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At least 379 records · Page 21Linked to original sources
PubMed2002

SubtiList: the reference database for the Bacillus subtilis genome.

SubtiList is the reference database dedicated to the genome of Bacillus subtilis 168, the paradigm of Gram-positive endospore-forming bacteria. Developed in the framework of the B.subtilis genome project, SubtiList provides a curated dataset of DNA and protein sequences, combined with the relevant annotations and functional assignments. Information about gene functions and products is continuously updated by linking relevant bibliographic references. Recently, sequence corrections arising from both systematic verifications and submissions by individual scientists were included in the reference genome sequence. SubtiList is based on a generic relational data schema and a World Wide Web interface developed for the handling of bacterial genomes, called GenoList. The World Wide Web interface was designed to allow users to easily browse through genome data and retrieve information according to common biological queries. SubtiList also provides more elaborate tools, such as pattern searching, which are tightly connected to the overall browsing system. SubtiList is accessible at http://genolist.pasteur.fr/SubtiList/. Similar bacterial databases are accessible at http://genolist.pasteur.fr/.

Bacillus subtilis↗
PubMed1993

Serum immunoglobulin E and sudden cardiac arrest during myocardial infarction.

BACKGROUND: While studying the immunological response to acute myocardial infarction (AMI) we noticed that patients who on admission had a high serum immunoglobulin E (IgE) level were less likely to die suddenly. This observation seemed to deserve verification since atopic patients whose production of IgE was excessive had been reported to have depressed haemostatic platelet function and impaired thrombinogenesis. METHODS: We measured levels of serum IgE in 386 patients with AMI at the time of admission to the coronary care unit. Patients were divided into two groups, depending on the presence (n = 55) or absence (n = 331) of sudden cardiac arrest. The two groups did not differ with respect to age, sex, or risk factors for coronary artery disease. RESULTS: The mean level of serum IgE was significantly higher in the group without sudden cardiac arrest than in the group with this complication. In a separate study we found that high serum IgE levels were associated with delayed thrombin generation in the clotting blood of survivors of myocardial infarction. CONCLUSION: Early determination of serum IgE levels might help to detect patients at risk of sudden cardiac arrest during myocardial infarction. Patients with high serum IgE levels might be protected against sudden cardiac death through the depression of clot formation because of the late appearance of thrombin in their coronary arteries.

Aged↗
PubMed2005

RealSpot: software validating results from DNA microarray data analysis with spot images.

The spot images from DNA microarray highly affect the discovery of biological knowledge from gene expression data. However, results from quality analysis, normalization, differential expression, and cluster analysis are rarely validated with spot images in current data analysis methods or software packages. We designed RealSpot, a software package, to validate the results by directly associating spot quality and data with spot images in a spreadsheet table. RealSpot splits hybridization images into individual spots stored in a spreadsheet table. It subsequently associates microarray data with spot images and performs data validation through the standard table operation such as sorting, searching, and editing. RealSpot has several built-in functions to facilitate data validation, including spot quality analysis, data organization, one-way ANOVA, gene ontology association, verification, import, and export. We used RealSpot to evaluate 77 slides (30,000 features each) from real hybridization experiments and to validate results from each step of data analysis. It took approximately 10 min to validate results of spot quality after initial evaluation and correct approximately 0.3% of falsely assigned qualities of 10,000 spots. We validated 1,641 of 2,110 differentially expressed genes identified by SAM analysis in approximately 1/2 h by comparing each gene with its respective spot image. Furthermore, we found that 6 of 48 genes in one cluster from k-mean clustering method showed inconsistent trends of spot images. RealSpot is efficient for validating microarray results and thus helpful for improving the reliability of the whole microarray experiment for experimentalists.

Algorithms↗
PubMed1965

DIFFERENTIAL RENAL FUNCTION STUDY: AN AID IN PREOPERATIVE EVALUATION OF HYPERTENSIVE PATIENTS.

Non-occlusive ureteral catheters were placed bilaterally in the renal pelves of 30 patients known to have hypertension. Samples of urine were collected under conditions of normal hydration, of urea-PAH-saline diuresis and, in some cases, mannitol diuresis. The samples were analyzed for indications of impaired flow of blood to the kidneys. Aortograms were obtained in all cases. This placement of non-occlusive catheters up into the renal pelves was felt to have caused only minimal disturbance of renal function, and was not accompanied by ureteral edema with the concomitant complications caused by occlusive catheters. Under conditions of normal hydration, leakage was insignificant. Of the 20 patients in whom urea-PAH-saline infusion revealed an ischemic pattern, 19 had an ischemic pattern under conditions of normal hydration. Since in the one exception an aortographic examination did not show a surgically reparable renal lesion, it may be inferred that the use of urea-PAH-saline diuresis is not essential in the preoperative evaluation of hypertensive renal disease. Correlation of the results of differential renal function studies and aortographic findings was possible in 19 of the 30 patients. Lack of correlation in the remaining 11 patients emphasized the importance of obtaining both types of study. Aortographic examination combined with differential renal function studies, using small ureteral catheters under conditions of normal hydration, should give the urologist a practical and yet accurate method of determining differential renal blood flow. If desired, further verification could be obtained by administering contrast medium and performing serial measurements of urine density.

Angiography↗
PubMed2003

Complete proteinogram of cerebrospinal fluid and its contribution to the diagnostics of inflammatory and autoimmune diseases of the central nervous system.

Complete evaluation of cerebrospinal fluid proteinogram represents a routine request of the clinician in the analysis of CSF in the Czech Republic. It comprises the measurement of concentrations of acute phase proteins (CRP, orosomucoid, haptoglobin, transferrin, prealbumin), immunoglobulins (IgG, IgA, IgM), compressive markers (albumin, fibrinogen), markers of CNS tissue destruction (apolipoproteins A-I, A-II, Apo B), complement components (C3, C4), alpha-1-microglobulin, beta-2-microglobulin, and proteinase inhibitors (alpha-1-antitrypsin, antithrombin III). Therefore, 19 CSF proteins of precisely verified clinical relevance are routine parameters for the assessment of the functional state of the blood-CSF barrier, presence of the intrathecal synthesis of immunoglobulins, inflammatory changes and verification of CNS tissue destruction. Evidence of these clinically relevant and independent parameters enabled the detection of the presence of autoimmune and neuroinfective diseases of CNS, even in clinical cases where the basic CSF parameters do not express relevant changes, or they are of a bordering or non-specific character. Clinically typical and the most significant abnormalities in the CSF proteinogram represent themselves a new access to a contemporary CSF analysis. Despite the fact that assessment of CSF proteins and their analysis is quite a difficult field in laboratory medicine, it is now routinely requested and routinely performed in the Czech Republic.

Autoimmune Diseases of the Nervous System↗
PubMed2006

[Verification of normative values for the Swiss version of the Freiburg speech intelligibility test].

BACKGROUND AND OBJECTIVE: In the Swiss version of the Freiburg speech intelligibility test five test words from the original German recording which are rarely used in Switzerland have been exchanged. Furthermore, differences in the transfer functions between headphone and loudspeaker presentation are not taken into account during calibration. New settings for the levels of the individual test words in the recommended recording and small changes in calibration procedures led us to make a verification of the currently used normative values. PATIENTS AND METHODS: Speech intelligibility was measured in 20 subjects with normal hearing using monosyllabic words and numbers via headphones and loudspeakers. RESULTS: On average, 50% speech intelligibility was reached at levels which were 7.5 dB lower under free-field conditions than for headphone presentation. The average difference between numbers and monosyllabic words was found to be 9.6 dB, which is considerably lower than the 14 dB of the current normative curves. CONCLUSIONS: There is a good agreement between our measurements and the normative values for tests using monosyllabic words and headphones, but not for numbers or free-field measurements.

Adult↗
PubMed2005

An annotation update via cDNA sequence analysis and comprehensive profiling of developmental, hormonal or environmental responsiveness of the Arabidopsis AP2/EREBP transcription factor gene family.

AP2/EREBP transcription factors (TFs) play functionally important roles in plant growth and development, especially in hormonal regulation and in response to environmental stress. Here we reported verification and correction of annotation through an exhaustive cDNA cloning and sequence analysis performed on 145 of 147 gene family members. A RACE analysis performed on genes with potential in-frame up-stream ATG codon resulted in identification of At2g28520 as an authentic AP2/EREBP member and corrected ORF annotations for three other members. A further phylogenetic analysis of this updated and likely complete family divided it into three major subfamilies. The expression patterns of the AP2/EREBP family members among the 11 organ or tissue types were examined using an oligo microarray and their hormonal and environmental responsiveness were further characterized using cDNA custom macroarrays. These detailed expression profile results provide strong support for a role for AP2/EREBP family members in development and in response to environmental stimuli, and a foundation for future functional analysis of this gene family.

Algorithms↗
PubMed1998

Xeroderma pigmentosum group C protein complex is the initiator of global genome nucleotide excision repair.

The XPC-HR23B complex is specifically involved in global genome but not transcription-coupled nucleotide excision repair (NER). Its function is unknown. Using a novel DNA damage recognition-competition assay, we identified XPC-HR23B as the earliest damage detector to initiate NER: it acts before the known damage-binding protein XPA. Coimmunoprecipitation and DNase I footprinting show that XPC-HR23B binds to a variety of NER lesions. These results resolve the function of XPC-HR23B, define the first NER stages, and suggest a two-step mechanism of damage recognition involving damage detection by XPC-HR23B followed by damage verification by XPA. This provides a plausible explanation for the extreme damage specificity exhibited by global genome repair. In analogy, in the transcription-coupled NER subpathway, RNA polymerase II may take the role of XPC. After this subpathway-specific initial lesion detection, XPA may function as a common damage verifier and adaptor to the core of the NER apparatus.

Base Sequence↗
PubMed2007

Development of a three-dimensional finite element model of a human mandible containing endosseous dental implants. I. Mathematical validation and experimental verification.

The purpose of this study was to mathematically validate and clinically verify a finite element model (FEM) of the human mandible and to compare the functional deformation predicted by the model with that detected clinically. Mandibular surface strain, using 11 single strain gauges, and medial convergence (MC), using a custom-fabricated linear variable differential transformer (LVDT), were recorded in a dried human jaw. The mandible was treated with two endosseous implants, placed bilaterally in the premolar area, and mounted in a rig that simulated natural function of the jaw. Measurements were made in real time using a multichannel analogue/digital converter and a personal computer for data storage and analysis. A FEM of the mandible was constructed, using commercially available finite element software, based on CT scan images of the jaw. MC was predicted as the linear change in the orientation of the two implants in the horizontal plane. Predicted and measured values of MC ranged between 60 and 109 microm. The differences between the measured and predicted strain magnitudes were expressed as absolute percentages of the measured values and ranged between 3 and 18%. The limits of agreement between the predicted and measured strain values, as suggested by Bland and Altman (Lancet 1986; 1:307-310), were small enough for the predictions from the FEM to be considered clinically acceptable. The good agreement between the predicted and measured strain values indicates the accuracy of the present FEM. Finite element analysis is a powerful technique that provides a better insight into understanding the complex phenomena of mandibular functional deformation.

Computer Simulation↗
PubMed2003

Surgical verification of percutaneous maxacalcitol injection therapy on enlarged parathyroid glands in chronic dialysis patients.

Selective percutaneous ethanol injection therapy (PEIT) has been used to control parathyroid function in patients with secondary hyperparathyroidism (2HPT) when one or more parathyroid gland (PTG) progresses to the nodular hyperplasia stage. However, PEIT can have adverse side effects, such as nerve paralysis and adhesion, because the ethanol is destructive. Intraparathyroid injection of a vitamin D analogue has been designed as a treatment to control parathyroid function without destruction of the PTG or causing adhesions to the surrounding tissue, and the present study aimed to verify the effect of percutaneous maxacalcitol (22-oxacalcitriol) as the vitamin D analogue. The study group comprised two haemodialysis patients who needed parathyroidectomy for uncontrolled 2HPT with a maximal PTG diameter >20 mm. The treatment began with an ultrasonographically guided injection of 10 microg of maxacalcitol solution into the largest PTG and, 1 week later, parathyroidectomy was performed to examine the effect of the maxacalcitol injection both macroscopically and microscopically. The injected glands were swollen and inflamed, and adhesions made it difficult to remove them. There was macroscopic and microscopic evidence of haemorrhagic necrosis and adhesions to the surrounding tissue. Direct vitamin D analogue injection should not be performed as a primary treatment option because the adverse side effects are not overcome by this technique.

Calcitriol↗
PubMed1997

[Neurophysiologic diagnosis in proctology].

Functional diagnostic exploration in proctology is ever-expanding and becoming more differentiating. Neurophysiologic examinations can take over an essential share. They have in part already been introduced into routine diagnostic workup. Both afference and efference, as well as the muscular system can be investigated in functional neurologic disorders of the pelvic floor. The electromyogram using concentric needle electrodes constitutes the most significant tool. It provides us with a better verification of the neurogenic lesion, and enables us to discriminate between acute and chronic and comment on severity and prognosis. The diagnostic program is additionally supplemented by motor and sensory evoked potentials, electroneurography of the pudendal nerve, and measurements of vegetative nerve paths.

Afferent Pathways↗
PubMedDate not supplied

Quantal analysis of synaptic processes in the neocortex.

The application of fluctuation analysis to studies of synaptic function in the neocortex is discussed. Analysis of failures of transmission has been valuable in indicating whether a presynaptic or a postsynaptic site is responsible for a change in synaptic efficacy. When combined with detailed ultrastructural verification of all synapses involved in an individual cell to cell connection, a reasonable estimate of quantal size and release probability under conditions of low frequency activity can be obtained. However, both the number of available release sites in functional terms and the probability that an action potential (AP) will release transmitter from any given site can vary from AP to AP at higher frequencies. A variety of presynaptic mechanisms that modulate release are now apparent. For example, one mechanism dominates release patterns at one class of connection which is insensitive to absolute firing frequency, but responsive to changes in frequency. At another class of connection, a different mechanism dominates, resulting in high sensitivity to frequency.

Animals↗
PubMed1993

Quantification and statistical verification of neuronal stimulus responses from noisy spike train data.

Usually neuronal responses to short-lasting stimuli are displayed as peri-stimulus time histogram. The function estimated by such a histogram allows to obtain informations about stimulus-induced postsynaptic events as long as the interpretation is restricted to the first response component after the stimulus. The interpretation of secondary response components is much more difficult, as they may be either due to stimulus effects or represent an "echo" of the primary response. In the present paper two output functions are developed that do not show such an echoing of responses. The first one, the interspike interval change function, represents an ideal way to quantify a neuronal stimulus response as its amplitude was found to be almost independent of the stimulation strategy used during acquisition of the spike train data. The other function, the displaced impulses function, allows to verify the statistical significance of an observed response component. Both functions may be estimated from stimulus-correlated spike train data, even if the neuron under investigation shows considerable interspike-interval variability in the absence of stimulation. The concepts underlying these neuronal output functions are developed on simulated responses of a Hodgkin-Huxley-type model for a mammalian neuron at body temperature that is exposed to a transient excitatory conductance increase. Additionally, estimation of these output functions is also demonstrated on responses of human soleus motoneurons that were exposed to electrical stimuli of the tibial nerve in the popliteal fossa.

Action Potentials↗
PubMed2004

Experimental verification of conformational variation of human fatty acid synthase as predicted by normal mode analysis.

Fatty acid synthase (FAS) is a 550 kDa homodimeric enzyme with multiple functional and structural domains. Normal mode analysis of a previously determined 19 A structure of FAS suggested that this enzyme might assume different conformational states with several distinct hinge movements. We have used a simultaneous multiple-model refinement method to search for the presence of the structural conformers from the electron images of FAS. We have demonstrated that the resulting models observed in the electron images are consistent with the predicted conformational changes. This technique demonstrates the potential of the combination of normal mode analysis with multiple model refinement to elucidate the multiple conformations of flexible proteins. Since each of these structures is based on a more homogeneous particle set, this technique has the potential, provided that sufficient references are used, to improve the resolution of the final reconstructions of single particles from electron cryomicroscopy.

Cryoelectron Microscopy↗
PubMed1996

Symptomatology and energy intake during the menstrual cycle in smoking women.

This study extends our understanding of smoking behavior, withdrawal, and premenstrual symptomatology in smoking women, as well as energy intake as a function of cycle phase. Thirty-two women age 18 to 40 years, smoking ad lib, were followed for an average of two menstrual cycles with hormonal verification. Withdrawal and premenstrual symptomatology as well as energy intake were reported during the follicular (F), luteal (L), and late luteal (LL) cycle phases. Both premenstrual symptomatology and withdrawal symptomatology were higher during the LL phase. Subject response on measurements of craving, irritability, restlessness, increased appetite, and depressed mood tended to be higher in the LL phase. Energy intake did not vary as a function of cycle phase. Participants perceived that they smoked more and had increased appetite in the LL phase but related measurements did not confirm this. Premenstrual and withdrawal symptoms are highly correlated and one needs to be cautious in interpreting cycle effects on withdrawal. Overall symptomatology seems to be lower during the F phase, indicating that this may be a more opportune time for women to quit smoking.

Adolescent↗
PubMed2005

Gene expression analysis of peripheral blood leukocytes from discordant sib-pairs with schizophrenia and bipolar disorder reveals points of convergence between genetic and functional genomic approaches.

We performed global RNA transcript analysis and comprehensive gene group analysis of peripheral blood leukocyte (PBL) RNA from two groups of matched sib-pairs that were discordant for either schizophrenia (n = 33 sib-pairs) or bipolar disorder (n = 5 sib-pairs). The pairs chosen for these analyses were selected from families with known patterns of genetic linkage (5q for schizophrenia and 6q for bipolar disorder). At the single gene level, we obtained lists of the transcripts with the most significant changes in expression and from these lists determined those with the highest degree of predictive power for classifying subjects according to diagnosis in these samples. At the gene group level, we comprehensively analyzed pairwise expression changes of more than 4,000 functional groups and cytogenetic locations, and present a novel method of displaying these data that we term "cytogenomic" mapping. Verification of selected changes in expression was performed using quantitative real-time RT-PCR. Our results provide compelling evidence for the utility of analyzing PBL RNA for changes in expression in neuropsychiatric disorders.

Adult↗
PubMed1982

Disruption of passive avoidance memory by REM sleep deprivation: methodological and pharmacological considerations.

The present experiments were designed to examine more closely the variables responsible for the disruption of passive avoidance memory produced by REM sleep deprivation. In the pharmacological study it was found that imipramine could reverse the memory disruption exhibited by rats maintained on large platforms (presumably not REM-deprived) while both imipramine and physostigmine were required to reverse the memory disruption exhibited by rats maintained on small platforms. In the methodological study it was found that those animals maintained on the smallest platforms and therefore having the largest weight to area ratio exhibited the greatest degree of memory disruption. It is concluded that further modification and verification of the platform techniques of REM deprivation is required before firm conclusions about its neurochemical basis and behavioural functions can be made.

Animals↗
PubMed2006

LC-MS/MS based proteomic analysis and functional inference of hypothetical proteins in Desulfovibrio vulgaris.

High efficiency capillary liquid chromatography-tandem mass spectrometry (LC-MS/MS) was used to examine the proteins extracted from Desulfovibrio vulgaris cells across six treatment conditions. While our previous study provided a proteomic overview of the cellular metabolism based on proteins with known functions [W. Zhang, M.A. Gritsenko, R.J. Moore, D.E. Culley, L. Nie, K. Petritis, E.F. Strittmatter, D.G. Camp II, R.D. Smith, F.J. Brockman, A proteomic view of the metabolism in Desulfovibrio vulgaris determined by liquid chromatography coupled with tandem mass spectrometry, Proteomics 6 (2006) 4286-4299], this study describes the global detection and functional inference for hypothetical D. vulgaris proteins. Using criteria that a given peptide of a protein is identified from at least two out of three independent LC-MS/MS measurements and that for any protein at least two different peptides are identified among the three measurements, 129 open reading frames (ORFs) originally annotated as hypothetical proteins were found to encode expressed proteins. Functional inference for the conserved hypothetical proteins was performed by a combination of several non-homology based methods: genomic context analysis, phylogenomic profiling, and analysis of a combination of experimental information, including peptide detection in cells grown under specific culture conditions and cellular location of the proteins. Using this approach we were able to assign possible functions to 20 conserved hypothetical proteins. This study demonstrated that a combination of proteomics and bioinformatics methodologies can provide verification of the expression of hypothetical proteins and improve genome annotation.

Amino Acid Sequence↗