Miracle-dz/UniFAR-FTUs huggingface dataset:
Dual Field Calibration of Capacitance and Neutron Soil Water Sensors in a Shrinking–Swelling Clay Soil

Multisensor capacitance sensors (MCS) are now popular alternatives to neutron scattering (NS) soil water–monitoring devices. The objectives of this study were to (i) quantify the effect of clay shrinkage–swelling on the soil bulk density; (ii) determine field calibration equations for an MCS and an NS device; and (iii) compare the performance of the MCS with a NS meter under field conditions. The calibration was conducted in a duplex soil with sandy clay loam overlying clay in South Australia. Six access tubes were installed in a 6 by 8 m grid. Three moisture treatments were replicated twice for every moisture level. The bulk density of the top 20 cm increased with increasing water content; this increase was more pronounced in the upper 10‐cm horizon, which could be attributed to soil compaction. However, a negative correlation was obtained between bulk density and water content in the 30‐ to 100‐cm depth layers reflecting the shrinking and swelling properties of the fine‐textured subsoil. Results also show highly significant effects of sampling depth and moisture level on NS and MCS readings. Compared with linear calibration, a three‐parameter model improved NS calibration and/or minimized the root mean square errors for 6 out of the 10 sampling depths. Except for the 10‐cm sampling depth, individual calibration for each 10‐cm soil layer improved the accuracy of the MCS as compared with the use of single calibration equation for the entire profile. Site‐specific calibration improved the accuracy of both the NS and MCS soil water–monitoring devices.
The Role of Interferon Antagonist, Non-Structural Proteins in the Pathogenesis and Emergence of Arboviruses

A myriad of factors favor the emergence and re-emergence of arthropod-borne viruses (arboviruses), including migration, climate change, intensified livestock production, an increasing volume of international trade and transportation, and changes to ecosystems (e.g., deforestation and loss of biodiversity). Consequently, arboviruses are distributed worldwide and represent over 30% of all emerging infectious diseases identified in the past decade. Although some arboviral infections go undetected or are associated with mild, flu-like symptoms, many are important human and veterinary pathogens causing serious illnesses such as arthritis, gastroenteritis, encephalitis and hemorrhagic fever and devastating economic loss as a consequence of lost productivity and high mortality rates among livestock. One of the most consistent molecular features of emerging arboviruses, in addition to their near exclusive use of RNA genomes, is the inclusion of viral, non-structural proteins that act as interferon antagonists. In this review, we describe these interferon antagonists and common strategies that arboviruses use to counter the host innate immune response. In addition, we discuss the complex interplay between host factors and viral determinants that are associated with virus emergence and re-emergence, and identify potential targets for vaccine and anti-viral therapies.
A Preliminary Evaluation of a Computerized Maze Task with Multiple Complexity Levels.

Abstract : To complete a series of experiments on multiple-task performance, it became necessary to identify a spatial task that did not require extensive use of visual short-term memory. The task had to be presented on a computer but, because of the limitations of the available graphics systems, the task could not require color discriminations or movement in three-dimensional space. Very few tasks met these requirements. Of these, the most promising were maze tasks. However, there was one serious problem associated with the use of mazes as experimental tasks: There was no way to describe a maze quantitatively. Such a description is necessary to relate maze characteristics to solution behavior. If the problem of maze quantification could be solved, several other problems remained. One problem was strictly practical in nature: To use mazes in research, it was necessary to develop a computer program that could generate a large number of mazes with specified characteristics. These characteristics could subsequently be quantified and related to solution behavior. A second problem was that the cognitive processes required to solve mazes had never been identified. To use mazes as spatial tasks, it was necessary to demonstrate that verbal information processing is not required to solve mazes.
Structure and Function of CutC Choline Lyase from Human Microbiota Bacterium Klebsiella pneumoniae*

Background: The bacterial glycyl radical enzyme CutC converts choline to trimethylamine, a metabolite involved in pathogenesis of several diseases. Results: The structures of substrate-bound and substrate-free CutC revealed significant differences. Conclusion: Choline binding to the active site triggers a conformational change from the open to closed form. Significance: A novel substrate-driven conformational mechanism and a potential target for drug design have been identified. CutC choline trimethylamine-lyase is an anaerobic bacterial glycyl radical enzyme (GRE) that cleaves choline to produce trimethylamine (TMA) and acetaldehyde. In humans, TMA is produced exclusively by the intestinal microbiota, and its metabolite, trimethylamine oxide, has been associated with a higher risk of cardiovascular diseases. Therefore, information about the three-dimensional structures of TMA-producing enzymes is important for microbiota-targeted drug discovery. We have cloned, expressed, and purified the CutC GRE and the activating enzyme CutD from Klebsiella pneumoniae, a representative of the human microbiota. We have determined the first crystal structures of both the choline-bound and choline-free forms of CutC and have discovered that binding of choline at the ligand-binding site triggers conformational changes in the enzyme structure, a feature that has not been observed for any other characterized GRE.
CENTRIFUGE MODELING OF GRANULAR SOIL RESPONSE OVER ACTIVE CIRCULAR TRAPDOORS

The trapdoor problem is a useful model for providing a clearer understanding of stress distribution around basic geotechnical engineering structures such as tunnels, conduits and anchor plates. The interest is mainly directed towards the determination of soil load on the trapdoor, which can be substantially different from the initial geostatic loads, when the trapdoor is moved even slightly. Development of shear bands around the yielding trapdoor is also of interest. A series of centrifuge and 1g model tests were conducted to study active arching in dry granular soil on circular trapdoors. The study was undertaken mainly because of two reasons: (i) limited success in earlier centrifuge modeling studies of a trapdoor problem, and (ii) a lack of understanding of the load-displacement characteristics under axisymmetric conditions. A trapdoor assembly and in-flight precompression technique were developed to perform a series of tests involving different overburden soil thickness on circular doors of different diameters. Correct initial geostatic loads were measured. Greater confidence in the experimental results was obtained because modeling of models type experiments were also successful. A parametric study involving different overburden soil thickness to trapdoor diameter ratios (H/D) ranging from 0.67 to 6 was conducted. The pattern of shear bands in sand above the trapdoor observed in a centrifuge model under a high gravity field differed considerably from that in a 1g model. Maximum arching was completely mobilized at movements of only 1.5% of trapdoor diameter. The minimum load on the trapdoor became constant at H/D equal to 5 regardless of the initial overburden pressure or height of the soil model.
Prevalence and dissemination of Salmonella serotypes along the slaughtering process in Brazilian small poultry slaughterhouses.

Salmonella is the leading cause of human foodborne infections in Latin America, and poultry meat is one of the main vehicles. Small poultry slaughterhouses (fewer than 200 birds slaughtered per day) represent an important economic activity in certain regions. The slaughtering process in these abattoirs is manual and rudimentary, and frequently the hygienic conditions are poor. This study reports results of a detailed evaluation of the prevalence of Salmonella serotypes in carcasses, utensils, and environmental samples collected in 60 small Brazilian slaughterhouses. In the second step of the study, one of these slaughterhouses was selected to monitor the dissemination of Salmonella along the slaughtering process. For testing, conventional procedures were used: preenrichment in buffered peptone water (35 degrees C for 24 h), selective enrichment in Selenite-cystine (35 degrees C for 24 h), tetrathionate and Rappaport-Vassiliadis broths (42 degrees C for 24 h), plating on bismuth-sulfite and brilliant green agars (35 degrees C for 24 h), proper biochemical testing, and complete serotyping. Forty-one percent of samples harbored Salmonella spp. , including 42% of carcasses, 23.1% of utensils, 71.4% of water, and 71.4% of freezers and refrigerators. Seventeen serotypes were detected. Salmonella Enteritidis predominated (30%), followed by Salmonella Albany (12%), Salmonella Hadar (12%), Salmonella Indiana (10%), and I 4,12:z:- (8%). All samples collected along the slaughtering process in the selected slaughterhouse were Salmonella positive. Five serotypes were detected, including Salmonella Albany, Salmonella Hadar, Salmonella Agona, Salmonella Emek, and Salmonella Indiana. More than 30% of the samples contained more than one serotype, and 12.5% presented three serotypes. The widespread occurrence of Salmonella in small slaughterhouses reinforces the need for implementation of effective control measures.
The tertiary creep of polycrystalline ice: experimental evidence for stress-dependent levels of strain-rate enhancement

Laboratory creep deformation experiments have been conducted on initially isotropic laboratory-made samples of polycrystalline ice. Steady-state tertiary creep rates, ∈ · ter , were determined at strains exceeding 10% in either uniaxial-compression or simple-shear experiments. Isotropic minimum strain rates, ∈ · min , determined at ∼1% strain, provide a reference for comparing the relative magnitude of tertiary creep rates in shear and compression through the use of strain-rate enhancement factors, E , defined as the ratio of corresponding tertiary and isotropic minimum creep rates, i.e. E = ∈ · ter / ∈ · min . The magnitude of strain-rate enhancement in simple shear was found to exceed that in uniaxial compression by a constant factor of 2.3. Results of experiments conducted at octahedral shear stresses of τ o = 0.04–0.80 MPa indicate a creep power-law stress exponent of n = 3 for isotropic minimum creep rates and n = 3.5 for tertiary creep rates. The difference in stress exponents for minimum and tertiary creep regimes can be interpreted as a τ o stress-dependent level of strain-rate enhancement, i.e. E α τ 1/2 o . The implications of these results for deformation in complex multicomponent stress configurations and at stresses below those used in the current experiments are discussed.
A fast two-pass HDL simulation with on-demand dump

Simulation-based functional verification is characterized by two inherently conflicting targets: the signal visibility and simulation performance. Achieving a proper trade-off between these two targets is of paramount importance. Even though HDL simulators are the most widely used verification platform at the RTL and gate level, their major drawback is the low performance in verifying complex SOCs, especially when the high visibility over the design under verification is required. This paper presents a new, fast simulation method as an effective way to achieve both high simulation speed and full signal visibility. It is based on an original two-pass simulation approach. During the 1st pass, with the simulation running at full speed, a set of design states is saved periodically at predetermined checkpoints. During the 2nd pass, another simulation is performed, using any of saved checkpoints and providing 100% signal visibility for debugging. Our method differs from the traditional simulation snapshot approach in the amount and the way the design state is saved. Experimental results show significant speed-up compared to existing traditional simulation methods while maintaining 100% visibility.
Antibodies to West Nile Virus in Wild and Farmed Crocodiles in Southeastern Mexico

Surveillance for evidence of West Nile virus (WNV) infection in Morelet’s crocodiles (Crocodylus moreletii) was conducted in Campeche State, Mexico, in 2007. Sera from 62 crocodiles (32 free-ranging and 30 captive) were assayed for antibodies to WNV by epitope-blocking enzyme-linked immunosorbent assay. Antibodies to WNV were detected in 13 (41%) wild and nine (30%) captive crocodiles, and the overall antibody prevalence was 35%. Although evidence of WNV infection in captive crocodiles has been reported in Mexico, we provide the first evidence of WNV exposure in wild crocodiles in Mexico.
A corpus-based approach to language learning

A CORPUS BASED APPROACH TO LANGUAGE LEARNING Eric Brill Supervisor Mitchell Marcus One goal of computational linguistics is to discover a method for assigning a rich struc tural annotation to sentences that are presented as simple linear strings of words meaning can be much more readily extracted from a structurally annotated sentence than from a sentence with no structural information Also structure allows for a more in depth check of the well formedness of a sentence There are two phases to assigning these structural annotations rst a knowledge base is created and second an algorithm is used to generate a structural annotation for a sentence based upon the facts provided in the knowledge base Until recently most knowledge bases were created manually by language experts These knowledge bases are expensive to create and have not been used e ectively in structurally parsing sentences from other than highly restricted domains The goal of this dissertation is to make signi cant progress toward designing automata that are able to learn some struc tural aspects of human language with little human guidance In particular we describe a learning algorithm that takes a small structurally annotated corpus of text and a larger unannotated corpus as input and automatically learns how to assign accurate structural descriptions to sentences not in the training corpus The main tool we use to automati cally discover structural information about language from corpora is transformation based error driven learning The distribution of errors produced by an imperfect annotator is examined to learn an ordered list of transformations that can be applied to provide an accurate structural annotation We demonstrate the application of this learning algorithm
Seeing It My Way or Your Way: Frontoparietal Brain Areas Sustain Viewpoint-independent Perspective Selection Processes

A hallmark of human social interaction is the ability to consider other people's mental states, such as what they see, believe, or desire. Prior neuroimaging research has predominantly investigated the neural mechanisms involved in computing one's own or another person's perspective and largely ignored the question of perspective selection. That is, which brain regions are engaged in the process of selecting between self and other perspectives? To address this question, the current fMRI study used a behavioral paradigm that required participants to select between competing visual perspectives. We provide two main extensions to current knowledge. First, we demonstrate that brain regions within dorsolateral prefrontal and parietal cortices respond in a viewpoint-independent manner during the selection of task-relevant over task-irrelevant perspectives. More specifically, following the computation of two competing visual perspectives, common regions of frontoparietal cortex are engaged to select one's own viewpoint over another's as well as select another's viewpoint over one's own. Second, in the absence of conflict between the content of competing perspectives, we showed a reduced engagement of frontoparietal cortex when judging another's visual perspective relative to one's own. This latter finding provides the first brain-based evidence for the hypothesis that, in some situations, another person's perspective is automatically and effortlessly computed, and thus, less cognitive control is required to select it over one's own perspective. In doing so, we provide stronger evidence for the claim that we not only automatically compute what other people see but also, in some cases, we compute this even before we are explicitly aware of our own perspective.
Risk Factors for Self-Reported Adverse Drug Events Among Medicare Enrollees

Background: Adverse drug events (ADEs) occur in older adults. ADEs occur in up to 6.5% of all hospitalized patients and outpatients, and about 28% of these events are preventable. The proportion of outpatients with an ADE ranges from 5% to 35%, depending on the exact definition used. There is a critical need to examine the risk factors associated with having an ADE to increase awareness about medication safety among older adults. Objective: To quantify the association between risk factors such as the number of pharmacies used by patients and their concern and necessity beliefs about medicines, and self-reported ADEs. Methods: A cross-sectional Internet survey was administered by Harris Interactive. Harris Interactive asked individuals from their online panel who were 65 years of age or older, US residents, and enrolled in Medicare to complete the survey. A convenience sample of 1220 anonymous surveys was obtained. Multiple logistic regression analysis was performed. The dependent variable was self-reported ADEs, defined as the patient's visiting a physician to report an unwanted reaction or medicine problem in the past year. Independent variables included sociodemographics, self-rated health, number of medications, sum of symptoms experienced, concern and necessity beliefs about medicines, number of pharmacies, and whether subjects skipped doses of their medications to save money or stopped taking the drugs due to cost. Results: Eighteen percent of respondents reported an ADE. ADEs were related to being female (OR 1.56; 95% CI 1.05 to 2.33), number of pharmacies (OR 3.40; 95% CI 1.56 to 7.41), number of symptoms experienced (OR 3.39; 95% CI 1.87 to 6.14), concern beliefs about medicines (OR 1.14; 95% CI 1.08 to 1.20), and having a graduate academic degree (OR 2.17; 95% CI 1.41 to 3.36). Conclusions: The number of pharmacies, concern beliefs about medicines, and number of symptoms experienced in the past month were associated with self-reported ADEs. Discussing patients’ beliefs about their drug therapy with them is likely to affect their expectations and interpretation of symptoms, as well as future attributions regarding drug therapy.
Sequence Typing and Comparison of Population Biology of Campylobacter coli and Campylobacter jejuni

ABSTRACT A multilocus sequence typing (MLST) scheme that uses the same loci as a previously described system for Campylobacter jejuni was developed for Campylobacter coli. The C. coli-specific primers were validated with 53 isolates from humans, chickens, and pigs, together with 15 Penner serotype reference isolates. The nucleotide sequence of the flaA short variable region (SVR) was determined for each isolate. These sequence data were compared to equivalent information for 17 C. jejuni isolates representing the known genetic diversity of this species. C. coli and C. jejuni share approximately 86.5% identity at the nucleotide sequence level within the MLST loci. There is evidence of genetic exchange of the housekeeping genes between the two species, but at a very low rate; only one sequence type from each species showed evidence of imported DNA. The flaA gene was more variable and has been exchanged many times between the two species, making it an unreliable marker for species identification but useful for distinguishing closely related strains. All but 3 of 21 human C. coli clinical isolates were distinct, according to the combined MLST and SVR sequences. The use of a common MLST scheme allows direct comparisons of the population biology and molecular epidemiology of these two closely related human pathogens.
Effectiveness/efficiency tradeoffs for candidate generation in multi-stage retrieval architectures

This paper examines a multi-stage retrieval architecture consisting of a candidate generation stage, a feature extraction stage, and a reranking stage using machine-learned models. Given a fixed set of features and a learning-to-rank model, we explore effectiveness/efficiency tradeoffs with three candidate generation approaches: postings intersection with SvS, conjunctive query evaluation with WAND, and disjunctive query evaluation with WAND. We find no significant differences in end-to-end effectiveness as measured by NDCG between conjunctive and disjunctive WAND, but conjunctive query evaluation is substantially faster. Postings intersection with SvS, while fast, yields substantially lower end-to-end effectiveness, suggesting that document and term frequencies remain important in the initial ranking stage. These findings show that conjunctive WAND is the best overall candidate generation strategy of those we examined.
Conversion of sub-surface reflectances to above-surface MERIS reflectance

Factors for converting sub-surface reflectances to above-surface MERIS reflectances have been determined both as analytic functions and average numbers for solar zenith angles in the range 30°–75°, wind speeds up to 10 m s−1, and the spectral domain 400–700 nm. The conversion factors have been obtained by numerical and statistical computations based on field observations of spectral radiance and irradiance, above and below the surface of the sea. The estimated maximum errors of the different algorithms range from ≤0.1% up to 10%, depending on the chosen method and the types of optical quantities that are available. The errors are smallest for solar zenith angles between 30° and 60° and increase when the solar zenith angle approaches 75°. The influence of the wind on the conversion factors is practically negligible. The algorithms, which have been derived for conditions representative of the Skagerrak and the adjacent seas, are assumed to be valid for both Case 1 and 2 waters.
The Global Geopotential Models in the Region of Korean Peninsula

The purpose of this paper is to establish the optimum reference field as testing some geopotential model, gravity data and GPS data. We have to decide a best fitting geopotential model as a reference surface for establishing the optimum geoid solutions. We conduct some tests on the Korean Peninsula gravity data to establish which of the model would be prove to be the best one. Three ways were used to compare the geopotential coefficient solutions. One of the tests is to compare the residual gravity anomaly remaining after the anomaly computed from the geopotential model has been subtracted from the "observed" gravity anomaly. The second method is a comparison of several geopotential solutions in terms of differences in gravity anomalies and quasi-geoid undulations. The third method is a comparison between the undulation obtained by GPS and the corresponding undulation from each geopotential model. The result showed that OSU91A model is a best fitting model as a reference in the region of Korean Peninsula.Peninsula.