bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dissecting dynamics and differences of selective pressures in the evolution of human pigmentation
Authors: Huang Xin , He Yungang , Wang Sijia , Jin Li 
Published: January 2018

AbstractHuman pigmentation is a highly diverse and complex trait among populations, and has drawn particular attention from both academic and non-academic investigators for thousands of years. Previous studies detected selection signals in several human pigmentation genes, but few studies have integrated contribution from multiple genes to the evolution of human pigmentation. Moreover, none has quantified selective pressures on human pigmentation over epochs and between populations. Here, we dissect dynamics and differences of selective pressures during different periods and between distinct populations with new approaches. We propose a new model with multiple populations to estimate historical selective pressures by summarizing selective pressures on multiple genes. We use genotype data of 19 genes associated with human pigmentation from 17 datasets, and obtain data for 2346 individuals of six representative population groups from worldwide. Our results quantify selective pressures on light pigmentation not only in modern Europeans (0.0249/generation) but also in proto-Eurasians (0.00665/generation). Our results also support several derived alleles associated with human dark pigmentation may under directional selection by quantifying differences of selective pressures between populations. Our study provides a first attempt to quantitatively investigate the dynamics of selective pressures during different time periods in the evolution of human pigmentation, and may facilitate studies of the evolution of other complex traits.Author SummaryThe color variation of human skin, hair, and eye is affected by multiple genes with different roles. This diversity may be shaped by natural selection and adapted for ultraviolet radiation in different environments around the world. As human populations migrated out from Africa, the ultraviolet radiation in the environment they encountered also changed. It is possible that the selective pressures on human pigmentation varied throughout human evolutionary history. In this study, we develop a new approach and estimate historical selective pressures on light pigmentation not only in modern Europeans but also in proto-Eurasians. To our best knowledge, this is the first study that quantifies selective pressures during different time periods in the evolution of human pigmentation. Besides, we provide statistical evidence to support several genes associated with human dark pigmentation may be favored by natural selection. Thus, natural selection may not only affect light pigmentation in Eurasians, but also influence dark pigmentation in Africans.
Parametric and Non-parametric Gradient Matching for Network Inference
Authors: Dony Leander , He Fei , Stumpf Michael PH 
Published: January 2018

AbstractReverse engineering of gene regulatory networks from time series gene-expression data is a challenging problem, not only because of the vast sets of candidate interactions but also due to the stochastic nature of gene expression. To avoid the computational cost of large-scale simulations, a two-step Gaussian process interpolation based gradient matching approach has been proposed to solve differential equations approximately. Based on this gradient matching approach, we evaluate the fits of parametric as well as non-parametric candidate models to the data under various settings for different inference objectives. We also use model averaging, based on the Bayesian Information Criterion (BIC), in order to combine the different inferences. We found that parametric methods can provide comparable, and often improved inference compared to non-parametric methods; the latter, however, require no kinetic information and are computationally more efficient.The code used in this work is available athttps://github.com/ld2113/Final-Project.
Genome-wide analysis of consistently RNA edited sites in human blood reveals interactions with mRNA processing genes and suggests correlations with cell types and biological variables
Authors: Giacopuzzi Edoardo , Gennarelli Massimo , Sacco Chiara , Filippini Alice , Mingardi Jessica , Magri Chiara , Barbon Alessandro 
Published: January 2018

AbstractBackgroundA-to-I RNA editing is a co-/post-transcriptional modification catalyzed by ADAR enzymes, that deaminates Adenosines (A) into Inosines (I). Most of known editing events are located within inverted ALU repeats, but they also occur in coding sequences and may alter the function of encoded proteins. RNA editing contributes to generate transcriptomic diversity and it is found altered in cancer, autoimmune and neurological disorders. Emerging evidences indicate that editing process could be influenced by genetic variations, biological and environmental variables.ResultsWe analyzed RNA editing levels in human blood using RNA-seq data from 459 healthy individuals and identified 2,079 sites consistently edited in this tissue. As expected, analysis of gene expression revealed thatADARis the major contributor to editing on these sites, explaining ∼13% of observed variability. After removingADAReffect, we found significant associations for 1,122 genes, mainly involved in RNA processing. These genes were significantly enriched in genes encoding proteins interacting with ADARs, including 276 potential ADARs interactors and 9 ADARs direct partners. In addition, our analysis revealed several factors potentially influencing RNA editing in blood, including cell composition, age, Body Mass Index, smoke and alcohol consumption. Finally, we identified genetic loci associated with editing levels, including knownADAReQTLs and a small region on chromosome 7, containingLOC730338,a lincRNA gene that appears to modulate ADARs mRNA expression.ConclusionsOur data provides a detailed picture of the most relevant RNA editing events and their variability in human blood, giving interesting insights on potential mechanisms behind this post-transcriptional modification and its regulation in this tissue.
Deciphering noise amplification and reduction in open chemical reaction networks
Authors: Pucci Fabrizio , Rooman Marianne 
Published: January 2018

AbstractThe impact of fluctuations on the dynamical behavior of complex biological systems is a longstanding issue, whose understanding would elucidate how evolutionary pressure tends to modulate intrinsic noise. Using the Itō stochastic differential equation formalism, we performed analytic and numerical analyses of model systems containing different molecular species in contact with the environment and interacting with each other through mass-action kinetics. For networks of zero deficiency, which admit a detailed- or complex-balanced steady state, all molecular species are uncorrelated and their Fano factors are Poissonian. Systems of higher deficiency have non-equilibrium steady states and non-zero reaction fluxes flowing between the complexes. When they model homooligomerization, the noise on each species is reduced when the flux flows from the oligomers of lowest to highest degree, and amplified otherwise. In the case of hetero-oligomerization systems, only the noise on the highest-degree species shows this behavior.
Triple Representation of Language, Working Memory, Social and Emotion Processing in the Cerebellum: Convergent Evidence from Task and Seed-Based Resting-State Fmri Analyses in a Single Large Cohort
Authors: Guell Xavier , Gabrieli John D.E. , Schmahmann Jeremy D. 
Published: January 2018

ABSTRACTDelineation of functional topography is critical to the evolving understanding of the cerebellum’s role in a wide range of nervous system functions. We used data from the Human Connectome Project (n=787) to analyze cerebellar fMRI task activation (motor, working memory, language, social and emotion processing) and resting-state functional connectivity calculated from cerebral cortical seeds corresponding to the peak Cohen’s d of each task contrast. The combination of exceptional statistical power, activation from both motor and multiple non-motor tasks in the same participants, and convergent resting-state networks in the same participants revealed novel aspects of the functional topography of the human cerebellum. Consistent with prior studies there were two distinct representations of motor activation. Newly revealed were three distinct representations each for working memory, language, social, and emotional task processing that were largely separate for these four cognitive and affective domains. In most cases, the task-based activations and the corresponding resting-network correlations were congruent in identifying the two motor representations and the three non-motor representations that were unique to working memory, language, social cognition, and emotion. The definitive localization and characterization of distinct triple representations for cognition and emotion task processing in the cerebellum opens up new basic science questions as to why there are triple representations (what different functions are enabled by the different representations?) and new clinical questions (what are the differing consequences of lesions to the different representations?).HIGHLIGHTS-We analyzed motor and multiple nonmotor task fMRI activations in the cerebellum.-Resting-state seeds were placed at each task activation peak in the cerebral cortex.-We describe cerebellar task topography in the largest single cohort studied to date.-Nonmotor cerebellar task activation revealed a pattern of triple representation.-Resting-state analysis revealed an overlapping pattern of triple representation.
The yeast GRASP Grh1 displays a high polypeptide backbone mobility along with an amyloidogenic behavior
Authors: Fontana N. A. , Fonseca-Maldonado R. , Mendes L.F.S , Meleiro L. P. , Costa-Filho A. J. 
Published: January 2018

AbstractGRASPs are proteins involved in cell processes that seem paradoxical, such as being responsible for shaping the Golgi cisternae and also involved in unconventional secretion mechanisms that bypass the Golgi, among other functions in the cell. Despite its involvement in several relevant cell processes, there is still a considerable lack of studies on full-length GRASPs. Our group has previously reported an unexpected behavior of the full-length GRASP from the fungus C. neoformans: its intrinsically-disordered characteristic. Here, we generalize this finding by showing that is also observed in the GRASP from the yeast S. cerevisae (Grh1), which strongly suggests it may be a general property within the GRASP family. Furthermore, Grh1 is also able to form amyloid fibrils either upon heating or when submitted to changes in the dielectric constant of its surroundings, a condition that is experienced by the protein when in close contact with membranes of cell compartments, such as the Golgi apparatus. Intrinsic disorder and amyloid fibril formation can thus be two structural properties exploited by GRASP during its functional cycle.
Whole genome sequence of an edible and potential medicinal fungus, Cordyceps guangdongensis
Authors: Zhang Chenghua , Deng Wangqiu , Yan Wenjuan , Li Taihui 
Published: January 2018

ABSTRACTCordyceps guangdongensis is an edible fungus which has been approved as a Novel Food by the Chinese Ministry of Public Health in 2013. It also has a broad application prospect in pharmaceutical industries with many medicinal activities. In this study, the whole genome of C. guangdongensis GD15, a single spore isolate from a wild strain, was sequenced and assembled with Illumina and PacBio sequencing technology. The generated genome is 29.05 Mb in size, comprising 9 scaffolds with an average GC content of 57.01%. It is predicted to contain a total of 9150 protein-coding genes. Sequence identification and comparative analysis indicated that the assembled scaffolds contained two complete chromosomes and four single-end chromosomes, showing a high level assembly. Gene annotation revealed a diversity of transporters that could contribute to the genome size and evolution. Besides, approximately 15.49% and 13.70% genes involved in metabolic processes were annotated by KEGG and COG respectively. Genes belonging to CAZymes accounted for a proportion of 2.84% of the total genes. In addition, 435 transcription factors (TFs) were identified, which were involved in various biological processes. Among the identified TFs, the fungal transcription regulatory proteins (18.39%) and fungal-specific TFs (19.77%) represented the two largest classes of TFs. These data provided a much needed genomic resource for studying C. guangdongensis, laying a solid foundation for further genetic and biological studies, especially for elucidating the genome evolution and exploring the regulatory mechanism of fruiting body development.
DeepNeuron: An Open Deep Learning Toolbox for Neuron Tracing
Authors: Zhou Zhi , Kuo Hsien-Chi , Peng Hanchuan , Long Fuhui 
Published: January 2018

AbstractReconstructing three-dimensional (3D) morphology of neurons is essential to understanding brain structures and functions. Over the past decades, a number of neuron tracing tools including manual, semi-automatic, and fully automatic approaches have been developed to extract and analyze 3D neuronal structures. Nevertheless, most of them were developed based on coding certain rules to extract and connect structural components of a neuron, showing limited performance on complicated neuron morphology. Recently, deep learning outperforms many other machine learning methods in a wide range of image analysis and computer vision tasks. Here we developed a new open source toolbox, DeepNeuron, which uses deep learning networks to learn features and rules from data and trace neuron morphology in light microscopy images. DeepNeuron provides a family of modules to solve basic yet challenging problems in neuron tracing. These problems include but not limited to: (1) detecting neuron signal under different image conditions, (2) connecting neuronal signals into tree(s), (3) pruning and refining tree morphology, (4) quantifying the quality of morphology, and (5) classifying dendrites and axons in real time. We have tested DeepNeuron using light microscopy images including bright-field and confocal images of human and mouse brain, on which DeepNeuron demonstrates robustness and accuracy in neuron tracing.
Antagonism between the dynein and Ndc80 complexes at kinetochores controls the stability of kinetochore-microtubule attachments during mitosis
Authors: Amin Mohammed A. , McKenney Richard J. , Varma Dileep 
Published: January 2018

AbstractChromosome alignment and segregation during mitosis depends critically on kinetochoremicrotubule (kMT) attachments that are mediated by the function of the molecular motor cytoplasmic dynein, and the kinetochore microtubule (MT) binding complex, Ndc80. The RZZ (Rod-ZW10-Zwilch) complex is central to this coordination as it has an important role in dynein recruitment and has recently been reported to have a key function in the regulation of stable kMT attachment formation in C. elegans. However, the mechanism by which kMT attachments are controlled by the coordinated function of these protein complexes to drive chromosome motility during early mitosis is still unclear. In this manuscript, we provide evidence to show that Ndc80 and dynein directly antagonize each other’s MT-binding. We also find that severe chromosome alignment defects induced by depletion of dynein, or the dynein adapter spindly, are rescued by codepletion of the RZZ component, Rod, in human cells. Interestingly, the rescue of chromosome alignments defects was independent of Rod function in activation of the spindle assembly checkpoint and was accompanied by a remarkable restoration of stable kMT attachments. Furthermore, rescue of chromosome alignment was critically dependent on the plus-end-directed motility of CENP-E, as cells codepleted of CENP-E along with Rod and dynein were unable to establish stable kMT attachments or align their chromosomes properly. Taken together, our findings support the idea that the dynein motor may control the function of the Ndc80 complex in stabilizing kMT attachments either directly by interfering with Ndc80-MT binding, and/or indirectly by modulating the Rod-mediated inhibition of Ndc80.
Comprehensive characterization of transcript diversity at the humanNODALlocus
Authors: Findlay Scott D , Postovit Lynne-Marie 
Published: January 2018

AbstractNODAL, a morphogen belonging to the transforming growth factor beta (TGβ) superfamily, is essential during embryogenesis where it induces axis formation and left-right asymmetry.NODALis also required for the maintenance of human embryonic stem cell pluripotency, and emerges in many cancer types concomitant with metastasis and therapy resistance. Several enhancer elements have been shown to regulate mouseNodalexpression and studies have delineated mechanisms by which mRNA splicing and translation of NODAL homologues are regulated in model organisms. However, little is known regarding the co-transcriptional and post-transcriptional processing of human NODAL. Herein, we describe hitherto unreported RNAs which are transcribed from theNODALlocus, including an antisense transcript, a circular transcript, and multiple splice variants. These transcripts demonstrate the complexity ofNODALexpression and highlight the need to consider each NODAL variant when attempting to quantify or target this morphogen.
Attracting Chinese FDI in Africa
Authors: Shan Shan , Lin Zhibin , Li Yulei , Zeng Yan 
Published: January 2018

PurposeThe purpose of this paper is to examine the effect of natural resources, market size and five major institutional factors (voice and accountability; political stability and absence of violence; regulatory quality; rule of law and control of corruption) on Chinese foreign direct investment (FDI) in Africa.Design/methodology/approachThis study uses regression analysis on panel data across 22 countries for the period 2008-2014.FindingsNatural resources did not play a significant role in attracting Chinese investments, but market size did. Among the institutional factors, only voice and accountability had a significant and positive effect on attracting Chinese FDI; the effects of rule of law and control of corruption were not significant and political stability and regulatory quality had a significant and negative effect.Research limitations/implicationsChinese investment in Africa is only a recent phenomenon, and is growing rapidly; further studies should examine factors that are unique to the context such as bilateral political link.Practical implicationsAfrican countries that are struggling with improving their poor institutional quality in the short term could effectively attract Chinese investment by reducing investor psychic distance, e.g. establishing a closer political link with China. Nevertheless, in the long term, measures of improving institutional quality are important.Originality/valueThis study reveals for the first time that what attracts Chinese investment is market size rather than natural resources, and different institutional factors of an African country show varying effects on attracting Chinese FDI.
New time-based model to identify the influential users in online social networks
Authors: Mahmoudi Amin , Yaakub Mohd Ridzwan , Abu Bakar Azuraliza 
Published: January 2018

Purpose
Users are the key players in an online social network (OSN), so the behavior of the OSN is strongly related to their behavior. User weight refers to the influence of the users on the OSN. The purpose of this paper is to propose a method to identify the user weight based on a new metric for defining the time intervals.

Design/methodology/approach
The behavior of an OSN changes over time, thus the user weight in the OSN is different in each time frame. Therefore, a good metric for estimating the user weight in an OSN depends on the accuracy of the metric used to define the time interval. New metric for defining the time intervals is based on the standard deviation and identifies that the user weight is based on a simple exponential smoothing model.

Findings
The results show that the proposed method covers the maximum behavioral changes of the OSN and is able to identify the influential users in the OSN more accurately than existing methods.

Research limitations/implications
In event detection, when a terrorist attack occurs as an event, knowing the influential users help us to know the leader of the attack. Knowing the influential user in each time interval based on this study can help us to detect communities which formed around these people. Finally, in marketing, this issue helps us to have a targeted advertising.

Practical implications
User effect is a significant issue in many OSN domain problems, such as community detection, event detection and recommender systems.

Originality/value
Previous studies do not give priority to the recent time intervals in identifying the relative importance of users. Thus, defining a metric to compute a time interval that covers the maximum changes in the network is a major shortcoming of earlier studies. Some experiments were conducted on six different data sets to test the performance of the proposed model in terms of the computed time intervals and user weights.
Firefighters as first incident persons
Authors: Svensson Anders , Österberg Sofia Almerud , Fridlund Bengt , Stening Kent , Elmqvist Carina 
Published: January 2018

PurposeIn order to shorten the response time, two part-time fire departments (FDs) in Sweden initialize a first incident person (FIP) assignment. This is done by alarming the crew manager as an FIP, responding in a separate emergency vehicle, and by arriving at the scene before rest of the crew. The purpose of this paper is to explore and describe experiences of the FIP assignment within an FD.Design/methodology/approachA multimethod design was used, influenced by Creswell and Plano Clark’s (2011) explanatory sequential mixed method design including emergency reports, a questionnaire and interviews.FindingsThe results show that the FIP assignment was a function that secured an early presence at the scene of an accident or emergency situations, which is beneficial for society in the form of a safety factor, for the firefighters in the form of early prior information on what to expect at the scene and for the patient in the form of early existential support and increased chances of survival.Originality/valueIn order to prevent full scenarios to happen and get the chance to save lives, an early response must be ensured. Hence, studies must be made in different settings, based on its unique conditions. This study indicates that by implementing FIP in FDs placed in a rural area, the FIP can break the chain of events and becoming a new link in the chain of survival.