JIB.tools 2.0 – A Bioinformatics Registry for Journal Published Tools with Interoperability to bio.tools

JIB.tools 2.0 is a new approach to more closely embed the curation process in the publication process. This website hosts the tools, software applications, databases and workflow systems published in the Journal of Integrative Bioinformatics (JIB). As soon as a new tool-related publication is published in JIB, the tool is posted to JIB.tools and can afterwards be easily transferred to bio.tools, a large information repository of software tools, databases and services for bioinformatics and the life sciences. In this way, an easily-accessible list of tools is provided which were published in JIB a well as status information regarding the underlying service. With newer registries like bio.tools providing these information on a bigger scale, JIB.tools 2.0 closes the gap between journal publications and registry publication. (Reference: https://jib.tools)

Treatment with obestatin : a ghrelin gene-encoded peptide : reduces the severity of experimental colitis evoked by trinitrobenzene sulfonic acid

Obestatin is a 23-amino acid peptide derived from proghrelin, a common prohormone for ghrelin and obestatin. Previous studies showed that obestatin exhibited some protective and therapeutic effects in the gut. The aim of our presented study was to examine the effect of treatment with obestatin on trinitrobenzene sulfonic acid (TNBS)-induced colitis. In rats anesthetized with ketamine, colitis was induced through intrarectal administration of 25 mg of 2,4,6-trinitrobenzene sulfonic acid (TNBS). Obestatin was administered intraperitoneally at doses of 4, 8, or 16 nmol/kg, twice per day for four consecutive days. The first dose of obestatin was given one day before the induction of colitis, and the last one was given two days after administration of TNBS. Fourteen days after the induction of colitis, rats were anesthetized again with ketamine, and the severity of colitis was determined. The administration of obestatin had no effect on the parameters tested in rats without the induction of colitis. In rats with colitis, administration of obestatin at doses of 8 or 16 nmol/kg reduced the area of colonic damage, and improved mucosal blood flow in the colon. These effects were accompanied by a reduction in the colitis-evoked increase in the level of blood leukocytes, and mucosal concentration of pro-inflammatory interleukin-1β. Moreover, obestatin administered at doses of 8 or 16 nmol/kg reduced histological signs of colonic damage. The administration of obestatin at a dose of 4 nmol/kg failed to significantly affect the parameters tested. Overall, treatment with obestatin reduced the severity of TNBS-induced colitis in rats. This effect was associated with an improvement in mucosal blood flow in the colon, and a decrease in local and systemic inflammatory processes

A patient with the hepatorenal syndrome treated with a liver transplant — case description with duties of the nursing staff

Transplantacja wątroby (LTx) jest leczeniem z wyboru w przypadku zespołu wątrobowo-nerkowego (HRS). Pacjenci oczekujący na przeszczep w stanie zdekompensowanej marskości wątroby z niewydolnością nerek stanowią grupę potencjalnych biorców wysokiego ryzyka rozwoju poważnych powikłań i zgonu w okresie oczekiwania na przeszczep. W pracy przedstawiono przypadek pacjenta z niewydolną marską wątrobą w przebiegu toksycznego jej uszkodzenia, u którego doszło do rozwoju HRS typu I. Chorego zakwalifikowano do pilnego przeszczepu wątroby. W okresie oczekiwania na zabieg poddany był hemodializom. Po transplantacji nastąpiła normalizacja parametrów wątrobowych i nerkowych. W dalszym okresie potransplantacyjnym stężenie kreatyniny obniżyło się do 0,6–1,0 mg/dl. U chorego w okresie oczekiwania na transplantację dominowały problemy wynikające z marskości wątroby oraz niewydolności nerek: żółtaczka, wodobrzusze, obrzęki kończyn dolnych, wyniszczenie, encefalopatia, zaburzenia krzepnięcia, zaburzenia hemodynamiczne, bezmocz. Zadania podejmowane przez personel pielęgniarski zależały od zmieniającego się stanu zdrowia pacjenta i stosowaną terapią mającą na celu utrzymanie go przy życiu i zapewnienie mu opieki do czasu uzyskania przeszczepu.Liver transplantation (LTx) is the first-line treatment for hepatorenal syndrome (HRS). Patients awaiting LTx with decompensated cirrhosis and renal failure are a group of potential recipients with a high risk of developing serious complications and death in the period of expecting for a transplant. The work presents the case of a patient with cirrhosis and a failing liver due to toxic-induced damage; the patient developed HRS type 1. The patient required urgent LTx. During the waiting period s/he undergone haemodialyses. After LTx, there was a normalization in the hepatic and renal parameters. In the ensuing post-transplantation period, the concentration of creatine went down to 0,6–1,0 mg/dl. During waiting for treatment, the patient suffered chiefly from conditions related to cirrhosis and renal failure: jaundice, abdominal dropsy, edema of lower extremity, emaciation, encephalopathy, coagulation disorder, hemodynamic disorder, and anuria. The activities of medical personnel were subject to the patient’s changing condition and employed therapy that was to keep the patient alive and provide safety until the transplantation

Impact of marathon performance on muscles stiffness in runners over 50 years old

IntroductionThe research examines the relationship between marathon performance and muscle stiffness changes from pre to marathon in recreational runners aged 50+ years.MethodsThirty-one male long-distance runners aged 50–73 years participated in the experiment. The muscle stiffness of quadriceps and calves was measured in two independent sessions: the day before the marathon and 30 min after the completed marathon run using a Myoton device.Results and DiscussionThe 42.195-km run was completed in 4.30,05 h ± 35.12 min, which indicates an intensity of 79.3% ± 7.1% of HRmax. The long-term, low-intensity running exercise (marathon) in older recreational runners and the low level of HRmax and VO2max showed no statistically significant changes in muscle stiffness (quadriceps and calves). There was reduced muscle stiffness (p = 0.016), but only in the triceps of the calf in the dominant (left) leg. Moreover, to optimally evaluate the marathon and adequately prepare for the performance training program, we need to consider the direct and indirect analyses of the running economy, running technique, and HRmax and VO2max variables. These variables significantly affect marathon exercise

Study protocol : Minimum effective low dose: anti-human thymocyte globulin (MELD-ATG): phase II, dose ranging, efficacy study of antithymocyte globulin (ATG) within 6 weeks of diagnosis of type 1 diabetes

Introduction Type 1 diabetes (T1D) is a chronic autoimmune disease, characterised by progressive destruction of the insulin-producing beta cells of the pancreas. One immunosuppressive agent that has recently shown promise in the treatment of new-onset T1D subjects aged 12-45 years is antithymocyte globulin (ATG), Thymoglobuline, encouraging further exploration in lower age groups. Methods and analysis Minimal effective low dose (MELD)-ATG is a phase 2, multicentre, randomised, double-blind, placebo-controlled, multiarm parallel-group trial in participants 5-25 years diagnosed with T1D within 3-9 weeks of planned treatment day 1. A total of 114 participants will be recruited sequentially into seven different cohorts with the first cohort of 30 participants being randomised to placebo, 2.5 mg/kg, 1.5 mg/kg, 0.5 mg/kg and 0.1 mg/kg ATG total dose in a 1:1:1:1:1 allocation ratio. The next six cohorts of 12-15 participants will be randomised to placebo, 2.5 mg/kg, and one or two selected middle ATG total doses in a 1:1:1:1 or 1:1:1 allocation ratio, as dependent on the number of middle doses, given intravenously over two consecutive days. The primary objective will be to determine the changes in stimulated C-peptide response over the first 2 hours of a mixed meal tolerance test at 12 months for 2.5 mg/kg ATG arm vs the placebo. Conditional on finding a significant difference at 2.5 mg/kg, a minimally effective dose will be sought. Secondary objectives include the determination of the effects of a particular ATG treatment dose on (1) stimulated C-peptide, (2) glycated haemoglobin, (3) daily insulin dose, (4) time in range by intermittent continuous glucose monitoring measures, (5) fasting and stimulated dry blood spot (DBS) C-peptide measurements. Ethics and dissemination MELD-ATG received first regulatory and ethical approvals in Belgium in September 2020 and from the German and UK regulators as of February 2021. The publication policy is set in the INNODIA (An innovative approach towards understanding and arresting Type 1 diabetes consortium) grant agreement (www.innodia.eu).Peer reviewe

Novel variation and <i>de novo </i>mutation rates in population-wide <i>de novo</i> assembled Danish trios

Building a population-specific catalogue of single nucleotide variants (SNVs), indels and structural variants (SVs) with frequencies, termed a national pan-genome, is critical for further advancing clinical and public health genetics in large cohorts. Here we report a Danish pan-genome obtained from sequencing 10 trios to high depth (50 × ). We report 536k novel SNVs and 283k novel short indels from mapping approaches and develop a population-wide de novo assembly approach to identify 132k novel indels larger than 10 nucleotides with low false discovery rates. We identify a higher proportion of indels and SVs than previous efforts showing the merits of high coverage and de novo assembly approaches. In addition, we use trio information to identify de novo mutations and use a probabilistic method to provide direct estimates of 1.27e−8 and 1.5e−9 per nucleotide per generation for SNVs and indels, respectively