gebhart/patrepeval huggingface dataset:
Mammalian Dengue Virus Receptors (2005)

It has been estimated that some 3 billion people live in areas at the risk of infection with the dengue virus, and that up to 100 million infections occur each year, making dengue the most common arthropod-borne viral disease. Humans become infected following the bite of an infected mosquito, and infection can either be essentially without symptoms, or can result in severe, life-threatening manifestations. The initial interaction between a susceptible host cell and the dengue virus is a critical determinant of cell tropism and thus of pathogenicity. As such, considerable effort has been expended on trying to determine the nature of the initial cell: virus interaction and in particular to identify the nature of the receptor proteins used by dengue virus to enter into the cell. Over the last few years a number of proteins, including DC-SIGN, GRP-78, the 37/67kDa high-affinity laminin receptor and heat shock proteins 70 and 90, have all been implicated as dengue virus receptors in a number of cell types. In addition, the specific role of heparan sulfate in dengue virus binding and internalization of dengue still remains to be fully elucidated. This review seeks to provide an overview of the current state of research into mammalian dengue virus receptors, as an increased understanding of which molecules can function as dengue virus receptors and how their expression leads to cell susceptibility will potentially provide novel insights into the pathogenic mechanism of dengue virus infection.
Single crystal nano-resonators at 100 MHz fabricated by a simple batch process (2005)

Nanoresonators with resonant frequency until 100 MHz and with Q-factors until 15000 were realized in a single crystal <100> standard silicon wafer, using standard UV photolithography and anisotropic etching with TMAH. Their cross-section is triangular, with edges following <111> and <100> planes, and they are aligned along the {110} direction. While the resonant frequency decreases with the increase of the length, as expected, the Q factor shows quite different values between the two tested batch process. This is due to the connecting parts of the resonators to the bulk, which differs in the two batch process, with one giving more dissipation losses than the other one.
Enabling deep-tissue networking for miniature medical devices (2018)

We present IVN (In-Vivo Networking), a system that enables powering up and communicating with miniature sensors implanted or injected in deep tissues. IVN overcomes fundamental challenges which have prevented past systems from powering up miniature sensors beyond superficial depths. These challenges include the significant signal attenuation caused by bodily tissues and the miniature antennas of the implantable sensors.
Knowledge-based quantification of pericardial fat in non-contrast CT data (2010)

Recent studies show that pericardial fat is associated with vascular calcification and cardiovascular risk. The fat is imaged with Computed Tomography (CT) as part of coronary calcium scoring but it is not included in routine clinical analysis due to the lack of automatic tools for fat quantification. Previous attempts to create such an automated tool have the limitations of either assuming a preset threshold or a Gaussian distribution for fat. In order to overcome these limitations, we present a novel approach using a classification-based method to discriminate fat from other tissues. The classifier is constructed from three binary SVM classifiers trained separately for multiple tissues (fat, muscle/blood and calcium), and a specific code is assigned to each tissue type based on the number of classifiers. The decisions of these binary classifiers are combined and compared with previously determined codes using a minimum Hamming decoding distance to identify fat. We also present an improved method for detection of a compact region-of-interest around the heart to reduce the number of false positives due to neighboring organs. The proposed method UH-PFAT attained a maximum overlap of 87%, and an average overlap of 76% with expert annotations when tested on unseen data from 36 subjects. Our method can be improved by identifying additional discriminative features for fat and muscle/blood separation, or by using more advanced classification approaches such as cascaded classifiers to reduce the number of false detections.
What Constitutes Adequate Oxygenation? (1990)

In an attempt to avoid the substantial risks of pulmonary injury associated with the use of high ventilator pressures and high oxygen concentrations, physicians often ask such questions as "What is the optimal Pao2?" and "What treatment should be used to achieve an optimal Pao2?" Although the intent to minimize secondary, ventilator-induced lung injury is laudable, any attempt to provide a fixed numeric response to this query is misguided not only because the oxygen requirements and clinical circumstances of our patients vary, but because the Pao2 is a particularly poor indicator of these needs. An example is the large full-term neonate admitted to a newborn intensive care unit from the delivery room with obvious tachypnea and an arterial Po2 of 60 mm Hg in room air. Is this Pao2 acceptable? A more appropriate question may be whether the infant's "oxygenation" is adequate. But what is "oxygenation"? If by this vaguely applied term we mean the partial pressure of oxygen in the arterial blood, and if we define the acceptable limits for this parameter as being between 50 and 80 mm Hg, as is often done, then the answer must clearly be in the affirmative. If, on the other hand, we take oxygenation to mean the balance between the rate of oxygen delivery to the tissues and their rate of oxygen consumption, then we must admit that we cannot know on the basis of the information provided by the Pao2 alone. Oxygen delivery is determined by the concentration o hemoglobin in the blood, its oxygen saturation, the rate at which this blood is circulated to the tissues (generally, the cardiac output), and the efficiency with which the oxygen is "unloaded" from hemoglobin to the tissues.
Simulation of the Governance of Complex Systems (SimCo): Basic Concepts and Experiments on Urban Transportation (2018)

The current paper is positioned at the intersection of computer simulation, governance research, and research on infrastructure systems, such as transportation or energy. It proposes a simulation framework, "Simulation of the governance of complex systems" (SimCo), to study the governability of complex socio-technical systems experimentally by means of agent-based modelling (ABM). SimCo is rooted in a sociological macromicro-macro model of a socio-technical system, taking into account the interplay of agents' choices (micro) and situational constraints (macro). The paper presents the conceptualization of SimCo, its elements and subsystems as well as their interactions. SimCo depicts the daily routines of users performing their tasks (e.g. going to work) by choosing among di erent technologies (e.g. modes of transportation), occasionally deciding to replace a worn-out technology. All components entail di erent dimensions that can be adjusted, thus allowing operators to purposefully intervene, for instance in the case of risk management (e.g. preventing congestion) or system transformation (e.g. towards sustainable mobility). Experiments with a basic scenario of an urban road transport system demonstrate the e ects of di erent modes of governance (so control, strong control and a combination of both), revealing that so control may be the best strategy to govern a complex socio-technical system.
Planar approximation for the least reliable bit log-likelihood ratio of 8-PSK modulation (2000)

The optimum decoding of component codes in block coded modulation (BCM) schemes requires the use of the log-likelihood ratio (LLR) as the signal metric. An approximation to the LLR for the least reliable bit (LRB) in an 8-PSK modulation based on planar equations with fixed-point arithmetic is developed that is both accurate and easily realisable for practical BCM schemes. Through an error power analysis and an example simulation it is shown that the approximation results in less than 0.06 dB in degradation over the exact expression at an Es/N0 of 10 dB. It is also shown that the approximation can be realised in combinatorial logic using roughly 7300 transistors. This compares favourably to a look-up table approach in typical systems.
The Lysine Decarboxylase CadA Protects <i>Escherichia coli</i> Starved of Phosphate against Fermentation Acids (2007)

Conflicting results have been reported for the rate and extent of cell death during a prolonged stationary phase. It is shown here that the viability of wild-type cells (MG1655) could decrease >or=10(8)-fold between days 1 and 14 and between days 1 and 6 of incubation under aerobic and anaerobic phosphate (P(i)) starvation conditions, respectively, whereas the cell viability decreased moderately under ammonium and glucose starvation conditions. Several lines of evidence indicated that the loss of viability of P(i)-starved cells resulted primarily from the catabolism of glucose into organic acids through pyruvate oxidase (PoxB) and pyruvate-formate lyase (PflB) under aerobic and anaerobic conditions, respectively. Weak organic acids that are excreted into the medium can reenter the cell and dissociate into protons and anions, thereby triggering cell death. However, P(i)-starved cells were efficiently protected by the activity of the inducible GadABC glutamate-dependent acid resistance system. Glutamate decarboxylation consumes one proton, which contributes to the internal pH homeostasis, and removes one intracellular negative charge, which might compensate for the accumulated weak acid anions. Unexpectedly, the tolerance of P(i)-starved cells to fermentation acids was markedly increased as a result of the activity of the inducible CadBA lysine-dependent acid resistance system that consumes one proton and produces the diamine cadaverine. CadA plays a key role in the defense of Salmonella at pH 3 but was thought to be ineffective in Escherichia coli since the protection of E. coli challenged at pH 2.5 by lysine is much weaker than the protection by glutamate. CadA activity was favored in P(i)-starved cells probably because weak organic acids slowly reenter cells fermenting glucose. Since the environmental conditions that trigger the death of P(i)-starved cells are strikingly similar to the conditions that are thought to prevail in the human colon (i.e., a combination of low levels of P(i) and oxygen and high levels of carbohydrates, inducing the microbiota to excrete high levels of organic acids), it is tempting to speculate that E. coli can survive in the gut because of the activity of the GadABC and CadBA glutamate- and lysine-dependent acid resistance systems.
A Convenient Synthesis of 1-(4-Fluorophenyl)-2-(4-pyridyl)cyclopentene from Cyclopentanone (2008)

In the framework of investigating the role of pyridyl-substituted five-membered heterocycles as potential p38 mitogen-activated protein kinase inhibitors, we synthesized the disubstituted carbocyclic analogue, 1-(4-fluorophenyl)-2-(4-pyridyl)cyclopentene. A multistep synthesis of this compound starting from cyclopentanone is reported. Cyclopentanone was converted into 1-cy-­clo­pentenyl-4-fluorobenzene using a Grignard reaction. The oxidation of this product with hydrogen peroxide and formic acid gave 2-(4-fluorophenyl)cyclopentanone. This ketone was activated using a neodymium salt (NdCl3·2LiCl) and subsequently reacted with a complexed Grignard reagent (pyMgCl·LiCl) to give the corresponding cyclopentanol derivative. Finally, dehydration of the latter alcohol led to the title compound.
The Improvisational State of Mind: A Multidisciplinary Study of an Improvisatory Approach to Classical Music Repertoire Performance (2018)

The recent re-introduction of improvisation as a professional practice within classical music, however cautious and still rare, allows direct and detailed contemporary comparison between improvised and "standard" approaches to performances of the same composition, comparisons which hitherto could only be inferred from impressionistic historical accounts. This study takes an interdisciplinary multi-method approach to discovering the contrasting nature and effects of prepared and improvised approaches during live chamber-music concert performances of a movement from Franz Schubert's "Shepherd on the Rock," given by a professional trio consisting of voice, flute, and piano, in the presence of an invited audience of 22 adults with varying levels of musical experience and training. The improvised performances were found to differ systematically from prepared performances in their timing, dynamic, and timbral features as well as in the degree of risk-taking and "mind reading" between performers, which included moments of spontaneously exchanging extemporized notes. Post-performance critical reflection by the performers characterized distinct mental states underlying the two modes of performance. The amount of overall body movements was reduced in the improvised performances, which showed less unco-ordinated movements between performers when compared to the prepared performance. Audience members, who were told only that the two performances would be different, but not how, rated the improvised version as more emotionally compelling and musically convincing than the prepared version. The size of this effect was not affected by whether or not the audience could see the performers, or by levels of musical training. EEG measurements from 19 scalp locations showed higher levels of Lempel-Ziv complexity (associated with awareness and alertness) in the improvised version in both performers and audience. Results are discussed in terms of their potential support for an "improvisatory state of mind" which may have aspects of flow (as characterized by Csikszentmihalyi, 1997) and primary states (as characterized by the Entropic Brain Hypothesis of Carhart-Harris et al., 2014). In a group setting, such as a live concert, our evidence suggests that this state of mind is communicable between performers and audience thus contributing to a heightened quality of shared experience.
<i>Ptf1a</i>is essential for the differentiation of GABAergic and glycinergic amacrine cells and horizontal cells in the mouse retina (2007)

Basic helix-loop-helix (bHLH) transcription factors are important regulators of retinal neurogenesis. In the developing retina, proneural bHLH genes have highly defined expressions, which are influenced by pattern formation and cell-specification pathways. We report here that the tissue-specific bHLH transcription factor Ptf1a (also known as PTF1-p48) is expressed from embryonic day 12.5 of gestation (E12.5) to postnatal day 3 (P3) during retinogenesis in the mouse. Using recombination-based lineage tracing, we provide evidence that Ptf1a is expressed in precursors of amacrine and horizontal cells. Inactivation of Ptf1a in the developing retina led to differentiation arrest of amacrine and horizontal precursor cells in addition to partial transdifferentiation of Ptf1a-expressing precursor cells to ganglion cells. Analysis of late cell-type-specific markers revealed the presence of a small population of differentiated amacrine cells, whereas GABAergic and glycinergic amacrine cells, as well as horizontal cells, were completely missing in Ptf1a-knockout retinal explants. We conclude that Ptf1a contributes to the differentiation of horizontal cells and types of amacrine cells during mouse retinogenesis.
Revised Calibration for High Pressure Electrical Resistance Cell (1970)

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Lck associates with and is activated by Kit in a small cell lung cancer cell line: inhibition of SCF-mediated growth by the Src family kinase inhibitor PP1. (1998)

At least 70% of small cell lung cancers (SCLCs) express the Kit receptor tyrosine kinase and its ligand, stem cell factor (SCF). In an effort to define the signal transduction pathways activated by Kit in SCLC, we focused on Src family kinases and, in particular, Lck, a Src-related tyrosine kinase that is expressed in hemopoietic cells and certain tumors, including SCLC. SCF treatment of the H526 cell line induced a physical association between Kit and Lck that, in vitro, was dependent on phosphorylation of the juxtamembrane domain of Kit. Stimulation of Kit with recombinant SCF resulted in a rapid 3-6-fold increase in the specific activity of Lck, which was similar in magnitude to the activation of Lck resulting from the cross-linking of the T-cell receptor complex of Jurkat cells. Lck activity peaked by 5 min after SCF addition, and the elevated activity persisted for at least 30 min in the presence of SCF, with kinetics similar to the activation of mitogen-activated protein kinase. PP1, an inhibitor of Src family kinases with selectivity for Lck, completely inhibited SCF-mediated growth but had little effect on insulin-like growth factor-I-mediated growth. PP1 antagonized both SCF-mediated proliferation and inhibition of apoptosis. PP1 had no effect on Kit kinase activity but was shown to block total Lck activity by at least 90% by immune complex kinase assay. Low levels of Src, Hck, and Yes were also expressed in the H526 cell line; only Yes showed a consistent increase in specific activity, which was also inhibited by PP1 following SCF treatment. These data demonstrate that, in the H526 SCLC cell line, Lck and, possibly, Yes are downstream of Kit in a signal transduction pathway; the inhibition by PP1 of SCF-mediated proliferation and inhibition of apoptosis suggests that Src family kinases are intermediates in the signaling pathways that regulate these processes.
Nanometer-scale patterning of self-assembled monolayer films on native silicon oxide (1998)

A nanoscale-patterning method on silicon oxide using a self-assembled monolayer (SAM) was developed. The silicon surface with native oxide was additionally oxidized locally in dry nitrogen atmosphere by the field-induced oxidation (FIO) technique using an atomic force microscope with a conductive cantilever, and then immersed in octadecyltrichlorosilane (OTS) solution. The contact angle and topography image revealed that the OTS layer was formed only on the native oxide. In contrast, when FIO was performed under the humidity of 88%, OTS SAM was formed on both FIO and native oxide. These results indicate that SAM formation on silicon oxides can be locally suppressed by FIO in a dry environment. By using this technique, we could fabricate a line structure of OTS SAM as narrow as 22 nm.
An Inductively Powered Converter for Implantable Biochemical Sensor Signal Processing System (2009)

In this paper, we propose an inductively powered converter to convert the incoming RF energy into a DC voltage (3.3 V) which powers up the biochemical sensor signal processing system. The converter, which is constructed by clamper, voltage limiter, rectifier, and LDO regulator, is capable of delivering more than 330 muW from a receiver coil to the implant circuitry. The chip area is 0.12times0.48 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> in the 0.35 mum CMOS process. The performance of the integrated converter has been tested, by using carrier signal in 13.56 MHz. The proposed converter has the merit of low cost, due to its use of the standard CMOS process, without the necessary of adding an extra ESD process.
Mechanisms of Olefin Metathesis Catalyst Decomposition and Methods of Catalyst Reactivation (2015)

Since their discovery, homogeneous olefin metathesis catalysts have been the object of intense research which has led to many improvements in their activity, selectivity, and stability. One important aspect of this research concerns the area of catalyst decomposition. Detailed mechanisms of catalyst decomposition in the absence and presence of substrates have been unveiled. These studies have played an important role in the development of olefin metathesis catalysts by guiding the design of improved and more stable systems. This chapter reviews the decomposition mechanisms of well-defined, homogeneous, high-oxidation state molybdenum and tungsten catalysts as well as of homogeneous ruthenium-based catalysts, strategies used to avert catalyst decomposition, and possible modes of catalyst reactivation or regeneration.
Initiation of electroless Cu plating on nonmetallic surfaces (1984)

Electroless plating of a metal on a dielectric substrate requires the prior deposition of a catalyst such as a Pd-Sn colloid consisting of a metallic Pd core surrounded by a stabilizing layer of Sn ions. The activation step (deposition of the colloid) is usually followed by an acceleration step (removal of excess ionic tin). Adhesion of the deposit to the substrate is improved by mechanical and chemical pretreatment steps. An electrochemical method has been developed for assessing the catalytic activity of Pd-Sn colloids. Hydrogen sorption in the Pd in the colloid can be correlated with catalytic activity, since Pd accessible for the H-sorption reaction is also accessible as the catalyst for the electroless deposition reaction. These conclusions have been confirmed by surface analytical techniques and by functional tests. The efficacy of various accelerating solutions has also been assessed.
Finite bisimulation of reactive untimed infinite state systems modeled as automata with variables (2006)

Some discrete event systems such as software are typically infinite state systems, and a commonly used technique for performing formal analysis such as automated verification is based on their finite abstractions. In this paper, we consider a model for reactive untimed infinite state systems called input-output extended finite automaton (I/O-EFA), which is an automaton extended with discrete variables such as inputs, outputs, and data. Using I/O-EFA as a model many value-passing processes can be represented by finite graphs. We study the problem of finding a finite abstraction that is bisimilar to a given I/O-EFA. We present a sufficient condition under which the underlying transition system of an I/O-EFA admits a finite bisimilar quotient. This sufficient condition is existential as it relies on the existence of a suitable partition of the state space. We then identify a class of I/O-EFAs for which a partition satisfying our sufficient condition can be constructed by inspecting the structure of the given I/O-EFA
COMPARISON BETWEEN TACROLIMUS AND CYCLOSPORINE AS IMMUNOSUPPRESSIVE AGENTS COMPATIBLE WITH TOLERANCE INDUCTION BY CD4/CD8 BLOCKADE (2000)

The induction of tolerance by blocking CD4 and CD8 was not prevented by tacrolimus. However, combination of cyclosporine with the same tolerogenic protocol was toxic to mice.
A novel filter design for suppression of high voltage gradient in voltage-fed PWM inverter (1997)

This paper proposes a new filter topology that suppresses the high voltage gradient (dv/dt) in AC motor terminals when a cable feeding a motor is very long. By using the proposed filter in the inverter terminal, the rising and the falling edge of the PWM waveform of the inverter are smoothed, resulting in less voltage gradient to the AC motor. The effectiveness of the proposed filter is compared to that of the conventional scheme and its effectiveness is verified by computer simulation, as well as by prototype experiments.