gebhart/patrepeval huggingface dataset:
Enzymic cleavage of a CD4 immunoadhesin generates crystallizable, biologically active Fd-like fragments (1990)

CD4, the cell-surface receptor for the human immunodeficiency virus (HIV), is a member of the immunoglobulin (Ig) gene superfamily. It contains four extracellular sequences homologous to Ig VL domains. The first of these (V1) is sufficient for binding to HIV; however, the structural basis for this binding has yet to be elucidated. While several models for the structure of Ig-like domains in CD4 have been proposed on the basis of crystal structures of Ig VL domains, direct evidence that CD4 and VL domains fold similarly has not been obtained. To produce individual domains of CD4 for structural studies, we used molecular fusions of such domains with Ig heavy chain (CD4 immunoadhesins), which are very efficiently expressed and secreted in mammalian cells and can be easily isolated in single-step purification with protein A. Since these fusion molecules are antibody-like homodimeric proteins, we investigated the possibility that they might be cleaved enzymatically to produce Fd-like and Fc fragments. We found that cleavage with papain releases an Fd-like fragment containing the V1 and V2 CD4 domains; this fragment fully retains the ability to bind to the HIV-1 envelope glycoprotein gp120 and to block HIV infection in vitro. Moreover, folding of the CD4 domains in the Fd-like fragment and in the parent immunoadhesin is indistinguishable, as indicated by circular dichroism. Spectral analysis of the Fd-like fragment suggests that secondary structure content is identical with that predicted from the known structure of Ig VL domains; this directly supports the hypothesis that the V1 and V2 domains of CD4 fold similarly to Ig VL domains.(ABSTRACT TRUNCATED AT 250 WORDS)
IFN-gamma-inducing factor up-regulates Fas ligand-mediated cytotoxic activity of murine natural killer cell clones (1996)

NK cells, non-T non-B immune effector lymphocytes, are localized in many organs, including liver, as well as in the circulation. To investigate the regulatory mechanism of killing apparatus in hepatic NK cells, we established IL-2-dependent NK cell clones from liver lymphocytes of BALB/c nude mice. To generate the NK cell clones, we incubated liver lymphocytes with a high dose of IL-2 in the presence of irradiated Kupffer cells, as feeder cells and as the source of IL-12, originally identified as NK cell stimulatory factor. Unless liver lymphocytes were incubated with both IL-2 and Kupffer cells, no cell growth was observed. Hepatic NK cell clones were established from this cell line by limiting dilution. The surface phenotypes of cloned NK cells were IL-2R beta-chain+ CD16+ CD3- IgM-. The clones did not express NK2.1, which is expressed by a half of NK-enriched spleen cells of BALB/c mice. Although the cells contained dense granules reactive to mAb against perforin, they exerted no conventional cytolytic activity against YAC-1. They constitutively expressed Fas ligand (FasL) and specifically killed Fas-positive target cells by fragmenting DNA. This Fas-FasL-mediated killing activity was enhanced by IFN-gamma-inducing factor, a recently identified novel cytokine produced by activated Kupffer cells, but was not affected by other Kupffer cell-produced cytokines, such as IL-12, IL-1beta, and TNF-alpha. Taken together, these findings suggest that hepatic NK cells participate in the immune response as effector cells through the Fas-FasL system in collaboration with cytokines from Kupffer cells.
Interfacial synthesis of luminescent 7 kDa silver clusters (2009)

We report the synthesis of luminescent Ag clusters through the interfacial etching of mercaptosuccinic acid (MSA) protected silver nanoparticles, Ag@MSA, with guanine at the water-toluene interface. The clusters exhibiting well-defined absorption emit in the near-infrared (NIR) region. Crude clusters were separated using polyacrylamide gel electrophoresis (PAGE). The cluster solid, prepared by freeze drying, is highly hygroscopic. Biomolecular markers were used to identify the approximate mass of the cluster which was found to be 7 kDa, as mass spectrometry did not reveal specific signatures. The clusters were investigated using UV-Vis spectroscopy, transmission electron microscopy (TEM), energy dispersive analysis of X-rays (EDAX), X-ray photoelectron spectroscopy (XPS), infrared spectroscopy (IR), and fluorescence spectroscopy. Elemental analysis and IR studies reveal the protection of the cluster by two types of ligands, namely MSA and guanine. Fluorescence of the cluster is highly temperature dependent, with an increase in intensity with decrease in temperature. Influence of different ratios of reactants, etching capacity of different nucleobases and effect of temperature on the synthesis as well as possible single-phase etching were investigated. Sensitivity of the cluster to certain metal ions has been monitored using fluorescence spectroscopy.
NMPdb: Database of Nuclear Matrix Proteins (2004)

The nuclear matrix (NM) is a structure resulting from the aggregation of proteins and RNA in the nucleus of eukaryotic cells; it is the 'sticky bit' that remains after aggressive DNAse digestion and salt extraction protocols. Owing to the important role of the NM in DNA replication, DNA transcription and RNA splicing, the expression pattern of NM proteins has become an important early indicator for numerous cancers/tumors. Recent descriptions of the NM structure distinguish between a network-like 'internal nuclear matrix' (INM) and a 'nuclear shell' that connects the INM to the inner and outer nuclear membranes. A cautious NM preparation protocol reveals a coat of proteins on top of the INM; these proteins are usually referred to as the 'nuclear matrix-associated proteins'. Here, we describe a new database (NMPdb at http://www.rostlab.org/db/NMPdb/) that currently contains details of 398 NM proteins. We collected these data through a semi-automated analysis of over 3000 scientific articles in PubMed. We could match these 398 proteins to 302 protein sequences in UniProt or GenBank. Our NMPdb repository annotates these links along with the following annotations: organism, cell type, PubMed identifier, sequence-based predictions of structural and functional features and for some entries the explicit sequence segment that is responsible for localization (nuclear matrix targeting signal).
Joint and actuator design for enhanced stability in robotic force control (1990)

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Aeronautics and Astronautics, 1990.
Dose-Response Relationship of Oral Insulin Spray in Healthy Subjects (2005)

Oral insulin was absorbed in direct relation to the amount given and had a faster onset and a shorter duration of action compared with subcutaneous regular insulin. A dose-response relationship in the absorption and metabolic effect of the oral insulin was noted.
Developing protective textile materials as barriers to liquid penetration using melt‐electrospinning (2006)

Abstract Electrospun polypropylene fiber webs and laminates were developed using melt‐electrospinning, to explore an alternative way of manufacturing protective clothing materials for agricultural workers. Electrospun polypropylene webs were fabricated in two levels of thickness. To examine the effect of lamination on the protection/thermal comfort properties, the webs were laminated on nonwoven fabric substrates. Barrier performance was evaluated for the electrospun webs and laminates, using two pesticide mixtures that represent a range of surface tension and viscosity. Effects of web thickness and lamination on air permeability and water vapor transmission were assessed as indications of thermal comfort performance. Penetration testing shows that electrospun polypropylene webs provide excellent barrier performance against the high surface tension challenge liquid, whereas the laminated fabrics of electrospun polypropylene webs exhibited performance of 90–100% for challenge liquids with varying surface tension. Air permeability of electrospun polypropylene webs decreased by ∼20% because of the lamination and web thickness, but was still higher than most of the materials currently in use for protective clothing. Water vapor transmission of electrospun polypropylene webs reduced by up to 12% from the lamination and web thickness as well, but was still in a range comparable to woven work clothing fabrics. © 2006 Wiley Periodicals, Inc. J Appl Polym Sci 102: 3430–3437, 2006
Crossflow microfiltration of animal cells (1991)

Laminar shear is the primary mechanism of cell damage, limiting flow rate (and hence flux) in crossflow microfiltration of animal cells. Sensitivity to hydrodynamic and interfacial stress is reduced by the addition of 0.1% Pluronic polyol. A critical average wall shear rate of 3000 s(-1) (above which damage occurs) is found for several cell types, including mammalian and insect cells. Hydrodynamic stress also limits the maximum tip speed in a rotary lobe pump to less than 350 cm/s. Turbulent flow in the recirculation loop piping at Reynolds numbers of up to 71,000 does not cause cell damage. Maximum sustainable flux decreases with cell concentration and increases with cell size (in qualitative agreement with the hydrodynamic lift model). A flux of 30 to 75 L/m(2) h (depending on cell size) can be sustained during 20-fold concentration from 2.5 x 10(6) cells/ml, while maintaining high cell viability.
Overproduction of Rb Protein after the G 1 /S Boundary Causes G 2 Arrest (1993)

The Rb protein is known to exert its activity at decision points in the G1 phase of the cell cycle. To investigate whether it may also play some role(s) at later points in the cell cycle, we used a system of rapid inducible gene amplification to conditionally overexpress Rb protein during G2 phase. A cell line expressing a temperature-sensitive simian virus 40 large T antigen (T-Ag) was stably transfected with plasmids containing the Rb cDNA linked to the simian virus 40 origin of replication: pRB-wt, pRB-fs, and pRB-Dra, carrying wild-type murine Rb cDNA, a frameshift mutation close to the beginning of the Rb coding region, and a single-amino-acid deletion in the E1A/T-Ag binding pocket, respectively. Numerous independent cell lines were isolated at the nonpermissive temperature; cell lines displaying a high level of episomal amplification of an intact Rb expression cassette following shiftdown to the permissive temperature were chosen for further analysis. Plasmid pRB-fs did not express detectable Rb antigen, while pRB-Dra expressed full-length Rb protein. The Dra mutation has previously been shown to abrogate phosphorylation as well as T-Ag binding. Fluorescence-activated cell sorting (FACS) analysis revealed that cultures induced to overexpress either wild-type or Dra mutant Rb proteins were significantly enriched for cells with a G2 DNA content. Cultures that amplified pRB-fs or rearranged pRB-wt and did not express Rb protein had normal cell cycle profiles. Double-label FACS analysis showed that cells overexpressing Rb or Rb-Dra proteins were uniformly accumulating in G2, whereas cells expressing endogenous levels of Rb were found throughout the cell cycle. These results indicate that Rb protein is interacting with some component(s) of the cell cycle-regulatory machinery during G2 phase.
Affecting Protein Charge State Distributions in Nano-Electrospray Ionization via In-Spray Solution Mixing Using Theta Capillaries (2014)

Borosilicate theta glass capillaries pulled to serve as nanoelectrospray ionization emitters are used for short time-scale mixing of protein and acid solutions during the electrospray process to alter protein charge state distributions (CSDs) without modifying the sample solution. The extent of protein CSD shifting/denaturing can be tailored by acid identity and concentration. The observed CSD(s) are protein dependent, and the short mixing time-scale enables the study of short-lived unfolding intermediates and higher charge states of noncovalent protein complexes, including those of holomyoglobin. Additionally, the theta tips provide a simple and inexpensive method for mixing nonvolatile reagents such as supercharging agents, which cannot be used with previously developed vapor leak-in techniques, with protein solutions during the electrospray process.
Safety of iron polymaltose given as a total dose iron infusion (2006)

An audit of the in-hospital safety and tolerability of 401 infusions of iron polymaltose in 386 patients has shown no cases of anaphylaxis or other cardiorespiratory compromise. The infusion was terminated prematurely because of adverse events in six patients (1.6%). No adverse events occurred within the first 15 min of the infusion. Premedication (in 24%) was not associated with fewer adverse events. Fear of anaphylaxis should not inhibit the use of total dose iron infusion and the practices of premedication and of medical supervision during the first 15 min of the infusion should be abandoned.
Mechanisms of drug-induced lupus. II. T cells overexpressing lymphocyte function-associated antigen 1 become autoreactive and cause a lupuslike disease in syngeneic mice. (1996)

Current theories propose that systemic lupus erythematosus develops when genetically predisposed individuals are exposed to certain environmental agents, although how these agents trigger lupus is uncertain. Some of these agents, such as procainamide, hydralazine, and UV-light inhibit T cell DNA methylation, increase lymphocyte function-associated antigen 1 (LFA-1) (CD11a/CD18) expression, and induce autoreactivity in vitro, and adoptive transfer of T cells that are made autoreactive by this mechanism causes a lupuslike disease. The mechanism by which these cells cause autoimmunity is unknown. In this report, we present evidence that LFA-1 overexpression is sufficient to induce autoimmunity. LFA-1 overexpression was induced on cloned murine Th2 cells by transfection, resulting in autoreactivity. Adoptive transfer of the transfected, autoreactive cells into syngeneic recipients caused a lupuslike disease with anti-DNA antibodies, an immune complex glomerulonephritis and pulmonary alveolitis, similar to that caused by cells treated with procainamide. These results indicate that agents or events which modify T cell DNA methylation may induce autoimmunity by causing T cell LFA-1 overexpression. Since T cells from patients with active lupus have hypomethylated DNA and overexpressed LFA-1, this mechanism could be important in the development of human autoimmunity.
Design of a SOI memory cell (1997)

In this paper a quantitative analysis has been used for describing and discussing design characterizations of an SOI flash memory cell. Mathematical expressions for the front gate threshold voltage of the SOI memory cell are derived using the equations for a standard SOI MOSFET. Coupling coefficients which exist between the control gate and source and drain regions, are the same as for the silicon body, through stored charge at the floating gate has to be included in these equations and the mathematical expressions for the flash memory cell can be obtained. Implementing this, the voltage of the front gate of a standard SOI MOSFET is equal to the voltage of the floating gate of the memory cell. During analysis, the emphasis is put on the case where the back channel is depleted, because then coupling between the front and back gate can control the threshold voltage of the control gate.
Studies on Antidiabetic Agents. X. Synthesis and Biological Activities of Pioglitazone and Related Compounds. (1991)

Various analogues of a new antidiabetic agent, pioglitazone (AD-4833, U-72107), were synthesized in order to study in more detail the structure-activity relationships of this class of drug. 5-(4-Pyridylalkylthiobenzyl)-2,4-thiazolidinediones (I), thia-analogues of pioglitazone, were prepared via Meerwein arylation of the alkylthioanilines (IV). 5-(4-Pyridylalkoxybenzylidene)-2,4-thiazolidinediones (IIa) and related heterocyclic analogues (IIb) were synthesized by Knoevenagel condensation of the aldehydes (VIII) with the corresponding azolidinones. Compounds I and II were evaluated for hypoglycemic and hypolipidemic activity in genetically obese and diabetic yellow KK (KKAy) mice. Several 5-[4-[2-(2-pyridyl)ethoxy]-benzylidene]-2,4- thiazolidinediones (IIa) were equipotent to pioglitazone. However, the thia-analogues (I) and the benzylideneheterocycles (IIb) had decreased activity. Catalytic hydrogenation of the 5-benzylidene analogue (14) was found to be a convenient new synthetic method for pioglitazone. The configuration of 14 is also discussed.
Acoustic Purification of Extracellular Microvesicles (2015)

Microvesicles (MVs) are an increasingly important source for biomarker discovery and clinical diagnostics. The small size of MVs and their presence in complex biological environment, however, pose technical challenges in sample preparation, particularly when sample volumes are small. We herein present an acoustic nanofilter system that size-specifically separates MVs in a continuous and contact-free manner. The separation uses ultrasound standing waves to exert differential acoustic force on MVs according to their size and density. By optimizing the design of the ultrasound transducers and underlying electronics, we were able to achieve a high separation yield and resolution. The "filter size-cutoff" can be controlled electronically in situ, which enables versatile MV-size selection. We applied the acoustic nanofilter to isolate nanoscale (<200 nm) vesicles from cell culture media as well as MVs in stored red blood cell products. With the capacity for rapid and contact-free MV isolation, the developed system could become a versatile preparatory tool for MV analyses.
Network Monitoring with Software Defined Networking: Towards OpenFlow network monitoring (2013)

Network monitoring is becoming more and more important as more Internet Service Providers and Enterprise networks deploy real-time services, like voice and video. Network operators need to have an up-to-date view of the network and to measure network performance with metrics like link usage, packet loss and delay, in order to assure the quality of service for such applications. Obtaining accurate and meaningful network statistics helps the service providers to estimate the "health" of their network, to find service degradation due to congestion and could even use them for routing optimization. Finally, a more accurate picture of the nature of the Internet traffic is important for continued research and innovation. In this thesis, Software Defined Networking is used as a unified solution to measure link utilization, packet loss and delay. Currently, there is no single solution capable to measure all the mentioned metrics, but a collection of multiple different methods. They all need separate infrastructure which needs additional installations and expenses. Furthermore, those methods are not capable to meet all the requirements for a monitoring solution, some are not accurate or granular enough, others are adding additional network load or lack scalability. Software Defined Networking is still in an early development stage. Unfortunately, obtaining network statistics is a problem that has not been discussed very much. Nevertheless, OpenFlow protocol is already gaining a lot of popularity and it could be used as a unified monitoring solution. Its built-in features are already sufficient to provide accurate measurements. This thesis explores what are the current monitoring methods with and without Software Defined Networking and how monitoring could be archived in an OpenFlow enabled topology. It proposes methods to measure link usage, packet loss and delay. In terms of link usage statistics several approaches are proposed to reduce the generated overhead. Furthermore, the thesis also suggests how to measure how packet loss in networks that use OpenFlow.
The cDNA sequence of mouse LAMP-2. Evidence for two classes of lysosomal membrane glycoproteins. (1990)

We describe the isolation and sequencing of a cDNA encoding the mouse lysosomal membrane glycoprotein mLAMP-2 and the sequence differences that distinguish this molecule from the LAMP-1 class of proteins. An oligonucleotide probe corresponding to the NH2-terminal amino acid sequence of purified mLAMP-2 was synthesized by the polymerase chain reaction and used to screen several cDNA libraries. cDNA clones with an insert of 1,700 nucleotides were identified and sequenced. The deduced amino acid sequence of mLAMP-2 comprises a signal sequence of 25 residues and a 390-amino acid polypeptide (Mr 43,017) with the following putative domains: a large intraluminal region (residues 1-354) with 17 N-linked glycosylation sites (Asn-X-Ser/Thr), a hydrophobic transmembrane-spanning region of 24 residues (355-378), and a COOH-terminal cytoplasmic tail of 12 residues (379-390). When this sequence is compared with those of other lysosomal membrane glycoproteins, it is apparent that mouse LAMP-2 and human LAMP-2 form one homology class (LAMP-2) that is separated from the LAMP-1 class of proteins. The sequence differences in these two classes provide a basis for comparing the structure of the proteins with their biochemical and biological properties.
Aziridines. XIII. Reactions of Cyclohexenimine Derivatives1 (1965)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAziridines. XIII. Reactions of Cyclohexenimine Derivatives1Paul E. Fanta and Edward N. WalshCite this: J. Org. Chem. 1965, 30, 10, 3574–3575Publication Date (Print):October 1, 1965Publication History Published online1 May 2002Published inissue 1 October 1965https://pubs.acs.org/doi/10.1021/jo01021a512https://doi.org/10.1021/jo01021a512research-articleACS PublicationsRequest reuse permissionsArticle Views108Altmetric-Citations14LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Simulation and Comparison of Various Lossless Data Compression Techniques based on Compression Ratio and Processing Delay (2013)

With increasing need to store data in lesser memory several lossless compression techniques are developed. This paper intends to provide the performance analysis of lossless compression techniques over various parameters like compression ratio, delay in processing, size of image etc. It provides the relevant data about variations in them as well as to describe the possible causes for it. It describes the basic lossless techniques as Huffman encoding, run length encoding, arithmetic encoding and Lempel-ziv-welch encoding briefly with their effectiveness under varying parameters. Considering the simulation results of grayscale image compression achieved in MATLAB software, it also focused to propose the possible reasons behind differences in comparison.