High order expression dependencies finely resolve cryptic states and subtypes in single cell data.

Single cells are typically typed by clustering into discrete locations in reduced dimensional transcriptome space. Here we introduce Stator, a data-driven method that identifies cell (sub)types and states without relying on cells' local proximity in transcriptome space. Stator labels the same single cell multiply, not just by type and subtype, but also by state such as activation, maturity or cell cycle sub-phase, through deriving higher-order gene expression dependencies from a sparse gene-by-cell expression matrix.

Investigation of the iridium adsorption process with functionalized magnetic nanoparticles using triisobutylphosphine sulfide extractors.

In this research work, the adsorption process of iridium using magnetic nanoparticles functionalized with Cyanex 471X has been investigated. In this regard, parameters affecting the adsorption process such as pH, initial concentration of iridium ions, contact time and adsorbent dosage were assessed. According to the results, pH 6, adsorbent dosage 1.

A TGFβ-ECM-integrin signaling axis drives structural reconfiguration of the bile duct to promote polycystic liver disease.

The formation of multiple cysts in the liver occurs in a number of isolated monogenic diseases or multisystemic syndromes, during which bile ducts develop into fluid-filled biliary cysts. For patients with polycystic liver disease (PCLD), nonsurgical treatments are limited, and managing life-long abdominal swelling, pain, and increasing risk of cyst rupture and infection is common. We demonstrate here that loss of the primary cilium on postnatal biliary epithelial cells (via the deletion of the cilia gene ) drives ongoing pathological remodeling of the biliary tree, resulting in progressive cyst formation and growth.

Computational fluid dynamics simulation of two-phase flow patterns in a serpentine microfluidic device.

In the current research work, the flow behavior of a liquid-liquid extraction (LLE) process in a serpentine microchannel was analyzed. The simulation was performed using a 3D model and the results were found to be consistent with experimental data. The impact of the flow of chloroform and water on the flow model was also examined.

Investigation of kinetic, isotherm and adsorption efficacy of thorium by orange peel immobilized on calcium alginate.

In this research work the thorium uptake on immobilized protonated orange peel was studied in a batch system. The effects of effective parameters such as biosorbent dosage, initial metal ion concentration, and contact time on the biosorption of thorium were analyzed. The biosorption capacity of the immobilized orange peel for thorium at optimal conditions of initial pH 3.

A novel multi-objective robust fuzzy stochastic programming model for sustainable agri-food supply chain: case study from an emerging economy.

On the one hand, supply chain management of agri-food products under uncertain conditions has a significant impact on food security and, on the other hand, increases the profits of supply chain components. Moreover, considering the sustainability concepts leads to more social and environmental benefits. The present study investigates the canned food supply chain under uncertain conditions and sustainability concepts by considering strategic and operational decisions and different characteristics.

Characterization of occult hepatitis B infection among Iranian liver transplant recipients.

Background: The prevalence of occult hepatitis B infection (OBI) among Iranian liver transplant recipient patients has not been explored yet. The present study aimed to determine the OBI prevalence among Iranian liver transplant recipients.

Methods: This study encompassed 97 patients having undergone liver transplantation due to several clinical backgrounds in the Liver Transplantation Center, Tehran, Iran.

Comparative transcriptome in large-scale human and cattle populations.

Background: Cross-species comparison of transcriptomes is important for elucidating evolutionary molecular mechanisms underpinning phenotypic variation between and within species, yet to date it has been essentially limited to model organisms with relatively small sample sizes.

Results: Here, we systematically analyze and compare 10,830 and 4866 publicly available RNA-seq samples in humans and cattle, respectively, representing 20 common tissues. Focusing on 17,315 orthologous genes, we demonstrate that mean/median gene expression, inter-individual variation of expression, expression quantitative trait loci, and gene co-expression networks are generally conserved between humans and cattle.

Identifying Potential New Gene Expression-Based Biomarkers in the Peripheral Blood Mononuclear Cells of Hepatitis B-Related Hepatocellular Carcinoma.

Objective: The analysis of the gene expression of peripheral blood mononuclear cells (PBMCs) is important to clarify the pathogenesis of hepatocellular carcinoma (HCC) and the detection of suitable biomarkers. The purpose of this investigation was to use RNA-sequencing to screen the appropriate differentially expressed genes (DEGs) in the PBMCs for the HCC.

Methods: The comprehensive transcriptome of extracted RNA of PBMC ( = 20) from patients with chronic hepatitis B (CHB), liver cirrhosis, and early stage of HCC (5 samples per group) was carried out using RNA-sequencing.

Prevalence of human papilloma virus (HPV) genotypes between outpatients males and females referred to seven laboratories in Tehran, Iran.

Background: Human papilloma virus (HPV) causes the most common sexually-transmitted infection especially among sexually-active individuals. The aim of study was to characterize the molecular characterization of HPV genotypes between 5176 female and male patients.

Methods: HPV DNA was extracted from genital swabs of the study participants and amplified by Real Time Polymerase Chain Reaction (PCR).

Social innovation based on collaboration between government and non-governmental organizations in COVID-19 crisis: evidence from Iran.

Background: One of the effective ways to attract social collaboration to provide effective, prompt, and coordinated interventions in emergencies is through social innovation. The present study seeks to identify the factors affecting the implementation of the social innovation plan based on the collaboration between government and non-governmental organizations (NGOs) for saving people's lives in crises. The initial idea of this research was obtained from the best practice "Every Home Is a Health Base" which was implemented in Iran.

Higher-order interactions in statistical physics and machine learning: A model-independent solution to the inverse problem at equilibrium.

The problem of inferring pairwise and higher-order interactions in complex systems involving large numbers of interacting variables, from observational data, is fundamental to many fields. Known to the statistical physics community as the inverse problem, it has become accessible in recent years due to real and simulated big data being generated. Current approaches to the inverse problem rely on parametric assumptions, physical approximations, e.

Pervasive lesion segregation shapes cancer genome evolution.

Cancers arise through the acquisition of oncogenic mutations and grow by clonal expansion. Here we reveal that most mutagenic DNA lesions are not resolved into a mutated DNA base pair within a single cell cycle. Instead, DNA lesions segregate, unrepaired, into daughter cells for multiple cell generations, resulting in the chromosome-scale phasing of subsequent mutations.

An insight to HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP) pathogenesis; evidence from high-throughput data integration and meta-analysis.

Background: Human T-lymphotropic virus 1-associated myelopathy/tropical spastic paraparesis (HAM/TSP) is a progressive disease of the central nervous system that significantly affected spinal cord, nevertheless, the pathogenesis pathway and reliable biomarkers have not been well determined. This study aimed to employ high throughput meta-analysis to find major genes that are possibly involved in the pathogenesis of HAM/TSP.

Results: High-throughput statistical analyses identified 832, 49, and 22 differentially expressed genes for normal vs.

Zebrafish MITF-Low Melanoma Subtype Models Reveal Transcriptional Subclusters and MITF-Independent Residual Disease.

The melanocyte-inducing transcription factor (MITF)-low melanoma transcriptional signature is predictive of poor outcomes for patients, but little is known about its biological significance, and animal models are lacking. Here, we used zebrafish genetic models with low activity of Mitfa (MITF-low) and established that the MITF-low state is causal of melanoma progression and a predictor of melanoma biological subtype. MITF-low zebrafish melanomas resembled human MITF-low melanomas and were enriched for stem and invasive (mesenchymal) gene signatures.

IL-17 and IL-22 genetic polymorphisms in HBV vaccine non- and low-responders among healthcare workers.

Background: Healthcare workers constitute a population at high risk for HBV infection. Efficient vaccination options are available; however, the individual response to HBV vaccination may vary widely between subjects, potentially due to cytokine profiles and genetic variations. In the present study, we investigated the relationship between IL-17 and IL-22 gene polymorphisms versus non- and low-responsiveness to HBV vaccination in healthcare workers.

Identification of occult hepatitis B virus (HBV) infection and viral antigens in healthcare workers who presented low to moderate levels of anti-HBs after HBV vaccination.

Background: Worldwide, healthcare workers (HCWs) show different levels of response to hepatitis B virus (HBV) vaccine. One of the factors associated with vaccine unresponsiveness may be the existence of current or past HBV infection. Regardless of the presence of HBsAg (overt infection), occult HBV infection (OBI, defined as presence of HBV DNA in the absence of HBsAg) might also account for some non- or hypo-response cases.

Evolution of hepatitis B virus surface gene and protein among Iranian chronic carriers from different provinces.

Background And Objectives: Iranian chronic HBV carrier's population has shown a unique pattern of genotype D distribution all around the country. The aim of this study was to explore more details of evolutionary history of carriers based on structural surface proteins from different provinces.

Materials And Methods: Sera obtained from 360 isolates from 12 Different regions of country were used for amplification and sequencing of surface proteins.

Lamivudine Resistance and Precore Variants in Iranian Patients With Chronic Hepatitis B: Correlation With Virological and Clinical Features.

Background: Long-term lamivudine therapy, despite its initial effectiveness against hepatitis B virus (HBV), is associated with the emergence of drug resistance mutations in polymerase protein.

Objectives: The aim of the present study was to determine the prevalence of precore and lamivudine drug resistance mutations in lamivudine treated patients with chronic B hepatitis.

Patients And Methods: Sequential sera were obtained from 88 chronic HBV carriers who received lamivudine for more than 24 months.

Symptoms of obsessive-compulsive disorder in a sample of Iranian patients.

Background: Characteristic features of the obsessive-compulsive disorder (OCD) occur with remarkable consistency in different cultural settings. The content of symptoms, however, seems to vary across cultures.

Aims: To examine the content of symptoms in a sample of OCD patients from Iran.