bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nanojunctions: Specificity of Ca2+signalling requires nano-scale architecture of intracellular membrane contact sites
Authors: Fameli Nicola , van Breemen Cornelis , Groschner Klaus 
Published: February 2023

AbstractSpecificity of control over virtually all essential cellular functions by Ca2+is based on the existence of separated, autonomic signaling modules. Spatiotemporal definition of Ca2+signals involves the assembly of signaling complexes within the nano-architecture of contact sites between the sarco/endoplasmic (SR/ER) reticulum and the plasma membrane (PM). While the requirement of precise spatial assembly and positioning of the junctional signaling elements is well documented, the role of the nano-scale membrane architecture itself, as an ion reflecting confinement of the signaling unit, remains as yet elusive. Utilizing the NCX1/SERCA2-mediated ER Ca2+refilling process as a junctional signalling paradigm, we provide here the first evidence for an indispensable cellular function of the junctional membrane architecture. Our stochastic modeling approach demonstrates that junctional ER Ca2+refilling operates exclusively at nano-scale membrane spacing, with a strong inverse relationship between junctional width and signaling efficiency. Our model predicts a breakdown of junctional Ca2+signaling with loss of reflecting membrane confinement, irrespective of the spatial positioning of the molecular signaling elements. Alterations in the molecular and nano-scale membrane organization at organelle-PM contacts are suggested as new concept in pathophysiology.
Substrate evaporation drives collective construction in termites
Authors: Facchini G. , Rathery A. , Douady S. , Sillam-Dussès D. , Perna A. 
Published: February 2023

AbstractTermites build complex nests which are an impressive example of self-organization. We know that the coordinated actions involved in the construction of these nests by multiple individuals are primarily mediated by signals and cues embedded in the structure of the nest itself. However, to date there is still no scientific consensus about the nature of the stimuli that guide termite construction, and how they are sensed by termites. In order to address these questions, we studied the early building behavior ofCoptotermes gestroitermites in artificial arenas, decorated with topographic cues to stimulate construction. Pellet collections were evenly distributed across the experimental setup, compatible with a collection mechanism that is not affected by local topography, but only by the distribution of termite occupancy (termites pick pellets at the positions where they are). Conversely, pellet depositions were concentrated at locations of high surface curvature and at the boundaries between different types of substrate. The single feature shared by all pellet deposition regions was that they correspond to local maxima in the evaporation flux. We can show analytically and we confirm experimentally that evaporation flux is directly proportional to the local curvature of nest surfaces. Taken together, our results indicate that surface curvature is sufficient to organize termite building activity, and that termites likely sense curvature indirectly through substrate evaporation. Our findings reconcile the apparently discordant results of previous studies.
Design and Validation of an Open Loop Controlled Positive-Displacement Pump for Vascular Flow Modelling
Authors: O’Brien Thomas 
Published: February 2023

ABSTRACTRealistic vascular flow-rates are highly patient dependent. There is a need, when evaluating vascular medical devices, to study variable physiological flow-rates corresponding to specific patients. This study presents an experimental analysis of a positive-displacement piston pump designed for generating patient-specific vascular flow-rate wave-forms. Open loop control is used to drive a positive-displacement piston pump according to user-input physiological wave-forms. Transient and frequency analyses are performed for simple and complex inputs. Theoretical analysis of the system shows that it may be modelled as a linear first order system and the response of the system for various inputs shows that the real system approximates a linear first order response, however, higher order effects are noted. These higher order effects do not have any particular detrimental effect on the generation of physiologically realistic flow-rate waveforms.
Proliferating cell nuclear antigen involves in temperature stress tolerance ofUlva prolifera
Authors: He Hongyan , Yang Juanjuan , He Yuan , Li Zhiyong , Fu Caiwei , Zhang Dongren , Li Mengru , Lu Aiming , Dong Jingwei , Liu Jiasi , Gu Huiyue , Shen Songdong 
Published: February 2023

AbstractUlva proliferais the dominant species of “green tide”, and has higher tolerance to environmental stresses such as temperature. However, the molecular mechanisms are still unclear. Here, transcriptome analysis, Western blot and RT-qPCR analysis ofU. proliferasuggested that, under temperature stresses (4°C, 36°C), the expression ofPCNAandCyclinAwas promoted, and the MAPK signaling was activated. Besides, the results showed that PCNA interacted with CyclinA. Interestingly, the expression ofmiR-2916, which was predicted to bind PCNA at -552∼-772, was negatively correlated with the expression ofPCNAunder temperature stresses (4°C, 36°C). In addition, the results showed that low temperature (4°C) had no obvious effect on the survival, the formation of cell walls, and the division of protoplasts. However, high temperature (36°C) had obvious effect on them. PCNA inhibitors increased the sensitivity of the protoplasts under temperature stresses. Together, our results suggested PCNA regulating the proliferation in response to the temperature stress ofU. proliferawas associated with miR-2916/PCNA/CyclinA/MAPK pathway. In conclusion, the study preliminarily illuminates the molecular mechanism in response to temperature stress ofU. prolifera, and may provide a new insight for prevention of green tide.
NTpred: A robust and precise machine learning framework for in-silico identification of Tyrosine nitration sites in protein sequences
Authors: Datta Sourajyoti , Asim Muhammad Nabeel , Dengel Andreas , Ahmed Sheraz 
Published: February 2023

AbstractPost-translational modifications (PTMs) either enhance a protein’s activity in various sub-cellular processes, or degrade their activity which leads towards failure of intracellular processes. Tyrosine nitration (NT) modification degrades protein’s activity that initiate and propagate various diseases including Neurodegenerative, Cardiovascular, Autoimmune diseases, and Carcinogenesis. Identification of NT modification support development of novel therapies and drug discoveries for associated diseases. Identification of NT modification in biochemical labs is expensive, time consuming, and error-prone. To supplement this process, several computational approaches have been proposed. However these approaches remain fail to precisely identify NT modification, due to the extraction of irrelevant, redundant and less discriminative features from protein sequences. The paper in hand presents NTpred framework competent in extracting comprehensive features from raw protein sequences using four different sequence encoders. To reap the benefits of different encoders, it generates four additional feature spaces by fusing different combinations of individual encodings. Furthermore, it eradicates irrelevant and redundant features from eight different feature spaces through a Recursive Feature Elimination process. Selected features of four individual encodings and four feature fusion vectors are used to train eight different Gradient Boosted Tree classifiers. The probability scores from the trained classifiers are utilized to generate a new probabilistic feature space, that is utilized to train a Logistic Regression classifier. On BD1 benchmark dataset, the proposed framework outperform existing best performing predictor in 5-fold cross validation and independent test evaluation with combined improvement of 13.7% in MCC and 20.1% in AUC. Similarly, on BD2 benchmark dataset, the proposed framework outperform existing best performing predictor with combined improvement of 5.3% in MCC and 1.0% in AUC.
Respiratory virus concentrations in human excretions that contribute to wastewater: A systematic review
Authors: Lowry Sarah A. , Wolfe Marlene K. , Boehm Alexandria B. 
Published: February 2023

AbstractConcentrations of nucleic acids from a range of respiratory viruses including human influenza A and B, respiratory syncytial virus (RSV), metapneumovirus, parainfluenza virus, rhinovirus, and seasonal coronaviruses in wastewater solids collected from wastewater treatment plants correlate to clinical data on disease occurrence in the community contributing to the wastewater. Viral nucleic acids enter wastewater from various excretions including stool, urine, mucus, sputum, and saliva deposited in toilets or other drains in buildings. In order to relate the measured concentrations in wastewater at a treatment plant to actual number of infections in a community, concentrations of the viral nucleic acids in these human excretions are needed as inputs to a mass balance model. In this study, we carried out a systematic review and meta-analysis to characterize the concentrations and presence of influenza A and B, respiratory syncytial virus (RSV), metapneumovirus, parainfluenza virus, rhinovirus, and seasonal coronaviruses in stool, urine, mucus, sputum, and saliva. The systematic review protocol can be accessed athttps://doi.org/10.17605/OSF.IO/ESVYC. We identified 220 data sets from 50 unique articles that met inclusion criteria and reported information on viral concentrations and presence in these excretions. Data were unevenly distributed across virus type (with the most available for influenza) and excretion type (with the most available for respiratory excretions). The majority of data sets only reported the presence or absence of the virus in an excretion in a cross-sectional study design. There is a need for more concentration data, including longitudinal data, across all respiratory virus and excretion types. Such data would allow quantitatively linking virus wastewater concentrations to numbers of infected individuals.
Crane fly semiochemical overrules plant control over cyanobiont inAzollasymbioses
Authors: Güngör Erbil , Savary Jérôme , Adema Kelvin , Dijkhuizen Laura W. , Keilwagen Jens , Himmelbach Axel , Mascher Martin , Koppers Nils , Bräutigam Andrea , Hove Charles van , Riant Olivier , Nierzwicki-Bauer Sandra , Schluepmann Henriette 
Published: February 2023

AbstractSemiochemicals from insects that restrict plant symbiont dinitrogen fixation had not been known. Here we report on a the glycosylated triketide δ-lactone only found inNephrotoma cornicinacrane flies, cornicinine, that causes chlorosis in the floating-fern symbioses from the genusAzolla.Cornicinine was chemically synthesized, as well as its aglycone and diastereoisomer. Only the glycosylated trans-A form was active: 500 nM cornicinine in the growth medium turned the dinitrogen-fixing cyanobacterial filaments fromNostoc azollaeinside the host leaf cavities into akinete-like cells. Cornicinine further inhibited akinete germination inAzollasporelings, precluding re-establishment of the symbiosis during sexual reproduction. It did not affect the plantArabidopsis thalianaor several free-living cyanobacteria from the generaAnabaenaorNostoc. Chlorosis occurred in hosts on nitrogen with and devoid of cyanobiont. Cornicinine, therefore, targeted host mechanisms resulting in coordinate cyanobiont differentiation.Sequence profiling of messenger RNA from isolated leaf cavities confirmed high NH4-assimilation and proanthocyanidin biosynthesis in this trichome-rich tissue. Leaf-cavity transcripts in ferns grown on cornicinine reflected activation of Cullin-RING ubiquitin-ligase pathways, known to mediate metabolite signaling and plant elicitation consistent with the chlorosis phenotype. Transcripts accumulating when akinetes are induced, in leaf cavities of ferns on cornicinine and in megasporocarps, were consistent with increased JA-oxidase, sulfate transport and exosome formation.The work begins to uncover molecular mechanisms of cyanobiont differentiation in a seed-free plant symbiosis important for wetland ecology or circular crop-production today, that once caused massive CO2draw-down during the Eocene geological past.SignificanceCoordinated differentiation of host and filamentous cyanobacteria underlies the development of ecologically important symbioses; this includes the floating fernsAzollawhich share their wetland habitat withNephrotoma cornicinacraneflies containing the glycosylated triketide δ-lactone semiochemical, cornicinine. Cornicinine overrules cyanobiont differentiation thus inhibiting symbiosis N2-fixation and sexual reproduction; its mode of action resembles plant elicitation as suggested by transcriptional profiling of cells lining the cyanobiont cavities using a new release of the fern host genome.
Updating TCGA glioma classification through integration of molecular profiling data following the 2016 and 2021 WHO guidelines
Authors: de Mendonça Mónica Leiria , Coletti Roberta , Gonçalves Céline S. , Martins Eduarda P. , Costa Bruno M. , Vinga Susana , Lopes Marta B. 
Published: February 2023

AbstractThe understanding of glioma disease has been evolving drastically with dedicated research into the genetic and molecular profiling of glioma tumour tissue. Molecular biomarkers have gained progressive and substantial importance in providing diagnostic information, leading to groundbreaking changes in the tumour classification system, criteria and taxonomy standardised by the 2016 and 2021 editions of the World Health Organization Classification of Tumours of the Central Nervous System’s guidelines (WHO-2016 and WHO-2021, respectively). Some of the insights into glioma disease derived from extensive research on open-source multi-omics databases, such as the Cancer Genome Atlas (TCGA). However, given the substantial changes in glioma classification, retrospective databases may harbour outdated diagnostic annotations, suboptimal for further research. Here we propose two methods for updating the tumour classification of TCGA glioma samples in accordance with WHO-2016 and WHO-2021 guidelines, through the integration of curated molecular profiling information. Our methods allowed for the diagnostic update of 98% and 87% of evaluated TCGA glioma cases according to WHO-2016 and -2021, respectively, and highlighted changes in patient-specific diagnosis across both guidelines’ editions. Our reclassification pipelines are provided in R scripts, facilitating direct reproduction or tailoring upon new releases of WHO guidelines.
Structural basis of bifunctional CTP/dCTP synthase
Authors: Guo Chen-Jun , Zhang Zherong , Zhong Jiale , Liu Ji-Long 
Published: February 2023

AbstractNucleotides are important molecules of life. According to the sugar, nucleotides can be divided into nucleotides and deoxynucleotides, which are the basic components of RNA and DNA respectively. CTP synthase (CTPS) catalyzes the last step in the de novo synthesis of CTP, which can form cytoophidia in cells from all three domains of life. We have recently found that CTPS combines with NTPs to form filaments, and solved the structures of CTPS bound with NTPs. Previous biochemical studies have shown that CTPS can also serve as dCTPS, i.e. CTPS/dCTPS can not only bind UTP, ATP and GTP to generate CTP, but also bind deoxynucleotides to generate dCTP. However, the structural basis of the bifunctional enzyme CTPS/dCTPS binding deoxynucleotide is not clear. In this study, we find that CTPS/dCTPS can form filaments bound with deoxynucleotides. Biochemically, we compare the binding and reaction characteristics of the corresponding nucleotides/deoxynucleotides and CTPS/dCTPS. Using cryo-electron microscopy, we solve the the structure of CTPS/dCTPS bound with deoxynucleotides at near-atomic resolution. This study not only provides a structural basis for understanding the catalysis and regulation of bifunctional CTPS/dCTPS, but also opens a door for further exploration the compartmentation of CTPS/dCTPS inside a cell.
S1000: A better taxonomic name corpus for biomedical information extraction
Authors: Luoma Jouni , Nastou Katerina , Ohta Tomoko , Toivonen Harttu , Pafilis Evangelos , Jensen Lars Juhl , Pyysalo Sampo 
Published: February 2023

AbstractMotivationThe recognition of mentions of species names in text is a critically important task for biomedical text mining. While deep learning-based methods have made great advances in many named entity recognition tasks, results for species name recognition remain poor. We hypothesize that this is primarily due to the lack of appropriate corpora.ResultsWe introduce the S1000 corpus, a comprehensive manual re-annotation and extension of the S800 corpus. We demonstrate that S1000 makes highly accurate recognition of species names possible (F-score=93.1%), both for deep learning and dictionary-based methods.AvailabilityAll resources introduced in this study are available under open licenses fromhttps://jensenlab.org/resources/s1000/. The webpage contains links to a Zenodo project and two GitHub repositories associated with the study.Contactsampo.pyysalo@utu.fi,lars.juhl.jensen@cpr.ku.dkSupplementary informationSupplementary data are available atBioinformaticsonline.
Tracing cancer evolution and heterogeneity using Hi-C
Authors: Erdmann-Pham Dan Daniel , Batra Sanjit Singh , Turkalo Timothy K. , Durbin James , Blanchette Marco , Yeh Iwei , Shain Hunter , Bastian Boris C. , Song Yun S. , Rokhsar Daniel S. , Hockemeyer Dirk 
Published: February 2023

ABSTRACTChromosomal rearrangements can initiate and drive cancer progression, yet it has been challenging to evaluate their impact, especially in genetically heterogeneous solid cancers. To address this problem we developed HiDENSEC, a new computational framework for analyzing chromatin conformation capture in heterogeneous samples, which can infer somatic copy number alterations, characterize large-scale chromosomal rearrangements, and estimate cancer cell fractions. We validated HiDENSEC within silicoandin vitrocontrols, and then characterized chromosome-scale evolution during melanoma progression in formalin-fixed tumor samples from three patients. The resulting comprehensive annotation of the genomic events includes copy number neutral translocations that disrupt tumor suppressor genes such as NF1, whole chromosome arm exchanges that result in loss of CDKN2A, and whole-arm copy-number neutral loss of homozygosity involving PTEN. These findings show that large-scale chromosomal rearrangements occur throughout cancer evolution and characterizing these events yields insights into drivers of melanoma progression.
Crosstalk between Rac and Rho GTPase activity mediated by Arhgef11 and Arhgef12 coordinates cell protrusion-retraction cycles
Authors: Nanda Suchet , Calderon Abram , Duong Thanh-Thuy , Koch Johannes , Sachan Arya , Xin Xiaoyi , Solouk Djamschid , Wu Yao-Wen , Nalbant Perihan , Dehmelt Leif 
Published: February 2023

AbstractRho GTPase crosstalk is thought to play a key role in the spatio-temporal coordination of cytoskeletal dynamics during cell migration. Here, we directly investigated crosstalk between the major Rho GTPases Rho, Rac and Cdc42 by combining acute activity perturbation with activity measurements in individual, mammalian cells. As expected for their proposed mutual inhibition, we confirmed that Rho inhibits Rac activity. However, surprisingly, we found that Rac strongly stimulates Rho activity. We hypothesized that this crosstalk might play a role in mediating the tight spatio-temporal coupling between cell protrusions and retractions that are typically observed during mesenchymal cell migration. Using new, improved activity sensors for endogenous Rho GTPases, we find that Rac activation is tightly and precisely coupled to local cell protrusions, followed by Rho activation during retraction. In a screen for potential crosstalk mediators, we find that a subset of the Rho activating Lbc-type GEFs, in particular Arhgef11 and Arhgef12, are enriched at transient cell protrusions and retractions. Furthermore, via an optogenetic approach, we show that these Lbc GEFs are recruited to the plasma membrane by active Rac, suggesting that they might link cell protrusion and retraction by mediating Rac/Rho activity crosstalk. Indeed, depletion of these GEFs impaired cell protrusion-retraction dynamics, which was accompanied by a decrease in migration distance and an increase in migration directionality. Thus, our study shows that Arhgef11 and Arhgef12 facilitate effective exploratory cell migration by coordinating the central cell morphogenic processes of cell protrusion and retraction by coupling the activity of the associated small GTPases Rac and Rho.
STRategy: A support system for collecting and analyzing short tandem repeats for forensic science
Authors: Kulthammanit Nuttachai , Sukawutthiya Poonyapat , Noh Hasnee , Vongpaisarnsin Kornkiat , Wichadakul Duangdao 
Published: February 2023

AbstractShort tandem repeats (STRs) are short repeated sequences commonly found in the human genome. They provide many advantages to forensic sciences, such as identifying individuals, estimating the likelihood of kinship, and analyzing mixtures. Next-generation sequencing (NGS) technologies, e.g., ForenSeq Signature Prep, have been proposed for sequencing STRs, obtaining the sequence of each locus and SNPs, and inferring length-based alleles. However, even though the sequenced STRs from ForenSeq offer more insights into the STRs, which lead to the genetic analysis of population and sub-population structures, no open-source software platform enables the collection and management of STR data from NGS and incorporates related analysis tools in one place.Here, we introduce STRategy, a standalone web-based application supporting essential STR data management and analysis capabilities. The analyzed data will be visualized in various forms, for example, charts, maps, and pattern alignments. The system implemented a role-based access control that allows users to search or access specific data depending on their responsibilities. It enables public users to search for data. In addition, they can view statistical data, for example, detailed alleles and genetic variation. Lab users can add, update, and see the information of individuals and explore pattern alignments for a specific locus within the population. Administrators can customize the system, for example, configure maps according to the samples’ geographic data, and manage reference STR repeat motifs.We designed and developed the STRategy using software engineering principles for flexible extension and easy deployment utilizing the Docker container. The source code is publicly available athttps://github.com/cucpbioinfo/STRategy. Also, we deployed a showcase system on a cloud computing service where its URL is included on the GitHub repository. The current version only supports the ForenSeq sample detail report files.