gebhart/patrepeval huggingface dataset:
Molecular Cloning, Sequencing, and Expression of a Novel Multidomain Mannanase Gene from <i>Thermoanaerobacterium polysaccharolyticum</i> (1999)

The manA gene of Thermoanaerobacterium polysaccharolyticum was cloned in Escherichia coli. The open reading frame of manA is composed of 3,291 bases and codes for a preprotein of 1,097 amino acids with an estimated molecular mass of 119,627 Da. The start codon is preceded by a strong putative ribosome binding site (TAAGGCGGTG) and a putative -35 (TTCGC) and -10 (TAAAAT) promoter sequence. The ManA of T. polysaccharolyticum is a modular protein. Sequence comparison and biochemical analyses demonstrate the presence of an N-terminal leader peptide, and three other domains in the following order: a putative mannanase-cellulase catalytic domain, cellulose binding domains 1 (CBD1) and CBD2, and a surface-layer-like protein region (SLH-1, SLH-2, and SLH-3). The CBD domains show no sequence homology to any cellulose binding domain yet reported, hence suggesting a novel CBD. The duplicated CBDs, which lack a disulfide bridge, exhibit 69% identity, and their deletion resulted in both failure to bind to cellulose and an apparent loss of carboxymethyl cellulase and mannanase activities. At the C-terminal region of the gene are three repeats of 59, 67, and 56 amino acids which are homologous to conserved sequences found in the S-layer-associated regions within the xylanases and cellulases of thermophilic members of the Bacillus-Clostridium cluster. The ManA of T. polysaccharolyticum, besides being an extremely active enzyme, is the only mannanase gene cloned which shows this domain structure.
[Photoluminescence of nano-SiC annealed by pulse laser]. (2005)

Nanocrystalline silicon carbon (nc-SiC) from amorphous silicon carbon films was obtained through XeCl excimer laser annealing. The photoluminescence (PL) of the nc-SiC was analyzed at different annealing laser energy density. It was observed that PL presented a wide luminescence band from 300-600 nm in the nc-SiC films. The two main luminescence bands, situated at 398 and 470 nm respectively, are attributed to band to band and defect recombination in the 6H-SiC based on the structure changes of the nc-SiC films. The relative PL intensity of these two bands was determined by the surface state density in the nc-SiC films and their irradiative life
Optical Coherence Tomography Imaging in Acute Coronary Syndromes (2011)

Optical coherence tomography (OCT) is a high-resolution imaging technique that offers microscopic visualization of coronary plaques. The clear and detailed images of OCT generate an intense interest in adopting this technique for both clinical and research purposes. Recent studies have shown that OCT is useful for the assessment of coronary atherosclerotic plaques, in particular the assessment of plaque rupture, erosion, and intracoronary thrombus in patients with acute coronary syndrome. In addition, OCT may enable identifying thin-cap fibroatheroma, the proliferation of vasa vasorum, and the distribution of macrophages surrounding vulnerable plaques. With its ability to view atherosclerotic lesions in vivo with such high resolution, OCT provides cardiologists with the tool they need to better understand the thrombosis-prone vulnerable plaques and acute coronary syndromes. This paper reviews the possibility of OCT for identification of vulnerable plaques in vivo.
Performance advantages of distributed antennas in indoor wireless communication systems (2002)

With the smaller physical scale of distributing the radio frequency signal in buildings, distributed antenna systems, which may be too expensive in outdoor systems, become affordable. This paper explores quantitatively and qualitatively the advantages of distributed antenna systems over single point source antenna systems, and develops theorems comparing the two systems based on a two slope path loss model.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Decision-making in cold chain logistics using data analytics: a literature review (2018)

Purpose The purpose of the paper is to identify the multiple types of data that can be collected and analyzed by practitioners across the cold chain, the ICT infrastructure required to enable data capture and how to utilize the data for decision making in cold chain logistics. Design/methodology/approach Content analysis based literature review of 38 selected research articles, published between 2000 and 2016, was used to create an overview of data capture, technologies used for collection and sharing of data, and decision making that can be supported by the data, across the cold chain and for different types of perishable food products. Findings There is a need to understand how continuous monitoring of conditions such as temperature, humidity, and vibration can be translated to support real-time assessment of quality, determination of actual remaining shelf life of products and use of those for decision making in cold chains. Firms across the cold chain need to adopt appropriate technologies suited to the specific contexts to capture data across the cold chain. Analysis of such data over longer periods can also unearth patterns of product deterioration under different transportation conditions, which can lead to redesigning the transportation network to minimize quality loss or to take precautions to avoid the adverse transportation conditions. Research limitations/implications The findings need to be validated through further empirical research and modeling. There are opportunities to identify all relevant parameters to capture product condition as well as transaction data across the cold chain processes for fish, meat and dairy products. Such data can then be used for supply chain (SC) planning and pricing products in the retail stores based on product conditions and traceability information. Addressing some of the above research gaps will call for multi-disciplinary research involving food science and engineering, information technologies, computer science and logistics and SC management scholars. Practical implications The findings of this research can be beneficial for multiple players involved in the cold chain like food processing companies, logistics service providers, ports and wholesalers and retailers to understand how data can be effectively used for better decision making in cold chain and to invest in the specific technologies, which will suit the purpose. To ensure adoption of data analytics across the cold chain, it is also important to identify the player in the cold chain, which will drive and coordinate the effort. Originality/value This paper is one of the earliest to recognize the need for a comprehensive assessment for adoption and application of data analytics in cold chain management and provides directions for future research.
FAM19A5 Expression During Embryogenesis and in the Adult Traumatic Brain of FAM19A5-LacZ Knock-in Mice (2019)

FAM19A5 is a secretory protein that is predominantly expressed in the brain. Although the <i>FAM19A5</i> gene has been found to be associated with neurological and/or psychiatric diseases, only limited information is available on its function in the brain. Using <i>FAM19A5-LacZ</i> knock-in mice, we determined the expression pattern of FAM19A5 in developing and adult brains and identified cell types that express FAM19A5 in naïve and traumatic brain injury (TBI)-induced brains. According to X-gal staining results, FAM19A5 is expressed in the ventricular zone and ganglionic eminence at a very early stage of brain development, suggesting its functions are related to the generation of neural stem cells and oligodendrocyte precursor cells (OPCs). In the later stages of developing embryos and in adult mice, FAM19A5 expression expanded broadly to particular regions of the brain, including layers 2/3 and 5 of the cortex, cornu amonis (CA) region of the hippocampus, and the corpus callosum. X-gal staining combined with immunostaining for a variety of cell-type markers revealed that FAM19A5 is expressed in many different cell types, including neurons, OPCs, astrocytes, and microglia; however, only some populations of these cell types produce FAM19A5. In a subpopulation of neuronal cells, TBI led to increased X-gal staining that extended to the nucleus, marked by slightly condensed content and increased heterochromatin formation along the nuclear border. Similarly, nuclear extension of X-gal staining occurred in a subpopulation of OPCs in the corpus callosum of the TBI-induced brain. Together, these results suggest that FAM19A5 plays a role in nervous system development from an early stage and increases its expression in response to pathological conditions in subsets of neurons and OPCs of the adult brain.
System design for automation in semiconductor manufacturing. (1990)

The objective of this study is the presentation and characterization of the constructs necessary for system design of automated semiconductor manufacturing facilities. This system design is broken into four distinct tasks. The first task is a determination of the appropriate facility structure and subsequent characterization of global facility structure properties. The second task is the development and description of a communication protocol for the automated semiconductor manufacturing facility. The third task is the development of a facility database for process information storage and flow in the facility. The final task is the development and detailed description of a generic architecture for each controller in the facility. A facility automation concept simulation has been developed in parallel with research in the above tasks to support the developed theories from an experimental viewpoint. A hierarchical facility structure is determined as ideal for the automated facility. Its attractive properties of distribution and separation of knowledge, ease of update (due to a limited scope of influence), modularity and transparency are characterized. Results in facility communication include the SECS Message Service (SMS), an International Standards Organization (ISO) compliant protocol that provides for the high speed communication of messages tailored for the semiconductor manufacturing arena. As a further result of the SMS effort, a methodology has been developed for protocol incorporation of features of a non-ISO protocol into an ISO framework. Results in facility database development include an entity relationship (E-R) model of process recipe information flow in the facility. The model includes new E-R model extensions developed to represent time sequence ordering aspects of the information flow. The interpretation of the model to database implementation is presented. Research in the development of a generic controller architecture has led to a structure that maximizes the generic attributes of the controller. The architecture is conditional upon the facility being hierarchical, the various facility communication protocols being well-defined (e.g., ISO compatible), and the facility message format being well-defined and consistent throughout the facility. The facility automation concept simulation incorporates results from each of the above four areas, shows feasibility of the many concepts presented, and identifies initial performance parameters.
The novel dihydroorotate dehydrogenase (DHODH) inhibitor BAY 2402234 triggers differentiation and is effective in the treatment of myeloid malignancies (2019)

Acute myeloid leukemia (AML) is a devastating disease, with the majority of patients dying within a year of diagnosis. For patients with relapsed/refractory AML, the prognosis is particularly poor with currently available treatments. Although genetically heterogeneous, AML subtypes share a common differentiation arrest at hematopoietic progenitor stages. Overcoming this differentiation arrest has the potential to improve the long-term survival of patients, as is the case in acute promyelocytic leukemia (APL), which is characterized by a chromosomal translocation involving the retinoic acid receptor alpha gene. Treatment of APL with all-trans retinoic acid (ATRA) induces terminal differentiation and apoptosis of leukemic promyelocytes, resulting in cure rates of over 80%. Unfortunately, similarly efficacious differentiation therapies have, to date, been lacking outside of APL. Inhibition of dihydroorotate dehydrogenase (DHODH), a key enzyme in the de novo pyrimidine synthesis pathway, was recently reported to induce differentiation of diverse AML subtypes. In this report we describe the discovery and characterization of BAY 2402234 - a novel, potent, selective and orally bioavailable DHODH inhibitor that shows monotherapy efficacy and differentiation induction across multiple AML subtypes. Herein, we present the preclinical data that led to initiation of a phase I evaluation of this inhibitor in myeloid malignancies.
This POODLE Bites: Exploiting The SSL 3.0 Fallback (2014)

This document discusses how attackers can exploit the downgrade dance and break the cryptographic security of SSL 3.0.
The mechanism of fungal cellulase action. Synergism between enzyme components of <i>Penicillium pinophilum</i> cellulase in solubilizing hydrogen bond-ordered cellulose (1989)

Studies on reconstituted mixtures of extensively purified cellobiohydrolases I and II and the five major endoglucanases of the fungus Penicillium pinophilum have provided some new information on the mechanism by which crystalline cellulose in the form of the cotton fibre is rendered soluble. It was observed that there was little or no synergistic activity either between purified cellobiohydrolases I and II, or, contrary to previous findings, between the individual cellobiohydrolases and the endoglucanases. Cotton fibre was degraded to a significant degree only when three enzymes were present in the reconstituted enzyme mixture: these were cellobiohydrolases I and II and some specific endoglucanases. The optimum ratio of the cellobiohydrolases was 1:1. Only a trace of endoglucanase activity was required to make the mixture of cellobiohydrolases I and II effective. The addition of cellobiohydrolases I and II individually to endoglucanases from other cellulolytic fungi resulted in little synergistic activity; however, a mixture of endoglucanases and both cellobiohydrolases was effective. It is suggested that current concepts of the mechanism of cellulase action may be the result of incompletely resolved complexes between cellobiohydrolase and endoglucanase activities. It was found that such complexes in filtrates of P. pinophilium or Trichoderma reesei were easily resolved using affinity chromatography on a column of p-aminobenzyl-1-thio-beta-D-cellobioside.
Isocitrate dehydrogenase mutations: new opportunities for translational research (2015)

Over the last decade, comprehensive genome-wide sequencing studies have enabled us to find out unexpected genetic alterations of metabolism in cancer. An example is the identification of arginine missense mutations of isocitrate dehydrogenases-1 and -2 (IDH1/2) in glioma, acute myeloid leukemia (AML), chondrosarcomas, and cholangiocarcinoma. These alterations are closely associated with the production of a new stereospecific metabolite, (R)-2-hydroxyglutarate (R-2HG). A large number of follow-up studies have been performed to address the molecular mechanisms of IDH1/2 mutations underlying how these events contribute to malignant transformation. In the meanwhile, the development of selective mutant IDH1/2 chemical inhibitors is being actively pursued in the scientific community and pharmaceutical industry. The present review article briefly discusses the important findings that highlight the molecular mechanisms of IDH1/2 mutations in cancer and provides a current status for development of selective mutant IDH1/2 chemical inhibitors.
Successful use of emicizumab in a patient with refractory acquired hemophilia A and acute coronary syndrome requiring percutaneous coronary intervention (2019)

We report a patient with a high-titer factor VIII inhibitor refractory to immunosuppression. He initially presented with myocardial infarction requiring percutaneous coronary intervention (PCI) with bare metal stent placement. Despite Feiba prophylaxis, inadequate hemostasis prompted premature discontinuation of dual antiplatelet therapy (DAPT). Fifteen weeks later, the patient presented with a left anterior descending artery in-stent restenosis. This case report examines the Key Clinical Question of how to manage in-stent restenosis in a patient with acquired hemophilia A (AHA). After multidisciplinary discussions including hematology, cardiology, cardiac surgery, laboratory medicine, and pharmacy, emicizumab was initiated to facilitate PCI. Four weeks after emicizumab initiation, the patient underwent successful PCI with drug-eluting stent placement. Five months after discharge, he remains without signs or symptoms of cardiac disease or bleeding on DAPT and emicizumab. This case provides evidence of the potential of emicizumab for bleeding prophylaxis in AHA.
Energy-Efficient Neuron, Synapse and STDP Integrated Circuits (2012)

Ultra-low energy biologically-inspired neuron and synapse integrated circuits are presented. The synapse includes a spike timing dependent plasticity (STDP) learning rule circuit. These circuits have been designed, fabricated and tested using a 90 nm CMOS process. Experimental measurements demonstrate proper operation. The neuron and the synapse with STDP circuits have an energy consumption of around 0.4 pJ per spike and synaptic operation respectively.
Bias-Dependent Radio Frequency Performance for 40 nm InAs High-Electron-Mobility Transistor with a Cutoff Frequency Higher than 600 GHz (2012)

Bias-Dependent Radio Frequency Performance for 40 nm InAs High-Electron-Mobility Transistor with a Cutoff Frequency Higher than 600 GHz, Faiz Fatah, Chien-I Kuo, Heng-Tung Hsu, Che-Yang Chiang, Ching-Yi Hsu, Yasuyuki Miyamoto, Edward Yi Chang
On Knock Intensity and Superknock in SI Engines (2017)

<div class="section abstract"><div class="htmlview paragraph">Most studies on knock ignore the stochastic nature of knock and focus on the onset of knock which is determined by chemical kinetics. This paper focuses on knock intensity (<i>KI</i>) which is determined by the evolution of the pressure wave following knock onset in a hot spot and highlights the stochastic processes involved.</div><div class="htmlview paragraph"><i>KI</i> is defined in this study as the maximum peak-to-peak pressure fluctuation that follows the onset of knock. It depends on <i>ξ</i> = (<i>a</i>/<i>u<sub>a</sub></i>) where <i>u<sub>a</sub></i> is the speed of the autoignition front and <i>a</i> is the speed of sound. When <i>u<sub>a</sub></i> is small, <i>KI</i> can be related to the product of a parameter <i>Z</i>, which depends on <i>P<sub>ko</sub></i>, the pressure at knock onset and the square of (∂x/∂<i>T</i>), which is the inverse of the gradient of temperature with distance in the hot spot. Both <i>Z</i> and (∂<i>x</i>/∂<i>T</i>) were calculated using measured <i>KI</i> and <i>P<sub>ko</sub></i> for hundreds of individual knocking cycles for different fuels. The model for ignition delay as a function of pressure <i>P</i> and <i>T</i> in the hot spot and other data needed to calculate <i>Z</i> were available from a previous study (SAE 2016-01-0702). For a given fuel and operating condition, <i>Z</i> varies because <i>P<sub>ko</sub></i> varies, because of cyclic variation of combustion - a stochastic process. (∂<i>x</i>/∂<i>T</i>) depends on the evolution of the hot spot during the engine cycle and depends on flow and turbulence - another stochastic process. All else being equal, <i>Z</i> increases and hence the probability of high <i>KI</i> increases as <i>P<sub>ko</sub></i> increases, e.g., by more advanced spark timing and/or faster flame development. For a given <i>P<sub>ko</sub>, Z</i> is lower for a fuel with higher <i>RON</i>. In modern turbocharged engines extremely high intensity knock, informally termed superknock is observed to occur occasionally even though operating conditions are chosen to avoid knock. Superknock is caused by developing detonation (DD) which results when the value of <i>ξ</i> decreases and the pressure wave begins to couple with the autoignition front and gets amplified. Autoignition has to be initiated at high <i>P</i> and <i>T</i> for superknock to occur. At practical operating conditions, this can only happen via another abnormal stochastic phenomenon - preignition, when a flame is established before the spark plug fires. Both preignition and superknock become more likely as <i>P</i> increases. All else being equal, the probability of superknock decreases as the fuel <i>RON</i> is increased. However, even with high <i>RON</i>, high <i>KI</i> and superknock could occur with the right combination of <i>P</i> and (∂<i>x</i>/∂<i>T</i>).</div></div>
Pharmacokinetics, tissue distribution and bioavailability of imatinib in mice after administration of a single oral and an intravenous bolus dose (2010)

Imatinib inhibits Bcr-Abl, c-KIT and PDGFR kinases involved in chronic myelogenous leukemia and gastrointestinal stromal tumors. Mice were given imatinib PO (50 mg/kg) or IV (12.5 mg/kg) and plasma, liver, brain, spleen, kidney disposition profiles analyzed. Plasma t1/2 was 4.5 h. IV plasma AUC0→∞ was 11.59 μg·h/mL, MRT was 4.87 h, Cl was 1.08 l/h/kg and VSS was 5.23 l/kg. PO AUC0→∞ was 12.82 μg·h/mL, MRT 5.1 h, CMAX was 6.99 ± 2.84 μg/mL, absorption rate constant, Ka was 4.348 h–1, bioavailability was 27.7%, VSS was 5.51 l/kg. The hepatic extraction ratio was 0.384 and the minimum dose fraction absorbed was 0.450. IV AUC0→∞ tissue-to-plasma ratios were 2.59 (spleen, kidney) and 2.91 (liver) but increased after PO administration in spleen (3.68) and kidney (3.49) and decreased in liver (2.75). Liver and kidney correlations with plasma concentrations suggests perfusion-limited uptake. Spleen counter-clockwise profile suggests non-concentration dependent uptake. Brain penetration was minimal.
Evaluation of protective effect of myricetin, a bioflavonoid in dimethyl benzanthracene-induced breast cancer in female Wistar rats (2014)

Myricetin was found to be either equieffective or more effective than vincristine in all the parameters studied. Myricetin proved the capacity of flavonols to act as antioxidant in cells represents a potential treatment in the field of oncology.
Zinc-Containing Neurons (1994)

Zinc-containing neurons are cells that sequester zinc in their presynaptic vesicles and release it in a calcium- and impulse-dependent manner. The zinc-containing neurons are a subclass of the glutaminergic neurons: all known zinc-containing pathways are also glutaminergic pathways. With a few exceptions, zinc-containing neurons are located only in the telencephalon. The major glutaminergic systems of the brain stem, thalamus, and cerebellum, for example, all lack vesicular zinc, whereas many cerebrocortical systems are zinc containing. Within the telencephalon, the zinc-containing fiber systems form a vast associational network that reciprocally interconnects isocortical, allocortical and 'limbic' structures. Because the hippocampal, amygdalar, and perirhinal regions are prominent nodes in this network, it is presumed that vesicular zinc is involved in epileptic phenomena (in pathology) and (in normal function) in the synaptic plasticity of developmental and experiential learning. Zinc ions are potent modulators of amino acid receptors [especially the N-methyl-D-aspartate (NMDA) receptor] and corelease of zinc along with glutamate would provide a mechanism for modulating postsynaptic excitability levels. One useful hypothesis is that synaptically released zinc controls a 'window' of postsynaptic excitability, having little or no effect at physiological firing rates, but selectively depressing excitability (by NMDA receptor depression) when firing rates reach dangerous, paroxysmal levels.