bluuebunny/crossref_metadata_2025_split huggingface dataset:
High metabolic rates drive tiny genomes in plants (and birds): a commentary on ‘The smallest angiosperm genomes may be the price for effective traps of bladderworts’
Authors: Givnish Thomas J 
Published: October 2024

This article comments on:
František Zedek, Jakub Šmerda, Aneta Halasová, Lubomír Adamec, Adam Veleba, Klára Plačková and Petr Bureš, The smallest angiosperm genomes may be the price for effective traps of bladderworts, Annals of Botany, Volume 134, Issue 7, 31 December 2024, Pages 1131–1138, https://doi.org/10.1093/aob/mcae107
Clutch attendance and call parameters are linked to mating success in a glassfrog with paternal care
Authors: Garrido-Priego Marina , Tószeghi Moric , Angiolani-Larrea Francesca N , Valencia-Aguilar Anyelet , Bégué Lauriane , Núñez Raby , Culebras Jaime , Ringler Max , Stynoski Jennifer L , Ringler Eva 
Published: October 2024

Abstract
Females of some species improve their reproductive success not only by being choosy and selecting males with certain traits, but also by sequentially mating with multiple males within one reproductive season. However, it is relatively unknown whether females also evaluate parental care during mate choice and, if they do, whether males actively communicate their care status to approaching females. We monitored a natural population of the glassfrog Hyalinobatrachium valerioi, a species with sequential polyandry and paternal care, to assess the role of parental care and advertisement calling on male mating success. Using field observations and acoustic analysis, we found that even in this species which has single-note calls, variations in call parameters allow for individual discrimination. Calling was strongly associated with mating success in H. valerioi males. Males with longer calls achieved the highest total mating success over the entire study period, indicating that females might have a preference for longer calls. Moreover, active calling and the presence of clutches were both linked to male mating success on a given night, although we cannot fully exclude that the link between presence of clutches and mating success is due to attractive call features alone. Call parameters differed between males when they were calling on top of their clutches, compared to sitting on the leaf directly, which might provide reliable cues about parental state to approaching females. These findings demonstrate the prominent role of acoustic communication and female choice in a species with male parental care and sequential polyandry.
A modern multi-omics data exploration experience with Panomicon
Authors: Allendes Osorio Rodolfo S , Kosugi Yuji , Nyström-Persson Johan T , Mizuguchi Kenji , Natsume-Kitatani Yayoi 
Published: October 2024

Abstract

Summary
To address the challenges of the storage, sharing, and analysis of multi-omics data, here we introduce the newest version of Panomicon, which includes the improvement of the underlying data model, the introduction of new registration and control access service, together with the seamless integration with other services (like TargetMine for data enrichment analysis), integrated in a completely new, more user friendly web application.

Availability and implementation
Panomicon is available online at https://panomicon.nibiohn.go.jp. Unregistered users can access the publicly available data uploaded to Panomicon using the following account: user: guest, password: anonymous. Source code for the application is also freely available under a GNU license at https://github.com/Toxygates/Panomicon/. A brief user guide for the new features of Panomicon is provided as supplementary material online.
ABodyBuilder3: improved and scalable antibody structure predictions
Authors: Kenlay Henry , Dreyer Frédéric A , Cutting Daniel , Nissley Daniel , Deane Charlotte M 
Published: October 2024

Abstract

Summary
In this article, we introduce ABodyBuilder3, an improved and scalable antibody structure prediction model based on ABodyBuilder2. We achieve a new state-of-the-art accuracy in the modelling of CDR loops by leveraging language model embeddings, and show how predicted structures can be further improved through careful relaxation strategies. Finally, we incorporate a predicted Local Distance Difference Test into the model output to allow for a more accurate estimation of uncertainties.

Availability and implementation
The software package is available at https://github.com/Exscientia/ABodyBuilder3 with model weights and data at https://zenodo.org/records/11354577.
BatchFLEX: feature-level equalization of X-batch
Authors: Davis Joshua T , Obermayer Alyssa N , Soupir Alex C , Hesterberg Rebecca S , Duong Thac , Yang Ching-Yao , Dao Ken Phong , Manley Brandon J , Grass G Daniel , Avram Dorina , Rodriguez Paulo C , Fridley Brooke L , Yu Xiaoqing , Teng Mingxiang , Wang Xuefeng , Shaw Timothy I 
Published: October 2024

Abstract

Motivation
Integrative analysis of heterogeneous expression data remains challenging due to variations in platform, RNA quality, sample processing, and other unknown technical effects. Selecting the approach for removing unwanted batch effects can be a time-consuming and tedious process, especially for more biologically focused investigators.

Results
Here, we present BatchFLEX, a Shiny app that can facilitate visualization and correction of batch effects using several established methods. BatchFLEX can visualize the variance contribution of a factor before and after correction. As an example, we have analyzed ImmGen microarray data and enhanced its expression signals that distinguishes each immune cell type. Moreover, our analysis revealed the impact of the batch correction in altering the gene expression rank and single-sample GSEA pathway scores in immune cell types, highlighting the importance of real-time assessment of the batch correction for optimal downstream analysis.

Availability and implementation
Our tool is available through Github https://github.com/shawlab-moffitt/BATCH-FLEX-ShinyApp with an online example on Shiny.io https://shawlab-moffitt.shinyapps.io/batch_flex/.
Castanet: a pipeline for rapid analysis of targeted multi-pathogen genomic data
Authors: Mayne Richard , Secret Shannah , Geoghegan Cyndi , Trebes Amy , Kean Kai , Reid Kaitlin , Lin Gu-Lung , Ansari M Azim , de Cesare Mariateresa , Bonsall David , Elliott Ivo , Piazza Paolo , Brown Anthony , Bray James , Knight Julian C , Harvala Heli , Breuer Judith , Simmonds Peter , Bowden Rory J , Golubchik Tanya 
Published: October 2024

Abstract

Motivation
Target enrichment strategies generate genomic data from multiple pathogens in a single process, greatly improving sensitivity over metagenomic sequencing and enabling cost-effective, high-throughput surveillance and clinical applications. However, uptake by research and clinical laboratories is constrained by an absence of computational tools that are specifically designed for the analysis of multi-pathogen enrichment sequence data. Here we present an analysis pipeline, Castanet, for use with multi-pathogen enrichment sequencing data. Castanet is designed to work with short-read data produced by existing targeted enrichment strategies, but can be readily deployed on any BAM file generated by another methodology. Also included are an optional graphical interface and installer script.

Results
In addition to genome reconstruction, Castanet reports method-specific metrics that enable quantification of capture efficiency, estimation of pathogen load, differentiation of low-level positives from contamination, and assessment of sequencing quality. Castanet can be used as a traditional end-to-end pipeline for consensus generation, but its strength lies in the ability to process a flexible, pre-defined set of pathogens of interest directly from multi-pathogen enrichment experiments. In our tests, Castanet consensus sequences were accurate reconstructions of reference sequences, including in instances where multiple strains of the same pathogen were present. Castanet performs effectively on standard computers and can process the entire output of a 96-sample enrichment sequencing run (50M reads) using a single batch process command, in $&lt;$2 h.

Availability and implementation
Source code freely available under GPL-3 license at https://github.com/MultipathogenGenomics/castanet, implemented in Python 3.10 and supported in Ubuntu Linux 22.04. The data underlying this article are available in Europe Nucleotide Archives, at https://www.ebi.ac.uk/ena/browser/view/PRJEB77004.
Pediatric wrist fractures: variations in management across countries. An evidence-based summary of evidence
Authors: Labianca Luca , Calderaro Cosma , Maffulli Nicola 
Published: October 2024

Abstract

Introduction
Fractures of the distal radius are common in pediatric population, with considerable variation in the management of pediatric wrist fractures across different countries. It is crucial to consider the different approaches to conservative management and surgical intervention. The decision on the appropriate treatment method often depends on the type and severity of the fracture, as well as the available healthcare resources and expertise in each country. This article tries to identify these variations, so the various healthcare systems can work toward implementing best practices in the management of pediatric wrist fractures on a global scale.

Source of data
Published peer-reviewed articles identified in electronic databases, including PubMed Scopus and Google Scholar.

Areas of agreement
The management of pediatric wrist fractures can differ significantly among countries given the high variability in healthcare resources and cultural practices.

Areas of controversy
The management of pediatric wrist fractures can be challenging in certain countries, especially in developing regions with limited resources.

Growing points
Challenges such as long therapeutic delays, lack of appropriate anesthesia, and the absence of fluoroscopy can complicate the treatment process. Randomized controlled clinical trials (RCTs) are vital in providing high-quality evidence to guide clinical decision-making, especially in the field of pediatric wrist fractures.

Areas timely for developing research
Efforts to support and prioritize the conduct and dissemination of RCTs in pediatric wrist fracture management can ultimately lead to more consistent, effective, and evidence-based care for children with wrist fractures worldwide.
Extraordinary 99Mo adsorption: utilizing spray-dried mesoporous alumina for clinical-grade generator development
Authors: Alowasheeir Azhar , Eguchi Miharu , Fujita Yoshitaka , Tsuchiya Kunihiko , Wakabayashi Ryutaro , Kimura Tatsuo , Ariga Katsuhiko , Hatano Kentaro , Fukumitsu Nobuyoshi , Yamauchi Yusuke 
Published: October 2024

Abstract
Mesoporous alumina spherical particles, synthesized via spray-drying with the self-assembly of EOnPOmEOn, have been utilized for the development of clinical-grade molybdenum-99/technetium-99 m (99Mo/99mTc) generators. When evaluated as molybdenum (Mo) adsorbents, the mesoporous alumina spherical particles are useful for effective adsorption of Mo ions rather than commercially available particulate alumina. The effects of surfactant removal methods on the Mo adsorption property are also systematically investigated using the batch method. Batch adsorption studies reveal practical adsorption capacities ranging from 45.9 to 91.2 mg Mo g−1 in a Mo solution (1000 mg Mo L−1) at pH 3. The experimental results indicate the following trend in Mo adsorption capacity: solvent extraction &gt;calcination (400 °C and 800 °C) &gt;commercially available alumina (Medical Al2O3 used as is). To explore the feasibility of developing a clinical-scale generator, a novel tandem column generator concept is employed. Using the spray-dried and extracted mesoporous alumina, 99mTc eluted from the generator exhibits high radionuclidic, radiochemical, and chemical purity, making it suitable for the preparation of 99mTc-labeled radiopharmaceuticals.
Expert opinion on characteristics of vulval lichen sclerosus: initial identification of important clinical features through an international electronic Delphi consensus study
Authors: Simpson Rosalind C , Birchall­­ Michael , Daniels Jane , Gran Sonia , Kirtschig Gudula , Thomas Kim S 
Published: October 2024

Abstract

Background
Lichen sclerosus (LS) is a chronic inflammatory condition that mainly affects genital skin. It causes distressing symptoms that impact daily quality of life, as well as progressive anatomical changes and a potential risk of cancer. Vulval LS is often misdiagnosed and treatment delayed. If nonexperts can be supported to identify clinical features of LS, they may diagnose the condition sooner and commence timely treatment or refer a patient for assessment and confirmatory biopsy.

Objectives
To reach international expert consensus on clinical diagnostic features for vulval LS.

Methods
Between March and May 2023, a four-stage electronic Delphi consensus exercise was conducted. In the first three rounds, participants were asked to rate the importance of a list of clinical features. Responses from round 1 were summarized and presented in rounds 2 and 3, along with additional features suggested by participants. Any items rated as ‘very important/critical’ or ‘not important’ that met the definition of consensus were removed from subsequent rounds. In round 4, items that were rated ‘important but not critical’ were ranked in order of their importance. Consensus was defined a priori, and all rounds were conducted anonymously.

Results
In total, 47 participants from 14 countries completed round 1, with 42 (89%) retained by round 3 when consensus was determined. Round 4 was completed by 36 (77%) participants. Participants completing all four rounds predominantly included healthcare professionals (n = 28/36; 78%) and patient support group representatives (n = 7/36; 19%). In round 1, 21 diagnostic features were rated. Participants suggested an additional 10 features, which were subsequently added to the round 2 survey. After three rounds, consensus was achieved for five diagnostic features: whiteness, itch, changes in anatomy, burying of the clitoral area and improvement in response to topical steroids. There were also 12 features rated as ‘important but not critical’ and participants subsequently ranked them in the fourth round.

Conclusions
Experts agreed on 5 critical diagnostic features for vulval LS in adults and an additional 12 features that may also be important. Future research should assess these clinical features for diagnostic validity through a multicentre diagnostic test accuracy study.
The effects of dialysate calcium prescription on mortality outcomes in incident patients on hemodialysis
Authors: ter Meulen Karlien J , Carioni Paola , Bellocchio Francesco , van der Sande Frank M , Bouman Heleen J , Stuard Stefano , Neri Luca , Kooman Jeroen P 
Published: October 2024

ABSTRACT

Background
The appropriate prescription of dialysate calcium concentration for hemodialysis is debated. We investigated the association between dialysate calcium and all-cause, cardiovascular mortality and sudden cardiac death.

Methods
In this historical cohort study, we included adult incident hemodialysis patients who initiated dialysis between 1 January 2010 and 30 June 2017 who survived for at least 6 months (grace period). We evaluated the association between dialysate calcium 1.25 or 1.50 mmol/l and outcomes in the 2 years after the grace period, using multivariable Cox regression models. Moreover, we examined the association between the serum dialysate to calcium gradient and outcomes.

Results
We included 12 897 patients with dialysate calcium 1.25 mmol/l and 26 989 patients with dialysate calcium 1.50 mmol/l. The median age was 65 years, and 61% were male. The unadjusted risk of all-cause mortality was higher for dialysate calcium 1.50 mmol/l [hazard ratio (HR) 1.07, 95% confidence intervals (CI) 1.01–1.12]. However, in the fully adjusted model, no significant differences were noted (HR 1.05, 95% CI 0.99–1.12). Similar results were observed for the risk of cardiovascular mortality (HR 1.03, 95% CI 0.94–1.13). Adjusted risk of sudden cardiac death was lower for dialysate calcium 1.50 mmol/l (HR 0.81, 95% CI 0.67–0.97). Significant and positive associations with all outcomes were observed with larger serum-to-dialysate calcium gradients, primarily mediated by the serum calcium level.

Conclusions
In contrast to the unadjusted analysis that showed a higher risk for dialysate calcium of 1.50 mmol/l, after adjusting for confounders, there were no significant differences in the risk of all-cause and cardiovascular mortality between dialysate calcium concentrations of 1.50 and 1.25 mmol/l. After adjustment, a lower risk of sudden cardiac death was observed in patients with dialysate calcium 1.50 mmol/l. A higher serum-to-dialysate calcium gradient is associated with an increased risk for adverse outcomes.
Disentangling Anemia in Frailty: Exploring the Role of Inflammation
Authors: Herpich Catrin , Göger Lea , Faust Lea , Kalymon Magdalena , Ott Christiane , Walter Sophia , Lehmkuhl Elke , Grune Tilman , Moskiou Varvara , Müller-Werdan Ursula , Norman Kristina 
Published: October 2024

Abstract

Background
In older patients, frailty and anemia frequently coexist. However, only few studies have been conducted in older patients with multimorbidity and several overlapping causes of anemia, such as inflammation, inadequate nutrition, or certain pathologies. This analysis aims to decipher potential factors associated with anemia in older hospital patients with frailty.

Methods
Patients (n = 208, age: 62–98 years) were categorized as prefrail (n = 68) and frail (n = 140) using the Fried frailty phenotype. We quantified serum concentrations of markers of iron metabolism (iron, ferritin, transferrin, soluble transferrin receptor, and hepcidin), inflammation (interleukin [IL]-6 and IL-10 C-reactive protein), and hematology (hemoglobin). Principal component analysis was conducted to evaluate biomarker patterns and associations with frailty were assessed with logistic regression analysis.

Results
Anemia prevalence was higher in patients with frailty (84.3% vs 70.6%, p = .021). Three principal components (PC1–3) were identified. PC1 was characterized by high factor loadings representing inflammation and factor scores differed between patients with prefrailty and frailty (−0.04 (interquartile range [IQR]: 1.45) vs −0.51 (IQR: 0.87), p &lt; .001]. PC2 represents macrocytic anemia and thus vitamin B12 or folate deficiency, whereas PC3 indicates hematological pathologies. Only PC1 was associated with frailty status when controlled for age, sex, number of drugs, and comorbidities (OR: 2.018, 95% CI: 1.316; 3.094, p = .001). PC2 and PC3 were not associated with frailty.

Conclusions
Our results suggest that anemia in patients with frailty is driven by inflammation rather than being disease-related or solely the result of micronutrient deficiencies.
Biopharmaceutical pipeline funded by venture capital firms, 2014 to 2024
Authors: Kang So-Yeon , Liu Mingqian , Ballreich Jeromie , Gupta Ravi , Anderson Gerard 
Published: October 2024

Abstract
Venture capital (VC) firms fund biopharmaceutical research and development (R&D) while incurring substantial financial risk. VC firms seek to invest in clinical areas with the greatest potential for financial return. Using a combination of data for clinical trials and VC investment deals between January 2014 and March 2024, we found that approximately 75% of VC investments were allocated to clinical trials studying small-molecule drugs compared to biologics or gene therapies, without substantial changes over the study period. Most of VC firms’ investment in biopharmaceutical R&D was concentrated in phase 1 and phase 2 clinical trials. This trend has increased in recent years, with phase 1 trials accounting for nearly half of total deals and capital investments in 2023. VC investments were concentrated in several therapeutic areas, including cancer.
Understanding the factors that impact federal rulemaking: a survey of former EPA regulators
Authors: Topazian Rachel J , McGinty Emma E , Hearne Shelley A 
Published: October 2024

Abstract
While federal rulemaking is an essential part of American governance, it is not well understood by researchers and advocates. We surveyed 115 former regulators at the Environmental Protection Agency to understand their views on the kinds of information they valued most and their communication preferences (June-August 2023). Respondents highly valued information about the scope of a problem (96%), legal analysis (97%), technology assessments (96%), and impacts of a proposed rule (99%). Regulators had difficulty accessing several kinds of information: 16% of respondents viewed racial equity information as easy to access and 30% thought financial information was easy to access. Respondents valued communications that provided data (99% viewed as effective), made compelling arguments (97%) or technical recommendations (93%), and storytelling (88%). Respondents indicated that the content of comment letters was important: 94% viewed letters containing data as important and 90% valued technical recommendations. Only 22% thought that repetition of the same comments across letters was important. Our findings reveal opportunities for researchers and advocates to help fill information gaps and identify communication strategies that might resonate with federal regulators.
Changes in hospital-supported substance use services across US nonprofit hospitals, 2015-2021
Authors: Cronin Cory E , Franz Berkeley , Lindenfeld Zoe , Yuanhong Lai Alden , Pagán José A , Chang Ji 
Published: October 2024

Abstract
Substance use remains a timely and important community need to understand and address. Nonprofit hospitals are in a unique position to identify needs and develop programs in response to substance use challenges in their communities. To better understand how nonprofit hospitals do this, we collected data from community health needs assessments and their corresponding implementation strategy (IS) to address these needs for a 20% random sample of hospitals in each state of the United States over 2 periods (2015-2018 and 2019-2021). The sample of nonprofit hospitals came from the American Hospital Association's (AHA) Annual Survey Database. Community health needs assessment and IS documents were coded for the inclusion of substance use programs using a systematic protocol and analyzed quantitatively. We found that the percentage of nonprofit hospitals in our sample with at least 1 substance use program increased from 66.5% in 2015-2018 to 73.6% in 2019-2021. Of the types of programs analyzed, harm reduction approaches saw the greatest increase in implementation in the time period studied, while primary care approaches decreased. This indicates that hospitals are continuing or even increasing their responses to community needs regarding substance use, but there is evidence that their approaches in doing so are shifting over time.