bluuebunny/crossref_metadata_2025_split huggingface dataset:
LPAD: using network construction and label propagation to detect topologically associating domains from Hi-C data
Authors: Liu Jian , Li Pingjing , Sun Jialiang , Guo Jun 
Published: May 2023

Abstract
With the development of chromosome conformation capture technique, the study of spatial conformation of a genome based on Hi-C technique has made a quantum leap. Previous studies reveal that genomes are folded into hierarchy of three-dimensional (3D) structures associated with topologically associating domains (TADs), and detecting TAD boundaries is of great significance in the chromosome-level analysis of 3D genome architecture. In this paper, we propose a novel TAD identification method, LPAD, which first extracts node correlations from global interactions of chromosomes based on the random walk with restart and then builds an undirected graph from Hi-C contact matrix. Next, LPAD designs a label propagation-based approach to discover communities and generates TADs. Experimental results verify the effectiveness and quality of TAD detections compared with existing methods. Furthermore, experimental evaluation of chromatin immunoprecipitation sequencing data shows that LPAD performs high enrichment of histone modifications remarkably nearby the TAD boundaries, and these results demonstrate LPAD’s advantages on TAD identification accuracy.
SLHSD: hybrid scaffolding method based on short and long reads
Authors: Luo Junwei , Guan Ting , Chen Guolin , Yu Zhonghua , Zhai Haixia , Yan Chaokun , Luo Huimin 
Published: May 2023

Abstract
In genome assembly, scaffolding can obtain more complete and continuous scaffolds. Current scaffolding methods usually adopt one type of read to construct a scaffold graph and then orient and order contigs. However, scaffolding with the strengths of two or more types of reads seems to be a better solution to some tricky problems. Combining the advantages of different types of data is significant for scaffolding. Here, a hybrid scaffolding method (SLHSD) is present that simultaneously leverages the precision of short reads and the length advantage of long reads. Building an optimal scaffold graph is an important foundation for getting scaffolds. SLHSD uses a new algorithm that combines long and short read alignment information to determine whether to add an edge and how to calculate the edge weight in a scaffold graph. In addition, SLHSD develops a strategy to ensure that edges with high confidence can be added to the graph with priority. Then, a linear programming model is used to detect and remove remaining false edges in the graph. We compared SLHSD with other scaffolding methods on five datasets. Experimental results show that SLHSD outperforms other methods. The open-source code of SLHSD is available at https://github.com/luojunwei/SLHSD.
Impact of house dust mite in vitiligo skin: environmental contribution to increased cutaneous immunity and melanocyte detachment
Authors: Bzioueche Hanene , Boniface Katia , Drullion Claire , Marchetti Sandrine , Chignon-Sicard Bérengère , Sormani Laura , Rocchi Stéphane , Seneschal Julien , Passeron Thierry , Tulic Meri K 
Published: May 2023

Abstract

Background
Vitiligo is an autoimmune skin disorder characterized by loss of melanocytes. Protease-mediated disruption of junctions between keratinocytes and/or keratinocyte intrinsic dysfunction may directly contribute to melanocyte loss. House dust mite (HDM), an environmental allergen with potent protease activity, contributes to respiratory and gut disease but also to atopic dermatitis and rosacea.

Objectives
To verify if HDM can contribute to melanocyte detachment in vitiligo and if so, by which mechanism(s).

Methods
Using primary human keratinocytes, human skin biopsies from healthy donors and patients with vitiligo, and 3D reconstructed human epidermis, we studied the effect of HDM on cutaneous immunity, tight and adherent junction expression and melanocyte detachment.

Results
HDM increased keratinocyte production of vitiligo-associated cytokines and chemokines and increased expression of toll-like receptor (TLR)-4. This was associated with increased in situ matrix-metalloproteinase (MMP)-9 activity, reduced cutaneous expression of adherent protein E-cadherin, increased soluble E-cadherin in culture supernatant and significantly increased number of suprabasal melanocytes in the skin. This effect was dose-dependent and driven by cysteine protease Der p1 and MMP-9. Selective MMP-9 inhibitor, Ab142180, restored E-cadherin expression and inhibited HDM-induced melanocyte detachment. Keratinocytes from patients with vitiligo were more sensitive to HDM-induced changes than healthy keratinocytes. All results were confirmed in a 3D model of healthy skin and in human skin biopsies.

Conclusions
Our results highlight that environmental mite may act as an external source of pathogen-associated molecular pattern molecules in vitiligo and topical MMP-9 inhibitors may be useful therapeutic targets. Whether HDM contributes to the onset of flares in vitiligo remains to be tested in carefully controlled trials.
Destined for the intestine: thymic selection of TCRαβ CD8αα intestinal intraepithelial lymphocytes
Authors: Joannou Kevin , Baldwin Troy A 
Published: May 2023

Summary
The immune system is composed of a variety of different T-cell lineages distributed through both secondary lymphoid tissue and non-lymphoid tissue. The intestinal epithelium is a critical barrier surface that contains numerous intraepithelial lymphocytes that aid in maintaining homeostasis at that barrier. This review focuses on T-cell receptor αβ (TCRαβ) CD8αα intraepithelial lymphocytes, and how recent advances in the field clarify how this unique T-cell subset is selected, matures, and functions in the intestines. We consider how the available evidence reveals a story of ontogeny starting from agonist selection of T cells in the thymus and finishing through the specific signaling environment of the intestinal epithelium. We conclude with how this story raises further key questions about the development of different ontogenic waves of TCRαβ CD8αα IEL and their importance for intestinal epithelial homeostasis.
Interactive effects of temperature and bisphenol A on phytoplankton growth and community structure
Authors: Theus Meredith E , Michaels Julia , Fey Samuel B 
Published: May 2023

Abstract
Environmental contamination of bisphenol A (BPA) is a widespread and multifaceted issue with vast ecological, social and economic consequences. Thus, understanding how local environmental conditions, such as temperature, interact with BPA to affect populations and community dynamics remain important areas of research. Here, we conduct laboratory experiments aimed at understanding how environmental gradients of both temperature and BPA concentration influence freshwater phytoplankton population growth and community structure. We exposed phytoplankton assemblages comprised of three common species of green algae (Chlorella vulgaris, Ankistrodesmus braunii and Scenedesmus quadricauda) as well as isolates of each individual species to three BPA concentrations (0, 2, 13 mg/L BPA) and three temperatures (18, 23, 27°C) monitoring population growth and community structure (via biovolume). We observed antagonistic interactions between BPA and warmer temperatures, such that when warmer temperatures decreased growth (observed with A. braunii), high concentrations of BPA elevated growth at these warm temperatures; however, when warmer temperatures increased growth (C. vulgaris, S. quadricauda), high BPA concentrations diminished these gains. Although BPA exposure inhibited the growth of most C. vulgaris populations, growth was not reduced in A. braunii or S. quadricauda populations exposed to 2 mg/L BPA. Phytoplankton assemblage evenness (Pielou evenness index) decreased as BPA concentration increased and was consistently lowest under 27°C. Community composition was similar in assemblages cultured under 0 and 2 mg/L BPA under 18 and 23°C but was most similar between assemblages cultured under 2 and 13 mg/L BPA under 27°C. These results indicate that local environmental temperatures can mediate the consequences of BPA for freshwater phytoplankton growth rates and community structure and that BPA can diminish potential gains of increased growth rate for warm-adapted phytoplankton species at high environmental temperatures.
Friend or foe? Using eye-tracking technology to investigate the visual discrimination ability of giant pandas
Authors: Huang Xinrui , Li Guo , Zhang Guiquan , Li Zixiang , Zhao Lin , Zhu Mengdie , Xiang Qinghua , Liu Xuefeng , Tian Mei , Zhang Hemin , Buesching Christina D , Liu Dingzhen 
Published: May 2023

Abstract
The role that visual discriminative ability plays among giant pandas in social communication and individual discrimination has received less attention than olfactory and auditory modalities. Here, we used an eye-tracker technology to investigate pupil fixation patterns for 8 captive male giant pandas Ailuropoda melanoleuca. We paired images (N = 26) of conspecifics against: 1) sympatric predators (gray wolves and tigers), and non-threatening sympatric species (golden pheasant, golden snub-nosed monkey, takin, and red panda), 2) conspecifics with atypical fur coloration (albino and brown), and 3) zookeepers/non-zookeepers wearing either work uniform or plain clothing. For each session, we tracked the panda’s pupil movements and measured pupil first fixation point (FFP), fixation latency, total fixation count (TFC), and duration (TFD) of attention to each image. Overall, pandas exhibited similar attention (FFPs and TFCs) to images of predators and non-threatening sympatric species. Images of golden pheasant, snub-nosed monkey, and tiger received less attention (TFD) than images of conspecifics, whereas images of takin and red panda received more attention, suggesting a greater alertness to habitat or food competitors than to potential predators. Pandas’ TFCs were greater for images of black-white conspecifics than for albino or brown phenotypes, implying that familiar color elicited more interest. Pandas reacted differently to images of men versus women. For images of women only, pandas gave more attention (TFC) to familiar combinations (uniformed zookeepers and plain-clothed non-zookeepers), consistent with the familiarity hypothesis. That pandas can use visual perception to discriminate intra-specifically and inter-specifically, including details of human appearance, has applications for panda conservation and captive husbandry.
CineECG analysis provides new insights into Familial ST-segment Depression Syndrome
Authors: Frosted Rasmus , Paludan-Müller Christian , Vad Oliver Bundgaard , Olesen Morten Salling , Bundgaard Henning , van Dam Peter , Christensen Alex Hørby 
Published: May 2023

Abstract

Aims
Familial ST-segment Depression Syndrome (Fam-STD) is a novel inherited cardiac disease associated with arrhythmias and sudden cardiac death. This study aimed at investigating the cardiac activation pathway in patients with Fam-STD, modelling the electrocardiogram (ECG) phenotype, and performing in-depth ST-segment analyses.

Methods and results
CineECG analysis of patients with Fam-STD and age- and sex-matched controls. The groups were compared using the CineECG software which included the trans-cardiac ratio and the electrical activation pathway. We simulated the Fam-STD ECG phenotype by adjusting action potential duration (APD) and action potential amplitude (APA) in specific cardiac regions. High-resolution ST-segment analyses were performed per lead by dividing the ST-segment into nine 10 ms subintervals. Twenty-seven Fam-STD patients (74% females, mean age 51.6 ± 6.2 years) and 83 matched controls were included. Among Fam-STD patients, electrical activation pathway analysis in the anterior-basal orientation showed significantly abnormal direction toward the basal areas of the heart starting from QRS 60–89 ms until Tpeak-Tend (all P &lt; 0.001). Simulations with shortened APD and reduced APA in the left ventricle basal regions recapitulated the Fam-STD ECG phenotype. Detailed ST-segment analyses showed significant differences in all nine 10 ms subintervals (all P &lt; 0.01), with the most prominent findings during the 70–79/80–89 ms intervals.

Conclusion
CineECG analyses indicated abnormal repolarization with basal directions, and the Fam-STD ECG phenotype was simulated by reducing APD and APA in the left ventricle basal regions. Detailed ST-analysis showed amplitudes consistent with the proposed diagnostic criteria for Fam-STD patients. Our findings provide new insight into the electrophysiological abnormalities of Fam-STD.
Coverage by examinations associated with early detection of colorectal neoplasia in the Czech Republic
Authors: Ngo Ondřej , Hejcmanová Kateřina , Suchánek Štěpán , Pehalová Lucie , Dušek Ladislav , Zavoral Miroslav , Bureš Jan , Seifert Bohumil , Hejduk Karel , Král Norbert , Májek Ondřej 
Published: May 2023

Abstract

Background
Coverage by examinations is a crucial indicator of the future impact on the burden of colorectal cancer (CRC). The study aimed to evaluate coverage by examinations associated with CRC screening and early cancer detection of CRC in the Czech Republic. The burden of CRC was also assessed.

Methods
The novel nationwide administrative registry with individual data (period 2010–19) was used to evaluate coverage by examinations for screening faecal occult blood test and colonoscopy. In the second step, additional examinations for early CRC detection were included in the coverage calculation (complete coverage). Age-specific trends in CRC incidence (period 1977–2018) were investigated using Joinpoint regression.

Results
Coverage by screening examinations within recommended interval was around 30%. Complete coverage reached &gt;37% and &gt;50% at the 3-year interval. The coverage by examinations for the non-screening population aged 40–49 years was almost 4% and 5% (most of them were colonoscopies) at the 3-year interval. In age groups aged ≥50 years, we observed a significant annual decline, especially in the 50–69 age group, with recent annual decreases reaching up to 5–7%. The change in trend and the recent decline were also observed in the age group 40–49.

Conclusions
More than half of the target screening population was covered by examinations potentially associated with early detection and subsequent treatment of colorectal neoplasms. The substantial coverage by potentially prophylactic examinations might be an explanation for the considerable decrease in CRC incidence.
“Participation Is Fun and Empowering”: A Participatory Approach to Co-Design a Cultural Art Program for Older Chinese at Risk of Depression in Hong Kong
Authors: Liu Tianyin , Chan Rachel , Yeung Crystal , Lee Ling Cheun Bianca , Chan Tristan Nga Chee , Welton Keturah , Lum Terry Yat-Sang , Wong Gloria Hoi Yan 
Published: May 2023

Abstract

Background and Objectives
Internalized ageism and stigma of mental illness may disempower older people and impede help-seeking among those at risk of depression. Arts are deemed enjoyable, stigma-free, and conducive to mental health, and a participatory approach can engage and empower potential service users. This study aimed to co-design a cultural art program and test its feasibility in empowering older Chinese people in Hong Kong and preventing depression.

Research Design and Methods
Adopting a participatory approach and guided by the Knowledge-to-Action framework, we co-designed a 9-session group art program using Chinese calligraphy as the channel for gaining emotional awareness and facilitating expression. The iterative participatory co-design process engaged 10 older people, 3 researchers, 3 art therapists, and 2 social workers through multiple workshops and interviews. We tested the program’s acceptability and feasibility in 15 community-dwelling older people at risk of depression (mean age = 71.6). Mixed methods were used, including pre- and postintervention questionnaires, observation, and focus groups.

Results
Qualitative findings suggest the feasibility of the program, and quantitative findings indicated its effects in increasing empowerment (t(14) = 2.82, p &lt; .05), but not in other mental health-related measurements. Participants reflected that active participation and learning new art skills were fun and empowering, arts enabled them to gain insight into and express deeper feelings, and groups with peers made them feel relatable and accepted.

Discussion and Implications
Culturally appropriate participatory arts groups can effectively promote empowerment in older people, and future research should balance eliciting meaningful personal experiences and measurable changes.
Posting and Transfer: the experiences of public sector doctors in two Indian states
Authors: Purohit Bhaskar , Hill Peter S 
Published: May 2023

Abstract
Posting and Transfer (PT) refers to deployment of the health workforce in ways that ensure appropriate numbers and distribution. Although PT is a crucial aspect of health workforce governance, it remains under-researched from the viewpoint of implementation, health workforce and governance. The aim of this paper is to examine public sector doctors’ experience of their initial postings, in the context of local policy from two Indian states. We carried out a review search for policy documentation. A total 61 in-depth interviews were conducted in both states with 33 doctors, as subjects of the study. There were 28 key informant (KI) interviews of health administrators and other policy actors to understand their perspectives of PT policies and implementation. Thematic analysis was used to analyse data. Job histories were constructed from the doctors’ interviews to track their experience with the PT system, and analysed using location, duration and postings. Despite search for state policy for PT, we were unable to identify any policy documentation. However, participants referred to PT practices that suggested expectations of what the poliy meant to them. These expectations were corroborated by KI, and the job histories and interview data enabled the authors to construct a series of norms, interpreted as evidence of implied policy. The main norms identified relate to service need, native place, request, gender and posting duration. The norm related to state need had strong face validity, while other norms based on request, gender and duration were less consistent in application. In the absence of documented policies, the construction of norms from the qualitative data proved useful to examine the dynamics of health workers’ interactions with the initial PT systems This construction of norms provides a methodological innovation allowing health policy and systems researchers to compensate for the absence of documented policy in exploring PT functions.
Sustaining youth physical activity in times of challenge and change: lessons from COVID-19
Authors: Trask Suzanne , Lockyer Peg , Hildreth Jillian , D’Souza Erica , Buklijas Tatjana , Menzies Rochelle , Vickers Mark , Bay Jacquie L 
Published: May 2023

Abstract
Physical activity (PA) is recognized as essential for positive physical and mental well-being in young people. However, participation in PA is known to decline as adolescents emerge into adulthood under the influence of complex social and structural factors. Globally, COVID-19 restrictions resulted in changes to PA and PA participation levels in youth populations, providing a unique opportunity for gaining insight into PA barriers and enablers in circumstances of challenge, limitation and change. This article details young people’s self-reported PA behaviours during the 4-week 2020 COVID-19 lockdown in New Zealand. Taking a strengths-based view and drawing on the COM-B (capabilities, opportunity and motivation behaviour) model for behaviour change, the study explores factors enabling young people to sustain or increase PA during lockdown. Findings are drawn from qualitative-dominant mixed-methods analyses of responses to an online questionnaire: New Zealand Youth Voices Matter (16–24 years; N = 2014). Key insights included the importance of habit and routine, time and flexibility, social connections, incidental exercise and awareness of links between PA and well-being. Of note were the positive attitudes, creativity and resiliency demonstrated as young people substituted or invented alternatives to their usual PA. PA needs to change to adapt to new circumstances over the life course, and youth understanding and knowledge of modifiable factors may provide support for this. Thus these findings have implications for sustaining PA during late adolescence and emerging adulthood, a life phase that can be associated with significant challenge and change.
Intercostal artery’s access for type II endoleak embolization
Authors: Lorenz Veronica , Muzzi Luigi , Candeloro Laura , Ricci Carmelo , Cini Marco , Alba Giuseppe , Tucci Enrico , Neri Eugenio 
Published: May 2023

Abstract
Endoleaks represent a main issue of endovascular approach of thoracic aorta diseases and their treatment continue to be challenging. According to some authors, type II endoleaks sustained by intercostal arteries should not be treated because of the technical difficulties. However, the persistence of a pressurized aneurysmal may confer an ongoing risk of enlargement and/or aortic rupture. We describe the successful treatment of type II endoleak in 2 patients with an intercostal artery’s access. In both cases, the endoleak was discovered during follow-up and was treated with its direct coil embolization under local anaesthesia.
Emergence of tet(X2) in Acinetobacter pittii confers clinical resistance to tigecycline
Authors: Qian Changrui , Ma Zhexiao , Feng Luozhu , Guo Wenhui , Han Yijia , Zhang Yi , Xu Chunquan , Cao Jianming , Zhou Tieli 
Published: May 2023

Abstract

Objectives
To characterize a novel transposon Tn7533 carrying the tet(X2) gene in a tigecycline-resistant Acinetobacter pittii BM4623 of clinical origin.

Methods
Gene knockout and in vitro cloning were used to verify the function of tet(X2). WGS and comparative genomic analysis were used to explore the genetic characteristics and molecular evolution of tet(X2). Inverse PCR and electroporation experiments were used to evaluate the excision and integration capabilities of Tn7533.

Results
A. pittii BM4623 belonged to a novel ST, ST2232 (Pasteur scheme). Knockout of tet(X2) in BM4623 restored its susceptibility to tigecycline. Cloning of the tet(X2) gene into Escherichia coli DH5α and Acinetobacter baumannii ATCC 17978 resulted in 16-fold or more increases in MICs of tigecycline. Sequence analysis showed that the region upstream of tet(X2) exhibited a high degree of diversity, while there was a 145 bp conserved region downstream of tet(X2). tet(X2) in BM4623 was located on a novel composite transposon Tn7533, which also contains multiple resistance genes including blaOXA-58. Tn7533 could be excised from the chromosome to form a circular intermediate and transferred into A. baumannii ATCC 17978 by electroporation.

Conclusions
Our study demonstrates that tet(X2) is a determinant conferring clinical resistance to tigecycline in Acinetobacter species. The emergence of Tn7533 may lead to the potential dissemination of tigecycline and carbapenem resistance in Acinetobacter, which requires continuous monitoring.
194 Leveraging Animal Nutrition to Enhance Sustainability of Food Production Systems
Authors: White Robin R 
Published: May 2023

Abstract
Dr. White’s research focuses on the animal/environment interface with the broad goal of leveraging animal nutrition to enhance sustainability of food production systems. This work focuses at three levels: 1) basic research evaluating factors regulating rumen fermentation; 2) applied research testing strategies to enhance feed efficiency; and 3) systems-level research evaluating the wider socioeconomic impacts of livestock production and management.