gebhart/patrepeval huggingface dataset:
Methylation-Specific PCR (2008)

Methylation-specific polymerase chain reaction (MSP) is a technique that has facilitated the detection of promoter hypermethylation at CpG islands in cell lines and clinical samples, including fresh/frozen tissues. The ability of MSP to differentiate methylated from unmethylated cytosine is dependent upon sodium bisulfite treatment of DNA which retains the methylation marks of cytosines together with the specific amplification of this modified DNA using primer sets complimentary only to the formerly methylated or unmethylated alleles. Nested-MSP (MN-MSP) is an alternative method that overcomes the limitations of MSP, especially when it comes to analyzing samples with low quality/quantity of starting DNA (e.g., paraffin-embedded specimens). MN-MSP includes a first round of amplification using primers unbiased toward the methylation status of a single (MN-MSP) or multiple (multiplex MN-MSP) genes followed by conventional MSP. Although MSP and NM-MSP are simple techniques that can easily be incorporated in most molecular biology laboratories, the ability to accurately determine the promoter methylation status of genes largely depends upon the careful design of MSP primers as well as other steps outlined in this chapter.
Feasibility investigation of Fabry-Perot Interferometer as Weigh-in-Motion Sensor (2006)

Fiber Fabry-Perot interferometer application in weight-in-motion sensor is presented. Sensors embedded in metal bars show linear dependence on axial displacement; and consistently reproduced the expected characteristics of truck wheel crossings in road tests.
Sub-nanosecond single line-of-sight (SLOS) x-ray imagers (invited) (2018)

A new generation of fast-gated x-ray framing cameras have been developed that are capable of capturing multiple frames along a single line-of-sight with 30 ps temporal resolution. The instruments are constructed by integrating pulse-dilation electron imaging with burst mode hybrid-complimentary metal-oxide-semiconductor sensors. Two such instruments have been developed, characterized, and fielded at the National Ignition Facility and the OMEGA laser. These instruments are particularly suited for advanced x-ray imaging applications in Inertial Confinement Fusion and High energy density experiments. Here, we discuss the system architecture and the techniques required for tuning the instruments to achieve optimal performance. Characterization results are also presented along with planned future improvements to the design.
Data from Histone Deacetylase HDAC8 Promotes Insulin Resistance and β-Catenin Activation in NAFLD-Associated Hepatocellular Carcinoma (2023)

&lt;div&gt;Abstract&lt;p&gt;The growing epidemic of obesity, which causes nonalcoholic fatty liver disease (NAFLD) and the more severe phenotype nonalcoholic steatohepatitis (NASH), has paralleled the increasing incidence of hepatocellular carcinoma (HCC). Accumulating evidence demonstrates that overnutrition and metabolic pathways can trigger modifications of DNA and histones via deregulation of chromatin modifiers, resulting in aberrant transcriptional activity. However, the epigenetic regulation of HCC development in NAFLD remains obscure. Here, we uncover key epigenetic regulators using both dietary and genetic obesity-promoted HCC models through quantitative expression profiling and characterize the oncogenic activities of histone deacetylase HDAC8 in NAFLD-associated hepatocarcinogenesis. HDAC8 is directly upregulated by the lipogenic transcription factor SREBP-1 where they are coexpressed in dietary obesity models of NASH and HCC. Lentiviral-mediated HDAC8 attenuation &lt;i&gt;in vivo&lt;/i&gt; reversed insulin resistance and reduced NAFLD-associated tumorigenicity. HDAC8 modulation by genetic and pharmacologic approaches inhibited p53/p21-mediated apoptosis and G&lt;sub&gt;2&lt;/sub&gt;–M phase cell-cycle arrest and stimulated β-catenin–dependent cell proliferation. Mechanistically, HDAC8 physically interacted with the chromatin modifier EZH2 to concordantly repress Wnt antagonists via histone H4 deacetylation and H3 lysine 27 trimethylation. In human NAFLD-associated HCC, levels of SREBP-1, HDAC8, EZH2, H4 deacetylation, H3K27me3, and active β-catenin were all correlated positively in tumors compared with nontumor tissues. Overall, our findings show how HDAC8 drives NAFLD-associated hepatocarcinogenesis, offering a novel epigenetic target to prevent or treat HCC in obese patients. &lt;i&gt;Cancer Res; 75(22); 4803–16. ©2015 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Light-extraction enhancement of vertical-injection GaN-based light-emitting diodes fabricated with highly integrated surface textures (2008)

We report on the fabrication of high-efficiency vertical-injection GaN-based light-emitting diodes (LEDs) fabricated with integrated surface textures. An optical ray-tracing simulation shows that the high integration of surface textures can effectively enhance the light-extraction efficiency. The integrated surface textures are fabricated on the top surface of LEDs by generating hexagonal cones on the periodically corrugated surfaces of n-GaN. Compared to reference LEDs without textures, LEDs fabricated with integrated surface textures show an enhancement of the output power by a factor of 2.59, which is in agreement with the calculated results.
A bio-orthogonal functionalization strategy for site-specific coupling of antibodies on vesicle surfaces after self-assembly (2019)

Attaching targeting ligands on the surface of self-assembled drug delivery systems is one of the key requests for a controlled transport of the drug to a desired location.
Quantitative Analysis of Microstructure of Self-Reinforced Silicon Nitride Ceramics (1993)

β-Si3N4 powders containing 0.5mol% Y2O3 and 0.5mol% Nd2O3 were gas-pressure sintered at 2000°C for 2, 4, and 8h. The obtained materials presented the microstructure of self-reinforced composites consisting of some large rod-like grains in a fine matrix, as it was observed by scanning electron microscopy of plasma-etched surfaces. Two-dimensional distributions of grain diameter, grain length, and cross-sectional area were quantitatively analyzed using an image analyzer. The distribution curve of grain number and grain cross-sectional area did not reflect the presence of large grains, and therefore this method is not suitable for evaluation of self-reinforced materials. The volume fractions of large grains and fine matrix grains were estimated from the relation between the grain size and the two-dimentional distribution curve of grain cross-sectional area.
Supplementary Figure from Perioperative Influenza Vaccination Reduces Postoperative Metastatic Disease by Reversing Surgery-Induced Dysfunction in Natural Killer Cells (2023)

&lt;p&gt;PDF file, 190K, Prophylactic vaccines enhance NK cell cytotoxicity.&lt;/p&gt;
Profitable deployment of regenerators as traffic grows in WDM elastic networks featuring 32/64 GBaud carriers (2018)

We investigate the progressive regenerator deployment throughout traffic growth in two WDM core networks, by illustrating how this strategy is more profitable with 64 GBaud Elastic Optical Transponders (EOT) than with 32 GBaud EOTs.
Matrix-isolation studies of the iron/cyclopentadiene system: infrared detection of cyclopentadienyliron hydride (1985)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMatrix-isolation studies of the iron/cyclopentadiene system: infrared detection of cyclopentadienyliron hydrideDavid W. Ball, Zakya H. Kafafi, Robert H. Hauge, and John L. MargraveCite this: Inorg. Chem. 1985, 24, 22, 3708–3710Publication Date (Print):October 1, 1985Publication History Published online1 May 2002Published inissue 1 October 1985https://doi.org/10.1021/ic00216a049Request reuse permissionsArticle Views178Altmetric-Citations16LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (410 KB) Get e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Ethanol (2011)

The article contains sections titled: 1. Introduction 2. Physical Properties 3. Chemical Properties 4. Synthesis 4.1. Direct Catalytic Hydration of Ethylene 4.1.1. Chemistry 4.1.2. Catalysts 4.1.3. Production Process 4.2. Indirect Hydration of Ethylene 4.2.1. Chemistry 4.2.2. Production Process 4.3. Other Methods 4.3.1. Homologation of Methanol 4.3.2. Carbonylation of Methanol and Methyl Acetate 4.3.3. Conversion of Synthesis Gas 4.3.3.1. Synthesis by Heterogeneous Catalysis 4.3.3.2. Synthesis by Homogeneous Catalysis 5. Fermentation 5.1. Production by Yeast 5.1.1. Nutrients 5.1.2. Fermentation Pathways 5.1.3. Fermentation Variables 5.1.4. Direct Fermentation 5.2. Production by Bacteria 5.2.1. Ethanol Tolerance 5.2.2. Fermentation of Glucose by Z. mobilis 5.2.3. Fermentation of Other Sugars by Recombinant Z. mobilis Strains 5.2.4. Ethanol Production by Recombinant Enterobacteria 5.2.5. Comparison of Recombinant Bacterial Strains 5.3. Fermentation Modes 5.3.1. Batch Processes 5.3.2. Continuous Processes 5.3.3. Other Processes 5.4. Raw Materials and Processes 5.4.1. Readily Fermentable Carbohydrates 5.4.2. Starch 5.4.3. Lignocellulosic Materials 5.4.4. Waste Materials and Residues 6. Recovery and Purification 6.1. Distillation 6.1.1. Distillation of Azeotropic Ethanol 6.1.2. Dehydration by Azeotropic Distillation 6.1.3. Motor Fuel Ethanol 6.1.4. Reduction of Energy Costs 6.2. Nondistillative Methods 6.2.1. Solvent Extraction 6.2.2. Carbon Dioxide Extraction 6.2.3. Adsorptive Dehydration 6.2.4. Membrane Technology 6.2.5. Yarn-Filled Column 6.3. Storage and Transportation 7. Comparison of Process Economics for Synthetic and Fermentation Ethanol 7.1. Summary of Cost Analysis for Synthetic and Fermentation Ethanol 7.2. Production Costs of Synthetic Ethanol 7.3. Production Costs of Fermentation Ethanol 8. Analysis 9. Uses 10. Economic Aspects 10.1. Worldwide Production of Synthetic and Fermentation Ethanol 10.2. Major Producers of Fermentation Ethanol from Regenerable Resources 11. Toxicology
Phosphorylation of theStreptococcus pneumoniaecell wall biosynthesis enzyme MurC by a eukaryotic-like Ser/Thr kinase (2012)

Streptococcus pneumoniae contains a single Ser/Thr kinase-phosphatase pair known as StkP-PhpP. Here, we report the interaction of StkP-PhpP with S. pneumoniae UDP-N-acetylmuramoyl:L-alanine ligase, MurC, an enzyme that synthesizes an essential intermediate of the cell wall peptidoglycan pathway. Combinatorial phage display using StkP as target selected the peptide sequence YEVCGSDTVGC as an interacting partner and subsequently confirmed by ELISA. The phage peptide sequence YEVCGSDTVGC aligns closely with the MurC motif spanning S. pneumoniae amino acid coordinates 31-37. We show that MurC is phosphorylated by StkP and that phosphoMurC is dephosphorylated by PhpP. These data suggest a link between StkP-PhpP with the coordinated regulation of cell wall biosynthesis via MurC.
P3‐079: INVESTIGATING DIAGNOSTIC BIOMARKERS OF COGNITIVE IMPAIRMENT BY UTILIZING VASCULAR AND NEUROGENIC CHANGES IN THE RETINA (2018)

Previous studies have demonstrated that Alzheimer's disease (AD) it is not limited to the brain but also affects the retina. We investigated the correlation between the retinal vascular complexity and neurodegenerative changes in patients with mild cognitive impairment (MCI). Quantification of the retinal structure and function using advanced retinal imaging and full-field electroretinogram (ERG) was performed. Also, visual performance exams were conducted using the Rabin cone contrast test (CCT). Retinal images and ERGs from each subject were obtained. Retinal vascular parameters were calculated using the Singapore Institute Vessel Assessment (SIVA) software which was also used to calculate the fractal dimension (FD) of the retinal vasculature network and retinal vascular caliber, summarized as central retinal artery equivalent (CRAE) and central retinal vein equivalent (CRVE). The Montreal Cognitive Assessment (MoCA) was used to assess cognitive dysfunction. Spearman's linear correlation was performed between variables, the level of significance was set at 5%. For the analysis, Statistics 7.0 software was used (Statsoft Inc., Tulsa, OK). Of the 55 participants, 21 had cognitive impairment (38%), 34 served as healthy controls. We found that the complexity of the branching pattern and caliber of retinal vessels were lower in patients with MCI (FD (mean±SE): 1.310±0.020; CRVE (92.65±1.60; age range [76-86]) in comparison to healthy controls (FD: 1.382±0.002; CRVE: 202.15±0.76; age range [76-86]). Also, drusen and retinal pigment mottling were noted in some elderly MCI subjects. For all full-field ERG measurements, smaller amplitudes and larger peak times were observed in the MCI subjects. The visual performance test with the computerized Rabin CCT revealed functional loss in color vision. Interestingly, FD significantly correlated with CRVE (p=0.0212, r=-0.4628) and with the ERG's implicit time (p=0.0240, r=0.4910) in MCI individuals. To our knowledge, this is the first study to examine the association between FD and full field ERG implicit time in patients with MCI. Our preliminary findings also show that our approach to evaluating visual capacities in elderly individuals may add predictive value of early visual pathway injury associated with MCI and facilitate the introduction of a novel multimodal eye biomarker for the early detection of AD.
The Impact of MEMS on the Chemical and Pharmaeutical Industries (2000)

Microfabrication techniques are increasingly used in different fields of chemistry to realize structures with capabilities exceeding those of conventional macroscopic systems. In addition to already demonstrated analysis applications (j.tTAS), MEMS microreactor systems are expected to have a number of advantages for chemical synthesis, chemical kinetics studies, and process development. Current efforts in microfabrication and application of microchemical systems are reviewed.
Investigating the Cyclic Bending of PCB Subassembly During Board Level Drop Test (2006)

The dynamic responses of printed circuit boards (PCBs) mounted with thin-profile fine-pitch BGA (TFBGA) packages under board level drop tests were investigated. Data captured during the tests include accelerations, in-plane strains and in-situ change in solder joint resistance. PCBs were mounted on the drop table using either 4-screw or 6-screw supports. A high-speed charge-coupled device (CCD) camera was used to capture the drop impact process. The PCB bending modes, frequency, velocities before and after impact, impact duration, and deflection were derived from the high-speed photographs. The results are consistent with the measured strain and acceleration. In-situ solder joint resistance is monitored using an oscilloscope. In-situ resistance measurement is important as a solder joint crack may close up again after the impact. For the 4- and 6-screw supports, the in-plane strains are found to be similar, but the flexural frequency and failure rate of the solder joints are different. This is attributed to the bending of the PCB that resulted in solder joint failure.
Characterization of SiO<sub>2</sub>/4H-SiC Interface by Device Simulation and Temperature Dependence of On-Resistance of SiC MOSFET (2014)

MOS interface traps are characterized by device simulation on the basis of temperature dependence of lateral MOS-TEG devices on the same Al-implanted p-type region as vertical device. The simulation shows fairly large D it in SiO 2 /4H-SiC interface, corresponding to the suggested trap density inside the conduction band. Temperature dependence of on-resistance is explained by application of evaluated interface properties to calculation of current voltage properties of vertical DMOSFET.
CAD-model recognition and 6DOF pose estimation using 3D cues (2011)

This paper focuses on developing a fast and accurate 3D feature for use in object recognition and pose estimation for rigid objects. More specifically, given a set of CAD models of different objects representing our knoweledge of the world - obtained using high-precission scanners that deliver accurate and noiseless data - our goal is to identify and estimate their pose in a real scene obtained by a depth sensor like the Microsoft Kinect. Borrowing ideas from the Viewpoint Feature Histogram (VFH) due to its computational efficiency and recognition performance, we describe the Clustered Viewpoint Feature Histogram (CVFH) and the cameras roll histogram together with our recognition framework to show that it can be effectively used to recognize objects and 6DOF pose in real environments dealing with partial occlusion, noise and different sensors atributes for training and recognition data. We show that CVFH out-performs VFH and present recognition results using the Microsoft Kinect Sensor on an object set of 44 objects.
Characterization of Reaction Products and Mechanisms between Serotonin and Methylglyoxal in Model Reactions and Mice (2020)

Serotonin is an important endogenous regulatory neurotransmitter and has also been found in fruits, vegetables, and nuts. Methylglyoxal (MGO) is a reactive dicarbonyl metabolite and also a food toxin that modifies protein and DNA to cause the development of many chronic diseases. The objective of this study is to understand the reaction mechanisms between serotonin and MGO and determine whether serotonin could trap MGO <i>in vivo</i>. Five products were detected in phosphate buffer (pH 7.4) at 37 °C. Four products (compounds <b>2</b> and <b>4</b>-<b>6</b>) were purified from the reaction mixture, and their structures were characterized by the analysis of their high-resolution mass and one- and two-dimensional nuclear magnetic resonance spectra. One product (compound <b>3</b>), as a result of its instability, could not be properly purified and was tentatively characterized on the basis of its high-resolution mass spectrum and corresponding mass fragments. On the basis of the structures of these five products, two reaction pathways were proposed. Compounds <b>2</b>, <b>3</b>, <b>5</b>, and <b>6</b> were produced through the Pictet-Spengler condensation pathway between the primary amine of serotonin and the ketone of MGO, and compound <b>3</b> was identified as the intermediate product to form products <b>2</b>, <b>5</b>, and <b>6</b>, whereas compound <b>4</b> was formed through nucleophilic substitution by the benzene ring of serotonin, which is a new reaction pathway between biogenic amines and reactive carbonyl species. More importantly, the detection of adducts <b>2</b> and <b>4</b>-<b>6</b> in mice supports our hypothesis that the reaction between serotonin and MGO also happens <i>in vivo</i> through the same pathways as those in model reactions, suggesting that dietary or endogenous serotonin has the capacity to trap MGO <i>in vivo</i>.
Prospective comparison of various radiological response criteria and pathological response to preoperative chemotherapy and survival in operable high-grade soft tissue sarcomas in the Japan Clinical Oncology Group study JCOG0304 (2018)

UMIN Clinical Trials Registry C000000096. Registered 30 August, 2005 (retrospectively registered).
Three-Dimensional Printing of Highly Stretchable and Tough Hydrogels into Complex, Cellularized Structures (2015)

A 3D printable and highly stretchable tough hydrogel is developed by combining poly(ethylene glycol) and sodium alginate, which synergize to form a hydrogel tougher than natural cartilage. Encapsulated cells maintain high viability over a 7 d culture period and are highly deformed together with the hydrogel. By adding biocompatible nanoclay, the tough hydrogel is 3D printed in various shapes without requiring support material.
Validation of Pre-operative Templating for Total Disc Replacement Surgery (2019)

FE analyses accurately predicted ROM in this cohort and can facilitate selection of the optimal implant size and location that we believe will increase the chance of achieving clinical success with the application of this technology.
Improving Cancer Immunotherapy by Targeting the Hypoxic Tumor Microenvironment: New Opportunities and Challenges (2019)

Initially believed to be a disease of deregulated cellular and genetic expression, cancer is now also considered a disease of the tumor microenvironment. Over the past two decades, significant and rapid progress has been made to understand the complexity of the tumor microenvironment and its contribution to shaping the response to various anti-cancer therapies, including immunotherapy. Nevertheless, it has become clear that the tumor microenvironment is one of the main hallmarks of cancer. Therefore, a major challenge is to identify key druggable factors and pathways in the tumor microenvironment that can be manipulated to improve the efficacy of current cancer therapies. Among the different tumor microenvironmental factors, this review will focus on hypoxia as a key process that evolved in the tumor microenvironment. We will briefly describe our current understanding of the molecular mechanisms by which hypoxia negatively affects tumor immunity and shapes the anti-tumor immune response. We believe that such understanding will provide insight into the therapeutic value of targeting hypoxia and assist in the design of innovative combination approaches to improve the efficacy of current cancer therapies, including immunotherapy.