gebhart/patrepeval huggingface dataset:
Hemizygosity for the COP9 signalosome subunit gene, SGN3, in the Smith‐Magenis syndrome (1999)

Smith-Magenis syndrome (SMS) is a multiple congenital anomaly/mental retardation syndrome associated with an interstitial deletion of chromosome band 17p11.2. The critical region is extremely gene-rich and spans approximately 1.5-2.0 Mb of DNA. Here we report the localization and partial characterization of the gene for subunit 3 of the COP9 signalosome, SGN3. SGN3 maps to the distal portion of the SMS critical interval, between SREBF1 and cCI17-638. We assessed the potential effect of haploinsufficiency of SGN3 in SMS patient lymphoblastoid cell lines through transfection studies and western analysis. Our results indicate that the COP9 signalosome assembles properly in these cells and appears to have normal expression and a kinase function intact. However, because the role of the COP9 signalosome in embryogenesis or differentiation is still uncertain, we cannot rule out the involvement of this gene in the Smith-Magenis syndrome. Am. J. Med. Genet. 87:342–348, 1999. © 1999 Wiley-Liss, Inc.
Influence of substrate polarity on growth of InN films by RF‐MBE (2003)

We have investigated influence of substrate polarity on the growth of InN films by RF-MBE. It was found that the temperature required for successful growth of InN strongly depended on the substrate polarity. InN could be grown on C-face SiC at 550 °C, whereas no InN growth occurred on Si-face SiC at 550 °C. InN growth on Si-face SiC was realized at lower temperature of 450 °C. In the case of the growth on free-standing GaN substrates, InN could be grown on N-face GaN at 550 °C, whereas InN growth on Ga-face GaN was realized at 450 °C. It was found that InN with N polarity can be grown at higher temperature than that with In polarity. These results indicate that control of polarity is essential for successful growth of InN.
Performance of a 6-degree-of-freedom active microsurgical manipulator in handheld tasks (2013)

This paper presents the first experimental results from human users of a new 6-degree-of-freedom handheld micromanipulator. This is the latest prototype of a fully-handheld system, known as "Micron," which performs active compensation of hand tremor for microsurgery. The manipulator is a miniature Gough-Stewart platform incorporating linear ultrasonic motors that provide a cylindrical workspace 4 mm long and 4 mm wide. In addition, the platform allows the possibility of imposing a remote center of motion for controlling motion not only at the tip but also at the entry point in the sclera of the eye. We demonstrate hand tremor reduction in both static and dynamic micromanipulation tasks on a rubber pad. The handheld performance is also evaluated in an artificial eye model while imposing a remote center of motion. In all cases, hand tremor is significantly reduced.
Quantitative and Qualitative Differences in DNA Complementary to Avian Myeloblastosis Virus between Normal and Leukemic Chicken Cells (2015)

Hybridization of avian myeloblastosis virus (AMV) RNA with DNA immobilized on filters or in liquid with a vast DNA excess was used to measure the viral specific DNA sequences in chicken cells. Newly synthesized viral DNA (v-DNA) appears within an hour after infection of chicken embryo fibroblasts (CEF) with avian oncornaviruses. A fraction of newly synthesized v-DNA becomes integrated into the cellular genome and the remainder gradually disappears. A covalent linkage between v-DNA and cellular DNA was demonstrated to exist in CEF and in leukemic myeloblasts by alkaline sucrose velocity sedimentation. Hybridization of AMV RNA in DNA excess has revealed that there are 2 clases of viral specific sequences within normal as well as in leukemic cells. The 2 types of sequences differ in their rate of hybridization. The amount of both types of DNA sequences is about 2 times higher in leukemic cells than in normal cells. Both the fast- and slowly reacting sequences in leukemic cells exhibit a higher Tm (2 degrees C) than the respective DNA sequences in normal cells. Furthermore, when nucleotide sequences in AMV RNA complementary to normal DNA are removed first by exhaustive hybridization with normal DNA, the residual RNA only hybridizes with leukemic DNA but not with normal DNA. These results suggest that leukemic cells contain viral specific DNA sequences which are absent in normal cells. Endogenous v-DNA has been shown to be integrated in cellular DNA region(s) with a reiteration frequency of approximately 1,200 copies per cell and each integration unit appears to have a size approximately equivalent to the 35S RNA subunit of the viral genome. Viral sequences acquired after infection appear to be integrated in the unique region of cell DNA, or in tandem with the endogenous viral sequences.
Biomedical applications of sodium MRI in vivo (2013)

In this article we present an up-to-date overview of the potential biomedical applications of sodium magnetic resonance imaging (MRI) in vivo. Sodium MRI is a subject of increasing interest in translational imaging research as it can give some direct and quantitative biochemical information on the tissue viability, cell integrity and function, and therefore not only help the diagnosis but also the prognosis of diseases and treatment outcomes. It has already been applied in vivo in most human tissues, such as brain for stroke or tumor detection and therapeutic response, in breast cancer, in articular cartilage, in muscle, and in kidney, and it was shown in some studies that it could provide very useful new information not available through standard proton MRI. However, this technique is still very challenging due to the low detectable sodium signal in biological tissue with MRI and hardware/software limitations of the clinical scanners. The article is divided in three parts: 1) the role of sodium in biological tissues, 2) a short review on sodium magnetic resonance, and 3) a review of some studies on sodium MRI on different organs/diseases to date.
The thermally activated distortion with amplification effect and related variant selection in red gold alloys (2020)

Variant selection during the A1→L10 transformation in a polycrystalline red gold alloy close to equiatomic Au-Cu composition has been extensively studied by Electron Backscatter Diffraction (EBSD) in our previous work. The use of a mathematical description of the lattice distortion and the maximal work criterion allowed us to quantify the degree of selection. With the same approach, we investigate here an interesting shape distortion effect, discovered twenty years ago in equiatomic AuCu-Ga. The shape distortion of thin samples placed in bending condition and then heat-treated under stress is studied in details. The singular shape memory effect and the remarkable distortion amplification, which we call TADA effect, are explored by monitoring the sample radius of curvature and the advancement of the transformation. The underlying mechanisms of variant selection are revealed by EBSD analysis across the samples. The experimental crystallographic variant selection distribution is compared with the expected profile calculated with the Euler-Bernoulli beam theory. The good agreement demonstrates that variant selection during the transformation is at the origin of the macroscopic distortion of red gold alloys. The TADA effect was found to occur when external stresses are released, and strongly depends on the stress at the initial stage of the transformation. This unusual effect is assumed to result from the persistence of variant selection throughout the transformation.
Isoform Diversity and Tandem Duplication of the Glycoprotein A Gene in Ferret Pneumocystis carinii (1995)

Two ferret P. carinii gpA cDNA clones were identified that reacted identically with a panel of anti-gpA monoclonal antibodies, although their nucleotide sequences were 22% divergent. Each clone hybridized to a single mRNA species of 3,600 nucleotides only in P. carinii-infected lung mRNA, but RT-PCR analysis demonstrated that these cDNA clones were derived from two distinct gpA mRNA transcripts. Further PCR analysis demonstrated that the ferret P. carinii genome contains at least two gpA genes lying in tandem on a single chromosome separated by a 329-bp intergenic region. Based on the terminal gene sequences of this tandem repeat and the cDNA clones, a composite full-length ferret P. carinii gpA coding sequence was constructed. The intergenic region immediately downstream of the stop codon of the first gpA gene contains three putative polyadenylation signals, and constitutes the 3' untranslated region (UTR) of the gpA mRNA. Primer extension of the gpA mRNA resulted in products extending 74 and 244 nucleotides into the 5' UTR. However, the intergenic region lying greater than 25 nucleotides upstream of the first methionine of the second gpA gene was found to be absent from the 5' UTR.
A Survey of Air-to-Ground Propagation Channel Modeling for Unmanned\n Aerial Vehicles (2018)

In recent years, there has been a dramatic increase in the use of unmanned\naerial vehicles (UAVs), particularly for small UAVs, due to their affordable\nprices, ease of availability, and ease of operability. Existing and future\napplications of UAVs include remote surveillance and monitoring, relief\noperations, package delivery, and communication backhaul infrastructure.\nAdditionally, UAVs are envisioned as an important component of 5G wireless\ntechnology and beyond. The unique application scenarios for UAVs necessitate\naccurate air-to-ground (AG) propagation channel models for designing and\nevaluating UAV communication links for control/non-payload as well as payload\ndata transmissions. These AG propagation models have not been investigated in\ndetail when compared to terrestrial propagation models. In this paper, a\ncomprehensive survey is provided on available AG channel measurement campaigns,\nlarge and small scale fading channel models, their limitations, and future\nresearch directions for UAV communication scenarios.\n
An Ionic-Radical Approach to Vicinally Functionalized Cyclopentanones and Cyclohexanones (2022)

A versatile strategy to access vicinally functionalized cyclopentanones and cyclohexanones is described. It takes advantage of new reagents, α-xanthyl enones, which can be prepared from the reaction of xanthate salts with the corresponding epoxyketones under mild conditions. β-Functionalization of these compounds can be performed by conjugate additions without affecting the xanthate moiety. This significantly expands the pool of xanthate substrates, allowing the synthesis of open chain and fused bicyclic building blocks useful in the synthesis of natural products.
A3adenosine receptors regulate Cl−channels of nonpigmented ciliary epithelial cells (1999)

Adenosine stimulates Cl- channels of the nonpigmented (NPE) cells of the ciliary epithelium. We sought to identify the specific adenosine receptors mediating this action. Cl- channel activity in immortalized human (HCE) NPE cells was determined by monitoring cell volume in isotonic suspensions with the cationic ionophore gramicidin present. The A3-selective agonist N6-(3-iodobenzyl)-adenosine-5'-N-methyluronamide (IB-MECA) triggered shrinkage (apparent Kd = 55 +/- 10 nM). A3-selective antagonists blocked IB-MECA-triggered shrinkage, and A3-antagonists (MRS-1097, MRS-1191, and MRS-1523) also abolished shrinkage produced by 10 microM adenosine when all four known receptor subtypes are occupied. The A1-selective agonist N6-cyclopentyladenosine exerted a small effect at 100 nM but not at higher or lower concentrations. The A2A agonist CGS-21680 triggered shrinkage only at high concentration (3 microM), an effect blocked by MRS-1191. IB-MECA increased intracellular Ca2+ in HCE cells and also stimulated short-circuit current across rabbit ciliary epithelium. A3 message was detected in both HCE cells and rabbit ciliary processes using RT-PCR. We conclude that human HCE cells and rabbit ciliary processes possess A3 receptors and that adenosine can activate Cl- channels in NPE cells by stimulating these A3 receptors.
ChemInform Abstract: 20 Years of DNA‐Encoded Chemical Libraries (2012)

Abstract Review: 59 refs.
Efficient detection and post-surgical monitoring of colon cancer with a multi-marker DNA methylation liquid biopsy (2021)

Multiplex assays, involving the simultaneous use of multiple circulating tumor DNA (ctDNA) markers, can improve the performance of liquid biopsies so that they are highly predictive of cancer recurrence. We have developed a single-tube methylation-specific quantitative PCR assay (mqMSP) that uses 10 different methylation markers and is capable of quantitative analysis of plasma samples with as little as 0.05% tumor DNA. In a cohort of 179 plasma samples from colorectal cancer (CRC) patients, adenoma patients, and healthy controls, the sensitivity and specificity of the mqMSP assay were 84.9% and 83.3%, respectively. In a head-to-head comparative study, the mqMSP assay also performed better for detecting early-stage (stage I and II) and premalignant polyps than a published SEPT9 assay. In an independent longitudinal cohort of 182 plasma samples (preoperative, postoperative, and follow-up) from 82 CRC patients, the mqMSP assay detected ctDNA in 73 (89.0%) of the preoperative plasma samples. Postoperative detection of ctDNA (within 2 wk of surgery) identified 11 of the 20 recurrence patients and was associated with poorer recurrence-free survival (hazard ratio, 4.20; <i>P</i> = 0.0005). With subsequent longitudinal monitoring, 14 patients (70%) had detectable ctDNA before recurrence, with a median lead time of 8.0 mo earlier than seen with radiologic imaging. The mqMSP assay is cost-effective and easily implementable for routine clinical monitoring of CRC recurrence, which can lead to better patient management after surgery.
Estimation of Particle Deposition in the Airways from Different Inhaler Formulations Using an In Silico Model (2021)

The objective of these studies was to evaluate the use of an in silico model for predicting lung deposition of inhaled therapeutic aerosols. A range of input data derived from our own in vitro data and published clinical studies was utilized. The in silico model ran simulations for these propellant driven metered dose inhaler formulations across a range of conditions. Firstly, a range of pressurized metered dose inhaler formulations were evaluated in the in silico model and compared to the in vitro aerosol performance data. Limitations of using in vitro cascade impaction data were observed. Then, using in vivo data from healthy human subjects using metered dose inhalers, lung deposition profiles were compared with the in silico model predictions. Despite differences in oropharyngeal deposition the model predicted lung deposition accurately. We conclude that the in silico model can be applied to various conditions for particulate based inhalation aerosol systems.
MLC/3LC NAND flash SSD cache with asymmetric error reduction huffman coding for tiered hierarchical storage (2017)

Asymmetric Error Reduction Huffman Coding (AERH) is proposed for MLC/3LC NAND flash memory used as SSD cache in the tiered hierarchical storage. AERH compresses data, reduces asymmetric memory cell errors by modulating Vth distribution and thus enhances reliability and endurance of memory cells. AERH decreases data-retention errors by 72.6% and 82.6% of MLC and 3LC NAND flash, respectively. In addition, this paper analyzes the compression ratio and the cost (effective bits/cell) of proposed AERH. Proposed MLC/3LC NAND flash with AERH realizes the utmost reliability of enterprise SSD cache where SLC NAND flash is commonly used.
Real-time Hardware-in-the-Loop simulation of convertible static transmission controller for transmission grid management (2013)

We propose a Convertible Static Transmission Controller (CSTC) concept that enables coordinated power flow control with emphasis on large penetration of renewable energy resources based transmission in a meshed network. CSTS can be connected across the substation power transformer and reconfigured for different modes of operation to perform as a versatile transmission controller with several functions including: power flow control for transmission of renewable resources, and as a transformer back-up for disaster management and/or life extension purposes. Different connecting configuration options, i.e. shunt-shunt, series-shunt, and series-series can be obtained. In this paper, we demonstrated the viability of the proposed concept using Typhoon HIL400 ultra-high fidelity Hardware-in-the-Loop (HIL) system in three different modes of operation. HIL simulations are used to verify the validity of the proposed control architecture for CSTC operation during both normal and unbalanced power system conditions for different connecting configurations.
Influence of Cooling Rate on Primary Particle and Solute Distribution in High-Speed Twin-Roll Cast Al-Mn Based Alloy Strip (2017)

Binary Al-Mn, ternary Al-Mn-Fe and Al-Mn-Si alloys were prepared by different cooling rates during solidification using direct chill-casting and high-speed twin-roll casting. Mn concentration and solute distribution in Al matrix were examined. The Mn concentration in solid solution was considered almost equivalent in as-cast condition. In contrast, much amount of decomposition of supersaturated Mn in solid solution occurred in high-speed twin-roll cast alloys after homogenization. In high-speed twin-roll cast strips, fine distribution of constituent particles in Al-Mn-Fe alloy and homogeneous solute distribution in Al matrix in Al-Mn-Si alloy were obtained due to the high cooling rate of the high-speed twin-roll casting. After homogenization treatment, coarsening and spheroidization of the constituent particles were mainly observed in Al-Mn-Fe alloy, while formation of fine dispersoids was predominantly observed in Al-Mn-Si alloy. Such differences in microstructure resulted from the decomposition behavior of supersaturated Mn in solid solution.
An experimental investigation of the nonlinear transient electric field response induced in thin-walled cylindrical ferromagnetic shields by short-duration surface current pulses (2004)

The paper presents results of an experimental investigation of the transient electric field induced at the interior surface of long, thin-walled, cylindrical, electrically-conductive ferromagnetic shields by axially-directed, unipolar, short-duration current pulses along the exterior surface. For an applied pulse having a duration that was sufficiently short compared to the shield response, the transient electric field response approached a result that depended on the total charge transported along the surface of the cylinder during the applied current pulse but was essentially independent of the particular time variation of the applied pulse. For practical purposes, such pulses can be regarded as impulses, and the resultant electric field response can be regarded as an impulse response for that charge level. Experimental results for a wide range of injected charge levels on a mildly ferromagnetic specimen are presented. Unlike the impulse response for the linear problem with a constant permeability, the impulse response exhibits nonlinear variation with applied charge level.
Surgical treatment for pancreatic cystic lesions—implications from the multi-center and prospective German StuDoQ|Pancreas registry (2023)

With respect to unclear findings frequently present in PCL, diagnostic means recommended in guidelines should always be considered in the preoperative phase. The therapy of PCL should be decided upon in the light of patient-specific factors, and the surgical strategy needs to be adapted accordingly.
Sn Corrosion and Its Influence on Whisker Growth (2007)

The microstructure and crystal structure of condensation-induced corrosion products, vapor phase induced oxidation products, Cu-Sn intermetallics, and Sn whiskers that formed on electroplated matte Sn on Cu-alloy after exposure 2500 h in a 60 degC/93%RH ambient were characterized with scanning electron microscopy, (SEM), focused ion beam (FIB) microscopy, energy dispersive spectroscopy (EDS), transmission electron microscopy (TEM), and selected area electron diffraction (SAD). The corrosion product was identified as crystalline SnO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> . The oxidation of Sn in condensed water was at least four orders of magnitude larger than that in moist vapor at 60 degC. All Sn whiskers were found to be within 125 mum of the corrosion product. Based on these observations, a theory was developed. The theory assumes that oxidation leads to the displacement of Sn atoms within the film. Because the grain boundaries and free surfaces of the film are pinned, the oxidation-induced excess Sn atoms are constrained within the original volume of the Sn-film. The trapped excess Sn atoms create localized stress, excess strain energy, in the Sn-film. If and when the pinning constraint is relaxed, as for example would occur when the surface oxide on the film cracks, then the Sn atoms can diffuse to lower energy configurations. When this occurs, whisker nucleation and growth begins. The theory was tested by detailed measurements and comparison of the corrosion volume and the whisker volume in two different samples. The volume comparisons were consistent with the theory
Effects of tunneling on groundwater flow and swelling of clay‐sulfate rocks (2011)

Swelling of clay‐sulfate rocks is a major threat in tunneling. It is triggered by the transformation of the sulfate mineral anhydrite into gypsum as a result of water inflow in anhydrite‐containing layers after tunnel excavation. The present study investigates the hydraulic effects of tunneling on groundwater flow and analyzes how hydraulic changes caused by excavation lead to water inflow into anhydrite‐containing layers in the tunnel area. Numerical groundwater models are used to conduct scenario simulations that allow one to relate hydrogeological conditions to rock swelling. The influence of the topographic setting, the excavation‐damaged zone around the tunnel, the sealing effect of the tunnel liner, and the geological configuration are analyzed separately. The analysis is performed for synthetic situations and is complemented by a case study from a tunnel in Switzerland. The results illustrate the importance of geological and hydraulic information when assessing the risk of swelling at an actual site.
0929 Transversely Isotropic Material Parameter Estimation for Soft Tissue Using Inverse FEM (2007)

Mechanical simulations of soft biological tissue required proper material properties. In this study, we performed material parameter estimation of transversely isotropic incompressible hyperelastic model for soft tissue using Inverse FEM technique for the purpose of estimating in vivo material parameters. A set of material parameters were estimated from a cited stress-strain curvature of liver tissue as proper parameters. Then, cubic models with different fiber directions and the proper material parameters were compressed using FEM, and a loading force and internal distortions at some observation points. Finally, the estimated parameters by Inverse FEM were compared with the proper parameters. As the results, the parameter estimation strongly depended on the angle between the loading and fiber direction, and worked better when the loading direction was close to the diagonal of the fiber direction.