Miracle-dz/UniFAR-FTUs huggingface dataset:
The MC@NLO 3.4 Event Generator

This is the user's manual of MC@NLO 3.4. This package is a practical implementation, based upon the HERWIG event generator, of the MC@NLO formalism, which allows one to incorporate NLO QCD matrix elements consistently into a parton shower framework. Processes available in this version include the hadroproduction of single vector and Higgs bosons, vector boson pairs, heavy quark pairs, single top, single top in association with a W, lepton pairs, and Higgs bosons in association with a W or Z. Spin correlations are included for all processes except ZZ and WZ production. This document is self-contained, but we emphasise the main differences with respect to previous versions.
Prevalence, Enterotoxin Gene and Antimicrobial Resistance of Staphylococcus aureus and Methicillin-Resistant Staphylococcus aureus from Clinical Healthy Dairy Cows

Received: Revised: Accepted: Published online: April 08, 2015 February 11, 2016 February 12, 2016 March 30, 2016 Coagulasepositive Staphylococcus aureus (CPS) is a leading cause of both clinical and subclinical bovine mastitis. Moreover, methicillinresistant Staphylococcus aureus (MRSA) have been identified as an emerging mastitis pathogen in dairy cows. In our study, 121 raw milk samples were collected from individual clinical healthy cows from five commercial farms. 52 samples (42.98%) were positively detected as CPS. Fifty-two strains of CPS were isolated and identified using phenotypic and molecular approaches. Their coagulase gene (coa gene) amplification showed a single amplicon of a size between 600 and 1000 bp. Five CPS isolated strains from YZ farm, which was resistant to oxacillin and contained a specific 310-bp for the mecA gene, were identified as MRSA. The staphylococcal enterotoxin a (SEa) gene was detected in 18 strains. None of the isolates carried the gene SEb, SEc, SEd and SEe. All isolates including the five MRSA isolates were uniformly susceptible to Cephalothin (KF), Ofloxacin (OFX) and Vancomycin hydrochloride (VA) at minimum inhibitory concentrations (MIC). Besides P and CIP, the resistance of these isolates resistances to Oxacillin (OX), rifampicin (RIF), Cefotaxime (CTX), Azithromycin (AZM) and Clindamycin (DA) were relatively low (<20%). Together, our findings demonstrated that there was high prevalence of CPS and ten MRSA contaminations in raw milk from clinical healthy cows. ©2016 PVJ. All rights reserved
Study of Hydraulic Disturbances From Single-Unit Load Rejection in a Pumped-Storage Hydropower Station With a Shared Water Delivery System

The transient characteristics of load rejection process in pumped-storage hydropower (PSH) stations have a close relation to the safety of electric power system and hydraulic facilities. A large portion of PSHs consist of multiple units sharing one tunnel (MUSOT). In this paper, a three-dimensional numerical simulation method for hydraulic disturbance caused by single unit load rejection transition process based on the volume of fluid (VOF) two phase flow model was proposed and a filed test was carried out in a PSH station with a two units sharing one tunnel (TUSOT) setting. The power output from the unit that operates in normal condition (UNC), the pressure fluctuations of the spiral casing inlet and tailrace tunnel outlet, the water level variation and flow pattern in surge tank were obtained through the numerical simulation and field test. The results showed that the highest and lowest water level in surge tank from the numerical method agreed well with the measured data obtained in the field test. The guide vanes closing law of the unit that runs in load rejection (ULR) mainly impacts on the variation of the above parameters. To reduce the influence of single-load load-rejection hydraulic disturbance, a more elaborate guide vanes adjustment scheme of the UNC should be proposed in the next step to avoid large short-time fluctuations in the power output and pressure.
Photodynamic Therapy Using Topical Methyl Aminolevulinate vs Surgeryfor Nodular Basal Cell Carcinoma: Results of a Multicenter Randomized Prospective Trial

Results: Data from 97 patients (105 lesions) were included in the 3-month per-protocol analysis. Complete response rates did not differ significantly between groups (51/52 [98%] lesions with surgery vs 48/53 [91%] lesions with methyl aminolevulinate PDT; difference [95% confidence interval], 4.8% (−3.4% to 13.0%]; P=.25). At 12 months, tumor-free rates were 50 (96%) of 52 lesions with surgery vs 44 (83%) of 53 with methyl aminolevulinate PDT (P=.15). More patients treated with methyl aminolevulinate PDT than surgery had an excellent or good cosmetic outcome at all time points (significant at 12 and 24 months on patient assessment, P .05, and at 3, 12, and 24 months on investigator evaluation, P .001). At 24 months, 5 lesions that had initially cleared with methyl aminolevulinate PDT had recurred, compared with 1 after surgery.
An End-to-End-Based Low Dimensional Binary Embedding for Chrysanthemum Phenotypic Petal Similarity Evaluation

Plant phenotyping is widely used to identify the genotype differences and the environmental conditions of plants. These pieces of information can be gathered by various sensors conveniently and easily. The similarity evaluation of phenotypic data is essential for category classifications and stress sensitivity analysis of plants. Chrysanthemum is a flower with great varieties and petal types. The similarity evaluation of chrysanthemum flowers plays a key role in the phenotypic research. For improving the performance and effectiveness of phenotypic similarity evaluation of high-throughput chrysanthemum flower images, this paper proposes an end-to-end based low dimensional binary embedding framework by using deep learning and hash encoding approaches. Within this framework, compact binary codes are learned by deep convolutional neural networks. Firstly, features of chrysanthemum images are extracted by deep neural networks, then a binary layer is embedded for converting the features into lower dimensional bit codes. Finally, the phenotypic similarity of the chrysanthemum flower is evaluated in Hamming space with the binary codes. Extensive experiments are conducted and the results show that the performance and effectiveness of similarity evaluations are improved greatly. In summary, our research provides an end-to-end pipeline for the similarity evaluation of chrysanthemum petal phenotypes, and the proposed method is practically applicable to the high-throughput similarity evaluation. The proposed method can be used as a foundation for the in-depth research on chrysanthemum flower petals as well.
PREVALENCE AND CHARACTERIZATION OF ASPERGILLUS SPP. FROM RICE GRAINS IN SOUTH INDIA

Rice is one of the most important staple foods in Asian and African countries. It is prone to many pre and post-harvest biotic stresses. The rice samples are associated with a number of storage fungi like Aspergillus, Rhizopus, Fusarium, Curvularia and Penicillium species. Therefore, identification of fungi associated with discoloured rice grains and their characterization is needed. Hence, morphological characterization was carried out to identify toxigenic and non-toxigenic species of Aspergilli. The present study indicated that the dominant colonies included parrot green (A. flavus, 40%), black (A. niger, 30%), olive green (A. parasiticus, 9%) and yellow (A. ochraceus, 7%) coloured along with some other coloured colonies/ species. Among the four media tested, CY20S favoured luxurious growth whereas suppressed and slow growth of the fungi was observed on CZ medium, but provided additional clues on the identity of Aspergilli species. These systematic data on macroscopic and microscopic characters of the isolates were compared with each other and also with neo type cultures of Aspergillus species obtained from Mycological Type Culture Centre (MTCC), Chandigarh. These two sets of data were compared to arrive at and confirm the identity of the fungus isolated from discoloured rice grains. From all these data, it was concluded that the parrot green colonies were A. flavus (with few A. flavus var. columnaris and A. fumigatus), olive green colonies were A. parasiticus, some of the black colonies were A. niger, A. aculeatus A. carbonarius and yellow colonies were A. ochraceus species.
Cytomegalovirus Infection and Pneumonitis: Impact after Isolated Lung Transplantation

Using aggressive surveillance of blood, bronchoalveolar lavage (BAL) fluid, and lung tissue, we sought to determine the incidence of cytomegalovirus (CMV) pneumonitis in isolated lung transplant recipients and to characterize its impact on pulmonary function, chronic rejection, and survival. Forty-six lung transplant recipients who survived greater than 30 days had prospective documentation of CMV infection in blood and BAL fluid and regular surveillance with transbronchial lung biopsy. CMV infection was documented in 92% of patients who were D−/R+, D+/R+, or D+/R−, and the incidence of historically confirmed CMV pneumonitis among these patients was 75%. No D−/R− patient experienced CMV infection or disease. D+/R− patients experienced more frequent and severe episodes, and ganciclovir prophylaxis during the first 2 wk was not useful. CMV pneumonitis was accompanied by detectable radiographic changes in less than one third of cases. The detection of CMV in BAL fluid was not predictive of CMV pneumonitis on.
Functional Plant Biology

Identification of an orthologous clade of peroxidases that respond to feeding by greenbugs (Schizaphis graminum) in C4 grasses Erin D. Scully, Teresa Donze-Reiner, Haichuan Wang, Thomas E. Eickhoff, Frederick Baxendale, Paul Twigg, Frank Kovacs, Tiffany Heng-Moss, Scott E. Sattler and Gautam Sarath 1134–1148 For a plant to persist in saline soil, leaves should accumulate sodium and chloride to high concentrations, thus allowing energy-efficient osmotic adjustment. Adverse effects of these ions must be avoided, a situation known as ‘tissue tolerance’. This viewpoint considers the concept of tissue tolerance and how to measure it, to identify useful genetic variation that can be harnessed for plant breeding.
Finite Element Modeling of Stator Winding Faults in Permanent Magnet Synchronous Motor: Part II

Stator Winding Faults (SWFs) in Permanent Magnet Synchronous Motors (PMSMs) adversely affect the performance of the machine. The machine quantities in terms of stator phase currents, back-EMF, magnetic flux density and flux lines changes significantly. This paper shall investigate in detail the adverse affect on different electrical and magnetic quantities during the SWFs in PMSM. Earlier in Part I, the authors have modeled the machine using analytical approach to draw the inferences on the performance of PMSM during healthy and faulty conditions. This paper shall discuss in detail about the validation of those results with the outcomes obtained through Finite Element (FE) modeling of PMSM using Maxwell 2D tool. FE modeling of PMSM involves Numerical Method (NM) approach which though takes high computational time but deliver better accuracy. FE model of PMSM with an emulation of different SWFs viz. Stator Inter-turn Fault (SITF), coil-to-coil fault and phase-to-phase faults are developed. The performance of the machine is then compared under healthy and faulty conditions. The performance deductions are further analyzed and compared with the analytical outcomes thereby giving a validation of SWFs in PMSM. The significant outcomes like changes in phase currents, back-EMF and magnetic flux density, thus encountered are further used to define fault index for the detection and identification of SWFs in PMSM.
L O ] 2 3 A ug 2 01 0 A Generic Scheme for Qualified Logic Programming ⋆ Technical Report SIC-108

Uncertainty in Logic Programming has been investigated since about 25 years, publishing papers dealing with various approaches to semantics and different applications. This report is intended as a first step towards the investigation of qualified computations in Constraint Functional Logic Programming, including uncertain computations as a particular case. We revise an early proposal, namely van Emden’s Quantitative Logic Programming [24], and we improve it in two ways. Firstly, we generalize van Emden’s QLP to a generic scheme QLP (D) parameterized by any given Qualification Domain D, which must be a lattice satisfying certain natural axioms. We present several interesting instances for D, one of which corresponds to van Emden’s QLP . Secondly, we generalize van Emden’s results by providing stronger ones, concerning both semantics and goal solving. We present Qualified SLD Resolution over D, a sound and strongly complete goal solving procedure for QLP (D), which is applicable to open goals and can be efficiently implemented using CLP technology over any constraint domain CD able to deal with qualification constraints over D. We have developed a prototype implementation of some instances of the QLP (D) scheme (including van Emden’s QLP ) on top of the CFLP system T OY .
Sleep Spindle-dependent Functional Connectivity Correlates with Cognitive Abilities

Abstract EEG studies have shown that interindividual differences in the electrophysiological properties of sleep spindles (e.g., density, amplitude, duration) are highly correlated with trait-like “reasoning” abilities (i.e., “fluid intelligence”; problem-solving skills; the ability to employ logic or identify complex patterns), but not interindividual differences in STM or “verbal” intellectual abilities. Previous simultaneous EEG-fMRI studies revealed brain activations time-locked to spindles. Our group has recently demonstrated that the extent of activation in a subset of these regions was related to interindividual differences in reasoning intellectual abilities, specifically. However, spindles reflect communication between spatially distant and functionally distinct brain areas. The functional communication among brain regions related to spindles and their relationship to reasoning abilities have yet to be investigated. Using simultaneous EEG-fMRI sleep recordings and psychophysiological interaction analysis, we identified spindle-related functional communication among brain regions in the thalamo-cortical-BG system, the salience network, and the default mode network. Furthermore, the extent of the functional connectivity of the cortical–striatal circuitry and the thalamo-cortical circuitry was specifically related to reasoning abilities but was unrelated to STM or verbal abilities, thus suggesting that individuals with higher fluid intelligence have stronger functional coupling among these brain areas during spontaneous spindle events. This may serve as a first step in further understanding the function of sleep spindles and the brain network functional communication, which support the capacity for fluid intelligence.
Translating Systems Medicine Into Clinical Practice: Examples From Pulmonary Medicine With Genetic Disorders, Infections, Inflammations, Cancer Genesis, and Treatment Implication of Molecular Alterations in Non-small-cell Lung Cancers and Personalized Medicine

Non-small-cell lung cancers (NSCLC) represent 85% of all lung cancers, with adenocarcinoma as the most common subtype. Since the 2000's, the discovery of molecular alterations including epidermal growth factor receptor (EGFR) mutations and anaplastic lymphoma kinase (ALK) rearrangements together with the development of specific tyrosine kinase inhibitors (TKIs) has facilitated the development of personalized medicine in the management of this disease. This review focuses on the biology of molecular alterations in NSCLC as well as the diagnostic tools and therapeutic alternatives available for each targetable alteration. Rapid and sensitive methods are essential to detect gene alterations, using tumor tissue biopsies or liquid biopsies. Massive parallel sequencing or Next Generation Sequencing (NGS) allows to simultaneously analyze numerous genes from relatively low amounts of DNA. The detection of oncogenic fusions can be conducted using fluorescence in situ hybridization, reverse-transcription polymerase chain reaction, immunohistochemistry, or NGS. EGFR mutations, ALK and ROS1 rearrangements, MET (MET proto-oncogenereceptor tyrosine kinase), BRAF (B-Raf proto-oncogen serine/threonine kinase), NTRK (neurotrophic tropomyosin receptor kinase), and RET (ret proto-oncogene) alterations are described with their respective TKIs, either already authorized or still in development. We have herein paid particular attention to the mechanisms of resistance to EGFR and ALK-TKI. As a wealth of diagnostic tools and personalized treatments are currently under development, a close collaboration between molecular biologists, pathologists, and oncologists is crucial.
Developmental Roles of AUX1/LAX Auxin Influx Carriers in Plants

Plant hormone auxin regulates several aspects of plant growth and development. Auxin is predominantly synthesized in the shoot apex and developing leaf primordia and from there it is transported to the target tissues e.g. roots. Auxin transport is polar in nature and is carrier-mediated. AUXIN1/LIKE-AUX1 (AUX1/LAX) family members are the major auxin influx carriers whereas PIN-FORMED (PIN) family and some members of the P-GLYCOPROTEIN/ATP-BINDING CASSETTE B4 (PGP/ABCB) family are major auxin efflux carriers. AUX1/LAX auxin influx carriers are multi-membrane spanning transmembrane proteins sharing similarity to amino acid permeases. Mutations in AUX1/LAX genes result in auxin related developmental defects and have been implicated in regulating key plant processes including root and lateral root development, root gravitropism, root hair development, vascular patterning, seed germination, apical hook formation, leaf morphogenesis, phyllotactic patterning, female gametophyte development and embryo development. Recently AUX1 has also been implicated in regulating plant responses to abiotic stresses. This review summarizes our current understanding of the developmental roles of AUX1/LAX gene family and will also briefly discuss the modelling approaches that are providing new insight into the role of auxin transport in plant development.
The Cotton GhWRKY91 Transcription Factor Mediates Leaf Senescence and Responses to Drought Stress in Transgenic Arabidopsis thaliana

WRKY transcription factors (TFs) play essential roles in the plant response to leaf senescence and abiotic stress. However, the WRKY TFs involved in leaf senescence and stress tolerance in cotton (Gossypium hirsutum L.) are still largely unknown. In this study, a WRKY gene, GhWRKY91, was isolated and thoroughly characterized. Transcriptional activity assays showed that GhWRKY91 could activate transcription in yeast. The expression pattern of GhWRKY91 during leaf senescence, and in response to abscisic acid (ABA) and drought stress was evaluated. β-Glucuronidase (GUS) activity driven by the GhWRKY91 promoter in transgenic Arabidopsis was reduced upon exposure to ABA and drought treatments. Constitutive expression of GhWRKY91 in Arabidopsis delayed natural leaf senescence. GhWRKY91 transgenic plants exhibited increased drought tolerance and presented delayed drought-induced leaf senescence, as accompanied by reinforced expression of stress-related genes and attenuated expression of senescence-associated genes (SAGs). Yeast one-hybrid (Y1H) assays and electrophoretic mobility shift assays (EMSAs) revealed that GhWRKY91 directly targets GhWRKY17, a gene associated with ABA signals and reactive oxygen species (ROS) production. A transient dual-luciferase reporter assay demonstrated that GhWRKY91 activated the expression of GhWRKY17. Our results suggest that GhWRKY91 might negatively regulate natural and stress-induced leaf senescence and provide a foundation for further functional studies on leaf senescence and the stress response in cotton.
A ug 2 01 0 Group Variable Selection via a Hierarchical Lasso and Its Oracle Property Nengfeng Zhou Consumer Credit Risk Solutions Bank of America Charlotte , NC 28255

In many engineering and scientific applications, prediction variables are grouped, for example, in biological applications where assayed genes or proteins can be grouped by biological roles or biological pathways. Common statistical analysis methods such as ANOVA, factor analysis, and functional modeling with basis sets also exhibit natural variable groupings. Existing successful group variable selection methods such as Antoniadis and Fan (2001), Yuan and Lin (2006) and Zhao, Rocha and Yu (2009) have the limitation of selecting variables in an “all-in-all-out” fashion, i.e., when one variable in a group is selected, all other variables in the same group are also selected. In many real problems, however, we may want to keep the flexibility of selecting variables within a group, such as in gene-set selection. In this paper, we develop a new group variable selection method that not only removes unimportant groups effectively, but also keeps the flexibility of selecting variables within a group. We also show that the new method offers the potential for achieving the theoretical “oracle” property as in Fan and Li (2001) and Fan and Peng (2004).
The Biotic and Abiotic Carbon Monoxide Formation During Aerobic Co-digestion of Dairy Cattle Manure With Green Waste and Sawdust

Carbon monoxide (CO), an air pollutant and a toxic gas to humans, can be generated during aerobic digestion of organic waste. CO is produced due to thermochemical processes, and also produced or consumed by cohorts of methanogenic, acetogenic, or sulfate-reducing bacteria. The exact mechanisms of biotic and abiotic formation of CO in aerobic digestion (particularly the effects of process temperature) are still not known. This study aimed to determine the temporal variation in CO concentrations during the aerobic digestion as a function of process temperature and activity of microorganisms. All experiments were conducted in controlled temperature reactors using homogeneous materials. The lab-scale tests with sterilized and non-sterilized mix of green waste, dairy cattle manure, sawdust (1:1:1 mass ratio) were carried out for 1 week at 10, 25, 30, 37, 40, 50, 60, 70°C to elucidate the biotic vs. abiotic effect. Gas concentrations of CO, O2, and CO2 inside the reactor were measured every 12 h. The CO concentrations observed for up to 30°C did not exceed 100 ppm v/v. For 50 and 60°C, significantly (p < 0.05) higher CO concentrations, reaching almost 600 ppm v/v, were observed. The regression analyses showed in both cases (sterile and non-sterile) a statistically significant effect (p < 0.05) of temperature on CO concentration, confirming that the increase in temperature causes an increase in CO concentration. The remaining factors (time, O2, and CO2 content) were not statistically significant (p > 0.05). A new polynomial model describing the effect of temperature, O2, and CO2 concentration on CO production during aerobic digestion of organic waste was formulated. It has been found that the proposed model for sterile variant had a better fit (R2 = 0.86) compared with non-sterile (R2 = 0.71). The model predicts CO emissions and could be considered for composting process optimization. The developed model could be further developed and useful for ambient air quality and occupational exposure to CO.