gebhart/patrepeval huggingface dataset:
Internet as Clinical Information System: Application Development Using the World Wide Web (1995)

Clinical computing application development at Columbia-Presbyterian Medical Center has been limited by the lack of a flexible programming environment that supports multiple client user platforms. The World Wide Web offers a potential solution, with its multifunction servers, multiplatform clients, and use of standard protocols for displaying information. The authors are now using the Web, coupled with their own local clinical data server and vocabulary server, to carry out rapid prototype development of clinical information systems. They have developed one such prototype system that can be run on most popular computing platforms from anywhere on the Internet. The Web paradigm allows easy integration of clinical information with other local and Internet-based information sources. The Web also simplifies many aspects of application design; for example, it includes facilities for the use of encryption to meet the authors' security and confidentiality requirements. The prototype currently runs on only the Web server in the Department of Medical Informatics at Columbia University, but it could be run on other Web servers that access the authors' clinical data and vocabulary servers. It could also be adapted to access clinical information from other systems with similar server capabilities. This approach may be adaptable for use in developing institution-independent standards for data and application sharing.
Weak value amplified optical activity measurements (2011)

We present a new form of optical activity measurement based on a modified weak value amplification scheme. It has recently been shown experimentally that the left- and right-circular polarization components refract with slightly different angles of refraction at a chiral interface causing a linearly polarized light beam to split into two. By introducing a polarization modulation that does not give rise to a change in the optical rotation it is possible to differentiate between the two circular polarization components even after post-selection with a linear polarizer. We show that such a modified weak value amplification measurement permits the sign of the splitting and thus the handedness of the optically active medium to be determined. Angular beam separations of Δθ ∼ 1 nanoradian, which corresponds to a circular birefringence of Δn ∼ 1 × 10(-9), could be measured with a relative error of less than 1%.
Reinforcement learning in a large-scale photonic recurrent neural network (2018)

Photonic neural network implementation has been gaining considerable attention as a potentially disruptive future technology. Demonstrating learning in large-scale neural networks is essential to establish photonic machine learning substrates as viable information processing systems. Realizing photonic neural networks with numerous nonlinear nodes in a fully parallel and efficient learning hardware has been lacking so far. We demonstrate a network of up to 2025 diffractively coupled photonic nodes, forming a large-scale recurrent neural network. Using a digital micro mirror device, we realize reinforcement learning. Our scheme is fully parallel, and the passive weights maximize energy efficiency and bandwidth. The computational output efficiently converges, and we achieve very good performance.
Deterministic Langevin Monte Carlo with Normalizing Flows for Bayesian Inference (2022)

We propose a general purpose Bayesian inference algorithm for expensive likelihoods, replacing the stochastic term in the Langevin equation with a deterministic density gradient term. The particle density is evaluated from the current particle positions using a Normalizing Flow (NF), which is differentiable and has good generalization properties in high dimensions. We take advantage of NF preconditioning and NF based Metropolis-Hastings updates for a faster convergence. We show on various examples that the method is competitive against state of the art sampling methods.
Hydrogen Peroxide Fluxes and Compartmentalization inside Growing <i>Escherichia coli</i> (2001)

Escherichia coli generates about 14 microM hydrogen peroxide (H(2)O(2)) per s when it grows exponentially in glucose medium. The steady-state intracellular concentration of H(2)O(2) depends on the rates at which this H(2)O(2) is dissipated by scavenging enzymes and by efflux from the cell. The rates of H(2)O(2) degradation by the two major scavenging enzymes, alkyl hydroperoxide reductase and catalase, were quantified. In order to estimate the rate of efflux, the permeability coefficient of membranes for H(2)O(2) was determined. The coefficient is 1.6 x 10(-3) cm/s, indicating that permeability is substantial but not unlimited. These data allowed internal H(2)O(2) fluxes and concentrations to be calculated. Under these growth conditions, Ahp scavenges the majority of the endogenous H(2)O(2), with a small fraction degraded by catalase and virtually none persisting long enough to penetrate the membrane and exit the cell. The robust scavenging activity maintains the H(2)O(2) concentration inside glucose-grown cells at <10(-7) M, substantially below the level (10(-6) M) at which toxicity is evident. When extracellular H(2)O(2) is present, its flux into the cell can be rapid, but the internal concentration may still be an order of magnitude lower than that outside. The presence of such gradients was confirmed in experiments that revealed different degrees of oxidative stress in cocultured scavenger-deficient mutants. The limited permeability of membranes to H(2)O(2) rationalizes the compartmentalization of scavenging systems and predicts that bacteria that excrete redox-cycling drugs do not experience the same H(2)O(2) dose that they impose on their competitors.
Increased Melanocytic Nevi in Patients with Inherited Ichthyoses: Report of a Previously Undescribed Association (2010)

Ichthyosis is a heterogeneous cornification disorder. Melanocytic lesions have not been previously described in association with ichthyosis. Their clinical importance lies in the fact that they may simulate melanoma clinically and dermoscopically, as seen in epidermolysis bullosa. The objective of this study was to evaluate the clinical, dermoscopic, and histopathologic features of nevi and lentigines in 16 patients with autosomal recessive congenital ichthyosis-lamellar ichthyosis and nonbullous ichthyosiform congenital erythroderma. Patients underwent general clinical examination dermoscopy. The more suspicious lesions were excised and to histopathologic examination. Most patients (n = 13) reported no personal or familial history of melanoma or atypical nevi. All of the patients had at least five atypical melanocytic lesions. Ten of the 16 patients had at least one atypical nevus or lentigo. This study suggests that increased atypical melanocytic nevi may be a feature of long-standing congenital ichthyoses. Whether this finding is disease-related or a coincidental observation is difficult to ascertain. As an unequivocal discrimination from malignant melanoma in vivo is not always possible, regular clinical follow-up of patients with ichthyosis and increased or unusual nevi is recommended.
Xanthohumol suppresses oestrogen-signalling in breast cancer through the inhibition of BIG3-PHB2 interactions (2014)

Xanthohumol (XN) is a natural anticancer compound that inhibits the proliferation of oestrogen receptor-α (ERα)-positive breast cancer cells. However, the precise mechanism of the antitumour effects of XN on oestrogen (E2)-dependent cell growth, and especially its direct target molecule(s), remain(s) largely unknown. Here, we focus on whether XN directly binds to the tumour suppressor protein prohibitin 2 (PHB2), forming a novel natural antitumour compound targeting the BIG3-PHB2 complex and acting as a pivotal modulator of E2/ERα signalling in breast cancer cells. XN treatment effectively prevented the BIG3-PHB2 interaction, thereby releasing PHB2 to directly bind to both nuclear- and cytoplasmic ERα. This event led to the complete suppression of the E2-signalling pathways and ERα-positive breast cancer cell growth both in vitro and in vivo, but did not suppress the growth of normal mammary epithelial cells. Our findings suggest that XN may be a promising natural compound to suppress the growth of luminal-type breast cancer.
Label-Free Protein Recognition Two-Dimensional Array Using Nanomechanical Sensors (2008)

We demonstrate two-dimensional multiplexed real-time, label-free antibody-antigen binding assays by optically detecting nanoscale motions of two-dimensional arrays of microcantilever beams. Prostate specific antigen (PSA) was assayed using antibodies covalently bound to one surface of the cantilevers by two different surface chemistries, while the nonreaction surfaces were passivated by poly(ethylene glycol)-silane. PSA as low as 1 ng/mL was detected while 2 mg/microl of bovine serum albumin induced only negligible deflection on the cantilevers.
Systematic Analysis of the Combinatorial Nature of Epitopes Recognized by TCR Leads to Identification of Mimicry Epitopes for Glutamic Acid Decarboxylase 65-Specific TCRs (2003)

Accumulating evidence indicates that recognition by TCRs is far more degenerate than formerly presumed. Cross-recognition of microbial Ags by autoreactive T cells is implicated in the development of autoimmunity, and elucidating the recognition nature of TCRs has great significance for revelation of the disease process. A major drawback of currently used means, including positional scanning synthetic combinatorial peptide libraries, to analyze diversity of epitopes recognized by certain TCRs is that the systematic detection of cross-recognized epitopes considering the combinatorial effect of amino acids within the epitope is difficult. We devised a novel method to resolve this issue and used it to analyze cross-recognition profiles of two glutamic acid decarboxylase 65-autoreactive CD4(+) T cell clones, established from type I diabetes patients. We generated a DNA-based randomized epitope library based on the original glutamic acid decarboxylase epitope using class II-associated invariant chain peptide-substituted invariant chains. The epitope library was composed of seven sublibraries, in which three successive residues within the epitope were randomized simultaneously. Analysis of agonistic epitopes indicates that recognition by both TCRs was significantly affected by combinations of amino acids in the antigenic peptide, although the degree of combinatorial effect differed between the two TCRs. Protein database searching based on the TCR recognition profile proved successful in identifying several microbial and self-protein-derived mimicry epitopes. Some of the identified mimicry epitopes were actually produced from recombinant microbial proteins by APCs to stimulate T cell clones. Our data demonstrate the importance of the combinatorial nature of amino acid residues of epitopes in molecular mimicry.
The crystal structure of 1-methyltriphenylene (1990)

The crystal structure of 1-methyltriphenylene, C 19 H 14 , has been determined by application of direct methods to single-crystal X-ray diffractometric data, with refinement by least-squares to R = 0.087 over 987 independent reflections to give apparent estimated standard deviations of 0.01 Å in C – C bond lengths and 0.6° in C – C – C angles. In the methyl-substituted bay region, molecular overcrowding is relieved by a long beach bond C13 – C14 = 1.50(1) Å and a C14 – C1 – C19 bond angle of 126° to the methyl group, with the beach-arm bond angles C12 – C13 – C14 = 122° and C13 – C14 – C1 = 124° compared with about 121° in the unsubstituted bay regions. Substitution of the methyl group into nearly planar triphenylene also causes ring-carbon atoms in all three peripheral rings to deviate by as much as ± 0.3 Å from the mean molecular plane; the methyl-carbon atom is 0.8 Å below this plane. The ring-methyl C1 – C19 bond is long [1.53(1) Å]; and, in the unsubstituted rings, the peripheral bonds C6 – C7 and C10 – C11 at 1.35(1) Å and 1.36(1) Å, respectively, are slightly shorter than in triphenylene.
Photoluminescence Properties of Eu[sup 3+]-Activated Y[sub 2]GeO[sub 5] Phosphors (2003)

The luminescence and energy transfer properties of in have been investigated. The critical concentration at which the concentration quenching occurred under UV excitation were in To investigate the distinction of photoluminescence behavior of two transitions (i.e., and transition) for the ion, the decay curves for both and transition have been analyzed. Furthermore the energy migration process of this sample was investigated using Yokota and Tanimoto's formula based on diffusion limited quenching. © 2003 The Electrochemical Society. All rights reserved.
Identification and characterization of multiple mdm-2 proteins and mdm-2-p53 protein complexes. (1993)

A protein product of the mdm-2 oncogene (p90) has been recently shown to associate with the protein encoded by the tumor-suppressor gene p53. The mdm-2 gene was originally identified as a gene amplified in a spontaneously transformed Balb/c 3T3 cell line (3T3DM). This report describes the characterization of mdm-2 gene products and their interactions with the p53 protein. Polyclonal and monoclonal antibodies were generated against murine and human mdm-2 protein. These antibodies detected the mdm-2 p90 protein and at least four additional polypeptides (p85, p76, p74, p58-p57) in cultured cells. These additional proteins may arise from different spliced mRNA forms of the mdm-2 gene or post-translational modifications of the mdm-2 protein. The monoclonal antibodies distinguished at least three sets of mdm-2 proteins with distinct combinations of epitopes (p90 and p85; p76 and p74; p58-57). One or two of these proteins forms a complex with the p53 protein (p90, p58). These mdm-2 proteins were found to be overexpressed in 3T3DM cells and a subset of these proteins were complexed with p53. In 3T3DM cells, p90, like p53, had a short half-life of approximately 20 min and was localized to the cell nucleus. In resting cells stimulated with serum p90 levels and p90/p53 complex levels increased in the late G1 phase of the cell cycle. The p90 mdm-2 protein could regulate p53 activity in the late G1 phase of the cell cycle.
An Enzyme-Immunoassay for Human Interleukin-2 (1987)

A highly sensitive enzyme-immunoassay (EIA) for human interleukin-2 (IL-2) has been established. The assay is based on a sandwich method that uses two kinds of anti-IL-2 antibodies raised against Escherichia coli-derived recombinant IL-2 (rIL-2). An affinity-purified-anti-IL-2 goat IgG was used as the first antibody and the Fab' fragment of an affinity-purified-anti-IL-2 rabbit IgG was used as the second antibody after being coupled with horseradish peroxidase (HRP). As little as 30 pg/ml of IL-2 was detected by the EIA, indicating that this method was about 100 times more sensitive than the bioassay using an IL-2-dependent murine natural killer cell line, NKC3. There was a good correlation between the EIA and the bioassay (r = 0.998).
Testing postcombustion CO2 capture with CaO in a 1.7 MWt pilot facility (2013)

Calcium looping, CaL, is a new and rapidly developing technology that makes use of CaO as a high temperature regenerable sorbent of CO2. Previous theoretical and lab scale studies have shown that this technology could lead to a substantial reduction in the cost of CO2 capture and energy penalties because heat can be effectively recovered from this high temperature solid looping system. We report in this paper on the first results from a pilot plant designed to demonstrate the viability of postcombustion capture of CO2 using CaL under conditions comparable to those expected in a large scale plant. The pilot includes two interconnected circulating fluidized bed reactors of 15 m height: a CO2 absorber (carbonator) able to treat up to 2400 kg/h (equivalent to about 1.7 MWth), and an oxy-fired CFB calciner with a firing power between 1-3 MWth. CO2 capture efficiencies over 90% have been experimentally observed, including continuous operation with highly cycled solids in the system (i.e. with modest CO2 carrying capacities). SO2 capture is shown to be extremely high, with concentrations of SO2 well below 10 ppmv at the exit of the carbonator. Closure of carbon and sulfur balances is satisfactory. These results should be valuable base for model validation and scaling up purposes in future stages of the EU FP7 "CaOling" project, under which this investigation has been carried out.
Isolation of specific peptides from Mycobacterium paratuberculosis protoplasm and their use in an enzyme-linked immunosorbent assay for the detection of paratuberculosis (Johne's disease) in cattle (1983)

An antigen was isolated from the protoplasm of Mycobacterium paratuberculosis by a combination of gel filtration, ion exchange, and affinity chromatography. The purified antigen constituted 7.8% of the total protein in the protoplasm. The specificity and sensitivity of the enzyme-linked immunosorbent assay (ELISA) for paratuberculosis, using the purified antigen, were evaluated with sera from 104 cattle which were examined (surveyed) for M paratuberculosis infection by fecal cultural technique. The ELISA was positive in 50 of 60 infected animals. Five of 44 noninfected animals were also test-positive. When a crude protoplasmic extract was used as antigen in the ELISA, sera from 37 infected and from 18 noninfected animals were test-positive. Cross-reactions were encountered in both complement-fixation test and the ELISA between crude or partially purified M paratuberculosis antigens and antisera to Nocardia asteroides, M avium, M phlei, and M fortuitum. The purified antigen gave no complement-fixation reaction with any of these antisera. In the ELISA, cross-reaction was not found when purified antigen was used and the sera were screened at 1:40 dilution.
Current R&D Challenges for Fluidized Bed Processes in the Refining Industry (2009)

Fluidized bed processes are widely used in the refining industry, mostly for conversion applications (e.g. fluid catalytic cracking, fluid coking, residue hydroconversion, Fischer-Tropsch Synthesis, etc.). These are large scale processes operating under severe conditions. Fluidized bed processes involve many complex phenomena that need to be considered in order to ensure proper design, operation and reliability. There have been thousands of publications over many years in the field of fluidization, but some of the fundamentals of fluid-particle flows still remain to be clarified. As a consequence, scale-up and industrialization of new technologies or processes remain a difficult, challenging and risky task.IFP is deeply involved with fluidized bed processes used in the refining industry. Over the last twenty years, industrial developments and PhD studies were conducted to explore new concepts, to develop new technologies, to scale-up hydrodynamics, to understand and quantify key phenomena. This paper discusses R&D practices in the field and current challenges encountered, mostly based on IFP experience. It does not intend, however, to provide an extensive literature review of all topics addressed in this paper.Interactions between particles, multiphase flow and reactor geometries are complex issues in fluidized beds. Therefore, experimentation is required to study new concepts such as downflow systems, complex phenomena such as vaporization of droplets in contact with gas-particle systems. The design of the experiment and the development of appropriate instrumentation are never simple and in the absence of simple similarities, anticipation of the main flow features is unavoidable. Modeling of results is then mandatory in order to translate results to industrial perspectives. Over the last 15 years, CFD has appeared as a promising tool to describe multiphase flow phenomena in complex geometries. Unfortunately, the lack of theoretical models to describe gas particle flow, at least for Group A powders, still leads researchers to conduct experiments to validate simulations or to adjust the gas-particle closure equations to validate results. Furthermore, observation in industrial units, during start-up or under steady conditions, when possible, greatly aids in validating research efforts and methodology.Despite its maturity, our industry is moving forward. There are ongoing developments in the energy and fuels market as well as in environmental fields, but also in the scientific background available to describe multiphase flow. Therefore, evolutionary R&D in the field is still needed to progress in the description of complex phenomena in order to optimize reactors and technologies and to face the changes of our industry.
Double heterostructure GaAs/AlGaAs thin film diode lasers on glass substrates (1989)

The epitaxial liftoff approach has been attracting increasing interest as an alternative to lattice-mismatched heteroepitaxy. A thin-film GaAs double heterostructure injection diode laser fabricated on a glass substrate by the epitaxial liftoff technique is reported. This presages the integration of the two major optical communication materials, III-V semiconductor crystals with SiO/sub 2/ glass.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Montelukast and Churg-Strauss syndrome (2001)

I read with interest the case report by Tuggey and Hosker where Churg-Strauss syndrome was associated with the use of montelukast in an asthmatic patient in whom there was no recent exposure to oral corticosteroid.1 However, it is worth noting that the patient was using a high dose of inhaled fluticasone propionate (1.5 mg/day) via a large volume spacer prior to the introduction of montelukast. In this respect, a large volume spacer has been shown to double the systemic bioavailability of fluticasone propionate compared with a metered dose inhaler, in terms of its propensity for adrenal suppression.2 In a dose ranging study in asthmatic patients a comparison was made between inhaled fluticasone propionate via a 750 ml large volume spacer (Volumatic) and oral prednisolone.3 Regression analysis showed significant (p<0.05) dose-response relationships with both drugs for suppression of peripheral blood eosinophils (fig 1), in keeping with their systemic bioavailability. At the highest doses studied for prednisolone (20 mg/day) and fluticasone propionate (2 mg/day nominal dose) there was a 1.5-fold (95% CI 0.8 to 2.7) greater suppression of blood eosinophils with prednisolone than with fluticasone although, as indicated by the confidence interval (which included unity), this did not represent a significant …