nils-herrmann/clean_scirepeval huggingface dataset:
Frequent Occurrence of Tomato Leaf Curl New Delhi Virus in Cotton Leaf Curl Disease Affected Cotton in Pakistan
Venue: PloS one

Cotton leaf curl disease (CLCuD) is the major biotic constraint to cotton production on the Indian subcontinent, and is caused by monopartite begomoviruses accompanied by a specific DNA satellite, Cotton leaf curl Multan betasatellite (CLCuMB) Since the breakdown of resistance against CLCuD in 2001/2002, only one virus, the "Burewala" strain of Cotton leaf curl Kokhran virus (CLCuKoV Bur) and a recombinant form of CLCuMB have consistently been identified in cotton across the major cotton growing areas of Pakistan. Unusually a bipartite isolate of the begomovirus Tomato leaf curl virus was identified in CLCuD affected cotton recently. In the study described here we isolated the bipartite begomovirus Tomato leaf curl New Delhi virus (ToLCNDV) from CLCuD affected cotton. To assess the frequency and geographic occurrence of ToLCNDV in cotton, CLCuD symptomatic cotton plants were collected from across the Punjab and Sindh provinces between 2013 and 2015. Analysis of the plants by diagnostic PCR showed the presence of CLCuKoV Bur in all 31 plants examined and ToLCNDV in 20 of the samples. Additionally, a quantitative real time PCR analysis of the levels of the two viruses in co infected plants suggests that coinfection of ToLCNDV with the CLCuKoV Bur/CLCuMB complex leads to an increase in the levels of CLCuMB, which encodes the major pathogenicity (symptom) determinant of the complex. The significance of these results are discussed.
The Cross Section of Expected Returns on Penny Stocks: Are Low Hanging Fruits Not So Sweet?

In this paper, we study the determinants of expected returns on the listed penny stocks from two perspectives. Traditionally financial economics literature has been devoted to study the macro and micro determinants of expected returns on stocks (Subrahmanyam, 2010) Very few research has been carried out on penny stocks (Liu, Rhee, Zhang, 2011; Nofsinger Verma, 2014) Our study is an effort to contribute more empirical evidence on penny stocks in the emerging market context. We see the return dynamics of penny stocks from corporate governance perspective. Issues such as shareholding patters are considered to be of much significance when it comes to understand the price movements. Using cross sectional data on 167 penny stocks listed in the National Stock Exchange of India, we show that (i) Returns of portfolio of lower market cap penny stocks are significantly different(higher) than that of higher market cap penny stocks. (ii)Returns of portfolio lower P/E stocks are significantly different (higher) than that of higher P/E stocks. Similarly, returns of portfolio of lower P/B stocks are significantly different (higher) than that of higher P/B stocks, and returns of portfolio of lower priced penny stocks are significantly different(higher) than that of higher priced penny stocks. (iii) Trading volume differences due to alphabetism are insignificant. (iv)Differences in returns of portfolios based on beta and shareholding patterns are insignificant.
Down regulation of a signaling mediator in association with lowered plasma arachidonic acid levels in individuals with autism spectrum disorders
Venue: Neuroscience Letters

Previous studies have indicated that the altered composition of polyunsaturated fatty acids (PUFAs) might contribute to the pathophysiology of autism spectrum disorder (ASD) We examined the relationship between the plasma fatty acid levels, expressed as mg/ml, and the plasma levels of biomarkers of AA related signaling mediators, such as ceruloplasmin, transferrin and superoxide dismutase, and assessed the behavioral symptoms of 30 individuals with ASD (mean age, 13.6 4.3 years old) compared with 20 age and gender matched normal controls (mean age, 13.2 5.4 years old) using Aberrant Behavior Checklists (ABC) The plasma levels of EPA and the plasma ratios of EPA/AA were significantly higher, while the plasma levels of AA and metabolites, such as 5,8,11,14 eicosatetraenoic acid, adrenic acid, and ceruloplasmin (Cp) were significantly lower in the 30 individuals with ASD compared with the 20 normal controls. The ABC scores were significantly increased in the ASD group compared with those of the control group. Thus, the results of the present study revealed that reduced plasma levels of AA and metabolites in association with high plasma EPA/AA ratios might down regulate AA related signaling mediators, such as Cp. Subsequently, reduced plasma Cp levels might reduce the protective capacity for brain damage, resulting in the pathophysiology underlying the behavioral symptoms in individuals with ASD. These findings suggest that reduced plasma AA levels may downregulate Cp.
On the application of higher order symplectic integrators in Hamiltonian Monte Carlo

We explore the construction of new symplectic numerical integration schemes to be used in Hamiltonian Monte Carlo and study their efficiency. Two integration schemes from Blanes et al. (2014) and a new scheme based on optimal acceptance probability, are considered as candidates to the commonly used leapfrog method. All integration schemes are tested within the framework of the No U Turn sampler (NUTS) both for a logistic regression model and a student $t$ model. The results show that the leapfrog method is inferior to all the new methods both in terms of asymptotic expected acceptance probability for a model problem and the and efficient sample size per computing time for the realistic models.
Robust Online Model Predictive Control for a Constrained Image Based Visual Servoing
Venue: IEEE Transactions on Industrial Electronics

This paper presents an online image based visual servoing (IBVS) controller for a 6 degrees of freedom (DOF) robotic system based on the robust model predictive control (RMPC) method. The controller is designed considering the robotic visual servoing system's input and output constraints, such as robot physical limitations and visibility constraints. The proposed IBVS controller avoids the inverse of the image Jacobian matrix and hence can solve the intractable problems for the classical IBVS controller, such as large displacements between the initial and the desired positions of the camera. To verify the effectiveness of the proposed algorithm, real time experimental results on a 6 DOF robot manipulator with eye in hand configuration are presented and discussed.
Associations of Extrinsic and Intrinsic Components of Work Stress with Health: A Systematic Review of Evidence on the Effort Reward Imbalance Model
Venue: International journal of environmental research and public health

Mainstream psychological stress theory claims that it is important to include information on people's ways of coping with work stress when assessing the impact of stressful psychosocial work environments on health. Yet, some widely used respective theoretical models focus exclusively on extrinsic factors. The model of effort reward imbalance (ERI) differs from them as it explicitly combines information on extrinsic and intrinsic factors in studying workers' health. As a growing number of studies used the ERI model in recent past, we conducted a systematic review of available evidence, with a special focus on the distinct contribution of its intrinsic component, the coping pattern "over commitment" towards explaining health. Moreover, we explore whether the interaction of intrinsic and extrinsic components exceeds the size of effects on health attributable to single components. Results based on 51 reports document an independent explanatory role of "over commitment" in explaining workers' health in a majority of studies. However, support in favour of the interaction hypothesis is limited and requires further exploration. In conclusion, the findings of this review support the usefulness of a work stress model that combines extrinsic and intrinsic components in terms of scientific explanation and of designing more comprehensive worksite stress prevention programs.
High Brightness Solid State Lasers for Compact Short Wavelength Sources

Various types of compact short wavelength sources are emerging in the region from EUV to hard X ray and further to gamma ray. These high energy photons are usually accessible in a large scale facility such as SR or FEL, and the compactness of these new technologies provides new possibilities for broader applications in dedicated laborato ries or factories. Laser produced plasma is used for soft X ray laser and high average power EUV sources for lithography. Laser Compton short wavelength sources are now entering into practical applications in medical imaging. The performance of these sources critically depends on the laser driver performance. This chapter describes the recent progress of high brightness, short pulse solid state laser technology in close relation to these new compact short wavelength sources. Pulsed picosecond thin disc laser progress is reviewed with kW average power specifications. Cryogenic laser is reported for the advantage of higher beam quality in large pulse energy operation.
Cryogenic nanosecond and picosecond high average and peak power (HAPP) pump lasers for ultrafast applications

Using cryogenic laser technology, it is now possible to design and demonstrate lasers that have concomitant high average and peak powers, with near diffraction limited beam quality. We refer to these new laser systems as HAPP lasers. In this paper, we review important laser crystal materials properties at cryogenic temperature, with an emphasis on Yb lasers, and discuss the important design considerations, including the laser induced damage threshold, nonlinear effects and thermal effects. A comprehensive model is presented to describe diode pulsed pumping with arbitrary duration and repetition rate, and is used with the Frantz Nodvik equation to describe, to first order, the performance of HAPP laser systems. A computer code with representative results is also described.
High energy diode pumped solid state laser development at the Central Laser Facility
Venue: SPIE Photonics Europe

In this paper we review the development of high energy, nanosecond pulsed diode pumped solid state lasers within the Central Laser Facility (CLF) based on cryogenic gas cooled multi slab ceramic Yb:YAG amplifier technology. To date two 10J scale systems, the DiPOLE prototype amplifier and an improved DIPOLE10 system, have been developed, and most recently a larger scale system, DiPOLE100, designed to produce 100 J pulses at up to 10 Hz. These systems have demonstrated amplification of 10 ns duration pulses at 1030 nm to energies in excess of 10 J at 10 Hz pulse repetition rate, and over 100 J at 1 Hz, with optical to optical conversion efficiencies of up to 27% We present an overview of the cryo amplifier concept and compare the design features of these three systems, including details of the amplifier designs, gain media, diode pump lasers and the cryogenic gas cooling systems. The most recent performance results from the three systems are presented along with future plans for high energy DPSSL development within the CLF.
Laser cooling in solids: advances and prospects.
Venue: Reports on progress in physics. Physical Society

This review discusses the progress and ongoing efforts in optical refrigeration. Optical refrigeration is a process in which phonons are removed from a solid by anti Stokes fluorescence. The review first summarizes the history of optical refrigeration, noting the success in cooling rare earth doped solids to cryogenic temperatures. It then examines in detail a four level model of rare earth based optical refrigeration. This model elucidates the essential roles that the various material parameters, such as the spacing of the energy levels and the radiative quantum efficiency, play in the process of optical refrigeration. The review then describes the experimental techniques for cryogenic optical refrigeration of rare earth doped solids employing non resonant and resonant optical cavities. It then examines the work on laser cooling of semiconductors, emphasizing the differences between optical refrigeration of semiconductors and rare earth doped solids and the new challenges and advantages of semiconductors. It then describes the significant experimental results including the observed optical refrigeration of CdS nanostructures. The review concludes by discussing the engineering challenges to the development of practical optical refrigerators, and the potential advantages and uses of these refrigerators.
DESIGN, DEVELOPMENT AND CHARACTERIZATION OF MUCOADHESIVE GASTRO SPHERES OF CARVEDILOL

The purpose of this study was to design mucoadhesive gastro spheres of carvedilol targeting to upper GIT, and optimize it in terms of its entrapment efficiency and drug release. A 3 2 full factorial design was employed to study the effect of independent variables like sodium alginate and sodium carboxyl methyl cellulose on entrapment efficiency and in vitro drug release.  Mucoadhesive gastro spheres were prepared by Orifice Ionic gelation method, in which drug is uniformly distributed in the polymer solution so drug can be loaded easily in the polymer.3 2 full factorial designs were used to study the effect of process variables on formulation characteristics by applying statistical analysis.  FTIR, XRD and DSC analyses apparently did not indicate any interaction of the drug with the polymers. However, the drug content, drug entrapment efficiency and morphology of the gastro spheres were found to be influenced by the method of preparation, composition of gastro spheres as well as exposure to the cross linking agent. In vitro drug release study showed that drug release can be modified by varying drug to polymer ratio. The release rate was found to be decreased in accordance with the increase in the ratio of polymer used.  From the study, we successfully developed carvedilol gastro spheres by using mucoadhesive polymer like SCMC and rate retardant sodium alginate polymer.
Crystal structure of glycogen debranching enzyme and insights into its catalysis and disease causing mutations
Venue: Nature communications

Glycogen is a branched glucose polymer and serves as an important energy store. Its debranching is a critical step in its mobilization. In animals and fungi, the 170 kDa glycogen debranching enzyme (GDE) catalyses this reaction. GDE deficiencies in humans are associated with severe diseases collectively termed glycogen storage disease type III (GSDIII) We report crystal structures of GDE and its complex with oligosaccharides, and structure guided mutagenesis and biochemical studies to assess the structural observations. These studies reveal that distinct domains in GDE catalyse sequential reactions in glycogen debranching, the mechanism of their catalysis and highly specific substrate recognition. The unique tertiary structure of GDE provides additional contacts to glycogen besides its active sites, and our biochemical experiments indicate that they mediate its recruitment to glycogen and regulate its activity. Combining the understanding of the GDE catalysis and functional characterizations of its disease causing mutations provides molecular insights into GSDIII.
CD44 and RHAMM are essential for rapid growth of bladder cancer driven by loss of Glycogen Debranching Enzyme (AGL)
Venue: BMC Cancer

BackgroundLoss of Amylo alpha 1 6 glucosidase 4 alpha glucanotransferase (AGL) drives rapid proliferation of bladder cancer cells by upregulating Hyaluronic acid(HA) Synthase (HAS2) mediated HA synthesis. However the role of HA receptors CD44 and Hyaluronan Mediated Motility Receptor (RHAMM) in regulating the growth of bladder cancer cells driven by loss of AGL has not been studied.MethodsWestern blot analysis and Terminal deoxynucleotidyl transferase (TdT) dUTP Nick End Labeling (TUNEL) assay was carried out to study cellular apoptosis with HAS2, CD44 and RHAMM loss in bladder cancer cells with and without AGL expression. Proliferation and softagar assays were carried out to study cellular anchorage dependent and independent growth. Clinicopathologic analysis was carried out on bladder cancer patient datasets.ResultsHigher amounts of cleaved Cas3, Cas9 and PARP was observed in AGL low bladder cancer cell with loss of HAS2, CD44 or RHAMM. TUNEL staining showed more apoptotic cells with loss of HAS2, CD44 or RHAMM in AGL low bladder cancer cells. This revealed that bladder cancer cells whose aggressive growth is mediated by loss of AGL are susceptible to apoptosis with loss of HAS2, CD44 or RHAMM. Interestingly loss of either CD44 or RHAMM induces apoptosis in different low AGL expressing bladder cancer cell lines. Growth assays showed that loss of CD44 and RHAMM predominantly inhibit anchorage dependent and independent growth of AGL low bladder cancer cells. Clinicopathologic analysis revealed that high RHAMM mRNA expression is a marker of poor patient outcome in bladder cancer and patients with high RHAMM and low AGL tumor mRNA expression have poor survival.ConclusionOur findings strongly point to the importance of the HAS2 HA CD44/RHAMM pathway for rapid growth of bladder cancer cells with loss of AGL and provides rational for targeting this pathway at various steps for "personalized" treatment of bladder cancer patients based of their AGL expression status.
Transmission characteristics of CRLH rectangular waveguides constructed by the cutoff modes of TM and TE waves
Venue: 2016 International Conference on Electromagnetics in Advanced Applications (ICEAA)

Composite right/left handed (CRLH) rectangular waveguides has been proposed. In the waveguides, negative permeability is realized by the cutoff TM11 mode, of which electromagnetic field distribution is similar to that of a coaxial line TEM mode. On the other hand, negative permittivity is realized by the cutoff TE mode in the waveguides divided into 4 sections by an H shaped conductor partition. It is verified from the dispersion diagram and the transmission characteristics that the proposed guides successfully possess the left handed nature.
Quality of Health Services and Patients' Satisfaction in Accredited and Non Accredited Hospitals

The majority of hospitals follow voluntary or mandatory accreditation standards; these standards are widely believed to improve the quality of hospital services (QHS) and thereby increase patient satisfaction (PS) The current descriptive comparative study explored patients' opinions and beliefs with regard to QHS and PS at accredited and non accredited Jordanian public hospitals in 2016. Data of discharged patients were collected using a structured questionnaire; 250 patients from four hospitals participated (response rate: 83% SPSS v.15 was used calculate mean values, standard deviations, and Pearson's correlation coefficient, and to conduct t tests. Patients indicated medium levels of QHS and PS in both accredited and non accredited hospitals; additionally, QHS and PS were significantly correlated (p 0.05) in both types of hospitals. These results suggest that QHS and PS require improvement in all Jordanian public hospitals; future research should identify causal relationships between implementing accreditation standards and patient satisfaction.
Graph Based Compression of Dynamic 3D Point Cloud Sequences
Venue: IEEE Transactions on Image Processing

This paper addresses the problem of compression of 3D point cloud sequences that are characterized by moving 3D positions and color attributes. As temporally successive point cloud frames share some similarities, motion estimation is key to effective compression of these sequences. It, however, remains a challenging problem as the point cloud frames have varying numbers of points without explicit correspondence information. We represent the time varying geometry of these sequences with a set of graphs, and consider 3D positions and color attributes of the point clouds as signals on the vertices of the graphs. We then cast motion estimation as a feature matching problem between successive graphs. The motion is estimated on a sparse set of representative vertices using new spectral graph wavelet descriptors. A dense motion field is eventually interpolated by solving a graph based regularization problem. The estimated motion is finally used for removing the temporal redundancy in the predictive coding of the 3D positions and the color characteristics of the point cloud sequences. Experimental results demonstrate that our method is able to accurately estimate the motion between consecutive frames. Moreover, motion estimation is shown to bring a significant improvement in terms of the overall compression performance of the sequence. To the best of our knowledge, this is the first paper that exploits both the spatial correlation inside each frame (through the graph) and the temporal correlation between the frames (through the motion estimation) to compress the color and the geometry of 3D point cloud sequences in an efficient way.
Climate change is the primary driver of white tailed deer (Odocoileus virginianus) range expansion at the northern extent of its range; land use is secondary
Venue: Ecology and evolution

Quantifying the relative influence of multiple mechanisms driving recent range expansion of non native species is essential for predicting future changes and for informing adaptation and management plans to protect native species. White tailed deer (Odocoileus virginianus) have been expanding their range into the North American boreal forest over the last half of the 20th century. This has already altered predator prey dynamics in Alberta, Canada, where the distribution likely reaches the northern extent of its continuous range. Although current white tailed deer distribution is explained by both climate and human land use, the influence each factor had on the observed range expansion would depend on the spatial and temporal pattern of these changes. Our objective was to quantify the relative importance of land use and climate change as drivers of white tailed deer range expansion and to predict decadal changes in white tailed deer distribution in northern Alberta for the first half of the 21st century. An existing species distribution model was used to predict past decadal distributions of white tailed deer which were validated using independent data. The effects of climate and land use change were isolated by comparing predictions under theoretical "no change between decades" scenarios, for each factor, to predictions under observed climate and land use change. Climate changes led to more than 88% by area, of the increases in probability of white tailed deer presence across all decades. The distribution is predicted to extend 100 km further north across the northeastern Alberta boreal forest as climate continues to change over the first half of the 21st century.
Active exploration in parameterized reinforcement learning
Venue: ArXiv

Online model free reinforcement learning (RL) methods with continuous actions are playing a prominent role when dealing with real world applications such as Robotics. However, when confronted to non stationary environments, these methods crucially rely on an exploration exploitation trade off which is rarely dynamically and automatically adjusted to changes in the environment. Here we propose an active exploration algorithm for RL in structured (parameterized) continuous action space. This framework deals with a set of discrete actions, each of which is parameterized with continuous variables. Discrete exploration is controlled through a Boltzmann softmax function with an inverse temperature \beta$ parameter. In parallel, a Gaussian exploration is applied to the continuous action parameters. We apply a meta learning algorithm based on the comparison between variations of short term and long term reward running averages to simultaneously tune \beta$ and the width of the Gaussian distribution from which continuous action parameters are drawn. When applied to a simple virtual human robot interaction task, we show that this algorithm outperforms continuous parameterized RL both without active exploration and with active exploration based on uncertainty variations measured by a Kalman Q learning algorithm.