gebhart/patrepeval huggingface dataset:
<title>Diffractive-refractive lens system for age-related macular degeneration</title> (1993)

Age-related macular degeneration is a disease that affects the retina in eye of the older adult, causing central visual field loss. This can result in reduced visual acuity. A magnified image effectively appears as if the visual field loss is small relative to that image. The magnification is provided by an ocular telephoto system consisting of a diffractive and refractive hybrid spectacle lens and a dual-purpose intraocular lens. Without the spectacle lens, the intraocular lens functions as an implant for the treatment of cataracts. With the spectacle the system assists the patient in visual near tasks, such as reading or writing. The application of diffractive optics on the spectacle permits the correction of optical aberrations while reducing the size and weight of the high-power spectacle lens.
Zonal-Centrifuged Purified Duck Embryo Cell Culture Rabies Vaccine for Human Vaccination (1971)

Rabies virus produced in duck embryo cell culture was concentrated from volumes of 14 to 30 liters to 400 to 800 ml by zonal centrifugation. Virus titers of peak fractions were from 100- to 1,000-fold greater than those of the starting material. Vaccines were prepared by combining fractions with peak virus titers and diluting back to 10 times concentration. The resulting beta-propiolactone-inactivated vaccines, when prepared as lyophilized vaccines with AlPO(4) adjuvant diluents, were low in protein nitrogen (0.01 mg/ml), and three of four lots passed the National Institutes of Health potency test when tested as equivalent to a standard 10% suspension of duck embryo or mouse brain tissue vaccine. These vaccines also induced good sero-conversion in adult rabbits after a single 1-ml dose of vaccine. Guinea pigs sensitized with zonal-centrifuged purified duck embryo vaccine (with AlPO(4) adjuvant) did not exhibit anaphylactic shock reactions when challenged with homologous vaccine. Also, no anaphylactic shock reactions were observed when guinea pigs were sensitized with either a 10% experimental duck embryo vaccine or cell culture vaccine and then challenged with the zonal-purified vaccine. However, guinea pigs sensitized with cell culture or zonal-purified vaccine and then challenged with the 10% experimental vaccine did show slight transitory congestion. The 10% experimental whole duck embryo vaccine was responsible for all observed anaphylactic shock reactions whether homologous or heterologous.
Pkd1 and Pkd2 Are Required for Normal Placental Development (2010)

Placental abnormalities contribute to the fetal demise of Pkd(-/-) embryos. Endothelial cell specific deletion of Pkd1 or Pkd2 recapitulates a subset of findings seen in Pkd null animals. Our studies reveal a complex role for polycystins in maintaining vascular integrity.
Raman imaging of human macular pigments (2002)

We have imaged the spatial distribution of macular carotenoid pigments (MPs) in the human retina, employing Raman spectroscopy. Using excised human eyecups as initial test samples and resonant excitation of the pigment molecules with narrow-bandwidth blue light from a mercury arc lamp, we record Raman images originating from the carbon-carbon double-bond stretch vibrations of the molecules. Preliminary Raman images reveal significant differences in the MPs of different samples in regard to absolute levels as well as spatial variation. This technique holds promise as a method of rapid screening of MPs in large populations at risk for vision loss from age-related macular degeneration, a leading cause of blindness.
Insertion element IS986 from Mycobacterium tuberculosis: a useful tool for diagnosis and epidemiology of tuberculosis (1990)

IS986 of Mycobacterium tuberculosis belongs to the IS3-like family of insertion sequences, and it has previously been shown to be present in multiple copies in the chromosome of M. tuberculosis. In this study we investigated the value of a IS986-based DNA probe in the diagnosis and epidemiology of tuberculosis. IS986 was found only in species belonging to the M. tuberculosis complex. Independent isolates of M. tuberculosis complex strains showed a very high degree of polymorphism of restriction fragments which contained IS986 DNA. In contrast, Mycobacterium bovis BCG vaccine strains as well as clinical isolates of M. bovis BCG contained one copy of IS986, which was present at the same location in the chromosome. Different M. tuberculosis isolates from a recent M. tuberculosis outbreak showed an identical banding pattern. We concluded that IS986 is an extremely suitable tool for the diagnosis and epidemiology of tuberculosis.
Fast three-dimensional black-blood MR imaging for carotid artery intra-plaque haemorrhage using DANTE-prepared FLASH (3D-DASH) (2014)

Background DANTE (Delays Alternating with Nutation for Tailored Excitation) pulse trains are a rapid series of low flip angle RF pulses interspersed with gradients. We have previously demonstrated that when using DANTE pulse trains as a preparation module prior to imaging readout, the longitudinal magnetization of flowing spins is substantially attenuated, whereas the longitudinal magnetization of static tissue/fluid is mostly preserved [1]. In this study we introduce a new DANTE-prepared 3D FLASH T1 weighted (T1w) sequence (denoted ‘3DDASH’) [2] that is able to generate 0.6 mm isotropic resolution images with an average imaging speed better than 2 sec/slice.
4,4′,5,5′-Tetracarboxy-2,2′-bipyridine Ru(II) Sensitizers for Dye-Sensitized Solar Cells (2014)

Two Ru(II) sensitizers TCR-1 and TCR-2 bearing four carboxy anchoring groups were prepared using 4,4',5,5'-tetraethoxycarbonyl-2,2'-bipyridine chelate and 4-(5-hexylthien-2-yl)-2-(3-trifluoromethyl-1H-pyrazol-5-yl)pyridine and 6-t-butyl-1-(3-trifluoromethyl-1H-pyrazol-5-yl)isoquinoline, respectively. Dissolution of these sensitizers in DMF solution afforded a light green solution up to 10(-5) M, for which their color gradually turned red upon further dilution and deposition on the surface of a TiO2 photoanode due to the spontaneous deprotonation of carboxylic acid groups. These sensitizers were characterized using electrochemical means and structural analysis time-dependent density functional theory (TDDFT) simulation and were also subjected to actual device fabrication. The as-fabricated DSC devices showed overall efficiencies η = 6.16% and 6.23% versus their 4,4'-dicarboxy counterparts TFRS-2 and TFRS-52 with higher efficiencies of 7.57% and 8.09%, using electrolyte with 0.2 M LiI additive. Their inferior efficiencies are possibly caused by the combination of blue-shifted absorption on TiO2, inadequate dye loading, and the perpendicularly oriented central carboxy groups.
Preparation and characterization of aromatic polyamides from 4,4'-(2,6-naphthylenedioxy)dibenzoic acid and aromatic diamines (1998)

A new aromatic dicarboxylic acid, 4,4′-(2,6-naphthylenedioxy)dibenzoic acid (3), was synthesized by the fluoro-displacement reaction of p-fluorobenzonitrile with 2,6-naphthalenediol in the presence of potassium carbonate, followed by alkaline hydrolysis. A series of aromatic polyamides having inherent viscosities of 1.30–2.19 dL/g were prepared by the triphenyl phosphite activated polycondensation from the diacid 3 with sixteen aromatic diamines. Most of the resulting polymers were noncrystalline and readily soluble in a variety of polar solvents such as N,N-dimethylacetamide (DMAc) and N-methyl-2-pyrrolidone (NMP). Except for those polymers derived from p-phenylenediamine, benzidine, and 4,4′-bis(p-aminophenoxy)biphenyl, transparent, tough, and flexible films were cast from the DMAc or NMP solutions. The films had tensile strengths ranging from 70 to 91 MPa, elongations at break from 6 to 50%, and initial moduli from 1.35 to 2.32 GPa. The polyamides exhibit glass transition temperatures in the range of 178–300°C. Almost all polymers are stable up to 400°C, with 10% weight loss being recorded above 500°C, in air and nitrogen atmosphere.
Microwave Selective Heating Enhancement for Cancer Hyperthermia Therapy Based on Lithographically Defined Micro/Nanoparticles (2016)

Hyperthermia therapy is a promising approach for cancer treatment that uses external electromagnetic fields to heat up the tumor region in order to preferentially weaken or kill cancer cells. However, achieving localized heating of the cancer tissue without damaging the nearby healthy tissue remains a challenge. This study proposes to use lithographically defined micro/nanoparticles as microwave absorbers to achieve localized heating under microwave radiation for hyperthermia therapy. The particle structures, including both geometry and material, have been designed, tested, and optimized by the finite element method using Ansoft HFSS to obtain high microwave absorption efficiency. Based on the numerical studies, the magnetic dipoles have been chosen as the microwave‐absorbing particles. The fabrication and collection processes of the particles have been developed. The measurements in this study, based on particle‐suspended hydrogel setup, have demonstrated that the micro/nanoparticles can absorb the external electromagnetic field efficiently and greatly enhance the localized heat generation compared to control groups without particles.
Nonstoichiometric calcium pyrophosphate: a highly efficient and selective catalyst for dehydration of lactic acid to acrylic acid (2014)

Lactic acid dehydration using a non-stoichiometric calcium pyrophosphate catalyst (Ca/P ratio 0.78) has resulted in 78% acrylic acid yield due to formation of calcium lactate as an intermediate on the catalyst surface.
Investigation of the pattern of hepatitis C virus sequence diversity in different geographical regions: implications for virus classification (1995)

Genotypes of hepatitis C virus (HCV) present within 104 samples from HCV-infected individuals from Africa, the Middle East, the Indian subcontinent and South-East Asia were identified by sequence comparisons in the core and NS-5 regions. Relatively short sequences (such as the 222 bp fragment of NS-5) provided effective discrimination of types, subtypes and isolates, and produced equivalent relationships between genotypes as were found upon comparison of longer sequences of NS-5, of the core region, and by comparison of the limited number of complete genomic sequences currently available. Measurement of evolutionary distances in the core and NS-5 regions allowed 79 of the 104 samples to be identified as examples of known genotypes, while 17 of the remainder could be provisionally classified as new subtypes of types 1 (Nigeria), 2 (Gambia), 3 (India, Pakistan and Bangladesh) and 4 (Middle East) on the basis of sequence comparison in core and NS-5 (n = 9) or provisionally using core alone (n = 8). The remaining sequences from Thailand made up two groups showing no close similarity to any of the six major genotypes classified to date, although one corresponded to an as yet unclassified variant of HCV also found in Thailand. However, phylogenetic analysis of the core and NS-5 regions indicated a distant relationship between these sequences with variants found in Vietnam and with type 6a, and collectively they formed a diverse single phylogenetic group. The existence of great diversity within a single genotype was also found amongst type 3 sequences in the Indian subcontinent, amongst type 4 variants in Central Africa and the Middle East, and amongst type variants in Nigeria. These findings may provide clues for understanding the origins and mechanisms of transmission of HCV.
<title>Novel aerodynamic window with a pump cavity and a supersonic jet</title> (1990)

In order to minimize the mass flow rate and the optical distortion of aerodynamic windows, a novel type with a pump cavity and a supersonic as jet has been deve- loped. Prototypes of this window with an aperture of 4x4 mm have been designed and fabricated. With it, a 80 mbar laser cavity can be sealed up using a gas jet of 5 g/s mass rate at 5.4 bar while the pressue in pump cavity is about 600 mbar and the volume to be pumped is less than 7.2 m /h. It can be operated stably if the pressure variation is less than 25 mbar. A wide range of operation pressure of the laser cavity can be realized easily by adjusting the supply pressure for the gas jet and the pressure in the pump cavity.
788. Imaging of Adenoviral Replication with a Fluorescent Reporter in the E3 Region (2004)

Top of pageAbstract
Adenoviral vectors offer promise for gene therapy of various diseases. One recent development in this area is conditionally replicative adenoviruses (CRAds) which selectively kill cancer cells through tumor-specific replication. To maintain safety and practically apply these agents in a clinical context, a non-invasive detection system of viral replication is required. Current adenovirus detection methods used in virotherapy clinical trials include in situ hybridization, immuno-histochemistry, electron microscopy, and DNA amplification. Although these techniques are useful for examining the presence of adenovirus in a laboratory setting, they are not suitable for monitoring dynamic events and isolated such as viral replication in clinical context. These methods can only provide static data on replication since they rely on invasive biopsies. To address these issues, we hypothesized that expression of a reporter gene from a replicative adenovirus would yield valuable information on viral replication and localization. We chose a strategy to incorporate the EGFP fluorescent protein into the E3 region so that transgene expression under the adenovirus major late promoter would closely mimic the viral replication profile. In addition, the chosen fluorescent reporter protein has potential to be detected noninvasively. We constructed Ad5ΔE3ADPF by deleting proteins 6.7K, gp19K, RIDα (10.4K), RIDβ (14.5K), and a portion of 12.5K from the E3 region while retaining the adenovirus death protein (ADP) since this viral product is required for efficient cell lysis and viral release. This construct has been reported to overexpress ADP and cause enhanced cytopathic effect. Using this construct, we generated six different vectors with EGFP in six different configurations (forward / reverse directions and three reading frames). Vectors with the EGFP cassette in the forward direction (F0, F1, F2: left to right) expressed EGFP 12 hours after infection in A549 (adenovirus permissive human lung carcinoma cell line). On the other hand, no EGFP expression was seen in BNL1NGA.4 (mouse hepatoma cell line) in which human adenovirus can infect but not replicate productively. Of the three frames, F1 showed the clearest correlation of EGFP expression with viral replication. Vectors with reverse direction cassettes (R0, R1, R2: right to left) did not demonstrate any EGFP expression. In the context of cytocidal effect, viruses with ΔE3ADP structure showed same level of cell killing effect as Ad5 wild type in A549 cells. Our data suggest that our novel imaging system may provide a simple and convenient way to monitor viral replication in preclinical and clinical settings. Additionally, deletion of the E3 region while remaining ADP would yield more cloning capacity for transgenes in a replicative adenovirus without hampering cell killing effect. We are currently testing the functionality of our system in several CRAd configurations for noninvasive imaging purposes.
Repetitively pulsed X-ray laser operating on the 3<i>p</i>— 3<i>s</i>transition of the Ne-like argon in a capillary discharge (2003)

The paper is devoted to a 469-Å X-ray laser excited by a fast capillary discharge in neon. The basic characteristics of the active medium and laser beam are presented. Applications of the laser in the studies of plasmas with densities of up to 1020 cm-3, in interferometry, reflectometry, for analysis of materials, etc. are described. A brief historical review is presented and the current state of the art in the development of laboratory X-ray lasers is considered.
Peer-to-Peer Streaming Capacity (2011)

Peer-to-peer (P2P) systems provide a scalable way to stream content to multiple receivers over the Internet. The maximum rate achievable by all receivers is the capacity of a P2P streaming session. We provide a taxonomy of sixteen problem formulations, depending on whether there is a single P2P session or there are multiple concurrent sessions, whether the given topology is a full mesh graph or an arbitrary graph, whether the number of peers a node can have is bounded or not, and whether there are nonreceiver relay nodes or not. In each formulation, computing P2P streaming capacity requires the computation of an optimal set of multicast trees, with an exponential complexity, except in three simplest formulations that have been recently solved with polynomial time algorithms. These solutions, however, do not extend to the other more general formulations. In this paper, we develop a family of constructive, polynomial-time algorithms that can compute P2P streaming capacity and the associated multicast trees, arbitrarily accurately for seven formulations, to a factor of 4-approximation for two formulations, and to a factor of log of the number of receivers for two formulations. The optimization problem is reformulated in each case so as to convert the combinatorial problem into a linear program with an exponential number of variables. The linear program is then solved using a primal-dual approach. The algorithms combine an outer loop of primal-dual update with an inner loop of smallest price tree construction, driven by the update of dual variables in the outer loop. We show that when the construction of smallest price tree can be carried out arbitrarily accurately in polynomial time, so can the computation of P2P streaming capacity. We also develop several efficient algorithms for smallest price tree construction. Using the developed algorithms, we investigate the impact of several factors on P2P streaming capacity using topologies derived from statistics of uplink capacities of Internet hosts.
Computational Identification and Characterization of New microRNAs in Human Platelets Stored in a Blood Bank (2020)

Platelet concentrate (PC) transfusions are widely used to save the lives of patients who experience acute blood loss. MicroRNAs (miRNAs) comprise a class of molecules with a biological role which is relevant to the understanding of storage lesions in blood banks. We used a new approach to identify miRNAs in normal human platelet sRNA-Seq data from the GSE61856 repository. We identified a comprehensive miRNA expression profile, where we detected 20 of these transcripts potentially expressed in PCs stored for seven days, which had their expression levels analyzed with simulations of computational biology. Our results identified a new collection of miRNAs (miR-486-5p, miR-92a-3p, miR-103a-3p, miR-151a-3p, miR-181a-5p, and miR-221-3p) that showed a sensitivity expression pattern due to biological platelet changes during storage, confirmed by additional quantitative real-time polymerase chain reaction (qPCR) validation on 100 PC units from 500 healthy donors. We also identified that these miRNAs could transfer regulatory information on platelets, such as members of the let-7 family, by regulating the <i>YOD1</i> gene, which is a deubiquitinating enzyme highly expressed in platelet hyperactivity. Our results also showed that the target genes of these miRNAs play important roles in signaling pathways, cell cycle, stress response, platelet activation and cancer. In summary, the miRNAs described in this study, have a promising application in transfusion medicine as potential biomarkers to also measure the quality and viability of the PC during storage in blood banks.
A Hammerstein-Type Equalizer for Concatenated Fiber-Wireless Uplink (2005)

In optical fiber-based wireless access schemes, the radio signal is transmitted through fiber without frequency conversion radio-over-fiber (ROF). Although the fiber has adequate bandwidth, nonlinear distortion due to electrical to optical (E/O) conversion is a concern. In the uplink, the dynamic multipath wireless channel is followed by this static memoryless ROF link; this forms a Wiener system. In this paper, we propose a Hammerstein type decision feedback equalizer (HDFE) for the fiber-wireless uplink to combat the nonlinear distortion and the wireless channel dispersion. The proposed equalizer is less complex because it handles static and dynamic distortions separately. The nonlinear distortion is compensated first, reducing the power of cross modulation products significantly. Analytical results show that the lower bound of the mean squared error depends on the optical and wireless channel noise. The bit error rate (BER) performance of the HDFE for the nonlinear channel approaches the performance of a decision feedback equalizer (DFE) in a linear channel when the nonlinearity is adequately compensated.
Space-borne Observations of Atmospheric Pre-Earthquake Signals in Seismically Active Areas: Case Study for Greece 2008-2009 (2013)

We are conducting theoretical studies and practical validation of atm osphere/ionosphere phenomena preceding major earthquakes. Our approach is based on monitoring of two physical parameters from space: outgoi ng long-wavelength radiation (OLR) on the top of the atmosphere and e lectron and electron density variations in the ionosphere via GPS Tot al Electron Content (GPS/TEC). We retrospectively analyzed the temporal and spatial variations of OLR an GPS/TEC parameters characterizing the state of the atmosphere and ionosphere several days before four m ajor earthquakes (M>6) in Greece for 2008-2009: M6.9 of 02.12.08, M6. 2 02.20.08; M6.4 of 06.08.08 and M6.4 of 07.01.09.We found anomalous behavior before all of these events (over land and sea) over regions o f maximum stress. We expect that our analysis reveal the underlying p hysics of pre-earthquake signals associated with some of the largest earthquakes in Greece.
Sequence similarity‐driven proteomics in organisms with unknown genomes by LC‐MS/MS and automated <b><i>de novo</i></b> sequencing (2007)

LC-MS/MS analysis on a linear ion trap LTQ mass spectrometer, combined with data processing, stringent, and sequence-similarity database searching tools, was employed in a layered manner to identify proteins in organisms with unsequenced genomes. Highly specific stringent searches (MASCOT) were applied as a first layer screen to identify either known (i.e. present in a database) proteins, or unknown proteins sharing identical peptides with related database sequences. Once the confidently matched spectra were removed, the remainder was filtered against a nonannotated library of background spectra that cleaned up the dataset from spectra of common protein and chemical contaminants. The rectified spectral dataset was further subjected to rapid batch de novo interpretation by PepNovo software, followed by the MS BLAST sequence-similarity search that used multiple redundant and partially accurate candidate peptide sequences. Importantly, a single dataset was acquired at the uncompromised sensitivity with no need of manual selection of MS/MS spectra for subsequent de novo interpretation. This approach enabled a completely automated identification of novel proteins that were, otherwise, missed by conventional database searches.
On broadcast disk paging (1998)

Broadcast disks are an emerging paradigm for mastive information dissemination. In a broadcast disk, data is divided into n equal-sized pages and pages are broadcast in a roundrobin manner by a server. Broadcast disks are effective because many clients can simultaneously retrieve any transmitted information. Paging is used by the clients to improve performance, much as in virtual memory systems. However, paging on broadcast disks differs from virtual memory paging in at least two fundamental aspects: l A page fault in the broadcast disk model has a variable cost that depends on the requested page as well as the current state of the broadcast.