Signal

Abstract: The strength of phylogenetic signal in extinction risk can give insight into the mechanisms behind species’ declines. Nevertheless, no existing measure of phylogenetic pattern in a binary trait, such as extinction-risk status, measures signal strength in a way that can be compared among data sets. We developed a new measure for phylogenetic signal of binary traits, D, which simulations show gives robust results with data sets of more than 50 species, even when the proportion of threatened species is low. We applied D to the red-list status of British birds and the world's mammals and found that the threat status for both groups exhibited moderately strong phylogenetic clumping. We also tested the hypothesis that the phylogenetic pattern of species threatened by harvesting will be more strongly clumped than for those species threatened by either habitat loss or invasive species because the life-history traits mediating the effects of harvesting show strong evolutionary pattern. For mammals, our results supported our hypothesis; there was significant but weaker phylogenetic signal in the risk caused by the other two drivers (habitat loss and invasive species). We conclude that D is likely to be a useful measure of the strength of phylogenetic pattern in many binary traits.Resumen: La intensidad de la señal filogenética en el riesgo de extinción puede proporcionar perspectivas acerca de los mecanismos subyacentes en la declinación de las especies. Sin embargo, ninguna medida existente del patrón filogenético en un atributo binario, como el estatus de riesgo de extinción, cuantifica la intensidad de la señal de modo que pueda ser comparada entre conjuntos de datos. Desarrollamos una nueva medida de la señal filogenética para atributos binarios, D, que en simulaciones proporciona resultados robustos con conjuntos de datos de más de 50 especies, aun cuando la proporción de especies amenazadas sea baja. Aplicamos D a la lista roja de aves británicas y de mamíferos del mundo y encontramos que el estatus de amenaza para ambos grupos mostró un agrupamiento filogenético moderadamente fuerte. También probamos la hipótesis de que el patrón filogenético de especies amenazadas por la cosecha estará agrupado más estrechamente que las especies amenazadas por la pérdida de hábitat o por especies invasoras porque los atributos de la historia de vida que intervienen en los efectos de la cosecha muestran un fuerte patrón evolutivo. Para mamíferos, nuestros resultados soportaron nuestra hipótesis; hubo señal filogenética significativa pero más débil en el riesgo causado por los otros dos factores (pérdida de hábitat y especies invasoras). Concluimos que D es una medida útil de la intensidad del patrón filogenético en muchos atributos binarios.Resumen: La intensidad de la señal filogenética en el riesgo de extinción puede proporcionar perspectivas acerca de los mecanismos subyacentes en la declinación de las especies. Sin embargo, ninguna medida existente del patrón filogenético en un atributo binario, como el estatus de riesgo de extinción, cuantifica la intensidad de la señal de modo que pueda ser comparada entre conjuntos de datos. Desarrollamos una nueva medida de la señal filogenética para atributos binarios, D, que en simulaciones proporciona resultados robustos con conjuntos de datos de más de 50 especies, aun cuando la proporción de especies amenazadas sea baja. Aplicamos D a la lista roja de aves británicas y de mamíferos del mundo y encontramos que el estatus de amenaza para ambos grupos mostró un agrupamiento filogenético moderadamente fuerte. También probamos la hipótesis de que el patrón filogenético de especies amenazadas por la cosecha estará agrupado más estrechamente que las especies amenazadas por la pérdida de hábitat o por especies invasoras porque los atributos de la historia de vida que intervienen en los efectos de la cosecha muestran un fuerte patrón evolutivo. Para mamíferos, nuestros resultados soportaron nuestra hipótesis; hubo señal filogenética significativa pero más débil en el riesgo causado por los otros dos factores (pérdida de hábitat y especies invasoras). Concluimos que D es una medida útil de la intensidad del patrón filogenético en muchos atributos binarios.

Proteins mediate transmission of signals along intercellular and intracellular pathways and between the exterior and the interior of a cell. The dynamic properties of signaling proteins are crucial to their functions. We discuss emerging paradigms for the role of protein dynamics in signaling. A central tenet is that proteins fluctuate among many states on evolutionarily selected energy landscapes. Upstream signals remodel this landscape, causing signaling proteins to transmit information to downstream partners. New methods provide insight into the dynamic properties of signaling proteins at the atomic scale. The next stages in the signaling hierarchy---how multiple signals are integrated and how cellular signaling pathways are organized in space and time---present exciting challenges for the future, requiring bold multidisciplinary approaches.

Clonal deletion provides an important mechanism for the elimination of autoreactive T cells. Deletion is accomplished by programmed cell death directed by interaction of the T-cell receptor (TCR) of the developing thymocyte with major histocompatibility complex elements in the thymic environment. In this report we present evidence to support the hypothesis that the activation and the maturation state of the T cell may be important in coupling the TCR to the "death program." We show that coupling of the TCR to the death program is open during maturation but closed in naive mature T cells. However, during primary antigenic stimulation, coupling between the TCR and the death program is reopened, as demonstrated by the stimulation of the death of these cells by immobilized anti-TCR. Our results suggest that further examination of mature cells that are either resistant or sensitive to receptor-stimulated death may lead to the identification of the components of the death pathwa...

Salicylic acid-binding protein 2 (SABP2) is essential for the establishment of systemic acquired resistance (SAR) in tobacco; SABP2’s methyl salicylate (MeSA) esterase activity is required in healthy systemic tissues of infected plants to release the active defense phytohormone SA from MeSA, which serves as a long-distance signal for SAR. In the current study, we characterize a new gene family from Arabidopsis thaliana encoding 18 potentially active α/β fold hydrolases that share 32–57% identity with SABP2. Of 14 recombinant AtMES (MES for methyl esterase) proteins tested, five showed preference for MeSA as a substrate and displayed SA inhibition of MeSA esterase activity in vitro (AtMES1, -2, -4, -7, and -9). The two genes encoding MeSA esterases with the greatest activity, AtMES1 and -9, as well as AtMES7 were transcriptionally upregulated during infection of Arabidopsis with avirulent Pseudomonas syringae. In addition, conditional expression of AtMES1, -7, or -9 complemented SAR deficiency in SABP2-silenced tobacco, suggesting that these three members of the AtMES family are SABP2 functional homologs (orthologs). Underexpression by knockout mutation and/or RNAi-mediated silencing of multiple AtMES genes, including AtMES1, -2, -7, and -9, compromised SAR in Arabidopsis and correlated with enhanced accumulation of MeSA in the systemic tissue of SAR-induced plants. Together, the data show that several members of the AtMES gene family are functionally homologous to SABP2 and redundant for MeSA hydrolysis and probably SAR. These data suggest that MeSA is a conserved SAR signal in Arabidopsis and tobacco.

Follicular lymphoma (FL) is a cancer of lymph system and it is the second most common lymphoid malignancy in the western world. Currently, the risk stratification of FL relies on histological grading method, where pathologists evaluate hematoxilin and eosin (H&E) stained tissue sections under a microscope as recommended by the World Health Organization. This manual method requires intensive labor in nature. Due to the sampling bias, it also suffers from inter- and intra-reader variability and poor reproducibility. We are developing a computer-assisted system to provide quantitative assessment of FL images for more consistent evaluation of FL. In this study, we proposed a statistical framework to classify FL images based on their histological grades. We introduced model-based intermediate representation (MBIR) of cytological components that enables higher level semantic description of tissue characteristics. Moreover, we introduced a novel color-texture analysis approach that combines the MBIR with low level texture features, which capture tissue characteristics at pixel level. Experimental results on real follicular lymphoma images demonstrate that the combined feature space improved the accuracy of the system significantly. The implemented system can identify the most aggressive FL (grade III) with 98.9% sensitivity and 98.7% specificity and the overall classification accuracy of the system is 85.5%.

This experiment investigated the effect of signal modality on time perception in 5- and 8-year-old children as well as young adults using a duration bisection task in which auditory and visual signals were presented in the same test session and shared common anchor durations. Durations were judged shorter for visual than for auditory signals by all age groups. However, the

This study examined a signal amplification assay, the Invader assay, for the quantitation of hepatitis B virus (HBV) covalently closed circular DNA (cccDNA) in liver biopsies and sera. DNA was extracted from liver biopsy and serum samples were collected from 16 hepatitis B e antigen (HBeAg)-positive and 36 antibody-to-HBeAg-positive (anti–HBe-positive) chronic hepatitis B patients. The amount of total HBV DNA and cccDNA was measured using the Invader assay. Anti–HBe-positive patients had lower median total intrahepatic HBV DNA (P < .001) and intrahepatic cccDNA levels (P = .001) than HBeAg-positive patients. Intrahepatic cccDNA correlated positively with the total intrahepatic HBV DNA (r = 0.950, P < .001). However, the proportion of intrahepatic HBV DNA in the form of cccDNA was inversely related to the amount of total intrahepatic HBV DNA (r = −0.822, P < .001). A small amount of cccDNA was detected in 39 of 52 (75%) serum samples. Anti-HBe-positive patients had lower median serum cccDNA levels than HBeAg-positive patients (P = .002). Serum HBV DNA correlated positively with intrahepatic total HBV DNA (r = 0.778, P < .001) and intrahepatic cccDNA (r = 0.481, P = .002). In conclusion, the Invader assay is a reliable assay for the quantitation of cccDNA. Serum and intrahepatic total HBV DNA and cccDNA levels become lower as the disease progresses from HBeAg-positive to anti–HBe-positive phase, with cccDNA becoming the predominant form of intrahepatic HBV DNA. (HEPATOLOGY 2004;40:727–737.)

Human voice pitch is sexually dimorphic and therefore conveys important information about its owner’s sex. Since people often associate voice pitch with age, body size, attractiveness and, in the case of men, level of dominance, it is assumed that voice pitch signals biological condition. We tested (1) how female voice pitch is related to perceptions of dominance and (2) whether female voice pitch correlates linearly with its attractiveness assessment. We recorded five vowels {A [a], E [ɛ], I [i], O [ɔ], U [u]} and measured the voice fundamental frequency (F0) of 58 young women. The following voices of four women were selected: low (184.6 Hz), medium (223.7 Hz), high (261.9 Hz) and very high (310.3 Hz). Each of these voices was lowered and raised by 20 Hz. The modified voices and the original voices were rated for attractiveness by men, and were rated for dominance by both men and women. We found that women with lower voices were perceived as more dominant and that this relationship was linear. An interaction between the sexes in the dominance assessment indicates that women are more sensitive than men to the dominance cues present in female voices. We also found that, contrary to other studies, the relationship between female voice pitch and its attractiveness is not linear. Higher pitched voices were assessed as more attractive up to an optimal pitch; female voices above ca. 280 Hz were rated as less attractive. We suggest that female voices that have too high a pitch sound babyish and are associated with sexual immaturity.