gebhart/patrepeval huggingface dataset:
Cardioprotective effects of thioredoxin in myocardial ischemia and the reperfusion role of S-nitrosation (2004)

Apoptosis contributes to myocardial ischemia/reperfusion (MI/R) injury, and both thioredoxin (Trx) and nitric oxide have been shown to exert antiapoptotic effects in vitro. Recent evidence suggests that this particular action of Trx requires S-nitrosation at Cys-69. The present study sought to investigate whether or not exogenously applied Trx reduces MI/R injury in vivo and to which extent this effect depends on S-nitrosation. Adult mice were subjected to 30 min of MI and treated with either vehicle or human Trx (hTrx, 2 mg/kg, i.p.) 10 min before reperfusion. Native hTrx was incorporated into myocardial tissue as shown by immunostaining, and reduced MI/R injury as evidenced by decreased terminal deoxynucleotidyltransferase-mediated dUTP nick end labeling (TUNEL) staining, DNA fragmentation, caspase-3 activity, and infarct size. When hTrx was partially S-nitrosated by preincubation with S-nitrosoglutathione, its cardioprotective effect was markedly enhanced. Treatment with hTrx significantly reduced p38 mitogen-activated protein kinase (MAPK) activity, and this effect was also potentiated by S-nitrosation. To further address the role of S-nitrosation for the overall antiapoptotic effect to Trx, the action of Escherichia coli Trx (eTrx) was investigated in the same model. Whereas eTrx inhibited MI/R-induced apoptosis to a degree similar to hTrx, S-nitrosation of this protein, which lacks Cys-69, failed to further enhance its antiapoptotic action. Collectively, our results demonstrate that systemically applied Trx is taken up by the myocardium to exert potent cardioprotective effects in vivo, offering interesting therapeutic avenues. In the case of hTrx, these effects are further potentiated by S-nitrosation, but this posttranslational modification is not essential for protection.
Unpinned GaAs MOS capacitors and transistors (1988)

Metal-oxide-semiconductor (MOS) capacitors and field-effect transistors (MOSFETs) in the GaAs semiconductor system using an unpinned interface are described. The structures utilize plasma-enhanced chemical-vapor deposition (PECVD) for the silicon-dioxide insulator on GaAs that has been terminated with a few monolayers of silicon during growth by molecular beam epitaxy. Interface densities in the structures have been reduced to approximately 10/sup 12/ cm/sup -2/.eV/sup -1/. High-frequency characteristics indicate strong inversion of both p-type and n-type GaAs. The excellent insulating quality of the oxide has allowed demonstration of quasi-static characteristics. MOSFETs operating in depletion mode with a transconductance of 60 mS/mm at 8.0- mu m gate lengths have been fabricated.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Introduction to Risk Calculation in Genetic Counselling (1991)

Abstract Genetic counselling is widely accepted as an integral part of the management of every patient with an inherited disorder. This book describes in detail how the risk can be estimated or calculated for most counselling situations, using nothing more complex than a knowledge of the simple laws of probability and a pocket calculator. All patterns of inheritance are considered. Particular attention is paid to the segregation of balanced chromosome rearrangements and risk calculation in single gene inheritance taking into account factors such as reduced penetrance, late age of onset, consanguinity, and the extended family. Also covered at length is the use of linked markers, an area of rapidly increasing importance in carrier detection and prenatal diagnosis. The text has been written in a straightforward "user-friendly" style with liberal use of worked examples and will be of benefit to everyone involved in the provision and delivery of genetic counselling services.
Substrate specificity of bovine liver formaldehyde dehydrogenase. (1986)

Formaldehyde dehydrogenases isolated from several different biological sources have been reported to catalyze the NAD+-dependent oxidative acylation of glutathione by methylglyoxal to form S-pyruvylglutathione, suggesting the involvement of this enzyme in the metabolism of methylglyoxal. However, formaldehyde dehydrogenase from bovine liver is found not to use methylglyoxal or related alpha-ketoaldehydes as substrates. Using methylglyoxal with the enzyme under conditions favoring the forward reaction did not result in the formation of S-pyruvylglutathione. Using independently synthesized S-pyruvylglutathione with the enzyme under conditions favoring the reverse reaction did not result in the production of methylglyoxal. In addition, methylglyoxal and several related alpha-ketoaldehydes did not exhibit detectable activity with formaldehyde dehydrogenase partially purified from human liver, contrary to a previous report. Some, if not all, past reports that methylglyoxal serves as a substrate for the dehydrogenase may be due to the demonstrated presence of contaminating formaldehyde in some commercially available preparations of methylglyoxal. In a related study, S-hydroxymethylglutathione, formed by pre-equilibrium addition of formaldehyde to glutathione, is concluded to be direct substrate for the dehydrogenase. This follows from the observation that the catalytic turnover number of the enzyme in the forward direction exceeds by a factor of approximately 20 the first order rate constant for decomposition of S-hydroxymethylglutathione to glutathione and formaldehyde (k = 5.03 +/- 0.30 min-1, pH 8, 25 degrees C).
Atom Transfer Radical Polymerization: Billion Times More Active Catalysts and New Initiation Systems (2018)

Approaching 25 years since its invention, atom transfer radical polymerization (ATRP) is established as a powerful technique to prepare precisely defined polymeric materials. This perspective focuses on the relation between structure and activity of ATRP catalysts, and the consequent choice of the initiating system, which are paramount aspects to well-controlled polymerizations. The ATRP mechanism is discussed, including the effect of kinetic and thermodynamic parameters and side reactions affecting the catalyst. The coordination chemistry and activity of copper complexes used in ATRP are reviewed in chronological order, while emphasizing the structure-activity correlation. ATRP-initiating systems are described, from normal ATRP to low ppm Cu systems. Most recent advancements regarding dispersed media and oxygen-tolerant techniques are presented, as well as future opportunities that arise from progressively more active catalysts and deeper mechanistic understanding.
The Synergistic Anti-Tumor Activity of EZH2 Inhibitor SHR2554 and HDAC Inhibitor Chidamide through ORC1 Reduction of DNA Replication Process in Diffuse Large B Cell Lymphoma (2021)

SHR2554, a potent, highly selective small molecule inhibitor of EZH2, inhibited EZH2-mutant DLBCL more significantly in vitro and in vivo. The combination of HDAC inhibitor HBI8000 with EZH2 inhibitor SHR2554 exhibited dramatic anti-tumor activity in both mutant and wild-type DLBCL, which may become a potential therapeutic modality for the treatment of DLBCL patients.
Magnetic properties of Sm-Fe-N bulk magnets prepared from Sm2Fe17N3 melt-spun ribbons (2015)

Sm-Fe-N bulk magnets were prepared from Sm2Fe17N3 melt-spun ribbon using the spark plasma sintering method. The bulk materials thus obtained had high densities of 90%–94%. The Sm-Fe-N bulk magnets produced at 723 K or lower retained the Sm2Fe17N3 phase of the melt-spun ribbon and exhibited a high coercivity. In contrast, the Sm2Fe17N3 phase decomposed during sintering at 773 K or higher, resulting in Sm-Fe-N bulk magnets with a lower coercivity. The Sm-Fe-N bulk magnets prepared from the Sm2Fe17N3 melt-spun ribbons sintered at 673 K exhibited an attractively high coercivity of 16.9 kOe with a remanence of 94.4 emu/g.
Hyperspectral colon tissue cell classification (2004)

A novel algorithm to discriminate between normal and malignant tissue cells of the human colon is presented. The microscopic level images of human colon tissue cells were acquired using hyperspectral imaging technology at contiguous wavelength intervals of visible light. While hyperspectral imagery data provides a wealth of information, its large size normally means high computational processing complexity. Several methods exist to avoid the so-called curse of dimensionality and hence reduce the computational complexity. In this study, we experimented with Principal Component Analysis (PCA) and two modifications of Independent Component Analysis (ICA). In the first stage of the algorithm, the extracted components are used to separate four constituent parts of the colon tissue: nuclei, cytoplasm, lamina propria, and lumen. The segmentation is performed in an unsupervised fashion using the nearest centroid clustering algorithm. The segmented image is further used, in the second stage of the classification algorithm, to exploit the spatial relationship between the labeled constituent parts. Experimental results using supervised Support Vector Machines (SVM) classification based on multiscale morphological features reveal the discrimination between normal and malignant tissue cells with a reasonable degree of accuracy.
The ABC Transporter Protein OppA Provides Protection against Experimental <i>Yersinia pestis</i> Infection (2006)

The identification of Yersinia pestis as a potential bioterrorism agent and the emergence of antibiotic-resistant strains have highlighted the need for improved vaccines and treatments for plague. The aim of this study was to evaluate the potential for ATP-binding cassette (ABC) transporter proteins to be exploited as novel vaccines against plague. Western blotting of ABC transporter proteins using sera from rabbits immunized with killed whole Y. pestis cells or human convalescent-phase sera identified four immunologically reactive proteins: OppA, PstS, YrbD, and PiuA. Mice immunized with these proteins developed antibody to the immunogen. When the immunized mice were challenged with Y. pestis, the OppA-immunized mice showed an increased time to death compared to other groups, and protection appeared to correlate with the level of immunoglobulin G antibody to OppA.
Carrier Phase Tracking of OFDM-Based DVB-T Signals for Precision Ranging (2017)

In general, the carrier phase of orthogonal frequency division multiplexing (OFDM) signals is not tracked for at least two reasons. First, the dc component of most baseband OFDM symbols is a null subcarrier so as to avoid the effect of dc bias at reception. Second, generation and transmission of OFDM symbols are independent from one symbol to next. As a result, no phase continuity is required to be maintained at any subcarriers. For communications, demodulation of OFDM symbols with cyclic prefix (CP) is tolerant to small timing errors and insensitive to the absolute phase but relative phase at data subcarriers, which can be easily calibrated with the help of pilot subcarriers. However, the OFDM signaling adopted by the Terrestrial Digital Video Broadcast (DVB-T) retains the dc component. Besides, the CP duration is specified in such a way that a whole number of cycles is ensured for the middle carrier. It happens in DVB- T that the middle carrier is assigned as a continual pilot subcarrier, which has a constant value across OFDM symbols. As a result, the baseband center frequency (dc component) has no phase discontinuity, which gives rise to the opportunity for carrier phase tracking. Carrier phase tracking has the potential to provide more accurate timing for ranging and ultimately for positioning than cross-correlation of CP and pilot subcarriers in coarse and fine time of arrival (TOA) estimation, respectively. In this paper, in-the air DVB-T signals collected in experimental tests are used to show the functionality and performance of DVB-T signal carrier phase tracking.
Cephalopod biology and fisheries in Europe (2010)

Over the past two decades, cephalopod molluscs have attracted increased attention from marine biologists and fishery scientists. Several species are important for European fisheries, as targets of small‐scale coastal fisheries and/or as bycatch in multispecies fisheries for demersal fish. The present report draws on a series of reviews prepared in 2005 for the CEPHSTOCK project (see Section 1). The taxonomy of the main resource species is reviewed (Section 2), and brief descriptions of each species are provided, along with information from studies of population genetics, habitat requirements of paralarvae and adults, and health and ecotoxicology (Section 3). The main fisheries are described, including illustration of gears used in specialized small‐scale fisheries and a discussion of the socio-economic importance of the fisheries. The current status of cephalopod aquaculture is reviewed, highlighting notable advances in commercial culture of octopus and cuttlefish (Section 4). Current fishery data collection and fishery management are described, noting that there is no setting of landings quotas and no routine assessment of stock status. Optns for stock assessment are discussed, drawing on one off assessments made during specific projects and current practice elsewhere in the world. The “live fast, die yong” lifehistory strategies of cephalopods present particular challenges, buparallels can be drawn with shortlived fish (Section 5). Finally, the report looks to the future, reviewing possible effects of climate change on cephalopods. It discusses the future development of aquaculture and fisheries for cephalopods, including prospects for fishery forecasting and fishery management - especially in relation to the small-scale directed fisheries. Various knowledge gaps are identified, and ideas for research to fill these gaps are presented
Joint unscented Kalman filter for state and parameter estimation in Managed Pressure Drilling (2013)

Drilling into offshore deep water, high-pressure high-temperature reservoirs is a very challenging process. The most important task in these drilling operations is to control bottomhole pressure. Many automatic control systems for drilling operations are based on models calculating wellbore pressure, flow and downhole hydraulics. Closed loop control systems, for example Managed Pressure Drilling, are examples of systems that may involve such real-time calculations. Therefore a high degree of accuracy in pressure and flow predictions is crucial to the performance of automatic drilling applications. In this paper the key uncertain model parameters and the bottom-hole pressure are estimated using joint unscented Kalman filter based on only available top-side measurements. The results of simulations show accurate estimation of the bottom-hole pressure and uncertain parameters, even in transient periods for example the scenario of pipe connection operations, where there is no available bottom-hole pressure measurement, and flow through the bit.
Performance analysis in CoDe-X partitioning for structural programmable accelerators (1997)

Presents the performance analysis process within the parallelizing compilation environment CoDe-X (CoDesign of Xputers) for simultaneous programming of transputer-based accelerators and their hosts. This paper briefly introduces its hardware/software co-design strategies at two levels of partitioning. CoDe-X performs, at the first level, a profiling-driven host/accelerator partitioning for performance optimization and, at the second level, a resource-driven sequential/structural partitioning of the accelerator source code in order to optimize the utilization of its reconfigurable resources. The analysis of candidate (task) performances in CoDe-X has to be done for both a procedural (sequential) programmable host processor and a structural programmable data-driven accelerator processor. In complete application time estimation, data dependencies for parallel task execution (hosts/accelerators) are considered. To stress the significance of this application development methodology, this paper gives an introduction to the target hardware platform.
Artificial intelligence and indoor air quality: better health with new technologies (2020)

Although many people imagine that enclosed spaces offer protection from outdoor pollution, the indoor air is very often contaminated by harmful substances created by everyday household cleaning and cooking activities as well as from outdoor pollution from sources such as vehicles and industry, particularly in the megacities of Asia.Founded in 2015 by two French entrepreneurs, AirVisual is a company whose primary mission is to raise awareness of air quality. By offering connected sensors for measuring indoor air quality, the company makes it possible for everybody to optimize their indoor air quality, which in turn limits health risks from exposure to fine particles and excessive concentrations of CO2. In addition, aggregating data from governments, satellite images and outdoor sensors that AirVisual has installed worldwide has enabled the startup to create an interactive world map of air quality on our planet, helping to increase awareness of the importance of air quality and encouraging solutions that are relevant to local contexts.
Arbitrary bit permutations in one or two cycles (2004)

Symmetric-key block ciphers encrypt data, providing data confidentiality over the public Internet. For interoperability reasons, it is desirable to support a variety of symmetric-key ciphers efficiently. We show the basic operations performed by a variety of symmetric-key cryptography algorithms. Of these basic operations, only bit permutation is very slow using existing processors, followed by integer multiplication. New instructions have been proposed recently to accelerate bit permutations in general-purpose processors, reducing the instructions needed to achieve an arbitrary n-bit permutation from O(n) to O(log(n)). However, the serial data-dependency between these log(n) permutation instructions prevents them from being executed in fewer than log(n) cycles, even on superscalar processors. Since application specific instruction processors (ASIPs) have fewer constraints on maintaining standard processor datapath and control conventions, can we achieve even faster permutations? We propose six alternative ASIP approaches to achieve arbitrary 64 bit permutations in one or two cycles, using new BFLY and IBFLY instructions. This reduction to one or two cycles is achieved without increasing the cycle time. We compare the latencies of different permutation units in a technology independent way to estimate cycle time impact. We also compare the alternative ASIP architectures and their efficiency in performing arbitrary 64 bit permutations.
On the analysis of clonogenic survival data: Statistical alternatives to the linear-quadratic model (2016)

Undoubtedly, LQ regression is a robust method for the analysis of clonogenic survival data. Nevertheless, alternative approaches including non-linear regression and multivariate techniques such as cluster analysis and principal component analysis represent versatile tools for the extraction of parameters and/or scores of the cellular response towards ionizing irradiation with a more intuitive biological interpretation. The latter are highly informative for correlation analyses with other types of data, including functional genomics data that are increasingly being generated.
Denoising seismic noise cross correlations (2009)

Seismic noise cross correlations have become a novel way of probing the elastic structure of the Earth without relying on an often highly nonuniform and sporadic distribution of earthquakes. By circumventing this restriction, one can determine the elastic Green's function between any two points where instruments exist. For tomography, this will allow for a larger distribution of crossing paths and therefore better resolution in the inversions. One can also monitor the same station pair Green's functions for changes in the state of the Earth, an application that has been employed in volcanic monitoring. One limitation of this cross‐correlation technique is that the input time series are frequently very long to recover high‐fidelity signals. We present two time‐frequency stacking algorithms to denoise the correlated signals and to alleviate this problem; increasing signal‐to‐noise ratios allows for high‐fidelity Green's functions to be constructed from shorter time series. We demonstrate the increase in signal fidelity by applying these routines to seismic data, first to ambient noise across southern California and then to data from le Piton de la Fournaise volcano on La Réunion Island. In the former, we find that denoising the data allows for more traveltimes to be measured, particularly at longer station separations, across all passbands examined except for long‐period Love waves, where no data are recovered. In the latter, we apply a time‐frequency denoising algorithm to resolve subtle shifts in phase in cross correlations between seismic stations that occur before eruptions: we see a clear precursor to the June 2000 eruption.
Point mutations in a nucleoside transporter gene from <i>Leishmania donovani</i> confer drug resistance and alter substrate selectivity (2001)

Leishmania parasites lack a purine biosynthetic pathway and depend on surface nucleoside and nucleobase transporters to provide them with host purines. Leishmania donovani possess two closely related genes that encode high affinity adenosine-pyrimidine nucleoside transporters LdNT1.1 and LdNT1.2 and that transport the toxic adenosine analog tubercidin in addition to the natural substrates. In this study, we have characterized a drug-resistant clonal mutant of L. donovani (TUBA5) that is deficient in LdNT1 transport and consequently resistant to tubercidin. In TUBA5 cells, the LdNT1.2 genes had the same sequence as wild-type cells. However, because LdNT1.2 mRNA is not detectable in either wild-type or TUBA5 promastigotes, LdNT1.2 does not contribute to nucleoside transport in this stage of the life cycle. In contrast, the TUBA5 cells were compound heterozygotes at the LdNT1.1 locus containing two mutant alleles that encompassed distinct point mutations, each of which impaired transport function. One of the mutant LdNT1.1 alleles encoded a G183D substitution in predicted TM 5, and the other allele contained a C337Y change in predicted TM 7. Whereas G183D and C337Y mutants had only slightly elevated adenosine K(m) values, the severe impairment in transport resulted from drastically ( approximately 20-fold) reduced V(max) values. Because these transporters were correctly targeted to the plasma membrane, the reduction in V(max) apparently resulted from a defect in translocation. Strikingly, G183 was essential for pyrimidine nucleoside but not adenosine transport. A mutant transporter with a G183A substitution had an altered substrate specificity, exhibiting robust adenosine transport but undetectable uridine uptake. These results suggest that TM 5 is likely to form part of the nucleoside translocation pathway in LdNT1.1