Home About us Contact
|
Home About us Contact | ||
|
|
||
Pair Members (pair + member)
Selected AbstractsEvaluation of PSI-BLAST alignment accuracy in comparison to structural alignmentsPROTEIN SCIENCE, Issue 11 2000Iddo Friedberg Abstract The PSI-BLAST algorithm has been acknowledged as one of the most powerful tools for detecting remote evolutionary relationships by sequence considerations only. This has been demonstrated by its ability to recognize remote structural homologues and by the greatest coverage it enables in annotation of a complete genome. Although recognizing the correct fold of a sequence is of major importance, the accuracy of the alignment is crucial for the success of modeling one sequence by the structure of its remote homologue. Here we assess the accuracy of PSI-BLAST alignments on a stringent database of 123 structurally similar, sequence-dissimilar pairs of proteins, by comparing them to the alignments defined on a structural basis. Each protein sequence is compared to a nonredundant database of the protein sequences by PSI-BLAST. Whenever a pair member detects its pair-mate, the positions that are aligned both in the sequential and structural alignments are determined, and the alignment sensitivity is expressed as the per-centage of these positions out of the structural alignment. Fifty-two sequences detected their pair-mates (for 16 pairs the success was bi-directional when either pair member was used as a query). The average percentage of correctly aligned residues per structural alignment was 43.5 ± 2.2%. Other properties of the alignments were also examined, such as the sensitivity vs. specificity and the change in these parameters over consecutive iterations. Notably, there is an improvement in alignment sensitivity over consecutive iterations, reaching an average of 50.9 + 2.5% within the five iterations tested in the current study. [source] The Mechanics of Duetting in a New Zealand Endemic, the Kokako (Callaeas cinerea wilsoni): Song at a Snail's PaceETHOLOGY, Issue 5 2006Laura E. Molles New Zealand's endemic, duetting kokako (Callaeas cinerea wilsoni) produce one of the longest known bird songs (ca 30 s) and duets that differ strikingly from those of most duetters in their unusual length and non-repetitive structure, long pauses between component phrases, and the great flexibility in sex roles. Here we present a structural analysis of the vocalizations of 17 kokako pairs collected during natural song bouts and in response to conspecific playback, to gain insight into the functional role of this extraordinary vocal behavior. Males tend to sing a greater proportion of the duet than females. Like many duetting species, kokako have a moderately sized repertoire of phrases (mean repertoire size =18) and pair members tend to sing antiphonally rather than in unison. Sharing of phrase types is high among neighboring kokako ( = 86%) and repertoires are not sex specific, as is typical of some but not all duetting species. Timing characteristics, broad sharing of phrase types, and countersinging behavior strongly suggest that kokako duets play an important role in territory defense. Additionally, differences in pairs' sex role and phrase sequence flexibility suggest that these aspects of duet performance may reflect pair-bond length or commitment, and require a time investment by pair members. [source] Long-Term Leisure Time Physical Activity and Properties of Bone: A Twin Study,,JOURNAL OF BONE AND MINERAL RESEARCH, Issue 8 2009Hongqiang Ma Abstract Effects of physical activity on bone properties, when controlled for genetic effects, are not fully understood. We aimed to study the association between long-term leisure time physical activity (LTPA) and bone properties using twin pairs known to be discordant for leisure time physical activity for at least 30 yr. Volumetric BMD and geometric properties were measured at the tibia shaft and distal end using pQCT in 16 middle-aged (50,74 yr) same-sex twin pairs (seven monozygotic [MZ] and nine dizygotic [DZ] pairs) selected from a population-based cohort. Paired differences between active and inactive co-twins were studied. Active members of MZ twin pairs had larger cortical bone cross-sectional area (intrapair difference: 8%, p = 0.006), thicker cortex (12%, p = 0.003), and greater moment of inertia (Imax, 20%, p = 0.024) at the tibia shaft than their inactive co-twins. At the distal tibia, trabecular BMD (12%, p = 0.050) and compressive strength index (18%, p = 0.038) were also higher in physically active MZ pair members than their inactive co-twins. The trends were similar, but less consistently so, in DZ pairs as in MZ pairs. Our genetically controlled study design shows that LTPA during adulthood strengthens bones in a site-specific manner, that is, the long bone shaft has a thicker cortex, and thus higher bending strength, whereas the distal bone has higher trabecular density and compressive strength. These results suggest that LTPA has a potential causal role in decreasing the long-term risk of osteoporosis and thus preventing osteoporotic fractures. [source] Secrets in the eyes of Black Oystercatchers: a new sexing techniqueJOURNAL OF FIELD ORNITHOLOGY, Issue 2 2008Brian M. Guzzetti ABSTRACT Sexing oystercatchers in the field is difficult because males and females have identical plumage and are similar in size. Although Black Oystercatchers (Haematopus bachmani) are sexually dimorphic, using morphology to determine sex requires either capturing both pair members for comparison or using discriminant analyses to assign sex probabilistically based on morphometric traits. All adult Black Oystercatchers have bright yellow eyes, but some of them have dark specks, or eye flecks, in their irides. We hypothesized that this easily observable trait was sex-linked and could be used as a novel diagnostic tool for identifying sex. To test this, we compared data for oystercatchers from genetic molecular markers (CHD-W/CHD-Z and HINT-W/HINT-Z), morphometric analyses, and eye-fleck category (full eye flecks, slight eye flecks, and no eye flecks). Compared to molecular markers, we found that discriminant analyses based on morphological characteristics yielded variable results that were confounded by geographical differences in morphology. However, we found that eye flecks were sex-linked. Using an eye-fleck model where all females have full eye flecks and males have either slight eye flecks or no eye flecks, we correctly assigned the sex of 117 of 125 (94%) oystercatchers. Using discriminant analysis based on morphological characteristics, we correctly assigned the sex of 105 of 119 (88%) birds. Using the eye-fleck technique for sexing Black Oystercatchers may be preferable for some investigators because it is as accurate as discriminant analysis based on morphology and does not require capturing the birds. SINOPSIS El sexado de ostreros en el campo es sumamente difícil dado el caso de que tanto hembras como machos tienen plumaje idéntico y son similares en tamaño. Aunque los ostreros negros (Haematopus bachmani) son sexualmente dimórficos, el utilizar morfometría para determinar su sexo requiere capturar a ambos miembros de la pareja para compararlos, utilizando una análisis discriminativo a modo de asignar un sexo por probabilidad, basado en características morfométricas. Todos los adultos del ostrero negro tienen ojos amarillos y brillantes, pero algunos tienen manchas oscuras en el iris. Tomamos como hipótesis que estas peculiaridades observables estaban ligada al sexo, y que podían ser utilizadas como una herramienta novel de diagnóstico para identificar el sexo en dichas aves. Para poner a pruebas lo mencionado, comparamos datos de ostreros donde se utilizaron marcadores genéticos moleculares (CHD-W/CHD-Z y HINT-W/HINT-Z), análisis morfométrico, y categorías en las manchas en los ojos (manchas marcadas en los ojos, algunas manchitas en los ojos, sin manchas en los ojos). Comparado a marcadores moleculares, encontramos que el análisis discriminativo basado en características morfológicas ofrecía resultados variables asociados a diferencias morfológicas geográficas. Sin embargo, encontramos que las manchas en los ojos estaban ligadas al sexo. Utilizando un modelo de manchas en los ojos, en donde clasificamos como hembras aquellos individuos con manchas pronunciadas en los ojos y a machos con muy pocas manchitas o sin manchitas, le pudimos asignar correctamente el sexo a 117 de 125 (94%) individuos. Utilizando una análisis discriminativo basado en características morfológicas, le asignamos el sexo correctamente a 105 de 119 (88%) individuos. El utilizar la técnica de manchas en los ojos para el sexado de ostreros negros pudiera ser preferible para algunos investigadores porque es más exacto que el análisis discriminativo basado en morfología y porque no requiere que se tenga que capturar a las aves. [source] Increased realism in eyewitness confidence judgements: the effect of dyadic collaborationAPPLIED COGNITIVE PSYCHOLOGY, Issue 5 2003Carl Martin Allwood This study investigated to what extent, and under what circumstances, pair collaboration influences the realism in eyewitness confidence in event memory. The participants first saw a short film clip and then confidence rated their answers to questions on its content. A condition (the Individual,Pair condition) where individual effort preceded pair collaboration showed better calibration compared with a condition (the Simple Pair condition) where no individual effort took place. Furthermore, within the Individual,Pair condition, better calibration, and lower overconfidence, were found in the pair phase compared with the individual phase. The eyewitnesses in the Individual,Pair condition made more realistic judgements of the total number of questions answered correctly. In a control experiment no effect on realism in confidence was found when individuals performed the same task twice. The improved realism in the Individual,Pair condition may partly be explained in terms of the increased accuracy and lowered confidence found for such items where the pair members' had given different answers in the individual phase, and by a risky shift effect for such items where they had given the same answer. Copyright © 2003 John Wiley & Sons, Ltd. [source] | ||||||||||