Miracle-dz/UniFAR-FTUs huggingface dataset:
Home Range, Habitat Use and Food Habits of Re-Introduced Gaur (Bos Gaurus Gaurus) in Bandhavgarh Tiger Reserve, Central India

Gaur, which became locally extinct before 1995 in Bandhavgarh Tiger Reserve (BTR), Central India, is an endangered animal per Schedule - I of the Indian Wildlife Protection Act (1972). A re-introduction program was therefore created to rebuild the gaur population in BTR, both to enhance the long-term survival of the species and to restore natural biodiversity. After re-introduction, the home range, habitat use and food habits of gaur (Bos gaurus gaurus) were studied in BTR, India, from January 2011 to January 2012. Nineteen gaurs (five males - three radio-collared and 14 females - nine radio-collared) were re-introduced from Kanha Tiger Reserve to Bandhavgarh Tiger Reserve in January 2011. The reintroduced gaurs were monitored periodically through ground tracking and satellite GPS fixes. The mean annual group size of gaur was estimated at 7.3 ± 0.76 (SE). The overall estimated summer, monsoon and winter home ranges of gaur were 290 km2, 137 km2 and 155 km2 (Minimum Convex Polygon) respectively. The overall individual male home ranges varied from 135 to 142 km2, and overall individual female home ranges varied from 32 to 169 km2. Radio collared locations were plotted on a classified (LISS III) habitat map of Bandhavgarh Tiger Reserve to evaluate the habitat use and availability in each season. Habitat preference was computed using Bonferroni confidence interval method, compositional analysis and Ivlev's index. In summer, gaur largely preferred grassland (P<0.0001), whereas in monsoon and winter, gaur preferred bamboo mixed forest (P<0.0001). Gaur avoi ded open mixed forest (P<0.0001) and agricultural land in all three seasons. Data on food habits were collected through opportunistic sightings. In total, gaur fed on 68 plant species. The present study has reported first-time information on ranging patterns of reintroduced gaur and their degree of preferences for different vegetation and terrain types across seasons, which will be very useful to the park administration for future conservation of this endangered species and for habitat intervention.
Biodiversity of ectomycorrhizal fungi in surface mine spoil restoration stands in Poland – first time recorded, rare, and red-listed species

Results of mycological research conducted in the years 2001–2013 in the restoration stands growing on reclaimed mine spoils are presented. Four opencast lignite mine spoil heaps in Poland were examined: Pątnow-Joźwin, Adamow, Mt Kamiensk, and Turow. The paper focuses on 71 species of ectomycorrhizal fungi: recorded for the first time in the country (16 taxa), currently red-listed (23 taxa), known from few localities only (32 taxa). Notes on their ecology and habitats are provided, as well as their distribution in Europe and in Poland. Restoration tree stands, established as part of the reclamation process of mine spoils, form a unique habitat for many rare and interesting fungal taxa. Among them are pioneer species, species known mainly from Northern Europe or mountainous locations, highly specialized and narrow-niche taxa, and many threatened species. Afforested mine spoils contribute significantly to the fungal biodiversity, both at a local and at a larger scale.
Clinically-weighted transcriptomic signatures for protein kinase inhibitor associated cardiotoxicity

Cardiotoxicity (CT) involving diminished cardiac contractility and heart failure is a major adverse event associated with otherwise efficacious protein kinase inhibitors (KIs). Here, we sought to develop clinically-weighted transcriptomic signatures to predict risk of CT and to better understand the biological processes associated with CT risk. We obtained transcriptome-wide response profiles in four human primary cardiomyocyte cell lines that were treated with 22 different KIs using mRNA sequencing with 3’ digital gene expression. The FDA Adverse Event Reporting System was used to derive relative risk scores for four types of CT for different KIs. We used elastic net regression to associate these transcriptomic profiles with KI-associated risk scores for CT subtypes to obtain clinically-weighted transcriptomic signatures, which showed good predictive properties (cross-validation R2 >0.87). Our clinically-weighted transcriptomic signatures for KI-associated CT may be of relevance in early drug development for the prediction of KI-associated CT.
An Enzyme-Linked Immunosorbent Assay for the Rapid Detection of Vibrio parahaemolyticus.

A sandwich enzyme-linked immunosorbent assay (ELISA) was developed for the rapid detection of Vibrio parahaemolyticus in foods. The assay was based on the detection of two outer-membrane proteins (molecular weights 36,000 and 34,000) of V. parahaemolyticus . Following an 18-h incubation in alkaline peptone salt broth containing 0.1%Teepol, the culture supernatant was added to the microtiter plate coated with antibodies against the two outer-membrane proteins. After washing, the same antibodies absorbed with V. alginolyticus and labeled with horsemdish peroxidase were used as secondary antibodies. The detection limit of the assay for total outer-membrane proteins was 10 ng/ml. For 29 strains of V. parahaemolyticus and 73 strains (including 27 isolates of vibrios) of other bacteria tested, the sensitivity and specificity of the ELISA were 100 and 96%, respectively. Strains producing false positives were V. tubiashii , V. campbellii , and V. vulnificus . Of 23 seafood samples tested, V. parahaemolyticus was detected in 17 and 15 samples, respectively, by the ELISA and by a conventional culture method. V. parahaemolyticus was also detected in samples artificially inoculated with the microorganism at levels less than 10 colony-forming units (CFU) per g. Compared to the conventional culture methods, which may take 4 to 6 days to complete, the ELISA can detect low numbers of V.parahaemolyticus in foods with a total analytical time of only 24 h. The ELISA is recommended as a rapid screening method.
Octopus sinensis d'Orbigny, 1841 (Cephalopoda: Octopodidae): Valid Species Name for the Commercially Valuable East Asian Common Octopus

The East Asian common octopus has long been synonymized with the Atlantic and Mediterranean species Octopus vulgaris Cuvier, 1797 . However, evidence from molecular genetic studies has firmly established that the so-called cosmopolitan common octopus is in fact a group of several biogeographically distinct populations which form a complex of species with closely similar morphology. Here, a diagnosis and brief description are provided which distinguish the East Asian common octopus from O. vulgaris, and as a suitable name for it a former junior synonym of O. vulgaris is identified as a valid species: Octopus sinensis d'Orbigny, 1841 . A neotype is designated. Voucher material includes specimens collected in Japan by Philipp Franz von Siebold and deposited in the National Museum of Natural History - Naturalis - in Leiden; and others that were studied by Madoka Sasaki in preparation for the detailed description of this species (as O. vulgaris) in a monograph on Japanese Cephalopoda published in 1929. At present, all species in this complex (particularly O. vulgaris and the East Asian species here identified as O. sinensis) are highly vulnerable to overfishing, so recognizing O. sinensis as a species distinct from O. vulgaris is an important step towards improving sustainable fisheries management policies for each species in this group of commercially valuable octopuses.
Comparative and Computer Assisted Drug Designing of Fatty Acids Isolated from Flowers, Leaves, Stem Bark, Root Bark and Nuts of Semecarpus anacardium L. f. （Anacardiaceae）

Objectives: Computational study will help us in reducing the experimental work. The process of drug discovery involves the designing of molecules with appropriate pharmacophores with the help of various soft wares. The purpose of this paper is to study the probable binding modes of fatty acids on fatty acids after enzymatic hydrolysis of the FAAH (fatty acid amide hydrolase) in different extracts of flowers, leaves, stem bark, root bark and nuts of Semecarpus anacardium L. f. by using molecular modeling study and computer assisted drug designing. Nuts yielded 20 fatty acids including saturated, ω-3 unsaturated, ω-6 unsaturated, ω-7 unsaturated and ω−9 unsaturated fatty acids. Based on IR, H NMR, C NMR, MS (mass) spectrometry, GC analysis, the structural elucidation of these isolated fatty acids was established. Methods: A dataset comprising of 20 fatty acids were drawn in ChemDraw and converted into 3D-molecules with all possible tautomers and chiral centers. The minimization of molecules was carried out using PRCG (Polak-Ribiere Conjugate Gradient) method with maximum of 5000 iterations. The minimized compounds were used for protein preparation. The crystal structure of human FAAH (PDB ID: 3K84) is prepared and selected for the docking studies of 20 fatty acids using Schrödinger docking program module. Conclusions: In this study, we carried out the molecular docking studies in order to understand the probable binding mode of 20 fatty acids in FAAH from which we identified key active site residues for FAAH, thereby it can be used to design the novel compounds for FAAH targets.
Effect of Indian Ocean Dipole signal on freshwater cyanobacterial dynamics

Abstract The proliferation of freshwater cyanobacteria is a serious environmental problem that often reduces water quality. In this study, we observed the possible influence of the Indian Ocean Dipole (IOD), represented by the Dipole Mode Index (DMI), on the dynamics of cyanobacterial blooms in a river system (the lower Nakdong River). Korean monsoon rainfall (KMR) was preceded by 5-month moving average DMI of ~1.5 years, and the KMR and DMI were negatively associated (r2 = 0.53, n = 15, p < 0.01). In turn, a decrease in KMR was responsible for a decrease in total dam discharge (r2 = 0.64, n= 15, p < 0.01), resulting in an abrupt increase in cyanobacterial cell density at the study site (r2 = 0.94, n = 15, p < 0.01). We found a strong and significant positive correlation between cyanobacterial density of the Nakdong River and a 5-month moving average DMI (r2 = 0.95, n = 15, p < 0.01). These correlations suggest that a positive DMI decreased KMR and therefore water discharge, resulting in an excessive proliferation of the cyanobacterial density during the monsoon period. Despite a variety of uncertainties, the presence of the IOD is believed to play a role in triggering freshwater cyanobacterial proliferation through a signal propagation pathway during summer drought occurrence in the monsoon period.
THE COMPOSITION OF PLANT AND RATOON CROPS OF VARIETY N14 AT PONGOLA

Material harvested from a growth analysis experiment conducted with sugarcane variety N14 under irrigation at Pongolawas used to determine the composition of plant and firstratoon crops that grewconcurrently from 12 November 1986 to 12 October 1987. Harvesting took place when the crops were 70, 125, 188, 251 and 334days old. The amounts of dry matter, fibre, brix, sucrose, glucose, and fructose were determined in the harvested stalks. The proportions of glu­ cose and fructose relative to that of sucrose declined pro­ gressively as the crops grew older. The proportions of fibre and brix were reversed as the crop aged from 125 to 334 days. The inorganic constituents of foliage, trash and stalks were alsodeterminedat eachtime of harvesting. The amounts of the major elements contained in the above-ground crops werecompared with those of comparable plant crops of va­ riety NC0376 grown at Shakaskraal and Pongola. The most noteworthy features were the high nitrogen content of a crop of NC0376 which was the first crop to be planted on pre­ viously uncultivated land on the farm at Pongola, and the high potassium contents of all three crops studied in growth analysis experiments at Pongola.
Effect of co-culture with enterocinogenic E. faecium on L. monocytogenes key virulence gene expression

The aim of the present study was to assess the expression of key virulence genes during co-culture of L. monocytogenes with a bacteriocinogenic E. faecium strain in liquid growth medium. For that purpose, BHI broth was inoculated with 7 log CFU·mL –1 L. monocytogenes and 4, 5 or 6 log CFU·mL –1 E. faecium . Sampling took place after 8 and 24 h of incubation, corresponding to the maximum and minimum of enterocin production, respectively. The RNA was extracted, stabilized and expression of prfA , sigB , hly , plcA , plcB , inlA , inlB , inlC and inlJ , was assessed by RT-qPCR. Most of the genes were downregulated during co-culture at 5 °C. Moreover, a statistically significant effect of the inoculum level was evident in most of the cases. On the contrary, no effect on the transcription level of most of the genes was observed during co-culture at 37 °C.
Differential organization of taxonomic and functional diversity in an urban woody plant metacommunity

Questions Urban ecosystems present an opportunity to study ecological communities in the context of unprecedented environmental change. In the face of urban land conversion, ecologists observe new patterns of species composition, dominance, behaviour and dispersal. We propose a hypothetical socioeconomic template that describes a gradient in human investment in community composition to aid in organizing the human role in shaping urban biodiversity. We asked: (1) what is the relative magnitude of taxonomic and functional turnover of urban woody plant communities across different land-use types; and (2) do land uses exhibiting higher intensity of human management of biodiversity support higher turnover over those with less human influence? Location Baltimore, MD, USA (39°17′ N, 76°38′ W). Methods We examined patterns in woody plant biodiversity across 209 plots of different urban land uses. Six land-use types were arranged along a gradient in the intensity through which humans are hypothesized to manage species composition at the plot scale. We calculated local, or α-diversity, and compositional turnover, or β-diversity, of taxonomic and functional diversity across plots within each land-use type. We compared the magnitude of these biodiversity measures between land uses to test our conceptual template for how the intensity of human management can predict urban woody plant biodiversity. Results We observed high taxonomic turnover in residential and commercial plots compared with vacant or open space land-use areas. This was associated with a weaker, but similar, pattern in functional diversity. This was associated with low total abundance in residential and commercial plots. Furthermore, the number of unique species was extremely high in the same land-use types. Conclusions Our observations help explain why turnover can be high in heavily managed plots relative to vacant land. In patches without heavy human management, we found low levels of turnover. This highlights the importance of assessing diversity both locally and at the level of turnover between patches. Management and policy can benefit from the perspective embodied in the conceptual approach tested here.
Successful Amplification of DNA Using Recombinase-Aided Amplification (RAA) and its Application to Seven Horticultural Crops

The amplification of nucleic acid is essential for many analyses requiring DNA. Current techniques require sophisticated equipment or complex experimental procedures whose implementation may be limited to outsourcing to other laboratories, or a continuous electricity supply that is expensive and inaccessible in many regions. In this study, a novel approach, recombinase-aided amplification (RAA), was used to rapidly amplify DNA. Since primer length is one factor that can influenc e the success of DNA amplification, i n this assay, 18 primer pairs were tested between 18 and 28 base pairs in length. Four of these were applied to seven horticultural crops: mango (Mangifera indica L. var. ‘Tainong no.1’), Manchurian walnut (Juglans mandshurica Maxim.), Chinese pear (Pyruspyrifolia (Burm.) Nak), grape (Vitisvinifera L. var. ‘Thompson ’), Cattley guava (Psidium cattleianum Sabine var. ‘Littorale’), lychee (Litchi chinensis Sonn. var.‘Bobaitangbo’) and Chinese sugarcane (Saccharum sinense L.). RAA could successfully and consistently amplify the DNA of all seven horticultural crops.
CONTRIBUTION TO THE PHYLOGENY OF THE PANGASIIDAE BASED ON MITOCHONDRIAL 12S RDNA

Catfishes are generally one of the economically important groups of fresh and brackish water fishes in the world. In many countries, they form a significant part of inland fisheries, and several species have been introduced in fish culture. Judging from literature, the main constraint to cultivate wild species and to optimise the production of pangasiid catfishes is due to the poorly documented systematics of this family. In the present contribution, the phylogenetic relationships within Pangasiidae are studied to contribute to a better insight in their taxonomy and evolution. The genetic relatedness is inferred using mitochondrial 12S rDNA gene sequences. To resolve the phylogenetic position of Laides in this group of catfish, five genera of Asian and African Schilbeidae are also considered. The results showed that a species group (complex) could be clearly seen in the genetic tree. Pangasius is more derive than the other genera. By using approximate molecular clock/evolutionary calibration from mitochondrial gene, a new episode of speciation for the family marked explosive radiation about 5- 8 million years ago (mya). This adaptive radiation extended until the Late Pleistocene. Regarding the relationships between the Pangasiidae and Schilbeidae, two families show an allopatric distribution with slight overlap. The Pangasiidae occur mainly in Southeast Asia, while the Schilbeidae are seen mainly on the Indian subcontinent (including Myanmar) and Africa. It confirms the separation between Schilbeidae and Pangasiidae occurred in the Early Miocene.
Marine food-web structure and community patterns in high-latitude marine ecosystems

A food web is an ecological network and its topological description consists of the list of nodes, i.e., trophospecies, the list of links, i.e., trophic interactions, and the direction of interactions (who is the prey and who is the predator). Food web topologies are widely used in ecology to describe structural properties of communities or ecosystems. The selection of trophospecies and trophic interactions can be realized in different manners so that many different food webs may be constructed for the same community. In the Barents Sea, many simple food webs have been constructed. We present a comprehensive food web topology for the Barents Sea ecosystem, from plankton to marine mammals. The protocol used to compile the data set includes rules for the selection of taxa and for the selection and documentation of the trophic links. The resulting topology, which includes 244 taxa and 1589 trophic links, can serve as a basis for topological analyses, comparison with other marine ecosystems, or as a basis to build simulation models of the Barents Sea ecosystem. The data set consists of three related tables: (1) the list of taxa, (2) the list of pairwise interactions, and (3) the list of bibliographical references.
Effects of glyceollin on mRNA expression in the female mouse brain.

EFFECTS OF GLYCEOLLIN ON MRNA EXPRESSION IN THE FEMALE MOUSE BRAIN Sanaya F. Bamji August 9, 2016 Glyceollins (Glys), produced by soy plants in response to stress, have antiestrogenic activity in breast and ovarian cancer cell lines in vitro and in vivo. In addition to known anti-estrogenic effects, Glys exhibit mechanisms of action not involving estrogen receptor (ER) signaling. To date, effects of Glys on brain physiology and function are unknown. The purpose of the experiments summarized in this dissertation was to gain an understanding of the effects of Gly on brain-related functions in the female mouse brain through the observation of changes in gene expression. For our initial studies, we treated ovariectomized Swiss Webster (CFW) mice with 17-β estradiol (E2) or placebo pellets, followed by 11 days of exposure to Glys or vehicle i.p. injections. We then performed microarray (Chapter 2) and RNA-sequencing analyses (Chapter 3) on total RNA extracted from whole brain hemispheres and identified differentially expressed genes (DEGs) between our treatment groups. Our results suggested that Glys, when in combination with E2 (E2+Gly), can oppose the E2 effects on gene expression and vice versa, can regulate genes similarly to E2, and can also have E2-independent effects on gene expression in the female brain. However, the whole brain experiments did not take into account the heterogeneity of the brain. Different brain regions perform unique and
Reconstructing phylogenetic trees from clustering trees

MOTIVATION In the context of phylogenetic tree reconstruction, divisive clustering methods can be used to infer phylogenetic trees in a top-down way. These methods have the important advantage of providing an explanation for the resulting topology, since the splits are described by polymorphic locations in the sequences. However, the quality of the resulting trees is rather variable. In this work, we argue that trees induced by top-down methods can be viewed not just as phylogenetic trees, but also as identifying constraints that the real phylogenetic tree must satisfy.
Mécanismes de tri et d’adressage des protéines vers les deux domaines membranaires des cellules épithéliales polarisées

La polarite est une caracteristique fondamentale de la plupart des cellules eucaryotes. Le caractere primordial de cette polarite est l’individualisation de la membrane plasmique en domaines separes: le domaine apical et le domaine basolateral. Ces deux surfaces exercent des fonctions differentes qui correspondent a une composition tres specifique de chaque domaine en lipides et en proteines. Pour etablir et maintenir leur polarite, les cellules epitheliales doivent trier et envoyer les proteines et les lipides vers la surface cellulaire correcte. Les donnees recentes concernant le transport polarise montrent que le trafic intracellulaire des lipides et des proteines sont deux evenements etroitement lies et qui ne doivent donc pas etre abordes separement. Dans cette revue nous discuterons de quelques mecanismes impliques dans le transport polarise, nous aborderons plus particulierement les donnees recentes concernant le role des microdomaines lipidiques (Rafts) dans le trafic des proteines vers la surface apicale des cellules epitheliales polarisees.
The Laying Cycle of Brown-Headed Cowbirds: Passerine Chickens?

We collected 270 female Brown-headed Cowbirds (Molothrus ater) in southern Ontario in 1976 to determine ovarian and oviducal growth during the breeding season and 188 female cowbirds in 1977 to estimate clutch size and the interval between clutches. Ovaries and oviducts grew rapidly in April, reached breeding size in early May, and remained at this size, without regression between clutches, until the end of the breeding season in early July. Ovaries and oviducts then regressed rapidly and by the end of July weighed about the same as those in early April. The clutch size averaged about 4.0-4.6 eggs, similar to clutch sizes of nonparasitic icterids. It varied greatly from 1 egg, in about 10% of the birds, to about 7 eggs. Two days without laying usually separated consecutive clutches, but some birds appeared to miss laying for only 1 day. Although atresia of large yolky follicles was common in birds between clutches, it did not always precede the end of a clutch. The long reproductive period without regression and the short interval between clutches are atypical of passerine reproduction. Rather, the laying cycle of cowbirds is similar to that of domestic chickens (Gallus gallus). The laying cycle of cowbirds seems adapted to a continuous supply of host nests; atresia may be related to a shortage of nests. Received 16 June 1982, accepted 18