Miracle-dz/UniFAR-FTUs huggingface dataset:
Aurora B couples chromosome alignment with anaphase by targeting BubR1, Mad2, and Cenp-E to kinetochores

The Aurora/Ipl1 family of protein kinases plays multiple roles in mitosis and cytokinesis. Here, we describe ZM447439, a novel selective Aurora kinase inhibitor. Cells treated with ZM447439 progress through interphase, enter mitosis normally, and assemble bipolar spindles. However, chromosome alignment, segregation, and cytokinesis all fail. Despite the presence of maloriented chromosomes, ZM447439-treated cells exit mitosis with normal kinetics, indicating that the spindle checkpoint is compromised. Indeed, ZM447439 prevents mitotic arrest after exposure to paclitaxel. RNA interference experiments suggest that these phenotypes are due to inhibition of Aurora B, not Aurora A or some other kinase. In the absence of Aurora B function, kinetochore localization of the spindle checkpoint components BubR1, Mad2, and Cenp-E is diminished. Furthermore, inhibition of Aurora B kinase activity prevents the rebinding of BubR1 to metaphase kinetochores after a reduction in centromeric tension. Aurora B kinase activity is also required for phosphorylation of BubR1 on entry into mitosis. Finally, we show that BubR1 is not only required for spindle checkpoint function, but is also required for chromosome alignment. Together, these results suggest that by targeting checkpoint proteins to kinetochores, Aurora B couples chromosome alignment with anaphase onset.
Phosphorylation of Vanilloid Receptor 1 by Ca2+/Calmodulin-dependent Kinase II Regulates Its Vanilloid Binding*

Vanilloid receptor 1 (VR1), a capsaicin receptor, is known to play a major role in mediating inflammatory thermal nociception. Although the physiological role and biophysical properties of VR1 are known, the mechanism of its activation by ligands is poorly understood. Here we show that VR1 must be phosphorylated by Ca2+-calmodulin dependent kinase II (CaMKII) before its activation by capsaicin. In contrast, the dephosphorylation of VR1 by calcineurin leads to a desensitization of the receptor. Moreover, point mutations in VR1 at two putative consensus sites for CaMKII failed to elicit capsaicin-sensitive currents and caused a concomitant reduction in VR1 phosphorylation in vivo. Such mutants also lost their high affinity binding with [3H]resiniferatoxin, a potent capsaicin receptor agonist. We conclude that the dynamic balance between the phosphorylation and dephosphorylation of the VR1 channel by CaMKII and calcineurin, respectively, controls the activation/desensitization states by regulating VR1 binding. Furthermore, because sensitization by protein kinase A and C converge at these sites, phosphorylation stress in the cell appears to control a wide range of excitabilities in response to various adverse stimuli.
Optics of light dosimetry for PDT in superficial lesions versus bulky tumors

The light dosimetry for photodynamic therapy (PDT)for superficial lesions is concerned with ensuring sufficient light in the superficial tissue layer to achieve efficacious PDT. The light dosimetry for bulky tumors is concerned with the maximum depth of effective treatment while expecting over exposure of the tumor surface. The light delivered to a tissue surface does not equal the light received by the superficial region of that tissue. Backscattered light from the underlying tissues augments the surface irradiance to yield a higher fluence rate (W/cm2)in the target superficial tissue layer. The effective irradiance of treatment light, E [W/cm2 ],seen by a superficial lesion is approximated: E =Eo(1 + 2R(1 +ri)/(1 -ri))=Eo(1 +6R)where Eo is the irradiance delivered to the surface, R is the fraction of incident light that escapes the tissue as observable reflectance (typically about 0.30-0.60),and ri is the total internal reflection of light attempting to escape at the air/tissue surface (about 0.50). Hence the factor (1 +6R)varies from 2.8-4.6. The backscattered light significantly affects the treatment light dose for superficial lesions. The light within a bulky tumor is approximated: E =Eo k exp(-z/delta),where z is the depth in the tissue, k is a backscatter term, k =3 +5.1R -2exp(- 9.7R)(eg.,k =4.1-5.9 for R =0.30-0.60),and delta is the 1/e optical penetration depth (typically about 0.3-0.5 cm).
An Experiment Setup for Collecting Data for Adaptive Output Planning in a Multimodal Dialogue System

We describe a Wizard-of-Oz experiment setup for the collection of multimodal interaction data for a Music Player application. This setup was developed and used to collect experimental data as part of a project aimed at building a flexible multimodal dialogue system which provides an interface to an MP3 player, combining speech and screen input and output. Besides the usual goal of WOZ data collection to get realistic examples of the behavior and expectations of the users, an equally important goal for us was to observe natural behavior of multiple wizards in order to guide our system development. The wizards’ responses were therefore not constrained by a script. One of the challenges we had to address was to allow the wizards to produce varied screen output a in real time. Our setup includes a preliminary screen output planning module, which prepares several versions of possible screen output. The wizards were free to speak, and/or to select a screen output.
Exponential bounds with applications to call admission

In this paper, we develop a framework for computing upper and lower bounds of an exponential form for a large class of single resource systems with Markov additive inputs. Specifically, the bounds are on quantities such as backlog, queue length, and response time. Explicit or computable expressions for our bounds are given in the context of queuing theory and numerical comparisons with other bounds and exact results are presented. The paper concludes with two applications to admission control in multimedia systems.
Fault attack on AES with single-bit induced faults

This work presents a differential fault attack against AES employin any key size, regardless of the key scheduling strategy. The presented attack relies on the injection of a single bit flip, and is able to check for the correctness of the injection of the fault a posteriori. This fault model nicely fits the one obtained through underfeeding a computing device employing a low cost tunable power supply unit. This fault injection technique, which has been successfully applied to hardware implementations of AES, receives a further validation in this paper where the target computing device is a system-on-chip based on the widely adopted ARM926EJ-S CPU core. The attack is successfully carried out against two different devices, etched in two different technologies (a generic 130nm and a low-power oriented 90nm library) running a software implementation of AES-192 and AES-256 and has been reproduced on multiple instances of the same chip.
A reference governor approach for path tracking of nonholonomic mobile robot

In this study, a reference governor approach is proposed for path tracking of nonholonomic mobile robot considering prescribed constraints. The proposed approach is designed to minimize the tracking error with a desired speed while satisfying all other constraints such as bounds on linear and angular velocities, acceleration. This approach determines the control inputs of a path tracking algorithm based on current-state, reference trajectory and prescribed constraints. This is achieved by designing a reference governor module addition to the classical path tracking approaches.
Lowering Power at 28 nm with Xilinx 7 Series Devices

www.xilinx. com 1 © Copyright 2011–2015 Xilinx, Inc. Xilinx, the Xilinx logo, Artix, ISE, Kintex, Spartan, Virtex, Vivado, Zynq, and other designated brands included herein are trademarks of Xilinx in the United States and other countries. PCI, PCIe, and PCI Express are trademarks of PCI-SIG and used under license. All other trademarks are the property of their respective owners. All other trademarks are the property of their respective owners. This white paper describes several aspects of power related to the Xilinx® 28 nm 7 series FPGAs and Zynq®-7000 devices, including the TSMC 28 nm high-k metal gate (HKMG), high performance, low power (28 nm HPL or 28 HPL) process choice.
ProteinHistorian: Tools for the Comparative Analysis of Eukaryote Protein Origin

The evolutionary history of a protein reflects the functional history of its ancestors. Recent phylogenetic studies identified distinct evolutionary signatures that characterize proteins involved in cancer, Mendelian disease, and different ontogenic stages. Despite the potential to yield insight into the cellular functions and interactions of proteins, such comparative phylogenetic analyses are rarely performed, because they require custom algorithms. We developed ProteinHistorian to make tools for performing analyses of protein origins widely available. Given a list of proteins of interest, ProteinHistorian estimates the phylogenetic age of each protein, quantifies enrichment for proteins of specific ages, and compares variation in protein age with other protein attributes. ProteinHistorian allows flexibility in the definition of protein age by including several algorithms for estimating ages from different databases of evolutionary relationships. We illustrate the use of ProteinHistorian with three example analyses. First, we demonstrate that proteins with high expression in human, compared to chimpanzee and rhesus macaque, are significantly younger than those with human-specific low expression. Next, we show that human proteins with annotated regulatory functions are significantly younger than proteins with catalytic functions. Finally, we compare protein length and age in many eukaryotic species and, as expected from previous studies, find a positive, though often weak, correlation between protein age and length. ProteinHistorian is available through a web server with an intuitive interface and as a set of command line tools; this allows biologists and bioinformaticians alike to integrate these approaches into their analysis pipelines. ProteinHistorian's modular, extensible design facilitates the integration of new datasets and algorithms. The ProteinHistorian web server, source code, and pre-computed ages for 32 eukaryotic genomes are freely available under the GNU public license at http://lighthouse.ucsf. edu/ProteinHistorian/.
Surface modification of conductive PEDOT coated textile yarns with silicone resin

Abstract Electroactive textile fibres and fabrics have been used in smart and interactive clothing for medical, military and sports applications. The improved surface properties of conductive textiles are required for their successful integration in all of the above mentioned applications. This paper presents the production of conductive poly(3,4-ethylenedioxythiophene) (PEDOT) coated viscose yarns in longer length, i.e. 5 m, and the surface modification of the coated yarns by treating with silicone solution. The structural properties of silicone coated conductive yarns were then investigated by Fourier transform infrared spectroscopy and thermogravimetric analysis. The effect of silicone coating on the mechanical, electrical and hydrophobic properties was also evaluated and then compared with the PEDOT coated viscose yarns without surface treatment. Results show that the mechanical and hydrophobic properties of conductive yarns were improved by surface modification with silicone without affecting their structural properties. The surface modified PEDOT coated yarns could be used as pressure and stretch sensors in health care applications.
An explicit RC-circuit delay approximation based on the first three moments of the impulse response

Due to its simplicity, the ubiquitous Elmore delay, or first moment of the impulse response, has been an extremely popular delay metric for analyzing RC trees and meshes. Its inaccuracy has been noted however and it has been demonstrated that higher order moments can be mapped to dominant pole approximations (e.g. AWE) in the general case. The first three moments can be mapped to a two pole approximation, but stability is an issue and even a stable model results in a transcendental equation that must be iteratively evaluated to determine the delay. We describe an explicit delay approximation based on the first three moments of the impulse response. We begin with the development of a provably stable two pole transfer function/impedance model based on the first three moments (about s=0) of the impulse response. Then, since the model form is known, we evaluate the delay (any waveform percentage point) in terms of an analytical approximation that is consistently within a fraction of 1 percent of the "exact" solution for this model. The result is an accurate, explicit delay expression that will be an effective metric for high speed interconnect circuit models.
Towards dynamic pricing-based collaborative optimizations for green data centers

Increased demand for cloud computing services has ushered power management schemes into the frontlines of data center research. Meanwhile, market penetration of intermittent renewable energy sources (e.g., wind and solar) is on the rise. While clean and abundant, their intermittency is troubling for utility companies, requiring power balancing reserves to be deployed at anytime to precisely match consumer demand with energy availability. However, a transformative redesign of our power grid is looming, calling for the use of dynamic energy pricing to resolve this issue by possibly shaping demand. Data centers, being significant consumers with the ability to adjust power utilization in real-time (e.g., by migrating its jobs to and from other locations), are ideal candidates to participate in dynamic pricing markets. We propose a collaborative cost optimization framework by coupling utilities with data centers via dynamic pricing. We develop models describing the information exchange framework for utilities and data centers and employ a distributed constraint optimization solver, Cologne, to negotiate a mutually optimal price. An evaluation of our system has been performed using real intermittent-energy-generation trace data. Modeling the dynamic price over this trace, we show that our technique could reduce a participating data center's costs by 75%. On the side of utilities, we further show that consumer power demand can be shaped to reveal a 17% improvement on average.
Completely Opportunistic Approach to Network Coding Using in Wireless Network

Network coding is a new method by which a multicast network can achieve the network capacity determined by the max-flow and min-cut theorem. This paper shows the mutual exchange of independent information between two nodes in a wireless network which can be efficiently combined with network coding and broadcast property offered by wireless medium. It introduces COPE, an opportunistic approach to network coding. Compared with traditional routing, COPE can increase the network and apply for multiple unicast flow efficiently and robustly.
Optimizing the Signal-to-Noise Ratio of Scoring Functions for Protein-Ligand Docking

Empirical scoring functions provide estimates of the free energy of protein-ligand binding in situations when atomic-scale simulations are intractable, for example, in virtual high-throughput screening. Currently, such scoring functions are often inaccurate, and further improvements are complicated by the lack of reliable training data, the complex interplay between scoring functions and docking algorithms, and an inconsistent statistical treatment of positive and negative training data. In comparison to various other performance measures of scoring functions, "analysis of variance" provides a well-behaved objective function for optimization, which focuses on the signal-to-noise ratio of ligand-decoy discrimination. In combination with a large database of ligands and decoys, an in situ optimization of scoring function parameters was able to generate improved, target-specific scoring functions for three different proteins of pharmaceutical interest: cyclin-dependent kinase 2, the estrogen receptor, and cyclooxygenase-2. Statistical analysis of the improvements observed in "receiver-operating characteristic" curves showed that the optimized scoring functions achieved a significantly (between p < 0.0001 and p < 0.05) higher enrichment of true ligands. A scaffold dependence of the resulting binding modes was observed, which is discussed in conjunction with the rigid receptor hypothesis commonly made in protein-ligand docking. In summary, the approach described here represents a well-adapted statistical method for setting up scoring functions.
Self-Organised Recruitment and Deployment with Aerial and Ground-Based Robotic Swarms

We tackle the problem of forming and deploying groups of robots in a dynamic task allocation scenario. In our approach, wheeled robots carry out tasks and flying robots coordinate the formation and subsequent deployment of groups of wheeled robots. Our recruitment system is based on simple probabilistic rules inspired by the aggregation behaviour of cockroaches under shelters. The system successfully forms stable groups of the desired size and copes with the dynamic addition and removal of either wheeled robots or tasks. The system includes a deadlock resolution mechanism that allows it to continue to function even when there are not enough wheeled robots to carry out all tasks simultaneously. As the robotic hardware is still under development, our experiments are conducted in a physically realistic embodied simulation environment.
Measurement and Analysis of Wireless Channel Impairments in DSRC Vehicular Communications

We present a GPS-enabled channel sounding platform for measuring both vehicle-to-vehicle and vehicle-to- roadside wireless channels. This platform was used to conduct an extensive field measurement campaign involving vehicular wireless channels across a wide variety of speeds and line-of-sight conditions. From the data, we present statistical characterizations of several classes of these channels at 5.9 GHz. This analysis suggests that while the proposed DSRC standard may account for Doppler and delay spreads in vehicular channels, large packets may face higher error rates due to time-varying channels.
Rapid cryogenic fixation of biological specimens for electron microscopy

This thesis describes investigations into cryofixation by the plungecooling technique, at ambient pressure. The objective was to characterise coolants which are commonly used for cryofixation, so that the structure and chemistry of biological specimens may be preserved in a more life-like state. The work began with the design of a suitable cooling device. This was developed further into a large test-bed apparatus which was used in both biological and methodological experiments. The large cooling apparatus demonstrated for the first time that ethane was a superior coolant under forced convection, compared to propane or Freon 22, for bare thermocouples, for exposed hydrated specimens and for metal-sandwiched hydrated specimens. Ice crystal formation was monitored in sandwiched specimens and found to correspond closely to modelling predictions. A biological application was the X-ray microanalysis of body fluids in "indicator" species of Chaetognaths, where results obtained from cryoscanning electron microscopy revealed ecophysiological differences. The use of low thermal mass supports demonstrated that good freezing can occur in the centre of specimens. A new cryomounting method was developed to load well-frozen specimens into the microscope. The effect of post-freeze processing temperature was investigated by monitoring ice crystals in red blood cells. Exposure to 213 K (-60°C) over a 48 hour period did not induce crystal growth and exposure to 233 K (-40°C) for 8 days showed minimal ice crystal damage. The progress of cryosubstitution was monitored over 48 h at 193 K ( -80°C), this showed that uranium ingressed to a depth of 320 1J.D1 which could be doubled when shrinkage was allowed for. The conclusion was that observed ice crystal damage originated during the initial freezing and not during subsequent cryoprocessing.
Acupuncture for postoperative pain following total knee arthroplasty: a systematic review protocol

Introduction Total knee arthroplasty (TKA) is a common surgical method in orthopaedics; however, pain management after TKA remains a significant challenge. This review provides a comprehensive evaluation of the effects of acupuncture for postoperative pain after TKA. Methods and analysis The following 10 databases will be searched until August 2015: MEDLINE, EMBASE, CENTRAL, AMED, CINAHL, three Chinese databases (the China National Knowledge Infrastructure Database, the Chongqing VIP Chinese Science and Technology Periodical Database, and Wanfang Database) and five Korean databases (the Korean Medical Database, the Korean Studies Information Service System, the National Discovery for Science Leaders, the Database Periodical Information Academic, and the Oriental Medicine Advanced Searching Integrated System). All eligible randomised controlled trials related to the use of acupuncture for postoperative pain after TKA will be included. Assessment of risk of bias will be performed with the Cochrane risk-of-bias method. Mean differences or standardised mean differences will be calculated with 95% CIs for continuous data; the risk ratio will be used with 95% CIs for dichotomous data. Dissemination This systematic review will be presented in a peer-reviewed journal. The result of this review will also be disseminated at a relevant conference presentation. Trial registration number PROSPERO 2015: CRD42015020924.
Inherited Thrombophilia and First Venous Thromboembolism during Pregnancy and Puerperium

Summary Venous thromboembolism is a rare but threatening complication of pregnancy. Little conclusive information is available on the actual risk of venous thromboembolism during pregnancy or puerperium in women with inherited thrombophilia, particularly in carriers of factor V Leiden and of the G20210A prothrombin gene mutation. To determine the pregnancy-related and puerperium-related risk of venous thromboembolism in women with inherited thrombophilia, we performed a case-control study on 119 women who had a first episode of deep vein thrombosis and/or pulmonary embolism during pregnancy or puerperium and 232 healthy women who had at least one pregnancy without thrombosis. Inherited thrombophilia was diagnosed in 47 patients (39.5%) and 15 controls (6.5%). The relative risk of venous thromboembolism was 10.6 (95% CI, 5.6-20.4) for heterozygous carriers of factor V Leiden, 2.9 (95% CI, 1.0-8.6) for heterozygous carriers of the prothrombin mutation and 13.1 (95% CI, 5.0-34.2) for those with antithrombin, protein C or protein S deficiency taken together. Sixty-eight of the 119 women (57%) had thrombosis after delivery, confirming the puerperium as a particularly high-risk period. When women were divided into two groups of those with antenatal or postnatal thrombosis, the relative risks associated with each type of inherited thrombophilia were of similar magnitude. In conclusion, women with inherited thrombophilia have an increased risk of venous thromboembolism during pregnancy. Among thrombophilic abnormalities, the prothrombin mutation was the weakest risk factor. Thrombosis occurred more frequently in puerperium than in pregnancy, whether or not thrombophilia was diagnosed.