bluuebunny/crossref_metadata_2025_split huggingface dataset:
Changes in rumen microbiota of cows in response to dietary supplementation with nitrate, linseed and saponin alone or in combination
Authors: Popova Milka , Guyader Jessie , Silberberg Mathieu , Seradj Ahmad Reza , Saro Cristina , Bernard Aurélien , Gérard Christine , Martin Cécile , Morgavi Diego P 
Published: August 2018

AbstractDietary supplementation with linseed, saponins and nitrate is a promising methane mitigation strategy in ruminant production. The main objective of this work was to assess the effects of these additives on the rumen microbiota in order to understand underlying microbial mechanisms of methane abatement. Two 2 × 2 factorial design studies were conducted simultaneously, which also allowed us to make a broad-based assessment of microbial responses. Eight non-lactating cows were fed diets supplemented with linseed or saponin in order to decrease hydrogen production and nitrate to deviate hydrogen consumption; also, combinations of linseed plus nitrate or saponin plus nitrate were used to explore the interaction between dietary treatments. Amplicon sequencing of 18S and 16S rRNA genes was employed to characterise rumen microbes. Nitrate fed alone or in combination in both studies dramatically affected the composition and structure of rumen microbiota, though impacts were more evident in one of the studies. Linseed moderately modified bacterial community structure with no effect on rumen methanogens and protozoa. Indicator OTU analysis revealed that both linseed and nitrate reduced the relative abundance of hydrogen-producingRuminococcaceae. Linseed increased the proportion of bacteria known to reduce succinate to propionate, whereas nitrate supplementation increased nitrate-reducing bacteria and decreased the metabolic activity of rumen methanogens. Saponins had no effect on the microbiota. Inconsistency found between the two studies, when nitrate was fed to the cows could be explained by changes in microbial ecosystem functioning rather than changes in microbial community structure.ImportanceThis study aimed at identifying the microbial mechanisms of enteric methane mitigation when linseed, nitrate and saponins were fed to non-lactating cows alone or in a combination. Hydrogen is a limiting factor in rumen methanogenesis. We hypothesised that linseed and saponins would affect hydrogen producers and nitrate would deviate hydrogen consumption thus leading to reduced methane production in the rumen. Contrary to what was foreseen, both linseed and nitrate had a deleterious effect on hydrogen producers; linseed also redirected hydrogen consumption towards propionate production, whereas nitrate stimulated the growth of nitrate reducing and hence hydrogen-consuming bacterial taxa. Fundamental knowledge of microbial mechanism involved in rumen methanogenesis, provides novel insights for the development of new or the optimisation of existing methane mitigation strategies.
Polymer coil-globule phase transition is a universal folding principle of Drosophila epigenetic domains
Authors: Lesage Antony , Dahirel Vincent , Victor Jean-Marc , Barbi Maria 
Published: August 2018

AbstractBackgroundLocalized functional domains within chromosomes, known astopologically associating domains(TADs), have been recently highlighted. InDrosophila, TADs are biochemically defined by epigenetic marks, this suggesting that the 3D arrangement may be the “missing link” between epigenetics and gene activity. Recent observations (Boettiger et al., Nature 2016) provide access to structural features of these domains with unprecedented resolution thanks to super-resolution experiments. In particular, they give access to thedistributionof the radii of gyration for domains of different linear length and associated with different transcriptional activity states: active, inactive or repressed. Intriguingly, the observed scaling laws lack consistent interpretation in polymer physics.ResultsWe develop a new methodology conceived to extract the best information from such super-resolution data by exploiting the whole distribution of gyration radii, and to place these experimental results on a theoretical framework. We show that the experimental data are compatible with thefinite-sizebehavior of aself-attracting polymer. The same generic polymer model leads to quantitative differences between active, inactive and repressed domains. Active domains behave as pure polymer coils, while inactive and repressed domains both lie at the coil-globule crossover. For the first time, the “colo-specificity” of both the persistence length and the mean interaction energy are estimated, leading to important differences between epigenetic states.ConclusionsThese results point toward a crucial role of criticality to enhance the system responsivity, resulting in both energy transitions and structural rearrangements. We get strong indications that epigenetically induced changes in nucleosome-nucleosome interaction can cause chromatin to shift between different activity states.
Information Theory as a consistent framework for quantification and classification of landscape patterns
Authors: Nowosad Jakub , Stepinski Tomasz F. 
Published: August 2018

AbstractContextQuantitative grouping of similar landscape patterns is an important part of landscape ecology due to the relationship between a pattern and an underlying ecological process. One of the priorities in landscape ecology is a development of the theoretically consistent framework for quantifying, ordering and classifying landscape patterns.ObjectiveTo demonstrate that the Information Theory as applied to a bivariate random variable provides a consistent framework for quantifying, ordering, and classifying landscape patterns.MethodsAfter presenting Information Theory in the context of landscapes, information-theoretical metrics were calculated for an exemplar set of landscapes embodying all feasible configurations of land cover patterns. Sequences and 2D parametrization of patterns in this set were performed to demonstrate the feasibility of Information Theory for the analysis of landscape patterns.ResultsUniversal classification of landscape into pattern configuration types was achieved by transforming landscapes into a 2D space of weakly correlated information-theoretical metrics. An ordering of landscapes by any single metric cannot produce a sequence of continuously changing patterns. In real-life patterns, diversity induces complexity – increasingly diverse patterns are increasingly complex.ConclusionsInformation theory provides a consistent, theory-based framework for the analysis of landscape patterns. Information-theoretical parametrization of landscapes offers a method for their classification.
Individual susceptibility to TMS affirms the precuneual role in metamemory upon recollection
Authors: Ye Qun , Zou Futing , Dayan Michael , Lau Hakwan , Hu Yi , Kwok Sze Chai 
Published: August 2018

AbstractBackgroundA recent virtual-lesion study using inhibitory repetitive transcranial magnetic stimulation (rTMS) confirmed the causal behavioral relevance of the precuneus in the evaluation of one’s own memory performance (aka mnemonic metacognition).ObjectiveThis study’s goal is to elucidate how these TMS-induced neuromodulatory effects might relate to the neural correlates and be modulated by individual anatomical profiles in relation to meta-memory.MethodsIn a within-subjects design, we assessed the impact of 20-min rTMS over the precuneus, compared to the vertex, across three magnetic resonance imaging (MRI) neuro-profiles on 18 healthy subjects during a memory versus a perceptual task.ResultsTask-based functional MRI revealed that BOLD signal magnitude in the precuneus is associated with variation in individual meta-memory efficiency, and such correlation diminished significantly following TMS targeted at the precuneus. Moreover, individuals with higher resting-state functional connectivity (rs-fcMRI) between the precuneus and the hippocampus, or smaller grey matter volume in the stimulated precuneal region exhibit considerably higher vulnerability to the TMS effect. These effects were not observed in the perceptual domain.ConclusionWe provide compelling evidence in outlining a possible circuit encompassing the precuneus and its mnemonic midbrain neighbor the hippocampus at the service of realizing our meta-awareness during memory recollection of episodic details.HighlightsTMS on precuneus reduces meta-memory ability during memory retrieval.TMS disrupts the correlation between BOLD activity and meta-memory ability.TMS effect is modulated by rs-fcMRI between precuneus and hippocampus.Individuals with greater precuneal grey matter volume more immune to TMS effect.
Mesenchymal Stem Cell Chondroinduction on Cellulose-Silk Composites is Driven by Substrate Elasticity
Authors: Begum Runa , Kafienah Wael 
Published: August 2018

AbstractBiomaterials that can physically control the fate of stem cells are critical for the application ofin situtissue engineering. However, the mechanisms underlying this phenomenon remain unclear. In this study, cellulose and silk composite substrates, known to induce physically the chondrogenic differentiation of human mesenchymal stem cells (MSCs), were regenerated to fabricate two-dimensional film surfaces. MSCs were grown on these surfaces in the presence of chemicals that interfere with the biochemical and mechanical signalling pathwys of MSCs. The data shows that preventing substrate surface elasticity transmission results in significant downregulation of chondrogenic gene expression. Interference with the classical, chondrogenic Smad2/3 Phosphorylation pathway does not impact the chondrogenic capacity of the substrates. The results highlight the importance of the substrate mechanical elasticity on chondrogenic MSCs and its independence of known chondrogenic biochemical pathways.
Functional dynamics underlying near-threshold perception of facial emotions: a magnetoencephalography investigation
Authors: Kajal Diljit Singh , Fioravanti Chiara , Elshahabi Adham , Ruiz Sergio , Sitaram Ranganatha , Braun Christoph 
Published: August 2018

AbstractConscious perception of emotional valence of faces has been proposed to involve top-down and bottom-up information processing. Yet, the underlying neuronal mechanisms of these two processes and the implementation of their cooperation is still unclear. We hypothesized that the networks activated during the interaction of top-down and bottom-up processes are the key substrates responsible for perception. We assessed the participation of neural networks involved in conscious perception of emotional stimuli near the perceptual threshold using a visual-backward-masking paradigm in 12 healthy individuals using magnetoencephalography. Providing visual stimulation near the perceptual threshold enabled us to compare correctly and incorrectly recognized facial emotions and assess differences in top-down modulation for these stimuli using coherence analysis. We found a fronto-parietal network oscillating in the lower gamma band and exerting top-down control as determined by the causality measure of phase slope index. We demonstrated that correct recognition of facial emotions involved high-beta and low-gamma activity in parietal networks, Incorrect recognition was associated with enhanced coupling in the gamma band between left frontal and right parietal regions. Our results indicate that fronto-parietal control of the perception of emotional face stimuli relies on the right-hemispheric dominance of synchronized gamma band activity.
FactorialHMM: Fast and exact inference in factorial hidden Markov models
Authors: Schweiger Regev , Erlich Yaniv , Carmi Shai 
Published: August 2018

MotivationHidden Markov models (HMMs) are powerful tools for modeling processes along the genome. In a standard genomic HMM, observations are drawn, at each genomic position, from a distribution whose parameters depend on a hidden state; the hidden states evolve along the genome as a Markov chain. Often, the hidden state is the Cartesian product of multiple processes, each evolving independently along the genome. Inference in these so-called Factorial HMMs has a naïve running time that scales as the square of the number of possible states, which by itself increases exponentially with the number of subchains; such a running time scaling is impractical for many applications. While faster algorithms exist, there is no available implementation suitable for developing bioinformatics applications.ResultsWe developed FactorialHMM, a Python package for fast exact inference in Factorial HMMs. Our package allows simulating either directly from the model or from the posterior distribution of states given the observations. Additionally, we allow the inference of all key quantities related to HMMs: (1) the (Viterbi) sequence of states with the highest posterior probability; (2) the likelihood of the data; and (3) the posterior probability (given all observations) of the marginal and pairwise state probabilities. The running time and space requirement of all procedures is linearithmic in the number of possible states. Our package is highly modular, providing the user with maximal flexibility for developing downstream applications.Availabilityhttps://github.com/regevs/factorialhmm
Detection of Amyotrophic Lateral Sclerosis (ALS) via Acoustic Analysis
Authors: Norel Raquel , Pietrowicz Mary , Agurto Carla , Rishoni Shay , Cecchi Guillermo 
Published: August 2018

ABSTRACTALS is a fatal neurodegenerative disease with no cure. Experts typically measure disease progression via the ALSFRS-R score, which includes measurements of various abilities known to decline. We propose instead the use of speech analysis as a proxy for ALS progression. This technique enables 1) frequent non-invasive, inexpensive, longitudinal analysis, 2) analysis of data recorded in the wild, and 3) creation of an extensive ALS databank for future analysis. Patients and trained medical professionals need not be co-located, enabling more frequent monitoring of more patients from the convenience of their own homes. The goals of this study are the identification of acoustic speech features in naturalistic contexts which characterize disease progression and development of machine models which can recognize the presence and severity of the disease. We evaluated subjects from the Prize4Life Israel dataset, using a variety of frequency, spectral, and voice quality features. The dataset was generated using the ALS Mobile Analyzer, a cell-phone app that collects data regarding disease progress using a self-reported ALSFRS-R questionnaire and several active tasks that measure speech and motor skills. Classification via leave-five-subjects-out cross-validation resulted in an accuracy rate of 79% (61% chance) for males and 83% (52% chance) for females.
Gramicidin increases lipid flip-flop in symmetric and asymmetric lipid vesicles
Authors: Doktorova M. , Heberle F. A. , Marquardt D. , Rusinova R. , Sanford L. , Peyear T. A. , Katsaras J. , Feigenson G. W. , Weinstein H. , Andersen O. S. 
Published: August 2018

ABSTRACTUnlike most transmembrane proteins, phospholipids can migrate from one leaflet of the membrane to the other. Because this spontaneous lipid translocation (flip-flop) tends to be very slow, cells facilitate the process with enzymes that catalyze the transmembrane movement and thereby regulate the transbilayer lipid distribution. Non-enzymatic membrane-spanning proteins with unrelated primary functions have also been found to accelerate lipid flip-flop in a nonspecific manner and by various hypothesized mechanisms. Using deuterated phospholipids, we examined the acceleration of flip-flop by gramicidin channels which have well-defined structures and known function, features that make them ideal candidates for probing the protein-membrane interactions underlying lipid flip-flop. To study compositionally and isotopically asymmetric proteoliposomes containing gramicidin, we expanded a recently developed protocol for the preparation and characterization of lipid-only asymmetric vesicles. Channel incorporation, conformation, and function were examined with small-angle X-ray scattering, circular dichroism and a stopped-flow spectrofluorometric assay, respectively. As a measure of lipid scrambling we used differential scanning calorimetry to monitor the effect of gramicidin on the melting transition temperatures of the two bilayer leaflets. The two calorimetric peaks of the individual leaflets merged into a single peak over time suggestive of scrambling activity, and the effect of the channel on the transbilayer lipid distribution in both symmetric POPC and asymmetric POPC/DMPC vesicles was quantified from proton NMR measurements. Our results show that gramicidin increases lipid flip-flop in a complex, concentration-dependent manner. To determine the molecular mechanism of the process we used molecular dynamics simulations and further computational analysis of the trajectories to estimate the amount of membrane deformation in the samples. Together, the experimental and computational approaches were found to constitute an effective means for studying the effects of transmembrane proteins on lipid distribution in both symmetric and asymmetric model membranes.
Powerful and Efficient Strategies for Genetic Association Testing of Symptom and Questionnaire Data in Psychiatric Genetic Studies
Authors: Holleman Aaron M. , Broadaway K. Alaine , Duncan Richard , Almli Lynn M. , Bradley Bekh , Ressler Kerry J. , Ghosh Debashis , Mulle Jennifer G. , Epstein Michael P. 
Published: August 2018

ABSTRACTGenetic studies of psychiatric disorders often deal with phenotypes that are not directly measurable. Instead, researchers rely on multivariate symptom data from questionnaires and surveys like the PTSD Symptom Scale (PSS) and Beck Depression Inventory (BDI) to indirectly assess a latent phenotype of interest. Researchers subsequently collapse such multivariate questionnaire data into a univariate outcome to represent a surrogate for the latent phenotype. However, when a causal variant is only associated with a subset of collapsed symptoms, the effect will be challenging to detect using the univariate outcome. We describe a more powerful strategy for genetic association testing in this situation that jointly analyzes the original multivariate symptom data collectively using a statistical framework that compares similarity in multivariate symptom-scale data from questionnaires to similarity in common genetic variants across a gene. We use simulated data to demonstrate this strategy provides substantially increased power over standard approaches that collapse questionnaire data into a single surrogate outcome. We also illustrate our approach using GWAS data from the Grady Trauma Project and identify genes associated with BDI not identified using standard univariate techniques. The approach is computationally efficient, scales to genome-wide studies, and is applicable to correlated symptom data of arbitrary dimension (thereby aligning with National Institute of Mental Health’s Research Domain Criteria).
A scoping review of health-based survey instruments validated in Brunei Darussalam
Authors: Alhaji Mohammed M. , Tan Jackson , Naing Lin , Tuah Nik AA 
Published: August 2018

ABSTRACTThis study sought to map and review validated health-based survey instruments in Brunei Darussalam. A scoping search of relevant articles was carried out. Six health-based survey tools have been psychometrically evaluated in Brunei Darussalam, 4 in Brunei-Malay (SF-36v2, EQ-5D/VAS, CPQπ_14, and m-SEQ-12) and 2 in English (OFER and WPBA) languages. Two studies (m-SEQ-12, CPQ11–14) translated tools in English into Brunei-Malay. Two studies (SF-36v2, EQ-5D) cross-culturally adapted the Malaysian and Singaporean versions of the tools into Brunei-Malay. Four studies were adult- and hospital-based, among healthcare workers (OFER,WPBA) and patients with chronic diseases (SF-36v2, EQ-5D); and 2 studies (m-SEQ-12, CPQ11–14) were non-adult-and secondary school-based. Pretesting was carried out in 4 studies (SF-36v2, EQ-5D, CPQ11–14, and m-SEQ-12) on a sample of 5 to 20 volunteers. The sample size for validation ranged from 40 to 457. Reliability tests, Cronbach’s alpha and intra-class coefficient (n=3), Cohen’s Kappa (n=1), and 5-point scale qualitative assessment (n=1) were measured. Validity tests included face validity (n=2), discriminant validity (n=2), convergent validity (n=2), construct validity (n=2), factorial validity (n=2), and 5-point scale qualitative assessment (n=1). There is a need for more psychometric evaluation of questionnaires in Brunei Darussalam. Importantly, large heterogeneous participants, more languages, and varied psychometric tests should be considered.
Opposing Roles of the Fork-head box genes FoxM1 and FoxA2 in Hepatocellular Carcinoma
Authors: Chand Vaibhav , Pandey Akshay , Kopanja Dragana , Guzman Grace , Raychaudhuri Pradip 
Published: August 2018

ABSTRACTThe fork-head box transcription factor FoxMl is essential for hepatocellular carcinoma (HCC) development and its overexpression coincides with poor prognosis. Here, we show that the mechanisms by which FoxM1 drives HCC progression involve overcoming the inhibitory effects of the liver differentiation gene FoxA2. First, the expression patterns of FoxM1 and FoxA2 in human HCC are opposite. We show that FoxM1 represses expression of FoxA2 in G1 phase, a phase in the cell cycle in which cells can undergo differentiation. Repression of FoxA2 in G1 phase is important, as it is capable of inhibiting expression of the pluripotency genes that are expressed mainly in S/G2 phases. Using a transgenic mouse model for oncogenic Ras-driven HCC, we provide genetic evidence for a repression of FoxA2 by FoxM1. Conversely, FoxA2 inhibits expression of FoxM1, and inhibits FoxM1-induced tumorigenicity of HCC cells. Moreover, expression of FoxA2 in mouse liver expressing activated Ras inhibits FoxM1 expression and inhibits HCC progression. The observations provide strong genetic evidence for an opposing role of FoxM1 and FoxA2 in HCC progression.AUTHOR SUMMARYLiver cancer remains untreatable because it is diagnosed at a stage when the cancer is aggressive and resistant to therapeutics. The mechanism that drives aggressive liver cancer is poorly understood. These cancers are made up of poorly differentiated cancer cells. Interestingly, the FoxM1 gene is overexpressed in the aggressive liver cancers. Although FoxM1 is important for expression of the proliferation genes, it does not explain why it is overexpressed mainly in the undifferentiated cancers. The current study addresses this puzzle. Our previous studies demonstrated that FoxM1 increases expression of the pluripotency genes that are expressed mainly in the stem-like cells. In the current manuscript we show that, in addition to activating the pluripotency genes, FoxM1 inhibits expression of the liver differentiation gene FoxA2. Overexpression of FoxM1 is important for this inhibition function, as it involves the retinoblastoma family of proteins, which are often inactivated in cancer cells, and thus, are of low-abundance. Moreover, the inhibition of FoxA2 is significant because FoxA2 could inhibit expression of the pluripotency genes as well as FoxM1. The observations provide new insights into how FoxM1 drives progression of aggressive liver cancer.