bluuebunny/crossref_metadata_2025_split huggingface dataset:
Risk prediction strategies using intraoperative physiological data in adults undergoing surgery: a systematic review study protocol
Authors: Yong Shun Qi , Ang Gauri , Stubbs Daniel J 
Published: May 2024

Abstract
Postoperative mortality accounts for 7.7% of all global deaths, while postoperative complications increase 1-year mortality by 60%. Risk prediction models for postoperative complications and mortality can facilitate tailored risk mitigation strategies. However, most models incorporate only preoperative patient-related factors as predictors and do not capture dynamic risks or intraoperative events. This systematic review seeks to evaluate the predictive capability of intraoperative physiology derived from routine anaesthetic monitoring and the feature extraction methods for these variables. This review will include both prospective and retrospective studies that incorporate intraoperative physiological measurements into the development, validation or updating of a statistical prediction model, to identify those at risk of major end-organ (cardiovascular, pulmonary, renal and neurological) complications and mortality up-to 90 days postoperatively. We will identify models developed in two settings: those undergoing cardiac surgery and heterogeneous adult patient cohorts undergoing non-cardiac surgery. The review will be reported according to the 2020 Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. This review will evaluate the available literature on intraoperative physiology as predictor variables, to improve feature extraction methods for risk prediction models development while understanding how to capitalize on the vast routinely collected intraoperative physiological data sets that are increasingly available. This review is registered on PROSPERO, registration number CRD42023474384.
Emerging into the world: regulation and control of dormancy and sprouting in geophytes
Authors: Kumari Nirupma , Kumari Manhas Sonali , Jose-Santhi Joel , Kalia Diksha , Sheikh Firdous Rasool , Singh Rajesh Kumar 
Published: May 2024

AbstractGeophytic plants synchronize growth and quiescence with the external environment to survive and thrive under changing seasons. Together with seasonal growth adaptation, dormancy and sprouting are critical factors determining crop yield and market supply, as various geophytes also serve as major food, floriculture, and ornamental crops. Dormancy in such crops determines crop availability in the market, as most of them are consumed during the dormant stage. On the other hand, uniform/maximal sprouting is crucial for maximum yield. Thus, dormancy and sprouting regulation have great economic importance. Dormancy–sprouting cycles in geophytes are regulated by genetic, exogenous (environmental), and endogenous (genetic, metabolic, hormonal, etc.) factors. Comparatively, the temperature is more dominant in regulating dormancy and sprouting in geophytes, unlike above-ground tissues, where both photoperiod and temperature control are involved. Despite huge economic importance, studies concerning the regulation of dormancy and sprouting are scarce in the majority of geophytes. To date, only a few molecular factors involved in the process have been suggested. Recently, omics studies on molecular and metabolic factors involved in dormancy and growth regulation of underground vegetative tissues have provided more insight into the mechanism. Here, we discuss current knowledge of the environmental and molecular regulation and control of dormancy and sprouting in geophytes, and discuss challenges/questions that need to be addressed in the future for crop improvement.
The Feasibility and Efficacy of Warrior Health and Fitness: A 3-Month Fitness and Nutrition Program for Veterans
Authors: Horwitz Sarah D , Millstein Rachel A , McCarthy Megan D , Vanderweit Ryan , Fernandez Jaime , Hernandez Armando R , Wilson Victoria , Maggiolo Nicolette , Collins Emily , Hirschberg Ron , Cefalo Philip , Sylvia Louisa G 
Published: May 2024

ABSTRACT

Introduction
Veterans are at risk for mental and physical health problems but may not seek traditional health care services. Wellness-based interventions, including exercise and nutrition, have been associated with improvements in physical and mental health among this population. This study explores the acceptability, feasibility, and efficacy of a 3-month health and fitness program for veterans.

Materials and Methods
Participants in 2 time-based cohorts from 2019 to 2023 (cohort 1: n = 261; cohort 2: n = 256) were cleared by a physician to participate. Participants then completed a fitness test and self-reported surveys (e.g., quality of life, sleep, and pain) before and after the 3-month program. Participants were recruited to participate at one of three sites: Boston, MA Fort Myers, FL, or Tampa, FL. The 3-month program consisted of weekly, supervised group fitness and one-on-one sessions, nutritional consultations, yoga, and other wellness activities. Primary program outcomes were measured by fitness assessments, self-report surveys, program completion, and program satisfaction. Fitness assessments included measures of weight, body mass index, grip strength, waist to hip ratio, body fat, lean mass, fat mass, heart rate, and blood pressure (BP). Self-report measures included quality of life, depression, loneliness, sleep quality, pain intensity, and pain interference.

Results
In cohort 1, significant improvements were found for measures of weight (P = .01), left-handed grip strength (P &lt; .01), body fat percent (P &lt; .01), and quality of life (P &lt; .01). In cohort 2, significant improvements were found for measures of waist:hip ratio (P = .02), right and left-handed grip strength (P &lt; .01), body mass index (P = .02), body fat percent (P &lt; .01), and quality of life (P = .02). For both cohorts, pain intensity (cohort 1: P = .01, cohort 2: P &lt; .001) and pain interference (cohort 1: P = .02, cohort 2: P &lt; .001) increased significantly.

Conclusions
These data suggest that a 3-month health and fitness program for veterans is acceptable and feasible and may improve physical and mental health outcomes. Considerations for program retention and assessment completion are discussed.
Schopenhauer on the Futility of Suicide
Authors: Marshall Colin 
Published: May 2024

Abstract
Schopenhauer repeatedly claims that suicide is both foolish and futile. But while many commentators express sympathy for his charge of foolishness, most regard his charge of futility as indefensible even within his own system. In this paper, I offer a defence of Schopenhauer’s futility charge, based on metaphysical and psychological considerations. On the metaphysical front, Schopenhauer’s view implies that psychological connections extend beyond the death of an individual. Drawing on Parfit’s discussion of personal identity, I argue that those connections have personal significance, such that suicide does not allow one, as Hamlet hopes, simply ‘not to be’. On the psychological front, I argue that a distinction between agents’ intentions and underlying desires makes room for Schopenhauer’s claim that paradigmatic suicidal agents ultimately desire the opposite of what suicide accomplishes. I conclude by showing how this understanding of futility can buttress Schopenhauer’s charge of foolishness. My interpretation still leaves Schopenhauer vulnerable to certain objections, but shows that his account is more defensible than previous commentators have realized.
Diversity and Molecular Evolution of Nonvisual Opsin Genes across Environmental, Developmental, and Morphological Adaptations in Frogs
Authors: Boyette John L , Bell Rayna C , Fujita Matthew K , Thomas Kate N , Streicher Jeffrey W , Gower David J , Schott Ryan K 
Published: May 2024

Abstract
Nonvisual opsins are transmembrane proteins expressed in the eyes and other tissues of many animals. When paired with a light-sensitive chromophore, nonvisual opsins form photopigments involved in various nonvisual, light-detection functions including circadian rhythm regulation, light-seeking behaviors, and seasonal responses. Here, we investigate the molecular evolution of nonvisual opsin genes in anuran amphibians (frogs and toads). We test several evolutionary hypotheses including the predicted loss of nonvisual opsins due to nocturnal ancestry and potential functional differences in nonvisual opsins resulting from environmental light variation across diverse anuran ecologies. Using whole-eye transcriptomes of 81 species, combined with genomes, multitissue transcriptomes, and independently annotated genes from an additional 21 species, we identify which nonvisual opsins are present in anuran genomes and those that are also expressed in the eyes, compare selective constraint among genes, and test for potential adaptive evolution by comparing selection between discrete ecological classes. At the genomic level, we recovered all 18 ancestral vertebrate nonvisual opsins, indicating that anurans demonstrate the lowest documented amount of opsin gene loss among ancestrally nocturnal tetrapods. We consistently found expression of 14 nonvisual opsins in anuran eyes and detected positive selection in a subset of these genes. We also found shifts in selective constraint acting on nonvisual opsins in frogs with differing activity periods, habitats, distributions, life histories, and pupil shapes, which may reflect functional adaptation. Although many nonvisual opsins remain poorly understood, these findings provide insight into the diversity and evolution of these genes across anurans, filling an important gap in our understanding of vertebrate opsins and setting the stage for future research on their functional evolution across taxa.
SimRNAweb v2.0: a web server for RNA folding simulations and 3D structure modeling, with optional restraints and enhanced analysis of folding trajectories
Authors: Moafinejad S Naeim , de Aquino Belisa R H , Boniecki Michał J , Pandaranadar Jeyeram Iswarya P N , Nikolaev Grigory , Magnus Marcin , Farsani Masoud Amiri , Badepally Nagendar Goud , Wirecki Tomasz K , Stefaniak Filip , Bujnicki Janusz M 
Published: May 2024

Abstract
Research on ribonucleic acid (RNA) structures and functions benefits from easy-to-use tools for computational prediction and analyses of RNA three-dimensional (3D) structure. The SimRNAweb server version 2.0 offers an enhanced, user-friendly platform for RNA 3D structure prediction and analysis of RNA folding trajectories based on the SimRNA method. SimRNA employs a coarse-grained model, Monte Carlo sampling and statistical potentials to explore RNA conformational space, optionally guided by spatial restraints. Recognized for its accuracy in RNA 3D structure prediction in RNA-Puzzles and CASP competitions, SimRNA is particularly useful for incorporating restraints based on experimental data. The new server version introduces performance optimizations and extends user control over simulations and the processing of results. It allows the application of various hard and soft restraints, accommodating alternative structures involving canonical and noncanonical base pairs and unpaired residues, while also integrating data from chemical probing methods. Enhanced features include an improved analysis of folding trajectories, offering advanced clustering options and multiple analyses of the generated trajectories. These updates provide comprehensive tools for detailed RNA structure analysis. SimRNAweb v2.0 significantly broadens the scope of RNA modeling, emphasizing flexibility and user-defined parameter control. The web server is available at https://genesilico.pl/SimRNAweb.
Visualization of oxidized guanine nucleotides accumulation in living cells with split MutT
Authors: Fujikawa Yoshihiro , Kawai Hidehiko , Suzuki Tetsuya , Kamiya Hiroyuki 
Published: May 2024

Abstract
Cancer cells produce vast quantities of reactive oxygen species, leading to the accumulation of toxic nucleotides as 8-oxo-7,8-dihydro-2′-deoxyguanosine 5′-triphosphate (8-oxo-dGTP). The human MTH1 protein catalyzes the hydrolysis of 8-oxo-dGTP, and cancer cells are dependent on MTH1 for their survival. MTH1 inhibitors are possible candidates for a class of anticancer drugs; however, a reliable screening system using live cells has not been developed. Here we report a visualization method for 8-oxo-dGTP and its related nucleotides in living cells. Escherichia coli MutT, a functional homologue of MTH1, is divided into the N-terminal (1–95) and C-terminal (96–129) parts (Mu95 and 96tT, respectively). Mu95 and 96tT were fused to Ash (assembly helper tag) and hAG (Azami Green), respectively, to visualize the nucleotides as fluorescent foci formed upon the Ash-hAG association. The foci were highly increased when human cells expressing Ash-Mu95 and hAG-96tT were treated with 8-oxo-7,8-dihydro-2′-deoxyguanosine (8-oxo-dG) and 8-oxo-dGTP. The foci formation by 8-oxo-dG(TP) was strikingly enhanced by the MTH1 knockdown. Moreover, known MTH1 inhibitors and oxidizing reagents also increased foci. This is the first system that visualizes damaged nucleotides in living cells, provides an excellent detection method for the oxidized nucleotides and oxidative stress, and enables high throughput screening for MTH1 inhibitors.
GPSFun: geometry-aware protein sequence function predictions with language models
Authors: Yuan Qianmu , Tian Chong , Song Yidong , Ou Peihua , Zhu Mingming , Zhao Huiying , Yang Yuedong 
Published: May 2024

Abstract
Knowledge of protein function is essential for elucidating disease mechanisms and discovering new drug targets. However, there is a widening gap between the exponential growth of protein sequences and their limited function annotations. In our prior studies, we have developed a series of methods including GraphPPIS, GraphSite, LMetalSite and SPROF-GO for protein function annotations at residue or protein level. To further enhance their applicability and performance, we now present GPSFun, a versatile web server for Geometry-aware Protein Sequence Function annotations, which equips our previous tools with language models and geometric deep learning. Specifically, GPSFun employs large language models to efficiently predict 3D conformations of the input protein sequences and extract informative sequence embeddings. Subsequently, geometric graph neural networks are utilized to capture the sequence and structure patterns in the protein graphs, facilitating various downstream predictions including protein–ligand binding sites, gene ontologies, subcellular locations and protein solubility. Notably, GPSFun achieves superior performance to state-of-the-art methods across diverse tasks without requiring multiple sequence alignments or experimental protein structures. GPSFun is freely available to all users at https://bio-web1.nscc-gz.cn/app/GPSFun with user-friendly interfaces and rich visualizations.
Aggrescan4D: structure-informed analysis of pH-dependent protein aggregation
Authors: Bárcenas Oriol , Kuriata Aleksander , Zalewski Mateusz , Iglesias Valentín , Pintado-Grima Carlos , Firlik Grzegorz , Burdukiewicz Michał , Kmiecik Sebastian , Ventura Salvador 
Published: May 2024

Abstract
Protein aggregation is behind the genesis of incurable diseases and imposes constraints on drug discovery and the industrial production and formulation of proteins. Over the years, we have been advancing the Aggresscan3D (A3D) method, aiming to deepen our comprehension of protein aggregation and assist the engineering of protein solubility. Since its inception, A3D has become one of the most popular structure-based aggregation predictors because of its performance, modular functionalities, RESTful service for extensive screenings, and intuitive user interface. Building on this foundation, we introduce Aggrescan4D (A4D), significantly extending A3D’s functionality. A4D is aimed at predicting the pH-dependent aggregation of protein structures, and features an evolutionary-informed automatic mutation protocol to engineer protein solubility without compromising structure and stability. It also integrates precalculated results for the nearly 500,000 jobs in the A3D Model Organisms Database and structure retrieval from the AlphaFold database. Globally, A4D constitutes a comprehensive tool for understanding, predicting, and designing solutions for specific protein aggregation challenges. The A4D web server and extensive documentation are available at https://biocomp.chem.uw.edu.pl/a4d/. This website is free and open to all users without a login requirement.
PROSCA: an online platform for humanized scaffold mining facilitating rational protein engineering
Authors: Wang Xiaona , Zhang Yintao , Li Zengpeng , Duan Zixin , Guo Menghan , Wang Zhen , Zhu Feng , Xue Weiwei 
Published: May 2024

Abstract
Protein scaffolds with small size, high stability and low immunogenicity show important applications in the field of protein engineering and design. However, no relevant computational platform has been reported yet to mining such scaffolds with the desired properties from massive protein structures in human body. Here, we developed PROSCA, a structure-based online platform dedicated to explore the space of the entire human proteome, and to discovery new privileged protein scaffolds with potential engineering value that have never been noticed. PROSCA accepts structure of protein as an input, which can be subsequently aligned with a certain class of protein structures (e.g. the human proteome either from experientially resolved or AlphaFold2 predicted structures, and the human proteins belonging to specific families or domains), and outputs humanized protein scaffolds which are structurally similar with the input protein as well as other related important information such as families, sequences, structures and expression level in human tissues. Through PROSCA, the user can also get excellent experience in visualizations of protein structures and expression overviews, and download the figures and tables of results which can be customized according to the user's needs. Along with the advanced protein engineering and selection technologies, PROSCA will facilitate the rational design of new functional proteins with privileged scaffolds. PROSCA is freely available at https://idrblab.org/prosca/.
Healthcare worker burnout during a persistent crisis: a case–control study
Authors: Appelbom S , Nordström A , Finnes A , Wicksell R K , Bujacz A 
Published: May 2024

Abstract

Background
During the immediate outbreak of the COVID-19 pandemic, burnout symptoms increased among healthcare workers. Knowledge is needed on how early symptoms developed during the persistent crisis that followed the first pandemic wave.

Aims
To investigate if high levels of burnout symptoms during the first pandemic wave led to high burnout and depressive symptoms up to a year later, and if participation in psychological support was related to lower levels of symptoms.

Methods
A longitudinal case–control study followed 581 healthcare workers from two Swedish hospitals. Survey data were collected with a baseline in May 2020 and three follow-up assessments until September 2021. The case group was participants reporting high burnout symptoms at baseline. Logistic regression analyses were performed separately at three follow-ups with case–control group assignment as the main predictor and burnout and depression symptoms as outcomes, controlling for frontline work, changes in work tasks and psychological support participation.

Results
One out of five healthcare workers reported high burnout symptoms at baseline. The case group was more likely to have high burnout and depressive symptoms at all follow-ups. Participation in psychological support was unrelated to decreased burnout and depressive symptoms at any of the follow-ups.

Conclusions
During a persistent crisis, healthcare organizations should be mindful of psychological reactions among staff and who they place in frontline work early in the crisis. To better prepare for future healthcare crises, preventive measures on burnout are needed, both at workplaces and as part of the curricula in medical and nursing education.
Putative rhamnogalacturonan-II glycosyltransferase identified through callus gene editing which bypasses embryo lethality
Authors: Zhang Yuan , Sharma Deepak , Liang Yan , Downs Nick , Dolman Fleur , Thorne Kristen , Black Ian M , Pereira Jose Henrique , Adams Paul , Scheller Henrik V , O’Neill Malcolm , Urbanowicz Breeanna , Mortimer Jenny C 
Published: May 2024

Abstract
Rhamnogalacturonan II (RG-II) is a structurally complex and conserved domain of the pectin present in the primary cell walls of vascular plants. Borate cross-linking of RG-II is required for plants to grow and develop normally. Mutations that alter RG-II structure also affect cross-linking and are lethal or severely impair growth. Thus, few genes involved in RG-II synthesis have been identified. Here, we developed a method to generate viable loss-of-function Arabidopsis (Arabidopsis thaliana) mutants in callus tissue via CRISPR/Cas9-mediated gene editing. We combined this with a candidate gene approach to characterize the male gametophyte defective 2 (MGP2) gene that encodes a putative family GT29 glycosyltransferase. Plants homozygous for this mutation do not survive. We showed that in the callus mutant cell walls, RG-II does not cross-link normally because it lacks 3-deoxy-D-manno-octulosonic acid (Kdo) and thus cannot form the α-L-Rhap-(1→5)-α-D-kdop-(1→sidechain). We suggest that MGP2 encodes an inverting RG-II CMP-β-Kdo transferase (RCKT1). Our discovery provides further insight into the role of sidechains in RG-II dimerization. Our method also provides a viable strategy for further identifying proteins involved in the biosynthesis of RG-II.
SMEs, Trade Finance Markets and Instruments: A Review of the Issues with Reference to Asia
Authors: Cavoli Tony , Christian David , Shrestha Rashesh 
Published: May 2024

Abstract
Small and Medium Enterprises (SMEs) are an important source of employment and economic activity, but their expansion and growth may be limited by the existence of trade finance constraints due mainly to a lack of access to external sources of finance. We present a conceptual framework for understanding trade finance transactions, instruments, and participants; and map this framework to the available data used to measure trade finance. Finally, we present some stylized facts on the relationship between various trade finance instruments, and their possible links to SME outcomes with reference to ASEAN countries. We find that there are many (though imperfect) proxies for trade finance activities; and that improving trade finance is associated with more desirable SME outcomes.