gebhart/patrepeval huggingface dataset:
Human immunodeficiency viruses [letter] (1986)

This statement by some members of a subcommittee empowered by the International Committee on the Taxonomy of Viruses proposes that the acquired immunodeficiency syndrome (AIDS) retroviruses be officially designated as the human immunodeficiency viruses (HIV). Adoption of an internationally acceptable name for this group of viruses has become important in view of the multiplicity of names currently in use. Several isolates of what are evidently closely related members of the same virus group have been called lymphadenopathy-associated virus (LAV) human T-lymphotropic virus type III (HTLV-III) HTLV-III/LAV and several other designations. The name HIV conforms to common nomenclature for retroviruses in that it begins with the host species ends with virus and contains a word that denotes the major pathogenic property of members of the virus group. It is readily distinguishable from all existing names for this group of viruses and was chosen without regard to priority of discovery. The name is sufficiently distinct from the names of other retroviruses to imply an independent virus species. Retroviruses isolated from subhuman primates and found to be genetically related and biologically similar to HIVs should be designated as immunodeficiency viruses of the host species eg simian immunodeficiency virus (SIV). Since HIV isolates are numerous and display considerable genetic heterogeneity particularly in the env gene each laboratory will have to assign subspecies designations to their isolates. It is recommended that each laboratory adopt a code with geographically informative letters and sequential numbers to identify their isolates. Initially existing well characterized isolates such as HTLV-IIIB should be so identified in publications to ease the transition to a unified nomenclature.
Gray Apertures for Holographic Data Storage System (2008)

In this paper, we propose the idea of gray optical apertures in contrast to the conventional binary apertures for holographic data storage (HDS). A gray aperture can be realized by a liquid crystal display or a binary aperture with a coating near the edge. In our simulation, HDS with a gray aperture shows a better page signal-to-noise ratio and modeling accuracy than HDS using a binary aperture.
Examination of Aglycone-Binding Site of Human Salivary α-Amylase by Means of Transglycosylation Reactions (1991)

The active site of human salivary alpha-amylase is composed of tandem subsites (S3, S2, S1, S1',S2', etc.) geometrically complementary to several glucose residues, and the glycosidic linkage of the substrate is split between S1 and S1'. As a matter of convenience, the subsites to which the non-reducing-end part (glycone) and the reducing-end part (aglycone) of the substrate being hydrolyzed are bound are named the glycone-binding site (S3, S2, S1) and the aglycone-binding site (S1', S2'), respectively. The features of the aglycone-binding site of human salivary alpha-amylase were examined by means of transglycosylation reaction using phenyl alpha-maltoside (GG phi: G-G-phi) and its derivatives (GAG phi: G-AG-phi, GCG phi: G-CG-phi, AGG phi: AG-G-phi, and CGG phi: CG-G-phi) in which one of the glucose residues (G) has been converted to 6-amino-6-deoxy-glucose (AG) or glucuronic acid (CG) residue as the acceptor. A fluorogenic derivative of maltotetraose, p-nitrophenyl O-6-deoxy-6-[(2-pyridyl)amino]-alpha-D-glucopyranosyl-(1----4)-O-alpha-D -glucopyranosyl-(1----4)-O-alpha-D-glucopyranosyl-(1----4)-alpha-D- glucopyranosyl-(1----4)-alpha-D-glucopyranoside (FG4P, FG-G-G-G-P), was used as the substrate. HSA catalyzed both hydrolysis of FG4P to FG3 (FG-G-G) and p-nitrophenyl alpha-glucoside (G-P) and transfer of the FG3 residue of FG4P to the acceptors. Transfer to GAG phi occurred more effectively than to GG phi. Transfers to GCG phi and CGG phi were less than to GG phi and very little transfer to AGG phi occurred.(ABSTRACT TRUNCATED AT 250 WORDS)
Multi-spectral imaging with infrared sensitive organic light emitting diode (2014)

Commercially available near-infrared (IR) imagers are fabricated by integrating expensive epitaxial grown III-V compound semiconductor sensors with Si-based readout integrated circuits (ROIC) by indium bump bonding which significantly increases the fabrication costs of these image sensors. Furthermore, these typical III-V compound semiconductors are not sensitive to the visible region and thus cannot be used for multi-spectral (visible to near-IR) sensing. Here, a low cost infrared (IR) imaging camera is demonstrated with a commercially available digital single-lens reflex (DSLR) camera and an IR sensitive organic light emitting diode (IR-OLED). With an IR-OLED, IR images at a wavelength of 1.2 µm are directly converted to visible images which are then recorded in a Si-CMOS DSLR camera. This multi-spectral imaging system is capable of capturing images at wavelengths in the near-infrared as well as visible regions.
Metallic Conduction through Engineered DNA: DNA Nanoelectronic Building Blocks (2001)

A novel way of engineering DNA molecules involves substituting the imino proton of each base pair with a metal ion to obtain M-DNA with altered electronic properties. We report the first direct evidence of metalliclike conduction through 15 microm long M-DNA. In contrast, measurements on B-DNA give evidence of semiconducting behavior with a few hundred meV band gap at room temperature. The drastic change of M-DNA conductivity points to a new degree of freedom in the development of future molecular electronics utilizing DNA, such as creating all-DNA junction devices for use as nanoelectronic building blocks.
P‐118: Ellipsoidal Light Diffusing Film with Narrow Louver Micro Structure of Refractive index (2014)

Abstract Optical diffusers consisting of a microstructured refractive index are promising materials because of their unique optical properties. Existing Anisotropic diffusers formed of such films merely have straight‐line diffusion properties, and exhibit very little ellipticity. Here we describe ellipsoidal diffuser films, together with a method to control the ellipticity.
Multi-azimuth Prestack Time Migration for General Anisotropic, Weakly Heterogeneous Media - Field Data Examples (2013)

Multi-azimuth data acquisition has shown benefits in noise reduction and structure illumination, which leads generally to improved seismic images. However the current time processing, which is based on independent processing of the data from the different predominant azimuths, may lead to destructive interferences and deterioration of the final stacked image when the earth model is anisotropic or laterally heterogeneous. In order to solve this problem a prestack time migration for anisotropic, weakly heterogeneous media has been recently introduced and tested on synthetic data. In this work, we ran a first field data application on a multi-azimuth data set. From data in three different acquisition azimuths we performed migration velocity analysis to build azimuth-dependent migration operators. We processed the data in parallel also with conventional narrow azimuth prestack time migration in order to assess the performance of the new approach.
Non-invasive, multi-modal sensing of skin stretch and bioimpedance for detecting infiltration during intravenous therapy (2016)

Intravenous infiltration is a condition wherein an infused solution leaks inadvertently into soft tissue surrounding a hypodermic needle site. This occurrence affects approximately 6.5% of patients in hospitals worldwide, and can lead to severe tissue damage if not treated immediately. The methods currently used by medical staff to detect an infiltration are subjective and can potentially be prone to error. Infiltration is an even larger concern in pediatric patients, who have smaller veins than adults and have more difficulty in communicating pain or other discomfort associated with the infiltration with medical staff. For these reasons, automatic IV infiltration detection could potentially reduce the risk associated with this damaging condition. This paper proposes a novel proof-of-concept system that uses non-invasive sensing in conjunction with a low-power embedded computing platform to deliver continuous infiltration monitoring around the IV catheter site. This kind of system could be able to detect an infiltration by non-invasively monitoring for known symptoms: swelling of soft tissue and increased skin firmness; these symptoms can be sensed by measuring skin stretch and local bioimpedance. Moreover, the low-power design and wireless capabilities can potentially enable continuous wear. The proposed automatic IV infiltration detection system could significantly improve the number of infiltrations identified and treated on time.
Identification of Elongin C Sequences Required for Interaction with the von Hippel-Lindau Tumor Suppressor Protein (1997)

Elongin C is a 112-amino acid protein that is found in mammalian cells as a positive regulatory subunit of heterotrimeric RNA polymerase II elongation factor Elongin (SIII) and as a component of a multiprotein complex containing the von Hippel-Lindau (VHL) tumor suppressor protein. As a subunit of the Elongin complex, Elongin C interacts directly with the transcriptionally active Elongin A subunit and potently induces its elongation activity; in addition, Elongin C interacts with the ubiquitin-like Elongin B subunit, which regulates the interaction of Elongin C with Elongin A. As a component of the VHL complex, Elongin C interacts directly with both Elongin B and the VHL protein. Binding of the VHL protein to Elongin C was found to prevent Elongin C from interacting with and activating Elongin A in vitro, leading to the proposal that one function of the VHL protein may be to regulate RNA polymerase II elongation by negatively regulating the Elongin complex. In this report, we identify Elongin C sequences required for its interaction with the VHL protein. We previously demonstrated that the ability of Elongin C to bind and activate Elongin A is sensitive to mutations in the C-terminal half of Elongin C, as well as to mutations in an N-terminal Elongin C region needed for formation of the Elongin BC complex. Here we show that interaction of Elongin C with the VHL tumor suppressor protein depends strongly on sequences in the C terminus of Elongin C but is independent of the N-terminal Elongin C region required for binding to Elongin B and for binding and activation of Elongin A. Taken together, our results are consistent with the proposal that the VHL protein negatively regulates Elongin C activation of the Elongin complex by sterically blocking the interaction of C-terminal Elongin C sequences with Elongin A. In addition, our finding that only a subset of Elongin C sequences required for its interaction with Elongin A are critical for binding to VHL may offer the opportunity to develop reagents that selectively interfere with Elongin and VHL function.
Molecular Target Therapy For Synovial Sarcoma (2005)

Although the specific chromosomal translocation and fusion gene SYT-SSX in synovial sarcoma (SS) has been identified, the molecular mechanism of its tumorigenesis is largely unknown. Recent gene-expression profiles of soft-tissue tumors using cDNA microarray demonstrated that SS has the distinct gene-expression pattern from other sarcomas and has a similar pattern to that of malignant peripheral nerve sheath tumors, indicating that the origin of SS is likely to be the neural crest cells. Through this analysis, several genes were found to be specifically upregulated in SS and considered to play an important role in the proliferation of SS cells. Among them, Frizzled homolog 10 was identified as a good candidate molecule for the development of novel therapies to treat SS patients.
Small CD4 Mimetics Prevent HIV-1 Uninfected Bystander CD4 + T Cell Killing Mediated by Antibody-dependent Cell-mediated Cytotoxicity (2015)

Human immunodeficiency virus type 1 (HIV-1) infection causes a progressive depletion of CD4 + T cells. Despite its importance for HIV-1 pathogenesis, the precise mechanisms underlying CD4 + T-cell depletion remain incompletely understood. Here we make the surprising observation that antibody-dependent cell-mediated cytotoxicity (ADCC) mediates the death of uninfected bystander CD4 + T cells in cultures of HIV-1-infected cells. While HIV-1-infected cells are protected from ADCC by the action of the viral Vpu and Nef proteins, uninfected bystander CD4 + T cells bind gp120 shed from productively infected cells and are efficiently recognized by ADCC-mediating antibodies. Thus, gp120 shedding represents a viral mechanism to divert ADCC responses towards uninfected bystander CD4 + T cells. Importantly, CD4-mimetic molecules redirect ADCC responses from uninfected bystander cells to HIV-1-infected cells; therefore, CD4-mimetic compounds might have therapeutic utility in new strategies aimed at specifically eliminating HIV-1-infected cells.
Immunolocalization of islet amyloid polypeptide (IAPP) in pancreatic beta cells by means of peroxidase-antiperoxidase (PAP) and protein A-gold techniques. (1988)

A novel putative polypeptide hormone identified as islet amyloid polypeptide (IAPP) was recently purified from islet amyloid (IA) of diabetic humans and cats, and also from amyloid of a human insulinoma. Although the function of IAPP is yet unknown, its occurrence in pancreatic endocrine tissue and its partial amino acid sequence identity with calcitonin gene-related peptide (CGRP) suggests an endocrine regulatory effect. In the present investigation, the authors utilized antisera to insulin, glucagon, somatostatin, pancreatic polypeptide, synthetic human CGRP, and a synthetic human IAPP (7-17) undecapeptide to immunohistochemically (PAP technique) document the presence of IAPP immunoreactive cells in the islets of the cat, dog, mouse, and rat, but not in the islets of the horse or calf. In serial sections of islets from these species it was shown that IAPP immunoreactivity occurred in insulin-reactive beta cells. This observation was confirmed immunocytochemically in cat islets by means of protein A-gold probes. With protein A-gold labeling techniques, IAPP immunoreactivity was localized to the outer lucent compartment of the beta cell secretory granule, whereas insulin immunoreactivity was associated with the electron-dense core. These findings provide strong evidence that IAPP or an IAPP precursor is synthesized by beta cells and is stored in beta cell granules for subsequent co-secretion with insulin. The conservation of IAPP in humans and multiple animal species and the localization of IAPP to pancreatic beta cells provide further evidence that IAPP has an important endocrine regulatory function. The propensity of IAPP to polymerize and form IA fibrils in diabetes associated with aging may indicate that IAPP is in some way also linked to the development of Type 2 diabetes.
Energy-based Position Estimation of Microphones and Speakers (2007)

We present a novel energy-based algorithm to estimate the positions of microphones and speakers in an ad hoc microphone array setting. Compared to traditional time-of-flight based approaches, energy-based approach has the advantage that it does not require accurate time synchronization. This property is particularly useful for ad hoc microphone arrays because highly accurate synchronization across microphones may be difficult to obtain since these microphones usually belong to different devices. This new algorithm extends our previous energy-based position estimation algorithm [1] in that it does not assume the speakers are in the same positions as their corresponding microphones. In fact, our new algorithm estimates both the microphones and speakers simultaneously. Experiment results are shown to demonstrate its performance improvement over the previous approach in [1], and evaluate its robustness against time synchronization errors.
Grahamimycins: antibiotics from Cytospora sp. Ehrenb. W.F.P.L. 13A (1981)

Aerobic fermentation of cultures of Cytospora sp. Ehrenb. W.F.P.L. 13A produces a group of novel, broad-spectrum, dilactone, macrocyclic antibiotics. These compounds, named grahamimycins, were isolated from the culture medium by extraction with organic solvents and separated by chromatography. Three active components have been obtained in crystalline form and have been designated grahamimycins A, A1, and B. The most active of these, grahamimycin A, exhibited activity against 36 species of bacteria, 8 species of blue-green algae (cyanobacteria), and 2 species of green algae, and antifungal activity against 5 fungi. Studies on the growth of the Cytospora with respect to formation of antibiotic activity, and the isolation, characterization, and structure elucidation of the grahamimycins are described. These studies indicate that the grahamimycins are distinct from other known antibiotics and represent a new class of antibiotic structures.
Efficient Recombinant Parvovirus Production with the Help of Adenovirus-derived Systems (2012)

Rodent parvoviruses (PV) such as rat H-1PV and MVM, are small icosahedral, single stranded, DNA viruses. Their genome includes two promoters P4 and P38 which regulate the expression of non-structural (NS1 and NS2) and capsid proteins (VP1 and VP2) respectively1. They attract high interest as anticancer agents for their oncolytic and oncosuppressive abilities while being non-pathogenic for humans2. NS1 is the major effector of viral cytotoxicity3. In order to further enhance their natural antineoplastic activities, derivatives from these vectors have been generated by replacing the gene encoding for the capsid proteins with a therapeutic transgene (e.g. a cytotoxic polypeptide, cytokine, chemokine, tumour suppressor gene etc.)4. The recombinant parvoviruses (recPVs) vector retains the NS1/2 coding sequences and the PV genome telomeres which are necessary for viral DNA amplification and packaging. Production of recPVs occurs only in the producer cells (generally HEK293T), by co-transfecting the cells with a second vector (pCMV-VP) expressing the gene encoding for the VP proteins (Fig. 1)4. The recPV vectors generated in this way are replication defective. Although recPVs proved to possess enhanced oncotoxic activities with respect to the parental viruses from which they have been generated, their production remains a major challenge and strongly hampers the use of these agents in anti-cancer clinical applications. We found that introduction of an Ad-5 derived vector containing the E2a, E4(orf6) and the VA RNA genes (e.g. pXX6 plasmid) into HEK293T improved the production of recPVs by more than 10 fold in comparison to other protocols in use. Based on this finding, we have constructed a novel Ad-VP-helper that contains the genomic adenoviral elements necessary to enhance recPVs production as well as the parvovirus VP gene unit5. The use of Ad-VP-helper, allows production of rec-PVs using a protocol that relies entirely on viral infection steps (as opposed to plasmid transfection), making possible the use of cell lines that are difficult to transfect (e.g. NB324K) (Fig. 2). We present a method that greatly improves the amount of recombinant virus produced, reducing both the production time and costs, without affecting the quality of the final product5. In addition, large scale production of recPV (in suspension cells and bioreactors) is now conceivable.
Pharmacokinetic Evaluation of a 1-Day Treatment Initiation Option for Starting Long-Acting Aripiprazole Lauroxil for Schizophrenia (2018)

The 1-day initiation regimen resulted in plasma aripiprazole concentrations consistent with the 21-day initiation regimen. Therefore, a single dose of ALNCD with a single 30-mg oral dose of aripiprazole provides an alternative initiation regimen for starting AL.
Self-aligned silicon fins in metallic slits as a platform for planar wavelength-selective nanoscale resonant photodetectors (2012)

We propose and demonstrate a novel nanoscale resonant metal-semiconductor-metal (MSM) photodetector structure based on silicon fins self-aligned to metallic slits. This geometry allows the center wavelength of the photodetector's spectral response to be controlled by the silicon fin width, allowing multiple detectors, each sensitive to a different wavelength, to be fabricated in a single-step process. In addition, the detectors are highly efficient with simulations showing ~67% of the light (λ = 800 nm) incident on the silicon fin being absorbed in a region of thickness ~170 nm whereas the absorption length at the same wavelength is ~10 µm. This approach is promising for the development of multispectral imaging sensors and low-capacitance photodetectors for short-range optical interconnects.
Work function of Ni silicide phases on HfSiON and SiO/sub 2/: NiSi, Ni/sub 2/Si, Ni/sub 31/Si/sub 12/, and Ni/sub 3/Si fully silicided gates (2005)

A complete determination of the effective work functions (WF) of NiSi, Ni/sub 2/Si, Ni/sub 31/Si/sub 12/ and Ni/sub 3/Si on HfSiON and on SiO/sub 2/ is presented. Conditions for formation of fully silicided (FUSI) gates for NiSi/sub 2/, NiSi, Ni/sub 3/Si/sub 2/, Ni/sub 2/Si, Ni/sub 31/Si/sub 12/ and Ni/sub 3/Si crystalline phases were identified. A double thickness series (HfSiON/SiO/sub 2/) was used to extract WF on HfSiON accounting for charge effects. A strong effect on WF of Ni content is observed for HfSiON, with higher WF for the Ni-rich silicides suggesting unpinning of the Fermi level. A mild dependence is observed for SiO/sub 2/. While all Ni-rich silicides have adequate WF for pMOS applications, Ni/sub 2/Si is most attractive due to its low formation temperature, lower volume expansion and ease of integration. Similar threshold voltages (-0.3 V) were obtained on Ni/sub 2/Si and Ni/sub 31/Si/sub 12/ FUSI HfSiON pMOSFETS.
Hardware-in-the-Loop End-to-End Optimization of Camera Image Processing Pipelines (2020)

Commodity imaging systems rely on hardware image signal processing (ISP) pipelines. These low-level pipelines consist of a sequence of processing blocks that, depending on their hyperparameters, reconstruct a color image from RAW sensor measurements. Hardware ISP hyperparameters have a complex interaction with the output image, and therefore with the downstream application ingesting these images. Traditionally, ISPs are manually tuned in isolation by imaging experts without an end-to-end objective. Very recently, ISPs have been optimized with 1st-order methods that require differentiable approximations of the hardware ISP. Departing from such approximations, we present a hardware-in-the-loop method that directly optimizes hardware image processing pipelines for end-to-end domain-specific losses by solving a nonlinear multi-objective optimization problem with a novel 0th-order stochastic solver directly interfaced with the hardware ISP. We validate the proposed method with recent hardware ISPs and 2D object detection, segmentation, and human viewing as end-to-end downstream tasks. For automotive 2D object detection, the proposed method outperforms manual expert tuning by 30% mean average precision (mAP) and recent methods using ISP approximations by 18% mAP.
Direct Synthesis of Naltrexone by Palladium‐Catalyzed <i>N</i>‐Demethylation/Acylation of Oxymorphone: The Benefit of CH Activation and the Intramolecular Acyl Transfer from C‐14 Hydroxy (2012)

Abstract Oxymorphone was converted to naltrexone in three steps by palladium‐catalyzed oxidative N ‐demethylation and intramolecular acyl transfer from C‐14 hydroxy to N‐17. Vitride™ reduction of N ‐acylamide to N ‐alkylamine proceeded with concomitant reductive deprotection of C‐6 and O‐3 functionalities.