Miracle-dz/UniFAR-FTUs huggingface dataset:
The use of a generalized born model for the analysis of protein conformational transitions: A comparative study with explicit solvent simulations for chemotaxis Y protein (CheY)

To investigate whether implicit solvent models are appropriate for mechanistic studies of conformational transition in proteins, a recently developed generalized Born model (GBSW) was applied to a small signaling protein, chemotaxis protein Y (CheY), with different combinations of the phosphorylation state and conformation of the system; the results were compared to explicit solvent simulations using a stochastic boundary condition. The subtle but distinct conformational transitions involved in CheY activation makes the system ideally suited for comparing implicit and explicit solvent models because these conformational transitions are potentially accessible in both types of simulations. The structural and dynamical properties analyzed include not only those localized to the active site region but also throughout the protein, such as sidechain methyl group order parameters, backbone hydrogen bonding lifetime and occupancy as well as principal components of the trajectories. Overall, many properties were well reproduced by the GBSW simulations when compared with the explicit solvent calculations, although a number of observations consistently point to the suggestion that the current parameterization of the GBSW model tends to overestimate hydrogen‐bonding interactions involving both charged groups and (charge‐neutral) backbone atoms. This deficiency led to overstabilization of certain secondary structural motifs and more importantly, qualitatively different behaviors for the active site groups (Thr 87, Ala 88, the β4–α4 loop) in response to phosphorylation, when compared with explicit solvent simulations. The current study highlights the value of carrying out both explicit and implicit solvent simulations for complementary mechanistic insights in the analysis of conformational transition in biomolecules. © 2006 Wiley Periodicals, Inc. J Comput Chem, 2006
The exclusion of WMAP's Hubble constant by laser interferometry

In a recent laser interferometry experiment, the light from a specific forbidden transition was frequency compared with that from a highly stable cryogenic laserresonator coupling for a period of τ ≈ 200 days. Through a detailed analysis, we demonstrate that while the free transition source emits light to set a frequency standard, the wavelength of the other source, being rigidly fixed by the physical size of the resonator box when a prescribed number of wavecycles must fit into the box, would have caused the emitted frequency to blueshift with time if there is Hubble expansion, because the physical distance propagated by light per unit time increases with time as space expands, thereby driving the frequency upwards if the wavelength is not allowed to change. Over the duration τ of the experiment, and given that the initial frequencies of the two sources were calibrated to be the same, the frequency of the laser-resonator should have blueshifted w.r. t. that of the reference source by the fractional amount H0τ/2 ≈ 2 × 10 −11 for H0 = 70 km s Mpc. Their non-detection of a frequency shift δν/ν = (4.8 ± 5.3) × 10 puts to question the reality of space expansion at the rate inferred from WMAP data. The 2σ upper limit for the Hubble constant from this precision optical bench is ≈ 50 km s Mpc. In an interesting laboratory experiment performed recently (Braxmaier et al 2002) the Lorentz complying line element in Minkowski space:
College Sexuality Education Promotes Future Discussions About Sexuality Between Former Students and Their Children

The study examined whether completion of a college human sexuality course would have long-term effects on students' willingness to discuss sexuality with their children. Fifty-two former students with children aged 5 years or older were surveyed 2½ to 3 years after completion of the course, and their responses were compared with those of a control group of 50 parents surveyed on the first day of the course. Only 10 of the 102 subjects indicated that they had ever had a single meaningful discussion about sex with their parents while growing up. While only 18% of the parents who had not yet had sexuality education had begun discussions with their own children, 86.5% of the sexuality-educated parents had done so (p < .001). Of 34 sexuality-educated parents with children aged 12 years or older, three-fourths or more had discussed menstruation, sexual intercourse and reproduction, birth control, sexually transmitted diseases, homosexuality, and sexual abuse. Masturbation was the only surveyed subject that had .
Uncovering stem cell differentiation factors for salivary gland regeneration by quantitative analysis of differential proteomes

Severe xerostomia (dry mouth) compromises the quality of life in patients with Sjögren’s syndrome or radiation therapy for head and neck cancer. A clinical management of xerostomia is often unsatisfactory as most interventions are palliative with limited efficacy. Following up our previous study demonstrating that mouse BM-MSCs are capable of differentiating into salivary epithelial cells in a co-culture system, we further explored the molecular basis that governs the MSC reprogramming by utilizing high-throughput iTRAQ-2D-LC-MS/MS-based proteomics. Our data revealed the novel induction of pancreas-specific transcription factor 1a (PTF1α), muscle, intestine and stomach expression-1 (MIST-1), and achaete-scute complex homolog 3 (ASCL3) in 7 day co-cultured MSCs but not in control MSCs. More importantly, a common notion of pancreatic-specific expression of PTF1 α was challenged for the first time by our verification of PTF1 α expression in the mouse salivary glands. Furthermore, a molecular network simulation of our selected putative MSC reprogramming factors demonstrated evidence for their perspective roles in salivary gland development. In conclusion, quantitative proteomics with extensive data analyses narrowed down a set of MSC reprograming factors potentially contributing to salivary gland regeneration. Identification of their differential/synergistic impact on MSC conversion warrants further investigation.
Attention‐Deficit/Hyperactivity Disorder in Young French Male Prisoners

While forensic studies have reported higher than community rates of mental disorders in imprisoned populations, few studies have focused on attention‐deficit/hyperactivity disorder (ADHD) in these subjects. The aim of this study was to investigate ADHD prevalence among young French male prisoners. A specific diagnostic interview (Conners' Adult ADHD Diagnostic Interview for DSM‐IV, CAADID) was used. Correlations between ADHD, subsyndromal ADHD, and criminal features were investigated. 11% of young male prisoners among 93 male subjects aged 18–35 years met the criteria for actual ADHD, and 17% met those for childhood ADHD. Considering ADHD and subsyndromal ADHD, prevalence was about 43% in adulthood. ADHD and subsyndromal ADHD in adulthood were significantly associated with a higher number of imprisonments and a younger age at first arrest. It could be advisable to better identify subjects with ADHD symptoms among prison populations.
Clinical Features and Genetic Analysis of 20 Chinese Patients with X-Linked Hyper-IgM Syndrome

X-linked hyper-IgM syndrome (XHIGM) is one type of primary immunodeficiency diseases, resulting from defects in the CD40 ligand/CD40 signaling pathways. We retrospectively analyzed the clinical and molecular features of 20 Chinese patients diagnosed and followed up in hospitals affiliated to Shanghai Jiao Tong University School of Medicine from 1999 to 2013. The median onset age of these patients was 8.5 months (range: 20 days–21 months). Half of them had positive family histories, with a shorter diagnosis lag. The most common symptoms were recurrent sinopulmonary infections (18 patients, 90%), neutropenia (14 patients, 70%), oral ulcer (13 patients, 65%), and protracted diarrhea (13 patients, 65%). Six patients had BCGitis. Six patients received hematopoietic stem cell transplantations and four of them had immune reconstructions and clinical remissions. Eighteen unique mutations in CD40L gene were identified in these 20 patients from 19 unrelated families, with 12 novel mutations. We compared with reported mutation results and used bioinformatics software to predict the effects of mutations on the target protein. These mutations reflected the heterogeneity of CD40L gene and expanded our understanding of XHIGM.
Validation of an Online Food Frequency Questionnaire against Doubly Labelled Water and 24 h Dietary Recalls in Pre-School Children

The development of easy-to-use and accurate methods to assess the intake of energy, foods and nutrients in pre-school children is needed. KidMeal-Q is an online food frequency questionnaire developed for the LifeGene prospective cohort study in Sweden. The aims of this study were to compare: (i) energy intake (EI) obtained using KidMeal-Q to total energy expenditure (TEE) measured via doubly labelled water and (ii) the intake of certain foods measured using KidMeal-Q to intakes acquired by means of 24 h dietary recalls in 38 children aged 5.5 years. The mean EI calculated using KidMeal-Q was statistically different (p < 0.001) from TEE (4670 ± 1430 kJ/24 h and 6070 ± 690 kJ/24 h, respectively). Significant correlations were observed for vegetables, fruit juice and candy between KidMeal-Q and 24 h dietary recalls. Only sweetened beverage consumption was significantly different in mean intake (p < 0.001), as measured by KidMeal-Q and 24 h dietary recalls. In conclusion, KidMeal-Q had a relatively short answering time and comparative validity to other food frequency questionnaires. However, its accuracy needs to be improved before it can be used in studies in pre-school children.
DERIVATION OF A SIX-STEP BLOCK METHOD FOR DIRECT SOLUTION OF SECOND ORDER ORDINARY DIFFERENTIAL EQUATIONS

A new six-step block method for solving second order initial value problems of ordinary differential equations is proposed using interpolation and collocation strategies. In developing this method, the power series adopted as an approximate solution is employed as interpolation equation while its second derivative is used as collocation equation. In addition, the stability properties of the developed method are also established. The numerical results reveal that the new method produces better accuracy if compared to existing methods when solving the same problems.
Opposite malaria and pregnancy effect on oral bioavailability of artesunate – a population pharmacokinetic evaluation

Aim The aim was to compare the pharmacokinetic properties of artesunate and dihydroartemisinin in the same women: i) pregnant with acute uncomplicated malaria on day 1 and 2, ii) pregnant with convalescent malaria on day 7 and iii) in a healthy state 3 months post-partum on day 1, 2 and 7. Methods Non-linear mixed-effects modelling was used to compare plasma concentration–time profiles of artesunate and dihydroartemisinin over 7 days of treatment following oral and intravenous artesunate administration to pregnant women with uncomplicated Plasmodium falciparum malaria during their second or third trimesters of pregnancy. The same women were restudied 3 months after delivery when fully recovered. Non-compartmental results of the same study have been published previously. Results Twenty pregnant patients on the Thailand-Myanmar border were studied and 15 volunteered to be restudied 3 months post-partum. Malaria and pregnancy had no effect on the pharmacokinetic properties of artesunate or dihydroartemisinin after intravenous artesunate administration. However, malaria and pregnancy had opposite effects on the absorption of orally administered artesunate. Malaria increased the absolute oral bioavailability of artesunate by 87%, presumably by inhibiting first pass effect, whereas pregnancy decreased oral bioavailability by 23%. Conclusions The population pharmacokinetic analysis demonstrated opposite effects of malaria and pregnancy on the bioavailability of orally administered artesunate. Lower drug exposures during the second and third trimesters of pregnancy may contribute to lower cure rates and thus the development of drug resistance. Dose optimization studies are required for artesunate containing artemisinin-based combination therapies (ACTs) in later pregnancy.
How Life History Can Sway the Fixation Probability of Mutants

In this work, we study the effects of demographic structure on evolutionary dynamics when selection acts on reproduction, survival, or both. In contrast to the previously discovered pattern that the fixation probability of a neutral mutant decreases while the population becomes younger, we show that a mutant with a constant selective advantage may have a maximum or a minimum of the fixation probability in populations with an intermediate fraction of young individuals. This highlights the importance of life history and demographic structure in studying evolutionary dynamics. We also illustrate the fundamental differences between selection on reproduction and selection on survival when age structure is present. In addition, we evaluate the relative importance of size and structure of the population in determining the fixation probability of the mutant. Our work lays the foundation for also studying density- and frequency-dependent effects in populations when demographic structures cannot be neglected.
The Indirect Association Between Television Exposure and Self-Protective Behavior as a Result of Worry About Crime: The Moderating Role of Gender

Persistent fear of crime can have serious consequences for one’s social behavior. Previous research has shown that people who fear crime are more likely to engage in self-protective behavior. Although a substantial amount of research has examined the relationship between television exposure and fear of crime, research on the association between television exposure and self-protective behavior is scarce. Based on cultivation theory and the mediated fear model, the current study aimed to examine whether news and crime drama television viewing are indirectly related to self-protective behavior via fear of crime. Structural equation modeling of data from 392 undergraduate students showed that news viewing and crime drama viewing is indirectly associated with self-protective behavior. The current study provided evidence for the importance of accounting for gender when investigating the complex issue of media effects on fear of crime and self-protective behavior.
Lawrence Berkeley National Laboratory Recent Work Title Comparative analysis of SN 2012 dn optical spectra : Days-14 to + 114 Permalink

SN 2012dn is a super-Chandrasekhar mass candidate in a purportedly normal spiral (SAcd) galaxy, and poses a challenge for theories of type Ia supernova diversity. Here we utilize the fast and highly parametrized spectrum synthesis tool, SYNAPPS, to estimate relative expansion velocities of species inferred from optical spectra obtained with six facilities. As with previous studies of normal SN Ia, we find that both unburned carbon and intermediate-mass elements are spatially coincident within the ejecta near and below 14 000 km s−1. Although the upper limit on SN 2012dn’s peak luminosity is comparable to some of the most luminous normal SN Ia, we find a progenitor mass exceeding ∼1.6 M is not strongly favoured by leading merger models since these models do not accurately predict spectroscopic observations of SN 2012dn and more normal events. In addition, a comparison of light curves and host-galaxy masses for a sample of literature and Palomar Transient Factory SN Ia reveals a diverse distribution of SN Ia subtypes where carbon-rich material remains unburned in some instances. Such events include SN 1991T, 1997br, and 1999aa where trace signatures of C III at optical wavelengths are presumably detected.
Experimental Test of Postfire Management in Pine Forests: Impact of Salvage Logging versus Partial Cutting and Nonintervention on Bird–Species Assemblages

Abstract: There is an intense debate about the effects of postfire salvage logging versus nonintervention policies on regeneration of forest communities, but scant information from experimental studies is available. We manipulated a burned forest area on a Mediterranean mountain to experimentally analyze the effect of salvage logging on bird–species abundance, diversity, and assemblage composition. We used a randomized block design with three plots of approximately 25 ha each, established along an elevational gradient in a recently burned area in Sierra Nevada Natural and National Park (southeastern Spain). Three replicates of three treatments differing in postfire burned wood management were established per plot: salvage logging, nonintervention, and an intermediate degree of intervention (felling and lopping most of the trees but leaving all the biomass). Starting 1 year after the fire, we used point sampling to monitor bird abundance in each treatment for 2 consecutive years during the breeding and winter seasons (720 censuses total). Postfire burned‐wood management altered species assemblages. Salvage logged areas had species typical of open‐ and early‐successional habitats. Bird species that inhabit forests were still present in the unsalvaged treatments even though trees were burned, but were almost absent in salvage‐logged areas. Indeed, the main dispersers of mid‐ and late‐successional shrubs and trees, such as thrushes (Turdus spp.) and the European Jay (Garrulus glandarius) were almost restricted to unsalvaged treatments. Salvage logging might thus hamper the natural regeneration of the forest through its impact on assemblages of bird species. Moreover, salvage logging reduced species abundance by 50% and richness by 40%, approximately. The highest diversity at the landscape level (gamma diversity) resulted from a combination of all treatments. Salvage logging may be positive for bird conservation if combined in a mosaic with other, less‐aggressive postfire management, but stand‐wide management with harvest operations has undesirable conservation effects.
The effect of L2 teaching method on motivation and proficiency

Although motivational research determined an evident link between motivation and instructional practice in the second language classroom, no study so far provided empirical evidence for the prevalence of a teaching method among others in terms of its effect on learning motivation. This study attempts to fill this gap in the motivational research by means of an investigation of the relationship between teaching method, L2 learning motivation and proficiency over the course of two academic years. The participants in this study were 107 Dutch students from four different classes instructed French at beginner level with either an implicit (AIM) or explicit (Grandes Lignes) instructional method. As suggested by the results of this research, the teaching method by itself does not play a role in directing students’ beliefs and attitudes towards language learning, and in contributing to shape students’ L2 motivational self; the combination of the method with a specific teacher, however, seems to be the main factor accounting for differences in motivation and proficiency in our participants.
PENGARUH KEADILAN ORGANISASI DAN BUDAYA ORGANISASI TERHADAP PERILAKU KEWARGAAN ORGANISASI MELALUI KOMITMEN ORGANISASI DAN KEPUASAN KERJA

This study aims to determine the relationship between variables of organizational justice, organizational culture, organizational commitment, job satisfaction and organizational citizenship behavior at PT. Pos Indonesian. The use of these variables with the results of previous studies provide reason for the different conclusions, there is theory that direct effect and did not. For example justice organizations significant effect on organizational citizenship behavior, and also say is not significant. Besides, these variables are expected to change for the better in improving the fairness of the organization and the organizational culture of the OCB through commitment and job satisfaction at PT. Pos Indonesian. The population’s research was all employees of PT. Pos using simple random method, so that the members of a population of 130 employees, the research sample of 100 people. Penelitian ini bertujuan untuk mengetahui hubungan antar variabel keadilan organisasi, budaya organisasi, komitmen organisasi, kepuasan kerja dengan perilaku kewargaan organisasi di PT. Pos Indonesia. Penggunaan variabel-variabel tersebut dengan alasan hasil penelitian terdahulu memberikan kesimpulan yang berbeda-beda, ada yang mengatakan berpengaruh langsung dan juga tidak. Misalnya keadilan organisasi berpengaruh signifikan terhadap perilaku kewargaan organisasi, dan juga ada yang mengatakan tidak signifikan. Disamping itu variabel-variabel tersebut diharapkan memberi perubahan ke arah yang lebih baik dalam meningkatkan keadilan organisasi dan budaya organisasi terhadap OCB melalui komitmen dan kepuasan kerja pada PT. Pos Indonesia. Populasi penelitian adalah seluruh karyawan PT. Pos dengan menggunakan metode acak sederhana, sehingga anggota populasi yang berjumlah 130 orang karyawan yang dijadikan sampel penelitian 100 orang.
Authentication and key agreement protocol for UMTS with low bandwidth consumption

Radio interface and wireless service accesses are two areas, in which wireless networks do not provide the same level of protection as wired networks. It may result in the wireless networks being vulnerable to various attacks. For example, the first generation cellular mobile communication systems, such as advanced mobile phone service (AMPS), and the second generation cellular mobile communication systems, such as global system for mobile (GSM), do not take account of security issues comprehensively. It brings about an intruder to be able to eavesdrop user traffic or even change the identities of mobile phones to gain fraudulent services. Therefore, the Universal Mobile Telecommunication System (UMTS), which is known as the third generation (3G) cellular mobile communication system, is proposed. UMTS adopts the security feature of GSM in order to interwork with GSM smoothly. Furthermore, the UMTS adds new security features to design an authentication and key agreement protocol, which is called UMTS AKA protocol. However, it is found that the UMTS AKA has some problems, including bandwidth consumption between a serving network and a user's home network, space overhead of the serving network and sequence number synchronization. Therefore, in this paper, we propose an extension of UMTS AKA protocol, called UMTS X-AKA to overcome the aforementioned problems of UMTS AKA.
The Stable Long-Run CAPM and the Cross-Section of Expected Returns

The capital-asset-pricing model (CAPM) is one of the most popular methods of financial market analysis. But, evidence of the poor empirical performance of the CAPM has accumulated in the literature. For example, based on their empirical results regarding the relation between market Beta and average return, Fama and French (1996) conclude that the CAPM is no longer a useful tool for empirical financial market analysis. Most empirical studies of the conventional CAPM take, however, neither the fat-tails of return data nor the price relationship between an asset of interest and the bench market portfolio into account. In the framework of a univariate Beta-model we consider a stable long-run CAPM taking account of the fat-tails of stock returns and the common stochastic trends between stock prices. Using the same data used by Fama and French (1996), the stable long-run CAPM demonstrates that Markowitz rule of the expected returns and variance of returns can (still) -without any use of firm specific variables- explain the variation of the cross-sectional average returns.