gebhart/patrepeval huggingface dataset:
NTRK1-3 point mutations in poor prognosis thyroid cancers. (2017)

6087 Background: NTRK1-3 fusions, identified in pediatric radiation-associated thyroid cancers, are low frequency oncogenic drivers that can trigger constitutive activation of TrK1-3 tyrosine kinase domains with responsively heightened downstream signaling through RAS-MAPK, PI3K-AKT, and/or PLCγ-PKC. NTRK point mutations are rare and of largely uninvestigated oncogenic potential, but some appear oncogenic. Methods: Advanced thyroid cancer (TC) patients (pts) requiring systemic therapy at Mayo Clinic sites underwent tumor genetic interrogation using Foundation One analyses with the goal of informing salvage therapeutic strategies. In this IRB-approved study, data from pts with TCs bearing NTRK point mutations were retrospectively analyzed, as this occurrence was unexpected but potentially of prognostic and/or therapeutic relevance. Results: Five of 55 pts (9%) with advanced TCs subject to Foundation One tumor interrogation had NTRK1-3 point mutations (allele frequency, AF, 15-49%); none had fusions. All 5 tumors had microsatellite stability; 4/5 had low tumor mutation burden (2-5 mutations/megabase). NTRK mutations in 3 anaplastic TC (ATC) pts (15% prevalence) were: NTRK3 I749M (AF 15%; overall survival, OS, 15 mos), NTRK1 R744H (AF not available; OS 9.5 mos), and NTRK1 R583H (AF 20.1%; OS &gt; 4.9 mos); NTRK2 S167Y (AF 49%; OS &gt; 51 mos) or NTRK1 R6W (AF 42%; OS &gt; 60 mos) were found in one papillary (PTC) and one Hürthle cell (HCC) TC pt respectively (summary table below). Conclusions: NTRK point mutations, but not fusions, were unexpectedly identified in 9% of assessed advanced TCs - but remarkably in 15% of ATCs. Mutated NTRKs, along with oncogenic p53 and TERT, may contribute to TC progression, especially in ATC, consequent to downstream activation of MAPK and PI3K-AKT pathways. We posit that NTRK point mutations may have therapeutic implications for treatment of refractory disease. [Table: see text]
MISSA Is a Highly Efficient in Vivo DNA Assembly Method for Plant Multiple-Gene Transformation (2010)

We describe a highly efficient in vivo DNA assembly method, multiple-round in vivo site-specific assembly (MISSA), which facilitates plant multiple-gene transformation. MISSA is based on conjugational transfer, which is driven by donor strains, and two in vivo site-specific recombination events, which are mediated by inducible Cre recombinase and phage lambda site-specific recombination proteins in recipient strains, to enable in vivo transfer and in vivo assembly of multiple transgenic DNA. The assembly reactions can be performed circularly and iteratively through alternate use of the two specially designed donor vectors. As proof-of-principle experiments, we constructed a few plant multigene binary vectors. One of these vectors was generated by 15 rounds of MISSA reactions and was confirmed in transgenic Arabidopsis (Arabidopsis thaliana). As MISSA simplifies the tedious and time-consuming in vitro manipulations to a simple mixing of bacterial strains, it will greatly save time, effort, and expense associated with the assembly of multiple transgenic or synthetic DNA. The principle that underlies MISSA is applicable to engineering polygenic traits, biosynthetic pathways, or protein complexes in all organisms, such as Escherichia coli, yeast, plants, and animals. MISSA also has potential applications in synthetic biology, whether for basic theory or for applied biotechnology, aiming at the assembly of genetic pathways for the production of biofuels, pharmaceuticals, and industrial compounds from natural or synthetic DNA.
The effect of species and species distribution on the layer characteristics of OSB. (2000)

Southern pine and aspen are widely utilized species for oriented strandboard (OSB) production in North America. In general, aspen with a relatively low specific gravity and uniform cell structure arrangement is considered more suitable for composite panel manufacture than is southern pine. Aspen OSB typically is lower in density and has better dimensional stability when compared to pine OSB. The purpose of this study was to investigate the effects of species use and distribution within OSB panels on the formation of the vertical density profile, resulting layer thickness swelling, and end-product layer characteristics. Five species configurations were used in this study (by weight): all pine, all aspen, 50/50 percent mixture, 25 percent aspen faces/50 percent pine core, and 25 percent pine faces/50 percent aspen core. Results show that the shape of the vertical density profile was considerably affected by species and species distribution. Resulting shapes of the vertical density profile were described as steep or gradual, referring to the densification of the face layers relative to the core. A steep profile has high density surface layers relative to the core and a gradual profile exhibits less difference between the face and core layers. The face density region of the density profile was further described as either a narrow density peak or a wide density peak, referring to the degree of density change within the face itself. The all-aspen panel had a steep density profile with a very narrow density peak. The 25 percent pine faces/50 percent aspen core panel had a more gradual density profile with a wide density peak. There was a strong relationship between layer density and layer thickness swelling. Physical and strength properties for all species combinations of panel types are reported.
Numerical Measurement of Viable and Nonviable Adipocytes and Other Cellular Components in Aspirated Fat Tissue (2008)

Single use or a combination of the viability assays used in this study can appropriately determine the number of adipocytes and other cells, although it remains difficult to assess original cells directly without tissue dissociation.
Highly Efficient Saturated Power Amplifier (2012)

In this article, a high-efficiency saturated amplifier has been presented. This amplifier takes advantage of the nonlinear output capacitor to shape the voltage waveform. The nonlinear capacitor generates substantial second harmonic voltage with small higher order harmonics. Thus, using √2 times larger fundamental load and the proper second harmonic termination, the resultant voltage waveform can be half-sinusoidal. For high efficiency, the PA should be driven by the large input power. Therefore, the current of the PA is bifurcated, resulting in the quasirectangular current shape. The resultant output waveforms are similar to those of class-F <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sup> amplifiers, whose waveforms are optimal for high efficiencies. Based on harmonic source/ load-pull simulation, the saturated amplifier has been designed using Cree's GaN HEMT CGH40006P packaged model. The matching networks for the input and output were optimized using the Momentum simulator. The implemented amplifier delivered a PAE of 80.1% at 3.475 GHz. The simulation and measurement results verify that the saturated amplifier is suitable for a high-efficiency PA over a relatively high frequency band.
Mutations in the androgen receptor gene are associated with progression of human prostate cancer to androgen independence. (1996)

Progression to androgen-independent growth of human prostate cancers may be mediated by alterations in the structure and/or expression of the androgen receptor (AR) gene. To date, mutations in the AR gene have largely been identified in hormone refractory tumors. In this study, single-strand conformational polymorphism analysis and DNA sequencing of the entire AR gene coding region was performed on 25 primary prostate tumors sampled prior to initiation of hormonal (i.e. , androgen ablation) therapy. Base changes leading to amino acid substitutions in the AR were identified in 11 (44%) tumors. The presence of AR amino acid substitutions was associated with decreased immunohistochemical staining for AR in tumor cells and the rapid failure of subsequent hormonal therapies. Single-strand conformational polymorphism analysis of exons 2, 3, and 8 of the X-linked hypoxanthine guanine phosphoribosyl transferase (HPRT) gene in the same samples revealed no bandshifts, suggesting that the high frequency of AR gene mutations detected was not a consequence of generalized genetic instability. These data indicate that AR gene mutations occur commonly in advanced prostate cancers prior to endocrine treatment of disease and may contribute to altered androgen responsiveness of the tumors.
Enterohaemorrhagic Escherichia coli and Shigella dysenteriae type 1-induced haemolytic uraemic syndrome (2008)

Haemolytic uraemic syndrome (HUS) can be classified according to the aetiology of the different disorders from which it is composed. The most prevalent form is that induced by shigatoxin producing Escherichia coli (STEC) and, in some tropical regions, by Shigella dysenteriae type 1. STEC cause a zoonosis, are widely distributed in nature, enter the food chain in different ways, and show regional differences. Not all STEC are human pathogens. Enterohaemorrhagic E. coli usually cause attachment and effacing lesions in the intestine. This is not essential, but production of a shigatoxin (Stx) is. Because Stx are encoded by a bacteriophage, this property is transferable to naïve strains. Laboratory methods have improved by identifying STEC either via the toxin or its bacteriophage. Shigella dysenteriae type 1 produces shigatoxin, identical to Stx-1, but also has entero-invasive properties that enterohaemorrhagic Escherichia coli (EHEC) do not. Shigella patients risk bacteremia and benefit from early antibiotic treatment, unlike those with EHEC.
Optical nano-antennas: Fabrication, characterization and applications (2011)

As optical counterpart of microwave antennas, optical nano-antennas are important devices for converting propagating radiation into confined/enhanced fields at nanoscale. The recent advances in resonant sub-wavelength optical antennas have now offered researchers a continuum of electromagnetic spectrum—from radio frequencies all the way up to X-rays—to design, analyze and predict new phenomena that were previously unknown. Their applications in areas with pressing needs, e.g., in sensing, imaging, energy harvesting, and disease cure and prevention, have brought revolutionary improvements. This dissertation investigates important characteristics of these plasmonic resonators through optical and electron-beam excitation using nanostructures defined by lithography as well as a newly developed direct metal patterning technique.&#13;\n&#13;\nThe important challenges in optical antenna research include both fundamental understanding of the underlying physics as well as issues related to fabrication of low cost, high throughput nanostructures beyond the diffraction limit. The nanoscale feature size of optical antennas limits our ability to design, manufacture, and characterize their resonant behavior. In this regard, I demonstrate how electron-beam lithography can be coupled with a new solid-state electrochemical process to directly pattern metal nanostructures with possibility of sub-10 nm features at low cost, minimal infrastructure, and ambient conditions.&#13;\n&#13;\nUsing bowtie antennas as representative of the general class of optical nano-antennas, I show how optical imaging can be used as a simple tool to characterize their resonant behavior. Further understanding of their spatial and spectral modes is gathered using finite-difference time domain simulations. The extremely high fields generated in gaps of closely coupled bowties are used in non-linear signal generation and several sum-frequency phenomena are identified.&#13;\n&#13;\nThe sub-wavelength confinement of fields in optical antennas requires new techniques that can image beyond diffraction limited optical imaging. One such technique, cathodoluminescence (CL) imaging spectroscopy, which has been demonstrated to resolve sub-25 nm antenna modes, is used to map various modes of triangular and bowtie antennas. The highly localized electron-beam in CL is used to excite and map the hybridized modes of bowtie dimers, including anti-parallel “dark” modes. These high quality dark modes are critical for overcoming the fundamental limitations associated with wideband resonances in plasmonic resonators. &#13;\n&#13;\nFinally, I discuss the role of CL in characterizing metal nano-disks which show multiple modes and have sizes comparable to their resonance wavelengths. CL provides a unique opportunity to map the enhanced fields from interference of surface plasmons sustained on the disks. The understanding of these modes is critical for the application of resonant metal cavities for the next generation of optical devices including nano-lasers.
High resolution CsI(Tl)/Si-PIN detector development for breast imaging (1998)

High resolution multi-element (8/spl times/8) imaging arrays with collimators, size matched to discrete CsI(TI) scintillator arrays and Si-PIN photodetector arrays (PDA's) were developed as prototypes for larger arrays for breast imaging. Photodetector pixels were each 1.5/spl times/1.5 mm/sup 2/ with 0.25 mm gaps. A 16-element quadrant of the detector was evaluated with a segmented CsI(TI) scintillator array (1.5/spl times/1.5/spl times/6 mm/sup 3/ segments with 0.25 mm septa) coupled to the silicon array. The scintillator thickness of 6 mm corresponds to >85% total gamma efficiency at 140 keV. Pixel energy resolution of <8% FWHM was obtained for Tc-99m (140 keV). Electronic noise was 41 e/sup -/ RMS corresponding to a 3% FWHM contribution to the 140 keV photopeak. Detection efficiency uniformity (/spl plusmn//spl sigma/%) measured with a Tc-99m flood source was 4.3% for a /spl sim/10% energy photopeak window. Spatial resolution was 1.53 mm FWHM and pitch was 1.75 mm as measured from the Co-57 (122 keV) line spread function. Signal to background was 34 and contrast ([max-min]/[max+min]) was 0.94. The energy resolution and spatial characteristics of the new imaging detector exceed those of other scintillator based imaging detectors. A camera based on this technology will allow: (1) Improved Compton scatter rejection; (2) Detector positioning in close proximity to the breast to increase signal to noise; (3) Improved spatial resolution; and (4) Improved efficiency compared to high resolution collimated gamma cameras for the anticipated compressed breast geometries.
X‐ray crystal structures of the oxidized and reduced forms of the rubredoxin from the marine hyperthermophilic archaebacterium pyrococcus furiosus (1992)

The structures of the oxidized and reduced forms of the rubredoxin from the archaebacterium, Pyrococcus furiosus, an organism that grows optimally at 100 degrees C, have been determined by X-ray crystallography to a resolution of 1.8 A. Crystals of this rubredoxin grow in space group P2(1)2(1)2(1) with room temperature cell dimensions a = 34.6 A, b = 35.5 A, and c = 44.4 A. Initial phases were determined by the method of molecular replacement using the oxidized form of the rubredoxin from the mesophilic eubacterium, Clostridium pasteurianum, as a starting model. The oxidized and reduced models of P. furiosus rubredoxin each contain 414 nonhydrogen protein atoms comprising 53 residues. The model of the oxidized form contains 61 solvent H2O oxygen atoms and has been refined with X-PLOR and TNT to a final R = 0.178 with root mean square (rms) deviations from ideality in bond distances and bond angles of 0.014 A and 2.06 degrees, respectively. The model of the reduced form contains 37 solvent H2O oxygen atoms and has been refined to R = 0.193 with rms deviations from ideality in bond lengths of 0.012 A and in bond angles of 1.95 degrees. The overall structure of P. furiosus rubredoxin is similar to the structures of mesophilic rubredoxins, with the exception of a more extensive hydrogen-bonding network in the beta-sheet region and multiple electrostatic interactions (salt bridge, hydrogen bonds) of the Glu 14 side chain with groups on three other residues (the amino-terminal nitrogen of Ala 1; the indole nitrogen of Trp 3; and the amide nitrogen group of Phe 29). The influence of these and other features upon the thermostability of the P. furiosus protein is discussed.
Field-controllable liquid-crystal phase grating (1979)

A new liquid-crystal phase-grating mode has been found. The grating is formed by the application of a spatially periodic electric field to a uniformly aligned liquid-crystal layer with dielectric and optical anisotropy. The fundamental diffraction characteristics of this liquid-crystal phase grating were measured by using a Schlieren optical system, and analyzed based on Fraunhofer diffraction theory with the assumption that the refractive indices vary periodically in the liquid-crystal layer. The incident light is diffracted under the electric field in particular directions determined by the spatial frequency of the periodic electrode, and the intensity of the diffracted light increases abruptly or gradually above the threshold depending on the cell thickness. The applicability of this liquid-crystal phase grating to a light valve in a projection display system is also considered.
Scientific essentials of reproductive medicine (1996)

Basic Sciences: Gene Expression. Cell Structure and Function. Cell Cycle. Hormone Receptors. Intracellular Signalling. Fundamental Immunology. Chromosomes. Genetic Inheritance. Molecular Techniques. Development and Function of the Genital Tract: Gonadal Differentiation. The Hypothalamo-Pituitary Axis. The Ovary: Endocrine Function. The Ovary: Genesis. The Testis: Endocrine Function. The Testis: Spermatogenesis. Uterus and Tubes. Puberty. Menstruation. Fertilization and Early Embryogenesis. Assisted Reproduction. Nutrition, Metabolism and Reproduction in Women. Menopause. Fetal Development and Pregnancy: The Molecular Basis of Mammalian Embryogenesis. Human Embryogenesis. Immunology and Reproduction. Chromosomes and Reproduction. Laboratory Techniques for Prenatal Diagnosis. The Placenta. Control of Fetal Growth. Fetal Cardiovascular Function. Fetal Lung Development. Parturition. Acid-Base Balance in the Fetus. Physiological Adaption at Birth. Infection During Pregnancy. HIV Infection and AIDS. Fetal and Placental Pathology. Principles of Imaging. Fetal Behavior. Maternal Respiratory and Cardiovascular Changes During Pregnancy. Reproductive Cancers: Epidemiology of Reproductive Cancers. Human Papillomavirus and Cervical Neoplasia. Hormones and Cancer. Pathology of Uterus and Ovaries. Molecular Genetics of Ovarian Cancer. Growth Factors and Oncogenes. Pathology of Gestational Trophoblastic Disease. Molecular Analysis in Gynaecological Pathology. Principles of Radiotherapy. Principles of Chemotherapy. Applied Science: Clinical Trials. Statistics.
An integrated hybrid interference and absorption filter for fluorescence detection in lab-on-a-chip devices (2009)

We present a hybrid optical filter design that combines interference and absorbing components for enhanced fluorescence detection in miniaturized highly-integrated lab-on-a-chip devices. The filter is designed in such a way that the advantages of each technology are used to offset the disadvantages of the other. The filter is fabricated with microfabrication compatible processes and materials for monolithic integration with microelectronics and microfluidics devices. The particular embodiment of the filter described herein is designed to discriminate fluorescence emission at 650 nm from excitation at 532 nm. The 9-layer interference filter component is fabricated with alternating TiO(2) and SiO(2) thin-film layers and has an attenuation of -12.6 dB at 532 nm and -0.76 dB at 650 nm. The absorbing filter component is fabricated using a dyed photopolymer (KMPR + Orasol Red) having an attenuation of -32.6 dB at 532 nm and -1.28 dB at 650 nm. The total rejection ratio of the hybrid filter is 43 dB. The filter exhibits very low autofluorescence and performs equally well at off-axis incidence angles.
Bayesian Modeling of Facial Similarity (1998)

In previous work [6, 9, 10], we advanced a new technique for direct visual matching of images for the purposes of face recognition and image retrieval, using a probabilistic measure of similarity based primarily on a Bayesian (MAP) analysis of image differences, leading to a &amp;quot;dual&amp;quot; basis similar to eigenfaces [13]. The performance advantage of this probabilistic matching technique over standard Euclidean nearest-neighbor eigenface matching was recently demonstrated using results from DARPA&amp;apos;s 1996 &amp;quot;FERET&amp;quot; face recognition competition, in which this probabilistic matching algorithm was found to be the top performer. We have further developed a simple method of replacing the costly compution of nonlinear (online) Bayesian similarity measures by the relatively inexpensive computation of linear (offline) subspace projections and simple (online) Euclidean norms, thus resulting in a significant computational speed-up for implementation with very large image databases as typically encountered in real-world applications.
Role of bone morphogenetic protein-2 in osteogenic differentiation of mesenchymal stem cells (2015)

Bone mesenchymal stem cells (BMSCs) have been an area of interest in biomedical research and tissue engineering due to their diverse differentiation abilities. In osteogenesis, bone morphogenetic proteins (BMPs), particularly BMP‑2, are important. However, the effect of BMP‑2 on the osteogenetic capacity of BMSCs remains to be fully elucidated. In the present study, primary rat BMSCs were infected with a recombinant lentivirus carrying the BMP‑2 gene (Lenti‑BMP‑2), and the effects of BMP‑2 on the activity of alkaline phosphatase (ALP) on days 3, 7, 14 and 21, and on mineralization on day 21 were evaluated. In addition, the adhesive ability of BMP‑2‑overexpressed BMSCs was detected using an adhesion assay. Following forced expression of BMP‑2 in the BMSCs, the levels of osteogenic genes, including osteopontin (OPN), osteocalcin (OC) and collagen type I (Col‑Ⅰ), were detected and the nuclear accumulation of Runt‑related transcription factor (Runx)‑2 and phosphorylated small mothers against decapentaplegic (p‑Smad) 1/5/8 was also evaluated. The results demonstrated that the rat BMSCs had been isolated, cultured and passaged from Sprague‑Dawley rat bone marrow successfully, and the third‑generation BMSCs were identified using flow cytometry with CD29 staining. The osteogenetic phenotype of the BMSCs, expressing ALP and osteocalcin, was significantly induced by BMP‑2, and the proliferation of the BMSCs was enhanced by BMP‑2. Furthermore, the adhesive potential of the BMP‑2‑overexpressed BMSCs was increased, the expression levels of OPN, OCN and Col‑Ⅰe osteogenetic factors were upregulated and the nuclear accumulation of Runx‑2 and p‑Smads1/5/8 were increased significantly. These data suggested that BMP‑2 may facilitate the osteogenetic differentiation of rat BMSCs and provide a favorable cell resource for tissue engineering.
Sound Strategies for Hearing Restoration (2014)

Hearing loss is the most common sensory deficit in humans, with some estimates suggesting up to 300 million affected individuals worldwide. Both environmental and genetic factors contribute to hearing loss and can cause death of sensory cells and neurons. Because these cells do not regenerate, the damage tends to accumulate, leading to profound deafness. Several biological strategies to restore auditory function are currently under investigation. Owing to the success of cochlear implants, which offer partial recovery of auditory function for some profoundly deaf patients, potential biological therapies must extend hearing restoration to include greater auditory acuity and larger patient populations. Here, we review the latest gene, stem-cell, and molecular strategies for restoring auditory function in animal models and the prospects for translating these approaches into viable clinical therapies.