Sensitivity of polarization fluctuations to the nature of protein-water interactions: Study of biological water in four different protein-water systems

Since the time of Kirkwood, observed deviations in magnitude of the dielectric constant of aqueous protein solution from that of neat water (similar to 80) and slower decay of polarization have been subjects of enormous interest, controversy, and debate. Most of the common proteins have large permanent dipole moments (often more than 100 D) that can influence structure and dynamics of even distant water molecules, thereby affecting collective polarization fluctuation of the solution, which in turn can significantly alter solution's dielectric constant. Therefore, distance dependence of polarization fluctuation can provide important insight into the nature of biological water. We explore these aspects by studying aqueous solutions of four different proteins of different characteristics and varying sizes, chicken villin headpiece subdomain (HP-36), immunoglobulin binding domain protein G (GB1), hen-egg white lysozyme (LYS), and Myoglobin (MYO). We simulate fairly large systems consisting of single protein molecule and 20000-30000 water molecules (varied according to the protein size), providing a concentration in the range of similar to 2-3 mM. We find that the calculated dielectric constant of the system shows a noticeable increment in all the cases compared to that of neat water. Total dipole moment auto time correlation function of water < dM(W) (0)delta M-W (t) > is found to be sensitive to the nature of the protein. Surprisingly, dipole moment of the protein and total dipole moment of the water molecules are found to be only weakly coupled. Shellwise decomposition of water molecules around protein reveals higher density of first layer compared to the succeeding ones. We also calculate heuristic effective dielectric constant of successive layers and find that the layer adjacent to protein has much lower value (similar to 50). However, progressive layers exhibit successive increment of dielectric constant, finally reaching a value close to that of bulk 4-5 layers away. We also calculate shellwise orientational correlation function and tetrahedral order parameter to understand the local dynamics and structural re-arrangement of water. Theoretical analysis providing simple method for calculation of shellwise local dielectric constant and implication of these findings are elaborately discussed in the present work. (C) 2014 AIP Publishing LLC.

Effect of Molecular Flexibility on the Nematic-to-Isotropic Phase Transition for Highly Biaxial Molecular Non-Symmetric Liquid Crystal Dimers

In this work, a study of the nematic (N)-isotropic (I) phase transition has been made in a series of odd non-symmetric liquid crystal dimers, the alpha-(4-cyanobiphenyl-4'-yloxy)-omega-(1-pyrenimine-benzylidene-4'-oxy) alkanes, by means of accurate calorimetric and dielectric measurements. These materials are potential candidates to present the elusive biaxial nematic (N-B) phase, as they exhibit both molecular biaxiality and flexibility. According to the theory, the uniaxial nematic (N-U)-isotropic (I) phase transition is first-order in nature, whereas the N-B-I phase transition is second-order. Thus, a fine analysis of the critical behavior of the N-I phase transition would allow us to determine the presence or not of the biaxial nematic phase and understand how the molecular biaxiality and flexibility of these compounds influences the critical behavior of the N-I phase transition.

Watershed monitoring and the TMDL modeling to assess bacterial loading in estuarine environments to improve management

Shellfish bed closures along the North Carolina coast have increased over the years seemingly concurrent with increases in population (Mallin 2000). More and faster flowing storm water has come to mean more bacteria, and fecal indicator bacterial (FIB) standards for shellfish harvesting are often exceeded when no source of contamination is readily apparent (Kator and Rhodes, 1994). Could management reduce bacterial loads if the source of the bacteria where known? Several potentially useful methods for differentiating human versus animal pollution sources have emerged including Ribotyping and Multiple Antibiotic Resistance (MAR) (US EPA, 2005). Total Maximum Daily Load (TMDL) studies on bacterial sources have been conducted for streams in NC mountain and Piedmont areas (U.S. EPA, 1991 and 2005) and are likely to be mandated for coastal waters. TMDL analysis estimates allowable pollutant loads and allocates them to known sources so management actions may be taken to restore water to its intended uses (U.S. EPA, 1991 and 2005). This project sought first to quantify and compare fecal contamination levels for three different types of land use on the coast, and second, to apply MAR and ribotyping techniques and assess their effectiveness for indentifying bacterial sources. Third, results from these studies would be applied to one watershed to develop a case study coastal TMDL. All three watershed study areas are within Carteret County, North Carolina. Jumping Run Creek and Pettiford Creek are within the White Oak River Basin management unit whereas the South River falls within the Neuse River Basin. Jumping Run Creek watershed encompasses approximately 320 ha. Its watershed was a dense, coastal pocosin on sandy, relic dune ridges, but current land uses are primarily medium density residential. Pettiford Creek is in the Croatan National Forest, is 1133 ha. and is basically undeveloped. The third study area is on Open Grounds Farm in the South River watershed. Half of the 630 ha. watershed is under cultivation with most under active water control (flashboard risers). The remaining portion is forested silviculture.(PDF contains 4 pages)

Estresse no trabalho e lesões por esforços repetitivos (LER) em servidores públicos de uma Universidade no Estado do Rio de Janeiro: Estudo Pró-Saúde

O presente estudo avalia a associação entre estresse no trabalho e auto-relato de diagnóstico médico de lesão por esforço repetitivo (LER). Trata-se de um estudo seccional, inserido no Estudo Pró-Saúde, que consiste no acompanhamento de uma coorte de funcionários técnico-administrativos de uma universidade no Estado do Rio de Janeiro. Os dados foram obtidos, no ano de 2001, a partir da aplicação de um questionário auto-preenchível. A população de estudo constou de 3.314 funcionários, dentre os quais, 485 apresentaram auto-relato de diagnóstico médico de LER, após sua admissão como funcionários da universidade. A prevalência de LER foi maior entre as mulheres (19,4%) do que entre os homens (8,8%). O estresse no trabalho foi avaliado através da versão reduzida do Job Content Questionnaire, desenvolvido por Karasek e Theorell, cujas questões se destinam a avaliar a demanda psicológica, o controle sobre o próprio trabalho e, o apoio social no trabalho. A análise do estresse no trabalho foi realizada de acordo com os quadrantes propostos por Karasek (1979): baixa exigência (baixa demanda e alto controle); trabalho passivo (baixa demanda e baixo controle); alta exigência (alta demanda e baixo controle) e; trabalho ativo (alta demanda e alto controle). Nesta análise, utilizou-se como categoria de referência, a baixa exigência, por compor um cenário ideal de trabalho. Após ajuste por variáveis socioeconômicas e demográficas (idade, escolaridade e renda familiar per capita) e, ocupacionais (anos de trabalho na universidade e ocupação), homens e mulheres com alta exigência no trabalho, apresentaram uma chance maior de serem acometidos por LER (homens: OR= 1,88; IC95% 1,07-3,29 e mulheres: OR= 1,90; IC95% 1,32-2,02). No ajuste adicional pelo apoio social no trabalho, houve redução da força da associação, para ambos os sexos. Para as mulheres com alta exigência no trabalho, esta associação manteve-se significativa (OR= 1,63; IC95%= 1,12-2,37); enquanto que para os homens, esta associação ficou marginalmente significante (OR= 1,62; IC95%= 0,91-2,87). Este estudo reforça que o desequilíbrio entre a demanda psicológica no trabalho e o controle sobre o próprio trabalho é importante na ocorrência de LER e, portanto, pode ser útil na elaboração de medidas preventivas desse crescente problema de sáude pública. Espera-se que as hipóteses geradas neste estudo possam ser testadas em novas investigações que incorporem o desenho longitudinal, como o Estudo Pró-Saúde, no qual este se insere.

Learning to perceive in the sensor motor approach: Piaget's theory of equilibration interpreted dynamically

Learning to perceive is faced with a classical paradox: if understanding is required for perception, how can we learn to perceive something new, something we do not yet understand? According to the sensorimotor approach, perception involves mastery of regular sensorimotor co-variations that depend on the agent and the environment, also known as the "laws" of sensorimotor contingencies (SMCs). In this sense, perception involves enacting relevant sensorimotor skills in each situation. It is important for this proposal that such skills can be learned and refined with experience and yet up to this date, the sensorimotor approach has had no explicit theory of perceptual learning. The situation is made more complex if we acknowledge the open-ended nature of human learning. In this paper we propose Piaget's theory of equilibration as a potential candidate to fulfill this role. This theory highlights the importance of intrinsic sensorimotor norms, in terms of the closure of sensorimotor schemes. It also explains how the equilibration of a sensorimotor organization faced with novelty or breakdowns proceeds by re-shaping pre-existing structures in coupling with dynamical regularities of the world. This way learning to perceive is guided by the equilibration of emerging forms of skillful coping with the world. We demonstrate the compatibility between Piaget's theory and the sensorimotor approach by providing a dynamical formalization of equilibration to give an explicit micro-genetic account of sensorimotor learning and, by extension, of how we learn to perceive. This allows us to draw important lessons in the form of general principles for open-ended sensorimotor learning, including the need for an intrinsic normative evaluation by the agent itself. We also explore implications of our micro-genetic account at the personal level.

Proteomic analysis of differentially expressed proteins in lymphoid organ of Fenneropenaeus chinensis response to Vibrio anguillarum stimulation

To gain an insight into the function of shrimp lymphoid organ at protein level, we analyzed the proteome of lymphoid organ in healthy Chinese shrimp Fenneropenaeus chinensis (F. chinensis) through two-dimensional gel electrophoresis (2-DE) based proteomic approach. A total of 95 spots representing 75 protein entries were identified by liquid chromatography tandem mass spectrometry (LC-MS/MS) with both online and in-house database. According to Gene Ontology (GO) annotation of biological process, the identified proteins were classified into 13 categories. Among them, approximately 36% of proteins related to cytoskeleton are noticeable. Then, a comparative proteomic approach was employed to investigate the differentially expressed proteins in lymphoid organ of Vibrio anguillarum-challenged F. chinensis. At 24 h post-injection (hpi), 17 differentially expressed protein spots were successfully identified, including 4 up-regulated protein spots (represent 4 proteins: cathepsin L protein similar to squid CG16901-PC, protein kinase C and protein similar to T-complex Chaperonin 5 CG8439-PA), and 13 down-regulated protein spots (represent 9 proteins: actin, beta-actin, cytoplasmic actin CyII, alpha tubulin, beta tubulin, protein similar to proteasome delta, vacuolar ATP synthase subunit B, elongation factor 2, carboxypeptidase B). These data may help us to understand the function of lymphoid organ and the molecular immune mechanism of shrimp responsive to pathogen infection. (C) 2010 Elsevier Ltd. All rights reserved.

Inferring Intersection Typings that are Equivalent to Call-by-Name and Call-by-Value Evaluations

We present a procedure to infer a typing for an arbitrary λ-term M in an intersection-type system that translates into exactly the call-by-name (resp., call-by-value) evaluation of M. Our framework is the recently developed System E which augments intersection types with expansion variables. The inferred typing for M is obtained by setting up a unification problem involving both type variables and expansion variables, which we solve with a confluent rewrite system. The inference procedure is compositional in the sense that typings for different program components can be inferred in any order, and without knowledge of the definition of other program components. Using expansion variables lets us achieve a compositional inference procedure easily. Termination of the procedure is generally undecidable. The procedure terminates and returns a typing if the input M is normalizing according to call-by-name (resp., call-by-value). The inferred typing is exact in the sense that the exact call-by-name (resp., call-by-value) behaviour of M can be obtained by a (polynomial) transformation of the typing. The inferred typing is also principal in the sense that any other typing that translates the call-by-name (resp., call-by-value) evaluation of M can be obtained from the inferred typing for M using a substitution-based transformation.

From the demise of theory to its resurgence. A retrospective on the postmodern turn to rethink the 'desire for narrative' and the sublime untimeliness of emancipation

Cultural Marxist Theory, commonly known as theory, enjoyed a moment of extraordinary success in the 1970s, when the works of leading post-war French philosophers were published in English. After relocating to Anglophone academia, however, theory disavowed its original concerns and lost its ambition to understand the world as a whole, becoming the play of heterogeneities associated with postcolonialism, multiculturalism and identity politics, commonly referred to as postmodern theory. This turn, which took place during a period that seemed to have spelt the death of Marxism, the 1990s, induced many of its supporters to engage in an ongoing funeral wake designating the merits of theory and dreaming its resurgence. According to them, had theory been resurrected in historical circumstances completely different from those which had led to its rise, it would have never reacquired the significance that had originally connoted it. This thesis demonstrates how theory has survived its demise and entirely regained its prominence in our socio-political context marked by the effects of the latest crisis of capitalism and by the global threat of terrorisms rooted in messianic eschatologies. In its current form theory does no longer need to show allegiance to certain intellectual stances or political groupings in order to produce important reformulations of the projects it once gave life to. Though less overtly radical and epistemologically bounded, theory remains a necessary form of enquiry justified by the political commitment which originated it in the first place. Its voice continues to speak to us about justice ‘where it is not yet, not yet there, where it is no longer’ (Derrida, 1993, XVIII).

Contribution of the North Atlantic subtropical high to regional climate model (RCM) skill in simulating southeastern United States summer precipitation

© 2014, Springer-Verlag Berlin Heidelberg.This study assesses the skill of advanced regional climate models (RCMs) in simulating southeastern United States (SE US) summer precipitation and explores the physical mechanisms responsible for the simulation skill at a process level. Analysis of the RCM output for the North American Regional Climate Change Assessment Program indicates that the RCM simulations of summer precipitation show the largest biases and a remarkable spread over the SE US compared to other regions in the contiguous US. The causes of such a spread are investigated by performing simulations using the Weather Research and Forecasting (WRF) model, a next-generation RCM developed by the US National Center for Atmospheric Research. The results show that the simulated biases in SE US summer precipitation are due mainly to the misrepresentation of the modeled North Atlantic subtropical high (NASH) western ridge. In the WRF simulations, the NASH western ridge shifts 7° northwestward when compared to that in the reanalysis ensemble, leading to a dry bias in the simulated summer precipitation according to the relationship between the NASH western ridge and summer precipitation over the southeast. Experiments utilizing the four dimensional data assimilation technique further suggest that the improved representation of the circulation patterns (i.e., wind fields) associated with the NASH western ridge substantially reduces the bias in the simulated SE US summer precipitation. Our analysis of circulation dynamics indicates that the NASH western ridge in the WRF simulations is significantly influenced by the simulated planetary boundary layer (PBL) processes over the Gulf of Mexico. Specifically, a decrease (increase) in the simulated PBL height tends to stabilize (destabilize) the lower troposphere over the Gulf of Mexico, and thus inhibits (favors) the onset and/or development of convection. Such changes in tropical convection induce a tropical–extratropical teleconnection pattern, which modulates the circulation along the NASH western ridge in the WRF simulations and contributes to the modeled precipitation biases over the SE US. In conclusion, our study demonstrates that the NASH western ridge is an important factor responsible for the RCM skill in simulating SE US summer precipitation. Furthermore, the improvements in the PBL parameterizations for the Gulf of Mexico might help advance RCM skill in representing the NASH western ridge circulation and summer precipitation over the SE US.

Retrospective assessment of dryland soil stability in relation to grazing and climate change

Accelerated soil erosion is an aspect of dryland degradation that is affected by repeated intense drought events and land management activities such as commercial livestock grazing. A soil stability index (SSI) that detects the erosion status and susceptibility of a landscape at the pixel level, i.e., stable, erosional, or depositional pixels, was derived from the spectral properties of an archived time series (from 1972 to 1997) of Landsat satellite data of a commercial ranch in northeastern Utah. The SSI was retrospectively validated with contemporary field measures of soil organic matter and erosion status that was surveyed by US federal land management agencies. Catastrophe theory provided the conceptual framework for retrospective assessment of the impact of commercial grazing and soil water availability on the SSI. The overall SSI trend was from an eroding landscape in the early drier 1970s towards stable conditions in the wetter mid-1980s and late 1990s. The landscape catastrophically shifted towards an extreme eroding state that was coincident with the “The Great North American Drought of 1988”. Periods of landscape stability and trajectories toward stability were coincident with extremely wet El Niño events. Commercial grazing had less correlation with soil stability than drought conditions. However, the landscape became more susceptible to erosion events under multiple droughts and grazing. Land managers now have nearly a year warning of El Niño and La Niña events and can adjust their management decisions according to predicted landscape erosion conditions.

Effect of a clinical pathway to reduce hospitalizations in nursing home residents with pneumonia:A randomized controlled trial

Context: Nursing home residents with pneumonia are frequently hospitalized. Such transfers may be associated with multiple hazards of hospitalization as well as economic costs. Objective: To assess whether using a clinical pathway for on-site treatment of pneumonia and other lower respiratory tract infections in nursing homes could reduce hospital admissions, related complications, and costs. Design, Setting, and Participants: A cluster randomized controlled trial of 680 residents aged 65 years or older in 22 nursing homes in Hamilton, Ontario, Canada. Nursing homes began enrollment between January 2, 2001, and April 18, 2002, with the last resident follow-up occurring July 4, 2005. Residents were eligible if they met a standardized definition of lower respiratory tract infection. Interventions: Treatment in nursing homes according to a clinical pathway, which included use of oral antimicrobials, portable chest radiographs, oxygen saturation monitoring, rehydration, and close monitoring by a research nurse, or usual care. Main Outcome Measures: Hospital admissions, length of hospital stay, mortality, health-related quality of life, functional status, and cost. Results: Thirty-four (10%) of 327 residents in the clinical pathway group were hospitalized compared with 76 (22%) of 353 residents in the usual care group. Adjusting for clustering of residents in nursing homes, the weighted mean reduction in hospitalizations was 12% (95% confidence interval [CI], 5%-18%; P=.001). The mean number of hospital days per resident was 0.79 in the clinical pathway group vs 1.74 in the usual care group, with a weighted mean difference of 0.95 days per resident (95% CI, 0.34-1.55 days; P=.004). The mortality rate was 8% (24 deaths) in the clinical pathway group vs 9% (32 deaths) in the usual care group, with a weighted mean difference of 2.9% (95% CI, -2.0% to 7.9%; P=.23). There were no significant differences between the groups in health-related quality of life or functional status. The clinical pathway resulted in an overall cost savings of US $1016 per resident (95% CI, $207-$1824) treated. Conclusion: Treating residents of nursing homes with pneumonia and other lower respiratory tract infections with a clinical pathway can result in comparable clinical outcomes, while reducing hospitalizations and health care costs. ©2006 American Medical Association. All rights reserved.

Aspects of dietary carbohydrate intake are not related to risk of colorectal polyps in the Tennessee Colorectal Polyp Study

Purpose: High digestible carbohydrate intakes can induce hyperglycemia and hyperinsulinemia and collectively have been implicated in colorectal tumor development. Our aim was to explore the association between aspects of dietary carbohydrate intake and risk of colorectal adenomas and hyperplastic polyps in a large case–control study.

Methods: Colorectal polyp cases (n = 1,315 adenomas only, n = 566 hyperplastic polyps only and n = 394 both) and controls (n = 3,184) undergoing colonoscopy were recruited between 2003 and 2010 in Nashville, Tennessee, USA. Dietary intakes were estimated by a 108-item food frequency questionnaire. Unconditional logistic regression analysis was applied to determine odds ratios (OR) and corresponding 95 % confidence intervals (CI) for colorectal polyps according to dietary carbohydrate intakes, after adjustment for potential confounders.

Results: No significant associations were detected for risk of colorectal adenomas when comparing the highest versus lowest quartiles of intake for total sugars (OR 1.03; 95 % CI 0.84–1.26), starch (OR 1.01; 95 % CI 0.81–1.26), total or available carbohydrate intakes. Similar null associations were observed between dietary carbohydrate intakes and risk of hyperplastic polyps, or concurrent adenomas and hyperplastic polyps.

Conclusion: In this US population, digestible carbohydrate intakes were not associated with risk of colorectal polyps, suggesting that dietary carbohydrate does not have an etiological role in the early stages of colorectal carcinogenesis.

'"To have its cake and eat it too:" US policy toward South Africa during the Kennedy administration

The assumption that US policy toward Africa was characterized by continuity during the cold war has recently been challenged by scholars who argue that President John F. Kennedy embarked on an African policy that was distinct from his predecessors. This may be true for black Africa, but Kennedy’s support for African nationalism did not extend to South Africa. This article reveals that Kennedy’s cold war priorities ensured continuity in US policy toward the apartheid state and, in some cases, additional cooperation as cold war crises increased the perceived importance of South Africa as an ideological and strategic ally and bastion against communism on a rapidly changing continent. This article also explores the role South Africa’s apartheid government played in this cold war alliance. The ruling National Party recognized its importance to US foreign policy goals and used this to stave off serious American criticism of its racial policies, deflect attention in the United Nations, and ensure continued economic and military cooperation with the United States.

Phase transitions and nonlinear phenomena in neuronal network models

Communication and cooperation between billions of neurons underlie the power of the brain. How do complex functions of the brain arise from its cellular constituents? How do groups of neurons self-organize into patterns of activity? These are crucial questions in neuroscience. In order to answer them, it is necessary to have solid theoretical understanding of how single neurons communicate at the microscopic level, and how cooperative activity emerges. In this thesis we aim to understand how complex collective phenomena can arise in a simple model of neuronal networks. We use a model with balanced excitation and inhibition and complex network architecture, and we develop analytical and numerical methods for describing its neuronal dynamics. We study how interaction between neurons generates various collective phenomena, such as spontaneous appearance of network oscillations and seizures, and early warnings of these transitions in neuronal networks. Within our model, we show that phase transitions separate various dynamical regimes, and we investigate the corresponding bifurcations and critical phenomena. It permits us to suggest a qualitative explanation of the Berger effect, and to investigate phenomena such as avalanches, band-pass filter, and stochastic resonance. The role of modular structure in the detection of weak signals is also discussed. Moreover, we find nonlinear excitations that can describe paroxysmal spikes observed in electroencephalograms from epileptic brains. It allows us to propose a method to predict epileptic seizures. Memory and learning are key functions of the brain. There are evidences that these processes result from dynamical changes in the structure of the brain. At the microscopic level, synaptic connections are plastic and are modified according to the dynamics of neurons. Thus, we generalize our cortical model to take into account synaptic plasticity and we show that the repertoire of dynamical regimes becomes richer. In particular, we find mixed-mode oscillations and a chaotic regime in neuronal network dynamics.

To Hell with Herbert Read

Freee write manifestos by taking a pencil (or a laptop) to an historical text, usually belonging to the entwined traditions of the avant-garde and political activism. Sometimes, as Tristan Tzara advised, we choose the text according to its length, while other times, such as in this instance, we selected the text according to the conditions of the invitation that triggered the writing of the manifesto. Our manifesto ‘To Hell with Herbert Read’ was written originally as a contribution to a conference held in Manchester that took its title from Herbert Read’s book ‘To Hell with Culture’. ‘To Hell with Culture’ is a book that cuts itself off from the world whereas ‘To Hell with Herbert Read’ relocates Read’s book in a world of cultural, social, economic and political actualities that are part of common experience. Read rejects culture because he thinks it is a useless, wasteful, elitist, puffed-up, decorative supplement to the functional, factual, palpable, purposeful world of things. He is a positivist kind of modernist who presents himself as the opposite, an enemy of the status quo. He is an anarchist of a particularly bourgeois hue: he wants us all to have decent pots and pans, not the inferior ones that are supplied by market forces cheaply. Rather than taking his aim precisely to target the dominant forces of his day - the industrial capitalists and their financiers - he rejects the world and all its inhabitants. He not only despises elitist culture but popular culture too.