bluuebunny/crossref_metadata_2025_split huggingface dataset:
Local adaptation can cause both peaks and troughs in nucleotide diversity within populations
Authors: Jasper Russ J , Yeaman Sam 
Published: September 2024

Abstract
The amount of standing variation present within populations is a fundamental quantity of interest in population genetics, commonly represented by calculating the average number of differences between pairs of nucleotide sequences (nucleotide diversity, π). It is well understood that both background and positive selection can cause reductions in nucleotide diversity, but less clear how local adaptation affects it. Depending on the assumptions and parameters, some theoretical studies have emphasized how local adaptation can reduce nucleotide diversity, while others have shown that it can increase it. Here, we explore how local adaptation shapes genome-wide patterns in within-population nucleotide diversity, extending previous work to study the effects of polygenic adaptation, genotypic redundancy, and population structure. We show that local adaptation produces two very different patterns depending on the relative strengths of migration and selection, either markedly decreasing or increasing within-population diversity at linked sites at equilibrium. At low migration, regions of depleted diversity can extend large distances from the causal locus, with substantially more diversity eroded than expected with background selection. With higher migration, peaks occur over much smaller genomic distances but with much larger magnitude changes in diversity. Across spatially extended environmental gradients, both patterns can be found within a single species, with increases in diversity at the center of the range and decreases towards the periphery. Our results demonstrate that there is no universal diagnostic signature of local adaptation based on within-population nucleotide diversity, so it will not be broadly useful for explaining increased FST. However, given that neither background nor positive selection inflate diversity, when peaks are found they suggest local adaptation may be acting on a causal allele in the region.
Optimizing architectural designs for energy efficiency in Jeddah: a comparative analysis of building forms
Authors: Ismaail Amal Dawoud , Mahboob Abdullah Mohamed 
Published: September 2024

Abstract
This research paper investigates the impact of residential building forms, including high-density, balanced urban design, and eco-friendly designs, on energy efficiency in Jeddah, Saudi Arabia, through a comparative analysis utilizing parametric numerical analysis with Autodesk Revit. The study aims to address the unique challenges posed by Jeddah’s rapid population growth, climatic conditions, and economic diversification efforts under Saudi Vision 2030. By examining different building configurations, the research highlights how urban building forms influence energy consumption, providing valuable insights for urban planners and designers during the conceptual design phase. The findings underscore the importance of optimizing urban parameters to promote high-density urban growth, maximize land use efficiency, and support sustainable energy consumption, aligning with the strategic objectives of Saudi Vision 2030.
A mesh-independent method for second-order potential mean field games
Authors: Liu Kang , Pfeiffer Laurent 
Published: September 2024

Abstract
This article investigates the convergence of the Generalized Frank–Wolfe (GFW) algorithm for the resolution of potential and convex second-order mean field games. More specifically, the impact of the discretization of the mean-field-game system on the effectiveness of the GFW algorithm is analyzed. The article focuses on the theta-scheme introduced by the authors in a previous study. A sublinear and a linear rate of convergence are obtained, for two different choices of stepsizes. These rates have the mesh-independence property: the underlying convergence constants are independent of the discretization parameters.
A rapid method to assess the in vivo multi-functionality of adoptively transferred engineered TCR T cells
Authors: Tan Anthony T , Hang Shou Kit , Tan Nicole , Krishnamoorthy Thinesh L , Chow Wan Cheng , Wong Regina Wanju , Wai Lu-En , Bertoletti Antonio 
Published: September 2024

Abstract

Introduction
The clinical efficacy of chimeric antigen and T cell receptor (TCR) T cell immunotherapies is attributed to their ability to proliferate and persist in vivo. Since the interaction of the engineered T cells with the targeted tumour or its environment might suppress their function, their functionality should be characterized not only before but also after adoptive transfer.

Materials and methods
We sought to achieve this by adapting a recently developed Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) rapid whole blood T cell assay to stimulate engineered TCR T cells in small volumes of whole blood (&lt;1 ml) without in vitro cellular purification. As a proof-of-concept, we used this method to longitudinally study two patients with primary Hepatitis B Virus (HBV)-related hepatocellular carcinoma who received multiple dose-escalating infusions of transiently functional mRNA-engineered HBV-TCR T cells.

Results
We demonstrated that a simple pulsing of whole blood with a peptide corresponding to the epitope recognized by the specific HBV-TCR elicited Th1 cytokine secretion in both patients only after HBV-TCR T cell treatment and not before. The amount of cytokines secreted also showed an infusion-dose-dependent association.

Discussions
These findings support the utility of the whole blood cytokine release assay in monitoring the in vivo function and quantity of engineered T cell products following adoptive transfer.
Bacterial Inactivation Studies in Shrimp Pond Water by Using Different Disinfectant Agents
Authors: Nadella Ranjit Kumar , Panda Satyen Kumar , Uchoi Devananda , Kishore Pankaj , V. R. Madhu , Ayyappan Minimol Valamattath , Badireddy Madhusudana Rao , Kuricheti Pani Prasad , Raman Ram Prakash , Mothadaka Mukteswar Prasad 
Published: September 2024

Abstract

Background
Aquaculture water plays an important role in the dissemination of antibiotic-resistant bacteria during harvest of shrimps. Mitigation of bacteria through discharge is essential to prevent dissemination downstream. Chemical disinfection of culture water is feasible compared to other methods of bacterial inactivation.

Objective
To study the effect of different disinfectant agent’s viz., chlorine, Fenton’s reagent, and hydrogen peroxide (H2O2) on inactivation of bacteria from shrimp pond water.

Methods
The water samples were subjected to treatment with various concentrations of chlorine (0.0, 1.0, 2.5, 5.0, and 10.0 mg/L), Fenton’s reagent (1:10 mM ratio of Fe2+:H2O2; 2:20, 3:30, 4:40, 5:50) and H2O2 (20, 30, 40, and 50 mM) for different time durations (5, 15, 30, and 60 min).

Results
The results indicated that all the disinfecting agents inactivated both the total heterotrophic bacteria and tetracycline-resistant bacteria with increased concentrations and time. At the end of 60 min treatment with chlorination (2.5 mg Cl2/L), Fenton’s reagent (2 mM Fe2+ + 20 mM H2O2), and H2O2 (50 mM H2O2), the total heterotrophic bacterial count in the water samples gradually decreased by 2.35, 2.65, and 1.38 Log10 CFU/mL, and tetracycline-resistant bacterial count reduced by 1.57, 1.66, and 1.43 Log10 CFU/mL respectively, from initial bacterial load.

Conclusion
The study revealed that disinfection agents can be successfully employed in the inactivation of antibiotic-resistant bacteria discharged through aquaculture water. Among three disinfection agents, Fenton’s reagent has been found effective in inhibiting both heterotrophic bacteria and tetracycline-resistant bacteria from water samples.

Highlights
Bacterial inactivation studies were carried with chlorination, Fenton’s reagent, and hydrogen peroxide. The highest reduction in Heterotrophic Plate Count (HPC) (2.65 Log) and tetracycline-resistant count (1.66 Log) was noticed in the water samples treated with Fenton’s reagent. The use of disinfection agents effectively mitigates antibiotic-resistant bacteria from aquaculture wastewater.
Corrected generalized cross-validation for finite ensembles of penalized estimators
Authors: Bellec Pierre C , Du Jin-Hong , Koriyama Takuya , Patil Pratik , Tan Kai 
Published: September 2024

Abstract
Generalized cross-validation (GCV) is a widely used method for estimating the squared out-of-sample prediction risk that employs scalar degrees of freedom adjustment (in a multiplicative sense) to the squared training error. In this paper, we examine the consistency of GCV for estimating the prediction risk of arbitrary ensembles of penalized least-squares estimators. We show that GCV is inconsistent for any finite ensemble of size greater than one. Towards repairing this shortcoming, we identify a correction that involves an additional scalar correction (in an additive sense) based on degrees of freedom adjusted training errors from each ensemble component. The proposed estimator (termed CGCV) maintains the computational advantages of GCV and requires neither sample splitting, model refitting, or out-of-bag risk estimation. The estimator stems from a finer inspection of the ensemble risk decomposition and two intermediate risk estimators for the components in this decomposition. We provide a non-asymptotic analysis of the CGCV and the two intermediate risk estimators for ensembles of convex penalized estimators under Gaussian features and a linear response model. Furthermore, in the special case of ridge regression, we extend the analysis to general feature and response distributions using random matrix theory, which establishes model-free uniform consistency of CGCV.
Interventions to reduce surgical site infection following elective colorectal surgery: protocol for a systematic review with narrative synthesis and GRADE recommendations
Authors: Dean Harry , Drami Ioanna , Shamsiddinova Amira , Alkizwini Eman , Kinross James , Wilson Ana , Tozer Phil , Vaizey Carolynne 
Published: September 2024

Abstract
Surgical site infection (SSI) is frequently associated with adverse patient outcomes. SSI is often perceived as a preventable complication following elective surgery, and a wide array of strategies have been reported to reduce its occurrence. Despite this, colorectal surgery continues to have among the highest incidences of SSI, and there is considerable variation in the use of evidence-based practices in its prevention. There are currently no systematic reviews describing the full range of interventions to reduce SSI across the perioperative period of elective colorectal surgery. To determine which perioperative interventions are effective in reducing SSI following elective colorectal surgery. A systematic search of MEDLINE, EMBASE, Cochrane Central Register of Controlled Trials and Web of Science databases as well as grey literature sources will be performed. Data extraction, risk of bias assessments and narrative synthesis will be performed by a team of trained, independent reviewers. Certainty of evidence will be assessed using the Grading of Recommendations, Assessment, Development and Evaluations framework. This review will form the most comprehensive assessment to date of measures to reduce SSI following elective colorectal surgery. This will promote the adoption of evidence-based practice and the identification of future research needs.
Model-Based Prediction for Small Domains Using Covariates: A Comparison of Four Methods
Authors: Michal Victoire , Wakefield Jon , Schmidt Alexandra M , Cavanaugh Alicia , Robinson Brian E , Baumgartner Jill 
Published: September 2024

Abstract
We consider methods for model-based small area estimation when the number of areas with sampled data is a small fraction of the total areas for which estimates are required. Abundant auxiliary information is available from the survey for all the sampled areas. Further, through an external source, there is information for all areas. The goal is to use auxiliary variables to predict the outcome of interest for all areas. We compare areal-level random forests and LASSO approaches to a frequentist forward variable selection approach and a Bayesian shrinkage method using a horseshoe prior. Further, to measure the uncertainty of estimates obtained from random forests and the LASSO, we propose a modification of the split conformal procedure that relaxes the assumption of exchangeable data. We show that the proposed method yields intervals with the correct coverage rate and this is confirmed through a simulation study. This work is motivated by Ghanaian data available from the sixth Ghana Living Standards Survey (GLSS) and the 2010 Population and Housing Census, in the Greater Accra Metropolitan Area (GAMA) region, which comprises eight districts that are further divided into enumeration areas (EAs). We estimate the areal mean household log consumption using both datasets. The outcome variable is measured only in the GLSS for 3 percent of all the EAs (136 out of 5019) and 174 potential covariates are available in both datasets. In the application, among the four modeling methods considered, the Bayesian shrinkage performed the best in terms of bias, mean squared error (MSE), and prediction interval coverages and scores, as assessed through a cross-validation study. We find substantial between-area variation with the estimated log consumption showing a 1.3-fold variation across the GAMA region. The western areas are the poorest while the Accra Metropolitan Area district has the richest areas.
Natural variation in the adjustment of primary metabolism determines ammonium tolerance in the model grass Brachypodium distachyon
Authors: De la Peña Marlon , Poucet Théo , Montardit-Tarda Francesc , Urmeneta Leyre , Urbano-Gámez Jose Alberto , Cassan Cédric , Vega-Mas Izargi , Catalán Pilar , Igartua Ernesto , Gibon Yves , Gonzalez-Moro M Begoña , Marino Daniel 
Published: September 2024

Abstract
Nitrogen (N) fertilization is essential to maximize crop production. However, around half of the applied N is lost to the environment, causing water and air pollution and contributing to climate change. Understanding the natural genetic and metabolic basis underlying plants N use efficiency is of great interest to attain an agriculture with less N demand and thus more sustainable. The study of ammonium (NH4+) nutrition is of particular interest, because it mitigates N losses due to nitrate (NO3–) leaching or denitrification. In this work, we studied Brachypodium distachyon, the model plant for C3 grasses, grown with NH4+ or NO3– supply. We performed gene expression analysis in the root of the B. distachyon reference accession Bd21 and examined the phenotypic variation across 52 natural accessions through analyzing plant growth and a panel of 22 metabolic traits in leaf and root. We found that the adjustment of primary metabolism to NH4+ nutrition is essential for the natural variation of NH4+ tolerance, notably involving NH4+ assimilation and phosphoenolpyruvate carboxylase (PEPC) activity. Additionally, genome-wide association studies (GWAS) indicated several loci associated with B. distachyon growth and metabolic adaptation to NH4+ nutrition. We found that the GDH2 gene was associated with the induction of root glutamate dehydrogenase activity under NH4+ nutrition and that two genes encoding malic enzyme were associated with leaf PEPC activity. Altogether, our work underlines the value of natural variation and the key role of primary metabolism to improve NH4+ tolerance.
Buprenorphine for the Treatment of Military-related PTSD With Treatment-resistant Depression and Unexpected Benefit for Chronic Pain: Case Report
Authors: Skorzewska Anna , Younger William A , Dempster Kylie S , Nazarov Anthony , Richardson J Don 
Published: September 2024

ABSTRACT
The prevalence of treatment-resistant depression within global and military populations highlights the need for novel treatment approaches beyond monoamine neurotransmitter modulators. Buprenorphine (BUP), a semi-synthetic partial opioid agonist, is approved for the treatment of opioid use disorder and has shown promise in treating both depression and chronic pain. This case report discusses the use of transdermal BUP in treating a 36 year-old man with treatment-resistant depression with prominent anhedonia, military-related posttraumatic stress disorder, and chronic pain because of barosinusitis. Significant reductions in anxious and depressive symptoms, including in anhedonia, were observed with lasting effects. An unexpected finding was the discontinuation of prescribed hydromorphone for pain, suggesting the potential unique benefit of BUP in treating chronic pain and treatment resistant depression comorbidities. These findings implicate the diverse beneficial potential of BUP in psychiatric treatments for military populations.
Thermodynamic origin of the affinity, selectivity, and domain specificity of metallothionein for essential and toxic metal ions
Authors: Quinn Colette F , Wilcox Dean E 
Published: September 2024

Abstract
The small Cys-rich protein metallothionein (MT) binds several metal ions in clusters within two domains. While the affinity of MT for both toxic and essential metals has been well studied, the thermodynamics of this binding has not. We have used isothermal titration calorimetry measurements to quantify the change in enthalpy (ΔH) and change in entropy (ΔS) when metal ions bind to the two ubiquitous isoforms of MT. The seven Zn2+ that bind sequentially at pH 7.4 do so in two populations with different coordination thermodynamics, an initial four that bind randomly with individual tetra-thiolate coordination and a subsequent three that bind with bridging thiolate coordination to assemble the metal clusters. The high affinity of MT for both populations is due to a very favourable binding entropy that far outweighs an unfavourable binding enthalpy. This originates from a net enthalpic penalty for Zn2+ displacement of protons from the Cys thiols and a favourable entropic contribution from the displaced protons. The thermodynamics of other metal ions binding to MT were determined by their displacement of Zn2+ from Zn7MT and subtraction of the Zn2+-binding thermodynamics. Toxic Cd2+, Pb2+, and Ag+, and essential Cu+, also bind to MT with a very favourable binding entropy but a net binding enthalpy that becomes increasingly favourable as the metal ion becomes a softer Lewis acid. These thermodynamics are the origin of the high affinity, selectivity, and domain specificity of MT for these metal ions and the molecular basis for their in vivo binding competition.
Secondhand Tobacco Exposure Assessed Using Urinary Cotinine Among 10-Year-Old Children in Japan: An 11-Year Repeated Cross-sectional Study
Authors: Tamada Yudai , Takeuchi Kenji , Tabuchi Takahiro 
Published: September 2024

Abstract

Introduction
The emergence of heated tobacco products (HTPs) has made it important to monitor HTP-generated aerosols in addition to combustible cigarette (CC) smoke as a source of secondhand tobacco (SHT) exposure. We investigated the trend of SHT exposure in school-aged children and assessed whether SHT exposure depended on household tobacco use status.

Aims and Methods
This repeated cross-sectional study from 2011 to 2021 (15 927 participants) was based on data from an annual survey of fourth-grade students (aged 10 years) in Kumagaya City, Japan. In addition to a questionnaire which includes questions about household tobacco use status, we measured the urinary cotinine levels of each participant by their first-morning urine sample to objectively assess SHT exposure. We defined the participants with urinary cotinine levels ≥5.0 ng/mL as being exposed to SHT.

Results
The prevalence of SHT exposure decreased over the 11-year period from 18.6% in 2011 to 5.3% in 2021. It was significantly higher in households with tobacco users than without tobacco users (t-test p&lt; .001). Prevalence of SHT exposure was 1.4% among the 68.1% of households not using tobacco, 22.9% among the 16.5% using only CC, 3.1% among the 12.3% using only HTP, and 27.6% among the 3.9% of households using CC and HTP.

Conclusions
While the prevalence of SHT exposure showed a decreasing trend from 2011 to 2021, the prevalence of SHT exposure was higher in children with household members using tobacco products, regardless of the type of tobacco product, than in those without tobacco users.

Implications
This study observed that the prevalence of SHT exposure was higher among children in households with tobacco users than among those without tobacco users, regardless of the type of tobacco product. Our findings highlight the importance of advocating that HTPs do not reduce the likelihood of SHT exposure to bystanders.
Adherence to CDC Guidelines for mpox Evaluation: Practice Patterns Across an Academic Medical System During the 2022 Epidemic
Authors: Garneau William M , Jones Joyce L , Dashler Gabriella M , Kwon Nathan , Hamill Matthew M , Gilliams Elizabeth A , Rudolph David S , Keruly Jeanne C , Klein Eili Y , Wang Nae-Yuh , Hansoti Bhakti , Gebo Kelly A 
Published: September 2024

Abstract

Background
Patients with suspected mpox presented to different venues for evaluation during the 2022 outbreak. We hypothesized that practice patterns may differ across venue of care.

Methods
We conducted an observational study of patients undergoing mpox testing between 1 June 2022 and 15 December 2022. We assessed concomitant sexually transmitted infection (STI) testing, sexual history, and anogenital examination and a composite outcome of all 3, stratified by site. Venue of care was defined as ED (emergency department or urgent care), ID (infectious disease clinic), or PCP (primary care or other outpatient clinic).

Results
Of 276 patients included, more than half (62.7%) were evaluated in the ED. Sexual history, anogenital examination, and STI testing were documented as performed at a higher rate in ID clinic compared to ED or PCP settings. STIs were diagnosed in 20.4% of patients diagnosed with mpox; syphilis was the most common STI among patients diagnosed with mpox (17.5%). Patients evaluated in an ID clinic had higher odds ratio of completing all 3 measures (adjusted odds ratio, 3.6 [95% confidence interval, 1.4–9.3]) compared to PCP setting adjusted for age, gender, and men who have sex with men status. Cisgender men who have sex with men, transgender males, and transgender females had higher odds ratio of completing all 3 measures compared to cisgender females (adjusted odds ratio, 4.0 [95% confidence interval, 1.9–8.4]) adjusted for age and venue of care.

Conclusions
Care varied across clinical sites. ID clinics performed a more thorough evaluation than other venues. Rates of STI coinfection were high. Syphilis was the most common STI. Efforts to standardize care are important to ensure optimal outcomes for patients.