Rapid Sampling of Molecular Motions with Prior Information Constraints

Proteins are active, flexible machines that perform a range of different functions. Innovative experimental approaches may now provide limited partial information about conformational changes along motion pathways of proteins. There is therefore a need for computational approaches that can efficiently incorporate prior information into motion prediction schemes. In this paper, we present PathRover, a general setup designed for the integration of prior information into the motion planning algorithm of rapidly exploring random trees (RRT). Each suggested motion pathway comprises a sequence of low-energy clash-free conformations that satisfy an arbitrary number of prior information constraints. These constraints can be derived from experimental data or from expert intuition about the motion. The incorporation of prior information is very straightforward and significantly narrows down the vast search in the typically high-dimensional conformational space, leading to dramatic reduction in running time. To allow the use of state-of-the-art energy functions and conformational sampling, we have integrated this framework into Rosetta, an accurate protocol for diverse types of structural modeling. The suggested framework can serve as an effective complementary tool for molecular dynamics, Normal Mode Analysis, and other prevalent techniques for predicting motion in proteins. We applied our framework to three different model systems. We show that a limited set of experimentally motivated constraints may effectively bias the simulations toward diverse predicates in an outright fashion, from distance constraints to enforcement of loop closure. In particular, our analysis sheds light on mechanisms of protein domain swapping and on the role of different residues in the motion

Effector and Naturally Occurring Regulatory T Cells Display No Abnormalities in Activation Induced Cell Death in NOD Mice

BACKGROUND: Disturbed peripheral negative regulation might contribute to evolution of autoimmune insulitis in type 1 diabetes. This study evaluates the sensitivity of naïve/effector (Teff) and regulatory T cells (Treg) to activation-induced cell death mediated by Fas cross-linking in NOD and wild-type mice. PRINCIPAL FINDINGS: Both effector (CD25(-), FoxP3(-)) and suppressor (CD25(+), FoxP3(+)) CD4(+) T cells are negatively regulated by Fas cross-linking in mixed splenocyte populations of NOD, wild type mice and FoxP3-GFP trangeneess. Proliferation rates and sensitivity to Fas cross-linking are dissociated in Treg cells: fast cycling induced by IL-2 and CD3/CD28 stimulation improve Treg resistance to Fas-ligand (FasL) in both strains. The effector and suppressor CD4(+) subsets display balanced sensitivity to negative regulation under baseline conditions, IL-2 and CD3/CD28 stimulation, indicating that stimulation does not perturb immune homeostasis in NOD mice. Effective autocrine apoptosis of diabetogenic cells was evident from delayed onset and reduced incidence of adoptive disease transfer into NOD.SCID by CD4(+)CD25(-) T cells decorated with FasL protein. Treg resistant to Fas-mediated apoptosis retain suppressive activity in vitro. The only detectable differential response was reduced Teff proliferation and upregulation of CD25 following CD3-activation in NOD mice. CONCLUSION: These data document negative regulation of effector and suppressor cells by Fas cross-linking and dissociation between sensitivity to apoptosis and proliferation in stimulated Treg. There is no evidence that perturbed AICD in NOD mice initiates or promotes autoimmune insulitis

Apoptosis of Purified CD4+ T Cell Subsets Is Dominated by Cytokine Deprivation and Absence of Other Cells in New Onset Diabetic NOD Mice

BACKGROUND: Regulatory T cells (Treg) play a significant role in immune homeostasis and self-tolerance. Excessive sensitivity of isolated Treg to apoptosis has been demonstrated in NOD mice and humans suffering of type 1 diabetes, suggesting a possible role in the immune dysfunction that underlies autoimmune insulitis. In this study the sensitivity to apoptosis was measured in T cells from new onset diabetic NOD females, comparing purified subsets to mixed cultures. PRINCIPAL FINDINGS: Apoptotic cells are short lived in vivo and death occurs primarily during isolation, manipulation and culture. Excessive susceptibility of CD25(+) T cells to spontaneous apoptosis is characteristic of isolated subsets, however disappears when death is measured in mixed splenocyte cultures. In variance, CD25(-) T cells display balanced sensitivity to apoptosis under both conditions. The isolation procedure removes soluble factors, IL-2 playing a significant role in sustaining Treg viability. In addition, pro- and anti-apoptotic signals are transduced by cell-to-cell interactions: CD3 and CD28 protect CD25(+) T cells from apoptosis, and in parallel sensitize naïve effector cells to apoptosis. Treg viability is modulated both by other T cells and other subsets within mixed splenocyte cultures. Variations in sensitivity to apoptosis are often hindered by fast proliferation of viable cells, therefore cycling rates are mandatory to adequate interpretation of cell death assays. CONCLUSIONS: The sensitivity of purified Treg to apoptosis is dominated by cytokine deprivation and absence of cell-to-cell interactions, and deviate significantly from measurements in mixed populations. Balanced sensitivity of naïve/effector and regulatory T cells to apoptosis in NOD mice argues against the concept that differential susceptibility affects disease evolution and progression

Perceptual Learning Based on a Temporal Stimulus

Purpose: Studies have shown that amblyopic subjects can greatly benefit from Perceptual Learning (PL) to improve visual functions. The focus of these studies has mainly been on the spatial aspect of visual performance; however, less work has been devoted to evaluate the effect of PL on temporal performance. Here we aimed at determining whether a simple flickering stimulus can be utilized in PL to enhance temporal function performance and whether enhancement will transfer to spatial functions in amblyopic subjects. Methods: Six amblyopic and six normally sighted subjects underwent an evaluation of baseline psychophysics spatial function performance (VA, contrast sensitivity), temporal function performance (critical fusion frequency (CFF) test), static and flickering stereopsis test, and an electrophysiological evaluation (VEP). Next, the subjects underwent 5 training sessions, which included a task similar to the CFF test using the method of constant stimuli. After completing the training sessions, subjects repeated the initial performance evaluation tasks. Results: All amblyopic subjects showed improved temporal visual performance (CFF) in the amblyopic eye (on average, 17%, p<<0.01), following temporal PL. Evidence for generalization to spatial, spatio-temporal, and binocular tasks was also found. The results were further electrophysiologically manifested by an increase in VEP amplitude, increased SNR in amblyopes to levels not different from normally sighted subjects and increased inter-ocular synchronization. In contrast, no significant effect of training was found in the normally sighted group.Conclusions: These results highlight the potential of PL to improve the temporal and spatial visual performance. Future work is needed to optimize this method for clinical applications.THIS DATASET IS ARCHIVED AT DANS/EASY, BUT NOT ACCESSIBLE HERE. TO VIEW A LIST OF FILES AND ACCESS THE FILES IN THIS DATASET CLICK ON THE DOI-LINK ABOV

Matlab code - CFF test

Recent studies highlight the importance of the temporal domain in visual processing. Critical Flicker Frequency (CFF), the frequency at which a flickering light is perceived as continuous, is a widely used measure for evaluating visual temporal processing. Another important issue to investigate is the cortical interactions arising between the flicker stimuli of both eyes.This data presents a robust and reliable dichoptic tool for evaluating the CFF threshold in both eyes. This system is based on an analog output device used to independently drive two LEDs through a custom-written MATLAB code (using a laptop PC) for eliciting sinusoidal flickering stimuli and for psychophysically measuring the perceived CFF threshold. The luminance and phases of each LED are individually controlled, enabling the investigation of the effect of phase and luminance differences on binocular summation in subjects with different ocular pathologies. Experiments were designed to evaluate the CFF threshold through a psychophysical test, based on a discrimination task with a stimulus duration of 1 sec, based on a temporal alternative forced-choice paradigm. The target stimulus temporal features were modulated using the staircase method. Subjects were requested to discriminate between a target stimulus (a flickering light at various frequencies) and a flickering light at a frequency of 120Hz, which is significantly higher than the CFF in humans; therefore, it is perceived as constant.One of the main advantages of the introduced dichoptic presentation system is that it enables the visual temporal performance to be measured under both monocular and binocular conditions where phenomena such as temporal binocular summation (BS) can be evaluated. Moreover, the system offers great flexibility by introducing a stimulus phase shift, which enables studying how stimulus timing affects the temporal function at millisecond scale resolution.Here we provide all necessary computer code that will enable an easy and quick adaptation of the method by scientists interested in studying the temporal resolution of the visual system in general, and in studying inter-ocular differences or interactions in particular.THIS DATASET IS ARCHIVED AT DANS/EASY, BUT NOT ACCESSIBLE HERE. TO VIEW A LIST OF FILES AND ACCESS THE FILES IN THIS DATASET CLICK ON THE DOI-LINK ABOV

Group decision-making theories for child and family social work

There is increasing interest in decision making in social work. Much of the attention has been on individual professional judgement rather than on group decisions processes. This paper outlines key theoretical approaches from diverse fields of knowledge for conceptualising professional group decision processes in child and family social work, as a framework for future research and more focused theoretical developments. The main theoretical approaches considered include (1) group consensus processes; (2) exchange and the use of information; (3) naturalistic studies emphasising group complexity; and (4) incremental improvement processes. The analysis highlights the possible impact of individual, organisational and contextual factors, as well as their complex interconnections, on group decision making. The paper provides a valuable resource for reflecting on group decision processes in child and family social work, and how they complement individual professional judgements and the interactive processes with children and families. Next steps for the development of practice, policy, and research to improve group decision making are discussed. Using theoretical models to underpin empirical research will enable greater connection to be made between studies, and hence further the knowledge base for social work in this field