gebhart/patrepeval huggingface dataset:
Overexpression of mutant ras in human melanoma increases invasiveness, proliferation and anchorage-independent growth in vitro and induces tumour formation and cachexia in vivo (1999)

Malignant melanoma is the deadliest form of skin cancer. Previous studies have shown that the incidence of ras mutation increases with progression of melanoma, but that such mutations may not be present in the earliest radial growth phase melanomas. Recently it has been proposed that introduction of ras mutations into cells deficient in tumour suppressor genes such as p16 (INK4a) is sufficient to induce characteristics of cellular transformation such as anchorage-independent growth and tumour formation in vivo. To test this hypothesis in human melanoma, mutant N-ras, mutant H-ras or wild-type H-ras genes were transfected by electroporation into WM35 cells, a p16-deficient human melanoma cell line of low invasive potential. Increased expression of mutant ras p21 enhanced anchorage-dependent cell growth on tissue culture plastic. In addition, overexpression of mutant N-ras and H-ras, but not of wild-type H-ras, increased the experimental invasive potential, inducing anchorage-independent growth in soft agar, increasing cell motility measured by time-lapse video microscopy, and increasing invasiveness through reconstituted basement membranes. Finally, overexpression of mutant H-ras in melanoma cells was shown to increase tumorigenicity and to induce cachexia when H-ras transfected cell lines were injected subcutaneously in severe combined immunodeficiency (SCID) mice. Thus the addition of activating ras mutations to a melanoma cell line already deficient in p16 leads to enhanced proliferation, survival and migration in vitro and to enhanced subcutaneous tumour formation in vivo. This phenotype is typical of the behaviour of vertical growth phase (VGP) melanoma, and we propose that activation of the ras signalling pathway in the presence of deletions in p16 or related tumour suppressors can induce the VGP melanoma phenotype.
Curcumin-Loaded PLGA Nanoparticles Coating onto Metal Stent by Electrophoretic Deposition Techniques (2007)

Restenosis after percutaneous coronary intervention (PCI) continues to be a serious problem in clinical cardiology. To solve this problem, drug eluting stents (DES) with antiproliferative agents have been developed. Variable local drug delivery systems in the context of stenting require the development of stent manufacture, drug pharmacology and coating technology. We have worked on a system that integrates electrophoretic deposition (EPD) technology with the polymeric nanoparticles in DES for local drug delivery and a controlled release system. The surface morphology and drug loading amount of DES by EPD have been investigated under different operational conditions, such as operation time, voltage and the composition of media. We prepared poly-D,L-lactide-co-glycolic acid (PLGA) nanoparticles embedded with curcumin, which was done by a modified spontaneous emulsification method and used polyacrylic acid (PAA) as a surfactant because its carboxylic group contribute negative charge to the surface of CPNPs (?53.5 ± 5.8 mV). In the process of ‘trial and error' endeavors, we found that it is easy to control the drug loading amount deposited onto the stent while keeping uniform surface morphology. Accordingly, stent coating by EPD has a wide application to the modification of DES using various kinds of nanoparticles and drugs.
Reversible Light Switching of Cell Signalling by Genetically Encoded Protein Dimerization (2010)

Let there be light! Light control provides precise spatial and temporal regulation of cellular events. A genetically encoded system based on the photoswitchable Arabidopsis thaliana PhyB–PIF interaction has been applied to the reversible photocontrol of protein translocation and cellular morphology in mammalian cells.
Taci Is a Traf-Interacting Receptor for Tall-1, a Tumor Necrosis Factor Family Member Involved in B Cell Regulation (2000)

We and others recently reported tumor necrosis factor (TNF) and apoptosis ligand-related leukocyte-expressed ligand 1 (TALL-1) as a novel member of the TNF ligand family that is functionally involved in B cell proliferation. Transgenic mice overexpressing TALL-1 have severe B cell hyperplasia and lupus-like autoimmune disease. Here, we describe expression cloning of a cell surface receptor for TALL-1 from a human Burkitt's lymphoma RAJI cell library. The cloned receptor is identical to the previously reported TNF receptor (TNFR) homologue transmembrane activator and calcium modulator and cyclophilin ligand (CAML) interactor (TACI). Murine TACI was subsequently isolated from the mouse B lymphoma A20 cells. Human and murine TACI share 54% identity overall. Human TACI exhibits high binding affinities to both human and murine TALL-1. Soluble TACI extracellular domain protein specifically blocks TALL-1-mediated B cell proliferation without affecting CD40- or lipopolysaccharide-mediated B cell proliferation in vitro. In addition, when injected into mice, soluble TACI inhibits antibody production to both T cell-dependent and -independent antigens. By yeast two-hybrid screening of a B cell library with TACI intracellular domain, we identified that, like many other TNFR family members, TACI intracellular domain interacts with TNFR-associated factor (TRAF)2, 5, and 6. Correspondingly, TACI activation in a B cell line results in nuclear factor kappaB and c-Jun NH(2)-terminal kinase activation. The identification and characterization of the receptor for TALL-1 provides useful information for the development of a treatment for B cell-mediated autoimmune diseases such as systemic lupus erythematosus.
PIE: an online prediction system for protein-protein interactions from text (2008)

Protein-protein interaction (PPI) extraction has been an important research topic in bio-text mining area, since the PPI information is critical for understanding biological processes. However, there are very few open systems available on the Web and most of the systems focus on keyword searching based on predefined PPIs. PIE (Protein Interaction information Extraction system) is a configurable Web service to extract PPIs from literature, including user-provided papers as well as PubMed articles. After providing abstracts or papers, the prediction results are displayed in an easily readable form with essential, yet compact features. The PIE interface supports more features such as PDF file extraction, PubMed search tool and network communication, which are useful for biologists and bio-system developers. The PIE system utilizes natural language processing techniques and machine learning methodologies to predict PPI sentences, which results in high precision performance for Web users. PIE is freely available at http://bi.snu.ac.kr/pie/.
Third-order elastic constants for an inviscid fluid (1993)

In dealing with nonlinear problems involving fluids and solids, whether of a static or dynamic nature, a common description of the fields in terms of Eulerian or Lagrangian variables is desirable. Usually the former is used for fluids and the latter for solids. The choice of primitive variables also differs when dealing with fluids or solids. The material constants describing the constitutive behavior of these media will thus depend on the description adopted. In this paper, explicit relations are provided between third-order elastic constants for an inviscid fluid and the more common coefficients, A and B, appearing in the Taylor expansion of the equation of state. The essential results are c111=−(5A+B), c112=−(A+B), and c123=A−B.
In vitro-engineered non-antibody protein therapeutics (2017)

Antibodies have proved to be a valuable mode of therapy for numerous diseases, mainly owing to their high target binding affinity and specificity. Unfortunately, antibodies are also limited in several respects, chief amongst those being the extremely high cost of manufacture. Therefore, non-antibody binding proteins have long been sought after as alternative therapies. New binding protein scaffolds are constantly being designed or discovered with some already approved for human use by the FDA. This review focuses on protein scaffolds that are either already being used in humans or are currently being evaluated in clinical trials. Although not all are expected to be approved, the significant benefits ensure that these molecules will continue to be investigated and developed as therapeutic alternatives to antibodies. Based on the location of the amino acids that mediate ligand binding, we place all the protein scaffolds under clinical development into two general categories: scaffolds with ligand-binding residues located in exposed flexible loops, and those with the binding residues located in protein secondary structures, such as α-helices. Scaffolds that fall under the first category include adnectins, anticalins, avimers, Fynomers, Kunitz domains, and knottins, while those belonging to the second category include affibodies, β-hairpin mimetics, and designed ankyrin repeat proteins (DARPins). Most of these scaffolds are thermostable and can be easily produced in microorganisms or completely synthesized chemically. In addition, many of these scaffolds derive from human proteins and thus possess very low immunogenic potential. Additional advantages and limitations of these protein scaffolds as therapeutics compared to antibodies will be discussed.
Fast voice-coil scanning optical-resolution photoacoustic microscopy (2011)

We developed a photoacoustic imaging system that has real-time imaging capability with optical resolution. The imaging system is capable of scanning at 20 Hz over a 9 mm range and up to 40 Hz over a 1 mm scanning range. A focused laser beam provides a lateral resolution of 3.4 μm as measured in an optically nonscattering medium. Flows of micrometer-sized carbon particles or whole blood in a silicone tube and individual red blood cells (RBCs) in mouse ear capillaries were also imaged in real time, demonstrating the capability to image highly dynamic processes in vivo at a micrometer-scale resolution.
Bioassays: A Handbook of Quantitative Pharmacology. (1931)

A few decades ago it was considered heretical for the Pharmacopeia to have any assays other than chemical. Today no modern work dealing with determinations of the potency of drugs is complete without the assays of those indefinite but active mixtures so widely used in medicine, such as digitalis, pituitary and ergot. The important place that has been assumed by bio-assays is revealed in the issuance of this book of nearly a thousand pages dealing with only that portion of pharmacology. The book cannot be classed with such critical works on pharmacology as those of Cushny, Edmunds and Gunn, and Sollmann. It should be looked on in much the same relation to the pharmacologic library as Beilstein is looked on by chemists. It is a compilation that required a prodigious amount of bibliographic work. In the descriptions, the various methods of bio-assays are briefly given with complete references to the
An introduction to optical dating: the dating of Quaternary sediments by the use of photon-stimulated luminescence (1999)

Chapter 1: Introduction Chapter 2 2.1 Natural radioactivity 2.2 The natural dose-rate 2.3 Evaluation of dose-rate 2.4 Artificial irradiation 2.5 Dependence on rate at which dose is delivered, and on temperature Chapter 3 3.1 Sample collection 3.2 Preparation of aliquots for OSL measurement 3.3 Measurement of OSL Chapter 4 4.1 Unwanted signals: backgrounds and residuals 4.2 Irradiation and preheating 4.3 Multi-aliquot methods 4.4 The single-aliquot Chapter 5 5.1 Aeolian deposits 5.2 Water-laid sediment 5.3 Organic-rich sediment 5.4 Glaciation-related deposits 5.5 Earthquake-related studies 5.6 Two unusual applications 5.7 Applications other than sediment dating Chapter 6 6.1 Factors affecting rapidity of bleaching 6.2 The level reached 6.3 Intrinsic indications about zeroing - analysis of the shine-down curve 6.4 Other intrinsic indications about zeroing Chapter 7 7.1 Thermal transfer 7.2 Shine-curve analysis revisited 7.3 Reasons for preheating 7.4 Preheating of feldspars and polymineral fine-grains 7.5 Preheating of quartz 7.6 Quartz preheating and sensitivity change 7.7 Retention lifetimes
Electro-optically tunable, narrowband Ti:LiNbO 3 wavelength filter (1987)

We report a tunable optical transmission filter for 1.5μn with a bandwidth of 12 Å and a tuning range of at least 80 Å. The filter is based on wavelength-dependent polarisation conversion in a birefringent waveguide and employs a periodic electrode structure with interleaved birefringence tuning electrodes.
Seaglider: a long-range autonomous underwater vehicle for oceanographic research (2001)

Seagliders are small, reusable autonomous underwater vehicles designed to glide from the ocean surface to a programmed depth and back while measuring temperature, salinity, depth-averaged current, and other quantities along a sawtooth trajectory through the water. Their low hydrodynamic drag and wide pitch control range allow glide slopes in the range 0.2 to 3. They are designed for missions in a range of several thousand kilometers and durations of many months. Seagliders are commanded remotely and report their measurements in near real time via wireless telemetry. The development and operation of Seagliders and the results of field trials in Puget Sound are reported.
A Simple Cycloaddition Approach to a Racemate of the Natural Sweetener Monatin (1994)

Abstract The reaction of methyl 2-(3-indolylmethyl)-acrylate 2 with carbethoxyformonitrile oxide 3, followed by saponification and reduction, gives mainly racemic monatin 1. Preliminary attempts to adapt the 2+3 cycloaddition to a new chiral synthesis of monatin, is described.
Central N-acetyl aspartylglutamate deficit: a possible pathogenesis of schizophrenia. (2005)

The "glutamate hypothesis" of schizophrenia has emerged from the finding that phencyclidine (PCP) induces psychotic-like behaviors in rodents, possibly by blocking the N-methyl-D-aspartate (NMDA) subtype of glutamate receptor, thereby causing increased glutamate release. N-acetyl aspartylglutamate (NAAG), an endogenous peptide abundant in mammalian nervous systems, is localized in certain brain cells, including cortical and hippocampal pyramidal neurons. NAAG is synthesized from N-acetylaspartate (NAA) and glutamate, and NAA availability may limit the rate of NAAG synthesis. Although NAAG is known to have some neurotransmitter-like functions, NAA does not. NAAG is a highly selective agonist of the type 3 metabotropic glutamate receptor (mGluR3, a presynaptic autoreceptor) and can inhibit glutamate release. In addition, at low levels, NAAG is an NMDA receptor antagonist, and blocking of NMDA receptors may increase glutamate release. Taken together, low central NAAG levels may antagonize the effect of glutamate at NMDA receptors and decrease its agonistic effect on presynaptic mGluR3; both activities could increase glutamate release, similar to the increase demonstrated in the PCP model of schizophrenia. In this report, it is suggested that the central NAAG deficit, possibly through decreased synthesis or increased degradation of NAAG, may play a role in the pathogenesis of schizophrenia. Evidence is presented and discussed from magnetic resonance, postmortem, animal model, schizophrenia treatment, and genetic studies. The central NAAG deficit model of schizophrenia could explain the disease process, from the perspectives of both neurodevelopment and neurodegeneration, and may point to potential treatments for schizophrenia.
Bone formation using novel interconnected porous calcium hydroxyapatite ceramic hybridized with cultured marrow stromal stem cells derived from Green rat (2004)

The clinical use of cultured marrow stromal stem cells (MSCs) has recently attracted attention in the field of tissue engineering. For the clinical use of the MSCs, a prominent scaffold is needed. A scaffold hybridized with MSCs is transformed into a "bioactive bone substitute," and this provides good osteoconduction. In this study, a novel calcium hydroxyapatite ceramic with an interconnected porous structure (IP-CHA) was used as a scaffold. MSCs were harvested from Green rats containing Green Fluorescent Protein (GFP), and then these hybrids were implanted into the tibias of Sprague-Dawley rats. The purposes of this study were to examine the osteogenic ability of these hybrids without coculture, and to evaluate whether the resulting bone formation originated from the grafted MSCs or the recipient's cells. The hybridized group showed excellent bone formation compared with the IP-CHA-only implant group. Observation of the implanted MSCs revealed that they survived 8 weeks after surgery, and differentiated into osteoblast-like cells, thus providing bone formation. This implantation of the MSCs/IP-CHA composite provides excellent osteoconduction, and is expected to have extensive clinical applications.
Air and water stable ionic liquids in physical chemistry (2006)

Ionic liquids are defined today as liquids which solely consist of cations and anions and which by definition must have a melting point of 100 °C or below. Originating from electrochemistry in AlCl3 based liquids an enormous progress was made during the recent 10 years to synthesize ionic liquids that can be handled under ambient conditions, and today about 300 ionic liquids are already commercially available. Whereas the main interest is still focussed on organic and technical chemistry, various aspects of physical chemistry in ionic liquids are discussed now in literature. In this review article we give a short overview on physicochemical aspects of ionic liquids, such as physical properties of ionic liquids, nanoparticles, nanotubes, batteries, spectroscopy, thermodynamics and catalysis of/in ionic liquids. The focus is set on air and water stable ionic liquids as they will presumably dominate various fields of chemistry in future.
A rapid finite difference algorithm, utilizing successive over‐relaxation to solve the Poisson–Boltzmann equation (1991)

Abstract An efficient algorithm is presented for the numerical solution of the Poisson–Boltzmann equation by the finite difference method of successive over‐relaxation. Improvements include the rapid estimation of the optimum relaxation parameter, reduction in number of operations per iteration, and vector‐oriented array mapping. The algorithm has been incorporated into the electrostatic program DelPhi, reducing the required computing time by between one and two orders of magnitude. As a result the estimation of electrostatic effects such as solvent screening, ion distributions, and solvation energies of small solutes and biological macromolecules in solution, can be performed rapidly, and with minimal computing facilities.
Involvement of KU80 in T-DNA integration in plant cells (2005)

In Agrobacterium-mediated genetic transformation of plant cells, the bacterium exports a well defined transferred DNA (T-DNA) fragment and a series of virulence proteins into the host cell. Following its nuclear import, the single-stranded T-DNA is stripped of its escorting proteins, most likely converts to a double-stranded (ds) form, and integrates into the host genome. Little is known about the precise mechanism of T-DNA integration in plants, and no plant proteins specifically associated to T-DNA have been identified. Here we report the direct involvement of KU80, a protein that binds dsT-DNA intermediates. We show that ku80-mutant Arabidopsis plants are defective in T-DNA integration in somatic cells, whereas KU80-overexpressing plants exhibit increased susceptibility to Agrobacterium infection and increased resistance to DNA-damaging agents. The direct interaction between dsT-DNA molecules and KU80 in planta was confirmed by immunoprecipitation of KU80 dsT-DNA complexes from Agrobacterium-infected plants. Transformation of KU80-overexpressing plants with two separate T-DNA molecules resulted in an increased rate of extrachromosomal T-DNA to T-DNA recombination, indicating that KU80 bridges between dsT-DNAs and double-strand breaks. This last result further supports the notion that integration of T-DNA molecules occurs through ds intermediates and requires active participation of the host's nonhomologous end-joining repair machinery.
Disruption of circadian insulin secretion is associated with reduced glucose uptake in first-degree relatives of patients with type 2 diabetes. (1999)

The objective of this study was to evaluate whether first-degree relatives (FDRs) of patients with type 2 diabetes had abnormal circadian insulin secretion and, if so, whether this abnormality affected their glucose metabolism. Six African-American FDRs with normal glucose tolerance and 12 matched normal control subjects (who had no family history of diabetes) were exposed to 48 h of hyperglycemic clamping (approximately 12 mmol/l). Insulin secretion rates (ISRs) were determined by deconvolution of plasma C-peptide levels using individual C-peptide kinetic parameters. Detrending and smoothing of data (z-scores) and computation of autocorrelation functions were used to identify ISR cycles. During the initial hours after start of glucose infusions, ISRs were approximately 60% higher in FDRs than in control subjects (585 vs. 366 nmol/16 h, P < 0.05), while rates of glucose uptake were the same (5.6 mmol x kg(-1) x h(-1)), indicating that the FDRs were insulin resistant. Control subjects had well-defined circadian (24 h) cycles of ISR and plasma insulin that rose in the early morning, peaked in the afternoon, and declined during the night. In contrast, FDRs had several shorter ISR cycles of smaller amplitude that lacked true periodicity. This suggested that the lack of a normal circadian ISR increase had made it impossible for the FDRs to maintain their compensatory insulin hypersecretion beyond 18 h of hyperglycemia. As a result, ISR decreased to the level found in control subjects, and glucose uptake fell below the level of control subjects (61 vs. 117 micromol x kg(-1) x min(-1), P < 0.05). In summary, we found that FDRs with normal glucose tolerance had defects in insulin action and secretion. The newly recognized insulin secretory defect consisted of disruption of the normal circadian ISR cycle, which resulted in reduced insulin secretion (and glucose uptake) during the ascending part of the 24 h ISR cycle.
Additive amelioration of ALS by co‐targeting independent pathogenic mechanisms (2017)

Our data suggest that a combinatorial approach co-targeting different pathogenic mechanisms in independent cell types is a beneficial therapeutic strategy for ALS.
Determining anatomical connectivities between cortical and brainstem pain processing regions in humans: A diffusion tensor imaging study in healthy controls (2006)

Neuroimaging methods have so far identified various structures in the brain involved in the processing of pain and its control. However, our understanding of their anatomical connectivities is relatively weak. Diffusion tensor imaging (DTI), a magnetic resonance imaging-based method, allows in vivo mapping of the anatomical connections in the human brain and was used to investigate the white matter connections originating from the periaquaductal grey (PAG) and nucleus cuneiformis (NCF). We performed DTI on 8 healthy right-handed male volunteers. Group analysis showed that tract paths could be defined and their likelihood quantified for connections between the PAG and separately for the NCF, to the prefrontal cortex, amygdala, thalamus, hypothalamus and rostroventral medial medulla bilaterally. The connections identified confirm the existence of an anatomical circuitry for the functionally characterised top-down influences on pain processing via brainstem structures in humans.