Miracle-dz/UniFAR-FTUs huggingface dataset:
The Non-Fimbriate Phenotype Is Predominant among Salmonella enterica Serovar Choleraesuis from Swine and Those Non-Fimbriate Strains Possess Distinct Amino Acid Variations in FimH

Although most Salmonella serovars are able to infect a range of animal hosts, some have acquired the ability to cause systemic infections of specific hosts. For example, Salmonella enterica serovar Choleraesuis is primarily associated with systemic infection in swine. Adherence to host epithelial cells is considered a prerequisite for initial infection, and fimbrial appendages on the outer membrane of the bacteria are implicated in this process. Although type 1 fimbriae encoded by the fim gene cluster are commonly found in Salmonella serovars, it is not known whether S. Choleraesuis produces this fimbrial type and if and how fimbriae are involved in pathogenesis. In the present study, we demonstrated that only four out of 120 S. Choleraesuis isolates from pigs with salmonellosis produced type 1 fimbriae as assayed by the yeast agglutination test and electron microscopy. One of the 116 non-type 1 fimbria-producing isolates was transformed with plasmids carrying different fim genes from S. Typhimurium LB5010, a type 1 fimbria-producing strain. Our results indicate that non-type 1 fimbria-producing S. Choleraesuis required only an intact fimH to regain the ability to produce fimbrial appendages. Sequence comparison revealed six amino acid variations between the FimH of the non-type 1 fimbria-producing S. Choleraesuis isolates and those of the type 1 fimbria-producing S. Choleraesuis isolates. S. Choleraesuis that produced type 1 fimbriae contained FimH with an amino acid sequence identical to that of S. Typhimurium LB5010. Site-directed mutagenesis leading to the replacement of the non-conserved residues revealed that a change from glycine to valine at position of 63 (G63V) resulted in a non-type 1 fimbria-producing S. Choleraesuis being able to express type 1 fimbriae on its outer membrane. It is possible that this particular amino acid change prevents this polypeptide from proper interaction with other Fim subunits required for assembly of an intact type 1 fimbrial shaft in S. Choleraesuis; however, it remains to be determined if and how the absence of type 1 fimbriae production is related to the systemic infection of the swine host by S. Choleraesuis.
Get out but don’t fall down: verb-particle constructions in child language

Much has been discussed about the challenges posed by Multiword Expressions (MWEs) given their idiosyncratic, flexible and heterogeneous nature. Nonetheless, children successfully learn to use them and eventually acquire a number of Multiword Expressions comparable to that of simplex words. In this paper we report a wide-coverage investigation of a particular type of MWE: verb-particle constructions (VPCs) in English and their usage in child-produced and child-directed sentences. Given their potentially higher complexity in relation to simplex verbs, we examine whether they appear less prominently in child-produced than in child-directed speech, and whether the VPCs that children produce are more conservative than adults, displaying proportionally reduced lexical repertoire of VPCs or of verbs in these combinations. The results obtained indicate that regardless of any additional complexity VPCs feature widely in children data following closely adult usage. Studies like these can inform the development of computational models for language acquisition.
Incremental Maintenance of Association Rule Bases

Association rule mining from transaction databases (TDB) is a classical data mining task, whereby the most computationally intensive step is the detection of frequently occurring patterns, called frequent itemsets (FIs), from which the rules are further extracted. The number of FIs may be potentially large, leading to an even greater number of rules. Approaches based on closure operators, Galois conections and Galois (concept) lattices have been proposed in an attempt to reduce the size of the resulting rule set. Thus, the search for frequent patterns has been limited to closed itemsets, while looking for a representative and reduced set of association rules, called a basis, which nevertheless conveys all the relevant information. In thess approaches, the minimal generators of a closed itemset play a key role for the itemset/rule construction. In our paper, we present a straightforward method for the maintenance of an association rule basis when a new transaction is added to the TDB. To that end, we utilize results on the incremental update of lattices and extend them with new properties to form a complete framework for association rule base maintenance. In particular, we define a simple and efficient method for on-line computation of the generators for closed itemsets and show how its output is used in the update of the rule basis.
Keratin attenuates tumor necrosis factor–induced cytotoxicity through association with TRADD

Keratin 8 and 18 (K8/18) are the major components of intermediate filament (IF) proteins of simple or single-layered epithelia. Recent data show that normal and malignant epithelial cells deficient in K8/18 are nearly 100 times more sensitive to tumor necrosis factor (TNF)–induced cell death. We have now identified human TNF receptor type 1 (TNFR1)–associated death domain protein (TRADD) to be the K18-interacting protein. Among IF proteins tested in two-hybrid systems, TRADD specifically bound K18 and K14, type I (acidic) keratins. The COOH-terminal region of TRADD interacted with the coil Ia of the rod domain of K18. Endogenous TRADD coimmunoprecipitated with K18, and colocalized with K8/18 filaments in human mammary epithelial cells. Overexpression of the NH2 terminus (amino acids 1–270) of K18 containing the TRADD-binding domain as well as overexpression of K8/18 in SW13 cells, which are devoid of keratins, rendered the cells more resistant to killing by TNF. We also showed that overexpressed NH2 termini of K18 and K8/18 were associated with endogenous TRADD in SW13 cells, resulting in the inhibition of caspase-8 activation. These results indicate that K18 may sequester TRADD to attenuate interactions between TRADD and activated TNFR1 and moderate TNF-induced apoptosis in simple epithelial cells.
An Enlarged Economic and Monetary Union: Effects and Policy Implications

We calculate an "enlarged" Phillips curve for a theoretical EMU with 12+8 Member States. Both the empirical evidence and the econometric analysis show the worsening of the trade-off between inflation and unemployment, and hence the need to revise, at least temporarily, the stance of the ECB monetary policy. Also, the estimates point to a modified responsiveness of the money-demand function to the changes of the interest rates, given, however, a greater stability of such a function in the long-run.
Towards Semantic Requirement Engineering

It is widely acknowledged that most of problems occurring in requirement engineering activities mainly results from the lack of a semantic agreement among stakeholders. It implies to find an effective mechanism to integrate existing theory, techniques and resources accumulated in requirement engineering, and furthermore to provide a favorable base to develop novel theory and techniques. This paper proposes an integrated framework for semantic requirement engineering, and points out several interesting research avenues.
Polymyxin B, in combination with fluconazole, exerts a potent fungicidal effect.

OBJECTIVES The objective of this study was to identify existing clinical compounds that either possess a fungicidal activity alone or can act synergistically with fungistatic antifungals. METHODS We screened a clinical compound library for drugs that exhibited anti-Aspergillus activity. Among selected compounds, the cationic peptide antibiotic polymyxin B was chosen for further characterization because it can be used parenterally and topically. The fungicidal effect of polymyxin B and its synergistic interactions with azole antifungals were tested against a variety of fungal species. The toxicity of the drug combination of polymyxin B and fluconazole was compared with that of each drug alone in mammalian cell cultures. RESULTS We found that polymyxin B possesses a broad-spectrum antifungal activity at relatively high concentrations. However, because of its synergistic interactions with azole antifungals, polymyxin B at much lower concentrations exerts a potent fungicidal effect against Cryptococcus neoformans, Candida albicans and non-albicans Candida species and moulds when combined with azoles. The combination of polymyxin B and fluconazole at concentrations within susceptible breakpoints is particularly potent against C. neoformans isolates, including fluconazole-resistant strains. The drug combination displayed no additional toxicity compared with polymyxin B alone when tested in cell culture. CONCLUSIONS The combination of polymyxin B and fluconazole has the potential to be used in the clinic to treat systemic cryptococcosis. Our findings suggest that combining cationic peptide antibiotics with azole antifungals could provide a new direction for developing novel antifungal therapies.
Industry or Class Cleavages Over Trade Policy? Evidence from the Britishgeneral Election of 1923

Economists and political scientists have frequently attempted to determine whether trade policy-related political action takes place along factor-lines (such as capital versus labor, as implied by the Stolper-Samuelson theorem) or along industry-lines (as implied by models with imperfect factor mobility). This paper examines voting patterns in the British general election of 1923, an election that hinged on free trade versus protection. The election provides an opportunity to distinguish between the two hypotheses because either an industry or a factor alignment among voters is plausible: rigidities in the interwar labor market have often been discussed, and electoral politics has often been viewed as having a class basis. This paper exploits data from the British census of 1921, which divides the population into categories of occupation (by industry) and categories of economic class (by income and/or skill level), and relates these data to cross-country variation in voting for the contending political parties. The results indicate that county differences in the occupational structure of the electorate account for the election outcome better than differences in class structure.
Multi-omic landscape of rheumatoid arthritis: re-evaluation of drug adverse effects

Objective: To provide a frame to estimate the systemic impact (side/adverse events) of (novel) therapeutic targets by taking into consideration drugs potential on the numerous districts involved in rheumatoid arthritis (RA) from the inflammatory and immune response to the gut-intestinal (GI) microbiome. Methods: We curated the collection of molecules from high-throughput screens of diverse (multi-omic) biochemical origin, experimentally associated to RA. Starting from such collection we generated RA-related protein-protein interaction (PPI) networks (interactomes) based on experimental PPI data. Pharmacological treatment simulation, topological and functional analyses were further run to gain insight into the proteins most affected by therapy and by multi-omic modeling. Results: Simulation on the administration of MTX results in the activation of expected (apoptosis) and adverse (nitrogenous metabolism alteration) effects. Growth factor receptor-bound protein 2 (GRB2) and Interleukin-1 Receptor Associated Kinase-4 (IRAK4, already an RA target) emerge as relevant nodes. The former controls the activation of inflammatory, proliferative and degenerative pathways in host and pathogens. The latter controls immune alterations and blocks innate response to pathogens. Conclusions: This multi-omic map properly recollects in a single analytical picture known, yet complex, information like the adverse/side effects of MTX, and provides a reliable platform for in silico hypothesis testing or recommendation on novel therapies. These results can support the development of RA translational research in the design of validation experiments and clinical trials, as such we identify GRB2 as a robust potential new target for RA for its ability to control both synovial degeneracy and dysbiosis, and, conversely, warn on the usage of IRAK4-inhibitors recently promoted, as this involves potential adverse effects in the form of impaired innate response to pathogens.
Functional Selection of shRNA Loops from Randomized Retroviral Libraries

Gene silencing by RNA interference (RNAi) can be achieved by the ectopic expression of tailored short hairpin RNAs (shRNAs) which after export to the cytoplasm are processed by Dicer and incorporated into the RNA induced silencing complex (RISC). Design rules for shRNAs have been the focus of several studies, but only a few reports have turned the attention to the sequence of the loop-region. In this work we selected high-functional and low-functional shRNA loops from retroviral hairpin-loop-libraries in an RNAi reporter assay. The procedure revealed a very significant and stem sequence-dependent effect of the loop on shRNA function and although neither strong consensus loop sequence nor structural motifs could be identified, a preferred loop sequence (5′-UGUGCUU-3′) was found to support robust knock down with little stem sequence dependency. These findings will serve as a guide for designing shRNAs with improved knock down capacity.
Effects of Emotional Response on Adherence to Antihypertensive Medication and Blood Pressure Improvement

Background. Developing interventions to improve medication adherence may depend upon discovery of novel behavioral risk factors for nonadherence. Objective. Explore the effects of emotional response (ER) on adherence to antihypertensive medication and on systolic blood pressure (SBP) improvement. Design. We studied 101 adults with diabetes and hypertension. The primary outcome, 90-day “percentage of days covered” adherence score, was determined from pharmacy refill records. The secondary outcome was change in SBP over 90 days. ER was classified as positive, negative, or neutral. Results. Average adherence was 71.6% (SD 31.4%), and negative and positive ER were endorsed by 25% and 9% of subjects, respectively. Gender moderated the effect of positive or negative versus neutral ER on adherence (interaction P = 0.003); regardless of gender, negative and positive ER were associated with similarly high and low adherence, respectively, but males endorsing neutral ER had significantly higher adherence than their female counterparts (85.6% versus 57.1%, F value = 15.3, P = 0.0002). Adherence mediated ER's effect on SBP improvement: among participants with negative, but not positive or neutral, ER, increasing adherence and SBP improvement were correlated (Spearman's r = 0.49, P = 0.02). Conclusions. Negative, but not positive or neutral, ER predicted better medication adherence and a correlation between medication adherence and improvement in SBP.
Attention selection model using Weight Adjusted Topological properties and quantification evaluating criterion

Topological properties have important function in human beings visual attention. TPQFT (Topological properties based Phase spectrum of Quaternion Fourier Transform) model is an attention selection model using topological properties expression we have introduced. A new quantification criterion to evaluate every channel's contribution and model's performance is proposed in this paper and used in TPQFT. This paper improves TPQFT model in several aspects and WTPQFT (Weight Adjusted Topological properties based Phase spectrum of Quaternion Fourier Transform) model is introduced. The experimental results show that WTPQFT model reflects the real attention selection more accurately than TPQFT and PQFT (Phase spectrum of Quaternion Fourier Transform) method.
Configurable applications for satellite graphics

This paper advocates a configurable approach to software for satellite graphics in which the division of labor between the host and satellite computers can be easily changed after an application program has been written. A software system, CAGES (Configurable Applications for Graphics Employing Satellites), implements this approach. CAGES can substantially simplify the application programmer's task of programming a host and satellite computer by making the intercomputer interface relatively invisible to him, while at the same time allowing him the efficiency and flexibility that can result from direct application programming of the satellite computer.Proper design of configurable programs is facilitated by a mathematical model defining a pairwise measure of program module inter-dependence. Experience with this model has resulted in a set of programming guidelines that further aid the application programmer in producing a suitable program structure.
Evaluation of Commercial and Field-Expedient Baited Traps for House Flies, Musca domestica L. (Diptera: Muscidae)

ABSTRACT: A comparison of nine commercial baited fly traps on Florida dairy farms demonstrated that Terminator traps collected significantly more (13,323/trap) house flies (Musca domestica L.) than the others tested. Final Flight, Fly Magnet, and FliesBeGone traps collected intermediate numbers of flies (834–2,166), and relatively few were caught with ISCA, Advantage, Fermone Big Boy, Squeeze & Snap, or OakStump traps (<300). Terminator traps collected about twice as many flies (799.8/trap) as FliesBeGone traps (343.8) when each trap was baited with its respective attractant, but when the attractants were switched between the two trap types, collections were significantly lower (77–108) than was observed with traps baited with their respective attractant. Solutions of molasses were significantly more attractive to house flies than honey, maple syrup, or jaggery (date palm sugar). Field-expedient traps constructed from discarded PET water bottles were much less effective than commercial traps, but painting the tops of such traps with black spray paint resulted in a six-fold increase in trap capture.
Medical image segmentation using analysis of isolable-contour maps

A common challenge for automated segmentation techniques is differentiation between images of close objects that have similar intensities, whose boundaries are often blurred due to partial-volume effects. The authors propose a novel approach to segmentation of two-dimensional images, which addresses this challenge. Their method, which they call intrinsic shape for segmentation (ISeg), analyzes isolabel-contour maps to identify coherent regions that correspond to major objects. ISeg generates an isolabel-contour map for an image by multilevel thresholding with a fine partition of the intensity range. ISeg detects object boundaries by comparing the shape of neighboring isolabel contours from the map. ISeg requires only little effort from users; it does not require construction of shape models of target objects. In a formal validation with computed-tomography angiography data, the authors showed that ISeg was more robust than conventional thresholding, and that ISeg's results were comparable to results of manual tracing.
Simulating Mechanics to Study Emergence in Games

This paper presents the latest version of the Machinations framework. This framework uses diagrams to represent the flow of tangible and abstract resources through a game. This flow represents the mechanics that make up a game’s interbal economy and has a large impact on the emergent gameplay of most simulation games, strategy games and board games. This paper shows how Machinations diagrams can be used simulate and balance games before they are built.
Mendel versus malthus: research, productivity and food prices in the long run.

Over the past 50 years and longer, the supply of food commodities has grown faster than the effective market demand, in spite of increasing population and per capita incomes. Consequently, the real (deflated) prices of food commodities have steadily trended down. The past increases in agricultural productivity and production, and the resulting real price trends, are attributable in large part to technological changes enabled by investments in agricultural R&D. Evidence is beginning to emerge of a slowdown in the long-term path of agricultural productivity growth. These productivity patterns mirror a progressive slowing down in the growth rate of total spending on agricultural R&D and a redirection of the funds away from farm productivity that began 20-30 years ago.
Artificial neural network modelling and flood water level prediction using extended Kalman filter

Accurate flood water level prediction are essential for reliable flood forecasting modelling. Although back propagation neural network (BPN) offer advantages for flood water level prediction, nonlinearity due to input parameters are the major issue to this modelling. A novel Extended Kalman Filter (EKF) optimization algorithm was employed in this study to overcome the nonlinearity problem and come out with an optimal ANN for the prediction of flood water level 3 hours in advance. The inputs used in the algorithm were current values of rainfall at the flood location and three upstream locations of river water levels. The BPN model was trained and tested successfully with Root Mean Square Error (RMSE) and loss function (V) close to zero.