Miracle-dz/UniFAR-FTUs huggingface dataset:
Study of the Cd complexation mechanism by glutathione in Rhizobium leguminosarum

The symbiotic association of leguminous plants and rhizobia also has a crucial impact on the nitrogen cycle: estimates are that rhizobial symbioses, with a number greater than 100 important agronomical legumes, contribute nearly half to the annual quantity of nitrogen fixed biologically entering soil ecosystems (Somasegaran and Hoben, 1994; Zahran, 1999). Nevertheless, the permanent increased of metal pollution in agriculture soils, due to the current use of fertilizers and industrial and domestic sludge, is becoming one of the most troublesome environmental problems (Alloway, 1995a; Giller et al., 1998; Permina et al., 2006; Thorsen et al., 2009; Wani et al., 2008), has a negative impact in rhizobia persistence in agricultural soils and its ability to form nitrogen-fixing nodules (Broos et al., 2005; Wani et al., 2008; Zhengwei et al., 2005). So, the study of the tolerance mechanisms of soil bacteria to metals arises as a research area with great importance. In this thesis it was intended to draw attention to the tolerance to Cd of Rhizobium leguminosarum, a specific soil bacteria that establish symbiotic associations with legumes. The present study focused on a particular strategy that Rhizobium leguminosarum possess to tolerate Cd: the intracellular chelation of Cd by the tripetide GSH. Thus the elucidation of the role of GSH as a metal chelating agent in bacteria tolerance to Cd was considered to be the main aim of this work. Higher intracellular Cd and GSH levels were observed in the tolerant strain as it had already been demonstrated by others authors (Figueira et al., 2005; Lima et al., 2006). It was also demonstrated that Rhizobium leguminosarum tolerance to Cd was dependent on the higher efficiency of the chelation mechanism exhibited by the tolerant strain. This mechanism was activated at the beginning of the lag phase (12 h of growth). As the accumulation of GSH-Cd complexes may inhibit intracellular Cd uptake (Gomes et al., 2002), which was not observed in the tolerant strain, the GSHCd complexes were suggested to be transported into the periplasmic space. The results point out this hypothesis as the most viable as high levels of GSH and Cd were found in the periplasmic space but only a small percentage of GSH-Cd complexes were quantified. It was also established that the chelation mechanism occurred in the cytoplasm, and its efficiency appeared to be dependent on the enzymatic activity of a specific GST isoform. So, the ability of the tolerant strain to induce GSH synthesis under Cd exposure and, simultaneously, to increment the activity of a specific GST was point out as the main reasons behind the differences the tolerance to Cd observed between the two strains.
Examining the linguistic and multicultural practices of refugee children in a primary school in Cyprus: A sociocultural approach to language learning

As a result of the 2015 refugee crisis, classrooms in the Republic of Cyprus are now becoming more linguistically and culturally diverse. Cyprus, as one of the neighbouring host countries, should be working on developing the appropriate conditions for the educational support of children with refugee trajectories. Following a sociocultural approach to second language learning, this ethnographic study is the first to provide empirical evidence of the linguistic and multicultural practices that a group of refugee primary school children develop in order to learn the target language (Greek) and also to become members of their learning community. The data come from an in-depth analysis of spoken classroom interactions and semi-structured interviews following a discourse analysis approach. The study suggests that multilingual research in education settings presupposes reflecting on participants’ multilingual complexities and that is why a multilingual transcription and presentation of spoken discourse is provided. Multimodal artefacts were also examined and provided valuable insights for children’s learning. The findings suggest that children experienced their languages coming together holistically and used them in a flexible way that mediated their learning and communicative interactions. The linguistic practices derived from this juxtaposition of languages were code-switching, translating and repeating. These linguistic practices were seen as scaffolding tools that enhanced children’s learning of Standard Modern Greek, as the interactional data provide ample evidence of children’s metalinguistic awareness. This study also provides examples of good teaching practices and considers that, when classrooms are seen as sites of multilingualism, refugee children’s linguistic and cultural backgrounds become visible tools and have positive learning outcomes not only for the minority but also for the majority of learners. I argue that the understanding of the Communities of Practices concept goes beyond assimilationist perspectives on learning as the data suggest that this flexible use of linguistic and multicultural resources enabled the participants’ roles to be reversed. I show that refugee children were not only expected to join in with the school’s learning practices, but their linguistic and cultural experiences were actively implemented in the learning process. Thus, in some cases, the majority of children also needed to claim their legitimacy during teaching. The study considers pedagogical implications and emphasises the need for a better understanding of issues of multilingual education for policy makers, researchers and educators in Cyprus and beyond to recognise the rich value of children’s available linguistic repertoires. This recognition will not only provide opportunities for language learning but will also add to the multilingual discourse that aims for social justice in education and wider society.
Identification and Validation of Stable Reference Genes for Gene Expression Analysis in Sword-leaf Dogbane Using Quantitative Reverse Transcriptase Polymerase Chain Reaction

Sword-leaf dogbane (Apocynum venetum) is a traditional Chinese herb with increasingly recognized potential to enhance health, but no study of stable reference genes in this herb has been reported. Based on a homologous cloning strategy, we have successfully cloned five candidate reference genes from sword-leaf dogbane: glyceraldehyde-3-phosphate dehydrogenase (AvGAPDH), beta tubulin (AvbTUB), polyubiquitin (AvUBQ), elongation factor 1-alpha (AvEF1α), and actin (AvACTIN). Three distinct algorithms, geNorm, NormFinder, and BestKeeper, were used to estimate the expression stability of candidate reference primer pairs. We found that AvACTIN-2 and AvACTIN-3 presented the highest stability of expression in different tissue samples, and AvGAPDH-2 was most stable under salinity stress. In addition, we illustrated the application of these new reference genes by assaying the expression levels of two hyperoside biosynthesis terminal enzyme genes, flavonoid 3′-hydroxylase (F3′H) and flavonol synthase (FLS), under salinity stress. Our study is the first to report stable expression of internal reference genes in sword-leaf dogbane in multiple experimental sample sets.
Breeding management of mares in late reproductive age considering improvement of welfare. A review

Mares retain the ability to produce offspring for a relatively long period of time. The average horse lifespan is 25–30 years and it is estimated that mare can give birth to a healthy foal till the age of 20 years, or even later. Nevertheless, fertility in older mares decreases significantly every year and so the possibility of obtaining offspring is an individual feature (Scoggin, 2015). When comparing two mares with different reproductive statuses at the same age (over 15 years old) it is estimated that mare which foaled in the previous breeding season will have a greater chance to get pregnant than mare with fertilization or gestation problems. It cannot be assumed that mare which has never given birth will be fertile at an older age (Bosh et al., 2009). Therefore, breeding management of older mares is difficult and requires investment of time, money, and a lot of effort (Byszewski and Gromnicka, 1994).
Distribution of GnRH and Kisspeptin Immunoreactivity in the Female Llama Hypothalamus

Llamas are induced non-reflex ovulators, which ovulate in response to the hormonal stimulus of the male protein beta-nerve growth factor (β-NGF) that is present in the seminal plasma; this response is dependent on the preovulatory gonadotrophin-releasing hormone (GnRH) release from the hypothalamus. GnRH neurones are vital for reproduction, as these provide the input that controls the release of luteinizing hormone (LH) and follicle-stimulating hormone (FSH) from the pituitary gland. However, in spontaneous ovulators, the activity of GnRH cells is regulated by kisspeptin neurones that relay the oestrogen signal arising from the periphery. Here, we investigated the organisation of GnRH and kisspeptin systems in the hypothalamus of receptive adult female llamas. We found that GnRH cells exhibiting different shapes were distributed throughout the ventral forebrain and some of these were located in proximity to blood vessels; sections of the mediobasal hypothalamus (MBH) displayed the highest number of cells. GnRH fibres were observed in both the organum vasculosum laminae terminalis (OVLT) and median eminence (ME). We also detected abundant kisspeptin fibres in the MBH and ME; kisspeptin cells were found in the arcuate nucleus (ARC), but not in rostral areas of the hypothalamus. Quantitative analysis of GnRH and kisspeptin fibres in the ME revealed a higher innervation density of kisspeptin than of GnRH fibres. The physiological significance of the anatomical findings reported here for the ovulatory mechanism in llamas is still to be determined.
Triticum polonicum L. as potential source material for the biofortification of wheat with essential micronutrients

Abstract The grain of modern wheat cultivars has a significantly lower mineral content, including the content of copper, iron, magnesium, manganese, phosphorous, selenium and zinc. For this reason cereal breeders, are constantly searching for new genetic sources of minerals that are essential in human nutrition. Triticum polonicum, which is grown on a small scale in Spain, southern Italy, Algeria, Ethiopia and warm regions of Asia, deserves special attention in this context. The micronutrient and macronutrient content of T. polonicum versus T. durum and T. aestivum was compared in this study. Polish wheat grain was characterized by the significantly highest content of phosphorus (4.55 g/kg), sulphur (1.82 g/kg), magnesium (1.42 g/kg), zinc (49.5 mg/kg), iron (39.1 mg/kg) and boron (0.56 mg/kg) as well as a low content of aluminium (only 1.04 mg/kg). The macronutrient profile of most T. polonicum lines differed completely from that of common wheat and durum wheat. The principal component analysis supported discrimination of seven Polish wheat lines with a particularly beneficial micronutrient profile (P2, P3, P5, P7, P9, P22 and P25). These lines were characterized by the highest content of copper, iron and zinc, as well as the lowest concentrations of strontium, aluminium and barium which are undesirable in food products. The above lines can be potentially applied as source materials for breeding new wheat varieties. The results of this study indicate that Polish wheat could be used in genetic biofortification of durum wheat and common wheat.
“Nose-metrics” of wild southern elephant seal (Mirounga leonina) males using image analysis and geometric morphometrics

The elephant seal (genus Mirounga) proboscis has been a textbook example of an exaggerated secondary sexual trait from the very beginning of evolutionary biology (Darwin, 1871). In both species of elephant seal (the southern, M. leonina (Linneaus, 1758), and the northern, M. angustirostris Gill, 1866) males develop an elongation of the nostrils that results in a true proboscis in breeding males. The sexual dimorphism in the nostrils becomes evident at age three to four (Laws, 1953), but the proboscis shows a significant enlargement and shape change during the postpubertal growth spurt showed by males between sexual maturity and adulthood (McLaren, 1993). Although the basic anatomy and development of the elephant seal proboscis are well known (Laws, 1953), a demonstration of its function(s) remains elusive. We previously showed that both body size and age have an independent effect on the proboscis size that is apparently under a positive directional phenotypic selection (Sanvito, Galimberti, & Miller, 2007a). In fact, the proboscis development is a rather accurate morphological cue of male age, permitting the assessment Received: 7 September 2018 | Revised: 18 December 2018 | Accepted: 6 January 2019 DOI: 10.1111/jzs.12276
Age- and Sex-Specific Standard Scores for the Reading the Mind in the Eyes Test

The reliable, valid and economic assessment of social cognition is more relevant than ever in the field of clinical psychology. Theory of Mind is one of the most important socio-cognitive abilities but standardized assessment instruments for adults are rare. The Reading the Mind in the Eyes Test (RMET) is well-established and captures the ability to identify mental states from gaze. Here, we computed standard scores for the German version of the RMET derived from a large, community-dwelling sample of healthy adults (20–79 years). The standardization sample contains 966 healthy adult individuals of the population-based Leipzig Research Center for Civilization Diseases (LIFE) study. Before standardization, weighting factors were applied to match the current sample with distribution characteristics of the German population regarding age, sex, and education. RMET scores were translated into percentage ranks for men and women of five age groups (20–29, 30–39, 40–49, 50–59, 60+ years). Age-specific percentage ranks are provided for men and women. Independent of age, men present a larger variance in test scores compared to women. Within the specific age groups, women score higher and their scoring range is less variable. With increasing age, the scoring variance increases in both men and women. This is the first study providing age- and sex-specific RMET standard scores. Data was weighted to match German population characteristics, enabling the application of standard scores across German-speaking areas. Our results contribute to the standardized assessment of socio-cognitive abilities in clinical diagnostics.
Diversität von aphidophagen Insekten im Bayerischen Wald. Welchen Beitrag leistet die Tanne im Vergleich zur Fichte

Diversity of aphidophagous insects in the Bavarian Forest – what contributions does White fir make in comparison to spruce? In the present study the impact of White fir (Abies alba) as compared to spruce (Picea abies) on the diversity of aphidophagous insects was analysed. To this end, tree crown communities of five trees each were sampled by flight interception traps in the Bavarian Forest National Park in the year 2004. Altogether 386 specimens of 31 aphidophagous species, including: Heteroptera, Neuropterida, and Coccinellidae (Coleoptera) were captured on the two coniferous species. Number of specimens and species as well as diversity (Fisher’s alpha) of aphidophagous insects was significantly higher on White fir as compared to spruce. With the exception of three species, all species where found in higher numbers in tree crowns of White fir. The favourable microclimatic conditions of the more open crown structure of White fir compared to spruce as well as the quality and quantity of aphid resource availability are discussed as possible abiotic and biotic factors affecting the observed patterns of aphidophagous communities.
Effects of dietary mannan oligosaccharides on growth, body composition, and intestine and liver histology of rainbow trout, Oncorhynchus mykiss

This study investigated the effects of dietary mannan oligosaccharides (MOS) on growth, body composition, and small intestine and liver histology of rainbow trout (Oncorhynchus mykiss Walbaum). Experimental diets were supplemented with 0 (control), 1.5, 3.0, or 4.5 g MOS per kg commercial trout feed and randomly assigned to treatment groups. Enhanced growth performance was generally observed in fish fed the diet supplemented with 1.5‰ MOS. Villi of fish fed diets supplemented with 1.5 or 3.0‰ MOS were longer than those of fish fed 4.5‰ or no dietary MOS (p<0.05). Protein contents increased as the rate of MOS increased (p<0.05). There were no significant differences in feed conversion ratio, protein efficiency ratio, or hepatosomatic index (p>0.05) and MOS had no detrimental effects on the intestine. * Corresponding author. Tel. : +90-326-2455845 ext. 1302, fax: +90-326-2455817, e-mail: agenc@mku.edu. tr
The Effect of Media Professionalization on Cognitive Neurodynamics During Audiovisual Cuts

Experts apply their experience to the proper development of their routine activities. Their acquired expertise or professionalization is expected to help in the development of those recurring tasks. Media professionals spend their daily work watching narrative contents on screens, so learning how they manage visual perception of those contents could be of interest in an increasingly audiovisual society. Media works require not only the understanding of the storytelling, but also the decoding of the formal rules and presentations. We recorded electroencephalographic (EEG) signals from 36 participants (18 media professionals and 18 non-media professionals) while they were watching audiovisual contents, and compared their eyeblink rate and their brain activity and connectivity. We found that media professionals decreased their blink rate after the cuts, suggesting that they can better manage the loss of visual information that blinks entail by sparing them when new visual information is being presented. Cuts triggered similar activation of basic brain processing in the visual cortex of the two groups, but different processing in medial and frontal cortical areas, where media professionals showed a lower activity. Effective brain connectivity occurred in a more organized way in media professionals–possibly due to a better communication between cortical areas that are coordinated for decoding new visual content after cuts.
A taxonomic study of the genus Fimbristylis Vahl (Cyperaceae) in Korea

A morphological study of Korean Fimbristylis was conducted in order to clarify the taxonomical position and scientific names among species. It was determined that the anther size and style length are important characteristics for the species-level identification of Fimbristylis. It was confirmed that Fimbristylis ovata (Burm.f.) J. Kern, which is recorded in the literature but which has no sampling specimens in Korea, grows on the grassland on Marado Island. According to this study, the genus Fimbristylis in Korea is classified into a total of 21 taxa, including four sections, nineteen species, and two varieties.
Bivalve mollusks as tools for monitoring antibiotic resistance in the marine environment

Antibiotic resistance (AR) is a major global health concern, especially in clinical and veterinary settings. Environmental niches, including the aquatic environment, serve as a source of and/or a dissemination route for antibiotic resistance genes (ARGs) and resistant bacteria. Bivalves are suspension feeders that actively filter, retain and concentrates particles from their surrounding water, including free living or particlebound bacteria. The main aim of this thesis was to evaluate bivalve mollusks as tools for monitoring Escherichia coli and associated AR, in the marine environment in Norway. Sampling of bivalves were conducted from several sites along the Norwegian coast and the samples were examined for the presence of E. coli, according to the most probable number (MPN) EU reference method. More than half (61%) of the samples were positive for E. coli, and a selection of 200 E. coli isolates were further identified by matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDITOF MS). The majority (90%) were confirmed as E. coli, while the remaining isolates (10%) were identified as other species mostly belonging to the Enterobacteriaceae family. The isolates were antibiotic susceptibility tested (AST) using the disk diffusion method recommended by the European Committee on Antimicrobial Susceptibility Testing (EUCAST). Seventy-five bacterial isolates (38%) showed phenotypic resistance to at least one antibiotic, while multidrug-resistance was observed in eight isolates (4%). Based on resistance phenotypes, selected E. coli isolates were subjected to whole-genome sequencing (WGS). Two isolates revealed to carry CTX-M-type extended-spectrum β-lactamases (ESBLs). Accordingly, the two E. coli isolates were subjected to long-read sequencing, and a hybrid de novo assembly using long-reads and short-reads to obtain complete and closed genome sequences. One isolate harbored four identical chromosomal copies of the blaCTX-M-14 gene, while the other isolate carried the blaCTX-M-15 gene on a conjugative plasmid. Another aim of this thesis was to generate knowledge regarding the prevalence of antibiotic and heavy metal resistance, and associated resistance genes, among
LEMMI: A Live Evaluation of Computational Methods for Metagenome Investigation

Metagenomics promotes our understanding of microbial communities. The methodology profoundly relies on computational interpretation of the sequencing reads in the light of our evolving understanding of microbial taxonomy. The fast growing volumes of such readouts and the reference databases prompted development of a multitude of computational procedures over recent years. Only a subset of these has appeared in independent benchmarking assessments, which are also quickly becoming obsolete. This is obscuring an informed choice of a method for biologists as well as the impact of certain innovations for method developers. Here we present the LEMMI benchmarking platform (https://lemmi.ezlab.org) enabling the continuous integration of taxonomic profilers and binners, their assessment on a variety of data, as well as dynamic presentation of their ranking according to alternative objectives of required analyses or technical limitations. The platform is container-based and exploits the ability of many methods to construct a reference database on demand to compare them under highly controlled conditions and with identical inputs. Curated references can also be provided by method developers, enabling the advantages of particular databases to be highlighted. LEMMI creates a link between method developers and their users. It provides automated and unbiased benchmarking that are valuable to both. Moreover, the standardised and easy-to-use containers created by us or developers can be downloaded by metagenomic tool users, who will get exactly the same software as it appears in evaluation.
Understanding US Export Dynamics: Does Modelling the Extensive Margin of Exports Help?

This paper evaluates whether recent advances in modelling the extensive margin of exports contribute to our understanding of export fluctuations over the business cycle. Using US and euro-area data, we estimate a general equilibrium model in which the extensive margin of exports varies over the business cycle. A comparison of its performance to two similar models that differ in their modelling of the extensive margin of exports shows that, while recent advances in modelling the extensive margin of trade help replicate exports dynamics, this is not the result of a good fit to the observed extensive margin of exports: the model-implied extensive margin of exports varies considerably more than the data suggests.