gebhart/patrepeval huggingface dataset:
Optically Transparent Nanofiber Paper (2009)

Optically transparent paper of densely packed cellulose nanofibers is prepared without any additives. This material has the same chemical constituents as conventional paper, the only difference being the fiber width and the size of the interstitial cavities. This optically transparent paper exhibits high Young's modulus, high strength, ultralow CTE, and high foldability.
Characterization of ARF-BP1/HUWE1 Interactions with CTCF, MYC, ARF and p53 in MYC-Driven B Cell Neoplasms (2012)

Transcriptional activation of MYC is a hallmark of many B cell lineage neoplasms. MYC provides a constitutive proliferative signal but can also initiate ARF-dependent activation of p53 and apoptosis. The E3 ubiquitin ligase, ARF-BP1, encoded by HUWE1, modulates the activity of both the MYC and the ARF-p53 signaling pathways, prompting us to determine if it is involved in the pathogenesis of MYC-driven B cell lymphomas. ARF-BP1 was expressed at high levels in cell lines from lymphomas with either wild type or mutated p53 but not in ARF-deficient cells. Downregulation of ARF-BP1 resulted in elevated steady state levels of p53, growth arrest and apoptosis. Co-immunoprecipitation studies identified a multiprotein complex comprised of ARF-BP1, ARF, p53, MYC and the multifunctional DNA-binding factor, CTCF, which is involved in the transcriptional regulation of MYC, p53 and ARF. ARF-BP1 bound and ubiquitylated CTCF leading to its proteasomal degradation. ARF-BP1 and CTCF thus appear to be key cofactors linking the MYC proliferative and p53-ARF apoptotic pathways. In addition, ARF-BP1 could be a therapeutic target for MYC-driven B lineage neoplasms, even if p53 is inactive, with inhibition reducing the transcriptional activity of MYC for its target genes and stabilizing the apoptosis-promoting activities of p53.
Deducing ink thickness variations by a spectral prediction model (2009)

Abstract Most existing techniques for regulating the ink flow in offset presses rely on density measurements carried out on specially printed patches. In the present contribution, we develop a methodology to deduce ink thickness variations from spectral measurements of multichromatic halftone patches located within the printed page. For this purpose, we extend the Clapper‐Yule spectral reflectance prediction model by expressing the transmittance of the colorants composed of superposed inks as a function of the ink transmittances and of fitted ink layer thicknesses. We associate to each ink an ink thickness variation factor. At print time, this ink thickness variation factor can be fitted to minimize a difference metric between predicted reflection spectrum and measured reflection spectrum. The ink thickness variations deduced from multichromatic halftones allow to clearly distinguish between normal ink volume, reduced ink volume, or increased ink volume. This information can then be used for performing control operations on the printing press. © 2009 Wiley Periodicals, Inc. Col Res Appl, 34, 432–442, 2009
A2A Adenosine Receptor and its Modulators: Overview on a Druggable GPCR and on Structure-Activity Relationship Analysis and Binding Requirements of Agonists and Antagonists (2008)

Since the discovery of the biological effects of adenosine, the development of potent and selective agonists and antagonists of adenosine receptors has been the subject of medicinal chemistry research for several decades, even if their clinical evaluation has been discontinued. Main problems include side effects due to the ubiquity of the receptors and the possibility of side effects, or to low brain penetration (in particular for the targeting of CNS diseases), short half-life of compounds, lack of effects. Furthermore, species differences in the affinity of ligands make difficult preclinical testing in animal models. Nevertheless, adenosine receptors continue to represent promising drug targets. A(2A) receptor has proved to be a promising pharmacological target for small synthetic ligands, and while A(2A) agonists are undergoing clinical trials for myocardial perfusion imaging and as anti-inflammatory agents, A(2A) antagonists represent an attractive field of research to discover new drugs for the treatment of neurodegenerative disorders, such as Parkinson's disease. Furthermore, the information coming from bioinformatics and molecular modeling studies for the A(2A) receptor has made easier the understanding of ligand-target interaction and the rational design of agonists and antagonists for this subtype. The aim of this review is to show an overview of the most significant steps and progresses in developing A(2A) adenosine receptor agonists and antagonists.
Engineering Graphene‐Ceramic 3D Composite Foams by Freeze Drying (2021)

A 3D graphene foam produced by the chemical vapor deposition (CVD) technique is recognized as an effective nanofiller material, as it does not agglomerate in the matrix. Though CVD facilitates pristine graphene foam production, the method poses limitations in developing large‐scale 3D graphene composite foams as advanced engineering materials. Herein, a freeze‐drying (FD) process is used to produce a composite 3D foam, which is a mixture of graphene nanoplatelet (GNP) and a low‐temperature co‐fired ceramic (LTCC). The freeze‐dried GNP‐LTCC reticulated 3D composite foam has an average pore size ranging from 70 to 100 μm. Pore size is varied by regulating the heat transfer rate during the freezing process using a thermally conductive aluminum (Al) mold and a thermally insulating acrylonitrile butadiene styrene (ABS) mold. Computational thermal modeling is used to visualize the heat transfer and its effect on foam pore size. Subsequently, a freeze‐dried GNP‐LTCC composite foam is embedded into the LTCC matrix to form a hierarchical assembly by a spark plasma technique without compromising the 3D structure of the FD foam. This study established that a simple, eco‐friendly, and scalable processing methodology can produce advanced graphene‐based 3D composite foams as the future tailorable nanofillers for designing multimatrix materials.
Adjustable spectrum LED solar simulator (2014)

An LED solar simulator containing LEDs emitting at 23 different wavelengths is described. Taking into account the natural spectral width of each of the LED wavelengths, a reasonably well-behaved and spike-free spectral continuum is demonstrated. The LED light source is based on a modular design that facilitates fabrication of arbitrarily large area simulators for both single solar cell and multi-cell module test and evaluation. The spectral tunability of this simulator makes it an attractive instrument for use in evaluating the performance of both conventional solar cells and tandem solar cells. The basic modular building block is a 10 cm x 10 cm “tile” consisting of the LED emitter platform with reflecting side mirrors and driver electronics conveniently located directly underneath the emitter platform in a compact yet flexible configuration. Combinations of tiles facilitate manufacture of solar simulators of arbitrarily large size and shape, with the advantages of high reliability, spectral tunability, lighter weight, no water cooling requirements and absence of high voltages. Excellent spectral mixing and intensity uniformity is obtained on the measurement plane, resulting in a simulator that meets Class AAA specifications according to ASTM and IEC standards.
Real-Time PCR Assay for a Unique Chromosomal Sequence of <i>Bacillus anthracis</i> (2004)

Real-time PCR has become an important method for the rapid identification of Bacillus anthracis since the 2001 anthrax mailings. Most real-time PCR assays for B. anthracis have been developed to detect virulence genes located on the pXO1 and pXO2 plasmids. In contrast, only two published chromosomal targets exist, the rpoB gene and the gyrA gene. In the present study, subtraction-hybridization with a plasmid-cured B. anthracis tester strain and a Bacillus cereus driver was used to find a unique chromosomal sequence. By targeting this region, a real-time assay was developed with the Ruggedized Advanced Pathogen Identification Device. Further testing has revealed that the assay has 100% sensitivity and 100% specificity, with a limit of detection of 50 fg of DNA. The results of a search for sequences with homology with the BLAST program demonstrated significant alignment to the recently published B. anthracis Ames strain, while an inquiry for protein sequence similarities indicated homology with an abhydrolase from B. anthracis strain A2012. The importance of this chromosomal assay will be to verify the presence of B. anthracis independently of plasmid occurrence.
Towards predicting query execution time for concurrent and dynamic database workloads (2013)

Predicting query execution time is crucial for many database management tasks including admission control, query scheduling, and progress monitoring. While a number of recent papers have explored this problem, the bulk of the existing work either considers prediction for a single query, or prediction for a static workload of concurrent queries, where by "static" we mean that the queries to be run are fixed and known. In this paper, we consider the more general problem of dynamic concurrent workloads. Unlike most previous work on query execution time prediction, our proposed framework is based on analytic modeling rather than machine learning. We first use the optimizer's cost model to estimate the I/O and CPU requirements for each pipeline of each query in isolation, and then use a combination queueing model and buffer pool model that merges the I/O and CPU requests from concurrent queries to predict running times. We compare the proposed approach with a machine-learning based approach that is a variant of previous work. Our experiments show that our analytic-model based approach can lead to competitive and often better prediction accuracy than its machine-learning based counterpart.
Hypoxia-Inducible Protein 2 ( <i>HIG2</i> ), a Novel Diagnostic Marker for Renal Cell Carcinoma and Potential Target for Molecular Therapy (2005)

To identify molecules to serve as diagnostic markers for renal cell carcinoma (RCC) and as targets for novel therapeutic drugs, we investigated genome-wide expression profiles of RCCs using a cDNA microarray. We subsequently confirmed that hypoxia-inducible protein-2 (HIG2) was expressed exclusively in RCCs and fetal kidney. Induction of HIG2 cDNA into COS7 cells led to secretion of the gene product into culture medium and resulted in enhancement of cell growth. Small interfering RNA effectively inhibited expression of HIG2 in human RCC cells that endogenously expressed high levels of the protein and significantly suppressed cell growth. Moreover, addition of polyclonal anti-HIG2 antibody into culture medium induced apoptosis in RCC-derived cell lines. By binding to an extracellular domain of frizzled homologue 10 (FZD10), HIG2 protein enhanced oncogenic Wnt signaling and its own transcription, suggesting that this product is likely to function as an autocrine growth factor. ELISA analysis of clinical samples identified secretion of HIG2 protein into the plasma of RCC patients even at an early stage of tumor development, whereas it was detected at significantly lower levels in healthy volunteers or patients with chronic glomerulonephritis. The combined evidence suggests that this molecule represents a promising candidate for development of molecular-targeting therapy and could serve as a prominent diagnostic tumor marker for patients with renal carcinomas.
Isolation and Characterization of a Novel ConusPeptide with Apparent Antinociceptive Activity (2000)

Cone snails are tropical marine mollusks that envenomate prey with a complex mixture of neuropharmacologically active compounds. We report the discovery and biochemical characterization of a structurally unique peptide isolated from the venom of Conus marmoreus. The new peptide, mr10a, potently increased withdrawal latency in a hot plate assay (a test of analgesia) at intrathecal doses that do not produce motor impairment as measured by rotarod test. The sequence of mr10a is NGVCCGYKLCHOC, where O is 4-trans-hydroxyproline. This sequence is highly divergent from all other known conotoxins. Analysis of a cDNA clone encoding the toxin, however, indicates that it is a member of the recently described T-superfamily. Total chemical synthesis of the three possible disulfide arrangements of mr10a was achieved, and elution studies indicate that the native form has a disulfide connectivity of Cys1-Cys4 and Cys2-Cys3. This disulfide linkage is unprecedented among conotoxins and defines a new family of Conus peptides.
Evaluation of Pore Size Distribution Effects on Phase Behavior of Hydrocarbons Produced in Shale Gas Condensate Reservoirs (2017)

Abstract This paper presents a novel method that quantifies the pore confinement effects on fluid properties and phase behavior of hydrocarbons produced in shale gas condensate reservoirs. This method takes into account the rock pore size distribution derived from core or log measurements. The new method is applied to quantify the effects of pore size distribution on saturation pressures, fluid saturations, and molar fractions of components in liquid and vapor phases for a constant composition expansion (CCE) process of confined hydrocarbons. The pressure/volume/temperature (PVT) data of reservoir fluids for constant volume depletion (CVD) processes are generated and analyzed, including condensate windows of Eagle Ford and Marcellus shale formations. Primary modeling and analysis results show that the pore confinement has no significant effects on the phase behavior and fluid properties of hydrocarbons produced in shale gas condensate reservoirs.
2B-1 Solutions for Reconfigurable Arrays in Ultrasound (2006)

A reconfigurable array may involve a relatively large 2D array of transducer sub-elements and a layer of electronics which uses switches to connect certain sub-elements together, to a single system channel [Fischer et al., 2005 and Thomenius et al., 2005]. An annular array pattern, consisting of ring-shaped element groups, may be electronically scanned, or stepped, across the surface of such a reconfigurable array. The array could use 20 to 32 system channels and provide image quality comparable to a 128 channel linear array [Hazard et al., 2003 amd Dietz et al., 1979], This paper discusses some of the unique challenges and solutions pertaining to reconfigurable two-dimensional ultrasound arrays. Size constraints of the electronics result in some non-ideal aspects to the switch array; namely, there are constraints on the distribution of system channel access points across the array, and that these switches have a certain on-resistance which introduces non-ideal signal propagation delays. Some solutions will be discussed in this paper which aim to reduce the effect of these non-ideal constraints, and may suggest certain design tradeoffs which can be made in the design of future reconfigurable switch arrays
Process Design for Tough Ductile Martensitic Steels through Direct Quenching and Partitioning (2015)

A novel processing route comprising of thermomechanical rolling followed by direct quenching and partitioning (DQP) has been established for developing tough ductile high strength steels with yield strengths ≈1100 MPa. Suitable compositions were designed based on high silicon and/or aluminum contents and the microstructural mechanisms and DQP parameters established through physical simulation on a Gleeble simulator. Based on these results, suitable laboratory rolling trials were designed that also enabled coiling simulation. Desired martensite-austenite microstructures in respect of refined and randomized martensite packets/laths and finely divided austenite resulted in excellent mechanical properties, particularly at low quenching temperatures.
A morphing active surface model for automatic re-contouring in 4D radiotherapy (2007)

Delineation of tumor and organs at risk on each phase of 4D CT images is an essential step in adaptive radiotherapy planning. Manual contouring of the large amount of data is time-consuming and impractical. (Semi-) automated methods typically rely on deformable image registration techniques to automatically map the manual contours drawn in one image to all the other phases in order to get complete 4D contouring, a procedure known as <i>automatic re-contouring</i>. Disadvantages of such approaches are that the manual contouring information is not used in the registration process and the whole volume registration is highly inefficient. In this work, we formulate the automatic re-contouring in a deformable surface model framework, which effectively restricts the computation to a lower dimensional space. The proposed framework was inspired by the <i>morphing active contour model </i>proposed by Bertalmio <i>et al</i>. [1], but we address some limitations of the original method. First, a surface-based regularization is introduced to improve robustness with respect to noise. Second, we design a multi-resolution approach to further improve computational efficiency and to account for large deformations. Third, discrete meshes are used to represent the surface model instead of the implicit level set framework for better computational speed and simpler implementation. Experiment results show that the new morphing active surface model method performs as accurately as a volume registration based re-contouring method but is nearly an order of magnitude faster. The new formulation also allows easy combination of registration and segmentation techniques for further improvement in accuracy and robustness.
ESD protection design using a mixed-mode simulation for advanced devices (2004)

In this paper, we propose a new ESD protection design methodology using a mixed-mode ESD simulation that takes account of a coupling effect for both device and circuit. As a result, we can analysis the each protection unit operation and select the optimized protection circuits in prevention of ESD failure on separated power supply units by prediction of the simulation.
Enhancing the Power Output of Bifacial Solar Modules by Applying Effectively Transparent Contacts (ETCs) With Light Trapping (2018)

We have performed a computational study on the enhancement of the power output of bifacial solar modules with effectively transparent contacts (ETCs). ETCs are triangular cross-sectional silver grid fingers that redirect light to the active area of the solar cell, therefore mitigating grid finger shading losses. Furthermore, ETCs can be spaced densely leading to light trapping. We modeled bifacial silicon heterojunction solar modules with varying front and rear illumination and ETC coverages. We determined that shading losses can be almost fully mitigated and that light absorption can be increased by up to 4.7% compared with state-of-the-art screen-printed bifacial modules. Furthermore, we calculated that grid resistance and silver usage can be improved when using ETCs.
High power ultrasounds: A powerful, non-thermal and green technique for improving the phenolic extraction from grapes to must during red wine vinification (2019)

Wine color is one of the main organoleptic characteristics influencing its quality. It is of especial interest in red vinifications due to the economic resources that wineries have to invest for the extraction of the phenolic compounds. To increase this extraction, some chemical (maceration enzymes) or physical technologies (thermovinification, criomaceration, flash-expansion) can be applied. In this work, the results of the application of high power ultrasounds to the crushed grapes to increase the extraction of phenolic compounds are presented. Crushed grapes (400 kg) from the 2017 harvest were treated with ultrasound, and three different lengths of skin maceration period (2, 3 or 7 days) and the results were compared with a control vinification, where grapes were not subjected to any treatment and were skin macerated during 7 days. The wine chromatic characteristics and the individual phenolic compounds were followed during all the maceration period, at the end of alcoholic fermentation and after bottle storage. The wines made with ultrasound treated grapes presented differences with control wine, especially as regard color and total phenol and tannin content, the wines with three days of maceration time presenting similar chromatic characteristics than control wines with 7 days of maceration time.
Muscle Tension Line Concept in Nasolabial Muscle Complex—Based on 3-Dimensional Reconstruction of Nasolabial Muscle Fibers (2015)

Based on the 2-dimensional images obtained from the micro-computed tomographic scans, we suggest the concept of nasolabial muscle complex and muscle tension line group theory: there is a close relationship among the alar part of the nasalis, depressor septi muscle, orbicularis oris muscle, and levator labii superioris alaeque nasi. The tension line groups are 3 tension line structures in the nasolabial muscle complex that interlock with each other at the intersections and maintain the specific shape and aesthetics of the lip and nose.
Structural Basis for Aza-Glycine Stabilization of Collagen (2017)

Previously, we have demonstrated that replacement of the strictly conserved glycine in collagen with aza-glycine provides a general solution for stabilizing triple helical collagen peptides (Chenoweth, D. M.; et al. J. Am. Chem. Soc. 2016, 138, 9751 ; 2015, 137, 12422 ). The additional hydrogen bond and conformational constraints provided by aza-glycine increases the thermal stability and rate of folding in collagen peptides composed of Pro-Hyp-Gly triplet repeats, allowing for truncation to the smallest self-assembling peptide systems observed to date. Here we show that aza-glycine substitution enhances the stability of an arginine-containing collagen peptide and provide a structural basis for this stabilization with an atomic resolution crystal structure. These results demonstrate that a single nitrogen atom substitution for a glycine alpha-carbon increases the peptide's triple helix melting temperature by 8.6 °C. Furthermore, we provide the first structural basis for stabilization of triple helical collagen peptides containing aza-glycine and we demonstrate that minimal alteration to the peptide backbone conformation occurs with aza-glycine incorporation.
Perlecan domain V is neuroprotective and proangiogenic following ischemic stroke in rodents (2011)

Stroke is the leading cause of long-term disability and the third leading cause of death in the United States. While most research thus far has focused on acute stroke treatment and neuroprotection, the exploitation of endogenous brain self-repair mechanisms may also yield therapeutic strategies. Here, we describe a distinct type of stroke treatment, the naturally occurring extracellular matrix fragment of perlecan, domain V, which we found had neuroprotective properties and enhanced post-stroke angiogenesis, a key component of brain repair, in rodent models of stroke. In both rat and mouse models, Western blot analysis revealed elevated levels of perlecan domain V. When systemically administered 24 hours after stroke, domain V was well tolerated, reached infarct and peri-infarct brain vasculature, and restored stroke-affected motor function to baseline pre-stroke levels in these multiple stroke models in both mice and rats. Post-stroke domain V administration increased VEGF levels via a mechanism involving brain endothelial cell α5β1 integrin, and the subsequent neuroprotective and angiogenic actions of domain V were in turn mediated via VEGFR. These results suggest that perlecan domain V represents a promising approach for stroke treatment.