gebhart/patrepeval huggingface dataset:
Wideband leaky-mode resonance reflectors: Influence of grating profile and sublayers (2008)

We apply inverse numerical methods to design compact wideband reflectors in which a periodic silicon layer supports resonant leaky modes. Using particle swarm optimization to determine appropriate device thickness, period, and fill factors, we arrive at example reflector designs for both TE and TM polarized input light. As a properly configured grating profile provides added design freedom, we design reflectors with two and four subparts in the period. In TM polarization, a particular single-layer two-part reflector has 520 nm bandwidth whereas the four-part device reaches 600 nm bandwidth. In TE polarization, the corresponding numbers are 125 nm and 495 nm, respectively. We provide a qualitative explanation for the smaller TE-reflector bandwidth. We quantify the effects of deviation from the design parameters and compute the angular response of the elements. As the angle of incidence deviates from normal incidence, narrow transmission channels emerge in the response yielding a bandpass filter with low sidebands. The effects of adding a silica sublayer between a silicon substrate and the periodic silicon layer is investigated. It is found that a properly designed sublayer can extend the reflection bandwidth significantly.
Eicosapentanoic acid inhibits hypoxia-reoxygenation-induced injury by attenuating upregulation of MMP-1 in adult rat myocytes (2003)

These observations suggest that EPA attenuates an increase in MMP-1 following H-R, which may be a basis of protection of myocytes from the adverse effects of H-R. p38MAPK phosphorylation may be an important signaling event in this process.
Storage of Hydrogen, Methane, and Carbon Dioxide in Highly Porous Covalent Organic Frameworks for Clean Energy Applications (2009)

Dihydrogen, methane, and carbon dioxide isotherm measurements were performed at 1-85 bar and 77-298 K on the evacuated forms of seven porous covalent organic frameworks (COFs). The uptake behavior and capacity of the COFs is best described by classifying them into three groups based on their structural dimensions and corresponding pore sizes. Group 1 consists of 2D structures with 1D small pores (9 A for each of COF-1 and COF-6), group 2 includes 2D structures with large 1D pores (27, 16, and 32 A for COF-5, COF-8, and COF-10, respectively), and group 3 is comprised of 3D structures with 3D medium-sized pores (12 A for each of COF-102 and COF-103). Group 3 COFs outperform group 1 and 2 COFs, and rival the best metal-organic frameworks and other porous materials in their uptake capacities. This is exemplified by the excess gas uptake of COF-102 at 35 bar (72 mg g(-1) at 77 K for hydrogen, 187 mg g(-1) at 298 K for methane, and 1180 mg g(-1) at 298 K for carbon dioxide), which is similar to the performance of COF-103 but higher than those observed for COF-1, COF-5, COF-6, COF-8, and COF-10 (hydrogen at 77 K, 15 mg g(-1) for COF-1, 36 mg g(-1) for COF-5, 23 mg g(-1) for COF-6, 35 mg g(-1) for COF-8, and 39 mg g(-1) for COF-10; methane at 298 K, 40 mg g(-1) for COF-1, 89 mg g(-1) for COF-5, 65 mg g(-1) for COF-6, 87 mg g(-1) for COF-8, and 80 mg g(-1) for COF-10; carbon dioxide at 298 K, 210 mg g(-1) for COF-1, 779 mg g(-1) for COF-5, 298 mg g(-1) for COF-6, 598 mg g(-1) for COF-8, and 759 mg g(-1) for COF-10). These findings place COFs among the most porous and the best adsorbents for hydrogen, methane, and carbon dioxide.
Transactional auto scaler (2012)

In this paper we introduce TAS (Transactional Auto Scaler), a system for automating elastic-scaling of in-memory transactional data grids, such as NoSQL data stores or Distributed Transactional Memories. Applications of TAS range from on-line self-optimization of in-production applications to automatic generation of QoS/cost driven elastic scaling policies, and support for what-if analysis on the scalability of transactional applications.
PHOTOBIOLOGICAL ACTIVITIES OF 5‐A‐LKOXYPSORALENS WITH RESPECT TO THE ACTION ON Escherichia coli (1986)

Abstract— Near‐UV induced activities of a series of 5‐a‐lkoxypsoralen derivatives (C 1 to C 8 ) and 5‐h‐ydroxypsoralen were compared with respect to lethal, mutagenic and prophage inducing effects on E. coli . Although 5‐a‐lkoxypsoralen derivatives having an alkoxyl chain longer than C 2 were slightly soluble, their saturated solutions containing their insoluble portion showed the significant photolethal effect on E. coli . 5‐E‐thoxypsoralen was less photoactive in inducing phenotypic reversion of the arginine auxotrophy than 5‐m‐ethoxypsoralen but it photoinduced prophage lambda from the lysogenic bacteria as well as 5‐m‐ethoxypsoralen. Photomutagenesis by the derivatives of C 3 to C 8 could not be detected but ca . 10% of the lysogenic bacteria photoinduced prophage in the presence of the derivatives at the maximum induction.
Further evidence for increased macrophage migration inhibitory factor expression in prostate cancer (2005)

Increased serum MIF was associated with prostate cancer. Diluent reagents that included BSA resulted in MIF serum immunoassay interference. In addition, significant amounts of complexed MIF (180 kDa under denaturing conditions by Western blot) found in the serum do not bind to the MIF capture antibody. Increased MIF mRNA expression was observed in prostatic adenocarcinoma compared to benign tissue from matched samples, supporting our earlier finding of increased MIF gene expression in prostate cancer.
Email worm modeling and defense (2005)

Email worms constitute one of the major Internet security problems. We present an email worm model that accounts for the behaviors of email users by considering email checking time and the probability of opening email attachments. Email worms spread over a logical network defined by email address relationship, which plays an important role in determining the spreading dynamics of an email worm. Our observations suggest that the node degrees of an email network are heavy-tailed distributed. We compare email worm propagation on three topologies: power law, small world and random graph topologies; and then study how the topology affects immunization defense on email worms. The impact of the power law topology on the spread of email worms is mixed: email worms spread more quickly on a power law topology than on a small world topology or a random graph topology, but immunization defense is more effective on a power law topology than on the other two.
11 Structure and Mechanism of the Large Catalytic RNAs: Group I and Group II Introns and Ribonuclease P (1993)

Living cells require thousands of different chemical reactions to grow, store energy, move, respond to external stimuli, and reproduce. These reactions may take place spontaneously, but they rarely occur at a rate fast enough to support life. Biological catalysts accelerate these reactions, often by a factor of a billion or even a trillion, and also impart on them exquisite specificity. Biological catalysis is mostly the realm of protein enzymes, at least in modern cells. During the past decade, however, we have come to see that proteins do not have a monopoly on biological catalysis. Some RNA molecules are able to fold up to form active sites that catalyze chemical reactions, perhaps including a key reaction of protein synthesis. Furthermore, there is much speculation that RNA catalysis may have made an essential contribution to the establishment of self-replication and information-directed protein synthesis in early evolution. The purpose of this chapter is to describe what we know and what we would like to know about some of these catalytic RNAs, or “ribozymes” (Kruger et al. 1982). The specific questions are those of structure (How do these RNAs fold to form an active site?) and mechanism (What chemical reactions occur and how are they catalyzed?). The decision to cover the group I and group II introns and the catalytic RNA subunit of RNase P in a single review is justifiable on two grounds. First, these are all large ribozymes compared, for example, to the hammerhead (see Pan et al., this volume). Although size...
Bilateral diffuse pulmonary ectopic ossification after marrow allograft in a dog. Evidence for allotransplantation of hemopoietic and mesenchymal stem cells. (1983)

In light of recent studies showing successful transplantation of both bony and stromal elements by marrow transplantation, we report an unexpected phenomenon occurring in a canine radiation chimera. Nine hundred fifty-six days after a successful and uneventful DLA-matched marrow allograft, a dog suddenly died of respiratory failure. Autopsy revealed extensive ossification of the lungs with multiple sites of trilineage marrow engraftment. The entire complement of bony elements can apparently be allografted using marrow grafting techniques.
Genetic heterogeneity in benign familial neonatal convulsions: identification of a new locus on chromosome 8q. (1993)

The syndrome of benign familial neonatal convulsions (BFNC) is a rare autosomal dominant disorder characterized by unprovoked seizures in the first few weeks of life. One locus for BFNC has been mapped to chromosome 20 in several pedigrees, but we have excluded linkage to chromosome 20 in one large kindred. In order to identify this novel BFNC locus, dinucleotide repeat markers distributed throughout the genome were used to screen this family. Maximum pairwise LOD scores of 4.43 were obtained with markers D8S284 and D8S256 on chromosome 8q. Multipoint analysis placed the BFNC locus in the interval spanned by D8S198-D8S274. This study establishes the presence of a new BFNC locus and confirms genetic heterogeneity of this disorder.
Nitric oxide regulation of mitochondrial oxygen consumption I: cellular physiology (2006)

Mitochondrial biochemistry is complex, expanding from oxygen consumption, oxidative phosphorylation, lipid catabolism, heme biosynthesis, to apoptosis, calcium homeostasis, and production of reactive oxygen species, including nitric oxide (NO). The latter molecule is produced by a mitochondrial NO synthase (mtNOS). The rates of consumption and production determine the steady-state concentration of NO at subcellular levels, leading to regulation of mitochondrial events. Temporospatial processes tightly regulate production of NO in mitochondria to maximize target effects and minimize deleterious reactions. Temporal regulatory mechanisms of mtNOS include activation by calcium signaling and transcriptional/translational regulations. Calcium-activated mtNOS inhibits mitochondrial respiration, resulting in a decrease of the oxygen consumption. This negative regulation antagonizes the effects of calcium on calcium-dependent dehydrogenases in the citric acid cycle, preventing the formation of anoxic foci. Temporal regulation of NO production by intracellular calcium signaling is a complex process, considering the heterogeneous intracellular calcium response and distribution. NO production in mitochondria is spatially regulated by mechanisms that determine subcellular localization of mtNOS, likely acylation and protein-protein interactions, in addition to transcriptional regulation as neuronal NOS. Because NO rapidly decays in mitochondria, subcellular localization of mtNOS is crucial for NO to function as a signal molecule. These temporospatial processes are biologically important to allow NO to act as an effective signal molecule to regulate mitochondrial events such as oxygen consumption and reactive oxygen species production.
Esterification of 1,4-dichlorobutane with sodium formate under solid–liquid phase transfer catalysis. A kinetic study (1989)

Kinetic data are reported regarding the esterification of 1,4-dichlorobutane with sodium formate catalyzed by quaternary ammonium salts as a model for reactions in series, under solid–liquid phase transfer conditions. The process was found to follow a consecutive first-order mechanism of the general type A → R → S. The reactivity of the quaternary ammonium salts with regard to the counteranion was Cl − &gt; Br − &gt; 1 − &gt; HSO 4 − . The reaction rate was linearly dependent on catalyst concentration up to 12 mol% of catalyst relative to the substrate. Above this concentration the rate was constant and independent of the amount of the catalyst. The activation energy of the two consecutive steps was found to be similar (21 kcal/mol). Therefore, the product distribution (R/S) is not appreciably affected by temperature. A mechanism termed "Thin aqueous boundary layer" is suggested for nucleophilic displacement reactions under solid–liquid phase transfer conditions. Keywords: phase transfer catalysis, series reactions, kinetic study.
SoK: Research Perspectives and Challenges for Bitcoin and Cryptocurrencies (2015)

Bit coin has emerged as the most successful cryptographic currency in history. Within two years of its quiet launch in 2009, Bit coin grew to comprise billions of dollars of economic value despite only cursory analysis of the system's design. Since then a growing literature has identified hidden-but-important properties of the system, discovered attacks, proposed promising alternatives, and singled out difficult future challenges. Meanwhile a large and vibrant open-source community has proposed and deployed numerous modifications and extensions. We provide the first systematic exposition Bit coin and the many related crypto currencies or 'altcoins.' Drawing from a scattered body of knowledge, we identify three key components of Bit coin's design that can be decoupled. This enables a more insightful analysis of Bit coin's properties and future stability. We map the design space for numerous proposed modifications, providing comparative analyses for alternative consensus mechanisms, currency allocation mechanisms, computational puzzles, and key management tools. We survey anonymity issues in Bit coin and provide an evaluation framework for analyzing a variety of privacy-enhancing proposals. Finally we provide new insights on what we term disinter mediation protocols, which absolve the need for trusted intermediaries in an interesting set of applications. We identify three general disinter mediation strategies and provide a detailed comparison.
The 1999 SWISS-2DPAGE database update (2000)

SWISS-2DPAGE (http://www.expasy.ch/ch2d/ ) is an annotated two-dimensional polyacrylamide gel electro-phoresis (2-DE) database established in 1993. The current release contains 24 reference maps from human and mouse biological samples, as well as from Saccharomyces cerevisiae, Escherichia coli and Dictyostelium discoideum origin. These reference maps have now 2824 identified spots, corresponding to 614 separate protein entries in the database, in addition to virtual entries for each SWISS-PROT sequence or any user-entered amino acids sequence. Last year improvements in the SWISS-2DPAGE database are as follows: three new maps have been created and several others have been updated; cross-references to newly built federated 2-DE databases have been added; new functions to access the data have been provided through the ExPASy proteomics server.
Turbulent Flows (2000)

This is a graduate text on turbulent flows, an important topic in fluid dynamics. It is up-to-date, comprehensive, designed for teaching, and is based on a course taught by the author at Cornell University for a number of years. The book consists of two parts followed by a number of appendices. Part I provides a general introduction to turbulent flows, how they behave, how they can be described quantitatively, and the fundamental physical processes involved. Part II is concerned with different approaches for modelling or simulating turbulent flows. The necessary mathematical techniques are presented in the appendices. This book is primarily intended as a graduate level text in turbulent flows for engineering students, but it may also be valuable to students in applied mathematics, physics, oceanography and atmospheric sciences, as well as researchers and practising engineers.
Spectral embedding based active contour (SEAC): application to breast lesion segmentation on DCE-MRI (2011)

Spectral embedding (SE), a graph-based manifold learning method, has previously been shown to be useful in high dimensional data classification. In this work, we present a novel SE based active contour (SEAC) segmentation scheme and demonstrate its applications in lesion segmentation on breast dynamic contrast enhance magnetic resonance imaging (DCE-MRI). In this work, we employ SE on DCE-MRI on a per voxel basis to embed the high dimensional time series intensity vector into a reduced dimensional space, where the reduced embedding space is characterized by the principal eigenvectors. The orthogonal eigenvector-based data representation allows for computation of strong tensor gradients in the spectrally embedded space and also yields improved region statistics that serve as optimal stopping criteria for SEAC. We demonstrate both analytically and empirically that the tensor gradients in the spectrally embedded space are stronger than the corresponding gradients in the original grayscale intensity space. On a total of 50 breast DCE-MRI studies, SEAC yielded a mean absolute difference (MAD) of 3.2±2.1 pixels and mean Dice similarity coefficient (DSC) of 0.74±0.13 compared to manual ground truth segmentation. An active contour in conjunction with fuzzy c-means (FCM+AC), a commonly used segmentation method for breast DCE-MRI, produced a corresponding MAD of 7.2±7.4 pixels and mean DSC of 0.58±0.32. In conjunction with a set of 6 quantitative morphological features automatically extracted from the SEAC derived lesion boundary, a support vector machine (SVM) classifier yielded an area under the curve (AUC) of 0.73, for discriminating between 10 benign and 30 malignant lesions; the corresponding SVM classifier with the FCM+AC derived morphological features yielded an AUC of 0.65.
Activity of Minocycline Against R Factor-Carrying Enterobacteriaceae (1970)

Minocycline (Min) and other tetracyclines were tested in vivo and in vitro for activity against strains of salmonellae harboring R factor-mediated chlortetracycline (A) resistance. Minocycline was more active in vitro against these strains than the other tetracyclines. Mice infected with these cultures responded to treatment with Min, but there was little or no response to treatment with the other tetracyclines. Various A-resistant field isolates of Salmonella typhimurium and Escherichia coli were all shown to be more susceptible in vitro to Min than to A. Several of these cultures were shown to transfer A resistance. Cultures of normal bacterial flora were isolated from swine fecal matter after plating on Min-supplemented Mac-Conkey agar. All recovered cultures were more susceptible in vitro to Min than to A. Several isolates were able simultaneously to transfer Min and A resistances into S. choleraesuis var. kunzendorf; however, the levels of Min resistance in either the donors or exconjugants were no higher than in those cultures of salmonellae which responded in vivo to Min therapy. The same was true for the levels of Min resistance in the field isolates of S. typhimurium and E. coli. The increased potency of Min, as compared to tetracycline, against R factor-carrying bacteria was not observed for organisms made resistant (presumably chromosomally) to A by successive transfers in increasing concentrations of the agent, suggesting different mechanisms as the basis for chromosomal versus R factor-mediated A resistances.
Dynamic Changes in Splanchnic Blood Flow and Blood Volume in Dogs during Activation of Sympathetic Nerves (1971)

Arterial inflow to and venous outflow from the vascularly isolated splanchnic region were measured simultaneously by using cannulating electromagnetic square-wave flow transducers in 25 anesthetized dogs with intact abdomens. Change in splanchnic blood volume (SBV) was calculated as the instantaneous difference between inflow and outflow. Addition of the respective increases and decreases in SBV induced by changing carotid sinus pressure from the control value (mean, 136 mm Hg) to 200 or to 40 mm Hg gave an average total volume of 93 ml of blood ( SD , ±21.7) that could be mobilized reflexly from the splanchnic circulation, Electrical stimulation (15 v, 2 cps, 3 msec duration) of the left thoracic splanchnic nerve for 2 to 10 minutes decreased SBV by 159 ml of blood ( SD , ±84). These mean values represent 32 and 48%, respectively, of the calculated total SBV. In both situations the translocation of blood was rapid, 50% of the total change in splanchnic blood flow and SBV occurring within 30 seconds. During a 2-minute hemorrhage (7.2 ml/kg), a mean volume of 56 ml of blood ( SD , ±16) was mobilized from the splanchnic region. This represented 54% of the total volume bled. Under these circumstances, blood moved out of the splanchnic circulation at a fairly constant rate.
Dinuclear Zinc Complexes Based on Parallel β-Diiminato Binding Sites:  Syntheses, Structures, and Properties as CO2/Epoxide Copolymerization Catalysts (2007)

With the background that β-diketiminato zinc complexes efficiently catalyze the CO2/epoxide copolymerization via a mechanism involving two catalyst molecules, a ligand system containing two parallel β-diiminato binding sites linked by a xanthene backbone ([RXanthdim]2- with residues R = 2,3-dimethylphenyl and 2,4-difluorophenyl at the iminato units, respectively) was investigated with respect to its zinc coordination chemistry. The corresponding diimines [RXanthdim]H2 were treated with diethylzinc to yield the complexes [Me2C6H3Xanthdim](ZnEt)2, 4, and [F2C6H3Xanthdim](ZnEt(thf))2, 5, respectively. In order to convert these compounds into polymerization catalysts, they were subsequently treated with SO2, which indeed resulted in the corresponding ethylsulfinates. Due to aggregation via intermolecular bridging of ethylsulfinate ligands, the product after the reaction of 5 represents an insoluble coordination polymer. Aggregation does take place also for the primary product obtained from the reaction of 4, as evidenced by the isolation of the tetramer [{[Me2C6H3Xanthdim]Zn2(μ-O2SEt)}μ-O2SEt]4, 6, and the precipitation of an insoluble solid on storing of such mixtures. 4, 5, and 6 display moderate activities as catalysts for the copolymerization of cyclohexene oxide and CO2. A bimodal molecular weight distribution points to two effective mechanisms, one of which probably involves two cooperating Zn centers as anticipated. Possible structural reasons for these catalytic results are discussed.