Miracle-dz/UniFAR-FTUs huggingface dataset:
Quantitative MR Analysis of Changes in the Radius Bone Marrow in Osteoporosis

Purpose This pilot study aimed to explore the feasibility of scanning the human distal radius bone marrow in vivo to detect osteoporosis-related changes using magnetic resonance and evaluate whether the radius may serve as an accessible probing site for osteoporosis. This may lead in the future to the use of affordable means such as low-field MRI scanners for the monitoring of disease progression. Methods A clinical trial was performed using a 3T MR scanner, including 26 women assigned into three study groups: healthy-premenopausal (n = 7; mean age 48.6 ± 3.5 years), healthy-postmenopausal (n = 10; mean age 54.5 ± 5.6 years), and osteoporotic-postmenopausal (n = 9; mean age 61.3 ± 5.6 years). Marrow fat composition was evaluated using T2 maps, a two-compartment model of T1, and a Dixon pulse sequence. Results The osteoporotic group exhibited higher fat content than the other two groups and lower T2 values than the healthy-premenopausal group. Conclusions Osteoporosis-related changes in the composition of the distal radius bone marrow may be detected in vivo using MRI protocols. The scanning protocols chosen here can later be repeated using low-field MRI scanners, thus offering the potential for early detection and treatment monitoring, using an accessible, affordable means that may be applied in small clinics. This trial is registered with MOH_2018-05-23_002247, NCT03742362.
Global research trends in DNA methylation in rheumatoid arthritis: A bibliometric analysis and visual analysis

Rheumatoid arthritis (RA) is a prevalent autoimmune disorder with a significant global economic burden. Epigenetic modifications, particularly DNA methylation, play a crucial role in RA. This study conducted a bibliometric analysis to explore the evolving trends and predominant themes in RA and DNA methylation research over the past two decades. A total of 1800 articles met the inclusion criteria, and the analysis revealed consistent growth in the literature, with a notable increase in output after 2019. The research involved 70 countries, 2139 academic institutions, 23,365 unique authors, and 58,636 co-cited authors. The United States emerged as a dominant contributor in this research domain. The significance of DNA methylation in shaping research directions for RA management is increasingly evident. Recent investigations have shed light on the pivotal role of DNA methylation in RA, particularly in characterizing synovial tissue and exploring the underlying mechanisms of disease pathogenesis. This study provides valuable insights into the landscape of DNA methylation research in RA and highlights the importance of epigenetics in autoimmune diseases.
Effects of a Novel Glucokinase Activator, Dorzagliatin, on Glycemic Control and Glucose Fluctuation in Drug-Naïve Patients with Type 2 Diabetes Mellitus

Aim The prevalence rate of type 2 diabetes mellitus (T2DM) has been increasing and a large proportion of patients still do not achieve adequate or sustainable glycemic control on the basis of previous hypoglycemic treatment. In this present study, we explored whether dorzagliatin, a novel glucokinase activator (GKA), could improve glycemic control and lessen glucose fluctuation in drug-naïve patients with T2DM. Methods A self-comparative observational study of 25 drug-naïve patients with T2DM (aged 18–75 years and HbA1c of 7.5%–11.0%) treated with dorzagliatin 75 mg twice daily for 52 weeks. Before and after dorzagliatin intervention, the serum levels of hemoglobin A1c (HbA1c), insulin, and C-peptide were measured repeatedly during fasting and after a mixed meal. The continuous glucose monitoring (CGM) device was also used to obtain 24-hour glucose profiles and assess the changes in glycemic variability parameters. Results After 52 weeks of treatment with dorzagliatin, a numerally greater reduction in HbA1c of 1.03% from the baseline was observed in patients with T2DM, accompanied by significant improvement in insulin resistance and insulin secretion. Moreover, the standard deviation of blood glucose (SDBG) and the mean amplitude of glycemic excursion (MAGE) derived from CGM data were significantly decreased after dorzagliatin therapy. The 24-h glucose variation profile showed that study patients had obviously lower mean glucose levels during the postprandial period from the baseline to week 52, an effect also demonstrated by the significant decrease in the incremental area under glucose concentration versus time curve for 2 h (iAUC0–2 h) after meals. Conclusions This study suggests that dorzagliatin therapy could effectively improve glycemic control and glucose fluctuation in drug-naïve patients with T2DM.
In-silico evaluation of natural alkaloids against the main protease and spike glycoprotein as potential therapeutic agents for SARS-CoV-2

Severe Acute Respiratory Syndrome Corona Virus (SARS-CoV-2) is the causative agent of COVID-19 pandemic, which has resulted in global fatalities since late December 2019. Alkaloids play a significant role in drug design for various antiviral diseases, which makes them viable candidates for treating COVID-19. To identify potential antiviral agents, 102 known alkaloids were subjected to docking studies against the two key targets of SARS-CoV-2, namely the spike glycoprotein and main protease. The spike glycoprotein is vital for mediating viral entry into host cells, and main protease plays a crucial role in viral replication; therefore, they serve as compelling targets for therapeutic intervention in combating the disease. From the selection of alkaloids, the top 6 dual inhibitory compounds, namely liensinine, neferine, isoliensinine, fangchinoline, emetine, and acrimarine F, emerged as lead compounds with favorable docked scores. Interestingly, most of them shared the bisbenzylisoquinoline alkaloid framework and belong to Nelumbo nucifera, commonly known as the lotus plant. Docking analysis was conducted by considering the key active site residues of the selected proteins. The stability of the top three ligands with the receptor proteins was further validated through dynamic simulation analysis. The leads underwent ADMET profiling, bioactivity score analysis, and evaluation of drug-likeness and physicochemical properties. Neferine demonstrated a particularly strong affinity for binding, with a docking score of -7.5025 kcal/mol for main protease and -10.0245 kcal/mol for spike glycoprotein, and therefore a strong interaction with both target proteins. Of the lead alkaloids, emetine and fangchinoline demonstrated the lowest toxicity and high LD50 values. These top alkaloids, may support the body’s defense and reduce the symptoms by their numerous biological potentials, even though some properties naturally point to their direct antiviral nature. These findings demonstrate the promising anti-COVID-19 properties of the six selected alkaloids, making them potential candidates for drug design. This study will be beneficial in effective drug discovery and design against COVID-19 with negligible side effects.
Genomic and functional insights into antibiotic resistance genes floR and strA linked with the SXT element of Vibrio cholerae non-O1/non-O139

The emergence and spread of antibiotic-resistant bacterial pathogens are a critical public health concern across the globe. Mobile genetic elements (MGEs) play an important role in the horizontal acquisition of antimicrobial resistance genes (ARGs) in bacteria. In this study, we have decoded the whole genome sequences of multidrug-resistant Vibrio cholerae clinical isolates carrying the ARG-linked SXT, an integrative and conjugative element, in their large chromosomes. As in others, the SXT element has been found integrated into the 5′-end of the prfC gene (which encodes peptide chain release factor 3 involved in translational regulation) on the large chromosome of V. cholerae non-O1/non-O139 strains. Further, we demonstrate the functionality of SXT-linked floR and strAB genes, which confer resistance to chloramphenicol and streptomycin, respectively. The floR gene-encoded protein FloR belongs to the major facilitator superfamily efflux transporter containing 12 transmembrane domains (TMDs). Deletion analysis confirmed that even a single TMD of FloR is critical for the export function of chloramphenicol. The floR gene has two putative promoters, P1 and P2. Sequential deletions reveal that P2 is responsible for the expression of the floR. Deletion analysis of the N- and/or C-terminal coding regions of strA established their importance for conferring resistance against streptomycin. Interestingly, qPCR analysis of the floR and strA genes indicated that both of the genes are constitutively expressed in V. cholerae cells. Further, whole genome-based global phylogeography confirmed the presence of the integrative and conjugative element SXT in non-O1/non-O139 strains despite being non-multidrug resistant by lacking antimicrobial resistance (AMR) gene cassettes, which needs monitoring.
Comparison of scissor-type knife to non-scissor-type knife for endoscopic submucosal dissection: a systematic review and meta-analysis

Background/Aims: Scissor-type endoscopic submucosal dissection (ST-ESD) knives can reduce the adverse events associated with ESDs. This study aimed to compare ST-ESD and non-scissor-type (NST)-ESD knives. Methods: We identified ten studies that compared the performance characteristics and safety profiles of ST-ESD and NST-ESD knives. Fixed- and random-effects models were used to calculate the pooled proportions. Heterogeneity was assessed using the I2 test. Results: On comparing ST-ESD knives to NST-ESD knives, the weighted odds of en bloc resection was 1.61 (95% confidence interval [CI], 0.90–2.90; p=0.14), R0 resection was 1.10 (95% CI, 0.71–1.71; p=0.73), delayed bleeding was 0.40 (95% CI, 0.17–0.90; p=0.03), perforation was 0.35 (95% CI, 0.18–0.70; p<0.01) and ESD self-completion by non-experts was 1.89 (95% CI, 1.20–2.95; p<0.01). There was no heterogeneity, with an I2 score of 0% (95% CI, 0%–54.40%). Conclusions: The findings of reduced odds of perforation, a trend toward reduced delayed bleeding, and an improvement in the rates of en bloc and R0 resection with ST-ESD knives compared to NST-ESD knives support the use of ST-ESD knives when non-experts perform ESDs or as an adjunct tool for challenging ESD procedures.
A Coarse-to-Fine Framework for Cloud Removal in Remote Sensing Image Sequence

Clouds and accompanying shadows, which exist in optical remote sensing images with high possibility, can degrade or even completely occlude certain ground-cover information in images, limiting their applicabilities for Earth observation, change detection, or land-cover classification. In this paper, we aim to deal with cloud contamination problems with the objective of generating cloud-removed remote sensing images. Inspired by low-rank representation together with sparsity constraints, we propose a coarse-to-fine framework for cloud removal in the remote sensing image sequence. Leveraging on group-sparsity constraint, we first decompose the observed cloud image sequence of the same area into the low-rank component, group-sparse outliers, and sparse noise, corresponding to cloud-free land-covers, clouds (and accompanying shadows), and noise respectively. Subsequently, a discriminative robust principal component analysis (RPCA) algorithm is utilized to assign aggressive penalizing weights to the initially detected cloud pixels to facilitate cloud removal and scene restoration. Moreover, we incorporate geometrical transformation into a low-rank model to address the misalignment of the image sequence. Significantly superior to conventional cloud-removal methods, neither cloud-free reference image(s) nor additional operations of cloud and shadow detection are required in our method. Extensive experiments on both simulated data and real data demonstrate that our method works effectively, outperforming many state-of-the-art approaches.
Evaluation of Changes in Prices and Purchases Following Implementation of Sugar-Sweetened Beverage Taxes Across the US

Key Points Question What changes occurred in sugar-sweetened beverage (SSB) prices and purchase volume after SSB taxes were implemented in 5 large US cities? Findings In this cross-sectional study, SSB taxes in Boulder, Colorado; Philadelphia, Pennsylvania; Oakland, California; San Francisco, California; and Seattle, Washington, were associated with a 33.1% composite increase in SSB prices (92% pass-through of taxes to consumers) and a 33% reduction in purchase volume, without increasing cross-border purchases. The results were sustained in the months following tax implementation. Meaning The results suggest substantial, consistent declines in SSB purchases across several US cities; insofar as reducing SSB consumption can improve population health, scaling SSB taxes more broadly should be considered.
MindOpt Adapter for CPLEX Benchmarking Performance Analysis

This report provides a comprehensive analysis of the performance of MindOpt Adapter for CPLEX 12.9 in benchmark testing. CPLEX, recognized as a robust Mixed Integer Programming (MIP) solver, has faced some scrutiny regarding its performance on MIPLIB 2017 when configured to default settings. MindOpt Adapter aims to enhance CPLEX's performance by automatically applying improved configurations for solving optimization problems. Our testing demonstrates that MindOpt Adapter for CPLEX yields successfully solved 232 of the 240 problems in the MIPLIB 2017 benchmark set. This performance surpasses all the other solvers in terms of the number of problems solved and the geometric mean of running times. The report provides a comparison of the benchmark results against the outcomes achieved by CPLEX under its default configuration.
Living well with dementia: An exploratory matched analysis of minority ethnic and white people with dementia and carers participating in the IDEAL programme

Abstract Objectives The increasing heterogeneity of the population of older people is reflected in an increasing number of people with dementia and carers drawn from minority ethnic groups. Data from the IDEAL study are used to compare indices of ‘living well’ among people with dementia and carers from ethnic minority groups with matched white peers. Methods We used an exploratory cross‐sectional case‐control design to compare ‘living well’ for people with dementia and carers from minority ethnic and white groups. Measures for both groups were quality of life, life satisfaction, wellbeing, loneliness, and social isolation and, for carers, stress, relationship quality, role captivity and caring competence. Results The sample of people with dementia consisted of 20 minority ethnic and 60 white participants and for carers 15 and 45 respectively. People with dementia from minority ethnic groups had poorer quality of life (−4.74, 95% CI: −7.98 to −1.50) and higher loneliness (1.72, 95% CI: 0.78–2.66) whilst minority ethnic carers had higher stress (8.17, 95% CI: 1.72–14.63) and role captivity (2.00, 95% CI: 0.43–3.57) and lower relationship quality (−9.86, 95% CI: −14.24 to −5.48) than their white peers. Conclusion Our exploratory study suggests that people with dementia from minority ethnic groups experience lower quality of life and carers experience higher stress and role captivity and lower relationship quality than their white peers. Confirmatory research with larger samples is required to facilitate analysis of the experiences of specific minority ethnic groups and examine the factors contributing to these disadvantages.
Proteomic analysis shows decreased type I fibers and ectopic fat accumulation in skeletal muscle from women with PCOS

Background: Polycystic ovary syndrome’s (PCOS) main feature is hyperandrogenism, which is linked to a higher risk of metabolic disorders. Gene expression analyses in adipose tissue and skeletal muscle reveal dysregulated metabolic pathways in women with PCOS, but these differences do not necessarily lead to changes in protein levels and biological function. Methods: To advance our understanding of the molecular alterations in PCOS, we performed global proteomic and phosphorylation site analysis using tandem mass spectrometry, and analyzed gene expression and methylation. Adipose tissue and skeletal muscle were collected at baseline from 10 women with and without PCOS, and in women with PCOS after 5 weeks of treatment with electrical stimulation. Results: Perilipin-1, a protein that typically coats the surface of lipid droplets in adipocytes, was increased whereas proteins involved in muscle contraction and type I muscle fiber function were downregulated in PCOS muscle. Proteins in the thick and thin filaments had many altered phosphorylation sites, indicating differences in protein activity and function. A mouse model was used to corroborate that androgen exposure leads to a shift in muscle fiber type in controls but not in skeletal muscle-specific androgen receptor knockout mice. The upregulated proteins in muscle post treatment were enriched in pathways involved in extracellular matrix organization and wound healing, which may reflect a protective adaptation to repeated contractions and tissue damage due to needling. A similar, albeit less pronounced, upregulation in extracellular matrix organization pathways was also seen in adipose tissue. Conclusions: Our results suggest that hyperandrogenic women with PCOS have higher levels of extra-myocellular lipids and fewer oxidative insulin-sensitive type I muscle fibers. These could be key factors leading to insulin resistance in PCOS muscle while electric stimulation-induced tissue remodeling may be protective. Funding: Swedish Research Council (2020-02485, 2022-00550, 2020-01463), Novo Nordisk Foundation (NNF22OC0072904), and IngaBritt and Arne Lundberg Foundation. Clinical trial number NTC01457209.
Impaired oligodendrogenesis in the white matter of aged mice following diffuse traumatic brain injury.

Senescence is a negative prognostic factor for outcome and recovery following traumatic brain injury (TBI). TBI-induced white matter injury may be partially due to oligodendrocyte demise. We hypothesized that the regenerative capacity of oligodendrocyte precursor cells (OPCs) declines with age. To test this hypothesis, the regenerative capability of OPCs in young [(10 weeks ±2 (SD)] and aged [(62 weeks ±10 (SD)] mice was studied in mice subjected to central fluid percussion injury (cFPI), a TBI model causing widespread white matter injury. Proliferating OPCs were assessed by immunohistochemistry for the proliferating cell nuclear antigen (PCNA) marker and labeled by 5-ethynyl-2'-deoxyuridine (EdU) administered daily through intraperitoneal injections (50 mg/kg) from day 2 to day 6 after cFPI. Proliferating OPCs were quantified in the corpus callosum and external capsule on day 2 and 7 post-injury (dpi). The number of PCNA/Olig2-positive and EdU/Olig2-positive cells were increased at 2dpi (p < .01) and 7dpi (p < .01), respectively, in young mice subjected to cFPI, changes not observed in aged mice. Proliferating Olig2+/Nestin+ cells were less common (p < .05) in the white matter of brain-injured aged mice, without difference in proliferating Olig2+/PDGFRα+ cells, indicating a diminished proliferation of progenitors with different spatial origin. Following TBI, co-staining for EdU/CC1/Olig2 revealed a reduced number of newly generated mature oligodendrocytes in the white matter of aged mice when compared to the young, brain-injured mice (p < .05). We observed an age-related decline of oligodendrogenesis following experimental TBI that may contribute to the worse outcome of elderly patients following TBI.
MAGE-A11 is a potential prognostic biomarker and immunotherapeutic target in gastric cancer

Gastric cancer poses a serious threat to human health and affects the digestive system. The lack of early symptoms and a dearth of effective identification methods make diagnosis difficult, with many patients only receiving a definitive diagnosis at a malignant stage, causing them to miss out on optimal therapeutic interventions. Melanoma-associated antigen-A (MAGE-A) is part of the MAGE family and falls under the cancer/testis antigen (CTA) category. The MAGE-A subfamily plays a significant role in tumorigenesis, proliferation and migration. The expression, prognosis and function of MAGE-A family members in GC, however, remain unclear. Our research and screening have shown that MAGE-A11 was highly expressed in GC tissues and was associated with poor patient prognosis. Additionally, MAGE-A11 functioned as an independent prognostic factor in GC through Cox regression analysis, and its expression showed significant correlation with both tumour immune cell infiltration and responsiveness to immunotherapy. Our data further indicated that MAGE-A11 regulated GC cell proliferation and migration. Subsequently, our findings propose that MAGE-A11 may operate as a prognostic factor, having potential as an immunotherapy target for GC.
Small polymorphisms are a source of ancestral bias in structural variant breakpoint placement

High-quality genome assemblies and sophisticated algorithms have increased sensitivity for a wide range of variant types, and breakpoint accuracy for structural variants (SVs, ≥50 bp) has improved to near base pair precision. Despite these advances, many SV breakpoint locations are subject to systematic bias affecting variant representation. To understand why SV breakpoints are inconsistent across samples, we reanalyzed 64 phased haplotypes constructed from long-read assemblies released by the Human Genome Structural Variation Consortium (HGSVC). We identify 882 SV insertions and 180 SV deletions with variable breakpoints not anchored in tandem repeats (TRs) or segmental duplications (SDs). SVs called from aligned sequencing reads increase breakpoint disagreements by 2×–16×. Sequence accuracy had a minimal impact on breakpoints, but we observe a strong effect of ancestry. We confirm that SNP and indel polymorphisms are enriched at shifted breakpoints and are also absent from variant callsets. Breakpoint homology increases the likelihood of imprecise SV calls and the distance they are shifted, and tandem duplications are the most heavily affected SVs. Because graph genome methods normalize SV calls across samples, we investigated graphs generated by two different methods and find the resulting breakpoints are subject to other technical biases affecting breakpoint accuracy. The breakpoint inconsistencies we characterize affect ∼5% of the SVs called in a human genome and can impact variant interpretation and annotation. These limitations underscore a need for algorithm development to improve SV databases, mitigate the impact of ancestry on breakpoints, and increase the value of callsets for investigating breakpoint features.