Miracle-dz/UniFAR-FTUs huggingface dataset:
Fast multiresolution methods for density functional theory in nuclear physics

We describe a fast real-analysis based O(N) algorithm based on multiresolution analysis and low separation rank approximation of functions and operators for solving the Schrodinger and Lippman-Schwinger equations in 3-D with spin-orbit potential to high precision for bound states. Each of the operators and wavefunctions has its own structure of refinement to achieve and guarantee the desired finite precision. To our knowledge, this is the first time such adaptive methods have been used in computational physics, even in 1-D. Accurate solutions for each of the wavefunctions are obtained for a sample test problem. Spin orbit potentials commonly occur in the simulations of semiconductors, quantum chemistry, molecular electronics and nuclear physics. We compare our results with those obtained by direct diagonalization using the Hermite basis and the spline basis with an example from nuclear structure theory.
Impact of exercise and a complex environment on hippocampal dendritic morphology, Bdnf gene expression, and DNA methylation in male rat pups neonatally exposed to alcohol

Alcohol exposure in utero can result in Fetal Alcohol Spectrums Disorders (FASD). Measures of hippocampal neuroplasticity, including long‐term potentiation, synaptic and dendritic organization, and adult neurogenesis, are consistently disrupted in rodent models of FASD. The current study investigated whether third trimester‐equivalent binge‐like alcohol exposure (AE) [postnatal days (PD) 4–9] affects dendritic morphology of immature dentate gyrus granule cells, and brain‐derived neurotrophic factor (Bdnf) gene expression and DNA methylation in hippocampal tissue in adult male rats. To understand immediate impact of alcohol, DNA methylation was measured in the PD10 hippocampus. In addition, two behavioral interventions, wheel running (WR) and environmental complexity (EC), were utilized as rehabilitative therapies for alcohol‐induced deficits. AE significantly decreased dendritic complexity of the immature neurons, demonstrating the long‐lasting impact of neonatal alcohol exposure on dendritic morphology of immature neurons in the hippocampus. Both housing conditions robustly enhanced dendritic complexity in the AE animals. While Bdnf exon I DNA methylation was lower in the AE and sham‐intubated animals compared with suckle controls on PD10, alterations to Bdnf DNA methylation and gene expression levels were not present at PD72. In control animals, exercise, but not exercise followed by housing in EC, resulted in higher levels of hippocampal Bdnf gene expression and lower DNA methylation. These studies demonstrate the long‐lasting negative impact of developmental alcohol exposure on hippocampal dendritic morphology and support the implementation of exercise and complex environments as therapeutic interventions for individuals with FASD. © 2016 Wiley Periodicals, Inc. Develop Neurobiol 77: 708–725, 2017
Many Pathways from Land Use to Health: Associations between Neighborhood Walkability and Active Transportation, Body Mass Index, and Air Quality

Abstract The literature shows single-use, low-density land development and disconnected street networks to be positively associated with auto dependence and negatively associated with walking and transit use. These factors in turn appear to affect health by influencing physical activity, obesity, and emissions of air pollutants. We evaluated the association between a single index of walkability that incorporated land use mix, street connectivity, net residential density, and retail floor area ratios, with health-related outcomes in King County, Washington. We found a 5% increase in walkability to be associated with a per capita 32.1% increase in time spent in physically active travel, a 0.23-point reduction in body mass index, 6.5% fewer vehicle miles traveled, 5.6% fewer grams of oxides of nitrogen (NOx) emitted, and 5.5% fewer grams of volatile organic compounds (VOC) emitted. These results connect development patterns with factors that affect several prevalent chronic diseases.
Statistical models for natural sounds

It is important to understand the rich structure of natural sounds in order to solve important tasks, like automatic speech recognition, and to understand auditory processing in the brain. This thesis takes a step in this direction by characterising the statistics of simple natural sounds. We focus on the statistics because perception often appears to depend on them, rather than on the raw waveform. For example the perception of auditory textures, like running water, wind, fire and rain, depends on summary-statistics, like the rate of falling rain droplets, rather than on the exact details of the physical source. In order to analyse the statistics of sounds accurately it is necessary to improve a number of traditional signal processing methods, including those for amplitude demodulation, time-frequency analysis, and sub-band demodulation. These estimation tasks are ill-posed and therefore it is natural to treat them as Bayesian inference problems. The new probabilistic versions of these methods have several advantages. For example, they perform more accurately on natural signals and are more robust to noise, they can also fill-in missing sections of data, and provide error-bars. Furthermore, free-parameters can be learned from the signal. Using these new algorithms we demonstrate that the energy, sparsity, modulation depth and modulation time-scale in each sub-band of a signal are critical statistics, together with the dependencies between the sub-band modulators. In order to validate this claim, a model containing co-modulated coloured noise carriers is shown to be capable of generating a range of realistic sounding auditory textures. Finally, we explored the connection between the statistics of natural sounds and perception. We demonstrate that inference in the model for auditory textures qualitatively replicates the primitive grouping rules that listeners use to understand simple acoustic scenes. This suggests that the auditory system is optimised for the statistics of natural sounds.
Cognitive behavioral stress management effects on injury and illness among competitive athletes: A Randomized Clinical trial

Cognitive behavioral stress management (CBSM) has previously been found to reduce fatigue, depression, and cortisol response to heavy exercise training among competitive collegiate athletes and to speed physical and psychological recovery from surgery (1,2). Our study assessed the efficacy of a CBSM program to reduce the frequency of injury and illness among collegiate athletes in a randomized, single-blind, controlled clinical trial. Following assessment of baseline medical history, mood state, stress, cortisol, sleep, alcohol use, and exercise training, collegiate rowers were stratified by gender and competitive level and randomly assigned to either a control group or a CBSM group. Exercise training information and psychosocial assessments were repeated immediately following the intervention period, and health care providers who were blinded to participant assignment recorded the frequency of medical visits and the number of days injured or ill until the end of the season. Athletes randomly assigned to a CBSM group experienced significant reductions in the number of illness and injury days as compared to control group athletes. CBSM participants also had half the number of health service visits as did controls. The data suggest that a time-limited CBSM intervention designed specifically for an athlete population may be an effective prophylactic treatment to reduce the incidence of injury and illness among competitive collegiate athletes.
Adverse events reported following live, cold-adapted, intranasal influenza vaccine.

CONTEXT In June 2003, the US Food and Drug Administration licensed a trivalent live, attenuated influenza vaccine (LAIV-T) for intranasal administration to healthy persons 5 to 49 years of age. Although prelicensure testing involved 20 228 vaccinees, clinical trials were not of sufficient size to detect rare adverse events reliably. OBJECTIVE To identify adverse events reported following LAIV-T administration after licensure. DESIGN, SETTING, AND PARTICIPANTS All adverse events reported to the US Vaccine Adverse Event Reporting System (VAERS) during the 2003-2004 and the 2004-2005 influenza seasons. MAIN OUTCOME MEASURES Numbers and proportions of reported adverse events and reporting rates of adverse events per 100,000 vaccinees. RESULTS Approximately 2,500,000 persons received LAIV-T during the first 2 postlicensure seasons. As of August 16, 2005, VAERS received 460 adverse event reports for vaccinations received from August 2003 through July 2005. No fatalities were reported. There were 7 reports of possible anaphylaxis, 2 reports of Guillain-Barré syndrome, 1 report of Bell palsy, and 8 reports of asthma exacerbation among individuals with a prior asthma history. Events in individuals for whom the vaccine was not indicated accounted for 73 reports (16%). CONCLUSIONS Reports to VAERS in the first 2 seasons of LAIV-T use did not identify any unexpected serious risks with this vaccine when used according to approved indications. Like many vaccines and other medical products, LAIV-T may rarely cause anaphylaxis. Secondary transmission of the vaccine virus merits further investigation. Reports of asthma exacerbations in vaccinees with prior asthma history highlight the risks of vaccine use inconsistent with approved labeling.
The Jingle and Jangle of Emotion Assessment: Imprecise Measurement, Casual Scale Usage, and Conceptual Fuzziness in Emotion Research

Although affective science has seen an explosion of interest in measuring subjectively experienced distinct emotional states, most existing self-report measures tap broad affect dimensions and dispositional emotional tendencies, rather than momentary distinct emotions. This raises the question of how emotion researchers are measuring momentary distinct emotions in their studies. To address this question, we reviewed the self-report measurement practices regularly used for the purpose of assessing momentary distinct emotions, by coding these practices as observed in a representative sample of articles published in Emotion from 2001–2011 (n = 467 articles; 751 studies; 356 measurement instances). This quantitative review produced several noteworthy findings. First, researchers assess many purportedly distinct emotions (n = 65), a number that differs substantially from previously developed emotion taxonomies. Second, researchers frequently use scales that were not systematically developed, and that include items also used to measure at least 1 other emotion on a separate scale in a separate study. Third, the majority of scales used include only a single item, and had unknown reliability. Together, these tactics may create ambiguity regarding which emotions are being measured in empirical studies, and conceptual inconsistency among measures of purportedly identical emotions across studies. We discuss the implications of these problematic practices, and conclude with recommendations for how the field might improve the way it measures emotions.
Concrete At Elevated Temperatures FOLAGBADE

This paper modelled the experimental results of Ehm (1986) and Thelandersson (1987) on transient thermal creep of concrete specimens, under sustained load, at elevated temperatures and investigated the relevance of transient thermal creep on the behaviour of concrete at elevated temperatures. Numerical investigations were carried out on steady state and transient state models using the ‘Finite Element Analysis Programme’ (FEAP). The investigations included observing the effect of degraded coefficient of thermal expansion and modulus of elasticity of concrete with and without the inclusion of the effect of transient thermal creep (assumed equivalent to the effect of thermo mechanical strain) on the behaviour of concrete, observing the relevance of the transient thermal creep on the behaviour of concrete and observing the effect of sustained compressive stress on the temperature dependent compressive strength of concrete. The study showed that the model predictions fit the experimental results and confirmed i) the absence of transient thermal creep in steady state specimens, ii) that the coefficient of thermal expansion and modulus of elasticity of concrete are degraded at elevated temperatures, iii) that the coefficients of thermo mechanical strain and free thermal expansion changed respectively at 469 o C and 619 o C and iv) that the critical temperature of concrete decreases with increase in the magnitude of the sustained compressive stress.
Numerical simulations of sawteeth in tokamaks

Numerical simulations of sawteeth in tokamaks have been carried out using reduced magnetohydrodynamics and a simple transport model. The electron temperature is evolved self-consistently, including Ohmic heating and a highly anisotropic thermal diffusivity. The sawtooth period and collapse time found in the simulations for Lundquist numbers S below 107 compare favourably with experimental results from small and medium size ohmically heated tokamaks. The sawtoothing is found to be sensitive to the values of the transport coefficients. In particular, the perpendicular viscosity must be comparable to, or larger than, the perpendicular thermal diffusivity for distinct relaxation oscillations to occur. To study the scaling with S, the viscosity and perpendicular thermal conductivity have been scaled as 1/S, and S has been varied. Modifications of the equilibrium, caused by the sawteeth, play an important role in the scaling of the collapse time and period with the Lundquist numnber. The self-consistently computed q-profiles are very flat in the central region where q ≈ 1. Outside the low-shear region, the shear rises sharply. This q-profile allows a resistive mode to be turned on quickly with a high growth rate. The deviation of the central q from unity over the sawtooth cycle decreases with increasing S, and the collapse time shows a weaker dependence than the S½ scaling of Sweet and Parker.
A Comparison of Request Process and Outcomes in Donation After Cardiac Death and Donation After Brain Death: Results From a National Study

Available literature points to healthcare providers’ discomfort with donation after cardiac death (DCD) and their perception of public reluctance toward the procedure. Using a national sample, we report on the communication content of actual DCD and donation after brain death (DBD) approaches by organ procurement organization (OPO) requesters and compare family decision makers’ (FDMs’) experiences of both modalities. We recruited 1601 FDMs using a validated protocol; 347 (21.7%) were of potential DCD donors. Semistructured telephone interviews yielded FDMs’ sociodemographic data, donation attitudes, assessment of approach, final outcomes, and substantiating reasons. Initial analysis consisted of bivariate analyses. Multilevel mixture models compared groups representing authorization outcome and DCD/DBD status. No significant differences in family authorization were found between DCD and DBD cases. Statistically significant associations were found between sociodemographic characteristics and authorization, with white FDMs more likely to authorize DCD or DBD than black FDMs. FDMs of both modalities had similar evaluations of requester skills, topics discussed, satisfaction, and refusal reasons. The findings suggest that the DCD/DBD distinction may not be notable to families. We recommend the use of similar approach strategies and communication skills and the development of education campaigns about the public's acceptance of DCD.
Promotion of Wheat Growth under Salt Stress by Halotolerant Bacteria Containing ACC deaminase

Salinity is a major abiotic stress that reduces crop productivity in arid and semiarid soils. About 25% of the country's arable land is affected by different levels of salt. A considerable part of this land is under wheat cultivation each year as the country's most important crop. ACC deaminase producing bacteria increase plant resistance to stress condition by reducing stress ethylene in a variety of environmental stresses such as salinity. In this study, 167 halotolerant bacterial strains were isolated from the saline habitats and screened for growth at different NaCl concentrations. These halotolerant bacterial strains were then tested for 1 AminoCyclopropane-1-Carboxylic acid (ACC) deaminase activity. Among six isolates of halotolerant bacteria containing ACC deaminase, the K78 strain produced the highest level of this enzyme. Phylogenetic analysis of the 16S rRNA gene sequence of this bacterium indicated that this strain belonged to Bacillus mojavensis . Inoculation of Bacillus mojavensis to salt stressed wheat plants produced an increase in root and shoot weight, chlorophyll content, and nutrient uptake in comparison with the un-inoculated soils. In summary, this study indicates that the use of ACC deaminase-producing halotolerant bacteria mitigates salinity stress effects on growth of wheat plants by reducing salt-stress-induced ethylene production.
In vitro evaluation of controlled‐release 14% doxycycline gel for decontamination of machined and sandblasted acid‐etched implants

BACKGROUND Peri-implant infections are associated with the establishment and maturation of a bacterial biofilm characterized by a predominance of Gram-negative fusiform anaerobic species. The decontamination of implant surfaces is then crucial for a successful peri-implant therapy. METHODS Twenty-one smooth and 21 rough implants, divided into four groups according to surface and treatment modality, were contaminated with Streptococcus sanguinis and then placed in an incubator with the atmosphere of 5% CO2 at 37°C for 24 hours to allow the bacteria to grow. After 24 hours, the test groups were treated with controlled release 14% doxycycline gel injecting the gel circumferentially over the surface of the implant for 3 minutes, while the control groups were irrigated with sterile saline for 1 minute. The implants were then vortexed into triptych soy broth to allow the bacteria to detach from the surface, diluted 1:100 and plated. Colony forming units (CFU) were counted 48 hours after incubation. RESULTS The use of a 14% doxycycline gel minimized CFU counts compared to control groups, with the difference being statistically significant (P < 0.05). The reduction of CFUs in the smooth test group is more marked than in the rough test group, but the difference doesn't reach statistically significance (P = 0.215). CONCLUSIONS The use of 14% doxycycline gel in implant surface decontamination was efficacious in this in-vitro study. Adjunctive use of locally delivered 14% doxycycline gel might be a viable option in the management of peri-implantitis and peri-implant mucositis considering its efficacy in reducing bacterial colonization.
Palmitoylation and p8-Mediated Human T-Cell Leukemia Virus Type 1 Transmission

ABSTRACT The orf-I gene of human T-cell leukemia type 1 (HTLV-1) encodes p8 and p12 and has a conserved cysteine at position 39. p8 and p12 form disulfide-linked dimers, and only the monomeric forms of p8 and p12 are palmitoylated. Mutation of cysteine 39 to alanine (C39A) abrogated dimerization and palmitoylation of both proteins. However, the ability of p8 to localize to the cell surface and to increase cell adhesion and viral transmission was not affected by the C39A mutation.
Next generation multilocus sequence typing ( NGMLST ) and the Mitchell b , analytical software program MLSTEZ enable efficient , cost-effective , high-throughput , multilocus sequencing typing

http://dx.doi. org/10.1016/j.fgb. 2015.01. 005 1087-1845/ 2015 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). ⇑ Corresponding authors at: Division of Infectious Diseases, Department of Medicine, Duke University Medical Center, Durham, NC, USA (Y. Chen and J.R. Perfect). Fax: +1 919 6848902. E-mail addresses: ychenbioinfo@gmail.com (Y. Chen), perfe001@mc.duke. edu (J.R. Perfect). 1 Present address: Oregon Health and Science University, School of Medicine, Portland, OR, USA. 2 Present address: Mycotic Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA. Deborah J. Springer , Yun Ding , George Yuan , John R. Perfect a,⇑
Self-appraised problem solving and pain-relevant social support as predictors of the experience of chronic pain

The purpose of this study was to examine the contributions of self-appraised problem-solving competence and pain-relevant social support to the prediction of pain, depression, and disability. The 234 chronic pain patients referred for participation in a comprehensive pain management program were administered self-report measures of pain, depression, disability, pain-relevant social support, and problem solving. Hierarchical multiple-regression analyses revealed that lower self-appraised problem-solving competence was related to increased pain, depression, and disability. Pain-relevant social support was directly related to pain and disability but indirectly related to depression. High levels of pain-relevant social support were found to buffer the relation between poorer self-appraised problem-solving competence and depressive symptoms. The results support the assessment of problem-solving skills in chronic pain patients and the investigation and utility of interventions aimed at increasing adaptive pain-relevant social support.
Ideal versus real: simulated annealing of experimentally derived and geometric platinum nanoparticles

Platinum nanoparticles find significant use as catalysts in industrial applications such as fuel cells. Research into their design has focussed heavily on nanoparticle size and shape as they greatly influence activity. Using high throughput, high precision electron microscopy, the structures of commercially available Pt catalysts have been determined, and we have used classical and quantum atomistic simulations to examine and compare them with geometric cuboctahedral and truncated octahedral structures. A simulated annealing procedure was used both to explore the potential energy surface at different temperatures, and also to assess the effect on catalytic activity that annealing would have on nanoparticles with different geometries and sizes. The differences in response to annealing between the real and geometric nanoparticles are discussed in terms of thermal stability, coordination number and the proportion of optimal binding sites on the surface of the nanoparticles. We find that annealing both experimental and geometric nanoparticles results in structures that appear similar in shape and predicted activity, using oxygen adsorption as a measure. Annealing is predicted to increase the catalytic activity in all cases except the truncated octahedra, where it has the opposite effect. As our simulations have been performed with a classical force field, we also assess its suitability to describe the potential energy of such nanoparticles by comparing with large scale density functional theory calculations.