Efficient dynamic variation graphs.

MOTIVATION: Pangenomics is a growing field within computational genomics. Many pangenomic analyses use bidirected sequence graphs as their core data model. However, implementing and correctly using this data model can be difficult, and the scale of pangenomic datasets can be challenging to work at. These challenges have impeded progress in this field. RESULTS: Here, we present a stack of two C++ libraries, libbdsg and libhandlegraph, which use a simple, field-proven interface, designed to expose elementary features of these graphs while preventing common graph manipulation mistakes. The libraries also provide a Python binding. Using a diverse collection of pangenome graphs, we demonstrate that these tools allow for efficient construction and manipulation of large genome graphs with dense variation. For instance, the speed and memory usage are up to an order of magnitude better than the prior graph implementation in the VG toolkit, which has now transitioned to using libbdsg's implementations. AVAILABILITY AND IMPLEMENTATION: libhandlegraph and libbdsg are available under an MIT License from https://github.com/vgteam/libhandlegraph and https://github.com/vgteam/libbdsg.

Cystic Adventitial Disease of the Common Femoral Vein Successfully Treated with Resection, Synthetic Graft Reconstruction, and Fistula Creation.

Cystic adventitial disease (CAD) is a rare, benign disease of blood vessels which most commonly affects the popliteal artery. Less than 50 cases of CAD affecting veins have ever been described in the literature to date. We report the case of a 56-year-old woman who presented with unilateral lower extremity swelling and varicosities due to CAD of her common femoral vein. Resection and reconstruction with a venous interposition graft, employing a polytetrafluoroethylene graft and arteriovenous fistula in order to maintain venous bypass patency, were performed successfully. The patient recovered well without any evidence of recurrence or postoperative complications.

An online review of plastic surgeons in southern California.

BACKGROUND: It has become commonplace for patients to access online reviews of physicians when making choices about health care, just as any consumer would in today's computer-dependent world. Previous studies have shown that online reviews of physicians are generally positive. However, 1 negative review has the potential to adversely affect business and reputations. OBJECTIVES: To characterize the online presence of plastic surgeons in Southern California as portrayed by physician rating websites (PRWs). METHODS: An extensive online database of board-certified plastic surgeons was used to generate a list of surgeons within a 50-mile radius of Pomona, CA. Ratings from the PRWs HealthGrades.com, Vitals.com, and UCompareHealthcare.com were cataloged by number of reviews and ratings. RESULTS: Two hundred sixty-three surgeons were evaluated with the most-represented cities being Beverly Hills (N=47), Los Angeles (N=31), and Newport Beach (N=27). Ninety-seven percent of the surgeons were rated on at least 1 of the 3 PRWs chosen. In general, surgeons were rated highly, with a mean rating of 85%, SD, 14% (P<0.01), with a mean of 11.0 ratings per PRW, SD 10.9 (P<0.01). Total online ratings ranged from 0 to 222 per surgeon. The median number of total reviews was 25 and the mean rating for those surgeons above and below the median were equivocal, at 86% and 85%, respectively (P=0.284). CONCLUSIONS: In this study, we found that plastic surgeons in Southern California have an online presence that can be influenced by their patients; they should be aware of this and conscious of their online reputations. Overall, the ratings were high, regardless of the number of reviews.

Unification of Efforts to Improve Global Access to Cancer Therapeutics: Report From the 2022/2023 Access to Essential Cancer Medicines Stakeholder Summit.

PURPOSE: There is an urgent need to improve access to cancer therapy globally. Several independent initiatives have been undertaken to improve access to cancer medicines, and additional new initiatives are in development. Improved sharing of experiences and increased collaboration are needed to achieve substantial improvements in global access to essential oncology medicines. METHODS: The inaugural Access to Essential Cancer Medicines Stakeholder Meeting was organized by ASCO and convened at the June 2022 ASCO Annual Meeting in Chicago, IL, with two subsequent meetings, Union for International Cancer Control World Cancer Congress held in Geneva, Switzerland, in October 2022 and at the ASCO Annual Meeting in June of 2023. Invited stakeholders included representatives from cancer institutes, physicians, researchers, professional societies, the pharmaceutical industry, patient advocacy organizations, funders, cancer organizations and foundations, policy makers, and regulatory bodies. The session was moderated by ASCO. Past efforts and current and upcoming initiatives were initially discussed (2022), updates on progress were provided (2023), and broad agreement on resulting action steps was achieved with participants. RESULTS: Summit participants recognized that while much work was ongoing to enhance access to cancer therapeutics globally, communication and synergy across projects and organizations could be enhanced by providing a platform for collaboration and shared expertise. CONCLUSION: The summit resulted in new cross-stakeholder insights and planned collaboration addressing barriers to accessing cancer medications. Specific actions and timelines for implementation and reporting were established.

Accuracy and Glycemic Efficacy of Continuous Glucose Monitors in Critically Ill COVID-19 Patients: A Retrospective Study.

BACKGROUND: Continuous glucose monitoring (CGM) is approved for insulin dosing decisions in the ambulatory setting, but not currently for inpatients. CGM has the capacity to reduce patient-provider contact in inpatients with coronavirus disease 2019 (COVID-19), thus potentially reducing in hospital virus transmission. However, there are sparse data on the accuracy and efficacy of CGM to titrate insulin doses in inpatients. METHODS: Under an emergency use protocol, CGM (Dexcom G6) was used alongside standard point-of-care (POC) glucose measurements in patients critically ill from complications of COVID-19 requiring intravenous (IV) insulin. Glycemic control during IV insulin therapy was retrospectively assessed comparing periods with and without adjunctive CGM use. Accuracy metrics were computed and Clarke Error Grid analysis performed comparing CGM glucose values with POC measurements. RESULTS: Twenty-four critically ill patients who met criteria for emergency use of CGM resulted in 47 333 CGM and 5677 POC glucose values. During IV insulin therapy, individuals' glycemic control improved when CGM was used (mean difference -30.7 mg/dL). Among 2194 matched CGM: POC glucose pairs, a high degree of concordance was observed with a mean absolute relative difference of 14.8% and 99.5% of CGM: POC pairs falling in Zones A and B of the Clarke Error Grid. CONCLUSIONS: Continuous glucose monitoring use in critically ill COVID-19 patients improved glycemic control during IV insulin therapy. Continuous glucose monitoring glucose data were highly concordant with POC glucose during IV insulin therapy in critically ill patients suggesting that CGM could substitute for POC measurements in inpatients thus reducing patient-provider contact and mitigating infection transmission.

Assessment of barriers to optimal cancer control in adult cancer treatment centres in Cameroon.

Approximately 20,745 new cases of cancer were registered annually with 13,199 (64%) deaths in 2020 in Cameroon. Despite the increasing cancer burden, there is a paucity of reliable data that can enhance decision-making for cancer control in Cameroon. This assessment was, therefore, designed to generate data that may enable stakeholders, policymakers and funders to make data-driven decisions on cancer control. We conducted a cross-sectional survey in July 2020, which enabled us to collect data on key cancer variables from six adult cancer treatment centres in Cameroon. The key components of the assessment included case detection, service availability, human resource capacity, cost of chemotherapy and radiotherapy, the safety of chemotherapy sessions, data systems, patient education, palliative care, funding for chemotherapy and chemotherapy stock. Data were compiled and analysed using Microsoft Excel 2016. Data from four of the 6 sites show that 1,636 new cases were recorded representing an annual case detection rate of 11.8%. All the six assessed facilities offered chemotherapy services, 5/6 (83.3%) offered surgery for cancers, while just 1 (16.7%) offered radiotherapy services. In addition, none offered nuclear medicine services for cancer care and treatment. Similarly, none of the facilities had the WHO-recommended number of human resources for optimal cancer care. Overall, there were only 6 medical oncologists, 2 surgical oncologists, 3 radiation oncologists and 14 oncology nurses providing services across the 6 cancer treatment centres. Treatment services are expensive for an average national, with a complete course of chemotherapy followed by radiotherapy costing ~XAF 1,240,000 (~$2,480). None of the survey facilities had a recommended safe biosafety cabinet and clean room for the preparation of chemotherapies, rendering the preparation of chemotherapies suboptimal and hazardous. Data collection tools were manual, relatively available and very different across all the surveyed sites and the interval for data collection and transmission was collectively undefined. Optimal cancer care in adult cancer treatment centres is limited by several health systems and socio-economic factors. The identification of these barriers has enabled the formulation of action-oriented interventions, leveraging on the recently adopted national strategy for the prevention and control of cancers in the country.

Achieving the cancer moonshot in Africa.

For decades now, the United States (US) has been a leading contributor in global health with the government, academic institutions, foundations, non-profits and industry investing and partnering with African countries, as seen with the US President's Emergency Plan for AIDS Relief (PEPFAR) program. Now as more people survive HIV/AIDs and other infectious diseases in Africa and live longer, non-communicable diseases like cancer are on the rise, in what can be described as a growing health iceberg, hidden under epidemics of infectious diseases. There is now more urgent need for international collaborations on cancer, which has become a leading cause of death in both Africa and the US, underpinned by poignant disparities in access to care. The re-ignited Cancer Moonshot in the USA and publication of the Lancet Oncology Commission report for sub-Saharan Africa in 2022 provide a timely and valuable framework for growing US-Africa collaborations in the coming years towards attaining the goal of the cancer moonshot both in the US and Africa. This goal is to reduce cancer death rate by at least 50% over the next 25 years, and to improve the experience of those living with and surviving cancer. The US-Africa summit taking place in Washington in December 2022 provides a momentous opportunity to identify recommendations or priority areas, some of them included in this article, and initiating action for win-win collaborations towards achieving the cancer moonshot in Africa.

Willingness to use PrEP among female university students in Lesotho.

Oral pre-exposure prophylaxis (PrEP) for HIV-negative individuals at high risk was introduced in Lesotho in April 2016. To assess the feasibility and acceptability of PrEP in Lesotho and to study the attitudes and beliefs around HIV risk and prevention measures among young women, between September and December 2016 we asked 302 female university students at fourteen higher education institutions in Lesotho about their sexual behavior, experiences of sexual coercion and abuse, HIV risk perception, willingness to use PrEP, as well as their attitudes toward condom use and self-administration of daily medications. Overall, 57.3% of the sample reported perceiving themselves at risk of acquiring HIV and 32.1% reported being strongly willing to use PrEP if it were available in their community. In a multivariate mediation analysis, perceived HIV risk was associated with 11.5 percentage points increase in likelihood of using PrEP (p = 0.041). Multiple concurrent sexual partnership was associated with 16.1 percentage points increase in likelihood of self-perceived HIV risk (p = 0.007), while having sexual partners in polygamous relationships was associated with 17.8 percentage points increase in likelihood of self-perceived HIV risk (p = 0.002) and the mediated indirect effect accounted for 18.2% of its total effect. Those who reported strong adherence to antibiotics were 23.1 percentage points more likely to express willingness to use PrEP than those who did not (p = 0.004), and those who reported to dislike condoms were 19.1 percentage points more likely to be willing to use PrEP than those who did not report aversion to condom use: these effect were direct and not mediated by HIV risk perception. Intimate partner violence (IPV) in the network of peers was also directly associated with willingness to use PrEP and its effect was not significantly mediated by HIV risk perception: those who had friends who experienced intimate partner violence were 14.9 percentage points more likely to be willing to use PrEP than those who did not report IPV in their network of peers (p = 0.009). These findings support the inclusion of individuals with multiple concurrent sexual partners among the key populations for PrEP provision and confirm that willingness to use PrEP is not solely driven by HIV risk perception. They also indicate that the presence of IPV in peer networks is related to one's willingness to use PrEP. PrEP service provision may generate synergies with IPV prevention programs when offered within this framework.

Does the implementation of a pediatric appendicitis pathway promoting ultrasound work outside of a children's hospital?

BACKGROUND: Efficacy of care pathways for pediatric appendicitis is well established in children's hospitals, but not in community Emergency Departments (EDs). METHODS: A diagnostic pathway combining the Pediatric Appendicitis Score (PAS) with selective ultrasound was implemented. The charts of 2201 pediatric patients seen at four general EDs before and after implementation were retrospectively reviewed, identifying 611 children seriously considered for appendicitis. RESULTS: There were no cases of missed appendicitis within the pathway cohort (0/72). Low-PAS children on pathway had fewer computed tomography (CT) scans (0% vs. 21%; p < 0.02). Moderate-PAS patients also had a reduced CT-first rate (2.4% vs. 23%; p < 0.01). However, pathway adoption in 2016 was only 24%. Correct pathway application would have avoided 58 ultrasounds and 17 CTs over three months (annual savings $281,276). CONCLUSION: A pediatric appendicitis pathway is safe, rules out low suspicion patients without imaging, and is cost effective in a general hospital setting.

The composition of demand for newly launched vaccines: results from the pneumococcal and rotavirus vaccine introductions in Ethiopia and Malawi.

Understanding post-launch demand for new vaccines can help countries maximize the benefits of immunization programmes. In particular, low- and middle-income countries (LMICs) should ensure adequate resource planning with regards to stock consumption and service delivery for new vaccines, whereas global suppliers must produce enough vaccines to meet demand. If a country underestimates the number of children seeking vaccination, a stock-out of commodities will create missed opportunities for saving lives. We describe the post-launch demand for the first dose of pneumococcal conjugate vaccine (PCV1) in Ethiopia and Malawi and the first dose of rotavirus vaccine (Rota1) in Malawi, with focus on the new birth cohort and the 'backlog cohort', comprised of older children who are still eligible for vaccination at the time of launch. PCV1 and Rota1 uptake were compared with the demand for the first dose of pentavalent vaccine (Penta1), a routine immunization that targets the same age group and immunization schedule. In the first year, the total demand for PCV1 was 37% greater than that of Penta1 in Ethiopia and 59% greater in Malawi. In the first 6 months, the demand of Rota1 was only 5.9% greater than Penta1 demand in Malawi. Over the first three post-introduction months, 70.7% of PCV1 demand in Ethiopia and 71.5% of demand in Malawi came from children in the backlog cohort, whereas only 28.0% of Rota1 demand in Malawi was from the backlog cohort. The composition of demand was impacted by time elapsed since vaccine introduction and age restrictions. Evidence suggests that countries' plans should account for the impact of backlog demand, especially in the first 3 months post-introduction. LMICs should request for higher stock volumes when compared with routine needs, plan social mobilization activities to reach the backlog cohort and allocate human resources and cold chain capacity to accommodate high demand following vaccine introduction.

Mother-infant pair clinic and SMS messaging as innovative strategies for improving access to and retention in eMTCT care and Option B+ in Malawi: a cluster randomized control trial (the PRIME study).

UNAIDS has set a goal of achieving the elimination of mother-to-child transmission (eMTCT) of HIV by 2015 and keeping HIV-positive (HIV+) mothers alive. In pursuit of this goal, in 2011, the Malawi Ministry of Health (MoH) adopted the Option B+ strategy, which entails lifelong antiretroviral treatment for all HIV+ mothers, irrespective of severity of HIV infection. Poor mother-child pair retention is one of the major challenges against achieving this goal. To improve retention of mother-infant pairs in the eMTCT continuum of care, the Promoting Retention among Infants and Mothers Effectively (PRIME) study is evaluating the effectiveness of 3 models of health care delivery namely, mother-infant pair clinics, which deliver integrated HIV and non-HIV services, mother-infant pair clinics plus electronic text message (SMS) reminders for mother-infant pairs who miss scheduled eMTCT follow-up clinics, and current standard of care. The primary outcome is "the proportion of HIV+ mothers and/or HIV-exposed infants (HEI) retained in eMTCT care at 12 months postpartum and received recommended HIV and non-HIV services during preceding scheduled visits." This 3-arm cluster randomized intervention study is being implemented in 30 primary health facilities (10 facilities per arm) in Mangochi and Salima districts, Malawi. At each clinic, a total of 41 HIV+ mothers attending maternal and child health services are being recruited and followed up for 18 months postpartum. This article describes the study methodology and interventions, successes and challenges experienced during the first 12 months of study implementation and relevance of study results to Malawi and other countries adopting the Option B+ strategy.