bluuebunny/crossref_metadata_2025_split huggingface dataset:
Homologous Pairs of Low and High Temperature Originating Proteins Spanning the Known Prokaryotic Universe
Authors: Komp Evan , Alanzi Humood , Francis Ryan , Vuong Chau , Roberts Logan , Mossallenejad Amin , Beck David A. C. 
Published: August 2023

AbstractStability of proteins at high temperature has been a topic of interest for many years, as this attribute is favourable for applications ranging from therapeutics to industrial chemical manufacturing. Our current understanding and methods for designing high-temperature stability into target proteins are inadequate. To drive innovation in this space, we have curated a large dataset, learn2thermDB, of protein-temperature examples, totalling 24 million instances, and paired proteins across temperatures based on homology, yielding 69 million protein pairs - orders of magnitude larger than the current largest. This important step of pairing allows for study of high-temperature stability in a sequence-dependent manner in the big data era. The data pipeline is parameterized and open, allowing it to be tuned by downstream users. We further show that the data contains signal for deep learning. This data offers a new doorway towards thermal stability design models.
Evolution of parent-of-origin effects on placental gene expression in house mice
Authors: Rodriguez-Caro Fernando , Moore Emily C. , Good Jeffrey M. 
Published: August 2023

AbstractThe mammalian placenta is a hotspot for the evolution of genomic imprinting, a form of gene regulation that involves the parent-specific epigenetic silencing of one allele. Imprinted genes are central to placental development and are thought to contribute to the evolution of reproductive barriers between species. However, it is unclear how rapidly imprinting evolves or how functional specialization among placental tissues influences the evolution of imprinted expression. We compared parent-of-origin expression bias across functionally distinct placental layers sampled from reciprocal crosses within three closely related lineages of mice (Mus). Using genome-wide gene expression and DNA methylation data from fetal and maternal tissues, we developed an analytical strategy to minimize pervasive bias introduced by maternal contamination of placenta samples. We corroborated imprinted expression at 42 known imprinted genes and identified five candidate imprinted genes showing parent-of-origin specific expression and DNA methylation. Paternally-biased expression was enriched in the labyrinth zone, a layer specialized in nutrient transfer, and maternally-biased genes were enriched in the junctional zone, which specializes in modulation of maternal physiology. Differentially methylated regions were predominantly determined through epigenetic modification of the maternal genome and were associated with both maternally- and paternally-biased gene expression. Lastly, comparisons between lineages revealed a small set of co-regulated genes showing rapid divergence in expression levels and imprinted status in theM. m. domesticuslineage. Together, our results reveal important links between core functional elements of placental biology and the evolution of imprinted gene expression among closely related rodent species.
Temperature and intraspecific variation affect host-parasite interactions
Authors: Ismail Sherine , Farner Johannah , Couper Lisa , Mordecai Erin , Lyberger Kelsey 
Published: August 2023

AbstractParasites play key roles in regulating aquatic ecosystems, yet the impact of climate warming on their ecology and disease transmission remains poorly understood. Isolating the effect of warming is challenging as transmission involves multiple interacting species and potential intraspecific variation in temperature responses of one or more of these species. Here, we leverage a wide-ranging mosquito species and its facultative parasite as a model system to investigate the impact of temperature on host-parasite interactions and disease transmission. We conducted a common garden experiment measuring parasite growth and infection rates at seven temperatures using 12 field-collected parasite populations and a single mosquito population. We find that both free-living growth rates and infection rates varied with temperature, which were highest at 18-24.5°C and 13°C, respectively. Further, we find intraspecific variation in peak performance temperature reflecting patterns of local thermal adaptation—parasite populations from warmer source environments typically had higher thermal optima for free-living growth rates. For infection rates, we found a significant interaction between parasite population and nonlinear effects of temperature. These findings underscore the need to consider both host and parasite thermal responses, as well as intraspecific variation in thermal responses, when predicting the impacts of climate change on disease in aquatic ecosystems.
RNA-dependent RNA polymerase of predominant human norovirus forms liquid-liquid phase condensates as viral replication factories
Authors: Kaundal Soni , Anish Ramakrishnan , Ayyar B. Vijayalakshmi , Shanker Sreejesh , Kaur Gundeep , Crawford Sue E. , Pollet Jeroen , Stossi Fabio , Estes Mary K. , Prasad B.V. Venkataram 
Published: August 2023

AbstractMany viral proteins form biomolecular condensates via liquid-liquid phase separation (LLPS) to support viral replication and evade host antiviral responses, and thus, they are potential targets for designing antivirals. In the case of non-enveloped positive-sense RNA viruses, forming such condensates for viral replication is unclear and less understood. Human noroviruses (HuNoV) are positive-sense RNA viruses that cause epidemic and sporadic gastroenteritis worldwide. Here, we show that the RNA-dependent-RNA polymerase (RdRp) of pandemic GII.4 HuNoV forms distinct condensates that exhibit all the signature properties of LLPS with sustained polymerase activity and the capability of recruiting components essential for viral replication. We show that such condensates are formed in HuNoV-infected human intestinal enteroid cultures and are the sites for genome replication. Our studies demonstrate the formation of phase separated condensates as replication factories in a positive-sense RNA virus, which plausibly is an effective mechanism to dynamically isolate RdRp replicating the genomic RNA from interfering with the ribosomal translation of the same RNA.TeaserPolymerase of a positive-sense RNA virus forms LLPS to regulate replication as an elegant solution for an enigmatic question.
Nitrate-driven anaerobic oxidation of ethane and butane by bacteria
Authors: Wu Mengxiong , Li Jie , Lai Chun-Yu , Leu Andy O , Sun Shengjie , Gu Rui , Erler Dirk V , Liu Lian , Li Lin , Tyson Gene W. , Yuan Zhiguo , McIlroy Simon J. , Guo Jianhua 
Published: August 2023

AbstractThe short-chain gaseous alkanes (ethane, propane and butane; SCGAs) are important components of natural gas, yet our understanding of their fate in environmental systems is poorly understood. Microbially mediated anaerobic oxidation of SCGAs coupled to nitrate reduction has been demonstrated for propane, but is yet to be shown for ethane or butane – despite being energetically feasible. Here we report two independent bacterial enrichments performing anaerobic ethane and butane oxidation, respectively, coupled to nitrate reduction to dinitrogen gas and ammonium. Isotopic13C-and15N-labelling experiments, mass and electron balance tests, and metabolite and meta-omics analyses collectively reveal that the recently described propane-oxidising ‘CandidatusAlkanivorans nitratireducens’ was also responsible for nitrate-dependent anaerobic oxidation of the SCGAs in both these enrichments. The complete genome of this species encodes alkylsuccinate synthase genes for the activation of ethane/butane via fumarate addition. Further substrate range tests confirm ‘Ca.A. nitratireducens’ is metabolically versatile, being able to degrade ethane, propane and butane under anaerobic conditions. Moreover, our study proves nitrate as an additional electron sink for ethane and butane in anaerobic environments, and for the first time demonstrates the use of the fumarate addition pathway in anaerobic ethane oxidation. These findings significantly contribute to our understanding of microbial metabolism of SCGAs in anaerobic environments.
A deep learning phenotyping method for genetic analysis of 3D micro-CT data
Authors: Karshenas A. , Linderoth T. , Zatha R. , Rusuwa B. , Durbin R. 
Published: August 2023

AbstractThe number of Genome-Wide Association Studies (GWAS) has been growing rapidly in recent years due to developments in genotyping and sequencing platforms. When applied to quantitative traits, these and other statistical genetics approaches require large amounts of consistently and accurately measured phenotypes. Here, we introduce a computational toolbox based on deep convolutional neural networks that we have developed to phenotype quantitative traits describing morphology from micro-CT-scan image datasets. We illustrate the use of this Deep Learning Phenotyper (DLP) on a sample set of craniofacial CT scans of 118 samples from two very closely related species of Lake Malawi cichlid fish,Maylandia zebroidesandCynotilapia zebroides. We show that the pipeline constructed and implemented here is capable of measuring morphological skeletal phenotypes with high accuracy. We also demonstrate how this pipeline can be integrated with existing GWAS frameworks to identify candidate association loci. We believe the methods we present here will be valuable for groups studying quantitative morphological traits not only in fishes, but in other vertebrates using CT scan datasets.
Mucosal antibody responses to SARS-CoV-2 booster vaccination and breakthrough infection
Authors: Bhavsar Disha , Singh Gagandeep , Sano Kaori , Gleason Charles , Srivastava Komal ,   PARIS Study Group, Carreño Juan Manuel , Simon Viviana , Krammer Florian 
Published: August 2023

AbstractCoronavirus disease 2019 (COVID-19) vaccines have saved millions of lives. However, variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have emerged causing large numbers of breakthrough infections. These developments necessitated the rollout of COVID-19 vaccine booster doses. It has been reported that mucosal antibody levels in the upper respiratory tract, especially for secretory IgA (sIgA), correlate with protection from infection with SARS-CoV-2. However, it is still unclear how high levels of mucosal antibodies can be induced. In this study, we measured serum IgG, saliva IgG and saliva sIgA responses in individuals who received COVID-19 mRNA booster vaccinations or who experienced breakthrough infections. We found that mRNA booster doses could induce robust serum and saliva IgG responses, especially in individuals who had not experienced infections before, but saliva sIgA responses were weak. In contrast, breakthrough infections in individuals who had received the primary mRNA vaccination series induced robust serum and saliva IgG as well as saliva sIgA responses. Individuals who had received a booster dose and then had a breakthrough infection showed low IgG induction in serum and saliva but still responded with robust saliva sIgA induction. These data suggest that upper respiratory tract exposure to antigen is an efficient way of inducing mucosal sIgA while exposure via intramuscular injection is not.ImportanceAntibodies on mucosal surfaces of the upper respiratory tract have been shown to be important for protection from infection with SARS-CoV-2. Here we investigate the induction of serum IgG, saliva IgG and saliva sIgA after COVID-19 mRNA booster vaccination or breakthrough infections.
txtools: an R package facilitating analysis of RNA modifications, structures, and interactions
Authors: Garcia-Campos Miguel Angel , Schwartz Schraga 
Published: August 2023

AbstractWe present txtools, an R package that enables the processing, analysis, and visualization of RNA-seq data at the nucleotide-level resolution, seamlessly integrating alignments to the genome with transcriptomic representation. txtools’ main inputs are BAM files and a transcriptome annotation, and the main output is a table, capturing mismatches, deletions, and the number of reads beginning and ending at each nucleotide in the transcriptomic space. txtools further facilitates downstream visualization and analyses. We showcase, using examples from the epitranscriptomic field, how a few calls to txtools functions can yield insightful and ready-to-publish results. txtools is of broad utility also in the context of structural mapping and RNA:protein interaction mapping. By providing a simple and intuitive framework, we believe that txtools will be a useful and convenient tool and pave the path for future discovery. txtools is available for installation from its GitHub repository athttps://github.com/AngelCampos/txtools.
RADAR-IoT: An open-source, interoperable and extensible IoT gateway framework for healthcare and beyond
Authors: Ranjan Yatharth , Chang Jiangeng , Sankesara Heet , Conde Pauline , Rashid Zulqarnain , Sun Shaoxiong , Dobson Richard , Folarin Amos 
Published: August 2023

AbstractIoT sensors offer a wide range of sensing capabilities, many of which have the potential for health or medical applications. Existing solutions for IoT in healthcare have notable limitations, such as limited I/O protocols, limited cloud platform support, and limited extensibility. Therefore, the development of an open-source Internet of Medical Things (IoMT) gateway solution that addresses these limitations and provides reliability, broad applicability, and utility would be highly desirable. Combining a wide range of sensor data streams from IoT devices with ambulatory mHealth data would open the potential for providing a detailed 360-degree view of the relationship between patient physiology, behaviour, and environment. To harness this potential, RADAR-IoT has been developed as an open-source IoT gateway framework. Its purpose is to connect multiple IoT devices at the edge, perform on-device data analysis, and integrate with cloud-based mobile health platforms such as RADAR-base, enabling real-time data processing.
Patients’ preference and time to finish injection for GnRH agonist and GnRH antagonist in Japanese prostate cancer patients
Authors: Kawahara Takashi , Uemura Hiroji 
Published: August 2023

ABSTRACTHuggins et al. introduced surgical castration for prostate cancer treatment in 1941. Currently, androgen deprivation therapy (ADT) is key in treating advanced prostate cancer, especially in elderly patients. With the development of gonadotropin-releasing hormone (GnRH) medications, ADT transitioned from surgical to medical castration. From 1985 onwards, various GnRH agonists like Leuprorelin and Goserelin acetate have been used as ADT for prostate cancer. By 2012, a GnRH antagonist, degarelix, was introduced in Japan.A study at Yokohama City University Medical Center analyzed 851 hormonal injections between August 2018 and February 2019. It assessed the duration from prescription to injection completion and the perceived physical and mental load on patients. Results showed degarelix injections took significantly longer than other treatments. Leuprorelin 22.5mg reduced hospital stays the most, largely due to its 6-month duration and kit formulation. The lengthy process for degarelix, which requires drug dilution and cooling at the injection site due to potential skin reactions, increases its administration time.Concerning patient burden, leuprorelin 22.5mg ranked the lowest, with little variance from the oral form. A limitation of this study is the administration method of leuprorelin in Japan, which differs from other countries. In summary, the 6-month leuprorelin 22.5mg regimen minimizes hospital time, while degarelix tends to cause the most discomfort for patients.
The Iberian Roma genetic variant server; population structure, susceptibility to disease and adaptive traits
Authors: Mavillard Fabiola , Pérez-Florido Javier , Ortuño Francisco M , Valladares Amador , Álvarez-Villegas Miren L , Roldán Gema , Carmona Rosario , Soriano Manuel , Susarte Santiago , Fuentes Pilar , López-López Daniel , Nuñez-Negrillo Ana María , Carvajal Alejandra , Morgado Yolanda , Arteaga Daniel , Ufano Rosa , Mir Pablo , Gamella Juan F , Dopazo Joaquín , Paradas Carmen , Cabrera-Serrano Macarena 
Published: August 2023

ABSTRACTThe Roma are the most numerous ethnic minority in Europe. The Iberian Roma arrived in the Iberian Peninsula five centuries ago and still today, they keep a strong group identity. Demographic and cultural reasons lie behind a high rate of Mendelian disease often related to founder variants. We have analysed exome data from 119 Iberian Roma individuals collected from 2018 to 2020. A database of variant frequency has been implemented (IRPVS) and made available online. We have analysed the carrier rate of founder private alleles as well as pathogenic variants present in the general population. Significant enrichment in structural variants involving gene clusters related to keratinization and epidermal growth suggest that evolutive mechanisms have developed towards climate and environmental adaptation. IRPVS can be accessed athttp://irpvs.clinbioinfosspa.es/AUTHOR SUMMARYReference data is necessary for the correct interpretation of genetic studies. Although most genetic variants are present in all populations, ancestry has an important impact in the genetic background. For that reason databases of genetic variant in populations are developed specifically for different ethnicities, being an important tool for genetic diagnosis. The Roma are the most numerous ethnic minority in Europe. In this study we have collected samples from healthy Roma individuals from Iberian descent and implemented a database of genetic variant to facilitate genetic diagnosis in this population. Analysis of structural variants that are specific to the Iberian Roma not found in other healthy population for which genetic data are available suggest evolution towards environmental adaptation.
A systematic review evaluating the effectiveness of virtual reality-based well-being interventions for stress reduction in young adults
Authors: Xu Joy , Khanotia Areej , Juni Shmuel , Ku Josephine , Sami Hana , Lin Vallen , Walterson Roberta , Payne Evelyn , Jo Helen , Rahimpoor-Marnani Parmin 
Published: August 2023

ABSTRACTBackgroundAdolescents can be especially vulnerable to various stressors as they are still in their formative years and transitioning into adulthood. Hence, it is important for them to have effective stress management strategies. This systematic review investigates current well-being interventions that are aimed at reducing stress among young adults. In particular, interventions using the medium of virtual reality are explored.MethodsThis mixed-methods systematic review follows the PRISMA-P guidelines and articles were gathered for the databases PsycInfo, PubMed, Science Direct, Web of Science, Open Grey and Edutopia. Predetermined criteria and specific keywords were used to search for the articles. Search results were screened and extracted by two independent authors. Any disagreements after reconciliation were settled by a third author. The quality and risk of bias of included studies were assessed using the GRADE Quality Assessment Tool for Quantitative Studies. Studies were analyzed qualitatively.ResultsAmong the appraised studies, the effectiveness of virtual reality-based interventions was measured in three contexts: nature, stress, and academics.ConclusionStudies using virtual reality interventions, overall, promoted a reduction in stress and an increase in well-being. The findings suggest VR may serve as an accessible and affordable medium of stress reduction for students and young adults. Larger sample sizes, and a greater number of included studies, may be required in future directions.
Microscopic and metatranscriptomic analyses revealed unique cross-domain symbiosis betweenCandidatusPatescibacteria/candidate phyla radiation (CPR) and methanogenic archaea in anaerobic ecosystems
Authors: Kuroda Kyohei , Nakajima Meri , Nakai Ryosuke , Hirakata Yuga , Kagemasa Shuka , Kubota Kengo , Noguchi Taro Q.P. , Yamamoto Kyosuke , Satoh Hisashi , Nobu Masaru K. , Narihiro Takashi 
Published: August 2023

AbstractTo verify the parasitic lifestyle ofCandidatusPatescibacteria in the enrichment cultures derived from a methanogenic bioreactor, we applied multifaceted approaches combining cultivation, microscopy, metatranscriptomic, and protein structure prediction analyses. Cultivation experiments with the addition of exogenous methanogenic archaea with acetate, amino acids, and nucleoside monophosphates and 16S rRNA gene sequencing confirmed the increase in the relative abundance ofCa. Patescibacteria and methanogens. The predominantCa. Patescibacteria wereCa. Yanofskybacteria and 32-520 lineages (to which belongs to classCa. Paceibacteria) and positive linear relationships (r2≥ 0.70) between the relative abundance ofCa. Yanofskybacteria andMethanothrix, suggesting that the tendency of the growth rate is similar to that of the host. By fluorescencein situhybridization (FISH) observations, the FISH signals ofMethanothrixandMethanospirillumcells withCa. Yanofskybacteria and with 32-520 lineages, respectively, were significantly lower than those of the methanogens withoutCa. Patescibacteria, suggesting their parasitic interaction. The TEM and SEM observations also support parasitism in that the cell walls and plugs of these methanogens associated with submicron cells were often deformed. In particular, someMethanothrix-like filamentous cells were dented where the submicron cells were attached. Metatranscriptomic and protein structure prediction analyses identified highly expressed secreted genes from the genomes ofCa. Yanofskybacteria and 32-520, and these genes contain adhesion-related domains to the host cells. Considering the results through the combination of microscopic observations, gene expression, and computational protein modeling, we propose that the interactions betweenCa. Yanofskybacteria and 32-520 belonging to classCa. Paceibacteria and methanogenic archaea are parasitism.
Sputum-spotted solid matrix designed to release diagnostic-gradeMycobacterium tuberculosisDNA demonstrate optimal biocontainment property
Authors: Goyani Krishna H. , Mukhopadhyaya Pratap N. 
Published: August 2023

AbstractBiosafety quotient of a reagent-coated cellulose matrix designed to releaseMycobacterium tuberculosis(Mtb) DNA from sputum deposited onto it, was determined. Thirty-seven sputum samples infected withMtband 5 sputum samples from healthy individuals were processed and spotted onto the TBSend cards. LiveMtbbacilli were attempted for rescue from the spotted TBSend cards by washing them in phosphate buffer under mild shaking conditions. No liveMtbbacilli could be detected by the BACTEC™ MGIT 960™ TB System from bothMtbinfected as well as non-infected, sample-spotted TBSend cards when they were washed at two different time-points,viz., 1 minute and 15 hours from the time of spotting of the cards with sputum mixed with the preprocessing “spotting” buffer. The study reiterated published finding that chaotropic agents, which is an active component of the TBSend card module, have cent per cent bactericidal properties with regard toMtb.