Miracle-dz/UniFAR-FTUs huggingface dataset:
Revealing Interaction Mode Between HIV‐1 Reverse Transcriptase and Diaryltriazine Analog Inhibitor

HIV‐1 reverse transcriptase is a key enzyme playing an important role in the HIV‐1 life cycle for the replication of the RNA genome into DNA form. Lys103Asn (K103N) mutant frequently is observed in HIV‐1 reverse transcriptase. Therefore, a series of novel non‐nucleoside reverse transcriptase inhibitors were designed and synthesized. In vitro experimental results show that diaryltriazine analogs have potent anti‐HIV activity with moderate to high selectivity. In order to design anti‐HIV drug, docking and molecular dynamics simulation were used to investigate the binding mode between ligand and HIV‐1 reverse transcriptase. The results suggest that the analogs might have a similar interaction mechanism with HIV‐1 reverse transcriptase. Then comparative molecular field analysis and comparative molecular similarity indices analysis were used to construct quantitative structure–activity models. These models were evaluated by eight test set compounds. These models are helpful in making quantitative prediction of their activity for new lead compounds before resorting in vitro and in vivo experimentation.
Characterization of WbpB, WbpE, and WbpD and Reconstitution of a Pathway for the Biosynthesis of UDP-2,3-diacetamido-2,3-dideoxy-d-mannuronic Acid in Pseudomonas aeruginosa*

The lipopolysaccharide of Pseudomonas aeruginosa PAO1 contains an unusual sugar, 2,3-diacetamido-2,3-dideoxy-d-mannuronic acid (d-ManNAc3NAcA). wbpB, wbpE, and wbpD are thought to encode oxidase, transaminase, and N-acetyltransferase enzymes. To characterize their functions, recombinant proteins were overexpressed and purified from heterologous hosts. Activities of His6-WbpB and His6-WbpE were detected only when both proteins were combined in the same reaction. Using a direct MALDI-TOF mass spectrometry approach, we identified ions that corresponded to the predicted products of WbpB (UDP-3-keto-d-GlcNAcA) and WbpE (UDP-d-GlcNAc3NA) in the coupled enzyme-substrate reaction. Additionally, in reactions involving WbpB, WbpE, and WbpD, an ion consistent with the expected product of WbpD (UDP-d-GlcNAc3NAcA) was identified. Preparative quantities of UDP-d-GlcNAc3NA and UDP-d-GlcNAc3NAcA were enzymatically synthesized. These compounds were purified by high-performance liquid chromatography, and their structures were elucidated by NMR spectroscopy. This is the first report of the functional characterization of these proteins, and the enzymatic synthesis of UDP-d-GlcNAc3NA and UDP-d-GlcNAc3NAcA.
Impact of the Present-on-Admission Indicator on Hospital Quality Measurement: Experience With the Agency for Healthcare Research and Quality (AHRQ) Inpatient Quality Indicators

Background:The Agency for Healthcare Research and Quality (AHRQ) has constructed Inpatient Quality Indicator (IQI) mortality measures to measure hospital quality using routinely available administrative data. With the exception of California, New York State, and Wisconsin, administrative data do not include a present-on-admission (POA) indicator to distinguish between preexisting conditions and complications. The extent to which the lack of a POA indicator biases quality assessment based on the AHRQ mortality measures is unknown. Objective:To examine the impact of the POA indicator on hospital quality assessment based on the AHRQ mortality measures using enhanced administrative data from California, which includes a POA indicator. Methods:Retrospective cohort study based on 2.07 million inpatient admissions between 1998 and 2000 in the California State Inpatient Database. The AHRQ IQI software was used to calculate risk-adjusted mortality rates using either (1) routine administrative data that included all the International Classification of Diseases (ICD)-9-CM codes or (2) enhanced administrative data that included only the ICD-9-CM codes representing preexisting conditions. Results:The inclusion of the POA indicator frequently results in changes in the quality ranking of hospitals classified as high-quality or low-quality using routine administrative data. Twenty-seven percent (stroke) to 94% (coronary artery bypass graft) of hospitals classified as high-quality using routine administrative data were reclassified as intermediate- or low-quality hospitals using the enhanced administrative data. Twenty-five percent (congestive heart failure) to 76% (percutaneous coronary intervention) of hospitals classified as low-quality hospitals using enhanced administrative data were misclassified as intermediate-quality hospitals using routine administrative data. Conclusions:Despite the fact that the AHRQ IQIs were primarily intended to serve as a screening tool, they are being increasingly used to publicly report hospital quality. Our findings emphasize the need to improve the “quality” of administrative data by including a POA indicator if these data are to serve as the information infrastructure for quality reporting.
PERFORMANCE ANALYSIS OF STATE-DEPENDENT ROUTING IN CIRCUIT-SWITCHED NETWORKS

We present a new methodology for the steady-state performance analysis of circuit-switched networks with nonhierarchical state-dependent rout ing. The main features are: a distributed approach, where each link is examined in turn; the quantification, through a set of coefficients, of the percentage of usage each network link undergoes over a long time inter val under · the routing scheme; and, the establishment of connections between the above coefficients and parameters of the stochastic process which is selected to model the merged traffic streams on the link under consideration. The blocking probabilities (grade of service) are calcu lated through an . iterative procedure. With appropriate changes, this methodology can be used to provide a long-term-equivalent fixed routing for every type of dynamic routing. The algorithm can be used for net work design and for on-line monitoring of the performance of an operat ing network.
Adaptive Control Design for Hydrogen Production via Autothermal Reforming of Methanol

Autothermal reforming of methanol is considered to be a promising choice for hydrogen production. However, due to the fact that a series of complex chemical reactions are involved, an exact mathematical model is extremely hard to be established, which makes the control of the process a recognized difficulty. Therefore, an adaptive feedback control method is proposed in this work for the control of hydrogen production through autothermal reforming of methanol without the requirement of an accurate model. Theoretical analysis proves that this control strategy can achieve very good performance even when the system’s parameters change significantly. Moreover, simulation results demonstrate the feasibility of this approach.
Numerical Investigation of Temperature and Phase Development of (Deformation-) Dilatometer Specimens

The Gleeble 3500 thermo-mechanical testing machine with ISO-Q dilatometer set-up allows the creation of time temperature transformation diagrams at high cooling rates, after deformation and under constant load with a simple experimental set-up. An isothermal plane with temperature gradients perpendicular to this plane arises in the sample which is used for dilatometrical evaluation. The homogeneity and size of this isothermal region has a decisive influence on the measurement results, but cannot be measured with sufficient accuracy. To gain an accurate understanding of the processes in the sample, a coupled thermo-electrical, thermo-metallurgical, thermo-mechanical finite element model of the experiments is set up. To map the temperature control circuit of the machine, a PID controller is implemented, which controls the voltage of the conductive sample heating between the simulation steps. By comparing the temperature and hardness distribution with the experiments, it is shown that in this way the temperature distribution and phase transformation can be mapped. By the findings, the experimental setup was adjusted. This led to an improvement of the measurement results.
The Real-time Judging System of Figure Skating Based-on WLAN

Wireless LAN can quickly and conveniently resolve the problems of network connectivity, which are difficult for LAN based on wire. Basing on above advantages and the application of Figure Skating, we develop the real-time judging system of Figure Skating. It implements the video replaying which bases on DirectShow technology of COM criteria. The system is not only characterized by excellent mobility, but also efficiency, accuracy and equity during the judging process. In the experiment, the system is able to perfectly finish the real-time judging work for Figure Skating, and has a great instructing significance for skaters to improve their skills
The significance of Tenascin-C serum level as tumor marker in squamous cell carcinoma of the head and neck.

BACKGROUND Tenascin, an extracellular matrix glycoprotein, is transiently present in embryonic tissue, in benign granulation tissue, but also in several highly anaplastic tumors like fibrosarcoma, melanoma and squamous cell carcinoma of the skin. This study was performed to validate elevated Tenascin serum levels as a possible marker for head and neck squamous cell carcinomas (HNSCC). PATIENTS AND METHODS Tenascin serum levels were evaluated in patients with primary (n = 92) and with recurrent (n = 28) HNSCC. Patients with benign, non inflammatory ear, nose and throat diseases (n = 16) served as the control. The Tenascin serum levels were measured by ELISA (Aventis). RESULTS Serum Tenascin concentrations of patients with benign ENT diseases ranged between 0.37 and 2.19 micrograms/ml (n = 16, mean +/- SD: 1.23 +/- 0.59 micrograms/ml), of patients with HNSCC (primary diagnosis) between 0.05 and 8.75 micrograms/ml (n = 92, mean +/- SD: 1.81 (1.36 micrograms/ml) and of patients with recurrent HNSCC between 0.53 and 10.0 micrograms/ml (n = 28, mean +/- SD: 2.78 +/- 2.2 micrograms/ml). CONCLUSION We found a significant elevation of Tenascin serum levels only in patients with higher tumor stages (T4/UICC4) (p < 0.01/p < 0.1) or recurrent disease compared to Tenascin serum levels in healthy controls. Thereby Tenascin serum levels cannot be used clinically as a routine serum marker for the control of head and neck cancer. Further investigations are necessary to evaluate whether the measurement of Tenascin levels as tumor markers could offer additional information to the clinical outcome of patients with HNSCC.
A linearity enhanced broadband Class-F power amplifier with high harmonic suppressed matching circuits for S-band applications

A broadband power amplifier (PA) with linearity enhanced technology for S-band applications, is presented. For good linearity and high efficiency performance, a Class-F PA core with improved linearizing bias circuits is employed and integrated on a 1.1×1.1×0.82 mm3 die using an InGaP/GaAs HBT process. The linearizing bias circuit is composed of current mirrors, compensated inductor and capacitor, thus that the overall power gain is enhanced as well as the gain flatness. Furthermore, several LC serial harmonic traps are immersed into the broadband output matching circuit for good harmonic suppression performance. To demonstrate the feasibility of the concept, the PA was tested with a continuous wave (CW) signal and generated an output power of 34 dBm and achieved a PAE of 54.5% at 2GHz. In addition, excellent harmonic suppression levels of less than -57 dBc across the second to fifth harmonic are obtained.
Spot Price Modeling and the Valuation of Electricity Forward Contracts: The Role of Demand and Capacity

We propose a model where wholesale electricity prices are explained by two state variables: demand and capacity. We derive analytical expressions to price forward contracts and to calculate the forward premium. We apply our model to the PJM, England and Wales, and Nord Pool markets. Our empirical findings indicate that volatility of demand is seasonal and that the market price of demand risk is also seasonal and positive, both of which exert an upward (seasonal) pressure on the price of forward contracts. We assume that both volatility of capacity and the market price of capacity risk are constant and find that, depending on the market and period under study, it could either exert an upward or downward pressure on forward prices. In all markets we find that the forward premium exhibits a seasonal pattern. During the months of high volatility of demand, forward contracts trade at a premium. During months of low volatility of demand, forwards can either trade at a relatively small premium or, even in some cases, at a discount, i.e. they exhibit a negative forward premium.
TCAD ready density gradient calculation of channel charge for Si/strained Si/sub 1-x/Ge/sub x/ dual channel pMOSFETs on [001] relaxed Si/sub 1-y/Ge/sub y/

The dual channel MOSFET with strained Si/Si/sub 1-x/Ge/sub x/ layers on relaxed Si/sub 1-y/Ge/sub y/ is a promising structure for the improvement of CMOS performance because of its enhanced carrier mobilities (Hargrove, 1994). In order to obtain the correct threshold voltage and gate capacitance of these devices, it is essential to accurately model the channel charge distribution. In our study a dual channel MOSFET with an n-type substrate doping of 5 /spl middot/ 10/sup 17//cm/sup 3/ and a metal gate is investigated. The confinement of the holes to the strained SiGe region depends on the gate bias. For the first time accurate CV-characteristics for strained Si/SiGe dual channel pMOSFETs are calculated based on the density gradient method. These results make the direct application of commercially available TCAD tools feasible for the calculation of CV characteristics of such complicated structures.
A smartphone-based fall risk assessment tool: Measuring One Leg Standing, Sit to Stand and Falls Efficacy Scale

Falls are not an inevitable consequence of ageing. Several fall risk factors can be identified and effective fall prevention techniques applied, which offer an opportunity to reduce falls among older persons. In this paper, the smartphone is proposed as an alternative to traditional methods in the assessment of fall risk factors, including decline in balance, reduced lower limb strength and fear of falling. As such, clinical fall risk assessment tests were adapted to the smartphone in order to measure One Leg Standing, Sit to Stand and Falls Efficacy Scale. Experimental results of the system support the feasibility of a reliable phone-based fall predictor, which constitutes an alternative to evaluate fall risk factors in ageing.
Herpesvirus Genome Recognition Induced Acetylation of Nuclear IFI16 Is Essential for Its Cytoplasmic Translocation, Inflammasome and IFN-β Responses

The IL-1β and type I interferon-β (IFN-β) molecules are important inflammatory cytokines elicited by the eukaryotic host as innate immune responses against invading pathogens and danger signals. Recently, a predominantly nuclear gamma-interferon-inducible protein 16 (IFI16) involved in transcriptional regulation has emerged as an innate DNA sensor which induced IL-1β and IFN-β production through inflammasome and STING activation, respectively. Herpesvirus (KSHV, EBV, and HSV-1) episomal dsDNA genome recognition by IFI16 leads to IFI16-ASC-procaspase-1 inflammasome association, cytoplasmic translocation and IL-1β production. Independent of ASC, HSV-1 genome recognition results in IFI16 interaction with STING in the cytoplasm to induce interferon-β production. However, the mechanisms of IFI16-inflammasome formation, cytoplasmic redistribution and STING activation are not known. Our studies here demonstrate that recognition of herpesvirus genomes in the nucleus by IFI16 leads into its interaction with histone acetyltransferase p300 and IFI16 acetylation resulting in IFI16-ASC interaction, inflammasome assembly, increased interaction with Ran-GTPase, cytoplasmic redistribution, caspase-1 activation, IL-1β production, and interaction with STING which results in IRF-3 phosphorylation, nuclear pIRF-3 localization and interferon-β production. ASC and STING knockdowns did not affect IFI16 acetylation indicating that this modification is upstream of inflammasome-assembly and STING-activation. Vaccinia virus replicating in the cytoplasm did not induce nuclear IFI16 acetylation and cytoplasmic translocation. IFI16 physically associates with KSHV and HSV-1 genomes as revealed by proximity ligation microscopy and chromatin-immunoprecipitation studies which is not hampered by the inhibition of acetylation, thus suggesting that acetylation of IFI16 is not required for its innate sensing of nuclear viral genomes. Collectively, these studies identify the increased nuclear acetylation of IFI16 as a dynamic essential post-genome recognition event in the nucleus that is common to the IFI16-mediated innate responses of inflammasome induction and IFN-β production during herpesvirus (KSHV, EBV, HSV-1) infections.
Parallelized multiple alignment

UNLABELLED Multiple sequence alignment is a frequently used technique for analyzing sequence relationships. Compilation of large alignments is computationally expensive, but processing time can be considerably reduced when the computational load is distributed over many processors. Parallel processing functionality in the form of single-instruction multiple-data (SIMD) technology was implemented into the multiple alignment program Praline by using 'message passing interface' (MPI) routines. Over the alignments tested here, the parallelized program performed up to ten times faster on 25 processors compared to the single processor version. AVAILABILITY Example program code for parallelizing pairwise alignment loops is available from http://mathbio.nimr.mrc.ac.uk/~jkleinj/tools/mpicode. The 'message passing interface' package (MPICH) is available from http:/www.unix. mcs.anl. gov/mpi/mpich. CONTACT jhering@nimr.mrc.ac.uk SUPPLEMENTARY INFORMATION Praline is accessible at http://mathbio.nimr.mrc.ac.uk/praline.
Cardiac Memory Evolves With Age in Association With Development of the Transient Outward Current

Background—Calcium-insensitive transient outward current (Ito) is important to the development of cardiac memory (CM), which itself reflects the capacity of the heart to remodel electrophysiologically. We used cardiac pacing to test the hypothesis that CM evolution can be explained by developmental maturation of Ito. Methods and Results—Acutely anesthetized dogs from 1 day old to adult were paced from the left ventricle (VP, n=29) or left atrial appendage (AP, n=12) to induce CM. T-wave vector displacement (TVD) obtained during VP was greater than with AP (adults, 0.39±0.06 mV; neonates, 0.04±0.01 mV; P<0.05). TVD began to increase at ≈40 days of age, reaching adult levels by ≈200 days. Microelectrode studies performed in 18 dogs (ages 3 to 94 days) after completing the CM protocol and 20 additional dogs (1 day old to adult) revealed that the epicardial action potential notch was absent in neonates, became apparent in the young, and was deepest in adults. The relationship between TVD and epicardial notch was such that as notch magnitude increased, TVD increased (r=−0.65, P<0.05). KChIP2 and Kv4.3 mRNA (measured via reverse transcription–polymerase chain reaction) also increased with age. Conclusions—The inducibility of CM gradually increases with age in association with evolution of the epicardial action potential notch and mRNA expression for KChIP2 and Kv4.3. This suggests that the capacity of the heart to remodel electrophysiologically and to manifest memory during development depends in part on evolution of the determinants of Ito.
The initiation and propagation behaviour of short fatigue cracks in Waspaloy subjected to bending

The fatigue crack growth behaviour of a nickel base superalloy, Waspaloy, has been studied using four point bending specimens in laboratory air. Two groups of tests, for which the span/width ratios were 1 and 2.5, were conducted and the results compared. Surface crack lengths were measured from plastic replicas of the surface. Equations which describe both short and long cracks have been derived and used to predict the fatigue life for the Waspaloy specimens. From plastic replication studies and scanning electron microscope examinations, a physical understanding of the relationship between crack growth and microstructural features was enhanced.
Reactive collision avoidance for navigation with dynamic constraints

We address the problem of applying reactive navigation methods for collision avoidance to systems where the dynamics cannot be neglected: mobile robots with slow dynamic capabilities, or systems working at high speeds. Rather than embedding the motion constraints when designing a navigation method, we propose to introduce the robot dynamic constraints directly into the spatial representation. In this space the dynamic capabilities of the robot are implicitly represented. With minor modifications, standard reactive navigation methods can be used in this space implicitly taking into account the robot dynamic constraints. To validate this framework, we show experimental results using two reactive navigation methods whose original formulation do not take the robot dynamic constraints into account (the nearness diagram navigation and the potential field method).
On the Conditions of Sparse Parameter Estimation via Log-Sum Penalty Regularization

For high-dimensional sparse parameter estimation problems, Log-Sum Penalty (LSP) regularization effectively reduces the sampling sizes in practice. However, it still lacks theoretical analysis to support the experience from previous empirical study. The analysis of this article shows that, like ‘0-regularization, O(s) sampling size is enough for proper LSP, where s is the non-zero components of the true parameter. We also propose an efficient algorithm to solve LSP regularization problem. The solutions given by the proposed algorithm give consistent parameter estimations under less restrictive conditions than‘1-regularization.
Multivariable MPC design based on a frequency response approximation approach

This paper presents an improvement to the MPC tuning approach presented in [1]. The drawbacks of the former approach are discussed and a new tuning approach is proposed to overcome them. The primary aim is to treat linear MPC as a classical controller design problem and to use the tools of linear control theory for determining the tuning parameters. MPC tuning is performed for a desired open-loop frequency response which results from an achievable closed-loop performance determined using the Youla parameterization technique. The tuning approach is performed in two steps and both resulting minimization problems are convex optimization problems. The approach is tested on a challenging example.