Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparison of Different Tests to Diagnose Feline Infectious Peritonitis

Clinical data from 488 cats (1979–2000) with histopathologically confirmed feline infectious peritonitis (FIP) and 620 comparable controls were evaluated retrospectively to assess the value of several diagnostic tests frequently used in the evaluation of cats with suspected FIP. Diagnostic utility of serum albumin to globulin ratio for the diagnosis of FIP was greater than of the utility of serum total protein and ‐/‐globulin concentrations. Diagnostic utility of these variables was higher when performed on effusion. On effusion, positive and negative predictive values of Rivalta's test, a test that distinguishes between exudates and transudates (0.86 and 0.97), anti‐coronavirus antibody detection (0.90 and 0.79), and immunofluorescence staining of coronavirus antigen in macrophages (1.00 and 0.57) were investigated. The positive and negative predictive values of presence of anti‐coronavirus antibodies were 0.44 and 0.90, respectively, antibody concentrations (1:1,600) were 0.94 and 0.88, presence of immune complexes measured by a competitive enzyme‐linked immunosorbent assay were 0.67 and 0.84, and detection of viral RNA by serum reverse‐transcrip‐tase polymerase chain reaction (RT‐PCR) were 0.90 and 0.47. Effusion RT‐PCR was performed in 6 cats; it was positive in all 5 cats with FIP and negative in the cat with another disease. Diagnostic assays on the fluid in cats with body effusion had good predictive values. Definitive diagnosis of FIP on the basis of measurement of various variables in serum was not possible. Serum tests can only be used to facilitate the decision for more invasive diagnostic methods.
Alternate row sowing: a novel approach to maintain sown species in mixed pasture swards

Establishing and maintaining a balanced mixture of perennial and annual pasture species is often difficult, especially in drier environments. One method to reduce the competition between pasture species and to improve the potential productivity and nitrogen fixed by the pasture is to establish pasture species in separate rows (alternate row sowings). An experimental field site was established in the autumn of 2012 near Mirrool in southern NSW. Medicago sativa and Phalaris aquatica were sown in combination with a range of annual legumes either as a monoculture, mixture, or arranged in alternate rows in 1:1 or 1:2 ratios. Legumes were inoculated with appropriate rhizobia and the sites were fertilised with Starter 15 at 150 kg/ ha. Seedling establishment, regeneration and dry matter (DM) were measured each year until 2014. Annual legume seed reserves and nitrogen fixation (N-fix) were measured in 2013. Alternate row sowing improved seedling regeneration and annual legume seed reserves in some situations; however, it did not significantly improve mean DM, mean legume DM or N-fix. In contrast the choice of species combinations impacted on these responses. For example, the inclusion of P. aquatica in the pasture mix tended to increase mean DM, although if N-fix and mean legume DM were to be maintained at acceptable levels, M. sativa and Trifolium subterraneum were important inclusions in combination with P. aquatica.
Near-infrared Raman spectroscopy of human coronary arteries: histopathological classification based on Mahalanobis distance.

OBJECTIVE In this study, near-infrared Raman spectroscopy (NIRS) was used for evaluation of human atherosclerotic lesions using a simple algorithm based on discriminant analysis. The Mahalanobis distance was used to classify the clustered spectral features extracted from NIRS of a total of 111 arterial fragments of human coronary arteries. BACKGROUND DATA Raman spectroscopy has been used for diagnosis of a variety of diseases. For real-time applications, it is important to have a simple algorithm that could perform fast data acquisition and analysis. The ultimate goal is to obtain a feasible diagnosis, which discriminates various atherosclerotic lesions with high sensitivities and specificities. MATERIALS AND METHODS Non-atherosclerotic (NA) arteries, atherosclerotic plaques without calcification (NC), and atherosclerotic plaques with classification (C) were obtained and scanned with an NIR Raman spectrometer with 830-nm laser excitation. An algorithm based on the discriminant analysis using the Mahalanobis distance of the clustered spectral features was used for tissue classification into three categories: Na, NC, and C. RESULTS Human coronary arteries exhibit different spectral signatures depending on different bio-chemicals present in each tissue type such as collagen, cholesterol, and calcium hydroxyapatite, respectively. It is shown that our algorithm has a maximum sensitivity and specificity of 85% and 89%, respectively, for the diagnosis of the NA tissue type, 85% and 89% for the NC tissue type, and 100% and 100% for the C tissue type. CONCLUSION An algorithm (with a minimum of mathematical and computational requirements) based on the discriminant analysis of spectral features has been developed to classify atherosclerotic lesions with high sensitivities and specificities.
Variations in Student Mental Health and Treatment Utilization Across US Colleges and Universities

Abstract Objective: On US college campuses, mental health problems are highly prevalent, appear to be increasing, and are often untreated. Concerns about student mental health are well documented, but little is known about potential variations across the diversity of institutions of higher education. Participants: Participants were 43,210 undergraduates at 72 campuses that participated in the Healthy Minds Study from 2007 to 2013. Methods: Multivariable logistic regressions focus on associations between institutional characteristics and student mental health and treatment utilization. Results: The following institutional characteristics are associated with worse mental health: doctoral-granting, public, large enrollment, nonresidential, less competitive, and lower graduation rates. Among students with apparent mental health problems, treatment utilization is higher at doctorate-granting institutions, baccalaureate colleges, institutions with small enrollments, and schools with strong residential systems. Conclusions: Although high rates of mental health problems and low treatment utilization are major concerns at all types of institutions of higher education, substantial variation occurs across campuses.
An Analytic Connector Loss Model for Step-Index Polymer Optical Fiber Links

The authors report on an analytic connector loss model for step-index polymer optical fibers (SI-POF). The model describes the non-linear dependencies for combinations of the most important intrinsic and extrinsic influence parameters like Fresnel reflections, mismatches in numerical aperture (NA) and core diameters, as well as lateral, longitudinal and angular offsets. As connector losses strongly depend on the mode distribution, expressions for the mode-dependent coupling efficiencies for the various influence parameters are derived. This way, the model can handle any rotationally symmetric mode distribution including the uniform mode distribution (UMD) and the equilibrium mode distribution (EMD) in the steady-state. It is shown that for step-index fibers, lateral and longitudinal offsets can be handled in a similar way, which reduces the overall effort for the mathematical description. For the typical case of identical fibers, the authors also derive easy-to-apply approximations for a combination of lateral and longitudinal offsets under UMD and EMD conditions. The results are in good agreement with ray-tracing simulations and are evaluated for the cases of identical fibers and the worst case parameter constellation for the SI-POF in the IEC A4a.2 fiber class.
The Effects of Economic News on Commodity Prices: Is Gold Just Another Commodity?

The paper uses an event study methodology to investigate which and how macroeconomic announcements affect commodity prices. Results show that gold is unique among commodities, with prices reacting to specific scheduled announcements in the United States and the Euro area (such as indicators of activity or interest rate decisions) in a manner consistent with gold's traditional role as a safe-haven and store of value. Other commodity prices, where such news is significant, exhibit pro-cyclical sensitivities and these have risen somewhat as commodities have become increasingly financialized. These results are important for those trading in the commodity markets on a frequent basis and long-term market participants that take their decisions based on information on price fundamentals, which are reflected in the release of macroeconomic announcements.
Lattice-reduction-aided broadcast precoding

A precoding scheme for multiuser broadcast communications is described, which fills the gap between the low-complexity Tomlinson-Harashima precoding and the sphere decoder-based system of Peel et al. Simulation results show that, replacing the closest-point search with the Babai approximation, the full diversity order supported by the channel is available to each user, as in the system of Peel et al., and unlike Tomlinson-Harashima precoding, which suffers some diversity penalty. The complexity of the scheme is similar to that of Tomlinson-Harashima precoding.
Potential for Porphyry Copper Mineralization Below the Kasuga Lithocap, Nansatsu District, Japan

Lithocaps consist of vuggy residual quartz and advanced argillic alteration formed at shallow depths and potentially related to porphyry copper‐bearing intrusions at depth, meaning that, conceptually, porphyry copper deposits may exist beneath the lithocap‐hosted Nansatsu‐type gold deposits. The Kasuga lithocap extends for about 5 km NE–SW by 2 km width; beyond the northeastern edge of this lithocap, there are contemporaneous epithermal gold‐quartz veins. A 1200‐m hole was drilled in 1999 beneath the main orebody at Kasuga but did not intersect porphyry copper mineralization. On the basis of detailed examination of the alteration pattern and paleothermal environment of the Kasuga area, a paleo high‐temperature zone appears to lie in a NE‐ward direction from the deep drilling site.
The ASPIC+ framework for structured argumentation: a tutorial

This article gives a tutorial introduction to the ASPIC+ framework for structured argumentation. The philosophical and conceptual underpinnings of ASPIC+ are discussed, the main definitions are illustrated with examples and several ways are discussed to instantiate the framework and to reconstruct other approaches as special cases of the framework. The ASPIC+ framework is based on two ideas: the first is that conflicts between arguments are often resolved with explicit preferences, and the second is that arguments are built with two kinds of inference rules: strict, or deductive rules, whose premises guarantee their conclusion, and defeasible rules, whose premises only create a presumption in favour of their conclusion. Accordingly, arguments can in ASPIC+ be attacked in three ways: on their uncertain premises, or on their defeasible inferences, or on the conclusions of their defeasible inferences. ASPIC+ is not a system but a framework for specifying systems. A main objective of the study of the ASPIC+ f.
An in vitro study on the genotoxic effect of substituted furans in cells transfected with human metabolizing enzymes: 2,5-dimethylfuran and furfuryl alcohol

2,5-Dimethylfuran (DMF) and furfuryl alcohol (FFA) are two substituted furans that are formed during the processing of foods and have also been used as food flavorings. DMF and FFA are proposed to be bioactivated by human sulfotransferases (SULTs) which are not expressed in conventional cell lines used for genotoxicity testing. Therefore, in addition to the standard V79 cell line, we used a transfected V79 derived cell line co-expressing human cytochrome P450 (CYP) 2E1 and human SULT1A1 to assess the genotoxicity of DMF and FFA. The alkaline single cell gel electrophoresis (SCGE) assay was used to detect DNA damage in the form of single strand breaks and alkali-labile sites after exposure to DMF (0.5h; 0.5, 1, 1.5 or 2mM) or FFA (3h; 1, 3, 6 or 15mM). DMF induced DNA damage in V79 cells in a concentration-dependent manner irrespective of the expression of human CYP2E1 and SULT1A1. Almost no increase in the level of DNA damage was detected after exposure to FFA, except for a weak effect at the highest concentration in the transfected cell line. The results suggest that DNA damage in V79 cells from exposure to DMF detected by the alkaline SCGE assay is independent of human CYP2E1 and SULT1A1, and the genotoxic effect of FFA, as assessed by SCGE, is minimal in V79 cells.
Spatial stochastic modelling of the phosphoenolpyruvate-dependent phosphotransferase (PTS) pathway in Escherichia coli

MOTIVATION Many biochemical networks involve reactions localized on the cell membrane. This can give rise to spatial gradients of the concentration of cytosolic species. Moreover, the number of membrane molecules can be small and stochastic effects can become relevant. Pathways usually consist of a complex interaction network and are characterized by a large set of parameters. The inclusion of spatial and stochastic effects is a major challenge in developing quantitative and dynamic models of pathways. RESULTS We have developed a particle-based spatial stochastic method (GMP) to simulate biochemical networks in space, including fluctuations from the diffusion of particles and reactions. Gradients emerging from membrane reactions can be resolved. As case studies for the GMP method we used a simple gene expression system and the phosphoenolpyruvate:glucose phosphotransferase system pathway. AVAILABILITY The source code for the GMP method is available at http://www.science. uva.nl/research/scs/CellMath/GMP.
Role of Hydrophobic Residues in the Central Ectodomain of gp41 in Maintaining the Association between Human Immunodeficiency Virus Type 1 Envelope Glycoprotein Subunits gp120 and gp41

ABSTRACT The interaction between the gp120 and gp41 subunits of the human immunodeficiency virus envelope glycoprotein serves to stabilize the virion form of the complex and to transmit receptor-induced conformational changes in gp120 to trigger the membrane fusion activity of gp41. In this study, we used site-directed mutagenesis to identify amino acid residues in the central ectodomain of gp41 that contribute to the stability of the gp120-gp41 association. We identified alanine mutations at six positions, including four tryptophan residues, which result in mutant envelope glycoprotein complexes that fail to retain gp120 on the cell surface. These envelope glycoproteins readily shed their gp120 and are unable to mediate cell-cell fusion. These findings suggest an important role for the conserved bulky hydrophobic residues in stabilizing the gp120-gp41 complex.
Seeing the Destination but Not the Path: Effects of Socioeconomic Disadvantage on School-focused Possible Self Content and Linked Behavioral Strategies

Low-income children perform better in school when school-focused future identities are a salient aspect of their possible self for the coming year and these school-focused future identities are linked to behavioral strategies (Oyserman et al., 2006). Hierarchical linear modeling of data from a four-state low-income neighborhood sample of eighth-graders suggests two central consequences of family and neighborhood socioeconomic deprivation on children's school-focused possible identities and strategies. First, higher neighborhood disadvantage is associated with greater salience of school in children's possible self for the coming year. Second, disadvantage clouds the path to school-success; controlling for salience of school-focused possible identities, children living in lower socioeconomic status families and boys living in more economically disadvantaged neighborhoods were less likely to have strategies to attain their school-focused possible identities. The influence of family socioeconomic status was seen particularly with regard to strategies to attain academic success and teacher engagement aspects of school-focused identities.
EIGER™: An open-source frequency-domain electromagnetics code

EIGERtrade is a general-purpose, 3D frequency-domain electromagnetics code suite consisting of a pre-processor (Jungfrau), the physics code (EIGER), and post processor (Moench). In order to better enable collaborative development, EIGERtrade version 2.0 has been approved for release as open source software under a GNU Public License. EIGERtrade is primarily an integral-equation code for both frequency-domain electromagnetics and electrostatics. This version includes the following Green's functions: 2D and 3D free space, symmetry-planes, periodic and layered media. There is a thin-wire algorithm as well as junction basis functions for attachment of a wire to a conducting surface, and also thin-slot models for coupling into cavities. The code is written in Fortran 90 using object-oriented design and has the capability to run both in parallel and serial.
Multi-Trait and Multi-Environment QTL Analyses for Resistance to Wheat Diseases

Background Stripe rust, leaf rust, tan spot, and Karnal bunt are economically significant diseases impacting wheat production. The objectives of this study were to identify quantitative trait loci for resistance to these diseases in a recombinant inbred line (RIL) from a cross HD29/WH542, and to evaluate the evidence for the presence loci on chromosome region conferring multiple disease resistance. Methodology/Principal Findings The RIL population was evaluated for four diseases and genotyped with DNA markers. Multi-trait (MT) analysis revealed thirteen QTLs on nine chromosomes, significantly associated with resistance. Phenotypic variation explained by all significant QTLs for KB, TS, Yr, Lr diseases were 57%, 55%, 38% and 22%, respectively. Marginal trait analysis identified the most significant QTLs for resistance to KB on chromosomes 1BS, 2DS, 3BS, 4BL, 5BL, and 5DL. Chromosomes 3AS and 4BL showed significant association with TS resistance. Significant QTLs for Yr resistance were identified on chromosomes 2AS, 4BL and 5BL, while Lr was significant on 6DS. MT analysis revealed that all the QTLs except 3BL significantly reduce KB and was contributed from parent HD29 while all resistant QTLs for TS except on chromosomes 2DS.1, 2DS.2 and 3BL came from WH542. Five resistant QTLs for Yr and six for Lr were contributed from parents WH542 and HD29 respectively. Chromosome region on 4BL showed significant association to KB, TS, and Yr in the population. The multi environment analysis for KB identified three putative QTLs of which two new QTLs, mapped on chromosomes 3BS and 5DL explained 10 and 20% of the phenotypic variation, respectively. Conclusions/Significance This study revealed that MT analysis is an effective tool for detection of multi-trait QTLs for disease resistance. This approach is a more effective and practical than individual QTL mapping analyses. MT analysis identified RILs that combine resistance to multiple diseases from parents WH542 and/or HD29.
Does vigabatrin possess an anticonvulsant action against pentylenetetrazol-induced seizures in developing rats?

Anticonvulsant action of vigabatrin (300, 600, 900 and/or 1200 mg/kg i.p.), an inhibitor of GABA-transaminase, was studied in a model of motor sezures elicited by pentylenetetrazol. Five age groups of rats (7, 12, 18, 25 and 90 days old) received a s.c. injection of pentylenetetrazol 4, 6 and/or 24 hours after vigabatrin administration. The incidence of minimal, predominantly clonic seizures was not changed in any age group, but their latencies were prolonged in 18- and 25-day-old rats. Generalized tonic-clonic seizures were influenced in a more complex manner. Incidence of these seizures was decreased in 7-day-old rat pups 24 hours after vigabatrin administration. Higher doses of vigabatrin exhibited a similar effect in adult rats at all intervals studied. Specific suppression or at least restriction of the tonic phase was observed in all groups of immature rats, the effect was more marked 24 hours after vigabatrin than at shorter intervals. The anticonvulsant action of vigabatrin, which could be demonstrated mainly against generalized tonic-clonic seizures, varies markedly during development.
The BEHAVE video dataset: ground truthed video for multi-person behavior classification

Although there is much research on behaviour recognition in time-varying video, there are few ground truthed datasets for assessing multi-person behavioral interactions. This short paper presents the BEHAVE project’s dataset, which has around 90,000 frames of humans identified by bounding boxes, with interacting groups classified into one of 5 different behaviors. An example of its use is also presented.
Tea consumption and risk of type 2 diabetes: a dose–response meta-analysis of cohort studies

Tea consumption has inconsistently been shown to be associated with the risk of type 2 diabetes (T2D). The aim of the present study was to conduct a dose–response meta-analysis of cohort studies assessing the association between consumption of tea and risk of developing T2D. Pertinent studies were identified by searching PubMed, Web of Science and EMBASE through 31 March 2013. A total of sixteen cohorts from fifteen articles that reported 37 445 cases of diabetes among 545 517 participants were included. A significant linearly inverse association between tea consumption and T2D risk was found (P for linear trend = 0·02). An increase of 2 cups/d in tea consumption was found to be associated with a 4·6 (95 % CI 0·9, 8·1) % reduced risk of T2D. On the basis of the dose–response meta-analysis, the predicted relative risks of diabetes for 0, 1, 2, 3, 4, 5 and 6 cups of tea consumed per d were 1·00 (referent), 0·97 (95 % CI 0·94, 1·01), 0·95(95 % CI 0·92, 0·98), 0·93 (95 % CI 0·88, 0·98), 0·90 (95 % CI 0·85, 0·96), 0·88 (95 % CI 0·83, 0·93) and 0·85 (95 % CI 0·80, 0·91), respectively. There was a statistically significant heterogeneity within the selected studies (Q= 45·32, P< 0·001, I 2= 60·3 %). No evidence of substantial small-study bias was found (P= 0·46). Our findings suggest that tea consumption could be linearly inversely associated with T2D risk. Future well-designed observational studies that account for different characteristics of tea such as tea types, preparation methods and tea strength are needed to fully characterise such an association.
A Consideration of the Biological and Psychological Foundations of Autonomous Robotics

The new wave of robotics aims to provide robots with the capacity to learn, develop and evolve in interaction with their environments using biologically inspired techniques. This work is placed in perspective by considering its biological and psychological basis with reference to some of the grand theorists of living systems. In particular, we examine what it means to have a body by outlining theories of the mechanisms of bodily integration in multicellular organisms and their means of solidarity with the environment. We consider the implications of not having a living body for current ideas on robot learning, evolution, and cognition and issue words of caution about wishful attributions that can smuggle more into observations of robot behaviour than is scientifically supportable. To round off the arguments we take an obligatory swipe at ungrounded artificial intelligence but quickly move on to assess physical grounding and embodiment in terms of the rooted cognition of the living.