bluuebunny/crossref_metadata_2025_split huggingface dataset:
Neuropsychological Test Performance and MRI Markers of Dementia Risk
Authors: Walter Stefan , Dufouil Carole , Gross Alden L. , Jones Richard N. , Mungas Dan , Filshtein Teresa J. , Manly Jennifer J. , Arpawong Thalida E. , Glymour M. Maria 
Published: June 2019

Background:
To use neuropsychological assessments for studying the underlying disease processes contributing to dementia, it is crucial that they correspond to magnetic resonance imaging (MRI)-based measures of dementia, regardless of educational level.

Methods:
French 3-City Dijon MRI study cohort members (n=1782) with assessments of white matter lesion volume (WMLV), hippocampal volume (HCV), and cerebrospinal fluid volume (CSFV), and 6 waves of neuropsychological assessments over 11 years, including Mini-Mental State Examination (MMSE), plus 5 other tests combined using a Z-score or item-response theory (IRT-cognition) comprised the study cohort. We evaluated, testing interactions, whether education modified associations of MRI markers with intercept or rate of change of MMSE, Z-score composite, or IRT-cognition.

Results:
In linear models, education modified the associations of WMLV and CSFV with MMSE and CSFV and Z-score composite. In mixed models, education modified the associations of WMLV and CSFV with level of MMSE and the association of HCV with slope of MMSE. Education also modified the association with CSFV and slope of Z-score composite decline. There was no evidence that education modified associations between MRI measures and level or slope of IRT-cognition.

Conclusions:
Longitudinal analysis of correctly scaled neuropsychological assessments may provide unbiased proxies for MRI-based measures of dementia risk.
Thermal performance across levels of biological organization
Authors: Rezende Enrico L. , Bozinovic Francisco 
Published: June 2019

Thermal performance curves are widely used to describe how ambient temperature impacts different attributes of ectothermic organisms, from protein function to life-history traits, and to predict the potential effects of global warming on ecological systems. Nonetheless, from an analytical standpoint, they remain primarily heuristic and few attempts have been made to develop a formal framework to characterize these curves and disentangle which factors contribute to their variation. Here we employ a nonlinear regression approach to assess if they vary systematically in shape depending on the performance proxy of choice. We compare curves at contrasting levels of organization, namely photosynthetic rates in plants (n= 43), running speeds in lizards (n= 51) and intrinsic rates of population increase in insects (n= 47), and show with discriminant analyses that differences lie in a single dimension accounting for 99.1% of the variation, resulting in 75.8% of classification accuracy. Differences revolve primarily around the thermal range for elevated performance (greater than or equal to 50% of maximum performance), which is broader for photosynthetic rates (median of 26.4°C), intermediate for running speeds (19.5°C) and narrower for intrinsic rates of increase (12.5°C). We contend, confounding taxonomic factors aside, that these differences reflect contrasting levels of biological organization, and hypothesize that the thermal range for elevated performance should decrease at higher organization levels. In this scenario, instantaneous or short-term measures of performance may grossly overestimate the thermal safety margins for population growth and reproduction. Taken together, our analyses suggest that descriptors of the curve are highly correlated and respond in tandem, potentially resulting in systematic variation in shape across organization levels. Future studies should take into consideration this potential bias, address if it constitutes a general pattern and, if so, explain why and how it emerges.This article is part of the theme issue ‘Physiological diversity, biodiversity patterns and global climate change: testing key hypotheses involving temperature and oxygen’.
Scaling of thermal tolerance with body mass and genome size in ectotherms: a comparison between water- and air-breathers
Authors: Leiva Félix P. , Calosi Piero , Verberk Wilco C. E. P. 
Published: June 2019

Global warming appears to favour smaller-bodied organisms, but whether larger species are also more vulnerable to thermal extremes, as suggested for past mass-extinction events, is still an open question. Here, we tested whether interspecific differences in thermal tolerance (heat and cold) of ectotherm organisms are linked to differences in their body mass and genome size (as a proxy for cell size). Since the vulnerability of larger, aquatic taxa to warming has been attributed to the oxygen limitation hypothesis, we also assessed how body mass and genome size modulate thermal tolerance in species with contrasting breathing modes, habitats and life stages. A database with the upper (CTmax) and lower (CTmin) critical thermal limits and their methodological aspects was assembled comprising more than 500 species of ectotherms. Our results demonstrate that thermal tolerance in ectotherms is dependent on body mass and genome size and these relationships became especially evident in prolonged experimental trials where energy efficiency gains importance. During long-term trials, CTmax was impaired in larger-bodied water-breathers, consistent with a role for oxygen limitation. Variation in CTmin was mostly explained by the combined effects of body mass and genome size and it was enhanced in larger-celled, air-breathing species during long-term trials, consistent with a role for depolarization of cell membranes. Our results also highlight the importance of accounting for phylogeny and exposure duration. Especially when considering long-term trials, the observed effects on thermal limits are more in line with the warming-induced reduction in body mass observed during long-term rearing experiments.
This article is part of the theme issue ‘Physiological diversity, biodiversity patterns and global climate change: testing key hypotheses involving temperature and oxygen’.
Phenome-wide search for pleiotropic loci highlights key genes and molecular pathways for human complex traits
Authors: Shikov Anton E. , Predeus Alexander V. , Barbitoff Yury A. 
Published: June 2019

AbstractOver recent decades, genome-wide association studies (GWAS) have dramatically changed the understanding of human genetics. A recent genetic data release by UK Biobank has allowed many researchers worldwide to have comprehensive look into the genetic architecture of thousands of human phenotypes. In this study, we developed a novel statistical framework to assess phenome-wide significance and genetic pleiotropy across the human phenome based on GWAS summary statistics. We demonstrate widespread sharing of genetic architecture components between distinct groups of traits. Apart from known multiple associations inside the MHC locus, we discover high degree of pleiotropy for genes involved in immune system function, apoptosis, hemostasis cascades, as well as lipid and xenobiotic metabolism. We find several notable examples of novel pleiotropic loci (e.g., the MIR2113 microRNA broadly associated with cognition), and provide several possible mechanisms for these association signals. Our results allow for a functional phenome-wide look into the shared components of genetic architecture of human complex traits, and highlight crucial genes and pathways for their development.
TWIST1 homodimers and heterodimers orchestrate lineage-specific differentiation
Authors: Fan Xiaochen , Waardenberg Ashley J. , Demuth Madeleine , Osteil Pierre , Sun Jane , Loebel David A.F. , Graham Mark , Tam Patrick P.L. , Fossat Nicolas 
Published: June 2019

AbstractThe extensive array of bHLH transcription factors and their combinations as dimers underpin the diversity of molecular function required for cell type specification during embryogenesis. The bHLH factor TWIST1 plays pleiotropic roles during development. However, which combinations of TWIST1 dimers are involved and what impact each dimer imposes on the gene regulation network controlled by TWIST1 remain elusive. In this work, proteomic profiling of human-TWIST1 expressing cell lines and transcriptome analysis of mouse cranial mesenchyme have revealed that TWIST1 homodimer and heterodimers with TCF3, TCF4 and TCF12 E-proteins are the predominant dimer combinations. Dimers formation or their balance are altered by disease-causing mutations in TWIST1 helix domains, which may account for the defective differentiation of the craniofacial mesenchyme observed in patients. Functional analyses of the loss and gain of TWIST1-E-protein dimer activity have revealed previously unappreciated roles in guiding lineage differentiation of embryonic stem cells: TWIST1-E-protein heterodimers activate the differentiation of mesoderm and neural crest cells which is accompanied by epithelial-to-mesenchymal transition, while TWIST1 homodimers maintain the stem cells in a progenitor state and block entry to the endoderm lineage.
SS-31 Reverses Mitochondrial Fragmentation in Fibroblasts from Patients with DCMA, a Mitochondrial Cardiomyopathy
Authors: Machiraju Pranav , Wang Xuemei , Sabouny Rasha , Huang Joshua , Zhao Tian , Iqbal Fatima , King Melissa , Prasher Dimple , Lodha Arijit , Ravandi Amir , Argiropoulos Bob , Sinasac David , Khan Aneal , Shutt Timothy , Greenway Steven C. 
Published: June 2019

ABSTRACTObjectivesWe used patient dermal fibroblasts to characterize the mitochondrial abnormalities associated with the dilated cardiomyopathy with ataxia syndrome (DCMA) and to study the effect of the mitochondrially-targeted peptide SS-31 as a potential novel therapeutic.BackgroundDCMA is an understudied autosomal recessive disorder thought to be related to Barth syndrome but caused by mutations in DNAJC19, a protein of unknown function localized to the mitochondria. The clinical disease is characterized by 3-methylglutaconic aciduria, dilated cardiomyopathy, abnormal neurological development and other heterogeneous features. Until recently no effective therapies had been identified and affected patients frequently died in early childhood from intractable heart failure.MethodsDermal fibroblasts from four pediatric patients with DCMA were used to establish parameters of mitochondrial dysfunction. Mitochondrial structure, reactive oxygen species (ROS) production, cardiolipin composition and gene expression were evaluated.ResultsImmunocytochemistry with semi-automated quantification of mitochondrial structural metrics and transmission electron microscopy demonstrated mitochondria to be highly fragmented in DCMA fibroblasts compared to healthy control cells. Live-cell imaging demonstrated significantly increased ROS production in patient cells. These structural and functional abnormalities were reversed by treating DCMA fibroblasts with SS-31, a synthetic peptide that localizes to the inner mitochondrial membrane. Levels of cardiolipin were not significantly different between control and DCMA cells and were unaffected by SS-31 treatment.ConclusionsOur results demonstrate the abnormal mitochondrial structure and function in fibroblasts from patients with DCMA and suggest that SS-31 may represent a potential therapy for this devastating disease.
How to build a fast and highly sensitive sound detector that remains robust to temperature shifts
Authors: Chen Minghui , von Gersdorff Henrique 
Published: June 2019

AbstractFrogs must have sharp hearing abilities during the warm summer months to successfully find mating partners. This study aims to understand how frog hair cell ribbon-type synapses preserve both sensitivity and temporal precision during temperature changes. We performedin vitropatch-clamp recordings of hair cells and their afferent fibers in bullfrog amphibian papillae under room (23-25°C) and high (30-33°C) temperature. Afferent fibers exhibited a wide heterogeneity in membrane input resistance (Rin) from 100 MΩ to 1000 MΩ, which may contribute to variations in spike threshold and firing frequency. At higher temperatures, most fibers increased their frequency of action potential firing due to an increase in spontaneous EPSC frequencies. Hair cell resting membrane potential (Vrest) remained surprisingly stable during temperature increases, although both inward Ca2+current and outward K+current increased in amplitude. This increase in Ca2+current may explain the higher spontaneous EPSC frequencies. The larger “leak currents” at Vrestlowered Rinand produced higher electrical resonant frequencies. However, lower Rinshould decrease sensitivity to sound detection via smaller receptor potentials. Using membrane capacitance measurements, we suggest that hair cells can partially compensate for this reduced sensitivity by increasing exocytosis efficiency and the size of the readily releasable pool of synaptic vesicles. Furthermore, paired recordings of hair cells and their afferent fibers showed that synaptic delays become shorter and multivesicular release becomes more synchronous at higher temperatures, which should improve temporal precision. Altogether, our results explain many previousin vivoobservations on the temperature dependence of spikes in auditory nerves.Significance StatementThe vertebrate inner ear detects and transmits auditory information over a broad dynamic range of sound frequency and intensity. It achieves remarkable sensitivity to soft sounds and precise frequency selectivity. How does the ear of cold-blooded vertebrates maintain its performance level as temperature changes? More specifically, how does the hair cell to afferent fiber synapse in bullfrog amphibian papilla adjust to a wide range of physiological temperatures without losing its sensitivity and temporal fidelity to sound signals? This study usesin vitroexperiments to reveal the biophysical mechanisms that explain many observations made fromin vivoauditory nerve fiber recordings. We find that higher temperature facilitates vesicle exocytosis and electrical tuning to higher sound frequencies, which benefits sensitivity and selectivity.
Untargeted metabolite analysis of Ocimum leaves shows species specific variations
Authors: Shree Manu , Nanda Ranjan K , Masakapalli Shyam K 
Published: June 2019

ABSTRACTTulsi (Ocimum species), the queen of herbs is a common ingredient in beverages with perceived health benefits. Recently published Ocimum genome highlighted the presence of several genes that contributes to important phytochemicals but a comprehensive metabolite profiling to study the water soluble metabolites of Ocimum is lacking. In this study, untargeted metabolic profiling of hot water extract of fresh and air dried leaves of O. basilicum, O. sanctum and O. kilimandscharicum species employing gas chromatography and mass spectrometry (GC-MS) was attempted. Analysis of hot water extracts of Ocimum leaves will provide details of molecules consumed and species specific differences, if any. Several metabolic features including amino acids (glycine, serine glutamate), organic and other acids (succinic acid, fumaric acid, 4-amino butanoic acid), sugars and their derivatives (glucose, sucrose, mannitol, fructose) and secondary metabolites (shikimic acid, quinic acid, catechol, gamma amino butyric acid, eugenol) were identified. Multivariate statistical analysis of GC-MS data indicated several species specific metabolic similarities and differences. Based on variable importance parameter score of >1, it was observed that in case of air dried extracts, glucose, fumaric acid, and D-mannitol displayed as important variables for species specific variation. Whereas in case of fresh leaves extracts, the variation was prominent due to xylose, D-allose and an unknown metabolic feature detected at 24 min (metabolite@24 with highest m/z 75). Phytochemical phenotype of Ocimum leaves not only shows species specific variations but these may partly explain their difference in taste and health benefits from their use as hot beverages.
Easy Kinetics: a novel enzyme kinetic characterization software
Authors: Morabito Gabriele 
Published: June 2019

AbstractHere will be presented the software Easy Kinetics, a publicly available graphical interface that allows rapid evaluation of the main kinetics parameters in an enzyme catalyzed reaction. In contrast to other similar commercial software using algorithms based on non-linear regression models to reach these results, Easy Kinetics is based on a completely different original algorithm, requiring in input the spectrophotometric measurements of ΔAbs/min taken twice at only two different substrate concentrations. The results generated show however a significant concordance with those ones obtained with the most common commercial software used for enzyme kinetics characterization, GraphPad Prism 8©, suggesting that Easy Kinetics can be used for routine tests in enzyme kinetics as an alternative valid software.
The succession pattern of bacterial diversity in compost using pig manure mixed with wood chips analyzed by 16S rRNA gene analysis
Authors: Li Zhengfeng , Yang Yan , Xia Yuzhen , Wu Tao , Zhu Jie , Wang Zhaobao , Yang Jianming 
Published: June 2019

AbstractThe pig manure mixed with wood chips and formed compost by means of fermentation. We found that the protease activity, organic matter content and ammonium nitrogen concentration were higher in the early stage of composting. Meanwhile, the urease activity was highest in the high temperature period. The carbon to nitrogen ratio of the compost decreased continuously with fermentation. The dynamic change in the composition of bacterial overtime in the compost of a 180 kg piles were explored using microbial diversity analysis. The results showed that the microbial species increased with the compost fermentation. At the early stage of composting, the phyla of Firmicutes and Actinomycetes were dominant. The microbes in the high temperature period were mainly composed of Firmicutes and Proteobacteria while the proportion ofBacteroideswas increased during the cooling period. In the compost of maturity stage, the proportion ofChloroflexiincreased, becoming dominant species with other microorganisms includingFirmicutes, Proteobacteria, Bacteroides, Chloroflexibut notActinomycetes. Bacteria involved in lignocellulose degradation, such as those of theThermobifida, Cellvibrio, Mycobacterium, StreptomycesandRhodococcus, were concentrated in the maturity stages of composting. Through correlation analysis, the environmental factors including organic matter, ammonium nitrogen and temperature were consistent with the succession of microbial includingRhodocyclaceae, Anaerolineaceae, Thiopseudomonas, SinibacillusandTepidimicrobium. The change of urease activity and carbon to nitrogen ratio corresponded to microbial communities, mainly containingAnaerolineaceae, Rhodocyclaceae, Luteimoas, Bacillaceae, Corynebacterium, Bacillus, Anaerococcus, Lactobacillus, Ignatzschineria, andBacillaceae.
Can Cynodon dactylon be used to suppress invasive weeds? The effects of density-dependent on the growth and development of Tagetes minuta and Gutenbergia cordifolia
Authors: Ngondya Issakwisa B. , Treydte Anna C. , Ndakidemi Patrick A. , Munishi Linus K. 
Published: June 2019

AbstractPlant-Plant competitive interactions have been reported to be among the forces that shape plant community structure. We studied the effects of varying the density of Cynodon dactylon on the growth and development of the invasive plant species Tagetes minuta and Gutenbergia cordifolia in pot and field plot experiments following a completely randomized design. Increasing densities of C. dactylon strongly reduced T. minuta and G. cordifolia growth and development, leaf total chlorophyll and increased leaf anthocyanin of both invasive species. These detrimental effects may have contributed to poorer T. minuta and G. cordifolia performance under C. dactylon densities of more than 8 individuals per pot/plot compared to those in pots/plots without C. dactylon. This study suggests that C. dactylon can be successfully used to manage the two invasive plants, thus, improving forage production and biomass in affected rangelands.
Total quality index of commercial oyster mushroomPleurotus sapidusin modified atmosphere packaging
Authors: Wan-Mohtar Wan Abd Al Qadr Imad , Klaus Anita , Cheng Acga , Salis Shardana Aiga , Abdul Halim-Lim Sarina 
Published: June 2019

PurposeThe purpose of this paper is to identify the strain of oyster mushroom (OM)Pleurotus sapiduscultivated in a local (commercial) farm, and to generate a total quality index (TQI) on the strain using different modified atmosphere packaging (MAP) gas mixtures.Design/methodology/approachA phylogenetic tree was constructed using the MEGA software to identify the specific strain ofP. sapidusgrown in a local farm. The effects of MAP on fresh fruiting bodies of the identified strain were determined under three conditions: high carbon dioxide packaging (HCP: 20 per cent CO2, 15 per cent O2), low carbon dioxide packaging (LCP: 2 per cent CO2, 30 per cent O2) and high nitrogen packaging (HNP: 85 per cent N2, 15 per cent O2). All samples were stored at 4oC for up to ten days, and subjected to total phenolic content (TPC), colour retention (CR) and sensory analysis. Quality parameters such as chewiness and odour were used to obtain the TQI.FindingsFrom the phylogenetic analysis, a new strain (P. sapidusstrain QDR) with 99 per cent similarity toP. sapiduswas identified. Among the three MAP treatments, HCP recorded the highest TPC (2.85 mg GAE/g) and CR (60.36) after ten days, although only its CR was significantly different (p<0.05) from the control. Feedback from 30 sensory panellists indicated that both HCP and LCP were generally more effective in retaining the colour–odour of OM. The optimum TQI for HCP was obtained based on the observed parameters, which is useful for the large-scale packaging of OM.Originality/valueScientific evidence has revealed that packaging trend for commercially grown OM affects consumer’s acceptance.