Simulation studies of a phenomenological model for elongated virus capsid formation

We study a phenomenological model in which the simulated packing of hard, attractive spheres on a prolate spheroid surface with convexity constraints produces structures identical to those of prolate virus capsid structures. Our simulation approach combines the traditional Monte Carlo method with a modified method of random sampling on an ellipsoidal surface and a convex hull searching algorithm. Using this approach we identify the minimum physical requirements for non-icosahedral, elongated virus capsids, such as two aberrant flock house virus (FHV) particles and the prolate prohead of bacteriophage $\phi_{29}$, and discuss the implication of our simulation results in the context of recent experimental findings. Our predicted structures may also be experimentally realized by evaporation-driven assembly of colloidal spheres

A Computational Model of Reactive Oxygen Species and Redox Balance in Cardiac Mitochondria

AbstractElevated levels of reactive oxygen species (ROS) play a critical role in cardiac myocyte signaling in both healthy and diseased cells. Mitochondria represent the predominant cellular source of ROS, specifically the activity of complexes I and III. The model presented here explores the modulation of electron transport chain ROS production for state 3 and state 4 respiration and the role of substrates and respiratory inhibitors. Model simulations show that ROS production from complex III increases exponentially with membrane potential (ΔΨm) when in state 4. Complex I ROS release in the model can occur in the presence of NADH and succinate (reverse electron flow), leading to a highly reduced ubiquinone pool, displaying the highest ROS production flux in state 4. In the presence of ample ROS scavenging, total ROS production is moderate in state 3 and increases substantially under state 4 conditions. The ROS production model was extended by combining it with a minimal model of ROS scavenging. When the mitochondrial redox status was oxidized by increasing the proton permeability of the inner mitochondrial membrane, simulations with the combined model show that ROS levels initially decline as production drops off with decreasing ΔΨm and then increase as scavenging capacity is exhausted. Hence, this mechanistic model of ROS production demonstrates how ROS levels are controlled by mitochondrial redox balance

Using RNA-seq to characterize responses to 4 hydroxyphenylpyruvate dioxygenase (HPPD) inhibitor herbicide resistance in waterhemp (Amaranthus tuberculatus)

Background: Waterhemp (Amaranthus tuberculatus (Moq.) J.D. Sauer) is a problem weed commonly found in the Midwestern United States that can cause crippling yield losses for both maize (Zea mays L.) and soybean (Glycine max L. Merr). In 2011, 4-hydroxyphenylpyruvate-dioxygenase (HPPD, EC 1.13.11.27) inhibitor herbicide resistance was first reported in two waterhemp populations. Since the discovery of HPPD-herbicide resistance, studies have identified the mechanism of resistance and described the inheritance of the herbicide resistance. However, no studies have examined genome-wide gene expression changes in response to herbicide treatment in herbicide resistant and susceptible waterhemp. Results: We conducted RNA-sequencing (RNA-seq) analyses of two waterhemp populations (HPPD-herbicide resistant and susceptible), from herbicide-treated and mock-treated leaf samples at three, six, twelve, and twenty-four hours after treatment (HAT). We performed a de novo transcriptome assembly using all sample sequences. Following assessments of our assembly, individual samples were mapped to the de novo transcriptome allowing us to identify transcripts specific to a genotype, herbicide treatment, or time point. Our results indicate that the response of HPPDherbicide resistant and susceptible waterhemp genotypes to HPPD-inhibiting herbicide is rapid, established as soon as 3 hours after herbicide treatment. Further, there was little overlap in gene expression between resistant and susceptible genotypes, highlighting dynamic differences in response to herbicide treatment. In addition, we used stringent analytical methods to identify candidate single nucleotide polymorphisms (SNPs) that distinguish the resistant and susceptible genotypes. Conclusions: The waterhemp transcriptome, herbicide-responsive genes, and SNPs generated in this study provide valuable tools for future studies by numerous plant science communities. This collection of resources is essential to study and understand herbicide effects on gene expression in resistant and susceptible weeds. Understanding how herbicides impact gene expression could allow us to develop novel approaches for future herbicide development. Additionally, an increased understanding of the prolific traits intrinsic in weed success could lead to crop improvement

A Novel Approach for Ellipsoidal Outer-Approximation of the Intersection Region of Ellipses in the Plane

In this paper, a novel technique for tight outer-approximation of the intersection region of a finite number of ellipses in 2-dimensional (2D) space is proposed. First, the vertices of a tight polygon that contains the convex intersection of the ellipses are found in an efficient manner. To do so, the intersection points of the ellipses that fall on the boundary of the intersection region are determined, and a set of points is generated on the elliptic arcs connecting every two neighbouring intersection points. By finding the tangent lines to the ellipses at the extended set of points, a set of half-planes is obtained, whose intersection forms a polygon. To find the polygon more efficiently, the points are given an order and the intersection of the half-planes corresponding to every two neighbouring points is calculated. If the polygon is convex and bounded, these calculated points together with the initially obtained intersection points will form its vertices. If the polygon is non-convex or unbounded, we can detect this situation and then generate additional discrete points only on the elliptical arc segment causing the issue, and restart the algorithm to obtain a bounded and convex polygon. Finally, the smallest area ellipse that contains the vertices of the polygon is obtained by solving a convex optimization problem. Through numerical experiments, it is illustrated that the proposed technique returns a tighter outer-approximation of the intersection of multiple ellipses, compared to conventional techniques, with only slightly higher computational cost

Casting Light Upon The Great Endarkenment

While the Enlightenment promoted thinking for oneself independent of religious authority, the ‘Endarkenment’ (Millgram 2015) concerns deference to a new authority: the specialist, a hyperspecializer. Non-specialists need to defer to such authorities as they are unable to understand their reasoning. Millgram describes how humans are capable of being serial hyperspecializers, able to move from one specialism to another. We support the basic thrust of Millgram’s position, and seek to articulate how the core idea is deployed in very different ways in relation to extremely different philosophical areas. We attend to the issue of the degree of isolation of different specialists and we urge greater emphasis on parallel hyperspecialization, which describes how different specialisms can be embodied in one person at one time

Does bariatric surgery improve adipose tissue function?

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/134250/1/obr12429_am.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/134250/2/obr12429.pd

Unregulated provider perceptions of audit and feedback reports in long-term care: cross-sectional survey findings from a quality improvement intervention

Abstract Background Audit with feedback is a moderately effective approach for improving professional practice in other health care settings. Although unregulated caregivers give the majority of direct care in long-term care settings, little is known about how they understand and perceive feedback reports because unregulated providers have not been directly targeted to receive audit with feedback in quality improvement interventions in long-term care. The purpose of this paper is to describe unregulated care providers’ perceptions of usefulness of a feedback report in four Canadian long-term care facilities. Methods We delivered monthly feedback reports to unregulated care providers for 13 months in 2009–2010. The feedback reports described a unit’s performance in relation to falls, depression, and pain as compared to eight other units in the study. Follow-up surveys captured participant perceptions of the feedback report. We conducted descriptive analyses of the variables related to participant perceptions and multivariable logistic regression to assess the association between perceived usefulness of the feedback report and a set of independent variables. Results The vast majority (80%) of unregulated care providers (n = 171) who responded said they understood the reports. Those who discussed the report with others and were interested in other forms of data were more likely to find the feedback report useful for making changes in resident care. Conclusions This work suggests that unregulated care providers can understand and feel positively about using audit with feedback reports to make changes to resident care. Further research should explore ways to promote fuller engagement of unregulated care providers in decision-making to improve quality of care in long-term care settings.http://deepblue.lib.umich.edu/bitstream/2027.42/112596/1/12877_2012_Article_825.pd