Miracle-dz/UniFAR-FTUs huggingface dataset:
OryR Is a LuxR-Family Protein Involved in Interkingdom Signaling between Pathogenic Xanthomonas oryzae pv. oryzae and Rice

ABSTRACT Xanthomonas oryzae pv. oryzae, the causal agent of bacterial leaf blight in rice, contains a regulator that is encoded in the genome, designated OryR, which belongs to the N-acyl homoserine lactone (AHL)-dependent quorum-sensing LuxR subfamily of proteins. However, we previously reported that X. oryzae pv. oryzae does not make AHLs and does not possess a LuxI-family AHL synthase and that the OryR protein is solubilized by a compound present in rice. In this study we obtained further evidence that OryR interacts with a rice signal molecule (RSM) and that the OryR concentration increases when rice is infected with X. oryzae pv. oryzae. We also describe three OryR target promoters which are regulated differently: (i) the neighboring proline iminopeptidase (pip) virulence gene, which is positively regulated by OryR in the presence of the RSM; (ii) the oryR promoter, which is negatively autoregulated independent of the RSM; and (iii) the 1,4-β-cellobiosidase cbsA gene, which is positively regulated by OryR independent of the RSM. We also found that the RSM for OryR is small, is not related to AHLs, and is not able to activate the broad-range AHL biosensor Agrobacterium tumefaciens NT1(pZLQR). Furthermore, OryR does not regulate production of the quorum-sensing diffusible signal factor present in the genus Xanthomonas. Therefore, OryR has unique features and is an important regulator involved in interkingdom communication between the host and the pathogen.
Experimental Studies of the Molecular Pathways Regulated by Exercise and Resveratrol in Heart, Skeletal Muscle and the Vasculature

Regular exercise contributes to healthy aging and the prevention of chronic disease. Recent research has focused on the development of molecules, such as resveratrol, that activate similar metabolic and stress response pathways as exercise training. In this review, we describe the effects of exercise training and resveratrol on some of the organs and tissues that act in concert to transport oxygen throughout the body. In particular, we focus on animal studies that investigate the molecular signaling pathways induced by these interventions. We also compare and contrast the effects of exercise and resveratrol in diseased states.
Modeling of Purchase and Sales Contracts in Supply Chain Optimization

This work presents a novel approach for modeling of different types of contracts that a company may sign with its suppliers and customers. The main objective is to expand the scope of current planning and supply chain optimization models by including the selection of the types of contracts as an additional decision. The solution approach relies on representing the decision of choosing different contracts using disjunctive programming for both short-term and long-term production planning models. The resulting formulation is converted into a mixed-integer linear programming (MILP) problem. The advantages of the proposed models are highlighted in two case studies of increasing complexity
Categorizing Sources of Risk and the Estimated Magnitude of Risk

The social perception of risk is considered a multidimensional task, yet little attention has been paid to the cognitive components that organize sources of risk, despite their having been discovered in various research studies. This study attempts to concretely analyze the cultural dimension involved in those processes. In the first phase, we tried to discover to what extent sources of risk are organized into the same categories by people from different countries. In order to do so, two groups of participants were formed: 60 Spanish psychology students and 60 Chilean psychology students classified 43 sources of risk into different groups according to the criteria they found appropriate. The two samples classified risk into identical groups: acts of violence, drugs, electricity and home appliances, household chemicals, chemicals in the environment, public construction projects, transportation, sports, and natural disasters. In a second study, 100 Spanish and 84 Chilean students were asked to evaluate the magnitude of the damage incurred by 17 sources of risk. In both groups, it was observed that the evaluation of damage resulting from each source of risk was affected by its category. La percepción social del riesgo se considera una tarea multidimensional, sin embargo se ha prestado poca atención a los componentes cognitivos que organizan las fuentes del riesgo, a pesar de que se han descubierto en varios estudios de investigación. Concretamente, este estudio intenta analizar la dimensión cultural implicada en esos procesos. En primer lugar, intentamos descubrir hasta qué punto personas de diferentes países organizan las fuentes de riesgo en las mismas categorías. Para ello, se formaron dos grupos de participantes: 60 estudiantes de psicología españoles y 60 estudiantes de psicología chilenos clasificaron 43 fuentes de riesgo en diferentes grupos según los criterios más apropiados para ellos. Las dos muestras clasificaron el riesgo en grupos idénticos: actos de violencia, drogas, electricidad y electrodomésticos, productos químicos domésticos, productos químicos en el medioambiente, proyectos de construcción públicos, transporte, deportes y desastres naturales. En un segundo estudio, 100 estudiantes españoles y 84 chilenos evaluaron la magnitud del daño provocado por 17 fuentes de riesgo. En ambos grupos, se observó que la categoría afectaba la evaluación del daño resultante de cada fuente de riesgo.
A Practical Quality Index Based on the Octahedral Manipulator

The octahedral manipulator is a "3-3" device that is fully in parallel. It has a linear actuator on each of its six legs. The legs connect an equilateral platform triangle to a similar base triangle in a zigzag pattern between vertices. Our proposed quality index takes a maximum value of 1 at a central symmet rical configuration that is shown to correspond to the maxi mum value of the determinant of the 6 x 6 Jacobian matrix of the manipulator. This matrix is none other than that of the nor malized line coordinates of the six leg-lines; for its determi nant to be a maximum, the platform triangle is found to be half of the size of the base triangle, and the perpendicular distance between platform and base is equal to the side of the platform triangle. When the manipulator is actuated so that the octahedron departs from this central configuration, the determinant al ways diminishes, and, as is well known, it becomes zero when a special configuration is reached (the platform then gain ing one or more uncontrollable freedoms). Our quality index λ, 0 ≤ λ ≤ 1, is a constructive measure of acceptable design proportions. The double-spherical joints (there are six) are the source of the critical practical difficulties. Kinematic substitutions can circumvent this problem, but often there is no reasonable alternative to accepting a reduction of maximum quality index through separation by fairly short distances of some or all of the double-ball joints. Too great a separation easily leads too far toward generality; any fully-in-parallel manipulator of more general proportions should be tested for quality against our octahedral form simply because no different form can be superior to a well-designed octahedron from the points of view of structural soundness and ability to apply both forces and controlled displacements to the end-effector platform.
Employees are ambivalent about health checks in the occupational setting.

BACKGROUND Employees are increasingly provided with preventive health checks. However, participation rates are low and several ethical issues arise, such as a potential perceived threat to autonomy and privacy. AIMS To assess what employees think about preventive health checks in the occupational setting. METHODS Samples of construction workers and the general working population in the Netherlands completed a survey about preventive health checks in the occupational setting. We asked half of each sample about potential benefits and drawbacks of health checks, and the other half about how they should be offered. We employed explorative factor analysis to identify constructs related to perceived benefits and drawbacks, and the way health checks should be provided. We then conducted descriptive analyses and t-tests to compare subgroups of respondents. RESULTS A total of 482 (27%) of construction workers and 738 (65%) employees from the general population responded. The overall survey response rate was 42% with 41% completing the first questionnaire and 42% the second. We identified three constructs related to perceived benefits and drawbacks: self-control over health, disturbance and negative emotion and lack of autonomy. Participants rated 'self-control over health' as the highest potential benefit (mean = 3.40; SD = 0.69), and 'your employer interfering in your personal life' as the most important potential drawback (mean = 3.27; SD = 1.00). Participants indicated that they would like to receive help from their occupational physician when an increased health risk is identified (mean = 4.02; SD = 0.69). CONCLUSIONS Employees are ambivalent and hesitant concerning preventive health checks in the occupational setting.
Cache-efficient dynamic programming algorithms for multicores

We present cache-efficient chip multiprocessor (CMP) algorithms with good speed-up for some widely used dynamic programming algorithms. We consider three types of caching systems for CMPs: D-CMP with a private cache for each core, S-CMP with a single cache shared by all cores, and Multicore, which has private L1 caches and a shared L2 cache. We derive results for three classes of problems: local dependency dynamic programming (LDDP), Gaussian Elimination Paradigm (GEP), and parenthesis problem. For each class of problems, we develop a generic CMP algorithm with an associated tiling sequence. We then tailor this tiling sequence to each caching model and provide a parallel schedule that results in a cache-efficient parallel execution up to the critical path length of the underlying dynamic programming algorithm. We present experimental results on an 8-core Opteron for two sequence alignment problems that are important examples of LDDP. Our experimental results show good speed-ups for simple versions of our algorithms.
The grand coalition versus competing coalitions: trade-offs in how to standardize

The standardization landscape in the information and communication technology industries is fragmented in many different standardization bodies, industry consortia, and alliances. The existence of competing standardization coalitions may prevent coordination on a common standard. There is a lot of debate among practitioners and analysts about whether this fragmentation creates a coordination failure. Competition between standardization coalitions may harm compatibility. It also helps to mitigate coordination failures that occur within industry-wide standardization bodies and coalitions. The negotiation process in a coalition can cause coordination failures of its own. Technology sponsors may insist on their preferred technology being accepted as standard. Their intransigence slows down the selection of a standard. Introducing competition between coalitions can speed up negotiations within them, and thus help to overcome this infra-committee coordination failure. A game theoretic model formalises this view. It explores the effect of competition between coalitions on the speed of decision-making and standardization. It finds that a fear for incompatibility may hold back competing committees to the point that a grand coalition may actually adopt a standard faster than competing committees would. This result debunks sweeping statements that industry-wide coalitions or standards bodies are necessarily slow compared to strategic alliances and consortia.
Comparative social cognition: From wolf and dog to humans

Dogs’ special domestication processes, their natural socialization to humans, and the possibility of tracing evolutionary changes by comparing dogs’ behavior to that of wolves, make dogs altogether unique for studying the evolution of complex social behavior. Here the authors report some much needed comparisons between the behavior of dogs and wolves. The authors reveal some dog-specific behaviors, especially with regard to their interactions with humans, by comparing dogs and wolves hand-reared identically. This approach ensures that behavioral differences between dogs and wolves will be due to species-specific (genetic) differences, and not to differences in experience. The results indicate that social attraction, presumably synchronizing behavior, and communicative abilities of dogs changed markedly during the process of domestication. The authors suggest that this model of dog behavior has the potential to provide new insights into the evolution of human socio-cognitive behavior.
A Role for Poly(ADP-ribose) Polymerase in the Transcriptional Regulation of the Melanoma Growth Stimulatory Activity (CXCL1) Gene Expression*

The melanoma growth stimulatory activity/growth-regulated protein, CXCL1, is constitutively expressed at high levels during inflammation and progression of melanocytes into malignant melanoma. It has been shown previously that CXCL1 overexpression in melanoma cells is due to increased transcription as well as stability of the CXCL1 message. The transcription ofCXCL1 is regulated through several cis-acting elements including Sp1, NF-κB, HMGI(Y), and the immediate upstream region (IUR) element (nucleotides −94 to −78), which lies immediately upstream to the nuclear factor κB (NF-κB) element. Previously, it has been shown that the IUR is necessary for basal and cytokine-induced transcription of the CXCL1 gene. UV cross-linking and Southwestern blot analyses indicate that the IUR oligonucleotide probe selectively binds a 115-kDa protein. In this study, the IUR element has been further characterized. We show here that proximity of the IUR element to the adjacent NF-κB element is critical to its function as a positive regulatory element. Using binding site oligonucleotide affinity chromatography, we have selectively purified the 115-kDa IUR-F. Mass spectrometry/mass spectrometry/matrix-assisted laser desorption ionization/time of flight spectroscopy and amino acid analysis as well as microcapillary reverse phase chromatography electrospray ionization tandem mass spectrometry identified this protein as the 114-kDa poly(ADP-ribose) polymerase (PARP1). Furthermore, 3-aminobenzamide, an inhibitor of PARP-specific ADP-ribosylation, inhibits CXCL1 promoter activity and reduces levels of CXCL1 mRNA. The data point to the possibility that PARP may be a coactivator of CXCL1 transcription.
The multimodulus blind equalization and its generalized algorithms

This paper presents a new blind equalization algorithm called multimodulus algorithm (MMA). This algorithm combines the benefits of the well-known reduced constellation algorithm (RCA) and constant modulus algorithm (CMA). In addition, MMA provides more flexibility than RCA and CMA, and is better suited to take advantage of the symbol statistics of certain types of signal constellations, such as nonsquare constellations, very dense constellations, and some wrong solutions.
1 FASH and MASH : F emale and M ale A dult human phantoms based on polygon me SH surfaces Part II : Dosimetric calculations

Female and male adult human phantoms, called FASH (Female Adult meSH) and MASH (Male Adult meSH), have been developed in the first part of this study using 3D animation software and anatomical atlases to replace the image-based FAX06 and the MAX06 voxel phantoms. 3D modelling methods allow for phantom development independent from medical images of patients, volunteers or cadavers. The second part of this study investigates the dosimetric implications for organ and tissue equivalent doses due to the anatomical differences between the new and the old phantoms. These differences are mainly caused by the supine position of human bodies during scanning in order to acquire digital images for voxel phantom development. Compared to an upright standing person, in image-based voxel phantoms organs are often coronally shifted towards the head and sometimes the sagittal diameter of the trunk is reduced by a gravitational change of the fat distribution. In addition, volumes of adipose and muscle tissue shielding internal organs are sometimes too small, because adaptation of organ volumes to ICRP-based organ masses often occurs at the expense of general soft tissues, such as adipose, muscle or unspecified soft tissue. These effects have dosimetric consequences, especially for partial body exposure, such as in X-ray diagnosis, but also for whole body external exposure and for internal exposure. Using the EGSnrc Monte Carlo code, internal and external exposure to photons and electrons has been simulated with both pairs of phantoms. The results show differences between organ and tissue equivalent doses for the upright standing FASH/MASH and the image-based supine FAX06/MAX06 phantoms of up to 80% for external exposure and up to 100% for internal exposure. Similar differences were found for external exposure between FASH /MASH and REGINA/REX, the reference voxel phantoms of the International Commission on Radiological Protection. Comparison of effective doses for external photon exposure showed good agreement between FASH/MASH and REGINA/REX, but large differences between FASH/MASH and the mesh-based RPI_AM and the RPI_AF phantoms, developed at the Rensselaer Polytechnic Institute (RPI).
Occurrence of anthelmintic resistant nematodes on sheep farms in England and goat farms in England and Wales

A survey in 1992 showed that 44 per cent of the sheep farms tested in the south west and 15 per cent of those in the north east of England had parasitic nematode worm burdens which were resistant to benzimidazole anthelmintics, and that 65 per cent of the non-dairy goat farms tested in England and Wales had resistant worms. Ostertagia circumcincta was the main species in sheep and Haemonchus contortus in goats. The resistance to benzimidazoles was diagnosed by a combination of an egg hatch assay and a larval develop ment test. A simplified faecal egg count reduction test was used to investigate sheep and goat farms for signs of ivermectin resistance but no positive cases were detected. The initial identification of levamisole resistance on one farm, both from a faecal egg count reduction test and a positive larval development test, was confirmed by a ‘dose and slaughter’ trial.
E-commerce diffusion in high-income developing countries : determinants of e-commerce adoption and post-adoption of Saudi enterprises

The ubiquitous nature of e-commerce in developing countries demands an innovative conceptualisation of its adoption and post-adoption that responds to various contextual circumstances. Despite efforts made to investigate e-commerce adoption in developing countries, the literature suggests that the focus is mostly on a single perspective of a single adoption stage and concentrates on specific locations. To extend our understanding of the phenomenon, an exploratory phase is undertaken through a literature review as well as an exploratory investigation. Consequently, a holistic framework is integrated that includes organisational and environmental factors, in addition to innovation attributes. The framework is empirically validated using a statistically representative sample size of 384 enterprises of various sizes and industries in a high-income developing country from a poorly investigated region. The empirical analysis shows that perceived benefits as well as mimetic pressure are more influential for the adoption of e-commerce and scope of use than the utilisation amongst adopter organisations. In addition to coercive pressure, the readiness of financial institutions, IT industry and the government affect the scope of e-commerce use. For adopter firms, the extent of e-commerce adoption is influenced by business process readiness, government readiness and security. Commitment, especially from top managers, is a key determinant that links e-commerce adoption to the extent of adoption and the scope of e-commerce use. The findings indicate that the proposed models are sufficiently reliable in discriminating not only adopters from non-adopters, but also the extent of adoption and use across the value chain. Together, this research offers a multi-perspective framework of e-commerce adoption and post-adoption in high-income developing countries and identifies the factors that affect e-commerce adoption, and how these effects vary across adoption stages. It presents insight into various issues that influence e-commerce adoption and post-adoption in this little-explored region, which will be of interest to researchers, practitioners and policy makers.
Blood Genomics in Human Stroke

Advances in microarray technology and the sequencing of the human genome are opening up new possibilities for applying genomic information in clinical medicine, using information about structural polymorphisms in DNA and changes in gene expression as measured by mRNA. Gene expression profiling studies in cancer samples have led to the identification of clinical signatures that are already being applied in some centers. In stroke, it may be possible to use peripheral blood as a source of mRNA to study gene expression. After stroke, there is a selective recruitment and migration of white blood cells to the ischemic focus in the brain. This appears to involve all white cell types and is believed to impact significantly on tissue and clinical outcome through the exacerbation of ischemic injury, particularly after reperfusion, on the one hand, and conversely contributing to tissue remodeling and repair days to weeks after stroke. The first results from clinical studies in ischemic stroke suggest that a gene expression signature can be demonstrated from peripheral white blood cells and that this represents at least a partial adaptation to the altered cerebral microenvironment. Further studies are indicated to see whether these methods may lead to new management approaches for stroke.
First Identification of “Brachyspira hampsonii” in Wild European Waterfowl

Anseriformes deserve special attention in the epidemiology of Brachyspira spp. because diverse Anseriformes species have been described to act as highly efficient carriers of several Brachyspira spp. that can also infect livestock. The aim of this study was to investigate the prevalence and diversity of Brachyspira spp. in waterfowl that winter in Spain. Brachyspira spp. were isolated from 51 of the 205 faecal samples collected from graylag geese and mallards in the Villafáfila Lagoons Nature Reserve (Northwestern Spain). The Brachyspira species identified through phenotyping, PCR and sequencing of the nox gene were B. pilosicoli (5.9%), B. alvinipulli (11.8%), "B. hampsonii" (19.6%), B. murdochii (23.5%) and B. innocens (39.2%). The most relevant finding of this study is the description of "B. hampsonii" in specimens from birds for the first time. Phylogenetic analysis of the nox gene sequences grouped all of the obtained "B. hampsonii" isolates into a cluster with Brachyspira strains previously identified by others as "B. hampsonii" and separated from other Brachyspira spp. isolates and reference strains. Additionally, this cluster was related to clades that grouped B. murdochii and B. innocens isolates. The identification of “B. hampsonii” was also achieved in 8 of the 10 isolates by sequencing the16S rRNA gene and tlyA gene. Regardless of the species identified, no antimicrobial resistance was observed in any of the enteropathogenic isolates recovered. This is the first description of “B. hampsonii” in European waterfowl, which might represent hosts that serve as natural reservoirs of this Brachyspira species. This finding indicates that this spirochete is not limited to North America, and its presence in wild birds in Europe poses a risk of transmission to livestock.