gebhart/patrepeval huggingface dataset:
Murine Gammaherpesvirus 68 Open Reading Frame 31 Is Required for Viral Replication (2004)

Murine gammaherpesvirus 68 (MHV-68) is genetically related to the human gammaherpesviruses, Kaposi's sarcoma-associated herpesvirus (KSHV/HHV-8) and Epstein-Barr virus (EBV). It has been proposed as a model for gammaherpesvirus infection and pathogenesis. Open reading frame 31 (ORF31) is conserved among the Beta- and Gammaherpesvirinae subfamily, and there is no known mammalian homologue of this protein. The function of MHV-68 ORF31 and its viral homologues has not yet been determined. We described here a primary characterization of this protein and its requirement for lytic replication. The native MHV-68 ORF31 was detected at peak levels by 24 h postinfection, and the FLAG-tagged and green fluorescent protein fusion ORF31 were localized in the cytoplasm and nucleus in a diffuse pattern. Two independent experimental approaches were then utilized to demonstrate that ORF31 was required for lytic replication. First, small interfering RNA generated against ORF31 expression blocked protein expression and virus production in transfected cells. Then, two-independent bacterial artificial chromosome-derived ORF31-null MHV-68 mutants (31STOP) were generated and found to be defective in virus production in fibroblast cells. This defect can be rescued in trans by MHV-68 ORF31 and importantly by its KSHV homologue. A repair virus of 31STOP was also generated by homologous recombination in fibroblast cells. Finally, we showed that the defect in ORF31 blocked late lytic protein expression. Our results demonstrate that MHV-68 ORF31 is required for viral lytic replication, and its function is conserved in its KSHV homologue.
Food science sourcebook (1991)

2 v. : ill. ; 26 cm
Making Ricotta Cheese by Ultrafiltration (1978)

The principles of the uhrafihration process of Maubois, Mocquot, and Vassal were employed in production of Ricotta cheese. Effects on cheese quality of degree of acidification of the cheese milk, conditions of ultrafihration, and heat treatment of liquid pre-cheeses were studied. Cheeses produced under optimal conditions were similar to traditional Ricotta cheeses. The method lends itself to continuous operation.
Efficient broadband intracore grating LP_01–LP_02 mode converters for chromatic-dispersion compensation (1998)

LP(01)-LP(02) mode converters based on UV-written intracore gratings have been fabricated for chromatic-dispersion compensation. The mode converters operate in transmission at wavelengths near 150 nm with spectral bandwidths of 14-25 nm and coupling efficiencies of as much as 90%. A large negative dispersion of -335 ps/(nm km) is obtained for a compensator consisting of the mode converter and a 1490-m-long few-mode fiber. The compensator shows negative dispersion over a wavelength region of 5 nm. Its figure of merit is estimated to be 370 ps/(nm dB).
Cell cycle checkpoints, chromosome stability and the progression of cancer. (1997)

During the evolution of normal cells into cancer cells, the occurrence of multiple mutations results in genetic instability. Mutations in DNA repair genes such as those of mismatch and excision repair predispose the carriers of these mutations to cancer by increasing the level of genomic instability. A variety of chromosome aberrations, such as abnormal ploidy, whole chromosome loss or chromosome amplification are commonly observed in cancer cells. From one cell division to the next, mammalian cells pass through an organized series of controlled events referred to as the cell cycle. In order to pursue an ordered series of molecular events, the initiation of an event during cell cycle progression is dependent on the successful completion of an earlier event. The cell cycle is divided into two major phases, namely, M(mitotic) phase and interphase. Interphase can be further divided into three distinct phases termed G1 (gap 1), S(DNA synthesis) and G2(gap2) phases (Fig. 1). Along with the machinery that promotes cell cycle progression, cells are also equipped with cell cycle checkpoints that ensure correct ordering of events in the cell cycle. The idea of "the cell cycle checkpoint" was first introduced by Hartwell and Weinert (1989) as "the arrest of a cell at a particular phase of the cycle due to a lack of appropriate signals for cell cycle progression". Until the checkpoint machinery receives the appropriate signal, the cell will not be allowed to make transition from one phase of the cell cycle to the next. Thus, the major role of checkpoint control is to minimize somatic genetic alterations and/or events affecting cellular survival. When one or more components of a cell cycle checkpoint are mutated, the chances of genetic instability during one round of the cell cycle increase accordingly with consequent acceleration of cellular evolution from the normal to the cancerous state. Therefore, mutations in checkpoint controls may predispose cells to cancer by causing genomic instability. In this review, I will focus on the potential roles of cell cycle checkpoints in the progression of malignancy.
Electrical characteristics of low temperature polysilicon TFT with a novel TEOS/oxynitride stack gate dielectric (2003)

This investigation is the first to demonstrate a novel tetraethylorthosilicate (TEOS)/oxynitride stack gate dielectric for low-temperature poly-Si (LTPS) thin film transistors (TFTs), composed of a plasma-enhanced chemical vapor deposition (PECVD) thick TEOS oxide/ultrathin oxynitride grown by PECVD N/sub 2/O-plasma. The stack oxide shows a very high electrical breakdown field of 8.4 MV/cm, which is approximately 3 MV/cm larger than traditional PECVD TEOS oxide. The field effective mobility of stack oxide LTPS TFTs is over 4 times than that of traditional TEOS oxide LTPS TFTs. These improvements are attributed to the high quality N/sub 2/O-plasma grown ultrathin oxynitride forming strong Si/spl equiv/N bonds, as well as to reduce the trap density in the oxynitride/poly-Si interface.
A Modified Census Transform Based on the Neighborhood Information for Stereo Matching Algorithm (2013)

Census transform is a non-parametric local transform. Its weakness is that the results relied on the center pixel too much. This paper proposes a modified Census transform based on the neighborhood information for stereo matching. By improving the classic Census transform, the new technique utilizes more bits to represent the differences between the pixel and its neighborhood information. The result image of the modified Census transform has more detailed information at depth discontinuity. After stereo correspondence, sub-pixel interpolation and the disparity refinement, a better dense disparity map can be obtained. The experiments present that the proposed algorithm has simple mechanism and strong robustness. It can improve the accuracy of matching and is applicable to hardware systems.
Dynamic redistribution of raft domains as an organizing platform for signaling during cell chemotaxis (2004)

Spatially restricted activation of signaling molecules governs critical aspects of cell migration; the mechanism by which this is achieved nonetheless remains unknown. Using time-lapse confocal microscopy, we analyzed dynamic redistribution of lipid rafts in chemoattractant-stimulated leukocytes expressing glycosyl phosphatidylinositol-anchored green fluorescent protein (GFP-GPI). Chemoattractants induced persistent GFP-GPI redistribution to the leading edge raft (L raft) and uropod rafts of Jurkat, HL60, and dimethyl sulfoxide-differentiated HL60 cells in a pertussis toxin-sensitive, actin-dependent manner. A transmembrane, nonraft GFP protein was distributed homogeneously in moving cells. A GFP-CCR5 chimera, which partitions in L rafts, accumulated at the leading edge, and CCR5 redistribution coincided with recruitment and activation of phosphatidylinositol-3 kinase gamma in L rafts in polarized, moving cells. Membrane cholesterol depletion impeded raft redistribution and asymmetric recruitment of PI3K to the cell side facing the chemoattractant source. This is the first direct evidence that lipid rafts order spatial signaling in moving mammalian cells, by concentrating the gradient sensing machinery at the leading edge.
Rationally Combining Anti-VEGF Therapy with Checkpoint Inhibitors in Hepatocellular Carcinoma (2016)

Hepatocellular carcinoma (HCC) is a fatal disease with rising incidence in the world. For advanced HCC, sorafenib, a multikinase inhibitor, is the only systemic therapy with proven survival benefits. Sorafenib is a pan-VEGF receptor inhibitor, and thus many studies have focused its antivascular effects. But VEGF also acts as an immunosuppressive molecule. VEGF can inhibit maturation of dendritic cells, promote immune suppressive cell infiltration and enhance immune checkpoint molecules expression. On the other hand, potent VEGF inhibition may increase tumor hypoxia, which could hinder antitumor immunity or immunotherapy. Thus, achieving synergy when combining anti-VEGF therapy with immunotherapy may require proper polarization of the tumor microenvironment by dose titration or combination with other immunomodulating agents.
Effective Stabilization of a High-Loading Sulfur Cathode and a Lithium-Metal Anode in Li-S Batteries Utilizing SWCNT-Modulated Separators (2015)

A custom single-wall carbon nanotube (SWCNT)-modulated separator is employed to directly suppress the polysulfide migration and indirectly protect the lithium-metal anode from severe polysulfide contamination. The conductive sp(2) -carbon scaffold continuously reactivates and reutilizes the trapped active material, so the SWCNT-modulated separator provides a facile way to facilitate the implementation of pure sulfur cathodes with high sulfur contents and loadings.
Contribution of Each of Four Superantigens to<i>Streptococcus equi</i>-Induced Mitogenicity, Gamma Interferon Synthesis, and Immunity (2010)

Streptococcus equi is the causative agent of strangles, the most frequently diagnosed infectious disease of horses worldwide. The disease is characterized by abscessation and swelling of the lymph nodes of the head and neck, which can literally strangle the horse to death. S. equi produces four recently acquired phage-associated bacterial superantigens (sAgs; SeeH, SeeI, SeeL, and SeeM) that share homology with the mitogenic toxins of Streptococcus pyogenes. The aim of this study was to characterize the contribution of each of these S. equi sAgs to mitogenic activity in vitro and quantify the sAg-neutralizing capacity of sera from naturally infected horses in order to better understand their role in pathogenicity. Each of the sAgs was successfully cloned, and soluble proteins were produced in Escherichia coli. SeeI, SeeL, and SeeM induced a dose-dependent proliferative response in equine CD4 T lymphocytes and synthesis of gamma interferon (IFN-gamma). SeeH did not stimulate equine peripheral blood mononuclear cells (PBMC) but induced proliferation of asinine PBMC. Allelic replacement mutants of S. equi strain 4047 with sequential deletion of the superantigen genes were generated. Deletion of seeI, seeL, and seeM completely abrogated the mitogenic activity and synthesis of IFN-gamma, in equine PBMC, of the strain 4047 culture supernatant. Sera from naturally infected convalescent horses had only limited sAg-neutralizing activities. We propose that S. equi sAgs play an important role in S. equi pathogenicity by stimulating an overzealous and inappropriate Th1 response that may interfere with the development of an effective immune response.
Zwitterionic and acidic glycosphingolipids of the <i>Drosophila melanogaster</i> embryo (2000)

Defining glycosphingolipid structures in species amenable to genetic manipulation, such as Drosophila melanogaster, provides a foundation for investigating mechanisms that regulate glycolipid expression. Therefore, eight of the 12 major glycosphingolipids, accounting for 64% of lipid-linked carbohydrate in Drosophila embryos, were purified after separation into acidic and zwitterionic pools. The zwitterionic lipids possess phosphoethanolamine (PEtn) linked to one or more GlcNAc residues and comprise a family of serially related structures. The longest characterized glycolipid, an octaosylceramide, designated Nz28, has the structure: GalNAcbeta, 4(PEtn-6)GlcNAcbeta,3Galbeta,3GalNAcalpha,4Ga lNAcbeta, 4(PEtn-6)GlcNAcbeta,3Manbeta,4GlcbetaCer. Heptaosyl (Nz7), hexaosyl (Nz6), pentaosyl (Nz5) and tetraosyl (Nz4) forms of Nz28, sequentially truncated from the nonreducing terminus, possess only one PEtn moiety. The major acidic lipid, designated Az29, possesses two PEtn moieties and a glucuronic acid linked to a Gal-extended Nz28. Two other acidic glycolipids, Az9 and Az6, exhibit one PEtn moiety and the same hexose and N-acetylhexosamine composition as Az29 and Nz6, respectively. The fully extended Drosophila core oligosaccharide differs from that of other dipterans in the linkage at a single glycosidic bond, a distinction with significant structural and biosynthetic consequences. Furthermore, acidic species account for a larger proportion of total glycosphingolipid, and PEtn substitution of GlcNAc is more complete in the Drosophila embryo. Divergent characteristics may reflect interspecies variation or stage-specific glycosphingolipid expression in dipterans.
Post-transcriptional regulation across human tissues (2017)

Transcriptional and post-transcriptional regulation shape tissue-type-specific proteomes, but their relative contributions remain contested. Estimates of the factors determining protein levels in human tissues do not distinguish between (i) the factors determining the variability between the abundances of different proteins, i.e., mean-level-variability and, (ii) the factors determining the physiological variability of the same protein across different tissue types, i.e., across-tissues variability. We sought to estimate the contribution of transcript levels to these two orthogonal sources of variability, and found that scaled mRNA levels can account for most of the mean-level-variability but not necessarily for across-tissues variability. The reliable quantification of the latter estimate is limited by substantial measurement noise. However, protein-to-mRNA ratios exhibit substantial across-tissues variability that is functionally concerted and reproducible across different datasets, suggesting extensive post-transcriptional regulation. These results caution against estimating protein fold-changes from mRNA fold-changes between different cell-types, and highlight the contribution of post-transcriptional regulation to shaping tissue-type-specific proteomes.
Rhodopsin–lipid interactions (1973)

Abstract Purified, lipid‐free rhodopsin has been incorporated into bilayers of natural and synthetic phosphatidyl cholines and a natural digalactosyl diglyceride. Successful incorporation and high regenerability of rhodopsin appears to depend on the nature of the hydrocarbon chains and not specifically on the type of polar head group of the lipids. Electron paramagnetic resonance spectra of recombinant membranes containing small amounts of spin labeled phosphatidyl cholines reveals that rhodopsin interacts directly with the hydrocarbon chains of the phospholipids in the bilayer, resulting in a dramatically decreased motional freedom of the chains. In studies of the recombinant membranes using freeze–fracture electron microscopy, the presence of rhodopsin is detected as discrete particles in the plane of fracture. The particle distribution is dependent on the nature of the lipid hydrocarbon chains and whether or not the rhodopsin has been photolyzed. From these studies, it is concluded that the rhodopsin‐bilayer structure is stabilized primarily by direct interaction of the hydrocarbon chains with the protein molecule, and that structural parameters in this model system are subject to modulation by visible light.
Inorganic–organic hybrid materials through post-synthesis modification: Impact of the treatment with azides on the mesopore structure (2011)

Hybrid, hierarchically organized, monolithic silica gels, comprising periodically arranged mesopores and a cellular macroscopic network, have been prepared through a co-condensation reaction of tetrakis(2-hydroxyethyl)orthosilicate with chloromethyl-trimethoxysilane or 3-(chloropropyl)-triethoxysilane. Subsequent conversion of the chloro groups into azido groups, by nucleophilic substitution with NaN(3) in N,N-dimethylformamide, was conducted upon preservation of the monolithic structure. However, treatment with NaN(3) had a strong influence on the structure in the mesoporous regime, with changes such as an increase of mesopore diameter, pore volume and lattice constants, as well as a concomitant decrease of the pore wall thickness, as confirmed by small angle X-ray scattering, transmission electron microscopy, and nitrogen sorption analysis. Similar effects were observed for unmodified silica gels by simple ageing in azide-containing media, whether a relatively small or a sterically demanding counter ion (Na(+) or (H(3)C)(4)N(+)) was used. The structural modification did not seem to depend greatly on whether an organic aprotic solvent (N,N-dimethylformamide, 1,1,3,3-tetramethylurea, 1,3-dimethyl-2-imidazolidinone) or a protic solvent that can form hydrogen bonds, such as water, was used.
Endoplasmic reticulum stress in chondrodysplasias caused by mutations in collagen types II and X (2016)

The endoplasmic reticulum is primarily recognized as the site of synthesis and folding of secreted, membrane-bound, and some organelle-targeted proteins. An imbalance between the load of unfolded proteins and the processing capacity in endoplasmic reticulum leads to the accumulation of unfolded or misfolded proteins and endoplasmic reticulum stress, which is a hallmark of a number of storage diseases, including neurodegenerative diseases, a number of metabolic diseases, and cancer. Moreover, its contribution as a novel mechanistic paradigm in genetic skeletal diseases associated with abnormalities of the growth plates and dwarfism is considered. In this review, I discuss the mechanistic significance of endoplasmic reticulum stress, abnormal folding, and intracellular retention of mutant collagen types II and X in certain variants of skeletal chondrodysplasia.
Real-Time 3D Sonar Image Recognition for Underwater Vehicles (2007)

The recognition of objects and environment are one of keys to automate underwater tasks. This paper presents a predictor based image recognition method using high-resolution sonar images. They are very sensitive to sonar's view point changes. The proposed predictor predicts an object images depending on the view point. Using the object model, it modifies a template for optimal recognition. To estimate the accuracy and reliability of the proposed method, indoor tank tests were carried out using various shapes of objects.
10 × 10 GHz simultaneously modelocked multiwavelengthfibre ring laser (1999)

A simple, multiwavelength, fibre ring laser source is demonstrated which is capable of generating 10 simultaneous, synchronised wavelength channels, each modelocked at 10 GHz and producing 20 ps pulses.
LY293558, a Novel AMPA/GluR5 Antagonist, is Efficacious and Well-Tolerated in Acute Migraine (2004)

Glutamatergic hyperactivity is implicated migraine pathogenesis. Also, LY293558, an alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA)/kainate (KA) receptor antagonist, is effective in preclinical models of migraine. We therefore tested LY293558 in acute migraine. We conducted a randomized, triple-blind, parallel-group, double-dummy, multicentre trial of 1.2 mg/kg intravenous (IV) LY293558, 6 mg subcutaneous (SC) sumatriptan, or placebo in the treatment of acute migraine. The primary efficacy variable was the headache response rate, i.e. headache score improvement from moderate/severe at baseline to mild/none at 2 h. Of 45 enrolled patients, 44 patients (20M:24F; mean age +/- SD = 40 +/- 9 years) completed the study. Response rates were 69% for LY293558 (P = 0.017 vs. placebo), 86% for sumatriptan (P < 0.01 vs. placebo) and 25% for placebo. LY293558 and sumatriptan were superior to placebo (P < 0.01 for all comparisons) on all other measures of improvement in pain and migraine associated symptoms. Fifteen percent of patients who took LY293558 reported adverse events (AEs) (n = 2; one mild, one severe). Fifty-three percent of patients who took sumatriptan (n = 8; seven mild, one moderate) and 31% of those who received placebo reported AEs (n = 5; four mild, one severe). The efficacy and safety results of LY293558 in this small migraine proof of concept trial, together with supportive preclinical data, provide evidence for a potential role of nonvasoactive AMPA/KA antagonists in treating migraine. Larger trials are needed to further test the hypothesis.
Developing for privacy (2000)

The Sunday Boston Globe of January 30, 2000 was very representative of current newspapers.In addition to the usual mayhem, fires, weather, traffic accidents, and sports, the newspaper contained a number of Internet related stories, all roughly on a similar topic.A page one story discussed Internet gambling.Even though it is illegal in US, Internet gambling has merely moved offshore.Another story reports the widow of Frank Malina, an artist, has been sued over the word "Leonardo."Malina founded an academic journal called "Leonardo" in 1968, but a French corporation is claiming trademark damages because the journal shows up in Web searches for their site "Leonardo".Another story tells people how to avoid auction scams on e-bay and similar Web sites.
A Note on the Fragility of the “Michael” Message Integrity Code (2004)

The IEEE 802.11 wireless local area network standard did not incorporate a cryptographic message integrity code into its wired equivalent privacy (WEP) protocol, and relied upon CRC-32 for message integrity. This was shown to be completely insecure since WEP uses a stream cipher (RC4) for encryption. The latest IEEE 802.11i draft addresses this, and other, weaknesses discovered in WEP. IEEE 802.11i suggests three new modes of operation: two based on the Advanced Encryption Standard cipher and one [temporal key integrity protocol (TKIP)] still based on RC4. The TKIP mode is intended for use on legacy hardware, which is computationally weak. TKIP uses a new, keyed, 64-b, message integrity code called Michael. In this letter, we highlight a weakness in Michael and suggest a simple fix.
Image recovery from signal-dependent noise (1983)

It is well known that the noise processes corrupting an image are, in general, signal dependent. Under low signal to-noise-ratio situations, the amount of signal information present in the signal-dependent noise may become a significant fraction of the total signal information. A simple technique designed to demonstrate the potential for signal extraction from signal-dependent noise is presented.