bluuebunny/crossref_metadata_2025_split huggingface dataset:
Vitamin D status in Sudanese pregnant women: a cross-sectional study
Authors: Gaffer Ahmed A , Rayis Duria A , Elhussein Osama G , Adam Ishag 
Published: June 2019

Abstract

Background
Maternal vitamin D deficiency is associated with maternal and perinatal adverse effects. This study was conducted to assess the vitamin D status among pregnant Sudanese women.

Methods
A total of 180 pregnant women were enrolled in a cross-sectional study in Saad Abualila Hospital, Khartoum, Sudan. The medical history of each woman was collected and 25-hydroxyvitamin D [25(OH)D] was measured using an electrochemiluminescence immunoassay.

Results
The median age, gravidity and gestational age was 27.7 y, 1.0 and 10.7 weeks, respectively. Of the 180 woman, 169 (93.9%) had vitamin D deficiency (≤20 ng/ml). There was no correlation between the 25(OH)D level and body mass index (r=−0.135, p=0.071) or haemoglobin level (r= 0.001, p=0.999).

Conclusions
The current study showed a high prevalence of vitamin D deficiency. Further studies investigating the risk factors for vitamin D deficiency and the outcome of pregnancy are needed.
Cranial morphology and phylogenetic relationships of the Middle Permian pareiasaur Embrithosaurus schwarzi from the Karoo Basin of South Africa
Authors: Van den Brandt Marc Johan , Abdala Fernando , Rubidge Bruce Sidney 
Published: June 2019

AbstractPareiasaurs were globally distributed, abundant, herbivorous parareptiles of the Middle to Late Permian, with the basal-most members found in the Middle Permian of South Africa. These basal taxa were particularly abundant and went extinct at the end of the Gaudalupian (Capitanian) at the top of the Tapinocephalus Assemblage Zone. Currently four taxa are recognized in this group: Bradysaurus seeleyi, B. baini, Nochelesaurus alexanderi and Embrithosaurus schwarzi, but they are all poorly understood. We here present the first detailed cranial description and updated diagnosis for Embrithosaurus schwarzi. No cranial autapomorphies were identified. However, Embrithosaurus schwarzi is a distinct taxon in this group, based on its unique dentition and using a combination of cranial features. It has nine marginal cusps on all maxillary and mandibular teeth, and wider maxillary teeth than in the co-occurring taxa, due to the marginal cusps being arranged more regularly around the crown, and the apex of the crown lacking the long, central, three-cusped trident. Our updated phylogenetic analysis recovers the four Middle Permian South African taxa as a monophyletic group for the first time, which we call Bradysauria, comprising a clade including Embrithosaurus, Bradysaurus baini and a polytomy including Nochelesaurus and Bradysaurus seeleyi.
A Bayesian framework for identifying consistent patterns of microbial abundance between body sites
Authors: Meier Richard , Thompson Jeffrey A , Chung Mei , Zhao Naisi , Kelsey Karl T. , Michaud Dominique S. , Koestler Devin C. 
Published: June 2019

AbstractRecent studies have found that the microbiome in both gut and mouth are associated with diseases of the gut, including cancer. If resident microbes could be found to exhibit consistent patterns between the mouth and gut, disease status could potentially be assessed non-invasively through profiling of oral samples. Currently, there exists no generally applicable method to test for such associations. Here we present a Bayesian framework to identify microbes that exhibit consistent patterns between body sites, with respect to a phenotypic variable. For a given operational taxonomic unit (OTU), a Bayesian regression model is used to obtain Markov-Chain Monte Carlo estimates of abundance among strata, calculate a correlation statistic, and conduct a formal test based on its posterior distribution. Extensive simulation studies demonstrate overall viability of the approach, and provide information on what factors affect its performance. Applying our method to a dataset containing oral and gut microbiome samples from 77 pancreatic cancer patients revealed several OTUs exhibiting consistent patterns between gut and mouth with respect to disease subtype. Our method is well powered for modest sample sizes and moderate strength of association and can be flexibly extended to other research settings using any currently established Bayesian analysis programs.
Network Topology Dynamics of Circulating Biomarkers and Cognitive Performance in Older Cytomegalovirus-seropositive or -seronegative Men and Women
Authors: Benedetto Svetlana Di , Müller Ludmila , Rauskolb Stefanie , Sendtner Michael , Fassnacht Martin , Pawelec Graham , Müller Viktor 
Published: June 2019

AbstractBackgroundCytokines are signaling molecules operating within complex cascade patterns and having exceptional modulatory functions. They impact various physiological processes such as neuroendocrine and metabolic interactions, neurotrophins’ metabolism, neuroplasticity, and may affect behavior and cognition. In our previous study, we found that sex and Cytomegalovirus (CMV)-serostatus may modulate levels of circulating pro- and anti-inflammatory cytokines, metabolic factors, immune cells, and cognitive performance, as well as associations between them.ResultsIn the present study, we used a graph-theoretical approach to investigate the network topology dynamics of 22 circulating biomarkers and 11 measures of cognitive performance in 161 older participants recruited to undergo a six-months training intervention. For network construction, we applied coefficient of determination (R2) that was calculated for all possible pairs of variables (N = 33) in four groups (CMV− men and women; CMV+ men and women). Network topology has been evaluated by clustering coefficient (CC) and characteristic path length (CPL) as well as local (Elocal) and global (Eglobal) efficiency, showing the degree of network segregation (CC and Elocal) and integration (CPL and Eglobal). We found that networks under consideration showed small-world networks properties with more random characteristics. Mean CC, as well as local and global efficiency were highest and CPL shortest in CMV− males (having lowest inflammatory status and highest cognitive performance). CMV− and CMV+ females did not show any significant differences. Modularity analyses showed that the networks exhibit in all cases highly differentiated modular organization (with Q-value ranged between 0.397 and 0.453).ConclusionsIn this work, we found that segregation and integration properties of the network were notably stronger in the group with balanced inflammatory status. We were also able to confirm our previous findings that CMV-infection and sex modulate multiple circulating biomarkers and cognitive performance and that balanced inflammatory and metabolic status in elderly contributes to better cognitive functioning. Thus, network analyses provide a useful strategy for visualization and quantitative description of multiple interactions between various circulating pro- and anti-inflammatory biomarkers, hormones, neurotrophic and metabolic factors, immune cells, and measures of cognitive performance and can be in general applied for analyzing interactions between different physiological systems.
Adiabatic invariants drive rhythmic human motion in variable gravity
Authors: Boulanger N. , Buisseret F. , Dehouck V. , Dierick F. , White O. 
Published: June 2019

AbstractNatural human movements are stereotyped. They minimise cost functions that include energy, a natural candidate from mechanical and physiological points of view. In time-changing environments, however, motor strategies are modified since energy is no longer conserved. Adiabatic invariants are relevant observables in such cases, although they have not been investigated in human motor control so far. We fill this gap and show that the theory of adiabatic invariants explains how humans move when gravity varies.
Nucleus Basalis Stimulation Enhances Working Memory by Stabilizing Attractor Networks in Prefrontal Cortex
Authors: Qi Xue-Lian , Liu Ruifeng , Singh Balbir , Bestue David , Compte Albert , Vazdarjanova Almira I. , Blake David T. , Constantinidis Christos 
Published: June 2019

SummaryAcetylcholine in the neocortex is critical for executive function. Degeneration of the basal forebrain cholinergic system is associated with cognitive decline in aging and Alzheimer’s disease. Cholinergic agonists and acetylcholinesterase inhibitors improve cognitive performance as does intermittent electrical stimulation of the cortical source of acetylcholine, the Nucleus Basalis (NB) of Meynert. Here we tested how NB stimulation improves working memory behavior and alters its neural code. NB stimulation increased dorsolateral prefrontal activity during the delay period of working memory tasks but did not strengthen phasic responses to the optimal visual stimulus of each neuron. Unexpectedly, improvement of behavioral performance was not the result of increased neural selectivity. Tuning of neuronal responses broadened, which rendered an attractor network more stable and filtered distracting visual stimuli more effectively. Thus, the effects of acetylcholine on prefrontal neural activity and selectivity in working memory contrast those of dopamine and stabilize neural ensembles based on neuromodulatory tone.
Neural Multi-Scale Self-Supervised Registration for Echocardiogram Dense Tracking
Authors: Zhu Wentao , Huang Yufang , Vannan Mani A , Liu Shizhen , Xu Daguang , Fan Wei , Qian Zhen , Xie Xiaohui 
Published: June 2019

AbstractEchocardiography has become routinely used in the diagnosis of cardiomyopathy and abnormal cardiac blood flow. However, manually measuring myocardial motion and cardiac blood flow from echocar-diogram is time-consuming and error-prone. Computer algorithms that can automatically track and quantify myocardial motion and cardiac blood flow are highly sought after, but have not been very successful due to noise and high variability of echocardiography. In this work, we propose a neural multi-scale self-supervised registration (NMSR) method for automated myocardial and cardiac blood flow dense tracking. NMSR incorporates two novel components: 1) utilizing a deep neural net to parameterize the velocity field between two image frames, and 2) optimizing the parameters of the neural net in a sequential multi-scale fashion to account for large variations within the velocity field. Experiments demonstrate that NMSR yields significantly better registration accuracy than the state-of-the-art methods, such as advanced normalization tools (ANTs) and Voxel Morph, for both myocardial and cardiac blood flow dense tracking. Our approach promises to provide a fully automated method for fast and accurate analyses of echocardiograms.
Catabolism of alkylphenols inRhodococcusvia ameta-cleavage pathway associated with genomic islands
Authors: Levy-Booth David J. , Fetherolf Morgan M. , Stewart Gordon , Liu Jie , Eltis Lindsay D. , Mohn William W. 
Published: June 2019

AbstractThe bacterial catabolism of aromatic compounds has considerable promise to convert lignin depolymerization products to commercial chemicals. Alkylphenols are a key class of depolymerization products whose catabolism is not well elucidated. We isolatedRhodococcus rhodochrousEP4 on 4-ethylphenol and applied genomic and transcriptomic approaches to elucidate alkylphenol catabolism in EP4 andRhodococcus jostiiRHA1. RNA-Seq and RT-qPCR revealed a pathway encoded by theaphABCDEFGHIQRSgenes that degrades 4-ethylphenol via themeta-cleavage of 4-ethylcatechol. This process was initiated by a two-component alkylphenol hydroxylase, encoded by theaphABgenes, which were up-regulated ~3,000-fold. Purified AphAB from EP4 had highest specific activity for 4-ethylphenol and 4-propylphenol (~2000 U/mg) but did not detectably transform phenol. Nevertheless, a ΔaphAmutant in RHA1 grew on 4-ethylphenol by compensatory up-regulation of phenol hydroxylase genes (pheA1-3). Deletion ofaphC, encoding an extradiol dioxygenase, prevented growth on 4-alkylphenols but not phenol. Disruption ofpcaLin the β-ketoadipate pathway prevented growth on phenol but not 4-alkylphenols. Thus, 4-ethylphenol and 4-propylphenol are catabolized exclusively viameta-cleavage in rhodococci while phenol is subject toortho-cleavage. Putative genomic islands encodingaphgeneswere identified in EP4 and several other rhodococci. Overall, this study identifies a 4-alkylphenol pathway in rhodococci, demonstrates key enzymes involved, and presents evidence that the pathway is encoded in a genomic island. These advances are of particular importance for wide-ranging industrial applications of rhodococci, including upgrading of lignocellulose biomass.ImportanceElucidation of bacterial alkylphenol catabolism is important for the development of biotechnologies to upgrade the lignin component of plant biomass. We isolated a new strain,Rhodococcus rhodochrousEP4, on 4-ethylphenol, an alkylphenol that occurs in lignin-derived streams, including reductive catalytic fractionation products of corn stover. We further demonstrated its degradation via ameta-cleavage pathway (Aph) with transcriptomics. A new class of Actinobacterial hydroxylase, AphAB, acts specifically on alkylphenols. Phylogenomic analysis indicated that theaphgenes occur on putative genomic islands in several rhodococcal strains. These genes were identified in the genetically-tractable strainRhodococcus jostiiRHA1. Strains missing this element cannot metabolise 4-ethylphenol and 4-propylphenol. Overall, we advanced the understanding of how aromatic compounds are degraded by environmental bacteria and identified enzymes that can be employed in the transition away from petro-chemicals towards renewable alternatives.
Protein function prediction in genomes: Critical assessment of coiled-coil predictions based on protein structure data
Authors: Simm Dominic , Hatje Klas , Waack Stephan , Kollmar Martin 
Published: June 2019

AbstractCoiled-coil regions were among the first protein motifs described structurally and theoretically. The beauty and simplicity of the motif gives hope to detecting coiled-coil regions with reasonable accuracy and precision in any protein sequence. Here, we re-evaluated the most commonly used coiled-coil prediction tools with respect to the most comprehensive reference data set available, the entire Protein Data Base (PDB), down to each amino acid and its secondary structure. Apart from the thirtyfold difference in number of predicted coiled-coils the tools strongly vary in their predictions, across structures and within structures. The evaluation of the false discovery rate and Matthews correlation coefficient, a widely used performance metric for imbalanced data sets, suggests that the tested tools have only limited applicability for large data sets. Coiled-coil predictions strongly impact the functional characterization of proteins, are used for functional genome annotation, and should therefore be supported and validated by additional information.
Genetic dissection reveals the role of Ash1 domains in counteracting Polycomb repression
Authors: Dorafshan Eshagh , Kahn Tatyana G. , Glotov Alexander , Savitsky Mikhail , Schwartz Yuri B. 
Published: June 2019

AbstractAntagonistic functions of Polycomb and Trithorax proteins are essential for proper development of all metazoans. While the Polycomb proteins maintain the repressed state of key developmental genes, the Trithorax proteins ensure that these genes stay active in cells where they have to be expressed. Ash1 is the Trithorax protein that was proposed to counteract Polycomb repression by methylating lysine 36 of histone H3. However, recently it was shown that genetic replacement ofDrosophilahistone H3 with the variant that carried Arginine instead of Lysine at position 36 did not impair the ability of Ash1 to counteract Polycomb repression. This argues that Ash1 counteracts Polycomb repression by methylating, yet unknown, non-histone proteins. To find these substrates, one may need to look beyond the function of the Ash1 histone methyltransferase SET domain at other evolutionary conserved parts of the protein that received little attention. Here we usedDrosophilagenetics to demonstrate that Ash1 requires each of the BAH, PHD and SET domains to counteract Polycomb repression, while AT hooks are dispensable. Our findings argue that,in vivo, Ash1 acts as a multimer. Thereby, it can combine the input of the SET domain and PHD-BAH cassette residing in different peptides. Finally, using new loss of function alleles, we show that zygotic Ash1 is required to prevent erroneous repression of homeotic genes.
Single-cell based elucidation of molecularly-distinct glioblastoma states and drug sensitivity
Authors: Ding Hongxu , Burgenske Danielle M. , Zhao Wenting , Subramaniam Prem S. , Bakken Katrina K. , He Lihong , Alvarez Mariano J. , Laise Pasquale , Paull Evan O. , Spinazzi Eleonora F. , Dovas Athanassios , Marie Tamara , Upadhyayula Pavan , Cruz Filemon Dela , Diolaiti Daniel , Kung Andrew , Bruce Jeffrey N. , Canoll Peter , Sims Peter A. , Sarkaria Jann N. , Califano Andrea 
Published: June 2019

AbstractGlioblastoma heterogeneity and plasticity remain controversial, with proposed subtypes representing the average of highly heterogeneous admixtures of independent transcriptional states. Single-cell, protein-activity-based analysis allowed full quantification of >6,000 regulatory and signaling proteins, thus providing a previously unattainable single-cell characterization level. This helped identify four novel, molecularly distinct subtypes that successfully harmonize across multiple GBM datasets, including previously published bulk and single-cell profiles and single cell profiles from seven orthotopic PDX models, representative of prior subtype diversity. GBM is thus characterized by the plastic coexistence of single cells in two mutually-exclusive developmental lineages, with additional stratification provided by their proliferative potential. Consistently, all previous subtypes could be recapitulated by single-cell mixtures drawn from newly identified states. Critically, drug sensitivity was predicted and validated as highly state-dependent, both in single-cell assays from patient-derived explants and in PDX models, suggesting that successful treatment requires combinations of multiple drugs targeting these distinct tumor states.SignificanceWe propose a new, 4-subtype GBM classification, which harmonizes across bulk and single-cell datasets. Single-cell mixtures from these subtypes effectively recapitulate all prior classifications, suggesting that the latter are a byproduct of GBM heterogeneity. Finally, we predict single-cell level activity of three clinically-relevant drugs, and validate them in patient-derived explant.
NemaLife: A structured microfluidic culture device optimized for aging studies in crawlingC. elegans
Authors: Rahman Mizanur , Edwards Hunter , Birze Nikolajs , Gabrilska Rebecca , Rumbaugh Kendra P. , Blawzdziewicz Jerzy , Szewczyk Nathaniel J. , Driscoll Monica , Vanapalli Siva A. 
Published: June 2019

AbstractCaenorhabditis elegansis a powerful animal model in aging research. Standard longevity assays on agar plates involve the tedious task of picking and transferring animals to prevent younger progeny from contaminating age-synchronized adult populations. Large-scale studies employ progeny-blocking drugs or sterile mutants to avoid progeny contamination, but such manipulations change adult physiology and alter the influence of reproduction on normal aging. Moreover, for some agar growth-based technology platforms, such as automated lifespan machines, reagents such as food or drugs cannot be readily added/removed after initiation of the study. Current microfluidic approaches are well-suited to address these limitations, but in their liquid-based environments animals swim rather than crawl, introducing swim-induced stress in the lifespan analysis. Here we report a simple microfluidic device that we call NemaLife that features: 1) an optimized micropillar arena in which animals can crawl, 2) sieve channels that separate progeny and prevent the loss of adults from the arena during culture maintenance, and 3) ports which allow rapid accessibility to feed the adult-only population and introduce reagents as needed. Culture maintenance and liquid manipulation are performed with simple hand-held syringes to facilitate integration of our technology into general laboratory protocols. Additionally, device geometry and feeding protocols were designed to emulate the body gait, locomotion, and lifespan of animals reared on agar. We validated our approach with longevity analyses of classical aging mutants (daf-2,age-1,eat-2, anddaf-16) and animals subjected to RNAi knockdown of age-related genes (age-1anddaf-16). We also showed that healthspan measures such as pharyngeal pumping and tap-induced stimulated reversals can be scored across the lifespan. Overall, the capacity to generate reliable lifespan and physiological data from the NemaLife chip underscores the potential of this device to accelerate healthspan and lifespan investigations inC. elegans.
Choice suppression is achieved through opponent but not independent function of the striatal indirect pathway in mice
Authors: Delevich Kristen , Hoshal Benjamin , Collins Anne GE , Wilbrecht Linda 
Published: June 2019

AbstractThe dorsomedial striatum (DMS) plays a key role in action selection, but little is known about how direct and indirect pathway spiny projection neurons (dSPNs and iSPNs) contribute to choice suppression in freely moving animals. Here, we used pathway-specific chemogenetic manipulation during a serial choice foraging task to test opposing predictions for iSPN function generated by two theories: 1) the ‘select/suppress’ heuristic which suggests iSPN activity is required to suppress alternate choices and 2) the network-inspired Opponent Actor Learning model (OpAL) which proposes that the weighted difference of dSPN and iSPN activity determines choice. We found that chemogenetic activation, but not inhibition, of iSPNs disrupted learned suppression of nonrewarded choices, consistent with the predictions of the OpAL model. Our findings suggest that iSPNs’ role in stopping and freezing does not extend in a simple fashion to choice suppression. These data may provide insights critical for the successful design of interventions for addiction or other conditions in which suppression of behavior is desirable.