gebhart/patrepeval huggingface dataset:
Designing Enzyme-like Catalysts: A Rhodium(II) Metallopeptide Case Study (2012)

Chemists have long been fascinated by metalloenzymes and their chemistry. Because enzymes are essential for biological processes and to life itself, they present a key to understanding the world around us. At the same time, if chemists could harness the reactivity and selectivity of enzymes in designed transition-metal catalysts, we would have access to a powerful practical advance in chemistry. But the design of enzyme-like catalysts from scratch presents enormous challenges. Simplified, designed systems often don't provide the opportunity to mimic the complex features of enzymes such as selectivity in polyfunctional environments and access to reactive intermediates incompatible with bulk aqueous solution. Extensive efforts by numerous groups have led to remarkable designed metalloproteins that contain complex folds, including well-defined secondary and tertiary structure surrounding complex polymetallic centers. These structural achievements, however, have not yet led to general approaches to useful catalysts; continued efforts and new insights are needed. Our efforts have combined the attributes of enzymatic and traditional catalysis, bringing the benefits of polypeptide ligands to bear on completely nonbiological transition-metal centers. With a focus on designing useful catalytic activity, we have examined rhodium(II) carboxylates, bound to peptide chains through carboxylate side chains. Among other advantages, these complexes are stable and catalytically active in water. Our efforts have centered on two main interests: (1) understanding how Nature's ligand of choice, polypeptides, can be used to control the chemistry of nonbiological metal centers, and (2) mimicking metalloenzyme characteristics in designed, nonbiological catalysts. This Account conveys our motivation and goals for these studies, outlines progress to date, and discusses the future of enzyme-like catalyst design. In particular, these studies have resulted in on-bead, high-throughput screens for asymmetric metallopeptide catalysts. In addition, peptide-based molecular recognition strategies have facilitated the site-specific modification of protein substrates. Molecular recognition enables site-specific, proximity-driven modification of a broad range of amino acids, and the concepts outlined here are compatible with natural protein substrates and with complex, cell-like environments. We have also explored rhodium metallopeptides as hybrid organic-inorganic inhibitor molecules that block protein-protein interactions.
A Configurable Rete-OO Engine for Reasoning with Different Types of Imperfect Information (2010)

The RETE algorithm is a very efficient option for the development of a rule-based system, but it supports only boolean, first order logic. Many real-world contexts, instead, require some degree of vagueness or uncertainty to be handled in a robust and efficient manner, imposing a trade-off between the number of rules and the cases that can be handled with sufficient accuracy. Thus, in the first part of the paper, an extension of RETE networks is proposed, capable of handling a more general inferential process, which actually includes several types of schemes for reasoning with imperfect information. In particular, the architecture depends on a number of configuration parameters which could be set by the user, individually or as a whole for the entire rule base. The second part, then, shows how an appropriate combination of parameters can be used to emulate some of the most common, specialized engines: 3-valued logic, classical certainty factors, fuzzy, many-valued logic and Bayesian networks.
Trunk Injection: A Discriminating Delivering System for Horticulture Crop IPM (2014)

Trunk injection technology represents an alternative delivery system to provide crop protection for horticultural crops of commercial and smallholder farmers in the developed and developing world. Field studies, laboratory bioassays, and residue profile analysis were used to determine the seasonal effectiveness of trunk injected insecticides against key apple insect pests. Insecticides formulated for trunk injection, imidacloprid, rynaxypyr, and emamectin benzoate were injected into semi dwarf Empire apple trees and evaluated for a wide range of insect pests. Imidacloprid controlled piercing and sucking pests, and emamectin benzoate controlled leaf rollers, Oriental fruit moth, and leafhoppers, and rynaxypyr controlled Oriental fruit moth and leaf rollers. The residue profiles for insecticides showed that vascular delivery was predominantly to foliage, with fruit residues far below the EPA maximum residue limits, and low to no residues detected in apple flower parts. These results suggest that trunk injection is a promising delivering system for plant protection materials for control of foliar pests, while minimizing impacts on natural enemies, eliminating spray drift, and reducing the pesticide load in the agro-ecosystem. For smallholder farmers this low-capital investment technology has the potential to significantly reduce the human health risks associated with pesticide use, while protecting high value horticultural crops from pests
The Use of Chemical Spot Tests Kits for the Presumptive Identification of Narcotics and Drugs of Abuse (1974)

Abstract It is well known that chemical spot tests contribute to and are used for the identification of various substances [1–5]. From this information, chemical spot test kits have been commercially developed which are used by many law enforcement agencies for the identification of narcotics and drugs of abuse. There are basically two types of problems associated with the use of these kits, one which is inherent in the color reaction and the other which lies with color interpretation.
Resistance of adults to challenge with influenza A wild-type virus after receiving live or inactivated virus vaccine (1986)

The efficacy of live attenuated cold-adapted (ca) reassortant influenza A H3N2 and H1N1 virus vaccines against experimental challenge with homologous wild-type virus 7 months after vaccination was compared with that of licensed inactivated virus vaccine in 106 seronegative (hemagglutination-inhibiting antibody titer less than or equal to 1:8) college students. The live attenuated virus vaccines induced as much resistance against illness as did the inactivated vaccine. Vaccine efficacy, measured by reduction in febrile or systemic illness in vaccines, compared with that in controls was 100% for ca H3N2 vaccine, 84% for inactivated H3N2 vaccine, 79% for ca H1N1 vaccine, and 67% for inactivated H1N1 vaccine. Less protection was conferred against upper respiratory tract illness; there was 50 and 77% protection in ca and inactivated H3N2 vaccines, respectively, but there was no protection in ca or inactivated H1N1 vaccinees. The duration, but not the magnitude, of H1N1 wild-type virus shedding in both ca and inactivated vaccinees was significantly reduced compared with controls. In contrast, a significant reduction in the duration and magnitude of H3N2 virus shedding was observed in ca vaccinees but not in inactivated vaccines. After wild-type virus challenge, live ca virus vaccinees demonstrated resistance at least as great 7 months postvaccination as did inactivated virus vaccinees. These observations indicate that live virus vaccines may be a satisfactory alternative to inactivated vaccines for healthy persons.
A 6T SRAM with a carrier-injection scheme to pinpoint and repair fails that achieves 57% faster read and 31% lower read energy (2012)

Decreasing operating margins due to random variations is a key issue for voltage scaling in SRAM technology. It is particularly severe for half-select disturb because both write and read occur at the same row. While a wordline (WL) voltage assist technique [1] does not improve half-select disturbs, a negative bitline (BL) scheme [2] or asymmetric pass gate (PG) transistor with higher V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">TH</sub> during read [3] can be effective for mitigating half-select disturbs. While these techniques can increase operating margins, they cannot specifically target cells to correct for random variations.
Carcinoembryonic Antigen as a Selective Enhancer of Colorectal Cancer Metastasis (1990)

Although the serum level of carcinoembryonic antigen (CEA) is directly associated with a poor prognosis in human colorectal carcinoma (CRC), its function is obscure. As a member of the immunoglobulin supergene family, CEA may be involved with intercellular recognition and binding and facilitate attachment of CRC to sites of metastasis. In an experimental metastasis model of CRC in athymic nude mice, a systemic injection of CEA enhanced experimental liver metastasis and implantation in liver by a weakly metastatic CRC. This CRC also selectively bound to CEA that was attached to plastic. Thus, CEA may function as an attachment factor for CRC.
Comparison of performance of location-aware and traditional handoff-decision algorithms in CDPD networks (2002)

Traditional handoff algorithms based on stochastic and heuristic models perform poorly as they do not account for the rapid changes in the radio environments. Adaptive handoff algorithms are being developed to solve this problem with a corresponding tradeoff in terms of computational complexity. This paper suggests a location-aware handoff decision algorithm. The performance of the traditional and proposed handoff algorithm in a cellular digital packet data network (CDPD) are compared using simulations. The results indicate that the location-aware algorithm performs better than the traditional handoff algorithm.
Single-View Metrology: Algorithms and Applications (2002)

Abstract. This paper addresses the problem of extracting three-dimensional geometric information from a single, uncalibrated image of a scene. This work, building upon [7], is divided into two parts. The first part describes, in simple steps, the basic algorithms to obtain partial or complete geometric reconstruction from single perspective images of a scene. The second part presents a panorama of applications of single-view metrology and discusses its relationship with different disciplines such as architecture, history of art and forensic science. Furthermore, techniques for increasing the level of automation of the reconstruction process are herein described. Several examples on photographs and historical paintings demonstrate the power and flexibility of the proposed techniques. 1
<i>mik1</i><sup>+</sup> G1–S transcription regulates mitotic entry in fission yeast (2001)

In the fission yeast Schizosaccharomyces pombe Mik1p, in combination with Wee1p, is an important inhibitor of mitosis through direct phosphorylation of Cdc2p. Here we present the observation that mik1(+) is transcribed during G1- and S-phase in normally dividing cells. mik1(+) transcription is regulated by the MCB-DSC1 system, which controls expression of other genes at the G1-S interval. mik1(+) is shown to be an important target of MCB-DSC1 as it is epistatic for the mitotic delay phenotype displayed in cdc10-C4 cells, which are mutated in a component of DSC1. The mitotic delay in cdc10-C4 cells is bypassed by cdc2-1w, suggesting that mik1(+) acts directly on cdc2(+), with no checkpoint function involved. Thus, mik1(+) represents a new type of MCB-DSC1 regulated gene in fission yeast, whose gene product is exclusively expressed during G1- and S-phase to prevent premature mitosis during this cell cycle stage.
Fabrication of periodically reversed domain structure for SHG in LiNbO <sub>3</sub> , by direct electron beam lithography at room temperature (1991)

For the first time, the fabrication of a periodically reversed domain structure for LiNbO3 has been achieved at room temperature. The domain boundary is perpendicular to the positive c-face and is very deep which is advantageous for quasiphasematching SHG.
Variable selection in clustering and other contexts (1987)

Oxidative stress is a main cause of tissue damage and highly associated with incidence of human chronic diseases. Among the major target organs attacked by reactive oxygen species (ROS) is the liver. Protocatechuic acid (PCA) is a phenolic compound found in green tea, acai oil and some mushroom species that possesses strong antioxidative and anti-inflammatory activity and may have benefits as a natural phytochemical for prevention of human diseases. However, the protective effect of PCA on hydrogen peroxide (H<sub>2</sub>O<sub>2</sub>)-induced oxidative stress specifically in the liver has not yet been investigated. The current study aims to observe if PCA possesses protective activity against H<sub>2</sub>O<sub>2</sub>-induced oxidative stress in HepG2 human liver cancer cells. Relative to untreated control cells, treatment of HepG2 cells with PCA reduced H<sub>2</sub>O<sub>2</sub>-induced cell death and mitigated H<sub>2</sub>O<sub>2</sub>-induced production of ROS; furthermore, it mitigated the H<sub>2</sub>O<sub>2</sub>-induced increase of caspase-3/7 enzyme activity, expression of cleaved poly(ADP-ribose) polymerase (PARP), expression of endoplasmic reticulum (ER) stress genes including activating transcription factor 4 (ATF4), serine/threonine-protein kinase/endoribonuclease inositol-requiring enzyme 1 α (IRE1α) and phosphorylation of p38 mitogen-activated protein kinases (MAPK). These findings indicate that PCA effectively protects hepatic cells from H<sub>2</sub>O<sub>2</sub>-induced oxidative stress and cell death.
Wordpress- A convenient content-management system (CMS) (2018)

The objective of this study was to discuss about WordPress in detail and how custom integrations can be implemented with WordPress. Content Management Systems have made it easy-peasy to develop a web-site of any organization within a short period of time without having any knowledge of programming. There are several Content Management Systems which has great popularity. Some of them are WordPress, Drupal, Joomla. In this entire study I have focused on WordPress as it is quite famous among the other Content Management Systems (CMS). \n\nThe main theme of the study was to explain about WordPress in detail and the security issues or checks needed before launching a WordPress web-site. Additionally, the paper also discuss about how a custom integration can be implemented with WordPress. For instance, a custom integration has been elaborated which was to connect a contact form of a WordPress powered web-site to a database of Customer relationship management system (CRM) and sending the submitted contact form data to that database.
MADINA Y CHACÓN SE DISPUTAN LOS APOYOS PARA LAS PRIMARIAS: Los chaconistas, divididos entre el vasco y la catalana (2014)

Aunque la consigna es no mover ficha hasta despues de las europeas, ya hay revuelo entre algunos aspirantes a las primarias del PSOE. El primero en abrir fuego ha sido el vasco Eduardo Madina. pese a que aun no ha hecho oficial su paso al frente, mantiene una intensa actividad en busca de apoyos para su candidatura, que ya se da por mas que probable. Por lo tanto, cuenta con aliados entre los diputados mas jovenes y en federaciones como Extremadura o Madrid, donde podria estar robando antiguos aliados de Chacon, desencantados por la ausencia de la exdiputada. Tambien en Valencia, donde algunos miembros del grupo de cercanos a la chaconista y exministra Leire Pain -como su exjefe de gabinete, David del Campo- estan volviendo sus ojos hacia el diputado vasco.
Future Development of Technology in Dye-Sensitized Solar Cells (2011)

Reference EPFL-ARTICLE-170831View record in Web of Science Record created on 2011-12-16, modified on 2017-05-12
Constant linear velocity spiral scanning for near video rate 4D OCT ophthalmic and surgical imaging with isotropic transverse sampling (2018)

Ultrahigh speed optical coherence tomography (OCT) systems with >100 kHz A-scan rates can generate volumes rapidly with minimal motion artifacts and are well suited for 4D imaging (volumes through time) applications such as intra-operative imaging. In such systems, high OCT data acquisition efficiency (defined as the fraction of usable A-scans generated during the total acquisition time) is desired to maximize the volumetric frame rate and sampling pitch. However, current methods for beam scanning using non-resonant and resonant mirror scanners can result in severe scan distortion and transverse oversampling as well as require acquisition dead times, which limit the acquisition efficiency and performance of ultrahigh speed 4D OCT. We introduce constant linear velocity spiral scanning (CLV-SC) as a novel beam scanning method to maximize the data acquisition efficiency of ultrahigh speed 4D OCT systems. We demonstrate that CLV-SC does not require acquisition dead times and achieves more uniform transverse sampling compared to raster scanning. To assess its clinical utility, we implement CLV-SC with a 400 kHz OCT system and image the anterior eye and retina of healthy adults at up to 10 volumes per second with isotropic transverse sampling, allowing B-scans with equal sampling pitch to be extracted from arbitrary locations within a single volume. The feasibility of CLV-SC for intra-operative imaging is also demonstrated using a 800 kHz OCT system to image simulated retinal surgery at 15 volumes per second with isotropic transverse sampling, resulting in high quality volume renders that enable clear visualization of surgical instruments and manipulation of tissue.
Increased leukotriene A<sub>4</sub> hydrolase expression in the heart of angiotensin II‐induced hypertensive rat (1999)

Leukotriene A(4) (LTA(4)) hydrolase is essential for the conversion of LTA(4) to LTB(4), an inflammatory lipid mediator. We investigated whether LTA(4) hydrolase was regulated in the heart by angiotensin II (ang II) infusion. Continuous ang II infusion via an osmotic minipump for up to 7 days upregulated mRNA and protein levels of LTA(4) hydrolase ( approximately 3.5-fold of control) in the heart in a pressor-dependent manner. Immunohistochemistry demonstrated intense LTA(4) hydrolase staining in the myofibroblast as well as migrated monocytes/macrophages. These data suggest that the cardiac LTA(4) hydrolase-LTB(4) system plays a positive role in the promotion of cardiac inflammation in hypertension.
Arabidopsis Actin-Depolymerizing Factor AtADF4 Mediates Defense Signal Transduction Triggered by the<i>Pseudomonas syringae</i>Effector AvrPphB     (2009)

The actin cytoskeleton has been implicated in plant defenses against pathogenic fungi and oomycetes with limited, indirect evidence. To date, there are no reports linking actin with resistance against phytopathogenic bacteria. The dynamic behavior of actin filaments is regulated by a diverse array of actin-binding proteins, among which is the Actin-Depolymerizing Factor (ADF) family of proteins. Here, we demonstrate that actin dynamics play a role in the activation of gene-for-gene resistance in Arabidopsis (Arabidopsis thaliana) following inoculation with the phytopathogenic bacterium Pseudomonas syringae pv tomato. Using a reverse genetics approach, we explored the roles of Arabidopsis ADFs in plant defenses. AtADF4 was identified as being specifically required for resistance triggered by the effector AvrPphB but not AvrRpt2 or AvrB. Recombinant AtADF4 bound to monomeric actin (G-actin) with a marked preference for the ADP-loaded form and inhibited the rate of nucleotide exchange on G-actin, indicating that AtADF4 is a bona fide actin-depolymerizing factor. Exogenous application of the actin-disrupting agent cytochalasin D partially rescued the Atadf4 mutant in the AvrPphB-mediated hypersensitive response, demonstrating that AtADF4 mediates defense signaling through modification of the actin cytoskeleton. Unlike the mechanism by which the actin cytoskeleton confers resistance against fungi and oomycetes, AtADF4 is not involved in resistance against pathogen entry. Collectively, this study identifies AtADF4 as a novel component of the plant defense signaling pathway and provides strong evidence for actin dynamics as a primary component that orchestrates plant defenses against P. syringae.
Raf/MEK/MAPK signaling stimulates the nuclear translocation and transactivating activity of FOXM1c (2005)

The forkhead box (FOX) transcription factor FOXM1 is ubiquitously expressed in proliferating cells. FOXM1 expression peaks at the G2/M phase of the cell cycle and its functional deficiency in mice leads to defects in mitosis. To investigate the role of FOXM1 in the cell cycle, we used synchronized hTERT-BJ1 fibroblasts to examine the cell cycle-dependent regulation of FOXM1 function. We observed that FOXM1 is localized mainly in the cytoplasm in cells at late-G1 and S phases. Nuclear translocation occurs just before entry into the G2/M phase and is associated with phosphorylation of FOXM1. Consistent with the dependency of FOXM1 function on mitogenic signals, nuclear translocation of FOXM1 requires activity of the Raf/MEK/MAPK signaling pathway and is enhanced by the MAPK activator aurintricarboxylic acid. This activating effect was suppressed by the MEK1/2 inhibitor U0126. In transient reporter assays, constitutively active MEK1 enhances the transactivating effect of FOXM1c, but not FOXM1b, on the cyclin B1 promoter. RT-PCR analysis confirmed that different cell lines and tissues predominantly express the FOXM1c transcript. Mutations of two ERK1/2 target sequences within FOXM1c completely abolish the MEK1 enhancing effect, suggesting a direct link between Raf/MEK/MAPK signaling and FOXM1 function. Importantly, inhibition of Raf/MEK/MAPK signaling by U0126 led to suppression of FOXM1 target gene expression and delayed progression through G2/M, verifying the functional relevance of FOXM1 activation by MEK1. In summary, we provide the first evidence that Raf/MEK/MAPK signaling exerts its G2/M regulatory effect via FOXM1c.
Substrate recognition by oligosaccharyltransferase. Studies on glycosylation of modified Asn-X-Thr/Ser tripeptides. (1983)

The minimum primary structural requirement for N-glycosylation of proteins is the sequence -Asn-X-Thr/Ser-. In the present study, NH2-terminal derivatives of Asn-Leu-Thr-NH2 and peptides with asparagine replacements have been tested as substrates or inhibitors of N-glycosylation. The glycosylation of a known acceptor, N alpha-[3H]Ac-Asn-Leu-Thr-NHCH3, was optimized in chicken oviduct microsomes. The reaction was shown to be dependent upon Mn2+ and linear for 10 min at 30 degrees C; the apparent Km for the peptide was found to be 10 microM. N alpha-Acyl derivatives of Asn-Leu-Thr-NH2 (N-acetyl, N-benzoyl, N-octanoyl, or N-t-butoxycarbonyl) inhibited the glycosylation of N alpha-[3H] Ac-Asn-Leu-Thr-NHCH3 in a dose-dependent manner; additional experiments demonstrated that these compounds were alternative substrates rather than true inhibitors. The benzoyl and octanoyl derivatives were 10 times as effective as N alpha-Ac-Asn-Leu-Thr-NH2 in inhibiting glycosylation. In contrast, peptides containing asparagine modifications or substitutions were neither substrates nor inhibitors of N-glycosylation. They did not compete for glycosylation of 3H-peptide at 100-fold greater concentrations, and did not deplete endogenous pools of oligosaccharide-lipid. Thus, the asparagine side chain is an absolute requirement for recognition by the transferase. The majority of the glycosylated product (61%), but only 1% of the unglycosylated peptide, remained associated with the microsomes after high speed centrifugation. A large 41-amino acid residue acceptor peptide, alpha-lac17-58, was a poor substitute for glycosylation unless detergent was added to the microsomes. In contrast, glycosylation of tripeptide acceptors was not stimulated by detergent. Both of these findings suggest that the tripeptides are freely permeable to the microsomal membrane and support the earlier conclusion that glycosylation of proteins occurs at the luminal face of the microsomes.