bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mesoscale simulation of biomembranes with FreeDTS
Authors: Pezeshkian Weria , Ipsen John H. 
Published: January 2024

AbstractWe present FreeDTS software for performing computational research on biomembranes at the mesoscale. In this software, a membrane is represented by a dynamically triangulated surface equipped with vertex-based inclusions to integrate the effects of integral and peripheral membrane proteins. Several algorithms are included in the software to simulate complex membranes at different conditions such as framed membranes with constant tension, vesicles and high-genus membranes with various fixed volumes or constant pressure differences and applying external forces to membrane regions. Furthermore, the software allows the user to turn off the shape evolution of the membrane and focus solely on the organization of proteins. As a result, we can take realistic membrane shapes obtained from, for example, cryo-electron tomography and backmap them into a finer simulation model. In addition to many biomembrane applications, this software brings us a step closer to simulating realistic biomembranes with molecular resolution. Here we provide several interesting showcases of the power of the software but leave a wide range of potential applications for interested users.
HHV-6B detection and host gene expression implicate HHV-6B as pulmonary pathogen after hematopoietic cell transplant
Authors: Hill Joshua A. , Lee Yeon Joo , Vande Vusse Lisa K. , Xie Hu , Chung E. Lisa , Waghmare Alpana , Cheng Guang-Shing , Zhu Haiying , Huang Meei-Li , Hill Geoffrey R. , Jerome Keith R. , Leisenring Wendy M. , Zerr Danielle M. , Gharib Sina A. , Dadwal Sanjeet , Boeckh Michael 
Published: January 2024

AbstractLimited understanding of the immunopathogenesis of human herpesvirus 6B (HHV-6B) has prevented its acceptance as a pulmonary pathogen after hematopoietic cell transplant (HCT). In this prospective multicenter study of patients undergoing bronchoalveolar lavage (BAL) for pneumonia after allogeneic HCT, we test blood and BAL fluid (BALF) for HHV-6B DNA and mRNA transcripts associated with lytic infection and perform RNA-seq on paired blood. Among 116 participants, HHV-6B DNA is detected in 37% of BALs, 49% of which also have HHV-6B mRNA detection. We establish HHV-6B DNA viral load thresholds in BALF that are highly predictive of HHV-6B mRNA detection and associated with increased risk for overall mortality and death from respiratory failure. Participants with HHV-6B DNA in BALF exhibit distinct host gene expression signatures, notable for enriched interferon signaling pathways in participants clinically diagnosed with idiopathic pneumonia. These data implicate HHV-6B as a pulmonary pathogen after allogeneic HCT.
Optimizing drug combination and mechanism analysis based on risk pathway crosstalk in pan cancer
Authors: Hu Congxue , Mi Wanqi , Li Feng , Zhu Lun , Ou Qi , Li Maohao , Li Tengyue , Ma Yuheng , Zhang Yunpeng , Xu Yingqi 
Published: January 2024

AbstractCombination therapy can greatly improve the efficacy of cancer treatment, so identifying the most effective drug combination and interaction can accelerate the development of combination therapy. Here we developed a computational network biological approach to identify the effective drug which inhibition risk pathway crosstalk of cancer, and then filtrated and optimized the drug combination for cancer treatment. We integrated high-throughput data concerning pan-cancer and drugs to construct miRNA-mediated crosstalk networks among cancer pathways and further construct networks for therapeutic drug. Screening by drug combination method, we obtained 687 optimized drug combinations of 83 first-line anticancer drugs in pan-cancer. Next, we analyzed drug combination mechanism, and confirmed that the targets of cancer-specific crosstalk network in drug combination were closely related to cancer prognosis by survival analysis. Finally, we save all the results to a webpage for query (http://bio-bigdata.hrbmu.edu.cn/oDrugCP/). In conclusion, our study provided an effective method for screening precise drug combinations for various cancer treatments, which may have important scientific significance and clinical application value for tumor treatment.
Multi-cohort shotgun metagenomic analysis of oral and gut microbiota overlap in healthy adults
Authors: Rashidi Armin , Gem Hakan , McLean Jeffrey S. , Kerns Kristopher , Dean David R. , Dey Neelendu , Minot Samuel 
Published: January 2024

AbstractThe multitude of barriers between the mouth and colon may eliminate swallowed oral bacteria. Ascertaining the presence of the same bacteria in the mouth and colon is methodologically challenging partly because 16S rRNA gene sequencing – the most commonly used method to characterize the human microbiota – has low confidence in taxonomic assignments deeper than genus for most bacteria. As different species of the same genus can have low-level variation across the same 16S rRNA gene region, shotgun sequencing is needed to identify a true overlap. We analyzed a curated, multi-cohort, shotgun metagenomic database with species-level taxonomy and clade-specific marker genes to fill this knowledge gap. Using 500 paired fecal/oral (4 oral sites) samples from 4 healthy adult cohorts, we found a minute overlap between the two niches. Comparing marker genes between paired oral and fecal samples with species-level overlap, the pattern of overlap in only 7 individuals was consistent with same-strain colonization. These findings argue against ectopic colonization of oral bacteria in the distal gut in healthy adults.
National-scale remotely sensed lake trophic state from 1984 through 2020
Authors: Meyer Michael F. , Topp Simon N. , King Tyler V. , Ladwig Robert , Pilla Rachel M. , Dugan Hilary A. , Eggleston Jack R. , Hampton Stephanie E. , Leech Dina M. , Oleksy Isabella A. , Ross Jesse C. , Ross Matthew R. V. , Woolway R. Iestyn , Yang Xiao , Brousil Matthew R. , Fickas Kate C. , Padowski Julie C. , Pollard Amina I. , Ren Jianning , Zwart Jacob A. 
Published: January 2024

AbstractLake trophic state is a key ecosystem property that integrates a lake’s physical, chemical, and biological processes. Despite the importance of trophic state as a gauge of lake water quality, standardized and machine-readable observations are uncommon. Remote sensing presents an opportunity to detect and analyze lake trophic state with reproducible, robust methods across time and space. We used Landsat surface reflectance data to create the first compendium of annual lake trophic state for 55,662 lakes of at least 10 ha in area throughout the contiguous United States from 1984 through 2020. The dataset was constructed with FAIR data principles (Findable, Accessible, Interoperable, and Reproducible) in mind, where data are publicly available, relational keys from parent datasets are retained, and all data wrangling and modeling routines are scripted for future reuse. Together, this resource offers critical data to address basic and applied research questions about lake water quality at a suite of spatial and temporal scales.
Genesis of ectosymbiotic features based on commensalistic syntrophy
Authors: Krishnan Nandakishor , Csiszár Villő , Móri Tamás F. , Garay József 
Published: January 2024

AbstractThe symbiogenetic origin of eukaryotes with mitochondria is considered a major evolutionary transition. The initial interactions and conditions of symbiosis, along with the phylogenetic affinity of the host, are widely debated. Here, we focus on a possible evolutionary path toward an association of individuals of two species based on unidirectional syntrophy. With the backing of a theoretical model, we hypothesize that the first step in the evolution of such symbiosis could be the appearance of a linking structure on the symbiont’s membrane, using which it forms an ectocommensalism with its host. We consider a commensalistic model based on the syntrophy hypothesis in the framework of coevolutionary dynamics and mutant invasion into a monomorphic resident system (evolutionary substitution). We investigate the ecological and evolutionary stability of the consortium (or symbiotic merger), with vertical transmissions playing a crucial role. The impact of the ‘effectiveness of vertical transmission’ on the dynamics is also analyzed. We find that the transmission of symbionts and the additional costs incurred by the mutant determine the conditions of fixation of the consortia. Additionally, we observe that small and highly metabolically active symbionts are likely to form the consortia.
An analysis of national media coverage of a parental leave reform investigating sentiment, semantics and contributors
Authors: Vermillet Arnault-Quentin , Krejberg Sara Engsig , Nielsen Julie Svinth , Parsons Christine E. 
Published: January 2024

AbstractWhile paid leave for fathers after the birth of a child has become increasingly available, mothers still take most of the parental leave. A recent European Union (EU) reform addresses the unequal sharing of leave between parents via earmarking of paid, non-shareable leave to each parent. Given that the reform’s success will depend on uptake by families, we analysed Danish national media coverage to understand how journalists were writing about the reform. We assessed the sentiment and semantics of leave reform coverage compared to general news from the same period, also considering the inferred journalist gender and newspaper political orientation. Parental leave reform articles were slightly more emotional than general news, independent of who authored the article, or the newspaper where it was published. We found a robust difference in the semantics of how female journalists wrote about the reform, relative to male journalists, and that female journalists contributed to media coverage at a higher-than-expected rate. The tendency for media coverage to be written with a non-neutral sentiment can be understood in terms of the enduring political tensions over gender equality, the role of the EU and families’ rights to self-organization. That female journalists over-contributed to media coverage is interesting in understanding topic assignments or interest in parental leave.
Physical, mechanical, and microstructural characterisation of tungsten carbide-based polymeric composites for radiation shielding application
Authors: Abualroos Nadin Jamal , Idris Mohd Idzat , Ibrahim Haidi , Kamaruzaman Muhammad Izzat , Zainon Rafidah 
Published: January 2024

AbstractPolymeric based composites have gained considerable attention as potential candidates for advanced radiation shielding applications due to their unique combination of high-density, radiation attenuation properties and improved mechanical strength. This study focuses on the comprehensive characterisation of polymeric based composites for radiation shielding applications. The objective of this study was to evaluate the physical, mechanical and microstructural properties of tungsten carbide-based epoxy resin and tungsten carbide cobalt-based epoxy resin for its efficiency in shielding against gamma-rays ranging from 0.6 up to 1.33 MeV. Polymeric composites with different weight percentages of epoxy resin (40 wt%, 35 wt%, 30 wt%, 25 wt%, 20 wt%, 15 wt% and 10 wt%) were fabricated, investigated and compared to conventional lead shield. The attenuation of the composites was performed using NaI (Tl) gamma-ray spectrometer to investigate the linear and mass attenuation coefficients, half value layer, and mean free path. High filler loadings into epoxy resin matrix (90% filler/10% epoxy) exhibited excellent gamma shielding properties. Mechanical properties, such as hardness were examined to assess the structural integrity and durability of the composites under various conditions. The fabricated composites showed a good resistance, the maximum hardness was attributed to composites with small thickness. The high loading of fillers in the epoxy matrix improved the microhardness of the composites. The distribution of the filler powder within the epoxy matrix was investigated using FESEM/EDX. The results revealed the successful incorporation of tungsten carbide and cobalt particles into the polymer matrix, leading to increased composite density and enhanced radiation attenuation. The unique combination of high-density, radiation attenuation, and improved mechanical properties positions polymeric based composites as promising candidates for radiation protection field.
Novel species of Triatoma (Hemiptera: Reduviidae) identified in a case of vectorial transmission of Chagas disease in northern Belize
Authors: Gunter Sarah M. , Nelson Alisa , Kneubehl Alexander R. , Justi Silvia A. , Manzanero Russell , Zielinski-Gutierrez Emily , Herrera Claudia , Thompson Julie , Mandage Rajendra , Desale Hans , Maliga Adrianna , Bautista Kim , Ronca Shannon E. , Morey Francis , Fuentes Rafael Chacon , Lopez Beatriz , Dumonteil Eric , Morazan Gerhaldine H. , Murray Kristy O. 
Published: January 2024

AbstractChagas disease is a leading cause of non-ischemic cardiomyopathy in endemic regions of Central and South America. In Belize, Triatoma dimidiata sensu lato has been identified as the predominate taxon but vectorial transmission of Chagas disease is considered to be rare in the country. We recently identified an acute case of vector-borne Chagas disease in the northern region of Belize. Here we present a subsequent investigation of triatomines collected around the case-patient’s home. We identified yet undescribed species, closely related to Triatoma huehuetenanguensis vector by molecular systematics methods occurring in the peridomestic environment. The identification of a T. cruzi-positive, novel species of Triatoma in Belize indicates an increased risk of transmission to humans in the region and warrants expanded surveillance and further investigation.
Dynamics of technology emergence in innovation networks
Authors: Ho Martin , Price Henry C. W. , Evans Tim S. , O’Sullivan Eoin 
Published: January 2024

AbstractTo create the next innovative product, participants in science need to understand which existing technologies can be combined, what new science must be discovered, and what new technologies must be invented. Knowledge of these often arrives by means of expert consensus or popularity metrics, masking key information on how intellectual efforts accumulate into technological progress. To address this shortcoming, we first present a method to establish a mathematical link between technological evolution and complex networks: a path of events that narrates innovation bottlenecks. Next, we quantify the position and proximity of documents to these innovation paths. The result is an innovation network that more exhaustively captures deterministic knowledge flows with respect to a marketed innovative product. Our dataset, containing over three million biomedical citations, demonstrates the possibility of quantifying the accumulation, speed, and division of labour in innovation over a sixty-year time horizon. The significance of this study includes the (i) use of a purpose-generated dataset showing causal paths from research to development to product; (ii) analysis of the innovation process as a directed acyclic graph; (iii) comparison between calendar time and network time; (iv) ordering of science funders along technology lifecycles; (v) quantification of innovative activities’ importance to an innovative outcome; and (vi) integration of publication, patent, clinical trial, regulatory data to study innovation holistically.
Transcriptional profile of ribosome-associated quality control components and their associated phenotypes in mammalian cells
Authors: Dos Santos Otávio Augusto Leitão , Carneiro Rodolfo L. , Requião Rodrigo D. , Ribeiro-Alves Marcelo , Domitrovic Tatiana , Palhano Fernando L. 
Published: January 2024

AbstractDuring protein synthesis, organisms detect translation defects that induce ribosome stalling and result in protein aggregation. The Ribosome-associated Quality Control (RQC) complex, comprising TCF25, LTN1, and NEMF, is responsible for identifying incomplete protein products from unproductive translation events, targeting them for degradation. Although RQC disruption causes adverse effects on vertebrate neurons, data regarding mRNA/protein expression and regulation across tissues are lacking. Employing high-throughput methods, we analyzed public datasets to explore RQC gene expression and phenotypes. Our findings revealed widespread expression of RQC components in human tissues; however, silencing of RQC yielded only mild negative effects on cell growth. Notably, TCF25 exhibited elevated mRNA levels that were not reflected in the protein content. We experimentally demonstrated that this disparity arose from post-translational protein degradation by the proteasome. Additionally, we observed that cellular aging marginally influenced RQC expression, leading to reduced mRNA levels in specific tissues. Our results suggest the necessity of RQC expression in all mammalian tissues. Nevertheless, when RQC falters, alternative mechanisms seem to compensate, ensuring cell survival under nonstress conditions.
High quality of SARS-CoV-2 molecular diagnostics in a diverse laboratory landscape through supported benchmark testing and External Quality Assessment
Authors: Sluimer John , van den Akker Willem M. R. , Goderski Gabriel , Swart Arno , van der Veer Bas , Cremer Jeroen , Chung Ngoc Hoa , Molenkamp Richard , Voermans Jolanda , Guldemeester Judith ,   Working Group SARS-CoV-2 Diagnostics The Netherlands, van der Eijk Annemiek , de Jong Menno D. , Mithoe Glen , Hermans Mirjam H. A. , de Beer Jessica L. , Wessels Els , von Wintersdorff Christian , Pas Suzan , Verweij Jaco J. , Melchers Willem J. G. , van de Bovenkamp Jeroen H. B. , Vahidnia Ali , Gard Lilli , Schuurman Rob , Wintermans Bas , Leversteijn-van Hall Maurine , Smits Paul , de Groot Theun , Deiman Birgit A. L. M. , Bart Aldert , van der Reijden Wil , Svraka-Latifovic Sanela , van der Zanden Adri G. M. , Thijsen Steven , Schubbert Rainer , Dreesens Lisa L. , van Duijn Gert , Ong David S. Y. , Oostra Monique , Bruisten Sylvia , van Trijp Marijke , Pettersson Annika , van Burgel Nathalie D. , Oudbier Joke , van der Linden Michael , van Rijn Michiel , Bos Martine P. , Rossen John , Schuurs Theo A. , Grosser Roger , Smit Pieter , Nijhuis Roel H. T. , Rozemeijer Wouter , van de Laar Thijs , Scheepers Theodoor M. M. , Smeets Leonard C. , Flipse Jacky , de Leeuw Bertie , Dijkman Remco , van Maarseveen Noortje , Koppelman Marco , Postma Bent , van Hannen Erik J. , Thai Khoa , Braun Kathrin , Schepers Raf J. F. , Henning Jana , van Hees Eva R. , Tacken Mirriam G. J. , Mol Jaqueline , Heddema Edou R. , Eggink Dirk , Presser Lance D. , Meijer Adam 
Published: January 2024

AbstractA two-step strategy combining assisted benchmark testing (entry controls) and External Quality Assessments (EQAs) with blinded simulated clinical specimens to enhance and maintain the quality of nucleic acid amplification testing was developed. This strategy was successfully applied to 71 diagnostic laboratories in The Netherlands when upscaling the national diagnostic capacity during the SARS-CoV-2 pandemic. The availability of benchmark testing in combination with advice for improvement substantially enhanced the quality of the laboratory testing procedures for SARS-CoV-2 detection. The three subsequent EQA rounds demonstrated high quality testing with regard to specificity (99.6% correctly identified) and sensitivity (93.3% correctly identified). Even with the implementation of novel assays, changing workflows using diverse equipment and a high degree of assay heterogeneity, the overall high quality was maintained using this two-step strategy. We show that in contrast to the limited value of Cq value for absolute proxies of viral load, these Cq values can, in combination with metadata on strategies and techniques, provide valuable information for laboratories to improve their procedures. In conclusion, our two-step strategy (preparation phase followed by a series of EQAs) is a rapid and flexible system capable of scaling, improving, and maintaining high quality diagnostics even in a rapidly evolving (e.g. pandemic) situation.
Immunoinformatics-guided approach for designing a pan-proteome multi-epitope subunit vaccine against African swine fever virus
Authors: Simbulan Alea Maurice , Banico Edward C. , Sira Ella Mae Joy S. , Odchimar Nyzar Mabeth O. , Orosco Fredmoore L. 
Published: January 2024

AbstractDespite being identified over a hundred years ago, there is still no commercially available vaccine for the highly contagious and deadly African swine fever virus (ASFV). This study used immunoinformatics for the rapid and inexpensive designing of a safe and effective multi-epitope subunit vaccine for ASFV. A total of 18,858 proteins from 100 well-annotated ASFV proteomes were screened using various computational tools to identify potential epitopes, or peptides capable of triggering an immune response in swine. Proteins from genotypes I and II were prioritized for their involvement in the recent global ASFV outbreaks. The screened epitopes exhibited promising qualities that positioned them as effective components of the ASFV vaccine. They demonstrated antigenicity, immunogenicity, and cytokine-inducing properties indicating their ability to induce potent immune responses. They have strong binding affinities to multiple swine allele receptors suggesting a high likelihood of yielding more amplified responses. Moreover, they were non-allergenic and non-toxic, a crucial prerequisite for ensuring safety and minimizing any potential adverse effects when the vaccine is processed within the host. Integrated with an immunogenic 50S ribosomal protein adjuvant and linkers, the epitopes formed a 364-amino acid multi-epitope subunit vaccine. The ASFV vaccine construct exhibited notable immunogenicity in immune simulation and molecular docking analyses, and stable profiles in secondary and tertiary structure assessments. Moreover, this study designed an optimized codon for efficient translation of the ASFV vaccine construct into the Escherichia coli K-12 expression system using the pET28a(+) vector. Overall, both sequence and structural evaluations suggested the potential of the ASFV vaccine construct as a candidate for controlling and eradicating outbreaks caused by the pathogen.
Multivalent next generation influenza virus vaccines protect against seasonal and pre-pandemic viruses
Authors: Uno Naoko , Ross Ted M. 
Published: January 2024

AbstractEach year, new influenza virus vaccine formulations are generated to keep up with continuously circulating and mutating viral variants. A next-generation influenza virus vaccine would provide long-lasting, broadly-reactive immune protection against current and future influenza virus strains for both seasonal and pre-pandemic viruses. Next generation immunogens were designed using computationally optimized broadly reactive antigen (COBRA) methodology to protect against a broad range of strains over numerous seasons. Novel HA and NA amino acid sequences were derived from multilayered consensus sequence alignment for multiple subtypes of influenza. This multivalent formulation was hypothesized to elicit broadly protective immune responses against both seasonal and pre-pandemic influenza viruses. Mice were vaccinated with multivalent mixtures of HA and NA (H1, H2, H3, H5, H7, N1, N2) proteins. Multivalent COBRA vaccinations elicited antibodies that recognized a broad panel of strains and vaccinated mice were protected against viruses representing multiple subtypes. This is a promising candidate for a universal influenza vaccine that elicits protective immune responses against seasonal and pre-pandemic strains over multiple seasons.