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PubMed2006

Timecourse microarray analyses reveal global changes in gene expression of susceptible Glycine max (soybean) roots during infection by Heterodera glycines (soybean cyst nematode).

Changes in gene expression within roots of Glycine max (soybean), cv. Kent, susceptible to infection by Heterodera glycines (the soybean cyst nematode [SCN]), at 6, 12, and 24 h, and 2, 4, 6, and 8 days post-inoculation were monitored using microarrays containing more than 6,000 cDNA inserts. Replicate, independent biological samples were examined at each time point. Gene expression was analyzed statistically using T-tests, ANOVA, clustering algorithms, and online analytical processing (OLAP). These analyses allow the user to query the data in several ways without importing the data into third-party software. RT-PCR confirmed that WRKY6 transcription factor, trehalose phosphate synthase, EIF4a, Skp1, and CLB1 were differentially induced across most time-points. Other genes induced across most timepoints included lipoxygenase, calmodulin, phospholipase C, metallothionein-like protein, and chalcone reductase. RT-PCR demonstrated enhanced expression during the first 12 h of infection for Kunitz trypsin inhibitor and sucrose synthase. The stress-related gene, SAM-22, phospholipase D and 12-oxophytodienoate reductase were also induced at the early time-points. At 6 and 8 dpi there was an abundance of transcripts expressed that encoded genes involved in transcription and protein synthesis. Some of those genes included ribosomal proteins, and initiation and elongation factors. Several genes involved in carbon metabolism and transport were also more abundant. Those genes included glyceraldehyde 3-phosphate dehydrogenase, fructose-bisphosphate aldolase and sucrose synthase. These results identified specific changes in gene transcript levels triggered by infection of susceptible soybean roots by SCN.

Animals↗

PubMed2006

Major differences observed in transcript profiles of blueberry during cold acclimation under field and cold room conditions.

Our laboratory has been working toward increasing our understanding of the genetic control of cold hardiness in blueberry (Vaccinium section Cyanococcus) to ultimately use this information to develop more cold hardy cultivars for the industry. Here, we report using cDNA microarrays to monitor changes in gene expression at multiple times during cold acclimation under field and cold room conditions. Microarrays contained over 2,500 cDNA inserts, approximately half of which had been picked and single-pass sequenced from each of two cDNA libraries that were constructed from cold acclimated floral buds and non-acclimated floral buds of the fairly cold hardy cv. Bluecrop (Vaccinium corymbosum L.). Two biological samples were examined at each time point. Microarray data were analyzed statistically using t tests, ANOVA, clustering algorithms, and online analytical processing (OLAP). Interestingly, more transcripts were found to be upregulated under cold room conditions than under field conditions. Many of the genes induced only under cold room conditions could be divided into three major types: (1) genes associated with stress tolerance; (2) those that encode glycolytic and TCA cycle enzymes, and (3) those associated with protein synthesis machinery. A few of the genes induced only under field conditions appear to be related to light stress. Possible explanations for these differences are discussed in physiological context. Although many similarities exist in how plants respond during cold acclimation in the cold room and in the field environment, there are major differences suggesting caution should be taken in interpreting results based only on artificial, cold room conditions.

Acclimatization↗

PubMed2005

Examination of ancestry and ethnic affiliation using highly informative diallelic DNA markers: application to diverse and admixed populations and implications for clinical epidemiology and forensic medicine.

We and others have identified several hundred ancestry informative markers (AIMs) with large allele frequency differences between different major ancestral groups. For this study, a panel of 199 widely distributed AIMs was used to examine a diverse set of 796 DNA samples including self-identified European Americans, West Africans, East Asians, Amerindians, African Americans, Mexicans, Mexican Americans, Puerto Ricans and South Asians. Analysis using a Bayesian clustering algorithm (STRUCTURE) showed grouping of individuals with similar ethnic identity without any identifier other than the AIMs genotyping and showed admixture proportions that clearly distinguished different individuals of mixed ancestry. Additional analyses showed that, for the majority of samples, the predicted ethnic identity corresponded with the self-identified ethnicity at high probability (P > 0.99). Overall, the study demonstrates that AIMs can provide a useful adjunct to forensic medicine, pharmacogenomics and disease studies in which major ancestry or ethnic affiliation might be linked to specific outcomes.

Algorithms↗

PubMed2005

Location-dependent analysis of porosity and pore direction in tablets.

PURPOSE: Several phenomena in tablets indicate that an inhomogeneous pore distribution is formed during the compaction process. Examples are lamination and the capping of corners. In order to gain an understanding of the relation between structure and compact properties, analyzing the structure in a location dependent manner would be extremely useful. Our aim was to visualize and to quantitatively analyze the pore distribution in compacts. METHODS: This was done by embedding a cubic (sodium chloride) compact with polymer, allowing the compact to be cut without disrupting the structure. By doing so, it was possible to make scanning electron microscopic images from different angles at different locations in the compact. These images were made binary with a two-means cluster algorithm (Isodata) after which the porosity could be calculated. Counting the number of transitions from the pixels in the pores to the pixels in the sodium chloride particles in two perpendicular directions allows us to construct a measure for the anisotropic connectivity of the particles. RESULTS: The results show an increase in porosity toward the bottom of the compact and showed a preferred orientation of the pores in the direction of compression. CONCLUSIONS: The proposed method is suitable for analyzing the pore distribution quantitatively and for evaluating anisotropy.

Anisotropy↗

PubMed1989

Depressive episodes in premenstrual syndrome.

Episodic depression, a prominent but poorly defined symptom of premenstrual syndrome, was quantitated in 24-hour cortisol secretory episodes (determined by sampling at 20-minute intervals) as biochemical markers, as well as the Beck Depression Inventory and Profile of Mood States as psychometric measures. Results of 16 patients with premenstrual syndrome were compared with six age-matched women with endogenous depression and 16 control women. On both the Profile of Mood States and Beck Depression Inventory, women with premenstrual syndrome showed a marked worsening of scores (p less than 0.01) during the luteal phase compared with either their own follicular phase scores or the scores of controls in either cycle phase. However, Beck Depression Inventory scores were threefold higher (p less than 0.005) in women with depression than in those with luteal phase premenstrual syndrome (3.37 +/- 3.6 vs. 11.9 +/- 2.5). The Profile of Mood States depression scale was also higher (p less than 0.05) in women with depression than in those with premenstrual syndrome, while scores on other Profile of Mood States scales were similar. The numbers of cortisol secretory pulses identified by the cluster algorithm were similar (5 to 6 per 24 hours) in all groups, and the time of circadian nadirs as determined by cosinor rhythmometry were comparable. While the mean amplitude and duration of the cortisol pulses were also similar in women with premenstrual syndrome and controls, both were significantly higher (p less than 0.05) in women with depression. This resulted in markedly enhanced (p less than 0.005) cortisol secretion during a given secretory episode in women with depression and in higher 24-hour transverse mean cortisol values in women with depression (87.8 +/- 5.8 ng/ml) than in either those with premenstrual syndrome (66.7 +/- 3.3 ng/ml) or controls (58.9 +/- 3.3 ng/ml). These data affirm the clinical impression that depressive episodes occurring selectively in the luteal phase of the cycle in women with premenstrual syndrome are not present in controls and demonstrate, for the first time, that these episodes are distinct from endogenous depression as measured by both cortisol secretory parameters and psychological indices.

Adult↗

PubMed1985

An attempt to differentiate female relatives of Duchenne type dystrophy from healthy subjects using an automatic EMG analysis.

A new automatic EMG analysis and on-line assignment of MUAP into 8 dynamic cluster algorithm classes (P1......P8) were applied to female relatives of patients with Duchenne type dystrophy. Promising results are given. MUAP amplitude and duration differed significantly in the female relatives compared to the control subjects. MUAP distribution patterns found in the carrier population were significantly different from those found in controls; the carrier population exhibited higher percentages of MUAP (than healthy subjects) in the classes where were assigned the great majority of the potentials obtained from patients with Duchenne type dystrophy. All the known carriers and 55.5% of the possible carriers were detected using these methods. Nevertheless, the absolute accuracy of the results cannot yet be considered achieved because no recognizable distribution pattern was observed in carrier's daughters. No correlation was found between CK levels and EMG distribution.

Adult↗

PubMed1989

Androgen-dependent somatotroph function in a hypogonadal adolescent male: evidence for control of exogenous androgens on growth hormone release.

A 14(10/12)-year-old white male with primary gonadal failure following testicular irradiation for acute lymphocytic leukemia was evaluated for poor growth. He had received 2400 rad of prophylactic cranial irradiation. The growth velocity had decelerated from 7 to 3.2 cm/yr over 3 years. His bone age was 12(0/12) years (by TW2-RUS), and his peak growth hormone (GH) response to provocative stimuli was 1.4 ng/mL. The 24-hour GH secretion was studied by drawing blood every 20 minutes for 24 hours. The resulting GH profile was analyzed by a computerized pulse detection algorithm, CLUSTER. Timed serum GH samples were also obtained after a 1 microgram/kg IV bolus injection of the GH releasing factor (GRH). The studies showed a flat 24-hour profile and a peak GH response to GRH of 3.9 ng/ml. Testosterone enanthate treatment was started, 100 mg IM every 4 weeks. Ten months after the initiation of therapy the calculated growth rate was 8.6 cm/yr. The 24-hour GH study and GRH responses were repeated at the time, showing a remarkably normal 24-hour GH secretory pattern and a peak GH response to GRH of 14.4 ng/mL. Testosterone therapy was discontinued, and 4 months later similar studies were repeated. A marked decrease in the mean 24-hour GH secretion and mean peak height occurred, but with maintenance of the GH pulse frequency. The GH response to GRH was intermediate, with a peak of 8 ng/mL. There was no further growth during those 4 months despite open epiphyses.(ABSTRACT TRUNCATED AT 250 WORDS)

Adolescent↗

PubMed1994

Acute pharmacologic blockade of lipolysis normalizes nocturnal growth hormone levels and pulsatility in obese subjects.

Obesity is associated with blunted growth hormone (GH) levels and pulsatility and elevated plasma free fatty acids (FFA) levels. To evaluate whether the two phenomena are correlated, in the present study we investigated the effects of an acute pharmacologic blockade of lipolysis on nocturnal GH levels and pulsatility in 10 obese and 10 control subjects. At 9 PM on two different nights with a 1-night interval in between, all subjects received either a single oral tablet of placebo or acipimox slow release (ACX-SR, 500 mg) in randomized order. Blood samples were drawn from 10 PM to 6 AM for evaluation of FFA, glycerol, GH, immunoreactive insulin (IRI), glucose, and insulin-like growth factor-I (IGF-I) levels. After placebo, FFA and glycerol levels were higher (P < .02) and GH levels, areas, peak amplitude, and peak increment (assessed by the Cluster algorithm) were lower in obese than in control subjects (P < .01). After ACX-SR, FFA and glycerol levels were reduced in both groups (P < .02 v placebo), and in obese subjects they became similar to those observed in control subjects after placebo. ACX-SR had no effect on GH levels and pulsatility in control subjects. GH levels, areas, peak, amplitude, peak increment, and interpeak valley levels were all increased after ACX-SR in obese subjects (P < .05 or less v placebo) and became similar to those observed in normal subjects after placebo, but no correlation was found between the reduction in FFA levels and the increase in GH levels and pulsatility.(ABSTRACT TRUNCATED AT 250 WORDS)

Administration, Oral↗

PubMed1987

A method for automatic classification of large and small myelinated fibre populations in peripheral nerves.

The statistical analysis of morphometric data collected from biopsies of human superficial peroneal nerve is complicated by the heterogeneity of the population of myelinated fibres. In order to make separate statistical analyses of the subpopulations of large and small fibres we have developed a computer program (written in PASCAL) for their automatic separation. The method is based on a dynamic centres clustering algorithm and was applied to the multifactorial space defined by the principal component analysis of the morphometric variables: axonal diameter, myelin sheath thickness, circularity index and g-ratio. The classification technique was applied to measurements obtained from 5 control nerves, and to simulated data, and in each case it gave consistent Gaussian subpopulations with no need for the introduction of supplementary variables.

Algorithms↗

PubMed1988

Individual differences in cardiovascular responses to intermittent noise in human females.

In a group of 13 female subjects submitted in three sessions to regularly alternating pink noise-steps, different techniques were proposed to cope with individual differences in cardiovascular responses. Application of a clustering algorithm to intercorrelation data of individual heart rates (HR) resulted in three subsets of 'sensitive' (S), 'moderately sensitive' (MS) and 'poorly sensitive' (PS) subjects. Only one pattern of HR changes under intermittent noise was observed, but clear-cut differences appeared between sensitivity subgroups which differed for amplitudes of HR responses to noise-steps and for adaptivity to repeated exposures. S subjects always reacted strongly (in fact, progressively strongly); PS subjects always reacted poorly; MS subjects reacted moderately but some of them with exposures either seemed to adapt to the noise or tolerated the noise less and less easily. Although exposure to intermittent noise for 35 min did not prevent a slowing trend of HR in all subjects, no sign of habituation of HR responses to noise-steps was present in any subgroup with repeated exposures. Mean levels of measured systolic and diastolic blood pressure decreased significantly with repeated exposures in MS and PS subjects, but not in S subjects.

Adult↗

PubMed1986

Mental disorders and ecological structure in Nottingham.

This paper presents the findings of a specifically geographical investigation of the incidence, distribution and social/environmental correlates of mental disorder in Nottingham. Three diagnostic groups were examined, namely schizophrenia and paranoia, the effective psychoses (or manic depression) and the non-psychotic mental disorders. Analysis of two distinct cohorts of first contact patients for both the schizophrenia and affective psychoses diagnoses yielded markedly dissimilar incidence rates. It is therefore suggested that observed variations in the incidence of specific mental disorders between cities probably reflect such nosocomial (i.e. service related) factors as diagnostic accuracy and the levels of local psychiatric services. It is therefore dangerous to ascribe the variations solely to the contrasting social/environmental milieux found in these cities. The spatial distributions of the selected mental disorders within Nottingham were analysed in the context of a set of 12 distinct ecological areas. These areas were derived from a matrix comprising 105 sub-areas and 40 variables via principal components analysis and a non-hierarchical clustering algorithm. Marked spatial variation in the incidence of all the mental disorders was demonstrated via both traditional mapping and probability mapping techniques. Pearson product-moment analysis revealed that the distributions of the two diagnostically distinct schizophrenia and affective psychoses cohorts were virtually identical. The relationships between the inception rates for the mental disorders and social/environmental attributes were analysed. Stepwise multiple regression models for both the principal components and the individual census variables revealed strong and systematic relationships with all the mental disorders. Although such ecological analysis has limited explanatory power it nevertheless provides useful insights into mental disorder-environmental relationships. It is argued that these can be subsequently best examined at a disaggregated (i.e. behavioural) level.

Affective Disorders, Psychotic↗

PubMed1991

How do androgens affect episodic gonadotrophin secretion in postmenopausal women?

In the absence of any significant ovarian oestrogen secretion, as in post-menopausal women, the hypothalamic-pituitary axis may still be influenced by the androgens which continue to be produced. The episodic secretion of luteinizing hormone (LH) and follicle-stimulating hormone (FSH) by postmenopausal women was accordingly assessed following short-term androgen antagonism induced by flutamide, a specific androgen receptor blocker. Blood samples were collected at 10-min intervals for 10 h in nine women before and during flutamide administration (750 mg/day for 6 days) for the determination of gonadotrophin and sex hormone concentrations by radioimmunoassay. On both occasions, 25 micrograms of gonadotrophin-releasing-hormone (GnRH) was injected intravenously 8 h after initiation of the blood collections. Flutamide administration decreased (P less than 0.01 or less) androgen concentrations (testosterone, androstenedione and dehydroepiandrosterone sulphate) in relation to baseline values, but did not alter oestrogen (oestrone and oestradiol) or sex-hormone-binding globulin levels. The LH and FSH pulse characteristics (frequency, amplitude, interpulse interval and transverse mean levels) determined by a cluster algorithm in the gonadotrophin secretory profiles did not differ before and during androgen blockade. By contrast, androgen antagonism increased LH (P less than 0.01) and tended to enhance FSH (P = 0.10) FSH release in response to GnRH stimulation. Hence, short-term androgen receptor blockade with flutamide did not greatly affect episodic gonadotrophin secretion. However, the combined evidence of the enhanced gonadotrophin release observed in response to GnRH stimulation and the unchanged gonadotrophin secretion during androgen antagonism suggests that alterations in the magnitude, but not the frequency, of hypothalamic GnRH release had occurred. Even in the presence of substantial serum androgen concentrations, the gonadotrophin pulse rhythm in hypogonadal women constitutes the maximal-rate GnRH-LH release pattern.

Androgens↗

PubMed2005

Perceptually based FROC analysis.

RATIONALE AND OBJECTIVES: Analysis of reading data when cases have multiple targets and/or the reader is required to localize targets is difficult. One approach to this free-response operating characteristic (FROC) problem is for images to be segmented (eg, with quadrants) by the investigator and a segment-level analysis be conducted with the case as a nesting factor. In this report, we introduce an alternative method that uses the visual scan path of the reader to segment the image. We evaluate the new method by applying it to data from a mammography reading experiment. MATERIALS AND METHODS: The gaze scan path of one radiologist was recorded as she scanned 40 mammograms for masses and microcalcifications. The observer is an experienced mammographer and was not one of the authors. In addition, the reader provided a rating indicating the degree of suspicion for any suspected targets she identified and localized. We then established "perceptual regions" by using a clustering algorithm on the visual fixations. We combined ratings given to specific locations indicated by the reader with the segmentation from the visual scan to generate a series of ratings classified for whether the perceptually based region associated with the rating contained or did not contain a known target. We analyzed data generated by our method from all 40 cases by using the conventional maximum-likelihood method based on the binormal model. Finally, we tested goodness-of-fit of the binormal model to the data by using chi-square. RESULTS: Maximum-likelihood estimation led to a model that did not fit the data (P < .001). However, examination of the observed and expected counts suggests that the binormal assumption does not hold for segments that contain targets and a bimodal distribution model might be preferred. CONCLUSION: Our new method provides an alternative approach to analysis of the FROC experiment. It needs to be developed further. Specifically, we propose that a mixture model extension of the binormal model be developed for ratings data arising from perceptually based FROC experiments. A disadvantage to our method is the requirement to record the scan path of the reader. However, we believe that adding such information to receiver operating characteristic (ROC) curve analysis will pay off when appropriate statistical models have been identified because we believe our data support our hypothesis that the perceptual scanning of images by humans deconvolves interpretation correlation. If true, this hypothesis implies that conventional statistical methods for ROC analysis based on independent data can be applied to the analysis of FROC data after conditioning on the scan path of the observer.

Data Interpretation, Statistical↗

PubMed2006

Cell-nuclear data reduction and prognostic model selection in bladder tumor recurrence.

OBJECTIVE: The paper aims at improving the prediction of superficial bladder recurrence. To this end, feedforward neural networks (FNNs) and a feature selection method based on unsupervised clustering, were employed. MATERIAL AND METHODS: A retrospective prognostic study of 127 patients diagnosed with superficial urinary bladder cancer was performed. Images from biopsies were digitized and cell nuclei features were extracted. To design FNN classifiers, different training methods and architectures were investigated. The unsupervised k-windows (UKW) and the fuzzy c-means clustering algorithms were applied on the feature set to identify the most informative feature subsets. RESULTS: UKW managed to reduce the dimensionality of the feature space significantly, and yielded prediction rates 87.95% and 91.41%, for non-recurrent and recurrent cases, respectively. The prediction rates achieved with the reduced feature set were marginally lower compared to the ones attained with the complete feature set. The training algorithm that exhibited the best performance in all cases was the adaptive on-line backpropagation algorithm. CONCLUSIONS: FNNs can contribute to the accurate prognosis of bladder cancer recurrence. The proposed feature selection method can remove redundant information without a significant loss in predictive accuracy, and thereby render the prognostic model less complex, more robust, and hence suitable for clinical use.

Algorithms↗

PubMed2004

Pregnancy-associated changes in genome-wide gene expression profiles in the liver of cow throughout pregnancy.

The objective of the present study was to fabricate and use a bovine liver complementary DNA (cDNA) microarray to profile genome-wide gene expressions in the liver of cow throughout pregnancy. A cDNA library was prepared from liver total RNA collected from cows during estrous cycle and pregnancy, and from fetuses at different stages of pregnancy. The sequenced clones were compiled and annotated by basic local alignment search tool (BLASTn) and spotted onto glass slides. The annotated liver array represented 2675 genes. Of which, 1442 were known genes while 617 sequences had matches with sequences found in expressed sequence tags databases. In addition, 616 unknown sequences were found and these sequences may possibly be identified as candidates for novel bovine genes. For gene expression profiling studies, total RNA from livers of cows slaughtered on days 19, 27-28, 49-58, 150, and 245 of pregnancy (test RNAs) was separately reverse transcribed and labeled with either cyanine 5-fluorescent dye (Cy5) or Cy3. The test samples were individually compared with liver total RNA collected from nonpregnant cycling cows (control RNA) after reverse transcription and labeling with the opposite dye following a two-color hybridization method. After scanning, image acquisition, and normalization, genes that showed either more than 1.5-fold (test/control) induction or repression were selected for further analyses. Hierarchical clustering algorithm showed a clear induction of most liver genes on days 27-28 of pregnancy. Self-organizing maps algorithm identified groups of genes whose differential expression patterns were similar across pregnancy. In conclusion, we described fabrication of a bovine liver cDNA microarray, and demonstrate, for the first time, differential expression patterns of a large number of coregulated liver genes in parallel throughout pregnancy in the bovine.

Algorithms↗

PubMed2006

Transcriptional pulsing of a developmental gene.

It has not been possible to view the transcriptional activity of a single gene within a living eukaryotic cell. It is therefore unclear how long and how frequently a gene is actively transcribed, how this is modulated during differentiation, and how transcriptional events are dynamically coordinated in cell populations. By means of an in vivo RNA detection technique , we have directly visualized transcription of an endogenous developmental gene. We found discrete "pulses" of gene activity that turn on and off at irregular intervals. Surprisingly, the length and height of these pulses were consistent throughout development. However, there was strong developmental variation in the proportion of cells recruited to the expressing pool. Cells were more likely to re-express than to initiate new expression, indicating that we directly observe a transcriptional memory. In addition, we used a clustering algorithm to reveal synchronous transcription initiation in neighboring cells. This study represents the first direct visualization of transcriptional pulsing in eukaryotes. Discontinuity of transcription may allow greater flexibility in the gene-expression decisions of a cell.

Animals↗

PubMed2005

Identification of HNP3 as a tumour marker in CD4+ and CD4- lymphocytes of patients with cutaneous T-cell lymphoma.

Cutaneous T-cell lymphomas (CTCL) are characterized by malignant proliferation of skin homing T-cells. Although prognosis is generally good, reliable markers are needed to identify patients at risk for a more aggressive course. ProteinChip (SELDI) technology was used as a tool for the discovery of protein patterns in lymphocytes from patients with CTCL (n=25) and unaffected controls (n=25). Lymphocytes were separated in CD4+ and CD4- fractions by magnetic cell sorting (MACS). Each whole protein extract was analysed by ProteinChip technology. The resulting protein profiles were submitted for bioinformatic analysis including a clustering algorithm, a rule extraction, a rating and a rule-base construction step. For the generated combined rule base for the CD4- cell fraction, both the sensitivity and specificity for the prediction of CTCL reached 96%, while for the CD4+ fraction they were 92% and 84%, respectively, for sensitivity and specificity. The most significant peak at 3489Da could be identified as HNP3, an alpha-defensin, by immunocapturing. These results open up both the possibility for the use of this protein signature, especially HNP3, to more effectively monitor and screen CTCL, and the avenue to identify the other relevant peaks for a better understanding of the development of this tumour.

Biomarkers, Tumor↗

PubMed2005

Peak pressure curve: an effective parameter for early detection of foot functional impairments in diabetic patients.

A clinical investigation was conducted on 61 diabetic patients and 22 healthy volunteers. Joint mobility, muscular function of the foot-ankle complex and plantar pressure measurements were characterised. A clustering algorithm was applied to obtain patient classification based on the shape and amplitude of the time curve of the instantaneous maximum pressure the foot experienced during gait. Results indicate that a screening test based on the peak pressure curve might be an effective way to detect diabetic patients at risk of foot ulceration.

Algorithms↗