gebhart/patrepeval huggingface dataset:
Expression of dystroglycan correlates with tumor grade and predicts survival in renal cell carcinoma (2007)

The dystroglycan (DG) complex is a transmembrane glycoprotein that forms a continuous link from the extracellular matrix to the actin cytoskeleton. Deregulated expression of DG has been reported in a variety of human malignancies and related to tumor aggressiveness. In this study expression of the DG subunit was evaluated by immunostaining in a series of renal epithelial cancers and its relation with traditional prognostic indicators and with the clinical outcome of the patients was evaluated. alphaDG expression was undetectable in a significant fraction of tumors (54%). In renal cell carcinomas (RCC) loss of alpha-DG staining correlated with higher tumor grade (p = 0.02) but not with tumor stage nor tumor size. In clear cell RCC patients loss of alphaDG staining correlated with an increased risk of recurrence (p = 0.002 by log-rank test) and death (p = 0.004) also when patients with lower grade or stage tumors were analyzed separately. In a multivariate analysis loss of DG staining confirmed to be and independent predictor of shorter disease-free (p = 0.001; RR = 4.9) and overall (p = 0.009; RR = 4.9) survival stronger than tumor grade and size. These findings demonstrate that loss of alphaDG expression, which correspond to loss of a functional DG complex, is a frequent event in human renal tumorigenesis and is an independent predictor of early recurrence and death for patients with clear cell RCC.
Thermotropic Hydrocarbon Liquid Crystalline Monomers and Model Compounds (1988)

Abstract A versatile synthesis of hydrocarbon liquid crystalline monomers and model compounds has been developed. The general formula of the monomers is . Some of these compounds are 1iquid crystal1ine at room temperature and generally exhibit smectic B phases. A synthetic modification allows the preparation of model compounds with the general formula Several of these latter compounds are liquid crystalline and exhibit well defined smectic mesophases. Data obtained from differential scanning calorimetry, polarized light optical microscopy and X-ray diffraction are discussed.
Dual farnesoid X receptor/TGR5 agonist INT-767 reduces liver injury in the Mdr2 −/− ( Abcb4 −/−) mouse cholangiopathy model by promoting biliary HCO Symbol output (2011)

This study shows that FXR activation improves liver injury in a mouse model of chronic cholangiopathy by reduction of biliary BA output and promotion of HCO 3--rich bile secretion.
Different Signaling Pathways Stimulate a Disintegrin and Metalloprotease-17 (ADAM17) in Neutrophils during Apoptosis and Activation (2011)

ADAM17 is a membrane-associated metalloprotease that cleaves proteins from the surface of neutrophils and modulates the density of various receptors and adhesion molecules. The protease activity of ADAM17 is highly inducible and occurs upon neutrophil activation as well as apoptosis. At this time, little is known about the signal transduction pathway that promotes ADAM17 activity in neutrophils upon the induction of apoptosis. We show that caspase-8 activation, Bid cleavage, and the release of mitochondrial reactive oxygen species are sequential transduction components of the Fas signaling cascade that induces ADAM17. This is different from ADAM17 stimulation upon overt neutrophil activation, which requires MAPK p38 or ERK, but not caspases and reactive oxygen species. ADAM17 activity in apoptotic neutrophils may serve to inactivate select effector molecules that promote the pro-inflammatory activity of recruited neutrophils. For instance, TNFα receptors TNF-RI and TNF-RII are substrates of ADAM17, and we show that they are shed during apoptosis, decreasing neutrophil sensitivity to TNFα. Altogether, our findings provide significant new insights into the signal transduction pathway that stimulates ADAM17 during induced neutrophil apoptosis. ADAM17 induction during apoptosis may rapidly diminish neutrophil sensitivity to the inflammatory environment, complementing other anti-inflammatory activities by these cells during inflammation resolution.
A fully automated design of binary decision tree for land cover classification (2002)

A fully automated design method of binary decision tree is proposed for land cover classification of remote sensing data. The proposed method has the following features: (1) all possible binary combinations of identification classes are tested as splitting pattern of classes; (2) additional variables by linear combination of paired bands are applied in data segmentation; (3) automatic interaction detector technique is utilized to divide the data set into binary tree nodes. Completely enumerated Landsat MSS data with land-cover data are used for the test of the method and classification accuracy. The authors' new method is compared with Bayesian discriminant classifier in terms of accuracy and training sample set sizes.
Model for<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" id="M1"><mml:mrow><mml:mrow><mml:mi>B</mml:mi></mml:mrow><mml:mrow><mml:mn>1</mml:mn></mml:mrow></mml:mrow></mml:math>Imaging in MRI Using the Rotating RF Field (2014)

Conventionally, magnetic resonance imaging (MRI) is performed by pulsing gradient coils, which invariably leads to strong acoustic noise, patient safety concerns due to induced currents, and costly power/space requirements. This modeling study investigates a new silent, gradient coil-free MR imaging method, in which a radiofrequency (RF) coil and its nonuniform field (B 1 (+)) are mechanically rotated about the patient. The advantage of the rotating B 1 (+) field is that, for the first time, it provides a large number of degrees of freedom to aid a successful B 1 (+) image encoding process. The mathematical modeling was performed using flip angle modulation as part of a finite-difference-based Bloch equation solver. Preliminary results suggest that representative MR images with intensity deviations of <5% from the original image can be obtained using rotating RF field approach. This method may open up new avenues towards anatomical and functional imaging in medicine.
An economical solution to the cache coherence problem (1984)

In this paper we review and qualitatively evaluate schemes to maintain cache coherence in tightly-coupled multiprocessor systems. This leads us to propose a more economical (hardware-wise), expandable and modular variation of the “global directory” approach. Protocols for this solution are described. Performance evaluation studies indicate the limits (number of processors, level of sharing) within which this approach is viable.
Impacts of application lookahead on distributed network emulation (2013)

Large-scale and high-fidelity testbeds play critical roles in analyzing large-scale networks such as data centers, cellular networks, and smart grid control networks. Our prior work combines parallel simulation and virtual-time-integrated emulation, such that it offers both functional and temporal fidelity to the critical software execution in large scale network settings. To achieve better scalability, we have developed a distributed emulation system. However, as the number of computing servers grows, so does too the synchronization overhead. Application lookahead, the ability to predict future behaviors of software, may help reducing overhead for performance gain. In this paper, we study the impacts of application lookahead on our distributed emulation testbed. We find that application lookahead can greatly reduce synchronization overhead and improve speed by up to 3 times in our system, but incorrect lookahead may affect application fidelity to different degrees, depending on application sensitivity to timing.
An iterative maximum-likelihood polychromatic algorithm for CT (2001)

A new iterative maximum-likelihood reconstruction algorithm for X-ray computed tomography is presented. The algorithm prevents beam hardening artifacts by incorporating a polychromatic acquisition model. The continuous spectrum of the X-ray tube is modeled as a number of discrete energies. The energy dependence of the attenuation is taken into account by decomposing the linear attenuation coefficient into a photoelectric component and a Compton scatter component. The relative weight of these components is constrained based on prior material assumptions. Excellent results are obtained for simulations and for phantom measurements. Beam-hardening artifacts are effectively eliminated. The relation with existing algorithms is discussed. The results confirm that improving the acquisition model assumed by the reconstruction algorithm results in reduced artifacts. Preliminary results indicate that metal artifact reduction is a very promising application for this new algorithm.
<title>Ultrasonic imaging of corrosion and fatigue cracks in multilayered airplane structures</title> (1996)

Application of ultrasonic imaging to the inspection of multilayered airplane structures can provide comprehensive information on possible defects such as corrosion and cracks. A quantitative assessment of defects in internal layers of airplane structures using this technique can be accomplished form an external surface of the airplane skin. No disassembly is required for component evaluation. Therefore this ultrasonic technique can be extremely useful for cost-effective maintenance of airplanes. Three different ultrasonic techniques developed for inspection of the DC-9 and DC-10 airplanes are discussed in this paper. One of the techniques was used for evaluation of corrosion and stress corrosion cracks in a DC-9 tee cap, other techniques have been developed for fatigue crack characterization in a DC-9 rear spar and a DC-10 spar-cap/strap connection, respectively. All three techniques were developed to be applied with the same type of data acquisition and imaging system. However for each kind of flaw and structural configuration substantial modifications of the scanning and the data acquisition procedures have been made. {Peculiarities of each ultrasonic technique will be discussed. The ultrasonic technique for the inspection of the DC-9 tee cap has been approved by the FAA as an alternate means of compliance to meet the requirements of the DC-9 Service Bulletin.
Detection of Serum p53 Protein in Lung Cancer Patients (1994)

Serum levels of p53 protein were examined in 23 cases of lung cancer (many with potential asbestos exposure), 23 unexposed matched hospital control subjects, 58 unmatched general population control subjects, and 4 people with nonmalignant lung disease using an enzyme-linked immunosorbent assay and Western immunoblotting. Average levels of serum p53 in the lung cancer patients (0.55 ng/mL) were higher than in the cases of nonmalignant lung disease (0.42 ng/mL) or in the matched (0.32 ng/mL) or unmatched (0.31 ng/mL) control subjects, but the differences were not statistically significant. However, three of the cases of lung cancer (13%) were found to have serum p53 levels much greater than those of the control subjects (> 2 SD above the mean) and to have confirmatory positive Western blots for p53. The tumors from these subjects demonstrated increased levels of p53 in the tissue by immunohistochemistry and/or the presence of mutations in the p53 gene. These results suggest that p53 protein can be detected in serum in a portion of lung cancer cases with p53 alterations in the tumor tissue.
Antenna research at the Communications Research Centre (1996)

An overview is presented of the antenna research carried out by the Directorate of Antennas and Integrated Electronics (DAIE) of the Communications Research Centre (CRC). The antenna research within the DAIE can be categorized into two groups: antenna-hardware development and electromagnetic-software development. Research in antenna hardware has focused on printed multi-layer arrays, dielectric-resonator antennas, ferrite antennas, active-circuit integration, and low-loss feed networks. Research in electromagnetic software includes the development of three-dimensional transmission-line-matrix (TLM) code, and the application of cellular automata (CA) techniques for the analysis and modeling of antennas, microwave circuits, and general electromagnetic phenomena, such as scattering. This article concentrates on the antenna-hardware research and development within the DAIE. Radiation patterns are considered.
A Review of Condensation Frosting (2016)

The accretion of ice and frost on various infrastructure is ubiquitous in cold and humid environments, causing economic losses amounting to billions of dollars every year worldwide. The past couple of decades have seen unprecedented advances in the fields of surface chemistry and micro/nanofabrication, enabling the development of hydrophobic and superhydrophobic surfaces that promote facile deicing and/or passive anti-icing. However, in the light of new discoveries regarding the incipient stages of frost formation, it is becoming increasingly clear that the problems of icing and frosting are not one and the same. Thus, passive anti-icing strategies do not exhibit anti-frosting behavior, and the development of passive anti-frosting surfaces remains an unsolved problem. In this review, we provide a critical discussion of condensation frosting and show how the emerging new phenomena of frost halos, interdroplet ice bridges, and dry zones that comprise the incipient stages of frosting set it apart from the conventional problem of icing. Subsequently, we discuss possible strategies to break the sequential chain of events leading to pervasive frost growth.
Bioinformatic and experimental survey of 14-3-3-binding sites (2010)

More than 200 phosphorylated 14-3-3-binding sites in the literature were analysed to define 14-3-3 specificities, identify relevant protein kinases, and give insights into how cellular 14-3-3/phosphoprotein networks work. Mode I RXX(pS/pT)XP motifs dominate, although the +2 proline residue occurs in less than half, and LX(R/K)SX(pS/pT)XP is prominent in plant 14-3-3-binding sites. Proline at +1 is rarely reported, and such motifs did not stand up to experimental reanalysis of human Ndel1. Instead, we discovered that 14-3-3 interacts with two residues that are phosphorylated by basophilic kinases and located in the DISC1 (disrupted-in-schizophrenia 1)-interacting region of Ndel1 that is implicated in cognitive disorders. These data conform with the general findings that there are different subtypes of 14-3-3-binding sites that overlap with the specificities of different basophilic AGC (protein kinase A/protein kinase G/protein kinase C family) and CaMK (Ca2+/calmodulin-dependent protein kinase) protein kinases, and a 14-3-3 dimer often engages with two tandem phosphorylated sites, which is a configuration with special signalling, mechanical and evolutionary properties. Thus 14-3-3 dimers can be digital logic gates that integrate more than one input to generate an action, and coincidence detectors when the two binding sites are phosphorylated by different protein kinases. Paired sites are generally located within disordered regions and/or straddle either side of functional domains, indicating how 14-3-3 dimers modulate the conformations and/or interactions of their targets. Finally, 14-3-3 proteins bind to members of several multi-protein families. Two 14-3-3-binding sites are conserved across the class IIa histone deacetylases, whereas other protein families display differential regulation by 14-3-3s. We speculate that 14-3-3 dimers may have contributed to the evolution of such families, tailoring regulatory inputs to different physiological demands.
All refractory NbN integrated circuit process (1993)

The authors describe the fabrication and electrical performance of an eight mask step, 2.5- mu m*2.5- mu m minimum junction size, all refractory NbN integrated circuit process. NbN/MgO/NbN trilayers sputtered in situ are patterned by reactive ion etching to form Josephson tunnel junctions. A two-level dielectric process has been developed to ensure low defect densities. Sputtered molybdenum films form a resistor layer. NbN wire J/sub c/ enhancement and improved step coverage have been achieved. This process has been used to successfully fabricate SQUID amplifier circuits, digital modified variable threshold logic circuits, arrays of 256 SQUIDs, SFQ counters, and 4000 junction strings. NbN logic circuit operation above 10 K was demonstrated.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Normal human urothelial cells in vitro: proliferation and induction of stratification. (1994)

We describe a simplified technique for the isolation and long-term culture of human urothelial cells. Urothelial cells in vitro are capable of rapid proliferation and can be induced to form integrated stratifying cell layers in high calcium medium. Stratification-related changes are not necessarily accompanied by urothelial cell maturation and differentiation.
Involvement of a High-Mobility-Group Protein in the Transcriptional Activity of Herpes Simplex Virus Latency-Active Promoter 2 (1996)

Latency-active promoter 2 (LAP 2) is a TATA-less promoter in herpes simplex virus type 1 (HSV-1) that can express genes during viral latency. Four regions of LAP2 are protected from DNase I digestion in vitro by either HeLa cell nuclear extracts or purified Sp1. Transient gene expression assays of LAP2 substitution mutants demonstrate that two of the regions protected by Sp1 and three other regions protected by nuclear extract are important for promoter function. The mutation causing the most significant reduction in expression alters a stretch of 23 thymidine residues (T23) that binds a protein with several properties common to high-mobility-group (HMG) proteins. The T23 binding activity is heat stable, can be inhibited by poly(dA-dT).poly(dA-dT), and is inhibited by minor-groove-binding drugs. Antiserum directed against HMG I(Y) blocked the formation of one of the DNA-protein complexes on the T23 oligonucleotide, suggesting that a protein antigenically related to HMG I(Y) binds to LAP2 in vitro. Direct evidence of HMG I(Y) involvement in LAP2 function is provided by the findings that recombinant HMG I(Y) protein facilitates Sp1 binding to LAP2 in mobility shift assays and that antisense HMG I(Y) RNA specifically inhibits LAP2 function in vivo. These results suggest that DNA structure may be an important determinant of the activity of a promoter that is capable of escaping the global shutoff of transcription that occurs during viral latency.
Body-worn sensor based surrogates of minimum ground clearance in elderly fallers and controls (2011)

Falls in the elderly are a major problem worldwide with enormous associated economic and societal costs. Minimum ground clearance (MGC) is an important gait variable when considering trip-related falls risk. This study aimed to investigate the clinical relevance of inertial sensor derived parameters, previously shown to be related to MGC. Previous research by the authors reported a surrogate method for assessing minimum ground clearance (MGC) using shank-mounted inertial sensors in young controls. The present study tests this method on a cohort of 114 community dwelling elderly adults, with and without a history of falls, completing a 30 m continuous walk. Parameters based on the shank angular velocity signals that were shown to be associated with MGC showed significant differences (p<0.05) between fallers and non-fallers yet did not correlate strongly (r<0.7) with two standard measures of falls risk (TUG & BBS). Weak correlations were observed between the angular velocity derived parameters and gait velocity. We conclude that these parameters are clinically meaningful and therefore may constitute a new measure of falls risk.
Quantitative assessments of geometric errors for rapid prototyping in medical applications (2012)

Purpose In medical applications, it is crucial to evaluate the geometric accuracy of rapid prototyping (RP) models. Current research on evaluating geometric accuracy has focused on identifying two or more specific anatomical landmarks on the original structure and the RP model, and comparing their corresponding linear distances. Such kind of accuracy metrics is ambiguous and may induce misrepresentations of the actual errors. The purpose of this paper is to propose an alternative method and metrics to measure the accuracy of RP models. Design/methodology/approach The authors propose an accuracy metric composed of two different approaches: a global accuracy evaluation using volumetric intersection indexes calculated over segmented Computed Tomography scans of the original object and the RP model. Second, a local error metric that is computed from the surfaces of the original object and the RP model. This local error is rendered in a 3D surface using a color code, that allow differentiating regions where the model is overestimated, underestimated, or correctly estimated. Global and local error measurements are performed after rigid body registration, segmentation and triangulation. Findings The results show that the method can be applied to different objects without any modification, and provide simple, meaningful and precise quantitative indexes to measure the geometric accuracy of RP models. Originality/value The paper presents a new approach to characterize the geometric errors in RP models using global indexes and a local surface distribution of the errors. It requires minimum human intervention and it can be applied without any modification to any kind of object.
Vitreous cryo‐sectioning of cells facilitated by a micromanipulator (2006)

Summary Sectioning vitrified cells and tissues for cryo‐electron microscopy is more challenging than room‐temperature sectioning of plastic‐embedded samples. As the sample must be kept very cold (<−130 °C) and because there is no liquid upon which the sections can float as they are cut, transferring the sections from the knife edge to a grid is one of the more difficult steps in the process. We employed a micromanipulator to hold and control the cryo‐sections as they come off the knife. This allows slower cutting speeds than are typically used in vitreous cryo‐sectioning and contributes to better control during cutting, which facilitates repeatable placement of a ribbon of sections onto a grid. The ribbon is kept under tension during the entire cutting process, which may decrease folding and/or compression, features that are inherent to vitreous sections. Furthermore, the added control afforded by this technique makes it easier for multiple ribbons to be placed on a single grid, thereby increasing the number of sections that can be examined and imaged during a microscopy session. It even allows for serial cryo‐electron microscopy. As such, this approach is an advance in the cryo‐microtomy of vitreous sections.