gebhart/patrepeval huggingface dataset:
Electric field induced piezoelectric resonance in the micrometer to millimeter waveband in a thin film SrTiO3 capacitor (2003)

Thin film SrTiO3 metal–insulator–metal (MIM) capacitors were fabricated in order to characterize the piezoelectric resonance in the micrometer to millimeter waveband arising from electric field induced ferroelectricity in the SrTiO3 film. The specimens showed a second-order phase transition, and the piezoelectric resonance appeared when an electric field of 250 kV/cm was applied at room temperature. Finite element method (FEM) analysis was used to interpret the piezoelectric resonance observed in the capacitors. The FEM analysis data basically agrees well with the experimental data, and the few differences between the theoretical and experimental data are interpreted mainly as artifacts caused by overlapping of resonant/antiresonant peaks during the measurement. The piezoelectric resonance of thin film MIM capacitors is strongly influenced by the longitudinal stacked structure of the MIM.
Nuclear Hormone Receptor Regulation of MicroRNAs Controls Developmental Progression (2009)

In response to small-molecule signals such as retinoids or steroids, nuclear receptors activate gene expression to regulate development in different tissues. MicroRNAs turn off target gene expression within cells by binding complementary regions in messenger RNA transcripts, and they have been broadly implicated in development and disease. Here we show that the Caenorhabditis elegans nuclear receptor DAF-12 and its steroidal ligand directly activate promoters of let-7 microRNA family members to down-regulate the microRNA target hbl-1, which drives progression of epidermal stem cells from second to third larval stage patterns of cell division. Conversely, the receptor without the ligand represses microRNA expression during developmental arrest. These findings identify microRNAs as components of a hormone-coupled molecular switch that shuts off earlier developmental programs to allow for later ones.
On the influence of the shape of anode voltage pulse on the operation stability of spatial-harmonic magnetron with cold secondary emission cathode (2018)

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HIV-1 Neutralization Coverage Is Improved by Combining Monoclonal Antibodies That Target Independent Epitopes (2012)

HIV-1 neutralizing monoclonal antibodies (MAbs) define key targets for vaccine development and are being considered for passive prevention of infection. We analyzed the interaction of MAbs to two independent epitopes on the viral envelope glycoprotein. Potently neutralizing MAbs to the CD4 binding site and V1V2 region displayed no in vitro cross-competition and displayed additive, though not synergistic, neutralization activity. Predicted neutralization coverage of a combination of two MAbs reached 97% on a 208-isolate panel.
Trellis precoding for MIMO broadcast signaling (2009)

Channel inversion, and its minimum mean square error (MMSE) variation, are low complexity methods for space division multiple access (SDMA) in multiple input multiple output broadcast channel (MIMO-BC). As the channel matrix deviates from orthogonal, these methods result in a waste of transmit power. This paper proposes a trellis precoding method (across time and space) to improve the power efficiency. Adopting a 4-state trellis shaping method, the complexity of the proposed method, which is entirely at the transmitter side, is equivalent to the search in a trellis with 4 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">N</sup> states where N is the number of transmit antennas. Numerical results are presented showing that the achievable gains, which depend on the channel realization, can be significantly higher than the traditional shaping gain which is limited to 1.53 dB.
Identification of Chikungunya virus nucleocapsid core assembly modulators (2019)

Abstract: The alphavirus Chikungunya virus is transmitted to humans via infected mosquitos. Most infected humans experience symptoms which can range from short-term fatigue and fever to debilitating arthritis that can last for months or years. Some patients relapse and experience symptoms months or years after the initial bout of disease. The capsid protein of Chikungunya virus forms a shell around the viral RNA genome; this structure is called the nucleocapsid core. The core protects the genome during virus transmission and with the correct environmental trigger, this proteinaceous shell dissociates and releases the viral genome to initiate infection. We hypothesized that targeting compounds to interfere with the nucleocapsid core’s function would constrain virus spread either by inhibiting the release of viral genomes during entry or by reducing the number of infectious virus particles assembled. We implemented a high throughput, in vitro, FRET-based assay to monitor nucleic acid packaging by purified Chikungunya capsid protein as a proxy for nucleocapsid core assembly and disassembly. We screened 10,000 compounds and found 45 that substantially modulated the assembly of core-like particles. A subset of compounds was selected to study their effects in virus-infected vertebrate cells. Our results show that four compounds inhibit infectious virus production by at least 90% in a dose-dependent manner. The most promising inhibitor was tested and found to reduce the amount of nucleocapsid cores inside the cell during Chikungunya virus infection. These compounds could be the foundation for anti-viral therapeutics. Highlights A FRET-based assay to detect nucleic acid packaging by Chikungunya virus capsid protein Identification of small molecules that modulate core-like particle assembly A subset of compounds that interfere with in vitro assembly also inhibit Chikungunya virus production in cell culture Identification of antiviral molecules that may not be identified by assays using reporter viruses Potential starting compounds for developing direct-acting antivirals
Analyses of Sonic Data in an Indonesian Well for Formation Damage, Stresses, and Bedding (2002)

To help design the completion of an Indonesian development well, we have carried out cross-dipole dispersion analyses over a depth interval of approximately 500 ft. Dispersion analyses provide estimates of radial extent of formation damage and indicators of stress- and bedding-induced anisotropies. Most of these sections of this vertical well exhibit sand and shale lithology with shear slowness anisotropy ranging from 5 to 10%. Above the angular unconformity in the deeper section of the well, a clean sand interval (Sand A) shows evidence of cross-dipole dispersion crossovers. Crossing dipole dispersions are indicators of stress-induced anisotropy dominating the sonic data. We have developed a new technique for estimating the maximum horizontal SH, and minimum horizontal Sh stress magnitudes using multi-frequency inversion of wideband cross-dipole dispersions. At the mid-point of sand A, we estimate the overburden stress SV=-2278 psi; the maximum horizontal stress SH=-1843; and minimum horizontal stress Sh=-1698. The fast shear direction is NW5 in this depth interval. Radial profiling of formation shear velocity indicates varying degrees of mechanical alteration extending from one to two borehole diameters in the entire depth.A second clean sand interval B, 300 ft above sand A, shows dipole shear anisotropy on the order of 10%. However, cross-dipole dispersions appear to merge together at high frequencies instead of showing a cross-over. Radial profiling of shear velocity in the two orthogonal directions confirms mechanical damage extending to about 2x the borehole diameter. The near-wellbore region in this interval appears to have deformed (material creep) in an attempt to reduce shear stresses and attain hydrostatic equilibrium. Using the same stress sensitivity coefficients as estimated in the lower sand A, the differential stress (SH-Sh) is estimated to be about 20% larger in the upper interval, than the corresponding value in the lower interval.The fast-shear direction varies abruptly across the angular unconformity, changing from NW5 to NW75. Below the unconformity, this section exhibits beds with dips ranging from 10° to 30°. Cross-dipole dispersions show significant anisotropy and are non-intersecting at higher frequencies. Non-intersecting dispersions indicate bedding-induced anisotropy dominating the cross-dipole data. We have inverted borehole sonic velocities for four combinations of the TI-shale anisotropy, which can be combined with walk away VSPs to obtain all the shale anisotropy constants. These constants are needed in generating synthetic AVO gathers in anisotropic shale formations. Quantitative estimates of the radial extent of near-wellbore damage in this well suggest that perforations should penetrate deeper than twice the borehole diameter to avoid potential permeability impairment caused by near-wellbore mechanical damage.
Low voltage active pressure sensor based on polymer space-charge-limited transistor (2009)

Low voltage active pressure sensor is realized by vertically stacking a pressure sensitive rubber on a polymer space-charge-limited transistor. The sensor can be turned on and off by modulating the metal-grid base voltage within the range of 3 V. The output current is irrelevant to the pressure as the sensor is off. As the sensor is turned on, the output current values can be used to monitor the pressure. Reversible pressure sensing characteristics is observed below the pressure of 7.11 psi. The response time of the sensor to the pressure is as short as 22 ms.
Characterization of the human Ig V lambda II gene family and analysis of V lambda II and C lambda polymorphism in systemic lupus erythematosus (1991)

We report the cDNA sequence of an expressed human V lambda II gene and present an RFLP analysis of the Ig gene family defined by this clone. This V lambda II gene was expressed in a monoclonal B cell line generated from a patient with SLE by transformation with EBV. The encoded lambda L chain displays the 8.12 Id, an Id common to anti-DNA antibodies from patients with SLE. Using a coding region probe we estimate from Southern blot analysis that the germline V lambda II gene family contains at least 15 members. Many of the V lambda II restriction fragments are polymorphic both in SLE patients and in nonautoimmune individuals. EcoRI, HindIII, and TaqI RFLP analyses of the V lambda II gene family and EcoRI analysis of the C lambda gene family reveal no polymorphisms specific to SLE. Observed V lambda II and C lambda allele frequencies are the same among SLE patients and nonautoimmune individuals, and show no evidence of linkage disequilibrium between the two loci.
B14 Neurotrophic factors secreting mesenchymal stem cells attenuate quinolinic acid induced striatal lesion model suggesting autologous therapy for HD (2010)

<h3>Background</h3> We have been studying the potential of utilising the patients9 own bone marrow derived mesenchymal stem cells (MSCs) which are transformed into cellular vectors secreting neurotrophic factors (NTF+ cells) in order to protect diseased neurons. Differentiated cells were shown to produce and secrete higher levels of BDNF and GDNF compared with naive MSCs. <h3>Aims</h3> To evaluate the efficacy of NTF+ cell based therapy for the quinolinic acid (QA) induced striatal model for excitotoxicity. To evaluate the capability of cultivating MSCs from HD patients, transforming them into NTF+ cells and transplanting them into the QA model. <h3>Methods</h3> Human MSC went through a two phase medium based differentiation protocol containing N2, growth factors, IBMX and cAMP. The protocol9s output was assessed using immunocytochemistry and ELISA analysis of the medium post differentiation. Rats were treated with 150 nmol QA injected into the left striatum. A total of 450 000 cells (either MSCs of NTF+ cells) were transplanted into the lesioned striatum. Behavioural assessment included apomorphine induced rotations, followed by a histological study. <h3>Results</h3> Transplanting NTF+ cells, but not naive MSCs, ameliorated apomorphine induced rotations by over 80%. Moreover, we found that NTF+ cells transplantation reduced QA induced striatal atrophy. One of the inherent advantages of the use of MSCs is the possibility of autotransplantation. Indeed, MSC obtained from four Huntington9s disease (HD) patients demonstrated similar membrane markers and differentiation capacity. Moreover, in the QA induced striatal lesion model, we found that HD patients9 NTF+ cells altered apomorphine induced rotational behaviour as well as cells derived from healthy controls. <h3>Conclusions</h3> Our preliminary data suggest that NTF+ cells may be utilised for cellular autologous treatment for HD in the future. Further research is needed in order to fully prove its efficacy, mechanism and mode of delivery in various animal models for HD.
Compact Low-Profile Wearable Antennas For Breast Cancer Detection (2018)

Many lives can be saved if tumors are detected in early stages, which can result in a bigger chance for recovery. Many patients find it irritating to get regular checkups due to the fact that the majority of the monitoring systems are complicated, not available everywhere and not mobile. Furthermore, for medical field applications, micro-strip antennas are efficient and have flexible properties that are utilized in imaging, diagnosis and treatment. It is known that breast cancer is the most common type of cancer in the world, and the earlier its been detected the better. In the early stages of breast cancer, getting rid of from the tumors is much easier and more guaranteed. Nowadays, the main method that is used in the hospitals for breast cancer detection is the Ultra-Wideband method (UWB). However, Many patients find it irritating to get regular check ups due to the fact that the majority of the monitoring systems are complicated and not mobile.
A Survey on Automated Software Vulnerability Detection Using Machine Learning and Deep Learning (2023)

Software vulnerability detection is critical in software security because it identifies potential bugs in software systems, enabling immediate remediation and mitigation measures to be implemented before they may be exploited. Automatic vulnerability identification is important because it can evaluate large codebases more efficiently than manual code auditing. Many Machine Learning (ML) and Deep Learning (DL) based models for detecting vulnerabilities in source code have been presented in recent years. However, a survey that summarises, classifies, and analyses the application of ML/DL models for vulnerability detection is missing. It may be difficult to discover gaps in existing research and potential for future improvement without a comprehensive survey. This could result in essential areas of research being overlooked or under-represented, leading to a skewed understanding of the state of the art in vulnerability detection. This work address that gap by presenting a systematic survey to characterize various features of ML/DL-based source code level software vulnerability detection approaches via five primary research questions (RQs). Specifically, our RQ1 examines the trend of publications that leverage ML/DL for vulnerability detection, including the evolution of research and the distribution of publication venues. RQ2 describes vulnerability datasets used by existing ML/DL-based models, including their sources, types, and representations, as well as analyses of the embedding techniques used by these approaches. RQ3 explores the model architectures and design assumptions of ML/DL-based vulnerability detection approaches. RQ4 summarises the type and frequency of vulnerabilities that are covered by existing studies. Lastly, RQ5 presents a list of current challenges to be researched and an outline of a potential research roadmap that highlights crucial opportunities for future work.
Learning Deep Generative Models with Doubly Stochastic MCMC (2015)

We present doubly stochastic gradient MCMC, a simple and generic method for (approximate) Bayesian inference of deep generative models (DGMs) in a collapsed continuous parameter space. At each MCMC sampling step, the algorithm randomly draws a mini-batch of data samples to estimate the gradient of log-posterior and further estimates the intractable expectation over hidden variables via a neural adaptive importance sampler, where the proposal distribution is parameterized by a deep neural network and learnt jointly. We demonstrate the effectiveness on learning various DGMs in a wide range of tasks, including density estimation, data generation and missing data imputation. Our method outperforms many state-of-the-art competitors.
Online Deterministic Annealing for Classification and Clustering (2022)

Inherent in virtually every iterative machine learning algorithm is the problem of hyperparameter tuning, which includes three major design parameters: 1) the complexity of the model, e.g., the number of neurons in a neural network; 2) the initial conditions, which heavily affect the behavior of the algorithm; and 3) the dissimilarity measure used to quantify its performance. We introduce an online prototype-based learning algorithm that can be viewed as a progressively growing competitive-learning neural network architecture for classification and clustering. The learning rule of the proposed approach is formulated as an online gradient-free stochastic approximation algorithm that solves a sequence of appropriately defined optimization problems, simulating an annealing process. The annealing nature of the algorithm contributes to avoiding poor local minima, offers robustness with respect to the initial conditions, and provides a means to progressively increase the complexity of the learning model, through an intuitive bifurcation phenomenon. The proposed approach is interpretable, requires minimal hyperparameter tuning, and allows online control over the performance-complexity tradeoff. Finally, we show that Bregman divergences appear naturally as a family of dissimilarity measures that play a central role in both the performance and the computational complexity of the learning algorithm.
Study of ammonia removal in coal gasification processes, literature review: Topical report (1987)

In the combustion and gasification of coal, oxides of nitrogen (NO/sub x/) are formed from two sources: fixation of atmospheric nitrogen in high-temperature flames, and oxidation of nitrogen compounds that are part of the coal feedstock. Because US coals contain from 0.5 to 2 wt % nitrogen, the possible contribution of this source to NO/sub x/ emissions is not trivial. In the reducing environment near the exit of a gasifier, fuel-bound nitrogen appears largely as ammonia. Removal of ammonia from the hot coal gas will eliminate subsequent production of NO/sub x/ from the fuel-bound nitrogen in downstream appliances such as a gas turbine or a molten carbonate fuel cell. A comprehensive survey was performed of the scientific literature, patents, and government and industrial reports to determine process concepts that might be suitable for hot coal gas ammonia removal. Candidate ammonia removal processes resulting from the survey include: catalytic decomposition of ammonia; sorption/reaction of ammonia with metals and oxides; partial oxidation of ammonia to nitrogen; and staged combustion processes. Catalytic decomposition and staged combustion were judged to be the only processes with potential practical utility. A process based on catalytic decomposition will be independent of coal gas end use. Staged combustionmore » methods can be used to reduce ultimate NO/sub x/ emissions during oxidation of NH/sub 3/-containing coal gas, but they require modifications in the combustion process that may impair efficient energy use of the fuel for further testing. 112 refs., 12 figs., 6 tabs.« less
Enhanced Energy Storage and Suppressed Dielectric Loss in Oxide Core–Shell–Polyolefin Nanocomposites by Moderating Internal Surface Area and Increasing Shell Thickness (2012)

Dielectric loss in metal oxide core/Al(2)O(3) shell polypropylene nanocomposites scales with the particle surface area. By moderating the interfacial surface area between the phases and using increasing shell thicknesses, dielectric loss is significantly reduced, and thus the energy stored within, and recoverable from, capacitors fabricated from these materials is significantly increased, to as high as 2.05 J/cm(3).
Developmentally regulated expression of a Giardia lamblia cyst wall protein gene (1995)

The protozoan Giardia lamblia is an obligate parasite of the mammalian small intestine. We studied the expression of a gene that encodes a protein component of the cyst wall, a complex structure assembled during the differentiation of trophozoites to cysts and which is critical to survival of the parasite outside its mammalian host. Transcripts from the cyst wall protein gene increase more than 100-fold during encystation, reaching a maximum between 5 and 24 hours after induction. Cyst wall protein expression also increases dramatically during encystation, and, prior to its incorporation into the nascent cyst wall, the protein is contained within the encystation-specific vesicles of encysting trophozoites. The sequence of the cloned gene predicts an acidic, leucine-rich polypeptide of M(r) 26,000 that contains 5.3 tandemly arranged copies of a degenerate 24-amino-acid repeat. A hydrophobic amino-terminal peptide probably serves as the initial signal that targets this protein to a secretory pathway involving vesicular localization during encystation and, ultimately, secretion to form the cyst wall.
A Digitally Controlled Oscillator System for SAW-Less Transmitters in Cellular Handsets (2006)

A complete digitally controlled oscillator (DCO) system for mobile phones is presented with a comprehensive study. The DCO is part of a single-chip fully compliant quad-band GSM transceiver realized in a 90-nm digital CMOS process. By operating the DCO at a 4 /spl times/ GSM low-band frequency followed by frequency dividers, the requirement of on-chip inductor Q and the amount of gate oxide stress are relaxed. It was found that a dynamic divider is needed for stringent TX output phase noise while a source-coupled-logic divider can be used for RX to save power. Both dividers are capable of producing a tight relation between four quadrature output phases at low voltage and low power. Frequency tuning is achieved through digital control of the varactors which serve as an RF DAC. Combining a MIM capacitor array and two nMOS transistor arrays of the varactors for the RF DAC, a highly linear oscillator gain which is also insensitive to process shift is achieved. The finest varactor step size is 12 kHz at the 1.6-2.0 GHz output. With a sigma-delta dithering, high frequency resolution is obtained while having negligible phase noise degradation. The measured phase noise of -167 dBc/Hz at 20 MHz offset from 915 MHz carrier and frequency tuning range of 24.5% proves that this DCO system can be used in SAW-less quad-band transmitters for mobile phones.