Miracle-dz/UniFAR-FTUs huggingface dataset:
Growth response of different tree species (oaks, beech and pine) from SE Europe to precipitation over time

Changing climatic conditions can have various consequences for forest ecosystems, from increasing frequencies of forest fires, ice and windstorm events to pathogen outbreaks and mass mortalities. The Standardized Precipitation Index (SPI) was chosen for the evaluation of drought impact on the radial growth of trees after extensive preliminary testing of various calculated monthly climate parameters from the CARPATCLIM database. SPI was calculated for periods between 3 and 36 months for different sites (lowland and mountainous parts of Serbia, Southeast Europe), from which Quercus robur, Q. cerris, Fagus sylvatica and Pinus sylvestris samples were acquired. Bootstrapped Pearson’s correlations between SPI monthly indices and radial growth of tree species were calculated. We found that 12-month SPI for summer months may be a good predictor of positive and negative growth of different species at different sites. The strongest positive correlations for five of six tree-ring width chronologies were between 12-month June and 14-month September SPI, which implies that high growth rates can be expected when the autumn of the previous year, and winter, spring and summer of the current year, are well supplied with precipitation, and vice versa (low precipitation in given period/low growth rates).
Effect of applying a biostimulant containing seaweed and amino acids on the content of fiber fractions in three soybean cultivars

The experiment was conducted in the years 2014-2016 with the aim to evaluate the influence of a biostimulant based on seaweed and amino acids on the content of neutral and acid detergent fiber, lignin, cellulose and hemicellulose in three cultivars of soybean. In the vegetative season, 0.7% and 1.0% solutions of the biostimulant were used in single and double spraying. Based on the determined fiber fraction contents it was evaluated whether treating soybean with the biostimulant may enhance the quality of forages obtained from it. It was found that the level of fiber fractions and contents of hemicellulose and cellulose were influenced by biostimulant application. Differences in the content of fiber fractions resulted from the number of biostimulant doses and its concentration. Mavka cultivar treated with Fylloton was characterized by the highest mean content of fiber fraction. Evaluation of the forage quality indexes demonstrated that biostimulant use caused their reduction, and the highest values were found for Annushka cultivar.
Searching for Rewards Like a Child Means Less Generalization and More Directed Exploration

How do children and adults differ in their search for rewards? We considered three different hypotheses that attribute developmental differences to (a) children’s increased random sampling, (b) more directed exploration toward uncertain options, or (c) narrower generalization. Using a search task in which noisy rewards were spatially correlated on a grid, we compared the ability of 55 younger children (ages 7 and 8 years), 55 older children (ages 9–11 years), and 50 adults (ages 19–55 years) to successfully generalize about unobserved outcomes and balance the exploration–exploitation dilemma. Our results show that children explore more eagerly than adults but obtain lower rewards. We built a predictive model of search to disentangle the unique contributions of the three hypotheses of developmental differences and found robust and recoverable parameter estimates indicating that children generalize less and rely on directed exploration more than adults. We did not, however, find reliable differences in terms of random sampling.
MXP: Modular eXpandable framework for building bioinformatics Pipelines

Background Pipelines are a natural tool in bioinformatics applications. Virtually any meaningful processing of biological data involves the execution of multiple software tools, and this execution must be arranged in a coherent manner. Many tools for the building of pipelines were developed over time and used to facilitate work with increasing volume of bioinformatics data. Here we present a flexible and expandable framework for building pipelines, MXP, which we hope will find its own niche in bioinformatics applications. Results We developed MXP and tested it on various tasks in our organization, primarily for building pipelines for GWAS (Genome-Wide Association Studies) and post-GWAS analysis. It was proven to be sufficiently flexible and useful. Conclusions MXP implements a number of novel features which, from our point of view, make it to be more suitable and more convenient for building bioinformatics pipelines.
Agave americana and Furcraea andina: Key Species to Andean Cultures in Ecuador

<p><strong>Background:</strong> The rich Agaveae-based culture that exists in the Ecuadorian Andes is little known. Wild and cultivated rosettes of <em>Agave americana </em>and <em>Furcraea andina </em>coexist in arid Andean landscapes. <em>A. americana </em>is considered an introduced species to Ecuador. </p><p><strong>Questions:</strong> What are Agaveae use patterns and cultural importance in the Ecuadorian Andes? Is the ethnobotanical significance of <em>Agave</em> in Ecuador comparable to that in Mexico and other Andean countries? </p><p><strong>Species studied:</strong> <em>Agave americana, Furcraea andina</em></p><p><strong>Study site, dates:</strong> Ecuadorian Andes, 2016. </p><p><strong>Methods:</strong> Semi-structured interviews to Agaveae users (37) and a review of literature on ethnobotanical research conducted in Ecuador since the 18<sup>th</sup> century. </p><p><strong>Results:</strong><em> A. americana </em>is more diversely and widely used than <em>F. andina </em>(124 <em>vs</em> 36 uses and 548 <em>vs</em> 140 use records, respectively). The versatility of <em>A. americana</em> lies in its <em>mishki </em>(sap extracted from its heart) which has multiple medicinal, edible and ceremonial applications. We found significant variation of its use patterns throughout the region. The main use of <em>F. andina</em> as a source of fiber is disappearing. Most productive initiatives involve <em>A. americana</em> (92 %, n = 53). </p><p><strong>Conclusion:</strong> The importance of <em>A. americana </em>in the Ecuadorian Andes is comparable to that of agaves in Mexico, but not to its importance in other Andean countries where it is used sporadically. It<em> </em>can be considered a cultural keystone species. <em>F. andina</em> could have had that role in the past. <em>A. americana</em> versatility and availability through cultivation could explain why, irrespective of whether or not it is introduced, it remains an icon of identity and cultural cohesion in the Ecuadorian Andes. </p>
Tourist and Local Resident Preferences for the Northern Yellow-Cheeked Gibbon (Nomascus annamensis) Conservation Program in the Bach Ma National Park, Central Vietnam

Successful biodiversity conservation is closely linked to the support received from society. Therefore, a better understanding of public preferences for conservation activities facilitates successful conservation efforts. The objective of the study is to determine the preferences of tourists and local residents regarding the proposed conservation program of the northern yellow-cheeked gibbon (Nomascus annamensis) and its economic value in the Bach Ma National Park, as well as to examine the factors that determine their willingness to pay (WTP) for the gibbon conservation. The WTP was estimated with the dichotomous choice contingent valuation method, and data were collected using face-to-face interviews with 710 participations, including 352 Vietnamese tourists and 358 local residents. The logistic regression model was applied to predict the probability of WTP for the program. A number of factors were found to be significant predictors of WTP that included bid level, visit, awareness, knowledge, distance, family size, and education. The mean WTP amount was estimated at about $US3.81/tourist and $US 2.93/household for one-time support of the gibbon conservation program. A significant difference was also found between the tourists and local residents in terms of the estimated WTP. Our findings suggest that there is a strong public support within Vietnamese society for the conservation of gibbons, which should be considered in the design of social policies for biodiversity conservation and natural resource management.
Assessment or Evaluation of Genetic Diversity among 66 Cultivars of Chickpea (Cicer arietinum L.) of Indian Origin Using SSR Markers

Chickpea (Cicer arietinum L.) is the third most important winter season [diploid plant (2n = 2x = 16)] self pollinated with an estimated haploid genome size of 738 Mb pulse crop (Varshney et al., 2013). Two main types of cultivated chickpea are Kabuli (white seeded) and desi (brown seeded), representing two diverse gene pools. It is cultivated in about 44 countries and regions including South Europe, Ethiopia, North Africa, Australia, and Central-West Asia, with India being the largest producer (FAO, 2013; ICRISAT, 2013). It contains high nutritive value and cheap source of protein in developing countries and play important role to improving land fertility in dry rainfed area International Journal of Current Microbiology and Applied Sciences ISSN: 2319-7706 Volume 7 Number 02 (2018) Journal homepage: http://www.ijcmas. com
Study of the DiI method accuracy on the example of the afferent connections of the Habenula in P6 F1-C57Bl6 / CBA mice

DiI (1,1’-dioctadecyl-3,3,3’3’-tetramethylindocarbocyanine perchlorate) is a lipophilic carbocyanine stain diffusing in the plasma membrane and coloring the cell as a whole. The DiI injection method is an alternative to stereotaxis in the study of the neural connections of higher vertebrates. However, despite a number of studies performed to identify the neural connections of embryos and fetuses of different animals, the question of the accuracy of the DiI method remains open. The main goal of this study is to investigate the accuracy of the DiI method by examining the afferent Habenula (Hb) connections in P6 F1-C57Bl6/CBA mice. Hb is a paired structure of the intermediate brain, consisting of two nuclei - the medial (MHb) and lateral (LHb). At P6, the main Hb tracts are already formed but not yet myelinated. To estimate the accuracy of the method, two groups of cases with different types of application on different Hb nuclei were compared: bilateral applications of several DiI crystals - group 1 (26 applications); Unilateral applications of a single crystal DiI - control group 2 (7 applications). It is known that MHb is strictly innervated by Triangular septal nuclei (TS) and Septofimbrial septal nuclei (SFi); LHb is strictly innervated by the Lateral preopteic area (LPA). Any deviation from this scheme is a false positive result. When applying the marker to different Hb nuclei in group 1, the number of successful cases without deviations was -0%; in group 2 (control) - 28.57%. Unilateral applications of a single DiI crystal are more accurate. However, there are still a number of unavoidable problems, such as the fragmentation or loss of a single DiI crystal during application and the super-strong diffusion of the marker at the application site. Given this, the overall accuracy of the DiI injection method, even in the form of a single crystal, remains low.
New species of subterranean and endogean terrestrial isopods (Crustacea, Oniscidea) from Tuscany (central Italy)

ABSTRACT Seven new species of subterranean and endogean terrestrial isopods from Tuscany (central Italy) are described in the families Trichoniscidae Sars, 1899 (Leucocyphoniscus pisanus n. sp., Moserius gruberae n. sp., Moserius talamonensis n. sp.) and Armadillidiidae Brandt, 1833 (Typhlarmadillidium occidentale n. sp., Paraschizidium ferrarai n. sp., Trogleluma pilosa n. sp. and Alloschizidium labronicum n. sp.). The diagnostic characters and the affinities of the new species are discussed.
A plug-and-play system for enzyme production at commercially viable levels in fed-batch cultures of Escherichia coli BL21 (DE3)

Commercial exploitation of enzymes in biotransformation necessitates a robust method for enzyme production that yields high enzyme titer. Nitrilases are a family of hydrolases that can transform nitriles to enantiopure carboxylic acids, which are important pharmaceutical intermediates. Here, we report a fed-batch method that uses a defined medium and involves growth under carbon limiting conditions using DO-stat feeding approach combined with an optimized post-induction strategy, yielding high cell densities and maximum levels of active and soluble enzyme. This strategy affords strict control of nutrient feeding and growth rates, and ensures sustained protein synthesis over a longer period. The method was optimized for highest titer of nitrilase reported so far (247 kU/l) using recombinant E. coli expressing the Alcaligenes sp. ECU0401 nitrilase. The fed-batch protocol presented here can also be employed as template to produce a wide variety of enzymes with minimal modification, as demonstrated for alcohol dehydrogenase and formate dehydrogenase.
Nutritional requirement of digestible lysine for brown-egg laying hens in the 2nd production cycle

ABSTRACT - With the objective of determining the nutritional requirement of digestible lysine for brown-egg layinghens from 79 to 95 weeks of age, an experiment was carried out using 180 commercial Lohmann Brown laying hens, distribuitedin five treatments (0.555; 0.605; 0.655; 0.705 and 0.755%), six replications and six birds birds/replication. The feed intakeand the food conversion per dozen of eggs were not influenced by the lysine levels. There was a positive linear effect on lysineintake and quadratic on feed conversion for egg mass. Egg mass and weight presented a quadratic response to the lysine levels.The egg component percentage and the internal quality were not influenced by the levels of lysine, except for the yolk index,which showed quadratic effect. The digestible lysine requirement for brown-egg laying hens on the 2 nd production cycle ofproduction was 0.681% lysine, that corresponds to a daily intake of 783 mg digestible lysine.Key Words: amino acids, egg production, egg quality
Characterization of high anthocyanin-producing tetraploid potato cultivars selected for breeding using morphological traits and microsatellite markers

Purple- and red-fleshed potato cultivars constitute a great source of phenolic compounds, which may promote human health. Since the characterization of potato germplasm is a key step during the breeding process, the classification of high anthocyanin-producing tetraploid genotypes may facilitate the incorporation of phenolic-related traits in a potato breeding programme. A set of 18 high anthocyanin-producing underutilized tetraploid cultivars, which have been previously classified in terms of phytochemical content, have been characterized by both microsatellite markers (simple sequence repeat, SSR) and morphological descriptors. A wide genetic variability was found using 11 highly discriminatory SSR markers. The collection also displayed a large amount of variation for most morphological traits. The neighbour-joining trees defined by SSR markers and morphological descriptors revealed genetic and phenotypic relatedness of the potato genotypes. Despite the complexity of tetrasomic inheritance, high anthocyanin-producing tetraploid cultivars should be considered for potato breeding since they are adapted to long-day conditions and do not present undesirable characteristics that are found in native accessions or landraces.
Engineering Photosynthetic Enzymes Involved in CO 2 -Assimilation by Gene Shuffling

Summary Enhancing photosynthesis is a promising approach for increasing plant productivity. Advances in plant transformation technology make it possible to manipulate photosynthesis by overexpressing particular genes for alleviating bottleneck steps, diverting the flux of Calvin cycle intermediates and photoassimilates, or introducing new enzymes and pathways that can positively influence photosynthesis. Furthermore, directed molecular evolution makes it possible to target selected key enzymes in photosynthetic pathways for modifying their specific catalytic or protein properties and tailoring them to best function under specified growth conditions. In this chapter, advances in directed molecular evolution technology and the use of gene shuffling methodology to modify Rubisco and Rubisco activase to enhance plant photosynthesis and growth are described. By shuffling the Chlamydomonas reinhardtii Rubisco large subunit and utilizing competitive growth selection, several mutated Rubisco enzymes with increased carboxylase activity or CO 2 /O 2 specificity were identified. The mutations identified in the modified Chlamydomonas Rubisco variants were then introduced into the tobacco enzyme by site-directed mutagenesis. Enzyme kinetic assays indicated that the modified tobacco Rubisco enzymes displayed increased CO 2 /O 2 specificity, carboxylase activity and reduced K m for CO 2 . Similarly, gene shuffling technology was used to generate several Arabidopsis thaliana Rubisco activase variants exhibiting improved thermostability in order to alleviate the
Size-mediated, density-dependent cannibalism in the signal crayfish Pacifastacus leniusculus (Dana, 1852) (Decapoda, Astacidea), an invasive crayfish in Britain

The role of cannibalism in crayfish populations is not well understood, despite being a potentially key density-dependent process underpinning population dynamics. We studied the incidence of cannibalism in an introduced signal crayfish Pacifastacus leniusculus population in a Scottish lowland river in September 2014. Animals were sampled using six different sampling techniques simultaneously, revealing variable densities and size distributions across the site. Cannibalism prevalence was estimated by analysing the gut contents of crayfish >20 mm CL for the presence of crayfish fragments, which was found to be 20% of dissected individuals. When seeking evidence of relationships between the sizes of cannibals and ‘prey’, the density of conspecifics <56% the size of a dissected individual yielded the best fit. The relationship between cannibalism probability and crayfish size and density was equally well described by three different metrics of crayfish density. Cannibalism increased with crayfish size and density but did not vary according to sex. These results suggest that large P. leniusculus frequently cannibalize smaller (prey) conspecifics, and that the probability of cannibalism is dependent upon the relative size of cannibal-to-prey and the density of the smaller crayfish. We suggest that removing large individuals, as targeted by many traditional removal techniques, may lead to reduced cannibalism and therefore a compensatory increase in juvenile survival.
Caracterização de duas proteínas pertencentes ao operon toxina-antitoxina e de um fator de transcrição do tipo LysR de Xylella fastidiosa : Functional characterization of two proteins belonging to toxin-antitoxin operon and a LysR-type transcription factor from Xylella fastidiosa

Apos sequenciamento do genoma da bacteria Xylella fastidiosa linhagem 9a5c, houve um grande aumento de informacoes relacionadas a fisiologia e patogenia deste microrganismo, porem muitas das proteinas identificadas na analise de seu genoma ainda nao apresentam funcoes preditas. A caracterizacao de tais proteinas pode contribuir para o melhor conhecimento do processo de patogenicidade bacteriana. Sendo assim, este trabalho teve como objetivo caracterizar tres proteinas, XfYcjZ (ORF Xf1480) a qual apresenta alta similaridade com membros da familia de reguladores de transcricao do tipo LysR (LTTR) e das proteinas toxina (XfMqsR) e antitoxina (XfMqsA), as quais possuem similaridade com o sistema toxina-antitoxina MsqR/MqsA de Escherichia coli. Tais proteinas desempenham, entre outras funcoes, papel preponderante na regulacao de genes envolvidos no metabolismo celular, divisao celular, quorum sensing, formacao de biofilme, virulencia e resposta ao estresse oxidativo. A caracterizacao estrutural destas proteinas baseou-se em dados provenientes de ensaios de dicroismo circular (CD), cromatografia de filtracao em gel e ultracentrifugacao analitica. Ja a caracterizacao funcional baseou-se na producao de anticorpos contra cada umas das proteinas estudadas, seguida de experimentos de imunodeteccao durante as diferentes fases de formacao do biofilme de X. fastidiosa. A proteina XfYcjZ-like apresentou-se na forma tetramerica em solucao, sendo diferencialmente expressa nas fases de crescimento de X. fastidiosa, foi observado o seu papel na resposta ao estresse oxidativo, quando induzida por cobre II. Foi tambem demonstrado que a interacao entre as proteinas toxina-antitoxina ocorre na razao molar 1:1, sendo o complexo mais termoestavel, quando comparado as duas proteinas individualmente, dados estes obtidos por analise de desenovelmanto termico por CD. Dados funcionais confirmaram a anotacao das proteinas deste sistema, uma vez que a antitoxina possuiu dominio HTH na regiao N-terminal, o que lhe confere capacidade de se ligar ao promotor do operon; a toxina apresentou atividade de RNAse e tambem foi inibida pela antitoxina. Em adicao, foi mostrado pela primeira vez que a antitoxina e secretada por meio de vesiculas da membrana externa, o que e uma forte evidencia que ela possa ter uma nova funcao em X. fastidiosa. Assim, esperamos que nossos resultados contribuam para o melhor entendimento do envolvimento dessas proteinas no ciclo de vida de X. fastidiosa e suas possiveis implicacoes para a patogenicidade bacteriana. Abstract
The Effect of the Structure of Jazz Music on Anxiety

This project won third place in the 2019 Signature Course Information Literacy Award. The award recognizes exemplary student work that achieves the learning outcomes of the Signature Course information literacy requirement, that students will be able to create and execute a research strategy, critically evaluate information, and navigate the scholarly conversation. The paper was nominated by Laura I. Gonzalez from the Department of Integrative Biology, and was completed in her fall 2019 course, “Scientific Inquiry Across Disciplines. ” Buck, Punske, and Shah’s project was chosen for their excellent literature review and interesting research question that did seem to fit into a gap in the existing literature. Dr. Gonzalez supported this project by saying "Students demonstrated amazing creativity in developing their question, methodology and analysis. They used scholarly journals to reference their methods and ideas. The whole final product is one of the best examples of how to ask interesting scientific questions and use interdisciplinary approaches to tackle them. ”