Analysis of the hierarchical structure of the B. subtilis transcriptional regulatory network

The transcriptional regulation of gene expression is orchestrated by complex networks of interacting genes. Increasing evidence indicates that these `transcriptional regulatory networks' (TRNs) in bacteria have an inherently hierarchical architecture, although the design principles and the specific advantages offered by this type of organization have not yet been fully elucidated. In this study, we focussed on the hierarchical structure of the TRN of the gram-positive bacterium Bacillus subtilis and performed a comparative analysis with the TRN of the gram-negative bacterium Escherichia coli. Using a graph-theoretic approach, we organized the transcription factors (TFs) and sigma-factors in the TRNs of B. subtilis and E. coli into three hierarchical levels (Top, Middle and Bottom) and studied several structural and functional properties across them. In addition to many similarities, we found also specific differences, explaining the majority of them with variations in the distribution of s-factors across the hierarchical levels in the two organisms. We then investigated the control of target metabolic genes by transcriptional regulators to characterize the differential regulation of three distinct metabolic subsystems (catabolism, anabolism and central energy metabolism). These results suggest that the hierarchical architecture that we observed in B. subtilis represents an effective organization of its TRN to achieve flexibility in response to a wide range of diverse stimuli.

Gamma oscillations in the midbrain spatial attention network: linking circuits to function

Gamma-band (25-140 Hz) oscillations are ubiquitous in mammalian forebrain structures involved in sensory processing, attention, learning and memory. The optic tectum (01) is the central structure in a midbrain network that participates critically in controlling spatial attention. In this review, we summarize recent advances in characterizing a neural circuit in this midbrain network that generates large amplitude, space-specific, gamma oscillations in the avian OT, both in vivo and in vitro. We describe key physiological and pharmacological mechanisms that produce and regulate the structure of these oscillations. The extensive similarities between midbrain gamma oscillations in birds and those in the neocortex and hippocampus of mammals, offer important insights into the functional significance of a midbrain gamma oscillatory code.

Interaction of a vortex ring with a single bubble: bubble and vorticity dynamics

The interaction of a single bubble with a single vortex ring in water has been studied experimentally. Measurements of both the bubble dynamics and vorticity dynamics have been done to help understand the two-way coupled problem. The circulation strength of the vortex ring (Gamma) has been systematically varied, while keeping the bubble diameter (D-b) constant, with the bubble volume to vortex core volume ratio (V-R) also kept fixed at about 0.1. The other important parameter in the problem is a Weber number based on the vortex ring strength. (We = 0.87 rho(Gamma/2 pi a)(2)/(sigma/D-b); a = vortex core radius, sigma = surface tension), which is varied over a large range, We = 3-406. The interaction between the bubble and ring for each of the We cases broadly falls into four stages. Stage I is before capture of the bubble by the ring where the bubble is drawn into the low-pressure vortex core, while in stage II the bubble is stretched in the azimuthal direction within the ring and gradually broken up into a number of smaller bubbles. Following this, in stage III the bubble break-up is complete and the resulting smaller bubbles slowly move around the core, and finally in stage IV the bubbles escape. Apart from the effect of the ring on the bubble, the bubble is also shown to significantly affect the vortex ring, especially at low We (We similar to 3). In these low-We cases, the convection speed drops significantly compared to the base case without a bubble, while the core appears to fragment with a resultant large decrease in enstrophy by about 50 %. In the higher-We cases (We > 100), there are some differences in convection speed and enstrophy, but the effects are relatively small. The most dramatic effects of the bubble on the ring are found for thicker core rings at low We (We similar to 3) with the vortex ring almost stopping after interacting with the bubble, and the core fragmenting into two parts. The present idealized experiments exhibit many phenomena also seen in bubbly turbulent flows such as reduction in enstrophy, suppression of structures, enhancement of energy at small scales and reduction in energy at large scales. These similarities suggest that results from the present experiments can be helpful in better understanding interactions of bubbles with eddies in turbulent flows.

Deciphering complex patterns of class-I HLA-peptide cross-reactivity via hierarchical grouping

T-cell responses in humans are initiated by the binding of a peptide antigen to a human leukocyte antigen (HLA) molecule. The peptide-HLA complex then recruits an appropriate T cell, leading to cell-mediated immunity. More than 2000 HLA class-I alleles are known in humans, and they vary only in their peptide-binding grooves. The polymorphism they exhibit enables them to bind a wide range of peptide antigens from diverse sources. HLA molecules and peptides present a complex molecular recognition pattern, as many peptides bind to a given allele and a given peptide can be recognized by many alleles. A powerful grouping scheme that not only provides an insightful classification, but is also capable of dissecting the physicochemical basis of recognition specificity is necessary to address this complexity. We present a hierarchical classification of 2010 class-I alleles by using a systematic divisive clustering method. All-pair distances of alleles were obtained by comparing binding pockets in the structural models. By varying the similarity thresholds, a multilevel classification was obtained, with 7 supergroups, each further subclassifying to yield 72 groups. An independent clustering performed based only on similarities in their epitope pools correlated highly with pocket-based clustering. Physicochemical feature combinations that best explain the basis of clustering are identified. Mutual information calculated for the set of peptide ligands enables identification of binding site residues contributing to peptide specificity. The grouping of HLA molecules achieved here will be useful for rational vaccine design, understanding disease susceptibilities and predicting risk of organ transplants.

Activity-travel behaviour of non-workers from Bangalore City in India

This paper presents exploratory and statistical analyses of the activity-travel behaviour of non-workers in Bangalore city in India. The study summarises the socio-demographic characteristics as well as the activity-travel behaviour of non-workers using a primary activity-travel survey data collected by the authors. Where possible, the research also compares the analysis findings with the case studies on activity-travel behaviour of non-workers, carried out in developed and developing countries. This gives an opportunity to understand the differences/similarities in the activity-travel behaviour of non-workers across diverse socio-cultural settings. The preliminary exploratory analysis shed light on the differences in activity participation, trip chaining, time-of-day preference for trip departure, and mode use behaviour of non-workers in Bangalore city. Statistical models were developed for investigating the effects of individual and household socio-demographics, land use parameters, and travel context attributes on activity participation, trip chaining, time-of-day choice, and mode choice decisions of non-workers. A few important results of the analysis are the influence of viewing television at home on out-of-home activity participation and trip-chaining behaviour, and the impact of in-home maintenance activity duration on time-of-day choice. Further, based on the findings of the initial analyses, an attempt has been made in this study to develop an integrated model that links time allocation, time-of-day choice, and trip chaining behaviour of non-workers. The study also discusses the implications of the research findings for transportation planning and policy for Bangalore city. (C) 2015 Elsevier Ltd. All rights reserved.

Inter-comparison and performance evaluation of chemistry transport models over Indian region

Aerosol loading over the South Asian region has the potential to affect the monsoon rainfall, Himalayan glaciers and regional air-quality, with implications for the billions in this region. While field campaigns and network observations provide primary data, they tend to be location/season specific. Numerical models are useful to regionalize such location-specific data. Studies have shown that numerical models underestimate the aerosol scenario over the Indian region, mainly due to shortcomings related to meteorology and the emission inventories used. In this context, we have evaluated the performance of two such chemistry-transport models: WRF-Chem and SPRINTARS over an India-centric domain. The models differ in many aspects including physical domain, horizontal resolution, meteorological forcing and so on etc. Despite these differences, both the models simulated similar spatial patterns of Black Carbon (BC) mass concentration, (with a spatial correlation of 0.9 with each other), and a reasonable estimates of its concentration, though both of them under-estimated vis-a-vis the observations. While the emissions are lower (higher) in SPRINTARS (WRF-Chem), overestimation of wind parameters in WRF-Chem caused the concentration to be similar in both models. Additionally, we quantified the under-estimations of anthropogenic BC emissions in the inventories used these two models and three other widely used emission inventories. Our analysis indicates that all these emission inventories underestimate the emissions of BC over India by a factor that ranges from 1.5 to 2.9. We have also studied the model simulations of aerosol optical depth over the Indian region. The models differ significantly in simulations of AOD, with WRF-Chem having a better agreement with satellite observations of AOD as far as the spatial pattern is concerned. It is important to note that in addition to BC, dust can also contribute significantly to AOD. The models differ in simulations of the spatial pattern of mineral dust over the Indian region. We find that both meteorological forcing and emission formulation contribute to these differences. Since AOD is column integrated parameter, description of vertical profiles in both models, especially since elevated aerosol layers are often observed over Indian region, could be also a contributing factor. Additionally, differences in the prescription of the optical properties of BC between the models appear to affect the AOD simulations. We also compared simulation of sea-salt concentration in the two models and found that WRF-Chem underestimated its concentration vis-a-vis SPRINTARS. The differences in near-surface oceanic wind speeds appear to be the main source of this difference. In-spite of these differences, we note that there are similarities in their simulation of spatial patterns of various aerosol species (with each other and with observations) and hence models could be valuable tools for aerosol-related studies over the Indian region. Better estimation of emission inventories could improve aerosol-related simulations. (C) 2015 Elsevier Ltd. All rights reserved.

Joint modeling of lithosphere and mantle dynamics: Evaluation of constraints from global tomography models

With the advances in technology, seismological theory, and data acquisition, a number of high-resolution seismic tomography models have been published. However, discrepancies between tomography models often arise from different theoretical treatments of seismic wave propagation, different inversion strategies, and different data sets. Using a fixed velocity-to-density scaling and a fixed radial viscosity profile, we compute global mantle flow models associated with the different tomography models and test the impact of these for explaining surface geophysical observations (geoid, dynamic topography, stress, and strain rates). We use the joint modeling of lithosphere and mantle dynamics approach of Ghosh and Holt (2012) to compute the full lithosphere stresses, except that we use HC for the mantle circulation model, which accounts for the primary flow-coupling features associated with density-driven mantle flow. Our results show that the seismic tomography models of S40RTS and SAW642AN provide a better match with surface observables on a global scale than other models tested. Both of these tomography models have important similarities, including upwellings located in Pacific, Eastern Africa, Iceland, and mid-ocean ridges in the Atlantic and Indian Ocean and downwelling flows mainly located beneath the Andes, the Middle East, and central and Southeast Asia.

An experimental study on turbulent coherent structures near a sheared air-water interface

The turbulence structures near a sheared air-water interface were experimentally investigated with the hydrogen bubble visualization technique. Surface shear was imposed by an airflow over the water flow which was kept free from surface waves. Results show that the wind shear has the main influence on coherent structures under air-water interfaces. Low- and high- speed streaks form in the region close to the interface as a result of the imposed shear stress. When a certain airflow velocity is reached, "turbulent spots" appear randomly at low-speed streaks with some characteristics of hairpin vortices. At even higher shear rates, the flow near the interface is dominated primarily by intermittent bursting events. The coherent structures observed neat sheared air-water interfaces show qualitative similarities with those occurring in near-wall turbulence. However, a few distinctive phenomena were also observed, including the fluctuating thickness of the instantaneous boundary layer and vertical vortices in bursting processes, which appear to be associated with the characteristics of air-water interfaces.

A key role for similarity in vicarious reward.

Humans appear to have an inherent prosocial tendency toward one another in that we often take pleasure in seeing others succeed. This fact is almost certainly exploited by game shows, yet why watching others win elicits a pleasurable vicarious rewarding feeling in the absence of personal economic gain is unclear. One explanation is that game shows use contestants who have similarities to the viewing population, thereby kindling kin-motivated responses (for example, prosocial behavior). Using a game show-inspired paradigm, we show that the interactions between the ventral striatum and anterior cingulate cortex subserve the modulation of vicarious reward by similarity, respectively. Our results support studies showing that similarity acts as a proximate neurobiological mechanism where prosocial behavior extends to unrelated strangers.

Measurement and simulation of surface roughness noise using phased microphone arrays

A turbulent boundary-layer flow over a rough wall generates a dipole sound field as the near-field hydrodynamic disturbances in the turbulent boundary-layer scatter into radiated sound at small surface irregularities. In this paper, phased microphone arrays are applied to the measurement and simulation of surface roughness noise. The radiated sound from two rough plates and one smooth plate in an open jet is measured at three streamwise locations, and the beamforming source maps demonstrate the dipole directivity. Higher source strengths can be observed on the rough plates which also enhance the trailing-edge noise. A prediction scheme in previous theoretical work is used to describe the strength of a distribution of incoherent dipoles and to simulate the sound detected by the microphone array. Source maps of measurement and simulation exhibit satisfactory similarities in both source pattern and source strength, which confirms the dipole nature and the predicted magnitude of roughness noise. However, the simulations underestimate the streamwise gradient of the source strengths and overestimate the source strengths at the highest frequency. © 2008 Elsevier Ltd. All rights reserved.

Style and the “Idea” of the sophist after Plato : the impact of form typology on sophistic teaching and writing on interdisciplinary scholarly work

Resumen: Después de la primera sofística, los sofistas actuaron entre el resto de los pensadores del Mediterráneo como un grupo definido. Dado que hay muchos ejemplos que muestran que los sofistas ejercían sus prácticas y que también eran personas comprometidas en otras actividades, vamos a examinar aquí diversos casos de semejanzas y diferencias entre ellos y otros grupos de pensadores. Nuestras tres preguntas fundamentales son: qué, cómo y por qué los sofistas escribían y enseñaban. Intentaremos responder haciendo un análisis diacrónico de las principales formas y géneros de escritura que produjeron (qué). El cómo lo responderemos en su desenvolvimiento como una actividad comunicativa más allá de las fronteras de las disciplinas de la época. El por qué tendrá su respuesta al enfatizar la necesidad de la actividad de los sofistas en la socialización de la época y en la educación de la antigüedad. Al aseverar que el estilo era la idea de los sofistas, ponemos la noción de idea en Platón en el contexto de idea derivado de los sofistas contemporáneos a él y de los sofistas posteriores (segunda sofística) y centramos el foco en la función de visualidad expresada en su concepto de idea desde las obras sofísticas más tempranas en la época de Platón hasta las contribuciones posteriores.

Alfonso Henriques y Roger II de Sicilia, dos vidas paralelas : de condes a reyes: una clave para la comprensión del nacimiento del Reino de Portugal

Resumen: Este trabajo busca comparar los dos procesos de independencia de los condados de Sicilia y de Portugal. Las similitudes y diferencias, como las estrategias comunes para alcanzar el reconocimiento de la Cristiandad como nuevos reinos, forman parte de este trabajo que parte del parentesco dinástico entre las dos casas de Hauteville y de Borgoña, desde finales del siglo XI y la primera mitad del XII.

Saber y poder, prodigios ambiguos e interpretación medieval en el Libro de Alexandre y el Poema de Fernán Gonçález

Resumen: Tanto en el Libro de Alexandre como en el Poema de Fernán Gonçález se presentan prodigios de signifi cación ambigua: el eclipse en el LA, el caballero tragado por la tierra y la serpiente voladora en el PFG. Los episodios en que aparecen insertos estos elementos extraordinarios o sobrenaturales ofrecen una serie de similitudes: el temor de los ejércitos y la habilidad retórica que se despliega para reinterpretar el signo, volverlo a favor del héroe y enardecer así a sus hombres. El objetivo de este trabajo es examinar estos episodios y su signifi cación en el marco de cada uno de los poemas, centrándonos en los problemas de la interpretación y la asignación de sentido, y la relación entre saber y poder que se postula.

La teoría de la justicia de Amartya Sen y los orígenes del concepto católico de justicia social en Antonio Rosmini

Resumen: El autor propone en este artículo reflexionar sobre algunos aspectos del libro The Idea of Justice de Amartya Sen a la luz d e la obra del filósofo italiano Antonio Rosmini, difusor de la expresión “justicia social” en los orígenes del pensamiento social católico. En primer lugar, el autor muestra las coincidencias de Sen y Rosmini sobre el lugar de la razón en el análisis de la idea de justicia social frente a los planteos puramente emocionales y pragmáticos. En segundo lugar, propone una comparación entre las críticas que desarrollan Sen y Rosmini a las denominadas por el primero “teorías trascendentales” de la justicia y a los llamado s “cambios estructurales” así como la necesidad de cambios graduales para llegar a una sociedad justa. En tercer lugar, intenta mostrar cómo la opción por las personas y sus capacidades elegida por Sen puede ser iluminada y profundizada desde la teoría rosminiana de las capacidades. En cuarto lugar, describe el giro cognitivo que propone Sen para las instituciones y las políticas públicas. Finalmente, el autor enuncia algunas objeciones que pudieran hacerse al planteo propuesto en el artículo junto con unos comentarios finales sobre las mismas.

Toward a new synthesis of the god of Edom and Yahweh

This article deals primarily with two things: 1) the history and nature of the Edomite deity Qos, as far as these can be determined from the known archaeological and textual evidence, and 2) the similarities between Qos and Yahweh, the god of Israel, particularly in regard to the theories concerning the origins of the deities. Through the article I will consider some of the recent suggestions concerning the origin of Qos and how this may relate to the origin of Yahweh. I will suggest that both deities originated in the northwestern portion of the Arabian Peninsula and, that ultimately, the mutual origin of the deities accounts for the fact that the Bible makes no reference to Qos as the god of Edom.