gebhart/patrepeval huggingface dataset:
Restriction of the human in vivo immune response against the mouse monoclonal antibody OKT3. (1986)

The murine monoclonal antibody OKT3 (IgG2a) was administered prophylactically to 17 renal allograft recipients (5 mg/day, i.v.), either alone or in association with corticosteroids (0.25 mg/kg/day) and azathioprine (3 mg/kg/day). In all patients the kinetics of the IgM and IgG anti-OKT3 response was monitored by means of immunofluorescence and ELISA. All patients treated with OKT3 alone showed a rapid and strong sensitization that completely neutralized the therapeutic effectiveness of the monoclonal antibody. The anti-OKT3 sensitization was manifested by accelerated OKT3 clearance and abrupt reappearance of circulating OKT3+ cells before the end of treatment. This immune response was significantly delayed and reduced in its incidence and intensity in patients receiving low dose corticosteroids and azathioprine in association to OKT3; mainly IgM anti-OKT3 antibodies that did not accelerate OKT3 clearance were then observed. The fine specificity of the antibodies produced was studied, using patients whole sera and various mouse IgG2a-affinity chromatography-purified serum fractions. The results obtained showed that the anti-OKT3 response was remarkably restricted to two main categories of antibodies: a) anti-idiotypic antibodies that inhibited OKT3 binding to T cells and abrogated its therapeutic activity and b) anti-mouse IgG2a (anti-isotypic) antibodies that did not neutralize OKT3 immunosuppressive activity. These results suggest that OKT3-immunized patients might still be sensitive to the immunosuppressive effect of other anti-T cell monoclonals that do not share the OKT3 idiotype and possibly isotype.
Peptidyl prolyl cis-trans isomerase activity of cyclophilin A in functional homo-oligomeric receptor expression (1997)

The functional expression of homo-oligomeric alpha7 neuronal nicotinic and type 3 serotonin receptors is dependent on the activity of a cyclophilin. In this paper we demonstrate that the mechanism of cyclophilin action during functional homo-oligomeric receptor expression in Xenopus oocytes is distinct from the calcineurin-dependent immunosuppressive mechanism by showing that a nonimmunosuppressive analog of cyclosporin A (CsA), SDZ 211-811, reduces functional receptor expression to the same extent as CsA. The cytoplasmic subtype of cyclophilin, cyclophilin A (CyPA), appears to be required for functional receptor expression. This is because overexpression of CyPA and a CyPA mutant that is deficient in CsA binding activity reverses CsA-induced reduction in functional receptor expression. The mechanism of action of CyPA is likely to involve its prolyl isomerase activity because a mutant CyPA with a single amino acid substitution (arginine 55 to alanine) that is predicted to produce a 1000-fold attenuation in isomerase activity fails to reverse the cyclosporin A effect. Our data also suggest that CyPA does not form a stable complex with receptor subunits.
Structure of a feruloyl esterase fromAspergillus niger (2004)

The crystallographic structure of feruloyl esterase from Aspergillus niger has been determined to a resolution of 1.5 A by molecular replacement. The protein has an alpha/beta-hydrolase structure with a Ser-His-Asp catalytic triad; the overall fold of the protein is very similar to that of the fungal lipases. The structure of the enzyme-product complex was determined to a resolution of 1.08 A and reveals dual conformations for the serine and histidine residues at the active site.
Immunization of HLA-A2+ melanoma patients with MAGE-3 or MelanA peptide-pulsed autologous peripheral blood mononuclear cells plus recombinant human interleukin 12. (2001)

Vaccination with dendritic cells (DCs) pulsed with tumor antigen peptides has shown promise in the treatment of melanoma. Interleukin (IL)-12 production by DCs is a key component for their efficacy. Murine studies have shown that IL-12 promotes potent antitumor immunization when coadministered with peptides loaded onto other class I MHC+ cells, thus bypassing the need to use DCs. The easiest cell source to obtain in large quantity from human patients is peripheral blood mononuclear cells (PBMCs). A Phase I clinical trial was thus performed in patients with metastatic melanoma using immunization with autologous PBMCs pulsed with a MAGE-3 or a MelanA peptide, coadministered with various doses of recombinant human (rh)IL-12. Patients receiving low-to-moderate doses of rhIL-12 developed increased specific CD8+ T-cell responses. Of the eight patients showing increased immunity, six had evidence of clinical activity, with one complete, one partial, one minor, and three mixed responses observed. In two patients with mixed responses, growing tumors were found to lack expression of the antigen used to immunize. Thus, vaccination with peptide-pulsed PBMCs plus rhIL-12 induces specific immunity and has clinical activity, without the need to generate DCs. Outgrowth of antigen-negative tumors argues for the future development of polyepitope vaccines.
Open Core Dislocations and Surface Energy of SiC (2006)

More than fifty years ago Frank proposed that a dislocation with a Burgers vector larger than a critical value would have an open core. Since then, there has been controversy as to whether micropipes in SiC are examples of open core screw dislocations. In this work open core dislocations in 4H-SiC material are investigated by AFM. The results are interpreted on the basis of Frank’s theory and the surface energy of SiC is estimated from the critical value of Burgers vector. Finally, the extracted surface energy is compared with the results of other research.
Elements of Scientific Visualization in Basic Neuroscience Research (2004)

Abstract Scientific imaging systems have undergone a revolution over the last century since Wilhelm Röntgen's discovery of X rays in 1895. However, deciding which imaging system will do the job and assist in solving a scientific question—not just produce beautiful graphics with little practical use—can be difficult. This article serves as a minireview of methods and applications of imaging techniques for basic research. It identifies some of the popular types of imaging systems; describes briefly how they work; and illustrates their past, present, and potential future applications. It also attempts to identify inherent pitfalls associated with some of these systems. Finally, it demonstrates some of the specific applications of scientific imaging techniques in neuroscience research.
Emission characteristics of a low-density plasma based on a helium-chlorine mixture (2004)

The emission from the plasma (λ=195–670 nm) of a high-frequency longitudinal discharge in a helium-chlorine mixture has been studied. The emission intensity of the characteristic bands of the chlorine molecule (at 200, 257, and 307 nm) has been optimized in relation to the pumping conditions, pressure, and the composition of the working mixture. The dynamics of the discharge current and the plasma emission have been investigated.
CD39/Adenosine Pathway Is Involved in AIDS Progression (2011)

HIV-1 infection is characterized by a chronic activation of the immune system and suppressed function of T lymphocytes. Regulatory CD4+ CD25(high) FoxP3+CD127(low) T cells (Treg) play a key role in both conditions. Here, we show that HIV-1 positive patients have a significant increase of Treg-associated expression of CD39/ENTPD1, an ectoenzyme which in concert with CD73 generates adenosine. We show in vitro that the CD39/adenosine axis is involved in Treg suppression in HIV infection. Treg inhibitory effects are relieved by CD39 down modulation and are reproduced by an adenosine-agonist in accordance with a higher expression of the adenosine A2A receptor on patients' T cells. Notably, the expansion of the Treg CD39+ correlates with the level of immune activation and lower CD4+ counts in HIV-1 infected patients. Finally, in a genetic association study performed in three different cohorts, we identified a CD39 gene polymorphism that was associated with down-modulated CD39 expression and a slower progression to AIDS.
Retrotransposon-Related DNA Sequences in the Centromeres of Grass Chromosomes (1998)

Abstract Several distinct DNA fragments were subcloned from a sorghum (Sorghum bicolor) bacterial artificial chromosome clone 13I16 that was derived from a centromere. Three fragments showed significant sequence identity to either Ty3/gypsy- or Ty1/copia-like retrotransposons. Fluorescence in situ hybridization (FISH) analysis revealed that the Ty1/copia-related DNA sequences are not specific to the centromeric regions. However, the Ty3/gypsy-related sequences were present exclusively in the centromeres of all sorghum chromosomes. FISH and gel-blot hybridization showed that these sequences are also conserved in the centromeric regions of all species within Gramineae. Thus, we report a new retrotransposon that is conserved in specific chromosomal regions of distantly related eukaryotic species. We propose that the Ty3/gypsy-like retrotransposons in the grass centromeres may be ancient insertions and are likely to have been amplified during centromere evolution. The possible role of centromeric retrotransposons in plant centromere function is discussed.
Group specific sequences and conserved secondary structures at the 3′ end of HCV genome and its implication for viral replication (1992)

Journal Article Group specific sequences and conserved secondary structures at the 3′ end of HCV genome and its implication for viral replication Get access Jang H. Han, Jang H. Han Chiron Corporation, 4560 Horton Street, Emeryville, CA 94608, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Michael Houghton Michael Houghton Chiron Corporation, 4560 Horton Street, Emeryville, CA 94608, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 20, Issue 13, 11 July 1992, Page 3520, https://doi.org/10.1093/nar/20.13.3520 Published: 11 July 1992 Article history Received: 28 April 1992 Published: 11 July 1992
An implementation of the virtual wires interconnect scheme (1994)

A complete software system using Virtual Wires technology for FPGA-based logic emulation has been constructed. This system has been successfully used to emulate an 18K-gate ASIC implementation of a Sparc microprocessor. The use of Virtual Wires overcomes the pincount limitation that formerly restricted the efficiency of FPGA-based logic emulators. The Virtual Wires emulation compiler accepts a netlist description of the circuit to be emulated and compiles programming information for the FPGA hardware. The compiler also provides support for an interface to standard logic simulator tools for hardware accelerated simulation. Innovative features of the compiler system and knowledge gained during its construction are presented. A comparison is made of different implementations of the on-chip Virtual Wires circuitry synthesized by the compiler. A user&amp;apos;s guide to the compiler and its supporting tools is provided. Future improvements to further enhance emulation speed and FPGA utilization are ...
Inducible Gene Targeting in Postnatal Myocardium by Cardiac-Specific Expression of a Hormone-Activated Cre Fusion Protein (2001)

Cardiac-restricted expression of Cre recombinase can provoke lineage-specific gene excision in the myocardium. However, confounding early lethality may still preclude using loss-of-function models to study the postnatal heart. Here, we have tested whether inducible, heart-specific recombination can be triggered after birth by transgenic expression of a Cre fusion protein that incorporates a mutated progesterone receptor ligand binding domain (PR1) that is activated by the synthetic antiprogestin, RU486, but not by endogenous steroid hormones. CrePR1 driven by the alpha-myosin heavy chain (alphaMHC) promoter was expressed specifically in heart. Translocation of CrePR1 from cytoplasm to nuclei in ventricular myocytes was induced by RU486. To establish whether this approach can mediate cardiac-specific, drug-dependent excision between loxP sites in vivo, we mated alphaMHC-CrePR1 mice with a ubiquitously expressed (ROSA26) Cre reporter line. Offspring harboring alphaMHC-CrePR1 and/or the floxed allele were injected with RU486 versus vehicle, and the prevalence of beta-galactosidase (beta-gal)-positive cells was determined, indicative of Cre-mediated excision. Little or no baseline recombination was seen 1 week after birth. Cardiac-restricted, RU486-inducible recombination was demonstrated in bigenic mice at age 3 and 6 weeks, using each of 3 independent CrePR1 lines. Recombination in the absence of ligand paralleled the levels of CrePR1 protein expression and was more evident at 6 weeks. Thus, conditional, posttranslational activation of a Cre fusion protein can bypass potential embryonic and perinatal effects on the heart and permits inducible recombination in cardiac muscle. High levels of the chimeric Cre protein, in particular, were associated with progressive recombination in the absence of drug.
Unsupervised learning of time–frequency patches as a noise-robust representation of speech (2009)

We present a self-learning algorithm using a bottom-up based approach to automatically discover, acquire and recognize the words of a language. First, an unsupervised technique using non-negative matrix factorization (NMF) discovers phone-sized time-frequency patches into which speech can be decomposed. The input matrix for the NMF is constructed for static and dynamic speech features using a spectral representation of both short and long acoustic events. By describing speech in terms of the discovered time-frequency patches, patch activations are obtained which express to what extent each patch is present across time. We then show that speaker-independent patterns appear to recur in these patch activations and how they can be discovered by applying a second NMF-based algorithm on the co-occurrence counts of activation events. By providing information about the word identity to the learning algorithm, the retrieved patterns can be associated with meaningful objects of the language. In case of a small vocabulary task, the system is able to learn patterns corresponding to words and subsequently detects the presence of these words in speech utterances. Without the prior requirement of expert knowledge about the speech as is the case in conventional automatic speech recognition, we illustrate that the learning algorithm achieves a promising accuracy and noise robustness.
Efficient Management of Parallelism in Object-Oriented Numerical Software Libraries (1997)

Parallel numerical software based on the message-passing model is enormously complicated. This paper introduces a set of techniques to manage the complexity, while maintaining high efficiency and ease of use. The PETSc 2.0 package uses object-oriented programming to conceal the details of the message passing, without concealing the parallelism, in a high-quality set of numerical software libraries. In fact, the programming model used by PETSc is also the most appropriate for NUMA shared-memory machines, since they require the same careful attention to memory hierarchies as do distributed-memory machines. Thus, the concepts discussed are appropriate for all scalable computing systems. The PETSc libraries provide many of the data structures and numerical kernels required for the scalable solution of PDEs, offering performance portability. 1 Introduction Currently the only general-purpose, efficient, scalable approach to programming distributed-memory parallel systems is the message-pass...
Advanced cellular Internet service (ACIS) (1998)

The public's desire for mobile communications and computing, as evidenced by the popularity of cellular phones and laptop computers combined with the explosive demand for Internet access suggest a very promising future for wireless data services. The key to realizing this potential is the development and deployment of high-performance radio systems. In this article we describe a basic service concept, advanced cellular Internet service (ACIS), and the technologies for achieving reliable high-speed transmission to wide-area mobile and portable cellular subscribers with very high spectrum efficiency. Such a wireless service, optimized to meet the needs of a client-server model for information retrieval and Web browsing, and combined with evolutionary enhancements in second-generation technologies, can provide an attractive option for third-generation systems. The radio link design combines OFDM with transmit and receive antenna diversity and Reed-Solomon coding to overcome the link budget and dispersive fading limitations of the cellular mobile radio environment. For access, a dynamic packet assignment algorithm is proposed which combines rapid interference measurements, priority ordering, and a staggered frame assignment schedule to provide spectrum efficiencies of two-to-four times existing approaches.
CIP2A overexpression is associated with c-Myc expression in colorectal cancer (2012)

Overexpression of CIP2A in colorectal cancer patients may be an important step in colorectal carcinogenesis. Based on our findings, CIP2A shows no association with patient prognosis in colorectal cancer, but is associated with nuclear c-Myc.
MicroSAGE Analysis of 2,353 Expressed Genes in a Single Cell‐Derived Colony of Undifferentiated Human Mesenchymal Stem Cells Reveals mRNAs of Multiple Cell Lineages (2001)

Mesenchymal stem cells (MSCs) isolated from the bone marrow of adult organisms are capable of differentiating into adipocytes, chondrocytes, myoblasts, osteoblasts, and hematopoiesis-supporting stroma. We recently demonstrated that MSCs also adopt glial cell fates when transplanted into the developing central nervous system and hence can produce tissue elements derived from a separate embryonic layer. Despite these remarkable properties, it has been difficult to establish specific criteria to characterize MSCs. Using a modified protocol for micro-serial analysis of gene expression, we cataloged 2,353 unique genes expressed by a single cell-derived colony of undifferentiated human MSCs. This analysis revealed that the MSC colony simultaneously expressed transcripts characteristic of various mesenchymal cell lineages including chondrocytes, myoblasts, osteoblasts, and hematopoiesis-supporting stroma. Therefore, the profile of expressed transcripts reflects the developmental potential of the cells. Additionally, the MSC colony expressed mRNAs characteristic of endothelial, epithelial and neuronal cell lineages, a combination that provides a unique molecular signature for the cells. Other expressed transcripts included various products involved in wound repair as well as several neurotrophic factors. A total of 268 novel transcripts were also identified, one of which is the most abundantly expressed mRNA in MSCs. This study represents the first extensive gene expression analysis of MSCs and as such reveals new insight into the biology, ontogeny, and in vivo function of the cells.
Highly Sensitive, Mechanically Stable Nanopore Sensors for DNA Analysis (2009)

Highly sensitive, mechanically robust Al2O3 nanopores are fabricated and characterized. These sensors allow for size control with sub-nanometer precision, chemical modification, and exhibit superior noise performance and increased lifetime over their solid-state counterparts. This new class of nanopore sensor is used in dsDNA studies and finds broad application in bio-nanotechnology. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Rhodium(II)-Catalyzed Aziridination of Allyl-Substituted Sulfonamides and Carbamates (2004)

Several unsaturated sulfonamides underwent intramolecular aziridination when treated with PhI(OAc)(2), MgO, and catalytic Rh(2)(OAc)(4) to give bicyclic aziridines in excellent yield. Treatment of the resulting azabicyclic sulfonamides in methanol in the presence of p-TsOH resulted in exclusive opening of the aziridine ring at the most substituted position affording six- and seven-membered ring products in high yield. In contrast, the intramolecular aziridination of several cycloalkenyl-substituted carbamates did not require a Rh(II) catalyst and proceeded via an iminoiodinane intermediate. The resulting tricyclic aziridines underwent ring opening when treated with various nucleophiles to give anti-derived products as expected for nucleophilic attack at the three-membered ring. The iodine(III)-mediated reaction of a 3-indolyl-substituted carbamate, however, required a Rh(II) catalyst. The expected aziridine was not observed, but rather simultaneous spirocyclization of C(3) and stereoselective syn-acylation at C(2) occurred to give compound 41, whose structure was unequivocally established by an X-ray crystallographic study. The reaction proceeds in a stepwise manner via a metal-free zwitterionic intermediate which is attacked by a nucleophilic reagent on the same side of the amide anion. Related reactions occurred with both a 2-indolyl- and 3-benzofuranyl-substituted carbamate but with lower stereoselectivity.
Left Ventricular Hypertrophy in Ascending Aortic Stenosis Mice (2000)

Our findings indicate that myocyte apoptosis develops during the transition from hypertrophy to early failure in mice with chronic biomechanical stress and support the hypothesis that the disruption of normal myocyte anchorage to adjacent extracellular matrix and cells, a process called anoikis, may signal apoptosis.
Direct electrical communication between chemically modified enzymes and metal electrodes. I. Electron transfer from glucose oxidase to metal electrodes via electron relays, bound covalently to the enzyme (1987)

ADVERTISEMENT RETURN TO ISSUEArticleNEXTDirect electrical communication between chemically modified enzymes and metal electrodes. I. Electron transfer from glucose oxidase to metal electrodes via electron relays, bound covalently to the enzymeY. Degani and Adam. HellerCite this: J. Phys. Chem. 1987, 91, 6, 1285–1289Publication Date (Print):March 1, 1987Publication History Published online1 May 2002Published inissue 1 March 1987https://pubs.acs.org/doi/10.1021/j100290a001https://doi.org/10.1021/j100290a001research-articleACS PublicationsRequest reuse permissionsArticle Views2884Altmetric-Citations496LEARN 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 options Get e-Alerts