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Andrade, Juan, Anna Waller, and Marcela Gaytan Martinez. "In-Country Method Validation of a Paper-based, Smartphone-assisted Iron Sensor for the Food Fortification Programs." Current Developments in Nutrition 4, Supplement_2 (May 29, 2020): 1158. http://dx.doi.org/10.1093/cdn/nzaa056_005.
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Abstract Objectives Food fortification programs and food companies in low-income settings, such as in the case of Mexico, lack the ability to monitor the micronutrients added to staples entering local markets. The purpose of the present work is to validate a user-friendly sampling kit and quantify the final error parameters of a paper-based, smartphone-assisted sensor (Nu3px) for the determination of iron in corn flours within the context of Mexico's food fortification program. Methods Corn flour samples (n = 45) from local brands (n = 6) were collected from supermarkets, convenience stores, and directly from companies in the States of Querétaro, Cuautitlán, Saltillo, and Cuetzalan, Mexico. Iron content was analyzed using atomic emission spectroscopy (AES) and Nu3px. The final error parameters were quantified via method validation final experiments, i.e., replication and comparison of methods experiments. Qualitative categorization of samples (i.e., accept/reject batch) was applied to evaluate Nu3px's against Mexico's fortification policy (cutoff = 40 μg Fe/g flour). A user-centered design process was applied to develop and evaluate a sampling kit consisting of low-cost measuring utensils. Results Iron content in fortified Mexican corn flours varied widely (23–39%). Nu3px's random error was 12% (replication experiment, n = 5) and its bias was 1.79 ± 9.99 μg Fe/g flour (comparison of methods experiment, n = 45). The true mean difference between Nu3px and AES was zero (p > 0.05) and both methods had similar variance (F = 2.40; P > 0.05). AES and Nu3px classified the iron content above/below the cutoff in the same way (100% match, Χ2 = 16.41, P = 0.01). The affordable and user-friendly sampling kit added some random error, but the mean difference was equal to zero (P > 0.05). Both sampling procedures were correlated (r = 0.952, P = 0.01). Conclusions An affordable, user-friendly, and equipment-free sample preparation kit for corn flour samples showed similar precision to using analytical tools. The sample preparation kit along with the paper-based, smartphone-assisted assay measure iron within the performance parameters required for its application to monitor batch quality in the corn flour fortification program in Mexico. Funding Sources Fulbright Garcia-Robles Fellowship, 2019.
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Trunov, Alexandr, Volodymyr Beglytsia, Gennady Gryshchenko, Viktor Ziuzin, and Vitalii Koshovyi. "Methods and tools of formation of general indexes for automation of devices in rehabilitative medicine for post-stroke patients." Eastern-European Journal of Enterprise Technologies 4, no. 2(112) (August 31, 2021): 35–46. http://dx.doi.org/10.15587/1729-4061.2021.239288.
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The current processes of recovery of post-infarction and post-stroke patients in the context of the establishment of the institution of family doctors and insurance medicine are considered. It was proposed to introduce modules for automation of recovery devices (MARD) to ensure procedures, quality of life and reduce labor costs during the period of long-term recovery. The forms of presentation of the model of the integral indicator are substantiated, which, in accordance with the requirements of the Ministry of Health, assesses the generalized indicator of the patient's statement (GIPS), the quality of medical services and increases the efficiency of data compression. A consistent application of two Euclidean norms is proposed, which leads indicators of dissimilar physical nature to a limited metric space. The relationship between the lower and upper bounds of the GIPS, the error, the width of the sliding window, and the values of the derivatives was established on the basis of the Taylor series expansion, geometric inequality and limited space. The model for evaluating the GIPS as a lower bound and the method for generating information about its properties are substantiated. A three-level comparator is applied and an vector- indicator (VI) is introduced as an informational addition to the time series. Additional capabilities for intelligent analysis are demonstrated. The model of GIPS through VI is presented. The examples of VI values are used to demonstrate its applicability to the intelligent analysis of the recovery process. Openness, accessibility, transparency of GIPS and VI as tools of KIT is implemented by the princes of public administration (PA) by reducing it to quantitative control and comparison if there are quantitative and qualitative indicators in the list. VI, sliding windows, as PA and KIT tools in software (SW) for a diagnostic conclusion and correction of the course of procedures, are numerically investigated. It is demonstrated on examples of a numerical experiment with software how the combined application of the method for calculating the GIPS and VI effectively affects the compression ratio, increasing it to 60–75 %
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Godfrey-Smith, Peter. "Cephalopods and the evolution of the mind." Pacific Conservation Biology 19, no. 1 (2013): 4. http://dx.doi.org/10.1071/pc130004.
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IN thinking about the nature of the mind and its evolutionary history, cephalopods — especially octopuses, cuttlefish, and squid — have a special importance. These animals are an independent experiment in the evolution of large and complex nervous systems — in the biological machinery of the mind. They evolved this machinery on a historical lineage distant from our own. Where their minds differ from ours, they show us another way of being a sentient organism. Where we are similar, this is due to the convergence of distinct evolutionary paths. I introduced the topic just now as ‘the mind.’ This is a contentious term to use. What is it to have a mind? One option is that we are looking for something close to what humans have — something like reflective and conscious thought. This sets a high bar for having a mind. Another possible view is that whenever organisms adapt to their circumstances in real time by adjusting their behaviour, taking in information and acting in response to it, there is some degree of mentality or intelligence there. To say this sets a low bar. It is best not to set bars in either place. Roughly speaking, we are dealing with a matter of degree, though ‘degree’ is not quite the right term either. The evolution of a mind is the acquisition of a tool-kit for the control of behaviour. The tool-kit includes some kind of perception, though different animals have very different ways of taking in information from the world. It includes some form of memory and learning, means by which past experiences can be brought to bear on the present. In some cases it includes problem-solving and planning. Some tool-kits are more elaborate and expensive than others, but they can be sophisticated in different ways, with different tools present and more investment in one technology than another. One animal might have better ways of tracking the environment through its senses, while another may have simpler senses but more sophisticated learning. Different tool kits go with different ways of making a living. The ordinary term ‘mind’ is awkwardly or misleadingly applied to an animal with a very simple behavioural repertoire, but it is parochial to apply it only to humans.
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Deng, Yang, Li Li Ji, Lin Li, Bing Li, and Jian Yu Su. "Development and Application of a Novel Nucleic Amplification Kit on Detection of Several Pathogens." Applied Mechanics and Materials 618 (August 2014): 293–97. http://dx.doi.org/10.4028/www.scientific.net/amm.618.293.
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Escherichia coliO157,Psuedomonas aeruginosa,Salmonella,Vibrio parahaemolyticusandListeriaare important pathogens for human. With increased awareness in public health, development of a rapid, sensitive, cost-effective and easy-operating bacteriological detection is of the utmost importance and urgent necessity. In this study, we developed and applied a simple amplification kit based on loop-mediated isothermal amplification (LAMP) methods for rapid detection of various pathogens includingEscherichia coliO157,Psuedomonas aeruginosa,Salmonella,Vibrio parahaemolyticusandListeria, as well as related virulence. Nine targets, includingrfbE(E. coli-specific),stx1 (coding for Shiga toxin 1),stx2 (coding for Shiga toxin 2),oprI(P. aeruginosa–specific),invA(Salmonella-specific),hlyA(Listeria-specific),tlh(coding for thermolable haemolysin),tdh(coding for thermostable direct haemolysin) andtrh(coding for TDH-related haemolysin), were selected for identification forEscherichia coliO157,Psuedomonas aeruginosa,Salmonella,Vibrio parahaemolyticusandListeria, as well as related virulence.. Six primers, including outer primers, inner primers and loop primers, were specially designed for recognizing eight distinct sequences on the targets. Three solutions labeled A, B and C was included in the kit. The experiment were carried out in a total of 25 μl reaction mixture: solution A containing 1.6 μM (each) of the primers FIP and BIP, 0.2 μM (each) of the primers F3 and B3, 0.8 μM (each) of primers LF and LB; solution B containing 1.6 mM of deoxynucleoside triphosphates, 6 mM MgSO4, 1 M betain (Sigma, St. Louis, MO, USA), 1 X thermopol buffer (New England Biolabs, Ipswich, MA, USA); solution C containing BST polymerase. Twenty-two reference strains, including various species of gram-negative and-positive isolates, were included in this study to evaluate and optimize LAMP assays. Application of the optimized LAMP assays was performed on a total of 200 strains (with 40 strains for each species of the pahtogens). The optimal reaction condition was found to be 65°C for 45 min. Application of the kit assays were performed on various types of pathogens, the sensitivity for the 9 targets was found to be 100%; with a 100% specificity and positive predictive value (PPV) for all the 9 targets targets. In conclusion, the isothermal amplification kits were demonstrated to be useful and powerful tools for rapid differentiation of various pathogens (includingEscherichia coliO157,Psuedomonas aeruginosa,Salmonella,Vibrio parahaemolyticusandListeria), and undoubtedly, the rapidness, easiness and cost-effectiveness of LAMP assay will aid in the broad application of bacteriological detection of common pathogens.
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Poth, Alexander, Mario Kottke, and Andreas Riel. "The implementation of a digital service approach to fostering team autonomy, distant collaboration, and knowledge scaling in large enterprises." Human Systems Management 39, no. 4 (November 11, 2020): 573–88. http://dx.doi.org/10.3233/hsm-201049.
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BACKGROUND: Autonomous acting of individuals and as teams are key elements of agile, distributed, and partly or entirely distant working environments. The availability of relevant processes, methods, tools, and guidelines is key to leveraging team autonomy. OBJECTIVE: This article presents the design and implementation of a digital self-service kit (SSK) approach featuring high scalability, as well as a quality assurance and continuous improvement mechanism. As consumers, the teams within an organization can use these SSK’s anytime and on-demand without any constraints in location, time, or quota. As producers (of knowledge and experience), they can also assume active roles in the extension and continuous improvement of the SSK’s. METHODS: This has been achieved in open community networks where feedback is actively leveraged and constantly integrated in the SSK’s design. Such open Communities of Practices (CoP) ensure that all interested parties can contribute to the adequateness of both the content and the provision of the SSK’s in both local and distant corporate settings. Both the design and implementation have been done and evaluated in a large-scale international corporate environment where high cultural diversity, as well as distant collaboration are of key importance. RESULTS: The results presented in this article include a generic digital self-service approach to distance learning and coaching of teams in the particular context of the agile transformation of large corporate organizations. Key elements include a strong and systematic expert team involvement in the process of the setup and design of such digital SSK’s, as well as a well-explained and understood kit structure for efficient and effective utilization and re-contextualization of the contained knowledge into team-specific project contexts. This contributes to team autonomy as a major prerequisite for the agile transformation, as well as knowledge scaling across the organisation. CONCLUSIONS: The key insights gained from this experiment confirm the high relevance and effectivity of the approach especially during periods where distant collaborations are essential (e.g. during a pandemic crisis).
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Yuan, Haibin, Fengli Liu, Tongsheng Ma, Zhandong Zeng, and Ning Zhang. "miR-338-3p inhibits cell growth, invasion, and EMT process in neuroblastoma through targeting MMP-2." Open Life Sciences 16, no. 1 (January 1, 2021): 198–209. http://dx.doi.org/10.1515/biol-2021-0013.
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Abstract This study aimed to explore the regulatory mechanisms of miR-338-3p and matrix metalloproteinase-2 (MMP-2) in neuroblastoma. Putative target interaction regions of miR-338-3p on MMP-2 were predicted by miRcode and miRbase bioinformatics tools. Relative expression of miRNA-338-3p and MMP-2 in neuroblastoma tissues and GI-LI-N and SK-N-SH cells was determined by reverse transcription polymerase chain reaction experiment. Furthermore, the cell proliferation was determined by Cell Counting Kit-8 assay, the cell apoptosis rate was analyzed by flow cytometry assay, and the cell invasion was evaluated by transwell assay. miR-338-3p expression was downregulated, whereas MMP-2 expression was upregulated in metastasis tissue site compared to that in primary tissue site in total. Furthermore, miR-338-3p overexpression suppressed proliferation, invasion, and epithelial–mesenchymal transition (EMT) of neuroblastoma cells but promoted apoptosis, and the knockdown of MMP-2 triggered similar effects. Furthermore, MMP-2 was directly targeted by miR-338-3p, and overexpression of MMP-2 rescued the inhibitory effects of miR-338-3p on human neuroblastoma cell progression. Collectively, these data demonstrated that miR-338-3p could suppress cell growth, invasion, and EMT pathway and induce apoptosis in neuroblastoma cells by targeting MMP-2. MiR-338-3p sponged MMP-2 to regulate the PI3K/AKT pathway in human neuroblastoma cells.
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Zou, Wei, and Jun Cheng. "MiR-887 Promotes the Progression of Hepatocellular Carcinoma via Targeting VHL." Technology in Cancer Research & Treatment 19 (January 1, 2020): 153303382094042. http://dx.doi.org/10.1177/1533033820940425.
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Background: MiR-887 has been proved to promote the tumorigenesis in diverse cancers, but its function and downstream mechanism in hepatocellular carcinoma remain obscure. Methods: Quantitative real-time polymerase chain reaction was performed to detect the expression levels of miR-887 in hepatocellular carcinoma tissues and cell lines. MiR-887 mimics and miR-887 inhibitor were transfected into Huh7 and MHCC97H to establish miR-887 overexpression or inhibition models. Cell Counting Kit-8 and colony formation experiment were conducted to monitor cell proliferation. Subcutaneous xenotransplanted tumor model and tail vein injection model in mice were also established to further verify the effect of miR-887 on hepatocellular carcinoma in vivo. The targeting relationship between miR-887 and von Hippel-Lindau tumor suppressor (VHL) was determined by quantitative real-time polymerase chain reaction, Western blot, and luciferase reporter gene assay. Results: miR-887 expression in hepatocellular carcinoma tissues was significantly upregulated. Compared with the control cells, the proliferation and metastasis of cancer cells were enhanced by miR-887 mimics and suppressed by miR-887 inhibitor. Compared with control mice, the volume and weight of subcutaneous tumors of mice in the miR-887 mimics group were significantly elevated, and the significant increase was found in the occurrence of lung metastasis. Moreover, bioinformatics tools showed that miR-887 and VHL had 2 binding sites. Luciferase activity assay demonstrated that miR-887 can inhibit the luciferase activity of VHL, and miR-887 mimics could reduce the expressions of VHL at both messenger RNA and protein levels to increase hypoxia-inducible factor α expression. Conclusion: The upregulation of miR-887 could facilitate the proliferation and metastasis of hepatocellular carcinoma cells via targeting VHL.
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Fanela, Thiago Luis Martins, Edson Luiz Lopes Baldin, and Ricardo Toshio Fujihara. "New experimental tools for bioassays with whitefly in laboratory." Pesquisa Agropecuária Brasileira 47, no. 12 (December 2012): 1782–84. http://dx.doi.org/10.1590/s0100-204x2012001200015.
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The objective of this work was to develop an experimental kit for assessments of repellency, deterrence for oviposition, and insecticidal activity on adults of the whitefly Bemisia tabaci biotype B. The kit, which consisted of arenas and nebulizer, was effective for conducting bioassays, and the application of aqueous extracts by inhaler was adequate. The techniques are simple, cheap, and may contribute to research on this insect.
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Velychko, Stepan P., and Sergii V. Shulga. "КОМП'ЮТЕРНО-ОРІЄНТОВАНІ ЗАСОБИ ПІДТРИМКИ САМОСТІЙНОЇ ДІЯЛЬНОСТІ СТУДЕНТІВ У НАВЧАННІ КВАНТОВОЇ ФІЗИКИ." Information Technologies and Learning Tools 65, no. 3 (July 1, 2018): 103. http://dx.doi.org/10.33407/itlt.v65i3.2225.
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The introduction of modern innovative training technologies in the training of highly skilled specialists involves a significant expansion and increase of the significance of cognitive activity in the educational process of each student, and in particular his individual activity during the implementation of a laboratory practice on the course of general physics, including the study of the section "Quantum Physics". Our scientific researches convincingly prove the expediency of widespread use of computer-oriented means for the purpose of development of independent activity of students in physics and in their high efficiency in solving the problem of integration of the real and virtual experiment from the given section. For this purpose, our computer-oriented training tools and corresponding software products take into account the obligatory availability of successive modules that provide the multifunctionality of the proposed training kit for the physical workshop and practical training tasks from the corresponding section as autonomously (independently of others), for example and integrated with other modules. The isolated modules, on the one hand, are consistent with the types of educational activity of the student, and on the other hand, they contribute to the purposeful management of research work during the physical practice and thus are an important factor in the organization and management of the student's independent work. Such a technique allows the student to attain a sufficiently high level of understanding of each module and, accordingly, at the appropriate level, to master laboratory research on quantum physics, where the subject of study can be presented real or virtual, which simultaneously enhances the professional expertise of future physics teachers and professionals whose activities are " with physics, and also improves the efficiency of independent work of a future specialist.
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Pantilimonescu, Florin, Lucian Constantin Hanganu, Mihaita Peptanariu, Stefan Grigoras, Irina Ionescu, Georgeta Lidia Potop, Alina Iovan-Dragomir, and Stela Carmen Hanganu. "Modular Student Learning Kit for Internet of Things." Applied Mechanics and Materials 659 (October 2014): 601–6. http://dx.doi.org/10.4028/www.scientific.net/amm.659.601.
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The term Internet of Things as a component of Future Internet is a recent fast growing global network infrastructure which extends Internet with a sensors and actuators shield. The paper presents a hands-on learning kit based on an open standard embedded computer connected to Internet enabling live data processing. The system uses cloud programming tools to add significant value to the education purpose, by including up-to-date innovative technical approaches and pedagogical values for improving the attractiveness and efficiency of the education activities in the engineering area. The learning goal intends to develop the Internet of things as new universe based on smart objects, connected to the Internet via adequate sensors and actuators. This can be an essential tool for a deeper understanding of the main concepts in physics, informatics and math, even in the early steps of learning. Based on cloud programming resources, the hardware-software components use the latest version of low power 32-bit embedded computer development platform and process interfaces to allow data monitoring, remote physical experiments, mobile world supervising, and collaborative project development. As an open standard learning tool, the kit offers a new computational framework able to serve in scientific experiments and discovery-based learning. This study was strongly motivated by the European Union recommendation to support and enrich the university curriculum by engaging students in hands-on engineering and design activities.
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Athiyyah, Royhanun, Taufiq Al Farizi, and Dwi Nanto. "Improvement of Science Process Skills Through Sound Variable Intensity Level Tool Kit." Jurnal Penelitian & Pengembangan Pendidikan Fisika 6, no. 1 (June 30, 2020): 89–96. http://dx.doi.org/10.21009/1.06110.
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Science process skills (SPS) are essential to assist the learning of senior high school students according to the 2013 curriculum, which prioritizes a scientific approach. The learning method that supports SPS is experiment methods. Nevertheless, learning with experimental methods is still rarely applied in schools, especially in the sound intensity level concept. The reason is the limited number and variant of experiment tool kits to support learning in schools. This study aims to develop a sound variable intensity level sound tool kit based on development procedures proposed by Jan van de Akker (2006). Sound variable intensity level kit was developed based on tool kit, which was developed before by Fikri Habibi. Sound variable intensity level experiment kit was evaluated by several learning media and learning material experts before being tested on high school students in several stages, including the one-on-one evaluation stages, small group evaluations, and field tests. The researcher revised the sound variable intensity level kit based on suggestions from the experts and the students. After being revised, the sound variable intensity level kit was tested on summative evaluation. Based on the results of summative evaluations, the sound variable intensity level kit becomes a successful, practical, and effective learning support tool kit for improving the science process skills of the student in the concept of sound intensity level.
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Santos, Fabio P. S., Renato D. Puga, Ricardo Helman, Welbert Oliveira Pereira, Tarcila S. Datoguia, Bianca Lisboa, Mariana Miyagi, et al. "Whole Exome Sequencing of Philadelphia-Negative (Ph-negative) Myeloproliferative Neoplasms (MPNs) and Myelodysplastic/Myeloproliferative Disorders (MDS/MPD)." Blood 124, no. 21 (December 6, 2014): 4593. http://dx.doi.org/10.1182/blood.v124.21.4593.4593.
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Abstract Introduction: The development of next-generation sequencing has made it feasible to interrogate the entire genome or exome (coding genome) in a single experiment. Accordingly, our knowledge of the somatic mutations that cause cancer has increased exponentially in the last years. MPNs and MDS/MPD are chronic myeloid neoplasms characterized by an increased proliferation of one or more hematopoietic cell lineages, and an increased risk of transformation to acute myeloid leukemia (AML). MPNs and MDS/MPDs are heterogenous disorders, both in clinical presentation and in prognosis. We sought to determine the genetic landscape of Ph-negative MPNs and MDS/MPD through next-generation sequencing. Methods: Paired DNA (sorted CD66b-granulocytes/skin biopsy) from 102 patients with MPNs or MDS/MPD was subjected to whole exome sequencing on a Illumina HiSeq 2000 platform using Agilent SureSelect kit. Diagnosis included primary myelofibrosis (MF; N=42), essential thrombocythemia (ET; N=28), polycythemia vera (PV; N=12), chronic myelomonocytic leukemia (CMML; N=10), systemic mastocytosis (MS; N=6), MDS/MPD-Unclassified (N=2) and post-MPN AML (N=2). Tumor coverage was 150x and germline coverage was 60x. Somatic variants calls were generated by combining the output of Somatic Sniper (Washington University), Mutect (Broad Institute) and Pindel (Washington University). The combined output of these 3 tools was further filtered by in-house criteria in order to reduce false-positive calls (minimum coverage at both tumor/germline ≥8 reads; fraction of reads supporting alternate allele ≥10% in tumor and ≤10% in germline; ratio of allele fraction tumor:germline >2; excluding mutations seen in SNP databases). All JAK2 and CALR mutations were validated through Sanger sequencing. Validation of other somatic mutations is currently underway. Analysis of driver mutations was made with the Intogen web-based software, using the Oncodrive-FM and Oncodrive-cluster algorithms (www.intogen.org). Significantly mutated genes were considered as those with a q-value of <0.10. Results: We identified a total of 309 somatic mutations in all patients, with each patient having an average of 3 somatic abnormalities, fewer than most solid tumors that have been sequenced so far. Mutations occurred in 166 genes, and 40 of these were recurrently somatically mutated in Ph-negative MPNs. By the Oncodrive-FM algorithm, the following genes were identified as the most significantly mutated driver genes in Ph-negative MPNs and MDS/MPDs (in order of significance): CALR, ASXL1, JAK2, CBL, DNMT3A, U2AF1, TET2, TP53, RUNX1, EZH2, SH2B3 and KIT. By the Oncodrive-cluster algorithm, which considers clustering of mutations at a hotspot, the following genes were significantly mutated: KIT, JAK2, SRSF2 and U2AF1. Somatic mutations were seen in genes that are mutated at a low frequency in Ph-negative MPNs, including ATRX, BCL11A, BCORL1, BIRC5, BRCC3, CSF2RB, CUX1, IRF1, KDM2B, ROS1 and SUZ12. Consistent with the clinical phenotype, 96 patients (94%) had mutations that lead to increased cellular proliferation, either through activation of the JAK-STAT pathway (e.g. JAK2, CALR) or mutations that activated directly or indirectly signaling by receptor tyrosine kinases (e.g. FLT3, KIT, CBL). Besides biological pathways regulating cell proliferation, the most commonly implicated pathways included regulation of DNA methylation (e.g. DNMT3A, TET2), mRNA splicing (e.g. U2AF1, SRSF2) and histone modifications (e.g. ASXL1, EZH2), seen in 27%, 25% and 22% of patients, respectively. Abnormalities in these 3 pathways were more often seen in MF, MDS/MPD and CMML, as compared to PV and ET (65% vs. 20%; p<0.0001). Conclusions: Our study represents one of the largest series of patients with these neoplasms evaluated by whole exome sequencing, and together with the published data helps to delineate the genomic landscape of Ph-negative MPNs and MDS/MPDs. The majority of the most frequent mutations seen in Ph-negative MPNs have already been reported. Nevertheless, there are several low frequency mutations that need to be further studied and functionally validated in vitro and in vivo for a deeper knowledge of the pathophysiology of MPNs. Besides activation of cellular proliferation, abnormalities of DNA methylation, histone modification and mRNA splicing emerge as the most important biological pathways in these disorders. Disclosures No relevant conflicts of interest to declare.
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Le Bourhis, D., Y. Amigues, F. Charreaux, S. Lacaze, M. Tissier, C. Guyader-Joly, G. Mervant, et al. "187 EMBRYO GENOTYPING FROM IN VIVO BIOPSIED BOVINE EMBRYOS AFTER WHOLE GENOME AMPLIFICATION." Reproduction, Fertility and Development 21, no. 1 (2009): 192. http://dx.doi.org/10.1071/rdv21n1ab187.
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Genomic tools are now available for most livestock species and used routinely for marker-assisted selection (MAS) in cattle. The detection of a large number of markers that are widespread over the genome is generally limited by the amount of genomic DNA available in an embryo biopsy of a small size not to be detrimental to embryonic survival. Amplification of DNA from such a biopsy is then necessary. In this study, the efficiency of embryo genotyping for 45 microsatellites (MS) following whole-genome amplification (WGA) was evaluated from samples of a variable number of cells isolated from cattle embryos. In a second part, this work aims to test the reliability of the MAS method for 45 MS and 13 single nucleotide polymorphisms (SNP) from bovine embryo biopsies under field conditions. In experiment 1, in vitro bovine morulae (n = 10) were produced, and 1, 5, and 10 embryonic cells were removed from each morula. Cells were dry frozen in tubes before further processing. Whole-genome amplification was performed using the commercial Qiagen REPLI-g® Mini Kit according to the manufacturer instructions (Qiagen, Valencia, CA, USA). WGA solution was then diluted, processed by PCR with 45 markers, and the resulting data were genotyped with GeneMapper software® (Applied Biosystems Europe). Accuracy and reliability of genotyping were assessed using different samples of cells from the same embryo. In experiment 2, after superovulation (10 cows), bovine embryos were in vivo-produced and collected at day 6 or day 7 of pregnancy. Only grade 1 embryos were washed and biopsied using a microblade. Biopsied embryos were either frozen or transferred back to synchronized recipients. Individual biopsies were transferred as dry samples to the laboratory. Genomic DNA was amplified using WGA, and embryos were genotyped. The results of experiment 1 clearly indicate that a conventional biopsy of 5 to 10 cells was sufficient for multi-markers detection after whole-genome amplification as 98% of the 45 markers were detected compared to 45% of marker detection using 1 cell (P < 0.01). In experiment 2, from 123 collected embryos, 79 were classified as grade I or II transferable embryos (64.2%) and 57 were biopsied (34 were classified as stage 4–5 and 23 as stage 5–6, according to the IETS criteria). Using the stereomicroscopic analysis, 44 biopsies had a number of cells ranging from 4 to 7 (5.6 ± 1.4) and 13 biopsies from 8 to 10 (8.4 ± 1.6). Overall, at least 95% of markers (MS + SNP) were detected in 49.1% of biopsies (28/57). The total detection rate for SNP was significantly higher than for MS; 70.2% (40/57) v. 31.6% (18/57), respectively, (chi-square, P < 0.01). The detection rate of the markers was not significantly affected by the embryo stage or the biopsy size. Our results confirm that genotyping a large number of markers from biopsy samples after whole-genome amplification is possible under field conditions. A larger number of biopsies is required to assess the reliability of this method that may allow the development of MAS from early embryo. This work has been performed through the programme TYPAGENAE (GENANIMAL 4-03) with the financial support of FRT/ANR and Apis-Genes.
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Wheeler, Bob. "Algorithmic Tool Kit: Software for the Algorithmic Design of Experiments." American Statistician 39, no. 2 (May 1985): 144. http://dx.doi.org/10.2307/2682824.
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Sanmartin, Jaime. "TREC: A tool kit for programming cognitive experiments in Applesoft BASIC." Behavior Research Methods, Instruments, & Computers 19, no. 5 (September 1987): 467–68. http://dx.doi.org/10.3758/bf03205617.
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Silberstein, Lev, Peter Kharchenko, Youmna Kfoury, Francois Mercier, Masatake Osawa, Jonathan Hoggatt, Tiffany Tate, Charles Lin, and David T. Scadden. "Proximity-Based Single Cell Analysis of the Bone Marrow Niche Identifies Interleukin-18 As a Quiescence Regulator of Early Hematopoietic Progenitors." Blood 124, no. 21 (December 6, 2014): 773. http://dx.doi.org/10.1182/blood.v124.21.773.773.
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Abstract Background. Niche-derived signals are essential for maintenance and expansion of stem/progenitor cells in the bone marrow. Recently published studies used elegant genetic tools to dissect predominant cellular sources of known HSPC regulators, such as CXCL12 and kit-ligand (Ding et al, Nature 2012, Greenbaum et al, Nature 2013). However, strategies enabling identification of novel niche-derived factors are lacking. Here, we describe an approach which utilizes spatial proximity between osteolineage cells (OLC) and HSPC in the post-transplant bone marrow niche as a guide to niche factor discovery and reveals the role of Interleukin-18 (IL18) as a quiescence regulator of early hematopoietic progenitors. Results. We established a neonatal bone marrow (BM) transplantation model, in which adult BM-derived LKS CD34-Flk2- HSPCs fluorescently labeled with DiI were transplanted into irradiated newborn col2.3GFP recipients (in this mouse strain, the majority of OLCs are labeled with GFP). Forty-eight hours later, we obtained sections of femoral trabecular bone from transplanted mice and located rare OLCs harboring DiI-positive HSPCs in their immediate proximity. We harvested individual OLCs located within two cell diameters (proximal OLCs) and greater than five cell diameters (distal OLCs) from DiI-labeled HSPCs and performed comparative transcriptome analysis by single cell RNA-Seq. Remarkably, we found that proximal OLCs were distinct from their distal counterparts and showed a higher expression levels of known niche-associated molecules, as well as secreted factors not previously linked to regulatory niche function, including a pro-inflammatory cytokine IL18. Quantification of primitive subsets in the BM of IL18 knock-out (IL18KO) mice showed no abnormalities. However, cell cycle studies revealed that while long-term HSCs (which did not express the IL18 receptor) were unaffected by IL18 deletion, early progenitors - short-term HSC, multi-potent progenitor and common lymphoid progenitor – were more actively cycling. Accordingly, following sublethal exposure to 5-fluorouracil (5FU), IL18KO animals displayed a 2-fold increase in frequency of lin-kit+Sca1+ (LKS) cells, lin-kit+ myeloid progenitors and CLPs, as compared wild-type (WT) controls (Figure 1). On the other hand, exogenous administration of recombinant IL18 to 5FU-treated WT animals was associated with 25% mortality, while no deaths were observed in the vehicle-treated group. Taken together, these data illustrate that IL18 constrains the ability of the progenitor pool to respond to a genotoxic stress. Next, we tested if IL18 acts in a non cell-autonomous fashion. We transplanted progenitor-enriched bone marrow fraction (LKS cells) into IL18KO or WT hosts and observed an approximately 2-fold increase in both myeloid and lymphoid cells in peripheral blood of IL18KO animals. This finding was recapitulated in a reciprocal experiment, when LKS cells from IL18 receptor knock-out animals were transplanted into WT hosts, supporting the possibility that the effect of IL18 on progenitor proliferation is direct. Finally, we investigated if the loss of IL18-mediated quiescence can be therapeutically exploited in the transplant setting. To this end, we assessed survival of lethally irradiated WT and IL18KO mice following transplantation with a limiting BM dose, i.e. predicted to confer survival to 50% or less of WT animals. Notably, we observed reduced 30-day post-transplant mortality (33% versus 72%, p value = 0.05) in IL18KO animals, which likely resulted from accelerated progenitor expansion in the absence of IL18 in the host microenvironment (Figure 2). Conclusions. Our study demonstrates the capability of proximity-based single cell analysis of the post-transplant bone marrow microenvironment to identify a novel niche factor – IL 18. We show that IL18 specifically regulates quiescence of early hematopoietic progenitors, particularly under the conditions of stress hematopoiesis, such as exposure to 5FU or post-transplant hematopoietic expansion. The results presented here provide an insight into poorly understood molecular mechanisms of progenitor regulation by the niche. Moreover, improved post-transplant survival of animals in the absence of IL18 suggests that pharmacological inhibition of IL18 has the potential of improving clinical outcomes in transplant recipients. Figure 2 Figure 2. Figure 1 Figure 1. Disclosures No relevant conflicts of interest to declare.
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Suyatman, Suyatman. "Analisis Kebutuhan Pengembangan Laboratorium PGMI dalam Perkuliahan IPA." At-Tarbawi: Jurnal Kajian Kependidikan Islam 1, no. 1 (June 28, 2016): 57. http://dx.doi.org/10.22515/attarbawi.v1i1.35.
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Based on documentation of pgmi mentioned that college students are derived from background science class is 36,98 % , less than 50 % of the student PGMI .This has led consequence that lecture believe in science ranging from the base and supported by the laboratory adequate .The laboratory adequate will build real kosep students in understand science.Steps analysis needs research laboratory PGMI in lecture ipa is as follows: 1) analysis of need assessment, 2) the literature study, 3) study komparasi , 4) expert judgment, 5) improvement. Based on analysis of the data can pull conclusions as follows: 1) The lab PGMI FITK IAIN Surakarta especially for science laboratory having 85 set equipment consisting of 737 the tools and can be used to 121 title science experiments. 2) Additional needs necessary the 25 set equipment science experiments, with details as follows: kit science less 24 set, consisting of the balance KIT 4 sets, mineral KIT 5 sets, Sound KIT 4 sets, coal KIT 6 sets, and heat engine KIT 5 sets, and science integrated KIT less 1 set, and 5 the microscopes.Keywords: analysis needs , the development of a laboratory, IPA lecture
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Wheeler, Bob. "Regression Tool Kit: Software for the Design and Analysis of Regression Experiments." American Statistician 39, no. 2 (May 1985): 144. http://dx.doi.org/10.2307/2682823.
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Stilman, Boris, Vladimir Yakhnis, and Oleg Umanskiy. "Linguistic Geometry: The Age of Maturity." Journal of Advanced Computational Intelligence and Intelligent Informatics 14, no. 6 (September 20, 2010): 684–99. http://dx.doi.org/10.20965/jaciii.2010.p0684.
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This paper describes the current status of research and applications of Linguistic Geometry (LG), a type of game theory scalable to the level of real life defense systems. LG is compared to conventional gaming approaches with respect to their applicability to real world problems. LG generates winning strategies for all sides in a conflict in real time by constructing them out of a limited set of blocks called zones. Several examples of zones are introduced. The paper describes the process of discovery of new zones essential for various types of military operations, which represent different classes of abstract board games. We also included a brief explanation of scalability of the LG applications. This paper describes a universal tool kit, LG-PACKAGE, which allows a user to build his/her own applications of LG. This tool kit includes GDK (Game Development Kit), GIK (Game Integration Kit), GRT (Game Resource Tool), GST (Game Solving Tool), GNS (Game Network Services) and GMI (Game Mobile Interface). In the end we included a description of the most advanced experiments with the LG applications conducted by DARPA and US Army and assessments of these experiments by military experts.
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Talegaonkar, Purva, David Saucier, Will Carroll, Preston Peranich, Erin Parker, Carver Middleton, Samaneh Davarzani, et al. "Closing the Wearable Gap-Part VII: A Retrospective of Stretch Sensor Tool Kit Development for Benchmark Testing." Electronics 9, no. 9 (September 7, 2020): 1457. http://dx.doi.org/10.3390/electronics9091457.
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This paper presents a retrospective of the benchmark testing methodologies developed and accumulated into the stretch sensor tool kit (SSTK) by the research team during the Closing the Wearable Gap series of studies. The techniques developed to validate stretchable soft robotic sensors (SRS) as a means for collecting human kinetic and kinematic data at the foot-ankle complex and at the wrist are reviewed. Lessons learned from past experiments are addressed, as well as what comprises the current SSTK based on what the researchers learned over the course of multiple studies. Three core components of the SSTK are featured: (a) material testing tools, (b) data analysis software, and (c) data collection devices. Results collected indicate that the stretch sensors are a viable means for predicting kinematic data based on the most recent gait analysis study conducted by the researchers (average root mean squared error or RMSE = 3.63°). With the aid of SSTK defined in this study summary and shared with the academic community on GitHub, researchers will be able to undergo more rigorous validation methodologies of SRS validation. A summary of the current state of the SSTK is detailed and includes insight into upcoming experiments that will utilize more sophisticated techniques for fatigue testing and gait analysis, utilizing SRS as the data collection solution.
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Li, Haichao, Kun Wu, Chenchen Ruan, Jiao Pan, Yujin Wang, and Hongan Long. "Cost-reduction strategies in massive genomics experiments." Marine Life Science & Technology 1, no. 1 (November 2019): 15–21. http://dx.doi.org/10.1007/s42995-019-00013-2.
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Abstract Many modern biology studies require deep, whole-genome sequencing of hundreds to thousands of samples. Although per-sample costs have dramatically decreased, the total budget for such massive genome sequencing constitutes a significant barrier for poorly funded labs. The costly lab tools required for genomics experiments further hinder such studies. Here, we share two strategies for extensively reducing the costs of massive genomics experiments, including miniaturization of the NEBNext Ultra II FS DNA Library Prep Kit for Illumina (reducing the per-sample total costs to ~ 1/6 of that charged by service providers) and in-lab 3D model-designing of genomics tools. These strategies not only dramatically release funding pressure for labs, but also provide students with additional training in hands-on genomics and 3D-model-designing skills, demonstrating the high potential for their application in genomics experiments and science education.
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Bullynck, Maarten. "Johann Heinrich Lambert's Scientific Tool Kit, Exemplified by His Measurement of Humidity, 1769–1772." Science in Context 23, no. 1 (January 26, 2010): 65–89. http://dx.doi.org/10.1017/s026988970999024x.
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ArgumentJohann Heinrich Lambert (1728–1777) developed a very detailed theory of science and experiment. Using Lambert's hygrometric studies, this article provides an introduction to Lambert's theory and its practice. Of special interest is his well-founded theory on the emergence and definition of concepts and his neat eye for heuristics that should ultimately lead to a mathematization of physical phenomena. His use of visualizations in this context is especially remarkable.
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Fisher, Ann, William J. Wheeler, and Rami Zwick. "Experimental Methods in Agricultural and Resource Economics: How Useful are They?" Agricultural and Resource Economics Review 22, no. 2 (October 1993): 103–16. http://dx.doi.org/10.1017/s106828050000469x.
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Experimental economics has the potential to fill some of the gaps in the economist's tool kit. This article describes experimental economics, its advantages and disadvantages, and why this tool might be a good choice in some situations. The article summarizes the history of its use by agricultural and resource economists. An illustrative example compares laboratory experiment data with survey data.
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Golkar, Zhabiz. "CRISPR: a journey of gene-editing based medicine." Genes & Genomics 42, no. 12 (October 22, 2020): 1369–80. http://dx.doi.org/10.1007/s13258-020-01002-x.
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AbstractCRISPR (Clustered Regularly Interspaced Short Palindromic Repeat) is one of the hallmark of biological tools, contemplated as a valid and hopeful alternatives to genome editing. Advancements in CRISPR-based technologies have empowered scientists with an editing kit that allows them to employ their knowledge for deleting, replacing and lately “Gene Surgery”, and provides unique control over genes in broad range of species, and presumably in humans. These fast-growing technologies have high strength and flexibility and are becoming an adaptable tool with implementations that are altering organism’s genome and easily used for chromatin manipulation. In addition to the popularity of CRISPR in genome engineering and modern biology, this major tool authorizes breakthrough discoveries and methodological advancements in science. As scientists are developing new types of experiments, some of the applications are raising questions about what CRISPR can enable. The results of evidence-based research strongly suggest that CRISPR is becoming a practical tool for genome-engineering and to create genetically modified eukaryotes, which is needed to establish guidelines on new regulatory concerns for scientific communities.
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Supasorn, Saksri. "Grade 12 students' conceptual understanding and mental models of galvanic cells before and after learning by using small-scale experiments in conjunction with a model kit." Chemistry Education Research and Practice 16, no. 2 (2015): 393–407. http://dx.doi.org/10.1039/c4rp00247d.
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This study aimed to develop the small-scale experiments involving electrochemistry and the galvanic cell model kit featuring the sub-microscopic level. The small-scale experiments in conjunction with the model kit were implemented based on the 5E inquiry learning approach to enhance students' conceptual understanding of electrochemistry. The research tools consisted of (1) four small-scale experiments involving electrochemistry, which were oxidation and reduction reactions, galvanic cells, cathodic protection of iron nails, and connecting batteries in series, and (2) the galvanic cell model kit with the ability to generate various galvanic cells. The data collecting tools included (1) a conceptual test of electrochemistry and (2) the mental model drawing of a galvanic cell. Thirty-four grade 12 students participated in the series of four 5E learning activities for a total of 10 hours. Paired samplesT-test analysis revealed that the mean scores of the post-conceptual test (mean 36.63, SD 7.69) was statistically higher than that of the pre-conceptual test (mean 21.51, SD 6.83) at the significance level of 0.05. In addition, the mean scores of the post-mental models in both the macroscopic (mean 3.56, SD 1.30) and sub-microscopic features (mean 5.98, SD 2.93) were statistically higher than those of the pre-mental models (mean 1.85, SD 1.11 and mean 2.20, SD 2.45) at the significance level of 0.05. Prior to intervention, most students were in the categories of less correct conceptions, Partial Understanding with Specific Misunderstanding (PMU) to No Understanding (NU). However, after the intervention, they moved to the categories of more correct conceptions, Partial Understanding (PU) to Sound Understanding (SU). This indicated that this intervention can enhance students' conceptual understanding of electrochemistry and mental models of galvanic cells.
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O'Day, Sharyn Jones, and William F. Keegan. "Expedient Shell Tools from the Northern West Indies." Latin American Antiquity 12, no. 3 (September 2001): 274–90. http://dx.doi.org/10.2307/971633.
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Our work in the Bahamas, Turks and Caicos, Haiti, and Jamaica has revealed significant patterning in apparently unretouched molluscan shell objects. In the present paper we conclude that repetitive patterns in shell breakage, especially of queen conch (Strombus gigas), reflect the specific manufacture of forms for use as expedient tools. Expedient tools exhibit only primary modification in which a portion of the source material is removed and shaped, but there is no specific evidence for the preparation of a work edge. Alternatively, expedient tools may display no modification of the raw material except that produced through use. We hypothesize that through controlled breakage large S. gigas and other mollusk shells were modified to create numerous smaller pieces for everyday domestic activities. The key factor here is human intent. Experiments clearly demonstrate that controlled breakage of adult shells produces predictable fragments. Among these are forms that occurred in prehistoric sites throughout the West Indies; many of these forms also exhibit signs of use wear. This type of regional comparison and analysis is important for all archaeologists who work in coastal settings. It is only through such general studies that the sample size is sufficient to facilitate a more complete reconstruction of the aboriginal tool kit.
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Smith, Jeff, and R. Fredrik Inglis. "Evaluating kin and group selection as tools for quantitative analysis of microbial data." Proceedings of the Royal Society B: Biological Sciences 288, no. 1951 (May 19, 2021): 20201657. http://dx.doi.org/10.1098/rspb.2020.1657.
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Kin selection and multilevel selection theory are often used to interpret experiments about the evolution of cooperation and social behaviour among microbes. But while these experiments provide rich, detailed fitness data, theory is mostly used as a conceptual heuristic. Here, we evaluate how kin and multilevel selection theory perform as quantitative analysis tools. We reanalyse published microbial datasets and show that the canonical fitness models of both theories are almost always poor fits because they use statistical regressions misspecified for the strong selection and non-additive effects we show are widespread in microbial systems. We identify analytical practices in empirical research that suggest how theory might be improved, and show that analysing both individual and group fitness outcomes helps clarify the biology of selection. A data-driven approach to theory thus shows how kin and multilevel selection both have untapped potential as tools for quantitative understanding of social evolution in all branches of life.
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Banasiak, Małgorzata, and Małgorzata Karczmarzyk. "Games as a Tool in Education. Experiment in Teaching/Learning Competences by Student in the School." Kultura i Edukacja 114, no. 4 (December 31, 2016): 102–12. http://dx.doi.org/10.15804/kie.2016.04.07.
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Oltova, Jana, Ondrej Svoboda, Olga Machonova, Petra Svatonova, David Traver, Michal Kolar, and Petr Bartunek. "Zebrafish Kit ligands cooperate with erythropoietin to promote erythroid cell expansion." Blood Advances 4, no. 23 (December 1, 2020): 5915–24. http://dx.doi.org/10.1182/bloodadvances.2020001700.
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Abstract Kit ligand (Kitlg) is pleiotropic cytokine with a prominent role in vertebrate erythropoiesis. Although the role of Kitlg in this process has not been reported in Danio rerio (zebrafish), in the present study we show that its function is evolutionarily conserved. Zebrafish possess 2 copies of Kitlg genes (Kitlga and Kitlgb) as a result of whole-genome duplication. To determine the role of each ligand in zebrafish, we performed a series of ex vivo and in vivo gain- and loss-of-function experiments. First, we tested the biological activity of recombinant Kitlg proteins in suspension culture from zebrafish whole-kidney marrow, and we demonstrate that Kitlga is necessary for expansion of erythroid progenitors ex vivo. To further address the role of kitlga and kitlgb in hematopoietic development in vivo, we performed gain-of-function experiments in zebrafish embryos, showing that both ligands cooperate with erythropoietin (Epo) to promote erythroid cell expansion. Finally, using the kita mutant (kitab5/b5 or sparse), we show that the Kita receptor is crucial for Kitlga/b cooperation with Epo in erythroid cells. In summary, using optimized suspension culture conditions with recombinant cytokines (Epo, Kitlga), we report, for the first time, ex vivo suspension cultures of zebrafish hematopoietic progenitor cells that can serve as an indispensable tool to study normal and aberrant hematopoiesis in zebrafish. Furthermore, we conclude that, although partial functional diversification of Kit ligands has been described in other processes, in erythroid development, both paralogs play a similar role, and their function is evolutionarily conserved.
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Han, Xiu Li, Lei Liu, Wen Chen, and Jin Hua Wang. "Optimized Analysis of Orthogonal Experiment of Continuous Casting Powder Components Based on Matlab." Advanced Materials Research 774-776 (September 2013): 1301–5. http://dx.doi.org/10.4028/www.scientific.net/amr.774-776.1301.
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The optimal design of mineral composition of mould powder is significant for the improvement of quality of slab. This paper applies Matlab computing platform into mould powder proportioning scheme; designs multi-factor and multilevel orthogonal experiment based on CaO-SiO2-Al2O3mould powder system; prepares mould powder with the same content change of proportioning components and measures the melting temperature and viscosity of each mould powder; and establishes the regression relationship between viscosity and chemical components of mould powder by using Matlab to provide multiple pure quadratic regression analysis function of tool kit; analyzes the dynamic relationship between the viscosity of slag system and the content of various chemical components and provides quantitative analysis method for the optimal design of mould powder.
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Pramudyawan, Muhammad Tegar Septiaji, Aris Doyan, and Jannatin 'Ardhuha. "Effect of Guided Inquiry Learning Model Assisted by Work and Energy Experiment Tool Kit on Mastery of Physics Concepts Student." Jurnal Penelitian Pendidikan IPA 6, no. 1 (November 8, 2019): 40. http://dx.doi.org/10.29303/jppipa.v6i1.290.
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Gui, Wen Ming, Rui Fan Liu, Guang Yi Bai, and Xi Shao. "A Novel Approach to Improve the Frequency Resolution Based on Sparse Representation." Advanced Materials Research 756-759 (September 2013): 3336–40. http://dx.doi.org/10.4028/www.scientific.net/amr.756-759.3336.
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How to improve the frequency resolution, especially in the low frequency bands, is an important problem for many applications. A novel approach based on sparse representation was proposed for this problem. In this work, we first discussed the design of the over-completed dictionary with the high frequency resolution, and then Matching Pursuit was advised to perform sparse decomposition using Matching Pursuit Tool Kit. Next, the frequency information was extracted from the code book of the results of Matching Pursuit. Finally, the experiments demonstrated the improvement of the frequency resolution for the proposed approach.
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Vo-Phamhi, Jenny M., Kevin A. Yamauchi, and Rafael Gómez-Sjöberg. "Validation and tuning of in situ transcriptomics image processing workflows with crowdsourced annotations." PLOS Computational Biology 17, no. 8 (August 9, 2021): e1009274. http://dx.doi.org/10.1371/journal.pcbi.1009274.
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Recent advancements in in situ methods, such as multiplexed in situ RNA hybridization and in situ RNA sequencing, have deepened our understanding of the way biological processes are spatially organized in tissues. Automated image processing and spot-calling algorithms for analyzing in situ transcriptomics images have many parameters which need to be tuned for optimal detection. Having ground truth datasets (images where there is very high confidence on the accuracy of the detected spots) is essential for evaluating these algorithms and tuning their parameters. We present a first-in-kind open-source toolkit and framework for in situ transcriptomics image analysis that incorporates crowdsourced annotations, alongside expert annotations, as a source of ground truth for the analysis of in situ transcriptomics images. The kit includes tools for preparing images for crowdsourcing annotation to optimize crowdsourced workers’ ability to annotate these images reliably, performing quality control (QC) on worker annotations, extracting candidate parameters for spot-calling algorithms from sample images, tuning parameters for spot-calling algorithms, and evaluating spot-calling algorithms and worker performance. These tools are wrapped in a modular pipeline with a flexible structure that allows users to take advantage of crowdsourced annotations from any source of their choice. We tested the pipeline using real and synthetic in situ transcriptomics images and annotations from the Amazon Mechanical Turk system obtained via Quanti.us. Using real images from in situ experiments and simulated images produced by one of the tools in the kit, we studied worker sensitivity to spot characteristics and established rules for annotation QC. We explored and demonstrated the use of ground truth generated in this way for validating spot-calling algorithms and tuning their parameters, and confirmed that consensus crowdsourced annotations are a viable substitute for expert-generated ground truth for these purposes.
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Ford, Ian. "Commentary and Opinion: III. Some Nonontological and Functionally Unconnected Views on Current Issues in the Analysis of PET Datasets." Journal of Cerebral Blood Flow & Metabolism 15, no. 3 (May 1995): 371–77. http://dx.doi.org/10.1038/jcbfm.1995.46.
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Strother et al. (1995) and Friston (1995) both raise important issues and provide useful reviews of various aspects of PET data analysis. Statisticians would not assume that any single piece of methodology would answer all questions about a type of data in a variety of experimental and observational contexts. The fundamental importance of hypothesis-driven inference, based on well designed experiments, cannot be overestimated for its ability to progress scientific understanding in an orderly manner. However, hypothesis-generating experiments are also vital in their own right. In practice, we generally do not have the luxury of both types of experiment, and we should note Strother et al.'s comment on the importance of extracting as much information as possible from each dataset. Friston (1995) also sees formal testing methods and exploratory methods such as principal components analysis as complementary. The correct approach would therefore seem to be (a) to select methods for formal and exploratory data analysis from the rich existing tool kit of statistical procedures, (b) to modify these as necessary to deal with special PET problems such as multiplicity, (c) to be aware of the assumptions underlying the methods being used and to investigate the problems that can arise if these assumptions fail to hold, (d) to appreciate the complexity of both PET data and of the potential questions that can be asked of it, and (e) to be aware of the limitations of any statistical analysis and the need for caution in interpreting conclusions not based on any predefined hypothesis.
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Furness, Caroline L., Marcela B. Mansur, Victoria J. Weston, Sarah Jenkinson, Frederik W. van Delft, Lyndal Kearney, Ian Titley, et al. "The Sub-Clonal Complexity of STIL-TAL1 T-ALL." Blood 124, no. 21 (December 6, 2014): 3788. http://dx.doi.org/10.1182/blood.v124.21.3788.3788.
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Abstract Introduction The STIL-TAL1 fusion is found in 16% cases of paediatric and adolescent T-ALL, making it one of the most common T-ALL subgroups. Our study considers this leukaemia subtype in the context of a complex ecosystem that is diverse, evolving and subject to selective pressures. We used single cell methods to understand the order of co-operating mutational events and the clonal evolution of mutations in genes that are re-iteratively targeted, such as PTEN. Methods Diagnostic DNA from five STIL-TAL1 positive T-ALL cases was exome sequenced using Agilent SureSelect Human all Exon kit plus Illumina paired end sequencing. Driver copy number alterations and NOTCH1/PTEN exon 7 mutation status had been identified in a previous study and candidate driver mutations for inclusion in single cell experiments were validated by sequencing or Q-PCR using custom assays. Where more than one mutation was present within the same exon of a candidate driver gene, cloning experiments were carried out to verify the independent mutation sequences. Material from xenograft transplants was available in three of the five cases to assess their clonal heterogeneity in the leukaemia initiating cell compartment. Single cell multiplex Q-PCR was used to examine the single cell genetics of the pre-defined mutation events. Briefly, single cells were sorted and lysed prior to multiplex specific (DNA) target amplification and Q-PCR using the 96.96 dynamic microfluidic array and the BioMark HD (Fluidigm, UK). Copy number assays for the 1p33 deletion and custom assays for the patient specific STIL-TAL1 fusion breakpoints were used to confirm that the 1p33 deletion leading to this gene fusion was a clonal event. Results The only aberrant events common to all five samples were CKDN2A copy number loss and the 1p33 deletion that results in the STIL-TAL1 fusion. Exome sequencing revealed further mutations in known T-ALL drivers including NOTCH1, PTEN and PHF6 as well as candidate driver mutations in FREM2, PIK3CD, RPL14, BMPR1A and CDH18. Both NOTCH1 and PTEN demonstrated re-iterative inactivation and this was investigated in detail for PTEN. Case 1 had multiple PTEN exon 7 mutations and sub-clonal copy number loss. Case 2 had parallel frameshift mutations in PTEN exons 5 and 7. Case 3 contained an exon 8 mutation and multiple PTEN exon 7 mutations. In this case the three most frequent PTEN exon 7 indels were validated and tracked in a single cell multiplex Q-PCR experiment. This revealed a branching sub-clonal genetic architecture (see figure 1) in which all malignant cells at the proposed apex of the branching architecture harboured the STIL-TAL1 fusion and CDKN2A deletion with copy number losses of 4p, 6q and FREM2 and PTEN mutations occurring as sub-clonal events. PTEN indels 2 and 3 were found co-localised in the same sub-clone. Preliminary analysis of the paired mouse xenograft bone marrow did not detect PTEN exon 7 indels 1 – 3 in 84 single cells. However, bulk Sanger Sequencing analysis did identify the PTEN exon 8 mutation in the mouse. Ongoing work is in progress to determine whether single cells of the xenograft carry alternative PTEN exon 7 mutations detected in the diagnostic sample exome data and to characterise in which diagnostic sub-clone the PTEN exon 8 mutation resides. Conclusions This study demonstrates how exome sequencing and single cell multiplex Q-PCR can be used as complementary tools to understand the sub-clonal complexity of STIL-TAL1 T-ALL. PTEN inactivation is sub-clonal by single cell analysis, demonstrating the parallel evolution of multiple independent PTEN inactivated sub-clones, highlighting PTEN inactivation as a key event in this T-ALL subgroup. In a wider cohort of 20 patients collected by our group at least 50% had PTEN inactivation as assessed by sequencing of exon 7 and copy number data alone. Results indicate a strong evolutionary pressure selecting for mutational events that result in inactivation of the PTEN-PI3Kinase pathway. These events occur via multiple mechanisms, including copy number loss and truncating mutations, which are not limited to the known T-ALL hotspot in exon 7. Current work is focussing on using a similar approach to examine the clonal evolution of NOTCH1 mutations in STIL-TAL1 T-ALL samples in diagnostic and xenograft samples of cases 4 and 5. Figure 1 Figure 1. Disclosures No relevant conflicts of interest to declare.
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Janecka-Widła, Anna, Agnieszka Adamczyk, Kaja Majchrzyk, Anna Cichocka, and Joanna Niemiec. "Qproteome FFPE Tissue Kit is not suitable for protein analysis using Agilent 2100 Bioanalyzer." Diagnostyka Laboratoryjna 54, no. 3 (September 20, 2018): 145–50. http://dx.doi.org/10.5604/01.3001.0013.7699.
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Introduction: The chip-based protein separation using Agilent 2100 Bioanalyzer is a promising tool for proteomic analysis. However, it has not been defined if the above-mentioned device is suitable for analysis of formalin-fixed paraffin-embedded (FFPE) proteins extracts.<br>The aim of the study: Therefore we performed the analysis aimed at testing if extracts from FFPE tissues are suitable for proteins detection using Agilent 2100 Bioanalyzer.<br>Material and methods: FFPE tissues and cell cultures were used for experiments. Proteins were extracted from them using Qproteome FFPE Tissue Kit and RIPA buffer, respectively. For protein analysis Bioanalyzer Instrument, Western Blot and immunohistochemistry (IHC) were applied.<br>Results: In FFPE extracts, using Bioanalyzer we failed to detect β-actin. However, Western Blot analysis proved β-actin presence in them. One of possible explanations of this phenomenon might be lack of antibody-antigen interaction during immunoprecipitation preceding Bioanalyzer analysis. We suspected that, Extraction Buffer (from Qproteome FFPE Tissue Kit) or β-mercaptoethanol (both present in FFPE protein extracts) might be responsible for the above-mentioned blockade. Therefore, we applied IHC with detection of CD34 because, CD34 staining is robust against small methodological variations and this marker is always present in tumor tissue sections. Anti-CD34 antibody was diluted in Tris saline buffer with Extraction Buffer, β-mercaptoethanol or without. We did not observe CD34 immunopositivity only in the presence of Extraction Buffer.<br>Conclusion: Qproteome FFPE Tissue Kit is not suitable for protein analysis using Agilent 2100 Bioanalyzer, because the Extraction Buffer from the kit prevents an interaction between antibody and antigen during immunoprecipitation procedure.
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Kastenmüller, Gabi, Werner Römisch-Margl, Brigitte Wägele, Elisabeth Altmaier, and Karsten Suhre. "metaP-Server: A Web-Based Metabolomics Data Analysis Tool." Journal of Biomedicine and Biotechnology 2011 (2011): 1–7. http://dx.doi.org/10.1155/2011/839862.
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Metabolomics is an emerging field that is based on the quantitative measurement of as many small organic molecules occurring in a biological sample as possible. Due to recent technical advances, metabolomics can now be used widely as an analytical high-throughput technology in drug testing and epidemiological metabolome and genome wide association studies. Analogous to chip-based gene expression analyses, the enormous amount of data produced by modern kit-based metabolomics experiments poses new challenges regarding their biological interpretation in the context of various sample phenotypes. We developedmetaP-serverto facilitate data interpretation.metaP-serverprovides automated and standardized data analysis for quantitative metabolomics data, covering the following steps from data acquisition to biological interpretation: (i) data quality checks, (ii) estimation of reproducibility and batch effects, (iii) hypothesis tests for multiple categorical phenotypes, (iv) correlation tests for metric phenotypes, (v) optionally including all possible pairs of metabolite concentration ratios, (vi) principal component analysis (PCA), and (vii) mapping of metabolites onto colored KEGG pathway maps. Graphical output is clickable and cross-linked to sample and metabolite identifiers. Interactive coloring of PCA and bar plots by phenotype facilitates on-line data exploration. For users of commercial metabolomics kits, cross-references to the HMDB, LipidMaps, KEGG, PubChem, and CAS databases are provided.metaP-serveris freely accessible athttp://metabolomics.helmholtz-muenchen.de/metap2/.
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Gu, Zhimin, Amie S. Corbin, Thomas O'Hare, Anna M. Eiring, Tian yi Zhang, Brian J. Druker, and Michael W. Deininger. "Suppression of CML Progenitor but Not Stem Cells Requires Simultaneous Inhibition of KIT and BCR-ABL1." Blood 120, no. 21 (November 16, 2012): 2778. http://dx.doi.org/10.1182/blood.v120.21.2778.2778.
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Abstract Abstract 2778 In chronic myeloid leukemia (CML), imatinib and other tyrosine kinase inhibitors (TKIs) inhibit BCR-ABL1 tyrosine kinase activity but also target additional kinases including KIT. The role of KIT inhibition in the therapeutic efficacy of TKIs is controversial. We used TKIs with selective activity against ABL (PPY-A) or KIT (BAW667) and genetic tools to assess the role of KIT signaling for growth of CML cell lines and primary CML progenitor and stem cells. In Mo7eBCR-ABL1 or newly diagnosed CML CD34+ progenitor cells, immunoblotting confirmed that PPY-A (1 μM) suppresses BCR-ABL1 phosphorylation but not KIT tyrosine phosphorylation. In contrast, treatment of cells with a KIT-blocking antibody (K44.2, 200ng/mL), shRNA targeting KIT (shKIT), or the KIT selective inhibitor BAW667 (1 μM), suppressed KIT activity without affecting BCR-ABL1 kinase activity. Therefore, these systems are suitable to isolate the role of BCR-ABL1 vs. KIT inhibition. Treatment of Mo7eBCR-ABL1 cells with PPY-A resulted in suppression of growth by 91.7% (p<0.003). When PPY-A was combined with KIT activation by SCF, proliferation was restored, indicating KIT signaling must be inactivated to induce cell death by BCR-ABL1 inhibition. Immunoblot analysis of Mo7eBCR-ABL1 cells revealed that culture in SCF rapidly activated AKT and ERK1/2 in the presence but not absence of PPY-A. Simultaneous inhibition of AKT with LY294002 abolished SCF-mediated rescue of cell proliferation, whereas ERK1/2 inhibition with PD98059 only partially abrogated SCF rescue. These data indicate that SCF rescue of Mo7eBCR-ABL1 cells upon BCR-ABL1 inhibition critically depends on AKT. To assess BCR-ABL1 vs. KIT inhibition in primary cells, CD34+ cells from newly diagnosed CML patients (n=4) and normal controls (n=3) were cultured in semisolid medium supplied with IL-3 and GM-CSF (no SCF), in the presence of 1 μM PPY-A combined with shKIT or 1 μM BAW667. KIT inhibition by shKIT or 1 μM BAW667 reduced CFU-GM formation by 40% compared to controls (p<0.04) even in the absence of SCF, with no effects were seen in normal CD34+ cells, indicating that BCR-ABL1-dependent KIT activation occurs in the absence of SCF stimulation. PPY-A reduced colony formation by 54.7%, while PPY-A plus shKIT and PPY-A plus BAW667 suppressed CFU-GM colony formation by 79.7% and 72.1%, comparable to the effects of imatinib (71.9%). Addition of SCF partially rescued colony growth from the effects of PPY-A, consistent with results on Mo7eBCR-ABL1 cells. In a separate set of experiments lineage-negative (Lin−) cells from newly diagnosed patients (n=4) were cultured on HS-5 stromal cells containing K44.2, PPY-A, K44.2 plus PPY-A or 2 mM imatinib, followed by clonogenic assays. Only the PPY-A / K44.2 combination suppressed CFU-GM; isolated BCR-ABL1 or KIT block did not. These data demonstrate that both BCR-ABL1 and KIT contribute to CML progenitor cell survival under physiologically relevant conditions, and that inhibition of both pathways is required for imatinib-mediated suppression of CML progenitor cells. To assess the role of KIT vs. BCR-ABL1 inhibition on primitive CML cells we performed long-term culture-initiating cell (LTC-IC) assays on M2–10B4 murine stromal cells, using Lin− cells from newly diagnosed patients (n=3). Cultures were performed with K44.2, PPY-A, K44.2 plus PPY-A or 2 mM imatinib, with colonies plated at 1, 3, and 6 weeks. At 1 week colonies were reduced by 30% with K44.2 and 70% with PPY-A, but by 90% with the PPY-A / K44.2 combination or with imatinib. In contrast, at 6 weeks colony formation was unaffected by K44.2 but reduced by >95% with PPY-A, the PPY-A / K44.2 combination or imatinib. Week 3 colony growth was intermediate. Consistent with the LTC-IC assay, KIT inhibition with BAW667 enhanced PPY-A suppression of colony formation in Lin−CD34+CD38+ progenitor cells from newly diagnosed patients (n=3) by 18.7% (p<0.05), with no significant effect on primitive Lin−CD34+CD38− cells (7.7%, p=ns). Our findings suggest KIT inhibition is much more critical for suppression of mature progenitors compared to primitive CML cells. Since AKT is active in CML progenitors but suppressed by TGFβ in stem cells (Nature, 2010;463(7281):676; JCI, 2011;121(1):396), we speculate that upon BCR-ABL1 inhibition CML progenitors but not stem cells switch to an SCF-dependent mode of AKT activation, which renders these cells uniquely sensitive to dual inhibition of BCR-ABL1 and KIT signaling. Disclosures: No relevant conflicts of interest to declare.
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Arkani, Mohammad, Hossein Khalafi, Naser Vosoughi, and Samad Khakshournia. "Development and Experimental Validation of a Correlation Monitor Tool Based on the Endogenous Pulsed Neutron Source Technique." Metrology and Measurement Systems 24, no. 3 (September 1, 2017): 441–61. http://dx.doi.org/10.1515/mms-2017-0043.
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AbstractA correlation measuring tool for an endogenous pulsed neutron source experiment is developed in this work. Paroxysmal pulses generated by a bursts of neutron chains are detected by a 10-kbit embedded shift register with a time resolution of 100 ns. The system is implemented on a single reprogrammable device making it a compact, cost-effective instrument, easily adaptable for any case study. The system was verified experimentally in theEsfahan heavy-water zero power reactor(EHWZPR). The results obtained by the measuring tool are validated by the Feynman-α experiment, and a good agreement is seen within the boundaries of statistical uncertainties. The theory of the methods is briefly initiated in the text. Also, the system structure is described, the experimental results and their uncertainties are discussed, and neutron statistics in EHWZPR is examined experimentally.
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Beiter, Philip, and Peter Groche. "On the Development of Novel Light Weight Profiles for Automotive Industries by Roll Forming of Tailor Rolled Blanks." Key Engineering Materials 473 (March 2011): 45–52. http://dx.doi.org/10.4028/www.scientific.net/kem.473.45.
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Due to continuously increasing demands on safety, comfort and ecological performance, different lightweight construction concepts have been searched for and applied by the automotive industry lately. This paper focuses on the development of novel light weight profiles by roll forming of tailor rolled blanks (TRBs). It covers analytics, experiments and FE analysis. At the beginning, state of the art tools were used for a fundamental process layout. The results show, that their application with respect to the varying sheet thicknesses within the blanks is generally acceptable. However, it may be concluded that TRBs as semi-finished products for roll forming operations call for a well adapted pre-cut of the blank. In a second step, roll forming of TRBs to a symmetrical U-profile with constant roll gap was investigated. For this purpose, experiments on a conventional roll forming line and corresponding FE simulations were conducted. Both show very similar results for the final bending angle of the part. Nevertheless, variability in bending angle of up to 14.3° is witnessed between the areas of different sheet thickness on one part. Thus, one may conclude, that a sheet thickness dependent adaptation of the roll gap is necessary for closer tolerances. A vertical and horizontal adjustability of the rolls seems appropriate to meet this purpose. With respect to these findings, two different tool kit concepts were developed and investigated by means of FE analysis. Both aim at a real-time adjustment of the roll gap to the actual sheet thickness within the stand. On the one hand, a force-driven self-positioning of the rolls was simulated. On the other hand the positioning of the rolls was preset in accordance to the feed of the sheet and its thickness distribution. Both concepts are discussed by their effect on the final bending angle of the roll formed U-profile.
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Koulaouzidis, Anastasios, Dimitris Iakovidis, Diana Yung, Emanuele Rondonotti, Uri Kopylov, John Plevris, Ervin Toth, et al. "KID Project: an internet-based digital video atlas of capsule endoscopy for research purposes." Endoscopy International Open 05, no. 06 (May 31, 2017): E477—E483. http://dx.doi.org/10.1055/s-0043-105488.
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Abstract Background and aims Capsule endoscopy (CE) has revolutionized small-bowel (SB) investigation. Computational methods can enhance diagnostic yield (DY); however, incorporating machine learning algorithms (MLAs) into CE reading is difficult as large amounts of image annotations are required for training. Current databases lack graphic annotations of pathologies and cannot be used. A novel database, KID, aims to provide a reference for research and development of medical decision support systems (MDSS) for CE. Methods Open-source software was used for the KID database. Clinicians contribute anonymized, annotated CE images and videos. Graphic annotations are supported by an open-access annotation tool (Ratsnake). We detail an experiment based on the KID database, examining differences in SB lesion measurement between human readers and a MLA. The Jaccard Index (JI) was used to evaluate similarity between annotations by the MLA and human readers. Results The MLA performed best in measuring lymphangiectasias with a JI of 81 ± 6 %. The other lesion types were: angioectasias (JI 64 ± 11 %), aphthae (JI 64 ± 8 %), chylous cysts (JI 70 ± 14 %), polypoid lesions (JI 75 ± 21 %), and ulcers (JI 56 ± 9 %). Conclusion MLA can perform as well as human readers in the measurement of SB angioectasias in white light (WL). Automated lesion measurement is therefore feasible. KID is currently the only open-source CE database developed specifically to aid development of MDSS. Our experiment demonstrates this potential.
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Zheng, Zhe, Li Hong Lv, Jie Jiang, and Yang Zhou. "Research and Realization of Highly Accurate Data Generation Based on Channel Simulator." Advanced Materials Research 588-589 (November 2012): 1316–19. http://dx.doi.org/10.4028/www.scientific.net/amr.588-589.1316.
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With high accuracy, the channel simulator plays an important role in the docking experiment between the ground and the responder beacon. To begin with, this paper introduces the data generation algorithm including the data generation based on simulation technology, the principle of the linear least squares algorithm and then proposes the least squares quadratic spline method to generate highly accurate data in this channel simulator. Secondly, this paper introduces the system design to realize the data generation. Finally, a case which studies the approximation and an error analysis of the data generation algorithm is realized. The algorithm is considered to be accurate and easy to get the source data. The core of the algorithm is using data from Satellite Tool Kit to generate distance and speed sequence, and using the least squares to approximate real data and quadratic spline to fit for obtaining highly accurate data.
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Savage-Knepshield, Pamela A. "Usability Testing for Rapid Fielding with Small Ns: Lessons Learned during an Army Operational Field Experiment." Proceedings of the Human Factors and Ergonomics Society Annual Meeting 51, no. 26 (October 2007): 1622–26. http://dx.doi.org/10.1177/154193120705102605.
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The Army's acquisition process is transforming to meet the needs of a force that must be agile, adaptive, and responsive to asymmetric threats. Advanced capabilities and technologies, which are urgently needed to enable rapid response to evolving military needs, are being developed and pushed out to troops at unprecedented rates. As a result, not all systems have undergone an iterative design process, received usability feedback from their target users, or had design support from human factors engineers to ensure that unit and Soldier considerations have been addressed. Subsequently, these systems may possess characteristics that induce high cognitive workload, fatigue, detectability, or trigger events that lead to fratricide. When human factors engineers encounter a system that has not derived these benefits, they too must become more agile, adaptive, and responsive to ensure that Soldier feedback is collected and that serious issues are identified and resolved before the system makes its way to the battlefield. Lessons learned while participating in advanced technology and experimentation programs include techniques that facilitate working with small Ns, institutional review boards, rapid survey instrument development, and the collection of qualitative feedback as well as the importance of having a “usability tool kit” available to facilitate data collection efforts in an operational field environment.
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Mamo, S., C. A. Sargent, N. A. Affara, K. Wimmers, S. Ponsuksili, M. Gilles, and K. Schellander. "227 CONSTRUCTION OF STAGE-SPECIFIC cDNA MICROARRAY, AND ANALYSIS OF IN VITRO PRODUCED PRE-IMPLANATION STAGE BOVINE EMBRYOS FOR DEVELOPMENTAL COMPETENCE." Reproduction, Fertility and Development 17, no. 2 (2005): 264. http://dx.doi.org/10.1071/rdv17n2ab227.
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Microarray technology currently has wide acceptance as a research tool in the study of gene expression profiling, mainly as a result of its use for monitoring the expression profiles of thousands of genes in a single experiment. However, its use in analyzing gene expression in the pre-implantation stage of bovine embryo development has been limited for reasons such as the large amount of RNA required and the lack of bovine specific cDNA clone collections (Smith L and Greenfield A 2003 Hum. Mol. Genet. 12, 1–8). In this study, with the objectives of producing pre-implantation-stage-specific bovine cDNA clones and examining the developmental competence, eighty-two selected target clones of pre-implantation-stage-specific genes were prepared and spotted on the glass slide. Embryos were produced in vitro and mRNAs were isolated from contrasting probes of good quality matured oocytes and blastocyst-stage embryos using a Dynabead mRNA isolation kit by following the manufacturer's instructions. First-strand cDNA syntheses were primed with T7 Oligo d(T)21 primer, followed by random primed second-strand syntheses using a DOP master kit (Roche Diagnostics, Mannheim, Germany) and global amplification using the same primers used for the first- and second-strand syntheses. In vitro transcription was performed to amplify the RNA by using the AmpliScribe T7 transcription kit (EPICENTRE Technologies, Oldendorf, Germany), and the amplified RNA (aRNA) was purified using a RNeasy Mini kit (Qiagen, Hilden, Germany). Finally, the results of different RNA amplifications (aRNA) were tested by hybridization on microarrays and also using real-time PCR techniques. With these analyses, the sufficiency of the yield and linearity of amplification procedures were confirmed. Three micrograms each of aRNA were labelled with Cy3 and Cy5 dyes and hybridized to the array. After overnight incubation at 42°C, the slides were sequentially washed and scanned using an ArrayWorx biochip reader (Applied Precision, Marlborough, UK), and quantifications as well as all analyses were carried out using different TIGR software modules (Saeed AI et al. 2003 Biotechniques 34(2), 374–378). Analyses of the results of repeated hybridizations showed that 35 genes (43%), which belong to different functional groups, were differentially expressed between the two stages. Further independent analyses using real-time PCR confirmed the results of 25 genes. Hence, it is possible to conclude that the established methods can be used for large scale gene expression analysis, and the identified genes can be potential candidates for characterizing developmental competence.
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Pallares, Luisa F., Serge Picard, and Julien F. Ayroles. "TM3’seq: A Tagmentation-Mediated 3’ Sequencing Approach for Improving Scalability of RNAseq Experiments." G3: Genes|Genomes|Genetics 10, no. 1 (November 1, 2019): 143–50. http://dx.doi.org/10.1534/g3.119.400821.
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RNA-seq has become the standard tool for collecting genome-wide expression data in diverse fields, from quantitative genetics and medical genomics to ecology and developmental biology. However, RNA-seq library preparation is still prohibitive for many laboratories. Recently, the field of single-cell transcriptomics has reduced costs and increased throughput by adopting early barcoding and pooling of individual samples —producing a single final library containing all samples. In contrast, RNA-seq protocols where each sample is processed individually are significantly more expensive and lower throughput than single-cell approaches. Yet, many projects depend on individual library generation to preserve important samples or for follow-up re-sequencing experiments. Improving on currently available RNA-seq methods we have developed TM3′seq, a 3′-enriched library preparation protocol that uses Tn5 transposase and preserves sample identity at each step. TM3′seq is designed for high-throughput processing of individual samples (96 samples in 6h, with only 3h hands-on time) at a fraction of the cost of commercial kits ($1.5 per sample). The protocol was tested in a range of human and Drosophila melanogaster RNA samples, recovering transcriptomes of the same quality and reliability than the commercial NEBNext kit. We expect that the cost- and time-efficient features of TM3′seq make large-scale RNA-seq experiments more permissive for the entire scientific community.
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Wang, Xiaofeng, Xinyu Chen, Haiyang Ye, Yuan Liu, and Guizhu Zhang. "Cloud-Based Experimental Platform for the Space-Ground Integrated Network." Wireless Communications and Mobile Computing 2020 (October 21, 2020): 1–20. http://dx.doi.org/10.1155/2020/8893187.
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The space-ground integrated network (SGIN) is an important direction of future network development and is expected to play an important role in edge computing for the Internet of Things (IoT). Through integration with an SGIN, IoT applications can provide services with long-distance and wide-coverage features. However, SGINs are typical large-scale and time-varying networks for which new network technologies, protocols, and applications must be rigorously evaluated and validated. Therefore, a reliable experimental platform is necessary for SGINs. This paper presents a cloud-based experimental platform for the SGIN context named SGIN-Stack. First, the architecture of SGIN-Stack, which combines the Systems Tool Kit (STK) and OpenStack, is described. Based on this architecture, a seamless linkage between OpenStack and STK is achieved to realize synchronous, dynamic, and real-time network emulation for an SGIN, and the dynamic differential compensation technology and a random number generation algorithm are applied to improve the emulation accuracy for satellite links. Finally, an emulation scenario is constructed that includes six space-based backbone nodes, sixty-six space-based access nodes, and a ground station. Based on this emulation scenario, experiments concerning the satellite link delays, bit error ratio (BER), and throughput are carried out to prove the high fidelity of our SGIN-Stack platform. Emulation experiments involving satellite orbital maneuvers and attitude adjustments show that SGIN-Stack can be used for dynamic and real-time SGIN emulation.
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Allain, Ariane, Isaure Chauvot de Beauchêne, Florent Langenfeld, Yann Guarracino, Elodie Laine, and Luba Tchertanov. "Allosteric pathway identification through network analysis: from molecular dynamics simulations to interactive 2D and 3D graphs." Faraday Discuss. 169 (2014): 303–21. http://dx.doi.org/10.1039/c4fd00024b.
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Allostery is a universal phenomenon that couples the information induced by a local perturbation (effector) in a protein to spatially distant regulated sites. Such an event can be described in terms of a large scale transmission of information (communication) through a dynamic coupling between structurally rigid (minimally frustrated) and plastic (locally frustrated) clusters of residues. To elaborate a rational description of allosteric coupling, we propose an original approach – MOdular NETwork Analysis (MONETA) – based on the analysis of inter-residue dynamical correlations to localize the propagation of both structural and dynamical effects of a perturbation throughout a protein structure. MONETA uses inter-residue cross-correlations and commute times computed from molecular dynamics simulations and a topological description of a protein to build a modular network representation composed of clusters of residues (dynamic segments) linked together by chains of residues (communication pathways). MONETA provides a brand new direct and simple visualization of protein allosteric communication. A GEPHI module implemented in the MONETA package allows the generation of 2D graphs of the communication network. An interactive PyMOL plugin permits drawing of the communication pathways between chosen protein fragments or residues on a 3D representation. MONETA is a powerful tool for on-the-fly display of communication networks in proteins. We applied MONETA for the analysis of communication pathways (i) between the main regulatory fragments of receptors tyrosine kinases (RTKs), KIT and CSF-1R, in the native and mutated states and (ii) in proteins STAT5 (STAT5a and STAT5b) in the phosphorylated and the unphosphorylated forms. The description of the physical support for allosteric coupling by MONETA allowed a comparison of the mechanisms of (a) constitutive activation induced by equivalent mutations in two RTKs and (b) allosteric regulation in the activated and non-activated STAT5 proteins. Our theoretical prediction based on results obtained with MONETA was validated for KIT by in vitro experiments. MONETA is a versatile analytical and visualization tool entirely devoted to the understanding of the functioning/malfunctioning of allosteric regulation in proteins – a crucial basis to guide the discovery of next-generation allosteric drugs.
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Chatzidaki, Eleni, Michalis Xenos, and Charikleia Machaira. "Let’s Play a Game! Kin-LDD: A Tool for Assisting in the Diagnosis of Children with Learning Difficulties." Multimodal Technologies and Interaction 3, no. 1 (March 11, 2019): 16. http://dx.doi.org/10.3390/mti3010016.
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This paper presents an alternative approach for the diagnosis of learning difficulties in children. A game-based evaluation study, using Kinaesthetic Learning Difficulties Diagnosis (Kin-LDD), was performed during the actual diagnosis procedure for the identification of learning difficulties. Kin-LDD is a serious game that provides a gesture-based interface and incorporates spatial and time orientation activities. These activities assess children’s cognitive attributes while they are using their motor skills to interact with the game. The aim of this work was to introduce the fun parameter to the diagnostic process, provide a useful tool for the special educators and investigate potential correlations between in-game metrics and the diagnosis outcome. An experiment was conducted in which 30 children played the game during their official assessment for the diagnosis of learning difficulties at the Center for Differential Diagnosis, Diagnosis and Support. Performance metrics were collected automatically while the children were playing the game. These metrics, along with questionnaires appropriate for children and post-session interviews were later analyzed and the findings are presented in the paper. According to the results: (a) children evaluated the game as a fun experience, (b) special educators claimed it was helpful to the diagnostic procedure, and (c) there were statistically significant correlations between in-game metrics and the category of learning difficulty the child was characterized with.
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Djajanegara, Ira, Wayan Artama, Retno Lestari, and Sabar Pambudi. "VERIFIKASI cDNA T29 SEBAGAI KANDIDAT GEN PENGKODE PROTEIN Toxoplasma gondii DENGAN METODE SDS PAGE." Berkala Penelitian Hayati 11, no. 1 (December 31, 2005): 61–66. http://dx.doi.org/10.23869/bphjbr.11.1.200510.
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The process of cDNA construction from mRNA isolated from Toxoplasma gondii has been done. There were 7 candidates cDNA which one of them is called T29. Since Toxoplasma gondii is the cause of toxoplasmosis infection, cloning the gene encoding protein from this parasite provides an important tool for developing diagnostic kit for detection of toxoplasmosis. Digestion of the cDNA T29 with EcoRI which is the restriction site where the cDNA was inserted yielded a 1.862 bp fragment. The fragment was subcloned into E. coli expression vector pMal-p2x and transformed into E.coli strain TB1. Colonies of TB1 were grown on ampicillin plates and the recombinant plasmid was extracted using the standard procedure. The plasmid was digested using EcoRI and PstI, checked by PCR amplification using malE and M13/pUC primers. The recombinant plasmid was expressed in TB1 and the protein extracted was ran in SDS PAGE to observe the presence of the expressed protein. Based on the data from this experiment, there was no expression result of the expressed cDNA which was confirm by the PCR result. Therefore, it was concluded that cDNA T29 was not carrying the gene coding for protein from parasite Toxoplasma gondii.
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Stemplewska-Żakowicz, Katarzyna, Bartosz Zalewski, Hubert Suszek, Dorota Kobylińska, and Bartosz Szymczyk. "The Discursive Mind Model." Psychology of Language and Communication 18, no. 1 (May 1, 2014): 1–21. http://dx.doi.org/10.2478/plc-2014-0001.
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AbstractThe paper proposes the model of discursive mind and describes the cognitive architecture of the dialogically structured mind. The model draws on Hermans’ (1999) theory of the dialogical self (DS) and Wertsch’s (1991) vision of mind as a “tool kit” with socio-cultural instruments, and also on the socio-cognitive approach to personality in experimental psychology. An I-position is understood here as an active totality of experience, shaped in a particular social context and represented in a separate representation module. Th ere are many modules in the mind because in the course of socialization, the individual comes across many different social contexts. Th e described model and its preliminary empirical verification not only gives support to the DS theory, but can also be a leverage of its contribution to general theories of mind stemming from other theoretical traditions