bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optimizing nurse staffing in thoracic surgery: the imperative of Enhanced Recovery Programs—a statement of the European Society of Thoracic Surgeons Nursing & Allied Health Professionals Working Group
Authors: Fehlmann Florian , Moons Johnny , Missel Malene 
Published: November 2024

Abstract
Enhanced Recovery Programs (ERPs) have revolutionized thoracic surgery by reducing hospital stays and fostering quicker patient recoveries through minimally invasive procedures. However, the perception that patients in ERPs are less complex and require fewer nursing resources is misleading. Despite shorter hospital stays, the complexity of postoperative care remains high, with patients often needing vigilant monitoring and timely interventions. This article challenges the assumption of reduced nursing needs in ERPs, arguing that the fast-paced nature of these programmes intensifies the demand for skilled nursing care. The European Society of Thoracic Surgeons (ESTS) Nurses & Allied Health Professionals Working Group emphasizes that nurse staffing levels must be maintained or even increased to ensure quality care in ERPs. Adequate staffing is crucial for supporting not only the technical aspects of care but also the patient’s experience of illness and recovery. Failure to recognize this complexity could compromise patient outcomes, eroding the benefits of ERPs. This paper advocates for a comprehensive approach that balances efficiency with sufficient nursing support to optimize outcomes in thoracic surgery ERPs. It calls for a reassessment of staffing models to meet the evolving demands of these programmes, ensuring that the advantages of shorter recovery times are not undermined by insufficient care.
ProtPipe: A Multifunctional Data Analysis Pipeline for Proteomics and Peptidomics
Authors: Li Ziyi , Weller Cory A , Shah Syed , Johnson Nicholas L , Hao Ying , Jarreau Paige B , Roberts Jessica , Guha Deyaan , Bereda Colleen , Klaisner Sydney , Machado Pedro , Zanovello Matteo , Prudencio Mercedes , Oskarsson Björn , Staff Nathan P , Dickson Dennis W , Fratta Pietro , Petrucelli Leonard , Narayan Priyanka , Cookson Mark R , Ward Michael E , Singleton Andrew B , Nalls Mike A , Qi Yue A 
Published: November 2024

Abstract
Mass spectrometry (MS) is a technique widely employed for the identification and characterization of proteins, with personalized medicine, systems biology, and biomedical applications. The application of MS-based proteomics advances our understanding of protein function, cellular signaling, and complex biological systems. MS data analysis is a critical process that includes identifying and quantifying proteins and peptides and then exploring their biological functions in downstream analyses. To address the complexities associated with MS data analysis, we developed ProtPipe to streamline and automate the processing and analysis of high-throughput proteomics and peptidomics datasets with DIA-NN preinstalled. The pipeline facilitates data quality control, sample filtering, and normalization, ensuring robust and reliable downstream analyses. ProtPipe provides downstream analyses, including protein and peptide differential abundance identification, pathway enrichment analysis, protein–protein interaction analysis, and major histocompatibility complex (MHC)–peptide binding affinity analysis. ProtPipe generates annotated tables and visualizations by performing statistical post-processing and calculating fold changes between predefined pairwise conditions in an experimental design. It is an open-source, well-documented tool available at https://github.com/NIH-CARD/ProtPipe, with a user-friendly web interface.
What is the relationship between hospital management practices and quality of care? A systematic review of the global evidence
Authors: Ward Charlotte , Phiri Elias Rejoice Maynard , Goodman Catherine , Nyondo-Mipando Alinane Linda , Malata Monica , Manda Wanangwa Chimwaza , Mwapasa Victor , Powell-Jackson Timothy 
Published: November 2024

Abstract
There is a widely held view that good management improves organizational performance. However, hospitals are complex organizations, and the relationship between management practices and health service delivery is not straightforward. We conducted a global, systematic literature review of the quantitative evidence on the link between the adoption of management practices and quality of care in hospitals. We searched in PubMed, EMBASE, EconLit, Global Health, and Web of Science on 16 October 2024, without language or country restrictions. We included empirical studies from 1 January 2000 onwards, examining the quantitative association between hospital management practices and quality of care. Outcomes included structural quality (availability of resources such as drugs and equipment), clinical quality (adherence to guidelines), health outcomes, and patient satisfaction or experience with care. In every study, each tested association was categorized as significantly positive (at the 5% level), null, or significantly negative. The study was registered with PROSPERO (CRD42022301462). Of 11 731 articles, 25 studies met the inclusion criteria and had an acceptable risk of bias. Studies were equally distributed between high-income and low- and middle-income countries, with 22 cross-sectional and three intervention studies. Of 111 associations, 55 (49.5%) were significantly positive, one (1%) was significantly negative, and 55 (49.5%) were null. Among the associations tested, the majority were significantly positive for structural quality (79%), clinical quality (60%), and health outcomes (57%), while most associations between hospital management and patient satisfaction (80%) were null. The findings are mixed, with a similar proportion of positive and null associations between management practices and quality of care across studies. The evidence is limited by the risk of bias introduced by nonrandomized study designs. Evidence of positive associations in some settings warrants further investigation of the association through intervention studies or natural experiments. This could leverage methodological developments in quantitatively measuring management, highlighted by this review.
Australian parents’ perceptions of the risks posed by harmful products to the health of children
Authors: Pitt Hannah , McCarthy Simone , Hume Emily , Arnot Grace , Thomas Samantha 
Published: November 2024

Abstract
Cigarettes, alcohol, vaping and gambling products can cause significant harm to children and young people. The industries that make these products employ a range of tactics that aim to normalize their products and resist policy and regulatory reform. This includes ‘responsibility’ framing, in which parents are often held responsible for educating their children about the risks of these products. However, there has been very little research, which has investigated parents’ perceptions of these industries. A qualitatively led online panel survey was conducted with n = 455 Australian parents who had at least one child aged between 11 and 17 years. Participants were asked questions relating to concerns about harmful products; what they talked about with their children; other potential sources of risk information; and who were responsible for protecting young people from these industries. Four themes were constructed. (i) Parents identified that parental influence, peer pressure, social media and advertising influenced children’s attitudes towards these products. (ii) They had concerns about the short- and long-term consequences of these products. (iii) Parents actively engaged in educating their children about these products but recognized that it was difficult to counter industry messages. (iv) Parents emphasized the need for a collective approach, advocating for increased information and government regulations, particularly relating to marketing. This study demonstrates that parents are concerned about these industries and do their best to protect their children from harm but recognize that they need more support. Evidence-based education and comprehensive regulations particularly around marketing are needed to de-normalize products and protect young people.
Health and Economic Impacts of Introducing Vaccae and Enhanced Drug-Resistant Tuberculosis Management Strategies in China
Authors: Zhai Pei-Yao , Zang Xiao , Jiang Ting , Feng Jian , Zhang Bin , Zhang Lei , Chen Zhi-Xian , Zhao Yan-Lin , Qin Gang 
Published: November 2024

Abstract

Background
China faces high burden of multidrug-resistant or rifampicin-resistant tuberculosis (MDR/RR-TB). We aimed to evaluate the impacts of Vaccae vaccination and enhanced drug-resistant TB (DR-TB) management strategies.

Methods
Using a compartmental model calibrated with national TB data, we evaluated 9 interventions: enhanced DR-TB management (S1); Vaccae vaccination for those with latent TB infection, targeting specific age groups (S2: adolescents, S3: adolescents and young adults, S4: working-age adults, S5: elderly); and combined strategies S6-S9. Vaccae's efficacy was 0.547 for the first 5 years, then waning annually. Costs were US$28/dose for Vaccae, US$87/test for Xpert MTB/RIF, and US$13 818/course for BPaLM.

Results
Strategy S1 is projected to reduce MDR/RR-TB incidence and mortality by 21% (95% UI, 8%–46%) and 54% (38%–67%), respectively, by 2050. Strategy S9 (S5+S1) is more effective, reducing the incidence by 44% (35%–61%) and mortality by 68% (52%–78%), with an ICER of US$7222 (4460–10 779) per DALY averted compared with S1. Additionally, S9 could prevent 24.2 (13.5–32.9) million patient-months of second-line treatment from 2025 to 2050.

Conclusions
Prioritizing Vaccae vaccination for the elderly and enhancing DR-TB management offer a promising and cost-effective opportunity for China. The findings may have policy implications for other low- and middle-income countries with high MDR/RR-TB burden.
Numerical simulation study on the evolutionary law of energy zones in deep-buried roadway excavation surrounding rock
Authors: Sun Peng , Zhang Dongxiao , Guo Weiyao , Ding Ke , Xiong Feng , Zhang Ruijie 
Published: November 2024

Abstract
Rockburst disasters in deep-buried roadways significantly threaten mine safety. To uncover the evolutionary laws of energy zoning, this paper employs analytical theory and numerical modeling to investigate the static distribution characteristics and dynamic energy evolution in deep-buried roadway surrounding rock. The near-field energy storage model for roadways is established, and the large-diameter drillhole pressure relief measures based on energy zoning is designed. The results are as follows: (i) after the formation of deep-buried roadways, the roof on both sides and the coal mass of the elastic zone in the deep region became energy storage zones, while the coal mass in the shallow plastic area became energy-release zones. Rockbursts release stored elastic energy, causing crack propagation and kinetic energy transfer. (ii) The surrounding rock was divided into release, transitional, and energy storage zones during roadway excavation. Exceeding energy storage limits triggered the instantaneous release of elastic energy, leading to rockbursts. (iii) The large-diameter pressure relief drillhole parameters designed based on the energy zoning range of roadway surrounding rock can effectively destroy the energy storage zone of roadway surrounding rock, improve the safety of working face mining, and have important engineering guiding significance for rock burst prevention.
The link between changing news use and trust: longitudinal analysis of 46 countries
Authors: Fletcher Richard , Andı Simge , Badrinathan Sumitra , Eddy Kirsten A , Kalogeropoulos Antonis , Mont'Alverne Camila , Robertson Craig T , Ross Arguedas Amy , Schulz Anne , Toff Benjamin , Nielsen Rasmus Kleis 
Published: November 2024

Abstract
Changing levels of public trust in the news are of deep concern to both researchers and practitioners. We use data from 2015 to 2023 in 46 countries to explore how trust in news has changed, while also exploring the links with sociodemographic variables, differences by media system, and changing patterns of news use. We find that (a) there has been a small overall decline in trust in news since 2015, but also that (b) there are different trends in different countries. More specifically, trust has declined more in media environments that have become less structured by television news use, and increasingly structured by social media news use. Our findings underscore how changing structures of media use may be central to explaining trust dynamics in recent years, which suggests new avenues for restoring trust where it has eroded.
Cultural evolution via iterated learning and communication explains efficient color naming systems
Authors: Carlsson Emil , Dubhashi Devdatt , Regier Terry 
Published: November 2024

Abstract
It has been argued that semantic systems reflect pressure for efficiency, and a current debate concerns the cultural evolutionary process that produces this pattern. We consider efficiency as instantiated in the Information Bottleneck (IB) principle, and a model of cultural evolution that combines iterated learning and communication. We show that this model, instantiated in neural networks, converges to color naming systems that are efficient in the IB sense and similar to human color naming systems. We also show that some other proposals such as iterated learning alone, communication alone, or the greater learnability of convex categories, do not yield the same outcome as clearly. We conclude that the combination of iterated learning and communication provides a plausible means by which human semantic systems become efficient.
Worldwide study reveals fluid sexual preferences in females and no association between gynephilia and non-heterosexuality
Authors: Camperio Ciani Andrea S , Colledani Daiana 
Published: November 2024

Abstract

Background
Social factors and a lack of clearself-awareness may prevent women from explicitly reporting their non-heterosexuality, and implicit measures could provide more reliable data.

Aim
This study examined non-heterosexuality and gynephilia in a large, global sample of women using implicit and explicit methods.

Methods
A sample of 491 women participated in this cross-sectional study. Participants completed a biographical questionnaire, the Autobiographical-Implicit Association Test, the Sexual Preference-Implicit Association Test (SP-IAT), and an explicit measure of sexual orientation. In a follow-up study, 263 participants were recontacted and completed the Autobiographical Sexual Orientation IAT and answered additional questions about their sexual behavior and preferences related to the stimuli on the SP-IAT.

Outcomes
The main outcome measures were D-scores on implicit association tests and scores on explicit measures of sexual orientation and behaviors.

Results
Implicit measures showed a higher rate of gynephilia (67.8%) than explicit non-heterosexuality (19.6%), with consistent results across continents. The findings suggest that women may be attracted to other women without necessarily desiring sexual encounters with them. Furthermore, the results suggest a degree of fluidity in sexual preferences in the female population.

Clinical Implications
Studying the prevalence of gynephilia and non-heterosexuality in adult women can inform the development of health promotion programs tailored to women's diverse sexual experiences and preferences.

Strengths & Limitations
Strengths include the global sample and the use of both implicit and explicit measures. Limitations involve the cross-sectional web-based design, potential sample biases, and aspects related to the validity of the SP-IAT.

Conclusion
Implicit measures of non-heterosexuality appear to be less tied to social factors than explicit assessments. In women, gynephilia may not necessarily serve as a proxy for non-heterosexuality. Moreover, women seem to exhibit greater fluidity in sexual preferences and behaviors than men.
Photoperiodic control of growth and reproduction in non-flowering plants
Authors: Biswal Durga Prasad , Panigrahi Kishore Chandra Sekhar 
Published: November 2024

Abstract
Photoperiodic responses shape plant fitness to the changing environment and are important regulators of growth, development, and productivity. Photoperiod sensing is one of the most important cues to track seasonal variations. It is also a major cue for reproductive success. The photoperiodic information conveyed through the combined action of photoreceptors and the circadian clock orchestrates an output response in plants. Multiple responses such as hypocotyl elongation, induction of dormancy, and flowering are photoperiodically regulated in seed plants (eg. angiosperms). Flowering plants such as Arabidopsis or rice have served as important model systems to understand the molecular players involved in photoperiodic signalling. However, photoperiodic responses in non-angiosperm plants have not been investigated and documented in detail. Genomic and transcriptomic studies have provided evidence on the conserved and distinct molecular mechanisms across the plant kingdom. In this review, we have attempted to compile and compare photoperiodic responses in the plant kingdom with a special focus on non-angiosperms.
The PIWI-interacting protein Gtsf1 controls the selective degradation of small RNAs in Paramecium
Authors: Charmant Olivia , Gruchota Julita , Arnaiz Olivier , Nowak Katarzyna P , Moisan Nicolas , Zangarelli Coralie , Bétermier Mireille , Anielska-Mazur Anna , Legros Véronique , Chevreux Guillaume , Nowak Jacek K , Duharcourt Sandra 
Published: November 2024

Abstract
Ciliates undergo developmentally programmed genome elimination, in which small RNAs direct the removal of transposable elements (TEs) during the development of the somatic nucleus. Twenty-five nucleotide scanRNAs (scnRNAs) are produced from the entire germline genome and transported to the maternal somatic nucleus, where selection of scnRNAs corresponding to germline-specific sequences is thought to take place. Selected scnRNAs then guide the elimination of TEs in the developing somatic nucleus. How germline-specific scnRNAs are selected remains to be determined. Here, we provide important mechanistic insights into the scnRNA selection pathway by identifying a Paramecium homolog of Gtsf1 as essential for the selective degradation of scnRNAs corresponding to retained somatic sequences. Consistently, we also show that Gtsf1 is localized in the maternal somatic nucleus where it associates with the scnRNA-binding protein Ptiwi09. Furthermore, we demonstrate that the scnRNA selection process is critical for genome elimination. We propose that Gtsf1 is required for the coordinated degradation of Ptiwi09-scnRNA complexes that pair with target RNA via the ubiquitin pathway, similarly to the mechanism suggested for microRNA target-directed degradation in metazoans.
BFVD—a large repository of predicted viral protein structures
Authors: Kim Rachel Seongeun , Levy Karin Eli , Mirdita Milot , Chikhi Rayan , Steinegger Martin 
Published: November 2024

Abstract
The AlphaFold Protein Structure Database (AFDB) is the largest repository of accurately predicted structures with taxonomic labels. Despite providing predictions for over 214 million UniProt entries, the AFDB does not cover viral sequences, severely limiting their study. To address this, we created the Big Fantastic Virus Database (BFVD), a repository of 351 242 protein structures predicted by applying ColabFold to the viral sequence representatives of the UniRef30 clusters. By utilizing homology searches across two petabases of assembled sequencing data, we improved 36% of these structure predictions beyond ColabFold’s initial results. BFVD holds a unique repertoire of protein structures as over 62% of its entries show no or low structural similarity to existing repositories. We demonstrate how a substantial fraction of bacteriophage proteins, which remained unannotated based on their sequences, can be matched with similar structures from BFVD. In that, BFVD is on par with the AFDB, while holding nearly three orders of magnitude fewer structures. BFVD is an important virus-specific expansion to protein structure repositories, offering new opportunities to advance viral research. BFVD can be freely downloaded at bfvd.steineggerlab.workers.dev and queried using Foldseek and UniProt labels at bfvd.foldseek.com.
Identifying key underlying regulatory networks and predicting targets of orphan C/D box SNORD116 snoRNAs in Prader–Willi syndrome
Authors: Gilmore Rachel B , Liu Yaling , Stoddard Christopher E , Chung Michael S , Carmichael Gordon G , Cotney Justin 
Published: November 2024

Abstract
Prader-Willi syndrome (PWS) is a rare neurodevelopmental disorder characterized by neonatal hypotonia, followed by hyperphagia and obesity. Most PWS cases exhibit megabase-scale deletions of paternally imprinted 15q11-q13 locus. However, several PWS patients have been identified harboring much smaller deletions encompassing the SNORD116 gene cluster, suggesting these genes are direct drivers of PWS phenotypes. This cluster contains 30 copies of individual SNORD116 C/D box small nucleolar RNAs (snoRNAs). Many C/D box snoRNAs have been shown to guide chemical modifications of RNA molecules, often ribosomal RNA (rRNA). Conversely, SNORD116 snoRNAs show no significant complementarity to rRNA and their targets are unknown. Since many reported PWS cases lack their expression, it is crucial to identify the targets and functions of SNORD116. To address this we modeled PWS in two distinct human embryonic stem cell (hESC) lines with two different sized deletions, differentiated each into neurons, and compared differential gene expression. This analysis identified a novel set of 42 consistently dysregulated genes. These genes were significantly enriched for predicted SNORD116 targeting and we demonstrated impacts on FGF13 protein levels. Our results demonstrate the need for isogenic background comparisons and indicate a novel gene regulatory network controlled by SNORD116 is likely perturbed in PWS patients.