Miracle-dz/UniFAR-FTUs huggingface dataset:
Dust-scattered X-ray halos around two Swift gamma-ray bursts: GRB 061019 and GRB 070129

Two new expanding X-ray rings were detected by the Swift XRT instrument during early follow-up observations of GRB 061019 and GRB 070129, increasing to 5 the number of dust scattering X-ray halos observed around GRBs. Although these two halos were particularly faint, a sensitive analysis can be performed that optimizes the method originally developed by Tiengo & Mereghetti (2006, A&A, 449, 203) to analyze dust scattering rings observed with XMM-Newton for the Swift satellite. In the case of GRB 061019, a known giant molecular cloud is identified as the one responsible for the scattering process, and its distance is accurately measured (d = 940 ± 40 pc) through the dynamics of the expanding ring. In the second case, XRT observed both the main peak of the prompt emission of GRB 070129 and the scattering halo, but the small number of detected halo photons prevents us from distinguish between different dust models.
Fingerprint enhancement by directional Fourier filtering

A new method of enhancing fingerprint images is described, based upon nonstationary directional Fourier domain filtering. Fingerprints are first smoothed using a directional filter whose orientation is everywhere matched to the local ridge orientation. Thresholding then yields the enhanced image. Various simplifications lead to efficient implementation on general-purpose digital computers. Results of enhancement are presented for fingerprints of various pattern classifications. A comparison is made with the enhancement used within the automated fingerprint identification system (AFIS) developed by the UK Home Office. Use of the proposed enhancement method leads to significant improvements in the speed and accuracy of the AFIS.
Soil microbiome analysis reveals effects of periodic waterlogging stress on sugarcane growth

Sugarcane is one of the major agricultural crops with high economic importance in Thailand. Periodic waterlogging has a long-term negative effect on sugarcane development, soil properties, and microbial diversity, impacting overall sugarcane production. Yet, the microbial structure in periodically waterlogged sugarcane fields across soil compartments and growth stages in Thailand has not been documented. This study investigated soil and rhizosphere microbial communities in a periodic waterlogged field in comparison with a normal field in a sugarcane plantation in Ratchaburi, Thailand, using 16S rRNA and ITS amplicon sequencing. Alpha diversity analysis revealed comparable values in periodic waterlogged and normal fields across all growth stages, while beta diversity analysis highlighted distinct microbial community profiles in both fields throughout the growth stages. In the periodic waterlogged field, the relative abundance of Chloroflexi, Actinobacteria, and Basidiomycota increased, while Acidobacteria and Ascomycota decreased. Beneficial microbes such as Arthrobacter, Azoarcus, Bacillus, Paenibacillus, Pseudomonas, and Streptomyces thrived in the normal field, potentially serving as biomarkers for favorable soil conditions. Conversely, phytopathogens and growth-inhibiting bacteria were prevalent in the periodic waterlogged field, indicating unfavorable conditions. The co-occurrence network in rhizosphere of the normal field had the highest complexity, implying increased sharing of resources among microorganisms and enhanced soil biological fertility. Altogether, this study demonstrated that the periodic waterlogged field had a long-term negative effect on the soil microbial community which is a key determining factor of sugarcane growth.
A refactoring categorization model for software quality improvement

Refactoring, a widely adopted technique, has proven effective in facilitating and reducing maintenance activities and costs. Nonetheless, the effects of applying refactoring techniques on software quality exhibit inconsistencies and contradictions, leading to conflicting evidence on their overall benefit. Consequently, software developers face challenges in leveraging these techniques to improve software quality. Moreover, the absence of a categorization model hampers developers’ ability to decide the most suitable refactoring techniques for improving software quality, considering specific design goals. Thus, this study aims to propose a novel refactoring categorization model that categorizes techniques based on their measurable impacts on internal quality attributes. Initially, the most common refactoring techniques used by software practitioners were identified. Subsequently, an experimental study was conducted using five case studies to measure the impacts of refactoring techniques on internal quality attributes. A subsequent multi-case analysis was conducted to analyze these effects across the case studies. The proposed model was developed based on the experimental study results and the subsequent multi-case analysis. The model categorizes refactoring techniques into green, yellow, and red categories. The proposed model, by acting as a guideline, assists developers in understanding the effects of each refactoring technique on quality attributes, allowing them to select appropriate techniques to improve specific quality attributes. Compared to existing studies, the proposed model emerges superior by offering a more granular categorization (green, yellow, and red categories), and its range is wide (including ten refactoring techniques and eleven internal quality attributes). Such granularity not only equips developers with an in-depth understanding of each technique’s impact but also fosters informed decision-making. In addition, the proposed model outperforms current studies and offers a more nuanced understanding, explicitly highlighting areas of strength and concern for each refactoring technique. This enhancement aids developers in better grasping the implications of each refactoring technique on quality attributes. As a result, the model simplifies the decision-making process for developers, saving time and effort that would otherwise be spent weighing the benefits and drawbacks of various refactoring techniques. Furthermore, it has the potential to help reduce maintenance activities and associated costs.
Pulmonary Hypertension Is Associated With a Higher Risk of Heart Failure Hospitalization and Mortality in Patients With Chronic Kidney Disease: The Jackson Heart Study

Background— African Americans develop chronic kidney disease and pulmonary hypertension (PH) at disproportionately high rates. Little is known whether PH heightens the risk of heart failure (HF) admission or mortality among chronic kidney disease patients, including patients with non–end-stage renal disease. Methods and Results— We analyzed African Americans participants with chronic kidney disease (estimated glomerular filtration rate <60 mL/min per 1.73 m2 or urine albumin/creatinine >30 mg/g) and available echocardiogram-derived pulmonary artery systolic pressure (PASP) from the Jackson Heart Study (N=408). We used Cox models to assess whether PH (PASP>35 mm Hg) was associated with higher rates of HF hospitalization and mortality. In a secondary, cross-sectional analysis, we examined the relationship between cystatin C (a marker of renal function) and PASP and potential mediators, including BNP (B-type natriuretic peptide) and endothelin-1. In our cohort, the mean age was 63±13 years, 70% were female, 78% had hypertension, and 22% had PH. Eighty-five percent of the participants had an estimated glomerular filtration rate >30 mL/min per 1.73 m2. During follow-up, 13% were hospitalized for HF and 27% died. After adjusting for potential confounders, including BNP, PH was found to be associated with HF hospitalization (hazard ratio, 2.37; 95% confidence interval, 1.15–4.86) and the combined outcome of HF hospitalization or mortality (hazard ratio, 1.84; confidence interval, 1.09–3.10). Log cystatin C was directly associated with PASP (adjusted &bgr; =2.5 [95% confidence interval, 0.8–4.1] per standard deviation change in cystatin C). Mediation analysis showed that BNP and endothelin-1 explained 56% and 40%, respectively, of the indirect effects between cystatin C and PASP. Conclusions— Among African Americans with chronic kidney disease, PH, which is likely pulmonary venous hypertension, was associated with a higher risk of HF admission and mortality.
Upregulation of human GD3 synthase (hST8Sia I) gene expression during serum starvation-induced osteoblastic differentiation of MG-63 cells

In this study, we have firstly elucidated that serum starvation augmented the levels of human GD3 synthase (hST8Sia I) gene and ganglioside GD3 expression as well as bone morphogenic protein-2 and osteocalcin expression during MG-63 cell differentiation using RT-PCR, qPCR, Western blot and immunofluorescence microscopy. To evaluate upregulation of hST8Sia I gene during MG-63 cell differentiation by serum starvation, promoter area of the hST8Sia I gene was functionally analyzed. Promoter analysis using luciferase reporter assay system harboring various constructs of the hST8Sia I gene proved that the cis-acting region at -1146/-646, which includes binding sites of the known transcription factors AP-1, CREB, c-Ets-1 and NF-κB, displays the highest level of promoter activity in response to serum starvation in MG-63 cells. The -731/-722 region, which contains the NF-κB binding site, was proved to be essential for expression of the hST8Sia I gene by serum starvation in MG-63 cells by site-directed mutagenesis, NF-κB inhibition, and chromatin immunoprecipitation (ChIP) assay. Knockdown of hST8Sia I using shRNA suggested that expressions of hST8Sia I and GD3 have no apparent effect on differentiation of MG-63 cells. Moreover, the transcriptional activation of hST8Sia I gene by serum starvation was strongly hindered by SB203580, a p38MAPK inhibitor in MG-63 cells. From these results, it has been suggested that transcription activity of hST8Sia I gene by serum starvation in human osteosarcoma MG-63 cells is regulated by p38MAPK/NF-κB signaling pathway.
Exploration of an Prognostic Signature Related to Endoplasmic Reticulum Stress in Colorectal Adenocarcinoma and Their Response Targeting Immunotherapy

Background: Endoplasmic reticulum (ER) stress plays a pro-apoptotic role in colorectal adenocarcinoma (COAD). This study aimed to develop a novel ER-stress-related prognostic risk model for COAD and provide support for COAD cohorts with different risk score responses to immune checkpoint inhibitor therapies. Methods: TCGA-COAD and GSE39582 were included in this prospective study. Univariate and multivariate Cox analyses were performed to identify prognostic ER stress-related genes (ERSGs). Accordingly, the immune infiltration landscape and immunotherapy response in different risk groups were assessed. Finally, the expression of prognostic genes in 10 normal and 10 COAD tissue samples was verified using reverse transcription-quantitative polymerase chain reaction. Results: Eight prognostic genes were selected to establish an ERSG-based signature in the training set of the TCGA-COAD cohort. The accuracy of this was confirmed using a testing set of TCGA-COAD and GSE39582 cohorts. Gene set variation analysis indicated that differential functionality in high–low-risk groups was related to immune-related pathways. Corresponding to this, CD36, TIMP1, and PTGIS were significantly associated with 19 immune cells with distinct proportions between the different risk groups, such as central memory CD4T cells and central memory CD8T cells. Moreover, the risk score was considered effective for predicting the clinical response to immunotherapy, and the immunotherapy response was significantly and negatively correlated with the risk score of individuals with COAD. Furthermore, the immune checkpoint inhibitor treatment was less effective in the high-risk group, where the expression levels of PD-L1 and tumor immune dysfunction and exclusion scores in the high-risk group were significantly increased. Finally, the experimental results demonstrated that the expression trends of prognostic genes in clinical samples were consistent with the results from public databases. Conclusion: Our study established a novel risk signature to predict the COAD prognosis of patients and provide theoretical support for the clinical treatment of COAD.
Can machine learning methods be used for identification of at-risk neonates in low-resource settings? A prospective cohort study

Introduction Timely identification of at-risk neonates (ARNs) in the community is essential to reduce mortality in low-resource settings. Tools such as American Academy of Pediatrics pulse oximetry (POx) and WHO Young Infants Clinical Signs (WHOS) have high specificity but low sensitivity to identify ARNs. Our aim was assessing the value of POx and WHOS independently, in combination and with machine learning (ML) from clinical features, to detect ARNs in a low/middle-income country. Methods This prospective cohort study was conducted in a periurban community in Pakistan. Eligible live births were screened using WHOS and POx along with clinical information regarding pregnancy and delivery. The enrolled neonates were followed for 4 weeks of life to assess the vital status. The predictive value to identify ARNs, of POx, WHOS and an ML model using maternal and neonatal clinical features, was assessed. Results Of 1336 neonates, 68 (5%) had adverse outcomes, that is, sepsis (n=40, 59%), critical congenital heart disease (n=2, 3%), severe persistent pulmonary hypertension (n=1), hospitalisation (n=8, 12%) and death (n=17, 25%) assessed at 4 weeks of life. Specificity of POx and WHOS to independently identify ARNs was 99%, with sensitivity of 19% and 63%,respectively. Combining both improved sensitivity to 70%, keeping specificity at 98%. An ML model using clinical variables had 44% specificity and 76% sensitivity. A staged assessment, where WHOS, POx and ML are sequentially used for triage, increased sensitivity to 85%, keeping specificity 75%. Using ML (when WHOS and POx negative) for community follow-up detected the majority of ARNs. Conclusion Classic screening, combined with ML, can help maximise identifying ARNs and could be embedded in low-resource clinical settings, thereby improving outcome. Sequential use of classic assessment and clinical ML identifies the most ARNs in the community, still optimising follow-up clinical care.
A Meta-Analysis of the Effects of Taekwondo on Physical Self-Concept

In this meta-analysis we explored whether Taekwondo practice has improved its participants’ physical self-concepts. We also tested the mediating influence of factors in past research such as country, participant age, and measurement properties in their associations with these taekwondo effects. We reviewed extensive data collected from Chinese, English and Korean participants in articles listed in Cnki, Wanfang, PubMed, Web of Science, KISS, RISS, and DBPIA databases. First, we evaluated the methodological quality of these published articles with Review Manager 5.4 software according to the Cochrane System Evaluation Manual. Then, we used Comprehensive Meta-Analysis 3.7 software for statistical analysis. We based these analyses on nine research studies containing a total of 1154 participants. We found a significant association between taekwondo activity and an improved body self-concept (ES = .688, p < .001). Subgroup analyses showed a stronger association between these variables in Korea (ES = .90, p < .001) than in China (ES = .34, p < .001), a stronger association for children (ES = 1.04, p < .001) compared to adults (ES = .46, p < .001), and a stronger association with the modified version of the Physical Self-Description Questionnaire (PSDQ) (ES = .99, p < .001) than with the original PSDQ (ES = .57, p < .001). We concluded that practicing Taekwondo led to improved physical self-concept, especially in a younger population. In addition, the experimental design and measurement methods may influence the apparent link between these variables.
Successful MRI-Guided Focused Ultrasound Thalamotomy after Ipsilateral Gamma Knife Radiosurgery for Essential Tremor: A Case Report with Video

We report the case of a 67-year-old left-handed female patient with disabling medically refractory essential tremor who underwent successful right-sided magnetic resonance-guided focused ultrasound (MRgFUS) of the ventral intermediate nucleus after ipsilateral gamma knife radiosurgery (GKRS) thalamotomy performed 3 years earlier. The GKRS had a partial effect on her postural tremor without side effects, but there was no reduction of her kinetic tremor or improvement in her quality of life (QoL). The patient subsequently underwent a MRgFUS thalamotomy, which induced an immediate and marked reduction in both the postural and kinetic tremor components, with minor complications (left upper lip hypesthesia, dysmetria in her left hand, and slight gait ataxia). The MRgFUS-induced lesion was centered more medially than the GKRS-induced lesion and extended more posteriorly and inferiorly. The MRgFUS-induced lesion interrupted remaining fibers of the dentatorubrothalamic tract (DRTT). The functional improvement 1-year post-MRgFUS was significant due to a marked reduction of the patient’s kinetic tremor. The QoL score (Quality of Life in Essential Tremor) improved by 88% and her Clinical Rating Scale for Tremor left hand score by 62%. The side effects persisted but were minor, with no impact on her QoL. The explanation for the superior efficacy of MRgFUS compared to GKRS in our patient could be due to either a poor response to the GKRS or to a better localization of the MRgFUS lesion with a more extensive interruption of DRTT fibers. In conclusion, MRgFUS can be a valuable therapeutic option after unsatisfactory GKRS, especially because MRgFUS has immediate clinical effectiveness, allowing intra-procedural test lesions and possible readjustment of the target if necessary.
Intraperitoneal administration of a modified vaccinia virus Ankara confers single-chain interleukin-12 expression to the omentum and achieves immune-mediated efficacy against peritoneal carcinomatosis

Background Peritoneal carcinomatosis is an advanced stage of cancer in which the disease has spread to the peritoneal cavity. In order to restore antitumor immunity subverted by tumor cells in this location, we evaluated intraperitoneal administrations of modified vaccinia virus Ankara (MVA) engineered to express single-chain interleukin 12 (scIL-12) to increase antitumor immune responses. Methods MVA encoding scIL-12 (MVA.scIL-12) was evaluated against peritoneal carcinomatosis models based on intraperitoneal engraftment of tumor cells. CD8-mediated immune responses, elucidated antitumor efficacy, and safety were evaluated following intravenous, intratumoral, or intraperitoneal administration of the viral vector. The immune response was measured by ELISpot (enzyme-linked immunosorbent spot), RNA sequencing, flow cytometry, intravital microscopy, and depletion of lymphocyte subsets with monoclonal antibodies. Safety was assessed by body-weight follow-up and blood testing. Tissue tropism on intravenous or intraperitoneal administration was assessed by bioluminescence analysis using a reporter MVA encoding luciferase. Results Intraperitoneal or locoregional administration, but not other routes of administration, resulted in a potent immune response characterized by increased levels of tumor-specific CD8+ T lymphocytes with the ability to produce both interferon-γ and tumor necrosis factor-α. The antitumor immune response was detectable not only in the peritoneal cavity but also systemically. As a result of intraperitoneal treatment, a single administration of MVA.scIL-12 encoding scIL-12 completely eradicated MC38 tumors implanted in the peritoneal cavity and also protected cured mice from subsequent subcutaneous rechallenges. Bioluminescence imaging using an MVA encoding luciferase revealed that intraperitoneal administration targets transgene to the omentum. The omentum is considered a key tissue in immune protection of the peritoneal cavity. The safety profile of intraperitoneal administration was also better than that following intravenous administration since no weight loss or hematological toxicity was observed when the vector was locally delivered into the peritoneal cavity. Conclusion Intraperitoneal administration of MVA vectors encoding scIL-12 targets the omentum, which is the tissue where peritoneal carcinomatosis usually begins. MVA.scIL-12 induces a potent tumor-specific immune response that often leads to the eradication of experimental tumors disseminated to the peritoneal cavity.
The apelin-apelin receptor signaling pathway in fibroblasts is involved in tumor growth via p53 expression of cancer cells

Cancer-associated fibroblasts (CAFs) are pivotal in tumor progression. TP53-deficiency in cancer cells is associated with robust stromal activation. The apelin-apelin receptor (APJ) system has been implicated in suppressing fibroblast-to-myofibroblast transition in non-neoplastic organ fibrosis. The present study aimed to elucidate the oncogenic role of the apelin-APJ system in tumor fibroblasts. APJ expression and the effect of APJ suppression in fibroblasts were investigated for p53 status in cancer cells using human cell lines (TP53-wild colon cancer, HCT116, and Caco-2; TP53-mutant colon cancer, SW480, and DLD-1; and colon fibroblasts, CCD-18Co), resected human tissue samples of colorectal cancers, and immune-deficient nude mouse xenograft models. The role of exosomes collected by ultracentrifugation were also analyzed as mediators of p53 expression in cancer cells and APJ expression in fibroblasts. APJ expression in fibroblasts co-cultured with p53-suppressed colon cancer cells (HCT116sh p53 cells) was significantly lower than in control colon cancer cells (HCT116sh control cells). APJ-suppressed fibroblasts treated with an antagonist or small interfering RNA showed myofibroblast-like properties, including increased proliferation and migratory abilities, via accelerated phosphorylation of Sma- and Mad-related protein 2/3 (Smad2/3). In addition, xenografts of HCT116 cells with APJ-suppressed fibroblasts showed accelerated tumor growth. By contrast, apelin suppressed the upregulation of phosphorylated Smad2/3 in fibroblasts. MicroRNA 5703 enriched in exosomes derived from HCT116sh p53 cells inhibited APJ expression, and inhibition of miR-5703 diminished APJ suppression in fibroblasts caused by cancer cells. APJ suppression from a specific microRNA in cancer cell-derived exosomes induced CAF-like properties in fibroblasts. Thus, the APJ system in fibroblasts in the tumor microenvironment may be a promising therapeutic target.