gebhart/patrepeval huggingface dataset:
Rapid activation of G 2 /M checkpoint after hypertonic stress in renal inner medullary epithelial (IME) cells is protective and requires p38 kinase (2001)

Cells in the kidney medulla are subject to variable and often extreme osmotic stress during concentration of the urine. Previous studies showed that renal inner medullary epithelial (IME) cells respond to hypertonicity by G(2) arrest. The purpose of the present study was to investigate the mechanisms involved in initiation and maintenance of G(2) arrest. Rapid initiation of G(2) arrest after UV radiation is mediated by p38 kinase. Here we find that p38 kinase is responsible for rapid initiation of the G(2) delay in IME cells after the hypertonic stress created by adding NaCl. High NaCl, but not high urea, rapidly initiates G(2) arrest. Inhibition of p38 kinase by SB202190 (10 microM) blocks the rapid initiation of this checkpoint both in an immortalized cell line (mIMCD3) and in second-passage IME cells from mouse renal inner medulla. p38 inhibition does not affect exit from G(2) arrest. The rapid initiation of G(2) arrest is followed by inhibition of cdc2 kinase, which is also prevented by SB202190. To assess the possible protective role of G(2) arrest, we measured DNA strand breaks as reflected by immunostaining against phospho-histone H2AX, which becomes phosphorylated on Ser-139 associated with DNA breaks. Abrogation of rapid G(2)/M checkpoint activation by SB202190 increases the histone H2AX phosphorylation in G(2)/M cells. We propose that the rapid initiation of G(2) delay by p38 kinase after hypertonicity protects the cells by decreasing the level of DNA breaks caused by aberrant mitosis entry.
Mesenchymal Stem Cells for Treatment of Therapy-Resistant Graft-versus-Host Disease (2006)

MSC is a very promising treatment for severe steroid-resistant acute GVHD.
Hepatitis C virus receptor expression in normal and diseased liver tissue (2007)

HCV infection of Huh-7.5 hepatoma cells in vitro significantly increased CLDN1 expression levels, consistent with a direct modulation of CLDN1 by virus infection. In HCV infected livers, immunohistochemical studies revealed focal patterns of CLDN1 staining, suggesting localized areas of increased CLDN1 expression in vivo which may potentiate local viral spread within the liver.
ARGUS: Efficient Scalable Continuous Query Optimization for Large-Volume Data Streams (2006)

We present the architecture of ARGUS, a stream processing system implemented atop commercial DBMSs to support large-scale complex continuous queries over data streams. ARGUS supports incremental operator evaluation and incremental multi-query plan optimization as new queries arrive. The latter is done to a degree well beyond the previous state-of-the-art via a suite of techniques such as query-algebra canonicalization, indexing, and searching, and topological query network optimization with join order optimization, conditional materialization, minimal column projection, and transitivity inference. Building on top of a DBMS, the system provides a value-adding package to the existing database applications where the needs of stream processing become increasingly demanding. Compared to directly running the continuous queries on the DBMS, ARGUS achieves well over a 100-fold improvement in performance
VeriTrust (2013)

Hardware Trojans (HTs) implemented by adversaries serve as backdoors to subvert or augment the normal operation of infected devices, which may lead to functionality changes, sensitive information leakages, or Denial of Service attacks. To tackle such threats, this paper proposes a novel verification technique for hardware trust, namely VeriTrust, which facilitates to detect HTs inserted at design stage. Based on the observation that HTs are usually activated by dedicated trigger inputs that are not sensitized with verification test cases, VeriTrust automatically identifies such potential HT trigger inputs by examining verification corners. The key difference between VeriTrust and existing HT detection techniques is that VeriTrust is insensitive to the implementation style of HTs. Experimental results show that VeriTrust is able to detect all HTs evaluated in this paper (constructed based on various HT design methodologies shown in the literature) at the cost of moderate extra verification time, which is not possible with existing solutions.
Matched filter limits and code performance in digital magnetic recording (1991)

Presents a method for evaluating the performance of recording channels and codes for systems with additive spectral Gaussian noise. Starting with a noise-whitened isolated pulse, matched filters are calculated for the amplitude and timing channels which have the maximum signal-to-noise ratio (SNR) and minimum jitter, respectively. In high-density recording systems, the pulse slimming equalization required to control intersymbol interference degrades the SNR and jitter. For the timing channel, a detector SNR is defined whose error statistics are nearly identical to the amplitude channel SNR. Procedures for calculating losses relative to the matched filter SNR are developed that facilitate performance comparisons of both channels. A series of runs for the Lorentzian input pulse and cos/sup n/ equalized output pulses compares the performance of several modulation codes and detection techniques. Write equalization and partial response type four equalization are examined.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Requirement of JNK for Stress- Induced Activation of the Cytochrome c-Mediated Death Pathway (2000)

The c-Jun NH2-terminal kinase (JNK) is activated when cells are exposed to ultraviolet (UV) radiation. However, the functional consequence of JNK activation in UV-irradiated cells has not been established. It is shown here that JNK is required for UV-induced apoptosis in primary murine embryonic fibroblasts. Fibroblasts with simultaneous targeted disruptions of all the functional Jnk genes were protected against UV-stimulated apoptosis. The absence of JNK caused a defect in the mitochondrial death signaling pathway, including the failure to release cytochrome c. These data indicate that mitochondria are influenced by proapoptotic signal transduction through the JNK pathway.
Spinal Fusion in the United States (2011)

Frequency, utilization, and hospital charges of spinal fusion have increased at a higher rate than other notable inpatient procedures, as seen in this study from 1998 to 2008. In addition, patient demographics and hospital characteristics changed significantly; in particular, whereas the average age for spinal fusion increased, the in-hospital mortality rate decreased.
Total Synthesis of Anti-microtubule Diketopiperazine Derivatives:  Phenylahistin and Aurantiamine (2000)

ADVERTISEMENT RETURN TO ISSUEPREVNoteNEXTTotal Synthesis of Anti-microtubule Diketopiperazine Derivatives: Phenylahistin and AurantiamineYoshio Hayashi, Sumie Orikasa, Koji Tanaka, Kaneo Kanoh, and Yoshiaki KisoView Author Information Department of Medicinal Chemistry, Center for Frontier Research in Medicinal Science, Kyoto Pharmaceutical University, Yamashina-Ku, Kyoto 607-8412, Japan, and Shimizu Laboratories, Marine Biotechnology Institute, 1900 Sodeshi-Cho, Shimizu, Shizuoka, 424-0037, Japan [email protected]Cite this: J. Org. Chem. 2000, 65, 24, 8402–8405Publication Date (Web):November 8, 2000Publication History Received25 August 2000Published online8 November 2000Published inissue 1 December 2000https://pubs.acs.org/doi/10.1021/jo0012905https://doi.org/10.1021/jo0012905brief-reportACS PublicationsCopyright © 2000 American Chemical SocietyRequest reuse permissionsArticle Views2443Altmetric-Citations58LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Aldehydes,Chemical structure,Condensation,Imidazoles,Reaction products Get e-Alerts
Measuring single molecule conductance with break junctions (2005)

Single-molecule conductance measurements made under potential control provide a critical link between chemical and molecular electronic data. These measurements are made possible by the STM break-junction method introduced recently, but questions remain about its reliability. Here we report the use of a logarithmic current-to-voltage converter to examine a wide range of currents in an STM break junction study of octanedithiol, clearly showing both the gold-quantum wire regime and the single molecule conductance regime. We find two sets of molecular currents that we tentatively ascribe to different bonding geometries of the molecules in the break junction.
Efficient Synthesis of Light-Harvesting Arrays Composed of Eight Porphyrins and One Phthalocyanine (1999)

Effective light-harvesting arrays require multiple photoactive energy donors that funnel energy to an energy acceptor. Porphyrins and phthalocyanines are attractive components for light-harvesting arrays due to their strong absorption in the blue and red regions, respectively, and because energy transfer can occur from porphyrin to phthalocyanine regardless of their respective metalation states. Star-shaped light-harvesting arrays comprised of eight peripheral porphyrins and one core phthalocyanine have been prepared by a streamlined synthesis involving minimal reliance on protecting groups, a high degree of convergence, and facile chromatographic purification. The synthesis involves three distinct stages of complementary chemistries (porphyrin formation, Pd-mediated porphyrin dimer formation, phthalocyanine formation). Statistical reaction of p-iodobenzaldehyde, a phthalonitrile-linked benzaldehyde, and 5-mesityldipyrromethane afforded the desired trans-iodo/phthalonitrile-substituted porphyrin, which underwent Pd-mediated coupling with a monoethynyl porphyrin to give the porphyrin dimer bearing a phthalonitrile unit. Reaction of the dimer in 1-pentanol in the presence of MgCl2 and DBU for 48 h at 145 °C afforded the all-magnesium (porphyrin)8−phthalocyanine nonamer (MgP)8MgPc in 5.0% yield. The same reaction with lithium pentoxide in 1-pentanol for 2 h at 145 °C gave the all-free base nonamer (H2P)8H2Pc in 34% yield. The all-zinc nonamer (ZnP)8ZnPc was prepared by addition of zinc acetate at the end of the reaction. Similar treatment of a monomeric porphyrin−phthalonitrile afforded the pentameric (ZnP)4ZnPc in 58% yield. The (MgP)8MgPc was also obtained by magnesium insertion of (H2P)8H2Pc. The three nonamers were readily purified and are soluble in solvents such as toluene, THF, and CH2Cl2. Each nonamer absorbs strongly across the solar spectrum and exhibits efficient energy transfer from the porphyrins to the phthalocyanine.
Singapore Academy of Law Annual Lecture 1997: Hong Kong in 2002 (1997)

I have come in humility, to learn from you and to share with you some of my thoughts on the future of my beloved city: Hong Kong. With the assurance that Hong Kong's present system will not change for 50 years from the change of sovereignty on 1 July 1997, my attitude may be summed up in a few words: Confidence, coupled with a determination to face the challenges ahead. Now I must go straight to the Basic Law and examine with you those provisions which deal with the legal system.
Development of Biocompatible Interpenetrating Polymer Networks Containing a Sulfobetaine-Based Polymer and a Segmented Polyurethane for Protein Resistance (2006)

Interpenetrating polymer networks (IPNs) were prepared by the modification of a segmented polyurethane (SPU) with a cross-linked sulfobetaine methacrylate (SBMA) polymer. The IPN films that were prepared can effectively resist nonspecific protein adsorption when the distribution of SBMA units within the SPU film is well controlled, and they retain high mechanical strengths inherent from the base SPU films. Furthermore, the zwitterionic and biomimetic nature of sulfobetaine and the ease of SBMA preparation make SBMA-based materials very attractive for a wide range of applications. It is challenging to control the diffusion of highly polar SBMA into the hydrophobic network of SPU. In this study, various parameters governing the formation of IPNs containing SBMA were studied. The chemical composition depth profile of the IPN films was determined by confocal Raman microscopy. The morphology and thickness of these IPN films were examined by atomic force microscopy and scanning electron microscopy. The amount of adsorbed proteins on the IPN films was determined by an enzyme-linked immunosorbent assay. Results show that the amount of adsorbed proteins on the IPN films depends on the incubation conditions, including solvent polarity, incubation time, SBMA monomer ratio, and incubation concentration. It appears that the IPN films prepared in a mixed solvent of higher polarity with long incubation time lead to very low protein adsorption. This study not only introduces a new IPN system containing SBMA, but also provides a fundamental understanding of various parameters governing the formation of IPNs.
Hand-Held Video Deblurring Via Efficient Fourier Aggregation (2015)

Videos captured with hand-held cameras often suffer from a significant amount of blur, mainly caused by the inevitable natural tremor of the photographer's hand. In this work, we present an algorithm that removes blur due to camera shake by combining information in the Fourier domain from nearby frames in a video. The dynamic nature of typical videos with the presence of multiple moving objects and occlusions makes this problem of camera shake removal extremely challenging, in particular when low complexity is needed. Given an input video frame, we first create a consistent registered version of temporally adjacent frames. Then, the set of consistently registered frames is blockwise fused in the Fourier domain with weights depending on the Fourier spectrum magnitude. The method is motivated from the physiological fact that camera shake blur has a random nature; therefore, nearby video frames are generally blurred differently. Experiments with numerous videos recorded in the wild, along with extensive comparisons, show that the proposed algorithm achieves state-of-the-art results while at the same time being much faster than its competitors.
A versatile toolkit for high throughput functional genomics with Trichoderma reesei (2012)

Using this strategy and the materials provided, high throughput gene deletion in T. reesei becomes feasible. Moreover, with the application of sexual development, the NHEJ-defect can be removed efficiently and without the need for additional selection markers. The same advantages apply for the construction of multiple mutants by crossing of strains with different gene deletions, which is now possible with considerably less hands-on time and minimal screening effort compared to a transformation approach. Consequently this toolkit can considerably boost research towards efficient exploitation of the resources of T. reesei for cellulase expression and hence second generation biofuel production.
Hybrid adaptive procedure for estimation of psychometric functions (1981)

Adaptive psychophysical procedures that have been described in the literature generally fall into one of two categories. (1) Simple procedures, such as UDTR and PEST, can be implemented without an on-line computer. The decision to change testing level is based on the outcome of the few most recent trials, and the final estimate of threshold is given by the final testing level or the average of a few testing levels. (2) "Maximum likelihood" methods require an on-line computer. A parametric form of the psychometric function is assumed, and after each trial a maximum-likelihood estimate of the parameters of the psychometric function is made on the basis of all preceding trials. This estimate is used to set the next testing level and to estimate threshold. We describe here a hybrid procedure, in which testing levels are determined by PEST and the final estimate of threshold is made by fitting an assumed psychometric function to all preceding trials. The PEST rules were tuned to yield results that were accurate and insensitive to errors in initial estimates of the psychometric function. These parameters differ from those that yield optimum results with classical PEST. Results of computer simulations and of experiments with human subjects are presented.
Network analyses structure genetic diversity in independent genetic worlds (2009)

DNA flows between chromosomes and mobile elements, following rules that are poorly understood. This limited knowledge is partly explained by the limits of current approaches to study the structure and evolution of genetic diversity. Network analyses of 119,381 homologous DNA families, sampled from 111 cellular genomes and from 165,529 phage, plasmid, and environmental virome sequences, offer challenging insights. Our results support a disconnected yet highly structured network of genetic diversity, revealing the existence of multiple "genetic worlds." These divides define multiple isolated groups of DNA vehicles drawing on distinct gene pools. Mathematical studies of the centralities of these worlds' subnetworks demonstrate that plasmids, not viruses, were key vectors of genetic exchange between bacterial chromosomes, both recently and in the past. Furthermore, network methodology introduces new ways of quantifying current sampling of genetic diversity.
Pushing the Envelope of Modern Methods for Bundle Adjustment (2011)

In this paper, we present results and experiments with several methods for bundle adjustment, producing the fastest bundle adjuster ever published in terms of computation and convergence. From a computational perspective, the fastest methods naturally handle the block-sparse pattern that arises in a reduced camera system. Adapting to the naturally arising block-sparsity allows the use of BLAS3, efficient memory handling, fast variable ordering, and customized sparse solving, all simultaneously. We present two methods; one uses exact minimum degree ordering and block-based LDL solving and the other uses block-based preconditioned conjugate gradients. Both methods are performed on the reduced camera system. We show experimentally that the adaptation to the natural block sparsity allows both of these methods to perform better than previous methods. Further improvements in convergence speed are achieved by the novel use of embedded point iterations. Embedded point iterations take place inside each camera update step, yielding a greater cost decrease from each camera update step and, consequently, a lower minimum. This is especially true for points projecting far out on the flatter region of the robustifier. Intensive analyses from various angles demonstrate the improved performance of the presented bundler.
Alveolar stem cell transduction by an adeno-associated viral vector. (1995)

In inherited disorders such as surfactant protein deficiencies or cystic fibrosis (CF), where lung damage develops progressively after birth, gene replacement is best accomplished in the neonatal period. We use the adeno-associated virus (AAV) as a vector for gene transfer in the newborn rabbit lung where stem cells are activated for lung growth and differentiation. AAV-mediated gene transfer as assayed by lacZ gene expression occurred preferentially in alveoli in the alveolar epithelial progenitor cell, the type II cell, and in the large airway tracheobronchial basal and ciliated cells. Cell proliferation was confirmed by 5-bromo-deoxyuridine (BRDU) labeling in regions undergoing alveolarization and airway branch points. Regions of cell proliferation coincided with areas of significant lacZ expression. Thus, dividing and differentiating cells can be targeted by AAVlacZ delivery to newborn lung.
Cancer-associated mucins and mucin-type glycoproteins (1991)

Cancer-associated mucins and mucin-type glycoproteins Get access V. P. Bhavanandan V. P. Bhavanandan Department of Biological Chemistry and the Cell and Molecular Biology Program, The Milton S.Hershey Medical Center, Pennsylvania State UniversityHershey, PA 17033, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Glycobiology, Volume 1, Issue 5, November 1991, Pages 493–503, https://doi.org/10.1093/glycob/1.5.493 Published: 01 November 1991 Article history Received: 30 August 1991 Accepted: 30 August 1991 Published: 01 November 1991
Performance of Graceful Degradation for Cache Faults (2007)

In sub-90nm technologies, more frequent hard faults pose a serious burden on processor design and yield control. In addition to manufacturing-time chip repair schemes, microarchitectural techniques to make processor components resilient to hard faults become increasingly important. This paper considers defects in cache memory and studies their impact on program performance using a fault degradable cache model. We first describe how defects at the circuit level in cache manifest themselves at the microarchitecture level. We then examine several strategies for masking faults, by disabling faulty resources, such as lines, sets, ways, ports, or even the whole cache. We also propose an efficient cache set remapping scheme to recover lost performance due to failed sets. Using a new simulation tool, called CAFE, we study how the cache faults impact program performance under the various masking schemes
Rupture of a calcified, non-parasitic splenic cyst after indirect trauma. (1986)

A 31 year old man sustained head injuries in a motor vehicle accident. Subsequent events led to paracentesis of bloody fluid and exploratory laparotomy and splenectomy. Pathological examination disclosed rupture of a calcified, non-parasitic splenic cyst, which, in retrospect, could have been diagnosed on the admission chest roentgenogram. The incidence, origin and pathology of splenic cysts is discussed.