bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of the inaccessible genome on genotype imputation and genome-wide association studies
Authors: König Eva , Mitchell Jonathan Stewart , Filosi Michele , Fuchsberger Christian 
Published: April 2024

Abstract
Genotype imputation is widely used in genome-wide association studies (GWAS). However, both the genotyping chips and imputation reference panels are dependent on next-generation sequencing (NGS). Due to the nature of NGS, some regions of the genome are inaccessible to sequencing. To date, there has been no complete evaluation of these regions and their impact on the identification of associations in GWAS remains unclear. In this study, we systematically assess the extent to which variants in inaccessible regions are underrepresented on genotyping chips and imputation reference panels, in GWAS results and in variant databases. We also determine the proportion of genes located in inaccessible regions and compare the results across variant masks defined by the 1000 Genomes Project and the TOPMed program. Overall, fewer variants were observed in inaccessible regions in all categories analyzed. Depending on the mask used and normalized for region size, only 4%–17% of the genotyped variants are located in inaccessible regions and 52 to 581 genes were almost completely inaccessible. From the Cooperative Health Research in South Tyrol (CHRIS) study, we present a case study of an association located in an inaccessible region that is driven by genotyped variants and cannot be reproduced by imputation in GRCh37. We conclude that genotyping, NGS, genotype imputation and downstream analyses such as GWAS and fine mapping are systematically biased in inaccessible regions, due to missed variants and spurious associations. To help researchers assess gene and variant accessibility, we provide an online application (https://gab.gm.eurac.edu).
For-profit or for-CSR: decisions of power batteries recovery in the supply chain
Authors: Xing Ruxiao , Zhuang Mengmeng , Li Bo 
Published: April 2024

Abstract
Accepted by: M. Zied Babai
The importance of recovering retired batteries from new energy vehicles (NEVs) has garnered widespread attention in both scholarly literature and practical applications. This paper discusses the decisions of battery recovery in a supply chain consisting of a supplier and a manufacturer. Utilizing the Stackelberg game, we construct relevant models and compare the equilibrium solutions in two decision-making modes, for-profit and for-CSR (corporate social responsibility). We shows that the firms’ pursuit of CSR contributes to increasing collection prices. However, if environmental damage is severe, the firms’ pursuit of CSR leads to high retail prices, which is detrimental to the sale of NEVs. Furthermore, although not all members’ collection amounts increase when considering CSR, the overall collection effect will be better. Meanwhile, we find that both the supplier and the manufacturer have incentives to practice CSR because their pursuit of CSR leads to high profits. Finally, this paper has verified all the above conclusions using theoretical data.
Antibody Titers and the Risk of Infection During the SARS-CoV-2 Omicron Phase in Bizen City, Japan
Authors: Kadowaki Tomoka , Sasaki Ayako , Matsumoto Naomi , Mitsuhashi Toshiharu , Hagiya Hideharu , Takao Soshi , Yorifuji Takashi 
Published: April 2024

Abstract

Background
Understanding the association between the immune response and the risk of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has implications for forthcoming prevention strategies. We evaluated the association between antibody titers and the risk of infection for the general population during the Omicron-dominant phase.

Methods
This was a prospective cohort study of residents or people affiliated with institutions in Bizen City, which included 1899 participants. We measured the titers of antibodies against SARS-CoV-2 repeatedly every 2 months from June 2022 to March 2023. Infection status was obtained from self-reported questionnaires and the official registry. We estimated risk ratios (RRs) for infection within 2 months of the date of each antibody measurement with 95% confidence intervals (CIs) based on antibody titer categories and spline functions.

Results
Compared with the &lt;2500 arbitrary unit (AU)/mL category, the 2500–5000, 5000–10 000, and ≥10 000 AU/mL categories had adjusted RRs of 0.81 (95% CI, .61–1.08), 0.51 (95% CI, .36–.72), and 0.41 (95% CI, .31–.54), respectively. The spline function showed a nonlinear relationship between antibody titer and risk.

Conclusions
Higher antibody titers were associated with a lower risk. We demonstrate the usefulness of measuring an antibody titers to determine the appropriate timing for future prevention strategies.
Foreign Military Training and Socialization: An Examination of Human Capital and Norm Transmission Between Allies
Authors: Fábián Sándor , Boutton Andrew 
Published: April 2024

Abstracts
Foreign military personnel routinely participate in educational and cultural programs administered by the U.S. military. In addition to bolstering the capacity of the recipient military, one of the primary goals of these programs is to professionalize the military of the recipient state. It is hoped not only that the soldiers will internalize norms of human rights and democracy themselves but also that they will become influential members of the military in the future. Existing cross-national research, along with selective anecdotes of U.S.-trained soldiers leading coups and rebellions, suggests that military aid may be ineffective. To date, however, a nuanced understanding of the more granular effects of military aid on the recipient country has been hindered by a lack of data and a focus on the macro-level. We address this lacuna by examining norm transmission among a sample of the Hungarian officer corps. We show that while soldiers who graduated from IMET programs display more favorability toward human rights and democracy, they do not believe the military should remain insulated from policymaking. We believe this is a valuable step toward a deeper understanding of how U.S. military aid shapes recipient militaries and, more broadly, how norms are transmitted between allies.
Fear or Anger? Leaders’ Childhood War Trauma and Interstate Conflict Initiation
Authors: Kim James D 
Published: April 2024

Abstract
How does a leader’s childhood exposure to war influence their propensity to initiate conflicts? While much research explains leaders’ national security policies using their combat and rebel experiences, few scholars have examined the effects of childhood wartime violence. I develop and test two competing arguments about the effects of childhood war trauma on future conflict behavior. One argument expects that leaders exposed to war at a young age will be less likely to initiate conflict because they fear its consequences. An alternative perspective expects that these leaders are more likely to initiate conflict out of anger and a desire for revenge. I test my hypotheses using an original dataset and a research design that reduces inference barriers. Leveraging variations in the level of violence experienced during wartime, I only compare leaders who were exposed to foreign military invasions as children. I find that those who experienced severe war trauma, such as family deaths, injuries, or displacement, are less likely to initiate interstate conflicts than those who did not experience such traumatic events. These effects are substantial, particularly when political constraints are weak. My results suggest that childhood war trauma has a long-term impact on leaders’ conservatism about using force.
Bioactive metabolites of Asparagopsis stabilized in canola oil completely suppress methane emissions in beef cattle fed a feedlot diet
Authors: Cowley Frances C , Kinley Robert D , Mackenzie Sigrid L , Fortes Marina R S , Palmieri Chiara , Simanungkalit Gamaliel , Almeida Amelia K , Roque Breanna M 
Published: April 2024

Abstract
Asparagopsis taxiformis (Asparagopsis) has been shown to be highly efficacious at inhibiting the production of methane (CH4) in ruminants. To date, Asparagopsis has been primarily produced as a dietary supplement by freeze-drying to retain the volatile bioactive compound bromoform (CHBr3) in the product. Steeping of Asparagopsis bioactive compounds into a vegetable oil carrier (Asp-Oil) is an alternative method of stabilizing Asparagopsis as a ruminant feed additive. A dose–response experimental design used 3 Asp-Oil-canola oil blends, low, medium, and high Asp-Oil which provided 17, 34, and 51 mg Asparagopsis derived CHBr3/kg dry matter intake (DMI), respectively (in addition to a zero CHBr3 canola oil control), in a tempered-barley based feedlot finisher diet, fed for 59 d to 20 Angus heifers (five replicates per treatment). On four occasions, live weight was measured and CH4 emissions were quantified in respiration chambers, and blood, rumen fluid, and fecal samples were collected. At the end of the experiment, all animals were slaughtered, with carcasses graded, and samples of meat and edible offal collected for testing of consumer sensory qualities and residues of CHBr3, bromide, and iodide. All Asp-Oil treatments reduced CH4 yield (g CH4/kg DMI, P = 0.008) from control levels, with the low, medium, and high Asp-Oil achieving 64%, 98%, and 99% reduction, respectively. Dissolved hydrogen increased linearly with increasing Asp-Oil inclusion, by more than 17-fold in the high Asp-Oil group (P = 0.017). There was no effect of Asp-Oil treatment on rumen temperature, pH, reduction potential, volatile fatty acid and ammonia production, rumen pathology, and histopathology (P &gt; 0.10). There were no differences in animal production and carcass parameters (P &gt; 0.10). There was no detectable CHBr3 in feces or any carcass samples (P &gt; 0.10), and iodide and bromide residues in kidneys were at levels unlikely to lead to consumers exceeding recommended maximum intakes. Overall, Asp-Oil was found to be safe for animals and consumers of meat, and effective at reducing CH4 emissions and yield by up to 99% within the range of inclusion levels tested.
Calcineurin-NFAT signaling controls neutrophils’ ability of chemoattraction upon fungal infection
Authors: Vymazal Ondrej , Papatheodorou Ioanna , Andrejčinová Ivana , Bosáková Veronika , Vascelli Gianluca , Bendíčková Kamila , Zelante Teresa , Hortová-Kohoutková Marcela , Frič Jan 
Published: April 2024

Abstract
Calcineurin–nuclear factor of activated T cells (CN-NFAT) inhibitors are widely clinically used drugs for immunosuppression, but besides their required T cell response inhibition, they also undesirably affect innate immune cells. Disruption of innate immune cell function can explain the observed susceptibility of CN-NFAT inhibitor–treated patients to opportunistic fungal infections. Neutrophils play an essential role in innate immunity as a defense against pathogens; however, the effect of CN-NFAT inhibitors on neutrophil function was poorly described. Thus, we tested the response of human neutrophils to opportunistic fungal pathogens, namely Candida albicans and Aspergillus fumigatus, in the presence of CN-NFAT inhibitors. Here, we report that the NFAT pathway members were expressed in neutrophils and mediated part of the neutrophil response to pathogens. Upon pathogen exposure, neutrophils underwent profound transcriptomic changes with subsequent production of effector molecules. Importantly, genes and proteins involved in the regulation of the immune response and chemotaxis, including the chemokines CCL2, CCL3, and CCL4 were significantly upregulated. The presence of CN-NFAT inhibitors attenuated the expression of these chemokines and impaired the ability of neutrophils to chemoattract other immune cells. Our results amend knowledge about the impact of CN-NFAT inhibition in human neutrophils.
Effects of stubble height on stump sprouting and nutrient accumulation and allocation of Hippophae rhamnoides ssp. sinensis
Authors: Liu Shenghong , Li Zhongmu , Nie Kaihong , Lu Sai , Yao Zengyu , Li Genqian 
Published: April 2024

Abstract
As a main method of forest regeneration, stump sprouting plays a crucial role in forest community succession and vegetation restoration. We aimed to investigate the response of stump sprouting capacity to stubble height, unveil its nutrient-accumulation and allocation strategies and determine the appropriate stubble height most favorable for stump sprouting of Hippophae rhamnoides ssp. sinensis. Fifteen-year plants with signs of premature aging were coppiced at 0, 10 and 20 cm from the ground level. With the increase in stubble height, the number of stump sprouts increased linearly, and the survival rate decreased linearly. The height, diameter and cluster width of stump sprouts first increased, reached the highest level at a stubble height of 10 cm and then decreased. The contents and reserves of N, P, K, Ca and Mg showed a similar trend as the growth, positively correlating with each other. Compared with the control (no coppicing), the coppicing increased the nutrient element allocation of leaves, vertical roots and horizontal roots. Magnesium plays an important role in stump sprouting. The findings suggest that coppicing changed the accumulation ability and allocation pattern of nutrient elements, and further affected the sprouting ability of stumps. The best stubble height for stump sprouting and nutrient accumulation potential was 11.0–14.0 cm estimated by the regression.
SifiNet: a robust and accurate method to identify feature gene sets and annotate cells
Authors: Gao Qi , Ji Zhicheng , Wang Liuyang , Owzar Kouros , Li Qi-Jing , Chan Cliburn , Xie Jichun 
Published: April 2024

Abstract
SifiNet is a robust and accurate computational pipeline for identifying distinct gene sets, extracting and annotating cellular subpopulations, and elucidating intrinsic relationships among these subpopulations. Uniquely, SifiNet bypasses the cell clustering stage, commonly integrated into other cellular annotation pipelines, thereby circumventing potential inaccuracies in clustering that may compromise subsequent analyses. Consequently, SifiNet has demonstrated superior performance in multiple experimental datasets compared with other state-of-the-art methods. SifiNet can analyze both single-cell RNA and ATAC sequencing data, thereby rendering comprehensive multi-omic cellular profiles. It is conveniently available as an open-source R package.
Decreased glucagon in diabetic peripheral neuropathy patients with long duration type 2 diabetes
Authors: Shen Ziyang , Chen Mengxing , Li Qian , Ma Jianhua 
Published: April 2024

Abstract

Objective
The aim of this study was to investigate the association of fasting C-peptide and glucagon with diabetic peripheral neuropathy (DPN) in patients with type 2 diabetes (T2DM).

Methods
A comprehensive evaluation was conducted on 797 patients with T2DM to assess the various risk factors affecting DPN. The subjects were categorized into short duration and long duration group according to the duration of diabetes with a threshold of 10 years. Logistic regression analysis was employed to examine the association between DPN and islet function, as well as other parameters. Receiver operating characteristic curve analysis was performed to evaluate the predictive capability of glucagon.

Results
The fasting C-peptide levels were significantly lower in the DPN patients with short duration of diabetes, but lost significance in the long duration group. Conversely, a decreased level of glucagon was only observed in DPN patients with long duration of diabetes. For the group with long duration of diabetes, glucagon was the sole risk factor associated with DPN. The receiver operating characteristic curve analysis revealed that glucagon in the long duration group exhibited a moderate area under the curve of 0.706.

Conclusions
The serum glucagon levels in T2DM patients with DPN exhibited bidirectional changes based on the duration of diabetes. Decreased glucagon was associated with DPN in T2DM patients with long duration of diabetes.
A Theory of Socially Responsible Investment
Authors: Oehmke Martin , Opp Marcus M 
Published: April 2024

AbstractWe characterize the conditions under which a socially responsible (SR) fund induces firms to reduce externalities, even when profit-seeking capital is in perfectly elastic supply. Such impact requires that the SR fund’s mandate permits the fund to trade off financial performance against reductions in social costs—relative to the counterfactual in which the fund does not invest in a given firm. Based on such an impact mandate, we derive the social profitability index, an investment criterion that characterizes the optimal ranking of impact investments when SR capital is scarce. If firms face binding financial constraints, the optimal way to achieve impact is by enabling a scale increase for clean production. In this case, SR and profit-seeking capital are complementary: Surplus is higher when both investor types are present.
Association of Lamotrigine Plasma Concentrations With Efficacy and Toxicity in Patients With Epilepsy: A Retrospective Study
Authors: Lee Ze-Ning , van Nuland Merel , Bognàr Tim , Leijten Frans S. S. , van der Elst Kim C. M. 
Published: April 2024

Background:
There is limited evidence to support the currently suggested lamotrigine (LTG) therapeutic reference range of 2.5–15 mg/L for the treatment of seizures. The objective of this study was to evaluate the association of LTG plasma concentrations with the efficacy and toxicity of the treatment in patients with epilepsy.

Methods:
Patients whose LTG plasma concentration was measured between January 2013 and February 2022 were included. Efficacy was defined as seizure freedom for at least 6 months around the time of measured LTG concentration. Toxicity was defined as any LTG-related adverse drug effect documented in each patient's health record or when the reason for measuring the LTG concentration was toxicity. In addition, the dose–concentration relationship of LTG was assessed.

Results:
In total, 549 concentrations from 259 patients with epilepsy were included. The most common reasons for therapeutic drug monitoring were suspected inefficacy (39%) and pregnancy (21%). The LTG plasma concentration was not associated with efficacy (adjusted odds ratio = 0.94; 95% confidence interval, 0.85–1.04). The LTG plasma concentration was positively associated with the incidence of toxicity after adjusting for age, sex, and number of antiepileptic drugs (odds ratio = 1.11; 95% confidence interval, 1.04–1.19). The daily dose had a significant linear correlation with the LTG plasma concentration (P < 0.001).

Conclusions:
The LTG plasma concentration was associated with toxicity, whereas no association with efficacy was found. A reference range of 2.5–10 mg/L may be considered to decrease the risk of toxicity while maintaining similar efficacy. Therapeutic drug monitoring may be useful when LTG-related toxicity is suspected and in cases of pharmacokinetic changes (eg, pregnancy and concomitant use of interacting drugs) that can influence the LTG plasma concentration.
The “Ukiyo” of Moxibustion Reflected in the Ukiyo-e
Authors: JIANG Shan 
Published: April 2024

Abstract

Ukiyo-e (浮世絵) was a genre of popular art during the Edo and Meiji periods in Japan. Moxibustion, which was originally introduced from China, was also in its heyday and became one of the popular topics for ukiyo-e artists at that time. Using the images as historical evidence perspective, this article focuses on the moxibustion used in daily life in Japan depicted in the ukiyo-e arts. With the perspective of acu-moxa therapy, one may identify some specific issues in the acupoint selection, leading to the discovery of special application of moxibustion used by the group of yūjo (遊女) at that time. The article concludes by exploring gender issues in ukiyo-e arts and the implications of punishment attached to moxibustion treatment.
Determinants of Nurse Managers' Transformational Leadership
Authors: Labrague Leodoro J. 
Published: April 2024

OBJECTIVE
The aim of this study was to examine the relationship between various factors and self-perceived transformational leadership among a sample of Filipino nurse managers (NMs).

BACKGROUND
Transformational leadership plays a crucial role in promoting positive outcomes in healthcare settings, particularly for NMs. Understanding the factors that influence NMs' self-perceived transformational leadership is essential for improving leadership practices and enhancing organizational effectiveness.

METHODS
A cross-sectional research design was used to collect data from 260 NMs using standardized measures.

RESULTS
Employment status, the number of units managed, the type of hospital employment, psychological distress, and job satisfaction were factors that significantly influenced their leadership perceptions.

CONCLUSION
By addressing the identified factors, nursing organizations can create an environment that promotes effective leadership practices, ultimately enhancing patient outcomes, staff satisfaction, and overall organizational performance.
Trends of Antimicrobial Susceptibility of Neisseria gonorrhoeae Isolates Between 2012 and 2023: Results From an Open Italian Cohort
Authors: Lucente Maria Francesca , Raccagni Angelo Roberto , Galli Laura , Lolatto Riccardo , Ranzenigo Martina , Ripa Marco , Ponta Giacomo , Monardo Roberta , Gona Floriana , Clementi Nicola , Burioni Roberto , Carletti Silvia , Castagna Antonella , Nozza Silvia 
Published: April 2024

Background

Neisseria gonorrhoeae (Ng) is a public health priority because of the rapid evolution of antimicrobial resistance, the emergence of antibiotic resistance, and the absence of a vaccine against Ng. The aim of this study was to investigate trends in the minimum inhibitory concentration and resistance (R) or reduced susceptibility (DS) of Ng cases to ceftriaxone (CRO), azithromycin (AZM), tetracycline (TET), benzylpenicillin (PenG), and ciprofloxacin (CIP) during a 10-year period.

Methods
We conducted a retrospective analysis on an open cohort of Ng cases diagnosed on rectal, urethral, and pharyngeal samples at San Raffaele Scientific Institute, between September 2012 and February 2023. Minimum inhibitory concentrations of antibiotics were determined by gradient-test strips. Bivariate linear regression models were applied on logarithmic minimum inhibitory concentrations values; Cochran-Armitage test was used to determine a linear trend in the proportions of resistant strains.

Results
A total of 436 Ng isolates from 352 individuals were analyzed. Minimum inhibitory concentrations of CRO and PenG reduced over time (P < 0.001, P = 0.030), AZM increased (P = 0.001), and CIP and TET did not change (P = 0.473, P = 0.272). The percentages of resistant strains were as follows: PenG, 89.9%; TET, 90.8%; CIP, 48.2%; AZM, and 4.4%. CRO-DS strains were 8.7%, and only 1 case of CRO-R was identified. The proportion of resistant strains increased over time for AZM (P = 0.007), TET (P = 0.001), and CIP (P < 0.001), whereas it decreased for PenG (P < 0.001) and CRO-DS/R strains (P < 0.001).

Conclusions
Ng strains showed high susceptibility to CRO, although we identified cases of DS/R and observed high levels of susceptibility to AZM. Overall, the recommended primary regimen for Ng treatment was confirmed to be effective.