Miracle-dz/UniFAR-FTUs huggingface dataset:
What is the relationship between the global structures of apo and holo proteins?

It is well known that ligand binding and release may induce a wide range of structural changes in a receptor protein, varying from small movements of loops or side chains in the binding pocket to large‐scale domain hinge‐bending and shear motions or even partial unfolding that facilitates the capture and release of a ligand. An interesting question is what in general are the conformational changes triggered by ligand binding? The aim of this work is analyze the magnitude of structural changes in a protein resulting from ligand binding to assess if the state of ligand binding needs to be included in template‐based protein structure prediction algorithms. To address this issue, a nonredundant dataset of 521 paired protein structures in the ligand‐free and ligand‐bound form was created and used to estimate the degree of both local and global structure similarity between the apo and holo forms. In most cases, the proteins undergo relatively small conformational rearrangements of their tertiary structure upon ligand binding/release (most root‐mean‐square‐deviations from native, RMSD, are <1 Å). However, a clear difference was observed between single‐ and multiple‐domain proteins. For the latter, RMSD changes greater than 1 Å and sometimes larger were found for almost 1/3 of the cases; these are mainly associated with large‐scale hinge‐bending movements of entire domains. The changes in the mutual orientation of individual domains in multiple‐domain proteins upon ligand binding were investigated using a mechanistic model based on mass‐weighted principal axes as well as interface buried surface calculations. Some preferences toward the anticipated mechanism of protein domain movements are predictable based on the examination of just the ligand‐free structural form. These results have applications to protein structure prediction, particularly in the context of protein domain assembly, if additional information concerning ligand binding is exploited. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Work factors as predictors of sickness absence: a three month prospective study of nurses’ aides

Aims: To identify the work factors that predict sickness absence in nurses’ aides. Methods: The sample comprised 5563 Norwegian nurses’ aides, not on leave because of illness or pregnancy when they completed a mailed questionnaire in 1999. Of these, 4931 (88.6%) completed a second questionnaire three months later. The outcome measure was the three month incidence proportion of certified sickness absence (>3 days), as assessed by self reports at follow up. Results: Perceived lack of encouraging and supportive culture in the work unit (odds ratio (OR) 1.73; 95% confidence interval (CI) 1.28 to 2.34), working in psychiatric and paediatric wards, having injured the neck in an accident, and health complaints were associated with higher risk of sickness absence, after adjustments for a series of physical, psychological, and organisational work factors, personal engagement in the work unit, demographic characteristics, and daily consumption of cigarettes. Having untraditional jobs (for nurses’ aides) (OR 0.53; 95% CI 0.36 to 0.77), and engaging in aerobics or gym were associated with a lower risk of sickness absence. Conclusions: The study suggests that the three month effects of work factors on rates of certified sickness absence are modest in nurses’ aides. The most important work factor, in terms of predicting sickness absence, seems to be perceived lack of encouraging and supportive culture in the work unit.
SPATIAL ENVIRONMENTAL CORRELATES OF INTERTIDAL RECRUITMENT: A TEST USING BARNACLES IN NORTHERN CHILE

Nearshore circulation processes and local geomorphological patterns are thought to be important correlates of spatial variation in larval recruitment of benthic organisms. However, few studies have attempted to quantitatively separate their relative influences upon recruitment dynamics. Here we use 12 study sites spanning 250 km of the northern Chile upwelling ecosystem and the intertidal barnacles Jehlius cirratus and Notochthamalus scabrosus to examine the extent to which spatial variation in larval recruitment is related to environmental variability and how these relationships depend on spatial autocorrelation. We find that upwelling intensity and wind velocity are negatively related to larval recruitment while surface slicks showed a positive correlation. However, the pure effect of each environmental variable was lower than its combined effects. Taking spatial autocorrelation into account, we find that the spatially structured variation of upwelling dynamics, distance to upwelling fronts, wind velocity, and slick occurrence explained most of the variation in barnacle recruitment. Spatial variation in recruitment rates of barnacles showed a characteristic length scale of 60-70 km, similar to the scale estimated for the spatially structured variables (upwelling, wind velocity, and surface slicks). We find that conditions for the occurrence of surface slicks (as surrogates of internal waves activity) seem to operate across several sites, suggesting a meso- instead local-scale influence over spatial variation in barnacle recruitment. Our results suggest that spatial variation in barnacle recruitment is modulated by the combined influence of several spatially structured nearshore processes operating at scales of 60-70 km and that spatial autocorrelation must be taken into account in the study of the recruitment-environment relationship. However, the influence of local and small-scale factors on recruitment dynamics of benthic invertebrates should be interpreted cautiously.
BEHAVIORAL OPERATIONS MANAGEMENT: A BLIND SPOT AND A RESEARCH PROGRAM

Behavioral operations management, or simply behavioral operations (BOps), aims at understanding the decision-making of managers and at using this understanding to generate interventions that improve the operation of the supply chain. To do so, BOps imports knowledge from a number of fields such as economics, psychology and other social and behavioral sciences. We point out a blind spot in this knowledge: In BOps, the heuristics that people use are typically, although not always, viewed as a liability. The issue with this view is that it does not explain when and in what way heuristics can be an asset. We propose, as a research program for BOps, uncovering the conditions under which the heuristics that supply chain managers use are an asset, as well as the conditions under which they are a liability. We briefly discuss some research on heuristics in BOps and show how the study of quantitative models of heuristics can complement it.
Learning to Diagnose: Assimilating Clinical Narratives using Deep Reinforcement Learning

Clinical diagnosis is a critical and non-trivial aspect of patient care which often requires significant medical research and investigation based on an underlying clinical scenario. This paper proposes a novel approach by formulating clinical diagnosis as a reinforcement learning problem. During training, the reinforcement learning agent mimics the clinician’s cognitive process and learns the optimal policy to obtain the most appropriate diagnoses for a clinical narrative. This is achieved through an iterative search for candidate diagnoses from external knowledge sources via a sentence-by-sentence analysis of the inherent clinical context. A deep Q-network architecture is trained to optimize a reward function that measures the accuracy of the candidate diagnoses. Experiments on the TREC CDS datasets demonstrate the effectiveness of our system over various non-reinforcement learning-based systems.
Organizational Stressors and Job Stress among Managers : the Moderating Role of Neuroticism

The purpose of this paper is to: first, determine the influence of organizational variables (conflict, blocked career, alienation, work overload, and unfavourable work environment) on job stress among managers and, second, to examine whether this relationship varies according to the individual’s level of neuroticism. Analyses of 285 responses using hierarchical regression revealed that three of the five organizational variables (conflict, blocked career, and alienation) had significant positive effects on job stress. Neuroticism was found to moderate the effects of the three organizational stressors (alienation, work overload, and unfavourable work environment) on job stress. Implications for managerial practice and future research are discussed.
Immunologic NO Synthase: Elevation in Severe AIDS Dementia and Induction by HIV-1 gp41

Indirect mechanisms are implicated in the pathogenesis of the dementia associated with human immunodeficiency virus-type 1 (HIV-1) infection. Proinflammatory molecules such as tumor necrosis factor α and eicosanoids are elevated in the central nervous system of patients with HIV-1-related dementia. Nitric oxide (NO) is a potential mediator of neuronal injury, because cytokines may activate the immunologic (type II) isoform of NO synthase (iNOS). The levels of iNOS in severe HIV-1-associated dementia coincided with increased expression of the HIV-1 coat protein gp41. Furthermore, gp41 induced iNOS in primary cultures of mixed rat neuronal and glial cells and killed neurons through a NO-dependent mechanism. Thus, gp41-induced NO formation may contribute to the severe cognitive dysfunction associated with HIV-1 infection.
Intercellular Calcium Waves in Neurons

Spontaneous intercellular Ca2+ waves were observed in groups of neurons in two different culture preparations: primary mouse cortical neurons and GT1-1 immortalized neurons. Waves of increased intracellular Ca2+ concentration propagated at rates of 100-200 microns/s over as many as 200 cells and were abolished by the removal of extracellular calcium, by nimodipine, by tetrodotoxin, and by the gap junction inhibitor octanol. A sister clone of the GT1 line, GT1-7 neurons, showed no intercellular Ca2+ waves and were found to have a significantly lower level of connexin26 mRNA than the GT1-1 line. Although we cannot definitively rule out a role for synaptic communication, we propose that intercellular Ca2+ waves in cultured neurons are generated by Ca2+ influx caused primarily by the propagation of depolarization via gap junctions. Intercellular Ca2+ signaling via gap junctions may represent an important mechanism for nonsynaptic neuronal signaling.
Adaptation to Antifaces and the Perception of Correct Famous Identity in an Average Face

Previous experiments have examined exposure to anti-identities (faces that possess traits opposite to an identity through a population average), finding that exposure to antifaces enhances recognition of the plus-identity images. Here we examine adaptation to antifaces using famous female celebrities. We demonstrate: that exposure to a color and shape transformed antiface of a celebrity increases the likelihood of perceiving the identity from which the antiface was manufactured in a composite face and that the effect shows size invariance (experiment 1), equivalent effects are seen in internet and laboratory-based studies (experiment 2), adaptation to shape-only antifaces has stronger effects on identity recognition than adaptation to color-only antifaces (experiment 3), and exposure to male versions of the antifaces does not influence the perception of female faces (experiment 4). Across these studies we found an effect of order where aftereffects were more pronounced in early than later trials. Overall, our studies delineate several aspects of identity aftereffects and support the proposal that identity is coded relative to other faces with special reference to a relatively sex-specific mean face representation.
Optical Properties of Aerosols by Cavity Ring down Optical Properties of Absorbing and Non-absorbing Aerosols Retrieved by Cavity Ring down (crd) Spectroscopy Acpd Optical Properties of Aerosols by Cavity Ring Down

Application of cavity ring down (CRD) spectrometry for measuring the optical properties of pure and mixed laboratory-generated aerosols is presented. The extinction coefficient (α ext), extinction cross section (σ ext) and extinction efficiency (Q ext) were measured for polystyrene spheres (PSS), ammonium sulphate ((NH 4) 2 (SO 4)), sodium 5 chloride (NaCl), glutaric acid (GA), and Rhodamine-590 aerosols. The refractive indices of the different aerosols were retrieved by comparing the measured extinction efficiency of each aerosol type to the extinction predicted by Mie theory. Aerosols composed of sodium chloride and glutaric acid in different mixing ratios were used as model for mixed aerosols of two non-absorbing materials, and their extinction and 10 complex refractive index were derived. Aerosols composed of Rhodamine-590 and ammonium sulphate in different mixing ratios were used as model for mixing of absorbing and non-absorbing species, and their optical properties were derived. The refractive indices of the mixed aerosols were also calculated by various optical mixing rules and a core plus shell Mie model. We found that for non-absorbing mixtures, the 15 linear rule, Maxwell-Garnett rule, extended effective medium approximation (EEMA), and core plus shell model give comparable results, with the linear mixing rule giving a slightly better fit than the others. Overall, calculations for the mixed aerosols are not as good as for single component aerosols. For absorbing mixtures, the differences between the refractive indices calculated using the mixing rules and those retrieved by 20 CRD are generally higher.
The safety and tolerability of atypical antipsychotics in bipolar disorder

Atypical antipsychotics (aAPs), have become a first-line treatment option, both in schizophrenia and bipolar disorders. Almost all aAPs now have proven efficacy in acute mania, some also in bipolar depression and in maintenance treatment. This provides reliable data on their safety and tolerability in this particular group of patients. This review focuses on the safety and tolerability of aAPs in the treatment of bipolar disorders. Both tolerability, for example, extrapyramidal symptoms, and safety issues, for example, occurrence of weight gain and hyperglycaemia, will be highlighted for olanzapine, quetiapine, risperidone, ziprasidone and aripiprazole.
POLYPHASIC CHARACTERIZATION OF DOLICHOSPERMUM SPP. AND SPHAEROSPERMOPSIS SPP. (NOSTOCALES, CYANOBACTERIA): MORPHOLOGY, 16S rRNA GENE SEQUENCES AND FATTY ACID AND SECONDARY METABOLITE PROFILES 1

The genera Dolichospermum (Ralfs ex Bornet et Flahault) Wacklin, L. Hoffm. et Komárek and Sphaerospermopsis Zapomělová, Jezberová, Hrouzek, Hisem, K. Řeháková et Komárk. ‐Legn. represent a highly diversified group of planktonic cyanobacteria that have been recently separated from the traditional genus Anabaena Bory ex Bornet et Flahault. In this study, morphological diversity, phylogeny of the 16S rRNA gene, production of fatty acids, and secondary metabolite profiles were evaluated in 33 strains of 14 morphospecies isolated from the Czech Republic. Clustering of the strains based on 16S rRNA gene sequences corresponded to wider groups of species in terms of morphology. The overall secondary metabolite and fatty acid profiles, however, were not correlated to each other and neither were they correlated to the 16S rRNA phylogeny nor the morphology of the strains. Nevertheless, a minor part of the detected secondary metabolites (19% of all compounds) was present only in close relatives and can be thus considered as autapomorphic features.
Modeling Duct Flow for Molecular Communication

Active transport such as fluid flow is sought in molecular communication to extend coverage, improve reliability, and mitigate interference. Flow models are often over-simplified, assuming one-dimensional diffusion with constant drift. However, diffusion and flow are usually encountered in three-dimensional bounded environments where the flow is highly non-uniform such as in blood vessels or microfluidic channels. For a qualitative understanding of the relevant physical effects inherent to these channels, based on the Péclet number and the transmitter-receiver distance, we study when simplified models of uniform flow and advection-only transport are applicable. For these two regimes, analytical expressions for the channel impulse response are derived and validated by particle-based simulation. Furthermore, as advection-only transport is typically overlooked and hence not analyzed in the molecular communication literature, we evaluate the symbol error rate for exemplary on-off keying as performance metric.
Isolation of type I and II DNA topoisomerase mutants from fission yeast: single and double mutants show different phenotypes in cell growth and chromatin organization.

We have isolated mutants defective in DNA topoisomerases and an endonuclease from the fission yeast Schizosaccharomyces pombe by screening individual extracts of mutagenized cells. Two type I topoisomerase mutants (top1) and three endonuclease mutants (end1) were all viable. The double mutant top1 end1 was also viable and, in its extract, Mg2+‐ and ATP‐ dependent type II activity could be detected. Three temperature‐sensitive (ts‐) mutants having heat‐sensitive (hs‐) type II enzymes were isolated, and the ts‐ marker cosegregated with the hs‐ type II activity. All the ts‐ mutations fell in one gene (top2) tightly linked to leul in chromosome II. The nuclear division of single top2 mutants was blocked at the restrictive temperature, but the formation of a septum was not inhibited so that the nucleus was cut across with the cell plate. In contrast, the double top1 top2 mutants were rapidly arrested at various stages of the cell cycle, showing a strikingly altered nuclear chromatin region. The type II topoisomerase may have an essential role in the compaction and/or segregation of chromosomes during the nuclear division but also complement the defect of the type I enzyme whose major function is the maintenance of chromatin organization throughout the cell cycle.
Dose-dependent fluoxetine effects on boldness in male Siamese fighting fish

ABSTRACT As the use of pharmaceuticals and personal care products (PPCPs) continues to rise, these compounds enter the environment in increasing frequency. One such PPCP, fluoxetine, has been found in detectable amounts in aquatic ecosystems worldwide, where it may interfere with the behavior of exposed organisms. Fluoxetine exposure has been found to influence boldness and exploration in a range of fish species; however, how it might alter behavior in multiple contexts or over time is rarely examined. To this end, the effects of fluoxetine on boldness over time were studied in male Siamese fighting fish. Three different groups of males (0, 0.5 and 5 µg l−1 fluoxetine) were tested in multiple boldness assays (empty tank, novel environment and shoal) once a week for 3 weeks to collect baseline measures and then at three different time points post-exposure. The effects of these varying exposure amounts on behavior were then examined for overall response, consistency and across-context correlations. Unexposed males were bolder in all contexts, were more consistent within a context, and had stronger between-context correlations than exposed males. Fluoxetine had dose-dependent effects on behavior, as males that received the higher dose exhibited greater behavioral effects. This study stresses the potential fitness consequences of fluoxetine exposure and suggests that examining behavioral effects of PPCPs under different dosing regimens and in multiple contexts is important to gain an increased understanding of how exposure affects behavior. Highlighted Article: Multiple assays show that fluoxetine alters boldness on multiple levels and over time in male Siamese fighting fish. This altered boldness could generate negative fitness consequences.
Salt Taste Sensitivity and Stimulus Volume: Sips and Drops. Some Implications for the Henkin Taste Test

Various presentation procedures and stimulus volumes were compared in their effect on salt taste sensitivity. For sodium chloride (NaCl) stimuli pipetted onto the tongue, subjects had comparable measured sensitivity to 10 ml and 1 ml volumes but a reduced sensitivity to 0.1 ml volumes. The greatest sensitivity was achieved with 10 ml sipped volumes. Modification of the Henkin dropwise triangluar taste test, by increasing the stimulus volumes, increased subjects' sensitivity. Only the 1 ml pipette presentation increased the sensitivity of the Henkin procedure, albeit slightly, to the detection of changes in taste sensitivity, the purpose for which the procedure was actually designed. Such modification did not perturb salivary NaCl levels more than the regular Henkin procedure, so it would not be expected to introduce sensitivity drift.
Evaluation of a comprehensive behavior management program to improve school-wide positive behavior support

This paper describes the cvalu nificantly decre<±sed for 7th gruders u.nd fur ha­ rJssment u.mong males. Students' perceptions of school snfety improved at the target school but not <±t compnrison schools. Students' reports of being physicnlly or verbnlly attncked the previous d<±y were reduced at the target school us well, but these changes were nlso seen at the comparison schooL
Emotional perception as a component of emotional intelligence : its role in academic achievement, social interaction, and focus of attention

The ability to perceive emotion in others has been proposed as an important component of emotional intelligence (EI). Indeed, perhaps the only independent aspect of EI which is not simply a manifestation of personality or cognitive ability. The ability to perceive emotion in others has been proposed as an important component of emotional intelligence (EI). Indeed, perhaps the only independent aspect of EI which is not simply a manifestation of personality or cognitive ability. This thesis investigates the status of emotional perception (EP) within the EI framework. Chapter 1 discusses a number of controversies within the EI literature and identifies EP as the most important aspect of EI. Chapter 2 describes the difficulties with the measurement of EP and evaluates its potential theoretical contributions. It then reports the development and validation of a scale designed to measure EP. Successive Chapters investigate the influence of EP in three main theoretical areas. First, the role of EP in academic performance and its potential longitudinal effects are evaluated in two longitudinal studies. EP is compared with scales measuring other aspects of EI, a personality inventory, a measure of cognitive ability, a well-being scale and a coping scale in order to assess the reliability and validity of the measures, and to evaluate their intercorrelations. Additionally, the relationship between EP and various types of academic achievement is explored in order to assess the predictive validity of EP. Second, a quasi-experimental design is employed in order to investigate the role of EP in social interaction. The experience of embarrassment when delivering class presentations is used to investigate these effects. Third, a series of experimental studies, using the attentional bias framework, consider the effects of EP on the focus of attention to emotionally meaningful stimuli. The thesis presents evidence to suggest that EP is a semi-independent construct within EI. It can be assessed reliably, demonstrates validity, is a practically useful construct, and influences moment-by-moment regulation of behaviour.