gebhart/patrepeval huggingface dataset:
DNA Methylation Based Biomarkers in Non-Invasive Cancer Screening (2010)

DNA methylation plays a critical role in the regulation of gene expression, differentiation and in the development of cancer and other diseases. Hypermethylation of CpG islands located in the promoter regions of tumor suppressor genes is now firmly established as the most frequent mechanism for gene inactivation in cancers. Feasibility of using DNA methylation based biomarkers for early detection of cancer has been shown. Potential of using DNA methylation for prediction of therapeutic outcome and patient survival has also been shown. DNA originated from cancer cells has been routinely detected in clinical specimens (ex. Plasma/serum, sputum, urine etc.) from cancer patients. Presence of methylated DNA sequences in clinical specimens and potential of using them as biomarkers have been recognized. Novel methylation based biomarkers that can be used in clinical specimens, obtained non-invasively from cancer patients, offer significant practical advantages. More resources need to be committed to this area of biomarker research. Thus, we review recent findings on DNA methylation based cancer biomarkers with particular focus on these applicable to the clinical specimens obtained non-invasively from cancer patients.
Learning probabilistic document template models via interaction (2013)

Document aesthetics measures are key to automated document composition. Recently we presented a probabilistic document model (PDM) which is a micro-model for document aesthetics based on a probabilistic modeling of designer choice in document design. The PDM model comes with efficient layout synthesis algorithms once the aesthetic model is defined. A key element of this approach is an aesthetic prior on the parameters of a template encoding aesthetic preferences for template parameters. Parameters of the prior were required to be chosen empirically by designers. In this work we show how probabilistic template models (and hence the PDM cost function) can be learnt directly by observing a designer making design choices in composing sample documents. From such training data our learning approach can learn a quality measure that can mimic some of the design tradeoffs a designer makes in practice.
Facet-Dependent Catalytic Activity of MnFe Prussian Blue Analogues in Peroxymonosulfate-Activated System for Efficient Degradation of Acetamiprid (2023)

MnFe Prussian blue analogues (MnFe PBAs) were fabricated for acetamiprid degradation with peroxymonosulfate (PMS) as an oxidant. MnFe PBAs (200) are the most active facets for PMS activation due to the superior chemisorption affinity and electron-transfer ability. Density functional theory calculation verified that Mn(III) served as an electron donor and acceptor to adjust the electron density between Fe and Mn, which played a crucial role in the high activation performance of MnFe PBAs (200). PBA lattice (−C═N) did not exhibit direct PMS activation capability in this system, which differed from previously reported Fenton counterparts. Based on the electronic localization function calculation and probe experiments, the O–O of HSO5– was broken, and the bonds of PBA could be restored during the activation reaction, leading to the continuous generation of reactive oxygen species in the MnFe PBAs/PMS system. Transformation product studies indicated that the oxidized products were primarily the result of aromatic hydroxylation, N–C bond cleavage, azo reaction, and so forth, achieving the mineralization and ecotoxicity mitigation of acetamiprid efficiently. Findings in this study provided new insights into developing advanced facet-dependent catalysts to activate PMS for the efficient degradation of emerging contaminants in the aqueous environment.
Biologically Active Hen Egg Components in Human Health and Disease (2004)

It is widely recognized that eggs are more than a source of dietary nutrients, and extensive studies identifying and characterizing the biologically active components of eggs have been carried out. Numerous biological activities have now been associated with egg components, including antibacterial and antiviral activity, immunomodulatory activity, and anti-cancer activity, indicating the importance of eggs and egg components in human health, and disease prevention and treatment. The potential of some of these biologically active components has already been realized, including egg white lysozyme and avidin, and yolk IgY and lecithin, which are currently produced on an industrial scale, and have been applied for the prevention and treatment of various medical conditions. The information presented here serves to demonstrate the significant potential of biologically active egg components, for medical, nutraceutical, and food-fortification applications.
Calibrating an intracranial pressure dynamics model with clinical data - a progress report (2005)

We describe the calibration of a computer model of intracranial pressure (ICP) dynamics to correspond with annotated clinical data taken from a patient being treated for elevated ICP due to a traumatic brain injury. The research protocol employed during treatment includes adjusting the elevation of the head of the bed, adjusting the ventilator settings to induce mild hyperventilation and hypoventilation, and adjusting the height of the cerebrospinal fluid drainage system. The model behavior corresponds to the experimental data quite well in the case of the changing the head of the bed, but less well in the case of changing the ventilator settings.
415 Verification of Dynamic Characteristics for Mount Combined Air-Spring with Viscous Fluid (2006)

現在,油圧ショベルのキャブマウントとしては,防振ゴムによる弾性支持力と高粘度オイルの圧力差によって生じる粘性減衰力を利用したビスカスマウントが一般に用いられている.しかしながら,このビスカスマウントは搭載重量が大きくなると中立位置が押し下げられ,同じ外力振動でもストロークエンドのゴムストッパに達する頻度が多くなり,オペレータはゴムストッパの衝撃を受ける.また,高粘度オイルを密封した構造となっており,衝撃的な大負荷時においては狭い環状隙間にオイルが流れにくくオイルの圧縮反発力を受けるため粘性減衰力が発揮されにくいなどの課題があり,多種多様なアプリケーションに対応したマウント開発が難しい.そこで搭載負荷に応じた中立位置が調整可能で,幅広い外力振動に対しても流体の粘性力を発揮できるマウントとして,Fig.A-1に示すような空気ばねと粘性流体の粘性せん断力を組み合わせた複合マウントを考案した.この複合マウントは,空気ばねに円筒状の容器を内蔵したものであり,搭載物は空気ばねによって支持される.円筒内の粘性流体は密封されておらず,高粘度オイルのせん断粘性力を重視した構造となっている.本研究では,上記ような目的で考案した複合マウントの試作回数を低減するための設計指針を与えることを目的として,その動特性を設計パラメータを用いて算出する方法を提案する.まず複合マウントを試作し,定常波加振試験を実施した.加振試験によって得た変位振幅,加振力の波形から複合マウントの動剛性,損失剛性を算出し,さらに実験条件を変更することにより周波数,変位振幅,空気ばねの内圧,粘性流体の粘度に対する依存性を明らかにした.次に設計パラメータを用いた動特性算出式を導出し,動剛性および損失剛性を算出した.最後に,設計パラメータによって算出された動特性と加振実験によって計測された動特性を比較することによって,動特性算出式を検証した.
Understanding Polymer Processing (2010)

You have accessUnderstanding Polymer ProcessingOct 2010Understanding Polymer ProcessingTim A. OsswaldTim A. Osswaldhttps://doi.org/10.3139/9783446446038.fmSectionsAboutPDF ToolsAdd to FavoritesDownload CitationTrack CitationsCopy LTI LinkPDF ShareFacebookTwitterEmailLinkedIn next chapter FiguresReferencesRelatedDetails 2010Pages: I-XIVPrint ISBN: 978-3-446-42404-3eISBN: 978-3-446-44603-8 Copyright & Permissions© 2011 Carl Hanser Verlag GmbH & Co. KGPDF DownloadLoading ...
From the DNA Gyrase Inhibitor Cyclothialidine to a New Class of Antibacterial Agents (2003)

Cyclothialidine (Ro 09-1437) is a potent DNA gyrase inhibitor that was isolated from S. filipinensis NR0484. In this account we describe the identification of potent antibacterials structurally derived from this virtually neat enzyme inhibitor.
Gemini Observations of Mid-IR Emission from the Nucleus of Centaurus A (2006)

Peer reviewed: Yes
Dynamic Wavelength-Tunable Photodetector Using Subwavelength Graphene Field-Effect Transistors (2017)

Dynamic wavelength tunability has long been the holy grail of photodetector technology. Because of its atomic thickness and unique properties, graphene opens up new paradigms to realize this concept, but so far this has been elusive experimentally. Here we employ detailed quantum transport modeling of photocurrent in graphene field-effect transistors (including realistic electromagnetic fields) to show that wavelength tunability is possible by dynamically changing the gate voltage. We reveal the phenomena that govern the behavior of this type of device and show significant departure from the simple expectations based on vertical transitions. We find strong focusing of the electromagnetic fields at the contact edges over the same length scale as the band-bending. Both of these spatially-varying potentials lead to an enhancement of non-vertical optical transitions, which dominate even in the absence of phonon or impurity scattering. We also show that the vanishing density of states near the Dirac point leads to contact blocking and a gate-dependent modulation of the photocurrent. Several of the effects discussed here should be applicable to a broad range of one- and two-dimensional materials and devices.
Vitamin C estimation with standard 1H spectroscopy using a clinical 3T MR system: Detectability and reliability within the human brain (2008)

This study demonstrates the ability to detect vitamin C in the human brain under common clinical magnetic resonance spectroscopy (MRS) standards in combination with LCModel. Furthermore, it supports the need to include Asc in the standard MRS analysis.
Passive mode-locking of a Nd:GdVO4 laser by intracavity SHG in periodically-poled stoichiometric lithium tantalate (2010)

Stable and self-starting mode-locking is achieved by cascaded second order nonlinearity using PPMgSLT nonlinear crystal in a Nd:GdVO 4 laser, achieving average powers up to 5.1 W and pulse durations as short as 3.8 ps.
Abstract 33: Cancer-associated IDH1 mutations produce 2-hydroxyglutarate (2010)

Abstract Mutations in the enzyme isocitrate dehydrogenase 1 (IDH1) are a common feature of most gliomas and secondary glioblastomas, as well as approx 10% acute myeloid leukemias. This event results in loss of the enzyme's ability to catalyze conversion of isocitrate to α -ketoglutarate. However, these mutations are all heterozygous and occur at a single amino acid residue of the IDH1 active site consistent with an enzymatic gain of function rather than a simple loss of function. To test this hypothesis we characterized mutant IDH1 (IDH1m) biochemically. We have shown that cancer-associated IDH1 mutations result in a new ability of the enzyme to catalyze the NADPH-dependent reduction of α-ketoglutarate to R(-)-2-hydroxyglutarate (2-HG). Patients with an inherited, neurometabolic disorders called 2-hydroxyglutaric aciduria exhibit an accumulation of 2-HG in their CNS, and an increased risk of developing malignant brain tumors. Similarly, in human malignant gliomas harboring IDH1 mutations, we find elevated levels of 2-HG. Altogether our data demonstrate that the IDH1 mutations result in production of 2-HG, and suggest that the excess 2HG which accumulates in vivo contributes to the formation and malignant progression of gliomas. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 33.
Assessment of Gaussian-3 and density-functional theories on the G3/05 test set of experimental energies (2005)

The G3/99 test set [L. A. Curtiss, K. Raghavachari, P. C. Redfern, and J. A. Pople, J. Chem. Phys. 112, 7374 (2000)] of thermochemical data for validation of quantum chemical methods is expanded to include 78 additional energies including 14 enthalpies of formation of the first- and second-row nonhydrogen molecules, 58 energies of molecules containing the third-row elements K, Ca, and Ga-Kr, and 6 hydrogen-bonded complexes. The criterion used for selecting the additional systems is the same as before, i.e., experimental uncertainties less than +/- 1 kcal/mol. This new set, referred to as the G3/05 test set, has a total of 454 energies. The G3 and G3X theories are found to have mean absolute deviations of 1.13 and 1.01 kcal/mol, respectively, when applied to the G3/05 test set. Both methods have larger errors for the nonhydrogen subset of 79 species for which they have mean absolute deviations of 2.10 and 1.64 kcal/mol, respectively. On all of the other types of energies the G3 and G3X methods are very reliable. The G3/05 test set is also used to assess density-functional methods including a series of new functionals. The most accurate functional for the G3/05 test set is B98 with a mean absolute deviation of 3.33 kcal/mol, compared to 4.14 kcal/mol for B3LYP. The latter functional has especially large errors for larger molecules with a mean absolute deviation of 9 kcal/mol for molecules having 28 or more valence electrons. For smaller molecules B3LYP does as well or better than B98 and the other functionals. It is found that many of the density-functional methods have significant errors for the larger molecules in the test set.
First-in-human phase I study of the antiangiogenic vaccine (OTS11101) targeting VEGFR-1 in patients with solid tumors. (2011)

2568 Background: OTS11101 is a novel peptide vaccine which acts as an angiogenesis inhibitors by specifically targeting vascular endothelial cells with vascular endothelial growth factor receptor (VEGFR)-1 expressing target by inducing cytotoxic T cell lymphocyte (CTL). The objectives of this phase I study is to evaluate the safety, tolerability, maximum tolerated dose (MTD), and pharmacodynamics of this agent. Methods: Nine patients with advanced solid tumors received OTS11101 1.0 mg/ml, 2.0 mg/ml, or 3.0 mg/ml subcutaneously once a week of a 28-day cycle. Also, we explored the induction of specific activated CTL, and the alternation of the serum concentration of VEGFR-1 and VEGFR-2, and various kinds of cytokines. Results: Three patients were enrolled in each dose level, respectively. A total of three patients experienced the reaction of injection site of grade 1, which was the most frequent adverse event in this study. As the other toxicities were also generally mild, MTD was not reached. No objective response was observed, but five had stable disease. According to the biomarker analysis, induction of specific CTL was observed in both levels of 2.0 mg/ml and 3.0 mg/ml, respectively. Conclusions: OTS11101 was well tolerated in patients with advanced tumors up to 3.0 mg/ml once a week. Further investigations are recommended to confirm efficacy of the vaccine.
Residues Comprising the Enhanced Aromatic Sequon Influence Protein N-Glycosylation Efficiency (2017)

N-Glycosylation is an important co- and/or post-translational modification that occurs on the vast majority of the one-third of the mammalian proteome that traverses the cellular secretory pathway, regulating glycoprotein folding and functions. Previous studies on the sequence requirements for N-glycosylation have yielded the Asn-X-Ser/Thr (NXS/T) sequon and the enhanced aromatic sequons (Phe-X-Asn-X-Thr and Phe-X-X-Asn-X-Thr), which can be efficiently N-glycosylated. To further investigate the influence of sequence variation on N-glycosylation efficiency in the context of a five-residue enhanced aromatic sequon, we used the human CD2 adhesion domain (hCD2ad) to screen the i-2, i-1, i+1, and i+2 residues flanking Asn at the i position. We found that aromatic residues, especially Trp, and sulfur-containing residues at the i-2 position improved N-glycosylation efficiency, while positively charged residues such as Arg suppressed N-glycosylation. Thiol, hydroxyl, and aliphatic-based side chains at the i-1 position had higher N-glycosylation efficiency, and Cys, in particular, compensated for the negative effect of Arg at the i-2 position. Small residues and Ser at the i+1 position increased the likelihood of N-glycosylation, and Thr is better than Ser at the i+2 position. We devised an algorithm for prediction of N-glycosylation efficiency using the SAS software, employing the 120 sequences studied as a training set. We then introduced the optimized-enhanced aromatic sequons into other glycoproteins and observed an enhancement in N-glycan occupancy that was further supported by modeling the high-affinity interaction between the optimized sequence on hCD2ad and a human oligosaccharyltransferase (OST) subunit. The findings in this study provide useful information for enhancing or suppressing N-glycosylation at a site of interest and valuable data for a better understanding of OST-catalyzed N-glycosylation.
Low Viscosity Retarded Acid System: A Novel Alternative to Emulsified Acids (2018)

Abstract Acid systems are widely recognized by the oil and gas industry as an attractive class of fluids for efficient stimulation of carbonate reservoirs. One of the major challenges in carbonate acidizing treatments is adjusting the convective transport of acid deep into the reservoir while achieving a minimum rock face dissolution. Conventional emulsified acids are hindered by several limitations; low stability at high temperatures, a high viscosity that limits pumping rate due to frictional losses, the potential of formation damage, and the difficulty to achieve homogenous field-scale mixing. The objective of this paper is to introduce an engineered low-viscosity retarded acid system without the need for gelation by a polymer or surfactant, or emulsification by diesel. The proposed acid system combines the use of a strong mineral acid (i.e. hydrochloric acid "HCl") with an organic compound that is highly soluble in the acid. It is based on reducing the free water in the system and, consequently, restricting the ionic separation of the proton from the acid. This results in a retardation behavior that is necessary to maintain a controlled reaction for the system used. The retardation behavior testing includes dissolution experiments, compatibility testing (using X-Ray Diffraction "XRD" and inductively coupled plasma "ICP"), coreflood study (at rates of 2 and 5 cm3/min at 300°F and 3000 psi) and corrosion rate testing (conducted at 300°F). Finally, a reaction kinetics analysis (at disc rotational speeds of 250 rpm, 500 rpm, 700 rpm and 1500 rpm) was performed to evaluate the retarded acid performance. The new acid system showed 4 times reduction in the core weight loss due to dissolution in acid compared to plain 15wt% HCl. XRD and Computed Tomography (CT) scans illustrated the acid compatibility with dolomite by forming no precipitation that is attributed to the organic compound used in the system. The proposed acid can create a dominant wormhole pattern requiring only 0.53 Pore Volume (PV) of acid to achieve breakthrough in the Indiana limestone core. It is important to note that emulsified acids require 0.8 PV of fluid compared to 1.4 PV for 15 wt.% HCl acid package. The proposed system was determined to have negligible corrosion rate of 0.002 lb/ft2 after 4 hours exposure at 300°F. Reaction kinetics study proved the delayed acid reaction with calcite by an order of magnitude compared to 32 wt.% HCl. Conventional emulsified acids require expensive energization, through nitrogen (N2) or carbon dioxide (CO2), to overcome frictional losses and meet high injection rates requirement for fracturing and stimulation in deep formations. This novel system is characterized by having a low-viscosity and high thermal stability system that can be mixed on the fly. This approach addresses the main challenges of emulsified acid systems and will offer a cost-effective solution to cover a wide range of applications in matrix or fracturing applications, and high-temperature conditions that require a thermally-stable acid system.
Systematic Design and Experimental Demonstration of Transmission‐Type Multiplexed Acoustic Metaholograms (2021)

Abstract Acoustic holograms have promising applications in sound‐field reconstruction, particle manipulation, ultrasonic haptics, and therapy. This study reports on the theoretical, numerical, and experimental investigation of multiplexed acoustic holograms at both audio and ultrasonic frequencies via a rationally designed transmission‐type acoustic metamaterial. The proposed metahologram is composed of two Fabry–Pérot resonant channels per unit cell, which enables the simultaneous modulation of the transmitted amplitude and phase at two desired frequencies. In contrast to conventional acoustic metamaterial‐based holograms, the design strategy proposed here provides a new degree of freedom (frequency) that can actively tailor holograms that are otherwise completely passive and significantly enhances the information encoded in acoustic metamaterials. To demonstrate the multiplexed acoustic metamaterial, the projection of two different high‐quality metaholograms is first shown at 14 and 17 kHz, with the patterns of the letters N and S. Then, two‐channel ultrasound focusing and annular beams generation for the incident ultrasonic frequencies of 35 and 42.5 kHz are demonstrated. These multiplexed acoustic metaholograms offer a technical advance to tackle the rising challenges in the fields of acoustic metamaterials, architectural acoustics, and medical ultrasound.
Search for neutral Higgs bosons of the minimal supersymmetric standard model in pp collisions at s = 8 $$ \sqrt{s}=8 $$ TeV with the ATLAS detector (2014)

A search for the neutral Higgs bosons predicted by the Minimal Supersymmetric Standard Model (MSSM) is reported. The analysis is performed on data from proton-proton collisions at a centre-of-mass energy of 8 TeV collected with the ATLAS detector at the Large Hadron Collider. The samples used for this search were collected in 2012 and correspond to integrated luminosities in the range 19.5-20.3 fb -1 . The MSSM Higgs bosons are searched for in the final state. No significant excess over the expected background is observed, and exclusion limits are derived for the production cross section times branching fraction of a scalar particle as a function of its mass. The results are also interpreted in the MSSM parameter space for various benchmark scenarios.
Evidence that a 'memory' for glucose metabolism desensitizes A-cell responsiveness in the perfused pancreas of the rat (1985)

A-cell sensitivity to glucose is diminished and enhanced by prior fuel abundance and deprivation, respectively. Such effects could be due to persisting changes in A-cell energy availability rather than to pertubations in insulin or somatostatin secretion.
Information Fusion for Diabetic Retinopathy CAD in Digital Color Fundus Photographs (2009)

The purpose of computer-aided detection or diagnosis (CAD) technology has so far been to serve as a second reader. If, however, all relevant lesions in an image can be detected by CAD algorithms, use of CAD for automatic reading or prescreening may become feasible. This work addresses the question how to fuse information from multiple CAD algorithms, operating on multiple images that comprise an exam, to determine a likelihood that the exam is normal and would not require further inspection by human operators. We focus on retinal image screening for diabetic retinopathy, a common complication of diabetes. Current CAD systems are not designed to automatically evaluate complete exams consisting of multiple images for which several detection algorithm output sets are available. Information fusion will potentially play a crucial role in enabling the application of CAD technology to the automatic screening problem. Several different fusion methods are proposed and their effect on the performance of a complete comprehensive automatic diabetic retinopathy screening system is evaluated. Experiments show that the choice of fusion method can have a large impact on system performance. The complete system was evaluated on a set of 15,000 exams (60,000 images). The best performing fusion method obtained an area under the receiver operator characteristic curve of 0.881. This indicates that automated prescreening could be applied in diabetic retinopathy screening programs.