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At least 55 records · Page 3Linked to original sources
PubMed1998

Dexamethasone treatment prior to reperfusion improves the survival of skin flaps subjected to secondary venous ischaemia.

The potential use of the anti-inflammatory glucocorticoid, dexamethasone, to treat ischaemic skin flaps prior to reperfusion was investigated. Island flaps were raised in rats, subjected to arteriovenous ischaemia for 2 h, normal blood flow for 24 h, secondary venous ischaemia for 4 h and secondary reperfusion for 7 days. This sequence mimics the clinical sequence of free flap transfer followed by a subsequent venous thrombosis. Groups of 10 rats were administered with an intraperitoneal dose of either saline (controls) or dexamethasone (2.5 mg/kg) 30 min before the end of the venous ischaemia. Compared with viability of 70.0% in controls, dexamethasone treatment increased viability significantly to 92.0% (P < 0.01). In skin flap tissue harvested at 24 h reperfusion, dexamethasone treatment resulted in significant attenuation of tissue water content, tissue myeloperoxidase activity and tissue hydroperoxide levels. Thus the protective effect of this agent may be explained by the combined reduction of oedema formation, neutrophil infiltration and free radical production, respectively. We conclude that a single systemic dose of dexamethasone prior to reperfusion may be beneficial in treating skin flaps that have undergone secondary venous ischaemia.

Animals↗
PubMed2005

Fatty infiltration of the liver. Detection and grading using dual T1 gradient echo sequences on clinical MR system.

AIM: To evaluate the relationship between histopathology results and magnetic resonance imaging (MRI) on in and opposed-phase sequences grading of fat deposition within human liver. MATERIALS AND METHODS: In and opposed-phase T1-weighted gradient-echo sequences (double echo time 2.3 ms and 4.6 ms) were performed in 25 patients, using a 1.5-T clinical MR imaging system. Fat/water ratio on in- and opposed-phase images of the liver was compared with pathologically defined degree of steatosis. The signal intensity in the images was acquired with operator-defined regions of interest at the same location in both fat and water images and the ratio was calculated by dividing signal intensity of liver in opposed phased sequence on signal intensity of liver in phased sequence. Fat/water ratio and the degree of steatosis were compared using linear regression. The sensitivity and specificity of opposed-phase for diagnosing steatosis were defined by ROC analysis. Furthermore, a correlation between visual signal intensity variation and the degree of steatosis was assessed using Pearson correlation coefficient. RESULTS: Histology demonstrated fatty liver infiltrations in 81% of specimens. The percentage of fatty hepatocytes was 28 +/- 30%. Fat/water ratio was significantly correlated with the pathologic grading of steatosis (r = 0.816, P < 0.001). The opposed phase MR imaging sensibility and specificity for the diagnosis of hepatic steatosis were respectively 80% and 71%. We obtained a statistically significant correlation between visual SIV and fatty liver grading (P = 0.017). CONCLUSION: We demonstrated a significant correlation between fat/water ratio and histological findings for the detection and grading of fatty liver.

Adipose Tissue↗
PubMed2005

Comparative bioavailability/ bioequivalence of two different sertraline formulations: a randomised, 2-period x 2-sequence, crossover clinical trial in healthy volunteers.

An open-label, randomised, crossover single dose study, using 2 periods x 2 sequences, with a minimum washout period of 4 weeks, was conducted in order to assess the comparative bioavailability of two formulations of sertraline hydrochloride (CAS 79617-96-2) 100 mg tablets. Plasma samples were obtained at intake (baseline) and at +1 h, +2 h, +3 h, +4 h, +5 h, +6 h, +7 h, +8 h, +9 h, +12 h, +24 h, +48 h, +72 h and +96 h post administration. Sertraline plasma concentrations were determined by high pressure liquid chromatography with tandem mass detection (HPLC-MS/MS) and the lower limit of quantification was set at 100.15 pg/mL. Pharmacokinetic parameters used for bioequivalence assessment (AUClast, AUCinf and Cmax) were determined by non-compartmental analysis. Classical 90 % confidence intervals (90CI) were calculated for the overall sample, and for males and females separately, and gender effects were investigated using an appropriate model. The results showed that overall classical 90CI were 84.55-100.32 % for Cmax 86.96-98.68 % for AUClast, and 86.79-98.93 for AUCinf, that is, they were all within the predefined ranges for bioequivalence acceptance. Separate gender analysis showed very similar results for males and females when analysed independently, and no gender effects were detected in bioequivalence analysis (p > 0.05). It may be therefore concluded that the evaluated formulations are bioequivalent in terms of rate and extent of absorption.

Adolescent↗
PubMedDate not supplied

Metal artifact reduction sequence: early clinical applications.

Artifact arising from metal hardware remains a significant problem in orthopedic magnetic resonance imaging. The metal artifact reduction sequence (MARS) reduces the size and intensity of susceptibility artifacts from magnetic field distortion. The sequence, which is based on view angle tilting in combination with increased gradient strength, can be conveniently used in conjunction with any spin-echo sequence and requires no additional imaging time. In patients with persistent pain after femoral neck fracture, the MARS technique allows visualization of marrow adjacent to hip screws, thus enabling diagnosis or exclusion of avascular necrosis. Other applications in the hip include assessment of periprosthetic soft tissues after hip joint replacement surgery, postoperative assessment after resection of bone tumors and reconstruction, and localization of unopacified methyl methacrylate cement prior to hip arthroplasty revision surgery. In the knee, the MARS technique allows visualization of structures adjacent to implanted metal staples, pins, or screws. The technique can significantly improve visualization of periprosthetic bone and soft-tissue structures even in patients who have undergone total knee arthroplasty. In patients with spinal fixation hardware, the MARS technique frequently allows visualization of the vertebral bodies and spinal canal contents. The technique can be helpful after wrist fusion or screw fixation of scaphoid fractures.

Adult↗
PubMed2001

Comparison of antifungal activities and 16S ribosomal DNA sequences of clinical and environmental isolates of Stenotrophomonas maltophilia.

In recent years, the gram-negative bacterium Stenotrophomonas maltophilia has become increasingly important in biotechnology and as a nosocomial pathogen, giving rise to a need for new information about its taxonomy and epidemiology. To determine intraspecies diversity and whether strains can be distinguished based on the sources of their isolation, 50 S. maltophilia isolates from clinical and environmental sources, including strains of biotechnological interest, were investigated. The isolates were characterized by in vitro antagonism against pathogenic fungi and the production of antifungal metabolites and enzymes. Phenotypically the strains showed variability that did not correlate significantly with their sources of isolation. Clinical strains displayed remarkable activity against the human pathogenic fungus Candida albicans. Antifungal activity against plant pathogens was more common and generally more severe from the environmental isolates, although not exclusive to them. All isolates, clinical and environmental, produced a range of antifungal metabolites including antibiotics, siderophores, and the enzymes proteases and chitinases. From 16S ribosomal DNA sequencing analysis, the isolates could be separated into three clusters, two of which consisted of isolates originating from the environment, especially rhizosphere isolates, and one of which consisted of clinical and aquatic strains. In contrast to the results of other recent investigations, these strains could be grouped based on their sources of isolation, with the exception of three rhizosphere isolates. Because there was evidence of nucleotide signature positions within the sequences that are suitable for distinguishing among the clusters, the clusters could be defined as different genomovars of S. maltophilia. Key sequences on the 16S ribosomal DNA could be used to develop a diagnostic method that differentiates these genomovars.

Antibiosis↗
PubMed1999

Abstraction on clinical data sequences: an object-oriented data model and a query language based on the event calculus.

In this work, we deal with temporal abstraction of clinical data. Abstractions are, for example, blood pressure state (e.g. normal, high, low) and trend (e.g. increasing, decreasing and stationary) over time intervals. The goal of our work is to provide clinicians with automatic tools to extract high-level, concise, important features of available collections of time-stamped clinical data. This capability is especially important when the available collections constantly increase in size, as in long-term clinical follow-up, leading to information overload. The approach we propose exploits the integration of the deductive and object-oriented approaches in clinical databases. The main result of this work is an object-oriented data model based on the event calculus to support temporal abstraction. The proposed approach has been validated building the CARDIOTABS system for the abstraction of clinical data collected during echocardiographic tests.

Databases, Factual↗
PubMed2005

A refined long RT-PCR technique to amplify complete viral RNA genome sequences from clinical samples: application to a novel hepatitis C virus variant of genotype 6.

The goal of this study was to adapt a long RT-PCR technique to amplify large PCR fragments from the genome of hepatitis C virus (HCV) isolates using clinical samples. This was done by using a reverse transcriptase devoid of RNase H activity and a mixture of two antibody-bound thermostable polymerases to combine the high processivity of Taq and the high fidelity of Pwo with its 3'-->5' exonuclease activity. Other modifications included gentle handling during RNA extraction, the absence of tRNA and random primers, a two-step reverse transcription procedure to optimize cDNA synthesis, and increasing the annealing temperature for primers. With this approach, the HCV-1 genome (nucleotides 35-9282) was amplified consistently as two overlapping fragments of 5344 and 4675 bp from a pooled chimpanzee plasma sample containing approximately 10(6) genome copies of HCV RNA/ml. Using the conditions that we identified, 96% of the complete genomic sequence of a distinct HCV genotype 6 variant (km45) was determined from less than 300 microl of serum. This method should prove useful for molecular, epidemiological and clinical studies of hepatitis C where samples are limited but complete virus sequence is required, for example, identifying mutational hot spots of HCV under specific clinical conditions.

Animals↗
PubMed2026

Age-related genomic characterization and therapeutic targets in Chinese breast cancer: insights from prospective targeted sequencing and clinical data analysis.

BACKGROUND: In China, breast cancer occurs at a much younger age and has a higher recurrence and mortality rate. However, with changes in lifestyle, there has been a trend towards an older age of breast cancer incidence in Chinese women. There is a paucity of large-scale next-generation sequencing cohorts for the analysis of genomic characterization in these populations and the identification of potential therapeutic targets. METHODS: To address this gap, we performed prospective targeted sequencing of tumor and blood samples from Chinese patients and collected detailed clinical information. We then categorized patients into two groups based on age (<&#x2009;40&#xa0;years, n&#x2009;=&#x2009;637;&#x2009;&#x2265;&#x2009;40&#xa0;years, n&#x2009;=&#x2009;3442) and proceeded to provide comprehensive descriptions of somatic and germline mutations in both groups. RESULTS: The somatic mutation analysis revealed that PIK3CA, FOXA1, and TBX3 mutations were more prevalent in elderly patients. By leveraging the aforementioned mutational characteristics, we employed our institution's FUTURE-SUPER clinical trial, an umbrella study targeting metastatic breast cancer, to confirm the potential benefits of PI3K-AKT-mTOR pathway inhibitors among elderly patients with breast cancer. Furthermore, TP53 and ERBB2 were more likely to be co-mutated in young women. Patients with TP53 and ERBB2 co-mutation tend to have a poorer prognosis, but through investigation of the SPARK cohort, patients carrying the TP53 and ERBB2 co-mutation are more likely to benefit from immune checkpoint inhibitor combination with tyrosine kinase inhibitor therapy. In our study, we observed a higher frequency of mutations in the DNA homology-dependent recombination pathway in young patients with breast cancer, which was associated with an elevated Ki67 index. Additionally, we confirmed a significant prevalence of germline breast cancer susceptibility gene 1 (gBRCA1) mutations in young patients, whereas germline checkpoint kinase 2 (gCHEK2) mutations are more common in elderly patients. CONCLUSIONS: Our study, which makes use of the largest Chinese breast cancer sequencing cohort, sought to characterize the age-related genomic profile of breast cancer patients and identify novel therapeutic opportunities for individuals with breast cancer.

Adult↗
PubMed2026

Molecular DNA enrichment methods for parasite genomic sequencing in clinical samples: a systematic review.

Parasitic diseases such as malaria, Chagas disease, leishmaniases, and helminthiases are major causes of sickness and death in low- and middle-income countries. The high genetic diversity of these pathogens affects virulence, immune evasion, and diagnostic accuracy. Although Whole Genome Sequencing (WGS) is a powerful tool for tracking genetic variants and drug resistance, low parasitemia and the predominance of host DNA limit its application to clinical samples. This study systematically reviewed molecular strategies to improve the recovery of parasite DNA from clinical samples, following PRISMA 2020 guidelines and registered in PROSPERO. Searches of PubMed, Scopus, Web of Science, and LILACS up to December 2025 identified 20 eligible studies, most of which focused on protozoa, particularly Plasmodium spp. The main approaches included hybridization capture, selective whole-genome amplification, host DNA depletion, and in silico enrichment via adaptive sampling. Overall, no single method is suitable for all parasites analyzed; the optimal approach depends on the pathogen, sample type, and research objective. The review emphasizes that parasite DNA enrichment is essential for enabling WGS in clinical settings, underscoring the need for protocol standardization and cost-effectiveness analyses to support public health genomic surveillance.

Adaptive sampling↗
PubMed2004

Substernal epicardial echocardiography: a recommended examination sequence and clinical evaluation in patients undergoing cardiac surgery.

BACKGROUND: Substernal epicardial echocardiography is a novel echocardiography window, utilizing a modified mediastinal drain incorporating a sleeve for the insertion of a transesophageal echocardiography probe. METHODS: Forty-six patients undergoing cardiac surgery from two institutions were evaluated, and an examination sequence was developed. RESULTS: An 11-view examination is presented as a consensus between the two institutions. In clinical usage, there were no major complications attributable to use of the device. Minor air leaks occurred in 6 patients, and 2 cases of sternal wound infection occurring in a cluster of infections are reported, but causation was not attributed to use of the device. There were no significant differences in measurements of the aortic valve area, pulmonary artery diameter, left ventricular outflow tract dimension, or the sinotubular junction between substernal and transesophageal examinations. All 16 wall-motion segments were well visualized in most patients with substernal epicardial echocardiography. CONCLUSIONS: Substernal epicardial echocardiography is a safe device for use in the postoperative environment.

Cardiac Surgical Procedures↗
PubMed2006

Comparative study on the bioequivalence of two different gabapentin formulations. A randomised, two-period, two-sequence, crossover clinical trial in healthy volunteers.

The bioequivalence of two capsule formulations containing 400 mg gabapentin (CAS 60142-96-3) was assessed in 24 healthy volunteers in an open, randomised, crossover, 2 periods x 2 sequences, with a minimum washout period of 7 days, single-dose study. Plasma samples were obtained at fixed time points, over 48 h (baseline (pre-dose), +0.5 h, +1 h, +1.5, +2, +2.5, +3, +3.5, +4, +8, +5, +6, +8, +10, +12, +24, +36 and +48 h after administration) and gabapentin concentrations were determined by means of an HPLC-MS method (LLOQ 50.2 ng/mL). Pharmacokinetic parameters used for bioequivalence assessment (AUCtlast, AUCinf and Cmax) were determined from the gabapentin concentration data using non-compartmental analysis. The results showed that all 90 % confidence intervals (obtained by ANOVA) were all within the predefined ranges: 93.87-111.87 % for Cmax 94.04-108.21 % for AUCtlast and 94.23-108.29 % for AUCinf. Consequently, this bioequivalence study was well designed in order to conclude that the test formulation and reference formulation were bioequivalent in terms of rate and extent of absorption.

Adolescent↗
PubMed2000

Cytogenetics, immunostaining for fibroblast growth factors, p53 sequencing, and clinical features of two cases of cystosarcoma phyllodes.

BACKGROUND: We present cytogenetics and fibroblast growth factor immunohistochemistry in one case of cystosarcoma phyllodes with localized disease and one with metastatic spread. The p53 gene was sequenced in the malignant case. METHODS AND RESULTS: Karyotype analysis used trypsin-Giemsa banding. Immunohistochemistry of FGF1, FGF2, FGFR1 and p53 used avidin-biotin detection of the primary antibody. One case had a mosaic female karyotype and three clones: one normal, one with trisomy 7, and one with both trisomy 5 and a rearranged chromosome 1. In the second case, a resected pulmonary metastasis had the karyotype 43-47,XX,+mar1,+mar2[6]/43-46,XX, +del(7)(p10)[3],+mar2[1][cp3]/46,XX[10]. These tumors expressed FGF1, FGF2, and FGFR1. The malignant case showed immunostaining for p53 protein, but a wild-type gene sequence. CONCLUSION: The karyotype of cystosarcoma phyllodes is complex, with wide case-to-case variation. These tumors express members of the FGF family. Metastatic behavior can occur in the presence of a wild-type p53 gene.

Adult↗
PubMed2005

A multi-exonic BRCA1 deletion identified in multiple families through single nucleotide polymorphism haplotype pair analysis and gene amplification with widely dispersed primer sets.

The identification of intragenic rearrangements is important for a comprehensive understanding of mutations that occur in some clinically important genes. Single nucleotide polymorphism haplotypes obtained from clinical sequence data have been used to identify patients at high risk for rearrangement mutations. Application of this method identified a novel 26-kb deletion of BRCA1 exons 14 through 20 in patients from multiple families with hereditary breast and ovarian cancer. Clinical sequence data from 5911 anonymous patients were screened for genotypes that were inconsistent with known pairs of canonical haplotypes in BRCA1 that could be explained by hemizygous deletions involving exon 16. Long-range polymerase chain reaction demonstrated that two of six samples identified by this search contained a deletion in the expected region encompassing exons 14 through 20. The breakpoint was fully characterized by DNA sequencing and demonstrated that the deletion resulted from Alu-mediated recombination. This mutation was also identified twice in a set of 982 anonymous specimens that had negative clinical test results, but uninformative haplotypes. Three additional occurrences of this mutation were found by testing 10 other patients with the indicative genotype. An assay for this mutation was added to a comprehensive clinical breast/ovarian cancer test and eight more instances were found in 20,649 probands. This multiexon deletion has therefore been detected in 15 different North American families with hereditary breast/ovarian cancer. In conclusion, this primarily computational approach is highly effective and identifies specimens using existing data that are enriched for deletion mutations.

BRCA1 Protein↗
PubMed2024

A comparison of software for analysis of rare and common short tandem repeat (STR) variation using human genome sequences from clinical and population-based samples.

Short tandem repeat (STR) variation is an often overlooked source of variation between genomes. STRs comprise about 3% of the human genome and are highly polymorphic. Some cause Mendelian disease, and others affect gene expression. Their contribution to common disease is not well-understood, but recent software tools designed to genotype STRs using short read sequencing data will help address this. Here, we compare software that genotypes common STRs and rarer STR expansions genome-wide, with the aim of applying them to population-scale genomes. By using the Genome-In-A-Bottle (GIAB) consortium and 1000 Genomes Project short-read sequencing data, we compare performance in terms of sequence length, depth, computing resources needed, genotyping accuracy and number of STRs genotyped. To ensure broad applicability of our findings, we also measure genotyping performance against a set of genomes from clinical samples with known STR expansions, and a set of STRs commonly used for forensic identification. We find that HipSTR, ExpansionHunter and GangSTR perform well in genotyping common STRs, including the CODIS 13 core STRs used for forensic analysis. GangSTR and ExpansionHunter outperform HipSTR for genotyping call rate and memory usage. ExpansionHunter denovo (EHdn), STRling and GangSTR outperformed STRetch for detecting expanded STRs, and EHdn and STRling used considerably less processor time compared to GangSTR. Analysis on shared genomic sequence data provided by the GIAB consortium allows future performance comparisons of new software approaches on a common set of data, facilitating comparisons and allowing researchers to choose the best software that fulfils their needs.

Humans↗
PubMed1992

Practical choices of fast spin echo pulse sequence parameters: clinically useful proton density and T2-weighted contrasts.

With the development of fast spin echo (FSE) MRI techniques, T2-weighted images of the brain may be obtained much more quickly than when using conventional spin echo techniques (CSE), because made the individual echoes on the FSE pulse sequence are phase encoded, allowing acquisition of the same spatial information as in CSE with less excitations. The pulse sequence parameters (echo train length, bandwidth, echo spacing) are discussed. Images were obtained on four volunteers using both CSE and FSE while varying repetition time, echo time and matrix. Comparison for signal intensity gray-white differentiation, fat and CSE signal, arifacts and vascular resolution showed that FSE images comparable in quality to those of CSE can be obtained in less than half the time. A practical choice of FSE parameters is recommended for clinical use. However, artifacts, possibly related to CSF and vascular pulsation, of which the radiologist should be aware, were identified on the FSE images.

Artifacts↗
PubMed1992

Anti-C100-3 antibody status, viral genomic sequences, and clinical features in chronic hepatitic patients with hepatitis C virus RNA in sera.

Since detection of hepatitis C virus RNA by the polymerase chain reaction (PCR) showed that there existed anti-C100-3 (anti-HCV) antibody negative patients infected with HCV, we attempted to find out whether there were any clinical or viral genomic differences between the anti-HCV antibody positive and negative groups. One hundred and fifty-nine patients with chronic liver diseases with hepatitis C virus RNA in their sera were selected. Anti-HCV antibody was tested for anti-C100-3 antibody by an enzyme linked immunosorbent assay. The incidence of anti-HCV antibody was 129/159. The concentration of serum gamma-globulin, the titier of ZTT, and the positive rate of the PCR with the primers of the NS3/4 region (NS3/4PCR) were significantly higher in the anti-HCV antibody positive group than in the negative group. However, the other data such as alanine aminotransferase activity or past history were not significantly different. Nucleotide sequence of the cDNA fragments of NS3/4 region amplified by the PCR did not differ significantly between isolates from anti-HCV antibody positive and negative sera. The sequences observed in the present study did not differ significantly from those reported previously. Although there remains the possibility that the variation of viral genomic sequences may cause the absence of anti-HCV antibody, these results suggested that the individual clinical backgrounds or immunoreactivity of the patients might influence the antibody development.

Adult↗
PubMed1993

Detection of foot-and-mouth disease viral sequences in clinical specimens and ethyleneimine-inactivated preparations by the polymerase chain reaction.

The polymerase chain reaction method (PCR) has been applied to the diagnosis of foot-and-mouth disease viral RNA in tissues and, particularly, oesophageal-pharyngeal fluid (probang) samples from cattle. Using primer sets which corresponded to conserved regions of the VP1 sequence of the viral genome, it was possible to amplify sequences regardless of the serotype/strain of the virus. In comparison with infectivity assays, the PCR was generally more sensitive although there were a number of examples where only infectivity was detectable. In experiments with uninfected probang samples deliberately seeded with a dilution series of virus, the PCR proved to be approximately 10(4) times more sensitive than infectivity assays. This greater sensitivity was attributed, in part, to the ability of the PCR to amplify specifically from non-infectious RNA preparations. This enabled the identification, by sequencing, of viral RNA from chemically inactivated virus concentrates typical of those used for commercial vaccine production. Amplification of specific PCR products was also achieved with virus eluted from commercial vaccine, including preparations which had been stored for more than 10 years at 4 degrees C. The PCR technique is of considerable value, therefore, both as a complement to infectivity assays and as a powerful tool in vaccine-associated studies.

Amino Acid Sequence↗