Miracle-dz/UniFAR-FTUs huggingface dataset:
Resistance to copper toxicity in populations of the earthworms Lumbricus rubellus and Dendrodrilus rubidus from contaminated mine wastes

Two arsenic and heavy metal—contaminated mine spoil sites, at Carrock Fell, Cumbria, United Kingdom, and Devon Great Consols Mine, Devon, United Kingdom, have been found to support populations of the earthworms Lumbricus rubellus Hoffmeister and Dendrodrilus rubidus (Savigny). Lumbricus rubellus and D. rubidus collected from the Devon site and an uncontaminated site were kept for 28 d in uncontaminated soil and in soil containing 750 mg/kg CuCl2, the state of the specimens being recorded using a semiquantitative assessment of earthworm health (condition index). The condition index remained high for all specimens except those of L. rubellus and D. rubidus from uncontaminated sites, which displayed 100% mortality. Bioavailability of Cu in the soils from one uncontaminated and two contaminated sites and in the uncoutaminated soil treated with CuCl2 was determined using sequential extraction. Soils from Devon Great Consols had the greatest availability of Cu, Carrock Fell the lowest. Total tissue Cu for L. rubellus and D. rubidus from the contaminated sites did not change significantly for each species during the experiment. Total tissue concentrations of Cu for L. rubellus and D. rubidus from uncontaminated sites increased significantly during the first 7 d, after which mortality was 90%, making it impossible to continue the analysis.
Selenium and the Methionine Sulfoxide Reductase System

Selenium is a chemical element participating in the synthesis of selenocysteine residues that play a pivotal role in the enzymatic activity efficiency of selenoproteines. The methionine sulfoxide reductase (Msr) system that reduces methionine sulfoxide (MetO) to methionine comprises the selenoprotein MsrB (MsrB1) and the non-selenoprotein MsrA, which reduce the R- and the S- forms of MetO, respectively. The effects of a selenium deficient (SD) diet, which was administrated to wild type (WT) and MsrA knockout mice (MsrA-/-), on the expression and function of Msr-related proteins are examined and discussed. Additionally, new data about the levels of selenium in brain, liver, and kidneys of WT and MsrA-/- mice are presented and discussed.
The Evolution of Price Dispersion in the European Car Market

Car prices in Europe are characterized by large and persistent differences across countries. The purpose of this paper is to document and explain this price dispersion. Using a panel data set extending from 1980 to 1993, we first demonstrate two main facts concerning car prices in Europe: (1) The existence of significant differences in quality adjusted prices across countries, with Italy and the U.K. systematically representing the most expansive markets; (2) Substantial year-to-year volatility that is to a large extent accounted for by exchange rate fluctuation and the incomplete response of local currency prices to these fluctuations. These facts are analyzed within the framework of a multiproduct oligopoly model with product differentiation. The model identifies three potential sources for the international price differences: price elasticities generating differences in markups, costs, and import quota constraints. Local currency price stability can be attributed either to the presence of a local component in marginal costs, or to markup adjustment that is correlated with exchange rate volatility; the latter requires that the perceived elasticity of demand is increasing in price. We find that the primary reason for the higher prices in Italy is the existence of a strong bias for domestic brands that generates high markups for the domestic firm (Fiat). In the U.K. higher prices are mainly attributed to better equipped cars and/or differences in the dealer discount practices. The import quota constraints are found to have a significant impact on Japanese car prices in Italy, France, and the U.K. With respect to local currency price stability, 2/3 of the documented price inertia are attributed to local costs, and 1/3 to markup adjustment that is indicative of price discrimination. Based on these results, we conjecture that the EMU will substantially reduce the year-to -year volatility observed in the car price data, but without further measures to increase European integration, it will not completely eliminate existing cross-country price differences.
Does actually mean chromosome number increase with latitude in vascular plants? An answer from the comparison of Italian, Slovak and Polish floras

Abstract We compared chromosome number (CN) variation among vascular floras of three different countries with increasing latitude in the Boreal hemisphere: Italy, Slovakia, Poland. Aim of the study was to verify whether the patterns of CN variation parallel the differences in latitudinal ranges. The three datasets comprised 3426 (Italy), 3493 (Slovakia) and 1870 (Poland) distinct cytotypes. Standard statistics (ANOVA, Kruskal–Wallis tests) evidenced significant differences among the three countries, mean CN increasing together with latitude. On the contrary, an inverse relation (r = -1) was evidenced among the frequency of odd CNs and latitude. Our results show that the hypothesis of a polyploid increase proportional with distance from the Equator seems to be confirmed, when territories from the same hemisphere are compared.
Numerical 3D modeling of heat transfer in human tissues for microwave radiometry monitoring of brown fat metabolism

Background: Brown adipose tissue (BAT) plays an important role in whole body metabolism and could potentially mediate weight gain and insulin sensitivity. Although some imaging techniques allow BAT detection, there are currently no viable methods for continuous acquisition of BAT energy expenditure. We present a non-invasive technique for long term monitoring of BAT metabolism using microwave radiometry. Methods: A multilayer 3D computational model was created in HFSSTM with 1.5 mm skin, 3-10 mm subcutaneous fat, 200 mm muscle and a BAT region (2-6 cm3) located between fat and muscle. Based on this model, a log-spiral antenna was designed and optimized to maximize reception of thermal emissions from the target (BAT). The power absorption patterns calculated in HFSSTM were combined with simulated thermal distributions computed in COMSOL® to predict radiometric signal measured from an ultra-low-noise microwave radiometer. The power received by the antenna was characterized as a function of different levels of BAT metabolism under cold and noradrenergic stimulation. Results: The optimized frequency band was 1.5-2.2 GHz, with averaged antenna efficiency of 19%. The simulated power received by the radiometric antenna increased 2-9 mdBm (noradrenergic stimulus) and 4-15 mdBm (cold stimulus) corresponding to increased 15-fold BAT metabolism. Conclusions: Results demonstrated the ability to detect thermal radiation from small volumes (2-6 cm3) of BAT located up to 12 mm deep and to monitor small changes (0.5 °C) in BAT metabolism. As such, the developed miniature radiometric antenna sensor appears suitable for non-invasive long term monitoring of BAT metabolism.
Fine-Scale Dissection of Functional Protein Network Organization by Statistical Network Analysis

Revealing organizational principles of biological networks is an important goal of systems biology. In this study, we sought to analyze the dynamic organizational principles within the protein interaction network by studying the characteristics of individual neighborhoods of proteins within the network based on their gene expression as well as protein-protein interaction patterns. By clustering proteins into distinct groups based on their neighborhood gene expression characteristics, we identify several significant trends in the dynamic organization of the protein interaction network. We show that proteins with distinct neighborhood gene expression characteristics are positioned in specific localities in the protein interaction network thereby playing specific roles in the dynamic network connectivity. Remarkably, our analysis reveals a neighborhood characteristic that corresponds to the most centrally located group of proteins within the network. Further, we show that the connectivity pattern displayed by this group is consistent with the notion of “rich club connectivity” in complex networks. Importantly, our findings are largely reproducible in networks constructed using independent and different datasets.
DROSOPHILA SALIVARY GLANDS IN VITRO

The salivary glands of larval dipterans with their giant polytene chromosomes have been used extensively in cytogenetic studies, analysis of chromosome structure, and in the analysis of gene activity during differentiation (1, 4-7, 21, 29, 30, 35, 39). Specific local modifications at given gene loci, which are related to differentiation, are sites of RNA synthesis, and have been shown to be dependent upon the following parameters: extracellular environment, cytoplasmic environment, ions in the nuclear sap, as well as the state of reactivity inherent in the cell and chromosomes (3, 10-13, 23-26, 31, 36, 37). Investigations on the factors involved in chromosome puffing have been facilitated by in vitro techniques in which salivary glands have been maintained in Ephrussi-Beadle saline for 1-2 hr (3, 36). The uptake of radioactive precursors has also been studied in explanted glands in EphrussiBeadle saline (16, 17, 32-34, 37). The maintenance of salivary glands during 24 hr of explantation to tissue culture media has been demonstrated in Sciara coprophila by Cannon (9, 10), who observed DNA synthesis and puff formation and condensation (DNA puffs) in chromosomes. The purpose of the present research is to compare various insect tissue culture media to see whether morphological integrity and DNA synthesis can be obtained during extended explantation of salivary glands of Drosophila melanogaster.
Intraspecific ITS Variability in the Kingdom Fungi as Expressed in the International Sequence Databases and Its Implications for Molecular Species Identification

The internal transcribed spacer (ITS) region of the nuclear ribosomal repeat unit is the most popular locus for species identification and subgeneric phylogenetic inference in sequence-based mycological research. The region is known to show certain variability even within species, although its intraspecific variability is often held to be limited and clearly separated from interspecific variability. The existence of such a divide between intra- and interspecific variability is implicitly assumed by automated approaches to species identification, but whether intraspecific variability indeed is negligible within the fungal kingdom remains contentious. The present study estimates the intraspecific ITS variability in all fungi presently available to the mycological community through the international sequence databases. Substantial differences were found within the kingdom, and the results are not easily correlated to the taxonomic affiliation or nutritional mode of the taxa considered. No single unifying yet stringent upper limit for intraspecific variability, such as the canonical 3% threshold, appears to be applicable with the desired outcome throughout the fungi. Our results caution against simplified approaches to automated ITS-based species delimitation and reiterate the need for taxonomic expertise in the translation of sequence data into species names.
Very Fast Kernel SVM under Budget Constraints

In this paper we propose a fast online Kernel SVM algorithm under tight budget constraints. We propose to split the input space using LVQ and train a Kernel SVM in each cluster. To allow for online training, we propose to limit the size of the support vector set of each cluster using different strategies. We show in the experiment that our algorithm is able to achieve high accuracy while having a very high number of samples processed per second both in training and in the evaluation.
It Takes Three to Tango: Triangulation Approach to Answer Ranking in Community Question Answering

We address the problem of answering new questions in community forums, by selecting suitable answers to already asked questions. We approach the task as an answer ranking problem, adopting a pairwise neural network architecture that selects which of two competing answers is better. We focus on the utility of the three types of similarities occurring in the triangle formed by the original question, the related question, and an answer to the related comment, which we call relevance, relatedness , and appropriateness . Our proposed neural network models the interactions among all input components using syntactic and semantic embeddings, lexical matching, and domain-speciﬁc features. It achieves state-of-the-art results, showing that the three similarities are important and need to be modeled together. Our experiments demonstrate that all feature types are relevant, but the most important ones are the lexical similarity features, the domain-speciﬁc features, and the syntactic and semantic embeddings.
The value of clitics in non-native Spanish

One of the tasks of second language acquisition research is to determine the ‘linguistic’ nature of interlanguage systems. To achieve this goal it is mandatory to formulate the properties of learners' grammars in terms of the theoretical constructs proposed by linguistic theory. I have proposed elsewhere (Liceras, 1985) that, permeability, one of those properties, is related to parameter setting. In this paper, it is hypothesized that the location of a given process in the different components of the grammar may also be relevant in the determination of permeability. In the light of conflicting evidence provided by the Spanish interlanguage of French and English speakers with respect to the value of clitics in the non-native grammar, it is suggested that, due to the nature of ‘intake’, L2 learners of Spanish may locate clitics in the lexicon (as affix-like elements) or postlexically (as words in the syntax) rather than giving them a unidimensional value. I have also suggested that non-native clitics may not share all the properties that are assigned to Modern Spanish clitic pronouns.
Identification and Characterization of All-trans-retinol Dehydrogenase from Photoreceptor Outer Segments, the Visual Cycle Enzyme That Reduces All-trans-retinal to All-trans-retinol*

Retinol dehydrogenase (RDH), the enzyme that catalyzes the reduction of all-trans-retinal to all-trans-retinol within the photoreceptor outer segment, was the first visual cycle enzymatic activity to be identified. Previous work has shown that this enzyme utilizes NADPH, shows a marked preference for all-trans-retinal over 11-cis-retinal, and is tightly associated with the outer segment membrane. This paper reports the identification of a novel member of the short chain dehydrogenase/reductase family, photoreceptor RDH (prRDH), using subtraction and normalization of retina cDNA, high throughput sequencing, and data base homology searches to detect retina-specific genes. Bovine and human prRDH are highly homologous and are most closely related to 17-β-hydroxysteroid dehydrogenase 1. The enzymatic properties of recombinant bovine prRDH closely match those previously reported for RDH activity in crude bovine rod outer segment preparations. In situ hybridization and RNA blotting show that the PRRDH gene is expressed specifically in photoreceptor cells, and protein blotting and immunocytochemistry show that prRDH localizes exclusively to both rod and cone outer segments and that prRDH is tightly associated with outer segment membranes. Taken together, these data indicate that prRDH is the enzyme responsible for the reduction of all-trans-retinal to all-trans-retinol within the photoreceptor outer segment.
Factors influencing bacterial adhesion to contact lenses

The process of any contact lens related keratitis generally starts with the adhesion of opportunistic pathogens to contact lens surface. This article focuses on identifying the factors which have been reported to affect bacterial adhesion to contact lenses. Adhesion to lenses differs between various genera/species/strains of bacteria. Pseudomonas aeruginosa, which is the predominant causative organism, adheres in the highest numbers to both hydrogel and silicone hydrogel lenses in vitro. The adhesion of this strain reaches maximum numbers within 1h in most in vitro studies and a biofilm has generally formed within 24 h of cells adhering to the lens surface. Physical and chemical properties of contact lens material affect bacterial adhesion. The water content of hydroxyethylmethacrylate (HEMA)-based lenses and their iconicity affect the ability of bacteria to adhere. The higher hydrophobicity of silicone hydrogel lenses compared to HEMA-based lenses has been implicated in the higher numbers of bacteria that can adhere to their surfaces. Lens wear has different effects on bacterial adhesion, partly due to differences between wearers, responses of bacterial strains and the ability of certain tear film proteins when bound to a lens surface to kill certain types of bacteria.
Temporal Autonomy in a Laboring Society

Abstract The aim of this paper is to discuss which stance towards the allocation of labor and leisure would be defensible from the perspective of modern liberal political theory. There is a long tradition in philosophy defending an ideal of leisure, but this tradition has been rightly criticized for being too perfectionist. A liberal perspective seems more attractive in not dictating how much time people spend in labor or leisure, but leaving this choice to individuals. The question is whether this is possible. After scrutinizing the traditional philosophical defense of leisure I focus on Robert Goodin and his collaborators' recent proposal to think about labor and leisure in terms of “temporal autonomy”. I show that their concept is a great improvement over the older philosophical theories, both in its conceptualization of labor and leisure and in its ambition to leave labor/leisure choices to individuals. Nonetheless, it contains an important unresolved ambiguity about whether discretionary time maximization is a desirable end. Since the exercise of one's temporal autonomy can undercut the temporal autonomy of others in society, this leads to a dilemma. This dilemma can be resolved either in a libertarian or in a sufficientarian direction. I provide a cautious defense of the sufficientarian conception of temporal autonomy, because it accounts for the intuition in the older tradition of leisure that it is important not to be overwhelmed by the demands of labor, while also retaining the liberal emphasis on individual choice.
Biochemistry and molecular genetics of Leishmania glucose transporters

SUMMARY Glucose is utilized as a significant source of metabolic energy by Leishmania parasites. This sugar is accumulated by the parasite via a specific carrier-mediated transport system located in the parasite membrane. Parasites may also contain another transporter that shuttles glucose between the cytoplasm and the glycosome, a membrane-bound organelle where the early steps of glycolysis occur. The transport systems of both the insect stage promastigotes and the intracellular amastigotes have been characterized and shown to have kinetic properties that are consistent with the different physio-logical environments of the insect gut and the macrophage phagolysosome. Several genes have been cloned from Leishmania species which encode proteins with substantial sequence similarity to glucose transporters from mammals and lower eukaryotes. Two of these genes are expressed preferentially in the promastigote stage of the life cycle, where glucose is more readily available and more rapidly transported and metabolized than in the intracellular amastigotes. One of these two developmentally-regulated genes has been functionally expressed in Xenopus oocytes and shown to encode a glucose transporter. A third gene encodes a protein that is also a member of the glucose transporter family on the basis of sequence similarity and proposed secondary structure. However, the significant differences between this protein and the other two suggest that it is likely to transport a different substrate. Functional expression will be required to define the specific biochemical role of each gene within the parasite.
Effects of methanol extraction residue and therapeutic irradiation against established isografts and simulated local recurrence of mammary carcinomas.

Female BALB/c mice carrying established isografts or simulated local recurrence implants of 2 rapidly growing mammary adenocarcinomas were treated either by injection of the methanol extraction residue (MER) fraction of killed Bacillus Calmette-Guérin organisms (given s.c. or into the tumor) or by focal X-irradiation or by both. None of the modalities of therapy effected cures, but in many instances there was a significant retardation of tumor cevelopment and prolongation of the lives of the mice. Administration of MER alone offered protection in a number of cases but less often than the other forms of treatment. Combined therapy with MER and irradiation was, on the whole, the most successful therapeutic intervention. MER or irradiation administered alone enhanced the neoplastic process only on rare occasions; this appeared to be the case even more infrequently with combined treatment. MER was most likely to be effective alone or in combination when small quantities were used and when only 1 treatment or 1 cycle of combined therapy was given. The therapeutic action of MER was not dependent on direct introduction of the agent into a neoplastic focus; s.c. administration distal to the tumor site was almost always at least as satisfactory as injection directly into the tumor mass and indeed was often more efficacious.
A functional magnetic resonance imaging study of amygdala and medial prefrontal cortex responses to overtly presented fearful faces in posttraumatic stress disorder.

BACKGROUND Previous functional neuroimaging studies have demonstrated exaggerated amygdala responses and diminished medial prefrontal cortex responses during the symptomatic state in posttraumatic stress disorder (PTSD). OBJECTIVES To determine whether these abnormalities also occur in response to overtly presented affective stimuli unrelated to trauma; to examine the functional relationship between the amygdala and medial prefrontal cortex and their relationship to PTSD symptom severity in response to these stimuli; and to determine whether responsivity of these regions habituates normally across repeated stimulus presentations in PTSD. DESIGN Case-control study. SETTING Academic medical center. PARTICIPANTS Volunteer sample of 13 men with PTSD (PTSD group) and 13 trauma-exposed men without PTSD (control group). MAIN OUTCOME MEASURES We used functional magnetic resonance imaging (fMRI) to study blood oxygenation level-dependent signal during the presentation of emotional facial expressions. RESULTS The PTSD group exhibited exaggerated amygdala responses and diminished medial prefrontal cortex responses to fearful vs happy facial expressions. In addition, in the PTSD group, blood oxygenation level-dependent signal changes in the amygdala were negatively correlated with signal changes in the medial prefrontal cortex, and symptom severity was negatively related to blood oxygenation level-dependent signal changes in the medial prefrontal cortex. Finally, relative to the control group, the PTSD group tended to exhibit diminished habituation of fearful vs happy responses in the right amygdala across functional runs, although this effect did not exceed our a priori statistical threshold. CONCLUSIONS These results provide evidence for exaggerated amygdala responsivity, diminished medial prefrontal cortex responsivity, and a reciprocal relationship between these 2 regions during passive viewing of overtly presented affective stimuli unrelated to trauma in PTSD.