The Encyclopedia of DNA elements (ENCODE): data portal update.

The Encyclopedia of DNA Elements (ENCODE) Data Coordinating Center has developed the ENCODE Portal database and website as the source for the data and metadata generated by the ENCODE Consortium. Two principles have motivated the design. First, experimental protocols, analytical procedures and the data themselves should be made publicly accessible through a coherent, web-based search and download interface. Second, the same interface should serve carefully curated metadata that record the provenance of the data and justify its interpretation in biological terms. Since its initial release in 2013 and in response to recommendations from consortium members and the wider community of scientists who use the Portal to access ENCODE data, the Portal has been regularly updated to better reflect these design principles. Here we report on these updates, including results from new experiments, uniformly-processed data from other projects, new visualization tools and more comprehensive metadata to describe experiments and analyses. Additionally, the Portal is now home to meta(data) from related projects including Genomics of Gene Regulation, Roadmap Epigenome Project, Model organism ENCODE (modENCODE) and modERN. The Portal now makes available over 13000 datasets and their accompanying metadata and can be accessed at: https://www.encodeproject.org/.

Midline Cleft of Lip With Preaxial Polydactyly in One Hand: A Possible New Variation of Thurston Syndrome?

Oral-facial-digital syndromes are a group of disorders with various subtypes. Type V, also known as the Thurston syndrome, is an autosomal recessive condition characterized by median cleft of the upper lip, postaxial polydactyly of hands and feet, and oral manifestations. Majority of the cases reported in the literature have been of Indian ethnic origin. We report a case of a possible variation of this syndrome in a 5-month-old Indian girl who presented with severe midline clefting, cleft palate, and atypically, preaxial polydactyly of the right hand.

Enhancing value and lowering costs of care: a qualitative exploration of a randomized linkage to care intervention in South Africa.

While interventions to improve HIV linkage and retention in care exist, none have demonstrated results sufficient to reach UNAIDS 90-90-90 goals. We explored values and costs of seeking clinical care through testing three strategies to improve linkage to care: Point of care CD4 testing alone (POC-CD4), POC-CD4 combined with transportation support and combined with care facilitation. We conducted in-depth interviews with participants and transcribed audio-recordings of care facilitation sessions. Participants described values and costs enhanced or addressed by the three interventions. Psychosocial support provided through the care facilitation intervention appeared salient. Participants named other values and costs of seeking care unrelated to the intervention, such as encouragement from healthcare workers and aversion to lifelong treatment. Combined with the quantitative results of this trial, these findings may point to why the care facilitation arm was successful but not the POC-CD4 only or transportation arms. It also provides guidance for future interventions.

Cost-Utility of Access to Care, a National HIV Linkage, Re-engagement and Retention in Care Program.

Linkage to HIV medical care and on-going engagement in HIV medical care are vital for ending the HIV epidemic. However, little is known about the cost-utility of HIV linkage, re-engagement and retention (LRC) in care programs. This paper presents the cost-utility analysis of Access to Care, a national HIV LRC program. Using standard methods from the US Panel on Cost-Effectiveness in Health and Medicine, we calculated the cost-utility ratio. Seven Access to Care programs were cost-effective and two were cost-saving. This study adds to a small but growing body of evidence to support the cost-effectiveness of LRC programs.

The Cost and Threshold Analysis of Retention in Care (RiC): A Multi-Site National HIV Care Program.

Persons diagnosed with HIV but not retained in HIV medical care accounted for the majority of HIV transmissions in 2009 in the United States (US). There is an urgent need to implement and disseminate HIV retention in care programs; however little is known about the costs associated with implementing retention in care programs. We assessed the costs and cost-saving thresholds for seven Retention in Care (RiC) programs implemented in the US using standard methods recommended by the US Panel on Cost-effectiveness in Health and Medicine. Data were gathered from accounting and program implementation records, entered into a standardized RiC economic analysis spreadsheet, and standardized to a 12 month time frame. Total program costs for from the societal perspective ranged from $47,919 to $423,913 per year or $146 to $2,752 per participant. Cost-saving thresholds ranged from 0.13 HIV transmissions averted to 1.18 HIV transmission averted per year. We estimated that these cost-saving thresholds could be achieved through 1 to 16 additional person-years of viral suppression. Across a range of program models, retention in care interventions had highly achievable cost-saving thresholds, suggesting that retention in care programs are a judicious use of resources.

Cost-Utility Analysis of Three U.S. HIV Linkage and Re-engagement in Care Programs from Positive Charge.

Linking and retaining people living with HIV in ongoing, HIV medical care is vital for ending the U.S. HIV epidemic. Yet, 41-44 % of HIV+ individuals are out of care. In response, AIDS United initiated Positive Charge, a series of five HIV linkage and re-engagement projects around the U.S. This paper investigates whether three Positive Charge programs were cost effective and calculates a return on investment for each program. It uses standard methods of cost utility analysis and WHO-CHOICE thresholds. All three projects were found to be cost effective, and two were highly cost effective. Cost utility ratios ranged from $4439 to $137,271. These results suggest that HIV linkage to care programs are a productive and efficient use of public health funds.

Cost and cost threshold analyses for 12 innovative US HIV linkage and retention in care programs.

Out of >1,000,000 people living with HIV in the USA, an estimated 60% were not adequately engaged in medical care in 2011. In response, AIDS United spearheaded 12 HIV linkage and retention in care programs. These programs were supported by the Social Innovation Fund, a White House initiative. Each program reflected the needs of its local population living with HIV. Economic analyses of such programs, such as cost and cost threshold analyses, provide important information for policy-makers and others allocating resources or planning programs. Implementation costs were examined from societal and payer perspectives. This paper presents the results of cost threshold analyses, which provide an estimated number of HIV transmissions that would have to be averted for each program to be considered cost-saving and cost-effective. The methods were adapted from the US Panel on Cost-effectiveness in Health and Medicine. Per client program costs ranged from $1109.45 to $7602.54 from a societal perspective. The cost-saving thresholds ranged from 0.32 to 1.19 infections averted, and the cost-effectiveness thresholds ranged from 0.11 to 0.43 infections averted by the programs. These results suggest that such programs are a sound and efficient investment towards supporting goals set by US HIV policy-makers. Cost-utility data are pending.

Individual-Level and Partner-Level Predictors of Newly Diagnosed HIV Infection Among Black and White Men Who Have Sex with Men in Baltimore, MD.

Black MSM continue to be the group most disproportionately impacted by HIV in the United States. This study assesses the relationship between partner-level and respondent-level characteristics and newly diagnosed HIV infection among a sample of MSM. Ego-centric data were gathered using venue-based time-space sampling on 335 men who reported on a total of 831 male anal sex partners. In multivariate analyses, age of partner, HIV status of partner, and respondent having had an STD in the past twelve months were associated with a newly diagnosed HIV infection among black MSM. Efforts for black MSM are needed that aim to increase HIV and STD testing, foster open communication between partners about HIV status, and address social determinants of health.

Positive Charge: Filling the Gaps in the U.S. HIV Continuum of Care.

Adequate engagement in HIV care is necessary for the achievement of optimal health outcomes and for the reduction of HIV transmission. Positive Charge (PC) was a national HIV linkage and re-engagement in care program implemented by AIDS United. This study describes three PC programs, the characteristics of their participants, and the continuum of engagement in care for their participants. Eighty-eight percent of participants were engaged in care post PC enrollment. Sixty-nine percent were retained in care, and 46 % were virally suppressed at follow-up. Older participants were more likely to be engaged, retained, and virally suppressed. Differences by race and gender in HIV care and treatment varied across PC programs, reflecting the diverse target populations, locations, and strategies employed by the PC grantees. There is an urgent need for programs that promote HIV care and treatment among vulnerable populations, including young people living with HIV. There is also an urgent need for additional research to test the effectiveness of promising linkage and retention in care strategies, such as peer navigation.

Cost and threshold analysis of positive charge, a multi-site linkage to HIV care program in the United States.

Positive Charge (PC) is a linkage to HIV care initiative implemented by AIDS United with sites in New York, Chicago, Louisiana, North Carolina, and the San Francisco/Bay Area. This study employed standard methods of cost and threshold analyses, as recommended by the US Panel on Cost-effectiveness in Health and Medicine, to calculate cost-saving and cost effective thresholds of the initiative. The overall societal cost of the linkage to care programs ranged from $48,490 to $370,525. The study found that PC's five unique evidence-based linkage to care programs have relatively low costs per client served and highly achievable cost-saving and cost-effectiveness thresholds. The findings from this study suggest that HIV linkage to care programs have the potential to be a highly productive use of public health resources.

Diurnal Preference Predicts Phase Differences in Expression of Human Peripheral Circadian Clock Genes.

BACKGROUND: Circadian rhythms play an integral role in human behavior, physiology and health. Individual differences in daily rhythms (chronotypes) can affect individual sleep-wake cycles, activity patterns and behavioral choices. Diurnal preference, the tendency towards morningness or eveningness among individuals, has been associated with interpersonal variation in circadian clock-related output measures, including body temperature, melatonin levels and clock gene mRNA in blood, oral mucosa, and dermal fibroblast cell cultures. METHODS: Here we report gene expression data from two principal clock genes sampled from hair follicle cells, a peripheral circadian clock. Hair follicle cells from fourteen individuals of extreme morning or evening chronotype were sampled at three time points. RNA was extracted and quantitative PCR assays were used to measure mRNA expression patterns of two clock genes, Per3 and Nr1d2. RESULTS: We found significant differences in clock gene expression over time between chronotype groups, independent of gender or age of participants. Extreme evening chronotypes have a delay in phase of circadian clock gene oscillation relative to extreme morning types. Variation in the molecular clockwork of chronotype groups represents nearly three-hour phase differences (Per3: 2.61 hours; Nr1d2: 3.08 hours, both: 2.86) in circadian oscillations of these clock genes. CONCLUSIONS: The measurement of gene expression from hair follicles at three time points allows for a direct, efficient method of estimating phase shifts of a peripheral circadian clock in real-life conditions. The robust phase differences in temporal expression of clock genes associated with diurnal preferences provide the framework for further studies of the molecular mechanisms and gene-by-environment interactions underlying chronotype-specific behavioral phenomena, including social jetlag.

Mind the gap: social media engagement by public health researchers.

BACKGROUND: The traditional vertical system of sharing information from sources of scientific authority passed down to the public through local health authorities and clinicians risks being made obsolete by emerging technologies that facilitate rapid horizontal information sharing. The rise of Public Health 2.0 requires professional acknowledgment that a new and substantive forum of public discourse about public health exists on social media, such as forums, blogs, Facebook, and Twitter. OBJECTIVE: Some public health professionals have used social media in innovative ways: to surveil populations, gauge public opinion, disseminate health information, and promote mutually beneficial interactions between public health professionals and the lay public. Although innovation is on the rise, most in the public health establishment remain skeptical of this rapidly evolving landscape or are unclear about how it could be used. We sought to evaluate the extent to which public health professionals are engaged in these spaces. METHODS: We conducted a survey of professorial- and scientist-track faculty at the Johns Hopkins Bloomberg School of Public Health in Baltimore, Maryland, USA. We asked all available faculty via email to complete a 30-question survey about respondent characteristics, beliefs about social media, and usage of specific technologies, including blogs, Facebook, Twitter, and YouTube. RESULTS: A total of 181 (19.8%) of 912 professor- and scientist-track faculty provided usable responses. The majority of respondents rarely used major social media platforms. Of these 181 respondents, 97 (53.6%) had used YouTube, 84 (46.4%) had used Facebook, 55 (30.4%) had read blogs, and 12 (6.6%) had used Twitter in the prior month. More recent degree completion was the best predictor of higher usage of social media. In all, 122 (67.4%) agreed that social media is important for disseminating information, whereas only 55 (30.4%) agreed that social media is useful for their research. In all, 43 (23.8%) said social media was helpful for professional career advancement, whereas 72 (39.8%) said it was not. Only 43 (23.8%) faculty said they would employ a full- or part-time social media consultant, and 30 (16.6%) currently employed one. CONCLUSIONS: Despite near-universal appreciation of the potential for social media to serve as a component of public health strategy, a small minority are actually engaged in this space professionally, whereas most are either disinterested or actively opposed to professional engagement. Social media is seen by most as more useful for spreading information than obtaining it. As public discourse on a number of critical health topics continues to be influenced and sometimes shaped by discussions online from Twitter to Facebook, it would seem that greater discourse is needed about when and how public health professionals should engage in these media, and also how personal, institutional, and professional barriers to greater use of social media may be overcome.

Successful management of an unusual hypopigmented scar after surgical repair of a unilateral Tessier 7 cleft.

Tessier No. 7 cleft is the most common atypical craniofacial cleft with an incidence of 1:3000-5642 births. This clinical report describes the successful management of a delayed, unusually hypopigmented postoperative facial scar following the surgical closure of a Tessier 7 cleft using the Pfeiffer wave line incision. In the absence of any other associated systemic lesions, the scar was treated as a localized leucoderma. The scar coloration improved dramatically with the chosen line of conservative medical treatment, and a surgical revision was not required. This report highlights the need for continuous follow up despite seemingly good short-term results. The medical management of the hypopigmented scar will aid fellow practitioners who may face similar dilemmas.

Cumulative Violence and PTSD Symptom Severity Among Urban Street-Based Female Sex Workers.

Female sex workers (FSW) are a marginalized and vulnerable population at high risk of gender-based violence within and outside of their occupation. However, FSW remain underrepresented in the trauma and mental health literature. The aims of this study were to (a) characterize exposure to violence among street-based FSW, including violence type, patterns over the life course, and key perpetrator groups, and (b) examine the multivariate associations between posttraumatic stress disorder (PTSD) symptom severity and two constructs (revictimization across life stages and cumulative violence). Data were drawn from the Sex Workers and Police Promoting Health in Risky Environments (SAPPHIRE) study, an observational community-based cohort of street-based FSW recruited through targeted sampling across Baltimore, Maryland (USA) in 2016 to 2017. PTSD symptom severity was measured using the PTSD Checklist for Diagnostic and Statistical Manual of Mental Disorders-Fifth Edition (PCL-5). At baseline, 61% of FSW screened positive for PTSD symptoms. The mean PCL-5 score was 38.6. We documented extensive histories of sexual and physical violence (lifetime: 81.8%; childhood and adult revictimization: 15.0% for sexual and 37.7% for physical). The vast majority of perpetrators were male and included paying clients, police officers, family members, and intimate partners. Exposure to childhood and adult sexual violence were independently associated with higher PTSD severity (p < .05), with marginal associations observed for physical violence. Data supported a cumulative violence model of PTSD severity (p < .05). Binge drinking also appeared to be a contributing factor (p < .05). The levels of PTSD observed among our sample were comparable with that reported among treatment-seeking war veterans. Our findings underscore the urgent need for tailored trauma-informed interventions and policies to address violence among urban street-based FSW, a population experiencing extremely high levels of violence, PTSD, and substance use.

Exploring the role of epidermal growth factor receptor variant III in meningeal tumors.

Meningioma is the second most common type of intracranial brain tumor. Immunohistochemical techniques have shown prodigious results in the role of epidermal growth factor receptor variant III (EGFR vIII) in glioma and other cancers. However, the role of EGFR vIII in meningioma is still in question. This study attempt the confer searches for the position attained by EGFR vIII in progression and expression of meningioma. Immunohistochemistry technique showed that EGFR vIII is highly expressed in benign tumors as compared to the atypical meningioma with a highly significant p-value (p<0.05). Further analysis by flow cytometry results supported these findings thus presented high intensity of EGFR vIII in low grades of meningioma. The study revealed that the significant Ki 67 values, to predictor marker for survival and prognosis of the patients. Higher expression of EGFR vIII in low grades meningiomas as compared to high-grade tumors indicate towards its oncogenic properties. To our knowledge, limited studies reported in literature expressing the EGFR vIII in meningioma tumors. Hence, Opinions regarding the role that EGFR vIII in tumorigenesis and tumor progression are clearly conflicting and, therefore, it is crucial not only to find out its mechanism of action, but also to definitely identify its role in meningioma.

Extending access to care across the rural US south: Preliminary results from the Alabama eHealth programme.

PURPOSE: Using a mixed-methods formative evaluation, the purpose of this study was to provide a broad overview of the Alabama eHealth programme set-up and initial patient outcomes. The Alabama eHealth programme uses telemedicine to provide medical care to people living with HIV in rural Alabama. It was led by a community-based organisation, Medical Advocacy and Outreach (MAO), and supported by AIDS United and the Corporation for National Community Service's Social Innovation Fund with matching support from non-federal donors. METHODS: We conducted and transcribed in-depth interviews with Alabama eHealth staff and then performed directed content analysis. We also tracked patients' ( n = 240) appointment attendance, CD4 counts, and viral loads. FINDINGS: Staff described the steps taken to establish the programme, associated challenges (e.g., costly, inadequate broadband in rural areas), and technology enabling this programme (electronic medical records, telemedicine equipment). Of all enrolled patients, 76% were retained in care, 88% had antiretroviral therapy and 75% had a suppressed viral load. Among patients without missing data, 96% were retained in care, 97% used antiretroviral therapy and 93% had suppressed viral loads. There were no statistically significant demographic differences between those with and without missing data. CONCLUSIONS: Patients enrolled in a telemedicine programme evaluation successfully moved through the HIV continuum of care.

Post-Traumatic Stress Disorder, Neighborhood Residency and Satisfaction, and Social Network Characteristics among Underserved Women in Baltimore, Maryland.

BACKGROUND: Post-traumatic stress disorder (PTSD) prevalence is high, but not well-understood, among women living in urban, impoverished areas. Although previous studies have established social support as an important factor in PTSD development and maintenance, little is known about how perceptions of neighborhood are linked to PTSD. This study examined the relationship between PTSD and social network and neighborhood factors among women with a low socioeconomic status. METHODS: We analyzed cross-sectional data collected from a human immunodeficiency virus/sexually transmitted infection peer network study in Baltimore, Maryland (n = 438). We used bivariate analyses to examine the associations between PTSD and social network characteristics and time in neighborhood and satisfaction. We then constructed multivariable regression models that controlled for the following with PTSD: homelessness, cocaine/heroin use, and unemployment. MAIN FINDINGS: Overall, 30% of women had PTSD symptom severity consistent with a clinical diagnosis. In the multivariable model, dissatisfaction with neighborhood block (odds ratio [OR], 1.80; p = .03) and living in one's neighborhood for more than 5 years (OR, 1.69; p = .03) were associated with PTSD. Social network factors that were significantly associated with PTSD included a higher number of network members in conflict with the participant (OR, 1.28; p = .02), presence of a network member who would let the participant stay with them (OR, 0.4; p = .004), and the number of network members with whom the participant socialized (OR, 0.6; p = .04). CONCLUSIONS: In this sample of impoverished urban women with a high prevalence of PTSD, duration of residency, satisfaction with neighborhood, and network characteristics were found to be strongly associated with PTSD symptom severity.

Barriers and Facilitators to the Implementation of a National HIV Linkage, Re-Engagement, and Retention in Care Program.

The 2020 National HIV AIDS Strategy (NHAS) sets a target of 90% of diagnosed people living with HIV (PLWH) retained in HIV care. Access to Care (A2C) was a national HIV linkage, re-engagement, and retention in care program funded by AIDS United with support from the Corporation for National and Community Service that aimed to link and retain the most vulnerable PLWH into high-quality HIV care. This study explores the barriers and facilitators of implementing the A2C program from the perspective of program staff. Ninety-eight qualitative interviews were conducted with staff at implementing organizations over the 5 years of the project. Barriers included challenges with recruiting and retaining participants, staffing and administration, harmonizing partnerships, and addressing the basic and psychosocial needs of participants. Facilitators included strong relationships with partner organizations, flexible program models, and the passion and dedication of staff. Findings will inform the development of future programs and policy.

Phaco-nucleotomy techniques in management of pseudoexfoliation syndrome.

INTRODUCTION: Pseudoexfoliation syndrome is a common clinically important systemic condition characterized by the pathological production and accumulation of an abnormal fibrillar extracellular material in many intraocular and extra ocular tissues. Many studies have shown that pseudoexfoliation syndrome patients have higher rates of intraoperative complications during cataract surgery compared to the patients without it. OBJECTIVES: To compare Phaco-chop and Divide and Conquer techniques of phacoemulsification, in the management of pseudoexfoliation syndrome in terms of intraoperative complications. MATERIALS AND METHODS: It is a hospital based prospective study of 90 patients with cataract and pseudoexfoliation syndrome attending ophthalmology outpatient department in our hospital. RESULTS: The mean age of patients in the study was 61.7 years with equal number of unilateral and bilateral cases. Intra operative complications noted in vertical chopping technique was only pupil constriction in 6.7%, no other complications were seen in this technique, whereas in horizontal chopping, 13.3% had pupil constriction, 6.7% had difficulty in chopping, 3.3% had zonular dehiscence and 3.3% had posterior capsular rent . In divide and conquer technique 16.7% had pupil constriction, 10% had difficulty in trenching, 3.3% had posterior capsular rent. Almost all the patients (97.8%) were implanted with intraocular lens after employment of various surgical modifications. CONCLUSION: Vertical chopping techniques scores over horizontal chopping and divide and conquer technique of phacoemulsification with good surgical outcome because of less complications.