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PubMed2001

Stiles-Crawford effect of the first kind: assessment of photoreceptor alignments following dark patching.

Properties of presumed mechanisms controlling photoreceptor alignments are partially defined. A phototropic mechanism normally dominates alignment, but do modest changes in orientations occur with dark patching? Here, new photopic Stiles-Crawford (SCE-I) determinations were made before patching (pre-patch), just after 8-days of dark-patching (post-patch), and 3 days after patch removal (recovery test). We tested at 0, 11 and 22 degrees in the temporal retina of both eyes. Ten eyes of adult subjects were tested. SCE-I peak positions and Stile's parameter 'rho' were assessed. Dark-patching effects were small. Observations revealed meaningful corrective alignment overshoots with recovery in the light. Results suggest (1) the presence of multiple weak mechanisms affecting receptor alignments in the dark; (2) the phototropic mechanism to be dominant in the light; (3) the need for multiple test loci to be sampled in such studies, and (4) small changes in the SCE-I in the pupil plane can reflect meaningful events occurring at the retina.

Adaptation, Ocular↗

PubMed2006

Genotyping of Campylobacter spp. from retail meats by pulsed-field gel electrophoresis and ribotyping.

AIMS: To determine the genetic relatedness of Campylobacter spp. from retail meat products, and compare the discriminatory power of pulsed-field gel electrophoresis (PFGE) and automatic ribotyping. METHODS AND RESULTS: A total of 378 Campylobacter isolates recovered from 159 raw meats (130 chicken, 25 turkey, three pork and one beef) sampled from 50 retail grocery stores of four supermarket chains in the Maryland suburban area from August 1999 to July 2000 were analysed by PFGE with SmaI, 120 isolates of which were also characterized by ribotyping with PstI using RiboPrinter system. A total of 148 unique PFGE patterns were identified, 91 of which were present in multiple Campylobacter isolates and 24 in multiple meat samples. Nineteen Campylobacter clones with identical PFGE patterns recurred frequently (up to nine times) throughout the sampling period. Comparing ribotyping with PFGE, we identified 44 PFGE patterns and 22 RiboGroups among the 120 isolates tested. Multiple PFGE patterns within one RiboGroup were commonly observed, as well as multiple RiboGroups within one PFGE pattern. CONCLUSIONS: Although Campylobacter present in retail meats were genetically diverse, certain clones persisted in poultry meats. PFGE had a greater discriminatory power than ribotyping, and the two methods were complementary in genotyping Campylobacter. SIGNIFICANCE AND IMPACT OF THE STUDY: Genomic DNA fingerprinting of Campylobacter confirmed diverse and recurrent Campylobacter clones in the retail meats, which provides additional data for a better understanding of the epidemiological aspect of Campylobacter infection.

Animals↗

PubMed2002

Measurable differences between sequential and parallel diagnostic decision processes for determining stroke subtype: a representation of interacting pathologies.

Stroke diagnosis depends on causal subtype. The accepted classification procedure is a succession of diagnostic tests administered in an order based on prior reported frequencies of the subtypes. The first positive test result completely determines diagnosis. An alternative approach tests multiple concomitant diagnostic hypotheses in parallel. This method permits multiple simultaneous pathologies in the patient. These two diagnostic procedures can be compared by novel numeric criteria presented here. Thrombosis, a type of ischemic stroke, results from interaction between endothelium, blood flow and blood components. We tested for ischemic stroke on thirty patients using both methods. For each patient the procedure produced an assessment of severity as an ordered set of three numbers in the interval [0, 1]. We measured the difference in diagnosis between the sequential and parallel diagnostic algorithms. The computations reveal systematic differences: The sequential procedure tends to under-diagnose and excludes any measure of interaction between pathologic elements.

Algorithms↗

PubMed2006

Association of warfarin dose with genes involved in its action and metabolism.

We report an extensive study of variability in genes encoding proteins that are believed to be involved in the action and biotransformation of warfarin. Warfarin is a commonly prescribed anticoagulant that is difficult to use because of the wide interindividual variation in dose requirements, the narrow therapeutic range and the risk of serious bleeding. We genotyped 201 patients for polymorphisms in 29 genes in the warfarin interactive pathways and tested them for association with dose requirement. In our study, polymorphisms in or flanking the genes VKORC1, CYP2C9, CYP2C18, CYP2C19, PROC, APOE, EPHX1, CALU, GGCX and ORM1-ORM2 and haplotypes of VKORC1, CYP2C9, CYP2C8, CYP2C19, PROC, F7, GGCX, PROZ, F9, NR1I2 and ORM1-ORM2 were associated with dose (P < 0.05). VKORC1, CYP2C9, CYP2C18 and CYP2C19 were significant after experiment-wise correction for multiple testing (P < 0.000175), however, the association of CYP2C18 and CYP2C19 was fully explained by linkage disequilibrium with CYP2C9*2 and/or *3. PROC and APOE were both significantly associated with dose after correction within each gene. A multiple regression model with VKORC1, CYP2C9, PROC and the non-genetic predictors age, bodyweight, drug interactions and indication for treatment jointly accounted for 62% of variance in warfarin dose. Weaker associations observed for other genes could explain up to approximately 10% additional dose variance, but require testing and validation in an independent and larger data set. Translation of this knowledge into clinical guidelines for warfarin prescription will be likely to have a major impact on the safety and efficacy of warfarin.

Adult↗

PubMed1994

Methylphenidate treatment following ablation-induced hemiplegia in rat: experience during drug action alters effects on recovery of function.

Two experiments examined the effects of single or multiple administrations of methylphenidate (MPH; Ritalin) and differing amounts of beam-walking trials (symptom relevant experience) during the period of drug action on recovery from hemiplegia following unilateral sensorimotor cortex ablation in rat. The first study tested multiple doses of MPH (10 mg/kg) or sterile saline given once daily, followed by four beam-walk (BW) trials at 1, 2, 3, and 6 h on 3 consecutive days. A significant and enduring enhancement of recovery was only observed 24 h after the third administration of MPH, compared to saline controls. In the second study, a single dose of MPH (10 mg/kg) or saline was administered 24 h after ablation, followed by 12 BW trials beginning 1 h and continuing at 15-min intervals until 3 h after MPH or saline administration. A significant and enduring facilitation of BW ability was produced by this single MPH treatment regimen. These data further support the importance of an interaction between symptom-relevant experience and drugs that increase norepinephrine transmission to enhance functional recovery after brain damage.

Animals↗

PubMed2026

Cross-target and cell-preferential CRISPR-Cas9 inhibition with carbohydrate-tagged oligonucleotides.

Precise control of clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9) activity is important for limiting off-target effects and chromosomal rearrangements. Existing inhibitors, including anti-CRISPR proteins and spacer-targeting oligonucleotides, can be constrained by immunogenicity, target-sequence dependence, or delivery challenges. Here, we developed single-stranded DNA oligonucleotides that target conserved regions of the Streptococcus pyogenes Cas9 single-guide RNA (sgRNA) scaffold rather than the variable spacer. Screening identified single-stranded DNA 7 (ssDNA7), which targets stem-loop-1 and the adjacent linker and inhibits Cas9 activity across multiple tested spacer sequences and genomic loci without redesigning the inhibitor. Carbohydrate conjugation improved oligonucleotide stability and preferentially enhanced inhibitory activity in selected liver-derived or cancer cell models. Amplicon sequencing confirmed inhibition of endogenous editing in multiple cell models and normal liver-derived organoids, and supported cell-preferential inhibition in matched cell comparisons. These findings establish sgRNA-scaffold targeting as a strategy for cross-target inhibition of Cas9 and show that carbohydrate conjugation can tune its cellular activity.

CRISPR-Cas9↗

PubMed2004

Identifying periodically expressed transcripts in microarray time series data.

MOTIVATION: Microarray experiments are now routinely used to collect large-scale time series data, for example to monitor gene expression during the cell cycle. Statistical analysis of this data poses many challenges, one being that it is hard to identify correctly the subset of genes with a clear periodic signature. This has lead to a controversial argument with regard to the suitability of both available methods and current microarray data. METHODS: We introduce two simple but efficient statistical methods for signal detection and gene selection in gene expression time series data. First, we suggest the average periodogram as an exploratory device for graphical assessment of the presence of periodic transcripts in the data. Second, we describe an exact statistical test to identify periodically expressed genes that allows one to distinguish periodic from purely random processes. This identification method is based on the so-called g-statistic and uses the false discovery rate approach to multiple testing. RESULTS: Using simulated data it is shown that the suggested method is capable of identifying cell-cycle-activated genes in a gene expression data set even if the number of the cyclic genes is very small and regardless the presence of a dominant non-periodic component in the data. Subsequently, we re-examine 12 large microarray time series data sets (in part controversially discussed) from yeast, human fibroblast, human HeLa and bacterial cells. Based on the statistical analysis it is found that a majority of these data sets contained little or no statistical significant evidence for genes with periodic variation linked to cell cycle regulation. On the other hand, for the remaining data the method extends the catalog of previously known cell-cycle-specific transcripts by identifying additional periodic genes not found by other methods. The problem of distinguishing periodicity due to generic cell cycle activity and to artifacts from synchronization is also discussed. AVAILABILITY: The approach has been implemented in the R package GeneTS available from http://www.stat.uni-muenchen.de/~strimmer/software.html under the terms of the GNU General Public License.

Algorithms↗

PubMed1994

Malignancies that occur before and after anal cancer: clues to their etiology.

With the use of two different approaches to study multiple primaries in anal cancer patients, the authors sought clues to the etiology of anal cancer. Based on data from the Danish Cancer Registry for 1943-1989, previous cancers in 831 anal cancer patients were compared with cancers in 12,376 matched population controls, and subsequent cancers in 955 anal cancer patients were compared with expected numbers based on population rates. Overall, previous cancers were in excess among anal cancer patients (odds ratio (OR) = 1.7, 95% confidence interval (CI) 1.3-2.1). Elevated risks were observed especially for the vulva/vagina (OR = 15.4, 95% CI 4.9-48.0), cervix (OR = 4.3, 95% CI 2.7-6.9), and lymphoma/leukemia (OR = 3.9, 95% CI 1.5-10.4). Subsequent cancers were also in excess (relative risk (RR) = 1.4, 95% CI 1.1-1.7), particularly for the lung (RR = 2.3, 95% CI 1.3-3.7), bladder (RR = 2.3, 95% CI 1.0-4.6), breast (RR = 2.0, 95% CI 1.2-3.3), vulva/vagina (RR = 12.3, 95% CI 4.0-28.7), and small intestine (two cases) (RR = 10.8, 95% CI 1.2-39.0). Colorectal cancers were reduced (RR = 0.3, 95% CI 0.1-0.9). The data support a multifactorial etiology for anal cancer, in which an infectious agent and smoking may be involved. The association with lymphatic/hematopoietic cancers may indicate a possible role for immunodeficiency in anal cancer development. Multiple cancers occurred predominantly in patients diagnosed with anal cancer at a young age (< 60 years), which raises the possibility of a genetic predisposition for some cases. The authors recommend that, in future hypothesis generating and hypothesis testing multiple cancer studies of rare malignancies, the combined study of cancer events both prior to and following an index cancer should be considered.

Age Factors↗

PubMed2000

Pasteurized, monoclonal antibody factor VIII concentrate: establishing a new standard for purity and viral safety of plasma-derived concentrates.

A factor VIII concentrate (Monoclate-P) manufactured using a combination of pasteurization and immunoaffinity chromatography has been chosen to compare and contrast manufacturing aspects of plasma-derived factor VIII concentrates. Pasteurization is a virucidal method with a long safety record in clinical practice, while immuno-affinity chromatography selectively isolates and purifies the procoagulant protein of factor VIII, and partitions potential viral contaminants and nonessential proteins to the unbound fraction. The complete Monoclate-P production process reduces human immunodeficiency virus by > or = 10.5 log10, Sindbis (a model for hepatitis C virus) by > or = 6.5 log10, and murine encephalomyocarditis virus (a non-enveloped model virus) by 7.1 log10. The viral safety of Monoclate-P has been further demonstrated in clinical studies in patients not previously treated with blood or plasma-derived products. Additionally, the manufacture of Monoclate-P includes careful donor screening and plasma testing for antibodies to syphilis and human immunodeficiency, hepatitis B, and hepatitis C viruses to enhance source plasma safety. Combined with donor selection and plasma testing, multiple viral reduction steps effectively eliminate both lipid-enveloped viruses (e.g. human immunodeficiency, hepatitis B and C) and non-lipid-enveloped viruses (e.g. hepatitis A). In addition, polymerase chain reaction-based nucleic acid detection tests for hepatitis B and C viruses and for human immunodeficiency virus-1 have been introduced as part of an investigational new drug mechanism.

Antibodies, Monoclonal↗

PubMed1986

Prediction of death, myocardial infarction, and worsening chest pain using thallium scintigraphy and exercise electrocardiography.

Although used extensively, there is little published information on the prognostic ability of exercise 201Tl scintigraphy. Accordingly, 1 yr after testing we contacted 819 patients without previous MI or CABG seen in our laboratory during a 2-yr period. Events were defined as death from a cardiovascular cause, nonfatal MI, or worsening clinical state requiring CABG. The event rate was 3.9 events per 100 patients per year. There was univariate prognostic information when comparing the highest and lowest categories as risk ratios for chest pain characteristics (2.7), sex (2.3), exercise duration (3.1), ST slope (2.5), and thallium pattern (11.6), intensity of perfusion defect (17.2), and number of abnormal regions (8.7). However, the strongest predictors were also the least common. Prognostic ability was improved by combining the results categorically, as the number of abnormal tests (13.9). The highest risk ratio, 20.5:1, was obtained by combining results through discriminant function analysis. We conclude that exercise thallium scintigraphy provides prognostic information, although the most predictive patterns are uncommon. Combining the results of multiple test results improves the prognostic ability.

Adult↗

PubMedDate not supplied

The influence of polysomnography on the Multiple Sleep Latency Test and other measures of daytime sleepiness.

INTRODUCTION: According to its guidelines, the Multiple Sleep Latency Test (MSLT) should be performed following an all-night polysomnography (PSG). However, the sleep quality and consequently the MSLT results may be affected by PSG and by the fact that a subject sleeps under unfamiliar conditions. The aim of this study was to examine whether PSG performed in a sleep laboratory has any influence on the MSLT and other measures of daytime sleepiness. METHODS: Twenty healthy subjects with a mean age of 35.9+/-10.1 years underwent two MSLT examinations, and the 2 examination days were at least 4 weeks apart. In addition, on each occasion a monotonous vigilance task (VT) was performed and the subjects were asked to fill out the Epworth Sleepiness (ESS) and Visual Analogue Scales (VAS). In a cross-over design, a group of 10 subjects underwent a MSLT (MSLT-P) following a PSG and, on a second occasion, a MSLT (MSLT-N) was performed without a prior PSG. Vice versa, a second group of 10 subjects underwent first MSLT-N and then MSLT-P. RESULTS: None of the MSLT parameters differed significantly between MSLT-P and MSLT-N. The other measures of daytime sleepiness (VT, ESS, VAS) also showed no evidence of significant differences between days with and without a prior PSG. CONCLUSIONS: The results of MSLT and other measures of daytime sleepiness in healthy subjects are not influenced by the fact whether or not the subjects had a PSG the night prior to MSLT.

Adult↗

PubMed2003

Multiple regression modelling of mineral base oil biodegradability based on their physical properties and overall chemical composition.

A set of 38 mineral base oils was characterized by a number of chemical (i.e., overall chemical composition) and physical parameters used routinely in industry. Their primary biodegradability was evaluated using the CEC L-33-A-93 test. Multiple (stepwise) linear regression (MLR) analyses were performed to describe the relationships between the biodegradability values and the chemical or physical properties of oils. Chemical, physical, and both types of parameters were successively used as independent variables. Using chemical descriptors as variables, a four-variable model equation was obtained that explained only 68.2% (adjusted R-squared statistic=68.2%) of the variability in biodegradability. The fitting was improved by using either the physical or the whole parameters as variables. MLR analyses led to three-descriptor model equations involving kinematic viscosity (as log), Noack volatility (as log) and either the viscosity index (pure physical model) or the paraffinic carbon percentage (mixed chemical-physical model). These two models displayed very similar adjusted R-squared statistics, of approximately 91%. Their predicting ability was verified using 25 additional base oils or oil blends. For 80% of oils on a total of 63, the absolute percentage error on biodegradability predicted by either model was lower than 20%. Kinematic viscosity was by far the most influential parameter in the two models.

Biodegradation, Environmental↗

PubMed2005

The (CA)n polymorphism of the TNFR2 gene is associated with peak bone density in Chinese nuclear families.

Low peak bone density (PBD) in adulthood is an important determinant of osteoporotic fracture (OF) in the elderly. The tumor necrosis factor receptor 2 (TNFR2) gene has been considered as an important candidate gene for PBD due to its important role in bone turnover. In this study, we recruited a total of 1,263 subjects from 402 Chinese nuclear families composed of both parents and at least one daughter, and tested the association of the (CA)(n) polymorphism in intron 4 of the TNFR2 gene with PBD using a more contemporary quantitative transmission disequilibrium test (QTDT). Significant within-family association was detected between the CA16 allele and bone mineral density (BMD) at the lumbar spine with the P-value of 0.005 after permutations, which is still significant after correction for multiple testing. Some evidence of total-family association between the CA16 allele and lumbar spine BMD was found (P=0.021), although the significant level did not reach the empirical threshold (P< or =0.007). About 3.14% of lumbar spine BMD variation can be explained by the CA16 allele. In summary, our results suggest that the TNFR2 gene may play an important role in determining lumbar spine BMD variation in Chinese women.

Bone Density↗

PubMed1995

The relation between thermal and pH changes in alginate impression materials.

OBJECTIVES: The purpose of this study was to determine if pH changes are related to thermal changes during setting in alginate impression materials, and to investigate the possibility of establishing a mathematical model between thermal and pH changes. METHODS: Thermal and pH changes were recorded during the 20 min gelation period following the mixing of five commercial alginate materials. The data obtained were plotted and statistically analyzed using a student's T-test, multiplicative, linear and reciprocal analyses at a significance level of p<0.05. These analyses were used to determine the differences between various materials and to establish regression models between thermal and pH changes for each of the materials tested. RESULTS: For all samples, the pH values fell within the first minutes from the alkaline range into the neutral and even into the acidic range, while the initial sharp fall in temperature was followed by a subsequent gradual increase. Differences in the final gel structures of the alginate materials were shown to be related to the differences in thermal and pH changes during setting. This could be expected from their various chemical compositions such as the variety of components, the chemical forms of principal components and the proportion of each component. SIGNIFICANCE: This work contributes to the development of a mathematical model relating pH changes and thermal changes to form a basis for the correlation between chemical properties and characteristics in practical use.

Alginates↗

PubMed1996

Mucosal allergy: role of mast cells and eosinophil granulocytes in the gut.

Despite the progress made in understanding the mechanisms of allergic disease, the pathophysiology and clinical significance of intestinal allergic reactions is largely unclear. The intestinal mucosa is pre-destined for allergic reactions against food proteins and other antigens, and a number of studies indicate that allergic reactions occur in the GI tract. However, only a few epidemiological data are available, and the mechanisms are poorly understood. Intestinal allergic reactions may be different to classical IgE-mediated reactions because patients with intestinal allergy often have negative skin tests and low levels of serum IgE. There is increasing evidence that, as with the findings in the skin and lung, mast cells and eosinophils play a central role in mediating intestinal allergic reactions. Furthermore, both types of cell are found to be activated in a number of other GI inflammatory diseases such as inflammatory bowel disease, celiac disease and eosinophilic gastroenteritis. However, the relationship between these pathologies and intestinal allergy is largely unclear. A major clinical problem is the lack of appropriate means for confirming the diagnosis of intestinal allergy. However, new test systems have been developed--such as the measurement of eosinophil mediators in stool samples or endoscopic provocation tests performed locally at the intestinal mucosa, which may improve the possibility of identifying afflicted patients on an objective basis. Since symptoms of intestinal allergic reactions are variable and non-specific, the diagnosis requires the use of multiple tests and the exclusion of other pathologies such as infectious disease or non-immunological intolerance reactions. The preferred therapeutic option is avoidance of the allergens of relevance; however, this approach can be realized only in some patients, whereas others require additional treatment, for example, with oral cromoglycate or corticosteroids. Although we do not yet know to what extent intestinal allergic reactions may be an aetiological factor in GI diseases, such reactions should be considered in the differential diagnosis of unclear intestinal inflammation and irritable bowel syndrome.

Animals↗

PubMed2003

Multilocus statistics to uncover epistasis and heterogeneity in complex diseases: revisiting a set of multiple sclerosis data.

New statistics are developed to gather the contribution of many alleles at different loci to common diseases. Both inferential and descriptive statistics are included in order to uncover epistatic effects as well as heterogeneity. The problem of multiple testing is circumvented by considering a global null hypothesis. Global testing is supplemented by descriptive methods that make use of measures like odds ratio or the P-value of individually tested allele combinations. Visualization helps to reflect complex data sets. The methods described here have been scrutinized by statistical simulations, and we show that power gains can be substantial as compared to single locus statistics. Typing data of multiple sclerosis patients and controls are investigated, representing an example of larger scale information in screening candidate genes for their impact on complex diseases. New insights emerge from this data set demonstrating genetic heterogeneity and evidence for epistasis.

Adult↗

PubMed2007

Dual selection pressure by drugs and HLA class I-restricted immune responses on human immunodeficiency virus type 1 protease.

To determine the influence of human immunodeficiency virus type 1 (HIV-1)-specific CD8+ T cells on the development of drug resistance mutations in the HIV-1 protease, we analyzed protease sequences from viruses from a human leukocyte antigen class I (HLA class I)-typed cohort of 94 HIV-1-positive individuals. In univariate statistical analyses (Fisher's exact test), minor and major drug resistance mutations as well as drug-associated polymorphisms showed associations with HLA class I alleles. All correlations with P values of 0.05 or less were considered to be relevant without corrections for multiple tests. A subset of these observed correlations was experimentally validated by enzyme-linked immunospot assays, allowing the definition of 10 new epitopes recognized by CD8+ T cells from patients with the appropriate HLA class I type. Several drug resistance-associated mutations in the protease acted as escape mutations; however, cells from many patients were still able to generate CD8+ T cells targeting the escape mutants. This result presumably indicates the usage of different T-cell receptors by CD8+ T cells targeting these epitopes in these patients. Our results support a fundamental role for HLA class I-restricted immune responses in shaping the sequence of the HIV-1 protease in vivo. This role may have important clinical implications both for the understanding of drug resistance pathways and for the design of therapeutic vaccines targeting drug-resistant HIV-1.

Alleles↗

PubMed2001

CSF antiretroviral drug penetrance and the treatment of HIV-associated psychomotor slowing.

The authors evaluated whether highly active antiretroviral therapy (HAART) with multiple CSF-penetrating drugs results in greater improvement in HIV-associated psychomotor slowing than HAART with a single CSF-penetrating drug. Both groups had improvement in CD4 count, plasma viral load, as well as two tests of psychomotor speed. Comparing the two groups, there were no differences in the mean change for CD4 count, viral load, or any of the neuropsychological tests. Multiple and single CSF-penetrating HAART may be equivalent for treating HIV-associated psychomotor slowing.

Adult↗