gebhart/patrepeval huggingface dataset:
Formation of Silicon Structures by Plasma-Activated Wafer Bonding (2000)

A room temperature wafer bonding process based on oxygen plasma treatment or argon plasma treatment has been studied for surfaces of silicon, silicon dioxide, and crystalline quartz. The surface energy of the bonded samples was observed at different storage times. Atomic force microscope measurements, multiple internal reflection infrared spectroscopy, electrical characterization, secondary ion mass spectroscopy, and post‐processing steps were performed to evaluate the plasma‐treated surfaces and the formed bonded interfaces. Electrical measurements were used to investigate the usefulness of plasma‐bonded interfaces for electronic devices. The bonded interfaces exhibit high surface energies, comparable to what can be achieved with annealing steps in the range of 600–800°C using normal wet chemical activation before bonding. The high mechanical stability obtained after bonding at room temperature is explained by an increased dynamic in water removal from the bonded interface allowing covalent bonds to be formed. © 2000 The Electrochemical Society. All rights reserved.
Aberrant expression of B-lymphocyte stimulator by B chronic lymphocytic leukemia cells: a mechanism for survival (2002)

B-cell chronic lymphocytic leukemia (B-CLL) is defined by the accumulation of CD5(+) B cells in the periphery and bone marrow. This disease is not characterized by highly proliferative cells but rather by the presence of leukemic cells with significant resistance to apoptosis and, therefore, prolonged survival. B-lymphocyte stimulator (BLyS) is a newly identified tumor necrosis factor (TNF) family member shown to be critical for maintenance of normal B-cell development and homeostasis and it shares significant homology with another TNF superfamily member, APRIL. The striking effects of BLyS on normal B-cell maintenance and survival raises the possibility that it may be involved in pathogenesis and maintenance of hematologic malignancies, including B-CLL. In this study, we investigated the status of APRIL and BLyS expression, as well as their receptors, in this disease. All B-CLL patient cells studied expressed one or more of 3 known receptors for BLyS; however, the pattern of expression was variable. In addition, we demonstrate for the first time that B-CLL cells from a subset of patients aberrantly express BLyS and APRIL mRNA, whereas these molecules were not detectable in normal B cells. Furthermore, we provide in vitro evidence that BLyS protects B-CLL cells from apoptosis and enhances cell survival. Because these molecules are key regulators of B-cell homeostasis and tumor progression, leukemic cell autocrine expression of BLyS and APRIL may be playing an important role in the pathogenesis of this disease.
State of the Art in Example-based Texture Synthesis (2009)

Recent years have witnessed significant progress in example-based texture synthesis algorithms. Given an example texture, these methods produce a larger texture that is tailored to the users needs. In this state-of-the-art report, we aim to achieve three goals: (1) provide a tutorial that is easy to follow for readers who are not already familiar with the subject, (2) make a comprehensive survey and comparisons of different methods, and (3) sketch a vision for future work that can help motivate and guide readers that are interested in texture synthesis research. We cover fundamental algorithms as well as extensions and applications of texture synthesis.
An algorithm for distributed computation of a spanningtree in an extended LAN (1985)

A protocol and algorithm are given in which bridges in an extended Local Area Network of arbitrary topology compute, in a distributed fashion, an acyclic spanning subset of the network. The algorithm converges in time proportional to the diameter of the extended LAN, and requires a very small amount of memory per bridge, and communications bandwidth per LAN, independent of the total number of bridges or the total number of links in the network. Algorhyme I think that I shall never see A graph more lovely than a tree. A tree whose crucial property Is loop-free connectivity. A tree which must be sure to span So packets can reach every LAN. First the Root must be selected By ID it is elected. Least cost paths from Root are traced. In the tree these paths are placed. A mesh is made by folks like me Then bridges find a spanning tree.
Ontology versioning in an ontology management framework (2004)

Ontologies have become ubiquitous in information systems. They constitute the semantic Web's backbone, facilitate e-commerce, and serve such diverse application fields as bioinformatics and medicine. As ontology development becomes increasingly widespread and collaborative, developers are creating ontologies using different tools and different languages. These ontologies cover unrelated or overlapping domains at different levels of detail and granularity. A uniform framework, which we present here, helps users manage multiple ontologies by leveraging data and algorithms developed for one tool in another. For example, by using an algorithm we developed for structural evaluation of ontology versions, this framework lets developers compare different ontologies and map similarities and differences among them. Multiple-ontology management includes these tasks: maintain ontology libraries, import and reuse ontologies, translate ontologies from one formalism to another, support ontology versioning, specify transformation rules between different ontologies and version, merge ontologies, align and map between ontologies, extract an ontology's self-contained parts, support inference across multiple ontologies, support query across multiple ontologies.
Abstract 2451: A novel humanized anti-CD40 RabMAb exhibits potent efficacy in preclinical models (2010)

Abstract Monoclonal antibodies directed against B cell antigens have shown clinical benefits to hematologic malignancies. CD40 is a member of the TNFR superfamily and is a target for potential treatment of B cell lineage hematological malignancies as well as certain carcinomas. To date, majority of the therapeutic monoclonal antibodies are of murine origin. To evaluate the therapeutic potential of rabbit monoclonal antibodies (RabMAb®), we generated functional RabMAbs against CD40 using Epitomics' RabMAb® platform. Here we report the characterization of EPI0050, a novel humanized anti-CD40 rabbit monoclonal antibody. EPI0050 specifically recognizes the CD40 ligand binding domain and selectively blocks the ligand binding to CD40. EPI0050 itself exhibits modest agonist effects as shown in the up-regulation of CD80, CD83 and CD86 in differentiated dendritic cells and direct inhibition of CD40 positive malignant B cells. EPI0050 bound CD40 strongly without much internalization, which conferred to a potent ADCC effect in vitro. In an established preclinical Ramos lymphoma model, EPI0050 significantly inhibited tumor growth with a long-term stabilization of the tumor post dosing as compared with Rituximab and another anti-CD40 antibody. EPI0050 was also able to regress established rebound tumors post Rituximab treatment. More animal models and MOA are being explored for EPI0050. Both in vitro and in vivo results support the preclinical and clinical development of EPI0050 as a bio-better tumor therapy. Note: This abstract was not presented at the AACR 101st Annual Meeting 2010 because the presenter was unable to attend. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2451.
Information Extraction (2008)

The automatic extraction of information from unstructured sources has opened up new avenues for querying, organizing, and analyzing data by drawing upon the clean semantics of structured databases and the abundance of unstructured data. The field of information extraction has its genesis in the natural language processing community where the primary impetus came from competitions centered around the recognition of named entities like people names and organization from news articles. As society became more data oriented with easy online access to both structured and unstructured data, new applications of structure extraction came around. Now, there is interest in converting our personal desktops to structured databases, the knowledge in scientific publications to structured records, and harnessing the Internet for structured fact finding queries. Consequently, there are many different communities of researchers bringing in techniques from machine learning, databases, information retrieval, and computational linguistics for various aspects of the information extraction problem. This review is a survey of information extraction research of over two decades from these diverse communities. We create a taxonomy of the field along various dimensions derived from the nature of the extraction task, the techniques used for extraction, the variety of input resources exploited, and the type of output produced. We elaborate on rule-based and statistical methods for entity and relationship extraction. In each case we highlight the different kinds of models for capturing the diversity of clues driving the recognition process and the algorithms for training and efficiently deploying the models. We survey techniques for optimizing the various steps in an information extraction pipeline, adapting to dynamic data, integrating with existing entities and handling uncertainty in the extraction process.
A novel MTJ for STT-MRAM with a dummy free layer and dual tunnel junctions (2012)

A novel magnetic tunnel junction (MTJ) for embedded memory applications such as spin transfer torque magneto-resistive random access memory (STT-MRAM) is proposed. It consists of a dummy free layer and dual tunnel junctions using perpendicular magnetic anisotropy at the CoFeB/MgO interface. A fabricated MTJ with 53 nm diameter exhibited a high thermal stability factor Δ = 52 and a small switching current I <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">c0</inf> = 57 μA, resulting in an Δ/I <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">c0</inf> ratio of 0.91, which is more than twice that of the reference MTJ. This MTJ simultaneously provides an excellent Δ/I <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">c0</inf> ratio, low-voltage switching (0.34 V at 100 ns), and good manufacturability.
Transfer and Integration of T-DNA without Cell Injury in the Host Plant. (1997)

Agrobacterium colonizes plant cells via a gene transfer mechanism that results in plant tumorigenesis. Virulence (vir) genes are transcriptionally activated in the bacteria by plant metabolites released from the wound site. Hence, it is believed that agrobacteria use injuries to facilitate their entrance into the host plant and that the wounded state is required for plant cell competence for Agrobacterium-mediated gene delivery. However, our experiments using vir gene-activated bacteria sprayed onto tobacco plantlets demonstrated that cells in unwounded plants could also be efficiently transformed. The condition of the plant cells was monitored using [beta]-glucuronidase under the control of a wound-inducible promoter. Infection of leaf tissue is light dependent, and it is drastically reduced when abscisic acid is exogenously applied to the plant. Under these experimental conditions, stomatal opening seems to be used by Agrobacterium to circumvent the physical barrier of the cuticle. These results thus show that the proposed cellular responses evoked by wounding in higher plants are not essential for Agrobacterium-mediated transformation.
Loss of Trop2 Promotes Carcinogenesis and Features of Epithelial to Mesenchymal Transition in Squamous Cell Carcinoma (2011)

Trop2, an oncogenic cell surface protein under investigation as a therapeutic target, is commonly overexpressed in several epithelial tumor types yet its function in tumor biology remains relatively unexplored. To investigate the role of Trop2 in epithelial carcinogenesis, we generated Trop2(-/-) mice, which are viable and possess a normal lifespan. Contrary to expectations, Trop2 loss fails to suppress keratinocyte transformation. Instead, ras-transformed Trop2(-/-) keratinocytes preferentially pass through an epithelial to mesenchymal transition (EMT) and form tumors with spindle cell histology. Furthermore, Trop2 loss renders Arf-null mice susceptible to the formation of biphasic sarcomatoid carcinomas containing both squamous and spindle cell components upon carcinogen exposure in an otherwise skin cancer-resistant strain (C57BL/6). Immortalized keratinocytes derived from Trop2(-/-)Arf(-/-) mice exhibit enhanced proliferative and migratory capacity as well as increased activation of mitogen-activated protein kinase and Src prior to transformation. The clinical relevance of these findings was supported by studying the molecular epidemiology of Trop2 in primary head and neck squamous cell carcinomas. This analysis revealed that Trop2 mRNA levels are decreased in a subset of tumors with features of EMT, and total loss of Trop2 protein expression is observed in the spindle cell component of sarcomatoid carcinomas. Therefore, while previous studies have emphasized the potential importance of Trop2 gain of function, these results uncover a role for Trop2 loss in tumorigenesis and the mesenchymal transdifferentiation observed in a subset of squamous cell carcinomas.
J chain is covalently bound to both monomer subunits in human secretory IgA. (1981)

Previous work has established that the secretory component (SC) in human secretory IgA is covalently linked to only one of the two IgA monomer subunits, but it has not been clear whether the J chain is covalently linked to one or to both of these subunits. In view of the asymmetry in the disulfide bonding between SC and the IgA subunits, an arrangement which follows disulfide interchange, several models for the disulfide linkage of J chain and the bonds between IgA subunits were envisaged and investigated. When sIgA was gel filtered through Sephadex G-200 in acetic acid, a single major symmetrical peak eluted at the front. This material contained SC, alpha and L chains, and all of the J chain. The greater resolution afforded by polyacrylamide gel electrophoresis in detergent confirmed that human sIgA contains no major noncovalently linked components in the 150,000-200,000 molecular weight range. In another series of experiments the Fc monomer, which is not covalently attached to SC, isolated after treatment of sIgA with IgA protease and cyanogen bromide, was investigated to learn whether alpha chain COOH-terminal octapeptides could be released by reduction. The results were negative. The available data thus favor a model in which J chain is disulfide-bonded to both IgA monomer subunits in sIgA.
How hydrogen bonds impact P-glycoprotein transport and permeability (2012)

The requirement to cross a biological membrane can be a complex process especially if multidrug transporters such as P-gp must be considered. Drug partitioning into the lipid membrane and efflux by P-gp are tightly coupled processes wherein H-bonding interactions play a key role. All H-bond donors and acceptors are not equal in terms of the strength of the H-bonds that they form, hence it is important to consider their relative strength. Using various examples from literature, we illustrate the benefits of considering the relative strengths of individual H-bonds and introducing intramolecular H-bonds to increase membrane permeability and/or decrease P-gp efflux.
Structural and Functional Characterization of Oversulfated Chondroitin Sulfate/Dermatan Sulfate Hybrid Chains from the Notochord of Hagfish (2004)

Oversulfated chondroitin sulfate (CS)/dermatan sulfate (DS) hybrid chains were purified from the notochord of hagfish. The chains (previously named CS-H for hagfish) have an average molecular mass of 18 kDa. Composition analysis using various chondroitinases demonstrated a variety of D-glucuronic acid (GlcUA)- and L-iduronic acid (IdoUA)-containing disaccharides variably sulfated with a higher proportion of GlcUA/IdoUA-GalNAc 4,6-O-disulfate, revealing complex CS/DS hybrid features. The hybrid chains showed neurite outgrowth-promoting activity of an axonic nature, which resembled the activity of squid cartilage CS-E and which was abolished fully by chondroitinase ABC digestion and partially by chondroitinase AC-I or B digestion, suggesting the involvement of both GlcUA and IdoUA in neuritogenic activity. Purified CS-H exhibited interactions in a BIAcore system with various heparin-binding proteins and neurotrophic factors (viz. fibroblast growth factor-2, -10, -16, and -18; midkine; pleiotrophin; heparin-binding epidermal growth factor-like growth factor; vascular endothelial growth factor; brain-derived neurotrophic factor; and glial cell line-derived neurotrophic factor), most of which are expressed in the brain, although fibroblast growth factor-1 and ciliary neurotrophic factor showed no binding. Kinetic analysis revealed high affinity binding of these growth factors and, for the first time, of the neurotrophic factors. Competitive inhibition revealed the involvement of both IdoUA and GlcUA in the binding of these growth factors, suggesting the importance of the hybrid nature of CS-H for the efficient binding of these growth factors. These findings, together with those from the recent analysis of brain CS/DS chains from neonatal mouse and embryonic pig (Bao, X., Nishimura, S., Mikami, T., Yamada, S., Itoh, N., and Sugahara, K. (2004) J. Biol. Chem. 279, 9765-9776), suggest physiological roles of the hybrid chains in the development of the brain.
Isolation and Culture of Mouse Cortical Astrocytes (2013)

Astrocytes are an abundant cell type in the mammalian brain, yet much remains to be learned about their molecular and functional characteristics. In vitro astrocyte cell culture systems can be used to study the biological functions of these glial cells in detail. This video protocol shows how to obtain pure astrocytes by isolation and culture of mixed cortical cells of mouse pups. The method is based on the absence of viable neurons and the separation of astrocytes, oligodendrocytes and microglia, the three main glial cell populations of the central nervous system, in culture. Representative images during the first days of culture demonstrate the presence of a mixed cell population and indicate the timepoint, when astrocytes become confluent and should be separated from microglia and oligodendrocytes. Moreover, we demonstrate purity and astrocytic morphology of cultured astrocytes using immunocytochemical stainings for well established and newly described astrocyte markers. This culture system can be easily used to obtain pure mouse astrocytes and astrocyte-conditioned medium for studying various aspects of astrocyte biology.
Functionally Different Agonists Induce Distinct Conformations in the G Protein Coupling Domain of the β2Adrenergic Receptor (2001)

G protein-coupled receptors represent the largest class of drug discovery targets. Drugs that activate G protein-coupled receptors are classified as either agonists or partial agonists. To study the mechanism whereby these different classes of activating ligands modulate receptor function, we directly monitored ligand-induced conformational changes in the G protein-coupling domain of the beta(2) adrenergic receptor. Fluorescence lifetime analysis of a reporter fluorophore covalently attached to this domain revealed that, in the absence of ligands, this domain oscillates around a single detectable conformation. Binding to an antagonist does not change this conformation but does reduce the flexibility of the domain. However, when the beta(2) adrenergic receptor is bound to a full agonist, the G protein coupling domain exists in two distinct conformations. Moreover, the conformations induced by a full agonist can be distinguished from those induced by partial agonists. These results provide new insight into the structural consequence of antagonist binding and the basis of agonism and partial agonism.
Drug-induced DNA repair: X-ray structure of a DNA-ditercalinium complex. (1991)

Ditercalinium is a synthetic anticancer drug that binds to DNA by bis-intercalation and activates DNA repair processes. In prokaryotes, noncovalent DNA-ditercalinium complexes are incorrectly recognized by the uvrABC repair system as covalent lesions on DNA. In eukaryotes, mitochondrial DNA is degraded by excess and futile DNA repair. Using x-ray crystallography, we have determined, to 1.7 A resolution, the three-dimensional structure of a complex of ditercalinium bound to the double-stranded DNA fragment [d(CGCG)]2. The DNA in the complex with ditercalinium is kinked (by 15 degrees) and severely unwound (by 36 degrees) with exceptionally wide major and minor grooves. Recognition of the DNA-ditercalinium complex by uvrABC in prokaryotes, and by mitochondrial DNA repair systems in eukaryotes, might be related to drug-induced distortion of the DNA helix.
The BET Bromodomain Inhibitor OTX015 Affects Pathogenetic Pathways in Preclinical B-cell Tumor Models and Synergizes with Targeted Drugs (2015)

Together with the data coming from the ongoing phase I study, the in vitro and in vivo data presented here provide the basis for further clinical investigation of OTX015 as single agent and in combination therapies.
Actopaxin (α-Parvin) Phosphorylation Is Required for Matrix Degradation and Cancer Cell Invasion (2012)

Dysregulation of cell adhesion and motility is known to be an important factor in the development of tumor malignancy. Actopaxin (α-parvin) is a paxillin, integrin-linked kinase, and F-actin binding focal adhesion protein with several serine phosphorylation sites in the amino terminus that contribute to the regulation of cell spreading and migration. Here, phosphorylation of actopaxin is shown to contribute to the regulation of matrix degradation and cell invasion. Osteosarcoma cells stably expressing wild type (WT), nonphosphorylatable (Quint), and phosphomimetic (S4D/S8D) actopaxin demonstrate that actopaxin phosphorylation is necessary for efficient Src and matrix metalloproteinase-driven degradation of extracellular matrix. Rac1 was found to be required for actopaxin-induced matrix degradation whereas inhibition of myosin contractility promoted degradation in the phosphomutant-expressing Quint cells, indicating that a balance of Rho GTPase signaling and regulation of cellular tension are important for the process. Furthermore, actopaxin forms a complex with the Rac1/Cdc42 GEF β-PIX and Rac1/Cdc42 effector PAK1, to regulate actopaxin-dependent matrix degradation. Actopaxin phosphorylation is elevated in the invasive breast cancer cell line MDA-MB-231 compared with normal breast epithelial MCF10A cells. Expression of the nonphosphorylatable Quint actopaxin in MDA-MB-231 cells inhibits cell invasion whereas overexpression of WT actopaxin promotes invasion in MCF10A cells. Taken together, this study demonstrates a new role for actopaxin phosphorylation in matrix degradation and cell invasion via regulation of Rho GTPase signaling.