OpenFluor- an online spectral library of auto-fluorescence by organic compounds in the environment

An online repository of published organic fluorescence spectra has been developed, which can be searched for quantitative matches with any set of unknown spectra. It fills a critical gap by increasing access to measured and modelled (PARAFAC) spectra, and linking across studies and systems to reveal "global" fluorescence trends

Lameness detection challenges in automated milking systems addressed with partial least squares discriminant analysis

AbstractLameness causes decreased animal welfare and leads to higher production costs. This study explored data from an automatic milking system (AMS) to model on-farm gait scoring from a commercial farm. A total of 88 cows were gait scored once per week, for 2 5-wk periods. Eighty variables retrieved from AMS were summarized week-wise and used to predict 2 defined classes: nonlame and clinically lame cows. Variables were represented with 2 transformations of the week summarized variables, using 2-wk data blocks before gait scoring, totaling 320 variables (2×2×80). The reference gait scoring error was estimated in the first week of the study and was, on average, 15%. Two partial least squares discriminant analysis models were fitted to parity 1 and parity 2 groups, respectively, to assign the lameness class according to the predicted probability of being lame (score 3 or 4/4) or not lame (score 1/4). Both models achieved sensitivity and specificity values around 80%, both in calibration and cross-validation. At the optimum values in the receiver operating characteristic curve, the false-positive rate was 28% in the parity 1 model, whereas in the parity 2 model it was about half (16%), which makes it more suitable for practical application; the model error rates were, 23 and 19%, respectively. Based on data registered automatically from one AMS farm, we were able to discriminate nonlame and lame cows, where partial least squares discriminant analysis achieved similar performance to the reference method

Why use component-based methods in sensory science?

This paper discusses the advantages of using so-called component-based methods in sensory science. For instance, principal component analysis (PCA) and partial least squares (PLS) regression are used widely in the field; we will here discuss these and other methods for handling one block of data, as well as several blocks of data. Component-based methods all share a common feature: they define linear combinations of the variables to achieve data compression, interpretation, and prediction. The common properties of the component-based methods are listed and their advantages illustrated by examples. The paper equips practitioners with a list of solid and concrete arguments for using this methodology.publishedVersio

Experienced and inexperienced observers achieved relatively high within-observer agreement on video mobility scoring of dairy cows

AbstractAssessment of lameness prevalence and severity requires visual evaluation of thelocomotion of a cow. Welfare schemes including locomotion assessments are increasingly being adopted, and more farmers and their veterinarians might implement a locomotion-scoring routine together. However, high within-observer agreement is a prerequisite for obtaining valid mobility scorings, and within-observer agreement cannot be estimated in a barn, because the gait of cows is dynamic and may change between 2 occasions. The objective of this study was to estimate the within-observer agreement according to the observers’ educational background and experience with cattle, based on video recordings with very diverse types of gait. Groups of farmers, bovine veterinarians, first- and fourth-year veterinary students, researchers, and cattle-inexperienced sensory assessors evaluated mobility using a 5-point mobility score system developed specifically for walking cows (n=102 observers). The evaluation sessions were similar for all groups, lasted 75 min, and were organized as follows: introduction, test A, short training session, break, and test B. In total, video recordings of 22 cows were displayed twice in a random order (11 cows in each test × 2 replicates). Data were analyzed applying kappa coefficient, logistic regression, and testing for random effects of observers. The crude estimates of 95% confidence interval for weighted kappa in test A and B ranged, respectively, from 0.76 to 0.80 and 0.70 to 0.75. When adjusting for the fixed effects of video sample and gait scoring preferences, the probability of assigning the same mobility score twice to the same cow varied from 55% (sensory assessors) to 72% (fourth-year veterinary students). The random effect of the individual observers was negligible. That is, in general observers could categorize the mobility characteristics of cows quite well. Observers who preferred to assess the attributes back arch or the overall mobility score (based on uneven gait) had the highest agreement, respectively, 69 or 68%. The training session seemed insufficient to improve agreement. Nonetheless, even novice observers were able to achieve perfect agreement up to 60% of the 22 scorings with merely the experience obtained during the study (introduction and training session). The relatively small differences between groups, together with a high agreement, demonstrate that the new system is easy to follow compared with previously described scoring systems. The mobility score achieves sufficiently high within-observer repeatability to allow between-observer agreement estimates, which are reliable compared with other more-complex scoring systems. Consequently, the new scoring scale seems feasible for on-farm applications as a tool to monitor mobility within and between cows, for communication between farmers and veterinarians with diverse educational background, and for lamenessbenchmarking of herds

Approximating a Wavefunction as an Unconstrained Sum of Slater Determinants

The wavefunction for the multiparticle Schr\"odinger equation is a function of many variables and satisfies an antisymmetry condition, so it is natural to approximate it as a sum of Slater determinants. Many current methods do so, but they impose additional structural constraints on the determinants, such as orthogonality between orbitals or an excitation pattern. We present a method without any such constraints, by which we hope to obtain much more efficient expansions, and insight into the inherent structure of the wavefunction. We use an integral formulation of the problem, a Green's function iteration, and a fitting procedure based on the computational paradigm of separated representations. The core procedure is the construction and solution of a matrix-integral system derived from antisymmetric inner products involving the potential operators. We show how to construct and solve this system with computational complexity competitive with current methods.Comment: 30 page

Education in the working-class home: modes of learning as revealed by nineteenth-century criminal records

The transmission of knowledge and skills within the working-class household greatly troubled social commentators and social policy experts during the first half of the nineteenth century. To prove theories which related criminality to failures in working-class up-bringing, experts and officials embarked upon an ambitious collection of data on incarcerated criminals at various penal institutions. One such institution was the County Gaol at Ipswich. The exceptionally detailed information that survives on families, literacy, education and apprenticeships of the men, women and children imprisoned there has the potential to transform our understanding of the nature of home schooling (broadly interpreted) amongst the working classes in nineteenth-century England. This article uses data sets from prison registers to chart both the incidence and ‘success’ of instruction in reading and writing within the domestic environment. In the process, it highlights the importance of schooling in working-class families, but also the potentially growing significance of the family in occupational training

Determination of dichlobenil and its major metabolite (BAM) in onions by PTV–GC–MS using PARAFAC2 and experimental design methodology

The optimization of a GC–MS analytical procedure which includes derivatization, Quick Easy Cheap Effective Rugged and Safe (QuEChERS) and programmed temperature vaporization (PTV) using design of experiments is performed to determine 2,6-dichlorobenzonitrile (dichlobenil) and 2,6-dichlorobenzamide (BAM) in onions, using 3,5-dichlorobenzonitrile and 2,4-dichlorobenzamide as internal standards. The use of a central composite design and two D-optimal designs, together with the desirability function, makes it possible to significantly reduce the economic, time and environmental cost of the study. The usefulness of PARAFAC2 for solving problems as the interference of unexpected derivatization artifacts unavoidably linked to some derivatization agents, or the presence of coeluents from the complex matrix, which share m/z ratios with the target compounds, is shown. The limits of decision (CCα) of the optimized procedure, 5.00 μg kg− 1 for dichlobenil and 1.55 μg kg− 1 for BAM (α = 0.05), are below the maximum residue limit (MRL) established by the EU for dichlobenil (20 μg kg− 1) in this commodity.Ministerio de Economía y Competitividad (CTQ2011-26022) and Junta de Castilla y León (BU108A11-2

Competition-induced stress does not explain deceptive alarm calling in tufted capuchin monkeys

Tactical deception has long attracted interest because it is often assumed to entail complex cognitive mechanisms. However, systematic evidence of tactical deception is rare and no study has attempted to determine whether such behaviours may be underpinned by relatively simple mechanisms. This study examined whether deceptive alarm calling among wild tufted capuchin monkeys, Cebus apella nigritus, feeding on contestable food resources can be potentially explained by a physiological mechanism, namely increased activation in the adrenocortex and the resulting production of glucocorticoids (GCs; ‘stress hormones’). This was tested experimentally in Iguazu? National Park, Argentina, by manipulating the potential for contest competition over food and noninvasively monitoring GC production through analysis of faecal hormone metabolites. If deceptive false alarms are indeed associated with adreno- cortical activity, it was predicted that the patterns of production of these calls would match the patterns of GC output, generally being higher in callers than noncallers in cases in which food is most contestable, and specifically being higher in callers on those occasions when a deceptive false alarm was produced. This hypothesis was not supported, as (1) GC output was significantly lower in association with the experimental introduction of contestable resources than in natural contexts wherein the potential for contest is lower, (2) within experimental contexts, there was a nonsignificant tendency for noncallers to show higher GC output than callers when food was most contestable, and (3) individuals did not show higher GC levels in cases in which they produced deceptive alarms relative to cases in which they did not. A learned association between the production of alarms and increased access to food may be the most likely cognitive explanation for this case of tactical deception, although unexplored physiological mechanisms also remain possible