bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative transcriptomics provides insights into molecular mechanisms of zinc tolerance in the ectomycorrhizal fungus Suillus luteus
Authors: Smith Alexander , Fletcher Jessica , Swinnen Janne , Jonckheere Karl , Bazzicalupo Anna , Liao Hui-Ling , Ragland Greg , Colpaert Jan , Lipzen Anna , Tejomurthula Sravanthi , Barry Kerrie , V. Grigoriev Igor , Ruytinx Joske , Branco Sara 
Published: July 2024

Abstract
Zinc (Zn) is a major soil contaminant and high Zn levels can disrupt growth, survival, and reproduction of fungi. Some fungal species evolved Zn tolerance through cell processes mitigating Zn toxicity, although the genes and detailed mechanisms underlying mycorrhizal fungal Zn tolerance remain unexplored. To fill this gap in knowledge, we investigated the gene expression of Zn tolerance in the ectomycorrhizal fungus Suillus luteus. We found that Zn tolerance in this species is mainly a constitutive trait that can also be environmentally dependent. Zinc tolerance in S. luteus is associated with differences in the expression of genes involved in metal exclusion and immobilization, as well as recognition and mitigation of metal-induced oxidative stress. Differentially expressed genes were predicted to be involved in transmembrane transport, metal chelation, oxidoreductase activity, and signal transduction. Some of these genes were previously reported as candidates for S. luteus Zn tolerance, while others are reported here for the first time. Our results contribute to understanding the mechanisms of fungal metal tolerance and pave the way for further research on the role of fungal metal tolerance in mycorrhizal associations.
Selection with two alleles of X-linkage and its application to the fitness component analysis of OdsH in Drosophila
Authors: Sun Sha , Ting Chau-Ti , Wu Chung-I 
Published: July 2024

Abstract
In organisms with the XY sex-determination system, there is an imbalance in the inheritance and transmission of the X chromosome between males and females. Unlike an autosomal allele, an X-linked recessive allele in a female will have phenotypic effects on its male counterpart. Thus, genes located on the X chromosome are of particular interest to researchers in molecular evolution and genetics. Here we present a model for selection with two alleles of X-linkage to understand fitness components associated with genes on the X chromosome. We apply this model to the fitness analysis of an X-linked gene, OdsH (16D), in the fruit fly Drosophila melanogaster. The function of OdsH is involved in sperm production and the gene is rapidly evolving under positive selection. Using site-directed gene targeting, we generated functional and defective OdsH variants tagged with the eye-color marker gene white. We compare the allele frequency changes of the two OdsH variants, each directly competing against a wild-type OdsH allele in concurrent but separate experimental populations. After 20 generations, the two genetically modified OdsH variants displayed a 40% difference in allele frequencies, with the functional OdsH variant demonstrating an advantage over the defective variant. Using maximum likelihood estimation, we determined the fitness components associated with the OdsH alleles in males and females. Our analysis revealed functional aspects of the fitness determinants associated with OdsH, and that sex-specific fertility and viability consequences both contribute to selection on an X-linked gene.
People-centered primary care measures in health equity: a perspective of urban–rural comparison in Beijing, China
Authors: Peng Yingchun , Zhai Shaoqi , Zhang Zhiying , Zhang Ruyi , Zhang Jiaying , Jin Qilin , Zhou Jiaojiao , Chen Jingjing 
Published: July 2024

Abstract
Person-centered primary care measures (PCPCM) facilitate high-quality and culturally appropriate primary care. Access to PCPCM remains unequal between rural and urban areas, and the available evidence on rural PCPCM is still lacking. A cross-sectional survey was conducted with stratified sampling by regions, and four districts (Xicheng, Fengtai, Huairou, and Daxing) in Beijing were selected to test the performance of PCPCM in both urban and rural areas. Descriptive statistical methods were used to compare the urban–rural differences in the demographic characteristics of PCPCM. Correlation and regression analyses were performed to determine the associations between PCPCM in demographics and utilization of primary care. The PCPCM showed good reliability and validity in both urban and rural areas (P &lt; .001), slightly lower in rural areas, but scores of rural PCPCM (R-PCPCM) in all items were lower than urban PCPCM (U-PCPCM). Patients in either the preferred urban or rural health centers all showed the highest PCPCM scores, with U-PCPCM= 3.31 for CHCs and R-PCPCM= 3.10 for RHCs, respectively. Patients in urban areas were more likely to receive higher-quality primary care than in rural areas (P &lt; .001). Patients who preferred hospitals (β = 2.61, P &lt; .001) or CHCs (β = 0.71, P = .003) as providers was a significant positive predictor of U-PCPCM but it was the preference for hospitals (β = 2.95, P &lt; .001) for R-PCPCM. Urban–rural differences existed in the performance of PCPCM, with rural areas typically more difficult to access better PCPCM. To promote health equity in rural areas, healthcare providers should strive to minimize urban–rural differences in the quality and utilization of primary care services as much as feasible.
Christian Addiction: The Metaphor of Debt-Bondage in Roman Theology
Authors: McCracken Lucas 
Published: July 2024

Abstract
What exactly is addiction? Scholars, clinicians, and addicts themselves consistently arrive at a fork in the road in their respective quests for the meaning of addiction: choice or compulsion, crime or disease? Despite these many inquiries, one important aspect of addiction’s past remains unexamined—its deep theological history. Christian theologians writing in Latin from the second to the seventeenth century used the term addiction metaphorically to describe the sinful human condition. In this article, I uncover the genesis and development of the Christian addiction metaphor in the writings of Roman theologians Tertullian, Ambrose, and Augustine. I analyze their theologies of addiction to show how the language and logic of Roman pecuniary jurisprudence structures their thinking about sin, salvation, and free will. To conclude, I suggest that the disease-crime ambivalence constitutive of our contemporary understanding of addiction originated in their oxymoronic definition of sin as both generational enslavement and willful servitude.
Rationalizing irrational prescribing—infection-related attitudes and practices across paediatric surgery specialties in a hospital in South India
Authors: Surendran Surya , Nampoothiri Vrinda , Dhar Puneet , Holmes Alison , Singh Sanjeev , Charani Esmita 
Published: July 2024

Abstract

Background and objectives
Antibiotic use in paediatric surgical specialties is understudied. We investigated the antibiotic prescribing practices of paediatric general and cardiovascular surgical teams in a tertiary hospital in South India.

Methods
Mixed-methods study including observations from ward rounds, semi-structured interviews, and review of antibiotic prescribing. Field notes from observations and interview transcripts were coded using NVivo and thematically analysed. Data collection and analysis were iterative and continued until thematic saturation. Quantitative data were analysed using descriptive statistics.

Results
Data included 62 h of observation, 24 interviews, one case study and 200 patient chart reviews (100/specialty). Senior surgeons make key decisions, referring to their own experience when prescribing antibiotics. Being outcome-driven, the doctors often prescribe antibiotics at the earliest indication of infection with a reluctance to de-escalate, even when an infection is not diagnosed. This practice is more acute among surgeons who consider themselves responsible for their patients’ health and attribute the consistently low surgical site infection rates to this practice.
In general surgery, 83.3% (80/96; 4 lost to follow-up) of patients were prescribed antibiotics for the duration of their stay with oral antibiotics prescribed at discharge. The surgeons use antibiotics prophylactically for patients who may be vulnerable to infection. The antimicrobial stewardship team was considered to have limited influence in the decision-making process.

Conclusions
Outcome-driven decision-making in surgery leads to overprescription of antibiotics and prolonged surgical prophylaxis. The rationale for suboptimal practices is complicated by the surgeons’ beliefs about the contextual determinants of health in India.
Performance Evaluation of 2 FDA-Approved Fentanyl Immunoassays against LC-MS/MS Reference
Authors: Militello Leah , Gqamana Putuma P , McLean Betty , Laurey Jesse , Rudy Daniel , McMaster Jeffrey M , Zhang Y Victoria 
Published: July 2024

Abstract

Background
Fentanyl, a synthetic opioid, has caused many recent overdose deaths. Diagnosis of fentanyl abuse is not served by traditional opiate assays due to differences in chemical structure between synthetics and natural opioids. To our knowledge, this is the first study that uses liquid chromatography-tandem mass spectrometry (LC-MS/MS) as the reference method to evaluate and compare the ARK Fentanyl II Assay (ARK II) and the Fentanyl II Enzyme Immunoassay by Roche (FEN2). The ARK II is designed to detect fentanyl in urine samples, whereas the FEN2 is designed to detect norfentanyl, which is the major metabolite.

Methods
Two hundred patient urine samples including 100 positive and 100 negative samples according to an in-house LC-MS/MS assay were selected for the study. These samples were tested using the ARK II and the FEN2 to determine their performances relative to LC-MS/MS results.

Results
The FEN2 showed a positive and negative predictive value of 100% and 97% and a concordance with LC-MS/MS of 98.5% (kappa 0.97). The ARK II showed a positive and negative predictive value of 100% and 95% and a concordance with LC-MS/MS of 97.5% (kappa 0.95). Additionally, the FEN2 accurately identified 9 positive samples with a range of fentanyl concentrations from 0 to 18 ng/mL for which norfentanyl levels were less than the cutoff of 5 ng/mL, indicating potentially greater sensitivity than otherwise stated.

Conclusions
The FEN2 and the ARK II were evaluated to be similar in terms of positive and negative predictive value during the analysis of 200 patient samples, as well as equally concordant with the LC-MS/MS reference, despite differences in design.
Measuring cognitive effort using tabular transformer-based language models of electronic health record-based audit log action sequences
Authors: Kim Seunghwan , Warner Benjamin C , Lew Daphne , Lou Sunny S , Kannampallil Thomas 
Published: July 2024

Abstract

Objectives
To develop and validate a novel measure, action entropy, for assessing the cognitive effort associated with electronic health record (EHR)-based work activities.

Materials and Methods
EHR-based audit logs of attending physicians and advanced practice providers (APPs) from four surgical intensive care units in 2019 were included. Neural language models (LMs) were trained and validated separately for attendings’ and APPs’ action sequences. Action entropy was calculated as the cross-entropy associated with the predicted probability of the next action, based on prior actions. To validate the measure, a matched pairs study was conducted to assess the difference in action entropy during known high cognitive effort scenarios, namely, attention switching between patients and to or from the EHR inbox.

Results
Sixty-five clinicians performing 5 904 429 EHR-based audit log actions on 8956 unique patients were included. All attention switching scenarios were associated with a higher action entropy compared to non-switching scenarios (P &lt; .001), except for the from-inbox switching scenario among APPs. The highest difference among attendings was for the from-inbox attention switching: Action entropy was 1.288 (95% CI, 1.256-1.320) standard deviations (SDs) higher for switching compared to non-switching scenarios. For APPs, the highest difference was for the to-inbox switching, where action entropy was 2.354 (95% CI, 2.311-2.397) SDs higher for switching compared to non-switching scenarios.

Discussion
We developed a LM-based metric, action entropy, for assessing cognitive burden associated with EHR-based actions. The metric showed discriminant validity and statistical significance when evaluated against known situations of high cognitive effort (ie, attention switching). With additional validation, this metric can potentially be used as a screening tool for assessing behavioral action phenotypes that are associated with higher cognitive burden.

Conclusion
An LM-based action entropy metric—relying on sequences of EHR actions—offers opportunities for assessing cognitive effort in EHR-based workflows.
Telemedicine appointments are more likely to be completed than in-person healthcare appointments: a retrospective cohort study
Authors: Cummins Mollie R , Tsalatsanis Athanasios , Chaphalkar Chaitanya , Ivanova Julia , Ong Triton , Soni Hiral , Barrera Janelle F , Wilczewski Hattie , Welch Brandon M , Bunnell Brian E 
Published: July 2024

AbstractObjectivesMissed appointments can lead to treatment delays and adverse outcomes. Telemedicine may improve appointment completion because it addresses barriers to in-person visits, such as childcare and transportation. This study compared appointment completion for appointments using telemedicine versus in-person care in a large cohort of patients at an urban academic health sciences center.Materials and MethodsWe conducted a retrospective cohort study of electronic health record data to determine whether telemedicine appointments have higher odds of completion compared to in-person care appointments, January 1, 2021, and April 30, 2023. The data were obtained from the University of South Florida (USF), a large academic health sciences center serving Tampa, FL, and surrounding communities. We implemented 1:1 propensity score matching based on age, gender, race, visit type, and Charlson Comorbidity Index (CCI).ResultsThe matched cohort included 87 376 appointments, with diverse patient demographics. The percentage of completed telemedicine appointments exceeded that of completed in-person care appointments by 9.2 points (73.4% vs 64.2%, P &lt; .001). The adjusted odds ratio for telemedicine versus in-person care in relation to appointment completion was 1.64 (95% CI, 1.59-1.69, P &lt; .001), indicating that telemedicine appointments are associated with 64% higher odds of completion than in-person care appointments when controlling for other factors.DiscussionThis cohort study indicated that telemedicine appointments are more likely to be completed than in-person care appointments, regardless of demographics, comorbidity, payment type, or distance.ConclusionTelemedicine appointments are more likely to be completed than in-person healthcare appointments.
Smart Chemometric-Assisted Spectrophotometric Approaches for Simultaneous Quantification of Tertiary Combination Recommended for COVID-19 Supportive Treatments With Their Greenness Assessment
Authors: Soliman Rabab M , Tantawy Mahmoud A , Mostafa Nadia M , Fayez Yasmin M , Monir Hany H , Rostom Yasmin 
Published: July 2024

Abstract

Background
There is an increasing interest of the scientific community in developing innovative methodologies for their analysis needs within a green analytical chemistry framework. UV spectrophotometry is one of the most promising eco-friendly methods, which is integrated with advanced chemometric tools to enhance the selectivity of the analysis of complex mixtures with severe overlapped signals.

Objective
Simultaneous determination of a triple-combination of pseudoephedrine hydrochloride (PSE), carbinoxamine maleate (CRX), and paracetamol (PAR) using an artificial intelligence system and multivariate calibration methods. This combination has been recently recommended for COVID-19 home-treated patients as part of a symptomatic treatment.

Methods
Namely, the suggested models are artificial neural networks, partial least-squares, and principal component regression. The proposed algorithms were optimized and developed with the aid of a five-level, three-factor experimental design.

Results
The investigated methods were applied over the concentration range of 100–180 μg/mL, 18–16 μg/mL, and 4–12 μg/mL for PSE, CRX, and PAR, respectively. The models’ validation results demonstrated excellent recoveries (around 98 to 102%), signaling the approaches’ outstanding resolution capacity for the cited compounds in the presence of common excipients. The outcomes of the studied methods were statistically compared to the official approaches, and no significant difference was found.

Conclusions
The suggested models were efficiently employed to determine the selected drugs in their combined tablets without any initial separation steps. The impact of these methods on the environment was evaluated via greenness tools: namely, the National Environmental Method Index, Raynie and Driver’s green assessment method, Analytical Eco-Scale, Green Analytical Procedure Index, and Analytical Greenness Metric.

Highlights
Green chemometric quality assessment of PSE, CRX, and PAR in their pure and pharmaceutical dosage forms. The established approaches are innovative, sustainable, smart, fast, selective, and cost-effective. These models are potential green nominees for routine analysis of the investigated mixture in quality control laboratories.
Effect of cordyceps militaris on growth performance, antioxidant capacity, and intestinal epithelium functions in weaned pigs
Authors: Li YanPing , Lu Yang , Yu Bing , Huang Zhiqing , Luo Yuheng , Zheng Ping , Mao Xiangbing , Yu Jie , Luo Junqiu , Yan Hui , He Jun 
Published: July 2024

Abstract
To explore the effects of cordyceps militaris (CM) on growth performance and intestinal epithelium functions, 180 weaned pigs were randomly assigned into 5 treatments with 6 replicate pens per treatment (6 pigs per pen). Pigs were fed with basal diet (control) or basal diet supplemented with 100, 200, 400, and 800 mg/kg CM. The trial lasted for 42 d, and pigs from the control and optimal-dose groups (based on growth performance) were picked for blood and tissue collection (n = 6). Results showed that CM elevated the average daily gain (ADG) and decreased the ratio of feed intake to gain (F:G) in the weaned pigs (P &lt; 0.05). CM supplementation at 100 mg/kg improved the digestibilities of dry matter (DM), crude protein (CP), and gross energy (GE) (P &lt; 0.05). CM not only increased the activities of superoxide dismutase (SOD), glutathione (GSH), and catalase (CAT) but also increased the concentration of interleukin-10 (IL-10) in serum (P &lt; 0.05). The serum concentrations of malondialdehyde (MDA), d-lactate, and diamine oxidase (DAO) were reduced by CM (P &lt; 0.05). Interestingly, CM elevated the villus height and the ratio of villus height to crypt depth in the duodenum and jejunum and increased the activities of duodenal sucrase and maltase (P &lt; 0.05). Moreover, CM elevated the expression levels of tight-junction proteins ZO-1, claudin-1, and occluding, as well as critical functional genes such as the fatty acid transport protein (FATP1), cationic amino acid transporter 1 (CAT1), and NF-E2-related factor 2 (Nrf2) in the duodenum and jejunum (P &lt; 0.05). Importantly, CM increased the concentrations of acetic acid and butyric acid, and elevated the abundances of Bacillus and Lactobacillus in the cecum and colon, respectively (P &lt; 0.05). These results indicated potential benefits of CM in improving the growth of weaned pigs, and such effect may be tightly associated with improvement in antioxidant capacity and intestinal epithelium functions.
Carboxyfullerene C60 preserves porcine sperm by enhancing antioxidant capacity and inhibiting apoptosis and harmful bacteria
Authors: Li Yuqing , Xiao Haoqi , Qin Xue , Zhang Haize , Zheng Yi , Cai Rui , Pang Weijun 
Published: July 2024

Abstract
This study used a porcine model to systematically investigate whether carboxyfullerene C60(CF-C60) can be used for sperm preservation. The results indicated that CF-C60 supplementation can preserve porcine sperm quality during storage at 17 °C. This effect was attributable to an improvement in the antioxidant capacity of sperm through a decrease in the reactive oxygen species (ROS) level. Additionally, CF-C60 can maintain mitochondrial function, inhibit sperm apoptosis through the ROS/Cytochrome C (Cyt C)/Caspase 3 signaling pathway, and mediate suppression of bacterial growth through the effects of ROS. Finally, the results of artificial insemination experiments indicated that insemination with CF-C60-treated sperm can increase the total number of offspring born and reduce the number of deformed piglets. Thus, CF-C60 is safe for use as a component of semen diluent for sperm storage.
Qualitative and quantitative determination of xylazine in oral fluid
Authors: Levitas Matthew , Thomas Christopher , Widman Corey , DeColumna Joseph , Allgaier Brandi , Conley Eric , deHagen Troy , Freitas Isabela , Horvath Hannah , Lemberg Bridget , Lemberg Dave 
Published: July 2024

AbstractXylazine has emerged in recent years as a dangerous adulterant in illicit fentanyl use, and methods for the detection of xylazine in toxicology panels are still lagging. We developed methods for the screening and quantitation of xylazine in oral fluid (OF), a popular testing medium due to its ease of collection and reflection of presence in blood for many classes of drugs. Enzyme-linked immunosorbent assays were employed for the rapid screening of xylazine directly from the collection device buffer with a cutoff of 1 ng/mL. Solid-phase extraction coupled with liquid chromatography–tandem mass spectrometry facilitated the confirmation and quantification of xylazine as low as 0.1 ng/mL and a dynamic range of 0.1–25 ng/mL. Selectivity, ionization suppression, processed sample stability, and dilution effect were also assessed. The method was validated through the American National Standards Institute/American Academy of Forensic Sciences Standards Board (ANSI/ASB) Standard 036, first edition from 2019, and found to be accurate, precise, and robust. Living human subject OF samples collected within substance use disorder and therapeutic drug monitoring clinics received between September 2023 and January 2024, with the specific request to test for xylazine (n = 57), were screened. Presumptive positive samples were confirmed using the validated method. Xylazine confirmed living human subject OF sample concentrations ranged from 1.2 to 23.3 ng/mL.