bluuebunny/crossref_metadata_2025_split huggingface dataset:
The scaling limit of random cubic planar graphs
Authors: Stufler Benedikt 
Published: November 2024

AbstractWe study the random cubic planar graph with an even number of vertices. We show that the Brownian map arises as Gromov–Hausdorff–Prokhorov scaling limit of as tends to infinity, after rescaling distances by for a specific constant . This is the first time a model of random graphs that are not embedded into the plane is shown to converge to the Brownian map. Our approach features a new method that allows us to relate distances on random graphs to first‐passage percolation distances on their 3‐connected core.
Core-Temperature Responses at the 3-km World Aquatics Open-Water Swimming Masters Championships in Doha 2024
Authors: Esh Chris J. , Dablainville Valentin , Dalansi Feriel , Kathuria Sayyam , Cardinale Marco 
Published: November 2024

Purpose: This study aimed to characterize core-temperature (Tc) responses of swimmers competing at the 2024 3-km World Aquatics Masters Open Water Swimming Championships. Methods: Within a cross-sectional observational study design, swimmers (n = 48 [23 male, 25 female]) ingested a telemetric Tc pill 4 hours before their race. Water temperatures were 20.9 °C (male; mean wet-bulb-globe temperature 25.9 °C) and 20.5 °C (female; mean wet-bulb-globe temperature: 25.4 °C). Linear mixed models determined differences between males and females for race-start, mean in-race, and peak Tc. Random coefficient models determined relationships between (1) sex, race time, body mass index (BMI), body-mass change or age, and Tc peak; (2) sex, race time, BMI, body-mass change or age, and Tc nadir; (3) sex, Tc peak, BMI, body-mass change or age, and race time, and (4) sex, Tc peak, BMI, body-mass change, or age and race ranking. Results: The mean in-race Tc was 37.8 °C (36.1–38.8 °C); however, there were highly variable individual Tc responses (−3.1 to +2.7 °C). One swimmer experienced mild hypothermia (Tc ≤ 35.0 °C), and 5 exceeded 39.0 °C, a risk factor for heat-related illness. There were no statistical differences between males and females for race-start, mean, and peak Tc (P ≥ .243). Higher peak Tc was associated with faster race time (P = .05), higher race rank (P = .027), and higher BMI (P = .001). Conclusions: Highly variable Tc responses (−3.1 to +2.7 °C) were observed, demonstrating that organizers of mass-participation open-water swimming events should always be prepared for, and provide facilities to treat, swimmers experiencing cold-/heat-related health incidents during competition.
Architectural dissection of adhesive bacterial cell surface appendages from a “molecular machines” viewpoint
Authors: Smith Olivia E. R. , Bharat Tanmay A. M. 
Published: November 2024

ABSTRACT

The ability of bacteria to interact with and respond to their environment is crucial to their lifestyle and survival. Bacterial cells routinely need to engage with extracellular target molecules, in locations spatially separated from their cell surface. Engagement with distant targets allows bacteria to adhere to abiotic surfaces and host cells, sense harmful or friendly molecules in their vicinity, as well as establish symbiotic interactions with neighboring cells in multicellular communities such as biofilms. Binding to extracellular molecules also facilitates transmission of information back to the originating cell, allowing the cell to respond appropriately to external stimuli, which is critical throughout the bacterial life cycle. This requirement of bacteria to bind to spatially separated targets is fulfilled by a myriad of specialized cell surface molecules, which often have an extended, filamentous arrangement. In this review, we compare and contrast such molecules from diverse bacteria, which fulfil a range of binding functions critical for the cell. Our comparison shows that even though these extended molecules have vastly different sequence, biochemical and functional characteristics, they share common architectural principles that underpin bacterial adhesion in a variety of contexts. In this light, we can consider different bacterial adhesins under one umbrella, specifically from the point of view of a modular molecular machine, with each part fulfilling a distinct architectural role. Such a treatise provides an opportunity to discover fundamental molecular principles governing surface sensing, bacterial adhesion, and biofilm formation.
Cellular NONO protein binds to the flavivirus replication complex and promotes positive-strand RNA synthesis
Authors: Yuan Honggen , Luo Yun , Zou Jiahui , Zhang Junmei , Zhang Jinhua , Cao Gang , Cao Shengbo , Chen Huanchun , Song Yunfeng 
Published: November 2024

ABSTRACT

A cellular protein, non-POU-domain-containing octamer binding protein (NONO), bound to the replication complex of Japanese encephalitis virus (JEV) by directly interacting with the viral 3’ UTR RNA and NS3 protein. These interactions were also identified in West Nile virus (WNV) and Zika virus (ZIKV). The infection of JEV or the expression of JEV NS3 protein in cells could induce relocation of NONO protein from the nucleus to the cytoplasm. In JEV-infected cells, the NS3, NS5, and viral RNA could be concurrently detected in the immunoprecipitation by the NONO-specific antibody, suggesting that NONO could integrate into the replication complex of JEV. Further results of co-immunoprecipitation assays showed that NONO protein interacted with NS3 helicase domains 1 and 2 by its two RNA recognize motifs (RRMs). The knockdown and knockout of NONO in cells could significantly reduce the replication of JEV and ZIKV but had no effect on the replication of vesicular stomatitis virus (VSV). The effect of NONO protein on JEV proliferation occurred during the replication stage, rather than the attachment and entry stages. The level of viral positive-strand RNA in NONO knockout cells was significantly reduced than that in wild-type cells at 12–48 h post-JEV infection. However, the level of negative-strand virus RNA had no difference between NONO knockout and wild-type cells at 12–24 h post-infection. In summary, our study identified a cellular protein that bound to the replication complex of flavivirus and facilitated the synthesis of positive-strand RNA.

IMPORTANCE
Over half of the world’s population is at risk of flaviviruses infection, posing a serious global health concern. To date, there are no antiviral drugs or treatments for the severe symptoms caused by the infection of flaviviruses. Some cellular proteins could participate in the replication of virus, and these cellular proteins were also ideal targets in antiviral strategy. Here, we identified cellular NONO protein was recruited by flavivirus NS3 protein to the cytoplasm, serving as a “scaffold” for viral replication complex. Our findings also revealed that NONO protein was critical for flavivirus positive-strand RNA synthesis. Specific areas where NONO interacted with flavivirus NS3 proteins and viral UTRs have also been identified. These results propose a new mechanism for cellular protein to participate in flavivirus replication and also raise a new potential anti-flavivirus strategy.
Shotgun metagenomics analysis indicates
Bradyrhizobium
spp. as the predominant genera for heavy metal resistance and bioremediation in a long-term heavy metal-contaminated ecosystem
Authors: Agashe Rohan , George Jonathan , Pathak Ashish , Fasakin Olasunkanmi , Seaman John , Chauhan Ashvini 
Published: November 2024

ABSTRACT

Ten soil cores were collected from the long-term heavy metal-contaminated Savannah River Site (SRS) and studied using shotgun metagenomics. In-line with our previous reports,
Bradyrhizobium
spp. dominated the SRS soils, and thus we recommend that SRS bioremediation studies target the
Bradyrhizobium
genus.
ITSxpress version 2: software to rapidly trim internal transcribed spacer sequences with quality scores for amplicon sequencing
Authors: Einarsson Sveinn V. , Rivers Adam R. 
Published: November 2024

ABSTRACT

The nuclear ribosomal RNA (rRNA) internal transcribed spacer (ITS) regions are commonly used to identify fungi and other eukaryotic taxa in amplicon sequencing. The highly conserved rRNA regions flanking the ITS are often trimmed before being used for taxonomic assignment. The Python software package ITSxpress rapidly trims single-end or paired-end sequences in FASTQ format for use in amplicon sequence variant clustering methods like DADA2. This new major release of ITSxpress improves the paired-end merging method, simplifies installation of the QIIME 2 ITSxpress plugin, removes major dependencies, adds use cases, and is compatible with newer compression formats. This article discusses the modifications to ITSxpress that improve the output and user experience, leading to a major version increase.

IMPORTANCE
ITSxpress is a sequence trimming method applied to internal transcribed spacer (ITS) amplicon sequences before calling amplicon sequence variants (ASVs). The ITS region is used to understand the composition of eukaryotic microbial communities. ITS sequences provide good taxonomic resolution due to their hypervariability, but are flanked by conserved regions that allow their primers to be more universal. Amplicons generated with such primers contain regions with different evolutionary rates, and trimming these conserved regions results in better taxonomic classification and a more valid set of ASVs. This package can be used for most amplicon sequencing methods including for newer long-read sequencing formats, such as PacBio. ITSxpress can be installed from Bioconda, used as a Docker image, or installed from source code. The package works well with high-performance computing clusters or laptops due to its low-resource requirements.
The efficacy of valproate in acute mania, bipolar depression and maintenance therapy for bipolar disorder: an overview of systematic reviews with meta-analyses
Authors: Mari Jair , Dieckmann Luiz Henrique Junqueira , Prates-Baldez Daniel , Haddad Michel , Rodrigues da Silva Naielly , Kapczinski Flavio 
Published: November 2024

ObjectiveThis study aims to conduct an overview on the comparative efficacy of valproate in acute mania, bipolar depression and maintenance treatment of bipolar disorder (BD).MethodWe performed an overview of systematic reviews with meta-analyses of randomised controlled trials (RCTs), registered in PROSPERO (CRD42024497749). We searched Medline and Cochrane Database of Systematic Reviews. Summary measures comparing valproate with placebo or other active drugs were described.ResultsWe included 26 systematic reviews. For acute mania (31 RCTs, n=4376), valproate showed a significantly better response than placebo in two high-quality systematic reviews (RR=1.42; 95% CI: 1.19 to 1.71) (OR=2.05; 95% CI: 1.32 to 3.20). No significant differences with lithium were found in most outcomes. Valproate had similar efficacy to quetiapine and lower efficacy compared with risperidone, with conflicting results when compared with olanzapine. In bipolar depression (7 RCTs, n=399), valproate was more effective than placebo in reducing depressive symptoms (OR=2.80; 95% CI: 1.26 to 6.18) and achieving remission (OR=2.4; 95% CI: 1.09 to 5.29) (OR=2.15; 95% CI: 0.82 to 5.6), considering the results of three high-quality systematic reviews. No significant difference was observed with lithium, lurasidone, quetiapine or olanzapine plus fluoxetine, but valproate showed superior efficacy to aripiprazole, ziprasidone and agomelatine. In maintenance treatment (11 RCTs, n=1063), valproate was superior to placebo in preventing relapse of any mood episode in two high-quality systematic reviews (RR=0.63; 95% CI: 0.48 to 0.83) (RR=0.63; 95% CI: 0.47 to 0.83). No significant difference was found with lithium, olanzapine or lamotrigine.ConclusionThis overview highlights favourable results for valproate compared with placebo in all phases of BD, as well as presenting specific results in comparison with other active drugs. However, these results must be interpreted considering the methodological limitations of our study.
Identifying priorities for future research on reducing and stopping psychiatric medication: results of a James Lind Alliance priority-setting partnership
Authors: Boland Miriam , Higgins Agnes , Beecher Claire , Bracken Pat , Burn Wendy , Cody Anne , Framer Adele , Gronlund Toto , Horowitz Mark , Huff Christy , Jayacodi Sandra , Keating Dolores , Kessler David , Konradsson-Geuken Åsa , Lamberson Nicole , Montagu Luke , Smith Ruth , Cadogan Cathal 
Published: November 2024

ObjectiveThe objective of this study is to identify the top 10 research priorities on reducing and stopping psychiatric medication that reflect the perspectives and unmet needs of three key stakeholder groups (people with lived experience, family members/carers/supporters and healthcare professionals).MethodsA priority-setting partnership was conducted using the James Lind Alliance’s seven-step process. This involved (1) creating an international Steering Group of key stakeholder representatives and (2) identifying potential partners; (3) gathering stakeholders’ uncertainties about reducing and stopping psychiatric medication using an online survey and summarising the survey responses; (4) checking the summary questions against existing evidence and verifying uncertainties; (5) shortlisting the questions using a second online survey; (6) determining the top 10 research questions through a prioritisation workshop; and (7) disseminating the results.ResultsA total of 3635 questions were collected in the initial survey from 884 respondents of which 32 questions were verified as uncertainties. These questions were then ranked in a second online survey by 526 respondents and the findings discussed in a final prioritisation workshop by 30 participants to produce the final top 10 list of research questions. These questions cover a range of areas including the most effective ways of safely reducing/stopping psychiatric medication and providing support to individuals undergoing the discontinuation process, as well as the best ways to educate healthcare professionals on this topic.ConclusionThe top 10 list of research priorities was produced through extensive engagement with key stakeholders and highlights important uncertainties and gaps in the existing evidence base that need to be addressed by future research.
Cost-effectiveness of falls prevention strategies for older adults: protocol for a living systematic review
Authors: Davis Jennifer C , Husdal Kirsten , Rice Jordyn , Loomba Sohail , Falck Ryan Stanley , Dimri Vrinda , Pinheiro Marina , Cameron Ian , Sherrington Catherine , Madden Kenneth M , Liu-Ambrose Teresa 
Published: November 2024

IntroductionOne-third of adults aged 65+ fall annually. Injuries from falls can be devastating for individuals and account for 1.5% of annual healthcare spending. With the growing ageing population, falls place increased strain on scarce health resources. Prevention strategies that target individuals at high risk for falls demonstrate the best value for money; however, limited efficiency (ie, cost-effectiveness) information for fall prevention interventions hinders the implementation of effective falls prevention programmes. Living systematic reviews provide a timely up-to-date evidence-based resource to inform clinical guidelines and health policy decisions. This protocol details the methodology for a living systematic review of the efficiency (ie, cost-effectiveness) of fall prevention interventions for older adults in three settings: community-dwelling, aged care and hospitals.Methods and analysisThis protocol used the reporting guidelines from the Preferred Reporting Items for Systematic Reviews and Meta-Analysis Protocol. Peer-reviewed economic evaluations of controlled clinical trials or health state models will be included. Reports will be obtained through monthly systematic searches of CENTRAL (Ovid), CINAHL (EBSCO), Embase (Ovid), MEDLINE (Ovid), SCOPUS (Elsevier) and Web of Science (Clarivate) alongside snowballing and handsearching EconLit and the Tufts Cost Effectivness Analysis Registry. Screening, data extraction, quality assessment and risk of bias will be assessed by multiple reviewers. The primary outcomes will be the incremental cost-effectiveness (ie, incremental cost per fall prevented), incremental cost-utility (ie, incremental cost per quality-adjusted life year gained) or cost-benefit ratio. Additional outcomes will include falls and cost-related measures. All economic outcomes will be reported in a common year and currency. Results will be reported as a narrative synthesis; meta-analysis will be considered based on data quality, suitability and availability.Ethics and disseminationEthical approval is not required as primary human data will not be collected. Results will be disseminated through peer-reviewed publications and a dedicated website.PROSPERO registration numberCRD42024532485.
What factors are associated with early childhood development in Thailand? A cross-sectional analysis using the 2022 Multiple Indicator Cluster Survey
Authors: Topothai Thitikorn , Phisanbut Napat , Topothai Chompoonut , Suphanchaimat Rapeepong , Müller-Riemenschneider Falk , Cetthakrikul Nisachol , Tangcharoensathien Viroj 
Published: November 2024

BackgroundEarly childhood development is essential for lifelong health and well-being. This study aims to assess the proportion of children aged 24–59 months in Thailand who are developmentally on track using the Early Childhood Development Index 2030 (ECDI2030) and to explore associations with household socioeconomic characteristics and environments.MethodsA cross-sectional analysis was conducted using data from the 2022 Multiple Indicator Cluster Survey by the Thailand National Statistical Office. The developmental progress of 6557 children was evaluated across health, learning and psychosocial domains using ECDI2030 criteria. Multivariable logistic regression was used to assess associations between developmental status and household and participant characteristics.ResultsThe study found that 81.3% of children were developmentally on track. Factors positively associated with being on track included being female (adjusted OR (AOR)=1.49), higher maternal education (AOR=2.02 for above secondary education), more books at home (AOR=1.59 for 3–9 books; AOR=2.40 for 10+ books) and increased screen time (AOR=1.68). Living in the Northern (AOR=0.45) and Northeastern (AOR=0.56) regions decreased the likelihood of being on track.ConclusionAround 20% of children did not meet ECDI2030 milestones, highlighting the need for targeted policy interventions. Gender, region, maternal education, access to books and screen time were significant factors for developmental outcomes. Policies should prioritise support for parents, nurturing care and educational resources, particularly for socioeconomically disadvantaged groups.
“That’s not how abortions happen”: a qualitative study exploring how young adults navigate abortion misinformation in the post-Roe era
Authors: John Jennifer N , Westley Allie , Blumenthal Paul D , Sanders Lee M 
Published: November 2024

BackgroundMisinformation about abortion is widespread and was exacerbated by the overturn ofRoe v Wade. Young adults are among those facing the most direct impacts of new abortion restrictions and are more likely to access health information from online sources, where misinformation is prevalent. We explored how young adults perceive and evaluate abortion-related information in a time of heightened abortion restrictions.MethodsWe conducted in-depth, semi-structured interviews with 25 young adults (aged 18–24 years, 56% assigned female at birth), recruited across 17 US states (44% living in states with restrictive abortion policies), between June and September 2022. We derived themes from the interviews using reflexive thematic analysis.ResultsWhile many participants were aware of and had personally encountered abortion misinformation, their susceptibility to false claims varied substantially based on their previous knowledge of abortion and exposure to anti-abortion rhetoric. Participants tended to reject some common myths regarding the medical risks of abortion (eg, association with breast cancer), while expressing a wider range of views regarding its impacts on fertility and mental health. When presented with contradictory sources of abortion information, most participants were unable to confidently reject the misleading source. Knowledge gaps left participants vulnerable to misinformation, while prior scepticism of anti-abortion rhetoric protected participants against misinformation.ConclusionsIn this diverse national sample, young adults demonstrated a range of perceptions of abortion misinformation and approaches to identify it. These results lay the groundwork for future observational and experimental research in public health communication.
Cancer-associated fibroblasts shape early myeloid cell response to chemotherapy-induced immunogenic signals in next generation tumor organoid cultures
Authors: Kabiljo Julijan , Theophil Anna , Homola Jakob , Renner Annalena F , Stürzenbecher Nathalie , Ammon Daphni , Zirnbauer Rebecca , Stang Simone , Tran Loan , Laengle Johannes , Kulu Askin , Chen Anna , Fabits Markus , Atanasova Velina S , Pusch Oliver , Weninger Wolfgang , Walczak Henning , Herndler Brandstetter Dietmar , Egger Gerda , Dolznig Helmut , Kusienicka Anna , Farlik Matthias , Bergmann Michael 
Published: November 2024

BackgroundPatient-derived colorectal cancer (CRC) organoids (PDOs) solely consisting of malignant cells led to major advances in the understanding of cancer treatments. Yet, a major limitation is the absence of cells from the tumor microenvironment, thereby prohibiting potential investigation of treatment responses on immune and structural cells. Currently there are sparse reports describing the interaction of PDOs, cancer-associated fibroblasts (CAFs) and tumor-associated macrophages (TAMs) in complex primary co-culture assay systems.MethodsPrimary PDOs and patient matched CAF cultures were generated from surgical resections. Co-culture systems of PDOs, CAFs and monocytic myeloid cells were set up to recapitulate features seen in patient tumors. Single-cell transcriptomics and flow cytometry was used to show effects of culture systems on TAM populations in the co-culture assays under chemotherapeutic and oncolytic viral treatment.ResultsIn contrast to co-cultures of tumor cells and monocytes, CAF/monocyte co-cultures and CAF/monocyte/tumor cell triple cultures resulted in a partial differentiation into macrophages and a phenotypic switch, characterized by the expression of major immunosuppressive markers comparable to TAMs in CRC. Oxaliplatin and 5-fluorouracil, the standard-of-care chemotherapy for CRC, induced polarization of macrophages to a pro-inflammatory phenotype comparable to the immunogenic effects of treatment with an oncolytic virus. Monitoring phagocytosis as a functional proxy to macrophage activation and subsequent onset of an immune response, revealed that chemotherapy-induced cell death, but not virus-mediated cell death, is necessary to induce phagocytosis of CRC cells. Moreover, CAFs enhanced the phagocytic activity in chemotherapy treated CRC triple cultures.ConclusionsPrimary CAF-containing triple cultures successfully model TAM-like phenotypesex vivoand allow the assessment of their functional and phenotypic changes in response to treatments following a precision medicine approach.