ExpansionHunter: a sequence-graph-based tool to analyze variation in short tandem repeat regions.

SUMMARY: We describe a novel computational method for genotyping repeats using sequence graphs. This method addresses the long-standing need to accurately genotype medically important loci containing repeats adjacent to other variants or imperfect DNA repeats such as polyalanine repeats. Here we introduce a new version of our repeat genotyping software, ExpansionHunter, that uses this method to perform targeted genotyping of a broad class of such loci. AVAILABILITY AND IMPLEMENTATION: ExpansionHunter is implemented in C++ and is available under the Apache License Version 2.0. The source code, documentation, and Linux/macOS binaries are available at https://github.com/Illumina/ExpansionHunter/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Investigation of Dopamine Analogues: Synthesis, Mechanistic Understanding, and Structure-Property Relationship.

Dopamine, perhaps the simplest molecule that covalently links catechol and amine, together with its derivatives, has shown impressive adhesive and coating properties with its polymers. However, the scope of the molecules is rather limited, and the polymerization mechanisms are still elusive. We designed a general synthetic scheme and successfully synthesized a series of dopamine analogues with different alkyl chain lengths between the catechol and amine. Taking these new dopamine analogues, together with the molecular systems that have separate catechol and alkyl amine, we show that having both catechol and amine in the molecular system, whether covalently linked via an alkyl chain or not, is sufficient to polymerize under a similar reaction condition to that of dopamine polymerization. However, the time-dependent UV-vis characterization of the individual polymerization indicates that the polymerization for individual molecular systems likely proceeds via different reaction intermediates, depending on the length of the alkyl chain and whether there is a covalent linkage. Interestingly, whereas the covalent linkage via an alkyl chain is not necessary for showing the adhesive property, it is required to achieve the impressive coating property. Our results offer new insights into the design and synthesis of dopamine analogues for future applications, as well as a further mechanistic understanding of the polymerization of these dopamine analogues.

Brief report on a systematic review of youth violence prevention through media campaigns: Does the limited yield of strong evidence imply methodological challenges or absence of effect?

BACKGROUND: We present a brief report on a systematic review which identified, assessed and synthesized the existing evidence of the effectiveness of media campaigns in reducing youth violence. METHODS: Search strategies made use of terms for youth, violence and a range of terms relating to the intervention. An array of academic databases and websites were searched. RESULTS: Although media campaigns to reduce violence are widespread, only six studies met the inclusion criteria. There is little strong evidence to support a direct link between media campaigns and a reduction in youth violence. Several studies measure proxies for violence such as empathy or opinions related to violence, but the link between these measures and violence perpetration is unclear. Nonetheless, some evidence suggests that a targeted and context-specific campaign, especially when combined with other measures, can reduce violence. However, such campaigns are less cost-effective to replicate over large populations than generalised campaigns. CONCLUSIONS: It is unclear whether the paucity of evidence represents a null effect or methodological challenges with evaluating media campaigns. Future studies need to be carefully planned to accommodate for methodological difficulties as well as to identify the specific elements of campaigns that work, especially in lower and middle income countries.

Mitigating Matrix Effects in LC-ESI-MS-MS Analysis of a Urinary Biomarker of Xylenes Exposure.

Liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS-MS) with stable isotope-labeled internal standards (SIL-ISs) is the gold standard for quantitative analysis of drugs and metabolites in complex biological samples. Significant isotopic effects associated with deuterium labeling often cause the deuterated IS to elute at a different retention time from the target analyte, diminishing its capability to compensate for matrix effects. In this study, we systematically compared the analytical performance of deuterated (2H) SIL-IS to non-deuterated (13C and 15N) SIL-ISs for quantifying urinary 2-methylhippuric acid (2MHA) and 4-methylhippuric acid (4MHA), biomarkers of xylenes exposure, with an LC-ESI-MS-MS assay. Analytical method comparison between ISs demonstrated a quantitative bias for urinary 2MHA results, with concentrations generated with 2MHA-[2H7] on average 59.2% lower than concentrations generated with 2MHA-[13C6]. Spike accuracy, measured by quantifying the analyte-spiked urine matrix and comparing the result to the known spike concentration, determined that 2MHA-[2H7] generated negatively biased urinary results of -38.4%, whereas no significant bias was observed for 2MHA-[13C6]. Post-column infusion demonstrated that ion suppression experienced by 2MHA and 2MHA-[13C6] was not equally experienced by 2MHA-[2H7], explaining the negatively biased 2MHA results. The quantitation of urinary 4MHA results between ISs exhibited no significant quantitative bias. These results underscore the importance of the careful selection of ISs for targeted quantitative analysis in complex biological samples.

Assessment of urinary 6-hydroxy-2,4-cyclohexadienyl mercapturic acid as a novel biomarker of benzene exposure.

Assessing benzene exposure is a public health priority due to its deleterious health effects and ubiquitous industrial and environmental sources of exposure. Phenyl mercapturic acid (PhMA) is a commonly used urinary biomarker to assess benzene exposure. However, recent work has identified significant interlaboratory variation in urinary PhMA concentrations related to methodological differences. In this study, we present urinary 6-hydroxy-2,4-cyclohexadienyl mercapturic acid (pre-PhMA), a metabolite that undergoes acid-catalyzed dehydration to form PhMA, as a novel and specific urinary biomarker for assessing benzene exposure. We developed and validated the first quantitative liquid chromatography-tandem mass spectrometry assay for measuring urinary concentrations of pre-PhMA. The pH effect on the method of ruggedness testing determined that pre-PhMA is stable across the normal human urine pH range and that neutral conditions must be maintained throughout quantification for robust and accurate measurement of urinary pre-PhMA concentrations. The method exhibited below 2 ng/mL sensitivity for pre-PhMA, linearity over three orders of magnitude, and precision and accuracy within 10%. Urinary pre-PhMA concentrations were assessed in 369 human urine samples. Smoking individuals exhibited elevated levels of pre-PhMA compared to non-smoking individuals. Furthermore, the relationship between benzene exposure and urinary pre-PhMA levels was explored by examining the correlation of pre-PhMA with 2-cyanoethyl mercapturic acid, a smoke exposure biomarker. The urinary biomarkers exhibited a positive correlation (r = 0.720), indicating that pre-PhMA levels increased with benzene exposure. The results of this study demonstrate that urinary pre-PhMA is a rugged and effective novel biomarker of benzene exposure that can be widely implemented for future biomonitoring studies.

South Africa's male homicide epidemic hiding in plain sight: Exploring sex differences and patterns in homicide risk in a retrospective descriptive study of postmortem investigations.

South Africa has an overall homicide rate six times the global average. Males are predominantly the victims and perpetrators, but little is known about the male victims. For the country's first ever study on male homicide we compared 2017 male and female victim profiles for selected covariates, against global average and previous estimates for 2009. We conducted a retrospective descriptive study of routine data collected through postmortem investigations, calculating age-standardised mortality rates for manner of death by age, sex and province and male-to-female incidence rate ratios with 95% confidence intervals. We then used generalised linear models and linear regression models to assess the association between sex and victim characteristics including age and mechanism of injury (guns, sharp and blunt force) within and between years. 87% of 19,477 homicides in 2017 were males, equating to seven male deaths for every female, with sharp force and firearm discharge being the most common cause of death. Rates were higher among males than females at all ages, and up to eight times higher for the age group 15-44 years. Provincial rates varied overall and by sex, with the highest comparative risk for men vs. women in the Western Cape Province (11.4 males for every 1 female). Male homicides peaked during December and were highest during weekends, underscoring the prominent role of alcohol as a risk factor. There is a massive, disproportionate and enduring homicide risk among South African men which highlights their relative neglect in the country's prevention and policy responses. Only through challenging the normative perception of male invulnerability do we begin to address the enormous burden of violence impacting men. There is an urgent need to address the insidious effect of such societal norms alongside implementing structural interventions to overcome the root causes of poverty, inequality and better control alcohol and firearms.

Non-COVID-19 vaccine hesitancy among migrant populations worldwide: a scoping review of the literature, 2000-2020.

INTRODUCTION: Migration can be linked to the transmission of vaccine-preventable diseases. Hence, monitoring migrants' vaccination-related concerns can inform needed interventions to support vaccine acceptance. AREAS COVERED: Along with Google and Google Scholar, we searched 13 bibliographic databases between 1 January 2000 and 10 October 2020, to identify published studies of vaccine hesitancy among migrant populations. From a total of 8,915 records, we screened 745 abstracts and included 112 eligible articles. We summarized extracted data using figures, tables, and narrations. Of the 112 articles, 109 were original quantitative (48%), qualitative (45%), and mixed-methods (7%) research, originating mainly from the United States (US) (68%), the United Kingdom (UK) (12%), and Scandinavia (6%). Most articles addressed human papillomavirus (63%), measles (13%), and influenzas (9%) vaccinations, and the leading sponsor of funded research was the US National Institutes of Health (50%). Discernable migrant groups with vaccine-specific concerns included Somali diasporas, UK-based Poles and Romanians, and US-based Haitians and Koreans. Among US-based Latina/Latino immigrants, lower vaccine uptake frequency was mostly associated with awareness levels, knowledge gaps, and uninsured status. EXPERT OPINION: Migrants' vaccine-related apprehensions may cascade well beyond their proximate social connections and influence vaccine attitudes and behaviors in their countries-of-origin.

Confession, psychology and the shaping of subjectivity through interviews with victims of female-perpetrated sexual violence.

Female-perpetrated sexual abuse (FSA) is often seen as rare and of little consequence. Confessing to being a victim of FSA is infrequent and often met with incredulity. Identifying as such a victim is thus often a response to an incitement to speak in the mode of confession. Interviews producing the possibility for such confessions were conducted with ten self-identified South African FSA victims and then analysed using a Foucauldian approach. In identifying as victims of FSA the participants drew on psychologised, gendered accounts of damage reflected in trauma, revictimisation, memory loss, the cycle of abuse and deviance. An analysis of these accounts demonstrates how confessional sites, such as the (psychological) interview, anchor victim worthiness in damage so that 'non-normative' victims of violence are able to see themselves in sexual violence discourse as forever compromised subjects whose healing requires rethinking the relationship between gender, sexuality, and violence in contemporary South Africa.

Vaccine hesitancy in migrant communities: a rapid review of latest evidence.

By refusing or delaying vaccination, vaccine hesitant individuals and communities undermine the prevention, and ultimately, elimination of communicable diseases against which safe and effective vaccines are available. We reviewed recent evidence of vaccine hesitancy within migrant communities in the context of increased human mobility and widespread anti-immigrant sentiment and manifest xenophobia. Among many immigrant parents and families, vaccine hesitancy is largely associated with fears and misinformation about vaccine harms, limited knowledge of both preventable diseases and vaccines, distrust of host countries' health systems and their attendant intentions, language barriers, and perceived incompatibility between vaccine uptake and migrants' religion. Hesitancy toward measles, influenza, and human papillomavirus vaccines are most discernible, and main migrant populations involved include Somalis and Poles.

Effects of feeding a novel alfalfa leaf pellet product (ProLEAF MAX) and alfalfa stems (ProFiber Plus) on performance in the feedlot and carcass quality of beef steers.

Alfalfa is often included in the diets of beef animals; however, the nutrient content of alfalfa is variable depending on the region in which it is grown, climate, soil, and many other factors. The leaf portion of alfalfa has a less variable nutrient composition than the stem portion of the plant. The variability that is present in the alfalfa plant can make the development of total mixed rations of consistent nutrient content difficult. As such, the purpose of this study was to determine how the inclusion of fractionated alfalfa leaves and alfalfa stems impacts performance and carcass quality of finishing beef steers. Twenty-four steers were allocated to one of three treatments: a control group fed a typical finishing diet with alfalfa as the forage (CON; n = 8), a typical diet that replaced alfalfa with fractionated alfalfa leaf pellets and alfalfa stems (ProLEAF MAX™ + ProFiber Plus™; PLM+PFP; n = 8), or a typical diet that replaced alfalfa with alfalfa stems (PFP; n = 8) for 63 days. Steers were fed individually once daily, weighed every 14 days and ultrasound images were collected every 28 days. At the end of the feeding trial, steers were harvested at a commercial facility and carcass data was obtained. Analysis of dry matter intake demonstrated that steers receiving the PFP and CON diets consumed more feed (P < 0.001) than steers consuming the PLM+PFP diet. Steers receiving the PLM+PFP diet gained less (P < 0.001) weight than the steers receiving the other two dietary treatments. No differences (P > 0.10) in feed efficiency or carcass characteristics were observed. Steers receiving the PFP diet had improved (P = 0.016) cost of gain ($0.93 per kg) when compared with steers receiving PLM+PFP ($1.08 per kg) diet. Overall, our findings demonstrate that the inclusion of PFP in place of alfalfa hay in a finishing diet has the potential to improve cost of gain, without negatively affecting growth, performance, or carcass characteristics of finishing feedlot steers.

Anabolic Implants Varying in Hormone Type and Concentration Influence Performance, Feeding Behavior, Carcass Characteristics, Plasma Trace Mineral Concentrations, and Liver Trace Mineral Concentrations of Angus Sired Steers.

Fifty Angus-sired steers were utilized to evaluate the effects of anabolic implants varying in hormone type and concentration on performance, carcass traits, and plasma and liver trace mineral concentrations over 129 d. Steers were stratified by weight into one of four (n = 12 or 13/treatment) implant treatments: (1) estradiol (E2; 25.7 mg E2; Compudose, Elanco Animal Health, Greenfield, IN, USA), (2) trenbolone acetate (TBA; 200 mg TBA; Finaplix-H, Merck Animal Health, Madison, NJ, USA), (3) combination implant (ETBA; 120 mg TBA + 24 mg E2; Revalor-S, Merck Animal Health), or (4) no implant (CON). Steers were randomly assigned to pens equipped with GrowSafe bunks and fed a corn and barley-based finishing ration. Overall average daily gain and body weight were greater for ETBA and TBA than CON (p ≤ 0.04), but not E2 (p ≥ 0.12). Feed efficiency and hot carcass weight were only greater than CON for ETBA (p ≤ 0.03). Plasma and d 2 liver Zn concentrations were lesser for ETBA than CON (p ≤ 0.01) and d 10 liver Mn was lesser (p = 0.0003) for TBA than CON. These data indicate that implants containing TBA influence growth and trace mineral parameters, though more work investigating this relationship is necessary.

Interactions between cattle breed type and anabolic implant strategy impact circulating serum metabolites, feedlot performance, feeding behavior, carcass characteristics, and economic return in beef steers.

Introducing Bos indicus (BI) genetics into a beef herd has the potential to increase environmental sustainability. When introducing BI genetics, there are concerns regarding negative impacts on temperament, growth, and carcass characteristics. Implants are routinely used in the United States, with majority of cattle on feed receiving an anabolic implant to improve growth and efficiency, however research regarding the interaction between cattle breed type and anabolic implants is limited. This research compared the use of implants in BI influenced animals versus Bos taurus in a feedlot setting. Twenty steers were stratified by initial weight in a 2 × 2 factorial design examining two different breeds: Angus (AN; n = 10) or Santa Gertrudis influenced (SG; n = 10), and two implant strategies: no implant (CON; n = 10) or a combined implant containing 120 mg TBA and 24 mg E2 (IMP; n = 10; Revalor-S, Merck Animal Health). We hypothesized that anabolic implants would improve growth and feedlot performance of BI influenced animals. Steers were randomly placed into covered pens equipped with GrowSafe bunks and fed the same ration for 129 d. Steers were weighed every 28 d. Dry matter intake, feeding behavior, and carcass data of the steers was collected. Blood was collected and harvested as serum on d 0, 2, 10, 28 and every 28 d after that, and analyzed for serum urea nitrogen (SUN), haptoglobin, and 25HydroxyVitamin D. Angus steers tended to gain more (P = 0.06) weight than SG, while IMP tended to gain more (P = 0.10) weight than CON with no breed × treatment interaction observed (P > 0.10). A breed × treatment interaction was observed when analyzing SUN (P = 0.05) and haptoglobin (P = 0.02) concentrations. Serum 25HydroxyVitmain D concentrations tended to be increased (P = 0.09) in SG-IMP steers compared to SG-CON steers. Angus steers tended (P = 0.10) to have greater amounts of marbling compared to SG steers, while SG steers had improved (P = 0.04) yield grade. Economic return was decreased by $46 a head when introducing SG genetics, while implanting steers improved economic return by $46 a head. This research provides evidence suggesting that BI influenced animals may respond differently to anabolic implants when compared to BT animals. Economic analyses demonstrate that anabolic implants improve economic return to beef producers, while introducing SG genetics decreases economic return in animals raised in more temperate climates.

Large Differences in Urinary Benzene Metabolite S-Phenylmercapturic Acid Quantitation: A Comparison of Five LC-MS-MS Methods.

Benzene is a known genotoxic carcinogen linked to many hematological abnormalities. S-phenylmercapturic acid (PHMA, N-acetyl-S-(phenyl)-L-cysteine, CAS# 4775-80-8) is a urinary metabolite of benzene and is used as a biomarker to assess benzene exposure. Pre-S-phenylmercapturic acid (pre-PHMA) is a PHMA precursor that dehydrates to PHMA at acidic pH. Published analytical methods that measure urinary PHMA adjust urine samples to a wide range of pH values using several types of acid, potentially leading to highly variable results depending on the concentration of pre-PHMA in a sample. Information is lacking on the variation in sample preparation among laboratories regularly measuring PHMA and the effect of those differences on PHMA quantitation in human urine samples. To investigate the differences in PHMA quantitation, we conducted an inter-laboratory comparison that included the analysis of 50 anonymous human urine samples (25 self-identified smokers and 25 self-identified non-smokers), quality control samples and commercially available reference samples in five laboratories using different analytical methods. Observed urinary PHMA concentrations were proportionally higher at lower pH, and results for anonymous urine samples varied widely among the methods. The method with the neutral preparation pH yielded results about 60% lower than the method using the most acidic conditions. Samples spiked with PHMA showed little variation, suggesting that the variability in results in human urine samples across methods is driven by the acid-mediated conversion of pre-PHMA to PHMA.

Urban upgrading and levels of interpersonal violence in Cape Town, South Africa: The violence prevention through urban upgrading programme.

Violence Prevention through Urban Upgrading applies second generation crime prevention through environmental design, which includes built environment interventions alongside social programmes and community participation initiatives in Khayelitsha, one of South Africa's poorest and most violent suburbs. We conducted a retrospective population-based study using survey data from 3625 geo-located households collected between 2013 and 2015 and mapped alcohol outlets to assess the association between the intervention and reported experience of violence. The analysis used generalised linear models to estimate and compare selfreported experience of violence adjusting for known confounders, which included area and household deprivation as well as alcohol outlet density. Living in close proximity to the upgraded urban infrastructure was associated with a 34% reduced exposure to interpersonal violence after adjusting for confounders. This association was consistent across age and gender. Access to additional social programmes alongside the urban upgrading intervention was not associated with further reduction in risk. The association between urban-upgrading and reduced exposure to interpersonal violence supports its inclusion among interventions in national and local crime prevention policies to address social and structural environments.

Amplification-free long-read sequencing of TCF4 expanded trinucleotide repeats in Fuchs Endothelial Corneal Dystrophy.

Amplification of a CAG trinucleotide motif (CTG18.1) within the TCF4 gene has been strongly associated with Fuchs Endothelial Corneal Dystrophy (FECD). Nevertheless, a small minority of clinically unaffected elderly patients who have expanded CTG18.1 sequences have been identified. To test the hypothesis that the CAG expansions in these patients are protected from FECD because they have interruptions within the CAG repeats, we utilized a combination of an amplification-free, long-read sequencing method and a new target-enrichment sequence analysis tool developed by Pacific Biosciences to interrogate the sequence structure of expanded repeats. The sequencing was successful in identifying a previously described interruption within an unexpanded allele and provided sequence data on expanded alleles greater than 2000 bases in length. The data revealed considerable heterogeneity in the size distribution of expanded repeats within each patient. Detailed analysis of the long sequence reads did not reveal any instances of interruptions to the expanded CAG repeats, but did reveal novel variants within the AGG repeats that flank the CAG repeats in two of the five samples from clinically unaffected patients with expansions. This first examination of the sequence structure of CAG repeats in CTG18.1 suggests that factors other than interruptions to the repeat structure account for the absence of disease in some elderly patients with repeat expansions in the TCF4 gene.

The impact of violence on health in low- to middle-income countries.

More than 90% of violence-related deaths occur in low- to middle-income countries (LMICs), where the mortality rate due to violence is almost 2.5 times greater than in high-income countries. Over and above the substantial contribution of violence as a cause of death and physical injuries, victims of violence are also more vulnerable to a range of mental and physical health problems. Several studies describe the deleterious impact of different types of violence on a range of health outcomes, but no review has yet been undertaken that presents a composite overview of the current state of knowledge in LMICs. This paper reviews the scientific literature describing the nature, magnitude and impact of violence on health, describing the current state of violence-prevention policy developments within the global health agenda and highlighting the health consequences, disease burden and economic costs of violence. Although data are limited, the review indicates that costs relating to violence deplete health care budgets considerably and that scarce resources could be better used to address other health threats that hamper development.

The impact of violence on development in low- to middle-income countries.

Along with the numerous trauma-related impacts of violence and its effects on other health outcomes, the social toll of violence is further exacerbated by economic costs that represent formidable threats to fiscal growth and development. A companion piece to a review of the scientific literature describing the nature, magnitude and impact of violence on health (Matzopoulos, Bowman, Butchart & Mercy, 2008) in this issue, this paper reviews the current knowledge base on violence and development with a specific focus on low- to middle-income countries. It describes how violence impacts on all eight goals of the Millennium Development Plan and exerts a considerable economic burden on already stressed state systems and social spending. Violence will become an increasingly important threat to development and is receiving growing recognition among the global health community and within health ministries. The near absence of violence prevention within the global development agenda is, however, cause for concern. There is an urgent need to mobilise the international development community to provide financial and technical support for intersectoral collaboration, multilateral research cooperation and the development of research capacity towards addressing violence as a significant threat to development.

Coming-Out Confessions: Negotiating the Burden of Lesbian Identity Politics in South Africa.

For lesbians, "coming out" or disclosing one's sexual orientation has come to be seen as a marker of self-acceptance, actualization, and the imperative first step in the authentication of a liberated subjectivity and social identity. However, other critical schools of thought, largely informed by Foucault's middle writings, have argued that "coming out" is merely a confessional response to an incitement to discourse about sex. This study explored constructions of coming out by a group of self-identified lesbians in South Africa. Data were collected via eight semistructured interviews and subjected to discourse analysis. Although the coming-out stories appear to conform to some discursive practices characterizing confessional modes of response to incitements to speak, they are also de-emphasized as central to the constitution of selfhood. The changing conditions of possibility for the production of sexual subjectivity in contemporary South Africa seem to disrupt understandings of coming out as either solely a confessional or liberatory practice.

Citizenship in a time of HIV: Understanding medical adult male circumcision in South Africa.

Medical adult male circumcision has been shown to offer men significant protection against HIV infection during peno-vaginal sex. This has resulted in calls for a national roll-out of medical adult male circumcision in South Africa, a rights-based constitutional democracy. This article explores the ways that the potential tensions between this call to circumcise as a practice of good health citizenship and the guaranteed right to bodily integrity are negotiated in interviews with 30 urban-based men in Johannesburg. The results suggest that despite its demonstrable biological efficacy, these tensions may paralyse decision- and policy-makers in grappling with the potential scaling up of medical adult male circumcision for HIV prevention in South Africa.