Data mining and clinical data repositories: Insights from a 667,000 patient data set

Clinical repositories containing large amounts of biological, clinical, and administrative data are increasingly becoming available as health care systems integrate patient information for research and utilization objectives. To investigate the potential value of searching these databases for novel insights, we applied a new data mining approach, HealthMiner, to a large cohort of 667,000 inpatient and outpatient digital records from an academic medical system. HealthMiner approaches knowledge discovery using three unsupervised methods: CliniMiner, Predictive Analysis, and Pattern Discovery. The initial results from this study suggest that these approaches have the potential to expand research capabilities through identification of potentially novel clinical disease associations.     

Care and treatment of HIV-infected children in Africa: issues and challenges at the district hospital level

More than 90% of pediatric HIV infection occurs in sub-Saharan Africa and 75% of these children currently die before their fifth birthday. Most HIV-infected children in Africa rely on district hospitals for HIV treatment, but insufficient attention has been paid to improving HIV/AIDS care at this level. Considerable confusion exists about optimal use of combination antiretroviral treatment, prophylaxis for opportunistic infections and other rational healthcare interventions that can greatly improve the quality of life for these children. A simple and inexpensive infant HIV diagnostic assay and alternative laboratory markers of pediatric HIV disease progression would be highly beneficial. Routine anthropometric and neurodevelopmental assessments could help guide initiation and monitoring of antiretroviral therapy. Even in the absence of antiretroviral therapy, interventions such as immunizations, provision of micronutrients and nutrition counseling, prevention and treatment of opportunistic as well as endemic infections (such as helminths and malaria) can substantially reduce pediatric HIV-related morbidity and mortality. The need for pain relief, palliative care, counseling and emotional support is often underestimated. Surmounting the sense of hopelessness by providing district healthcare workers with training in basic pediatric HIV/AIDS care is an urgent priority.     

An eight-week, open-label, uncontrolled, multicenter, Phase IV study of remission rates in outpatients and inpatients with major depression treated with venlafaxine

Background: Venlafaxine is a structurally novel antidepressant that is believed to potentiate monoamine activity in the central nervous system. In preclinical studies, venlafaxine was shown to inhibit the neuronal uptake of serotonin and norepinephrine and, to a lesser degree, dopamine reuptake, but was without effect on monoamine oxidase (MAO) activity. Clinical trial results from ∼3000 patients suggest that venlafaxine is a safe and effective antidepressant with the potential to invoke an early onset of clinical activity.Objective: The purpose of this 8-week, open-label, uncontrolled, multicenter, Phase IV study was to examine the extent of remission and symptom relief in outpatients and inpatients with major depressive disorder treated with venlafaxine.Methods: This study was conducted at 12 centers across Belgium and Luxembourg. Consecutive, severely depressed inpatients and moderately depressed outpatients aged 18 to 70 years were eligible. Patients were administered open-label venlafaxine for 8 weeks. Dosing was initiated at venlafaxine 75 mg/d (37.5 mg BID), with dose adjustments made throughout the study, to a maximum daily dose of 375 mg for inpatients and 225 mg for outpatients. Results were measured using the Hamilton Depression (HAM-D) scale, the Montgomery-Asberg Depression Rating Scale (MADRS), and the Clinical Global Impression (CGI) scale.Results: A total of 149 consecutive patients (84 females, 65 males; mean age, 46.5 years; 88 outpatients, 61 inpatients) were enrolled; the intent-to-treat (ITT) population comprised 144 patients (84 outpatients, 60 inpatients); 111 patients (64 outpatients, 47 inpatients) completed the study. At the week 8 visit, 71.3% of patients (77/108) were considered to be responders according to the HAM-D scale; 73.8% (79/107) according to the MADRS; and 78.7% (85/108) according to the CGI scale. A sustained response was achieved in 33.3% of the ITT population (48/144), and at week 8, 50.8% of outpatients (32/63) and 37.8% of inpatients (17/45) were in remission according to the HAM-D scale. Venlafaxine was well tolerated at all doses, with the most frequently experienced adverse events (AEs) being nausea, sweating, and headache. Fewer inpatients than outpatients reported ≥1 AE (57.4% [35/61] and 73.9% [65/88], respectively), despite receiving a higher maximum daily dose of venlafaxine.Conclusion: The results of this study indicate that venlafaxine was a tolerable and effective antidepressant in both outpatients and inpatients, with a significant proportion of patients achieving remission.     

Polyclonal antibodies from patients immunized with a globo H-keyhole limpet hemocyanin vaccine: isolation, quantification, and characterization of immune responses by using totally synthetic immobilized tumor antigens

We have previously reported on a carbohydrate-based vaccine program for immunotherapy in cancer patients. One such vaccine, based on the globo H antigen conjugated to the protein keyhole limpet hemocyanin (KLH), has been in clinical evaluation. Although this and other carbohydrate vaccines have been shown to induce antibody responses, there are currently no quantitative data on the antibody levels achieved in immunized patients by these or other anti-cancer vaccines. We report herein an efficient route to complex synthetic oligosaccharides attached to an affinity matrix for identifying and isolating antibodies elicited against such a carbohydrate-based vaccine in humans. Pre- and postvaccination profiles from serum samples of patients immunized with globo H-KLH were compared. All anti-globo H antibody activity was efficiently separated from other serum constituents. The isolated antibodies were readily quantified, and their specificities were analyzed. Since no comparable data were available on antibodies resulting from the vaccination of other cancer patients, we compared the observed levels with those quoted in studies with bacterial polysaccharide vaccines that had been quantified. Remarkably, cancer patients immunized with globo H-KLH produce anti-globo H antibody levels often exceeding those formed by immunization with bacterial polysaccharides. In addition, substantial quantities of both IgG and IgM antibodies were elicited, clearly indicating a class switch to IgG. Taken together, these analyses serve to clarify several aspects of the immune response to the vaccine and give several new insights to the carbohydrate-based vaccination strategy. Furthermore, antibodies so isolated could well have applications in clinical therapy.     

The carbohydrate domain of calicheamicin gamma I1 determines its sequence specificity for DNA cleavage.

We have investigated the DNA cleaving properties of calicheamicinone, the synthetic core aglycone of calicheamicin gamma I1, a natural product with extremely potent antitumor activity. Our experiments have shown that the synthetic analog binds and cleaves DNA, albeit without any sequence selectivity and with less efficiency than the natural compound. We propose that a key element in the sequence recognition process is the thiobenzoate ring present in the natural compound. We have demonstrated by one-dimensional NMR that there is direct hydrogen abstraction from DNA by calicheamicinone, with enhanced binding affinity contributed by the carbohydrate domain. The reduced efficiency of hydrogen abstraction from DNA by bound calicheamicinone, compared with the natural compound, implicates the carbohydrate moiety in positioning the drug for hydrogen abstraction.     

HIV prevention and care services for female sex workers: efficacy of a targeted community-based intervention in Burkina Faso

Introduction

Although interventions to control HIV among high-risk groups such as female sex workers (FSW) are highly recommended in Africa, the contents and efficacy of these interventions are unclear. We therefore designed a comprehensive dedicated intervention targeting young FSW and assessed its impact on HIV incidence in Burkina Faso.

Methods

Between September 2009 and September 2011 we conducted a prospective, interventional cohort study of FSW aged 18 to 25 years in Ouagadougou, with quarterly follow-up for a maximum of 21 months. The intervention combined prevention and care within the same setting, consisting of peer-led education sessions, psychological support, sexually transmitted infections and HIV care, general routine health care and reproductive health services. At each visit, behavioural characteristics were collected and HIV, HSV-2 and pregnancy were tested. We compared the cohort HIV incidence with a modelled expected incidence in the study population in the absence of intervention, using data collected at the same time from FSW clients.

Results

The 321 HIV-uninfected FSW enrolled in the cohort completed 409 person-years of follow-up. No participant seroconverted for HIV during the study (0/409 person-years), whereas the expected modelled number of HIV infections were 5.05/409 person-years (95% CI, 5.01–5.08) or 1.23 infections per 100 person-years (p=0.005). This null incidence was related to a reduction in the number of regular partners and regular clients, and by an increase in consistent condom use with casual clients (adjusted odds ratio (aOR)=2.19; 95% CI, 1.16–4.14, p=0.01) and with regular clients (aOR=2.18; 95% CI, 1.26–3.76, p=0.005).

Conclusions

Combining peer-based prevention and care within the same setting markedly reduced the HIV incidence among young FSW in Burkina Faso, through reduced risky behaviours.     

Carnitine palmitoyl transferase-I inhibition is not associated with cardiac hypertrophy in rats fed a high-fat diet

1. Cardiac lipotoxicity is characterized by hypertrophy and contractile dysfunction and can be triggered by impaired mitochondrial fatty acid oxidation and lipid accumulation. The present study investigated the effect of dietary fatty acid intake alone and in combination with inhibition of mitochondrial fatty acid uptake with the carnitine palmitoyl transferase (CPT)-I inhibitor oxfenicine. Long-chain fatty acids activate peroxisome proliferator-activated receptors (PPAR), thus mRNA levels of PPAR target genes were measured. 2. Rats were untreated or given the CPT-I inhibitor oxfenicine (150 mg/kg per day) and were fed for 8 weeks with either: (i) standard low-fat chow (10% of energy from fat); (ii) a long-chain saturated fatty acid diet; (iii) a long-chain unsaturated fatty acid diet; or (iv) a medium-chain fatty acid diet (which bypasses CPT-I). High-fat diets contained 60% of energy from fat. 3. Cardiac triglyceride content was increased in the absence of oxfenicine in the saturated fat group compared with other diets. Oxfenicine treatment further increased cardiac triglyceride stores in the saturated fat group and caused a significant increase in the unsaturated fat group. Despite elevations in triglyceride stores, left ventricular mass, end diastolic volume and systolic function were unaffected. 4. The mRNA levels of PPAR-regulated genes were increased by the high saturated and unsaturated fat diets compared with standard chow or the medium chain fatty acid chow. Oxfenicine did not further upregulate PPARalpha target genes within each dietary treatment group. 5. Taken together, the data suggest that consuming a high-fat diet or inhibiting CPT-I do not result in cardiac hypertrophy or cardiac dysfunction in normal rats.     

Insights into the Regulation of a Common Variant of HMGA2 Associated with Human Height During Embryonic Development

Early genetic studies in the mouse and chicken identified the HMGA oncogene as a candidate that regulates body height. Subsequent genome-wide SNP studies revealed a significant association of rs1042725 genotypes CT and CC in the 3’ UTR of HMGA2 with human height. Together, these studies indicated that HMGA2 expression levels during prenatal development might be a critical factor that contributes to the height phenotype. In the present study, we sought to gain insight into the regulation of HMGA2 during human embryonic development and provide evidence that the rs1042725 genotype is unlikely to affect HMGA2 levels in pluripotent human embryonic stem cells (hESCs). This implies that hESCs in the inner cell mass of blastocysts are most likely not involved in determining the human height phenotype associated with this SNP. By applying a computational approach and cell-based reporter assays, we then identified miR-196b as a candidate microRNA that could contribute to SNP-specific expression of HMGA2 during human prenatal development. We briefly discuss this result in the context of other known functions for miR-196b during vertebrate development.