bluuebunny/crossref_metadata_2025_split huggingface dataset:
Flies adaptively control flight to compensate for added inertia
Authors: Salem Wael , Cellini Benjamin , Jaworski Eric , Mongeau Jean-Michel 
Published: December 2022

AbstractAnimal locomotion is highly adaptive, displaying a large degree of flexibility, yet how this flexibility arises from the integration of mechanics, sensing and neural control remains elusive. For instance, animals require flexible strategies to maintain performance as changes in mass or inertia impact stability. Compensatory strategies to mechanical loading are especially critical for animals that rely on flight for survival. To shed light on the capacity and flexibility of flight neuromechanics to mechanical loading, we pushed the performance of fruit flies (Drosophila) near its limit and implemented a control theoretic framework to quantify how flies compensated for added inertia. Flies with added inertia were placed inside a virtual reality arena which enabled free rotation about the vertical (yaw) axis. Adding inertia increased the fly’s response time yet had little influence on overall gaze performance. Flies maintained stability following the addition of inertia by adaptively modulating both visuomotor gain and damping. In contrast, mathematical modeling predicted a significant decrease in flight stability and performance. Adding inertia altered saccades, however flies compensated for the added inertia by increasing yaw torque production, indicating that flies sense that they are mechanically loaded. Taken together, in response to added inertia flies trade off reaction time to maintain flight performance through adaptive neural modulation. Our work highlights the flexibility and capacity of motor control in flight.
SIMplyBee: R package for simulating honeybee populations and breeding programs
Authors: Obšteter Jana , Strachan Laura K. , Bubnič Jernej , Prešern Janez , Gorjanc Gregor 
Published: December 2022

AbstractBackgroundThe Western honeybee is an economically important species globally, but has been experiencing colony losses that lead to economical damage and decreased genetic variability. This situation is spurring additional interest in honeybee breeding and conservation programs. Stochastic simulators are essential tools for rapid and low-cost testing of breeding programs and methods, yet no existing simulator allows for a detailed simulation of honeybee populations. Here we describe SIMplyBee, a holistic simulator of honeybee populations and breeding programs. SIMplyBee is an R package and hence freely available for installation from CRANhttp://cran.r-project.org/package=SIMplyBee.ImplementationSIMplyBee builds upon the stochastic simulator AlphaSimR that simulates individuals with their corresponding genomes and quantitative genetic values. To enable a honeybee specific simulation, we extended AlphaSimR by developing classes for global simulation parameters,SimParamBee, for a honeybee colony,Colony, and multiple colonies,MultiColony. We also developed functions to address major specificities of the honeybees: honeybee genome, haplo-diploid inheritance, social organisation, complementary sex determination, polyandry, colony events, and quantitative genetics of honeybees.ResultsWe describe and show implementation regarding simulating a honeybee genome, creating a honeybee colony and its members, haplodiploid inheritance and complementary sex determination, colony events, creating and managing multiple colonies at once, and obtaining genomic data and honeybee quantitative genetics. Further documentation athttp://SIMplyBee.infoprovides details on these operations and describes additional operations related to genomics, quantitative genetics, and other functionality.DiscussionSIMplyBee is a holistic simulator of honeybee populations and breeding programs that simulates individual honeybees with their genomes, colonies with colony events, and individual- and colony-level quantitative values. SIMplyBee provides a research platform for testing breeding and conservation strategies and their effect on future genetic gain and variability. Future development of SIMplyBee will focus on improving the simulation of honeybee genomes, optimizing the performance of the simulator, and including spatial awareness to crossing functions and phenotype simulation. We welcome the honeybee genetics and breeding community to join us in the future development of SIMplyBee.
Ot2Rec: A Semi-Automatic, Extensible, Multi-Software Tomographic Reconstruction Workflow
Authors: Yee Neville B.-y. , Ho Elaine M. L. , Tun Win , Smith Jake L. R. , Dumoux Maud , Grange Michael , Darrow Michele C. , Basham Mark 
Published: December 2022

AbstractElectron cryo-tomography (cryo-ET) is an imaging technique for probing 3D structures with at the nanometre scale. This technique has been used extensively in the biomedical field to study the complex structures of proteins and other macromolecules. With the advancement in technology, microscopes are currently capable of producing images amounting to terabytes of data per day, posing great challenges for scientists as the speed of processing of the images cannot keep up with the ever-higher throughput of the microscopes. Therefore, automation is an essential and natural pathway on which image processing – from individual micrographs to full tomograms – is developing. In this paper, we present Ot2Rec, an open-source pipelining tool which aims to enable scientists to build their own processing workflows in a flexible and automatic manner. The basic building blocks of Ot2Rec are plugins which follow a unified API structure, making it simple for scientists to contribute to Ot2Rec by adding features which are not already available. In this paper, we also present three case studies of image processing using Ot2Rec, through which we demonstrate the speedup of using a semi-automatic workflow over a manual one, the possibility of writing and using custom (prototype) plugins, and the flexibility of Ot2Rec which enables the mix-and-match of plugins. We also demonstrate, in the supplementary information, a built-in reporting feature in Ot2Rec which aggregates the metadata from all process being run, and output them in the Jupyter Notebook and/or HTML formats for quick review of image processing quality. Ot2Rec can be found athttps://github.com/rosalindfranklininstitute/ot2rec.Impact StatementThe field of cryo electron tomography has grown substantially in recent years, bringing about new advances in hardware and software which enable visualisation of cell and tissue architecture and proteins found in their native context. These same advances have, in some ways, stratified the field into those with access and those without. On the software side, this has emphasised the need for open-source options that do not require high levels of computational literacy to access. Additionally, it has highlighted the need for ways to both mix-and-match software for easy prototyping and comparisons between parameters and methods. Ot2Rec addresses these needs through a simple, unified plugin structure allowing the addition of existing software or the development of new and does so in a way which democratises access.
Modeling a traffic light warning system for acute respiratory infections
Authors: Diaz-Infante Saul , Acuña-Zegarra M. Adrian , Velasco-Hernández Jorge X. 
Published: December 2022

ABSTRACTThe high morbidity of acute respiratory infections constitutes a crucial global health burden. In particular, for SARS-CoV-2, non-pharmaceutical intervention geared to enforce social distancing policies, vaccination, and treatments will remain an essential part of public health policies to mitigate and control disease outbreaks. However, the implementation of mitigation measures directed to increase social distancing when the risk of contagion is a complex enterprise because of the impact of NPI on beliefs, political views, economic issues, and, in general, public perception. The way of implementing these mitigation policies studied in this work is the so-called traffic-light monitoring system that attempts to regulate the application of measures that include restrictions on mobility and the size of meetings, among other non-pharmaceutical strategies. Balanced enforcement and relaxation of measures guided through a traffic-light system that considers public risk perception and economic costs may improve the public health benefit of the policies while reducing their cost. We derive a model for the epidemiological traffic-light policies based on the best response for trigger measures driven by the risk perception of people, instant reproduction number, and the prevalence of a hypothetical acute respiratory infection. With numerical experiments, we evaluate and identify the role of appreciation from a hypothetical controller that could opt for protocols aligned with the cost due to the burden of the underlying disease and the economic cost of implementing measures. As the world faces new acute respiratory outbreaks, our results provide a methodology to evaluate and develop traffic light policies resulting from a delicate balance between health benefits and economic implications.
A patterned human heart tube organoid model generated by pluripotent stem cell self-assembly
Authors: Volmert Brett , Riggs Ashlin , Wang Fei , Juhong Aniwat , Kiselev Artem , Kostina Aleksandra , O’Hern Colin , Muniyandi Priyadharshni , Wasserman Aaron , Huang Amanda , Lewis-Israeli Yonatan , Park Sangbum , Qiu Zhen , Zhou Chao , Aguirre Aitor 
Published: December 2022

AbstractHuman pluripotent stem cells can recapitulate significant features of mammalian organ developmentin vitro, including key aspects of heart development. We hypothesized that the organoids thus created can be made substantially more relevant by mimicking aspects ofin uterogestation, leading to higher physiological and anatomical resemblance to theirin vivocounterparts. Here, we report steps towards generating developmentally inspired maturation methodologies to differentiate early human heart organoids into patterned heart-tube-like structures in a reproducible and high-throughput fashion by complete self-organization. The maturation strategy consists of the controlled and stepwise exposure to metabolic (glucose, fatty acids) and hormonal signals (T3, IGF-1) as present during early heart development. These conditions elicit important transcriptomic, cellular, morphological, metabolomic, and functional changes over a 10-day period consistent with continuously increasing heart complexity, maturation, and patterning. Our data reveals the emergence of atrial and ventricular cardiomyocyte populations, valvular cells, epicardial cells, proepicardial-derived cells, endothelial cells, stromal cells, conductance cells, and cardiac progenitors, all of them cell types present in the primitive heart tube. Anatomically, the organoids elongate and develop well-differentiated atrial and ventricular chambers with compacted myocardial muscle walls and a proepicardial organ. For the first time in a completely self-organizing heart organoid, we show anterior-posterior patterning due to an endogenous retinoic acid gradient originating at the atrial pole, where proepicardial and atrial populations reside, mimicking the developmental process present within the primitive heart tube. Collectively, these findings highlight the ability of self-organization and developmental maturation strategies to recapitulate human heart development. Our patterned human heart tube model constitutes a powerfulin vitrotool for dissecting the role of different cell types and genes in human heart development, as well as disease modeling congenital heart defects, and represents a step forward in creating fully synthetic human hearts.
Abundant deep ocean heterotrophic bacteria are culturable
Authors: Sanz-Sáez Isabel , Sánchez Pablo , Salazar Guillem , Sunagawa Shinichi , de Vargas Colomban , Bowler Chris , Sullivan Matthew B. , Wincker Patrick , Karsenti Eric , Pedrós-Alió Carlos , Agustí Susana , Gojobori Takashi , Duarte Carlos M. , Gasol Josep M. , Sánchez Olga , Acinas Silvia G. 
Published: December 2022

ABSTRACTTraditional culture techniques usually retrieve only a small fraction of the environmental marine microbial diversity, which mainly belong to the so-called rare biosphere. However, this paradigm has not been fully tested at a broad scale, especially in the deep ocean. Here, we examined the fraction of heterotrophic bacterial communities in photic and deep ocean layers that could be recovered by culture-dependent techniques at a large scale. We compared 16S rRNA gene sequences from a collection of 2003 cultured isolates of heterotrophic marine bacteria with global 16S rRNA metabarcoding datasets (16S TAGs) covering surface, mesopelagic and bathypelagic ocean samples that included 16 of the 22 samples used for isolation. These global datasets represent 60,322 unique 16S amplicon sequence variants (ASVs). Our results reveal a significantly higher proportion of isolates identical to ASVs in deeper ocean layers reaching up to a 28% of the 16S TAGs of the bathypelagic microbial communities, which included the isolation of 3 of the top 10 most abundant 16S ASVs in the global bathypelagic ocean, related to the generaSulfitobacter, Halomonas and Erythrobacter. These cultured isolates contributed differently to the prokaryotic communities across different plankton size fractions, recruiting between 38% in the free-living size fraction (0.2-0.8 μm) and up to 45% in the largest plankton size fraction (20-200 μm) in the bathypelagic ocean. Our findings support the hypothesis that sinking particles in the bathypelagic realm act as resource-rich habitats, suitable for the growth of heterotrophic bacteria with a copiotroph lifestyle that can be cultured, and that these cultivable bacteria can also thrive as free-living bacteria.
Shark-dust: High-throughput DNA sequencing of processing residues unveils widespread trade in threatened sharks and rays
Authors: Prasetyo Andhika P. , Murray Joanna M. , Kurniawan Muh. Firdaus A. K. , Sales Naiara G. , McDevitt Allan D. , Mariani Stefano 
Published: December 2022

AbstractIllegal fishing, unregulated bycatch, and market demand for certain products (e.g. fins) are largely responsible for the rapid global decline of shark and ray populations. Controlling trade of endangered species remains difficult due to product variety, taxonomic ambiguity and trade complexity. The genetic tools traditionally used to identify traded species typically target individual tissue samples, are time-consuming and/or species-specific. Here, we performed high-throughput sequencing of trace DNA fragments retrieved from dust and scraps left behind by trade activities. We metabarcoded ‘shark-dust’ samples from seven processing plants in the world’s biggest shark landing site (Java, Indonesia), and identified 54 shark and ray taxa (representing half of all chondrichthyan orders), half of which could not be recovered from tissue samples collected in parallel from the same sites. Importantly, over 80% of shark-dust sequences were found to belong to CITES-listed species. We argue that this approach is likely to become a powerful and cost-effective monitoring tool wherever wildlife is traded.One-Sentence SummaryShark-dust, the traces of biological material left behind from the processing of shark products, can now be DNA-sequenced in bulk to accurately reconstruct the biodiversity underlying trade.
Transformer-based tool recommendation system in Galaxy
Authors: Kumar Anup , Grüning Björn , Backofen Rolf 
Published: December 2022

AbstractGalaxy is a web-based open-source platform for scientific analyses. Researchers use thousands of high-quality tools and workflows for their respective analyses. Tool recommender system predicts a collection of tools that can be used to extend an analysis. In this work, a tool recommender system is developed by training a Transformer-based neural network on workflows available on Galaxy Europe. Compared to the existing tool recommender system on Galaxy Europe that trains a recurrent neural network, the transformer-based neural network achieves two times faster convergence, has a four times lower model usage (model loading + prediction) time and shows a better generalisation that goes beyond training workflows. The scripts to create the recommendation model are available under MIT licence athttps://github.com/anuprulez/galaxy_tool_recommendation_transformers.
Biochemical activity is the default DNA state in eukaryotes
Authors: Luthra Ishika , Chen Xinyi E. , Jensen Cassandra , Rafi Abdul Muntakim , Salaudeen Asfar Lathif , de Boer Carl G. 
Published: December 2022

AbstractGenomes encode for genes and the regulatory signals that enable those genes to be transcribed, and are continually shaped by evolution. Genomes, including those of human and yeast, encode for numerous regulatory elements and transcripts that have limited evidence of conservation or function. Here, we sought to create a genomic null hypothesis by quantifying the gene regulatory activity of evolutionarily naïve DNA, using RNA-seq of evolutionarily distant DNA expressed in yeast and computational predictions of random DNA activity in human cells and tissues. In yeast, we found that >99% of bases in naïve DNA expressed as part of one or more transcripts. Naïve transcripts are sometimes spliced, and are similar to evolved transcripts in length and expression distribution, indicating that stable expression and/or splicing are insufficient to indicate adaptation. However, naïve transcripts do not achieve the extreme high expression levels as achieved by evolved genes, and frequently overlap with antisense transcription, suggesting that selection has shaped the yeast transcriptome to achieve high expression and coherent gene structures. In humans, we found that, while random DNA is predicted to have minimal activity, dinucleotide content-matched randomized DNA is predicted to have much of the regulatory activity of evolved sequences, including active chromatin marks at between half (DNase I and H3K4me3) and 1/16th (H3K27ac and H3K4me1) the rate of evolved DNA, and the repression-associated H3K27me3 at about twice the rate of evolved DNA. Naïve human DNA is predicted to be more cell type-specific than evolved DNA and is predicted to generate co-occurring chromatin marks, indicating that these are not reliable indicators of selection. However, extreme high activity is rarely achieved by naïve DNA, consistent with these arising via selection. Our results indicate that evolving regulatory activity from naïve DNA is comparatively easy in both yeast and humans, and we expect to see many biochemically active and cell type-specific DNA sequences in the absence of selection. Such naïve biochemically active sequences have the potential to evolve a function or, if sufficiently detrimental, selection may act to repress them.
SnapFISH: a computational pipeline to identify chromatin loops from multiplexed DNA FISH data
Authors: Lee Lindsay , Yu Hongyu , Jia Bojing Blair , Jussila Adam , Zhu Chenxu , Chen Jiawen , Xie Liangqi , Hafner Antonina , Strambio-De-Castillia Caterina , Boettiger Alistair , Ren Bing , Li Yun , Hu Ming 
Published: December 2022

AbstractMultiplexed DNA fluorescence in situ hybridization (FISH) imaging technologies have been developed to map the folding of chromatin fibers at tens of nanometer and tens of kilobase resolution in single cells. However, computational methods to reliably identify chromatin loops from such imaging datasets are still lacking. Here we present a Single-Nucleus Analysis Pipeline for multiplexed DNA FISH (SnapFISH), to process the multiplexed DNA FISH data and identify chromatin loops. SnapFISH can identify known chromatin loops from mouse embryonic stem cells with high sensitivity and accuracy. In addition, SnapFISH obtained comparable results of chromatin loops across datasets generated from diverse imaging technologies.
Indolent primary cutaneous B-cell lymphomas resemble persistent antigen reactions without signs of dedifferentiation
Authors: Griss Johannes , Gansberger Sabina , Oyarzun Inigo , Drach Mathias C. , Nguyen Vy , Shaw Lisa E. , Mann Ulrike , Porkert Stefanie , Farlik Matthias , Weninger Wolfgang , Dolak Werner , Aschenbrenner Bertram , Lichtenberger Beate M. , Wagner Christine , Simonitsch-Klupp Ingrid , Wagner Stephan N. , Jonak Constanze , Brunner Patrick M. 
Published: December 2022

AbstractPrimary cutaneous B-cell lymphomas comprise a heterogeneous group of extranodal non-Hodgkin lymphomas. While primary cutaneous diffuse large B-cell lymphoma leg type (pcDLBCL-LT) is highly aggressive, the two other subtypes, primary cutaneous follicle centre lymphoma (pcFCL) and primary cutaneous marginal zone lymphoma (pcMZL), usually follow an indolent course.To better understand the molecular landscape of these entities, we performed single-cell RNA sequencing of pcFCL, pcMZL, and pcDLBCL-LT skin lesions and compared them to B-cell rich lymphoid proliferation (rB-LP) lesions, gastric MALT lymphoma, nodal FCL, and nodal DLBCL.Our data show that these lymphomas can be clearly distinguished from each other on a transcriptomic level based on scRNA-seq. pcMZL, pcFCL, and rB-LP all exhibited a persistent germinal centre reaction as evidenced by the presence of required support cells and continuous somatic hypermutation within the expanded clone. By contrast, malignant clones of pcDLBCL-LT and gastric MALT lymphoma lesions lacked these features. Further, pcMZL top expanded clones were developing within lesions from naïve and not post-germinal centre B cells as currently presumed. Therefore, pcMZL may represent a non-malignant reaction against a yet to be determined antigen. Conversely, in pcFCL, B cells showed a larger amount of clonal expansion. The lack of further differentiation of these B cells may explain its indolent clinical course. In contrast to pcDLCBL-LT, our data thus indicate that pcMZL and pcFCL, similar to rB-LP are characterised by a functional germinal centre reaction likely driven by (a yet unknown) antigen recognition, which supports the classification of pcMZL as a lymphoproliferative disease.Key pointsIndolent B cell neoplasms are uniquely characterised by ongoing, antigen-driven germinal centre reactions.Primary cutaneous B cell lymphomas are distinct entities compared to their systemic counterparts.
Genomic insights intoPlasmodium vivaxpopulation structure and diversity in central Africa
Authors: Gartner Valerie , Redelings Benjamin D. , Gaither Claudia , Parr Jonathan B. , Kalonji Albert , Phanzu Fernandine , Brazeau Nicholas F. , Juliano Jonathan J. , Wray Gregory A. 
Published: December 2022

AbstractPlasmodium vivaxmalaria has not traditionally been a major concern in central Africa given the high prevalence of the human Duffy-negative phenotype that is believed to prevent infection. Increasing reports of asymptomatic and symptomatic infections in Duffy-negative individuals throughout Africa raise the possibility thatP. vivaxis evolving to evade host resistance, but there are few parasite samples with genomic data available from this part of the world. In this study, we perform whole genome sequencing of a newP. vivaxisolate from the Democratic Republic of the Congo (DRC) and assess how this central African isolate fits into the global context of this species. We use population genomics methods to show thatP. vivaxfrom DRC is similar to other African parasite populations and is not closely related to the non-human primate parasiteP. vivax-like.SignificanceThe second most common malaria species to infect humans,Plasmodium vivax, is not considered a major threat to human health in central Africa because people in this region frequently have a genetic variant that prevents theP. vivaxspecies from being able to cause illness. Recent research shows thatP. vivaxcan be found in individuals who should be immune, but there is insufficient data to understand why. Our study investigates the genome of oneP. vivaxsample collected from central Africa to show that the DRC population is closely related to otherP.vivaxpopulations in Africa.