Academic literature on the topic 'Differential download'
Create a spot-on reference in APA, MLA, Chicago, Harvard, and other styles
Consult the lists of relevant articles, books, theses, conference reports, and other scholarly sources on the topic 'Differential download.'
Next to every source in the list of references, there is an 'Add to bibliography' button. Press on it, and we will generate automatically the bibliographic reference to the chosen work in the citation style you need: APA, MLA, Harvard, Chicago, Vancouver, etc.
You can also download the full text of the academic publication as pdf and read online its abstract whenever available in the metadata.
Journal articles on the topic "Differential download"
1
Hammelman, Jennifer, and David K. Gifford. "Discovering differential genome sequence activity with interpretable and efficient deep learning." PLOS Computational Biology 17, no. 8 (August 9, 2021): e1009282. http://dx.doi.org/10.1371/journal.pcbi.1009282.
Full textAbstract:
Discovering sequence features that differentially direct cells to alternate fates is key to understanding both cellular development and the consequences of disease related mutations. We introduce Expected Pattern Effect and Differential Expected Pattern Effect, two black-box methods that can interpret genome regulatory sequences for cell type-specific or condition specific patterns. We show that these methods identify relevant transcription factor motifs and spacings that are predictive of cell state-specific chromatin accessibility. Finally, we integrate these methods into framework that is readily accessible to non-experts and available for download as a binary or installed via PyPI or bioconda at https://cgs.csail.mit.edu/deepaccess-package/.
2
Chabbert, Christophe D., Lars M. Steinmetz, and Bernd Klaus. "DChIPRep, an R/Bioconductor package for differential enrichment analysis in chromatin studies." PeerJ 4 (April 26, 2016): e1981. http://dx.doi.org/10.7717/peerj.1981.
Full textAbstract:
The genome-wide study of epigenetic states requires the integrative analysis of histone modification ChIP-seq data. Here, we introduce an easy-to-use analytic framework to compare profiles of enrichment in histone modifications around classes of genomic elements, e.g. transcription start sites (TSS). Our framework is available via the user-friendly R/Bioconductor packageDChIPRep.DChIPRepuses biological replicate information as well as chromatin Input data to allow for a rigorous assessment of differential enrichment.DChIPRepis available for download through the Bioconductor project athttp://bioconductor.org/packages/DChIPRep.Contact.DChIPRep@gmail.com.
3
Deller, J. R., Hayder Radha, and J. Justin McCormick. "Exploiting Identifiability and Intergene Correlation for Improved Detection of Differential Expression." ISRN Bioinformatics 2013 (June 3, 2013): 1–15. http://dx.doi.org/10.1155/2013/404717.
Full textAbstract:
Accurate differential analysis of microarray data strongly depends on effective treatment of intergene correlation. Such dependence is ordinarily accounted for in terms of its effect on significance cutoffs. In this paper, it is shown that correlation can, in fact, be exploited to share information across tests and reorder expression differentials for increased statistical power, regardless of the threshold. Significantly improved differential analysis is the result of two simple measures: (i) adjusting test statistics to exploit information from identifiable genes (the large subset of genes represented on a microarray that can be classified a priori as nondifferential with very high confidence], but (ii) doing so in a way that accounts for linear dependencies among identifiable and nonidentifiable genes. A method is developed that builds upon the widely used two-sample t-statistic approach and uses analysis in Hilbert space to decompose the nonidentified gene vector into two components that are correlated and uncorrelated with the identified set. In the application to data derived from a widely studied prostate cancer database, the proposed method outperforms some of the most highly regarded approaches published to date. Algorithms in MATLAB and in R are available for public download.
4
Ma, Guowei, Mingyan Liu, Ke Du, Xin Zhong, Shiqiang Gong, Linchi Jiao, and Minjie Wei. "Differential Expression of mRNAs in the Brain Tissues of Patients with Alzheimer’s Disease Based on GEO Expression Profile and Its Clinical Significance." BioMed Research International 2019 (February 26, 2019): 1–9. http://dx.doi.org/10.1155/2019/8179145.
Full textAbstract:
Background. Early diagnosis of Alzheimer’s disease (AD) is an urgent point for AD prevention and treatment. The biomarkers of AD still remain indefinite. Based on the bioinformatics analysis of mRNA differential expressions in the brain tissues and the peripheral blood samples of Alzheimer’s disease (AD) patients, we investigated the target mRNAs that could be used as an AD biomarker and developed a new effective, practical clinical examination program. Methods. We compared the AD peripheral blood mononuclear cells (PBMCs) expression dataset (GEO accession GSE4226 and GSE18309) with AD brain tissue expression datasets (GEO accessions GSE1297 and GSE5281) from GEO in the present study. The GEO gene database was used to download the appropriate gene expression profiles to analyze the differential mRNA expressions between brain tissue and blood of AD patients and normal elderly. The Venn diagram was used to screen out the differential expression of mRNAs between the brain tissue and blood. The protein-protein interaction network map (PPI) was used to view the correlation between the possible genes. GO (gene ontology) and KEGG (Kyoto Gene and Genomic Encyclopedia) were used for gene enrichment analysis to determine the major affected genes and the function or pathway. Results. Bioinformatics analysis revealed that there were differentially expressed genes in peripheral blood and hippocampus of AD patients. There were 4958 differential mRNAs in GSE18309, 577 differential mRNAs in GSE4226 in AD PBMCs sample, 7464 differential mRNAs in GSE5281, and 317 differential mRNAs in GSE129 in AD brain tissues, when comparing between AD patients and healthy elderly. Two mRNAs of RAB7A and ITGB1 coexpressed in hippocampus and peripheral blood were screened. Furthermore, functions of differential genes were enriched by the PPI network map, GO, and KEGG analysis, and finally the chemotaxis, adhesion, and inflammatory reactions were found out, respectively. Conclusions. ITGB1 and RAB7A mRNA expressions were both changed in hippocampus and PBMCs, highly suggested being used as an AD biomarker with AD. Also, according to the results of this analysis, it is indicated that we can test the blood routine of the elderly for 2-3 years at a frequency of 6 months or one year. When a patient continuously detects the inflammatory manifestations, it is indicated as a potentially high-risk AD patient for AD prevention.
5
Tran, Stephen S., Qing Zhou, and Xinshu Xiao. "Statistical inference of differential RNA-editing sites from RNA-sequencing data by hierarchical modeling." Bioinformatics 36, no. 9 (January 31, 2020): 2796–804. http://dx.doi.org/10.1093/bioinformatics/btaa066.
Full textAbstract:
Abstract Motivation RNA-sequencing (RNA-seq) enables global identification of RNA-editing sites in biological systems and disease. A salient step in many studies is to identify editing sites that statistically associate with treatment (e.g. case versus control) or covary with biological factors, such as age. However, RNA-seq has technical features that incumbent tests (e.g. t-test and linear regression) do not consider, which can lead to false positives and false negatives. Results In this study, we demonstrate the limitations of currently used tests and introduce the method, RNA-editing tests (REDITs), a suite of tests that employ beta-binomial models to identify differential RNA editing. The tests in REDITs have higher sensitivity than other tests, while also maintaining the type I error (false positive) rate at the nominal level. Applied to the GTEx dataset, we unveil RNA-editing changes associated with age and gender, and differential recoding profiles between brain regions. Availability and implementation REDITs are implemented as functions in R and freely available for download at https://github.com/gxiaolab/REDITs. The repository also provides a code example for leveraging parallelization using multiple cores.
6
Ovchinnikov, Alexey, Isabel Pérez Verona, Gleb Pogudin, and Mirco Tribastone. "CLUE: exact maximal reduction of kinetic models by constrained lumping of differential equations." Bioinformatics 37, no. 12 (February 3, 2021): 1732–38. http://dx.doi.org/10.1093/bioinformatics/btab010.
Full textAbstract:
Abstract Motivation Detailed mechanistic models of biological processes can pose significant challenges for analysis and parameter estimations due to the large number of equations used to track the dynamics of all distinct configurations in which each involved biochemical species can be found. Model reduction can help tame such complexity by providing a lower-dimensional model in which each macro-variable can be directly related to the original variables. Results We present CLUE, an algorithm for exact model reduction of systems of polynomial differential equations by constrained linear lumping. It computes the smallest dimensional reduction as a linear mapping of the state space such that the reduced model preserves the dynamics of user-specified linear combinations of the original variables. Even though CLUE works with non-linear differential equations, it is based on linear algebra tools, which makes it applicable to high-dimensional models. Using case studies from the literature, we show how CLUE can substantially lower model dimensionality and help extract biologically intelligible insights from the reduction. Availability and implementation An implementation of the algorithm and relevant resources to replicate the experiments herein reported are freely available for download at https://github.com/pogudingleb/CLUE. Supplementary information Supplementary data are available at Bioinformatics online.
7
Du, Yajing, Sujuan Yuan, Xibing Zhuang, Qi Zhang, and Tiankui Qiao. "Multiomics Differences in Lung Squamous Cell Carcinoma Patients with High Radiosensitivity Index Compared with Those with Low Radiosensitivity Index." Disease Markers 2021 (August 30, 2021): 1–11. http://dx.doi.org/10.1155/2021/3766659.
Full textAbstract:
Objectives. Radiosensitivity Index (RSI) can predict intrinsic radiotherapy sensitivity. We analyzed multiomics characteristics in lung squamous cell carcinoma between high and low RSI groups, which may help understand the underlying molecular mechanism of radiosensitivity and guide optional treatment for patients in the future. Methods. The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) data were used to download clinical data, mRNA, microRNA, and lncRNA expression. Differential analyses, including mRNA, miRNA, lncRNA, and G.O. and KEGG, and GSVA analyses, were performed with R. Gene set enrichment analysis was done by GSEA. miRNA-differentially expressed gene network and ceRNA network were analyzed and graphed by the Cytoscape software. Results. In TCGA data, 542 patients were obtained, including 171 in the low RSI group (LRSI) and 371 in the high RSI group (HRSI). In RNAseq, 558 significantly differentially expressed genes (DEGs) were obtained. KRT6A was the most significantly upregulated gene and IDO1 was the most significantly downregulated gene. In miRNAseq, miR-1269a was the most significantly upregulated. In lncRNAseq, LINC01871 was the most upregulated. A 66-pair interaction between differentially expressed genes and miRNAs and an 11-pair interaction between differential lncRNAs and miRNAs consisted of a ceRNA network, of which miR-184 and miR-490-3p were located in the center. In the GEO data, there were 40 DEGs. A total of 17 genes were founded in both databases, such as ADAM23, AHNAK2, BST2, COL11A1, CXCL13, FBN2, IFI27, IFI44L, MAGEA6, and PTGR1. GSVA analysis revealed 31 significant pathways. GSEA found 87 gene sets enriched in HRSI and 91 gene sets in LRSI. G.O. and KEGG of RNA expression levels revealed that these genes were most enriched in T cell activation and cytokine−cytokine receptor interaction. Conclusions. Patients with lung squamous cell carcinoma have different multiomics characteristics between two groups. These differences may have an essential significance with radiotherapy effect.
8
BREITLING, RAINER, and PAWEL HERZYK. "RANK-BASED METHODS AS A NON-PARAMETRIC ALTERNATIVE OF THE T-STATISTIC FOR THE ANALYSIS OF BIOLOGICAL MICROARRAY DATA." Journal of Bioinformatics and Computational Biology 03, no. 05 (October 2005): 1171–89. http://dx.doi.org/10.1142/s0219720005001442.
Full textAbstract:
We have recently introduced a rank-based test statistic, RankProducts (RP), as a new non-parametric method for detecting differentially expressed genes in microarray experiments. It has been shown to generate surprisingly good results with biological datasets. The basis for this performance and the limits of the method are, however, little understood. Here we explore the performance of such rank-based approaches under a variety of conditions using simulated microarray data, and compare it with classical Wilcoxon rank sums and t-statistics, which form the basis of most alternative differential gene expression detection techniques.We show that for realistic simulated microarray datasets, RP is more powerful and accurate for sorting genes by differential expression than t-statistics or Wilcoxon rank sums — in particular for replicate numbers below 10, which are most commonly used in biological experiments.Its relative performance is particularly strong when the data are contaminated by non-normal random noise or when the samples are very inhomogenous, e.g. because they come from different time points or contain a mixture of affected and unaffected cells.However, RP assumes equal measurement variance for all genes and tends to give overly optimistic p-values when this assumption is violated. It is therefore essential that proper variance stabilizing normalization is performed on the data before calculating the RP values. Where this is impossible, another rank-based variant of RP (average ranks) provides a useful alternative with very similar overall performance.The Perl scripts implementing the simulation and evaluation are available upon request. Implementations of the RP method are available for download from the authors website ().
9
Frodden, Ernesto, and Diego Hidalgo. "Surface charges toolkit for gravity." International Journal of Modern Physics D 29, no. 06 (April 2020): 2050040. http://dx.doi.org/10.1142/s0218271820500406.
Full textAbstract:
These notes provide a detailed catalog of surface charge formulas for different classes of gravity theories. The present catalog reviews and extends the existing literature on the topic. Part of the focus is on reviewing the method to compute quasi-local surface charges for gauge theories in order to clarify conceptual issues and their range of applicability. Many surface charge formulas for gravity theories are expressed in metric, tetrads-connection, Chern–Simons connection, and even BF variables. For most of them, the language of differential forms is exploited and contrasted with the more popular metric components language. The gravity theory is coupled with matter fields as scalar, Maxwell, Skyrme, Yang–Mills, and spinors. Furthermore, three examples with ready-to-download notebook codes, show the method in full action. Several new results are highlighted through the notes.
10
Li, Jun-Chen, Qiu-Han Chen, Rui Jian, Jiang-Rong Zhou, Yun Xu, Fang Lu, Jun-Qiao Li, and Hao Zhang. "The Partial Role of KLF4 and KLF5 in Gastrointestinal Tumors." Gastroenterology Research and Practice 2021 (July 27, 2021): 1–13. http://dx.doi.org/10.1155/2021/2425356.
Full textAbstract:
Background. KLF4 and KLF5 are members of the KLF transcription factor family, which play an important role in many gastrointestinal tumors. To gain a deeper insight into its function and role, bioinformatics was used to analyze the function and role of KLF4 and KLF5 in gastrointestinal tumors. Methods. Data were collected from several online databases. Gene Expression Profiling Interactive Analysis (GEPIA), UALCAN database analysis, Kaplan-Meier Plotter analysis, LOGpc system, the Pathology Atlas, and the STRING website were used to analyze the data. We download relevant data from TCGA and then perform GO enrichment and KEGG enrichment analysis. The effects of KLF5 on gastric cancer cell proliferation were measured by CCK-8 assay. The effect of KLF5 on the expression of CyclinD1 and MMP9 was detected by Western blot. Results. KLF4 and KLF5 were differentially expressed in normal and tumor tissues of the gastrointestinal tract, and their differential expression is related to several genes or pathways. KEGG analysis showed that KLF5 was coexpressed with endocytosis-related genes. KLF5 promotes the proliferation of gastric cancer cells and the expression of metastasis-related molecules. Conclusion. KLF4 and KLF5 are of great significance for developing gastrointestinal tumors and can be used as therapeutic targets.
Dissertations / Theses on the topic "Differential download"
1
Brawerman, Alessandro. "A Fraud-Prevention Framework for Software Defined Radio Mobile Devices." Diss., Georgia Institute of Technology, 2005. http://hdl.handle.net/1853/7162.
Full textAbstract:
The superior reconfigurability of software defined radio mobile devices has made it one of the most promising technology on the wireless network and in the mobile communication industry.
The evolution from a static and rigid system to a highly dynamic environment, which offers many advantages over current systems, has been made possible thanks to the concepts of programmability
and reconfigurability introduced by the software defined radio technology and the higher level of flexibility and openness of this technology's devices.
Clearly, the software defined radio mobile device's flexibility is a great advantage since the customer is able to use the same device in different parts of the world, with different wireless technologies.
Despite the advantages, there are still issues to be discussed regarding security. According to the Software Defined Radio Forum some of the concerns are the radio configuration download, storage and installation, user's privacy, and cloning.
To address the SDR Forum concerns a raud-prevention framework is proposed. The framework is composed by new pieces of hardware, new modules and new protocols that together greatly enhance the overall security of software defined radio mobile devices and this new highly dynamic environment.
The framework offers security monitoring against malicious attacks and viruses that may affect the configuration data; protects sensitive information through the use of protected storage; creates and protects an identity for the system; employs a secure and efficient protocol for radio configuration download and update; and finally, establishes an anti-cloning scheme, which not
only guarantees that no units can be cloned over the air but also elevates the level of difficulty to clone units if the attacker has physical access to those units. Even if cloned units exist, the anti-cloning scheme is able to identify them and deny any service.
2
Stucki, Christoph. "Die Therapiebeziehung differentiell gestalten : intuitive Reaktionen, Patientenwahrnehmung und Beziehungsverhalten von Therapeuten in der Psychotherapie /." Bern : [s.n.], 2004. http://www.zb.unibe.ch/download/eldiss/04stucki_c.pdf.
Full textConference papers on the topic "Differential download"
1
Akinyamoju, Benedict, Don Irving, Abiodun Olofin, Christopher Browne, Enrique Loo, and Jeremy Greenwood. "Comprehensive Operational Assessment Eliminates Significant Lost Time on a 3-Year Development Project in Nigeria." In IADC/SPE Asia Pacific Drilling Technology Conference. SPE, 2021. http://dx.doi.org/10.2118/201034-ms.
Full textAbstract:
Abstract A 3 year, 23 well project drilled by a major operator in Nigeria was challenged to develop methodologies to optimize every aspect of drilling for a development project to reduce total project time and costs. The team of operator and service company personnel created an approach that systematically examined and challenged the efficiency of all tasks. They then developed and implemented innovative methods to save time by both analyzing repetitive, lengthy, or troublesome operations and challenging many status quo rig activities. The culture of continually challenging the causes of invisible lost time (ILT) that developed resulted in the creation of several critical performance improvement methodologies each of which are explained in detail. The multiple focus areas where process improvements were made included hole cleaning efficiencies, optimizing the ROP to deliver shortest well time from drilling out the casing shoe to landing the next casing, anti-collision practices to drill out conductors with a separation factor of less than 1.0, BHA design efficiencies for equipment standardization and faster make up and break down times, managing differential sticking risks, improving survey times, and developing best practices to side-track with a point-the-bit Rotary steerable system. Exact times were tracked to establish the required baselines and drilling optimization services were introduced to modify the drilling practices to reach the technical limit. The technical limit for ROP was achieved and best practices developed in this environment for effective hole cleaning, ease of tripping, and improved tripping speeds of the BHA at the end of every run saved 38.25 days over 15 wells. Average ROP's were improved by 48% in the 17 ½" section and 57% in the 12 ¼" section. The new anti-collision methodology saved 5 hours per well. BHA assembly and tool download efficiencies saved 11.47 days. Wellbore strengthening techniques prevented seepage losses and reduced stuck pipe events. Surveying improvements saved 11.78 days and new sidetracking practices saved 5 hours per sidetrack. Tasks that could be done in parallel to the critical path were identified and tasks on the critical path were performed more efficiently. ILT elimination in drilling processes saved a total of 96 days of rig time over an established performance baseline during this 23 well project. The operator set two records for the fastest drilled and completed conventional offshore wells in Nigerian history.
2
Bird, Mathew, William F. Cook, George S. Hazen, and Britton Ward. "Yacht Design Software 2.0: The Open Source Movement." In SNAME 19th Chesapeake Sailing Yacht Symposium. SNAME, 2009. http://dx.doi.org/10.5957/csys-2009-006.
Full textAbstract:
This paper is a survey of the current state of the art of open source software for yacht design applications. Yacht design and design tools we use have undergone numerous transformations in recent decades, the most notable being the introduction of the personal computer. Since the advent of the PC, yacht designers have been forced to create their own programs from scratch or choosing from relatively few off-the-shelf programs. Commercial software has been characterized by high expense, closed systems, and limited interoperability between applications that are difficult to fully customize or use in a collaborative manner. A lot of sneaker-netting and custom conversion code is often required. For the last several years, users in many industries have been given a new option of joining the “open source movement,” where software and the underlying code is made available for users to download, modify, improve and again make available to others. With open source, the isolated approach to custom software development can be replaced with a broad base of core capability that can be extended and shared with the larger community. Industry players collaborate on the essential elements of tools for our profession - as the saying goes, "A rising tide will lift all boats." There is still plenty of room for individuals or companies to differentiate themselves by how they use the tools and by their niche areas of expertise or experience, but the return on investing in an 'open source' set of common tools is potentially greater than its cost. In doing so, software tools are developed and improved in a collaborative manner, resulting in shorter development time and applications that are more powerful, robust and interoperable for all users. Although working in a closed environment may feel safe and secure to private actors, the lack of adequate peer review and external contribution leads to situation specific myopia. In this paper, we will survey available open source tools both general and yacht design specific that can be used, present some suggestions on integrating them into the design process and explore how the industry can improve these tools in the future.