gebhart/patrepeval huggingface dataset:
Methylation Analysis by DNA Immunoprecipitation (MeDIP) (2009)

Alteration in epigenetic regulation of gene expression is a common event in human cancer and developmental disease. CpG island hypermethylation and consequent gene silencing is observed for many genes involved in a diverse range of functions and pathways that become deregulated in the disease state. Comparative profiling of the methylome is therefore useful in disease gene discovery. The ability to identify epigenetic alterations on a global scale is imperative to understanding the patterns of gene silencing that parallel disease progression. Methylated DNA immunoprecipitation (MeDIP) is a technique that isolates methylated DNA fragments by immunoprecipitating with 5'-methylcytosine-specific antibodies. The enriched methylated DNA can then be analyzed in a locus-specific manner using PCR assay or in a genome-wide fashion by comparative genomic hybridization against a sample without MeDIP enrichment. This article describes the detailed protocol for MeDIP and hybridization of MeDIP DNA to a whole-genome tiling path BAC array.
The Synthesis of Peptides of L-Glutamine by the Carbobenzoxy Azide Method<sup>1</sup> (1954)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe Synthesis of Peptides of L-Glutamine by the Carbobenzoxy Azide Method1Ernest Sondheimer and Robert W. HolleyCite this: J. Am. Chem. Soc. 1954, 76, 10, 2816–2818Publication Date (Print):May 1, 1954Publication History Published online1 May 2002Published inissue 1 May 1954https://pubs.acs.org/doi/10.1021/ja01639a063https://doi.org/10.1021/ja01639a063research-articleACS PublicationsRequest reuse permissionsArticle Views170Altmetric-Citations25LEARN 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 InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Microcrystalline diamond deposition using a combustion flame of acetylene and oxygen with a magnetic field (1991)

Microcrystalline diamonds were successfully deposited on an abraded molybdenum surface under a magnetic field using a combustion flame of acetylene (C2H2) and oxygen (O2) gases. The deposition rate was about 1 μm/min, which is an order larger than that obtained by conventional chemical-vapor-deposition methods. The magnetic field led to an increase of the deposited area and of the microcrystal diameter. The microcrystals show good crystallinity as observed from scanning electron microscopy, reflective electron diffraction, and x-ray diffraction measurements.
A phase I/II dose escalation study of apolizumab (Hu1D10) using a stepped-up dosing schedule in patients with chronic lymphocytic leukemia and acute leukemia (2009)

Apolizumab (Hu1D10), a humanized monoclonal anti- Human leukocyte antigen -DR beta-chain antibody, mediates apoptosis of chronic lymphocytic leukemia (CLL) cells in vitro. We conducted a phase I/II dose-escalation study of thrice-weekly apolizumab (1.5, 3.0, 5.0 mg/kg/dose) for 4 weeks in relapsed CLL. Two of six patients at 5.0 mg/kg/dose developed treatment-related dose-limiting toxicity (aseptic meningitis, hemolytic uremia). Other toxicities included infusion toxicity, urticaria, and headache. Eleven patients were enrolled in a phase I/II expansion to evaluate the maximum tolerated dose (MTD) of 3.0 mg/kg/dose. In total, 23 patients were enrolled (22 CLL, 1 ALL). Nineteen patients with CLL were treated at or above the MTD. One partial response was observed, and three patients had stable disease exceeding 6 months. Pharmacokinetic analysis demonstrated a dose-dependent C(max) increase and serum antibody accumulation after week 1 of therapy. Given the toxicity and lack of efficacy in this and other trials in lymphoma and solid tumors, further development of apolizumab was discontinued.
Analysis of genes encoding D-alanine-D-alanine ligase-related enzymes in Enterococcus casseliflavus and Enterococcus flavescens (1994)

Using degenerate oligonucleotides complementary to sequences encoding conserved amino acid motifs in D-alanine-D-alanine (Ddl) ligases, we have amplified ca. 600-bp fragments from Enterococcus casseliflavus ATCC 25788 and Enterococcus flavescens CCM439. Sequence analysis of the amplification products indicated that each strain possessed two genes, ddlE. cass. and vanC-2, and ddlE. flav. and vanC-3, respectively, encoding Ddl-related enzymes. The fragments internal to the vanC genes were 98.3% identical. The vanC-2 gene was cloned into Escherichia coli and sequenced. Extensive similarity (66% nucleotide identity) was detected between this gene and vanC-1 from Enterococcus gallinarum (S. Dutka-Malen, C. Molinas, M. Arthur, and P. Courvalin, Gene 112:53-58, 1992), suggesting that the vanC genes are required for intrinsic low-level resistance to vancomycin. The partial deduced amino acid sequences of ddlE. cass. and ddlE. flav. were identical and closely related to that of the Ddl ligase of Enterococcus faecalis (79% identity). In Southern hybridization experiments, only DNA from E. casseliflavus and E. flavescens hybridized to probes internal to the vanC-2 and ddlE. cass. genes.
High-resolution seismic geomorphology and stratigraphy of a tunnel valley confined ice-margin fan (Elsterian glaciation, Southern North Sea) (2016)

The deep Middle Pleistocene subglacial incisions of the Southern North Sea (SNS) are commonly infilled by northward gently dipping clinoforms oriented toward the former ice-sheet core. We have focused on the terminal sector of the largest tunnel valley (TV) of the SNS and offer the first high-resolution reconstruction of the geomorphology and stratigraphy of the infill of the glacial incision, as well as the detailed geomorphology of the incision to better understand the genetic mechanisms of these uncommon but peculiar large-scale (up to 13 km in length) bedforms. For this study, high-resolution 3D seismic data, the grain-size distribution from ditch cutting samples, and the gamma-ray wireline log of borehole K14-12 are used. The TV formed in the subglacial environment by steady state flows in a time-transgressive fashion. Meltwater flow transports the eroded material southward and eventually deposits it at the ice-sheet margin, in the lightly grounded ice-sheet environment where the adverse slope forces the flow to wane. The process results in an elongated ice-margin fan made of clinoforms, whose grain-size distribution fines progressively southward, in the downstream direction. The formation and filling of the TV occurred during the retreat of the ice-sheet margin and cyclic fluctuations of the meltwater mass flow rate, which affected the internal stratigraphy and created an undulated top of the clinoforms’ unit. Sparsely distributed, horizontally layered units interpreted as distal proglacial lacustrine deposits filled depressions on the top of the clinoforms-bearing unit. The sequence was then sealed by a chaotic seismic-stratigraphic unit that probably belongs to postglacial times. The ice-sheet-oriented clinoforms were thus formed by sustained meltwater flow resulting from large-size Scandinavian and British convergent ice sheet flows in the freshwater environment of SNS developed between the complex ice margins and the topographic highs inherited from continental Europe.
Femtosecond pulses from coherently combined parallel chirped pulse fiber amplifiers (2011)

Active coherent combining of femtosecond pulses from parallel chirped-pulse fiber amplifiers is demonstrated. This opens a new path for simultaneously increasing both energy and average power of ultrashort pulses from fiber based systems.
An efficient online path profiling framework for Java just-in-time compilers (2004)

Collecting hot paths is important for restructuring and optimizing the target program effectively. It is, however, challenging for just-in-time (JIT) compilers, which must collect path profiles on the fly at runtime. Here, we propose an efficient online path profiling technique, called structural path profiling (SPP), suitable for JIT compilers. The key idea is to partition the target method into a hierarchy of the nested graphs based on the loop structure, and then to profile each graph independently. With SPP, we can collect accurate path profiles efficiently with low overhead. The experimental results show that our technique can collect path profiles with an accuracy of around 90% compared to the offline complete path profiles, while it incurs only 2-3% overhead on average in the active profiling phase.
Heterochronic Mutants of the Nematode <i>Caenorhabditis elegans</i> (1984)

Mutations in the Caenorhabditis elegans genes lin-14, lin-28, and lin-29 cause heterochronic developmental defects: the timing of specific developmental events in several tissues is altered relative to the timing of events in other tissues. These defects result from temporal transformations in the fates of specific cells, that is, certain cells express fates normally expressed by cells generated at other developmental stages. The identification and characterization of genes that can be mutated to cause heterochrony support the proposal that heterochrony is a mechanism for phylogenetic change and suggest cellular and genetic bases for heterochronic variation.
Separation of absorption and scattering properties of turbid media using relative spectrally resolved cw radiance measurements (2012)

We present a new method for extracting the effective attenuation coefficient and the diffusion coefficient from relative spectrally resolved cw radiance measurements using the diffusion approximation. The method is validated on both simulated and experimental radiance data sets using Intralipid-1% as a test platform. The effective attenuation coefficient is determined from a simple algebraic expression constructed from a ratio of two radiance measurements at two different source-detector separations and the same 90° angle. The diffusion coefficient is determined from another ratio constructed from two radiance measurements at two angles (0° and 180°) and the same source-detector separation. The conditions of the validity of the method as well as possible practical applications are discussed.
X-ray Microscopy and Microtomography (2013)

It has been almost a decade since the first special issue on X-ray microscopy, organized by Günter Schmahl (SRN, Vol. 16, No. 3, 2003). That was a time of rapid expansion of scanning X-ray microscopes (STXM) and transmission microscopes (TXM). The special issue included articles on soft X-ray microscopes at BESSYII, ALS, NSLS, Aarhus, Ritsumeikan, Elettra, and on hard X-ray microscopes at ESRF, SPring-8, and the APS. Most of these instruments used zone plates to achieve high resolution, have thrived ever since, and many more have come on-line. Microscopes are now operating, or being commissioned at almost every light source around the world. X-ray microscopy has become a broadly utilized technique, with journal articles describing results appearing almost weekly. There are even commercial suppliers selling X-ray microscopes to be used at light sources, or at any home laboratory. There is a specialized International Conference on X-ray Microscopy that is held every two years, with the most recent one held in Shanghai in August 2012. Several review articles provide an overview of the field [1 Kaulich, B., Thibault, P., Gianoncelli, A. and Kiskinova, M. 2011. J. Phys: Condens. Matter, 23: 083002[Crossref] , [Google Scholar]–5 Spence, J., Weierstall, U. and Chapman, H. 2012. Rep. Prog. Phys., 75: 102601[Crossref], [PubMed] , [Google Scholar]].
SiteRank-Based Crawling Ordering Strategy for Search Engines (2007)

Search engines are playing a more and more important role in discovering information nowadays. Due to limitations of time-consuming, network bandwidth and hardwares, we cannot obtain the whole information on the Web and have to download important information first. In this paper we propose a novel crawling ordering strategy which is based on SiteRank. Experimental results running on over 15 million pages indicate that it can work efficiently in discovering important pages under the PageRank evaluation of page quality. Furthermore, it exhibits the ability of anti-spamming.
The efficiency and efficacy of IVF and GIFT (1991)

Data relating to the rate of clinical pregnancy obtained with in-vitro fertilization--embryo transfer (IVF-ET) and gamete intra-Fallopian transfer (GIFT) are available for Australia, UK, USA and France. For IVF-ET the value is not affected by the indication but is affected by the age of the woman. The rate of spontaneous abortion, at approximately 20-25% also increases with age and is an important consideration in view of the increased age of patients undergoing IVF-ET. A take-home baby rate of 30% is obtained from an estimated 70% of clinical pregnancies leading to live births and an estimate of 42.8% pregnancies after three attempts. The greater number of oocytes transferred with GIFT may be associated with the increased frequency of multiple pregnancies.
Prevention of Hydrogen Embrittlement in Steels (2016)

The essential facts about the nature of the hydrogen embrittlement of steels have now been known for 140 years. It is diffusible hydrogen that is harmful to the toughness of iron. It follows, therefore, that the harmful influence of diffusible hydrogen can be mitigated by preventing its entry into steel or by rendering it immobile once it penetrates the material. This review deals with the methods that might be implemented to design steels and components that resist hydrogen embrittlement by reducing the intake of hydrogen or rendering it innocuous when it does penetrate the steel.
Effects of alkyl substitutions of xanthine skeleton on bronchodilation (1992)

Structure-activity relationships in a series of 1,3,7-trialkyl-xanthine were studied with guinea pigs. Relaxant actions in the tracheal muscle were increased with alkyl chain length at the 1- and 3-positions of the xanthine skeleton, but decreased by alkylation at the 7-position. Positive chronotropic actions in the right atrium were potentiated with 3-alkyl chain length but tended to decrease with 1-alkylation and diminish by 7-substitution. Consequently, while the 1- and 3-substitutions were equally important for the tracheal smooth muscle relaxation, the substitution at the 1-position was more important than the 3-substitution for bronchoselectivity. The 7-alkylation may be significant to cancel heart stimulation. There were good correlations between the smooth muscle relaxant action and the cyclic AMP-PDE inhibitory activity in 3-substituents and the affinity for adenosine (A1) receptors in 1-, 3-, and 7-substituents. This suggests that not only the cyclic AMP-PDE inhibitory activity but also the adenosine antagonistic activity is important in the bronchodilatory effects of alkylxanthines. Among these xanthine derivatives, 1-butyl-3-propylxanthine and its 7-methylated derivative showed high bronchoselectivity in the in vitro and in vivo experiments compared to theophylline and enprofylline and may be new candidates for bronchodilator.
Thermodynamic Vapor Cycles for Converting Low- to Medium-grade Heat to Power: A State-of-the- art Review and Future Research Pathways (2014)

The moderate temperature of renewable energy sources and vast amounts of industrial waste heat demands implementing other thermodynamic heat to power cycles than the conventional power cycle. Various thermodynamic cycles for converting low-grade heat into power have been developed, in which the major ones are: zeotropic vapor cycle, organic Rankine cycle, Trilateral Flash cycle, supercritical Rankine cycle. This study serves the state-of-the-art review of thermodynamic vapor cycles for converting the low-grade heat into electrical power and present recommendations for future research and development to advance the conversion of low- to medium-grade heat to power.
Training and performance assessment of land mine detector operator using motion tracking and virtual mine lane (2000)

Landmine detection is a complex and highly dangerous task. Most demining operations are done using hand-held detectors, which means that the operator is always at risk of serious injury or death. One of the most important factor that determines the probability of detecting is the operator performance. Therefore, it is very important that we train the operator well and are able to assess their performance accurately. To achieve these objectives, we have been developing two training tools, the 3D tracker for real-time feedback during training, and the virtual mien lane for interactive training. We have been using the 3D tracker successfully to assess the performance of an operator as a prat of a successful training program.
IDENTIFICATION OF CYTOPLASMIC BASOPHILIA (RIBONUCLEIC ACID) BY FLUORESCENCE MICROSCOPY (1956)

1. The fluorochrome, acridin orange (AO), allows identification of basophilic cytoplasmic inclusions in the supravital state. 2. The fluorescence picture of hepatic cells after treatment with AO shows the hyaloplasm faint gray-green; flake-like or granular structures in the cytoplasm, bright red; the nuclei, with chromatin structures, green; the central part of the nucleoli red, their periphery green. 3. The red-fluorescent cytoplasmic inclusions correspond to those observed with the toluidine-blue technique, and shown, by the RNase test, to consist mainly of RNA. The same is demonstrated by the changes of AO fluorescence after application of RNase to fresh or fixed tissues. 4. The fluorescence picture given by other cell elements and tissues in the rat liver is described. 5. Changes in the AO fluorescence of liver tissue with varying pH, dye concentration, staining time, action of salts, prolonged U.V. illumination, fixation, as well as the fluorescence of some biologically important substances (RNA, DNA, heparin, albumin, glycogen), treated with AO, are indicated. 6. The advantages and limitations of the method, and the theories of AO staining are discussed. 7. As compared to conventional histochemical methods, the applicability to living or supravital tissues of the fluorochrome technique decreases errors due to fixation, dehydration, embedding and related procedures, and the low concentrations applied in fluorochrome staining further safeguard against histochemical artifacts.
A New Tire Model with an Application in Vehicle Dynamics Studies (1989)

<div class="htmlview paragraph">The behaviour of the tyre plays an important role in controlling the horizontal motion of the vehicle. In vehicle dynamics studies, a good representation of tyre behaviour is therefore a necessity. A series of tyre measurements have been carried out on the road in stationary conditions. The data obtained have been represented by mathematical expressions on the basis of a formula. The coefficients in the formula represent some of the typifying quantities of the tyre and the formula is capable of describing all characteristics of side force, brake force and self aligning torque with great accuracy. The behaviour of the tyre during combined cornering and braking has successfully been described by a model which makes use of the obtained mathematical expressions and some tyre-modelling theory. The side force characteristic governs the behaviour in lateral direction and the brake force characteristic in longitudinal direction. Thus, the non-isotropic properties of the tyre have been taken into account. Influences of ply steer, conicity, rolling resistance and camber are included as well. In this way a new and compact empirical model is obtained, enabling sensitivity studies to be performed. Vehicle dynamics studies have been carried out with the aid of simulations including the new model. This paper is a result of a joint project between Volvo Car Corporation, Sweden and the Delft University of Technology, The Netherlands.</div>
Expression of collagens I, II, X, and XI and aggrecan mRNAs by bovine growth plate chondrocytes <i>in situ</i> (1994)

The cells responsible for skeletal growth are the chondrocytes of the cartilaginous growth plate. These cells differentiate through a series of maturational stages, establishing different zones in the growth plate. Among the major functions of these cells is the production of appropriate extracellular matrix, primarily composed of collagens and proteoglycans. To determine whether matrix synthesis varies with respect to maturational stage and in which cell populations different collagens are expressed, bovine growth plates were analyzed by in situ hybridization to mRNA and by Northern blot hybridization. The most abundant collagen mRNA in the growth plate was type-II collagen. This mRNA was present at relatively low levels in the most immature cells of the growth plate but increased several-fold as cells entered the proliferative stage and remained high through subsequent phases of maturation. Type-XI collagen mRNA and mRNA for the cartilage-characteristic proteoglycan, aggrecan, were codistributed with the type-II collagen mRNA; however, both were present in much smaller quantities. Type-X procollagen mRNA was localized to chondrocytes late in their maturation and was expressed at levels similar to the expression of type-II collagen. In situ hybridization of serial sections revealed that growth plate chondrocytes in their more mature stages contain both type-II and type-X collagen mRNA. Type-I collagen mRNA was not observed in growth plate chondrocytes at any maturational stage; rather, it was localized to a morphologically distinct population of cells attached to calcifying cartilage septa in the region of vascular invasion.(ABSTRACT TRUNCATED AT 250 WORDS)
Screened Poisson Equation for Image Contrast Enhancement (2014)

In this work we propose a discussion and detailed implementation of a very simple gradient domain method that tries to eliminate the effect of nonuniform illumination and at the same time preserves the images details. This model, which to the best of our knowledge has not been explored in spite of its simplicity, acts as a high pass filter. We show that with a single contrast parameter (which keeps the same value in most experiments), the model delivers state of the art results. They compare favorably to results obtained with more complex algorithms. Our algorithm is designed for all kinds of images, but with the special specification of making minimal image detail alteration thanks to a first order fidelity term, instead of the usual zero order term. Experiments on non-uniform medical images and on hazy images illustrate significant perception gain.