gebhart/patrepeval huggingface dataset:
Radar tomography for environmental geotechnology: field and simulation tests (1994)

The ground wave in GPR can be used for reconnaissance studies of moisture in the subsurface. Wave velocity depends on moisture via the dielectric properties of the material. When using a small antenna separation, the ground wave may be superimposed by the air wave. On the other hand, the ground wave decays fast with distance. As a consequence, the ground wave can be observed in the radargram only within a limited antenna separation. We begin the field studies with a wide angle reflection and refraction 0NARR) measurement to identify the ground wave, to determine its velocity and to fmd the optimal antenna separation. This separation is kept throughout a profile when tracing out the lateral variation of ground wave velocity. The free volumetric water content is determined from the dielectric properties of subsurface matter by an empirical relation of Topp et al. (1980). Field data are usually influenced by several factors, such as antenna frequency, antenna separation and small inhomogeneties near the surface. Moisture in the subsurface can be determined more accurately using lower antenna frequencies in a humid subsurface than vice versa. We used the Pulse EKKO IV radar system with 50 and 200 MHz antennas for the field measurements. Reconnaissance studies of moisture with GPR ground wave are non-destructive, free of radiation hazard, fast and suitable for both soft and hard subsurface.
A Protein-Truncating HSD17B13 Variant and Protection from Chronic Liver Disease (2018)

A loss-of-function variant in HSD17B13 was associated with a reduced risk of chronic liver disease and of progression from steatosis to steatohepatitis. (Funded by Regeneron Pharmaceuticals and others.).
In-situ measurement of Poisson's ratio for germanium nano-bridge in TEM (2016)

In the work a microelectromechanical systems (MEMS) based in-situ tensile test for germanium nano-bridge in transmission electron microscope is presented. With a carefully designed electrostatic actuator, germanium nano-bridge can be stretched stably at a speed rate less than 0.05% per step in strain. Assisted with the selected area electron diffraction (SAED) images, Poisson's ratios measured from a local area whose diameter is less than 20 nm can be obtained. Three different sized samples (marked as a, b, c) were tested and the Poisson's ratios were measured to be 0.18, 0.25, 0.27, respectively, comparing to 0.28 for the bulk germanium. The smallest scaled sample (a) presents a remarkable lower Poisson's ratio than bulk germanium, which may result from the increasing radial stress caused by the decreasing dimension of the nano-bridge.
The Controlled Intradiscal Release of Simvastatin Retards the Progression of Degeneration and Facilitates Autogeneous Repair at Rat Caudal Intervertebral Disc Injured by Needle Stab (2008)

. To test the effectiveness of the drug in vivo, we developed a modified stab incision at the rat IVD to induce degeneration, followed by the injection of a simvastatin-loaded hydrogel. As this model has become widely used for the IVD degeneration due to the cost-efficiency and convenient procedure, the needle puncture model using small rodents has never been utilized. It has been recognized that needle puncture can induce mild and progressive disc degeneration that is suitable for testing the potential treatments for the degenerative disc disease (2) . The aims of this study are: (1) to develop an easier and less invasive disc degeneration model by need puncture at rat tails (2) to test the effectiveness of the controlled intradiscal release of simvastatin to retard or repair the perturbed disc using the proposed model. Materials and Methods Animals Male Sprague-Dawley rats (3 months old) obtained from Harlan were used in this study. Surgical Technique With the aid of fluoroscopy,18G or 21G needle was inserted in the middle of the nucelus pulposus (NP) of Co5/Co6 or Co7/Co8, rotated 180 o , and held for 5s. Depth of penetration was controlled at 5 mm from the needle. Co6/7 remained intact. Simvastatin Treatment 6 weeks after stabbed injury by 21G needle, 2 μl of simvastatin at the concentration of 5 mg/ml loaded in a thermo-sensitive PEG-PLGA-PEG hydrogel or hydrogel alone that degrades persistently in vivo was slowly injected into the injured NP using microsyringe attached with 31G needle. MRI Procedures and Processing In vivo MRI was serially scanned post-surgery using a 7.0T Varian MR scanner. T2-weighted midsagittal images of the intact and stabbed discs were processed and analyzed qualitatively using Analyze 7.0 and an IDL code. Histologic Analysis After animals were sacrificed, the control and stabbed discs with or without treatment were processed and sectioned. Sections were stained with H&E and safranin O. Statistical analysis: Data were expressed as mean ± SEM. One-way ANOVA and Dunnett post-hoc test were used to determine the significant difference. Results
Aesthetic Concrete Barrier Design (2006)

This report contains guidelines for aesthetic treatment of concrete safety shape barriers. The report will be of particular interest to design and safety practitioners with responsibility for roadside safety improvements.
Detecting mechanical loosening of total hip replacement implant from\n plain radiograph using deep convolutional neural network (2019)

Plain radiography is widely used to detect mechanical loosening of total hip\nreplacement (THR) implants. Currently, radiographs are assessed manually by\nmedical professionals, which may be prone to poor inter and intra observer\nreliability and low accuracy. Furthermore, manual detection of mechanical\nloosening of THR implants requires experienced clinicians who might not always\nbe readily available, potentially resulting in delayed diagnosis. In this\nstudy, we present a novel, fully automatic and interpretable approach to detect\nmechanical loosening of THR implants from plain radiographs using deep\nconvolutional neural network (CNN). We trained a CNN on 40 patients\nanteroposterior hip x rays using five fold cross validation and compared its\nperformance with a high volume board certified orthopaedic surgeon (AFC). To\nincrease the confidence in the machine outcome, we also implemented saliency\nmaps to visualize where the CNN looked at to make a diagnosis. CNN outperformed\nthe orthopaedic surgeon in diagnosing mechanical loosening of THR implants\nachieving significantly higher sensitively (0.94) than the orthopaedic surgeon\n(0.53) with the same specificity (0.96). The saliency maps showed that the CNN\nlooked at clinically relevant features to make a diagnosis. Such CNNs can be\nused for automatic radiologic assessment of mechanical loosening of THR\nimplants to supplement the practitioners decision making process, increasing\ntheir diagnostic accuracy, and freeing them to engage in more patient centric\ncare.\n
Linking physiological modeling of the stomach's electrical activity to in vitro measurements. (2014)

info:eu-repo/semantics/published
Mild Intramolecular Ring Opening of Oxetanes (2019)

Oxetanes have been increasingly used as stable motifs in medicinal chemistry as well as versatile synthetic intermediates. Herein, an intramolecular ring opening of oxetane carboxamides with mild nucleophiles, such as nitrogen heterocycles, is presented. The reaction proceeds under metal-free basic conditions which is highly unusual in ring opening reactions of oxetanes. Amide formation and oxetane ring opening/cyclization in a one-pot approach affords high levels of molecular complexity in a single step from simple, readily available substrates.
System Concepts and Circuits for a 60 GHz OFDM Transceiver (2009)

This chapter contains sections titled: Introduction System Design Aspects OFDM Baseband Processor Architecture and Simulation Results Medium Access Control (MAC) Implications Architecture and Performance of System Demonstrators Conclusions and Future Work Acknowledgements References
Overexpression of a Gene Encoding Hydrogen Peroxide-Generating Oxalate Oxidase Evokes Defense Responses in Sunflower (2003)

Oxalate oxidase (OXO) converts oxalic acid (OA) and O(2) to CO(2) and hydrogen peroxide (H(2)O(2)), and acts as a source of H(2)O(2) in certain plant-pathogen interactions. To determine if the H(2)O(2) produced by OXO can function as a messenger for activation of defense genes and if OXO can confer resistance against an OA-producing pathogen, we analyzed transgenic sunflower (Helianthus annuus cv SMF3) plants constitutively expressing a wheat (Triticum aestivum) OXO gene. The transgenic leaf tissues could degrade exogenous OA and generate H(2)O(2). Hypersensitive response-like lesion mimicry was observed in the transgenic leaves expressing a high level of OXO, and lesion development was closely associated with elevated levels of H(2)O(2), salicylic acid, and defense gene expression. Activation of defense genes was also observed in the transgenic leaves that had a low level of OXO expression and had no visible lesions, indicating that defense gene activation may not be dependent on hypersensitive response-like cell death. To further understand the pathways that were associated with defense activation, we used GeneCalling, an RNA-profiling technology, to analyze the alteration of gene expression in the transgenic plants. Among the differentially expressed genes, full-length cDNAs encoding homologs of a PR5, a sunflower carbohydrate oxidase, and a defensin were isolated. RNA-blot analysis confirmed that expression of these three genes was significantly induced in the OXO transgenic sunflower leaves. Furthermore, treatment of untransformed sunflower leaves with jasmonic acid, salicylic acid, or H(2)O(2) increased the steady-state levels of these mRNAs. Notably, the transgenic sunflower plants exhibited enhanced resistance against the OA-generating fungus Sclerotinia sclerotiorum.
In Vivo Cytochrome P450 3A Isoenzyme Activity and Pharmacokinetics of Imatinib in Relation to Therapeutic Outcome in Patients With Chronic Myeloid Leukemia (2015)

The CYP3A activity does not influence imatinib plasma concentrations or the therapeutic outcome. These results indicate that although imatinib is metabolized by CYP3A enzymes, this activity is not the rate-limiting step in imatinib metabolism and excretion. Future studies should focus on other pharmacokinetic processes so as to identify the major contributor to patient variability in imatinib plasma concentrations.
The loss of PPAR γ in immune cells abrogates the ability of abscisic acid to improve insulin sensitivity through a mechanism involving suppression of MCP‐1 expression and macrophage infiltration into white adipose tissue (2007)

Abcisic acid (ABA) is a natural phytohormone and PPAR γ agonist that significantly improves insulin sensitivity in db/db mice. Though it has become clear that obesity is associated with macrophage infiltration into white adipose tissue (WAT), the phenotype of adipose tissue macrophages (ATMs) and the mechanisms by which insulin‐sensitizing compounds modulate their infiltration remains unknown. We used a loss‐of‐function approach to investigate whether ABA ameliorates insulin resistance through a mechanism dependent on immune cell PPAR γ. We characterized two phenotypically distinct ATM subsets in db/db mice based on their surface expression of F4/80. The F4/80 hi ATMs were more abundant and expressed greater concentrations of chemokine receptor 2 (CCR2) and CCR5 when compared to F4/80 lo ATMs. ABA significantly decreased CCR2 + F4/80 hi infiltration into WAT and suppressed monocyte chemoattractant protein‐1 (MCP‐1) expression in WAT and plasma. Furthermore, the deficiency of PPAR γ in immune cells, including macrophages, impaired the ability of ABA to suppress infiltration of F4/80 hi ATMs into WAT, repress WAT MCP‐1 expression and improve glucose tolerance. We provide molecular evidence in vivo demonstrating that ABA improves insulin sensitivity and obesity‐related inflammation by inhibiting MCP‐1 expression and F4/80 hi ATM infiltration through a PPAR γ‐dependent mechanism.
Microlasers à cristaux photoniques en InP reporté sur silicium (2002)

Nous avons realise des microcavites a cristaux photoniques a 2D sur une heterostructure en InP reportee sur silicium. Les proprietes modales de ces structures ont ete etudiees theoriquement et experimentalement, en fonction de la taille de la cavite et du diametre des trous du cristal photonique. Un pompage de ces structures en regime pulse a temperature ambiante a permis d'atteindre une emission laser pour un seuil effectif de l'ordre de 2 mW.
Magnesium absorption in the human small intestine. Results in normal subjects, patients with chronic renal disease, and patients with absorptive hypercalciuria. (1976)

Magnesium absorption was studied in the normal human jejunum and ileum by in vivo intestinal perfusion, using test solutions containing from 0 to 20 mM Mg (as MgCl2). As luminal Mg concentration was increased, the rate of absorption in the jejunum rose progressively with a tendency towards saturation at the higher concentrations. The kinetics and rates of Mg absorption in the ileum were comparable to those in the jejunum, with the exception that at higher luminal concentrations the ileal absorptive process was fully saturated. Using test solutions containing various combinations of Ca and Mg, we found that Ca had little or no influence on Mg absorption, even through Mg depressed Ca absorption to a modest extent. Patients with end-stage renal disease, who had a reduced rate of Ca absorption (presumably due to deficiency of 1,25-dihydroxycholecalciferol) were found to have a severe depression of Mg absorption. On the other hand, patients with absorptive hypercalciuria and nephrolithiasis, who had an increased rate of Ca absorption, were found to absorb Mg normally. These results suggest that Mg absorption in the human is mediated by a transport process different from that which facilitates Ca absorption, and that normal Mg absorption may be dependent on vitamin D. Our results do not establish whether or not the normal intestine can absorb Mg against an electrochemical gradient.
Accelerated Blood Clearance of Lipid Nanoparticles Entails a Biphasic Humoral Response of B-1 Followed by B-2 Lymphocytes to Distinct Antigenic Moieties (2019)

Accelerated blood clearance (ABC) is a phenomenon in which certain pharmaceutical agents are rapidly cleared from the blood upon second and subsequent administrations. ABC has been observed for many lipid-delivery vehicles, including liposomes and lipid nanoparticles (LNP). Previous studies have demonstrated a role for humoral responses against the polyethylene glycol motifs in clearance, but significant gaps remain in our understanding of the mechanism of ABC, and strategies for limiting the impact of ABC in a clinical setting have been elusive. mRNA therapeutics have great promise, but require chronic administration in encapsulating delivery systems, of which LNP are the most clinically advanced. In this study, we investigate the mechanisms of ABC for mRNA-formulated LNP in vivo and in vitro. We present evidence that ABC of mRNA-formulated LNP is dramatic and proceeds rapidly, based on a previously unrecognized ability of LNP to directly activate B-1 lymphocytes, resulting in the production of antiphosphorylcholine IgM Abs in response to initial injection. Upon repeated injections, B-2 lymphocytes also become activated and generate a classic anti-polyethylene glycol adaptive humoral response. The ABC response to phosphorylcholine/LNP-encapsulated mRNA is therefore a combination of early B-1 lymphocyte and later B-2 lymphocyte responses.
Tea Polyphenols Modulate Antioxidant Redox System on Cisplatin‐induced Reactive Oxygen Species Generation in a Human Breast Cancer Cell (2013)

Tea polyphenols (TPP) have potent antioxidant and anticancer properties, particularly in patients undergoing radiation or chemotherapy. However, few studies have been conducted on treatments using a combination of TPP and the conventional chemical anticancer drug cisplatin (CP). This study was designed to investigate the mechanism of the cytotoxicity of total TPP and CP, which may synergistically induce cell death in cancer cells. Here, breast cancer cells (MCF-7) were treated with various concentrations of TPP alone or in combination with the chemotherapeutic drug CP. The effect of TPP on cell growth, intracellular reactive oxygen species (ROS) level, apoptosis and gene expression of caspase-3, caspase-8 and caspase-9 and p53 was investigated. The MTT (3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) assay revealed that the MCF-7 cells were less sensitive to growth inhibition by TPP treatment than either CP or the combination therapy. Propidium iodide nuclear staining indicated that exposure to this combination increased the proportion of apoptotic nuclei compared with a single-agent treatment. Flow cytometry analysis was used to quantify changes in intracellular ROS. Detection of activated caspases by fluorescently labelled inhibitors of caspases (FLICA) combined with the plasma membrane permeability assay demonstrated that the percentage of early and late apoptotic/secondary necrotic cells was higher in the cells treated with the combination than in those treated with either TPP or CP alone. The combined TPP and CP treatment synergistically induced apoptosis through both caspase-8 and caspase-9 activation and p53 over-expression. This suggests that TPP plus CP may be used as an efficient antioxidant-based combination therapy for estrogen receptor (ER)-positive and p53-positive breast cancer.
High Harmonic Generation from Isolated Bound States: Tunable Emission Spectra and Mollow Triplets (2022)

High harmonic generation (HHG) is a highly nonlinear emission process in which systems driven by intense laser pulses emit integer multiples (harmonics) of the driving field. This feature is considered universal to all occurrences of HHG. Here we show that a strong nonlinear response of certain systems can split the HHG spectrum into non-harmonic Mollow-type triplets, imprinting the internal electronic characteristics and confining potential on the HHG spectrum. The spectral lines become tunable by the driver field. These phenomena are universal to any material system with isolated bound states. We identify the conditions under which our predictions become accessible and propose experimental systems to observe them.
Systematic Profiling of Poly(A)+ Transcripts Modulated by Core 3’ End Processing and Splicing Factors Reveals Regulatory Rules of Alternative Cleavage and Polyadenylation (2015)

Alternative cleavage and polyadenylation (APA) results in mRNA isoforms containing different 3' untranslated regions (3'UTRs) and/or coding sequences. How core cleavage/polyadenylation (C/P) factors regulate APA is not well understood. Using siRNA knockdown coupled with deep sequencing, we found that several C/P factors can play significant roles in 3'UTR-APA. Whereas Pcf11 and Fip1 enhance usage of proximal poly(A) sites (pAs), CFI-25/68, PABPN1 and PABPC1 promote usage of distal pAs. Strong cis element biases were found for pAs regulated by CFI-25/68 or Fip1, and the distance between pAs plays an important role in APA regulation. In addition, intronic pAs are substantially regulated by splicing factors, with U1 mostly inhibiting C/P events in introns near the 5' end of gene and U2 suppressing those in introns with features for efficient splicing. Furthermore, PABPN1 inhibits expression of transcripts with pAs near the transcription start site (TSS), a property possibly related to its role in RNA degradation. Finally, we found that groups of APA events regulated by C/P factors are also modulated in cell differentiation and development with distinct trends. Together, our results support an APA code where an APA event in a given cellular context is regulated by a number of parameters, including relative location to the TSS, splicing context, distance between competing pAs, surrounding cis elements and concentrations of core C/P factors.
Efficient quantum computation of molecular forces and other energy gradients (2022)

While most work on the quantum simulation of chemistry has focused on computing energy surfaces, a similarly important application requiring subtly different algorithms is the computation of energy derivatives. Almost all molecular properties can be expressed an energy derivative, including molecular forces, which are essential for applications such as molecular dynamics simulations. Here, we introduce new quantum algorithms for computing molecular energy derivatives with significantly lower complexity than prior methods. Under cost models appropriate for noisy-intermediate scale quantum devices, we demonstrate how low-rank factorization and other tomography schemes can be optimized for energy derivative calculations. We numerically demonstrate that our techniques reduce the number of circuit repetitions required by many orders of magnitude for even modest systems, and that the cost of estimating an entire force vector may in some systems be lower than the cost of estimating the energy. In the context of fault-tolerant algorithms, we develop new methods of estimating energy derivatives with Heisenberg limited scaling, incorporating state-of-the-art techniques for block encoding fermionic operators. In contrast to our near-term results, we find that the cost of estimating forces with any of our Heisenberg-limited methods is bounded by the cost of estimating energies, due to inner loops requiring either energy estimation or reflections around the ground state. This implies that applications such as geometry optimization, coupling parameter estimation, and spectral prediction may be practical on fault-tolerant quantum devices, but tractable molecular dynamics simulations of large-scale systems requires further algorithmic advances.
Validation of the Prague C&M classification of Barrett's esophagus in clinical practice (2013)

Agreement was good for Barrett's esophagus and reasonable for hiatal hernia length. These findings strengthen the value of the Prague C&M classification to describe Barrett's esophagus and hiatal hernia length. Although absolute agreement during real-time endoscopy was high, one should anticipate that Barrett's values may vary by 1 - 2 cm between two endoscopies.
Supplementary Methods from Very Long-term Survival Following Resection for Pancreatic Cancer Is Not Explained by Commonly Mutated Genes: Results of Whole-Exome Sequencing Analysis (2023)

&lt;p&gt;Supplementary Methods. This document provides detailed methods for library preparation, sequencing, and SafeSeq.&lt;/p&gt;
Benzdiynes (1,2,4,5-Tetradehydrobenzenes):  Direct Observation by Wavelength-Selective Photolyses of Benzenetetracarboxylic Dianhydrides in Low-Temperature Nitrogen Matrixes (2002)

Toward direct observation of benzdiynes, we investigated the wavelength-selective photolyses of five kinds of benzenetetracarboxylic dianhydride derivatives in nitrogen matrixes at 13 K. In the first step of the photolyses, all dianhydrides were converted into benzynedicarboxylic anhydrides with loss of CO and CO2 upon irradiation at 308 nm. In the second step, the benzyne intermediates were photolyzed at 266 nm. In these photolyses, the generation of two kinds of benzdiynes, 3,6-difluoro-1,4-benzdiyne and 3,6-bis(trifluoromethyl)-1,4-benzdiyne, was confirmed by good correspondence between observed and calculated IR spectra. These benzdiynes were converted into the corresponding hexatriynes upon further irradiation at 266 nm. Benzdiynes were not observed in the photolyses of the other three dianhydrides: only hexatriynes were observed as major photoproducts. These results suggested that benzdiynes were generated first and then converted into hexatriynes and that the efficiency of the decomposition of benzdiynes depended on the substituents. The dynamics of the generation and decomposition of benzdiynes in the matrixes was analyzed by using a successive reaction scheme.
RNA Extraction and Analysis (2009)

This chapter contains sections titled: Transcription Translation Gene Regulation Use of siRNA to Investigate Gene Function References