gebhart/patrepeval huggingface dataset:
Photothermally triggered actuation of hybrid materials as a new platform for in vitro cell manipulation (2017)

Mechanical forces in the cell's natural environment have a crucial impact on growth, differentiation and behaviour. Few areas of biology can be understood without taking into account how both individual cells and cell networks sense and transduce physical stresses. However, the field is currently held back by the limitations of the available methods to apply physiologically relevant stress profiles on cells, particularly with sub-cellular resolution, in controlled in vitro experiments. Here we report a new type of active cell culture material that allows highly localized, directional and reversible deformation of the cell growth substrate, with control at scales ranging from the entire surface to the subcellular, and response times on the order of seconds. These capabilities are not matched by any other method, and this versatile material has the potential to bridge the performance gap between the existing single cell micro-manipulation and 2D cell sheet mechanical stimulation techniques.
A network-assisted dynamic packet assignment algorithm for wireless data networks (2002)

We propose a dynamic packet assignment algorithm, network-assisted dynamic packet assignment (NA-DPA), for wireless data networks with frame synchronized base stations. The basic idea of NA-DPA is to use interbase signaling to shift most of the burden of the resource allocation from the air interface to the backbone infrastructure. By exchanging path loss and channel assignment information in real time, each base can calculate the effect of a resource assignment on the overall system. As a result, rapid interference measurements, which are typically needed to implement dynamic channel assignment (DCA) schemes, are replaced by a limited amount of path loss measurements and the computation of interference conditions by the base stations. This significantly reduces the measurement and over-the-air signaling requirements. It also provides an opportunity for a better optimization of the system performance, than that permitted by other DCA algorithms. We show NA-DPA can provide a throughput that is 50% higher than that obtained by other proposed DCA algorithms.
Untangling the tau gene association with neurodegenerative disorders (2006)

Pathological tau protein inclusions have long been recognized to define the diverse range of neurodegenerative disorders called the tauopathies, which include Alzheimer's disease (AD), progressive supranuclear palsy (PSP) and frontotemporal lobar degeneration. Mutations in the tau gene, MAPT, cause familial frontotemporal dementia with parkinsonism linked to chromosome 17 (FTDP-17), and common variation in MAPT is strongly associated with the risk of PSP, corticobasal degeneration and, to a lesser extent, AD and Parkinson's disease (PD), implicating the involvement of tau in common neurodegenerative pathway(s). This review will discuss recent work towards the unravelling of the functional basis of this MAPT gene association. The region of chromosome 17q21 containing MAPT locus is characterized by the complex genomic architecture, including a large inversion that leads to a bipartite haplotype architecture, an inversion-mediated deletion and multiplications resulting from non-allelic homologous recombination between the MAPT family of low-copy repeats.
La Bible d'Alexandrie. LXX (Book) (1995)

Neither the omeprazole nor ranitidine plus bicarbonate plus amoxicillin therapies used here can be recommended for treatment of H. pylori infection.
Response functions for computing absorbed dose to skeletal tissues from photon irradiation—an update (2011)

A comprehensive set of photon fluence-to-dose response functions (DRFs) is presented for two radiosensitive skeletal tissues-active and total shallow marrow-within 15 and 32 bone sites, respectively, of the ICRP reference adult male. The functions were developed using fractional skeletal masses and associated electron-absorbed fractions as reported for the UF hybrid adult male phantom, which in turn is based upon micro-CT images of trabecular spongiosa taken from a 40 year male cadaver. The new DRFs expand upon both the original set of seven functions produced in 1985, and a 2007 update calculated under the assumption of secondary electron escape from spongiosa. In this study, it is assumed that photon irradiation of the skeleton will yield charged particle equilibrium across all spongiosa regions at energies exceeding 200 keV. Kerma coefficients for active marrow, inactive marrow, trabecular bone and spongiosa at higher energies are calculated using the DRF algorithm setting the electron-absorbed fraction for self-irradiation to unity. By comparing kerma coefficients and DRF functions, dose enhancement factors and mass energy-absorption coefficient (MEAC) ratios for active marrow to spongiosa were derived. These MEAC ratios compared well with those provided by the NIST Physical Reference Data Library (mean difference of 0.8%), and the dose enhancement factors for active marrow compared favorably with values calculated in the well-known study published by King and Spiers (1985 Br. J. Radiol. 58 345-56) (mean absolute difference of 1.9 percentage points). Additionally, dose enhancement factors for active marrow were shown to correlate well with the shallow marrow volume fraction (R(2) = 0.91). Dose enhancement factors for the total shallow marrow were also calculated for 32 bone sites representing the first such derivation for this target tissue.
Activation of the hole-forming toxin aerolysin by extracellular processing (1985)

A precursor-product relationship between aerolysin and a protein with a higher molecular weight was observed in culture supernatants of Aeromonas hydrophila. The larger protein was isolated by ammonium sulfate precipitation and ion-exchange and hydroxyapatite chromatography and compared with purified aerolysin. It was at least 250 times less hemolytic than aerolysin. Both proteins had the same amino acid sequence at the amino terminus. Cyanogen bromide fragments obtained from the two were identical except that each protein contained one unique fragment, and the fragment from the larger protein was 2,500 daltons larger than the fragment obtained from aerolysin. Treatment with trypsin or with an extracellular Aeromonas protease resulted in rapid conversion of the larger protein to a form corresponding in molecular weight and activity to aerolysin. The results indicate that aerolysin is exported to the culture supernatant as a protoxin which is later activated by proteolytic removal of a peptide from the C terminus.
Remote control catheter navigation: options for guidance under MRI (2012)

MR-guided endovascular interventions under remote control steering are in their infancy due to issues regarding safety and reliability. Additional experimental studies are needed prior to their use in humans.
Three-dimensional image sensing by chromatic confocal microscopy (1994)

In the image of a confocal microscope, only those parts of an object appear bright that are located in the focal plane of the objective. Because of an axial chromatic aberration deliberately introduced into the microscope objective, the location of the focal plane depends on the wavelength used. By using a white-light source and examining an object with a depth variation less than the axial range of the chromatic focus, we find that all parts of the object appear sharp and bright in the image, but according to its height they appear in different colors. A camera with black-and-white film sequentially combines, with three selected chromatic filters, intensity and tone of color of each object point. For each tone of color one can assign a height by using a calibration curve. This assignment could be made unequivocal by the selection of filters with adequate chromatic transmission.
Tenascin-C Aptamers Are Generated Using Tumor Cells and Purified Protein (2001)

Tenascin-C (TN-C) is an extracellular matrix protein that is overexpressed during tissue remodeling processes, including tumor growth. To identify an aptamer for testing as a tumor-selective ligand, SELEX (systematic evolution of ligands by exponential enrichment) procedures were performed using both TN-C and TN-C-expressing U251 glioblastoma cells. The different selection techniques yielded TN-C aptamers that are related in sequence. In addition, a crossover procedure that switched from tumor cell to purified protein selections was effective in isolating two high-affinity TN-C aptamers. When targeting tumor cells in vitro, the observed propensity of naive oligonucleotide pools to evolve TN-C aptamers may be due to the abundance of this protein. In vivo, TN-C abundance may also be well suited for aptamer accumulation in the tumor milieu. A size-minimized and nuclease-stabilized aptamer, TTA1, binds to the fibrinogen-like domain of TN-C with an equilibrium dissociation constant (K(d)) of 5 x 10(-9) m. At 13 kDa, this aptamer is intermediate in size between peptides and single chain antibody fragments, both of which are superior to antibodies for tumor targeting because of their smaller size. TTA1 defines a new class of ligands that are intended for targeted delivery of radioisotopes or chemical agents to diseased tissues.
Low-loss optical waveguides made with molecular beam epitaxial In0.012Ga0.988As and In0.2Ga0.8As-GaAs superlattices (1986)

We demonstrate for the first time low-loss optical guiding in In-doped GaAs. Ridge waveguides are made with single In0.012Ga0.988As ternary layers and In0.2Ga0.8As-GaAs superlattices. Attenuation constants of ∼1.3 dB/cm are measured and the principal loss mechanism is identified to be scattering at the ridge walls. It is expected that improved fabrication techniques will lead to guides with attenuation ≤0.5 dB/cm.
Structural prerequisites for serum amyloid A fibril formation. (1993)

Most studies of experimental amyloid A protein (AA) amyloidosis in mice have been performed in type A mice with BALB/c as the prototype. In these mice the products of two genes, SAA1 and SAA2, are the major apo-SAA isoforms on high density lipoprotein (HDL). Of these two isoforms, that differ at nine amino acids, only apo-SAA2 is rapidly cleared and deposited as amyloid fibrils. No mouse strain has ever been shown to be completely resistant to amyloid induction. We have found the CE/J mouse strain to be exceedingly resistant to amyloidogenesis. Data indicate that this resistance is not due to a lack of apo-SAA synthesis but rather resides in the unique apo-SAA isoform in this strain. CE/J mice have a single major apo-SAA isoform (pI 6.15) the product of a single gene. This is a hybrid molecule with features of both apo-SAA1 and apo-SAA2, differing from the latter at only six amino acids. When CD studies were performed to explore the structural relationship of this isoform to apo-SAA1 and apo-SAA2, we found that when bound to heparan sulfate proteoglycan the CE/J pI 6.15 isoform fails to undergo the beta-sheet folding typical for apo-SAA2. This evidence suggests that the folding effect of heparan sulfate proteoglycan on apo-SAA2 is important in amyloid formation.
Enhancement Of Immunogenicity of an Immunoprotective Glycophospholipid Antigen of Mycobacteria Using Liposomes Containing Lipid A (1993)

Role of liposomes as the carriers of mannophosphoino-sitides (PIMs) antigen of mycobacteria have been investigated. PIMs when incorporated in liposomes made of egg phosphatidylcholine (EPC) and cholesterol (CH)/ in a molar ratio of 2: 1. 5 respectively/ elicited both humoral (anti-PIMs IgG) and cell-mediated (DTH) immune responses in mice. Further/ lipid A containing liposomes as carriers of PIMs were observed to induce almost two times more anti-PIMs immune responses as compared to those without lipid A. These findings clearly establish that the lipid A containing liposomes not only replace FIA, but are even better adjuvants for PIMs.
Direct Analysis of Pharmaceutical Drug Formulations Using Ion Mobility Spectrometry/Quadrupole-Time-of-Flight Mass Spectrometry Combined with Desorption Electrospray Ionization (2005)

A novel approach to the rapid analysis of pharmaceutical drug formulations using hyphenated ion mobility spectrometry (IMS) and time-of-flight mass spectrometry (ToF-MS) that requires no sample pretreatment or chromatographic separation is described. A modified quadrupole time-of-flight mass spectrometer containing an ion mobility drift cell was used for gas-phase electrophoretic separation of ions prior to ToF-MS detection. The generation of sample ions directly from tablets and cream formulations was effected by desorption electrospray ionization (DESI) using a modified electrospray ion source. The analysis of a range of over-the-counter and prescription tablet formulations is described, including histamine H2 receptor antagonist (ranitidine), analgesic (paracetamol), opiate (codeine), and aromatase inhibitor anticancer (anastrozole) drugs. The successful determination of active drugs from soft formulations, such as an antiseptic cream (chlorhexidine) and a nicotine-containing skin patch, is also presented. Limits of detection for the active drugs using the DESI/IMS/ToF-MS method fell within the high-picomole to nanomole range. In all cases, the use of ion mobility drift tube separation showed increased selectivity for active drug responses (present as low as 0.14% w/w) over excipient responses such as poly(ethylene glycol). Tandem mass spectrometric analysis of precursor ions separated by IMS allowed positive confirmation of active drugs with little loss of ion mobility efficiency. The ability to analyze hard or soft pharmaceutical formulations directly by DESI combined with ion mobility spectrometry/mass spectrometry in approximately 2 min demonstrates the potential applicability of this novel method to pharmaceutical screening of low-molecular-weight drug formulations with high selectivity over the formulation vehicle.
A Critical Comparison of Models for Orientation and Ocular Dominance Columns in the Striate Cortex (1994)

More than ten of the most prominent for the structure and for the activity dependent formation of orientation and ocular dominance columns in the striate cortex have been evaluated. We implemented those on parallel machines, we extensively explored parameter space, and we quantitatively compared model predictions with experimental data which were recorded optically from macaque striate cortex.

In our contribution we present a summary of our results to date. Briefly, we find that (i) despite apparent differences, many are based on similar principles and, consequently, make similar predictions, (ii) certain pattern models as well as the developmental correlation-based learning disagree with the experimental data, and (iii) of the we have investigated, competitive Hebbian and the recent model of Swindale provide the best match with experimental data.
The Inducible G Protein-coupled Receptor edg-1 Signals via the Gi/Mitogen-activated Protein Kinase Pathway (1996)

The edg-1 gene encodes an inducible G protein-coupled receptor (GPR) homologue that is induced during the in vitro differentiation of human endothelial cells. The aim of this study was to investigate the G protein-coupling and -signaling properties of the edg-1 polypeptide. The third cytosolic loop (i3) of edg-1 associates with G(i) alpha and G(o) alpha polypeptides in a guanosine 5'-O-(thiotriphosphate)-sensitive manner. Immunoprecipitation of the edg-1 polypeptide in transfected cells results in the co-precipitation of G(i) alpha 1 and G(i) alpha 3 polypeptides. These data strongly suggest that edg-1 is capable of coupling to the Gi pathway. Overexpression of the edg-1 GPR in human embryonic kidney 293 cells results in the sustained activation of the MAP kinase activity that is blocked by pertussis toxin treatment. Moreover, NIH3T3 cells permanently transfected with edg-1 exhibit enhanced MAP kinase and phospholipase A2 activities. These data suggest that the G(i)/mitogen-activated protein kinase pathway is a major signaling pathway regulated by the orphan receptor edg-1.
Aggregation of alpha-synuclein in Lewy bodies of sporadic Parkinson's disease and dementia with Lewy bodies. (1998)

Lewy bodies (LBs) are hallmark lesions of degenerating neurons in the brains of patients with Parkinson's disease (PD) and dementia with Lewy bodies (DLB). Recently, a point mutation in the gene encoding the presynaptic alpha-synuclein protein was identified in some autosomal-dominantly inherited familial PD pedigrees, and light microscopic studies demonstrated alpha-synuclein immunoreactivity in LBs of sporadic PD and DLB. To characterize alpha-synuclein in LBs, we raised monoclonal antibodies (MAbs) to LBs purified from DLB brains and obtained a MAb specific for alpha-synuclein that intensely labeled LBs. Light and electron microscopic immunocytochemical studies performed with this MAb as well as other antibodies to alpha-and beta-synuclein showed that alpha-synuclein, but not beta-synuclein, is a component of LBs in sporadic PD and DLB. Western blot analyses of highly purified LBs from DLB brains showed that full-length as well as partially truncated and insoluble aggregates of alpha-synuclein are deposited in LBs. Thus, these data strongly implicate alpha-synuclein in the formation of LBs and the selective degeneration of neurons in sporadic PD and DLB.
Glutathione- and Cysteine-Induced Transverse Overgrowth on Gold Nanorods (2007)

We have demonstrated glutathione- and cysteine-induced transverse overgrowth on gold nanorods. In aqueous solutions, glutathione and cysteine are preferentially bound to the ends of gold nanorods that are stabilized by a cationic surfactant bilayer. This preferential end binding blocks the growth of the nanorods in the longitudinal direction completely and allows for the growth only in the transverse direction. As a result, the diameters of the nanorods become larger and larger while their lengths remain unchanged, as more and more gold precursor is supplied. In addition, the shape of the nanorods undergoes a gradual change from rods, peanuts, and truncated octahedra to faceted spheres during overgrowth. We believe that this transverse overgrowth provides an alternative means for tailoring the longitudinal plasmon wavelengths and extinction cross sections of gold nanoparticles and will therefore facilitate their use in optics, optoelectronics, and biotechnology.
Work-Flow Automation Enhances Job Performance and Improves Job-Execution Data (1997)

Summary We designed and implemented a work-flow automation system to automate the flow of operational data throughout a servicing operation. Work-flow automation enables well-service personnel who are rarely network-connected to access information systems containing updated job requirements and well data. As the service personnel perform their work, data from the job are stored on a personal computer by use of store-and-forward architecture. Once the computer connects to the wide area network (WAN), job data are forwarded to the service-center operations systems. Copies of these data also can be forwarded to the customer to demonstrate enhanced value or to track cost. In this pilot implementation, we decreased the number of paper forms substantially, increased the quality of data collection, distributed updates to the system to the field easily, and relayed key data to the customer quickly. This paper documents the pilot implementation of this system and the lessons learned from its implementation.
Materials for Pharmaceutical Dosage Forms: Molecular Pharmaceutics and Controlled Release Drug Delivery Aspects (2010)

Controlled release delivery is available for many routes of administration and offers many advantages (as microparticles and nanoparticles) over immediate release delivery. These advantages include reduced dosing frequency, better therapeutic control, fewer side effects, and, consequently, these dosage forms are well accepted by patients. Advances in polymer material science, particle engineering design, manufacture, and nanotechnology have led the way to the introduction of several marketed controlled release products and several more are in pre-clinical and clinical development.
Derivation of Embryonic Stem-Cell Lines from Human Blastocysts (2004)

Embryonic stem cells have the unique ability to form all adult cell types. Harnessing this potential may provide a source of cells to replace those that are lost or impaired as a result of disease. Moreover, the derivation of human embryonic stem cells opens a unique window into the study of early human development. At present, approximately 15 human embryonic stem-cell lines are publicly available, and they vary considerably in their usefulness for research and the extent of their characterization (see http://stemcells.nih.gov/registry/index.asp). To promote further research with human embryonic stem cells, we sought to derive and characterize more fully cell lines that meet strict criteria for ease of manipulation, including enzymatic passage with trypsin, streamlined freezing and thawing procedures, well-defined culture mediums, and straightforward methods for in vitro differentiation. We report the derivation and characterization of 17 additional human embryonic stem cell lines.
Morphology and Adsorbate Dependence of Ionic Transport in Dye Sensitized Mesoporous TiO2Films (1998)

By modeling the steady-state mass transport in a thin-layer cell configuration involving an electrochemically inactive mesoporous colloidal film, the limiting currents of an iodine containing electrolyte can be predicted, as a function of the film porosity. The porosity of the layer is then determined by best fit of the porosity parameter in the model, given the experimentally determined limiting currents. Satisfactory agreement is found with the porosity values obtained by BET measurements. In photoelectrochemical cell applications such as dye sensitized nanocrystalline photoelectrodes for solar energy conversion devices, the porosities of the dye loaded films of e.g. anatase TiO2 play an essential role with respect to their efficiency. In particular, the findings of this work demonstrate that the presence of adsorbed sensitizer cis-(SCN-)2 bis(2,2‘-bipyridyl-4,4‘-dicarboxylate)ruthenium(II) in TiO2 colloidal films appears to decrease the original naked film porosity by up to 30%. This depends on the initial bare film porosity and the dye diameter, thus resulting in a considerably lower effective mass-transport limit within the coated films. The effective diffusion coefficient of triiodide in these porous electrodes was found to not deviate significantly with respect to the free-stream values, suggesting an influence of mesoporosity on the transport mechanisms involved.
Data-Centric Automated Data Mining (2006)

Data mining is a difficult task. It requires complex methodologies, including problem definition, data preparation, model selection, and model evaluation. This has limited the adoption of data mining at large and in the database and business intelligence (BI) communities more specifically. The concepts and methodologies used in data mining are foreign to database and BI users in general. This paper proposes a new approach to the design of data mining applications targeted at these user groups. This approach uses a data-centric focus and automated methodologies to make data mining accessible to nonexperts. The automated methodologies are exposed through high-level interfaces. This hides the data mining concepts away from the users thus helping to bridge the conceptual gap usually associated with data mining. We illustrate the approach with two applications: the new Oracle Predictive Analytics feature of Oracle Database 10g Release 2 and the Oracle Spreadsheet Add-In for Predictive Analytics.