gebhart/patrepeval huggingface dataset:
Involvement of a Bifunctional, Paired-like DNA-binding Domain and a Transpositional Enhancer in Sleeping BeautyTransposition (2002)

Sleeping Beauty (SB) is the most active Tc1/mariner-like transposon in vertebrate species. Each of the terminal inverted repeats (IRs) of SB contains two transposase-binding sites (DRs). This feature, termed the IR/DR structure, is conserved in a group of Tc1-like transposons. The DNA-binding region of SB transposase, similar to the paired domain of Pax proteins, consists of two helix-turn-helix subdomains (PAI + RED = PAIRED). The N-terminal PAI subdomain was found to play a dominant role in contacting the DRs. Transposase was able to bind to mutant sites retaining the 3' part of the DRs; thus, primary DNA binding is not sufficient to determine the specificity of the transposition reaction. The PAI subdomain was also found to bind to a transpositional enhancer-like sequence within the left IR of SB, and to mediate protein-protein interactions between transposase subunits. A tetrameric form of the transposase was detected in solution, consistent with an interaction between the IR/DR structure and a transposase tetramer. We propose a model in which the transpositional enhancer and the PAI subdomain stabilize complexes formed by a transposase tetramer bound at the IR/DR. These interactions may result in enhanced stability of synaptic complexes, which might explain the efficient transposition of Sleeping Beauty in vertebrate cells.
Overview of current development in electrical energy storage technologies and the application potential in power system operation (2014)

Electrical power generation is changing dramatically across the world because of the need to reduce greenhouse gas emissions and to introduce mixed energy sources. The power network faces great challenges in transmission and distribution to meet demand with unpredictable daily and seasonal variations. Electrical Energy Storage (EES) is recognized as underpinning technologies to have great potential in meeting these challenges, whereby energy is stored in a certain state, according to the technology used, and is converted to electrical energy when needed. However, the wide variety of options and complex characteristic matrices make it difficult to appraise a specific EES technology for a particular application. This paper intends to mitigate this problem by providing a comprehensive and clear picture of the state-of-the-art technologies available, and where they would be suited for integration into a power generation and distribution system. The paper starts with an overview of the operation principles, technical and economic performance features and the current research and development of important EES technologies, sorted into six main categories based on the types of energy stored. Following this, a comprehensive comparison and an application potential analysis of the reviewed technologies are presented.
Biochemical analysis of human immunodeficiency virus-1 reverse transcriptase containing a mutation at position lysine 263. (1993)

Site-directed mutagenesis has been used to assess the importance of lysine 263 in substrate binding of human immunodeficiency virus-1 (HIV-1) reverse transcriptase. Previous studies have indicated that lysine 263 functions in the binding of 2'-deoxynucleoside 5'-triphosphate (dNTP) substrates (Basu, A., Tirumalai, R. S., and Modak, M. J. (1989) J. Biol. Chem. 264, 8746-8752). We studied this interaction directly by using site-specific mutagenesis to change lysine 263 to a serine. Highly purified mutant enzyme K263S bound natural dNTP substrates and primed polynucleic acid substrates with equal affinity when compared to the wild type reverse transcriptase. No difference was observed in the binding of 3'-azido-2',3'-dideoxythymidine 5'-triphosphate to the mutant reverse transcriptase on the basis of Km and Ki determinations. The serine substitution had no effect on RNase H activity. These results indicate that lysine 263 is not essential in the binding of substrates to HIV-1 reverse transcriptase.
Computing signal delay in general RC networks by tree/link partitioning (1990)

Most RC simulators handle only tree networks, not arbitrary networks. An algorithm is presented for computing signal delays in general RC networks using the RC-tree computation as the primary operation. The algorithm partitions a given network into a spanning tree and links. It computes the signal delay of the spanning tree, and updates the signal delay as it incrementally adds the links back to reconstruct the original network. If m is the number of links, this algorithm requires m(m+1)/2 updates and m+1 tree delay evaluations. All the tree delay evaluations involve computing signal delays with the same resistive spanning tree, but with different values for the capacitors.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Integration and packaging of GaAs MMIC subsystems using silicon motherboards (2002)

A technique has been developed for the integration and packaging of subsystems containing GaAs MMICs (monolithic microwave ICs) or a mix of MMIC, quasi-monolithic, and hybrid components on a single substrate of high-resistivity silicon. This silicon motherboard (SMB) technique differs from the monolithic GaAs-on-silicon approach in that, in this approach, conventional MMICs, FETs dielectric resonators, and other components are attached to a low-loss silicon substrate which contains etched recesses for MMIC chips and devices, vias, and monolithic overlay capacitors, resistors, air bridges, and other typical MMIC components and structures. The silicon acts as the transmission medium, chip carrier, and heat conductor. This integrated structure requires far fewer manual assembly operations than conventional approaches and exhibits fewer discontinuities, thus reducing cost and improving reliability, reproducibility, and performance. As a test vehicle for this technique, a three-stage, 2 W C-band power amplifier was adapted for implementation in an SMB form. The output power and gain of the amplifier closely match the predicted values of 33 dBm and 33 dB, respectively. The measured efficiency is 36%. Subsequent nonlinear analysis indicates that efficiency and output power can be improved by the addition of a third via under the output FETs.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
p53 Modulates RPA-Dependent and RPA-Independent WRN Helicase Activity (2005)

Werner syndrome is a hereditary disorder characterized by the early onset of age-related symptoms, including cancer. The absence of a p53-WRN helicase interaction may disrupt the signal to direct S-phase cells into apoptosis for programmed cell death and contribute to the pronounced genomic instability and cancer predisposition in Werner syndrome cells. Results from coimmunoprecipitation studies indicate that WRN is associated with replication protein A (RPA) and p53 in vivo before and after treatment with the replication inhibitor hydroxyurea or gamma-irradiation that introduces DNA strand breaks. Analysis of the protein interactions among purified recombinant WRN, RPA, and p53 proteins indicate that all three protein pairs bind with similar affinity in the low nanomolar range. In vitro studies show that p53 inhibits RPA-stimulated WRN helicase activity on an 849-bp M13 partial duplex substrate. p53 also inhibited WRN unwinding of a short (19-bp) forked duplex substrate in the absence of RPA. WRN unwinding of the forked duplex substrate was specific, because helicase inhibition mediated by p53 was retained in the presence of excess competitor DNA and was significantly reduced or absent in helicase reactions catalyzed by a WRN helicase domain fragment lacking the p53 binding site or the human RECQ1 DNA helicase, respectively. p53 effectively inhibited WRN helicase activity on model DNA substrate intermediates of replication/repair, a 5' ssDNA flap structure and a synthetic replication fork. Regulation of WRN helicase activity by p53 is likely to play an important role in genomic integrity surveillance, a vital function in the prevention of tumor progression.
Storage Physics and Noise Mechanism in Heat-Assisted Magnetic Recording (2018)

As cloud computing and massive-data machine learning are applied pervasively, ultra-high volume data storage serves as the foundation block. Every day, nearly 2.5 quintillion bytes (50000 GB/second in 2018) of data is created and stored. Hard Disk Drive (HDD) takes major part of this heavy duty. However, despite the amazing evolution of HDD technology during the past 50 years, the conventional Perpendicular Magnetic Recording (PMR), the state-of-the-art HDD technique, starts to have less momentum in increasing storage density because of the recording trilemma. To overcome this, Heat-Assisted Magnetic Recording (HAMR) was initially proposed in 1990s. With years of advancement, recent industrial demos have shown the potential of HAMR to actually break the theoretical limit of PMR. However, to fully take advantage of HAMR and realize the commercialization, there are still quite a few technical challenges, which motivated this thesis work. Via thermal coupled micromagnetic simulation based upon Landau-Lifshitz-Bloch (LLB) equation, the entire dynamic recording process has been studied systematically. The very fundamental recording physics theorem is established, which manages to elegantly interpret the previously conflicting experimental observations. The thermal induced field dependence of performance, due to incomplete switching and erase-after-write, is proposed for the first time and validated in industrial lab. The combinational effects form the ultimate physical limit of this technology. Meanwhile, this theorem predicts the novel noise origins, examples being Curie temperature distribution and temperature distribution, which are the key properties but ignored previously. To enhance performance, utilizations of higher thermal gradient, magnetically stiffer medium, optimal field etc. have been suggested based upon the theorem. Furthermore, a novel concept, Recording Time Window (RTW), has been proposed. It tightly correlates with performance and serves as a unified optimization standard, summarizing almost all primary parameters. After being validated via spin stand testing, the theorem has been applied to provide solutions for guiding medium design and relaxing the field and heating requirement. This helps solve the issues around writer limit and thermal reliability. Additionally, crosstrack varying field has been proposed to solve the well-known transition curvature issue, which may increase the storage density by 50%.
The Design of Dynamic Ship Positioning Control Systems Using Extended Kalman Filtering Techniques (1979)

Recent dynamic positioning systems have involved the use of a Kalman filter, in a state estimate feedback control scheme, based upon the separation principle of stochastic optimal control theory. Both linear and non-linear filtering schemes have been proposed for this application. A new extended Kalman filtering scheme is introduced which has an improved performance relative to previous designs. This system is compared with one based upon a linear Kalman filter.
Using β-Lactamase to Trigger Supramolecular Hydrogelation (2006)

This paper reports the rational design and synthesis of a β-lactam conjugate. Treating the conjugate with β-lactamase cleaves the scissile β-lactam amide bond, releases a hydrogelator, and results in enzymatic formation of a supramolecular hydrogel. The process involves the use of a bacterial enzymethe one causes antibiotic inactivation and accounts for resistance to β-lactams in many clinical important pathogensto catalyze the formation of the hydrogel. It offers an opportunity to investigate the kinetics of these types of enzymatic reactions, screen inhibitors of the enzyme, and provides a new candidate to generate hydrogels for biomedical applications.
Central Nervous System Active Medications and Risk for Fractures in Older Women (2003)

<h3>Background</h3> Use of central nervous system (CNS) active medications may increase the risk for fractures. Prior studies are limited by incomplete control of confounders. <h3>Methods</h3> To determine whether use of CNS active medications, including benzodiazepines, antidepressants, anticonvulsants, and narcotics, increases fracture risk in elderly, community-dwelling women, we examined use of these 4 categories of medications in a cohort of 8127 older women and followed the participants prospectively for incident nonspine fractures, including hip fractures. Current use of CNS active medications was assessed by interview with verification of use from containers between 1992 and 1994 and between 1995 and 1996. Use was coded as a time-dependent variable. Incident nonspine fractures occurring after the initial medication assessment until May 31, 1999, were confirmed by radiographic reports. <h3>Results</h3> During an average follow-up of 4.8 years, 1256 women (15%) experienced at least one nonspine fracture, including 288 (4%) with first hip fractures. Compared with nonusers, women taking narcotics (multivariate hazard ratio [HR], 1.40; 95% confidence interval [CI], 1.06-1.83) and those taking antidepressants (multivariate HR, 1.25; 95% CI, 0.99-1.58) had increases in the risks for any nonspine fractures. Women taking tricyclic antidepressants and those using selective serotonin reuptake inhibitors (SSRIs) had similar fracture rates. There were no independent associations between benzodiazepine use or anticonvulsant use and risk for nonspine fracture. Women taking antidepressants compared with nonusers had a 1.7-fold increase in the risk for hip fracture (multivariate HR, 1.65; 95% CI, 1.05-2.57). We did not observe independent associations between use of any of the other 3 classes of CNS active medications and risk of hip fracture. <h3>Conclusions</h3> Community-dwelling older women taking narcotics have an increased risk for any nonspine fracture, and those taking antidepressants have a greater risk for nonspine fractures, including hip fracture. Rates of fracture were similar in women taking tricyclic antidepressants and those using SSRIs. Benzodiazepine use and anticonvulsant use were not independently associated with an increased risk of nonspine fractures, including hip fracture.
Dissecting karyotypic patterns in colorectal tumors: two distinct but overlapping pathways in the adenoma-carcinoma transition. (2002)

More than 500 colorectal tumors with clonal chromosomal abnormalities have been reported. Although the pattern of aberrations is nonrandom, no specific primary or secondary karyotypic abnormality has been identified. Also, the chronological order in which the aberrations appear during disease progression is not well known. One reason why our understanding of the cytogenetic evolution is unclear is the high degree of karyotypic complexity seen in these tumors. To overcome some of these difficulties we have previously used several statistical methods that allow identification and interpretation of karyotypic pathways as well as establishment of a temporal order of appearance of the imbalances. These methods were applied on 531 colorectal tumor karyotypes. By using a resampling strategy, 1p-, +7, 7q-, and +12p were identified as early events. Two major and two minor cytogenetic pathways were identified by means of principal component analysis. The two major pathways were initiated with 1p- and +7, and the minor pathways were initiated with +12p and 7q-. The +7/+12p tumors were found to be hyperdiploid, whereas those with 1p-/7q- were pseudodiploid. We also show that the adenoma-carcinoma transition in the 1p- pathway is strongly linked to karyoytypic evolution, whereas the +7 pathway is not, and that the cytogenetic pathways are separated at both early and late stages.
Dielectric-assisted trilayer lift-off process for improved metal definition (1998)

We have developed a simple, trilayer lift-off process for obtaining metal of various thickness while retaining good feature definition down to 1 μm, using only standard photoresist and developer, and e-beam evaporated dielectric. This process has been implemented for fabrication of high speed circuits using InP/InGaAs/InP double heterojunction bipolar transistor devices. This structure is nonplanar, with a topography of about 1.3 μm from the top of the emitter to the substrate level for interconnects. Clean edges are obtained for all of the metallization steps. Metal lift-off with our trilayer process is easily accomplished by gentle rinsing with acetone, and does not require the use of high pressure spray or any heat treatment, such as boiling in a solvent to aid lift-off. This new process has greatly improved our circuit yield.
A New Test Sequence Generation Method for Interoperability Testing (1995)

A method for generating test sequences for interoperability testing of communication systems is proposed. In the proposed method, the system state graph, which shows behaviours of the whole system, is generated from protocol specifications, and test sequences that confirm each transition and the state based on this graph are generated. The method is characterized in that the states of individual processes are confirmed, considering independency of the two processes, which is a characteristic of the interoperability testing. An application for a simple protocol with a retransmission mechanism shows that we can improve testing reliability in interoperability testing. Using this method is expected to decrease cost for generating test sequences.
An In Vitro Coculture Model of Transmigrant Monocytes and Foam Cell Formation (1999)

To analyze in vitro the migration of monocytes to the subendothelial space, their differentiation into macrophages, and the subsequent formation of foam cells in vitro, we have developed a 2-coculture system with rabbit aortic endothelial cells (AECs), aortic smooth muscle cells (SMCs), and a mixture of matrix proteins on polyethylene filters in chemotaxis chambers. AECs were seeded on a mixture of type I and IV collagen with or without various types of serum lipoproteins (method 1) or on matrix proteins secreted by SMCs (method 2). In these coculture systems, rabbit AECs can maintain a well-preserved monolayer for up to 2 weeks. When human CD14-positive monocytes were added to the upper medium of the system, with monocyte chemotactic protein-1 treatment approximately 60% of the monocytes transmigrated within 24 hours and were retained for up to 7 days, whereas without MCP-1 treatment, <30% of monocytes transmigrated. On day 1, transmigrant monocytes were negative for immunostaining of type I and II macrophage scavenger receptors but by day 3, became positive for scavenger receptors as well as other macrophage markers. When oxidized low density lipoprotein was added to the matrix layer of the method I coculture, on day 4 transmigrant cells exhibited lipid deposit droplets, and by day 7, they had the appearance of typical foam cells. Some of the transmigrant cells recovered in the lower medium on day 7 also appeared to be foam cells, indicating foam cell motility and escape from the coculture layer through the filter. In summary, this coculture system is a useful in vitro tool to dissect the cellular and molecular events that make up the process of foam cell formation.
Isolation and immunisation studies of a canine parco-like virus from dogs with haemorrhagic enteritis (1979)

A newly recognised canine parvo like virus was isolated from faeces of dogs with haemorrhagic enteritis. Cell cultures from several species were susceptible to it. Virus infected cells could be demonstrated by staining with fluorescent antibody reagents (prepared against canine virus or feline panleucopenia virus) or by haemagglutination with pig or rhesus monkey red blood cells. Inhibition of haemagglutination by specific antiserum prepared in specific-pathogen-free beagles provided a convenient method for viral identification. Experimental inoculation of specific-pathogen-free beagles resulted in elevated body temperatures and caused lymphopenia lasting one to three days. Feline panleucopenia virus vaccines protected dogs against challenge with virulent canine parvo-like virus.
Electrochemical route to thermoelectric nanowires via organic electrolytes (2010)

Abstract Thermoelectric nanowires have been predicted to have superior properties compared to their bulk counterparts due to quantum confinement. We present the synthesis of chalcogenide nanowires A 2 B 3 (A = Bi, Sb; B = S, Se, Te) and PbB (B = S, Se, Te) by electrochemical deposition into highly ordered porous Al 2 O 3 membranes. The narrow pore size distribution of the templates reproducibly yields very homogeneous nanowires upon electrodeposition into the pores. The thermoelectric nanowires presented here were deposited from nonaqueous electrolytes based on Bi 3+ and S (and their heavier counterparts). The transmission electron microscopy investigations on released nanowires show the homogeneous growth behavior of the material. We will present data on the Seebeck coefficients of nanowire ensembles of various IV–VI and V–VI materials embedded in the porous template.
Synthesis of zero-aliasing elementary-tree space compactors (2002)

A new method is presented for designing space compactors for either deterministic testing or pseudo-random testing. A tree of elementary gates (AND, OR, NAND, NOR) is used to combine the outputs of the circuit-under-test (CUT) in a way that zero-aliasing is guaranteed with no modification of the CUT. The elementary-tree is synthesized by adding one gate at a time without introducing redundancy. The end result is a cascaded network CUT followed by space compactor, that is irredundant and has fewer outputs than the CUT alone. All faults in the CUT and space compactor can be tested. Only the outputs of the space compactor need to be observed during testing. Experimental results are surprising; they show that very high compaction ratios can be achieved with zero-aliasing elementary-tree space compactors. Compared with parity trees and other space compactor designs that have been proposed, the method presented here requires less overhead and yet guarantees zero-aliasing.
Isoenzymes of rat liver mitochondrial malate dehydrogenase evidence for the existence of nonidentical subunits (1970)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTIsoenzymes of rat liver mitochondrial malate dehydrogenase evidence for the existence of nonidentical subunitsKenneth G. Mann and Carl S. VestlingCite this: Biochemistry 1970, 9, 15, 3020–3025Publication Date (Print):July 21, 1970Publication History Published online1 May 2002Published inissue 21 July 1970https://doi.org/10.1021/bi00817a013RIGHTS & PERMISSIONSArticle Views35Altmetric-Citations13LEARN 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 InReddit PDF (2 MB) Get e-Alertsclose Get e-Alerts