gebhart/patrepeval huggingface dataset:
A survey of mobile phone sensing (2010)

Mobile phones or smartphones are rapidly becoming the central computer and communication device in people's lives. Application delivery channels such as the Apple AppStore are transforming mobile phones into App Phones, capable of downloading a myriad of applications in an instant. Importantly, today's smartphones are programmable and come with a growing set of cheap powerful embedded sensors, such as an accelerometer, digital compass, gyroscope, GPS, microphone, and camera, which are enabling the emergence of personal, group, and communityscale sensing applications. We believe that sensor-equipped mobile phones will revolutionize many sectors of our economy, including business, healthcare, social networks, environmental monitoring, and transportation. In this article we survey existing mobile phone sensing algorithms, applications, and systems. We discuss the emerging sensing paradigms, and formulate an architectural framework for discussing a number of the open issues and challenges emerging in the new area of mobile phone sensing research.
Concentrations of EpCAM ectodomain as found in sera of cancer patients do not significantly impact redirected lysis and T-cell activation by EpCAM/CD3-bispecific BiTE antibody MT110 (2011)

Ectodomains of target antigens for antibody-based therapies can be shed from the target cell surface and found in sera of patients. Shed ectodomains of therapeutic targets not only pose the risk of sequestering therapeutic antibodies but, in a multimeric form, of triggering T cell activation by bispecific antibodies binding to CD3 on T cells. Recently, epithelial cell adhesion molecule (EpCAM) has been shown to be activated by release of its ectodomain, called EpEX. Here, we show that only very low amounts of EpEX are detectable in sera of cancer patients. Among 100 cancer patient samples tested, only 17 (17%) showed serum levels of EpEX in excess of 0.05 ng/ml with highest EpEX concentrations of 5.29, 1.37 and 0.52 ng/ml. A recombinant form of human EpEX (recEpEX) was produced to assess its possible effect on redirected lysis and T cell activation by EpCAM/CD3-bispecific BiTE antibody MT110, currently being tested in patients with solid tumor malignancies. RecEpEX had a very minor effect on redirected lysis by MT110 with an approximate IC 50 value of 3,000 ng/ml, which is a concentration close to three orders of magnitude higher than the highest EpEX concentration found in cancer patients. Concentrations of 30 ng/ml EpEX in combination with 250 ng/ml MT110 were minimally required to induce a detectable activation of CD4 (+) and CD8 (+) T cells. We conclude that soluble EpEX in sera of cancer patients is unlikely to pose an issue for the efficacy or safety of MT110, and perhaps other antibodies binding to N-terminal epitopes of EpCAM.
PCR Detection of Escherichia coli O157:H7 Directly from Stools: Evaluation of Commercial Extraction Methods for Purifying Fecal DNA (2000)

Rapid identification of Escherichia coli O157:H7 is important for patient management and for prompt epidemiological investigations. We evaluated one in-house method and three commercially available kits for their ability to extract E. coli O157:H7 DNA directly from stool specimens for PCR. Of the 153 stool specimens tested, 107 were culture positive and 46 were culture negative. The sensitivities and specificities of the in-house enrichment method, IsoQuick kit, NucliSens kit, and QIAamp kit were comparable, as follows: 83 and 98%, 85 and 100%, 74 and 98%, and 86 and 100%, respectively. False-negative PCR results may be due to the presence of either inherent inhibitors or small numbers of organisms. The presence of large amounts of bacteria relative to the amount of the E. coli O157:H7 target may result in the lower sensitivities of the assays. All commercial kits were rapid and easy to use, although DNA extracted with the QIAamp kit did not require further dilution of the DNA template prior to PCR.
Output‐SensitiveVisibility Algorithms for Dynamic Scenes with Applications to Virtual Reality (1996)

Abstract An output‐sensitive visibility algorithm is one whose runtime is proportional to the number of visible graphic primitives in a scene model—not to the total number of primitives, which can be much greater. The known practical output‐sensitive visibility algorithms are suitable only for static scenes, because they include a heavy preprocessing stage that constructs a spatial data structure which relies on the model objects’ positions. Any changes to the scene geometry might cause significant modifications to this data structure. We show how these algorithms may be adapted to dynamic scenes. Two main ideas are used: first, update the spatial data structure to reflect the dynamic objects’ current positions; make this update efficient by restricting it to a small part of the data structure. Second, use temporal bounding volumes (TBVs) to avoid having to consider every dynamic object in each frame. The combination of these techniques yields efficient, output‐sensitive visibility algorithms for scenes with multiple dynamic objects. The performance of our methods is shown to be significantly better than previous output‐sensitive algorithms, intended for static scenes. TBVs can be adapted to applications where no prior knowledge of the objects’ trajectories is available, such as virtual reality (VR), simulations etc. Furthermore, they save updates of the scene model itself; notjust of the auxiliary data structure used by the visibility algorithm. They can therefore be used to greatly reduce the communications overhead in client‐server VR systems, as well as in general distributed virtual environments.
Importance of the character and configuration of residues B24, B25, and B26 in insulin-receptor interactions (1991)

By use of isolated canine hepatocytes and insulin analogs prepared by trypsin-catalyzed semisynthesis, we have investigated the importance of the aromatic triplet PheB24-PheB25-TyrB26 of the COOH-terminal B-chain domain of insulin in directing the affinity of insulin-receptor interactions. Analysis of the receptor binding potencies of analogs bearing transpositions or replacements (by Tyr, D-Tyr or their corresponding 3,5-diiodo derivatives) in this region demonstrates a wide divergence in the acceptance both of configurational change (with [D-TyrB24,PheB26]insulin and [D-TyrB25,PheB26]insulin exhibiting 160 and 0.1% of the receptor binding potency of insulin, respectively) and of detailed side chain structure (with [TyrB24,PheB26]insulin and [TyrB25,PheB26]insulin exhibiting 2 and 80% of the receptor binding potency of insulin, respectively). Additional experiments addressed the solvent accessibilities of the 4 tyrosine residues of insulin and the insulin analogs at selected peptide concentrations by use of analytical radioiodination. Whereas two analogs ([TyrB25,PheB26]insulin and [D-TyrB24,PheB26]insulin) were found to undergo self aggregation, no strict correlation was found between the ability of an analog to aggregate and its potency for interaction with the insulin receptor. Related findings are discussed in terms of the interplay between side chain and main chain structure in the COOH-terminal domain of the insulin B-chain and the structural attributes of insulin that determine the affinity of insulin-receptor interactions.
Serogroup B and C Serum Bactericidal Assays (2003)

Meningococci are usually classified based on serological reactivity of their polysaccharide capsules with serogroups A, B, and C, currently the most common causes of disease. Serogroup A meningococci can cause massive outbreaks particularly in areas such as the African meningitis belt, whereas other areas such as in the Americas and Europe, serogroups B and C predominate. Although licensed vaccines for serogroups A and C exist, based on the polysaccharide capsules, no such vaccine exists thus far for serogroup B owing to its poor immunogenicity in humans. This chapter discusses and details serum bactericidal assay protocols for measuring the complement-mediated lysis of serogroups B and C meningococci by human sera following vaccination or disease.
Link analysis of a deformable mirror device based optical crossbar switch (1992)

An optical crossbar switch is proposed that uses a semiconductor-addressed, deformable-mirror spatial light modulator to direct gigabit-per-second optical transmissions to several receivers. The switch performance is described in terms of size, number, and deflection range of micromechanical mirror elements, as well as emitter, detector, and lens dimensions. These parameters are incorporated in a link energy budget and estimates of system dimensions. Maximum-sized 128- to 1000-channel crossbars appear feasible based on current and projected performance limits of various lightwave components.
Preferential induction of polyclonal IgA secretion by murine Peyer's patch dendritic cell-T cell mixtures. (1984)

Polyclonal IgA secretion is inducible in murine B cells when DC-T from Peyer's patches (PP) provide the inducing stimulus. PP DC-T, which are composed predominantly of dendritic cells and Lyt-1+ T cells, are capable of dramatic augmentation of IgA secretion by PP or spleen B cells with minimal induction of IgM secretion. DC-T from spleen, however, are incapable of augmenting IgA secretion by either PP or spleen B cells. The level of IgA secretion is dependent upon the dose of DC-T providing the inducing stimulus and reaches a plateau with DC-T:B ratios of less than 1:1. This system for preferential induction of IgA responses should permit elucidation of cellular mechanisms involved in regulation of IgA secretion.
Highly Phosphorescent Bis-Cyclometalated Iridium Complexes:  Synthesis, Photophysical Characterization, and Use in Organic Light Emitting Diodes (2001)

The synthesis and photophysical study of a family of cyclometalated iridium(III) complexes are reported. The iridium complexes have two cyclometalated (C(**)N) ligands and a single monoanionic, bidentate ancillary ligand (LX), i.e., C(**)N2Ir(LX). The C(**)N ligands can be any of a wide variety of organometallic ligands. The LX ligands used for this study were all beta-diketonates, with the major emphasis placed on acetylacetonate (acac) complexes. The majority of the C(**)N2Ir(acac) complexes phosphoresce with high quantum efficiencies (solution quantum yields, 0.1-0.6), and microsecond lifetimes (e.g., 1-14 micros). The strongly allowed phosphorescence in these complexes is the result of significant spin-orbit coupling of the Ir center. The lowest energy (emissive) excited state in these C(**)N2Ir(acac) complexes is a mixture of (3)MLCT and (3)(pi-pi) states. By choosing the appropriate C(**)N ligand, C(**)N2Ir(acac) complexes can be prepared which emit in any color from green to red. Simple, systematic changes in the C(**)N ligands, which lead to bathochromic shifts of the free ligands, lead to similar bathochromic shifts in the Ir complexes of the same ligands, consistent with "C(**)N2Ir"-centered emission. Three of the C(**)N2Ir(acac) complexes were used as dopants for organic light emitting diodes (OLEDs). The three Ir complexes, i.e., bis(2-phenylpyridinato-N,C2')iridium(acetylacetonate) [ppy2Ir(acac)], bis(2-phenyl benzothiozolato-N,C2')iridium(acetylacetonate) [bt2Ir(acac)], and bis(2-(2'-benzothienyl)pyridinato-N,C3')iridium(acetylacetonate) [btp2Ir(acac)], were doped into the emissive region of multilayer, vapor-deposited OLEDs. The ppy2Ir(acac)-, bt2Ir(acac)-, and btp2Ir(acac)-based OLEDs give green, yellow, and red electroluminescence, respectively, with very similar current-voltage characteristics. The OLEDs give high external quantum efficiencies, ranging from 6 to 12.3%, with the ppy2Ir(acac) giving the highest efficiency (12.3%, 38 lm/W, >50 Cd/A). The btp2Ir(acac)-based device gives saturated red emission with a quantum efficiency of 6.5% and a luminance efficiency of 2.2 lm/W. These C(**)N2Ir(acac)-doped OLEDs show some of the highest efficiencies reported for organic light emitting diodes. The high efficiencies result from efficient trapping and radiative relaxation of the singlet and triplet excitons formed in the electroluminescent process.
Performance tuning of distributed applications with CoSMoS (2002)

Performance monitoring of distributed software executing on workstation cluster systems is a complex task because of the multitude of factors that can affect performance in these environments. For performance analysis to be done effectively, all runtime events which have an impact on performance have to be captured. We introduce an integrated monitoring system that is capable of recording performance data on the application level, the operating system level, and the network level. It is thus able to provide complete coverage of all subsystems relevant to application performance. One of the key features of the proposed monitoring system is its ability to correlate performance data with application source code, pointing the developer to the portions of his code that may be time-critical. The system thus supports a cyclic process of optimizing performance in multiple iterations of analysis and refinement. This method allows performance bottlenecks to be tracked down to source code instruction level.
Extraction and tracking of the tongue surface from ultrasound image sequences (2002)

This paper presents a system for automatic extraction and tracking of 2D contours of the tongue surfaces from digital ultrasound image sequences. The input to the system is provided by a Head and Transducer Support System (HATS), which is developed for use in ultrasound imaging of the tongue movement. We developed a novel active contour (snakes) model that uses several temporally adjacent images during the extraction of the tongue surface contour for an image frame. The user supplies an initial contour model for a single image frame in the whole sequence. Using optical flow and multi-resolution methods, this initial contour is then used to find the candidate contour points in the temporally immediate adjacent images. Subsequently, the new snake mechanism is applied to estimate optimal contours for each image frame using these candidate points. In turn, the extracted contours are used as models for the extraction process of new adjacent frames. Finally, the system uses a novel postprocessing technique to refine the positions of the contours. We tested the system on 11 different speech sequences, each containing about 25 images. Visual inspection of the detected contours by the speech experts shows that the results are very promising and this system can be effectively employed in speech and swallowing research.
Nuclear Overhauser Effect and Computational Characterization of the β-Spiral of the Polypentapeptide of Elastin (1989)

The structure of the elastin polypentapeptide, poly(VPGVG), was studied by nuclear Overhauser effect experiments using perdeuterated Val1 and Val4 samples under the condition where intermolecular interactions are absent. More extensive interaction was found between the Val1 gamma CH and Pro2 beta CH protons than between the Val4 gamma CH and Pro2 beta CH protons. The Val1 gamma CH3-Pro2 beta CH interaction does not occur within the same pentamer as previously shown experimentally and as expected from steric considerations. The results are incompatible with the presence of a random chain network in poly(VPGVG) at room temperature but are readily explicable in terms of interturn interactions in a beta-spiral structure. More specifically, the results indicate that the beta-spiral conformation with 2.9 pentamers/turn is more prevalent than that with 2.7 pentamers/turn. Using conformations developed by molecular mechanics calculations, molecular dynamics simulations were carried out to compare the relative energies of these two variants of this class of beta-spiral structures. It was found in vacuo that the structure with 2.9 pentamers/turn is indeed more stable than that of 2.7 pentamers/turn by approximately 1 kcal/mole-pentamer.
Secreted Klotho protein in sera and CSF: implication for post‐translational cleavage in release of Klotho protein from cell membrane (2004)

Klotho mutant mice exhibit a set of phenotypes resembling human ageing. Although the function of Klotho remains unclear, mediation of its pleiotropic functions by putative humoral factor(s) has been presumed. Newly established antibodies against Klotho allowed the detection of secreted Klotho, a candidate for the putative humoral factor, in sera and cerebrospinal fluid. Surprisingly the secreted Klotho was 130 kDa, in contrast to the 70 kDa predicted form from klotho gene transcripts. The secreted as well as the membrane-bound Klotho proteins were suggested to form oligomerized complex. These results delineate post-translation processing of Klotho and possible regulatory mechanisms for secretion of Klotho in vivo.
Glucose-Regulated Protein 78 and Platelet Deposition (2010)

These findings demonstrate that blockade of 3-hydroxy-3-methylglutaryl-coenzyme A reductase reduces platelet deposition and inhibits GRP78 translocation from the platelet surface after shear and collagen activation. For the first time to our knowledge, this study reports on the presence and functional role of GRP78 in platelets and indicates that GRP78 has additional functions beyond those of a molecular chaperone.
Human placental syncytiotrophoblast microvillous membranes impair maternal vascular endothelial function (1997)

STBM vesicle perfusion specifically altered the relaxation response of preconstricted maternal subcutaneous fat arteries to acetylcholine, suggesting an alteration in endothelial dependent relaxation. Deported microvilli may therefore be capable of producing endothelial cell damage and endothelial dysfunction observed in the maternal syndrome of pre-eclampsia.
The hematopoietic cytokine, colony‐stimulating factor 1, is also a growth factor in the CNS: Congenital absence of CSF‐1 in mice results in abnormal microglial response and increased neuron vulnerability to injury (1995)

In this study we used op/op mice, which are deficient in the hematopoietic cytokine, colony-stimulating factor 1 (CSF-1), to determine the effect of CSF-1 on neuronal survival and microglial response in injury. In normal mice microglia express the CSF-1 receptor and are primarily regulated by CSF-1, produced mainly by astrocytes. The CSF-1 deficiency in op/op mice results in a depletion in the number of monocytes and macrophages but does not affect the number or morphology of microglia. We produced an ischemic lesion in the cerebral cortex of mice by disrupting the pia-arachnoid blood vessels in a defined area. Using Nissl stain and astrocyte- and microglia-specific antibodies, we determined the number of viable neurons in such injury and the intensity of glial reaction. The cellular response to injury on the operated side of op/op mice was compared to that on the non-operated contralateral side and to the cellular response in similar lesions in CSF-1 producing C3H/HeJ mice. We found that the systemic lack of CSF-1 in op/op mice results in a significant increase in neuron vulnerability to ischemic injury and considerably reduced microglial response to neuron injury. Remedying the CSF-1 deficiency, either by grafting CSF-1 secreting astroglia into the brain or by implanting encapsulated CSF-1 secreting fibroblast-like cells into the peritoneum, partially restores the microglial response to neuron injury and significantly potentiates neuronal survival in cerebral cortex ischemic lesions. Astroglial reaction was approximately the same in the lesions in op/op mice, grafted and implanted op/op mice and C3H/HeJ mice, indicating that CSF-1 modulates microglia, but not the response of astrocytes to injury. The degree of neuronal survival was not correlated to the degree of microglial proliferation and intensity of their reaction. We report some indications that CSF-1, in addition to modulation of microglia, may also act directly on neurons.
Premetastatic Niches (2010)

This chapter contains sections titled: Introduction 'Seeds' influencing the 'Soil' Cellular components of premetastatic niches ECM components of premetastatic niches Premetastatic niche formation precedes metastatic growth Therapeutic targeting of the premetastatic niche Evidence for premetastatic niches in the clinic Concluding remarks References
A sea urchin gene encoding dystrophin-related proteins (1998)

The gene which is defective in Duchenne muscular dystrophy (DMD) is the largest known gene. The product of the gene in muscle, dystrophin, is a 427 kDa protein. The same gene encodes at least six additional products: two non-muscle dystrophin isoforms transcribed from promoters located in the 5'-end region of the gene and four smaller proteins transcribed from internal promoters located further downstream. Several other genes, encoding evolutionarily related proteins, have been identified. These include a structurally very similar gene in vertebrates encoding utrophin (DRP1), which is closely related to dystrophin, and a number of small and simple genes in vertebrates or invertebrates encoding proteins similar to some of the small products of the DMD gene. We have isolated a sea urchin gene showing very strong sequence and structural homology with the DMD and utrophin genes. Sequence and intron/exon structure similarities suggest that this gene is related to a precursor of both the DMD gene and the gene encoding utrophin. The sea urchin gene has the unique complex structure of the DMD gene. There is at least one, and possibly more, product(s) transcribed from internal promoters, as well as a large product of >300 kDa containing at least three of the four major domains of dystrophin. The small product seems to be evolutionarily related to Dp116, one of the small products of the human DMD gene. Partial characterization of this gene helped us to construct an evolutionary tree connecting the vertebrate dystrophin gene family with related genes in invertebrates. The constructed evolutionary tree also implies that the vertebrate small and simple structured gene encoding a Dp71-like protein, called DRP2 , evolved from the dystrophin/utrophin ancestral large and complex gene by a duplication of only a small part of the gene.
Nephritogenic antigen determinants in epidermal and renal basement membranes of kindreds with Alport-type familial nephritis. (1986)

We probed epidermal basement membranes (EBM) of acid-urea denatured skin from members of kindreds with Alport-type familial nephritis (FN) for the presence of antigens reactive with Goodpasture sera (GPS) and serum (FNS) from an Alport patient who developed anti-glomerular basement membrane (GBM) nephritis in a renal allograft. By immunoblotting, GPS reacted primarily with the 28,000 molecular weight (mol wt) monomer but also the 24,000 mol wt and 26,000 mol wt monomers of the noncollagenous globular domain (NC1) of type IV collagen from normal human GBM, while FNS identified only the 26,000-mol wt monomer. FNS reacted with EBM of 12 controls and nine unaffected male kindred members but not EBM of eight affected males. Five affected females exhibited interrupted reactivity of FNS with EBM. GPS showed variable reactivity with EBM and was not discriminating with respect to Alport-type FN. FNS did not stain renal basement members of five affected males. However, the EBM, tubular basement membrane, and Bowman's capsules of affected males contained antigens reactive with GPS. These immunochemical studies suggest that the FNS antigen is distinct from Goodpasture antigen(s). The expression of FNS antigen located on the NC1 domain of type IV collagen is altered in basement membranes of patients with Alport-type FN, and the distribution of this antigenic anomaly within kindreds suggests X-linked dominant transmission of a defective gene.