Miracle-dz/UniFAR-FTUs huggingface dataset:
Gastrointestinal Surgery for Inflammatory Bowel Disease Persistently Lowers Microbiome and Metabolome Diversity

Abstract Background Many studies have investigated the role of the microbiome in inflammatory bowel disease (IBD), but few have focused on surgery specifically or its consequences on the metabolome that may differ by surgery type and require longitudinal sampling. Our objective was to characterize and contrast microbiome and metabolome changes after different surgeries for IBD, including ileocolonic resection and colectomy. Methods The UC San Diego IBD Biobank was used to prospectively collect 332 stool samples from 129 subjects (50 ulcerative colitis; 79 Crohn’s disease). Of these, 21 with Crohn’s disease had ileocolonic resections, and 17 had colectomies. We used shotgun metagenomics and untargeted liquid chromatography followed by tandem mass spectrometry metabolomics to characterize the microbiomes and metabolomes of these patients up to 24 months after the initial sampling. Results The species diversity and metabolite diversity both differed significantly among groups (species diversity: Mann-Whitney U test P value = 7.8e-17; metabolomics, P-value = 0.0043). Escherichia coli in particular expanded dramatically in relative abundance in subjects undergoing surgery. The species profile was better able to classify subjects according to surgery status than the metabolite profile (average precision 0.80 vs 0.68). Conclusions Intestinal surgeries seem to reduce the diversity of the gut microbiome and metabolome in IBD patients, and these changes may persist. Surgery also further destabilizes the microbiome (but not the metabolome) over time, even relative to the previously established instability in the microbiome of IBD patients. These long-term effects and their consequences for health outcomes need to be studied in prospective longitudinal trials linked to microbiome-involved phenotypes.
Cutaneous manifestations of coronavirus disease 2019 in 458 confirmed cases: A systematic review

Background: The coronavirus disease 2019 (COVID-19) pandemic has affected the whole world for a short span of time. As it is a novel virus, its manifestations have been slowly revealed. Cutaneous manifestations of COVID-19 have gradually been reported from different regions of the world. However, their significance in diagnosis, as well as predicting prognosis, remains to be established. Objective: This review describes the cutaneous manifestations of COVID-19 patients from diverse regions with the aim of highlighting any important associations. Methods: A literature search was conducted using “PubMed” for original articles, case series, and case reports using the search terms “cutaneous manifestations” and “skin manifestations” in combination with “COVID-19” published up to 31 May. Results: Nine original research articles and 35 case series or case reports were identified, including 458 confirmed COVID-19 cases. The ratio of male to female patients was 0.94, and the patients' age ranged from 2 months to 84 years. In 10% of cases, skin lesions appeared before systemic manifestations. The most common cutaneous manifestation was macular/maculo-papular rash (42.5%), followed by acute urticaria (17.9%), vesicular rash (15.3%), pseudo-chilblain or acral purpuric lesions (15.1), and livedo-reticularis (4.4%). The majority of reported cases were located in Spain, Italy, and France. These manifestations do not seem to be sex-, age-, or country-specific. Conclusion: It is necessary to conduct worldwide registries and prospective studies to assess the true incidence of cutaneous manifestations of COVID-19 and to streamline their categorization based on their pathogenesis. There appears to be no specific manifestation at present, but a high index of suspicion can help in the diagnosis of patients presenting with cutaneous lesions as the first manifestation.
Comparison of effects of volume-controlled and pressure-controlled mode of ventilation on endotracheal cuff pressure and respiratory mechanics in laparoscopic cholecystectomies: A randomised controlled trial

Background and Aims: One of the pathophysiological consequences of pneumoperitoneum is variations in endotracheal cuff pressure (ETTc). Volume-controlled mode and pressure-controlled mode of ventilation being two modes of ventilatory strategies; we intended to find out variations in ETTc governed by respiratory mechanics between these two modes during laparoscopic cholecystectomies. Methods: After obtaining ethics committee approval, this randomised (1:1), active-controlled, parallel-assigned study was done on 60 patients undergoing laparoscopic cholecystectomies. These patients were allocated into two groups by computer-generated randomisation: Volume-controlled mode (V) and pressure-controlled mode (P). We observed for variations in ETTc which was the primary aim and haemodynamic parameters; respiratory mechanics at baseline (T1), at pneumoperitoneum (T2), after 10 min (T3), 20 min (T4) of pneumoperitoneum and at desufflation (T5). Post-operative laryngotracheal co-morbidities were also observed. Analysis was done using Statistical Package for the Social Sciences version 16.0 (IBM SPSS Statistics, Somers NY, USA). Results: No statistically significant difference was found in both groups either concerning ETTc, haemodynamic parameters or complications. In both groups, ETTc variation was statistically significant when compared from baseline to desufflation (T1 versus T5) and in group V additionally from baseline to time of pneumoperitoneum (T1 versus T2). Group P showed lower peak airway pressure at desufflation and higher mean airway pressure throughout at all the time intervals. Conclusions: There is no variation in ETTc between the two modes. Group P appears to be better in terms of lower Ppeak and better Pmean.
Medicinal characteristics of Smyrnium cordifolium Boiss. plant extract in rats

The most common sleep disorder is insomnia and about 35% of all people suffer from this disturbance. A trend in using herbal medications for this disorder is increasing globally. Current study aimed to investigate the hypnotic characteristics of Smyrnium cordifolium Boiss (SCB) plant extract. From an experimental study, 96 healthy male Wistar rats were equally divided into 12 groups. For hypnotic evaluations, a negative control with normal saline (10 mg/kg), a positive control with diazepam (1 mg/kg) and 3 treatment groups with different dosages of plant extract (100, 200 and 300 mg/kg) were selected and injected intraperitoneally. Sleep start time and sleep duration time were then measured in different groups. For relaxant effects of the plant, a negative control with normal saline (10 mg/kg), 3 positive controls with diazepam (0.125, 0.25 and 0.5 mg/kg) and 3 treatment groups of plant extract (200, 300 and 400 mg/kg) were allocated and injected intraperitoneally. Finally, the mean time of sleeping, sleep start time and holding bar (marker of muscle relation) were compared between treatment and control groups appropriately. SCB plant extract (300 mg/kg), compared to diazepam and normal saline (N/S) shortened the sleep start time significantly (p < 0.001). All 3 dosages of SCB plant extract (100, 200 and 300 mg/kg), compared to diazepam and normal saline, increased sleep duration significantly (p < 0.001) and as the SCB dosage was increased the sleep duration was increased too. The relaxant effects of the plant extract did not indicate a significant difference. SCB plant extract as a natural product showed hypnotic effects even better than diazepam and needs to be investigated in human by further studies. Key words: Smyrnium cordifolium Boiss, hypnotic, insomnia, relaxant, Iran.
Factors Associated with the Immunogenicity of Anti-Tumor Necrosis Factor Agents in Pediatric Patients with Inflammatory Bowel Disease

Background/Aims Anti-drug antibodies (ADAs) can develop during treatment with anti-tumor necrosis factor (TNF) agents. We aimed to investigate the factors associated with immunogenicity of anti-TNF agents in pediatric patients with inflammatory bowel disease (IBD) and observe the clinical course of ADA-positive patients. Methods Pediatric IBD patients receiving maintenance treatment with anti-TNF agents who had been tested for ADAs against infliximab (IFX) or adalimumab (ADL) were included in this cross-sectional study. Factors associated with ADA positivity were investigated by analyzing clinicodemographic, laboratory, and treatment-related factors. Results A total of 76 patients (Crohn’s disease, 65; ulcerative colitis, 11) were included. Among these, 59 and 17 patients were receiving IFX and ADL, respectively. ADAs were found in 10 patients (13.2%), all of whom were receiving IFX. According to multivariable logistic regression analysis, the IFX trough level (TL) was associated with ADA positivity (odds ratio, 0.25; 95% confidence interval [CI], 0.08 to 0.51; p=0.002). According to the receiver operating characteristic analysis, the optimal cutoff of the IFX TLs for stratifying patients based on the presence of ADAs against IFX was 1.88 μg/mL (area under curve, 0.941; 95% CI, 0.873 to 1.000; sensitivity, 80.0%; specificity, 95.9%; p<0.001). Among the 10 patients with ADAs against IFX, five patients (50%) switched to ADL within 1 year, while five patients (50%) kept receiving IFX. Transient ADAs were observed in three patients (30%). Conclusions IFX TL was the only factor associated with ADA formation in pediatric IBD patients receiving IFX. Future studies based on serial and proactive therapeutic drug monitoring are required in the future.
Occurrence of a human‐associated microbial source tracking marker and its relationship with faecal indicator bacteria in an urban estuary

One of the main impacts of urban sprawl in rapidly growing countries has been contamination of coastal environments by waterborne pathogens, posing a critical risk to ecosystem and human health. Microbial source tracking (MST) has been a robust tool to identify the origin of these pathogens globally. This study compared the occurrence of a human‐associated Bacteroides marker (BT‐α) with faecal indicator bacteria (FIB) in an urban estuary (Golden Horn, Istanbul, Turkey). Faecal coliform (culture method), enterococci (both culture and qPCR method) concentrations and physicochemical variables were compared with the BT‐α concentrations in monthly collected samples for a year (n = 108). Enterococci concentrations detected by culture and qPCR were positively correlated (r = 0·86, P < 0·01) suggesting that qPCR can be an alternative method for monitoring. BT‐α marker was positive for 30% of the samples and positively correlated with enterococci (r = 0·61 and r = 0·64 for culture and qPCR methods respectively, P < 0·01). Rainfall had a moderate positive correlation with all faecal/MST indicators suggesting combined sewer overflows also severely impacted estuarine water quality. The high FIB and BT‐α concentrations at upper estuary suggested that faecal pollution mainly originated from the peri‐urban settlements around two creeks entering the estuary.
Ubiquitin-Like Modifiers: Emerging Regulators of Protozoan Parasites

Post-translational protein regulation allows for fine-tuning of cellular functions and involves a wide range of modifications, including ubiquitin and ubiquitin-like modifiers (Ubls). The dynamic balance of Ubl conjugation and removal shapes the fates of target substrates, in turn modulating various cellular processes. The mechanistic aspects of Ubl pathways and their biological roles have been largely established in yeast, plants, and mammalian cells. However, these modifiers may be utilised differently in highly specialised and divergent organisms, such as parasitic protozoa. In this review, we explore how these parasites employ Ubls, in particular SUMO, NEDD8, ATG8, ATG12, URM1, and UFM1, to regulate their unconventional cellular physiology. We discuss emerging data that provide evidence of Ubl-mediated regulation of unique parasite-specific processes, as well as the distinctive features of Ubl pathways in parasitic protozoa. We also highlight the potential to leverage these essential regulators and their cognate enzymatic machinery for development of therapeutics to protect against the diseases caused by protozoan parasites.
Non‐sterile corn steep liquor a novel, cost effective and powerful culture media for Sporosarcina pasteurii cultivation for sand improvement

Microbial induced calcium carbonate precipitation (MICP) is one of the bio‐cementation methods for improving granular soils. This study evaluate the feasibility of obtaining a bacterial solution with high optical density and urease activity by an inexpensive corn steep liquor (CSL) medium in non‐sterile conditions in order to achieve sand improvement.
Transform-Based Multiresolution Decomposition for Degradation Detection in Cellular Networks

Anomaly detection in the performance of the huge number of elements that are part of cellular networks (base stations, core entities, and user equipment) is one of the most time consuming and key activities for supporting failure management procedures and ensuring the required performance of the telecommunication services. This activity originally relied on direct human inspection of cellular metrics (counters, key performance indicators, etc.). Currently, degradation detection procedures have experienced an evolution towards the use of automatic mechanisms of statistical analysis and machine learning. However, pre-existent solutions typically rely on the manual definition of the values to be considered abnormal or on large sets of labeled data, highly reducing their performance in the presence of long-term trends in the metrics or previously unknown patterns of degradation. In this field, the present work proposes a novel application of transform-based analysis, using wavelet transform, for the detection and study of network degradations. The proposed system is tested using cell-level metrics obtained from a real-world LTE cellular network, showing its capabilities to detect and characterize anomalies of different patterns and in the presence of varied temporal trends. This is performed without the need for manually establishing normality thresholds and taking advantage of wavelet transform capabilities to separate the metrics in multiple time-frequency components. Our results show how direct statistical analysis of these components allows for a successful detection of anomalies beyond the capabilities of detection of previous methods.
Short ELF-EMF Exposure Targets SIRT1/Nrf2/HO-1 Signaling in THP-1 Cells

Extremely low frequency electromagnetic fields (ELF-EMFs) have been known to modulate inflammatory responses by targeting signal transduction pathways and influencing cellular redox balance through the generation of oxidants and antioxidants. Here, we studied the molecular mechanism underlying the anti-oxidative effect of ELF-EMF in THP-1 cells, particularly with respect to antioxidant enzymes, such as heme oxygenase-1 (HO-1), regulated transcriptionally through nuclear factor E2-related factor 2 (Nrf2) activation. Cells treated with lipopolysaccharides (LPS) were exposed to a 50 Hz, 1 mT extremely low frequency electromagnetic fields for 1 h, 6 h and, 24 h. Our results indicate that ELF-EMF induced HO-1 mRNA and protein expression in LPS-treated THP-1 cells, with peak expression at 6 h, accompanied with a concomitant migration to the nucleus of a truncated HO-1 protein form. The immunostaining analysis further verified a nuclear enrichment of HO-1. Moreover, ELF-EMF inhibited the protein expressions of the sirtuin1 (SIRT1) and nuclear factor kappa B (NF-kB) pathways, confirming their anti-inflammatory/antioxidative role. Pretreatment with LY294002 (Akt inhibitor) and PD980559 (ERK inhibitor) inhibited LPS-induced Nrf2 nuclear translocation and HO-1 protein expression in ELF-EMF-exposed cells. Taken together, our results suggest that short ELF-EMF exposure exerts a protective role in THP-1 cells treated with an inflammatory/oxidative insult such as LPS, via the regulation of Nrf-2/HO-1 and SIRT1 /NF-kB pathways associated with intracellular glutathione (GSH) accumulation.
The Anti-Obesogenic Effect of Lean Fish Species Is Influenced by the Fatty Acid Composition in Fish Fillets

Fillets from marine fish species contain n-3 polyunsaturated fatty acids (PUFAs) in the form of phospholipids (PLs). To investigate the importance of PL-bound n-3 PUFAs in mediating the anti-obesogenic effect of lean seafood, we compared the anti-obesogenic properties of fillets from cod with fillets from pangasius, a fresh water fish with a very low content of PL-bound n-3 PUFAs. We prepared high-fat/high-protein diets using chicken, cod and pangasius as the protein sources, and fed male C57BL/6J mice these diets for 12 weeks. Mice fed the diet containing cod gained less adipose tissue mass and had smaller white adipocytes than mice fed the chicken-containing diet, whereas mice fed the pangasius-containing diet were in between mice fed the chicken-containing diet and mice fed the cod-containing diet. Of note, mice fed the pangasius-containing diet exhibited reduced glucose tolerance compared to mice fed the cod-containing diet. Although the sum of marine n-3 PUFAs comprised less than 2% of the total fatty acids in the cod-containing diet, this was sufficient to significantly increase the levels of eicosapentaenoic acid (EPA) and docosahexaenoic acids (DHA) in mouse tissues and enhance production of n-3 PUFA-derived lipid mediators as compared with mice fed pangasius or chicken.
COPD in the major nonsmoking adult: A systematic review and meta-analysis

Abstract Chronic Obstructive Pulmonary Disease (COPD) main cause is attributed to active smokers, but there's a small percentage that comes from risk factors that have been less considered. The aim of this research was to identify the risk factors and the clinical presentation of the population over 64 years of age that lead to the development of COPD. A systematic review and a meta-analysis was performed. From the 92 studies interpreted, we identified seven studies on the presence of COPD in nonsmokers older adults, having a universe of 14,920 patients. The primary risk factor to trigger the development of COPD was secondhand smoking. The study defined the most common risk factors that currently trigger COPD development among nonsmokers and provided an insight into the potential clinical differences between nonsmokers and smokers.
Knowledge and practice of hand hygiene among undergraduate students and junior doctors in the Regional Institute of Medical Sciences, Imphal

Context: Maintenance of proper hand hygiene among treating doctors and nurses is one of the most important measures to curb health-care-associated infections.Hand hygiene can prevent the spread of germs including those that are resistant to antibiotics and are becoming difficult, if not impossible, to treat.There are few published articles on similar topic in different settings in India but not in Manipur. Keeping this in mind, the study was conducted. Aims: To assess the knowledge and practice of hand hygiene among undergraduate students and junior doctors in rims, imphal and its association with the selected variables of interest. Settings and Design: Regional Institute of Medical Sciences (RIMS). Methods and Material: A cross-sectional study was done on 924 participants by using a self-administered questionnaire. The data was analyzed using the software SPSS 21 version. Results: Of the participants, 49.1% had poor knowledge about hand hygiene; 14.3% had average knowledge, and 36.6% had good knowledge. Knowledge was significantly associated with the frequency of washing hands after patient contact or any laboratory procedure or after the removal of hand gloves (P < 0.001) and the frequency of following the six steps of hand washing (P = 0.001). Conclusions: Nearly half (49.1%) of the participants had poor knowledge about hand hygiene; more than one-tenth (14.3%) had average knowledge, and more than one-third (36.6%) had good knowledge.
Prevalence of COVID-19-related anxiety among healthcare workers: A cross-sectional study

Introduction: COVID-19 was labeled as a pandemic in March 2020. Healthcare workers (HCW) are confronting great mental stressors in coping with the crisis. In Saudi Arabia, research on the psychological effect of COVID-19 on HCW is lacking. Aim: To evaluate COVID-19 psychological impact on HCW and determine anxiety predictors to identify high-risk individuals. Materials and Methods: A descriptive cross-sectional study was conducted on HCW in First Health Cluster Institutes in Eastern Province. An English self-administered questionnaire was adopted from similar research done in China. The original questionnaires were modified to meet the objectives of our study and suit Saudi sociodemographic differences. Generalized anxiety disorder-7 scale was incorporated to be the main tool for assessing the psychological impact. Results: One-third of HCW were classified as having anxiety disorder. In univariate analyses, the age group in years (P = 0.026), gender (P = 0.001), nationality (P = 0.033), and living with family (P = 0.007) significantly influenced anxiety disorder. However, in the multivariate regression model, gender (P = 0.004), living with family (P = 0.021), family history of COVID-19 (P = 0.022), and been suspected or confirmed with COVID-19 infection (P = 0.018) remained statistically significant when compared to anxiety disorder. Conclusion: During early COVID-19 pandemic, anxiety disorder among HCW was noticeable. Being a female, living with family members, and having a family history of COVID-19 increased the risk for anxiety disorder.
Which obesity index is a better predictor for cardiometabolic risk factors in a young adult rural population of Telangana State, India?

Background: Waist-to-height ratio (WHtR) has recently been found to be a useful marker of cardiovascular disease (CVD) risk in populations in developed countries; the comparison of various obesity indices, particularly WHtR, has received little study in India and other developing countries. Aim: This study aimed to compare the associations of common obesity indices, body mass index (BMI), waist circumference, waist-hip ratio (WHR), and WHtR, with cardiometabolic risk factors in a young, rural Indian population. Subjects and Methods: Anthropometric measurements and cardiometabolic risk factors (hypertension, diabetes, and dyslipidemia) were measured using standardized protocols at the baseline visit of the Longitudinal Indian Family hEalth Pilot Study, a population-based cohort study of child-bearing age women and their husbands in rural Telangana, India. Results: In comparison with most previously studied populations, this population sample (642 males and 980 females) was younger; had lower BMI; and lower rates of diabetes, hypertension, and abnormal lipids (exception of high rates of low high-density lipoprotein). With regard to each of the cardiometabolic risk factors, the associations across the obesity indices tended to be significant, but weak, and similar to each other, whereas the association with WHR was less strong. Conclusion: Although WHtR was not a better predictor of cardiometabolic risk than conventional obesity indices, in this young adult Indian population, it was equally good. This raises the prospect of using WHtR as an alternative to BMI for assessing cardiometabolic risk in Indians considering the ease with which it can be easily done and interpreted.