Miracle-dz/UniFAR-FTUs huggingface dataset:
Complete mitochondrial genome sequence of the Indian clouded leopard (Neofelis nebulosa)

Abstract The complete mitochondrial genome of sequence 16,859 bp of Indian clouded leopard (Neofelis nebulosa) has been sequenced using next generation sequencing technology Torrent PGM platform. The complete mitochondrial genome sequence of clouded leopard consists of 13 protein-coding, 22 tRNA, and two rRNA genes and a control region (CR). The mitochondrial genome is relatively similar to other felid mitochondrial genomes with respect to gene arrangement, composition, tRNA structures and skews of AT/GC bases to be typical of those reported for other mammals. The nucleotide composition of the genome shows that there is more A–T% than G–C% on the positive strand as revealed by positive AT and CG skews. The base composition of the mitochondrial genome of clouded leopard is as follows: A, 5362 bp (31.8%); C, 4560bp (27.0%); G, 2475 bp (14.6%); T, 4462 bp (26.4%). Most of the genes have ATG initiation codons, except ND1, ND2, ND3, ND4, ND6, and CYTB (ATA start codon).
EMPIRICAL MODEL BUILDING FOR THE OPTIMUM DESIGN OF ROTATING MACHINERY

This work shows the application of statistical modeling techniques to the optimum design of rotating machinery. The fundamentals of rotor dynamics are reviewed in order to present the physical quantities involved in the statement of an optimization problem aiming at improving the configuration of a rotor-bearing system, whose behavior is evaluated in terms of its critical speeds and strain energy. Objective and constraint functions belonging to this optimization procedure are represented by means of response surface meta-models, whose basic concepts are also briefly reviewed. The optimum values of the design variables (bearing stiffness/damping coefficients and inertia values/positions) are determined by several different optimization methods, spanning gradient based and heuristic strategies. The results obtained are analyzed, leading to the conclusions and some suggestions for future research work.
Remote sensing based crop inventory: A review of Indian experience

This paper reviews the approach and techniques of Remote Sensing (RS) based crop discrimination and area estimation including single date approach based on maximum likelihood classification as well as hierarchical/ growth profile for crop classification. Uniqueness of both optical and microwave data for crop identification in operational scenario in Rabi and Kharif season is presented. In the past two decades, studies on RS based crop inventory of more than 20 crops at various spatial scales (village to national) have been conducted. In most of the studies a sampling-based approach using optimally acquired single date satellite data and a supervised classifier has been used. More recently, national scale inventory of wheat and rice using multidate WiFS and Radarsat, Synthetic Aperture Radar (SAR) data have been carried out. Studies on accuracies of area inventory led to understanding of effects of sensor characteristics such as spatial, spectral and radiometric resolution and scene characteristics such as field sizes, acquisition date etc. These experiences in Crop Area and Production Estimation (CAPE) project over past decade suggests that remote sensing inventory has matured in operational use. Future perspective such as utilization of multi-source data and merging techniques, fraction area estimation approaches, as well as integration of conventional field survey information with remote sensing data towards the FASAL concept is also presented.
S PARSE R ECOVERY VIA B OOTSTRAPPING : C OLLABO - RATIVE OR I NDEPENDENT ?

Sparse regression problems have traditionally been solved using all available mea1 surements simultaneously. However, this approach fails in challenging scenarios 2 such as when the noise level is high or there are missing data / adversarial samples. 3 We propose JOBS (Joint-Sparse Optimization via Bootstrap Samples) – a collab4 orative sparse-regression framework on bootstrapped samples from the pool of 5 available measurements via a joint-sparse constraint to ensure support consistency. 6 In comparison to traditional bagging which solves sub-problems in an independent 7 fashion across bootstrapped samples, JOBS achieves state-of-the-art performance 8 with the added advantage of having a sparser solution while requiring a lower 9 number of observation samples. 10 Analysis of theoretical performance limits is employed to determine critical optimal 11 parameters: the number of bootstrap samples K and the number of elements L in 12 each bootstrap sample. Theoretical results indicate a better bound than Bagging 13 (i.e. higher probability of achieving the same or better performance). Simulation 14 results are used to validate this parameter selection. JOBS is robust to adversarial 15 samples that fool the baseline method, as shown by better generalization in an 16 image reconstruction task where the adversary has similar occlusions or alignment 17 as the test sample. Furthermore, JOBS also improves discriminative performance 18 in a facial recognition task in a sparse-representation-based classification setting. 19
Staphylococcus aureus and Lactobacillus crispatus: Adhesive characteristics of two Gram-positive bacterial species

DEPARTMENT OF BIOSCIENCES FACULTY OF BIOLOGICAL AND ENVIRONMENTAL SCIENCES DOCTORAL PROGRAMME IN MICROBIOLOGY AND BIOTECHNOLOGY UNIVERSITY OF HELSINKI Staphylococcus aureus and Lactobacillus crispatus: Adhesive Characteristics of Two Gram-Positive Bacterial Species RIIKKA KYLVÄJÄ dissertationes schola doctoralis scientiae circumiectalis, alimentariae, biologicae. universitatis helsinkiensis 17/2016
for predicting species ranges: a metamodelling framework

Aim Current interest in forecasting changes to species ranges has resulted in a multitude of approaches to species distribution models (SDMs). However, most approaches include only a small subset of the available information, and many ignore smaller-scale processes such as growth, fecundity and dispersal. Furthermore, different approaches often produce divergent predictions with no simple method to reconcile them. Here, we present a flexible framework for integrating models at multiple scales using hierarchical Bayesian methods.
Isolation and Characterization of Extracellular Enzyme Producing Bacilli in the Digestive Tracts of Rohu, Labeo rohita (Hamilton) and Murrel, Channa punctatus (Bloch)

Isolation of some extracellular enzyme producing aerobic bacteria in the digestive tracts of rohu (Labeo rohita, Cyprinidae) and murrel (Channa punctatus, Channidae) was carried out. Gut bacteria were isolated on tryptone soya agar (TSA) plates. The isolated strains were qualitatively screened based on their extracellular protease, amylase and cellulase producing ability using selective media. Among the strains isolated, LrB1 and CpB2 isolated from L. rohita and C. punctatus, respectively, seemed to be the superior strains. The strains were characterized based on morphological, physiological and biochemical characterization and identified as Bacillus subtilis (LrB1) and Bacillus cereus (CpB2). They tolerated a wide range of temperature (15-55°C), pH (5-11) and NaCl (125%). Biochemical characterization suggests that the isolates are capable of hydrolyzing proteins and carbohydrates indicating their importance in fish nutrition. The information generated from the present investigation could contribute towards the utilization of such autochthonous enzyme-producing bacteria for nutrition in fish with better efficiency.
Root Growth, Respiration and β-Glucosidase Activity in Maize (Zea mays) and Common Bean (Phaseolus vulgaris) Inoculated with Azospirillum brasilense

As Azospirillum is shown to improve plant growth, the influence of inoculation on plant metabolism in maize and common bean seedlings has been assessed. Respiration rates have been measured and changes in 13-glucosidase (which may be involved in phytohormone release from conjugates) activity detected. A trend of inoculum concentration-dependent increased respiration rates was detected in inoculated maize seeds in Petri dishes. A similar phenomenon was observed for coinmon bean seedlings grown in an hydroponic system, when growth promotion and enhanced respiration rates occurred after inoculation with Azospirillum at 106 du/ml. In the hydroponic growth system, Azospirillum inoculation at 106 du/ml, promoted root fresh weight as well as shoot fresh and dry weight of maize seedlings. Treatment with Azospirillum reduced the Km and Vmax values of 13glucosidase activity, in crude extracts from maize root tips. In vitro inoculation of detached root segments caused reduction in 13-glucosidase kinetic values. In this case, changes in Km and Vmax were already observed after 5 hand increased up to 24 h. This effect was promoted when inoculum concentration was increased. Reduction in *The author to whom correspondence should be sent. 0334-5114/99 /$05.50 ©1999 Balaban 364 D. VEDDER-WEISS ET AL. Vmax and Km may indicate lower total activity of ~-glucosidase, but higher affinity to the substrate of specific ~-glucosidases. Analysis of Zm-p60.1 gene expression, coding for the maize hormones involved in ~-glucosidase deglycosilation, did not indicate changes in the transcript level following inoculation with Azospirillum.
Phylogeny and diversification of the cloud forest Morpho sulkowskyi group (Lepidoptera, Nymphalidae) in the evolving Andes

The monophyletic Morpho sulkowskyi butterfly group, endemic of Andean cloud forests, was studied to test the respective contributions of Mio‐Pliocene intense uplift period and Pleistocene glacial cycles on Andean biodiversity. We sampled nine taxa covering the whole geographical range of the group. Two mitochondrial and two nuclear genes were analysed using a Bayesian method. We established a dated phylogeny of the group using a relaxed clock method and a wide‐outgroup approach. To discriminate between two hypotheses, we used a biogeographical probabilistic method. Results suggest that the ancestor of the M. sulkowskyi group originated during the Middle–Late Miocene uplift of the Eastern Cordillera in northern Peru. Biogeographical inference suggests that the M. sulkowskyi and Morpho lympharis clades diverged in the northern Peruvian Andes. The subsequent divergences, from the Late Miocene to the Late Pliocene, should have resulted from a dispersal towards the Northern Andes (M. sulkowskyi clade), after the closure of the West Andean Portal separating the Central and Northern Andes, and a southwards dispersal along the Peruvian and Bolivian Eastern Cordilleras (M. lympharis clade). Only a few divergences occurred at the very end of the Pliocene or during the Pleistocene, a period when the more recent uplifts interfered with Pleistocene glacial cycles.
Monoamine Oxidase Activity: A Genetic Marker of Schizophrenia?

The results of pilot studies of the activities of platelet monoamine oxidase {MAO) and catechol-0-methyl transferase (COMT) in the blood of selected schizophrenics and the families of schiz ophrenics is presented. No statistically significant difference was found between the blood COMT levels of 21 control subjects and 26 schizophrenics, whereas the values found for platelet MAO activity were signifi cantly lower for the schizophrenic group than for the control group. In one acutely disturbed first-admission schizophrenic the platelet MAO activity increased to a normal level in parallel with the clinical improvement, whereas in the relapsing schizophrenics the platelet MAO activity remained at its initial level although the clinical picture improved. No consistent findings with regard to the platelet MAO activity emerged from the study of 3 families having a history of schizophrenia.
Sur deux espèces de Copépodes Lernaeopodidae (Siphonostomatoida) parasites du marbré Lithognathus mormyrus (Linnaeus, 1758) (Pisces, Sparidae)

L'examen de marbres (Lithognathus mormyrus) captures sur les cotes de Tunisie a permis de decouvrir deux especes de copepodes parasites appartenant a la famille des Lernaeopodidae Olsson, 1869 (Siphonostomatoida Thorell, 1859). La premiere a ete, tout d'abord, identifiee comme appartenant a l'espece Sparidicola papilliferens Kabata & Tareen, 1987. L'etude d'un paratype d'une autre espece du meme genre, S. lithognathi (Kensley & Grindley, 1973) (= Brachiella lithognathae Kensley & Grindley, 1973) collecte sur des marbres (Lithognathus lithognathus [Cuvier, 1830]) d'Afrique du Sud a permis de montrer que Sparidicola papilliferens et S. lithognathi appartiennent a une seule espece qui doit, en consequence, etre appelee S. lithognathi. La seconde est une espece nouvelle pour la science, Clavellotis briani n. sp. , observee pour la premiere fois sur des marbres des cotes de Mauritanie par Brian (1924), qui ne l'a pas nommee. Sparidicola lithognathi et Clavellotis briani n. sp. ont ete egalement recoltees sur la cote mediterraneenne francaise (golfe du Lion), dans la region de Kenitra (Maroc) ainsi que dans la region de Dakar (Senegal), toujours sur le marbre.
The genus Strandesia and other Cypricercini (Crustacea, Ostracoda) in the West Indies. II. Carapace length, ecology, and distribution of two Strandesia species

Repartition geographique dans les Antilles de S. longula et de S. stocki. Trouvees surtout en eau douce, elles peuvent tolerer des taux de salinite de 3500 mg/l. Vivent dans les puits, dans des eaux stagnantes et dans le sous-ecoulement de cours d'eau. Les differences de longueur de la carapace seraient liees avec toute une combinaison de facteurs externes
LIGHT VERSUS HEAT: THERMOREGULATORY BEHAVIOR IN A NOCTURNAL LIZARD (GEKKO GECKO)

Tokay geckos (Gekko gecko) acclimatized to 25 ? 1 C and a LD 12:12 photoperiod exhibited significant diel cycles of temperature selection in a thermal gradient with either uniform light over the entire gradient (UL) or a point-source of light over the hot end of the gradient (LH). Both groups selected higher body temperatures at night than during the day. No diel cycle was observed in the geckos exposed to the paradoxical condition of a point-source of light over the cold end of the gradient (LC). The UL and LH groups showed greater precision in thermoregulation during the scotophase than during the photophase. The opposite was found for the LC group. We concluded that light has a definite impact on thermoregulatory behavior that is distinct from the role that heat plays in thermoregulation. We recommend that variance be used as a standardized measure of thermoregulatory precision.
Physicochemical and Reactive Oxygen Species Scavenging Properties of Collagen and Collagen Hydrolysates from Farmed Globefish (Fugu rubripes) Bone

ABSTRACT Globefish (Fugu rubripes) bone collagen (GBC) was isolated and characterized. Electrophoresis and Fourier transform infrared (FTIR) spectra indicated that GBC was high-purity type I collagen with an intact triple-helical structure. Amino acid analysis revealed that GBC contained higher glycine content (364 residues/1,000 residues) than that of other fishery bones, and the imino acid content was 189 residues/1,000 residues. The denaturation temperature (Td) of GBC was 27.1°C. GBC displayed a rapid fibril-forming rate and well-defined fibril morphology in vitro. Globefish bone collagen hydrolysates (GBCH) were optimized by neutral protease through response surface methodology (RSM) with the highest hydroxyl radical (•OH) scavenging capacity. The optimal hydrolysis condition was a reaction temperature of 48.4°C, time of 120 min, and enzyme/substrate ratio of 2520 U/g. Three fractions were collected by ultrafiltration, and the fraction GBCH-III (Mw<1 kDa) possessed the strongest •OH scavenging ability. Reactive oxygen species (ROS) scavenging capacities were evaluated with two model systems: •OH and nitric oxide (NO•). The ROS scavenging capacities increased in a dose-dependent manner. GBCH-III proved to be a more effective •OH scavenger than reduced glutathione (GSH). These findings demonstrated that GBC and GBCH have potential as an alternative source of collagen-derived materials for use in pharmaceutical, nutraceutical, and cosmetic industries.
Vegetation type and demography of low density willow ptarmigan populations

The willow ptarmigan (Lagopus lagopus) is an economically important and desired game species in Scandinavia. Its abundance varies considerably in time and space, but there has been a long-term population decline over recent decades. Earlier studies demonstrated willow ptarmigan select certain habitat features. We investigated the relationship between area-specific conditions (habitat and ownership status) and 2 variables describing willow ptarmigan demography (adult density and reproductive success). We found no connection between adult density and cover of 6 vegetation types. However, willow ptarmigan had lower reproductive success in survey areas dominated by mountain birch (Betula pubescens czerepanovii) forest. The lack of any clear association between willow ptarmigan density and vegetation types could be explained by relatively low population densities in our study areas. Thus, relative to years with higher population levels, resources (e.g., food and shelter) were plentiful and competition was low. We found strong indications in areas of similar vegetation composition that adult density was higher in areas managed by private landowners than on state-owned land. The difference in density was 2.56 birds/km2, equivalent to a 46% increase compared to adult density on state-owned land. This difference in density may be due to a difference in hunting pressure. We conclude that management actions to improve habitat will have little effect on willow ptarmigan populations during periods of relatively low densities. © 2016 The Wildlife Society.
Response to Plant Hormones of Senescence-related Genes for Cucumis sativus L. in Cotyledon Development

This study was carried out to discover the response of cucumber (Cucumis sativus L.) senescence- associated genes (SAGs) to several plant hormones in detached and developing cotyledon. Accordingly, a collection of cucumber SAGs were examined to characterize their gene expression response through semi-quantitative RT-PCR. Cotyledons were excised at day 14 after seed sowing from plantlets, then incubated in 100 μM each of IAA or zeatin solution for up to 4 days in light and darkness. They were collected at 2-day intervals and used for total RNA extraction and subjected to RT-PCR. Gene expression levels of several cucumber SAGs were significantly changed during the incubation period. More than five cucumber SAGs involving SAG 60 responded to the IAA and zeatin treatment. In the ethylene response study, cotyledons were exposed up to 10 days by ethylene gas. Most of the cucumber SAGs did not show immediate response to ethylene in green cotyledon. The exceptions were PCK, SAG 158, and SAG 288 genes, which responded after 1 day of exposure to green cotyledon, while ICL and SAG 281 revealed strong responses after 10 days of being exposed to yellowing cotyledon. These results suggest that several cucumber SAGs react actively in response to starvation or senescence against exogenously applied stimulus. This induced senescence response is able to understand the SAGs role in lipids and amino acids metabolism partly and function in organ senescence during development.
Variation in chlorophyll content in bearley mutants

A field study was conducted to investigate variation in chlorophyll content in barley mutants. A significant decrease in chlorophyll content was observed in the chlorina mutant compared to parent while in most of the other mutants there was significant increase. The individual values of chlorophyll a and chlorophyll b revealed interesting trends. In the mutants, an increase in the chlorophyll a content had been associated with a decrease in chlorophyll b content. The dwarf mutant with variable chlorophyll pattern from that of parental control could be of greater use in developmental studies. Correlation studies revealed a positive association of grain yield with total chlorophylls and flag leaf area.
Delayed Post Hatch Feeding Affects Performance, Intestinal Morphology and Expression Pattern of Nutrient Transporter Genes in Egg Type Chickens

Effect of post-hatch (PH) feed deprivation (FD) for 6, 12, 24 and 36 hrs. , on the performance, gut development and differential expression of nutrient transporter genes in egg type chickens (crosses of White Leghorn) was studied. Significant decrease (P=0.001) in yolk utilization (in all the FD chicks) and relative weight of gizzard, intestine, liver and pancreas was observed in 24 and 36 hrs FD chicks. The 36 hrs FD chicks recorded lower (P=0.001) body weight, lower feed intake and inferior FCR, decreased serum glucose, but higher cholesterol and uric acid level than the control (immediate fed group) or 6 hrs FD chicks. Villi height in duodenum, jejunum and ileum decreased (P=0.001) but villi width increased (P=0.001) with increase in FD period and significant changes were observed particularly in 24 or 36 hrs FD chicks. Relative expression of Cdx gene decreased with age of the bird and the feed restriction period. Expression of SGLT, FABP gene was not associated with the feed deprivation period, while that of EAAT3 gene increased in 24 or 36 hrs FD chicks. No difference was observed in bursa, spleen and thymus weight. In vivo humoral and cellular immune response was significantly better in chicks FD for 6, 12 and 24 hrs than control and 36 hrs FD chicks. Expression of immunity related genes IL-6 and TLR-2 increased as the FD period increased. It may concluded that PH feed deprival for first 12 hrs did not affect growth performance, intestinal morphology and immune response but feed withdrawal for 24 or 36 hrs adversely affect the intestinal morphology and few nutrient transporter genes expression in egg type chickens.
Sexual differentiation of the somatic gonad tissue in marine bivalve mollusks: esterase- and fibronectin-like recognition signals

Textbooks usually indicate that in many species sex determination starts with gonad differentiation, triggered during early embryonic development. Once a primary somatic gonad is formed, the gonad-derived inductive signals are used to maintain the sex differentiation of germ cells. In marine bivalves, sex is not determined until the germ cells are differentiated, whether that is in the larva or in the juvenile. As sex is often decided late in post-larval development, gonad differentiation starts in the adult state. It is generally accepted that bivalves have no great difficulty in transforming from hermaphroditism to gonochorism and vice versa (Mackie, 1984). Our results focus attention on the patterns of gene expression in the "common" gonad (i.e., ovotestis) of the simultaneous hermaphroditic scallop species, Pecten maximus, during maturation and reproduction periods. In this species, as in almost all marine bivalves, the connective-tissue cell types present in the testis and ovary of the "common" gonad are essentially identical. Using biochemical, immunochemical and molecular approaches, we demonstrate for the first time that the scallop ovotestis is characterized by germ-cell-associated somatic protein expression.