gebhart/patrepeval huggingface dataset:
The diagnostic application of RNA sequencing in patients with thyroid cancer: an analysis of 851 variants and 133 fusions in 524 genes (2016)

While the genomic landscape of all thyroid neoplasm subtypes will inevitably be elucidated, caution should be used in the early adoption of published mutations as the sole predictor of malignancy in thyroid. The largest set of such mutations known to date detects only a portion of thyroid carcinomas in preoperative FNAs in our cohort and thus is not sufficient to rule out cancer. Due to the finding that variants are also found in benign nodules, testing only GEC suspicious nodules may be helpful in avoiding false positives and altering the extent of treatment when selected mutations are found.
Analytical Solution to Steady-State Heat-Conduction Problems With Irregularly Shaped Boundaries (1971)

A method of obtaining an analytical solution to two-dimensional steady-state heat-conduction problems with irregularly shaped boundaries is presented. The technique of obtaining the coefficients to the series solution via a direct least-squares approach is compared to the “point-matching” scheme. The two methods were applied to problems with known solutions involving the three heat-transfer boundary conditions, temperature, heat flux, and convection coefficient specified. Increased accuracy with substantially fewer terms in the series solution was obtained via the least-squares technique.
Synthesis of S‐benzyl‐DL‐[1‐13C]cysteine and its incorporation into oxytocin and [8‐arginlne]vasopressin and related compounds by total synthesis. Separation of diastekeoisomers by partition chromatography and HPLC (1980)

Abstract S‐Benzyl‐DL‐[1‐ 13 C]cysteine was prepared from Na 13 CN by a three step synthesis and converted to the t‐butyloxycarbonyl derivative which was suitable for use in peptide synthesis. This compound was incorporated into the 1 and 6 positions of a variety of oxytocin and [8‐arginine]vasopressin derivatives and analogues via total synthesis using the solid phase method. The compounds were separated and purified by partition chromatography on Sephadex and their purity was checked by high pressure liquid chromatography. The compounds synthesized include [1‐hemi‐[1‐ 13 C]cystine]oxytocin, [1‐hemi‐ D ‐[1‐ 13 C]‐cystine]oxytocin, [1‐hemi‐[1‐ 13 C]cystine, 8‐arginine]vasopressin, [1‐hemi‐ D [1‐ 13 C]cystine, 8‐arginine]vasopressin, [6‐hemi‐[1‐ 13 C]cystine]oxytocin, [6‐hemi‐ D ‐[1‐ 13 C]cystine]oxytocin, [1‐hemi‐ D ‐[1‐ 13 C]cystine, 3‐ D ‐leucine]‐oxytocin, and [1‐hemi‐[1‐ 13 C]cystine, 3‐ D ‐leucine]oxytocin.
Cryogenic Infrared Radiance Instrumentation for Shuttle (CIRRIS 1A) Earth limb spectral measurements, calibration, and atmospheric O3, HNO3, CFC‐12, and CFC‐11 profile retrieval (1997)

During the Space Transportation System 39 (STS 39) flight of April 28 to May 6, 1991, the Cryogenic Infrared Radiance Instrumentation for Shuttle (CIRRIS 1A) measured spectral and spatial (“Earth limb scan”) distributions of the atmospheric infrared (IR) emissions using a Michelson interferometer. The IR spectral radiant emissions from the greenhouse gases were collected at a shuttle altitude of 260 km in the 9–13 μm atmosphere infrared window. Before and after the flight, the response of CIRRIS 1A to the IR spectral emission sources was calibrated using absolute and spectral source types. The Fast Atmospheric Signature Code 3, which used the HITRAN92 database and predetermined temperature‐pressure profiles from the National Meteorological Center, was used in an onion‐peeling routine to retrieve gas concentrations from absolutely calibrated spectral data (moderate resolution ∼1.0 cm −1 ). Vertical profiles of O 3 , HNO 3 , CFC‐12, and CFC‐11 are presented. An error analysis is presented to show the quality of the measured spectral data and the accuracy of these retrieval results. The concentrations of CFC‐11 (3.0×10 −4 ppmv) and CFC‐12 (4.9×10 −4 ppmv) in the tropopause region are consistent with a global flux increment rate of about 5% yr −1 . The observed concentrations of HNO 3 are consistent with previous reports for a relatively clean stratosphere.
Aerobic Copper Catalysis for Tandem Oxy‐N‐alkenylation of [1,2,3]Triazolo[1,5‐a]pyridines (2016)

Abstract N ‐Alkenylated triazolinone ylides were generated through copper‐catalyzed oxy‐ N ‐alkenylation of triazolopyridines. The mechanistic course of this aerobic tandem reaction has been experimentally elucidated and primary photophysical data of the ylide products are also given. magnified image
Berberine Alleviates Adiposity and Cardiac Dysfunction in Offspring Exposed to Gestational Diabetes Mellitus (2020)

Abstract The most robust risk factor for type 2 diabetes in childhood is prior exposure to diabetes during gestation. Currently, there are few evidence-based strategies to attenuate the of risk of metabolic syndrome in offspring exposed to gestational diabetes mellitus (GDM). Berberine (BBR) is an isoquinoline alkaloid extracted from Chinese herbs and exhibits glucose lowering properties. It has been used safely for centuries in humans. Our objective was to determine whether BBR treatment improves health outcomes in the mouse offspring of GDM dams. Dams were fed either a lean low-fat diet (Lean, LF,10% kcal fat) or a GDM-inducing high-fat/high sucrose diet (GDM, HF, 45% kcal fat) prior to breeding and throughout pregnancy. The resulting Lean and GDM-exposed offspring were randomly assigned a LF, HF or HF diet containing BBR (160 mg/kg/d) for 12 weeks. We determined that BBR treatment significantly reduced body weight (∼20%), % body fat (∼40%) and gonadal fat pad mass (∼60%) compared to HF-fed GDM offspring. Furthermore, BBR treatment of HF-fed GDM offspring normalized insulin levels in the plasma and isolated pancreatic islets. Differences in food consumption did not contribute to altered body composition in BBR treated mice, as levels remained similar between experimental groups. Alternatively, BBR-treatment was associated with increased whole-body oxygen consumption (VO2), activity and heat production. Additionally, we determined that HF-fed GDM offspring developed a cardiomyopathy, characterized by increased isovolumetric contraction (∼150%, IVCT), relaxation time (∼70%, IVRT), elevated cardiac triglyceride (∼120%) and reduced mitochondrial function (30%, spare capacity) compared to LF fed Lean controls. BBR treatment normalized heart function, reduced triglyceride levels and maintained mitochondrial function. Our data supports BBR as a potential pharmacotherapeutic approach to improve health outcomes in individuals exposed to GDM. Key Points Summary Gestational diabetes mellitus is a common metabolic complication of pregnancy which is increasing worldwide due to the prevalence of obesity. It is known that individuals exposed to gestational diabetes have elevated risk of developing metabolic syndrome however there are few evidence-based strategies which provide protection. Berberine is a natural compound found in Chinese herbs which has been safely used for centuries to treat type 2 diabetes mellitus. We determined that berberine treatment of offspring exposed to gestational diabetes attenuated weight gain, reduced insulin levels and normalized both heart and pancreatic function. Our data supports berberine as a potential pharmacotherapeutic approach to improve health outcomes in individuals exposed to gestational diabetes.
Intracellular MR Contrast Agents Based on Cationic Cell Penetrating Peptides: A Comparative Study (2006)

For the development of intracellular Magnetic Resonance contrast agents (CAs) it is a prerequisite that they cross the plasma membrane. Cell penetrating peptides (CPPs) are known to transport cargo molecules attached to it into cells. We synthesized intracellular CAs containing known CPPs or modified peptides. Gd-diethylenetriaminepenta-acetic acid (Gd-DTPA) was coupled to CPPs for MR visualization and fluorescence imaging agent fluorescein isothiocyanate (FITC) for tracking the agent inside cells by optical imaging. Compared on the basis of these measurements, modifications in CPPs enhanced the intracellular delivery ability of our CAs providing a tool for stable labeling of cells for MR imaging.
A Facile System for Encoding Unnatural Amino Acids in Mammalian Cells (2009)

Abstract Ein Shuttle‐System zur Verwendung von in E. coli selektierten Aminoacyl‐tRNA‐Synthetasen (aaRSs) für den Einbau von nichtnatürlichen Aminosäuren in Säugerzellen wurde entwickelt. Eine in E. coli selektierte Mutante der Pyrrolysyl‐tRNA‐Synthetase (PylRS) aminoacyliert selektiv eine Nonsense‐Suppressor‐tRNA mit einem photoaktivierbaren Lysinderivat. Durch Übertragung dieses orthogonalen tRNA‐aaRS‐Paares in Säugerzellen gelang es, diese nichtnatürliche Aminosäure selektiv in Proteine einzubauen. magnified image
Performance Improvement of HfAlOxN n-Channel Metal–Oxide–Semiconductor Field-Effect Transistors by Controlling the Bonding Configuration of Nitrogen Atoms Coordinated to Hf Atoms (2007)

A high-temperature oxygen annealing (HiTOA) process has been developed to recover the degradation of the electrical characteristics due to the nitrogen incorporation into the HfAlOx film. The HiTOA process was carried out after the introduction of the nitrogen atoms. This process affected the bonding configuration of the nitrogen atom coordinated to the hafnium atom, and reconverted the nitrogen atom into an oxygen one. Therefore, this substitution markedly recovered the gate leakage current through the HfAlOxN film with a slight increase in the equivalent oxide thickness. Additionally, it significantly improved the effective mobility of n+ polycrystalline silicon (poly-Si) gate n-channel metal–oxide–semiconductor field-effect transistors (nMOSFETs).
Implicit function-based phantoms for evaluation of registration algorithms (2005)

Medical image fusion is increasingly enhancing diagnostic accuracy by synergizing information from multiple images, obtained by the same modality at different times or from complementary modalities such as structural information from CT and functional from PET. An active, crucial research topic in fusion is validation of the registration (point-to-point correspondence) used. Phantoms and other simulated studies are useful in the absence of, or as a preliminary to, definitive clinical tests. Software phantoms in specific have the added advantage of robustness, repeatability and reproducibility. Our virtual-lung-phantom-based scheme can test the accuracy of any registration algorithm and is flexible enough for added levels of complexity (addition of blur/anti-alias, rotate/warp, and modality-associated noise) to help evaluate the robustness of an image registration/fusion methodology. Such a framework extends easily to different anatomies. The feature of adding software-based fiducials both within and outside simulated anatomies prove more beneficial when compared to experiments using data from external fiducials on a patient. It would help the diagnosing clinician make a prudent choice of registration algorithm.
Olive Oil Phenols (2019)

Olive oils contain numerous substances that have a beneficial role in human health. Phenols are natural compounds that are present in extra-virgin olive oil (EVOO), and they are produced at the malaxation step of the olive oil production. The four most abundant phenols in EVOO are oleocanthal, oleacein, ligstroside aglycon, and oleuropein aglycon. These phenols exhibit significant biological effects in many diseases, participating in various cellular and biochemical processes. Oleocanthal can protect and prevent against the Alzheimer disease, demonstrates acute antiplatelet effects, which has a vital role against cancer, and can act like ibuprofen. Oleacein has antioxidant and anti-inflammatory activities and helps against atherosclerosis. Moreover, it acts as an antiaging factor and as a 5-lipoxygenase inhibitor. Ligstroside aglycon implicates to mechanisms against breast cancer, while oleuropein aglycon shows activities against the Alzheimer disease and breast cancer.
Plasma C-Terminal Pro-Endothelin-1 and the Natriuretic Pro-Peptides NT-proBNP and MR-proANP in Very Preterm Infants with Patent Ductus Arteriosus (2011)

CT-proET-1 is a promising predictor in determining the need for PDA intervention.
Free-Form Nonrigid Image Registration Using Generalized Elastic Nets (2007)

We introduce a novel probabilistic approach for non-parametric nonrigid image registration using generalized elastic nets, a model previously used for topographic maps. The idea of the algorithm is to adapt an elastic net (a constrained Gaussian mixture) in the spatial-intensity space of one image to fit the second image. The resulting net directly represents the correspondence between image pixels in a probabilistic way and recovers the underlying image deformation. We regularize the net with a differential prior and develop an efficient optimization algorithm using linear conjugate gradients. The nonparametric formulation allows for complex transformations having local deformation. The method is generally applicable to registering point sets of arbitrary features. The accuracy and effectiveness of the method are demonstrated on different medical image and point set registration examples with locally nonlinear underlying deformations.
MicroRNAs and Corresponding Targets in Esophageal Cancer as ShownIn VitroandIn Vivoin Preclinical Models (2022)

Squamous cell carcinoma of the esophagus is associated with a dismal prognosis. Therefore, identification of new targets and implementation of new treatment modalities are issues of paramount importance. Based on a survey of the literature, we identified microRNAs conferring antitumoral activity in preclinical in vivo experiments. In the category of miRs targeting secreted factors and transmembrane receptors, four miRs were up-regulated and 10 were down-regulated compared with five out of nine in the category transcription factors, and six miRs were down-regulated in the category enzymes, including metabolic enzymes. The down-regulated miRs have targets which can be inhibited by small molecules or antibody-related entities, or re-expressed by reconstitution therapy. Up-regulated miRs have targets which can be reconstituted with small molecules or inhibited with antagomirs.
Abstract PR-009: Proteotranscriptomic classification and characterization of pancreatic neuroendocrine neoplasms (2020)

Abstract Background Pancreatic neuroendocrine neoplasms (PNENs) are biologically and clinically heterogeneous neoplasms with variable patient outcomes. Our study aims to uncover the molecular factors that underlie the clinical and biological heterogeneity among PNENs for a better understanding and potential classification of this disease. Methods Formalin-fixed paraffin-embedded primary tumour specimens from 92 patients with PNEN were procured for the study and split into two cohorts for discovery and validation purposes. Next-generation sequencing profiled the exome and transcriptome, and quantitative mass-spectrometry profiled the global proteome of specimens. Non-negative matrix factorization was used to identify subgroups, followed by differential analysis to identify subgroup-specific features. To corroborate subgroup-specific RNA- and protein- level distinctions, activities of key cellular regulators were inferred from target gene expression or co-expression signatures. Results Unsupervised clustering analysis of transcriptome data identified four robust molecular subgroups that were substantiated by proteome analysis (p=0.0005) within the discovery cohort and validated with the validation cohort and an external cohort of PNENs from a previous microarray-based gene expression study. A proliferative subgroup was enriched with neuroendocrine carcinomas and specimens with &amp;gt;20% Ki67, concomitant with reduced survival probability (p=0.0024; logrank test) and higher mRNA expression and protein abundance of cell cycle-related genes. Increased mRNA expression of ARX or PDX1 (adjusted p&amp;lt;0.05) was found in two of the subgroups similar to a previous report. The ARX-high subgroup was characterized by enrichment of oxidative phosphorylation genes and increased relative abundance of mitochondrial proteins, while oncogenic Ras mutations were found in the PDX1-high subgroup. A fourth subgroup exhibited enrichment of stromal/mesenchymal molecular features and Hippo signaling pathway. Inferred activities of key cellular regulators further supported observed alterations within subgroups. Conclusions We identified four robust molecular subgroups among PNENs with clinicopathological associations and biological distinctions that may provide potential new directions for patient stratification and treatment strategies to facilitate treatment decisions. Citation Format: Kevin C. Yang, Steve Kalloger, John Aird, Michael Lee, Christopher Rushton, Sandra E. Spencer Miko, Karen L. Mungall, Andrew J. Mungall, Shane Colborne, Ryan D. Morin, Jonathan M. Loree, Marco A. Marra, Daniel J. Renouf, Gregg B. Morin, David F. Schaeffer, Sharon M. Gorski. Proteotranscriptomic classification and characterization of pancreatic neuroendocrine neoplasms [abstract]. In: Proceedings of the AACR Virtual Special Conference on Pancreatic Cancer; 2020 Sep 29-30. Philadelphia (PA): AACR; Cancer Res 2020;80(22 Suppl):Abstract nr PR-009.
Surface Treatment for Leakage Reduction in AlGaN/GaN HEMTs (2007)

Development of AIGaN/GaN HEMTs has been largely advanced in recent years, leading to record microwave power performance from solid-state devices. With the AIGaN/GaN HEMTs emerging as a viable technology for high frequency low noise amplifiers and power amplifiers, there are still several problems to be solved. One key problem is the relatively high gate leakage current, which may cause extra noise and reliability problems. In this report, we present a technology which reproducibly reduces gate leakage by two orders without introducing any negative effect on the device performance.
UW Sinus Surgery Cadaver/Live Dataset (UW-Sinus-Surgery-C/L) (2020)

This dataset was developed at the University of Washington's BioRobotics Lab (http://brl.ee.washington.edu). It has endoscopic sinus surgery images with manual annotations for surgical instrument segmentation task. The challenging conditions of this dataset include specular reflections, blur from motion, blood, smoke and tools in shadow.
Theory, fabrication and testing of dual track complimentary type of thin-film recording heads for perpendicular magnetic recording system (1996)

A new type of recording head for a perpendicular magnetic recording system, a dual track complimentary (DTC) type of thin-film head, was proposed in this study. The magnetic core of the head has a ‘‘U’’ character shape which is provided with ‘‘a pair of’’ recording tracks and the efficiency to detect flux reversal in the media will become high enough to achieve high linear density. The two-dimensional analysis of DTC heads implied that the perpendicular component of the head field should become larger by using the double-layered media under a narrower spacing condition. Recording characteristics using conventional ring head were evaluated in order to determine the principle of DTC configuration. Several DTC heads were prepared using photolithography technique and their performances were examined. A typical DTC head has inductance of about 500 nH, which is relatively low, and constant up to 10 MHz. DTC heads seems to be one of the most hopeful candidates as the heads useful for perpendicular magnetic recording systems.
Modeling the Anomalous Flow Behavior of Ni3Al Intermetallic Single Crystals (2004)

In this study we present a new constitutive model for Ni3Al and Ni3(Al, X) alloys that was developed to represent many of the unusual plastic flow behavior found in L12 intermetallics while maintaining consistency with the experimentally‐observed evolution of dislocation substructure. In particular, we sought to develop a model that would not only predict the anomalous increase of the yield strength with increasing temperature, but would also capture other important flow characteristics such as extremely high work‐hardening rates that change anomalously with temperature, and a flow stress that is partially to fully reversible with temperature. For this model, we have treated work‐hardening as arising from two different sources. Thermally‐reversible work hardening is accounted for using the description of screw dislocation motion proposed by Caillard, which involves exhaustion of mobile dislocations by cross‐slip locking of the dislocation core and athermal unlocking. Thermally‐irreversible work hardening is accounted for using an approach consistent with the theoretical framework proposed by Ezz and Hirsch, which involves both the multiplication of Frank‐Reed sources and the interaction of edge‐dislocation segments with cross‐slip locking events and the dislocation forest. Both work‐hardening contributions were incorporated into the rate formulation for thermally‐activated plastic flow proposed by Kocks, Argon and Ashby. We will show simulation results for the flow response of Ni3(Al, X) crystals over a wide range of temperatures in the anomalous flow regime, and we will compare these findings with experimental data.
Growth dynamics of mammalian cells monitored with automated cell cycle staining and flow cytometry (2008)

To accurately observe high-frequency events during transient cell cycle kinetics, we have implemented a single step 15-min DNA staining protocol using automated flow cytometry. This protocol was used to sample and to analyze a Chinese hamster ovary cell culture for the DNA distribution, viable cell concentration, apoptotic cell concentration, and light scattering properties every 25 min over 4.5 days in response to a nutrient deprivation and a nutrient upshift. After the nutrient deprivation and exposure to fresh growth medium, two populations of cells started proliferating at different times likely corresponding to cells leaving the G0 and G1 cell cycle phases. After a nutrient upshift in late exponential growth, a cell cycle arrest occurred at the G1/S and G2/M boundary. The resulting cell cycle and proliferation kinetics followed damped oscillations that directly reveal the average time cells spend in each cell cycle phase. The observed detailed dynamics of the cell cycle progression is made possible through the high-frequency sampling enabled by automated flow cytometry. The approach should be useful in studying cell cycle perturbations in response to different environmental conditions resulting from exposure to specific nutrients or to drugs.
Supplementary Figure S3 from E7090, a Novel Selective Inhibitor of Fibroblast Growth Factor Receptors, Displays Potent Antitumor Activity and Prolongs Survival in Preclinical Models (2023)

&lt;p&gt;Western blot analysis of phospho-FGFR in SNU-16 tumors at the indicated times after treatment with the indicated concentrations of E7090. See also Figure 3D.&lt;/p&gt;
STRUCTURE OF MATTER AND QUANTUM CHEMISTRY SOLVENT-REAGENT EFFECT IN CHEMICAL DETECTION OF ENERGETIC MATERIALS TYPE CONTAMINANTS (2009)

Present study extended the list of solvent and reagents appropriate to use for the colorimetric de� tection and semi quantitative analysis of various energetic compounds. The new reagents used in this study include DMSO as solvent/reagent, and tetramethylammonium hydroxide and tetrabutylammonium hydrox� ide for the generation of a basic medium. The advantages of these reagents vs. older procedures are discussed in this paper. Also, a standardized procedure for the analysis of several classes of energetic compounds has been developed, allowing an excellent practical application of the recommended method. The influence of different solvents on the changes in the UVVIS spectra were evaluated and an attempt to interpret the result� ing absorption UV spectra based on quantum chemical calculations has been done.