bluuebunny/crossref_metadata_2025_split huggingface dataset:
Global linear and nonlinear gyrokinetic simulations of tearing modes
Authors: Jitsuk T. , Di Siena A. , Pueschel M.J. , Terry P.W. , Widmer F. , Poli E. , Sarff J.S. 
Published: February 2024

Abstract
To better understand multi-scale interactions between global tearing modes and microturbulence in the Madison Symmetric Torus (MST) reversed-field pinch (RFP), the global gyrokinetic code Gene is modified to describe global tearing mode instability via a shifted Maxwellian (SM) distribution consistent with experimental equilibria. The implementation of the SM is tested and benchmarked by comparisons with different codes and models. Good agreement is obtained in code-code and code-theory comparisons. Linear stability of tearing modes of a non-reversed MST discharge is studied. A collisionality scan is performed to the lowest order unstable modes (n = 5, n = 6) and shown to behave consistently with theoretical scaling. The nonlinear evolution is simulated, and saturation is found to arise from mode coupling and transfer of energy from the most unstable tearing mode to small-scale stable modes mediated by the m = 2 tearing mode. The work described herein lays the foundation for nonlinear simulation and analysis of the interaction of tearing modes and gyroradius-scale instabilities in RFP plasmas.
First measurements with monolithic active pixel test structures produced in a 65 nm CMOS process
Authors: Buckland M. ,   the ALICE collaboration
Published: February 2024

Abstract
The Inner Tracking System (ITS) of the ALICE experiment at CERN will undergo an upgrade during the LHC long shutdown 3, in which the three innermost tracking layers will be replaced. This upgrade, named the Inner Tracking System 3 (ITS3), employs stitched wafer-scale Monolithic Active Pixel Sensors fabricated in a 65 nm CMOS process. The sensors are 260 mm in length and thinned to less than 50 μm then bent to form truly half-cylindrical half-barrels. The feasibility of this process for the ITS3 was explored with the first test production run (MLR1) in 2021, whose goal was to evaluate the charged particle detection efficiency and the sensor performance under non-ionising and ionising radiation up to the expected levels for ALICE ITS3 of 1013 1 MeV neq cm-2 (NIEL) and 10 kGy (TID). Three sensor flavours were produced to investigate this process: Analog Pixel Test Structure (APTS), Circuit Exploratoire 65 (CE65) and Digital Pixel Test Structure (DPTS).
This contribution gives an overview of the MLR1 submission and test results, describing the different sensor flavours and presenting the results of the performance measurements done with particle beams for various chip variants and irradiation levels.
The climatological renewable energy deviation index (credi)
Authors: Stoop Laurens P , van der Wiel Karin , Zappa William , Haverkamp Arno , Feelders Ad J , van den Broek Machteld 
Published: February 2024

Abstract
We propose an index to quantify and analyse the impact of climatological variability on the energy system at different timescales. We define the climatological renewable energy deviation index (credi) as the cumulative anomaly of a renewable resource with respect to its climate over a specific time period of interest. For this we introduce the smooth, yet physical, hourly rolling window climatology that captures the expected hourly to yearly behaviour of renewable resources. We analyse the presented index at decadal, annual and (sub-)seasonal timescales for a sample region and discuss scientific and practical implications. credi is meant as an analytical tool for researchers and stakeholders to help them quantify, understand, and explain, the impact of energy-meteorological variability on future energy system. Improved understanding translates to better assessments of how renewable resources, and the associated risks for energy security, may fare in current and future climatological settings. The practical use of the index is in resource planning. For example transmission system operators may be able to adjust short-term planning to reduce adequacy issues before they occur or combine the index with storyline event selection for improved assessments of climate change related risks.
DP2LM: leveraging deep learning approach for estimation and hypothesis testing on mediation effects with high-dimensional mediators and complex confounders
Authors: Wang Shuoyang , Huang Yuan 
Published: February 2024

Summary
Traditional linear mediation analysis has inherent limitations when it comes to handling high-dimensional mediators. Particularly, accurately estimating and rigorously inferring mediation effects is challenging, primarily due to the intertwined nature of the mediator selection issue. Despite recent developments, the existing methods are inadequate for addressing the complex relationships introduced by confounders. To tackle these challenges, we propose a novel approach called DP2LM (Deep neural network-based Penalized Partially Linear Mediation). This approach incorporates deep neural network techniques to account for nonlinear effects in confounders and utilizes the penalized partially linear model to accommodate high dimensionality. Unlike most existing works that concentrate on mediator selection, our method prioritizes estimation and inference on mediation effects. Specifically, we develop test procedures for testing the direct and indirect mediation effects. Theoretical analysis shows that the tests maintain the Type-I error rate. In simulation studies, DP2LM demonstrates its superior performance as a modeling tool for complex data, outperforming existing approaches in a wide range of settings and providing reliable estimation and inference in scenarios involving a considerable number of mediators. Further, we apply DP2LM to investigate the mediation effect of DNA methylation on cortisol stress reactivity in individuals who experienced childhood trauma, uncovering new insights through a comprehensive analysis.
Systematic Bibliographic Database Searching for an Overview of Reviews: A Practical Guide Using Children’s Participation as a Case Study
Authors: McCafferty Paul , Mercado Garcia Esther 
Published: February 2024

Abstract
Systematic literature reviews are crucial in research. Identifying relevant research is the first stage in a systematic review, yet challenges exist hindering their efficacy. Through a case study search strategy addressing the question ‘What do we know about children’s participation in child welfare decision-making?’, this article seeks to promote efficiency in searching by building on existing conceptual and practical guidelines for conducting systematic literature searches and appraisal of database performance in social work research. Thirteen databases were utilised in this study. The total citations, unique hits, sensitivity and precision for each database were calculated to gauge database performance before conducting a cross-study comparison with five previously published social work systematic reviews to begin recognising emergent themes. Social Science Citation and PsycINFO are effective high-performing databases in social work. Social Services Abstracts, Applied Social Science Index and Abstracts are also recommended. The article emphasises the pitfalls of relying on a single database, highlighting the importance of comprehensive searches to avoid bias and increase relevance. The findings underscore the need for social work professionals to develop effective database searching skills, leveraging the information age to inform and enhance practice, promoting efficiency and addressing the challenges faced in this critical stage of research.
Tracking Cryptococcal Meningitis to Monitor HIV Program Success During the Treat All Era: An Analysis of National Data in Botswana
Authors: Milburn James , Ntwayagae Ookeditse , Suresh Rachita , Ngoni Kebatshabile , Northcott Cassie , Penney James , Kinsella Matthew , Mechie Imogen , Ensor Samuel , Thamae Goitseone , Leeme Tshepo , Lawrence David S , Chebani Tony , Grint Daniel , Tenforde Mark W , Avalos Ava , Ramaabya Dinah , Ogando Justus , Mokomane Margaret , Mine Madisa , Jarvis Joseph N 
Published: February 2024

Abstract

Background
Cryptococcal meningitis (CM) causes substantial mortality in African countries with a high prevalence of human immunodeficiency virus (HIV), despite advances in disease management and increasing antiretroviral therapy (ART) coverage. Reliable diagnosis of CM is cheap and more accessible than other indicators of advanced HIV disease burden such as CD4 testing or investigation for disseminated tuberculosis; therefore, monitoring CM incidence has the potential to serve as a valuable metric of HIV programmatic success.

Methods
Botswana national meningitis surveillance data from 2015 to 2022 were obtained from electronic health records. All electronic laboratory records from cerebrospinal fluid samples analyzed within government healthcare facilities in Botswana were extracted from a central online repository. Adjustments for missing data were made through triangulation with prospective cohort study datasets. CM case frequency was enumerated using a case definition and incidence calculated using national census data.

Results
A total of 1744 episodes of CM were identified; incidence declined from 15.0 (95% confidence interval [CI], 13.4–16.7) cases/100 000 person-years in 2015 to 7.4 (95% CI, 6.4–8.6) cases/100 000 person-years in 2022. However, the rate of decline slowed following the introduction of universal treatment in 2016. The highest incidence was observed in men and individuals aged 40–44 years. The proportion of cases diagnosed through cryptococcal antigen testing increased from 35.5% to 86.3%.

Conclusions
CM incidence has decreased in Botswana following expansion of ART coverage but persists at a stubbornly high incidence. Most cases are now diagnosed through the cheap and easy-to-use cryptococcal antigen test, highlighting the potential of using CM as key metric of program success in the Treat All era.
The effect of retrieval practice on vocabulary learning for DHH children
Authors: Reimer Casey K , Grantham Heather , Butler Andrew C 
Published: February 2024

Abstract
On average, deaf and hard-of-hearing (DHH) children have difficulty developing expressive spoken vocabulary comparable to hearing peers. Yet, there are no evidence-based practices to guide classroom instruction for teachers of the deaf. Retrieval practice—a robust learning strategy—has been shown to improve children’s retention of vocabulary, but it has not been investigated with DHH children who use listening and spoken language. The present study examined whether DHH children benefit from using retrieval practice to learn new vocabulary. Sixteen DHH children (in the age range of 5.0–8.11 years) were taught a set of new vocabulary words using retrieval practice or repeated exposure. A recall test was administered two days later. Results showed that DHH children were twice as likely to recall a word taught through retrieval practice than exposure (OR = 2.01, p = .02). Presence of an additional diagnosis and number of practice trials were also significant predicting factors of vocabulary learning.
The Births, Lives and Deaths of Corporations in Late Imperial Russia
Authors: Gregg Amanda , Nafziger Steven 
Published: February 2024

Abstract
Enterprise creation, destruction and evolution support the transition to modern economic growth, yet these processes are poorly understood in industrialising contexts. We investigate Imperial Russia's industrial development at the firm level by examining entry, exit and persistence of corporations. Relying on newly developed balance sheet panel data from every non-financial Russian corporation (more than 2,500 of them) between 1899 and 1914, we examine the characteristics of entering and exiting corporations, how new entrants evolved and the impact of founder identity on subsequent outcomes. Russian corporations evolved within a market environment, conditional on overcoming distortionary institutional barriers to entry that slowed the emergence of these leading firms in the Imperial economy.
Effects of orthopedic treatment (distraction splint) on dentofacial deformities in patients with juvenile idiopathic arthritis
Authors: Vassis Stratos , Sabljic Sanja , Noeldeke Beatrice , Sefidroodi Mohammedreza , Küseler Annelise , Klit Pedersen Thomas , Stoustrup Peter 
Published: February 2024

Abstract

Background
Juvenile idiopathic arthritis (JIA) frequently affects the temporomandibular joint (TMJ), which can alter mandibular growth and development and result in dentofacial deformities.

Objective
To assess the outcomes of orthopedic treatment with distraction splint (DS) in patients with JIA-related dentofacial deformity.

Methods
The retrospective study involved 30 patients with JIA and unilateral TMJ involvement, another study group of 20 patients with JIA and bilateral TMJ involvement, and a control group of 18 non-JIA orthodontic patients with Class II and III malocclusions. The inclusion criteria were DS treatment and cone-beam computed tomography (CBCT) scans before (T0) and 2 years after treatment (T1). Dentofacial morphology and deformity were evaluated based on a validated three-dimensional CBCT-based morphometric analysis. Intergroup differences in outcome measures were compared at T0 and T1, and intragroup changes between T0 and T1 were assessed using the Kruskal–Wallis test.

Results
Initial evaluations at T0 revealed significant differences between the unilateral and bilateral JIA groups and the control group for three out of eight dentofacial deformity variables: inter-side difference in total posterior mandibular height, mandibular axial angle, and posterior/anterior face height (ratio). At follow-up (T1), significant inter-group differences were only observed in total posterior mandibular height indicating that intergroup differences were less pronounced after splint treatment. Assessing inter-group changes between T0 and T1 showed that all parameters remained constant except posterior/anterior face height ratio, which significantly decreased between T0 and T1.

Conclusions
The findings demonstrate the potential of DS treatment for patients with JIA and unilateral or bilateral TMJ involvement to generally support normal dentofacial growth or at least limit further deterioration of dentofacial deformities.
Transglobal spread of an ecologically relevant sea urchin parasite
Authors: Ritchie Isabella T , Vilanova-Cuevas Brayan , Altera Ashley , Cornfield Kaileigh , Evans Ceri , Evans James S , Hopson-Fernandes Maria , Kellogg Christina A , Looker Elayne , Taylor Oliver , Hewson Ian , Breitbart Mya 
Published: February 2024

Abstract
Mass mortality of the dominant coral reef herbivore Diadema antillarum in the Caribbean in the early 1980s contributed to a persistent phase shift from coral- to algal-dominated reefs. In 2022, a scuticociliate most closely related to Philaster apodigitiformis caused further mass mortality of D. antillarum across the Caribbean, leading to &gt;95% mortality at affected sites. Mortality was also reported in the related species Diadema setosum in the Mediterranean in 2022, though the causative agent of the Mediterranean outbreak has not yet been determined. In April 2023, mass mortality of Diadema setosum occurred along the Sultanate of Oman's coastline. Urchins displayed signs compatible with scuticociliatosis including abnormal behavior, drooping and loss of spines, followed by tissue necrosis and death. Here we report the detection of an 18S rRNA gene sequence in abnormal urchins from Muscat, Oman, that is identical to the Philaster strain responsible for D. antillarum mass mortality in the Caribbean. We also show that scuticociliatosis signs can be elicited in Diadema setosum by experimental challenge with the cultivated Philaster strain associated with Caribbean scuticociliatosis. These results demonstrate the Philaster sp. associated with D. antillarum mass mortality has rapidly spread to geographically distant coral reefs, compelling global-scale awareness and monitoring for this devastating condition through field surveys, microscopy, and molecular microbiological approaches, and prompting investigation of long-range transmission mechanisms.
Unravelling novel and pleiotropic genes for cannon bone circumference and bone mineral density in Yorkshire pigs
Authors: Qiu Zijian , Cai Wenwu , Liu Qian , Liu Kaiyue , Liu Chenxi , Yang Huilong , Huang Ruihua , Li Pinghua , Zhao Qingbo 
Published: February 2024

Abstract
Leg weakness is a prevalent health condition in pig farms. The augmentation of cannon bone circumference and bone mineral density can effectively improve limb strength in pigs and alleviate leg weakness. This study measured forelimb cannon bone circumference (fCBC) and rear limb cannon bone circumference (rCBC) using an inelastic tapeline and rear limb metatarsal area bone mineral density (raBMD) using a dual-energy X-ray absorptiometry bone density scanner. The samples of Yorkshire castrated boars were genotyped using a 50K single-nucleotide polymorphism (SNP) array. The SNP-chip data were imputed to the level of whole-genome sequencing data (iWGS). This study used iWGS data to perform genome-wide association studies and identified novel significant SNPs associated with fCBC on SSC6, SSC12, and SSC13, rCBC on SSC12 and SSC14, and raBMD on SSC7. Based on the high phenotypic and genetic correlations between CBC and raBMD, multi-trait meta-analysis was performed to identify pleiotropic SNPs. A significant potential pleiotropic quantitative trait locus (QTL) regulating both CBC and raBMD was identified on SSC15. Bayes fine mapping was used to establish the confidence intervals for these novel QTLs with the most refined confidence interval narrowed down to 56 kb (15.11 to 15.17 Mb on SSC12 for fCBC). Furthermore, the confidence interval for the potential pleiotropic QTL on SSC15 in the meta-analysis was narrowed down to 7.45 kb (137.55 to137.56 Mb on SSC15). Based on the biological functions of genes, the following genes were identified as novel regulatory candidates for different phenotypes: DDX42, MYSM1, FTSJ3, and MECOM for fCBC; SMURF2, and STC1 for rCBC; RGMA for raBMD. Additionally, RAMP1, which was determined to be located 23.68 kb upstream of the confidence interval of the QTL on SSC15 in the meta-analysis, was identified as a potential pleiotropic candidate gene regulating both CBC and raBMD. These findings offered valuable insights for identifying pathogenic genes and elucidating the genetic mechanisms underlying CBC and BMD.
MHY1485 potentiates immunogenic cell death induction and anti-cancer immunity following irradiation
Authors: Sun Lue , Morikawa Kumi , Sogo Yu , Sugiura Yuki 
Published: February 2024

Abstract
Recent in vitro experiments showed that combined treatment with MHY1485, a low-molecular-weight compound, and X-ray irradiation significantly increased apoptosis and senescence in tumor cells, which was associated with oxidative stress, endoplasmic reticulum (ER) stress and p21 stabilization, compared to radiation treatment alone. However, evidence for MHY1485 treatment-mediated suppression of tumor growth in animals is still lacking. Furthermore, it has been shown that ER stress enhances immunogenic cell death (ICD) in tumor cells, as it can exert a favorable influence on the anti-cancer immune system. In the present study, we examined whether co-treatment of MHY1485 and X-ray irradiation induces ICD and in vivo tumor growth suppression using the CT26 and Lewis lung carcinoma murine tumor cell lines. We found that MHY1485 + X-ray treatment promotes ICD more effectively than X-ray treatment alone. MHY1485 suppresses tumor growth in vivo under co-treatment with X-rays and increases INF-γ, tumor necrosis factor, interleukin-2 and interleukin-12 levels in the spleen as well as the presence of CD8+ cells in the tumor. The results suggest that MHY1485 treatment leads to the conversion of irradiated tumors into effective vaccines. Thus, MHY1485 is a promising lead compound for use in combination with radiotherapy.
Noninvasive biomarkers for lupus nephritis
Authors: Liu Ting , Yang Yun-long , Zhou Yan , Jiang Yong-mei 
Published: February 2024

Abstract
Lupus nephritis (LN) is one of the most severe clinical manifestations of systemic lupus erythematosus (SLE). Notably, the clinical manifestations of LN are not always consistent with the histopathological findings. Therefore, the diagnosis and activity monitoring of this disease are challenging and largely depend on invasive renal biopsy. Renal biopsy has side effects and is associated with the risk of bleeding and infection. There is a growing interest in the development of novel noninvasive biomarkers for LN. In this review, we summarize most of the LN biomarkers discovered so far by correlating current knowledge with future perspectives. These biomarkers fundamentally reflect the biological processes of kidney damage and repair during disease. Furthermore, this review highlights the role of urinary cell phenotype detection in the diagnosis, monitoring, and treatment of LN and summarizes the limitations and countermeasures of this test.
Post-traumatic stress disorder in hospital doctors after the COVID-19 pandemic
Authors: Rollin L , Guerin O , Petit A , Bourdon L , Guillemette S , Gislard A , Clin B , Bachelet L , Rouget Mejjad I , Rouger F , Benichou J , Gehanno J F , Commune A 
Published: February 2024

Abstract

Background
Prior studies showed that during the coronavirus disease 2019 (COVID-19) pandemic healthcare workers had a higher risk of developing post-traumatic stress disorder (PTSD) symptoms. However, studies conducted among doctors several years after the beginning of the COVID-19 pandemic are scarce.

Aims
To evaluate the prevalence of PTSD among hospital doctors and to describe potential explanatory factors.

METHODS
The Protec-Cov study was an observational, cross-sectional, multicentre study, which used an anonymous online questionnaire to evaluate PTSD in doctors from six hospitals in France between December 2021 and March 2022. The presence of PTSD was assessed using the Post-traumatic Stress Disorder Checklist Scale (PCLS) questionnaire with a cut-off of 44.

RESULTS
Among the 307 doctors included, 18% presented a PCLS ≥44. The multivariate analysis showed that factors associated with a PCLS ≥44 were having a higher workload than before the COVID-19 pandemic (odds ratio [OR] = 4.75; 95% confidence interval [CI] 1.68–13.38), not feeling recognized within the professional environment (OR = 2.83; 95% CI 1.26–6.33), and feeling isolated because of the lockdown (OR = 4.2; 95% CI 1.97–8.95). Approximately 30% of hospital doctors (n = 91) felt a need for psychological support but only 31% of them (n = 28) received support.

Conclusions
Based on our findings, a high prevalence of PTSD was observed among hospital doctors 2 years after the beginning of the COVID-19 pandemic. This study supports an early diagnosis of PTSD in this category of healthcare workers and warrants further study.