HIV prevalence and awareness among adults presenting for enrolment into a study of people at risk for HIV in Kisumu County, Western Kenya

INTRODUCTION

Despite declines in new HIV diagnoses both globally and in Kenya, parts of Western Kenya still report high HIV prevalence and incidence. We evaluated HIV prevalence to inform the development of policies for strategic and targeted HIV prevention interventions.

METHODS

Adult participants aged 18-35 years were recruited in Kisumu County and screened for HIV for a prospective HIV incidence cohort. Questionnaires assessed HIV-associated risk behaviors. Participants who tested positive for HIV were disaggregated into groups based on prior knowledge of their HIV status: previously-diagnosed and newly-diagnosed. In separate analyses by prior knowledge, robust Poisson regression was used to estimate prevalence ratios (PRs) and 95% confidence intervals (CIs) for factors potentially associated with a positive HIV test in each group, as compared to participants without HIV.

RESULTS

Of 1059 participants tested for HIV, 196 (18.5%) had a positive HIV test. Among PLWH, 78 (39.8%) were newly diagnosed with HIV at screening. After adjusting for other variables, previously-diagnosed HIV was more common among females than males (PR 2.70, 95%CI 1.69-4.28), but there was no observed sex difference in newly-diagnosed HIV prevalence (PR 1.05, 95%CI 0.65-1.69). Previously-diagnosed HIV was also more common among people reporting consistent use of condoms with primary sexual partners as compared to inconsistent condom use (PR 3.19, 95%CI 2.09-4.86), but newly-diagnosed HIV was not associated with such a difference between consistent and inconsistent condom use (PR 0.73, 95%CI 0.25-2.10).

CONCLUSION

Prevalence of newly-diagnosed HIV was high, at approximately 8% of participants, and not statistically different between genders, highlighting the need for improved HIV case finding regardless of sex. The higher prevalence of previously-diagnosed HIV in female participants may reflect higher rates of HIV testing through more encounters with the healthcare system. Higher prevalence of consistent condom use amongst those previously-diagnosed suggests behavioral change to reduce HIV transmission, a potential benefit of policies to facilitate earlier HIV diagnosis.

Early sexual debut is associated with drug use and decreased educational attainment among males and females in Kisumu County, Kenya

Differing global sociocultural contexts of sexual relationships influence age at first sexual intercourse with potentially long-lasting region-specific effects such as increased risk of contracting HIV and other sexually transmitted infections (STIs). In these cross-sectional analyses of data from the screening and enrollment visits for an HIV incidence study in Kisumu County, Kenya, we evaluated factors associated with having experienced an early sexual debut (ESD) among males and females aged 18-35 years. Clinical evaluation was performed and sexual behaviors were assessed via questionnaire. ESD was defined as self-reported age 15 years or younger at first sexual intercourse. Robust Poisson regression was used to estimate prevalence ratios (PRs) and 95% confidence intervals (95% CIs) for factors associated with ESD. Of 1057 participants, 542 (51.3%) were female. Participants' median age at study screening was 25 years (interquartile range [IQR]: 22-29), and at sexual debut was 16 years (IQR: 14-17). Five hundred and four participants (47.7%) reported ESD. ESD was less common among females (PR 0.78, CI 0.67-0.90) and participants with more than primary education (PR 0.56, CI 0.47-0.66). ESD was more common in participants with a history of drug use (PR 1.28, CI 1.10-1.49). Drug use removed the protective effect of education (some secondary education or less, no drug use: PR 0.72, CI 0.61-0.85; some secondary education or less, drug use: PR 0.94, CI 0.74-1.18). ESD was common in our study and associated with lower educational attainment and increased likelihood of drug use. Interventions are needed early in life, well before 15 years of age, to encourage engagement in schooling and prevent drug use. Comprehensive sexual education and interventions to prevent drug use may be beneficial before the age of 15 years.

Emergeny Medicine Resident Trauma Intubation Success and Prior Intubation Experience

BACKGROUND

Emergency medicine residents are often involved in the management of trauma airways. There are few data on the correlation between prior intubation experience and first-pass trauma intubation success for emergency medicine residents.

OBJECTIVES

We attempted to elucidate a relationship between prior resident intubation experience and first-pass success for trauma patient intubation.

METHODS

We combined two data sets to assess for correlation between prior intubation experience for postgraduate year 2 and 3 residents and first-pass success for trauma patient intubation. Prior intubation experience was gathered from resident procedure logs and trauma intubation data were collected as part of a quality-monitoring program. A univariable logistic regression analysis for all available variables was performed, with first-pass intubation success as the outcome of interest.

RESULTS

We included 295 consecutive trauma patients intubated at a Level I trauma center where we could link the resident prior intubation experience (total intubations) with intubation attempt quality data. First-pass success for all emergency medicine residents was 82.3% (233/283). Overall successful intubation rate for emergency medicine residents was 90.4% (256/283). The combination of airway management by both the resident and emergency medicine attending provided an overall success rate of 97.3% (287/295). There was no statistically significant association between first-pass success and prior resident intubation experience or any of the other measured variables.

CONCLUSION

We did not demonstrate any significant correlation between first-pass intubation success and number of prior intubations performed by the emergency medicine resident.

Acute HIV-1 infection viremia associate with rebound upon treatment interruption

BACKGROUND

Analytic treatment interruption (ATI) studies evaluate strategies to potentially induce remission in people living with HIV-1 but are often limited in sample size. We combined data from four studies that tested three interventions (vorinostat/hydroxychloroquine/maraviroc before ATI, Ad26/MVA vaccination before ATI, and VRC01 antibody infusion during ATI).

METHODS

The statistical validity of combining data from these participants was evaluated. Eleven variables, including HIV-1 viral load at diagnosis, Fiebig stage, and CD4+ T cell count were evaluated using pairwise correlations, statistical tests, and Cox survival models.

FINDINGS

Participants had homogeneous demographic and clinical characteristics. Because an antiviral effect was seen in participants who received VRC01 infusion post-ATI, these participants were excluded from the analysis, permitting a pooled analysis of 53 participants. Time to viral rebound was significantly associated with variables measured at the beginning of infection: pre-antiretroviral therapy (ART) viral load (HR = 1.34, p = 0.022), time to viral suppression post-ART initiation (HR = 1.07, p < 0.001), and area under the viral load curve (HR = 1.34, p = 0.026).

CONCLUSIONS

We show that higher viral loads in acute HIV-1 infection were associated with faster viral rebound, demonstrating that the initial stage of HIV-1 infection before ART initiation has a strong impact on viral rebound post-ATI years later.

FUNDING

This work was supported by a cooperative agreement between the Henry M. Jackson Foundation for the Advancement of Military Medicine and the US Department of the Army (W81XWH-18-2-0040). This research was funded, in part, by the US National Institute of Allergy and Infectious Diseases (AAI20052001) and the I4C Martin Delaney Collaboratory (5UM1AI126603-05).

Creation of a protective space between the rectum and prostate prior to prostate radiotherapy using a hydrogel spacer

The placement of a polyethylene glycol (PEG) hydrogel spacer is a recently developed technique employed to reduce the radiation dose administered to the rectum during prostate radiotherapy. This procedure has been adopted by urologists and radiation oncologists involved in transperineal prostate biopsy and brachytherapy, and more recently by radiologists with experience in transperineal prostate procedures. Radiologists should be familiar with the product, which may be encountered on computed tomography (CT) or magnetic resonance imaging (MRI). Radiologists may wish to become involved in the delivery of this increasingly utilised procedure. This review familiarises radiologists with the technique and risks and benefits of the use of transperineal delivery of hydrogel spacers with imaging examples.

Young at risk-people in Maputo City, Mozambique, present a high willingness to participate in HIV trials: Results from an HIV vaccine preparedness cohort study

INTRODUCTION

Vaccine efficacy testing requires engagement of willing volunteers with high disease incidence. We evaluated factors associated with willingness to participate in potential future HIV vaccine trials in Maputo, Mozambique.

METHODS

Adults aged 18-35 years without HIV and who reported at least two sexual partners in the 3 months prior to screening were enrolled into a 24-month observational study. They were asked at screening and exit if they would be willing to participate in a theoretical HIV vaccine study. Bivariate and multivariate logistic regression analyses were done between willingness to participate, demographic, sexual behavior, and motivational factors for screening visit data. Logistic regression with generalized estimating equations (GEE) was used to estimate odds ratios (ORs) and 95% confidence intervals (CIs) for factors potentially associated with willingness to participate for data from both visits.

RESULTS

A total of 577 participants without HIV were eligible, including 275 (48%) women. The mean age was 22.2 (SD ± 3.9) years. At screening 529 (92%) expressed willingness to participate and the proportion remained stable at 378 (88%) of the 430 participants retained through the exit visit (p = 0.209). Helping the country (n = 556) and fear of needles (n = 26) were the top motive and barrier for willingness to participate, respectively. Results from the GEE binary logistic regression (screening visit and exit visit) showed that wanting to learn how to avoid risk behaviors (aOR 3.33, 95% CI: 1.61-6.86) and feeling protected against HIV infection (aOR 2.24, 95% CI: 1.07-4.7) were associated with willingness to participate in HIV vaccine studies.

CONCLUSION

The majority of our study population in Mozambique expressed willingness to participate in a theoretical HIV vaccine trial. Participation in a HIV vaccine trial was seen as a way to contribute to the fight against HIV but was associated with some unrealistic expectations such as protection against HIV. This reinforces the need for continuous mobilization and awareness of potential participants to HIV vaccine trial.

Epidemiological and clinical implications of asymptomatic malaria and schistosomiasis co-infections in a rural community in western Kenya

BACKGROUND

Malaria and schistosomiasis present considerable disease burden in tropical and sub-tropical areas and severity is worsened by co-infections in areas where both diseases are endemic. Although pathogenesis of these infections separately is well studied, there is limited information on the pathogenic disease mechanisms and clinical disease outcomes in co-infections. In this study, we investigated the prevalence of malaria and schistosomiasis co-infections, and the hematologic and blood chemistry abnormalities in asymptomatic adults in a rural fishing community in western Kenya.

METHODS

This sub-study used samples and data collected at enrollment from a prospective observational cohort study (RV393) conducted in Kisumu County, Kenya. The presence of malaria parasites was determined using microscopy and real-time-PCR, and schistosomiasis infection by urine antigen analysis (CCA). Hematological analysis and blood chemistries were performed using standard methods. Statistical analyses were performed to compare demographic and infection data distribution, and hematologic and blood chemistry parameters based on different groups of infection categories. Clinically relevant hematologic conditions were analyzed using general linear and multivariable Poisson regression models.

RESULTS

From February 2017 to May 2018, we enrolled 671 participants. The prevalence of asymptomatic Plasmodium falciparum was 28.2% (157/556) and schistosomiasis 41.2% (229/562), with 18.0% (100/556) of participants co-infected. When we analyzed hematological parameters using Wilcoxon rank sum test to evaluate median (IQR) distribution based on malarial parasites and/or schistosomiasis infection status, there were significant differences in platelet counts (p = 0.0002), percent neutrophils, monocytes, eosinophils, and basophils (p < 0.0001 each). Amongst clinically relevant hematological abnormalities, eosinophilia was the most prevalent at 20.6% (116/562), whereas thrombocytopenia was the least prevalent at 4.3% (24/562). In univariate model, Chi-Square test performed for independence between participant distribution in different malaria parasitemia/schistosomiasis infection categories within each clinical hematological condition revealed significant differences for thrombocytopenia and eosinophilia (p = 0.006 and p < 0.0001, respectively), which was confirmed in multivariable models. Analysis of the pairwise mean differences of liver enzyme (ALT) and kidney function (Creatinine Clearance) indicated the presence of significant differences in ALT across the infection groups (parasite + /CCA + vs all other groups p < .003), but no differences in mean Creatinine Clearance across the infection groups.

CONCLUSIONS

Our study demonstrates the high burden of asymptomatic malaria parasitemia and schistosomiasis infection in this rural population in Western Kenya. Asymptomatic infection with malaria or schistosomiasis was associated with laboratory abnormalities including neutropenia, leukopenia and thrombocytopenia. These abnormalities could be erroneously attributed to other diseases processes during evaluation of diseases processes. Therefore, evaluating for co-infections is key when assessing individuals with laboratory abnormalities. Additionally, asymptomatic infection needs to be considered in control and elimination programs given high prevalence documented here.

Hepatitis and tuberculosis testing are much less common than HIV testing among adults in Kisumu, Kenya: results from a cross-sectional assessment

Background

Kenya has a high burden of HIV, viral hepatitis, and tuberculosis. Screening is necessary for early diagnosis and treatment, which reduces morbidity and mortality across all three illnesses. We evaluated testing uptake for HIV, viral hepatitis, and tuberculosis in Kisumu, Kenya.

Methods

Cross-sectional data from adults aged 18–35 years who enrolled in a prospective HIV incidence cohort study from February 2017 to May 2018 were analyzed. A questionnaire was administered to each participant at screening for study eligibility to collect behavioral characteristics and to assess prior testing practices. Among participants without a history of previously-diagnosed HIV, multivariable robust Poisson regression was used to estimate prevalence ratios (PRs) and 95% confidence intervals (CIs) for factors potentially associated with HIV testing in the 12 months prior to enrollment. A hierarchical model was used to test for differential access to testing due to spatial location.

Results

Of 671 participants, 52 (7.7%) were living with HIV, 308 (45.9%) were female, and the median age was 24 (interquartile range 21–28) years. Among 651 (97.0%) who had ever been tested for HIV, 400 (61.2%) reported HIV testing in the past 6 months, 129 (19.7%) in the past 6–12 months, and 125 (19.1%) more than one year prior to enrollment. Any prior testing for viral hepatitis was reported by 8 (1.2%) participants and for tuberculosis by 51 (7.6%). In unadjusted models, HIV testing in the past year was more common among females (PR 1.08 [95% CI 1.01, 1.17]) and participants with secondary education or higher (PR 1.10 [95% CI 1.02, 1.19]). In the multivariable model, only secondary education or higher was associated with recent HIV testing (adjusted PR 1.10 [95% CI 1.02, 1.20]). Hierarchical models showed no geographic differences in HIV testing across Kisumu subcounties.

Conclusions

Prior HIV testing was common among study participants and most had been tested within the past year but testing for tuberculosis and viral hepatitis was far less common. HIV testing gaps exist for males and those with lower levels of education. HIV testing infrastructure could be leveraged to increase access to testing for other endemic infectious diseases.

Clinical laboratory reference values in adults in Kisumu County, Western Kenya; hematology, chemistry and CD4

Background

Clinical laboratory reference intervals (RIs) are essential for diagnosing and managing patients in routine clinical care as well as establishing eligibility criteria and defining adverse events in clinical trials, but may vary by age, gender, genetics, nutrition and geographic location. It is, therefore, critical to establish region-specific reference values in order to inform clinical decision-making.

Methods

We analyzed data from a prospective observational HIV incidence cohort study in Kombewa, Kenya. Study participants were healthy males and females, aged 18–35 years, without HIV. Median and 95% reference values (2.5^th percentile to 97.5^th percentile) were calculated for laboratory parameters including hematology, chemistry studies, and CD4 T cell count. Standard Deviation Ratios (SDR) and Bias Ratios (BR) are presented as measures of effect magnitude. Findings were compared with those from the United States and other Kenyan studies.

Results

A total of 299 participants were analyzed with a median age of 24 years (interquartile range: 21–28). Ratio of males to females was 0.9:1. Hemoglobin range (2.5^th—97.5^th percentiles) was 12.0–17.9 g/dL and 9.5–15.3 g/dL in men and women respectively. In the cohort, MCV range was 59-95fL, WBC 3.7–9.2×10³/μL, and platelet 154–401×10³/μL. Chemistry values were higher in males; the creatinine RI was 59–103 μmol/L in males vs. 46–76 μmol/L in females (BRUL>.3); and the alanine transferase range was 8.8–45.3 U/L in males vs. 7.5–36.8 U/L in females (SDR>.3). The overall CD4 T cell count RI was 491–1381 cells/μL. Some parameters including hemoglobin, neutrophil, creatinine and ALT varied with that from prior studies in Kenya and the US.

Conclusion

This study not only provides clinical reference intervals for a population in Kisumu County but also highlights the variations in comparable settings, accentuating the requirement for region-specific reference values to improve patient care, scientific validity, and quality of clinical trials in Africa.

Variation in the pelvic and pectoral girdles of Australian Oligo-Miocene mekosuchine crocodiles with implications for locomotion and habitus

Australian Oligo-Miocene mekosuchines (Crocodylia; Crocodyloidea) display wide diversity in cranial shape and inferred hunting strategies. Terrestrial habitus has been inferred for these distinctive predators. A direct morphological signal for locomotion can be expected in the postcrania, particularly the pelvic and pectoral girdles. Here we describe fossil materials of the girdles, which chart their morphological variation in the subfamily from Eocene through to Middle Miocene. Over this period, both girdles undergo significant morphological changes. Notably, an enclosed, ventrally orientated acetabulum in the ilium is developed in one lineage. This recapitulates the erect parasagittal configuration of the pelvic limb seen in many Mesozoic crocodylomorph lineages, suggesting consistent use of erect high-walking in these mekosuchines. Other pelves from the same Oligo-Miocene deposits display morphology closer to modern crocodilians, suggesting a partitioning of locomotory strategy among sympatric mekosuchines. Plesiomorphic and derived pelvic girdles are distinguishable by parsimony analysis, and the earliest examples of the mekosuchine pelvis more closely resemble gavialids and alligatorids while latter forms converge on crown group crocodylids in the morphology of the iliac crest. This suggests that a revaluation of the base relationship of Mekosuchinae within Eusuchia is necessary.

The EPIICAL project: an emerging global collaboration to investigate immunotherapeutic strategies in HIV-infected children

The EPIICAL (Early-treated Perinatally HIV-infected Individuals: Improving Children's Actual Life with Novel Immunotherapeutic Strategies) project arises from the firm belief that perinatally infected children treated with suppressive antiretroviral therapy (ART) from early infancy represent the optimal population model in which to study novel immunotherapeutic strategies aimed at achieving ART-free remission. This is because HIV-infected infants treated within 2-3 months of life have a much reduced viral reservoir size, and rarely show HIV-specific immunity but preserve normal immune development. The goal of EPIICAL is the establishment of an international collaboration to develop a predictive platform using this model to select promising HIV therapeutic vaccine candidates, leading to prioritisation or deprioritisation of novel immunotherapeutic strategies. To establish this platform, the EPIICAL Consortium aims to: develop predictive models of virological and immunological dynamics associated with response to early ART and to treatment interruption using available data from existing cohorts/studies of early-treated perinatally HIV-infected children; optimise methodologies to better characterise immunological, virological and genomic correlates/profiles associated with viral control; test novel immunotherapeutic strategies using in vivo proof-of-concept (PoC) studies with the aim of inducing virological, immunological and transcriptomic correlates/profiles equivalent to those defined by the predictive model. This approach will strengthen the capacity for discovery, development and initial testing of new therapeutic vaccine strategies through the integrated efforts of leading international scientific groups, with the aim of improving the health of HIV-infected individuals.

Polychlorinated biphenyl (PCB) and dioxin concentrations in residential dust of pregnant women

Polychlorinated biphenyls (PCBs) and dioxins are well known for their persistence in the environment. PCBs can be found in the residential environment long after the use of these chemicals in domestic products and industrial processes has ceased. Dioxins have been assessed in Australia as being of very low concentrations. Despite concerns about residential dust as a source of human exposure to persistent chemicals, there has been limited testing of PCBs and dioxins in dust in Australia. As part of an assessment of maternal exposure to a variety of persistent toxic substances, we analysed 30 residential dust samples from a variety of geographical settings for their dioxin and PCB concentrations. PCBs were found in most samples, the median and range concentrations (pg g(-1)) of dominant congeners of PCB were as follows: PCB118 (315; <35.0-29 000), PCB105 (130; 14.0-16 000) and PCB156 (440; <5.00-2800). Dioxin concentrations were generally low with median concentrations for the total sum of dioxin-like polychlorinated dibenzodioxins (PCDDs) and polychlorinated dibenzofurans (PCDFs) of 3.75 pg g(-1) each. There was a very high percentage of non-detects. Concentrations of both PCBs and dioxins were low compared with most studies reporting residential dust concentrations internationally. Age of dwelling was the only factor observed to influence both PCB congener concentrations and dioxin isomers in multivariate regression analyses. No other housing or sociodemographic variables, including proximity to industry, were important predictors in multivariate linear regression models.

Long-term survival of children less than six years of age enrolled on the CCG-945 phase III trial for newly-diagnosed high-grade glioma: a report from the Children's Oncology Group

BACKGROUND

We analyzed the long-term survival of children under 6 years of age (<6 years) enrolled upon the Children's Cancer Group (CCG)-945 high-grade glioma (HGG) study to determine the impact of intrinsic biological characteristics as well as treatment upon both survival and quality of life (QOL) in this younger age population.

PROCEDURE

Analyses were undertaken on patients <6 years with institutionally diagnosed HGG enrolled on the CCG-945 trial. Comparisons of survival were performed for patients <3 years of age (<3 years) (treated with intent to avoid irradiation) versus those between 3 and 6 years of age (3-6 years) (treated with irradiation and chemotherapy) at diagnosis. Discordance between the institutional diagnoses of HGG and consensus-reviewed diagnoses led us to perform further survival analyses for both groups. We compared the two groups of patients for biological markers, and evaluated the neuropsychological and QOL outcomes of long-term survivors.

RESULTS

Patients <3 years (n = 49, 19.5% of all enrolled patients) at diagnosis had a 10-year EFS and OS of 29 ± 6.5% and 37.5 ± 7%, respectively, while for patients 3-6 years (n = 34, 13.5% of all enrolled patients) 10-year EFS and OS were 35 ± 8% and 36 ± 8%, respectively. Molecular marker analysis showed that a smaller proportion of patients <3 years harbored TP53 mutations (P = 0.05). Analysis of QOL outcomes with a median length of follow-up of 15.1 years (9.5-19.2) showed comparable results.

CONCLUSIONS

QOL and survival data were similar for the two groups. A larger prospective study is justified to study the efficacy of chemotherapy only regimens in younger children.

Imaging pancreas transplants

Pancreas transplants are performed in multiple centres across the UK with good graft survival rates. This places an increasing demand on radiology services, particularly as the complication rates are not insignificant. The imaging appearances of pancreas transplants and their complications can be difficult to interpret. This review provides an illustrative journey through the anatomical appearances of a graft and the imaging appearances of complications, as a reference tool for radiologists.

Synchrotron Reveals Early Triassic Odd Couple: Injured Amphibian and Aestivating Therapsid Share Burrow

Fossorialism is a beneficial adaptation for brooding, predator avoidance and protection from extreme climate. The abundance of fossilised burrow casts from the Early Triassic of southern Africa is viewed as a behavioural response by many tetrapods to the harsh conditions following the Permo-Triassic mass-extinction event. However, scarcity of vertebrate remains associated with these burrows leaves many ecological questions unanswered. Synchrotron scanning of a lithified burrow cast from the Early Triassic of the Karoo unveiled a unique mixed-species association: an injured temnospondyl amphibian (Broomistega) that sheltered in a burrow occupied by an aestivating therapsid (Thrinaxodon). The discovery of this rare rhinesuchid represents the first occurrence in the fossil record of a temnospondyl in a burrow. The amphibian skeleton shows signs of a crushing trauma with partially healed fractures on several consecutive ribs. The presence of a relatively large intruder in what is interpreted to be a Thrinaxodon burrow implies that the therapsid tolerated the amphibian’s presence. Among possible explanations for such unlikely cohabitation, Thrinaxodon aestivation is most plausible, an interpretation supported by the numerous Thrinaxodon specimens fossilised in curled-up postures. Recent advances in synchrotron imaging have enabled visualization of the contents of burrow casts, thus providing a novel tool to elucidate not only anatomy but also ecology and biology of ancient tetrapods.

Esrrb is a direct Nanog target gene that can substitute for Nanog function in pluripotent cells

Embryonic stem cell (ESC) self-renewal efficiency is determined by the level of Nanog expression. However, the mechanisms by which Nanog functions remain unclear, and in particular, direct Nanog target genes are uncharacterized. Here we investigate ESCs expressing different Nanog levels and Nanog^−/− cells with distinct functionally inducible Nanog proteins to identify Nanog-responsive genes. Surprisingly, these constitute a minor fraction of genes that Nanog binds. Prominent among Nanog-reponsive genes is Estrogen-related receptor b (Esrrb). Nanog binds directly to Esrrb, enhances binding of RNAPolII, and stimulates Esrrb transcription. Overexpression of Esrrb in ESCs maintains cytokine-independent self-renewal and pluripotency. Remarkably, this activity is retained in Nanog^−/− ESCs. Moreover, Esrrb can reprogram Nanog^−/− EpiSCs and can rescue stalled reprogramming in Nanog^−/− pre-iPSCs. Finally, Esrrb deletion abolishes the defining ability of Nanog to confer LIF-independent ESC self-renewal. These findings are consistent with the functional placement of Esrrb downstream of Nanog.

Formation of artefacts while sampling emissions of PCDD/PCDF from open burning of biomass

Emission factors for PCDD/PCDF determined from open combustion are used to estimate national emission budgets; therefore, it is important to have confidence in their accuracy. It has been suspected that artefacts may form due to the presence of hot metal surfaces of sampling equipment, thus skewing emission factors. In this study, emissions of PCDD/PCDF from open burning of forest biomass over a brick hearth were sampled. Five experiments were carried out using a portable sampler. Experiments were designed where the key variable, sample hood and inlet temperatures were manipulated. Other variables such as fuel origin, type and density were consistent. The measured concentration of PCDD/PCDF in the smoke samples ranged from 0.01 μg TEQ (t fuel)(-1) at the lowest maximum hood temperature (185°C) to 15 μg TEQ (t fuel)(-1) at the highest maximum hood temperature (598°C). when hood inlet temperatures exceeded 400°C emission factors were significantly elevated and this is attributed to the formation of artefacts that can cause the over estimation of emission factors. The increase in hood temperature also resulted in a change in the PCDD/PCDF congener and homologue profile of the emissions. For example at the lowest temperature (Fire 1) the PCDD/PCDF ratio measured was 50:1, whereas at the highest temperature (Fire 5) this ratio was about 0.53:1. When the sampler hood and inlet temperatures were kept in the normal operating range of <200°C, emission factors were comparable to those observed in many previous studies in Australia with emissions dominated by PCDD.

An Oct4-centered protein interaction network in embryonic stem cells

Transcription factors, such as Oct4, are critical for establishing and maintaining pluripotent cell identity. Whereas the genomic locations of several pluripotency transcription factors have been reported, the spectrum of their interaction partners is underexplored. Here, we use an improved affinity protocol to purify Oct4-interacting proteins from mouse embryonic stem cells (ESCs). Subsequent purification of Oct4 partners Sall4, Tcfcp2l1, Dax1, and Esrrb resulted in an Oct4 interactome of 166 proteins, including transcription factors and chromatin-modifying complexes with documented roles in self-renewal, but also many factors not previously associated with the ESC network. We find that Esrrb associated with the basal transcription machinery and also detect interactions between transcription factors and components of the TGF-β, Notch, and Wnt signaling pathways. Acute depletion of Oct4 reduced binding of Tcfcp2l1, Dax1, and Esrrb to several target genes. In conclusion, our purification protocol allowed us to bring greater definition to the circuitry controlling pluripotent cell identity.

Ensembl Genomes: extending Ensembl across the taxonomic space

Ensembl Genomes (http://www.ensemblgenomes.org) is a new portal offering integrated access to genome-scale data from non-vertebrate species of scientific interest, developed using the Ensembl genome annotation and visualisation platform. Ensembl Genomes consists of five sub-portals (for bacteria, protists, fungi, plants and invertebrate metazoa) designed to complement the availability of vertebrate genomes in Ensembl. Many of the databases supporting the portal have been built in close collaboration with the scientific community, which we consider as essential for maintaining the accuracy and usefulness of the resource. A common set of user interfaces (which include a graphical genome browser, FTP, BLAST search, a query optimised data warehouse, programmatic access, and a Perl API) is provided for all domains. Data types incorporated include annotation of (protein and non-protein coding) genes, cross references to external resources, and high throughput experimental data (e.g. data from large scale studies of gene expression and polymorphism visualised in their genomic context). Additionally, extensive comparative analysis has been performed, both within defined clades and across the wider taxonomy, and sequence alignments and gene trees resulting from this can be accessed through the site.

Is K-O Tab 1-2-3((R)) long lasting on non-polyester mosquito nets?

Many societies use locally sourced mosquito nets made from a variety of materials. For protecting against malaria these require regular re-treatment with insecticide. K-O Tab 1-2-3 is a 'dip-it-yourself' long-lasting formulation with time-limited interim recommendation from WHO for treatment of washed white and coloured polyester nets for up to 15 washes. To determine wash-resistance on different fabrics, nets made of polyester, polyethylene, cotton or nylon were treated with K-O Tab 1-2-3 and washed up to 20 times using standard WHO washing procedures. Efficacy was assessed using cone and cylinder bioassays and tunnel tests, and deltamethrin content using high-pressure liquid chromatography. Polyethylene and cotton nets treated with K-O Tab 1-2-3 and washed 20 times achieved the WHO threshold of >80% mortality in tunnel tests. Polyethylene matched the performance of polyester in all bioassays in contrast to cotton and nylon which produced low mortality and knock-down in cone and cylinder bioassays. After 20 washes 16.5% of the loading dose of deltamethrin remained on the polyester nets compared with 28.7% on polyethylene, 38.9% on cotton and 2.2% on nylon. Cotton nets retained a high concentration of insecticide but the relatively poor performance in terms of knock-down and mortality suggest most insecticide is bound within the cotton fibres rather than on the surface. K-O Tab 1-2-3 renders insecticide wash fast on polyethylene nets, less so on cotton and nylon. Nets made from polyethylene can be treated in the home to render the insecticide long lasting.

Unsupervised Methods for Determining Object and Relation Synonyms on the Web

The task of identifying synonymous relations and objects, or synonym resolution, is critical for high-quality information extraction. This paper investigates synonym resolution in the context of unsupervised information extraction, where neither hand-tagged training examples nor domain knowledge is available. The paper presents a scalable, fully-implemented system that runs in O(KN log N) time in the number of extractions, N, and the maximum number of synonyms per word, K. The system, called Resolver , introduces a probabilistic relational model for predicting whether two strings are co-referential based on the similarity of the assertions containing them. On a set of two million assertions extracted from the Web, Resolver resolves objects with 78% precision and 68% recall, and resolves relations with 90% precision and 35% recall. Several variations of resolver's probabilistic model are explored, and experiments demonstrate that under appropriate conditions these variations can improve F1 by 5%. An extension to the basic Resolver system allows it to handle polysemous names with 97% precision and 95% recall on a data set from the TREC corpus.

BioJava: an open-source framework for bioinformatics

Summary: BioJava is a mature open-source project that provides a framework for processing of biological data. BioJava contains powerful analysis and statistical routines, tools for parsing common file formats and packages for manipulating sequences and 3D structures. It enables rapid bioinformatics application development in the Java programming language.

Availability: BioJava is an open-source project distributed under the Lesser GPL (LGPL). BioJava can be downloaded from the BioJava website (http://www.biojava.org). BioJava requires Java 1.5 or higher.

Contact:andreas.prlic@gmail.com. All queries should be directed to the BioJava mailing lists. Details are available at http://biojava.org/wiki/BioJava:MailingLists.

AutoCSA, an algorithm for high throughput DNA sequence variant detection in cancer genomes

The undertaking of large-scale DNA sequencing screens for somatic variants in human cancers requires accurate and rapid processing of traces for variants. Due to their often aneuploid nature and admixed normal tissue, heterozygous variants found in primary cancers are often subtle and difficult to detect. To address these issues, we have developed a mutation detection algorithm, AutoCSA, specifically optimized for the high throughput screening of cancer samples.

Chlorfenapyr: a pyrrole insecticide for the control of pyrethroid or DDT resistant Anopheles gambiae (Diptera: Culicidae) mosquitoes

Owing to the development and spread of pyrethroid resistance in Anopheles gambiae in Africa there is an urgent need to develop alternative insecticides to supplement the pyrethroids. Chlorfenapyr is a pyrrole insecticide first commercialized for the control of agricultural pests and termites. Performance against An. gambiae bearing kdr (pyrethroid and DDT resistance) or Ace-1(R) insensitive acetylcholinesterase (organophosphate and carbamate resistance) mechanisms was studied using a variety of adult bioassay tests including a simulated-experimental hut system (tunnel tests) that allows uninhibited mosquito behaviour/insecticide interactions. Strains resistant to pyrethroids and organophosphates showed no cross resistance to chlorfenapyr. In cone bioassays on treated netting the mortality of adult mosquitoes showed an unexpected curvilinear response, with highest mortality occurring at intermediate dosages. Adults expressed irritability to chlorfenapyr at higher dosages, which might explain the dosage-mortality trend. Toxic activity of chlorfenapyr was slow compared to conventional neurotoxic insecticides and additional mortality occurred between 24h and 72 h. In tunnel tests, the dosage-mortality trend showed a more typical sigmoid response and most mortality occurred during the first 24h. Mosquito penetration through the holed, treated netting showed only limited inhibition and blood-feeding was not inhibited. Mortality rates in the kdr strain exposed to chlorfenapyr treated netting in tunnel tests were much higher than with permethrin treated netting over the same 100-500 mg/m(2) dosage range. Chlorfenapyr has potential for malaria control in treated-net or residual spraying applications in areas where mosquitoes are pyrethroid resistant. For treated-net applications chlorfenapyr might be combined with pyrethroid as a mixture to provide personal protection as well as to give control of resistant mosquitoes.

Change in pancreatic B-cell function (HOMA-B) varies in different populations with similar genetic backgrounds but different environments

OBJECTIVE

To determine whether pancreatic B-cell function varies in different populations with similar genetic backgrounds but different environments.

RESEARCH DESIGN/METHODS

We compared a specific migrant Gujarati community in the UK (n = 205) with people still resident in the same villages of origin in Gujarat, India (n = 246). Pancreatic B-cell function (HOMA-B) was determined and the influence of age, migration and other factors was explored.

RESULTS

As anticipated, there was an age-related decline in log(HOMA-B) in both groups. However, the age-related fall in log(HOMA-B) was more pronounced in the UK than in Gujarat (normalized beta-0.29 vs. -0.14, P for difference = 0.03). The decline of HOMA-B with age persisted after adjustment for body mass index (UK beta = -0.31; Gujarat beta = -0.16, P = 0.015, P < 0.001). There was no significant change in insulin sensitivity (HOMA-S) with age at either site, although insulin sensitivity was lower in the UK. Fasting non-estrified fatty acid (NEFA) levels rose with age in the UK but not in Gujarat (P = 0.003 for difference in gradients). In multiple linear regression analysis, lower log(HOMA-B) was independently associated with higher fasting log(NEFA) levels; normalized beta = -0.24, P < 0.001, age; beta = -0.16, P = 0.005, higher log(insulin-like growth factor binding protein-1); beta = -0.19, P = 0.007 and lower body mass index; beta = 0.26, P = 0.001. This model accounted for 25% of the variability in HOMA-B.

CONCLUSIONS

HOMA-B as a measure of B-cell function declines more rapidly with age in the migrant UK group than in Gujarat. This may be a direct consequence of chronically higher NEFA exposure in the UK group.