bluuebunny/crossref_metadata_2025_split huggingface dataset:
Context-dependent DNA methylation signatures in animal livestock
Authors: Venkatesh Geetha , Tönges Sina , Hanna Katharina , Ng Yi Long , Whelan Rose , Andriantsoa Ranja , Lingenberg Annika , Roy Suki , Nagarajan Sanjanaa , Fong Steven , Raddatz Günter , Böhl Florian , Lyko Frank 
Published: January 2023

Abstract
DNA methylation is an important epigenetic modification that is widely conserved across animal genomes. It is widely accepted that DNA methylation patterns can change in a context-dependent manner, including in response to changing environmental parameters. However, this phenomenon has not been analyzed in animal livestock yet, where it holds major potential for biomarker development. Building on the previous identification of population-specific DNA methylation in clonal marbled crayfish, we have now generated numerous base-resolution methylomes to analyze location-specific DNA methylation patterns. We also describe the time-dependent conversion of epigenetic signatures upon transfer from one environment to another. We further demonstrate production system-specific methylation signatures in shrimp, river-specific signatures in salmon and farm-specific signatures in chicken. Together, our findings provide a detailed resource for epigenetic variation in animal livestock and suggest the possibility for origin tracing of animal products by epigenetic fingerprinting.
A reference genome for Bluegill (Centrarchidae: Lepomis macrochirus)
Authors: Ludt William B , Corbett Eamon C , Kattawar Jerry , Chakrabarty Prosanta , Faircloth Brant C 
Published: January 2023

Abstract
North American sunfishes (Family Centrarchidae) are among the most popular sportfish throughout the United States and Canada. Despite the popularity of sunfishes, their ecological importance, and their extensive stocking and aquacultural history, few molecular studies have examined the evolutionary relationships and species boundaries among members of this group, many of which are known to hybridize. Here, we describe a chromosome-scale genome assembly representing Bluegill (Lepomis macrochirus), one of the most widespread centrarchid species. By combining long-read, Oxford Nanopore sequencing data with short-insert, whole-genome and HiC sequence reads, we produced an assembly (Lm_LA_1.1) having a total length of 889 Mb including 1,841 scaffolds and having a scaffold N50 of 36 Mb, L50 of 12, N90 of 29 Mb, and L90 of 22. We detected 99% (eukaryota_odb10) and 98% (actinopterygii_odb10) universal single-copy orthologs (BUSCOs), and ab initio gene prediction performed using this new assembly identified a set of 17,233 genes that were supported by external (OrthoDB v10) data. This new assembly provides an important addition to the growing set of assemblies already available for spiny-rayed fishes (Acanthomorpha), and it will serve as a resource for future studies that focus on the complex evolutionary history of centrarchids.
Genomic view of the diversity and functional role of archaea and bacteria in the skeleton of the reef-building corals Porites lutea and Isopora palifera
Authors: Tandon Kshitij , Ricci Francesco , Costa Joana , Medina Mónica , Kühl Michael , Blackall Linda L , Verbruggen Heroen 
Published: January 2023

Abstract
At present, our knowledge on the compartmentalization of coral holobiont microbiomes is highly skewed toward the millimeter-thin coral tissue, leaving the diverse coral skeleton microbiome underexplored. Here, we present a genome-centric view of the skeleton of the reef-building corals Porites lutea and Isopora palifera, through a compendium of ∼400 high-quality bacterial and archaeal metagenome-assembled genomes (MAGs), spanning 34 phyla and 57 classes. Skeletal microbiomes harbored a diverse array of stress response genes, including dimethylsulfoniopropionate synthesis (dsyB) and metabolism (DMSP lyase). Furthermore, skeletal MAGs encoded an average of 22 ± 15 genes in P. lutea and 28 ± 23 in I. palifera with eukaryotic-like motifs thought to be involved in maintaining host association. We provide comprehensive insights into the putative functional role of the skeletal microbiome on key metabolic processes such as nitrogen fixation, dissimilatory and assimilatory nitrate, and sulfate reduction. Our study provides critical genomic resources for a better understanding of the coral skeletal microbiome and its role in holobiont functioning.
Are Italian Rules on Copyright Collective Management in Line with EU Law?
Authors: Meo Carlo 
Published: January 2023

Abstract
Directive (EU) 2014/26 liberalised the market for collective management of copyright and related rights in Europe. In doing so it distinguished collecting societies into two categories. ‘Collective Management Organisations’ (CMOs) are entities that are either controlled (or owned) by rightholders or organised on a ‘non-profit’ basis. Conversely, ‘Independent Management Entities’ (IMEs) operate ‘for profit’ and are not controlled by rightholders. Prior to the adoption of this Directive, Italian law entrusted SIAE (Italian Society of Authors and Publishers) with a legal monopoly for the collective management of copyright. In 2017 a reform put an end to this system by opening the market to new entrants. However, according to the new rules, an entity can only manage copyright in Italy if it qualifies as a CMO. IMEs are therefore still not allowed to manage copyright in the Italian market. Such a restriction has raised a lively debate in Italy and its compatibility with EU law has recently been the object of a request for a preliminary ruling of the CJEU by the Tribunal of Rome. This work deals with the question of whether the choice of preventing IMEs from entering the Italian market is compatible with the principles of Directive 2014/26 and with general principles of EU law on the Internal Market.
A Multicenter, Controlled Human Infection Study of Influenza A(H1N1)pdm09 in Healthy Adults
Authors: Ortiz Justin R , Bernstein David I , Hoft Daniel F , Woods Christopher W , McClain Micah T , Frey Sharon E , Brady Rebecca C , Bryant Christopher , Wegel Ashley , Frenck Robert W , Walter Emmanuel B , Abate Getahun , Williams Sarah R , Atmar Robert L , Keitel Wendy A , Rouphael Nadine , Memoli Mathew J , Makhene Mamodikoe K , Roberts Paul C , Neuzil Kathleen M 
Published: January 2023

Abstract

Background
We evaluated the associations between baseline influenza virus–specific hemagglutination inhibition (HAI) and microneutralization (MN) titers and subsequent symptomatic influenza virus infection in a controlled human infection study.

Methods
We inoculated unvaccinated healthy adults aged 18–49 years with an influenza A/California/04/2009/H1N1pdm-like virus (NCT04044352). We collected serial safety labs, serum for HAI and MN, and nasopharyngeal swabs for reverse-transcription polymerase chain reaction (RT-PCR) testing. Analyses used the putative seroprotective titer of ≥40 for HAI and MN. The primary clinical outcome was mild-to-moderate influenza disease (MMID), defined as ≥1 postchallenge positive qualitative RT-PCR test with a qualifying symptom/clinical finding.

Results
Of 76 participants given influenza virus challenge, 54 (71.1%) experienced MMID. Clinical illness was generally very mild. MMID attack rates among participants with baseline titers ≥40 by HAI and MN were 64.9% and 67.9%, respectively, while MMID attack rates among participants with baseline titers &lt;40 by HAI and MN were 76.9% and 78.3%, respectively. The estimated odds of developing MMID decreased by 19% (odds ratio, 0.81 [95% confidence interval, .62–1.06]; P = .126) for every 2-fold increase in baseline HAI. There were no significant adverse events.

Conclusions
We achieved a 71.1% attack rate of MMID. High baseline HAI and MN were associated with protection from illness.
Clinical Trials Registration. NCT04044352.
Striking differences in weight gain after cART initiation depending on early or advanced presentation: results from the ANRS CO4 FHDH cohort
Authors: Grabar Sophie , Potard Valérie , Piroth Lionel , Abgrall Sophie , Bernard Louis , Allavena Clotilde , Caby Fabienne , de Truchis Pierre , Duvivier Claudine , Enel Patricia , Katlama Christine , Khuong Marie-Aude , Launay Odile , Matheron Sophie , Melica Giovanna , Melliez Hugues , Meynard Jean-Luc , Pavie Juliette , Slama Laurence , Bregigeon Sylvie , Tattevin Pierre , Capeau Jacqueline , Costagliola Dominique 
Published: January 2023

AbstractBackgroundMany studies have reported weight gain in ART-naive people living with HIV (PWH) initiating an integrase strand-transfer inhibitor-based regimen. We studied the impact of early or advanced presentation and that of individual drugs in PWH initiating combined ART (cART) between 2012 and 2018.MethodsFrom the French Hospital Database HIV cohort, we assessed factors associated with a weight gain  ≥10%, weight change after cART initiation or BMI increase  ≥5 kg/m2 up to 30 months. The analyses were conducted overall, and among PWH with early (primary infection or CD4 &gt;350/mm3 and viral load  &lt;100 000 copies/mL, without AIDS) and advanced presentation (AIDS or CD4 &lt;200/mm3, not during primary infection).ResultsAt 30 months, 34.5% (95% CI: 33.5–35.6) of the 12 773 PWH had a weight gain ≥10%, with 20.9% (95% CI: 19.6–22.2) among the 5794 with early presentation and 63.1% (95% CI: 60.9–65.3) among the 3106 with advanced presentation. Weight gain was 2.8 kg (95% CI: 2.0–3.7) for those with early presentation and 9.7 kg (95% CI: 8.4–11.1) for those with advanced presentation. Most weight gain occurred in the first 12 months. Underweight and obese PWH were at significantly higher risk of a BMI increase  ≥5 kg/m2 than normal-weight PWH. Results differed within classes and by outcome. Raltegravir and dolutegravir were consistently associated with greater weight gain than the other third agents. Tenofovir alafenamide was also associated with higher weight gain than tenofovir disoproxil or abacavir.ConclusionsAfter initiating cART, PWH with early presentation exhibited a small weight gain, whereas it was large among those with advanced presentation. The choice of ART should account for the risk of weight gain, especially for PWH who present with advanced disease and/or are obese.
Bayesian multistate modelling of incomplete chronic disease burden data
Authors: Jackson Christopher , Zapata-Diomedi Belen , Woodcock James 
Published: January 2023

AbstractThe ‘multistate lifetable’ is a widely used model for the long-term health impacts of public health interventions. It requires estimates of the incidence, case fatality, and sometimes also remission rates, for multiple diseases by age and gender. The case fatality is the rate of death from a disease for people with a disease, and is commonly not observed directly. Instead, we often observe the mortality in the general population. Similarly, we might know the disease prevalence, but not the incidence. This paper presents Bayesian continuous-time multistate models for estimating transition rates between disease states based on incomplete data. It unifies and extends two previous methods, by using a formal statistical model, with more efficient computational algorithms. This allows rates for different ages, areas, and time periods to be related in more flexible ways, and allows models to be formally checked and compared. The methods are made more widely usable through an R package. The models are used to estimate case fatality for multiple diseases in the city regions of England, based on incidence, prevalence, and mortality data from the Global Burden of Disease study. The estimates can be used to inform health impact models relating to those diseases and areas.
Disease severity and genotype–phenotype correlation in adult patients with familial Mediterranean fever
Authors: Tuncer Kuru Fatma , Gokcen Neslihan , Yazici Ayten , Cefle Ayse 
Published: January 2023

ABSTRACT

Objectives
To assess the relationships of disease severity with genotype and phenotype in adult familial Mediterranean fever patients.

Methods
Two-hundred seventy-five patients included in the study were divided into four groups according to their mutations: Group 1, M694V homozygous; Group 2, M694V–other; Group 3, other–other; and Group 4, no meaningful gene variants. Disease severity was evaluated using the Pras disease severity score. The association between Pras scores and other possible predictors was assessed by the multiple linear regression analysis.

Results
In this study, 12.4% of all patients were in Group 1, 55.3% were in Group 2, 26.5% were in Group 3, and 5.8% were in Group 4. Pras scores were higher in Group 1 than in Groups 2, 3, and 4 (post hoc pairwise comparisons; P = .001, P &lt; .001, and P = .001, respectively). Age at disease onset and age at diagnosis were found moderately and strongly correlated with Pras scores. Patients with moderate and severe disease were intensely involved in Group 1.

Conclusions
Higher Pras scores, earlier age of symptoms and diagnosis, more frequent arthritis and erysipelas-like erythema, and higher colchicine dose are closely associated with M694V homozygous familial Mediterranean fever patients. These patients also have mostly moderate and severe disease severity.
Hyperglobulinemia predicts increased risk of mortality in primary Sjögren’s syndrome: Based on a Chinese multicentre registry
Authors: Zhong Hui , Wang Yanhong , Yang Pingting , Duan Xinwang , Wang Yongfu , Xu Jian , Wu Lijun , Li Qin , Kong Xiaodan , Zhang Liyun , Li Xiaomei , Xu Dong , Li Mengtao , Zhao Yan , Zeng Xiaofeng 
Published: January 2023

ABSTRACT

Objective
To investigate whether primary Sjögren’s syndrome (pSS) patients with hyperglobulinemia have an increased risk of all-cause mortality.

Methods
Patients who registered in the Chinese Rheumatism Data Centre from May 2016 to July 2021 and met the 2002 American European Consensus Group criteria or 2016 American College of Rheumatology /European League Against Rheumatism classification criteria for Sjögren’s syndrome were included. Hyperglobulinemia was defined as any elevated serum levels of immunoglobulin G (IgG), immunoglobulin A (IgA), or immunoglobulin M (IgM). The primary outcome was all-cause death. Data for demographic and clinical characteristics, laboratory results, disease activity, damage scores, and treatments were evaluated.

Results
A total of 9527 pSS patients were included in the analysis, of whom 4236 (44.5%) had at least one kind of elevated immunoglobulin level among IgG, IgA, and IgM. Patients with hyperglobulinemia had a significantly increased risk of death (crude hazard ratio 2.60; 95% confidence interval 1.91–3.55; adjusted hazard ratio 1.90; 95% confidence interval 1.20–3.01). The risk of death was positively correlated with IgG level (P trend &lt;.001). The 5-, 10-, and 15-year survival rates of patients with hyperglobulinemia were 96.9%, 92.3%, and 87.9%, respectively, and significantly lower than the corresponding rates of 98.8%, 97.9%, and 96.4% in patients without hyperglobulinemia.

Conclusions
Hyperglobulinemia is an independent risk factor for increased all-cause mortality in pSS patients. The risk of death is positively correlated with IgG level.
Clinical Correlation of Adenoviral Load in the Respiratory Tract Measured by Digital PCR in Immunocompromised Children
Authors: Hijano Diego R , Ferrolino Jose A , Hidinger Jennifer , Brazelton Jessica N , Gu Zhengming , Suganda Sri , Glasgow Heather L , Allison Kim J , Peterson Megan , Dallas Ronald H , Maron Gabriela , Hayden Randall T 
Published: January 2023

Abstract
Immunocompromised patients can have life-threatening adenoviral infection. Viral load in blood and stool is commonly used to guide antiviral therapy. We developed and evaluated a digital polymerase chain reaction assay to quantify human adenovirus in the respiratory tract and showed that higher peak load correlates with disseminated infection, mechanical ventilation, and death.
To Align or Misalign?: Interpreting INGO-State Partnership in Cambodia
Authors: Wilks Mary-Collier 
Published: January 2023

ABSTRACT
This article uses ethnographic and interview methods to compare two international nongovernmental organizations (INGOs) implementing public health programs in Cambodia. Both INGOs formally adopt the same policy, developing state partnership, but implement this policy very differently. One INGO successfully aligns the policy with on-the-ground practice, while the other organization is unable and unwilling to successfully cooperate with local state officials. I argue that previous research on international development organizations, policy convergence, and divergence in implementation needs to be expanded to analytically specify the process of policy alignment and misalignment. Drawing on the inhabited institutions perspective, I illustrate how global policies are made meaningful in intra- and inter-organizational interactions through a two-step process: (1) operationalization in which the broad policy is translated into specific programming and (2) implementation in which local actors do or do not align the policy with actual practice in Cambodia. This article offers a method for systematically theorizing policy alignment or misalignment with practice in international organizations.
NEW Soul in the neighborhood—reach and effectiveness of a dissemination and implementation feasibility study
Authors: Bernhart John A , Turner-McGrievy Gabrielle M , Wilson Mary J , Sentman Claudia , Wilcox Sara , Rudisill Caroline 
Published: January 2023

AbstractDissemination and implementation (D&I) studies of dietary interventions for African Americans are limited. Restaurants may be an innovative setting to deliver dietary interventions. Purpose: Assess weight loss, self-efficacy for healthy eating, diet quality, and quality of life in African Americans in two groups: virtual synchronous and virtual asynchronous. Guided by RE-AIM, the Nutritious Eating with Soul @ Rare Variety Café Feasibility study included nutrition education, accountability partners for support, and cooking demonstrations led by a community health worker and was delivered across two cohorts in a non-randomized design. The intervention was conducted over 12 consecutive weekly classes. Due to the COVID-19 pandemic, intervention delivery was online. African Americans between 18–65 years old with overweight/obesity, not currently following a plant-based diet or taking medications to control diabetes, and living in a southeastern city were recruited. Participants completed in-person weight assessments and online surveys at baseline and post-intervention. Linear mixed models analyzed changes in outcomes and differences in 3-month outcomes between groups. All models controlled for age and sex. Regarding Reach, 199 participants expressed interest, and 60 enrolled. Among the full sample, participants decreased body weight −2.6 ± 0.5 kg (p &lt; .0001) and increased self-efficacy 1.6 ± 0.7 points (p = .03). No differences in 3-month outcomes between groups were observed. This D&I feasibility study successfully recruited participants during the COVID-19 pandemic and produced significant results. The successful online intervention delivery compared to in-person suggests the potential for greater D&I in vegan soul food restaurants. As restrictions are loosened, future studies will test in-person delivery.
Predicting the severity of traffic accidents on mountain freeways with dynamic traffic and weather data
Authors: Li Juan , Guo Fengxiang , Zhou Yanning , Yang Wenchen , Ni Dingan 
Published: January 2023

Abstract
Traffic accident severity prediction is essential for dynamic traffic safety management. To explore the factors influencing the severity of traffic accidents on mountain freeways and to predict the severity of traffic accidents, four models based on machine learning algorithms are constructed using support vector machine (SVM), decision tree classifier (DTC), Ada_SVM and Ada_DTC. In addition, random forest (RF) is used to calculate the importance degree of variables and the accident severity influences with high importance levels form the RF dataset. The results show that rainfall intensity, collision type, number of vehicles involved in the accident and road section type are important variables influencing accident severity. The RF feature selection method improves the classification performance of four machine learning algorithms, resulting in a 9.3%, 5.5%, 7.2% and 3.6% improvement in prediction accuracy for SVM, DTC, Ada_SVM and Ada_DTC, respectively. The combination of the Ada_SVM integrated algorithm and RF feature selection method has the best prediction performance, and it achieves 78.9% and 88.4% prediction precision and accuracy, respectively.
Glycyrrhizic acid improves tacrolimus‐induced renal injury by regulating autophagy
Authors: Cao Rui , Li Yakun , Hu Xiaofan , Qiu Yang , Li Shanglin , Xie Yanan , Xu Cong , Lu Chenqi , Chen Gang , Yang Jun 
Published: January 2023

AbstractTacrolimus (TAC)‐induced renal injury is detrimental to long‐term kidney function, but a treatment medication is not available. Glycyrrhizic acid (GA) is an active ingredient in licorice widely used to treat kidney disease. Thus, this study explored the mechanisms of renoprotection by GA on TAC‐induced renal injury. C57BL/6 mice were subjected daily to TAC or a combination of TAC and GA for 4 weeks, and then renal function, histopathology, and autophagy were assessed to examine the effect of GA on a renal injury. Next, Human kidney proximal tubular epithelial (HK‐2) cells were pretreated with GA for 2 h and then treated with TAC for 24 h. The effect of GA on TAC‐induced HK‐2 cell injury was assessed by measuring cell viability, apoptosis, autophagy, and lysosomes. Mice exposed to TAC and treated with GA had significantly greater improvements in renal function and tubulointerstitial fibrosis in comparison to mice not treated with GA. In addition, fibrosis‐related protein expression, including α‐smooth muscle actin and fibronectin, decreased after GA treatment. GA treatment also relieved autophagic clearance in TAC‐induced renal injury. Several in vitro studies found that TAC inhibited cell viability, autophagy, lysosomal acidification, and promoted apoptosis. However, these results were less pronounced with GA pretreatment. In addition, bafilomycin A1 (which inhibits lysosomal function) reduced the protective effect of GA, indicating that lysosomal function plays an important role in this effect. Our data suggest that GA improves lysosomal function and regulates autophagy to protect against TAC‐induced renal injury.