Miracle-dz/UniFAR-FTUs huggingface dataset:
Co-infection With Hepatitis B in Tuberculosis Patients on Anti-tuberculosis Treatment and the Final Outcome

Background The occurrence of both tuberculosis (TB) and concomitant hepatitis B virus (HBV) is likely to be associated with poor patient outcomes and poor treatment response. Objective To assess whether tuberculosis patients with concomitant hepatitis B virus infection were prone to poorer outcomes and treatment response. Methodology A case-control study was undertaken at the Tuberculosis Centre, DHQ Bagh Azad Kashmir and Pulmonology Department, Lady Reading Hospital, Peshawar, between March 2020 and August 2020. All patients with diagnosed tuberculosis and coinfection with hepatitis B were labeled as the case group while those with only tuberculosis acted as the control. All patients with tuberculosis were managed on a directly observed treatment strategy (DOTS). Non-compliant patients and those without complete data were excluded from the study. All data regarding socio-demographics, laboratory investigations, and clinical characteristics were recorded in a predefined proforma. Patients were considered to have good treatment outcomes when patients completed the treatment or had a negative smear at six months of treatment. The Statistical Package for the Social Sciences (SPSS) version 26 (IBM Corp, Armonk, NY) was used for the data analysis. Results A total of 178 patients were enrolled in the study. It was found that patients with concomitant hepatitis B had significantly poorer outcomes as compared to patients who did not have hepatitis B (<0.001). Similarly, TB and hepatitis B patients were significantly associated with severe tuberculosis (<0.001) and required a higher frequency of retreatment (<0.001). Conclusion Our study reports a strong association between the treatment response of patients with tuberculosis with an added hepatitis B infection. Furthermore, a larger number of patients with hepatitis B had severe tuberculosis as compared to those without hepatitis B.
Breathing in vitro: Designs and applications of engineered lung models

The aim of this review is to provide a systematic design guideline to users, particularly engineers interested in developing and deploying lung models, and biologists seeking to identify a suitable platform for conducting in vitro experiments involving pulmonary cells or tissues. We first discuss the state of the art on lung in vitro models, describing the most simplistic and traditional ones. Then, we analyze in further detail the more complex dynamic engineered systems that either provide mechanical cues, or allow for more predictive exposure studies, or in some cases even both. This is followed by a dedicated section on microchips of the lung. Lastly, we present a critical discussion of the different characteristics of each type of system and the criteria which may help researchers select the most appropriate technology according to their specific requirements. Readers are encouraged to refer to the tables accompanying the different sections where comprehensive and quantitative information on the operating parameters and performance of the different systems reported in the literature is provided.
Modulation of Pro-inflammatory and Anti-inflammatory Cytokines in the Fat by an Aloe Gel-based Formula, QDMC, Is Correlated with Altered Gut Microbiota

Abnormal inflammatory responses are closely associated with intestinal microbial dysbiosis. Oral administration of Qmatrix-diabetes-mellitus complex (QDMC), an Aloe gel-based formula, has been reported to improve inflammation in type 2 diabetic mice; however, the role of the gut microbiota in ameliorating efficacy of QDMC remains unclear. We investigated the effect of QDMC on the gut microbiota in a type 2 diabetic aged mouse model that was administered a high-fat diet. Proinflammatory (TNF-α and IL-6) and anti-inflammatory (IL-4 and IL-10) cytokine levels in the fat were normalized via oral administration of QDMC, and relative abundances of Bacteroides, Butyricimonas, Ruminococcus, and Mucispirillum were simultaneously significantly increased. The abundance of these bacteria was correlated to the expression levels of cytokines. Our findings suggest that the immunomodulatory activity of QDMC is partly mediated by the altered gut microbiota composition.
Cannabinoid Receptor 1 rs1049353 Variant, Childhood Abuse, and the Heterogeneity of PTSD Symptoms: Results From the National Health and Resilience in Veterans Study

Background Accumulating evidence implicates the endocannabinoid system, including variants in the cannabinoid-1 receptor gene (CNR1), in the pathophysiology of posttraumatic stress disorder (PTSD). The synonymous G1359A variant (rs1049353) in the CNR1 gene has been linked to PTSD in individuals exposed to childhood abuse. In this study, the effects of the rs1049353 genotype and childhood abuse on overall PTSD symptoms, as well as PTSD symptom clusters were examined in order to examine how this interaction relates to the phenotypic expression of this disorder. Method Data were analyzed from 1,372 Caucasian U.S. veterans who participated in the National Health and Resilience in Veterans Study. Multivariable analyses were conducted to evaluate the association between rs1049353 genotype, childhood abuse, and their interaction in relation to PTSD symptoms. Results A significant interaction between rs1049353 genotype and childhood abuse was observed, with A allele carriers with histories of childhood abuse reporting greater severity of PTSD symptoms, most notably anxious arousal, relative to G/G homozygotes. Significant main effects of childhood abuse on overall PTSD symptoms, and re-experiencing, emotional numbing, and dysphoric arousal symptom clusters, as well as of A allele carrier status on anxious arousal symptoms were observed. Conclusions Results of this study replicate prior work and suggest that the rs1049353-by-childhood abuse interaction is particularly associated with the manifestation of anxious arousal symptoms of PTSD. Taken together, these findings underscore the importance of considering the phenotypic heterogeneity of PTSD in gene-environment studies of this multifaceted disorder.
Comparison Between Hip Arthroscopic Surgery and Periacetabular Osteotomy for the Treatment of Patients With Borderline Developmental Dysplasia of the Hip: A Systematic Review

Background: The treatment for borderline developmental dysplasia of the hip (BDDH) has historically been arthroscopic surgery or periacetabular osteotomy (PAO). As orthopaedic surgery is constantly evolving, a lack of comparison of outcomes for these 2 treatment methods could potentially be stalling the progression of treatment for patients with BDDH. Purpose: To evaluate the existing literature on patient characteristics, procedures, clinical outcomes, and failure rates for patients with BDDH and to determine whether PAO or hip arthroscopic surgery is a better treatment method for patients with BDDH. Study Design: Systematic review; Level of evidence, 4. Methods: Studies included were found using the following search words: “hip” and “borderline dysplasia,” “osteotomy” or “arthroscopy,” and “outcome” or “procedure. ” Articles were included if they detailed participants of all sexes and ages, reported on isolated hips, and had patients diagnosed with BDDH. Results: A search was conducted across 3 databases, resulting in 469 articles for consideration, from which 12 total studies (10 on arthroscopic surgery and 2 on PAO) were chosen for a review. There were 6 studies that included patients with a lateral center-edge angle of 18° to 25°, while the remainder included patients with a lateral center-edge angle of 20° to 25°. All the studies reviewing arthroscopic surgery reported concomitant/accessory procedures, while the articles on the topic of PAO did not. It was determined that, whether treated using arthroscopic surgery or PAO, outcomes improved across all patient-reported outcome measures. Revision surgery was also common in both procedures. Conclusion: There is a lack of consensus in the literature on the best treatment option for patients with BDDH. Preoperative patient characteristics and concomitant injuries should be considered when evaluating which surgical procedure will result in the most favorable outcomes.
Comparison of two methods for prolong storage of decellularized mouse whole testis for tissue engineering application: An experimental study

Abstract Background Biological scaffolds are derived by the decellularization of tissues or organs. Various biological scaffolds, such as scaffolds for the liver, lung, esophagus, dermis, and human testicles, have been produced. Their application in tissue engineering has created the need for cryopreservation processes to store these scaffolds. Objective The aim was to compare the two methods for prolong storage testicular scaffolds. Materials and Methods In this experimental study, 20 male NMRI mice (8 wk) were sacrificed and their testes were removed and treated with 0.5% sodium dodecyl sulfate followed by Triton X-100 0.5%. The efficiency of decellularization was determined by histology and DNA quantification. Testicular scaffolds were stored in phosphate-buffered saline solution at 4°C or cryopreserved by programmed slow freezing followed by storage in liquid nitrogen. Masson's trichrome staining, Alcian blue staining and immunohistochemistry, collagen assay, and glycosaminoglycan assay were done prior to and after six months of storage under each condition. Results Hematoxylin-eosin staining showed no remnant cells after the completion of decellularization. DNA content analysis indicated that approximately 98% of the DNA was removed from the tissue (p = 0.02). Histological evaluation conﬁrmed the preservation of extracellular matrix components in the fresh and frozen-thawed scaffolds. Extracellular matrix components were decreased by 4°C-stored scaffolds. Cytotoxicity tests with mouse embryonic fibroblast showed that the scaffolds were biocompatible and did not have a harmful effect on the proliferation of mouse embryonic fibroblast cells. Conclusion Our results demonstrated the superiority of the slow freezing method for prolong storage of testicular scaffolds.
Repeated ecological and life cycle transitions make salamanders an ideal model for evolution and development

Observations on the ontogeny and diversity of salamanders provided some of the earliest evidence that shifts in developmental trajectories have made a substantial contribution to the evolution of animal forms. Since the dawn of evo‐devo there have been major advances in understanding developmental mechanisms, phylogenetic relationships, evolutionary models, and an appreciation for the impact of ecology on patterns of development (eco‐evo‐devo). Molecular phylogenetic analyses have converged on strong support for the majority of branches in the Salamander Tree of Life, which includes 764 described species. Ancestral reconstructions reveal repeated transitions between life cycle modes and ecologies. The salamander fossil record is scant, but key Mesozoic species support the antiquity of life cycle transitions in some families. Colonization of diverse habitats has promoted phenotypic diversification and sometimes convergence when similar environments have been independently invaded. However, unrelated lineages may follow different developmental pathways to arrive at convergent phenotypes. This article summarizes ecological and endocrine‐based causes of life cycle transitions in salamanders, as well as consequences to body size, genome size, and skeletal structure. Salamanders offer a rich source of comparisons for understanding how the evolution of developmental patterns has led to phenotypic diversification following shifts to new adaptive zones.
Civil Commitment for Substance Use Disorders: A National Survey of Addiction Medicine Physicians

Background: Civil commitment (CC) for substance use disorders (SUDs) is a legal mechanism, initiated by family members, healthcare professionals, or others, that compels individuals with substance use problems into involuntary treatment. With the recent rise of US overdose deaths, more states are considering these laws. Yet little is known about physicians’ perspectives regarding CC in treating patients with SUDs. Methods: We conducted a web-based survey of American Society of Addiction Medicine (ASAM) physician members regarding their awareness of, attitudes towards, and experiences with CC for adults with SUDs. Results: One hundred sixty-five addiction physicians completed the survey; 60.7% favored, 21.5% opposed, and 17.8% were unsure regarding CC for SUDs. More than a third (38.4%) were unfamiliar with these laws and more than a quarter (28.8%) were unsure if CC for SUDs was permitted in their state. Support for CC was strongest for SUDs involving heroin (79.0%), alcohol (74.7%), and nonheroin opioids (74.7%). Those opposing CC were more likely to believe it would jeopardize patient rapport (P < 0.001), would be ineffective for unmotivated individuals (P < 0.001), and should only be permitted for certain substances (P = 0.007). A majority of respondents endorsed the need for more clinician education (91.5%) and research (87.1%) on this topic. Conclusions: Although most addiction physicians in this study approve of CC for SUDs, enthusiasm for this compulsory intervention is mixed with strongest support for patients with opioid and alcohol use disorders. At the same time, many respondents are unfamiliar with these laws and most believe more education and research are needed.
Functional Connectivity-Based Prediction of Autism on Site Harmonized ABIDE Dataset

Objective: The larger sample sizes available from multi-site publicly available neuroimaging data repositories makes machine-learning based diagnostic classification of mental disorders more feasible by alleviating the curse of dimensionality. However, since multi-site data are aggregated post-hoc, i.e. they were acquired from different scanners with different acquisition parameters, non-neural inter-site variability may mask inter-group differences that are at least in part neural in origin. Hence, the advantages gained by the larger sample size in the context of machine-learning based diagnostic classification may not be realized. Methods: We address this issue using harmonization of multi-site neuroimaging data using the ComBat technique, which is based on an empirical Bayes formulation to remove inter-site differences in data distributions, to improve diagnostic classification accuracy. Specifically, we demonstrate this using ABIDE (Autism Brain Imaging Data Exchange) multi-site data for classifying individuals with Autism from healthy controls using resting state fMRI-based functional connectivity data. Results: Our results show that higher classification accuracies across multiple classification models can be obtained (especially for models based on artificial neural networks) from multi-site data post harmonization with the ComBat technique as compared to without harmonization, outperforming earlier results from existing studies using ABIDE. Furthermore, our network ablation analysis facilitated important insights into autism spectrum disorder pathology and the connectivity in networks shown to be important for classification covaried with verbal communication impairments in Autism. Conclusion: Multi-site data harmonization using ComBat improves neuroimaging-based diagnostic classification of mental disorders. Significance: ComBat has the potential to make AI-based clinical decision-support systems more feasible in psychiatry.
Early Observation of Red Flags in 12-Month-Old Infant Siblings Later Diagnosed With Autism Spectrum Disorder.

Purpose Valid and reliable screening tools are needed to improve early detection and optimize developmental outcomes for toddlers at risk for autism spectrum disorder (ASD). The current study aimed to evaluate the utility of the Systematic Observation of Red Flags (SORF) for ASD at 12 months of age in a sample of high-risk infant siblings of children with ASD. Method As part of a prospective, longitudinal study, we examined the sensitivity and specificity of the SORF at 12 months for predicting a diagnosis of ASD at 24 months in a sample of 122 infants, 31 of whom were diagnosed with ASD. Results The optimal SORF Composite cutoff score of 18 correctly identified 24 of the 31 twelve-month-olds who were diagnosed with ASD, yielding a sensitivity of . 77 and a specificity of . 76. The optimal SORF Red Flags cutoff score of 7 correctly identified 20 of the 31 infants, yielding a sensitivity of . 65 and a specificity of . 75. Conclusion This preliminary study demonstrates the potential of the SORF as an effective observational screening measure for 12-month-olds at risk for ASD with good discrimination, sensitivity, and specificity.
Acute kidney injury in COVID-19: are kidneys the target or just collateral damage? A comprehensive assessment of viral RNA and AKI rate in patients with COVID-19

Purpose of review To investigate the possible effects of severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) on kidney function and assess the rate of viral ribonucleic acid (RNA) shedding/detection in urine. Recent findings Most of the research on the topic suggests that for the moment our ability to estimate whether SARS-CoV-2 is a direct causative agent in acute kidney injury (AKI) or whether it has a cytokine storm effect is limited. During our prospective assessment of 333 patients with COronaVIrus Disease 2019 (COVID-19) it was found that frequency of AKI of 9.6% (32 cases). Despite previous data suggestive of the ability to detect SARS-CoV-2 in urine, we were unable to identify any traces of messenger ribonucleic acid (mRNA) in our group. Both COVID-19 severity (odds ratio, OR = 23.09, confidence interval, CI 7.89–67.57, P < 0.001) and chronic kidney disease (CKD) history (OR = 7.17, CI 2.09–24.47, P = 0.002) were associated with the AKI rate. Summary AKI is a relatively frequent condition for patients with COVID-19 and is normally correlated with the severity of the disease and the patient's history of CKD. The available data fail to address whether SARS-CoV-2 mRNA is present in urine, whereas our prospective trial data suggest that mRNA is undetectable in urine irrespective of the severity of the disease.
Assessment of Imaging Modalities Against Liver Biopsy in Nonalcoholic Fatty Liver Disease: The Amsterdam NAFLD‐NASH Cohort

Noninvasive diagnostic methods are urgently required in disease stratification and monitoring in nonalcoholic fatty liver disease (NAFLD). Multiparametric magnetic resonance imaging (MRI) is a promising technique to assess hepatic steatosis, inflammation, and fibrosis, potentially enabling noninvasive identification of individuals with active and advanced stages of NAFLD.
Clinical and radiographic outcome of the root canal treatment of infected teeth with associated sinus tract: A retrospective study.

This retrospective study evaluated the outcome of the endodontic treatment/retreatment of teeth with intraoral sinus tracts. Seventy-two teeth from 70 individuals were included. One operator treated all teeth over about 20 years. Time for the sinus tract to heal was recorded. Treatment outcome was evaluated after at least 1 year and classified as healed, healing or diseased. The overall healed rate of periradicular lesions was 73.6% (74.1% for treatment and 72.2% for retreatment). In 6 (8.3%) teeth, lesions were healing. Thirteen teeth (18.1%) exhibited persistent disease. In 68/72 (94.4%) cases, the sinus tract healed in less than 1 month. No preoperative/intraoperative variable affected the outcome (P > 0.05). Missing restorations had a negative impact (P < 0.05). Healing of both the sinus tract quickly after treatment and the periradicular lesion later were usually achieved. Closure of the sinus tract in the first month was a good predictor of lesion healing.
Inhibiting xCT/SLC7A11 induces ferroptosis of myofibroblastic hepatic stellate cells but exacerbates chronic liver injury

The outcome of liver injury is dictated by factors that control the accumulation of myofibroblastic (activated) hepatic stellate cells (MF‐HSCs) but therapies that specifically block this process have not been discovered. We evaluated the hypothesis that MF‐HSCs and liver fibrosis could be safely reduced by inhibiting the cysteine/glutamate antiporter xCT.
Esophageal fistula after definitive concurrent chemotherapy and intensity modulated radiotherapy for esophageal squamous cell carcinoma

Background The literature regarding esophageal fistula after definitive concurrent chemotherapy and intensity modulated radiotherapy (IMRT) for esophageal squamous cell carcinoma (ESCC) remains lacking. We aimed to investigate the risk factors of esophageal fistula among ESCC patients undergoing definitive concurrent chemoradiotherapy (CCRT) via IMRT technique. Methods A total of 129 consecutive ESCC patients receiving definitive CCRT with IMRT between 2008 and 2018 were reviewed. The cumulative incidence of esophageal fistula and survival of patients were estimated by the Kaplan–Meier method and compared between groups by the log-rank test. The risk factors of esophageal fistula were determined with multivariate Cox proportional hazards regression analysis. Results Median follow-up was 14.9 months (IQR, 7.0–28.8). Esophageal perforation was identified in 20 (15.5%) patients, resulting in esophago-pleural fistula in nine, esophago-tracheal fistula in seven, broncho-esophageal fistula in two, and aorto-esophageal fistula in two patients. The median interval from IMRT to the occurrence of esophageal fistula was 4.4 months (IQR, 3.3–10.1). Patients with esophageal fistula had an inferior median overall survival (10.0 vs. 17.2 months, p = 0.0096). T4 (HR, 3.776; 95% CI, 1.383–10.308; p = 0.010) and esophageal stenosis (HR, 2.601; 95% CI, 1.053–6.428; p = 0.038) at baseline were the independent risk factors for esophageal fistula. The cumulative incidence of esophageal fistula was higher in patients with T4 (p = 0.018) and pre-treatment esophageal stenosis (p = 0.045). There was a trend toward better survival after esophageal fistula among patients receiving repair or stenting for the fistula than those only undergoing conservative treatments (median survival, 5.9 vs. 0.9 months, p = 0.058). Conclusions T4 and esophageal stenosis at baseline independently increased the risk of esophageal fistula in ESCC treated by definitive CCRT with IMRT. There existed a trend toward improved survival after the fistula among patients receiving repair or stenting for esophageal perforation.
Evolution of virulence in a novel family of transmissible mega-plasmids.

Some Serratia entomophila isolates have been successfully exploited in biopesticides due to their ability to cause amber disease in larvae of the Aotearoa (New Zealand) endemic pasture pest, Costelytra giveni. Anti-feeding prophage and ABC toxin complex virulence determinants are encoded by a 153-kb single-copy conjugative plasmid (pADAP; amber disease-associated plasmid). Despite growing understanding of the S. entomophila pADAP model plasmid, little is known about the wider plasmid family. Here, we sequence and analyze mega-plasmids from 50 Serratia isolates that induce variable disease phenotypes in the C. giveni insect host. Mega-plasmids are highly conserved within S. entomophila, but show considerable divergence in Serratia proteamaculans with other variants in S. liquefaciens and S. marcescens, likely reflecting niche adaption. In this study to reconstruct ancestral relationships for a complex mega-plasmid system, strong co-evolution between Serratia species and their plasmids were found. We identify twelve distinct mega-plasmid genotypes, all sharing a conserved gene backbone, but encoding highly variable accessory regions including virulence factors, secondary metabolite biosynthesis, Nitrogen fixation genes and toxin-antitoxin systems. We show that the variable pathogenicity of Serratia isolates is largely caused by presence/absence of virulence clusters on the mega-plasmids, but notably, is augmented by external chromosomally encoded factors. This article is protected by copyright. All rights reserved.