gebhart/patrepeval huggingface dataset:
Proteomic analysis of the <i>Escherichia coli</i> outer membrane (2000)

Outer membrane proteins (OMPs) of Gram-negative bacteria are key molecules that interface the cell with the environment. Traditional biochemical and genetic approaches have yielded a wealth of knowledge relating to the function of OMPs. Nonetheless, with the completion of the Escherichia coli genome sequencing project there is the opportunity to further expand our understanding of the organization, expression and function of the OMPs in this Gram-negative bacterium. In this report we describe a proteomic approach which provides a platform for parallel analysis of OMPs. We propose a rapid method for isolation of bacterial OMPs using carbonate incubation, purification and protein array by two-dimensional electrophoresis, followed by protein identification using mass spectrometry. Applying this method to examine E. coli K-12 cells grown in minimal media we identified 21 out of 26 (80%) of the predicted integral OMPs that are annotated in SWISS-PROT release 37 and predicted to separate within the range of pH 4-7 and molecular mass 10-80 kDa. Five outer membrane lipoproteins were also identified and only minor contamination by nonmembrane proteins was observed. Importantly, this research readily demonstrates that integral OMPs, commonly missing from 2D gel maps, are amenable to separation by two-dimensional electrophoresis. Two of the identified OMPs (YbiL, YeaF) were previously known only from their ORFs, and their identification confirms the cognate genes are transcribed and translated. Furthermore, we show that like the E. coli iron receptors FhuE and FhuA, the expression of YbiL is markedly increased by iron limitation, suggesting a putative role for this protein in iron transport. In an additional demonstration we show the value of parallel protein analysis to document changes in E. coli OMP expression as influenced by culture temperature.
Abstract 1221: Targeting interferon-λ1 with a stabilized dimer of anti-tumor Fab . (2013)

Abstract Background: The type-III interferons (IFNs), comprising IFN-λ1, IFN-λ2, and IFN-λ3, are functionally similar to the type-I IFN-α in eliciting anti-viral, anti-tumor, and immune-modulating activities. Due to its more restricted cellular targets, IFN-λ is being considered as a potential alternative to existing therapeutic regimens based on IFN-α, whose adverse effects in patients limit its use. The development of antibody-targeted IFN-λ may further improve its safety, potency and pharmacokinetics. Methods: We generated three DOC-AND-LOCKTM (DNLTM) complexes, designated (E1)-λ1, (15)-λ1, and (C2)-λ1, by conjugating IFN-λ1 site-specifically to a stabilized dimer of humanized Fab derived from hRS7 (anti-Trop-2), hMN-15 (anti-CEACAM6), and hL243 (anti-HLA-DR), respectively, which were affinity-purified and evaluated in human malignant cell lines of cervix (ME-180), colon (HT-29), esophagus (TE-11, T.Tn), lung (SK-MES-1, A549), liver (HepG2, Huh-7), and skin (A375). Results: As determined by flow cytometry, Trop-2 was highly expressed on the surface of ME-180, TE-11, and T.Tn; moderately on SK-MES-1 and HT-29; and negligibly on HepG2, Huh-7, A549, and A375. In comparison, CEACAM6 was undetectable on SK-MES-1 and A375, but positive on the remaining 7 cell lines, yet at a considerably lower level than Trop-2. Targeting of these immunocytokines to antigen-expressing cells markedly increased the amount of IFN-λ1 localized at the cell surface, as demonstrated by (E1)-λ1 on ME-180 (Trop-2+), (15)-λ1 on HepG2 (CEACAM6+), and (C2)-λ1 on A375 (HLA-DR+), respectively. In MTS assays, (E1)-λ1 inhibited the in vitro proliferation of ME-180, SK-MES-1, and TE-11, with EC50 &lt;1 pM, which was 1,000-fold more potent than commercial IFN-λ1. Likewise, the anti-proliferation activity of (15)-λ1 was enhanced ∼100-fold in ME-180 and TE-11, but not in CEACAM6-negative SK-MES-1. The observed potency was further substantiated by enhanced cell signaling, including STAT phosphorylation and MHC-I up-regulation induced by (15)-λ1 in HepG2 cells. In the Pk study, (E1)-λ1 showed a mean residence time of 12 h with a T1/2 of 8.6 h, and clearance of 2.2 ml/h in mouse serum, which is comparable to PEG-IFN-λ1. Conclusions: These promising results, attributable to increased localization and stronger binding to antibody-targeted cells, warrant further exploration of these novel immunocytokines as potential cancer therapeutics. Citation Format: Donglin Liu, Edmund A. Rossi, Thomas M. Cardillo, David M. Goldenberg, Chien-Hsing Chang. Targeting interferon-λ1 with a stabilized dimer of anti-tumor Fab . [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1221. doi:10.1158/1538-7445.AM2013-1221
Three-Dimensional Effective Elastic Constants for Thick Laminates (1988)

Equivalent homogeneous anisotropic solids are used to represent thick laminates con sisting of large numbers of a repeating sublaminate. The typical sublaminate is used for studying its load-deformation behavior from which the effective elastic constants are derived from the constituent lamina properties. Explicit expressions for effective elastic constants for general thick laminates are presented. Reduced expressions are also derived for balanced laminates containing a single composite system. Numerical examples are in cluded.
High-Throughput Study of the Effects of Celastrol on Activated Fibroblast-Like Synoviocytes from Patients with Rheumatoid Arthritis (2017)

Celastrol, a natural triterpene, exhibits potential anti-inflammatory activity in a variety of inflammatory diseases. The present study aimed to investigate its biological effect on activated fibroblast-like synoviocytes (FLSs) from patients with rheumatoid arthritis (RA). The primary FLSs of the synovial tissues were obtained from synovial biopsies of patients with RA. The normal human FLS line (HFLS) was used as a control. After the RA-FLSs and HFLSs were treated with or without celastrol, various approaches, including the WST-1 assay, transwell assay, real-time PCR and ELISA analysis, were performed to estimate proliferation, invasion and expression of pro-inflammatory cytokines of the RA-FLSs. Microarray analysis was performed to screen for differentially expressed genes in RA-FLSs before and after celastrol treatment. The results showed that treatment of celastrol attenuated both the proliferation and invasion of the RA-FLSs. The expression of several chemokine genes, including <i>CCL2</i> , <i>CXCL10</i> , <i>CXCL12</i> , <i>CCR2</i> and <i>CXCR4</i> , was significantly changed after celastrol treatment. The genes involved in the NF-κB signaling pathway appeared to be regulated by celastrol.
Crystallization of Dense Binary Hard-Sphere Mixtures with Marginal Size Ratio (2008)

Molecular dynamics simulations are performed for binary hard-sphere mixtures with a size ratio of gamma =0.9 and a volume fraction of phi=0.58 over a range of compositions. We show how, at this high volume fraction, crystallization depends sensitively on the composition. Evidence is presented that crystallization in these mixtures does not proceed by the standard nucleation and growth paradigm. Rather, some crystallite forms almost immediately and then an interplay between compositional fluctuations and crystal growth is able to dramatically extend the time scale on which further crystallization occurs. This can be seen as a form of geometric frustration.
Densification of Alumina and Silica in the Presence of a Liquid Phase (1981)

Alumina and silica powders were sintered at 1250° to 1460°C in the presence of liquid phases containing CaO, A1 2 O 3 , and SiO 2 . The data were analyzed using the equation D = K log t +C and the Arrhenius equation. The activation energy for sintering decreases with increasing amounts of liquid phase.
Carbon Nanotube Transistor Fabrication Assisted by Topographical and Conductive Atomic Force Microscopy (2006)

In this work, fully functional carbon nanotube field-effect transistors (CNT-FETs) have been fabricated using a simple and inexpensive process including in-situ chemical vapor deposition (CVD) growth of the nanotubes. The temperature used is 900 °C and the catalyst layer is nickel on aluminum. Simultaneously, the catalyst metal areas are used as source/drain electrodes. The CNT-FET fabrication is compatible with conventional complementary metal oxide semiconductor (CMOS) technology. For process optimization, every major process step is controlled by atomic force microscopy (AFM). The nondestructive AFM technique provides both a complete overview of the structures as well as the detailed geometrical properties of the nanotubes. We have also fabricated CNT-FET test structures in which the source/drain electrodes have a direct conductive path to the substrate, in order to perform electrical measurements at the nanoscale by conductive AFM (C-AFM). In this way, we obtain current images of the structures and the electrical characteristics of each individual nanotube can be measured.
A Single Pathway Targets Several Health Challenges of the Elderly (2014)

New avenues to modulate the autophagy-lysosomal route of protein clearance have the potential to help treat several disease states to which the elderly are particularly vulnerable. Two recent papers identified distinct ways to tap into the lysosomal degradation pathway of autophagy to reduce age-related protein accumulation events. Shoji-Kawata et al. (Nature 2013;494:201-206) describe a new autophagy-inducing peptide, Tat-Beclin 1, that enhances the clearance of polyglutamine aggregates related to Huntington's disease and, interestingly, suppresses viral and bacterial infections. Savolainen et al. (Neurobiol Dis 2014;68:1-15) describe a prolyl oligopeptidase inhibitor that reduces α-synuclein species related to Parkinson's disease and other α-synucleinopathies, and this inhibitor caused a concomitant increase in autophagic activation markers. Previous studies have also linked the autophagy-lysosomal pathway to the protective clearing of the Aβ peptides of Alzheimer's disease and tau species of tauopathies. Enhancing autophagy-lysosomal efficiency may provide a therapeutic avenue for diverse types of proteinopathies, including the most common neurodegenerative disorders of the elderly.
Revised record/playback interface systems for GA-HDTV, HD-VCR and D3 VTR (1996)

This paper describes the revised versions of the three recording/playback interface systems from the previous ones. Modifications were required to meet the current HDTV transport data formats which were significantly changed in accordance with the Grand Alliance (GA) specification. The interface is also modified to accept both 8 VSB and 16 VSB modes. It has three types of interface application: the first interface is for the GA-HDTV transmitter to D3 digital VTR, the second is for the GA-HDTV receiver to HD-VCR and the third is for the HD-VCR to D3 VTR. The interface hardware was fully developed and used for the GA-HDTV systems laboratory testing in April, 1995 at ATTC and field testing in Charlotte, North Carolina.
Rare-earth-doped fibre lasers and amplifiers (1988)

Rare-earth doped single-mode fibre lasers and amplifiers will form the basis of all-fibre optical circuits. Recent advances in the field and some possible applications will be described.
Rational design of a conformation‐switchable Ca<sup>2+</sup>‐ and Tb<sup>3+</sup>‐binding protein without the use of multiple coupled metal‐binding sites (2008)

Ca2+, as a messenger of signal transduction, regulates numerous target molecules via Ca2+-induced conformational changes. Investigation into the determinants for Ca2+-induced conformational change is often impeded by cooperativity between multiple metal-binding sites or protein oligomerization in naturally occurring proteins. To dissect the relative contributions of key determinants for Ca2+-dependent conformational changes, we report the design of a single-site Ca2+-binding protein (CD2.trigger) created by altering charged residues at an electrostatically sensitive location on the surface of the host protein rat Cluster of Differentiation 2 (CD2).CD2.trigger binds to Tb3+ and Ca2+ with dissociation constants of 0.3 +/- 0.1 and 90 +/- 25 microM, respectively. This protein is largely unfolded in the absence of metal ions at physiological pH, but Tb3+ or Ca2+ binding results in folding of the native-like conformation. Neutralization of the charged coordination residues, either by mutation or protonation, similarly induces folding of the protein. The control of a major conformational change by a single Ca2+ ion, achieved on a protein designed without reliance on sequence similarity to known Ca2+-dependent proteins and coupled metal-binding sites, represents an important step in the design of trigger proteins.
Detecting Moving Objects using a Single Camera on a Mobile Robot in an Outdoor Environment (2004)

Robust detection of moving objects from a mobile robot is required for safe outdoor navigation, but is not easily achievable since there are two motions involved: the motions of moving objects and the motion of the sensors used to detect the objects. We have experimented with a probabilistic approach for moving object detection from a mobile robot using a single camera in outdoor environments. The ego-motion of the camera is compensated using corresponding feature sets and outlier detection, and the positions of moving objects are estimated using an adaptive particle lter and EM al- gorithm. The algorithms are implemented and tested on three different robot platforms (robotic helicopter, Segway RMP, and Pioneer2 AT) in an outdoor environment, and the detection results are analyzed.
CXXXIII.—The chlorination of anilides. Part IV. The significance of velocity measurements in relation to the problem of benzene substitution (1928)

A. E. Bradfield and B. Jones, J. Chem. Soc., 1928, 1006 DOI: 10.1039/JR9280001006
Influence of Prior Structured Treatment Interruptions on the Length of Time without Antiretroviral Treatment in Chronically HIV-Infected Subjects (2004)

The influence of previous structured treatment interruptions (STIs) on the length of time off therapy when highly active antiretroviral treatment (HAART) is discontinued in chronically HIV-infected subjects was assessed. A comparative, retrospective clinical cohort study included patients with plasma viral load (VL) <50 copies/ml and CD4 cell count >500 cells/mm(3) who interrupted HAART. Fifteen patients interrupted HAART after six 2-weeks-off-/4-weeks-on therapy cycles (STI group) and 30 subjects discontinued HAART without previous STIs (NSTI group). The criteria for treatment resumption were development of AIDS-defining clinical events, VL >100,000 copies/ml or CD4 <350 cells/mm(3). Median (IQR) time off therapy was 48 (29-56) weeks in the STI group and 31 (8-77) weeks in the NSTI group (p < 0.15). After 48 weeks, 46% of the patients in the STI group and 40% in the NSTI group remained off HAART (p < 0.74). No patient developed AIDS-defining events and all but one achieved virological control after treatment resumption. The CD4 nadir was 341 (298-464) cells/mm(3) among patients who reinitiated HAART and 560 (364-682) cells/mm(3) in those who remained off therapy by week 48 (p <0.01). Likewise, CD4 count prior to treatment interruption was 902 (806-1040) cells/mm(3) and 1123 (924-1234) cells/mm(3) in subjects resuming and remaining off HAART, respectively (p = 0.03). No relationship between treatment resumption and pre-ART VL or with the time with undetectable VL before enrollment was found. CD4 nadir was a significant predictor for treatment reinitiation in a multivariate analysis. Previous STIs do not influence time off therapy when HAART is definitively discontinued in chronically HIV-infected subjects. CD4 nadir is an important factor in the treatment discontinuation decision.
Protocols for Nationally Coordinated Laboratory and Field Research on Manure Nitrogen Mineralization (2005)

Abstract The National Program structure of USDA‐ARS provides an opportunity to coordinate research on problems of national and global significance. A team of USDA‐ARS scientists is conducting nationally coordinated research to develop predictions of manure N availability to protect water quality and improve farm solvency. Experimental design and research protocols were developed and used in common across all participating locations. Laboratory incubations are conducted at each location with a minimum of three soils, three temperatures, two wetting/drying regimes, and two manure treatments. A soil from the central United States (Catlin silt loam, fine‐silty, mixed, superactive, mesic Oxyaquic Argiudoll) is used as an internal reference across all locations. Incubation data are compiled across locations to develop generalized predictions of manure nitrogen mineralization (Nmin). Field validation data are then obtained by monitoring nitrogen (N) transformations in manure‐amended soil cores equipped with anion exchange resin to capture leached nitrate. This field data will be used to compare laboratory‐based predictions with field observations of Nmin in each soil, climatic zone, and manure type represented. A Decision Support System will then be developed for predicting manure N mineralization across ranges in soil, climate, and manure composition. Protocols used by this research team are provided to 1) document the procedures used and 2) offer others detailed information for conducting research on nutrient transformation processes involving collaboration across locations or complementary research between laboratory and field environments.
An Acidic Polysaccharide Having Activity on the Reticuloendothelial System from the Root of Astragalus mongholicus. (1991)

An acidic polysaccharide, designated as AMon-S, was isolated from the roots of Astragalus mongholicus BUNGE. It was homogeneous on electrophoresis and gel chromatography, and its molecular mass was estimated to be 7.6 x 10(4). It showed significant reticuloendothelial system-potentiating activity in a carbon clearance test. It is composed of L-arabinose: D-galactose: D-galacturonic acid: D-glucuronic acid in the molar ratio of 18:18:1:1, in addition to small amounts of O-acetyl groups and peptide moiety. A part of the hexuronic acid residues exist as the methyl esters. Methylation analysis, carbon-13 nuclear magnetic resonance and periodate oxidation studies enabled elucidation of its structural features and revealed mainly alpha-arabino-beta-3,6-galactan type structural units.
Broadband wireless technology employment in Canada (2002)

Summary form only given, as follows. Canada has been aggressive in allocating frequency bands throughout the spectrum, from 2.5 GHz to 40 GHz, for the provision of terrestrial, wireless, broadband broadcasting and telecommunications services for both urban and rural applications-to compete with the conventional telephone, cable television and satellite infrastructures. This article overviews the technology and applications associated with a portfolio of some eight different bands allocated for various services, presenting the relative performance and economics of the spectrum alternatives and underlining the technical constraints associated with the higher frequency alternatives. The focus on provision of broadband services, employment of compression techniques for video transmission is outlined-with service capacities compared between the low and high frequency ends of the spectrum. Particular attention is focused on the new Local Multipoint Communications Service alternatives, with the equipment development and economic challenges associated with LMCS being presented.
Generalized electron emission model for field, thermal, and photoemission (2002)

Analysis of electron emission from photocathodes, field emitters under extreme fields, or thermionic emitters operated at reduced temperature, utilize thermionic (Richardson) or field emission (Fowler–Nordheim) approximations which become inaccurate for such atypical conditions. The computational overhead of advanced numerical transport models make them ill-suited for data analysis or simulations of extended areas of photocathode and thermionic emitters, or for nonplanar field emitters. In this letter, an analytic thermal-field emission equation is given for which the Fowler–Nordheim and Richardson–Laue–Dushman equations are asymptotic limits. The methodology can analytically address “warm” field and “cool” thermionic emission, photoemission, and electron transport between interfaces (e.g., Schottky barriers). The approximations developed are compared to an exact evaluation (the modified airy function approach).
A mouse model of anemia of inflammation: complex pathogenesis with partial dependence on hepcidin (2013)

Anemia is a common complication of infections and inflammatory diseases, but the few mouse models of this condition are not well characterized. We analyzed in detail the pathogenesis of anemia induced by an injection of heat-killed Brucella abortus and examined the contribution of hepcidin by comparing wild-type (WT) to iron-depleted hepcidin-1 knockout (Hamp-KO) mice. B abortus-treated WT mice developed severe anemia with a hemoglobin nadir at 14 days and partial recovery by 28 days. After an early increase in inflammatory markers and hepcidin, WT mice manifested hypoferremia, despite iron accumulation in the liver. Erythropoiesis was suppressed between days 1 and 7, and erythrocyte destruction was increased as evidenced by schistocytes on blood smears and shortened red blood cell lifespan. Erythropoietic recovery began after 14 days but was iron restricted. In B abortus-treated Hamp-KO compared with WT mice, anemia was milder, not iron restricted, and had a faster recovery. Similarly to severe human anemia of inflammation, the B abortus model shows multifactorial pathogenesis of inflammatory anemia including iron restriction from increased hepcidin, transient suppression of erythropoiesis, and shortened erythrocyte lifespan. Ablation of hepcidin relieves iron restriction and improves the anemia.
Autocrine VEGF-VEGF-R loop on podocytes during glomerulonephritis in humans (2010)

This study shows, for the first time, increased podocytic VEGF-VEGF-R binding during human GN, suggesting not only the existence of a glomerular paracrine proangiogenic, but also an autocrine role of the VEGF-VEGF-R system in diseased podocytes.
Charge loss after /sup 60/Co irradiation of flash arrays (2004)

Flash memories are the most important among modern nonvolatile memory technologies. We are showing new results on the threshold voltage shifts in Flash memory arrays after /sup 60/Co irradiation. A (relatively) high total dose, exceeding 100 krad (SiO/sub 2/), is needed to induce errors in the array, but threshold voltage shifts are all but negligible even at lower doses. These shifts can be accurately described by using a model which considers the charges generated by irradiation in all the oxides surrounding the floating gate. We are also showing that cycling (endurance) and total ionizing dose effects mutually add.
Multifrequency waveguide orthomode transducer (2005)

This paper presents the design and development of a multifrequency probe-coupled orthomode transducer (OMT) using a circular waveguide as the primary waveguide and a rectangular waveguide as the secondary waveguide. Design is presented for a common OMT operating at 6.6, 10.65, 18, and 21 GHz using four cascaded circular waveguide sections with different cross-sectional dimensions. An innovative design technique is used to minimize the inter-port coupling and to maximize the power in the dominant mode to get the required radiation performance at all the frequency bands using a common radiating aperture. The simulated and measured parameters of the OMT and the horn fed by this OMT have been presented.