gebhart/patrepeval huggingface dataset:
Molecular and Functional Analysis of a Conserved CTL Epitope in HIV-1 p24 Recognized from a Long-Term Nonprogressor: Constraints on Immune Escape Associated with Targeting a Sequence Essential for Viral Replication (1999)

It has been hypothesized that sequence variation within CTL epitopes leading to immune escape plays a role in the progression of HIV-1 infection. Only very limited data exist that address the influence of biologic characteristics of CTL epitopes on the emergence of immune escape variants and the efficiency of suppression HIV-1 by CTL. In this report, we studied the effects of HIV-1 CTL epitope sequence variation on HIV-1 replication. The highly conserved HLA-B14-restricted CTL epitope DRFYKTLRAE in HIV-1 p24 was examined, which had been defined as the immunodominant CTL epitope in a long-term nonprogressing individual. We generated a set of viral mutants on an HX10 background differing by a single conservative or nonconservative amino acid substitution at each of the P1 to P9 amino acid residues of the epitope. All of the nonconservative amino acid substitutions abolished viral infectivity and only 5 of 10 conservative changes yielded replication-competent virus. Recognition of these epitope sequence variants by CTL was tested using synthetic peptides. All mutations that abrogated CTL recognition strongly impaired viral replication, and all replication-competent viral variants were recognized by CTL, although some variants with a lower efficiency. Our data indicate that this CTL epitope is located within a viral sequence essential for viral replication. Targeting CTL epitopes within functionally important regions of the HIV-1 genome could limit the chance of immune evasion.
Diagnosing combinational logic designs using the single location at-a-time (SLAT) paradigm (2002)

A new way of diagnosing ICs that fail logic tests is described. It can handle bridging fault, opens, transition faults and many more complex defects as easily and as accurately as regular stuck-at faults.
Iron Chelators: In Vitro Inhibitory Effect on the Liver Stage of Rodent and Human Malaria (1988)

The activity of desferrioxamine (Desferal) and desferrithiocin (a newly developed oral iron chelator) was evaluated against the liver stage of Plasmodium yoelii and P. falciparum in the rodent and the human hepatocyte in vitro culture system. The two iron chelators were found to inhibit the liver schizogony of both the rodent and the human Plasmodium species at concentrations achievable in vivo. P. falciparum proved to be more sensitive (ic 95% below 20 micromol/l than P. yoelii (ic 95% 50-100 micromol/l). As assessed by electron microscopy, drug administration was associated with focal clarification of the cytoplasm thought to be reversible. As desferrioxamine and desferrithiocin are known to be equally active on the blood stage of rodent and human plasmodia, iron chelators are deserving of further investigation as potential alternative candidates to existing drugs for radical cure of malaria.
Virtual Reality Exposure Therapy for World Trade Center Post-traumatic Stress Disorder: A Case Report (2002)

Done properly by experienced therapists, re-exposure to memories of traumatic events via imaginal exposure therapy can lead to a reduction of Post-traumatic Stress Disorder (PTSD) symptoms. Exposure helps the patient process and habituate to memories and strong emotions associated with the traumatic event: memories and emotions they have been carefully avoiding. But many patients are unwilling or unable to self-generate and re-experience painful emotional images. The present case study describes the treatment of a survivor of the World Trade Center (WTC) attack of 9-11-01 who had developed acute PTSD. After she failed to improve with traditional imaginal exposure therapy, we sought to increase emotional engagement and treatment success using virtual reality (VR) exposure therapy. Over the course of six 1-h VR exposure therapy sessions, we gradually and systematically exposed the PTSD patient to virtual planes flying over the World Trade Center, jets crashing into the World Trade Center with animated explosions and sound effects, virtual people jumping to their deaths from the burning buildings, towers collapsing, and dust clouds. VR graded exposure therapy was successful for reducing acute PTSD symptoms. Depression and PTSD symptoms as measured by the Beck Depression Inventory and the Clinician Administered PTSD Scale indicated a large (83%) reduction in depression, and large (90%) reduction in PTSD symptoms after completing VR exposure therapy. Although case reports are scientifically inconclusive by nature, these strong preliminary results suggest that VR exposure therapy is a promising new medium for treating acute PTSD. This study may be examined in more detail at www.vrpain.com.
Multicolor Quantum Dot Encoding for Polymeric Particle-Based Optical Ion Sensors (2007)

Multicolor quantum dot-encoded polymeric microspheres are prepared with controllable and uniform doping levels that function as chemical sensors on the basis of bulk optode theory. TOP/TOPO-capped CdSe quantum dots and CdTe quantum dots capped with CdS (lambdaem = 610 and 700 nm, lambdaex = 510 nm) are blended with a THF solution of poly(methyl methacrylate-co-decyl methacrylate), poly(n-butylacrylate), or poly(vinyl chloride) plasticized with bis(2-ethylhexyl) sebacate without a need for ligand exchange. Polymeric microspheres are generated under mild, nonreactive conditions with a particle caster that breaks down a polymer stream containing the quantum dots into fine droplets by the vibration of a piezocrystal. The resulting microspheres exhibit uniform size and fluorescence emission intensities. Fluorescent bar codes are obtained by subsequent doping of two quantum dots with different colors and mass ratios into the microspheres. A linear relationship is found between the readout fluorescence ratio of the two types of nanocrystals and the mixing ratio. Quantum dot-encoded ion sensing optode microspheres are prepared by simultaneous doping of sodium ionophore X, chromoionophore II, a lipophilic tetraphenylborate cation exchanger, and TOPO-capped CdSe/CdS quantum dot as the fluorescent label. A net positive charge of the quantum dots is found to induce an anion-exchange effect on the sensor function, and therefore, an increased concentration of the lipophilic cation exchanger is required to achieve proper ion sensing properties. The modified quantum dot-labeled sodium sensing microspheres show satisfactory sodium response between 10(-4) and 0.1 M at pH 4.8, with excellent selectivity toward common interferences. The amount of the carried positive charges of the CdSe quantum dots is estimated as 2.8 mumol/g of quantum dots used in this study.
On the Inertial-Electrostatic Confinement of a Plasma (1959)

A system in which electrons are projected radially inwards from a spherical surface, has been proposed for the confinement of a plasma at thermonuclear temperatures. The equilibrium, economics, and stability of such a system are discussed theoretically. Although we conclude that it is of doubtful utility as a thermonuclear reactor, it may be possible to produce in this way small regions of thermonuclear plasma for study. The device appears to be unstable at economic densities. The stability is discussed in terms of a virial, which turns out to be mathematically tractable in this geometry.
An Analog Neural Network Computing Engine Using CMOS-Compatible Charge-Trap-Transistor (CTT) (2018)

An analog neural network computing engine based on CMOS-compatible charge-trap transistor (CTT) is proposed in this paper. CTT devices are used as analog multipliers. Compared to digital multipliers, CTT-based analog multiplier shows significant area and power reduction. The proposed computing engine is composed of a scalable CTT multiplier array and energy efficient analog-digital interfaces. By implementing the sequential analog fabric, the engine's mixed-signal interfaces are simplified and hardware overhead remains constant regardless of the size of the array. A proof-of-concept 784 by 784 CTT computing engine is implemented using TSMC 28-nm CMOS technology and occupies 0.68 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> . The simulated performance achieves 76.8 TOPS (8-bit) with 500 MHz clock frequency and consumes 14.8 mW. As an example, we utilize this computing engine to address a classic pattern recognition problem-classifying handwritten digits on MNIST database and obtained a performance comparable to state-of-the-art fully connected neural networks using 8-bit fixed-point resolution.
A Novel Member of the Netrin Family, β-Netrin, Shares Homology with the β Chain of Laminin (2000)

The netrins are a family of laminin-related molecules. Here, we characterize a new member of the family, beta-netrin. beta-Netrin is homologous to the NH(2) terminus of laminin chain short arms; it contains a laminin-like domain VI and 3.5 laminin EGF repeats and a netrin C domain. Unlike other netrins, this new netrin is more related to the laminin beta chains, thus, its name beta-netrin. An initial analysis of the tissue distribution revealed that kidney, heart, ovary, retina, and the olfactory bulb were tissues of high expression. We have expressed the molecule in a eukaryotic cell expression system and made antibodies to the expressed product. Both in situ hybridization and immunohistochemistry were used to describe the cellular source of beta-netrin and where beta-netrin is deposited. beta-Netrin is a basement membrane component; it is present in the basement membranes of the vasculature, kidney, and ovaries. In addition, beta-netrin is expressed in a limited set of fiber tracts within the brain, including the lateral olfactory tract and the vomeronasal nerve. Functional studies were performed and show that beta-netrin promotes neurite elongation from olfactory bulb explants. Together, these data suggest that beta-netrin is important in neural, kidney, and vascular development.
Distamycin-A derivatives potentiate tumor-necrosis-factor activityvia the modulation of tyrosine phosphorylation (1997)

The cytotoxic activities of 2 novel distamycin-A derivatives, FCE 24517 and FCE 25450A, alone and in combination with tumor-necrosis factor-alpha (TNF), were studied. Both drugs, especially FCE 25450A, analyzed extensively here, inhibited the growth of HL60 promyelocytic cells, and human SV80 and murine L929 transformed fibroblasts in a dose-dependent manner. The growth-inhibitory potential of sequential exposure to the distamycin-A analogs and TNF was determined. A 4-hr treatment of L929 fibroblasts with 100-1,000 ng/ml FCE 25450A, followed by 2 ng/ml TNF, resulted in a synergistic anti-proliferative effect. The synergism of FCE 24517 with TNF was less profound. Experiments to elucidate the mechanism underlying the cooperation revealed that FCE 25450A pre-treatment almost completely abolished the elevated tyrosine phosphorylation of a 137-kDa and other membranal proteins and prevented the de-phosphorylation of another protein band observed in L929 cells in the presence of TNF. FCE 25450A alone induced no changes in the phosphotyrosine profile of the cells. The effect of FCE 25450A was counteracted by the tyrosine-phosphatase inhibitor orthovanadate. In parallel, the inhibitor also diminished the antiproliferative action of the FCE 25450A/TNF combination. These findings suggest that, beyond their cytotoxic effects as single agents, the distamycin derivatives increase the sensitivity of cells to TNF. This effect is governed via the inhibition of TNF-induced tyrosine phosphorylation of specific proteins which are probably involved in the development of TNF resistance. Thus, protein de-phosphorylation might provide an additional mechanism of action of these novel distamycin-A-derived drugs.
Approximate Homomorphic Encryption over the Conjugate-Invariant Ring (2018)

The Ring Learning with Errors (RLWE) problem over a cyclotomic ring has been the most widely used hardness assumption for the construction of practical homomorphic encryption schemes. However, this restricted choice of a base ring may cause a waste in terms of plaintext space usage. For example, an approximate homomorphic encryption scheme of Cheon et al. (ASIACRYPT 2017) is able to store a complex number in each of the plaintext slots since its canonical embedding of a cyclotomic field has a complex image. The imaginary part of a plaintext is not underutilized at all when the computation is performed over the real numbers, which is required in most of the real-world applications such as machine learning.
Tinnitus and inferior colliculus activity in chinchillas related to three distinct patterns of cochlear trauma (2008)

A longstanding hypothesis is that tinnitus, the perception of sound without an external acoustic source, is triggered by a distinctive pattern of cochlear hair cell (HC) damage and that this subsequently leads to altered neural activity in the central auditory pathway. This hypothesis was tested by assessing behavioral evidence of tinnitus and spontaneous neural activity in the inferior colliculus (IC) after unilateral cochlear trauma. Chinchillas were assigned to four cochlear treatment groups. Each treatment produced a distinctive pattern of HC damage, as follows: acoustic exposure (AEx): sparse low-frequency inner hair cell (IHC) and outer hair cell (OHC) loss; round window cisplatin (CisEx): pronounced OHC loss mixed with some IHC loss; round window carboplatin (CarbEx): pronounced IHC loss without OHC loss; control: no loss. Compared with controls, all experimental groups displayed significant and similar psychophysical evidence of tinnitus with features resembling a 1-kHz tone. Contralateral IC spontaneous activity was elevated in the AEx and CisEx groups, which showed increased spiking and increased cross-fiber synchrony. A multidimensional analysis identified a subpopulation of neurons more prevalent in animals with tinnitus. These units were characterized by high bursting, low ISI variance, and within-burst peak spiking of approximately 1,000/sec. It was concluded that cochlear trauma in general, rather than its specific features, leads to multiple changes in central activity that underpin tinnitus. Particularly affected was a subpopulation ensemble of IC neurons with the described unique triad of features.
PROTOTIPE ALAT PENCUCI CARTRIDGE FILTER USAHA AIR MINUM ISI ULANG (2016)

Abstrak Mekanisme penyaringan air yang digunakan pengusaha air minum isi ulang di Kabupaten Bengkalis adalah perangkat pengolah depot air minum yang dijual oleh perusahaan atau agen grosir air minum. Dalam pemakaiannya, komponen terpenting pada pengolah air minum ini yaitu cartridge filter, apabila sudah banyak kotoran yang menempel, dibersihkan dengan cara manual. Hal ini disebabkan belum tersedianya alat pembersih atau pencuci khusus cartridge filter di pasaran. Pembersihan cartridge filter yang dilakukan saat ini dengan cara disemprot dengan air bertekanan, lalu cartridge filter tersebut dipukul berulang-ulang dengan kekuatan sedang pada permukaan lantai. Dalam penelitian ini dibuat sebuah prototip pencuci cartridge filter tanpa merusak dan dengan demikian menghasilkan air minum isi ulang yang higienis. Hasil ujicoba alat pencuci cartridge filter di tempat mitra diperoleh waktu rata-rata pencucian untuk 12 cartridge sebesar 02 jam 42 menit 17 detik, dengan tiga tahap pencucian. Sedangkan rata-rata Total Dissolved Solid (TDS) dengan prototip alat pencuci cartridge filter ini sebesar 6.6 ppm Kata kunci : alat pencuci cartridge filter, air minum isi ulang , TDS
Gene and Locus Structure and Chromosomal Localization of the Protease-activated Receptor Gene Family (1998)

Protease-activate receptors (PARs) mediate activation of platelets and other cells by thrombin and other proteases. Such protease-triggered signaling events are thought to be critical for hemostasis, thrombosis, and other normal and pathological processes. We report here the structure of the mouse and human PAR3 genes as well as the organization of a PAR gene cluster encompassing the genes encoding PARs 1, 2, and 3. We also report the structure of the mouse and human PAR4 genes, which map to distinct chromosomal locations and encode a new thrombin receptor. PARs 1-4 are all encoded by genes with the same two exon structure. In each case, exon 1 encodes a signal peptide, and exon 2 encodes the mature receptor protein. These are separated by an intron of variable size. The genes encoding PARs 1-3 all map to chromosome 13D2 in mouse and chromosome 5q13 in human. In mouse, all three genes are located within 80 kilobases of each other. The PAR1 gene is located centrally and is flanked upstream by the PAR3 gene and downstream by the PAR2 gene in both species. The proximity of the PAR1 and PAR3 genes suggests the possibility that these genes might share regulatory elements. A comparison of the structures of the PAR amino acid sequences, gene structures, locus organization, and chromosomal locations suggests a working model for PAR gene evolution.
Metal Mesh Scaffold for Tissue Engineering of Membranes (2011)

Engineering of the membrane-like tissue structures to be utilized in highly dynamic loading environments such as the cardiovascular system has been a challenge in the past decade. Scaffolds are critical components of the engineered tissue membranes and allow them being formed in vitro and remain secure in vivo when implanted in the body. Several approaches have been taken to develop scaffolds for tissue membranes. However, all methods entail limitations due to structural vulnerability, short-term functionality, and mechanical properties of the resulted membrane constructs. To overcome these issues, we have developed a novel hybrid scaffold made of an extra thin layer of metal mesh tightly enclosed by biological matrix components. This approach retains all the advantages of using biological scaffolds while developing a strong extracellular matrix that can stand various types of loads after implantation inside the body.
Assessment of collagen absorption and related potential diagnostic applications (2007)

The sensitivity to collagen may be useful for diagnostic purposes in mammography, as collagen seems to be involved in the development of breast cancer. Moreover, collagen content is expected to be related to breast density (i.e. breast parenchymal pattern) and its quantification could allow the classification of breast type. Thus we have measured the absorption properties of collagen from 610 to 1040 nm. Absorption spectra of breast from healthy volunteers were then interpreted adding collagen to the other absorbers previously considered (i.e. oxy- and deoxyhemoglobin, water, and lipids). A significant amount of collagen, depending on breast type, is estimated to be present and seems to correlate with breast type. Moreover, adding collagen to the fitting procedure affects remarkably the estimated values of blood content and oxygenation. We have also upgraded our time-resolved multi-wavelength optical mammograph, adding a long wavelength (1060 nm) to improve the spectral information and, in particular, the sensitivity to collagen. Breast measurements on volunteers have recently started.
Faster gaze prediction with dense networks and Fisher pruning (2018)

Predicting human fixations from images has recently seen large improvements by leveraging deep representations which were pretrained for object recognition. However, as we show in this paper, these networks are highly overparameterized for the task of fixation prediction. We first present a simple yet principled greedy pruning method which we call Fisher pruning. Through a combination of knowledge distillation and Fisher pruning, we obtain much more runtime-efficient architectures for saliency prediction, achieving a 10x speedup for the same AUC performance as a state of the art network on the CAT2000 dataset. Speeding up single-image gaze prediction is important for many real-world applications, but it is also a crucial step in the development of video saliency models, where the amount of data to be processed is substantially larger.
Characterization of an <i>ERAD</i> Gene as <i>VPS30/ATG6</i> Reveals Two Alternative and Functionally Distinct Protein Quality Control Pathways: One for Soluble Z Variant of Human α-1 Proteinase Inhibitor (A1PiZ) and Another for Aggregates of A1PiZ (2005)

The Z variant of human alpha-1 proteinase inhibitor (A1PiZ) is a substrate for endoplasmic reticulum-associated protein degradation (ERAD). To identify genes required for the degradation of this protein, A1PiZ degradation-deficient (add) yeast mutants were isolated. The defect in one of these mutants, add3, was complemented by VPS30/ATG6, a gene that encodes a component of two phosphatidylinositol 3-kinase (PtdIns 3-kinase) complexes: complex I is required for autophagy, whereas complex II is required for the carboxypeptidase Y (CPY)-to-vacuole pathway. We found that upon overexpression of A1PiZ, both PtdIns 3-kinase complexes were required for delivery of the excess A1PiZ to the vacuole. When the CPY-to-vacuole pathway was compromised, A1PiZ was secreted; however, disruption of autophagy led to an increase in aggregated A1PiZ rather than secretion. These results suggest that excess soluble A1PiZ transits the secretion pathway to the trans-Golgi network and is selectively targeted to the vacuole via the CPY-to-vacuole sorting pathway, but excess A1PiZ that forms aggregates in the endoplasmic reticulum is targeted to the vacuole via autophagy. These findings illustrate the complex nature of protein quality control in the secretion pathway and reveal multiple sites that recognize and sort both soluble and aggregated forms of aberrant or misfolded proteins.
Low temperature oxidation of silicon (1988)

Oxidation of silicon in dry oxygen ambient at temperatures between 25°C to 500°C, with a point-to-plane corona discharge is studied. The oxidation rate for this case is a strong function of temperature and is found to increase significantly in comparison to the conventional thermal oxidation rate. For the thicker films, refractive index of the grown oxide layer approaches the value obtained for high-temperature thermally grown oxide.
Influence of Composition and Texture on Compressive Strength Variations in the Travis Peak Formation (1992)

Abstract The evaluation of rock strength from geophysical well logs is fundamental to engineering problems associated with wellbore stability, sand control and hydraulic fracture containment. Meaningful inversion of geophysical data for rock strength requires a better understanding of how intrinsic rock properties affect rock strength as well as new models to capture this understanding. A study of the relationships between compressive strength and rock composition and texture was conducted on cores from the Travis Peak formation. Travis Peak lithologies vary from mudstones to quartz arenites, and porosities range from 5.5% to 8.5%. After identifying the dominant composition and texture elements controlling strength variations in the Travis Peak formation, we explain our results in terms of micromechanical deformation mechanisms. A simple predictive model of rock strength is developed, based on measurable quantities physically linked to the governing deformation mechanisms. We show that the most accurate strength models include explicit information on both extrinsic and intrinsic rock properties. Our method suggests a new approach to quantifying rock strength from well logs.
A Four-Cavity Elliptic Waveguide Filter (1970)

Realization of the bandpass fourth-order antimetric elliptic filter function in a waveguide structure is described. A mathematical model is shown to accurately predict the performance of the experimental narrow-bandpass waveguide filter.