bluuebunny/crossref_metadata_2025_split huggingface dataset:
HAPNEST: efficient, large-scale generation and evaluation of synthetic datasets for genotypes and phenotypes
Authors: Wharrie Sophie , Yang Zhiyu , Raj Vishnu , Monti Remo , Gupta Rahul , Wang Ying , Martin Alicia , O’Connor Luke J , Kaski Samuel , Marttinen Pekka , Palamara Pier Francesco , Lippert Christoph , Ganna Andrea 
Published: August 2023

Abstract

Motivation
Existing methods for simulating synthetic genotype and phenotype datasets have limited scalability, constraining their usability for large-scale analyses. Moreover, a systematic approach for evaluating synthetic data quality and a benchmark synthetic dataset for developing and evaluating methods for polygenic risk scores are lacking.

Results
We present HAPNEST, a novel approach for efficiently generating diverse individual-level genotypic and phenotypic data. In comparison to alternative methods, HAPNEST shows faster computational speed and a lower degree of relatedness with reference panels, while generating datasets that preserve key statistical properties of real data. These desirable synthetic data properties enabled us to generate 6.8 million common variants and nine phenotypes with varying degrees of heritability and polygenicity across 1 million individuals. We demonstrate how HAPNEST can facilitate biobank-scale analyses through the comparison of seven methods to generate polygenic risk scoring across multiple ancestry groups and different genetic architectures.

Availability and implementation
A synthetic dataset of 1 008 000 individuals and nine traits for 6.8 million common variants is available at https://www.ebi.ac.uk/biostudies/studies/S-BSST936. The HAPNEST software for generating synthetic datasets is available as Docker/Singularity containers and open source Julia and C code at https://github.com/intervene-EU-H2020/synthetic_data.
Biological interactions involving the myrmecophyte Hirtella physophora and its associates
Authors: Dejean Alain , Leroy Céline , Corbara Bruno , Azemar Frederic , Orivel Jérôme 
Published: August 2023

Abstract
In ecological communities, several species interact with one another to regulate their abundance. For example, mutualisms benefit all species involved, commensalism benefits one species but not the other, competition (for a resource) lowers the fitness of all species involved, whereas for predation, herbivory and parasitism one species is negatively affected by the other. We present the biological interactions between the myrmecophyte Hirtella physophora (i.e. a plant sheltering ants in hollow structures) and other organisms. Two Allomerus ants build gallery-shaped traps on this plant using hairs from its stems and the mycelium of an Ascomycota fungus to capture prey. They also use their refuse to provide their host plant and the fungi with nutrients (myrmecotrophy). Social wasps build their nests under the Hirtella leaves to benefit from the protection provided by Allomerus against army ants. Several insects can rob parts of Allomerus prey (cleptobiosis), but can be captured in turn. Finally, the reduviid Zelus annulosus, which foils attacks by Allomerus due to the production of a sticky substance that covers its egg masses and coats its legs, mostly attacks prey in groups and then shares them. Their populations are regulated by parasitoid wasps. Consequently, almost all possible biological interactions were noted in this study.
Trophic interactions between plants, pollinators, florivores and predators: a global systematic review
Authors: Camurça Letícia Menezes , Santos André Mauricio Melo , Castro Cibele Cardoso , Leite Ana Virgínia 
Published: August 2023

Abstract
The multitrophic relationships between plants, pollinators, florivores and spiders that predate floral visitors influence plant reproductive success, and some plant characteristics influence the choices of these animals. The aim of this study was to integrate the global data on these multitrophic relationships and answer the following questions. How are the studies distributed by biomes? What are the groups of plants, pollinators, florivores, spiders and prey recorded? What plant features explain the presence of florivores and spiders? What is the effect of spiders on fruit set? A systematic literature review was carried out to extract the necessary information. The most frequently observed families of plants, pollinators, florivores, spiders and prey were, respectively, herbaceous Asteraceae, Apidae (bees), Chrysomelidae (beetles), Thomisidae (spiders) and Bombyliidae (flies). The choice of flowers by florivores was explained by floral longevity. The choice of flowers by spiders was explained by life-form, symmetry, shape, pollination unit (more frequent in isolated flowers than in inflorescences) and resource (nectar). Spiders had a neutral general effect on fruit set, indicating that the study scale influenced the result. An important knowledge gap concerns the influence of florivores on fruit set. Studies that follow standardized methodologies are necessary.
Preconditioning program reduces the incidence of prolonged hospital stay after lung cancer surgery: Results from the Move For Surgery randomized clinical trial
Authors: Patel Yogita S , Sullivan Kerrie A , Churchill Isabella F , Beauchamp Marla K , Wald Joshua , Mbuagbaw Lawrence , Fahim Christine , Hanna Waël C 
Published: August 2023

Abstract

Background
Lung cancer resection is associated with high rates of prolonged hospital stay. It is presumed that preconditioning with aerobic exercise can shorten the postoperative duration of hospital stay, but this has not yet been demonstrated in trials after lung cancer surgery. The aim of this study was to perform a RCT to determine whether Move For Surgery (MFS), a home-based and wearable technology-enhanced preconditioning program before lung cancer surgery, is associated with a lower incidence of prolonged hospital stay when compared to usual preoperative care.

Methods
Patients undergoing lung resection for early-stage non-small cell lung cancer were enrolled before surgery into this blinded, single-site RCT, and randomized to either the MFS or control group in a 1 : 1 ratio. Patients in the MFS group were given a wearable activity tracker, and education about deep breathing exercises, nutrition, sleep hygiene, and smoking cessation. Participants were motivated/encouraged to reach incrementally increasing fitness goals remotely. Patients in the control group received usual preoperative care. The primary outcome was the difference in proportion of patients with hospital stay lasting more than 5 days between the MFS and control groups.

Results
Of 117 patients screened, 102 (87.2 per cent) were eligible, enrolled, and randomized (51 per trial arm). The majority (95 of 102, 93.1 per cent) completed the trial. Mean(s.d.) age was 67.2(8.8) years and there were 55 women (58 per cent). Type of surgery and rates of thoracotomy were not different between arms. The proportion of patients with duration of hospital stay over 5 days was 3 of 45 (7 per cent) in the MFS arm compared to 12 of 50 (24 per cent) in the control arm (P = 0.021).

Conclusion
MFS, a home-based and wearable technology-enhanced preconditioning program before lung cancer surgery, decreased the proportion of patients with a prolonged hospital stay. Registration number: NCT03689634 (http://www.clinicaltrials.gov).
318 Advancing Surgery in Africa Through Education, Mentorship and Research; the Surgery Interest Group of Africa (SIGAf)
Authors: Jesuyajolu D , Chineme-Anyaeze C , Abdullateef R , Opashola K , Moti T , Ekennia-Ebeh J , Adegbite O 
Published: August 2023

Abstract

Aim
Peer-to-peer surgical education has improved remarkably over the last decade with the aid of interest groups and charity organisations such as ASiT, IncisioN, NANSIG, and StarSURG. Despite these advances, there remains a lack of collaborative interest groups tailored to improving surgical education in Africa. The Surgery Interest Group of Africa (SIGAf) was established in response, and this study assesses its benefits in research, education, and mentorship.

Method
Feedback data from over 20 virtual sessions grouped into six categories over seven months in 2022 were analysed in this study. The categories included the surgical conference (Exposure to African Surgery), Career talks, Surgical lecture series, Exam preparation lectures, Research and audit lectures and Journal club activities. Data on participant confidence levels, helpfulness, engagement, and interest in the lecture content were examined using a 5-point Likert scale.

Results
705 responses were recorded across the six categories. The participants’ confidence level increased from an indeterminate pre-session to a statistically significant fairly confident level post-session. The attendees perceived the conference, career talks, lecture series, and journal club activities as helpful and had the highest level of interest. The surgical conference, career talk and surgical lecture series all had a reasonably good engagement.

Conclusions
This study has shown that the virtual sessions held by the Surgery Interest Group of Africa aimed at advancing surgery across the continent through education, mentorship, and research have achieved reasonable success.
829 Bariatric Surgery Versus Medical Therapy for the Management of Obesity in Patients With Type 2 Diabetes
Authors: Shirke M , Sreejith G , Ravikumar N , Roy S , Nizam Z , Tuli K 
Published: August 2023

Abstract

Aim
The risks associated with Type 2 Diabetes (T2DM) and obesity are increasingly becoming relevant across the world. This review aims to compare the clinical outcomes of the Bariatric surgery versus medical therapy in management of obese patients with diabetes.

Method
A systematic, electronic search was performed according to PRISMA guidelines to identify relevant articles that compared outcomes of medical therapy versus the Bariatric surgery procedures for obesity in diabetic patients.

Results
Twelve studies were included, enrolling 4097 patients. A greater reduction in HbA1c (SMD -12.27, 95% CI[-16.99, -7.56]) and BMI (SMD -10.77, 95% CI[-12.59, -8.95]), was observed in the surgical group. Secondary outcomes, weight (SMD -2.14, 95% CI [-6.30, -1.21]), total cholesterol (SMD -5.78, 95% CI[-9.92, -1.65]), waist circumference (SMD = -5.24 [-9.20, -1.28]) and fasting glucose (SMD -3.75, 95% CI [-6.79, -1.19]) were statistically significant in favour of the Bariatric surgery approach. No significant differences were observed in the triglycerides (SMD -1.55 [-4.53, 1.42], p = 0.31) and diastolic blood pressure (SMD -0.12 [-1.14, 0.90], p = 0.82). Systolic blood pressure (SMD 1.26, 95% CI[0.42, 2.11]) was significantly in favour of medical therapy.

Conclusions
The Bariatric surgery approach is associated with a reduced HbA1c and BMI. However, the long-term benefits of the procedure need to be evaluated. This review calls for robust trials comparing the two techniques to further strengthen the evidence.
682 Accidental Toothpick Ingestion Causing Liver Abscess – a Case Report and Review of Literature
Authors: Anwar S , Aldajani N , Alozaibi L 
Published: August 2023

Abstract

Introduction
Perforation due to foreign body ingestion leading to pyogenic liver abscess is an unusual but fatal event. We present a rare case of accidentally ingested toothpick that perforated the duodenum and migrated to the liver causing abscess.

Case Presentation
A 40-year-old gentleman presented with symptoms and signs of sepsis. He reported having eaten dry fish and chicken with bones 4 days prior to presentation. Abdominal computed tomography (CT) scan revealed hepatic collection containing a linear object in the middle. Non-operative management improved patient’s general condition but an increase in the size of collection lead to operative management.

Discussion
Usual course of formation of a pyogenic liver abscess is due to ascending cholangitis or infections causing hematogenous spread. Such an event due to a foreign body perforating the gastro-intestinal tract and migrating to liver is rarely seen. Presentation ranges from mild abdominal pain to full blown septicemia. Diagnosis is challenging as patients may present with vague symptoms, or sometimes don’t even remember having ingested an indigestible object. A trial of conservative management can be given to stable patients who improve, but deterioration necessitates surgical intervention.

Conclusions
Pyogenic liver abscess due to foreign body ingestion leading to intestinal perforation and displacing to liver is seldom encountered, and a toothpick leading to such an event is a very rare event. Patients may improve clinically with non-operative management; definitive management lies in the surgical removal of foreign body.
Individualized Antibiotic Plans as a Quality Improvement Initiative to Reduce Carbapenem Use for Hematopoietic Cell Transplant Patients at a Freestanding Pediatric Hospital
Authors: Brothers Adam W , Pak Daniel J , Poole Nicole M , Kronman Matthew P , Bettinger Brendan , Wilkes Jennifer J , Carpenter Paul A , Englund Janet A , Weissman Scott J 
Published: August 2023

Abstract

Background
Providers must balance effective empiric therapy against toxicity risks and collateral damage when selecting antibiotic therapy for patients receiving hematopoietic cell transplant (HCT). Antimicrobial stewardship interventions during HCT are often challenging due to concern for undertreating potential infections.

Methods
In an effort to decrease unnecessary carbapenem exposure for patients undergoing HCT at our pediatric center, we implemented individualized antibiotic plans (IAPs) to provide recommendations for preengraftment neutropenia prophylaxis, empiric treatment of febrile neutropenia, and empiric treatment for hemodynamic instability. We compared monthly antibiotic days of therapy (DOT) adjusted per 1000 patient-days for carbapenems, antipseudomonal cephalosporins, and all antibiotics during two 3-year periods immediately before and after the implementation of IAPs to measure the impact of IAP on prescribing behavior. Bloodstream infection (BSIs) and Clostridioides difficile (CD) positivity test rates were also compared between cohorts. Last, providers were surveyed to assess their experience of using IAPs in antibiotic decision making.

Results
Overall antibiotic use decreased after the implementation of IAPs (monthly reduction of 19.6 DOT/1000 patient-days; P = .004), with carbapenems showing a continuing decline after IAP implementation. BSI and CD positivity rates were unchanged. More than 90% of providers found IAPs to be either extremely or very valuable for their practice.

Conclusions
Implementation of IAPs in this high-risk HCT population led to reduction in overall antibiotic use without increase in rate of BSI or CD test positivity. The program was well received by providers.
Comparison of Bivalent and Monovalent mRNA Vaccine Boosters
Authors: Wong Carlos K H , Lau Kristy T K , Au Ivan C H , Lau Eric H Y , Cowling Benjamin J 
Published: August 2023

Abstract
In this cohort study conducted in Hong Kong where both bivalent and monovalent formulations of BNT162b2 were available, there were no significant differences in the mortality or hospitalization between those who received bivalent and monovalent mRNA as second boosters. Bivalent and monovalent mRNA boosters appear equally protective against clinical outcomes.
Predicting target lesion failure following percutaneous coronary intervention through machine learning risk assessment models
Authors: Mamas Mamas A , Roffi Marco , Fröbert Ole , Chieffo Alaide , Beneduce Alessandro , Matetic Andrija , Tonino Pim A L , Paunovic Dragica , Jacobs Lotte , Debrus Roxane , El Aissaoui Jérémy , van Leeuwen Frank , Kontopantelis Evangelos 
Published: August 2023

Abstract

Aims
Central to the practice of precision medicine in percutaneous coronary intervention (PCI) is a risk-stratification tool to predict outcomes following the procedure. This study is intended to assess machine learning (ML)-based risk models to predict clinically relevant outcomes in PCI and to support individualized clinical decision-making in this setting.

Methods and results
Five different ML models [gradient boosting classifier (GBC), linear discrimination analysis, Naïve Bayes, logistic regression, and K-nearest neighbours algorithm) for the prediction of 1-year target lesion failure (TLF) were trained on an extensive data set of 35 389 patients undergoing PCI and enrolled in the global, all-comers e-ULTIMASTER registry. The data set was split into a training (80%) and a test set (20%). Twenty-three patient and procedural characteristics were used as predictive variables. The models were compared for discrimination according to the area under the receiver operating characteristic curve (AUC) and for calibration. The GBC model showed the best discriminative ability with an AUC of 0.72 (95% confidence interval 0.69–0.75) for 1-year TLF on the test set. The discriminative ability of the GBC model for the components of TLF was highest for cardiac death with an AUC of 0.82, followed by target vessel myocardial infarction with an AUC of 0.75 and clinically driven target lesion revascularization with an AUC of 0.68. The calibration was fair until the highest risk deciles showed an underestimation of the risk.

Conclusion
Machine learning–derived predictive models provide a reasonably accurate prediction of 1-year TLF in patients undergoing PCI. A prospective evaluation of the predictive score is warranted.

Registration
Clinicaltrial.gov identifier is NCT02188355.
Building twenty-first century agricultural research and extension capacity in Africa
Authors: Jayne T S , Zingore Shamie , Niang Amadou Ibra , Palm Cheryl , Shah Saloni , Sanchez Pedro 
Published: August 2023

Abstract
This study explores the effectiveness of international efforts to build the capacities of national agricultural research and extension systems (NARES) in Africa and proposes actions to improve the performance of these systems. Analysis draws on agricultural research expenditure data in Africa, Asia and Latin America and key informant interviews of 26 senior representatives of international and African research organisations. We conclude that donors and international partners have increased the supply of professional African scientists while contributing relatively little to the institutional capacities of African NARES. We propose a transition to what we call a twenty-first century African-led agricultural research system and identify actions to manifest it.
Stroke risk in women with atrial fibrillation
Authors: Buhari Hifza , Fang Jiming , Han Lu , Austin Peter C , Dorian Paul , Jackevicius Cynthia A , Yu Amy Y X , Kapral Moira K , Singh Sheldon M , Tu Karen , Ko Dennis T , Atzema Clare L , Benjamin Emelia J , Lee Douglas S , Abdel-Qadir Husam 
Published: August 2023

AbstractBackground and aimsFemale sex is associated with higher rates of stroke in atrial fibrillation (AF) after adjustment for other CHA2DS2-VASc factors. This study aimed to describe sex differences in age and cardiovascular care to examine their relationship with stroke hazard in AF.MethodsPopulation-based cohort study using administrative datasets of people aged ≥66 years diagnosed with AF in Ontario between 2007 and 2019. Cause-specific hazard regression was used to estimate the adjusted hazard ratio (HR) for stroke associated with female sex over a 2-year follow-up. Model 1 included CHA2DS2-VASc factors, with age modelled as 66–74 vs. ≥ 75 years. Model 2 treated age as a continuous variable and included an age–sex interaction term. Model 3 further accounted for multimorbidity and markers of cardiovascular care.ResultsThe cohort consisted of 354 254 individuals with AF (median age 78 years, 49.2% female). Females were more likely to be diagnosed in emergency departments and less likely to receive cardiologist assessments, statins, or LDL-C testing, with higher LDL-C levels among females than males. In Model 1, the adjusted HR for stroke associated with female sex was 1.27 (95% confidence interval 1.21–1.32). Model 2 revealed a significant age–sex interaction, such that female sex was only associated with increased stroke hazard at age &gt;70 years. Adjusting for markers of cardiovascular care and multimorbidity further decreased the HR, so that female sex was not associated with increased stroke hazard at age ≤80 years.ConclusionOlder age and inequities in cardiovascular care may partly explain higher stroke rates in females with AF.
Erosional exhumation of carbonate rock facilitates dispersal-mediated allopatric speciation in freshwater fishes
Authors: Kim Daemin , Stokes Maya F , Ebersole Sandy , Near Thomas J 
Published: August 2023

Abstract
A fundamental goal of evolutionary biology is to understand the mechanisms that generate and maintain biodiversity. Discovery and delimitation of species represent essential prerequisites for such investigations. We investigate a freshwater fish species complex comprising Etheostoma bellator and the endangered E. chermocki, which is endemic to the Black Warrior River system in Alabama, USA, a global hotspot of temperate freshwater biodiversity. Phylogenomic analyses delimit five geographically disjunct species masquerading as E. bellator. Three of these new species exhibit microendemic distributions comparable to that of E. chermocki raising the possibility that they also require protection. The species of the complex are found in streams flowing over carbonate rock and they are separated by waterways flowing over siliciclastic rock, a geographic pattern dictated by the underlying stratigraphy and structural geology. Over time, rivers have eroded downward through layers of siliciclastic rocks in the basin, gradually exposing underlying carbonate rock, the substrate of suitable habitat today. Our results suggest that episodic dispersal to patches of suitable habitat set the stage for allopatric speciation in the species complex. Our study suggests that the presence of heterogeneous rock can facilitate dispersal-mediated allopatric speciation in freshwater organisms in the absence of external tectonic or climatic perturbations.
Identifying barriers to the production and use of routine health information in Western Province, Zambia
Authors: Lee Na-Mee , Singini Douglas , Janes Craig R , Grépin Karen A , Liu Jennifer A 
Published: August 2023

Abstract
Recent decades of improvements to routine health information systems in low- and middle-income countries (LMICs) have increased the volume of health data collected. However, countries continue to face several challenges with quality production and use of information for decision-making at sub-national levels, limiting the value of health information for policy, planning and research. Improving the quality of data production and information use is thus a priority in many LMICs to improve decision-making and health outcomes. This qualitative study identified the challenges of producing and using routine health information in Western Province, Zambia. We analysed the interview responses from 37 health and social sector professionals at the national, provincial, district and facility levels to understand the barriers to using data from the Zambian health management information system (HMIS). Respondents raised several challenges that we categorized into four themes: governance and health system organization, geographic barriers, technical and procedural barriers, and challenges with human resource capacity and staff training. Staff at the facility and district levels were arguably the most impacted by these barriers as they are responsible for much of the labour to collect and report routine data. However, facility and district staff had the least authority and ability to mitigate the barriers to data production and information use. Expectations for information use should therefore be clearly outlined for each level of the health system. Further research is needed to understand to what extent the available HMIS data address the needs and purposes of the staff at facilities and districts.