bluuebunny/crossref_metadata_2025_split huggingface dataset:
Co-option of a seed-like proteome by oil-rich tubers
Authors: Niemeyer Philipp William , Schmitt Kerstin , Valerius Oliver , Braus Gerhard H. , deVries Jan , Carlsson Anders Sven , Hofvander Per , Ischebeck Till 
Published: December 2020

AbstractCo-option is an important aspect of evolution that can occur on several levels. Genes, whose function was molded by selection in the evolutionary past, are readily observed to serve a new function when acting in a different context in an extant system. Whole organs can be co-opted for new roles as well. For example, roots that evolved from shoot-like axes. Finally a framework of genes and its coded proteins can be co-opted to serve a similar molecular function but in a completely different organ, drastically changing its properties. Here, we describe such an example, where a set of proteins important for desiccation tolerance and oil accumulation in seeds of most angiosperms was co-opted in the tubers of yellow nutsedge (Cyperus esculentus). These tubers are not only desiccation tolerant but also store a large amount of lipids—especially TAG, similar to seeds. We generated nanoLC-MS/MS-based proteomes in five replicates of four stages of tuber development and compared them to the proteomes of roots and leaves, yielding 2257 distinct protein groups. Our data reveal a striking upregulation of hallmark proteins of seeds in the tubers. A deeper comparison to a previously published proteome of Arabidopsis seeds and seedlings indicate that indeed a seed-like proteome was co-opted. This was further supported by an analysis of the proteome of a lipid-droplet enriched fraction of yellow nutsedge, which also displayed seed-like characteristics.
Comparison of sparse biclustering algorithms for gene expression datasets
Authors: Nicholls Kath , Wallace Chris 
Published: December 2020

AbstractGene clustering and sample clustering are commonly used to find patterns in gene expression datasets. However, in heterogeneous samples (e.g. different tissues or disease states), genes may cluster differently. Biclustering algorithms aim to solve this issue by performing sample clustering and gene clustering simultaneously. Existing reviews of biclustering algorithms have yet to include a number of more recent algorithms and have based comparisons on simplistic simulated datasets without specific evaluation of biclusters in real datasets, using less robust metrics.In this study we compared four classes of sparse biclustering algorithms on a range of simulated and real datasets. In particular we use a knockout mouse RNA-seq dataset to evaluate each algorithm’s ability to simultaneously cluster genes and cluster samples across multiple tissues. We found that Bayesian algorithms with strict sparsity constraints had high accuracy on the simulated datasets and didn’t require any post-processing, but were considerably slower than other algorithm classes. We assessed whether non-negative matrix factorisation algorithms can be repurposed for biclustering and found that, although the raw output was poor, after using a sparsity-inducing post-processing procedure we introduce, one such algorithm was one of the most highly ranked on real datasets. We also exhibit the limitations of biclustering algorithms by varying the complexity of simulated datasets. The algorithms generally struggled on simulated datasets with a large number of implanted factors, or with a large number of genes. In real datasets, the algorithms rarely returned clusters containing samples from multiple tissues, which highlights the need for further thought in the design and analysis of multi-tissue studies to avoid differences between tissues dominating the analysis.Code to run the analysis is available athttps://github.com/nichollskc/biclust_comp, including wrappers for each algorithm, implementations of evaluation metrics, and code to simulate datasets and perform pre- and post-processing. The full tables of results are available athttps://doi.org/10.5281/zenodo.4317556
Activity Budget and Postural Behaviours in Orangutans on Bukit Merah Orang Utan Island for Assessing Captive Great Ape Welfare
Authors: Kamaluddin Siti Norsyuhada , Matsuda Ikki , Md-Zain Badrul Munir 
Published: December 2020

ABSTRACTAssessments of the welfare status of captive and semi-captive animals often compare how their expression of natural behaviours differs from that of free-ranging conspecifics. Bukit Merah Orang Utan Island (BMOUI) is the only orangutan rehabilitation and conservation centre in the Malay Peninsula. We recorded and analyzed the activity budget and postural behaviours of orangutans moving freely in the enclosures on BMOUI to evaluate their welfare status. From December 2015 to December 2016, we observed three individuals: an adult male, an adult female and a subadult male, and collected 252 hours of focal data (84 hr/individual). The orangutans’ activity budget was dominated by resting (60%), feeding (13%), playing (14%) and moving (9%). The study individuals heavily relied on the artificial foods (79.2%), and they spent majority of their time on the ground (85.1%) with occasional arboreal observations like using the wooden tree platform or a rope. Despite some significant individual differences, behavioural categories followed a similar trend: resting > feeding > moving > playing, except that the subadult male spent significantly more time playing (35%) than the two adults (3–4%). The most predominant posture was sitting (47.0%), followed by pronograde standing (29.4%), lying (10.5%) and clinging (4.5%). Our results suggest that orangutans on BMOUI engage in less feeding but more resting, and show less postural diversity, than free-ranging individuals. We propose that appropriate interventions to shift activity budgets, especially feeding vs. resting, and postural behaviours of captive orangutans towards those found in free-ranging orangutans might be beneficial for their welfare and survival; however, the conclusions we can draw are limited due to the small sample size, and thus until the captive behaviours of a larger number of orang-utans has been described, these results must be considered preliminary and just a case study.
The rapid, massive growth of COVID-19 authors in the scientific literature
Authors: Ioannidis John P.A. , Salholz-Hillel Maia , Boyack Kevin W. , Baas Jeroen 
Published: December 2020

ABSTRACTWe examined the extent to which the scientific workforce in different fields was engaged in publishing COVID-19-related papers. According to Scopus (data cut, August 1, 2021), 210,183 COVID-19-related publications included 720,801 unique authors, of which 360,005 authors had published at least 5 full papers in their career and 23,520 authors were at the top 2% of their scientific subfield based on a career-long composite citation indicator. The growth of COVID-19 authors was far more rapid and massive compared with cohorts of authors historically publishing on H1N1, Zika, Ebola, HIV/AIDS and tuberculosis. All 174 scientific subfields had some specialists who had published on COVID-19. In 109 of the 174 subfields of science, at least one in ten active, influential (top-2% composite citation indicator) authors in the subfield had authored something on COVID-19. 52 hyper-prolific authors had already at least 60 (and up to 227) COVID-19 publications each. Among the 300 authors with the highest composite citation indicator for their COVID-19 publications, most common countries were USA (n=67), China (n=52), UK (n=32), and Italy (n=18). The rapid and massive involvement of the scientific workforce in COVID-19-related work is unprecedented and creates opportunities and challenges. There is evidence for hyper-prolific productivity.
The role of anatomical connection strength for interareal communication in macaque cortex
Authors: Vezoli Julien , Vinck Martin , Bosman Conrado Arturo , Bastos André Moraes , Lewis Christopher Murphy , Kennedy Henry , Fries Pascal 
Published: December 2020

SUMMARYWhat is the relationship between anatomical connection strength and rhythmic synchronization? Simultaneous recordings of 15 cortical areas in two macaque monkeys show that interareal networks are functionally organized in spatially distinct modules with specific synchronization frequencies, i.e. frequency-specific functional connectomes. We relate the functional interactions between 91 area pairs to their anatomical connection strength defined in a separate cohort of twenty six subjects. This reveals that anatomical connection strength predicts rhythmic synchronization and vice-versa, in a manner that is specific for frequency bands and for the feedforward versus feedback direction, even if interareal distances are taken into account. These results further our understanding of structure-function relationships in large-scale networks covering different modality-specific brain regions and provide strong constraints on mechanistic models of brain function. Because this approach can be adapted to non-invasive techniques, it promises to open new perspectives on the functional organization of the human brain.
A low-autofluorescence, transparent resin for multiphoton 3D printing
Authors: Flamourakis George , Kordas Antonis , Barmparis Georgios D. , Ranella Anthi , Farsari Maria 
Published: December 2020

AbstractMultiphoton lithography allows the high resolution, free-form 3D printing of structures such as micro-optical elements and 3D scaffolds for Tissue Engineering. A major obstacle in its application in these fields is material and structure autofluorescence. Existing photoresists promise near zero fluorescent in expense of poor mechanical properties, and low printing efficiency. Sudan Black B is a molecular quencher used as a dye for biological studies and as means of decreasing the autofluorescence of polymers. In our study we report the use of Sudan Black B as both a photoinitiator and as a post-fabrication treatment step, using the zirconium silicate SZ2080™ for the development of a non-fluorescent composite. We use this material for the 3D printing of micro-optical elements, and meso-scale scaffolds for Mesenchymal Stem Cell cultures. Our results show the hybrid, made photosensitive with Sudan Black B, can be used for the fabrication of high resolution, highly transparent, autofluorescence-free microstructures.
Choice of assemblers has a critical impact on de novo assembly of SARS-CoV-2 genome and characterizing variants
Authors: Islam Rashedul , Raju Rajan Saha , Tasnim Nazia , Shihab Md. Istiak Hossain , Bhuiyan Maruf Ahmed , Araf Yusha , Islam Tofazzal 
Published: December 2020

AbstractBackgroundCoronavirus Disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a global pandemic following its initial emergence in China. Using next-generation sequencing technologies, a large number of SARS-CoV-2 genomes are being sequenced at an unprecedented rate and being deposited in public repositories. For the de novo assembly of the SARS-CoV-2 genomes, a myriad of assemblers is being used, although their impact on the assembly quality has not been characterized for this virus. In this study, we aim to understand the variabilities on assembly qualities due to the choice of the assemblers.ResultsWe performed 6,648de novoassemblies of 416 SARS-CoV-2 samples using 8 different assemblers with different k-mers. We used Illumina paired-end sequencing reads and compared the genome assembly quality to that of different assemblers. We showed the choice of assemblers plays a significant role in reconstructing the SARS-CoV-2 genome. Two metagenomic assemblers e.g. MEGAHIT and metaSPAdes performed better compared to others in most of the assembly quality metrics including, recovery of a larger fraction of the genome, constructing larger contigs and higher N50, NA50 values etc. We showed that at least 09% (259/2,873) of the variants present in the assemblies between MEGAHIT and metaSPAdes are unique to the assembly methods.ConclusionOur analyses indicate the critical role of assembly methods for assembling SARS-CoV-2 genome using short reads and their impact on variant characterization. This study could help guide future studies to determine which assembler is best suited for the de novo assembly of virus genomes.
Python Interfaces for the Smoldyn Simulator
Authors: Singh Dilawar , Andrews Steven S. 
Published: December 2020

AbstractMotivationSmoldyn is a particle-based biochemical simulator that is frequently used for systems biology and biophysics research. Previously, users could only define models using text-based input or a C/C++applicaton programming interface (API), which were convenient, but limited extensibility.ResultsWe added a Python API to Smoldyn to improve integration with other software tools such as Jupyter notebooks, other Python code libraries, and other simulators. It includes low-level functions that closely mimic the existing C/C++API and higher-level functions that are more convenient to use. These latter functions follow modern object-oriented Python conventions.AvailabilitySmoldyn is open source and free, available athttp://www.smoldyn.org, and can be installed with the Python package managerpip. It runs on Mac, Windows, and Linux.Contactsteven.s.andrews@gmail.comSupplementary informationDocumentation is available athttp://www.smoldyn.org/SmoldynManual.pdfandhttps://smoldyn.readthedocs.io/en/latest/python/api.html.
Putative Pseudolysogeny-Dependent Phage Gene Implicated in the Superinfection Resistance ofCutibacterium acnes
Authors: Wottrich Stephanie , Mendonca Stacee , Safarpour Cameron , Nguyen Christine , Marinelli Laura J. , Modlin Robert L. , Parker Jordan Moberg 
Published: December 2020

AbstractBackgroundBacteriophage therapy is a promising option to minimize the risk of treatment-associated antibiotic resistance inCutibacterium acnes. A novel phage (Aquarius) was isolated and analyzed to explore characteristics ofC. acnesphages that may confer lysis-evasion properties.Materials and MethodsPhage superinfection resistance assays were performed with a range ofC. acnesphages, which were assayed for pseudolysogeny via phage release assays and episome PCR. Bioinformatics and qRT-PCR were used to identify candidate genes related to observed phenotypes.ResultsAssay findings indicated that infectedC. acnesstrains were broadly resistant to superinfection and were capable of forming stable pseudolysogens. A conserved Ltp family-like gene contained protein signatures which may be contributing to phage-mediated superinfection resistance in a pseudolysogeny-dependent manner.ConclusionsC. acnesbacteria are capable of harboring phage pseudolysogens, and this phenomenon may result in superinfection resistance, necessitating consideration in targeting optimization ofC. acnesphage-based therapy.
Identification of inhibitors of SARS-CoV-2 3CL-Pro enzymatic activity using a small molecule in-vitro repurposing screen
Authors: Kuzikov Maria , Costanzi Elisa , Reinshagen Jeanette , Esposito Francesca , Vangeel Laura , Wolf Markus , Ellinger Bernhard , Claussen Carsten , Geisslinger Gerd , Corona Angela , Iaconis Daniela , Talarico Carmine , Manelfi Candida , Cannalire Rolando , Rossetti Giulia , Gossen Jonas , Albani Simone , Musiani Francesco , Herzog Katja , Ye Yang , Giabbai Barbara , Demitri Nicola , Jochmans Dirk , De Jonghe Steven , Rymenants Jasper , Summa Vincenzo , Tramontano Enzo , Beccari Andrea R. , Leyssen Pieter , Storici Paola , Neyts Johan , Gribbon Philip , Zaliani Andrea 
Published: December 2020

AbstractCompound repurposing is an important strategy for the identification of effective treatment options against SARS-CoV-2 infection and COVID-19 disease. In this regard, SARS-CoV-2 main protease (3CL-Pro), also termed M-Pro, is an attractive drug target as it plays a central role in viral replication by processing the viral polyproteins pp1a and pp1ab at multiple distinct cleavage sites. We here report the results of a repurposing program involving 8.7 K compounds containing marketed drugs, clinical and preclinical candidates, and small molecules regarded as safe in humans. We confirmed previously reported inhibitors of 3CL-Pro, and have identified 62 additional compounds with IC50 values below 1 μM and profiled their selectivity towards Chymotrypsin and 3CL-Pro from the MERS virus. A subset of 8 inhibitors showed anti-cytopathic effect in a Vero-E6 cell line and the compounds thioguanosine and MG-132 were analysed for their predicted binding characteristics to SARS-CoV-2 3CL-Pro. The X-ray crystal structure of the complex of myricetin and SARS-Cov-2 3CL-Pro was solved at a resolution of 1.77 Å, showing that myricetin is covalently bound to the catalytic Cys145 and therefore inhibiting its enzymatic activity.Graphical abstractAbstract Figure.Workflow for identification and profiling of inhibitors of SARS-CoV-2 3CL-Pro using a large scale repurposing and bioactive compound collection (rhs). Primary assay principle based on quenched FRET peptide substrate of SARS-CoV-2 3CL-Pro (lhs). Inhibiting compounds reduce fluorescence signal relative to DMSO controls. Hit profiling using X-ray.
Sex-specific body mass ageing trajectories in adult Asian elephants
Authors: Lalande Lucas D. , Lummaa Virpi , Aung Htoo H. , Htut Win , Nyein U. Kyaw , Berger Vérane , Briga Michael 
Published: December 2020

AbstractIn species with marked sexual dimorphism and where one sex undergoes stronger intrasexual competition, that sex is expected to age earlier or quicker. Here, we utilise a unique, longitudinal dataset of a semi-captive population of Asian elephants (Elephas maximus), a species with marked male-biased intrasexual competition, with males being larger and living shorter, and test the hypothesis that males show earlier and/or faster body mass ageing than females. We show sex-specific body mass ageing trajectories: adult males gained weight up to the age of 48 years old, followed by a decrease in body mass until natural death. In contrast, adult females gained body mass with age until a body mass decline in the last year of life. Our study shows that sex-specific life-histories shape ageing patterns, consistent with the predictions of the classical theory of ageing.
Shape Morphing Technique Can Accurately Predict Pelvic Bone Landmarks
Authors: Kuchař Michal , Henyš Petr , Rejtar Pavel , Hájek Petr 
Published: December 2020

AbstractDiffeomorphic shape registration allows for the seamless geometric alignment of shapes. In this study, we demonstrated the use of a registration algorithm to automatically seed anthropological landmarks on the CT images of the pelvis. We found a high correlation between manually and automatically seeded landmarks. The registration algorithm makes it possible to achieve a high degree of automation with the potential to reduce operator errors in the seeding of anthropological landmarks. The results of this study represent a promising step forward in effectively defining the anthropological measures of the human skeleton.HighlightsThe clinical CT scan is a feasible alternative to skeletal collections and body donor programs.Pelvic morphology is complex, sexually dimorphic and is proven to being a good demonstration model for the performance analysis of registration algorithm for automatic landmark seeding.The landmark seeding using registration algorithm can save time and effort in anthropological analysis.
Motor planning brings human primary somatosensory cortex into action-specific preparatory states
Authors: Ariani Giacomo , Pruszynski J. Andrew , Diedrichsen Jörn 
Published: December 2020

AbstractMotor planning plays a critical role in producing fast and accurate movement. Yet, the neural processes that occur in human primary motor and somatosensory cortex during planning, and how they relate to those during movement execution, remain poorly understood. Here we used 7T functional magnetic resonance imaging (fMRI) and a delayed movement paradigm to study single finger movement planning and execution. The inclusion of no-go trials and variable delays allowed us to separate what are typically overlapping planning and execution brain responses. Although our univariate results show widespread deactivation during finger planning, multivariate pattern analysis revealed finger-specific activity patterns in contralateral primary somatosensory cortex (S1), which predicted the planned finger action. Surprisingly, these activity patterns were as informative as those found in contralateral primary motor cortex (M1). Control analyses ruled out the possibility that the detected information was an artifact of subthreshold movements during the preparatory delay. Furthermore, we observed that finger-specific activity patterns during planning were highly correlated to those during execution. These findings reveal that motor planning activates the specific S1 and M1 circuits that are engaged during the execution of a finger press, while activity in both regions is overall suppressed. We propose that preparatory states in S1 may improve movement control through changes in sensory processing or via direct influence of spinal motor neurons.Significance statementMotor planning is important for good behavioral performance, yet it is unclear which neural processes underlie the preparation of the nervous system for an upcoming movement. Using high-resolution functional neuroimaging, we investigated how motor planning for finger presses changes the activity state in primary motor and primary somatosensory cortex, and how brain responses during planning and execution relate to each other. We show that planning leads to finger-specific activation in both M1 and S1, which is highly similar to the finger-specific activity patterns elicited during execution. Our findings suggest that S1 is being specifically prepared for an upcoming action, either to actively contribute to the outflowing motor command or to enable action-specific sensory gating.