Efficient taxa identification using a pangenome index.

Tools that classify sequencing reads against a database of reference sequences require efficient index data-structures. The r-index is a compressed full-text index that answers substring presence/absence, count, and locate queries in space proportional to the amount of distinct sequence in the database: [Formula: see text] space, where r is the number of Burrows-Wheeler runs. To date, the r-index has lacked the ability to quickly classify matches according to which reference sequences (or sequence groupings, i.e., taxa) a match overlaps. We present new algorithms and methods for solving this problem. Specifically, given a collection D of d documents, [Formula: see text] over an alphabet of size σ, we extend the r-index with [Formula: see text] additional words to support document listing queries for a pattern [Formula: see text] that occurs in [Formula: see text] documents in D in [Formula: see text] time and [Formula: see text] space, where w is the machine word size. Applied in a bacterial mock community experiment, our method is up to three times faster than a comparable method that uses the standard r-index locate queries. We show that our method classifies both simulated and real nanopore reads at the strain level with higher accuracy compared with other approaches. Finally, we present strategies for compacting this structure in applications in which read lengths or match lengths can be bounded.

Sigmoni: classification of nanopore signal with a compressed pangenome index.

SUMMARY: Improvements in nanopore sequencing necessitate efficient classification methods, including pre-filtering and adaptive sampling algorithms that enrich for reads of interest. Signal-based approaches circumvent the computational bottleneck of basecalling. But past methods for signal-based classification do not scale efficiently to large, repetitive references like pangenomes, limiting their utility to partial references or individual genomes. We introduce Sigmoni: a rapid, multiclass classification method based on the r-index that scales to references of hundreds of Gbps. Sigmoni quantizes nanopore signal into a discrete alphabet of picoamp ranges. It performs rapid, approximate matching using matching statistics, classifying reads based on distributions of picoamp matching statistics and co-linearity statistics, all in linear query time without the need for seed-chain-extend. Sigmoni is 10-100× faster than previous methods for adaptive sampling in host depletion experiments with improved accuracy, and can query reads against large microbial or human pangenomes. Sigmoni is the first signal-based tool to scale to a complete human genome and pangenome while remaining fast enough for adaptive sampling applications. AVAILABILITY AND IMPLEMENTATION: Sigmoni is implemented in Python, and is available open-source at https://github.com/vshiv18/sigmoni.

Comparison of chest radiographs against minimum intensity projection reconstruction computed tomography scans for detection of airway stenosis in children with lymphobronchial tuberculosis.

BACKGROUND: Ideally, suspected airway compression in symptomatic children with lymphobronchial tuberculosis (TB) would be diagnosed using modern computed tomography (CT) assisted by coronal minimum intensity projection (MinIP) reconstructions. However, in TB-endemic regions with limited resources, practitioners rely on conventional radiography for diagnosing TB and its complications. Furthermore, airway compression detected on conventional radiographs would upgrade a patient into the severe category according to the new World Health Organization guidelines, precluding the patient from shorter treatment protocols. The accuracy of conventional radiographs in the context of detecting airway compression in children with TB has not been specifically evaluated against an imaging gold standard. OBJECTIVE: We aimed to compare frontal chest radiographs against thick-slab angled coronal CT MinIP in identifying airway stenosis at ten specific sites and to determine observer agreement between the modalities regarding the degree of stenosis. MATERIALS AND METHODS: This retrospective cross-sectional study compared chest radiographs with standardized angled coronal CT MinIP in children with symptomatic lymphobronchial TB at ten predetermined airway locations. Chest radiographs were evaluated by one pediatric radiologist and CT MinIP reconstructions were independently interpreted by three readers. Sensitivity and specificity were calculated using CT MinIP as the gold standard. Stenosis was graded as 1 for mild (1-50%), 2 for moderate (51-75%), 3a for severe (76-99%), and 3b for total occlusion (100%). Agreement between the two modalities regarding severity of stenosis was calculated using the kappa coefficient for each affected site. RESULTS: A total of 37 patients were included in the study. The median age of patients was 14.3 months (interquartile range 8.0-23.2). Three hundred and seventy individual bronchi (10 from each of the 37 patients) were evaluated for stenosis. Chest radiographs showed that 31 out of 37 (84%) patients had stenosis in at least one of ten evaluated sites, most commonly the left main bronchus and bronchus intermedius, and this was confirmed via CT MinIP. The gold standard (CT MinIP) demonstrated stenosis in at least one of ten sites in all 37 patients (100%). Left main bronchus stenosis was detected by chest radiography with a 92.9% sensitivity and 100% specificity. Sensitivity and specificity for bronchus intermedius stenosis were 80% and 75%, respectively. There was substantial agreement for grade of stenosis between chest radiographs and CT (kappa=0.67) for the left main bronchus and moderate agreement (kappa=0.58) for the bronchus intermedius. Severe stenosis was found in 78 bronchi on CT compared to 32 bronchi (Grade 3a: 9, Grade 3b: 23) on chest radiographs. CONCLUSION: The diagnosis of pulmonary TB in children continues to rely heavily on imaging, and we have shown that in young children, chest radiographs had a high sensitivity and specificity for detecting airway stenosis at certain anatomical sites, when adequately visualized, resulting from tuberculous lymph node compression at left main bronchus and bronchus intermedius. For most sites, the interobserver agreement was poor. Stenosis of the left main bronchus and bronchus intermedius should be the focus of chest radiograph interpretation and can assist both diagnosis and classification of patients for treatment.

Beyond Borders: A Global Microsurgery Training and Case Exposure Survey.

BACKGROUND: Microsurgery is essential in modern reconstructive surgery and plastic surgery training. Surgeon's proficiency and experience are crucial for effective microsurgical interventions. Despite anecdotal evidence of varying quality of microsurgery training globally, no empirical studies have investigated this. We conducted a global survey to investigate microsurgical training and clinical case exposure among plastic surgery trainees worldwide. METHODS: An online survey was conducted using a secure platform to gather information on microsurgical case exposure and training among plastic surgery trainees between August 2020 and April 2021. Participants provided consent and completed a 37-question survey across four themes: clinical caseload, surgical exposure to microsurgery, microsurgical simulation training exposure, and barriers and opportunities. RESULTS: A total of 202 responses were received, with most respondents in formal training programs (86.7%). The data highlighted regional variation in microsurgery case indications and flap types, with North America and Europe exhibiting the highest activity levels in microsurgery. Trainees in Asia have the highest cumulative practical exposure in microsurgery, followed by Australia and Oceania, and North America. Only 39.6% of respondents reported formal microsurgical simulation training, and almost one-third (29.7%) received no simulation training. Trainee access to practical experience is limited by several factors, including insufficient time and procedure complexity. Notably, practical experience was most commonly denied without reason being given. CONCLUSION: Our study highlights significant disparities in microsurgical training and exposure among plastic surgery trainees globally. Further research is needed to identify strategies for addressing these issues, given the growing demand for complex reconstructive microsurgery and its impact on health care inequalities.

Safety and Efficacy of Immune Checkpoint Inhibitors in Patients with Cancer and Viral Hepatitis: The MD Anderson Cancer Center Experience.

BACKGROUND: Despite the clinical benefit of immune checkpoint inhibitors (ICIs), patients with a viral hepatitis have been excluded from clinical trials because of safety concerns. The purpose of this study was to determine the incidence rate of adverse events (AEs) in patients with viral hepatitis who received ICIs for cancer treatment. MATERIALS AND METHODS: We conducted a retrospective study in patients with cancer and concurrent hepatitis B or C, who had undergone treatment with ICI at MD Anderson Cancer Center from January 1, 2010 to December 31, 2019. RESULTS: Of the 1076 patients screened, we identified 33 with concurrent hepatitis. All 10 patients with HBV underwent concomitant antiviral therapy during ICI treatment. Sixteen of the 23 patients with HCV received it before the initiation of ICI. The median follow-up time was 33 months (95% CI, 23-45) and the median duration of ICI therapy was 3 months (IQR, 1.9-6.6). Of the 33 patients, 12 (39%) experienced irAEs (immune-related adverse events) of any grade, with 2 (6%) having grade 3 or higher. None of the patients developed hepatitis toxicities. CONCLUSION: ICIs may be a therapeutic option with an acceptable safety profile in patients with cancer and advanced liver disease.

C reactive protein utilisation, a biomarker for early COVID-19 treatment, improves lenzilumab efficacy: results from the randomised phase 3 'LIVE-AIR' trial.

OBJECTIVE: COVID-19 severity is correlated with granulocyte macrophage colony-stimulating factor (GM-CSF) and C reactive protein (CRP) levels. In the phase three LIVE-AIR trial, lenzilumab an anti-GM-CSF monoclonal antibody, improved the likelihood of survival without ventilation (SWOV) in COVID-19, with the greatest effect in participants having baseline CRP below a median of 79 mg/L. Herein, the utility of baseline CRP to guide lenzilumab treatment was assessed. DESIGN: A subanalysis of the randomised, blinded, controlled, LIVE-AIR trial in which lenzilumab or placebo was administered on day 0 and participants were followed through Day 28. PARTICIPANTS: Hospitalised COVID-19 participants (N=520) with SpO2 ≤94% on room air or requiring supplemental oxygen but not invasive mechanical ventilation. INTERVENTIONS: Lenzilumab (1800 mg; three divided doses, q8h, within 24 hours) or placebo infusion alongside corticosteroid and remdesivir treatments. MAIN OUTCOME MEASURES: The primary endpoint was the time-to-event analysis difference in SWOV through day 28 between lenzilumab and placebo treatments, stratified by baseline CRP. RESULTS: SWOV was achieved in 152 (90%; 95% CI 85 to 94) lenzilumab and 144 (79%; 72 to 84) placebo-treated participants with baseline CRP <150 mg/L (HR: 2.54; 95% CI 1.46 to 4.41; p=0.0009) but not with CRP ≥150 mg/L (HR: 1.04; 95% CI 0.51 to 2.14; p=0.9058). A statistically significant interaction between CRP and lenzilumab treatment was observed (p=0.044). Grade ≥3 adverse events with lenzilumab were comparable to placebo in both CRP strata. No treatment-emergent serious adverse events were attributed to lenzilumab. CONCLUSION: Hospitalised hypoxemic patients with COVID-19 with baseline CRP <150 mg/L derived the greatest clinical benefit from treatment with lenzilumab. TRIAL REGISTRATION NUMBER: NCT04351152; ClinicalTrials.gov.

Clinical and Prognostic Biomarker Value of Blood-Circulating Inflammatory Cytokines in Hepatocellular Carcinoma.

INTRODUCTION: Circulating inflammatory cytokines play critical roles in tumor-associated inflammation and immune responses. Recent data have suggested that several interleukins (ILs) mediate carcinogenesis in hepatocellular carcinoma (HCC). However, the predictive and prognostic value of circulating ILs is yet to be validated. Our study aimed to evaluate the association of the serum ILs with overall survival (OS) and clinicopathologic features in a large cohort of HCC patients. METHODS: We prospectively collected data and serum samples from 767 HCC patients treated at the University of Texas MD Anderson Cancer Center between 2001 and 2014, with a median follow-up of 67.4 months (95% confidence interval [CI]: 52.5, 83.3). Biomarker association with OS was evaluated by the log-rank method. RESULTS: The median OS in this cohort was 14.2 months (95% CI: 12, 16.1 months). Clinicopathologic features were more advanced, and OS was significantly inferior in patients with high circulating levels of IL1-R1, IL-6, IL-8, IL-10, IL-15, IL-16, and IL-18. CONCLUSION: Our study shows that several serum IL levels are valid prognostic biomarker candidates and potential targets for therapy in HCC.

Novel APOE Mutation in a Moroccan Subject Suffering from Alzheimer Disease: A Case Study and Exploration of Pathogenic Implication.

Alzheimer disease (AD) is a major public health concern worldwide. It is a severe neurodegenerative disease that primarily affects the elderly and causes significant brain cell death. According to the most complete scientific research, the APOE gene, which encodes the APOE protein, maybe the key to identifying the likely cause of delayed AD. The development of plaques and tangles, as well as increased amyloid (amyloid-ß) levels and deposition, have been linked to APOE4. Pathogenic mutations in this gene can impact how beta-amyloid deposits and how they are cleared from the body. In this study, we report a novel pathogenic mutation, Arg160Leu, in APOE that was identified in a Moroccan patient. The magnetic resonance imaging of this 67-year-old woman revealed hippocampal shrinkage, and the results of her cognition testing revealed that she is suffering from severe AD. The current study may increase awareness of the genetic risk factors for AD caused by APOE4 mutations.

Prevalence of and factors associated with depression among adult patients living with HIV/AIDs undergoing ART unit in Banadir hospital, Mogadishu Somalia.

BACKGROUND: Depression is the most common psychiatric disorder in HIV/AIDs patients, and its prevalence is three times higher in HIV/AIDs patients. Globally, over 35 million people were living with HIV/AIDs, 24.7 million were in Sub-Saharan Africa. The study aims to estimate the prevalence and determine factors associated with depression among HIV/AIDs adult patients in the ART unit at Banadir Hospital Mogadishu, Somalia. METHOD: A hospital-based cross-sectional study was conducted between 1 May and 1 July 2022. Samples were recruited from the HIV/AIDs adult patients attending in ART unit at Banadir Hospital, Mogadishu, Somalia. A validated research tool, including sociodemographic, behavioral, clinical, and psycho-social characteristics, three items social support scale, an 11-item HIV stigma scale, and patient health questions-9 (PHQ-9) were used. The interview was conducted privet room in the ART unit. Logistic regression was used to determine factors associated with depression at the significance level a = 0.050. RESULT: The overall prevalence of depression among HIV/AIDs patients was 33.5% (95%CI = 28.1-39.0). In the multivariable logistic regression, three factors were associated with depression; the odds of depression were 3.415 times (95%CI=1.465-7.960) greater for those with poor social support than those with moderate-strong social support. Those with moderate and poor treatment adherence had 14.307 times (95%CI=5.361-38.182) greater odds of depression than those with good treatment adherence. Those who use substances had 3.422 times (95%CI=1.727-6.781) greater odds of having depression than those who did not. CONCLUSION: People living with HIV in Mogadishu, Somalia, suffer from depression. The implementation to reduce depression should be focused on empowering social support, developing an appropriate approach to increase treatment adherence, and reducing or eliminating substance use.

Assessment of healthcare workers' knowledge and attitude on Ebola virus disease in Somalia: a multicenter nationwide survey.

BACKGROUND: In September 2022, a new Ebola outbreak was reported in Uganda, East Africa, and 142 confirmed cases, including 19 Healthcare workers (HCWs) reported. Ebola is not endemic in Somalia, but the country is at a reasonable risk of the virus being introduced due to the direct connection with daily flights from Uganda without border health control and prevention activities. Therefore, evaluating HCWs' Knowledge and attitude is crucial since this is the first time being evaluated in Somalia. The study's objective is to evaluate the HCWs' Knowledge and attitude toward the Ebola virus disease in Somalia. METHOD: An online self-administrated cross-sectional survey was conducted among HCWs (n = 1103) in all six federal member states of Somalia using a validated, reliable, well-structured questionnaire. Data we analyzed using descriptive statistics and Logistic regression were used to determine sociodemographic characteristics associated with poor Knowledge and negative attitude. RESULT: Over one-third (37.3%) of HCWs had poor Knowledge; the mean knowledge score was 7.97 SD ± 2.15. Almost 40.1% of the HCWs had a negative attitude; the mean attitude was 27.81 SD ± 8.06. Low-income HCWs (AOR = 2.06, 95%CI:1.01-4.19), Married HCWs (AOR = 1.39, 95%CI: 1.110-1.963), Midwives (AOR = 2.76, 95%CI: 1.74-4.39), Lab technicians (AOR = 2.43, 95%CI: 1.43-4.14), HCWs work in Jubaland state of Somalia (AOR = 3.69, 95%CI: 2.39-5.70), Galmudug state (AOR = 8.50, 95%CI: 4.59-15.77), Hirshabelle state (AOR = 3.18, 95%CI: 2.15-4.71) were more likely to have poor Knowledge compared to their counterparts. HCWs who work in Hirshabelle state (AOR = 5.44,95%CI: 3.58-8.27), Jubaland state (AOR = 8.47, 95%CI: 4.69-15.29), and Galmudug state (AOR = 4.43, 95%CI: 3.03-6.48) was more likely to have a negative attitude than those working in the Banadir region administration. CONCLUSION: Most Somali healthcare workers showed good Knowledge and a positive attitude toward the Ebola virus. The implementation to enhance Knowledge and attitude must specifically focus on low-income HCWs, Midwives, Lab technicalities, and those who work in Hirshabelle, Jubaland, and Galmudug states of Somalia.

Sildenafil for congenital heart diseases induced pulmonary hypertension, a meta-analysis of randomized controlled trials.

BACKGROUND: Sildenafil was first prescribed for angina pectoris and then for erectile dysfunction from its effects on vascular smooth muscle relaxation and vasodilatation. Recently, sildenafil has been proposed for congenital heart diseases induced pulmonary hypertension, which constitutes a huge burden on children's health and can attribute to fatal complications due to presence of unoxygenated blood in the systemic circulation. Therefore, our meta-analysis aims to further investigate the safety and efficacy of sildenafil on children population. METHODS: We searched the following electronic databases: PubMed, Cochrane CENTRAL, WOS, Embase, and Scopus from inception to April 20th, 2022. Randomized controlled trials that assess the efficacy of using sildenafil in comparison to a placebo or any other vasodilator drug were eligible for inclusion. The inverse variance method was used to pool study effect estimates using the random effect model. Effect sizes are provided in the form of mean difference (MD) with 95% confidence intervals (CI). RESULTS: Our study included 14 studies with (n = 849 children) with a mean age of 7.9 months old. Sildenafil showed a statistically significant decrease over placebo in mean and systolic pulmonary artery pressure (PAP) with MD -7.42 (95%CI [-13.13, -1.71], P = 0.01) and -8.02 (95%CI [-11.16, -4.88], P < 0.0001), respectively. Sildenafil revealed a decrease in mean aortic pressure and pulmonary artery/aortic pressure ratio over placebo with MD -0.34 (95%CI [-2.42, 1.73], P = 0.75) and MD -0.10 (95%CI [-0.11, -0.09], P < 0.00001), respectively. Regarding post corrective operations parameters, sildenafil had a statistically significant lower mechanical ventilation time, intensive care unit stay, and hospital stay over placebo with MD -19.43 (95%CI [-31.04, -7.81], s = 0.001), MD -34.85 (95%CI [-50.84, -18.87], P < 0.00001), and MD -41.87 (95%CI [-79.41, -4.33], P = 0.03), respectively. Nevertheless, no difference in mortality rates between sildenafil and placebo with OR 0.25 (95%CI 0.05, 1.30], P = 0.10) or tadalafil with OR 1 (95%CI 0.06, 17.12], P = 1). CONCLUSION: Sildenafil is a well-tolerated treatment in congenital heart diseases induced pulmonary hypertension, as it has proven its efficacy not only in lowering both PAP mean and systolic but also in reducing the ventilation time, intensive care unit and hospital stay with no difference observed regarding mortality rates.

Enhanced Wound Healing Potential of Spirulina platensis Nanophytosomes: Metabolomic Profiling, Molecular Networking, and Modulation of HMGB-1 in an Excisional Wound Rat Model.

Excisional wounds are considered one of the most common physical injuries. This study aims to test the effect of a nanophytosomal formulation loaded with a dried hydroalcoholic extract of S. platensis on promoting excisional wound healing. The Spirulina platensis nanophytosomal formulation (SPNP) containing 100 mg PC and 50 mg CH exhibited optimum physicochemical characteristics regarding particle size (598.40 ± 9.68 nm), zeta potential (-19.8 ± 0.49 mV), entrapment efficiency (62.76 ± 1.75%), and Q6h (74.00 ± 1.90%). It was selected to prepare an HPMC gel (SPNP-gel). Through metabolomic profiling of the algal extract, thirteen compounds were identified. Molecular docking of the identified compounds on the active site of the HMGB-1 protein revealed that 12,13-DiHome had the highest docking score of -7.130 kcal/mol. SPNP-gel showed higher wound closure potential and enhanced histopathological alterations as compared to standard (MEBO® ointment) and S. platensis gel in wounded Sprague-Dawley rats. Collectively, NPS promoted the wound healing process by enhancing the autophagy process (LC3B/Beclin-1) and the NRF-2/HO-1antioxidant pathway and halting the inflammatory (TNF-, NF-κB, TlR-4 and VEGF), apoptotic processes (AIF, Caspase-3), and the downregulation of HGMB-1 protein expression. The present study's findings suggest that the topical application of SPNP-gel possesses a potential therapeutic effect in excisional wound healing, chiefly by downregulating HGMB-1 protein expression.

Exploring Medicinal Herbs' Therapeutic Potential and Molecular Docking Analysis for Compounds as Potential Inhibitors of Human Acetylcholinesterase in Alzheimer's Disease Treatment.

Background and Objectives: Alzheimer's disease (AD) stands as a pervasive neurodegenerative ailment of global concern, necessitating a relentless pursuit of remedies. This study aims to furnish a comprehensive exposition, delving into the intricate mechanistic actions of medicinal herbs and phytochemicals. Furthermore, we assess the potential of these compounds in inhibiting human acetylcholinesterase through molecular docking, presenting encouraging avenues for AD therapeutics. Materials and Methods: Our approach entailed a systematic exploration of phytochemicals like curcumin, gedunin, quercetin, resveratrol, nobiletin, fisetin, and berberine, targeting their capability as human acetylcholinesterase (AChE) inhibitors, leveraging the PubChem database. Diverse bioinformatics techniques were harnessed to scrutinize molecular docking, ADMET (absorption, distribution, metabolism, excretion, and toxicity), and adherence to Lipinski's rule of five. Results: Results notably underscored the substantial binding affinities of all ligands with specific amino acid residues within AChE. Remarkably, gedunin exhibited a superior binding affinity (-8.7 kcal/mol) compared to the reference standard. Conclusions: These outcomes accentuate the potential of these seven compounds as viable candidates for oral medication in AD treatment. Notably, both resveratrol and berberine demonstrated the capacity to traverse the blood-brain barrier (BBB), signaling their aptitude for central nervous system targeting. Consequently, these seven molecules are considered orally druggable, potentially surpassing the efficacy of the conventional drug, donepezil, in managing neurodegenerative disorders.

Online education via media platforms and applications as an innovative teaching method.

Online teaching has globally become a part of the learning process and has been more well-established in developed countries. In developing countries, online teaching or e-Learning is not practiced or recognized officially by educational organizations and policymakers. On the other hand, it is well-known that computers and technology are the future; in such a case, the advancement of distance-learning or online learning is immensely remarkable. It has reduced teachers' and students' introversion concerning e-learning and technology and has provided a platform for learning new technologies and developing new skills. The recent COVID-19 lockdown impelled governments to start implementing E-learning in schools, which resulted in several challenges. This study attempts to analyze and interpret the challenges and potentials of implementing online learning by surveying through an online questionnaire using 'Google Forms' (N = 968) with responses from high school and primary school English teachers during the first week of March through the last week of April. The findings revealed that most teachers had negative perceptions of implementing e-learning for several reasons, including lack of essential facilities such as electricity, electronic devices, and the absence of required skills. The actual contributions of students and educators are also among the major obstacles. This research suggests introducing Information Communication Technology modules across media platforms and applications in the education departments, opening intensive courses for teachers, and developing educational facilities in the education departments and schools to overcome these limitations and challenges.

Clinical course of non-alcoholic fatty liver disease and the implications for clinical trial design.

BACKGROUND & AIMS: The predicted risk and timeline to progression to liver-related outcomes in the population with NAFLD are not well-characterized. We aimed to examine the risk and time to progression to cirrhosis, hepatic decompensation and death in a contemporary population over a long follow-up period, to obtain information to guide endpoint selection and sample size calculations for clinical trials on NAFLD-related cirrhosis. METHODS: This is a retrospective study of prospectively collected data in a medical record linkage system, including all adults diagnosed with NAFLD between 1996-2016 by clinical, biochemical and radiological criteria in Olmsted County, Minnesota and followed until 2019. Liver-related outcomes and death were ascertained and validated by individual medical record review. Time and risk of progression from NAFLD to cirrhosis to decompensation and death were assessed using multistate modeling. RESULTS: A total of 5,123 individuals with NAFLD (median age 52 years, 53% women) were followed for a median of 6.4 (range 1-23) years. The risk of progression was as follows: from NAFLD to cirrhosis: 3% in 15 years; compensated cirrhosis to first decompensation: 33% in 4 years (8%/year); first decompensation to ≥2 decompensations: 48% in 2 years. Albumin, bilirubin, non-bleeding esophageal varices and diabetes were independent predictors of decompensation. Among the 575 deaths, 6% were liver related. Therapeutic trials in compensated cirrhosis would require enrolment of a minimum of 2,886 individuals followed for >2 years to detect at least a 15% relative decrease in liver-related endpoints. CONCLUSION: In this population-based cohort with 23 years of longitudinal follow-up, NAFLD was slowly progressive, with liver-related outcomes affecting only a small proportion of people. Large sample sizes and long follow-up are required to detect reductions in liver-related endpoints in clinical trials. LAY SUMMARY: For patients with compensated non-alcoholic steatohepatitis-related cirrhosis, the time spent in this state and the risk of progression to decompensation are not well-known in the population. We examined the clinical course of a large population-based cohort over 23 years of follow-up. We identified that adults with compensated cirrhosis spend a mean time of 4 years in this state and have a 10% per year risk of progression to decompensation or death. The risk of further progression is 3-fold higher in adults with cirrhosis and one decompensating event. These results are reflective of placebo arm risks in drug clinical trials and are essential in the estimation of adequate sample sizes.

Natural History of Nonalcoholic Fatty Liver Disease With Normal Body Mass Index: A Population-Based Study.

BACKGROUND & AIMS: The natural history of lean nonalcoholic fatty liver disease (NAFLD) is not well-understood. Consequently, patient counseling and disease management are limited. We aimed to compare the natural history of lean, overweight, and obese NAFLD in a U.S. population with long-term follow-up. METHODS: All adults diagnosed with NAFLD in Olmsted County, MN between 1996 and 2016 were identified, and all subsequent medical events were ascertained using a medical record linkage system. Subjects were divided on the basis of body mass index (BMI) at NAFLD diagnosis into 3 groups: normal, overweight, and obese. The probability to develop cirrhosis, decompensation, malignancies, cardiovascular events, or death among the 3 groups was estimated by using the Aalen-Johansen method, treating death as a competing risk. The impact of BMI categories on these outcomes was explored by using Cox proportional hazards regression analysis. RESULTS: A total of 4834 NAFLD individuals were identified: 414 normal BMI, 1189 overweight, and 3231 obese. Normal BMI NAFLD individuals were characterized by a higher proportion of women (66% vs 47%) and lower prevalence of metabolic comorbidities than the other 2 groups. In reference to obese, those with normal BMI NAFLD had a nonsignificant trend toward lower risk of cirrhosis (hazard ratio [HR], 0.33, 95% confidence interval [CI], 0.1-1.05). There were no significant differences in the risk of decompensation (HR, 0.79; 95% CI, 0.11-5.79), cardiovascular events (HR, 1.05; 95% CI, 0.73-1.51), or malignancy (HR, 0.87; 95% CI, 0.51-1.48). Compared with obese, normal BMI NAFLD had higher risk of all-cause mortality (HR, 1.96; 95% CI, 1.52-2.51). CONCLUSIONS: NAFLD with normal BMI is associated with a healthier metabolic profile and possibly a lower risk of liver disease progression but similar risk of cardiovascular disease and malignancy than obese NAFLD.

Megadepth: efficient coverage quantification for BigWigs and BAMs.

MOTIVATION: A common way to summarize sequencing datasets is to quantify data lying within genes or other genomic intervals. This can be slow and can require different tools for different input file types. RESULTS: Megadepth is a fast tool for quantifying alignments and coverage for BigWig and BAM/CRAM input files, using substantially less memory than the next-fastest competitor. Megadepth can summarize coverage within all disjoint intervals of the Gencode V35 gene annotation for more than 19 000 GTExV8 BigWig files in approximately 1 h using 32 threads. Megadepth is available both as a command-line tool and as an R/Bioconductor package providing much faster quantification compared to the rtracklayer package. AVAILABILITY AND IMPLEMENTATION: https://github.com/ChristopherWilks/megadepth, https://bioconductor.org/packages/megadepth. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

HepatoScore-14: Measures of Biological Heterogeneity Significantly Improve Prediction of Hepatocellular Carcinoma Risk.

BACKGROUND AND AIMS: Therapeutic, clinical trial entry and stratification decisions for hepatocellular carcinoma (HCC) are made based on prognostic assessments, using clinical staging systems based on small numbers of empirically selected variables that insufficiently account for differences in biological characteristics of individual patients' disease. APPROACH AND RESULTS: We propose an approach for constructing risk scores from circulating biomarkers that produce a global biological characterization of individual patient's disease. Plasma samples were collected prospectively from 767 patients with HCC and 200 controls, and 317 proteins were quantified in a Clinical Laboratory Improvement Amendments-certified biomarker testing laboratory. We constructed a circulating biomarker aberration score for each patient, a score between 0 and 1 that measures the degree of aberration of his or her biomarker panel relative to normal, which we call HepatoScore. We used log-rank tests to assess its ability to substratify patients within existing staging systems/prognostic factors. To enhance clinical application, we constructed a single-sample score, HepatoScore-14, which requires only a subset of 14 representative proteins encompassing the global biological effects. Patients with HCC were split into three distinct groups (low, medium, and high HepatoScore) with vastly different prognoses (medial overall survival 38.2/18.3/7.1 months; P < 0.0001). Furthermore, HepatoScore accurately substratified patients within levels of existing prognostic factors and staging systems (P < 0.0001 for nearly all), providing substantial and sometimes dramatic refinement of expected patient outcomes with strong therapeutic implications. These results were recapitulated by HepatoScore-14, rigorously validated in repeated training/test splits, concordant across Myriad RBM (Austin, TX) and enzyme-linked immunosorbent assay kits, and established as an independent prognostic factor. CONCLUSIONS: HepatoScore-14 augments existing HCC staging systems, dramatically refining patient prognostic assessments and therapeutic decision making and enrollment in clinical trials. The underlying strategy provides a global biological characterization of disease, and can be applied broadly to other disease settings and biological media.

Regulation of Nrf2 and Nrf2-related proteins by ganoderma lucidum in hepatocellular carcinoma.

BACKGROUND: HCC is among the most common cancer. Ganoderma lucidum (G.lucidum) has been essential in preventing and treating cancer. The Nrf2 signaling cascade is a cell protective mechanism against further damage, such as cancer development. This signaling pathway upregulates the cytoprotective genes and is vital in eliminating xenobiotics and reactive oxygen. This study aimed to show the potential cytotoxic activity of G. lucidum aqueous extract in HCC. METHODS AND RESULTS: MTT assay was used to detect cell viability. Nrf2-related proteins were measured by western blotting, and the flow cytometry method assayed cell population in different cycle phases. Cell viability was 49% and 47% following G. lucidum extract at 100 µg/ml at 24 and 48 h treatments, respectively. G. lucidum extract (aqueous, 100 or 50 µg/ml) treatments for 24, 48, or 72 h were able to significantly change the cytoplasmic/nuclear amount of Nrf2 and HO-1, NQO1 protein levels. Moreover, at both concentrations, arrest of the G0/G1 cell cycle was stimulated in HCC. CONCLUSIONS: The activation of the Nrf2 signaling pathways seems to be among the mechanisms underlining the protective and therapeutic action of G. lucidum against HCC.

Detection of Helicobacter pylori in Gastric Biopsies Among Sudanese Patients with Confirmed Gastric Disorders Using Three Diagnostic Methods.

BACKGROUND: Helicobacter pylori (H. pylori) infection represents one of the most common chronic bacterial infections in developing countries. However, in Sudan, the infection is not well diagnosed with standard laboratory methods in many parts of the country. This study aimed to detect H. pylori in gastric biopsies of patients with gastric disorders, using three diagnostic methods. MATERIALS AND METHODS: A cross-sectional study was conducted among 100 patients in Gezira state, central Sudan. Giemsa stain for histopathological examination (HPE), rapid urease test (RUT), and polymerase chain reaction (PCR) techniques were performed to detect H. pylori from the gastric biopsy samples as per standard assays. RESULTS: Most of the patients were males (66%), from rural areas (72%) and in the age group 31 to 50 years. H. pylori were identified in 85% of the samples by at least one of the three tests. The highest positivity was detected by HPE (83%), followed by PCR (67%) and RUT (63%), while 59% were positive by the three diagnostic methods. PCR showed higher sensitivity (80.72% vs. 73.49%) and specificity (100% vs. 88.24%) than RUT. Positive predictive values were reported as 100% for PCR and 96.83% for RUT. Considering PCR as a gold standard method, HPE revealed higher sensitivity (100%) than RUT (88.06%). On the contrary, RUT showed higher specificity (87.88%) than PCR (51.52%). There were no significant associations between H. pylori infection patients' gender (p = 0.747). Loss of weight (p = 0.007) and nausea (p = 0.032) were significantly associated with H. pylori infection. CONCLUSIONS: There was a high prevalence of H. pylori infection in central Sudan. This highlights the need to analyze epidemiological status, virulence factors, and strain characteristics to control disease transmission. PCR is a reliable and valuable technique in detecting H. pylori infection from gastric biopsy samples.