Miracle-dz/UniFAR-FTUs huggingface dataset:
The dynamics and flexibility of protein disulphide-isomerase (PDI): predictions of experimentally-observed domain motions

We have studied the mobility of the folding catalyst, protein disulphide-isomerase (PDI), by molecular dynamics and by a rapid approach based on flexibility. We analysed our simulations using measures of backbone movement, relative positions and orientations of domains, and distances between functional sites. Despite their different assumptions, the two methods are surprisingly consistent. Both methods agree that motion of domains is dominated by hinge and rotation motion of the a and a' domains relative to the central b-b' domain core. We identify the a' domain as showing the greatest intra-domain mobility. The flexibility method, which requires 10 4-fold less computer power, predicts 2 additional large-scale features of inter-domain motion that have been observed experimentally. We conclude that the methods offer complementary insight into the motion of this large protein and provide detailed structural models that characterise its functionally-significant conformational changes. • Flexibility of yeast PDI has been explored by MD and a new rapid all-atom approach • Both methods highlight PDI's capacity for notable inter-domain (twist/tilt) motion 3 • The rapid method predicts experimentally-observed extreme domain reorientations • Used in synergy, the methods can simulate fully the flexibility of large proteins 4
Opioid Prescription Is Associated With Increased Survival in Older Adult Patients With Pancreatic Cancer in the United States: A Propensity Score Analysis

PURPOSE: Few studies have assessed the interaction between pain treatment and mortality in pancreatic cancer. The aim of this study was to investigate the association between receipt of opioid prescriptions and survival in adults with pancreatic cancer. METHODS: The SEER-Medicare linked database was used to identify patients diagnosed with late-stage pancreatic cancer between 2007 and 2015. Kaplan-Meier models were used to assess the association between opioid prescriptions in the year after cancer diagnosis and survival. Cox proportional hazard models were used to determine the association between opioid receipt and survival, adjusting for propensity score and other relevant confounders including cancer-directed therapies and palliative care referral. RESULTS: A total of 5,770 older adults with pancreatic cancer were identified; 1,678 (29.1%) were prescribed opioids for at least 60 days. Median survival was increased in those with opioid prescriptions (6.0 months) compared with those without (4.0 months, P < .0001). After adjustment for confounders, opioid prescriptions were still associated with improved survival (hazard ratio 0.80; 95% CI, 0.75 to 0.86). On multivariable analysis, opioid prescriptions were associated with older age, female sex, residing in nonmetro areas, and treatment with celiac plexus neurolysis, chemotherapy, and radiation. CONCLUSION: Receipt of opioid prescriptions is associated with longer survival in patients with pancreatic cancer. This may be due to the impact of cancer-related pain, although further studies are needed to better understand the interaction between pain management, cancer-directed therapies, and systemic factors, such as palliative care, availability of opioids, and clinical practice culture.
A Model for Delivery of Orthopaedic Perioperative Education via Telehealth

With orthopaedic surgery, there is a risk of poor outcomes such as pain, decreased mobility, and decreased function, particularly if patients do not receive adequate preoperative and postoperative orthopaedic education. Healthcare education delivered via telehealth can be individualized to the patient's specific situation and health literacy level and is accessible, convenient, and timely for patients and providers. The purpose of this article is to combine two models of best practice, the EDUCATE model of patient education and Bashshur's Taxonomy of Telehealth, to describe a framework for improving delivery of preoperative and postoperative orthopaedic education. This innovative model presents a patient-centered approach to orthopaedic education that can increase patient comprehension and retention and address health literacy, through consideration of three dimensions essential for effective telehealth programs: functionality, application, and technology. Applications of the model are presented.
Identi�cation of hub genes and potential drugs in hepatocellular carcinoma through integrated bioinformatics analysis

Background Hepatocellular carcinoma (HCC) is the third cancer-related cause of death in the world. Until now, the involved mechanisms during the development of HCC are largely unknown. This study aims to explore the driven-genes and potential drugs in HCC. Methods Three mRNA expression datasets were used to analyze the differentially expressed genes (DEGs) in HCC. The bioinformatics approaches include identi�cation of DEGs and hub genes, GO terms analysis and KEGG enrichment analysis, construction of protein–protein interaction network. The expression levels of hub genes were validated based on TCGA, GEPIA and the Human Protein Atlas. Moreover, overall survival and disease-free survival analysis of the hub genes were further conducted by Kaplan-Meier plotter and the GEPIA. DGIdb database was performed to search the candidate drugs for HCC.
Night eating syndrome – characterization

The definition of the Polish National Food and Nutrition Institute indicates that proper human nutrition should completely satisfy the body's needs for energy as well as provide all nutrients needed for the development of life and preservation of health. This article is devoted to the relatively recently described issue, pertaining to eating disorders, that is night eating syndrome (NES). Nowadays, food has become a tool used for improving one’s well-being, which has contributed to an increase in the frequency of eating disorders and lifestyle diseases such as obesity. Night eating syndrome is important in the pathogenesis of obesity and for this reason, in the near future, it may become an important problem in public health. Night eating syndrome can be a difficult disorder to diagnose. Identification may be hindered by the lack of a unified definition, lack of coherent diagnostic criteria or diagnostic method, and problems with classification, which contributes to difficulties in fully understanding the disorder. Introduction The definition of the Polish National Food and Nutrition Institute indicates that proper human nutrition should completely satisfy the body's needs for energy as well as provide all nutrients needed for the development of life and preservation of health. This means that proper nutrition is of fundamental importance in our lives. A diet lacking in some ingredients, poor absorption, or poor digestion of foods can lead to malnutrition, becoming underweight,
Development of a multiplex PCR test-system for detection of BHV-1, BVDV, Chlamydia spp. and Mycoplasma spp.

This study describes development of a multiplex PCR assay for detection of BHV-1, BVDV, Chlamydia spp. and Mycoplasma spp. infections in bovines. The assay was developed using genomic DNA and RNA and four sets of PCR primers targeting 16S rRNA genes of Chlamydia spp. , Mycoplasma spp. , 5’-UTR of Bovine viral diarrhea virus, gE of Bovine herpesvirus-1, respectively. A total of 100 tissue samples were collected from cattle suspected to be infected with the viral and bacterial pathogens (BVDV, BHV-1, Chlamydia spp. and Mycoplasma spp.) from different regions of Ukraine. A part of sample was stored at –50°C for isolation of genomic DNA and RNA. The multiplex PCR assay was optimized in the study. The specific primers designed and used in the study were found sensitive and specific in amplifying target genes viz. 16S rRNA, gE, 5’-UTR of Chlamydia spp. , Mycoplasma spp. , BHV-1 and BVDV, respectively. The PCR primers used in the optimization of multiplex PCR assay for detection of Bovine viral diarrhea virus, Bovine herpesvirus-1, Chlamydia spp. , Mycolasma spp. could amplify 221 bp, 111 bp, 386 bp, 279 bp products, respectively. Non specific amplification was not observed
Gauged supergravities and the physics of extra dimensions

This thesis analyses gauged supergravities in various dimensions and their possible origin from compactifications of string theory. In the effective description the fluxes appear in the theory as deformation parameters generating a potential for the scalar fields. Physics after compactification is only sensitive to the orbits of the global symmetry group, in that gaugings lying in the same orbit are related by duality transformations. Given a certain gauged supergravity containing non-geometric fluxes, we discuss in dimension seven and higher whether there exists a duality transformation that rotates them away and, for those cases in which this is not possible, we give an interpretation as compactifications of Double Field Theory (DFT). Focusing then on our better understanding of geometric flux compactifications, we analyse further in this thesis a class of compactifications down to four dimensions which are compatible with half-maximal supersymmetry (orientifold compactifications) and discuss their embedding in maximal supergravity in the limit of vanishing local sources.
Adjusting Positions of Vehicle Parts based on Rules for Unknown Drivers

—This paper describes an inference engine used in a system and semantic representation for the system which automatically adjusts the positions of vehicle parts based on rules. The inference engine has rules stored in a knowledge base, which describe the relation between the position of the vehicle part and the driver’s body size. The inference engine receives the driver’s body sizes in real time, and ﬁnds a rule associated with the input values by matching a pattern between them. According to the value deﬁned in the rule, the position of the vehicle part is changed automatically. This rule is automatically modiﬁed by learning the relation between the driver’s preferred position and body size. The number of selected rules and reasoning time are selected as performance indicators of the inference engine. Also, an ontology is designed to share the development results with others. Automated vehicle parts control system can be used as a method that improves the driver’s satisfaction by automatically recommending the driver’s preferred position in an environment where many unknown people use the same vehicle like a shared car or a rental car.
Cerebral MR spectroscopy and patient-reported men- tal health outcomes in hepatitis C genotype 1 naïve patients treated with ledipasvir and sofosbuvir

miological, clinical, and antiviral efficacy data for children aged 1-5 years is very scarce. Methods: We collected detailed data of the epidemiological and clinical characteristics of 256 children aged 1-5 years with HCV infection during the period when they were hospitalized in our unit. Antiviral therapy with conventional interferon-α plus ribavirin was administered to 162 children with HCV RNA-positive chronic hepatitis C, and the efficacy was evaluated from the sustained virologic response (SVR) and side effects. Results: The median age of the 256 children was 2.7 years, and 165 (64.5%) were male. Ninety-three (36.3%, 93/256) HCV-infected children exhibited spontaneous clearance of HCV infection. Serum HCV RNA positivity with a mean level of 4.6 log10 IU/mL was observed in the remaining 63.7% (163/256) children, and HCV 1b and 2a were identified in 42% and 58% of the 133 genotype-determined cases. The favorable IL-28B rs12979860 CC and rs8099917 TT genotypes accounted for 88.7% and 90.3% cases, respectively. The levels of alanine and aspartate aminotransferases correlated positively with the HCV RNA levels (r = 0.43 and 0.38, respectively; p < 0.001 for both), and 100% had normal total bilirubin and albumin levels and prothrombin time activity. G1 histological inflammation and S1 fibrosis were seen in majority of the liver biopsy specimens of 219 children (79.9% and 60.7%, respectively). Overall, 97.5% (158/162) children achieved SVR at both 12 and 24 weeks after the cessation of therapy; the side effects were mild and the cost was low. Adherence was found to be an independently predictive factor associated with both SVR and viral breakthrough. Conclusions: This study fills the gap in the epidemiological and clinical features of iatrogenic HCV infection in children aged 1–5 years and shows that conventional interferon-α plus ribavirin therapy is the most cost-effective means of managing such patients, and earlier antiviral treatment can achieve the best efficacy for these patients. Shi-Shu Zhu, Qing-Lei Zeng, and Yi Dong contributed equally to this study. Correspondence to: Prof Fu-Sheng Wang, Research Center for Biological Therapy, fswang302@163.com, or Hong-Fei Zhang, Treatment and Research Center for Children’s Liver Disease, bjzhhf@aliyun. com, both in Beijing 302 Hospital, No. 100, the 4th Western Ring Middle Road, Beijing 100039, China.
Molecular and Genetic Evidence for the Key Role of AtCaM3 in Heat-Shock Signal Transduction in Arabidopsis

Heat shock (HS) is a common form of stress suffered by plants. It has been proposed that calmodulin (CaM) is involved in HS signal transduction, but direct evidence has been lacking. To investigate the potential regulatory function of CaM in the HS signal transduction pathway, T-DNA knockout mutants for AtCaM2, AtCaM3, and AtCaM4 were obtained and their thermotolerance tested. Of the three knockout mutant plants, there were no differences compared with wild-type plants under normal conditions. However, the AtCaM3 knockout mutant showed a clear reduction in thermotolerance after heat treatment at 45 C for 50 min. Overexpression of AtCaM3 in either the AtCaM3 knockout or wild-type background significantly rescued or increased the thermotolerance, respectively. Results from electrophoretic mobility-shift assays, real-time quantitative reverse transcription-polymerase chain reaction, and western-blot analyses revealed that, after HS, the DNA-binding activity of HS transcription factors, mRNA transcription of HS protein genes, and accumulation of HS protein were downregulated in the AtCaM3 knockout mutant and up-regulated in the AtCaM3-overexpressing transgenic lines. Taken together, these results suggest that endogenous AtCaM3 is a key component in the Ca-CaM HS signal transduction pathway.
Technical Report VICKEY: Mining Conditional Keys on RDF datasets

A conditional key is a key constraint that holds under certain circum-stances – such as “the given name and the family name uniquely identify the members of the European parliament”. In this paper, we show how such keys can be mined automatically on large knowledge bases (KBs). For this, we combine techniques from key mining with techniques from rule mining. We show that our method can scale to KBs of millions of facts. We also show that the conditional keys we mine can improve the quality of entity linking by up to 47 percentage points
for “Bayesian Ising Graphical Model for Variable Selection”

where aj = x T j y is considered as the signal. The coefficient κj’s represent how much shrinkage is placed on the initial estimation of βj’s. κj → 0, yields no shrinkage, and κj → 1 yields near-total shrinkage. With this definition of κj, it is easy to derive the density function of κj, p(κj). In the following discussions, we assume φ = 1. This is equivalent to say that y, aj’s and b are scaled by √ φ, respectively. The marginal odds for γj = 1 given b is calculated as
OP-PCPJ130190 1..12

Genome-wide single nucleotide polymorphism (SNP) analysis is a promising tool to examine the genetic diversity of rice populations and genetic traits of scientific and economic importance. Next-generation sequencing technology has accelerated the re-sequencing of diverse rice varieties and the discovery of genome-wide SNPs. Notably, validation of these SNPs by a high-throughput genotyping system, such as an SNP array, could provide a manageable and highly accurate SNP set. To enhance the potential utility of genome-wide SNPs for geneticists and breeders, analysis tools need to be developed. Here, we constructed an SNP haplotype database, which allows visualization of the allele frequency of all SNPs in the genome browser. We calculated the allele frequencies of 3,334 SNPs in 76 accessions from the world rice collection and 3,252 SNPs in 177 Japanese rice accessions; all these SNPs have been validated in our previous studies. The SNP haplotypes were defined by the allele frequency in each cultivar group (aus, indica, tropical japonica and temperate japonica) for the world rice accessions, and in non-irrigated and three irrigated groups (three variety registration periods) for Japanese rice accessions. We also developed web tools for finding polymorphic SNPs between any two rice accessions and for the primer design to develop cleaved amplified polymorphic sequence markers at any SNP. The ‘HapRice’ database and the web tools can be accessed at http://qtaro.abr. affrc.go. jp/index.html. In addition, we established a core SNP set consisting of 768 SNPs uniformly distributed in the rice genome; this set is of a practically appropriate size for use in rice genetic analysis.
Kinematic and dynamic patterns of human gait reference data for young women walking at low, preferred and high speeds

The purpose of this study was to presents reference data concerning gait speed for angular, kinematic and dynamic temporal and spatial parameters in patterns of groud reaction forces, knee joint moments of force and powers during a wide range of walking speeds of young womens. For the purpose of the study, comprehensive measurements and descriptive statistics were used to describe dynamic and kinematic variables at each walking speed tested. The tree walking velocities levels (low, preferred and high) were selected as the research objectives. The results showed that along with the increase in walking speed, the values of the analysed parameters also increase.
NBER WORKING PAPER SERIES GETTING INSIDE THE “BLACK BOX” OF HEAD START QUALITY: WHAT MATTERS AND WHAT DOESN’T?

Critics of Head Start contend that many programs spend too much money on programs extraneous to education. On the other hand, Head Start advocates argue that severely disadvantaged children need a broad range of services. Given the available evidence, it has been impossible to assess the validity of these claims. In this study, we match detailed administrative data with data on child outcomes from the National Longitudinal Survey of Youth 1979, including test scores, behavior problems, and grade repetition. We find that former Head Start children have higher reading scores and are less likely to have been retained in grade where Head Start spending was higher. Holding per capita expenditures constant, children in programs that devoted higher shares of their budgets to education and health have fewer behavior problems and are less likely to have been retained in grade. However, when we examine specific educational inputs holding per capita expenditures constant, only pupil/teacher ratios matter. Janet Currie Department of Economics UCLA 405 Hilgard Avenua Los Angeles, CA 90095-1477 and NBER currie@simba.sscnet. ucla.edu Matthew Neidell Department of Economics and CISES University of Chicago 5734 S. Ellis Avenue Chicago, IL 60637 mneidell@uchicago.edu 1 Authors’ calculations based on the 2000 Head Start Fact Sheet at http://www.acf. hhs.gov/programs/hsb/research/factsheets/00_hsfs. htm, and statistics on the number of children less than 6 in poverty at http://ferret.bls. census.gov/macro/032001/pov/new01_003. htm. 2 See Currie (2001), Barnett (1995) and Karoly et al. (1998) for reviews.
Robert, Hélène S and Grunewald, Wim and Sauer, Michael and Cannoot, Bernard and Soriano, Mercedes and Swarup, Ranjan and Weijers, Dolf and Bennett, Malcolm J. and Boutilier, Kim and Friml,

The plant hormone auxin and its directional transport are known to play a crucial role in defining the embryonic axis and subsequent development of the body plan. Although the role of the PIN auxin efflux transporters has been clearly assigned during embryonic shoot and root specification, the role of the auxin influx carriers, AUX1 and AUX1-LIKE (LAX) proteins, is not well established so far. Here we used chemical and genetic tools on Brassica napus microspore-derived embryos and Arabidopsis thaliana zygotic embryos, and demonstrate that AUX1, LAX1 and LAX2 are required for both shoot and root pole formation, in concert with the PIN efflux carriers. Furthermore, we uncovered a positive feedback loop between MONOPTEROS/ARF5-dependent auxin signalling and auxin transport. This MONOPTEROS-dependent transcriptional regulation of auxin influx (AUX1, LAX1 and LAX2) and auxin efflux (PIN1 and PIN4) carriers by MONOPTEROS helps to maintain proper auxin transport to the root tip. These results indicate that auxin-dependent cell specification during embryo development requires balanced auxin transport involving both influx and efflux mechanisms, and that this transport is maintained by a positive transcriptional feedback on auxin signalling.
Analysis of Possible Triggering Mechanisms of Severe Thunderstorms in the Tropical Central Andes of Peru,

The aim of the present study is to analyze the triggering mechanisms of three thunderstorms (TSs) associated with severe rainfall, hail and lightening in the tropical central Andes of Peru, specifically above the Huancayo observatory (12.04◦ S, 75.32◦ W, 3313 m a.s.l.) located in the Mantaro valley during the spring-summer season (2015–2016). For this purpose, we used a set of in-situ pluviometric observations, satellite remote sensing data, the Compact Meteorological Ka-Band Cloud Radar (MIRA-35C), the Boundary Layer Tropospheric Radar and downscaling model simulations with the Weather Research and Forecasting (WRF) Model (resolutions: 18 km, 6 km and 2 km), and the Advance Regional Prediction System (ARPS) (resolution: 0.5 km) models in order to analyze the dynamic of the atmosphere in the synoptic, meso and local scales processes that control the occurrence of the three TS events. The results show that at synoptic scale, the TSs are characterized by the southern displacement of the South-east Pacific Subtropical Anticyclone up to latitudes higher than 35◦ S, by the weakening and south-eastern displacement of the Bolivian high–North east low system and by the intrusion of westerly winds along the west side of the central Andes at upper and medium levels of the atmosphere. At meso-scale, apparently, two important moisture fluxes from opposite directions are filtered through the passes along the Andes: one from the north-west and the other from the south-east directions converge and trigger the deep convection into the Mantaro valley. These moisture fluxes are generated by the intrusion of the sea-breeze from the Pacific ocean along the west of the Andes coupling with upper and middle westerly winds and by the thermally induced moisture fluxes coming from the South American low level jet at the east side of the Andes. At the local scale, there is a low-level conditional instability in the previous hours as well as during the occurrence of the TSs above the Huancayo observatory. In addition, the simulation results indicated the possibility of generation of inertial gravity waves in the Amazon basin, associated with geostrophic adjustment which transports energy and moisture into the central Andes plateau and consequently intensifies the thunderstorms above the Mantaro valley.