Miracle-dz/UniFAR-FTUs huggingface dataset:
Impact of the Position of the Chemically Modified 5-Furyl-2′-Deoxyuridine Nucleoside on the Thrombin DNA Aptamer–Protein Complex: Structural Insights into Aptamer Response from MD Simulations

Aptamers are functional nucleic acids that bind to a range of targets (small molecules, proteins or cells) with a high affinity and specificity. Chemically-modified aptamers are of interest because the incorporation of novel nucleobase components can enhance aptamer binding to target proteins, while fluorescent base analogues permit the design of functional aptasensors that signal target binding. However, since optimally modified nucleoside designs have yet to be identified, information about how to fine tune aptamer stability and target binding affinity is required. The present work uses molecular dynamics (MD) simulations to investigate modifications to the prototypical thrombin-binding aptamer (TBA), which is a 15-mer DNA sequence that folds into a G-quadruplex structure connected by two TT loops and one TGT loop. Specifically, we modeled a previously synthesized thymine (T) analog, namely 5-furyl-2′-deoxyuridine (5FurU), into each of the six aptamer locations occupied by a thymine base in the TT or TGT loops of unbound and thrombin bound TBA. This modification and aptamer combination were chosen as a proof-of-principle because previous experimental studies have shown that TBA displays emissive sensitivity to target binding based on the local environment polarity at different 5FurU modification sites. Our simulations reveal that the chemically-modified base imparts noticeable structural changes to the aptamer without affecting the global conformation. Depending on the modification site, 5FurU performance is altered due to changes in the local environment, including the modification site structural dynamics, degree of solvent exposure, stacking with neighboring bases, and interactions with thrombin. Most importantly, these changes directly correlate with the experimentally-observed differences in the stability, binding affinity and emissive response of the modified aptamers. Therefore, the computational protocols implemented in the present work can be used in subsequent studies in a predictive way to aid the fine tuning of aptamer target recognition for use as biosensors (aptasensors) and/or therapeutics.
UvA-DARE ( Digital Academic Repository ) Progress with the LOFAR Imaging Pipeline

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Identification of the complete mitochondrial genome of the king penguin Aptenodytes patagonicus (Sphenisciformes: Spheniscidae: Aptenodytes)

Abstract The complete mitochondrial genome of the king penguin Aptenodytes patagonicus was firstly determined. The mitogenome is 17,477 bp in length and contains 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and a control region. The total nucleotide composition is 31.0% A, 22.2% T, 33.1% C, and 13.8% G, with a total A + T content of 53.2%. The phylogenetic analysis demonstrates a close relationship between A. patagonicus and A. forsteri. These results provide fundamental information for further phylogeny and genetic studies on Aptenodytes genus.
Contribution of landscape metrics to the assessment of scenic quality - the example of the landscape structure plan Havelland/Germany.

The scenic quality of a landscape is a natural resource that is to be preserved according to German and international law. One important indicator for the evaluation of this value is the structural diversity of the landscape. Although Landscape Metrics (LM) represent a well-known instrument for the quantification of landscape patterns, they are hardly used in applied landscape and environmental planning. This study shows possibilities for the integration of LM into a commonly used method to assess scenic quality by the example of a Landscape Structure Plan. First results indicate that especially Shannon’s Diversity Index and Edge Density are suitable to achieve an objective evaluation of the structural diversity as indicator for scenic quality. The addition of qualitative parameters to the objective structural analysis is discussed. Moreover, the use of landscape scenery units and raster cells as basic geometry has been compared. It shows that LM can support the evaluation of the aesthetic quality in environmental planning, especially when integrated into commonly used evaluation methods.
Reanalysis of nearby open clusters using Gaia DR1/TGAS and HSOY

Context. Open clusters have long been used to gain insights into the structure, composition, and evolution of the Galaxy. With the large amount of stellar data available for many clusters in the Gaia era, new techniques must be developed for analyzing open clusters, as visual inspection of cluster color-magnitude diagrams is no longer feasible. An automatic tool will be required to analyze large samples of open clusters. Aims. We seek to develop an automatic isochrone-fitting procedure to consistently determine cluster membership and the fundamental cluster parameters. Methods. Our cluster characterization pipeline first determined cluster membership with precise astrometry, primarily from TGAS and HSOY. With initial cluster members established, isochrones were fitted, using a χ2 minimization, to the cluster photometry in order to determine cluster mean distances, ages, and reddening. Cluster membership was also refined based on the stellar photometry. We used multiband photometry, which includes ASCC-2.5 BV, 2MASS JHKs, and Gaia G band. Results. We present parameter estimates for all 24 clusters closer than 333 pc as determined by the Catalogue of Open Cluster Data and the Milky Way Star Clusters catalog. We find that our parameters are consistent to those in the Milky Way Star Clusters catalog. Conclusions. We demonstrate that it is feasible to develop an automated pipeline that determines cluster parameters and membership reliably. After additional modifications, our pipeline will be able to use Gaia DR2 as input, leading to better cluster memberships and more accurate cluster parameters for a much larger number of clusters.
An evaluation of maternal influences on growth traits: the Zandi sheep breed of Iran as an example

An animal model was used to estimate direct and maternal genetic parameters for birth weight (BW), weaning weight (WW), 9-month weight (W9) and yearling weight (YW) for a population of Zandi sheep. The magnitude of estimates of these parameters was used to evaluate the importance of direct and maternal infl uences on body weight at various stages of Zandi lambs’ life. Results confi rmed the potential maternal infl uences to change pattern of body weight’s heritability with age. Maternal infl uences were signifi cant for early growth traits. The importance of maternal infl uences diminished with age, although for W9 and YW those effects did not disappear completely. In contrast to variation due to maternal effects, the variance of direct effects increased from birth to a year of age. Estimates of maternal breeding values averaged by year of birth decreased throughout the experiment for both BW and WW. It was concluded that for more precise designing selection programs and, in consequence, increasing effi ciency of selection, inclusion of maternal effects as well as direct-maternal genetic covariance into the model, especially for early growth traits, is necessary.
Natural Growth and Mortality of the Golden Grey Mullet Liza Aurata (Risso, 1810) In the Lagoon of Klisova-Messolonghi (W. Greece)

Growth and mortality of L. aurata (Risso,1810) were estimated in the lagoon of Klisova-Messolonghi (W. Greece), based on age estimation from scale readings of a total of 1048 individuals, ranging between 10 and 59 cm in total length (TL). Age determination revealed nine age classes (0+ to 8+). Maximum age was found to be 8 years for females and 6 years for males respectively. The growth pattern of L. aurata exhibited allometry (b=3.26). The species seems to achieve 34% of its growth during the first year; thereafter the annual growth rate drops. Both sexes presented similar von Bertalanffy growth curves. The von Bertalanffy growth function for the estimated total length-at-age was found Lt = 70.78 [1 - e -0.129(t+1.345)] for the combined sexes. Otolith weight, length and width were tested and they were found to be very good predictors for age. Between the present L. aurata growth parameters and those of other Mediterranean, Caspian and Atlantic Sea for the same species, there were found significant differences in its growth parameters. The total (Z) and natural (M) mortality rate was found to be 0.54 years-1 and 0.33 years-1 respectively. The estimated exploitation rate was found to be E=0.395 which suggests that the existing fishing pressure on L. aurata is rather moderate in the investigated region.
Antioxidant action in diets with ground soybeans on ruminal microbial production, digestion, and fermentation in buffaloes

ABSTRACT The objective of this study was to evaluate the effect of adding ground soybeans and antioxidants to diet of buffaloes on intake, ruminal microbial production, total and ruminal digestibility of nutrients, and ruminal fermentation parameters. Four crossbred buffaloes with a mean weight of 506±29 kg were distributed in a 4×4 Latin square. Four diets were tested: control; diet with ground soybeans; diet with ground soybeans and supplementation with yerba mate; and diet with ground soybeans and supplementation with yerba [. ]
The Family Innovator's Dilemma: How Family Influence Affects the Adoption of Discontinuous Technologies by Incumbent Firms

We integrate research on family business and discontinuous change to better explain why incumbents vary in when and how they adopt discontinuous technologies. Family influence induces companies to strive for continuity, command, community, and connections and, thus, alters the mix of constraints under which firms operate. Consequently, family influence weakens several of the inertial forces described in the discontinuous change literature, particularly the level of formalization, dependence on external capital providers, and political resistance. However, it also aggravates critical sources of organizational paralysis, specifically emotional ties to existing assets and the rigidity of mental models. We aggregate these seemingly contradictory effects to show that, overall, discontinuous change conflicts with essential goals and values of the family system, and, therefore, family influence entails fundamentally different dilemmas than those described in extant research. In turn, although highly family-influ.
Evaluation of Therapeutic Properties of a Low Energy Electron Beam Plus Spoiler for Local Treatment of Mycosis Fungoides: A Monte Carlo Study

Background: When using low-energy electron beams for the treatment of skin lesions, such as Mycosis Fungoides (MF), a beam spoiler is used to decrease electron therapeutic depth (R90) while increasing the surface dose. Objective: The aim of this study was to evaluate the characteristics of a 5 MeV electron beam when using a spoiler for the local treatment of MF skin lesions by Monte Carlo (MC) simulation. Material and Methods: In this experimental study, a Siemens Primus treatment head and an acrylic spoiler, positioned at the end of applicator, were simulated using BEAMnrc, an EGSnrc user code. The modelled beam was validated by measurement using MP3-M water tank, Roos parallel plate chamber and Semi flex Chamber-31013 (all from PTW, Freiburg, Germany). For different spoiler thicknesses, dose distributions in water were calculated for 2 field sizes and were compared to those for the corresponding open fields. Results: For a 1.3 cm spoiler, therapeutic range changed from 1.5 cm (open field) to 0.5 cm and 0.4 cm for 10 × 10 cm2 and 20 × 20 cm2 field sizes, respectively. Maximum increase in penumbra width was 2.8 and 3.8 cm for 10 × 10 cm2 and 20 × 20 cm2 field sizes, respectively. Maximum increase in bremsstrahlung contamination was %2 in both field sizes. Conclusion: R90 decreased exponentially with increase in spoiler thickness. The effect of field size on penumbra was much larger for spoiled beam compared to the open beam. The results of this research can be applied to optimize the radiation treatment of MF patients in our hospital.
A meta-analysis of inter-individual differences in innovation

The ability to innovate, and the social transmission of innovations, have played a central role in human evolution. However, innovation is also crucial for other animals, by allowing them to cope with novel socio-ecological challenges. Although innovation plays such a central role in animals' lives, we still do not know the conditions required for innovative behaviour to emerge. Here, we focused on interindividual differences in innovation by (i) extensively reviewing existing literature on innovative behaviour in animals and (ii) quantitatively testing the different evolutionary hypotheses that have been proposed to explain inter-individual variation in innovation propensity during foraging tasks. We ran a series of phylogenetically controlled mixed-effects meta-regression models to determine which hypotheses (if any) are supported by currently available empirical studies. Our analyses show that innovation is more common in individuals who are more neophilic and/or explorative. Moreover, age, sexual dimorphism and captivity had significant effect on innovation. Overall, our results suggest that captivity and inter-individual differences in traits related to personality are also important predictors of innovation, and likely interact with one another in complex ways.
Nutritional Immunology-Tocopherol and Selenium Facilitate Recovery from Lipopolysaccharide-Induced Sickness in Aged Mice 1 , 2

The elderly suffer a decline in immune function that increases their vulnerability to infections. Because antioxidants improve some age-related deficits in immune and cognitive function, our goal was to determine whether dietary -tocopherol ( -T) and selenium inhibit LPS-induced sickness behavior in aged mice. Male BALB/c mice were fed modified AIN93-M diets that were low, adequate, or high in both -T (10, 75, or 500 mg/kg) and selenium (0.05, 0.15, or 2 mg/kg) from 18 to 21 mo of age. Sickness was quantified by measuring time in social exploration of a novel juvenile conspecific. The lipopolysaccharide treatment reduced social exploration by 74% at 2 h, regardless of diet. By 4 h, aged mice fed the low diet were 88% less social, whereas mice fed the adequate and high diets displayed only 40% reductions due to LPS treatment. Mice fed the low diet had greater LPS-induced weight loss than mice fed the high diet. Plasma -T concentration and glutathione peroxidase (GPX) activity increased with each increment in -T and selenium 24 h post-LPS treatment. Brain -T concentration and GPX activity were lower in mice fed the low diet than in those fed the adequate or high diet. Regardless of diet, interleukin (IL)-6, IL-1 , and tumor necrosis factor (TNF) mRNA levels were elevated by LPS 3-fold in cortex, cerebellum, striatum, and hippocampus. Thus, antioxidants inhibit sickness behavior independently of IL-6, IL-1 , and TNF mRNA levels 2 h post-LPS in the brain regions analyzed. Taken together, these findings suggest that adequate intake of dietary -T and selenium may help promote recovery from gram-negative bacterial infection in the aged. J. Nutr. 135: 1157–1163, 2005.
Financial crises and volatility spillovers among emerging European equity markets

Financial crisis not only have statistically but also economically significant impact on global equity market returns. This study analyzes whether current financial crisis affect the equity market returns of Balkan transition economies and what is the extent of such impact by employing Generalized Autoregressive Conditional Heteroscedasticity model is employed on daily data spans from 2006 to 2012 for three transition economies which are Bosnia-Herzegovina, Croatia and Serbia. Empirical result indicates that volatility of Serbian stock price is influenced by the volatility of Bosnian and Croatian stock prices. There is one way volatility transmission from Bosnian and Croatian stock markets to Serbian stock market. High degree of volatility is observed in the stock markets during latest financial crises.
Predictive and Prognostic Value of Selected MicroRNAs in Luminal Breast Cancer

Breast cancer (BrC) is the most frequent malignancy and the leading cause of cancer death among women worldwide. Approximately 70% of BrC are classified as luminal-like subtype, expressing the estrogen receptor. One of the most common and effective adjuvant therapies for this BrC subtype is endocrine therapy. However, its effectiveness is limited, with relapse occurring in up to 40% of patients. Because microRNAs have been associated with several mechanisms underlying endocrine resistance and sensitivity, they may serve as predictive and/or prognostic biomarkers in this setting. Hence, the main goal of this study was to investigate whether miRNAs deregulated in endocrine-resistant BrC may be clinically relevant as prognostic and predictive biomarkers in patients treated with adjuvant endocrine therapy. A global expression assay allowed for the identification of microRNAs differentially expressed between luminal BrC patients with or without recurrence after endocrine adjuvant therapy. Then, six microRNAs were chosen for validation using quantitative reverse transcription polymerase chain reaction in a larger set of tissue samples. Thus, miR-30c-5p, miR-30b-5p, miR-182-5p, and miR-200b-3p were found to be independent predictors of clinical benefit from endocrine therapy. Moreover, miR-182-5p and miR-200b-3p displayed independent prognostic value for disease recurrence in luminal BrC patients after endocrine therapy. Our results indicate that selected miRNAs’ panels may constitute clinically useful ancillary tools for management of luminal BrC patients. Nevertheless, additional validation, ideally in a multicentric setting, is required to confirm our findings.
Performance Differences between Entrepreneurial and Non-Entrepreneurial Firms

This paper extends the strategy–structure–performance paradigm to examine the performance differences between entrepreneurial and non-entrepreneurial electrical distribution firms. The results indicate that both entrepreneurial and non-entrepreneurial electrical distributors with an optimal strategy–structure alignment tend to have a higher organizational performance than those entrepreneurial and non-entrepreneurial electrical distributors without such an alignment. The results are examined and conclusions are offered. Finally, the implications for future research are set out, as are the limitations of the present study.
RADIATION PATTERN SYNTHESIS FOR MAXIMUM MEAN EFFECTIVE GAIN WITH SPHERICAL WAVE EXPANSIONS AND PARTICLE SWARM TECHNIQUES

A new Mean Efiective Gain (MEG) expression using Spherical Wave Expansions (SWE) is presented in order to evaluate the impact of mobile environments on radiating structures. The proposed approach takes into account the pattern polarization and transforms a continuous functional optimization problem into an approximate discrete formulation. It allows to synthesize e-cient antenna radiation patterns in terms of the Mean Efiective Gain when it is combined with modern heuristic optimization techniques. In addition, antenna performance limits are evaluated by means of certain bounds. These depend on the modal number which is required to describe accurately far flelds and depend ultimately on the antenna size. The method estimates the optimum patterns for two difierent wireless scenarios that are characterized by the statistical probability density functions of incoming waves and particularized in the case of Gaussian statistics. The numerical evaluation has been performed by means of the Particle Swarm Optimization (PSO) technique, which is slightly modifled to include a speciflc constrain and whose parameters have been computed previously by solving a canonical problem. Finally, representative results in outdoor and mixed wireless scenarios are discussed, pointing out some useful consequences in antenna design.
Improving Soybean Yield in the Dry Land ofNorth Lombok Using Eggshell Waste andArbuscular Mycorrhiza

This study aims to determine soybean yield on dry land by utilizing eggshell waste and arbuscular mycorrhiza (AM). Factorial Randomized Block Design (RBD) consisting of 2 factors, namely the dose of AM and eggshell flour was used to design the study. AM (F) consists of three levels, namely f1 (AM dose 300 kg ha-1), f2 (dose AM 400 kg ha-1) and f3 (dose AM 500 kg ha-1) while that of eggshell flour (T), consists of five levels, namely t0 (without eggshell flour), t1 (with eggshell flour 50 kg ha-1), t2 (with eggshell flour 100 kg ha-1), t3 ( with eggshell flour 150 kg ha-1) and t4 (with eggshell flour 200 kg ha-1). The parameters observed were soil nutrient availability N, P, and pH before and after the experiment, wet and dry weight of plant stover at harvest, dry pod weight per plant, seed weight per plant, the weight of 100 seeds, number of AM spores per 10 g soil and degree of root colonization. The results showed that 500 kg AM ha-1 can increase seed weight per plant and weight of 100 seeds by 22.6% and 12.12% respectively, which is significantly different from 300 kg AM ha-1. The dose of 200 kg ha-1 eggshell flour can increase the weight of wet and dry biomass, dry pod weight p, seed weight per plant and weight of 100 seeds by 22.56%, 47.56%, 55.8%, 38.6 % and 23.62% with significant difference compared to controls. The interaction of the dose of 500 kg AM ha-1 and eggshell flour 200 kg ha-1 can increase the number of AM spores and the percentage of infections in the roots.
No evidence for differential maternal allocation to offspring in the house sparrow (Passer domesticus)

We tested the differential maternal allocation hypothesis in a population of house sparrows. We experimentally altered the attractiveness of males by treating them with implants filled with crystalline testosterone (T) or left empty (C). We subsequently monitored maternal investment as a function of male hormonal treatment and the size of the black patch of feathers on the throat (i.e., the badge), a sexually selected trait. The differential allocation hypothesis predicts that females should adjust their investment with respect to the benefits they receive by mating with an attractive male. Given that both circulating levels of T and badge size are condition-dependent traits, we expected that females mated with T males and/or with large-badged males should invest more into current reproduction. Contrary to this prediction, we found no evidence that suggested differential maternal allocation in this population of house sparrows. Female investment in yolk T, yolk mass, clutch size, chick brooding, and feeding was not affected by male hormonal treatment or by male badge size. As expected, T males invested less into chick brooding and feeding. More surprisingly, females did not compensate the reduced paternal contribution to chick feeding. As a consequence, the breeding success of T pairs was largely reduced compared with that of C pairs. The absence of differential allocation in a system in which it could have an adaptive role raises the question about the possible constraints or overriding factors operating on patterns of reproductive investment in this species. Copyright 2003.