Challenges and perspectives for naming lipids in the context of lipidomics.

INTRODUCTION: Lipids are key compounds in the study of metabolism and are increasingly studied in biology projects. It is a very broad family that encompasses many compounds, and the name of the same compound may vary depending on the community where they are studied. OBJECTIVES: In addition, their structures are varied and complex, which complicates their analysis. Indeed, the structural resolution does not always allow a complete level of annotation so the actual compound analysed will vary from study to study and should be clearly stated. For all these reasons the identification and naming of lipids is complicated and very variable from one study to another, it needs to be harmonized. METHODS & RESULTS: In this position paper we will present and discuss the different way to name lipids (with chemoinformatic and semantic identifiers) and their importance to share lipidomic results. CONCLUSION: Homogenising this identification and adopting the same rules is essential to be able to share data within the community and to map data on functional networks.

Budesonide Versus Mesalamine in Microscopic Colitis: A Comparative Meta-analysis of Randomized Controlled Trials.

BACKGROUND: Microscopic colitis (MC) is an inflammatory bowel disease of autoimmune origin that causes chronic watery diarrhea. Medications, including budesonide, mesalamine, loperamide, cholestyramine, and bismuth subsalicylate, are first-line therapies. Meanwhile, azathioprine, 6-mercaptopurine, and methotrexate are indicated for refractory MC. OBJECTIVE: We aim to assess the efficacy and safety of budesonide compared with mesalamine for induction of remission in MC patients. METHODS: We searched the Cochrane Library, Scopus, Web of Science, and PubMed for relevant clinical trials comparing either mesalamine or budesonide with a control group. We included the following outcomes: clinical remission (3 or fewer stools/day), daily stool weight, daily stool frequency, number of patients with clinical response <50% in the disease activity, and daily stool consistency. Safety end points included: any adverse event, serious adverse events, any adverse event-related discontinuation, abdominal discomfort, constipation, flatulence, nausea, dizziness, headache, bronchitis, nasopharyngitis, and depression. We conducted a meta-analysis model using the generic inverse variance method and performed a subgroup analysis based on the intervention administered. RESULTS: Nineteen randomized clinical trials were included. We found that after 6 weeks of follow-up, budesonide is associated with increased clinical remission rates compared with mesalamine [RR=2.46 (2.27, 2.67), and RR=2.24 (1.95, 2.57), respectively]. However, the test of subgroup difference revealed that the difference is not significant (P=0.25). After 8 weeks of follow-up, budesonide showed significantly higher clinical remission rates than mesalamine RR=2.29 (2.14, 2.45), and RR=1.7 (1.41, 2.05), respectively (P=0.003). Regarding the daily stool weight, patients in the budesonide group showed nonsignificant less stool weight [MD=-351.62 (-534.25, -168.99)] compared with mesalamine [MD=-104.3 (-372.34, 163.74)], P=0.14. However, daily stool frequency was significantly less in the budesonide group compared with mesalamine (P<0.001). Budesonide is associated with a significantly lower incidence of adverse events compared with mesalamine (P=0.002). Analysis of other safety endpoints was not significant between both groups. CONCLUSIONS: Budesonide was found to be better than mesalamine in MC patients in terms of clinical remission rate, especially after 8 weeks of follow-up. Budesonide also showed less incidence of adverse events. There is an urgent need for randomized, double-blinded clinical trials to provide direct and reliable evidence.

Efficacy and safety of terlipressin and albumin vs. noradrenaline and albumin in adult patients with hepatorenal syndrome: A systematic review and meta-analysis.

INTRODUCTION AND OBJECTIVES: Hepatorenal syndrome (HRS) is a serious complication of cirrhosis treated with various medications. We aim to evaluate terlipressin and albumin's effectiveness and safety compared to albumin and noradrenaline in adult hepatorenal disease patients. MATERIALS AND METHODS: Clinical trials from four databases were included. Cochrane's approach for calculating bias risk was utilized. We rated the quality evaluation by Grading of Recommendations Assessment, Development, and Evaluation (GRADE). We included the following outcomes: serum creatinine (mg/dl), urine output (ml/24 h), mean arterial pressure (mmHg), reversal rate of HRS, mortality rate, blood plasma renin activity (ng/ml/h), plasma aldosterone concentration (pg/ml), urine sodium (mEq/l), and creatinine clearance (ml/min). RESULTS: Our analysis of nine clinical studies revealed that the noradrenaline group was associated with higher creatinine clearance (MD = 4.22 [0.40, 8.05]), (P = 0.03). There were no significant differences in serum creatinine levels (MD = 0.03 [-0.07, 0.13]), urinary sodium (MD = -1.02 [-5.15, 3.11]), urine output (MD = 32.75 [-93.94, 159.44]), mean arterial pressure (MD = 1.40 [-1.17, 3.96]), plasma renin activity (MD = 1.35 [-0.17, 2.87]), plasma aldosterone concentration (MD = 55.35 [-24.59, 135.29]), reversal rate of HRS (RR = 1.15 [0.96, 1.37]), or mortality rate (RR = 0.87 [0.74, 1.01]) between the two groups (p-values > 0.05). CONCLUSIONS: Noradrenaline is a safe alternative medical therapy for HRS.

Effects of curcumin in patients with non-alcoholic fatty liver disease: A systematic review and meta-analysis.

Background: Curcumin is an anti-inflammatory that is proposed to have a positive impact on patients with non-alcoholic fatty liver disease (NAFLD). We aim to assess the effects of curcumin in patients with NAFLD. Methods: Clinical trials from PubMed, Scopus, the Web of Science, and Cochrane CENTRAL with variables alanine transferase, aspartate transaminase, alkaline phosphatase, glycated hemoglobin (HBA1c), BMI, waist circumference, total cholesterol, total glycerides, high-density lipoproteins, and low-density lipoproteins were included. Homogeneous and heterogeneous were analyzed under a fixed-effects model and the random-effects model, respectively. Results: Fourteen clinical trials found that curcumin has no statistically significant effect on alanine transferase (MD = -2.20 [-6.03, 1.63], p = 0.26], aspartate transaminase (MD = 1.37 [-4.56, 1.81], p = 0.4), alkaline phosphatase (MD = 3.06 [-15.85, 9.73], p = 0.64), glycated hemoglobin (HBA1c), (MD = -0.06 [-0.13, 0.02], p = 0.16], and BMI (MD = 0.04 [-0.38, 0.46], p = 0.86). Curcumin reduced the waist circumference (MD = -4.87 [-8.50, -1.25], p = 0.008). Lipid profile parameters were not significant, except the total glycerides (MD = -13.22 [-24.19, -2.24], p = 0.02). Conclusions: Curcumin significantly reduces total glycerides and waist circumference in NAFLD.

Effects of silymarin use on liver enzymes and metabolic factors in metabolic dysfunction-associated steatotic liver disease: a systematic review and meta-analysis.

Background: Fatty liver disease comprises a wide range of related liver disorders affecting mainly people who drink no or minimal amounts of alcohol. Silymarin is a member of the Carduus marianum family that has been used for centuries to treat different diseases. There is little evidence supporting its efficacy in humans. Objectives: To evaluate the effects of Silymarin in patients with non alcoholic fatty liver disease (NAFLD) or recently renamed metabolic dysfunction-associated steatotic liver disease (MASLD). Methods: We searched PubMed, SCOPUS, Web of Science, and Cochrane Library for relevant clinical trials assessing the use of silymarin in patients with NAFLD. A risk of bias assessment was performed using Cochrane's risk of bias tool. We included the following outcomes: alanine aminotransferase (ALT), aspartate aminotransferase (AST), γ-glutamyl transferase (GGT), total cholesterol (TC), triglyceride (TG), high-density lipoprotein (HDL) (mg/dL), degree of fibrosis resolution, low-density lipoprotein (LDL), and HOMA-IR. We analyzed continuous data using mean difference (MD) and relative 95% confidence interval (CI). Results: We included nine clinical trials. We found that silymarin significantly reduced the levels of ALT (MD= -17.12 [-28.81, -4.43]), (P < 0.004), AST (MD= -12.56 [-19.02, -6.10]), (P < 0.0001) and TG (MD = -22.60 [-23.83, -21.38]) (p < 0.00001). It also improved HDL (MD= 2.13 [1.60, 2.66]), (P < 0.01)). There was no significant difference regarding GGT (P=o.07), TC (P= 0.52), LDL (P= 0.06), HOMA-IR (P= 0.06) and BMI (p=0.1).One study reported significant improvement in the degree of fibrosis (P = 0.023). Conclusion: Silymarin treatment significantly reduces biochemical and transaminase levels in patients with MASLD.

The Risk of Infection-Caused Mortality in Gastric Adenocarcinoma: A Population-Based Study.

Background: Gastric adenocarcinoma (GAC) is a deadly tumor. Postoperative complications, including infections, worsen its prognosis and may affect overall survival. Little is known about perioperative complications as well as modifiable and non-modifiable risk factors. Early detection and treatment of these risk factors may affect overall survival and mortality. Methods: We extracted GAC patient's data from the Surveillance, Epidemiology, and End Results (SEER) database and analyzed using Pearson's Chi-square, Cox regression, Kaplan-Meier, and binary regression methods in SPSS. Results: At the time of analysis, 59,580 GAC patients were identified, of which 854 died of infection. Overall, mean survival in months was better for younger patients, age < 50 years vs. ≥ 50 years (60.45 vs. 56.75), and in females vs. males (65.23 vs. 53.24). The multivariate analysis showed that the risk of infectious mortality was higher in patients with age ≥ 50 years (hazard ratio (HR): 3.137; 95% confidence interval (CI): 2.178 - 4.517), not treated with chemotherapy (HR: 1.669; 95% CI: 1.356 - 2.056), or surgery (HR: 1.412; 95% CI:1.132 - 1.761) and unstaged patients (HR: 1.699; 95% CI: 1.278 - 2.258). In contrast, the mortality risk was lower in females (HR: 0.658; 95% CI: 0.561 - 0.773) and married patients (HR: 0.627; 95% CI: 0.506 - 0.778). The probability of infection was higher in older patients (odds ratio (OR) of 2.094 in ≥ 50 years), other races in comparison to Whites and Blacks (OR: 1.226), lesser curvature, not other specified (NOS) as a primary site (OR: 1.325), and patients not receiving chemotherapy (OR: 1.258). Conclusion: Older, unmarried males with GAC who are not treated with chemotherapy or surgery are at a higher risk for infection-caused mortality and should be given special attention while receiving treatment.

Histopathological features of idiopathic portal hypertension: A systematic review and meta-analysis.

BACKGROUND: Portal hypertension (PH) is a clinically significant entity that could present with life-threatening gastrointestinal bleeding. Cirrhosis is the most common cause of PH, with well-documented histopathology and etiology. However, in idiopathic portal hypertension (IPH), no single histopathologic finding is associated with PH. Our systematic review aims to identify and summarize the prevalence of the common histological findings of IPH. METHODS: We systematically searched PubMed, Cochrane CENTRAL, Web of Science, and Scopus till 1ST March 2022 for studies describing the histopathological features of IPH. Data were extracted from eligible studies and pooled as events rate and 95% confidence interval (CI) using binary random-effects model by open meta-analyst software. RESULTS: We included 23 retrospective studies with a total sample size of 813 patients. The overall incidence of nodular regenerative hyperplasia was 38.6%, 59.8% for portal fibrosis, 51.3% for periportal fibrosis, 39.3% for perisinusoidal fibrosis, 89.8% for portal vein sclerosis, 42.2% for portal inflammation, 53.3% for mega-sinusoids, 39.5% for thickening of portal vein branches, 93.8% for narrowing of portal veins, 53.3% for hepatic veins/venous outflow obstruction, 51.4% for aberrant portal/periportal vessels, 42.4% for shunt vessel, 50.9% for ductular proliferation, and 16.3% for steatosis. CONCLUSION: Due to the relatively non-pathognomonic and non-specific nature of IPH, a combination of different histological features such as the portal and periportal fibrosis, portal vein sclerosis, mega-sinusoids, narrowing of portal veins, hepatic venous outflow obstruction, aberrant portal or periportal vessels, and ductular proliferation may be of value in diagnosing IPH as the incidence rate of these features was at approximately 50%.

Incidental Diagnosis of Malignant Peritoneal Mesothelioma During Liver Transplantation Surgery: A Case Report.

BACKGROUND Malignant peritoneal mesothelioma (MPM) is a rare, lethal tumor of serous membranes. The most common factor reported in association with MPM is asbestos exposure, while viral infections, genetic predisposition, paraneoplastic syndrome, and altered immunity have been described as well. The diagnosis can be challenging among those with lower tumor burden as well as nonspecific symptoms, and it is not unusual to discover the diagnosis incidentally. CASE REPORT A middle-aged woman with decompensated cirrhosis underwent extensive pre-transplant workup, showing no evidence of malignancy. She had a personal history of asbestos exposure and family history of MPM in the extended family. During transplant surgery, a few peritoneal nodules were noted, leading to termination of the procedure. Pathological analysis confirmed malignant MPM. A multidisciplinary discussion led to following a conservative treatment approach without any intervention, due to higher risk of worsening hepatic decompensation associated with peritonectomy and intraperitoneal chemotherapy. The patient's hepatic decompensation resolved 6 months after the aborted liver transplant operation. Since the diagnosis of MPM, positron emission tomography scans have shown no recurrence of MPM for 3 consecutive years. CONCLUSIONS This is the first case of MPM diagnosed incidentally during a liver transplantation surgery. This case highlights the challenges in the diagnosis and management of MPM in a patient with decompensated liver disease. A multidisciplinary approach and following a consensus decision led to prolonged survival in the described patient.

Efficacy and safety of laparoscopic Heller's myotomy versus pneumatic dilatation for achalasia: A systematic review and meta-analysis of randomized controlled trials.

BACKGROUND AND OBJECTIVES: Achalasia has several treatment modalities. We aim to compare the efficacy and safety of laparoscopic Heller myotomy (LHM) with those of pneumatic dilatation (PD) in adult patients suffering from achalasia. METHODS: We searched Cochrane CENTRAL, PubMed, Web of Science, SCOPUS and Embase for related clinical trials about patients suffering from achalasia. The quality appraisal and assessment of risk of bias were conducted with GRADE and Cochrane's risk of bias tool, respectively. Homogeneous and heterogeneous data was analyzed under fixed and random-effects models, respectively. RESULTS: The pooled analysis of 10 studies showed that PD was associated with a higher rate of remission at three months, one year, three years and five years (RR = 1.25 [1.09, 1.42] (p = 0.001); RR = 1.13 [1.05, 1.20] (p = 0.0004); RR = 1.48 [1.19, 1.82] (p = 0.0003); RR = 1.49 [1.18, 1.89] (p = 0.001)), respectively. LHM was associated with lower number of cases suffering from adverse events, dysphagia and relapses (RR = 0.50 [0.25, 0.98] (p = 0.04); RR = 0.33 [0.16, 0.71] (p = 0.004); RR = 0.38 [0.15, 0.97] (p = 0.04)), respectively. There is no significant difference between both groups regarding the lower esophageal pressure, perforations, remission rate at two years, Eckardt score after one year and reflux. CONCLUSION: PD had higher remission rates than LHM at three months, one year and three years, but not at two years or five years. More research is needed to determine whether PD has a significant advantage over LHM in terms of long-term remission rates.

Impact of left ventricular assist devices on 30-day readmission and outcomes in non-variceal upper gastrointestinal bleeding: a nationwide analysis.

Introduction: Bleeding, especially non-variceal upper gastrointestinal bleeding (NVUGIB), remains the most common cause of readmission in left ventricular assist device (LVAD) patients. Any readmission after NVUGIB carries a worse prognosis. Aim: To compare readmission outcomes in NVUGIB patients with and without LVAD. Material and methods: We identified adult NVUGIB patients using the National Readmission Database 2018 employing International Classification of Diseases, Tenth Revision (ICD-10) codes. The patients were grouped based on LVAD history. Proportions were compared using the Fisher exact test, and multivariate Cox proportional regression analysis was used to compute adjusted p-values. We used Stata version 14.2 to perform analyses considering 2-sided p < 0.05 as statistically significant. Results: The analysis included 322,342 NVUGIB patients, 1403 had a history of LVAD (mean age 64.25 years). The 30-day all-cause readmission rate in NVUGIB with LVAD was higher (24.31% vs. 13.92%, p < 0.001). Gastrointestinal bleeding as a readmission cause was more prevalent in the LVAD group. In patients with LVAD, NVUGIB readmissions required more complex endoscopic procedures, either requiring intervention during endoscopy or enteroscopy. There was no difference in mortality in NVUGIB readmissions (1.51% vs. 4.49%, p = 0.36); however, the length and cost of stay were higher in the LVAD group. Additionally, we identified novel independent predictors of readmission from NVUGIB in patients with LVADs. Conclusions: Readmissions in NVUGIB patients after LVAD require complex haemostatic intervention and are associated with greater resource utilization. To reduce readmissions and associated healthcare costs, it is essential to identify high-risk patients.

Functional implications of glycans and their curation: insights from the workshop held at the 16th Annual International Biocuration Conference in Padua, Italy.

Dynamic changes in protein glycosylation impact human health and disease progression. However, current resources that capture disease and phenotype information focus primarily on the macromolecules within the central dogma of molecular biology (DNA, RNA, proteins). To gain a better understanding of organisms, there is a need to capture the functional impact of glycans and glycosylation on biological processes. A workshop titled "Functional impact of glycans and their curation" was held in conjunction with the 16th Annual International Biocuration Conference to discuss ongoing worldwide activities related to glycan function curation. This workshop brought together subject matter experts, tool developers, and biocurators from over 20 projects and bioinformatics resources. Participants discussed four key topics for each of their resources: (i) how they curate glycan function-related data from publications and other sources, (ii) what type of data they would like to acquire, (iii) what data they currently have, and (iv) what standards they use. Their answers contributed input that provided a comprehensive overview of state-of-the-art glycan function curation and annotations. This report summarizes the outcome of discussions, including potential solutions and areas where curators, data wranglers, and text mining experts can collaborate to address current gaps in glycan and glycosylation annotations, leveraging each other's work to improve their respective resources and encourage impactful data sharing among resources. Database URL: https://wiki.glygen.org/Glycan_Function_Workshop_2023.