gebhart/patrepeval huggingface dataset:
Discovery Systems in Ubiquitous Computing (2006)

Ubiquitous computing introduces unique requirements for discovery technologies, which let services and devices become aware of each other without explicit human administration. Discovery lets services and devices spontaneously become aware of the availability and capability of peers on the network without explicit administration. In practice, this means that a client can discover and potentially use a device without prior knowledge of it. Although discovery is a necessary component of ubiquitous computing, the wide range of discovery systems in use today reflects the varied needs of the communities from which they originated. Some of these features are appropriate for ubiquitous computing, but others require further research and development.
Age is an important determinant in humoral and T cell responses to immunization with hepatitis B surface antigen (2013)

The aging of the immune system, also named immunosenescence, affects vaccine responses. However, the onset of age-related immunosenescence has been uncertain, in particularly with regard to vaccine responses. Here, we show that the formation of antibodies in response to vaccination against hepatitis B virus infection was significantly reduced for donors with a mean age of 61 y compared with a group with a mean age of 33 y. Booster vaccination sero-converted the elderly donors, but only at a reduced level, while a stronger response was found for the group of young donors. Agreeing with these findings, the hepatitis B surface antigen-specific proliferative responses by donor-derived T cells were reduced for the elder donors. Interestingly, the association between expression of the adhesion molecule CD62L (L-selectin) on naïve and central memory T cells and the formation of antigen-specific antibodies differed significantly between younger and elder donors. This finding corresponds well with the observation made previously that CD62L gene ablation in animals alters the formation of antigen-specific antibodies. We suggest that a complex interplay between the expression of CD62L and its ligands is a determinant in early-age immunosenescence affecting the response to HBV vaccination.
Metabotropic NMDA receptor function is required for NMDA receptor-dependent long-term depression (2013)

NMDA receptor (NMDAR) activation controls long-term potentiation (LTP) as well as long-term depression (LTD) of synaptic transmission, cellular models of learning and memory. A long-standing view proposes that a high level of Ca(2+) entry through NMDARs triggers LTP; lower Ca(2+) entry triggers LTD. Here we show that ligand binding to NMDARs is sufficient to induce LTD; neither ion flow through NMDARs nor Ca(2+) rise is required. However, basal levels of Ca(2+) are permissively required. Lowering, but not maintaining, basal Ca(2+) levels with Ca(2+) chelators blocks LTD and drives strong synaptic potentiation, indicating that basal Ca(2+) levels control NMDAR-dependent LTD and basal synaptic transmission. Our findings indicate that metabotropic actions of NMDARs can weaken active synapses without raising postsynaptic calcium, thereby revising and expanding the mechanisms controlling synaptic plasticity.
Structural and functional similarities between the human cytoskeletal protein zyxin and the ActA protein of Listeria monocytogenes (1997)

The intracellular bacterial parasite Listeria monocytogenes produces ActA protein at its surface to facilitate the localized assembly of actin-filled comets that are required for movement. The organization of actin in Listeria comets shows striking similarity to the organization of actin at the plasma membrane of mammalian cells. Therefore we examined the possibility that an ActA-like protein is present in mammalian cells. By using antibodies directed against ActA, we identified zyxin as an ActA related protein in a number of cell types. We compared the functions of ActA and zyxin by transient expression of variants tagged with an inner plasma membrane localization sequence (a CAAX box). Targeting of the proline rich domain of zyxin to the plasma membrane disrupts the actin cytoskeleton and cell shape in a manner similar to that which occurs with membrane-targeted ActA sequences. A chimeric protein composed of the N-terminal domain of ActA fused to the N-terminal and central domains of zyxin induced a full ActA response in cells. Furthermore, zyxin and ActA exhibit common protein partners in vitro. On the basis of the shared properties of zyxin and ActA, we propose that zyxin enhances actin organizing activity in mammalian cells.
Enhanced expression of the tie receptor tyrosine kinase mesenger RNA in the vascular endothelium of metastatic melanomas. (1994)

Angiogenesis of human melanomas has been the focus of intense interest since it was shown that the spread and prognosis of primary tumors is correlated with their vascularization (N. Weidner, J. P. Semple, W. R. Welch, and J. Folkman, N. Engl. J. Med., 324: 1-8, 1991). Basic fibroblast growth factor (bFGF) and its high-affinity receptor FGFR-1 have been implicated in melanoma growth and angiogenesis (R. Halaban, Y. Funasaka, J. Lee, J. Rubin, D. Ron, and D. Birnbaum, Fibroblast Growth Factors in Normal and Malignant Melanocytes, pp. 232-243. New York: The New York Academy of Sciences, 1991). We have studied the expression of the Tie endothelial cell receptor tyrosine kinase mRNA in skin and primary cutaneous melanomas as well as in their skin and brain metastases by in situ hybridization. The Tie probe hybridized very weakly with the vascular endothelium of capillaries of normal skin, while it was detected in larger arteries and veins as well as in capillaries around sweat glands. However, capillaries and medium-sized vessels within cutaneous and brain metastases of melanoma were strongly positive for Tie mRNA. In contrast, endothelial cells contained very little or no FGFR-1 transcripts, whereas abundant FGFR-1 mRNA was present in melanoma tumor cells and in fibrovascular stroma. In agreement with these findings, a Tie-specific amplified cDNA band was obtained by reverse transcription-polymerase chain reaction from melanoma metastases but not from normal skin. These results suggest a role for the Tie receptor in the angiogenesis associated with melanoma metastases.
A multiple‐start Monte Carlo docking method (1992)

We present a method to search for possible binding modes of molecular fragments at a specific site of a potential drug target of known structure. Our method is based on a Monte Carlo (MC) algorithm applied to the translational and rotational degrees of freedom of the probe fragment. Starting from a randomly generated initial configuration, favorable binding modes are generated using a two-step process. An MC run is first performed in which the energy in the Metropolis algorithm is substituted by a score function that measures the average distance of the probe to the target surface. This has the effect of making buried probes move toward the target surface and also allows enhanced sampling of deep pockets. In a second MC run, a pairwise atom potential function is used, and the temperature parameter is slowly lowered during the run (Simulated Annealing). We repeat this procedure starting from a large number of different randomly generated initial configurations in order to find all energetically favorable docking modes in a specified region around the target. We test this method using two inhibitor-receptor systems: Streptomyces griseus proteinase B in complex with the third domain of the ovomucoid inhibitor from turkey, and dihydrofolate reductase from E. coli in complex with methotrexate. The method could consistently reproduce the complex found in the crystal structure searching from random initial positions in cubes ranging from 25 A to 50 A about the binding site. In the case of SGPB, we were also successful in docking to the native structure. In addition, we were successful in docking small probes in a search that included the entire protein surface.
Imaging radio frequency electron-spin-resonance spectrometer with high resolution and sensitivity for i n v i v o measurements (1989)

We report the development of a novel radio frequency electron-spin-resonance spectrometer designed to provide measurements with high molar sensitivity and resolution in vivo. Radio frequency (250 MHz) is chosen to obtain good penetration in animal tissue and large aqueous samples with modest sacrifice of sensitivity. The spectrometer has a lumped component resonator and operates in continuous-wave mode. The spectrometer is capable of two-dimensional imaging, and with a modest addition should be capable of three-dimensional imaging. We demonstrate 3-mm spatial resolution for DPPH samples. For 10-mℓ samples of aqueous nitroxide, we demonstrate sensitivity (normalized to spectral width of 1 G) to 3×10−8-M concentrations and spectral resolution of 0.1 G. Spectra from nitroxide spin label injected into a live mouse are shown.
Switching Kinetics in Nanoscale Hafnium Oxide Based Ferroelectric Field-Effect Transistors (2017)

The recent discovery of ferroelectricity in thin hafnium oxide films has led to a resurgence of interest in ferroelectric memory devices. Although both experimental and theoretical studies on this new ferroelectric system have been undertaken, much remains to be unveiled regarding its domain landscape and switching kinetics. Here we demonstrate that the switching of single domains can be directly observed in ultrascaled ferroelectric field effect transistors. Using models of ferroelectric domain nucleation we explain the time, field and temperature dependence of polarization reversal. A simple stochastic model is proposed as well, relating nucleation processes to the observed statistical switching behavior. Our results suggest novel opportunities for hafnium oxide based ferroelectrics in nonvolatile memory devices.
The Mechanism of Cutting in Electrosurgery (1975)

A detailed analysis shows how electrosurgical r-f power is localized in the vicinity of the cutting electrode. This localization requires a small radius of curvature for the surgical tip, relatively high r-f voltages, and rapid surgical tip motion. The erratic results sometimes encountered in electrosurgery may be due to a deficiency in the above procedures as well as a lack of care in the use of the r-f leads and ground plates. A further analysis supports the supposition that evolving steam bubbles in the tissue at the surgical tip continuously rupture the tissue and are responsible for the cutting mechanism.
Design and Synthesis of the Potent, Orally Available, Brain-Penetrable Arylpyrazole Class of Neuropeptide Y5 Receptor Antagonists (2003)

Novel arylpyrazole derivatives were synthesized and evaluated as neuropeptide Y (NPY) Y5 receptor antagonists. Compound (-)-7, which features a novel chiral 2,3-dihydro-1H-cyclopenta[a]naphthalene moiety, showed good binding affinity and antagonistic activity for the Y5 receptor. After intracerebroventricular administration in SD rats, (-)-7 significantly inhibited food intake that was induced by the centrally administered Y5-preferring agonist, bovine pancreatic polypeptide, but had only a negligible effect on NPY-induced feeding.
Growth retardation of tumors by adoptive transfer of cytotoxic T lymphocytes reprogrammed by CD44V6-specific SCFV: ζ-chimera (1996)

Variants of the CD44 protein family containing sequences encoded by variant exon 6 (v6) are involved in the metastatic spread of rat and human tumors. The rat-specific antibody 1.1ASML, which recognizes a v6 epitope, interferes with metastatic dissemination of a rat pancreatic carcinoma. The single-chain antigen-binding fragment of this monoclonal antibody was fused to the zeta-chain of the T-cell receptor complex. The appropriate fusion gene was incorporated into a retroviral gene transfer vector. Murine cytotoxic T lymphocytes (CTLs) were infected, and cellular clones which express the single-chain zeta-chain fusion protein on their cell surface were selected. These CTLs are not MHC-restricted in their CD44v6 recognition and exhibit in vitro lytic activity toward cells expressing CD44 variants comprising exon v6. Tumor cell xenografts grown in athymic nude mice are suppressed in their growth upon infusion of the genetically manipulated CTLs. Our data indicate that the CD44v6 epitope is an effective target for immune tumor therapy and demonstrate the efficacy of genetically engineered CTLs in targeting tumors expressing such epitopes.
Improved Synthesis of Aza‐bis(oxazoline) Ligands. (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
Isolation and characterization of a cDNA clone corresponding to bovine cellular retinoic‐acid‐binding protein and chromosomal localization of the corresponding human gene (1988)

A bovine adrenal cDNA library was constructed and a clone corresponding to cellular retinoic-acid-binding protein (CRABP) mRNA was isolated and sequenced. The insert of the clone corresponds to 75 bp of the 5' untranslated portion, the whole translated and the complete 3' untranslated portion of the bovine CRABP mRNA. A genomic Southern blot, probed with CRABP cDNA, indicated that only one copy of the gene is present in the human genome. Hybridizing bands in restricted chicken and fish DNA were also observed. Using the CRABP cDNA as probe we have located the human CRABP gene to chromosome 3 in hybridizations to mouse-human, hamster-human and rat-human cell hybrids. In situ hybridizations on rat testis cells probed with CRABP and cellular retinol-binding protein antisense mRNA indicate that both proteins are expressed in tubuli cells.
Monoclonal antibody to the C-terminus of β-amyloid (1994)

SOLUBLE amyloidβ-protein (Aβ) is normally produced, but forms deposits in the brain of Alzheimer's (AD) patients. The length of isolated Aβ in SDS-insoluble amyloid from AD brain is reported to vary between plaques and vessels ranging from 28 to 43, with major species being 40 and 42 residues. Because the Aβ C-terminus determines aggregation rates, we made an Aβ monoclonal antibody distinguishing β1–42 from β1–40. In AD cortex, the β1–42 antibody recognizes all the structures identified by monoclonal to β1–40 on adjacent sections: plaque cores, diffuse Aβ deposits and vascular amyloid. These antibodies help define variation in Aβ length between different deposits, regions and autopsied brains.
Novel multispecific heterodimeric antibody format allowing modular assembly of variable domain fragments (2016)

Multispecific antibody formats provide a promising platform for the development of novel therapeutic concepts that could facilitate the generation of safer, more effective pharmaceuticals. However, the production and use of such antibody-based multispecifics is often made complicated by: 1) the instability of the antibody fragments of which they consist, 2) undesired inter-subunit associations, and 3) the need to include recombinant heterodimerization domains that confer distribution-impairing bulk or enhance immunogenicity. In this paper, we describe a broadly-applicable method for the stabilization of human or humanized antibody Fv fragments that entails replacing framework region IV of a V<sub>κ</sub>1/V<sub>H</sub>3-consensus Fv framework with the corresponding germ-line sequence of a λ-type V<sub>L</sub> chain. We then used this stable Fv framework to generate a novel heterodimeric multispecific antibody format that assembles by cognate V<sub>L</sub>/V<sub>H</sub> associations between 2 split variable domains in the core of the complex. This format, termed multispecific antibody-based therapeutics by cognate heterodimerization (MATCH), can be applied to produce homogeneous and highly stable antibody-derived molecules that simultaneously bind 4 distinct antigens. The heterodimeric design of the MATCH format allows efficient in-format screening of binding domain combinations that result in maximal cooperative activity.
Carbon Isotope Discrimination and Photosynthesis (1989)

We discuss the physical and enzymatic bases of carbone isotope discrimination during photosynthesis, noting how knowledge of discrimination can be used to provide additional insight into photosynthetic metabolism and the environmental influences on that process
The PrpC Serine-Threonine Phosphatase and PrkC Kinase Have Opposing Physiological Roles in Stationary-Phase Bacillus subtilis Cells (2002)

Loss of the PrpC serine-threonine phosphatase and the associated PrkC kinase of Bacillus subtilis were shown to have opposite effects on stationary-phase physiology by differentially affecting cell density, cell viability, and accumulation of beta-galactosidase from a general stress reporter fusion. These pleiotropic effects suggest that PrpC and PrkC have important regulatory roles in stationary-phase cells. Elongation factor G (EF-G) was identified as one possible target of the PrpC and PrkC pair in vivo, and purified PrpC and PrkC manifested the predicted phosphatase and kinase activities against EF-G in vitro.
Tissue imprint imaging by desorption electrospray ionization mass spectrometry (2011)

Cross-sections of Myristica malabarica (Lam) seed and mouse brain tissue were imprinted on such ordinary surfaces as printer paper and TLC plates, and successfully imaged by desorption electrospray ionization mass spectrometry (DESI-MS) at 250 μm resolution. Chemical images representing the distribution of the alkaloid malabaricone C in the seed substructures and individual lipids in the substructures of the brain were obtained. Practical implications include analysis of irregular or soft materials, easy recording, transportation and storage of the latent image, and posterior analysis of the samples by different techniques without the requirement of addition of matrices or use of specific types of surfaces.
Large deflection dynamics and control for planar continuum robots (2003)

This paper focuses on a class of robot manipulators termed "continuum" robots - robots that exhibit behavior similar to tentacles, trunks, and snakes. In previous work, we studied details of the mechanical design, kinematics, path-planning and small-deflection dynamics for continuum robots such as the Clemson "tentacle manipulator". In this paper, we discuss the dynamics of a planar continuum backbone section, incorporating a large-deflection dynamic model. Based on these dynamics, we formulate a vibration-damping setpoint controller, and include experimental results to illustrate the efficacy of the proposed controller.
T‐DNA insertional mutagenesis for functional genomics in rice (2000)

We have produced 22 090 primary transgenic rice plants that carry a T-DNA insertion, which has resulted in 18 358 fertile lines. Genomic DNA gel-blot and PCR analyses have shown that approximately 65% of the population contains more than one copy of the inserted T-DNA. Hygromycin resistance tests revealed that transgenic plants contain an average of 1.4 loci of T-DNA inserts. Therefore, it can be estimated that approximately 25 700 taggings have been generated. The binary vector used in the insertion contained the promoterless beta-glucuronidase (GUS) reporter gene with an intron and multiple splicing donors and acceptors immediately next to the right border. Therefore, this gene trap vector is able to detect a gene fusion between GUS and an endogenous gene, which is tagged by T-DNA. Histochemical GUS assays were carried out in the leaves and roots from 5353 lines, mature flowers from 7026 lines, and developing seeds from 1948 lines. The data revealed that 1.6-2.1% of tested organs were GUS-positive in the tested organs, and that their GUS expression patterns were organ- or tissue-specific or ubiquitous in all parts of the plant. The large population of T-DNA-tagged lines will be useful for identifying insertional mutants in various genes and for discovering new genes in rice.
Gene transfer of the uroporphyrinogen III synthase cDNA into haematopoietic progenitor cells in view of a future gene therapy in congenital erythropoietic porphyria (1997)

Congenital erythropoietic porphyria (CEP) is an inherited metabolic disorder characterized by an overproduction and accumulation of porphyrins in bone marrow. This autosomal recessive disease results from a deficiency of uroporphyrinogen III synthase (UROIIIS), the fourth enzyme of the haem biosynthetic pathway. It is phenotypically heterogeneous: patients with mild disease have cutaneous involvement, while more severely affected patients are transfusion dependent. The cloning of UROIIIS cDNA and genomic DNA has allowed the molecular characterization of the genetic defect in a number of families. To date, 22 different mutations have been characterized. Allogeneic bone marrow transplantation is the only curative treatment available for the severe, transfusion-dependent, cases. When bone marrow transplantation cannot be performed owing to the absence of a suitable donor, the autografting of genetically modified cells is an appealing alternative. The best approach to somatic gene therapy in this disease involves the use of recombinant retroviral vectors to transduce cells ex vivo, followed by autologous transplantation of the genetically modified cells. We investigated retroviral transfer in deficient human fibroblasts, immortalized lymphoblasts as well as bone marrow cells, and obtained a complete restoration of the enzymatic activity and full metabolic correction. Using K562 cells, an erythroleukaemic cell line, the expression of the transgene remained stable during 3 months and during erythroid differentiation of the cells. Finally, a 1.6- to 1.9-fold increase in enzyme activity compared to the endogenous level was found in normal CD34+ cells, a population of heterogeneous cells known to contain the progenitor/stem cells for long-term expression. The future availability of a mouse model of the disease will permit ex vivo gene therapy experiments on the entire animal.
Cross-Bifix-Free Codes Within a Constant Factor of Optimality (2013)

A cross-bifix-free code is a set of words in which no prefix of any length of any word is the suffix of any word in the set. Cross-bifix-free codes arise in the study of distributed sequences for frame synchronization. We provide a new construction of cross-bifix-free codes which generalizes the construction by Bajic to longer code lengths and to any alphabet size. The codes are shown to be nearly optimal in size. We also establish new results on Fibonacci sequences, which are used in estimating the size of the cross-bifix-free codes.
Distinct Role of Macrophages in Different Tumor Microenvironments (2006)

Macrophages are prominent in the stromal compartment of virtually all types of malignancy. These highly versatile cells respond to the presence of stimuli in different parts of tumors with the release of a distinct repertoire of growth factors, cytokines, chemokines, and enzymes that regulate tumor growth, angiogenesis, invasion, and/or metastasis. The distinct microenvironments where tumor-associated macrophages (TAM) act include areas of invasion where TAMs promote cancer cell motility, stromal and perivascular areas where TAMs promote metastasis, and avascular and perinecrotic areas where hypoxic TAMs stimulate angiogenesis. This review will discuss the evidence for differential regulation of TAMs in these microenvironments and provide an overview of current attempts to target or use TAMs for therapeutic purposes.