bluuebunny/crossref_metadata_2025_split huggingface dataset:
Adherence to a Semiannual Surveillance Program for Hepatocellular Carcinoma in Patients With Liver Cirrhosis
Authors: Mancebo Alejo , González-Diéguez María Luisa , Navascués Carmen A. , Cadahía Valle , Varela María , Pérez Ramón , Rodrigo Luis , Rodríguez Manuel 
Published: October 2016

Background:
Patient adherence to screening for hepatocellular carcinoma (HCC) is not well known. Our aims were to analyze the adherence to a surveillance program in a prospective cohort of cirrhotic patients and to examine its association with HCC stage at diagnosis.

Materials and Methods:
A total of 770 patients with cirrhosis were examined semiannually by ultrasound and alpha-fetoprotein at a tertiary center. We collected data on 17 variables at baseline. Suboptimal adherence was defined as failure to complete 2 consecutive screening rounds.

Results:
Over a median follow-up period of 42.0 months (interquartile range: 60.0), 125 patients (16.2%) had suboptimal adherence. Active or previous intravenous drug use [hazard ratio (HR), 5.33; 95% confidence interval (CI), 3.07-9.23], active alcohol consumption (HR, 3.03; 95% CI, 2.03-4.51), absence of liver decompensation before the inclusion in the program (HR, 1.65; 95% CI, 1.07-2.55) and aspartate transaminase/alanine transaminase ratio ≥1.6 (HR, 1.82; 95% CI, 1.23-2.70) were independent predictors of suboptimal adherence. Compared with those with optimal adherence, patients with suboptimal adherence had a more advanced HCC stage at diagnosis (P=0.015), they were less frequently treated with curative intention (P=0.078) and survived less (median: 14.2 mo; IQR: 36.0 vs. 22.7 mo; IQR: 47.4; P=0.160), although these differences were not significant.

Conclusions:
The adherence to the process of HCC surveillance can be considered as adequate among cirrhotic patients. Active alcohol consumption and a history of intravenous drug use are the strongest predictors of suboptimal adherence. These patients have a more advanced HCC stage at diagnosis and tend to be less frequently treated with curative intention.
Real-Time Non-Intrusive Assessment of Viewing Distance during Computer Use
Authors: Argilés Marc , Cardona Genís , Pérez-Cabré Elisabet , Pérez-Magrané Ramon , Morcego Bernardo , Gispets Joan 
Published: October 2016

ABSTRACTPurposeTo develop and test the sensitivity of an ultrasound-based sensor to assess the viewing distance of visual display terminals operators in real-time conditions.MethodsA modified ultrasound sensor was attached to a computer display to assess viewing distance in real time. Sensor functionality was tested on a sample of 20 healthy participants while they conducted four 10-minute randomly presented typical computer tasks (a match-three puzzle game, a video documentary, a task requiring participants to complete a series of sentences, and a predefined internet search).ResultsThe ultrasound sensor offered good measurement repeatability. Game, text completion, and web search tasks were conducted at shorter viewing distances (54.4 cm [95% CI 51.3–57.5 cm], 54.5 cm [95% CI 51.1–58.0 cm], and 54.5 cm [95% CI 51.4–57.7 cm], respectively) than the video task (62.3 cm [95% CI 58.9–65.7 cm]). Statistically significant differences were found between the video task and the other three tasks (all p < 0.05). Range of viewing distances (from 22 to 27 cm) was similar for all tasks (F = 0.996; p = 0.413).ConclusionsReal-time assessment of the viewing distance of computer users with a non-intrusive ultrasonic device disclosed a task-dependent pattern.
The Visual Impact of Lens-Induced Astigmatism is Linked to Habitual Axis
Authors: Hughes Amy R. , Mallen Edward A. H. , Elliott David B. 
Published: October 2016

ABSTRACT

Purpose
Many studies have assessed the visual impact of astigmatism by inducing it using loose trial lenses at set axes. There are conflicting opinions and some confusion about the results, but the reduction in vision is typically least with lens-induced with-the-rule astigmatism. In this study, we determined whether a participant’s habitual astigmatism influences the impact of lens-induced astigmatism on distance visual acuity (VA).

Methods
Participants included 35 adults (age range 19–79, average 41.3 ± 15.4 years), who were either astigmats (≥0.75DC; N = 21) or non-astigmatic controls (N = 14). Distance VA was measured using an automated FrACT (Freiburg VA) system with the participant’s habitual correction, and then with the addition of a +1.00DC lens at either 90 or 180 degrees (control) or at and perpendicular to the axis of habitual astigmatism (astigmats).

Results
The reduction in VA with induced astigmatism was significantly affected by whether the participant was a with-the-rule astigmat, against-the-rule astigmat, or non-astigmat (p = 0.006). Lens-induced astigmatism axis ≈ 180 (160–20°) reduced the VA less than axis ≈ 90 (70–120°) in the control group (reduction in mean VA of 0.32 SD ± 0.10 with 95% confidence intervals of [0.27,0.37] compared to 0.42 ± 0.09 [0.37,0.47] logMAR) and with-the-rule astigmats (reduction in VA of 0.31 SD ± 0.06 [0.27,0.35] compared to 0.45 SD ± 0.12 [0.38,0.52] logMAR). The against-the-rule astigmats had a very similar reduction in VA with the ≈+1.00DC axis 180 condition compared to the ≈+1.00DC axis 90 condition (reduction in VA of 0.26 SD ± 0.09 [0.21,0.31] compared to 0.25 SD ± 0.14 [0.17,0.33] logMAR).

Conclusions
The impact of lens-induced astigmatism was dependent on the refractive status of the participants. When investigating the impact of lens-induced astigmatism, it is important to consider the participants’ habitual axis of astigmatism.
Studying vertical microbiome transmission from mothers to infants by strain-level metagenomic profiling
Authors: Asnicar Francesco , Manara Serena , Zolfo Moreno , Truong Duy Tin , Scholz Matthias , Armanini Federica , Ferretti Pamela , Gorfer Valentina , Pedrotti Anna , Tett Adrian , Segata Nicola 
Published: October 2016

AbstractThe gut microbiome starts to be shaped in the first days of life and continues to increase its diversity during the first months. Several investigations are assessing the link between the configuration of the infant gut microbiome and infant health, but a comprehensive strain-level assessment of vertically transmitted microbes from mother to infant is still missing. We longitudinally collected fecal and breast milk samples from multiple mother-infant pairs during the first year of life, and applied shotgun metagenomic sequencing followed by strain-level profiling. We observed several specific strains including those fromBifidobacterium bifidum,Coprococcus comes, andRuminococcus bromii, that were present in samples from the same mother-infant pair, while being clearly distinct from those carried by other pairs, which is indicative of vertical transmission. We further applied metatranscriptomics to study thein vivoexpression of vertically transmitted microbes, for exampleBacteroides vulgatusandBifidobacteriumspp., thus suggesting that transmitted strains are functionally active in the two rather different environments of the adult and infant guts. By combining longitudinal microbiome sampling and newly developed computational tools for strain-level microbiome analysis, we showed that it is possible to track vertical transmission of members of the microbiome from mother to infants and characterize their transcriptional activity. Our work poses the basis for surveying at larger scale the sources of microbial diversity in the infants and starts associating these transmissions with the subsequent longer-term development of a healthy or dysbiotic microbiome.ImportanceEarly infant exposure is important in the acquisition and ultimate development of a healthy infant microbiome. There is increasing support that the maternal microbial reservoir is a key route of microbial transmission, yet much is inferred from the observation of shared species in mother and infant. Common species,per se, does not necessarily equate vertical transmission as species exhibit considerable strain heterogeneity and it is therefore imperative to identify shared strains. We demonstrate here the potential of shotgun metagenomics and strain-level resolution to identify vertical transmission events via the maternal source. Combined with a metatranscriptomic approach, we show the potential not only to identify and track the fate of microbes in the early infant microbiome but also identify the metabolically active members. These approaches will ultimately provide important insights into the acquisition, development and community dynamics of the infant microbiome.
Transposable elements activity reveals punctuated patterns of speciation in mammals
Authors: Ricci Marco , Peona Valentina , Guichard Etienne , Taccioli Cristian , Boattini Alessio 
Published: October 2016

ABSTRACTTransposable elements (TEs) play an essential role in shaping eukaryotic genomes and generating variability. Our “Cold Genome” hypothesis postulates that speciation and TEs activity are strongly related in mammals. In order to test this hypothesis, we created two new parameters: the Density of Insertion (DI) and the Relative Rate of Speciation (RRS). The DI is the ratio between the number of TE insertions in a genome and its size, whereas the RRS is a conditional parameter designed to identify potential speciation bursts. Thus, by analyzing TEs insertions in mammals, we defined the genomes as “hot” (low DI) and “cold” (high DI). Then, comparing TEs activity among 16 intra-order pairs of mammalian species, 4 superorders of Eutheria and 29 taxonomical families of the whole Mammalia class, we showed that taxa with positive RRS correlate with “hot” genomes, whereas taxa with negative RRS correlate with “cold” genomes. In addition, our study supports the “Punctuated Equilibria” theory in mammals for both adaptive radiation and stasis.
The p150N domain of Chromatin Assembly Factor-1 regulates Ki-67 accumulation on the mitotic perichromosomal layer
Authors: Matheson Timothy D. , Kaufman Paul D. 
Published: October 2016

AbstractChromatin Assembly Factor 1 (CAF-1) deposits histones during DNA synthesis. The p150 subunit of human CAF-1 contains an N-terminal domain (p150N) that is dispensable for histone deposition but which promotes the localization of specific loci (Nucleolar-Associated Domains, or “NADs”) and proteins to the nucleolus during interphase. One of the p150N-regulated proteins is proliferation antigen Ki-67, whose depletion also decreases the nucleolar association of NADs. Ki-67 is also a fundamental component of the perichromosomal layer (PCL), a sheath of proteins surrounding condensed chromosomes during mitosis. We show here that a subset of p150 localizes to the PCL during mitosis, and that p150N is required for normal levels of Ki-67 accumulation on the PCL. This activity requires the Sumoylation Interacting Motif (SIM) within p150N, which is also required for the nucleolar localization of NADs and Ki-67 during interphase. In this manner, p150N coordinates both interphase and mitotic nuclear structures via Ki67.
Optimized functional annotation of ChIP-seq data
Authors: Khomtchouk Bohdan B. , Koehler William C. , Booven Derek J. Van , Wahlestedt Claes 
Published: October 2016

AbstractMotivationDifferent ChIP-seq peak callers often produce different output results from the same input. Since different peak callers are known to produce differentially enriched peaks with a large variance in peak length distribution and total peak count, accurately annotating peak lists with their nearest genes can be an arduous process. Functional genomic annotation of histone modification ChIP-seq data can be a particularly challenging task, as chromatin marks that have inherently broad peaks with a diffuse range of signal enrichment (e.g., H3K9me1, H3K27me3) differ significantly from narrow peaks that exhibit a compact and localized enrichment pattern (e.g., H3K4me3, H3K9ac). In addition, varying degrees of tissue-dependent broadness of an epigenetic mark can make it difficult to accurately and reliably link sequencing data to biological function. Thus, there exists an unmet need to develop a software program that can precisely tailor the computational analysis of a ChIP-seq dataset to the specific peak coordinates of the data and its surrounding genomic features.ResultsgeneXtendeRoptimizes the functional annotation of ChIP-seq peaks by exploring relative differences in annotating ChIP-seq peak sets to variable-length gene bodies. In contrast to prior techniques,geneXtendeRconsiders peak annotations beyond just the closest gene, allowing users to investigate peak summary statistics for the first-closest gene, second-closest gene, …,nth-closest gene whilst ranking the output according to biologically relevant events and iteratively comparing the fidelity of peak-to-gene overlap across a user-defined range of upstream and downstream extensions on the original boundaries of each gene’s coordinates. We testedgeneXtendeRon 547 human transcription factor ChIP-seq ENCODE datasets and 198 human histone modification ChIP-seq ENCODE datasets, providing the analysis results as case studies.AvailabilityThegeneXtendeRR/Bioconductor package (including detailed introductory vignettes) is available under the GPL-3 Open Source license and is freely available to download from Bioconductor at:https://bioconductor.org/packages/geneXtendeR/Author summarygeneXtendeRmakes functional annotation of ChIP-seq data more robust and precise, regardless of peak variability attributable to parameter tuning or peak caller algorithmic differences. Since different ChIP-seq peak callers produce differentially enriched peaks with large variance in peak length distribution and total peak count, annotating peak lists with their nearest genes can often be a noisy process where an adjacent second or third-closest gene may constitute a more viable biological candidate, e.g., during cases of linked genes that are located close to each other. As such, the goal ofgeneXtendeRis to robustly link differentially enriched peaks with their respective genes, thereby aiding experimental follow-up and validation in designing primers for a set of prospective gene candidates during qPCR.
The human functional genome defined by genetic diversity
Authors: Iulio Julia di , Bartha Istvan , Wong Emily H.M. , Yu Hung-Chun , Hicks Michael , Shah Naisha , Lavrenko Victor , Kirkness Ewen F. , Fabani Martin M. , Yang Dongchan , Jung Inkyung , Biggs William H. , Ren Bing , Venter J. Craig , Telenti Amalio 
Published: October 2016

ABSTRACTLarge scale efforts to sequence whole human genomes provide extensive data on the non-coding portion of the genome. We used variation information from 11,257 human genomes to describe the spectrum of sequence conservation in the population. We established the genome-wide variability for each nucleotide in the context of the surrounding sequence in order to identify departure from expectation at the population level (context-dependent conservation). We characterized the population diversity for functional elements in the genome and identified the coordination of conserved sequences of distal andcisenhancers, chromatin marks, promoters, coding and intronic regions. The most context-dependent conserved regions of the genome are associated with unique functional annotations and a genomic organization that spreads up to one megabase. Importantly, these regions are enriched by over 100-fold of non-coding pathogenic variants. This analysis of human genetic diversity thus provides a detailed view of sequence conservation, functional constraint and genomic organization of the human genome. Specifically, it identifies highly conserved non-coding sequences that are not captured by analysis of interspecies conservation and are greatly enriched in disease variants.
How to fold intricately: using theory and experiments to unravel the properties of knotted proteins
Authors: Jackson Sophie E. , Suma Antonio , Micheletti Cristian 
Published: October 2016

AbstractOver the years, advances in experimental and computational methods have helped us to understand the role of thermodynamic, kinetic and active (chaperone-aided) effects in coordinating the folding steps required to achieving a knotted native state. Here, we review such developments by paying particular attention to the complementarity of experimental and computational studies. Key open issues that could be tackled with either or both approaches are finally pointed out.
Probing the effect of uniaxial compression on cell migration
Authors: Srivastava Nishit , Kay Robert R , Kabla Alexandre J 
Published: October 2016

AbstractThe chemical, physical and mechanical properties of the extra-cellular environment have a strong effect on cell migration. Aspects such as pore-size or stiffness of the matrix influence the selection of the mechanism used by cells to propel themselves, including pseudopod or blebbing. How a cell perceives its environment, and how such a cue triggers a change in behaviour are largely unknown, but mechanics is likely to be involved. Because mechanical conditions are often controlled by modifying the composition of the environment, separating chemical and physical contributions is difficult and requires multiple controls. Here we propose a simple method to impose a mechanical compression on individual cells without altering the composition of the gel. Live imaging during compression provides accurate information about the cell’s morphology and migratory phenotype. UsingDictyosteliumas a model, we observe that a compression of the order of 500 Pa flattens the cells under gel by up to 50%. This uniaxial compression directly triggers a transition in the mode of migration, from primarily pseudopodial to bleb driven, in less than 30 sec. This novel device is therefore capable of influencing cell migration in real time and offers a convenient approach to systematically study mechanotransduction in confined environments.
Binary Relation Extraction from Biomedical Literature using Dependency Trees and SVMs
Authors: Sharma Anuj , Virvilis Vassilis , Lekka Tina , Andronis Christos 
Published: October 2016

AbstractThe goal of Biomedical relation extraction is to uncover high-quality relations from life science literature with diverse applications in the ﬁelds of Biology and Medicine. In the last decade, several methods can be found in published literature ranging from binary to complex relation extraction. In this work, we present a binary relation extraction system that relies on sentence level dependency features. We use a novel approach to map dependency tree based rules to feature vectors that can be used to train a classiﬁer. We build a SVM classiﬁer using these feature vectors and our experimental results show that it outperforms simple co-occurrence and rule-based systems. Through our experiments, using two ‘real-world’ examples, we quantify the positive impact of improved relation extraction on Literature Based Discovery.
Regulation of sleep plasticity by a thermo-sensitive circuit inDrosophila
Authors: Lamaze Angelique , Öztürk-Çolak Arzu , Fischer Robin , Peschel Nicolai , Koh Kyunghee , Jepson James E.C. 
Published: October 2016

AbstractSleep is a highly conserved and essential behaviour in many species, including the fruit fly Drosophila melanogaster. In the wild, sensory signalling encoding environmental information must be integrated with sleep drive to ensure that sleep is not initiated during detrimental conditions. However, the molecular and circuit mechanisms by which sleep timing is modulated by the environment are unclear. Here we introduce a novel behavioural paradigm to study this issue. We show that in male fruit flies, onset of the daytime siesta is delayed by ambient temperatures above 29°C. We term this effect Prolonged Morning Wakefulness (PMW). We show that signalling through the TrpA1 thermo-sensor is required for PMW, and that TrpA1 specifically impacts siesta onset, but not night sleep onset, in response to elevated temperatures. We identify two critical TrpA1-expressing circuits and show that both contact DN1p clock neurons, the output of which is also required for PMW. Finally, we identify the circadian blue-light photoreceptor CRYPTOCHROME as a molecular regulator of PMW. We propose a model in which the Drosophila nervous system integrates information encoding temperature, light, and time to dynamically control when sleep is initiated. Our results provide a platform to investigate how environmental inputs co-ordinately regulate sleep plasticity.
Reverse-engineering human olfactory perception from chemical features of odor molecules
Authors: Keller Andreas , Gerkin Richard C. , Guan Yuanfang , Dhurandhar Amit , Turu Gabor , Szalai Bence , Mainland Joel D. , Ihara Yusuke , Yu Chung Wen , Wolfinger Russ , Vens Celine , Schietgat Leander , De Grave Kurt , Norel Raquel ,   DREAM Olfaction Prediction Challenge Consortium, Stolovitzky Gustavo , Cecchi Guillermo , Vosshall Leslie B. , Meyer Pablo 
Published: October 2016

AbstractDespite 25 years of progress in understanding the molecular mechanisms of olfaction, it is still not possible to predict whether a given molecule will have a perceived odor, or what olfactory percept it will produce. To address this stimulus-percept problem for olfaction, we organized the crowd-sourced DREAM Olfaction Prediction Challenge. Working from a large olfactory psychophysical dataset, teams developed machine learning algorithms to predict sensory attributes of molecules based on their chemoinformatic features. The resulting models predicted odor intensity and pleasantness with high accuracy, and also successfully predicted eight semantic descriptors (“garlic”, “fish”, “sweet”, “fruit”, “burnt”, “spices”, “flower”, “sour”). Regularized linear models performed nearly as well as random-forest-based approaches, with a predictive accuracy that closely approaches a key theoretical limit. The models presented here make it possible to predict the perceptual qualities of virtually any molecule with an impressive degree of accuracy to reverse-engineer the smell of a molecule.One Sentence SummaryResults of a crowdsourcing competition show that it is possible to accurately predict and reverse-engineer the smell of a molecule.
CELL-TO-CELL MODELING OF THE INTERFACE BETWEEN ATRIAL AND SINOATRIAL ANISOTROPIC HETEROGENEOUS NETS
Authors: López Gabriel , Castellanos Norma P. , Godínez Rafael 
Published: October 2016

ABSTRACTThe transition between Sinoatrial cells and Atrial cells in the Heart is not fully undefirst ood. Here we focus in cell-to-cell mathematical models involving typical Sinoatrial cells and Atrial cells connected with experimentally observed conductance values exclusively. We are interested mainly in the geometry of the microstructure of the conduction paths in the Sinoatrial Node. We show with some models that appropriate source-sink relationships between Atrial and Sinoatrial cells may occur according to certain geometric arrangements.