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PubMed1999

Time-related effects of estrogen withdrawal on proliferation- and cell death-related events in MCF-7 xenografts.

Endocrine treatments for human breast cancer have been based largely upon the removal of estrogenic stimuli. The regression of tumors after estrogen deprivation has generally been characterized as being due to reduced proliferation but more recently has been recognized to also involve increased apoptosis. The aim of our experiments was to define the associated changes in certain proliferation- and cell death-related biological parameters after hormone withdrawal from estrogen-dependent MCF-7 xenografts in athymic nude mice using immunohistochemical techniques. The baseline estrogen receptor (ER) level of this MCF-7 xenograft was relatively low (average H score 23) but it was strongly Bcl-2-, PgR- and pS2-positive, indicating the functional integrity of estrogen signaling. Changes in proliferation (Ki-67), apoptosis, ER, progesterone receptor (PgR), cyclin D1, p27kip1, Bcl-2 and Bax expression were assessed during the 2 weeks after estrogen deprivation. ER levels rose markedly after estrogen ablation, whereas PgR levels fell to about 10% of baseline and pS2 levels halved. The proportion of Ki-67-positive cells was unchanged after 24 hr but by day 14 had reduced by about 80%. The normal levels of cyclin D1 also reduced after estrogen withdrawal in contrast to the rapid increase in levels of cyclin-dependent kinase inhibitor p27kip1. This latter increase appeared to occur in advance of the changes in Ki-67. The proportion of apoptotic cells increased from a mean 1.5% at baseline to 2.9% after 3 days and 4.7% after 14 days. There were reductions in both Bcl-2 and Bax staining but these appeared to be greater for Bcl-2, effectively decreasing the Bcl-2/Bax ratio. Our results provide a framework for the use of these parameters as intermediate markers in comparisons of hormonal agents for human breast cancer treatment.

Animals↗

PubMed2004

A genetic linkage map of microsatellite, gene-specific and morphological markers in diploid Fragaria.

Diploid Fragaria provide a potential model for genomic studies in the Rosaceae. To develop a genetic linkage map of diploid Fragaria, we scored 78 markers (68 microsatellites, one sequence-characterised amplified region, six gene-specific markers and three morphological traits) in an interspecific F2 population of 94 plants generated from a cross of F.vesca f. semperflorens x F. nubicola. Co-segregation analysis arranged 76 markers into seven discrete linkage groups covering 448 cM, with linkage group sizes ranging from 100.3 cM to 22.9 cM. Marker coverage was generally good; however some clustering of markers was observed on six of the seven linkage groups. Segregation distortion was observed at a high proportion of loci (54%), which could reflect the interspecific nature of the progeny and, in some cases, the self-incompatibility of F. nubicola. Such distortion may also account for some of the marker clustering observed in the map. One of the morphological markers, pale-green leaf (pg) has not previously been mapped in Fragaria and was located to the mid-point of linkage group VI. The transferable nature of the markers used in this study means that the map will be ideal for use as a framework for additional marker incorporation aimed at enhancing and resolving map coverage of the diploid Fragaria genome. The map also provides a sound basis for linkage map transfer to the cultivated octoploid strawberry.

Base Sequence↗

PubMed2026

Identification of Rare Noncoding Variants in Familial Nonmedullary Thyroid Carcinoma.

BACKGROUND: Familial nonmedullary thyroid carcinoma (FNMTC) occurs when three or more family members are affected by usually papillary thyroid carcinoma (PTC), the most common form of NMTC. While the heritability to NMTC is among the highest of all cancers, the genetic determinants among NMTC families are not well understood. Here, we aim to understand the contribution of rare noncoding germline variants in the etiology of FNMTC. METHODS: We previously reported whole-genome sequencing (WGS) and linkage analysis in 17 PTC families and reported on 41 protein-coding variants in 40 genes that cosegregated with PTC in 11 of the families. Herein, we further leveraged our WGS data to include noncoding variants in our analysis for all 17 families. We hypothesized that most of the pathogenic noncoding variants would be located in theoretical or empirically determined regulatory regions that demonstrate at a minimum, basal thyroid expression, a positive family linkage score, and co-segregation among PTC-affected individuals. To test this hypothesis, we adopted a unique filtering strategy to identify variants that occurred in known DNA elements and transcription factor binding sites, near regions known to impact on gene expression or splicing in thyroid tissue, and/or in characterized thyroid enhancers. We annotated variants using two analyses (ENCODE and transcription factor binding site) within the BasePlayer software. We separately analyzed (1) expression quantitative trait loci, (2) splicing quantitative trait loci, and (3) thyroid enhancers. We then ranked variants according to predicted pathogenicity and performed Sanger sequencing in all individuals of each family. RESULTS: In total, 121 variants were selected based on in-silico prediction and our custom ranking analysis in each pedigree. Of these, 56 variants showed cosegregation among all PTC-affected individuals and were absent from unaffected individuals. This included candidate variants from five of the six PTC families for whom no protein-coding variants were previously found. CONCLUSION: Our data suggest that noncoding variants are important in the etiology of FNMTC and provide a framework for identifying noncoding germline variants using a novel approach. Further studies are needed to functionally characterize these variants to better understand the molecular mechanism of their pathogenicity.

Humans↗

PubMed2026

Network-based stratification of allele-specific expression reveals patient subgroups in Huntington's disease.

MOTIVATION: Huntington's disease (HD) exhibits substantial variability in age of onset and disease progression that is not fully explained by CAG repeat length alone. Part of this residual variation is heritable, implicating additional genetic mechanisms. cis-regulatory variation, genetic variants that alter transcription and splicing of nearby genes, represents one such mechanism that can be quantified through allele-specific expression (ASE) analysis. However, methods for integrating ASE profiles into patient stratification frameworks remain underdeveloped, particularly for rare diseases with small cohorts and sparse data. RESULTS: We adapt a network-based stratification algorithm, originally developed for somatic tumour mutations, to ASE data. By propagating gene-level ASE imbalance profiles through a protein-protein interaction network, we stratified 20 HD patients into three distinct biological patient subgroups. Differential gene expression analysis highlights neuroinflammatory pathways, including microglial activation, immune cell activation, and cytokine regulation, as key sources of inter-patient heterogeneity, while differential ASE analysis implicates proteasomal and ubiquitin-dependent protein catabolic processes, immune activation, and central nervous system development. Intersection of differentially imbalanced and expressed genes identified FAM181B as a candidate gene with potential eQTL-mediated regulation, supported by independent cis-eQTL evidence for rs3780 in the caudate and putamen, the primary HD-affected striatal regions. FAM181B encodes a nuclear protein expressed in neural tissues acting as an interactor of the Hippo pathway TEAD transcription factors, implicating transcriptional regulatory variation as a potential contributor to molecular heterogeneity between patient subgroups. Differences in cortical and striatal neuropathological scores between clusters, even when adjusted for CAG repeat length, provide clinical support for the biological relevance of the identified subgroups. AVAILABILITY: All analysis code, Docker containers, and conda environments are available at https://github.com/macsbio/HD-ASE-NBS.

Huntington Disease↗

PubMed2005

Acupuncture for osteoarthritic pain: an observational study in routine care.

OBJECTIVE: To investigate characteristics and outcomes of patients undergoing acupuncture treatment for osteoarthritic pain under conditions of routine care in the framework of statutory health insurance in Germany. METHODS: Patients with chronic pain due to osteoarthritis (ICD-10 diagnoses M15 to M19) treated with acupuncture as the leading form of therapy were included in an observational study. Detailed questionnaires including instruments to measure pain intensity (numerical rating scales from 0 to 10), disability (Pain Disability Index) and quality of life (SF-36) were filled in before treatment, after treatment and at 6 months. Patients suffering from osteoarthritis of the knee and hip also filled in the Western Ontario and McMaster Universities (WOMAC) Osteoarthritis Index questionnaire. RESULTS: A total of 736 patients were included in the main analysis. Seventy (10%) patients and 278 (38%) patients, respectively, suffered exclusively from primary osteoarthritis of the hip or knee, 239 (33%) from another type of osteoarthritis and 149 (20%) had more than one affected joint. On average, patients received 8.7 +/- 3.1 acupuncture treatments. Statistically significant and clinically relevant improvements were seen in all subgroups both after treatment and at 6 months in all major outcome measures. In patients with osteoarthritis of the hip, the WOMAC sum score was 47.9 +/- 20.7 at baseline, 34.8 +/- 20.0 after treatment and 33.1 +/- 22.2 at 6 months. The respective values in patients with osteoarthritis of the knee were 51.7 +/- 20.9, 34.1 +/- 23.3 and 34.6 +/- 25.1. CONCLUSIONS: In this study, patients with chronic pain due to osteoarthritis reported clinically relevant improvements after acupuncture treatment. Due to the uncontrolled design and the high proportion of patients lost to follow-up, the study findings must be interpreted cautiously.

Acupuncture Therapy↗

PubMed1994

Constructing confidence intervals for QTL location.

We describe a method for constructing the confidence interval of the QTL location parameter. This method is developed in the local asymptotic framework, leading to a linear model at each position of the putative QTL. The idea is to construct a likelihood ratio test, using statistics whose asymptotic distribution does not depend on the nuisance parameters and in particular on the effect of the QTL. We show theoretical properties of the confidence interval built with this test, and compare it with the classical confidence interval using simulations. We show in particular, that our confidence interval has the correct probability of containing the true map location of the QTL, for almost all QTLs, whereas the classical confidence interval can be very biased for QTLs having small effect.

Chromosome Mapping↗

PubMed2005

Determining older people's needs for care by Registered Nurses: the Nursing Needs Assessment Tool.

AIMS: This paper reports a study to determine an appropriate framework for assessing older people's needs for nursing within the policy of 'free nursing', and to attempt to identify valid, reliable and usable assessment tool for determining this eligibility. BACKGROUND: In 2001, the United Kingdom government introduced 'free nursing care' legislation, eligibility for which was subject to a nursing needs assessment. This paper outlines the search for and subsequent development of an appropriate tool for assessing older people's eligibility for free nursing care in Northern Ireland. METHODS: Following a systematic search of the literature, existing tools used in ascertaining older people's nursing needs were identified. Each tool was systematically assessed in accordance with criteria of validity, reliability, usability, comprehensiveness of assessment and ability to quantify nursing care needs. From the findings, an assessment instrument, Nursing Needs Assessment Tool was subsequently developed and tested. Paired assessments of older people were undertaken independently by assessor dyads and evaluated statistically. Assessors' opinions on the usability of the instrument were sought through a focus group. RESULTS: One hundred and ten paired assessments were returned (63%). Overall there was 65% agreement between assessors. Kappa scores indicated good levels of inter-rater reliability. Correlation co-efficient measures reinforced these results. Findings from the focus group confirmed the validity, usability and comprehensiveness of the tool. CONCLUSIONS: The Nursing Needs Assessment Tool is a reliable, valid and usable instrument. This has major implications for the standardization of assessment for older people.

Aged↗

PubMed2006

Physicochemical descriptors to discriminate protein-protein interactions in permanent and transient complexes selected by means of machine learning algorithms.

Analyzing protein-protein interactions at the atomic level is critical for our understanding of the principles governing the interactions involved in protein-protein recognition. For this purpose, descriptors explaining the nature of different protein-protein complexes are desirable. In this work, the authors introduced Epic Protein Interface Classification as a framework handling the preparation, processing, and analysis of protein-protein complexes for classification with machine learning algorithms. We applied four different machine learning algorithms: Support Vector Machines, C4.5 Decision Trees, K Nearest Neighbors, and Naïve Bayes algorithm in combination with three feature selection methods, Filter (Relief F), Wrapper, and Genetic Algorithms, to extract discriminating features from the protein-protein complexes. To compare protein-protein complexes to each other, the authors represented the physicochemical characteristics of their interfaces in four different ways, using two different atomic contact vectors, DrugScore pair potential vectors and SFCscore descriptor vectors. We classified two different datasets: (A) 172 protein-protein complexes comprising 96 monomers, forming contacts enforced by the crystallographic packing environment (crystal contacts), and 76 biologically functional homodimer complexes; (B) 345 protein-protein complexes containing 147 permanent complexes and 198 transient complexes. We were able to classify up to 94.8% of the packing enforced/functional and up to 93.6% of the permanent/transient complexes correctly. Furthermore, we were able to extract relevant features from the different protein-protein complexes and introduce an approach for scoring the importance of the extracted features.

Algorithms↗

PubMed2026

Effects of continuous isomaltulose-containing gummy intake on interstitial glucose and salivary hormones during an 18-hole golf round: a randomized, double-blind controlled pilot study.

BACKGROUND: Golf is a prolonged, moderate-intensity sport requiring sustained physiological stability to manage cumulative stress and maintain performance. Although carbohydrate intake is commonly used to reduce fatigue, rapidly absorbed sugar-induced rapid blood glucose fluctuations may induce volatile arousal and latent metabolic stress. Isomaltulose, a slow-digesting disaccharide, provides a steadier glucose supply compared with sucrose. This exploratory pilot study examined the effects of isomaltulose intake on physiological stress markers, glycemic dynamics, and subjective responses during a competitive 18-hole golf round. METHODS: Twenty-three male collegiate golfers were randomized to either the isomaltulose group (ISO; n = 12) or the sucrose group (CON; n = 11) in a double-blind controlled trial. Participants consumed gummies containing isomaltulose or sucrose immediately after each hole (12.1 g carbohydrate per hole; total carbohydrate intake: 217.5 g). Primary outcomes were salivary stress markers [cortisol, testosterone, and dehydroepiandrosterone sulfate (DHEAS)] levels. Secondary outcomes included interstitial glucose concentration measured via continuous glucose monitoring, subjective assessments (i.e. sleepiness, relaxation, and concentration), and golf performance (18-hole score). Between-group comparisons at each time point were conducted using planned Welch's t-tests. RESULTS: No significant between-group differences were observed for 18-hole score (p = 0.38) or mean interstitial glucose concentration (p = 0.20). However, exploratory analyses revealed distinct hormonal variations; salivary DHEAS and testosterone levels were higher in the ISO group during the latter half of the round (p < 0.05), whereas both declined in the CON group. Regarding glycemic variability, the ISO group demonstrated a more stable glucose profile with a medium effect size for lower standard deviation (ISO: 14.7 ± 1.9 vs. CON: 16.7 ± 4.6 mg/dL; d = 0.58), although this difference was not significant. Conversely, subjective outcomes diverged; the CON group reported significantly greater subjective arousal (wakefulness and relaxation) (p < 0.01) relative to the ISO group. CONCLUSIONS: In conclusion, continuous intake of isomaltulose-containing gummies during an 18-hole golf round was associated with differences in selected physiological markers, including DHEAS and testosterone concentrations. However, these findings were not accompanied by improvements in objective golf performance outcomes compared with sucrose-containing gummies. Isomaltulose may influence glycemic dynamics and hormonal responses during prolonged golf play; however, the practical significance of these effects remains exploratory. Further studies with larger sample sizes and appropriate repeated-measures frameworks are needed to determine whether such physiological changes translate into meaningful performance or recovery benefits.

Humans↗

PubMed2002

General survey of intertumor linkages that connect the chronological changes of age-adjusted incidence rates of 13 neoplasia types from l975 to l993 in Japan.

We attempted a stochastic study of cancer risk change in time using the follow-up data of the age-adjusted incidence rate (AAIR) of cancer in Japan, which covered 13 neoplasia types of both sexes in scope, and ranged from 1975 to 1993 in time. The purpose of our study was to test whether or not there was any mathematical regularity that was to condition cancer risk changes in time in all the 13 human neoplasia types. We investigated the relation between 2 neoplasias as regards log AAIR changes in time by the direct successive elimination method of Gauss, a fitness test of a given pair data to an equilibrium model. The fitness test was repeated in each of 156 tumor pairs [P(13.2)] in both sexes, in each of 3 (x, y) coordinates - the original (x, y) coordinates, the rect- (x, y) coordinates and the para- (x, y) coordinates. Total number of fitness test in this study was estimated to be 156x2x3=936. The rect- (x, y) coordinates and the para- (x, y) coordinates were defined each as an (x, y) framework with its x axis crossed at a right angle to the regression line of the original log AAIR data, and as another framework with its x axis run in parallel with the regression line of the original log AAIR data. The fitness of a given tumor to an equilibrium system was assessed in terms of the correlation coefficient value r within the range of -1.000 (the oncogene-type equilibrium system) to +1.000 (the tumor suppressor gene-type equilibrium system). Results obtained are given as follows: i) the positivity rates of the fitness test to the oncogene-type equilibrium system and the tumor suppressor gene-type system in the male all-cancer population were each 95.5% (149/156 tumor pairs) and 79.5% (124/156 tumor pairs), and those in the female all-cancer population were each 91.0% (142/156 tumor pairs) and 83.3% (130/156 tumor pairs). Evidence was available to indicate that all of the 13 human neoplasia types of both sexes was associated with both oncogene activation and tumor suppressor gene inactivation at the level of individual tumors. In other words, clearance of both oncogene activation and tumor suppressor gene inactivation was the sine qua non premise of carcinogenesis. ii) The positivity score profiles of a given tumor (profile-like presentation of positivity score for each tumor), for each of 2 cancer genes and for each sex, was highly specific for each of the 26 tumor units (13 tumors of both sexes). The presence of a highly specific positivity score pattern might be taken as another expression of complex interaction of 2 cancer genes in carcinogenesis. iii) Evidence was presented to suggest that specified interactions of the oncogene-tumor suppressor gene complexes of both sexes might be causally related to the emergence of sex discrimination of cancer risk, as testified in a set of tumors with both male dominance of cancer risk and female dominance of cancer risk. iv) The significance of one tumor pair that failed to show fitness to both the oncogene-type equilibrium system and the tumor suppressor gene-type equilibrium system was discussed in terms of spacially restricted dissociation of the power center of the oncogene-type equilibrium system from that of the tumor suppressor gene-type equilibrium system in a given tumor pair.

Age Factors↗

PubMed2006

An integrated approach to the prediction of domain-domain interactions.

BACKGROUND: The development of high-throughput technologies has produced several large scale protein interaction data sets for multiple species, and significant efforts have been made to analyze the data sets in order to understand protein activities. Considering that the basic units of protein interactions are domain interactions, it is crucial to understand protein interactions at the level of the domains. The availability of many diverse biological data sets provides an opportunity to discover the underlying domain interactions within protein interactions through an integration of these biological data sets. RESULTS: We combine protein interaction data sets from multiple species, molecular sequences, and gene ontology to construct a set of high-confidence domain-domain interactions. First, we propose a new measure, the expected number of interactions for each pair of domains, to score domain interactions based on protein interaction data in one species and show that it has similar performance as the E-value defined by Riley et al. Our new measure is applied to the protein interaction data sets from yeast, worm, fruitfly and humans. Second, information on pairs of domains that coexist in known proteins and on pairs of domains with the same gene ontology function annotations are incorporated to construct a high-confidence set of domain-domain interactions using a Bayesian approach. Finally, we evaluate the set of domain-domain interactions by comparing predicted domain interactions with those defined in iPfam database that were derived based on protein structures. The accuracy of predicted domain interactions are also confirmed by comparing with experimentally obtained domain interactions from H. pylori. As a result, a total of 2,391 high-confidence domain interactions are obtained and these domain interactions are used to unravel detailed protein and domain interactions in several protein complexes. CONCLUSION: Our study shows that integration of multiple biological data sets based on the Bayesian approach provides a reliable framework to predict domain interactions. By integrating multiple data sources, the coverage and accuracy of predicted domain interactions can be significantly increased.

Algorithms↗

PubMed2026

Shared genetic basis and spatial cellular atlas of psoriasis and metabolic syndrome.

BACKGROUND: Psoriasis (PS) and metabolic syndrome (MetS) frequently co-occur. Characterizing their shared genetic architecture and spatially enriched cellular populations may clarify the context of their co-occurrence and generate hypotheses for functional validation. METHODS: We integrated genome-wide association study (GWAS) summary statistics for PS, MetS, and five related components with spatially resolved single-cell transcriptomic data. Global and local genetic correlations were assessed using linkage disequilibrium score regression, genetic covariance analysis, high-definition likelihood, and local analysis of variant association. A bivariate causal mixture model quantified polygenic overlap. Conditional/conjunctional false discovery rate and composite-null pleiotropy analyses identified shared susceptibility loci. Finally, gsMap evaluated trait-associated enrichment across annotated embryonic tissues at single-cell resolution. RESULTS: Genetic approaches identified significant genome-wide correlations and polygenic sharing between PS, MetS, and its components. Local and cross-trait analyses identified region-specific signals and cross-validated shared loci. gsMap revealed trait-specific tissue enrichment. PS showed the strongest enrichment in the epidermis (pCauchy = 1.0573 × 10  - ⁴), adipose tissue (pCauchy = 1.5366 × 10 - ⁴), and liver (pCauchy = 1.0167 × 10 - ³). Across MetS, FBG, HDL-C, hypertension, and TG, enriched regions mainly involved the liver, adipose tissue, and epidermis. WC enrichment was predominantly observed in adipose tissue (pCauchy = 1.7823 × 10 - ⁴), with no significant liver or epidermal enrichment. CONCLUSION: Integrating GWAS with single-cell transcriptomic and spatial information characterized shared genetic architecture between PS and MetS-related phenotypes and their spatial enrichment patterns. These findings provide a framework for generating testable hypotheses about comorbidity biology and guiding future functional and clinical validation.

Psoriasis↗

PubMed1997

Health-related quality of life: an indicator of quality of care?

There is an increasing interest in the use of outcome indicators to monitor the quality of care. Traditionally, outcome indicators have been based mainly on biological indicators reflecting death or disease. Now that various instruments for health status measurement have become available, questions have been raised as to the potential application of health status scores in monitoring the quality of care. This paper identifies conditions which should be fulfilled before such applications can be recommended. Firstly, the relationship between care delivery processes and health status outcomes must be established. In order to achieve this, health status measures which are clearly able to detect health status variations between groups of patients (i.e. discriminative ability) and variations over time (i.e. sensitivity to change) are needed. Secondly, health status data should be available, preferably from established data collection registries (e.g. computerized hospital records or national registries) where data relating to the description of variations in health status (between physicians, hospitals, regions, etc.) are routinely collected. Thirdly, methods should be found to collect additional data, including 'case-mix' information and health status reference data, in order to enable the interpretation of variations in health status. Because most of these conditions are currently not being fulfilled, we conclude that the state-of-the-art of health status measurement has not yet matured sufficiently to allow for the use of health status as an indicator of quality of care. The present paper provides a framework for both future research and data collection that is needed to improve the applicability of health status measures as quality-of-care indicators.

Decision Making↗

PubMed2002

Investigation of microleakage at the interface between a Co-Cr based alloy and four polymeric veneering materials.

STATEMENT OF PROBLEM: . Marginal adaptation and resistance to microleakage are important factors for clinical success in fixed prosthodontics. Alloy corrosion that sometimes occurs under a veneer in the cervical area may result in cervical staining, a metallic taste, or even failure of the interface. PURPOSE: This study investigated cervical microleakage between a Co-Cr alloy and 4 indirect polymeric veneering materials used with different conditioning systems. MATERIAL AND METHODS: Sixteen metallic frameworks (copings) were obtained by fabricating 0.6-mm calibrated wax patterns on a master cast abutment. The wax patterns were provided with 0.4-mm beaded retention on the veneering surfaces and cast in a Co-Cr based alloy (Biosil F) used for fixed partial dentures. The Co-Cr copings were divided equally into 4 groups and veneered with 4 polymeric materials (Signum, Solidex, Superpont C+B, and Targis). Three chemical conditioning systems (Siloc, Targis-Link, and Silicoater MD) were used with the respective veneering system recommended by the manufacturer; Conolar opaque was used for Superpont C+B. No control group was created. After 2 weeks of storage in distilled water at 37 degrees C, 2000 cycles at 5-55 degrees C, and 24 hours of storage in 0.5% basic fuchsine, specimens were embedded in clear liquid casting resin and sectioned along a perpendicular cervical-incisal plane through the middle of the cervical collar. The surfaces of the resulting sections were examined in the cervical area with a metallurgical microscope to detect dye penetration. Leakage was quantitatively evaluated with the use of a scoring system (established by the authors) that indicated the presence/absence of dye in 3 regions of the cervical interface from the collar to the incisal margin. Scores were compared and analyzed with the use of 1-way analysis of variance followed by post-hoc Tukey's honestly significant difference test (P=.05). RESULTS: Superpont C+B was associated with the highest microleakage scores (3.75 +/- 0.5). The least microleakage at the interface was produced by Targis (1 +/- 0.816), followed by Solidex (2.5 +/- 1.0) and Signum (2.25 +/- 0.975). Only the difference between Targis and Superpont C+B was significant (P<.05). CONCLUSION: Within the limitations of this in vitro study, the extent of cervical microleakage between the coping and veneer depended on the particular polymeric material used for veneering. The extremes of the study were Targis/Targis-Link (lowest leakage scores) and Superpont C+B (highest leakage scores). Differences among the chemical retention systems tested were not significant.

Analysis of Variance↗

PubMed2004

Denaturing-HPLC-based assay for detection of ABL mutations in chronic myeloid leukemia patients resistant to Imatinib.

BACKGROUND: Despite the efficacy of the BCR-ABL tyrosine kinase inhibitor Imatinib mesylate for the treatment of chronic myeloid leukemia (CML), resistance has been observed in a proportion of cases, especially those with advanced stages of the disease. Point mutations within the ABL kinase domain are emerging as the most frequent mechanism for reactivation of kinase activity within the leukemic clone. METHODS: We developed a denaturing-HPLC (D-HPLC)-based assay for screening for ABL point mutations. For each sample, two partially overlapping fragments of 393 and 482 bp corresponding to the kinase domain were amplified by nested reverse transcription-PCR and analyzed under selected temperature and acetonitrile gradient conditions. Fifty-one bone marrow and/or peripheral blood specimens from 27 CML patients who showed cytogenetic resistance to Imatinib were screened in parallel by D-HPLC and by direct sequencing. RESULTS: In 12 of 27 (44%) patients, D-HPLC showed an abnormal elution profile suggesting the presence of a nucleotide change. Direct sequencing confirmed the presence of a point mutation in all cases. Conversely, all samples scored as wild type by D-HPLC showed no evidence of mutations by direct sequencing. In two cases, novel amino acid substitutions at codons already known for being hot-spots of mutation were identified (F311I and E355D). CONCLUSIONS: The proposed D-HPLC-based assay is highly specific and at least as sensitive as sequencing; with respect to the latter, it provides a much faster and less expensive semiautomated system for mutational screening. It may therefore potentially be a valuable tool for regular, large-scale testing of patients undergoing Imatinib treatment.

Antineoplastic Agents↗

PubMed1987

DNA polymorphism patterns in the beta-globin gene cluster in the Japanese population.

Restriction site polymorphisms in the beta-globin gene cluster on chromosome #11 were analyzed in healthy Japanese. The beta A chromosomes were mapped by scoring the presence (+) or the absence (-) of seven different restriction sites (Hinc II site 5' to the epsilon-globin gene; Hind III sites in the G gamma- and A gamma-globin genes; Hinc II sites in and 3' to the psi beta 1-globin gene; Ava II site in the beta-globin gene; Bam HI site 3' to the beta-globin gene). No chromosomes with [- +] for two Hind III sites in the G gamma- and A gamma-globin genes, or those with [+ -] for two Hinc II sites in and 3' to the psi beta 1-globin gene, were observed. It was observed that homozygosity for the presence of the Hinc II site 5' to the epsilon-globin gene (+/+) always accompanied the homozygosity for the absence of the Hinc II sites in and 3' to the psi beta 1-globin gene (--/--). Almost all A gamma T chromosomes possessed a subhaplotype [- + + - +] 5' to the beta-globin gene. More than half of the beta A chromosomes observed in the Japanese showed haplotype VII, which may be characteristic for Asians. It was deduced that frameworks 1, 2, and 3 of the beta-globin gene in the Japanese comprised 16%, 18%, and 66%, respectively.

Adult↗

PubMed1994

Saturated molecular map of the rice genome based on an interspecific backcross population.

A molecular map has been constructed for the rice genome comprised of 726 markers (mainly restriction fragment length polymorphisms; RFLPs). The mapping population was derived from a backcross between cultivated rice, Oryza sativa, and its wild African relative, Oryza longistaminata. The very high level of polymorphism between these species, combined with the use of polymerase chain reaction-amplified cDNA libraries, contributed to mapping efficiency. A subset of the probes used in this study was previously used to construct an RFLP map derived from an inter subspecific cross, providing a basis for comparison of the two maps and of the relative mapping efficiencies in the two crosses. In addition to the previously described PstI genomic rice library, three cDNA libraries from rice (Oryza), oat (Avena) and barley (Hordeum) were used in this mapping project. Levels of polymorphism detected by each and the frequency of identifying heterologous sequences for use in rice mapping are discussed. Though strong reproductive barriers isolate O. sativa from O. longistaminata, the percentage of markers showing distorted segregation in this backcross population was not significantly different than that observed in an intraspecific F2 population previously used for mapping. The map contains 1491 cM with an average interval size of 4.0 cM on the framework map, and 2.0 cM overall. A total of 238 markers from the previously described PstI genomic rice library, 250 markers from a cDNA library of rice (Oryza), 112 cDNA markers from oat (Avena), and 20 cDNA markers from a barley (Hordeum) library, two genomic clones from maize (Zea), 11 microsatellite markers, three telomere markers, eleven isozymes, 26 cloned genes, six RAPD, and 47 mutant phenotypes were used in this mapping project. Applications of a molecular map for plant improvement are discussed.

Avena↗

PubMed2000

The impact of minor acute wounds on quality of life.

A study was undertaken to explore the experiences of patients with minor acute wounds following discharge from either inpatient or day care. The sample comprised patients attending the plastic surgery dressing clinic of a district general hospital. Patients whose wounds were considered to be chronic were not included. A conceptual framework was developed from the literature, postulating that the patient is 'eclipsed' by the wound and enters the sick role before healing and recovery take place. A self-administered questionnaire was used to collect data for a mainly quantitative analysis, with some open questions to indicate avenues for further study. Unfortunately, the response rate was low, and insufficient data were obtained for effective analysis. However, trends were identified which indicated that these wounds had a significant impact on patients and their families, and recommendations were made for future studies. The survey would need to be repeated on a larger, more representative sample and include semi-structured interviews to produce generalizable results.

Acute Disease↗