gebhart/patrepeval huggingface dataset:
Human Antibody Responses to Bacterial Antigens: Studies of a Model Conventional Antigen and a Proposed Model B Cell Superantigen (1992)

We have investigated the human antibody repertoires that bind to two different classes of bacterial antigens. Immunization with the conventional antigen, type b capsular polysaccharide of Haemophilus influenzae Hib PS, uniformly induces IgA and IgG responses dominated by clones that use heavy chains structurally related to two subsets of VH3 genes, while in a minority of subjects antibodies from the VH1 or VH4 families are co-induced. In contrast, the "alternative binding site" of Staphylococcal Protein A (SPA) represents an unconventional determinant, because; (i) SPA is bound by a large proportion of non-immune IgM, IgA and IgG F(ab')2, (ii) SPA is bound only to Fab from the VH3 family, which can be encoded by at least four different germline genes, (iii) SPA binding is independent of VL usage, (iv) by flow cytometry SPA is bound by > 15% of tonsilar B cells, but not to T cells. (v) In vitro stimulation with an SPA containing mitogen induces the preferentially production of Ig bearing a VH3 marker. Taken together, these studies characterize a VH family restricted binding interaction that is distinct from the properties associated with conventional antigens such as Hib PS. Based on these data we propose that SPA represents a prototype for a B cell superantigen.
Counterflow pipeline based dynamic instruction scheduling (2002)

This paper proposes a new dynamic instruction scheduler called the Asynchronous Fast Dispatch Stack (AFDS). This approach utilizes asynchronous design techniques to implement a dispatch stack-based dynamic instruction issue mechanism. To maintain throughput and simplify dependency computations, the AFDS architecture includes a counterflow pipeline, which is modeled after the Counterflow Pipeline Processor (CFPP) proposed by Sproull and Sutherland (1994). The AFDS counterflow pipeline, however, propagates instruction dependency and completion information, rather than results and source operands. Preliminary results indicate that the AFDS is a promising application of the CFPP architecture.
Antibacterial Nitric Oxide‐Releasing Polyester for the Coating of Blood‐Contacting Artificial Materials (2010)

The emergence of multidrug-resistant bacteria associated with blood-contacting artificial materials is a growing health problem, which demands new approaches in the field of biomaterials research. In this study, a poly(sulfhydrylated polyester) (PSPE) was synthesized by the polyesterification reaction of mercaptosuccinic acid with 3-mercapto-1,2-propanediol and blended with poly(methyl methacrylate) (PMMA) from solution, leading to solid PSPE/PMMA films, with three different PSPE : PMMMA mass ratios. These films were subsequently S-nitrosated through the immersion in acidified nitrite solution, yielding poly(nitrosated)polyester/PMMA (PNPE/PMMA) films. A polyurethane intravascular catheter coated with PNPE/PMMA was shown to release nitric oxide (NO) in phosphate buffered saline solution (pH 7.4) at 37 degrees C at rates of 4.6 nmol/cm(2)/h in the first 6 h and 0.8 nmol/cm(2)/h in the next 12 h. When used to coat the bottom of culture plates, NO released from these films exerted a potent dose- and time-dependent antimicrobial activity against Staphylococcus aureus and a multidrug-resistant Pseudomonas aeruginosa strains. This antibacterial effect of PSPE/PMMA films opens a new perspective for the coating of blood-contacting artificial materials, for avoiding their colonization with highly resistant bacteria.
Abstract 1876: Preclinical efficacy of fibroblast growth factor ligand trap HGS1036 in lung carcinoma models with genomic amplification of FGFR1 (2012)

Abstract Lung cancer is the most common cause of cancer-related death in industrialized countries. In 2010, it is estimated that cancer of the lung and bronchus will be responsible for 157,300 deaths in the US (Jermal et al. 2010). A number of recent publications have reported the genomic amplification of the fibroblast growth factor receptor 1 gene (FGFR1) in lung cancer (Weiss et al. 2010; Voortman et al. 2010). Subtype analysis indicates that approximately 22% of squamous non-small cell lung cell carcinomas (NSCLC) and 27-33% of small cell lung cancer (SCLC) have amplification of the FGFR1 gene. Amplification of the FGFR1 gene in lung cancer cell lines is associated with over-expression of the FGFR1 receptor protein and increased signaling through the FGFR1 pathway resulting in increased cell proliferation and tumorigenesis. HGS1036 (formerly FP-1039) is a soluble fusion protein consisting of the extracellular domain of human FGFR1 isoform α-IIIc linked to the Fc region of human immunoglobulin G1 (IgG1). HGS1036 acts as a ligand “trap” that sequesters multiple fibroblast growth factor (FGF) family ligands, blocking their ability to bind to and activate multiple FGF receptors. We investigated the preclinical efficacy of HGS1036 in preclinical lung cancer models with genomic FGFR1 amplification as a novel therapeutic strategy. A panel of lung cancer cell lines (n=5) were identified that displayed genomic FGFR1 amplification on chromosome 8. Two of the cell lines, DMS53 and DMS114, were derived from the tumors of patients with SCLC. The other three cell lines, NCI-H1581, NCI-H520 and NCI-H1703, were derived from the tumors of patients with NSCLC. Examination of in vitro drug sensitivity indicated that all 5 cell lines were sensitive to HGS1036. Treatment of NCI-H1581, NCI-H520, NCI-H1703, DMS53 and DMS114 cells with HGS1036 in vitro resulted in a 52%, 71%, 46%, 47% and 82% reduction in cell proliferation, respectively, as determined by CellTiterGlo. Sensitivity to HGS1036 in vitro generally correlated with FGFR1 copy number and total FGFR1 protein expression. HGS1036 treatment of mice bearing FGFR1 amplified lung cancer xenografts resulted in tumor growth inhibition in all five FGFR1-amplified models examined (p=&amp;lt;0.01). The degree of tumor growth inhibition, as assessed by area-under-the-curve analysis, varied from 31-84% depending on the FGFR1 amplified lung model examined. These experiments demonstrate that lung tumor cell lines with genomic FGFR1 amplification can be sensitive to FGF-ligand blockade by HGS1036 and provide preclinical rationale for the clinical study of HGS1036 in the treatment of lung cancer. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 1876. doi:1538-7445.AM2012-1876
Apical and basolateral transferrin receptors in polarized BeWo cells recycle through separate endosomes. (1991)

Contrary to most other epithelia, trophoblasts in the human placenta, which form the physical barrier between the fetal and the maternal blood circulation, express high numbers of transferrin receptors on their apical cell surface. This study describes the establishment of a polarized trophoblast-like cell line BeWo, which exhibit a high expression of transferrin receptors on the apex of the cells. Cultured on permeable filter supports, BeWo cells formed a polarized monolayer with microvilli on their apical cell surface. Across the monolayer a transepithelial resistance developed of approximately 600 omega.cm2 within 4 d. Depletion of Ca2+ from the medium decreased the resistance to background levels, showing its dependence on the integrity of tight junctions. Within the same period of time the secretion of proteins became polarized. In addition, the compositions of integral membrane proteins at the apical and basolateral plasma membrane domains were distinct as determined by domain-selective iodination. Similar to placental trophoblasts, binding of 125I-labeled transferrin to BeWo monolayers revealed that the transferrin receptor was expressed at both plasma membrane domains. Apical and basolateral transferrin receptors were found in a 1:2 surface ratio and exhibited identical dissociation constants and molecular weights. After uptake, transferrin recycled predominantly to the domain of administration, indicating separate recycling pathways from the apical and basolateral domain. This was confirmed by using diaminobenzidine cytochemistry, a technique by which colocalization of endocytosed 125I-labeled and HRP-conjugated transferrin can be monitored. No mixing of the two types of ligands was observed, when both ligands were simultaneously internalized for 10 or 60 min from opposite domains, demonstrating that BeWo cells possess separate populations of apical and basolateral early endosomes. In conclusion, the trophoblast-like BeWo cell line can serve as a unique model to compare the apical and basolateral endocytic pathways of a single ligand, transferrin, in polarized epithelial cells.
A Two-Terminal Active Capacitor (2017)

This letter proposes a concept of two-terminal active capacitor implemented by power semiconductor switches and passive elements. The active capacitor has the same level of convenience as a passive one with two power terminals only. It is application independent and can be specified by rated voltage, ripple current, equivalent series resistance, and operational frequency range. The concept, control method, self-power scheme, and impedance characteristics of the active capacitor are presented. A case study of the proposed active capacitor for a capacitive dc-link application is discussed. The results reveal a significantly lower overall energy storage of passive elements and a reduced cost to fulfill a specific reliability target, compared to a passive capacitor solution. Proof-of-concept experimental results are given to verify the functionality of the proposed capacitor.
Nanowire electronic and optoelectronic devices (2006)

Electronic and optoelectronic devices impact many areas of society, from simple household appliances and multimedia systems to communications, computing, and medical instruments. Given the demand for ever more compact and powerful systems, there is growing interest in the development of nanoscale devices that could enable new functions and/or greatly enhanced performance. Semiconductor nanowires are emerging as a powerful class of materials that, through controlled growth and organization, are opening up substantial opportunities for novel nanoscale photonic and electronic devices. We review the broad array of nanowire building blocks available to researchers and discuss a range of electronic and optoelectronic nanodevices, as well as integrated device arrays, that could enable diverse and exciting applications in the future.
Beta-arrestin2, a novel member of the arrestin/beta-arrestin gene family. (1992)

Homologous or agonist-specific desensitization of beta 2-adrenergic receptors (beta 2AR) is mediated by the beta-adrenergic receptor kinase (beta ARK) which specifically phosphorylates the agonist-occupied form of the receptor. However, the capacity of beta ARK-phosphorylated beta 2AR to stimulate Gs in a reconstituted system is only minimally impaired. Recently, a protein termed beta-arrestin, was cloned from a bovine brain cDNA library and found to quench phosphorylated beta 2AR-coupling to Gs. Utilizing a low stringency hybridization technique to screen a rat brain cDNA library, we have now isolated cDNA clones representing two distinct beta-arrestin-like genes. One of the cDNAs is the rat homolog of bovine beta-arrestin (beta-arrestin1). In addition, we have isolated a cDNA clone encoding a novel, beta-arrestin-related protein which we have termed beta-arrestin2. Overall, beta-arrestin2 exhibits 78% amino acid identity with beta-arrestin1. The primary structure of these proteins delineates a family of proteins that regulates receptor coupling to G proteins. The capacity of purified beta-arrestin1, beta-arrestin2, and arrestin to inhibit the coupling of phosphorylated receptors to their respective G proteins were assessed in a reconstituted beta 2AR-Gs system and in a reconstituted rhodopsin-GT system. beta-Arrestin2 was equipotent to beta-arrestin1 and specifically inhibited beta 2AR function. Conversely, arrestin inhibited rhodopsin coupling to GT, whereas beta-arrestin1 and beta-arrestin2 were at least 20-fold less potent in this system. beta-Arrestin1 and beta-arrestin2 are predominantly localized in neuronal tissues and in the spleen. However, low mRNA levels can be detected in most peripheral tissues. In the central nervous system, beta-arrestin2 appears to be even more abundant than beta-arrestin1. Immunohistochemical analysis of the tissue distribution of beta-arrestin1 and beta-arrestin2 in rat brain shows extensive, but heterogenous, neuronal labeling of the two proteins. They are found in several neuronal pathways suggesting that they have relatively broad receptor specificity regulating many G protein-coupled receptors. Furthermore, immunoelectron microscopy shows that the beta-arrestins are appropriately situated at postsynaptic sites to act in concert with beta ARK to regulate G protein-coupled neurotransmitter receptors.
Tailor-Made Pentablock Copolymer Based Formulation for Sustained Ocular Delivery of Protein Therapeutics (2014)

The objective of this research article is to report the synthesis and evaluation of novel pentablock copolymers for controlled delivery of macromolecules in the treatment of posterior segment diseases. Novel biodegradable PB copolymers were synthesized by sequential ring-opening polymerization. Various ratios and molecular weights of each block (polyglycolic acid, polyethylene glycol, polylactic acid, and polycaprolactone) were selected for synthesis and to optimize release profile of FITC-BSA, IgG, and bevacizumab from nanoparticles (NPs) and thermosensitive gel. NPs were characterized for particle size, polydispersity, entrapment efficiency, and drug loading. In vitro release study of proteins from NPs alone and composite formulation (NPs suspended in thermosensitive gel) was performed. Composite formulations demonstrated no or negligible burst release with continuous near zero-order release in contrast to NPs alone. Hydrodynamic diameter of protein therapeutics and hydrophobicity of PB copolymer exhibited significant effect on entrapment efficiency and in vitro release profile. CD spectroscopy confirmed retention of structural conformation of released protein. Biological activity of released bevacizumab was confirmed by in vitro cell proliferation and cell migration assays. It can be concluded that novel PB polymers can serve a platform for sustained delivery of therapeutic proteins.
Physiological Interactions Between Symbionts in Vesicular-Arbuscular Mycorrhizal Plants (1988)

Crop loss due to soil salinization is an increasing threat to agriculture worldwide. This review provides an overview of cellular and physiological mechanisms in plant responses to salt. We place cellular responses in a time- and tissue-dependent context ...Read More
The Rho-Rock-Myosin Signaling Axis Determines Cell-Cell Integrity of Self-Renewing Pluripotent Stem Cells (2008)

These findings demonstrate an essential role of the Rho-Rock-Myosin signaling axis for the regulation of basic cell-cell communications in both mouse and human ES cells, and would contribute to advance in medically compatible xeno-free environments for human pluripotent stem cells.
Effects of Topical Ethacrynic Acid Ointment vs Timolol on Intraocular Pressure in Glaucomatous Monkey Eyes (1994)

The ECA ointment reduced IOP in glaucomatous monkey eyes. This reduction was evident by the fifth day of treatment with all the concentrations tested. The reduction in IOP produced by once-daily treatment with 1.5% ECA ointment was comparable with that of 0.5% timolol maleate administered twice daily. Therefore, drugs in this class of compound may prove to be useful in glaucoma therapy.
The nucleocapsid protein isolated from HIV-1 particles binds zinc and forms retroviral-type zinc fingers (1990)

The role of zinc in retroviral gag protein function has been addressed through the application of high-resolution nuclear magnetic resonance spectroscopy to samples of the nucleocapsid protein (NCP, p7) isolated directly from infectious HIV-1 particles. Unlike reports for the NCP from avian myeloblastosis virus (AMV) particles [Jentoft et al. (1988) Proc. Natl. Acad. Sci. U.S.A. 85, 7094], we find that the HIV-1 NCP binds 2 equiv of zinc tightly and stoichiometrically. Two-dimensional NMR spectroscopic studies reveal that zinc binding induces formation of folded domains that are conformationally similar to (if not identical with) structures observed previously for relevant retroviral-type (RT) zinc finger peptides [formerly called zinc fingerlike peptides; Summers et al. (1990) Biochemistry 29, 329]. This finding is consistent with the hypothesis that the inability of mutant proteins (with substituted Cys and His residues) to package viral RNA results from deficient zinc-binding capability, which may have significant consequences in the development of vaccines for the prevention of AIDS.
The study on distributed speech recognition system (2002)

This paper focuses on the architecture design, implementation and optimisation of distributed speech recognition systems. Client-server DSR architecture is presented based on the analysis of alternative architectures and an integrated prototype system is investigated in the client, network and server parts. Finally system optimization is considered in transmission bandwidth, server workload control and client security aspects.
[Studies on RESA in Plasmodium falciparum culture medium]. (1991)

P. falciparum grown in the complete RPMI 1640 medium (containing about 10% normal rabbit serum) for 24 h was collected at about 5% parasitemia. The medium was centrifuged at 500g for 20 min and the supernatant was then centrifuged once more at 40,000g for 30 min. Ten serum samples from falciparum malaria patients with anti-RESA antibodies collected from Yunnan Province were mixed with different dilutions of the culture supernatant, incubated at 37 degrees C for 2h and then at 4 degrees C overnight, and used for conducting RESA-IFA test. The titers of RESA-IFA test of all samples were reduced as compared with controls. When heated supernatant was used in the test, the inhibitory activity remained unchanged. The results indicate that RESA in the supernatants was soluble and heat-stable. To establish the origin of the reacting antigens in the inhibition experiments, the soluble fraction of sonicated merozoite-enriched collection and sonicates of ghost made from normal O phenotype erythrocytes were used in the inhibition RESA-IFA test with sera containing anti-RESA antibodies. The results showed that merozoite-enriched preparations were fully inhibitory at the concentration of 3.1 micrograms/ml, while no inhibition was observed at 0.2 micrograms/ml. In contrast, similar extracts made from normal erythrocyte ghosts were not inhibitory until concentrations about 30 times higher than that of merozoite antigen.
BMP-6 inhibits growth of mature human B cells; induction of Smad phosphorylation and upregulation of Id1 (2005)

In mature human B cells, BMP-6 inhibited cell growth, and rapidly induced phosphorylation of Smad1/5/8 followed by an upregulation of Id1.
Alternative splicing of human cyclin E (1994)

Cyclin E is a regulatory subunit of the cdc2-related protein kinase cdk2, which is activated shortly before S-phase entry, thus defining it as a G1 cyclin. We report here the existence of a 43 kDa splice variant of human cyclin E, termed cyclin Es, which lacks 49 amino acids within the cyclin box compared to the known 48 kDa cyclin E. Cyclin Es is expressed at approximately 1/10 of the level of full-length cyclin E in several cell lines analysed. The two cyclin E forms differ functionally in that cyclin E, but not cyclin Es, is able to complex with cdk2, to activate the histone H1, pRb and p107 in vitro kinase activity of cdk2 and to rescue a triple CLN mutation in S. cerevisiae. Cyclin Es is the first splice variant of a cell cycle regulatory protein to be described. Our findings also indicate that the cyclin box in cyclin E mediates the interaction with cdk2.
Demystifying 3D ICs: The Pros and Cons of Going Vertical (2005)

This article provides a practical introduction to the design trade-offs of the currently available 3D IC technology options. It begins with an overview of techniques, such as wire bonding, microbumps, through vias, and contactless interconnection, comparing them in terms of vertical density and practical limits to their use. We then present a high-level discussion of the pros and cons of 3D technologies, with an analysis relating the number of transistors on a chip to the vertical interconnect density using estimates based on Rent's rule. Next, we provide a more detailed design example of inductively coupled interconnects, with measured results of a system fabricated in a 0.35-μm technology and an analysis of misalignment and crosstalk tolerances. Lastly, we present a case study of a fast Fourier transform (FFT) placed and routed in a 0.18-μm through-via silicon-on-insulator (SOI) technology, comparing the 3D design to a traditional 2D approach in terms of wire length and critical-path delay.
Myeloperoxidase: an inflammatory enzyme for generating dysfunctional high density lipoprotein (2006)

Oxidation of HDL by myeloperoxidase may represent a specific molecular mechanism for converting the cardioprotective lipoprotein into a dysfunctional form, raising the possibility that the enzyme represents a potential therapeutic target for preventing vascular disease in humans. Moreover, oxidized HDL might prove useful as a blood marker for clinically significant cardiovascular disease in humans.
Poly I: C-activated dendritic cells that were generated in CellGro for use in cancer immunotherapy trials (2011)

In this study, we identified monocyte-derived DCs that were generated in CellGro and activated using Poly I:C as the most potent clinical-grade DCs for the induction of antigen-specific T cells.
Restriction pattern of the major outer-membrane protein gene provides evidence for a homogeneous invasive group among ruminant isolates of Chlamydia psittaci (1991)

Thirty-six ruminant isolates of Chlamydia psittaci, previously classified as invasive or non-invasive in a mouse model of virulence, were compared by analysing AluI restriction patterns of the major outer-membrane protein (MOMP) gene after DNA amplification by the polymerase chain reaction. The 24 invasive isolates, although from various origins, all belonged to serotype 1 and represented a strictly homogeneous group sharing a specific MOMP-gene restriction pattern that was not observed in the non-invasive strains. On the other hand, the 12 non-invasive strains, although all belonging to serotype 2, constituted a heterogeneous group with eight distinct MOMP-gene restriction patterns. However, all eight patterns shared a 180 bp fragment or the corresponding restricted fragments of 110 and 70 bp. MOMP-gene restriction patterns also clearly distinguished the ruminant strains from an avian C. psittaci isolate, a C. pneumoniae isolate and two C. trachomatis isolates which were studied for comparison. The homogeneous character of the invasive C. psittaci strains argues strongly for their genetic relatedness. Our results illustrate the usefulness of the MOMP-gene restriction mapping in typing chlamydiae.