gebhart/patrepeval huggingface dataset:
Insights into the genomic nitrate response using genetics and the Sungear Software System (2007)

Nitrate is both a nutrient and a potent signal that stimulates plant growth. Initial experiments in the late 1950s showing that nitrate enhances nitrate reductase (NR) activity after several hours of treatment have now progressed to transcriptome studies identifying over 1000 genes that respond to muM levels of nitrate within minutes. The use of an Arabidopsis NR-null mutant allowed the identification of genes that respond to nitrate when the production of downstream metabolites of nitrate is blocked. Further dissection of the nitrate response is now possible using new bioinformatic tools such as Sungear to perform comparative studies of multiple transcriptome responses across different laboratories and environmental conditions. These analyses have identified genes and pathways (e.g. nitrate assimilation, pentose phosphate pathway, and glycolysis) that respond to nitrate under a variety of conditions (context-independent). Most of these genes and pathways are ones that were identified using the NR-null mutant as responding directly to nitrate. By contrast, other processes such as protein synthesis respond only under a subset of conditions (context-dependent). Data from the NR-null mutant suggest these latter processes may be regulated by downstream nitrogen metabolites.
Application of machine learning in recommendation systems (2018)

Study includes basic information about machine learning and recommender systems with their examples. More broadly addressed was the topic of machine learning's algorithms, which are used in such systems. The paper mainly focused on filtering algorithms based on the neighborhood of users or objects, and based on content. The description of these algorithms includes: similarities, disadvantages and advantages, measures for evaluating the algorithm, and calculation of the sample value of the evaluation prediction. The design part of the work begins with the description of the used databases from the MovieLens portal. Afterwards, the technology and practical implementation of the algorithms described above are then presented. The next part contains an analysis of the results and conclusions based on the simulations carried out on the computer to assess how the algorithms work. At the end of the work, there is a summary, performance evaluation of recommendation systems, and lessons learned from the project, as well as a proposal for further work on the issue of such systems.
Nitrite as a Substrate and Inhibitor of Myeloperoxidase (2000)

Myeloperoxidase is a heme enzyme of neutrophils that uses hydrogen peroxide to oxidize chloride to hypochlorous acid. Recently, it has been shown to catalyze nitration of tyrosine. In this study we have investigated the mechanism by which it oxidizes nitrite and promotes nitration of tyrosyl residues. Nitrite was found to be a poor substrate for myeloperoxidase but an excellent inhibitor of its chlorination activity. Nitrite slowed chlorination by univalently reducing the enzyme to an inactive form and as a consequence was oxidized to nitrogen dioxide. In the presence of physiological concentrations of nitrite and chloride, myeloperoxidase catalyzed little nitration of tyrosyl residues in a heptapeptide. However, the efficiency of nitration was enhanced at least 4-fold by free tyrosine. Our data are consistent with a mechanism in which myeloperoxidase oxidizes free tyrosine to tyrosyl radicals that exchange with tyrosyl residues in peptides. These peptide radicals then couple with nitrogen dioxide to form 3-nitrotyrosyl residues. With neutrophils, myeloperoxidase-dependent nitration required a high concentration of nitrite (1 mM), was doubled by tyrosine, and increased 4-fold by superoxide dismutase. Superoxide is likely to inhibit nitration by reacting with nitrogen dioxide and/or tyrosyl radicals. We propose that at sites of inflammation myeloperoxidase will nitrate proteins, even though nitrite is a poor substrate, because the co-substrate tyrosine will be available to facilitate the reaction. Also, production of 3-nitrotyrosine will be most favorable when the concentration of superoxide is low.
LATTICE PREDICTIONS FOR THE INTERQUARK POTENTIAL (1981)

The measured values of Wilson loops in Monte Carlo simulations of SU(3) lattice gauge theories are used to predict the qi potential. The relationship between ho and the short distance scale of the qq potential is also calculated. The predictions are in agreement with theoretical expectations but indicate that fermions must be incorporated into the lattice calculations before any realistic results relevant to QCD can be derived.
Generation and Detection of a 112-Gb/s Dual Polarization Signal Using a Directly Modulated Laser and Half-16-QAM Nyquist-Subcarrier-Modulation (2012)

A 56-Gb/s 16-QAM signal was generated using subcarrier modulation with a subcarrier frequency of half the symbol rate, Nyquist pulse shaping, and a directly modulated passive feedback laser. Using a pre-amplified direct detection receiver and digital signal processing, a loss margin of 12.6 dB was achieved for a 112-Gb/s dual polarization signal.
Highly Automated Method for Maintaining Expiring Records (2017)

This document describes a simple DNS cache optimization which keeps
the most popular Resource Records set (RRset) in the DNS cache: Highly
Automated Method for Maintaining Expiring Records (HAMMER). The
principle is that popular RRset in the cache are fetched, that is to
say resolved before their TTL expires and flushed. By fetching RRset
before they are being queried by an end user, that is to say
prefetched, HAMMER is expected to improve the quality of experience of
the end users as well as to optimize the resources involved in large
DNSSEC resolving platforms.
<i>Quillaja</i>Saponin Can Modulate Ovalbumin-Induced IgE Allergic Responses through Regulation of Th1/Th2 Balance in a Murine Model (2006)

Quillaja saponin is the extract from the balk of a South American tree, and it is considered to modulate immunological responses. We hypothesized that Quillaja saponin may change allergy-associated cytokine profile and antigen-specific immune responses. The purpose of this study is to investigate whether Quillaja saponin can suppress ovalbumin (OVA)-induced IgE-mediated allergic responses through promoting a dominant Th1 immune response. The spleen cells from BALB/c mice, which were primed by OVA, were used for an in vitro challenge test. The level of total and OVA-specific IgE, IL-4, IFN-gamma, and IL-12 was determined by enzyme-linked immunosorbent assay (ELISA). BALB/c mice were orally administered with saponin for 35 days. The mice were immunized intraperitoneally with OVA on days 14 and 21. After intraperitoneal challenge with OVA on day 35, anaphylactic symptoms were monitored. Total and specific IgE and IgG, specific IgG1 and IgG2a, and histamine levels in serum were analyzed by ELISA. The increase of IL-12 and IFN-gamma levels was observed in the presence of Quillaja saponin, while the IL-4 level was decreased. Furthermore, Quillaja saponin suppressed total and OVA-specific IgE secretion in spleen cells. Balb/c mice that were orally administered Quillaja saponin exhibited lower total and OVA-specific IgE and OVA-specific IgG secretions, whereas total IgG levels remained unchanged. Suppression of OVA-specific IgG1 and an increase of OVA-IgG2a were observed in mice fed saponin. Quillaja saponin also decreased serum histamine levels and diminished anaphylactic symptoms. The present study indicates that Quillajasaponin can suppress allergen-specific IgE-mediated reactivity in a murine model of food allergy, which results from shifting from a Th2-dominated to a Th1-dominated immune response.
Human Metapneumovirus Infection in Japanese Children (2004)

Human metapneumovirus (hMPV) has been recently discovered as an etiological agent of acute respiratory infections. Our purpose was to asses the virological and clinical features of children with respiratory infections caused by hMPV. We examined 658 nasopharyngeal swab samples obtained from 637 children with respiratory infections for hMPV by using reverse transcription-PCR (RT-PCR). A total of 268 samples from 637 children were inoculated onto tertiary monkey kidney cells. A total of 36 serum samples (26 in the acute phase and 10 in the convalescent phase) from the 26 hMPV-positive children were tested for immunoglobulin G (IgG) and IgM antibodies to hMPV by using an indirect immunofluorescence assay. We detected hMPV in 57 (8.9%) of the 637 samples by using RT-PCR and isolated 7 (2.6%) hMPV strains of the 268 samples in cell cultures. A total of 12 (46.2%) of 26 hMPV-positive children were suspected to have primary infection with hMPV as determined by an indirect immunofluorescence assay. The infected children were diagnosed as having wheezy bronchitis (36.8%), upper respiratory tract infection (26.3%), bronchitis (22.8%), and pneumonia (14.0%). We showed that two hMPV groups were circulating in different regions during the same period and that reinfection with hMPV frequently occurs in childhood. The RT-PCR test is the most sensitive test for detection of hMPV, and a serological test may be useful to differentiate between primary infection and reinfection with hMPV.
Increased cytotoxicity of normal rabbit serum for lectin-resistant mutants of animal cells. (1984)

Plant lectins are cytotoxic and can be used to select for mutants of animal cells that exhibit structural changes in cell surface carbohydrates reflecting glycosylation defects. We isolated eight lectin mutants of Chinese hamster ovary (CHO) cells that appear to represent three different phenotype classes. These lectin mutants were much more sensitive to the cytotoxic action of normal rabbit serum (NRS) than were the parental cells. This increased cytotoxicity was heat sensitive, specifically absorbed, and inhibited by simple and complex carbohydrates. No killing was observed under conditions in which only the alternate complement pathway was active. An NRS-resistant subclone that was isolated from one lectin mutant was shown to have also regained wild type behavior when tested with the lectins. The possibility that naturally occurring antibodies in rabbit serum are reacting with incomplete carbohydrate chains on the surface of the lectin mutants is discussed.
Automatic detection, identification, and registration of anatomical landmarks from 3-D laser digitizer body segment scans (2002)

Describes a signal processing method for automated detection, identification, and registration (ALDIR) of optically marked anatomical fiduciary landmarks from 3-D laser digitizer body segment measurements. The method described is a multistage process. In the first stage, body surface reflectivity and topography information is used to detect optical markers in digitizer measurement data. In the second stage, maximum likelihood identification is used to identify each of the detected landmarks. Finally, the identified landmarks and their relative spatial coordinates are registered and output. This can be used in a prosthetics-orthotics (or other) computer-aided design and computer-aided manufacturing (CAD/CAM) system to compute a quantitative diagnostic measure of the patient's physiological state; as a measure of efficacy of a given medical treatment regimen; or added to an anthropometric/medical data base.
Resistance of bulk alfalfa seeds to airflow (1994)

Northridge, CA). The manufacturer's specified pressure range for~Model DP 103-26 was 0 to about 3500 Pa. For low airflow rates of less than 0.02 m3*sI»m2, the long column shown in Fig. 2 was used. The pressure taps were placed at two levels 2 m apart along the height of the grain column. Four pressure taps 90 degrees apart were in stalled at each level. The grain column was hinged at the mid-section to facilitate filling and emptying of the container. The supply airflow from the compressed air line passed through a series of filters and pressure regulators before entering the grain column. The airflow rates were measured by four rotameter tubes (Fisher and Porter Co., Warminster. PA) that measured airflow rates as low as 7.54 x I0~s m3«s~'»m~2. The pressures along the depth of the grain column were measured using a pressure transducer (model DP 103-12,
Efficient generation of cytotoxic T lymphocytes against cervical cancer cells by adeno-associated virus/human papillomavirus type 16 E7 antigen gene transduction into dendritic cells (2002)

Adeno-associated virus (AAV) is able to efficiently deliver a cytokine gene into dendritic cells (DC). Improvements in T cell priming by DC might be effected by the delivery of antigen genes into DC, resulting in continuous protein expression, as most proteins have short half-lives. In this study, a recombinant AAV vector containing the human papillomavirus (HPV)-16 E7 gene was used to pulse/infect DC and compared to the pulsing of DC by the lipofection of bacterially produced E7 protein. Pulsing of DC with AAV/antigen (Ag) gene was found to be superior to pulsing with protein in six different assay systems: (1) the level of antigen transfer into DC as determined by intracellular staining; (2) the level of MHC class I-restricted killing in cytotoxic T lymphocyte (CTL) assays; (3) the level of IFN-gamma expression; (4) the level of DC-T cell priming clusters generated; (5) the level of CD80 and CD83 expression on DC; and (6) in the resulting CD8:CD4 ratio. Finally, AAV/Ag gene pulsing resulted in strong CTL activity after only 7 days of priming. These data suggest that AAV vectors may offer advantages over the commonly used protein-pulsing technique and that AAV vectors may be useful for the stimulation of CTL activity and adoptive immunotherapy protocols.
A lightweight network repair scheme for data collection applications in zigbee WSNs (2009)

Data collection is a fundamental operation in wireless sensor networks (WSNs). In, a quick convergecast solution is proposed for data collection in a ZigBee beacon-enabled tree-based WSN. However, it does not consider the network repair issue. When a ZigBee router loses its link to its parent, all its descendants have to rejoin the network. The rejoining procedure is time-consuming and may incur high communication overheads. The proposed network repair scheme consists of a regular repair and an instant repair schemes. Periodically, the network coordinator can issue regular repair to refresh the network (so as to keep the network in good shape). During normal operations, if a router loses its parent, it tries instant repair to reconnect to a new parent. Our design thus improves over ZigBee in that nodes can continue their operations even during instant repair.
Optimization of Al step coverage through computer simulation and scanning electron microscopy (1978)

Minute cracks in integrated circuit metallization at step edges constitute a very real hazard to device reliability. The computer simulations of metal film deposition reported in this study are in excellent agreement with SEM photographs of actual film step coverage obtained on unheated substrates. The use of the simulation technique to optimize step coverage has led to the modification of the planetary system used to support the wafers in the electron beam metal deposition apparatus. However, even with optimization of the planetary-source configuration, small cracks in metal films at steps occur if the step angles are greater than a maximum value determined by the system geometry. For the deposition system used in this work that maximum angle is 40°. However, steps with angles of 50° have been successfully coated with crack-free films when the substrates are heated above 300°C during deposition. We conclude that good step coverage may be obtained by optimization of the source-planetary configuration in the deposition apparatus, by controlling the substrate step profiles and by the use of elevated substrate temperatures.
Template free preparation of nanoporous organically modified silica thin films on flexible substrates (2011)

We report the preparation and characterization of nanoporous organically modified silica (ormosil) thin films at room temperature and neutral pH conditions from homogeneous methyl silsesquioxane (MSQ) gels. Universally applicable and stable colloidal ormosil suspensions are prepared from the gels by sonication and coated to the substrates including glass, paper and plastics. The nanoporosity and thickness of the films can be tuned, which makes them suitable for certain applications including sensing, functional coatings, and low-dielectric materials. We demonstrate the antireflection property of the films on glass, cellulose acetate (CA) and polyetherimide (PEI) substrates. The films on CA and PEI retain their antireflection property after multiple bending cycles. Furthermore, films are intrinsically hydrophobic, over a wide pH range, with static contact angles up to 143° on paper and 123° on glass and CA. Producing nanoporous ormosil thin films on flexible substrates may expand their use in low cost electronic, optical devices and sensors, and lab-on-paper applications.
Conversion of carbon oxides into methane in a nonthermal plasma-catalytic reactor (2011)

Nonthermal plasma created in a catalyst-packed bed reactor was applied to the conversion of carbon oxides (CO and CO2) into methane. The methanation was performed over a Ni/alumina catalyst with the molar ratios of H2/CO and H2/CO2 at 3.0 and 4.0, respectively. The present work focused on the effect of nickel loading (0–12.5 wt.%) on the methanation rate over the temperature range of 200–300 °C. The applied voltage for creating nonthermal plasma was 6.4–10.3 kV (operating frequency: 1 kHz). For both CO and CO2, the behavior of the methanation in the plasma-catalytic reactor greatly depended on the applied voltage, resulting in higher conversion efficiencies at higher voltages. There was optimal nickel content of 2.5–5.0 wt.% where the plasma effect on the methanation rate was maximized. It is believed that the plasma created in the catalytic reactor can change the rate-determining step by accelerating the dissociation of carbon oxides adsorbed on the catalyst surface.
The Long Side of the Market and the Short End of the Stick: Bargaining Power and Price Formation in Buyers', Sellers', and Balanced Markets (1995)

The determinants of bargaining power and price formation in a dynamic exchange market where new traders enter randomly over time are studied. When agents on the long side of the market possess the option to wait for the arrival of future partners, the terms of trade in the spot market must honor the value of this option. The equilibrium terms of trade are expressed in intuitive closed-form equations that highlight the distinct influences of short-run spot-market conditions and long-run market demographics.
An Architecture for Software-Based iSCSI on Multiprocessor Servers (2005)

To achieve IP-converged cluster deployments, the performance and scalability of iSCSI must approach that of FC SANs. We recognize and quantify that the major overhead of iSCSI comes from TCP/IP processing. Industry has largely responded with TCP offload engines (TOEs) and iSCSI storage adapters. As an alternative, this paper shows a software implementation of iSCSI on generic OSes and processors. The trend towards chip multiprocessing (CMP) and integrated memory controllers (MCH) largely motivated our direction. With CMP, increased processing power is delivered through multiple cores per processor; on-die MCH allows memory bandwidth to scale better with processor speeds. Our approach and analysis shows the effectiveness of partitioning the workload suitable for a CMP system, allowing iSCSI to scale with the increasing processing power and memory bandwidth of servers over time.
5(6)-Carboxyfluorescein Revisited:  New Protecting Group, Separation of Isomers, and their Spectral Properties on Oligonucleotides (2007)

Pentafluorophenyl esters of 5- and 6-carboxyfluorescein-3',6'-O-dipivalate can be easily separated in multigram quantities by column chromatography. The individual isomers were converted into stable phosphoramidites suitable for oligonucleotide synthesis. The use of the cyclohexylcarbonyl (Chc) protecting group instead of pivaloyl (Piv) facilitates the separation of isomers. The fluorescence spectra of 5- and 6-carboxyfluoresceins on oligonucleotides were compared.
Design of a 2.5kW 400V&#x2192;M2V high-efficiency DC/DC converter using a novel synchronous rectification control for electric vehicles (2013)

This paper proposes the design and development of a 2.5kW 400V→12V high-efficiency DC/DC converter with a wide input voltage range (450V~220VDC) and output voltage range (16V~6VDC). The designed DC/DC converter will be used in the electric vehicle as an electric alternator. An LLC half bridge topology is adopted as the primary side of the isolated DC/DC converter. For the secondary side, a novel rectification control strategy is developed to turn on/off the rectifier MOSFETs by actively tracking the exact triggering moments. A 2.5kW prototype to charge the on-board 12V battery was built to experimentally verify the theoretical analysis. The overall system efficiency was ~92% and the maximum is 93.2%.
Geotracker (2007)

The Web is rapidly moving towards a platform for mass collaboration in content production and consumption. Fresh content on a variety of topics, people, and places is being created and made available on the Web at breathtaking speed. Navigating the content effectively not only requires techniques such as aggregating various RSS-enabled feeds, but it also demands a new browsing paradigm. In this paper, we present novel geospatial and temporal browsing techniques that provide users with the capability of aggregating and navigating RSS-enabled content in a timely, personalized and automatic manner. In particular, we describe a system called GeoTracker that utilizes both a geospatial representation and a temporal (chronological) presentation to help users spot the most relevant updates quickly. Within the context of this work, we provide a middleware engine that supports intelligent aggregation and dissemination of RSS feeds with personalization to desktops and mobile devices. We study the navigation capabilities of this system on two kinds of data sets, namely, 2006 World Cup soccer data collected over two months and breaking news items that occur every day. We also demonstrate that the application of such technologies to the video search results returned by YouTube and Google greatly enhances a user.s ability in locating and browsing videos based on his or her geographical interests. Finally, we demonstrate that the location inference performance of GeoTracker compares well against machine learning techniques used in the natural language processing/information retrieval community. Despite its algorithm simplicity, it preserves high recall percentages.
Lack of Clinical Usefulness of the Limulus Test in the Diagnosis of Endotoxemia (1975)

Studies of the clinical value of the limulus amebocyte lysate test for the detection of endotoxemia are inconsistent. In an attempt to define the value of this test, a total of 237 plasma samples from 111 patients were tested for endotoxin with seven different lysate preparations. A total of 48 plasma samples yielded a positive test with one or more of the seven preparations. Two of eight samples positive with all seven preparations were from ambulatory patients. A significant positive correlation of the test with bacteremia, neutrophilia and elevated serum alkaline phosphatase was found. Only three of the 48 positive tests occurred by four hours of incubation, and only 12 were associated with positive blood cultures (eight contained gram-negative bacteria). The test now available has no clinical usefulness in the detection of endotoxemia or gram-negative septicemia.