Miracle-dz/UniFAR-FTUs huggingface dataset:
Psychometric Properties of the Turkish Version of the Environmentally Desirable Responding Scale (EDRS)

This study was aimed to test the reliability and validity of the Turkish version of the Environmentally Desirable Responding Scale (EDRS). The EDRS contained 18 items, which were expressed on a 4-point Likert scale. The study group consisted of 221 recreational outdoor sports participants from Ankara, Turkey. The participants included 78 females and 143 males, with a mean age of 23.2 years and a standard deviation of 3.92 years. Principal Axis Factoring (PAF) produced a 3-factor solution with the sub-dimensions self-deception/denial of negatives, image management and self-deception/assertion of positives. Confirmatory factor analysis (CFA) confirmed this 3-factor solution, AGFI=0.87, GFI=0.90, NFI=0.91, CFI=0.96, RMSEA=0.061 SRMR=0.053. Cronbach’s Alpha coefficient values for 3 sub-dimensions ranged from 0.74 to 0.87. These suggest that the Turkish version of the questionnaire is a valid and reliable data collection tool for recreational outdoor sports participants.
Response of Appetite and Appetite Regulating Hormones to Acute Hypoxia

AIM: To determine the acute response of appetite and appetite regulating hormones after exposure to simulated altitude. METHODS: Seven males and five females (height: 178.9 ¡ 2.3 cm; weight: 77.3 ¡ 7.2 kg; body fat: 18.4 ¡ 1.7%) participated in two, three-hour trials in a hypoxic (5000 m) and normoxic (350 m) environment. Blood samples were collected prior to and immediately following three hours of exposure for the measurement of leptin, adiponectin, and acylated ghrelin. Appetite, acute mountain sickness, heart rate, blood oxygenation, tissue oxygenation, respiration rate, and whole body gases were also measured. RESULTS: Leptin was not different between hypoxic (5.8 ¡ 1.8 ng ml 2 1 ) and normoxic trials (6.2 ¡ 2.0 ng ml 2 1 ; p 5 0.603). Adiponectin was not different between hypoxic (9.0 ¡ 0.2 m g ml 2 1 ) and normoxic trials (8.4 ¡ 0.7 m g ml 2 1 ; p 5 0.216). Acylated ghrelin was not different between hypoxic (15.0 ¡ 3.8 pg ml 2 1 ) and normoxic trials (16.3 ¡ 4.6 pg ml 2 1 ; p 5 0.285). Appetite scores were not different between trials ( p . 0.05) with the exception of fullness which was greater in the hypoxic condition ( p 5 0.027). Heart rate and symptoms of acute mountain sickness were higher while blood and tissue oxygenation were lower in the hypoxic trial ( p , 0.05). No differences were noted in other metabolic parameters ( p . 0.05). CONCLUSION: Appetite and appetite regulating hormones are not affected by three hours of hypoxic exposure, and thus some of these negative consequences of hypoxic exposure may not be evident with short exposure times.
Climate and rapid local adaptation as drivers of germination and seed bank dynamics of Alliaria petiolata (garlic mustard) in North America

Local differences in climate conditions may facilitate rapid evolutionary changes in introduced plants to optimize timing of germination or ability to survive in seed banks, which may constitute beneficial demographic adaptations during range expansions. Understanding differences in germination requirements and emergence patterns across a species’ range is critical for demographic modelling and potential invasive species control efforts. We assessed germination responses of Alliaria petiolata using seeds collected from 10 populations spanning much of the North American distribution of the species. We compared germination responses under different stratification regimes in a growth chamber over 2·5 years, and evaluated seedling emergence in a common garden in Ithaca, New York over 13 years. We further evaluated how climate overlap between Ithaca and original collection sites influenced emergence patterns. In the laboratory, germination of all populations was similar and highest at 4 °C stratification. Seeds exposed to sub‐zero temperatures delayed germination and population responses were variable. In the common garden, seedlings from most populations emerged over 13 years, and emergence patterns were strongly influenced by population. Annual emergence was positively correlated with spring temperature and inversely correlated with number of spring days with minimum temperature below freezing. Climate overlap between the common garden and original collection location enhanced germination, but common garden climate conditions over the course of the 13‐year experiment and population identity had greater explanatory power. Synthesis. Laboratory germination tests did not reflect seedling emergence under field conditions. After 150 years of residence time in North America, Alliaria petiolata populations have developed striking differences in their responses to local climates and stratification requirements suggesting that a complex interplay of pre‐adaptation, rapid evolutionary changes, and phenotypic plasticity result in locally adapted populations.
Effect of Ephedra foeminea active compounds on cell viability and actin structures in cancer cell lines

Ephedra is likely one of the oldest medicinal plants still currently in use. In folk medicine, extracts of Ephedra foeminea are commonly used to treat cancer patients. In relation to its traditional use, the aim of the present study was to determine the cytotoxic activity in vitro of E. foeminea extracts on cancer and non-cancer cells. Cell viability was determined using XTT assay, induction of apoptosis by cell sorting and caspase-3 inhibition, and the effects on cell cytoskeleton structure were detected using cell transfection utilizing different cytoskeleton markers. Chemical profiling, analysis of active extracts and identification of compounds was done using high pressure liquid chromatography (HPLC) and gas chromatography-mass spectroscopy (GCMS). E. foeminea leaf ethanol extract and E. foeminea fruit juice reduced cancer cell viability in vitro, whereas the water extract reduced cytotoxic activity in all cell lines. The extract's cytotoxic activity was conveyed at least partially via the induction of caspase 3-dependent cell apoptosis, and enhanced by the addition of Taxol. Both E. foeminea ethanol leaf extract and fruit juice affected actin-stained but not tubulin-stained filaments. Ethanol extract promoted the formation of invadopodia-like structures and fruit juice promoted the formation of large focal adhesion points in the treated cells. Active sub-fractions of E. foeminea extracts were found to contain several compounds including trans-sinapyl alcohol and trans-sinapaldehyde derivative. Key words: Ephedra foeminea, plant extract, cancer cells, actin, invadopodia, apoptosis.
Myostatin Gene Expression and Its Application on Goat Breeding Programme

Characteristics of double muscled growth in animals are influenced by myostatin gene (MSTN). Myostatin gene is known as a member of the growth gene's superfamily (TGF-β) which works to suppress the muscle growth. However, the presence of six mutations on MSTN cause the gene inactive, and trigger the occurrence of muscle hypertrophy. Identification of myostatin gene was conducted by molecular techniques, and the most common method is polymerase chain reaction followed by single-strand conformation polymorphism (PCR-SSCP). Research on sheep and goat in several countries showed that there had been several variations occurred in myostatin gene but further studies are required to correlate these variations to body weight gain and other important production parameters. For goat production in Indonesia, myostatin mutations cause double muscling that can be utilised for genetic improvement in goat breeding plan to produce a new breed with high quality meat.
Classifying cells with Scasat - a tool to analyse single-cell ATAC-seq

Motivation The assay for transposase-accessible chromatin using sequencing (ATAC-seq) reveals the landscape and principles of DNA regulatory mechanisms by identifying the accessible genome of mammalian cells. When done at single-cell resolution, it provides an insight into the cell-to-cell variability that emerges from identical DNA sequences by identifying the variability in the genomic location of open chromatin sites in each of the cells. Processing of single-cell ATAC-seq requires a number of steps and a simple pipeline to processes and analyse single-cell ATAC-seq is not yet available. Results This paper presents ScAsAT (single-cell ATAC-seq analysis tool), a complete pipeline to process scATAC-seq data with simple steps. The pipeline is developed in a Jupyter notebook environment that holds the executable code along with the necessary description and results. For the initial sequence processing steps, the pipeline uses a number of well-known tools which it executes from a python environment for each of the fastq files. While functions for the data analysis part are mostly written in R, it is robust, flexible, interactive and easy to extend. The pipeline was applied to a single-cell ATAC-seq dataset in order to identify different cell-types from a complex cell mixture. The results from Scasat showed that open chromatin location corresponding to potential regulatory elements can account for cellular heterogeneity and can identify regulatory regions that separates cells from a complex population. Availability The jupyter notebook with the complete pipeline applied to the dataset published with this paper are publicly available on the Github (https://github.com/ManchesterBioinference/Scasat). An additional notebook is also provided for analysis of a publicly available dataset. The fastq files are submitted at ArrayExpress database at EMBL-EBI (www.ebi.ac.uk/arrayexpress) under accession number E-MTAB-6116. Contact syed.murtuzabaker@manchester.ac.uk and magnus.rattray@manchester.ac.uk Supplementary information Supplementary data are available at bioRxiv online.
Pollen morphology of some Verbascum (Scrophulariaceae) taxa in Turkey.

Pollen morphology of six Verbascum (Scrophulariaceae) taxa belonging to five different groups in the genus [ V. georgicum (group E), V. nudatum var. nudatum (group F), V. cariense (group F), V. bithynicum (group H), V. pycnostachyum (group K), and V. lasianthum (group L)] was studied. Pollen slides were prepared according to the Woodhouse method and were examined with light-microscopy (LM) and Scanning Electron Microscopy (SEM). All studied pollen grains are generally monads, though tetrads (5 %) were observed in Verbascum nudatum var. nudatum . Pollen grains of all studied taxa were determined as isopolar and radially symmetric. In general terms, aperture types are trizonocolporate, but also trisyncolpate ( V. lasianthum 10 %, V. pycnostachum 1 %, and V. georgicum 4 %) and trizonocolpate ( V. cariense 10 %, V. bithynicum 10%, V. lasianthum 90%, V. pycnostachyum 9%, and V. georgicum 96 %) aperture types were observed. The shapes of the pollen grains were determined as prolate, subprolate, prolate-spheroidal and oblate-spheroidal. The sculpture was reticulate in all cases. The results of the study corroborate that morphological features, such as pollen shape, polar axis length (P), equatorial axis length (L), aperture type, surface ornamentation, muri thickness, and lumina shape, show differences which can be taken into consideration in the systematic discrimination within the groups, and also for discrimination of the groups in the genus.
A meta-analysis of Planarian: an animal model useful to understand the effect of magnetic field Planarian and magnetic field researches

The planarians research since the first description until nowadays has a broad spectrum of topics. The present paper deals on a meta-analysis which identified as a problem the lack of consolidate information and data analysis about the use of planarian as animal model, and specifically the use of magnetic field in regeneration experiments. To conduct the meta-analysis 1255 papers published since 1955 to 2017 were analysed, identifying the Stem cell biology and regeneration as the most published topic, with 276 papers, followed by molecular and cellular analyses (238), genetics (175), inter and transdisciplinary research (107), ecotoxicological evaluations (102), animal model (67), ecological and biological studies (56), magnetic field (57), developmental biology (32) and RNA regulation (31). Other statistics and metrics indicators were taken in to account like total of papers and distribution per year, distribution of paper by journals and selection of main journals according to the number of published papers, most cited papers, authors and countries and distribution of papers by countries. Finally, were analysed those papers with Planarians research using magnetic field, all of them published during the last three years. It was an evidence that this topic is becoming a trending with rising interest, being the most reported species to study the magnetic field effects Dugesia spp. and Girardia sp. Summary statement This work presents a meta-analysis which allows consolidating information and a better understanding of trends in Planarian researches, emphasizing in the use of magnetic field.
Northern Snakes Appear Much More Abundant in Old Fields than in Forests

Temperature is one of the most important factors regulating habitat selection by ectotherms. Through behavioural thermoregulation, reptiles maintain preferred body temperatures and thereby maximize fitness. At northern latitudes, small colubrids appear to use forest habitat rarely because of thermal constraints. In cool environments, open habitats such as old fields offer more favourable thermal conditions than forest. We studied two northern colubrid snakes, Red-bellied Snake ( Storeria occipitomaculata ) and Common Gartersnake ( Thamnophis sirtalis ), in Gatineau Park, Quebec, Canada, to test the hypothesis that small northern snakes are more abundant in open than in closed habitats because open habitats provide better opportunities for thermoregulation. Snakes were sampled using large arrays of tin and plywood coverboards. Snakes were indeed much more abundant in old fields than in forest, and fields offered more favourable thermal conditions. Most snakes were captured in spring and summer (May to August) when temperatures were highest. Storeria occipitomaculata preferred tin over plywood coverboards. We confirmed an apparent strong preference for open habitats in northern snakes.
Boron supply alleviates Al-induced inhibition of root elongation and physiological characteristics in rapeseed (Brassica napus L.)

ABSTRACT Aluminum (Al) toxicity is one of the major problems affecting crop production. Boron (B) is an essential micronutrient for higher plants. In the present study, we investigated the alleviation of Al-induced inhibition of root growth and physiological characteristics by B in rapeseed. The rapeseeds were grown in different Al concentrations (0 and 300 μM), and for every concentration, two B treatments (2.5 and 25 µM as H3BO3) were applied. The results showed that Al toxicity under low B drastically inhibited root growth. The supply of B improved root length, photosynthesis, root activity, total chlorophyll by 60.15%, 104.7%, 102%, and 106.3%, respectively under Al toxicity. This further resulted in improvement of peroxidase, catalase, and ascorbate peroxidase activities while decreasing malondialdehyde, H2O2, and Al contents in roots and leaves. It might be supposed that B alleviates Al toxicity by less mobilization of Al in plant parts and through improving antioxidant enzyme activities.
Additions to the Vascular Plant Flora of St. Lawrence Island, Alaska: New Records, Rare Species, and Phytogeographic Patterns

abstract St. Lawrence Island, in the northern Bering Sea, is an important biogeographic link between the flora of northeastern Asia and northwestern North America. A vascular plant inventory was conducted on St. Lawrence Island in the 1960s by Steven Young in which 250 taxa were documented. Since that time, very few collections have been made on the island. We conducted a vascular plant survey to improve our understanding of baseline floristics and identify populations of species of conservation concern. Of the 166 taxa we collected in late July 2012, a number of collections represent new or significant finds. Eritrichium villosum, a Siberian taxon not previously recognized from North America, was collected on north-central St. Lawrence Island. This taxon, however, had been collected under a different name by Young in the late 1960s. Iris setosa subsp. setosa is a new record for the island. Iris setosa, although common along the eastern Bering Sea coast from Kotzebue Sound south through the Aleutians, appears to be very restricted on St. Lawrence Island and has only been noted by residents in recent years. Erigeron humilis and Moehringia lateriflora are also new records for the island. New populations were located of the globally rare species: Cardamine blaisdellii, Claytonia arctica, Micranthes nudicaulis subsp. nudicaulis, Papaver gorodkovii, Potentilla fragiformis, Ranunculus camissonis, and R. turneri subsp. turneri. We have included an annotated species list of 281 taxa, illustrated under-sampled regions of the island, and described the biogeographic affinities of the flora to other high latitude regions. The island's flora has strong biogeographic affinities to eastern Beringia (Alaska and western Yukon), particularly to the Seward Peninsula and less strongly to the Russian Far East. Numerous circumpolar arctic and alpine species were also present, with a minority of East-Asian species known from very few populations in extreme western Alaska.
Species richness and composition of shrub-encroached grasslands in relation to environmental factors in northern China

Shrub encroachment has taken place in many of China’s northern grasslands. This study attempts to answer the following questions: which plant communities are present in these shrub-encroached grasslands (SEGs)? What are the species richness and composition of these communities? Which environmental factors determine the spatial distribution thereof? We investigated the community characteristics of 255 SEG plots with a size of 20 m × 20 m at 69 locations across grasslands in northern China. In each plot, paired 1-m² quadrats were established within shrub patches and the neighbouring grassy matrix to record herb species composition. The quantitative characteristics (abundance, coverage and height) of herbs were measured in 0.25-m² subquadrats, and soil samples were collected in the quadrats. Two-way indicator species analysis (TWINSPAN), detrended canonical analysis (DCA) and canonical correspondence analysis (CCA) were used for community clustering and ordination. The DCA and TWINSPAN results suggested that the SEGs in northern China can be divided into six community types: Potentilla fruticosa + Carex atrofusca, Spiraea hypericifolia + Festuca ovina, Caragana acanthophylla + Stipa sareptana, Caragana microphylla + Leymus chinensis, Caragana microphylla + Stipa klemenzii and Caragana tibetica + Cleistogenes songorica. At a regional scale, climate and soil nutrients controlled the spatial patterns of species richness and community composition of the SEGs in northern China. Temperature exerted a negative impact, whereas precipitation and nutrients had positive effects on species richness. Among the environmental factors used, climate was the major controller of the variations in community structure. These results provide new insights into the community composition of SEGs in China and enrich the global dataset of SEGs.
Summary of Philippine Eagle reproductive success, 1978-98

The Philippine Eagle (Pithecophagajefferyi) is one of the rarest eagles in the world. Its present status has always been regarded as critically endangered. Previous estimates of the Philippine Eagle population have been speculative (Alvarez 1970, Gonzales 1971, Rabor 1971). The most recent estimate suggests that the total population consists of between 300-500 individuals (Kennedy 1977, 1985). Philippine Eagles lay a single egg and have a 2-yr cycle between successive breedings when pairs breed successfully, but in cases when breeding attempts fail, adults breed the following year. Since work began in earnest on this species, a large amount of information on nesting successes and failures in Mindanao have been amassed.
Tree Seedling Survival Depends on Canopy Age, Cover and Initial Composition: Trade-offs in Forest Restoration Enrichment Planting

Recruitment of late-successional, shade-tolerant trees into early-successional plantings is a crucial step in long-term forest restoration, especially in urban areas where seed dispersal can be limiting. Enrichment plantings are an important strategy for diversifying the developing understory, but we lack clear guidance about when shade-tolerant species can be successfully introduced or how the initial canopy composition constrains the success of enrichment plantings. To address this knowledge gap, we conducted an experiment in a forest restoration project in a warm temperate forest region in New Zealand. We planted seedlings of six functionally-diverse species in restored sites that ranged from two to seven years since the initial restoration planting and analyzed 2-year seedling survival and growth rates as a function of planting age, canopy cover, and canopy composition. The canopy height of initial plantings grew at a linear rate of 1 meter per year. Within five years, initial plantings reached 80% canopy closure, a leaf area index of 5 m2 m−2, and a corresponding reduction of pasture weed cover to < 10%. Seedling survival was highest beneath young canopies dominated by tea tree (Myrtaceae) but also in older canopies with a more diverse composition. Our results show that the rate of canopy development is highly predictable despite differences in initial planting composition, but that enrichment planting seedling survival depends on both canopy age and composition. To enhance survival of enrichment plantings, we recommend using a balanced mixture of tea tree and broadleaved trees in the original planting to optimize seedling survival to facilitate long-term forest restoration.
Occurrence of non-native fish species in a Neotropical river under the influence of aquaculture activities

The introduction of non-native species is one of the greatest global changes and is a substantial threat to continental fish fauna. This study aimed to evaluate the composition and structure of the fish assemblage of the Azul River, a tributary along the left margin of the Piquiri River basin, to determine the occurrence, abundance and spatial distribution of non-native fish species. Sampling was carried out from February to November 2014 at three sites along the river using of electric fishing equipment. Thirty-two fish species belonging to 20 genera, 11 families and five orders were collected. Eight non-native fish species were recorded, and Gymnotus inaequilabiatus and Oreochromis niloticus were listed among the five most abundant species in the Azul River. The fish fauna followed a distribution pattern expected for the Neotropical region, with a predominance of Characiformes and Siluriformes. However, the high representativeness of the abundance of the non-native species of the Gymnotiformes and Perciformes orders highlights the potential negative impacts on the structure of the fish assemblages of the Azul River due to species introductions.