Meta-analysis of transcriptomic variation in T-cell populations reveals both variable and consistent signatures of gene expression and splicing.

Human CD4+ T cells are often subdivided into distinct subtypes, including Th1, Th2, Th17, and Treg cells, that are thought to carry out distinct functions in the body. Typically, these T-cell subpopulations are defined by the expression of distinct gene repertoires; however, there is variability between studies regarding the methods used for isolation and the markers used to define each T-cell subtype. Therefore, how reliably studies can be compared to one another remains an open question. Moreover, previous analysis of gene expression in CD4+ T-cell subsets has largely focused on gene expression rather than alternative splicing. Here we take a meta-analysis approach, comparing eleven independent RNA-seq studies of human Th1, Th2, Th17, and/or Treg cells to determine the consistency in gene expression and splicing within each subtype across studies. We find that known master-regulators are consistently enriched in the appropriate subtype; however, cytokines and other genes often used as markers are more variable. Importantly, we also identify previously unknown transcriptomic markers that appear to consistently differentiate between subsets, including a few Treg-specific splicing patterns. Together this work highlights the heterogeneity in gene expression between samples designated as the same subtype, but also suggests additional markers that can be used to define functional groupings.

Neurocysticercosis and HIV/AIDS co-infection: A scoping review.

OBJECTIVES: Neurocysticercosis (NCC) and human immunodeficiency virus (HIV) have a high disease burden and are prevalent in overlapping low- and middle-income areas. Yet, treatment guidance for people living with HIV/AIDS (PLWH/A) co-infected with NCC is currently lacking. This study aims to scope the available literature on HIV/AIDS and NCC co-infection, focusing on epidemiology, clinical characteristics, diagnostics and treatment outcomes. METHODS: The scoping literature review methodological framework, and the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines were followed. A total of 16,969 records identified through database searching, and 45 additional records from other sources were reduced to 52 included studies after a standardised selection process. RESULTS: Two experimental studies, ten observational studies, 23 case series/case reports and 17 reviews or letters were identified. Observational studies demonstrated similar NCC seroprevalence in PLWH/A and their HIV-negative counterparts. Of 29 PLWH/A and NCC co-infection, 17 (59%) suffered from epileptic seizures, 15 (52%) from headaches and 15 (52%) had focal neurological deficits. Eighteen (62%) had viable vesicular cysts, and six (21%) had calcified cysts. Fifteen (52%) were treated with albendazole, of which 11 (73%) responded well to treatment. Five individuals potentially demonstrated an immune-reconstitution inflammatory syndrome after commencing antiretroviral therapy, although this was in the absence of immunological and neuroimaging confirmation. CONCLUSIONS: There is a paucity of evidence to guide treatment of PLWH/A and NCC co-infection. There is a pressing need for high-quality studies in this patient group to appropriately inform diagnostic and management guidelines for HIV-positive patients with NCC.

COVID-19-related acute kidney injury; incidence, risk factors and outcomes in a large UK cohort.

BACKGROUND: Acute kidney injury (AKI) is common among patients hospitalised with COVID-19 and associated with worse prognosis. The aim of this study was to investigate the epidemiology, risk factors and outcomes of AKI in patients with COVID-19 in a large UK tertiary centre. METHODS: We analysed data of consecutive adults admitted with a laboratory-confirmed diagnosis of COVID-19 across two sites of a hospital in London, UK, from 1st January to 13th May 2020. RESULTS: Of the 1248 inpatients included, 487 (39%) experienced AKI (51% stage 1, 13% stage 2, and 36% stage 3). The weekly AKI incidence rate gradually increased to peak at week 5 (3.12 cases/100 patient-days), before reducing to its nadir (0.83 cases/100 patient-days) at the end the study period (week 10). Among AKI survivors, 84.0% had recovered renal function to pre-admission levels before discharge and none required on-going renal replacement therapy (RRT). Pre-existing renal impairment [odds ratio (OR) 3.05, 95%CI 2.24-4,18; p <  0.0001], and inpatient diuretic use (OR 1.79, 95%CI 1.27-2.53; p <  0.005) were independently associated with a higher risk for AKI. AKI was a strong predictor of 30-day mortality with an increasing risk across AKI stages [adjusted hazard ratio (HR) 1.59 (95%CI 1.19-2.13) for stage 1; p < 0.005, 2.71(95%CI 1.82-4.05); p < 0.001for stage 2 and 2.99 (95%CI 2.17-4.11); p < 0.001for stage 3]. One third of AKI3 survivors (30.7%), had newly established renal impairment at 3 to 6 months. CONCLUSIONS: This large UK cohort demonstrated a high AKI incidence and was associated with increased mortality even at stage 1. Inpatient diuretic use was linked to a higher AKI risk. One third of survivors with AKI3 exhibited newly established renal impairment already at 3-6 months.

Mapping RNA splicing variations in clinically accessible and nonaccessible tissues to facilitate Mendelian disease diagnosis using RNA-seq.

PURPOSE: RNA-seq is a promising approach to improve diagnoses by detecting pathogenic aberrations in RNA splicing that are missed by DNA sequencing. RNA-seq is typically performed on clinically accessible tissues (CATs) from blood and skin. RNA tissue specificity makes it difficult to identify aberrations in relevant but nonaccessible tissues (non-CATs). We determined how RNA-seq from CATs represent splicing in and across genes and non-CATs. METHODS: We quantified RNA splicing in 801 RNA-seq samples from 56 different adult and fetal tissues from Genotype-Tissue Expression Project (GTEx) and ArrayExpress. We identified genes and splicing events in each non-CAT and determined when RNA-seq in each CAT would inadequately represent them. We developed an online resource, MAJIQ-CAT, for exploring our analysis for specific genes and tissues. RESULTS: In non-CATs, 40.2% of genes have splicing that is inadequately represented by at least one CAT; 6.3% of genes have splicing inadequately represented by all CATs. A majority (52.1%) of inadequately represented genes are lowly expressed in CATs (transcripts per million (TPM) < 1), but 5.8% are inadequately represented despite being well expressed (TPM > 10). CONCLUSION: Many splicing events in non-CATs are inadequately evaluated using RNA-seq from CATs. MAJIQ-CAT allows users to explore which accessible tissues, if any, best represent splicing in genes and tissues of interest.

Systematic review and network meta-analysis of atrial fibrillation percutaneous catheter ablation technologies using randomized controlled trials.

AIMS: We sought out to make comparisons between all atrial fibrillation (AF) catheter ablation technologies using randomized controlled trial data. Our comparisons were freedom from AF, procedural duration, and fluoroscopy duration. METHODS: Searches were made of EMBASE, MEDLINE, and CENTRAL databases, and studies were selected which had cryoballoon, conventional radiofrequency (RF), multipolar RF catheters, and laser technology as an arm in the study and were identified as randomized controlled trials (RCTs). These studies were analyzed for direct comparisons using conventional meta-analysis and a combination of indirect and direct comparisons via a network meta-analysis (NMA). RESULTS: With respect to freedom from AF both direct comparisons and NMA did not demonstrate any significant difference. However in analysis of procedural and fluoroscopy duration (minutes) for the pulmonary vein ablation catheter (PVAC), both conventional analysis and NMA revealed significantly shorter procedure times, RF vs PVAC (conventional: 61.99 [38.03-85.94], P <.00001; NMA: 54.76 [36.64-72.88], P < .0001) and fluoroscopy times, RF vs PVAC (conventional: 12.96 [6.40-19.53], P = .0001; NMA: 8.89 [3.27-14.51], P < .01). The procedural duration was also shorter for the cryoballoon with NMA, RF vs CRYO (20.56 [3.47-37.65], P = .02). DISCUSSION: Our analysis demonstrated that while there was no difference in the efficacy of the individual catheter technologies, there are significant differences in the procedural duration for the PVAC and the cryoballoon. While they may seem an attractive solution for high-volume centers, further RCTs of next-generation technologies should be examined.

The Concept of Advocacy in Nursing: A Critical Analysis.

As health care professionals practice as a team, they take on responsibilities that are specific to their roles-responsibilities that are recognized and understood by the team and management as pertaining to their professional domain and expertise. Is advocacy part of the role of the nurse? Members of the nursing profession commonly maintain that it is, but is there a consensus on this issue, both within the profession and among other stakeholders? Is there a clear understanding of the term advocacy, and is this reflected in Codes of Practice and research into practice? An examination of significant documents and reports of empirical research reveals conflicting conceptions and opinions. There is potential for a common definition, but agreements need to be reached on whether advocacy is an essential function of nursing within the management of health care, and if so, what is advocacy's importance, focus, and limits.

Severe Disseminated Infection with Emerging Lineage of Methicillin-Sensitive Staphylococcus aureus.

We report a case of severe disseminated infection in an immunocompetent man caused by an emerging lineage of methicillin-sensitive Staphylococcus aureus clonal complex 398. Genes encoding classic virulence factors were absent. The patient made a slow recovery after multiple surgical interventions and a protracted course of intravenous flucloxacillin.

The Concept of Advocacy in Nursing: A Critical Analysis.

As health care professionals practice as a team, they take on responsibilities that are specific to their roles-responsibilities that are recognized and understood by the team and management as pertaining to their professional domain and expertise. Is advocacy part of the role of the nurse? Members of the nursing profession commonly maintain that it is, but is there a consensus on this issue, both within the profession and among other stakeholders? Is there a clear understanding of the term advocacy, and is this reflected in Codes of Practice and research into practice? An examination of significant documents and reports of empirical research reveals conflicting conceptions and opinions. There is potential for a common definition, but agreements need to be reached on whether advocacy is an essential function of nursing within the management of health care, and if so, what is advocacy's importance, focus, and limits.

Interferon-γ release assay screening in biologics: safe and reliable, but not perfect.

Background: Systemic biologic agents can increase the risk of re-activation of latent tuberculosis (TB). Prior to initiation, screening for latent TB using an interferon-γ release assay (IGRA) is recommended. There is concern that false-negative IGRAs may be more likely in this context. Methods: This retrospective analysis of IGRAs, specifically T-SPOT.TB, results and outcomes of patients already on or due to start biologics identifies the rate of TB re-activation in a low TB incidence setting. Additionally, we estimate the negative predictive value (NPV) of IGRAs in this population. Results: Patients on biologics were more likely to have a negative IGRA result than patients not on biologics. There was no statistically significant change in conversion or reversion rates between groups. Of 9263 patients on biologics, 19 developed active TB after starting biologics at an incidence rate of 55.1 per 100 000 patient-years. This occurred despite screening in half of the 16 patients for whom we were able to review medical records. Most drugs implicated were known to be high risk, although rituximab and natalizumab were being taken by five patients and one patient, respectively. The T-SPOT.TB NPV was 99.20% and dropped only slightly to 99.17% when we simulated an approach where all borderline IGRA results were regarded as being negative. Conclusions: Negative IGRA results confer a low risk of subsequent active TB in patients on biologics in a low TB incidence setting. However, continued awareness is needed given that a number of active TB cases will have had a prior negative result.

Risk of infective endocarditis after surgical and transcatheter aortic valve replacement.

OBJECTIVE: To define the incidence and risk factors for infective endocarditis (IE) following surgical aortic valve replacement (SAVR) and transcatheter aortic valve implantation (TAVI). METHODS: All patients who underwent first SAVR or TAVI in England between 2007 and 2016 were identified from the NICOR databases. Hospital admissions with a primary diagnosis of IE were identified by linkage with the NHS Hospital Episode Statistics database. Approval was obtained from the NHS Research Ethics Committee. RESULTS: 2057 of 91 962 patients undergoing SAVR developed IE over a median follow-up of 53.9 months-an overall incidence of 4.81 [95% CI 4.61 to 5.03] per 1000 person-years. Correspondingly, 140 of 14 195 patients undergoing TAVI developed IE over a median follow-up of 24.5 months-an overall incidence of 3.57 [95% CI 3.00 to 4.21] per 1000 person-years. The cumulative incidence of IE at 60 months was higher after SAVR than after TAVI (2.4% [95% CI 2.3 to 2.5] vs 1.5% [95% CI 1.3 to 1.8], HR 1.60, p<0.001). Across the entire cohort, SAVR remained an independent predictor of IE after multivariable adjustment. Risk factors for IE included younger age, male sex, atrial fibrillation, and dialysis. CONCLUSIONS: IE is a rare complication of SAVR and TAVI. In our population, the incidence of IE was higher after SAVR than after TAVI.

The conflict between accountability and confidentiality in Medicare's access to psychiatrists? notes.

OBJECTIVE: The aims of this paper were to identify a conflict between psychiatrists? obligations regarding patient confidentiality and Medicare's auditing procedures, and to examine potential resolutions to the conflict. CONCLUSION: While it is reasonable for Medicare, as a taxpayer-funded instrumentality, to require documentary evidence to substantiate and justify claims, such a requirement constitutes a significant breach of patient confidentiality. Obtaining patient consent appears to be the only ethical resolution of the issue.

MOCCASIN: a method for correcting for known and unknown confounders in RNA splicing analysis.

The effects of confounding factors on gene expression analysis have been extensively studied following the introduction of high-throughput microarrays and subsequently RNA sequencing. In contrast, there is a lack of equivalent analysis and tools for RNA splicing. Here we first assess the effect of confounders on both expression and splicing quantifications in two large public RNA-Seq datasets (TARGET, ENCODE). We show quantification of splicing variations are affected at least as much as those of gene expression, revealing unwanted sources of variations in both datasets. Next, we develop MOCCASIN, a method to correct the effect of both known and unknown confounders on RNA splicing quantification and demonstrate MOCCASIN's effectiveness on both synthetic and real data. Code, synthetic and corrected datasets are all made available as resources.

Atypical Clinical Manifestations of Loiasis and Their Relevance for Endemic Populations.

BACKGROUND: Loiasis is mostly considered a relatively benign infection when compared with other filarial and parasitic diseases, with Calabar swellings and eyeworm being the most common signs. Yet, there are numerous reports in the literature of more serious sequelae. Establishing the relationship between infection and disease is a crucial first step toward estimating the burden of loiasis. METHODS: We conducted a systematic review of case reports containing 329 individuals and detailing clinical manifestations of loiasis with a focus on nonclassical, atypical presentations. RESULTS: Results indicate a high proportion (47%) of atypical presentations in the case reports identified, encompassing a wide range of cardiac, respiratory, gastrointestinal, renal, neurological, ophthalmological, and dermatological pathologies. Individuals with high microfilarial densities and residing in an endemic country were at greater risk of suffering from atypical manifestations. CONCLUSIONS: Our findings have important implications for understanding the clinical spectrum of conditions associated with Loa loa infection, which extends well beyond the classical eyeworm and Calabar swellings. As case reports may overestimate the true rate of atypical manifestations in endemic populations, large-scale, longitudinal clinico-epidemiological studies will be required to refine our estimates and demonstrate causality between loiasis and the breadth of clinical manifestations reported. Even if the rates of atypical presentations were found to be lower, given that residents of loiasis-endemic areas are both numerous and the group most at risk of severe atypical manifestations, our conclusions support the recognition of loiasis as a significant public health burden across Central Africa.

Antibiotic prophylaxis for infective endocarditis: a systematic review and meta-analysis.

OBJECTIVE: The use of antibiotic prophylaxis (AP) for prevention of infective endocarditis (IE) is controversial. In recent years, guidelines to cardiologists and dentists have advised restriction of AP to high-risk groups (in Europe and the USA) or against its use at all (in the UK). The objective of this systematic review was to appraise the evidence for use of AP for prevention of bacteraemia or IE in patients undergoing dental procedures. METHODS: We conducted electronic searches in Medline, Embase, Cochrane Library and ISI Web of Science. We assessed the methodological characteristics of included studies using the Strengthening the Reporting of Observational Studies in Epidemiology criteria for observational studies and the Cochrane Risk of Bias Tool for trials. Two reviewers independently determined the eligibility of studies, assessed the methodology of included studies and extracted the data. RESULTS: We identified 178 eligible studies, of which 36 were included in the review. This included 10 time-trend studies, 5 observational studies and 21 trials. All trials identified used bacteraemia as an endpoint rather than IE. One time-trend study suggests that total AP restriction may be associated with a rising incidence of IE, while data on the consequences of relative AP restriction are conflicting. Meta-analysis of trials indicates that AP is effective in reducing the incidence of bacteraemia (risk ratio 0.53, 95% CI 0.49 to 0.57, p<0.01), but case-control studies suggest this may not translate to a statistically significant protective effect against IE in patients at low risk of disease. CONCLUSIONS: The evidence base for the use of AP is limited, heterogeneous and the methodological quality of many studies is poor. Postprocedural bacteraemia is not a good surrogate endpoint for IE. Given the logistical challenges of a randomised trial, high-quality case-control studies would help to evaluate the role of dental procedures in causing IE and the efficacy of AP in its prevention.

Medicare Item 319 after 10 years: a range of concerns.

OBJECTIVE: The aim of this paper was to re-examine, via a risk benefit analysis, the rationale of restrictions to long-term intensive psychotherapy and psychoanalytic treatment through the mechanism of the Commonwealth Medicare Benefits Scheme (CMBS) in light of side effects on patients' access to treatment, their self-esteem, and their privacy. CONCLUSION: The application of the Global Assessment of Functioning Scale and the specificity of CMBS Item 319 on individual patients' medical records carry risks that are not offset by demonstrable communal benefits that were predicted when the item was introduced 10 years ago.