gebhart/patrepeval huggingface dataset:
Peptide-induced conformational changes in class I heavy chains alter major histocompatibility complex recognition. (1992)

Small peptides, derived from endogenous proteins bind within the antigen binding groove created by the beta-pleated sheets and alpha helices of the alpha 1 and alpha 2 domains of the class I molecule of the major histocompatibility complex (MHC). However, the precise role of peptide in class I MHC conformation remains unclear. Here, we have shown that, in at least some instances, changes induced in the MHC molecule by the binding of distinct peptides can be identified as specific alterations in serological epitopes expressed on the class I protein. The nature of specific peptides expressed by class I-bearing cells may, therefore, have a dramatic influence on T cell development, self-tolerance, and alloreactivity.
Production of Spontaneous Diploid Lines from Isolated Microspores Following Cryopreservation in Spring Rapeseed (<i>Brassica napus</i> L.) (1992)

Abstract Cryopreservation of microspores provides a potentially powerful means for increasing percentage of spontaneous diploids in microspore‐derived populations in rapeseed ( Brassica napus L.). This study was to investigate the production of spontaneous diploid lines in relation to steps of cryopreserving micro‐spores of two spring rapeseed breeding lines G‐231 and M3‐124. Microspores of both genotypes were isolated and subjected to Cryopreservation. The step of cooling process (before liquid nitrogen immersion) in a Cryopreservation protocol resulted in high percentages of spontaneous diploids in lines regenerated from frozen microspores in both genotypes. Liquid nitrogen immersion and subsequent thawing process had no influence on the percentage of spontaneous diploids. A linear relationship between percentage of spontaneous diploids and cooling temperatures was detected. The lowest cooling temperature of −40 °C yielded the highest percentages of spontaneous diploids (51.1 % in G‐231 and 47.7 % in M3‐124, respectively), which were more than doubled in comparison to those in the corresponding unfrozen controls. The current study indicated that cold treatment may be utilized to greatly enhance the percentage of spontaneous diploids in rapeseed breeding programs.
Binding of Urokinase-type Plasminogen Activator to Its Receptor in MCF-7 Cells Activates Extracellular Signal-regulated Kinase 1 and 2 Which Is Required for Increased Cellular Motility (1998)

Binding of urokinase-type plasminogen activator (uPA) to its receptor, uPAR, regulates cellular adhesion, migration, and tumor cell invasion. Some of these activities may reflect the ability of uPAR to initiate signal transduction even though this receptor is linked to the plasma membrane only by a glycosylphosphatidylinositol anchor. In this study, we demonstrated that single-chain uPA activates extracellular signal-regulated kinase 1 (ERK1) and ERK2 in MCF-7 breast cancer cells. Phosphorylation of ERK1 and ERK2 was increased 1 min after adding uPA and returned to baseline levels by 5 min. The amino-terminal fragment (ATF) of uPA, which binds to uPAR but lacks proteinase activity, also activated ERK1 and ERK2. Responses to uPA and ATF were eliminated when the cells were pretreated with PD098059, an inhibitor of mitogen-activated protein kinase kinase. uPA and ATF promoted the migration of MCF-7 cells across serum-coated Transwell membranes in vitro. Migration was increased 2.1 +/- 0.4-fold when uPA was added to the top chamber, 4. 8 +/- 0.8-fold when uPA was added to the bottom chamber, and 7.7 +/- 1.0-fold when uPA was added to both chambers. MCF-7 cells that were pulse-exposed to uPA for 30 min, and then washed to remove unbound ligand, demonstrated increased motility even though migration was allowed to occur for 24 h. PD098059 completely neutralized the effects of uPA on MCF-7 cellular motility, irrespective of whether the uPA was present for the entire motility assay or administered by pulse-exposure. These results demonstrate a novel, receptor-dependent signaling activity which is required for uPA-stimulated breast cancer cell migration.
Evaluating image segmentation algorithms using monotonic hulls in fitness/cost space (2001)

Image segmentation is the first stage of processing in many practical computer vision systems. While development of particular segmentation algorithms has attracted considerable research interest, relatively little work has been published on the subject of their evaluation. In this paper we propose a framework for quantitative evaluation of segmentation algorithms which we believe addresses shortcomings of previous approaches, and use this framework to compare several state-of-the-art algorithms.
Fluorescence Resonance Energy Transfer in CdSe/ZnS−DNA Conjugates:  Probing Hybridization and DNA Cleavage (2005)

Nucleic-acid-functionalized CdSe/ZnS quantum dots (QDs) were hybridized with the complementary Texas-Red-functionalized nucleic acid. The hybridization was monitored by following the fluorescence resonance energy transfer from the QDs to the dye units. Treatment of the QD/dye DNA duplex structure with DNase I resulted in the cleavage of the DNA and the recovery of the fluorescence properties of the CdSe/ZnS QDs. The luminescence properties of the QDs were, however, only partially recovered due to the nonspecific adsorption of the dye onto the QDs. Similarly, nucleic-acid-functionalized Au nanoparticles (Au NPs) were hybridized with the complementary Texas-Red-labeled nucleic acid. The hybridization was followed by the fluorescence quenching of the dye by the Au NPs. Treatment of the Au NP/dye DNA duplex with DNase I resulted in the cleavage of the DNA and the partial recovery of the dye fluorescence. The incomplete recovery of the dye fluorescence originated from the nonspecific binding of the dye units to the Au NPs. The nonspecific binding of the dye to the CdSe/ZnS QDs and the Au NPs is attributed to nonprotected surface vacancies in the two systems.
Traffic analysis of Ethernet-PON in FTTH trial service (2003)

Applicability of Ethernet-PON systems providing real-time broadband services such as video streaming and voice over IP to the commercial FTTH service has been confirmed through the traffic analyses in the FTTH field trial.
Organization of Cortical and Thalamic Input to Pyramidal Neurons in Mouse Motor Cortex (2013)

Determining how long-range synaptic inputs engage pyramidal neurons in primary motor cortex (M1) is important for understanding circuit mechanisms involved in regulating movement. We used channelrhodopsin-2-assisted circuit mapping to characterize the long-range excitatory synaptic connections made by multiple cortical and thalamic areas onto pyramidal neurons in mouse vibrissal motor cortex (vM1). Each projection innervated vM1 pyramidal neurons with a unique laminar profile. Collectively, the profiles for different sources of input partially overlapped and spanned all cortical layers. Specifically, orbital cortex (OC) inputs primarily targeted neurons in L6. Secondary motor cortex (M2) inputs excited neurons mainly in L5B, including pyramidal tract neurons. In contrast, thalamocortical inputs from anterior motor-related thalamic regions, including VA/VL (ventral anterior thalamic nucleus/ventrolateral thalamic nucleus), targeted neurons in L2/3 through L5B, but avoided L6. Inputs from posterior sensory-related thalamic areas, including POm (posterior thalamic nuclear group), targeted neurons only in the upper layers (L2/3 and L5A), similar to inputs from somatosensory (barrel) cortex. Our results show that long-range excitatory inputs target vM1 pyramidal neurons in a layer-specific manner. Inputs from sensory-related cortical and thalamic areas preferentially target the upper-layer pyramidal neurons in vM1. In contrast, inputs from OC and M2, areas associated with volitional and cognitive aspects of movements, bypass local circuitry and have direct monosynaptic access to neurons projecting to brainstem and thalamus.
Characterization of polyesterurethane degradation products (1994)

Abstract Microthane foam, a poly(ester)urethane, used as a covering of some breast implants (Meme or Replicon by Surgitek) degrades readily in phosphate buffer pH 7.4 producing multiple unknown products in addition to 2,4 and 2,6 toluenediamine (TDA). The cumulative weight loss of the foam in buffer was 1.5% at 1 week and 2% at 2 weeks. Multiple peak molecular weights from 105 to 665 000 were found in the aqueous foam extracts following 2 weeks of incubation at 37°C using size exclusion chromatography (SEC). TDA was measured in the foam buffer extracts by high pressure liquid chromatography (HPLC) and confirmed by gas chromatography/mass spectroscopy (GC/MS). The total cumulative levels of 2,4 TDA and 2,6 TDA measured were 3 ± 0.65 μg/g of foam and 1.13 ± 0.19 μg/g of foam following 36 days of incubation at 37 °C. Higher amounts, 8.96 μg/g of 2,4 TDA and 3.3 μg/g of 2,6 TDA, were obtained at 50 °C. The cumulative release of TDA in aqueous extracts was found to correlate linearly with time suggesting a slow but continuous production of TDA under neutral conditions. However, less than 0.2 μg/g of TDA was detected as residual TDA in the methylene chloride extracts following up to 60 days at 37 °C. PU foam extracted with methylene chloride under similar conditions showed higher foam weight loss, 4.4 and 5% at 1 and 2 weeks, respectively. The results presented in this study provide further evidence that Microthane undergoes hydrolysis under neutral conditions in aqueous solutions producing TDA and other unknown low molecular weight components and oligomers. © 1994 John Wiley & Sons, Inc.
Antisense against Amyloid-β Protein Precursor Reverses Memory Deficits and Alters Gene Expression in Neurotropic and Insulin-Signaling Pathways in SAMP8 Mice (2015)

The senescence-accelerated mouse (SAMP8) strain exhibits an age-related decrease in memory accompanied by an increase in hippocampal amyloid-β protein precursor (AβPP) and amyloid-β peptide (Aβ). We have shown that administration of an antisense oligonucleotide against the Aβ region of AβPP (AβPP antisense) reverses the memory deficits. The purpose of this study was to determine the effect of peripheral (IV) administration of AβPP antisense on hippocampal gene expression. The AβPP antisense reversed the memory deficits and altered expression of 944 hippocampal genes. Pathway analysis showed significant gene expression changes in nine pathways. These include the MAPK signaling pathway (p = 0.0078) and the phosphatidylinositol signaling pathway (p = 0.043), which we have previously shown to be altered in SAMP8 mice. The changes in these pathways contributed to significant changes in the neurotropin (p = 0.0083) and insulin signaling (p = 0.015) pathways, which are known to be important in learning and memory. Changes in these pathways were accompanied by phosphorylation changes in the downstream target proteins p70S6K, GSK3β, ERK, and CREB. These changes in hippocampal gene expression and protein phosphorylation may suggest specific new targets for antisense therapy aimed at improving memory.
Vertical cavity lasers based on vertically coupledquantum dots (1997)

Ground state lasing is reported for vertical cavity lasers containing three-period InGaAs/GaAs vertically coupled quantum dot active regions. The structures include selectively oxidised AlO current apertures and AlO/GaAs reflectors. Experimental devices emitting near 1.0 µm operate continuous wave at 20°C with threshold currents <200 µA and peak power conversion efficiencies exceeding 10%.
Evidence of space weathering in regolith breccias I: Lunar regolith breccias (2005)

Abstract— We have analyzed a suite of lunar regolith breccias in order to assess how well space weathering products can be preserved through the lithification process and therefore whether or not it is appropriate to search for space weathering products in asteroidal regolith breccia meteorites. It was found that space weathering products, vapor/sputter deposited nanophase‐iron‐bearing rims in particular, are easily identified in even heavily shocked/compacted lunar regolith breccias. Such rims, if created on asteroids, should thus be preserved in asteroidal regolith breccia meteorites. Two additional rim types, glass rims and vesicular rims, identified in regolith breccias, are also described. These rims are common in lunar regolith breccias but rare to absent in lunar soils, which suggests that they are created in the breccia‐forming process itself. While not “space weathering products” in the strictest sense, these additional rims give us insight into the regolith breccia formation process. The presence or absence of glass and/or vesicular rims in asteroidal regolith breccias will likewise tell us about environmental conditions on the surface of the asteroid body on which the breccia was created.
Oxide Removal and Selective Etching of In from InSb(100) with TiCl<sub>4</sub> (2011)

The reaction of TiCl4 with a native oxide-covered InSb(100) film grown epitaxially on GaAs(100) was investigated using X-ray photoelectron spectroscopy, scanning electron microscopy, and atomic force microscopy. At room temperature and low pressure (∼3 × 10–7 Torr), TiCl4 reacted with In and Sb oxides, producing a stable indium chloride overlayer and removing a small amount of Sb, likely as SbCl3, after a subsequent vacuum annealing step at 500 K. About 25% of the O was removed, likely as TiOCl2, and a submonolayer of TiO2 was deposited, which competed with oxide etching. When TiCl4 was dosed with the substrate temperature maintained at 470–560 K, the etching reaction prevailed, resulting in complete removal of the native oxide without depositing TiO2. Heating alone could not account for the results because the oxide desorption onset was 550 K and some oxide was present even after annealing in vacuum to 650 K. TiCl4 exposure at elevated temperatures not only removed the native oxide but also preferentially etched substrate In atoms by forming volatile indium chlorides. Residual indium chlorides remained on the surface in the 470–530 K range but were completely removed at 500–560 K. The depletion of In from the surface promoted the out-diffusion of In from the substrate, allowing bulk etching and accumulation of at least a 72 Å thick Sb layer. Accumulation of Sb on the surface is consistent with a higher kinetic barrier for chlorination of Sb compared to In. The atomic ratio of Ti to Sb in elemental states was 0.43–0.46, suggesting TiSb2 alloy formation. Surface height modulations on the order of 100 nm and the presence of pits and grain boundaries were observed.
Two-Layer Electroplated Microcoils With a PECVD Silicon Dioxide Interlayer Dielectric (2008)

This paper covers the design, fabrication, and characterization of two-layer microcoils wherein an unannealed plasma-enhanced CVD SiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> functions as the insulator between silicon- and photoresist-molded copper coils. This design overcomes the thermal limitations placed upon coils that are embedded within polymer molds and thereby enables higher current carrying capability. The fabrication process is compatible with deep reactive-ion etching and may be used to integrate coils with flexures/compliant mechanisms. Thermal and mechanical limitations were determined experimentally and used to create design rules that limit the coil design space. The breakdown strength of the unannealed SiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> was measured at 4.6 MV/cm. Experiments show that coils with 40-mum pitch, 30 times 30-mum <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> winding cross section, and SiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> thickness of 1 mum may carry more than 1 A (larger than 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">9</sup> A/m <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> ) with less than 10degC temperature change. These characteristics make the coils useful in small-scale actuators and power systems.
Breast Cancer: Serum TPS as a Biomarker (2014)

Cytokeratin tumor markers are traditionally used as serological markers in various epithelial cell-associated carcinomas, such as breast, lung, colorectal, and bladder cancer. Cytokeratin reflects the proliferative activity of tumor cells (Barak et al. 2004). Tissue polypeptide-specific antigen (TPS) is a cytokeratin marker that quantitates a critical epitope structure of peptide in serum associated with human cytokeratin 18. TPS is detected using the monoclonal antibody, M3 (Bonfrer et al. 1994; Rydlander et al. 1996, D' Alessandro et al. 2001). The M3 epitope is related to the proliferative activity of the tumor (O'Hanlon et al. 1996). Since the well-known serum tumor markers in breast cancer, including CA 15-3 and CEA, do not reflect proliferative activity, TPS may be more beneficial as a prognostic indicator. TPS has consistently been reported as an effective serum marker for providing prognostic information and establishing patient responses to therapy. A main limitation of TPS is that it is not “organ specific,” which impedes diagnostic utility. Additionally, TPS levels are altered according to inflammation conditions, such as liver cirrhosis, ovulation, and menopausal status. Further clinical studies are required to fully establish the clinical utility of TPS, both alone and in combination with other established prognostic markers.
Synthetic Studies on Fostriecin and Related Natural Products (2007)

Fostriecin (CI-920), isolated from Streptomyces pulveraceus, shows in vitro antitumor activity against leukemia, lung breast and ovarian cancer, and in vivo against L 1210 and P 388 leukemia. Its analogous compounds, such as leustroducsins, phoslactomycins and cytostatin, are also known to show a variety of biological activities. One of the most characteristic biochemical features is a specific inhibitory activity against Ser/Thr protein phosphatase 2 A. Not only because of their interesting biological activities, but also in order to prove utility of new reactions and/or new synthetic methodologies, fostriecin and its analogs attract much attention as a synthetic target, and a number of synthetic studies on these compounds have been conducted, particularly since the stereostructure of fostriecin was revealed by Boger's group in 1997. In this review, we focus on the studies reported after Shibasaki's review in 2005. Recent synthetic studies on the analogous natural products, leustroducsins, phoslactomycins and cytostatin are also included.
Enhanced defense against <i>Pneumocystis carinii</i> mediated by a novel dectin-1 receptor Fc fusion protein (2007)

In the right panel of Figure
Nonlinear image processing: modeling and fast algorithm for regularization with edge detection (2002)

This paper deals with edge-preserving regularization. The definition of the regularizing functions and properties such as edge modeling or stability are studied in the variational approach (by minimizing of a criterion) and in the anisotropic diffusion approach (by solving a PDE). We propose sufficient conditions to define an edge-preserving regularizing function, and analyze comparatively several usual functions. We use the algorithm ARTUR based on the half-quadratic transform to solve the nonlinear equation. The image and the edge map are simultaneously estimated.
Ionophore A 23187-Induced Production of Slow Reacting Substance of Anaphylaxis (SRS-A) by Rat Peritoneal Cells <i>in Vitro</i>: Evidence for Production by Mononuclear Cells (1978)

Abstract A slow reacting substance is produced when mixed peritoneal cells from rats are incubated with low concentrations of the calcium ionophore A 23187 in the presence of 0.01 M cysteine. The product resembles slow reacting substance of anaphylaxis (SRS-A), if it is not identical to it, based on its behavior during chromatography on Amberlite XAD-2, silicic acid, and Sephadex LH-20; its destruction by dilute HCl and its stability in dilute alkali; its susceptibility to inactivation by aryl sulfatase; and its smooth muscle contracting activity on the guinea pig ileum and the gerbil colon. In vivo selective depletion procedures and in vitro cell isolation procedures were employed to identify the cells responsible for SRS-A production. Mast cells and mixtures of neutrophils and eosinophils produced only very small amounts of SRS-A; this could not be explained by the destruction of preformed SRS-A by these cells. The low yield of SRS-A from mast cells was also not explained by feedback inhibition caused by the histamine they released, because high concentrations of the H2 antagonist, Burimamide, caused only modest increases in SRS-A production by mast cell-containing cell suspensions. Granulocyte-depleted cell suspensions which were derived from thioglycolate-induced mononuclear cell exudates produced more SRS-A per cell than did comparable preparations from uninduced rats. The SRS-A production by induced monocytes was virtually abolished in tandem with the depletion of the phagocytic cells in the preparation. The possible implications of these findings on the source and role of SRS-A in the rat are briefly considered.
Tracking radar studies of bird migration (1972)

The application of tracking radar for determining the flight paths of migratory birds is discussed. The effects produced by various meteorological parameters are described. Samples of radar scope presentations obtained during tracking studies are presented. The characteristics of the radars and their limitations are examined.
Consistency Error Modeling-based Localization in Sensor Networks (2006)

We have developed a new error modeling and optimization-based localization approach for sensor networks in presence of distance measurement noise. The approach is solely based on the concept of consistency. The error models are constructed using non-parametric statistical techniques; they do not only indicate the most likely error, but also provide the likelihood distribution of particular errors occurring. The models are evaluated using the learn-and-test techniques and serve as the objective functions for the task of localization. The localization problem is formulated as task of maximizing consistency between measurements and calculated distances. We evaluated the approach in (i) both GPS-based and GPS-less scenarios; (ii) 1-D, 2-D and 3-D spaces, on sets of acoustic ranging-based distance measurements recorded by deployed sensor networks. The experimental evaluation indicates that localization of only a few centimeters is consistently achieved when the average and median distance measurement errors are more than a meter, even when the nodes have only a few distance measurements. The relative performance in terms of location accuracy compare favorably with respect to several state-of-the-art localization approaches. Finally, several insightful observations about the required conditions for accurate localization are deduced by analyzing the experimental results