bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evolutionary features of a prolific subtype of avian influenza A virus in European waterfowl
Authors: Wille Michelle , Tolf Conny , Latorre-Margalef Neus , Fouchier Ron A. M. , Halpin Rebecca A. , Wentworth David E. , Ragwani Jayna , Pybus Oliver G. , Olsen Björn , Waldenström Jonas 
Published: November 2021

AbstractAvian influenza A virus (AIV) is ubiquitous in waterfowl, and detected annually at high prevalence in waterfowl during the Northern Hemipshere autumn. Some AIV subtypes are globally common in waterfowl, such as H3N8, H4N6, and H6N2, and are detected in the same populations at high frequency, annually. In order to investigate genetic features associated to the long-term maintenance of common subtypes in migratory ducks, we sequenced 248 H4 viruses isolated across 8 years (2002-2009) from Mallards (Anas platyrhynchos) sampled in southeast Sweden. Phylogenetic analyses showed that both H4 and N6 sequences fell into in three distinct lineages, structured by year of isolation. Specifically, across the eight years of the study, we observed lineage replacement, whereby a different HA lineage circulated in the population each year. Analysis of deduced amino acid sequences of the HA lineages illustrated key differences in regions of the globular head of hemagglutinin that overlap with established antigentic sites in homologous hemagglutinin H3, suggesting the possibility of antigenic differences among these HA lineages. Beyond HA, lineage replacement was common to all segments, such that novel genome constellations were detected across years. A dominant genome constellation would rapidly amplify in the duck population, followed by unlinking of gene segments as a result of reassortment within 2-3 weeks following introduction. These data help reveal the evolutionary dynamics exhibited by AIV on both annual and decadal scales in an important reservoir host.
A Scalable and Modular Automated Pipeline for Stitching of Large Electron Microscopy Datasets
Authors: Mahalingam Gayathri , Torres Russel , Kapner Daniel , Trautman Eric T. , Fliss Tim , Seshamani Sharmishtaa , Perlman Eric , Young Rob , Kinn Samuel , Buchanan JoAnn , Takeno Marc , Yin Wenjing , Bumbarger Daniel , Gwinn Ryder P. , Nyhus Julie , Lein Ed , Smith Stephen , Reid Clay , Khairy Khaled , Saalfeld Stephan , Collman Forrest , Macarico da Costa Nuno 
Published: November 2021

AbstractSerial-section electron microscopy (ssEM) is the method of choice for studying macroscopic biological samples at extremely high resolution in three dimensions. In the nervous system, nanometer-scale images are necessary to reconstruct dense neural wiring diagrams in the brain, so calledconnectomes. In order to use this data, consisting of up to 108individual EM images, it must be assembled into a volume, requiring seamless 2D stitching from each physical section followed by 3D alignment of the stitched sections. The high throughput of ssEM necessitates 2D stitching to be done at the pace of imaging, which currently produces tens of terabytes per day. To achieve this, we present a modular volume assembly software pipelineASAP(Assembly Stitching and Alignment Pipeline) that is scalable to datasets containing petabytes of data and parallelized to work in a distributed computational environment. The pipeline is built on top of theRender[18] services used in the volume assembly of the brain of adultDrosophila melanogaster[2]. It achieves high throughput by operating on the meta-data and transformations of each image stored in a database, thus eliminating the need to render intermediate output. ASAP is modular, allowing for easy incorporation of new algorithms without significant changes in the workflow. The entire software pipeline includes a complete set of tools for stitching, automated quality control, 3D section alignment, and final rendering of the assembled volume to disk. ASAP has been deployed for continuous processing of several large-scale datasets of the mouse visual cortex and human brain samples including one cubic millimeter of mouse visual cortex [1, 25] at speeds that exceed imaging. The pipeline also has multi-channel processing capabilities and can be applied to fluorescence and multi-modal datasets like array tomography.
Multiple groups of methanotrophic bacteria mediate methane oxidation in anoxic lake sediments
Authors: Su Guangyi , Zopfi Jakob , Niemann Helge , Lehmann Moritz F. 
Published: November 2021

AbstractFreshwater lakes represent an important source of the potent greenhouse gas methane (CH4) to the atmosphere. Methane emissions are regulated to large parts by aerobic (MOx) and anaerobic (AOM) oxidation of methane that are important sinks in lakes. In contrast to marine benthic environments, our knowledge about the modes of AOM and the related methanotrophic microorganisms in anoxic lake sediments is still rudimentary. Here we demonstrate the occurrence of AOM in the anoxic sediments of Lake Sempach (Switzerland), with maximum in situ AOM rates observed within the surface sediment layers in presence of multiple groups of methanotrophic bacteria and various oxidants known to support AOM. However, substrate-amended incubations (with NO2−, NO3−, SO42–, Fe3+ and Mn4+) revealed that none of the electron acceptors previously reported to support AOM enhanced methane turnover in Lake Sempach sediments under anoxic conditions. In contrast, the addition of oxygen to the anoxic sediments resulted in an approximately tenfold increase in methane oxidation relative to the anoxic incubations. Phylogenetic and isotopic evidence indicate that both Type I and Type II aerobic methanotrophs were growing on methane under both oxic and anoxic conditions, although methane assimilation rates were an order of magnitude higher under oxic conditions. While the anaerobic electron acceptor responsible for AOM could not be identified, these findings expand our understanding of the metabolic versatility of canonically aerobic methanotrophs under anoxic conditions, with important implications for future investigations to identify methane oxidation processes. Bacterial AOM by facultative aerobic methane oxidizers might be of much larger environmental significance in reducing methane emissions than previously thought.
Annotation of Spatially Resolved Single-cell Data with STELLAR
Authors: Brbić Maria , Cao Kaidi , Hickey John W. , Tan Yuqi , Snyder Michael P. , Nolan Garry P. , Leskovec Jure 
Published: November 2021

AbstractAccurate cell type annotation from spatially resolved single cells is crucial to understand functional spatial biology that is the basis of tissue organization. However, current computational methods for annotating spatially resolved single-cell data are typically based on techniques established for dissociated single-cell technologies and thus do not take spatial organization into account. Here we present STELLAR, a geometric deep learning method for cell type discovery and identification in spatially resolved single-cell datasets. STELLAR automatically assigns cells to cell types present in the annotated reference dataset as well as discovers novel cell types and cell states. STELLAR transfers annotations across different dissection regions, different tissues, and different donors, and learns cell representations that capture higher-order tissue structures. We successfully applied STELLAR to CODEX multiplexed fluorescent microscopy data and multiplexed RNA imaging datasets. Within the Human BioMolecular Atlas Program, STELLAR has annotated 2.6 million spatially resolved single cells with dramatic time savings.
Activation of LH GABAergic inputs counteracts fasting-induced changes in tVTA/RMTG neurons
Authors: Godfrey Nathan , Qiao Min , Borgland Stephanie L. 
Published: November 2021

AbstractDopamine neurons in the ventral tegmental area (VTA) are strongly innervated by GABAergic neurons in the ‘tail of the VTA’ (tVTA), also known as the rostralmedial tegmental nucleus (RMTg). Disinhibition of dopamine neurons through firing of the GABAergic neurons projecting from the lateral hypothalamus (LH) leads to reward seeking and consumption through dopamine release in the nucleus accumbens. VTA dopamine neurons respond to changes in motivational state, yet less is known of whether tVTA/RMTg GABAergic neurons or the LH GABAergic neurons that project to them are also affected by changes in motivational state, such as fasting. An acute 16 h overnight fast decreased the excitability of tVTA/RMTg GABAergic neurons of male and female mice. In addition, fasting decreased synaptic strength at LH GABA to tVTA/RMTg GABAergic synapses, indicated by reduced amplitude of optically evoked currents, decreased readily releasable pool (RRP) size and replenishment. Optical stimulation of LH GABA terminals suppressed evoked action potentials of tVTA/RMTg GABAergic neurons in unfasted mice, but this effect decreased following fasting. Furthermore, during fasting, LH GABA inputs to tVTA/RMTg neurons maintained functional connectivity during depolarization, as depolarization block was reduced following fasting. Taken together, inhibitory synaptic transmission from LH GABA inputs onto tVTA/RMTg GABAergic neurons decreases following fasting, however ability to functionally inhibit tVTA/RMTg GABAergic neurons is preserved, allowing for possible disinhibition of dopamine neurons and subsequent foraging.Key PointsWhile dopamine neuronal activity changes with motivational state, it is unknown if fasting influences tVTA/RMTg GABAergic neurons, a major inhibitory input to VTA dopamine neurons.In unfasted mice, there were sex differences in inhibitory synaptic transmission onto tVTA/RMTg GABAergic neurons.Activation of LH GABAergic neurons decreases firing of tVTA/RMTg GABAergic neurons through a monosynaptic input.An acute fast decreased the excitability of tVTA/RMTg GABAergic neurons.An acute fast decreases inhibitory synaptic transmission of the LH GABA input to tVTA/RMTg GABAergic neurons in both male and female mice.
A high-density lineage tree reveals dynamics of expression differences accumulation in nondifferentiating clonal expansion
Authors: Chen Feng , Li Zizhang , Zhang Xiaoyu , Wu Peng , Yang Wenjing , Chen Xiaoshu , Yang Jian-Rong 
Published: November 2021

SummaryDifferences in gene expression levels among genetically identical cells naturally accumulate during cellular proliferation, forming the basis of expression noise or differentiation. Nevertheless, how transcriptome-wide noise accumulation is constrained to maintain homeostasis during continuous cell divisions has remained largely unresolved. We developed a novel method named “single-cell transcriptome and dense tree” (STADT) to simultaneously determines the transcriptomes and lineage tree of >50% single cells in a single-cell-seeded colony. This lineage tree revealed gradual accumulation of transcriptome differences that became saturated upon four cell divisions, reduced expression noise for sub-tree/sub-colonies closer to inferred expression boundaries, and transcriptionally modulated co-fluctuations among genes. These results collectively showed, for the first time, constrained dynamics of expression noise in the context of cell division.
Gut-testis axis: microbiota-(n-3) PUFA improving semen quality in type 1 diabetes
Authors: Hao Yanan , Feng Yanni , Yan Xiaowei , Chen Liang , Zhong Ruqing , Tang Xiangfang , Shen Wei , Sun Qingyuan , Sun Zhongyi , Ren Yonglin , Zhang Hongfu , Zhao Yong 
Published: November 2021

AbstractGut dysbiosis and type 1 diabetes (T1D) are closely related, and gut dysbiosis and male infertility are correlated, too. Moreover, most male T1D patients are of active reproductive age. Therefore, it is crucial to explore possible means for improving their semen quality. Here, we found that fecal microbiota transplantation (FMT) from alginate oligosaccharide (AOS) improved gut microbiota (A10-FMT) significantly decreased blood glucose and glycogen, and increased semen quality in streptozotocin-induced T1D subjects. A10-FMT improved T1D-disturbed gut microbiota, especially the increase in small intestinal lactobacillus, and blood and testicular metabolome to produce n-3 polyunsaturated fatty acid (PUFA) docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA) to ameliorate spermatogenesis and semen quality. Moreover, A10-FMT can improve spleen and liver function to strengthen the systemic environment for sperm development. FMT from gut microbiota of control animals (Con-FMT) produced some beneficial effects; however, to a smaller extent. Thus, AOS improved gut microbiota may be a useful protocol for improving semen quality and male fertility in T1D patients.ImportanceClinical data suggest that male reproductive dysfunction especially infertility is a critical issue for type 1 diabetic patient (T1D) because most of them are at the reproductive age. Gut dysbiosis is involved in T1D related male infertility. However, improved gut microbiota can be used to improve spermatogenesis and male fertility in T1D remains incompletely understood. We discovered that alginate oligosaccharide-improved gut microbiota (A10-FMT) significantly ameliorated spermatogenesis and semen quality. AOS-improved gut microbiota (specific microbes) may serve as a novel, promising therapeutic approach for the improvement of semen quality and male fertility in T1D patients.
Nutrigonometry I: using right-angle triangles to quantify nutritional trade-offs in multidimensional performance landscapes
Authors: Morimoto Juliano , Conceição Pedro , Mirth Christen , Lihoreau Mathieu 
Published: November 2021

AbstractAnimals regulate their diet in order to maximise the expression of fitness traits that often have different nutritional needs. These nutritional trade-offs have been experimentally uncovered using the Geometric framework for nutrition (GF). However, current analytical methods to measure such responses rely on either visual inspection or complex models applied to multidimensional performance landscapes, making these approaches subjective, or conceptually difficult, computationally expensive, and in some cases inaccurate. This limits our ability to understand how animal nutrition evolved to support life-histories within and between species. Here, we introduce a simple trigonometric model to measure nutritional trade-offs in multidimensional landscapes (‘Nutrigonometry’). Nutrigonometry is both conceptually and computationally easier than current approaches, as it harnesses the trigonometric relationships of right-angle triangles instead of vector calculations. Using landmark GF datasets, we first show how polynomial (Bayesian) regressions can be used for precise and accurate predictions of peaks and valleys in performance landscapes, irrespective of the underlying structure of the data (i.e., individual food intakes vs fixed diet ratios). Using trigonometric relationships, we then identified the known nutritional trade-off between lifespan and reproductive rate both in terms of nutrient balance and concentration. Nutrigonometry enables a fast, reliable and reproducible quantification of nutritional trade-offs in multidimensional performance landscapes, thereby broadening the potential for future developments in comparative research on the evolution of animal nutrition.
Tracing the development and lifespan change of population-level structural asymmetry in the cerebral cortex
Authors: Roe James M. , Vidal-Piñeiro Didac , Amlien Inge K. , Pan Mengyu , Sneve Markus H. , de Schotten Michel Thiebaut , Friedrich Patrick , Sha Zhiqiang , Francks Clyde , Wang Yunpeng , Walhovd Kristine B. , Fjell Anders M. , Westerhausen René 
Published: November 2021

AbstractCortical asymmetry is a ubiquitous feature of brain organization that is subtly altered in some neurodevelopmental disorders, yet we lack knowledge of how its development proceeds across life in health. Achieving consensus on the precise cortical asymmetries in humans is necessary to uncover the genetic and later influences that shape them, such as age. Here, we delineate population-level asymmetry in cortical thickness and surface area vertex-wise in 7 datasets and chart asymmetry trajectories longitudinally across life (4-89 years; observations = 3937; 70% longitudinal). We find replicable asymmetry interrelationships, heritability maps, and test asymmetry associations in large-scale data. Cortical asymmetry was robust across datasets. Whereas areal asymmetry is predominantly stable across life, thickness asymmetry grows in childhood and peaks in early adulthood. Areal asymmetry correlates phenotypically and genetically in specific regions, and is low-moderately heritable (max h2SNP∼19%). In contrast, thickness asymmetry is globally interrelated across the cortex in a pattern suggesting highly left-lateralized individuals tend towards left-lateralization also in population-level right-asymmetric regions (and vice versa), and exhibits low or absent heritability. We find less areal asymmetry in the most consistently lateralized region in humans associates with subtly lower cognitive ability, and confirm small handedness and sex effects. Results suggest areal asymmetry is developmentally stable and arises in early life through genetic but mainly subject-specific stochastic effects, whereas childhood developmental growth shapes thickness asymmetry and may lead to directional variability of global thickness lateralization in the population.
Evidence of positive and negative selection associated with DNA methylation
Authors: Hatcher Charlie ,   Genetics of DNA Methylation Consortium, Hemani Gibran , Rodriguez Santiago , Gaunt Tom R. , Lawson Daniel J. , Min Josine L. 
Published: November 2021

AbstractSignatures of negative selection are pervasive amongst complex traits and diseases. However, it is unclear whether such signatures exist for DNA methylation (DNAm) that has been proposed to have a functional role in disease. We estimate polygenicity, SNP-based heritability and model the joint distribution of effect size and minor allele frequency (MAF) to estimate a selection coefficient (S) for 2000 heritable DNAm sites in 1774 individuals from the Avon Longitudinal Study of Parents and Children. Additionally, we estimate S for meta stable epi alleles and DNAm sites associated with aging and mortality, birthweight and body mass index. Quantification of MAF-dependent genetic architectures estimated from genotype and DNAm reveal evidence of positive (S > 0) and negative selection (S < 0) and confirm previous evidence of negative selection for birthweight. Evidence of both negative and positive selection highlights the role of DNAm as an intermediary in multiple biological pathways with competing function.
Mesoscopic in vivo human T2* dataset acquired using quantitative MRI at 7 Tesla
Authors: Gulban Omer Faruk , Bollmann Saskia , Huber Renzo , Wagstyl Konrad , Goebel Rainer , Poser Benedikt A. , Kay Kendrick , Ivanov Dimo 
Published: November 2021

AbstractMesoscopic (0.1-0.5 mm) interrogation of the living human brain is critical for advancing neuroscience and bridging the resolution gap with animal models. Despite the variety of MRI contrasts measured in recent years at the mesoscopic scale, in vivo quantitative imaging of T2* has not been performed. Here we provide a dataset containing empirical T2* measurements acquired at 0.35 × 0.35 × 0.35 mm3voxel resolution using 7 Tesla MRI. To demonstrate unique features and high quality of this dataset, we generate flat map visualizations that reveal fine-scale cortical substructures such as layers and vessels, and we report quantitative depth-dependent T2* (as well as R2*) values in primary visual cortex and auditory cortex that are highly consistent across subjects. This dataset is freely available athttps://doi.org/10.17605/OSF.IO/N5BJ7, and may prove useful for anatomical investigations of the human brain, as well as for improving our understanding of the basis of the T2* -weighted (f)MRI signal.
Assembly process case matching based on a multilevel assembly ontology method
Authors: Gong Hanqing , Shi Lingling , Zhai Xiang , Du Yimin , Zhang Zhijing 
Published: November 2021

Purpose
The purpose of this study is to achieve accurate matching of new process cases to historical process cases and then complete the reuse of process knowledge and assembly experience.

Design/methodology/approach
By integrating case-based reasoning (CBR) and ontology technology, a multilevel assembly ontology is proposed. Under the general framework, the knowledge of the assembly domain is described hierarchically and associatively. On this basis, an assembly process case matching method is developed.

Findings
By fully considering the influence of ontology individual, case structure, assembly scenario and introducing the correction factor, the similarity between non-correlated parts is significantly reduced. Compared with the Triple Matching-Distance Model, the degree of distinction and accuracy of parts matching are effectively improved. Finally, the usefulness of the proposed method is also proved by the matching of four practical assembly cases of precision components.

Originality/value
The process knowledge in historical assembly cases is expressed in a specific ontology framework, which makes up for the defects of the traditional CBR model. The proposed matching method takes into account all aspects of ontology construction and can be used well in cross-ontology similarity calculations.
Insitu SVET studies on the current density distribution on dissolving of Mg, MgZn2, Mg2Si and Al4Cu2Mg8Si7 surfaces in NaCl solutions
Authors: Ikeuba Alexander I. , Okafor Peter C. , Ita Benedict , Obike Anthony I. , Abeng Fidelis E. , Essien Uduak , Bamigbola Abiola 
Published: November 2021

Purpose
This paper aims to acquire the current density distribution on dissolving of Mg, MgZn2 (η -phase), Mg2Si (ß-phase) and Al4Cu2Mg8Si7 (Q-phase) surface in NaCl solutions.

Design/methodology/approach
MgZn2 (η -phase), Mg2Si (ß-phase) and Al4Cu2Mg8Si7 (Q-phase) are important intermetallic compounds found in aluminum alloys. Insitu scanning vibrating electrode technique (SVET) was used to acquire the current density distribution on dissolving of Mg, MgZn2 (η -phase), Mg2Si (ß-phase) and Al4Cu2Mg8Si7 (Q-phase) surface in NaCl solutions scanning electron microscopy/energy-dispersive X-ray spectroscopy (SEM/EDX) was used to characterize the corroded surface.

Findings
SVET maps reveal that these compounds display characteristic dissolution features. Mg and MgZn2 displayed localized anodic and cathodic sites while that of Al4Cu2Mg8Si7 > Mg2Si displayed a diffused distribution of anodic and cathodic sites. The magnitude of the integrated anodic current densities on the compounds was noted to decrease with the progress of time, and the order of the magnitude of the current density with respect to the compounds is Mg > Mg2Si > Al4Cu2Mg8Si7 > MgZn2. SEM/EDX reveal that the highest mass loss recorded after the SVET test was manifested by Mg2Si followed by MgZn2 then Al4Cu2Mg8Si7.

Originality/value
Auxiliary information on the current density distribution on the corroding sample surface at the microscopic scale has been provided by SVET thereby taking care of certain limitations of traditional corrosion monitoring techniques such as gravimetric, hydrogen evolution and electrochemical measurements.