gebhart/patrepeval huggingface dataset:
A mouse analogue of the human carcinoembryonic antigen. (1989)

Functional human carcinoembryonic antigen (CEA)-like genes have been shown to be present in the mouse. Southern analyses of murine DNA using both human and murine CEA complementary DNA probes have revealed the presence of multiple CEA-like genes, while analyses of RNA from different mouse tissues showed CEA-like transcripts in adult colon and liver. Furthermore, a CEA-like protein, immunoprecipitable with a rabbit polyclonal serum raised against human CEA, has been detected in adult murine colon tissue. Several murine CEA complementary DNA clones have been isolated from a murine colon complementary DNA library, and characterization of one such clone demonstrates that both the N-terminal and the internal domains have been conserved between the two species. The existence of a murine counterpart of CEA strengthens the case for an essential function for this human tumor marker and provides an experimentally amenable system for elucidation of its biological properties.
Marinobufagenin Predicts and Resibufogenin Prevents Preeclampsia: A Review of the Evidence (2012)

Expanded human trials of MBG as a predictor of the later development of PE are warranted as are studies of the efficacy and safety of RBG as a preventative/therapy.
Transcription antitermination: the λ paradigm updated (1995)

Coliphage lambda employs systems of transcription termination and antitermination to regulate gene expression. Early gene expression is regulated by the phage-encoded N protein working with a series of Escherichia coli proteins, Nus, at RNA sites, NUT, to modify RNA polymerase to a termination-resistant form. Expression of lambda late genes is regulated by the phage-encoded Q antitermination protein. Q, which appears to use only one host factor, acts at a DNA site, qut, to modify RNA polymerase to a termination-resistant form. This review focuses on recent studies which show that: (i) N can mediate antitermination in vitro, independent of Nus proteins. (ii) Early genes in another lambdoid phage HK022 are also regulated by antitermination, where only an RNA signal appears necessary and sufficient to create a termination-resistant RNA polymerase. (iii) A part of the qut signal appears to be read from the non-template DNA strand. (iv) A host-encoded inhibitor of N antitermination appears to act through the NUT site as well as with the alpha subunit of RNA polymerase, and is antagonized by NusB protein.
Assessment of myocardial perfusion in coronary artery disease using myocardial contrast echocardiography (1995)

MCE has evolved over the past decade as a clinically useful technique for the assessment of myocardial perfusion in patients with coronary artery disease. At present, its applications are limited because of the necessity of injecting microbubbles directly into the arterial circulation. Newer contrast agents, capable of producing myocardial opacification from a venous injection, are likely to broaden significantly the application of this technique in patients with coronary artery disease. Advances in ultrasound technology, such as second-harmonic imaging will make MCE a valuable non-invasive method, capable of simultaneously assessing regional perfusion and function. The advent of ultrasound systems that provide a linear relationship between the tissue concentration of microbubbles and the video intensity will make the method truly quantitative. It is likely that MCE will replace nuclear cardiology for the assessment of myocardial dysfunction by the turn of the century in many patients with coronary artery disease.
RNF2 is the target for phosphorylation by the p38 MAPK and ERK signaling pathways (2009)

RNF2, a member of polycomb group (PcG) proteins, is involved in chromatin remodeling. However, mechanisms that regulate RNF2 function are unknown. To identify such mechanisms, RNF2 was expressed in HEK-293 cells and analyzed by 2-D electrophoresis. RNF2 was resolved into at least seven protein spots, migrating toward the lower pI from its expected pI of 6.38, suggesting that RNF2 undergoes post-translational modifications. Western blotting indicated that majority of these RNF2 spots contained phosphoserine(s), which were completely dephosphorylated upon treatment with a phosphatase. SB203580, a specific inhibitor of p38 MAPK, inhibited RNF2 phosphorylation at one site. On the other hand, PD98059, an inhibitor of MEK1/2, inhibited majority of the phosphorylation events in RNF2. Mass spectrometry analysis identified that RNF2 expressed in Sf9 insect cells undergoes co-translational excision of (1)Met coupled to N-acetylation of (2)Ser, and phosphorylation of (41)Ser. Interestingly, (41)Ser is a predicted p38/MAPK phosphorylation site, consistent with the loss of phosphorylation induced by SB203580. Further analysis indicated that RNF2 phosphorylation differentially modulates the expression of transcription factors and histone 2B acetylation. These results provide first evidence for phosphorylation of RNF2, and suggest that the mitogen activated protein kinases including p38 MAPK and ERK1/2 regulate growth, stress response, differentiation and other cellular processes, through phosphorylation of RNF2.
Nanoscale Morphology Revealed at the Interface Between Colloidal Quantum Dots and Organic Semiconductor Films (2010)

The degree of interpenetration at the interface between colloidal quantum dots (QDs) and organic semiconductor molecules commonly employed in hybrid light-emitting devices (QD-LEDs) has been examined using tapping-mode atomic force microscopy. Both phase separation-driven and Contact Printing-enabled QD/semiconductor heterojunction fabrication methodologies lead to significant QD embedment in the underlying organic film with the greatest degree of QD penetration observed for QD monolayers that have been contact printed. The relative performance of QD-LEDs fabricated via three different methods using the same materials set has also been investigated.
The design and implementation of fault insertion capabilities for ISPS (1980)

Fault tolerance is an important attribute of most computer systems, and to be effective it must be an explicit objective from the beginning of the design process. Inserting faults into a simulation of the machine and observing its behavior is a thorough and economical technique for evaluating prospective fault detection, diagnosis, recovery, and repair mechanisms. As systems become larger due to rising semiconductor integration, the expense of these fault simulations increasingly necessitates that they be performed at higher levels of abstraction (such as the register transfer level) rather than lower (such as the gate level). This can achieve major cost savings without significantly compromising fault coverage.
Bcl-2 Overexpression Protects Against Neuron Loss in Peri-infarct Regions Following Experimental Stroke (2001)

59 Purpose: Bcl-2 protects against both apoptotic and necrotic death induced by various insults, including cerebral ischemia. Ischemic injury with and without reperfusion may occur by different mechanisms, and protective strategies may be effective against one, but not the other. Here, we determine whether Bcl-2 protects against 2 different forms of focal cerebral ischemic injury within cortical penumbra in a model of experimental stroke. Methods: Bipromoter defective herpes simplex viral (HSV) vectors expressing Bcl-2 plus β-galactosidase (β-gal) as the reporter or β-gal only (control vector)were stereotaxically injected into left and right cortices using coordinates corresponding to the infarct border. 12 h later, focal ischemia was induced by occluding the middle cerebral artery (MCA) and both common carotid arteries (CCA). For the permanent occlusion model, the MCA was left occluded, but the CCAs were reopened after 2 h. For the reperfusion model, all 3 vessels were reopened after 2 h. 2 days later, brains were harvested and sections were reacted with X-gal followed by cresyl violet. X-gal positive neurons were counted in each hemisphere and expressed as the ratio of positive neurons in the ischemic side compared to the non-ischemic side. Results: Bcl-2 overexpression resulted in significantly improved cortical neuron survival within penumbral regions compared to control vector in both cases. Following reperfusion, Bcl-2 injected animals had 74±14%(n=5) survival compared to control 26±3% (n=6)(P Conclusion: Bcl-2 overexpression protects against experimental stroke with and without reperfusion. The extent of protection appears to be greater for ischemia with permanent MCA occlusion. Furthermore, we show that gene transfer to penumbral zones is possible, suggesting a potential therapeutic strategy for clinical application.
Combination of distributed camera network and laser-based 3D mapping for urban service robots (2009)

Presentado al IROS Workshop on Network Robot Systems (celebrado en Saint Louis (EE. UU.) del 11 al 15 de octubre de 2009.
Reclassification of Streptomyces diastaticus subsp. ardesiacus, Streptomyces gougerotii and Streptomyces rutgersensis (2020)

We investigated the taxonomic relationships among <i>Streptomyces diastaticus</i> subsp. <i>ardesiacus</i>, <i>Streptomyces diastaticus</i> subsp. <i>diastaticus</i>, <i>Streptomyces gougerotii</i> and <i>Streptomyces rutgersensis</i>. The 16S rRNA gene sequence similarity between <i>S. diastaticus</i> subsp. <i>ardesiacus</i> and <i>S. diastaticus</i> subsp. <i>diastaticus</i> was 97.7 %, whereas <i>S. diastaticus</i> subsp. <i>diastaticus</i>, <i>S. gougerotii</i> and <i>S. rutgersensis</i> showed 100 % nucleotide sequence identity. In addition, <i>S. diastaticus</i> subsp. diastaticus<i>, S. gougerotii</i> and <i>S. rutgersensis</i> formed a single clade in the phylogenetic tree. Digital DNA-DNA relatedness between <i>S. diastaticus</i> subsp. <i>diastaticus</i> and <i>S. diastaticus</i> subsp. <i>ardesiacus</i> was only 22.8%, indicative of different species. In comparison, DNA-DNA relatedness values for <i>S. diastaticus</i> subsp. <i>diastaticus</i>, <i>S. gougerotii</i> and <i>S. rutgersensis</i> ranged from 95.8 to 97.2 %, suggesting the three taxa belong to the same genomospecies. Previously reported phenotypic data also supported synonymy. Therefore, we propose that <i>S. diastaticus</i> subsp. <i>ardesiacus</i> should be classified as an independent species, <i>Streptomyces ardesiacus</i> sp. nov. The type strain is NBRC 13412<sup>T</sup> (=ATCC 3315<sup>T</sup>=CBS 713.72<sup>T</sup>=DSM 40496<sup>T</sup>=ISP 5496<sup>T</sup>=JCM 4745<sup>T</sup>=NBRC 3714<sup>T</sup>=NRRL B-1241<sup>T</sup>=RIA 1373<sup>T</sup>). Our data also suggests that <i>S. rutgersensis</i> and <i>S. gougerotii</i> should be reclassified as later heterotypic synonyms of <i>S. diastaticus</i>.
The sterlet sturgeon genome sequence and the mechanisms of segmental rediploidization (2020)

Sturgeons seem to be frozen in time. The archaic characteristics of this ancient fish lineage place it in a key phylogenetic position at the base of the ~30,000 modern teleost fish species. Moreover, sturgeons are notoriously polyploid, providing unique opportunities to investigate the evolution of polyploid genomes. We assembled a high-quality chromosome-level reference genome for the sterlet, Acipenser ruthenus. Our analysis revealed a very low protein evolution rate that is at least as slow as in other deep branches of the vertebrate tree, such as that of the coelacanth. We uncovered a whole-genome duplication that occurred in the Jurassic, early in the evolution of the entire sturgeon lineage. Following this polyploidization, the rediploidization of the genome included the loss of whole chromosomes in a segmental deduplication process. While known adaptive processes helped conserve a high degree of structural and functional tetraploidy over more than 180 million years, the reduction of redundancy of the polyploid genome seems to have been remarkably random.
On‐line molecular weight distribution estimation and control in batch polymerization (1994)

Abstract A molecular weight distribution (MWD) estimator for batch methyl methacrylate solution polymerization is implemented experimentally for on‐line control and estimation of the MWD. The estimator is based on an extended Kalman filter and provides current estimates of the entire MWD, reaction temperature, monomer conversion, and initiator conversion. It uses a detailed polymerization model, on‐line monomer conversion measurements, temperature measurements, and periodic, time‐delayed measurements of the MWD from an on‐line size‐exclusion chromatograph. The estimator is shown to perform well with several on‐line MWD estimation experiments. Real‐time feedback control of the molecular weight is presented by utilizing the on‐line MWD information. Temperature, monomer‐addition, and simultaneous temperature and monomer‐addition control are investigated experimentally to achieve a specific constant weight‐average molecular weight. The on‐line feedback control is effective in rejecting realistic disturbances which deteriorate molecular weight control.
Preface: Software defined environments (2014)

Presents the introductory welcome message from the conference proceedings. May include the conference officer(s) offer(s) congratulations to all involved with the conference event and publication of the proceedings record.
Minimizing Tip-Sample Contact Force in Automated Atomic Force Microscope Based Force Spectroscopy (2009)

In atomic force microscope based force spectroscopy, it is often necessary to minimize the tip-sample contact force. While it is possible to control the contact force using force feedback, this method is susceptible to sensor drift and is often under-utilized due to the noise associated with the feedback process. Here we present a method to control the tip-sample contact force for repeated pulling cycles without relying on force feedback or tedious user-controlled z-stage step increments. The custom pulling program uses the data recorded during the previous retraction cycle to automatically reposition the sample surface to account for changes in topography and system drift. Using this method we were able to complete 250 automated pulling cycles, 76% of which had evidence of tip-sample contact. Of those pulling cycles with tip-sample contact, the average contact force was 83 pN, with the maximum contact force not exceeding 292 pN.
Tests of systematic effects in an n-channel FPGA time-to-digital converter for continuous acquisition with high photon count rate using correlation measurements (2021)

The continuous time-tagging of photon arrival times for high count rate sources is necessary for applications such as optical communications, quantum key encryption, and astronomical measurements. Detection of Hanbury- Brown Twiss photon correlations from thermal sources such as stars requires a combination of high dynamic range, long integration times and low systematics in the photon detection and time tagging system. The continuous nature of the measurements and the need for highly accurate timing resolution requires a customized time-to-digital converter (TDC). We used a custom built, two-channel, FPGA-based TDC to continuously time tag single photons with sub clock cycle timing resolution for correlation measurements. We used autocorrelation and cross-correlation measurement tools to constrain spurious systematic effects in the pulse count data as a function of system variables. These variables included, but were not limited to, incident photon count rate, incoming signal attenuation, and measurements of fixed signals. We present an overview of the results of these tests, the types of systematic effects that the results imply, and how those effects may be accounted for and corrected to levels below those required for photon correlation measurements.
11.6 A multi-channel neural-recording amplifier system with 90dB CMRR employing CMOS-inverter-based OTAs with CMFB through supply rails in 65nm CMOS (2015)

In addition to minimizing input-referred noise and lowering power consumption, a good multi-channel neural amplifier system should be able to significantly reject common-mode electrical interference (CMI). The dominant source of CMI comes from capacitive coupling of electrical mains supply line or EMGs onto neural tissues and can be as high as 100mV <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">pp</inf> [1]. Thus any neural recording setup needs a total common-mode rejection ratio (TCMRR) of at least 70dB for a minimum detectable neural signal of 5uV <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">rms</inf> [1]. However, multi-channel neural amplifiers are commonly implemented with a shared reference input whose input impedance is several times lower than that of corresponding signal inputs [2]. This results in a large mismatch at the bipolar electrode-amplifier input interface [1]. As analysed in Fig. 11.6.1, the TCMRR is significantly degraded below 70dB, independent of an amplifier's intrinsic CMRR (ICMRR). In this work, we report a micro-power, low-noise 16-channel neural amplifier that eliminates this impedance mismatch problem by using single-ended CMOS inverter-based LNAs for both the reference and signal inputs. Compared to conventional replica channel works [3], when operating at 1V supply, the LNAs can accommodate a large input CMI of up to 220mV <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">pp</inf> through the use of a common-mode feedback (CMFB) loop implemented through the supply rails of the CMOS-inverter-based LNAs, which coincidentally leads to a high amplifier ICMRR.
Rescue of expression and signaling of human luteinizing hormone G protein-coupled receptor mutants with an allosterically binding small-molecule agonist (2011)

Naturally occurring mutations of G protein-coupled receptors (GPCRs) causing misfolding and failure to traffic to the cell surface can result in disease states. Some small-molecule orthosteric ligands can rescue such misfolded receptors, presumably by facilitating their correct folding and shuttling to the plasma membrane. Here we show that a cell-permeant, allosterically binding small-molecule agonist (Org 42599) rescues the folding and cell surface expression, and therefore target cell signaling, of mutant human luteinizing hormone (LH) receptors (A593P and S616Y) that cause Leydig cell hypoplasia in man. Both mutant receptors were retained in the cytoplasm whereas WT receptor localized at the cell membrane, and binding of LH to cells expressing the mutant receptors was markedly lower than to those expressing the WT receptor. Incubation with Org 42599 increased mutant receptor expression, cell surface localization, and the proportion of mutant receptor in the mature glycosylated form. Importantly, although LH stimulated little (S616Y) or no (A593P) activation of cells expressing mutant receptors, incubation of cells with Org 42599 facilitated rescue of expression and stimulation by the native ligand, LH. Although Org 42599 could activate these receptors, it could not displace (125)I-labeled human LH binding to the WT receptor, indicating that it acts in an allosteric manner. Here we demonstrate a small-molecule GPCR allosteric agonist that functionally rescues intracellularly retained mutant LH receptors by facilitating their cell surface expression. This approach may have application for treatment of infertile patients bearing such mutations and, more broadly, for other misfolded GPCR mutants resulting in human pathologic processes.
Multiple-mirror trap: Milestones and future (2016)

A fusion reactor concept on the basis of a linear trap is developing in BINP. These studies incorporate multiple-mirror sections which should reduce significantly longitudinal plasma losses from a confinement zone. In the paper, physics on the multiple-mirror confinement relevant to plasma behavior at reactor conditions will be discussed. Basic results were received in the GOL-3 multiple-mirror trap in which plasma of 1021 m−3 density was heated by a high-power electron beam up to 2 – 4 keV temperature. The key milestones were: the demonstration of effective plasma heating by the electron beam due to collective effects, the achievement of theoretically predicted level of energy confinement time under optimal conditions, and finally, the discovery of a bounce instability that improves longitudinal confinement. Direct demonstration of a confinement improvement by multi-mirror sections in the magnetic configuration relevant to the reactor one will be done in the GOL-NB facility that will be created in BINP. In addition, a new plasma device SMOLA with a helical multiple-mirror magnetic field for an active confinement control is discussed.
Native Oxide Growth and Organic Impurity Removal on Si Surface with Ozone‐Injected Ultrapure Water (1993)

To manufacture ULSI devices with high performance and reliability in large volume, further integration and miniaturization are being promoted. The key issue in realizing what we call "Noise‐Free Manufacturing" is to keep the wafer surface ultraclean all the time. To realize the ultraclean wafer, organic impurities adsorbed on the wafer surface must be removed first before other wafer cleaning procedures. This is because native oxide and metallic impurities on the wafer cannot be removed completely in the presence of residual organic impurities on the surface. The conventional wet cleaning process is designed to have the cleaning performed at the first stage to remove organic impurities on the wafer. Because the solution in this cleaning must be heated to about 130°C, the chemical composition of the solution cannot be maintained at a constant level. This means that the cleaning is not perfectly controlled. The cleaning has another serious problem: the cleaning step produces a large volume of chemical waste that must be treated properly. We have developed a cleaning technology using ozone‐injected ultrapure water. Ozone concentration in the water is 1–2 ppm. This process is capable of effectively removing organic contaminants from the wafer surface in a short time at room temperature. Processing waste from this process is simple. Chemical composition of the ozone‐injected ultrapure water can be controlled easily.
Cardiac Contractility Modulation by Non-Excitatory Currents: Studies in Isolated Cardiac Muscle (2005)

Like voltage clamping, extracellular currents applied during the ARP can similarly modulate action potential duration in-vitro and modulate myocardial contractility by similar intracellular mechanisms. This concept provides the potential of a therapeutic strategy in patients with heart failure to enhance contractility.
Control of charge dilution in turbocharged diesel engines via exhaust valve timing (2004)

Stringent constraints in oxides of nitrogen (NOx) and particulate emission require high levels of exhaust gas recirculation. In this paper we employ a Variable Valve Timing methodology that in steady-state achieves large levels of internal Exhaust Gas Recirculation (iEGR) or charge dilution in Diesel engines. We develop a crankangle based dynamic nonlinear model of a six-cylinder 12 liter turbocharged (TC) Diesel engine. This model captures the transient interactions between VVT actuation, the turbocharger dynamics, and the cylinder-to-cylinder breathing characteristics. Low order linear multi-input multi-output (MIMO) models are then identified using cycle-sampled or -averaged data from the higher order non-linear model. A model-based controller is designed that varies Exhaust Valve Closing (EVC) to maximize the internal exhaust gas recirculation under air-to-fuel ratio (AFR) constraints during transient fueling demands. The closed-loop controller is based on tracking optimal and achievable set-points of burned gas fraction. Simulation results are shown on the full order model.