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The National Microbiome Data Collaborative (NMDC) is a multi-organizational effort to integrate microbiome data across diverse areas in environmental science. Data provided by the NMDC can then undergo advanced analysis and provide new insights into metagenomics, metatranscriptomics, metaproteomics, and metabolomics. To address these challenges, we have developed our schema using the Linked data Modeling Language (LinkML). This allows us to easily map data to existing standards and ontologies.

The article presents a case study of a 29-year-old HIV negative woman who was diagnosed with ulcerative colitis (UC) in her teens and developed jaundice with pruritus at the age of 26. A pancolitis and low and high-grade dysplasia was shown during the diagnosis. The patient was found to be cachectic, mildly encephalopathic on examination.

The article describes the case of a 22-year-old male who had acute ethylene glycol intoxication.

Background: Home dialysis therapies have limited uptake in most regions despite recognized benefits such as increasing patients' independence, and several domains of quality of life with cost savings in some systems., Objective: To perform a scoping review of published literature to identify tools and guides used in systematically screening and assessing patient suitability for home dialysis. A secondary objective was to explore barriers and enablers associated with the home dialysis assessment process. It is important to identify gaps in current research to pose pertinent questions for future work in the field., Design: Online databases Embase, Medline (Ovid), and CINAHL were used to identify articles published between January 2007 to May 2023. A total of 23 peer-reviewed primary and secondary studies that investigated screening or selection for patients > 18 years old with kidney failure for home dialysis met the study inclusion criteria., Results: The studies consisted of secondary studies (n = 10), observational studies (n = 8), and survey-based studies (n = 5). The major themes identified that influence patient screening and assessment for home dialysis candidacy included: screening tools and guidelines (n = 8), relative contraindications (n = 4), patient or program education (n = 9), and socioeconomic factors (n = 2)., Limitations: Consistent with the scoping review methodology, the methodological quality of included studies was not assessed. The possible omission of evidence in languages other than English is a limitation., Conclusion: This scoping review identified tools and factors that potentially guide the assessment process for home dialysis candidacy. Patient screening and assessment for home dialysis requires a comprehensive evaluation of clinical, psychosocial, and logistical factors. Further research is required to validate and refine existing tools to establish standardized patient screening criteria and evaluation processes. Up-to-date training and education for healthcare providers and patients are needed to improve the utilization of home dialysis and ensure optimal outcomes., Competing Interests: Declaration of conflicting interestsThe authors declared no potential conflicts of interest with respect to the research, authorship, and/or publication of this article.

Purpose of the Review: The purpose of the review is to discuss current proven benefits and problems of integrating exercise in the care of people receiving dialysis by reviewing literature from the last few years and identifying important questions that still need to be asked and answered., Methods: A focused review and appraisal of the literature were done. Original peer-reviewed articles, review articles, opinion pieces and guidelines were identified from PubMed and Google Scholar databases. Only sources in English were accessed. Search terms "exercise" and "dialysis" were used to find active recruiting randomized trials in various clinical trial registry platforms., Key Findings: Numerous studies have demonstrated the benefits of exercise training in individuals receiving dialysis, limited by factors such as short duration of follow-up and inconsistent adverse event reporting and outcomes selected. Notable gaps in exercise research in dialysis include ways to maintain programs and patient motivation, studies in peritoneal dialysis and home hemodialysis patients, and how best to define and measure outcomes of interest., Implications: This review summarizes the current state of exercise in people receiving dialysis and serves as a call to action to conduct large, randomized controlled trials to improve the quality of evidence needed to implement and sustain innovative, exercise interventions, and programs for this population., Competing Interests: The author(s) declared no potential conflicts of interest with respect to the research, authorship, and/or publication of this article., (© The Author(s) 2024.)

The wave of kidney and heart outcome trials, showing multiple potential benefits for sodium-glucose co-transport 2 (SGLT2) inhibitors, have excluded patients with an estimated glomerular filtration rate below 25 ml/min/1.73 m 2 . However, dialysis patients are at the highest risk of cardiovascular disease and would benefit most from effective cardioprotective therapies. There is emerging evidence from experimental studies and post hoc analyses of randomised clinical trials that SGLT2 inhibitors are well tolerated and may also be effective in preventing cardiovascular and mortality outcomes in patients with severe chronic kidney disease, including patients receiving dialysis. As such, extending the usage of SGLT2 inhibitors to dialysis patients could provide a major advancement in their care. Peritoneal dialysis (PD) patients have an additional unmet need for effective pharmacotherapy to preserve their residual kidney function (RKF), with its associated mortality benefits, and for treatment options that help reduce the risk of transfer to haemodialysis. Experimental data suggest that SGLT2 inhibitors, via various mechanisms, may preserve RKF and protect the peritoneal membrane. There is sound physiological rationale and an urgent clinical need to execute robust randomised control trials to study the use of SGLT2 inhibitors in PD patients to answer important questions of relevance to patients and healthcare systems.

Background: Blood pressure (BP) management can decrease morbidity and mortality in chronic kidney disease (CKD) patients. Evidence-based hypertension guidelines endorse home BP monitoring (HBPM), and the growing use of virtual health has highlighted the need for HBPM. A comprehensive understanding of HBPM adoption in our province is lacking., Objective: To identify the baseline practices, perspectives, barriers, and enablers in both providers and patients in our kidney care clinics regarding HBPM. Ultimately, this will inform the development of a provincial intervention that empowers providers to both increase patient understanding and equip them for accurate and reliable home BP measurement., Design: Cross-sectional, descriptive study using online survey methodology., Setting: Kidney care clinic network in the province of British Columbia, Canada., Patients or Sample or Participants: Kidney care clinic staff and patients who perform HBPM., Methods: Data were collected using semi-structured online surveys, one for staff and one for patients and/or caregivers. These surveys were developed by an interdisciplinary working group that included patient partners and addressed some key components of the implementation of an HBPM program (including perceived barriers to uptake, education, and adoption of best practices)., Results: In all, 46 patients and 43 staff responded to the survey from 16 kidney care clinics. Of the patients 53% were women, and the most common age range was 60 to 69 years (25%); 93% of the staff respondents were women and 63% were nurses. We identified numerous areas of discordance between providers and patients and the need for improvement from the perspective of implementing best practices from hypertension guidelines, both in staff teaching and patient usage of HBPM. Blood pressure targets were not known to 18% of patients and 39% of patients had received a BP target from their kidney care clinic team; 89% of patients had not had their upper arm circumference measured for cuff size. Furthermore, 54% of patients knew what to do when their BP is off-target. All recognized the benefits of HBPM, providers were more likely to perceive anxiety as a barrier relative to patients, and patients were more likely to report expense as a barrier than providers., Limitations: This study includes only a single provincial health care system limiting generalizability to other jurisdictions and sampled a small subset of patients and providers., Conclusions: The systematic evaluation of education, understanding, implementation of best practices, and barriers and motivating factors for HBPM from both patient and clinician perspectives is an important step in designing strategies to improve the use of HBPM. Given differences in staff and patient perspectives, targeted interventions based on these responses may lead to improved use of HBPM, and ultimately enhance hypertension self-management and BP control in our CKD patients., Competing Interests: The author(s) declared no potential conflicts of interest with respect to the research, authorship, and/or publication of this article., (© The Author(s) 2023.)

Many advances have been made in the field of nephrology over the last decade. These include an increasing focus on patient-centred involvement in trials, exploration of innovative trial designs and methodology, the growth of personalized medicine and, most importantly, novel therapeutic agents that are disease-modifying for large groups of patients with and without diabetes and chronic kidney disease. Despite this progress, many questions remain unanswered and we have not critically evaluated some of our assumptions, practices and guidelines despite emerging evidence to challenge current paradigms and discrepant patient-preferred outcomes. How best to implement best practices, diagnose various conditions, examine better diagnostic tools, treat laboratory values versus patients and understand prediction equations in the clinical context remain unanswered. As we enter a new era in nephrology, there are extraordinary opportunities to change the culture and care. Rigorous research paradigms enabling both the generation and the use of new information should be explored. We identify here some key areas of interest and suggest renewed efforts to describe and address these gaps so that we can develop, design and execute trials of importance to all., (© The Author(s) 2022. Published by Oxford University Press on behalf of the ERA.)

Background: Vascular calcification is a major risk factor for cardiovascular morbidity and mortality in patients with end-stage renal disease (ESRD). In Western countries, Blacks appear to have lesser degrees of vascular calcification compared to non-Blacks. However, there is no published data from sub-Saharan Africa., Materials and Methods: This study assessed the 5-year change in vascular calcification and mortality in a previously published cohort of patients with ESRD. Vascular calcification was assessed by abdominal aortic calcification score and vascular stiffness by pulse wave velocity (PWV)., Results: 66 of the original 74 participants studied at baseline were identified. The median age was 46.6 years (37.6 - 59.2), and 57.6% were women. Abdominal aortic calcification showed no progression among Blacks (baseline range 0 - 5, follow-up range 0 - 8 (p = 1.00)), but a trend to progression among non-Blacks (baseline range 0 - 19, follow up range 0 - 22 (p = 0.066)). Black participants did not display a survival advantage (p = 0.870). Non-Blacks had higher parathyroidectomy rates than Blacks with 9/30 cases compared to 2/36 (p = 0.036). After adjustment for parathyroidectomy at follow-up, the odds ratio of having abdominal vascular calcification score of ≥ 1 amongst non-Blacks was 8.6-fold greater compared to Blacks (p = 0.03). A positive correlation (r = 0.5) was observed between PWV and abdominal aortic calcification (p = 0.047). Elevated baseline coronary artery calcification score and FGF-23 level at baseline were not associated with a difference in mortality., Conclusion: There was no significant progression in vascular calcification among Blacks. After adjusting for increased parathyroidectomy rates, there was a greater progression of vascular calcification amongst non-Blacks compared to Blacks.

HIV-associated distal sensory polyneuropathy (DSP), with or without neuropathic symptoms, can develop after anti-retroviral therapy (ART). Symptoms frequently involve small fibres but reports on autonomic dysfunction in HIV-DSP are sparse. We studied an HIV-infected cohort after 5 years of ART, and report on the frequency and severity of autonomic symptoms and the impact of DSP on everyday function. This cross-sectional study comprised of participants from a community-based South African HIV-clinic. The Brief Peripheral Neuropathy Screen and reduced Total Neuropathy Score evaluated neuropathic symptoms/signs. DSP was defined as ≥2 symmetrical DSP-signs, and symptomatic DSP when accompanied by neuropathic symptoms. Autonomic symptoms questionnaires, heart rate variability and postural blood pressure changes were assessed. The Lower Extremity Functional Scale (LEFS) was completed. The 67 participants had a median age of 42 years and median ART exposure of 7 years with viral suppression in 84%. Most (81%) met our criteria for DSP and 36% had additional neuropathic symptoms. Autonomic symptoms and signs (above normative values) were present in 15% and more likely in those with symptomatic DSP (P < .001). Participants with DSP, even without symptoms, had lower LEFS scores (P ≤ .039) than those without. HIV-DSP is prevalent and impacts on daily living., (Copyright © 2019 Elsevier B.V. All rights reserved.)

Background: Acute interstitial nephritis (AIN) is a common cause of acute kidney injury that has not been adequately characterized in Sub-Saharan Africa (SSA) despite an increasing use of potentially inciting agents for the treatment of human immunodeficiency virus (HIV) and tuberculosis in the region., Methods: A retrospective audit of records of patients with biopsy-proven AIN diagnosed at Groote Schuur Hospital, Cape Town from the 1 st of January, 2006, to the 31 st of December, 2015., Results: 54 patients with biopsy-proven AIN were reviewed. The majority were of black African origin (59.2%), with HIV (42.8%) and HIV-tuberculosis coinfection (30.5%) as the most common comorbidities. Drug-related AIN was seen in 38 (67.9%) patients, with rifampicin as the most often implicated medication. Probable drug-related AIN was seen in 3 (5.4%) patients, infection-related AIN in 8 (14.3%), and unspecified causes in 4 (7.4%). AIN was suspected in 44.6% of patients before biopsy. 18 patients (34%) received hemodialysis, while 19 (35.2%) were treated with corticosteroids. Complete renal recovery at 30 and 90 days was seen in 23 (42.6%) patients and 24 (45.3%) patients, respectively, with the majority seen among those with drug-induced AIN. Six (11.1%) patients died; 4 (10.5%) of the patients were in the drug-related group. There was no correlation between degree of interstitial inflammation and severity of renal failure (p = 0.10). On multivariate logistic regression, drug-related causes of AIN were predictive of complete recovery at day 30 (OR 16.63; 95% CI: 1.71 - 161.6, p = 0.02), and presence of interstitial fibrosis reduced likelihood of recovery (OR 0.03; 95% CI 0.002 - 0.46, p = 0.012). Steroid use did not influence partial recovery (OR 0.59, 95% CI 0.17 - 1.77; p = 0.32) or complete recovery (OR 3.38, 95% CI 0.38 - 30.39, p = 0.28)., Conclusions: AIN is common in patients with HIV or those on treatment for tuberculosis. Drug-related AIN is often associated with improved outcomes. This is particularly reassuring in the SSA region where the use of potentially-inciting medications is rife from a high burden of HIV and tuberculosis.
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Objectives: Human immunodeficiency virus (HIV) and antiretroviral therapy (ART) are associated with renal disease and increased cardiovascular risk. The relationship between HIV and ambulatory blood pressure (ABP) non-dipping status, a risk factor for cardiovascular events and target-organ damage, has never been assessed in South Africa. Study objectives were to establish the prevalence of chronic kidney disease, and assess the ABP profile in asymptomatic HIV-positive clinic out-patients., Methods: This was a prospective cohort study. Office blood pressure (BP), urinary microalbumin-creatinine ratio, urine dipsticks, serum creatinine and estimated glomerular filtration rate (eGFR) were measured at baseline and six months after ART initiation. A subset of HIV-positive subjects and an HIV-negative control group underwent 24-hour ABP monitoring., Results: No patient had an eGFR < 60 ml/min, three patients (4.7%) had microalbuminuria and one had macroalbuminuria. Mean office systolic BP was 111 ± 14 mmHg at baseline and increased by 5 mmHg to 116 ± 14 mmHg (p = 0.05) at six months. This increase was not confirmed by ABP monitoring. In the HIV-positive and -negative patients, the prevalences of non-dipping were 80 and 52.9%, respectively (p = 0.05, odds ratio = 3.56, 95% CI: 0.96-13.13). No relationship between dipping status and ART usage was found., Conclusion: The prevalence of chronic kidney disease (CKD) was lower than anticipated. HIV infection was associated with an ambulatory non-dipping status, which suggests an underlying dysregulation of the cardiovascular system. In the short term, ART does not seem to improve loss of circadian rhythm.

The aim of this study was to assess and analyse the attitudes and beliefs of medical students regarding organ donation, procurement, and transplantation. Medical students at the University of Cape Town were prospectively surveyed using a self-administered questionnaire. There were 346 study participants; the mean age was 21 (range 18-33) yr, 38% were male and 62% was female. Only 8% of respondents were registered donors; clinical and white students constituted the majority of this group. Of the 315 "non-donors," the main reason for not donating was "I have not really thought about organ donation" (59%). Most students (91%) would accept an artificial organ; and 87% and 52% of students would accept human and animal organs respectively. Muslim students (11%, p<0.05) and those who believe in an after-life or reincarnation (18%, p=0.00) were less willing to accept human or animal organs. About 95% of respondents stated that they would like to learn more about transplantation and would keep information about it in their practice but only 18% of respondents knew where to find information for potential donors and recipients. Most students have a favorable attitude toward organ transplantation; religion and belief systems impact on willingness to receive organs., (© 2011 John Wiley & Sons A/S.)

myExperiment (http://www.myexperiment.org) is an online research environment that supports the social sharing of bioinformatics workflows. These workflows are procedures consisting of a series of computational tasks using web services, which may be performed on data from its retrieval, integration and analysis, to the visualization of the results. As a public repository of workflows, myExperiment allows anybody to discover those that are relevant to their research, which can then be reused and repurposed to their specific requirements. Conversely, developers can submit their workflows to myExperiment and enable them to be shared in a secure manner. Since its release in 2007, myExperiment currently has over 3500 registered users and contains more than 1000 workflows. The social aspect to the sharing of these workflows is facilitated by registered users forming virtual communities bound together by a common interest or research project. Contributors of workflows can build their reputation within these communities by receiving feedback and credit from individuals who reuse their work. Further documentation about myExperiment including its REST web service is available from http://wiki.myexperiment.org. Feedback and requests for support can be sent to bugs@myexperiment.org.