Miracle-dz/UniFAR-FTUs huggingface dataset:
Rocky reef fish assemblage structure in coastal islands of southern Brazil

Within the Brazilian province, rocky reefs and submerged outcrops are among the most important habitats for reef fishes, providing suitable habitats for the development of reef fish communities and consequently sheltering a high ecological diversity. Rocky reef fish assemblages were sampled in seven coastal islands in South Brazil by strip transects of 40 m 2 by the underwater visual census to obtain density (fish 40 m -2 ) and biomass (g 40 m -2 ). Fish species were also categorized according to trophic category and geographical distribution. In total, 526 strip transects were performed, covering an area of 21,040 m 2 , providing 19,377 fish, distributed among 73 species of 34 families. Itacolomis Island presented the highest density, followed by Veado Island. Regarding biomass, Itacolomis Island and Pedra da Baleia were the most representative rocky reefs. Mobile invertebrate predator was the trophic category with the highest density and biomass. A total of 60% of the species occur in the Western Atlantic, 20% are Transatlantic and 9.6% are endemic to the Brazilian Province. Our results indicate that despite the similarity in the taxonomic composition among islands, the observed differences in densities and biomass, highlight singular assemblage structures, whether by environmental and/or anthropogenic factors, and dominated by few species, both in density and biomass.
BIOACTIVITY RESEARCHING ON NEW SPECIES OF ECHINOPS L. (ASTERACEAE): ANTIMICROBIAL AND ANTIOXIDANT ACTIVITY OF ECHINOPS ANTALYENSIS

The aim of this study was to investigate the antimicrobial and antioxidant activities of different extracts from Echinops antayensis C.Vural. Antimicrobial activity was estimated against several common human pathogenic bacterial strains using the agar disc diffusion and minimal inhibitory concentration assays. Antioxidant activity was evaluated using the DPPH radical-scavenging assay and total phenolic content methods. On the light of these experiments, E. antalyensis would seem to be an important natural antioxidant. This study is first report on the biological activity of E. antalyensis as regarded new species from Turkey.
A comprehensive comparison between single- and two-step GBLUP methods in a simulated beef cattle population

Abstract: The statistical methods used in the genetic evaluations are a key component of the process and can be best compared by using simulated data. The latter is especially true in grazing beef cattle production systems, where the number of proven bulls with highly reliable estimated breeding values is limited to allow for a trustworthy validation of genomic predictions. Therefore, we simulated data for 4980 beef cattle aiming to compare single-step genomic best linear unbiased prediction (ssGBLUP), which simultaneously incorporates pedigree, phenotypic, and genomic data into genomic evaluations, and two-step GBLUP (tsGBLUP) procedures and genomic estimated breeding values (GEBVs) blending methods. The greatest increases in GEBV accuracies compared with the parents’ average estimated breeding values (EBVPA) were 0.364 and 0.341 for ssGBLUP and tsGBLUP, respectively. Direct genomic value and GEBV accuracies when using ssGBLUP and tsGBLUP procedures were similar, except for the GEBV accuracies using Hayes’ blending method in tsGBLUP. There was no significant or slight bias in genomic predictions from ssGBLUP or tsGBLUP (using VanRaden’s blending method), indicating that these predictions are on the same scale compared with the true breeding values. Overall, genetic evaluations including genomic information resulted in gains in accuracy >100% compared with the EBVPA. In addition, there were no significant differences between the selected animals (10% males and 50% females) by using ssGBLUP or tsGBLUP.
Tolerance to humans of resting lynxes Lynx lynx in a hunted population

The tolerance of lynxes Lynx lynx to human presence and disturbance in a hunted population in Norway was studied using telemetry. Forest land within 200 metres from the nearest road or house was avoided by lynxes when resting (P < 0.01). The tolerance distance of resting lynxes towards intruding people was short (median 50 m), though strongly correlated with the horizontal vegetation cover (partial correlation, P < 0.02) and forest maturation stage (partial correlation, P < 0.02), but not with terrain inclination (partial correlation, P > 0.3). The lynxes did not enter steeper country (P > 0.4) or alter their daily walking distance (P > 0.7) after being disturbed. The data indicate that lynxes, even when suffering extensive, man-induced mortality, may tolerate high human activity within their range as long as sufficient stands of undisturbed, mature forest with dense horizontal cover are present.
Development of HAMLET-like Cytochrome c-Oleic Acid Nanoparticles for Cancer Therapy

In the literature, HAMLET (Human Alpha-lactalbumin Made LEthal to Tumor cells) is described as a tumoricidal complex composed of oleic acid (OA) non-covalently bound to α-lactalbumin. We recently demonstrated that OA is the real drug in this complex and that the protein solely serves as the drug carrier. We hypothesized that by replacing α-lactalbumin with a bioactive protein it should be possible to synergistically increase the efficiency of the complex. Consequently, we developed a HAMLET-like complex composed of OA coupled to the apoptosis-inducing protein cytochrome c (Cyt c). As control we coupled OA to the non-toxic protein bovine serum albumin (BSA). The syntheses of HAMLET-like Cyt c-OA and BSA-OA complexes micelles were performed at pH 8 and 45°C and we loaded 10 and 53 molecules of OA per molecule of Cyt c and BSA, respectively. We found that OA binding promotes protein structural changes characteristic of the protein-OA interactions in HAMLET. Cyt c-OA and BSA-OA complexes had a circular shape and a diameter of 123 and 169 nm, respectively. Cell viability tests showed less than 10% of viability after cancer cell (HeLa and A-549) incubation for 6 h with Cyt c-OA, while normal cells (Cho-K1 and NIH/3T3) showed more than 20% of viability. BSA-OA killed both cell types with less efficiency and no selectivity. The Cyt c-OA complex showed 50% of caspase-3 and caspase-9 activation in a cell-free assay while BSA-OA lacked any caspase activation. Confocal micrographs showed morphological changes indicative of late- and early-apoptosis by the action of Cyt-OA and BSAOA, respectively. This study demonstrates that using Cyt c increases the potency of OA in HAMLET-like complexes.
Measuring host plant selection and retention of Halyomorpha halys by a trap crop

Trap cropping may exploit a pest's dispersal and host selection behavior in order to protect a desired crop. Here, we used a combination of visual sampling, immunomarking, and harmonic radar to assess host plant selection and retention time of the highly mobile and invasive Halyomorpha halys (Stål) (Hemiptera: Pentatomidae), as it moves within and between a polyculture trap crop of sorghum and sunflower, and a bell pepper cash crop. Visual sampling demonstrated no significant differences in H. halys densities across crops, whereas dislodging stink bugs to collect for protein analysis revealed ca. 4× more bugs in the trap crop plants than in the peppers. In total 145 H. halys were collected and of these 6% were doubly marked with proteins, demonstrating that minimal movement occurred between the two planting systems. Tracking tagged H. halys with harmonic radar revealed that the trap crop retained adult H. halys within the plots 1.5× longer and reduced their movement by nearly half compared with bugs released in the pepper cash crop. The data suggest the trap crop of sunflower plus sorghum has the potential to attract and arrest the invasive H. halys, demonstrating that trap cropping may operate as an effective management tool.
Karyotype of the Neotropical mangrove species Pelliciera Rhizophorae Triana and Planchon (Tetrameristaceae)

Abstract Pelliciera rhizophorae is the sole survivor of the Eocene mangroves inhabiting the Isthmus of Panama. Two populations of Pelliciera rhizophorae, a small morphotype at the Pacific coast and a tall morphotype at the Caribbean coast, display significant morphological and molecular differences. The patterns of differentiation between these two morphotypes were not determined by the isthmus itself, but are probably due to a process of adaptation in response to the climate that resulted in specific traits for the two populations. Aiming to verify if the ecological isolation also caused changes in the karyotype of the two morphotypes, we investigated the number of chromosomes, size, morphology, distribution of CMA, DAPI bands and nuclear DNA content of the Atlantic and Pacific populations of P. rhizophorae. A diploid chromosome number of 2n = 34 was found in both morphotypes, exhibiting small metacentric, submetacentric and acrocentric chromosomes. The acrocentric chromosomes presented the largest CMA+bands which are often associated with the nucleolus. Nuclear DNA content was similar in both variants (2.52 pg and 2. 56 pg for the small and tall morphotypes respectively), evidencing a small genome. Although the two morphotypes were karyotypically very similar, we observed a consistent difference in digestibility of their root tips in cellulase–pectinase solution and in the stainability of their cytoplasm. The cytotaxonomical relationship between Pelliciera and the related taxa is also discussed.
Comparison and Combination of Mobile and Terrestrial Laser Scanning for Natural Forest Inventories

Terrestrial laser scanning (TLS) has been successfully used for three-dimensional (3D) data capture in forests for almost two decades. Beyond the plot-based data capturing capabilities of TLS, vehicle-based mobile laser scanning (MLS) systems have the clear advantage of fast and precise corridor-like 3D data capture, thus providing a much larger coverage within shorter acquisition time. This paper compares and discusses advantages and disadvantages of multi-temporal MLS data acquisition compared to established TLS data recording schemes. In this pilot study on integrated TLS and MLS data processing in a forest, it could be shown that existing TLS data evaluation routines can be used for MLS data processing. Methods of automatic laser scanner data processing for forest inventory parameter determination and quantitative structure model (QSM) generation were tested in two sample plots using data from both scanning methods and from different seasons. TLS in a multi-scan configuration delivers very high-density 3D point clouds, which form a valuable basis for generating high-quality QSMs. The pilot study shows that MLS is able to provide high-quality data for an equivalent determination of relevant forest inventory parameters compared to TLS. Parameters such as tree position, diameter at breast height (DBH) or tree height can be determined from MLS data with an accuracy similar to the accuracy of the parameter derived from TLS data. Results for instance in DBH determination by cylinder fitting yielded a standard deviation of 1.1 cm for trees in TLS data and 3.7 cm in MLS data. However, the resolution of MLS scans was found insufficient for successful QSM generation. The registration of MLS data in forests furthermore requires additional effort in considering effects caused by poor GNSS signal.
Morphological diversity and phylogenetic relationships within a South-American clade of iguanian lizards (Liolaemidae: Phymaturus )

With 36 species and at least nine potentially independent lineages (not formally described yet) occurring mostly in theAndes and adjacent Patagonia and Puna plateau areas, Phymaturus lizards represent one of the most endemic vertebrategroups of the arid southwestern region of South America. Phylogenetic relationships among species of Phymaturus areinferred using mainly a morphological data set of 206 characters. Also available sequences of mitochondrial DNA for sev-en terminals were added for a total evidence analysis. Most information is included in the discrete characters block; mostcharacters involve color pattern, osteology and squamation. Continuous characters were taken from body proportions,squamation and skeletons. Among morphological data, binary polymorphic characters were analyzed applying the scaledcoding criteria. Continuous characters were entered in the analysis using standardized ranges, a method that allows a sim-ple optimization to estimate distances/costs avoiding the arbitrary coding as discrete characters. For our parsimony anal-yses we chose the implied weights method, which underweights homoplastic characters. Several runs were madeanalyzing all the information combined and also separating morphological from molecular datasets. Binary polymor-phisms were also analyzed as missing data. All characters affected by sexual dimorphism were analyzed separating thesexes; female information was more congruent with the total evidence analysis. Characters involving continuous and poly-morphic information are relevant for searching and building phylogenetic hypotheses in Phymaturus. There exists signif-icant congruence between the molecular information analyzed in this study and previous published analyses. Within bothmain clades of Phymaturus, northern subgroups are those more recently originated during the genus diversification. Spe-cies belonging to the puna subclade of the palluma group are arranged in two natural groups, one distributed in the north(Catamarca and La Rioja provinces), and the other in the south, La Rioja and San Juan provinces. Within the patagonicus group, the majority of the species are arranged in a south-central Chubut clade, eastern-central Chubut clade, central Rio Negro clade and a Payunia clade.
TRPV4 interacts with mitochondrial proteins and acts as a mitochondrial structure-function regulator

TRPV4 has been linked with the development of sensory defects, neuropathic pain, neurodegenerative disorders such as Charcot Marie Tooth disease and various muscular dystrophies. In all these cases mitochondrial abnormalities were tagged as cellular hallmarks and such abnormalities have been reported as key factor for the pathophysiological conditions. Mitochondria also have the unique ability to sense and regulate their own temperature. Here, we demonstrate that TRPV4, a thermosensitive ion channels, localizes to a subpopulation of mitochondria in various cell lines, in primary cells and also in sperm cells. Improper expression and/or function of TRPV4 induce several mitochondrial abnormalities such as low oxidative potential, high Ca2+-influx and changes in electron transport chain functions. TRPV4 is also involved in regulation of mitochondrial morphology, smoothness, and fusion-fission events. The C-terminal cytoplasmic region of TRPV4 can localize it to mitochondria and interacts with mitochondrial proteins including Hsp60, Mfn1 and Mfn2. Regulation of mitochondria by TRPV4 may contribute to previously uncharacterized mitochondria-specific functions observed in various cell types. This discovery may help to link TRPV4-mediated channelopathies with mitochondria-mediated diseases. Abbreviations ER Endoplasmic Reticulum IMM Inner Mitochondrial Membrane MAM Mitochondria-associated ER membrane MCU Mitochondrial uniporters MOM Mitochondrial outer membrane NO Nitric Oxide ROS Reactive Oxygen Species TRPV4 Transient Receptor Potential Channel Vanilloid subfamily member 4 VDAC Voltage Gated Anion Channels
The critical role of ASD-related gene CNTNAP3 in regulating synaptic development and social behavior in mice

Accumulated genetic evidences indicate that the contactin associated protein-like (CNTNAP) family is implicated in autism spectrum disorders (ASD). In this study, we identified genetic mutations in the CNTNAP3 gene from Chinese Han ASD cohorts and Simons Simplex Collections. We found that CNTNAP3 interacted with synaptic adhesion proteins Neuroligin1 and Neuroligin2, as well as scaffolding proteins PSD95 and Gephyrin. Significantly, we found that CNTNAP3 played an opposite role in controlling the development of excitatory and inhibitory synapses in vitro and in vivo, in which ASD mutants exhibited loss-of-function effects. In this study, we showed that Cntnap3-null mice exhibited deficits in social interaction, spatial learning and prominent repetitive behaviors. These evidences elucidate the pivotal role of CNTNAP3 in synapse development and social behaviors, providing the mechanistic insights for ASD.
Methamphetamine Contaminated Currency in the Birmingham, Alabama Metropolitan Area

GC-MS Analyses of extracts of one dollar bills collected from in and nearby the Birmingham, Alabama metropolitan area in 2012 indicated that 42% of them were contaminated with methamphetamine. This is the first time that methamphetamine was identified on one dollar bills since the laboratory began testing them in 2008.
Disentangling the process of speciation using machine learning

Historically, investigations into the processes driving speciation have largely been isolated from systematic investigations into species limits. Recent advances in sequencing technology have led to a rapid increase in the availability of genomic data, and this, in turn, has led to the introduction of many novel methods for species delimitation. However, these methods have been limited to divergence-only scenarios and have not attempted to evaluate complex modes of speciation, such as those that include gene flow during early stages of divergence (sympatric speciation) or population size changes (founder effect speciation). To address this shortcoming, we introduce delimitR, an approach that enables biologists to infer species boundaries and evaluate the demographic processes that may have led to speciation. delimitR uses the binned multidimensional Site Frequency Spectrum and a machine-learning algorithm (Random Forests) to compare speciation models. We use simulations to evaluate the accuracy of delimitR. When comparing models that include lineage divergence and gene flow for three populations, error rates are near zero with recent divergence times (<100,000 generations) and a modest number of Single Nucleotide Polymorphisms (SNPs; 1,500). When applied to a more complex model set (including divergence, gene flow, and population size changes), error rates are moderate (~0.15 with 10,000 SNPs), and misclassifications are generally between highly similar models. We also evaluate the utility of delimitR using three previously published datasets and find results that corroborate previous findings. Our analyses indicate that delimitR can serve as an important conceptual bridge uniting various investigations into the process of speciation.
An unexpected twist: Sperm cells coil to the right in land snails and to the left in song birds

In animals, cell polarity may initiate symmetry breaking very early in development, ultimately leading to whole-body asymmetry. Helical sperm cells, which occur in a variety of animal clades, are one class of cells that show clearly visible bilateral asymmetry. We used scanning-electron microscopy to study coiling direction in helical sperm cells in two groups of animals that have figured prominently in the sperm morphology literature, namely land snails, Stylommatophora (514 spermatozoa, from 27 individuals, belonging to 8 species and 4 families) and songbirds, Passeriformes (486 spermatozoa, from 26 individuals, belonging to 18 species and 8 families). We found that the snail sperm cells were consistently dextral (clockwise), whereas the bird sperm cells were consistently sinistral (counterclockwise). We discuss reasons why this apparent evolutionary conservatism of sperm cell chirality may or may not be related to whole-body asymmetry.
Mapping of QTLs for traits related to leaf pubescence, jassid resistance and yield in cotton (Gossypium spp.).

Present investigation was carried out to find the QTLs associated with leaf pubescence, jassid resistance and yield traits in cotton. Available SNP based linkage map was used for QTL analysis. Single marker analysis and simple interval mapping identified 24 and 11 associated QTLs, respectively. Composite interval mapping detected only seven QTLs, of which five were associated with jassid injury resistance and leaf pubesence with 8.83–11.64% phenotypic variance explained. One QTL each for seed cotton yield and boll weight was detected. These identified QTLs and markers may be used in molecular breeding for improving yield and insect resistance in cotton.
Population density, activity patterns, and ecological importance of giant armadillos (Priodontes maximus) in Colombia

The giant armadillo (Priodontes maximus) is the largest extant armadillo species. This rare, cryptic, and poorly studied South American mammal is considered a physical ecosystem engineer. From February to August 2014, 10 camera traps were used to estimate population density, activity patterns, and the ecological importance of giant armadillos on private lands with riparian forests and natural savannas near Puerto Gaitán (Meta), in the Eastern Llanos of Colombia. A total of 5,728 records (photos and videos) were obtained during 1,335 trap nights, 7.4% of which corresponded to giant armadillos and 92.6% to other vertebrate species. The 426 records of Priodontes, grouped in 78 events (uncorrelated records), were used to individually identify 11 individuals in an area of 189 km2 and determine their activity periods. Population density was estimated at 5.8 animals/100 km2. Nocturnal habits, mainly between 22:00 and 00:00 h, were predominant. A total of 470 km walking transects, censuses of burrows and other indirect signs of presence, and camera trapping allowed determination of some aspects of habitat use. Priodontes prefers riparian forest habitats, makes burrows of 42.0 ± 5.9 cm width and 35.0 ± 5.9 cm height in sloped terrain, and re-uses burrows. More than 26 different species were associated with Priodontes burrows. The conservation of riparian forests is fundamental for the persistence of P. maximus populations and the ecological community that is associated with its burrows.
Range-wide Microsatellite Analysis of the Genetic Population Structure of Prairie Voles (Microtus ochrogaster)

Abstract Understanding population genetic structure provides insight into the evolutionary past, present, and future of a species. In this study, we examine the range-wide population genetic structure of the prairie vole, Microtus ochrogaster (n = 170). Early work divided M. ochrogaster into seven subspecies using morphological characteristics. We hypothesized polymorphic microsatellite data would reveal a genetic structure roughly congruent with the current classification of subspecies based on their geographic boundaries. We predicted populations within the geographic range of one subspecies would be genetically distinguishable from populations within the geographic range of another subspecies. Microsatellite data from the seven putative subspecies suggested ∼90% of molecular variation was within populations. A STRUCTURE cluster analysis had a best supported k = 3, but most individuals were admixed for the three genetic clusters, and only individuals of M. o. ohionensis were distinctive in being essentially represented by a single cluster. Therefore, our molecular data showed evidence of relatively high gene flow and little geographic differentiation throughout the range of the six contiguous subspecies. The subspecific classification of M. ochrogaster should be re-evaluated using a comprehensive taxonomic approach that combines molecular, morphometric, and other data.