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Biomedical subjects

Peter White

Publications and source records attributed to Peter White.

At least 19 recordsLinked to original sources

Genetic Determinants of Early Heart Failure in Hypoplastic Left Heart Syndrome: A Prospective NC-DEFINE Study.

BACKGROUND: Survivors of hypoplastic left heart syndrome (HLHS), the most severe form of congenital heart disease, are at high risk for heart failure (HF). HF in early life is a major contributor to mortality in this vulnerable population. However, reliable approaches to identify infants at highest risk for early HF are currently lacking. OBJECTIVES: The purpose of this study was to evaluate whether ultra-rare variants in cardiomyopathy-associated genes are associated with HF risk in HLHS. METHODS: Neonates with HLHS were prospectively enrolled within the first 21 days of life at Duke University Health System. Children and adults with HLHS who were older than 21 days were enrolled from Duke University Health System and the University of North Carolina into an ambispective cohort. External HLHS cohorts from Nationwide Children's Hospital and Vanderbilt University Medical Center were evaluated to assess for reproducibility across institutions. Participants underwent genome sequencing, and ultra-rare variants in dilated cardiomyopathy-associated genes (minor allele frequency &#x2264;0.01%) were evaluated. The primary outcome was HF, categorized as severe (ventricular assist device implantation, heart transplantation, or death) or medically managed (reduced systemic ventricular ejection fraction and/or HF diagnosis requiring initiation or escalation of HF therapy). Associations between variant status and HF risk were assessed using Cox regression. RESULTS: Among 35 neonates in the prospective cohort, 7 (20.0%) developed severe HF, 10 (28.6%) developed medically managed HF, and 18 (51.4%) remained HF free. The presence of a likely pathogenic/pathogenic variant was associated with a marked 9-fold increased risk of severe HF compared with genotype-negative individuals (P = 0.02). Most severe HF events occurred within the first month of life (67%). Similar associations between likely pathogenic/pathogenic variants and severe HF were observed in the Nationwide Children's Hospital and Vanderbilt University Medical Center cohorts (11- and 3-fold increased risk, respectively; all P < 0.05). Associations were attenuated in the ambispective cohort (all P > 0.05), which consisted of individuals significantly older than the prospective cohort (P < 0.0001). CONCLUSIONS: This study provides the first prospective evidence linking dilated cardiomyopathy-associated variants to early-onset HF in HLHS. These findings suggest that genetic variation may contribute to myocardial vulnerability in HLHS, highlighting the potential for genetic screening to enable early risk stratification and guide precision medicine approaches in this high-risk population.

Humans↗

PheBee: A Graph-Aware System for Scalable, Traceable, and Semantic Phenotyping.

OBJECTIVES: Phenotype-driven workflows in clinical and translational research require standardized ontology-based representation, ontology-aware cohort discovery, and provenance inspection for each assertion. Existing approaches optimize either for semantic traversal or scalable batch analytics, but not both. We describe PheBee, a hybrid system that links semantic assertions to scalable evidence storage via a deterministic identifier, preserving provenance while supporting ontology-aware discovery at cohort scale. MATERIALS AND METHODS: PheBee represents phenotype assertions in a knowledge graph as ontology-linked nodes with clinical modifier context (e.g., negated, family history), and stores supporting evidence records in a scalable row-oriented evidence table for cohort-scale access. The two layers are connected by a deterministic identifier enabling stable joins across repeated ingestions without duplicating high-volume evidence in the graph. We evaluated PheBee using synthetic datasets designed to exercise end-to-end ingestion and query workflows. RESULTS: Functional evaluation validated hierarchical term expansion, qualifier-aware retrieval, duplicate-free assertion handling under re-ingestion, and privacy-conscious management of subjects shared across multiple research projects. At scale (10,000 subjects producing 12M evidence records) PheBee completed ingestion in ~30 minutes and responded to interactive queries within 6 seconds under concurrent load. DISCUSSION: PheBee exposes a unified API for ontology-aware cohort discovery with hierarchical term expansion, subject-centric retrieval of phenotypes and clinical modifiers, and evidence and provenance queries. Its data model aligns with GA4GH Phenopackets, facilitating interoperability with phenotype exchange standards. CONCLUSION: By combining ontology-aware semantics with scalable, provenance-bearing evidence storage, PheBee provides a practical open-source foundation for phenotype-driven research workflows that demand both semantic precision and cohort-scale traceability.

cohort studies↗

Functional genomics of the beta-cell: short-chain 3-hydroxyacyl-coenzyme A dehydrogenase regulates insulin secretion independent of K+ currents.

Recent advances in functional genomics afford the opportunity to interrogate the expression profiles of thousands of genes simultaneously and examine the function of these genes in a high-throughput manner. In this study, we describe a rational and efficient approach to identifying novel regulators of insulin secretion by the pancreatic beta-cell. Computational analysis of expression profiles of several mouse and cellular models of impaired insulin secretion identified 373 candidate genes involved in regulation of insulin secretion. Using RNA interference, we assessed the requirements of 10 of these candidates and identified four genes (40%) as being essential for normal insulin secretion. Among the genes identified was Hadhsc, which encodes short-chain 3-hydroxyacyl-coenzyme A dehydrogenase (SCHAD), an enzyme of mitochondrial beta-oxidation of fatty acids whose mutation results in congenital hyperinsulinism. RNA interference-mediated gene suppression of Hadhsc in insulinoma cells and primary rodent islets revealed enhanced basal but normal glucose-stimulated insulin secretion. This increase in basal insulin secretion was not attenuated by the opening of the KATP channel with diazoxide, suggesting that SCHAD regulates insulin secretion through a KATP channel-independent mechanism. Our results suggest a molecular explanation for the hyperinsulinemia hypoglycemic seen in patients with SCHAD deficiency.

Animals↗

EPConDB: a web resource for gene expression related to pancreatic development, beta-cell function and diabetes.

EPConDB (http://www.cbil.upenn.edu/EPConDB) is a public web site that supports research in diabetes, pancreatic development and beta-cell function by providing information about genes expressed in cells of the pancreas. EPConDB displays expression profiles for individual genes and information about transcripts, promoter elements and transcription factor binding sites. Gene expression results are obtained from studies examining tissue expression, pancreatic development and growth, differentiation of insulin-producing cells, islet or beta-cell injury, and genetic models of impaired beta-cell function. The expression datasets are derived using different microarray platforms, including the BCBC PancChips and Affymetrix gene expression arrays. Other datasets include semi-quantitative RT-PCR and MPSS expression studies. For selected microarray studies, lists of differentially expressed genes, derived from PaGE analysis, are displayed on the site. EPConDB provides database queries and tools to examine the relationship between a gene, its transcriptional regulation, protein function and expression in pancreatic tissues.

Animals↗

Novel genes identified by manual annotation and microarray expression analysis in the pancreas.

The mouse PancChip, a microarray developed for studying endocrine pancreatic development and diabetes, represents over 13,000 cDNAs. After computationally assigning the cDNAs on the array to known genes, manual curation of the remaining sequences identified 211 novel transcripts. In microarray experiments, we found that 196 of these transcripts were expressed in total pancreas and/or pancreatic islets. Of 50 randomly selected clones from these 196 transcripts, 92% were confirmed as expressed by qRT-PCR. We evaluated the coding potential of the novel transcripts and found that 74% of the clones had low coding potential. Since the transcripts may be partial mRNAs, we examined their translated proteins for transmembrane or signal peptide domains and found that about 40 proteins had one of these predicted domains. Interestingly, when we investigated the novel transcripts for their overlap with noncoding microRNAs, we found that 1 of the novel transcripts overlapped a known microRNA gene.

Animals↗

PANDER-induced cell-death genetic networks in islets reveal central role for caspase-3 and cyclin-dependent kinase inhibitor 1A (p21).

PANcreatic DERived factor is an islet-specific cytokine that promotes apoptosis in primary islets and islet cell lines. To elucidate the genetic mechanisms of PANDER-induced cell death we performed expression profiling using the mouse PancChip version 5.0 in conjunction with Ingenuity Pathway Analysis. Murine islets were treated with PANDER and differentially expressed genes were identified at 48 and 72 h post-treatment. 64 genes were differentially expressed in response to PANDER treatment. 22 genes are associated with cell death. In addition, the genes with the highest fold change were linked with cell death or apoptosis. The most significantly affected gene at 48 h was the downregulated cyclin-dependent kinase inhibitor 1A (CDKN1A or p21). Approximately half of the genes impacted at 72 h were linked to cell death. Cell death differentially expressed genes were confirmed by quantitative RT-PCR. Further analysis identified cell death genetic networks at both time points with 21 of the 22 cell death genes related in various biological pathways. Caspase-3 (CASP3) was biologically linked to CDKN1A in several genetic networks and these two genes were further examined. Elevated cleaved CASP3 levels in PANDER-treated beta-TC3 insulinoma cells were found to abrogate CDKN1A expression. Levels of CDKN1A were not affected in the absence of cleaved CASP3. PANDER-induced downregulation of CDKN1A expression coupled with induced CASP3-activation may serve a central role in islet cell death and offers further insight into the mechanisms of cytokine-induced beta-cell apoptosis.

Animals↗

The synergy of ChemMatrix resin and pseudoproline building blocks renders RANTES, a complex aggregated chemokine.

Traditionally, solid-phase synthesis has relied on polystyrene-based resins for the synthesis of all kinds of peptides. However, due to their high hydrophobicity, these resins have certain limitations, particularly in the synthesis of complex peptides, and in such cases, poly(ethylene glycol) (PEG)-based resins are often found to give superior results. Another powerful strategy for expediting the assembly of complex peptides is to employ pseudoproline dipeptides. These derivatives disrupt the interactions among chains that are usually the cause of poor coupling yields in aggregated sequences. Here we report on an efficient stepwise solid-phase synthesis of RANTES (1-68) by combining the advantages of the totally PEG-based ChemMatrix resin and pseudoproline dipeptides.

Amino Acid Sequence↗

Otomicroscopic findings and systemic interleukin-6 levels in relation to etiologic agent during experimental acute otitis media.

The aim of the present study was to explore whether it was possible to differentiate the clinical course and the otomicroscopic appearance of acute otitis media (AOM) caused by common otitis pathogens in an animal model. Systemic interleukin (IL)-6 levels as early markers for bacterial AOM were also studied. Four groups of rats were inoculated with either Streptococcus pneumoniae, Streptococcus pyogenes, non-typeable Haemophilus influenzae or Moraxella catarrhalis. The animals were monitored by otomicroscopy, photos of the tympanic membrane, cultures and IL-6 detection in serum the following 4 days. The gram-positive S. pneumoniae and S. pyogenes induced severe AOM with opaque effusion behind the tympanic membrane, pronounced dilation of the vessels and spontaneous perforations. The gram-negative H. influenzae and M. catarrhalis induced a less severe infection with cloudy, sometimes foamy effusion, and no spontaneous perforations. With the otomicroscopic findings it was possible to distinguish between infections induced by gram-positive bacteria and gram-negative bacteria. Detection of interleukin-6 in serum appeared to be of limited use for all infections except the pneumococcal AOM, but this needs to be further investigated.

Acute Disease↗

A background to acupuncture and its use in chronic painful musculoskeletal conditions.

This article gives a brief description of the origins of acupuncture and describes some of the underlying philosophy behind this treatment and attempts to place it in context of the traditional Chinese medicine genre within which acupuncture is set. The article then explains the difference between traditional and Western style acupuncture and explains how point selection is made. The use of acupuncture is steadily increasing for a variety of reasons, it is a very safe intervention particularly when compared to conventional treatment and its lack of serious side effects might in part account for some of its popularity. The science behind acupuncture is also explored in terms of its underlying mechanisms and includes pain gate, endogenous opioids, diffuse noxious inhibitory control, serotonin and bioelectricity as possible explanations. The efficacy of acupuncture for a range of chronic musculoskeletal conditions is then explored and it is concluded that acupuncture has a place in the treatment of chronic musculoskeletal pain and in particular osteo-arthritis (OA). Where degenerative conditions are involved, acupuncture clearly cannot provide a 'cure' but can provide symptomatic relief, often over a prolonged period.

Acupuncture↗

Expectancy and belief modulate the neuronal substrates of pain treated by acupuncture.

Both specific and non-specific factors may play a role in acupuncture therapy for pain. We explored the cerebral consequences of needling and expectation with real acupuncture, placebo acupuncture and skin-prick, using a single-blind, randomized crossover design with 14 patients suffering from painful osteoarthritis, who were scanned with positron emission tomography (PET). The three interventions, all of which were sub-optimal acupuncture treatment, did not modify the patient's pain. The insula ipsilateral to the site of needling was activated to a greater extent during real acupuncture than during the placebo intervention. Real acupuncture and placebo (with the same expectation of effect as real acupuncture) caused greater activation than skin prick (no expectation of a therapeutic effect) in the right dorsolateral prefrontal cortex, anterior cingulate cortex, and midbrain. These results suggest that real acupuncture has a specific physiological effect and that patients' expectation and belief regarding a potentially beneficial treatment modulate activity in component areas of the reward system.

Acupuncture↗

Footprints.

Explore the source record for details and available documents.

Biopsy↗

Use of prostate-specific antigen (PSA) isoforms for the detection of prostate cancer in men with a PSA level of 2-10 ng/ml: systematic review and meta-analysis.

OBJECTIVE: Measurement of serum prostate-specific antigen (PSA) for the detection of prostate cancer has poor specificity in men with PSA levels between 2 and 10 ng/ml. It has been suggested that measurement of the ratio of free to total PSA (f/tPSA) or complexed PSA (cPSA) might offer an improvement. We performed a systematic review and meta-analysis to evaluate the diagnostic performance of these tests among men with PSA levels between 2 and 10 ng/ml. METHODS: Data on sensitivity and specificity were extracted from 66 eligible studies. Likelihood ratios and summary receiver operating characteristic curves were estimated and possible sources of heterogeneity between studies examined. RESULTS: Use of the f/tPSA or the cPSA test improved diagnostic performance among men with a total PSA (tPSA) of 2-4 or 4-10 ng/ml compared to tPSA alone. The diagnostic performance of the f/tPSA test was significantly higher in the tPSA range of 4-10 ng/ml compared to a tPSA range of 2-4 ng/ml (p < 0.01); at a sensitivity of 95%, the specificity was 18% in the 4-10 ng/ml tPSA range and 6% in the 2-4 ng/ml tPSA range. Among studies that measured both isoforms, the diagnostic performance of the f/tPSA test and the cPSA was equivalent in both PSA ranges. CONCLUSIONS: The use of the f/tPSA or cPSA test among men with PSA levels between 2 and 10 ng/ml can reduce the number of unnecessary biopsies whilst maintaining a high cancer detection rate.

Humans↗

Hearing loss after "refractory" secretory otitis media.

CONCLUSIONS: The results indicate that SOM of extreme duration, and maybe also the treatment of SOM, are risk factors for developing permanent hearing loss, both conductive and sensorineural. OBJECTIVE: Fluctuating or persisting hearing loss of varying degrees is known to accompany secretory otitis media (SOM). The aim of this study was to detect possible hearing sequelae in young adults who had suffered from "refractory" SOM during childhood. MATERIAL AND MEDTHODS: A total of 33 subjects (age 16-25 years) with previous SOM that had persisted for a mean of 11 years (range 6-19 years) were retrospectively examined at a mean of 18 years after their first myringotomy or tube insertion and compared to 15 healthy controls. The follow-up included audiometric examinations (pure-tone audiometry, distorted speech and impedance audiometry), otomicroscopy and scrutiny of medical records. RESULTS: The SOM group had poorer hearing at all frequencies with the exception of 1.5 kHz in the range 0.125-16 kHz. Those with the greatest number of myringotomies and tube insertions and those with the longest duration of SOM had significantly poorer hearing at high frequencies (8-16 kHz) than those with fewer tube insertions and a shorter duration of SOM. The SOM group scored lower on distorted speech tests than the controls.

Adolescent↗

Course and long-term outcome of 'refractory' secretory otitis media.

OBJECTIVE: The course and the long-term outcome of 'refractory' secretory otitis media (SOM), defined as continuous SOM for more than 6 years, were studied in 52 young patients. They had during childhood been treated for bilateral SOM on average for 12 years (range 6 to 26 years). The mean interval between resolution of SOM and examination was 7 years. METHODS: At follow up the patients' medical records were scrutinized with regards to transmyringeal ventilation tubes, adenoidectomy, sequelae and complications, and a questionnaire was filled in to document other diseases. RESULTS: The onset of SOM showed two peaks, one at the age of one year and one at the age of 3.5 years. Patients whose onset of SOM was related to an episode of acute otitis media (AOM) were younger at SOM onset than those who had no such relation. Otorrhoea and AOM episodes were more frequent during the SOM periods, with blocked or expelled tubes, than during periods with patent tubes. Cholesteatoma were seen in 3 per cent and perforations in 5 per cent of patients. CONCLUSIONS: Extremely long-standing SOM does not necessarily result in myringeal perforation or cholesteatoma to a greater extent than that seen in patients with shorter durations of SOM. However, at follow up one-third of the patients reported hearing impairment and a majority felt discomfort when flying or diving.

Acute Disease↗

Acupuncture versus placebo for the treatment of chronic mechanical neck pain: a randomized, controlled trial.

BACKGROUND: Despite substantial increases in its popularity and use, the efficacy of acupuncture for chronic mechanical neck pain remains unproved. OBJECTIVE: To compare acupuncture and placebo for neck pain. DESIGN: A randomized, single-blind, placebo-controlled, parallel-arm trial with 1-year follow-up. SETTING: The outpatient departments of 2 major hospitals in the United Kingdom, 1999 to 2001. PATIENTS: 135 patients 18 to 80 years of age who had chronic mechanical neck pain. Eleven patients withdrew from treatment, and 124 completed the primary end point. MEASUREMENTS: The primary outcome was pain 1 week after treatment, according to a visual analogue scale. Secondary outcomes were pain at other time points, score on the Neck Disability Index and the Short Form-36, and use of analgesic medications. INTERVENTIONS: Patients were randomly assigned to receive, over 4 weeks, 8 treatments with acupuncture or with mock transcutaneous electrical stimulation of acupuncture points using a decommissioned electroacupuncture stimulation unit. RESULTS: Both groups improved statistically from baseline, and acupuncture and placebo had similar credibility. For the primary outcome (weeks 1 to 5), a statistically significant difference in visual analogue scale score in favor of acupuncture (6.3 mm [95% CI, 1.4 to 11.3 mm]; P = 0.01) was observed between the 2 study groups, after adjustment for baseline pain and other covariates. However, this difference was not clinically significant because it demonstrated only a 12% (CI, 3% to 21%) difference between acupuncture and placebo. Secondary outcomes showed a similar pattern. LIMITATIONS: All treatments were provided by 1 practitioner. Although the control was credible, it did not mimic the process of needling. A nonintervention group was not present to control for regression to the mean. CONCLUSIONS: Acupuncture reduced neck pain and produced a statistically, but not clinically, significant effect compared with placebo. The beneficial effects of acupuncture for pain may be due to both nonspecific and specific effects.

Acetaminophen↗