bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessment of fatty liver and its correlation with glycemic control in patients with type 2 diabetes mellitus attending Dessie Comprehensive Specialized Hospital, Northeast Ethiopia
Authors: Abebe Gashaw , Ayanaw Daniel , Ayelgn Mengstie Tiget , Dessie Gashaw , Malik Tabarak 
Published: September 2022

Objectives: The purpose of conducting this study was to assess fatty liver disease and its correlation with glycemic control in type 2 diabetes mellitus patients. In addition, evaluation of associated factors and correlation analysis between the fatty liver index and hemoglobin A1C level in patients with type 2 diabetes mellitus was another aim of this study. Methods: A hospital-based cross-sectional study was conducted among type 2 diabetes mellitus patients attending at diabetes clinic of Dessie Comprehensive Specialized Hospital located in south Wollo, Ethiopia. It was conducted from July to August 2021. The fatty liver index was calculated to assess fatty liver disease. Simple descriptive statistics, multivariate analysis, and an independent sample t-test were utilized for statistical analysis. Multiple logistic regression analysis was used to determine the associated factors of fatty liver. The p value < 0.05 was considered as statistically significant. Results: In this study, the mean ± standard deviation values of body mass index among type 2 diabetes mellitus patients were 25.82 ± 3.64, 28.04 ± 2.43, and 22.70 ± 2.62 in both fatty and non-fatty liver cases, respectively. In this study, the prevalence of fatty liver among type 2 diabetes mellitus patients was 58.4%. There was a significant positive correlation between the level of Hemoglobin A1C or glycated hemoglobin and fatty liver index (p value = 0.008, r = 0.35). The development of fatty liver was 4.6 times more likely among patients with type 2 diabetes mellitus who had insufficient physical exercise than sufficient exercise. Patients with insulin and oral hypoglycemic drugs were 0.8 folds less likely to have a fatty liver as compared to oral hypoglycemic drug treatment. Conclusion: The results of this study showed that the prevalence of non-alcoholic fatty liver disease was elevated among patients with type 2 diabetes mellitus who had higher levels of body mass index, waist circumference, triglycerides, glycated hemoglobin, and gamma-glutamyltransferase. Therefore, glycemic control, sufficient physical exercise, and insulin treatment may reduce the risk of fatty liver disease in patients with type 2 diabetes mellitus.
Novel electrode design reduces sensory threshold current drift during peripheral nerve evaluation in patients considered for sacral nerve stimulation
Authors: Shin Je Song , Middleton Duncan G , Small Douglas , Cochrane Lisa , Morton Simon , Conn Ian G 
Published: September 2022

Objective: To retrospectively compare the efficacy and technical performance of a novel lead used for percutaneous nerve evaluation (PNE) during the testing phase for sacral nerve neuromodulation with the existing lead currently used. Materials and methods: Sixty-three PNE leads were inserted in 45 consecutive patients who underwent PNE with the novel helical electrodes, and the intra-operative and return clinic sensory threshold currents were recorded. This resulted in current measurements for 63 individual electrodes. Measurements were compared with 46 consecutive patients who previously underwent PNE using the standard lead with measurements for 63 individual electrodes. Current difference distributions for the two leads were compared using a Wilcoxon signed-rank test. Results: There was a statistically significant difference observed between the two types of PNE electrode. The new PNE lead demonstrated less drift in sensory threshold current during a 12-day test period in comparison to the old lead. Conclusion: The novel helical PNE electrodes demonstrate a significant improvement in current drift compared with the old style leads over a 12-day test period. Level of evidence: Level III
Intra-articular Hip Injuries in National Basketball Association Players: A Descriptive Epidemiological Study
Authors: Egger Anthony C. , Minkara Anas , Parker Richard , Rosneck James 
Published: September 2022

Background: Since the most recent epidemiologic study of injuries in National Basketball Association (NBA) players was completed in 2012, the understanding and diagnosis of intra-articular hip injury has advanced. Purpose: To report the epidemiology of intra- versus extra-articular hip injuries in NBA players with regard to missed games, risk factors for injury, and treatment types. Study Design: Cohort study; Level of evidence, 3. Methods: The NBA injury database was queried for all reported hip and groin injuries from 2013 to 2017. The injuries were then divided into intra-articular and extra-articular types. Variables compared between injury types included player age, NBA tenure, season schedule (preseason or offseason), onset type, injury mechanism, roster position, games missed, time to return to play, and need for surgery. Results: A total of 224 athletes sustaining 353 total hip pathologies were identified. Of these injuries, 216 (61.2%) were sustained during game competition and affected 156 (69.6%) of the athletes. Intra-articular injuries represented 39 (11.0%) cases and involved 36 (16.1%) players. The time to return to play was significantly longer after intra-articular versus extra-articular injury (44.6 ± 96.0 vs 11.8 ± 32.0 days; P = .03), and the number of games missed was significantly greater after intra-articular versus extra-articular injury (8.0 ± 18.7 vs 1.54 ± 4.9 games; P = .03). Patients with intra-articular hip injuries were more likely to undergo surgery (odds ratio, 5.5 [95% CI, 1.8-16.7]; P = .005). There was no statistically significant difference in the number of games missed due to surgery (35.2 ± 8.3 [intra-articular] vs 35.4 ± 11.6 [extra-articular]; P = .42) or nonoperative treatment (4.2 ± 3.4 [intra-articular] vs 1.3 ± 0.5 [extra-articular]; P = .11). Years of NBA tenure were not significantly different between intra-articular and extra-articular injuries (7.1 ± 3.7 vs 6.3 ± 4.0 years). For both types of hip injury, there was no correlation between player age and either days to return to play or number of games missed ( R 2 = 0.014). Conclusion: NBA players with intra-articular hip injuries underwent surgery more frequently and had a longer return-to-play time compared with those with extra-articular hip injuries. NBA tenure and player age were not correlated with the risk of developing hip injury or the need for surgery.
Structural and spectroscopic study of well-developed crystals of parahibbingite, β-Fe2(OH)3Cl, formed from terrestrial weathering of the Muonionalusta iron meteorite
Authors: Margheri Simone , Bindi Luca , Bonazzi Paola , Holtstam Dan 
Published: September 2022

AbstractParahibbingite [β-Fe2(OH)3Cl], a new mineral recently described from ultramafic rocks in the Bushveld Complex, South Africa, has been found to form millimetric well-developed crystals as a terrestrial weathering product of the Muonionalusta iron meteorite. The mineral, initially identified by means of Raman spectroscopy, was found in a small cavity within a crust of rust on a granitic rock fragment that was in direct contact with the alteration crust of a meteorite specimen, collected in the Kitkiöjärvi area, Sweden. Its crystal structure was refined from single-crystal X-ray diffraction data (R1 = 0.0331) in the space group R$\bar{3}$m [a = 6.9362(4), c = 14.673(1) Å and V = 611.35(7) Å3 for Z = 6], thus confirming the structural model of synthetic β-Fe2(OH)3Cl. It consists of a network of octahedrally coordinated Fe2+ atoms alternately arranged in triangular and Kagomé layers, stacked along the c axis. The H atom position was determined, showing O–H⋅⋅⋅Cl bonds, which provides a further link between layers. Parahibbingite is found to be not only an important constituent of the corrosion system of archaeological iron artefacts but can also play an important role as an alteration product of iron meteorites.
Missense mutations in PIEZO1, which encodes the Piezo1 mechanosensor protein, define Er red blood cell antigens
Authors: Karamatic Crew Vanja , Tilley Louise A. , Satchwell Timothy J. , AlSubhi Samah A. , Jones Benjamin , Spring Frances A. , Walser Piers J. , Martins Freire Catarina , Murciano Nicoletta , Rotordam Maria Giustina , Woestmann Svenja J. , Hamed Marwa , Alradwan Reem , AlKhrousey Mouza , Skidmore Ian , Lewis Sarah , Hussain Shimon , Jackson Jane , Latham Tom , Kilby Mark D. , Lester William , Becker Nadine , Rapedius Markus , Toye Ashley M. , Thornton Nicole M. 
Published: September 2022

Abstract
Despite the identification of the high-incidence red cell antigen Era nearly 40 years ago, the molecular background of this antigen, together with the other 2 members of the Er blood group collection, has yet to be elucidated. Whole exome and Sanger sequencing of individuals with serologically defined Er alloantibodies identified several missense mutations within the PIEZO1 gene, encoding amino acid substitutions within the extracellular domain of the Piezo1 mechanosensor ion channel. Confirmation of Piezo1 as the carrier molecule for the Er blood group antigens was demonstrated using immunoprecipitation, CRISPR/Cas9-mediated gene knockout, and expression studies in an erythroblast cell line. We report the molecular bases of 5 Er blood group antigens: the recognized Era, Erb, and Er3 antigens and 2 novel high-incidence Er antigens, described here as Er4 and Er5, establishing a new blood group system. Anti-Er4 and anti-Er5 are implicated in severe hemolytic disease of the fetus and newborn. Demonstration of Piezo1, present at just a few hundred copies on the surface of the red blood cell, as the site of a new blood group system highlights the potential antigenicity of even low-abundance membrane proteins and contributes to our understanding of the in vivo characteristics of this important and widely studied protein in transfusion biology and beyond.
Malignant T cells induce skin barrier defects through cytokine-mediated JAK/STAT signaling in cutaneous T-cell lymphoma
Authors: Gluud Maria , Pallesen Emil M. H. , Buus Terkild B. , Gjerdrum Lise Mette Rahbek , Lindahl Lise M. , Kamstrup Maria R. , Bzorek Michael , Danielsen Maria , Bech Rikke , Monteiro Madalena N. , Blümel Edda , Willerslev-Olsen Andreas , Lykkebo-Valløe Anders , Vadivel Chella Krishna , Krejsgaard Thorbjørn , Bonefeld Charlotte Menne , Geisler Carsten , Becker Jürgen C. , Koralov Sergei B. , Iversen Lars , Litman Thomas , Woetmann Anders , Ødum Niels 
Published: September 2022

AbstractCutaneous T-cell lymphoma (CTCL) is a devastating lymphoid malignancy characterized by the accumulation of malignant T cells in the dermis and epidermis. Skin lesions cause serious symptoms that hamper quality of life and are entry sites for bacterial infection, a major cause of morbidity and mortality in advanced diseases. The mechanism driving the pathological processes that compromise the skin barrier remains unknown. Here, we report increased transepidermal water loss and compromised expression of the skin barrier proteins filaggrin and filaggrin-2 in areas adjacent to TOX-positive T cells in CTCL skin lesions. Malignant T cells secrete mediators (including cytokines such as interleukin 13 [IL-13], IL-22, and oncostatin M) that activate STAT3 signaling and downregulate filaggrin and filaggrin-2 expression in human keratinocytes and reconstructed human epithelium. Consequently, the repression of filaggrins can be counteracted by a cocktail of antibodies targeting these cytokines/receptors, small interfering RNA–mediated knockdown of JAK1/STAT3, and JAK1 inhibitors. Notably, we show that treatment with a clinically approved JAK inhibitor, tofacitinib, increases filaggrin expression in lesional skin from patients with mycosis fungoides. Taken together, these findings indicate that malignant T cells secrete cytokines that induce skin barrier defects via a JAK1/STAT3-dependent mechanism. As clinical grade JAK inhibitors largely abrogate the negative effect of malignant T cells on skin barrier proteins, our findings suggest that such inhibitors provide novel treatment options for patients with CTCL with advanced disease and a compromised skin barrier.
Tracking the progeny of adoptively transferred virus-specific T cells in patients posttransplant using TCR sequencing
Authors: Huisman W. , Roex M. C. J. , Hageman L. , Koster E. A. S. , Veld S. A. J. , Hoogstraten C. , van Balen P. , van Egmond H. M. , van Bergen C. A. M. , Einsele H. , Germeroth L. , Amsen D. , Falkenburg J. H. F. , Jedema I. 
Published: September 2022

Abstract
Adoptive cellular therapies with T cells are increasingly used to treat a variety of conditions. For instance, in a recent phase 1/2 trial, we prophylactically administered multivirus-specific T-cell products to protect recipients of T-cell–depleted allogeneic stem cell grafts against viral reactivation. To establish treatment efficacy, it is important to determine the fate of the individual transferred T-cell populations. However, it is difficult to unequivocally distinguish progeny of the transferred T-cell products from recipient- or stem cell graft–derived T cells that survived T-cell depletion during conditioning or stem cell graft manipulation. Using messenger RNA sequencing of the T-cell receptor β-chains of the individual virus-specific T-cell populations within these T-cell products, we were able to track the multiple clonal virus-specific subpopulations in peripheral blood and distinguish recipient- and stem cell graft–derived virus-specific T cells from the progeny of the infused T-cell products. We observed in vivo expansion of virus-specific T cells that were exclusively derived from the T-cell products with similar kinetics as the expansion of virus-specific T cells that could also be detected before the T-cell product infusion. In addition, we demonstrated persistence of virus-specific T cells derived from the T-cell products in most patients who did not show viral reactivation. This study demonstrates that virus-specific T cells from prophylactically infused multiantigen-specific T-cell products can expand in response to antigen encounter in vivo and even persist in the absence of early viral reactivation.
Topology-enhanced molecular graph representation for anti-breast cancer drug selection
Authors: Gao Yue , Chen Songling , Tong Junyi , Fu Xiangling 
Published: September 2022

Abstract
Background
Breast cancer is currently one of the cancers with a higher mortality rate in the world. The biological research on anti-breast cancer drugs focuses on the activity of estrogen receptors alpha (ER$$\alpha$$
α
), the pharmacokinetic properties and the safety of the compounds, which, however, is an expensive and time-consuming process. Developments of deep learning bring potential to efficiently facilitate the candidate drug selection against breast cancer.

Methods
In this paper, we propose an Anti-Breast Cancer Drug selection method utilizing Gated Graph Neural Networks (ABCD-GGNN) to topologically enhance the molecular representation of candidate drugs. By constructing atom-level graphs through atomic descriptors for each distinct compound, ABCD-GGNN can topologically learn both the implicit structure and substructure characteristics of a candidate drug and then integrate the representation with explicit discrete molecular descriptors to generate a molecule-level representation. As a result, the representation of ABCD-GGNN can inductively predict the ER$$\alpha$$
α
, the pharmacokinetic properties and the safety of each candidate drug. Finally, we design a ranking operator whose inputs are the predicted properties so as to statistically select the appropriate drugs against breast cancer.

Results
Extensive experiments conducted on our collected anti-breast cancer candidate drug dataset demonstrate that our proposed method outperform all the other representative methods in the tasks of predicting ER$$\alpha$$
α
, and the pharmacokinetic properties and safety of the compounds. Extended result analysis demonstrates the efficiency and biological rationality of the operator we design to calculate the candidate drug ranking from the predicted properties.

Conclusion
In this paper, we propose the ABCD-GGNN representation method to efficiently integrate the topological structure and substructure features of the molecules with the discrete molecular descriptors. With a ranking operator applied, the predicted properties efficiently facilitate the candidate drug selection against breast cancer.
msPIPE: a pipeline for the analysis and visualization of whole-genome bisulfite sequencing data
Authors: Kim Heesun , Sim Mikang , Park Nayoung , Kwon Kisang , Kim Junyoung , Kim Jaebum 
Published: September 2022

Abstract
Background
DNA methylation is an important epigenetic modification that is known to regulate gene expression. Whole-genome bisulfite sequencing (WGBS) is a powerful method for studying cytosine methylation in a whole genome. However, it is difficult to obtain methylation profiles using the WGBS raw reads and is necessary to be proficient in all types of bioinformatic tools for the study of DNA methylation. In addition, recent end-to-end pipelines for DNA methylation analyses are not sufficient for addressing those difficulties.

Results
Here we present msPIPE, a pipeline for DNA methylation analyses with WGBS data seamlessly connecting all the required tasks ranging from data pre-processing to multiple downstream DNA methylation analyses. The msPIPE can generate various methylation profiles to analyze methylation patterns in the given sample, including statistical summaries and methylation levels. Also, the methylation levels in the functional regions of a genome are computed with proper annotation. The results of methylation profiles, hypomethylation, and differential methylation analysis are plotted in publication-quality figures. The msPIPE can be easily and conveniently used with a Docker image, which includes all dependent packages and software related to DNA methylation analyses.

Conclusion
msPIPE is a new end-to-end pipeline designed for methylation calling, profiling, and various types of downstream DNA methylation analyses, leading to the creation of publication-quality figures. msPIPE allows researchers to process and analyze the WGBS data in an easy and convenient way. It is available at https://github.com/jkimlab/msPIPE and https://hub.docker.com/r/jkimlab/mspipe.
Identification of thermogenesis-related lncRNAs in small extracellular vesicles derived from adipose tissue
Authors: Hong Pengyu , Wu Yue , Zhang Qi , Liu Pan , Zhang Siyuan , Yu Mei , Tian Weidong 
Published: September 2022

AbstractBackgroundBrown adipose tissue (BAT) is considered as a primary location of adaptive thermogenesis and the thermogenic activities of brown adipocytes are also connected to generating heat and counteracting obesity. Recent studies revealed that BAT could secrete certain batokines-like factors especially small extracellular vesicles (sEVs), which contributed to the systemic consequences of BAT activities. As a newly emerging class of mediators, some long non-coding RNAs (lncRNAs) have exhibited metabolic regulatory effects in adipocyte development. However, besides the well-studied lncRNAs, the lncRNAs carried by sEVs derived from brown adipose tissue (sEV-BAT) have not been identified yet. ResultsIn this study, we demonstrated that sEV-BAT could induce beige adipocyte differentiation both in ASCs and 3T3-L1 cells, while sEV-WAT had no corresponding effects. The lncRNA microarray assay on sEV-WAT and sEV-BAT revealed a total of 563 types of known lncRNAs were identified to be differentially expressed, among which 232 lncRNAs were upregulated and 331 lncRNAs were downregulated in sEV-BAT. Three novel candidates (AK029592, humanlincRNA1030 and ENSMUST00000152284) were selected for further validation. LncRNA–mRNA network analysis revealed candidate lncRNAs were largely embedded in cellular metabolic pathways. During adipogenic and thermogenic phenotype differentiation in ASCs and 3T3-L1 cells, only the expressions of AK029592 were upregulated. The three lncRNAs were all relatively enriched in brown adipose tissues and brown adipocytes. In different adipocytes, sEV and adipose tissue, the expression of AK029592 and ENSMUST00000152284 were remarkably decreased in obese mice compared to lean mice, while obesity state could not change the expression of humanlincRNA1030.ConclusionCollectively, our profiling study provided a comprehensive catalog for the study of lncRNAs specifically carried by sEV-BAT and indicated the potential regulatory role of certain sEV-BAT lncRNAs in thermogenesis.
The antimicrobial effect of a novel peptide LL-1 on Escherichia coli by increasing membrane permeability
Authors: Zhou Lingling , Lian Kaiqi , Wang Mengting , Jing Xueyi , Zhang Yuanchen , Cao Jinling 
Published: September 2022

AbstractBackgroundThe widespread use of antibiotics has led to the emergence of many drug-resistant strains; thus, the development of new antibacterial drugs is essential with antimicrobial peptides becoming the focus of research. This study assessed the antibacterial effect of a novel antimicrobial peptide, named LL-1 onEscherichia coli(E.coli) by determining the minimum inhibitory concentration (MIC) and the antibacterial curve. The interaction between LL-1 andE. coliDNA was then detected by nucleic acid gel electrophoresis. The effect of LL-1 on theE. colicell membrane was assessed by detecting the leakage of β-galactosidase, nucleic acid and protein. The influence of LL-1 on the intracellular ATP ofE. coliwas analysed by determining the concentration of intracellular ATP. Finally, the bacteria and colonies ofE. colitreated with LL-1 were observed using scanning and transmission electron microscopy.ResultsThe results suggested that the MIC value was 3.125 µg/ml, and the antibacterial effect was dose-dependent. LL-1 dose-dependently combined withE. coliDNA. LL-1 resulted in the leakage of intracellular β-galactosidase, nucleic acid and protein, and decreased intracellular ATP concentrations ofE. coli. Two MIC of LL-1 causedE. colito shrink, resulting in a rough surface, plasmolysis, and bacterial adhesion.ConclusionThis study indicated that LL-1 had a good bactericidal effect onE. coliby mainly increasing the permeability of the cell membrane, leading to leakage of the intracellular content. This will lay the foundation for an in-depth study on the antibacterial mechanism of LL-1 againstE. coliand its clinical application.