Close encounters with DNA

Over the past ten years, the all-atom molecular dynamics method has grown in the scale of both systems and processes amenable to it and in its ability to make quantitative predictions about the behavior of experimental systems. The field of computational DNA research is no exception, witnessing a dramatic increase in the size of systems simulated with atomic resolution, the duration of individual simulations and the realism of the simulation outcomes. In this topical review, we describe the hallmark physical properties of DNA from the perspective of all-atom simulations. We demonstrate the amazing ability of such simulations to reveal the microscopic physical origins of experimentally observed phenomena. We also discuss the frustrating limitations associated with imperfections of present atomic force fields and inadequate sampling. The review is focused on the following four physical properties of DNA: effective electric charge, response to an external mechanical force, interaction with other DNA molecules and behavior in an external electric field.

Molecular analysis, pathogenic mechanisms, and readthrough therapy on a large cohort of Kabuki syndrome patients

Kabuki syndrome (KS) is a multiple congenital anomalies syndrome characterized by characteristic facial features and varying degrees of mental retardation, caused by mutations in KMT2D/MLL2 and KDM6A/UTX genes. In this study, we performed a mutational screening on 303 Kabuki patients by direct sequencing, MLPA, and quantitative PCR identifying 133 KMT2D, 62 never described before, and four KDM6A mutations, three of them are novel. We found that a number of KMT2D truncating mutations result in mRNA degradation through the nonsense-mediated mRNA decay, contributing to protein haploinsufficiency. Furthermore, we demonstrated that the reduction of KMT2D protein level in patients’ lymphoblastoid and skin fibroblast cell lines carrying KMT2D-truncating mutations affects the expression levels of known KMT2D target genes. Finally, we hypothesized that the KS patients may benefit from a readthrough therapy to restore physiological levels of KMT2D and KDM6A proteins. To assess this, we performed a proof-of-principle study on 14 KMT2D and two KDM6A nonsense mutations using specific compounds that mediate translational readthrough and thereby stimulate the re-expression of full-length functional proteins. Our experimental data showed that both KMT2D and KDM6A nonsense mutations displayed high levels of readthrough in response to gentamicin treatment, paving the way to further studies aimed at eventually treating some Kabuki patients with readthrough inducers.

Self-perceived unmet health care needs of persons enrolled in HIV care

We examined the prevalence of, and factors associated with unmet health service needs among persons with HIV disease. Data were examined from 1,851 participants in the U.S. AIDS Cost and Service Utilization Study, drawn from 26 medical care providers in 10 cities. Geographic areas with large numbers of AIDS cases, and health care providers within them were chosen as study sites. After completing a screener questionnaire, potential participants at each site were stratifed by illness stage, HIV exposure route, and insurance status; a systematic random sample within those strata were selected for the study. Participants completed a comprehensive survey of HIV-related service use and costs, which also asked them to identify unmet health service needs. Analyses identified the relationship between unmet needs and: stage of illness, type of insurance, source of care, living arrangement, and AIDS prevalence of respondents' geographic region. At least one unmet need was reported by 20% of the sample. Needs for non-institutional services, e.g, dental care, mental health, and medications were more likely to be unmet than need for emergency room and hospital care. While most factors significantly affected the odds of having an unmet need, the greatest effects were found for private insurance and HIV asymptomatic status, both of which decreased the odds of unmet needs by approximately 50%. These findings suggest that insurance coverage for services required during the chronic phase of HIV illness is inadequate and should be augmented.

The impact of housing status on health care utilization among persons with HIV disease

This study sought to identify the prevalence of unstable housing situations, and for whom they occurred, and to examine differences in health care utilization by housing status. Housing status and inpatient and outpatient health care utilization of 1,851 HIV-infected individuals was ascertained through interviews. Nine percent of respondents were in unstable housing situations. Unstable housing was associated with significantly lower functional status. The unstably housed were more likely to visit an emergency room (p < 0.05) and had fewer ambulatory visits than persons with stable housing (p < 0.03). They incurred nearly five more hospital days and their average hospitalization was approximately 1.5 days longer than the stably housed, although these differences were not significant. Utilization of ambulatory care is lower among unstably housed persons with HIV disease, which may have led to their increased reliance upon emergency rooms and hospitals. Helping HIV-infected individuals maintain adequate housing could reverse this pattern.

Results of the ACSUS for pediatric AIDS patients: utilization of services, functional status, and social severity

OBJECTIVE

This study describes demographic characteristics of pediatric AIDS patients, describes hospital and community-based service utilization patterns, and analyzes medical and social support service usage patterns with respect to patient demographic characteristics, clinical trial participation, functional/developmental status, and social environment.

DATA SOURCES AND STUDY SETTING

Data reported in this study are from the AIDS Costs and Service Utilization Survey (ACSUS) and cover the six-month period beginning March 1991 (N = 135). Pediatric patients who sought care for HIV-related problems were sampled at seven different hospitals in five metropolitan regions of the United States. All of the participating hospitals had clinics specifically serving pediatric patients infected with HIV. The sample consists of HIV-positive patients who had had at least one HIV-related symptom or condition.

STUDY DESIGN

A stratified probability sample design guided the sampling strategy, which included oversampling in two large hospitals from two of the five metropolitan areas. Survey data cover an 18-month time period of health care utilization, cost, and financing information from HIV-infected patients and their providers. Utilization measures are standardized to a six-month period. Per capita income, family structure, informal personal network, functional status, and clinical trial participation are tested for associations with patterns of utilization. In addition, a weighted ten-point social severity scale was developed to assess family/household stability.

DATA COLLECTION

Data were collected through a screener instrument completed by the person accompanying the child to a hospital clinic visit (usually a a parent), and through two interviews conducted in person with the patients' primary caregivers. Data from the questionnaires were coded and assembled into computerized SAS analysis files by WESTAT:

PRINCIPAL FINDINGS

Children in this sample are 62 percent African American, 25 percent Hispanic, and 10 percent White. Medicaid is the primary payer for 92 percent. Mean per capita income is $3,440. Fewer than one-half (41 percent) of the families of the children receive Aid to Families with Dependent Children (AFDC). (AFDC). Within the six-month period, approximately one-third of the sample (29.6 percent) was hospitalized. Mean length of stay was 16.0 days. Clinical trial participation was positively related to mean number of hospital clinic visits and receipt of formal (paid) home care. There were no differences in use of community clinic, mental health, and inpatient facilities by clinical trial status. Participation in clinical trials was positively related to income and negatively related to social severity. In four cities, emergency room use was consistently lower for clinical trial participants than for nonparticipants.

CONCLUSIONS

Data from the first six months of the ACSUS pediatric sample suggest that participation in clinical trials may bring about access to social services that appear to reduce emergency room use. However, the findings reported here are descriptive and exploratory. Further multivariate, nonparametric analyses of the full 18-month provider-patient merged data set are necessary to confirm the simple correlations found in this study.

The strength of metal reinforced methylmethacrylate fixation of pathologic fractures

Fixation of the pathological fracture in terminal patients has in the past added the trauma of an extensive surgical procedure to an already weakened patient. Intramedullary fixation with single and double rods in conjuction with polymethylmethacrylate have been compared to ascertain the effect of different loading conditions using torque and analysis under compression measurements of the strength of repair bone. Extensive intramedullary reaming can be avoided with polymethylmethacrylate. The cement effectively transmits the load from the proximal to the distal fragment. The single large rod method would be more desirable for stiffer bones while the double thin rod technique may be applicable to more flexible bones.