Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparative Transcriptomic Analysis of Rectal Tissue from Beef Steers Revealed Reduced Host Immunity in Escherichia coli O 157 : H 7 Super-Shedders

Super-shedder cattle are a major disseminator of E. coliO157:H7 into the environment, and the terminal rectum has been proposed as the primary E. coliO157:H7 colonization site. This study aimed to identify host factors that are associated with the super-shedding process by comparing transcriptomic profiles in rectal tissue collected from 5 super-shedder cattle and 4 non-shedder cattle using RNA-Seq. In total, 17,859 ± 354 genes and 399 ± 16 miRNAs were detected, and 11,773 genes were expressed in all animals. Fifty-eight differentially expressed (DE) genes (false discovery rate < 0.05) including 11 up-regulated and 47 down-regulated (log 2 (fold change) ranged from -5.5 to 4.2), and 2 up-regulated DE miRNAs (log 2 (fold change) = 2.1 and 2.5, respectively) were identified in super-shedders compared to non-shedders. Functional analysis of DE genes revealed that 31 down-regulated genes were potentially associated with reduced innate and adaptive immune functions in super-shedders, including 13 lymphocytes membrane receptors, 3 transcription factors and 5 cytokines, suggesting the decreased key host immune functions in the rectal tissue of super-shedders, including decreased quantity and migration of immune cells such as lymphocytes, neutrophils and dendritic cells. The up-regulation of bta-miR-29d-3p and the down regulation of its predicted target gene, regulator of G-protein signaling 13, suggested a potential regulatory role of this miRNA in decreased migration of lymphocytes in supershedders. Based on these findings, the rectal tissue of super-shedders may inherently exhibit less effective innate and adaptive immune protection. Further study is required to confirm if such effect on host immunity is due to the nature of the host itself or due to actions mediated by E. coliO157:H7. PLOS ONE | DOI:10.1371/journal.pone.0151284 March 9, 2016 1 / 19 OPEN ACCESS Citation:Wang O, Liang G, McAllister TA, Plastow G, Stanford K, Selinger B, et al. (2016) Comparative Transcriptomic Analysis of Rectal Tissue from Beef Steers Revealed Reduced Host Immunity in Escherichia coli O157:H7 Super-Shedders. PLoS ONE 11(3): e0151284. doi:10.1371/journal. pone.0151284 Editor: Firas H Kobeissy, University of Florida, UNITED STATES Received: September 2, 2015 Accepted: February 25, 2016 Published: March 9, 2016 Copyright: © 2016 Wang et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Data Availability Statement: The RNA-Seq and miRNA-Seq data are available at NCBI Gene Expression Omnibus (GEO) database under accession number GSE67099 and GSE74627, respectively. Funding: This work was supported by Alberta Innovates Bio Solutions (http://bio.albertainnovates. ca; Project Number: FSC-12-017) to TAM, GP, KS, BS, and LLG.
Breaking Free from the Shackles of Embeddedness and Venturing into Exploration of Technology Domains

Extant literature explains that collaborations exert positive effects on innovation output, but relational embeddedness hinders exploration of technology domains. This paper hypothesized that knowledge diversity and access to a leading firm’s resources positively moderate the negative effect of relational embeddedness on exploration. Longitudinal data on patenting activity of 3,372 inventors in the Danish pharmaceutical industry from 1979 to 2016 is used to test the hypotheses. Results support hypotheses and show that some deeply embedded inventors can explore technology domains successfully whereas others in similar position cannot. A complementary analysis shows that knowledge diversity improves both exploration and exploitation, as well as that access to a leading firm’s resources contributes to exploration of remote technology domains, but not to exploration in less distant domains. Breaking Free from the Shackles of Embeddedness and Venturing into Exploration of Technology Domains
GENETIC DIVERSITY IN PEA GERMPLASM USING RANDOMLY AMPLIFIED POLYMORPHIC DNA MARKERS

Selection of the genotypes using plasmid assisted technology provides an efficient and useful tool for elaborating genetic relationships among genotypes. In present study, 48 Pea (Pisum sativum var sativum L.) genotypes obtained from different sources were analyzed through 20 RAPD, DNA markers for assessment of intraspecific DNA variations. Results revealed that significant variations were present in minor bands. Major bands also showed significant diversity. Considerable variations were also recorded in density of some common bands. Maximum and minimum genetic diversity i.e., 80% and 20% was found among 08 and 23 comparisons, respectively from banding profile. These variations can be used further for enhancing variability, a prerequisite for crop breeding. Phylogenetic clustering (through dendrogram analysis) of genotypes revealed that genetic diversity is independent of origin of genotypes. Forty eight genotypes of pea clustered in three main groups A, B and C comprising 23, 5 and 20 genotypes, respectively. Group A1 and C1 included the most distantly related genotypes and hence can be recommended for breeding to obtain genetically diverse segregating populations.
WP / 1 9 / 150 International Fiscal-financial Spillovers : The Effect of Fiscal Shocks on Cross-border Bank Lending by

This paper sheds new light on the degree of international fiscal-financial spillovers by investigating the effect of domestic fiscal policies on cross-border bank lending. By estimating the dynamic response of U.S. cross-border bank lending towards the 45 recipient countries to exogenous domestic fiscal shocks (both measured by spending and revenue) between 1990Q1 and 2012Q4, we find that expansionary domestic fiscal shocks lead to a statistically significant increase in cross-border bank lending. The magnitude of the effect is also economically significant: the effect of 1 percent of GDP increase (decrease) in spending (revenue) is comparable to an exogenous decline in the federal funds rate. We also find that fiscal shocks tend to have larger effects during periods of recessions than expansions in the source country, and that the adverse effect of a fiscal consolidation is larger than the positive effect of the same size of a fiscal expansion. In contrast, we do not find systematic and statistically significant differences in the spillover effects across recipient countries depending on their exchange rate regime, although capital controls seem to play some moderating role. The extension of the analysis to a panel of 16 small open economies confirms the finding from the U.S. economy. JEL Classification Numbers: E62, F21, F32, F42.
An Efficient Path Robustness Metric for Compliant Robots

Compliant robots are able to make contact with obstacles safely, but many compliant robots suffer from significant actuation uncertainty. When executing a path that is collision-free contact with a nearby obstacle, though safe, can lead to the robot becoming “stuck” and being unable to continue execution. It is very computationally expensive to compute the probability of being stuck through forward-simulation and impractical to capture the distribution over the robot state in contact with parametric probability distributions, precluding the use of existing methods to evaluate the robustness of the path. This paper presents a robustness metric for compliant robots that captures the probability of the robot completing a given path, i.e. the probability of avoiding stuck configurations. Our metric is intended to be used inside a motion planner to determine the quality more efficiently than forward simulation. Our approach constructs a set of reachable C-space volumes between the waypoints of a path that bound the set of configurations the robot could achieve given the actuation noise. We can then identify stuck configurations within these volumes and approximate their joint pre-image, which we then use to compute the probability of successfully reaching a way-point and subsequently the probability of reaching the path’s goal. In our experiments we compare our method to forward-simulation on 3DoF and 6DoF free-flying robots in a narrow passage environment. We find that our method computes similar robustness predictions to forwardsimulation but does so significantly more efficiently.
Statistica Sinica Preprint No : SS-2018-0075 Title The Broken Adaptive Ridge Procedure and Its Applications

In this paper, we study the broken adaptive ridge method to estimate lower-dimensional patterns of coefficients in regression models. Based on the re-weighted `2-penalization, the new method can simultaneously recover both the true sparsity and the inherent structures of the features, which makes it theoretically and practically appealing. The resulting estimate is shown to enjoy the oracle property. The proposed method also contains a set of variable selection or pattern estimation methods. As a special case, the fused broken adaptive ridge, which penalizes the differences between adjacent coefficients, is thoroughly discussed with applications in signal approximation and image processing. The associated algorithms are numerically easy to implement. Various simulation studies and real data analyses illustrate its advantages over the fused lasso method.
Nano fi bers for Water and Wastewater 3 Treatment : Recent Advances 4 and Developments

7 Abstract Materials of nanofibrous morphology and structure are attractive for 8 solving environmental problems including water-related issues. In recent years, 9 increasing interest is geared on the use of specially designed electrospun nanofibers 10 for water/wastewater treatment applications. The nanofibers can be used in the form 11 of nonwoven structures, as stand-alone membranes, as support layer or as a surface 12 modification layer that enables added functionality to a composite material. 13 Continuous research has been carried out in optimizing the nanofiber membrane 14 design and structure by manipulating material, process and surrounding parameters 15 in the electrospinning process. This chapter highlights the recent advances and 16 developments on the potential and application of electrospun nanofibers for water/ 17 wastewater treatment. Comprehensive discussion is presented here on various 18 designs and structures of nanofibers and their applications to water-related treat19 ment and the future prospects of such materials.
Dose-Adjusted EPOCH-R Compared With R-CHOP as Frontline Therapy for Diffuse Large B-Cell Lymphoma: Clinical Outcomes of the Phase III Intergroup Trial Alliance/CALGB 50303.

PURPOSE Alliance/CALGB 50303 (NCT00118209), an intergroup, phase III study, compared dose-adjusted etoposide, prednisone, vincristine, cyclophosphamide, doxorubicin, and rituximab (DA-EPOCH-R) with standard rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisone (R-CHOP) as frontline therapy for diffuse large B-cell lymphoma. PATIENTS AND METHODS Patients received six cycles of DA-EPOCH-R or R-CHOP. The primary objective was progression-free survival (PFS); secondary clinical objectives included response rate, overall survival (OS), and safety. RESULTS Between 2005 and 2013, 524 patients were registered; 491 eligible patients were included in the final analysis. Most patients (74%) had stage III or IV disease; International Prognostic Index (IPI) risk groups included 26% IPI 0 to 1, 37% IPI 2, 25% IPI 3, and 12% IPI 4 to 5. At a median follow-up of 5 years, PFS was not statistically different between the arms (hazard ratio, 0.93; 95% CI, 0.68 to 1.27; P = .65), with a 2-year PFS rate of 78.9% (95% CI, 73.8% to 84.2%) for DA-EPOCH-R and 75.5% (95% CI, 70.2% to 81.1%) for R-CHOP. OS was not different (hazard ratio, 1.09; 95% CI, 0.75 to 1.59; P = .64), with a 2-year OS rate of 86.5% (95% CI, 82.3% to 91%) for DA-EPOCH-R and 85.7% (95% CI, 81.4% to 90.2%) for R-CHOP. Grade 3 and 4 adverse events were more common ( P < .001) in the DA-EPOCH-R arm than the R-CHOP arm, including infection (16.9% v 10.7%, respectively), febrile neutropenia (35.0% v 17.7%, respectively), mucositis (8.4% v 2.1%, respectively), and neuropathy (18.6% v 3.3%, respectively). Five treatment-related deaths (2.1%) occurred in each arm. CONCLUSION In the 50303 study population, the more intensive, infusional DA-EPOCH-R was more toxic and did not improve PFS or OS compared with R-CHOP. The more favorable results with R-CHOP compared with historical controls suggest a potential patient selection bias and may preclude generalizability of results to specific risk subgroups.
Morphological, anatomical and karyological investigations on the genus Paris in Turkey.

This study presents morphological, anatomical and karyological characteristics of the genus Paris L. represented by 2 species in Turkey: P. incomplete M. Bieb. and P. quadrifolia L. Taxonomically detailed description of the species are based on collected and examined specimens; distributions and illustrations are presented along with anatomical cross sections of leaves, stems, rhizomes and roots and leaf surfaces. The differing anatomical structure of studied plant parts is suitable for use as an additional tool in their identification. Karyotypes of the species are determined, P. incompleta, as 2n = 10, diploid, chromosome formula is 2m+4sm+2st+2t and P. quadrifolia as 2n = 20, tetraploid, chromosome formula is 4m+8sm+2st+2t. Photographies of species in naturel habitat, distribution map of species in Turkey, detailed drawing of flowers and general view of species, drawings and microphotographies of the karyotypes are also presented.
Fertilization Effects on Potato Yield and Quality

At Agricultural Research Station Farm, Giza Governorate, Egypt, two field experiments were carried out during two successive winter seasons of 2013/2014 and 2014/2015 to study the effect of nitrogen (0, 90, 120 and 150 kg fed.), potassium (0, 72 and 96 kg K2O fed ) fertilizer rates and foliar application of boron in sthe form of H3BO3 (0 and 100 ppm) as well as their interactions on potato yield and its quality (Solanum tuberosum L.) cv. Spunta cultivar. A split-split-plot system in a randomized complete blocks design with three replicates was used in this respect. The obtained results indicated that significant increase in no. of tubers/plant, average tuber weight (g) and tuber yield was observed with 150 kg N fed over control. Increase in tuber yield with 96 kg K2O fed -1 was statistically significant compared to other treatments. The quality parameters like dry matter, specific gravity, total carbohydrate, reducing sugar and starch contents were improved with both nitrogen and K application. Spraying potato plants with boron at a rate of 100 ppm significantly increased yield and its components as well as quality of tubers. Interaction treatments among different rates of nitrogen, potassium fertilization and boron foliar application were significant on potato yield and quality. In general, the best interaction treatment among different rates of nitrogen, potassium fertilization and foliar application of boron was fertilization with 150 kg N fed in the form of ammonium sulphate, 96 kg K2O fed -1 in the form potassium sulphate and foliar application of boron to improve both yield and quality of potato crop as compared with other treatments.
Torsional vibration of size-dependent viscoelastic rods using nonlocal strain and velocity gradient theory

In this paper the torsional vibration of size-dependent viscoelastic nanorods embedded in an elastic medium with different boundary conditions is investigated. The novelty of this study consists of combining the nonlocal theory with the strain and velocity gradient theory to capture both softening and stiffening size-dependent behavior of the nanorods. The viscoelastic behavior is modeled using the so-called Kelvin–Voigt viscoelastic damping model. Three length-scale parameters are incorporated in this newly combined theory, namely, a nonlocal, a strain gradient, and a velocity gradient parameter. The governing equation of motion and its boundary conditions for the vibration analysis of nanorods are derived by employing Hamilton’s principle. It is shown that the expressions of the classical stress and the stress gradient resultants are only defined for different values of the nonlocal and strain gradient parameters. The case where these are equal may seem to result in an inconsistency to the general equation of motion and the related non-classical boundary conditions. A rigorous investigation is conducted to prove that the proposed solution is consistent with physics. Damped eigenvalue solutions are obtained both analytically and numerically using a Locally adaptive Differential Quadrature Method (LaDQM). Analytical results of linear free vibration response are obtained for various length-scales and compared with LaDQM numerical results.
Young Scientists Conference in HPC and Simulation , YSC 2017 , 1-3 November 2017 , Kotka , Finland Si ulation of verdrive Pacing in 2 Pheno enological odels of nisotropic yocardiu

Spiral waves in the heart underlie dangerous cardiac arrhythmias such as fibrillation. Low-voltage defibrillation and cardioversion are modern methods to treat such pathologies. This type of electrotherapy is based on the phenomenon of superseding spiral waves by a high-frequency source of excitation. In this paper, we numerically simulated the superseding process in a thin layer of the cardiac muscle. We captured the case of a sole spiral wave with a stable core at the centre of a square. We used different cell-level models as well as a variety of electrode configurations and studied the induced drift of the spiral wave. Regimes of the external stimulation were classified based on whether they provide an effective and safe, that is without break-up, way to shift the spiral toward the boundary. c 7 ut rs. lis ls i . responsibility of the scientifi co mittee of the 6th I ternational Young Scientist co fere ce in HPC and i lati .
What Have We Learned about the Employment Effects of Severance Pay ? Further Iterations of Lazear et al . w

Abstract. In this study we examine the effect of severance pay on employment and unemployment, using data on industrialized OECD countries. Our starting point is Lazear’s [(1990) Quarterly Journal of Economics 105, 699–726] dictum that severance payment requirements unfavorably impact the labor market. We extend his sample period and add to his parsimonious specification a variety of fixed and time-varying labor market institutions. While the positive effect of severance pay on unemployment garners some support, there is no real indication of adverse effects in respect of the other employment outcomes identified here, namely, the employment-population ratio, the labor force participation rate, and long-term unemployment. Moreover, with the possible exception of collective bargaining coordination, the role of institutions is also more muted than suggested in the literature.
A GLOBAL ANALYSIS OF IMMIGRATION BARRIERS’ EFFECTS ON POVERTY, WAGES, AND OUTPUT

Most rich nations maintain very tight restrictions on immigration despite widespread opening of trade and international capital flows since World War II. This paper uses a two-region, one-sector, dynastic growth model with a continuum of skills to assess the welfare effects and poverty implications of these barriers. Such a dynamic model allows me to take account of international capital flows, as well as domestic investment, which have important interactions with international migration. Similar to other global studies of migration, I find that rich nation migration barriers impose huge losses on the global economy. This paper also estimates, for the first time to my knowledge, the global poverty implications of those barriers and finds that freeing migration into rich nations would reduce global poverty by at least 40% and as much as 66%. This corroborates the conclusions drawn by others that opening rich nations to freer migration may do more to reduce poverty around the world than any other policy.
Interactive Natural Image Segmentation and Foreground Extraction

Interactive image segmentation is very practical and important problem in computer vision. In this paper a regressive based Green’s function is employed to formulate the problem of segmentation. The method is incorporated with different clustering approaches intended to extract the foreground regions from the natural images. The method performance is improved with proper labeling of foreground and background regions, and with more number of cluster regions. The method is evaluated with two standard benchmark datasets and found that the experimental results were promising.
Discussion Paper Series A No . 502 On Initial Conferment of Individual Rights

An extended social choice framework is proposed for the analysis of initial conferment of individual rights. It captures the intuitive conception of decisionmaking procedure as a carrier of intrinsic value along with the instrumental usefulness thereof in realizing valuable culmination outcomes. Our model of social decision-making consists of two stages. In the first stage, the society decides on the game form rights-system to be promulgated. In the second stage, the promulgated game form rights-system, coupled with the revealed profile of individual preference orderings over the set of culmination outcomes, determines a fully-fledged game, the play of which determines a culmination outcome at the Nash equilibrium. A set of sufficient conditions for the existence of a democratic social choice procedure, which chooses a game form in the first stage that is not only liberal, efficient and Nash solvable, but also uniformly workable for every revealed profile of individual preference orderings over the set of culmination outcomes, is identified. JEL Classification Numbers: D63, D71
DISCUSSION PAPER SERIES ON THE SMOOTH AMBIGUITY MODEL : A REPLY

Epstein (2009) describes three Ellsberg-style thought experiments and argues that they pose di¢ culties for the smooth ambiguity model of decision making under uncertainty developed by Klibano¤, Marinacci and Mukerji (2005). We revisit these thought experiments and nd, to the contrary, that they either point to strengths of the smooth ambiguity model compared to other models, such as the maxmin expected utility model (Gilboa and Schmeidler, 1989), or, in the case of one thought experiment, raise criticisms that apply equally to a broad range of current ambiguity models.