Miracle-dz/UniFAR-FTUs huggingface dataset:
Folding of a small helical protein using hydrogen bonds and hydrophobicity forces

A reduced protein model with five to six atoms per amino acid and five amino acid types is developed and tested on a three‐helix‐bundle protein, a 46‐amino acid fragment from staphylococcal protein A. The model does not rely on the widely used Gō approximation, which ignores non‐native interactions. We find that the collapse transition is considerably more abrupt for the protein A sequence than for random sequences with the same composition. The chain collapse is found to be at least as fast as helix formation. Energy minimization restricted to the thermodynamically favored topology gives a structure that has a root‐mean‐square deviation of 1.8 Å from the native structure. The sequence‐dependent part of our potential is pairwise additive. Our calculations suggest that fine‐tuning this potential by parameter optimization is of limited use. Proteins 2002;47:99–105. © 2002 Wiley‐Liss, Inc.
Long-lasting and rapid calcium changes during mitosis

A more complete understanding of calcium's role in cell division requires knowledge of the timing, magnitude, and duration of changes in cytoplasmic-free calcium, [Ca2+]i, associated with specific mitotic events. To define the temporal relationship of changes in [Ca2+]i to cellular and chromosomal movements, we have measured [Ca2+]i every 6-7 s in single-dividing Pt K2 cells using fura-2 and microspectrophotometry, coupling each calcium measurement with a bright- field observation. In the 12 min before discernable chromosome some separation, 90% of metaphase cells show at least one transient of increased [Ca2+]i, 72% show their last transient within 5 min, and a peak of activity is seen at 3 min before chromosome separation. The mean [Ca2+]i of the metaphase transients is 148 +/- 31 nM (61 transients in 35 cells) with an average duration of 21 +/- 14 s. The timing of these increases makes it unlikely that these transient increases in [Ca2+]i are acting directly to trigger the start of anaphase. However, it is possible that a transient rise in calcium during late metaphase is part of a more complex progression to anaphase. In addition to these transient changes, a gradual increase in [Ca2+]i was observed starting in late anaphase. Within the 2 min surrounding cytokinesis onset, 82% of cells show a transient increase in [Ca2+]i to 171 +/- 48 nM (53 transients in 32 cells). The close temporal correlation of these changes with cleavage is consistent with a more direct role for calcium in this event, possibly by activating the contractile system. To assess the specificity of these changes to the mitotic cycle, we examined calcium changes in interphase cells. Two- thirds of interphase cells show no transient increases in calcium with a mean [Ca2+]i of 100 +/- 18 nM (n = 12). However, one-third demonstrate dramatic and repeated transient increases in [Ca2+]i. The mean peak [Ca2+]i of these transients is 389 +/- 70 nM with an average duration of 77 s. The necessity of any of these transient changes in calcium for the completion of mitotic or interphase activities remains under investigation.
Anonymization of location data does not work: a large-scale measurement study

We examine a very large-scale data set of more than 30 billion call records made by 25 million cell phone users across all 50 states of the US and attempt to determine to what extent anonymized location data can reveal private user information. Our approach is to infer, from the call records, the "top N" locations for each user and correlate this information with publicly-available side information such as census data. For example, the measured "top 2" locations likely correspond to home and work locations, the "top 3" to home, work, and shopping/school/commute path locations. We consider the cases where those "top N" locations are measured with different levels of granularity, ranging from a cell sector to whole cell, zip code, city, county and state. We then compute the anonymity set, namely the number of users uniquely identified by a given set of "top N" locations at different granularity levels. We find that the "top 1" location does not typically yield small anonymity sets. However, the top 2 and top 3 locations do, certainly at the sector or cell-level granularity. We consider a variety of different factors that might impact the size of the anonymity set, for example the distance between the "top N" locations or the geographic environment (rural vs urban). We also examine to what extent specific side information, in particular the size of the user's social network, decrease the anonymity set and therefore increase risks to privacy. Our study shows that sharing anonymized location data will likely lead to privacy risks and that, at a minimum, the data needs to be coarse in either the time domain (meaning the data is collected over short periods of time, in which case inferring the top N locations reliably is difficult) or the space domain (meaning the data granularity is strictly higher than the cell level). In both cases, the utility of the anonymized location data will be decreased, potentially by a significant amount.
Evolution of a neuroprotective function of central nervous system myelin

The central nervous system (CNS) of terrestrial vertebrates underwent a prominent molecular change when a tetraspan membrane protein, myelin proteolipid protein (PLP), replaced the type I integral membrane protein, P0, as the major protein of myelin. To investigate possible reasons for this molecular switch, we genetically engineered mice to express P0 instead of PLP in CNS myelin. In the absence of PLP, the ancestral P0 provided a periodicity to mouse compact CNS myelin that was identical to mouse PNS myelin, where P0 is the major structural protein today. The PLP–P0 shift resulted in reduced myelin internode length, degeneration of myelinated axons, severe neurological disability, and a 50% reduction in lifespan. Mice with equal amounts of P0 and PLP in CNS myelin had a normal lifespan and no axonal degeneration. These data support the hypothesis that the P0–PLP shift during vertebrate evolution provided a vital neuroprotective function to myelin-forming CNS glia.
Stress and Mental Health in Families With Different Income Levels: A Strategy to Collect Multi-Actor Data

Background Several studies have focused on family stress processes, examining the association between various sources of stress and the mental health and well-being of parents and adolescents. The majority of these studies take the individual as the unit of analysis. Multi-actor panel data make it possible to examine the dynamics of the family context over time and the differentiating effects of individual roles within the same family. Accurate information about family processes allows practitioners to provide support that enhances family resilience and minimizes the risk of mental health problems. Objective Our study contributes to the research on family stress processes by focusing on families with different income levels, and by collecting panel data from mothers, fathers, and adolescents within the same family. Methods The relationship between mothers, fathers, and children (RMFC) study is an ongoing Flemish multi-actor panel study that aims to enhance our understanding of family processes that protect the mental health and well-being of two-parent families with a target adolescent between 11 and 17 years old. Mothers, fathers, and children provide information about various aspects of family life, including finances, sources of stress, health, mental health, parenting, and coping strategies. Measures have been chosen whenever possible that have sound conceptual underpinnings and robust psychometric properties. The study posed two challenges. First, economically disadvantaged families are difficult to reach. Second, the collection of multi-actor data is often plagued by high nonresponse. To ensure that the families were targeted as successfully as possible, the study employed a purposive nonprobability sampling method. Results The RMFC study is one of the largest triadic panel studies of its kind. The first wave of quantitative data collection was conducted between February 2012 and January 2013. A total of 2566 individuals of 880 families participated in our study. The second wave of data collection will be undertaken 6-12 months later. Conclusions The strength of the RMFC study is its multi-actor panel approach of data collection among families with different income levels. Strategies that were followed to address the empirical issues involved with the sampling design are discussed, together with theoretical and practical implications.
Polymorphisms of the CYP1B1 Gene as Risk Factors for Human Renal Cell Cancer

Purpose: CYP1B1 activates various environmental carcinogens in human tissues, including renal tissues. We hypothesize that certain polymorphisms of the CYP1B1 gene are risk factors for renal cell cancer. The rationale for this hypothesis is that chemical procarcinogenic compounds require metabolic activation by oxidative enzymes such as CYP1B1 to be transformed into potentially carcinogenic forms. To test this hypothesis, we investigated the genotypic distributions of six different loci on the CYP1B1 gene and their association with renal cell cancer. Experimental Design: DNA from 211 cases of human renal cell cancer and 200 healthy controls was analyzed by sequence-specific PCR and direct DNA sequencing to determine the genotypic frequencies of six different polymorphic loci on the CYP1B1 gene. Results: The results of this study demonstrate that the frequencies of genotype 119T/T and genotype 432G/G were significantly higher in renal cell cancer patients compared with healthy normal controls. The relative risks were calculated as 3.01 and 2.17 for genotypes 119T/T and 432G/G, respectively, in renal cell carcinoma patients. These genotypic distributions were also significantly different between male and female patients. The relative risks of genotype 119T/T were calculated as 3.95 in males and 1.92 in females, and the relative risks of genotype 432G/G were calculated as 2.81 in males and 1.35 in females. Conclusions: The present study demonstrates for the first time that the polymorphisms at codons 119 and 432 may be risk factors for renal cancer, especially in the male population.
Effects of memory colour on colour constancy for unknown coloured objects

The perception of an object's colour remains constant despite large variations in the chromaticity of the illumination—colour constancy. Hering suggested that memory colours, the typical colours of objects, could help in estimating the illuminant's colour and therefore be an important factor in establishing colour constancy. Here we test whether the presence of objects with diagnostical colours (fruits, vegetables, etc) within a scene influence colour constancy for unknown coloured objects in the scene. Subjects matched one of four Munsell papers placed in a scene illuminated under either a reddish or a greenish lamp with the Munsell book of colour illuminated by a neutral lamp. The Munsell papers were embedded in four different scenes—one scene containing diagnostically coloured objects, one scene containing incongruent coloured objects, a third scene with geometrical objects of the same colour as the diagnostically coloured objects, and one scene containing non-diagnostically coloured objects (eg, a yellow coffee mug). All objects were placed against a black background. Colour constancy was on average significantly higher for the scene containing the diagnostically coloured objects compared with the other scenes tested. We conclude that the colours of familiar objects help in obtaining colour constancy for unknown objects.
Social Need versus Local Opposition: Simulating Energy Infrastructure Siting Outcomes Using a Multi-Agent Decision Support System I,II

Siting new energy infrastructure projects to meet growing demand is becoming increasingly contentious and costly. This paper explicates the design and results of the Sustainable Energy Modeling Program (SEMPro), a decision support system for energy infrastructure siting. SEMPro makes two contributions to planning decision support: rst, SEMPro fuses geographical information system data with a multi agent-based model (ABM) of citizen attitude and behavior diusion, a powerful tool in predicting the outcome of planning decisions and explaining emergent opposition behavior. Second, it is the only planning model we are aware of that integrates an ABM with spatial bargaining models of stakeholder and regulatory decision making to simulate the real world complexity of infrastructure siting. Using a high voltage transmission line project in California for model development and validation, we nd emergent citizen interactions aects stakeholder and regulator decision making in siting processes. Monte Carlo simulations show that higher levels of project disruption result in a greater number of citizen comments sent to regulators. These messages have a greater impact on the preferences of regulators simulated in the spatial bargaining module than they do on stakeholder preferences. Stakeholder preferences are strongly inuenced by the community based organizations that arise to oppose the project. We also
Literary cynics: Borges, Beckett, Coetzee

Samuel Beckett’s last few plays were all written by invitation and performed before specialist audiences who were familiar with his work and knew what they could expect from him. Arthur Rose quite rightly points out that such expectation is constitutive in nature, that these audiences approached the plays with the baggage of a “preconceived Beckett” (112–13). He is also right when he argues that Beckett, in the plays in question, evinces an awareness of his reification as an author and of the authority of reputation. In this regard, Rose cites the following dialogue from the first draft of Ohio Impromptu:
STUDENTS’ ATTITUDES TOWARD STATISTICS ACROSS THE DISCIPLINES: A MIXED-METHODS APPROACH

Students’ attitudes toward statistics were investigated using a mixed-methods approach including a discovery-oriented qualitative methodology among 684 undergraduate students across business, criminal justice, and psychology majors where at least one course in statistics was required. Students were asked about their attitudes toward statistics and the reasons for their attitudes. Five categories resulted for those with positive and negative attitudes and were separated on the basis of discipline. Approximately 63% of students indicated a positive attitude toward statistics. Business majors were most positive and were more likely to believe statistics would be used in their future career. Multiple methodological approaches have now provided data on the various domains of attitudes toward statistics and those implications are discussed. First published November 2012 at Statistics Education Research Journal: Archives
Becoming active post-hospitalisation discharge – an exploration of motivational profiles during exercise change in obese patients

ABSTRACT Despite the urgent need to prevent weight regain in the long-term, it remains questionable whether inpatient multicomponent behavioural obesity treatments positively impact their patients, leaving them with favourable (i.e. autonomous) motivational profiles towards exercising. Based on Organismic Integration Theory, a sub-theory of Self-Determination Theory, this study retrospectively examined how exercise motivational profiles relate to exercise behaviour outcomes of a behavioural obesity treatment. Obese patients for whom outpatient treatment was deemed ineffective (N = 262; 34.2% female, body mass index >30 kg/m2) were administered to a 3-week inpatient obesity treatment. The study design incorporates both longitudinal and retrospective cross-sectional aspects. Patients completed questionnaires concerning exercise behaviour (pre-hospitalisation/6 months post-discharge) and behavioural regulations (6 months post-discharge). Exercise motivational profiles were generated based on the six behavioural regulations using K-means non-hierarchical cluster analysis. The self-reported dependent variable represents a change in patients’ exercise status (i.e. remaining inactive, becoming active). Chi-square tests related motivational profiles to exercise behaviour. Three profiles emerged: a moderate-controlled cluster (n = 80), a moderate-autonomous cluster (n = 78) and a high-autonomous cluster (n = 104). Of the patients who became active over time, the majority belonged to the high-autonomous cluster. No significant differences were found between patients who became active or remained inactive and whether they belonged to the moderate-controlled or moderate-autonomous cluster. Although the moderate-controlled and moderate-autonomous clusters differ greatly in their motivational quality, moderately controlled motivation does not seem detrimental regarding exercise change, as both clusters result in similar exercise behaviour outcomes.
Vehicle Routing Problem with Mixed Fleet of Conventional and Heterogenous Electric Vehicles and Time Dependent Charging Costs

In this paper, we consider a new real-life Heterogenous Electric Vehicle Routing Problem with Time Dependant Charging Costs and a Mixed Fleet (HEVRP-TDMF), in which a set of geographically scattered customers have to be served by a mixed fleet of vehicles composed of a heterogenous fleet of Electric Vehicles (EVs), having different battery capacities and operating costs, and Conventional Vehicles (CVs). We include the possibility of charging EVs in the available charging stations during the routes in order to serve all customers. Each charging station offers charging service with a known technology of chargers and time dependent charging costs. Charging stations are also subject to operating time windows constraints. EVs are not necessarily compatible with all available charging technologies and a partial charging is allowed. Intermittent charging at the depot is also allowed provided that constraints related to the electricity grid are satisfied. The objective is to minimize the number of employed vehicles and then minimize the total travel and charging costs. In this study, we present a Mixed Integer Programming Model and develop a Charging Routing Heuristic and a Local Search Heuristic based on the Inject-Eject routine with three different insertion strate-gies. All heuristics are tested on real data instances.
Emotional Labor in China: Relationships with Burnout, Job Satisfaction, and Perceived Group Membership as Predictors

With the prevalence of service jobs, researchers have begun to pay attention to emotional labor in the workplace. Emotional labor refers to spontaneous manipulation of one's feelings or/and expressions, in order to induce expected reaction of others (e.g. customers) or meet the organizational norms (Hochschild, 1983). Employees in service jobs commonly use emotional labor through two different strategies: surface acting and deep acting. Surface acting means the manipulation of the appeared expression; in contrast, deep acting refers to the adjustment of the internal feeling. In current study, we investigated the relationship between different acting strategies and burnout as well as job satisfaction. We also examined whether employees' perceptions of customers' social economic status and in-out group membership would affect their use of emotional labor strategies. Participants were employees from a jewelry store in China who completed surveys and interviews. Results showed that surface acting was positively correlated with emotional exhaustion, while deep acting was positively correlated with personal accomplishment. Employees used more deep acting if they perceived their customers as in-group members, indicating group membership as a predictor of deep acting. No correlation was found between acting strategies and depersonalization, job satisfaction, or perceived social economic status of customers. Several themes emerged from the interview responses. First, employees reported using emotional labor commonly at work and took it as a duty or a shaped habit. Second,
Steady State Analysis of 2-D LMS Adaptive Filters Using the Independence Assumption (Special Section on Selected Papers from the 11th Workshop on Circuits and Systems in Karuizawa)

SUMMARY In this paper, we consider the steady state mean square error (MSE) analysis for 2-DLMS adaptive filtering algorithm in which the filter’s weights are updated along both vertical and horizontal directions as a doubly-indexed dynamical system. The MSE analysis is conducted using the well-known independence assumption. First we show that computation of the weight-error covariance matrix for doubly-indexed 2-DLMS algorithm requires an approximation for the weight-error correlation coefficients at large spatial lags. Then we propose a method to solve this problem. Further discussion is carried out for the special case when the input signal is white Gaussian. It is shown that the convergence in the MSE sense occurs for step size range that is significantly smaller than the one necessary for the convergence of the mean. Simulation experiments are presented to support the obtained analytical results.
Touch Interacts with Vision during Binocular Rivalry with a Tight Orientation Tuning

Multisensory integration is a common feature of the mammalian brain that allows it to deal more efficiently with the ambiguity of sensory input by combining complementary signals from several sensory sources. Growing evidence suggests that multisensory interactions can occur as early as primary sensory cortices. Here we present incompatible visual signals (orthogonal gratings) to each eye to create visual competition between monocular inputs in primary visual cortex where binocular combination would normally take place. The incompatibility prevents binocular fusion and triggers an ambiguous perceptual response in which the two images are perceived one at a time in an irregular alternation. One key function of multisensory integration is to minimize perceptual ambiguity by exploiting cross-sensory congruence. We show that a haptic signal matching one of the visual alternatives helps disambiguate visual perception during binocular rivalry by both prolonging the dominance period of the congruent visual stimulus and by shortening its suppression period. Importantly, this interaction is strictly tuned for orientation, with a mismatch as small as 7.5° between visual and haptic orientations sufficient to annul the interaction. These results indicate important conclusions: first, that vision and touch interact at early levels of visual processing where interocular conflicts are first detected and orientation tunings are narrow, and second, that haptic input can influence visual signals outside of visual awareness, bringing a stimulus made invisible by binocular rivalry suppression back to awareness sooner than would occur without congruent haptic input.