gebhart/patrepeval huggingface dataset:
Capacity of MIMO systems with closely spaced antennas (2003)

Wide-band radio channel measurements at 5.2 GHz with four transmit and four receive antennas at variable element spacing are reported, aiming to evaluate the potential of compact antenna arrays at mobile terminals. We show that, for an element spacing d<0.5/spl middot//spl lambda/ (down to 0.2/spl middot//spl lambda/), the link capacity is not smaller than that for much larger d. This is explained by the observation that mutual coupling changes the radiation patterns of closely spaced antenna elements, individually. Compact multi-antenna terminals may thus become practical.
Mechanisms of cellular communication through intercellular protein transfer (2010)

In a multicellular system, cellular communication is a must for orchestration and coordination of cellular events. Advent of the latest analytical and imaging tools has allowed us to enhance our understanding of the intercellular communication. An intercellular exchange of proteins or intact membrane patches is a ubiquitous phenomenon, and has been the subject of renewed interest, particularly in the context of immune cells. Recent evidence implicates that intercellular protein transfers, including trogocytosis is an important mechanism of the immune system to modulate immune responses and transferred proteins can also contribute to pathology. It has been demonstrated that intercellular protein transfer can be through the internalization/pathway, dissociation-associated pathway, uptake of exosomes and membrane nanotube formations. Exchange of membrane molecules/antigens between immune cells has been observed for a long time, but the mechanisms and functional consequences of these transfers remain unclear. In this review, we will discuss the important findings concerning intercellular protein transfers, possible mechanisms and highlight their physiological relevance to the immune system, with special reference to T cells such as the stimulatory or suppressive immune responses derived from T cells with acquired dendritic cell membrane molecules.
Suppression of Retinal Neovascularization by Erythropoietin siRNA in a Mouse Model of Proliferative Retinopathy (2009)

Inhibiting EPO mRNA expression with siRNA is effective in suppressing retinal neovascularization, suggesting EPO siRNA is a potentially useful pharmaceutical intervention for treating proliferative retinopathy.
Effects of SH2 and SH3 deletions on the functional activities of wild-type and transforming variants of c-Src. (1992)

The amino-termina, noncatalytic half of Src contains two domains, designated the Src homology 2 (SH2) and Src homology 3 (SH3) domains, that are highly conserved among members of the Src family of tyrosine kinases. The SH2 domain (which can be further divided into the B and C homology boxes) and the SH3 domain (also referred to as the A box) are also found in several proteins otherwise unrelated to protein tyrosine kinases. It is believed that these domains are important for directing specific protein-protein interactions necessary for the proper functioning of Src. To determine the importance of the SH2 and SH3 domains in regulating the functions of c-Src, we evaluated mutants of c-Src lacking the A box (residues 88 to 137), the B box (residues 148 to 187) or the C box (residues 220 to 231). Each of these deletions caused a 14- to 30-fold increase in the in vitro level of kinase activity of c-Src. Chicken embryo fibroblasts expressing the deletion mutants displayed a transformed cell morphology, formed colonies in soft agar, and contained elevated levels of cellular phosphotyrosine-containing proteins. Src substrates p36, p85, p120, p125, the GTPase-activating protein (GAP), and several GAP-associated proteins were phosphorylated on tyrosine in cells expressing the A, B, or C box deletion mutant. p110 was highly phosphorylated in cells expressing the C box mutant, was weakly phosphorylated in cells expressing the B box mutant, and was not phosphorylated in cells expressing the A box mutant. Expression of the mutant proteins caused a reorganization of the actin cytoskeleton similar to that seen in v-Src-transformed cells. In addition, deletion of the A, B, or C box did not diminish the transforming or enzymatic activity of an activated variant of c-Src, E378G. These data indicate that deletion of the A, B, or C homology box causes an activation of the catalytic and transforming potential of c-Src and that while these mutations caused subtle differences in substrate phosphorylation, the homology boxes are not required for many of the phenotypic changes associated with transformation by Src.
Presentation of Exogenous Protein Antigens on Major Histocompatability Complex Class I Molecules by Dendritic Cells: Pathway of Presentation and Regulation by Cytokines (1997)

Several recent studies have shown that dendritic cells (DC) pulsed with soluble proteins can present peptide epitopes derived from these exogenous antigens on major histocompatability complex (MHC) class I molecules and induce an antigen-specific cytotoxic T lymphocyte (CTL) response. We provide evidence here that DC use macropinocytosis to capture soluble antigens that are then presented on MHC class I molecules. The presentation of an epitope derived from soluble ovalbumin was transporter associated with antigen presentation (TAP)-dependent, brefeldin A-sensitive, blocked by inhibitors of proteasomes, and resistant to chloroquine. These data suggest that exogenous antigens access the cytosol of DC and are proccessed for presentation via the same pathway described for conventional MHC class I-restricted cytosolic antigens. Proinflammatory mediators such as tumor necrosis factor-α (TNF-α) and lipopolysaccharide (LPS) reduced the efficiency of ovalbumin presentation via this pathway. This reduced presentation was not due to impaired expression of class I molecules because these substances upregulated the cell surface expression of Kb-molecules comparable to levels induced by interferon-γ (IFN-γ) treatment. The addition of IFN-γ increased ovalbumin presentation even in the presence of TNF-α or LPS. These results show that DC might be involved in the cross-priming phenomenon. This could offer the immune system an additional pathway for effective priming of cytotoxic T cells and provide the possibility to activate both CD4 and CD8 T-cell responses.
The Breadth of Cross Sub-Type Neutralisation Activity of a Single Domain Antibody to Influenza Hemagglutinin Can Be Increased by Antibody Valency (2014)

The response to the 2009 A(H1N1) influenza pandemic has highlighted the need for additional strategies for intervention which preclude the prior availability of the influenza strain. Here, 18 single domain VHH antibodies against the 2009 A(H1N1) hemagglutinin (HA) have been isolated from a immune alpaca phage displayed library. These antibodies have been grouped as having either (i) non-neutralising, (ii) H1N1 restricted neutralising or (iii) broad cross-subtype neutralising activity. The ability to neutralise different viral subtypes, including highly pathogenic avian influenza (H5N1), correlated with the absence of hemagglutination inhibition activity, loss of binding to HA at acid pH and the absence of binding to the head domain containing the receptor binding site. This data supports their binding to epitopes in the HA stem region and a mechanism of action other than blocking viral attachment to cell surface receptors. After conversion of cross-neutralising antibodies R1a-B6 and R1a-A5 into a bivalent format, no significant enhancement in neutralisation activity was seen against A(H1N1) and A(H5N1) viruses. However, bivalent R1a-B6 showed an 18 fold enhancement in potency against A(H9N2) virus and, surprisingly, gained the ability to neutralise an A(H2N2) virus. This demonstrates that cross-neutralising antibodies, which make lower affinity interactions with the membrane proximal stem region of more divergent HA sub-types, can be optimised by bivalency so increasing their breadth of anti-viral activity. The broad neutralising activity and favourable characteristics, such as high stability, simple engineering into bivalent molecules and low cost production make these single domain antibodies attractive candidates for diagnostics and immunotherapy of pandemic influenza.
The epitope space of the human proteome (2008)

In the post-genome era, there is a great need for protein-specific affinity reagents to explore the human proteome. Antibodies are suitable as reagents, but generation of antibodies with low cross-reactivity to other human proteins requires careful selection of antigens. Here we show the results from a proteome-wide effort to map linear epitopes based on uniqueness relative to the entire human proteome. The analysis was based on a sliding window sequence similarity search using short windows (8, 10, and 12 amino acid residues). A comparison of exact string matching (Hamming distance) and a heuristic method (BLAST) was performed, showing that the heuristic method combined with a grid strategy allows for whole proteome analysis with high accuracy and feasible run times. The analysis shows that it is possible to find unique antigens for a majority of the human proteins, with relatively strict rules involving low sequence identity of the possible linear epitopes. The implications for human antibody-based proteomics efforts are discussed.
Tolerability and efficacy of the first-in-class anti-CD47 antibody magrolimab combined with azacitidine in frontline TP53m AML patients: Phase 1b results. (2022)

7020 Background: Magrolimab is a monoclonal antibody blocking CD47, a “don’t eat me” signal overexpressed on cancer cells such as acute myeloid leukemia (AML). This blockade induces phagocytosis of tumor cells and is synergistic with azacitidine (AZA) via upregulation of “eat me” signals. We report data from a Phase 1b trial of magrolimab+AZA in frontline TP53-mutant ( TP53m) AML. Methods: Patients (pts) with frontline AML not suitable for intensive chemotherapy received IV magrolimab starting with a priming dose (1 mg/kg) followed by ramp-up to 30 mg/kg QW or Q2W as maintenance dose. AZA 75 mg/m 2 was given IV or SC on Days 1–7 of each 28-day cycle. Primary endpoints were safety/tolerability and complete remission (CR) rate by ELN 2017 criteria. Results: 72 TP53m AML pts were treated (Table). Common all-grade TEAEs were constipation (52.8%), diarrhea (47.2%), febrile neutropenia (45.8%), nausea (43.1%), fatigue (37.5%), decreased appetite (37.5%), thrombocytopenia (31.9%), peripheral edema (30.6%), and cough (30.6%). Most common Grade 3+ TEAEs were febrile neutropenia (37.5%), anemia (29.2%; Grade 3, 26.4%; Grade 4, 2.8%), thrombocytopenia (29.2%), pneumonia (26.4%), and neutropenia (20.8%). Objective response rate (ORR) by intent-to-treat was 48.6% (33.3% CR, 8.3% CR with incomplete hematologic recovery [CRi] / CR with partial hematologic recovery [CRh], 1.4% morphologic leukemia-free state [MLFS], 5.6% partial response). Stable disease was reported in 16.7%, progressive disease (PD) in 5.6%. 30- and 60-day mortalities were 8.3% and 18.1%, respectively. Response assessment was unavailable in 4.2% who discontinued due to AEs and 6.9% due to other, prior to the C3D1 assessment. Median time to CR/CRi was 2.2 months (mos; range 1.7–7.2) and to CR was 3.0 mos (range 1.8–9.6). 45.2% (14/31) of evaluable CR/CRi/CRh/MLFS pts achieved negative MRD by flow cytometry (investigator reported). Of 24 CR patients, 8 had a longitudinal TP53 VAF assessment, and 5/8 (63%) had VAF decreased to ≤5%. Treatment was stopped due to SCT in 9 pts (12.5%), PD 26 (36.1%), death 8 (11.1%), AE 13 (18.1%), and other 14 (19.4%). Median durations of CR and CR/CRi were 7.7 mos (95% CI: 4.7, 10.9) and 8.7 mos (95% CI: 5.3, 10.9), respectively. Median overall survival (OS) for the 72 pts was 10.8 mos (95% CI: 6.8, 12.8) with median follow up 8.3 mos. Conclusions: In high-risk frontline TP53m AML pts unsuitable for intensive chemotherapy, magrolimab+AZA showed durable responses and encouraging OS in a single-arm study. A Phase 3 trial in TP53m AML (ENHANCE-2; NCT04778397) of this combination vs standard of care is ongoing. Clinical trial information: NCT03248479. [Table: see text]
In Vitro ATP Regeneration from Polyphosphate and AMP by Polyphosphate:AMP Phosphotransferase and Adenylate Kinase from Acinetobacter johnsonii 210A (2000)

In vitro enzyme-based ATP regeneration systems are important for improving yields of ATP-dependent enzymatic reactions for preparative organic synthesis and biocatalysis. Several enzymatic ATP regeneration systems have been described but have some disadvantages. We report here on the use of polyphosphate:AMP phosphotransferase (PPT) from Acinetobacter johnsonii strain 210A in an ATP regeneration system based on the use of polyphosphate (polyP) and AMP as substrates. We have examined the substrate specificity of PPT and demonstrated ATP regeneration from AMP and polyP using firefly luciferase and hexokinase as model ATP-requiring enzymes. PPT catalyzes the reaction polyP(n) + AMP --> ADP + polyP(n-1). The ADP can be converted to ATP by adenylate kinase (AdK). Substrate specificity with nucleoside and 2'-deoxynucleoside monophosphates was examined using partially purified PPT by measuring the formation of nucleoside diphosphates with high-pressure liquid chromatography. AMP and 2'-dAMP were efficiently phosphorylated to ADP and 2'-dADP, respectively. GMP, UMP, CMP, and IMP were not converted to the corresponding diphosphates at significant rates. Sufficient AdK and PPT activity in A. johnsonii 210A cell extract allowed demonstration of polyP-dependent ATP regeneration using a firefly luciferase-based ATP assay. Bioluminescence from the luciferase reaction, which normally decays very rapidly, was sustained in the presence of A. johnsonii 210A cell extract, MgCl(2), polyP(n=35), and AMP. Similar reaction mixtures containing strain 210A cell extract or partially purified PPT, polyP, AMP, glucose, and hexokinase formed glucose 6-phosphate. The results indicate that PPT from A. johnsonii is specific for AMP and 2'-dAMP and catalyzes a key reaction in the cell-free regeneration of ATP from AMP and polyP. The PPT/AdK system provides an alternative to existing enzymatic ATP regeneration systems in which phosphoenolpyruvate and acetylphosphate serve as phosphoryl donors and has the advantage that AMP and polyP are stabile, inexpensive substrates.
Prevalence of <I>Ehrlichia chaffeensis</I> (Rickettsiales: Rickettsiaceae) in <I>Amblyomma americanum</I> (Acari: Ixodidae) from the Georgia Coast and Barrier Islands (2000)

Human monocytic ehrlichiosis is an emerging zoonosis caused by infection with Ehrlichia chaffeensis Anderson, Dawson, Jones & Wilson, which is transmitted to mammals by ixodid ticks. Prevalence of infected ticks and distribution of infection foci indicate relative risk of human exposure to ehrlichiosis and may be influenced by factors such as geographic isolation, human disturbance, and the availability of suitable mammalian reservoir hosts. To test, this, individual and pooled lone star ticks, Amblyomma americanum (L.), were collected from three populations from the Georgia coast (1 mainland site and two barrier islands) and screened for E. chaffeensis. A species-specific, nested polymerase chain reaction (PCR) assay was used to amplify a 572 bp fragment of the E. chaffeensis 16S rRNA gene from infected ticks. PCR product specificity was confirmed by nucleotide sequencing. Our results showed the prevalence of infected ticks to be 0.0% (n = 151), 0.9% (n = 111), and 9.3% (n = 129) for Sapelo Island, St. Catherine's Island, and Fort McAllister, respectively.
Lipid and Temperature Dependence of Membrane-Bound ATPase Activity of Acholeplasma laidlawii (1974)

Arrhenius plots (15–45 °C) of the ATPase activity of Acholeplasma laidlawii membranes enriched with either arachidoyl or saturated short-chain groups exhibited a pronounced discontinuity in slope around 25–30 °C, absent in oleoyl-enriched membranes. The membrane lipid fluidity was measured with a stearic acid spin label. At the growth temperature (37 °C) the membrane lipid fluidity was identical for all three kinds of enriched membranes. For membranes enriched with saturated acyl chains, a plot of the electron paramagnetic resonance anisotropy parameter 2T 11 vs. the reciprocal of temperature showed a biphasic profile with a discontinuity in slope around 25–30 °C. For oleoyl-group enriched membranes this plot yields only a straight line between 15 and 50 °C. Thus, lipids do play a role in the functioning of the membrane-bound ATPase. This enzyme is probably localized in the more fluid regions of the membrane.
Data Management for XML: Research Directions (1999)

This paper is a July 1999 snapshot of a &amp;quot;whitepaper&amp;quot; that I&amp;apos;ve been working on. The purpose of the whitepaper, which I initially drafted in April 1999, was to formulate and put into prose my thoughts on the research opportunities XML brings to the general area of data management. It is important to know that this paper is not a survey. It offers my personal opinions and thoughts on Data Management for XML, fully incorporating my biases and ignorances. Related work is not discussed, and references are not provided with the exception of a handful of URLs. Furthermore, I expect the whitepaper to evolve over time; please see [1] for the latest version. 1 The XML Revolution XML---the eXtensible Markup Language---has recently emerged as a new standard for data representation and exchange on the Internet [2]. The basic ideas underlying XML are very simple: tags on data elements identify the meaning of the data, rather than, e.g., specifying how the data should be formatted (as in HTML), and ...
Inhibition of tRNA Aminoacylation by 2‘-O-Methyl Oligonucleotides (1996)

A 2'-O-methyl oligonucleotide complementary to 18 nucleotides in the dihydrouridine stemloop of Escherichia coli tRNA(Cys) has been shown to stably bind to the tRNA. The binding inhibits aminoacylation of the tRNA by cysteine tRNA synthetase. The same oligonucleotide sequence but with the DNA deoxy backbone does not bind to the tRNA. This provides the basis for the design and test of a series of 2'-O-methyl oligonucleotides for their ability to bind to E. coli tRNA(Cys) and inhibit aminoacylation. We show here that different regions of the tRNA have different sensitivities to oligonucleotides. A 10-mer that targets G15 forms a stable complex with the tRNA. The Kd of the complex is several orders of magnitude lower than that of the tRNA-synthetase complex. Measurements of dissociation rate constants indicate that the stronger affinity of the 10-mer to tRNA(Cys) is due to a significantly slower rate of dissociation (by a factor of 10(6)) than that of the synthetase from the tRNA. Only a stoichiometric amount of the 10-mer is necessary to completely inhibit aminoacylation. Because tRNA aminoacylation is fundamental to cell growth, these results provide the rationale for the 10-mer and its derivatives as pharmaceutical agents that target specific cell growth.
Inverse Opals of Molecularly Imprinted Hydrogels for the Detection of Bisphenol A and pH Sensing (2011)

Inverse opal films of molecularly imprinted polymers (MIP) were elaborated using the colloidal crystal template method. The colloidal crystals of silica particles were built by the Langmuir-Blodgett technique, allowing a perfect control of the film thickness. Polymerization in the interspaces of the colloidal crystal in the presence of bisphenol A (BPA) and removal of the used template provides 3D-ordered macroporous methacrylic acid-based hydrogel films in which nanocavities derived from bisphenol A are distributed within the thin walls of the inverse opal hydrogel. The equilibrium swelling properties of the nonimprinted (NIPs) and molecularly imprinted polymers (MIPs) were studied as a function of pH and bisphenol A concentration, while the molecular structures of the bulk hydrogels were analyzed using a cross-linked network structure theory. This study showed an increase in nanopore (mesh) size in the MIPs after BPA extraction as compared to NIPs, in agreement with the presence of nanocavities left by the molecular imprints of the template molecule. The resulting inverse opals were found to display large responses to external stimuli (pH or BPA) with Bragg diffraction peak shifts depending upon the hydrogel film thickness. The film thickness was therefore shown to be a critical parameter for improving the sensing capacities of inverse opal hydrogel films deposited on a substrate.
Behavior of reaction mixtures under microwave conditions: use of sodium salts in microwave-induced N-[18F]fluoroalkylations of aporphine and tetralin derivatives (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTBehavior of reaction mixtures under microwave conditions: use of sodium salts in microwave-induced N-[18F]fluoroalkylations of aporphine and tetralin derivativesS. Zijlstra, T. J. De Groot, L. P. Kok, G. M. Visser, and W. VaalburgCite this: J. Org. Chem. 1993, 58, 7, 1643–1645Publication Date (Print):March 1, 1993Publication History Published online1 May 2002Published inissue 1 March 1993https://pubs.acs.org/doi/10.1021/jo00059a002https://doi.org/10.1021/jo00059a002research-articleACS PublicationsRequest reuse permissionsArticle Views131Altmetric-Citations32LEARN 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
Multifunctional metal-polymer nanoagglomerates from single-pass aerosol self-assembly (2016)

In this study, gold (Au)-iron (Fe) nanoagglomerates were capped by a polymer mixture (PM) consisting of poly(lactide-co-glycolic acid), protamine sulfate, and poly-l-lysine via floating self-assembly in a single-pass aerosol configuration as multibiofunctional nanoplatforms. The Au-Fe nanoagglomerates were directly injected into PM droplets (PM dissolved in dichloromethane) in a collison atomizer and subsequently heat-treated to liberate the solvent from the droplets, resulting in the formation of PM-capped Au-Fe nanoagglomerates. Measured in vitro, the cytotoxicities of the nanoagglomerates (>98.5% cell viability) showed no significant differences compared with PM particles alone (>98.8%), thus implying that the nanoagglomerates are suitable for further testing of biofunctionalities. Measurements of gene delivery performance revealed that the incorporation of the Au-Fe nanoagglomerates enhanced the gene delivery performance (3.2 × 10(6) RLU mg(-1)) of the PM particles alone (2.1 × 10(6) RLU mg(-1)), which may have been caused by the PM structural change from a spherical to a hairy structure (i.e., the change followed the agglomerated backbone). Combining the X-ray-absorbing ability of Au and the magnetic property of Fe led to magnetic resonance (MR)-computed tomography (CT) contrast ability in a phantom; and the signal intensities [which reached 64 s(-1) T2-relaxation in MR and 194 Hounsfield units (HUs) in CT at 6.0 mg mL(-1)] depended on particle concentration (0.5-6.0 mg mL(-1)).