gebhart/patrepeval huggingface dataset:
Manganese Substantially Alters the Dynamics of Translesion DNA Synthesis (2002)

The effect of metal ion substitution on the dynamics of translesion DNA synthesis catalyzed by the bacteriophage T4 DNA polymerase was quantitatively evaluated through steady-state and transient kinetic techniques. Substitution of Mn(2+) for Mg(2+) enhances the steady-state rate of dNMP misinsertion opposite an abasic site by 11-34-fold. At the molecular level, the enhancement in translesion DNA synthesis reflects a substantial increase in the rate of the conformational change preceding phosphoryl transfer for all dNTPs that were tested. This is best illustrated by the biphasic pre-steady-state time course of dAMP insertion opposite an abasic site which indicates that a step after chemistry is rate-limiting for steady-state enzyme turnover. Furthermore, the k(pol) value of 40 s(-1) measured under single-turnover reaction conditions is 20-fold greater than the k(cat) value of 2 s(-1) measured for steady-state enzyme turnover. Finally, the low elemental effect ( approximately 2.4-fold reduction in k(pol)) measured by substituting the alpha-thiotriphosphate analogue for dATP further argues that chemistry is not rate-limiting. In contrast to the biphasic insertion of dAMP, pre-steady-state time courses for the insertion of dCMP, dGMP, or dTMP opposite an abasic site were linear. Nearly identical k(pol) values ( approximately 1 s(-1)) were measured for the insertion of dCMP, dGMP, and dTMP opposite the abasic site using single-turnover conditions. However, the large elemental effects of 27 and 70 measured by substituting the alpha-thiotriphosphate analogues for dCTP and dGTP, respectively, suggest that phosphoryl transfer may be the rate-limiting step for their insertion opposite the abasic site. Various models are discussed in an attempt to explain the effect of metal ion substitution on the dynamics of translesion DNA replication.
Cyber-Physical Attacks Targeting Communication-Assisted Protection Schemes (2019)

The dependence of modern societies on electric energy is ever increasing by the emergence of smart cities and electric vehicles. This is while unprecedented number of cyber-physical hazards are threatening the integrity and availability of the power grid on a daily basis. On one hand, physical integrity of power systems is under threat by more frequent natural disasters and intentional attacks. On the other hand, the cyber vulnerability of power grids is on the rise by the emergence of smart grid technologies. This underlines an imminent need for the modeling and examination of power grid vulnerabilities to cyber-physical attacks. This paper examines the vulnerability of the communication-assisted protection schemes like permissive overreaching transfer trip to cyberattacks using a co-simulation platform. The simulation results show that the transient angle stability of power systems can be jeopardized by cyberattacks on the communication-assisted protection schemes. To address this vulnerability, two physical solutions including the deployment of communication channel redundancy, and a more advanced communicated-assisted protection scheme, i.e., directional comparison unblocking scheme (DCUB), are considered and tested. The proposed solutions address the vulnerability of the communication-assisted protection schemes to distributed denial of service attack to some extent. Yet, the simulation results show the vulnerability of the proposed solutions to sophisticated cyberattacks like false data injection attacks. This highlights the need for the development of cyber-based solutions for communication channel monitoring.
E-Business and Management Science: Mutual Impacts (Part 1 of 2) (2003)

This begins a two-part commentary on management science and e-business, the theme of this two-part special issue. After explaining the topical clusters that give organization to both parts, we pose two key questions concerning the impact of the emerging digital economy on management science research: What fundamentally new research questions arise, and what kind of research enables progress on them. We sketch the papers appearing in this part from the perspective of both these questions, and offer summary comments on the first question based on the papers in both parts. The principal conclusion is that the digital economy is giving birth to new research questions in three main ways (not all independent): by enabling and popularizing several types of technology-mediated interactions, by spawning large-scale digital data sources, and by creating recurring operational decisions that need to be automated.
Insights into thymic aging and regeneration (2005)

The deterioration of the immune system with progressive aging is believed to contribute to morbidity and mortality in elderly humans due to the increased incidence of infection, autoimmunity, and cancer. Dysregulation of T-cell function is thought to play a critical part in these processes. One of the consequences of an aging immune system is the process termed thymic involution, where the thymus undergoes a progressive reduction in size due to profound changes in its anatomy associated with loss of thymic epithelial cells and a decrease in thymopoiesis. This decline in the output of newly developed T cells results in diminished numbers of circulating naive T cells and impaired cell-mediated immunity. A number of theories have been forwarded to explain this 'thymic menopause' including the possible loss of thymic progenitors or epithelial cells, a diminished capacity to rearrange T-cell receptor genes and alterations in the production of growth factors and hormones. Although to date no interventions fully restore thymic function in the aging host, systemic administration of various cytokines and hormones or bone marrow transplantation have resulted in increased thymic activity and T-cell output with age. In this review, we shall examine the current literature on thymic involution and discuss several interventional strategies currently being explored to restore thymic function in elderly subjects.
Development and validation of a spectral library searching method for peptide identification from MS/MS (2007)

A notable inefficiency of shotgun proteomics experiments is the repeated rediscovery of the same identifiable peptides by sequence database searching methods, which often are time-consuming and error-prone. A more precise and efficient method, in which previously observed and identified peptide MS/MS spectra are catalogued and condensed into searchable spectral libraries to allow new identifications by spectral matching, is seen as a promising alternative. To that end, an open-source, functionally complete, high-throughput and readily extensible MS/MS spectral searching tool, SpectraST, was developed. A high-quality spectral library was constructed by combining the high-confidence identifications of millions of spectra taken from various data repositories and searched using four sequence search engines. The resulting library consists of over 30,000 spectra for Saccharomyces cerevisiae. Using this library, SpectraST vastly outperforms the sequence search engine SEQUEST in terms of speed and the ability to discriminate good and bad hits. A unique advantage of SpectraST is its full integration into the popular Trans Proteomic Pipeline suite of software, which facilitates user adoption and provides important functionalities such as peptide and protein probability assignment, quantification, and data visualization. This method of spectral library searching is especially suited for targeted proteomics applications, offering superior performance to traditional sequence searching.
Drive Systems for Multiaxial and Special Purpose Test Systems (1974)

In this chapter, examples are given of fatigue systems and machines which have been designed to apply more than one mode of loading that subjects the specimen to biaxial or triaxial stresses. In addition, there are discussions of a number of special purpose test systems.
A Reevaluation of the Key Factors That Influence Tomato Fruit Softening and Integrity (2007)

The softening of fleshy fruits, such as tomato (Solanum lycopersicum), during ripening is generally reported to result principally from disassembly of the primary cell wall and middle lamella. However, unsuccessful attempts to prolong fruit firmness by suppressing the expression of a range of wall-modifying proteins in transgenic tomato fruits do not support such a simple model. 'Delayed Fruit Deterioration' (DFD) is a previously unreported tomato cultivar that provides a unique opportunity to assess the contribution of wall metabolism to fruit firmness, since DFD fruits exhibit minimal softening but undergo otherwise normal ripening, unlike all known nonsoftening tomato mutants reported to date. Wall disassembly, reduced intercellular adhesion, and the expression of genes associated with wall degradation were similar in DFD fruit and those of the normally softening 'Ailsa Craig'. However, ripening DFD fruit showed minimal transpirational water loss and substantially elevated cellular turgor. This allowed an evaluation of the relative contribution and timing of wall disassembly and water loss to fruit softening, which suggested that both processes have a critical influence. Biochemical and biomechanical analyses identified several unusual features of DFD cuticles and the data indicate that, as with wall metabolism, changes in cuticle composition and architecture are an integral and regulated part of the ripening program. A model is proposed in which the cuticle affects the softening of intact tomato fruit both directly, by providing a physical support, and indirectly, by regulating water status.
Aptamers to <i>Escherichia coli</i> core RNA polymerase that sense its interaction with rifampicin, σ‐subunit and GreB (2004)

Bacterial RNA polymerase (RNAP) is the central enzyme of gene expression that is responsible for the synthesis of all types of cellular RNAs. The process of transcription is accompanied by complex structural rearrangements of RNAP. Despite the recent progress in structural studies of RNAP, detailed mechanisms of conformational changes of RNAP that occur at different stages of transcription remain unknown. The goal of this work was to obtain novel ligands to RNAP which would target different epitopes of the enzyme and serve as specific probes to study the mechanism of transcription and conformational flexibility of RNAP. Using in vitro selection methods, we obtained 13 classes of ssDNA aptamers against Escherichia coli core RNAP. The minimal nucleic acid scaffold (an oligonucleotide construct imitating DNA and RNA in elongation complex), rifampicin and the sigma70-subunit inhibited binding of the aptamers to RNAP core but did not affect the dissociation rate of preformed RNAP-aptamer complexes. We argue that these ligands sterically block access of the aptamers to their binding sites within the main RNAP channel. In contrast, transcript cleavage factor GreB increased the rate of dissociation of preformed RNAP-aptamer complexes. This suggested that GreB that binds RNAP outside the main channel actively disrupts RNAP-aptamer complexes by inducing conformational changes in the channel. We propose that the aptamers obtained in this work will be useful for studying the interactions of RNAP with various ligands and regulatory factors and for investigating the conformational flexibility of the enzyme.
Feed for dual-band printed dipole antenna (2004)

A dual-band printed dipole antenna is proposed for WLAN applications in the 2.4 and 5.2 GHz bands. A spur line was etched on the arms of the printed dipole to achieve the dual-band operation. The printed dipole antenna with a simplified matching network is proposed. The novel simplified feed structure consists of a pair of parallel metal strips printed on the opposite sides of the dielectric substrate and connected to a 50 Ω microstrip line with a truncated ground plane. This feeding network does not require additional transition devices, such as a T-junction, power divider, tuning stub or microstrip-to-coplanar stripline balun.
Activity-centric streaming of virtual environments and games to mobile devices (2011)

As mobile devices still have limited battery, processing power, memory, and display size, compared to their PC counterparts, they cannot yet execute Virtual Environment (VE) and Online Gaming applications with the same fidelity and quality as their PC counterpart. In response, we have recently witnessed some research with the goal of real-time delivery of VE and multiplayer game content specifically to fit mobile devices' limitations. In this paper, we present a novel approach to tackle the streaming of 3D objects for such environments. Our goal is to improve the real-time response and interactivity of networked VEs and games through an efficient context-aware 3D object selection and prioritization scheme, before streaming those objects over the network. In our architecture, we take advantage of game context for culling and streaming only the most relevant objects in each frame of gameplay and stream them from the server to a client. Our evaluations show that this technique not only leads to better performance in general, but also increases gameplay experience by helping the player to achieve a higher score in comparison with traditional approaches.
A novel protein from <i>Brassica napus</i> has a putative KID domain and responds to low temperature (2003)

To identify factors that interact with histone deacetylase (HDAC) in Brassica napus, a yeast two-hybrid library was screened using the Arabidopsis HDA19 as bait. A novel protein, bnKCP1, containing a putative kinase-inducible domain (KID) was found to interact with HDA19. Southern blot analysis indicated that the bnKCP1 gene belongs to a small gene family of at least three members. Northern blot analysis showed bnKCP1 to be strongly expressed in stems, flowers, roots, and immature siliques, but not in leaf blades of seedlings. The accumulation of bnKCP1 transcript in the leaf blades was induced significantly within 4 h of exposure of B. napus seedlings to cold stress, whereas treatment of leaf blades with inomycin, an ionophore of Ca2+, caused a rapid (30 min) but transient induction of bnKCP1 expression. In contrast to that observed in leaf blades, expression of bnKCP1 in the stems was repressed upon cold treatment. In vitro and in vivo protein-binding assays showed that bnKCP1 interacts with HDA19 via the KID domain, and that S188 is critical for bnKCP1-HDA19 interaction. BnKCP1 also exerted modest transactivation of the lacZ reporter gene in yeast through its N-terminal region. These assays suggest that bnKCP1 may function as a transcription factor, which regulates gene expression through interaction with HDA19.
Voice Profile for Internet Mail (VPIM) Addressing (2004)

This document lists the various Voice Profile for Internet Mail (VPIM)
email address formats that are currently in common use and defines
several new address formats for special case usage. Requirements are
imposed on the formats of addresses used in VPIM submission mode.
[STANDARDS-TRACK]
Retinoids in Cancer Chemoprevention (2004)

We review the therapeutic and preventive applications of a retinoid analog (vitamin A and its derivatives) for human cancers. Chemoprevention of cancer is an intervention in the carcinogenic process by chemical agents that block or reverse the malignant transformation of cells. Retinoids are prime candidates for cancer chemoprevention since cancer is characterized by abnormal growth with a lack of differentiation, which could be modified by retinoids. Retinoids exert their biological functions through nuclear receptors, retinoic acid receptor (RAR) and retinoid X receptor (RXR). A number of experimental and clinical studies have been performed in the past two decades with retinoids showing that they inhibit or reverse the carcinogenic process in some organs, including hematological malignancy as well as premalignant and malignant lesions in the oral cavity, head and neck, breast, skin and liver. We particularly focus upon the therapeutic application of all-trans RA (atRA) to acute promyelocytic leukemia (APL) and on the preventive approach to hepatocellular carcinoma (HCC) by a synthetic retinoid analog, acyclic retinoid. In both malignancies, malfunction of retinoid nuclear receptors is closely related to their carcinogenic process. In APL, a chromosomal translocation produces a chimeric protein between RAR alpha and a protein called promyelocyte leukemia protein (PML). PML-RAR alpha works as a dominant negative receptor in the leukemic cells, interfering with the normal function of RAR alpha and/or PML, which in turn results in the arrest of cell maturation at the stage of promyelocytes. Oral administration of atRA induces differentiation of promyelocytic leukemic cells to mature neutrophils, and leads to a high rates (over 90%) of complete remission. AtRA therapy has become standard in the treatment of APL. In the case of HCC, post-translational modification of RXR by phosphorylation impairs its function, which leads to uncontrolled cell growth. Acyclic retinoid suppresses the phosphorylation of RXR alpha, restores its function in the presence of its endogenous ligand, 9-cis RA, and thereby induces apoptosis of the cancer cells. Acyclic retinoid given orally successfully suppresses the development of second primary tumors in cirrhotic patients who undergo curative removal of preceding HCC. Eradication of (pre)malignant clones ('clonal deletion') from the liver is suggested as a mechanism of the chemopreventive effect. Further development of more effective retinoids as well as their use in combination with other classes of anticancer agents including immunopreventive drugs like interferons may provide strategies for cancer prevention.
The Central Enzymes of the Aspartate Family of Amino Acid Biosynthesis (2001)

The aspartate pathway is responsible for the biosynthesis of lysine, threonine, isoleucine, and methionine in most plants and microorganisms. The absence of this pathway in humans and animals makes the central enzymes potential targets for inhibition, with the aim of developing new herbicides and biocides, and also for enhancement, to improve the nutritional value of crops. Our current state of knowledge of these enzymes is reviewed, including recently determined structural information and newly constructed bifunctional fusion enzymes.
Identification of cytosolic aldehyde dehydrogenase 1 from non‐small cell lung carcinomas as a flavopiridol‐binding protein (1999)

The synthetic flavone flavopiridol can be cytostatic or cytotoxic to mammalian cells, depending on the concentration of the drug and the duration of exposure. It has been shown to inhibit the cyclin-dependent kinase (CDK) family of cell cycle regulatory enzymes. However, the existence of additional potential targets for drug action remains a matter of interest to define. To identify cellular targets, flavopiridol was immobilized. CDKs, particularly CDK 4, bound weakly to immobilized flavopiridol when ATP was absent but not in its presence. Two proteins with molecular weights of 40 kDa and 120 kDa had high affinities to the immobilized flavopiridol independent of the presence of ATP. They were present in all cell lines analyzed: cervical (HeLa), prostate and non-small cell lung carcinoma (NSCLC) cell lines. A 60-kDa protein, which was present only in NSCLC cells and bound similarly well to immobilized flavopiridol, was identified as cytosolic aldehyde dehydrogenase class 1 (ALDH-1). The level of this protein correlated with the resistance of NSCLC cell lines to cytotoxicity caused by 500 nM flavopiridol but not higher flavopiridol concentrations. Despite binding to ALDH-1, there was no inhibition of dehydrogenase activity by flavopiridol concentrations as high as 20 microM and flavopiridol was not metabolized by ALDH-1. The results suggest that high cellular levels of ALDH-1 may reduce cytotoxicity of flavopiridol and contribute to relative resistance to the drug. This is the first report that flavopiridol binds to proteins other than CDKs.
Principles and implementation of direct torque control by stator flux orientation of an induction motor (1995)

The field oriented control of an induction motor is sensitive to machine parameters and some detuning is expected in most rotor flux oriented systems. Consequently, direct torque control has been introduced to reduce parameter sensitivity problems, which are negligible at high speed. The authors of this paper present principles and implementation, with a digital signal processor, of the control system. They propose solutions to correct integrators, which cause some drift and operation errors, and they estimate the possibilities of the proposal. They describe the methods used to obtain good performance, even in the low speed range, where the stator resistance influence becomes critical.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Plasmon Line Shaping Using Nanocrosses for High Sensitivity Localized Surface Plasmon Resonance Sensing (2011)

The detection of small changes in the wavelength position of localized surface plasmon resonances in metal nanostructures has been used successfully in applications such as label-free detection of biomarkers. Practical implementations, however, often suffer from the large spectral width of the plasmon resonances induced by large radiative damping in the metal nanocavities. By means of a tailored design and using a reproducible nanofabrication process, high quality planar gold plasmonic nanocavities are fabricated with strongly reduced radiative damping. Moreover, additional substrate etching results in a large enhancement of the sensing volume and a subsequent increase of the sensitivity. Coherent coupling of bright and dark plasmon modes in a nanocross and nanobar is used to generate high quality factor subradiant Fano resonances. Experimental sensitivities for these modes exceeding 1000 nm/RIU with a Figure of Merit reaching 5 are demonstrated in microfluidic ensemble spectroscopy.
Traumatic brain injury (2016)

Abstract Traumatic brain injury remains the most common cause of trauma-related death and disability, disproportionately affecting young individuals, most often males. In addition, the cost to individuals and society in emotional, social, and financial terms is substantial as the disabling effects of the original injury may persist for many years. This chapter discusses the management of the critically ill patient with traumatic brain injury. It provides an overview of the changing epidemiology, systems of classification, resuscitation in the field, transfer, and the management in the intensive care unit. In particular, the chapter reviews intracranial pressure- versus cerebral perfusion pressure-guided management strategies, multimodal monitoring, limitations of current research methodologies, and strategies for the future.
Axicabtagene Ciloleucel as Second-Line Therapy for Large B-Cell Lymphoma (2021)

Axi-cel therapy led to significant improvements, as compared with standard care, in event-free survival and response, with the expected level of high-grade toxic effects. (Funded by Kite; ZUMA-7 ClinicalTrials.gov number, NCT03391466.).