bluuebunny/crossref_metadata_2025_split huggingface dataset:
poolHelper: An R package to help in designing Pool‐Seq studies
Authors: Carvalho João , Faria Rui , Butlin Roger K. , Sousa Vitor C. 
Published: July 2023

Abstract

Next‐generation sequencing of pooled samples (Pool‐seq) is an important tool in population genomics and molecular ecology. In Pool‐seq, the relative number of reads with an allele reflects the allele frequencies in the sample. However, unequal individual contributions to the pool and sequencing errors can lead to inaccurate allele frequency estimates, influencing downstream analysis. When designing Pool‐seq studies, researchers need to decide the pool size (number of individuals) and average depth of coverage (sequencing effort). An efficient sampling design should maximise the accuracy of allele frequency estimates while minimising the sequencing effort. We describe a novel tool to simulate single nucleotide polymorphism (SNP) data using coalescent theory and account for sources of uncertainty in Pool‐seq.

We introduce an R package, poolHelper, enabling users to simulate Pool‐seq data under different combinations of average depth of coverage and pool size, accounting for unequal individual contributions and sequencing errors, modelled by adjustable parameters. The mean absolute error is computed by comparing the sample allele frequencies obtained based on individual genotypes with the frequency estimates obtained with Pool‐seq.

poolHelper enables users to simulate multiple combinations of pooling errors, average depth of coverage, pool sizes and number of pools to assess how they influence the error of sample allele frequencies and expected heterozygosity. Using simulations under a single population model, we illustrate that increasing the depth of coverage does not necessarily lead to more accurate estimates, reinforcing that finding the best Pool‐seq study design is not straightforward. Moreover, we show that simulations can be used to identify different combinations of parameters with similarly low mean absolute errors. This can help users to define an effective sampling design by using those combinations of parameters that minimise the sequencing effort.

The poolHelper package provides tools for performing simulations with different combinations of parameters (e.g. pool size, depth of coverage, unequal individual contribution) before sampling and generating data, allowing users to define sampling schemes based on simulations. This allows researchers to focus on the best sampling scheme to answer their research questions. poolHelper is comprehensively documented with examples to guide effective use.
Biocarceral citizenship: Criminalizing through care in postapartheid South Africa
Authors: Rupcic Sonia 
Published: July 2023

AbstractThe story often told about HIV in South Africa is a celebratory one that foregrounds the relationship between seropositive citizens and health‐care institutions. In the last 20 years, the government has invested heavily in rolling out life‐sustaining antiretroviral medicines to all who need them, making HIV a firm ground upon which many residents claim protections from the state. This article explores the role of medicine in buttressing the carceral state. I proposebiocarceral citizenshipto characterize the way health‐care entitlements produce new relationships to the criminal legal system, not through active state surveillance but by extending the responsibilization expected of patients to the penal sphere. Drawing from 22 months of ethnographic research carried out in clinics and courtrooms in the town of Thohoyandou between 2014 and 2018, I apply this concept to both those who have experienced rape, for whom reporting to the (carceral) state is a condition of accessing HIV prophylaxis, and to those who are charged with rape, for whom adherence to antiretroviral medicines is used as evidence of weaponizing sickness. In parallel ways, therapeutic responsibilization exposes both groups to state violence. The article takes HIV‐related entitlements as a cipher for theorizing punishment beyond a critique of neoliberalism.
How does learners’ L2 utterance fluency relate to their L1? A meta‐analysis
Authors: Gao Jianmin , Sun Peijian Paul 
Published: July 2023

AbstractUnraveling how learners’ L2 fluency performance relates to their L1 is crucial for promoting L2 speaking assessment. Despite the consensus that learners’ L1 and L2 are correlated in several measures of utterance fluency, there have been variations in the correlation strength resulting from methodological differences. The current meta‐analysis aims to present an overall picture of the L1–L2 fluency relationship and investigate the moderating effect of methodological factors. We identified 16 studies with 137 effect sizes and 714 participants. Through a multi‐level meta‐analysis, we calculated the aggregate effect sizes of the relationship between L1 and L2 fluency and examined the potential moderating effect of five learner and task variables. The overall correlation was strongest in L1 and L2 breakdown fluency, followed by speed and composite fluency, and weakest in repair fluency. Based on the results of the moderator analyses, we assume that the relationship between L1 and L2 composite fluency may be affected by L2 learning context, task type, and task consistency. The findings have implications for future research design and L2 fluency assessment.
Melatonin in food allergy: Mechanism and potential therapy
Authors: Wang Hao , Yan Yuqi , Hung Ifen , Liu Chunxue , Yin Jie , Ge Liangpeng , Ren Wenkai 
Published: July 2023

AbstractFood allergy affects more than 500 million people in the world, and its prevalence is increasing at an alarming rate causing serious public health concerns; however, prevention and treatment methods are still under investigation and are relatively scarce so far. Insights on pathophysiology reveal a complex interplay of the immune cells (e.g., DCs, T cells, and B cells) resulting in allergy or tolerance. Studies have shown that melatonin metabolisms are altered in patients with allergic diseases, suggesting that melatonin might impact allergic diseases. Notably, melatonin can orchestrate the differentiation and function of immune cells. Additionally, the disease severities of many allergic diseases and the function of the immune system exhibit circadian rhythmicity. Therefore, melatonin, a rhythm regulator, may also act indirectly on the immune system through the circadian clock to regulate food allergies. Herein, we reviewed the impacts of melatonin on food allergy and its underlying regulatory mechanisms, providing a theoretical reference for melatonin as effective means of prevention and treatment for food allergy in the future.
Machine learning analysis of wing venation patterns accurately identifies Sarcophagidae, Calliphoridae and Muscidae fly species
Authors: Ling Min Hao , Ivorra Tania , Heo Chong Chin , Wardhana April Hari , Hall Martin Jonathan Richard , Tan Siew Hwa , Mohamed Zulqarnain , Khang Tsung Fei 
Published: July 2023

AbstractIn medical, veterinary and forensic entomology, the ease and affordability of image data acquisition have resulted in whole‐image analysis becoming an invaluable approach for species identification. Krawtchouk moment invariants are a classical mathematical transformation that can extract local features from an image, thus allowing subtle species‐specific biological variations to be accentuated for subsequent analyses. We extracted Krawtchouk moment invariant features from binarised wing images of 759 male fly specimens from the Calliphoridae, Sarcophagidae and Muscidae families (13 species and a species variant). Subsequently, we trained the Generalized, Unbiased, Interaction Detection and Estimation random forests classifier using linear discriminants derived from these features and inferred the species identity of specimens from the test samples. Fivefold cross‐validation results show a 98.56 ± 0.38% (standard error) mean identification accuracy at the family level and a 91.04 ± 1.33% mean identification accuracy at the species level. The meanF1‐score of 0.89 ± 0.02 reflects good balance of precision and recall properties of the model. The present study consolidates findings from previous small pilot studies of the usefulness of wing venation patterns for inferring species identities. Thus, the stage is set for the development of a mature data analytic ecosystem for routine computer image‐based identification of fly species that are of medical, veterinary and forensic importance.
Sedimentological and ichnological characterization of delta front mouth bars in a river‐dominated delta (Upper Cretaceous) from the La Anita Formation, Austral Basin, Argentina
Authors: Ponce Juan José , Carmona Noelia , Jait Damián , Cevallos Martín , Rojas Christian 
Published: July 2023

AbstractIntegrated sedimentological and ichnological studies in deltaic systems are key to determine whether a delta is river‐dominated, tide‐dominated, wave‐dominated or hybrid, and thus predict the distribution of their geometries and main reservoirs. The Austral Basin is one of the most important oil and gas basins from Argentina, and the Upper Cretaceous La Anita Formation has shown excellent attributes as a hydrocarbon reservoir. Analysis of eleven cores, supplemented by a large volume of well logging data and two‐dimensional and three‐dimensional seismic, allowed to recognize a river‐dominated deltaic system affected by hyperpycnal discharges and storm events. Four main facies associations were recognized (offshore, prodelta, delta front and interdistributary bay), being the delta front facies associations, the most recurrent facies and constituting the major reservoir of the La Anita Formation. Three types of deltaic mouth bars have been characterized in the delta front.Type Icorresponds to active mouth bars with preservation of sedimentary structures and bioturbated by suspension and deposit feeding organisms.Type IIrepresents the stopped progradation and the abandonment in the construction of mouth bars, which are completely reworked by suspension and deposit feeding organisms and, in some cases, affected by fair‐weather or storm‐wave processes at the top.Type IIIcomprises hyperpycnal mouth bars characterized by transitional and recurrent intervals of sedimentary structures, high concentration of phytodetritus, and paucity of bioturbation. The amalgamation and coalescence of these three types of sandy mouth bars produce lobe‐like geometries and are the main processes of delta front construction and progradation. This proposed model allows to explain the principal mechanism of construction of the delta front and can be applied to the analysis of other reservoirs where mouth bar architectural elements are dominant.
Prospective, observational study investigating the level of agreement between transcutaneous and invasive carbon dioxide measurements in critically ill emergency department patients
Authors: Farenden Scott , Chung Yewon , Cui Amy , Ferguson Ian 
Published: July 2023

BackgroundTranscutaneous carbon dioxide (Ptcco2) measurement is a non-invasive surrogate marker for arterial carbon dioxide (Paco2), which requires invasive arterial blood sampling. Use of Ptcco2has been examined in different clinical settings, however, most existing evidence in the adult emergency department (ED) setting shows insufficient agreement between the measurements. This study assessed the level of agreement between Ptcco2and Paco2in undifferentiated adult ED patients across multiple timepoints.MethodsThis prospective observational study (study period 2020–2021) assessed paired Ptcco2and Paco2measurements at four consecutive timepoints (0, 30, 60 and 90 min) in adult (aged 18 years or over) Australian ED patients requiring hospital admission and arterial catheter insertion. Agreement between the pairs was assessed using Bland-Altman analysis. It was prospectively determined by expert consensus that limits of ±4 mm Hg would be a clinically acceptable level of agreement between Ptcco2and Paco2.ResultsDuring the study period 168 paired Ptcco2and Paco2readings were taken from 42 adult ED patients. Bland-Altman analysis showed a mean Ptcco2reading 3.85 mm Hg higher than Paco2,although at each timepoint the 95% CIs breached the limit of 4 mm Hg difference. In addition, only 66% (111/168) of results fell within the clinically acceptable range.ConclusionThe level of agreement between Ptcco2and Paco2measurements may not be sufficiently precise for the adoption of Ptcco2monitoring in patients presenting to the ED.
Lung function tracking in children with perinatally acquired HIV following early antiretroviral therapy initiation
Authors: Gie André , Davies Claire , Vaida Florin , Morrison Julie , Maree David , Otwombe Kennedy , Browne Sara H , van der Zalm Marieke M , Cotton Mark F , Innes Steve , Goussard Pierre 
Published: July 2023

IntroductionLung disease remains a frequent complication in children with perinatal HIV infection (CHIV) and exposure without infection (CHEU), resulting in diminished lung function. In CHIV, early antiretroviral therapy (ART) initiation improves survival and extrapulmonary outcomes. However, it is unknown if there is benefit to lung function.MethodsCohorts of CHIV (ART initiated at median 4.0 months), CHEU and HIV-unexposed children (CHU) prospectively performed pulmonary function testing (PFT) consisting of spirometry, plethysmography and diffusing capacity from 2013 to 2020. We determined lung function trajectories for PFT outcomes comparing CHIV to CHU and CHEU to CHU, using linear mixed effects models with multiple imputation. Potential confounders included sex, age, height, weight, body mass index z-score, urine cotinine and Tanner stage.Results328 participants (122 CHIV, 126 CHEU, 80 CHU) performed PFT (ages 6.6–15.6 years). Spirometry (forced expiratory volume in 1 s, FEV1, forced vital capacity (FVC), FEV1/FVC) outcomes were similar between groups. In plethysmography, the mean residual volume (RV) z-score was 17% greater in CHIV than CHU (95% CI 1% to 33%, p=0.042). There was no difference in total lung capacity (TLC) or RV/TLC z-scores between groups. Diffusing capacity for carbon monoxide was similar in all groups, while alveolar volume (VA) differed between HIV groups by sex.ConclusionOur study indicates that early ART initiation can mitigate the loss of lung function in CHIV with lasting benefit through childhood; however, there remains concern of small airway disease. CHEU does not appear to disrupt childhood lung function trajectory.
Is $$d^*(2380)$$ a compact hexaquark state?
Authors: Pan Manying , Zhu Xinmei , Ping Jialun 
Published: July 2023

AbstractThe most fascinating dibaryon in the non-strange quark sector is$$d^*(2380)$$d∗(2380), which was reported by WASA-at-COSY Collaboration and confirmed by A2@MAMI Collaboration. The reported mass and decay width are$$M\approx 2.37$$M≈2.37GeV,$$\Gamma \approx 70$$Γ≈70MeV and the quantum numbers are$$IJ^P=03^+$$IJP=03+. The structure of$$d^*(2380)$$d∗(2380)is still in controversy. In the present calculation, the powerful method in few-body system, Gaussian expansion method (GEM) is employed to explore the structure of$$d^*(2380)$$d∗(2380)in the framework of constituent quark models without assuming the presupposed structure. The results show that the radius of$$d^*(2380)$$d∗(2380)is around 0.8 fm, it is a very compact object. Because of the compact structure, the color singlet-singlet component has a large overlap with the color octet-octet one, two colorless, large overlapped$$\Delta $$Δs dominate the state is possible.
Worry about Climate Change of Outdoor Recreation Participants: A Case Study in Türkiye
Authors: Aslan Ramazan , Köçer Musab Süleyman , Mizrak Sefa 
Published: July 2023

Abstract
Anthropogenic climate change (ACC) is considered to be one of the biggest threats to humanity in this century, with severe direct or indirect impacts on people’s lives. Such a significant threat causes serious concern, which can motivate low-level proenvironmental behavior and lead to serious health problems at high levels. Therefore, determining the level of this concern is crucial. Outdoor recreation participants, who are constantly in contact with nature, can closely witness the effects of ACC due to these interactions. Therefore, evaluating their ACC worry is essential. In this study, the aim was to determine the ACC worry levels of outdoor recreation participants. The research data were collected through an online survey from a sample reached through convenience sampling method throughout Türkiye. The data were analyzed using analysis of moment structures (AMOS) and Statistical Package for the Social Sciences (SPSS) software. The relationship between independent variables and ACC concern was revealed through ordinal logistic regression. The research found that the participants had a high level of concern about ACC, with a score of 3.50. It was also determined that this level of concern was influenced by variables such as the type of outdoor recreation, the duration of participation in outdoor recreation, and exposure to the effects of ACC. Considering that ACC can motivate proenvironmental behaviors, the research suggests that outdoor recreational participants with high levels of concern about ACC should not be ignored in the adaptation process.
Symptoms of depression and stress among migrant workers in Al Qassim, Saudi Arabia
Authors: Umar Anwar , Saquib Juliann , Haikal Amal Yassien Mohamed , Al Komi Omar , Alnajjar Anas Hasson , Rizky Wahyu Choirur , Muqresh Mohamad Ayham , Sayed Mustafa Mohamed , Almazrou Abdulrahman , Saquib Nazmus 
Published: July 2023

Background: Migrant workers make up a third of the population of Saudi Arabia, approximately 13 million. Mental health disorders among this population are common, but very limited data exist currently. Aims: To assess the prevalence of moderate to severe symptoms of depression and stress among a sample of migrant workers in Saudi Arabia. To identify whether migrant-specific factors, such as occupation, nationality, duration of migration, and work characteristics, are associated with depressive and stress symptoms. Methods: A cross-sectional study of 2,123 migrants was conducted in Al Qassim, Saudi Arabia. Depressive and stress symptoms were assessed with the Depression, Anxiety, and Stress Scale (DASS-21). The outcomes were categorized into two levels (i.e. mild or no symptoms versus moderate to severe symptoms). Univariate and multivariate binary logistic regressions were used to assess the relationship with potential covariates. Results: The prevalence of moderate to severe depressive and stress symptoms was 7.3% and 3.6%, respectively. These did not vary by the duration of stay in the country or weekly work hours. However, there was substantial variance in the symptoms by participants’ nationality and occupation. Participants from Bangladesh were 3.8 (95% CI [1.50, 9.62]) times more likely, and hospital cleaners were 6.5 (95% CI [2.12, 20.07]) times more likely to have depressive symptoms. Similarly, auto-repair workers were 6.3 times more likely to have symptoms of stress (95% CI [1.55, 25.90]). Conclusion: The prevalence of depressive and stress symptoms varied significantly depending on occupation and country of origin. It would behoove employers to screen for these mental health conditions and refer employees to the relevant healthcare services. Future studies could examine the feasibility of mental health screening programs among migrant employees.
Female directors and employment stability: A longitudinal analysis of the roles of ultimate owners and managers’ incentive compensation
Authors: Chen Ming-Yuan , Wang Yi-Ting 
Published: July 2023

This study examines the moderating role of ultimate owners in the relationship between female directors and employment stability, and tests whether this moderation can be achieved through a mediation process whereby female directors reduce top managers’ incentive compensation to enhance employment stability. We analyze longitudinal data of Taiwanese firms from 2005 to 2019 in a multilevel mediated-moderation model. Our results indicate that while female directors have a positive impact on employment stability, this effect is attenuated by ultimate owners’ private benefit-seeking control. We also find that this moderating effect can be realized by moderating the mediation process between female directors and employment stability. In addition, we explore the differences between family and non-family firms and consider the issue of critical mass. Overall, our study suggests that the value of a gender-diverse board for employment stability depends on appropriate governance structures. JEL Classification: D22, G30, J33, M51
Retinal changes after fluocinolone acetonide implant (ILUVIEN®) for DME: SD-OCT imaging assessment using ESASO classification
Authors: Leite João , Ferreira André , Castro Catarina , Coelho João , Borges Tânia , Correia Nuno , Pessoa Bernardete 
Published: July 2023

Introduction A detailed understanding of the anatomical and structural changes occurring in the retina following intravitreal fluocinolone acetonide implantation may help improve the management and prognosis of persistent or recurrent diabetic macular edema (DME). Methods Overall, 45 eyes (from 35 patients) with refractory center-involved DME received an intravitreal fluocinolone acetonide implant. They were monitored at baseline and at 6, 12, 24, and 36 months for best-corrected visual acuity (BCVA), central foveal thickness (CFT), and the seven retinal parameters used in the classification of diabetic maculopathy recently developed at the European School for Advanced Studies in Ophthalmology (ESASO). Results Within 6 months of implantation, significant improvements were evident in BCVA, CFT, maculopathy stage, and the percentage of eyes with: intraretinal cysts; CFT > 30% above the upper normal value; and disrupted or absent ellipsoid zone (EZ) and/or external limiting membrane (ELM). Significant improvements were still maintained at 36 months post-implantation. At month 36, early treatment with the implant (i.e., after < 6 previous intravitreal injections for DME) trended toward being more effective than later treatment in improving BCVA, CFT, maculopathy stage, and the percentage of eyes with CFT > 30% above the upper normal value. However, statistical significance was not achieved. Conclusion In persistent or recurrent DME, fluocinolone acetonide implantation can be effective in improving maculopathy stage and reducing the percentage of eyes with: intraretinal cysts; CFT > 30% above the upper normal value; and disrupted or absent EZ and/or ELM. It can also increase BCVA and reduce CFT.
Recanalization of occluded central veins in hemodialysis patients using a dual lumen microcatheter
Authors: Adiarto Suko 
Published: July 2023

Background: Percutaneous transluminal angioplasty (PTA) is the standard therapy for stenosis or occlusion of the central vein in patients with chronic kidney disease undergoing routine hemodialysis. In the case of chronic total occlusion (CTO) of the central vein, crossing the lesion might be the most challenging part of the procedure. Although several techniques have been successfully used, a new, additional strategy that is safer yet equally effective would be beneficial. Methods: We reported two cases of central vein occlusion in which the lesions could not be crossed by multiple escalating wires even with the support of a microcatheter. The wires could not penetrate the hardest part of the lesion and were always deflected to the false route. A dual lumen microcatheter was used as a support for the first wire and to facilitate the insertion of a second wire through the chronic occlusion. Results: The dual lumen microcatheter successfully facilitated wire crossing of the CTO lesion in two patients. Conclusions: Dual lumen microcatheters may serve as an alternative strategy to cross central vein occlusions during PTA.