gebhart/patrepeval huggingface dataset:
Iota-carrageenan and Xylitol inhibit SARS-CoV-2 in cell culture (2020)

Abstract COVID-19 (coronavirus disease 2019) is a pandemic caused by SARS-CoV-2 (severe acute respiratory syndrome-coronavirus 2) infection affecting millions of persons around the world. There is an urgent unmet need to provide an easy-to-produce, affordable medicine to prevent transmission and provide early treatment for this disease. The nasal cavity and the rhinopharynx are the sites of initial replication of SARS-CoV-2. Therefore, a nasal spray may be a suitable dosage form for this purpose. The main objective of our study was to test the antiviral action of three candidate nasal spray formulations against SARS-CoV-2. We have found that iota-carrageenan in concentrations as low as 6 µg/ mL inhibits SARS-CoV-2 infection in Vero cell cultures. The concentrations found to be active in vitro against SARS-CoV-2 may be easily achieved by the application of nasal sprays already marketed in several countries. Xylitol at a concentration of 5 % m/V has proved to be viricidal on its own and the association with iota-carrageenan may be beneficial, as well.
Epstein‐Barr Viral Latency and Cell Immortalization as Targets for Antisense Oligomersa (1992)

The approach of using an antisense oligonucleotide to oppose the synthesis of a single selected viral gene product needed to maintain the EBV episome in non-virus-producing cells appears to be promising not only for possible cure of latent viral infection, but also for reversal of EBV-driven cell proliferation. It is also possible that targeting multiple latent viral genes might mount a synergistic effect that would prove to be more efficient at curing latent infection. However, further work is needed to identify the reasons for the variable results that are observed as well as to prove specificity of the inhibitory effects. Finally, we are also working on other assays and methods to screen compounds rapidly.
<title>Analog electro-optic modulators for ferroelectric-liquid-crystal/VLSI spatial light modulators</title> (1993)

We report here on analog modulation effects in ferroelectric liquid crystal (FLC) materials and electrical drive schemes that are appropriate to FLC/VLSI spatial light modulations (SLMs). The deformable-helix ferroelectric (DHF) effect paired with fixed-charge drive can give sub- millisecond grey-scale response with VLSI-compatible drive voltages. New DHF materials with long-pitch nematic phases give superior alignment quality and contrast ratio. We present analog FLC driver circuits suitable for VLSI implementation, and show that providing adequate read/write isolation in optically addressed FLC/VLSI SLMs requires special care.
A novel LDPC decoder for DVB-S2 IP (2009)

In this paper a programmable Forward Error Correction (FEC) IP for a DVB-S2 receiver is presented. It is composed of a Low-Density Parity Check (LDPC), a Bose-Chaudhuri-Hoquenghem (BCH) decoder, and pre- and postprocessing units. Special emphasis is put on LDPC decoding, since it accounts for the most complexity of the IP core by far. We propose a highly efficient LDPC decoder which applies Gauss-Seidel decoding. In contrast to previous publications, we show in detail how to solve the well known problem of superpositions of permutation matrices. The enhanced convergence speed of Gauss-Seidel decoding is used to reduce area and power consumption. Furthermore, we propose a modified version of the lambda-Min algorithm which allows to further decrease the memory requirements of the decoder by compressing the extrinsic information. Compared to the latest published DVB-S2 LDPC decoders, we could reduce the clock frequency by 40% and the memory consumption by 16%, yielding large energy and area savings while offering the same throughput.
Successful immunotherapy of natural killer-resistant established pulmonary melanoma metastases by the intravenous adoptive transfer of syngeneic lymphocytes activated in vitro by interleukin 2. (1984)

In previous in vitro studies, we have shown that murine splenocytes or cancer patient lymphocytes incubated in IL-2 become lytic for fresh syngeneic or autologous tumors. We have now performed the adoptive transfer of such lymphokine-activated killer (LAK) cells in a murine B16 metastasis model to test their in vivo efficacy. 1 X 10(8) LAK cells, infused intravenously into C57BL/6 mice with established B16 pulmonary metastases, led to a marked decreased in the number of lung nodules and improved survival. LAK cells administered 3 d after amputation of a tumor-bearing limb also decreased the incidence of spontaneous pulmonary metastases. LAK cells generated from tumor-bearer splenocytes had effects equivalent to those from normal animals, and this antimetastatic effect of the LAK cells did not require the prior administration of cyclophosphamide or other immunosuppressants. Fresh or unstimulated splenocytes had no effect. The antitumor effectors and precursors in vivo and in vitro were Thy-1+. The lymphokine required for the activation appeared to be interleukin 2 (IL-2), since incubation in partially purified supernatants from PMA pulsed EL-4 or Con A-pulsed splenocytes or purified Jurkat IL-2 led to the generation of LAK cells equally active in vivo. The use of IL-2-activated cells may provide a valuable method for the adoptive therapy of human neoplasms as well.
Enhanced assessment of limb neuro-mechanics via a haptic display (2014)

Current state-of-the-art quantitative assessments of abnormal neuro-mechanics (e.g., spasticity, rigidity, dystonia) require sophisticated measurement systems that, together with the lengthiness of the data acquisition, make these approaches impractical for the clinical setting. Our long-term goal is to create a tool that enhances the capability of therapists to diagnose abnormal neuro-mechanics without the need of lengthy procedures and sophisticated equipment. Towards this direction, we present a haptic display of abnormal limb neuro-mechanics. This haptic display can be used as a training device for clinicians to understand the causality of the haptic sensation associated with neurological impairments and abnormal biomechanics during manipulation of a patients' limb. Other uses include the testing of operational research algorithms to maximize the exchange of haptic information, reproducing conditions of human-human interaction, and a test bed for developing novel assessment techniques and targeted interventions. Experimental results support the hypothesis that the best assessment of abnormalities can be obtained via specific manipulation strategies.
Semaphorin-1a Acts in Concert With the Cell Adhesion Molecules Fasciclin II and Connectin to Regulate Axon Fasciculation in Drosophila (2000)

Semaphorins comprise a large family of phylogenetically conserved secreted and transmembrane glycoproteins, many of which have been implicated in repulsive axon guidance events. The transmembrane semaphorin Sema-1a in Drosophila is expressed on motor axons and is required for the generation of neuromuscular connectivity. Sema-1a can function as an axonal repellent and mediates motor axon defasciculation. Here, by manipulating the levels of Sema-1a and the cell adhesion molecules fasciclin II (Fas II) and connectin (Conn) on motor axons, we provide further evidence that Sema-1a mediates axonal defasciculation events by acting as an axonally localized repellent and that correct motor axon guidance results from a balance between attractive and repulsive guidance cues expressed on motor neurons.
Local thermal conductivity in chemical-vapor-deposited diamond (1994)

The thermal conductivity has been measured in the temperature range 5–400 K for a series of chemical-vapor-deposited diamond samples differing only in thickness. By analyzing the conductance, a local conductivity is extracted as a function of height z above the substrate on which the samples were grown. An analysis of the temperature dependence of the conductivity at any given height yields the phonon scattering mechanisms as a function of z. Point defects and extended defects of approximately 1.5 nm diam appear to be the most important phonon scattering entities at room temperature, but their scattering strengths decrease with height above the substrate. At a height z≊300 μm, the material is sufficiently perfect that scattering from extended defects at room temperature is negligible and scattering from point defects is only slightly higher than that attributable to naturally occurring 13C. The observed anisotropy of the thermal conductivity is consistent with aggregation of point defects and extended defects at or near grain boundaries. The z dependence of the scattering from these defects suggests that the quality of the grain boundaries increases with z. For z≳300 μm, the conductivity is equal to that of single crystals of gem-quality type IIa diamond.
Feasibility of quantifying SDC2 methylation in stool DNA for early detection of colorectal cancer (2017)

Taken together, our result indicates that stool DNA-based <i>SDC2</i> methylation test by LTE-qMSP is a potential noninvasive diagnostic tool for early detection of CRC.
Interferometric polarization control (2006)

We develop the Jones and Mueller matrices for structures that allow control of the path length difference between two linear orthogonal polarizations and consider the effect of placing multiple devices in series. Specifically, we find that full polarization modulation (measurement of Stokes Q, U, and V) can be achieved by placing two such modulators in series if the relative angles of the beam-splitting grids with respect to the analyzer orientation are appropriately chosen. Such a device has several potential advantages over a spinning wave plate modulator for measuring astronomical polarization in the far infrared through millimeter: (i) The use of small, linear motions eliminates the need for cryogenic rotational bearings; (ii) the phase flexibility allows measurement of circular as well as linear polarization; and (iii) this architecture allows for both multiwavelength and broadband modulation. We also present initial laboratory results.
Refactoring Java programs for flexible locking (2011)

Recent versions of the Java standard library offer flexible locking constructs that go beyond the language's built-in monitor locks in terms of features, and that can be fine-tuned to suit specific application scenarios. Under certain conditions, the use of these constructs can improve performance significantly, by reducing lock contention. However, the code transformations needed to convert between locking constructs are non-trivial, and great care must be taken to update lock usage throughout the program consistently. We present Relocker, an automated tool that assists programmers with refactoring synchronized blocks into ReentrantLocks and ReadWriteLocks, to make exploring the performance tradeoffs among these constructs easier. In experiments on a collection of real-world Java applications, Relocker was able to refactor over 80% of built-in monitors into ReentrantLocks. Additionally, in most cases the tool could automatically infer the same ReadWriteLock usage that programmers had previously introduced manually.
Abstract 1362: Discovery of a novel structural class of compounds: HLM-030376 and its analogs as potent chymotrypsin-like proteasome inhibitors (2011)

Abstract The ubiquitin-proteasome pathway plays a critical role in the regulated degradation of proteins involved in cell cycle control and tumor growth. Proteasome inhibitors cause selective apoptosis of malignant cells and represent a new class of antineoplastic agents. In 2003 Bortezomib (peptide boronate), a proteasome inhibitor was approved by FDA for treatment of multiple myeloma. Toxicity and tumor cell resistance against Bortezomib demand development of less toxic proteasome inhibitors with broader spectrum of tumor activity. Our aim is to develop non-peptidic small drug-like molecules as proteasome inhibitors. To this end, we have identified through in-house screening efforts HLM-030376 as a small molecule proteasome inhibitor with phenanthridine pharmacophore. HLM-030376 showed in-vitro chymotrypsin like, trypsin like and PGPH inhibitory activities with IC50 values 0.26, 0.19 and 2.07 µM respectively. Extensive synthetic modifications around the HLM-030376 pharmacophore were undertaken to aid the cell activity of this class of compounds. We will describe the synthesis and activity of analogs of HLM-030376 as potent proteasome inhibitors. The analogs of HLM-030376 showed in-vivo CT-L inhibitory activities (IC50 between 0.6-6.0 µM) against MDA-MB 468 breast cancer cell line as well as improved (IC50 between 70-200 nM) in-vitro CT-L inhibitory activities. The detailed in-vitro structure activity relationship (SAR) data of HLM-030376 and analogs will be discussed to understand the structural moieties responsible for proteasome activity. The whole cell activity data of HLM-030376 as well as in-silico docking studies will be presented as potential proteasome inhibitors for further development. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 1362. doi:10.1158/1538-7445.AM2011-1362
Employing efficient techniques based on 2D DMWT/FastICA for supervised facial recognition (2016)

A supervised facial recognition system is proposed in this paper. There are three main phases in the proposed system, namely, Preprocessing, Feature Extraction, and Classification. Cropping, choosing appropriate dimensions, and prefiltering are performed in the first phase. In the feature extraction phase, Two Dimensional Discrete Multiwavelet Transform (2D DMWT) is applied to the facial images to compact the data and extract useful information. Then, Two Dimensional Fast Independent Component Analysis (2D FastICA) is applied to the extracted features to obtain efficient features with enhanced discriminating and independent properties. Finally, the efficient features are compressed in one single column by applying ℓ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> -Norm. Then, the computed ℓ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> -Norm features are fed into a Neural Network (NN) classifier, which employs Back Propagation Training Algorithm (BPTA) for the recognition task. The proposed techniques are evaluated using four different databases, namely, ORL, YALE, FERET, and FEI that have different facial expressions, light conditions, rotations, etc. The results of the proposed system are analyzed by using K-fold Cross Validation (CV). The experimental results of the proposed techniques are shown to improve the recognition rates, computational complexity, as well as the storage requirements compared to the some of the existing approaches.
Surface‐Mediated Release of a Small‐Molecule Modulator of Bacterial Biofilm Formation: A Non‐Bactericidal Approach to Inhibiting Biofilm Formation in <i>Pseudomonas aeruginosa</i> (2013)

We report an approach to preventing bacterial biofilm formation that is based on the surface-mediated release of 5,6-dimethyl-2-aminobenzimidazole (DMABI), a potent and non-bactericidal small-molecule inhibitor of bacterial biofilm growth. Our results demonstrate that DMABI can be encapsulated in thin films of a model biocompatible polymer [poly(lactide-co-glycolide), PLG] and be released in quantities that inhibit the formation of Pseudomonas aeruginosa biofilms by up to 75-90% on surfaces that otherwise support robust biofilm growth. This approach enables the release of this new anti-biofilm agent for over one month, and it can be used to inhibit biofilm growth on both film-coated surfaces and other adjacent surfaces (e.g., on other uncoated surfaces and at air/water interfaces). Our results demonstrate a non-bactericidal approach to the prevention of biofilm growth and provide proof of concept using a clinically relevant human pathogen. In contrast to coatings designed to kill bacteria on contact, this approach should also permit the design of strategically placed depots that disseminate DMABI more broadly and exert inhibitory effects over larger areas. In a broader context, the non-bactericidal nature of DMABI could also provide opportunities to address concerns related to evolved resistance that currently face approaches based on the release of traditional microbicidal agents (e.g., antibiotics). Finally, the results of initial in vitro mammalian cell culture studies indicate that DMABI is not toxic to cells at concentrations required for strong anti-biofilm activity, suggesting that this new agent is well suited for further investigation in biomedical and personal care contexts.
Contact Physics of Capacitive Interconnects (2007)

The resistance and capacitance of a typical multi-point contact interface has been used to assess the impact on high frequency signal integrity. In the past it was shown how fully degraded interfaces can still provide acceptable performance for high data rate signal transfers. In the case of fully degraded contacts, signals were shown to transfer by capacitive coupling and wave propagation. This paper focuses on the critical parameters of a capacitive coupled interface. Moreover, the physics of the contact interface is related to contacts that rely on capacitive (as opposed to metallic) coupling and electronic tunneling. These results help define the physics and design requirements for capacitive coupling. In addition, critical performance parameters such as real contact area, film thickness and the nature of dielectric films are defined for high frequency signal propagation. This paper provides a contrast between the requirements for high frequency signal transfer using capacitive coupling and electron tunneling versus traditional metallic contact.
MICROMACHINED POLYCRYSTALLINE SIGE-BASED THERMOPILES FOR MICROPOWER GENERATION ON HUMAN BODY (2008)

This paper presents a polycrystalline silicon germanium (poly-SiGe) thermopile specially designed for thermoelectric generators used on human body. Both the design of the single thermocouple and the arrangement of the thermocouple array have been described. A rim structure has been introduced in order to increase the temperature difference across the thermocouple junctions. The modeling of the thermocouple and the thermopile has been performed analytically and numerically. An output power of about 1 μW at an output voltage of more than 1 V is expected from the current design of thermopiles in a watch-size generator. The key material properties of the poly-SiGe have been measured. The thermopile has been fabricated and tested. Experimental results clearly demonstrate the advantage of the rim structure in increasing output voltage. In presence of forced convection, the output voltage of a non-released thermopile can increase from about 53 mV/K/cm 2 to about 130 mV/K/cm 2 after the rim structure is formed. A larger output voltage from the thermopile is expected upon process completion. 1.
Novel Upf2p Orthologues Suggest a Functional Link between Translation Initiation and Nonsense Surveillance Complexes (2000)

Transcripts harboring premature signals for translation termination are recognized and rapidly degraded by eukaryotic cells through a pathway known as nonsense-mediated mRNA decay (NMD). In addition to protecting cells by preventing the translation of potentially deleterious truncated peptides, studies have suggested that NMD plays a broader role in the regulation of the steady-state levels of physiologic transcripts. In Saccharomyces cerevisiae, three trans-acting factors (Upf1p to Upf3p) are required for NMD. Orthologues of Upf1p have been identified in numerous species, showing that the NMD machinery, at least in part, is conserved through evolution. In this study, we demonstrate additional functional conservation of the NMD pathway through the identification of Upf2p homologues in Schizosaccharomyces pombe and humans (rent2). Disruption of S. pombe UPF2 established that this gene is required for NMD in fission yeast. rent2 was demonstrated to interact directly with rent1, a known trans-effector of NMD in mammalian cells. Additionally, fragments of rent2 were shown to possess nuclear targeting activity, although the native protein localizes to the cytoplasmic compartment. Finally, novel functional domains of Upf2p and rent2 with homology to eukaryotic initiation factor 4G (eIF4G) and other translational regulatory proteins were identified. Directed mutations within these so-called eIF4G homology (4GH) domains were sufficient to abolish the function of S. pombe Upf2p. Furthermore, using the two-hybrid system, we obtained evidence for direct interaction between rent2 and human eIF4AI and Sui1, both components of the translation initiation complex. Based on these findings, a novel model in which Upf2p and rent2 effects decreased translation and accelerated decay of nonsense transcripts through competitive interactions with eIF4G-binding partners is proposed.
Construction of rubella virus genome-length cDNA clones and synthesis of infectious RNA transcripts (1994)

Plasmids containing a complete cDNA copy of the rubella virus (RUB) genomic RNA were constructed. Transfection into cell culture of genome-length RNA transcribed in vitro from one of these cDNA clones, Robo102, resulted in the production of virus which preserved the genetic and phenotypic characteristics of the parental virus from which the cDNA clone was derived. Prior to construction of the RUB genome-length cDNA clones, the 5'-terminal sequence of the RUB genomic RNA was determined to be 5'CAAUGG...3' following the cap structure. Analysis of the specific infectivity of RUB genomic RNA isolated from virions revealed that in Vero cells, the specific infectivity of RUB genomic RNA is roughly equivalent to that of Sindbis virus genomic RNA. In RUB virion RNA preparations, the subgenomic RNA was detected. It was demonstrated that subgenomic RNA was packaged into RUB virions; however, the presence of the subgenomic RNA was not essential for infectivity of the genomic RNA.
Information transfer in stochastic optimal control with randomized strategies and directed information criterion (2016)

We show that stochastic dynamical control systems are capable of information transfer from control processes to output processes, with operational meaning as defined by Shannon. Moreover, we show that optimal control strategies have a dual role, specifically, (i) to transfer information from the control process to the output process, and (ii) to stabilize the output process. We illustrate that information transfer is feasible by considering general Gaussian Linear Decision Models, and relate it to the well-known Linear-Quadratic-Gaussian (LQG) control theory.
Using Phase Retrieval to Determine the Intensity and Phase of an Ultrashort Laser Pulse (1992)

We have solved the long-standing problem of measuring the full electric field, E(t), of a single ultrashort laser pulse by reducing it to a two-dimensional phase-retrieval problem.
<title>Digital measurement of gene expression in a cDNA microarray</title> (1997)

Gene expression can be quantitatively analyzed by hybridizing fluor-tagged mRNA to targets on a cDNA micro- array. Comparison of expression levels arising from co- hybridized samples is achieved by taking ratios of average expression levels for individual genes. The present paper concerns image processing to automatically segment digitized micro-arrays and measure median gene expression levees across cDNA target sites. The main difficulty arises from determination of the target site when signal intensity is low. Segmentation must be accomplished for target sites that can possess highly unstable geometry and consist of a relatively small number of pixels. Segmentation must also be computationally efficient. The present paper proposes a nonparametric statistical method that separates target site from local background using the Mann-Whitney test.