Miracle-dz/UniFAR-FTUs huggingface dataset:
Evolution in the dark: A study of cave crickets in Southern Appalachia

In 1978 Hubbell and Norton described nine species of crickets in the Tribe Hadenoecini found in caves or forest litter in the Southern Appalachians. According to the model proposed by these authors new species formed during glaciation. Hubbell and Norton (1978) suggested that the crickets are thermophile relicts that dispersed in the area before and after glaciation but, during glaciation, formed new species in allopatric refugia of caves or forests south of their normal ranges. Our mitochondrial DNA sequence data—the first obtained for members of this group--tested several hypotheses: 1) The Tribe Hadenoecini is a monophyletic clade when compared with outgroups from their sister Tribe Dolocopodini, 2) The two genera Euhadenoecus and Hadenoecus are both monophyletic, 3) The forest Euhadenoecus and the trogloxenic Euhadenoecus are each monophyletic, 4) The two trogloxenes from Kentucky form a single clade, and the three most cave-adapted trogloxenes in Tennessee form a single clade. Our preliminary results support all four of these hypotheses. Our data, however, suggest that the divergence between the two genera and between the two clades of Hadenoecus occurred well before the Pleistocene and that only speciation within the two Hadenoecus clades occurred in the mid to late Pleistocene as suggested by Hubbell and Norton (1978).
UDPipe: Trainable Pipeline for Processing CoNLL-U Files Performing Tokenization, Morphological Analysis, POS Tagging and Parsing

Automatic natural language processing of large texts often presents recurring challenges in multiple languages: even for most advanced tasks, the texts are first processed by basic processing steps – from tokenization to parsing. We present an extremely simple-to-use tool consisting of one binary and one model (per language), which performs these tasks for multiple languages without the need for any other external data. UDPipe, a pipeline processing CoNLL-U-formatted files, performs tokenization, morphological analysis, part-of-speech tagging, lemmatization and dependency parsing for nearly all treebanks of Universal Dependencies 1.2 (namely, the whole pipeline is currently available for 32 out of 37 treebanks). In addition, the pipeline is easily trainable with training data in CoNLL-U format (and in some cases also with additional raw corpora) and requires minimal linguistic knowledge on the users’ part. The training code is also released.
Effect of vitreous fluidity on the measurement of blood‐retinal barrier permeability using contrast‐enhanced MRI

Breakdown of the blood‐retinal barrier (BRB), frequently an early clinical sign in retinopathy, can be accurately determined using contrast‐enhanced MRI. However, increased vitreous fluidity with age and disease may affect the accuracy of the MRI method. We compared the permeability surface area product per area of leaky retina in eyes with normal vitreous (5.42 ± 0.48 × 10−4 cm/min, mean ± SEM, n = 5) to the contralateral gas‐compressed vitrectomized eyes (5.41 ± 0.54 × 10−4 cm/min, n = 5). The effect of vitrectomy was not significant (P = 0.325) using a Wilcoxon matched pairs signed rank test on the signed differences of the PS' values.
Cardiovascular response to the i.v. administration of morphine in critically ill patients undergoing IPPV.

The haemodynamic changes following the administration of morphine 0.15 and 0.30 mg kg-1 i.v. were studied in 11 patients, free from known cardiac disease. All patients were acutely ill and their lungs were being ventilated mechanically. In those patients receiving 0.15 mg kg-1, the only haemodynamic change was a slight and transitory decrease in the systolic arterial pressure. In contrast, several changes were observed in patients receiving 0.30 mg kg-1: an immediate and prolonged decrease in the cardiac index was noted along with transient decreases in heart rate, stroke volume index, arterial pressure and left stroke work index. These results suggest that the haemodynamic cost of morphine 10 mg is negligible but could be significant when 20 mg has been administered and must be weighed against its beneficial effects in the critically ill patient.
Fast Response of the Tropics to an Abrupt Loss of Arctic Sea Ice via Ocean Dynamics

The role of ocean dynamics in the transient adjustment of the coupled climate system to an abrupt loss of Arctic sea ice is investigated using experiments with Community Climate System Model version 4 in two configurations: a thermodynamic slab mixed layer ocean and a full‐depth ocean that includes both dynamics and thermodynamics. Ocean dynamics produce a distinct sea surface temperature warming maximum in the eastern equatorial Pacific, accompanied by an equatorward intensification of the Intertropical Convergence Zone and Hadley Circulation. These tropical responses are established within 25 years of ice loss and contrast markedly with the quasi‐steady antisymmetric coupled response in the slab‐ocean configuration. A heat budget analysis reveals the importance of anomalous vertical advection tied to a monotonic temperature increase below 200 m for the equatorial sea surface temperature warming maximum in the fully coupled model. Ocean dynamics also rapidly modify the midlatitude atmospheric response to sea ice loss.
DNAshape: a method for the high-throughput prediction of DNA structural features on a genomic scale

We present a method and web server for predicting DNA structural features in a high-throughput (HT) manner for massive sequence data. This approach provides the framework for the integration of DNA sequence and shape analyses in genome-wide studies. The HT methodology uses a sliding-window approach to mine DNA structural information obtained from Monte Carlo simulations. It requires only nucleotide sequence as input and instantly predicts multiple structural features of DNA (minor groove width, roll, propeller twist and helix twist). The results of rigorous validations of the HT predictions based on DNA structures solved by X-ray crystallography and NMR spectroscopy, hydroxyl radical cleavage data, statistical analysis and cross-validation, and molecular dynamics simulations provide strong confidence in this approach. The DNAshape web server is freely available at http://rohslab.cmb. usc.edu/DNAshape/.
Multivariate analysis of allometry using point coordinates

For many years, the bivariate allometric equation has yielded insights about size and shape. Multivariate generalizations of the bivariate allometric equation are given by the principal components or factors extracted from a covariance matrix of the logarithms of the original measurements. The coefficients in the principal components or the factor loadings show the nature of changes in the variables, which may be isometric or allometric. A single suite of multivariate data may contain one or more sources of allometry. The relationships between the variables are shown by the principal components or factor loadings whereas the corresponding ordinations of specimens are revealed by the principal component or factor scores. In the examination of allometry, most workers have used measurements such as lengths, widths, areas, volumes, weights, etc. However, these parameters only provide indirect insights about size and shape. Instead, for many applications we prefer to analyze the coordinates of points, which are homologous and/or topographically constant relative to orthogonal X, Y and Z axes. An X coordinate is actually a distance or linear dimension parallel to the X axis. The other coordinates can be treated in the same way. Such data deal directly with size and shape. The information that can be derived from multivariate allometry of point coordinates is similar to that obtained from transformation grids. Two case studies are discussed, namely the growth of Eurypterus remipes remipes DeKay, a Silurian eurypterid, and the evolution of the Dicoelosia varica lineage of Silurian-Devonian brachiopods. The technique has been sucessfully applied to various groups of organisms including foraminifera, brachiopods, trilobites, eurypterids, and vertebrates, as well as various non-geological objects including hang gliders and vintage aircraft.
FPGAs: a new point in the database design space

In line with the insight that "one size" of databases will not fit all application needs [19] the database community is currently exploring various alternatives to commodity, CPU-based system designs. One particular candidate in this trend are field-programmable gate arrays (FPGAs), programmable chips that allow tailor-made hardware designs optimized for specific systems, applications, or even user queries. With a focus on database use, this tutorial introduces into FPGA technology, demonstrates its potential, but also pinpoints some challenges that need to be addressed before FPGA-accelerated database systems can go mainstream. The goal of this tutorial is to develop an intuition of an FPGA development cycle, receive guidelines for a "good" FPGA design, but also learn the limitations that hardware-implemented database processing faces. Our more high-level ambition is to spur a broader interest in database processing on novel hardware technology.
Hepatitis C virus-specific CD4+ T cell response after liver transplantation occurs early, is multispecific, compartmentalizes to the liver, and does not correlate with recurrent disease.

The role of hepatitis C virus (HCV)-specific CD4+ T cells in recurrent HCV infection after orthotopic liver transplantation (OLTx) is unclear. In parallel, 73 intrahepatic and 73 blood-derived T cell lines were established from 34 patients. At a single cell level, virus-specific interferon (IFN)-gamma production to various HCV proteins was determined by ELISPOT assay: 45 (62%) of 73 liver- or blood-derived T cell lines produced IFN-gamma in response to one of the HCV antigens. HCV specificity was detected mainly in the liver (47% vs. 23% in the blood; P<.05, chi(2) test) and was detectable earlier (< or =6 months) significantly more often than later (>6 months) after OLTx (78% vs 49%; P<.05, chi(2) test). Histology, histologic activity index, liver enzymes, and virus load did not correlate with the occurrence of HCV-specific CD4+ T cells. Despite strong immunosuppressive treatment, OLTx recipients can develop an early, multispecific, preferentially intrahepatic CD4+ T cell response that decreases over time, making it a potential candidate target for novel therapeutic approaches in the transplant setting.
Making Biographical Data in Wikipedia Readable: A Pattern-based Multilingual Approach

In this paper we present Biografix, a pattern based tool that simplifies parenthetical structures with biographical information, whose aim is to create simple, readable and accessible sentences. To that end, we analysed the parenthetical structures that appear in the first paragraph of the Basque Wikipedia, and concentrated on biographies. Although it has been designed and developed for Basque we adapted it and evaluated with other five languages. We also perform an extrinsic evaluation with a question generation system to see if Biografix improve its results.
Coexistence in two-type first-passage percolation models

We study the problem of coexistence in a two-type competition model governed by first-passage percolation on Zd or on the infinite cluster in Bernoulli percolation. We prove for a large class of ergodic stationary passage times that for distinct points x, y ∈ Zd, there is a strictly positive probability that {z ∈ Zd; d(y, z) d(x, z)} are both infinite sets. We also show that there is a strictly positive probability that the graph of time-minimizing path from the origin in first-passage percolation has at least two topological ends. This generalizes results obtained by Haggstrom and Pemantle for independent exponential times on the square lattice.
Pharmacological Modulation of Cortical Excitability Shifts Induced by Transcranial Direct Current Stimulation in Humans

Transcranial direct current stimulation (tDCS) of the human motor cortex results in polarity‐specific shifts of cortical excitability during and after stimulation. Anodal tDCS enhances and cathodal stimulation reduces excitability. Animal experiments have demonstrated that the effect of anodal tDCS is caused by neuronal depolarisation, while cathodal tDCS hyperpolarises cortical neurones. However, not much is known about the ion channels and receptors involved in these effects. Thus, the impact of the sodium channel blocker carbamazepine, the calcium channel blocker flunarizine and the NMDA receptor antagonist dextromethorphane on tDCS‐elicited motor cortical excitability changes of healthy human subjects were tested. tDCS‐protocols inducing excitability alterations (1) only during tDCS and (2) eliciting long‐lasting after‐effects were applied after drug administration. Carbamazepine selectively eliminated the excitability enhancement induced by anodal stimulation during and after tDCS. Flunarizine resulted in similar changes. Antagonising NMDA receptors did not alter current‐generated excitability changes during a short stimulation, which elicits no after‐effects, but prevented the induction of long‐lasting after‐effects independent of their direction. These results suggest that, like in other animals, cortical excitability shifts induced during tDCS in humans also depend on membrane polarisation, thus modulating the conductance of sodium and calcium channels. Moreover, they suggest that the after‐effects may be NMDA receptor dependent. Since NMDA receptors are involved in neuroplastic changes, the results suggest a possible application of tDCS in the modulation or induction of these processes in a clinical setting. The selective elimination of tDCS‐driven excitability enhancements by carbamazepine proposes a role for this drug in focussing the effects of cathodal tDCS, which may have important future clinical applications.
Effects of Benfotiamine and Methylcobalamin on Paclitaxel Induced Peripheral Neuropathy

Background: Reports indicate that paclitaxel causes a dose-limiting distal and symmetrical sensorimotor peripheral neuropathy. This study was designed to evaluate the protective effects of benfotiamine and methylcobalamin on prevention of paclitaxel induced peripheral neuropathy. Methods: Twenty four rats and twenty four mice were involved in this study. Each animal group was allocated to two main experimental groups [control group (n=6) and paclitaxel model group (n=18)]. The paclitaxel model group in rats was subdivided into 3 subgroups [paclitaxel group (6mg/kg i.p.) for 4 weeks, paclitaxel + benfotiamine (100mg/kg orally, daily for 8 weeks) and paclitaxel + methylcobalamin (500μg/kg i.p., twice weekly for 8 weeks)]. Whereas the paclitaxel model group of mice was subdivided into 3 sub groups [paclitaxel group (6mg/kg i.p. for 4 weeks), paclitaxel + benfotiamine (100mg/kg orally, daily for 6 weeks) and paclitaxel + methylcobalamin (500μg/kg orally, daily for 6 weeks)]. Electrophysiological and histological investigations, as well as a number of classical behavioural tests of nociception were performed. Results: Paclitaxel administration produced significant increase in latency, but decrease in amplitude and conduction velocity in peripheral motor nerves in rats. Degenerative changes of sciatic nerve were observed in rats. The paw withdrawal latency for heat hyperalgesia and the tail withdrawal latency for cold (allodynia and hyperalgesia) in mice were significantly reduced. Benfotiamine administration significantly ameliorated all electrophysiological changes induced by paclitaxel in peripheral motor nerves. Moreover benfotiamine decreased histological changes in rat’s sciatic nerve. In mice benfotiamine administration significantly ameliorated the reduced withdrawal latencies for cold and hot. Methylcobalamin administration together with paclitaxel attenuates the reduction in conduction velocity in rats but had no effect on the reduced amplitude. Methylcobalamin reduced degenerative changes in Schwann cells but had no effect on reduced myelin thickness. While in mice daily methylcobalamin administration significantly reduced the decreased withdrawal latencies for cold and hot. Conclusion: Benfotiamine 100mg/kg was very efficient in prevention of sensorimotor neuropathy induced by paclitaxel, whereas the suggested methylcobalamin (500μg/kg) twice weekly did not sufficiently prevent peripheral motor nerve destruction induced by paclitaxel, while the administration of high dose methylcobalamin every day is efficient in removal of thermal nociception induced during paclitaxel treatment.
The TREND experimental activities on “green” communication networks

Aimed at answering important questions about the energy demand of current telecom infrastructure and the design of sustainable and energy-efficient future networks, the research of a number of European partners is brought together in the TREND project. In this paper we present the achievements of the Work Package coordinating the experimental activities of the project - WP4. Although not presenting a completely finished portrait yet, the results shown help building a better global view on the “big picture” in the field of energy-efficient networking.
Potential usefulness of inflammatory markers to monitor respiratory functional impairment in sarcoidosis.

BACKGROUND Sarcoidosis is a multiorgan inflammatory granulomatous disorder of unknown origin for which adequate markers to monitor disease severity are lacking. The aim of this study was to evaluate the potential clinical usefulness of serologic markers of inflammation [high-sensitivity C-reactive protein (hs-CRP) and serum amyloid A (SAA)], T-cell activation [soluble interleukin-2 receptor (sIL2R)], and granuloma formation [angiotensin-converting enzyme (ACE)] for monitoring of sarcoidosis. METHODS Of the 185 sarcoidosis patients who visited the Sarcoidosis Management Center between 1999 and 2002, we selected 144 nonsmoking patients: 73 untreated (group I) and 71 treated (group II). Subgroups of the untreated patients [group Ia (nonchronic group with time since diagnosis < or = 2 years) and group Ib (chronic group with time since diagnosis >2 years)] were evaluated separately. ROC curves and logistic regression analyses were used to compare the diagnostic accuracy of different markers to assess disease severity. Pulmonary disease severity was defined by lung function test results. RESULTS In untreated subgroup Ia and the total untreated group (group I), sIL2R had the largest areas under the curves (AUCs; 0.891 and 0.799, respectively) and the highest sensitivity (82% and 64%), specificity (94% and 88%), and positive (82% and 70%) and negative (94% and 88%) predictive values among the evaluated markers in both untreated groups. Nevertheless, the confidence intervals for sIL2R AUC, sensitivity, and specificity were broad and partly overlapped those of ACE, hs-CRP, and SAA. In the treated group (group II), all four markers appeared to have comparable AUCs, ranging from 0.645 for SAA to 0.711 for sIL2R. CONCLUSION sIL2R appears to be useful for monitoring respiratory disease severity in sarcoidosis. We recommend sIL2R measurement in the follow-up of patients with sarcoidosis.
Alterations of Molecular and Behavioral Responses to Cocaine by Selective Inhibition of Elk-1 Phosphorylation

Activation of the extracellular signal-regulated kinase (ERK) signaling pathway in the striatum is crucial for molecular adaptations and long-term behavioral alterations induced by cocaine. In response to cocaine, ERK controls the phosphorylation levels of both mitogen and stress-activated protein kinase 1 (MSK-1), a nuclear kinase involved in histone H3 (Ser10) and cAMP response element binding protein phosphorylation, and Elk-1, a transcription factor involved in serum response element (SRE)-driven gene regulations. We recently characterized the phenotype of msk-1 knock-out mice in response to cocaine. Herein, we wanted to address the role of Elk-1 phosphorylation in cocaine-induced molecular, morphological, and behavioral responses. We used a cell-penetrating peptide, named TAT–DEF–Elk-1 (TDE), which corresponds to the DEF docking domain of Elk-1 toward ERK and inhibits Elk-1 phosphorylation induced by ERKs without modifying ERK or MSK-1 in vitro. The peptide was injected in vivo before cocaine administration in mice. Immunocytochemical, molecular, morphological, and behavioral studies were performed. The TDE inhibited Elk-1 and H3 (Ser10) phosphorylation induced by cocaine, sparing ERK and MSK-1 activation. Consequently, TDE altered cocaine-induced regulation of genes bearing SRE site(s) in their promoters, including c-fos, zif268, ΔFosB, and arc/arg3.1 (activity-regulated cytoskeleton-associated protein). In a chronic cocaine administration paradigm, TDE reversed cocaine-induced increase in dendritic spine density. Finally, the TDE delayed the establishment of cocaine-induced psychomotor sensitization and conditioned-place preference. We conclude that Elk-1 phosphorylation downstream from ERK is a key molecular event involved in long-term neuronal and behavioral adaptations to cocaine.
Total thrombin‐activatable fibrinolysis inhibitor (TAFI) antigen and pro‐TAFI in patients with haemophilia A

Pro‐thrombin‐activatable fibrinolysis inhibitor (pro‐TAFI), also known as TAFI, procarboxypeptidase U, or procarboxypeptidase B, is a relatively recently described plasma glycoprotein synthesized in the liver. It can be catalysed into its active form, TAFI (TAFIa, carboxypeptidase U or B) by a complex of thrombin/thrombomodulin. TAFI can potentially inhibit fibrinolysis by removing carboxyterminal lysine residues from partially degraded fibrin, decreasing plasminogen binding on the surface of fibrin, which thereby results in a decrease of the fibrinolytic activity. As TAFI represents a connection between coagulation and fibrinolysis, it can be expected that TAFI levels are altered in different thrombotic and haemorrhagic diseases, such as haemophilia A. Total TAFI antigen (including pro‐TAFI, TAFI and the inactive form of TAFI [TAFIi]) and pro‐TAFI were determined in 17 patients with haemophilia A. Thirteen healthy age‐matched volunteers served as controls. No significant difference in levels of total TAFI antigen was observed between controls and patients with haemophilia, although it was slightly decreased in patients with haemophilia. Pro‐TAFI was significantly reduced in haemophilia patients compared to controls (P=0.0113). TAFI antigen levels similar to controls have already been described in different clinical conditions, including haemophilia A. Decrease of pro‐TAFI in haemophilia A can be an additional factor, together with decrease in thrombin generation, which induces impaired activation of pro‐TAFI to TAFI, and could cause accelerated fibrinolysis. This supports the validity of usage of antifibrinolytics in the treatment of haemophilia A. In this paper we use new nomenclature for TAFI, and we believe that this recommended terminology for different forms of TAFI can simplify further standardization in TAFI investigation.