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https://www.readbyqxmd.com/read/28231515/computational-tools-for-enzyme-improvement-why-everyone-can-and-should-use-them
#1
REVIEW
Maximilian Ccjc Ebert, Joelle N Pelletier
This review presents computational methods that experimentalists can readily use to create smart libraries for enzyme engineering and to obtain insights into protein-substrate complexes. Computational tools have the reputation of being hard to use and inaccurate compared to experimental methods in enzyme engineering, yet they are essential to probe datasets of ever-increasing size and complexity. In recent years, bioinformatics groups have made a huge leap forward in providing user-friendly interfaces and accurate algorithms for experimentalists...
February 20, 2017: Current Opinion in Chemical Biology
https://www.readbyqxmd.com/read/28231405/three-dimensional-printing-of-x-ray-computed-tomography-datasets-with-multiple-materials-using-open-source-data-processing
#2
Ian M Sander, Matthew T McGoldrick, My N Helms, Aislinn Betts, Anthony van Avermaete, Elizabeth Owers, Evan Doney, Taimi Liepert, Glen Niebur, Douglas Liepert, W Matthew Leevy
Advances in three-dimensional (3D) printing allow for digital files to be turned into a "printed" physical product. For example, complex anatomical models derived from clinical or pre-clinical X-ray computed tomography (CT) data of patients or research specimens can be constructed using various printable materials. Although 3D printing has the potential to advance learning, many academic programs have been slow to adopt its use in the classroom despite increased availability of the equipment and digital databases already established for educational use...
February 23, 2017: Anatomical Sciences Education
https://www.readbyqxmd.com/read/28231339/limits-of-use-of-social-media-for-monitoring-biosecurity-events
#3
Marijke Welvaert, Omar Al-Ghattas, Mark Cameron, Peter Caley
Compared to applications that trigger massive information streams, like earthquakes and human disease epidemics, the data input for agricultural and environmental biosecurity events (ie. the introduction of unwanted exotic pests and pathogens), is expected to be sparse and less frequent. To investigate if Twitter data can be useful for the detection and monitoring of biosecurity events, we adopted a three-step process. First, we confirmed that sightings of two migratory species, the Bogong moth (Agrotis infusa) and the Common Koel (Eudynamys scolopaceus) are reported on Twitter...
2017: PloS One
https://www.readbyqxmd.com/read/28231335/immigrants-in-the-one-percent-the-national-origin-of-top-wealth-owners
#4
Lisa A Keister, Brian Aronson
BACKGROUND: Economic inequality in the United States is extreme, but little is known about the national origin of affluent households. Households in the top one percent by total wealth own vastly disproportionate quantities of household assets and have correspondingly high levels of economic, social, and political influence. The overrepresentation of white natives (i.e., those born in the U.S.) among high-wealth households is well-documented, but changing migration dynamics suggest that a growing portion of top households may be immigrants...
2017: PloS One
https://www.readbyqxmd.com/read/28231289/rehr-an-r-package-for-manipulating-and-analysing-electronic-health-record-data
#5
David A Springate, Rosa Parisi, Ivan Olier, David Reeves, Evangelos Kontopantelis
Research with structured Electronic Health Records (EHRs) is expanding as data becomes more accessible; analytic methods advance; and the scientific validity of such studies is increasingly accepted. However, data science methodology to enable the rapid searching/extraction, cleaning and analysis of these large, often complex, datasets is less well developed. In addition, commonly used software is inadequate, resulting in bottlenecks in research workflows and in obstacles to increased transparency and reproducibility of the research...
2017: PloS One
https://www.readbyqxmd.com/read/28231256/advancing-the-match-mismatch-framework-for-large-herbivores-in-the-arctic-evaluating-the-evidence-for-a-trophic-mismatch-in-caribou
#6
David Gustine, Perry Barboza, Layne Adams, Brad Griffith, Raymond Cameron, Kenneth Whitten
Climate-induced shifts in plant phenology may adversely affect animals that cannot or do not shift the timing of their reproductive cycle. The realized effect of potential trophic "mismatches" between a consumer and its food varies with the degree to which species rely on dietary income and stored capital. Large Arctic herbivores rely heavily on maternal capital to reproduce and give birth near the onset of the growing season but are they vulnerable to trophic mismatch? We evaluated the long-term changes in the temperatures and characteristics of the growing seasons (1970-2013), and compared growing conditions and dynamics of forage quality for caribou at peak parturition, peak lactation, and peak forage biomass, and plant senescence between two distinct time periods over 36 years (1977 and 2011-13)...
2017: PloS One
https://www.readbyqxmd.com/read/28230745/toward-improving-electrocardiogram-ecg-biometric-verification-using-mobile-sensors-a-two-stage-classifier-approach
#7
Robin Tan, Marek Perkowski
Electrocardiogram (ECG) signals sensed from mobile devices pertain the potential for biometric identity recognition applicable in remote access control systems where enhanced data security is demanding. In this study, we propose a new algorithm that consists of a two-stage classifier combining random forest and wavelet distance measure through a probabilistic threshold schema, to improve the effectiveness and robustness of a biometric recognition system using ECG data acquired from a biosensor integrated into mobile devices...
February 20, 2017: Sensors
https://www.readbyqxmd.com/read/28230161/robust-high-dimensional-bioinformatics-data-streams-mining-by-odr-iovfdt
#8
Dantong Wang, Simon Fong, Raymond K Wong, Sabah Mohammed, Jinan Fiaidhi, Kelvin K L Wong
Outlier detection in bioinformatics data streaming mining has received significant attention by research communities in recent years. The problems of how to distinguish noise from an exception and deciding whether to discard it or to devise an extra decision path for accommodating it are causing dilemma. In this paper, we propose a novel algorithm called ODR with incrementally Optimized Very Fast Decision Tree (ODR-ioVFDT) for taking care of outliers in the progress of continuous data learning. By using an adaptive interquartile-range based identification method, a tolerance threshold is set...
February 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28229969/microrna-144-inhibits-hepatocellular-carcinoma-cell-proliferation-invasion-and-migration-by-targeting-zfx
#9
Hongbin Bao, Xinguo Li, Hengli Li, Hongli Xing, Binghui Xu, Xianfeng Zhang, Zhaoming Liu
MicroRNA 144 (miR-144), a small non-coding RNA, is frequently dysregulated in human several tumour progression, but its role and the underlying mechanisms in hepatocellular carcinoma (HCC) is poorly investigated. In the present study, the expression of miR-144 was firstly analysed in datasets derived from GSE21362 and TCGA, and then detected in HCC tissues and cell lines by quantitative RT-PCR (qRT-PCR) analysis. MiR-144 was shown to be significantly down-regulated in HCC tissues and cell lines. Subsequently, overexpression of miR-144 was transfected into HCC cell lines so as to investigate its biological function, including MTT, colony formation, and transwell assays...
March 2017: Journal of Biosciences
https://www.readbyqxmd.com/read/28229558/microbial-diversity-of-a-full-scale-uasb-reactor-applied-to-poultry-slaughterhouse-wastewater-treatment-integration-of-16s-rrna-gene-amplicon-and-shotgun-metagenomic-sequencing
#10
Tiago Palladino Delforno, Gileno Vieira Lacerda Júnior, Melline F Noronha, Isabel K Sakamoto, Maria Bernadete A Varesche, Valéria M Oliveira
The 16S rRNA gene amplicon and whole-genome shotgun metagenomic (WGSM) sequencing approaches were used to investigate wide-spectrum profiles of microbial composition and metabolic diversity from a full-scale UASB reactor applied to poultry slaughterhouse wastewater treatment. The data were generated by using MiSeq 2 × 250 bp and HiSeq 2 × 150 bp Illumina sequencing platforms for 16S amplicon and WGSM sequencing, respectively. Each approach revealed a distinct microbial community profile, with Pseudomonas and Psychrobacter as predominant genus for the WGSM dataset and Clostridium and Methanosaeta for the 16S rRNA gene amplicon dataset...
February 23, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28229308/eeg-signatures-of-dynamic-functional-network-connectivity-states
#11
E A Allen, E Damaraju, T Eichele, L Wu, V D Calhoun
The human brain operates by dynamically modulating different neural populations to enable goal directed behavior. The synchrony or lack thereof between different brain regions is thought to correspond to observed functional connectivity dynamics in resting state brain imaging data. In a large sample of healthy human adult subjects and utilizing a sliding windowed correlation method on functional imaging data, earlier we demonstrated the presence of seven distinct functional connectivity states/patterns between different brain networks that reliably occur across time and subjects...
February 22, 2017: Brain Topography
https://www.readbyqxmd.com/read/28229175/survival-prediction-of-trauma-patients-a-study-on-us-national-trauma-data-bank
#12
I Sefrioui, R Amadini, J Mauro, A El Fallahi, M Gabbrielli
BACKGROUND: Exceptional circumstances like major incidents or natural disasters may cause a huge number of victims that might not be immediately and simultaneously saved. In these cases it is important to define priorities avoiding to waste time and resources for not savable victims. Trauma and Injury Severity Score (TRISS) methodology is the well-known and standard system usually used by practitioners to predict the survival probability of trauma patients. However, practitioners have noted that the accuracy of TRISS predictions is unacceptable especially for severely injured patients...
February 22, 2017: European Journal of Trauma and Emergency Surgery: Official Publication of the European Trauma Society
https://www.readbyqxmd.com/read/28229145/oxidation-potentials-of-phenols-and-anilines-correlation-analysis-of-electrochemical-and-theoretical-values
#13
Ania S Pavitt, Eric J Bylaska, Paul G Tratnyek
Phenols and anilines have been studied extensively as reductants of environmental oxidants (such as manganese dioxide) and as reductates (e.g., model contaminants) that are transformed by environmental oxidants (ozone, triple organic matter, etc.). The thermodynamics and kinetics of these reactions have been interpreted using oxidation potentials for substituted phenols and anilines, often using a legacy experimental dataset that is of uncertain quality. Although there are many alternative oxidation potential data, there has been little systematic analysis of the relevance, reliability, and consistency of the data obtained by different methods...
February 23, 2017: Environmental Science. Processes & Impacts
https://www.readbyqxmd.com/read/28229131/discovering-cortical-folding-patterns-in-neonatal-cortical-surfaces-using-large-scale-dataset
#14
Yu Meng, Gang Li, Li Wang, Weili Lin, John H Gilmore, Dinggang Shen
The cortical folding of the human brain is highly complex and variable across individuals. Mining the major patterns of cortical folding from modern large-scale neuroimaging datasets is of great importance in advancing techniques for neuroimaging analysis and understanding the inter-individual variations of cortical folding and its relationship with cognitive function and disorders. As the primary cortical folding is genetically influenced and has been established at term birth, neonates with the minimal exposure to the complicated postnatal environmental influence are the ideal candidates for understanding the major patterns of cortical folding...
October 2016: Medical Image Computing and Computer-assisted Intervention: MICCAI ..
https://www.readbyqxmd.com/read/28229116/short-and-long-term-changes-in-sugarbeet-beta-vulgaris-l-gene-expression-due-to-postharvest-jasmonic-acid-treatment-data
#15
Lucilene Silva de Oliveira, Karen Klotz Fugate, Jocleita Perruzo Ferrareze, Melvin D Bolton, Edward L Deckard, Fernando L Finger
Jasmonic acid is a natural plant hormone that induces native defense responses in plants. Sugarbeet (Beta vulgaris L.) root unigenes that were differentially expressed 2 and 60 days after a postharvest jasmonic acid treatment are presented. Data include changes in unigene expression relative to water-treated controls, unigene annotations against nonredundant (Nr), Swiss-Prot, Clusters of Orthologous Groups (COG), and Kyoto Encyclopedia of Genes and Genomes (KEGG) protein databases, and unigene annotations with Gene Ontology (GO) terms...
April 2017: Data in Brief
https://www.readbyqxmd.com/read/28229027/risk-analysis-of-colorectal-cancer-incidence-by-gene-expression-analysis
#16
Wei-Chuan Shangkuan, Hung-Che Lin, Yu-Tien Chang, Chen-En Jian, Hueng-Chuen Fan, Kang-Hua Chen, Ya-Fang Liu, Huan-Ming Hsu, Hsiu-Ling Chou, Chung-Tay Yao, Chi-Ming Chu, Sui-Lung Su, Chi-Wen Chang
BACKGROUND: Colorectal cancer (CRC) is one of the leading cancers worldwide. Several studies have performed microarray data analyses for cancer classification and prognostic analyses. Microarray assays also enable the identification of gene signatures for molecular characterization and treatment prediction. OBJECTIVE: Microarray gene expression data from the online Gene Expression Omnibus (GEO) database were used to to distinguish colorectal cancer from normal colon tissue samples...
2017: PeerJ
https://www.readbyqxmd.com/read/28228849/considerations-and-complications-of-mapping-small-rna-high-throughput-data-to-transposable-elements
#17
Alexandros Bousios, Brandon S Gaut, Nikos Darzentas
BACKGROUND: High-throughput sequencing (HTS) has revolutionized the way in which epigenetic research is conducted. When coupled with fully-sequenced genomes, millions of small RNA (sRNA) reads are mapped to regions of interest and the results scrutinized for clues about epigenetic mechanisms. However, this approach requires careful consideration in regards to experimental design, especially when one investigates repetitive parts of genomes such as transposable elements (TEs), or when such genomes are large, as is often the case in plants...
2017: Mobile DNA
https://www.readbyqxmd.com/read/28228543/characterization-of-dependencies-between-growth-and-division-in-budding-yeast
#18
Michael B Mayhew, Edwin S Iversen, Alexander J Hartemink
Cell growth and division are processes vital to the proliferation and development of life. Coordination between these two processes has been recognized for decades in a variety of organisms. In the budding yeast Saccharomyces cerevisiae, this coordination or 'size control' appears as an inverse correlation between cell size and the rate of cell-cycle progression, routinely observed in G1 prior to cell division commitment. Beyond this point, cells are presumed to complete S/G2/M at similar rates and in a size-independent manner...
February 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28228285/mass-spectrometry-profiling-of-hla-associated-peptidomes-in-mono-allelic-cells-enables-more-accurate-epitope-prediction
#19
Jennifer G Abelin, Derin B Keskin, Siranush Sarkizova, Christina R Hartigan, Wandi Zhang, John Sidney, Jonathan Stevens, William Lane, Guang Lan Zhang, Thomas M Eisenhaure, Karl R Clauser, Nir Hacohen, Michael S Rooney, Steven A Carr, Catherine J Wu
Identification of human leukocyte antigen (HLA)-bound peptides by liquid chromatography-tandem mass spectrometry (LC-MS/MS) is poised to provide a deep understanding of rules underlying antigen presentation. However, a key obstacle is the ambiguity that arises from the co-expression of multiple HLA alleles. Here, we have implemented a scalable mono-allelic strategy for profiling the HLA peptidome. By using cell lines expressing a single HLA allele, optimizing immunopurifications, and developing an application-specific spectral search algorithm, we identified thousands of peptides bound to 16 different HLA class I alleles...
February 21, 2017: Immunity
https://www.readbyqxmd.com/read/28228149/fasciolopsis-buski-digenea-fasciolidae-from-china-and-india-may-represent-distinct-taxa-based-on-mitochondrial-and-nuclear-ribosomal-dna-sequences
#20
Jun Ma, Miao-Miao Sun, Jun-Jun He, Guo-Hua Liu, Lin Ai, Mu-Xin Chen, Xing-Quan Zhu
BACKGROUND: Fasciolopsis buski is a zoonotic intestinal fluke infecting humans and pigs, but it has been seriously neglected. It is yet to know whether there is any genetic diversity among F. buski from different geographical locations, particularly in sequences of nuclear ribosomal DNA (rDNA) and mitochondrial (mt) DNA. Therefore, we determined the sequences of partial 18S, the complete internal transcribed spacer (ITS) rDNA and the complete mt genome of F. buski from China, compared the rDNA and mtDNA sequences with those of isolates from India and Vietnam, and assessed the phylogenetic relationships of this fluke and related fasciolid trematodes based on the mtDNA dataset...
February 22, 2017: Parasites & Vectors
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