gebhart/patrepeval huggingface dataset:
The short prodomain influences caspase-3 activation in HeLa cells (2000)

Proteolytic activation of caspases is a key step in the process of apoptosis. According to their primary structure, caspases can be divided into a group with a long prodomain and a group with a short prodomain. Whereas long prodomains play a role in autocatalytic processing, little is known about the function of the short prodomain, for example the prodomain of caspase-3. We constructed caspase-3 variants lacking the prodomain and overexpressed these in HeLa and yeast cells. We found that removal of the caspase-3 prodomain resulted in spontaneous proteolytic activation of the protein when expressed in HeLa cells. This processing was only partially autocatalytic, as demonstrated by a catalytically inactive caspase-3 mutant. Co-expression of the anti-apoptotic protein XIAP (X-chromosome-linked inhibitor of apoptosis protein) completely blocked the observed spontaneous activation, which excluded a direct involvement of caspase-8. Our findings indicate that the short prodomain of caspase-3 serves as a silencing component in mammalian cells by retaining this executioner caspase in an inactive state.
Adsorbability of Single-Wall Carbon Nanotubes onto Agarose Gels Affects the Quality of the Metal/Semiconductor Separation (2011)

Although the metal/semiconductor separation of single-wall carbon nanotubes (SWCNTs) using an agarose gel column has been successfully developed, little is known about the mechanism of the separation. In this study, we examined the agarose concentration dependence of the separation using this column. The amount of SWCNTs obtained from the eluate decreased with increasing agarose concentration, indicating that a smaller amount of SWCNTs was adsorbed onto the agarose gels at higher concentrations. To clarify the relation between the adsorbability of SWCNTs and the agarose concentration, various concentrations of SWCNTs were adsorbed onto 2, 4, and 6% agarose gels in a quasi-equilibrium state. The results showed that the concentration of the unadsorbed SWCNTs increased with increasing agarose concentration. By assuming that the adsorption follows the Langmuir isotherm, it was found that the effective gel volume for the adsorption was negatively correlated with the agarose concentration; specifically, the adsorbability was associated with the effective gel volume. Finally, an effect of the adsorbability on the separation using the agarose gel columns was considered. With decreasing adsorbability of SWCNTs onto agarose, the amount of SWCNTs adsorbed onto the top of the column decreased and the distribution of the SWCNTs became broadened along the column. Thus, the agarose concentration dependence of the separation quality is attributable to the adsorbability of SWCNTs onto the agarose gels.
Adaptive Routing for Dynamic On-Body Wireless Sensor Networks (2014)

Energy is scarce in mobile computing devices including wearable and implantable devices in a wireless body area network. In this paper, an adaptive routing protocol is developed and analyzed which minimizes the energy cost per bit of information by using the channel information to choose the best strategy to route data. In this approach, the source node will switch between direct and relayed communication based on the quality of the link and will use the relay only if the channel quality is below a certain threshold. The mathematical model is then validated through simulations which shows that the adaptive routing strategy can improve energy efficiency significantly compared with existing methods.
All-digital TX frequency synthesizer and discrete-time receiver for Bluetooth radio in 130-nm CMOS (2004)

We present a single-chip fully compliant Bluetooth radio fabricated in a digital 130-nm CMOS process. The transceiver is architectured from the ground up to be compatible with digital deep-submicron CMOS processes and be readily integrated with a digital baseband and application processor. The conventional RF frequency synthesizer architecture, based on the voltage-controlled oscillator and the phase/frequency detector and charge-pump combination, has been replaced with a digitally controlled oscillator and a time-to-digital converter, respectively. The transmitter architecture takes advantage of the wideband frequency modulation capability of the all-digital phase-locked loop with built-in automatic compensation to ensure modulation accuracy. The receiver employs a discrete-time architecture in which the RF signal is directly sampled and processed using analog and digital signal processing techniques. The complete chip also integrates power management functions and a digital baseband processor. Application of the presented ideas has resulted in significant area and power savings while producing structures that are amenable to migration to more advanced deep-submicron processes, as they become available. The entire IC occupies 10 mm/sup 2/ and consumes 28 mA during transmit and 41 mA during receive at 1.5-V supply.
Continuous ECG Transmission via Mobile Telephone Network and Waiting Time of Packets for Smooth Display (2012)

ECG signals received from a long distance call through mobile phone network need to be displayed instantaneously, smoothly and recorded. Due to non-uniform load and inherent time delay in the network the real-time display is incoherent. This will cause some discomfort or inaccuracies in observing the waveform at the critical moment, and then more or less affect the quality of work performed by the healthcare worker. This paper considers the process model as a queuing system which can be simplified as M/D/1 and identifies the dominant parameter as the receiver queueing time which may be dynamically adjusted. To simplify the procedure, the waiting time in the buffer was set to a constant value which was determined empirically by a network simulator and an open-source network analyzer. This was done together with a suitable data packet size selection to optimize the bandwidth utilization, and so a simple data flow management within the receiver can be achieved.
Double estimation of distribution guided sampling algorithm for de-novo protein structure prediction (2017)

Protein structure prediction is a long standing problem in the filed of structural bioinformatics. To address this problem, on the basis of Monte Carlo (MC), a double estimation of distribution guided sampling algorithm for de-novo protein structure prediction (DED) is proposed. Serval MC trajectories are launched simultaneously at the begining of DED. And two probability distribution are designed to decide which MC trajectory should be selected for further sampling in the conformational space. One of the probability distribution is called current energy probability distribution, which is calculated by analysing the distribution of energy of the latest conformation in each MC trajectory. Another is called historical acceptance probability distribution, which is calculated by counting the times that the conformation is been accepted in each MC trajectory. The two probability distribution make the inner information of the sampling algorithm could be used for guiding the sampling process. It means that the protein conformation with lower energy and more times been accepted has a relative higher probability been selected for further sampling. It gives more chance for sampling in the conformational space with lower energy, while the space with relative higher energy can also be sampled. DED finds an effective way out in spite of the inaccuracy of the energy modal. 12 target proteins are tested for verifying the proposed method, test results shows that DED can captures the near-native conformations effectively and efficiently.
Realization of Multi-port SDRAM Controller in LXI Data Acquisition System (2013)

Currently, the LXI data acquisition system often requires high speed, large capacity memory, but the internal storage resource of FPGA is not sufficient to meet the requirements. In order to solve above problems, a SDRAM controller is proposed in this paper, where the Multiple FIFO based on the on-chip resources of FPGA serves as the read and write cache to realize the multiple functional modules performing the read/write operation in LXI acquisition system by the design of priority algorithm and reasonable controlling the access of SDRAM from external device. At the same time, the SDRAM can still communicate at high frequency by the suitable time limitation. The simulation results show that the proposed SDRAM controller can not only realize reading and writing data, but also its operating frequency is able to meet the requirements of functional modules.
Cellulose Nanofibrils/Xyloglucan Bio-Based Aerogels with Shape Recovery (2021)

Bio-based aerogels containing cellulose nanofibrils (CNFs) are promising materials due to the inherent physical properties of CNF. The high affinity of cellulose to plant hemicelluloses (xyloglucan, xylan, pectin) is also an opportunity to develop biomaterials with new properties. Here, we prepared aerogels from gelled dispersions of CNFs and xyloglucan (XG) at different ratios by using a freeze-casting procedure in unidirectional (UD) and non-directional (ND) manners. As showed by rheology analysis, CNF and CNF/XG dispersions behave as true gels. We investigated the impact of the freezing procedure and the gel's composition on the microstructure and the water absorption properties. The introduction of XG greatly affects the microstructure of the aerogel from lamellar to cellular morphology. Bio-based aerogels showed high water absorption capacity with shape recovery after compression. The relation between morphology and aerogel compositions is discussed.
Unified Description of Charge-Carrier Mobilities in Disordered Semiconducting Polymers (2005)

From a numerical solution of the master equation for hopping transport in a disordered energy landscape with a Gaussian density of states, we determine the dependence of the charge-carrier mobility on temperature, carrier density, and electric field. Experimental current-voltage characteristics in devices based on semiconducting polymers are excellently reproduced with this unified description of the mobility. At room temperature it is mainly the dependence on carrier density that plays an important role, whereas at low temperatures and high fields the electric field dependence becomes important. Omission in the past of the carrier-density dependence has led to an underestimation of the hopping distance and the width of the density of states in these polymers.
Utility max-min fair flow control for multipath communication networks (2007)

Abstract — This paper considers flow control and resource allo-cation problem as applied to multipath communication networks. We propose a novel distributed algorithm, show and prove that among all the sources with generic increasing and bounded util-ities (no need to be concave) in steady state, the utility max-min fairness is achieved, which is essential in providing application QoS (Quality of Service) guarantee. In addition, by combining a first order Lagrangian method and filtering mechanism, the resulted approach eliminates typical oscillating behavior for the multipath network and possesses a rapid convergence property. I.
Transflective Configuration of Dual Mode Liquid Crystal Display for High Contrast Ratio (2009)

We propose a transflective dual mode liquid crystal display, which is composed of a transmissive part for dynamic mode and a reflective part for a memory mode in a pixel. The proposed configuration has single cell gap and single rubbing direction in both parts. In order to make the reflectance minimized and maximized for dark and bright states of memory part, the parameters of LC layer and retardation film are optimized by using the Jones matrix method. Moreover, the operating voltage of dynamic part is found to depend on the retardation values of compensation films. With this configuration, the dynamic and memory modes show high contrast ratio of 1100:1 and 20:1, respectively, by calculation, while 220:1 and 10:1, respectively, by experiment.
Natural Convection in Trapezoidal Enclosure Heated Partially from Below (2012)

Natural convection in a trapezoidal enclosure with partial heating from below and symmetrical cooling from the sides has been investigated numerically. The heating is simulated by a centrally located heat source on the bottom wall, and four different values of the dimensionless heat source length, 1/5, 2/5, 3/5, 4/5 are considered. The laminar flow field is analyzed numerically by solving the steady, two-dimensional incompressible Navier-Stokes and energy equations. The Cartesian velocity components and pressure on a collocated (non-staggered) grid are used as dependent variables in the momentum equations discretized by finite volume method; body fitted coordinates are used to represent the trapezoidal enclosure, and grid generation technique based on elliptic partial differential equations is employed. SIMPLE algorithm is used to adjust the velocity field to satisfy the conservation of mass. The range of Rayleigh number is (103? Ra ?105) and Prandtl number is 0.7. The results show that the average Nusselt number increases with the increases of the source length.
Blocking mitochondrial pyruvate import in brown adipocytes induces energy wasting via lipid cycling (2020)

Combined fatty acid esterification and lipolysis, termed lipid cycling, is an ATP-consuming process that contributes to energy expenditure. Therefore, interventions that stimulate energy expenditure through lipid cycling are of great interest. Here we find that pharmacological and genetic inhibition of the mitochondrial pyruvate carrier (MPC) in brown adipocytes activates lipid cycling and energy expenditure, even in the absence of adrenergic stimulation. We show that the resulting increase in ATP demand elevates mitochondrial respiration coupled to ATP synthesis and fueled by lipid oxidation. We identify that glutamine consumption and the Malate-Aspartate Shuttle are required for the increase in Energy Expenditure induced by MPC inhibition in Brown Adipocytes (MAShEEBA). We thus demonstrate that energy expenditure through enhanced lipid cycling can be activated in brown adipocytes by decreasing mitochondrial pyruvate availability. We present a new mechanism to increase energy expenditure and fat oxidation in brown adipocytes, which does not require adrenergic stimulation of mitochondrial uncoupling.
Effect of a declination angle of substrate position on magnetron sputter deposition from a YBa2Cu3O7−x target (1989)

Thin-film deposition by magnetron sputtering of a multielement target was carried out with respect to the geometrical factors between a target and the substrates. The thin films were deposited on substrates which were located semicircularly over a YBa2Cu3O7−x target in several declination angles measured from the normal to the target surface. The deposition rate decreased to about one-third with the change in the angle from 0° to 90°. In the angles of 45°, 60°, and 75°, films showed significant instability in the atmosphere, which appeared to be caused by an excessive concentration of Ba atoms in the films. Target composition was almost reproduced in the films deposited in the angle of 90°.
First glimpse at a calixarene clathrate (2012)

The 1979 X-ray crystal structure of the p-t-butylcalix[4]arene toluene 1 : 1 intra-cavity inclusion complex proved a landmark result that established the iconic calixarene shape, proved the tetrameric calixarene structure and showed that an intrinsic molecular cavity in an artificial receptor could contain a guest molecule.
4-Hydroxy-2-cyclopentenone: An Anti-Pseudomonas and Cytotoxic Component fromPassiflora tetrandra1 (1991)

4-Hydroxy-2-cyclopentenone is responsible for the anti-bacterial activity of an extract of leaves from Passiflora tetrandra with minimum inhibitory doses (MID) of ca. 10 micrograms/disk against Escherichia coli, Bacillus subtilis, and Pseudomonas aeruginosa. 4-Hydroxy-2-cyclopentenone is also cytotoxic to P388 murine leukemia cells (IC50 of less than 1 microgram/ml).
Evaluation of free modeling targets in CASP11 and ROLL (2015)

We present an assessment of 'template-free modeling' (FM) in CASP11and ROLL. Community-wide server performance suggested the use of automated scores similar to previous CASPs would provide a good system of evaluating performance, even in the absence of comprehensive manual assessment. The CASP11 FM category included several outstanding examples, including successful prediction by the Baker group of a 256-residue target (T0806-D1) that lacked sequence similarity to any existing template. The top server model prediction by Zhang's Quark, which was apparently selected and refined by several manual groups, encompassed the entire fold of target T0837-D1. Methods from the same two groups tended to dominate overall CASP11 FM and ROLL rankings. Comparison of top FM predictions with those from the previous CASP experiment revealed progress in the category, particularly reflected in high prediction accuracy for larger protein domains. FM prediction models for two cases were sufficient to provide functional insights that were otherwise not obtainable by traditional sequence analysis methods. Importantly, CASP11 abstracts revealed that alignment-based contact prediction methods brought about much of the CASP11 progress, producing both of the functionally relevant models as well as several of the other outstanding structure predictions. These methodological advances enabled de novo modeling of much larger domain structures than was previously possible and allowed prediction of functional sites. Proteins 2016; 84(Suppl 1):51-66. © 2015 Wiley Periodicals, Inc.
Adeno-Associated Viral Vectors as Versatile Tools for Parkinson’s Research, Both for Disease Modeling Purposes and for Therapeutic Uses (2021)

It is without any doubt that precision medicine therapeutic strategies targeting neurodegenerative disorders are currently witnessing the spectacular rise of newly designed approaches based on the use of viral vectors as Trojan horses for the controlled release of a given genetic payload. Among the different types of viral vectors, adeno-associated viruses (AAVs) rank as the ones most commonly used for the purposes of either disease modeling or for therapeutic strategies. Here, we reviewed the current literature dealing with the use of AAVs within the field of Parkinson's disease with the aim to provide neuroscientists with the advice and background required when facing a choice on which AAV might be best suited for addressing a given experimental challenge. Accordingly, here we will be summarizing some insights on different AAV serotypes, and which would be the most appropriate AAV delivery route. Next, the use of AAVs for modeling synucleinopathies is highlighted, providing potential readers with a landscape view of ongoing pre-clinical and clinical initiatives pushing forward AAV-based therapeutic approaches for Parkinson's disease and related synucleinopathies.
Network Softwarization and Management (2020)

The articles in this special section focus on network softwarization and management. This renewed series focuses on softwarization, management, and their integration in communication networks and their services. “Network Softwarization” advocates for network architectures that separate the software implementing network functions, protocols and services from the hardware running them. Propelled by the maturity of technologies like network function virtualization and software-defined networking, softwarization is radically changing the way communication infrastructures are designed, programmed, integrated and operated, enabling rapid and innovative service creation with easy deployment and opening the door to a faster pace of innovation.
Review on Pharmacological Properties of Abutilon indicum. (2012)

Abutilon indicum belonging to family Malvaceae is distributed throughout number of tropical and subtropical areas and subtropical zones and has been used for various disorders in traditional and folk medicine. The plant is used as demulcent, aphrodisiac, laxative, diuretic, pulmonary and sedative. The leaves are used as astringent. Bark is used as diuretic. Seeds are used as laxative, demulcent and expectorant.
Elevations in Troponin T and I Are Associated With Abnormal Tissue Level Perfusion (2002)

Similar to what has been observed in the setting of ST-elevation myocardial infarction, abnormal tissue level perfusion is also associated with adverse outcomes in the NSTE-ACS setting. Independent of the presence of thrombus and abnormal flow in the epicardial artery, impaired tissue level perfusion is associated with a 1.8-fold increased risk of cTnT elevation.
A Novel and Effective Strategy for the Isolation of Adipose-Derived Stem Cells (2014)

Adipose-derived stem cells are an ideal mesenchymal stem cell population for regenerative medical application. The isolation procedure is performed by mechanical isolation under a laminar air flow bench without using serum or animal-derived reagents; cells were characterized by flow cytometric analysis. Cell availability is improved compared with enzymatic digestion procedures. The adipose-derived stem cell mechanical isolating procedure presented here is easier, safer, cheaper, and faster than traditional currently performed enzymatic procedures.
A Portable Microfabricated GCxGC System for Vapor Sampling and Analysis. (2013)

Abstract not provided.
Progress in the Research of Cloning on Mammals and Effect in Animal Production (2001)

WT5”BZ]This paper reviews the progress in the research of the nuclear transfer of the embryo cell and somatic cell on mammals.The tendency of realization of cloning be analyzed,and point out the technological difficulty to promote the effect of the cloning.The cloning technology have positive and negative effect to animal production.Expectation and apprehension would been taken into account to the further development of cloning. [WT5”HZ]
Mitigation algorithm against black hole attack using Real Time Monitoring for AODV routing protocol in MANET (2015)

Adhoc On Demand Vector (AODV) is a demand driven routing protocol in Mobile Ad hoc Network (MANET). There is always a resource constraint in adhoc network and threat from malicious nodes and hence feasible solution is preferably needed. For this reason, in this paper, we propose a new method RTMAODV (Real Time Monitoring AODV). It does not introduce any overhead. Moreover neighbor node detects and prevents black hole attack using real time monitoring. The new proposed method is effective for multiple sessions. The concept of broadcasting is being used in the method. Node which replies to RouteRequest (RREQ) by source is being monitored in promiscuous mode. Detection of malicious node is actually done by neighbor node of RouteReply (RREP) sender node. In simulation, new method has shown outstanding result in terms of packet delivery ratio as compare to AODV routing protocol in presence of malicious node under black hole attack.
Kidney Biopsy Findings in Patients with COVID-19 (2020)

Patients with COVID-19 develop a wide spectrum of glomerular and tubular diseases. Our findings provide evidence against direct viral infection of the kidneys as the major pathomechanism for COVID-19-related kidney injury and implicate cytokine-mediated effects and heightened adaptive immune responses.