gebhart/patrepeval huggingface dataset:
Conformational changes in an epitope localized to the NH2-terminal region of protein C (1989)

Murine monoclonal antibodies, developed following immunization with human protein C, were characterized for their ability to bind antigen in the presence of either CaCl2 or excess EDTA. Three stable clones were obtained which produced antibodies that bound to protein C only in the presence of EDTA. All three antibodies bound to the light chain of protein C on immunoblots and also bound to the homologous proteins factor X and prothrombin in solid-phase radioimmunoassays. One antibody, 7D7B10 was purified and studied further. The binding of 7D7B10 to human protein C was characterized by a KD of 1.4 nM. In competition studies, it was found that the relative affinity of the antibody for protein C was 20-40-fold higher than for prothrombin, fragment 1 of prothrombin, or factor X. In contrast, 7D7B10 was unable to bind to factor IX or bovine protein C. The effect of varying Ca2+ concentration on the interaction of the antibody with protein C was complex. Low concentrations of Ca2+ enhanced the formation of the protein C-antibody complex with half-maximal effect occurring at approximately 60 microM metal ion. However, higher concentrations of Ca2+ completely inhibited 7D7B10 binding to protein C with a K0.5 of 1.1 mM. Furthermore, millimolar concentrations of Mn2+, Ba2+, or Mg2+ also completely abolished antibody binding to protein C. The location of the epitope was delineated by immunoblotting and peptide studies and found to be present in the NH2-terminal 15 residues of protein C. Although residues corresponding to positions 10-13 of human protein C were necessary for maximal binding of the antibody, they were not sufficient. No evidence could be found for involvement of the epitope in metal binding per se. Therefore, the effect of Ca2+ on antibody binding is thought to be due to metal-dependent conformational changes in protein C. It seems likely that Ca2+ occupation of a high affinity site, shown by others to be located in the epidermal growth factor-like domain, causes a conformational change in the NH2-terminal region of protein C which is favorable for antibody interaction, whereas Ca2+ binding to the low affinity site(s), known to be present in the gamma-carboxyglutamic acid domain, causes an unfavorable conformational change.
Reactivity of cyclic sulfamidates towards phosphonate-stabilised enolates: synthesis and applications of α-phosphono lactams (2007)

Five and six ring a-phosphono lactams 14-20 are available by reaction of 1,2- and 1,3-cyclic sulfamidates respectively with enolates derived from ethyl dialkylphosphonoacetates 3 and 4. Subsequent Wadsworth-Emmons olefination provides the enantiomerically pure exo-alkylidene variants e.g. 25, which is efficiently converted to vinyl triflate 29 (> 98% ee). Suzuki coupling of 29 to a range of aryl and vinyl boronic acids leads to a structurally diverse range of pyrrolidinones exemplified by 30 and 34. The degree of epimerisation at the base-sensitive C(5) stereocentre during the Suzuki coupling of 29 is shown to be dependent on both the nature of the aryl boronic acid and the reaction conditions used.
Data Supplement from Optimal Effector Functions in Human Natural Killer Cells Rely upon Autocrine Bone Morphogenetic Protein Signaling (2023)

&lt;p&gt;Supplemental Figure S1. BMP pathway gene expression in activated NK cells.&lt;/p&gt;
Placental Growth Factor-1 and -2 Induce Hyperplasia and Invasiveness of Primary Rheumatoid Synoviocytes (2015)

Inflammation-mediated oncogenesis has been implicated in a variety of cancer types. Rheumatoid synovial tissues can be viewed as a tumor-like mass, consisting of hyperplastic fibroblast-like synoviocytes (FLSs). FLSs of rheumatoid arthritis (RA) patients have promigratory and invasive characteristics, which may be caused by chronic exposure to genotoxic stimuli, including hypoxia and growth factors. We tested whether a transformed phenotype of RA-FLSs is associated with placental growth factor (PlGF), a representative angiogenic growth factor induced by hypoxia. In this study, we identified PlGF-1 and PlGF-2 as the major PlGF isoforms in RA-FLSs. Global gene expression profiling revealed that cell proliferation, apoptosis, angiogenesis, and cell migration were mainly represented by differentially expressed genes in RA-FLSs transfected with small interfering RNA for PlGF. Indeed, PlGF-deficient RA-FLSs showed a decrease in cell proliferation, migration, and invasion, but an increase in apoptotic death in vitro. PlGF gene overexpression resulted in the opposite effects. Moreover, exogeneous PlGF-1 and PlGF-2 increased survival, migration, and invasiveness of RA-FLSs by binding their receptors, Flt-1 and neuropilin-1, and upregulating the expression of antiapoptotic molecules, pErk and Bcl2. Knockdown of PlGF transcripts reduced RA-FLS proliferation in a xenotransplantation model. Collectively, in addition to their role for neovascularization, PlGF-1 and -2 promote proliferation, survival, migration, and invasion of RA-FLSs in an autocrine and paracrine manner. These results demonstrated how primary cells of mesenchymal origin acquired an aggressive and transformed phenotype. PlGF and its receptors thus offer new targets for anti-FLS therapy.
Cooperative shared memory (1993)

We believe the paucity of massively parallel, shared-memory machines follows from the lack of a shared-memory programming performance model that can inform programmers of the cost of operations (so they can avoid expensive ones) and can tell hardware designers which cases are common (so they can build simple hardware to optimize them). Cooperative shared memory, our approach to shared-memory design, addresses this problem. Our initial implementation of cooperative shared memory uses a simple programming model, called Check-In/Check-Out (CICO), in conjunction with even simpler hardware, called Dir 1 SW. In CICO, programs bracket uses of shared data with a check_in directive terminating the expected use of the data. A cooperative prefetch directive helps hide communication latency. Dir 1 SW is a minimal directory protocol that adds little complexity to message-passing hardware, but efficiently supports programs written within the CICO model.
Data from Ataxia Telangiectasia Mutated Down-regulates Phospho-Extracellular Signal-Regulated Kinase 1/2 via Activation of MKP-1 in Response to Radiation (2023)

&lt;div&gt;Abstract&lt;p&gt;Ataxia telangiectasia mutated (ATM) kinase plays a crucial role in the cellular response to DNA damage and in radiation resistance. Although much effort has focused on the relationship between ATM and other nuclear signal transducers, little is known about interactions between ATM and mitogenic signaling pathways. In this study, we show a novel relationship between ATM kinase and extracellular signal-regulated kinase 1/2 (ERK1/2), a key mitogenic stimulator. Activation of ATM by radiation down-regulates phospho-ERK1/2 and its downstream signaling via increased expression of mitogen-activated protein kinase phosphatase MKP-1 in both cell culture and tumor models. This dephosphorylation of ERK1/2 is independent of epidermal growth factor receptor (EGFR) activity and is associated with radioresistance. These findings show a new function for ATM in the control of mitogenic pathways affecting cell signaling and emphasize the key role of ATM in coordinating the cellular response to DNA damage. (Cancer Res 2006; 66(24): 11554-9)&lt;/p&gt;&lt;/div&gt;
Matrix metalloproteinase activity in the lung is increased in Hermansky-Pudlak syndrome (2019)

In summary, our findings indicate that MMP activity is dysregulated in the HPS lung, suggesting a role for these proteases as biological markers or pathogenic players in HPS lung disease.
The Extracellular Domain of CD83 Inhibits Dendritic Cell–mediated T Cell Stimulation and Binds to a Ligand on Dendritic Cells (2001)

CD83 is an immunoglobulin (Ig) superfamily member that is upregulated during the maturation of dendritic cells (DCs). It has been widely used as a marker for mature DCs, but its function is still unknown. To approach its potential functional role, we have expressed the extracellular Ig domain of human CD83 (hCD83ext) as a soluble protein. Using this tool we could show that immature as well as mature DCs bind to CD83. Since CD83 binds a ligand also expressed on immature DCs, which do not express CD83, indicates that binding is not a homophilic interaction. In addition we demonstrate that hCD83ext interferes with DC maturation downmodulating the expression of CD80 and CD83, while no phenotypical effects were observed on T cells. Finally, we show that hCD83ext inhibits DC-dependent allogeneic and peptide-specific T cell proliferation in a concentration dependent manner in vitro. This is the first report regarding functional aspects of CD83 and the binding of CD83 to DCs.
"Person, Shoes, Tree. Is the Person Naked?" What People with Vision Impairments Want in Image Descriptions (2020)

Access to digital images is important to people who are blind or have low vision (BLV). Many contemporary image description efforts do not take into account this population's nuanced image description preferences. In this paper, we present a qualitative study that provides insight into 28 BLV people's experiences with descriptions of digital images from news websites, social networking sites/platforms, eCommerce websites, employment websites, online dating websites/platforms, productivity applications, and e-publications. Our findings reveal how image description preferences vary based on the source where digital images are encountered and the surrounding context. We provide recommendations for the development of next-generation image description technologies inspired by our empirical analysis.
A Novel Anode Electrode for Direct Borohydride Fuel Cell (2009)

As part of the development of a portable fuel cell using direct Borohydride fuel, method for deposition of the catalysis on the diffusion layer have been studied. The undesirable tendency for pore clogging due to sodium metaborate formation in the small pores where the high reaction and low flow rate cause a high metaborate concentration is observed. As one alternative, a nickel substrate based diffusion layer with larger pore size is under evaluation. However, a revision of the catalyst deposition method is needed for the application of nickel substrate. Three diffusion layer materials including open weave carbon cloth, Nickel Micro Fiber felt (NMF), and a nickel foam, were used along with a new catalyst deposition method to realize maximum uniform surface coverage. The catalyst coated diffusion layers were then run and compared in a test cell. A significant increase in cell power was obtained with nickel foam compared to nickel felt, or with carbon cloth substrate. Run time test results of catalysis coated Ni felt-foam and carbon cloth diffusion layers will be presented.
Nfkb1 Plays a Tumor-Suppressing Role in BCR-ABL-Induced Leukemias (2012)

Abstract Abstract 1666 NF-κB activation has been linked to the promotion of an assortment of malignancies. While in vitro studies have supported a tumor-promoting role for NF-κB in leukemias, in vivo evidence has not been collected. NF-κB has also been proposed as a therapeutic target for Philadelphia chromosome-positive leukemias including chronic myeloid leukemia (CML) and B-cell acute lymphoblastic leukemia (B-ALL). In this study, we investigate the role the Nfkb1 gene plays in CML and B-ALL using mouse models for these leukemias induced by the BCR-ABL oncogene. Contrary to conventional thinking, we find a tumor-suppressing role for Nfkb1 in BCR-ABL leukemias. To induced CML, we transduced bone marrow cells from 5-FU-primed wild type or Nfkb1−/− mice with BCR-ABL-GFP retrovirus, followed by transplantation of the transduced cells into lethally irradiated recipient mice. We show that recipients of BCR-ABL-transduced Nfkb1−/− donor cells developed CML more rapidly than the wild type recipients, correlating to elevated percentages (82.3% vs 38.5%) and total numbers of Gr-1+GFP+ cells in peripheral blood of the mice. We next tested whether the loss of Nfkb1 also accelerated B-ALL development under the B-ALL-inducing conditions, and show that recipients of BCR-ABL-transduced Nfkb1−/− donor cells succumbed to B-ALL more quickly than the wild type recipients. These results suggest that Nfkb1 does not stimulate leukemia growth, and instead, it plays a tumor-suppressing role in CML and B-ALL. Because these findings are opposite from what people believe in the field, we confirmed our findings by conducting a rescue experiment. The Nfkb1 gene encodes the p105 protein; roughly half of p105 product is selectively proteolyzed to yield the p50 transcription factor. In this rescue experiment, we transduced Nfkb1−/− donor cells with BCR-ABL alone or BCR-ABL and p50 of Nfkb1 to induce leukemia, and we show that acceleration of leukemia development caused by the Nfkb1 loss is partially reversed by p50. To study the underlying mechanism, we focused on CARD11, because it plays a critical role in mediating NF-κB signaling in lymphocytes. We find that CARD11 expression is induced in myeloid and increased in lymphoid cell lines expressing BCR-ABL. Furthermore, we induced B-ALL using Card1−/− mice. We find that similar to the loss of Nfkb1, the loss of Card11 expression also accelerates the development of B-ALL. To increase human relevance of our findings, we overexpressed p50 in human K562 cells by retroviral transduction with p50-IRES-GFP or empty vector, and find that FACS-sorted p50/GFP K562 cells grow significantly slower than empty vector-transduced cells. These findings support an idea that Nfkb1 signaling suppresses BCR-ABL-induce leukemia at least partially through a CARD11-dependent mechanism. In summary, our results demonstrate that Nfkb1 plays a tumor-suppressing role in BCR-ABL-induced leukemias, arguing that we should be careful when targeting of Nfkb1 in leukemia treatment. Disclosures: No relevant conflicts of interest to declare.
ASAP: a transistor sizing tool for speed, area, and power optimization of static CMOS circuits (1994)

This paper introduces an automated transistor sizing tool (ASAP) that incorporates accurate gate-level functional models and can be used for delay, area, and power optimization of CMOS combinational logic circuits in a VLSI design environment. The optimization technique is based on simulated annealing and considers the performance improvement of VLSI circuits by optimally sizing the transistors on the N most critical paths.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
L’impact des concepts de Pierre-Gilles de Gennes sur l’innovation en France dans le domaine des matériaux (2018)

International audience
Spatial degrees-of-freedom in large-array full-duplex: the impact of backscattering (2016)

The key challenge for in-band full-duplex wireless communication is managing self-interference. Many designs have employed spatial isolation mechanisms, such as shielding or multi-antenna beamforming, to isolate the self-interference waveform from the receiver. Because such spatial isolation methods confine the transmit and receive signals to a subset of the available space, the full spatial resources of the channel may be under-utilized, expending a cost that may nullify the net benefit of operating in full-duplex mode. In this paper, we leverage an antenna-theory-based channel model to analyze the spatial degrees of freedom available to a full-duplex capable base station. We observe that whether or not spatial isolation out-performs time-division (i.e., half-duplex) depends heavily on the geometric distribution of scatterers. Unless the angular spread of the objects that scatter to the intended users is overlapped by the spread of objects that backscatter to the base station, then spatial isolation outperforms time division, otherwise time division may be optimal.
Greedy search for descriptive spatial face features (2017)

Facial expression recognition methods use a combination of geometric and appearance-based features. Spatial features are derived from displacements of facial landmarks, and carry geometric information. These features are either selected based on prior knowledge, or dimension-reduced from a large pool. In this study, we produce a large number of potential spatial features using two combinations of facial landmarks. Among these, we search for a descriptive subset of features using sequential forward selection. The chosen feature subset is used to classify facial expressions in the extended Cohn-Kanade dataset (CK+), and delivered 88.7% recognition accuracy without using any appearance-based features.
Offset‐to‐angle transformations for PP and PS AVO analysis (2001)

PreviousNext No AccessSEG Technical Program Expanded Abstracts 2001Offset‐to‐angle transformations for PP and PS AVO analysisAuthors: Richard BaleScott LeaneyGabriela DumitruRichard BaleWesternGeco, Scott LeaneySchlumberger, and Gabriela DumitruSchlumbergerhttps://doi.org/10.1190/1.1816579 SectionsAboutPDF/ePub ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinked InRedditEmail Permalink: https://doi.org/10.1190/1.1816579FiguresReferencesRelatedDetailsCited ByApplication of pre-stack simultaneous inversion to predict gas-bearing dolomite reservoir: a case study from Sichuan Basin, China5 April 2019 | Carbonates and Evaporites, Vol. 34, No. 33D Kirchhoff prestack time migration in average illumination-azimuth and incident-angle domain for isotropic and vertical transversely isotropic mediaJiubing Cheng, Jianhua Geng, Huazhong Wang, and Zaitian Ma13 January 2011 | GEOPHYSICS, Vol. 76, No. 1Post‐migration time‐domain offset‐to‐phase‐incidence‐angle transform in VTI mediaYilong Qin8 August 20113‐D angle‐domain imaging in Kirchhoff prestack time migrationCheng Jiubing and Ma Zaitian14 October 2009Simultaneous inversion of PP and PS seismic dataHelene Hafslund Veire and Martin Landrø22 May 2006 | GEOPHYSICS, Vol. 71, No. 3 SEG Technical Program Expanded Abstracts 2001ISSN (print):1052-3812 ISSN (online):1949-4645Copyright: 2001 Pages: 2135 publication data© 2001 Copyright © 2001 Society of Exploration GeophysicistsPublisher:Society of Exploration Geophysicists HistoryPublished: 03 Jan 2005 CITATION INFORMATION Richard Bale, Scott Leaney, and Gabriela Dumitru, (2001), "Offset‐to‐angle transformations for PP and PS AVO analysis," SEG Technical Program Expanded Abstracts : 235-238. https://doi.org/10.1190/1.1816579 Plain-Language Summary PDF DownloadLoading ...
Generation and Reactions of an Unsubstituted N‐Heterocyclic Carbene Boryl Anion (2010)

Lying low: A lithiated unsubstituted N-heterocyclic carbene (NHC) boryl anion can be generated by reduction, and trapped by electrophiles (see scheme; dipp=2,6-diisopropylphenyl) to provide new substituted NHC boranes. It is yet another example of a low-valent boron compound or boron-containing reactive intermediate stabilized by an NHC, thereby extending the scope of NHC borane chemistry. 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.
Engineering Th determinants for efficient priming of humoral and cytotoxic T cell responses (2003)

To engineer T(h) determinants (THd) to prime help for humoral or cytotoxic T cell responses, we modified ovalbumin [OVA(323-337)] and myoglobin [MYO(106-118)] eliciting T(h)1 and T(h)0 cytokine profiles respectively. Residues along the sequence of both THd were replaced with amino acids representative of different families. Replacements at positions P-1 and P5 pointing to the TCR in both THd afforded higher levels of IFN-gamma and IL-4 production. Peptides eliciting different proportions of IFN-gamma and IL-4 were co-immunized with a peptide hapten or a T cytotoxic determinant (TCd) respectively. OVA(323-337)- and MYO(106-118)-derived peptides afforded the best THd for the induction of cytotoxic T lymphocyte (CTL) and anti-hapten antibodies respectively. IFN-gamma and IL-4, primed by MYO(106-118)-derived peptides, correlated significantly with antibody production against the hapten (P < 0.05 for IFN-gamma and P < 0.05 for IL-4). Interestingly, two peptides derived from OVA(323-337), 323G and 327G, which induced the clearest T(h)2 cytokine profiles, were not the most efficient to prime cell help for the induction of anti-hapten antibodies. For CTL induction, OVA(323-337)-derived peptides, inducing a T(h)1-like profile, required a lower dose (5 nmol) than T(h)0 peptides (50 nmol). The dose of 50 nmol was detrimental for T(h)1-like peptides. Interestingly, IFN-gamma primed by the THd correlated significantly with that induced by the TCd (P < 0.01).
Role of Anconeus in the Stability of a Lateral Ligament Deficient Elbow: An In Vitro Biomechanical Study (2020)

Objectives/Interrogation: The role of anconeus in elbow stability has been a long-standing debate. Anatomical and electromyographic studies have suggested a potential role as a stabilizer. However, to our knowledge, no clinical or biomechanical studies have investigated its role in improving the[for full text, please go to the a.m. URL]
A new scheme for view-dependent data differentiation in fan-beam and cone-beam computed tomography (2007)

In computed tomography, analytical fan-beam (FB) and cone-beam (CB) image reconstruction often involves a view-dependent data differentiation. The implementation of this differentiation step is critical in terms of resolution and image quality. In this work, we present a new differentiation scheme that is robust to changes in the data acquisition geometry and to coarse view sampling. Our scheme was compared to two previously suggested methods, which we call the direct scheme and the chain-rule scheme. Image reconstructions were performed from computer-simulated data of the Shepp-Logan phantom, the FORBILD thorax phantom and a modified FORBILD head phantom. For FB reconstruction, we investigated three acquisition geometries: a circular, an ellipse-shaped and a square-shaped trajectory. For CB reconstruction, the circle-plus-line trajectory was considered. Image comparison showed that the new scheme performs consistently well when varying the scenario, in both FB and CB geometry, unlike the other two schemes.
Sequential Data Clustering (2008)

This chapter contains sections titled: Introduction Sequence Similarity Indirect Sequence Clustering Model-Based Sequence Clustering Applications—Genomic and Biological Sequence Clustering Summary