Miracle-dz/UniFAR-FTUs huggingface dataset:
Estimation of Abundance and Recommendations for Monitoring White-Cheeked Pintails in Wetlands of Puerto Rico and Territorial Islands

Abstract The white-cheeked pintail (Anas bahamensis) is listed as threatened, and survey data are needed to assess population status, estimate trends, and guide management on Puerto Rico and territorial islands. We surveyed 51 points in 29 wetland sites to estimate density and population size after the peak of reproduction (Mar–Jul) and before the waterfowl hunting season (Nov–Jan). Estimated density was 2.33 individuals/ha (SE = 0.27), and estimated population size was 3,755 individuals (SE = 435, log-normal 95% CI = 2,995 to 4,708) in 1,614 ha surveyed in August–October 2003–2005. Density differed between August–October 2003 (𝐷̂ = 3.07 individuals/ha, SE = 0.41) and 2004 (𝐷̂ = 1.26 individuals/ha, SE = 0.17) and between August–October 2004 and 2005 (𝐷̂ = 2.54 individuals/ha, SE = 0.47) but not between August–October 2003 and 2005. Spatial distribution ranged from nearly random (estimate of dispersion parameter [𝑏̂] = 0.99) to highly clumped (𝑏̂ = 3.71). We suggest that spatiotemporal variation of wetland hydrochemical conditions caused changes in foraging resources, which in turn caused changes in white-cheeked pintail density and spacing patterns. We recommend surveying 186 points 3 times in August–October for estimated density to have a coefficient of variation of 0.10, even when white-cheeked pintails are highly clustered (estimate of exp cluster size, Ê[s] = 16.1, SE = 2.8) and clumped (b = 4) in space. We provide additional recommendations for integrating monitoring, research, and management objectives to better understand the ecology and promote the conservation of white-cheeked pintails and their habitats locally and regionally.
MicroRNAs de sementes de soja maduras e em germinação e Transfer RNA- derived Fragments (tRFs) associados a proteínas argonautas de Arabidopsis

The microRNAs (miRNAs) are non-coding RNAs with 19 to 24 nt in length, acting as important regulators of gene expression. Soybean is a protein and oil rich crop used for animal and human feed, but despite domestication and availability of complete genome, there are few transcriptome and microRNA studies during vegetative growth and stress-conditions. Up to now no miRNAs related to germination process have been characterized. Using deep sequencing, we identified 142 known miRNAs and 36 new ones in mature and germinating seeds. Using the mature seed degradome, eight miRNAs were characterized with target transcript related with possible functions in soybean seed germination, involved in auxin and gibberellin pathways, lipid and nitrogen metabolism and redox homeostasis. This study contributes to the understanding of microRNAs functions in plants, relating them to the process of seed germination.
Abundancia relativa y selección de hábitat de Tapirus bairdii en las reservas de Calakmul y Balam Kú, Campeche, México

Resumen Se documenta la abundancia relativa y la seleccion de habitat de Tapirus bairdii en la Reserva de la Biosfera de Calakmul y en la Reserva Estatal de Balam Ku en Campeche, Mexico; en 3 sitios bajo el efecto del gradiente de humedad en la peninsula de Yucatan, donde la precipitacion y humedad se incrementan de norte a sur. Se establecieron 120 km de transectos lineales, donde se registro el indice de abundancia relativa a traves del registro de huellas de tapir y variables del habitat como alimento y vegetacion. El indice de abundancia se reforzo con la instalacion de camaras-trampa en 9 aguadas en los 3 sitios. Se obtuvo un indice de abundancia de 0.33 huellas/km y de 17 foto-capturas/1,000 dias-trampa. No se encontraron diferencias significativas en los indices de abundancia entre sitios al aplicar la prueba estadistica de Kruskall-Wallis, asi como tampoco se registro una preferencia de habitat en cuanto al tipo de vegetacion utilizando un analisis de χ2. Este trabajo aporta informacion sobre la abundancia del tapir centroamericano en Calakmul y Balam Ku, donde existen pocos estudios para esta especie. Sugiere ademas, que en estas reservas los tapires pueden distribuirse en zonas mas secas y que pueden llegar a ser generalistas en cuanto a la seleccion de su habitat.
How do paedomorphic newts cope with lake drying

Paedomorphosis, in which adult individuals retain larval traits, is widespread in newts and salamanders. Most evolutionary models predict the maintenance of this life-history trait in favourable aquatic habitats surrounded by hostile terrestrial environments. Nevertheless, numerous ponds inhabited by paedomorphic individuals are unpredictable and temporary. In an experimental framework, I showed that paedomorphic newts were able to metamorphose and thus survive in the absence of water. However, the mere decrease of water level or the life space do not seem to induce metamorphosis in paedomorphs. On the contrary, drying up induces almost all individuals to move on land and after that to colonize other aquatic sites located nearby. Such terrestrial migrations allow survival in drying conditions without metamorphosis as long as the distances of terrestrial migration are short. These results are consistent with the presence of paedomorphs in drying ponds and are in favor of classic optimality models predicting metamorphosis in unfavorable environments.
Ácidos grasos y parámetros de calidad del aceite de semilla de uva silvestre (Vitis spp.)

Mexico is one of the centers of origin of the genus Vitis. Most of the native species are in an underutilized or neglected status. Thus, this work was performed aiming the determination of the potential of Mexican native grapes as a source of plant oil. It was determined the amount of oil and its fatty acid composition in seeds of wild grapes (Vitis spp.) in fruits collected in Temascaltepec, Mexico and harvested from a cropped accession growing in Zumpahuacan, Mexico. The average content of oil in seeds was 16.7% presenting four main fatty acids, linoleic, oleic, palmitic and stearic (71.5, 17.2, 6.6 and 4.3%, respectively). In the oil obtained from Temascaltepec grapes, there were determined some oil quality indexes. Possibly, the unsaturated fatty acid content explains the index of iodine (57.9 g/100 g), soapy number (170.7 mg/g), as well as the peroxide value (30 mEq/kg). Nevertheless, the high content of unsaturated fatty acid was not related with the smoking point (211 °C), although this value might be related to the content of palmitic and stearic acid. Oil from wild grape shows similar quality parameters compared with V. vinifera seed oil, thus its culinary, agro-industrial and cosmetic potential is noted.
Anti‐tumor immunity induced by tumor cells express a membrane‐bound form of IL‐2 and SDF‐1

Abstract The eventual goal of tumor immunotherapy is to develop a vaccine inducing a specific anti‐tumor immunity. Cytokine gene therapy is an effective way at least in animal models, but limited efficacy and various side effects obstruct clinical applications. In this study, we developed a tumor vaccine expressing a membrane‐bound form of IL‐2 (mbIL‐2) and SDF‐1 in B16F10 melanoma cells. The tumor clones expressing mbIL‐2 showed reduced tumorigenicity, and additional expression of SDF‐1 to mbIL‐2 expressing tumor cells caused more severe reduction in tumorigenicity. However, expression of the SDF‐1 alone did not affect on the tumorigenicity, probably because of limited production of SDF‐1 in the SDF‐1 transfected clones. When the mice once rejected mbIL‐2/SDF‐1 expressing tumor clone were re‐challenged with wild type B16F10 tumor cells, all of the mice survived. This result suggests that mbIL‐2/SDF‐1 tumor clone is effective in inducing systemic anti‐tumor immunity against wild type B16 melanoma. Furthermore, culture supernatant of tumor clones expressing SDF‐1 induced lymphocyte migration in vitro. These results, all together, suggest that expression of mbIL‐2 and SDF‐1 in tumor cells enhances anti‐tumor immune responses through different roles; the secreted SDF‐1 may function as a chemoattractant to recruit immune cells to tumor vaccine injection site, and the mbIL‐2 on tumor cells may provide costimulatory signal for CTL activation in physical contacts.
Chemical Contributions to Understanding Heparin Activity: Synthesis of Related Sulfated Oligosaccharides

Heparin and heparan sulfate are complex polysaccharides that modulate several biological events through the recognition of a number of distinct proteins. Chemical synthesis is a powerful tool to identify the unique binding domains responsible for the specific interactions and to generate potent analogues of the natural sequences. The present review reports the synthetic efforts of the last decade that are focused on the preparation of tailored fragments of these two polymers and analogues thereof. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2003)
STREPTOCOCCOSIS CAUSED BYSTREPTOCOCCUS INIAE IN FARMED RAINBOW TROUT (ONCHORHYNCHUS MYKISS) IN IRAN: BIOPHYSICAL CHARACTERISTICS AND PATHOGENESIS

Outbreaks of disease in cultured rainbow trout were observed in two farms in southwest Iran. The affected fish showed erratic swimming, dark discoloration, haemorrhages on the base of fins and exophthalmia with cataract; mortality varied from 20% to 40%. Internally, there were pale and/or haemorrhagic livers, congestion of spleen and kidney and occasionally ascites in the peritoneal cavity. Neither external nor intestinal parasites were found. Gram-positive â haemolytic cocci were recovered from the diseased fish. The bacteria were identified as Streptococcus iniae by morphological, physiological and biochemical characterization. Using specific S. iniae primer sequences to the 16s rRNA gene revealed a 513bp fragment amplified by PCR. Intraperitonal injection of the recovered isolates in rainbow trout of 100-150 g caused 100% mortality within one week post-challenge at 17-19°C. This is the first report of S. iniae associated with rainbow trout disease in the Middle East.
Studies on diurnal air temperature pattern from daily maximum and minimum by estimating the parameters of sinusoidal and exponential models on weekly basis under semi arid climate of Hyderabad.

The sinusoidal and exponential models for day time and night time temperature pattern have been fitted to weekly mean hourly air temperature data recorded at Hayathnagar Research Farm of CRIDA, Hyderabad during 1995-2007 using an automatic weather station. The lag coefficient ‘a’ of the sinusoidal model ranged between 1.150 – 4.372 and night time temperature coefficient ‘b’ of exponential model ranged between 2.175 – 4.334 during 1 st - 52 nd standard meteorological weeks. Coefficient of determination (R 2 ) values were between 0.892 – 0.995 for the sinusoidal and between 0.931 – 0.988 for the exponential model. Goodness of fit was tested by Student’s ‘t’ statistics as well by the graphical plots of observed vs. estimated mean weekly diurnal temperatures during 2008.
Wood Chip-Polyacrylamide Medium for Biocontrol Bacteria Decreases Verticillium dahliae Infection on Potato

The lack of consistent success of biological control of soilborne plant pathogens may be due to the introduction of the organism into a foreign environment. We hypothesized that wood chip-polyacrylamide (PAM) cores surrounding host plant roots could alter the soil environment to favour growth of introduced biocontrol microorganisms, thereby reducing Verticillium dahliae infection of potato ( Solanum tuberosum L.) in a greenhouse. A 7cm diameter 2 15cm deep hole (core) was drilled in the center of a 20 2 30cm deep pot (1.9 kg) containing soil infested with V. dahliae inoculum. Cores were then filled with wood chip-PAM-biocontrol organism mixtures. Soils that had Streptomyces lydicus inoculated into wood chip-PAM cores had lower levels of V. dahliae symptoms ( V vis ) and V. dahliae isolations ( V iso ) than all other treatments in three soils. V vis and V iso on plants growing in soils amended with S. lydicus or Pseudomona corrugata inoculated into the soil itself (without wood chip-PAM cores) did not differ from soils that were unamended with these biocontrol organisms. V. dahliae biomass was lower in wood chip-PAM cores inoculated with S. lydicus than control or wood chip-PAM cores without biocontrol bacteria. Soils with wood chip-PAM cores inoculated with S. lydicus or P. corrugata generally had higher microbial biomass/ V. dahliae biomass (MB/VB) ratios than control soils, or soils with S. lydicus or P. corrugata inoculated into the soil. Wood chipPAM cores alone and wood chip-PAM cores inoculated with S. lydicus had higher MB/VB ratios than wood chip-PAM cores inoculated with P. corrugata . V vis and V iso were curvilinearly correlated with the MB/VB ratios in negative relationships, respectively (r 2 = 0.68, r 2 = 0.68). As the MB/VB ratio increased, V vis and V iso decreased. Although field studies and economic evaluations are necessary, amending soil with wood chips-PAM and a biocontrol bacterium may be a valuable method to increase the effectiveness of biocontrol organisms.
Growth and gastrointestinal nematode parasitism in lambs grazing either lucerne (Medicago sativa) or sulla (Hedysarum coronarium) which contains condensed tannins

SUMMARY Two grazing experiments were undertaken to evaluate the effects of sulla (Hedysarum coronarium) which contains condensed tannins (CT) and lucerne (Medicago sativa), which does not contain CT, on the performance of parasitized and non-parasitized lambs. The work was carried out near Palmerston North, New Zealand in 1992 and 1993. Experiment 1 used lambs which were either genetically ‘conventional’ or ‘resistant’ to gastrointestinal nematodes and which had a naturally acquired heavy parasite burden (faecal egg count (FEC) 1300–2500 eggs per gram faeces (epg)). They were either drenched to remove all the parasites or remained undrenched when allocated to pure swards of either sulla or lucerne for the 28-day experimental period. Liveweight gains of drenched lambs were higher with sulla (mean 302 g/day) than with lucerne (mean 245 g/day; P < 0·02) and rates of gain were not reduced (P = 0·10) by genetic resistance to nematodes. Undrenched lambs had mean faecal egg counts of 1090–2220 epg after 28 days, with higher counts in lambs grazing lucerne than in those grazing sulla (P < 0·05). Lambs grazing lucerne also had a much lower average daily gain (ADG) (mean 50 g/day) than those grazing sulla (mean 206 g/day; P < 0·0001). Resistant lambs had reduced (P = 0·07) ADG in the sulla treatment only. In Expt 2, lambs with a relatively low worm burden (average FEC 250 epg) were either drenched to remove all worms or dosed with 20 000 Trichostrongylus colubriformis infective larvae and grazed on pure sulla or lucerne swards for 42 days. Drenched lambs had a similar liveweight gain (mean 190 g/day) and wool growth when grazing either sulla or lucerne. Undrenched lambs grazing sulla had a greater ADG (mean 129 g/day) than those grazing lucerne (mean −39 g/day; P < 0·0001) and a higher rate of wool growth from mid-side patches (P < 0·009) and larger wool fibre diameter (P < 0·05) than those grazing lucerne. Undrenched lambs grazing sulla had lower FECs (P < 0·05) on days 14, 21, 35 and 42 than those grazing lucerne and lower (P < 0·05) Trichostrongylus colubriformis worm burdens at slaughter. Undrenched lambs had less perineal faecal contamination when grazing sulla rather than lucerne. Parasite-induced anorexia was evident in the lambs grazing lucerne but not in those grazing sulla. These findings demonstrate that the performance of lambs infected with nematode parasites can vary substantially when given feeds of a similar chemical composition. The superior performance of lambs grazing sulla was probably caused by condensed tannins, which decrease protein degradation in the rumen and can increase post-ruminal protein availability.
An inducible system for expression and validation of the specificity of short hairpin RNA in mammalian cells

RNA interference (RNAi) by means of short hairpin RNA (shRNA) has developed into a powerful tool for loss-of-function analysis in mammalian cells. The principal problem in RNAi experiments is off-target effects, and the most vigorous demonstration of the specificity of shRNA is the rescue of the RNAi effects with a shRNA-resistant target gene. This presents its own problems, including the unpredictable relative expression of shRNA and rescue cDNA in individual cells, and the difficulty in generating stable cell lines. In this report, we evaluated the plausibility of combining the expression of shRNA and rescue cDNA in the same vector. In addition to facilitate the validation of shRNA specificity, this system also considerably simplifies the generation of shRNA-expressing cell lines. Since the compensatory cDNA is under the control of an inducible promoter, stable shRNA-expressing cells can be generated before the knockdown phenotypes are studied by conditionally turning off the rescue protein. Conversely, the rescue protein can be activated after the endogenous protein is completely repressed. This approach is particularly suitable when prolonged expression of either the shRNA or the compensatory cDNA is detrimental to cell growth. This system allows a convenient one-step validation of shRNA and generation of stable shRNA-expressing cells.
Structure and assembly cues of Arabidopsis root-inhabiting bacterial communities and comparative genomics of selected Rhizobium members

The plant root defines the interface between a multicellular eukaryote and soil, one of the richest microbial ecosystems on earth. Soil bacteria are able to colonize the root surface and even multiply inside roots as benign endophytes. Some of these bacteria modulate plant growth and development, with implications ranging from enhanced nutrition to resistance against pathogens. In this study a high-resolution methodology based on pyrosequencing of the bacterial 16S rRNA marker gene was adopted to characterize and compare soil and root-inhabiting bacterial communities. Our results show that roots of Arabidopsis thaliana, grown in different natural soils under controlled environmental conditions, are preferentially colonized by Proteobacteria, Bacteroidetes and Actinobacteria, and each bacterial phylum is represented by a dominating class or family of bacteria. Soil type defines the composition of root-inhabiting bacterial communities whereas the host genotype modulates their profiles only to a limited extent. Furthermore, bacterial communities associated to wooden sticks, representing a metabolically inactive lignocellulosic matrix for bacterial colonization, were analyzed to deconvolute actively recruited from opportunistic root microbiota members. This comparison showed that plant cell wall features appear to provide a sufficient cue for the assembly of app. 40% of the Arabidopsis root microbiota. This root- and wood-shared sub-community was mainly composed by Betaproteobacteria. In contrast, specifically recruited members of the root-inhabiting bacteria, mostly Actinobacteria, depended on cues from metabolically active host cells, defining a root-specific sub-community. This culture-independent survey of the Arabidopsis root-associated bacteria was utilized to guide a targeted cultivation-based approach resulting in the isolation of members of both sub-communities of the Arabidopsis root-inhabiting bacterial microbiota. Several Rhizobium spp. , which are either members of the shared or specific sub-communities, were isolated from Arabidopsis roots in pure culture and tested for plant growth promotion capabilities. Upon inoculation in a gnotobiotic system, Rhizobium spp. isolated from the specific sub-community increased shoot fresh weight of Arabidopsis, while a Rhizobium strain from the shared sub-community was not able to promote plant growth. Comparative whole-genome analysis of independent exemplars of the isolated Rhizobium spp. revealed differential gene enrichments among members of both sub-communities. Particularly, the amplification and divergence of transcription factor genes might represent a signature of differential habitat adaptation. This culture-based approach backed by a broad scale culture-independent survey sets the stage to advance from descriptive characterization of bacterial communities to testing the functional significance of plant-microbiota interactions.
Microbial Gaia: a new model for the evolution of environmental regulation

Whether free-living, aggregated in biofilms, or packaged into higher organisms, microbes are the most prevalent form of life on Earth. They make up more than half the biomass on Earth and occupy every conceivable niche in the biosphere. Their metabolic diversity and adaptability means that microbes can live where other life is impossible, in extreme environments such as deep-sea thermal vents, beneath the Arctic and Antarctic ice-caps, and even inside other organisms. Microbial life is heavily implicated in all the biogeochemical cycles, dwarfing the contribution of multicellular organisms — which in any case have microbes at the root of their metabolism. Mitochondria and chloroplasts, the main energy-producing organelles in animal and plant cells, both have evolutionary origins as once-free bacteria annexed into the greater whole. (Of course, the architect of this theory of endosymbiosis is none other than the co-founder of Gaia theory, Lynn Margulis.) Inside the body (but outside of the cell) the microbial gut flora of many higher species is an essential part of the metabolic processes of the host organism; cows could not digest cellulose with the incredible microbial diversity of the rumen [8], while humans rely on bacteria to digest various carbohydrates and lipids [9]. In short, Gaia’s metabolism is microbial. In recent years technological advances have led to a much greater understanding of the microbial world. We now understand (a little) how microbes metabolise, grow, and reproduce, and comprehend (a bit) how microbial genetics works, complete with lateral gene transfer
Soybean genes involved in nickel insertion into urease

In soybean, mutation in the Eu2 or in the Eu3 gene eliminates the activities, but not the proteins, of the embryo-specific and the ubiquitous ureases, encoded by Eu1 and Eu4, respectively. This pleiotropic urease-negative phenotype is consistent with accessory gene functions encoded by Eu2 and Eu3, i.e. correct insertion of Ni into the metallocentre of each urease. To test an accessory gene function an examination was made of segregation of alleles at Eu2 and Eu3 with segregation of an RFLP revealed by a plant homologue of the bacterial urease accessory gene, ureG. The eu3-e1/eu3-e1 mutant, which has a urease activity-null phenotype, lacked a 1.4 kb EcoRV genomic fragment found in progenitor cultivar Williams, cv Williams 82 and in two mutants at the Eu2 locus, eu2/eu2 and EN24, the latter described here for the first time. The lack of the 1.4 kb band segregated with eu3-e1 in a cross of eu3-e1/eu3-e1 × EN24. The second approach was to attempt partial correction of the urease-negative trait by Ni supplementation in vitro. First, a small, reproducible stimulation of activity in mixed extracts of mutants which complement genetically, namely {eu2/eu2 plus eu3-e1/eu3-e1) and (EN24 plus eu3-e1/eu3-e1) was observed. Activation proceeded for several hours in these extracts containing endogenous Ni. In mixed extracts from Ni-free embryos, activation was dependent on added Ni; Ni had no effect on individual mutant extracts. By genetic and biochemical criteria the ubiquitous urease was the sole or major species activated, an activation which approached 10% normal activity.
TRENDS - A Tool for Recognition of Emotions in Neuropsychiatric DisorderS

Rishikesh V. Behere V.N. G.P Raghunandan Ganesan Venkatasubramanian D.K. Subbakrishna, P.N. Jayakumar B.N. Gangadhar ABSTRACT Defects in social cognition which includes Facial Emotion Recognition Deficits [FERD] have been consistently demonstrated in most neuropsychiatric disorders. Influences of culture, age & sex on emotional expression and perception necessitates that a tool standardized in the Indian population be developed to study these deficits in Indian patients.