cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.825653.v1
title: Multi-class determination of anthelmintics in soil and water by LC-MS/MS

description: The translocation of antiparasitic drugs from animal excrement through soil and water to crops and forages and their recycling to food-producing animals is a potential concern with respect to the contamination of the food chain. To facilitate the investigation of this problem, an LC-MS/MS method for selected anthelmintics in soil and water was developed. The soil sample preparation involved a simple solvent extraction and dispersive clean-up technique. The method was validated at 10, 20 and 40 µg kg<sup>−1</sup> for levamisole, fenbendazole, fenbendazole sulphoxide and fenbendazole sulphone and at 20, 40 and 80 µg kg<sup>−1</sup> for eprinomectin. LOQs were 10 µg kg<sup>−1</sup> for the first four compounds and 20 µg kg<sup>−1</sup> for eprinomectin. The overall mean recoveries ranged from 76.1% to 89% for loamy soils and from 79.9% to 96.9% for sandy soils. Analysis of water samples was performed by extraction/concentration on an Oasis-HLB (Aschaffenburg, Germany) cartridge. Validation was performed at 0.25, 0.5 and 1.0 µg l<sup>−1</sup>. The LOQ for all compounds was 0.25 µg l<sup>−1</sup>. Method recovery (and RSD) varied between 35.4% (28) for eprinomectin and 125.1% (16) for fenbendazole sulphone. The validated methods were applied to soil and water samples in a study on the behaviour of anthelmintic drugs in a soil-plant-water system (manuscript on “transport investigation of antiparasitic drugs based on a lysimeter experiment” in preparation).
DOI: 10.6084/m9.figshare.825656.v1
title: The Canadian total diet study design: 1992–1999

description: This paper describes the design of the fourth phase of the Canadian total diet study, conducted for the period 1992–1999. During this phase, complete sets of foods were purchased from eight cities (from one of them twice). For each of the sets, individual foods were prepared as for consumption into about 140 different food composites at Kemptville College, homogenised and bottled. Water from Kemptville, Ontario, was used for the preparation of the foods. The composites were stored frozen at −20°C and then analysed in the Food Research Division for chlorinated dioxins and dibenzofurans, pesticides, PCBs and trace elements. The analytical results were combined with average food consumption values for different age/sex groups, and dietary intakes were calculated. The design of the total diet study provided information to achieve the following goals: (a) background concentrations of the chemicals in the 140 different food composites, (b) average dietary intakes of the chemicals by the population and by different age/sex groups, (c) percent contribution of individual foods and food groups to the dietary intakes, (d) identification of individual contaminated foods and (e) identification of trends in human exposure with time.
DOI: 10.6084/m9.figshare.825641
title: Qualitative observations of Dungeness crabs, <i>Cancer magister</i>, in and around traps: evidence of resource guarding and clustering

description: Decapod crustaceans are well known for agonistic interactions where they commonly fight over resources. Accurate descriptions of crab behaviour are essential to the development of quantitative behavioural studies involving the Dungeness crab fishery. An underwater video system mounted over a commercial crab trap <i>in situ</i> was used to qualitatively describe several of the most common behaviours utilized by <i>Cancer magister</i> in and around traps, including the documentation of previously undescribed behaviours in this species. Crabs commonly guarded trap doors without entering the trap and prevented other inspecting crabs from entering the trap. Agonistic interactions in traps ceased when crabs ‘clustered’ together, creating a group of non-interacting, fairly motionless crabs sitting on or near each other. These observations indicate that crab behaviour merits further attention in future studies of gear saturation and the catchability of Dungeness crabs.
DOI: 10.6084/m9.figshare.825641.v1
title: Qualitative observations of Dungeness crabs, <i>Cancer magister</i>, in and around traps: evidence of resource guarding and clustering

description: Decapod crustaceans are well known for agonistic interactions where they commonly fight over resources. Accurate descriptions of crab behaviour are essential to the development of quantitative behavioural studies involving the Dungeness crab fishery. An underwater video system mounted over a commercial crab trap <i>in situ</i> was used to qualitatively describe several of the most common behaviours utilized by <i>Cancer magister</i> in and around traps, including the documentation of previously undescribed behaviours in this species. Crabs commonly guarded trap doors without entering the trap and prevented other inspecting crabs from entering the trap. Agonistic interactions in traps ceased when crabs ‘clustered’ together, creating a group of non-interacting, fairly motionless crabs sitting on or near each other. These observations indicate that crab behaviour merits further attention in future studies of gear saturation and the catchability of Dungeness crabs.
DOI: 10.6084/m9.figshare.825634
title: Sound Finder: a new software approach for localizing animals recorded with a microphone array

description: Acoustic localization is a powerful technique for monitoring the positions, movements and behaviours of terrestrial animals. However, its prevalence in biological studies has been constrained by hardware and software that are custom-built, expensive and difficult to use. We recently helped to relieve the hardware constraint by describing a microphone array that is affordable, portable, easy to use and commercially available. Here, we help to relieve the software constraint by developing an acoustic localization program called “Sound Finder”, which is easy to use, freely available and accurate for a variety of animals and recording conditions. It runs in the free software environment R, and in spreadsheet programs such as Microsoft Excel and the open-source software LibreOffice. In this study, we describe how Sound Finder functions, and then test its accuracy by localizing natural sounds that were broadcast through loudspeakers and re-recorded with microphone arrays. We quantify Sound Finder's accuracy by comparing its location estimates with known loudspeaker locations and with output from other localization approaches. We show that Sound Finder generates accurate location estimates for a variety of animal sounds, microphone array configurations and environmental conditions. Furthermore, Sound Finder generates an error value that allows the user to assess its accuracy. In conclusion, Sound Finder provides accurate estimates of a vocalizing animal's location. It is easy to use, requires only widespread and affordable software and is freely available in a standard form as Supplementary material to this article.
DOI: 10.6084/m9.figshare.825635
title: Utility of the phylotoxigenic relationships among trichothecene-producing <i>Fusarium</i> species for predicting their mycotoxin-producing potential

description: Species of the genus <i>Fusarium</i> are well-known plant pathogens and mycotoxigenic fusaria are associated with health hazards to humans and animals. There is a need to understand the mechanisms of mycotoxin production by <i>Fusarium</i> species and to predict which produce mycotoxins. In this study, the <i>Fusarium</i> phylogenetic tree was first inferred among trichothecene producers and related species. We reconstructed the maximum likelihood (ML) tree based on the combined data from nucleotide sequences of rDNA cluster regions, the β-tubulin gene (β-<i>tub</i>) and the elongation factor 1α gene (<i>EF-1</i>α). Second, based on this tree topology, the ancestral states of the producing potential of type A and B trichothecenes (TriA and TriB), zearalenone (ZEN), moniliformin (MON), beauvericin (BEA) and enniatins (ENN) were reconstructed using the maximum parsimony (MP) method based on the observed production by extant species as reported in the literature. Finally, the species having the potential to produce each of these six mycotoxins was predicted on the basis of the parsimonious analysis. The ML tree indicated that the <i>Fusarium</i> species analysed in this study could be divided into two major clades. Clade I was divided into four distinct subclades: I-a, I-b, I-c and I-d. Furthermore, the parsimony reconstruction suggested that the potential for producing MON and ZEN was gained or lost only once, and that the producing potential for TriA and TriB, BEA and ENN was repeatedly gained and lost during the evolutionary history of the <i>Fusarium</i> species analysed in this study. Interestingly, the results showed the possibility that several species, about which reports were scarce with regard to mycotoxin production, have the potential to produce one or more of the six evaluated in this study. The phylogenetic information therefore helps one to predict the mycotoxin-producing potential by <i>Fusarium</i> species, and these “phylotoxigenic relationships” may be useful for predicting the pathogenicity of fungi.
DOI: 10.6084/m9.figshare.825637
title: Area aggregation in map generalisation by mixed-integer programming

description: Topographic databases normally contain areas of different land cover classes, commonly defining a planar partition, that is, gaps and overlaps are not allowed. When reducing the scale of such a database, some areas become too small for representation and need to be aggregated. This unintentionally but unavoidably results in changes of classes. In this article we present an optimisation method for the aggregation problem. This method aims to minimise changes of classes and to create compact shapes, subject to hard constraints ensuring aggregates of sufficient size for the target scale. To quantify class changes we apply a semantic distance measure. We give a graph theoretical problem formulation and prove that the problem is NP-hard, meaning that we cannot hope to find an efficient algorithm. Instead, we present a solution by mixed-integer programming that can be used to optimally solve small instances with existing optimisation software. In order to process large datasets, we introduce specialised heuristics that allow certain variables to be eliminated in advance and a problem instance to be decomposed into independent sub-instances. We tested our method for a dataset of the official German topographic database ATKIS with input scale 1:50,000 and output scale 1:250,000. For small instances, we compare results of this approach with optimal solutions that were obtained without heuristics. We compare results for large instances with those of an existing iterative algorithm and an alternative optimisation approach by simulated annealing. These tests allow us to conclude that, with the defined heuristics, our optimisation method yields high-quality results for large datasets in modest time.
DOI: 10.6084/m9.figshare.825635.v1
title: Utility of the phylotoxigenic relationships among trichothecene-producing <i>Fusarium</i> species for predicting their mycotoxin-producing potential

description: Species of the genus <i>Fusarium</i> are well-known plant pathogens and mycotoxigenic fusaria are associated with health hazards to humans and animals. There is a need to understand the mechanisms of mycotoxin production by <i>Fusarium</i> species and to predict which produce mycotoxins. In this study, the <i>Fusarium</i> phylogenetic tree was first inferred among trichothecene producers and related species. We reconstructed the maximum likelihood (ML) tree based on the combined data from nucleotide sequences of rDNA cluster regions, the β-tubulin gene (β-<i>tub</i>) and the elongation factor 1α gene (<i>EF-1</i>α). Second, based on this tree topology, the ancestral states of the producing potential of type A and B trichothecenes (TriA and TriB), zearalenone (ZEN), moniliformin (MON), beauvericin (BEA) and enniatins (ENN) were reconstructed using the maximum parsimony (MP) method based on the observed production by extant species as reported in the literature. Finally, the species having the potential to produce each of these six mycotoxins was predicted on the basis of the parsimonious analysis. The ML tree indicated that the <i>Fusarium</i> species analysed in this study could be divided into two major clades. Clade I was divided into four distinct subclades: I-a, I-b, I-c and I-d. Furthermore, the parsimony reconstruction suggested that the potential for producing MON and ZEN was gained or lost only once, and that the producing potential for TriA and TriB, BEA and ENN was repeatedly gained and lost during the evolutionary history of the <i>Fusarium</i> species analysed in this study. Interestingly, the results showed the possibility that several species, about which reports were scarce with regard to mycotoxin production, have the potential to produce one or more of the six evaluated in this study. The phylogenetic information therefore helps one to predict the mycotoxin-producing potential by <i>Fusarium</i> species, and these “phylotoxigenic relationships” may be useful for predicting the pathogenicity of fungi.
DOI: 10.6084/m9.figshare.825632
title: Characterization of Yellow Seahorse <i>Hippocampus kuda</i> feeding click sound signals in a laboratory environment: an application of probability density function and power spectral density analyses

description: Do the sounds generated by different-sized fish of different sexes differ from each other in temporal, spectral or intensity patterns? Such differences would enable the development of passive acoustic techniques to locate seahorses in open water bodies. On the basis of this perspective, we characterize and present in this study Yellow Seahorse <i>Hippocampus kuda</i> (Syngnathidae) feeding click sounds, recorded in a controlled laboratory environment. The characterization involved analysis of the “probability density function” (PDF) and the “power spectral density” (PSD) of the seahorse feeding click sound signals of different sizes and sexes. The PDF describes the general distribution of the magnitude of a random process, and such analysis, using recorded seahorse clicks, points towards a multimodal statistical distribution, which is the existence of more than one fitting component for the majority of seahorse click signals above the tank ambient noise level. This fact has been appraised towards the involvement of more than one process in the seahorse click signal generation mechanism. However, lack of prior knowledge about the individual PDF components of the data leads towards the mismatch between the data of PDFs. The PDF gives no information on the time and frequency content of the processes as provided by the PSD. Under such conditions, curve fitting of the “power law” expressions to the PSD functions estimates “slope” and “intercept” parameters of the seahorse click signal. Striking differences in the feeding click characteristics of various sizes of the <i>H. kuda</i> and between the sexes were discernable based on the clustering pattern among the estimated “slope” and “intercept” parameters. Further studies using the seahorse body sizes and weight (wet) with respect to the peak frequencies estimated from the PSD distribution show results equivalent to those from previous studies.
DOI: 10.6084/m9.figshare.825631
title: Ultrasonic communication in Gliridae (Rodentia): the hazel dormouse (<i>Muscardinus avellanarius</i>) as a case study

description: Ultrasonic vocalizations (USVs) have been detected in a range of small mammals, particularly rodents, and are associated not only with different social behaviours, e.g. sexual behaviour and aggression, but also with non-social behaviour in several species of mammals, including echolocation and as a by-product of respiration. Rodents in the Gliridae family are known to broadcast a variety of signals, but the behavioural relevance of the latter is poorly known. The aim of our study was to describe the vocal signals of <i>Muscardinus avellanarius</i> and to assess their function. By recording vocal and non-vocal behaviour of captive individuals in different social contexts, we demonstrate that <i>M. avellanarius</i> emits USVs and provide contextual evidence that such sounds are largely used for social communication. We identified six different vocalizations with an overall frequency range between 6.5 and 52.1 kHz, five out of six being ultrasonic (&gt;18 kHz). The vocal repertoire in <i>M. avellanarius</i> was associated with social behaviours, e.g. mother–infant reunion, isolation and paired opposite-sex courtship, all activities involving individuals that are out of mutual visual contact. We therefore infer that this repertoire constitutes a medium-distance (in the range of a few metres) communication system. Further research testing different social contexts both in nature and in captivity is needed for a more complete assessment of the vocal repertoire of this species and its function.
DOI: 10.6084/m9.figshare.825637.v1
title: Area aggregation in map generalisation by mixed-integer programming

description: Topographic databases normally contain areas of different land cover classes, commonly defining a planar partition, that is, gaps and overlaps are not allowed. When reducing the scale of such a database, some areas become too small for representation and need to be aggregated. This unintentionally but unavoidably results in changes of classes. In this article we present an optimisation method for the aggregation problem. This method aims to minimise changes of classes and to create compact shapes, subject to hard constraints ensuring aggregates of sufficient size for the target scale. To quantify class changes we apply a semantic distance measure. We give a graph theoretical problem formulation and prove that the problem is NP-hard, meaning that we cannot hope to find an efficient algorithm. Instead, we present a solution by mixed-integer programming that can be used to optimally solve small instances with existing optimisation software. In order to process large datasets, we introduce specialised heuristics that allow certain variables to be eliminated in advance and a problem instance to be decomposed into independent sub-instances. We tested our method for a dataset of the official German topographic database ATKIS with input scale 1:50,000 and output scale 1:250,000. For small instances, we compare results of this approach with optimal solutions that were obtained without heuristics. We compare results for large instances with those of an existing iterative algorithm and an alternative optimisation approach by simulated annealing. These tests allow us to conclude that, with the defined heuristics, our optimisation method yields high-quality results for large datasets in modest time.
DOI: 10.6084/m9.figshare.825630
title: The vocal repertoire of infant giant pandas (<i>Ailuropoda melanoleuca</i>)

description: Infant giant pandas (<i>Ailuropoda melanoleuca</i>) are highly vocal during the first few weeks of their life. Despite this, no previous studies have attempted to systematically categorize infant giant panda vocalizations into different call types. In this study, we used acoustic and video analyses to split infant giant panda vocalizations into three distinct call types based on their acoustic structure as well as their use in different behavioural contexts. A discriminant functions analysis on the acoustic variables confirmed our initial subjective classification of 281 vocalizations into three call types: the harsh sounding “squawk”, the high-pitched “squall” and the pulsed “croak”. Based on the observed spectral acoustic characteristics, none of these three infant call types appears to be a precursor of an adult giant panda vocalization. In addition, individual call types could not be assigned to specific recording contexts. These findings suggest that infant giant panda vocalizations convey information about a cub's distress and need, rather than being tied to specific contexts of emission. Our objective demonstration that infant giant pandas have three basic call types provides a foundation for future studies of vocal ontogeny in this highly endangered species.
DOI: 10.6084/m9.figshare.825632.v2
title: Characterization of Yellow Seahorse <i>Hippocampus kuda</i> feeding click sound signals in a laboratory environment: an application of probability density function and power spectral density analyses

description: Do the sounds generated by different-sized fish of different sexes differ from each other in temporal, spectral or intensity patterns? Such differences would enable the development of passive acoustic techniques to locate seahorses in open water bodies. On the basis of this perspective, we characterize and present in this study Yellow Seahorse <i>Hippocampus kuda</i> (Syngnathidae) feeding click sounds, recorded in a controlled laboratory environment. The characterization involved analysis of the “probability density function” (PDF) and the “power spectral density” (PSD) of the seahorse feeding click sound signals of different sizes and sexes. The PDF describes the general distribution of the magnitude of a random process, and such analysis, using recorded seahorse clicks, points towards a multimodal statistical distribution, which is the existence of more than one fitting component for the majority of seahorse click signals above the tank ambient noise level. This fact has been appraised towards the involvement of more than one process in the seahorse click signal generation mechanism. However, lack of prior knowledge about the individual PDF components of the data leads towards the mismatch between the data of PDFs. The PDF gives no information on the time and frequency content of the processes as provided by the PSD. Under such conditions, curve fitting of the “power law” expressions to the PSD functions estimates “slope” and “intercept” parameters of the seahorse click signal. Striking differences in the feeding click characteristics of various sizes of the <i>H. kuda</i> and between the sexes were discernable based on the clustering pattern among the estimated “slope” and “intercept” parameters. Further studies using the seahorse body sizes and weight (wet) with respect to the peak frequencies estimated from the PSD distribution show results equivalent to those from previous studies.