Miracle-dz/UniFAR-FTUs huggingface dataset:
The NetViz terminology visualization tool and the use cases in karstology domain modeling

We present the NetViz terminology visualization tool and apply it to the domain modeling of karstology, a subfield of geography studying karst phenomena. The developed tool allows for high-performance online network visualization where the user can upload the terminological data in a simple CSV format, define the nodes (terms, categories), edges (relations) and their properties (by assigning different node colors), and then edit and interactively explore domain knowledge in the form of a network. We showcase the usefulness of the tool on examples from the karstology domain, where in the first use case we visualize the domain knowledge as represented in a manually annotated corpus of domain definitions, while in the second use case we show the power of visualization for domain understanding by visualizing automatically extracted knowledge in the form of triplets extracted from the karstology domain corpus. The application is entirely web-based without any need for downloading or special configuration. The source code of the web application is also available under the permissive MIT license, allowing future extensions for developing new terminological applications.
Nucleotide sequence comparison of the capsid Protein gene of severe and protective mild strains of Papaya ringspot virus

This study compared three mild and three severe strains of Papaya ringspot virus - type W (PRSV-W), based on nucleotide and amino acid sequences of the capsid protein (CP) gene. The CP nucleotide sequences of the mild strains shared 98% to 100% identity. When compared to the severe strains the identity ranged from 93% to 95%, except in the case of PRSV-W-2R, which resulted from reversion of the mild strains PRSV-W-2. The CP sequence of the reverting strain showed 100% identity with the sequence of its parental strain. An insertion of six nucleotides in the core region of the CP gene, which reflected the addition of two amino acids (Asn and Asp) in the deduced sequence of the protein, was found in all mild strains. These sequence comparisons were used to design strain-specific primers that were used to specifically amplify regions for either the mild or severe strains.
Sign Language Motion Capture Dataset for Data-driven Synthesis

This paper presents a new 3D motion capture dataset of Czech Sign Language (CSE). Its main purpose is to provide the data for further analysis and data-based automatic synthesis of CSE utterances. The content of the data in the given limited domain of weather forecasts was carefully selected by the CSE linguists to provide the necessary utterances needed to produce any new weather forecast. The dataset was recorded using the state-of-the-art motion capture (MoCap) technology to provide the most precise trajectories of the motion. In general, MoCap is a device capable of accurate recording of motion directly in 3D space. The data contains trajectories of body, arms, hands and face markers recorded at once to provide consistent data without the need for the time alignment.
Performance, Water Use and Effluent Output of Weaner Pigs Fed ad libitumwith Either Dry Pellets or Liquid Feed and the Role of Microbial Activity in the Liquid Feed

Forty eight and ninety six pigs weaned at 22.6 ± 2.6 days, were allocated to two trials to study the effect of feeding post-weaning diets ad libitum, either as dry pellets (DF) or as meal mixed with water in the ratio 2.5 :1 (LF). The trials, lasting 28 days, differed only in the type of trough used to present the liquid feed to the pigs. In both trials the daily gain of LF pigs over the 4 weeks of the trial was significantly (P < 0.001) better than that of the DF pigs. Daily gains for the two treatment groups were respectively 428 and 343 ± 15 g day -1 in Trial 1 and 454 and 397 ± 10 g day -1 in Trial 2. The feed conversion ratio (FCR) (corrected to fresh weight of dry feed) of LF pigs was significantly poorer (P<0.01) than that of DF pigs in both trials primarily as a result of feed wastage by the LF pigs. FCR for the DF and LF pigs was, respectively, 1.31 and 1.89 ± 0.05 in Trial 1. In Trial 2 improvements in the trough design reduced the difference in FCR. FCR for the DF and LF treatments was 1.37 and 1.44 ± 0.02 respectively. In Trials 1 and 2 LF pigs used on average 76% and 35% more water than DF pigs. LF pig produced 12% (Trial 1) and 5.7% (Trial 2) more effluent per unit of liveweight gain than DF pigs. Microbiological examination of the liquid feed system demonstrated that the system acted as a fermenter. Lactobacillus spp proliferated rapidly and became the dominant organism within 5 days and the populations remained relatively constant thereafter. The proliferation of lactobacilli reduced the pH of the liquid feed from approximately 6.0 to between 3.5 and 4.0. At the lower levels of pH the number of coliforms in the feed was significantly reduced.
Isolation and characterization of mutants of the citrus canker pathogen Xanthomonas axonopodis pv. citri that induce a distinct pattern of disease.

Random mutagenesis with the transposon Tn5tac 1i nXanthomonas axonopodis pathovar citri, the causal agent of citrus canker, generated four mutants with altered pathogenicity. These mutants were classified into three groups: (i) the nonpathogenic (NP) mutants XT10 and XT122, which did not induce any visible symptoms in the host; (ii) the WS - mutant XT27, which induced a callus-like lesion but not a watersoaked lesion; and (iii) the CL - mutant XT37, which was unable to induce a callus-like eruption but did induce the formation of a watersoaked lesion around the infection site. The NP mutants failed to grow in planta, whereas the WS - and CL - mutants showed a reduced growth rate relative to that of the wild type. Co-inoculation of leaves with the WS - and CL - mutants did not result in complementation of their respective defects. The extent of extracellular accumulation of polysaccharide, protease, and amylase activities by each of the mutants was similar to that of the wild type. The extracellular activity of polygalacturonate lyase of XT27 was reduced relative to that of the wild type and other mutants. Unlike the wild type and other mutants, XT27 also required glutamic acid for growth in culture. Southern blot hybridization revealed that each of the mutants resulted from transposon insertion at a single site; the insertion sites for XT10 and XT27 were lo - cated in the chromosome, whereas those for XT37 and XT122 were located in the indigenous plasmids. These results provide evidence that bacterial genes contribute independently to the pathogenesis of citrus canker.
Effect of immune stress on growth performance and energy metabolism in broiler chickens

This study was conducted to investigate the effects of different types of immune stress on the growth performance and energy metabolism in broiler chickens (Cobb 500). Three hundred and twenty one-day-old broilers were randomly assigned (n = 80 birds/group) to receive one of four treatments: (1) no vaccination, (2) conventional vaccination, (3) cyclophosphamide (CPM) stress and (4) lipopolysaccharide (LPS) stress. The results demonstrated that immune stress reduced the daily feed intake, average daily weight gain, plasma renin activity, serum angiotensin II and amylase activity of jejunal digesta (P < 0.05). The body temperature of broilers increased rapidly after LPS administration on days 16, 18 and 20, but attenuated on days 37, 39 and 41. The data suggested that immune stress can negatively affect the utilisation of energy in broilers, resulting in the decreased growth performance.
Corticosterone responses of hand‐reared and parent‐reared grey‐faced petrel chicks (Pterodroma macroptera gouldi)

Hand-reared grey-faced petrel (Pterodroma macroptera gouldi) chicks (Order Procellariformes) that were subjected to a standardised blood sampling protocol immediately before they fledged showed a reduced corticosterone response compared to parent-raised chicks. Serum corticosterone concentrations were lower in hand-reared than parent-reared birds 30 and 60 min after handling was initiated (21.5±6.7 vs. 105.4±7.4 ng/ml at 30 min, and 11.3±3.6 vs. 93.8±11.4 ng/ml at 60 min, respectively). The total integrated corticosterone response and the response corrected for initial corticosterone concentrations were similarly lower in hand-reared than parent-reared birds (927±489 vs. 4639±1924 ng/ml.min, and 529±352 vs. 4110±1896 ng/ml.min, respectively). Habituation to handling associated with hand-rearing, which is expressed as a subdued corticostrone response, is likely to reduce the physiological stress associated with the translocation and reintroduction of these birds. However, the longer-term consequences of this attenuated response remain unclear. Zoo Biol 0:1–8, 2005. © 2005 Wiley-Liss, Inc.
A Natural Language Processing System for Extracting Evidence of Drug Repurposing from Scientific Publications

More than 200 generic drugs approved by the U.S. Food and Drug Administration for non-cancer indications have shown promise for treating cancer. Due to their long history of safe patient use, low cost, and widespread availability, repurposing of these drugs represents a major opportunity to rapidly improve outcomes for cancer patients and reduce healthcare costs. In many cases, there is already evidence of efficacy for cancer, but trying to manually extract such evidence from the scientific literature is intractable. In this emerging applications paper, we introduce a system to automate non-cancer generic drug evidence extraction from PubMed abstracts. Our primary contribution is to define the natural language processing pipeline required to obtain such evidence, comprising the following modules: querying, filtering, cancer type entity extraction, therapeutic association classification, and study type classification. Using the subject matter expertise on our team, we create our own datasets for these specialized domain-specific tasks. We obtain promising performance in each of the modules by utilizing modern language processing techniques and plan to treat them as baseline approaches for future improvement of individual components.
One Side of the Coin: Development of an ASL-English Parallel Corpus by Leveraging SRT Files

We report on a method used to develop a sizable parallel corpus of English and American Sign Language (ASL). The effort is part of the Gallaudet University Documentation of ASL (GUDA) project, which is currently coordinated by an interdisciplinary team from the Department of Linguistics and the Department of Interpretation and Translation at Gallaudet University. Creation of the parallel corpus makes use of the available SRT (SubRip Subtitle) files of ASL videos that have been interpreted into or from English, or captioned into English. The corpus allows for one-way searches based on the English translation or interpretation, which is useful for translators, interpreters, and those conducting comparative analyses. We conclude with a discussion of important considerations for this method of constructing a parallel corpus, as well as next steps that will help to refine the development and utility of this type of corpus.
THE ANTIBIOTIC ACTIVITY OF SOIL MICROORGANISMS AS RELATED TO BACTERIAL PLANT PATHOGENS

In an attempted evaluation of the importance of soil antagonisms as a possible factor in the different survival capabilities of some bacterial plant pathogens in the soil environment, a comparison was made of the numbers of antagonists detected when different plant pathogenic species were used as test organisms in determining the "antibiotic potential" of nine "virgin" soils. It was found that there are present among the soil flora a great abundance of microorganisms intrinsically capable of antagonizing most of the bacterial pathogens tested and only for a few species are such antagonists relatively rare. There were great differences in the number of isolates antagonistic to the different pathogenic species, even in the same genus, and there seemed to be a correlation between the numbers of antagonists, as found here, and the capability of a species to maintain itself for long periods in the soil. For the most part the Xanthomonas species appeared to be most sensitive to the antagonistic soil microflora .
Effect of land use and climate on the diversity of moth guilds with different habitat specialization

An assemblage of moth species at a suburb of Prague (50°5’11”N,14°18’06”E) was monitored by a highly efficient mercury light trap for 23 years (1967–1976, 1980–1992). Species caught were divided into guilds according to habitat specialisation, and analysed using species richness S, Shannon’s diversity H and evenness J as the response variables, and the individual years of monitoring and effects of mean annual temperature and precipitation as the explanatory variables. Overall, 424 species were recorded: 25 early successional arable land species (43% of all caught individuals), 116 forest species feeding on trees and shrubs, 33 forest species feeding on woodland herbs and lichens, 92 forest-steppe species, 116 grassland species, 28 wetland species, and 14 non-specialized generalists. The diversity of habitat-specialised species responded mainly to land use changes, whereas the diversity of generalists reflected long-term meteorological trends. Species richness of specialists whose habitats in the vicinity of the trap have declined in extent decreased, the numbers of those whose habitats remained intact did not exhibit any particular trend, whereas the numbers of generalists increased, and their diversity positively responded to warming. It is concluded that the habitat specialists and generalists react to environmental changes differently. Non-specialised species appear more sensitive indicators of climate changes than habitat specialists because for the latter the indication of climate changes can be overlaid by changes in habitat use.
Towards a Representation of Verbal Semantics – An Approach Based on Near Synonyms

In this paper we propose using the distributional differences in the syntactic patterns of near-synonyms to deduce the relevant components of verb meaning. Our method involves determining the distributional differences in syntactic patterns, deducing the semantic features from the syntactic phenomena, and testing the semantic features in new syntactic frames. We determine the distributional differences in syntactic patterns through the following five steps: First, we search for all instances of the verb in the corpus. Second, we classify each of these instances into its type of syntactic function. Third, we classify each of these instances into its argument structure type. Fourth, we determine the aspectual type that is associated with each verb. Lastly, we determine each verb's sentential type. Once the distributional differences have been determined, then the relevant semantic features are postulated. Our goal is to tease out the lexical semantic features as the explanation, and as the motivation of the syntactic contrasts.
p53 Targets Chromatin Structure Alteration to Repress α-Fetoprotein Gene Expression*

Many of the functions ascribed to p53 tumor suppressor protein are mediated through transcription regulation. We have shown that p53 represses hepatic-specific α-fetoprotein (AFP) gene expression by direct interaction with a composite HNF-3/p53 DNA binding element. Using solid-phase, chromatin-assembled AFP DNA templates and analysis of chromatin structure and transcriptionin vitro, we find that p53 binds DNA and alters chromatin structure at the AFP core promoter to regulate transcription. Chromatin assembled in the presence of hepatoma extracts is activated for AFP transcription with an open, accessible core promoter structure. Distal (−850) binding of p53 during chromatin assembly, but not post-assembly, reverses transcription activation concomitant with promoter inaccessibility to restriction enzyme digestion. Inhibition of histone deacetylase activity by trichostatin-A (TSA) addition, prior to and during chromatin assembly, activated chromatin transcription in parallel with increased core promoter accessibility. Chromatin immunoprecipitation analyses showed increased H3 and H4 acetylated histones at the core promoter in the presence of TSA, while histone acetylation remained unchanged at the site of distal p53 binding. Our data reveal that p53 targets chromatin structure alteration at the core promoter, independently of effects on histone acetylation, to establish repressed AFP gene expression.
High-level gene expression in differentiating xylem of tobacco driven by a 2.0 kb Poplar COMT2 promoter and a 4×35S enhancer

Promoter constructs with high levels of xylem specific expression are needed to obtain efficient expression of candidate genes, microRNAs (miRNAs) and artificial microRNAs (amiRNAs) for the genetic modification of wood properties. The gene for caffeic acid O-methytransferase (PtrCOMT2) has the second most abundant transcript level of all the genes in monolignol biosynthesis in Populus trichocarpa and a high level of specificity in differentiating xylem. To characterize the PtrCOMT2 promoter, we cloned a short (2.0 kb) and a long (3.3 kb) promoter segment and compared their expression using GUS as a reporter gene in the differentiating xylem of Nicotiana tabacum. Both the 2.0 kb and the 3.3 kb promoter segments showed high specificity for differentiating xylem in this heterologous system. GUS activity increased as much as 5 times when the 4×35S enhancer was inserted in front of the 2.0 kb promoter, but GUS activity was only increased 2 times when the enhancer was inserted behind the promoter. The enhancer inserted upstream reduced the expression of the 3.3 kb promoter. While expression of some of the enhancer-plus-promoter constructs increased expression, there was a loss of specificity.
Learning to Find Translations and Transliterations on the Web based on Conditional Random Fields

In recent years, state-of-the-art cross-linguistic systems have been based on parallel corpora. Nevertheless, it is difficult at times to find translations of a certain technical term or named entity even with a very large parallel corpora. In this paper, we present a new method for learning to find translations on the Web for a given term. In our approach, we use a small set of terms and translations to obtain mixed-code snippets returned by a search engine. We then automatically annotate the data with translation tags, automatically generate features to augment the tagged data, and automatically train a conditional random fields model for identifying translations. At runtime, we obtain mixed-code webpages containing the given term and run the model to extract translations as output. Preliminary experiments and evaluation results show our method cleanly combines various features, resulting in a system that outperforms previous works.
Stimulation of Root Formation in Difficult-to-Root Woody Cuttings by Dithiothreitol

Shoot microcuttings of Malus domestica cv. Jork 9, Malus domestica cv. Cepiland, Mandevilla (Dipladenia) sanderi, and Daphne odora cv. variegata were induced to root by the addition of 0.1-1 mM dithiothreitol following an auxin (indole-3-acetic acid) treatment to initiate root formation. The most difficult to root, Malus domestica cv. Cepiland, required higher dithiothreitol concentrations to achieve optimum rooting than did the less difficult to root, Malus domestica cv. Jork 9, Mandevilla sanderi, or Daphne odora variegata. The roots induced by the combination of dithiothreitol and auxin treatment were approximately twofold longer and more robust than those induced with auxin treatment alone. The combination treatment of auxin and dithiothreitol has the potential to be of practical importance in root initiation in difficult-to-root cuttings of both woody and herbaceous horticultural varieties.
From Dictionary to Corpus and Back Again – Linking Heterogeneous Language Resources for DGS

The Public DGS Corpus is published in two different formats, that is subtitled videos for lay persons and lemmatized and annotated transcripts and videos for experts. In addition, a draft version with the first set of preliminary entries of the DGS dictionary (DW-DGS) to be completed in 2023 is now online. The Public DGS Corpus and the DW-DGS are conceived of as stand-alone products, but are nevertheless closely interconnected to offer additional and complementary informative functions. In this paper we focus on linking the published products in order to provide users access to corpus and corpus-based dictionary in various, interrelated ways. We discuss which links are thought to be useful and what challenges the linking of the products poses. In addition we address the inclusion of links to other, older lexical resources (LSP dictionaries).
Discriminating Zooplankton Communities in Lakes with Brook Trout (Salvelinus fontinalis) and in Fishless Lakes

Abstract: Natural geographic barriers and escarpments inhibited the post-glacial colonization of many lakes by fish on the eastern Canadian Boreal Shield. Hence, fishless lakes containing freshwater communities that evolved without fish predation are commonly found on the Boreal Shield next to fish-present lakes. The aim of this study was thus to assess how different top-down control from fish or invertebrate predation structure zooplankton communities in eastern Canadian Boreal Shield lakes throughout the ice-free season. We examined zooplankton community characteristics using univariate indices such as abundance, richness (S), evenness (J') diversity (H'), and multivariate species assemblages (Bray—Curtis dissimilarity) in 5 lakes with a single fish population, brook trout, Salvelinus fontinalis, and in 5 naturally fishless lakes throughout the ice-free season. The total abundance of zooplanktonic organisms was significantly higher in fishless lakes over the whole sampling period; this was related to the presence of small herbivorous species such as rotifers. Species assemblages of zooplankton were also significantly different between the 2 types of lakes throughout the season, principally due to the high abundance of rotifers and the scarcity of immature and mature daphnids in fishless lakes. Our results suggest that the low intensity of selective predation by brook trout on large herbivores and the heavy predation by Chaoborus americanus larvae on daphnids in fishless lakes appear to be the key factors for structuring the zooplankton community. Multivariate indicators identified patterns that were not revealed with the usual univariate indices, showing the importance of selecting appropriate indicators for the assessment of community structure. Nomenclature: Edmondson, 1959; Pennak, 1978; Bernatchez & Giroux, 2000.
Effect of storage period and exposure conditions on the quality of bosana extra-virgin olive oil

Changes in quality parameters, antioxidant compounds, oxidative stability and antioxidant activity during 18 months of storage of a monovarietal extra-virgin olive oil from Bosana cultivar, and exposed to light and dark, were studied. Analysis of data showed that all the parameters underwent significant changes during storage: free acidity, peroxide and ultraviolet (UV) spectrophotometric indexes remained below the limits reported in the EEC Regulations 2568/91 and 1989/03, and these are: ≤0.8% for acidity, ≤20 meq O 2 /kg for peroxide and ≤2.50 and ≤0.22 for K232 and K270, respectively. Phenol and α-tocopherol content decreased during storage (42.0 and 29.6%, respectively) while chlorophylls and carotenoids underwent a decrease until 8 months of storage (49% and 30%, respectively); after that, the values remained constant. Oxidative stability and antioxidant activity had not changed dramatically during 18 months. Phenols were significantly correlated to the antioxidant activity of the oil, while oxidative stability measured by Rancimat did not show any correlation with carotenoids, chlorophylls, phenols and α-tocopherol. Regarding exposure conditions, storage in the dark was better in retaining the quality of the oil, as expected.