Miracle-dz/UniFAR-FTUs huggingface dataset:
THE LIMITS OF AMINO ACID SEQUENCE DATA IN ANGIOSPERM PHYLOGENETIC RECONSTRUCTION

Amino acid sequence data are available for ribulose biphosphate carboxylase, plastocyanin, cytochrome c, and ferredoxin for a number of angiosperm families. Cladistic analysis of the data, including evaluation of all equally or almost equally parsimonious cladograms, shows that much homoplasy (parallelisms and reversals) is present and that few or no well supported monophyletic groups of families can be demonstrated. In one analysis of nine angiosperm families and 40 variable amino acid positions from three proteins, the most parsimonious cladograms were 151 steps long and contained 63 parallelisms and reversals (consistency index = 0.583). In another analysis of six families and 53 variable amino acid positions from four proteins, the most parsimonious cladogram was 161 steps long and contained 50 parallelisms and reversals (consistency index = 0.689). Single changes in both data matrices could yield most parsimonious cladograms with quite different topologies and without common monophyletic groups. Presently, amino acid sequence data are not comprehensive enough for phylogenetic reconstruction among angiosperms. More informative positions are needed, either from sequencing longer parts of the proteins or from sequencing more proteins from the same taxa.
Predicting Drug-Target Interaction Networks Based on Functional Groups and Biological Features

Background Study of drug-target interaction networks is an important topic for drug development. It is both time-consuming and costly to determine compound-protein interactions or potential drug-target interactions by experiments alone. As a complement, the in silico prediction methods can provide us with very useful information in a timely manner. Methods/Principal Findings To realize this, drug compounds are encoded with functional groups and proteins encoded by biological features including biochemical and physicochemical properties. The optimal feature selection procedures are adopted by means of the mRMR (Maximum Relevance Minimum Redundancy) method. Instead of classifying the proteins as a whole family, target proteins are divided into four groups: enzymes, ion channels, G-protein- coupled receptors and nuclear receptors. Thus, four independent predictors are established using the Nearest Neighbor algorithm as their operation engine, with each to predict the interactions between drugs and one of the four protein groups. As a result, the overall success rates by the jackknife cross-validation tests achieved with the four predictors are 85.48%, 80.78%, 78.49%, and 85.66%, respectively. Conclusion/Significance Our results indicate that the network prediction system thus established is quite promising and encouraging.
Enumeration of the Simian Virus 40 Early Region Elements Necessary for Human Cell Transformation

ABSTRACT While it is clear that cancer arises from the accumulation of genetic mutations that endow the malignant cell with the properties of uncontrolled growth and proliferation, the precise combinations of mutations that program human tumor cell growth remain unknown. The study of the transforming proteins derived from DNA tumor viruses in experimental models of transformation has provided fundamental insights into the process of cell transformation. We recently reported that coexpression of the simian virus 40 (SV40) early region (ER), the gene encoding the telomerase catalytic subunit (hTERT), and an oncogenic allele of the H-ras gene in normal human fibroblast, kidney epithelial, and mammary epithelial cells converted these cells to a tumorigenic state. Here we show that the SV40 ER contributes to tumorigenic transformation in the presence of hTERT and oncogenic H-ras by perturbing three intracellular pathways through the actions of the SV40 large T antigen (LT) and the SV40 small t antigen (ST). LT simultaneously disables the retinoblastoma (pRB) and p53 tumor suppressor pathways; however, complete transformation of human cells requires the additional perturbation of protein phosphatase 2A by ST. Expression of ST in this setting stimulates cell proliferation, permits anchorage-independent growth, and confers increased resistance to nutrient deprivation. Taken together, these observations define the elements of the SV40 ER required for the transformation of human cells and begin to delineate a set of intracellular pathways whose disruption, in aggregate, appears to be necessary to generate tumorigenic human cells.
Natural language processing resources: Using semantic web technologies

Natural language processing relies heavily on resources. Most common usage scenarios include using the resources for automated lexical tagging or named entity recognition. Also manually annotated language resources are used for benchmarking of new automated approaches. To allow any processing on a large scale and considering the complexity of natural language (words can have multiple meanings within the same general context) the resources have to be quite large. In this paper we focus on lexical resources in ontology form.
Using Image Morphing for Memory-Efficient Impostor Rendering on GPU

Real-time rendering of large animated crowds consisting thousands of virtual humans is important for several applications including simulations, games and interactive walkthroughs, but cannot be performed using complex polygonal models at interactive frame rates. For that reason, several methods using large numbers of pre-computed image-based representations, which are called as impostors, have been proposed. These methods take the advantage of existing programmable graphics hardware to compensate the computational expense while maintaining the visual fidelity. Making the number of different virtual humans, which can be rendered in real-time, not restricted anymore by the required computational power but by the texture memory consumed for the variety and discretization of their animations. In this work, we proposed an alternative method that reduces the memory consumption by generating compelling intermediate textures using image-morphing techniques. In order to demonstrate the preserved perceptual quality of animations, where half of the key-frames were rendered using the proposed methodology, we have implemented the system using the graphical processing unit and obtained promising results at interactive frame rates.
Tremor attenuation using FES-based joint stiffness control

In this paper, a strategy to attenuate tremor based on co-contraction of antagonist muscles using Functional Electrical Stimulation (FES) is fully presented. Both methods to track tremor features in real-time, while filtering voluntary motion, and to identify a suitable joint model are described. Using this information, the stimulation controller modulates joint stiffness based on tremor intensity, while preventing the generation of undesirable joint torque. An experimental evaluation of the system, which confirmed the effectiveness of the approach, is also presented.
Autotrophic and heterotrophic metabolism of microbial planktonic communities in an oligotrophic coastal marine ecosystem: seasonal dynamics and episodic events

Abstract. A 18 month study was performed in the Bay of Villefranche to assess the episodic and seasonal variation of autotrophic and heterotrophic ecosystem processes. A typical spring bloom was encountered, where maximum of gross primary production (GPP) was followed by maxima of bacterial respiration (BR) and production (BP). The trophic balance (heterotrophy vs. autotrophy) of the system did not exhibit any seasonal trend although a strong intra-annual variability was observed. On average, the community tended to be net heterotrophic with a GPP threshold for a balanced metabolism of 1.1 μmol O2 l−1 d−1. Extended forest fires in summer 2003 and a local episodic upwelling in July 2003 likely supplied orthophosphate and nitrate into the system. These events were associated with an enhanced bacterioplankton production (up to 2.4-fold), respiration (up to 4.5-fold) and growth efficiency (up to 2.9-fold) but had no effect on GPP. A Sahara dust wet deposition event in February 2004 stimulated bacterial abundance, production and growth efficiency but not GPP. Our study suggests that short-term disturbances such as wind-driven upwelling, forest fires and Sahara dust depositions can have a significant but previously not sufficiently considered influence on phytoplankton- and bacterioplankton-mediated ecosystem functions and can modify or even mask the seasonal dynamics. The study also indicates that atmospheric deposition of nutrients and particles not only impacts phytoplankton but also bacterioplankton and could, at times, also shift systems stronger towards net heterotrophy.
Mapping Semantic Information from FrameNet onto VALLEX

Mapping Semantic Information from FrameNet onto VALLEX In this article, we introduce a project aimed at enhancing a valency lexicon of Czech verbs with semantic information. For this purpose, we make use of FrameNet, a semantically oriented lexical resource. At the present stage, semantic frames from FrameNet have been mapped to eight groups of verbs with various semantic and syntactic properties. The feasibility of this task has been verified by the achieved inter-annotator agreement measured on two semantically and syntactically different groups of verbs - verbs of communication and exchange (85.9% and 78.5%, respectively). Based on the upper level semantic frames from the relation of ‘Inheritance’ built in FrameNet, the verbs of these eight groups have been classified into more coherent semantic classes. Moreover, frame elements from these upper level semantic frames have been assigned to valency complementations of the verbs of the listed groups as semantic roles. As in case of semantic frames, the achieved interannotator agreement concerning assigning frame elements measured on verbs of communication and exchange has been promising (95.6% and 91.2%, respectively). As a result, 1 270 lexical units pertaining to the verbs of communication, mental action, psych verbs, social interaction, verbs of exchange, motion, transport and location (2 129 Czech verbs in total if perfective and imperfective verbs being counted separately) have been classified into syntactically and semantically coherent classes and their valency complementations have been characterized by semantic roles adopted from the FrameNet lexical database.
Cyclosporine suppresses hepatitis C virus in vitro and increases the chance of a sustained virological response after liver transplantation

Cyclosporine is an immunosuppressive agent widely used in the management of liver transplant recipients. Cyclosporine has been shown to have antiviral activities against HIV, herpes simplex, and vaccinia viruses. The aim of this study was to determine the effect of Cyclosporine in viral clearance in the liver transplant recipients during therapy with combination of interferon and ribavirin, and to determine the anti‐viral potential of Cyclosporine in vitro. Immunosuppression consisted of either Cyclosporine or Tacrolimus‐based therapy. Both groups received therapy with interferon and ribavirin for 48 weeks when evidence of progressive histologic disease was determined. We found that subjects on Cyclosporine‐based immunosuppression (n = 56) had a higher sustained virological response of 46% compared to 27% in the patients on Tacrolimus‐based therapy (n=59, P = 0.03). In vitro studies were performed to evaluate the antiviral effect of Cyclosporine in the replicon system. These studies showed that Cyclosporine inhibits hepatitis C viral replication in a dose‐dependent manner. Combination of Cyclosporine with interferon showed additive effect, and its function is independent of interferon signaling pathways. In conclusion, Cyclosporine may offer an advantage to Tacrolimus in those patients undergoing interferon‐based therapy and should be studied in a prospective randomized trial. Liver Transpl 12:51–57, 2006. © 2005 AASLD.
Intersymbol Interference Due to the Atmospheric Turbulence for Free-Space Optical Communication System

Weak atmospheric turbulence causes pulse broadening of an optical signal. In this article, we drive the pulse broadening as a function of turbulence strength by temporal moments directly. We derive pulse broadening dependency on turbulence strength and propagation distance when an optical signal propagates through atmosphere. This pulse broadening induces intersymbol interference (ISI) between adjacent pulses. Based on this derived results, we develop some observation patterns using a practical example.
SPECT findings in the Kleine-Levin syndrome.

STUDY OBJECTIVES The Kleine-Levin Syndrome, is a rare disorder with onset during teenage years, but little is known on etiopathogenesis. Seven subjects with Kleine-Levin Syndrome accumulated over time had systematic SPECT studies during (n=5) and out (n=7) of the symptomatic period. SUBJECTS Seven boys with symptom onset between 11 and 17 years of age and at least 2 episodes per year were followed for a mean of 6 years. METHODS Electroencephalogram awake-asleep, computed tomography scan, and magnetic resonance imaging studies were performed before Tc-99m ECD single photon emission tomography (SPECT) obtained during day 4 or 5 (n=5) and at least 1 month away from the symptomatic period (n=7). RESULTS All imaging tests except SPECT were normal. Hypoperfusion of both thalami were seen during the symptomatic period that completely disappeared during the asymptomatic period. Hypoperfusion in other regions were also noted in some, but not all subjects. They persisted during the asymptomatic period in 2 cases over the temporal lobe (2/7 cases), frontal lobe (1/7 cases), and basal ganglia (1/7 cases). The largest amount of persistent hypoperfusion was seen in the subject with longest clinical evolution. CONCLUSION Hypoperfusion of the thalamus is a consistent finding during the symptomatic period, but perfusion abnormalities may persist even during the asymptomatic period. The longer the duration of the syndrome, the more extended the hypoperfusion regions during the asymptomatic period.
Evaluating and Improving the ElarmS Earthquake Early Warning Algorithm

Earthquake Alarm Systems, or ElarmS, is a network-based earthquake early warning (EEW) system developed in California. This dissertation concerns the transition of ElarmS from research prototype to production-grade code. We test ElarmS' performance for large earthquakes with an extensive dataset of large events from Japan. Using the Japanese dataset and results, we develop a statistical error model for the magnitude, location, and ground motion prediction algorithms. We adapt ElarmS to run continuously throughout the state and analyze system latencies due to various seismic networks and instruments. We then rewrite ElarmS completely in newer, more efficient code, while redesigning the association and alert algorithms for improved performance. Finally, we apply an Artificial Neural Network (ANN) at the end of system processing, to detect and block false alerts. The ANN allows ElarmS to send earlier, faster alert messages, when fewer stations have contributed data to an event estimate. ElarmS now sends realtime alert messages to the California Integrated Seismic Network's ShakeAlert EEW system.
The use of social gaze cues in real world scenes

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Doxorubicin in combination with fluorouracil and cyclophosphamide (i.v. FAC regimen, day 1, 21) versus methotrexate in combination with fluorouracil and cyclophosphamide (i.v. CMF regimen, day 1, 21) as adjuvant chemotherapy for operable breast cancer: a study by the GEICAM group.

BACKGROUND The purpose of this study was to determine the relative efficacy of doxorubicin versus methotrexate in combination with intravenous cyclophosphamide and 5-fluorouracil (FAC versus CMF) as adjuvant chemotherapy for operable breast cancer. PATIENTS AND METHODS Over a 4-year period, 985 women undergoing curative surgery for breast cancer (T1-3 N0-2 M0, stage I-IIIA, UICC) from nine hospitals were stratified with respect to axillary node involvement (node positive versus node negative) and randomized to receive either FAC (500/50/500/m(2)) every 3 weeks for six cycles or CMF (600/60/600/m(2)) every 3 weeks for six cycles. RESULTS The relative dose intensities of FAC and CMF were 87% and 85% of planned doses, respectively. Unadjusted data indicated a non-significant trend towards better results with FAC. In the prospectively formed subset of node-negative patients, disease-free survival and overall survival were statistically superior in the FAC treatment arm (P = 0.041 and 0.034, respectively), but this advantage was not seen in the subset of node-positive patients, probably because of a difference in the percentage of patients with four or more positive nodes. Adjusting data for size of treatment effect and potential interactions (number of positive nodes, tumor size, treatment center), the overall relative risk (RR) of disease recurrence and death were significantly lower with FAC treatment (RR 1.2, P = 0.03, and RR 1.3, P = 0.05, respectively). This result was mainly due to the difference observed in the node-negative patient population. Toxicity was mild: FAC induced more alopecia, emesis, mucositis and cardiotoxicity; this last was of clinical concern, but was infrequent and manageable. CMF induced more conjunctivitis and weight gain. There were no toxic deaths. CONCLUSIONS Doxorubicin in combination with day 1 i.v. cyclophosphamide and 5-fluorouracil is superior to methotrexate in combination with day 1 i.v. cyclophosphamide and 5-fluorouracil as adjuvant chemotherapy for operable breast cancer. A treatment effect is particularly evident in the node-negative patients. Although the clinical toxicity of FAC is greater than that of CMF, the levels were manageable and clinically acceptable.
The NcGRA7 gene encodes the immunodominant 17 kDa antigen of Neospora caninum

A Neospora caninum 17–19 kDa antigenic protein fraction (p17) in one-dimensional polyacrylamide gel electrophoresis (SDS-PAGE) is the immunodominant antigen recognized by sera from bovines naturally infected by N. caninum. To identify the proteins making up the p17 fraction, we screened a new N. caninum tachyzoite cDNA library with an affinity-purified antibody against p17 (APA17). We isolated several cDNA clones with 100% sequence identity to the NcGRA7 gene. This previously described gene encodes a dense granule protein with an apparent molecular mass of 33 kDa. A second line of evidence emerged through a combined proteomic approach associating two-dimensional PAGE (2D-PAGE) to Western blotting and to mass spectrometry to characterize the p17 fraction. Two acidic immunodominant but minority protein spots were recognized by APA17 and by bovine sera. These antigens of 17 and 33 kDa are respectively composed of 4 and 2 isoforms. Furthermore, p17 isolation by 2D-PAGE and peptide sequencing by tandem mass spectrometry yielded a partial sequence of 17 amino acids, which allowed the putative amino terminal region of the NcGRA7 protein to be identified unambiguously.The NcGRA7 protein, without the putative signal peptide at the NH2-terminus, was cloned and expressed in Escherichia coli and when the purified recombinant protein (rNcGRA7) was analysed by SDS-PAGE and mass spectrometry, 2 bands of 24 and 33 kDa were resolved and identified as NcGRA7. These results demonstrate that the immunodominant 17 kDa antigen of N. caninum is encoded by the NcGRA7 gene.
Efficiency of Leakage Reduction Techniques on Different Static Logic Styles for Embedded Portable Applications with High Standby to Active Time Ratio

Leakage power is emerging as a major portion of the total power consumption in battery operated embedded systems. Thus, the designers face critical challenges in choosing the best circuit topologies with the appropriate leakage reduction technique in order to optimally balance the power and performance. This paper evaluates and compares the different static logic styles, with dual-threshold voltage and power gating techniques to attain low power and high performance VLSI systems in terms of power delay product and standby leakage power. A PMOS header for power gating with and without gated input schemes are evaluated. The simulations are carried out using a 180nm dual threshold mixed mode process technology.
IEEE 802.11 protocol: design and performance evaluation of an adaptive backoff mechanism

In WLANs, the medium access control (MAC) protocol is the main element that determines the efficiency of sharing the limited communication bandwidth of the wireless channel. The fraction of channel bandwidth used by successfully transmitted messages gives a good indication of the protocol efficiency, and its maximum value is referred to as protocol capacity. In a previous paper we have derived the theoretical limit of the IEEE 802.11 MAC protocol capacity. In addition, we showed that if a station has an exact knowledge of the network status, it is possible to tune its backoff algorithm to achieve a protocol capacity very close to its theoretical bound. Unfortunately, in a real case, a station does not have an exact knowledge of the network and load configurations (i.e., number of active stations and length of the message transmitted on the channel) but it can only estimate it. In this work we analytically study the performance of the IEEE 802.11 protocol with a dynamically tuned backoff based on the estimation of the network status. Results obtained indicate that under stationary traffic and network configurations (i.e., constant average message length and fixed number of active stations), the capacity of the enhanced protocol approaches the theoretical limits in all the configurations analyzed. In addition, by exploiting the analytical model, we investigate the protocol performance in transient conditions (i.e., when the number of active stations sharply changes).
Catenary optics for achromatic generation of perfect optical angular momentum

The nanoscale structures inspired by the natural catenaries can achromatically spin light wave. The catenary is the curve that a free-hanging chain assumes under its own weight, and thought to be a “true mathematical and mechanical form” in architecture by Robert Hooke in the 1670s, with nevertheless no significant phenomena observed in optics. We show that the optical catenary can serve as a unique building block of metasurfaces to produce continuous and linear phase shift covering [0, 2π], a mission that is extremely difficult if not impossible for state-of-the-art technology. Via catenary arrays, planar optical devices are designed and experimentally characterized to generate various kinds of beams carrying orbital angular momentum (OAM). These devices can operate in an ultra-broadband spectrum because the anisotropic modes associated with the spin-orbit interaction are almost independent of the incident light frequency. By combining the optical and topological characteristics, our approach would allow the complete control of photons within a single nanometric layer.