A comparative study of algorithms detecting differential rhythmicity in transcriptomic data.

Rhythmic transcripts play pivotal roles in driving the daily oscillations of various biological processes. Genetic or environmental disruptions can lead to alterations in the rhythmicity of transcripts, ultimately impacting downstream circadian outputs, including metabolic processes and even behavior. To statistically compare the differences in transcript rhythms between two or more conditions, several algorithms have been developed to analyze circadian transcriptomic data, each with distinct features. In this study, we compared the performance of seven algorithms that were specifically designed to detect differential rhythmicity. We found that even when applying the same statistical threshold, these algorithms yielded varying numbers of differentially rhythmic transcripts. Nevertheless, the set of transcripts commonly identified as differentially rhythmic exhibited substantial overlap among algorithms. Furthermore, the phase and amplitude differences calculated by these algorithms displayed significant correlations. In summary, our study highlights a high degree of similarity in the results produced by these algorithms. Furthermore, when selecting an algorithm for analysis, it is crucial to ensure the compatibility of input data with the specific requirements of the chosen algorithm and to assess whether the algorithm's output fits the needs of the user.

Development of a Tool for Health Screening and Assessment in Orphanages in Lesotho.

In low- and middle-income countries that have high burdens of disease, simple interventions such as health screenings can have a significant impact on health outcomes. Among vulnerable children, orphans in particular, deaths are often caused by conditions preventable through early identification and provision of basic health and nutritional needs. After consulting local preventative care guidelines and medical providers, a health screening tool for use in orphanages was created. This tool was used to screen children in two orphanages in Lesotho. Overall, the tool was found to be easy, efficient, and valuable in identifying both preventable and immediately treatable conditions in orphans. As a result, orphans with long-term medical needs were linked to community-based providers by developing individualized care plans in collaboration with orphanage colleagues. This preventative tool offers a screening strategy that directly aligns with the United Nations Agency for Development's Sustainable Development Goals and helps to advance the goal of universal health coverage.

The Standardized Pediatric Expedited Encounters for ART Drugs Initiative (SPEEDI): description and evaluation of an innovative pediatric, adolescent, and young adult antiretroviral service delivery model in Tanzania.

BACKGROUND: As countries scale up antiretroviral therapy (ART) for children, innovative strategies to deliver quality services to children are needed. Differentiated ART delivery models have been successful in adults, but no such program has been described in children. We describe the Standardized Pediatric Expedited Encounters for ART Drugs Initiative (SPEEDI). METHODS: Descriptive analysis of patients eligible for SPEEDI was done via retrospective review of children, adolescents, and young adults on ART at the Baylor Centre of Excellence (COE) in Mbeya, Tanzania between January 2013 and December 2015. Eligibility for SPEEDI visits included the following: stable children, adolescents, and young adults on ART for approximately 3 months or longer, no medical or social complications, good adherence to ART, and presence of reliable caregiver. During a SPEEDI visit, patients were fast tracked in triage to collect medications directly without physically seeing a clinician. SPEEDI patients came to clinic every two months, and alternated SPEEDI visits with standard visits. Baseline characteristics, mortality, and lost-to-follow up rates of SPEEDI patients were analyzed. RESULTS: One thousand one hundred sixty-four patients utilized SPEEDI, totaling 3493 SPEEDI visits. SPEEDI reached 51.3% (1164/2269) of pediatric ART patients, accounting for 7.7% (3493/44489) of total patient encounters. SPEEDI patients were 52% (605/1164) female, median age of 11.7 years (range 1.2-25.5 yr), median time on ART of 21 months (range 4-130 months) and 83.5% (964/1155) categorized as no or mild HIV-associated immunodeficiency. SPEEDI patients had good outcomes (98.8%), low LTFU (0.1%) and low mortality rates (0.61 deaths per 100 patient-years). CONCLUSION: SPEEDI was an effective model for delivering ART to children, adolescents, and young adults in our setting, leading to good clinical outcomes, low mortality, and low LTFU. The SPEEDI program safely and effectively expedited and spaced out ART visits for children, adolescents, and young adults, and can serve as an adaptable ART delivery model for other resource limited settings.

Leveraging tuberculosis case relative locations to enhance case detection and linkage to care in Swaziland.

BACKGROUND: In Swaziland, as in many high HIV/TB burden settings, there is not information available regarding the household location of TB cases for identifying areas of increased TB incidence, limiting the development of targeted interventions. Data from "Butimba", a TB REACH active case finding project, was re-analyzed to provide insight into the location of TB cases surrounding Mbabane, Swaziland. OBJECTIVE: The project aimed to identify geographical areas with high TB burdens to inform active case finding efforts. METHODS: Butimba implemented household contact tracing; obtaining landmark based, informal directions, to index case homes, defined here as relative locations. The relative locations were matched to census enumeration areas (known location reference areas) using the Microsoft Excel Fuzzy Lookup function. Of 403 relative locations, an enumeration area reference was detected in 388 (96%). TB cases in each census enumeration area and the active case finders in each Tinkhundla, a local governmental region, were mapped using the geographic information system, QGIS 2.16. RESULTS: Urban Tinkhundla predictably accounted for most cases; however, after adjusting for population, the highest density of cases was found in rural Tinkhundla. There was no correlation between the number of active case finders currently assigned to the 7 Tinkhundla surrounding Mbabane and the total number of TB cases (Spearman rho = -0.57, p = 0.17) or the population adjusted TB cases (Spearman rho = 0.14, p = 0.75) per Tinkhundla. DISCUSSION: Reducing TB incidence in high-burden settings demands novel analytic approaches to study TB case locations. We demonstrated the feasibility of linking relative locations to more precise geographical areas, enabling data-driven guidance for National Tuberculosis Programs' resource allocation. In collaboration with the Swazi National Tuberculosis Control Program, this analysis highlighted opportunities to better align the active case finding national strategy with the TB disease burden.

School and household tuberculosis contact investigations in Swaziland: Active TB case finding in a high HIV/TB burden setting.

BACKGROUND: Investigation of household contacts exposed to infectious tuberculosis (TB) is widely recommended by international guidelines to identify secondary cases of TB and limit spread. There is little data to guide the use of contact investigations outside of the household, despite strong evidence that most TB infections occur outside of the home in TB high burden settings. In older adolescents, the majority of infections are estimated to occur in school. Therefore, as part of a project to increase active case finding in Swaziland, we performed school contact investigations following the identification of a student with infectious TB. METHODS: The Butimba Project identified 7 adolescent TB index cases (age 10-20) with microbiologically confirmed disease attending 6 different schools between June 2014 and March 2015. In addition to household contact investigations, Butimba Project staff worked with the Swaziland School Health Programme (SHP) to perform school contact investigations. At 6 school TB screening events, between May and October 2015, selected students underwent voluntary TB screening and those with positive symptom screens provided sputum for TB testing. RESULTS: Among 2015 student contacts tested, 177 (9%) screened positive for TB symptoms, 132 (75%) produced a sputum sample, of which zero tested positive for TB. Household contact investigations of the same index cases yielded 40 contacts; 24 (60%) screened positive for symptoms; 19 produced a sputum sample, of which one case was confirmed positive for TB. The odds ratio of developing TB following household vs. school contact exposure was significantly lower (OR 0.0, 95% CI 0.0 to 0.18, P = 0.02) after exposure in school. CONCLUSION: School-based contact investigations require further research to establish best practices in TB high burden settings. In this case, a symptom-based screening approach did not identify additional cases of tuberculosis. In comparison, household contact investigations yielded a higher percentage of contacts with positive TB screens and an additional tuberculosis case.

Why being an expert - despite xpert -remains crucial for children in high TB burden settings.

BACKGROUND: As access to Xpert expands in high TB-burden settings, its performance against clinically diagnosed TB as a reference standard provides important insight as the majority of childhood TB is bacteriologically unconfirmed. We aim to describe the characteristics and outcomes of children with presumptive TB and TB disease, and assess performance of Xpert under programmatic conditions against a clinical diagnosis of TB as a reference standard. METHODS: Retrospective review of children evaluated for presumptive TB in Mbeya, Tanzania. Baseline characteristics were compared by TB disease status and, for patients diagnosed with TB, by TB confirmation status using Wilcoxon rank sum test for continuous variables and the Chi-square test for categorical variables. Sensitivity and specificity were calculated to assess the performance of Xpert, smear, and culture against clinical TB. Kappa statistics were calculated to assess agreement between Xpert and smear to culture. RESULTS: Among children (N = 455) evaluated for presumptive TB, 70.3% (320/455) had Xpert and 62.8% (286/455) had culture performed on sputa. 34.5% (157/455) were diagnosed with TB: 80.3% (126/157) pulmonary TB, 13.4% (21/157) bacteriologically confirmed, 53.5% (84/157) HIV positive, and 48.4% (76/157) inpatients. Compared to the reference standard of clinical diagnosis, sensitivity of Xpert was 8% (95% CI 4-15), smear 6% (95% CI 3-12) and culture 16% (95% CI 9-24), and did not differ based on patient disposition, nutrition or HIV status. CONCLUSION: Despite access to Xpert, the majority of children with presumptive TB were treated based on clinical diagnosis. Reflecting the reality of clinical practice in resource limited settings, new diagnostics such as Xpert serve as important adjunctive tests but will not obviate the need for astute clinicians and comprehensive diagnostic algorithms.

BUTIMBA: Intensifying the Hunt for Child TB in Swaziland through Household Contact Tracing.

BACKGROUND: Limited data exists to inform contact tracing guidelines in children and HIV-affected populations. We evaluated the yield and additionality of household contact and source case investigations in Swaziland, a TB/HIV high-burden setting, while prioritizing identification of childhood TB. METHODS: In partnership with 7 local TB clinics, we implemented standardized contact tracing of index cases (IC) receiving TB treatment. Prioritizing child contacts and HIV-affected households, screening officers screened contacts for TB symptoms and to identify risk factors associated with TB. We ascertained factors moderating the yield of contact tracing and measured the impact of our program by additional notifications. RESULTS: From March 2013 to November 2015, 3,258 ICs (54% bacteriologically confirmed; 70% HIV-infected; 85% adults) were enrolled leading to evaluation of 12,175 contacts (median age 18 years, IQR 24-42; 45% children; 9% HIV-infected). Among contacts, 196 TB cases (56% bacteriologically confirmed) were diagnosed resulting in a program yield of 1.6% for all forms of TB. The number needed to screen (NNS) to identify a bacteriologically confirmed TB case or all forms TB case traced from a child IC <5 years was respectively 62% and 40% greater than the NNS for tracing from an adult IC. In year one, we demonstrated a 32% increase in detection of bacteriologically confirmed child TB. Contacts were more likely to have TB if <5 years (OR = 2.0), HIV-infected (OR = 4.9), reporting ≥1 TB symptoms (OR = 7.7), and sharing a bed (OR = 1.7) or home (OR = 1.4) with the IC. There was a 1.4 fold increased chance of detecting a TB case in households known to be HIV-affected. CONCLUSION: Contact tracing prioritizing children is not only feasible in a TB/HIV high-burden setting but contributes to overall case detection. Our findings support WHO guidelines prioritizing contact tracing among children and HIV-infected populations while highlighting potential to integrate TB and HIV case finding.

Culture is an imperfect and heterogeneous reference standard in pediatric tuberculosis.

BACKGROUND: In pediatric tuberculosis (pTB), culture is the accepted reference standard for assessing new diagnostic tests despite culture only confirming 10-50% of clinically diagnosed cases. METHODS: Using the studies previously included in the systematic review of Gene Xpert, we evaluated the diagnostic yield of culture. Children with symptoms and signs suggestive of TB were considered to have a clinical diagnosis if they were 1) culture positive or 2) followed clinically for at least one month and started on Anti-Tuberculosis Therapy (ATT). RESULTS: Of 1989 children with presumptive pTB, 229 (11.5%) had culture-confirmation. Of the remaining 1760 culture negative children, 710 (24.4) were classified as culture-negative clinical TB and 821 were classified as "not TB". Diagnostic yield of culture was 24.4% (median 28.7% IQR 15.6%-42.4%; range 1.5%-65%). CONCLUSION: Culture, the accepted reference standard for pediatric TB diagnostics, has a low and variable yield that impacts how diagnostic studies should be reported as well as everyday clinical care.

Selective suppression of the human aryl hydrocarbon receptor function can be mediated through binding interference at the C-terminal half of the receptor.

The human aryl hydrocarbon receptor is a cytosolic signaling molecule which affects immune response and aberrant cell growth. Canonical signaling of the receptor requires the recruitment of coactivators to the promoter region to remodel local chromatin structure. We predicted that interference of this recruitment would block the aryl hydrocarbon receptor function. To prove that, we employed phage display to identify nine peptides of twelve-amino-acid in length which target the C-terminal half of the human aryl hydrocarbon receptor, including the region where coactivators bind. Eight 12mer peptides, in the form of GFP fusion, suppressed the ligand-dependent transcription of six AHR target genes (cyp1a1, cyp1a2, cyp1b1, ugt1a1, nqo1, and ahrr) in different patterns in Hep3B cells, whereas the AHR antagonist CH-223191 suppressed all these target genes similarly. Three of the 12mer peptides (namely 11-3, 1-7, and 7-3) suppressed the 3MC-induced, CYP1A1-dependent EROD activity and the ROS production caused by benzo[a]pyrene. These 12mer peptides suppressed the AHR function synergistically with CH-223191. In conclusion, we provide evidence that targeting the C-terminal half of the human aryl hydrocarbon receptor is a viable, new approach to selectively block the receptor function.

Erythropoietin as a treatment of anemia in heart failure: systematic review of randomized trials.

BACKGROUND: Anemia in heart failure is both common and associated with worse symptoms and increased mortality. Several small randomized controlled trials (RCTs) have assessed erythropoiesis-stimulating agents (ESAs), but definitive evaluation and clinical guidance are required. We sought to systematically review the effects of ESAs in chronic heart failure. METHODS: An extensive search strategy identified 11 RCTs with 794 participants comparing any ESA with control over 2 to 12 months of follow-up. Published and additionally requested data were incorporated into a Cochrane systematic review (CD007613). RESULTS: Nine studies were placebo controlled, and 5, double blinded. Erythropoiesis-stimulating agent treatment significantly improved exercise duration by 96.8 seconds (95% CI 5.2-188.4, P = .04) and 6-minute walk distance by 69.3 m (95% CI 17.0-121.7, P = .009) compared with control. Benefit was also noted for peak oxygen consumption (+2.29 mL/kg per minute, P = .007), New York Heart Association class (-0.73, P < .001), ejection fraction (+5.8%, P < .001), B-type natriuretic peptide (-226.99 pg/mL, P < .001), and quality-of-life indicators with a mean increase in hemoglobin level of 2 g/dL. There was a significantly lower rate of heart failure-related hospitalizations with ESA therapy (odds ratio 0.56, 95% CI 0.37-0.84, P = .005). No associated increase in adverse events or mortality (odds ratio 0.58, 95% CI 0.34-0.99, P = .047) was observed, although the number of events was limited. CONCLUSION: Meta-analysis of small RCTs suggests that ESA treatment can improve exercise tolerance, reduce symptoms, and have benefits on clinical outcomes in anemic patients with heart failure. Confirmation requires larger, well-designed studies with careful attention to dose, attained hemoglobin level, and long-term outcomes.

Using sentinel surveillance system to monitor seasonal and novel H1N1 influenza infection in Houston, Texas: outcome analysis of 2008-2009 flu season.

The advent of the novel H1N1 virus prompted the Houston Department of Health and Human services (HDHHS) to use the existing sentinel surveillance system to effectively monitor the situation of novel H1N1 virus in the Houston metropolitan area. The objective of this study was to evaluate the demographic characteristics and common symptoms associated with confirmed cases of seasonal influenza and Novel H1N1 virus reported to HDHHS between October 2008 and October 2009. A total of 30 providers were randomly selected using the probability proportional to size (PPS) sampling technique to participate in a sentinel surveillance system. The system was used to effectively monitor both seasonal and novel H1N1 virus in the Houston metropolitan area. These providers collected and submitted specimens for testing at HDHHS laboratory from patients with influenza-like illness (ILI) symptoms who visited their clinics during the period, October 2008 and October 2009. These data formed the basis of the current study. Data obtained were subjected to both descriptive and inferential statistical analyses using SAS software version 9.1.3. Overall a total of 1,122 ILI cases were reported to HDHHS by sentinel providers and tested by HDHHS laboratory. Of this number 296 (67.5%) specimens tested positive for influenza A; 140 (32.0%) for influenza B, and 2 (0.46%) for influenza A/B. Two hundred and fifty-nine (59%) were confirmed cases of seasonal influenza and 179 (41%) were novel H1N1 subtype, respectively. The median ages for seasonal influenza and novel H1N1 virus were 7 and 8 years, with majority of the cases reported among children of age 5-9 years. Fever was the most common symptom reported among patients with seasonal flu and novel H1N1 virus, followed by cough. Twenty-three percent (23%) of patients who were vaccinated against seasonal flu prior to the epidemic were infected with seasonal flu virus. The sentinel surveillance system provided timely data on the circulating ILI that assisted in making decisions regarding response activities for both seasonal and novel H1N1 influenza.

Erythropoiesis-stimulating agents for anaemia in chronic heart failure patients.

BACKGROUND: Chronic heart failure (CHF) is a leading cause of morbidity and mortality worldwide. Anaemia is a common (12-55%) co-morbid condition and is associated with worsening symptoms and increased mortality. Anaemia is treatable and can be targeted in the treatment of patients with CHF. Erythropoiesis-stimulating agents (ESA), supplemented by iron therapy, are used to treat anaemia in chronic kidney disease and cancer, however safety concerns have been raised in these patients. The clinical benefit and safety of these agents in CHF remains unclear. OBJECTIVES: To assess the benefits and risks of ESA for CHF patients with anaemia. SEARCH STRATEGY: We searched the Cochrane Central Register of Controlled Trials (The Cochrane Library 2008, Issue 3), MEDLINE (1950 to October 2008), EMBASE (1980 to October 2008) and reference lists of articles. No language restrictions were applied. SELECTION CRITERIA: Randomised controlled trials of any ESA, with or without iron therapy, in CHF patients were eligible for inclusion. DATA COLLECTION AND ANALYSIS: Three reviewers independently assessed study quality and extracted data. Original authors were contacted for additional information. The outcomes of interest were: exercise tolerance, haemoglobin level, New York Heart Association (NYHA) functional class, quality of life, left-ventricular ejection fraction, B-type natriuretic peptide, CHF-related hospitalisations, all-cause mortality and adverse effects. Risk ratios (RR) were calculated for dichotomous data and weighted mean difference (WMD) for continuous data. MAIN RESULTS: Eleven studies (794 participants) were included. Overall quality of studies was moderate with nine studies being placebo-controlled but only five double-blinded. Compared to control, ESA treatment significantly improved exercise duration by 96.8 seconds (95% CI 5.2 to 188.4, p=0.04) and 6-minute walk distance by 69.3 metres (95% CI 17.0 to 121.7, p=0.009). Benefit was also noted in terms of peak VO2 (+2.29 mL/kg/min, p=0.007), NYHA class (-0.73, p<0.001), ejection fraction (+5.8%, p<0.001), B-type natriuretic peptide (-226.99 pg/mL, p<0.001) and quality-of-life indicators, with a mean increase in haemoglobin of 1.98 g/dL (p<0.0001). There was also a significantly lower rate of heart failure related hospitalisations (RR 0.62, 95% CI 0.44 to 0.87) and lower all-cause mortality (RR 0.61, 95% CI 0.37 to 0.99). No increase in adverse events with ESA therapy was observed, however studies were of small sample sizes and limited duration. AUTHORS' CONCLUSIONS: Meta-analysis of small RCTs suggests that ESA treatment in patients with symptomatic CHF and mild anaemia (haemoglobin more than 10g/dL) can improve anaemia and exercise tolerance, reduce symptoms and have benefits on clinical outcomes. Confirmation requires well-designed studies with careful attention to dose, haemoglobin treatment target and associated iron therapy.