Priti Parikh

Kino: A Generic Document Management System for Biologists Using SA-REST and Faceted Search

Document management has become an important consideration for the scientific community over the last decade. Human knowledge is central to many scientific domains, thus it is not possible to completely automate the document management process. Managing scientific documents require a semi-automatic approach to overcome issues of large volume, yet support the human participation in the process. In this paper we present Kino, a set of tools that streamline the document management process in life science domains. Kino is integrated with National Center for Biomedical On-to logy (NCBO), providing scientists access to quality domain models. Annotated documents are indexed using a faceted indexing and search engine that provides fine grained search capabilities to the scientists. We present two use cases that highlight the pain points in managing scientific literature and also include an empirical evaluation.

The Prevalence of Positive Drug and Alcohol Screens in Elderly Trauma Patients

BACKGROUND Alcohol and drug abuse are recognized to be significantly prevalent in trauma patients, and are frequent harbingers of injury. The incidence of substance abuse in elderly trauma patients has, however, been limitedly examined. The authors sought to identify the spectrum of positive alcohol and drug toxicology screens in patients ≥65 years admitted to a Level I trauma center. METHODS Patients ≥65 years old admitted to an American College of Surgeons (ACS) Level I trauma center over a 60--month period were identified from the trauma registry. Demographic data, blood alcohol content (BAC), and urine drug screen (UDS) results at admission were obtained and analyzed. The positive results were compared with individuals below 65 years in different substance categories using Fishers exact test. RESULTS In the 5-year period studied, of the 4139 patients ≥65 years, 1302 (31.5%) underwent toxicological substance screening. A positive BAC was present in 11.1% of these patients and a positive UDS in 48.3%. The mean BAC level in those tested was 163 mg/dL and 69% of patients had a level >80 mg/dL. CONCLUSIONS These data show that alcohol and drug abuse are an issue in patients ≥65 years in our institution, though not as pervasive a problem as in younger populations. Admission toxicology screens, however, are important as an aid to identify geriatric individuals who may require intervention.

Individualized Behavior Management Program for Alzheimer’s/Dementia Residents Using Behavior-Based Ergonomic Therapies

Person-centered, nonpharmacological interventions for managing Alzheimer’s/dementia-related behavioral disturbances have received significant attention. However, such interventions are quite often of a single type limiting their benefits. We develop a comprehensive nonpharmacological intervention, the Behavior-Based Ergonomic Therapy (BBET), which consists of multiple therapies. This low-cost, 24/7 program uses learning, personality, and behavioral profiles and cognitive function of each resident to develop a set of individualized therapies. These therapies are made available through an accessible resource library of music and video items, games and puzzles, and memory props to provide comfort or stimulation depending on an individual resident’s assessment. The quantitative and qualitative benefits of the BBET were evaluated at the dementia care unit in a not-for-profit continuing care retirement community in west central Ohio. The 6-month pilot study reduced falls by 32.5% and markedly reduced agitation through increased resident engagement.

The Ontology for Parasite Lifecycle (OPL): Towards a consistent vocabulary of lifecycle stages in parasitic organisms

BackgroundGenome sequencing of many eukaryotic pathogens and the volume of data available on public resources have created a clear requirement for a consistent vocabulary to describe the range of developmental forms of parasites. Consistent labeling of experimental data and external data, in databases and the literature, is essential for integration, cross database comparison, and knowledge discovery. The primary objective of this work was to develop a dynamic and controlled vocabulary that can be used for various parasites. The paper describes the Ontology for Parasite Lifecycle (OPL) and discusses its application in parasite research.ResultsThe OPL is based on the Basic Formal Ontology (BFO) and follows the rules set by the OBO Foundry consortium. The first version of the OPL models complex life cycle stage details of a range of parasites, such as Trypanosoma sp., Leishmania sp., Plasmodium sp., and Shicstosoma sp. In addition, the ontology also models necessary contextual details, such as host information, vector information, and anatomical locations. OPL is primarily designed to serve as a reference ontology for parasite life cycle stages that can be used for database annotation purposes and in the lab for data integration or information retrieval as exemplified in the application section below.ConclusionOPL is freely available at http://purl.obolibrary.org/obo/opl.owl and has been submitted to the BioPortal site of NCBO and to the OBO Foundry. We believe that database and phenotype annotations using OPL will help run fundamental queries on databases to know more about gene functions and to find intervention targets for various parasites. The OPL is under continuous development and new parasites and/or terms are being added.

Predictive Factors and Models for Trauma Patient Disposition

BACKGROUND Hospital length of stay for trauma patients can be unnecessarily prolonged due to delays in disposition planning. Demographic characteristics, comorbidities, and other patient variables may help in planning early during hospitalization. MATERIALS AND METHODS The data of 2836 trauma patients were retrospectively analyzed. Analysis of variance and the chi-square test were used to determine univariate predictors of discharge location (i.e., home, nonhome, and rehabilitation), and multivariable logistic regression was used to determine independent predictors. Clinical decision rules for discharge location were developed for two models: (1) a regular discharge (RD) model to predict discharge location based on demographic and clinical characteristics at the completion of hospital stay and (2) an admission planning discharge (APD) model based on data available shortly after admission. RESULTS The discharge locations differed on age, sex, certain comorbidities, and various hospital and clinical variables. Increased age, female sex, longer intensive care unit and hospital stays, and the comorbidities of neurologic deficiencies, coagulopathy, and diabetes were independent predictors of nonhome discharge in the RD model. For the APD model, increased age, female sex, the comorbidities of neurologic deficiencies, diabetes, coagulopathy, and obesity were independent predictors of nonhome discharge. The RD and APD models correctly predicted the discharge location 87.2% and 82.9% of the time, respectively. CONCLUSIONS Demographic and clinical information for trauma patients predicts disposition early in the hospital stay. If the clinical decision rules are validated, discharge steps can be taken earlier in the hospital course, resulting in increased patient satisfaction, timely rehabilitation, and cost savings.

From Questions to Effective Answers: On the Utility of Knowledge-Driven Querying Systems for Life Sciences Data

We compare two distinct approaches for querying data in the context of the life sciences. The first approach utilizes conventional databases to store the data and provides intuitive form-based interfaces to facilitate querying of the data, commonly used by the life science researchers that we study. The second approach utilizes a large OWL ontology and the same datasets associated as RDF instances of the ontology. Both approaches are being used in parallel by a team of cell biologists in their daily research activities, with the objective of gradually replacing the conventional approach with the knowledgedriven one. We describe several benefits of the knowledge-driven approach in comparison to the traditional one, and highlight a few limitations. We believe that our analysis not only explicitly highlights the benefits and limitations of semantic Web technologies in the context of life sciences but also contributes toward effective ways of translating a question in a researcher’s mind into precise queries with the intent of obtaining effective answers.

Successful Placement of Intracranial Pressure Monitors by Trauma Surgeons

BACKGROUND The Brain Trauma Foundation guidelines advocate for the use of intracranial pressure (ICP) monitoring following traumatic brain injury (TBI) in patients with a Glasgow Coma Scale (GCS) score of 8 or less and an abnormal computed tomographic scan finding. The absence of 24-hour in-house neurosurgery coverage can negatively impact timely monitor placement. We reviewed the safety profile of ICP monitor placement by trauma surgeons trained and credentialed in their insertion by neurosurgeons. METHODS In 2005, the in-house trauma surgeons at a Level I trauma center were trained and credentialed in the placement of ICP parenchymal monitors by the neurosurgeons. We abstracted all TBI patients who had ICP monitors placed during a 6-year period. Demographic information, Injury Severity Score (ISS), outcome, and monitor placement by neurosurgery or trauma surgery were identified. Misplacement, hemorrhage, infections, malfunctions, and dislodgement were considered complications. Comparisons were performed by &khgr;2 testing and Student’s t tests. RESULTS During the 6-year period, 410 ICP monitors were placed for TBI. The mean (SD) patient age was 40.9 (18.9) years, 73.7% were male, mean (SD) ISS was 28.3 (9.4), mean (SD) length of stay was 19 (16) days, and mortality was 36.1%. Motor vehicle collisions and falls were the most common mechanisms of injury (35.2% and 28.7%, respectively). The trauma surgeons placed 71.7 % of the ICP monitors and neurosurgeons for the remainder. The neurosurgeons placed most of their ICP monitors (71.8%) in the operating room during craniotomy. The overall complication rate was 2.4%. There was no significant difference in complications between the trauma surgeons and neurosurgeons (3% vs. 0.8%, p = 0.2951). CONCLUSION After appropriate training, ICP monitors can be safely placed by trauma surgeons with minimal adverse effects. With current and expected specialty shortages, acute care surgeons can successfully adopt procedures such as ICP monitor placement with minimal complications. LEVEL OF EVIDENCE Therapeutic/care management study, level IV.

A Semantic Problem Solving Environment for Integrative Parasite Research: Identification of Intervention Targets for Trypanosoma cruzi

Background Research on the biology of parasites requires a sophisticated and integrated computational platform to query and analyze large volumes of data, representing both unpublished (internal) and public (external) data sources. Effective analysis of an integrated data resource using knowledge discovery tools would significantly aid biologists in conducting their research, for example, through identifying various intervention targets in parasites and in deciding the future direction of ongoing as well as planned projects. A key challenge in achieving this objective is the heterogeneity between the internal lab data, usually stored as flat files, Excel spreadsheets or custom-built databases, and the external databases. Reconciling the different forms of heterogeneity and effectively integrating data from disparate sources is a nontrivial task for biologists and requires a dedicated informatics infrastructure. Thus, we developed an integrated environment using Semantic Web technologies that may provide biologists the tools for managing and analyzing their data, without the need for acquiring in-depth computer science knowledge. Methodology/Principal Findings We developed a semantic problem-solving environment (SPSE) that uses ontologies to integrate internal lab data with external resources in a Parasite Knowledge Base (PKB), which has the ability to query across these resources in a unified manner. The SPSE includes Web Ontology Language (OWL)-based ontologies, experimental data with its provenance information represented using the Resource Description Format (RDF), and a visual querying tool, Cuebee, that features integrated use of Web services. We demonstrate the use and benefit of SPSE using example queries for identifying gene knockout targets of Trypanosoma cruzi for vaccine development. Answers to these queries involve looking up multiple sources of data, linking them together and presenting the results. Conclusion/Significance The SPSE facilitates parasitologists in leveraging the growing, but disparate, parasite data resources by offering an integrative platform that utilizes Semantic Web techniques, while keeping their workload increase minimal.

Nursing Interruptions in a Trauma Intensive Care Unit: A Prospective Observational Study

OBJECTIVE The aims of this study were to identify and analyze elements that affect duration of an interruption and likelihood of activity switch as experienced by nurses in an ICU. BACKGROUND Although interruptions in the ICU impact patient safety, little is known regarding the complex situations that drive them. METHODS RNs were observed in a 23-bed surgical ICU. We observed 206 interruptions, and analyzed for duration and activity switch. RESULTS RNs were interrupted on the average every 21.8 minutes. Attending physicians/residents caused fewer, but longer, interruptions to the RN. Longer interruptions were more likely to result in an activity switch. During complex situations such as when an RN is documenting, interruptions by a physician led to longer durations. Interruptions by a device led to higher switches. CONCLUSIONS A deeper understanding of individual factors and their complex interactions related to interruptions experienced by ICU RNs are vital to understanding the clinical significance of these interruptions and intervention design.

A Novel Approach using Liquid Embolic Agent for the Treatment of Pancreatic-Cutaneous Fistulas: Report of a Case

Highlights • Novel approach for treating pancreatic-cutaneous fistulas developed post-pancreaticoduodenectomy.• Use of liquid embolic agent to treat a high-output pancreatic-cutaneous fistula after a Whipple procedure, which to the best of our knowledge, has not been performed before.• Minimally invasive treatment for a difficult problem that often results in additional surgery or prolonged drainage and TPN.