bluuebunny/crossref_metadata_2025_split huggingface dataset:
Twitter-generated Moral Panic and Its Effect on Pretrial Incarceration/ Bail: Contextualizing the Tale of ‘Folk Devil’ Aryan Khan
Authors: Gautam Upma , Das Priya 
Published: May 2023

The Narcotic Drugs and Psychotropic Substances (NDPS) Act, which was enacted with an intent to control drug abuse and prohibit its trade, has blurred the line between the offender and the victim, particularly in cases of addicts. Nonetheless, the focus of this study is the multifarious victimization of the offender: overcriminalization in terms of measures, lengthy pretrial incarceration and increased sensationalism in cases of offenders belonging to high strata of society, thus creating a moral panic. Incident of victimization is juxtaposed with public concern solicited by the reporting of cases. The stigmatization endured and the trauma suffered by the accused owing to the full media glare strike on their innocence and violate their right to life and dignity. Aim and Objective: A criminal justice system is an institutionalized means of rendering justice. One of the virtuous traits of a criminal justice system modelled on the ethos of due process is its attempt to achieve certainty and transparency in its process and the outcomes. However, no institution is infallible as manifested by the misuse of draconian provisions of the NDPS Act 1985. This study first evaluates whether disposal of bail matters in NDPS cases is a classic case of overcriminalization leading to the victimization of the offender; second, it gauges the impact of public reaction depicting ‘moral panic’ of the offender in the disposal of bail matters. Methodology: The study was conducted through a detailed content analysis of the public reaction in the Aryan Khan drug case on the micro-blogging site Twitter with the help of the content analysis tool NVivo. Findings: The outcome of the study manifests positive interrelationship between moral panic and public perception, positive interrelationship between moral panic and status of the person arrested which consequentially affects the period of pretrial incarceration (denial of bail).
Gulf War Illness: A Randomized Controlled Trial Combining Mindfulness Meditation and Auricular Acupuncture
Authors: Breneman Charity B. , Reinhard Matthew J. , Allen Nathaniel , Belouali Anas , Chun Timothy , Crock Lucas , Duncan Alaine D. , Dutton Mary Ann 
Published: May 2023

Background Many Gulf War (GW) Veterans report chronic symptoms including pain, fatigue, and cognitive impairment, commonly defined as Gulf War Illness (GWI). Complementary and integrative health (CIH) therapies may potentially improve multiple symptoms of GWI. Objective To examine the effectiveness of combining 2 commonly available CIH therapies, mindfulness meditation and auricular acupuncture, in improving health-related functioning and multiple symptom domains of GWI (e.g., pain, fatigue). Methods This study was a randomized controlled trial in which Veterans with GWI were randomly assigned to either the intervention group (n = 75), wherein they received 2 distinct CIH therapies – mindfulness meditation and auricular acupuncture, or the active control group, wherein they received a GW Health Education (GWHE) program (n = 74), each lasting 8 weeks. Self-report health measures were assessed at baseline, endpoint, and 3 month follow-up. Results In the intention-to-treat analyses, there were significant between-group differences for mental-health related functioning, fatigue, depression symptoms, and Kansas total severity scores for symptoms in which the CIH group had improved scores for these outcomes at endpoint compared to the GWHE group (all P ≤ .05). The CIH group also had significant reductions in pain interference at endpoint and follow-up compared to baseline (estimated marginal mean difference: −2.52 and −2.22, respectively; all P = .01), whereas no significant changes were observed in the GWHE group. For pain characteristics, the GWHE group had a worsening of pain at endpoint compared to baseline (estimated marginal mean difference: +2.83; P = .01), while no change was observed in the CIH group. Conclusion Findings suggest a possible beneficial effect of combining 2 CIH therapies, mindfulness meditation and auricular acupuncture, in reducing overall symptom severity and individual symptom domains of fatigue, musculoskeletal, and mood/cognition in Veterans with GWI. Trial Registration Clinical Trials identifier NCT02180243
Whole‐genome sequencing identifies interferon-induced protein IFI6/IFI27-like as a strong candidate gene for VNN resistance in European sea bass
Authors: Delpuech Emilie , Vandeputte Marc , Morvezen Romain , Bestin Anastasia , Besson Mathieu , Brunier Joseph , Bajek Aline , Imarazene Boudjema , François Yoannah , Bouchez Olivier , Cousin Xavier , Poncet Charles , Morin Thierry , Bruant Jean-Sébastien , Chatain Béatrice , Haffray Pierrick , Phocas Florence , Allal François 
Published: May 2023

Abstract
Background
Viral nervous necrosis (VNN) is a major disease that affects European sea bass, and understanding the biological mechanisms that underlie VNN resistance is important for the welfare of farmed fish and sustainability of production systems. The aim of this study was to identify genomic regions and genes that are associated with VNN resistance in sea bass.

Results
We generated a dataset of 838,451 single nucleotide polymorphisms (SNPs) identified from whole-genome sequencing (WGS) in the parental generation of two commercial populations (A: 2371 individuals and B: 3428 individuals) of European sea bass with phenotypic records for binary survival in a VNN challenge. For each population, three cohorts were submitted to a red-spotted grouper nervous necrosis virus (RGNNV) challenge by immersion and genotyped on a 57K SNP chip. After imputation of WGS SNPs from their parents, quantitative trait loci (QTL) were mapped using a Bayesian sparse linear mixed model (BSLMM). We found several QTL regions that were specific to one of the populations on different linkage groups (LG), and one 127-kb QTL region on LG12 that was shared by both populations and included the genes ZDHHC14, which encodes a palmitoyltransferase, and IFI6/IFI27-like, which encodes an interferon-alpha induced protein. The most significant SNP in this QTL region was only 1.9 kb downstream of the coding sequence of the IFI6/IFI27-like gene. An unrelated population of four large families was used to validate the effect of the QTL. Survival rates of susceptible genotypes were 40.6% and 45.4% in populations A and B, respectively, while that of the resistant genotype was 66.2% in population B and 78% in population A.

Conclusions
We have identified a genomic region that carries a major QTL for resistance to VNN and includes the ZDHHC14 and IFI6/IFI27-like genes. The potential involvement of the interferon pathway, a well-known anti-viral defense mechanism in several organisms (chicken, human, or fish), in survival to VNN infection is of particular interest. Our results can lead to major improvements for sea bass breeding programs through marker-assisted genomic selection to obtain more resistant fish.
Telomere-to-Telomere genome assemblies of human-infecting Encephalitozoon species
Authors: Mascarenhas dos Santos Anne Caroline , Julian Alexander Thomas , Liang Pingdong , Juárez Oscar , Pombert Jean-François 
Published: May 2023

Abstract
Background
Microsporidia are diverse spore forming, fungal-related obligate intracellular pathogens infecting a wide range of hosts. This diversity is reflected at the genome level with sizes varying by an order of magnitude, ranging from less than 3 Mb in Encephalitozoon species (the smallest known in eukaryotes) to more than 50 Mb in Edhazardia spp. As a paradigm of genome reduction in eukaryotes, the small Encephalitozoon genomes have attracted much attention with investigations revealing gene dense, repeat- and intron-poor genomes characterized by a thorough pruning of molecular functions no longer relevant to their obligate intracellular lifestyle. However, because no Encephalitozoon genome has been sequenced from telomere-to-telomere and since no methylation data is available for these species, our understanding of their overall genetic and epigenetic architectures is incomplete.

Methods
In this study, we sequenced the complete genomes from telomere-to-telomere of three human-infecting Encephalitozoon spp. —E. intestinalis ATCC 50506, E. hellem ATCC 50604 and E. cuniculi ATCC 50602— using short and long read platforms and leveraged the data generated as part of the sequencing process to investigate the presence of epigenetic markers in these genomes. We also used a mixture of sequence- and structure-based computational approaches, including protein structure prediction, to help identify which Encephalitozoon proteins are involved in telomere maintenance, epigenetic regulation, and heterochromatin formation.

Results
The Encephalitozoon chromosomes were found capped by TTAGG 5-mer telomeric repeats followed by telomere associated repeat elements (TAREs) flanking hypermethylated ribosomal RNA (rRNA) gene loci featuring 5-methylcytosines (5mC) and 5-hemimethylcytosines (5hmC), themselves followed by lesser methylated subtelomeres and hypomethylated chromosome cores. Strong nucleotide biases were identified between the telomeres/subtelomeres and chromosome cores with significant changes in GC/AT, GT/AC and GA/CT contents. The presence of several genes coding for proteins essential to telomere maintenance, epigenetic regulation, and heterochromatin formation was further confirmed in the Encephalitozoon genomes.

Conclusion
Altogether, our results strongly support the subtelomeres as sites of heterochromatin formation in Encephalitozoon genomes and further suggest that these species might shutdown their energy-consuming ribosomal machinery while dormant as spores by silencing of the rRNA genes using both 5mC/5hmC methylation and facultative heterochromatin formation at these loci.
Resequencing of Rosa rugosa accessions revealed the history of population dynamics, breed origin, and domestication pathways
Authors: Zang Fengqi , Ma Yan , Wu Qichao , Tu Xiaolong , Xie Xiaoman , Huang Ping , Tong Boqiang , Zheng Yongqi , Zang Dekui 
Published: May 2023

Abstract
Background
Rosa rugosa is a shrub that originated in China and has economic and ecological value. However, during the development of R. rugosa, the genetic background was chaotic, and the genetic structure among different wild populations was unclear, as well as wild and cultivated accessions. Here, we report whole-genome resequencing of wild and cultivated R. rugosa accessions.

Results
A total of 19,041,284 SNPs were identified in 188 R. rugosa accessions and 3 R. chinensis accessions by resequencing. Population genetic analysis revealed that cultivated and wild groups were separated very early. All R. rugosa accessions were divided into 8 categories based on genetic structure: (1) Weihai, Yantai, and Liaoning category, (2) Jilin category, and (3) Hammonasset category (above three are wild); (4) traditional varieties, (5) hybrids between R. rugosa and R. chinensis, (6) Zizhi Rose, (7) Kushui Rose, (8) hybrids between R. rugosa and R. multiflora. We found that the heterozygosity and genetic diversity of wild accessions were generally lower than those of cultivated individuals. The genes that were selected during cultivation were identified, and it was found that these genes were mainly related to environmental adaptation and growth.

Conclusions
The Jilin population was the oldest population and later migrated to Liaoning and then migrated to Yantai and Weihai by sea regression in the Bohai Basin. The Hammonasset naturalized population probably originated from the Jilin population and then experienced separate differentiation. The long-term asexual reproduction pattern of R. rugosa decreased genetic diversity in the wild population. During R. rugosa cultivation, the ancestors of the Jilin population were involved in breeding traditional varieties, after which almost no wild individuals were engaged in breeding. However, in recent decades, cross breeding of R. rugosa started the utilization of wild germplasms. In comparison, some other species play important roles in variety formation. Few genes related to economic traits were selected, suggesting no directional domestication in the R. rugosa cultivation process.
Quantitative bias analysis in practice: review of software for regression with unmeasured confounding
Authors: Kawabata Emily , Tilling Kate , Groenwold Rolf H. H. , Hughes Rachael A. 
Published: May 2023

AbstractBackgroundFailure to appropriately account for unmeasured confounding may lead to erroneous conclusions. Quantitative bias analysis (QBA) can be used to quantify the potential impact of unmeasured confounding or how much unmeasured confounding would be needed to change a study’s conclusions. Currently, QBA methods are not routinely implemented, partly due to a lack of knowledge about accessible software. Also, comparisons of QBA methods have focused on analyses with a binary outcome.MethodsWe conducted a systematic review of the latest developments in QBA software published between 2011 and 2021. Our inclusion criteria were software that did not require adaption (i.e., code changes) before application, was still available in 2022, and accompanied by documentation. Key properties of each software tool were identified. We provide a detailed description of programs applicable for a linear regression analysis, illustrate their application using two data examples and provide code to assist researchers in future use of these programs.ResultsOur review identified 21 programs with$$62\%$$62%created post 2016. All are implementations of a deterministic QBA with$$81\%$$81%available in the free software R. There are programs applicable when the analysis of interest is a regression of binary, continuous or survival outcomes, and for matched and mediation analyses. We identified five programs implementing differing QBAs for a continuous outcome: treatSens, causalsens, sensemakr, EValue, and konfound. When applied to one of our illustrative examples, causalsens incorrectly indicated sensitivity to unmeasured confounding whereas the other four programs indicated robustness.sensemakrperforms the most detailed QBA and includes a benchmarking feature for multiple unmeasured confounders.ConclusionsSoftware is now available to implement a QBA for a range of different analyses. However, the diversity of methods, even for the same analysis of interest, presents challenges to their widespread uptake. Provision of detailed QBA guidelines would be highly beneficial.
Complex association of self-rated health, depression, functional ability with loneliness in rural community-dwelling older people
Authors: Cao Wenwen , Cao Chenglin , Ren Bohua , Yang Jing , Chen Ruoling , Hu Zhi , Bai Zhongliang 
Published: May 2023

AbstractBackgroundThis study aimed to explore whether and how self-rated health, depression and functional ability interactively associated with loneliness using a sample group of older adults residing in China rural communities.MethodsData on socio-demographic information, self-rated health, depressive symptoms, functional ability and loneliness (quantified via a single question) were collected from 1009 participants. Cross-tabulations with chi-square test, bivariate correlations, and Classification and Regression Tree (CART) models were employed for analysis.ResultsWe found that 45.1% of the participants were classified as lonely. Our results gain insight into the hierarchical order of predictors for the presence of loneliness, suggesting that there was a significant interaction between functional ability and depressive symptoms while self-rated health was not a significant factor. The probability of loneliness increased with the combination of limited functional ability and depression, and varied with different interaction of functional ability, depressive symptoms, and marital status, respectively. Notably, while there were some differences, similar associations were observed among older male and female respondents.ConclusionTo delay or reduce loneliness, early detection which focuses on older people who report limitations in functional ability, depression, and being female, offers opportunities to start early interventions. Our findings might be helpful not only in designing and implementing loneliness prevention programs but also in improving healthcare for older rural community-dwelling people.
Association of serum uric acid and fasting plasma glucose with cognitive function: a cross-sectional study
Authors: Yuan Zelin , Liu Huamin , Zhou Rui , Gu Shanyuan , Wu Keyi , Huang Zhiwei , Zhong Qi , Huang Yining , Chen Haowen , Wu Xianbo 
Published: May 2023

Abstract
Background
The combined effect of serum uric acid (SUA) and blood glucose on cognition has not been explored. This study aimed to examine the separate and combined association of SUA and fasting plasma glucose (FPG) or diabetes mellitus (DM) with cognition in a sample of Chinese middle-aged and elderly population.

Methods
A total of 6,509 participants aged 45 years or older who participated in the China Health and Retirement Longitudinal Study (CHARLS, 2011) were included. The three cognitive domains assessed were episodic memory, mental status, and global cognition (the sum of the first two terms). Higher scores indicated better cognition. SUA and FPG were measured. The participants were grouped based on SUA and FPG quartiles to evaluate their combined associations of cognition with SUA Q1–Q3 only (Low SUA), with FPG Q4 only (High FPG), without low SUA and high FPG levels (Non), and with low SUA and high FPG levels (Both), multivariate linear regression models were used to analyze their association.

Results
Lower SUA quartiles were associated with poorer performance in global cognition and episodic memory compared with the highest quartile. Although no association was found between FPG or DM and cognition, high FPG or DM combined with low SUA levels in women (βFPG = -0.983, 95% CI: -1.563–-0.402; βDM = -0.800, 95% CI: -1.369–-0.232) had poorer cognition than those with low SUA level only (βFPG = -0.469, 95% CI: -0.926–-0.013; βDM = -0.667, 95% CI: -1.060–-0.275).

Conclusion
Maintaining an appropriate level of SUA may be important to prevent cognitive impairment in women with high FPG.
Design of effective outpatient sentinel surveillance for COVID-19 decision-making: a modeling study
Authors: Toh Kok Ben , Runge Manuela , Richardson Reese AK , Hladish Thomas J , Gerardin Jaline 
Published: May 2023

Abstract
Background
Decision-makers impose COVID-19 mitigations based on public health indicators such as reported cases, which are sensitive to fluctuations in supply and demand for diagnostic testing, and hospital admissions, which lag infections by up to two weeks. Imposing mitigations too early has unnecessary economic costs while imposing too late leads to uncontrolled epidemics with unnecessary cases and deaths. Sentinel surveillance of recently-symptomatic individuals in outpatient testing sites may overcome biases and lags in conventional indicators, but the minimal outpatient sentinel surveillance system needed for reliable trend estimation remains unknown.

Methods
We used a stochastic, compartmental transmission model to evaluate the performance of various surveillance indicators at reliably triggering an alarm in response to, but not before, a step increase in transmission of SARS-CoV-2. The surveillance indicators included hospital admissions, hospital occupancy, and sentinel cases with varying levels of sampling effort capturing 5, 10, 20, 50, or 100% of incident mild cases. We tested 3 levels of transmission increase, 3 population sizes, and conditions of either simultaneous transmission increase or lagged increase in the older population. We compared the indicators’ performance at triggering alarm soon after, but not prior, to the transmission increase.

Results
Compared to surveillance based on hospital admissions, outpatient sentinel surveillance that captured at least 20% of incident mild cases could trigger an alarm 2 to 5 days earlier for a mild increase in transmission and 6 days earlier for a moderate or strong increase. Sentinel surveillance triggered fewer false alarms and averted more deaths per day spent in mitigation. When transmission increase in older populations lagged the increase in younger populations by 14 days, sentinel surveillance extended its lead time over hospital admissions by an additional 2 days.

Conclusions
Sentinel surveillance of mild symptomatic cases can provide more timely and reliable information on changes in transmission to inform decision-makers in an epidemic like COVID-19.
Vogesella urethralis-induced aspiration pneumonia and bacteremia in an elderly man: a first case report and literature review
Authors: Matsuda Hironari , Katayama Isana , Watanabe Takayasu , Komatsu Arisa , Iwakami Naoko , Goto Yukiko , Suzuki Misako , Iwakami Shin-ichiro , Takahashi Kazuhisa 
Published: May 2023

Abstract
Background
Vogesella species are common aquatic Gram-negative rods that were first reported in 1997. Vogesella urethralis bacterium was first isolated from human urine in 2020. Only two cases of disease caused by Vogesella species have been reported with no case of Vogesella urethralis-caused disease being reported as yet. Herein, we report a case of aspiration pneumonia and bacteremia caused by Vogesella urethralis.

Case presentation
An 82-year-old male patient was admitted with dyspnea, increased sputum production, and hypoxia. Gram-negative rods were isolated from the blood and sputum cultures of the patient. He was diagnosed with aspiration pneumonia and bacteremia. Initially, Vogesella urethralis was wrongly identified as Comamonas testosteroni based on fully automated susceptibility testing; however, additional 16S rRNA gene sequencing identified the causative as Vogesella urethralis. The patient was treated with piperacillin and tazobactam. Unfortunately, he developed aspiration pneumonia again and died during hospitalization.

Conclusions
Since no database exists for rare bacteria in traditional clinical microbiology laboratories, 16S rRNA gene sequence analysis is useful. We report the first case of Vogesella urethralis-induced aspiration pneumonia and bacteremia.