BioThings SDK: a toolkit for building high-performance data APIs in biomedical research

SUMMARY

To meet the increased need of making biomedical resources more accessible and reusable, Web Application Programming Interfaces (APIs) or web services have become a common way to disseminate knowledge sources. The BioThings APIs are a collection of high-performance, scalable, annotation as a service APIs that automate the integration of biological annotations from disparate data sources. This collection of APIs currently includes MyGene.info, MyVariant.info and MyChem.info for integrating annotations on genes, variants and chemical compounds, respectively. These APIs are used by both individual researchers and application developers to simplify the process of annotation retrieval and identifier mapping. Here, we describe the BioThings Software Development Kit (SDK), a generalizable and reusable toolkit for integrating data from multiple disparate data sources and creating high-performance APIs. This toolkit allows users to easily create their own BioThings APIs for any data type of interest to them, as well as keep APIs up-to-date with their underlying data sources.

AVAILABILITY AND IMPLEMENTATION

The BioThings SDK is built in Python and released via PyPI (https://pypi.org/project/biothings/). Its source code is hosted at its github repository (https://github.com/biothings/biothings.api).

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

535 Are Routine Post-Operative Blood Tests Necessary Following Hip or Knee Arthroplasty in Fit and Well Patients?

Introduction

Enhanced recovery protocols in hip and knee arthroplasty have achieved same-day discharge in selected patients. However, abnormal serum sodium, haemoglobin and creatinine may affect postoperative management. In particular, Serum creatinine guides dosage of prophylactic direct oral anticoagulants (DOAC). In this study we aim to establish if post-operative blood tests following arthroplasty might affect management.

Method

Patients undergoing primary hip and knee arthroplasty surgery at our unit between April 2018 and March 2019 were included. National Joint Registry input forms were used to identify the patients and their American Society for Anaesthesiologists (ASA) grade. Patients with an ASA grade of 1 or 2 were included. The incidence of AKI, hyponatraemia, drop in haemoglobin below 80g/L (the threshold for consideration of transfusion) and altered DOAC dose were recorded. For statistical analysis, the z-test of single proportion was used to compare results to a hypothesised expected population proportion of 1% for group sizes greater than 10. The p-value was set to 0.05.

Results

Results leading to a change in management were seen in 19 of the 218 patients (8.7%) (p < 0.0001). Twelve patients (5.5%) developed stage 1 or 2 AKI (p < 0.0001). Three patients required a reduction in the DOAC dose in response to their post-operative creatinine result. Post-operative haemoglobin level was below 80 g/L in two patients. Hyponatraemia was observed in one fifth of the patients and required intervention in two patients.

Conclusions

Post-operative blood tests are essential prior to discharge for all patients following hip and knee arthroplasty, regardless of pre-operative status.

Precision medicine for mood disorders: objective assessment, risk prediction, pharmacogenomics, and repurposed drugs

Mood disorders (depression, bipolar disorders) are prevalent and disabling. They are also highly co-morbid with other psychiatric disorders. Currently there are no objective measures, such as blood tests, used in clinical practice, and available treatments do not work in everybody. The development of blood tests, as well as matching of patients with existing and new treatments, in a precise, personalized and preventive fashion, would make a significant difference at an individual and societal level. Early pilot studies by us to discover blood biomarkers for mood state were promising [1], and validated by others [2]. Recent work by us has identified blood gene expression biomarkers that track suicidality, a tragic behavioral outcome of mood disorders, using powerful longitudinal within-subject designs, validated them in suicide completers, and tested them in independent cohorts for ability to assess state (suicidal ideation), and ability to predict trait (future hospitalizations for suicidality) [3-6]. These studies showed good reproducibility with subsequent independent genetic studies [7]. More recently, we have conducted such studies also for pain [8], for stress disorders [9], and for memory/Alzheimer's Disease [10]. We endeavored to use a similar comprehensive approach to identify more definitive biomarkers for mood disorders, that are transdiagnostic, by studying mood in psychiatric disorders patients. First, we used a longitudinal within-subject design and whole-genome gene expression approach to discover biomarkers which track mood state in subjects who had diametric changes in mood state from low to high, from visit to visit, as measured by a simple visual analog scale that we had previously developed (SMS-7). Second, we prioritized these biomarkers using a convergent functional genomics (CFG) approach encompassing in a comprehensive fashion prior published evidence in the field. Third, we validated the biomarkers in an independent cohort of subjects with clinically severe depression (as measured by Hamilton Depression Scale, (HAMD)) and with clinically severe mania (as measured by the Young Mania Rating Scale (YMRS)). Adding the scores from the first three steps into an overall convergent functional evidence (CFE) score, we ended up with 26 top candidate blood gene expression biomarkers that had a CFE score as good as or better than SLC6A4, an empirical finding which we used as a de facto positive control and cutoff. Notably, there was among them an enrichment in genes involved in circadian mechanisms. We further analyzed the biological pathways and networks for the top candidate biomarkers, showing that circadian, neurotrophic, and cell differentiation functions are involved, along with serotonergic and glutamatergic signaling, supporting a view of mood as reflecting energy, activity and growth. Fourth, we tested in independent cohorts of psychiatric patients the ability of each of these 26 top candidate biomarkers to assess state (mood (SMS-7), depression (HAMD), mania (YMRS)), and to predict clinical course (future hospitalizations for depression, future hospitalizations for mania). We conducted our analyses across all patients, as well as personalized by gender and diagnosis, showing increased accuracy with the personalized approach, particularly in women. Again, using SLC6A4 as the cutoff, twelve top biomarkers had the strongest overall evidence for tracking and predicting depression after all four steps: NRG1, DOCK10, GLS, PRPS1, TMEM161B, GLO1, FANCF, HNRNPDL, CD47, OLFM1, SMAD7, and SLC6A4. Of them, six had the strongest overall evidence for tracking and predicting both depression and mania, hence bipolar mood disorders. There were also two biomarkers (RLP3 and SLC6A4) with the strongest overall evidence for mania. These panels of biomarkers have practical implications for distinguishing between depression and bipolar disorder. Next, we evaluated the evidence for our top biomarkers being targets of existing psychiatric drugs, which permits matching patients to medications in a targeted fashion, and the measuring of response to treatment. We also used the biomarker signatures to bioinformatically identify new/repurposed candidate drugs. Top drugs of interest as potential new antidepressants were pindolol, ciprofibrate, pioglitazone and adiphenine, as well as the natural compounds asiaticoside and chlorogenic acid. The last 3 had also been identified by our previous suicidality studies. Finally, we provide an example of how a report to doctors would look for a patient with depression, based on the panel of top biomarkers (12 for depression and bipolar, one for mania), with an objective depression score, risk for future depression, and risk for bipolar switching, as well as personalized lists of targeted prioritized existing psychiatric medications and new potential medications. Overall, our studies provide objective assessments, targeted therapeutics, and monitoring of response to treatment, that enable precision medicine for mood disorders.

Preimplantation genetic testing using Karyomapping for a paternally inherited reciprocal translocation: a case study

PURPOSE

Preimplantation genetic testing (PGT) using Karyomapping is used to screen embryos for single gene disorders prior to implantation. While Karyomapping is not designed to screen for abnormalities in chromosome copy number, this testing is based upon a genome-wide analysis of single nucleotide polymorphisms (SNP) and, as such, some chromosome abnormalities are detected. The aim of this study was to validate whether Karyomapping could provide reliable and accurate PGT for a paternal 46,XY,t(10;19)(p15;p13.3) reciprocal translocation.

METHODS

Feasibility/validation for PGT was performed using DNA from the couple, as well as DNA from the paternal parents and from a previous unbalanced pregnancy. Karyomapping was performed using Illumina's HumanKaryomap-12 BeadChip microarray technology. SNP analysis was performed using BlueFuse Multi software (Illumina). Transmission of the translocation was assessed through the analysis of SNP markers on the chromosome regions of interest.

RESULTS

PGT-SR was determined to be feasible as chromosomal SNP analysis could reliably distinguish normal/balanced outcomes from all unbalanced outcomes. The couple transferred a normal/balanced embryo in an elective single embryo transfer procedure following 2 IVF/PGT-SR cycles. A clinical pregnancy was achieved.

CONCLUSION

This is the first report of PGT-SR test validation using Karyomapping for a 46,XY,t(10;19)(p15;p13.3) reciprocal translocation. Karyomapping may offer a means of detecting unbalanced forms of chromosome rearrangements when other PGT platforms fail.

Development Review of the BACE1 Inhibitor Lanabecestat (AZD3293/LY3314814)

Several ongoing clinical development programs are investigating potential disease-modifying treatments for Alzheimer's disease (AD), including lanabecestat (AZD3293/LY3314814). Lanabecestat is a brain-permeable oral inhibitor of human beta-site amyloid (Aβ) precursor protein-cleaving enzyme 1 (BACE1) that reduces Aβ production. As a potent BACE1 inhibitor, lanabecestat significantly reduced soluble Aβ species and soluble amyloid precursor proteins (sAPPβ) in mouse, guinea pig, and dog in a time- and dose-dependent manner. Significant reductions in plasma and cerebrospinal fluid (CSF) Aβ1-40 and Aβ1-42 were observed in Phase 1 studies of healthy subjects and AD patients treated with lanabecestat. Three lanabecestat trials are ongoing and intended to support registration in Early AD: (1) Phase 2/3 study in patients with mild cognitive impairment (MCI) due to AD and mild AD dementia (AMARANTH, NCT02245737); (2) Delayed-start extension study (AMARANTH-EXTENSION, NCT02972658) for patients who have completed treatment in the AMARANTH Study; and (3) Phase 3 study in mild AD dementia (DAYBREAK-ALZ, NCT02783573). This review will discuss the development of lanabecestat, results from the completed nonclinical and clinical studies, as well as describe the ongoing Phase 3 clinical trials.

Biomechanical analysis of an interference screw and a novel twist lock screw design for bone graft fixation

BACKGROUND

Malpositioning of an anterior cruciate ligament graft during reconstruction can occur during screw fixation. The purpose of this study is to compare the fixation biomechanics of a conventional interference screw with a novel Twist Lock Screw, a rectangular shaped locking screw that is designed to address limitations of graft positioning and tensioning.

METHODS

Synthetic bone (10, 15, 20lb per cubic foot) were used simulating soft, moderate, and dense cancellous bone. Screw push-out and graft push-out tests were performed using conventional and twist lock screws. Maximum load and torque of insertion were measured.

FINDINGS

Max load measured in screw push out with twist lock screw was 64%, 60%, 57% of that measured with conventional screw in soft, moderate and dense material, respectively. Twist lock max load was 78% and 82% of that with conventional screw in soft and moderate densities. In the highest bone density, max loads were comparable in the two systems. Torque of insertion with twist lock was significantly lower than with conventional interference screw.

INTERPRETATION

Based on geometric consideration, the twist lock screw is expected to have 35% the holding power of a cylindrical screw. Yet, results indicate that holding power was greater than theoretical consideration, possibly due to lower friction and lower preloaded force. During graft push out in the densest material, comparable max loads were achieved with both systems, suggesting that fixation of higher density bone, which is observed in young athletes that require reconstruction, can be achieved with the twist lock screw.

Understanding and predicting suicidality using a combined genomic and clinical risk assessment approach

Worldwide, one person dies every 40 seconds by suicide, a potentially preventable tragedy. A limiting step in our ability to intervene is the lack of objective, reliable predictors. We have previously provided proof of principle for the use of blood gene expression biomarkers to predict future hospitalizations due to suicidality, in male bipolar disorder participants. We now generalize the discovery, prioritization, validation, and testing of such markers across major psychiatric disorders (bipolar disorder, major depressive disorder, schizoaffective disorder, and schizophrenia) in male participants, to understand commonalities and differences. We used a powerful within-participant discovery approach to identify genes that change in expression between no suicidal ideation and high suicidal ideation states (n=37 participants out of a cohort of 217 psychiatric participants followed longitudinally). We then used a convergent functional genomics (CFG) approach with existing prior evidence in the field to prioritize the candidate biomarkers identified in the discovery step. Next, we validated the top biomarkers from the prioritization step for relevance to suicidal behavior, in a demographically matched cohort of suicide completers from the coroner's office (n=26). The biomarkers for suicidal ideation only are enriched for genes involved in neuronal connectivity and schizophrenia, the biomarkers also validated for suicidal behavior are enriched for genes involved in neuronal activity and mood. The 76 biomarkers that survived Bonferroni correction after validation for suicidal behavior map to biological pathways involved in immune and inflammatory response, mTOR signaling and growth factor regulation. mTOR signaling is necessary for the effects of the rapid-acting antidepressant agent ketamine, providing a novel biological rationale for its possible use in treating acute suicidality. Similarly, MAOB, a target of antidepressant inhibitors, was one of the increased biomarkers for suicidality. We also identified other potential therapeutic targets or biomarkers for drugs known to mitigate suicidality, such as omega-3 fatty acids, lithium and clozapine. Overall, 14% of the top candidate biomarkers also had evidence for involvement in psychological stress response, and 19% for involvement in programmed cell death/cellular suicide (apoptosis). It may be that in the face of adversity (stress), death mechanisms are turned on at a cellular (apoptosis) and organismal level. Finally, we tested the top increased and decreased biomarkers from the discovery for suicidal ideation (CADM1, CLIP4, DTNA, KIF2C), prioritization with CFG for prior evidence (SAT1, SKA2, SLC4A4), and validation for behavior in suicide completers (IL6, MBP, JUN, KLHDC3) steps in a completely independent test cohort of psychiatric participants for prediction of suicidal ideation (n=108), and in a future follow-up cohort of psychiatric participants (n=157) for prediction of psychiatric hospitalizations due to suicidality. The best individual biomarker across psychiatric diagnoses for predicting suicidal ideation was SLC4A4, with a receiver operating characteristic (ROC) area under the curve (AUC) of 72%. For bipolar disorder in particular, SLC4A4 predicted suicidal ideation with an AUC of 93%, and future hospitalizations with an AUC of 70%. SLC4A4 is involved in brain extracellular space pH regulation. Brain pH has been implicated in the pathophysiology of acute panic attacks. We also describe two new clinical information apps, one for affective state (simplified affective state scale, SASS) and one for suicide risk factors (Convergent Functional Information for Suicide, CFI-S), and how well they predict suicidal ideation across psychiatric diagnoses (AUC of 85% for SASS, AUC of 89% for CFI-S). We hypothesized a priori, based on our previous work, that the integration of the top biomarkers and the clinical information into a universal predictive measure (UP-Suicide) would show broad-spectrum predictive ability across psychiatric diagnoses. Indeed, the UP-Suicide was able to predict suicidal ideation across psychiatric diagnoses with an AUC of 92%. For bipolar disorder, it predicted suicidal ideation with an AUC of 98%, and future hospitalizations with an AUC of 94%. Of note, both types of tests we developed (blood biomarkers and clinical information apps) do not require asking the individual assessed if they have thoughts of suicide, as individuals who are truly suicidal often do not share that information with clinicians. We propose that the widespread use of such risk prediction tests as part of routine or targeted healthcare assessments will lead to early disease interception followed by preventive lifestyle modifications and proactive treatment.

Successful Semi-Ambulatory Veno-Arterial Extracorporeal Membrane Oxygenation Bridge to Heart-Lung Transplantation in a Very Small Child

Lung transplantation (LTx) may be denied for children on extracorporeal membrane oxygenation (ECMO) due to high risk of cerebral hemorrhage. Rarely has successful LTx been reported in children over 10 years of age receiving awake or ambulatory veno-venous ECMO. LTx following support with ambulatory veno-arterial ECMO (VA ECMO) in children has never been reported to our knowledge. We present the case of a 4-year-old, 12-kg child with heritable pulmonary artery hypertension and refractory right ventricular failure. She was successfully bridged to heart-lung transplantation (HLTx) using ambulatory VA ECMO. Initial resuscitation with standard VA ECMO was converted to an ambulatory circuit using Berlin heart cannulae. She was extubated and ambulating around her bed while on VA ECMO for 40 days. She received an HLTx from an oversized marginal lung donor. Despite a cardiac arrest and Grade 3 primary graft dysfunction, she made a full recovery without neurological deficits. She achieved 104% force expiratory volume in 1 s 33 months post-HLTx. Ambulatory VA ECMO may be a useful strategy to bridge very young children to LTx or HLTx. Patient tailored ECMO cannulation, minimization of hemorrhage, and thrombosis risks while on ECMO contributed to a successful HLTx in our patient.

Successful lung transplant in a child with cystic fibrosis and persistent Blastobotrys rhaffinosifermentans infection

Fungal respiratory infections in patients with CF are a significant concern both pre- and post-lung transplantation (LTx). Fungal infection is associated with increased mortality post-LTx, and in the past decade, the prevalence of fungal colonization in Canadian pediatric patients with CF has increased. The emergence of novel fungal pathogens is particularly challenging to the transplant community, as little is known regarding their virulence and optimal management. We present a case of a successful double-lung transplant in a pediatric patient with CF who was infected pretransplantation with a novel yeast, Blastobotrys rhaffinosifermentans. This patient was treated successfully with aggressive antifungal therapy post-transplantation, followed by extended fungal prophylaxis. The significance of fungal colonization and infection in children with CF pre- and post-LTx is reviewed.

Use of lean principals to improve flow of patients with fractured neck of femur--the HOPE study

We describe the implementation of a care pathway for patients with fractured neck of femur (NOF) using Lean and Six Sigma principles. After introduction of the Lean pathway, 32 patients out a total of 86 (37%) with fractured NOF were admitted to the Trauma Ward within 4 hours of presentation to the hospital; prior to implementation this was 16 patients out of a total of 59 (27%). Post-Lean an earlier mean theatre start time of 8.40am was achieved, resulting in a 38 minute increase in daily theatre time. An additional 52 patients (12%) received surgery within 24 hours of admission, resulting in 1 night length of stay reduction. Lean methodology proved an effective method to guide change resulting in an improved journey for the patient and significant workflow gains.

Care of type 2 diabetes in unresourced general practice: current practice in the Mid-West

It is estimated that 4.5% of the Irish population have type 2 diabetes. The HSE intends to move the care of uncomplicated type 2 diabetes to General Practice (GP). The study reviewed current General Practice diabetes care in the Irish Mid-West. The files of randomly selected patients from 12 GP teaching practices attached to the University of Limerick were audited. 842 patients were identified (62% male, 38% female). The mean age was 66 years. 75% were GMS patients. A practice protocol was used in 71% of patients. Average Cholesterol (4.3 mmol/l), creatinine (85.3 mmol/l), HbA1c (56.7 mmol/mol) and systolic blood pressure (SBP) (134 mmHg) measurements were well documented and controlled. However the rates of and mean intervals for foot review (60.2%), BMI measurement (52.3%), retinopathy screening (62.0%) and influenza vaccination (63.0%) were unacceptably low. Current management of type 2 diabetes in unresourced general practices is suboptimal although some biochemical parameters are well controlled.

Structured care of diabetes in general practice: a qualitative study of the barriers and facilitators

This qualitative study explored general practitioner's and practice nurse's perceptions of barriers and facilitators to the proposed transfer of diabetes care to general practice. Qualitative data were collected through five focus groups. Participants included GPs (n = 55) and practice nurses (n = 11) representing urban (44%), rural (29%) and mixed (27%) practices, in the Irish Mid-West region. Barriers and facilitators were mentioned 631 times (100%). Barriers were mentioned 461 times (73%), facilitators 170 times (27%). The most frequently identified barriers were lack of financial incentive (119/631; 19%), lack of access to secondary resources (93/631; 15%), lack of staff and increased workload (59/631; 9%) and time constraints (52/631; 8%). Identified facilitators were access to secondary care (49/631;7.8%), the holistic nature of general practice and continuity of care (48/631;7.6%). Although many are enthusiastic, there remains significant reluctance among GPs and practice nurses to take responsibility for diabetes care without addressing these barriers.

Caries status in 16 year-olds with varying exposure to water fluoridation in Ireland

Most of the Republic of Ireland's public water supplies have been fluoridated since the mid-1960s while Northern Ireland has never been fluoridated, apart from some small short-lived schemes in east Ulster.

OBJECTIVE

This study examines dental caries status in 16 year-olds in a part of Ireland straddling fluoridated and non-fluoridated water supply areas and compares two methods of assessing the effectiveness of water fluoridation. The cross-sectional survey tested differences in caries status by two methods: 1, Estimated Fluoridation Status as used previously in national and regional studies in the Republic and in the All-Island study of 2002; 2, Percentage Lifetime Exposure, a modification of a system described by Slade in 1995 and used in Australian caries research.

METHODS

Adolescents were selected for the study by a two-part random sampling process. Firstly, schools were selected in each area by creating three tiers based on school size, and selecting schools randomly from each tier. Then random sampling of 16-year-olds from these schools, based on a pre-set sampling fraction for each tier of schools.

RESULTS

With both systems of measurement, significantly lower caries levels were found in those children with the greatest exposure to fluoridated water when compared to those with the least exposure.

CONCLUSIONS

The survey provides further evidence of the effectiveness in reducing dental caries experience up to 16 years of age. The extra intricacies involved in using the Percentage Lifetime Exposure method did not provide much more information when compared to the simpler Estimated Fluoridation Status method.

Vascular risk factors, HIV serostatus, and cognitive dysfunction in gay and bisexual men

BACKGROUND

The purpose of this study was to evaluate the relationship between cognitive performance, risk factors for cardiovascular and cerebrovascular disease (CVD), and HIV infection in the era of highly active antiretroviral therapy.

METHODS

We evaluated the cognitive functions of men enrolled in the cardiovascular disease substudy of the Multicenter AIDS Cohort Study who were aged > or =40 years, with no self-reported history of heart disease or cerebrovascular disease. Results from comprehensive neuropsychological evaluations were used to construct composite scores of psychomotor speed and memory performance. Subclinical CVD was assessed by measuring coronary artery calcium and carotid artery intima-media thickness (IMT), as well as laboratory measures, including total cholesterol, fasting glucose, glycosylated hemoglobin, glomerular filtration rate (estimated), and standardized blood pressure and heart rate measures.

RESULTS

After accounting for education, depression, and race, carotid IMT and glomerular filtration rate were significantly associated with psychomotor speed, whereas IMT was associated with memory test performance. HIV serostatus was not significantly associated with poorer cognitive test performance. However, among the HIV-infected individuals, the presence of detectable HIV RNA in plasma was linked to lower memory performance.

CONCLUSIONS

These findings suggest that HIV infection may not be the most important predictor of cognitive performance among older gay and bisexual men in the post-highly active antiretroviral therapy era, at least among those with access to medical care and to appropriate medications. Medical factors associated with normal aging are significantly associated with performance on neuropsychological tests, and good clinical management of these factors both in HIV-infected individuals and those at risk for infection may have beneficial effects in the short term and could reduce the risk of subsequent cognitive decline.

Effect of melanoma on immune function in regional lymph nodes (LN)

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Background: Metastatic melanoma is associated with various measures of systemic and local immune suppression. We hypothesized that immune suppression in the regional LN basin exists and may facilitate melanoma progression. Methods: We collected portions of regional LNs from tumor uninvolved sentinel LNs (USLN) (remote from primary melanoma removal) and from macroscopically involved nodes (TILN) from therapeutic node dissections in successive melanoma patients. Lymphocytes were extracted, stained using surface and internal antibodies to T cell receptor zeta chain (TCRζ), T regulatory cells (CD4+CD25+ Fox 3p+) (Tregs) and tumor associated myeloid cells (CD11b+ CD14- CD15+) (TAMC), and analyzed via flow cytometer. Results from USLN specimens were compared with TILN. Results: 30 LNs (14 USLN/16 TILN) from 30 patients were evaluated. Median age of patients was 48 years (range 30–83); 20 were male. USLN patients were stage IB (12) or IIA (2); TILN patients were stage IIIB (5), IIIC (5), and IV (6). 7 patients with TILN and none with USLN have progressed. TILN had significantly less TCRζ chain expression than SLN (62% vs. 85%; p = 0.0001). This amounts to a localized decrease of 23% of TCRζ expression (95% CI 13%; 34%). No significant relationship between lymph node involvement and Treg or TAMC was documented. Conclusion: Regional LN involvement with melanoma is associated with a significant reduction in lymphocyte TCRζ expression indicating immune suppression. The mechanism for this is uncertain, but does not appear to be related to changes in Tregs or TAMC (arginase producing cells). We plan to further investigate TCRζ expression in microscopically involved SLNs and SLNs removed at time of primary excision to see if immune changes precede macroscopic tumor involvement. Supported by Harvard Skin SPORE Project 5 and Immune Monitoring Core P50CA93683–01

No significant financial relationships to disclose.

Genotyping of B and non-B subtypes of human immunodeficiency virus type 1

Current HIV-1 genotyping assays were developed using subtype B viruses prevalent in Western countries. It is not clear whether these assays are appropriate for use among African patients, who are likely to be infected with non-B subtypes. We evaluated the Bayer TRUGENE HIV-1 genotyping (TG) assay using prospectively collected samples from HIV-1-infected individuals who acquired infection in either sub-Saharan Africa or the West (Europe, North America, and Australia). Plasma samples from 208 individuals with an HIV-1 viral load of >1,000 copies/ml were tested using version 1 primers supplied with the TG assay. If these failed, an alternative primer set version 1.5 was used. Of the 208 individuals, the likely origin of infection was Africa (n = 104), Western (n = 87) and "Others" (i.e., all other geographic locations or origin not certain; n = 17). Among the three groups, the version 1 primers were successful in 85 (82%), 77 (89%), and 13 (76%) individuals, respectively (P = 0.1). Of the remaining 32 samples, 30 were successfully amplified by using the version 1.5 primers. HIV-1 subtypes deduced from the reverse transcriptase sequences correlated with the likely origin of infection: Africa (28A, 3B, 33C, 13D, 6G, 4J, 2K, 5CRF01_AE, and 10CRF02_AG), Western (86B and 1K), and Others (1A and 16B). The success of the version 1 primers correlated with viral load (P < 0.014) and not with HIV-1 subtypes. A protocol based on version 1 primers, followed by 1.5 primers, was successful in sequencing 99% of the samples in this cohort.

What makes gambling news?

This paper examines print media coverage of casino and electronic gambling in one Canadian province from 1992 to 1997. It provides a theme analysis of content of 234 gambling stories printed in the top two daily newspapers in Nova Scotia. The findings of our content analysis indicate that pro-gambling corporate and political newspaper sources waged a successful media campaign and constructed a powerful public rhetoric in support of new gambling products, services, and institutions. The media, for their part, gave visibility and form to these structured messages. They helped create expectations about gambling and economics and gambling and government. Law and order, and moral and medical discourses about gambling, we discovered, were minor representations in the news coverage, although moral narratives were a pervasive secondary theme in much of the reporting. At bottom, the press produced a "politics of truth" about gambling that was both an external exercise of power and an internal organizational production.

A comparison of the relative safety, efficacy, and tolerability of quetiapine and risperidone in outpatients with schizophrenia and other psychotic disorders: the quetiapine experience with safety and tolerability (QUEST) study

BACKGROUND

The few published direct comparative studies of the tolerability and efficacy of atypical antipsychotic agents were performed in relatively homogeneous populations that may not be typical of patients seen in clinical practice.

OBJECTIVE

The Quetiapine Experience with Safety and Tolerability (QUEST) study compared the relative safety, tolerability, and efficacy of quetiapine and risperidone in outpatients with a broad range of psychotic symptoms.

METHODS

This was a multicenter, 4-month, open-label, randomized clinical trial. Patients were randomized in a 3:1 ratio to receive quetiapine or risperidone. Doses were adjusted to maximize efficacy and to minimize adverse events. Extrapyramidal symptoms (EPS) were assessed with an EPS checklist; adverse events were recorded. Efficacy was assessed using the Clinical Global Impression (CGI) scale, Positive and Negative Symptom Scale (PANSS), and Hamilton Rating Scale for Depression (HAM-D).

RESULTS

A total of 728 patients were randomized, 553 to quetiapine and 175 to risperidone. Mean prescribed doses over the study period were 253.9 mg/d quetiapine and 4.4 mg/d risperidone. At the end of 4 months, EPS declined in both treatment groups, but quetiapine-treated patients were significantly less likely to require dose adjustment or concurrent anti-EPS medication (P < 0.001). The most common adverse events in the quetiapine and risperidone groups were somnolence (31.3% and 15.4%, respectively), dry mouth (14.5% and 6.9%), and dizziness (12.7% and 6.9%). Overall, tolerance to side effects with the 2 drugs, measured by dropout rates, was comparable. At each visit, a higher percentage of quetiapine-treated patients showed improvement on the CGI scale, but there were no significant between-group differences on the PANSS. At end point, quetiapine-treated patients had significantly lower HAM-D scores (P = 0.028).

CONCLUSIONS

The results of this study suggest that quetiapine is as effective as risperidone for the treatment of psychotic symptoms, is more effective for depressive symptoms, may have a more favorable EPS profile, and has comparable overall tolerability.

Absent hematuria and expensive computerized tomography: case characteristics of emergency urolithiasis

PURPOSE

We validated the descriptive characteristics of emergency cases presenting with urolithiasis, determined the incidence of normal urinalysis in such cases and compared the expense of diagnostic computerized tomography (CT) and excretory urography (IVP).

MATERIALS AND METHODS

We retrospectively reviewed the charts of all consecutive patient visits to a community emergency department for 48 months. Explicit protocols for case selection, data abstraction and monitoring were used to maximize accuracy. Entry criteria were urolithiasis diagnosed by IVP, CT or stone passage, and urinalysis. Data analysis included descriptive statistics and the calculation of confidence intervals.

RESULTS

From 159,083 emergency visits during this period 397 met study entry criteria. Absent hematuria was noted in 9% (95% confidence interval 7% to 12%) of patients with proved urolithiasis. There was no correlation of the degree of obstruction with absent hematuria. Most patients presenting with painful urolithiasis were male (73%), in the fifth decade of life (mean age 47 years), had stones in the mid ureter (32%) or at the ureterovesicular junction (44%) and received opiates for pain control (91%). Of the patients 48% presented between 5 p.m. and 7 a.m. when the radiology department was available only for emergency imaging. The diagnosis was made by CT in half of the patients, who were charged $1,409. The maximal insurance reimbursement was $673. The diagnosis was made by IVP in half of the patients, who were charged $445. The maximal insurance reimbursement was $141.

CONCLUSIONS

Hematuria is not universally present in patients with painful urolithiasis and does not correspond to the degree of obstruction. Despite previous reports to the contrary, CT is significantly more expensive for patients than IVP.

Problems in the interpretation of HIV-1 viral load assays using commercial reagents

During routine monitoring of human immunodeficiency virus (HIV) viral load, two problems arose. First, a number of patients, the majority being African, were found to have low viral loads by the Chiron branched-chain DNA assay in conjunction with low CD4(+) cell numbers. In order to determine whether this was due to failure of the branched-chain DNA assay to detect non-B subtypes of HIV, selected samples were subtyped and HIV RNA quantified by branched-chain DNA, NASBA, and the Roche Monitor RT-PCR assay. Twenty-eight (97%) of 29 Africans were infected with a non-B subtype of HIV and 15 (93.7%) of 16 non-Africans with subtype B. Twenty-three samples had a low viral load by branched-chain DNA, which was confirmed by the NASBA and RT-PCR assays. All three assays detected B and non-B subtypes with similar efficiency; NASBA failed to detect HIV RNA in a small number of non-B samples. Discrepancies between viral load and CD4(+) cell numbers did not appear therefore to be related to subtype. Second, while quantification of HIV RNA was being conducted using version 2 of the branched-chain DNA assay (lower detection limit 500 HIV RNA copies/ml) the manufacturers had developed a more sensitive assay and a comparative evaluation was therefore conducted. In approximately 30% of samples the viral load was up to 10 times higher with the more sensitive assay. These experiences emphasise the importance of close collaboration between the clinic and the laboratory.

Evidence for horizontal and not vertical transmission of human herpesvirus 8 in children born to human immunodeficiency virus-infected mothers

A survey of antibody responses to human herpesvirus 8 (HHV-8) was undertaken to examine the mode of transmission of this virus to children born to mothers with HIV. Methods. Serum samples from a cohort of 92 mother-infant pairs and a cross-sectional cohort of 100 children (median age, 4 years) were tested. In the cohort of mother-infant pairs, 14 infants were HIV-infected, 72 were not and the HIV status was unknown for 6. In the cohort of children 70 were HIV-infected and 30 were vertically exposed but uninfected. Serologic responses to two HHV-8 antigens, latency-associated nuclear antigen and the structural antigen encoded by open reading frame 65 were detected by immunofluorescent antibody test and enzyme-linked immunoassay. Results were confirmed by Western blot. Results. All HHV-8-seropositive mothers were African (17 of 92, 18.5%). Six of their infants were HHV-8-seronegative and 11 had at least 1 HHV-8-seropositive sample. One of the 11 infants tested only at birth had a lower antibody titer than the mother; the remaining 10 infants had decreasing titers up to 7 months of age and 6 became seronegative. No infants born to HHV-8-seronegative mothers had antibodies to the virus. The seroprevalence to HHV-8 was 6% in the cohort of children. All had African mothers and their median age was greater than that of the cohort (8.4 vs. 4.0 years). Five were coinfected with HIV. Conclusions. HHV-8 was not vertically transmitted by any of the HIV-coinfected mothers. Acquisition of antibody to HHV-8 occurred in older children, implying a horizontal route of transmission.

Radiation treatment of advanced or recurrent granulosa cell tumor of the ovary

BACKGROUND

Because granulosa cell tumors of the ovary are rare, the optimal treatment for women with gross residual disease after primary surgery or recurrence is not known. Our objective was to review the results of radiotherapy for advanced or recurrent granulosa cell tumor of the ovary.

METHODS

This retrospective review identified 34 patients with ovarian granulosa cell tumors treated with radiation at the University of Texas M. D. Anderson Cancer Center between 1949 and 1988. Fourteen received treatment for clinically measurable disease; 20 received adjuvant radiotherapy after surgery for minimal residual (<1 cm) or microscopic residual disease. The 14 patients with measurable disease formed the basis for this review.

RESULTS

Ten of 14 patients were treated with moving-strip whole-abdomen radiation (27-28 Gy), 9 with 60Co, and 1 with 6-MeV photons and a pelvic boost of 28 Gy with 22-25 MeV photons. The other 4 patients were treated with pelvic radiotherapy (45-61 Gy) with 22-25 MeV photons. Six of 14 patients (43%) had a clinical complete response to radiotherapy, with a median follow-up of 13 years (range, 5-21 years). Three of 6 who responded to radiation had relapse 4-5 years later; 2 of these 3 died of disease and 1 was alive with disease at last follow-up. Three responders remain alive without evidence of disease 10-21 years after treatment. The 8 nonresponders had a median survival of 12.3 months (range, 1-60 months).

CONCLUSIONS

Radiotherapy can induce a clinical response with occasional long-term remission in patients with persistent or recurrent granulosa cell tumor of the ovary.

Determination of olanzapine in human plasma and serum by liquid chromatography/tandem mass spectrometry

A liquid chromatographic/tandem mass spectrometric (LC/MS/MS) assay was developed for the quantitative determination of olanzapine (LY170053, OLZ) in human plasma and serum. Bond Elut C2 solid-phase extraction cartridges (single cartridge or 96-well format), in conjunction with a positive pressure manifold, were used to extract OLZ and its internal standard, LY170222, from the biological matrix. Chromatographic resolution of OLZ from endogenous plasma interferences and its metabolites was accomplished with a MetaChem monochrom HPLC (4.6 x 150 mm, dp 5 microns). Detection was effected with a Perkin-Elmer SCIEX API III Plus mass spectrometer using positive ion atmospheric pressure chemical ionization and a multiple reaction monitoring protocol. The linear dynamic range was from 250 pg ml-1 to 50 ng ml-1 of human plasma/serum using a 0.5 ml aliquot. The inter-day precision (relative standard deviation) and accuracy (relative error) in plasma ranged from 6.26 to 7.66% and from -3.54 to 7.52%, respectively. The intra-day precision and accuracy in serum ranged from 3.46 to 8.76% and from -8.06 to 12.46%, respectively. This assay is sensitive and selective, and will be used to support both human clinical and toxicological analyses. Furthermore, using the 96-well solid-phase extraction format, sample preparation can be easily automated.

Case-control study of idiopathic pulmonary fibrosis and environmental exposures

The authors conducted a matched case-control study of interstitial lung disease (ILD) using a self-administered questionnaire. All cases in the practice of two pulmonary specialists were identified. Cases were excluded if they were thought to have occupational exposures as a contributor, hypersensitivity pneumonitis or sarcoidosis, or some other well-recognized cause. Three controls were matched by sex and age (one year) as identified through orthopedic surgeons at the same institutions. Two rounds of a questionnaire were mailed; 17 cases (37.7%) and 94 controls (32.4%) responded to the questionnaire, although many of the case addresses were no longer valid. Individuals with ILD were 16.0 times as likely to report mold exposure and 11.1 times as likely to report silica as were controls in their workplace. Odds ratios associating ILD with moisture indicators in the home were in the same range as previously published associations between such indicators and wheezing. ILD may have environmental and occupational causes that warrant more systematic exploration.

Maternal viral load, CD4 cell count and vertical transmission of HIV-1

HIV load and CD4 cell numbers were measured among 95 HIV infected women during pregnancy in order to determine their value as prognostic markers for transmission of virus from mother to infant. Among the 94 live births, 13 children were infected with HIV, 69 were uninfected and 12 were of unknown infection status. HIV RNA levels, as measured by nucleic acid sequence based amplification, were significantly higher (P < 0.001) in women who transmitted virus than among those who did not transmit and maternal viral load was a stronger predictor of transmission than CD4 cell number. The predicted rate of transmission relative to maternal HIV RNA was 2% at 1,000 copies, 11% at 10,000 copies and 40% at 100,000 copies/ml. Little variation in viral load occurred during pregnancy and there was an association between viral load and prematurity, the mean gestation at delivery decreasing by 1.3 weeks for every 10-fold increase in maternal HIV RNA (P = 0.007). This study demonstrates that a high level of maternal HIV RNA is a risk factor for transmission of virus to the infant and maternal viral load is of more value as a prognostic marker for transmission risk than CD4 cell number. High viral load is also associated with premature delivery. Maternal viral load is therefore a useful marker on which to base management decisions during pregnancy.

Determination of LY355703 in dog and mouse plasma by positive ion liquid chromatography/tandem mass spectrometry with atmospheric pressure chemical ionization

A liquid chromatographic/mass spectrometric assay was developed for the determination of LY355703, a potent anti-tumor drug, in mouse and dog plasma. Empore (3M) C18 solid-phase extraction cartridges were used for sample preparation in conjunction with a positive pressure manifold. Chromatographic separation was obtained with a cyano high-performance liquid chromatographic column and detection was conducted using atmospheric pressure chemical ionization tandem mass spectrometry in the selected reaction monitoring mode. A structural analog, compound LY354504, was used as the internal standard. The assay was validated for the determination of LY355703 in mouse (ICR and NuNu) and dog (beagle) plasma. The lower and upper limits of quantitation were 2.1 and 527 ng ml-1, respectively, using a 0.1 ml plasma aliquot. The signal-to-noise ratio of a typical 2.1 ng ml-1 standard was approximately 40:1. The inter-day precision (relative standard deviation) and accuracy (relative error) derived from the analysis of validation samples at five concentrations ranged from 2.7 to 7.6% and from 4.8 to 4.5%, respectively. Throughput is approximately one sample every 3 min. This assay is simple, sensitive, accurate, precise and is being used to support toxicokinetic studies in dog and mouse.

Lipoxygenase inhibitors block PDGF-induced mitogenesis: a MAPK-independent mechanism that blocks fos and egr

Hepatic Ito cells proliferate during liver injury and fibrogenesis. Platelet-derived growth factor (PDGF)-induced [3H]thymidine incorporation was studied as Ito cells express the PDGF receptor after injury and activation. Pretreatment with either the nonspecific lipoxygenase inhibitor (nordihydroguaiaretic acid) or specific inhibitors of 5-lipoxygenase (SC-41661 and ICI-230487) inhibited PDGF-induced mitogenesis. Ito cells predominantly produce the leukotriene (LT) C4 >> LTB4. The PDGF-induced signal transduction cascade was studied to determine the potential mechanism of action of the lipoxygenase inhibitors. It was found that PDGF receptor abundance and receptor activation were not altered by lipoxygenase inhibition, suggesting that a postreceptor mechanism was involved. The two-key cytoplasmic serine-threonine kinases Raf and MAPK (mitogen-activated protein kinase), which are induced by PDGF and transmit the signal to the nucleus, were also not altered. Because Raf and MAPK can independently induce nuclear signaling, this suggests that the mechanism of action lies parallel or distal to these secondary messengers. Lipoxygenase inhibition did result in the suppression of PDGF-induced fos and egr expression. Collectively, this work suggests that lipoxygenase inhibition leads to the suppression of mitogenesis in part by disrupting the nuclear signaling that is required for protooncogene transcription at a step distal or parallel to MAPK activation.