gebhart/patrepeval huggingface dataset:
Discordance in estrogen receptor status, progesterone receptor status, and HER2 status between primary breast cancer and recurrent breast cancer (2016)

Objective
To study intraindividual correlation of estrogen receptor (ER) status, progesterone receptor (PR) status, and human epidermal growth factor receptor-2 (HER2) status between primary and recurrent tumors in patients with recurrent breast cancer. To investigate patients’ characteristics, feasibility of histopathological evaluation in the recurrent setting, and to predict factors associated with receptors status discordance.


Methods
The clinicopathological data of 37 patients with regional recurrence were retrospectively analyzed. Immunohistochemistry (IHC) or FISH was used to detect the expression of ER, PR, and HER2 in primary and recurrent breast tumors.


Results
Among the 37 cases, 29 patients maintained the same tumor phenotype, whereas 8 patients (21.6%) changed during progression between primary breast cancer and relapse foci. Discordance for ER, PR, and HER2 was 13.5%, 37.8% and 10.8%, respectively.


Conclusions
This study confirms that there is discordance in ER and PR receptor expression between primary breast tumor and the corresponding recurrent lesions. Testing technical variability, intratumoral heterogeneity, cellular exposure to systemic agents such as chemotherapy, hormonal therapy or trastuzumab may be possible reasons. Whenever possible, a biopsy should be taken to confirm the diagnosis of a possible relapse as well as the receptor status of patients with breast cancer.


Key words: 
Breast cancer; Human epidermal growth factor receptor 2; Hormone receptor; Recurrent tumor
High capacity screening of pooled compounds: Identification of the active compound without re-assay of pool members (1996)

A matrix-based compound pooling and deconvolution method has been developed that significantly increased the efficiency of a high-capacity screening program. This method is based on screening pools of 10 compounds. The matrix used to assemble the pools resulted in each compound being assayed twice—each time with a completely different set of pooled compounds. The active compound in an active pool was accurately predicted by determining which compound was present in an active pool both times that a pool containing that compound was tested. This has eliminated the need to re-assay each individual member of active pools. This approach has been tested with a set of 6,680 compounds in three different assays: inhibition of Factor Xa, inhibition of gastrin-releasing peptide receptor binding, and inhibition of nitric oxide synthase (isoform II). Thus significant time is saved not only by pooling the compounds for the initial assay but also by avoiding the need to re-assay all compounds in active pools. Moreover, no false negatives occurred in these assays—an important consideration from a drug discovery perspective. © 1996 Wiley-Liss, Inc.
Simple Evaluation Method of Bipolar Diffusion Charging of Aerosol Particles and Its Application to Smoke Detectors (1987)

The diffusion charging of polydisperse and monodisperse aerosol particles by bipolar ions was theoretically studied under various conditions. Approximate equations in the simple form were derived to evaluate the changes in the particle charge and the ion number concentration. These approximate equations were applied to analyze the performance of the ionization-type smoke detector. The output response of an ionization-type smoke detector was experimentally tested with monodisperse aerosols, and the experimental response on the particle size and number concentration dependence were found to be explained by the simple approximate equations.
Highly flexible and miniaturized triple-band bandpass filter design using coupled stacked spiral resonators (2012)

This paper describes a triple-resonance stacked spiral resonator (SSR) structure for designing very compact tripleband bandpass filters. The resonant frequencies of the proposed SSR structure can be determined by designing the spiral geometry and controlling the mutual coupling in a stacked structure. The triple passband bandwidths can then be determined by the spacing of different layer patterns between two coupled SSRs. An adequately designed geometry of the input/output resonator with a tapped-line feed can achieve matching conditions for all passbands simultaneously. Moreover, multiple transmission zeros created on both sides of each passband provide high stopband roll-off rates.
Identification of the adduct between a 4-aza-3-ene-1,6-diyne and DNA using electrospray ionization mass spectrometry (2006)

The interactions between a novel enediyne [1-methyl-2-(phenylethynyl)-3-(3-phenylprop-2-ynyl)-3H-benzimidazolium] (1) and various cytosine-containing oligonucleotides were studied using electrospray ionization mass spectrometry (ESI-MS) in a flow injection analysis mode useful for small volumes. This enediyne ligand, developed as a potential alternative to the highly cytotoxic natural enediynes, some of which have been successfully used as anti-tumor agents, has previously been shown to interact with DNA through frank strand scission as well as via the formation of adducts that lead to 2'-deoxycytidine-specific cleavage. Through ESI-MS, the structures of these adducts were examined and a sequence dependence of the 2'-deoxycytidine-specific cleavage was noted. Collisionally activated dissociation of the observed adducts confirmed the strength of the interactions between the enediyne and DNA and supports a direct linkage between the enediyne and the cytosine nucleobase, likely the result of a nucleophilic attack of the phenylethynyl group by the cytosine amine.
Copper Binding to the Neurotoxic Peptide PrP106–126: Thermodynamic and Structural Studies (2004)

The human prion protein fragment PrP(106-126) is a highly fibrillogenic peptide, resistant to proteinases and toxic to neurons; it derives from the normal prion protein (PrP(C)), with which it can interact, thus inhibiting its superoxide dismutase-like activity. The same properties are also shown by the abnormal isoform of the prion protein (PrP(Sc)), and this similarity makes PrP(106-126) an interesting model for the neurotoxic action of PrP(Sc). A role for copper in PrP(106-126) aggregation and toxicity has recently been evidenced, and the interaction of terminal Lys, His and Met residues with the copper ion at neutral pH has been suggested. In order to shed more light on the complex-formation equilibria of PrP(106-126) with the copper ion, a thorough investigation has been carried out by means of several experimental techniques: potentiometry, solution calorimetry, VIS spectrophotometry, circular dichroism, EPR and NMR spectroscopy. A shorter and more soluble fragment-PrP(106-113), which lacks the hydrophobic C-terminal domain of PrP(106-126) but contains all the potential donor groups-has also been considered for the sake of comparison. The involvement of terminal amino, imidazolic and amido nitrogens in complex formation has been confirmed, while no evidence was found for the interaction of side chains of Met and Lys residues with the copper ion. Solution structures for the main complexes are suggested.
Estimating Effects with Rare Outcomes and High Dimensional Covariates: Knowledge is Power (2016)

Many of the secondary outcomes in observational studies and randomized trials are rare. Methods for estimating causal effects and associations with rare outcomes, however, are limited, and this represents a missed opportunity for investigation. In this article, we construct a new targeted minimum loss-based estimator (TMLE) for the effect or association of an exposure on a rare outcome. We focus on the causal risk difference and statistical models incorporating bounds on the conditional mean of the outcome, given the exposure and measured confounders. By construction, the proposed estimator constrains the predicted outcomes to respect this model knowledge. Theoretically, this bounding provides stability and power to estimate the exposure effect. In finite sample simulations, the proposed estimator performed as well, if not better, than alternative estimators, including a propensity score matching estimator, inverse probability of treatment weighted (IPTW) estimator, augmented-IPTW and the standard TMLE algorithm. The new estimator yielded consistent estimates if either the conditional mean outcome or the propensity score was consistently estimated. As a substitution estimator, TMLE guaranteed the point estimates were within the parameter range. We applied the estimator to investigate the association between permissive neighborhood drunkenness norms and alcohol use disorder. Our results highlight the potential for double robust, semiparametric efficient estimation with rare events and high dimensional covariates.
Electromagnetic radiation and scattering from elliptical torus knots (2002)

A mathematically rigorous approach for combining knot theory with Maxwell's theory of electromagnetism was reported by Werner (see IEEE Antennas and Propagation Society International Symposium Digest, vol.2, p.1468-71, Montreal, Canada, 1997). This analysis methodology was initially used to investigate the electromagnetic characteristics of a special class of knots, known as (p,q)-torus knots. A convenient set of parametric representations was developed by Werner for this particular family of knots by making use of the fact that they may be constructed on the surface of a standard circular torus in R/sup 3/. These parameterizations were then used in combination with Maxwell's equations to derive vector potential and field expressions which describe the radiation and scattering of electromagnetic waves from circular (p,q)-torus knots.
Tissue levels of S-adenosylmethionine and S-adenosylhomocysteine in rats fed methyl-deficient, amino acid-defined diets for one to five weeks (1983)

The levels of S-adenosylmethionine (AdoMet) and of S-adenosylhomocysteine (AdoHcy) as well as the ratio of AdoMet/AdoHcy were determined in the liver, lungs, testes and kidneys of weanling male rats fed a commercial chow diet or 5 different amino acid-defined diets for 1-5 weeks. The amino acid-defined diets used were as follows: diet 1, supplemented with methionine, choline, folic acid and vitamin B12; diet 2, deficient in methionine and choline; diet 3, deficient in methionine alone; diet 4, deficient in choline alone; diet 5, deficient in methionine, choline, folic acid and vitamin B12. All methionine-deficient diets were supplemented with an equimolar dose of its metabolic precursor, homocystine. The animals were sacrificed after 1, 3 and 5 weeks of treatment. In animals fed either the chow diet or diet 1, liver was the organ found to contain the highest levels of AdoMet and AdoHcy. Similarly, in animals fed diet 1 or chow, the testes and lungs contained the lowest level of AdoMet, while the lungs contained the lowest levels of AdoHcy. In general, the tissue levels of AdoHcy and AdoMet in rats fed diet 1 were very similar to the corresponding values found in chow-fed rats. Diet 1 feeding, however, led to higher hepatic levels of AdoMet than did the administration of the chow diet. The administration of the methyl-deficient diets generally led to decreased hepatic AdoMet contents at 3 and 5 weeks; the methyl-deficient diets also led to increased AdoHcy contents and decreased AdoMet:AdoHcy ratios when compared with diet 1. Linear regression analysis showed a significant direct correlation between the observed hepatic AdoMet levels and the methyl content of the diet as well as an inverse correlation between hepatic AdoHcy levels and dietary methyl contents. Unlike liver, the lung and testes did not show any decrease in AdoMet content following feeding of the methyl-deficient diets. These tissues did show, however, early significant increases in AdoHcy contents and corresponding decreases in the ratios of AdoMet:AdoHcy. These changes were found to be proportional to the dietary methyl content. The renal contents of AdoMet, AdoHcy and the ratio of AdoMet/AdoHcy were unaffected by any of the diets administered except for diet 5. The administration of diet 5 to rats for 5 weeks led to a significant increase in renal AdoHcy. These results provide evidence indicating that dietary methyl insufficiency may exert its role in carcinogenesis through a decreased availability of AdoMet in vivo.
Ex vivo evaluation of erythrocytosis‐enhanced platelet thrombus formation using the cone and plate(let) analyzer: effect of platelet antagonists (2004)

Red blood cells (RBC) contribute significantly to haemostasis and thrombosis under oscillatory flow conditions, and erythrocytosis has been associated with increased thrombotic risk. To measure the dynamic influences of RBC on platelets, we used a recently described cone and plate(let) analyzer (CPA), evaluating the effect of haematocrit (Hct) on platelet function in whole blood under arterial flow conditions (1800/s, 2 min, 25 degrees C). Anticoagulated blood, reconstituted to varying haematocrits with autologous RBC, demonstrated a significant increase in adherent platelet aggregate formation at Hct levels >45%. This increase was not affected by pretreatment of blood with 0.05 mmol/l aspirin, but was prevented by antagonists of P2Y1, P2Y12, or P2X1, ADP and ATP receptors, and by converting exogenous ADP to ATP with creatine phosphate/creatine phosphokinase. As negligible platelet granule secretion was measured during CPA analysis, but metabolic inhibition of RBC with sodium azide or glutaraldehyde fixation inhibited erythrocytosis-enhanced increases in platelet aggregate size, adenine nucleotides contributing to shear-induced platelet aggregate formation appear to be derived from erythrocytes. These findings support the use of CPA for ex vivo evaluation of the contribution of RBC to platelet function and its inhibition under physiological shear conditions.
Reliable execution of business processes on dynamic networks of service-enabled devices (2009)

It is expected that future shop-floors will be populated by thousands of networked embedded devices. Those will not only communicate using IP (as in TCP/IP), but also feature some autonomy, allowing them to collaborate among themselves and with enterprise systems. As they can offer both their mechatronic and higher-level functions as a service and support dynamic deployment of new code, they can execute business logic locally, allowing for new classes of business processes that are executed collaboratively by back-end and embedded systems. While some parts of a process will still be executed in the data centre, the rest will execute directly on embedded devices on the shop-floor. Business Process execution will therefore be more dynamic and context-based.We introduce an approach to manage efficient business process execution over such highly dynamic infrastructures.
Generalised subcomplementary sets of sequences (1987)

The generalisation of the constructive technique for generating the subcomplementary sets of sequences, previously introduced by Sivaswamy, is presented. In such a manner, still more efficient pulse compression and spread-spectrum waveforms can be designed.
MRI-Compatible Injection System for Magnetic Microparticle Embolization (2018)

This system has the capability to operate within the strong magnetic field of a clinical 3-T MRI, to form proper particle aggregates and to automatically inject these aggregates into the MRI bore. Moreover, the versatility of the proposed injector renders it suitable for selective injections of MDEBs during MR-guided embolization procedures.
Resonant coupling of electrons and excitons in an aperiodic superlattice under electric fields studied by photoluminescence spectroscopy (1995)

We report on a low-temperature (2 K) photoluminescence (PL) investigation of a nine-quantum-well ${\mathrm{Al}}_{0.4}$${\mathrm{Ga}}_{0.6}$As/GaAs aperiodic superlattice designed to obtain an electron quasiminiband in a desired electric field. The field dependence of the photoluminescence excitation spectra exhibits triple resonance of exciton states originally confined in three neighboring quantum wells and enhancement of the lowest energy exciton intensity due to localizing Coulomb interaction. In the vicinity of a field corresponding to the formation of the quasiminiband, we also observed a drastic quenching of the integrated PL intensity attributed to the fast carrier (electrons) escape through the high-mobility channel formed in the conduction miniband. A comparison of experimental results with numerical calculations of the exciton oscillator strength confirmed that exciton resonance occurred between strongly coupled Stark ladder states.
Roll Forward, Not Back A Case for Deterministic Conflict Resolution (2011)

Enabling applications to execute various tasks in parallel is difficult if those tasks exhibit read and write conflicts. In recent work, we developed a programming model based on concurrent revisions that addresses this challenge: each forked task gets a conceptual copy of all locations that are declared to be shared. Each such location has a specific isolation type; on joins, state changes to each location are merged deterministically based on its isolation type. In this paper, we study how to specify isolation types abstractly using operation-based compensation functions rather than statebased merge functions. Using several examples including a list with insert, delete and modify operations, we propose compensation tables as a concise, general and intuitively accessible mechanism for determining how to merge arbitrary operation sequences. Finally, we provide sufficient conditions to verify that a state-based merge function correctly implements a compensation table.
Mediator-Related Symptoms and Anaphylaxis in Children with Mastocytosis (2021)

Mastocytosis is characterized by pathological accumulation of mast cells (MC) in various organs. In these patients, MC may degranulate and thereby contribute to clinical symptoms, especially when a concomitant allergy is present. However, MC activation can not only be induced by high-affinity receptors for IgE, but also by anaphylatoxins, neuropeptides, IgG immune complexes, complement-components, drugs, products of bacteria or parasites, as well as physical factors such as heat, cold, vibration, stress, sun, or physical effort. Symptoms due to mediators released by activated MC may develop in adults suffering from systemic mastocytosis, but also evolve in children who usually have cutaneous mastocytosis (CM). Clinically, CM is otherwise characterized by typical brown, maculopapular skin lesions or mastocytoma associated with a positive Darier&amp;rsquo;s sign. Pruritus and flushing are common and blistering may also be recorded, especially in diffuse CM (DCM). Pediatric patients with mastocytosis may also have gastrointestinal, respiratory, and neurologic complaints. Although anaphylaxis is not a typical finding, pediatric patients with massive skin involvement and high tryptase levels have a relatively high risk to develop anaphylaxis. This paper reviews MC mediator-related symptoms and anaphylaxis in children with mastocytosis, with special emphasis on risk factors, triggers, and management.
Viral Suppression and Immune Restoration in the Gastrointestinal Mucosa of Human Immunodeficiency Virus Type 1-Infected Patients Initiating Therapy during Primary or Chronic Infection (2006)

Although the gut-associated lymphoid tissue (GALT) is an important early site for human immunodeficiency virus (HIV) replication and severe CD4+ T-cell depletion, our understanding is limited about the restoration of the gut mucosal immune system during highly active antiretroviral therapy (HAART). We evaluated the kinetics of viral suppression, CD4+ T-cell restoration, gene expression, and HIV-specific CD8+ T-cell responses in longitudinal gastrointestinal biopsy and peripheral blood samples from patients initiating HAART during primary HIV infection (PHI) or chronic HIV infection (CHI) using flow cytometry, real-time PCR, and DNA microarray analysis. Viral suppression was more effective in GALT of PHI patients than CHI patients during HAART. Mucosal CD4+ T-cell restoration was delayed compared to peripheral blood and independent of the time of HAART initiation. Immunophenotypic analysis showed that repopulating mucosal CD4+ T cells were predominantly of a memory phenotype and expressed CD11 alpha, alpha(E)beta 7, CCR5, and CXCR4. Incomplete suppression of viral replication in GALT during HAART correlated with increased HIV-specific CD8+ T-cell responses. DNA microarray analysis revealed that genes involved in inflammation and cell activation were up regulated in patients who did not replenish mucosal CD4+ T cells efficiently, while expression of genes involved in growth and repair was increased in patients with efficient mucosal CD4+ T-cell restoration. Our findings suggest that the discordance in CD4+ T-cell restoration between GALT and peripheral blood during therapy can be attributed to the incomplete viral suppression and increased immune activation and inflammation that may prevent restoration of CD4+ T cells and the gut microenvironment.
Sensitivity studies on 3.5-MeV alpha bombardment of a tokamak first wall (1977)

High-energy fusion-product losses to the first wall of a fusion reactor cause wall damage and may seriously contaminate the plasma with material ejected from the wall. Present studies extend previous results by considering the sensitivity of the loading to various parameters such as major-minor radii and plasma current. (MHR)
Photon‐Induced Near‐Field Electron Microscopy of Eukaryotic Cells (2017)

Abstract Photon‐induced near‐field electron microscopy (PINEM) is a technique to produce and then image evanescent electromagnetic fields on the surfaces of nanostructures. Most previous applications of PINEM have imaged surface plasmon‐polariton waves on conducting nanomaterials. Here, the application of PINEM on whole human cancer cells and membrane vesicles isolated from them is reported. We show that photons induce time‐, orientation‐, and polarization‐dependent evanescent fields on the surfaces of A431 cancer cells and isolated membrane vesicles. Furthermore, the addition of a ligand to the major surface receptor on these cells and vesicles (epidermal growth factor receptor, EGFR) reduces the intensity of these fields in both preparations. We propose that in the absence of plasmon waves in biological samples, these evanescent fields reflect the changes in EGFR kinase domain polarization upon ligand binding.
Deconvolution for multimode fiber imaging: modeling of spatially variant PSF (2020)

Focusing light through a step-index multimode optical fiber (MMF) using wavefront control enables minimally-invasive endoscopy of biological tissue. The point spread function (PSF) of such an imaging system is spatially variant, and this variation limits compensation for blurring using most deconvolution algorithms as they require a uniform PSF. However, modeling the spatially variant PSF into a series of spatially invariant PSFs re-opens the possibility of deconvolution. To achieve this we developed svmPSF: an open-source Java-based framework compatible with ImageJ. The approach takes a series of point response measurements across the field-of-view (FOV) and applies principal component analysis to the measurements' co-variance matrix to generate a PSF model. By combining the svmPSF output with a modified Richardson-Lucy deconvolution algorithm, we were able to deblur and regularize fluorescence images of beads and live neurons acquired with a MMF, and thus effectively increasing the FOV.