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Analysis matrix data collection

Alejandro Avilés-Reyes, Irlan Almeida Freires, Jessica K Kajfasz, Dicler Barbieri, James H Miller, José A Lemos, Jacqueline Abranches
We report the whole genome sequence (WGS) of the serotype e Cbm+ strain LAR01 of Streptococcus mutans, a dental pathogen frequently associated with extra-oral infections. The LAR01 genome is a single circular chromosome of 2.1 Mb with a GC content of 36.96%. The genome contains 15 PTS gene clusters, 7 cell wall-anchored (LPxTG) proteins, all genes required for the development of natural competence and genes coding for mutacins VI and K8. Interestingly, the cbm gene is genetically linked to a putative type VII secretion system that has been found in Mycobacteria and few other gram-positive bacteria...
March 9, 2018: Molecular Oral Microbiology
Lukas Krasny, Philip Bland, Naoko Kogata, Patty Wai, Beatrice A Howard, Rachael C Natrajan, Paul H Huang
Proteomic analysis of extracellular matrix (ECM) and ECM-associated proteins, collectively known as the matrisome, is a challenging task due to the inherent complexity and insolubility of these proteins. Here we present sequential window acquisition of all theoretical fragment ion spectra mass spectrometry (SWATH MS) as a tool for the quantitative analysis of matrisomal proteins in both non-enriched and ECM enriched tissue without the need for prior fractionation. Utilising a spectral library containing 201 matrisomal proteins, we compared the performance and reproducibility of SWATH MS over conventional data-dependent analysis mass spectrometry (DDA MS) in unfractionated murine lung and liver...
February 28, 2018: Journal of Proteomics
Jian Ji, Pei Zhu, Ivana Blaženović, Fangchao Cui, Morteza Gholami, Jiadi Sun, Jean Habimana, Yinzhi Zhang, Xiulan Sun
Urine metabolic profiling of mice was conducted utilizing gas chromatography-mass spectrometry (GC-MS) to investigate the combinatory effect of mycotoxins deoxynivalenol (DON) and zearalenone (ZEN) on the metabolism of the mice. Experiments were conducted by means of five-week-old mice which were individually exposed to 2 mg/kg DON, 20 mg/kg ZEN and the mixture of DON and ZEN (2 mg/kg and 20 mg/kg, respectively). The intragastric administration was applied for three weeks and urine samples were collected for metabolic analysis...
February 28, 2018: Scientific Reports
M Akbari, H Salehi, A Niazi
The main goals of the present study were to screen Iranian common bermudagrasses to find cold-tolerant accessions and evaluate their genetic and morphological variabilities. In this study, 49 accessions were collected from 18 provinces of Iran. One foreign cultivar of common bermudagrass was used as control. Morphological variation was evaluated based on 14 morphological traits to give information about taxonomic position of Iranian common bermudagrass. Data from morphological traits were evaluated to categorize all accessions as either cold sensitive or tolerant using hierarchical clustering with Ward's method in SPSS software...
February 26, 2018: Molecular Biotechnology
G Camps, M Mars, B J M Witteman, C de Graaf, P A M Smeets
BACKGROUND: Indirect methods to assess gastric emptying (GE), such as13 C breath tests (BT), are commonly used. However, BT usually use a sampling time of 4+ hours. The current study aims to assess the validity of BT for four liquid meals differing in physicochemical properties. To this aim, we compared them to MRI GE-measurements. METHODS: Fifteen healthy males (age 22.6 ± 2.4 years, BMI 22.6 ± 1.8 kg/m2 ) participated in a randomized 2 × 2 crossover experiment...
February 23, 2018: Neurogastroenterology and Motility: the Official Journal of the European Gastrointestinal Motility Society
Matthew S Harkey, J Troy Blackburn, Anthony C Hackney, Michael D Lewek, Randy J Schmitz, Brian Pietrosimone
INTRODUCTION: An in depth understanding of the healthy cartilage response to activities of daily living is needed to better understand the complex relationship between cartilage health and loading. The purpose was to assess the role of loading on the acute serum cartilage oligomeric matrix protein (COMP) response in recreationally active individuals. METHODS: 40 individuals without previous lower extremity injury participated in this repeated measures study in which each participant completed all conditions during independent data collection sessions separated by at least one week...
February 21, 2018: Medicine and Science in Sports and Exercise
Sean C P Coogan, David Raubenheimer, Gordon B Stenhouse, Nicholas C Coops, Scott E Nielsen
We combine a recently developed framework for describing dietary generalism with compositional data analysis to examine patterns of omnivory in a large widely distributed mammal. Using the brown bear ( Ursus arctos ) as a model species, we collected and analyzed data from the literature to estimate the proportions of macronutrients (protein, carbohydrate, and lipid) in the diets of bear populations. Across their range, bears consumed a diversity of foods that resulted in annual population diets that varied in macronutrient proportions, suggesting a wide fundamental macronutrient niche...
February 2018: Ecology and Evolution
Norihiko Masuda, Osamu Ogawa, Meyeon Park, Alvin Y Liu, Steve Goodison, Yunfeng Dai, Landon Kozai, Hideki Furuya, Yair Lotan, Charles J Rosser, Takashi Kobayashi
A 10-plex urine-based bladder cancer (BCa) diagnostic signature has the potential to non-invasively predict the presence of BCa in at-risk patients, as reported in various case-control studies. The present meta-analysis was performed to re-evaluate and demonstrate the robustness and consistency of the diagnostic utility of the 10-plex urine-based diagnostic assay. We re-analyzed primary data collected in five previously published case-control studies on the 10-plex diagnostic assay. Studies reported the sensitivity and specificity of ten urinary protein biomarkers for the detection of BCa, including interleukin 8, matrix metalloproteinases 9 and 10, angiogenin, apolipoprotein E, syndecan 1, alpha-1 antitrypsin, plasminogen activator inhibitor-1, carbonic anhydrase 9, and vascular endothelial growth factor A...
January 23, 2018: Oncotarget
S Taylor Fischer, Yunxuan Jiang, K Alaine Broadaway, Karen N Conneely, Michael P Epstein
There has been increasing interest in identifying genes within the human genome that influence multiple diverse phenotypes. In the presence of pleiotropy, joint testing of these phenotypes is not only biologically meaningful but also statistically more powerful than univariate analysis of each separate phenotype accounting for multiple testing. Although many cross-phenotype association tests exist, the majority of such methods assume samples composed of unrelated subjects and therefore are not applicable to family-based designs, including the valuable case-parent trio design...
February 20, 2018: Genetic Epidemiology
Zikuan Chen, Vince Calhoun
Spatial smoothing is a widely used preprocessing step in functional magnetic resonance imaging (fMRI) data analysis. In this work, we report on the spatial smoothing effect on task-evoked fMRI brain functional mapping and functional connectivity. Initially, we decomposed the task fMRI data into a collection of components or networks by independent component analysis (ICA). The designed task paradigm helps identify task-modulated ICA components (highly correlated with the task stimuli). For the ICA-extracted primary task component, we then measured the task activation volume at the task response foci...
2018: Frontiers in Neuroscience
Jeremy R Manning, Xia Zhu, Theodore L Willke, Rajesh Ranganath, Kimberly Stachenfeld, Uri Hasson, David M Blei, Kenneth A Norman
Recent research shows that the covariance structure of functional magnetic resonance imaging (fMRI) data - commonly described as functional connectivity - can change as a function of the participant's cognitive state (for review see (Turk-Browne, 2013)). Here we present a Bayesian hierarchical matrix factorization model, termed hierarchical topographic factor analysis (HTFA), for efficiently discovering full-brain networks in large multi-subject neuroimaging datasets. HTFA approximates each subject's network by first re-representing each brain image in terms of the activities of a set of localized nodes, and then computing the covariance of the activity time series of these nodes...
February 12, 2018: NeuroImage
Michael Keck, Roelof Maarten van Dijk, Cornelia A Deeg, Katharina Kistler, Andreas Walker, Eva-Lotta von Rüden, Vera Russmann, Stefanie M Hauck, Heidrun Potschka
Information about epileptogenesis-associated changes in protein expression patterns is of particular interest for future selection of target and biomarker candidates. Bioinformatic analysis of proteomic data sets can increase our knowledge about molecular alterations characterizing the different phases of epilepsy development following an initial epileptogenic insult. Here, we report findings from a focused analysis of proteomic data obtained for the hippocampus and parahippocampal cortex samples collected during the early post-insult phase, latency phase, and chronic phase of a rat model of epileptogenesis...
April 2018: Neurobiology of Disease
Mandira Saha, P K Bandyopadhyay
A new species of myxozoan, Thelohanellus goldi n. sp. is described using morphological and molecular data, parasitizing the fin filaments from 18 of 25 host specimens (72.5%) of Carassius auratus collected from different ornamental fish farms of India. Mature spore of the new species were oval to spherical in frontal view having rounded posterior ends and tapering anterior end measures 8.7-10.26 (9.50) × 4.10-7.89 (5.84) μm. The single large polar capsule, round to oval in shape but slightly pointed at the anterior end measuring 4...
February 1, 2018: Acta Tropica
Qiaolin Chen, Catherine A Sugar, Robert E Weiss
Researchers collected multiple measurements on patients with schizophrenia and their relatives, as well as control subjects and their relatives, to study vulnerability factors for schizophrenics and their near relatives. Observations across individuals from the same family are correlated, and also the multiple outcome measures on the same individuals are correlated. Traditional data analyses model outcomes separately and thus do not provide information about the interrelationships among outcomes. We propose a novel Bayesian family factor model (BFFM), which extends the classical confirmatory factor analysis model to explain the correlations among observed variables using a combination of family-member and outcome factors...
February 5, 2018: Statistics in Medicine
Farag Malhat, Konstantinos M Kasiotis, Shehata Shalaby
Cyantraniliprole is an anthranilic diamide insecticide, belonging to the ryanoid class, with a broad range of applications against several pests. In the presented work, a reliable analytical technique employing high-performance liquid chromatography coupled with photodiode array detector (HPLC-DAD) for analyzing cyantraniliprole residues in tomato was developed. The method was then applied to field-incurred tomato samples collected after applications under open field conditions. The latter aimed to ensure the safe application of cyantraniliprole to tomato and contribute the derived residue data to the risk assessment under field conditions...
February 5, 2018: Environmental Monitoring and Assessment
Ameena M Ali, Jack Atmaj, Alaa Adawy, Sergey Lunev, Niels Van Oosterwijk, Sun Rei Yan, Chris Williams, Matthew R Groves
Peroxisomes are a major cellular compartment of eukaryotic cells, and are involved in a variety of metabolic functions and pathways according to species, cell type and environmental conditions. Their biogenesis relies on conserved genes known as PEX genes that encode peroxin proteins. Peroxisomal membrane proteins and peroxisomal matrix proteins are generated in the cytosol and are subsequently imported into the peroxisome post-translationally. Matrix proteins containing a peroxisomal targeting signal type 1 (PTS1) are recognized by the cycling receptor Pex5p and transported to the peroxisomal lumen...
February 1, 2018: Acta Crystallographica. Section F, Structural Biology Communications
Rodolfo Rogelio Posadas-Domínguez, Oscar Enrique Del Razo-Rodríguez, Isaac Almaraz-Buendía, Armando Pelaez-Acero, Verónica Espinosa-Muñoz, Samuel Rebollar-Rebollar, Jesús Armando Salinas-Martínez
This article combines a Policy Analysis Matrix with a sensitivity and poverty line analysis with the objective of evaluating the economic contribution of comparative advantages to the private profitability and competitiveness of small-scale dairy systems. For 1 year, socioeconomic data were collected from 82 farms selected from four strata via statistical sampling. Two scenarios were established to determine the quantitative contribution of comparative advantages: (1) a simulated scenario, which accounted for the cost of purchasing the total food and the opportunity cost of the family labour force (FLF), and (2) an actual production scenario, which accounted for the cost of producing food and eliminating the payment of the FLF and included other income...
February 1, 2018: Tropical Animal Health and Production
Liping Wang, Yanfei Wang
Reconstruction of the seismic wavefield from sub-sampled data is important and necessary in seismic image processing; this is partly due to limitations of the observations which usually yield incomplete data. To make the best of the observed seismic signals, we propose a joint matrix minimization model to recover the seismic wavefield. Employing matrix instead of vector as weight variable can express all the sub-sampled traces simultaneously. This scheme utilizes the collective representation rather than an individual one to recover a given set of sub-samples...
February 1, 2018: Scientific Reports
Stacey N Doan, Gerrit DeYoung, Thomas E Fuller-Rowell, Cindy Liu, Jerrold Meyer
In the current study, we present data investigating the relationships among stress, sleep disturbance, self-control, and levels of cortisol (CORT) and dehydroepiandrosterone (DHEA) in fingernail clippings. Currently, hair CORT is the only routinely used noninvasive, validated, biomarker of chronic exposure to stress-related hormones. Nail clippings represent an important potential alternative sample matrix for assessing chronic hormone exposure, as it offers a different timeline of hormone incorporation than scalp hair, and may be obtainable from populations in which hair either is lacking or is unavailable for cultural reasons...
January 26, 2018: Stress: the International Journal on the Biology of Stress
Gisele Chicone, Viviane Fernandes de Carvalho, André Oliveira Paggiaro
OBJECTIVE: Diabetic wounds that do not heal completely usually exhibit inflammatory markers, increased protease activity, and reduced levels of growth factors and cell count. A systematic review was performed to determine whether there is enough evidence to support the use of an oxidized regenerated cellulose/collagen matrix (ORC+C) to treat diabetic foot ulcers (DFUs). METHODS: Study authors analyzed randomized controlled trials (RCTs) on ORC+C dressings for the treatment of DFUs...
February 2018: Advances in Skin & Wound Care
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