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Biomedical subjects

Kenneth Williams

Publications and source records attributed to Kenneth Williams.

At least 19 recordsLinked to original sources
PubMed2006

Characterization of lymphocytic infiltrates in progressive multifocal leukoencephalopathy: co-localization of CD8(+) T cells with JCV-infected glial cells.

We characterized inflammatory infiltrates in archival brain biopsy and autopsy samples from 26 HIV(+) and 20 HIV(-) patients with progressive multifocal leukoencephalopathy (PML). The predominant inflammatory cells were CD8(+) T lymphocytes. We defined CD8(+) T cell distribution with regard to JCV-infected glial cells, PML lesions and the extent of demyelination. In most samples from either HIV(+) and HIV(-) patients, we found positive correlations between the parenchymal CD8(+) T cells and JCV-infected glial cells and conversely, negative correlations between the perivascular CD8(+) T cells and JCV-infected glial cells in the surrounding brain. Most of these correlations remained significant after accounting for the degree of demyelination and location of the cells relative to lesions. Moreover, high numbers of CD8(+) T cells were found within and at the border of active PML lesions. These results suggest that CD8(+) T cells are primarily associated with JCV-infected glial cells in most PML cases and that an active ongoing recruitment of CD8(+) T cells and possibly viral antigen-specific retention could occur. These observations are discussed in the context of the recent evidence of PML in multiple sclerosis and Crohn's patients treated with natalizumab, underscoring the role of CD8(+) T lymphocytes in continued immunosurveillance of the CNS.

Adult↗
PubMed2006

CD163 identifies perivascular macrophages in normal and viral encephalitic brains and potential precursors to perivascular macrophages in blood.

Perivascular macrophages are uniquely situated at the intersection between the nervous and immune systems. Although combined myeloid marker detection differentiates perivascular from resident brain macrophages (parenchymal microglia), no single marker distinguishes perivascular macrophages in humans and mice. Here, we present the macrophage scavenger receptor CD163 as a marker for perivascular macrophages in humans, monkeys, and mice. CD163 was primarily confined to perivascular macrophages and populations of meningeal and choroid plexus macrophages in normal brains and in brains of humans and monkeys with human immunodeficiency virus or simian immunodeficiency virus (SIV) encephalitis. Scattered microglia in SIV encephalitis lesions and multinucleated giant cells were also CD163 positive. Consistent with prior findings that perivascular macrophages are primary targets of human immunodeficiency virus and SIV, all SIV-infected cells in the brain were CD163 positive. Using fluorescent dyes that definitively and selectively label perivascular macrophages in vivo, we confirmed that dye-labeled simian perivascular macrophages were CD163 positive and able to repopulate the central nervous system within 24 hours. Flow cytometric studies demonstrated a subset of monocytes (CD163(+)CD14(+)CD16(+)) that were immunophenotypically similar to brain perivascular macrophages. These findings recognize CD163(+) blood monocytes/macrophages as a source of brain perivascular macrophages and underscore the utility of this molecule in studying the biology of perivascular macrophages and their precursors in humans, monkeys, and mice.

Animals↗
PubMed2005

Detecting and aligning peaks in mass spectrometry data with applications to MALDI.

In this paper, we address the peak detection and alignment problem in the analysis of mass spectrometry data. To deal with the peak redundancy problem existing in the MALDI data acquired in the reflectron mode, we propose to use the amplitude modulation technique in peak detection. The alignment of two peak sets is formulated as a non-rigid registration problem and is solved using a robust point matching (RPM) approach. To align multiple peak sets, we first use a super set method to find a common peak set among all peak sets as a standard and then align all peak sets to the standard using the robust point matching approach in a sequential manner (i.e. We align only one peak set to the standard each time, thus reducing the multiple peak set alignment problem to a simpler two peak set alignment problem). Experimental results from a study of ovarian cancer data set show that the quantitative cross-correlation coefficients among technical replicates are increased after peak alignment. Additional comparisons also demonstrate that our method has a similar performance as the hierarchical clustering method, although the implementations of these methods are different.

Female↗
PubMed2005

Magnetic resonance spectroscopy reveals that activated monocytes contribute to neuronal injury in SIV neuroAIDS.

Difficulties in understanding the mechanisms of HIV neuropathogenesis include the inability to study dynamic processes of infection, cumulative effects of the virus, and contributing host immune responses. We used H magnetic resonance spectroscopy and studied monocyte activation and progression of CNS neuronal injury in a CD8 lymphocyte depletion model of neuroAIDS in SIV-infected rhesus macaque monkeys. We found early, consistent neuronal injury coincident with viremia and SIV infection/activation of monocyte subsets and sought to define the role of plasma virus and monocytes in contributing to CNS disease. Antiretroviral therapy with essentially non-CNS-penetrating agents resulted in slightly decreased levels of plasma virus, a significant reduction in the number of activated and infected monocytes, and rapid, near-complete reversal of neuronal injury. Robust macrophage accumulation and productive virus replication were found in brains of infected and CD8 lymphocyte-depleted animals, but no detectable virus and few scattered infiltrating macrophages were observed in CD8 lymphocyte-depleted animals compared with animals not receiving antiretroviruses that were sacrificed at the same time after infection. These results underscore the role of activated monocytes and monocyte infection outside of the brain in driving CNS disease.

AIDS Dementia Complex↗
PubMed2005

In vivo, nucleoside reverse-transcriptase inhibitors alter expression of both mitochondrial and lipid metabolism genes in the absence of depletion of mitochondrial DNA.

BACKGROUND: Nucleoside reverse-transcriptase inhibitors (NRTIs), which are used to treat human immunodeficiency virus (HIV) infection, can cause mitochondrial dysfunction and have been associated with lipoatrophy. The effects of this mitochondrial dysfunction on lipid metabolism, at a molecular level in vivo, have not been described. METHODS: We examined early changes (by 2 weeks after initiation of therapy) in expression of mitochondrial and nuclear genes in adipose tissue from 20 HIV-negative subjects randomized to receive dual-NRTI therapy (zidovudine/lamivudine or stavudine/lamivudine) for 6 weeks. RESULTS: We observed decreased transcription of mitochondrial (mt) RNA without significant depletion of mtDNA. Decreases in mtRNA coincided with simultaneous up-regulation of nuclear genes involved in transcriptional regulation of mtRNA (NRF1 and TFAM) and oxidation of fatty acids (PPARA and LPL), whereas PPARG, which is important for differentiation of adipose tissue, was down-regulated. Many nuclear changes correlated with changes in peroxisome proliferator-activated receptor-gamma coactivator-1 (PGC1), suggesting a central role for PGC1 in nuclear responses to mitochondrial dysfunction. Expression of peripheral blood monocyte mtRNA also decreased, suggesting that monocytes may be surrogates for NRTI-induced mitochondrial dysfunction in other tissues. CONCLUSIONS: Independent of HIV, NRTIs decrease transcription of mtRNA in vivo. The absence of depletion of mtDNA suggests that NRTIs cause mitochondrial dysfunction by means other than through inhibition of DNA polymerase- gamma , whereas disruption of expression of lipid metabolism genes offers an explanation for NRTI-induced lipoatrophy.

Adipose Tissue↗
PubMed2005

A glial endogenous cannabinoid system is upregulated in the brains of macaques with simian immunodeficiency virus-induced encephalitis.

Recent evidence supports the notion that the endocannabinoid system may play a crucial role in neuroinflammation. We explored the changes that some elements of this system exhibit in a macaque model of encephalitis induced by simian immunodeficiency virus. Our results show that profound alterations in the distribution of specific components of the endocannabinoid system occur as a consequence of the viral infection of the brain. Specifically, expression of cannabinoid receptors of the CB2 subtype was induced in the brains of infected animals, mainly in perivascular macrophages, microglial nodules, and T-lymphocytes, most likely of the CD8 subtype. In addition, the endogenous cannabinoid-degrading enzyme fatty acid amide hydrolase was overexpressed in perivascular astrocytes as well as in astrocytic processes reaching cellular infiltrates. Finally, the pattern of CB1 receptor expression was not modified in the brains of infected animals compared with that in control animals. These results resemble previous data obtained in Alzheimer's disease human tissue samples and suggest that the endocannabinoid system may participate in the development of human immunodeficiency virus-induced encephalitis, because activation of CB2 receptors expressed by immune cells is likely to reduce their antiviral response and thus could favor the CNS entry of infected monocytes.

Amidohydrolases↗
PubMed2005

YPED: a proteomics database for protein expression analysis.

We have developed the Yale Protein Expression Database (YPED) to address the storage, retrieval, and integrated analysis of proteomics data generated by Yale's Keck Protein Chemistry and Mass Spectrometry Facility. YPED is Web-accessible and currently handles sample requisition, result reporting and sample comparison for ICAT, DIGE and MUDPIT samples. Sample descriptions are compatible with the evolving MIAPE standards. Peptides and proteins identified using Sequest or Mascot are validated with the Trans-Proteomic Pipeline developed at the Institute of Systems Biology and data from the resulting XML file are stored in the database. Researchers can view, subset and download their data through a secure Web interface.

Databases, Protein↗
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

Complement synthesis and activation in the brain of SIV-infected monkeys.

Complement is one of the most critical defence tools against cerebral infections, but uncontrolled complement biosynthesis and activation can induce profound brain tissue damage. To clarify the role of complement in the pathogenesis of AIDS-associated neurological disorders, we analysed the synthesis of complement in the brains of SIV-infected rhesus macaques. Using immunohistochemical staining we could show that the cerebral synthesis of complement factors C1q and C3 was strongly upregulated in SIV-infected monkeys compared to the spontaneous synthesis in uninfected control monkeys. Astrocytes, neurons, microglia, infiltrating macrophages and multinuclear giant cells all contribute to the high amounts of C1q and C3 in the brain. Secreted C1q and C3 are also deposited on the membrane of neurons, a prerequisite for formation of the membrane-driven lytic membrane attack complex. The membrane deposition thus might suggest complement-induced lysis of bystander neurons as a potential mechanism for cell damage during viral infection of the brain.

Animals↗
PubMed2004

Recent advances in neuroproteomics and potential application to studies of drug addiction.

The rapidly growing field of proteomics seeks to track changes in protein expression function that underlie the growth and differentiation of individual cell types, both during normal development and during the onset and progression of disease. Recent years have seen great strides in mRNA expression analysis, and the development of new technologies for protein profiling. However, current methods are limited to analysis of the relative expression level of only a few hundred to perhaps 2000 proteins, well below the ability of DNA microarrays to potentially interrogate the mRNA expression of more than 25,000 genes. Proteomics faces a special challenge in studies of the nervous system, where cellular and sub-cellular architecture is among the most complex in the body. This article presents an overview of current proteomic profiling technologies, reviews the recent use of some of these approaches in studies of the nervous system, and discusses the potential application of neuroproteomics to studies of drug addiction.

Animals↗
PubMed2004

An assessment of public attitudes toward automated external defibrillators.

OBJECTIVE: We assessed the familiarity of the general public with automated external defibrillators (AEDs) and their willingness to use them. METHODS: Shoppers were asked to complete a survey in an AED-equipped suburban shopping mall. RESULTS: 359 surveys were analyzed. Of the participants, 11% were healthcare professionals, 51% had training in CPR or first aid, and 44% had no medical training. Sixty percent were able to define defibrillator adequately. Seventy-one percent stated they would be likely to use an AED to resuscitate a stranger. The most common concerns were fear of using the machine incorrectly (57%) and fear of legal liability (38%). After being told of liability protection from the federal Cardiac Arrest Survival Act, 84% stated they would be likely to use the AED. This increased further to 91% if the participants were given an opportunity to receive training. CONCLUSION: Although a substantial number of people in this setting were willing to use an AED, education regarding legal liability and proper use of the machines increased the reported likelihood of use. Further public education may be necessary to provide optimally effective public access defibrillation programs.

Adult↗
PubMed2004

Identification of T lymphocytes in simian immunodeficiency virus encephalitis: distribution of CD8+ T cells in association with central nervous system vessels and virus.

T lymphocytes are found within brains infected with human immunodeficiency virus (HIV) or simian immunodeficiency virus (SIV) where they are a minor, but consistently identified, population. However, little analysis of their phenotypes has been done, and questions concerning whether or not they are viral antigen specific has not been thoroughly examined. We investigated the central nervous system (CNS) of SIV-infected rhesus macaques to identify T-lymphocyte subsets in relation to virus-infected cells and brain microvessels. We have found that a sensitive antigen-retrieval technique greatly enhanced immunohistochemical detection of CD4+ and CD8+ T lymphocytes in control studies. In encephalitic brains of SIV-infected monkeys with acquired immunodeficiency syndrome (AIDS), we found a significant accumulation of CD8+ T lymphocytes but little-to-no accumulation of CD4+ T lymphocytes. CD4+ cells, when detected, were mostly monocyte/macrophages closely associated with CNS vessels. Using a combination of in situ hybridization for SIV RNA, and immunohistochemistry for CD8+ T lymphocytes and/or Glut-1 for endothelial cells on brain microvessels, we found CD8+ T lymphocytes with an angiocentric distribution often adjacent to virus-infected cells. In the CNS of animals with SIV encephalitis, there was a trend of CD8+ T lymphocytes that were not directly juxtaposed with CNS vessels. These data suggest that in brains of SIV-infected monkeys and HIV-infected humans, CD8+ T lymphocytes traffic to and are retained in the CNS in an angiocentric and possibly antigen-specific manner.

Animals↗
PubMed2003

Comparison of statistical methods for classification of ovarian cancer using mass spectrometry data.

MOTIVATION: Novel methods, both molecular and statistical, are urgently needed to take advantage of recent advances in biotechnology and the human genome project for disease diagnosis and prognosis. Mass spectrometry (MS) holds great promise for biomarker identification and genome-wide protein profiling. It has been demonstrated in the literature that biomarkers can be identified to distinguish normal individuals from cancer patients using MS data. Such progress is especially exciting for the detection of early-stage ovarian cancer patients. Although various statistical methods have been utilized to identify biomarkers from MS data, there has been no systematic comparison among these approaches in their relative ability to analyze MS data. RESULTS: We compare the performance of several classes of statistical methods for the classification of cancer based on MS spectra. These methods include: linear discriminant analysis, quadratic discriminant analysis, k-nearest neighbor classifier, bagging and boosting classification trees, support vector machine, and random forest (RF). The methods are applied to ovarian cancer and control serum samples from the National Ovarian Cancer Early Detection Program clinic at Northwestern University Hospital. We found that RF outperforms other methods in the analysis of MS data.

Algorithms↗
PubMed2003

Comparing protein abundance and mRNA expression levels on a genomic scale.

Attempts to correlate protein abundance with mRNA expression levels have had variable success. We review the results of these comparisons, focusing on yeast. In the process, we survey experimental techniques for determining protein abundance, principally two-dimensional gel electrophoresis and mass-spectrometry. We also merge many of the available yeast protein-abundance datasets, using the resulting larger 'meta-dataset' to find correlations between protein and mRNA expression, both globally and within smaller categories.

Animals↗
PubMed2003

Monocyte/macrophage traffic in HIV and SIV encephalitis.

This short review focuses on the role of central nervous system (CNS) perivascular macrophages as targets of productive infection of the CNS. Data discussed include the importance of these cells as early targets of infection and their productive infection with AIDS. Many of the immune molecules on perivascular macrophages are also found on subsets of blood monocyte/macrophages, some of which are expanded during human immunodeficiency virus (HIV) infection. These observations paired with the known bone marrow (BM) origin of perivascular macrophages and the BM as a site of HIV infection underscore the importance of the study of monocyte populations in the BM and blood, which are activated and infected as a source of virus that enters the CNS. Data presented and discussed herein suggest a role of HIV-infected BM-derived monocytes as "Trojan horse" cells that traffic to the CNS to become perivascular macrophages. The study of such cells including their timing of infection, activation, and traffic and the role of HIV-specific immune responses controlling their accumulation in the CNS warrant study with regard to CNS neuropathogenesis.

AIDS Dementia Complex↗
PubMed2003

Rhode Island Disaster Initiative.

In summary, RIDI is a multi-year research project to identify and develop solutions to some of the challenges posed by disaster response, with a focus on WMD incidents. September 11, 2001, changed the RIDI timeline with increased pressure to produce tangible results and recommendations rapidly. Phase 1 was an effort to identify problems and potential solutions through vulnerability assessment, literature review and expert panel discussion. Many disaster response "solutions" may fail because of a rush to use untested equipment or processes. RIDI is working cooperatively with other Rhode Island disaster experts to avoid these failures. Informed by Phase 1, RIDI Phase 2 will carefully and progressively test potential "solutions" during research trial disaster drills. Only after research can RIDI identify best practices in disaster response. As RIDI progresses to Phase 3, the demonstration project phase, specific improvements are expected in Rhode Island's readiness for disaster. A main feature of Phase 3 is use of a RIDI demonstration vehicle to bring identified solutions to the scene as requested by Rhode Island EMS agencies. Together with others working to improve Rhode Island readiness for disaster threats, RIDI hopes to improve the outcome for patients and providers in Rhode Island as they face the current disaster threats.

Computer Systems↗
PubMed2002

Proliferating cellular nuclear antigen expression as a marker of perivascular macrophages in simian immunodeficiency virus encephalitis.

Brain perivascular macrophages are a major target of simian immunodeficiency virus (SIV) infection in rhesus macaques and HIV infection in humans. Perivascular macrophages are distinct from parenchymal microglia in their location, morphology, expression of myeloid markers, and turnover in the CNS. In contrast to parenchymal microglia, perivascular macrophages are continuously repopulated by blood monocytes, which undergo maturation to macrophages on entering the central nervous system (CNS). We studied differences in monocyte/macrophages in vivo that might account for preferential infection of perivascular macrophages by SIV. In situ hybridization for SIV and proliferating cellular nuclear antigen (PCNA) immunohistochemistry demonstrated that SIV-infected and PCNA-positive cells were predominantly found in perivascular cuffs of viremic animals and in histopathological lesions that characterize SIV encephalitis (SIVE) in animals with AIDS. Multilabel techniques including double-label immunohistochemistry and combined in situ hybridization and immunofluorescence confocal microscopy revealed numerous infected perivascular macrophages that were PCNA-positive. Outside the CNS, SIV-infected, PCNA-expressing macrophage subpopulations were found in the small intestine and lung of animals with AIDS. While PCNA is used as a marker of cell proliferation it is also strongly expressed in non-dividing cells undergoing DNA synthesis and repair. Therefore, more specific markers for cell proliferation including Ki-67, topoisomerase IIalpha, and bromodeoxyuridine (BrdU) incorporation were used which indicated that PCNA-positive cells within SIVE lesions were not proliferating. These observations are consistent with perivascular macrophages as terminally differentiated, non-dividing cells and underscores biological differences that could potentially define mechanisms of preferential, productive infection of perivascular macrophages in the rhesus macaque model of neuroAIDS. These studies suggest that within CNS and non-CNS tissues there exist subpopulations of macrophages that are SIV-infected and express PCNA.

Animals↗