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Journal articles on the topic 'Parallel profiling tool'

Author: Grafiati

Published: 4 June 2021

Last updated: 5 February 2022

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1

Qawasmeh, Ahmad, Salah Taamneh, Ashraf H. Aljammal, Nabhan Hamadneh, Mustafa Banikhalaf, and Mohammad Kharabsheh. "Parallelism exploration in sequential algorithms via animation tool." Multiagent and Grid Systems 17, no. 2 (2021): 145–58. http://dx.doi.org/10.3233/mgs-210347.

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Different high performance techniques, such as profiling, tracing, and instrumentation, have been used to tune and enhance the performance of parallel applications. However, these techniques do not show how to explore the potential of parallelism in a given application. Animating and visualizing the execution process of a sequential algorithm provide a thorough understanding of its usage and functionality. In this work, an interactive web-based educational animation tool was developed to assist users in analyzing sequential algorithms to detect parallel regions regardless of the used parallel

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Ishiya, Koji, and Shintaroh Ueda. "MitoSuite: a graphical tool for human mitochondrial genome profiling in massive parallel sequencing." PeerJ 5 (May 30, 2017): e3406. http://dx.doi.org/10.7717/peerj.3406.

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Recent rapid advances in high-throughput, next-generation sequencing (NGS) technologies have promoted mitochondrial genome studies in the fields of human evolution, medical genetics, and forensic casework. However, scientists unfamiliar with computer programming often find it difficult to handle the massive volumes of data that are generated by NGS. To address this limitation, we developed MitoSuite, a user-friendly graphical tool for analysis of data from high-throughput sequencing of the human mitochondrial genome. MitoSuite generates a visual report on NGS data with simple mouse operations.

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BONE, PAUL, ZOLTAN SOMOGYI, and PETER SCHACHTE. "Estimating the overlap between dependent computations for automatic parallelization." Theory and Practice of Logic Programming 11, no. 4-5 (2011): 575–91. http://dx.doi.org/10.1017/s1471068411000184.

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AbstractResearchers working on the automatic parallelization of programs have long known that too much parallelism can be even worse for performance than too little, because spawning a task to be run on another CPU incurs overheads. Autoparallelizing compilers have therefore long tried to use granularity analysis to ensure that they only spawn off computations whose cost will probably exceed the spawn-off cost by a comfortable margin. However, this is not enough to yield good results, because data dependencies may also limit the usefulness of running computations in parallel. If one computatio

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Reinartz, Jeannette, Eddy Bruyns, Jing-Zhong Lin, et al. "Massively parallel signature sequencing (MPSS) as a tool for in-depth quantitative gene expression profiling in all organisms." Briefings in Functional Genomics 1, no. 1 (2002): 95–104. http://dx.doi.org/10.1093/bfgp/1.1.95.

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Wierbowski, Shayne D., Tommy V. Vo, Pascal Falter-Braun, et al. "A massively parallel barcoded sequencing pipeline enables generation of the first ORFeome and interactome map for rice." Proceedings of the National Academy of Sciences 117, no. 21 (2020): 11836–42. http://dx.doi.org/10.1073/pnas.1918068117.

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Systematic mappings of protein interactome networks have provided invaluable functional information for numerous model organisms. Here we developPCR-mediatedLinkage of barcodedAdaptersTo nucleic acidElements forsequencing (PLATE-seq) that serves as a general tool to rapidly sequence thousands of DNA elements. We validate its utility by generating the ORFeome forOryza sativacovering 2,300 genes and constructing a high-quality protein–protein interactome map consisting of 322 interactions between 289 proteins, expanding the known interactions in rice by roughly 50%. Our work paves the way for hi

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Aparicio-Puerta, Ernesto, Ricardo Lebrón, Antonio Rueda, et al. "sRNAbench and sRNAtoolbox 2019: intuitive fast small RNA profiling and differential expression." Nucleic Acids Research 47, W1 (2019): W530—W535. http://dx.doi.org/10.1093/nar/gkz415.

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Abstract Since the original publication of sRNAtoolbox in 2015, small RNA research experienced notable advances in different directions. New protocols for small RNA sequencing have become available to address important issues such as adapter ligation bias, PCR amplification artefacts or to include internal controls such as spike-in sequences. New microRNA reference databases were developed with different foci, either prioritizing accuracy (low number of false positives) or completeness (low number of false negatives). Additionally, other small RNA molecules as well as microRNA sequence and len

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Liu, G. F., H. J. Cheng, W. You, E. L. Song, X. M. Liu, and F. C. Wan. "Transcriptome profiling of muscle by RNA-Seq reveals significant differences in digital gene expression profiling between Angus and Luxi cattle." Animal Production Science 55, no. 9 (2015): 1172. http://dx.doi.org/10.1071/an14096.

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The development of massively parallel sequencing technologies enables the sequencing of total cDNA to identify unigene expression and to discover novel regions of transcription. Here, we report the first use of RNA sequencing (RNA-Seq) to find the digital gene expression profiles (DGEs) associated with the growth and development of muscle in Chinese Luxi and Angus beef cattle. More than 9 243 921 clean reads were found in samples of muscle tissue. We found 232 DGEs between Luxi cattle and Angus cattle (false discovery ratio ≤0.001 and |log2 ratio| ≥1). Among the DGEs, we determined that 147 ge

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Krainer, Julie, Andreas Weinhäusel, Karel Hanak, et al. "EPIC-TABSAT: analysis tool for targeted bisulfite sequencing experiments and array-based methylation studies." Nucleic Acids Research 47, W1 (2019): W166—W170. http://dx.doi.org/10.1093/nar/gkz398.

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Abstract DNA methylation is one of the major epigenetic modifications and has frequently demonstrated its suitability as diagnostic and prognostic biomarker. In addition to chip and sequencing based epigenome wide methylation profiling methods, targeted bisulfite sequencing (TBS) has been established as a cost-effective approach for routine diagnostics and target validation applications. Yet, an easy-to-use tool for the analysis of TBS data in combination with array-based methylation results has been missing. Consequently, we have developed EPIC-TABSAT, a user-friendly web-based application fo

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Sgorbini, Barbara, Cecilia Cagliero, Lorenzo Boggia, et al. "Parallel dual secondary-column-dual detection comprehensive two-dimensional gas chromatography: a flexible and reliable analytical tool for essential oils quantitative profiling." Flavour and Fragrance Journal 30, no. 5 (2015): 366–80. http://dx.doi.org/10.1002/ffj.3255.

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10

Zhao, Shanrong, Kurt Prenger, and Lance Smith. "Stormbow: A Cloud-Based Tool for Reads Mapping and Expression Quantification in Large-Scale RNA-Seq Studies." ISRN Bioinformatics 2013 (September 12, 2013): 1–8. http://dx.doi.org/10.1155/2013/481545.

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RNA-Seq is becoming a promising replacement to microarrays in transcriptome profiling and differential gene expression study. Technical improvements have decreased sequencing costs and, as a result, the size and number of RNA-Seq datasets have increased rapidly. However, the increasing volume of data from large-scale RNA-Seq studies poses a practical challenge for data analysis in a local environment. To meet this challenge, we developed Stormbow, a cloud-based software package, to process large volumes of RNA-Seq data in parallel. The performance of Stormbow has been tested by practically app

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Zhao, Weiqiang, Jorge Cortes, Christina Hannah, Hagop M. Kantarjian, and Dan Jones. "Kinase Profiling as a Tool in Molecular Dissection of Imatinib Resistant Chronic Myeloid Leukemia (CML)." Blood 108, no. 11 (2006): 2337. http://dx.doi.org/10.1182/blood.v108.11.2337.2337.

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Abstract Imatinib (Gleevec) resistance (IR) in CML is a multifactorial phenomenon related to ineffective blockage of the bcr-abl kinase through point mutation and/or gene amplification, or alternatively kinase bypass through clonal evolution or presently unknown mechanisms. The newer generation of bcr-abl small molecule inhibitors (dasatinib, nilotinib) may be useful in overcoming ineffective bcr-abl blockage in IR-CML but may not be effective in other mechanisms of resistance. As a tool in classifying the pattern of disease resistance, we profiled kinase levels in IR-CML following switch to n

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Boyle, Evan A., Johan O. L. Andreasson, Lauren M. Chircus, et al. "High-throughput biochemical profiling reveals sequence determinants of dCas9 off-target binding and unbinding." Proceedings of the National Academy of Sciences 114, no. 21 (2017): 5461–66. http://dx.doi.org/10.1073/pnas.1700557114.

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The bacterial adaptive immune system CRISPR–Cas9 has been appropriated as a versatile tool for editing genomes, controlling gene expression, and visualizing genetic loci. To analyze Cas9’s ability to bind DNA rapidly and specifically, we generated multiple libraries of potential binding partners for measuring the kinetics of nuclease-dead Cas9 (dCas9) interactions. Using a massively parallel method to quantify protein–DNA interactions on a high-throughput sequencing flow cell, we comprehensively assess the effects of combinatorial mismatches between guide RNA (gRNA) and target nucleotides, bot

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Khor, Jian Ming, Jennifer Guerrero-Santoro, William Douglas, and Charles A. Ettensohn. "Global patterns of enhancer activity during sea urchin embryogenesis assessed by eRNA profiling." Genome Research 31, no. 9 (2021): 1680–92. http://dx.doi.org/10.1101/gr.275684.121.

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We used capped analysis of gene expression with sequencing (CAGE-seq) to profile eRNA expression and enhancer activity during embryogenesis of a model echinoderm: the sea urchin, Strongylocentrotus purpuratus. We identified more than 18,000 enhancers that were active in mature oocytes and developing embryos and documented a burst of enhancer activation during cleavage and early blastula stages. We found that a large fraction (73.8%) of all enhancers active during the first 48 h of embryogenesis were hyperaccessible no later than the 128-cell stage and possibly even earlier. Most enhancers were

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Cao, M., K. W. Wang, Y. Fujii, and W. E. Tobler. "Development of a Friction Component Model for Automotive Powertrain System Analysis and Shift Controller Design based on Parallel-Modulated Neural Networks." Journal of Dynamic Systems, Measurement, and Control 127, no. 3 (2004): 382–405. http://dx.doi.org/10.1115/1.1978909.

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In this study, a new hybrid-neural-network-based friction component model is developed for powertrain (PT) dynamic analysis and controller design. This new model, with significantly improved input-output scalability over conventional neural network configuration, has the capability to serve as a forward as well as an inverse system model. The structural information of the available physical and empirical correlations is utilized to construct a parallel-modulated neural network (PMNN) architecture consisting of small parallel sub-networks reflecting specific mechanisms of the friction component

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Yazdanbakhsh, Nima, and Joachim Fisahn. "High throughput phenotyping of root growth dynamics, lateral root formation, root architecture and root hair development enabled by PlaRoM." Functional Plant Biology 36, no. 11 (2009): 938. http://dx.doi.org/10.1071/fp09167.

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Plant organ phenotyping by non-invasive video imaging techniques provides a powerful tool to assess physiological traits and biomass production. We describe here a range of applications of a recently developed plant root monitoring platform (PlaRoM). PlaRoM consists of an imaging platform and a root extension profiling software application. This platform has been developed for multi parallel recordings of root growth phenotypes of up to 50 individual seedlings over several days, with high spatial and temporal resolution. PlaRoM can investigate root extension profiles of different genotypes in

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Tsui, Nancy B. Y., Peiyong Jiang, Yuen Fei Wong, et al. "Maternal Plasma RNA Sequencing for Genome-Wide Transcriptomic Profiling and Identification of Pregnancy-Associated Transcripts." Clinical Chemistry 60, no. 7 (2014): 954–62. http://dx.doi.org/10.1373/clinchem.2014.221648.

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Abstract BACKGROUND Analysis of circulating RNA in the plasma of pregnant women has the potential to serve as a powerful tool for noninvasive prenatal testing and research. However, detection of circulating RNA in the plasma in an unbiased and high-throughput manner has been technically challenging. Therefore, only a limited number of circulating RNA species in maternal plasma have been validated as pregnancy- and placenta-specific biomarkers. METHODS We explored the use of massively parallel sequencing for plasma transcriptome profiling in first-, second-, and third-trimester pregnant women.

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Chan, KC Allen, Peiyong Jiang, Yama WL Zheng, et al. "Cancer Genome Scanning in Plasma: Detection of Tumor-Associated Copy Number Aberrations, Single-Nucleotide Variants, and Tumoral Heterogeneity by Massively Parallel Sequencing." Clinical Chemistry 59, no. 1 (2013): 211–24. http://dx.doi.org/10.1373/clinchem.2012.196014.

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BACKGROUND Tumor-derived DNA can be found in the plasma of cancer patients. In this study, we explored the use of shotgun massively parallel sequencing (MPS) of plasma DNA from cancer patients to scan a cancer genome noninvasively. METHODS Four hepatocellular carcinoma patients and a patient with synchronous breast and ovarian cancers were recruited. DNA was extracted from the tumor tissues, and the preoperative and postoperative plasma samples of these patients were analyzed with shotgun MPS. RESULTS We achieved the genomewide profiling of copy number aberrations and point mutations in the pl

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18

Churkin, A. A., and I. N. Lozovsky. "QUALITY ASSURANCE OF DIAPHRAGM AND PILE WALLS BY GEOPHYSICS." Construction and Geotechnics 11, no. 2 (2020): 49–61. http://dx.doi.org/10.15593/2224-9826/2020.2.05.

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Underground structures like diaphragm and pile walls are constructed to organize waterproof curtains, protect pit sides, and transfer loads from the structures. Violations of the construction technological process can lead to the formation of defects. To prevent adverse consequences, before excavation, it is necessary to control the integrity of the slurry walls using non-destructive geophysical methods. A review of geophysical slurry wall quality control methods based on the excitation and registration of physical fields through access tubes installed in the reinforcement cage, in wells drill

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Wang, Yuying, Jianchao Zheng, Zhilong Li, et al. "Development of a novel liquid biopsy test to diagnose and locate gastrointestinal cancers." Journal of Clinical Oncology 38, no. 15_suppl (2020): 1557. http://dx.doi.org/10.1200/jco.2020.38.15_suppl.1557.

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1557 Background: Cancers of the gastrointestinal (GI) system, including esophagus, stomach, pancreas, gallbladder, liver, bile duct, colon, and rectum are estimated to account for 38% of all cancer incidences and nearly 46% of cancer-related deaths in China. We conducted a multi-center study to evaluate the feasibility of using genetic and epigenetic abnormalities in plasma cfDNA to diagnose and locate GI cancers. Methods: We performed parallel genetic and epigenetic profiling of plasma cfDNA from hepatocellular carcinoma (HCC), colorectal cancer (CRC) and pancreatic cancer (PC) patients as we

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Stenson, Martin, Ulla Ruetschi, Sverker Hasselblom, Herman Nilsson-Ehle, and P.-O. Andersson. "Can Global Protein Expression Profiling Determine Prognosis in Diffuse Large B-Cell Lymphoma?" Blood 120, no. 21 (2012): 1537. http://dx.doi.org/10.1182/blood.v120.21.1537.1537.

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Abstract Abstract 1537 Background. With current rituximab-based treatment about 60 % of patients with diffuse large B-cell lymphoma (DLBCL) can be cured. However, for patients with early relapse or being refractory to such therapy outcome is very poor. The International Prognostic Index (IPI) is still the only prognostic tool used in daily clinical practice to risk stratify DLBCL patients. Yet, IPI has a limited ability to identify patients with risk of early relapse or refractory disease. Thus, there is a great need for reliable biomarkers capable of identifying high-risk patients for whom al

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Gasper, F., K. Goergen, P. Shrestha, et al. "Implementation and scaling of the fully coupled Terrestrial Systems Modeling Platform (TerrSysMP v1.0) in a massively parallel supercomputing environment – a case study on JUQUEEN (IBM Blue Gene/Q)." Geoscientific Model Development 7, no. 5 (2014): 2531–43. http://dx.doi.org/10.5194/gmd-7-2531-2014.

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Abstract. Continental-scale hyper-resolution simulations constitute a grand challenge in characterizing nonlinear feedbacks of states and fluxes of the coupled water, energy, and biogeochemical cycles of terrestrial systems. Tackling this challenge requires advanced coupling and supercomputing technologies for earth system models that are discussed in this study, utilizing the example of the implementation of the newly developed Terrestrial Systems Modeling Platform (TerrSysMP v1.0) on JUQUEEN (IBM Blue Gene/Q) of the Jülich Supercomputing Centre, Germany. The applied coupling strategies rely

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Bielecka, Monika, Bartosz Pencakowski, Marta Stafiniak, et al. "Metabolomics and DNA-Based Authentication of Two Traditional Asian Medicinal and Aromatic Species of Salvia subg. Perovskia." Cells 10, no. 1 (2021): 112. http://dx.doi.org/10.3390/cells10010112.

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Subgenus Perovskia of the extended genus of Salvia comprises several Central Asian medicinal and aromatic species, of which S. yangii and S. abrotanoides are the most widespread. These plants are cultivated in Europe as robust ornamentals, and several cultivars are available. However, their medicinal potential remains underutilized because of limited information about their phytochemical and genetic diversity. Thus, we combined an ultra-high performance liquid chromatography quadrupole time of flight mass spectrometry (UHPLC-QTOF-MS) based metabolomics with DNA barcoding approach based on trnH

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Kim, Min Jung, Jihye Lee, Seon Hee Kim, Haidong Kim, Kang-Bong Lee, and Yeonhee Lee. "Detection of Matrix Elements and Trace Impurities in Cu(In, Ga)Se2 Photovoltaic Absorbers Using Surface Analytical Techniques." Journal of Nanoscience and Nanotechnology 15, no. 10 (2015): 7722–26. http://dx.doi.org/10.1166/jnn.2015.11181.

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Chalcopyrite Cu(In,Ga)Se2 (CIGS) thin films are well known as the next-generation solar cell materials notable for their high absorption coefficient for solar radiation, suitable band gap, and ability for deposition on flexible substrate materials, allowing the production of highly flexible and lightweight solar panels. To improve solar cell performances, a quantitative and depth-resolved elemental analysis of photovoltaic thin films is much needed. In this study, Cu(In,Ga)Se2 thin films were prepared on molybdenum back contacts deposited on soda-lime glass substrates via three-stage evaporati

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Bielecka, Monika, Bartosz Pencakowski, Marta Stafiniak, et al. "Metabolomics and DNA-Based Authentication of Two Traditional Asian Medicinal and Aromatic Species of Salvia subg. Perovskia." Cells 10, no. 1 (2021): 112. http://dx.doi.org/10.3390/cells10010112.

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Subgenus Perovskia of the extended genus of Salvia comprises several Central Asian medicinal and aromatic species, of which S. yangii and S. abrotanoides are the most widespread. These plants are cultivated in Europe as robust ornamentals, and several cultivars are available. However, their medicinal potential remains underutilized because of limited information about their phytochemical and genetic diversity. Thus, we combined an ultra-high performance liquid chromatography quadrupole time of flight mass spectrometry (UHPLC-QTOF-MS) based metabolomics with DNA barcoding approach based on trnH

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Freeman, Sylvie D., and Christopher S. Hourigan. "MRD evaluation of AML in clinical practice: are we there yet?" Hematology 2019, no. 1 (2019): 557–69. http://dx.doi.org/10.1182/hematology.2019000060.

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Abstract MRD technologies increase our ability to measure response in acute myeloid leukemia (AML) beyond the limitations of morphology. When applied in clinical trials, molecular and immunophenotypic MRD assays have improved prognostic precision, providing a strong rationale for their use to guide treatment, as well as to measure its effectiveness. Initiatives such as those from the European Leukemia Network now provide a collaborative knowledge-based framework for selection and implementation of MRD assays most appropriate for defined genetic subgroups. For patients with mutated-NPM1 AML, qu

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Vladimer, Gregory Ian, Christian Schmidl, Andre Renderio, et al. "Integrated ATAC-Seq and Chemosensitivity Profiling Identifies Rational Drug Combinations in Ibrutinib-Treated CLL Patients." Blood 130, Suppl_1 (2017): 800. http://dx.doi.org/10.1182/blood.v130.suppl_1.800.800.

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Abstract Chronic lymphocytic leukemia (CLL) is characterized by clonal proliferation and accumulation of malignant B lymphocytes in the blood, bone marrow, spleen, and lymph nodes. This process is associated with constitutively activated B cell receptor (BCR) signaling, and interference with BCR signaling provides therapeutic benefit. Specifically, the Bruton's Tyrosine Kinase (BTK) inhibitor ibrutinib prevents BTK tyrosine phosphorylation and thereby interferes with pathways downstream of BCR. It has shown high clinical response rates in patients with relapsed and refractory CLL, including pa

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SPOONHOWER, DANIEL, GUY E. BLELLOCH, ROBERT HARPER, and PHILLIP B. GIBBONS. "Space profiling for parallel functional programs." Journal of Functional Programming 20, no. 5-6 (2010): 417–61. http://dx.doi.org/10.1017/s0956796810000146.

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AbstractWe present a semantic space profiler for parallel functional programs. Building on previous work in sequential profiling, our tools help programmers to relate runtime resource use back to program source code. Unlike many profiling tools, our profiler is based on a cost semantics. This provides a means to reason about performance without requiring a detailed understanding of the compiler or runtime system. It also provides a specification for language implementers. This is critical in that it enables us to separate cleanly the performance of the application from that of the language imp

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Gill, Upkar S., Laura J. Pallett, Niclas Thomas, et al. "Fine needle aspirates comprehensively sample intrahepatic immunity." Gut 68, no. 8 (2018): 1493–503. http://dx.doi.org/10.1136/gutjnl-2018-317071.

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ObjectiveIn order to refine new therapeutic strategies in the pipeline for HBV cure, evaluation of virological and immunological changes compartmentalised at the site of infection will be required. We therefore investigated if liver fine needle aspirates (FNAs) could comprehensively sample the local immune landscape in parallel with viable hepatocytes.DesignMatched blood, liver biopsy and FNAs from 28 patients with HBV and 15 without viral infection were analysed using 16-colour multiparameter flow cytometry.ResultsThe proportion of CD4 T, CD8 T, Mucosal Associated Invariant T cell (MAIT), Nat

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Haferlach, Torsten, Alexander Kohlmann, Susanne Schnittger, et al. "All Clinically Relevant Leukemia Subtypes Can Be Diagnosed and Classified Based Solely on Gene Expression Profiling with an Accuracy of 95.1%: A Study on 1337 Adult Patients." Blood 104, no. 11 (2004): 143. http://dx.doi.org/10.1182/blood.v104.11.143.143.

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Abstract So far, comprehensive diagnosis of leukemia requires a combination of cytomorphology, immunophenotyping, and genetic methods. We aimed at developing a new diagnostic tool based solely on gene expression profiling to accurately predict all clinically relevant subtypes of leukemia in adults and to distinguish these from normal bone marrow. Therefore, we analyzed samples from 1337 untreated patients at diagnosis and healthy donors using oligonucleotide microarrays. The first series of 937 cases was hybridized to HG-U133A+B microarrays (Affymetrix). The following 13 subgroups were include

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Cargo, Catherine, Matt Cullen, Jan Taylor, Mike Short, Paul Evans, and Simon Crouch. "Mutational Profiling of Peripheral Blood and Bone Marrow Samples Discriminates Reactive Monocytosis from Chronic Myelomonocytic Leukaemia." Blood 128, no. 22 (2016): 3181. http://dx.doi.org/10.1182/blood.v128.22.3181.3181.

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Abstract Background Chronic myelomonocytic leukaemia (CMML) presents a diagnostic challenge to the haematologist. Distinguishing between a reactive monocytosis and clonal expansion is difficult, and current diagnostic criteria allow for a diagnosis of CMML even in the absence of a clonal marker of disease as long as the monocytosis is persistent. This fails to correctly identify patients with prolonged reactive changes, increasing mis-diagnoses. More recently, large sequencing studies have identified somatic mutations in >90% of patients with CMML, providing potential objective evidence to

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Konecny, Gottfried E., Chen Wang, Boris Winterhoff, et al. "Prognostic relevance of gene signatures in high-grade serous ovarian carcinoma." Journal of Clinical Oncology 31, no. 15_suppl (2013): 5510. http://dx.doi.org/10.1200/jco.2013.31.15_suppl.5510.

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5510 Background: Transcriptional profiling of ovarian cancers has proven to be complex. As such it has been difficult to validate existing signatures across studies. Cancer Genome Atlas (TCGA) researchers have identified four molecular subtypes of high-grade serous ovarian cancer (HGSOC). However, survival duration did not differ significantly for the TCGA subtypes. Potential limitations of the TCGA data include short clinical follow-up (45% were alive at the time of last follow-up) and the need to unify gene expression measures from multiple platforms. Methods: Clinically annotated stage-II–I

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Hynst, Jakub, Karla Plevova, Lenka Radova, Vojtech Bystry, Karol Pal, and Sarka Pospisilova. "Bioinformatic pipelines for whole transcriptome sequencing data exploitation in leukemia patients with complex structural variants." PeerJ 7 (June 12, 2019): e7071. http://dx.doi.org/10.7717/peerj.7071.

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Background Extensive genome rearrangements, known as chromothripsis, have been recently identified in several cancer types. Chromothripsis leads to complex structural variants (cSVs) causing aberrant gene expression and the formation of de novo fusion genes, which can trigger cancer development, or worsen its clinical course. The functional impact of cSVs can be studied at the RNA level using whole transcriptome sequencing (total RNA-Seq). It represents a powerful tool for discovering, profiling, and quantifying changes of gene expression in the overall genomic context. However, bioinformatic

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Silva, Vítor, Leonardo Neves, Renan Souza, Alvaro L. G. A. Coutinho, Daniel de Oliveira, and Marta Mattoso. "Adding domain data to code profiling tools to debug workflow parallel execution." Future Generation Computer Systems 110 (September 2020): 422–39. http://dx.doi.org/10.1016/j.future.2018.05.078.

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MAHAJAN, REEMA, DIETER KRANZLMÜLLER, JENS VOLKERT, ULRICH H. E. HANSMANN, and SIEGFRIED HÖFINGER. "DETECTING SECONDARY BOTTLENECKS IN PARALLEL QUANTUM CHEMISTRY APPLICATIONS USING MPI." International Journal of Modern Physics C 19, no. 01 (2008): 1–13. http://dx.doi.org/10.1142/s0129183108011899.

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Profiling tools such as gprof and ssrun are used to analyze the run-time performance of a scientific application. The profiling is done in serial and in parallel mode using MPI as the communication interface. The application is a quantum chemistry program using Hartree Fock theory and Pulays DIIS method. An extensive set of test cases is taken into account in order to reach uniform conclusions. A known problem with decreased parallel scalability can thus be narrowed down to a single subroutine responsible for the reduction in Speed Up. The critical module is analyzed and a typical pitfall with

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Cario, Gunnar, Andre Schrauder, Anja Moericke, Jean-Pierre Bourquin, Martin Schrappe, and Martin Stanulla. "Early Diagnosis and Molecular-Based Treatment of Very Highly Resistant Acute Lymphoblastic Leukemia in Childhood." Blood 112, no. 11 (2008): 754. http://dx.doi.org/10.1182/blood.v112.11.754.754.

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Abstract In trial ALL-BFM 2000, high-risk (HR) acute lymphoblastic leukemia (ALL) is defined by inadequate initial response to induction treatment [poor prednisone response on treatment day eight (PPR), non remission on treatment day 33, and/or a high load of minimal residual disease (MRD, ≥10E-3) after 12 weeks of treatment (TP2) and/or by positive cytogenetics for a t(4;11) or t(9;22)]. Recently, we presented data on the prospective evaluation of MRD at additional time-points under HR-treatment and showed that patients with a persistently high MRD load after the application of three intensiv

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Geng, Huimin, Brice Tiret, Hua-Xin Gao, et al. "Application of Hyperpolarized 13C Magnetic Resonance Imaging to Detect Target Inhibition of NFkB Activation in Preclinical Patient-Derived Models of CNS Lymphoma." Blood 132, Supplement 1 (2018): 2840. http://dx.doi.org/10.1182/blood-2018-99-117625.

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Abstract To gain insights into the tumor microenvironment in primary and secondary CNS lymphomas, we applied LC/MS and GC/MS for differential metabolomic profiling of the cerebrospinal fluid (CSF) of CNS lymphoma patients compared to control subjects. Among 145 analytes identified, the majority were involved in energy metabolism; one of the most significantly upregulated metabolites in CNS lymphoma was lactate (1.8 fold, p<0.001). Subsequently we determined that baseline elevated CSF lactate, quantified by a Beckman Coulter Unicell Clinical Chemistry analyzer, correlated with short survival

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Jacobs, Cassandra L., Dereje D. Jima, Jenny Zhang, et al. "A Comprehensive Identification of the Microrna Transcriptome and Its Application in B Cell Malignancies." Blood 114, no. 22 (2009): 2403. http://dx.doi.org/10.1182/blood.v114.22.2403.2403.

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Abstract Abstract 2403 Poster Board II-380 Background MicroRNAs are 18-22 nucleotide-long RNA molecules that regulate expression of genes. We and others have previously demonstrated a role for microRNAs in the pathogenesis of B cell malignancies. Computational predictions suggest that the human genome encodes several thousand microRNAs. Thus far, about 700 microRNAs have been discovered in humans, including over 200 new microRNAs in the past year alone. The ongoing discovery of microRNAs makes it difficult to comprehensively study their role in a disease group. The advent of high throughput se

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Carlet, Michela, Jenny Vergalli, Cornelia Finkenzeller, Michaela Grunert, and Irmela Jeremias. "The Novel Technique of Genetically Engineered Patient-Derived Xenografts (GEPDX) Reveals That the X-Linked Inhibitor of Apoptosis Protein (XIAP) Plays an Essential Role for Maintenance and Growth of Patients' Acute Lymphoblastic Leukemia In Vivo." Blood 126, no. 23 (2015): 2632. http://dx.doi.org/10.1182/blood.v126.23.2632.2632.

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Abstract Expression profiling and next generation sequencing have enabled a detailed knowledge on alterations present in tumors from individual patients. In contrast, only limited understanding exists on the role that each alteration plays for the existing tumor. Of direct clinical interest, genes are of special interest which harbor an essential function for tumor maintenance and growth as they represent putative targets for anti-cancer therapy. Characterizing gene functions is demanding regarding both techniques and resources. Questions on gene function are often studied in established tumor

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Lim, Ha Jin, Jun Hyung Lee, Ju-Hyeon Shin, et al. "Diagnostic Validation of a Clinical Laboratory-Oriented Targeted RNA Sequencing System As a Comprehensive Assay for Hematologic Malignancies." Blood 136, Supplement 1 (2020): 38–39. http://dx.doi.org/10.1182/blood-2020-142264.

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Introduction Targeted RNA sequencing (RNA-seq) is a highly accurate method for sequencing transcripts of interest and can overcome limitations regarding resolution, throughput, and multistep workflow. However, RNA-seq has not been widely performed in clinical molecular laboratories due to the complexity of data processing and interpretation. We developed a customized targeted RNA-seq panel with a data processing protocol and validated its analytical performance for gene fusion detection using a subset of samples with different hematologic malignancies. Additionally, we investigated its applica

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Mercier, Francois, Jiantao Shi, David Sykes, et al. "Identification of a Gene Expression Signature Characterizing Clonal Fitness and Dominance in Vivo in a Murine Model of MLL-AF9 Leukemia." Blood 124, no. 21 (2014): 2383. http://dx.doi.org/10.1182/blood.v124.21.2383.2383.

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Abstract Rationale: Human malignancies are often composed of multiple, related clones that arise through a process of branching Darwinian evolution. In acute myeloid leukemia (AML), high-throughput DNA sequencing identifies clonal heterogeneity at the mutational level, but the downstream molecular pathways driving clonal fitness, and their impact on response to therapy are still poorly understood. We report on the development of a novel experimental tool that allows prospective tracking of clonal evolution at the functional level. Using a combination of murine models of AML and fluorescent pro

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Wannachalee, Taweesak, and Adina F. Turcu. "Developments in Primary Aldosteronism Subtyping Using Steroid Profiling." Hormone and Metabolic Research 52, no. 06 (2020): 373–78. http://dx.doi.org/10.1055/a-1141-3526.

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AbstractAdrenal venous sampling is the standard of care for identifying patients with unilateral primary aldosteronism, which is often caused by an aldosterone producing adenoma and can be cured with surgery. The numerous limitations of adrenal venous sampling, including its high cost, scarce availability, technical challenges, and lack of standardized protocols, have driven efforts to develop alternative, non-invasive tools for the diagnosis of aldosterone producing adenomas. Seminal discoveries regarding the pathogenesis of aldosterone producing adenomas made over the past decade have levera

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Hurtado López, Ana M., Tzu Hua Chen-Liang, Joaquín Panadero, et al. "TFDP3and DDX53 are Highly Re-Expressed after One Cycle of Azacitidine in Myelodysplastic Syndrome Patients Achieving Complete Response: A Cancer Testis Antigen RNA-Seq Screening." Blood 132, Supplement 1 (2018): 4340. http://dx.doi.org/10.1182/blood-2018-99-117851.

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Abstract Background and Aim: Azacitidine have shown clinical activity in myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML), particularly at low, non-cytotoxic doses favoring hypomethylation over cytotoxicity. Cancer/testis antigens (CTAs, encoding for immunogenic proteins which are normally expressed in the testicles and trophoblastic cells of the ovary, have been shown to undergo derepression after the use of demethylating agents in cancer cell line models. We took advantage of the unique model of Aza-treated high risk MDS to in vivocharacterize candidates for immunotherapy fol

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Gnatenko, Dmitri V., Peter L. Perrotta, and Wadie F. Bahou. "Proteomic approaches to dissect platelet function: half the story." Blood 108, no. 13 (2006): 3983–91. http://dx.doi.org/10.1182/blood-2006-06-026518.

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AbstractPlatelets play critical roles in diverse hemostatic and pathologic disorders and are broadly implicated in various biological processes that include inflammation, wound healing, and thrombosis. Recent progress in high-throughput mRNA and protein profiling techniques has advanced our understanding of the biological functions of platelets. Platelet proteomics has been adopted to decode the complex processes that underlie platelet function by identifying novel platelet-expressed proteins, dissecting mechanisms of signal or metabolic pathways, and analyzing functional changes of the platel

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Lehnert, S. A., Y. H. Wang, S. H. Tan, and A. Reverter. "Gene expression-based approaches to beef quality research." Australian Journal of Experimental Agriculture 46, no. 2 (2006): 165. http://dx.doi.org/10.1071/ea05226.

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Advances in mammalian genomics have permitted the application of gene expression profiling approaches to gene discovery for meat quality traits in cattle. The first custom cDNA microarray based on the transcriptome of bovine muscle and fat tissue was developed and applied to animal experimentation and cell culture experimentation between 1999 and 2005. Complementary DNA microarray tools for beef quality research were developed in parallel with bioinformatics tools that permit the analysis of microarray data obtained from complex experimental designs commonly encountered in large animal researc

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Morlock, Gertrud E., Julia Heil, Antonio M. Inarejos-Garcia, and Jens Maeder. "Effect-Directed Profiling of Powdered Tea Extracts for Catechins, Theaflavins, Flavonols and Caffeine." Antioxidants 10, no. 1 (2021): 117. http://dx.doi.org/10.3390/antiox10010117.

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The antioxidative activity of Camelia sinensis tea and especially powdered tea extracts on the market, among others used as added value in functional foods, can considerably vary due to not only natural variance, but also adulteration and falsification. Thus, an effect-directed profiling was developed to prove the functional effects or health-promoting claims. It took 3–12 min per sample, depending on the assay incubation time, for 21 separations in parallel. Used as a fast product quality control, it can detect known and unknown bioactive compounds. Twenty tea extracts and a reference mixture

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Sharples, Wendy, Ilya Zhukov, Markus Geimer, et al. "A run control framework to streamline profiling, porting, and tuning simulation runs and provenance tracking of geoscientific applications." Geoscientific Model Development 11, no. 7 (2018): 2875–95. http://dx.doi.org/10.5194/gmd-11-2875-2018.

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Abstract. Geoscientific modeling is constantly evolving, with next-generation geoscientific models and applications placing large demands on high-performance computing (HPC) resources. These demands are being met by new developments in HPC architectures, software libraries, and infrastructures. In addition to the challenge of new massively parallel HPC systems, reproducibility of simulation and analysis results is of great concern. This is due to the fact that next-generation geoscientific models are based on complex model implementations and profiling, modeling, and data processing workflows.

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Gasper, F., K. Goergen, S. Kollet, et al. "Implementation and scaling of the fully coupled Terrestrial Systems Modeling Platform (TerrSysMP) in a massively parallel supercomputing environment – a case study on JUQUEEN (IBM Blue Gene/Q)." Geoscientific Model Development Discussions 7, no. 3 (2014): 3545–73. http://dx.doi.org/10.5194/gmdd-7-3545-2014.

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Abstract. Continental-scale hyper-resolution simulations constitute a grand challenge in characterizing non-linear feedbacks of states and fluxes of the coupled water, energy, and biogeochemical cycles of terrestrial systems. Tackling this challenge requires advanced coupling and supercomputing technologies for earth system models that are discussed in this study, utilizing the example of the implementation of the newly developed Terrestrial Systems Modeling Platform (TerrSysMP) on JUQUEEN (IBM Blue Gene/Q) of the Jülich Supercomputing Centre, Germany. The applied coupling strategies rely on t

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Zielinska, Agnieszka K., Kenton Leigh, Horacio Gomez, and Ryan K. Van Laar. "Validation of the Nextseq 500 and Development of a High-Throughput NGS Pipeline for Identifying Clinically-Relevant Gene Variants in Multiple Myeloma Specimens." Blood 126, no. 23 (2015): 5346. http://dx.doi.org/10.1182/blood.v126.23.5346.5346.

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Abstract As molecular profiling technologies have evolved, our understanding of multiple myeloma heterogeneity and the relative effectiveness of treatment options have increased dramatically. Most recently, next generation sequencing (NGS) studies have provided a new degree of molecular resolution into this disease, however it remains a challenge to translate these methodologies and insights from research tools to widely-available clinical assays which can be performed as part of routine patient care. MyPRS® is a clinically and scientifically validated high-throughput gene-expression (Affymetr

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Dolnik, Anna, Andreas Gerhardinger, Ursula Botzenhardt, et al. "Genome-Wide Analysis of Alternative Splicing Points to Novel Leukemia Relevant Genes in Acute Myeloid Leukemia." Blood 114, no. 22 (2009): 2391. http://dx.doi.org/10.1182/blood.v114.22.2391.2391.

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Abstract Abstract 2391 Poster Board II-368 Alternative mRNA splicing represents an effective mechanism of regulating gene function as well as a key element to increase the coding capacity of the human genome. Today, an increasing number of reports illustrates that aberrant splicing events can contribute to human disease and that alterations in the splicing machinery are common and functionally important for cancer development. Aberrant splice forms can for example have genome-wide effects by deregulating key signaling pathways. However, for most of the aberrant mRNA transcripts detected it rem

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Auder, Benjamin, Jairo Cugliari, Yannig Goude, and Jean-Michel Poggi. "Scalable Clustering of Individual Electrical Curves for Profiling and Bottom-Up Forecasting." Energies 11, no. 7 (2018): 1893. http://dx.doi.org/10.3390/en11071893.

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Smart grids require flexible data driven forecasting methods. We propose clustering tools for bottom-up short-term load forecasting. We focus on individual consumption data analysis which plays a major role for energy management and electricity load forecasting. The first section is dedicated to the industrial context and a review of individual electrical data analysis. Then, we focus on hierarchical time-series for bottom-up forecasting. The idea is to decompose the global signal and obtain disaggregated forecasts in such a way that their sum enhances the prediction. This is done in three ste

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