gebhart/patrepeval huggingface dataset:
Phenyl Esters Are Potent Inhibitors of Caseinolytic Protease P and Reveal a Stereogenic Switch for Deoligomerization (2015)

Caseinolytic protease P (ClpP) represents a central bacterial degradation machinery that is involved in cell homeostasis and pathogenicity. The functional role of ClpP has been studied by genetic knockouts and through the use of beta-lactones, which remain the only specific inhibitors of ClpP discovered to date. Beta-lactones have served as chemical tools to manipulate ClpP in several organisms; however, their potency, selectivity and stability is limited. Despite detailed structural insights into the composition and conformational flexibility of the ClpP active site, no rational efforts to design specific non-beta-lactone inhibitors have been reported to date. In this work, an unbiased screen of more than 137 000 compounds was used to identify five phenyl ester compounds as highly potent ClpP inhibitors that were selective for bacterial, but not human ClpP. The potency of phenyl esters largely exceeded that of beta-lactones in ClpP peptidase and protease inhibition assays and displayed unique target selectivity in living S. aureus cells. Analytical studies revealed that while phenyl esters are cleaved like native peptide substrates, they remain covalently trapped as acyl-enzyme intermediates in the active site. The synthesis of 36 derivatives and subsequent structure-activity relationship (SAR) studies provided insights into conserved structural elements that are important for inhibition potency and acylation reactivity. Moreover, the stereochemistry of a methyl-substituent at the alpha position to the ester, resembling amino acid side chains in peptide substrates, impacted ClpP complex stability, causing either dissociation into heptamers or retention of the tetradecameric state. Mechanistic insights into this intriguing stereo switch and the phenyl ester binding mode were obtained by molecular docking experiments.
Generation of Silk Fibroin Nanoparticles via Solution-Enhanced Dispersion by Supercritical CO<sub>2</sub> (2013)

A solution-enhanced dispersion by supercritical CO2 (SEDS) was employed to prepare silk fibroin (SF) nanoparticles. The results of 24 full factorial experiment indicated that SF nanoparticles with particle size (PS) from 52.5 to 102.3 nm and particle size distribution (PSD) from 0.32 to 0.66 can be fabricated successfully. Moreover, reducing precipitation pressure or increasing concentration of SF solution, flow rate of SF solution, or precipitation temperature can increase PS and PSD of SF nanoparticles. The nanoparticle formation mechanism was elucidated through the formation and growth of SF nuclei in the gaseous miscible phase evolved from initial droplets generated by liquid–liquid phase split. Mass transfer between supercritical CO2 and SF solution superimposed on supersaturation was the most important process parameter affecting nanoparticle formation. Furthermore, Fourier transform infrared spectroscopy and X-ray powder diffraction analysis revealed that SF nanoparticles exhibited predominant random coil and α-helix structure with minor β-sheet conformation.
PRIMING HEPATITIS B SURFACE (HBSAG)- AND CORE ANTIGEN (HBCAG)-SPECIFIC IMMUNE RESPONSES BY CHIMERIC, HBCAG WITH A HBSAG ‘A’ DETERMINANT (2006)

We developed an immunogen to stimulate multivalent immunity against hepatitis B surface antigen (HBsAg) and hepatitis B core antigens (HBcAg). Immune responses specific for both HBsAg and HBcAg play an important role in controlling the infection. HBsAg-specific antibodies mediate elimination of virions at an early stage of infection and prevent the spread of virus. The immunogen was constructed by inserting the immunodominant, antibody-binding ‘a ’ determinant (aa 111-149) of HBsAg (with or without a poly-glycine (PG) linker) into the e2 epitope of HBcAg. Only the constructs in which the HBsAg ‘a ’ determinant was inserted into HBcAg, flanked by PG linkers, expressed a chimeric protein in human embryonic kidney cells with HBsAg and HBcAg antigenicity. Both glycosylated and non-glycosylated forms of the chimeric protein were immunoprecipitated from cell lysate. Intramuscular DNA vaccination of mice with plasmids expressing chimeric HBcAg primed antibody responses against well-defined serologically-defined determinants of both, native HBcAg, and native HBsAg. In addition, CD8+ T cell responses against HBcAg epitopes were primed by this chimeric HBV antigen. The e2 sequence of HBcAg can thus be used to present heterologous epitopes without loss of immunogenicity of the HBcAg protein. Iran. Biomed. J. 10 (2): 61-68, 2006
Application-level differentiated multimedia Web services using quality aware transcoding (2000)

The ability of a Web service to provide low-latency access to its content is constrained by available network bandwidth. While providing differentiated quality of service (QoS) is typically enforced through network mechanisms, in this paper we introduce a robust mechanism for managing network resources using application-specific characteristics of Web services. We use transcoding to allow Web servers to customize the size of objects constituting a Web page, and hence the bandwidth consumed by that page, by dynamically varying the size of multimedia objects on a per-client basis. We leverage our earlier work on characterizing quality versus size tradeoffs in transcoding JPEG images to supply more information for determining the quality and size of the object to transmit. We evaluate the performance benefits of incorporating this information in a series of bandwidth management policies using realistic workloads and access scenarios to drive our system. The principal contribution of this paper is the demonstration that it is possible to use informed transcoding techniques to provide differentiated service and to dynamically allocate available bandwidth among different client classes, while delivering good quality of information content for all clients. We also show that it is possible to customize multimedia objects to the highly variable network conditions experienced by mobile clients in order to provide acceptable quality and latency depending on the networks used in accessing the service. We show that policies that aggressively transcode the larger images can produce images with quality factor values that closely follow the untranscoded base case while still saving as much as 150 kB. A transcoding policy that has knowledge of the characteristics of the link to the client can avoid as many as 40% of (unnecessary) transcodings.
Saddlepoint Approximation for Calculating Performance of Spectrum-Sliced WDM Systems (1999)

Spectrum slicing is a novel technique for the implementation of wavelength-division multiplexing (WDM). While conventional WDM systems employ laser diodes operating at discrete wavelengths as carriers for the different data channels that are to be multiplexed, spectrum-sliced systems make use of spectral slices of a broadband noise source for the different data channels, thus being economically attractive. In spectrum-sliced WDM systems with an optical preamplifier receiver there is an optimum m=BoT (Bo = optical channel bandwidth, T = bit duration) to minimize the average number of photons-per-bit (Np) required at the receiver for a given error probability (Pe). Both the optimum m and the minimum increase as interchannel interference increases. This has been analyzed previously by using the Gaussian approximation, or by assuming that the signals at the decision point are chi-square distributed. Although the chi-square distribution is valid in the case where there is no interference, it is not valid in the presence of interference, since the interference from the neighboring channel has a smaller bandwidth than the signal. In this thesis, a different method is used to analyze this problem. This method is called the Saddlepoint Approximation, and while the exact analysis required determination of the probability density function (pdf) of the received signal, the saddlepoint method makes use of moment generating functions (MGFs) which have a much simpler form and don't require the convolution operations the pdfs require. The saddlepoint method is validated by comparing results obtained with the chi-square analysis for the no interchannel interference case when a rectangular shaped filter is used. The effect of non-rectangular spectra on receiver sensitivity with the use of the Saddlepoint Approximation is also investigated. After verifying its validity, the method is applied to the interchannel interference case caused by filter overlap. It is shown that for small filter overlap, use of an equivalent chi-square distribution is valid, but when the overlap becomes larger, the performance approaches that calculated using the Gaussian distribution. It is shown that there is an optimum filter overlap to maximize the total system throughput when total bandwidth is constrained. Operating at this optimum, the total system throughput is 135 Gbits/s when the total system bandwidth is 4.4 THz (35 nm) for a Bit Error Rate (BER) of 10e-9.
Entropy-constrained trellis-coded quantization (1992)

Trellis-coded quantization is generalized to allow noiseless coding of the trellis branch reproduction symbols. An entropy-constrained trellis-coded quantization (ECTCQ) design algorithm is presented, based on the generalized Lloyd algorithm for trellis code design and the entropy-constrained vector quantization design algorithm. ECTCQ systems are designed for memoryless Gaussian and Laplacian sources, and for first- and second-order Gauss-Markov sources. With an 8-state trellis, the mean-squared error ECTCQ encoding performance for memoryless sources with smooth densities is within about 0.5 dB of the rate-distortion function. Small additional improvements are achieved with larger trellises. Similar, though not quite as good, performance is achieved for the Gauss-Markov sources by using the ECTCQ in a predictive coding structure.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Target Plasma Formation for Magnetic Compression/Magnetized Target Fusion (1995)

Experimental observations of plasma behavior in a novel plasma formation chamber are reported. Experimental results are in reasonable agreement with two-dimensional magnetohydrodynamic computations suggesting that the plasma could subsequently be adiabatically compressed by a magnetically driven pusher to yield 1 GJ of fusion energy. An explosively driven helical flux compression generator mated with a unique closing switch/opening switch combination delivered a 2.7 MA, 347 $\ensuremath{\mu}\mathrm{s}$ magnetization current and an additional 5 MA, 2.5 $\ensuremath{\mu}\mathrm{s}$ electrical pulse to the chamber. A hot plasma was produced and 1${0}^{13}$ D-T fusion reactions were observed.
3D LASER SCANNERS: HISTORY, APPLICATIONS, AND FUTURE (2014)

A 3D scanner is a device that analyses a real-world object or environment to collect data on its shape and possibly its appearance (e.g. colour). The collected data can then be used to construct digital three-dimensional models. Many different technologies can be used to build these 3D-scanning devices; each technology comes with its own limitations, advantages and costs. Many limitations in the kind of objects that can be digitized are still present, for example, optical technologies encounter many difficulties with shiny, mirroring or transparent objects. For example, industrial computed tomography scanning can be used to construct digital 3D models, applying non-destructive testing. Collected 3D data is useful for a wide variety of applications. These devices are used extensively by the entertainment industry in the production of movies and video games. Other common applications of this technology include industrial design, orthotics and prosthetics, reverse engineering and prototyping, quality control/inspection and documentation of cultural artifacts.
Sensory pudendal nerve stimulation increases bladder capacity through sympathetic mechanisms in cyclophosphamide‐induced cystitis rats (2018)

Aims Interstitial cystitis and bladder pain syndrome is a prevalent health concern with inadequate treatments. Neuromodulation has emerged as a therapeutic option to treat patients refractory to standard care. The objective of this study was to determine the efficacy and mechanism(s) of sensory pudendal nerve stimulation on bladder function in cystitis rats. Methods Female rats were administered saline ( n = 8) or cyclophosphamide (CYP, 150 mg/kg IP, n = 16) and single‐trial cystometry experiments were conducted under urethane anesthesia 48 h after injection. Electrical stimulation (0.02‐0.22 mA, 10‐20 Hz) was delivered to the sensory branch of the pudendal nerve and its effect on the bladder and external urethral sphincter were measured. Stimulation trials were also conducted following bilateral hypogastric nerve transection (HGNT) or pharmacological inhibition of beta‐adrenergic receptors (propranolol, 1 mg/kg IV) to determine the mechanisms of bladder inhibition. Results CYP‐induced cystitis decreased bladder capacity ( P = 0.0352) and bladder compliance ( P = 0.024) by up to 38% of control. Electrical stimulation of the sensory pudendal nerve increased bladder capacity ( P < 0.0001) in control and CYP rats by up to 51‐52% of their respective baselines. HGNT did not influence bladder inhibition generated by sensory pudendal nerve stimulation in control rats, whereas HGNT and propranolol decreased the efficacy of electrical stimulation in CYP rats. Conclusions Sympathetic reflex activity mediates sensory pudendal nerve stimulation in CYP treated but not control rats. These studies demonstrate an alternative approach to neuromodulation in cystitis and establish mechanistic changes during stimulation that may enable the development of novel therapeutics.
Introduction (1996)

It is seven o’clock on a Friday evening in June. A group of teenagers — mainly though not exclusively boys — are hanging around outside the shops on a usually quiet residential street. Local residents, fed up with the noise and anxious about levels of street crime in the area, call the police. Some 20 minutes later two officers arrive at the scene; they talk to the youths, a few muffled complaints are heard and the young people are moved on. The residents, for the moment at least, are placated.
A review of uncertainty quantification in deep learning: Techniques, applications and challenges (2021)

Uncertainty quantification (UQ) methods play a pivotal role in reducing the impact of uncertainties during both optimization and decision making processes. They have been applied to solve a variety of real-world problems in science and engineering. Bayesian approximation and ensemble learning techniques are two widely-used types of uncertainty quantification (UQ) methods. In this regard, researchers have proposed different UQ methods and examined their performance in a variety of applications such as computer vision (e.g., self-driving cars and object detection), image processing (e.g., image restoration), medical image analysis (e.g., medical image classification and segmentation), natural language processing (e.g., text classification, social media texts and recidivism risk-scoring), bioinformatics, etc. This study reviews recent advances in UQ methods used in deep learning, investigates the application of these methods in reinforcement learning, and highlights fundamental research challenges and directions associated with UQ.
Spectral line shapes of J = 1 odd-parity autoionizing Rydberg series of Ge, Sn, and Pb (1986)

Dipole allowed photoabsorption from the mp 2 3 P 0 ground state of Ge ( m = 4), Sn ( m = 5), or Pb ( m = 6) terminates on mpns or mpnd , J = 1 odd-parity states. Between the first and second ionization limits of each of these elements, the absorption spectrum shows three autoionizing series associated with mp 3/2 ns 1/2 , mp 3/2 nd 3/2 , and mp 3/2 nd 5/2 . The observed line shapes 1 of these autoionizing series are parametrized using a profile formula which has a form analogous to the well-known Fano resonance formula while satisfying requirements of multichannel quantum-defect theory. The profile parameters, such as width and asymmetry parameters, are discussed and correlated with the eigenquantum defects obtained from the analysis of term values of bound levels and the associated eigenchannel dipole matrix elements.
An audio 91-dB THD third-order fully-differential class-D amplifier (2011)

Class-D amplifiers exhibit high efficiency in spite of their simple implementation and, therefore, they are often used in portable devices with typical THD performance of the order of -65 dB. Presently, the possibility of using class-D amplifiers in applications requiring better THD (THD <; -85 dB) is being investigated, in consideration of their possible application in huge markets (like high-performance audio). For this reason, the THD performance of conventional class-D structures is not enough and new topologies have to be analyzed and implemented. In this paper, high-order class-D structures have been investigated to achieve the target THD performance. Among them, we selected a 3 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">rd</sup> -order fully-differential class-D amplifier, which has been implemented in a 0.18-μm CMOS technology, starting from a previously available 1 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">st</sup> -order class-D structure. The measurements on the realized 3 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">rd</sup> -order device show a THD ≈ -91 dB with -1 dB <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">FS</sub> input signal, about 30 dB better than the 1 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">st</sup> -order structure.
Green2.0 (2016)

Professionals and researchers of the Architectural, Engi-neering & Construction (AEC) industry are challenged by the increasing complexity of designing, constructing and op-erating a building. This typically requires close cooperation of actors having different backgrounds and interests. Tra-ditionally, this cooperation happens in an ad-hoc way and information exchange occurs through conventional general-purpose communication channels, such as paper or email. This communication and collaboration process can be inad-equate and inefficient, as it makes room for many different interpretations, mistakes and errors and can eventually lead to schedule and cost alterations. We present Green2.0, a system that tries to leverage advancements in building in-formation modeling to facilitate the collaboration process. The system integrates energy-efficiency simulation tools, and methods for online social network analysis to enable a data-driven approach to building design, construction and operation. By sharing all information online, all project ac-tors can access relevant information when they need so that everyone can work efficient together. The system aims to advance the current state of the art by bringing about a fundamental shift in the way that AEC professionals work together throughout a building's lifecycle.
Stent technology in ischemic stroke (2017)

Atherosclerotic disease of the cerebral vasculature is a major cause of stroke worldwide. Atherosclerosis that is refractory to best medical management may require revascularization. In these instances, endovascular treatment provides a popular and safe alternative to open surgical techniques. The authors provide an overview of stent technology in the treatment of ischemic stroke, discussing the major studies evaluating stenting for extracranial carotid artery, vertebral artery, and intracranial atherosclerotic disease. The authors describe the commonly used stents with respect to their individual characteristics and technical limitations. Current and future developments in stent technology are also discussed, with areas for further innovation and clinical research.
Mechanically Assisted Exfoliation and Functionalization of Thermally Converted Graphene Sheets (2009)

Graphene sheets were exfoliated and functionalized by grinding thermally converted graphene (TCG, obtained by thermally expansion of graphite oxide) in ionic liquid with various aryl-diazonium salts. This method results in the separation of graphene layers and addition of aryl groups on the sheets to obtain single layer-graphene; the number of functional groups on the graphene was determined to be roughly 1 in 60 carbons. This solvent-dispersible graphene material could prove desirable for use in composite scaffolds.
Synthesis of N-substituted 2-[(1E)-alkenyl]-4-(1H)-quinolone derivatives as antimycobacterial agents against non-tubercular mycobacteria (2011)

In an effort to improve biological activities and to examine antimycobacterial-lipophilicity relationships of 2-[(1E)-alkenyl)]-4-(1H)-quinolones, we have synthesized a series of 30 quinolones by introducing several alkyl groups, an alkenyl and an alkynyl group at N-1. All synthetic compounds were first tested in vitro against Mycobacterium smegmatis and the most active compounds (MIC values ∼3.0-7.0 μM) were further examined against three other rapidly growing strains of mycobacteria using a microtiter broth dilution assay. The Clog P values of the synthetic compounds were calculated to provide an estimate of their lipophilicity. Compounds 18e, 19a and 19b displayed the most potent inhibitory effect against M. smegmatis mc(2)155 with an MIC value of ∼1.5 μM, which was twenty fold and thirteen fold more potent than isoniazid and ethambutol, respectively. On the other hand, compounds 17e, 18e and 19a were most active against Mycobacterium fortuitum and Mycobacterium phlei with an MIC value of ∼3.0 μM. In the human diploid embryonic lung cell line MRC-5 cytotoxicity assay, the derivatives showed moderate to strong cytotoxic activity. Although the antimycobacterial activity of our synthetic compounds could not be correlated with the calculated log P values, an increase in lipophilicity enhances the antimycobacterial activity and C13-C15 total chain length at positions 1 and 2 is required to achieve optimal inhibitory effect against the test strains.