On the discrete Peyrard-Bishop model of DNA: stationary solutions and stability

As a first step in the search of an analytical study of mechanical denaturation of DNA in terms of the sequence, we study stable, stationary solutions in the discrete, finite and homogeneous Peyrard-Bishop DNA model. We find and classify all the stationary solutions of the model, as well as analytic approximations of them, both in the continuum and in the discrete limits. Our results explain the structure of the solutions reported by Theodorakopoulos {\em et al.} [Phys. Rev. Lett. {\bf 93}, 258101 (2004)] and provide a way to proceed to the analysis of the generalized version of the model incorporating the genetic information.Comment: 15 pages, 12 figure

Variation in African American parents' use of early childhood physical discipline

Physical discipline is endorsed by a majority of adults in the U.S. including African American (AA) parents who have high rates of endorsement. Although many studies have examined physical discipline use among AA families, few have considered how early childhood physical discipline varies within the population. Individuals within a cultural group may differ in their engagement in cultural practices (Rogoff, 2003). Furthermore, AA families’ characteristics and their contexts, which are shaped by the interaction of social position, racism, and segregation (García Coll et al., 1996), likely influence how AA families physically discipline their young children. This study examined variation in early childhood physical discipline among AA families living in low-income communities and relations with demographic and contextual factors. Year 1 data from 310 AA parents living in three regionally distinct low-income communities were used from a sequential longitudinal intervention program study of the development and prevention of conduct disorder. Latent class analyses were conducted using parents’ responses on a measure, of the frequency of overall physical discipline, spanking, and hitting during prekindergarten and kindergarten. The associations between latent classes and six demographic and contextual factors were examined using the Bolck, Croon, and Hagenaars (BCH) method. The factors were: child gender (59% male); marital status (51% never married); parental education (66% high school graduates and beyond); income (mean = $16.66K, S.D. = 12.50), family stress, and perception of neighborhood safety. Measures included the Family Information Form, Life Changes, and the Neighborhood Questionnaire. After considering two to seven class solutions, five physical discipline classes or sub-groups were identified. Classes were defined by discipline frequency (‘Infrequent’, ‘Weekly’, ‘Monthly’, ‘Almost-Every-Day’ and ‘Weekly-All’) as well as by discipline type (only parents in the ‘Weekly-All’ class hit their children). Significant associations were found between class membership, and child gender, marital status, income, and perception of neighborhood safety. Girls were more likely to be physically disciplined infrequently, χ2(4, N = 310) = 11.88, p = .05. The ‘Weekly’ class had significantly fewer married parents than all classes except ‘Almost-Every-Day’, χ2(4, N = 310) = 21.56, p < .001. Parents in the ‘Almost-Every-Day’ class had a significantly lower income than parents in all other classes except “Weekly-All”, χ2(4, N = 310) = 10.88, p = .03. Finally, parents in the “Almost-Every-Day” class perceived their neighborhood as significantly less safe compared to those in all other classes except the ‘Weekly-All’ class, χ2(4, N = 310) = 14.13 p = .01. These findings suggest that AA families vary in physical discipline during early childhood; this variation may result in sub-groups with different demographic characteristics. Associations between frequent discipline classes and perceptions of neighborhood safety implies that some AA parents may use physical discipline to protect their children from being harmed if they believe their communities are unsafe. Future research should qualitatively examine how AA parents respond to unsafe neighborhoods in their parenting behaviors, including physical discipline

Regional requirements for Dishevelled signaling during Xenopus gastrulation: separable effects on blastopore closure, mesendoderm internalization and archenteron formation

During amphibian gastrulation, the embryo is transformed by the combined actions of several different tissues. Paradoxically, many of these morphogenetic processes can occur autonomously in tissue explants, yet the tissues in intact embryos must interact and be coordinated with one another in order to accomplish the major goals of gastrulation: closure of the blastopore to bring the endoderm and mesoderm fully inside the ectoderm, and generation of the archenteron. Here, we present high-resolution 3D digital datasets of frog gastrulae, and morphometrics that allow simultaneous assessment of the progress of convergent extension, blastopore closure and archenteron formation in a single embryo. To examine how the diverse morphogenetic engines work together to accomplish gastrulation, we combined these tools with time-lapse analysis of gastrulation, and examined both wild-type embryos and embryos in which gastrulation was disrupted by the manipulation of Dishevelled (Xdsh) signaling. Remarkably, although inhibition of Xdsh signaling disrupted both convergent extension and blastopore closure, mesendoderm internalization proceeded very effectively in these embryos. In addition, much of archenteron elongation was found to be independent of Xdsh signaling, especially during the second half of gastrulation. Finally, even in normal embryos, we found a surprising degree of dissociability between the various morphogenetic processes that occur during gastrulation. Together, these data highlight the central role of PCP signaling in governing distinct events of Xenopus gastrulation, and suggest that the loose relationship between morphogenetic processes may have facilitated the evolution of the wide variety of gastrulation mechanisms seen in different amphibian species

The Red River Gorge: The Existence of Recreational Niches and Their Management Implications

Until the late 1960\u27s, the Red River Gorge was just one of the more beautiful parts of the Daniel Boone National Forest. At this time, the Army Corps of Engineers proposed to dam the river for flood control, water supply, and recreation purposes. Intense opposition to the project generated considerable publicity and the Gorge area experienced substantial increases in visitation. The result has been not only severe environmental degradation but extensive overcrowding as well. These trends are presently overtaxing management capabilities of the United States Forest Service. The most pressing issue has come to be how to effectively manage this area to preserve both its ecological and social attractiveness. In an effort to provide management agencies with some important social parameters of recreation in Red River Gorge, this report examines the recreationists\u27 sociodemographic characteristics, the recreational activities engaged in, their density tolerance levels, and their preferences for development of the area. Eleven \u27\u27recreational niches (defined as a specific location within a recreation area occupied by visitors pursuing different kinds of leisure-time activities) were identified. Preservation of the niches are recommended as a means for maintaining both the ecological and social diversity of the Red River Gorge

Confronting the Challenge of Whale Detection from Large Vessels

As a result of a moratorium on commercial whaling, most populations of large whales are increasing across the globe. However, concurrent growth in shipping means that lethal ship-whale collisions constitute a significant threat to whale conservation efforts. This study investigates the ability of ship operators to detect and avoid whales by quantifying the predictability of whale surfacing behaviors, which are the cues used to determine whale presence. Whale avoidance is challenging because whales spend most of their time underwater and thus unavailable to be detected (the “availability process”), but must be detected at sufficiently large distances (the “detection process”) to enact an effective avoidance maneuver.  We quantified one of the main characteristics of whale behavior that governs detectability – time breaking the surface – to create a novel model of whale surfacing patterns around ships while accounting for the detection process. We then estimated the frequency with which cues go undetected (i.e. whales break the surface but ship operators are unaware of them), as well as the frequency with which whales are present but unavailable for detection (i.e. below the surface of the water). This work will enable the prediction of close ship-whale encounters given different combinations of detected and/or missed cues at varying ship speeds. It will support ship operators’ avoidance efforts by quantifying the availability and detection processes in a way that facilitates the development of whale avoidance protocols

The Ecological Niche of \u3ci\u3eEchinococcus multilocularis\u3c/i\u3e in North America: Understanding Biotic and Abiotic Determinants of Parasite Distribution with New Records in New Mexico and Maryland, United States

English abstract: Understanding the factors shaping the niche of parasites and its expression over geographical space and through time continues to be a modern scientific challenge with the results of research in this area directly influencing both theoretical and applied biology. This is especially important for proactive management of zoonotic parasites such as Echinococcus multilocularis, the etiologic agent of alveolar echinococcosis. Echinococcus multilocularis has a Holarctic distribution; with its geographic range and prevalence increasing recently in areas of the western Palearctic, while its distribution dynamics are poorly understood in the Nearctic. In this paper, we use an ecological niche modeling (ENM) approach to: i) estimate the current spatial distribution of suitable conditions for the parasite in the Nearctic. ii) Evaluate the abiotic and biotic factors influencing the species distribution. iii) Assess the potential impact of climatic change on the distribution of this species in the Nearctic. Additionally, we report two new occurrence records of this parasite that significantly expands its known geographic range. We reviewed the occurrence records of E. multilocularis for the Nearctic. This was complemented by two new records of the species from Maryland and New Mexico identified using morphology and multivariate morphometrics of the rostellar hooks. From these data we created two ENMs using the software Maxent. The first ENM included climatic variables, while the second included the same abiotic data plus biotic information consisting of four host community-related data sets. We evaluated model performance and variable importance to explore the relation of these variables to the parasite niche. Finally, we projected the resulting niche model onto future climate change scenarios. We found that an important portion of the Nearctic has suitable conditions for E. multilocularis with adequate habitat in the West and East of the continent where the parasite has not been detected. We also found that the proposed biotic variables improve the model performance and provide unique information, while the most critical abiotic variable was related to the amount of solar radiation. Finally, under the future emission scenarios explored, the distribution of suitable habitat for the parasite is predicted to increase by 56% to 76%. We obtained a robust model that provides detail on the distribution of suitable areas for E. multilocularis, including areas that have not been explored for the presence of the parasite. The host community variables included in this study seem a promising way to include biotic data for ecological parasite niche modeling. Resumen español: El estudio de los factores que moldean el nicho de los parásitos y como este se expresa en la distribución espacial y temporal de estos organismos es un reto de importancia para la biología aplicada y teórica. Esta información puede ser de especial importancia para parásitos zoonóticos tales como Echinococcus multilocularis, el cestodo causante de echinococcosis alveolar. Este parasito presenta una distribución Holártica, con un incremento reciente en rango geográfico y prevalencia documentados en Asia y Europa, mientras que en el Neártico, se desconoce la dinámica de distribución de la especie. En este estudio usamos modelos de nicho ecológico para: i) estimar la distribución actual de hábitat para la especie en Norteamérica. ii) Evaluar el efecto de factores bióticos y abióticos sobre la distribución de este parasito. iii) Evaluar el impacto potencial del cambio climático sobre su distribución. Adicionalmente, reportamos dos nuevos registros para la especie. En este trabajo revisamos los registros de ocurrencia de E. multilocularis en el Neártico. Esta información es complementada con dos nuevos registros provenientes de Maryland y Nuevo México identificados a partir de análisis morfológicos y morfométricos. Empleando el software Maxent, creamos dos modelos de nicho a partir de estos registros. El primer modelo se basó únicamente en variables abióticas, mientras que el segundo además de incluir las variables abióticas incluyó variables bióticas relacionadas con la comunidad de hospederos potenciales. Evaluamos el desempeño de cada modelo y la contribución de cada variable para explorar la relación de estas con el nicho del parásito. Finalmente, proyectamos los modelos al futuro bajo dos escenarios de emisiones de CO2. Encontramos que existen condiciones adecuadas para la especie en una porción importante del área de estudio, con áreas predichas al Este y Occidente del continente donde no se ha registrado el parásito. La inclusión de las variables bióticas resulta en modelos con mejor desempeño, así mismo, se evidencio que estas variables presentan información única no contenida en otras capas. La radiación solar fue la variable abiótica de mayor importancia. Finalmente, bajo los escenarios de cambio climático explorados, el área de hábitat adecuado para el parasito presenta un importante aumento de entre el 56% y 76%. En este trabajo obtuvimos un modelo robusto y detallado de la distribución de las condiciones ambientales adecuadas para E. multilocularis, el cual incluye zonas donde no ha sido reportada la presencia del parásito. Las variables relacionadas con la comunidad de hospederos incluidas en este trabajo parecen ser una manera prometedora de incluir información biótica en modelos de nicho de simbiontes

Imaging the Beating Heart with Macroscopic Phase Stamping

We present a novel approach for imaging the beating embryonic heart, based on combining two independent imaging channels to capture the full spatio-temporal information of the moving 3D structure. High-resolution, optically-sectioned image recording is accompanied by simultaneous acquisition of low-resolution, whole-heart recording, allowing the latter to be used in post-acquisition processing to determine the macroscopic spatio-temporal phase of the heart beating cycle. Once determined, or 'stamped', the phase information common to both imaging channels is used to reconstruct the 3D beating heart. We demonstrated our approach in imaging the beating heart of the zebrafish embryo, capturing the entire heart over its full beating cycle, and characterizing cellular dynamic behavior with sub-cellular resolution