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Biomedical subjects

N Stein

Publications and source records attributed to N Stein.

At least 19 recordsLinked to original sources
PubMed2006

SPINE workshop on automated X-ray analysis: a progress report.

The Structural Proteomics In Europe (SPINE) consortium contained a workpackage to address the automated X-ray analysis of macromolecules. The aim of this workpackage was to increase the throughput of three-dimensional structures while maintaining the high quality of conventional analyses. SPINE was able to bring together developers of software with users from the partner laboratories. Here, the results of a workshop organized by the consortium to evaluate software developed in the member laboratories against a set of bacterial targets are described. The major emphasis was on molecular-replacement suites, where automation was most advanced. Data processing and analysis, use of experimental phases and model construction were also addressed, albeit at a lower level.

Algorithms↗
PubMed2006

Genetic mapping and BAC assignment of EST-derived SSR markers shows non-uniform distribution of genes in the barley genome.

A set of 111,090 barley expressed sequence tags (ESTs) was searched for the presence of microsatellite motifs [simple sequence repeat (SSRs)] and yielded 2,823 non-redundant SSR-containing ESTs (SSR-ESTs). From this, a set of 754 primer pairs was designed of which 525 primer pairs yielded an amplicon and as a result, 185 EST-derived microsatellite loci (EST-SSRs) were placed onto a genetic map of barley. The markers show a uniform distribution along all seven linkage groups ranging from 21 (7H) to 35 (3H) markers. Polymorphism information content values ranged from of 0.24 to 0.78 (average 0.48). To further investigate the physical distribution of the EST-SSRs in the barley genome, a bacterial artificial chromosomes (BAC) library was screened. Out of 129 markers tested, BAC addresses were obtained for 127 EST-SSR markers. Twenty-seven BACs, forming eight contigs, were hit by two or three EST-SSRs each. This unexpectedly high incidence of EST-SSRs physically linked at the sub-megabase level provides additional evidence of an uneven distribution of genes and the segmentation of the barley genome in gene-rich and gene-poor regions.

Chromosomes, Artificial, Bacterial↗
PubMed2005

Repeatability of the sonographic assessment of fetal sucking and swallowing movements.

OBJECTIVE: To test the repeatability of sonography in the assessment of fetal sucking and swallowing movements. METHODS: Eighty normal fetuses of pregnant women with no systemic abnormalities were examined sonographically at 30-38 weeks of gestation. Sucking and swallowing movements were observed for 15 min and the face was visualized in frontal and lateral views. The examinations were recorded for later analysis by two independent observers and the 95% limits of agreement (Bland and Altman) method was used for inter- and intraobserver comparison. RESULTS: The mean +/- SD number of swallowing movements, sucking bursts and total sucking movements recorded by Observer 1 were 8.3 +/- 4.7, 9.9 +/- 9.3 and 35.8 +/- 48.0 and the equivalent values for Observer 2 were 8.2 +/- 4.8, 9.8 +/- 9.3 and 36.4 +/- 49.0, respectively. The mean (95% limits of agreement) interobserver difference was 0.1 (-1.4; 1.6), 0.1 (-2.2; 2.3) and -0.6 (-9.0; 7.9), and the mean (95% limits of agreement) intraobserver difference was 0.4 (-3.1; 3.9), 0.1 (-2.0; 2.2) and 1.0 (-10.7; 12.7) for swallowing movements, sucking bursts and total sucking movements, respectively. CONCLUSIONS: The high degree of intra- and interobserver repeatability disclosed in the sonographic analysis of fetal sucking and swallowing movements supports the applicability of sonographic assessment in normal fetuses.

Cross-Sectional Studies↗
PubMed2004

The gibberellic-acid insensitive dwarfing gene sdw3 of barley is located on chromosome 2HS in a region that shows high colinearity with rice chromosome 7L.

In this study, comparative high resolution genetic mapping of the GA-insensitive dwarfing gene sdw3 of barley revealed highly conserved macrosynteny of the target region on barley chromosome 2HS with rice chromosome 7L. A rice contig covering the sdw3-orthologous region was identified and subsequently exploited for marker saturation of the target interval in barley. This was achieved by (1) mapping of rice markers from the orthologous region of the rice genetic map, (2) mapping of rice ESTs that had been physically localized on the rice contig, or (3) mapping of barley ESTs that show strong sequence similarity to coding sequences present in the rice contig. Finally, the sdw3 gene was mapped to an interval of 0.55 cM in barley, corresponding to a physical distance of about 252 kb in rice, after employing orthologous EST-derived rice markers. Three putative ORFs were identified in this interval in rice, which exhibited significant sequence similarity to known signal regulator genes from different species. These ORFs can serve as starting points for the map-based isolation of the sdw3 gene from barley.

Blotting, Southern↗
PubMed2003

Snipping polymorphisms from large EST collections in barley (Hordeum vulgare L.).

The public EST (expressed sequence tag) databases represent an enormous but heterogeneous repository of sequences, including many from a broad selection of plant species and a wide range of distinct varieties. The significant redundancy within large EST collections makes them an attractive resource for rapid pre-selection of candidate sequence polymorphisms. Here we present a strategy that allows rapid identification of candidate SNPs in barley (Hordeum vulgare L.) using publicly available EST databases. Analysis of 271,630 EST sequences from different cDNA libraries, representing 23 different barley varieties, resulted in the generation of 56,302 tentative consensus sequences. In all, 8171 of these unigene sequences are members of clusters with six or more ESTs. By applying a novel SNP detection algorithm (SNiPpER) to these sequences, we identified 3069 candidate inter-varietal SNPs. In order to verify these candidate SNPs, we selected a small subset of 63 present in 36 ESTs. Of the 63 SNPs selected, we were able to validate 54 (86%) using a direct sequencing approach. For further verification, 28 ESTs were mapped to distinct loci within the barley genome. The polymorphism information content (PIC) and nucleotide diversity (pi) values of the SNPs identified by the SNiPpER algorithm are significantly higher than those that were obtained by random sequencing. This demonstrates the efficiency of our strategy for SNP identification and the cost-efficient development of EST-based SNP-markers.

Chromatography, High Pressure Liquid↗
PubMed2001

Analysis of a contiguous 211 kb sequence in diploid wheat (Triticum monococcum L.) reveals multiple mechanisms of genome evolution.

In plant species with large genomes such as wheat or barley, genome organization at the level of DNA sequence is largely unknown. The largest sequences that are publicly accessible so far from Triticeae genomes are two 60 kb and 66 kb intervals from barley. Here, we report on the analysis of a 211 kb contiguous DNA sequence from diploid wheat (Triticum monococcum L.). Five putative genes were identified, two of which show similarity to disease resistance genes. Three of the five genes are clustered in a 31 kb gene-enriched island while the two others are separated from the cluster and from each other by large stretches of repetitive DNA. About 70% of the contig is comprised of several classes of transposable elements. Ten different types of retrotransposons were identified, most of them forming a pattern of nested insertions similar to those found in maize and barley. Evidence was found for major deletion, insertion and duplication events within the analysed region, suggesting multiple mechanisms of genome evolution in addition to retrotransposon amplification. Seven types of foldback transposons, an element class previously not described for wheat genomes, were characterized. One such element was found to be closely associated with genes in several Triticeae species and may therefore be of use for the identification of gene-rich regions in these species.

Base Sequence↗
PubMed2000

Subgenome chromosome walking in wheat: a 450-kb physical contig in Triticum monococcum L. spans the Lr10 resistance locus in hexaploid wheat (Triticum aestivum L.).

For many agronomically important plant genes, only their position on a genetic map is known. In the absence of an efficient transposon tagging system, such genes have to be isolated by map-based cloning. In bread wheat Triticum aestivum, the genome is hexaploid, has a size of 1.6 x 10(10) bp, and contains more than 80% of repetitive sequences. So far, this genome complexity has not allowed chromosome walking and positional cloning. Here, we demonstrate that chromosome walking using bacterial artificial chromosome (BAC) clones is possible in the diploid wheat Triticum monococcum (A(m) genome). BAC end sequences were mostly repetitive and could not be used for the first walking step. New probes corresponding to rare low-copy sequences were efficiently identified by low-pass DNA sequencing of the BACs. Two walking steps resulted in a physical contig of 450 kb on chromosome 1A(m)S. Genetic mapping of the probes derived from the BAC contig demonstrated perfect colinearity between the physical map of T. monococcum and the genetic map of bread wheat on chromosome 1AS. The contig genetically spans the Lr10 leaf rust disease resistance locus in bread wheat, with 0.13 centimorgans corresponding to 300 kb between the closest flanking markers. Comparison of the genetic to physical distances has shown large variations within 350 kb of the contig. The physical contig can now be used for the isolation of the orthologous regions in bread wheat. Thus, subgenome chromosome walking in wheat can produce large physical contigs and saturate genomic regions to support positional cloning.

Chromosome Walking↗
PubMed1997

Microamplification of specific chromosome sequences; an improved method for genome analysis.

An improved method was developed for microdissection and cloning of metaphase as well as pachytene chromosomes. The protocol incorporates efficient ligation of chromosomal DNA with linker adaptors, abolishment of microcloning steps and the reduction of micromanipulation. The threshold for amplifying genomic DNA template was in the range of 2-20 femtogram. The amplification products had a size distribution between 200 and 1300 bp (average 500 bp). Using pachytene chromosomes of maize the selectivity for segment-specific libraries can be increased between 10- and 20-fold. The approach described here is being applied to the fine mapping and isolation of genes conveying resistance against plant pathogens.

Chromosomes↗
PubMed1997

Appraisal and goal processes as predictors of psychological well-being in bereaved caregivers.

Narratives of 30 caregivers were scored for appraisals and coping responses following the death of their partners from AIDS. Appraisals were identified as valenced beliefs, emotions, and goal outcomes, whereas coping responses included goals and plans of action. The proportion of positive appraisals predicted long-term goals and plans and psychological well-being at both bereavement and 12 months later. Positive appraisals were correlated with positive moral and positive states of mind. The latter were negatively correlated with partner-centered, short-term plans. Positive appraisals were negatively correlated with depressive mood. Caregivers, who reported proportionately more positive appraisals during caregiving and after the loss of their partner, were more likely to have future- and self-oriented goals and plans and to demonstrate positive well-being at bereavement and better recovery 12 months later than were those who reported more negative appraisals.

Acquired Immunodeficiency Syndrome↗
PubMed1996

Headache and human immunodeficiency virus infection: a case control study.

The new onset of headache in a person infected with human immunodeficiency virus (HIV) may be an ominous sign of a significant underlying neurological disorder. This case control study compares the prevalence of headache in HIV-seropositive persons without identifiable neurological disease on study entry to that in an HIV-seronegative control population with similar risk factors for HIV infection. Features of headache that were evaluated included frequency, duration, location, severity, and recent change in characteristics. In the HIV-seropositive population, the presence of headache and its specific features were correlated with the degree of immunosuppression as determined by absolute CD4 counts and Centers for Disease Control stages, the presence of other neurological symptoms and neurological signs, cranial magnetic resonance imaging (MRI) findings, and cerebrospinal fluid (CSF) values. Headaches were common; approximately 50% of all subjects reported headache at study entry and 2 years later. Headache frequency and characteristics were not different between HIV-seropositive and HIV-seronegative subjects. Headache was neither more frequent nor different in HIV-seropositive individuals with advanced immunosuppression. There was no correlation between headache and abnormal CSF parameters, cranial MRI abnormalities, including the presence of sinusitis, or the use of zidovudine.

Adolescent↗
PubMed1995

Relationship between suicide and myocardial infarction with regard to changing physical environmental conditions.

In recent years, the possible association of changes in mortality from cardiovascular disease and myocardial infarction (MI) and deaths related to violence and the suicide rate has been repeatedly discussed. This study examined the relationship between cosmic physical changes (solar, geomagnetic and other space activity parameters) and changes in the total number of in-hospital and MI-related deaths and deaths from suicide to determine if a relationship exists between the distribution of total and MI-related deaths with suicide over time; some differences in the serotonergic mechanisms involved in the pathogenesis of MI and suicide were also taken into account. All suicides (n = 2359) registered in the State of Israel from 1981 to 1989 (108 months) were analysed and compared with the total number of deaths (n = 15601) and deaths from MI (n = 1573) in a large university hospital over 180 months (1974-1989). The following were the main features of the Results. (1) Monthly suicide rate was correlated with space proton flux (r = 0.42, P = 0.0001) and with geomagnetic activity (r = -0.22, P = 0.03). (2) Total hospital and MI-related deaths were correlated with solar activity parameters (r = 0.35, P < 0.001) and radiowave propagation (r = 0.52-0.44, P < 0.001), an with proton flux (r = -0.3 to -0.26, P < 0.01). (3) Monthly suicide distribution over 108 months was correlated with MI (r = -0.33, P = 0.0005) and total hospital mortality (r = -0.22, P = 0.024). (4) Gender differences were prominent.(ABSTRACT TRUNCATED AT 250 WORDS)

Cardiovascular Diseases↗
PubMed1995

Selective suppression of cytokine secretion in patients with small-cell lung cancer.

BACKGROUND: Whether or not cytokine secretion is impaired in patients with small-cell lung cancer (SCLC), is unknown. We therefore investigated whether cytokine secretion by immunocompetent cells may be suppressed in patients with SCLC. PATIENTS AND METHODS: We determined cytokine secretion by lymphocytes and monocytes in whole blood cell cultures from 58 patients with SCLC, 95 patients with non-small-cell lung cancer (NSCLC), 10 patients with nonmalignant lung disease and from 44 normal healthy individuals by using an enzyme-linked immunosorbent assay (ELISA) specific for the different cytokines measured. RESULTS: Compares to normal controls, immunocompetent cells from patients with SCLC secreted significantly lower amounts of IL-2, IFN alpha, and IFN gamma upon mitogen stimulation. TNF alpha-secretion was significantly reduced in SCLC extensive disease but not in SCLC limited disease. In contrast, secretion of IL-1 alpha and IL-1 beta was not reduced. In patients with NSCLC, secretion of IL-2 and IFN alpha was significantly reduced. Reduction of IFN gamma secretion was significant in metastasized NSCLC and marginally significant in localized NSCLC. Secretion of TNF alpha, IL-1 alpha and IL-1 beta was not impaired. In addition, cytokine secretion in SCLC patients substantially improved upon successful reduction of tumor load by chemotherapy but not upon ineffective chemotherapy. Furthermore, TGF beta 1 suppressed secretion of IL-2, IFN alpha, IFN gamma, TNF alpha but not of IL-1 alpha and IL-1 beta in whole blood cell cultures from healthy individuals. CONCLUSIONS: Suppression of cytokine secretion in patients with SCLC was selective, dependent on tumor load, different from immunosuppression in NSCLC and seemed to be reconstituted upon reduction of tumor load. These results may suggest interactions between tumor cells and the immune system. TGF beta 1 secreted by SCLC cell lines induced the same selective cytokine suppression as that found in SCLC patients. However, whether or not tumor-derived TGF beta 1 is a factor inducing selective immunosuppression in SCLC patients is presently unclear.

Adult↗
PubMed1994

Topographical differences in sweetness sensitivity in the peripheral gustatory system of adults and children.

The sensitivity of localised areas of the anterior tongue of adults and 8-year-old males to the sweetener sucrose was determined, using a two-alternative forced choice psychophysical procedure. Stimulation of 12 areas by 0.2125 M sucrose or water, using a filter paper technique, indicated that the children were significantly more sensitive to the sweetener at eight of the areas. Counts of papillae at each of the 12 areas showed that there were similar numbers for adults and children at eight areas, whilst at three of the areas that exhibited a higher sensitivity to sucrose, children had significantly more papillae. Since 8-year-old males are less sensitive to sucrose when the stimulus is given as a whole-mouth stimulus [12], it is proposed that the children's gustatory system may be unable to integrate the information available at the tongue as efficiently as adults, or that the threshold and stimulus-response functions of receptor cells are different in the two groups.

Adult↗
PubMed1987

Functional vs. organic pain: a meaningful distinction?

This study examined the statistical and clinical validity of the distinction frequently made between "functional" pain and "real" pain. Earlier work has relied on the MMPI exclusively and results have been inconclusive, yet the distinction continues to be made and treatment is recommended on the basis of the label. Sixty-seven chronic back pain patients were administered questionnaires that assessed quantity and quality of depression, dimensions of illness behavior, and psychogenic attitudes. Scores of chronic pain patients were compared to normal subjects, and results indicate that the pain subjects experienced high levels of depression, anxiety, and social alienation. However, organic pain subjects did not differ from subjects with no organic findings. The authors suggest that the distinction between organic and functional pain be discarded in favor of an approach that assesses current emotional stressors and available coping mechanisms.

Adult↗
PubMed1987

Fine-needle aspiration cytology of prostatic embryonal rhabdomyosarcoma: a case report.

Fine-needle aspiration of the prostate has recently gained popularity as a reliable technique in the evaluation of prostatic nodules for malignancy. The cytologic features of adenocarcinoma have been described, but the features of other more unusual tumors have not been widely publicized. We report a case of embryonal rhabdomyosarcoma of the prostate gland with epithelioid cytologic features.

Adult↗