Miracle-dz/UniFAR-FTUs huggingface dataset:
Phylogeny and biogeography of Arabian populations of the Persian Horned Viper Pseudocerastes persicus (Duméril, Bibron & Duméril, 1854)

The Persian Horned Viper (Pseudocerastes persicus) is distributed from northeast Iraq through the Iranian Plateau to western Pakistan with isolated populations in the Hajar Mountains of south-eastern Arabia. Like the other members of the genus Pseudocerastes, P. persicus is a sit-and-wait ambush feeder with low vagility, a characteristic that often results in high levels of population differentiation. In order to clarify the level of genetic variability, phylogenetic relationships, and biogeography of the Arabian populations of P. persicus we sequenced 597 base pairs of the mitochondrial cytochrome b of four individuals from the Hajar Mountains in south-eastern Arabia and inferred their phylogenetic relationships including 10 samples of P. persicus from Iran and Pakistan, four P. urarachnoides and one P. fieldi downloaded from GenBank. The four Arabian samples are genetically very similar in the gene fragment analysed and are phylogenetically very closely related to populations of P. persicus from coastal south Iran. Biogeographically, it appears that colonisation of the Hajar Mountains by P. persicus took place from Iran very recently, most probably during the last glaciation, when most of the Persian Gulf was above sea level and did not represent a barrier for dispersal.
Fish community in a large coastal subtropical lake: how an environmental gradient may affect the structure of trophic guilds

Biological communities change in time and space under driving pressures from differences in habitat structure, resource availability, interspecific competition, predation and other factors. Spatial heterogeneity, or patchiness, has been recognized as an important feature in a number of lake systems. In this study, we analysed changes in the seasonal dynamics of fish community in a subtropical lake over one year, focusing on the spatial and temporal distribution of fish biomass and species composition. Mangueira is a large shallow lake (3 m deep in average, 90 km long, 3-10 km wide, ≈ 820 km2) located along the Atlantic coast-line in southern Brazil (33◦3122S 53◦0748W). Mangueira Lake presents longitudinal gradients in both biotic and abiotic factors, and a principal components analysis (PCA) showed temporal and spatial gradients in the system. Analysis of similarity (ANOSIM) showed significant differences between the north and south extremes of Mangueira Lake. Secchi transparency (p < 0.001), dissolved organic carbon (DOC) (p = 0.03) and chlorophyll a (p < 0.001) were identified as the driving factors for this spatial gradient. A two-way ANOVA was adjusted for each data set. Chlorophyll a (p = 0.017), fish captures (p = 0.033) and fish richness (p = 0.026) were different according to the sampling site (after removing the seasonal effect), while only fish richness presented significant seasonal variation after removing the sampling site effect (p = 0.041). This longitudinal gradient can be related to two main driving pressures. The first is prevailing winds from northeast to southwest, with predictable consequences for the whole trophic cascade. The other structuring pressure is the interface of the Taim wetland with northern Mangueira Lake. Thus, the northern part presents more turbid water, muddy sediments and increased chlorophyll a concentration, while the southern part is characterized by increased water transparency, less chlorophyll a concentration and more PVI (percent volume infested) of submerged macrophytes, demonstrating the spatial heterogeneity of the ecosystem.
RICHNESS, STRUCTURE AND VEGETATION RELATIONSHIPS OF THE WOODY LAYER IN AN UPPER MONTANE FOREST IN CAPARAÓ NATIONAL PARK, MINAS GERAIS STATE, BRAZIL

The Upper Montane Forests are located in environments with in high structural, soil and climatic variations and considered as indicative of susceptibility to potential weather changes. However, the floristic and biogeographical knowledge of this vegetation type are still scarce. Therefore, as the beginning of understanding the functioning of forest autoecology in this environment, we conducted a floristic and structural survey of woody component of a Dense Rain Forest in the Upper Montane from Caparao National Park, establishing the floristic links between this community and others that have occurrence of similar phytophysionomies. For sampling of vegetation, we allocated 10 transects with 50x2m each, in three different portions in the Park, in the locality called Macieira. All individuals of woody layer were measured (DBH ? 2,5cm). We founded 356 individuals of 40 species. The most important in terms of dominance among the population studied were Myrsine coriacea and Symplocos pubescens with 14.68 and 14.02%, respectively. The Shannon Diversity (H') was 2.79 nat.ind-1 and Pielou Evenness (J) 0.76. Given our results, this Upper Montane Forest has floristic constitution and structural organization inconsistent with its other Upper Montane Rain Forest in the country. The geographical distance and isolation by grassland environment makes this an "island" determined by floristic differentiation and structural organization.
Carbohydrate hydrolyzing enzymes inhibitory and free radical scavenging activities of substituted 2 H -chromene-3-carboxylates, 2 H -chromenyl Knoevenagel derivatives and 6 H -chromenoquinolinones

Three series of compounds namely ethyl 2-hydroxy-2-(trifluoromethyl)-2H-chromene-3-carboxylates 3a-q, 2H-chromenyl Knoevenagel derivatives 7a-j and 6H-chromenoquinolinones 9a-l have been prepared. The synthesized compounds 3a-q, 7a-j and 9a-g have been screened for anti-oxidant and anti-diabetic activity. Compound 3i shows the most potent ABTS inhibitory activity when compared to trolox. Compounds 3b, 3d, 3j and 3l show α-amylase inhibitory activity.
Apps for angiosperms: the usability of mobile computers and printed field guides for UK wild flower and winter tree identification

Abstract We investigated usability of mobile computers and field guide books with adult botanical novices, for the identification of wildflowers and deciduous trees in winter. Identification accuracy was significantly higher for wildflowers using a mobile computer app than field guide books but significantly lower for deciduous trees. User preference followed a similar pattern. These results suggest that the identification method and its design are more important for a field guide than its presentation medium (electronic or printed). We discuss the relative advantages of the presentation media used and their value as engagement tools for botany.
Historical distribution of 'Red List diatoms' (Bacillariophyceae) in Flanders (Belgium)

The former distribution (1852-1943) in Flemish standing waters of diatoms included in the Red List for Germany and Central Europe is assessed through a survey of diatom assemblages from herbarium exsiccata of macrophytes and old samples. With few exceptions, a good historical representation of Red List taxa is observed in the Campine ecoregion only, as nutrient-poor non- alkaline waters are scarce elsewhere in Flanders due to edaphic conditions. The German list therefore does not appear to be optimalfor general use in e.g. site evaluation, as it reflects the availability of a particular habitat much more strongly than habitat quality as such. Within the Campine region and where leached sandy topsoils are present, such applications are possible, however. This is illustrated by a comparison of historical and recent survey data showing that a considerable decline in Red List diatoms occurred here. This decline is especially apparent if relative abundance or abundance ranked data are considered, but less so at the level of species numbers. For regions with naturally more eutrophic waters, development of a specific list seems more appropriate. A more general case can be made to use only Red Lists compiled at the scale of ecologically more homogeneous regions (ecoregions) for applications that are sensitive to biogeographic bias. Whether the number of Red List diatoms, their percentage abundance, or both metrics should be considered in assessing biological impairment or conservation value depends on the water type in question. Accurate estimates of the number of taxa are, however, more difficult to obtain. The use of rank ratios may be considered to compare differently structured assemblages. Among the cryptobiota, diatoms appear to be an exceptionally accessible group for addressing historical changes in biodiversity.
Protein Profile and Hematological Parameters of Mice post Injected with Irradiated Plasmodium berghei

Indonesia had a high number of malaria cases where the treatments are only perceived by 10% of patients in health facilities. The resistance of Plasmodium sp. to drugs causes the difficulty of controlling malaria. The use of irradiation to produce malaria vaccine material is being explored until nowadays. In previously study that dose rate of gamma irradiation delivered to parasite was at the low dose rate (380 Gy/hour) which produced several doses that not be able to attenuate the parasite. This research aimed to increase dose rate (740 Gy/hour) and to determine the dose irradiation effect of 150-250 Gy to the protein profile, erythrocyte and leukocyte numbers in mouse blood infected by P. berghei erythrocytic stage. Results showed that there was an influence of dose rate of 740 Gy/hour for doses of 150-250 Gy in treated mice and no difference in erythrocyte, leucocyte and body weight with negative control. Dose of 150 Gy was the optimal dose to attenuate parasites, whereas doses more than 150 Gy effectively killed the parasites. The changes of protein profile marked by the appearance of higher number of bands at molecular weight of 30-37 kDa that predicted as merozoite surface protein of P. berghei and/or antibodies elicited in mouse. How to Cite Rosadi, I. , Syaifudin, M. , & Elfidasari, D. (2016). Protein Profile and Hematological Parameters of Mice post Injected with Irradiated Plasmodium berghei. Biosaintifika: Journal of Biology & Biology Education , 8(2), 155-164
Determination of gibberellic acid in tomatoes, processed tomato products and grapes.

A simple and reliable method was developed for gibberellic acid determination in agricultural products by reversed-phase high pressure liquid chromatography and UV detection. Good overall recovery (74-105%), satisfactory linearity (r 2 = 0.996) and precision (5-15%) in the useful working range of 0.1-20 ppm, and a low detection limit of O. 1 ppm were obtained for this widely used agricultural compound. The method was used to screen for gibberellic acid residues in different varieties of tomato and grape, and in various types of processed tomato products. In several cases, the results showed levels of gibberellic acid up to twenty times higher than the limit allowed by the Italian law for these products.
High Levels of Diversity in the Phytochemistry, Ploidy and Genetics of theMedicinal Plant Acorus calamus L.

Acorus calamus L. is an emergent aquatic macrophyte that is used in several medicines and food supplements. A. calamus ecotypes with low concentrations of β-asarone can be used for medicinal purposes. We investigated 50 populations of this species, representing the entire natural distribution range in Indian Himalayan Region (IHR), to understand natural variations in β-asarone concentration, ploidy level and genetic divergence. Our results showed that: 1) all four cytotypes (diploid, triploid, tetraploid and hexaploid) of A. calamus exist in natural populations in the IHR; 2) the β-asarone concentration is highly correlated with the ploidy level (diploid and hexaploid populations exhibit low β-asarone concentrations, whereas triploids and tetraploids show high β-asarone concentrations); 3) there is a significant correlation between the β-asarone concentration and its distribution along latitudinal and longitudinal ranges, but not ecological factors (mean annual temperature and mean annual precipitation); and 4) geographic boundaries play an important role in the population divergence of A. calamus. This study provides a foundation for understanding the genetic basis of natural variation in complex traits of A. calamus and for devising conservation strategies for this medically important plant.
Transitions in the morphological features, habitat use, and diet of young-of-the-year goosefish (Lophius americanus)

This study was designed to improve our understanding of transitions in the early life history and the distribution, habitat use, and diets for young-of-the-year (YOY) goosefish (Lophius americanus) and, as a result, their role in northeastern U.S. continental shelf ecosystems. Pelagic juveniles (>12 to ca. 50 mm total length [TL]) were distributed over most portions of the continental shelf in the Middle Atlantic Bight, Georges Bank, and into the Gulf of Maine. Most individuals settled by 50−85 mm TL and reached approximately 60−120 mm TL by one year of age. Pelagic YOY fed on chaetognaths, hyperiid amphipods, calanoid copepods, and ostracods, and benthic YOY had a varied diet of fishes and benthic crustaceans. Goosefish are widely scattered on the continental shelf in the Middle Atlantic Bight during their early life history and once settled, are habitat generalists, and thus play a role in many continental shelf habit
Phylogeography of a freshwater crustacean species complex reflects a long‐gone archipelago

The Carpathian Mountains are an important European biodiversity hotspot and are characterized by a dynamic geological history. Their freshwater amphipod fauna is ubiquitous and diverse, consisting of micro‐endemic lineages that apparently reflect historical geological events. In this study, we propose that the complementary distribution of two widespread morphotypes belonging to the Gammarus balcanicus species complex reflects two chronologically distinct uplift episodes of the Carpathian Archipelago during the Miocene.
Social sophistry : logos and mythos in the forms of cooperation

In Plato's cave, humans chained to a wall see gests that workers are aware of the importance the world only as flickering shadows of statof cave-shadows in defining societies. Indeed, ues, removed by several degrees from the 'real' recent authors are usually careful to explain world of ideas and forms. As the cave-dwellers their use of social terms (e.g., Burda et al. 2000), communicate thoughts about the statues, their probably more careful and explicit now than pre words add yet another layer of removal and 1995.1 see this as progress — at least we know distance, here between each others' perception that we are in a cave like Plato's, and thought-pictures. Over ten years ago, I asked Second, tabulation of how often various a number of the philosopher queens and kings social terms were used before vs. after 1995 of social insect biology how they conceived (Costa & Fitzgerald 2005) can demonstrate any and applied the term 'reproductive division of trends, though the connections between word use labor', the core of the traditional definition of and application of concepts is difficult to judge, eusociality. From each person I received a differThird, we can seek to assess conceptual ent answer. I reckoned then that social terminolimpact by determining if any of the specific ogy systems required an attempt at meeting of suggestions of the authors have been imple minds, to avoid implicit confusion and to foster mented. For example, Crespi and Yanega (1995) progress in recognizing social convergences. proposed that some 'traditionally eusocial' ants, Down the hall I went to Paul Sherman and bees, and termites should be considered as coop his erudite mind. We compared our flickering erative breeders. Search for the combined terms shadows, decided to write a paper together, and 'insects' and 'cooperative breeding' on BIOSIS started — but then realized that we viewed the for 1985 through 1994 yielded 12 citations, with wall quite differently, and two contrasting papers only one on social insects (ants). By contrast, were the ultimate result. 1996 to 2005 produced 27 hits, including two The conceptual impact of the papers by Sherpapers on ants, two on termites, five on wasps, man et al. (1995), Crespi and Yanega (1995), and and three on bees. A search for 'eusociality con later Costa and Fitzgerald (1996), Wcislo( 1997), tinuum' over this period gave only one empiri and Crespi and Choe (1997) may be assessed cal paper, on Zambian mole rats. I take this as in several ways. First, the papers have been suggestive evidence that some workers have cited 80, 45 and 22 times respectively (for the adopted at least one central idea of Crespi and first three papers, Web of Science), which sugYanega (1995), that insects can be cooperative
Differential sub-nuclear distribution of hypoxia-inducible factors (HIF)-1 and -2 alpha impacts on their stability and mobility

Cellular adaptation to hypoxia occurs via a complex programme of gene expression mediated by the hypoxia-inducible factor (HIF). The oxygen labile alpha subunits, HIF-1α/-2α, form a heterodimeric transcription factor with HIF-1β and modulate gene expression. HIF-1α and HIF-2α possess similar domain structure and bind to the same consensus sequence. However, they have different oxygen-dependent stability and activate distinct genes. To better understand these differences, we used fluorescent microscopy to determine precise localization and dynamics. We observed a homogeneous distribution of HIF-1α in the nucleus, while HIF-2α localized into speckles. We demonstrated that the number, size and mobility of HIF-2α speckles were independent of cellular oxygenation and that HIF-2α molecules were capable of exchanging between the speckles and nucleoplasm in an oxygen-independent manner. The concentration of HIF-2α into speckles may explain its increased stability compared with HIF-1α and its slower mobility may offer a mechanism for gene specificity.
Structure and dynamics of a predicted ferredoxin-like selenoprotein in Japanese encephalitis virus By: Haizhen Zhong and Ethan Will Taylor

Homologues of the selenoprotein glutathione peroxidase (GPx) have been previously identified in poxviruses and in RNA viruses including HIV-1 and hepatitis C virus (HCV). Sequence analysis of the NS4 region of Japanese encephalitis virus (JEV) suggests it may encode a structurally related but functionally distinct selenoprotein gene, more closely related to the ironbinding protein ferredoxin than to GPx, with three highly conserved UGA codons that align with essential Cys residues of ferredoxin. Comparison of the probe JEV sequence to an aligned family of ferredoxin sequences gave an overall 30.3% identity and 45.8% similarity, and was statistically significant at 4.9 S.D. (P < 10−6) above the average score computed for randomly shuffled sequences. A 3-dimensional model of the hypothetical JEV protein (JEV model) was constructed by homology modeling using SYBYL, based upon a high resolution X-ray structure of ferredoxin (PDB code: 1awd). The JEV model and the model from 1awd were subsequently subjected to molecular dynamics simulations in aqueous medium using AMBER 6. The solution structure of the JEV model indicates that it could fold into a tertiary structure globally similar to ferredoxin 1awd, with RMSD between the averaged structures of 1.8 Å for the aligned regions. The modeling and MD simulations data also indicate that this structure for the JEV protein is energetically favorable, and that it could be quite stable at room temperature. This protein might play a role in JEV infection and replication via TNF and other cellular stimuli mediated via redox mechanisms.
The complete plastome sequence of Pentactina rupicola Nakai (Rosaceae), a genus endemic to Korea

Abstract The complete plastid genome (plastome) of Pentactina rupicola Nakai, the sole member of genus Pentactina, endemic to Korea, was determined in this study. The plastome of P. rupicola is 156,612 bp in length and is composed of a pair of 26,351 bp inverted repeat regions (IRa and IRb) separating large (LSC) and small (SSC) single-copy regions of 84,970 and 18,940 bp, respectively (NCBI acc. no. NC 016921). The plastome encodes 129 genes, of which 112 are unique, including 78 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Seventeen genes contain one intron and the ycf3 gene has two introns. The second intron of clpP is absent in the P. rupicola plastome. The AT content of P. rupicola is 63% overall, and in the LSC, SSC, and IR regions is 65%, 69%, and 58%, respectively. A total of 63 simple sequence repeats (SSR) are distributed among the noncoding regions of the genome. Phylogenetic analysis of the combined 82-gene data set for 35 plastomes suggests that P. rupicola is sister to the Pyrusmalus clade.
Population study for monitoring the status of rarity of three aconite species in Garhwal Himalaya

Alpine and subalpine regions of Garhwal Himalaya were surveyed quantitatively for the population study to determine the status of three aconites viz., Aconitum balfourii, A. heterophyllum and A violaceum. Population data of these three aconites revealed that they are restricted to specific pockets and had very low population density. Illegal and over exploitation of these species pose threat to their existence. However, to assign the categories of threats population status of aconites has not been quantified so far. Present study summarizes the population dynamics of identified aconite species in Garhwal Himalaya. Observations reveal that on the basis of population density and degree of constancy (occurrence) used to assign threat categories, all the three Aconitum species are endangered. Furthermore, these observations would be helpful in monitoring the threat categories in future on the basis of population reduction.
Limnological description of four temporary ponds in the Doñana National Park (SW, Spain)

Temporary ponds of Donana are small, shallow water bodies with alkaline waters rich in Na + . Periodic wet and dry seasons force their biota to function within a wide range of physical and chemical conditions. The ponds are basically fed by ground water and by direct rainfall during rainy periods. Thus, they are largely influenced by water table fluctuations and groundwater chemical composition. These ponds are also subject to frequent allochthonous inputs of nutrients and organic matter from adjacent terrestrial ecosystems. Their dependence on groundwater feeding has recently led some ponds to an endangered situation.
Enzymatic hydrolysis of lignocellulosic biomass

Abstract: Enzymatic hydrolysis technologies for producing ethanol from lignocellulosic materials offer much greater scope for advancements than those using acid catalysts. However, technical barriers for enzymatic hydrolysis to cost-effectively hydrolyze cellulose to glucose must be overcome. This chapter begins by dicussing the mechanisms of enzymatic cellulose hydrolysis and the synergistic interactions of cellulolytic enzyme components. It then reviews factors affecting the hydrolysis efficiency and research efforts to enhance saccharification efficiencies.