gebhart/patrepeval huggingface dataset:
Xenon diffusion on a stepped Pt(11,11,9) surface (1994)

The surface diffusion of xenon was studied on a stepped Pt(11,11,9) surface. Laser-induced thermal desorption (LITD) techniques were employed to examine the coverage dependence and anisotropy of the Xe diffusion. The coverage dependence of the Xe desorption rate was also measured using isothermal LITD and isothermal mass spectrometric methods. Both the diffusion and desorption rates of Xe on Pt(11,11,9) were independent of Xe coverage. These coverage-independent results provide no evidence for Xe trapping on step sites and are inconsistent with the existence of Xe islands. The coverage-independent desorption kinetics were similar to the kinetics on Pt(111) at low coverage with Edes=5.7 kcal/mole and νd=3.7×1010 s−1. The Xe diffusion was anisotropic and overwhelmingly parallel to the step edges. The diffusion kinetic parameters parallel to the step edges were Edif=2.8 kcal/mole and D0=50 cm2/s. This diffusion barrier is much larger than earlier theoretical predictions. The diffusion pre-exponential is also much larger than the values predicted by transition state theory. These experimental results suggest that Xe diffuses on the stepped Pt(111) surface with a multiple-site hopping mechanism. The temperature dependence of this multiple-site hop length may dominate the measured diffusion activation energy. Consequently, in accordance with recent calculations, the experimentally measured diffusion barrier may not directly reflect the underlying potential energy surface.
Remote Management and Control of WDM-PON System for Fronthaul in Cloud-Radio Access Networks (2017)

We develop an evaluation platform of remote management and control for WDM-PON system and successfully demonstrate an ONU activation operation by means of exchanging AMCC signals superimposed on both downstream and upstream main signals.
POT1 Stimulates RecQ Helicases WRN and BLM to Unwind Telomeric DNA Substrates (2005)

Defects in human RecQ helicases WRN and BLM are responsible for the cancer-prone disorders Werner syndrome and Bloom syndrome. Cellular phenotypes of Werner syndrome and Bloom syndrome, including genomic instability and premature senescence, are consistent with telomere dysfunction. RecQ helicases are proposed to function in dissociating alternative DNA structures during recombination and/or replication at telomeric ends. Here we report that the telomeric single-strand DNA-binding protein, POT1, strongly stimulates WRN and BLM to unwind long telomeric forked duplexes and D-loop structures that are otherwise poor substrates for these helicases. This stimulation is dependent on the presence of telomeric sequence in the duplex regions of the substrates. In contrast, POT1 failed to stimulate a bacterial 3'-5'-helicase. We find that purified POT1 binds to WRN and BLM in vitro and that full-length POT1 (splice variant 1) precipitates a higher amount of endogenous WRN protein, compared with BLM, from the HeLa nuclear extract. We propose roles for the cooperation of POT1 with RecQ helicases WRN and BLM in resolving DNA structures at telomeric ends, in a manner that protects the telomeric 3' tail as it is exposed during unwinding.
Effect of Na+-channel blockade on the three-dimensional substrate of atrial fibrillation in a model of endo-epicardial dissociation and transmural conduction (2018)

This simple atrial model explains the loss of efficacy of sodium channel blockers in terminating AF in the presence of severe structural remodelling as has been observed experimentally and clinically. Atrial fibrillation termination in atria with moderate structural remodelling in the presence of sodium channel block is caused by reduction of AF complexity. With more severe structural remodelling, sodium channel block fails to promote synchronization of the two layers of the model.
Online Supplementary Materials from Genomics-Driven Precision Medicine for Advanced Pancreatic Cancer: Early Results from the COMPASS Trial (2023)

&lt;p&gt;Supplementary Methods, Tables and Figures Supplementary Table 1: Summary of whole genome sequencing results including performance metrics and time to reporting (N=62). Supplementary Table 2: Summary of GATA6 RNA in situ results and its correlation with RNA subtype and histologic grade. Supplementary Figure 1: WGS Performance Characteristics. Supplementary Figure 2: Both COMP-0037 and COMP-0057 had germline BRCA2 p.S1982fs mutations but only COMP-0037 had a second hit (somatic LOH of wild type allele) and showed hallmarks of double strand break repair deficiency. Supplementary Figure 3: BRCA2 mutation status of COMP-0057. Supplementary Figure 4: Subtypes of advanced PDAC by Moffitt tumour classification Supplementary Figure 5: Correlation between Moffitt tumor RNA subtypes and GATA6 gene expression. Supplementary Figure 6: Correlation between GATA6 expression measured by RNASeq and RNA in situ hybridization. Supplementary Figure 7: Differentially expressed pathways between Moffitt's basal like and classical RNA subtypes Supplementary Figure 8: CDK4 amplification identified in COMP-0008 (A) and CDK6 amplification identified in COMP-0010 (B) validated by fluorescence in-situ hybridization.&lt;/p&gt;
Synthesis and Antiviral Activity of Water‐Soluble Polycarboxylic Derivatives of [60]Fullerene Loaded with 3,4‐Dichlorophenyl Units (2018)

We have synthesized a series of water-soluble polycarboxylic derivatives of [60]fullerene with a gradually changed polarity by combining three to five polar (ionic) malonate addends with two to zero hydrophobic dichlorobenzene units and explored their antiviral activity. It has been shown that decreasing the number of the ionogenic carboxylic groups in the molecules enhanced their antiviral activity against HIV-1 and suppressed their action against HIV-2. The obtained results implied that the charged states and hydrophobicity of the water-soluble polycarboxylic fullerene derivatives affect significantly their biological properties.
Identification of new genes and pathways involved in the vasoregression mimicking diabetic retinopathy (2008)

Aims: Diabetic retinopathy is the most common microangiopathy in diabetes. It is morphologically characterized by vasoregression including pericyte loss and increased formation of acellular capillaries. Recently, we characterized a transgenic rat with a universal overexpression of PKD-2, in which c- terminal polycystein-2 is truncated. The transgenic rats showed severe vasoregression in the retinas at the second month of life. To elucidate the mechanisms of vasoregression in the retina, we analysed transcriptional alterations in this transgenic rats.
Large-scale Circulating microRNA Profiling for the Liquid Biopsy of Prostate Cancer (2019)

The model developed in this study may help improve the diagnosis of prostate cancer and reduce the number of unnecessary prostate biopsies.
A Weight Loss Intervention Augmented by a Wearable Device in Rural Older Adults With Obesity: A Feasibility Study (2020)

A multicomponent obesity intervention incorporating a wearable device is feasible and acceptable to older adults with obesity, and potentially holds promise in enhancing health.
Design and simulation of fast substation protection in IEC 61850 environments (2015)

The IEC 61850 protocol suite provides significant benefits in electrical substation design and enables formal validation of complex device configurations to ensure that design objectives are met. One important benefit is the potential for protective relays to react in a collaborative fashion to an observed fault current. Modern relays are networked cyber-physical devices with embedded systems, capable of sophisticated protection schemes that are not possible on legacy overcurrent relays. However, they may be subject to error or cyber attack. Herein, we introduce the CODEF (Collaborative Defense) project examining distributed substation protection. Under CODEF, we derive algorithms for distributed protection schemes based on distributed agreement. By leveraging Kirchhoff's laws, we establish that certain fast agreement protocols have important equivalences to linear coding and error correction theory. In parallel, we describe a cyber-physical simulation environment in which these algorithms are being validated with respect to the strict time constraints of substation protection.
The Feniks FPGA Operating System for Cloud Computing (2017)

Driven by explosive demand on computing power and slowdown of Moore's law, cloud providers have started to deploy FPGAs into datacenters for workload offloading and acceleration. In this paper, we propose an operating system for FPGA, called Feniks, to facilitate large scale FPGA deployment in datacenters. XFeniks provides abstracted interface for FPGA accelerators, so that FPGA developers can get rid of underlying hardware details. In addtion, Feniks also provides (1) development and runtime environment for accelerators to share an FPGA chip in efficient way; (2) direct access to server's resource like storage and coprocessor over PCIe bus; (3) an FPGA resource allocation framework throughout a datacenter. We implemented an initial prototype of Feniks on Catapult Shell and Altera Stratix V FPGA. Our experiements show that device-to-device communication over PCIe is feasible and efficient. A case study shows multiple accelerators can share an FPGA chip independently and efficiently.
Synthesis and Accumulation of the Essential Amino Acids Lysine and Threonine in Seeds (2017)

This chapter focuses on the regulation of synthesis and accumulation of the essential amino acids lysine and threonine in plants and in seeds as autonomous organs, and approaches to increase the content of these essential amino acids in seeds. Information on the regulation of synthesis of other essential amino acids in plants can be obtained from other excellent reviews. The pattern of free lysine accumulation in seeds from transgenic plants expressing the bacterial insensitive dihydrodipicolinate synthase was entirely different from that of free threonine accumulation in plants expressing the bacterial insensitive Aspartate Kinase. Although the catabolism of lysine has been studied quite extensively in microorganisms, fungi, and animals, very little is known on the pathways and regulation of lysine catabolism in plants. Molecular studies suggest that the levels of free amino acids, particularly lysine, in plant seeds may be determined not only by the efficiency of their synthesis but also by their stability in the free pool.
ChemInform Abstract: Host‐Guest Binding Capacity of Cucurbituril. Cycloaddition Induced by Cucurbituril. A Case of Pauling Principle Catalysis. (1984)

Abstract Die Käfigverbindung Cucurbituril (I) liefert mit zahlreichen Ammoniumverbindungen Einschlußverbindungen, deren Dissoziationskonstanten in Relation zur Raumbeanspruchung diskutiert werden.
Analysis of Minor Alkaloids in Tobacco: A Collaborative Study (2005)

Abstract A collaborative study regarding the analysis of minor alkaloids in tobacco and tobacco products was initiated by the Analytical Methods Committee of the Tobacco Science Research Conference (TSRC). One purpose of the study was to assess the reliability of methods used for the analysis of minor alkaloids and nicotine in tobacco and tobacco products, as practiced in different laboratories. A second purpose was to select a preferred method or to develop a hybrid method based on the best elements from the procedures currently used for the analysis of minor alkaloids. A hybrid method was developed and its results compared with the values from existing methods. The hybrid method proves to be reliable, has good repeatability, and is easy to implement. This new method can be used as a reference procedure for minor alkaloids and nicotine analysis using either flame ionization (FID) or mass spectrometric (MS) detection. A comparison with the older techniques shows that the hybrid method considerably improved the repeatability, but only marginally increased the reproducibility for different laboratories. This may be, in part, because any new method requires some time to become fully standardized and reliable. Also, the contribution of other sources of variation such as different standards and different equipment may have limited the improvement in reproducibility.
Integrating Objects into Monocular SLAM (2018)

We propose a novel Line based parameterization for category specific CAD models. The proposed parameterization associates 3D category-specific CAD model and object under consideration using a dictionary based RANSAC method that uses object Viewpoints as prior and edges detected in the respective intensity image of the scene. The association problem is posed as a classical Geometry problem rather than being dataset driven, thus saving the time and labour that one invests in annotating dataset to train Keypoint Network[25, 26] for different category objects. Besides eliminating the need of dataset preparation, the approach also speeds up the entire process as this method processes the image only once for all objects, thus eliminating the need of invoking the network for every object in an image across all images. A 3D-2D edge association module followed by a resection algorithm for lines is used to recover object poses. The formulation optimizes for shape and pose of the object, thus aiding in recovering object 3D structure more accurately. Finally, a Factor Graph formulation is used to combine object poses with camera odometry to formulate a SLAM problem.
Ciliary neurotrophic factor is an endogenous pyrogen. (1993)

Fever is initiated by the action of polypeptide cytokines called endogenous pyrogens, which are produced by the host during inflammation, trauma, or infection and which elevate the thermoregulatory set point in the hypothalamus. Ciliary neurotrophic factor (CNTF) supports the differentiation and survival of central and peripheral neurons. We describe the activity of CNTF as intrinsically pyrogenic in the rabbit. CNTF induced a monophasic fever which rose rapidly (within the first 12 min) following intravenous injection; CNTF fever was blocked by pretreatment with indomethacin. The fever induced by CNTF was not due to contaminating endotoxins. Increasing doses of CNTF resulted in prolongation of the fever, suggesting the subsequent induction of additional endogenous pyrogenic activity. After passive transfer of plasma obtained during CNTF-induced fever, endogenous pyrogen activity was not present in the circulation; CNTF also did not induce the endogenous pyrogens interleukin 1, tumor necrosis factor, or interleukin 6 in vitro. Nevertheless, a second endogenous pyrogen may originate within the central nervous system following the systemic injection of CNTF. Of the four endogenous pyrogens described to date (interleukin 1, tumor necrosis factor, interferon, and interleukin 6), CNTF, like interleukin 6, utilizes the cell-surface gp 130 signal-transduction apparatus.
Studies of Soil Mineral-Organic Matter Associations and Plant Nutrient Fixation Using Synchrotron X-ray Methods (2021)

Earth and Space Science Open Archive This is a preprint and has not been peer reviewed. ESSOAr is a venue for early communication or feedback before peer review. Data may be preliminary.Learn more about preprints preprintOpen AccessYou are viewing the latest version by default [v1]Studies of Soil Mineral-Organic Matter Associations and Plant Nutrient Fixation Using Synchrotron X-ray MethodsAuthorsTamasVargaiDRaviKukkadapuAliceDohnalkovaiDLiborKovarikMatthewMarcusAmirAhkamiRosalieChuKimHixsonCarrieNicoraTanyaWinklerLorenRenoAnilBattuMorganBarnesOlgaAntipovaSirineFakraDilworthParkinsonSharonDotyiDSee all authors Tamas VargaiDCorresponding Author• Submitting AuthorPacific Northwest National LaboratoryiDhttps://orcid.org/0000-0002-5492-866Xview email addressThe email was not providedcopy email addressRavi KukkadapuPacific Northwest National Labview email addressThe email was not providedcopy email addressAlice DohnalkovaiDPacific Northwest National LaboratoryiDhttps://orcid.org/0000-0003-1578-4015view email addressThe email was not providedcopy email addressLibor KovarikPacific Northwest National Laboratoryview email addressThe email was not providedcopy email addressMatthew MarcusLawrence Berkeley National Laboratoryview email addressThe email was not providedcopy email addressAmir AhkamiPacific Northwest National Laboratoryview email addressThe email was not providedcopy email addressRosalie ChuPacific Northwest National Laboratoryview email addressThe email was not providedcopy email addressKim HixsonPacific Northwest National Laboratoryview email addressThe email was not providedcopy email addressCarrie NicoraPacific Northwest National Laboratoryview email addressThe email was not providedcopy email addressTanya WinklerPacific Northwest National Laboratoryview email addressThe email was not providedcopy email addressLoren RenoPacific Northwest National Laboratoryview email addressThe email was not providedcopy email addressAnil BattuPacific Northwest National Laboratoryview email addressThe email was not providedcopy email addressMorgan BarnesUniversity of California Mercedview email addressThe email was not providedcopy email addressOlga AntipovaArgonne National Laboratoryview email addressThe email was not providedcopy email addressSirine FakraLawrence Berkeley National Laboratoryview email addressThe email was not providedcopy email addressDilworth ParkinsonLawrence Berkeley National Laboratoryview email addressThe email was not providedcopy email addressSharon DotyiDUniversity of Washington Seattle CampusiDhttps://orcid.org/0000-0002-9546-315Xview email addressThe email was not providedcopy email address
<title>Asynchronous spread spectrum communication for a micro-miniature transponder: implementation and test results</title> (2005)

While the field of wireless communication has developed dramatically over the past several decades, there are several notable applications of wireless technologies which impose constraints on power-consumption and form-factor that are not compatible with cutting edge technologies. These applications include implantable devices and remote monitoring devices. Using a well-defined set of functional needs and system restrictions, we have developed an ultra-compact and ultra-low-powered transponder which contains spread spectrum (SS) logic for wireless communications. The transponder chip was designed and built in the Jazz BiCMOS SiGe technology. The device is activated via a pure tone and emits a SS response which is modulated over the carrier with binary phase shift keying (BPSK). The SS signal is a gold-code generated from two 9-bit m-sequence generators. One of the m-sequences is seeded with a fixed value while the other 9-bit register is pinned out and can be a fixed ID or a bus to transmit data from a microcontroller. The data is received and decoded by a standard PC with a high-speed acquisition board. In order to support multiple devices at various distances, asynchronous decoding is applied. When active, the device draws less than 35 mA of current. Because the duty cycle of this device is likely less than 1%, the device can be powered for several hours using a very small coin battery. The device has been tested both in the lab and natural environment testing is underway. Future work will combine the device with a microcontroller in the field to achieve specific monitoring goals.
Synthesis of polyglycocarbonates through polycondensation of glucopyranosides with CO2 (2017)

Starting from α-methyl <sc>d</sc>-glucopyranoside (MDG), three strategies of synthesis of polyglycocarbonates through direct polycondensation with CO<sub>2</sub> were tried.
Atomic-Oxygen-Durable and Electrically-Conductive CNT-POSS-Polyimide Flexible Films for Space Applications (2015)

In low Earth orbit (LEO), hazards such as atomic oxygen (AO) or electrostatic discharge (ESD) degrade polymeric materials, specifically, the extensively used polyimide (PI) Kapton. We prepared PI-based nanocomposite films that show both AO durability and ESD protection by incorporating polyhedral oligomeric silsesquioxane (POSS) and carbon nanotube (CNT) additives. The unique methods that are reported prevent CNT agglomeration and degradation of the CNT properties that are common in dispersion-based processes. The influence of the POSS content on the electrical, mechanical, and thermo-optical properties of the CNT-POSS-PI films was investigated and compared to those of control PI and CNT-PI films. CNT-POSS-PI films with 5 and 15 wt % POSS content exhibited sheet resistivities as low as 200 Ω/□, and these resistivities remained essentially unchanged after exposure to AO with a fluence of ∼2.3 × 10(20) O atoms cm(-2). CNT-POSS-PI films with 15 wt % POSS content exhibited an erosion yield of 4.8 × 10(-25) cm(3) O atom(-1) under 2.3 × 10(20) O atoms cm(-2) AO fluence, roughly one order of magnitude lower than that of pure PI films. The durability of the conductivity of the composite films was demonstrated by rolling film samples with a tight radius up to 300 times. The stability of the films to thermal cycling and ionizing radiation was also demonstrated. These properties make the prepared CNT-POSS-PI films with 15 wt % POSS content excellent candidates for applications where AO durability and electrical conductivity are required for flexible and thermally stable materials. Hence, they are suggested here for LEO applications such as the outer layers of spacecraft thermal blankets.
Inhibition of pancreatic cancer-cell growth and metastasis in vivo by a pyrazole compound characterized as a cell-migration inhibitor by an in vitro chemotaxis assay (2022)

Pancreatic cancer is recalcitrant to treatment as it is highly metastatic and rapidly progressive. While observing the behavior of human pancreatic BxPC-3 cells using an optical assay device called TAXIScan, we found that several synthetic pyrazole and pyrimidine derivatives inhibited cell migration. One such compound, 14-100, inhibited metastasis of fluorescence-labeled BxPC-3 cells, which were transplanted into the pancreas of nude mice as a subcutaneously grown cancer fragment. Surprisingly, despite its low cytotoxicity, the compound also showed an inhibitory effect on cancer cell proliferation in vivo, suggesting that the compound alters cancer cell characteristics needed to grow in situ. Single-cell RNA-sequencing revealed changes in gene expression associated with metastasis, angiogenesis, inflammation, and epithelial-mesenchymal transition. These data suggest that the compound 14-100 could be a good drug candidate against pancreatic cancer.
Method of detecting kink-bearing vessels in a retinal fundus image (2010)

Glaucoma is the second leading cause of blindness worldwide. The risk of glaucoma can be determined by calculating the cup to disc ratio in retinal fundus images. To accurately detect the optic cup, kinks or bends in small and medium vessels are important indicators of the cup boundary. In this paper, we present a method of detecting such vessels, through the extraction of patches and generation of hybrid features in a SVM-based model. The segmentation results show good potential for the further development of this method.