bluuebunny/crossref_metadata_2025_split huggingface dataset:
Novel design of imputation-enabled SNP arrays for breeding and research applications supporting multi-species hybridisation
Authors: Keeble-Gagnère G , Pasam R , Forrest KL , Wong D , Robinson H , Godoy J , Rattey A , Moody D , Mullan D , Walmsley T , Daetwyler HD , Tibbits J , Hayden MJ 
Published: August 2021

AbstractArray-based SNP genotyping platforms have low genotype error and missing data rates compared to genotyping-by-sequencing technologies. However, design decisions used to create array-based SNP genotyping assays for both research and breeding applications are critical to their success. We describe a novel approach applicable to any animal or plant species for the design of cost-effective imputation-enabled SNP genotyping arrays with broad utility and demonstrate its application through the development of the Infinium Wheat Barley 40K SNP array. We show the approach delivers high-quality and high-resolution data for wheat and barley, including when samples are jointly hybridised. The new array aims to maximally capture haplotypic diversity in globally diverse wheat and barley germplasm while minimising ascertainment bias. Comprising mostly biallelic markers designed to be species-specific and single-copy, it permits highly accurate imputation in diverse germplasm to improve statistical power for GWAS and genomic selection. The SNP content captures tetraploid wheat (A- and B-genome) and Ae. tauschii (D-genome) diversity and delineates synthetic and tetraploid wheat from other wheats, as well as tetraploid species and subgroups. The content includes SNP tagging key trait loci in wheat and barley and that directly connect to other genotyping platforms and legacy datasets. The utility of the array is enhanced through the web-based tool Pretzel (https://plantinformatics.io/) which enables the array’s content to be visualised and interrogated interactively in the context of numerous genetic and genomic resources to more seamlessly connect research and breeding. The array is available for use by the international wheat and barley community.Short summaryDesigning SNP genotyping arrays for closely related species with broad applicability in both research and breeding is challenging. Here we describe a novel generic approach to select SNP content for such arrays and demonstrate its utility in wheat and barley to:
capture haplotypic diversity while minimising ascertainment bias;accurately impute to high SNP density in diverse germplasm;generate high-quality high-resolution genotypic data; andjointly hybridise samples to the same bead chip array.
Sift-PULs: A public repository for specific functional polysaccharide utilization loci
Authors: Song Tao , Wei Congchong , Yuan Dezhi , Xiang Shengwei , Lv Hua , Huang Ting , Zhao Kelei , Wang Xinrong , Chu Yiwen , Luo Dan , Lin Jiafu 
Published: August 2021

AbstractBackgroundPolysaccharide utilization loci (PULs) were bacterial gene clusters encoding genes responsible for polysaccharide utilization process. PUL studies are blooming in recent years but the biochemical characterization speed is relative slow. There is a growing demand for PUL database with function annotations.ResultsUsing signature genes corresponding for specific polysaccharide, 10422 PULs specific for 6 polysaccharides (agar, alginate, pectin, carrageenan, chitin and β-manan) from various bacterial phyla were predicted. Then online website of specific functional polysaccharide utilization loci (Sift-PULs) was constructed. Sift-PULs provides a repository where users could browse, search and download interested PULs without registration.ConclusionsThe key advantage of Sift-PULs is to assign a function annotation of each PUL, which is not available in existing PUL databases. PUL’s functional annotation lays a foundation for studying novel enzymes, new pathways, PUL evolution or bioengineering. The website is available on https://sift-puls.org
Super-resolution imaging of highly curved membrane structures in giant vesicles encapsulating molecular condensates
Authors: Zhao Ziliang , Roy Debjit , Steinkühler Jan , Robinson Tom , Lipowsky Reinhard , Dimova Rumiana 
Published: August 2021

ABSTRACTMolecular crowding is an inherent feature of the cell interior. Synthetic cells as provided by giant unilamellar vesicles (GUVs) encapsulating macromolecules (polyethylene-glycol and dextran) represent an excellent mimetic system to study membrane transformations associated with molecular crowding and protein condensation. Similarly to cells, such GUVs loaded with macromolecules exhibit highly curved structures such as internal nanotubes. In addition, upon liquid-liquid phase separation as inside living cells, the membrane of GUVs encapsulating an aqueous two-phase system deforms to form apparent kinks at the contact line of the interface between the two aqueous phases. These structures, nanotubes and kinks, have dimensions below optical resolution and if resolved, can provide information about material properties such as membrane spontaneous curvature and intrinsic contact angle describing the wettability contrast of the encapsulated phases to the membrane. Previous experimental studies were based on conventional optical microscopy which cannot resolve these membrane and wetting properties. Here, we studied these structures with super-resolution microscopy, namely stimulated emission depletion (STED) microscopy, together with microfluidic manipulation. We demonstrate the cylindrical nature of the nanotubes with unprecedented detail based on the superior resolution of STED and automated data analysis. The spontaneous curvature deduced from the nanotube diameters is in excellent agreement with theoretical predictions. Furthermore, we were able to resolve the membrane “kink” structure as a smoothly curved membrane demonstrating the existence of the intrinsic contact angle. We find very good agreement between the directly measured values and the theoretically predicted ones based on the apparent contact angles on the micrometer scale. During different stages of cellular events, biomembranes undergo a variety of shape transformations such as the formation of buds and nanotubes regulated by membrane necks. We demonstrate that these highly curved membrane structures are amenable to STED imaging and show that such studies provide important insights in the membrane properties and interactions underlying cellular activities.
Sparse Sonomyography-based Estimation of Isometric Force: A Comparison of Methods and Features
Authors: Kamatham Anne Tryphosa , Alzamani Meena , Dockum Allison , Sikdar Siddhartha , Mukherjee Biswarup 
Published: August 2021

AbstractNoninvasive methods for estimation of joint and muscle forces have widespread clinical and research applications. Surface electromyography or sEMG provides a measure of the neural activation of muscles which can be used to estimate the force produced by the muscle. However, sEMG based measures of force suffer from poor signal-to-noise ratio and limited spatiotemporal specificity. In this paper, we propose an ultrasound imaging or sonomyography-based approach for estimating continuous isometric force from a sparse set of ultrasound scanlines. Our approach isolates anatomically relevant features from A-mode ultrasound signals, greatly reducing the dimensionality of the feature space and the computational complexity involved in traditional ultrasound-based methods. We evaluate the performance of four regression methodologies for force prediction using the reduced feature set. We also evaluate the feasibility of a practical wearable sonomyography-based system by simulating the effect of transducer placement and varying the number of transducers used in force prediction. Our results demonstrate that Gaussian process regression models outperform other regression methods in predicting continuous force levels from just four equispaced transducers and are tolerant to speckle noise. These findings will aid in the design of wearable sonomyography-based force prediction systems with robust, computationally efficient operation.
cageminer: an R/Bioconductor package to prioritize candidate genes by integrating GWAS and gene coexpression networks
Authors: Almeida-Silva Fabricio , Venancio Thiago M. 
Published: August 2021

ABSTRACTSummaryAlthough genome-wide association studies (GWAS) identify variants associated with traits of interest, they often fail in identifying causative genes underlying a given phenotype. Integrating GWAS and gene coexpression networks can help prioritize high-confidence candidate genes, as the expression profiles of trait-associated genes can be used to mine novel candidates. Here, we present cageminer, the first R package to prioritize candidate genes through the integration of GWAS and coexpression networks. Genes are considered high-confidence candidates if they pass all three filtering criteria implemented in cageminer, namely physical proximity to SNPs, coexpression with known trait-associated genes, and significant changes in expression levels in conditions of interest. Prioritized candidates can also be scored and ranked to select targets for experimental validation. By applying cageminer to a real data set, we demonstrate that it can effectively prioritize candidates, leading to >99% reductions in candidate gene lists.Availability and implementationThe package is available at Bioconductor (http://bioconductor.org/packages/cageminer).
But Mouse, you are not alone: On some severe acute respiratory syndrome coronavirus 2 variants infecting mice
Authors: Kuiper Michael J. , Wilson Laurence OW , Mangalaganesh Shruthi , Lee Carol , Reti Daniel , Vasan Seshadri S 
Published: August 2021

AbstractIn silico predictions combined with in vitro, in vivo and in situ observations collectively suggest that mouse adaptation of the SARS-CoV-2 virus requires an aromatic substitution in position 501 or position 498 (but not both) of the spike protein’s receptor binding domain. This effect could be enhanced by mutations in positions 417, 484, and 493 (especially K417N, E484K, Q493K and Q493R), and to a lesser extent by mutations in positions 486 and 499 (such as F486L and P499T). Such enhancements due to more favourable binding interactions with residues on the complementary angiotensin-converting enzyme 2 (ACE2) interface, are however, unlikely to sustain mouse infectivity on their own based on theoretical and experimental evidence to date. Our current understanding thus points to the Alpha, Beta, Gamma, and Omicron variants of concern infecting mice, while Delta and ‘Delta Plus’ lack a similar biomolecular basis to do so. This paper identifies eleven countries (Brazil, Chile, Djibouti, Haiti, Malawi, Mozambique, Reunion, Suriname, Trinidad and Tobago, Uruguay and Venezuela) where targeted local field surveillance of mice is encouraged because they may have come in contact with humans who had the virus with adaptive mutation(s). It also provides a systematic methodology to analyze the potential for other animal reservoirs and their likely locations.
Multiscale model of the physiological control of myocardial perfusion to delineate putative metabolic feedback mechanisms
Authors: Gharahi Hamidreza , Figueroa C. Alberto , Tune Johnathan D. , Beard Daniel A. 
Published: August 2021

AbstractCoronary blood flow is tightly regulated to ensure that myocardial oxygen delivery meets local metabolic demand via the concurrent action of myogenic, neural, and metabolic mechanisms. While several competing hypotheses exist, the specific nature of the local metabolic mechanism(s) remains poorly defined. To gain insights into the viability of putative metabolic feedback mechanisms and into the coordinated action of parallel regulatory mechanisms, we applied a multi-scale modeling framework to analyze experimental data on coronary pressure, flow, and myocardial oxygen delivery in the porcine heart in vivo. The modeling framework integrates a previously established lumped-parameter model of myocardial perfusion used to account for transmural hemodynamic variations and a simple vessel mechanics model used to simulate the vascular tone in each of three myocardial layers. Vascular tone in the resistance vessel mechanics model is governed by input stimuli from the myogenic, metabolic, and autonomic control mechanisms. Seven competing formulations of the metabolic feedback mechanism are implemented in the modeling framework, and associated model simulations are compared to experimental data on coronary pressures and flows under a range of experimental conditions designed to interrogate the governing control mechanisms. Analysis identifies a maximally likely metabolic mechanism among the seven tested models, in which production of a metabolic signaling factor is proportional to MVO2 and delivery proportional to flow. Finally, the identified model is validated based on comparisons of simulations to data on the myocardial perfusion response to conscious exercise that were not used for model identification.
Trophic specialization on unique resources in one of the most celebrated examples of sympatric speciation, Barombi Mbo crater lake cichlids
Authors: Galvez Jacquelyn R. , McLean Keara , Touokong Cyrille Dening , Gonwouo Legrand Nono , Martin Christopher H. 
Published: August 2021

ABSTRACTDivergent ecological selection often results in trophic niche partitioning and is one of the central processes underlying sympatric speciation. However, there are still few studies of niche partitioning in putative examples of sympatric speciation in the wild. Here we conducted the first quantitative study of dietary niche partitioning in one of the most celebrated examples of sympatric speciation, Barombi Mbo cichlids, using stomach contents and stable isotope analyses. We found little evidence for trophic niche partitioning among any Barombi Mbo cichlids, even among the nine species coexisting in sympatry in the littoral zone. Stable isotope analyses supported these conclusions of minimal dietary overlap. However, we did find extraordinary dietary specialization in some species, including spongivory and feeding on terrestrial ants, both unique feeding strategies among freshwater fishes. Stomach contents of the spongivore (Pungu maclareni) were 20% freshwater sponge, notable considering that only 0.04% of all fishes consume sponges. Overall, we conclude that while there is less trophic niche partitioning than expected among Barombi Mbo cichlids, there is evidence for dietary specialization on rare resources in support of Liem’s paradox.
Embedded 3D printing in self-healing annealable composites for precise patterning of functionally mature human neural constructs
Authors: Kajtez Janko , Wesseler Milan Finn , Birtele Marcella , Khorasgani Farinaz Riyahi , Ottosson Daniella Rylander , Heiskanen Arto , Kamperman Tom , Leijten Jeroen , Martínez-Serrano Alberto , Larsen Niels B. , Angelini Thomas E. , Parmar Malin , Lind Johan U. , Emnéus Jenny 
Published: August 2021

AbstractHuman in vitro models of neural tissue with controllable cellular identity, tunable microenvironment, and defined spatial arrangement are needed to facilitate studies of brain development and disease. Towards this end, embedded printing in jammed microgel supports (i.e., granular gels) holds great promise as it allows precise and programmable patterning of extremely soft and compliant tissue constructs. However, in contrast to the vast material landscape available for bulk hydrogels, granular printing support formulations are restricted to a handful of materials without the ability for facile adjustment of biofunctional properties of the cellular microenvironment. Therefore, there has been a need for novel materials that take advantage of versatile biomimicry of bulk hydrogels while providing high-fidelity support for embedded printing akin to granular gels. To address this need, we present a modular platform for bioengineering of neuronal networks via direct embedded 3D printing of human stem cells inside Self-Healing Annealable Particle-Extracellular matrix (SHAPE) composites. SHAPE composites consist of soft microgels immersed in viscous extracellular-matrix solution to enable precise freeform patterning of human stem cells and consequent generation and long-term maintenance of mature subtype-specific neurons that extend projections within the volume of the annealed support. The developed approach further allows multi-ink deposition, live spatial and temporal monitoring of oxygen levels, as well as creation of vascular channels. Due to its modularity, SHAPE biomanufacturing toolbox not only offers a solution for functional modeling of mechanically sensitive neural constructs, but also has potential to be applied to a wide range of biomaterials with different crosslinking mechanisms to model tissues and diseases where recapitulation of complex architectural features and topological cues is essential.
The road not taken: disconnection of a human-unique cortical pathway in schizophrenia and its effects on naturalistic social cognition
Authors: Patel Gaurav H. , Gruskin David , Arkin Sophie C. , Jamerson Emery C. , Ruiz-Betancourt Daniel , Klim Casimir C. , Sanchez-Peña Juan P. , Bartel Laura P. , Lee Jessica K. , Grinband Jack , Martinez Antigona , Berman Rebecca A. , Ochsner Kevin N. , Leopold David A. , Javitt Daniel C. 
Published: August 2021

AbstractBackgroundEfficient processing of complex and dynamic social scenes relies on intact connectivity of many underlying cortical areas and networks, but how connectivity deficits affect this functioning in social cognition remains unknown. Here we measure these relationships using functionally based localization of social cognition areas, resting-state functional connectivity, and movie-watching data.MethodsIn 42 schizophrenia participants (SzP) and 41 healthy controls (HC), we measured the functional connectivity of areas localized by face-emotion processing, theory-of-mind, and attention tasks. We quantified the weighted shortest path length between visual and medial prefrontal theory-of-mind areas in both populations to assess the impact of functional connectivity deficits on network structure. We then correlated connectivity along the shortest path in each group with movie-evoked activity in a key node of the theory-of-mind network (TPJp).ResultsSzP had pronounced connectivity deficits in temporoparietal junction/posterior superior temporal sulcus (TPJ-pSTS) areas involved in face-emotion processing (t(81)=4.4, p=0.00002). In HC the shortest path connecting visual and medial prefrontal theory-of-mind areas passed through TPJ-pSTS, whereas in SzP the shortest path passed through prefrontal cortex (PFC). While movie-evoked TPJp activity correlated with connectivity along the TPJ-pSTS pathway in both groups (r=0.43, p=0.002), it additionally correlated with connectivity along the PFC pathway only in SzP (rSzP=0.56, p=0.003).ConclusionsConnectivity along the human-unique TPJ-pSTS pathway affects both the network architecture and functioning of areas involved in processing complex dynamic social scenes. These results demonstrate how focal deficits can have widespread impacts across cortex.
Multivariate Genomewide Association Analysis by Iterative Hard Thresholding
Authors: Chu Benjamin B. , Ko Seyoon , Zhou Jin J. , Jensen Aubrey , Zhou Hua , Sinsheimer Janet S. , Lange Kenneth 
Published: August 2021

1AbstractIn genome-wide association studies (GWAS), analyzing multiple correlated traits is potentially superior to conducting multiple univariate analyses. Standard methods for multivariate GWAS operate marker-by-marker and are computationally intensive. We present a penalized regression algorithm for multivariate GWAS based on iterative hard thresholding (IHT) and implement it in a convenient Julia packageMendelIHT.jl(https://github.com/OpenMendel/MendelIHT.jl). In simulation studies with up to 100 traits, IHT exhibits similar true positive rates, smaller false positive rates, and faster execution times thanGEMMA’s linear mixed models andmv-PLINK’s canonical correlation analysis. On UK Biobank data, our IHT software completed a 3-trait joint analysis in 20 hours and an 18-trait joint analysis in 53 hours, requiring up to 80GB of computer memory. In short, our software enables geneticists to fit a single regression model that simultaneously considers the effect of all SNPs and dozens of traits.
Evolution of a costly immunity to cestode parasites is a pyrrhic victory
Authors: Weber Jesse N. , Steinel Natalie C. , Peng Foen , Shim Kum Chuan , Lohman Brian K. , Fuess Lauren , de Lisle Stephen , Bolnick Daniel I. 
Published: August 2021

AbstractParasites impose fitness costs on their hosts. Biologists therefore tend to assume that natural selection favors infection-resistant hosts. Yet, when the immune response itself is costly, theory suggests selection may instead favor loss of resistance. Immune costs are rarely documented in nature, and there are few examples of adaptive loss of resistance. Here, we show that when marine threespine stickleback colonized freshwater lakes they gained resistance to the freshwater-associated tapeworm, Schistocephalus solidus. Extensive peritoneal fibrosis and inflammation contribute to suppression of cestode growth and viability, but also impose a substantial cost of reduced fecundity. Combining genetic mapping and population genomics, we find that the immune differences between tolerant and resistant populations arise from opposing selection in both populations acting, respectively, to reduce and increase resistance consistent with divergent optimization.One Sentence SummaryRecently-evolved freshwater populations of stickleback frequently evolve increased resistance to tapeworms, involving extensive fibrosis that suppresses parasite growth; because this fibrosis greatly reduces fish fecundity, in some freshwater populations selection has favored an infection-tolerant strategy with fibrosis suppression.
Does the rainbow trout ovarian fluid guide the spermatozoon on its way to the egg?
Authors: Kholodnyy Vitaliy , Dzyuba Borys , Rodina Marek , Bloomfield-Gadêlha Hermes , Yoshida Manabu , Cosson Jacky , Boryshpolets Sergii 
Published: August 2021

AbstractFertilization of freshwater fish occurs in an environment that may negatively affect the gametes; therefore, the specific mechanisms triggering the encounters of gametes would be highly expedient. The egg and ovarian fluid (OF) are likely the primary sources of these triggers in fish that we confirmed here for rainbow trout Oncorhynchus mykiss. The ovarian fluid significantly affected the spermatozoa performance: it supported high velocity for a more extended period and changed the motility pattern from tumbling in water to straightforward moving in the ovarian fluid. Rainbow trout OF induced a trapping chemotaxis-like effect on activated male gametes, and this effect depended on the properties of the activating media. The interaction of the spermatozoa with the attracting agents was accompanied by their “turn-and-run” behavior involving asymmetric flagellar beating and Ca2+ concentration bursts in the bent flagella segment, characteristic of the chemotactic response. Collectively, the ovarian fluid creates the optimal environment for rainbow trout spermatozoa performance, being an effective promoter of fertilization. The individual peculiarities of the egg (ovarian fluid) – sperm interaction in rainbow trout reflect the specific features of the spawning process in this species.