Miracle-dz/UniFAR-FTUs huggingface dataset:
The Molecular Biology Database Collection: 2003 update

The Molecular Biology Database Collection is an online resource listing key databases of value to the biological community. This Collection is intended to bring fellow scientists' attention to high-quality databases that are available throughout the world, rather than just be a lengthy listing of all available databases. As such, this up-to-date listing is intended to serve as the jumping-off point from which to find specialized databases that may be of use in advancing biological research. The databases included in this Collection provide new value to the underlying data by virtue of curation, new data connections or other innovative approaches. Short, searchable summaries and updates for each of the databases included in this Collection are available through the Nucleic Acids Research Web site at http://nar.oupjournals. org.
Continuous Thoracic Epidural Anesthesia Induces Segmental Sympathetic Block in the Awake Rat

Thoracic epidural anesthesia (TEA) is used increasingly in critical care, especially for cardiac and intestinal sympathetic block. In this study we evaluated cardiorespiratory function and sympathetic activity in a new model of continuous TEA in awake rats. Thirteen rats received epidural saline control (CON) or bupivacaine 0.5% epidural infusion (EPI) at 15 &mgr;l/h for 2 h on day 1 and day 3. Mean arterial blood pressure, heart rate, respiration rate, arterial Pco2, and motor score were recorded at baseline and after 30, 60, 90, and 120 min. Skin temperature was measured at front paws, high-thoracic, mid-thoracic, and low-thoracic, hind paws, and the proximal and distal tail. Changes in sympathetic activity were assessed by skin temperature changes from baseline (&Dgr;T). In the EPI group, hemodynamics and respiration remained unchanged and only mild motor deficits occurred. &Dgr;T in thoracic segments was higher in the EPI than in the CON group (P < 0.001 at all times at high-thoracic, mid-thoracic, and low-thoracic segments). Skin temperature decreased in the distal tail in the EPI group, e.g., after 90 min &Dgr;T = −0.86 ± 0.25°C (EPI) versus 0.4 ± 0.12°C (CON) (P < 0.05 at 60, 90, and 120 min). &Dgr;T on day 3 was comparable to day 1. TEA induced stable segmental sympathetic block without cardiorespiratory and motor side effects in awake rats. This new technique may be applied in prolonged models of critical illness.
Fabrication and Characterization of the Charge-Plasma Diode

We present a new lateral Schottky-based rectifier called the charge-plasma diode realized on ultrathin silicon-on-insulator. The device utilizes the workfunction difference between two metal contacts, palladium and erbium, and the silicon body. We demonstrate that the proposed device provides a low and constant reverse leakage-current density of about 1 fA/μm with ON/OFF current ratios of around 107 at 1-V forward bias and room temperature. In the forward mode, a current swing of 88 mV/dec is obtained, which is reduced to 68 mV/dec by back-gate biasing.
WINSOME: A middleware platform for the provision of secure monitoring services over Wireless Sensor Networks

This paper deals with the design and implementation of security mechanisms in networked embedded systems (e.g. Wireless Sensor Networks (WSN)), without the support of external “resource unconstrained” facilities. While most literature contributions propose to put intelligence (that is usually more consuming both in computational resources and in memory as well) outside the WSN, we have already reported in some previous works that, under certain limitations, a WSN can operate as a functionally “autonomous entity” not only for sensing operations. This paper provides a global overview of the related research project and then reports on recent design upgrades to what we denote as the “Secure Platform”, i.e. the SW platform over WSN that is able to support a wide range of applications in non-standard environment such as monitoring of critical infrastructures, data acquisition in hazardous environments under standard security conditions. The work presented here is a partial achievement of the internal project WINSOME (WIreless sensor Network-based Secure system fOr structural integrity Monitoring and AlErting) at our Centre DEWS, whose target is to develop a cross-layer secure framework for advanced monitoring and alerting applications.
Dirichlet-Enhanced Spam Filtering based on Biased Samples

We study a setting that is motivated by the problem of filtering spam messages for many users. Each user receives messages according to an individual, unknown distribution, reflected only in the unlabeled inbox. The spam filter for a user is required to perform well with respect to this distribution. Labeled messages from publicly available sources can be utilized, but they are governed by a distinct distribution, not adequately representing most inboxes. We devise a method that minimizes a loss function with respect to a user's personal distribution based on the available biased sample. A nonparametric hierarchical Bayesian model furthermore generalizes across users by learning a common prior which is imposed on new email accounts. Empirically, we observe that bias-corrected learning outperforms naive reliance on the assumption of independent and identically distributed data; Dirichlet-enhanced generalization across users outperforms a single ("one size fits all") filter as well as independent filters for all users.
A high step-up current fed multi-resonant converter with coupled inductor

The two input filter inductors of the previously proposed current fed multi-resonant converter (CFMRC) occupy too much volume and hence restrict the power density of the converter. In this paper, an integrated magnetic structure is adopted to the CFMRC's input inductors to cut down the size, cost and loss of the CFMRC. With proper design, the inverse coupling of input inductors apparently reduces the ripple of the current flowing through the inductors. Thereby, the inductance can be reduced to further decrease the core size and copper length, and hence farther improve the power density as well as the efficiency of the converter. The above mentioned merits are verified by a 150 W prototype with integrated input inductors operating at 255 kHz switching frequency, the volume of the input inductors is reduced from 25410 mm3 to 7056 mm3 after integrating, and the full load efficiency is increased from 95.4% to 95.9%.
A Hybrid Algorithm for Accurate Stream Entropy Estimation

Entropy estimation plays an important role in many network tasks, in particular, anomaly detection. Accurate estimation of entropy demands large memory. In this paper, we propose a novel hybrid algorithm that processes items with different frequencies separately. For items with frequency higher than a given threshold, counters are used while for items with lower frequency, the technique introduced by Alon, Matias and Szegedy is applied. We analyze the error and variance bounds of the estimations generated by this hybrid algorithm, proved to be more accurate than the pure random algorithm, at the cost of no significant increase in space complexity. As demonstrated by experiments, this entropy estimation may be used to detect traffic anomaly resulted from different types of attacks.
Molecular mechanisms controlling legume autoregulation of nodulation.

BACKGROUND High input costs and environmental pressures to reduce nitrogen use in agriculture have increased the competitive advantage of legume crops. The symbiotic relationship that legumes form with nitrogen-fixing soil bacteria in root nodules is central to this advantage. SCOPE Understanding how legume plants maintain control of nodulation to balance the nitrogen gains with their energy needs and developmental costs will assist in increasing their productivity and relative advantage. For this reason, the regulation of nodulation has been extensively studied since the first mutants exhibiting increased nodulation were isolated almost three decades ago. CONCLUSIONS Nodulation is regulated primarily via a systemic mechanism known as the autoregulation of nodulation (AON), which is controlled by a CLAVATA1-like receptor kinase. Multiple components sharing homology with the CLAVATA signalling pathway that maintains control of the shoot apical meristem in arabidopsis have now been identified in AON. This includes the recent identification of several CLE peptides capable of activating nodule inhibition responses, a low molecular weight shoot signal and a role for CLAVATA2 in AON. Efforts are now being focused on directly identifying the interactions of these components and to identify the form that long-distance transport molecules take.
Inhibition of 3‐hydroxy‐3‐methylglutaryl coenzyme A (HMG CoA) reductase does not inhibit the platelet procoagulant response

1 Haverkate F, Samama M. Familial dysfibrinogenemia and thrombophilia: report on a study of the SSC subcommittee on fibrinogen. Thromb Haemost 1995; 73: 151–61. 2 Mosesson MW. Dysfibrinogenemia and thrombosis. Semin Thromb Hemost 1999; 3: 311–9. 3 Hanss MM, Ffrench PO, Mornex JF, Chabuet M, Biot F, De Mazancourt P, Dechavanne M. Two novel fibrinogen variants found in patients with pulmonary embolism and their families. J Thromb Haemost 2003; 1: 1251–7. 4 Koopman J, Haverkate F, Grimbergen J, Engesser L, Novakova I, Kerst AF, Lord ST. Abnormal fibrinogens Ijmuiden (BbArg14 > Cys) and Nijmegen (BbArg44 > Cys) form disulfide-linked fibrinogen-albumin complexes. Proc Natl Acad Sci USA 1992; 89: 3478–82. 5 Koopman J, Haverkate F, Grimbergen J, Lord ST, Mosesson MW, DiOrio JP, Siebenlist KS, Legrand C, Soria J, Soria C, Caen JP. Molecular basis for fibrinogen Dusart (Aa554Arg > Cys) and its association with abnormal fibrin polymerization and thrombophilia. J Clin Invest 1993; 91: 1637–43. 6 Steinmann C, Bogli C, JungoM, Lammle B, Heinemann G, Wermuth B, Redaelli R, Baudo F, Furlan M. A new substitution, c358Ser > Cys, in fibrinogen Milano VII causes defective fibrin polymerization. Blood 1994; 84: 1874–80. 7 Terukina S, Matsuda M, Hirata H, Takeda Y, Miyata T, Takao T, Shimonishi Y. Substitution of cArg-275 by Cys in an abnormal fibrinogen, ‘‘fibrinogen Osaka-II’’. Evidence for a unique solitary cystine structure at the mutation site. J Biol Chem 1988; 263: 13579–87. 8 Boyer MH, Shainoff JR, Ratnoff OD. Acceleration of fibrin polymerization by calcium ions. Blood 1972; 39: 382–7. 9 Tarumi T, Martincic D, Thomas A, Janco R, Hudson M, Baxter P, Gailani D. Familial thrombophilia associated with fibrinogen Paris V: Dusart syndrome. Blood 2000; 96: 1191–3. 10 Wada Y, Lord ST. A correlation between thrombotic disease and a specific fibrinogen abnormality (Aalpha 554Arg > Cys) in two unrelated kindred, Dusart and Chapel Hill III. Blood 1994; 84: 3709–14. 11 MosessonMW, Siebenlist KR, Hainfeld JF, Wall JS, Soria J, Soria C, Caen JP. The relationship between the fibrinogen D domain selfassociation/cross-linking site (gXL) and the fibrinogen Dusart abnormality (AaR554C-albumin). Clues to thrombophilia in the ‘‘Dusart syndrome’’. J Clin Invest 1996; 97: 2342–50. 12 Marchi R, Lundberg U, Grimbergen J, Koopman J, Torres A, de Bosch NB, Haverkate F, Arocha Pinango CL. Fibrinogen Caracas V, an abnormal fibrinogen with an Aa 532Ser > Cys substitution associated with thrombosis. Thromb Haemost 2000; 84: 263–70. 13 Hanss M, Biot F. A database for human fibrinogen variants. Ann N Y Acad Sci 2001; 936: 89–90. 14 Walter S, Stabler S, Lefkowitz JB. Fibrinogen Denver: a dysfibrinogenemia associated with abnormal Reptilase time and significant bleeding. Haemophilia 2006; 12: 393–7.
An Ambulatory System for Gait Monitoring Based on Wireless Sensorized Insoles

A new gait phase detection system for continuous monitoring based on wireless sensorized insoles is presented. The system can be used in gait analysis mobile applications, and it is designed for real-time demarcation of gait phases. The system employs pressure sensors to assess the force exerted by each foot during walking. A fuzzy rule-based inference algorithm is implemented on a smartphone and used to detect each of the gait phases based on the sensor signals. Additionally, to provide a solution that is insensitive to perturbations caused by non-walking activities, a probabilistic classifier is employed to discriminate walking forward from other low-level activities, such as turning, walking backwards, lateral walking, etc. The combination of these two algorithms constitutes the first approach towards a continuous gait assessment system, by means of the avoidance of non-walking influences.
Determinants of voluntary executive stock option disclosure in Brazil

This study investigates whether the governance attributes of Brazilian companies are associated with voluntary executive stock option (ESO) disclosure. Results show that Brazilian companies voluntarily disclose very little about their ESO plans, and that board size, presence of a compensation committee, and auditing by a Big 4 firm are significantly related to the degree of voluntary ESO disclosure. We also show that family-controlled companies in Brazil are associated with low voluntary ESO disclosure. Results are robust to a number of specification tests, dependent and explanatory variable measurements, and sample composition. This study has professional and regulatory implications for Brazil and other emerging capital markets. The results underscore the need for stricter rules for executive compensation reporting in Brazil, and they invite policy makers and regulators in emerging markets to consider the effects of company-level governance factors on disclosure incentives.
Distortions in QoE Measurements of Ubiquitous Mobile Video Services Caused by the Preconceptions of Test Subjects

In telecommunication services, alongside QoS, QoE provision has become essential, thus performance and quality evaluation measurement results need to reflect reality as much as possible. Our goal is to enhance QoE evaluation schemes and enable improved QoE provision for video applications and services anytime and anywhere. In order to eliminate potential erroneous conclusions of QoE assessment techniques, our paper reveals a novel topic of distortions caused by preconceptions based on prior technical knowledge of QoE measurement test subjects. In our analysis we introduce the differences from genuine QoE measurement results in 3G ubiquitous mobile video service scenarios where test subjects were aware of the service parameters during measurements. We show how subjects' evaluations were affected and investigate the identified phenomenon in terms of Mean Opinion Score deviations and the overall QoE result distortion.
Nonparametric Inference of Hemodynamic Response for Multi-Subject fMRI Data under Multi-Stimulus Design

Many existing methods for estimating the hemodynamic response functions (HRF) break down when analyzing multi-subject fMRI data from multi-stimulus designs due to the large and inhomogeneous variances across subjects. Within the context of the General Linear Model (GLM), we propose two new nonparametric estimators of the HRF for fMRI data arising from such designs. We first introduce a kernel-smoothed nonparametric estimator, based on which we conduct hypothesis tests to identify task relevant neural activity. To cope with the inherent large data variance, we further impose a Tikhonov regularization to the kernel-smoothed HRF estimator, on top of which a bias-correction procedure is introduced by utilizing the multi-subject averaged HRF. A fast algorithm with linear computational time is also developed to select optimal regularization and smoothing parameters. We apply these methods to the fMRI data collected under a psychology design employing the Monetary Incentive Delay (MID) task. The proposed method successfully identified regions of neural activation related to affective responses to monetary incentives and penalties that were not identified using the traditional GLM approach. Moreover, the HRF estimates reveal that the magnitude of the penalty-related neural activity is significantly correlated with an individual state anxiety measure.
Numerical Study of Few-Cycle Pulses by Nonlinear Compression in Two-Photon Semiconductor Amplifiers

Optical pulse compression down to a few optical cycles by the ultrabroadband gain of nonlinear two-photon process in semiconductors is proposed. Recent experimental demonstration of semiconductor two-photon gain (TPG) has motivated this analysis of ultrashort pulse dynamics with realistic semiconductor parameters. Comprehensive material model, including TPG, carrier depletion, linear absorption, Kerr effect, plasma response of injected carriers, and the material dispersion were numerically simulated using the finite-difference time-domain method. Pulse compression down to a few optical cycles is theoretically predicted.
The Antibacterial Activity of Honey Derived from Australian Flora

Chronic wound infections and antibiotic resistance are driving interest in antimicrobial treatments that have generally been considered complementary, including antimicrobially active honey. Australia has unique native flora and produces honey with a wide range of different physicochemical properties. In this study we surveyed 477 honey samples, derived from native and exotic plants from various regions of Australia, for their antibacterial activity using an established screening protocol. A level of activity considered potentially therapeutically useful was found in 274 (57%) of the honey samples, with exceptional activity seen in samples derived from marri (Corymbia calophylla), jarrah (Eucalyptus marginata) and jellybush (Leptospermum polygalifolium). In most cases the antibacterial activity was attributable to hydrogen peroxide produced by the bee-derived enzyme glucose oxidase. Non-hydrogen peroxide activity was detected in 80 (16.8%) samples, and was most consistently seen in honey produced from Leptospermum spp. Testing over time found the hydrogen peroxide-dependent activity in honey decreased, in some cases by 100%, and this activity was more stable at 4°C than at 25°C. In contrast, the non-hydrogen peroxide activity of Leptospermum honey samples increased, and this was greatest in samples stored at 25°C. The stability of non-peroxide activity from other honeys was more variable, suggesting this activity may have a different cause. We conclude that many Australian honeys have clinical potential, and that further studies into the composition and stability of their active constituents are warranted.
Drug-Inducible, Dendritic Cell-Based Genetic Immunization1

Determining the mechanism of Ag loading of Langerhans cells (LC) for genetic immunization (GI) is complicated by the inability to distinguish between the response generated by direct transfection of LC from that due to exogenous uptake. To unravel this mechanism, we examined the impact of gene gun treatment on LC with respect to their activation and migration from skin, transgene expression, and ability to initiate humoral and cellular immune responses upon transfer to naive mice. To assess responses generated by direct LC transfection, an RU486-inducible expression system was used as a GI vector. In vitro skin organ cultures were developed from gene gun immunized mouse ear specimens to obtain LC. Gene gun treatment markedly augmented (3-fold) LC migration from ear skin, and these LC expressed the transgene at RNA and protein levels. Transfer of 2 × 105 migratory cells resulted in identical cellular responses to, but 10-fold lower humoral responses than, standard GI. Using an RU486-inducible system, we were able to measure responses generated by directly transfected LC. Our results indicate that direct transfection is a predominant pathway for LC Ag loading. The ability to regulate transgene expression with inducible DC-based vaccines demonstrates a new level of immunological control.
Effects of the direct thrombin inhibitor dabigatran on ex vivo coagulation time in orthopaedic surgery patients: a population model analysis.

AIMS To describe the pharmacokinetic-pharmacodynamic (PK-PD) characteristics of the direct thrombin inhibitor dabigatran in hip replacement patients by assessing coagulation parameters activated partial thromboplastin time (aPTT) and ecarin clotting time (ECT), interindividual variability and factors affecting PD responses. METHODS BISTRO I patients received oral dabigatran etexilate postsurgery for 6-10 days. Dabigatran plasma concentrations and aPTT/ECT were measured on the day of surgery, on subsequent days and at steady state. PK-PD characteristics of the dabigatran-aPTT/ECT relationships were evaluated using NONMEM V. RESULTS The dabigatran concentration-aPTT relationship was described combining a linear and an E(max) model. Mean baseline aPTT was 33.4 s and E(max) (maximum increase in aPTT contributed by the E(max) model) was 26.9 s. The dabigatran concentration needed to attain 50% of maximum effect (EC(50)) was 94.7 ng ml(-1) and the mean slope of the linear concentration-response relationship (SLOP) was 0.0509 s ng(-1) ml(-1). Baseline aPTT and E(max) were highest following surgery and declined with time. The dabigatran concentration-ECT relationship fitted a linear model. Mean baseline ECT was 28 s and decreased with time; 50% of the maximum effect was observed after 2.9 days. SLOP decreased from 0.38 to 0.27 s ng(-1) ml(-1) with a half-life of 1.1 day, indicating greater PD effects on the day of surgery. Interindividual and residual variability was low. Covariates could not explain variability of this model. CONCLUSIONS aPTT and ECT prolongation were directly correlated with dabigatran concentrations. Blood coagulation prolongation was most pronounced following surgery. Data suggest that ECT provides a more precise description of the anticoagulant effect than aPTT.
Wolbachia infection frequencies in insects: evidence of a global equilibrium?

Wolbachia are a group of cytoplasmically inherited bacteria that cause reproduction alterations in arthropods, including parthenogenesis, reproductive incompatibility, feminization of genetic males and male killing. Previous general surveys of insects in Panama and Britain found Wolbachia to be common, occurring in 16–22% of species. Here, using similar polymerase chain reaction methods, we report that 19.3% of a sample of temperate North American insects are infected with Wolbachia, a frequency strikingly similar to frequencies found in two other studies in widely separated locales. The results may indicate a widespread equilibrium of Wolbachia infection frequencies in insects whose maintenance remains to be explained. Alternatively, Wolbachia may be increasing in global insect communities. Within each of the three geographic regions surveyed, Hymenoptera are more frequently infected with A group Wolbachia and Lepidoptera more frequently infected with B group Wolbachia.