gebhart/patrepeval huggingface dataset:
Profiling Selective Packaging of Host RNA and Viral RNA Modification in SARS-CoV-2 Viral Preparations (2022)

Viruses package host RNAs in their virions which are associated with a range of functions in the viral life cycle. Previous transcriptomic profiling of host RNA packaging mostly focused on retroviruses. Which host RNAs are packaged in other viruses at the transcriptome level has not been thoroughly examined. Here we perform proof-of-concept studies using both small RNA and large RNA sequencing of six different SARS-CoV-2 viral isolates grown on VeroE6 cells to profile host RNAs present in cell free viral preparations and to explore SARS-CoV-2 genomic RNA modifications. We find selective enrichment of specific host transfer RNAs (tRNAs), tRNA fragments and signal recognition particle (SRP) RNA in SARS-CoV-2 viral preparations. Different viral preparations contain the same set of host RNAs, suggesting a common mechanism of packaging. We estimate that a single SARS-CoV-2 particle likely contains up to one SRP RNA and four tRNA molecules. We identify tRNA modification differences between the tRNAs present in viral preparations and those in the uninfected VeroE6 host cells. Furthermore, we find uncharacterized candidate modifications in the SARS-CoV-2 genomic RNA. Our results reveal an under-studied aspect of viral-host interactions that may be explored for viral therapeutics.
DRAM System Simulation Speed-Up by Effective-Cycle Selection (2014)

Full system simulation is a developing methodology that aids to find the optimized configurations of system design. Huge amount of data is collected to better characterize the performance of the system. This process requires both accuracy and speed. Cycle-accurate modeling is precise but time and resource consuming. Higher abstraction level of modeling, such as transaction-level modeling, trades accuracy for speed. We propose a novel approach called "Effective-cycle Selection" to reduce redundant check of command scheduler in memory controller without affecting the functionality. Redundant checks occur in the cycles in which no command would be issued by the command scheduler. By predicting effective cycles, the proposed method diminishes redundancy and speed up simulation by up to 40% in multi-program real workloads, while introducing zero error in simulation compared to the cycle-based simulator. To the best of our knowledge, this is the first research work which leverages the redundancy of memory command scheduling to accelerate simulation.
Effect of Interfacial Layers on the Performance of Cu-In Liquid Phase Sintered Composites as Thermal Interface and Interconnect Materials (2011)

In this study, a novel architecture composed of uniformly distributed high melting phase (HMP, e.g. Cu) in a low melting phase (LMP, e.g. In) matrix, which can be produced via liquid phase sintering (LPS), is proposed to produce next generation thermal interface materials (TIMs) and interconnect (IC) materials. The LMP determines the shear compliance of these composites whereas the HMP determines its thermal and electrical conductivities. The volume fraction of In was optimized to produce a Cu-In solder with suitable mechanical, electrical and thermal properties for TIM and IC applications. Since, Cu and In react to form several Cu-In intermetallic compounds (IMCs), which may deteriorate the long-term performance of these solders, interfacial-layers of Au and Al2O3 were applied on Cu to further improve the performance of the Cu-In solders. The effect of interfacial-layers on the reaction between Cu and In, during sintering at 160°C and during aging at 125°C, was studied and its impact on the mechanical, thermal and electrical properties was evaluated. Au interfacial layer (50∼200nm) quickly reacted with In to form AuIn2 IMC, which acted as a tenacious diffusion-barrier and slowed down the reactions between Cu and In. 8-monolayer thick Al2O3 did not react with either Cu or In and inhibited reactions between Cu and In. During short-time sintering, the effect of interfacial layer on the thicknesses of IMCs was insignificant to affect the yield strength of the as-sintered composites. However, IMC layer thickened rapidly in the Cu-In composites without an interfacial-layer, which led to a drastic decrease in the volume fraction of unreacted In leading to an increase in the yield strength of the solder. On the other hand, the interfacial-layers effectively suppressed the growth of IMCs during aging and hence the yield strength of such composites increased at slower rates. Since, the IMCs formed at the interface radically affect the contact resistance, significant differences in the thermal and electrical conductivities were recorded for the solders with different interfacial-layers.
Hepatitis C Virus‐Specific Cytolytic T Lymphocyte and T Helper Cell Responses in Seronegative Persons (1997)

Hepatitis C virus (HCV) is a common infection worldwide, and in most persons, it leads to persistent viremia and liver damage. Efforts to identify the correlates of protective immunity are hampered by this high rate of persistent infection in both infected humans and the only animal model, the chimpanzee. Peripheral blood mononuclear cells from seronegative persons were stimulated with synthetic peptides that represent epitopes recognized by HCV-specific cytotoxic T lymphocytes (CTL) after natural infection. In addition, CD4+ proliferative responses to recombinant HCV proteins were examined in these same persons. CTL responses directed against a peptide epitope of HCV and proliferative responses in 2 HCV-seronegative persons with possible occupational exposure to HCV were found. These otherwise healthy persons were not viremic, suggesting that they may have recovered from acute HCV infection. Characterization of virus-specific immune responses in exposed but seronegative persons may provide important clues as to the nature of protective immunity in HCV.
The outer-membrane export signal of Porphyromonas gingivalis type IX secretion system (T9SS) is a conserved C-terminal β-sandwich domain (2016)

In the recently characterized Type IX Secretion System (T9SS), the conserved C-terminal domain (CTD) in secreted proteins functions as an outer membrane translocation signal for export of virulence factors to the cell surface in the Gram-negative Bacteroidetes phylum. In the periodontal pathogen Porphyromonas gingivalis, the CTD is cleaved off by PorU sortase in a sequence-independent manner, and anionic lipopolysaccharide (A-LPS) is attached to many translocated proteins, thus anchoring them to the bacterial surface. Here, we solved the atomic structure of the CTD of gingipain B (RgpB) from P. gingivalis, alone and together with a preceding immunoglobulin-superfamily domain (IgSF). The CTD was found to possess a typical Ig-like fold encompassing seven antiparallel β-strands organized in two β-sheets, packed into a β-sandwich structure that can spontaneously dimerise through C-terminal strand swapping. Small angle X-ray scattering (SAXS) revealed no fixed orientation of the CTD with respect to the IgSF. By introducing insertion or substitution of residues within the inter-domain linker in the native protein, we were able to show that despite the region being unstructured, it nevertheless is resistant to general proteolysis. These data suggest structural motifs located in the two adjacent Ig-like domains dictate the processing of CTDs by the T9SS secretion pathway.
Motion Generation in MRI Using an Electrostatic Linear Motor for Visualizing Internal Deformation of Soft Objects by tagged cine-MRI (2007)

This paper introduces a new actuating system for MRI study, combining the linear electrostatic film motor and tagged cine-MRI process to visualize internal deformation of soft objects. The linear electrostatic film motor is MR-compatible, simple structure, and easily controlled by open-loop. Motion of the motor and MR scanning are synchronized by a trigger and the motor conducts more than 250 cycles of reciprocating movements to create deformation in the soft subjects. A force sensor is developed using shielded strain gauges to monitor the applied force to the objects during MR scanning and the MR-compatibility of the newly made sensor was evaluated. The developed system was tested against gel samples. The obtained images using the system clearly showed the internal deformation of the soft samples under pushing force given by the electrostatic motor. Although further modifications are desirable, the pushing force was successfully measured by the newly made force sensor during MR scanning.
Safety and efficacy of ustekinumab or golimumab in patients with chronic sarcoidosis (2014)

Sarcoidosis is characterised by non-caseating granulomas that secrete pro-inflammatory cytokines, including interleukin (IL)-12, IL-23, and tumour necrosis factor (TNF)-α. Ustekinumab and golimumab are monoclonal antibodies that specifically inhibit IL-12/IL-23 and TNF-α, respectively. Patients with chronic pulmonary sarcoidosis (lung group) and/or skin sarcoidosis (skin group) received either 180 mg ustekinumab at week 0 followed by 90 mg every 8 weeks, 200 mg golimumab at week 0 followed by 100 mg every 4 weeks, or placebo. Patients underwent corticosteroid tapering between weeks 16 and 28. The primary end-point was week 16 change in percentage predicted forced vital capacity (ΔFVC % pred) in the lung group. Major secondary end-points were: week 28 for ΔFVC % pred, 6-min walking distance, St George's Respiratory Questionnaire (lung group), and Skin Physician Global Assessment response (skin group). At week 16, no significant differences were observed in ΔFVC % pred with ustekinumab (-0.15, p = 0.13) or golimumab (1.15, p = 0.54) compared with placebo (2.02). At week 28, there were no significant improvements in the major secondary end-points, although a nonsignificant numerically greater Skin Physician Global Assessment response was observed following golimumab treatment (53%) when compared with the placebo (30%). Serious adverse events were similar in all treatment groups. Although treatment was well tolerated, neither ustekinumab nor golimumab demonstrated efficacy in pulmonary sarcoidosis. However, trends towards improvement were observed with golimumab in some dermatological end-points.
Endocrine Effects of Dietary Restriction and Aging: The National Institute on Aging Study (2001)

Calorie restriction (CR) has been shown repeatedly to extend lifespan and reduce the incidence of age-related disease in a variety of animal models. Rhesus monkeys experience many age-related changes in hormone function that parallel those observed in humans and evidence suggests that CR is a safe and effective means for slowing many of these aging changes. In the National Institute on Aging (NIA) long-term study on rhesus monkeys, CR improved glucoregulatory function and disrupted both the thyroid and growth hormone axis, all of which may be important for mediating the effects of CR. Male monkeys experienced delayed puberty. However, data from old females indicated that restriction did not alter hormone levels or cycling—thus, reducing the potential risk of reproductive dysfunction due to lower caloric intake. While it is certainly advantageous to document improved health and longevity, the long lifespan of nonhuman primates dictates the need to develop physiological biomarkers of aging. Dehydroepiandrosterone (DHEA) and melatonin have met criteria as such and CR was shown to attenuate the age-related decline of these hormones in monkeys. This review summarizes selected findings on the hormonal changes elicited by CR in aging rhesus monkeys.
Evaluation of Porous ZrO 2 ‐SiO 2 and Monazite Coatings Using Nextel TM 720‐Fiber‐Reinforced Blackglas™ Minicomposites (2001)

A procedure was developed to fabricate oxide‐fiber‐reinforced minicomposites with a dense matrix and evaluate two oxidation‐resistant interface coatings, porous oxide (zirconia‐silica mixture) and monazite. The coatings were evaluated using Nextel TM 720‐fiber‐reinforced Blackglas TM ‐matrix minicomposites. Boron nitride (BN) coated and uncoated fibers were used as controls for comparison. The evaluation was based on ultimate failure strengths, fractography, and fiber pushin tests. All the composites that used fiber coatings had ultimate strengths significantly better than the control that used uncoated fibers. In addition, porous‐oxide‐coated fibers were found to be similar to BN‐coated fibers in strength, fractography, and fiber pushin behavior. Monazite‐coated fibers resulted in similar ultimate strengths but showed no appreciable fiber pullout. Fiber pushin tests showed that monazite debonds readily but frictional resistance is higher than for BN or porous oxide fiber coatings.
Construction of white-rot fungal-bacterial consortia with improved ligninolytic properties and stable bacterial community structure (2023)

It is believed that wood-rot fungi change their wood decay activities due to influences from co-existing bacterial communities; however, it is difficult to elucidate experimentally the interaction mechanisms in fungal-bacterial consortia because the bacterial community structure is quite unstable and readily changes. Indeed, the wood decay properties of fungal-bacterial consortia consisting of a white-rot fungus Phanerochaete sordida YK-624 and a natural bacterial community changed dramatically during several sub-cultivations on wood. Therefore, development of a sub-cultivation method that imparts stability to the bacterial community structure and fungal phenotype was attempted. The adopted method using agar medium enabled maintenance of fungal phenotypes relating to wood decay and the bacterial community even through dozens of repetitive sub-cultures. Some bacterial metabolic pathways identified based on gene predictions were screened as candidates involved in P. sordida-bacterial interactions. In particular, pathways related to prenyl naphthoquinone biosynthesis appeared to be involved in an interaction that promotes higher lignin degradation selectivity by the consortia, as naphthoquinone derivatives induced phenol-oxidizing activity. Based on these results, it is expected that detailed analyses of the relationship between the wood-degrading properties of white-rot fungal-bacterial consortia and bacterial community structures will be feasible using the sub-cultivation method developed in this study.
Research on An Innovative Communication Power System Integrated with Hybrid Battery Management (2018)

With the development of communication technology and battery technology, the application of hybrid battery is more and more, but the traditional independent HBTS solution has some problems. This paper proposes a new power system, which integrates the hybrid battery management function. While solving the problems of the traditional hybrid battery solution, it has many advantages such as system simplification, unified control, less space occupation, increased reliability and maintainability. These would bring tangible value to users such as CAPEX and OPEX reduction.
Crafting a Critical Technical Practice (2010)

In recent years, the category of “practice-based research” has become an essential component of discourse around public funding and evaluation of the arts in British higher education. When included under the umbrella of public policy concerned with “the creative industries", technology researchers often find themselves collaborating with artists who consider their own participation to be a form of practice-based research. We are conducting a study under the “Creator” Digital Economies project asking whether technologists, themselves, should be considered as engaging in “practice-based” research, whether this occurs in collaborative situations, or even as a component of their own personal research [1].
Practical Syntheses of 13-O-[(2-Methoxyethoxy)methyl]-22,23-dihydroavermectin B1 Aglycon [Dimedectin Isopropanol, MK-324] and 13-epi-O-(Methoxymethyl)-22,23-Dihydroavermectin B1 Aglycon [L-694,554], Flea Active Ivermectin Analogues (1997)

ADVERTISEMENT RETURN TO ISSUEPREVAddition/CorrectionNEXTPractical Syntheses of 13-O-[(2-Methoxyethoxy)methyl]-22,23-dihydroavermectin B1 Aglycon [Dimedectin Isopropanol, MK-324] and 13-epi-O-(Methoxymethyl)-22,23-Dihydroavermectin B1 Aglycon [L-694,554], Flea Active Ivermectin AnaloguesRaymond J. Cvetovich, Chris H. Senanayake, Joseph S. Amato, Lisa M. DiMichele, Timothy J. Bill, Ji Liu, Sheo B. Singh, Robert D. Larsen, R. F. Shuman, Thomas R. Verhoeven, and Edward J. J. GrabowskiCite this: J. Org. Chem. 1997, 62, 26, 9388Publication Date (Web):December 26, 1997Publication History Published online26 December 1997Published inissue 1 December 1997https://pubs.acs.org/doi/10.1021/jo974017khttps://doi.org/10.1021/jo974017kcorrectionACS PublicationsCopyright © 1997 American Chemical Society. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views322Altmetric-Citations-LEARN 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 Get e-Alertsclose Get e-Alerts
ChemInform Abstract: Fabrication and Use of Nanometer‐Sized Electrodes in Electrochemistry (1991)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Synthesis of Lanthanide(III) Chelates by Using ‘Click’ Chemistry (2007)

Abstract The copper(I)‐catalyzed dipolar [2+3] cycloaddition reaction of an azide and a terminal alkyne is exploited in the preparation of various europium(III), terbium(III), and dysprosium(III) chelates ( Schemes 1–3 ). By changing the nature of the alkyne and the azide, a wide range of chelates and biomolecule‐labeling reactants were obtained. The photophysical properties ( Table ) of the synthesized chelates are also discussed.
Temperature-limited microprocessors: Measurements and design implications (2007)

The details of the power distribution of state of the art CMOS chips (e.g., local regions of high power (or hotspots), which disproportionally drive up junction temperatures) can have a severe impact on reliability, manufacturing yield and chip performances. In this paper we discuss the results of a recently developed technique (spatially-resolved imaging of microprocessor power (SIMP)), which can measure power and temperature distributions of high power chips (e.g., microprocessors) under full operating conditions. Specifically, we present detailed microprocessor power distributions for different workloads with and without power/thermal management. The data yields a more comprehensive understanding of the relationships between hotspots and the respective designs, layouts, floorplans, micro-architectures and thermal/power management schemes, which is discussed in detail
Suzuki−Miyaura Coupling of NHC−Boranes: A New Addition to the C−C Coupling Toolbox (2009)

Complexes of triaryl- and trialkylboranes with N-heterocyclic carbenes (NHCs) participate in Suzuki-Miyaura cross-coupling reactions and provide coupled products in good yields under base-free conditions. The reaction can be applied to Csp(2)-Csp(2) and Csp(2)-Csp(3) carbon-carbon bond formation with triflates, iodides, bromides, and chlorides. These results enrich the utility of NHC-borane complexes, which can be added to the toolkit of Suzuki-Miyaura cross-couplings, along with boronic acids and organotrifluoroborates.
Activity monitoring of people in buildings using distributed smart cameras (2010)

Systems for monitoring the activity of people inside buildings (e.g., how many people are there, where are they, what are they doing, etc.) have numerous (potential) applications including domotics (control of lighting, heating, etc.), elderly-care (gathering statistics on the daily live) and video teleconferencing.\nWe will discuss the key challenges and present the preliminary results of our ongoing research on the use of distributed smart cameras for activity monitoring of people in buildings.\nThe emphasis of our research is on:\n- the use of smart cameras (embedded devices): video is processed locally (distributed algorithms), and only meta-data is send over the network (minimal data exchange)\n- camera collaboration: cameras with overlapping views work together in a network in order to increase the overall system performance\n- robustness: system should work in real conditions (e.g., robust to lighting changes)\nOur research setup consists of cameras connected to PCs (to simulate smart cameras), each connected to one central PC. The system builds in real-time an occupancy map of a room (indicating the positions of the people in the room) by fusing the information from the different cameras in a Dempster-Shafer framework.
Requirements for Scalable Access Control and Security Management Architectures (2005)

Maximizing local autonomy has led to a scalable Internet.Scalability and the capacity for distributed control have unfortunately not extended well to resource access control policies and mechanisms.Yet management of security is becoming an increasingly challenging problem, in no small part due to scaling up of measures such as number of users, protocols, applications, network elements, topological constraints, and functionality expectations.In this paper we discuss scalability challenges for traditional access control mechanisms and present a set of fundamental requirements for authorization services in large scale networks.We show why existing mechanisms fail to meet these requirements, and investigate the current design options for a scalable access control architecture.We argue that the key design options to achieve scalability are the choice of the representation of access control policy, the distribution mechanism for policy and the choice of access rights revocation scheme.
RECONSTITUTION OF HUMAN CORPORAL SMOOTH MUSCLE AND ENDOTHELIAL CELLS IN VIVO (1999)

Human corporal smooth muscle and endothelial cells seeded on biodegradable polymer scaffolds formed vascularized corpus cavernosum muscle when implanted in vivo. To our knowledge this is the first demonstration in tissue engineering in which capillary formation was facilitated by the addition of endothelial cells in composite tissue in vivo.
Editorial: Novel immunotherapies to treat gastrointestinal solid tumor cancers (2022)

gastrointestinal cancer (GI cancer), immunotherapies and
Kalman filtering for black-box identification of nonlinear ODE models (2006)

Two techniques for recursive identification of systems described by nonlinear ordinary differential equation models are discussed. The model is of black–box state space type, where the right–hand side function is estimated as a multi–variate polynomial in the states and input, with the parameters selected to be the polynomial coefficients. An algorithm based on Kalman filtering techniques is evaluated and compared to an RPEM. The Kalman filter based algorithm is e.g. suitable for initiation of the RPEM method as they are both based on the same model. In the paper the algorithm performance of the Kalman filter based methodis compared to that of the RPEM using a numerical example and live data from a cascaded tanks process.