gebhart/patrepeval huggingface dataset:
Arg-Tyr-Asp (RYD) and Arg-Cys-Asp (RCD) motifs in dendroaspin promote selective inhibition of β1 and β3 integrins (2001)

Arg-Gly-Asp (RGD) is a unique minimal integrin-binding sequence that is found within several glycoprotein ligands. This sequence has also been found in snake-venom anti-platelet proteins, including the disintegrins and dendroaspin, a natural variant of short-chain neurotoxins isolated from the venom of Dendroaspis jamesonii. In the present study, the motifs RYD and RCD were introduced into the dendroaspin scaffold to replace RGD. Both motifs in dendroaspin caused inhibition of ADP-induced platelet aggregation with IC50 values of 200 and 300nM respectively, similar to that of the wild-type RGD motif (170nM). In comparison with wild-type dendroaspin, both RYD- and RCD-containing dendroaspins were more selective in the inhibition of the adhesion of K562 cells to laminin rather than to fibrinogen and fibronectin, even though they were 10–30-fold less potent at inhibiting K562 cell (containing α5β1 integrin) adhesion to laminin compared with wild-type. Interestingly, the RYD motif produced a similar IC50 value to the RGD motif at inhibiting A375-SM cell (β3 integrin) adhesion to collagen, whereas the RCD motif was approx. 2–6-fold less potent compared with either RGD or RYD. These findings show that the selectivity of dendroaspin binding to β1 and β3 integrins can be modulated by the introduction of alternative cell recognition sequences.
The Mobile Sensing Platform: An Embedded Activity Recognition System (2008)

Activity-aware systems have inspired novel user interfaces and new applications in smart environments, surveillance, emergency response, and military missions. Systems that recognize human activities from body-worn sensors can further open the door to a world of healthcare applications, such as fitness monitoring, eldercare support, long-term preventive and chronic care, and cognitive assistance. Wearable systems have the advantage of being with the user continuously. So, for example, a fitness application could use real-time activity information to encourage users to perform opportunistic activities. Furthermore, the general public is more likely to accept such activity recognition systems because they are usually easy to turn off or remove.
Impaired B-lymphopoiesis, myelopoiesis, and derailed cerebellar neuron migration in CXCR4- and SDF-1-deficient mice (1998)

The chemokine stromal cell-derived factor 1, SDF-1, is an important regulator of leukocyte and hematopoietic precursor migration and pre-B cell proliferation. The receptor for SDF-1, CXCR4, also functions as a coreceptor for T-tropic HIV-1 entry. We find that mice deficient for CXCR4 die perinatally and display profound defects in the hematopoietic and nervous systems. CXCR4-deficient mice have severely reduced B-lymphopoiesis, reduced myelopoiesis in fetal liver, and a virtual absence of myelopoiesis in bone marrow. However, T-lymphopoiesis is unaffected. Furthermore, the cerebellum develops abnormally with an irregular external granule cell layer, ectopically located Purkinje cells, and numerous chromophilic cell clumps of abnormally migrated granule cells within the cerebellar anlage. Identical defects are observed in mice lacking SDF-1, suggesting a monogamous relationship between CXCR4 and SDF-1. This receptor-ligand selectivity is unusual among chemokines and their receptors, as is the function in migration of nonhematopoietic cells.
Adult zebrafish as a model for successful central nervous system regeneration (2008)

Adult fish, in contrast to mammals, are capable of regenerating axonal tracts as well as cells and even entire tissues in the central nervous system (CNS). The zebrafish is a powerful genetic model for studies on the developing CNS and is now emerging as a CNS regeneration model. Here we review recent progress in adult regeneration paradigms in zebrafish ranging from axonal re-growth models to those of tissue regeneration. Moreover, we review the tools that have become available in zebrafish to elucidate the factors contributing to successful CNS regeneration. Since many molecular pathways are shared between zebrafish and mammals, it is hoped that insights from zebrafish may contribute to future therapeutic approaches in CNS injury and disease.
Autoimmunity in multiple sclerosis (1988)

Multiple sclerosis reportedly coexists with disorders of autoimmune origin. The prevalence with which such disorders occur in the MS population has not been adequately investigated. We reviewed the medical records of 828 patients with definite MS and found that 4.8% had a past or present associated disorder in which autoimmune mechanisms presumably play a role. The cumulative prevalence of these disorders was no higher than that estimated for the general population. Serum from 105 patients, without clinical evidence of an associated autoimmune disorder, was tested for the presence of antinuclear, thyroid, parietal cell, smooth muscle, and mitochondrial antibodies. A significantly higher prevalence (p less than 0.01) of generally low titers of one or more autoantibodies was found in serum from the MS group, compared with a control group of 105 patients with other neurologic disorders. The increased frequency of serum autoantibodies probably reflects the existence of a nonspecific B cell overactivity in MS.
Attachment of Bacteroides melaninogenicus subsp. asaccharolyticus to Oral Surfaces and Its Possible Role in Colonization of the Mouth and of Periodontal Pockets (1978)

This investigation examined the ability of cells of Bacteroides melaninogenicus subsp. asaccharolyticus 381 to adhere to surfaces that might be important for its initial colonization of the mouth and its subsequent colonization in periodontal pockets. Of 48 asaccharolytic strains of B. melaninogenicus , 47 agglutinated human erythrocytes, whereas none of 20 fermentative strains, which included reference cultures of the subspecies intermedius and melaninogenicus , were active. Electron microscopy indicated that both asaccharolytic and fermentative strains possessed pili; hence, the presence of pili did not correlate with the hemagglutinating activities of B. melaninogenicus strains. Both asaccharolytic and fermentative B. melaninogenicus strains suspended in phosphate-buffered saline adhered in high numbers to buccal epithelial cells and to the surfaces of several gram-positive bacteria tested, including Actinomyces viscosus, A. naeslundii, A. israelii, Streptococcus sanguis , and S. mitis. B. melaninogenicus subsp. asaccharolyticus 381 also attached, but in comparatively low numbers, to untreated and to saliva-treated hydroxyapatite. Addition of clarified whole saliva to suspensions of strain 381 almost completely eliminated adherence to buccal epithelial cells and to hydroxyapatite surfaces, but saliva had no detectable effect on attachment to gram-positive plaque bacteria. Both fermentative and nonfermentative strains of B. melaninogenicus also attached in high numbers to crevicular epithelial cells derived from human periodontal pockets, but normal human serum strongly inhibited attachment. Serum also inhibited attachment of strain 381 to saliva- and serum-treated hydroxyapatite, but it had little effect upon attachment to gram-positive bacteria. These observations suggested that salivary and serum components would strongly inhibit the attachment of B. melaninogenicus cells to several oral surfaces, but not to the surfaces of certain gram-positive bacteria commonly present in human dental plaque. This was confirmed by an in vivo experiment in which streptomycin-labeled cells of B. melaninogenicus 381-R were introduced into the mouths of two volunteers. After 10 min, several hundred-fold higher numbers of the organism were recovered from preformed bacterial plaque present on teeth than from clean tooth surfaces or from the buccal mucosa and tongue dorsum. High numbers of B. melaninogenicus cells were also recovered from preformed plaque after 150 min, but virtually no cells of the organism were recovered from the other surfaces studied. These data suggest that the presence of dental plaque containing Actinomyces and other gram-positive bacteria may be essential for the attachment and colonization of B. melaninogenicus cells after their initial introduction into the mouth. Similarly, the presence of subgingival plaque containing gram-positive bacteria may be necessary for its secondary colonization in periodontal pockets.
Multi-layer SDN on a commercial Network Control Platform for Packet Optical Networks (2014)

We apply a hierarchical SDN controller to demonstrate multi-layer orchestration of a commercial Optical Network Control platform. We show dynamic allocation of transport resources for bandwidth on demand and congestion control of packet services.
Aspirin and Colon Cancer — Targeting Prevention? (2007)

The compelling evidence that chronic use of aspirin or certain nonsteroidal antiinflammatory drugs (NSAIDs) can substantially lower the risk of colon cancer has important implications, especially because colon cancer is the second leading cause of cancer death. Aspirin and nonselective NSAIDs each inhibit the generation of prostaglandins by inhibiting the two cyclooxygenase (COX) enzymes that initiate prostaglandin synthesis, COX-1 and COX-2. NSAIDs that are selective for COX-2 also inhibit the generation of prostaglandins. COX-1 is constitutively expressed in the colon, but COX-2 is inducible and markedly up-regulated in many colon cancers. Interventional trials have shown a decreased risk of the . . .
Does Nasal Cocolonization by Methicillin-Resistant Coagulase-Negative Staphylococci and Methicillin-Susceptible Staphylococcus aureus Strains Occur Frequently Enough To Represent a Risk of False-Positive Methicillin-Resistant S. aureus Determinations by Molecular Methods? (2006)

By analyzing the colonization of the anterior nares in cardiothoracic surgery patients on admission, nasal cocolonization by methicillin-susceptible Staphylococcus aureus and methicillin-resistant coagulase-negative staphylococci was detected in 8/235 (3.4%) specimens. Consequently, in a low-methicillin-resistant S. aureus (MRSA) setting, a molecular MRSA screening test targeting the mecA gene and an S. aureus-specific gene in parallel and applied directly to clinical specimens would be associated with an unacceptable positive predictive value of about 40%.
Synthesis of Optically Active Nine‐Membered Ring Lactams by a Zwitterionic Aza‐Claisen Reaction (1995)

Ring expansion with complete chirality transfer takes place in the title reaction in which proline derivatives 1 are converted into lactams 2 under mild conditions.
Improved Determination of Total Serum Lipids by the Sulfo-Phospho-Vanillin Reaction (1972)

Abstract We have modified and improved a colorimetric method for determining total serum lipids [Amer. J. Clin. Pathol. 53, 89 (1970)]. The improved procedure requires only 20 µl of serum, and the entire determination is done in one tube, thus eliminating the tedious pipetting of a concentrated sulfuric acid-serum digest. The phospho-vanillin reagent has been modified so that the linearity of the method now extends to 1250 mg/dl. Concentrations up to 1240 mg/dl or of bilirubin up to 20 mg/dl in the serum do not interfere. The relative standard deviation for the method (day-to-day) is 4.9%.
Toward a Practice of Autonomous Systems: Proceedings of the First European Conference on Artificial Life (1992)

Part 1 Autonomous robots: artificial life and real robots, Rodney A. Brooks concept formation as emergent phenomena, Mukesh J. Patel and Uwe Schnepf distributed adaptive control - a paradigm for designing autonomous agents, Rolf Pfeifer and Paul Verschure taking eliminative materialism seriously - a methodology for autonomous systems research, Tim Smithers an adaptable mobile robot, Leslie Pack Kaelbling learning behaviour networks from experience, Pattie Maes characterizing adaptation by constraint, Ian Horswill on the self-organizing properties of topological maps, Didier Keymeulen and Jo Decuyper massively parallel evolution of recurrent networks - an approach to temporal processing, Piet Spiessens and Jan Torreele neural networks for visual tracking in an artificial fly, Dave Cliff an approach to sensorimotor relevance, Eric Dedieu and Emmanuel Mazer using motor actions for location recognition, Ulrich Nehmzow and Tim Smithers the application of temporal difference learning to the neural control of quadruped locomotion, Martin Snaith and Owen Holland evolution of subsumption using genetic programming, John R. Koza. Part 2 Swarm intelligence: warm-made architectures, Jean-Louis Deneubourg, et al distributed optimization by ant colonies, Alberto Colorni, et al emergent colonization in an artificial ecology, Andrew M. Assad and Norman H. Packard the maximum entropy principle and sensing in swarm intelligence, Gerardo Beni and Susan Hackwood a behavioural simulation model for the study of emergent social structures, Alexis Drogoul, et al interactive evolution of dynamical systems, Karl Sims simulating co-evolution with mimetism, Nicolas Meuleau dynamics of artificial markets - speculative markets and emerging Common Sense knowledge, Christian Nottola, et al harvesting by a group of robots, S. Goss and J.L. Deneubourg. Part 3 Learning and evolution: learning, behaviour and evolution, Domenico Parisi, et al immune network and adaptive control, Hugues Bersini genetic self-learning, Frank Hoffmeister and Thomas Back Darwin's continent cycle theory and its simulation by the prisoner's dilemma, Heinz Muhlenbein the royal road for genetic algorithms - fitness landscapes and GA performance, Melanie Mitchell, et al using marker-based genetic encoding of neural networks to evolve finite-state behaviour, Brad Fullmer and Risto Miikkulainen self-adaptation in genetic algorithms, Thomas Back steerable GenNets - the genetic programming of steerable behaviours in GenNets, Hugo de Garis an action based neural network for adaptive control - the tank case study, Antonio Rizzo and Neil Burgess a model of formal neural network for non-supervised learning and recognition of temporal sequences, Bruno Gas. (Part contents)
Inconsistency of the immunophenotype of Reed-Sternberg cells in simultaneous and consecutive specimens from the same patients. A paraffin section evaluation in 56 patients. (1992)

Both immunophenotypic overlaps between Hodgkin's disease (HD) and non-Hodgkin's lymphoma (NHL), and evolution of one into the other have been reported. However, the underlying assumption that the antigenic expression of Reed-Sternberg (RS) cells is consistent in the same patient has not been evaluated. Such an evaluation was undertaken by immunophenotyping paraffin-embedded lymphoid tissue biopsies with HD from 56 patients in whom multiple specimens were obtained, either simultaneously from different sites or at different times. The panel of antibodies we used included: CD3 polyclonal antiserum, DAKO-M1 (CD15), L26 (CD20), BerH2 (CD30), MT1 (CD43), DAKO-LCA (CD45RB), UCHL1 (CD45R0), LN2 (CD74), and DAKO-EMA. The phenotype of RS cells was identical in simultaneous biopsies in only 11 of 39 patients (28%) and remained constant in consecutive biopsies in only 4 of 21 patients (19%). Major differences (relative to cell lineage specific antigens) were observed in 10 of 39 patients with simultaneous biopsies and in 10 of 21 patients over time; they mainly involved expression of T-cell antigens. Minor differences (relative to any other antigen) were observed in 22 of 39 patients with simultaneous biopsies and in 15 of 21 patients over time; these mainly involved CD15 or CD74. This striking variability of the immunophenotype of RS cells in the same patient may be due to aberrant marker expression, as a result of the neoplastic state, and/or to modulation of antigenic expression in relation to the host environment. This inconsistency suggests caution when interpreting the relationship between HD and NHL by paraffin immunophenotyping alone.
Tim-3 is an inducible human natural killer cell receptor that enhances interferon gamma production in response to galectin-9 (2012)

NK-cell function is regulated by the integration of signals received from activating and inhibitory receptors. Here we show that a novel immune receptor, T-cell Ig and mucin-containing domain-3 (Tim-3), is expressed on resting human NK cells and is up-regulated on activation. The NK92 NK-cell line engineered to overexpress Tim-3 showed a marked increase in IFN-γ production in the presence of soluble rhGal-9 or Raji tumor cells engineered to express Gal-9. The Tim-3(+) population of low-dose IL-12/IL-18-activated primary NK cells significantly increased IFN-γ production in response to soluble rhGal-9, Gal-9 presented by cell lines, and primary acute myelogenous leukemia (AML) targets that endogenously express Gal-9. This effect is highly specific as Tim-3 Ab blockade significantly decreased IFN-γ production, and Tim-3 cross-linking induced ERK activation and degradation of IκBα. Exposure to Gal-9-expressing target cells had little effect on CD107a degranulation. Reconstituted NK cells obtained from patients after hematopoietic cell transplantation had diminished expression of Tim-3 compared with paired donors. This observation correlates with the known IFN-γ defect seen early posttransplantation. In conclusion, we show that Tim-3 functions as a human NK-cell coreceptor to enhance IFN-γ production, which has important implications for control of infectious disease and cancer.
Formation of diamond-like carbon films and carbon foam by ultrafast laser ablation (2000)

The ultra-fast ablation of a graphite target using high repetition rate Nd:YAG lasers allows us to deposit two distinctly different carbonaceous structures, depending on the ambient Ar pressure: a diamond-like carbon film with the surface finish down to atomic level at a pressure below 0.1 Torr, and a fractal C nanofoam with air-like density and diamond-like resistivity at higher pressure. The experimental characterization of vapors and carbonaceous materials produced is presented and compared to the theoretical predictions. The analysis of the formation conditions leads to the qualitative understanding of the formation mechanism for both C structures.
Characterization of electrowetting actuation on addressable single-side coplanar electrodes (2006)

This paper studies and characterizes electrowetting-on-dielectric (EWOD) actuations on coplanar electrodes with an electrode-free cover plate or no cover plate. By arranging driving and reference electrodes on one plate, such an EWOD configuration can accommodate more sensing mechanisms from above and thus allows increased flexibility for system development. Various coplanar electrodes are tested for contact angle changes by EWOD with a focus on the effect of the percentage gap between electrodes and are found to be in good agreement with a simple analytical model. The droplet-moving devices demonstrate the successful moving, cutting and merging of droplets (∼0.1 µl) in a parallel-plate configuration, i.e., between the driving plate with coplanar electrodes and the passive plate with no electrode. EWOD actuation in single plate configuration, i.e. no cover plate, is also demonstrated, adding additional flexibility for the system design.
Experimental studies on wavelength division bidirectional optical amplifiers using an Er/sup 3+/-doped fiber (1994)

This paper presents a novel structure of an Er/sup 3+/-doped fiber amplifier capable of bidirectional operation through the wavelength division multiplex method. The idea is to combine an Er/sup 3+/-doped fiber, pump devices, optical isolators, and wavelength selective couplers so that two lightwaves having different wavelengths pass each proper isolator. The suitable structure was determined from experimental studies on several basic amplifier configurations. Optical gains of more than 25 dB were attained in both wavelength regions of 1.533 /spl mu/m and 1.55 /spl mu/m. Successful bidirectional operation of the amplifier was confirmed by means of a 2.488-Gbit/s-signal transmission experiment.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A Synthesizable IP Core for WIMAX 802.16E LDPC Code Decoding (2006)

The upcoming IEEE WiMax 802.16e standard, also referred to as WirelessMAN (2005), is the next step toward very high throughput wireless backbone architectures, supporting up to 500 Mbps. It features as an advanced channel coding scheme low-density parity-check codes. The decoding of LDPC codes is an iterative process, hence many data have to be exchanged between processing units within each iteration. The variety of the specified codes and the envision of different decoding schedules for different codes pose significant challenges to an LDPC decoder hardware realization. In this paper, we present to the best of our knowledge the first published LDPC decoder architecture capable to process all specified WiMax LDPC codes. Detailed synthesis and communications performance results are shown in addition
Safety and immunotoxicity assessment of immunomodulatory monoclonal antibodies (2010)

Most therapeutic monoclonal antibodies (mAbs) licensed for human use or in clinical development are indicated for treatment of patients with cancer and inflammatory/autoimmune disease and as such, are designed to directly interact with the immune system. A major hurdle for the development and early clinical investigation of many of these immunomodulatory mAbs is their inherent risk for adverse immune-mediated drug reactions in humans such as infusion reactions, cytokine storms, immunosuppression and autoimmunity. A thorough understanding of the immunopharmacology of a mAb in humans and animals is required to both anticipate the clinical risk of adverse immunotoxicological events and to select a safe starting dose for first-in-human (FIH) clinical studies. This review summarizes the most common adverse immunotoxicological events occurring in humans with immunomodulatory mAbs and outlines non-clinical strategies to define their immunopharmacology and assess their immunotoxic potential, as well as reduce the risk of immunotoxicity through rational mAb design. Tests to assess the relative risk of mAb candidates for cytokine release syndrome, innate immune system (dendritic cell) activation and immunogenicity in humans are also described. The importance of selecting a relevant and sensitive toxicity species for human safety assessment in which the immunopharmacology of the mAb is similar to that expected in humans is highlighted, as is the importance of understanding the limitations of the species selected for human safety assessment and supplementation of in vivo safety assessment with appropriate in vitro human assays. A tiered approach to assess effects on immune status, immune function and risk of infection and cancer, governed by the mechanism of action and structural features of the mAb, is described. Finally, the use of immunopharmacology and immunotoxicity data in determining a minimum anticipated biologic effect Level (MABEL) and in the selection of safe human starting dose is discussed.
Atomic-resolution transmission electron microscopy of electron beam–sensitive crystalline materials (2018)

High-resolution imaging of electron beam-sensitive materials is one of the most difficult applications of transmission electron microscopy (TEM). The challenges are manifold, including the acquisition of images with extremely low beam doses, the time-constrained search for crystal zone axes, the precise image alignment, and the accurate determination of the defocus value. We develop a suite of methods to fulfill these requirements and acquire atomic-resolution TEM images of several metal organic frameworks that are generally recognized as highly sensitive to electron beams. The high image resolution allows us to identify individual metal atomic columns, various types of surface termination, and benzene rings in the organic linkers. We also apply our methods to other electron beam-sensitive materials, including the organic-inorganic hybrid perovskite CH<sub>3</sub>NH<sub>3</sub>PbBr<sub>3</sub>.