gebhart/patrepeval huggingface dataset:
Utility of electrophoretically derived protein mass estimates as additional constraints in proteome analysis of human serum based on MS/MS analysis (2005)

The proteome of a HUPO human serum reference sample was analyzed using multidimensional separation techniques at both the protein and the peptide levels. To eliminate false-positive identifications from the search results, we employed a data filtering method using molecular weight (MW) correlations derived from denaturing 1-DE. First, the six most abundant serum proteins were removed from the sample using immunoaffinity chromatography. 1-DE was then used to fractionate the remaining serum proteins according to the MW. Gel bands were isolated and in-gel digested with trypsin, and the resulting peptides were analyzed by 2-D LC/ESI-MS/MS. A SEQUEST search using the MS/MS results identified 494 proteins. Of these, 202 were excluded formally using protein data filtering as they were single-assignment proteins and their theoretical and electrophoretically-derived MWs did not correlate at high confidence. To evaluate this method, the results were compared with those of 1-D LC/MALDI-TOF/TOF and HUPO Plasma Proteome Project analyses. Our data filtering approach proved valuable in analysis of complex, large-scale proteomes such as human serum.
980-nm Monolithic Passively Mode-Locked Diode Lasers With 62 pJ of Pulse Energy (2007)

Passively mode-locked 980-nm slab-coupled optical waveguide lasers have been demonstrated with pulse energies as high as 62 pJ and average powers of 489 mW at 7.92 GHz from a 5-mm device with a 300-mum absorber. Mode-locking has been observed with devices ranging from 3 to 10 mm in length
Clonal Hematopoiesis and Blood-Cancer Risk Inferred from Blood DNA Sequence (2020)

Cancers arise from multiple acquired mutations, which presumably occur over many years. Early stages in cancer development might be present years before cancers become clinically apparent.
Use of a Randomized Hybrid Ribozyme Library for Identification of Genes Involved in Muscle Differentiation (2004)

We have employed the hybrid hammerhead ribozyme-based gene discovery system for identification of genes functionally involved in muscle differentiation using in vitro myoblast differentiation assay. The major muscle regulatory genes (MyoD1, Mylk, myosin, myogenin, and Myf5) were identified endorsing the validity of this method. Other gene targets included tumor suppressors and cell cycle regulators (p19ARF and p21WAF1), FGFR-4, fibronectin, Prkg2, Pdk4, fem, and six novel proteins. Functional involvement of three of the identified targets in myoblast differentiation was confirmed by their specific knockdown using ribozymes and siRNA. Besides demonstrating a simple and an effective method of isolation of gene functions involved in muscle differentiation, we report for the first time that overexpression of Fem, a member of the sex-determining family of proteins, caused accelerated myotube formation, and its targeting deferred myoblast differentiation. This functional gene screening is not only helpful in understanding the molecular pathways of muscle differentiation but also to design molecular strategies for myopathologic therapies.
Preparation of Liposomes Surface-Loaded with Cationic Manganese Porphyrins as SOD Mimics (2005)

A water-soluble cationic 5,10,15,20-tetrakis(N-methylpyridinium-4- yl)porphinatomanganese(III) ion (MnT4MPyP) and water-insoluble 5,10,15,20-tetrakis(N-3-furyl)porphinatomanganese(III) ion (MnT3FuP) were prepared and ion-complexed with an anionic phospholipid membrane to enhance the circulation persistence of the porphyrin complexes in vivo. Fluorescence spectra and fluorescence depolarization experiments indicated MnT3FuP to be situated within the hydrophobic interior of the vesicle composed of the phospholipid membrane, while MnT4MPyP was anchored to the membrane by lipophilic tails with the metalloporphyrin head-group located on the interface between the membrance and aqueous solvent. SOD activity was determined by stopped-flow analysis and cytochrome c assay, which allowed the determination of IC50 and kcat values for the reaction of the metalloporphyrins with superoxide anion radical (O2-·). Sodium stearate-linked MnT4MPyP was the most effective catalyst as an SOD mimic to decompose O2-· at a second-order rate constant of 1.9×107 M-1s-1 in dimyristoylphosphatidylcholine (DMPC) liposomes. SOD activity of MnT3FuP was less than that of MnT4MPyP.
Wireless link shaping for service guarantees (2002)

Providing quality of service (QoS) guarantees on heterogeneous networks with both wireless and wireline networks involves accounting for the statistical fluctuations on wireless channels, in addition to the traffic fluctuations of interest in a purely wireline setting. We develop a detailed framework for QoS provisioning for delay constrained (real time) applications over a Rayleigh faded wireless downlink. Forward error correction (FEC) coding based link layer error recovery with interleaving is used for link shaping (i.e., for converting a link with high symbol error rates and correlations of symbol errors into a link with almost wireline characteristics). Tradeoffs between choice of code rate and interleaving depth, and the buffering used at the wireless-wireline interface, are examined. In addition to considering static bandwidth sharing as in conventional time division multiplexed (TDM) systems, we provide two mechanisms for statistical multiplexing that lead to significant capacity gains.
Suppression of spurious modes for performance enhancement of hybrid planar∕NRD-guide integrated circuits (2003)

A technique for suppressing spurious modes is presented with experimental and analysis results. It is simple and very effective in rejecting spurious modes for performance enhancement of hybrid planar/NRD-guide integrated circuits. As a practical example, a millimetre–wave planar/NRD-guide filter is designed to evaluate features of the proposed technique, which yields good results. It is found through preliminary analysis and experiments that the rejection of all spurious modes (including TE and LSE modes) can be better than −35 dB for a single microstrip-to-NRD-guide transition over the broadband frequency range of interest, and performance can be further enhanced using optimised design procedures. This new technique provides an alternative solution to the inherent problem of spurious modes occurring (especially TE modes) in the standard NRD-guide circuit design.
Liquid Oil That Flows in Spaces of Aqueous Foam without Defoaming (2014)

A very interesting phenomenon has been observed in which foam formed from an aqueous fatty acid potassium salt solution spontaneously absorbs liquid oil immediately upon contact without defoaming. Although this phenomenon initially appeared to be based on capillary action, it was clarified that the liquid oil that flows in foam film did not wet the air/water interface. In this study, it is discussed why aqueous foam can spontaneously soak up liquid oil without defoaming using equilibrium surface tension, dynamic oil/water interfacial tension, and image analysis techniques. The penetration of oil was attributed both to the dynamic decrease in the surface tension at the oil/water interface and to Laplace pressure, depending on the curvature of the plateau border. Therefore, the foam does not absorb the oil, but the oil spontaneously penetrates the foam. This interesting behavior can be expected to be applied to aqueous detergents for liquid oil removal.
Long Cycle Stability of Conversion Metal Fluoride Cathodes in Polymer Electrolytes (2020)

The development of Li-ion batteries (LIBs) has been slowed down to a mere 1-2% per year. The skyrocketing price of Co (&gt;30 $USD kg -1 ) and Ni (&gt;15 $USD kg -1 ), their limited resources, and accompanying to that low energy density of intercalation-chemistry batteries make it difficult the pack cost to fall to $90-100 kWh -1 or even below. The improvements in LIB energy density (&gt; 1.0 kWh/L) at a reduced cost (&lt;$50-70 kWh -1 ) can be sought from conversion metal fluoride cathodes (FeF 2(3) , CuF 2 or MF x ), which exhibit 2-3 times higher energy density (in Si-/Li-anodes based cells) and low cost (6-9 USD cents for Fe and 6-7 $USD fro Cu per kg, respectively). To streamline these battery chemistries, intrinsically poor ionic conductivity of MF x , substantial volume (up to 30%) and morphological changes during cycling, active material dissolution, substantial resistance buildup, and irreversible growth of the cathode electrolyte interphase (CEI) need to be minimized. By utilizing strong and tough ionically conducting polymer electrolyte matrix and elevated temperature cycling conditions (50 °C), we demonstrated formation of thin conformal CEI, substantial mechanical resilience, decreased internal resistance, reducing of active material dissolution, and overall improvement in performance of FeF 2 to 300 cycles at ~400 mAh g -1 . Figure 1
Telomerase repeat addition processivity is increased at critically short telomeres in a Tel1-dependent manner in Saccharomyces cerevisiae (2007)

Telomerase is the ribonucleoprotein enzyme that elongates telomeres to counteract telomere shortening. The core enzyme consists of a reverse transcriptase protein subunit and an RNA subunit. The RNA subunit contains a short region that is used as a template by the reverse transcriptase to add short, tandem, G-rich repeats to the 3' ends of telomeres. By coexpressing two RNA subunits that differ in the telomeric repeat sequence specified and examining the telomere extensions after one cell cycle, we determined that Saccharomyces cerevisiae telomerase can dissociate and reassociate from a given telomere during one cell cycle. We also confirmed that telomerase is nonprocessive in terms of telomeric repeat addition. However, repeat addition processivity is significantly increased at extremely short telomeres, a process that is dependent on the ATM-ortholog Tel1. We propose that this enhancement of telomerase processivity at short telomeres serves to rapidly elongate critically short telomeres.
Characterization of LDL and VLDL Binding Sites on Human Basophils and Mast Cells (1995)

Recent data suggest that basophils and mast cells play a potential role in the processing and accumulation of plasma lipoproteins. This study investigated the interactions of 111In-low-density lipoprotein (LDL), 111In-acetyl-LDL, and 111In-very-low-density lipoprotein (VLDL) with purified primary human blood basophils, immortalized human basophils (KU812 cell line), and a human mast cell line, HMC-1. Binding sites for 111In-LDL resolved into curvilinear Scatchard plots indicating two classes of specific binding sites on primary basophils (Bmax1, 7404 sites/cell; Kd1, 1.9 nmol/L; Bmax2, 39,611 sites/cell; Kd2, 29 nmol/L), on KU812 cells (Bmax1, 8290 +/- 2690 sites/cell; Kd1, 2.4 +/- 0.6 nmol/L; Bmax2, 46,470 sites/cell; Kd2, 33.4 +/- 7.8 nmol/L), and on HMC-1 cells (Bmax1, 7840 +/- 360 sites/cell; Kd1, 1.8 +/- 0.8 nmol/L; Bmax2, 61,450 +/- 9900 sites/cell; Kd2, 28.4 +/- 9.4 nmol/L). On KU812 cells, binding of 111In-LDL was displaced by apolipoprotein (apo)-E-rich high-density lipoprotein (HDL) (IC50, 14 +/- 6 nmol/L), LDL (IC50, 29 +/- 11 nmol/L), VLDL (IC50, 55 +/- 21 nmol/L), HDL2 (IC50, 420 +/- 140 nmol/L), and heparin (IC50, 67 +/- 28 nmol/L), whereas no competition was produced by HDL, HDL3, or acetyl-LDL (IC50, > 1 mumol/L). Western blot analysis using the monoclonal antibody C7 confirmed the presence of the LDL receptor on human basophils and HMC-1 cells. 111In-acetyl-LDL binding sites (scavenger receptor) could be detected neither on human basophils nor on HMC-1 cells. 111In-VLDL bound to a single class of high-affinity binding sites on primary basophils (Bmax, 4320 sites/cell; Kd, 10 nmol/L), KU812 cells (Bmax, 4020 +/- 840 sites/cell; Kd, 8 +/- 3 nmol/L), and HMC-1 cells (Bmax, 6143 +/- 1866 sites/cell; Kd, 4 +/- 2 nmol/L). 111In-VLDL binding was displaced by VLDL > LDL > apoE-rich HDL but not by heparin (IC50 > 1 mmol/L). In the presence of prostaglandin E1, the number of 111In-LDL receptors increased by 150% (P < .05) in the high-affinity range and by 170% (P < .01) in the low-affinity range, whereas the number of 111In-VLDL binding sites remained unchanged. VLDL, LDL, HDL, and the subclasses HDL2 and HDL3 inhibited immunological histamine release by primary normal basophils (n = 3) and mast cells (n = 3). Our results provide evidence for the existence of LDL and VLDL binding sites on human basophils and HMC-1 mast cells. The exact biological and pathophysiological roles of these sites remain to be elucidated.
WriteShield: A Pseudo Thin Client for Prevention of Information Leakage (2012)

While thin-client systems are diffusing as an effective security method in enterprises and organizations, there is a new approach called pseudo thin-client system. In this system, local disks of clients are write-protected and user data is forced to save on the central file server to realize the same security effect of conventional thin-client systems. Since it takes purely the software-based simple approach, it does not require the hardware enhancement of network and servers to reduce the installation cost. However there are several problems such as no write control to external media, memory depletion possibility, and lower security because of the exceptional write permission to the system processes. In this paper, we propose WriteShield, a pseudo thin-client system which solves these issues. In this system, the local disks are write-protected with volume filter driver and it has a virtual cache mechanism to extend the memory cache size for the write protection. This paper presents design and implementation details of WriteShield. Besides we describe the security analysis and simulation evaluation of paging algorithms for virtual cache mechanism and measure the disk I/O performance to verify its feasibility in the actual environment.
Enhancement of mouse immune system by pyrrolomycin B. (1984)

Pyrrolomycin B enhanced both humoral immune response and delayed-hypersensitivity against sheep red blood cells in mice. In spleen cell culture it was a weak inhibitor of mitogenesis. However, in combination with concanavalin A, there was stimulation of mitogenesis in spleen cell culture. Pyrrolomycin B also enhanced phagocytosis of yeasts by peritoneal macrophages after in vivo administration to mice. Thus, pyrrolomycin B, formerly isolated as an antibiotic agent, is an immunopotentiator possibly acting on the membrane of lymphocytes or macrophages.
Plate Fixation of Fractures of the Proximal Ulna (2000)

Hand and Upper Limb Centre Division of Orthopaedic Surgery University of Western Ontario London, Ontario, Canada Address correspondence and reprint requests to Dr. Graham King, Hand and Upper Limb Centre, 268 Grosvenor St., London, Ontario N6A 4L6, Canada.
Hybrid Electro-Optic Resonator for Image Classification (1995)

Optical resonators are a powerful tool for object classification. Using a volume hologram to store and simultaneously probe thousands of reference images, they can take an input image and find the best matched reference object from a vast stored library. Developments in this field are proceeding rapidly in numerous laboratories 1-3 . These research efforts are confined, however, to all-optical resonator systems which suffer from the speed and gain limitations of photorefractives, and from the lack of shift invariance of the inner-product function performed when the input image is used to read a volume hologram.
Heterozygous loss of function of IQSEC2/Iqsec2 leads to increased activated Arf6 and severe neurocognitive seizure phenotype in females (2019)

Clinical presentations of mutations in the <i>IQSEC2</i> gene on the X-chromosome initially implicated to cause non-syndromic intellectual disability (ID) in males have expanded to include early onset seizures in males as well as in females. The molecular pathogenesis is not well understood, nor the mechanisms driving disease expression in heterozygous females. Using a CRISPR/Cas9-edited <i>Iqsec2</i> KO mouse model, we confirm the loss of <i>Iqsec2</i> mRNA expression and lack of Iqsec2 protein within the brain of both founder and progeny mice. Both male (52%) and female (46%) <i>Iqsec2</i> KO mice present with frequent and recurrent seizures. Focusing on <i>Iqsec2</i> KO heterozygous female mice, we demonstrate increased hyperactivity, altered anxiety and fear responses, decreased social interactions, delayed learning capacity and decreased memory retention/novel recognition, recapitulating psychiatric issues, autistic-like features, and cognitive deficits present in female patients with loss-of-function <i>IQSEC2</i> variants. Despite Iqsec2 normally acting to activate Arf6 substrate, we demonstrate that mice modelling the loss of Iqsec2 function present with increased levels of activated Arf6. We contend that loss of Iqsec2 function leads to altered regulation of activated Arf6-mediated responses to synaptic signalling and immature synaptic networks. We highlight the importance of IQSEC2 function for females by reporting a novel nonsense variant c.566C > A, p.(S189*) in an elderly female patient with profound intellectual disability, generalised seizures, and behavioural disturbances. Our human and mouse data reaffirm <i>IQSEC2</i> as another disease gene with an unexpected X-chromosome heterozygous female phenotype. Our Iqsec2 mouse model recapitulates the phenotypes observed in human patients despite the differences in the IQSEC2/Iqsec2 gene X-chromosome inactivation between the species.
Production of Andean-Patagonic edible mushroom Grifola gargal on wood-based substrates (2015)

Grifola gargal is an edible mushroom with a characteristic almond flavor, and is found naturally in only limited areas of southern Argentina and Chile. The fruit body formations of G. gargal on wood-based substrates composed of a mixture of various hardwoods (mainly Quercus serrata) and/or Crytomeria japonica (sugi) were investigated. All 13 strains of G. gargal formed fruit bodies in the mixed hardwood medium, but the colors and morphological features of the fruit bodies were different for each strain. Of the strains tested, the strains GG010, GG006 and GG004 were suitable for commercial cultivation in mixed hardwood medium judging from their yield, biological efficiency (BE), cultivation period, color and mushroom shape. The fruit bodies of G. gargal (GG010) were formed even when sugi was added to the mixed hardwood medium (hardwood:sugi, 4:1 v/v). These results show that the Andean-Patagonic edible mushroom G. gargal can be produced at a reasonable cost in Japan using several strains and the commercially available mixed hardwood used for Lentinula edodes cultivation.
A simple microbiological assay for the stereospecific differentiation of ? and ? isomers of arteether (2000)

A new rapid bioassay has been developed which can precisely differentiate between stereospecific alpha and beta isomers of the antimalarial drug arteether. This method was developed through the disc diffusion bioactivity tests wherein semisynthetically produced alpha arteether was able to inhibit the growth of E. coli strains which are defective in DNA gyrase enzyme. The wild type E. coli with intact DNA gyrase did not show this sensitivity to alpha arteether. The beta isomer of arteether was, however, ineffective against both the mutant and wild type strains. Direct experimental proof of gyrase involvement was obtained through mobilization of gyr genes by transformation of E. coli gyr- mutant strains with wild type gyrA clone pMK90 (carried on the thermo-inducible lambda Col E1 vector). This resulted in alpha arteether resistant and nalidixic acid sensitive phenotype clearly demonstrating the use of gyrA mutant strains in differentiating alpha and beta isomers of arteether by this simple bioassay.
Detection of murine immunoglobulin in human tissues following therapeutic infusion of monoclonal antibody. (1986)

A class switch variant of hybridoma CO19-9 secreting IgG2a antibodies was shown to have the same immunoperoxidase binding pattern in human tissue as the IgG1 antibody secreted by the parental hybridoma. The IP tissue binding of GA73.3 and 17-1A monoclonal antibodies which have been suggested to bind to structurally related antigens were compared; although quite similar in distribution, some differences were noted. GA73.3 bound to 12/12 colon carcinomas compared to 17-1A which reacted with 11/12 tumors. In several cases, the percentage of cells reactive with GA73.3 (90-100%) exceeded those reactive with 17-1A (10-25%). Additionally, the intensity of reactivity for GA73.3 was consistently greater than that seen with 17-1A. The detection of murine antibody bound to human tissues following therapeutic infusion of 19-9 IgG2a or GA73.3 differed. Detection of antibody-antigen complexes was seen less often in patients who had received 19-9 IgG2a (2/6) than in patients who had received GA73.3 (5/5). Additionally, the presence of murine immunoglobulin was seen only in the extracellular mucin of the patients receiving 19-9 IgG2a, whereas strong cellular binding of murine immunoglobulin was noted following infusion with GA73.3.
MONOAMINE OXIDASE INHIBITORS ISOLATED FROM FERMENTED BROTHS (1973)

Cultured broths were screened by measuring the inhibition of monoamine oxidase. Using serotonin as the substrate, two active agents were isolated from Actinomycetes and shown to be pimprinine and trans-cinnamic acid amide, and a compound isolated from a mushroom was identified to be harman. Using benzylamine as the substrate, an inhibitor was isolated from a Streptomyces and shown to be phenethylamine.
A Micromachined High-Q Microstrip Line with a Broadband Microstrip-to-CPW Transistion (2009)

A high-Q micromachined microstrip line with its corresponding broadband microstrip-to-CPW transition is presented. The micromachined suspended-ground microstrip line is fabricated monolithically to eliminate the usage of multiple substrates and more complicated processes including wafer bonding and thru-substrate vias. Furthermore, via-less connections between the signal line and ground plane of the microstrip can be easily implemented. The fabricated 1-mm long suspended ground microstrip line with back-to-back transition shows an excellent RF performance with insertion loss of less than 0.36 dB and reflection below -18 dB over a broad bandwidth from dc to 30 GHz.
The in vitro antibody response to cell surface antigens. I. The xenogeneic response to human leukemia cells. (1977)

An in vitro spleen fragment culture system has been developed for the production and analysis of xenogeneic antibody responses to cell surface antigens. Depending on the methods of immunization and in vitro stimulation employed, mouse spleen fragments can produce antibody of both IgG and IgM classes directed against human cell surface antigens for more than 30 days in culture. A saturation binding analysis of the antibody products indicates that their range of specificities was more restricted than that of serum antibody. Approximately 5% of the in vitro antibody products raised against a homogeneous population of human leukemia cells could distinguish between the antigens present on the leukemia cells and those present on normal human lymphocytes. Methods previously employed to influence the range of serum antibodies expressed against complex immunogens, such as suppression of certain responses by passive administration of antibody at the time of immunization, were tested in the in vitro spleen culture system and resulted in successful modulation of the antibody response patterns observed.