bluuebunny/crossref_metadata_2025_split huggingface dataset:
spectrum_utils: A Python package for mass spectrometry data processing and visualization
Authors: Bittremieux Wout 
Published: August 2019

AbstractGiven the wide diversity in applications of biological mass spectrometry, custom data analyses are often needed to fully interpret the results of an experiment. Such bioinformatics scripts necessarily include similar basic functionality to read mass spectral data from standard file formats, process it, and visualize it. Rather than having to reimplement this functionality, to facilitate this task,spectrum_utilsis a Python package for mass spectrometry data processing and visualization. Its high-level functionality enables developers to quickly prototype ideas for computational mass spectrometry projects in only a few lines of code. Notably, the data processing functionality is highly optimized for computational efficiency to be able to deal with the large volumes of data that are generated during mass spectrometry experiments. The visualization functionality makes it possible to easily produce publication-quality figures as well as interactive spectrum plots for inclusion on web pages.spectrum_utilsis available for Python 3.6+, includes extensive online documentation and examples, and can be easily installed using conda. It is freely available as open source under the Apache 2.0 license athttps://github.com/bittremieux/spectrum_utils.
TVA-based modeling of short-term memory capacity, speed of processing and perceptual threshold in chronic stroke patients: Case-control differences, reliability, and sensitivity to cognitive training
Authors: Richard Geneviève , Petersen Anders , Ulrichsen Kristine M. , Kolskår Knut , Alnæs Dag , Sanders Anne-Marthe , Dørum Erlend S. , Ihle-Hansen Hege , Nordvik Jan Egil , Westlye Lars T. 
Published: August 2019

AbstractAttentional deficits following stroke are common and pervasive, and are important predictors for functional recovery. Attentional functions comprise a set of specific cognitive processes allowing to attend, filter and select among a continuous stream of stimuli. These mechanisms are fundamental for more complex cognitive functions such as learning, planning and cognitive control, all crucial for daily functioning, including social interactions. The distributed functional neuroanatomy of these processes is a likely explanation for the high prevalence of attentional impairments following stroke, and underscores the importance of a clinical implementation of computational approaches allowing for sensitive and specific modeling of attentional sub-processes. The Theory of Visual Attention (TVA) offers a theoretical, computational, neuronal and practical framework to assess the efficiency of visual selection performance and parallel processing of multiple objects. Here, using a whole-report experimental paradigm in a cross-sectional case-control comparison and in six repeated assessments over the course of a three-week intensive computerized cognitive training (CCT) intervention in chronic stroke patients (> 6 months since hospital admission, NIHSS < 7 at hospital discharge), we assessed the sensitivity and reliability of TVA parameters reflecting short-term memory capacity (K), processing speed (C) and perceptual threshold (t0). Cross-sectional group comparisons documented lower short-term memory capacity, slower processing speed and higher perceptual threshold in patients compared to age-matched healthy controls. Further, longitudinal analyses revealed high reliability of the TVA parameters in stroke patients, and higher processing speed at baseline was associated with larger cognitive benefits of the CCT. The results support the feasibility, reliability and sensitivity of TVA-based assessment of attentional functions in chronic stroke patients.
The evolution of paternal care: a role for microbes?
Authors: Gurevich Yael , Lewin-Epstein Ohad , Hadany Lilach 
Published: August 2019

AbstractPaternal care is an evolutionary mystery. Despite extensive research, both theoretical and experimental, the reasons for its ubiquity remain unclear. Common explanations include kin selection and limited accuracy in parentage assessment. However, these explanations do not cover the breadth of circumstances in which paternal care has been observed, particularly in cases of uncertain paternity. Here we propose that microbes may play a key role in the evolution of paternal care among their hosts. Using computational models, we demonstrate that microbes associated with increased paternal care could be favoured by natural selection. We find that microbe-induced paternal care could evolve under wider conditions than suggested by genetic models. Moreover, we show that microbe-induced paternal care is more likely to evolve when considering paternal care interactions that increase microbial transmission, such as feeding and grooming. Our results imply that factors affecting the composition of host microbiome may also alter paternal behaviour.
Genome-wide analysis of polymorphisms identified domestication-associated polymorphism desert carrying important rice grain size/weight QTL
Authors: Kumar Angad , Daware Anurag , Kumar Arvind , Kumar Vinay , Krishnan S Gopala , Mondal Subhasish , Patra Bhaskar Chandra , Singh Ashok. K. , Tyagi Akhilesh K. , Parida Swarup K. , Thakur Jitendra K. 
Published: August 2019

AbstractRice grain size and weight are major determinant of grain quality and yield and so have been under rigorous selection since domestication. However, genetic basis for contrasting grain size/weight trait among indian germplasm, and their association with domestication shaped evolutionary region is not studied before. To identify genetic basis of grain size/weight two long (LGG) and two short grain genotypes (SGG) were resequenced. LGG (LGR and Pusa Basmati 1121) differentiated from SGG (Sonasal and Bindli) by 504439 SNPs and 78166 InDels. TheLRKgene cluster was significantly affected and a truncation mutation in the LRK8 kinase domain was uniquely associated with LGG. Phylogeny with 3000 diverse rice accessions revealed four sequenced genotypes belonged tojaponicagroup and were at the edge of clades indicating source of genetic diversity available in Asian rice population. Five SNPs significantly were associated with grain size/weight and top three SNPs were validated in RIL mapping populations, suggesting this study as a valuable resource for high-throughput genotyping. A contiguous ∼6 Mb polymorphism desert region carrying a major grain weight QTL was identified on chromosome 5 in four sequenced genotypes. Further, among 3000, this region was identified as evolutionary important site with significant positive selection, elevated LD, and multiple selection sweeps, stabilising many domestication-related traits including grain size/weight. Theausgroup genotype retained more allelic variations in the desert region thanjaponicaandindica, and likely to be one of the differentiation point forausgroup. We suggest this desert region as an important evolutionary node that can be selected in breeding programs for improvement of grain yield and quality. All data and analysis can be accessed from RiceSzWtBase database.Significance statementBeing an important trait, rice grain size/weight has been under rigorous selection since domestication. However, a link between this trait and domestication is not so directly established. In addition to characterization of novel grain size/weight-associated SNPs, in this study, ∼ 6 Mb polymorphism desert region harboring major grain weight QTL was identified on chromosome 5, which turned out to be an evolutionary important site with multiple selection sweeps and introgression events, significantly correlated with domestication-related traits.
Overtone focusing in biphonic Tuvan throat singing
Authors: Bergevin Christopher , Narayan Chandan , Williams Joy , Mhatre Natasha , Steeves Jennifer , Story Brad 
Published: August 2019

AbstractKhoomei is a unique singing style originating from the Central Asian republic of Tuva. Singers produce two pitches simultaneously: a booming low-frequency rumble alongside a hovering high-pitched whistle-like tone. The biomechanics of this biphonation are not well-understood. Here, we use sound analysis, dynamic magnetic resonance imaging, and vocal tract modeling to demonstrate how biphonation is achieved by modulating vocal tract morphology. Tuvan singers show remarkable control in shaping their vocal tract to narrowly focus the harmonics (or overtones) emanating from their vocal cords. The biphonic sound is a combination of the fundamental pitch and a focused filter state, which is at the higher pitch (1-2 kHz) and formed by merging two formants, thereby greatly enhancing sound-production in a very narrow frequency range. Most importantly, we demonstrate that this biphonation is a phenomenon arising from linear filtering rather than a nonlinear source.
Widespread arginine phosphorylation in human cells - a novel protein PTM revealed by mass spectrometry
Authors: Fu Songsen , Fu Chuan , Zhou Quan , Lin Rongcan , Ouyang Han , Wang Minning , Sun Ying , Liu Yan , Zhao Yufen 
Published: August 2019

ABSTRACTArginine phosphorylation (pArg) is recently discovered as a ubiquitous protein N- phosphorylation in bacteria. However, its prevalence and roles in mammalian cells remain largely unknown due to the lack of established workflow and the inherent lability of the phosphoramidate (P-N) bond. Emerging evidence suggests that N-phosphorylation may extensively exist in eukaryotes and play crucial roles. We report an experimental phosphoproteomic workflow, which for the first time allowed to reveal the widespread occurrence of pArg in human cells by mass spectrometry. By virtue of this approach, we identified 152 high-confidence pArg sit]es derived from 118 proteins. Remarkably, the discovered phosphorylation motif and gene ontology of pArg hint a possible cellular function of arginine phosphorylation by regulating the favorability of propeptide convertase substrate. The generated extensive data set should enable a better understanding of the biological functions of eukaryotic pArg in the future.Abstract Figure
A widely distributed metalloenzyme class enables gut microbial metabolism of host- and diet-derived catechols
Authors: Rekdal Vayu Maini , Bernardino Paola Nol , Luescher Michael U. , Kiamehr Sina , Turnbaugh Peter J. , Bess Elizabeth N. , Balskus Emily P. 
Published: August 2019

AbstractCatechol dehydroxylation is a central chemical transformation in the gut microbial metabolism of plant- and host-derived small molecules. However, the molecular basis for this transformation and its distribution among gut microorganisms are poorly understood. Here, we characterize a molybdenum-dependent enzyme from the prevalent human gut bacteriumEggerthella lentathat specifically dehydroxylates catecholamine neurotransmitters available in the human gut. Our findings suggest that this activity enablesE. lentato use dopamine as an electron acceptor under anaerobic conditions. In addition to characterizing catecholamine dehydroxylation, we identify candidate molybdenum-dependent enzymes that dehydroxylate additional host-and plant-derived small molecules. These gut bacterial catechol dehydroxylases are specific in their substrate scope and transcriptional regulation and belong to a distinct group of largely uncharacterized molybdenum-dependent enzymes that likely mediate both primary and secondary metabolism in multiple environments. Finally, we observe catechol dehydroxylation in the gut microbiotas of diverse mammals, suggesting that this chemistry is present in habitats beyond the human gut. Altogether, our data reveal the molecular basis of catechol dehydroxylation among gut bacteria and suggest that the chemical strategies that mediate metabolism and interactions in the human gut are relevant to a broad range of species and habitats.
The Integrator complex terminates promoter-proximal transcription at protein-coding genes
Authors: Elrod Nathan D. , Henriques Telmo , Huang Kai-Lieh , Tatomer Deirdre C. , Wilusz Jeremy E. , Wagner Eric J. , Adelman Karen 
Published: August 2019

SUMMARYThe transition of RNA polymerase II (Pol II) from initiation to productive elongation is a central, regulated step in metazoan gene expression. At many genes, Pol II pauses stably in early elongation, remaining engaged with the 25-60 nucleotide-long nascent RNA for many minutes while awaiting signals for release into the gene body. However, a number of genes display highly unstable promoter Pol II, suggesting that paused polymerase might dissociate from template DNA at these promoters and release a short, non-productive mRNA. Here, we report that paused Pol II can be actively destabilized by the Integrator complex. Specifically, Integrator utilizes its RNA endonuclease activity to cleave nascent RNA and drive termination of paused Pol II. These findings uncover a previously unappreciated mechanism of metazoan gene repression, akin to bacterial transcription attenuation, wherein promoter-proximal Pol II is prevented from entering productive elongation through factor-regulated termination.HighlightsThe Integrator complex inhibits transcription elongation at ∼15% of mRNA genesIntegrator targets promoter-proximally paused Pol II for terminationThe RNA endonuclease of Integrator subunit 11 is critical for gene attenuationIntegrator-repressed genes are enriched in signaling and growth-responsive pathways
Seroprevalence and parasite rates ofPlasmodium malariaein a high malaria transmission setting of southern Nigeria
Authors: Oriero Eniyou C. , Olukosi Adeola Y. , Oduwole Olabisi A. , Djimde Abdoulaye , D’Alessandro Umberto , Meremikwu Martin M. , Amambua-Ngwa Alfred 
Published: August 2019

AbstractWhilePlasmodium falciparumcontinues to be the main target for malaria elimination, otherPlasmodiumspecies persist in Africa. Their clinical diagnosis is uncommon while rapid diagnostic tests (RDTs), the most widely used malaria diagnostic tool, are only able to distinguish betweenP. falciparumand non-falciparum species, the latter as ‘pan-species’. Blood samples, both from clinical cases and communites, were collected in southern Nigeria (Lagos and Calabar) in 2017 (October-December) and 2018 (October–November), and analysed by several methods, namely microscopy, quantitative real-time PCR (qPCR), and peptide serology targeting candidate antigens (PmAMA1, PmLDH and PmCSP). The sensitivity of the diagnostic approaches for the dominantP. falciparumwere comparable, detecting approx. 80% infection, but not so for non-falciparum species – 3% and 10% infection forP. malariae; 0% and 3% infection forP. ovaleby microscopy and qPCR respectively, across communities.P. ovaleprevalence was less than 5%. Infection rates forP. malariaevaried between age groups, with the highest rates in individuals > 5 years.P. malariaespecific seroprevalence rates fluctuated in those < 10 years but generally reached the peak around 20 years of age for all peptides. The heterogeneity and rates of these non-falciparum species calls for increased specific diagnosis and targeting by elimination strategies.
SNAPPy: a snakemake pipeline for scalable HIV-1 subtyping by phylogenetic pairing
Authors: Araújo Pedro M.M. , Martins Joana S. , Osório Nuno S. 
Published: August 2019

AbstractHuman immunodeficiency virus 1 (HIV-1) genome sequencing is routinely done for drug resistance monitoring in hospitals worldwide. Subtyping these extensive datasets of HIV-1 sequences is a critical first step in molecular epidemiology and surveillance studies. The clinical relevance of HIV-1 subtypes is increasingly recognized. Several studies suggest subtype-related differences in disease progression, transmission route efficiency, immune evasion, and even therapeutic outcomes. HIV-1 subtyping is mainly done using web servers. These tools have limitations in scalability and potential noncompliance with data protection legislation. Thus, the aim of this work was to develop an efficient method for local and high-throughput HIV-1 subtyping. We designed SNAPPy: a snakemake pipeline for scalable HIV-1 subtyping by phylogenetic pairing. It contains several tasks of phylogenetic inference and BLAST queries, which can be executed sequentially or in parallel, taking advantage of multiple-core processing units. Although it was built for subtyping, SNAPPy is also useful to perform extensive HIV-1 alignments. This tool facilitates large-scale sequence-based HIV-1 research by providing a local, resource efficient and scalable alternative for HIV-1 subtyping. It is capable of analysing full-length genomes or partial HIV-1 genomic regions (GAG, POL, ENV) and recognizes more than 90 circulating recombinant forms. SNAPPy is freely available at:https://github.com/PMMAraujo/snappy.
Axon-like protrusions promote small cell lung cancer migration and metastasis
Authors: Yang Dian , Qu Fangfei , Cai Hongchen , Chuang Chen-Hua , Lim Jing Shan , Jahchan Nadine , Grüner Barbara M. , Kong Christina , Oudin Madeleine J. , Winslow Monte M. , Sage Julien 
Published: August 2019

SUMMARYMetastasis is the main cause of death in cancer patients but remains a poorly understood process. Small cell lung cancer (SCLC) is one of the most lethal and most metastatic types of human cancer. SCLC cells normally express neuroendocrine and neuronal gene programs but accumulating evidence indicates that these cancer cells become relatively more neuronal and less neuroendocrine as they gain the ability to metastasize. Here we show that mouse and human SCLC cells in culture andin vivocan grow cellular protrusions that resemble axons. The formation of these protrusions is controlled by multiple neuronal factors implicated in axonogenesis, axon guidance, and neuroblast migration. Disruption of these axon-like protrusions impairs cell migration in culture and inhibits metastatic abilityin vivo. The co-option of developmental neuronal programs is a novel molecular and cellular mechanism that contributes to the high metastatic ability of SCLC.
Bayesian inference of reassortment networks reveals fitness benefits of reassortment in human influenza viruses
Authors: Müller Nicola F. , Stolz Ugnė , Dudas Gytis , Stadler Tanja , Vaughan Timothy G. 
Published: August 2019

AbstractReassortment is an important source of genetic diversity in segmented viruses and is the main source of novel pathogenic influenza viruses. Despite this, studying the reassortment process has been constrained by the lack of a coherent, model-based inference framework. We here introduce a novel coalescent based model that allows us to explicitly model the joint coalescent and reassortment process. In order to perform inference under this model, we present an efficient Markov chain Monte Carlo algorithm to sample rooted networks and the embedding of phylogenetic trees within networks. Together, these provide the means to jointly infer coalescent and reassortment rates with the reassortment network and the embedding of segments in that network from full genome sequence data. Studying reassortment patterns of different human influenza datasets, we find large differences in reassortment rates across different human influenza viruses. Additionally, we find that reassortment events predominantly occur on selectively fitter parts of reassortment networks showing that on a population level, reassortment positively contributes to the fitness of human influenza viruses.
Altered visual population receptive fields in human albinism
Authors: Alvarez Ivan , Smittenaar Rebecca , Handley Sian E. , Liasis Alki , Sereno Martin I. , Schwarzkopf D. Samuel , Clark Chris A. 
Published: August 2019

1AbstractAlbinism is a congenital disorder where misrouting of the optic nerves at the chiasm gives rise to abnormal visual field representations in occipital cortex. In typical human development, the left occipital cortex receives retinal input predominantly from the right visual field, and vice-versa. In albinism, there is a more complete decussation of optic nerve fibers at the chiasm, resulting in partial representation of the temporal hemiretina (ipsilateral visual field) in the contralateral hemisphere. In this study, we characterize the receptive field properties for these abnormal representations by conducting detailed fMRI population receptive field mapping in a rare subset of participants with albinism and no ocular nystagmus. We find a nasal bias for receptive field positions in the abnormal temporal hemiretina representation. In addition, by modelling responses to bilateral visual field stimulation in the overlap zone, we found evidence in favor of discrete unilateral receptive fields, suggesting a conservative pattern of spatial selectivity in the presence of abnormal retinal input.HighlightsWe characterized population receptive fields in albinotic participants with no ocular nystagmusConfirmed overlapping representations of left and right visual fields in cortexDetected nasal bias in receptive field location for temporal hemiretina representationEvidence in favor of discrete unilateral receptive fields and against double coding
Biological Pathways and Gene Networks Link Inflammation and Vascular Remodeling to Both Heart Failure with Preserved and Reduced Ejection Fraction in Women across Ethnicities
Authors: Liu Qing , Chan Kei Hang K. , Morrison Alan R. , McGarvey Stephen T. , Luo Xi , Wilson James G. , Correa Adolfo , Reiner Alexander P. , Li Jie , Liu Simin , Wu Wen-Chih 
Published: August 2019

AbstractIntroductionHeart failure (HF) is understudied among women; especially, genomic evidence implicating shared or unique mechanisms of HF with respect to reduced or preserved ejection fraction (HFrEF, HFpEF) is lacking across ethnic populations of women. Prior genome-wide association studies (GWAS) have identified approximately 30 suggestive genetic variants for HF, although none have been specifically linked to HFrEF or HFpEF.ObjectivesWe aimed to define, replicate, and annotate genetic variants to HFrEF, HFpEF, or both, as well as to investigate potential biological mechanisms underlying HFrEF and HFpEF among African American (AA) and European American (EA) women in three well-characterized, high-quality prospective cohorts, the Women’s Health Initiative (WHI) study, the Jackson Heart Study (JHS), and the Framingham Heart Study (FHS).MethodsGWAS analysis on HFrEF and HFpEF were first performed among 7,982 AA and 4,133 EA in the WHI, followed by pathway analysis employing two independent methodological platforms (GSA-SNP and Mergeomics) curating KEGG, Reactome, and BioCarta pathway databases. GWAS signals and biological pathways identified using the WHI were replicated in the JHS and FHS. For all replicated pathways, we performed cross-phenotype and cross-ethnicity validation analyses to examine shared pathways between HFrEF and HFpEF, and phenotype-specific pathways, across ethnicities. We further prioritized key driver genes for HF according to specific pathways identified.ResultsWe validated one previously reported genetic locus and identified six new ones, among which one locus was allocated to HFrEF and five to HFpEF. Additionally, we defined five biological pathways shared between HFrEF and HFpEF and discovered six HFpEF-specific pathways. These pathways overlapped in two main domains for molecular signaling: 1) inflammation and 2) vascular remodeling (including angiogenesis and vascular patterning), involving key driver genes from collagen and HLA gene families.ConclusionsOur network analysis of three large prospective cohorts of women in the United States defined several novel loci for HF and its subtypes. In particular, several key driver genes reinforce the mechanistic role of inflammation and vascular remodeling in the development of HF, especially HFpEF. Given that therapeutic strategies developed for left ventricular dysfunction have had limited success for HFpEF, several new targets and pathways identified and validated in this study should be further assessed in risk stratification as well as the design of potential new HF interventions.