Evaluating robustness of a generalized linear model when applied to electronic health record data accessed using an Open API

The Integrated Clinical and Environmental Exposures Service (ICEES) provides open regulatory-compliant access to clinical data, including electronic health record data, that have been integrated with environmental exposures data. While ICEES has been validated in the context of an asthma use case and several other use cases, the regulatory constraints on the ICEES open application programming interface (OpenAPI) result in data loss when using the service for multivariate analysis. In this study, we investigated the robustness of the ICEES OpenAPI through a comparative analysis, in which we applied a generalized linear model (GLM) to the OpenAPI data and the constraint-free source data to examine factors predictive of asthma exacerbations. Consistent with previous studies, we found that the main predictors identified by both analyses were sex, prednisone, race, obesity, and airborne particulate exposure. Comparison of GLM model fit revealed that data loss impacts model quality, but only with select interaction terms. We conclude that the ICEES OpenAPI supports multivariate analysis, albeit with potential data loss that users should be aware of.

ARAX: a graph-based modular reasoning tool for translational biomedicine

MOTIVATION

With the rapidly growing volume of knowledge and data in biomedical databases, improved methods for knowledge-graph-based computational reasoning are needed in order to answer translational questions. Previous efforts to solve such challenging computational reasoning problems have contributed tools and approaches, but progress has been hindered by the lack of an expressive analysis workflow language for translational reasoning and by the lack of a reasoning engine-supporting that language-that federates semantically integrated knowledge-bases.

RESULTS

We introduce ARAX, a new reasoning system for translational biomedicine that provides a web browser user interface and an application programming interface (API). ARAX enables users to encode translational biomedical questions and to integrate knowledge across sources to answer the user's query and facilitate exploration of results. For ARAX, we developed new approaches to query planning, knowledge-gathering, reasoning and result ranking and dynamically integrate knowledge providers for answering biomedical questions. To illustrate ARAX's application and utility in specific disease contexts, we present several use-case examples.

AVAILABILITY AND IMPLEMENTATION

The source code and technical documentation for building the ARAX server-side software and its built-in knowledge database are freely available online (https://github.com/RTXteam/RTX). We provide a hosted ARAX service with a web browser interface at arax.rtx.ai and a web API endpoint at arax.rtx.ai/api/arax/v1.3/ui/.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

RTX-KG2: a system for building a semantically standardized knowledge graph for translational biomedicine

BACKGROUND

Biomedical translational science is increasingly using computational reasoning on repositories of structured knowledge (such as UMLS, SemMedDB, ChEMBL, Reactome, DrugBank, and SMPDB in order to facilitate discovery of new therapeutic targets and modalities. The NCATS Biomedical Data Translator project is working to federate autonomous reasoning agents and knowledge providers within a distributed system for answering translational questions. Within that project and the broader field, there is a need for a framework that can efficiently and reproducibly build an integrated, standards-compliant, and comprehensive biomedical knowledge graph that can be downloaded in standard serialized form or queried via a public application programming interface (API).

RESULTS

To create a knowledge provider system within the Translator project, we have developed RTX-KG2, an open-source software system for building-and hosting a web API for querying-a biomedical knowledge graph that uses an Extract-Transform-Load approach to integrate 70 knowledge sources (including the aforementioned core six sources) into a knowledge graph with provenance information including (where available) citations. The semantic layer and schema for RTX-KG2 follow the standard Biolink model to maximize interoperability. RTX-KG2 is currently being used by multiple Translator reasoning agents, both in its downloadable form and via its SmartAPI-registered interface. Serializations of RTX-KG2 are available for download in both the pre-canonicalized form and in canonicalized form (in which synonyms are merged). The current canonicalized version (KG2.7.3) of RTX-KG2 contains 6.4M nodes and 39.3M edges with a hierarchy of 77 relationship types from Biolink.

CONCLUSION

RTX-KG2 is the first knowledge graph that integrates UMLS, SemMedDB, ChEMBL, DrugBank, Reactome, SMPDB, and 64 additional knowledge sources within a knowledge graph that conforms to the Biolink standard for its semantic layer and schema. RTX-KG2 is publicly available for querying via its API at arax.rtx.ai/api/rtxkg2/v1.2/openapi.json . The code to build RTX-KG2 is publicly available at github:RTXteam/RTX-KG2 .

Epidemiology and impact of frailty in patients with atrial fibrillation in Europe

BACKGROUND

Frailty is a medical syndrome characterised by reduced physiological reserve and increased vulnerability to stressors. Data regarding the relationship between frailty and atrial fibrillation (AF) are still inconsistent.

OBJECTIVES

We aim to perform a comprehensive evaluation of frailty in a large European cohort of AF patients.

METHODS

A 40-item frailty index (FI) was built according to the accumulation of deficits model in the AF patients enrolled in the ESC-EHRA EORP-AF General Long-Term Registry. Association of baseline characteristics, clinical management, quality of life, healthcare resources use and risk of outcomes with frailty was examined.

RESULTS

Among 10,177 patients [mean age (standard deviation) 69.0 (11.4) years, 4,103 (40.3%) females], 6,066 (59.6%) were pre-frail and 2,172 (21.3%) were frail, whereas only 1,939 (19.1%) were considered robust. Baseline thromboembolic and bleeding risks were independently associated with increasing FI. Frail patients with AF were less likely to be treated with oral anticoagulants (OACs) (odds ratio 0.70, 95% confidence interval 0.55-0.89), especially with non-vitamin K antagonist OACs and managed with a rhythm control strategy, compared with robust patients. Increasing frailty was associated with a higher risk for all outcomes examined, with a non-linear exponential relationship. The use of OAC was associated with a lower risk of outcomes, except in patients with very/extremely high frailty.

CONCLUSIONS

In this large cohort of AF patients, there was a high burden of frailty, influencing clinical management and risk of adverse outcomes. The clinical benefit of OAC is maintained in patients with high frailty, but not in very high/extremely frail ones.

Biolink Model: A universal schema for knowledge graphs in clinical, biomedical, and translational science

Within clinical, biomedical, and translational science, an increasing number of projects are adopting graphs for knowledge representation. Graph‐based data models elucidate the interconnectedness among core biomedical concepts, enable data structures to be easily updated, and support intuitive queries, visualizations, and inference algorithms. However, knowledge discovery across these “knowledge graphs” (KGs) has remained difficult. Data set heterogeneity and complexity; the proliferation of ad hoc data formats; poor compliance with guidelines on findability, accessibility, interoperability, and reusability; and, in particular, the lack of a universally accepted, open‐access model for standardization across biomedical KGs has left the task of reconciling data sources to downstream consumers. Biolink Model is an open‐source data model that can be used to formalize the relationships between data structures in translational science. It incorporates object‐oriented classification and graph‐oriented features. The core of the model is a set of hierarchical, interconnected classes (or categories) and relationships between them (or predicates) representing biomedical entities such as gene, disease, chemical, anatomic structure, and phenotype. The model provides class and edge attributes and associations that guide how entities should relate to one another. Here, we highlight the need for a standardized data model for KGs, describe Biolink Model, and compare it with other models. We demonstrate the utility of Biolink Model in various initiatives, including the Biomedical Data Translator Consortium and the Monarch Initiative, and show how it has supported easier integration and interoperability of biomedical KGs, bringing together knowledge from multiple sources and helping to realize the goals of translational science.

374 Are Operative Notes Adhering to the Standards of Good Practice?

Aim

Thorough documentation is imperative for postoperative care, quality improvement, research, and medico-legal enquiries. For these reasons this closed loop audit aimed to assess whether the local Trauma and Orthopaedic departments’ operative notes were adhering to the guidance outlined by The Royal College of Surgeons, in order to to follow good practice.

Method

This was a random data collection, single centre study performed which analysed 50 operative notes from a variety of Trauma and Orthopaedic surgical procedures (not including neck of femur fractures and elective surgeries). The next cycle of the audit was completed after departmental re-education and a new operative note pro forma was created and put in place.

Results

The first audit cycle demonstrated that 8 categories in the operative note were below 96 % compliance with the guidance, of these being: time, name of operating surgeon/anaesthetist, operative procedure, incision, operative diagnosis, DVT prophylaxis, signature. Furthermore, an interesting finding showed no complications were identified in any operative note, similarly no extra procedures were documented. The second audit cycle showed that there was 100% compliance gained across all categories. Additionally, the new pro forma had an option to specify if there was/or not any complications, which had 100 % compliance in the second cycle and identified one complication.

Conclusions

Overall this audit was able to standardise the operative notes and improve quality and structure in order to follow good practice, by implementing a new pro forma and re-educating the department. This ensures that the best standard of care is being delivered.

A Real-World Comparative Effectiveness Analysis of Thromboprophylactic Use of Enoxaparin Versus Unfractionated Heparin in Abdominal Surgery Patients in a Large U.S. Hospital Database

Introduction: Little is known about outcomes associated with enoxaparin versus unfractionated heparin (UFH) for venous thromboembolism (VTE) prophylaxis in abdominal surgery patients in U.S. clinical practice. The purpose of this study was to compare VTE, all-cause mortality, PE-related in-hospital mortality, and hospital costs during abdominal surgery hospitalization and the 90 days post-discharge between patients who received enoxaparin versus UFH prophylaxis. Materials and Methods: Using the Premier Healthcare Database, abdominal surgery patients who received at least 1 day of VTE prophylaxis with enoxaparin or UFH were identified between January 1, 2010 and September 30, 2016. Clinical outcomes were assessed using multivariable logistic regression models and cost outcomes were assessed using generalized linear models. Results: Of 363,669 patients identified, 59% received enoxaparin and 41% UFH. In adjusted analyses, there were statistically significant lower odds of VTE (OR 0.80; 95% CI 0.65-0.97), all-cause mortality (OR 0.67; 95% CI 0.60-0.75), and major bleeding (OR 0.88; 95% CI 0.82-0.94) during the hospitalization for enoxaparin versus UFH, but no differences during the 90-days post-discharge or for PE-related mortality. There was a statistically significant lower total hospital cost with enoxaparin versus UFH during index hospitalization ($8,913 vs $9,017, P < .0001), but not post-discharge ($3,342 vs $3,368, P = .42). Unadjusted rates of heparin-induced thrombocytopenia (index:0.1% vs 0.3%; post-discharge: 0.02% vs 0.06%) were reported for enoxaparin and UFH, respectively. Conclusion: In contemporary U.S. hospital practice, statistically significant lower odds of VTE, all-cause mortality and major bleeding with enoxaparin versus UFH prophylaxis were found during abdominal surgery hospitalizations.

Open Application of Statistical and Machine Learning Models to Explore the Impact of Environmental Exposures on Health and Disease: An Asthma Use Case

ICEES (Integrated Clinical and Environmental Exposures Service) provides a disease-agnostic, regulatory-compliant approach for openly exposing and analyzing clinical data that have been integrated at the patient level with environmental exposures data. ICEES is equipped with basic features to support exploratory analysis using statistical approaches, such as bivariate chi-square tests. We recently developed a method for using ICEES to generate multivariate tables for subsequent application of machine learning and statistical models. The objective of the present study was to use this approach to identify predictors of asthma exacerbations through the application of three multivariate methods: conditional random forest, conditional tree, and generalized linear model. Among seven potential predictor variables, we found five to be of significant importance using both conditional random forest and conditional tree: prednisone, race, airborne particulate exposure, obesity, and sex. The conditional tree method additionally identified several significant two-way and three-way interactions among the same variables. When we applied a generalized linear model, we identified four significant predictor variables, namely prednisone, race, airborne particulate exposure, and obesity. When ranked in order by effect size, the results were in agreement with the results from the conditional random forest and conditional tree methods as well as the published literature. Our results suggest that the open multivariate analytic capabilities provided by ICEES are valid in the context of an asthma use case and likely will have broad value in advancing open research in environmental and public health.

128 Rapidly Proliferative Pilomatrixoma On the Eyebrow of A 7-Year-Old Boy – A Case Report

Pilomatrixoma or calcifying epithelioma of Malherbe is a benign tumour originating from pluripotent precursors of hair matrix cells. We present a paediatric patient with a rapidly enlarging eyebrow mass with a differential diagnosis of sebaceous cyst, pyogenic granuloma, or malignancy.

A 7-year-old boy presented in primary care with a 0.5cm non-inflammatory nodule on his medial brow present for 2-3 months. History of previous trauma was not elicited and there were no features of bleeding or ulceration. It was then lanced, following diagnosis of an infected sebaceous cyst. Within weeks, the nodule underwent rapid proliferation, enlarging to 2cm in diameter. He was urgently referred to secondary care pending further investigation for possible trauma-induced pyogenic granuloma or malignancy.

Upon presentation in secondary care, we observed a protruding erythematous and ulcerated mass, indurated in texture and adherent to overlying skin. The patient was submitted to excisional biopsy with a vertical elliptical approach to minimise distortion of the brow. Small, calcified deposits were observed in the tumour substance. Histologically, basaloid basophilic cells were predominant and mixed with ghost cells and foci of giant multinucleate cells, verifying diagnosis of a pilomatrixoma.

Pilomatrixoma exhibits tendency towards mimicry of lesions such as epidermoid, sebaceous, dermoid cyst, pyogenic granuloma or even keratoacanthoma with a pre-operative detection rate as low as 11%. With a bimodal age distribution, arising in the first and sixth decades of life, this case highlights a need for a high degree of suspicion in young patients with careful clinical examination in order to aid diagnosis and prompt appropriate treatment.

Voting-based integration algorithm improves causal network learning from interventional and observational data: An application to cell signaling network inference

In order to increase statistical power for learning a causal network, data are often pooled from multiple observational and interventional experiments. However, if the direct effects of interventions are uncertain, multi-experiment data pooling can result in false causal discoveries. We present a new method, "Learn and Vote," for inferring causal interactions from multi-experiment datasets. In our method, experiment-specific networks are learned from the data and then combined by weighted averaging to construct a consensus network. Through empirical studies on synthetic and real-world datasets, we found that for most of the larger-sized network datasets that we analyzed, our method is more accurate than state-of-the-art network inference approaches.

An approach for open multivariate analysis of integrated clinical and environmental exposures data

The Integrated Clinical and Environmental Exposures Service (ICEES) provides regulatory-compliant open access to sensitive patient data that have been integrated with public exposures data. ICEES was designed initially to support dynamic cohort creation and bivariate contingency tests. The objective of the present study was to develop an open approach to support multivariate analyses using existing ICEES functionalities and abiding by all regulatory constraints. We first developed an open approach for generating a multivariate table that maintains contingencies between clinical and environmental variables using programmatic calls to the open ICEES application programming interface. We then applied the approach to data on a large cohort (N = 22,365) of patients with asthma or related conditions and generated an eight-feature table. Due to regulatory constraints, data loss was incurred with the incorporation of each successive feature variable, from a starting sample size of N = 22,365 to a final sample size of N = 4,556 (20.4%), but data loss was < 10% until the addition of the final two feature variables. We then applied a generalized linear model to the subsequent dataset and focused on the impact of seven select feature variables on asthma exacerbations, defined as annual emergency department or inpatient visits for respiratory issues. We identified five feature variables—sex, race, obesity, prednisone, and airborne particulate exposure—as significant predictors of asthma exacerbations. We discuss the advantages and disadvantages of ICEES open multivariate analysis and conclude that, despite limitations, ICEES can provide a valuable resource for open multivariate analysis and can serve as an exemplar for regulatory-compliant informatic solutions to open patient data, with capabilities to explore the impact of environmental exposures on health outcomes.

Left ventricular involvement in arrhythmogenic right ventricular cardiomyopathy

Background

Arrhythmogenic right ventricular cardiomyopathy (ARVC) is not an isolated RV disease. Left ventricular (LV) or biventricular involvement is being increasingly diagnosed in such patients. There is available research to show that the LV peak strain calculated from feature tracking (FT) cardiac MRI is impaired even before the impairment of function. If present, such involvement is an adverse prognostic marker.

Purpose

The aim of this study is to calculate LV involvement in patients with ARVC using FT cardiac MRI.

Methods

27 patients of ARVC who underwent cardiac MRI with late gadolinium enhancement (LGE) in our department were identified. 10 healthy volunteers (controls) were also assessed using non-contrast cardiac MRI. LV strain analysis was performed using Cvi42 Circle cardiovascular imaging software; and global LV peak radial, circumferential and longitudinal strain values were calculated. Patients were divided into two sub groups: those with preserved LV ejection fraction (LVEF) and those with reduced LVEF. Peak LV strain values were compared between the two groups of ARVC patients; and between ARVC patients with preserved LVEF and healthy volunteers.

Results

The LV peak global longitudinal strain (GLS), global circumferential strain (GCS) and global radial strain (GRS) were −17.7±2.47, −18.16±2.65, 31.04±6.07 respectively in healthy volunteers. LV global longitudinal (GLS), circumferential (GCS), and radial strain (GRS) were significantly impaired in ARVC/D patients (GLS: −11.97±4.34%, GCS: −14.35±4.32%, GRS: 22.1±7.39%). ARVC patients were divided into 2 subgroups: the preserved LV ejection fraction (LVEF) group (LVEF ≥55%, n=9) and the reduced LVEF group (LVEF &lt;55%, n=18). In ARVC patients with reduced LVEF, the peak GLS was −9.99±3.94, GCS was −12.88±4.08 and GRS was 19.57±7.56. With preserved LVEF these values were −15.1±3.02, −17.3±3.3 and 27.1±3.67 respectively. In ARVC patients with preserved LVEF, the peak LV strain were impaired when compared with healthy volunteers with significant difference in peak GLS in between the two groups (p=0.05).

Conclusion

In patients with ARVC, cardiac MRI feature tracking can detect early LV dysfunction and thus adverse prognostic marker. Even in patients with normal LVEF, GLS was found to be significantly impaired as compared to healthy controls.

Calculation of longitudinal strain

Funding Acknowledgement

Type of funding source: None

The TRIXS end-station for femtosecond time-resolved resonant inelastic x-ray scattering experiments at the soft x-ray free-electron laser FLASH

We present the experimental end-station TRIXS dedicated to time-resolved soft x-ray resonant inelastic x-ray scattering (RIXS) experiments on solid samples at the free-electron laser FLASH. Using monochromatized ultrashort femtosecond XUV/soft x-ray photon pulses in combination with a synchronized optical laser in a pump-probe scheme, the TRIXS setup allows measuring sub-picosecond time-resolved high-resolution RIXS spectra in the energy range from 35 eV to 210 eV, thus spanning the M-edge (M₁ and M_2,3) absorption resonances of 3d transition metals and N_4,5-edges of rare earth elements. A Kirkpatrick-Baez refocusing mirror system at the first branch of the plane grating monochromator beamline (PG1) provides a focus of (6 × 6) μm² (FWHM) at the sample. The RIXS spectrometer reaches an energy resolution of 35-160 meV over the entire spectral range. The optical laser system based on a chirped pulse optical parametric amplifier provides approximately 100 fs (FWHM) long photon pulses at the fundamental wavelength of 800 nm and a fluence of 120 mJ/cm² at a sample for optical pump-XUV probe measurements. Furthermore, optical frequency conversion enables experiments at 400 nm or 267 nm with a fluence of 80 and 30 mJ/cm², respectively. Some of the first (pump-probe) RIXS spectra measured with this setup are shown. The measured time resolution for time-resolved RIXS measurements has been characterized as 287 fs (FWHM) for the used energy resolution.

Online survey about anesthesia-related practice and patient safety in Indian hospitals

BACKGROUND

Patient safety is a global concern, and anaesthesiologists are critically involved in patient safety-related measures and practices. Although anesthesia service has improved a lot over the last few decades, the information on the anesthesia practice and patient safety in India is lacking. The present survey was aimed to get the information on these aspects.

METHODS

A cross-sectional, questionnaire-based survey including both postgraduate trainees and anaesthesiologists, working across the different hospitals of India was conducted during February-May 2019. Google form was used as the survey; responses were directly downloaded as an Excel file and calculated in absolute numbers and percentages. Autonomous teaching institutes (ATI) were taken as standard, and Fisher's exact test was used for comparisons; P<0.05 was considered significant.

RESULTS

Six-hundred (86.1%) responses were included for analysis. Pulse oximetry and non-invasive blood pressure (NIBP) were available in nearly 99% set-ups, but end-tidal carbon-di-oxide (EtCO₂), temperature, oxygen, and anesthesia gas analyzer were lacking. ATI and corporate teaching hospitals were having almost all standard monitoring, but patient safety-related advanced equipment and medications were not present in many of the hospitals. The lack was highest in both public and private non-teaching hospitals (P<0.0001).

CONCLUSION

Patient safety and anesthesia-related services in India are unsatisfactory. Except for pulse oximetry and NIBP, the public and private sector non-teaching hospitals were lacking even the standard monitoring. Referral and top-level corporate and public sector institutes also have scope for improvement.

P2797Clinical outcomes of an ultra-thin strut sirolimus-eluting stent with biodegradable polymer in all-comers patients undergoing coronary intervention

Background

Thin stent struts may be associated with reduced vessel injury and use of biodegradable polymers may further improve long term outcomes. However, data with earlier stents has been inconsistent; thus further studies with newer devices are needed.

Purpose

To evaluate the efficacy and safety of a new ultra-thin (65um) strut cobalt chromium sirolimus-eluting stent with a hybrid design (closed cell at ends and open cells in middle to reduce edge injury and optimise conformability) in all-comers patients undergoing percutaneous coronary intervention (PCI).

Methods

We enrolled 752 patients from 14 sites undergoing PCI into a prospective, non-randomised, multi-centre, open-label, observational registry. Inclusion of patients with complex anatomy (long stent lengths, bifurcations and chronic total occlusions) was encouraged. Clinical follow-up was scheduled at 1, 9, 12 and 24 months. The primary endpoint was incidence of major adverse cardiac events (MACE) - cardiac death, non-fatal myocardial infarction (MI), or target vessel revascularization (TVR) - at 9 months.

Results

Mean patient age was 64.7±12.2 years, 20.7% had diabetes, 58.8% had dyslipidaemia, 40.4% had multi-vessel disease, 22% had previous PCI, 4.7% had previous coronary-artery bypass graft, and 19.6% had a clinical history of previous MI. Mean lesion length was 25.7±17.3 mm. The primary endpoint of cumulative MACE up to 9 months (from 624 patients reaching 9 months follow-up) occurred in 12 patients (1.92%), including 6 (0.96%) cardiac death, 5 (0.80%) MI and 6 (0.96%) clinically indicated TVR. Definite stent thrombosis was reported in 3 patients (0.48%) and probable stent thrombosis in 2 patients (0.32%).

Conclusions

Use of an ultra-thin strut biodegradable polymer sirolimus-eluting stent in all-comers patients undergoing PCI was associated with good clinical efficacy and safety.

Acknowledgement/Funding

Meril Life

Cardiometabolic risk profile based on body mass index in American Indian children and adolescents

BACKGROUND

Childhood obesity is associated with increased cardiometabolic risk.

OBJECTIVE

To study the relationship between body mass index (BMI) and cardiometabolic risk factors in American Indian children and adolescents.

METHODS

Differences in metabolic variables by age and sex-specific BMI percentiles (2000 Centers for Disease Control and Prevention Growth Charts) were examined in a cross-sectional analysis of 2977 individuals across three age categories. Children with an exam in two consecutive age categories were included in a longitudinal analysis. Spearman's correlations were used to test the association of BMI percentile with anthropometric and biochemical variables.

RESULTS

Body mass index percentile correlated with systolic (r = 0.24 to 0.38) and diastolic (r = 0.13 to 0.22) blood pressure, fasting plasma glucose (r = 0.20 to 0.33), 2-h plasma glucose (r = 0.30 to 0.46), total cholesterol (r = 0.12 to 0.23), serum triglycerides (r = 0.40 to 0.51) and HDL cholesterol (r = -0.36 to -0.43) in each age group (5-9, 10-13 and 14-17 years). Among participants examined in multiple age categories, BMI percentile increased over time. Change in BMI percentile from one age category to the next was associated with an increase in fasting glucose, 2-h glucose and triglycerides and a decrease in HDL cholesterol.

CONCLUSION

Higher BMI was associated with blood pressure elevation, hyperglycaemia and dyslipidaemia in American Indian children and adolescents.

Clinical and microbiological profile of febrile neutropenia in solid tumors and hematological malignancies at a tertiary cancer care center in South India

BACKGROUND

Febrile neutropenia (FN) is a common but serious complication of chemotherapy in patients with solid tumors (ST) and hematological malignancies (HM). The epidemiology of FN keeps changing.

OBJECTIVE

The objective was to study the epidemiology of FN in adult patients with ST and HM at Kidwai Memorial Institute of Oncology, Bangalore - A tertiary cancer care center.

MATERIALS AND METHODS

Data of all episodes of FN that occurred during the period July 2011 to December 2011 were collected prospectively and analyzed.

RESULTS

A total of 75 episodes of FN was observed during study period involving 55 patients. Febrile neutropenic episodes were more frequent in HM than in ST (57% vs. 43%). The rate of bloodstream infection was 14.7%. Gram-negative organisms were the predominant isolates (56.25%). Overall mortality rate was 13.3%. Presence of medical co-morbidity and positive culture predicted high mortality. Mortality rate did not differ significantly between HM and ST (14% vs. 12.5%; P = 1.0). Gram-positive bacteremia was associated with greater mortality than Gram-negative bacteremia (P = 0.02).

CONCLUSION

Empiric antibiotic treatment for FN should be tailored to the locally prevalent pathogens and their susceptibility patterns.

Differential inflammasome activation signatures following intracellular infection of human macrophages with Mycobacterium bovis BCG or Trypanosoma cruzi

Pathogens frequently exploit or evade inflammasome activation in order to survive and proliferate. Alternatively, inadequate inflammasome activation by attenuated microorganisms or adjuvanted subunit vaccines may contribute to poor longevity of protection. To further understand these pathways, we determined the differential inflammasome transcriptome of human THP monocyte-derived macrophages in response to Mycobacterium bovis BCG, as compared to LPS or Trypanosoma cruzi. The results identify the highly specific innate recognition programs associated with inflammasome activation by human macrophages exposed to these microbial stimuli. BCG, T. cruzi, and LPS strongly induced expression of both unique and overlapping genes downstream of TLR signaling pathways including cytokines and chemokines that mediate inflammation and regulate cell death pathways. Compared to LPS, BCG failed to directly activate anti-apoptotic molecules and multiple NLR and inflammasome complex components including caspase-1, and actively repressed important signaling intermediates in AP-1 and NFκB transcription factor pathways. Both BCG and T. cruzi repressed expression of TXNIP, an anti-oxidant inhibitor that recruits caspase-1 to the NLRP3 inflammasome, while T. cruzi infection uniquely failed to activate TNF-α. These results identify unique pathogen specific strategies to activate inflammation and modulate cell death that may drive inflammatory outcomes and suggest avenues of investigation to optimize host immunity.

No evidence of association of xenotropic murine leukemia virus-related virus with oral cancers: Experience from a tertiary care center in South India

BACKGROUND

Development of oral cancer, a widely prevalent cancer in India, is multifactorial with increased risk in those habituated to smoking, consuming alcohol and chewing paan and tobacco. This does not preclude other etiological factors in the causation of this cancer. Exploratory studies on several oncogenic viruses have found varied associations with oral cancers.

AIM

The aim of this study was to explore the association of xenotropic murine leukemia virus-related virus, (XMRV) a retrovirus recently implicated in oncogenesis in humans, with oral cancers.

SETTINGS AND DESIGN

The presence of XMRV proviral deoxyribonucleic acid (DNA) was evaluated by standard nucleic acid amplification from DNA extracted from representative bits of tumor tissues and adjacent normal tissues from surgically resected specimens sent post-operatively for routine histopathological testing.

MATERIALS AND METHODS

This prospective study comprised 109 patients with a provisional diagnosis of oral cancer who were operated at the Oral Oncology Department of Kidwai Memorial Institute of Oncology, over a period of 10 months.

RESULTS

XMRV was not found in any of the tumor tissues (squamous cell carcinomas - 98; verrucous carcinomas - 4) nor in any of the normal tissues. It is thus important that the absence of this oncogenic virus in all the cases makes the association of XMRV with oral cancers very unlikely.

CONCLUSIONS

There is a need to investigate potentially oncogenic viruses in other solid tumors and in larger sample sizes. Any such association could have implications in detecting, preventing and treating these cancers.

Rare Presentation of Chorioadenoma Destruens as Acute Haemoperitoneum Mimicking Ruptured Ectopic Pregnancy

Gestational trophoblastic neoplasms (GTN) are proliferative degenerative disorders of placental elements and include complete or partial mole (90%), invasivemole (5-8%), choriocarcinoma (1-2%) and placental site tumor (1-2%). Chorioadenoma destruens is a trophoblastic tumor, characterized by myometrial invasion through direct extension or via venous channels. We present a case of invasive mole eroding uterus and uterine vasculature, causing sudden rupture of uterus with massive haemoperitoneum mimicking ectopic pregnancy. A 20 year old G1P0 at 6 weeks gestation presented in Casualty of Kasturba Hospital complaining of severe acute onset lower abdominal pain for one hour. Clinical examination revealed shock. Sonography suggested ectopic pregnancy and immediate exploratory laparotomy was decided. On laparotomy, 2000cc of haemoperitoneum was noted. Grape like vesicles protruding through fundal perforation with profuse active bleeding was seen. Bleeding persisted despite evacuation. Step wise uterine devascularisation failed to achieve haemostasis. Total abdominal hysterectomy was performed as a life saving measure.

Influence of Carbon and Microbial Community Priming on the Attenuation of Uranium in a Contaminated Floodplain Aquifer

The capacity for subsurface sediments to sequester radionuclide contaminants, such as uranium (U), and retain them after bioremediation efforts are completed is critical to the long-term stewardship of re-mediated sites. In U bioremediation strategies, carbon amendment stimulates bioreduction of U(VI) to U(IV), immobilizing it within the sediments. Sediments enriched in natural organic matter are naturally capable of sequestering significant U, but may serve as sources to the aquifer, contributing to plume persistence. Two types of organic-rich sediments were compared to better understand U release mechanisms. Sediments that were artificially primed for U removal were retrieved from an area previously biostimulated while detrital-rich sediments were collected from a location never subject to amendment. Batch incubations demonstrated that primed sediments rapidly removed uranium from the groundwater, whereas naturally reduced sediments released a sizeable portion of U before U(VI)-reduction commenced. Column experiments confirmed that U release persisted for 65 pore volumes in naturally reduced sediments, demonstrating their sink-source behavior. Acetate addition to primed sediments shifted the microbial community from sulfate-reducing bacteria within Desulfobacteraceae to the iron-reducing Geobacteraceae and Firmicutes, associated with efficient U(VI) removal and retention, respectively. In contrast, Geobacteraceae communities in naturally reduced sediments were replaced by sequences with similarity to Pseudomonas spp. during U release, while U(VI) removal only occurred with enrichment of Firmicutes. These investigations stress the importance of characterizing zones with heterogeneous carbon pools at U-contaminated sites prior to the determination of a remedial strategy to identify areas, which may contribute to long-term sourcing of the contaminants.

Oxidative stress and amyloid beta toxicity in Alzheimer's disease: intervention in a complex relationship by antioxidants

The elucidation of the intriguing relationship between oxidative stress and Alzheimer's disease is crucial to understand the pathogenesis of the disease as also to design a suitable drug trial with antioxidants against this condition. We begin by reviewing the basic facts about Alzheimer's disease and the chemistry and biology of oxygen free radicals with particular reference to the cellular adaptive response through redox-signalling pathways. The post-mortem evidence of oxidative damage in the brain of Alzheimer's disease patients is overwhelming which is also supported by the similar changes in transgenic mice models of this disease. However, the causal relationship of oxidative stress with amyloid beta pathology or the genesis of Alzheimer's disease is not clear. Considering the available evidence the review suggests that the oxidative stress could be an early event in the disease process and may trigger various adaptive responses such as the alterations of amyloid beta metabolism and the activation of stress responsive kinases which can subsequently lead to neuronal degeneration and AD pathology. Further, we have presented a large body of evidence from various studies to highlight the beneficial effects of antioxidants against amyloid beta toxicity or AD pathology in animal or cell based models of AD. The failure of clinical trials with antioxidants against AD has been mentioned and the possible causes of such failures have been analysed.

Effect of sub-maximal exercise stress on cold pressor pain: a gender based study

BACKGROUND

Analgesic effect of exercise is a well established fact; however available reports are contradictory on gender differences in pain perception following exercise stress test.

OBJECTIVE

The current study is prospectively designed to evaluate and compare the effect of acute bout of sub-maximal exercise stress on cold pressor pain in normal adult males and females.

METHOD

The experimental study design involved healthy adults (n= 41); females (n = 18) and males (n=23) aged between 18 to 25 years and included them into four sets of experiments: SET I (Control), "resting blood pressure, radial pulse and respiratory rate were recorded after 15 minutes of complete supine relaxation. SET II (Cold Pressor Pain Test): Pain Threshold, Pain Tolerance, and Pain Duration in seconds were taken. SET III (Exercise Stress Test): Sub-maximal exercise of 70 to 75% of maximum predicted heart rate was given for 6 minutes. SET IV (Cold Pressor Pain Test immediately after Exercise Stress Test): At 0 minute of recovery again the pain parameters; Pain Threshold, Pain Tolerance, and Pain Duration in seconds were taken. SET I, SET II were performed in order on the first day and SET III and SET IV on the second day to ensure only a single Cold Pressor Pain Test is performed in each day.

RESULT

The data (Mean ± SD) analysis showed significant increased in pain threshold (males: 14.36 ± 10.6 Vs 21.47 ± 13 seconds, p< 0.001, females: 14.1 ± 11.5 Vs 23.81 ± 20.22 seconds, p<0.001) and pain tolerance time (males: 41.3 ± 19.31 Vs 54.1 ± 21.7 seconds, p<0.001) in both sexes after 6 min of acute bout of sub-maximal exercise stress test with comparable age, BMI and baseline resting values of pain parameters and pulse rate and blood pressure. The percentage increment pain tolerance time following the exercise stress in female is higher than male (78.6 Vs 68.9%).

CONCLUSION

The result suggests that pain sensation decreases immediately after a brief period of exercise challenge irrespective of gender, and the analgesic effect of the acute bout of exercise in terms of pain tolerant time is more enhanced in females than males.

Bacteraemia caused by Sciscionella marina in a lymphoma patient: phenotypically mimicking Nocardia

A 55-year-old female patient with malignant lymphoma after induction chemotherapy developed fever. Blood culture yielded an organism biochemically identified as representing Nocardia spp., but molecular identification (16S rRNA gene sequencing) later identified it as representing Sciscionella marina. This is the first report, to the best of our knowledge, of Sciscionella being isolated from a human sample.

Skeletal muscle stem cells: effects of aging and metabolism on muscle regenerative function

Homeostatic and regenerative replacement of skeletal muscle fibers requires the activity of a dedicated pool of myogenic stem cells, called satellite cells, that are activated by muscle injury and act as a renewable source of muscle-forming cells throughout adult life. Satellite cell function is controlled by both intrinsic and extrinsic regulatory cues, whose integration determines the success of muscle regenerative responses. Pathological deregulation of satellite cell function through perturbation of these signaling pathways appears to play an important role in age-dependent deterioration of muscle function and in muscle dystrophic disease. The regenerative activity of skeletal muscle also appears to be tightly linked to metabolism, and alterations in metabolic state can directly influence the activity of these tissue-specific stem cells. Here, we review recent and emerging insights into the molecular and biochemical signals that control satellite cell function and discuss these in the context of muscle degenerative diseases such as dystrophy and sarcopenia. Novel discoveries from this ongoing work bring new opportunities to enhance or restore muscle repair and are likely to facilitate satellite cell transplantation in clinical applications.

Anaphylactic shock following intraurethral lidocaine administration during transurethral resection of the prostate

Anaphylactic shock was noted following an apparently uneventful transurethral resection of the prostate (TURP). Lidocaine jelly was used prior to urethral dilatation and before placement of three-way Foley. Lidocaine sensitivity was diagnosed serendipitously when lidocaine jelly was used for application of ECG electrodes. Anaphylaxis may be one of the rare differentials to be considered in a patient with postoperative shock following TURP. This report highlights a potentially fatal complication of an apparently innocuous and ubiquitous urological use of lidocaine.