bluuebunny/crossref_metadata_2025_split huggingface dataset:
Processing genome-wide association studies within a repository of heterogeneous genomic datasets
Authors: Bernasconi Anna , Canakoglu Arif , Comolli Federico 
Published: March 2023

Abstract
Background
Genome Wide Association Studies (GWAS) are based on the observation of genome-wide sets of genetic variants – typically single-nucleotide polymorphisms (SNPs) – in different individuals that are associated with phenotypic traits. Research efforts have so far been directed to improving GWAS techniques rather than on making the results of GWAS interoperable with other genomic signals; this is currently hindered by the use of heterogeneous formats and uncoordinated experiment descriptions.

Results
To practically facilitate integrative use, we propose to include GWAS datasets within the META-BASE repository, exploiting an integration pipeline previously studied for other genomic datasets that includes several heterogeneous data types in the same format, queryable from the same systems. We represent GWAS SNPs and metadata by means of the Genomic Data Model and include metadata within a relational representation by extending the Genomic Conceptual Model with a dedicated view. To further reduce the gap with the descriptions of other signals in the repository of genomic datasets, we perform a semantic annotation of phenotypic traits. Our pipeline is demonstrated using two important data sources, initially organized according to different data models: the NHGRI-EBI GWAS Catalog and FinnGen (University of Helsinki). The integration effort finally allows us to use these datasets within multi-sample processing queries that respond to important biological questions. These are then made usable for multi-omic studies together with, e.g., somatic and reference mutation data, genomic annotations, epigenetic signals.

Conclusions
As a result of the our work on GWAS datasets, we enable 1) their interoperable use with several other homogenized and processed genomic datasets in the context of the META-BASE repository; 2) their big data processing by means of the GenoMetric Query Language and associated system. Future large-scale tertiary data analysis may extensively benefit from the addition of GWAS results to inform several different downstream analysis workflows.
KDM4A, involved in the inflammatory and oxidative stress caused by traumatic brain injury-hemorrhagic shock, partly through the regulation of the microglia M1 polarization
Authors: Cai Jimin , Yang Yang , Han Jiahui , Gao Yu , Li Xin , Ge Xin 
Published: March 2023

Abstract
Background
Microglial polarization and the subsequent neuroinflammatory response and oxidative stress are contributing factors for traumatic brain injury (TBI) plus hemorrhagic shock (HS) induced brain injury. In the present work, we have explored whether Lysine (K)-specific demethylase 4 A (KDM4A) modulates microglia M1 polarization in the TBI and HS mice.

Results
Male C57BL/6J mice were used to investigate the microglia polarization in the TBI + HS model in vivo. Lipopolysaccharide (LPS)-induced BV2 cells were used to examine the mechanism of KDM4A in regulating microglia polarization in vitro. We found that TBI + HS resulted in neuronal loss and microglia M1 polarization in vivo, reflected by the increased level of Iba1, tumor necrosis factor (TNF)-α, interleukin (IL)-1β, malondialdehyde (MDA) and the decreased level of reduced glutathione (GSH). Additionally, KDM4A was upregulated in response to TBI + HS and microglia were among the cell types showing the increased level of KDM4A. Similar to the results in vivo, KDM4A also highly expressed in LPS-induced BV2 cells. LPS-induced BV2 cells exhibited enhanced microglia M1 polarization, and enhanced level of pro-inflammatory cytokines, oxidative stress and reactive oxygen species (ROS), while this enhancement was abolished by the suppression of KDM4A.

Conclusion
Accordingly, our findings indicated that KDM4A was upregulated in response to TBI + HS and microglia were among the cell types showing the increased level of KDM4A. The important role of KDM4A in TBI + HS-induced inflammatory response and oxidative stress was at least partially realized through regulating microglia M1 polarization.
Surgery-related anxiety on geriatric patients undergoing total knee arthroplasty: a retrospective observational study
Authors: Jung Kwang-Hwan , Park Jang-Ho , Ahn Jae-Woo , Park Ki-Bong 
Published: March 2023

Abstract
Background
The prevalence of anxiety in patients undergoing total knee arthroplasty (TKA) and its association with postoperative functions are well known; however, the levels of anxiety or anxiety-related characteristics are unknown. This study aimed to investigate the prevalence of clinically significant state anxiety in geriatric patients undergoing TKA for osteoarthritis (OA) of the knee and to evaluate the anxiety-related characteristics experienced by these patients pre- and post-operatively.

Methods
This retrospective observational study recruited patients who had undergone TKA for knee OA using general anesthesia between February 2020 and August 2021. The study participants were geriatric patients older than 65 years who had moderate or severe OA. We evaluated patient characteristics including age, sex, body mass index, smoking status, hypertension, diabetes, and cancer. We assessed their levels of anxiety status using the STAI-X which comprises 20-item scales. Clinically meaningful state anxiety was defined as a total score of 52 or higher. An independent Student’s t-test was used to determine differences of STAI score between subgroups in terms of patient characteristics. And patients were asked to complete questionnaires, which assessed four areas: (1) the main cause of anxiety; (2) the most helpful factor in overcoming anxiety before surgery; (3) the most helpful factor in reducing anxiety after surgery; and (4) the most anxious moment during the entire process.

Results
The mean STAI score of patients who underwent TKA was 43.0 points and 16.4% of patients experienced clinically significant state anxiety. The current smoking status affect STAI score and the proportion of patients with clinically meaningful state anxiety. The most common cause of preoperative anxiety was the surgery itself. Overall, 38% of patients reported that they experienced the greatest level of anxiety when the surgeon had recommended TKA in the outpatient clinic. The trust in the medical staff before surgery and the surgeon’s explanations after surgery helped the most in reducing anxiety.

Conclusions
One in six patients before TKA experience clinically meaningful state anxiety, and about 40% of patients experience anxiety from the time they are recommended for surgery. Patients tended to overcome anxiety before TKA through trust in the medical staff, and the surgeon’s explanations after surgery was found to be helpful in reducing anxiety.
A fully human connective tissue growth factor blocking monoclonal antibody ameliorates experimental rheumatoid arthritis through inhibiting angiogenesis
Authors: Qin Yang , Wu Gan , Jin Jiayi , Wang Hao , Zhang Jiani , Liu Li , Zhao Heping , Wang Jianguang , Yang Xinyu 
Published: March 2023

Abstract
Background
Connective tissue growth factor (CTGF) plays a pivotal role in the pathogenesis of rheumatoid arthritis (RA) by facilitating angiogenesis and is a promising therapeutic target for RA treatment. Herein, we generated a fully human CTGF blocking monoclonal antibody (mAb) through phage display technology.

Results
A single-chain fragment variable (scFv) with a high affinity to human CTGF was isolated through screening a fully human phage display library. We carried out affinity maturation to elevate its affinity for CTGF and reconstructed it into a full-length IgG1 format for further optimization. Surface plasmon resonance (SPR) data showed that full-length antibody IgG mut-B2 bound to CTGF with a dissociation constant (KD) as low as 0.782 nM. In the collagen-induced arthritis (CIA) mice, IgG mut-B2 alleviated arthritis and decreased the level of pro-inflammatory cytokines in a dose-dependent manner. Furthermore, we confirmed that the TSP-1 domain of CTGF is essential for the interaction. Additionally, the results of Transwell assays, tube formation experiments, and chorioallantoic membrane (CAM) assays showed that IgG mut-B2 could effectively inhibit angiogenesis.

Conclusion
The fully human mAb that antagonizes CTGF could effectively alleviate arthritis in CIA mice, and its mechanism is tightly associated with the TSP-1 domain of CTGF.
Dietary selenium intake in relation to non-alcoholic fatty liver disease assessed by fatty liver index and hepatic steatosis index; a cross-sectional study on the baseline data of prospective PERSIAN Kavar cohort study.
Authors: Shojaei Zarghani Sara , Rahimi Kashkooli Nima , Bagheri Zahra , Tabatabaei Mahdy , Fattahi Mohammad Reza , Safarpour Ali Reza 
Published: March 2023

Abstract
Background
There is limited and conflicting evidence on the association between selenium and non-alcoholic fatty liver disease (NAFLD). Therefore, the present population-based cross-sectional study aimed to explore the relationship between dietary selenium intake and the risk of NAFLD.

Methods
A total of 3026 subjects from the PERSIAN (Prospective Epidemiological Research Studies in IrAN) Kavar cohort study were included in the analysis. The daily selenium intake was evaluated using a semi-quantitative food frequency questionnaire, and energy-adjusted quintiles of selenium intake (µg/day) were calculated. NAFLD was defined as the fatty liver index (FLI) ≥ 60 or the hepatic steatosis index (HSI) > 36. The association between dietary selenium intake and NAFLD was evaluated using logistic regression analysis.

Results
The prevalence rates of NAFLD were 56.4% and 51.9%, based on the FLI and HSI markers, respectively. The odds ratios (ORs) for FLI-defined NAFLD were 1.31 (95% confidence interval (CI): 1.01–1.70) and 1.50 (95% CI: 1.13–1.99) for the fourth and fifth quintiles of selenium intake, respectively, after adjustment for sociodemographic variables, smoking status, alcohol drinking, physical activity, and dietary factors (P trend = 0.002). There was also a similar association between selenium intakes and HSI-defined NAFLD (OR = 1.34 (95% CI: 1.03–1.75) for the fourth quintile and OR = 1.50 (95% CI: 1.12–2.01) for the fifth quintile of selenium intake) (P trend = 0.006).

Conclusion
In this large sample study, we observed a weak positive association between dietary selenium intake and NAFLD risk.
Leveraging the vantage point – exploring nurses’ perception of residents’ communication skills: a mixed-methods study
Authors: Rahim Komal Abdul , Lakhdir Maryam Pyar Ali , Afzal Noreen , Merchant Asma Altaf Hussain , Shaikh Namra Qadeer , Noorali Ali Aahil , Tariq Umar , Ahmad Rida , Bakhshi Saqib Kamran , Mahmood Saad bin Zafar , Khan Muhammad Rizwan , Tariq Muhammed , Haider Adil H. 
Published: March 2023

AbstractIntroductionEffective communication is key to a successful patient-doctor interaction and improved healthcare outcomes. However, communication skills training in residency is often subpar, leading to inadequate patient-physician communication. There is a dearth of studies exploring the observations of nurses – key members of healthcare teams with a special vantage point to observe the impact of residents’ communication with patients. Thus, we aimed to gauge the perceptions of nurses regarding residents’ communication skills expertise.MethodsThis study employed a sequential mixed-methods design, and was conducted at an academic medical center in South Asia. Quantitative data was collected via a REDCap survey using a structured validated questionnaire. Ordinal logistic regression was applied. For qualitative data, In-depth interviews were conducted with nurses using a semi-structured interview guide.ResultsA total of 193 survey responses were obtained from nurses hailing from various specialties including Family Medicine (n = 16), Surgery (n = 27), Internal Medicine (n = 22), Pediatrics (n = 27), and Obstetrics/Gynecology (n = 93). Nurses rated long working hours, infrastructural deficits, and human failings as the main barriers to effective patient-resident communication. Residents working in in-patient settings were more likely to have inadequate communication skills (P-value = 0.160). Qualitative data analysis of nine in-depth interviews revealed two major themes: existing status-quo of residents’ communication skills (including deficient verbal and non-verbal communication, bias in patient counselling and challenging patients) and recommendations for improving patient-resident communication.ConclusionThe findings from this study highlight significant gaps in patient-resident communication from the perception of nurses and identify the need for creating a holistic curriculum for residents to improve patient-physician interaction.
Construct validity of advanced practice nurse core competence scale: an exploratory factor analysis
Authors: Chair Sek Ying , Wong Frances Kam Yuet , Bryant-Lukosius Denise , Liu Ting , Jokiniemi Krista 
Published: March 2023

Abstract
Background
Determining the core competence of advanced practice nurses is foundational for promoting optimal design and implementation of advanced practice nursing roles. Core competencies specific to the contexts of the advanced practice nurse in Hong Kong have been developed, but not yet validated. Thus, this study aims to assess the construct validity of advanced practice nurse core competence scale in Hong Kong.

Methods
We performed a cross-sectional study using an online self-report survey. Exploratory factor analysis was used to examine the factor structure of a 54-item advanced practice nurse core competence scale through principal axis factoring with direct oblique oblimin rotation. A parallel analysis was conducted to determine the number of factors to be extracted. The Cronbach’s α was computed to evaluate the internal consistency of the confirmed scale. The STROBE checklist was used as reporting guideline.

Results
A total of 192 advanced practice nurse responses were obtained. Exploratory factor analysis led to the final 51-item scale with a three-factor structure, which accounted for 69.27% of the total variance. The factor loadings of all items ranged from 0.412 to 0.917. The Cronbach’s alpha of the total scale and three factors ranged from 0.945 to 0.980, indicating robust internal consistency.

Conclusion
This study identified a three-factor structure of the advanced practice nurse core competency scale: client-related competencies, advanced leadership competencies, and professional development and system-related competencies. Future studies are recommended to validate the core competence content and construct in different contexts. Moreover, the validated scale could provide a cornerstone framework for advanced practice nursing roles development, education, and practice, and inform future competency research nationally and internationally.
Resilience in keeping the balance between demand and capacity in the COVID-19 pandemic, a case study at a Swedish middle-sized hospital
Authors: Rosenbäck Ritva Gisela , Svensson Ann 
Published: March 2023

Abstract
Background
In pandemics, it is critical to find a balance between healthcare demand, and capacity, taking into consideration the demands of the patients affected by the pandemic, as well as other patients (in elective or emergency care). The purpose of this paper is to suggest conceptual models for the capacity requirements at the emergency department, the inpatient care, and intensive care unit as well as a model for building staff capacity in pandemics.

Methods
This paper is based on a qualitative single case study at a middle-sized hospital in Sweden. The primary data are collected from 27 interviewees and inductively analyzed.

Results
The interviewees described a large difference between the immediate catastrophe scenario described in the emergency plan (which they had trained for), and the reality during the COVID-19 pandemic. The pandemic had a much slower onset and lasted longer compared to, for example, an accident, and the healthcare demand fluctuated with the societal infection. The emergency department and inpatient care could create surge capacity by reducing elective care. Lower inflow of other emergency patients also helped to create surge capacity. The number of intensive care beds increased by 350% at the case hospital. At the same time, the capacity of the employees decreased due to infection, exhaustion, and fear. The study contributes to knowledge of conceptional models and key factors affecting the balance between demand and capacity.

Conclusion
The framework suggests conceptual models for balancing surge capacity during a pandemic Health care practitioners need to provide assumptions of the key factors to find the balance between the demand and capacity corresponding to the reality and maintain the delivery of high-quality healthcare services.
Molecular investigation of Feline Panleukopenia in an endangered leopard (Panthera pardus) – a case report
Authors: Kolangath S. M. , Upadhye S. V. , Dhoot V. M. , Pawshe M. D. , Bhadane B. K. , Gawande A. P. , Kolangath R. M. 
Published: March 2023

AbstractBackgroundFeline Panleukopenia is an important disease of cats and has been reported worldwide. The disease is caused by a non-enveloped, single-stranded DNA virus; Feline Panleukopenia Virus (FPLV), belonging to the Parvoviridae family. The disease causes significant mortality in unvaccinated kittens. The disease has been well documented in companion animals. However, only a few reports have surfaced from the wild.Case presentationAn orphan leopard cub was presented to Wildlife Rescue Centre, Nagpur, for further care; the leopard was kept under quarantine. On day 22 of the quarantine, the leopard showed inappetence, lethargy and depression and did not consume the offered carabeef (Day 0 of treatment). The leopard was examined clinically and was found to have a temperature of 102°F; blood was collected and analysed. On day one, the leopard exhibited bloody diarrhoea, inappetence, fever and depression. The leopard was rationally treated with fluids, antibiotics, multi-vitamins, haemostatics and haematinics. To gain qualitative insights into the epidemiological aspect of the disease, molecular investigation, including Polymerase Chain Reaction (PCR) and qPCR (Quantitative Polymerase Chain Reaction), were utilized to confirm the infection. The amplicon was sequenced and was found to be similar to sequences of FPLV reported domestic cats and other wild felids from India and abroad. Phylogenetic analysis was performed to understand the evolutionary relationship of the virus with previously reported sequences of FPLV. Sequences were submitted to National Center for Biotechnology Information (NCBI) and were allotted accession numbers.ConclusionThe infection in endangered leopard cubs could be managed with prompt fluid therapy, antibiotics and support treatment, ensuring an uneventful recovery. Molecular investigation and sequencing efforts can provide valuable data on epidemiology and the evolutionary relationship of the virus with the circulating strains in the field. The study has implications in the preventive management of FPLV in captivity and the selection of strains for inclusion in vaccines meant for the wild felids.
Low carbohydrate high fat-diet in real life assessed by diet history interviews
Authors: Hagström Henrik , Hagfors Linda Nyström , Tellström Anna , Hedelin Rikard , Lindmark Krister 
Published: March 2023

AbstractBackgroundLow carbohydrate high fat (LCHF) diet has been a popular low carbohydrate diet in Sweden for 15 years. Many people choose LCHF to lose weight or control diabetes, but there are concerns about the effect on long-term cardiovascular risks. There is little data on how a LCHF diet is composed in real-life. The aim of this study was to evaluate the dietary intake in a population with self-reported adherence to a LCHF diet.MethodsA cross-sectional study of 100 volunteers that considered themselves eating LCHF was conducted. Diet history interviews (DHIs) and physical activity monitoring for validation of the DHIs were performed.ResultsThe validation shows acceptable agreement of measured energy expenditure and reported energy intake. Median carbohydrate intake was 8.7 E% and 63% reported carbohydrate intake at potentially ketogenic levels. Median protein intake was 16.9 E%. The main source of energy was dietary fats (72.0 E%). Intake of saturated fat was 32 E% and cholesterol was 700 mg per day, both of which exceeded the recommended upper limits according to nutritional guidelines. Intake of dietary fiber was very low in our population. The use of dietary supplements was high, and it was more common to exceed the recommended upper limits of micronutrients than to have an intake below the lower limits.ConclusionsOur study indicates that in a well-motivated population, a diet with very low carbohydrate intake can be sustained over time and without apparent risk of deficiencies. High intake of saturated fats and cholesterol as well as low intake of dietary fiber remains a concern.
Recent advances of CREKA peptide-based nanoplatforms in biomedical applications
Authors: Zhang Nannan , Ru Bin , Hu Jiaqi , Xu Langhai , Wan Quan , Liu Wenlong , Cai WenJun , Zhu Tingli , Ji Zhongwei , Guo Ran , Zhang Lin , Li Shun , Tong Xiangmin 
Published: March 2023

AbstractNanomedicine technology is a rapidly developing field of research and application that uses nanoparticles as a platform to facilitate the diagnosis and treatment of diseases. Nanoparticles loaded with drugs and imaging contrast agents have already been used in clinically, but they are essentially passive delivery carriers. To make nanoparticles smarter, an important function is the ability to actively locate target tissues. It enables nanoparticles to accumulate in target tissues at higher concentrations, thereby improving therapeutic efficacy and reducing side effects. Among the different ligands, the CREKA peptide (Cys-Arg-Glu-Lys-Ala) is a desirable targeting ligand and has a good targeting ability for overexpressed fibrin in different models, such as cancers, myocardial ischemia-reperfusion, and atherosclerosis. In this review, the characteristic of the CREKA peptide and the latest reports regarding the application of CREKA-based nanoplatforms in different biological tissues are described. In addition, the existing problems and future application perspectives of CREKA-based nanoplatforms are also addressed.