Miracle-dz/UniFAR-FTUs huggingface dataset:
Coherent correction of inconsistent conditional probability assessments

In this paper we suggest a procedure to adjust an incoherent conditional probability assessment given on a partial domain. We look for a solution that tries to attain two separate goals: on one hand the solution should be as close as possible to the initial assessments, on the other hand we do not want to insert more information than we had at the beginning. The first goal is achieved by minimizing an appropriately defined distance among assessments, while for the second we look for a “maximum entropy” like solution.
Large-eddy Simulation of Wall-bounded Turbulent Flow with High-order Discrete Uni(cid:12)ed Gas-Kinetic Scheme

In this paper, we introduce the incompressible discrete Maxwellian equilibrium distribution function and external forces into the two-stage third-order Discrete Uni(cid:12)ed Gas-Kinetic Scheme (DUGKS) for simulating low-speed incompressible turbulent (cid:13)ows with forcing term. The Wall-Adapting Local Eddy-viscosity (WALE) and Vreman sub-grid models for Large-Eddy Simulations (LES) of wall-bounded turbulent (cid:13)ows are coupled within the present framework. In order to simulate the three-dimensional turbulent (cid:13)ows associated with great computational cost, a parallel implementation strategy for the present framework is developed, and is validated by three canonical wall-bounded turbulent (cid:13)ows, viz., the fully developed turbulent channel (cid:13)ow at a friction Reynolds number (Re) about 180, the turbulent plane Couette (cid:13)ow at a friction Re number about 93 and three-dimensional lid-driven cubical cavity (cid:13)ow at a Re number of 12000. The turbulence statistics are computed by the present approach with both WALE and Vreman models, and their predictions match precisely with each other. Especially, the predicted (cid:13)ow physics of three-dimensional lid-driven cavity are consistent with the description from abundant literatures. While, they have small discrepancies in comparison to the Direct Numerical Simulation (DNS) due to the relatively low grid resolution. The present numerical results verify that the present two-stage third-order DUGKS-based LES method is capable for simulating inhomogeneous wall-bounded turbulent (cid:13)ows and getting reliable results with relatively coarse grids.
Robustly Transitive Sets and Heterodimensional Cycles

— It is known that all non-hyperbolic robustly transitive sets have a dominated splitting and, generically, contain periodic points of different indices. We show that, for a C1 -dense open subset of diffeomorphisms the indices of periodicpoints in a robust transitive set Â form an interval in N. We also prove that the homoclinic classes of two periodic points in Â are robustly equal. Finally, we describe what sort of homoclinic tangencies may appear in Â by studying its dominated splittings.
University of Birmingham The mechanisms governing the activation of dislocation sources in aluminum at different strain rates

This article examines the time to activate Frank – Read sources in response to macroscopic strain rates ranging from 10 1 s (cid:1) 1 to 10 10 s (cid:1) 1 in aluminium under athermal conditions. We develop analytical models of the bowing of a pinned dislocation segment as well as nu- merical simulations of three dimensional dislocation dynamics. We find that the strain rate has a direct influence on both the activation time and the source strength of Frank – Read sources at strain rates up to 10 6 s (cid:1) 1 , and the source strength increases in almost direct proportion to the strain rate. This contributes to the increase in the yield stress of materials at these strain rates. Above 10 6 s (cid:1) 1 , the speed of the bowing segments reaches values that exceed the domain of validity of the linear viscous drag law, and the drag law is modified to account for inertial effects on the motion of the dislocation. As a result the activation times of Frank – Read sources reach a finite limit at strain rates greater than 10 8 s (cid:1) 1 , suggesting that Frank – Read sources are unable to operate before homogeneous nucleation relaxes elastic stresses at the higher strain rates of shock loading. Elastody- namic calculations are carried out to compare the contributions of Frank – Read sources and homogeneous nucleation of dislocations to plastic relaxation. We find that at strain rates of 5 (cid:3) 10 7 s (cid:1) 1 homogeneous nucleation becomes the dominant generation mechanism. & 2015 The Authors. Published by Elsevier Ltd. This is an open access article
Simultaneous quantification of N-2, NH3 and N2O emissions from a flooded paddy field under different N fertilization regimes

: Gaseous nitrogen (N) emissions, especially emissions of dinitrogen (N 2 ) 35 and ammonia (NH 3 ), have long been considered as the major pathways of N loss from 36 flooded rice paddies. However, no studies have simultaneously evaluated the overall 37 response of gaseous N losses to improved N fertilization practices due to the 38 difficulties to directly measure N 2 emissions from paddy soils. We simultaneously 39 quantified emissions of N 2 (using membrane inlet mass spectrometry), NH 3 and 40 nitrous oxide (N 2 O) from a flooded paddy field in southern China over an entire 41 rice-growing season. Our field experiment included three treatments: a control treatment (no N addition) and two N fertilizer (220 kg N ha −1 ) application methods, the traditional surface application of N fertilizer and the incorporation of N fertilizer 44 into the soil. Our results show that over the rice-growing season, the cumulative 45 gaseous N losses from the surface application treatment accounted for 13.5% (N 2 ), 19.1% (NH 3 ), 0.2% (N 2 O) and 32.8% (total gaseous N loss) of the applied N fertilizer. Compared with the surface application treatment, the incorporation of N fertilizer into the soil decreased the emissions of NH 3 , N 2 and N 2 O by 14.2%, 13.3% and 42.5%, respectively. Overall, the incorporation of N fertilizer into the soil significantly reduced the total gaseous N loss by 13.8%, improved the fertilizer N use efficiency by 51 14.4%, increased the rice yield by 13.9% and reduced the gaseous N loss intensity 52 (gaseous N loss/rice yield) by 24.3%. Our results indicate that the incorporation of N 53 fertilizer into the soil is an effective agricultural management practice in ensuring 54 food security and environmental sustainability in flooded paddy ecosystems. fertilization methods. Our study shows that about one-third of the applied fertilizer N is lost to the environment via gaseous pathways if the fertilizer is applied to the soil surface. The incorporation of N fertilizer into the soil decreased gaseous N emissions by 13.3–42.5% relative to surface application, while simultaneously improving rice yield and decreasing gaseous N loss intensity. Our results clearly show that the incorporation of N fertilizer into the soil is effective in increasing NUE and reducing environmental N losses from paddy rice ecosystems, and should therefore be widely adopted.
The local Propolis as protective and therapeutic modulator on some biochemical parameters in diabetic nephropathic rats

The aim of the present study was to investigate the effect of daily oral administration of local Ethanolic Extract of Propolis (EPP) on blood glucose, antioxidant defense system and kidney function in streptozotocin (STZ)-induced diabetic rats to show the ameliorating and partly curative effects in STZ-induced rats(60mg/kg) intrapretonial (i.p). Seventy five rats (150-160gm) were divided into 5 groups, normal rats, diabetic rats, normal treated with local EEP for 6 weeks, pretreated with local EEP for 3 weeks then induced diabetic in rats for 3 weeks and the last group, after 3 weeks(normal) induced diabetic in rats then post- treated with local EEP for 3 weeks. The dose of EEP 200mg/kg for the last three groups, and groups 2, 4 and 5 were induced diabetes in the same time at the end of the first 3 weeks.After 6 weeks , serum of samples were collected from anesthetic rats to determined the biochemical alterations.Antioxidant status in rats were estimated by determined the Glutathione(GSH) concentration, and Glutathion peroxidase (GPx) activity, and also measured renal function by the tests of Serum Urea and Creatinine concentrations, the result of this research indicated the effect of local EEP as protective or therapeutic in this experiment, the diabetic group showed decreased significantly(p<0.05) in body weight gain, increased(p<0.05) blood glucose, decreased significantly(p<0.05) activity of GPx and GSH concentration and increased significantly(p<0.05) serum Urea and Creatinine concentrations, as well as local EEP was moderated and effected significantly decrease(p<0.05) glucose level, Urea and Creatinine concentrations, increased significantly(p<0.05) activity of GPx and GSH concentration, as a result, it led to protect the kidney from damage by moderated their functions.
in Acutely ill and Recovered Pa- tients W ith Major Depressive Disorder and Matched Healthy Com parison Subjects a

Background: Modulation of nicotinic acetylcholine receptors (nAChRs), spe-cifically t hose c ontaining t he b 2 subunit, may be effective in treating patients with major depressive disorder. Using [ 123 I]5-I-A-85380 single photon emission computed tomography (SPECT), the authors studied the availability of b 2 -subunit-con-taining nAChRs ( b 2 *-nAChRs) in depressed patients. To understand its molecular basis, the authors also studied b 2 *-nAChR binding in postmortem brain samples from depressed subjects. M ethod: The participants were 23 med-ication-free, nonsmoking subjects with familial, early-onset depression (eight acutely ill and 15 recovered) and 23 age- and gender-matched nonsmoking comparison subjects. Each received one [ 123 I]5-I-A-85380 SPECT scan and an MRI scan. The availability of b 2 *-nAChRs was quantified as V T /f P . Postmortem analysis of b 2 *-nAChR binding was conducted with [ 123 I]5-I-A-85380 on prefrontal cortex samples from 14 depressed subjects and 14 age-matched comparison subjects. Results: The b 2 *-nAChR availability in both the acutely ill and recovered depressed subjects was significantly lower across all brain regions than in the respective comparison subjects, and it was lower in the acutely ill subjects than in those w ho w ere r ecovered. I n t he d epressed patients, b 2 *-nAChR
Evaluation of different turfgrass genotypes for growth and physiological parameters under the hilly zone of Karnataka

An investigation was carried out to evaluate different turfgrass genotypes for growth and physiological parameters under the hilly zone of Karnataka was carried out at College of Horticulture, Sirsi (UHS, Bagalkote) during the year 2019-20. Among different genotypes earliest to new growth appearance (6.00 days), longest stolon at 60 days after planting and longest root length (18.23 cm) was observed in Cynodon dactylon L . (STGC-4). Shortest leaf and highest chlorophyll content was recorded in Cynodon dactylon L (STGC-5). Highest number of leaves at 60 days after planting was recorded in Eremochloa ophiuroides . Higher number of roots per culm were recorded in Cynodon genotypes. Pennisetum clandestinum recorded highest shoot fresh and dry weight at complete stage of establishment. The Cynodon genotypes were found to be most suitable under the hill zone of Karnataka.
NAR Breakthrough Article The double PHD finger domain of MOZ/MYST3 induces a -helical structure of the histone H3 tail to facilitate acetylation and methylation sampling and modification

Histone tail modifications control many nuclear processes by dictating the dynamic exchange of regulatory proteins on chromatin. Here we report novel insights into histone H3 tail structure in complex with the double PHD finger (DPF) of the lysine acetyltransferase MOZ/ MYST3/KAT6A. In addition to sampling H3 and H4 modification status, we show that the DPF cooperates with the MYST domain to promote H3K9 and H3K14 acetylation, although not if H3K4 is trimethylated. Four crystal structures of an extended DPF alone and in complex with unmodified or acetylated forms of the H3 tail reveal the molecular basis of crosstalk between H3K4me3 and H3K14ac. We show for the first time that MOZ DPF induces a -helical conformation of H3K4-T11, revealing a unique mode of H3 recognition. The helical structure facilitates sampling of H3K4 methylation status, and proffers H3K9 and other residues for modification. Additionally, we show that a conserved double glycine hinge flanking the H3 tail helix is required for a conformational change enabling docking of H3K14ac with the DPF. In summary, our data provide the first observations of extensive helical structure in a histone tail, revealing the inherent ability of the H3 tail to adopt alternate conformations in complex with chromatin acetylation by MOZ regulates its occupancy on chromatin. PTM sampling by the MOZ DPF facilitates histone substrate selection for acetylation. Acetylation of H3K14 stabilizes residency of MOZ on chromatin, whereas acetylation of H4 by MOZ or other regulators is non-permissive for MOZ recruitment. Histone PTMs generated by other factors such as the MLL histone methyltransferase complex that catalyses H3K4 trimethylation, also impact on MOZ residency. Thus, chromatin modifying proteins generate ‘Hire’ and ‘Fire’ PTM signatures that regulate their interactions with chromatin.
Cross-Sectional Dating of Novel of and Indicate These Proviruses Originated in Africa before Homo sapiens

The human genome, human endogenous retroviruses (HERV), of which HERV-K113 and HERV-K115 are the only known full-length proviruses that are insertionally polymorphic. Although a handful of previously published papers have documented their prevalence in the global population; to date, there has been no report on their prevalence in the United States population. Here, we studied the geographic distribution of K113 and K115 among 156 HIV-1 þ subjects from the United States, including African Americans, Hispanics, and Caucasians. In the individuals studied, we found higher insertion frequencies of K113 (21%) and K115 (35%) in African Americans compared with Caucasians (K113 9% and K115 6%) within the United States. We also report the presence of three single nucleotide polymorphism sites in the K113 5 # long terminal repeats (LTRs) and four in the K115 5 # LTR that together constituted four haplotypes for K113 and ﬁve haplotypes for K115. HERV insertion times can be estimated from the sequence differences between the 5 # and 3 # LTR of each insertion, but this dating method cannot be used with HERV-K115. We developed a method to estimate insertion times by applying coalescent inference to 5 # LTR sequences within our study population and validated this approach using an independent estimate derived from the genetic distance between K113 5 # and 3 # LTR sequences. Using our method, we estimated the insertion dates of K113 and K115 to be a minimum of 800,000 and 1.1 million years ago, respectively. Both these insertion dates predate the emergence of anatomically modern Homo sapiens . of K115 is 2-fold lower in age-matched healthy controls compared with breast cancer patients. Moyes et al. (2005) suggested that the prevalence of K113 is increased in people with Sjorgen’s syndrome.
Accuracy of models of hmF2 used for long‐term trend analyses

One of the largest expected ionospheric effects of the increasing concentrations of greenhouse gases is a decrease in the height of the F2 region peak density, hmF2, by ∼20 km. Analyses of long‐term trends of hmF2 in historical data to confirm this change must rely on models of hmF2 based on a limited number of ionogram characteristics, because a full analysis of historical analog (pre–digital age) ionograms to derive the plasma frequency profiles and hmF2 was a tedious and usually rare procedure. This paper discusses the accuracy of three models/formulas of hmF2 that have been used for long‐term trend studies, namely (1) the simple parabolic model, which sets hmF2 equal to the ionogram virtual height at 0.834 foF2, (2) the Dudeney (1974, 1983) model, and (3) the Bilitza et al. (1979) model. The models have been validated using ionograms calculated from plasma frequency profiles given by the International Reference Ionosphere (IRI). The best model would be the one with the smallest seasonal and solar cycle variations in the errors, even if it has a systematic error. Analysis of the errors (relative to the IRI) in the three models shows that all three are useful, but at different times of day.
DETECTION AND CONFIRMATION OF PLASMID MEDIATED ANTIBIOTIC RESISTANCE AND RESTRICTION ENZYME ANALYSIS OF PLASMIDS EXTRACTED FROM β-LACTAMASE PRODUCING UROPATHOGENS

Extended spectrum β-lactamases (ESBL) are functionally defined as β-lactamases that are able to hydrolyze extended-spectrum cephalosporins (ceftazidime or cefotaxime) and monobactams (aztreonam) and, are inhibited by β-lactamase inhibitors, such as clavulanic acid, whereas they cannot hydrolyze cephamycins (cefoxitin or cefotetan) or carbapenems (imipenem or meropenem) efficiently. ESBLs can arise as a point mutation in bla TEM gene, however, a number of these enzymes are recently found to be encoded by plasmid mediated resistance mechanisms that allow increased spread of antibiotic resistance through efficient plasmid transfer. In the current study, plasmid mediated antibiotic resistance was confirmed by PCR amplification of resistant genes from extracted plasmids and plasmid loss studies carried out on 167 ESBL producing uropathogens. Restriction digestion analysis of plasmids from ESBL producer’s using EcoRI, BamHI and HindIII revealed similar band patterns in most of the E.coli and K.pneumoniae isolates indicating their clonal relatedness whereas P.aeruginosa revealed different band patterns indicating clonal un-relatedness and more than one source of origin for spread of antibiotic resistance. Conjugation and transformation studies revealed both intra as well as inter-species plasmid transfer indicating ease of transfer of antibiotic resistance. Our study hence gives an insight into the growing problem of antibiotic resistance and an urgent need for efficient control practices and prevention of such outbreaks.
Nme SI Restriction-Modiﬁcation System Identiﬁed by Representational Difference Analysis of a Hypervirulent Neisseria meningitidis Strain

Neisseria meningitidis is a gram-negative bacterium that may cause meningitis, sepsis, or both. The increase in the incidence of meningococcal disease in various countries in the past 2 decades is mainly due the genotypically related lineage III meningococci. The chromosomal DNA differences between lineage III strains and non-lineage III strains were identiﬁed using representational difference analysis. Thus, a 1.8-kb locus that is speciﬁc for lineage III meningococci was identiﬁed. The locus contains three open reading frames encoding the Nme SI restriction-modiﬁcation system. The methyltransferase gene was cloned and expressed in Esche- richia coli . Site AGTACT was found to be modiﬁed by the enzyme. In conclusion, lineage III strains differ from endemic strains by the presence of a speciﬁc restriction-modiﬁcation system. This restriction-modiﬁcation system may contribute to the clonal and hypervirulent character of lineage III strains by inﬂuencing horizontal gene transfer and transcription.
Surface and Mechanical Properties of Different Dental Composites

Due to the unlimited revolution in dental composites technology, a wide variety of materials are available in the market. Materials’ selection is therefore a challenge and requires proper analysis of material properties. This study investigated the compressive, flexure, hardness and surface roughness of six commercially available dental composites (Filtek Z250 and 350 XT and P90, Tetric-N-Ceram and Tetric-N-Ceram Bulk Fill and IPS Impress Direct). The results showed that the highest strength and modulus (compressive and flexure) was observed for Filtek Z250 and 350XT. All tested composites showed bottom/ top hardness ratios above the minimum acceptable level (0.8) and surface roughness below the minimum acceptable level (0.2m) except Filtek P90. Accordingly, for high stress bearing applications, the materials of choice would be Filtek Z250 and Z350 XT. For low stress-bearing applications, IPS Empress and Tetric N-Ceram would be materials of choice. With P90 composites, high plaque accumulations would be expected. investigate the compressive and flexure properties as well as surface hardness, hardness ratio (as an of bottom to top conversion ratio) and roughness of six different commercially available dental composites having different
ANALYSIS OF LONGITUDINAL BINARY DATA: AN APPLICATION TO A DISEASE PROCESS

The analysis of longitudinal binary data can be undertaken using any of the three families of models namely, marginal, random effects and conditional models. Each family of models has its own respective merits and demerits. The models are applied in the analysis of binary longitudinal data for childhood disease data namely the Respiratory Syncytial Virus (RSV) data collected from a study in Kilifi, coastal Kenya. The marginal model was fitted using generalized estimating equations (GEE). The random effects models were fitted using ‘Proc GLIMMIX’ and ‘NLMIXED’ in SAS and then again in Genstat. Because the data is a state transition type of data with the Markovian property the conditional model was used to capture the dependence of the current response to the previous response which is known as the history. The data set has two main complicating issues. Firstly, there is the question of developing a stochastically based probability model for the disease process. In the current work we use direct likelihood and generalized linear modelling (GLM) approaches to estimate important disease parameters. The force of infection and the recovery rate are the key parameters of interest. The findings of the current work are consistent and in agreement with those in White et al. (2003). The aspect of time dependence on the RSV disease is also highlighted in the thesis by fitting monthly piecewise models for both parameters. Secondly, there is the issue of incomplete data in the analysis of longitudinal data. Commonly used methods to analyze incomplete longitudinal data include the well known available case analysis (AC) and last observation carried forward (LOCF). However, these methods rely on strong assumptions such as missing completely at random (MCAR) for AC analysis and unchanging profile after dropout for LOCF analysis. Such assumptions are too strong to generally hold. In recent years, methods
Nearby Supernova Factory : Calibration of SNIFS data and spectrophotometric Type Ia supernovae light curves.

Type Ia supernovae (SNe Ia) are one of the pillars of modern observational cosmology, since they are good standard candles for distance measurements in the universe. The cosmological analysis using SNe Ia requires the observation of both high and low-redshift objects, and the smaller statistic of events on the latter case represents a major source of uncertainties. This thesis takes place within the SNfactory project, which aims to study nearby (0.03 An extraction pipeline of the differential photometric ratios between nights, needed for the flux calibration of the spectra, was built. The systematic errors affecting these ratios are estimated to be below 2%, and spectrophotometric light curves of standard stars show a 5% photometric precision of the full flux calibration on non-photometric conditions. The obtained nearby Hubble diagram presents a smaller residual scatter than the one made using currently available data. A K-correction free cosmological fit shows an additional reduction of 5% on the scatter, until now undistinguishable from the SNe Ia "intrinsic dispersion".