bluuebunny/crossref_metadata_2025_split huggingface dataset:
The impact of psoriasis on wellbeing and clinical outcomes in juvenile psoriatic arthritis
Authors: Low Jie Man , Hyrich Kimme L , Ciurtin Coziana , McErlane Flora , Wedderburn Lucy R , Geifman Nophar , Shoop-Worrall Stephanie J W ,   CAPS Principal Investigators, Cleary G , Baildam E , Wedderburn L , Davidson J , Chieng A , McErlane F , Foster H , Ciurtin C , Ioannou Y , Thomson W , Hyrich K 
Published: July 2023

Abstract

Objectives
Juvenile PsA (JPsA) has varied clinical features that are distinctive from other JIA categories. This study investigates whether such features impact patient-reported and clinical outcomes.

Methods
Children and young people (CYP) were selected if recruited to the Childhood Arthritis Prospective Study, a UK multicentre JIA inception cohort, between January 2001 and March 2018. At diagnosis, patient/parent-reported outcomes (as age-appropriate) included the parental global assessment (10 cm visual analogue scale), functional ability (Childhood Health Assessment Questionnaire (CHAQ)), pain (10 cm visual analogue scale), health-related quality of life (Child Health Questionnaire PF50 psychosocial score), mood/depressive symptoms (Moods and Feelings Questionnaire) and parent psychosocial health (General Health Questionnaire 30). Three-year outcome trajectories have previously been defined using active joint counts, physician and parent global assessments (PGA and PaGA, respectively). Patient-reported outcomes and outcome trajectories were compared in (i) CYP with JPsA vs other JIA categories and (ii) CYP within JPsA, with and without psoriasis via multivariable linear regression.

Results
There were no significant differences in patient-reported outcomes at diagnosis between CYP with JPsA and non-JPsA. Within JPsA, those with psoriasis had more depressive symptoms (coefficient = 9.8; 95% CI: 0.5, 19.0) than those without psoriasis at diagnosis. CYP with JPsA had 2.3 times the odds of persistent high PaGA than other ILAR categories, despite improving joint counts and PGA (95% CI: 1.2, 4.6).

Conclusion
CYP with psoriasis at JPsA diagnosis report worse mood, supporting a greater disease impact in those with both skin and joint involvement. Multidisciplinary care with added focus to support wellbeing in children with JPsA plus psoriasis may help improve these outcomes.
Virulence of NovelRalstonia pseudosolanacearum(Phylotype I) Strains from Rose, Blueberry, and Mandevilla on Seed Potato
Authors: Overeem Remco , Pel Chiel , Tjou-Tam-Sin Napoleon , van de Bilt Jeroen , Gorkink-Smits Peggy , Landman Marco , Bocsanczy Ana Maria B. , Norman David , Bergsma-Vlami Maria 
Published: July 2023

Potato (Solanum tuberosum L.) ranks fourth among the most important staple food in the world. Ralstonia solanacearum (phylotype [phy] IIB, sequevar [seq] 1 and 2), also known as R3B2, the causal agent of brown rot disease on potato, is extremely damaging, causing great economical losses to potato in temperate regions. It is thought that members of Ralstonia pseudosolanacearum (phy I) are not pathogenic at low temperatures and are usually found in warmer climates. R. pseudosolanacearum strain PD 7123 (seq 33) isolated from roses in the Netherlands, strain P824 (seq 13) isolated from blueberry, and strain P781 (seq 14) from mandevilla in Florida are phylogenetically closely related and could share the same host. The virulence and ability of these novel strains to multiply latently in potato in temperate regions is unknown. The objective of this work was to assess the virulence and presence of latent infections of the mentioned R. pseudosolanacearum strains on three commercial seed potato cultivars under warmer (28°C) and temperate (20°C) temperatures. At 28°C, all three R. pseudosolanacearum strains caused severe symptoms on all potato cultivars. Overall disease severity on potato was lower at 20°C than 28°C, but major differences in virulence of the three strains were observed at 42 days postinoculation (dpi) among potato cultivars. All asymptomatic potato plants and most of their daughter tubers had latent infections at 20°C. Altogether, these results show that the phy I strains from rose, blueberry, and mandevilla may pose a threat to potato production in temperate climates and the worldwide movement of seed potatoes.[Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .
A Cross-Sectional Evaluation of Publication Bias in the Plastic Surgery Literature
Authors: Wu Shannon S. , Katabi Leila , Desimone Robert , Borsting Emily , Ascha Mona 
Published: July 2023

Background:
Publication bias (PB) is the preferential publishing of studies with statistically significant results. PB can skew findings of systematic reviews (SR) and meta-analyses (MA), with potential consequences for patient care and health policy. This study aims to determine the extent by which SRs and MAs in the plastic surgery literature evaluate and report PB.

Methods:
This cross-sectional study assessed PB reporting and analysis from plastic surgery studies published between January 1, 2015 and June 19, 2020. Full-texts of SRs and MAs were assessed by two reviewers for PB assessment methodology and analysis. Post-hoc assessment of studies that did not originally analyze PB was performed using Egger’s regression, Duval and Tweedie’s trim-and-fill, and Copas selection models.

Results:
There were 549 studies evaluated, of which 531 full-texts were included. PB was discussed by 183 (34.5%) studies, and formally assessed by 97 (18.3%) studies. Among SR and MAs that formally assessed PB, PB was present in 24 (10.7%), not present in 52 (23.1%), and inconclusive in 8 (3.6%) studies; 141 (62.7%) studies did not report the results of their PB assessment. Funnel plots were the most common assessment method (n=88, 39.1%), and 60 (68.2%) studies published funnel plots. The post-hoc assessment revealed PB in 17/20 (85.0%) studies.

Conclusion:
PB is inadequately reported and analyzed amongst studies in the plastic surgery literature. Most studies that assessed PB found PB, as did post-hoc analysis of non-reporting studies. Increased assessment and reporting of PB amongst SRs and MAs would improve quality of evidence in plastic surgery.
Impact of health disparity on pediatric infections
Authors: Rogo Tanya , Holland Sabina 
Published: July 2023

Purpose of review
The COVID-19 pandemic highlighted the health disparities among minoritized children due to structural racism and socioeconomic inequalities. This review discusses how health disparities affect pediatric infections and how they can be addressed.

Recent findings
In addition to disparities in healthcare access due to poverty, geography, and English-language proficiency, implicit and explicit bias affects the healthcare quality and subsequent outcomes in children and adolescents with infections. Disparities in clinical trial enrollment affect the generalizability of research findings. Physicians who understand their patients’ languages and the contexts of culture and socioeconomic conditions are better equipped to address the needs of specific populations and the health disparities among them.

Summary
Addressing disparities in pediatric infections requires prioritization of efforts to increase physician workforce diversity in Pediatric Infectious Diseases, as well as education in bias reduction and culturally sensitive clinical practice, in addition to socioeconomic interventions that improve healthcare access, delivery, and outcomes.
Validation of the PROMIS-29 Questionnaire as a Measure of Recovery after Pancreatic Surgery
Authors: Pecorelli Nicolò , Guarneri Giovanni , Vallorani Alessia , Limongi Chiara , Licinio Alice W. , Di Salvo Francesca , Tamburrino Domenico , Partelli Stefano , Crippa Stefano , Falconi Massimo 
Published: July 2023

Objective:
To contribute evidence for the reliability, construct validity and responsiveness of the PROMIS-29 profile questionnaire as a measure of recovery after pancreatic surgery.

Summary Background Data:
PROMIS questionnaires have been recommended to evaluate post-discharge recovery after surgery. Evidence supporting their measurement properties in pancreatic surgery is missing.

Methods:
An observational validation study designed according to the COSMIN checklist was conducted including data from a prospective clinical trial. Patients undergoing pancreatectomy completed PROMIS-29 preoperatively and on postoperative days (PODs) 15, 30, 90, 180. Reliability was assessed by internal consistency using Cronbach’s alpha. Construct validity was assessed by known-groups comparison. Responsiveness was evaluated hypothesizing that scores would be higher (1) preoperatively versus POD15, (2) on POD30 versus POD15, (3) on POD90 versus POD30, and (4) on POD180 versus POD90.

Results:
Overall, 510 patients were included in the study. Reliability was good to excellent (alpha values ranged from 0.82 to 0.97). Data supported 4 of 5 hypotheses tested for construct validity for five domains (physical function, anxiety, depression, fatigue and ability to participate in social roles) at most time points. Responsiveness hypotheses 1, 2, 3 were supported by the data for physical function, fatigue, sleep disturbance, pain interference and ability to participate in social roles domains.

Conclusion:
PROMIS had excellent reliability, discriminated between most groups expected to have different recovery trajectories and was responsive to the expected trajectory of recovery up to 90 days after surgery. Our findings support the use of PROMIS-29 profile as a patient reported outcome measure of post-discharge recovery after pancreatectomy.
IL-35 Stabilizes Treg Phenotype to Protect Cardiac Allografts in Mice
Authors: Huang Ai , Liu Kewei , Yin Ziyi , Liu Jie , Wei Hongyan , Xing Shijie , Qu Yue , Huang Lei , Li Liancheng , Li Chang , Zhang Lei , Li Xiaoshi , Zheng Cunni , Liu Quan , Jiang Ke 
Published: July 2023

Background.
Interleukin-35 (IL-35), secreted by regulatory T cells (Treg) and B cells, is immunosuppressive under both physiological and pathological conditions. However, the role of IL-35 in all responses has yet to be investigated. Here, we demonstrate that IL-35 protects allografts by stabilizing the Treg phenotype and suppressing CD8+ T-cell activation in a mouse heart transplantation model.

Methods.
The effect of IL-35 on immune cell infiltration in grafts and secondary lymphoid organs was examined using mass cytometry, flow cytometry, and immunofluorescence. Moreover, using quantitative real-time polymerase chain reaction, flow cytometry, and phospho-flow assays, we demonstrated that IL-35 maintains Treg phenotypes to restrain CD8+ T cells via the gp130/signal transducer and activator of transcription 1 pathway.

Results.
Mass cytometry analysis of intragraft immune cells showed that IL-35 decreased CD8+ T-cell infiltration and increased Foxp3 and IL-35 expressions in Treg. In vitro, we demonstrated that IL-35 directly promoted Treg phenotypic and functional stability and its IL-35 secretion, generating a positive feedback loop. However, Treg are required for IL-35 to exert its suppressive effect on CD8+ T cells in vitro. After depleting Treg in the recipient, IL-35 did not prolong graft survival or decrease CD8+ T-cell infiltration. Mechanistically, we found that IL-35 sustained Treg stability via the gp130/signal transducer and activator of transcription 1 signaling pathway.

Conclusions.
Our findings highlight that IL-35 stabilizes the Treg phenotype to ameliorate CD8+ T-cell infiltration in the allograft, which has never been described in the transplanted immunological milieu.
Development of a mobile, high-throughput, and low-cost image-based plant growth phenotyping system
Authors: Yu Li’ang , Sussman Hayley , Khmelnitsky Olga , Ishka Maryam Rahmati , Srinivasan Aparna , Nelson Andrew D.L. , Julkowska Magdalena M. 
Published: July 2023

AbstractNondestructive plant phenotyping is fundamental for unraveling molecular processes underlying plant development and response to the environment. While the emergence of high-through phenotyping facilities can further our understanding of plant development and stress responses, their high costs significantly hinder scientific progress. To democratize high-throughput plant phenotyping, we developed sets of low-cost image- and weight-based devices to monitor plant growth and evapotranspiration. We paired these devices with a suite of computational pipelines for integrated and straightforward data analysis. We validated the suitability of our system for large screens by evaluating a cowpea diversity panel for responses to drought stress. The observed natural variation was subsequently used for Genome-Wide Association Study, where we identified nine genetic loci that putatively contribute to cowpea drought resilience during early vegetative development. We validated the homologs of the identified candidate genes in Arabidopsis using available mutant lines. These results demonstrate the varied applicability of this low-cost phenotyping system. In the future, we foresee these setups facilitating identification of genetic components of growth, plant architecture, and stress tolerance across a wide variety of species.
DNA satellite and chromatin organization at house mouse centromeres and pericentromeres
Authors: Packiaraj Jenika , Thakur Jitendra 
Published: July 2023

ABSTRACTCentromeres are essential for faithful chromosome segregation during mitosis and meiosis. However, the organization of satellite DNA and chromatin at mouse centromeres and pericentromeres is poorly understood due to the challenges of sequencing and assembling repetitive genomic regions. Using recently available PacBio long-read sequencing data from the C57BL/6 strain and chromatin profiling, we found that contrary to the previous reports of their highly homogeneous nature, centromeric and pericentromeric satellites display varied sequences and organization. We find that both centromeric minor satellites and pericentromeric major satellites exhibited sequence variations within and between arrays. While most arrays are continuous, a significant fraction is interspersed with non-satellite sequences, including transposable elements. Additionally, we investigated CENP-A and H3K9me3 chromatin organization at centromeres and pericentromeres using Chromatin immunoprecipitation sequencing (ChIP-seq). We found that the occupancy of CENP-A and H3K9me3 chromatin at centromeric and pericentric regions, respectively, is associated with increased sequence abundance and homogeneity at these regions. Furthermore, the transposable elements at centromeric regions are not part of functional centromeres as they lack CENP-A enrichment. Finally, we found that while H3K9me3 nucleosomes display a well-phased organization on major satellite arrays, CENP-A nucleosomes on minor satellite arrays lack phased organization. Interestingly, the homogeneous class of major satellites phase CENP-A and H3K27me3 nucleosomes as well, indicating that the nucleosome phasing is an inherent property of homogeneous major satellites. Overall, our findings reveal that house mouse centromeres and pericentromeres, which were previously thought to be highly homogenous, display significant diversity in satellite sequence, organization, and chromatin structure.
Response Surface Methodology-Based High-Throughput BioLector Fermentation Screening of Rosetta™-2 for Enhanced Production of Insulin Variant: Towards Improved Production Efficiency
Authors: Ayan Esra , Aytekin Ali Özhan , Kati Ahmet , DeMirci Hasan 
Published: July 2023

AbstractBackgroundIn order to obtain high yields of recombinant insulin and advancing therapeutic avenues for diabetes patients, the development of innovative designer insulin analogs have critical importance. The modified insulin analog presents a cost-effective remedy by being produced as inclusion bodies (IBs) withinEscherichia coliBL21 (DE3) Rosetta-2 strain. This approach to production not only offers reduced production time but also yields high recovery rates. The prime aim of this investigation was to optimize the composition of the cultivation media, thereby accomplishing higher cell density fermentation of the proinsulin, that is fused with a cleavable hexa histidine purification tag.ResultVarious factors, including carbon and nitrogen sources, salts, metal ions, and pH, were systematically investigated through experimental screening using the BioLector multiwell bright plate. Additionally, computational analysis employing thePlackett-Burman Designwithin theDesign Expertsoftware was utilized to assess their effectiveness in terms of insulin concentration as a surrogate measure of insulin yield. Among the tested variables, glucose, glycerol, MgSO4, and lower Luria-Bertani mix concentration have a significant influence on insulin production, as determined by the screening experiment. Subsequently, theCentral Composite Designapproach was operated to further evaluate and optimize the precise levels of these influential variables. This systematic methodology achieved an optimized cultivation media formulation, resulting in a remarkable enhancement of insulin production, with levels reaching up to 13 mg/ml when applied in BioLector fermentation.ConclusionThe formulated cultivation media exhibited suitability for promoting high cell density fermentation of the modified insulin, thereby facilitating the attainment of optimal yields for the proinsulin expression.
afila, the origin and nature of a major innovation in the history of pea breeding
Authors: Tayeh Nadim , Hofer Julie , Aubert Grégoire , Jacquin Françoise , Turner Lynda , Kreplak Jonathan , Paajanen Pirita , Le Signor Christine , Dalmais Marion , Pflieger Stéphanie , Geffroy Valérie , Ellis Noel , Burstin Judith 
Published: July 2023

AbstractTheafila(af) mutation ofPisum sativumL. (pea) is characterised by leaves that are composed of a basal pair of stipules, a petiole and a branched mass of tendrils. These are bipinnate leaves in which the leaflet primordia are replaced by midrib-like, or terminal tendril, primordia. The phenotype was first reported as a spontaneous mutation in 1953, and several reports of spontaneously occurringafmutants and induced mutations have been published since then. Despite its wide-scale introgression to improve standing ability in combine-harvested dry pea crops, the molecular basis ofafhas remained unknown. Here, we show that the deletion of two tandemly-arrayed Q-type Cys(2)His(2)-zinc finger transcription factors, viz.PsPALM1aandPsPALM1b, is responsible for the af phenotype. Based on molecular evidence for the presence/absence of seven consecutive pea genes, we identified eight haplotypes in the genomic region of chromosome 2 that harboursaf. These haplotypes differ in the presence or absence ofPsPALM1a-band close genes and in the size of the deletion. Representative cultivars and spontaneous or induced mutants were assigned to the different haplotypes. The hitherto unrecognised diversity at theaflocus reveals highly rich, unexplored, potential for pea improvement and sheds light on the breeding history of pea. This knowledge can also be used to breed innovative cultivars in related crops.
The human genome’s vocabulary as proposed by the DNA language model GROVER
Authors: Sanabria Melissa , Hirsch Jonas , Poetsch Anna R. 
Published: July 2023

AbstractLarge Language Models (LLMs) on natural language have achieved a level of performance that allows the generation of coherent and syntactically correct text. DNA sequence of genomes follows rules similar to natural language, but a distinguishing factor is the absence of a concept analogous to words. We established byte-pair tokenization on the human genome and trained a foundation language model called GROVER (“GenomeRulesObtainedViaExtractedRepresentations”) to select the optimal vocabulary with a custom fine-tuning task of next-k-mer prediction. We thus defined a dictionary of words/tokens in the human genome that best carries the information content for DNA language models. Analyzing GROVER’s learned representations, we observed that token embeddings primarily encode information related to their frequency, sequence content, and length. Some tokens are almost exclusively localized in repeats, while the vast majority widely distributes over the genome. The model also learns context and lexical ambiguity. Average embeddings of genomic regions relate to functional genomics annotation and thus indicate that GROVER has learned these structures purely from the contextual relationships of tokens. That we can extract functional annotations from the genome, purely based on sequence representation to the trained model, highlights the extent of information content encoded by the sequence. This is supported by fine-tuning tasks on genome biology with questions of promoter identity and protein-DNA binding. GROVER learns sequence context, a sense for grammatical structures and language rules in the genome. This knowledge can be extracted and used to compose a grammar book for the code of life.
Does disaster contribute to armed conflict? A quantitative analysis of disaster–conflict co-occurrence between 1990 and 2017
Authors: Caso Nicolás , Hilhorst Dorothea , Mena Rodrigo , Papyrakis Elissaios 
Published: July 2023

Purpose
Disasters and armed conflict often co-occur, but does that imply that disasters trigger or fuel conflict? In the small but growing body of literature attempting to answer this question, divergent findings indicate the complex and contextual nature of a potential answer to this question. The purpose of this study is to contribute a robust cross-country analysis of the co-occurrence of disaster and conflict, with a particular focus on the potential role played by disaster.

Design/methodology/approach
Grounded in a theoretical model of disaster–conflict co-occurrence, this study merges data from 163 countries between 1990 and 2017 on armed conflict, disasters and relevant control variables (low human development, weak democratic institutions, natural resource dependence and large population size/density).

Findings
The main results of this study show that, despite a sharp increase in the co-occurrence of disasters and armed conflict over time, disasters do not appear to have a direct statistically significant relation with the occurrence of armed conflict. This result contributes to the understanding of disasters and conflicts as indirectly related via co-creation mechanisms and other factors.

Originality/value
This study is a novel contribution, as it provides a fresh analysis with updated data and includes different control variables that allow for a significant contribution to the field.