Miracle-dz/UniFAR-FTUs huggingface dataset:
Historical Presence of Israeli Acute Paralysis Virus in the United States

High bee colony losses in the United States this past year can be attributed in part to an unresolved syndrome termed Colony Collapse Disorder (CCD). An extensive genetic survey found one virus, Israeli Acute Paralysis Virus (IAPV), to be strongly associated with CCD. Using DNA sequencing and phylogenetic analyses, we provide evidence that IAPV was present in U.S. bees collected several years prior to CCD, and prior to the recent importation into the U.S. of honey bees from Australia and New Zealand. While downplaying the importance of bee importation for the appearance of CCD, these results indicate an urgent need to test specific strains of IAPV for their disease impacts.
Ontogenia dos ossos do esqueleto da tartaruga-da-amazônia Podocnemis expansa Schweigger, 1812 (Testudines, Podocnemididae)

CAPITULO 2: O cagado Podocnemis expansa esta distribuido pela bacia amazonica e ocorre em quase todos os seus afluentes. O esqueleto dos vertebrados e composto de cartilagem e osso e representa o produto de celulas de tres linhagens embrionarias distintas. O crânio e formado por celulas da crista neural. O conhecimento do criterio biologico para a sequencia de formacao ossea e de suma importância para o entendimento da ontogenia. Assim, o proposito do presente estudo foi estabelecer etapas normais da formacao da sequencia de ossificacao dos elementos osseos do crânio em P. expansa, nos diferentes estagios de desenvolvimento pre e pos-natal. Coletaram-se embrioes a partir do 18 dia de incubacao natural. Efetuou-se morfometria e os embrioes foram submetidos a tecnica de diafanizacao e coloracao dos ossos. Neurocrânio: no estagio 19 o basisfenoide e o basioccipital apresentam centro de ossificacao; no estagio 20 o supra-occipital e o opistotico, no estagio 21 o exoccipital e somente no estagio 24 o prootico. Dermatocrânio: o esquamosal, o pterigoide e a maxila sao os primeiros elementos a iniciar o processo de ossificacao, isso ocorre no estagio 16. Mas a maioria desses elementos osseos apresenta centros de ossificacao no estagio 17, sao eles: frontal, jugal, pos-orbital, parietal, pre-maxila, pre-frontal, seguido do palatino e quadradojugal no estagio 19 e por ultimo o vomer no estagio 25. O osso quadrado do esplancnocrânio, no estagio 23. Ossificacao da mandibula e aparelho hioide: tanto o dentario, coronoide e o supra-angular apresentam centros de ossificacao no estagio 16 e o corpo branquial I no estagio 17. A sequencia e a sincronizacao da ossificacao em P. expansa exibem similaridades, bem como diferencas, quando comparada com outras especies de Testudines. Fica evidente que mais estudos quantitativos sao necessarios para documentar a variabilidade natural de formacao dos ossos. CAPITULO 3: Os ossiculos da esclera sao pequenas placas osseas localizadas no globo ocular de muitos vertebrados e diferem em sua morfologia, desenvolvimento e posicao dentro de diferentes grupos de vertebrados. Com objetivo de investigar o desenvolvimento, o numero, a forma e a disposicao dos ossiculos da esclera, em Podocnemis expansa coletou-se 15 embrioes, a partir do 18 dia de incubacao natural e 16 especimes adultos, pertencentes ao acervo do LAPAS, dos quais foram removidos os globos oculares. Os embrioes e os globos oculares foram submetidos a tecnica de diafanizacao e coloracao dos ossos. Apurou-se que os ossiculos da esclera, nessa especie de Testudines, possuem forma quadrangular, variam de 10 a 13 com 11,25 0,93 e 11,43 0,81, no olho direito e no olho esquerdo, respectivamente, e ocupam posicao fixa, proximos a borda anterior da esclera. Os ossiculos se desenvolvem de forma intramembranosa e comecam a apresentar centros de ossificacao no estagio 21, com dez centros de ossificacao no olho direito e oito no olho esquerdo. No estagio 23, todos os ossiculos do anel esclerotico aumentam em comprimento e se aproximam dos ossiculos…
Functional Characterization and Anatomical Identification of Motion Sensitive Neurons in the Lobula plate of the Blowfly Calliphora erythrocephala

8 classes of homo- and heterolateral wide field neurons of the Lobula plate of Calliphora erythrocephala were investigated electrophysiologically and identified by intracellular injection of procion yellow. All recorded neurons were motion-sensitive. Some of the homolateral neurons respond only with graded potentials to visual stimulation; all heterolateral elements generate spike potentials. Connections between identified neurons were investigated by means of simultaneous double recordings. The described neurons are compared with units known from earlier extracellular studies.
Oil characteristics and fatty acid profile of seeds from three varieties of date palm ( Phoenix dactylifera ) cultivars in Bushehr-Iran

Studies were conducted on properties of seed oils extracted from three date palm ( Phoenix dactylifera ) varieties Shahabi, Shekar and Kabkab, grown in Bushehr-Iran. The primary objective of this study was to extract seed-oil from the three native date varieties and then analyzed their fatty acids (FAs). Also the chemical parameters of PV, AV, p-anisidin, and Totox values of oils, as indicators of the quality and safety, and oxidative status of edible oils, as well as refractive index as an objective method for evaluation of rancidity were also evaluated. Date seeds are approximately 10% of the fruits weight. Seeds contained about 8.5% fat that can serve as a useful source of fatty acids to replace other vegetable oils. The following mean of values from the three varieties were obtained from samples: peroxide value (1.05), acid value (1.4), p-anisidine value (2.54), Totox (4.64) and refractive index (1.46). Also, flame ionization based detection gas chromatography (GC-FID) revealed that oleic acid was the primary fatty acid in all varieties. It was followed by lauric, myristic, palmitic, linoleic and stearic acids and trace amounts of the other fatty acids like undecylic, capric, nonanoic (pelargonic) and caprylic acids. Depending on the regional industry, these data suggest that the potential applications of date seed oil for humans and animals are feeding, cosmetic formulations such as in body creams, shaving soap and shampoos, and pharmaceutical products. Keywords: Seed oil ( Phoenix dactylifera ), fatty acid, gas chromatography
Study on DGAT1-exon8 Polymorphism in Iranian Buffalo

Objective: Diacylglycerol acyltransferase 1 is a microsomal enzyme that catalyzes the final step of triglyceride synthesis. The objective of this project is to check out the polymorphism at the exon 8 region of DGAT1 gene using PCR-SSCP technique in Iranian water buffaloes (Bubalus bubalis). Recent activities have shown that a significant association between lysine at amino acid position 232 with higher milk fat content, whereas an alanine at this position is marker data of lower milk fat content and higher milk yield. Methods: In this study we analyzed buffaloes from 5 provinces of Iran. Three PCR-SSCP patterns were found. Results: DNA sequencing analysis showed that all of the patterns had the motif “AA” at position 6962-6963 (K allele) encoding lysine, which is similar to “AA” at position 10433-10434 in Bos indicus and also different buffalo breeds at position 6962-6963. Therefore exon 8 is a conservative region in Bos indicus and all buffalo breeds which is associated with higher milk fat content. Moreover, we found a base transition at position 7036 C/T and we have heterozygosity of both “C and T”, which is located at intron 8 of DGAT1 gene in few samples. Conclusions: this transition is a nonsense mutation which causes no change in amino acid sequence. This mutation has occurred at the intron 8 of DGAT1 gene in Iranian buffaloes.
LINKING BIODIVERSITY AND ECOSYSTEM FUNCTIONING OF DUNG BEETLES IN SOUTH AND SOUTHEAST ASIAN TROPICAL RAINFORESTS

We investigated the impacts of habitat disturbance and the resulting changes in biodiversity on ecosystem function in South and Southeast Asian forests using dung beetles (Coleoptera: Scarabaeidae: Scarabaeinae) as a focal taxon. Dung beetle sampling and dung burial experiments were conducted in intact, modifi ed, and fragmented forest habitats in three different countries: Sri Lanka, Malaysia, and Singapore. Data analysis was split into two themes for analysis: the effect of habitat modifi cation, and the effect of fragmentation. The proportion of dung mass removed was modelled against habitat modifi cation, and the species richness and abundances of the entire dung beetle community, the tunneller communities, and the roller communities. Abundance and richness of tunnellers and the degree of habitat disturbance were the main determinants of dung burial in the habitat modifi cation analysis. Total dung beetle abundance was the main determinant of dung burial in the fragmentation analysis. Through our combined analysis, we show that habitat modifi cation and forest fragmentation impact dung removal activity, albeit through different aspects of the dung beetle community structure.
Abundance and diversity of ammonia-oxidizing bacteria in rhizosphere and bulk paddy soil under different duration of organic management

Denaturing gradient gel electrophoresis (DGGE) and quantitative real-time PCR (qPCR) approaches were used to assess respectively the molecular diversity and quantity of the nifH gene sequences in rhizosphere and bulk paddy soil under conventional management and different duration of organic management (2, 3, 5, 9 years). The phylogenetic distribution of clones based on nifH gene sequence showed that taxonomic groups were consisted of Alphaproteobacteria (27.6%), Betaproteobacteria (24.1%) and Gammaproteobacteria (48.3%). Members of the order Rhizobiales and Pseudomonadales were prevalent among the dominant diazotrophs. When the quantity of the nifH gene sequences was determined by qPCR, 2.27 × 105 to 1.14 × 106 copies/g of soil were detected. Except for 2 years organically managed soil, nifH gene copy numbers in organic soil, both rhizosphere and bulk, were significantly higher than in CM soil. Moreover, nifH gene copy numbers in the organic rhizosphere soil (3, 5, 9 years) were significantly higher than in bulk soil. The abundance and diversity of nitrogen-fixing bacteria tended to increase with duration of organic management but the highest number of nifH gene copies was observed in the rhizosphere and bulk soil of 5 years organic management. In addition, analysis of variance and canonical correspondence analysis (CCA) showed that C/N, C and N were important factors influencing the abundance and community structure of nitrogen-fixing bacterial.
Interaction Effects of Arbuscular Mycorrhizal Fungi and Different Phosphate Levels on Growth Performance of Catharanthus roseus Linn.

Catharanthus roseus L. (Apocynaceae), a valuable medicinal plant with potential therapeutic value was inoculated with AM fungi Glomus fasciculatum under three different phosphate conditions. Catharanthus roseus plants raised in presence of the AM fungi showed increased growth in terms of (shoot length, root length, leaf number, fresh weight and dry weight). Total chlorophyll content and phosphate content of the shoot was found to be significantly higher in AM inoculated plants as compared to non AM Catharanthus plants. The activities of phosphatase enzymes were found to be increased in AM inoculated plants as compared to non AM plants. Root colonization percent was significantly higher in AM inoculated plants at zero and at all three phosphate levels after 60, 90 and 120 days of AM inoculation, but decreased at third phosphate level after 120 days of AM inoculation. The study suggests that Catharanthus roseus is dependent on the mycorrhizal fungi to a large extent for its growth and survival and also shows the potential of AM fungi Glomus fasciculatum in increasing growth and biomass of Catharanthus roseus L.
Sequences of Probes Revealing Mapped Restriction Fragment-length Polymorphisms in Cucumber

PstI-genomic and cDNA clones revealing mapped restriction fragment-length polymorphisms (RFLP) in cucumber (Cucumis sativus L.) were sequenced in order to ensure that these clones remain available and to determine if any clones showing genetic linkage in cucumber are physically linked in Arabidopsis thaliana. Sequence comparisons using translated searches revealed that 80% of the cucumber cDNA clones showed significant (≤e-20) similarities to Arabidopsis expressed sequence tags (ESTs) or genomic sequences, as opposed to relatively few (32%) of the cucumber genomic clones. Two clones revealing RFLPs linked at 2 cM in cucumber showed significant (<e-20) similarities to sequences separated by 347,616 basepairs on chromosome 4 of Arabidopsis.
Growth and Yield of Eggplants Grafted by a Newly Developed Robot

Eggplant (Solanum melongena L.) at the two-leaf stage were grafted on scarlet eggplant (Solanum integrifolium Poir.) by hand or a newly developed robot. The scion and rootstock were fixed with an elastic tube for hand grafting or with an adhesive and a hardener for robotic grafting. After acclimatization, the grafted plants were planted at the three- or 11-leaf stage in a glasshouse. Plants grafted by the robot showed a higher percentage of survival, and attained the three- and 11-leaf stages 8 days earlier on average than those grafted by hand. Stems were longer, and shoot fresh mass and fruit yield of plants were higher for the three-leaf- than for the 11-leaf-stage planting, irrespective of the grafting method. Such vigorous growth and high yield by robotic grafting were absent for the 11-leaf-stage planting but obvious for the three-leaf-stage planting.
Sperm competition, cryptic female choice and prolonged mating in the Eucalyptus Snout-Beetle, Gonipterus scutellatus (Coleoptera, Curculionidae)

The Eucalyptus weevil, Gonipterus scutellatus, shows a complex copulation behaviour whose duration is extremely variable, from less than one hour to more than two days. We tested different hypotheses that could explain the adaptive significance of prolonged copulations. Male genitalia is unable to reach to the interior of the espermatheca of the female, where the sperm of previous matings are stored, so prolonged copulation does not function to remove rivals' sperm. Neither the duration of the copulation nor the volume of the ejaculate were affected by the density of rivals, nor was there a significant relationship between copulation duration and volume of sperm ejaculated. The percentage of eggs fertilized by the second male to copulate with a female is very variable, even among different clutches of the same female. These results suggest, by a process of elimination, that prolonged copulation in G. scutellatus has evolved under sexual selection by cryptic female choice.
Economics of Controlling Invasive Species: A Stochastic Optimization Model for a Spatial‐dynamic Process

&NA; We analyze the dynamic process of invasive‐species control in a spatially explicit and stochastic setting. An integer optimization model is applied to identify optimal strategies to deal with invasive species at a steady state. Optimal strategies depend on the spatial location of invasion as well as on stochastic characteristics of spread and control. Previous studies of invasive‐species control have been stochastic or spatial, but not both. We model a landscape as consisting of multiple cells, each of which may be subject to border control or eradication within the cell. Optimal strategies from the model are characterized as eradication, containment, or abandonment of control. Representing the rate of species spread as stochastic rather than deterministic results in less‐intensive control becoming optimal at equilibrium. The optimal strategy may switch from eradication to containment or from containment to abandonment. If an infestation occurs at the boundary of the region within which it may spread, it is more likely to be optimal to eradicate or contain the species, compared to an infestation in the interior of the region. If the effectiveness of border control is stochastic, then containment is not feasible in the long term, but it is still optimal as a temporary measure in some scenarios.
Anti-inflammatory activity of Anthemis aciphylla var. aciphylla Boiss.

Ethanolic (EEAA) and sesquiterpene lactone (SEAA) extracts of the aerial parts of Anthemis aciphylla var. aciphylla Boiss. (Asteraceae) were evaluated for anti-inflammatory activity on carrageenin-induced paw edema (acute model) and cotton pellet-induced granuloma (chronic model) in rats. In carrageenin-induced paw edema, EEAA and SEAA at intraperitoneal doses of 50, 100, and 200 mg/kg dose-dependently inhibited the paw edema. In cotton pellet-induced granuloma, the oral administration of EEAA and SEAA at 50, 100, and 200 mg/kg dosages was also found to significantly inhibit granuloma tissue formation.
EVALUATION OF ALTERNATIVE LIFE HISTORY HYPOTHESES FOR THE SAND SHRIMP Crangon franciscorum (DECAPODA: CARIDEA)

Abstract Caridean shrimps are unique among decapod crustaceans in showing a great diversity of sexual systems, including gonochorism, protandry, protandry with primary females and simultaneous hermaphroditism. Crangon franciscorum (Stimpson, 1859) (Crangonidae), an ecologically and economically significant species from the Pacific coast of North America, has been assumed to be gonochoristic. Earlier population studies concluded that average lifespan is longer in females than in males, and that the latter die in or emigrate from estuaries after mating. This was believed to explain a recurrently observed “shrinking” of average male size starting during the fall of the first year of life. We investigated an alternative hypothesis according to which this species is a protandric hermaphorodite, and disappearance of large males from the population reflects sex change rather than death or emigration. We present several pieces of evidence in support of the alternative hypothesis: (i) ovarian development in males undergoing sex change, (ii) presence of atrophied vas deferens in secondary females, and (iii) observation of sex change in individuals kept in captivity. Our results are supported by histological study of the gonads, careful description of secondary sexual characters, and monthly sampling of an estuarine population (Grays Harbor, Washington). Tracking an identifiable year-class (1980) and combining field and laboratory data allowed us to assemble a life history schedule, including growth and a calendar of significant reproductive events. We discuss the implications of our results for the interpretation of survey data and studies on population dynamics.
Testing nest deterrents for Chihuahuan ravens on H‐frame transmission structures

Chihuahuan ravens (Corvus cryptoleucus) regularly perch and nest on electric utility structures. Because ravens perch on overhead shield wires, for which no perch discourager exists, management focuses on nests. When nests occur above energized wires (phase wires), risk of line faults, pole fires, and power outages develop. In southeastern Colorado, USA, Chihuahuan ravens nesting on H-frame transmission structures historically nested exclusively above the center phase. Nest deterrents prevent ravens from nesting over the center phase on short line segments (1.5 km), but effectiveness over longer line segments is unknown. We installed nest deterrents over the center phase on all structures within a 25.7-km line segment (n = 93 structures), and compared nesting there with nesting on two 0.75-km untreated segments adjacent to each end of the treated segment (n = 10 adjacent structures) and on a 25.6-km untreated segment (n = 93 distant structures). Data were collected over 7 surveys in Bent, Kiowa, and Crowley counties in southeastern Colorado, spring 2012. Ravens placed nest material on 25.8% of treated structures, 90.0% of adjacent untreated structures, and 78.5% of distant untreated structures. Used nests (containing eggs or nestlings) occurred on 2.1% of treated structures, 40.0% of adjacent untreated structures, and 17.2% of distant untreated structures. No used nest occurred above the center phase on any treated tangent structure, whereas all used nests occurred above the center phase on untreated structures. Future research should evaluate whether placing deterrents above all phases further reduces nesting. If so, this application could also be used in areas where ravens are potential predators of species of special concern. © 2015 The Wildlife Society.
Proteasome inhibitors as therapeutic agents

Highly regulated intracellular proteolysis is necessary for cell-cycle progression and cell division. The ubiquitin–proteasome pathway (UPP) plays a central role in the degradation of proteins and has therefore become an important, novel therapeutic target for diseases involving cell proliferation, most notably cancer. Proteasome inhibitors were initially used as research tools in cell biology to characterise the properties of the UPP. It was later determined that proteasome inhibition induced cell-cycle arrest and programmed cell death (apoptosis) in cancer cells in vitro and could inhibit tumour growth in animal xenograft models. Several classes of molecules that have proteasome-inhibiting characteristics have been studied. The dipeptidyl boronic acid bortezomib (Velcade™ Millennium Pharmaceuticals, Inc.), formerly known as PS-341, LDP-341 and MLN-341, is a potent and specific inhibitor of the proteasome that holds promise as a potential human therapeutic. It is the first proteasome inhibitor to be examined in human clinical trials and according to preliminary Phase I and II data, the drug has exhibited both manageable toxicities and biological activity.
NegFinder: A Web Service for Identifying Negation Signals and Their Scopes

: More and more biomedical documents are digitally written and stored. To make the most of the rich resources, it is crucial to precisely locate the information pertinent to user’s interests. An obstacle in ﬁnding information in natural language text is negations, which deny or reverse the meaning of a sentence. This is especially problematic in the biomedical domain since scientiﬁc ﬁndings and clinical records often contain negated expressions to state negative e ﬀ ects or the absence of symptoms. This paper reports on our work on a hybrid approach to negation identiﬁcation combining statistical and heuristic approaches and describes an implementation of the approach, named NegFinder, as a Web service.
Taxon-specific responses of soil bacteria to the addition of trace or low amounts of glucose.

When small or trace amounts of labile C substrates enter the soils either a priming effect or a triggering effect is induced but the identities of the microorganisms involved remains largely unknown. Here, we modified the Stable Isotope Probing (SIP) protocol to accommodate low level carbon pulses, such that their fate within the microbial community could be determined. Soils were amended with different concentrations of [ 14 C] glucose (150, 50 and 15 and 0 μg C /g soil) prior to rRNA extraction and equilibrium density centrifugation. Subsequent denaturing gradient gel electrophoresis (DGGE) analysis, sequencing of bands and multivariate statistics was then used to identify the taxon specific responses at different glucose concentrations. [ 14 C] RNA enrichment was restricted to Bacillus, Pseudomonas, Burkholderia and βproteobacteria and the concentration of glucose determined the magnitude of the community response. Pseudomonas was only enriched at 150 μg C /g soil whilst Bacillus and Burkholderia although present at 150 μg C /g soil, were more abundant at trace amounts (15-50 μg C /g soil). Glucose amendment also impacted indirectly on the community changing the [ 12 C] RNA signal of Bradyrhizobium, Actinobacteria Nitrosomonas and Acidobacteria which probably reflects changes in substrate availability and microbial interactions.