Miracle-dz/UniFAR-FTUs huggingface dataset:
Demographic and Psychological Predictors of Panel Attrition: Evidence from the New Zealand Attitudes and Values Study

This study examines attrition rates over the first four years of the New Zealand Attitudes and Values Study, a longitudinal national panel sample of New Zealand adults. We report the base rate and covariates for the following four distinct classes of respondents: explicit withdrawals, lost respondents, intermittent respondents and constant respondents. A multinomial logistic regression examined an extensive range of demographic and socio-psychological covariates (among them the Big-Six personality traits) associated with membership in these classes (N = 5,814). Results indicated that men, Māori and Asian peoples were less likely to be constant respondents. Conscientiousness and Honesty-Humility were also positively associated with membership in the constant respondent class. Notably, the effect sizes for the socio-psychological covariates of panel attrition tended to match or exceed those of standard demographic covariates. This investigation broadens the focus of research on panel attrition beyond demographics by including a comprehensive set of socio-psychological covariates. Our findings show that core psychological covariates convey important information about panel attrition, and are practically important to the management of longitudinal panel samples like the New Zealand Attitudes and Values Study.
PSI‐DOCK: Towards highly efficient and accurate flexible ligand docking

We have developed a new docking method, Pose‐Sensitive Inclined (PSI)‐DOCK, for flexible ligand docking. An improved SCORE function has been developed and used in PSI‐DOCK for binding free energy evaluation. The improved SCORE function was able to reproduce the absolute binding free energies of a training set of 200 protein–ligand complexes with a correlation coefficient of 0.788 and a standard error of 8.13 kJ/mol. For ligand binding pose exploration, a unique searching strategy was designed in PSI‐DOCK. In the first step, a tabu‐enhanced genetic algorithm with a rapid shape‐complementary scoring function is used to roughly explore and store potential binding poses of the ligand. Then, these predicted binding poses are optimized and compete against each other by using a genetic algorithm with the accurate SCORE function to determine the binding pose with the lowest docking energy. The PSI‐DOCK 1.0 program is highly efficient in identifying the experimental binding pose. For a test dataset of 194 complexes, PSI‐DOCK 1.0 achieved a 67% success rate (RMSD <2.0 Å) for only one run and a 74% success rate for 10 runs. PSI‐DOCK can also predict the docking binding free energy with high accuracy. For a test set of 64 complexes, the correlation between the experimentally observed binding free energies and the docking binding free energies for 64 complexes is r = 0.777 with a standard deviation of 7.96 kJ/mol. Moreover, compared with other docking methods, PSI‐DOCK 1.0 is extremely easy to use and requires minimum docking preparations. There is no requirement for the users to add hydrogen atoms to proteins because all protein hydrogen atoms and the flexibility of the terminal protein atoms are intrinsically taken into account in PSI‐DOCK. There is also no requirement for the users to calculate partial atomic charges because PSI‐DOCK does not calculate an electrostatic energy term. These features are not only convenient for the users but also help to avoid the influence of different preparation methods. Proteins 2006. © 2006 Wiley‐Liss, Inc.
Low frequency ultrasonic voice activity detection using convolutional neural networks

Low frequency ultrasonic mouth state detection uses reflected audio chirps from the face in the region of the mouth to determine lip state, whether open, closed or partially open. The chirps are located in a frequency range just above the threshold of human hearing and are thus both inaudible as well as unaffected by interfering speech, yet can be produced and sensed using inexpensive equipment. To determine mouth open or closed state, and hence form a measure of voice activity detection, this recently invented technique relies upon the difference in the reflected chirp caused by resonances introduced by the open or partially open mouth cavity. Voice activity is then inferred from lip state through patterns of mouth movement, in a similar way to video-based lip-reading technologies. This paper introduces a new metric based on spectrogram features extracted from the reflected chirp, with a convolutional neural network classification back-end, that yields excellent performance without needing the periodic resetting of the template closed-mouth reflection required by the original technique.
Coating of Polyetheretherketone Films with Silver Nanoparticles by a Simple Chemical Reduction Method and Their Antibacterial Activity

The coating of polymeric substrate polyetheretherketone (PEEK) with silver nanoparticles (AgNPs) was carried out by a wet chemical route at room temperature. The coating process was developed from the Tollens reagent and D-glucose as reducing agent. The resulting composite exhibited antimicrobial activity. The PEEK films were coated with a single layer and two layers of silver nanoparticles in various concentrations. The crystallographic properties of the polymer and the silver nanoparticles were analyzed by X-ray diffraction (XRD). Fourier transform infrared spectra (FTIR) show the interaction between the silver nanoparticles with the polymeric substrate. Transmission electron microscope (TEM) images confirmed the obtaining of metallic nanoparticles with average sizes of 25 nm. It was possible to estimate the amount of silver deposited on PEEK with the help of thermogravimetric analysis. The morphology and shape of the AgNPs uniformly deposited on the PEEK films was ascertained by the techniques of scanning electron microscopy (SEM) and atomic force microscopy (AFM), evidencing the increase in the amount of silver by increasing the concentration of the metal precursor. Finally, the antibacterial activity of the films coated with Ag in Escherichia coli, Serratia marcescens and Bacillus licheniformis was evaluated, evidencing that the concentration of silver is crucial in the cellular replication of the bacteria.
Mechanical properties and microstructure of oil-well cement stone enhanced with submicron SiC whiskers

Abstract In order to improve the intrinsically brittle nature of the oil-well cement stone, a new type of submicron-fibrous whisker, referred to as the silicon carbide whisker (SiC whisker) was added into cement paste. The cement-based composites were prepared with the various amounts of submicron SiC whiskers. The composites were analyzed via scanning electron microscopy (SEM), mechanical testing, X-ray diffraction (XRD), infrared spectrum analysis (FTIR), and thermal stability analysis in order to understand the enhanced effect that the submicron SiC whiskers had on the applied properties and mechanisms of oil-well cement stone. The compressive strength, the tensile strength, and the flexural strength of the sample with 1% of additional submicron SiC whiskers increased by 9%, 104%, and 26%. The ultimate strain was more than 5%, which increased 194%. The elasticity modulus was 4648.4MPa, which decreased 31.1% after 28 curing days. These improved the mechanical properties of the cement-based composites primarily because of the microscopic mechanism of reinforcement via the submicron SiC whisker, including the bridging effect, the crack deflection, and the pull-out effect. HIGHLIGHTS A submicron SiC whisker was used to enhance the oil-well cement The submicron SiC whisker could significantly increase the mechanical behaviors of the oil-well cement The reinforcing mechanism that the submicron SiC whisker had on the oil-well cement was discussed in detail. The influence that the submicron SiC whisker had on the integrity of the cement sheaths were evaluated
Fuzzy Rules and Evidence Theory for Satellite Image Analysis

Design of a fuzzy rule based classifier is proposed. The performance of the classifier for multispectral satellite image classification is improved using Dempster- Shafer theory of evidence that exploits information of the neighboring pixels. The classifiers are tested rigorously with two known images and their performance are found to be better than the results available in the literature. We also demonstrate the improvement of performance while using D-S theory along with fuzzy rule based classifiers over the basic fuzzy rule based classifiers for all the test cases.
Comprehensive Analysis of PPARα-Dependent Regulation of Hepatic Lipid Metabolism by Expression Profiling

PPARα is a ligand-activated transcription factor involved in the regulation of nutrient metabolism and inflammation. Although much is already known about the function of PPARα in hepatic lipid metabolism, many PPARα-dependent pathways and genes have yet to be discovered. In order to obtain an overview of PPARα-regulated genes relevant to lipid metabolism, and to probe for novel candidate PPARα target genes, livers from several animal studies in which PPARα was activated and/or disabled were analyzed by Affymetrix GeneChips. Numerous novel PPARα-regulated genes relevant to lipid metabolism were identified. Out of this set of genes, eight genes were singled out for study of PPARα-dependent regulation in mouse liver and in mouse, rat, and human primary hepatocytes, including thioredoxin interacting protein (Txnip), electron-transferring-flavoprotein β polypeptide (Etfb), electron-transferring-flavoprotein dehydrogenase (Etfdh), phosphatidylcholine transfer protein (Pctp), endothelial lipase (EL, Lipg), adipose triglyceride lipase (Pnpla2), hormone-sensitive lipase (HSL, Lipe), and monoglyceride lipase (Mgll). Using an in silico screening approach, one or more PPAR response elements (PPREs) were identified in each of these genes. Regulation of Pnpla2, Lipe, and Mgll, which are involved in triglyceride hydrolysis, was studied under conditions of elevated hepatic lipids. In wild-type mice fed a high fat diet, the decrease in hepatic lipids following treatment with the PPARα agonist Wy14643 was paralleled by significant up-regulation of Pnpla2, Lipe, and Mgll, suggesting that induction of triglyceride hydrolysis may contribute to the anti-steatotic role of PPARα. Our study illustrates the power of transcriptional profiling to uncover novel PPARα-regulated genes and pathways in liver.
Evolution of the β‐propeller fold

β‐Propellers are toroidal folds, in which repeated, four‐stranded β‐meanders are arranged in a circular and slightly tilted fashion, like the blades of a propeller. They are found in all domains of life, with a strong preponderance among eukaryotes. Propellers show considerable sequence diversity and are classified into six separate structural groups by the SCOP and CATH databases. Despite this diversity, they often show similarities across groups, not only in structure but also in sequence, raising the possibility of a common origin. In agreement with this hypothesis, most propellers group together in a cluster map of all‐β folds generated by sequence similarity, because of numerous pairwise matches, many of which are individually nonsignificant. In total, 45 of 60 propellers in the SCOP25 database, covering four SCOP folds, are clustered in this group and analysis with sensitive sequence comparison methods shows that they are similar at a level indicative of homology. Two mechanisms appear to contribute to the evolution of β‐propellers: amplification from single blades and subsequent functional differentiation. The observation of propellers with nearly identical blades in genomic sequences show that these mechanisms are still operating today. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Naturally Occurring DNA Transfer System Associated with Membrane Vesicles in Cellulolytic Ruminococcus spp. of Ruminal Origin

ABSTRACT A genetic transformation system with similarities to those reported for gram-negative bacteria was found to be associated with membrane vesicles of the ruminal cellulolytic genus Ruminococcus. Double-stranded DNA was recovered from the subcellular particulate fraction of all the cellulolytic ruminococci examined. Electron microscopy revealed that the only particles present resembled membrane vesicles. The likelihood that the DNA was associated with membrane vesicles (also known to contain cellulosomes) was further supported by the adherence of the particles associated with the subcellular DNA to cellulose powder added to culture filtrates. The particle-associated DNA comprised a population of linear molecules ranging in size from <20 kb to 49 kb (Ruminococcus sp. strain YE73) and from 23 kb to 90 kb (Ruminococcus albus AR67). Particle-associated DNA from R. albus AR67 represented DNA derived from genomic DNA of the host bacterium having an almost identical HindIII digestion pattern and an identical 16S rRNA gene. Paradoxically, particle-associated DNA was refractory to digestion with EcoRI, while the genomic DNA was susceptible to extensive digestion, suggesting that there is differential restriction modification of genomic DNA and DNA exported from the cell. Transformation using the vesicle-containing fraction of culture supernatant of Ruminococcus sp. strain YE71 was able to restore the ability to degrade crystalline cellulose to two mutants that were otherwise unable to do so. The ability was heritable and transferred to subsequent generations. It appears that membrane-associated transformation plays a role in lateral gene transfer in complex microbial ecosystems, such as the rumen.
The Fatality and Morbidity Components of the Value of Statistical Life

The fatality risk-money tradeoff that is the value of a statistical life (VSL) may vary with the nature of the fatality event. While all fatalities involve loss of future life expectancy, the morbidity effects and their duration may differ. This article analyzes fatality risks accompanied by morbidity effects of different duration to disentangle the mortality and morbidity components of VSL using data from the Census of Fatal Occupational Injuries (CFOI). The VSL is comprised of the sum of the value of the fatality risk and the value of the morbidity risk. Labor market valuations of morbidity risks are positive, even for fatalities that are caused by traumatic injuries. The value of the fatality risk is the dominant component of VSL, rather than the value of the morbidity risk.
Flashbulb Memories for September 11th can be Preserved in Older Adults

ABSTRACT Flashbulb memories (FMs) are vivid, long-lasting memories for the source of surprising, arousing news. Laboratory studies have consistently found that older adults, especially those with below-average frontal lobe (FL) function, are impaired in source memory relative to young. We tested memory for the source of news concerning the September 11th terrorist attacks in older adults with high or low frontal lobe function and in young people. We found no age differences in source memory a year after the event and no differences related to FL function. Flashbulb memories may be different from usual cases of source memory because of their emotional content, personal importance, or social relevance.
PLA Crystallization Kinetics and Morphology Development

Abstract This paper investigates the crystallization kinetics and morphology development of PLA. The transitory stages in the evolving flow-induced crystallization of PLA are identified and classified in terms of the overall crystallization kinetics and the crystalline morphologies. Under quiescent conditions, temperature governs the crystallization process and the slow crystallization kinetics of PLA is highlighted under these conditions, whereas under shearing conditions, the crystallization is highly enhanced due to the promotion of the nucleation mechanism. The enhancement of the crystallization implies also morphological modifications. Depending on the shear rate and the shearing time the microstructure changes dramatically: spherulitic microstructure, fine grained microstructure and oriented microstructure. For a specific shear rate, depending on the magnitude of the shearing time the microstructure assumes the following states: for low shearing time only an increase of the number of nuclei is observed (leading to fine grained microstructure), followed by a saturation of point-like nuclei, and for a relatively long shearing time (i. e. beyond a critical shearing time) the development of oriented structures looking like “shish-kebabs” is observed. The critical shearing time for the formation of oriented structures in PLA is determined as a function of the shear rate.
The role of conservative versus innovative nesting behavior on the 25‐year population expansion of an avian predator

Abstract Species ranges often change in relation to multiple environmental and demographic factors. Innovative behaviors may affect these changes by facilitating the use of novel habitats, although this idea has been little explored. Here, we investigate the importance of behavior during range change, using a 25‐year population expansion of Bonelli's eagle in southern Portugal. This unique population is almost exclusively tree nesting, while all other populations in western Europe are predominantly cliff nesting. During 1991–2014, we surveyed nest sites and estimated the year when each breeding territory was established. We approximated the boundaries of 84 territories using Dirichlet tessellation and mapped topography, land cover, and the density of human infrastructures in buffers (250, 500, and 1,000 m) around nest and random sites. We then compared environmental conditions at matching nest and random sites within territories using conditional logistic regression, and used quantile regression to estimate trends in nesting habitats in relation to the year of territory establishment. Most nests (>85%, n = 197) were in eucalypts, maritime pines, and cork oaks. Nest sites were farther from the nests of neighboring territories than random points, and they were in areas with higher terrain roughness, lower cover by agricultural and built‐up areas, and lower road and powerline densities. Nesting habitat selection varied little with year of territory establishment, although nesting in eucalypts increased, while cliff nesting and cork oak nesting, and terrain roughness declined. Our results suggest that the observed expansion of Bonelli's eagles was facilitated by the tree nesting behavior, which allowed the colonization of areas without cliffs. However, all but a very few breeding pairs settled in habitats comparable to those of the initial population nucleus, suggesting that after an initial trigger possibly facilitated by tree nesting, the habitat selection remained largely conservative. Overall, our study supports recent calls to incorporate information on behavior for understanding and predicting species range shifts.
Local partial likelihood estimation in proportional hazards regression

Fan, Gijbels and King [Ann. Statist. 25 (1997) 1661-1690] considered the estimation of the risk function ψ(x) in the proportional hazards model. Their proposed estimator is based on integrating the estimated derivative function obtained through a local version of the partial likelihood. They proved the large sample properties of the derivative function, but the large sample properties of the estimator for the risk function itself were not established. In this paper, we consider direct estimation of the relative risk function ψ(x 2 ) - ψ(x 1 ) for any location normalization point x 1 . The main novelty in our approach is that we select observations in shrinking neighborhoods of both x 1 and x 2 when constructing a local version of the partial likelihood, whereas Fan, Gijbels and King [Ann. Statist. 25 (1997) 1661-1690] only concentrated on a single neighborhood, resulting in the cancellation of the risk function in the local likelihood function. The asymptotic properties of our estimator are rigorously established and the variance of the estimator is easily estimated. The idea behind our approach is extended to estimate the differences between groups. A simulation study is carried out.
Sleep Deprivation and Psychomotor Performance among Night-Shift Nurses

This study examined how sleep deprivation influenced psychomotor performance of nurses who worked the night shift. Psychomotor performance was measured with the d2 Test of Attention, which quantifies attention, concentration, processing speed, and quality of performance. A sample of 289 licensed nurses was tested with the instrument. Fifty-six percent of the sample was sleep deprived. Mean psychomotor performance scores (26.6 for men and 11.4 for women) were above the normative means (44.4 for men and 41.03 for women). A significant (p < .0001) inverse relationship was found between psychomotor performance and hours of sleep. Nurses reported more hours of sleep on a general self-report sleep item than in a sleep diary.
Bacterial community of cushion plant Thylacospermum ceaspitosum on elevational gradient in the Himalayan cold desert

Although bacterial assemblages are important components of soils in arid ecosystems, the knowledge about composition, life-strategies, and environmental drivers is still fragmentary, especially in remote high-elevation mountains. We compared the quality and quantity of heterotrophic bacterial assemblages between the rhizosphere of the dominant cushion-forming plant Thylacospermum ceaspitosum and its surrounding bulk soil in two mountain ranges (East Karakoram: 4850–5250 m and Little Tibet: 5350–5850 m), in communities from cold steppes to the subnival zone in Ladakh, arid Trans-Himalaya, northwest India. Bacterial communities were characterized by molecular fingerprinting in combination with culture-dependent methods. The effects of environmental factors (elevation, mountain range, and soil physico-chemical parameters) on the bacterial community composition and structure were tested by multivariate redundancy analysis and conditional inference trees. Actinobacteria dominate the cultivable part of community and represent a major bacterial lineage of cold desert soils. The most abundant genera were Streptomyces, Arthrobacter, and Paenibacillus, representing both r- and K-strategists. The soil texture is the most important factor for the community structure and the total bacteria counts. Less abundant and diverse assemblages are found in East Karakoram with coarser soils derived from leucogranite bedrock, while more diverse assemblages in Little Tibet are associated with finer soils derived from easily weathering gneisses. Cushion rhizosphere is in general less diverse than bulk soil, and contains more r-strategists. K-strategists are more associated with the extremes of the gradient, with drought at lowest elevations (4850–5000 m) and frost at the highest elevations (5750–5850 m). The present study illuminates the composition of soil bacterial assemblages in relation to the cushion plant T. ceaspitosum in a xeric environment and brings important information about heterotrophic bacteria in Himalayan soil.