bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phylogeography and reassortment patterns of human influenza A viruses in sub-Saharan Africa
Authors: Owuor D. Collins , de Laurent Zaydah R. , Oketch John W. , Murunga Nickson , Otieno James R. , Chaves Sandra S. , Nokes D. James , Agoti Charles N. 
Published: January 2024

AbstractBackgroundThe role of sub-Saharan Africa in the global spread of influenza viruses remains unclear due to insufficient spatiotemporal sequence data.MethodsHere, we analyzed 222 codon-complete sequences of influenza A viruses (IAVs) sampled between 2011 and 2013 from five countries across sub-Saharan Africa (Kenya, Zambia, Mali, Gambia, and South Africa); these genomes were compared with 1,209 contemporaneous global genomes using phylogeographical approaches.ResultsThe spread of influenza in sub-Saharan Africa was characterized by (i) multiple introductions of IAVs into the region over consecutive influenza seasons, with viral importations originating from multiple global geographical regions, some of which persisted in circulation as intra-subtype reassortants for multiple seasons, (ii) virus transfer between sub-Saharan African countries, and (iii) virus export from sub-Saharan Africa to other geographical regions.ConclusionDespite sparse data from influenza surveillance in sub-Saharan Africa, our findings support the notion that influenza viruses persist as temporally structured migrating metapopulations in which new virus strains can emerge in any geographical region, including in sub-Saharan Africa; these lineages may have been capable of dissemination to other continents through a globally migrating virus population. Further knowledge of the viral lineages that circulate within understudied sub-Saharan Africa regions is required to inform vaccination strategies in those regions.
A revised mathematical model of pre-diagnostic glioma growth incorporating vascularization and tumor mutational burden
Authors: Jain Rishab K. 
Published: January 2024

AbstractGliomas, a type of brain tumor, have become increasingly important in oncology as they are difficult to treat due to their location deep in the brain. While some research has been done on spatiotemporal prediction of future glioma growth—something that can aid in surgical resections of gliomas once a patient has been diagnosed—modeling efforts for pre-diagnostic gliomas remain limited. The lack of retrospective, pre-diagnostic data makes this a challenging task; yet, pre-symptomatic serum glucose levels in patients have been shown to have a relationship with the emergence of gliomas, motivating this area of research. In 2015, Sturrock et al. presented an ordinary differential equation model of pre-diagnostic glioma growth that describes glioma-glucose-immune interactions. This report reproduces the major findings of Sturrock et al., revising their model to incorporate more biological phenomena—namely vascularization and mutational burden—testing additional medically relevant patient scenarios, and providing an extended discussion on the implications of the model.In-silicosimulations performed in this report provide further insight into models describing glioma-glucose-immune interactions, and how they can be expanded to incorporate physiologically relevant features. Future work is necessary to refine model parameters and validate predictions with the limited, albeit steadily growing, amount of longitudinal patient data.
Changes in risk factor status and risk of future ASCVD events in primary prevention
Authors: Hwang In-Chang , Kim Chee Hae , Kim Jae-Young , Park Jiesuck , Choi Hye Jung , Choi Hong-Mi , Yoon Yeonyee E. , Cho Goo-Yeong 
Published: January 2024

AbstractPrimary cardiovascular prevention highlights the management of risk factors through lifestyle changes and therapeutic interventions. While most previous studies focused on the presence of risk factors assessed only at baseline, temporal changes in the risk factor status were not considered. We aimed to evaluate the prognostic impact of temporal changes in risk factor status in primary prevention settings. A population-based cohort of 211,077 individuals who underwent repetitive 10-year atherosclerotic cardiovascular disease (ASCVD) risk assessments over 4–5 years, was identified from National Health Insurance Services claims data of South Korea. Changes in risk-factor status for blood pressure, glycemic control, cholesterol levels, smoking status, body-mass index, and physical activity were assessed. Hazard ratios (HR) for ASCVD events after follow-up screening were calculated based on increased or decreased risk factors between baseline and follow-up. Regardless of baseline status, increased risk factors correlated with higher future ASCVD risk, while a decrease corresponded to a lower risk. Notably, individuals initially without risk factors but developing three at follow-up faced significantly higher ASCVD risk (adjusted HR 2.74, 95% CI: 1.31– 5.76). Conversely, those decreasing three risk factors from 5 or 6 exhibited almost a 50% reduction in ASCVD risk. These findings show that primary prevention effects can be reflected by changes in risk factor status, underscoring the need to monitor temporal changes in risk factors for effective primary prevention.
Modularity of the segmentation clock and morphogenesis
Authors: Hammond James E. , Baker Ruth E. , Verd Berta 
Published: January 2024

AbstractVertebrates have evolved great diversity in the number of segments dividing the trunk body, however the developmental origin of the evolvability of this trait is poorly understood. The number of segments is thought to be determined in embryogenesis as a product of morphogenesis of the pre-somitic mesoderm (PSM) and the periodicity of a molecular oscillator active within the PSM known as the segmentation clock. Here we explore whether the clock and PSM morphogenesis exhibit developmental modularity, as independent evolution of these two processes may explain the high evolvability of segment number. Using a computational model of the clock and PSM parameterised for zebrafish, we find that the clock is broadly robust to variation in morphogenetic processes such as cell ingression, motility, compaction, and cell division. We show that this robustness is in part determined by the length of the PSM and the strength of phase coupling in the clock. As previous studies report no changes to morphogenesis upon perturbing the clock, we suggest that the clock and morphogenesis of the PSM exhibit developmental modularity.
Integrated immunogenomic analyses of high-grade serous ovarian cancer reveal vulnerability to combination immunotherapy
Authors: Gronauer Raphael , Madersbacher Leonie , Monfort-Lanzas Pablo , Floriani Gabriel , Sprung Susanne , Zeimet Alain Gustave , Marth Christian , Fiegl Heidelinde , Hackl Hubert 
Published: January 2024

AbstractBackgroundHigh-grade serous ovarian cancer (HGSOC) remains the most lethal gynecologic malignancy despite new therapeutic concepts, including poly-ADP-ribose polymerase inhibitors (PARPis) and antiangiogenic therapy. The efficacy of immunotherapies is modest, but clinical trials investigating the potential of combination immunotherapy with PARPis are underway. Homologous recombination repair deficiency (HRD) or BRCAness and the composition of the tumor microenvironment appear to play a critical role in determining the therapeutic response.MethodsWe conducted comprehensive immunogenomic analyses of HGSOC using data from several patient cohorts, including a new cohort from the Medical University of Innsbruck (MUI). Machine learning methods were used to develop a classification model for BRCAness from gene expression data. Integrated analysis of bulk and single-cell RNA sequencing data was used to delineate the tumor immune microenvironment and was validated by immunohistochemistry. The impact of PARPi andBRCA1mutations on the activation of immune-related pathways was studiedin vitrousing ovarian cancer cell lines, RNA sequencing, and immunofluorescence analysis.ResultsWe identified a predictive 24-gene signature to determine BRCAness. Comprehensive analysis of the tumor microenvironment allowed us to identify patient samples with BRCAness and high immune infiltration. Further characterization of these samples revealed increased infiltration of immunosuppressive cells, including tumor-associated macrophages (TAMs) expressingTREM2,C1QA,andLILRB4,as identified by further analysis of single-cell RNA sequencing data and gene expression analysis of samples from patients receiving combination therapy with PARPi and anti-PD-1. PARPi activated the cGAS-STING signaling pathway and the downstream innate immune response in a similar manner to HGSOC patients with BRCAness status. We have developed a web application (https://ovrseq.icbi.at) and an associated R package OvRSeq, which allow for comprehensive characterization of ovarian cancer patient samples and assessment of a vulnerability score that enables stratification of patients to predict response to the mentioned combination immunotherapy.ConclusionsGenomic instability in HGSOC affects the tumor immune environment, and TAMs play a crucial role in modulating the immune response. Based on various datasets, we have developed a diagnostic application that uses RNA sequencing data not only to comprehensively characterize HGSOC but also to predict vulnerability and response to combination immunotherapy.
Active Engagement: The Impact of Group-Based Physical Activities on Resilience of Israeli Adolescents with ADHD
Authors: Tamir Yair , Novak Anne Marie , Cohen Itzhak , Adini Bruria , Lev-Ari Shahar 
Published: January 2024

AbstractBackgroundAttention Deficit Hyperactivity Disorder (ADHD) is a pressing concern in contemporary pediatric public health, with its prevalence rising among children and teenagers. This study explored the relationship between group-based physical activity and the well-being, resilience, and distress levels of Israeli youth, with a specific focus on those with ADHD.MethodsThis was a survey-based, cross-sectional study that included 699 Jewish Israeli teenagers aged 16 to 19. In addition to quantitative questionnaires that examined sociodemographic factors, resilience, distress, and well-being levels, the youth were asked about participation in group-based physical activities and the significance they ascribe to various facets of the activities.ResultsOur findings indicated that structured and group-based physical activities, especially the Five Fingers program which emphasizes psychosocial development and leadership skills, are associated with higher resilience (p<.01) and lower distress levels (p<.01) in adolescents. Generally, Israeli adolescents with ADHD exhibited lower levels of resilience (p<.001) and well-being (p<.001), and higher levels of distress (p<.001) compared to their counterparts. However, adolescents with ADHD who participated in group-based activities fared better in terms of distress (p<.01) and well-being (p=.018) than adolescents with ADHD who did not participate in organized sports. Further, participation in any form of sport activity, older age, male gender, and a higher socio-economic status predicted greater resilience in youth generally.ConclusionsThe study presents the potential of structured, engaging physical activities that involve psychosocial training and group integration activities to improve the mental health of adolescents, especially in the context of ADHD.
Evaluation of aortic valve calcification in patients with suspected cardiac amyloidosis
Authors: Ng Daniel , Moussa Karine , Allinson Francis W. , Behroozian Adam A. , Jordan Timothy M. , Puglisi Leah , Stinis Curtiss T. , Teirstein Paul S. , Mohan Rajeev C. 
Published: January 2024

AbstractBackgroundThe association between transthyretin cardiac amyloidosis (TTR-CA) and aortic stenosis (AS) has been described, although the mechanism by which they interact remains unclear. It has previously been proposed that this may be secondary to excess valvular calcification.ObjectivesWe propose that patients with suspected cardiac amyloidosis will have increased aortic valve calcification, as evidenced by elevated aortic valve calcium score on CT imaging.MethodsWe retrospectively identified patients with severe AS referred for transcatheter aortic valve implantation (TAVI) from January 2017 to November 2022. This population was divided into two cohorts; the Likely CA cohort had suspected TTR-CA by echocardiogram while the Unlikely CA cohort did not. Baseline characteristics, echocardiographic data, CT aortic valve calcium scores, and post-procedural complications were compared.ResultsOf the 496 patients analyzed, 145 (29.2%) patients met echocardiographic criteria (interventricular septal thickness (IVS) ≥1.2 cm and average mitral annular systolic s’ ≤ 6 cm/s) for the Likely CA cohort. The Likely CA cohort was more likely to be older, be male, have atrial fibrillation, and have worse renal function. On echocardiogram, the Likely CA cohort had increased hypertrophy, worsened diastolic function, and decreased systolic function. Aortic valve calcium score by CT was not significantly different between the Likely CA and Unlikely CA cohort (2834.95 AU compared to 2852.27 AU, p=0.914). There was no statistically significant difference in post-TAVI complications.ConclusionsPatients with an echocardiographic profile consistent with TTR-CA had no difference in aortic valve calcification in comparison to a population unlikely to have TTR-CA.
The SV40 virus enhancer functions as a somatic hypermutation-targeting element with potential oncogenic activity
Authors: Šenigl Filip , Soikkeli Anni , Prost Salomé , Schatz David G. , Slavková Martina , Hejnar Jiří , Alinikula Jukka 
Published: January 2024

AbstractSimian virus 40 (SV40) is a monkey virus associated with several types of human cancers. SV40 is most frequently detected in mesotheliomas, brain and bone tumors and lymphomas, but the mechanism for SV40 tumorigenesis in humans is not clear. SV40 relative Merkel cell polyomavirus (MCPyV) causes Merkel cell carcinoma (MCC) in humans by expressing truncated large tumor antigen (LT) caused by APOBEC cytidine deaminase family enzymes induced mutations. AID (activation-induced cytidine deaminase), a member of the APOBEC family, is the initiator of the antibody diversification process known as somatic hypermutation (SHM) and its aberrant expression and targeting is a frequent source of lymphomagenesis. In this study, we investigated whether AID-induced mutations could cause truncation of SV40 LT. We demonstrate that the SV40 enhancer has strong SHM targeting activity in several cell types and that AID-induced mutations accumulate to SV40 LT in B cells and kidney cells and cause truncated LT expression in B cells. Our results argue that the ability of the SV40 enhancer to target SHM to LT is a potential source of LT truncation events in various cell types that could contribute to carcinogenesis.
Cryptic genetic structure of the coral host is the primary driver of holobiont assembly in massivePorites
Authors: Scott Carly B , Schott Raegen , Matz Mikhail V 
Published: January 2024

AbstractThe fate of coral reefs in response to climate change depends on their ability to adapt to new environments. The coral animal is buffered from environmental stress by its algal endosymbionts and microbial partners (together, the “holobiont”). However, the flexibility of holobiont community assembly is not well understood, making it difficult to estimate its contribution to coral adaptation. To clarify these processes, we genetically profiled holobiont components (coral, algal symbiont, and microbiome) of massive Porites sampled across two size classes (>2m and <30cm) and ecologically distinct reef sites near Orpheus and Pelorus Islands, Australia. We recovered five major genetic clusters in the coral host, with additional splits within them potentially defining up to ten distinct subclusters. We estimated the relative contributions of the host genetic structure, site, and size class to holobiont community composition. Host genetic structure was the primary driver of both Symbiodiniaceae and microbial communities, indicating strong holobiont specificity in cryptic lineages. In addition, the microbial community was associated with reef site and size class, unlike Symbiodiniaceae that were not significantly affected by either factor. As environmentally segregated, cryptic genetic lineages emerge as a common feature of scleractinian corals, these results emphasize that failure to assess cryptic genetic structure of the coral host may lead to dramatic overestimation of holobiont flexibility.
Prevotellaare major contributors of sialidases in the human vaginal microbiome
Authors: Pelayo Paula , Hussain Fatima A. , Werlang Caroline A. , Wu Chloe , Woolston Benjamin M. , Ribbeck Katharina , Kwon Douglas S. , Balskus Emily P. 
Published: January 2024

AbstractElevated bacterial sialidase activity in the female genital tract is strongly associated with poor health outcomes including preterm birth and bacterial vaginosis. These negative effects may arise from sialidase-mediated degradation of the protective mucus layer in the cervicovaginal environment. Prior biochemical studies of vaginal bacterial sialidases have focused solely on the bacterial vaginosis-associated organismGardnerella vaginalis. Despite their implications for sexual and reproductive health, sialidases from other vaginal bacteria have not been characterized. Here, we show that vaginalPrevotellaspecies produce active sialidases that possess variable activity toward mucin. These sialidases are highly conserved across clades ofPrevotellafrom different geographies, hinting at their importance globally. Finally, we find thatPrevotellasialidases, including mucin-degrading enzymes fromPrevotella timonensis, are highly prevalent and abundant in human vaginal metagenomes and metatranscriptomes, Together, our results identifyPrevotellaas a critical source of sialidases in the vaginal microbiome, improving our understanding of this detrimental bacterial activity.Significance StatementSialidase activity in the vaginal microbiome is increased in bacterial vaginosis and strongly associated with other adverse health outcomes. Sialidase enzymes release sialic acid from host-derived glycans in the vaginal environment, altering their structures and functions. However, biochemical studies of vaginal bacterial sialidases have been limited to one genus,Gardnerella. In this work, we identify and characterize multiple active sialidase enzymes in vaginal bacteria of the genusPrevotella. We find thatPrevotellasialidases are more prevalent and abundant in vaginal microbial communities thanGardnerellasialidases. Our work highlightsPrevotellabacteria as an underappreciated source of sialidase activity with important implications for both our understanding of vaginal health and therapeutic development.
Unified description of the
Qsq¯q¯
molecular bound states, molecular resonances, and compact tetraquark states in the quark potential model
Authors: Chen Yan-Ke , Wu Wei-Lin , Meng Lu , Zhu Shi-Lin 
Published: January 2024

We calculate the mass spectrum of the Qsq¯q¯ (Q=c, b) tetraquark states with JP=(0,1,2)+ using the AL1 quark potential model, which successfully describes the conventional hadron spectrum. We employ the Gaussian expansion method to solve the four-body Schrödinger equation and use the complex scaling method to identify the resonances. With the notation TQs,I(J)Theo.(M), we find several near-threshold bound states and resonances, including Tcs,0(0)Theo.(2350), Tcs,0(0)Theo.(2906), Tbs,0(0)Theo.(5781), Tbs,0(1)Theo.(5840), and Tbs,0(0)Theo.(6240), which are close to the DK¯, D*K¯*, B¯K¯, B¯*K¯, and B¯*K¯* thresholds, respectively. Furthermore, their spatial structures clearly support their molecular natures. The resonance Tcs,0(0)Theo.(2906) with a mass of 2906 MeV, a width of 20 MeV, and quantum numbers I(JP)=0(0+) may serve as a good candidate for the experimental Tcs0(2900) state. We strongly urge the experimental search of the predicted states.

Published by the American Physical Society
2024
Correlation function for the
Tbb
state: Determination of the binding, scattering lengths, effective ranges, and molecular probabilities
Authors: Feijoo A. , Dai L. R. , Abreu L. M. , Oset E. 
Published: January 2024

We perform a study of the B*+B0,B*0B+ correlation functions using an extension of the local hidden gauge approach which provides the interaction from the exchange of light vector mesons and gives rise to a bound state of these components in I=0 with a binding energy of about 21 MeV. After that, we face the inverse problem of determining the low energy observables, scattering length and effective range for each channel, the possible existence of a bound state, and, if found, the couplings of such a state to each B*+B0,B*0B+ component as well as the molecular probabilities of each of the channels. We use the bootstrap method to determine these magnitudes and find that, with errors in the correlation function typical of present experiments, we can determine all these magnitudes with acceptable precision. In addition, the size of the source function of the experiment from where the correlation functions are measured can be also determined with a high precision.

Published by the American Physical Society
2024
Energy consumption and carbon emission of conventional and green buildings using building information modelling (BIM)
Authors: Kusi Elijah , Boateng Isaac , Danso Humphrey 
Published: January 2024

PurposeUsing building information modelling (BIM) technology, a conventional structure in this study was converted into a green building to measure its energy usage and CO2 emissions.Design/methodology/approachDigital images of the existing building conditions were captured using unmanned aerial vehicle (UAV), and were fed into Meshroom to generate the building’s geometry for 3D parametric model development. The model for the existing conventional building was created and converted to an energy model and exported to gbXML in Autodesk Revit for a whole building analysis which was carried out in the Green Building Studio (GBS). In the GBS, the conventional building was retrofitted into a green building to explore their energy consumption and CO2 emission.FindingsBy comparing the green building model to the conventional building model, the research found that the green building model saved 25% more energy while emitting 46.8% less CO2.Practical implicationsThe study concluded that green building reduces energy consumption, thereby reducing the emission of CO2 into the environment. It is recommended that buildings should be simulated at the design stage to know their energy consumption and carbon emission performance before construction.Social implicationsOccupant satisfaction, operation cost and environmental safety are essential for sustainable or green buildings. Green buildings increase the standard of living and enhance indoor air quality.Originality/valueThis investigation aided in a pool of information on how to use BIM methodology to retrofit existing conventional buildings into green buildings, showing how green buildings save the environment as compared to conventional buildings.