gebhart/patrepeval huggingface dataset:
<i>In Vitro</i> Anti-Plasmodium falciparum Properties of the Full Set of Human Secreted Phospholipases A <sub>2</sub> (2015)

We have previously shown that secreted phospholipases A2 (sPLA2s) from animal venoms inhibit the in vitro development of Plasmodium falciparum, the agent of malaria. In addition, the inflammatory-type human group IIA (hGIIA) sPLA2 circulates at high levels in the serum of malaria patients. However, the role of the different human sPLA2s in host defense against P. falciparum has not been investigated. We show here that 4 out of 10 human sPLA2s, namely, hGX, hGIIF, hGIII, and hGV, exhibit potent in vitro anti-Plasmodium properties with half-maximal inhibitory concentrations (IC50s) of 2.9 ± 2.4, 10.7 ± 2.1, 16.5 ± 9.7, and 94.2 ± 41.9 nM, respectively. Other human sPLA2s, including hGIIA, are inactive. The inhibition is dependent on sPLA2 catalytic activity and primarily due to hydrolysis of plasma lipoproteins from the parasite culture. Accordingly, purified lipoproteins that have been prehydrolyzed by hGX, hGIIF, hGIII, and hGV are more toxic to P. falciparum than native lipoproteins. However, the total enzymatic activities of human sPLA2s on purified lipoproteins or plasma did not reflect their inhibitory activities on P. falciparum. For instance, hGIIF is 9-fold more toxic than hGV but releases a lower quantity of nonesterified fatty acids (NEFAs). Lipidomic analyses of released NEFAs from lipoproteins demonstrate that sPLA2s with anti-Plasmodium properties are those that release polyunsaturated fatty acids (PUFAs), with hGIIF being the most selective enzyme. NEFAs purified from lipoproteins hydrolyzed by hGIIF were more potent at inhibiting P. falciparum than those from hGV, and PUFA-enriched liposomes hydrolyzed by sPLA2s were highly toxic, demonstrating the critical role of PUFAs. The selectivity of sPLA2s toward low- and high-density (LDL and HDL, respectively) lipoproteins and their ability to directly attack parasitized erythrocytes further explain their anti-Plasmodium activity. Together, our findings indicate that 4 human sPLA2s are active against P. falciparum in vitro and pave the way to future investigations on their in vivo contribution in malaria pathophysiology.
A Benchmark Study Of Backdoor Data Poisoning Defenses For Deep Neural Network Classifiers And A Novel Defense (2019)

While data poisoning attacks on classifiers were originally proposed to degrade a classifier's usability, there has been strong recent interest in backdoor data poisoning attacks, where the classifier learns to classify to a target class whenever a backdoor pattern (e.g., a watermark or innocuous pattern) is added to an example from some class other than the target class. In this paper, we conduct a benchmark experimental study to assess the effectiveness of backdoor attacks against deep neural network (DNN) classifiers for images (CIFAR-10 domain), as well as of anomaly detection defenses against these attacks, assuming the defender has access to the (poisoned) training set. We also propose a novel defense scheme (cluster impurity (CI)) based on two ideas: i) backdoor patterns may cluster in a DNN's (e.g. penultimate) deep layer latent space; ii) image filtering (or additive noise) may remove the backdoor patterns, and thus alter the class decision produced by the DNN. We demonstrate that largely imperceptible single-pixel backdoor attacks are highly successful, with no effect on classifier usability. However, the CI approach is highly effective at detecting these attacks, and more successful than previous backdoor detection methods.
Toward the Synthesis of Noroxymorphone via Aerobic Palladium-Catalyzed Continuous Flow <i>N</i>-Demethylation Strategies (2016)

The palladium-catalyzed N-demethylation of the opioid alkaloids oxymorphone 3,14-diacetate and 14-hydroxymorphinone 3,14-diacetate to their nor-derivatives with oxygen as the terminal oxidant has been investigated. Palladium(II) acetate forms colloidal palladium(0) particles upon heating in N,N-dimethylacetamide. The palladium(0) particles are effective catalysts for the aerobic N-demethylation of these opiate alkaloids. Demethylation of 14-hydroxymorphinone 3,14-diacetate with pure oxygen as oxidant in a continuous flow reactor provided the demethylated product with excellent selectivity after residence times of only 10–20 min with 2.5–5 mol % palladium acetate as catalyst on a laboratory scale. Scale-up of the oxidation in a 100 mL flow reactor (combination of FlowPlate A6 and coiled tube to enhance the gas–liquid mass transfer), hydrogenation in a packed bed reactor, and subsequent hydrolysis afforded the desired noroxymorphone in high quality and good yield on a kg scale. The reaction sequence consumes only oxygen, hydrogen, and water as stoichiometric reagents.
Preclinical Development of a Fusion Peptide Conjugate as an HIV Vaccine Immunogen (2020)

The vaccine elicitation of broadly neutralizing antibodies against HIV-1 is a long-sought goal. We previously reported the amino-terminal eight residues of the HIV-1-fusion peptide (FP8) - when conjugated to the carrier protein, keyhole limpet hemocyanin (KLH) - to be capable of inducing broadly neutralizing responses against HIV-1 in animal models. However, KLH is a multi-subunit particle derived from a natural source, and its manufacture as a clinical product remains a challenge. Here we report the preclinical development of recombinant tetanus toxoid heavy chain fragment (rTTHC) linked to FP8 (FP8-rTTHC) as a suitable FP-conjugate vaccine immunogen. We assessed 16 conjugates, made by coupling the 4 most prevalent FP8 sequences with 4 carrier proteins: the aforementioned KLH and rTTHC; the H. influenzae protein D (HiD); and the cross-reactive material from diphtheria toxin (CRM197). While each of the 16 FP8-carrier conjugates could elicit HIV-1-neutralizing responses, rTTHC conjugates induced higher FP-directed responses overall. A Sulfo-SIAB linker yielded superior results over an SM(PEG)2 linker but combinations of carriers, conjugation ratio of peptide to carrier, or choice of adjuvant (Adjuplex or Alum) did not significantly impact elicited FP-directed neutralizing responses in mice. Overall, SIAB-linked FP8-rTTHC appears to be a promising vaccine candidate for advancing to clinical assessment.
Wireless network coding in multi-cell networks: Analysis and performance (2008)

Network coding has recently attracted a lot of interest from the research community, mainly due to its simplicity of application and the large number of applications it can be suited for. Research in network coding started on wired networks, but the researchers soon came to realize that the inherent properties of the wireless medium render it a fertile ground for the application of network coding, and the resulting efforts mainly targeted bidirectional traffic scenarios. In this work, we focus on practical implementation issues for network coding when applied to uplink cellular traffic. We provide our own relaying scheme based on decode-and-forward relays and network coding, with a specially designed method of decoding at the receiver. We complement this method with user grouping in order to make better use of the application of network coding. We measure the SINR and capacity performances of our proposed scheme and compare them to the classical decode-and-forward algorithm in a system level simulator. We show that user grouping should complement a network coding solution in order to translate the decrease in the number of transmissions offered by network coding into capacity gains.
Utility of Adenovirus-Based Vectors for Multiple Cancer Vaccine Approaches (2004)

The fact that adenovirus (Ad) vectors have been utilized in over 164 clinical trials to date (at least 644 subjects) substantiates the claim that these vectors are potentially useful in a variety of gene transfer strategies (1). Ad vectors are constructed in a manner such that one can insert desired recombinant DNA sequences into the El region of the wildtype Ad genome (Fig. 1). Since the El genes only encompass a small fraction of the Ad genome, approx 90% of the wildtype Ad genome is retained in the resultant [E1-]Ad vector. For a complete review of the numerous methods to genetically engineer a firstgeneration, or [E1-]Ad-based vector, see Imperiale et al. (2). The recombinant [E1-]Ad vector genomes are introduced into human cells that express the El proteins in trans, allowing for helper virus independent [E1-]Ad vector replication and packaging, and high-level production (3).
Femtosecond IR Laser Inscription of Bragg Gratings in Photonic Crystal Fibre Tapers (2006)

Fibre Bragg gratings were written in pure silica photonic crystal fibre tapers with 125 fs, 800 nm IR radiation. High reflectivity single and multimode responses were achieved with short exposure times.
Colorimetry-based retardation measurement method with white-light interference (2002)

A colorimetry-based retardation measurement (CBRM) method is presented. The specimen, between crossed polarizers, is illuminated with a white-light source. The retardation that is due to the birefringence of the specimen produces a white-light interference color. The x, y chromaticity coordinates of the color produced are measured with a spectrophotometer. The resulting x, y values are compared with a retardation x, y database that we obtained by measuring the retardation with an accurate Senarmont compensator and the x, y chromaticity values along the length of a 0-4-order quartz wedge. The technique was validated by the measurement of a variety of retardation plates. The retardation accuracy (mean error) of the CBRM method is shown to be 3.6 nm. The resolution is +/-0.2 nm, and the measurement range is 5-2150 nm. The method substitutes for a polariscope and eliminates errors associated with quarter-wave plates. The CBRM method does not utilize any moving parts and thus is fast and can be automated.
Proton computed tomography reconstruction using a backprojection-then-filtering approach (2014)

A novel approach to proton CT reconstruction using backprojection-then-filtering (BPF) is proposed. A list-mode algorithm is formulated accommodating non-linear proton paths. The analytical form is derived for the deblurring kernel necessary for the filtering step. Further, a finite matrix correction is derived to correct for the limited size of the backprojection matrix. High quantitative accuracy in relative stopping power is demonstrated (⩽0.1%) using Monte Carlo simulations. This accuracy makes the algorithm a promising candidate for future proton CT systems in proton therapy applications. For the purposes of reconstruction, each proton path in the object-of-interest was estimated based on a cubic spline fit to the proton entry and exit vectors. The superior spatial-resolution of the BPF method over the standard filtering-then-backprojection approach is demonstrated. As the BPF algorithm requires only one backprojection and filtering operation on a scan data set, it also offers computational advantages over an iterative reconstruction approach.
Cloning and Characterization of Ancylostoma-secreted Protein (1996)

The developmentally arrested third stage infective larva of hookworms resumes development upon entry into the definitive host. This transition to parasitism can be modeled in vitro by stimulating infective larvae with a low molecular weight ultrafiltrate of host serum together with methylated glutathione analogues. When stimulated to resume development in vitro, activated larvae of the hookworm Ancylostoma caninum released a 42-kDa protein, termed Ancylostoma-secreted protein (ASP). ASP was the major protein released by activated hookworm larvae. Degenerate oligonucleotide primers, based on a partial internal amino acid sequence of the protein, were used together with flanking vector sequence primers to amplify a fragment from a third stage larval cDNA library by polymerase chain reaction. The fragment was used as a probe to isolate a longer clone from the larval cDNA library. The full-length ASP cDNA was found to encode a 424-amino acid protein with homology to the antigen 5/antigen 3 family of proteins from hymenopteran venoms and a family of cysteine-rich secretory proteins. ASP was expressed in bacterial cells, and a polyclonal antiserum against purified recombinant ASP was produced. The antiserum, which was demonstrated to be specific for ASP, was used as a probe to measure the kinetics of ASP release by hookworm larvae. ASP is released within 30 min of stimulation, with the majority released by 4 h. Low levels of ASP were released continuously following activation, but only if the stimuli were present in the incubation medium. The compound 4,7-phenanthroline, previously shown to inhibit larval activation, also inhibited release of ASP. The specific, rapid release of ASP by activated infective larvae suggests that this molecule occupies a critical and central role in the transition from the external environment to parasitism.
Rapidly switchable optical filter for color generation (1991)

A ferroelectric liquid-crystal (FLC) color filter is described and experimentally demonstrated. The device consists of three polarizers and five smectic C* FLC cells. With the application of an appropriate electric field to each FLC cell, five outputs are observed. These consist of the three primary colors (red, green, and blue) along with white and black. With the rapid addressing speed of the FLC's, the FLC color filter can be used for color display applications, such as backlighting FLC television.
Activation of Tumor Antigen-Specific Cytotoxic T Lymphocytes (CTLs) by Human Dendritic Cells Infected with an Attenuated Influenza A Virus Expressing a CTL Epitope Derived from the HER-2/neu Proto-Oncogene (2003)

The development of cancer vaccines requires approaches to induce expansion and functional differentiation of tumor antigen-specific cytotoxic T lymphocyte (CTL) effectors which posses cytolytic capability and produce cytokines. Efficient induction of such cells is hindered by the poor immunogenicity of tumor antigens and by the poor transduction efficiency of dendritic cells (DCs) with current nonreplicating vectors. We have investigated the use of influenza A virus, a potent viral inducer of CTLs, as a vector expressing the immunodominant HER-2 CTL epitope KIF (E75). For this purpose, an attenuated influenza A/PR8/34 virus with a truncated nonstructural (NS1) gene was generated containing the E75 epitope in its neuraminidase protein (KIF-NS virus). Stimulation of peripheral blood mononuclear cells from healthy donors and of tumor-associated lymphocytes from ovarian and breast cancer patients with DCs infected with KIF-NS virus (KIF-NS DC) induced CTLs that specifically recognized the peptide KIF and HER-2-expressing tumors in cytotoxicity assays and secreted gamma interferon (IFN-gamma) and interleukin-2 at recall with peptide. Priming with KIF-NS DCs increased the number of E75(+) CD45RO(+) cells by more than 10-fold compared to nonstimulated cells. In addition, KIF-NS virus induced high levels of IFN-alpha in DCs. This is the first report demonstrating induction of human epitope-specific CTLs against a tumor-associated antigen with a live attenuated recombinant influenza virus vector. Such vectors may provide a novel approach for tumor antigen delivery, lymphocyte activation, and differentiation in human cancer vaccine development.
Heparanase: One Molecule with Multiple Functions in Cancer Progression (2008)

Mammalian heparanase, an endoglycosidase-degrading heparan sulfate, is synthesized as a latent 65 kDa precursor that undergoes proteolytic processing, primarily by cathepsin-L, yielding 8 kDa and 50 kDa subunits that heterodimerize to form a highly active enzyme. Enhanced heparanase expression in human tumors correlates with metastatic potential, tumor vascularity, and reduced postoperative survival of cancer patients, attributed to enzymatic and nonenzymatic activities of the heparanase protein. Urinary and plasma levels of heparanase are elevated in cancer patients and suppressed in response to effective anticancer treatments. These observations and the anticancerous effect of heparanase gene silencing and of heparanase-inhibiting molecules suggest that the enzyme is a promising target for anticancer drug development.
Intra‐articular gene delivery and expression of interleukin‐1Ra mediated by self‐complementary adeno‐associated virus (2009)

scAAV-mediated intra-articular gene transfer is robust and similarly efficient in both normal and inflamed joints; the resulting transgenic expression is sufficient to achieve biological relevance in joints of human proportion.
Recording characteristics of a magneto-optical super-resolution disk. (1994)

ABSTRACT To reduce recording magnetic field of a magneto-optical super-resolution disk which uses an in-plane magnetization readout layer, we developed a new disk structure. By preparing a DyFeCo intermediate layer between the readout layer andthe recording layer, the recording magnetic field was greatly reduced and then both super-resolution readout and mark-edge recording by a magnetic field modulation method were achieved. By using the new triple-layered disk for super-resolution readout, a carrier to noise ratio of 45dB at a 0.4 a m mark length was obtained and the recording magnetic field became 1 5kA/m. 1 . INTRODUCTION In magneto-optical (MO) disks, higher recording density is needed for makingcompact MO driver and handling digitized data of moving pictures. To meet the demand, three types of a magnetically induced super-resolution (MSR) readout method, FAD (front aperture detection), RAD (rear aperture detection)1 and CAD (center aperture detection)2 , were already proposed. Comparing with the FAD method and theRAD method, the CAD method has an advantage that does not need external magneticfield for readout.
Expansion microscopy: enabling single cell analysis in intact biological systems (2019)

There is a need for single cell analysis methods that enable the identification and localization of different kinds of biomolecules throughout cells and intact tissues, thereby allowing characterization and classification of individual cells and their relationships to each other within intact systems. Expansion microscopy (ExM) is a technology that physically magnifies tissues in an isotropic way, thereby achieving super-resolution microscopy on diffraction-limited microscopes, enabling rapid image acquisition and large field of view. As a result, ExM is well-positioned to integrate molecular content and cellular morphology, with the spatial precision sufficient to resolve individual biological building blocks, and the scale and accessibility required to deploy over extended 3-D objects like tissues and organs.
Laser and spectroscopic properties of Yb-doped apatite crystals (1993)

Favorable spectroscopic and laser properties have been measured in several Yb-doped crystals with the apatite structure.
ChemInform Abstract: New Functionalized Imidazolium‐Based Room‐Temperature Ionic Liquids and Composite Materials for Gas Separation and Selective Transport Applications (2012)

Abstract Review: 39 refs.
C-Lysine Conjugates: pH-Controlled Light-Activated Reagents for Efficient Double-Stranded DNA Cleavage with Implications for Cancer Therapy (2009)

Double-stranded DNA cleavage of light-activated lysine conjugates is strongly enhanced at the slightly acidic pH (<7) suitable for selective targeting of cancer cells. This enhancement stems from the presence of two amino groups of different basicities. The first amino group plays an auxiliary role by enhancing solubility and affinity to DNA, whereas the second amino group, which is positioned next to the light-activated DNA cleaver, undergoes protonation at the desired pH threshold. This protonation results in two synergetic effects which account for the increased DNA-cleaving ability at the lower pH. First, lysine conjugates show tighter binding to DNA at the lower pH, which is consistent with the anticipated higher degree of interaction between two positively charged ammonium groups with the negatively charged phosphate backbone of DNA. Second, the unproductive pathway which quenches the excited state of the photocleaver through intramolecular electron transfer is eliminated once the donor amino group next to the chromophore is protonated. Experiments in the presence of traps for diffusing radicals show that reactive oxygen species do not contribute significantly to the mechanism of DNA cleavage at the lower pH, which is indicative of tighter binding to DNA under these conditions. This feature is valuable not only because many solid tumors are hypoxic but also because cleavage which does not depend on diffusing species is more localized and efficient. Sequence-selectivity experiments suggest combination of PET and base alkylation as the chemical basis for the observed DNA damage. The utility of these molecules for phototherapy of cancer is confirmed by the drastic increase in toxicity of five conjugates against cancer cell lines upon photoactivation.
The camera offset space (2019)

Potential visibility has historically always been of importance when rendering performance was insufficient. With the rise of virtual reality, rendering power may once again be insufficient, e.g., for integrated graphics of head-mounted displays. To tackle the issue of efficient potential visibility computations on modern graphics hardware, we introduce the camera offset space (COS). Opposite to how traditional visibility computations work---where one determines which pixels are covered by an object under all potential viewpoints---the COS describes under which camera movement a sample location is covered by a triangle. In this way, the COS opens up a new set of possibilities for visibility computations. By evaluating the pairwise relations of triangles in the COS, we show how to efficiently determine occluded triangles. Constructing the COS for all pixels of a rendered view leads to a complete potentially visible set (PVS) for complex scenes. By fusing triangles to larger occluders, including locations between pixel centers, and considering camera rotations, we describe an exact PVS algorithm that includes all viewing directions inside a view cell. Implementing the COS is a combination of real-time rendering and compute steps. We provide the first GPU PVS implementation that works without preprocessing, on-the-fly, on unconnected triangles. This opens the door to a new approach of rendering for virtual reality head-mounted displays and server-client settings for streaming 3D applications such as video games.
Amorphous silicon TFT circuit integration for OLED displays on glass and plastic (2003)

This paper reviews design considerations along with measurement results pertinent to amorphous silicon (a-Si:H) thin film transistor (TFT) drive circuits for active matrix organic light emitting diode (AMOLED) displays. We describe both pixel architectures and TFT circuit topologies that are amenable for vertically integrated, high aperture ratio pixels. Here, the OLED layer is integrated directly above the TFT circuit layer, to provide an active pixel area that is at least 90% of the total pixel area with an aperture ratio that remains virtually independent of scaling. Both voltage-programmed and current-programmed drive circuits are considered. The latter provides compensation for shifts in device characteristics due to metastable shifts in the threshold voltage of the TFT. Integration of on-panel gate drivers is also discussed where we present the architecture of an a-Si:H based gate de-multiplexer that is threshold voltage shift invariant. In addition, a programmable current mirror with good linearity and stability is presented. Programmable current sources are an essential requirement in the design of source driver output stages.