Miracle-dz/UniFAR-FTUs huggingface dataset:
Structure of Zr-Cu and Zr-Ni Liquid Alloys Studied by High-Energy X-Ray Diffraction

In order to obtain an insight into the high glass-forming ability of bulk metallic glasses, we have analyzed liquid structures of the Zr-Cu and the Zr-Ni binary alloys with different compositions. High-energy (E = 113 keV) x-ray diffraction experiments were carried out for the liquid alloys levitated by a conical nozzle levitation (CNL) technique. While a peculiar shoulder on the second peak was observed in the structure factors of the Zr-Cu liquid alloys, those of the Zr70Ni30 and the Zr50Ni50 liquids exhibit an asymmetric shape of the second peak. In addition, it was found that the effect of concentration variation in the liquid Zr-Ni alloys was significantly different from that of the liquid Zr-Cu alloys. The liquid structure analyses using the reverse Monte Carlo (RMC) simulation have clarified that a degree of the short-range correlation between the constituents in the liquids affects substantially the glass-forming ability of the binary Zr alloys.
Removal of the PsaF Polypeptide Biases Electron Transfer in Favor of the PsaB Branch of Cofactors in Triton X‐100 Photosystem I Complexes from Synechococcus sp. PCC 7002 †

Continuous wave (CW) and transient electron paramagnetic resonance studies have implied that when PsaF is removed genetically, the double reduction of A1A is facile, the lifetime of A1A− is shorter and the ratio of fast to slow kinetic phases increases in PS I complexes isolated with Triton X‐100 (Van der Est, A., A. I. Valieva, Y. E. Kandrashkin, G. Shen, D. A. Bryant and J. H. Golbeck [2004] Biochemistry43, 1264–1275). Changes in the lifetimes of A1A− and A1B− are characteristic of mutants involving the quinone binding sites, but changes in the relative amplitudes of A1A− and A1B− are characteristic of mutants involving the primary electron acceptors, A0A and A0B. Here, we measured the fast and slow phases of electron transfer from A1B− and A1A− to FX in psaF and psaE psaF null mutants using time‐resolved CW and pump‐probe optical absorption spectroscopy. The lifetime of the fast kinetic phase was found to be unaltered, but the lifetime of the slow kinetic phase was shorter in the psaF null mutant and even more so in the psaE psaF null mutant. Concomitantly, the amplitude of the fast kinetic phase increased by a factor of 1.8 and 2.0 in the psaF and psaE psaF null mutants, respectively, at the expense of the slow kinetic phase. The change in ratio of the fast to slow kinetic phases is explained as either a redirection of electron transfer through A1B at the expense of A1A, or a shortening of the lifetime of A1A− to become identical to that of A1B−. The constant lifetime and the characteristics of the near‐UV spectrum of the fast kinetic phase favor the former explanation. A unified hypothesis is presented of a displacement of the A‐jk(1) α‐helix and switchback loop, which would weaken the H‐bond from Leu722 to A1A, accounting for the acceleration of the slow kinetic phase, as well as weaken the H‐bond from Tyr696 to A0A, accounting for the bias of electron transfer in favor of the PsaB branch of cofactors.
Diagnosis/Classification Criteria for Behcet's Disease

Historical Background. The ISG criteria for Behcet's, created in 1990, have excellent specificity, but lack sensitivity. The International Criteria for Behcet's Disease (ICBD) was created in 2006, as replacement to ISG. The aim of this study was to compare their performance. ISG and ICBD Criteria. For ISG oral aphthosis is mandatory. The presence of any two of the following (genital aphthosis, skin lesions, eye lesions, and positive pathergy test) will diagnose/classify the patient as BD. For ICBD, vascular lesions were added, while oral aphthosis is no more mandatory. Getting 3 or more points diagnose/classify the patient as BD (genital aphthosis 2 points, eye lesions 2 points, and the remaining each one point). Performance and Comparison of ISG and ICBD. Their sensitivity, specificity, and accuracy (percent agreement), were tested in three independent cohort of patients from Far-East (China), Middle-East (Iran), and Europe (Germany). The sensitivity for ISG was respectively 65.4%, 78.1%, 83.7% and for ICBD 87%, 98.2%, and 96.5%. The specificity for ISG was 99.2%, 98.8%, 89.5% and for ICBD 94.1%, 95.6%, and 73.7%. The accuracy for ISG was 74.2%, 85.5%, 85.5% and for ICBD 88.9%, 97.3%, and 89.5%. Conclusion. ICBD has better sensitivity, and accuracy than ISG.
The contribution of stress to the comorbidity of migraine and major depression: results from a prospective cohort study

Objectives To assess how much the association between migraine and depression may be explained by various measures of stress. Design National Population Health Survey is a prospective cohort study representative of the Canadian population. Eight years of follow-up time were used in the present analyses. Setting Canadian adult population ages 18–64. Participants 9288 participants. Outcome Incident migraine and major depression. Results Adjusting for sex and age, depression was predictive of incident migraine (HR: 1.62; 95% CI 1.03 to 2.53) and migraine was predictive of incident depression (HR: 1.55; 95% CI 1.15 to 2.08). However, adjusting for each assessed stressor (childhood trauma, recent marital problems, recent unemployment, recent household financial problems, work stress, chronic stress and change in social support) decreased this association, with chronic stress being a particularly strong predictor of outcomes. When adjusting for all stressors simultaneously, both associations were largely attenuated (depression–migraine HR: 1.30; 95% CI 0.80 to 2.10; migraine–depression HR: 1.19; 95% CI 0.86 to 1.66). Conclusions Much of the apparent association between migraine and depression may be explained by stress.
Linear Regression for Dependently Censored Panel Duration Models with Nonadditive Fixed E ff ects

This paper proposes estimators for a class of panel duration models with induced dependent censoring and fixed effects which may appear nonadditively in the model. No parametric assumptions are made about the distribution of the random error. The dependent censoring implies that the usual differencing approach common in fixed-effects models will lead to disproportionate weighting of the errors, and will not yield an unbiased estimating equation. Under mild assumptions on the conditional distribution of the errors, an estimator is proposed by proportionately trimming the marginal error distributions. It is proved that the estimators are consistent and asymptotically normal. Standard error estimators are constructed by using a resampling approach that repeatedly perturbs the minimand, thus avoiding the need for density estimation or numerical differentiation. Extensive simulations show that the estimators can have very good finite sample properties, and the resampling approach is reliable and efficient. The proposed approach is also applied to an unemployment duration problem using NLSY data.
An experimental study of the effects of heating and burning on the hard tissues of the human body and its implications for anthropology and forensic science

An understanding of heat-induced transformation of hard tissue is vital before a full interpretation of burned human remains can be successfully achieved. While some studies have examined this issue a lack of understanding continues to exist within the discipline. This study addresses a number of fundamental questions concerning the effect of heat on bone using a broad spectrum of analytical techniques. These include experimental burning, radiography, scanning electron microscopy, x-ray diffraction and for the first time mercury intrusion porosimetry and small angle x-ray scattering. These methods assisted in the study of heat-induced transformations in bone colour, mechanical strength, microstructure and dimension. Samples of modem sheep (n=60), modem human permanent and deciduous teeth and archaeological human permanent teeth (n=128) were analysed resulting in 5440 data points. An holistic experimental approach was undertaken exploring the bi-variable impact of heating temperature and duration of burning. Subsequent heat-induced bone changes included the progression of colour from natural through to blue-white, the significant loss of weight, the reduction in mechanical strength, the development of distinct fracture patterns, alterations in the microscopic porosity, substantial alterations in crystalline structure and the reduction and expansion in size. Collation and integration of this information demanded a fundamental revision of the four stages of heat-induced degradation of bone previously presented by Mayne Correia (1997) and Thompson (1999). The results of this study suggested that new approaches to the analysis of burned and cremated human remains within the forensic and archaeological arenas should be adopted. An examination of the role of the forensic anthropologist in mass fatality incidents alongside a retrospective study of regional fire-related deaths provides the context for this doctoral research.
B7H Costimulates Clonal Expansion of, and Cognate Destruction of Tumor Cells by, CD8+ T Lymphocytes In Vivo

B7H/B7RP (hereby called B7H) is a new member of the B7 family of costimulatory molecules and interacts with inducible costimulatory molecule (ICOS). Its function for CD8 T cells has not been reported. We report here that expression of B7H on the tumor cells reduced tumorigenicity and induced immunity to subsequent challenge with parental tumor cells. The immune protection correlates with an enhanced cytotoxic T lymphocyte (CTL) response against P1A, the major tumor antigen expressed in the J558 tumor. To understand the mechanism of immune protection, we adoptively transferred transgenic T cells specific for tumor antigen P1A into mice that bore P1A-expressing tumors. We found that while the transgenic T cells divided faster in mice bearing the B7H+ tumors, optimal B7H-induced clonal expansion of P1CTL required costimulation by B7–1 and B7–2 on the endogenous host antigen-presenting cells (APCs). Interestingly, when B7H+ and B7H− tumors were coinjected, P1CTL selectively eliminated the B7H+ tumor cells. Moreover, B7H expressed on the tumor cells made them highly susceptible to destruction by CTL in vivo, even if the CTL was administrated into mice with large tumor burdens. Tumors that recurred in the P1CTL-treated mice lost transfected B7H and/or H-2Ld, the class I molecule that presents the P1A peptide. Taken together, our results reveal that B7H costimulates clonal expansion of, and cognate destruction by CD8+ T lymphocytes in vivo.
Higher social class predicts increased unethical behavior

Seven studies using experimental and naturalistic methods reveal that upper-class individuals behave more unethically than lower-class individuals. In studies 1 and 2, upper-class individuals were more likely to break the law while driving, relative to lower-class individuals. In follow-up laboratory studies, upper-class individuals were more likely to exhibit unethical decision-making tendencies (study 3), take valued goods from others (study 4), lie in a negotiation (study 5), cheat to increase their chances of winning a prize (study 6), and endorse unethical behavior at work (study 7) than were lower-class individuals. Mediator and moderator data demonstrated that upper-class individuals’ unethical tendencies are accounted for, in part, by their more favorable attitudes toward greed.
YODA System for WMT16 Shared Task: Bilingual Document Alignment

In this paper, we address the task of automatically aligning/detecting the bilingual documents that are translations of each other from a single web-domain as part of WMT 2016. 1 Given the large amounts of data available in each web-domain, a brute force approach like finding similarities between every possible pair is a computationally expensive operation. Therefore, we start with a simple approach on matching just the web page urls after some pre-processing to reduce the number of possible pairings to a small extent. This simple approach obtained a recall of 50% and the exact matches from this approach are removed from further consideration. We built on top of this using an n-gram based approach that uses the partial English translations of French web pages and achieved a recall of 93.71% on the training pairs provided. We also outline an IR-based approach that uses both content and the meta data of each web page url, thereby obtaining a recall of 56.31%. Our final submission to this shared task using n-gram based approach achieved a recall of 93.92%.
Identifying Known and Unknown Peer-to-Peer Traffic

Class-of-service identification is a very useful task for enterprise, university and ISP networks. Peer-to-peer (P2P) traffic, being a significant portion of the network traffic today, constitutes a highly desirable class for identification. Accurate classification of P2P traffic is a challenging problem, and becomes even more challenging when we are constrained to use only transport-layer header information. In this paper, we present a new approach for P2P traffic identification, that uses fundamental characteristics of P2P protocols, such as a large network diameter and the presence of many hosts acting both as servers and clients. We do not use any application-specific information, but we are however able to identify both known and unknown P2P protocols in a simple and efficient way
Increasing horizontal resolution in numerical weather prediction and climate simulations: illusion or panacea?

The steady path of doubling the global horizontal resolution approximately every 8 years in numerical weather prediction (NWP) at the European Centre for Medium Range Weather Forecasts may be substan- tially altered with emerging novel computing architectures. It coincides with the need to appropriately address and determine forecast uncertainty with increasing resolution, in particular, when convective-scale motions start to be resolved. Blunt increases in the model resolution will quickly become unaffordable and may not lead to improved NWP forecasts. Consequently, there is a need to accordingly adjust proven numerical techniques. An informed decision on the modelling strategy for harnessing exascale, massively parallel computing power thus also requires a deeper understanding of the sensitivity to uncertainty—for each part of the model—and ultimately a deeper understanding of multi-scale interactions in the atmosphere and their numerical realization in ultra-high-resolution NWP and climate simulations. This paper explores opportunities for substantial increases in the forecast efficiency by judicious adjustment of the formal accuracy or relative resolution in the spectral and physical space. One path is to reduce the formal accuracy by which the spectral transforms are computed. The other pathway explores the importance of the ratio used for the horizontal resolution in gridpoint space versus wavenumbers in spectral space. This is relevant for both high-resolution simulations as well as ensemble-based uncertainty estimation.
Endoplasmic Reticulum Stress Induced Synthesis of a Novel Viral Factor Mediates Efficient Replication of Genotype-1 Hepatitis E Virus

Hepatitis E virus (HEV) causes acute hepatitis in many parts of the world including Asia, Africa and Latin America. Though self-limiting in normal individuals, it results in ~30% mortality in infected pregnant women. It has also been reported to cause acute and chronic hepatitis in organ transplant patients. Of the seven viral genotypes, genotype-1 virus infects humans and is a major public health concern in South Asian countries. Sporadic cases of genotype-3 and 4 infection in human and animals such as pigs, deer, mongeese have been reported primarily from industrialized countries. Genotype-5, 6 and 7 viruses are known to infect animals such as wild boar and camel, respectively. Genotype-3 and 4 viruses have been successfully propagated in the laboratory in mammalian cell culture. However, genotype-1 virus replicates poorly in mammalian cell culture and no other efficient model exists to study its life cycle. Here, we report that endoplasmic reticulum (ER) stress promotes genotype-1 HEV replication by inducing cap-independent, internal initiation mediated translation of a novel viral protein (named ORF4). Importantly, ORF4 expression and stimulatory effect of ER stress inducers on viral replication is specific to genotype-1. ORF4 protein sequence is mostly conserved among genotype-1 HEV isolates and ORF4 specific antibodies were detected in genotype-1 HEV patient serum. ORF4 interacted with multiple viral and host proteins and assembled a protein complex consisting of viral helicase, RNA dependent RNA polymerase (RdRp), X, host eEF1α1 (eukaryotic elongation factor 1 isoform-1) and tubulinβ. In association with eEF1α1, ORF4 stimulated viral RdRp activity. Furthermore, human hepatoma cells that stably express ORF4 or engineered proteasome resistant ORF4 mutant genome permitted enhanced viral replication. These findings reveal a positive role of ER stress in promoting genotype-1 HEV replication and pave the way towards development of an efficient model of the virus.
Finding Vanishing Points via Point Alignments in Image Primal and Dual Domains

We present a novel method for automatic vanishing point detection based on primal and dual point alignment detection. The very same point alignment detection algorithm is used twice: First in the image domain to group line segment endpoints into more precise lines. Second, it is used in the dual domain where converging lines become aligned points. The use of the recently introduced PClines dual spaces and a robust point alignment detector leads to a very accurate algorithm. Experimental results on two public standard datasets show that our method significantly advances the state-of-the-art in the Manhattan world scenario, while producing state-of-the-art performances in non-Manhattan scenes.
Use of CHROMagar Candida for the presumptive identification of Candida species directly from clinical specimens in resource-limited settings

Introduction: Identification of yeast isolated from clinical specimens to the species level has become increasingly important. Ever-increasing numbers of immuno-suppressed patients, a widening range of recognized pathogens, and the discovery of resistance to antifungal drugs are contributing factors to this necessity. Material and methods: A total of 487 yeast strains were studied for the primary isolation and presumptive identification, directly from clinical specimen. Efficacy of CHROMagar Candida has been evaluated with conventional methods including morphology on Corn meal–tween 80 agar and biochemical methods by using API 20 C AUX. Results: The result of this study shows that CHROMagar Candida can easily identify three species of Candida on the basis of colonial color and morphology, and accurately differentiate between them i.e. Candida albicans, Candida tropicalis, and Candida krusei. The specificity and sensitivity of CHROMagar Candida for C. albicans calculated as 99%, for C. tropicalis calculated as 98%, and C. krusei it is 100%. Conclusion: The data presented supports the use of CHROMagar Candida for the rapid identification of Candida species directly from clinical specimens in resource-limited settings, which could be very helpful in developing appropriate therapeutic strategy and management of patients.
Cytotoxic activities of CD8+ T cells collaborate with macrophages to protect against blood-stage murine malaria

The protective immunity afforded by CD8+ T cells against blood-stage malaria remains controversial because no MHC class I molecules are displayed on parasite-infected human erythrocytes. We recently reported that rodent malaria parasites infect erythroblasts that express major histocompatibility complex (MHC) class I antigens, which are recognized by CD8+ T cells. In this study, we demonstrate that the cytotoxic activity of CD8+ T cells contributes to the protection of mice against blood-stage malaria in a Fas ligand (FasL)-dependent manner. Erythroblasts infected with malarial parasites express the death receptor Fas. CD8+ T cells induce the externalization of phosphatidylserine (PS) on the infected erythroblasts in a cell-to-cell contact-dependent manner. PS enhances the engulfment of the infected erythroid cells by phagocytes. As a PS receptor, T-cell immunoglobulin-domain and mucin-domain-containing molecule 4 (Tim-4) contributes to the phagocytosis of malaria-parasite-infected cells. Our findings provide insight into the molecular mechanisms underlying the protective immunity exerted by CD8+ T cells in collaboration with phagocytes. DOI: http://dx.doi. org/10.7554/eLife.04232. 001
Solitary pulmonary nodules: detection, characterization, and guidance for further diagnostic workup and treatment.

OBJECTIVE The purpose of our study is to improve radiologists' understanding of the clinical issues involved in making a diagnosis and to guide further diagnostic workup and treatment of solitary pulmonary nodules (SPNs). CONCLUSION Information on the morphologic and hemodynamic characteristics of SPNs provided by dynamic helical CT, with high specificity and reasonably high accuracy, can be used for initial assessment. PET/CT is more sensitive at detecting malignancy than dynamic helical CT, and all malignant nodules may be potentially diagnosed as malignant by both techniques. Therefore, PET/CT may be selectively performed to characterize SPNs that show indeterminate results at dynamic helical CT.
Energy Absorption in Gold Nanoshells

A modeling study on energy absorption and transport in an isolated nanoshell and aggregates of nanoshells under localized surface plasma resonance (SPR) conditions is presented. A comprehensive model for multi-scattering of electromagnetic waves by a cluster of multilayered nanoshells is developed, which applies the Wigner-Eckart theorem for the calculation of the total scattering cross sessions of nanoshell aggregates. Absorption by an isolated nanoshell and by nanoshell clusters is studied using the model. Results show that the inter-nanoshell coupling results in strong field enhancement near the particle surface. Energy absorption in a nanoshell can be tuned by varying the structural parameters of the nanoshell. Smaller particles are more absorbing than the large ones, other conditions being equal. Because of the presence of a dielectric cavity, the radial distribution of the absorbed power in the metal shell may differ from the classical skin depth phenomena. The interaction among particles in close proximity causes the energy absorption efficiency and the resonance position of a nanoshell cluster to differ from those of an isolated nanoshell.
Similarity of phylogenetic trees as indicator of protein-protein interaction.

Deciphering the network of protein interactions that underlines cellular operations has become one of the main tasks of proteomics and computational biology. Recently, a set of bioinformatics approaches has emerged for the prediction of possible interactions by combining sequence and genomic information. Even though the initial results are very promising, the current methods are still far from perfect. We propose here a new way of discovering possible protein-protein interactions based on the comparison of the evolutionary distances between the sequences of the associated protein families, an idea based on previous observations of correspondence between the phylogenetic trees of associated proteins in systems such as ligands and receptors. Here, we extend the approach to different test sets, including the statistical evaluation of their capacity to predict protein interactions. To demonstrate the possibilities of the system to perform large-scale predictions of interactions, we present the application to a collection of more than 67 000 pairs of E.coli proteins, of which 2742 are predicted to correspond to interacting proteins.