gebhart/patrepeval huggingface dataset:
Biocolloids with Ordered Urease Multilayer Shells as Enzymatic Reactors (2001)

The preparation of biocolloids with organized enzyme-containing multilayer shells for exploitation as colloidal enzymatic nanoreactors is described. Urease multilayers were assembled onto submicrometer-sized polystyrene spheres by the sequential adsorption of urease and polyelectrolyte, in a predetermined order, utilizing electrostatic interactions for layer growth. The catalytic activity of the biocolloids increased proportionally with the number of urease layers deposited on the particles, demonstrating that biocolloid particles with tailored enzymatic activities can be produced. It was further found that precoating the latex spheres with nanoparticles (40-nm silica or 12-nm magnetite) enhanced both the stability (with respect to adsorption) and enzymatic activity of the urease multilayers. The presence of the magnetite nanoparticle coating also provided a magnetic function that allowed the biocolloids to be easily and rapidly separated with a permanent magnet. The fabrication of such colloids opens new avenues for the application of bioparticles and represents a promising route for the creation of complex catalytic particles.
Epitaxial growth of a nanoscale, vertically faceted, one-dimensional, high-aspect ratio grating in III-V materials for integrated photonics (2005)

Homoepitaxial selective growth of a GaAs nanoscale, high-aspect ratio, one-dimensional (1D) grating with vertical facets is reported. For a pattern direction along [110], the kinetics of faceting in selective molecular-beam epitaxy (MBE) induce (11¯0)-type facets vertical to a GaAs(001) substrate near the boundary between an SiO2 mask and an open substrate area. On a 1.25-μm period, 1D stripe, SiO2-patterned GaAs(001) substrate with an opening width of ∼300nm, vertical faceting results in a grating structure consisting of 2.8-μm-high, 820-nm-wide features. Kinetics of faceting in selective MBE is explained as a result of the minimization of total surface energy.
Application of Tumbling Melt Granulation Method to Prepare Controlled-Release Beads by Coating with Mixture of Functional Non-meltable and Meltable Materials. (1998)

A new coating method for use in preparing controlled-release beads was developed by modifying the tumbling melt granulation technique. The dissolution rate of the drug from the beads was controlled by coating the mixture of meltable and non-meltable materials by heating in a centrifugal fluidizing granulator without using any solvent. In experiments using talc as the non-meltable material, the resultant beads showed the sufficient ability to suppress the dissolution of the drug and no change in the dissolution characteristics by wetting agent and in a stability test at high temperature. Using functional polymer as the non-meltable material, the controlled-release beads with various dissolution characteristics could be prepared: entero-soluble-release beads using entero-soluble polymer, and zero-order-release beads using hydrophilic gel-forming agent and talc.
Fourier transform measurement of two-photon excitation spectra: applications to microscopy and optimal control (2005)

We report a novel Fourier transform method for measuring two-photon excitation spectra. We demonstrate this method using simple dye molecules and discuss its applications in two-photon fluorescence microscopy and optimal control. This method facilitates an intuitive interpretation of recent control experiments in terms of tuning the nonlinear spectrum of the exciting laser source.
Versatile Anion–π Interactions between Halides and a Conformationally Rigid Bis(tetraoxacalix[2]arene[2]triazine) Cage and Their Directing Effect on Molecular Assembly (2010)

Interactive halides: Bis(tetraoxacalix[2]arene[2]triazine), a conformationally rigid cage molecule of three V-shaped electron-deficient clefts, forms 1:1 complexes with fluoride (361 M−1), chloride (146 M−1) and bromide (95 M−1) in acetonitrile. Different anion–π interactions along with multiple hydrogen bonding, halogen bonding and lone-pair-electrons–π interactions directed the formation of different molecular assemblies (an example is shown here). Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Pico- and femtosecond laser-induced crosslinking of protein microstructures: evaluation of processability and bioactivity (2011)

This study reports the pico- and femtosecond laser-induced photocrosslinking of protein microstructures. The capabilities of a picosecond Nd:YAG laser to promote multiphoton excited crosslinking of proteins were evaluated by fabricating 2D and 3D microstructures of avidin, bovine serum albumin (BSA) and biotinylated bovine serum albumin (bBSA). The multiphoton absorption-induced photocrosslinking of proteins was demonstrated here for the first time with a non-toxic biomolecule flavin mononucleotide (FMN) as the photosensitizer. Sub-micrometer and micrometer scale structures were fabricated from several different compositions of protein and photosensitizer by varying the average laser power and scanning speed in order to determine the optimal process parameters for efficient photocrosslinking. In addition, the retention of ligand-binding ability of the crosslinked protein structures was shown by fluorescence imaging of immobilized biotin or streptavidin conjugated fluorescence labels. The surface topography and the resolution of the protein patterns fabricated with the Nd:YAG laser were compared to the results obtained with a femtosecond Ti:Sapphire laser. Quite similar grain characteristics and comparable feature sizes were achieved with both laser sources, which demonstrates the utility of the low-cost Nd:YAG microlaser for direct laser writing of protein microstructures.
Silencing of Thrombospondin-1 Is Critical for Myc-Induced Metastatic Phenotypes in Medulloblastoma (2010)

Mechanisms by which c-Myc (Myc) amplification confers aggressive medulloblastoma phenotypes are poorly defined. Here, we show using orthotopic models that high Myc expression promotes cell migration/invasion and induces metastatic tumors, which recapitulate aggressive histologic features of Myc-amplified primary human medulloblastoma. Using ChIP-chip analysis, we identified cell migration and adhesion genes, including Tsp-1/THBS1, ING4, PVRL3, and PPAP2B, as Myc-bound loci in medulloblastoma cells. Expression of Tsp-1 was most consistently and robustly diminished in medulloblastoma cell lines and primary human tumors with high Myc expression (n = 101, P = 0.032). Strikingly, stable Tsp-1 expression significantly attenuated in vitro transformation and invasive/migratory properties of high Myc-expressing medulloblastoma cells without altering cell proliferation, whereas RNA interference-mediated Myc knockdown was consistently accompanied by increased Tsp-1 levels and reduced cell migration and invasion in medulloblastoma cells. Chromatin immunoprecipitation (ChIP) assays revealed colocalization of Myc and obligate partner Max and correlated diminished RNA polymerase II occupancy (∼3-fold decrease, P < 0.01) with increased Myc binding at a core Tsp-1 promoter. Reporter gene and/or gel shift assays confirmed direct repression of Tsp-1 transcription by Myc and also identified JPO2, a Myc interactor associated with metastatic medulloblastoma, as a cofactor in Myc-mediated Tsp-1 repression. These findings indicate the Myc-regulatory network targets Tsp-1 via multiple mechanisms in medulloblastoma transformation, and highlight a novel critical role for Tsp-1 in Myc-mediated aggressive medulloblastoma phenotypes.
Towards an implantable brain-machine interface based on epicortical field potentials (2004)

* These authors contributed equally to this work. Abstract ⎯ Today, a major challenge in neuro-engineering is to develop a brain-machine interface (BMI) suitable to restore communication and motor control in paralyzed patients. One fundamental, unresolved question is which neuronal signal type should be recorded and decoded for such purposes. Here we review work on neuronal population activity, i.e. the ensemble activity of local groups of neurons, as a control signal for BMIs. Further, we propose a BMI approach based on population activity recorded directly from the human cortical surface. Using a finger movement task, we evaluate movement related changes in epicortical potentials across a broad frequency range and we show that the side of index finger flexions can be inferred from primary motor cortex population activity with up to 100 % accuracy from single trial data.
Differential CD40/CD40L Expression Results in Counteracting Antitumor Immune Responses (2007)

Establishment of host-protective memory T cells against tumors is the objective of an antitumor immunoprophylactic strategy such as reinforcing T cell costimulation via CD40-CD40L interaction. Previous CD40-targeted strategies assumed that T cell costimulation is an all-or-none phenomenon. It was unknown whether different levels of CD40L expression induce quantitatively and qualitatively different effector T cell responses. Using mice expressing different levels of CD40L, we demonstrated that the greater the T cell CD40L expression the less tumor growth occurred; the antitumor T cell response was host-protective. Lower levels of CD40L expression on T cells induced IL-10-mediated suppression of tumor-regressing effector CD8(+) T cells and higher productions of IL-4 and IL-10. Using mice expressing different levels of CD40 or by administering different doses of anti-CD40 Ab, similar observations were recorded implying that the induction of protumor or antitumor T cell responses was a function of the extent of CD40 cross-linking. IL-10 neutralization during priming with tumor Ags resulted in a stronger tumor-regressing effector T cell response. Using IL-10(-/-) DC for priming of mice expressing different levels of CD40L and subsequent transfer of the T cells from the primed mice to nu/nu mice, we demonstrated the protumor role of IL-10 in the induction of tumor-promoting T cells. Our results demonstrate that a dose-dependent cross-linking of a costimulatory molecule dictates the functional phenotype of the elicited effector T cell response. The T cell costimulation is a continuum of a function that induces not only graded T cell responses but also two counteracting responses at two extremes.
Hypertension caused by chronic intermittent hypoxia – influence of chemoreceptors and sympathetic nervous system (1997)

Our data imply that repetitive hypoxemia in SAS is probably the cause of the high prevalence of systemic hypertension in this population and that peripheral chemoreceptors and the sympathetic nervous system play important roles in this pathophysiologic process.
Nizatidine ameliorates gastroparesis in Parkinson's disease: A pilot study (2013)

Although this is a pilot study, we found a significant shortening of gastric emptying time after administration of NZT in PD patients.
Bulk Planar Junctionless Transistor (BPJLT): An Attractive Device Alternative for Scaling (2011)

We propose a novel highly scalable source-drain-junction-free field-effect transistor that we call the bulk planar junctionless transistor (BPJLT). This builds upon the idea of an isolated ultrathin highly doped device layer of which volume is fully depleted in the off-state and is around flatband in the on-state. Here, the leakage current depends on the effective device layer thickness, and we show that with well doping and/or well bias, this can be controllably made less than the physical device layer thickness in a bulk planar junction-isolated structure. We demonstrate by extensive device simulations that these additional knobs for controlling short-channel effects reduce the off-state leakage current by orders of magnitude for similar on-state currents, making the BPJLT highly scalable.
Clinical experience with ferric carboxymaltose in the treatment of cancer- and chemotherapy-associated anaemia (2012)

Background: Intravenous (i.v.) iron can improve anaemia of chronic disease and response to erythropoiesisstimulating agents (ESAs), but data on its use in practice and without ESAs are limited. This study evaluated effectiveness and tolerability of ferric carboxymaltose (FCM) in routine treatment of anaemic cancer patients.
Stimuli-Responsive Hydrogel Membranes Coupled with Biocatalytic Processes (2009)

A nanostructured signal-responsive thin hydrogel membrane was coupled with enzyme-based systems to yield "smart" multisignal-responsive hybrid systems with built-in "logic". The enzyme systems transduce biochemical input signals into structural changes of the membrane, thus resulting in the amplification of the biochemical signals and their transformation into the gated transport of molecules through the membrane. Coupling of the biocatalytic systems with a stimuli-responsive membrane is a promising approach for the development of materials that can regulate transport and release of chemicals/drugs by receiving and processing the biochemical information via biochemical reactions.
Potential Role for ADAM15 in Pathological Neovascularization in Mice (2003)

ADAM15 (named for a disintegrin and metalloprotease 15, metargidin) is a membrane-anchored glycoprotein that has been implicated in cell-cell or cell-matrix interactions and in the proteolysis of molecules on the cell surface or extracellular matrix. To characterize the potential roles of ADAM15 during development and in adult mice, we analyzed its expression pattern by mRNA in situ hybridization and generated mice carrying a targeted deletion of ADAM15 (adam15(-/-) mice). A high level of expression of ADAM15 was found in vascular cells, the endocardium, hypertrophic cells in developing bone, and specific areas of the hippocampus and cerebellum. However, despite the pronounced expression of ADAM15 in these tissues, no major developmental defects or pathological phenotypes were evident in adam15(-/-) mice. The elevated levels of ADAM15 in endothelial cells prompted an evaluation of its role in neovascularization. In a mouse model for retinopathy of prematurity, adam15(-/-) mice had a major reduction in neovascularization compared to wild-type controls. Furthermore, the size of tumors resulting from implanted B16F0 mouse melanoma cells was significantly smaller in adam15(-/-) mice than in wild-type controls. Since ADAM15 does not appear to be required for developmental angiogenesis or for adult homeostasis, it may represent a novel target for the design of inhibitors of pathological neovascularization.
Differential absorption imaging with optical coherence tomography (1998)

The spatial variation of the backscattering cross section is the primary source of contrast in present applications of optical coherence tomography (OCT). We introduce and analyze a technique for obtaining OCT images of the local concentration of an absorbing compound in biological tissues and other highly scattering media. A pair of light-emitting diodes, one emitting in a vibrational absorption band of the chemical compound of interest and the other emitting just outside this band, are used as sources at the input of the interferometer. The differential absorption of the probe beam is determined by Fourier transformation and ratiometric processing of the measured interference signals. The ability of the technique to distinguish lipid and water inclusions in a scattering material is demonstrated with an OCT system that uses a pair of light-emitting-diode sources with center wavelengths of 1.3 µm and 1.46 µm.
Metaprotein expression modeling for label-free quantitative proteomics (2012)

Mass-spectrometry proteomics is quickly becoming a powerful tool for studying biological and translational questions. Making use of all of the information contained in a particular set of data will be critical to the success of those endeavors. Our proposed model represents an advance in the ability of statistical models of proteomic data to identify and utilize correlation between features. This allows validation of predictors without translation to targeted assays in addition to informing the choice of targets when it is appropriate to generate those assays.
Use of Hybridization Chain Reaction-Fluorescent In Situ Hybridization To Track Gene Expression by Both Partners during Initiation of Symbiosis (2015)

The establishment of a productive symbiosis between Euprymna scolopes, the Hawaiian bobtail squid, and its luminous bacterial symbiont, Vibrio fischeri, is mediated by transcriptional changes in both partners. A key challenge to unraveling the steps required to successfully initiate this and many other symbiotic associations is characterization of the timing and location of these changes. We report on the adaptation of hybridization chain reaction-fluorescent in situ hybridization (HCR-FISH) to simultaneously probe the spatiotemporal regulation of targeted genes in both E. scolopes and V. fischeri. This method revealed localized, transcriptionally coregulated epithelial cells within the light organ that responded directly to the presence of bacterial cells while, at the same time, provided a sensitive means to directly show regulated gene expression within the symbiont population. Thus, HCR-FISH provides a new approach for characterizing habitat transition in bacteria and for discovering host tissue responses to colonization.
HSV-1-Based Vectors for Gene Therapy of Neurological Diseases and Brain Tumors: Part II. Vector Systems and Applications (1999)

Many properties of HSV-1 are especially suitable for using this virus as a vector to treat diseases affecting the central nervous system (CNS), such as Parkinson's disease or malignant gliomas. These advantageous properties include natural neurotropism, high transduction efficiency, large transgene capacity, and the ability of entering a latent state in neurons. Selective oncolysis in combination with modulation of the immune response mediated by replication-conditional HSV-1 vectors appears to be a highly promising approach in the battle against malignant glioma. Helper virus-free HSV/AAV hybrid amplicon vectors have great promise in mediating long-term gene expression in the PNS and CNS for the treatment of various neurodegenerative disorders or chronic pain. Current research focuses on the design of HSV-1-derived vectors which are targeted to certain cell types and support transcriptionally regulatable transgene expression. Here, we review the recent developments on HSV-1-based vector systems and their applications in experimental and clinical gene therapy protocols.
Integrating case-based reasoning and decision theory (1997)

Case-based reasoning (CBR) and decision-theoretic techniques can be complementary. Decision theory helps CBR deal with uncertainties in the problem domain, while CBR helps decision theory handle complicated problems with many variables. The goal of integrating CBR and decision theory is to improve the ability of CBR systems to solve problems in domains of incomplete information. Our methodology views the retrieval of old cases in CBR as a decision problem, where each case from the case base provides an alternative solution and a prediction of the possible outcomes for the problem. When case-based problem solving encounters uncertainty, our methodology applies decision theory to evaluate each case in terms of the attributes that are significant for the problem, so that the most desirable case can be selected. We implemented our methodology in a case-based design assistant that helps chemists design pharmaceuticals.
Future directions of electrotherapy for atrial fibrillation. (1998)

Suboptimal treatment of atrial fibrillation (AF) by pharmacotherapy alone has given rise to multiple novel electrotherapeutic modalities including pacing, ablation, and atrial defibrillation. These treatment approaches offer physicians the opportunity to evaluate their patients more extensively to better optimize therapy. AV junctional node ablation followed by full-time pacing improves quality of life and reduces the incidence of tachycardia-induced cardiomyopathy. Physicians who are reluctant to ablate the AV node may opt for either an AV nodal modification procedure or therapeutic modalities that attempt to maintain sinus rhythm. Both biatrial and dual site pacing have met with some success in preventing AF in a limited patient population. Studies also have evaluated the extent to which pacing may be used to terminate AF. These initial studies showed that, in general, pacing was ineffective. Radiofrequency catheter ablation is another therapeutic modality receiving considerable interest. The creation of multiple lesions mimicking the maze procedure, isthmus ablation to prevent the onset of atrial flutter that may degrade into AF, and ablation of tachycardia foci are all potential treatment alternatives to consider either as the primary therapy or as a synergistic procedure designed to augment another electrical therapy. Internal atrial defibrillation is being shown to be both safe and efficacious. This therapy appears uniquely able to repeatedly restore sinus rhythm in a segment of the AF population. Any of these therapies, either alone or more likely in some form of combined therapy, is likely to significantly influence and improve the care of patients with AF in the future.
Identification of differentially expressed genes in pancreatic cancer cells using cDNA microarray. (2002)

To identify new diagnostic markers and drug targets for pancreatic cancer, we compared the gene expression patterns of pancreatic cancer cell lines growing in tissue culture with those of normal pancreas using cDNA microarray analysis. Fluorescently (cyanine 5) labeled cDNA probes, made individually from mRNA samples of nine pancreatic cell lines, were each combined with fluorescently (cyanine 3) labeled universal reference mRNA. The mixed probes of each sample were then hybridized with 5760 cDNA arrays (5289 unique cDNA sequences) printed on individual microscope slides. Fluorescently (cyanine 5) labeled normal pancreas mRNA was also compared with the same universal reference mRNA reference pool. The expression ratios of neoplastic versus normal pancreas cells were then calculated by multiplying the ratio of cancer versus the universal reference mRNA and the ratio of the universal reference mRNA cell versus normal pancreas. For 5289 different genes interrogated by the arrays, 30 of them showed an expression ratio 2 SD from the mean in at least three of the nine pancreatic cell lines studied. To confirm the expression profiles of these genes, quantitative reverse transcription-PCR and Northern blot were carried out for 25 of the overexpressed genes. To verify the overexpression in patient samples, two of the overexpressed genes, c-Myc and Rad51, were selected to undergo analysis by reverse transcription-PCR in frozen tumor tissues and by immunostaining in paraffin-embedded tissue section microarrays. The results of these experiments are in agreement with the microarray data. Potential up-regulated targets of note from this study include urokinase-type plasminogen activator receptor, serine/threonine kinase 15, thioredoxin reductase, and CDC28 protein kinase 2, as well as several others.