gebhart/patrepeval huggingface dataset:
A 1H-NMR study of the activity expressed by lactate dehydrogenase in the human erythrocyte (1986)

The activity expressed by lactate dehydrogenase in the human erythrocyte has been compared with the activity displayed by the isolated enzyme in vitro. Enzyme activity was measured by using 1H spin-echo NMR to measure non-invasively the velocity of hydrogen label exchange between the C-2 positions of two methyl-labelled lactate species. This method has significant advantages over a method which has been described previously. The exchange velocity observed in the cell was much lower than that expected based on a comparison with measurements of the exchange velocity in vitro under conditions thought to simulate the intracellular environment. Measurements of enzyme inhibition in cell extracts suggest that the low intracellular activity is due to inhibition of the enzyme by low-molecular-mass compounds present in the cell.
Physiological Properties of hERG 1a/1b Heteromeric Currents and a hERG 1b-Specific Mutation Associated With Long-QT Syndrome (2008)

Cardiac I Kr is a critical repolarizing current in the heart and a target for inherited and acquired long-QT syndrome (LQTS). Biochemical and functional studies have demonstrated that I Kr channels are heteromers composed of both hERG 1a and 1b subunits, yet our current understanding of I Kr functional properties derives primarily from studies of homooligomers of the original hERG 1a isolate. Here, we examine currents produced by hERG 1a and 1a/1b channels expressed in HEK-293 cells at near-physiological temperatures. We find that heteromeric hERG 1a/1b currents are much larger than hERG 1a currents and conduct 80% more charge during an action potential. This surprising difference corresponds to a 2-fold increase in the apparent rates of activation and recovery from inactivation, thus reducing rectification and facilitating current rebound during repolarization. Kinetic modeling shows these gating differences account quantitatively for the differences in current amplitude between the 2 channel types. Drug sensitivity was also different. Compared to homomeric 1a channels, heteromeric 1a/1b channels were inhibited by E-4031 with a slower time course and a corresponding 4-fold shift in the IC50. The importance of hERG 1b in vivo is supported by the identification of a 1b-specific A8V missense mutation in 1/269 unrelated genotype-negative LQTS patients that was absent in 400 control alleles. Mutant 1bA8V expressed alone or with hERG 1a in HEK-293 cells dramatically reduced 1b protein levels. Thus, mutations specifically disrupting hERG 1b function are expected to reduce cardiac I Kr and enhance drug sensitivity, and represent a potential mechanism underlying inherited or acquired LQTS.
Preparation and Characterization of Cellulose Nanofibers from Two Commercial Hardwood and Softwood Pulps (2009)

The aim of this work was to study the mechanical fibrillation process for the preparation of cellulose nanofibers from two commercial hard- and softwood cellulose pulps. The process consisted of initial refining and subsequent high-pressure homogenization. The progress in fibrillation was studied using different microscopy techniques, mechanical testing, and fiber density measurements of cellulose films prepared after different processing stages. The mechanical properties of cellulose films showed an increase in strength and stiffness with decreasing fiber size, and this stabilized after a certain number of passes in the homogenizer. Atomic force microscopy studies showed that the obtained cellulose nanofibers had diameters in the 10−25-nm range. The significant difference between the two samples was that the ultimate failure strain for cellulose films made of softwood fibers increased during the process whereas it remained constantly low for hardwood cellulose films. This difference could be due to the presence of shorter fibers and more defects in the films. An important point to note is that excessive processing reduced properties, as seen by the decrease in failure strain of softwood fiber films, and could also decrease other properties such as strength if the number of processing steps were further increased.
Zero Defects Needs Third Party Software to Succeed (2006)

The challenge of achieving zero defects cannot be achieved by semiconductor OEMs acting on their own. Semiconductor test needs to understand and embrace the role that third party vendors can play in overcoming such challenges
Unsupervised Joint Alignment of Complex Images (2007)

Many recognition algorithms depend on careful positioning of an object into a canonical pose, so the position of features relative to a fixed coordinate system can be examined. Currently, this positioning is done either manually or by training a class-specialized learning algorithm with samples of the class that have been hand-labeled with parts or poses. In this paper, we describe a novel method to achieve this positioning using poorly aligned examples of a class with no additional labeling. Given a set of unaligned examplars of a class, such as faces, we automatically build an alignment mechanism, without any additional labeling of parts or poses in the data set. Using this alignment mechanism, new members of the class, such as faces resulting from a face detector, can be precisely aligned for the recognition process. Our alignment method improves performance on a face recognition task, both over unaligned images and over images aligned with a face alignment algorithm specifically developed for and trained on hand-labeled face images. We also demonstrate its use on an entirely different class of objects (cars), again without providing any information about parts or pose to the learning algorithm.
BeF\documentclass[12pt]{minimal}\usepackage{amsmath}\usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy}\usepackage{mathrsfs}\setlength{\oddsidemargin}{-69pt}\begin{document}\begin{equation*}{\mathrm{_{3}^{-}}}\end{equation*}\end{document} acts as a phosphate analog in proteins phosphorylated on aspartate: Structure of a BeF\documentclass[12pt]{minimal}\usepackage{amsmath}\usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy}\usepackage{mathrsfs}\setlength{\oddsidemargin}{-69pt}\begin{document}\begin{equation*}{\mathrm{_{3}^{-}}}\end{equation*}\end{document} complex with phosphoserine phosphatase (2001)

Protein phosphoaspartate bonds play a variety of roles. In response regulator proteins of two-component signal transduction systems, phosphorylation of an aspartate residue is coupled to a change from an inactive to an active conformation. In phosphatases and mutases of the haloacid dehalogenase (HAD) superfamily, phosphoaspartate serves as an intermediate in phosphotransfer reactions, and in P-type ATPases, also members of the HAD family, it serves in the conversion of chemical energy to ion gradients. In each case, lability of the phosphoaspartate linkage has hampered a detailed study of the phosphorylated form. For response regulators, this difficulty was recently overcome with a phosphate analog, BeF(3)(-), which yields persistent complexes with the active site aspartate of their receiver domains. We now extend the application of this analog to a HAD superfamily member by solving at 1.5-A resolution the x-ray crystal structure of the complex of BeF(3)(-) with phosphoserine phosphatase (PSP) from Methanococcus jannaschii. The structure is comparable to that of a phosphoenzyme intermediate: BeF(3)(-) is bound to Asp-11 with the tetrahedral geometry of a phosphoryl group, is coordinated to Mg(2+), and is bound to residues surrounding the active site that are conserved in the HAD superfamily. Comparison of the active sites of BeF(3)(-) x PSP and BeF(3)(-) x CeY, a receiver domain/response regulator, reveals striking similarities that provide insights into the function not only of PSP but also of P-type ATPases. Our results indicate that use of BeF(3)(-) for structural studies of proteins that form phosphoaspartate linkages will extend well beyond response regulators.
Large-scale lattice Boltzmann simulations of complex fluids: advances through the advent of computational Grids (2005)

During the last 2.5 years, the RealityGrid project has allowed us to be one of the few scientific groups involved in the development of computational Grids. Since smoothly working production Grids are not yet available, we have been able to substantially influence the direction of software and Grid deployment within the project. In this paper, we review our results from large-scale three-dimensional lattice Boltzmann simulations performed over the last 2.5 years. We describe how the proactive use of computational steering, and advanced job migration and visualization techniques enabled us to do our scientific work more efficiently. The projects reported on in this paper are studies of complex fluid flows under shear or in porous media, as well as large-scale parameter searches, and studies of the self-organization of liquid cubic mesophases.
Creep Damage in a Cr-Mo-V Steel as Measured by Retained Stress Rupture Properties (1957)

Abstract It is well known that a material subjected to progressive creep eventually fractures at a time determined by the applied stress and temperature. However, the processes which exhaust the metal ductility in creep are very poorly understood. Until these processes are clearly defined it is not possible to arrive at a satisfactory fracture theory for creep nor is it possible to predict intelligently the effects of creep history on the rupture life. In this investigation the progressive metal deterioration occurring during creep at 1000 F is measured by the retained 1100 F stress-rupture properties. This “creep damage” is shown to be both strain and time-sensitive. The creep conditions producing large damages are defined and a mechanism for the damage suggested. It is also shown that reheat treatment is able to heal the most severe damages produced in this investigation.
Methylthio- and ethanediyldithio-substituted 1,6-dithiapyrenes and their charge-transfer complexes: new organic molecular metals (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMethylthio- and ethanediyldithio-substituted 1,6-dithiapyrenes and their charge-transfer complexes: new organic molecular metalsKazuhiro Nakasuji, Mitsuru Sasaki, Tomoyuki Kotani, Ichiro Murata, Toshiaki Enoki, Kenichi Imaeda, Hiroo Inokuchi, Atsushi Kawamoto, and Jiro TanakaCite this: J. Am. Chem. Soc. 1987, 109, 23, 6970–6975Publication Date (Print):November 1, 1987Publication History Published online1 May 2002Published inissue 1 November 1987https://pubs.acs.org/doi/10.1021/ja00257a011https://doi.org/10.1021/ja00257a011research-articleACS PublicationsRequest reuse permissionsArticle Views399Altmetric-Citations52LEARN 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
Automated elemental analysis using energy dispersive X-ray fluorescence analysis (1977)

The application of energy dispersive x-ray fluorescence analysis to the measurements of air particulate samples has been described in several recent publications.Among its many advantages, the possibility of automatic analysis for large scale monitoring programs has not been widely discussed.We describe the completion of a program in which a total of 34,000 air particulate samples have been collected and analyzed over the past two years.An automatic photonexcited energy di spers ive spectrometer was used to obtain elemental concentrations for 27 elements on each sample.The sensitivity of the system is adequate to detect quantities of 10 ngm/cm 2 or less in a measurement time of approximately six minutes per sample.The precision and accuracy of the results will be compared to statistical analyses of the data set.Summaries of the results are presented and the implications for air particulate monitoring discussed.
The intricate side of systems biology (2006)

The combination of high-throughput methods of molecular biology with advanced mathematical and computational techniques has propelled the emergent field of systems biology into a position of prominence. Unthinkable a decade ago, it has become possible to screen and analyze the expression of entire genomes, simultaneously assess large numbers of proteins and their prevalence, and characterize in detail the metabolic state of a cell population. Although very important, the focus on comprehensive networks of biological components is only one side of systems biology. Complementing large-scale assessments, and sometimes at the risk of being forgotten, are more subtle analyses that rationalize the design and functioning of biological modules in exquisite detail. This intricate side of systems biology aims at identifying the specific roles of processes and signals in smaller, fully regulated systems by computing what would happen if these signals were lacking or organized in a different fashion. We exemplify this type of approach with a detailed analysis of the regulation of glucose utilization in Lactococcus lactis. This organism is exposed to alternating periods of glucose availability and starvation. During starvation, it accumulates an intermediate of glycolysis, which allows it to take up glucose immediately upon availability. This notable accumulation poses a nontrivial control task that is solved with an unusual, yet ingeniously designed and timed feedforward activation system. The elucidation of this control system required high-precision, dynamic in vivo metabolite data, combined with methods of nonlinear systems analysis, and may serve as a paradigm for multidisciplinary approaches to fine-scaled systems biology.
On the performance of submitting excess traffic to ATM networks (2002)

The author presents performance study results on forward congestion notification (FCN) in ATM (asynchronous transfer mode) networks; FCN is an element of an overall set of mechanisms that can be employed in ATM network traffic management. When a network element (e.g. a switch) becomes congested, it sets a notification indicator in chosen cell headers to inform destination terminals that there is congestion en-route. Terminal-to-terminal protocols may use this information to adapt their use of network resources to the prevailing conditions. The author investigates the efficacy of this scheme; in view of propagation delays that may affect the timeliness of the congestion information, it is not clear whether or not the mechanism would be useful in ATM networks. A simple terminal-to-terminal protocol that uses the FC indicator is described, and the behavior of network and terminal queues is investigated. It is found that FCN has significant value in helping terminal-to-terminal protocols adapt to the state of the network. Even when propagation delays are long, the use of the mechanism results in better behavior than if an open-loop mechanism is used.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Effect of Anaerobic Stabilization of Activated Sludge on its Production under Batch Conditions at Various So/Xo Ratios (1991)

The effect of anaerobic stabilization of returned activated sludge in a continuous system on biomass production under batch conditions at various So/Xo ratios was studied. A system without anaerobic sludge stabilization was also operated as a control unit. All experiments were carried out with Toulouse settled wastewater. Biomass growth, substrate removal, oxygen uptake and carbon dioxide production were measured using a quadrupole mass spectrometer (Inficon IQ 200) coupled to a 15-liter fermentor (Biolafitte). The results confirmed that one of the most important parameters in batch cultivation is the initial So/Xo ratio. It was found that anaerobic treatment of activated sludge changed its behaviour during batch cultivation. As a consequence, the observed biomass yield (Yobs) decreased with increasing So/Xo while it remained constant with the sludge from the control unit. In the anaerobic reactor, microorganisms are subject to a physiological shock due to lack of oxygen and food. Under the above conditions, they use ATP as a source of energy. After they are returned to aerobiosis and supplied with exogenous substrate, they rebuild energy reserves at the expense of growth.
Colour matching for ink-jet prints on paper (1998)

Predicting the colour of trichromatic prints by measuring the colour of the primaries and their areas has been shown to be possible using large area textile prints. This approach has been extended to paper printing with much smaller coloured areas, in a predetermined array of squares. As before, the light reflected from the coloured areas mixed additively within the integrating sphere of a spectrophotometer. Cyan, magenta, and yellow were used, with the addition of red, green, blue, and black, to simulate the typical situation likely to arise in commercial paper ink-jet printers. Partitive colour-mixing theory was used to predict the colours, and the results compared well with those obtained by measurement. However, unwanted overlaps of the printed coloured squares caused all the measured results to be darker and of higher chroma. The reverse process, whereby the area of each colour was calculated for a given target colour, specified by its tristimulus values, was also carried out. The results were generally in agreement with the actual number of squares used to produce the target, within one square out of 16. © 1998 John Wiley & Sons, Inc. Col Res Appl, 23, 18–26, 1998
Depth perception from motion parallax in the peripheral vision (2002)

The depth perception produced by motion parallax in the peripheral vision was investigated. To examine the effects of head movements on the depth perception, two observational conditions were settled, observation with head movements and without them. In experiment 1, the stimuli which simulated the identical amounts of depth were presented at various eccentricities. The results showed that the perceived depth generally decreased with the eccentricity. These results were discussed in relation to the perceived relative velocities. In experiment 2 the motion parallax stimuli which produced the identical relative velocities perceptions at each eccentricity were used. As a results, the amounts of the perceived depth decreased with the eccentricity as experiment 1. These results indicate that the perceived depth decreased with the eccentricity, though the perceived relative velocities were equal. The differences of the perceived depth in the observational conditions were not shown, while the angles of perceived rocking motion with head movements were smaller than that without them. It is suggested that the relation between the perception of depth and of motion obtained from motion parallax can't be explained by a simple trade-off relation.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Selective Inhibition of Hypoxia-Inducible Factor (HIF) Prolyl-Hydroxylase 1 Mediates Neuroprotection against Normoxic Oxidative Death via HIF- and CREB-Independent Pathways (2009)

Oxidative stress contributes to tissue injury in conditions ranging from cardiovascular disease to stroke, spinal cord injury, neurodegeneration, and perhaps even aging. Yet the efficacy of antioxidants in human disease has been mixed at best. We need a better understanding of the mechanisms by which established antioxidants combat oxidative stress. Iron chelators are well established inhibitors of oxidative death in both neural and non-neural tissues, but their precise mechanism of action remains elusive. The prevailing but not completely substantiated view is that iron chelators prevent oxidative injury by suppressing Fenton chemistry and the formation of highly reactive hydroxyl radicals. Here, we show that iron chelation protects, rather unexpectedly, by inhibiting the hypoxia-inducible factor prolyl 4-hydroxylase isoform 1 (PHD1), an iron and 2-oxoglutarate-dependent dioxygenase. PHD1 and its isoforms 2 and 3 are best known for stabilizing transcriptional regulators involved in hypoxic adaptation, such as HIF-1alpha and cAMP response element-binding protein (CREB). Yet we find that global hypoxia-inducible factor (HIF)-PHD inhibition protects neurons even when HIF-1alpha and CREB are directly suppressed. Moreover, two global HIF-PHD inhibitors continued to be neuroprotective even in the presence of diminished HIF-2alpha levels, which itself increases neuronal susceptibility to oxidative stress. Finally, RNA interference to PHD1 but not isoforms PHD2 or PHD3 prevents oxidative death, independent of HIF activation. Together, these studies suggest that iron chelators can prevent normoxic oxidative neuronal death through selective inhibition of PHD1 but independent of HIF-1alpha and CREB; and that HIF-2alpha, not HIF-1alpha, regulates susceptibility to normoxic oxidative neuronal death.
C/EBPβ (CCAAT/Enhancer Binding Protein) Controls Cell Fate Determination during Mammary Gland Development (2000)

Abstract Deletion of the transcription factor CCAAT/enhancer binding protein (C/EBP)β results in a severe inhibition of lobuloalveolar development in the mouse mammary gland. Because progesterone receptor (PR) is requisite for alveolar development, the expression of PR was investigated in C/EBPβ−/− mice. Unexpectedly, the number of PR-positive cells, as well as the levels of PR mRNA, were elevated 3-fold in the mammary glands of C/EBPβ−/− mice. Furthermore, in contrast to wild-type nulliparous mice, in which PR distribution shifted from a uniform to nonuniform pattern between 8–12 weeks of age, C/EBPβ−/− mice exhibited uniform PR distribution throughout all stages of mammary development analyzed. No change in C/EBPβ mRNA levels was observed in the mammary glands of PR−/− mice, suggesting that PR acts in a pathway either in parallel to or downstream of C/EBPβ. The overexpression and disrupted cellular distribution of PR in C/EBPβ−/− mice were coincident with a striking 10-fold decrease in cell proliferation after acute steroid hormone treatment, assayed by incorporation of bromodeoxyuridine. In wild-type mice, PR and bromodeoxyuridine-positive cells were adjacent to each other and rarely colocalized. No differences in the level or pattern of PR expression were observed in the uterus, suggesting that C/EBPβ influences PR in a mam-mary-specific fashion. Together, these data suggest that C/EBPβ may control cell fate decisions in the mammary gland through the appropriate temporal and spatial expression of molecular markers, such as PR, that induce the proliferation of alveolar progenitor cells via juxtacrine mechanisms.