gebhart/patrepeval huggingface dataset:
Data from Mutations in BRAF and KRAS Converge on Activation of the Mitogen-Activated Protein Kinase Pathway in Lung Cancer Mouse Models (2023)

&lt;div&gt;Abstract&lt;p&gt;Mutations in the &lt;i&gt;BRAF&lt;/i&gt; and &lt;i&gt;KRAS&lt;/i&gt; genes occur in ∼1% to 2% and 20% to 30% of non–small-cell lung cancer patients, respectively, suggesting that the mitogen-activated protein kinase (MAPK) pathway is preferentially activated in lung cancers. Here, we show that lung-specific expression of the BRAF V600E mutant induces the activation of extracellular signal–regulated kinase (ERK)-1/2 (MAPK) pathway and the development of lung adenocarcinoma with bronchioloalveolar carcinoma features &lt;i&gt;in vivo&lt;/i&gt;. Deinduction of transgene expression led to dramatic tumor regression, paralleled by dramatic dephosphorylation of ERK1/2, implying a dependency of BRAF-mutant lung tumors on the MAPK pathway. Accordingly, &lt;i&gt;in vivo&lt;/i&gt; pharmacologic inhibition of MAPK/ERK kinase (MEK; MAPKK) using a specific MEK inhibitor, CI-1040, induced tumor regression associated with inhibition of cell proliferation and induction of apoptosis in these &lt;i&gt;de novo&lt;/i&gt; lung tumors. CI-1040 treatment also led to dramatic tumor shrinkage in murine lung tumors driven by a mutant &lt;i&gt;KRas&lt;/i&gt; allele. Thus, somatic mutations in different signaling intermediates of the same pathway induce exquisite dependency on a shared downstream effector. These results unveil a potential common vulnerability of BRAF and KRas mutant lung tumors that potentially affects rational deployment of MEK targeted therapies to non–small-cell lung cancer patients. [Cancer Res 2007;67(10):4933–9]&lt;/p&gt;&lt;/div&gt;
Soluble suppressor supernatants elaborated by concanavalin A-activated human mononuclear cells. II. Characterization of a soluble suppressor of B cell immunoglobulin production. (1981)

Human peripheral blood mononuclear cells (PBMC) activated with the mitogenic lectin concanavalin A (Con A) elaborate a soluble immune suppressor supernatant (SISS) that contains at least 2 distinct suppressor factors. One of these, SISS-B, inhibits polyclonal B cell immunoglobulin production whereas the other, SISS-T, suppresses T cell proliferation to both mitogens and antigens. The latter mediator is discussed in the companion paper. Characteristics of the human soluble suppressor of B cell immunoglobulin production (SISS-B) include: 1) inhibition by a noncytotoxic mechanism, 2) loss of activity in the presence of the monosaccharide L-rhamnose, 3) appearance within 8 to 16 hr after the addition of Con A, 4) elaboration by cells irradiated with 500 or 2000 rads, 5) production by highly purified T cells, 6) stability at pH 2.5 but instability at 56 degrees C, and 7) m.w. of 60 to 80,000. These data indicate that after Con A activation, selected T cells not only become potent suppressor cells, but also generate a soluble saccharide-specific factor(s) that inhibits polyclonal immunoglobulin production by human B cells.
Amphipathic, Amphiphilic (2016)

This Glossary of Terms Related to Pharmaceutics is needed by practitioners in the field of pharmaceutics as this field fulfills an important and crucial role, different from the roles of other scientific disciplines involved in the drugmaking process. The glossary contains 168 definitions used in pharmaceutics. These are related to various aspects of this discipline, such as: (1) physicochemical characterization of pharmaceutical preparations and the active ingredients they contain; (2) unit operations used in the practice of pharmaceutics; (3) terms related to the various dosage forms; (4) terms related to the various modes and routes of drug delivery; (5) terms used in pharmacokinetics and biopharmaceutics in general; and additional miscellaneous terms. The field of pharmaceutics itself is of a multidisciplinary nature as its practitioners come from a variety of disciplines, such as chemistry or various biological sciences, thus a glossary containing authoritative definitions would be useful for them. The terms used in pharmaceutics are rarely covered by existing glossaries, and in the cases they are, their definitions are often inappropriate for the field of pharmaceutics and require new or modified definitions to better fit the new context.
LONGITUDINAL PENALIZED FUNCTIONAL REGRESSION (2010)

We propose a new regression model and inferential tools for the case when both the outcome and the functional exposures are observed at multiple visits. This data structure is new but increasingly present in applications where functions or images are recorded at multiple times. This raises new inferential challenges that cannot be addressed with current methods and software. Our proposed model generalizes the Generalized Linear Mixed Effects Model (GLMM) by adding functional predictors. Smoothness of the functional coefficients is ensured using roughness penalties estimated by Restricted Maximum Likelihood (REML) in a corresponding mixed effects model. This method is computationally feasible and is applicable when the functional predictors are measured densely, sparsely or with error; code implementing the proposed procedure is freely available. Methods are applied to a longitudinal diffusion tensor imaging (DTI) study relating changes in the microstructure of intracranial white matter tracts to cognitive disability in multiple sclerosis patients, but we note that the discussed data structure is increasingly common and our methods apply generally. An online appendix compares two implementations, one likelihood-based and the other Bayesian, and provides the software used in simulations.
Study of field-driven wall-configuration conversions for laminated Permalloy in the easy-axis state (1988)

Laminated Permalloy, with edge-curling walls replacing closure domains, has been proposed to increase permeability and reduce wall noise in recording. However, in structures meeting the criteria for Slonczewski’s ‘‘easy-axis’’ state, normal walls often coexist with edge-curling walls. We have used our laser magneto-optic microscope to study inductive-head-yoke shaped elements of two and four Permalloy layers separated by nonmagnetic, metallic spacers. In the four-magnetic-layer sample a state with a single wall, terminating at the edge-curling regions and lying along the easy-axis direction, is often observed on the top and bottom layers. Some elements may be driven into an easy-axis state with no observed domain walls. The two-magnetic-layer sample also exhibited simultaneous one-wall structures on the top and bottom layers. The other stable configuration was a no-wall state on the top layer and a two-wall (three-domain) state on the lower layer. These ‘‘coupled’’ states were exceptionally stable in both samples; fields on the order of 300 Oe were required to switch between configurations.
Biological subtyping of early breast cancer: a study comparing RT-qPCR with immunohistochemistry (2016)

The biological subtype of breast cancer influences the selection of systemic therapy. Distinction between luminal A and B cancers depends on consistent assessment of Ki-67, but substantial intra-observer and inter-observer variability exists when immunohistochemistry (IHC) is used. We compared RT-qPCR with IHC in the assessment of Ki-67 and other standard factors used in breast cancer subtyping. RNA was extracted from archival breast tumour tissue of 769 women randomly assigned to the FinHer trial. Cancer ESR1, PGR, ERBB2 and MKI67 mRNA content was quantitated with an RT-qPCR assay. Local pathologists assessed ER, PgR and Ki-67 expression using IHC. HER2 amplification was identified with chromogenic in situ hybridization (CISH) centrally. The results were correlated with distant disease-free survival (DDFS) and overall survival (OS). qPCR-based and IHC-based assessments of ER and PgR showed good concordance. Both low tumour MKI67 mRNA (RT-qPCR) and Ki-67 protein (IHC) levels were prognostic for favourable DDFS [hazard ratio (HR) 0.42, 95 % CI 0.25-0.71, P = 0.001; and HR 0.56, 0.37-0.84, P = 0.005, respectively] and OS. In multivariable analyses, cancer MKI67 mRNA content had independent influence on DDFS (adjusted HR 0.51, 95 % CI 0.29-0.89, P = 0.019) while Ki-67 protein expression had not any influence (P = 0.266) whereas both assessments influenced independently OS. Luminal B patients treated with docetaxel-FEC had more favourable DDFS and OS than those treated with vinorelbine-FEC when the subtype was defined by RT-qPCR (for DDFS, HR 0.52, 95 % CI 0.29-0.94, P = 0.031), but not when defined using IHC. Breast cancer subtypes approximated with RT-qPCR and IHC show good concordance, but cancer MKI67 mRNA content correlated slightly better with DDFS than Ki-67 expression. The findings based on MKI67 mRNA content suggest that patients with luminal B cancer benefit more from docetaxel-FEC than from vinorelbine-FEC.
MR Spectroscopy in Diagnosis and Neurological Decision-Making (2008)

One of the most prolific chemical and anatomical imaging techniques of recent decades, magnetic resonance imaging (MRI), includes the ability to noninvasively assess neurochemical changes with magnetic resonance spectroscopy (MRS). Practical concerns are paramount in applying MRS, such as what the manufacturer provides with a routine MRI scanner, what methods are well tolerated by patients, and what has proved most diagnostically productive over a 25 year span of preliminary exploration of the technology. In this review, the authors explain the technical and neurochemical aspects of MRS and critically discuss its clinical neuroimaging applications.
TEAD1 and c-Cbl are novel prostate basal cell markers that correlate with poor clinical outcome in prostate cancer (2008)

Prostate cancer is the most frequently diagnosed male cancer, and its clinical outcome is difficult to predict. The disease may involve the inappropriate expression of genes that normally control the proliferation of epithelial cells in the basal layer and their differentiation into luminal cells. Our aim was to identify novel basal cell markers and assess their prognostic and functional significance in prostate cancer. RNA from basal and luminal cells isolated from benign tissue by immunoguided laser-capture microdissection was subjected to expression profiling. We identified 112 and 267 genes defining basal and luminal populations, respectively. The transcription factor TEAD1 and the ubiquitin ligase c-Cbl were identified as novel basal cell markers. Knockdown of either marker using siRNA in prostate cell lines led to decreased cell growth in PC3 and disrupted acinar formation in a 3D culture system of RWPE1. Analyses of prostate cancer tissue microarray staining established that increased protein levels of either marker were associated with decreased patient survival independent of other clinicopathological metrics. These data are consistent with basal features impacting on the development and clinical course of prostate cancers.
MAGNETIZATION DISTRIBUTION IN THE VICINITY OF IMPLANTATION BOUNDARIES IN FERRIMAGNETIC GARNETS SUPPORTING BUBBLES (1985)

Néel lines in (TbY)3(FeAl)5O12 epitaxial layers with orthorhombic anisotropy and canted magnetization are observed by the presence of an apparent kink of the wall plane. It has been shown [1] that the sense of the kink does not depend on the average magnetization direction along the Néel line, but rather on the charge distribution around the line. In the present communication, a numerical calculation of the magnetization configuration around such a line is presented. The model is essentially similar to previous models such as introduced by Labonte [2,3] : the magnetization configuration is assumed to be independent of the Z coordinate, parallel to the line and for each iteration loop, the torque acting on the magnetization at location (X,Y) is calculated. The magnetization is then allowed to rotate slightly under the action of that torque. After a sufficiently large number of iterations, the equilibrium configuration is obtained. It will be shown that, in the present situation, two origins do contribute to the apparent Bloch wall kinking namely : - the charge distribution, as already mentioned, - the particular anisotropy characteristic of our samples where the easy and hard directions in the wall plane are not orthogonal. Finally, computed configurations will be confronted with the observed kink widths.
Development of a ZnS (Ag)-Silicon Photomultiplier Fast Neutron Detector for the Neutron Hodoscope at TREAT (2019)

The Transient Reactor Test (TREAT) Facility at Idaho National Laboratory is being restored to support the mission of advanced reactor and fuel development in the United States. A key part of this restoration is the fast neutron hodoscope which images the fuel tested during extreme transient conditions. Traditionally, this testing has been done with ZnS(Ag)-based proton recoil scintillators (PRS) coupled to photomultiplier tubes (PMTs). Recently, silicon photomultipliers (SiPMs) have emerged as a new candidate to replace PMTs in this application. This work develops, tests, and evaluates a SiPM-based PRS detector for incorporation into the updated fast neutron hodoscope, also known as the Fuel Motion Monitoring System (FMMS). The primary characteristics to be optimized are the gamma rejection and neutron detection efficiency of the detector, which will be done using a pulse shape discrimination (PSD) technique. Five types of SiPMs are tested and compared using standard PSD figures of merit, and the Hamamatsu 6075 is selected as the ideal SiPM. PSD performance for the Hamamatsu 6075 SiPM with the PRS detector is also characterized as a function of temperature. Finally, the gamma rejection and neutron detection efficiency are characterized for this SiPM and benchmarked to the traditional PMT-based PRS detectors. Both light sensors exhibit excellent gamma rejection and neutron detection efficiency. However, the SiPM-based detectors exhibit a greater ability to discriminate neutrons from gammas based only on pulse height which is important in operating at high count rates. This motivates the development of a SiPM-based PRS detector in a fully self-contained assembly to test directly with TREAT or in similar environments.
PRIMARY BLADDER NECK DYSFUNCTION IN CHILDREN AND ADOLESCENTS: RESULTS OF LONG TERM ALPHA BLOCKER THERAPY (2009)

You have accessJournal of Urology1 Apr 2009PRIMARY BLADDER NECK DYSFUNCTION IN CHILDREN AND ADOLESCENTS: RESULTS OF LONG TERM ALPHA BLOCKER THERAPY Jason P Van Batavia, Andrew J Combs, Mark Horowitz, and Kenneth I. Glassberg Jason P Van BataviaJason P Van Batavia More articles by this author , Andrew J CombsAndrew J Combs More articles by this author , Mark HorowitzMark Horowitz More articles by this author , and Kenneth I. GlassbergKenneth I. Glassberg More articles by this author View All Author Informationhttps://doi.org/10.1016/S0022-5347(09)60887-9AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "PRIMARY BLADDER NECK DYSFUNCTION IN CHILDREN AND ADOLESCENTS: RESULTS OF LONG TERM ALPHA BLOCKER THERAPY." The Journal of Urology, 181(4S), pp. 311–312 © 2009 by American Urological AssociationFiguresReferencesRelatedDetails Volume 181Issue 4SApril 2009Page: 311-312 Advertisement Copyright & Permissions© 2009 by American Urological AssociationMetrics Author Information Jason P Van Batavia More articles by this author Andrew J Combs More articles by this author Mark Horowitz More articles by this author Kenneth I. Glassberg More articles by this author Expand All Advertisement PDF downloadLoading ...
Dual-Source Computed Tomography for Assessing Cardiac Function (2007)

DSCT allows reliable quantification of global ventricular function independent of the heart rate. Multisegmental image reconstruction is not needed for DSCT assessment of global ventricular function.
High-resolution physicochemical characterization of different intravenous immunoglobulin products (2017)

Intravenous immunoglobulin (IVIg) is a complex mixture drug comprising diverse immunoglobulins and non-IgG proteins purified from the plasma of thousands of healthy donors. Approved IVIg products on the market differ regarding source of plasma, isolation process, and formulation. These products are used widely, and often interchangeably, for the treatment of immunodeficiency and autoimmune and inflammatory diseases, but their mechanisms of action in different indications are not well understood. A primary limitation to understanding the therapeutic relevance of specific components within IVIg has been the limited resolution of analytics historically implemented to characterize its complex mixture. In this study, high-resolution analytics were applied to better understand the composition of IVIg and product variations. We characterized three approved IVIg products: Gammagard®, Privigen®, and Octagam®. Differences in the distribution of molecular weight species, IgG sequence variants, isoforms, glycoforms, and the repertoire of previously reported antibody specificities were identified. We also compared the effect of aging on these products to identify changes in size distribution and posttranslational modifications. This type of characterization may provide insights into the specific factors and components of IVIg that may influence its activity and ultimately lead to optimization of IVIg products for use in autoimmune diseases.
Real time Structure from Motion for Driver Assistance System (2017)

Understanding of 3D surrounding is an important problem in Advanced Driver Assistance Systems (ADAS). Structure from Motion (SfM) is well known computer vision technique for estimating 3D structure from 2D image sequences. Inherent complexities of the SfM pose different algorithmic and implementation challenges to have an efficient enablement on embedded processor for real time processing. This paper focuses on highlighting such challenges and innovative solutions for them. The paper proposes an efficient SfM solution that has been implemented on Texas Instrument's TDA3x series of System on Chip (SoC). The TDA3x SoC contains one vector processor (known as EVE) and two C66x DSPs as co-processors which are useful for computationally intensive vision processing. The proposed SfM solution which performs Sparse Optical Flow, Fundamental matrix estimation, Triangulation, 3D points pruning consumes 42% of EVE and 10% of one DSP for 25 fps processing of one mega pixel image resolution.
Integration of physiologically relevant photosynthetic energy flows into whole genome models of light‐driven metabolism (2022)

Characterizing photosynthetic productivity is necessary to understand the ecological contributions and biotechnology potential of plants, algae, and cyanobacteria. Light capture efficiency and photophysiology have long been characterized by measurements of chlorophyll fluorescence dynamics. However, these investigations typically do not consider the metabolic network downstream of light harvesting. By contrast, genome-scale metabolic models capture species-specific metabolic capabilities but have yet to incorporate the rapid regulation of the light harvesting apparatus. Here, we combine chlorophyll fluorescence parameters defining photosynthetic and non-photosynthetic yield of absorbed light energy with a metabolic model of the pennate diatom Phaeodactylum tricornutum. This integration increases the model predictive accuracy regarding growth rate, intracellular oxygen production and consumption, and metabolic pathway usage. Through the quantification of excess electron transport, we uncover the sequential activation of non-radiative energy dissipation processes, cross-compartment electron shuttling, and non-photochemical quenching as the rapid photoacclimation strategy in P. tricornutum. Interestingly, the photon absorption thresholds that trigger the transition between these mechanisms were consistent at low and high incident photon fluxes. We use this understanding to explore engineering strategies for rerouting cellular resources and excess light energy towards bioproducts in silico. Overall, we present a methodology for incorporating a common, informative data type into computational models of light-driven metabolism and show its utilization within the design-build-test-learn cycle for engineering of photosynthetic organisms.
Real-time Watermarking Techniques for Sensor Networks (2003)

Wireless sensor networks have emerged as the major criteria that enable the next scientific, technological, engineering, and economic revolution. Since digital rights management is of the crucial importance for sensor networks, there is an urgent need for development of intellectual property protection (IPP) techniques. We have developed the first system of watermarking techniques to embed cryptologically encoded authorship signatures into data and information acquired by wireless embedded sensor networks. The key idea is to impose additional constraints during the data acquisition or sensor data processing. Constraints correspond to the encrypted signature and are selected in such a way that they provide favorable tradeoffs between the accuracy and the strength of proof of the authorship. The
Abstract 15357: Detection of Aoritc Wall Inflammation in Patients With Acute Aortic Intramural Hematoma by 18F-Fluorodeoxyglucose Positoron Emission Tomography (FDG-PET) (2014)

Background: Elevated serological markers of inflammation were reported to be associated with adverse outcome in patients with acute aortic intramural hematoma (IMH). The combined anatomic and metabolic information of 18F-fluorodeoxyglucose positron emission tomography (FDG-PET) has shown potential in the imaging of aortic wall instability and underlying inflammation in aortic disease. The present study aimed to investigate the clinical significance of FDG-PET in patients with IMH.

Methods: A total of consecutive 46 patients with acute aortic syndrome were admitted within 24 hours from the symptom onset between September 2013 and May 2014. Patients who had uncontrolled systemic inflammation or surgical site infection were excluded. FDG-PET of the body trunk and CT angiography of the entire aorta was performed in acute phase. The maximal SUV values (SUVmax) were assessed within aortic wall in the entire descending thoracic aorta, and segmentally analyzed in each slice at proximal descending aorta (PD), mid descending aorta (MD) and distal descending aorta (DD).

Results: Twenty-one patients (age: 71±13, male/female: 13/8) including 7 patients with classic aortic dissection (AD) and 14 patients with aortic intramural hematoma (IMH), were included in the final analysis. The SUVmax were significantly higher in patients with IMH than those with AD at entire descending thoracic aorta (3.29±0.48 vs 2.73±0.37, P=0.01). Besides, segmental analysis showed greater uptake of 18F-FDG in PD (3.08±0.42 vs 2.58±0.35, P=0.01) and DD (3.06±0.50 vs 2.49±0.48, P=0.02). However, the serological levels of C-reactive protein and D-dimer at the time of PET scan were similar between the groups.

Conclusions: FDG-PET revealed greater vessel wall inflammation in patients with IMH than AD patients. These results may suggest the different pathophysiology between AD and IMH.

 ![][1] [1]: /embed/graphic-1.gif
Enhancement of the Supercurrent at a Finite Voltage in a Sandwich-Type Ballistic SINIS Junction (2007)

A large, reentrant, Josephson current is observed in SINIS (Nb/Al/AlOx/Al/AlOx/Al/Nb) junctions at a finite voltage close to Delta/e (where Delta is the superconducting energy gap in S) and a bias current exceeding the zero-voltage Josephson current. The effect is studied using a multiterminal device configuration. A theoretical interpretation in terms of quantized electron states in the N layer is provided.