Miracle-dz/UniFAR-FTUs huggingface dataset:
Note types and coding in parid vocalizations. II: The chick-a-dee call of the mountain chickadee (Poecile gambeli)

We describe the chick-a-dee call of the mountain chickadee, Poecile gambeli (Ridgway, 1886), by classifying the various call notes into six types (A, A/B, B, C, Dh, and D). Note-type analyses identify a high degree of similarity among A and A/B notes in the ascending duration, descending duration, and note peak frequency, and among A/B and B notes in the end frequency. This statistical result paralleled disagreements between human sorters where A, A/B, and B notes were most often misclassified. Moreover, virtually all parameters measured showed significant variation across individuals. Therefore, the particular acoustic cues used in the discrimination of note types and individuals remain un - known, but it is likely that a constellation of features is used rather than one or two particularly salient features. Resume : Nous decrivons le chant d'appel de la mesange des montagnes, Poecile gambeli (Ridgway, 1886), en classi- fiant les differentes notes en six categories (A, A/B, B, C, D h et D). Une analyse comparative de ces differents types de notes a permis d'identifier un haut degre de similarite entre les notes A et A/B dans la duree des parties ascendante et descendante, ainsi que dans la frequence la plus haute de la note et entre les notes A/B et B dans la frequence fi - nale. Ce resultat statistique corrobore les desaccords qui surviennent lors du tri visuel par des humains, ou les notes de type A, A/B et B sont souvent mal classees. Si toutes les caracteristiques mesurees presentent une variation significa- tive entre individus, on ne connait toujours pas celles qui sont effectivement utilisees dans la differenciation des notes et dans le processus de reconnaissance individuelle. Il semble plus probable qu'une combinaison de plusieurs caracte- ristiques soit utilisee plutot qu'une ou deux caracteristiques en particulier.
Probabilistic historical biogeography: new models for founder-event speciation, imperfect detection, and fossils allow improved accuracy and model-testing

Historical biogeography has been characterized by a large diversity of methods and unresolved debates about which processes, such as dispersal or vicariance, are most important for explaining distributions. A new R package, BioGeoBEARS, implements many models in a common likelihood framework, so that standard statistical model selection procedures can be applied to let the data choose the best model. Available models include a likelihood version of DIVA (“DIVALIKE”), LAGRANGE’s DEC model, and BAYAREA, as well as “+J” versions of these models which include founder-event speciation, an important process left out of most inference methods. I use BioGeoBEARS on a large sample of island and non-island clades (including two fossil clades) to show that founder-event speciation is a crucial process in almost every clade, and that most published datasets reject the non-J models currently in widespread use. BioGeoBEARS is open-source and freely available for installation at the Comprehensive R Archive Network at http://CRAN.R-project.org/package=BioGeoBEARS. A step-by-step tutorial is available at http://phylo.wikidot. com/biogeobears.
Building a basidiocarp: a case study of Laccaria spp. fruitbodies in the extraradical mycelium of Pinus ectomycorrhizas

The extraradical mycelium of ectomycorrhizas is comprised of a network of hyphae that may initiate rhizomorphs, sclerotia and sexual reproductive structures. The development of these structures requires photosynthates produced by host trees. In this study, the initiation and early development of Laccaria bicolor (Maire) Orton fruitbodies (basidiocarps) were studied. Seedlings of Pinus resinosa Ait. and Pinus sylvestris L. were colonized by L. bicolor , a broad host epigeous ectomycorrhizal basidiomycetous fungal species, in growth pouches. Ectomycorrhizas with an extensive extraradical mycelium formed on short roots within 7-12 days after fungal inoculum was introduced. Numerous sites of hyphal aggregation, many of which subsequently developed into basidiocarp primordia, were initiated in the extraradical mycelium. Initial changes in aggregating hyphae included swelling and branching followed by growth of hyphae perpendicular to the paper wick in growth pouches. A stipe and a pileus primordium developed but none of these basidiocarp primordia matured. Distinct regions were evident in the stipe and pileus when sections were stained by various methods. Loose hyphae at the apex and periphery of the pileus were separated by mucilage. In Petri dishes with vermiculite as the substrate, basidiocarps of Laccaria laccata formed in ectomycorrhizal associations with Pinus sylvestris , developed a mature pileus with an hymenium and mature basidiospores.
Distribution of PCBs in Sediment from Different Bottom Types and Water Depths in Stockholm Archipelago, Baltic Sea

Abstract PCBs associate with organic matter in the aquatic environment. Sediment of different bottom types at different water depths may have organic matter with different properties. Also the different bottoms can be either oxic/bioturbated or anoxic/laminated, depending on water depth. To investigate if these circumstances would influence the distribution of PCBs in sediment, samples were collected from different bottom types at different water depths in two areas in the Stockholm Archipelago in the Baltic Sea. The bottom types were classified according to their water content. It was concluded that the concentration of PCBs on an organic carbon basis is the same for the different bottom types and the two areas. The possible differences in properties of the organic matter in different sediments is of minor importance, as are the influences of bioturbation and redox conditions. Instead, it is the properties of the PCB congeners which determine their distribution in the sediments.
Effect of cooling and freezing temperatures on microbial and chemical properties of chicken meat during storage

Cooling and freezing temperatures are considered two of the most efficient methods to delay or inhibit growth of microorganisms in chicken meat and meat products during transport or storage. It can help improve the safety and prolong shelf life of such products. The purpose of this study was to evaluate chicken meat quality under freezing and different cooling temperatures. The data showed that the values of the chemical and microbial indicators were affected by freezing and cooling temperatures. Total viable bacteria, Pseudomonas and fecal Streptococcus counts (log 10 CFU/g) in chicken meat at day 0 were 5.5, 4.2 and 3.8, respectively. These counts (log 10 CFU/g) increased after 3 days of storage at 4±1oC to 6.0, 5.9 and 5.5, respectively, also they increased to 7.1, 7.4 and 5.6, respectively, when chicken meat was stored at 7±1oC. Total viable count, Pseudomonas and fecal Streptococcus count were significantly decreased when chicken meat was stored at -10oC, -18oC and -18oC in vacuum package. The results indicated that the staphylococci and Staphylococcus aureus counts were higher in winter season compared to summer season. Total viable bacteria, Pseudomonas and fecal Streptococcus and coliform counts were lower in winter samples. Salmonella was positive in both winter and summer season samples. At day 0 the TBARS in chicken meat samples was 0.10±0.03 mg malonaldehyde/kg. After 3 days of storage at 4oC, 7oC, -10oC and -18oC, the TBARS increased to 0.22±0.05, 0.28±0.03, 0.18±0.05 and 0.15±0.03 mg malonaldehyde/kg, respectively. The TBARS in the chicken meats that were packaged under vacuum and kept at 4 o C and -18oC for six days were 0.23±0.01 and 0.20±0.07 mg malonaldehyde/kg, respectively. Free fatty acids in chicken meat increased from 0.75±0.11% at day 0 to 0.93±0.15%, 0.87±0.21%, 0.90±0.28%, 1.1±0.15%, 1.7±0.15% and 0.87±0.13% in samples preserved at -10oC, -18oC, -18oC with vacuum package, 4oC, 7oC and 4oC with vacuum package, respectively.
Effect of mindfulness trait factors on sleep quality of college students: the mediating role of cognitive emotion regulation strategies and anxiety

Objective To explore the effect of mindfulness traits on sleep quality of college students, and to investigate the mediating mechanism of cognitive emotion regulation and anxiety for mindfulness trait factors, and sleep quality in college students. Methods Totally 397 college students from five colleges were investigated using Five Facet Mindfulness Questionnaire, Cognitive Emotion Regulation Questionnaire, Self-Rating Anxiety Scale and Pittsburgh Sleep Quality Index.SPSS 22.0 version and Bootstrap method were used to analysis data and test intermediate effect. Results (1)The total score of mindfulness trait and the score of describe, act with awareness and non-judge factors in mindfulness traits were(118.44±9.38), (24.82±3.87), (27.41±5.53) and (25.07±4.60), respectively.The total score of sleep quality was (5.57±2.62), and it was negatively related to the above three factors (r=-0.13--0.37, all P<0.05). (2)Anxiety played a complete mediating role between describe factor and sleep quality.Negative cognitive emotion regulation and anxiety played multiple mediating roles between the total score of mindfulness trait, the act with awareness factor and sleep quality.Negative cognitive emotion regulation and anxiety played a complete chain mediated role between non-judge factor and sleep quality. Conclusion The describe, act with awareness and non-judge factors in mindfulness traits can affect sleep quality through mediation of negative cognitive emotion regulation and / or anxiety. Key words: Mindfulness trait; Sleep quality; Cognitive emotion regulation; Anxiety; College students
Life-history of Gnopharmia kasrunensis Wehrli, 1939 and G. colchidaria Lederer, 1870 (Geometridae, Ennominae) and their distribution in Iran, with first host-plant records for the genus

For the first time, observations on the life-history of the little known species Gnopharmia kasrunensis Wehrli, 1939 and G. colchidaria Lederer, 1870 are reported; eggs, larvae, pupae, adults and habitats are illustrated. Suitable dif- ferential features for a correct identification of both Iranian Gnopharmia species as well as a distribution map are pro- vided. Zusammenfassung. Erstmals wird uber Beobachtungen zur Biologie der wenig bekannten Arten Gnopharmia kasrunen- sis Wehrli, 1939 und G. colchidaria Lederer, 1870 berichtet. Eier, Larven, Puppen, Imagines und ihre Lebensraume wer- den beschrieben. Fur die korrekte Bestimmung der beiden iranischen Gnopharmia-Arten werden geeignete differential- diagnostische Merkmale sowie eine Verbreitungskarte vorgelegt.
Etude acoustique de la production de la parole chez des patients glossectomisés

Le present travail porte sur la production de la parole apres exerese chirurgicale d’une tumeur de la cavite buccale et oro-pharyngee afin de deceler les differentes perturbations articulatori-acoustiques qu’entraine cette operation chirurgicale. Cette etude longitudinale vise a mettre au jour les possibles strategies de compensation ou de reajustements que le patient peut mettre en place, seul ou a l’aide d’une reeducation orthophonique. L’originalite de ce travail reside dans la place importante accordee au niveau de l’organisation spatiotemporelle de la parole, a partir de l’exploitation de plusieurs parametres articulatori-acoustiques, inter et intra segmentaux. Trois tâches linguistiques ont ete etudiees : 1) la production de voyelles tenues [i, a, u] ; 2) la production de sequences VCV dans deux contextes differents, la consonne etant l’une des occlusives ou des fricatives du francais [p, t, k, b, d, g, s, ʃ, z, ʒ] ; 3) l’evaluation subjective de la qualite de parole apres glossectomie. Les enregistrements acoustiques des productions des patients ont ete effectues pendant 4 phases : 1) en preoperatoire (la veille de l’intervention) ; 2) en Postop1 (entre 1 et 1, 5 mois) ; 3) en Postop2 (3 mois apres la chirurgie) ; et 4) en Postop3 (6mois apres l’intervention). Dix patients et trois sujets sains ont ete enregistres. Les donnees recueillies aupres des patients, informant sur les perturbations et les ajustements en parole, correspondaient aux mesures temporelles et spectrales effectuees sur le signal acoustique, ainsi que l’auto-evaluation par les patients de la qualite de leur parole (Speech Handicap Index ou SHI). Les perturbations des gestes articulatoires et les ajustements releves, propres a chaque patient, a partir des donnees acoustiques nous ont permis de mettre en exergue les caracterisations des production vocaliques et consonantiques apres exerese carcinologique localisee dans le systeme de production de la parole. Il s’est revele interessant que les modifications de la synergie linguale avec differentes structures dans le conduit vocal, ainsi que les changements anatomophysiologiques des cavites orales, apportees par la glossectomie, empechent certains patients d’atteindre les cibles articulatoires attendues. Neanmoins, les productions demeurent, de maniere generale, dans des zones de viabilite, correspondant au bout du compte a des realisations articulatori-acoustiques intelligibles.
PRODUCTION BY THREE POPULATIONS OF WILD BROOK TROUT WITH EMPHASIS ON INFLUENCE OF RECRUITMENT RATES

Populations of wild brook trout, Salvelinus fontinalis, in three small ponds in northern Wisconsin were studied for 4 yr to determine annual production with particular emphasis on influence of recruitment rates. Recruitment included trout hatched in ponds and immigrants from adjacent waters. Age-specific growth rates and densities of trout were estimated in spring and fall. Harvest of trout was estimated through partial creel surveys. Among populations annual production ranged from 26 to 331 kg/ha and was directly related to recruitment rates. Production was most influenced by population biomass. Instantaneous growth rates did not vary significantly within or among populations despite large differences in population densities; hence, variations in production appeared unrelated to growth rates. Among populations, yield of trout ranged from 25 to 72 kg/ha and fishing pressure ranged from 154 to 1,405 hlha. Proportion of annual production that was harvested was directly related to fishing pressure. Production of fry during the first 9 mo of life may have been overestimated because mortality rates from emergence to fall were assumed constant. Estimates of production of adult trout could have been positively or negatively biased depending upon immigration patterns. Despite these possible errors, it was clear that recruitment was the most important factor affecting production.
Imagine That! Leveraging Emergent Affordances for 3D Tool Synthesis

In this paper we explore the richness of information captured by the latent space of a vision-based generative model. The model combines unsupervised generative learning with a task-based performance predictor to learn and to exploit task-relevant object affordances given visual observations from a reaching task, involving a scenario and a stick-like tool. While the learned embedding of the generative model captures factors of variation in 3D tool geometry (e.g. length, width, and shape), the performance predictor identifies sub-manifolds of the embedding that correlate with task success. Within a variety of scenarios, we demonstrate that traversing the latent space via backpropagation from the performance predictor allows us to imagine tools appropriate for the task at hand. Our results indicate that affordances-like the utility for reaching-are encoded along smooth trajectories in latent space. Accessing these emergent affordances by considering only high-level performance criteria (such as task success) enables an agent to manipulate tool geometries in a targeted and deliberate way.
PHYTOCHEMISTRY AND ANTIMICROBIAL COMPOUNDS OF HYMENOCRATER CALYCINUS

The genus, Hymenocrater, belongs to the plant family Lamiaceae which contains eleven shrub species, of which H. calycinus belonges and grows wildly in Northeastern Iran. From the ethyl acetate and methanol extracts of the flowered aerial parts of Hymenocrater calycinus, four compounds were isolated using chromatographic methods and identified by spectroscopic data (MS, 1 H- and 13 C-NMR, HMQC, HMBC and 1 H- 1 H COSY). The effect of rosmarinic acid, as the main component in our study was applied to Staphylococcus aureus, Escherichia coli, Candida albicans and Aspergillus niger by the broth dilution method. Isolated compounds were identified as s-sitosterol (1), ursolic acid (2), rosmarinic acid (3) and quercetin-3-O- rutinoside (4). The results of our assay against bacteria and fungi show that, rosmarinic acid has an antifungal property against Candida albicans (MIC, 250 μg mL -1 ).
Revisiting the Taxonomic Synonyms and Populations of Saccharomyces cerevisiae—Phylogeny, Phenotypes, Ecology and Domestication

Saccharomyces cerevisiae—the most emblematic and industrially relevant yeast—has a long list of taxonomical synonyms. Formerly considered as distinct species, some of the synonyms represent variants with important industrial implications, like Saccharomyces boulardii or Saccharomyces diastaticus, but with an unclear status, especially among the fermentation industry, the biotechnology community and biologists not informed on taxonomic matters. Here, we use genomics to investigate a group of 45 reference strains (type strains) of former Saccharomyces species that are currently regarded as conspecific with S. cerevisiae. We show that these variants are distributed across the phylogenetic spectrum of domesticated lineages of S. cerevisiae, with emphasis on the most relevant technological groups, but absent in wild lineages. We analyzed the phylogeny of a representative and well-balanced dataset of S. cerevisiae genomes that deepened our current ecological and biogeographic assessment of wild populations and allowed the distinction, among wild populations, of those associated with low- or high-sugar natural environments. Some wild lineages from China were merged with wild lineages from other regions in Asia and in the New World, thus giving more resolution to the current model of expansion from Asia to the rest of the world. We reassessed several key domestication markers among the different domesticated populations. In some cases, we could trace their origin to wild reservoirs, while in other cases gene inactivation associated with domestication was also found in wild populations, thus suggesting that natural adaptation to sugar-rich environments predated domestication.
Effect of dietary benzoic acid supplementation on growth performance and intestinal wall morphology of broilers.

The research was conducted to determine the influence of benzoic acid on growth performance and intestinal wall morphology of broiler birds. The research was carried out using 120 day-old broilers divided into five (5) groups, each having 24 broiler birds, and eight (8) birds per replicate. The levels of inclusion of the benzoic acid was based on control 0%, Treatment 1 = 0.6%, Treatment 2 = 1.2%, Treatment 3 = 1.8% and Treatment 4 = 2.4%. After six weeks, 2 animals from each replicate were killed. The carcasses weights, the pH of the digester and organ proportions were determined. Result showed that the body weight gain of birds in Treatment 1 and Treatment 2 were the highest (T1=1.44kg, T2=1.76kg), but T2 had the best growth performance which was significantly different (P<0.05) in the final body weight of other birds in other treatments. The different segment of the gastro-intestinal tract had different pH concentration which differed significantly (P<0.05) between the control and the treatments. Benzoic acid supplementation improved (P< 0.05) duodenal and jejuna villous height. This study showed that feeding benzoic acid at 1.2% inclusion level in broiler feed improved weight gain and also suppressed some microbes, which compete with the host animal for nutrient, thereby improving the growth performance and gut health of broiler birds.
Distribution of Calliophis melanueus, Boiga trigonata, Coluber grascilis and Coronella brachyera in Western region of Khed Tahsil, MS, India

Reptiles are termed as cold blooded, meaning that their body temperature varies with the outside temperature reptiles have low metabolic rate and there for produce less heat than a mammals or birds of comparable size. They have poor body insulation and cooling mechanism as they lack sweat glands yet they have considerable capacity for regulating their body temperature. The Western region is commercial crop growing area of Khed Tahsil. The present study observed in which 04 species belonging to 01 order, 02 families of 04 genera were recorded during June 2010 to May 2011. The Calliophis melanueus, Boiga trigonata, Coluber gracilis and Coronella brachyura species are rare in Khed Tahasil which is part of Northern western Ghats, Pune (MS).
Development and Challenges in Animal Tuberculosis Vaccination

Vaccination with Bacillus Calmette–Guérin (BCG) constituted a major advance in the prevention of human tuberculosis (TB) in the beginning of the past century. BCG has also a clear potential for use in animals and, in particular, in the main domestic species subjected to TB control programs, cattle. Nowadays, the use of BCG vaccination against TB in cattle is not permitted by European Union legislation because BCG can induce a cellular immune response producing diagnostic interference in the eradication programs based on tuberculin single and comparative intradermal tests imposed worldwide. In this review, we recall the history of TB vaccination as well as different vaccine trials and the response to vaccination in both domestic and wild animals. Promising potential inactivated vaccines are also reviewed. Research studies are mainly focused to improve vaccine efficacy, and at the same time to ensure its easy administration, safety and stability in the environment. Great challenges remain, particularly in terms of vaccine candidates and also in the acceptance of vaccination. Vaccination should be included in a strategic plan for integrated control of TB under a “one health” perspective, which also includes other measures such as improved biosafety on farms to avoid or decrease contact between domestic and wild animals or control of wildlife reservoirs to avoid overabundance that may favor infection maintenance.
Mining Business Process Information from Email Logs for Business Process Models Discovery

—Exchanged information in emails’ texts is usually concerned by complex events or business processes in which the entities exchanging emails are collaborating to achieve the processes’ ﬁnal goals. Thus, the ﬂow of information in the sent and received emails constitutes an essential part of such processes i.e. the tasks or the business activities. An email can be harvested for understanding the undocumented business process information it contains. Our goal in this work is to recast emails into a resource of business-oriented information. We describe a framework that is constituted of several analytical approaches able to extract such kind of information from email logs i.e. transforming an email log into an event log. The efﬁciency of all approaches is studied by applying different experiments on the open Enron email dataset.