gebhart/patrepeval huggingface dataset:
Cellular Uptake and Localization of Polymyxins in Renal Tubular Cells Using Rationally Designed Fluorescent Probes (2015)

Polymyxins are cyclic lipopeptide antibiotics that serve as a last line of defense against Gram-negative bacterial superbugs. However, the extensive accumulation of polymyxins in renal tubular cells can lead to nephrotoxicity, which is the major dose-limiting factor in clinical use. In order to gain further insights into the mechanism of polymyxin-induced nephrotoxicity, we have rationally designed novel fluorescent polymyxin probes to examine the localization of polymyxins in rat renal tubular (NRK-52E) cells. Our design strategy focused on incorporating a dansyl fluorophore at the hydrophobic centers of the polymyxin core structure. To this end, four novel regioselectively labeled monodansylated polymyxin B probes (MIPS-9541, MIPS-9542, MIPS-9543, and MIPS-9544) were designed, synthesized, and screened for their antimicrobial activities and apoptotic effects against rat kidney proximal tubular cells. On the basis of the assessment of antimicrobial activities, cellular uptake, and apoptotic effects on renal tubular cells, incorporation of a dansyl fluorophore at either position 6 or 7 (MIPS-9543 and MIPS-9544, respectively) of the polymyxin core structure appears to be an appropriate strategy for generating representative fluorescent polymyxin probes to be utilized in intracellular imaging and mechanistic studies. Furthermore, confocal imaging experiments utilizing these probes showed evidence of partial colocalization of the polymyxins with both the endoplasmic reticulum and mitochondria in rat renal tubular cells. Our results highlight the value of these new fluorescent polymyxin probes and provide further insights into the mechanism of polymyxin-induced nephrotoxicity.
XML data partitioning strategies to improve parallelism in parallel holistic twig joins (2009)

Parallel XML query processing systems that process numerous queries over large heterogeneous XML documents often experience under-performance due to workload imbalance and low CPU/system utilization, because conventional partitioning strategies cannot serve well for state-of-the-art query processing algorithms, such as holistic twig joins. Consequently, partitioning and distributing heterogeneous XML documents onto a parallel cluster system have lead to such an intricacy issue for maintaining good query performance. In this paper, we propose XML data partitioning strategies that are able to alleviate system performance degradation due to workload imbalance, especially for parallel holistic twig joins processing. The proposed XML data partitioning strategies aim at improving workload balance on both static data distribution and dynamic data distribution. In the first strategy we refine an XML partition having a high cost by series of XML data partition refinements with various levels of granularities from document, query, and subquery, up to node streams. The selection of the granularity level for refining a high cost partition is contextually dependent on the overall workload balance in the system. In the second strategy for dynamic data distribution, we dynamically handle low system utilization when there are many idle nodes in the system. We propose an XML data redistribution approach by partitioning XML data on the fly at the stream nodes-based granularity.
Zinc Requirement During Meiosis I-Meiosis II Transition in Mouse Oocytes Is Independent of the Mos-MAPK Pathway. (2010)

Zinc is an essential cofactor in hundreds of molecules needed for many biological processes, including formation and maturation of gametes. Our laboratory has recently demonstrated an important role for zinc during oocyte meiotic maturation. The first meiotic division is normally asymmetric and produces a large oocyte and a much smaller polar body. However, the attenuation of intracellular zinc availability during in vitro maturation of mouse oocytes using the membrane permeable heavy metal chelator N,N,N',N'-tetrakis(2-pyridylmethyl) ethylenediamine (TPEN) causes formation of large polar bodies and failure to form a meiosis II spindle. Oocytes matured in the presence of TPEN display a peculiar spindle phenotype in which a telophase-I-like conformation of spindle microtubules is maintained while chromatin begins to decondense. Formation of the cortical granule free domain is also impaired in these zinc-insufficient oocytes. Features of this phenotype resemble those of Mos null oocytes. Mos protein normally accumulates after germinal vesicle breakdown and phosphorylates mitogen activated kinase kinase 1 and 2 (MAP2K1/2) which, in turn, phosphorylate and activate mitogen activated kinase 1 and 3 (MAPK1/3). In Mos null oocytes, this pathway is disrupted and MAPK1/3 does not become phosphorylated; the phenotype of these oocytes is attributed mainly to absence of MAPK activation. The goal of this project was to investigate the mechanism by which zinc insufficiency causes abnormal meiotic maturation, focusing on components of the Mos-MAPK pathway. Reduced levels of both Mos protein and phospho-MAP2K1/2 are observed in zinc-insufficient oocytes; however, these differences appear only after completion of the first meiotic division. In addition, activation of downstream effector of the Mos pathway, MAPK1/3, is unaffected by zinc-insufficiency, and reduced Mos levels are observed only with the presence of TPEN after first polar body extrusion. These data are inconsistent with the hypothesis that reduced Mos mediates the observed phenotype. Finally, Mos overexpression does not rescue the phenotype of zinc-insufficient oocytes. Combined, these data lead us to conclude that reduced Mos levels are not responsible for the failure of asymmetric division and spindle abnormalities observed in our model of oocyte zinc-insufficiency. Zinc-insufficient oocytes fail to increase maturation promoting factor activity following the first meiotic division, indicating a failure to establish cytostatic factor (CSF), rather than the failure to maintain CSF observed in Mos null oocytes. Although we have shown that zinc has a novel role as a key regulator of the meiotic cell cycle, this role is not mediated through the Mos-MAPK pathway. Further work will be necessary to determine what pathways are impacted by zinc insufficiency and the mechanism by which disruption of meiotic maturation is occurring. This research was supported by NIH/NICHD P01 HD021921 and T32 HD07068 and by the W. M. Keck Foundation. (poster)
Towards a Functional Integration of Document Analysis and Understanding in Workflow Management Systems (1999)

. The integration of business applications into workflow management systems (WfMSs) is a recent topic in workflow management. Today, most efforts are concerned mainly with the integration itself. However, considering the information need of knowledge intensive applications, new possibilities arise when using information available in workflows. With the example of document analysis and understanding (DAU) as knowledge intensive business application, this paper introduces a concept for providing context information from workflows -- so-called workflow context - to DAU in order to enhance both, namely application and workflow. This concept can be seen as a first step towards a functional integration of these two systems which focuses on the satisfaction of DAU&apos;s information need. The paper defines the content of a workflow context, states how it can be arranged in workflows and represented to DAU. The representation uses the concept of expectations which have to be stated by ...
Synthesis of (R)-(-)-3-Methoxymethyl-3-propyl-3,4-dihydrocoumarin from a Chiral Michael Adduct: Absolute Configurations of the Allylated Products of Enantioselective Radical-Mediated Reactions. (1999)

(R)-3-Methoxymethyl-3-propyl-3, 4-dihydrocoumarin was synthesized, starting from a chiral Michael adduct [(S)-methyl 2, 3-dihydro-1-oxo-2-(3-oxobutyl)-1H-indene-2-carboxylate], in order to determine the absolute configurations of the products obtained by enantioselective radical-mediated allylation. Aldol cyclization of the Michael adduct proceeded smoothly with suppression of the retro Michael reaction to afford an optically active cyclized product. The Baeyer-Villiger reaction of (R)-2-methoxymethyl-2-propylindanone in the presence of BF3·Et2O afforded the desired dihydrocoumarin.
Excavando la web (2004)

The is the internet's most important phenomenon, as demonstrated by its exponential growth and diversity.
Hence, due to the volume and wealth of its data, search engines have become among the web's main tools. They are useful when we know what we are looking for. However, certainly the holds answers to questions never imagined. The process of finding relations or interesting patterns within a set is called data and in the case of the web, web mining. In this article we present the main ideas behind mining and some of its applications.
High-speed optical sampling using a silicon-chip temporal magnifier (2009)

We demonstrate a single-shot technique for optical sampling based on temporal magnification using a silicon-chip time lens. We demonstrate the largest reported temporal magnification factor yet achieved (>500) and apply this technique to perform 1.3 TS/s single-shot sampling of ultrafast waveforms and to 80-Gb/s performance monitoring. This scheme offers the potential of developing a device that can transform GHz oscilloscopes into instruments capable of measuring signals with THz bandwidths.
Promoted hydrogen release from ammonia borane with mannitolvia a solid-state reaction route (2011)

Promoted hydrogen release from ammonia borane (NH(3)BH(3), AB) with mannitol (C(6)H(8)(OH)(6), MA) additive is reported. It is found that for the MA/2AB sample, the dehydrogenation temperature is lowered by ~25 °C compared to that of neat AB, the liberation of undesired byproduct borazine is suppressed, and the released ammonia can be removed by using anhydrous MgCl(2) as absorber. The analyses of Raman, Fourier transform infrared spectroscopy and (11)B nuclear magnetic resonance spectroscopy demonstrate the breaking of B-N, B-H and O-H bonds and the formation of B-O bonds for the dehydrogenation process of MA/2AB. These results suggest a solid-state dehydrogenation reaction between AB and MA: the B-H(δ-) bonds in AB and the O-H(δ+) bonds in MA combine with each other to release H(2). Furthermore, the use of the perfect -OH carrier MA as additive leads to a straightforward understanding of the improved dehydrogenation of AB under the effect of hydroxyl groups in the solid state.
Pub - point upon body (2011)

This paper presents a novel interaction system, PUB (Point Upon Body), to explore eyes-free interaction in a personal space by allowing users tapping on their own arms to be provided with haptic feedback from their skin. Two user studies determine how users can interact precisely with their forearms and how users behave when operating in their arm space. According to those results, normal users can divide their arm space at most into 6 points between their wrists and elbows with iterative practice. Experimental results also indicate that the divided pattern of each user is unique from that of other ones. Based on the design principles from the observations, an interaction system, PUB, is designed to demonstrate how interaction design benefits from those findings. Two scenarios, remote display control and mobile device control, are demonstrated through the UltraSonic device attached on the users' wrists to detect their tapped positions.
Predictive Rollover Index Based on Frontal Road Geometry and On-Line Driver Information (2013)

A predictive rollover index is investigated in this work. The vehicle frontal road geometry and the on-line estimated driver information are incorporated into an existing rollover index to provide the rollover indication at an early stage. Both the frontal road curvature and the current road bank angle are considered in the road information. The on-line estimated driver model needs to be selected by a screening process to rule out incorrectly estimated driver models. Driving simulator experiments and physical vehicle road tests are both conducted to collect human driving data to evaluate the proposed predictive rollover index. The preliminary results show promising benefits in generating a reasonable predictive rollover index.
Randomized Phase 3 Trial of Fluorouracil, Epirubicin, and Cyclophosphamide Alone or Followed by Paclitaxel for Early Breast Cancer (2008)

Among patients with operable breast cancer, FEC-P treatment statistically significantly reduced the risk of relapse compared with FEC as adjuvant therapy.
Edge-Enhanced Error Diffusion Halftoning using Human Visual Properties (2006)

Digital halftoning is the technique to obtain a bilevel-toned image from continuous-toned image. Among halftoning methods, the error diffusion method gives better subjective quality than other halftoning ones. But it also makes edges of objects blurred. To overcome the defect, we proposes the modified error diffusion to enhance the edges using the property that human vision perceives the local average luminance and doesn't perceive a little variation of the spatial information. The proposed method computes a local activity measure, which is the difference between a pixel luminance and the average of its 3times3 neighborhood pixels' luminance weighted according to the spatial positioning. The system also uses information of edge enhancement (IEE), which is computed from the normalized spatial activity measure multiplied by the average luminance. The IEE is added to the quantizer's input pixel and feeds into the halftoning quantizer. The quantizer produces the halftone image having the enhanced edge. The computer experimental results show that the proposed method produces clearer bilevel-toned images than conventional methods and the edge of objects is preserved well. Also the performance of the proposed method is improved, compared with that of the conventional method by measuring the edge correlation and the local average accordance at some ranges of viewing distance
Optical pick-up for DVD (1996)

The optical pick-up for DVD with CD (compact disc) compatibility is discussed. The difference of the substrate thickness between DVD and CD causes the different spherical aberration and prevents the laser beam from being focused into a diffraction limit spot size with only one objective lens. Several methods of reducing this aberration and possessing compatibility with CD are proposed. The twin lens type optical pick-up is one solution in overcoming this problem. It incorporates objective lenses for both DVD and CD. Each lens results in an optimum focused spot without the extra spherical aberration for each type of disc.
Effect of sequential treatment with syndrome differentiation on acute exacerbation of chronic obstructive pulmonary disease and "AECOPD Risk-Window": study protocol for a randomized placebo-controlled trial (2012)

This study is registered at ClinicalTrials.gov, ChiCTR-TRC-11001460.
Specific checkpoints regulate plant cell cycle progression in response to oxidative stress (1999)

Summary The effects of oxidative stress on plant cell cycle progression were studied both in cell suspensions and in planta . Oxidative stress of variable severity was imposed by the addition of different concentrations of the methyl‐quinone, menadione, into the growth media. In cell suspensions, flow cytometry analyses demonstrated that low concentrations (20–50 μM) of menadione impaired the G1/S transition, slowed DNA replication, and delayed the entry into mitosis. Furthermore, cells in G1 were more sensitive to menadione‐mediated oxidative stress than cells in S phase. Cell cycle arrest was associated with an inhibition of the activity of cyclin‐dependent kinases, cell cycle gene expression, and a concomitant activation of stress genes. Menadione‐mediated oxidative stress was shown to have very similar effects on tobacco plants, suggesting that a general regulation mechanism takes place in plants. These results define an oxidative stress checkpoint pathway that modulates both the expression of the core cell cycle genes and oxidative defence genes. Redox sensing could be of key importance in controlling cell cycle progression in environmental stress conditions.
Thermal Spreading Resistance and Heat Source Temperature in Compound Orthotropic Systems With Interfacial Resistance (2013)

In this paper, a new and more general solution for thermal spreading resistance in compound, orthotropic systems with interfacial resistance is considered. This new solution, which extends beyond previously published results, is obtained for a finite rectangular heat source of uniform strength arbitrarily located on a rectangular substrate. By means of superposition, one can obtain the temperature field in the source plane for multiple heat sources as well as the source mean and centroid temperatures. By means of orthotropic transformations, systems containing orthotropic materials can be easily modeled. Extension of the present solutions using a computationally efficient influence coefficient method is also given, such that the effects of large numbers of heat sources are superimposed. The application of these closed-form expressions for the temperature rise is demonstrated with calculations for Gallium nitride (GaN) high electron mobility transistors (HEMTs). These solutions are shown to be more flexible than previously reported analytical expressions and much more computationally efficient than 3-D finite element analysis, especially for a large number of discrete heat sources associated with multifinger GaN HEMTs.
Flow Configurations in Colliding Plates: Explosive Bonding (1963)

The collision of plates at high velocity sometimes causes them to be metallurgically bonded. A study has been made of the nature of the bonds and of the conditions required to produce bonding. A necessary requirement is the formation of a jet in the space ahead of the region of impact. When the collision region moves along the plates at a velocity which exceeds the bulk sound velocity of both materials, the relative velocity of the plates must exceed a critical value for jetting. Clarification of these critical conditions in symmetric collisions, and a correct extension to asymmetric collisions have been obtained by consideration of the effect of downstream boundary conditions on the configuration of the shock waves attached to the collision line in the jetless case. When the velocity of the collision is subsonic, bonding is obtained when the elastic strength of the material is exceeded. Metallographic examination shows that three types of bond may be formed: (1) a direct bond, (2) a uniform layer of solidified melt, and (3) a wavy interface with discrete regions of solidified melt alternating with regions of direct bond. Consideration of the flow indicates the following: (1) the direct bond results from the removal of the surface layers as part of the jet, (2) the alloy results from the melting caused by entrapment of the high-velocity jet between the plates, and (3) the wavy interface is caused by an oscillation in the jet flow which produces the mixed type of bonding. The thickness of the continuous alloy layer, which greatly exceeds the calculated jet thickness, indicates that entrapment of the jet dissipates most of the kinetic energy lost in the collision. Analysis of the layer indicates a composition and structure which is expected from the rapid quenching of a well-mixed melt.
Submarine cable telegraphy (1922)

The history of the development of the subject is first outlined, and methods of operation of cables are described. The technical side is introduced with a statement of the various conditions which limit operation of cables, and a general method of analysis is developed, based upon an extension of ordinary alternating-current theory. The theory is made use of to analyze the action of cable types and of apparatus which at this time can be regarded as standard. The fundamental theory of the method of analysis, with information on the calculation of transients in electrical circuits, is given in the Appendix.
Efficient M-QAM Transmission Using Compacted Magnitude Modulation Tables (2008)

Magnitude Modulation is a technique proposed with success for QPSK and OQPSK in order to maximize power and bandwidth of small satellite earth stations, by reducing PAPR of the modulated signal at the HPA input. To meet the ever growing demand for higher data rates, higher order modulations have been considered. This paper shows that it is possible to use the magnitude modulation concept for the M-QAM case, even considering the huge number of symbol combinations. The constellation and RRC symmetries are explored, allowing considerable reduction on look-up table computation complexity and storage requirements. Experimental results show considerable gains (>2dB) in PAPR and back-off reduction for 16-QAM with negligible BER losses.
MaxDIA enables library-based and library-free data-independent acquisition proteomics (2021)

MaxDIA is a software platform for analyzing data-independent acquisition (DIA) proteomics data within the MaxQuant software environment. Using spectral libraries, MaxDIA achieves deep proteome coverage with substantially better coefficients of variation in protein quantification than other software. MaxDIA is equipped with accurate false discovery rate (FDR) estimates on both library-to-DIA match and protein levels, including when using whole-proteome predicted spectral libraries. This is the foundation of discovery DIA-hypothesis-free analysis of DIA samples without library and with reliable FDR control. MaxDIA performs three- or four-dimensional feature detection of fragment data, and scoring of matches is augmented by machine learning on the features of an identification. MaxDIA's bootstrap DIA workflow performs multiple rounds of matching with increasing quality of recalibration and stringency of matching to the library. Combining MaxDIA with two new technologies-BoxCar acquisition and trapped ion mobility spectrometry-both lead to deep and accurate proteome quantification.
Video Super-Resolution via Residual Learning (2018)

Convolutional neural networks have been widely applied in many low level vision tasks. In this paper, we propose a video super-resolution (SR) method named enhanced video SR network with residual blocks (EVSR). The proposed EVSR fully exploits spatio-temporal information and can implicitly capture motion relations between consecutive frames. Therefore, unlike conventional methods to video SR, EVSR does not require an explicit motion compensation process. In addition, residual learning framework exhibits excellence in convergence rate and performance improvement. Based on this, residual blocks and long skip-connection with dimension adjustment layer are proposed to predict high-frequency details. Extensive experiments validate the superiority of our approach over state-of-the-art algorithms.