gebhart/patrepeval huggingface dataset:
tmVar: a text mining approach for extracting sequence variants in biomedical literature (2013)

tmVar software and its corpus of 500 manually curated abstracts are available for download at http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/pub/tmVar
POCS-based restoration of space-varying blurred images (1994)

We propose a new method for space-varying image restoration using the method of projection onto convex sets (POCS). The formulation allows the use of a different blurring function at each pixel of the image in a computationally efficient manner. We illustrate the performance of the proposed approach by comparing the new results with those of the ROMKF method on simulated images. We also present results on a real-life image with unknown space-varying out-of-focus blur.
Tumor-derived matrix metalloproteinase-13 (MMP-13) correlates with poor prognosis of invasive breast cancer (2008)

Tumor-derived, but not stromal fibroblast-derived, MMP-13 correlated with aggressive tumor phenotypes, and inversely correlated with the overall survival of breast cancer patients. MMP-13 may serve as an independent prognostic factor for invasive breast cancer patients. MMP-13 may be particularly useful as a prognostic marker when evaluated along with Her-2/neu and lymph node status.
MR-guided focused ultrasound surgery, present and future (2013)

MR-guided focused ultrasound surgery (MRgFUS) is a quickly developing technology with potential applications across a spectrum of indications traditionally within the domain of radiation oncology. Especially for applications where focal treatment is the preferred technique (for example, radiosurgery), MRgFUS has the potential to be a disruptive technology that could shift traditional patterns of care. While currently cleared in the United States for the noninvasive treatment of uterine fibroids and bone metastases, a wide range of clinical trials are currently underway, and the number of publications describing advances in MRgFUS is increasing. However, for MRgFUS to make the transition from a research curiosity to a clinical standard of care, a variety of challenges, technical, financial, clinical, and practical, must be overcome. This installment of the Vision 20∕20 series examines the current status of MRgFUS, focusing on the hurdles the technology faces before it can cross over from a research technique to a standard fixture in the clinic. It then reviews current and near-term technical developments which may overcome these hurdles and allow MRgFUS to break through into clinical practice.
Cycle slip tolerant hybrid turbo differential decoding (2014)

We experimentally investigate the cycle slip tolerance of an enhanced Turbo Differential Decoding algorithm in nonlinear transmission. Error-free post-FEC measurements using a 100G QPSK DWDM module show excellent tolerance against cycle slips without a differential encoding penalty.
COX2 Activity Promotes Organic Osmolyte Accumulation and Adaptation of Renal Medullary Interstitial Cells to Hypertonic Stress (2003)

The mechanism by which COX2 inhibition decreases renal cell survival is poorly understood. In the present study we examined the effect of COX2 activity on organic osmolyte accumulation in renal medulla and in cultured mouse renal medullary interstitial cells (MMICs) and its role in facilitating cell survival. Hypertonicity increased accumulation of the organic osmolytes inositol, sorbitol, and betaine in cultured mouse medullary interstitial cells. Pretreatment of MMICs with a COX2-specific inhibitor (SC58236, 10 micromol/liter) dramatically reduced osmolyte accumulation (by 79 +/- 9, 57 +/- 12, and 96 +/- 10% for inositol, sorbitol, and betaine respectively, p < 0.05). Similarly, 24 h of dehydration increased inner medullary inositol, sorbitol, and betaine concentrations in vivo by 85 +/- 10, 197 +/- 28, and 190 +/- 24 pmol/microg of protein, respectively, but this increase was also blunted (by 100 +/- 5, 66 +/- 15, and 81 +/- 9% for inositol, sorbitol, and betaine, respectively, p < 0.05) by pretreatment with an oral COX2 inhibitor. Dehydrated COX2-/- mice also exhibited an impressive defect in sorbitol accumulation (88 +/- 9% less than wild type, p < 0.05) after dehydration. COX2 inhibition (COX2 inhibitor-treated or COX2-/- MMICs) dramatically reduced the expression of organic osmolyte uptake mechanisms including betaine (BGT1) and sodium-myo-inositol transporter and aldose reductase mRNA expression under hypertonic conditions. Importantly, preincubation of COX2 inhibitor-treated MMICs with organic osmolytes restored their ability to survive hypertonic stress. In conclusion, osmolyte accumulation in the kidney inner medulla is dependent on COX2 activity, and providing exogenous osmolytes reverses COX2-induced cell death. These findings may have implications for the pathogenesis of analgesic nephropathy.
Gated multiplanar cardiac computed tomography. (1982)

Multiplanar reformatting was combined with electrocardiographically gated computed tomography (CT) to provide a three-dimensional assessment of the beating heart of a live dog. Separate systolic and diastolic images were made in transverse, sagittal, coronal, and paraxial views. Three-dimensional contour images that outlined the cardiac chambers and the myocardium were then made using a separate research computer. This three-dimensional appreciation of cardiac morphology could be extended to assess regional function. Practical problems that limit the application of these methods are discussed, along with the proposed solutions.
The B subunit of Shiga toxin coupled to full-size antigenic protein elicits humoral and cell-mediated immune responses associated with a Th1-dominant polarization (2003)

A number of studies in animal models and humans have shown that both humoral andcell-mediated immune responses play an important role in the control of viral infection and tumor development. In most cases, vaccination with non-vectorized peptides or proteins induces low antibody responses and fails to elicit specific cytotoxic T lymphocytes (CTL). In order to make vaccination more efficient, we chemically coupled the non-toxic B subunit of Shiga toxin (STxB) to a full-size antigenic model protein, ovalbumin (OVA), yielding STxB-OVA. We found that STxB-OVA delivers OVA-derived peptides into both the MHC class I- and II-restricted presentation pathways in mouse dendritic cells. Accordingly, the study of STxB trafficking in these cells revealed that, after internalization, a fraction of STxB followed the retrograde transport pathway to the endoplasmic reticulum, while another fraction was targeted to late endosomes/lysosomes. Vaccination of mice with STxB-OVA primed a specific anti-OVA CTL response without the use of adjuvants. Splenocytes and, particularly, CD4(+) T cells from mice immunized with STxB-OVA also produced higher amounts of the T(h)1 cytokine IFN-gamma and IgG2a-type antibodies than mice immunized with non-vectorized ovalbumin. In conclusion, this study identifies a unique non-live vaccine delivery system for polyepitopic antigens that elicits antigen-specific CTL, a humoral immune response and a T(h)1-type polarization without the use of adjuvant.
Implementation of a Parallel Algorithm for Protein Pairwise Alignment Using Reconfigurable Computing (2006)

This paper describes the design and implementation of a parallel pairwise alignment hardware, implemented in a FPGA device. This system is aimed at aligning pairs of proteins, using a dynamic programming algorithm. The alignment is done in parallel thanks to a pipelined approach. All functional blocks are described in detail. Experiments were done to access the performance of the system for up to pairs of 2000-amino acids-long proteins. Hardalign was compared with a similar algorithm implemented in software and running in a PC, resulting in a 1:10 speed-up ratio. Results encourage the continuity of the work, showing that reconfigurable computing can offer interesting solutions for bioinformatics problems.
Susceptibility gradient quantization by MRI signal response mapping (SIRMA) to dephaser (2010)

The proposed method is a promising technique for a wide range of applications especially in molecular or cellular imaging with respect to its quantitative nature and its computational simplicity.
Special Modified Silazanes for Coatings, Fibers and CMC'S (2008)

Tailored precursors in the systems Si-C-N(Ti) were synthesized for various appli- cations by different reaction types by using the same two chlorosilanes. For the liquid phase infiltration (LP1)-process coammonolysis of CH3Cl2SiH and CH3Cl2SiCH=CH2 leads to a liquid cross-linkable precursor with a high ceramic yield (75 %) after pyrolysis at 1400°C. Therefore, this precursor is excellent as matrix source for CMCs. Hydrosilylation of the chlorosilanes as the first step and subsequent ammonolysis result in a meltable solid (∼ 100°C). This precursor was produced in a pilot plant and continuously meltspun to fibers with small diameters (∼ 20 μm). Curing of the polymer fibers and subsequent pyrolysing at 1000°C (N2) lead to non-oxide SiCN fibers. The liquid SiCN precursor modified by organometallic compounds (e.g. Ti(NR2)4) results in unmeltable but soluble solids. These polymers are suitable for applications as inorganic polymer-, and at higher temperatures, as ceramic-like-coatings (CLC). With corresponding precursor solutions different substrates (metals, ceramics, glass, plastics) with complex-shaped geometry can be coated by using simple dip- and spray-coating techniques. In all cases the adhesion to the substrate is very strong. Selected results from the research areas mentioned above are presented in order to illustrate the potential of these silazane-based materials, with particular emphasis on the latest results of coating investigations.
WHICH PROCESS TO FREE RARE EARTHS FROM RAW MONAZITE ORE (1959)

A caustic soda process and a sulfuric acid process for separating rare earths and thorium compounds from monazite ore are discussed in relation to flexibilities of the processes, drawbacks, and separation procedures. (C.J.G.)
Effects on proliferation and melanogenesis by inhibition of mutant <i>BRAF</i> and expression of wild‐type <i>INK4A</i> in melanoma cells (2005)

Activating BRAF mutations and loss of wild-type INK4A expression both occur at high frequencies in melanomas. Here, we present evidence that BRAF and INK4A have different effects on melanogenesis, a marker of melanocytic differentiation. Human melanoma cell line 624Mel harbors mutations in both BRAF and INK4A. The in vitro and in vivo growth of these cells was inhibited by either reduced expression of mutant BRAF using stable retroviral RNA interference (RNAi) or retrovirus-mediated stable expression of wild-type INK4A cDNA. Consistent with the observed growth inhibition, phosphorylation of S780 and S795 in pRB, both CDK4/6 targets, was suppressed in cells expressing either mutant BRAF RNAi or wild-type INK4A. Interestingly, melanoma cells expressing mutant BRAF RNAi had increased pigmentation, produced more mature melanosomes and melanin and expressed higher levels of tyrosinase and tyrosinase-related protein-1, whereas melanogenesis was not induced by wild-type INK4A. We found that the melanocyte lineage-specific master control protein microphthalmia-associated transcription factor was upregulated by inhibition of mutant BRAF, which may be the cause for the melanogenic effect of BRAF RNAi. The results suggest that, although both BRAF and INK4A lesions promote cell growth and tumor formation, mutant BRAF may also induce dedifferentiation in melanoma cells.
THE REACTION OF BENZOYL CHLORIDE WITH CERTAIN ALIPHATIC ORTHO ESTERS AND ACETALS (1936)

ADVERTISEMENT RETURN TO ISSUEArticleNEXTTHE REACTION OF BENZOYL CHLORIDE WITH CERTAIN ALIPHATIC ORTHO ESTERS AND ACETALSHOWARD W. POSTCite this: J. Org. Chem. 1936, 01, 3, 231–235Publication Date (Print):July 1, 1936Publication History Published online1 May 2002Published inissue 1 July 1936https://pubs.acs.org/doi/10.1021/jo01232a001https://doi.org/10.1021/jo01232a001research-articleACS PublicationsRequest reuse permissionsArticle Views324Altmetric-Citations20LEARN 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
Electronic Commerce Modeling Language (ECML): Version 2 Requirements (2003)

This document lists the design principles, scope, and requirements for the Electronic Commerce Modeling Language (ECML) version 2 specification. It includes requirements as they relate to Extensible Markup Language (XML) syntax, data model, format, and payment processing.
Causal temporal order in HCI (2011)

This paper proposes applying principles of human causal reasoning to graphical interface design to make interfaces more intuitive. In particular, we present a design guideline for making graphical interfaces consistent with causal temporal order and demonstrate its effectiveness in an experiment where participants solve a puzzle with a novel interface. We also present preliminary results of its application to a text formatting task and propose several other causal principles that are directly applicable to interface design.
Sentire: A Framework for Building Middleware for Sensor and Actuator Networks (2005)

Sentire represents a framework for building extensible middleware for sensor and actuator networks (SANET). The fundamental principle behind Sentire is the partitioning of SANET middleware into logically related components in order to allow developers of different aspects of the middleware to share a common plug-in infrastructure where their developed artifacts can interact. In this paper, an extended introduction of Sentire is presented, followed by a practical illustration of how this framework can be used to build SANET middleware.
Advanced CIM environment for manufacturing data analysis (2003)

An environment for performing complex analyses of semiconductor manufacturing processes and IC products is described. This innovative analysis toolset has increased the productivity of product engineering, process engineering and design organizations by providing a method for complex manufacturing data reduction without the need for exhaustive training. The interactive, forms-based interface utility has also provided significant reductions in the time required to isolate parameters and identify relationships that significantly influence manufacturing yields. The foundation of the system is the internally developed, Unix-based Manufacturing and Engineering Data Base (MEDB). MEDB is a fully automated system for collecting and loading in-line manufacturing parameters and sample probe, wafer probe, and package test data from a variety of equipment platforms.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Effect of Recent Changes in Atomic Bomb Survivor Dosimetry on Cancer Mortality Risk Estimates (2004)

The Radiation Effects Research Foundation has recently implemented a new dosimetry system, DS02, to replace the previous system, DS86. This paper assesses the effect of the change on risk estimates for radiation-related solid cancer and leukemia mortality. The changes in dose estimates were smaller than many had anticipated, with the primary systematic change being an increase of about 10% in gamma-ray estimates for both cities. In particular, an anticipated large increase of the neutron component in Hiroshima for low-dose survivors did not materialize. However, DS02 improves on DS86 in many details, including the specifics of the radiation released by the bombs and the effects of shielding by structures and terrain. The data used here extend the last reported follow-up for solid cancers by 3 years, with a total of 10,085 deaths, and extends the follow-up for leukemia by 10 years, with a total of 296 deaths. For both solid cancer and leukemia, estimated age-time patterns and sex difference are virtually unchanged by the dosimetry revision. The estimates of solid-cancer radiation risk per sievert and the curvilinear dose response for leukemia are both decreased by about 8% by the dosimetry revision, due to the increase in the gamma-ray dose estimates. The apparent shape of the dose response is virtually unchanged by the dosimetry revision, but for solid cancers, the additional 3 years of follow-up has some effect. In particular, there is for the first time a statistically significant upward curvature for solid cancer on the restricted dose range 0-2 Sv. However, the low-dose slope of a linear-quadratic fit to that dose range should probably not be relied on for risk estimation, since that is substantially smaller than the linear slopes on ranges 0-1 Sv, 0-0.5 Sv, and 0- 0.25 Sv. Although it was anticipated that the new dosimetry system might reduce some apparent dose overestimates for Nagasaki factory workers, this did not materialize, and factory workers have significantly lower risk estimates. Whether or not one makes allowance for this, there is no statistically significant city difference in the estimated cancer risk.
Surface modification of polypropylene sheets by UV‐radiation grafting polymerization (2005)

Abstract 1,6‐Hexanediol diacrylate (HDDA) was grafted onto polypropylene (PP) substrates in the presence of benzophenone (BP) and isopropylthioxanthone (ITX) photoinitiators, and then polyurethane acrylate formulations were coated onto the HDDA‐ g ‐PP substrates, using UV radiation. The amount grafted and the grafting efficiency of the polymerizations were determined gravimetrically. The effects of the photoinitiator concentration and the UV radiation intensity on the physicochemical surface properties and the grafting efficiency of the UV‐radiation grafting polymerizations were characterized in detail using contact‐angle measurements, Fourier transform infrared spectroscopy with attenuated total internal reflection, and scanning electron microscopy. The results showed that the amount grafted and the surface polarity of the HDDA‐ g ‐PP substrates both increased linearly with increasing BP photoinitiator concentration and UV radiation intensity, and that the addition of a small amount of ITX markedly enhanced both parameters, probably due to photosensitization. The adhesion of the UV‐cured coating onto the HDDA‐ g ‐PP substrates was evaluated using the crosshatch adhesion test. The results indicated that the amount of HDDA grafted onto the PP substrates should exceed about 1 mmol/cm 2 for satisfactory adhesion with the UV‐cured coating. © 2005 Wiley Periodicals, Inc. J Appl Polym Sci 99: 1446–1461, 2006
Self-calibration of a differential wheeled robot using only a gyroscope and a distance sensor (2015)

Research in mobile robotics often demands platforms that have an adequate balance between cost and reliability. In the case of terrestrial robots, one of the available options is the GNBot, an open-hardware project intended for the evaluation of swarm search strategies. The lack of basic odometry sensors such as wheel encoders had so far difficulted the implementation of an accurate high-level controller in this platform. Thus, the aim of this thesis is to improve motion control in the GNBot by incorporating a gyroscope whilst maintaining the requisite of no wheel encoders. Among the problems that have been tackled are: accurate in-place rotations, minimal drift during linear motions, and arc-performing functionality. Additionally, the resulting controller is calibrated autonomously by using both the gyroscope module and the infrared rangefinder on board each robot, greatly simplifying the calibration of large swarms. The report first explains the design decisions that were made in order to implement the self-calibration routine, and then evaluates the performance of the new motion controller by means of off-line video tracking. The motion accuracy of the new controller is also compared with the previously existing solution in an odor search experiment.
Superstructure Evolution in Poly(ethylene terephthalate) during Uniaxial Deformation above Glass Transition Temperature (2006)

The evolution of superstructure and its relationship with the phase transition during uniaxial deformation of poly(ethylene terephthalate) (PET) at temperatures (90 and 100 °C) above its glass transition temperature were investigated by in-situ small-angle X-ray scattering (SAXS) and wide-angle X-ray diffraction (WAXD). It appears that deformation at lower temperatures enhances the metastability of mesophase but narrows the strain window for phase transition. Very similar superstructure evolution pathways were observed at both temperatures. In zone I (the plastic deformation zone), WAXD did not show any crystal diffraction peak; however, SAXS exhibited an equatorial streak at the later stage, indicating the formation of a microfibrillar structure. Strain hardening took place in zone II, which could be categorized in two substages. In zone II-a, SAXS showed an X-shaped pattern that coincided with the appearance of crystal diffraction peaks in WAXD. The initial X-shaped patterns possessed strong intensity near the beam stop; the later patterns exhibited a scattering maximum that shifted toward larger angles with increasing strain. Results indicated the formation of a tilted lamellar structure within the microfibrils in conjunction with lamellar insertion. In zone II-b, oval spots appeared at the edges of the X-shaped pattern, which essentially became four-point. In this stage, the crystallinity still increased linearly with strain, but the invariant gradually reached an asymptotic value, indicating that lamellar insertion took place at a slower rate. In the final strain-hardening zone (III), the load became linear with strain even though crystallization was reduced. The equatorial long period was found to decrease drastically, suggesting that some microfibrils were split. In addition, a two-point pattern appeared near the central streak, corresponding to a periodic structure with long period of 100 nm. The formation of such a large layered structure and the microfibrillar splitting can be attributed to structural defects such as kinks in microfibrils.
Agent technology in communications systems: an overview (1999)

Telecommunications infrastructures are a natural application domain for the distributed software agent paradigm. The authors clarify the potential application of software agent technology in legacy and future communications systems, and provide an overview of publicly available research on software agents used for communications management. The authors focus on the intelligent agent type of software agent, although the paper also reviews the reasons why mobile agents have made an impact in this domain. The author's objective is to describe some of the intricacies of using the software agent approach for the management of communications systems. The paper is in four main sections. The first section provides a brief introduction to software agent technology. The second section considers general problems of network management and the reasons why software agents may provide a suitable solution. The third section reviews some selected research on agents in a telecommunications management framework. The final section concludes the paper by discussing some of the problems encountered and some future directions for further research.