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Scoring Scheme (scoring + scheme)
Selected AbstractsA new magnetic resonance imaging scoring method for assessment of haemophilic arthropathyHAEMOPHILIA, Issue 4 2004B. Lundin Summary., In a European multicentre study, 39 ankles in 28 haemophilic boys were investigated by magnetic resonance imaging (MRI). A new MRI score was developed in the format A(e:s:h) for evaluating haemophilic arthropathy. This scheme provides high resolution and allows separation of different pathological components. The factor A is calculated as the sum of scores for subchondral cysts (maximum value 6), irregularity/erosion of subchondral cortex (maximum 4) and chondral destruction (maximum 6); e, s and h, respectively, represent effusion/haemarthrosis, synovial hypertrophy and haemosiderin deposition, and they are separately evaluated on a scale of 0,4. Working independently, two radiologists scored the 39 ankles twice using both this new ,European' scoring method and a previously published ,Denver' scoring scheme. Final classification was achieved by consensus. The reproducibility of the readings was assessed, and for both scoring methods the results indicated good or moderate intraobserver agreement, and good, moderate or fair interobserver agreement. These findings suggest that MRI can be useful for semiquantitative evaluation of haemophilic arthropathy, providing the examination is performed according to an appropriate protocol, and the images are evaluated by specially trained radiologists. [source] Continuous, age-related plumage variation in male Kirtland's WarblersJOURNAL OF FIELD ORNITHOLOGY, Issue 1 2007John R. Probst ABSTRACT The ability to age individual birds visually in the field based on plumage variation could provide important demographic and biogeographical information. We describe an approach to infer ages from a distribution of plumage scores of free-ranging male Kirtland's Warblers (Dendroica kirtlandii). We assigned ages to males using a scoring scheme (0,12 points) based on variation in plumage coloration, brightness, and contrast on three dorsal and three ventral body regions presumed to be age-related. The distribution of total additive plumage scores for 875 breeding males was normally distributed, indicating no distinct age classes. Thus, we developed provisional plumage-age classes of second year (SY) and after second-year (ASY), and compared them to the total plumage scores of a smaller subsample of known age (N= 92) and minimum age (N= 143) males. Plumage scores of known-age male Kirtland's Warblers increased nonlinearly with age (rs= 0.67), but with some overlap. The median plumage score for SY males (median = 5.0) was significantly lower than for third-year (TY) males (median = 7.0) and after third-year (3 year and older) males (median = 8.0), indicating that the plumage of male Kirtland's Warblers becomes more distinctive and brighter with age. Linear discriminant function analysis differentiated ASY male Kirtland's Warbler from SY males with 78.3% accuracy. Investigators could use the distribution of plumage scores and approximate age structures to document changes in male age structure during colonization, use, and abandonment of habitats by Kirtland's Warblers or other species that occupy early successional habitats. Aging free-ranging birds based on a plumage scoring scheme may be especially critical for demographic studies of less-studied species where it is unlikely that a banding program will be initiated, but where plumage-age inferences or management decisions must be made. SINOPSIS Describimos una forma para inferir la edad a través de una distribución de marcadores en machos silvestres de la reinita Dendroica kirtlandii. Utilizando dicho acercamiento, asignamos edad relativa a machos basándonos en un esquema de puntuación (0,12) para la coloración del plumaje, su brillantez, y contraste en tres localidades del dorso y la parte ventral, que han sido relacionadas con la edad de estos. La distribución de las puntuaciones de 875 machos fue normal, lo que indica que no hubo forma de distinguir las diferentes edades. Por ende, desarrollamos un divisiones de clases, basándonos en diferencias en el plumaje para individuos de segundo año (SA) y posterior al segundo año (PSA) y los comparamos a las puntuaciones de una pequeña muestra de aves (N= 92) cuya edad era conocida y a otra en que sabíamos la edad mínima (N= 143). La puntuación total para individuos de edad conocida aumento de forma no-lineal con la edad (Rs = 0.67), con un pequeño solapamiento en el plumaje total. La puntuación para machos de segundo año (SA) (mediana = 5.0) fue significativamente menor que para aves de tercer año (mediana = 7.0) y esta a su vez que para aves mayores a tres años (mediana = 8.0), lo que indica que el plumaje de los machos, en las aves estudiadas, se torna más brillante con la edad. Un análisis lineal de función discriminativa pudo diferenciar entre aves PSA y SA con un 78.3% de exactitud. Los investigadores han utilizado estas diferencias en el plumaje para clasificar entre los grupos machos territoriales que no han sido anillados. También pudieran utilizar estas particularidades y diferencias en el plumaje para aproximar la estructura de edades entre machos silvestres y hacer inferencias sobre la demografía y reclutamiento de aves en habitats de diferente calidad. [source] Optimization of pathogenicity assays to study the Arabidopsis thaliana,Xanthomonas campestris pv. campestris pathosystemMOLECULAR PLANT PATHOLOGY, Issue 3 2005DAMIEN MEYER SUMMARY The cruciferous weed Arabidopsis thaliana and the causal agent of black rot disease of Crucifers Xanthomonas campestris pv. campestris (Xcc) are both model organisms in plant pathology. Their interaction has been studied successfully in the past, but these investigations suffered from high variability. In the present study, we describe an improved Arabidopsis,Xcc pathosystem that is based on a wound inoculation procedure. We show that after wound inoculation, Xcc colonizes the vascular system of Arabidopsis leaves and causes typical black rot symptoms in a compatible interaction, while in an incompatible interaction bacterial multiplication is inhibited. The highly synchronous and reproducible symptom expression allowed the development of a disease scoring scheme that enabled us to analyse the effects of mutations in individual genes on plant resistance or on bacterial virulence in a simple and precise manner. This optimized Arabidopsis,Xcc pathosystem will be a robust tool for further genetic and post-genomic investigation of fundamental questions in plant pathology. [source] PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometryRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 20 2003Bin Ma A number of different approaches have been described to identify proteins from tandem mass spectrometry (MS/MS) data. The most common approaches rely on the available databases to match experimental MS/MS data. These methods suffer from several drawbacks and cannot be used for the identification of proteins from unknown genomes. In this communication, we describe a new de novo sequencing software package, PEAKS, to extract amino acid sequence information without the use of databases. PEAKS uses a new model and a new algorithm to efficiently compute the best peptide sequences whose fragment ions can best interpret the peaks in the MS/MS spectrum. The output of the software gives amino acid sequences with confidence scores for the entire sequences, as well as an additional novel positional scoring scheme for portions of the sequences. The performance of PEAKS is compared with Lutefisk, a well-known de novo sequencing software, using quadrupole-time-of-flight (Q-TOF) data obtained for several tryptic peptides from standard proteins. Copyright © 2003 John Wiley & Sons, Ltd. [source] Clinical outcomes of single-fraction stereotactic radiation therapy of lung tumors,CANCER, Issue 6 2006Ryusuke Hara M.D. Abstract BACKGROUND The objective of the current study was to investigate the effects and the morbidities of single-fraction stereotactic radiation therapy (SRT) for lung tumors. METHODS A Microtron device was modified to deliver stereotactic irradiation under respiratory gating. Between August 1998 and December 2004, 59 malignant lung tumors (11 primary tumors, 48 metastases) that measured < 40 mm in greatest dimension were treated by single-fraction SRT. Nine tumors received a minimal dose of < 30 grays (Gy), and 50 tumors received a minimal dose of , 30 Gy. The macroscopic target volume ranged from 1 cc to 19 cc (mean, 5 cc). RESULTS The 1-year and 2-year local progression-free rates (LPFRs) were 93% and 78%, respectively. The overall survival rate was 76.5% at 1 year and 41% at 2 years. Local regrowth of the irradiated tumor was a direct cause of death in two patients. Only the minimal radiation dose to the reference target volume tended to have an influence on the LPFR (P = 0.068). The 2-year LPFRs for patients who received irradiation doses of , 30 Gy and < 30 Gy were 83% and 52%, respectively. With regard to morbidities, Grade 3 respiratory symptoms (according to the Radiation Therapy Oncology Group/European Organization for Research and Treatment of Cancer late radiation morbidity scoring scheme) were noted in one patient. CONCLUSIONS The results from the current study suggested that single-fraction SRT was tolerable and was capable of attaining excellent local control in patients who had malignant lung tumors that measured < 4 cm in greatest dimension. Cancer 2006. © 2006 American Cancer Society. [source] OLAV: Towards high-throughput tandem mass spectrometry data identificationPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 8 2003Jacques Colinge Abstract Mass spectrometry combined with database searching has become the preferred method for identifying proteins in proteomics projects. Proteins are digested by one or several enzymes to obtain peptides, which are analyzed by mass spectrometry. We introduce a new family of scoring schemes, named OLAV, aimed at identifying peptides in a database from their tandem mass spectra. OLAV scoring schemes are based on signal detection theory, and exploit mass spectrometry information more extensively than previously existing schemes. We also introduce a new concept of structural matching that uses pattern detection methods to better separate true from false positives. We show the superiority of OLAV scoring schemes compared to MASCOT, a widely used identification program. We believe that this work introduces a new way of designing scoring schemes that are especially adapted to high-throughput projects such as GeneProt large-scale human plasma project, where it is impractical to check all identifications manually. [source] | ||||||||||||||||