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At least 739 records · Page 41Linked to original sources
PubMed2004

Structure and function of a hypothetical Pseudomonas aeruginosa protein PA1167 classified into family PL-7: a novel alginate lyase with a beta-sandwich fold.

Structural and functional analyses of alginate lyases are important in the clarification of the biofilm-dependent ecosystem in Pseudomonas aeruginosa and in the development of therapeutic agents for bacterial disease. Most alginate lyases are classified into polysaccharide lyase (PL) family-5 and -7 based on their primary structures. Family PL-7 enzymes are still poorly characterized especially in structural properties. Among family PL-7, a gene coding for a hypothetical protein (PA1167) homologous to Sphingomonas alginate lyase A1-II was found to be present in the P. aeruginosa genome. PA1167 overexpressed in Escherichia coli cleaved glycosidic bonds in alginate and released unsaturated saccharides, indicating that PA1167 is an alginate lyase catalyzing a beta-elimination reaction. The enzyme acted preferably on heteropolymeric regions endolytically and worked most efficiently at pH 8.5 and 40 degrees C. The specific activity of PA1167, however, was much weaker than that of the known alginate lyase AlgL, suggesting that AlgL plays a main role in alginate depolymerization in P. aeruginosa. In addition to this specific activity, differences were found between PA1167 and AlgL in enzyme properties such as molecular mass, optimum pH, salt effect, and substrate specificity. The first crystal structure of the family PL-7 alginate lyase was determined at 2.0 A resolution. PA1167 was found to form a glove-like beta-sandwich composed of 15 beta-strands and 3 alpha-helices. The structural difference between the beta-sandwich PA1167 of family PL-7 and alpha/alpha-barrel AlgL of family PL-5 may be responsible for the enzyme characteristics. Crystal structures of polysaccharide lyases determined so far indicate that they can be assigned to three folding groups having parallel beta-helix, alpha/alpha-barrel, and alpha/alpha-barrel + antiparallel beta-sheet structures as basic frames. PA1167 is the fourth novel folding structure found among polysaccharide lyases.

Amino Acid Sequence↗
PubMed2003

Task-specific motor performance and musculoskeletal response in self-classified right handers.

We examined the difference between the left and right hand motor performance (in terms of erg produced) of self-classified right handers (15 men, 15 women) for power (task involving muscle force) and skilled (task involving precision and eye hand coordination) tasks. Musculoskeletal response during task performance was measured by electromyogram to test the hypothesis that performance with the nondominant hand would trigger more generalized muscle tension. The difference between the left and right hand performance of men was nonsignificant for power task; for women, right hand performance was significantly superior than left for such task. Men excelled in power and women excelled in skilled tasks relative to their counterparts. Generalized muscle tension was significantly more during the left than the right hand performance for power but not for skilled tasks.

Adult↗
PubMedDate not supplied

Revision of hypo-osmotic swelling (HOS) test with a proposition of classified grading system: its comparisons with four different types of human sperm separation technique.

In this study, we arbitrarily classified the morphological changes of sperm under hypo-osmotic condition and compared the results with four different sperm separation techniques. The morphology of classification ranged from a good swelling (SG 3 > SG 2 > SG 1), to non-swelling but reactive (SG 0-R), and completely non-swelling (SG 0). Thirty fresh semen from patients were divided into 4 groups and each processed by washing, swim up, 2-layer column and real time micro-separation system. The prevalent patterns of the swollen sperm in sequence after treatment was SG 0 > SG 1 > SG 3 > SG2 > SG 0-R in fresh semen, and the proportion of SG 0 was almost half of the total % HOS test results. However, SG 3 became the most common swollen form with a significant increase in number with any method of sperm preparation after treatment. The real time technique yielded the highest % rate of SG 3 type of swollen spermatozoa and was the richest in concentration (53+/-3.9%, P < 0.05) as compared with that of swim up (26+/-4.6%), 2-layer (20+/-4.4%), sperm washing (23+/-3.9%), and fresh semen (17+/- 2.8%), respectively. By contrast, 2-layer collected more number of SG0-R (5.3+/-1.2%, P < 0.05) pattern of spermatozoa when compared to real time and swim up. A positive correlation (r = 0.81, P < 0.002) was shown between the % total HOS spermatozoa and total motility of fresh semen but not with morphology. Collectively, an abnormally functional sperm may exist in almost half of a total sperm count from men. It would appear that a better potential fertilization capacity may reside in the more swollen sperm from HOS test than the less swollen sperm and that may be more related with the motility rather than the morphology. The HOS classification and grading system appears valuable in further evaluating sperm quality.

Cell Culture Techniques↗
PubMedDate not supplied

Classifying, identifying and enumerating arbitrary relationships.

In studies of human genetic isolates, or pedigrees, it is often required to examine the relationships that exist between two individuals in the isolate. This may be of interest in connection with inbreeding, or in its own right, for example in the study of mating patterns. A scheme is developed for classifying any relationship between two individuals in a pedigree as a pair of integers. Relative to a common ancestor, the first integer counts the level of the relationship and the second the difference in generation between the individuals. The scope of this scheme is broad enough to encompass cases of multiplicity of relationships and half-relationships. An algorithm for counting the number of times a given relationship occurs between two individuals is outlined. This algorithm assumes that recursion is possible and that the information on the pedigree is stored in such a way that the parents of an individual can be readily traced. It has been implemented in Algol 68 and in C. The method is illustrated by an example from the complex Samaritan pedigree.

Adult↗
PubMed2002

Application of molecular methods for identification of strains classified as Salmonella enterica serovar 6, 7:-:- by conventional serotyping.

An increased prevalence of Salmonella enterica serovar Tennessee (6, 7: z(29):-) was observed in broiler flocks in Denmark in 1994 and a parallel increase in the prevalence of Salmonella enterica serovar 6, 7:-:- was demonstrated, albeit at a lower level. Plasmid profiling and ribotyping revealed similar genotypes and it was speculated that serovar 6, 7:-:- could represent a non-motile variant of Salmonella Tennessee. Re-testing of the Salmonella 6, 7:-:- isolates demonstrated the presence of flagella through positive motility. All isolates but one demonstrated motility using both tube tests and light microscopy of overnight broth cultures. Molecular characterization indicated that all but two isolates previously classified as Salmonella 6, 7:-:, were isolates of Salmonella Tennessee and Salmonella Infantis, exhibiting reduced motility. Re-serotyping and multiplex polymerase chain reaction analysis for the phase 2 gene fljB demonstrated variants of Salmonella Infantis (6, 7: r: z(49)) expressing the R-phase antigen (Rz(49)) and possessing the gene for normal phase 2 antigen H: 1, 5. One of the two undefined strains demonstrated genotypic identity with a Salmonella Livingstone reference strain. The remaining putative 6, 7:-:- strain could not be identified and was genuinely non-motile. Diagnostic procedures performed initially were thus insufficient to differentiate between the different levels of motility and also resulted in mis-serotyping. As similar observations were made with two of 14 isolates received from a foreign laboratory, this may represent a general diagnostic problem.

Animals↗
PubMed1999

A clinical study of specific signs and symptoms of CMD in bruxers classified by the degree of severity.

Two hundred and seventy-six CMD patients referred consecutively for diagnosis and treatment over a period of four years were assessed. Two hundred and eleven were classified as bruxers according to the use of a questionnaire and clinical examination. One hundred (47.39%) presented clinical characteristics of mild bruxers, 66 (31.27%) presented moderate bruxism and 45 (21.32%) demonstrated severe bruxism. Severe bruxers presented the lowest degree of jaw opening (39.21 mm) and highest prevalence of capsulitis (97.77%), retrodiskal pain (84.44%) and disk-attachment pain (48.88%). As compared to the mild and moderate groups, severe bruxers also demonstrated significantly higher prevalence of protective splinting and transient locking or recent history of intermittent locking, masticatory pain, reciprocal clicking and signs and symptoms of Myofascial Pain Dysfunction Syndrome (MPDS). Because higher prevalence of specific muscle and joint disorders were observed in bruxers and such prevalence was progressive from the mild to the moderate and severe group, it may be concluded that bruxing behavior is a significant factor in the etiology and progression of muscle and joint disorders. Based on the review of the literature, the analysis of our data in comparison to other studies allowed us to conclude that severe bruxers are more impaired by muscular and joint disorders as compared to mild and moderate bruxers.

Adolescent↗
PubMed2002

Diffuse large B-cell lymphoma: a clinicopathologic analysis of 444 cases classified according to the updated Kiel classification.

The purpose of this study was: to compare the survival of diffuse large B-cell lymphomas (DLBCL) stratified according to the up-dated Kiel classification. A retrospective study of a cohort of 1378 cases was organized in 1996 by the Non-Hodgkin's Lymphoma Classification Project, and the DLBCL were classified according to the updated Kiel classification. The distribution of the different types and subtypes was as follows: centroblastic (CB, 85.4%), composed of the polymorphic (CB-PM, 58.6%), monomorphic (CB-MM, 17.1%) and multilobated (CB-ML, 9.7%) subtypes; immunoblastic (IB, 11.2%), with (8.3%) or without (2.9%) plasmacytoid differentiation; and anaplastic large cell lymphoma (ALCL) of B-cell type (3.4%). The rate of diagnostic agreement between pathologists was 78% for CB and 65% for IB lymphoma. The 5-year overall survival (OAS) for the entire group was 47% and the 5-year failure-free survival (FFS) was 42%. No significant differences in survival were found between the three major groups (CB, IB, ALCL). However, the 5-year OAS and FFS of patients with DLBCL not containing immunoblasts (CB-MM+CB-ML) was 51 and 52%, respectively, and was significantly better than the survival of those containing immunoblasts (CB-PM+IB+ALCL), which was 44 and 38% (p = 0.06 and p = 0.037), respectively. These results did not appear to be due to differences in the clinical features of the two groups, and was most significant for patients with low stage or low risk disease. However, histologic subtyping was not an independent risk factor for the entire group by multivariate analysis. In conclusion, patients with CB-MM and CB-ML (without immunoblasts) had a significantly better OAS and FFS than those with CB-PM, IB and ALCL (with immunoblasts). Therefore, we conclude that additional studies are still needed to further evaluate the importance of immunoblastic differentiation in DLBCL.

Adolescent↗
PubMed2000

Particulate penetration of porous foam used as a low flow rate respirable dust size classifier.

Porous foam has been used as a material for classification of particulate matter into various size fractions. The penetration characteristics of a nominal 90 pores per inch porous foam were studied at various flow rates, face velocities, and foam plug diameters and compared to the aerosol penetration of a 10 mm Dorr Oliver cyclone operated at 1.7 L/min. Poly-dispersed triethanolamine spheres were classified through porous foam plugs and the resulting penetration was determined using an aerodynamic particle sizer. Results showed that for a given plug diameter, as face velocity increased from 26 to 39 cm/sec, the 50 percent cut point decreased from 4.5 to 3.8 microns. Furthermore, as the diameter of the plug increased from 4 to 12 mm, the 50 percent cut points were similar to other plug diameters at equivalent face velocities. The best match to the 1.7 L/min cyclone penetration characteristics occurred at a flow rate of 250 ml/min through a 25 mm by 4 mm diameter section of 90 pore per inch foam. Because of the need to provide short-term or real-time estimates of worker respirable dust exposure, porous foam may be a viable classification media for a low flow rate, disposable respirable dust sampler for use in the coal mining industry.

Aerosols↗
PubMed2000

Daily mortality in the Philadelphia metropolitan area and size-classified particulate matter.

Time-series of daily mortality data from May 1992 to September 1995 for various portions of the seven-county Philadelphia, PA, metropolitan area were analyzed in relation to weather and a variety of ambient air quality parameters. The air quality data included measurements of size-classified PM, SO4(2-), and H+ that had been collected by the Harvard School of Public Health, as well as routine air pollution monitoring data. Because the various pollutants of interest were measured at different locations within the metropolitan area, it was necessary to test for spatial sensitivity by comparing results for different combinations of locations. Estimates are presented for single pollutants and for multiple-pollutant models, including gaseous pollutants and mutually exclusive components of PM (PM2.5 and coarse particles, SO4(2-) and non-SO4(2-) portions of total suspended particulate [TSP] and PM10), measured on the day of death and the previous day. We concluded that associations between air quality and mortality were not limited to data collected in the same part of the metropolitan area; that is, mortality for one part may be associated with air quality data from another, not necessarily neighboring, part. Significant associations were found for a wide variety of gaseous and particulate pollutants, especially for peak O3. Using joint regressions on peak O3 with various other pollutants, we found that the combined responses were insensitive to the specific other pollutant selected. We saw no systematic differences according to particle size or chemistry. In general, the associations between daily mortality and air pollution depended on the pollutant or the PM metric, the type of collection filter used, and the location of sampling. Although peak O3 seemed to exhibit the most consistent mortality responses, this finding should be confirmed by analyzing separate seasons and other time periods.

Adolescent↗
PubMed2006

Factors that predict infant disorganization in mothers classified as U in pregnancy.

The unresolved (U) state of mind in parents has been validated by its association with infant attachment disorganization (D), yet all studies show a transmission gap, and a proportion of individuals classified as U have infants who are not D. This paper reports on 31 mothers who showed the characteristic lapses in thinking and reasoning of the unresolved/disorganized state of mind in relation to stillbirth (U(sb)), when assessed with the Adult Attachment Interview (AAI) in the pregnancy after stillbirth. Seventeen (55%) of their infants were D at 1 year old. We evaluate social, attachment, and psychiatric variables to establish whether there are differences in U(sb) individuals that will predict infant D. In this population of U mothers, social and attachment factors did not predict infant D, but U(sb) mothers of non-D infants showed significantly higher levels of depression and of intrusive thoughts on the posttraumatic stress disorder (PTSD) scale in pregnancy, and showed higher levels of intrusive thoughts when the infant was 1 year old. We discuss possible interpretations of these findings.

Adjustment Disorders↗
PubMed2004

An efficient rhythmic component expression and weighting synthesis strategy for classifying motor imagery EEG in a brain-computer interface.

The recognition of mental states during motor imagery tasks is crucial for EEG-based brain-computer interface research. We have developed a new algorithm by means of frequency decomposition and weighting synthesis strategy for recognizing imagined right- and left-hand movements. A frequency range from 5 to 25 Hz was divided into 20 band bins for each trial, and the corresponding envelopes of filtered EEG signals for each trial were extracted as a measure of instantaneous power at each frequency band. The dimensionality of the feature space was reduced from 200 (corresponding to 2 s) to 3 by down-sampling of envelopes of the feature signals, and subsequently applying principal component analysis. The linear discriminate analysis algorithm was then used to classify the features, due to its generalization capability. Each frequency band bin was weighted by a function determined according to the classification accuracy during the training process. The present classification algorithm was applied to a dataset of nine human subjects, and achieved a success rate of classification of 90% in training and 77% in testing. The present promising results suggest that the present classification algorithm can be used in initiating a general-purpose mental state recognition based on motor imagery tasks.

Algorithms↗
PubMed2005

The spectrum of therapeutic influences and integrative health care: classifying health care practices by mode of therapeutic action.

The growing popularity of complementary and alternative medicine (CAM) and integrative medicine (IM) highlight the need for a clinically relevant system for classifying health care practices. All systems, modalities, and techniques of health care (conventional, complementary, alternative, and traditional) can be organized in categories of "primary mode of therapeutic action." This results in six categories: biochemical; biomechanical; mind-body; energy; psychological (symbolic); and nonlocal. In each category, there are subdivisions. Organizing health care by primary mode of therapeutic action has numerous benefits: (1) conventional and CAM practitioners, and the public, can readily see some of the general similarities and differences among practices; (2) health care educators gain a common foundation and shared language for explaining CAM and IM; (3) professionals and the public, wishing to combine dissimilar practices, gain a common framework for evaluating the meaning of integration; and (4) the crossover problem can be understood as a natural occurrence in health care, not a confusing intellectual dilemma. The National Center for Complementary and Alternative Medicine (NCCAM) system of categories for CAM is briefly critiqued.

Complementary Therapies↗
PubMed2004

Robust sparse hyperplane classifiers: application to uncertain molecular profiling data.

Molecular profiling studies can generate abundance measurements for thousands of transcripts, proteins, metabolites, or other species in, for example, normal and tumor tissue samples. Treating such measurements as features and the samples as labeled data points, sparse hyperplanes provide a statistical methodology for classifying data points into one of two categories (classification and prediction) and defining a small subset of discriminatory features (relevant feature identification). However, this and other extant classification methods address only implicitly the issue of observed data being a combination of underlying signals and noise. Recently, robust optimization has emerged as a powerful framework for handling uncertain data explicitly. Here, ideas from this field are exploited to develop robust sparse hyperplanes, i.e., classification and relevant feature identification algorithms that are resilient to variation in the data. Specifically, each data point is associated with an explicit data uncertainty model in the form of an ellipsoid parameterized by a center and covariance matrix. The task of learning a robust sparse hyperplane from such data is formulated as a second order cone program (SOCP). Gaussian and distribution-free data uncertainty models are shown to yield SOCPs that are equivalent to the SCOP based on ellipsoidal uncertainty. The real-world utility of robust sparse hyperplanes is demonstrated via retrospective analysis of breast cancer related transcript profiles. Data-dependent heuristics are used to compute the parameters of each ellipsoidal data uncertainty model. The generalization performance of a specific implementation, designated "robust LIKNON," is better than its nominal counterpart. Finally, the strengths and limitations of robust sparse hyperplanes are discussed.

Breast Neoplasms↗
PubMed1997

Subtypes of anti-TSH receptor antibodies classified by various assays using CHO cells expressing wild-type or chimeric human TSH receptor.

To analyze the heterogeneity of anti-TSH receptor antibodies (TSHRAb), we measured serum TSH-binding inhibitory immunoglobulin (TBII), thyroid-stimulating antibody (TSAb), and thyroid stimulation blocking antibody (TSBAb) activities in 31 patients with positive TSHRAb, using CHO cells expressing wild-type TSHR (WT) or TSHR chimera (Mc2) wherein residues 90-165 were substituted by the LH/CG receptor. Using membranes from WT cells, we detected TBII activity in all 31 patients; 10 (32%), all with TSAb activity only, completely lost TBII activity using Mc2 membranes. TSAb activity was found in 26 sera using WT cells; 20 (77%) completely lost TSAb activity in Mc2 cells. Comparisons of TBII and TSAb activity in WT cells did not exhibit a strong positive correlation (r = 0.52). Of the 20 sera that completely lost TSAb activity in Mc2 cells, 10 retained some TBII activity in Mc2 cells. In each of the sera with retained TBII activity, TSAb activity was recovered in Mc2 cells using the conversion assay, which measures the conversion of a nonstimulating TSHRAb to a TSAb by the action of an anti-human IgG. Additionally, the TBII and conversion assay values in Mc2 cells exhibited a strong positive correlation (r = 0.86). Of the 31 sera, TSBAb was found in 7 samples, with no difference in WT and Mc2 cells. TBII activity was detected in all 7 sera with WT cells; TSAb activity in only 2. In the 5 sera with TSBAb but no TSAb activity, and with only a minimal or no decrease in TBII activity in Mc2 cell membranes, the in vitro conversion assay uncovered TSAb activity. Analyzing these data, we classify the sera into 5 groups containing multiple, different TSHR autoantibodies, including two different TSAbs, three different TBIIs, and one nonfunctional antibody. The heterogeneity of TBIIs as well as TSAbs provides a basis to explain the lack of correlation between TBII and TSAb activities in some past studies of Graves' sera.

Animals↗
PubMed1994

CD34 immunostaining of bone marrow biopsy specimens is a reliable way to classify the phases of chronic myeloid leukemia.

Flow cytometry studies have shown that high expression of CD34 antigen in patients with chronic myeloid leukemia (CML) is indicative of accelerated or blastic phases. It has also been suggested that similar information can be obtained by CD34 immunostaining of bone marrow biopsy specimens. To test this hypothesis, the authors studied 59 conventionally fixed, paraffin-embedded bone marrow trephine biopsy specimens, representing the three phases of the disease (stable, accelerated, and blast crisis). Immunohistochemical staining for CD34 was performed using QBEnd10, a monoclonal antibody reactive in routine paraffin-embedded tissue. The differences in CD34 positivity among chronic, accelerated, and blastic phases of CML were highly significant (P = .0001). This study demonstrated that CD34 immunohistochemical staining of bone marrow biopsy specimens represents a reliable method for classifying patients with CML and may provide essential diagnostic and prognostic information when a marrow aspirate is unavailable.

Antigens, CD↗
PubMed2002

Risk of breast cancer classified by joint estrogen receptor and progesterone receptor status among women 20-44 years of age.

To gain insight into whether breast cancer tumors jointly classified by estrogen receptor (ER) and progesterone receptor (PR) status represent diseases with differing etiologies, data from a population-based case-control study of US women 20-44 years of age were analyzed. Cases included 1,556 women diagnosed between 1990 and 1992. Age- and geographic-frequency-matched controls included 1,397 women identified by random digit dialing. Heterogeneity between ER+PR+ and ER-PR- tumors was most pronounced in relation to age, race, and recreational exercise at 12-13 years of age. Multivariate-adjusted odds ratios for ER+PR+ tumors were 0.64 (95% confidence interval (CI): 0.47, 0.89) for 30-34 versus 40-44 years of age, 0.89 (95% CI: 0.63, 1.25) for Black versus White race, and 0.84 (95% CI: 0.68, 1.03) for exercise at 12-13 years of age above versus at or below the median. Corresponding odds ratios for ER-PR- tumors were 1.24 (95% CI: 0.86, 1.77), 1.51 (95% CI: 1.07, 2.14), and 1.15 (95% CI: 0.90, 1.48). Risk of ER-PR- cancer in relation to menstrual and reproductive (parity and lactation) characteristics, alcohol consumption, and family history of breast cancer was similar to that observed for ER+PR+ tumors. These findings only modestly support the hypothesis that hormonally related risk factors have differing relations with ER+PR+ versus ER-PR- tumors among younger women.

Adult↗
PubMed1998

Self-organizing tree growing network for classifying amino acids.

UNLABELLED: A self-organizing tree growing neural network was applied to classify amino acids and amino acid exchange matrices. AVAILABILITY: SOTA, is freely available by anonymous FTP or at http://www.cnb.uam.es/bioinfo/Software/so ta. CONTACT: carazo@cnb.uam.es

Algorithms↗
PubMed2000

Browsing the SLoop database of structurally classified loops connecting elements of protein secondary structure.

We describe a web server, which provides easy access to the SLoop database of loop conformations connecting elements of protein secondary structure. The loops are classified according to their length, the type of bounding secondary structures and the conformation of the mainchain. The current release of the database consists of over 8000 loops of up to 20 residues in length. A loop prediction method, which selects conformers on the basis of the sequence and the positions of the elements of secondary structure, is also implemented. These web pages are freely accessible over the internet at http://www-cryst.bioc.cam.ac.uk/ approximately sloop.

Amino Acid Sequence↗