Miracle-dz/UniFAR-FTUs huggingface dataset:
Response of soil organic carbon fractions, microbial community composition and carbon mineralization to high-input fertilizer practices under an intensive agricultural system

Microbial mechanisms associated with soil organic carbon (SOC) decomposition are poorly understood. We aim to determine the effects of inorganic and organic fertilizers on soil labile carbon (C) pools, microbial community structure and C mineralization rate under an intensive wheat-maize double cropping system in Northern China. Soil samples in 0–10 cm layer were collected from a nine-year field trial involved four treatments: no fertilizer, CK; nitrogen (N) and phosphorus (P) fertilizers, NP; maize straw combined with NP fertilizers, NPS; and manure plus straw and NP fertilizers, NPSM. Soil samples were analyzed to determine labile C pools (including dissolved organic C, DOC; light free organic C, LFOC; and microbial biomass C, MBC), microbial community composition (using phospholipid fatty acid (PLFA) profiles) and SOC mineralization rate (from a 124-day incubation experiment). This study demonstrated that the application of chemical fertilizers (NP) alone did not alter labile C fractions, soil microbial communities and SOC mineralization rate from those observed in the CK treatment. Whereas the use of straw in conjunction with chemical fertilizers (NPS) became an additional labile substrate supply that decreased C limitation, stimulated growth of all PLFA-related microbial communities, and resulted in 53% higher cumulative mineralization of C compared to that of CK. The SOC and its labile fractions explained 78.7% of the variance of microbial community structure. Further addition of manure on the top of straw in the NPSM treatment did not significantly increase microbial community abundances, but it did alter microbial community structure by increasing G+/G- ratio compared to that of NPS. The cumulative mineralization of C was 85% higher under NPSM fertilization compared to that of CK. Particularly, the NPSM treatment increased the mineralization rate of the resistant pool. This has to be carefully taken into account when setting realistic and effective goals for long-term soil C stabilization.
North-South Technology Diffusion, Regional Integration, and the Dynamics of the 'Natural Trading Partners' Hypothesis

Based on static analysis, a number of studies argue that forming a RTA is more likely to raise welfare if member countries are “natural trading partners,” while other studies claim the opposite. This paper considers the argument from a dynamic viewpoint by examining the impact of trade with Japan, North America and the EU on technology diffusion and TFP in Korea, Mexico and Poland. Using industry-level data, we show that i) technology diffusion and productivity gains tend to be regional: Korea (Mexico) (Poland) benefits mainly from trade with Japan (North America) (the EU); and ii) the dynamic version of the “natural trading partners” hypothesis seems to hold for Korea and Mexico though not necessarily for Poland.
Ontology enrichment by discovering multi-relational association rules from ontological knowledge bases

In the Semantic Web context, OWL ontologies represent the conceptualization of domains of interest while the corresponding assertional knowledge is given by the heterogeneous Web resources referring to them. Being strongly decoupled, ontologies and assertion can be out-of-sync. An ontology can be incomplete, noisy and sometimes inconsistent with regard to the actual usage of its conceptual vocabulary in the assertions. Data mining can support the discovery of hidden knowledge patterns in the data, to enrich the ontologies. We present a method for discovering multi-relational association rules, coded in SWRL, from ontological knowledge bases. Unlike state-of-the-art approaches, the method is able to take the intensional knowledge into account. Furthermore, since discovered rules are represented in SWRL, they can be straight-forwardly integrated within the ontology, thus (i) enriching its expressive power and (ii) augmenting the assertional knowledge that can be derived. Discovered rules may also suggest new axioms to be added to the ontology. We performed experiments on publicly available ontologies validating the performances of our approach.
Comparison of Metal and Plastic Stents for Preoperative Biliary Drainage in Resectable and Borderline Resectable Periampullary Cancer: A Meta-Analysis and System Review.

AIM The aim of this study was to compare the plastic stents with metal stents for preoperative biliary drainage (PBD) in terms of the rate of endoscopic reintervention and PBD-related pre- and postoperative complications in patients with resectable and borderline resectable periampullary cancer. METHODS We conducted a comprehensive search of the PubMed, EMBASE, and the Cochrane Library database to identify relevant available articles from their inception to September 2017. The odds ratio (OR) with 95% confidence interval (CI) was calculated to compare the incidence of endoscopic reintervention and stent-related complications between the plastic and metal stents groups. Also, we used RevMan 5.3 to perform the pooled analyses. RESULTS Four trials (three randomized controlled trials [RCT] and one prospective clinical trial) with 392 patients were included. One hundred seventy-four patients received metal stents for PBD, and 218 patients received plastic stents. The metal stents group had a significant lower rate of endoscopic reintervention (OR = 0.30, 95% CI = 0.13-0.73, P = .008) and preoperative cholangitis (OR = 3.60, 95% CI = 1.62-7.98, P = .002) compared with the plastic stents group. But there was a significantly higher rate of PBD-related pancreatitis (OR = 3.60, 95% CI = 1.62-7.98, P = .002) in the metal stents group. CONCLUSIONS The present meta-analysis revealed that metal stents have significantly lower rate of reintervention and cholangitis than plastic stents. But plastic stents have an obvious superiority over metal stents in terms of the incidence of preoperative pancreatitis. More RCTs are required to support this conclusion and provide more detailed information about the complications and treatment. Meanwhile, a uniform standard for the PBD is required in patients with malignant distal biliary obstruction.
Dark matter as a ghost free conformal extension of Einstein theory

We discuss ghost free models of the recently suggested mimetic dark matter theory. This theory is shown to be a conformal extension of Einstein general relativity. Dark matter originates from gauging out its local Weyl invariance as an extra degree of freedom which describes a potential flow of the pressureless perfect fluid. For a positive energy density of this fluid the theory is free of ghost instabilities, which gives strong preference to stable configurations with a positive scalar curvature and trace of the matter stress tensor. Instabilities caused by caustics of the geodesic flow, inherent in this model, serve as a motivation for an alternative conformal extension of Einstein theory, based on the generalized Proca vector field. A potential part of this field modifies the inflationary stage in cosmology, whereas its rotational part at the post inflationary epoch might simulate rotating flows of dark matter.
Anticancer Activities of Six Selected Natural Compounds of Some Cameroonian Medicinal Plants

Background Natural products are well recognized as sources of drugs in several human ailments. In the present work, we carried out a preliminary screening of six natural compounds, xanthone V1 (1); 2-acetylfuro-1,4-naphthoquinone (2); physcion (3); bisvismiaquinone (4); vismiaquinone (5); 1,8-dihydroxy-3-geranyloxy-6-methylanthraquinone (6) against MiaPaCa-2 pancreatic and CCRF-CEM leukemia cells and their multidrug-resistant subline, CEM/ADR5000. Compounds 1 and 2 were then tested in several other cancer cells and their possible mode of action were investigated. Methodology/Findings The tested compounds were previously isolated from the Cameroonian medicinal plants Vismia laurentii (1, 3, 4, 5 and 6) and Newbouldia laevis (2). The preliminary cytotoxicity results allowed the selection of xanthone V1 and 2-acetylfuro-1,4-naphthoquinone, which were then tested on a panel of cancer cell lines. The study was also extended to the analysis of cell cycle distribution, apoptosis induction, caspase 3/7 activation and the anti-angiogenic properties of xanthone V1 and 2-acetylfuro-1,4-naphthoquinone. IC50 values around or below 4 µg/ml were obtained on 64.29% and 78.57% of the tested cancer cell lines for xanthone V1 and 2-acetylfuro-1,4-naphthoquinone, respectively. The most sensitive cell lines (IC50<1 µg/ml) were breast MCF-7 (to xanthone V1), cervix HeLa and Caski (to xanthone V1 and 2-acetylfuro-1,4-naphthoquinone), leukemia PF-382 and melanoma colo-38 (to 2-acetylfuro-1,4-naphthoquinone). The two compounds showed respectively, 65.8% and 59.6% inhibition of the growth of blood capillaries on the chorioallantoic membrane of quail eggs in the anti-angiogenic assay. Upon treatment with two fold IC50 and after 72 h, the two compounds induced cell cycle arrest in S-phase, and also significant apoptosis in CCRF-CEM leukemia cells. Caspase 3/7 was activated by xanthone V1. Conclusions/Significance The overall results of the present study provided evidence for the cytotoxicity of compounds xanthone V1 and 2-acetylfuro-1,4-naphthoquinone, and bring supportive data for future investigations that will lead to their use in cancer therapy.
A novel approach for the convergence analysis of the least-mean fourth algorithm

The convergence analysis of the least-mean fourth (LMF) algorithm is derived. A novel approach is used to study the convergence behavior of the algorithm. As a by-product of this novel approach, expressions for more general and new sufficient conditions for convergence and the excess steady-state error for the LMF algorithm are derived.
Natural Hazards and Earth System Sciences Simulation of the effect of defence structures on granular flows using

This paper presents the SPH (Smoothed Particles Hydrodynamics) numerical method adapted to complex rheology and free surface flow. It has been developped to simulate the local effect of a simple obstacle on a granular flow. We have introduced this specific rheology to the classical formalism of the method and thanks to experimental devices, we were able to validate the results. Two viscosity values have been simultaneously computed to simulate “plugs” and “dead zone” with the same code. First, some experiments have been done on a simple inclined slope to show the accuracy of the numerical results. We have fixed the mass flow rate to see the variations of the flow depth according to the channel slope. Then we put a weir to block the flow and we analysed the dependence between the obstacle height and the length of influence upstream from the obstacle. After having shown that numerical results were consistent, we have studied speed profiles and pressure impact on the structure. Also results with any topography will be presented. This will have a great interest to study real flow over natural topography while using the model for decision help.
A Dependency Parser for Tweets

We describe a new dependency parser for English tweets, TWEEBOPARSER. The parser builds on several contributions: new syntactic annotations for a corpus of tweets (TWEEBANK), with conventions informed by the domain; adaptations to a statistical parsing algorithm; and a new approach to exploiting out-of-domain Penn Treebank data. Our experiments show that the parser achieves over 80% unlabeled attachment accuracy on our new, high-quality test set and measure the benefit of our contributions. Our dataset and parser can be found at http://www.ark. cs.cmu. edu/TweetNLP.
Druggable negative allosteric site of P2X3 receptors

Significance Allosteric regulation, produced by the binding of a ligand at an allosteric site topographically distinct from the orthosteric site, represents a direct and efficient means for modulation of biological macromolecule function. Because allosteric modulators have advantages over classic orthosteric ligands as therapeutic agents, understanding the mechanism underlying allosteric modulation may open new therapeutic avenues. Here, we focused on allosteric regulation of P2X receptors, which are implicated in diverse pathophysiological processes, such as blood clotting, pain sensation, inflammation, and rheumatoid arthritis. Combining structural determination, molecular modeling, and mutagenesis, we identified a druggable allosteric site on P2X3. Our findings will facilitate the development of novel therapeutics targeting these receptors. Allosteric modulation provides exciting opportunities for drug discovery of enzymes, ion channels, and G protein-coupled receptors. As cation channels gated by extracellular ATP, P2X receptors have attracted wide attention as new drug targets. Although small molecules targeting P2X receptors have entered into clinical trials for rheumatoid arthritis, cough, and pain, negative allosteric modulation of these receptors remains largely unexplored. Here, combining X-ray crystallography, computational modeling, and functional studies of channel mutants, we identified a negative allosteric site on P2X3 receptors, fostered by the left flipper (LF), lower body (LB), and dorsal fin (DF) domains. Using two structurally analogous subtype-specific allosteric inhibitors of P2X3, AF-353 and AF-219, the latter being a drug candidate under phase II clinical trials for refractory chronic cough and idiopathic pulmonary fibrosis, we defined the molecular interactions between the drugs and receptors and the mechanism by which allosteric changes in the LF, DF, and LB domains modulate ATP activation of P2X3. Our detailed characterization of this druggable allosteric site should inspire new strategies to develop P2X3-specific allosteric modulators for clinical use.
Developing a theory-based taxonomy of methods for implementing change in practice.

AIM In this paper we present a theory-based taxonomy of the methods used to implement change in practice. BACKGROUND Implementation research is characterized by inconsistent terminology for the methods employed and inattention to differences in the relevance of methods across different disciplines. Studies of the effectiveness of implementation have yielded mixed results. Positive effects shown have been small. The limited success of many efforts to implement change in practice may be due, in part, to the absence of a framework to guide the use of implementation methods. METHOD A provisional taxonomy of implementation methods, derived from theory and existing taxonomies, was used to content analyse a convenience sample of 43 reports of empirical studies of the implementation of one or more research-based practice changes involving nurses that had been published between 1995 and 2005. This taxonomy was revised throughout the course of analysis to capture more completely the information in each report. FINDINGS Following the analysis, nine of the 11 methods in the provisional taxonomy were retained, two were removed and five new methods were identified. The final taxonomy includes 14 implementation methods organized into five categories: (a) increasing coordination; (b) raising awareness; (c) persuasion via interpersonal channels; (d) persuasion via reinforcing belief that behaviour will lead to desirable results and (e) increasing behavioural control. CONCLUSIONS The taxonomy presented here differs from prior taxonomies by focusing on nursing and by providing a clear and mutually exclusive guide to implementation methods. By deriving the initial coding strategy from theory, the taxonomy links the methods to theoretical constructs that may inform the selection of methods across different practice changes and settings.
Rank-based optimal tests of the adequacy of an elliptic VARMA model

We are deriving optimal rank-based tests for the adequacy of a vector autoregressive-moving average (VARMA) model with elliptically contoured innovation density. These tests are based on the ranks of pseudo-Mahalanobis distances and on narmed residuals computed from Tyler's [Ann. Statist. 15 (1987) 234-251] scatter matrix; they generalize the univariate signed rank procedures proposed by Hallin and Puri [J. Multivariate Anal. 39 (1991) 1-29]. Two types of optimality properties are considered, both in the local and asymptotic sense, a la Le Cam: (a) (fixed-score procedures) local asymptotic minimaxity at selected radial densities, and (b) (estimated-score procedures) local asymptotic minimaxity uniform over a class F of radial densities. Contrary to their classical counterparts, based on cross-covariance matrices, these tests remain valid under arbitrary elliptically symmetric innovation densities, including those with infinite variance and heavy-tails. We show that the AREs of our fixed-score procedures, with respect to traditional (Gaussian) methods, are the same as for the tests of randomness proposed in Hallin and Paindaveine [Bernoulli 8 (2002b) 787-815]. The multivariate serial extensions of the classical Chernoff-Savage and Hodges-Lehmann results obtained there thus also hold here; in particular, the van der Waerden versions of our tests are uniformly more powerful than those based on cross-covariances. As for our estimated-score procedures, they are fully adaptive, hence, uniformly optimal over the class of innovation densities satisfying the required technical assomptions.
Unlinking information from 4‐manifolds

We generalize theorems of Cochran–Lickorish and Owens–Strle to the case of links with more than one component. This enables the use of linking forms on double branched covers, Heegaard Floer correction terms, and Donaldson's diagonalization theorem to complete the table of unlinking numbers for nonsplit prime links with crossing number nine or less.
Incorporation of Caseinoglycomacropeptide and Caseinophosphopeptide into the Salivary Pellicle Inhibits Adherence of Mutans Streptococci

The protective effects of milk and milk products against dental caries have been demonstrated in many animal studies. We have shown that this effect was mediated by micellar casein or caseinopeptide derivatives. A reduction in the Streptococcus sobrinus population in the oral microbiota of animals fed diets supplemented with these milk components was consistently observed. A possible explanation for these findings is that milk components are incorporated into the salivary pellicle, thereby reducing the adherence of S. sobrinus. This hypothesis was tested in vitro by the incubation of bovine enamel discs with unstimulated saliva. The resulting pellicle was washed and incubated with caseinoglycomacropeptide (CGMP) and/or caseinophosphopeptide (CPP) labeled with 17- and 12-nm gold particles. All samples were prepared for electron microscopy by high-pressure freezing followed by freeze-substitution. It was demonstrated by high-resolution scanning electron microscopy with back-scattered electron imaging, as well as by transmission electron microscopy, that both peptides were incorporated into the pellicle in exchange for albumin, confirming previous findings. This protein was identified with a mouse anti-human serum albumin followed by goat anti-mouse IgG labeled with 25-nm gold particles. Incorporation of CGMP and/or CPP into sali\ arv pellicles reduced the adherence of both S. sobrinus and S. mutans significantly. It is suggested that the calcium-and phosphate-rich micellar casein or caseinopeptides are incorporated into the pellicle. The resulting ecological shifts, together with the increased remineralization potential of this biofilm, may explain its modified cariogenic potential.
Mixed-Integer PDE-Constrained Optimal Control of Gas Networks ∗

We develop a mixed-integer optimal control model with partial differential equation (PDE) constraints for gas transport networks, designed for controlling extreme state transitions, such as flow reversals. Our model shows how to combine binary compressor controls with PDE flow models. We model the flow of gas using a variant of the Euler equations, which we discretize using a finite volume scheme, which obeys conservation of mass and average impulse independent of the direction of flow. The resulting large-scale mixed-integer nonlinear optimization problem is difficult to solve by using standard branch-and-bound solvers, and we propose a new tree-search strategy that allow us to solve realistic instances. We compare the performance of several solution schemes on twelve test instances, showing that our custom tree-search strategy greatly outperforms a generic strategy in most instances.
THE TRANSCENDENCE DEGREE OF THE MOD p COHOMOLOGY OF FINITE POSTNIKOV SYSTEMS

In this paper we examine the transcendence degree of the mod p cohomology of a nite Postnikov system E. We prove that, under mild assumptions on E, the transcendence degree of H(E; Fp) is always positive, and give a complete classication of the Postnikov systems where the transcen- dence degree of H(E; Fp) is nite. More precisely we prove that H(E; Fp )i s of nite transcendence degree i E is Fp-equivalent to the classifying space of a p-toral group. As an application of these results we derive statements about the n-connected cover Xhni of a nite complex X. We show for instance that, under suitable connectivity assumptions on X, the LS category of Xhni is always innite assuming Xhni6= X. Finally we discuss generalizations of the obtained results to polyGEMs.
Episomal Vectors for Rapid Expression and Purification of Proteins in Mammalian Cells

Research projects in life sciences aim at studying and better understanding biological systems. Over the past 50 years, tremendous advances in molecular biology and biochemistry have provided essential tools to dissect biological processes down to the molecular level. Most of the time, when studying the structure and function of proteins, obtaining sufficient quantities of the native form of the protein isolated from the relevant cells or tissue is not feasible. The development of recombinant DNA technologies to clone and express genes encoding proteins of interest has revolutionized the design and execution of research projects (Cohen et al., 1973). Indeed, access to purified recombinant proteins enables a wide spectrum of studies, ranging from structural characterization of proteinproteinand protein-nucleic acid interactions to immunization programs to generate antibodies as research tools. The availability of sufficient quantities of purified recombinant proteins is often key to success. Furthermore, recombinant approaches for the production of proteins have profoundly impacted biomedical research and drug development as they have opened the possibility of producing clinical grade proteins as drugs. This has subsequently paved the way for the emergence and fast development of protein biologics that today represent a very successful and quickly expanding class of drugs (Saladin et al., 2009; Chiverton et al., 2010).
Stationary shoulder tool in friction stir processing: a novel low heat input tooling system for magnesium alloy

ABSTRACT Present work aims to propose a new and novel low heat input stationary shoulder friction stir processing (SSFSP) for grain refinement. It uses stationary shoulder and rotating probe tool, which generates low heat input and small temperature gradient across thickness of material. In this study, SSFSP was performed in 6.35 mm thick AZ31B magnesium alloy without use of external cooling. The homogenous grain refinement occurred throughout the thickness (top, middle, and bottom). Enhancement in hardness and ductility exhibited minimum anisotropy across the processing thickness. Furthermore, fractography confirmed the similar fracture modes with dimples and tear ridges in all tensile specimens across the thickness. Graphical Abstract