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Biomedical subjects

Kevin White

Publications and source records attributed to Kevin White.

11 recordsLinked to original sources
PubMed2006

Intraoperative adverse events and related postoperative complications in spine surgery: implications for enhancing patient safety founded on evidence-based protocols.

STUDY DESIGN: Prospective observational study. OBJECTIVE: To assess the incidence and clinical consequence of intraoperative adverse events from a wide variety of spinal surgical procedures. SUMMARY OF BACKGROUND DATA: In this study, adverse events were defined as any unexpected or undesirable event(s) occurring as a result of spinal surgery. A complication was defined as a disease or disorder, which, as a consequence of a surgical procedure, will negatively affect the outcome of the patient. We hypothesized that most adverse events would not result in complications that would be normally flagged through traditional practice audit approaches. By defining the incidence and types of adverse events seen in a spine surgical practice, we hope to develop preventative approaches to enhance patient safety. METHODS: All postoperative clinical sequelae (i.e., complications) were prospectively identified, classified as to type, and graded (0 [none] to IV [death]) in 700 consecutive patients who underwent spine surgery (excluding > 300-day surgery microdiscectomies) at a university center from January 2002 to June 2003. To confirm data accuracy and assess the clinical sequelae of any adverse events, the medical records of these 700 patients were reviewed. RESULTS: The overall incidence of intraoperative adverse events was 14% (98/700). A total of 23 adverse events led to postoperative clinical sequelae for an overall intraoperative complication incidence of 3.2% (23/700). Specific adverse events included dural tears (n = 58), spinal instrumentation-related events (n = 12), blood loss exceeding 5000 mL (n = 10), anesthesia/medical (n = 4), suspected or actual vertebral artery injury (n = 3), approach-related events (n = 3), esophageal/pharyngeal injury (n = 2), and miscellaneous (n = 6). CONCLUSIONS: Adverse events can frequently occur (14%) during spinal surgery, however, the majority (76.5%) are not associated with complications. Improved patient safety can only be maximized by independent practice audit and the development of prospective methods to record adverse event data so that enhanced, evidence-based, clinical protocols can be developed.

Clinical Protocols↗
PubMed2004

A high productivity/low maintenance approach to high-performance computation for biomedicine: four case studies.

The rapid advances in high-throughput biotechnologies such as DNA microarrays and mass spectrometry have generated vast amounts of data ranging from gene expression to proteomics data. The large size and complexity involved in analyzing such data demand a significant amount of computing power. High-performance computation (HPC) is an attractive and increasingly affordable approach to help meet this challenge. There is a spectrum of techniques that can be used to achieve computational speedup with varying degrees of impact in terms of how drastic a change is required to allow the software to run on an HPC platform. This paper describes a high- productivity/low-maintenance (HP/LM) approach to HPC that is based on establishing a collaborative relationship between the bioinformaticist and HPC expert that respects the former's codes and minimizes the latter's efforts. The goal of this approach is to make it easy for bioinformatics researchers to continue to make iterative refinements to their programs, while still being able to take advantage of HPC. The paper describes our experience applying these HP/LM techniques in four bioinformatics case studies: (1) genome-wide sequence comparison using Blast, (2) identification of biomarkers based on statistical analysis of large mass spectrometry data sets, (3) complex genetic analysis involving ordinal phenotypes, (4) large-scale assessment of the effect of possible errors in analyzing microarray data. The case studies illustrate how the HP/LM approach can be applied to a range of representative bioinformatics applications and how the approach can lead to significant speedup of computationally intensive bioinformatics applications, while making only modest modifications to the programs themselves.

Amino Acid Sequence↗
PubMed2004

Exploring the portability of informatics capabilities from a clinical application to a bioscience application.

This report describes XDesc (eXperiment Description), a pilot project that serves as a case study exploring the degree to which an informatics capability developed in a clinical application can be ported for use in the biosciences. In particular, XDesc uses the Entity-Attribute-Value database implementation (including a great deal of metadata-based functionality) developed in TrialDB, a clinical research database, for use in describing the samples used in microarray experiments stored in the Yale Microarray Database (YMD). XDesc was linked successfully to both TrialDB and YMD, and was used to describe the data in three different microarray research projects involving Drosophila. In the process, a number of new desirable capabilities were identified in the bioscience domain. These were implemented on a pilot basis in XDesc, and subsequently "folded back" into TrialDB itself, enhancing its capabilities for dealing with clinical data. This case study provides a concrete example of how informatics research and development in clinical and bioscience domains has the potential for synergy and for cross-fertilization.

Clinical Medicine↗
PubMed2003

Results of triple therapy with interferon-alpha, cytarabine, and homoharringtonine, and the impact of adding imatinib to the treatment sequence in patients with Philadelphia chromosome-positive chronic myelogenous leukemia in early chronic phase.

BACKGROUND: Before the discovery of imatinib mesylate, a Bcr-Abl selective tyrosine kinase inhibitor, three agents, interferon-alpha (IFN-alpha), cytarabine (ara-C), and homoharringtonine (HHT), had demonstrated activity against Philadelphia chromosome (Ph)-positive chronic myelogenous leukemia (CML) as single agents and in couplet combinations. The goals of the current study were to evaluate the efficacy of the triple combination regimen with IFN-alpha, ara-C, and HHT in newly diagnosed Ph-positive CML and to assess the impact of the added sequential therapy with imatinib on overall prognosis. METHODS: Ninety patients with Ph-positive CML in early chronic phase received the triple regimen. Therapy consisted of 5 million units (MU)/m(2) IFN-alpha subcutaneously (s.c. daily, ara-C 10 mg s.c. daily, and HHT 2.5 mg/m(2) by continuous infusion over 24 hours daily x 5 every month. After a median duration of 16.5 months of therapy, 78 patients had their therapy changed to 400 mg orally administered imatinib daily. RESULTS: With the triple regimen, 85 patients (94%) achieved complete hematologic response and 67 patients (74%) had a cytogenetic response (Ph suppression to < or = 90%) which was complete (Ph 0%) in 20 patients (22%) and major in 42 patients (46%). Myelosuppression was significant, resulting in considerable reductions in the dose schedules. After 12 months of therapy, the median IFN-alpha dose was 1.6 MU/m(2) daily, the median ara-C dose was 1.85 mg daily, and the median number of HHT days was 2 every month. Only three patients developed blastic phase while receiving the triple regimen. With the change to imatinib therapy, currently 57 patients (63%) are in complete cytogenetic response and 69 patients (76%) in major cytogenetic response. With a median follow-up time of 46 months for the total study group, the estimated 5-year survival rate was 88%, and only 8 patients (9%) to date have developed blastic phase. CONCLUSIONS: The sequence of IFN-alpha, ara-C, and HHT followed by imatinib (imposed by the discovery of the latter drug) resulted in an estimated 5-year survival rate of 88%. This finding suggests that imatinib combination regimens may improve the prognosis in CML.

Adult↗
PubMed2003

Prediction of initial cytogenetic response for subsequent major and complete cytogenetic response to imatinib mesylate therapy in patients with Philadelphia chromosome-positive chronic myelogenous leukemia.

BACKGROUND: Obtaining a major (Philadelphia chromosome [Ph] of < 35%) or a complete cytogenetic response (Ph of 0%) has been associated with excellent long-term survival. Cytogenetic response may continue to improve with therapy. Because early allogeneic stem cell transplantation (SCT) may be associated with a better outcome, early parameters predicting for subsequent cytogenetic responses would optimize the treatment decision-making. METHODS: The current study was performed to analyze whether early cytogenetic responses may be predictive of later major or complete cytogenetic responses to imatinib mesylate therapy in patients with Ph-positive chronic myelogenous leukemia (CML). RESULTS: Two hundred sixty-one patients with Ph-positive, chronic-phase CML after failure with interferon therapy who were treated with imatinib mesylate therapy were analyzed. A persistence of 100% Ph-positive cells after > or = 6 months of imatinib mesylate therapy was associated with a major cytogenetic response rate of 9-13% and a complete cytogenetic response rate of 0-4%. However, a minor cytogenetic response after 3-12 months of therapy still was associated with high rates of major (68-83%) or complete (35-54%) cytogenetic response rates. CONCLUSIONS: Patients with Ph-positive, chronic-phase CML who have persistent 100% Ph-positive disease after > or = 6 months of imatinib mesylate therapy may be offered allogeneic SCT or considered for alternative investigational therapies.

Benzamides↗
PubMed2002

YMD: a microarray database for large-scale gene expression analysis.

The use of microarray technology to perform parallel analysis of the expression pattern of a large number of genes in a single experiment has created a new frontier of medical research. The vast amount of gene expression data generated from multiple microarray experiments requires a robust database system that allows efficient data storage, retrieval, secure access, data dissemination, and integrated data analyses. To address the growing needs of microarray researchers at Yale and their collaborators, we have built the Yale Microarray Database (YMD). YMD is Web-accessible with the following features: (i) a Web program that tracks DNA samples between source plates and arrays, (ii) the capability of finding common genes/clones across different array platforms, (iii) an image file server, (iv) laboratory-based user management and access privileges, (v) project management, (vi) template data entry, (vii) linking gene expression data to annotation databases for functional analysis. YMD is currently being used on a pilot basis by several laboratories for different organisms and array platforms.

Databases, Nucleic Acid↗
PubMedDate not supplied

A dynamic approach to mapping coordinates between microplates and microarrays.

The retrieval of useful data from spotted microarray slides requires keeping track of which microplate wells and DNA sample corresponds to each spot on each array slide. Existing approaches are closely coupled with the type of arrayer in use and are computer operating-system-specific. To support the microarray researcher community at large who use different arrayers and computer platforms, increased flexibility, generality, and portability of these approaches are required. In this paper, we describe a general algorithm that correlates the well positions of DNA samples in each microplate to the positions of the spots on each array slide. Based on this algorithm, we have implemented a flexible and platform-independent program named MicroArray Convolutor (MAC) that provides a Web solution allowing the user to: (a) import a text file that identifies the DNA samples and their well locations, (b) select a transformation method that converts data in 96-well plate format into 384-well plate format, and (c) specify the output format of the array lists dependant on the configuration of the array platform as well as the downstream analysis software chosen for the array. MAC and its source code can be accessed via the following Web address: http://ymd.med.yale.edu/kei-cgi/kc_mac_dev8.pl.

Algorithms↗