A Bayesian phylogenetic hidden Markov model for B cell receptor sequence analysis.

The human body generates a diverse set of high affinity antibodies, the soluble form of B cell receptors (BCRs), that bind to and neutralize invading pathogens. The natural development of BCRs must be understood in order to design vaccines for highly mutable pathogens such as influenza and HIV. BCR diversity is induced by naturally occurring combinatorial "V(D)J" rearrangement, mutation, and selection processes. Most current methods for BCR sequence analysis focus on separately modeling the above processes. Statistical phylogenetic methods are often used to model the mutational dynamics of BCR sequence data, but these techniques do not consider all the complexities associated with B cell diversification such as the V(D)J rearrangement process. In particular, standard phylogenetic approaches assume the DNA bases of the progenitor (or "naive") sequence arise independently and according to the same distribution, ignoring the complexities of V(D)J rearrangement. In this paper, we introduce a novel approach to Bayesian phylogenetic inference for BCR sequences that is based on a phylogenetic hidden Markov model (phylo-HMM). This technique not only integrates a naive rearrangement model with a phylogenetic model for BCR sequence evolution but also naturally accounts for uncertainty in all unobserved variables, including the phylogenetic tree, via posterior distribution sampling.

AIRR Community Standardized Representations for Annotated Immune Repertoires.

Increased interest in the immune system's involvement in pathophysiological phenomena coupled with decreased DNA sequencing costs have led to an explosion of antibody and T cell receptor sequencing data collectively termed "adaptive immune receptor repertoire sequencing" (AIRR-seq or Rep-Seq). The AIRR Community has been actively working to standardize protocols, metadata, formats, APIs, and other guidelines to promote open and reproducible studies of the immune repertoire. In this paper, we describe the work of the AIRR Community's Data Representation Working Group to develop standardized data representations for storing and sharing annotated antibody and T cell receptor data. Our file format emphasizes ease-of-use, accessibility, scalability to large data sets, and a commitment to open and transparent science. It is composed of a tab-delimited format with a specific schema. Several popular repertoire analysis tools and data repositories already utilize this AIRR-seq data format. We hope that others will follow suit in the interest of promoting interoperable standards.

Costs and savings of parenting interventions: results of a systematic review.

BACKGROUND: This systematic review of economic evaluations of universal preventative or targeted treatment parenting interventions that aim to enhance parent-infant interaction is primarily intended to inform decision makers who have to make difficult spending decisions, especially at a time of reduced spending allocations. A synthesis of available costs and savings about parenting interventions that set out to enhance parent-infant interaction is presented. This topic is important specifically in view of the UK Governments' emphasis on the equalities agenda and the early years. The benefits of positive early life experiences, which include good parent-infant interaction, are far reaching and may be positively correlated with improved educational, health and well-being outcomes and reduced criminality. METHODS: A literature search was undertaken using on-line indexing databases between 2004 and 2014 that included the search terms 'parent', 'infant', 'interaction', 'cost benefit analysis' and their synonyms. RESULTS: Despite existing economic studies generally focusing upon targeted short-run outcomes, significant savings were observed in the included studies. Parenting interventions could save the health service around £2.5k per family over 25 years and could save the criminal justice system over £145k per person over the life course. In light of the escalating costs of remedial services, these potential savings may provide the UK and other governments with a robust incentive to invest in early years parenting interventions. CONCLUSIONS: Parenting interventions can be economically efficient and return savings on investment. Moreover, and one might argue as a moral imperative of democratic societies, population health can be improved and health inequalities reduced. An important debate is needed about early years policy, to include acknowledgement of the differences between UK and international healthcare systems and the potential savings from the synergistic and spin-off effects of early years interventions to inform decision-making to fund and implement appropriate action.

Global health training among U.S. residency specialties: a systematic literature review.

BACKGROUND: Interest in global health training during residency is increasing. Global health knowledge is also becoming essential for health-care delivery today. Many U.S. residency programs have been incorporating global health training opportunities for their residents. We performed a systematic literature review to evaluate global health training opportunities and challenges among U.S. residency specialties. METHODS: We searched PubMed from its earliest dates until October 2015. Articles included were survey results of U.S. program directors on global health training opportunities, and web-based searches of U.S. residency program websites on global health training opportunities. Data extracted included percentage of residency programs offering global health training within a specialty and challenges encountered. RESULTS: Studies were found for twelve U.S. residency specialties. Of the survey based studies, the specialties with the highest percentage of their residency programs offering global health training were preventive medicine (83%), emergency medicine (74%), and surgery (71%); and the lowest were orthopaedic surgery (26%), obstetrics and gynecology (28%), and plastic surgery (41%). Of the web-based studies, the specialties with the highest percentage of their residency programs offering global health training were emergency medicine (41%), pediatrics (33%), and family medicine (22%); and the lowest were psychiatry (9%), obstetrics and gynecology (17%), and surgery (18%). The most common challenges were lack of funding, lack of international partnerships, lack of supervision, and scheduling. CONCLUSION: Among U.S. residency specialties, there are wide disparities for global health training. In general, there are few opportunities in psychiatry and surgical residency specialties, and greater opportunities among medical residency specialties. Further emphasis should be made to scale-up opportunities for psychiatry and surgical residency specialties.

A Bayesian Multinomial Probit MODEL FOR THE ANALYSIS OF PANEL CHOICE DATA.

A new Bayesian multinomial probit model is proposed for the analysis of panel choice data. Using a parameter expansion technique, we are able to devise a Markov Chain Monte Carlo algorithm to compute our Bayesian estimates efficiently. We also show that the proposed procedure enables the estimation of individual level coefficients for the single-period multinomial probit model even when the available prior information is vague. We apply our new procedure to consumer purchase data and reanalyze a well-known scanner panel dataset that reveals new substantive insights. In addition, we delineate a number of advantageous features of our proposed procedure over several benchmark models. Finally, through a simulation analysis employing a fractional factorial design, we demonstrate that the results from our proposed model are quite robust with respect to differing factors across various conditions.

Does delay to theatre for medical reasons affect the peri-operative mortality in patients with a fracture of the hip?

We have investigated how medical postponement, the time to surgery and the correction of medical abnormalities, according to McLaughlin criteria, before operation affected peri-operative mortality after fracture of the hip. From February to December 2007, in addition to core data, the Scottish Hip Fracture Audit collected information relating to surgical delay. Data were available for 4284 patients which allowed 30-day survival analysis to be performed. Multivariable logistic regression models were used to control for differences in case-mix. Patients with major clinical abnormalities were more likely to have a postponement and had a lower unadjusted 30-day survival. The time to operation and postponement were not associated with higher mortality after adjustment for case-mix. Correction of major clinical abnormalities before surgery improved the adjusted survival, but this improvement was not significant (p = 0.10). Postponement without correction of a medical abnormality before surgery was associated with a significantly lower (p = 0.006) 30-day adjusted survival. The possible benefits of postponement need to be weighed against prolonged discomfort for the patient and the possibility of the development of other complications.

Changes in population demographics and the future incidence of hip fracture.

BACKGROUND: During the first three decades of the 21st century the combination of increasing life expectancy and falling birth rates will result in substantial demographic changes within the population of the United Kingdom. A large increase in the elderly population is likely to have significant effects on the number of patients who sustain a hip fracture. AIM: To predict future changes in hip fracture burden in Scotland. MATERIALS AND METHODS: Data was obtained from the Scottish Hip Fracture Audit database for a 12 month period between April 2004 and March 2005. All orthopaedic units in Scotland participated in the audit during this period. This data was used to calculate the incidence of hip fracture by 5 year age/gender cohorts. Outcome data was analysed in a similar manner. Population prediction data obtained from the Registrar General's Office was then used to predict hip fracture numbers for the year 2031. Two separate prediction models were used. The first model assumed that the age/gender specific incidence of hip fracture observed in 2004 would remain constant. Between 1999 and 2004, a 9.6% decrease in the population incidence of hip fracture was observed. Therefore a second prediction model was used which assumed a continuation in the fall in population incidence of hip fracture between 2004 and 2031. RESULTS: The population aged 50 years and above is predicted to increase 28% by 2031, with the most significant increases occurring in the over 1980s. The number of hip fractures is predicted to rise by 45% to 75% (from 6164 to 8829-10756 cases per annum) requiring an additional 287-474 hospital beds. By 2031 approximately 45% of fractures will occur in those aged 85 years and above, compared to 34% in 2004. Predicted changes in population demographics are highly variable by region and so local planning of resource provision will be essential. CONCLUSION: Changes in population demographics will have significant implications for health care provision for the care of hip fracture patients. An increase in the capacity of acute orthopaedic care and a review of care models will be required to ensure adequate resource provision.

Outcome after surgery for the treatment of hip fracture in the extremely elderly.

BACKGROUND: As a consequence of changes in population demographics, the extremely elderly represent one of the fastest growing groups in Western society. Previous studies have associated advanced age with increased mortality after hip fracture; however, this finding has not been consistent. METHODS: The Scottish Hip Fracture Audit is a prospective, national, multicenter study that collects data on patients over the age of fifty years who are admitted to the hospital with a hip fracture. For the present study, we used data collected from twenty-two acute-care orthopaedic units between January 1998 and December 2005. The extremely elderly cohort consisted of 919 individuals with an age of ninety-five years or more. Case-mix variables and outcomes were compared with those for a modal control group of 15,461 individuals who were seventy-five to eighty-nine years of age. Outcome measures included thirty and 120-day mortality rates, the length of the hospital stay, the place of residence, and mobility. A multivariable logistic regression model was used to compare outcomes between groups while controlling for significant case-mix variables. RESULTS: The extremely elderly presented with poorer indicators of health status as demonstrated by higher American Society of Anesthesiologists scores. In addition, this group was less likely to be independently mobile and more likely to be in institutional care at the time of the fracture (p < 0.001). Mortality at thirty and 120 days was higher in the extremely elderly even after adjusting for case-mix variables. The extremely elderly also were less likely to return home or to return to previous levels of mobility. CONCLUSIONS: Although the extremely elderly exhibited a higher prevalence of prefracture indicators of poor outcome, statistical control for these case-mix variables showed further age-related deterioration in survival and outcomes after surgery for the treatment of a hip fracture.

Epidemiology and outcome after hip fracture in the under 65s-evidence from the Scottish Hip Fracture Audit.

AIM: To report the epidemiology and outcomes after hip fractures in the patients under 65 years of age. PATIENTS AND METHODS: We performed a prospective, multi-centre observational study using the Scottish Hip Fracture Audit Database. Case-mix, process and outcome data was collected by dedicated coordinators on site at the time of admission, at 120 days after the injury and on any re-operations within 12 months. The study cohort consisted of 1896 individuals aged 50-64 years. Patient variables and outcomes were compared to a control group of 15,461 individuals aged 75-89 years of age. The control group consisted of three modal 5-year age groups centred about a median age of 83 years, equal to the database value, excluding the effects of the extreme elderly who may act as confounders. Outcomes measures included 30- and 120-day mortality, length of hospital stay, place of residence and ambulatory status. A multivariate logistic regression model was used to compare outcome between groups while controlling for significant case-mix variables. RESULTS: Patients in the study cohort presented with lower ASA scores and were more likely to be independently mobile and live in their own home at the time of fracture (p<0.001). Pathological fractures were more common in younger patients and accounted for more than 1 in 20 fractures. Mortality at 30 and 120 days was significantly lower (p<0.0001) in the study cohort, however it was increased compared to age and gender adjusted mortality rates for the general population (p<0.001) Younger patients were more likely to recover independent mobility and living. CONCLUSION: Patients aged 50-64 years have significantly better outcome measures after surgery for hip fracture in terms of survival and function. Such differences exist even after controlling for differences in patient case-mix variables.

Gender differences in epidemiology and outcome after hip fracture: evidence from the Scottish Hip Fracture Audit.

We report gender differences in the epidemiology and outcome after hip fracture from the Scottish Hip Fracture Audit, with data on admission and at 120 days follow-up from 22 orthopaedic units across the country between 1998 and 2005. Outcome measures included early mortality, length of hospital stay, 120-day residence and mobility. A multivariate logistic regression model compared outcomes between genders. The study comprised 25 649 patients of whom 5674 (22%) were men and 19 975 (78%) were women. The men were in poorer pre-operative health, despite being younger at presentation (mean 77 years (60 to 101) vs 81 years (50 to 106)). Pre-fracture residence and mobility were similar between genders. Multivariate analysis indicated that the men were less likely to return to their home or mobilise independently at the 120-day follow-up. Mortality at 30 and 120 days was higher for men, even after differences in case-mix variables between genders were considered.

An oral health education programme based on the National Curriculum.

AIM: The aim of this study was to develop and evaluate a teaching programme based on the national curriculum for use in a primary school setting. DESIGN: National Curriculum guidelines were combined with oral health education messages to draw up lesson plans for teachers to deliver. A questionnaire was used to demonstrate children's oral health knowledge prior to the teaching programme, and at 1 and 7 weeks following the programme. The study took place in inner-city, state-run primary schools in Manchester and North London, UK. The subjects were children between the ages of 7 and 8 years from Manchester (n = 58) and North London (n = 30). The main outcome measure was change in knowledge attributable to a newly developed teaching programme. RESULTS: The children in Manchester had a higher level of knowledge prior to the teaching programme. Following the teaching programme, children in both schools showed a significant improvement in dental health knowledge (P < 0.001). Seven weeks later, the Manchester children showed no significant loss of knowledge (P < 0.001). CONCLUSIONS: The aims of the National Curriculum were easily integrated with oral health messages. A more widely available teaching resource, such as the one described in this study, would be useful to encourage the teaching profession to take on oral health education without more costly input from dental professionals.

Infants exposed to MRI in utero have a normal paediatric assessment at 9 months of age.

Any differences in detailed paediatric assessment at 9 months of age in infants exposed to echo planar MRI in utero from 20 weeks gestation to term were investigated by performing a case controlled prospective observational study of 20 infants. They had all had serial echo planar MRI in the antenatal period and were compared with a control group born at the same time who had not. Statistical analysis employed likelihood ratios, odds ratios and 95% confidence intervals. The mothers of the control infants had a significantly higher standard of educational attainment (p = 0.005). A small but significant decrease in length (p = 0.047), and an increase in gross motor function (p = 0.023) of the fetuses exposed to echo planar imaging were demonstrated. No other significant developmental or social differences were seen between the two groups. Infants at 9 months of age did not demonstrate any gross abnormality likely to be related to exposure to echo planar MRI in utero.

The financial abuse of mentally incompetent older adults: a canadian study.

ABSTRACT This article reports the results of a pilot study on the financial abuse of mentally incompetent seniors. The objectives of the study were to: (1) establish the incidence of suspected financial abuse among the clientele of the Office of Public Trustee, Province of Manitoba, (2) identify the characteristics of mentally incompetent older adults most at risk, and (3) identify indicators of financial abuse. Approximately 20% of the cases opened in a one year period were under suspicion of abuse. Findings were consistent with those of other research projects on elder abuse, in general, showing an over-representation of women over the age of eighty as victims of financial abuse. Unpaid personal care home bills when money should have been available was the most common indicator. In addition to providing a list of indicators of financial abuse that are of potential use to professionals, devising prevention programs, practical implications for service providers are presented.

Assessment of fetal lung growth in utero with echo-planar MR imaging.

PURPOSE: To measure changes in normal fetal lung volume with increasing gestation by using echo-planar magnetic resonance (MR) imaging. MATERIALS AND METHODS: Fifty-six singleton fetuses were examined longitudinally with respect to lung volume by using echo-planar MR imaging between 19 weeks gestation and term. RESULTS: Lung volume increased exponentially with gestation from 8 to 125 mL. Volume was related to gestation by using the equation, volume = 0.8375e0.1249g (R2 = 0.77), where g = gestation. Lung volume had a direct relationship to fetal volume with increasing gestation (R2 = 0.75). There was no significant relationship between amniotic fluid volume and lung volume (R2 = 0.11). CONCLUSION: Variation in lung volumes can be assessed by using echo-planar MR imaging, regardless of variations in amniotic fluid volume. These measurements are less than those obtained from postmortem and neonatal studies but are similar to those obtained by using three-dimensional ultrasonography. Lung volume estimations obtained by using echo-planar imaging may have important clinical and research applications when noninvassive assessment of lung volume is required.

Creating clinical opportunities in a managed care environment.

The Continuum of Care clinical experience was developed to provide future nurses with practice in a managed care environment. Students see how the critical care patient's needs change during the recovery process and assist the patient with the transition to self-care at home. Patient and student evaluations indicate the experience increases students' understanding of the role of the nurse in managed care while facilitating patients' transition to the self-care environment.

The provision of enabling services to higher-risk pregnant women and children in Medicaid managed care.

As managed care organizations become the major payer model for the higher-need, higher-risk population of Aid to Families with Dependent Children women and children, they would benefit from looking at lessons learned during the past decade as policy makers and providers struggled to identify less costly, but effective strategies to reduce morbidity and mortality associated with poor birth outcomes. This article discusses the experience of one community in providing enabling services, the opportunity for new partnerships, measuring the outcomes, and the financing of enabling services in a managed care model.

Preoperative assessment of the elderly patient.

Preoperative assessment of the elderly patient for surgery is vital to the success of the surgical procedure. A thorough evaluation must first begin with an understanding of the physiologic and pathophysiologic changes unique to the elderly patient and the aging skin. A complete preoperative assessment entails assessing the patient and dermatologic problem, preparing the patient and caregivers for the surgery and its expected outcomes, and highlighting issues and problems that need to be managed prior to the procedure. With the continued growth of the geriatric population, all dermatologic surgeons should be aware of the special issues related to their geriatric patients. With heightened awareness of and screening for potential pitfalls in the elderly surgical patient, adverse outcomes can be avoided.

CHINs in the context of an evolving health care system.

Community Health Information Network (CHIN) developments have slowed, due to the chaotic change in the health care system and stakeholders' attendant short-sighted focus. CHINs are a long-term investment that is necessary for the health care system's evolution to maturity. Several arenas of essential CHIN activity are given that would be characteristic of a mature, goal-directed health care system Lack of enterprise-wide computer-based patient record systems is a major barrier. Even in the short term, however, trends and incentives exist that are likely to push stakeholders toward CHIN development. Some of these trends include changes in organizational structure and political pressures. Practical incentives include the need for stakeholder cooperation to achieve healthy communities, the prospects for telemedicine, and the demand for greater quality assurance.

Evolving community health information networks.

A community health information network (CHIN) provides technology-based information services to help maintain optimal health for all the residents of a community. Defining features of a CHIN are that its services are available to all stakeholders and that competitors collaborate to share information. The initial impetus for a CHIN is usually to facilitate paying for health care or to share clinical records. Complex legal, organizational, funding, and control issues confront CHIN initiators, and reliable models do not exist today. During development, issues of program focus and technology selection arise, followed by concerns about information privacy and the CHIN's role in quality of care. Once basic capabilities are implemented, a mature CHIN can offer extensive cost-recovering health-related services to providers, related agencies, and consumers. Developments are underway that eventually will allow a CHIN to support a fully integrated longitudinal health record. A national network of mature CHINs would offer health care professionals further collaborative possibilities that could change the shape of future health care.