gebhart/patrepeval huggingface dataset:
High Density O-Glycosylation on Tandem Repeat Peptide from Secretory MUC1 of T47D Breast Cancer Cells (1999)

The site-specific O-glycosylation of MUC1 tandem repeat peptides from secretory mucin of T47D breast cancer cells was analyzed. After affinity isolation on immobilized BC3 antibody, MUC1 was partially deglycosylated by enzymatic treatment with alpha-sialidase/beta-galactosidase and fragmented by proteolytic cleavage with the Arg-C-specific endopeptidase clostripain. The PAP20 glycopeptides were isolated by reversed phase high pressure liquid chromatography and subjected to the structural analyses by quadrupole time-of-flight electrospray ionization mass spectrometry and to the sequencing by Edman degradation. All five positions of the repeat peptide were revealed as O-glycosylation targets in the tumor cell, including the Thr within the DTR motif. The degree of substitution was estimated to average 4.8 glycans per repeat, which compares to 2.6 glycosylated sites per repeat for the mucin from milk (Müller, S., Goletz, S., Packer, N., Gooley, A. A., Lawson, A. M., and Hanisch, F.-G. (1997) J. Biol. Chem. 272, 24780-24793). In addition to a modification by glycosylation, the immunodominant DTR motif on T47D-MUC1 is altered by amino acid replacements (PAPGSTAPAAHGVTSAPESR), which were revealed in about 50% of PAP20 peptides. The high incidence of these replacements and their detection also in other cancer cell lines imply that the conserved tandem repeat domain of MUC1 is polymorphic with respect to the peptide sequence.
Photon nanojet lens: design, fabrication and characterization (2016)

In this paper, a novel nanolens with super resolution, based on the photon nanojet effect through dielectric nanostructures in visible wavelengths, is proposed. The nanolens is made from plastic SU-8, consisting of parallel semi-cylinders in an array. This paper focuses on the lens designed by numerical simulation with the finite-difference time domain method and nanofabrication of the lens by grayscale electron beam lithography combined with a casting/bonding/lift-off transfer process. Monte Carlo simulation for injected charge distribution and development modeling was applied to define the resultant 3D profile in PMMA as the template for the lens shape. After the casting/bonding/lift-off process, the fabricated nanolens in SU-8 has the desired lens shape, very close to that of PMMA, indicating that the pattern transfer process developed in this work can be reliably applied not only for the fabrication of the lens but also for other 3D nanopatterns in general. The light distribution through the lens near its surface was initially characterized by a scanning near-field optical microscope, showing a well defined focusing image of designed grating lines. Such focusing function supports the great prospects of developing a novel nanolithography based on the photon nanojet effect.
DCT BASIS FUNCTION VISIBILITY: EFFECTS OF VIEWING DISTANCE AND CONTRAST MASKING (1994)

Several recent image compression standards rely upon the Discrete Cosine Transform (DCT). Models of DCT basis function visibility can be used to design quantization matrices for arbitrary viewing conditions and images. Here we report new results on the effects of viewing distance and contrast masking on basis function visibility. We measured contrast detection thresholds for DCT basis functions at viewing distances yielding 16, 32, and 64 pixels/degree. Our detection model has been elaborated to incorporate the observed effects. We have also measured detection thresholds for individual basis functions when superimposed upon another basis function of the same or a different frequency. We find considerable masking between nearby DCT frequencies. A model for these masking effects will also be presented. 1.
Cytotoxicity and anti-inflammatory activity of cyclosporine A loaded PLGA nanoparticles for ocular use. (2014)

Cyclosporine A loaded poly(lactide-co-glycolide) nanoparticles were prepared using the o/w emulsification solvent evaporation method and the effect of four preparation parameters on particle size and zeta potential was investigated. Release properties of the nanoparticles were examined and in vitro experiments were performed in order to evaluate the cytotoxicity and anti-inflammatory activity of the nanoparticles developed. Particle sizes varied between 191 and 303 nm depending on the different preparation parameters and all nanoparticle dispersions were monodisperse. The nanoparticles showed negative zeta potential values varying between -16 and -35 mV and 57 to 70 % of the amount of loaded cyclosporine A was released after 24 h. None of the nanoparticle formulations showed significant cytotoxicity compared to the negative control using human epithelial cells (HaCaT). Cyclosporine A incorporated in the various nanoparticle formulations retained its anti-inflammatory activity as significant suppression of interleukine-2 secretion in concanavalin A stimulated Jurkat T cells was measured. As the overall influence of the freeze-drying process on the characteristics of nanoparticles was limited, trehalose and carnitine should be preferred as cryoprotectants in ocular formulations for treatment of dry eye disease.
Untethered micro-robotic coding of three-dimensional material composition (2014)

Complex functional materials with three-dimensional micro- or nano-scale dynamic compositional features are prevalent in nature. However, the generation of three-dimensional functional materials composed of both soft and rigid microstructures, each programmed by shape and composition, is still an unsolved challenge. Here we describe a method to code complex materials in three-dimensions with tunable structural, morphological and chemical features using an untethered magnetic micro-robot remotely controlled by magnetic fields. This strategy allows the micro-robot to be introduced to arbitrary microfluidic environments for remote two- and three-dimensional manipulation. We demonstrate the coding of soft hydrogels, rigid copper bars, polystyrene beads and silicon chiplets into three-dimensional heterogeneous structures. We also use coded microstructures for bottom-up tissue engineering by generating cell-encapsulating constructs.
RETRACTED: The RasGAP-associated endoribonuclease G3BP assembles stress granules (2003)

Stress granules (SGs) are formed in the cytoplasm in response to various toxic agents, and are believed to play a critical role in the regulation of mRNA metabolism during stress. In SGs, mRNAs are stored in an abortive translation initiation complex that can be routed to either translation initiation or degradation. Here, we show that G3BP, a phosphorylation-dependent endoribonuclease that interacts with RasGAP, is recruited to SGs in cells exposed to arsenite. G3BP may thus determine the fate of mRNAs during cellular stress. Remarkably, SG assembly can be either dominantly induced by G3BP overexpression, or on the contrary, inhibited by expressing a central domain of G3BP. This region binds RasGAP and contains serine 149, whose dephosphorylation is induced by arsenite treatment. Critically, a phosphomimetic mutant (S149E) fails to oligomerize and to assemble SGs, whereas a nonphosphorylatable G3BP mutant (S149A) does both. These results suggest that G3BP is an effector of SG assembly, and that Ras signaling contributes to this process by regulating G3BP dephosphorylation.
Randomly Ordered Addressable High-Density Optical Sensor Arrays (1998)

Array-based sensors provide an architecture for multianalyte sensing. In this paper, we report a new approach for array fabrication. Sensors are made by immobilizing different reactive chemistries on the surfaces of microspheres. Sensor arrays are prepared by randomly distributing a mixture of microsphere sensors on an optical substrate containing thousands of micrometer-scale wells. The sensors occupy a different location from array to array; thus the identity of each sensor is ascertained and registered on the detector using encoding schemes, rather than by a predetermined location in the array. The approach thereby shifts the demand from fabrication to signal processing. The availability of commercial image analysis software makes such a shift both cost-effective and time efficient.
Coagulation Activation Markers in the Prediction of Venous Thrombosis after Elective Hip Surgery (1997)

Preoperative F1 + 2, TAT and D-dimer levels are associated with the risk of development of DVT after total hip replacement.
A Versatile Synthetic Route to Substituted Thianthrenes (1983)

Abstract 2,7-Dinitrothianthrene has been prepared by the base-catalyzed cyclization of 2-chloro-5-nitrobenzenethiol and proves to be a versatile starting point for the preparation of several 2,7-disubstituted thianthrenes, both symmetrically and unsymmetrically substituted.
RAPID EXPANSION OF ALLOSPECIFIC CYTOTOXIC T CELL CLONES USING NONSPECIFIC FEEDER CELL LINES WITHOUT FURTHER ADDITION OF EXOGENOUS IL2 (1984)

The availability of large numbers of functionally defined cloned T cells would facilitate biochemical and molecular studies and might be a prerequisite for in vivo immunotherapy with cytotoxic lymphocytes. Exogenous interleukin-2 (IL-2) is generally considered to be the most important medium supplement for the growth of human T cells or cloned T cells. We have studied the role of particular feeder cells or stimulator cells, or both, on the expansion of a panel of cytotoxic and noncytotoxic human T cell clones. By using a combination of peripheral blood lymphocytes (PBL) and Epstein-Barr virus (EBV)-transformed B cell lines (B-LCL) as feeder cells in the presence of lectins, we were able to achieve continuous and rapid expansion of phenotypically different allospecific cytotoxic and noncytotoxic T cell clones even without (further) addition of exogenous IL-2. This culture system allows expansion of cloned cells for up to 60 generations within two months with full retention of cytolytic activity and the original target cell specificity, and without the obligatory addition of the original stimulator cell. It was found that, in principle, all combinations of EBV-transformed B cell lines (or even leukemia-derived B cell lines) and PBL feeder cells could serve the purpose, although some B cell lines gave better results than others. No evidence for HLA restriction between responder and feeder or between feeder cells was found, because cells could also be expanded with autologous feeder cells alone. The system appeared to be suitable for the expansion of various types of cytotoxic and non cytotoxic T cells, including cloned directed against major histocompatibility complex (MHC) class I or MHC class II antigens as well as MHC-nonrestricted activated killer (AK) clones.
Recombinant human hemoglobins designed for gene therapy of sickle cell disease. (1994)

Two human hemoglobins designed to inhibit the polymerization of sickle hemoglobin (Hb S; alpha 2 beta S2) have been produced. Mutations that disrupt the ability of Hb S to form polymers were introduced into the normal human beta-globin gene by site-specific mutagenesis. These mutations affect the axial and lateral contacts in the sickle fiber. The recombinant hemoglobin designated anti-sickling hemoglobin 1 (Hb AS1) contains the mutations beta 22 glutamic acid to alanine and beta 80 asparagine to lysine. Hb AS2 has the same beta 22 glutamic acid to alanine mutation combined with beta 87 threonine to glutamine. Human alpha- and beta AS-globin genes were separately fused downstream of beta-globin locus control region sequences and these constructs were coinjected into fertilized mouse eggs. Transgenic mouse lines that synthesize high levels of each anti-sickling hemoglobin were established and anti-sickling hemoglobins were purified from hemolysates and characterized. Both AS hemoglobins bind oxygen cooperatively and the oxygen affinities of these molecules are in the normal range. Delay time experiments demonstrate that Hb AS2 is a potent inhibitor of Hb S polymerization; therefore, locus control region beta AS2-globin gene constructs may be suitable for future gene therapy of sickle cell disease.
Ginkgolides (1967)

Three bitter principles, ginkgolides A, B, and C, were isolated from the leaves of Ginkgo biloba L. Since the structure of ginkgolide A was established by X-ray analysis of its p-bromobenzoate, structures of the other two were deduced by comparison of the n.m.r. spectra of the three compounds. The structures of ginkgolides A and B were correlated by chemical methods. Owing to its complex structure, ginkgolide A gave an unusual oxidation product, the structure of which was determined.
Effective suppression of hippocampal seizures in rats by direct hippocampal cooling with a Peltier chip (2008)

Selective hippocampal cooling effectively suppresses the KA-induced hippocampal EDs. Direct hippocampal cooling with a permanently implantable system is potentially useful as a minimally invasive therapy for temporal lobe epilepsy and therefore could be an alternative to the temporal lobectomy.
Identification and characterization of the orf virus type I topoisomerase (1995)

Vaccinia virus (VV) and Shope fibroma virus (SFV), representatives of the orthopox and leporipox genera, respectively, encode type I DNA topoisomerases. Here we report that the 957-nt F4R open reading frame of orf virus (OV), a representative of the parapox genus, is predicted to encode a 318-aa protein with extensive homology to these enzymes. The deduced amino acid sequence of F4R has 54.7 and 50.6% identity with the VV and SFV enzymes, respectively. One hundred forty amino acids are predicted to be conserved in all three proteins. The F4R protein was expressed in Escherichia coli under the control of an inducible T7 promoter, partially purified, and shown to be a bona fide type I topoisomerase. Like the VV enzyme, the OV enzyme relaxed negatively supercoiled DNA in the absence of divalent cations or ATP and formed a transient covalent intermediate with cleaved DNA that could be visualized by SDS-PAGE. Both the noncovalent and covalent protein/DNA complexes could be detected in an electrophoretic mobility shift assay. The initial PCR used to prepare expression constructs yielded a mutant allele of the OV topoisomerase with a G-A transition at nt 677 that was predicted to replace a highly conserved Tyr residue with a Cys. This allele directed the expression of an enzyme which retained noncovalent DNA binding activity but was severely impaired in DNA cleavage and relaxation. Incubation of pUC19 DNA with the wild-type OV or VV enzyme yielded an indistinguishable set of DNA cleavage fragments, although the relative abundance of the fragments differed for the two enzymes. Using a duplex oligonucleotide substrate containing the consensus site for the VV enzyme, we demonstrated that the OV enzyme also cleaved efficiently immediately downstream of the sequence CCCTT.
Acute coagulopathy of trauma: mechanism, identification and effect (2007)

Acute coagulopathy results in increased transfusion requirements, incidence of organ dysfunction, critical care stay and mortality. Recognition of an early coagulopathic state has implications for the care of shocked patients and the management of massive transfusion. Identification of novel mechanisms for traumatic coagulopathy may lead to new avenues for drug discovery and therapeutic intervention.
Study of the correlation of ET and CGRP in cough variant asthma patients (2010)

Objective To understand the levels of plasma endothelin (ET) and calcitonin gene-related peptide (CGRP) in cough variant asthma(CVA) patients, and to investigate their correlation and clinical implications. Methods Thirty CVA patients,30 typical bronchial asthma patients and 25 healthy controls were recruited. Three milliliter limosis venous blood were drawn from each patient to measure the levels of plasma ET and CGRP by radioimmanity. Results ①The levels of ET in the CVA group and typical bronchial asthma group were higher than that in healthy controls (P 0.05). ②ET and CGRP were negatively correlated in both CVA group(r= -0.819,P<0.05) and typical bronchial asthma group(r= -0.738,P<0.05). Conclusions ET and CGRP were negatively correlated in both CVA group and typical bronchial asthma group, which means that ET and CGRP were a couple of antagonistic factors participated in the regulation of CVA, and may play an important role in the process of CVA.

Key words: 
Cough variant asthma; Bronchial asthma; Endotbelin; Calcitonin gene-related peptide
Measurements of small-signal photo-EMF of Si and Ge MIS structures using scanning light probe (1978)

Small-signal high-frequency photo-e.m.f. of AlSiO2Si and AlSi3N4SiO2–Ge structures is measured using a 30 μm diameter light probe. The measurements are carried out during continuous scanning of the investigated surface with displaying of the results as “three-dimensional” plots by XY recorder. The surface potential and its fluctuations over the sample area are determined. [Russian Text Ignored].
MimoDB 2.0: a mimotope database and beyond (2011)

Mimotopes are peptides with affinities to given targets. They are readily obtained through biopanning against combinatorial peptide libraries constructed by phage display and other display technologies such as mRNA display, ribosome display, bacterial display and yeast display. Mimotopes have been used to infer the protein interaction sites and networks; they are also ideal candidates for developing new diagnostics, therapeutics and vaccines. However, such valuable peptides are not collected in the central data resources such as UniProt and NCBI GenPept due to their 'unnatural' short sequences. The MimoDB database is an information portal to biopanning results of random libraries. In version 2.0, it has 15,633 peptides collected from 849 papers and grouped into 1818 sets. Besides the core data on panning experiments and their results, broad background information on target, template, library and structure is included. An accompanied benchmark has also been compiled for bioinformaticians to develop and evaluate their new models, algorithms and programs. In addition, the MimoDB database provides tools for simple and advanced searches, structure visualization, BLAST and alignment view on the fly. The experimental biologists can easily use the database as a virtual control to exclude possible target-unrelated peptides. The MimoDB database is freely available at http://immunet.cn/mimodb.
Force mapping on a partially H-covered Si(111)-(7×7) surface: Influence of tip and surface reactivity (2013)

We report force mapping experiments on Si(111)-(7$\ifmmode\times\else\texttimes\fi{}$7) surfaces with adsorbed hydrogen, using atomic force microscopy at room temperature supported by density functional theory (DFT) simulations. On the basis of noncontact atomic force microscopy (NC-AFM) images as well as force versus distance curves measured over both hydrogen-passivated and bare Si adatoms, we identified two types of tip termination, which result in different modes of interaction with the surface. The statistics of the tip dependence of the measured forces, which are effectuated using various tip states with different cantilevers, reveal the typical values of the force and their distribution in the two characteristic interaction modes. The experimental results are corroborated by DFT calculations performed for different tip structures. As a reactive tip, the dimer-terminated Si tip yields results in satisfactory agreement with experimental force curves for hydrogen-passivated and nonpassivated Si adatom sites. An oxidized Si dimer tip that bears a hydroxyl group on its apex reproduces well the experimental force curves acquired by nonreactive tips. This tip model could thus be used to interpret the experimentally obtained weak image contrast for the Si(111)-(7$\ifmmode\times\else\texttimes\fi{}$7) surface. The forces are thought to arise as a result of a weak electrostatic interaction involving a permanent dipole at the tip apex enhanced by the charge density redistribution due to the interaction with surface adatoms.
Modeling and dimensioning hierarchical storage systems for low-delay video services (2003)

In order to cost-effectively accommodate a large number of titles in a video system, a hierarchical storage system can be used. In this system, not-so-popular video files are stored in a tertiary level such as a disk/tape library. These files are transferred, or "staged," to a secondary level composed of magnetic disks before being streamed to the users. This system overcomes the current limitations in using disk/tape libraries to stream videos and resolves the bandwidth difference between staging and streaming. We present, via analysis, a model of the system and determine the minimum storage and bandwidth required, at each level, to meet a given user delay goal. We also analyze a number of system operations pertaining to whether or not a file is played while it is being staged (i.e., stage-streaming) and whether or not the displayed segments are deleted (i.e., trail-deletion). We show that stage-streaming and trail-deletion can achieve substantially lower bandwidth and storage requirements. In order to further increase the streaming and storage scalability, a distributed storage system can be used where multiple local servers are put close to user pools and get their files from one of the libraries through a network. We extend the models developed to such a system and specify the resource requirements to meet a given delay goal.
Advances in Intracranial Pressure Monitoring and Its Significance in Managing Traumatic Brain Injury (2015)

Intracranial pressure (ICP) measurements are essential in evaluation and treatment of neurological disorders such as subarachnoid and intracerebral hemorrhage, ischemic stroke, hydrocephalus, meningitis/encephalitis, and traumatic brain injury (TBI). The techniques of ICP monitoring have evolved from invasive to non-invasive-with both limitations and advantages. Some limitations of the invasive methods include short-term monitoring, risk of infection, restricted mobility of the subject, etc. The invasiveness of a method limits the frequency of ICP evaluation in neurological conditions like hydrocephalus, thus hampering the long-term care of patients with compromised ICP. Thus, there has been substantial interest in developing noninvasive techniques for assessment of ICP. Several approaches were reported, although none seem to provide a complete solution due to inaccuracy. ICP measurements are fundamental for immediate care of TBI patients in the acute stages of severe TBI injury. In severe TBI, elevated ICP is associated with mortality or poor clinical outcome. ICP monitoring in conjunction with other neurological monitoring can aid in understanding the pathophysiology of brain damage. This review article presents: (a) the significance of ICP monitoring; (b) ICP monitoring methods (invasive and non-invasive); and (c) the role of ICP monitoring in the management of brain damage, especially TBI.
Atlas of Lung Cancer (1998)

Heterogeneity of lung cancer papillomas, polyps and non-salivary adenomas squamous cell carcinoma neuroendocrine tumours adenocarcinoma large cell lung cancer adenosquamous carcinoma bronchial gland tumours mesothelioma hamartomas pulmonary blastoma carcinomas benign clear cell (sugar) tumours basaloid tumours melanomas vascular tumours lymphomas soft tissue tumours and pseudotumours.
Facile Routes to Patterned Surface Neutralization Layers for Block Copolymer Lithography (2007)

A new crosslinking system based on azide-functionalized random copolymers has been defined for the preparation of substrates with controllable surface interactions. The azido group is used for both thermal- and photo-crosslinking, which is found to be very efficient. Furthermore, the use of UV irradiation for crosslinking enables the preparation of patterned surfaces by conventional photolithographic techniques, combining the “bottom-up” self-assembly of block copolymer strategies with traditional “top-down” photolithographic methods.