gebhart/patrepeval huggingface dataset:
Tricin inhibits proliferation of human hepatic stellate cells in vitro by blocking tyrosine phosphorylation of PDGF receptor and its signaling pathways (2012)

4',5,7-Trihydroxy-3',5'-dimethoxyflavone (Tricin), a naturally occurring flavone, has anti-inflammatory potential and exhibits diverse biological activities including antigrowth activity in several human cancer cell lines and cancer chemopreventive effects in the gastrointestinal tract of mice. The present study aimed to investigate the biological actions of tricin on hepatic stellate cells (HSCs) in vitro, exploring its potential as a treatment of liver fibrosis, since HSC proliferation is closely related to the progression of hepatic fibrogenesis in chronic liver diseases leading to irreversible liver cirrhosis and hepatocellular carcinoma. Tricin inhibited platelet-derived growth factor (PDGF)-BB-induced cell proliferation by blocking cell cycle progression and cell migration in the human HSC line LI90 and culture-activated HSCs. It also reduced the phosphorylation of PDGF receptor β and the downstream signaling molecules ERK1/2 and Akt, which might be due to its tyrosine kinase inhibitor properties rather than inhibition of the direct binding between PDGF-BB and its receptor. Our findings suggest that tricin might be beneficial in HSC-targeting therapeutic or chemopreventive applications for hepatic fibrosis.
On using eye tracking in empirical assessment of software visualizations (2007)

The paper advocates the use of eye movement measurements in conducting empirical studies of software engineering tools, especially visualization techniques. Traditionally, measures such as accuracy and performance time have been used to assess and compare different tools for a given set of tasks. These measures are typically collected after the conclusion of an assigned task. Eye tracking adds a new additional dimension to the assessment arsenal by allowing access to the gaze activity of human subjects. The gaze activities can be captured quite precisely while a task is being performed. Thus, providing a unique opportunity to include measures of how exactly humans use a tool and ratiocinate their conclusions. A brief discussion on using the eye movements for assessing UML class diagram layouts is also presented.
Architecture for a Secure Distributed Repository (2006)

This paper presents and discusses the design and implementation of authorization mechanisms for a data repository service for grid environments that supports secure sharing of possibly confidential data by members of ad-hoc created groups. Such a system requires the separation of the repository into independent components thus adding to the complexity of the authorization mechanisms that protect both the storage service against unauthorized and possible malicious use, and intellectual property and confidentiality of the user's data. The solution proposed here extends the VOMS architecture, in favor of the other architectures for efficiency. The authorization is group-based with group membership authorization service responsible for maintaining the user roles in a virtual organization (i.e., the membership in a group). The user can now securely access data in a distributed repository by collecting SAML assertions from the component services and creating a complete assertion document that allows it to retrieve data from a data service
Fault diagnosis in vehicle engines using sound recognition techniques (2010)

Vehicle engine faults are serious faults that occur inside the engine, the ability to successfully perform fault diagnosis is highly dependent on technician skills. Some experienced technicians have some failure rate, which can lead to serious waste in time and money. Accordingly, an improved diagnosing methods is highly needed. In this paper, we develop an algorithm for fault diagnosis in vehicle engines using sounds techniques, since each engine fault has a specific sound that is distinguished. We collect and analyze sound samples from different types of cars, which represent different types of fault, to create a database of sound prints that will make the whole process of diagnosing engine faults based on sound easier and less time consuming. Different features from the sound samples are extracted and used for diagnosis. The fault under test is compared with the faults in the database according to their correlation, normalized mean square error, and formant frequencies values. The best match is considered the detected fault. The developed system can be useful for the inexperienced technicians and engineers and can be used as a training module for them. The simulation results show the high fault detection rates of the proposed algorithm.
Iopamidol: Exploring the potential use of a well‐established x‐ray contrast agent for MRI (2005)

Iopamidol is one of the most common contrast media used for diagnostic CT-based clinical protocols. Chemically, this molecule contains two pools of mobile protons (amide and alcoholic) that are in exchange with water. At 7.05 T, pH 7.4, and 312 K, the exchange rate of the alcoholic protons is too fast to affect the NMR properties of water protons, whereas the slowly exchanging amide protons induce a T(2)-shortening effect on the "bulk" water signal that is detectable when the concentration is about 12 mM. Moreover, a more pronounced contrast is observed when the amide resonances are saturated by the application of an appropriate RF irradiation field, making iopamidol a potential chemical exchange saturation transfer (CEST) agent whose effect can be detected at a concentration as low as 7 mM (at 7.05 T). The exploitation of the MRI properties of iopamidol could facilitate novel and interesting diagnostic applications for combined MRI and CT studies.
Selectivity and selectivity tuning in capillary gas chromatography (1985)

Abstract The selection of stationary phases in capillary gas chromatography is discussed. Methyl silicone, phenyl methyl silicone, trifluoropropylmethyl silicone, biscyanopropyl silicone, and high molecular weight (HMW) polyethylene glycol are considered to be the basic phases. Selectivities and polarities between these phases are obtained by selectivity tuning. Selectivity tuning can be performed in three different ways, namely by synthesizing a tuned stationary phase, by mixing the basic phases, or by coupling capillary columns of different selectivities. In coupling capillary columns the variables are column length, β‐value, temperature, and/or pressure.
Enzyme activities in experimental gingivitis in man (1971)

abstract – The purpose of the present investigation was to study hyaluronidase, protease, and lysozyme in dental plaque material and gingival fluid during the initial stages of gingivitis. Ten persons with healthy gingiva were subjected to a three‐week period without oral hygiene. During this period they developed abundance of plaque and generalized gingivitis. Hyaluronidase activity in dental plaque was highest on day 3 and then decreased during the whole experimental period. Protease and lysozyme activities varied during the experiment. An apparent trend towards higher lysozyme activity of gingival fluid with increased severity of gingival inflammation was noticed. No hyaluronidase and protease activities were detected in the gingival fluid. The hyaluronidases from plaque material of different days were separated by isoelectric focusing into at least two different fractions (pI 5.0 and pI 8.0). Proteolytic fractions were found over a wide pi interval (4.2–6.8) during all days. In all separations one lysozyme peak between pH 9.5–10.0 was found.
Structural basis for TNA synthesis by an engineered TNA polymerase (2017)

Darwinian evolution experiments carried out on xeno-nucleic acid (XNA) polymers require engineered polymerases that can faithfully and efficiently copy genetic information back and forth between DNA and XNA. However, current XNA polymerases function with inferior activity relative to their natural counterparts. Here, we report five X-ray crystal structures that illustrate the pathway by which α-(L)-threofuranosyl nucleic acid (TNA) triphosphates are selected and extended in a template-dependent manner using a laboratory-evolved polymerase known as Kod-RI. Structural comparison of the apo, binary, open and closed ternary, and translocated product detail an ensemble of interactions and conformational changes required to promote TNA synthesis. Close inspection of the active site in the closed ternary structure reveals a sub-optimal binding geometry that explains the slow rate of catalysis. This key piece of information, which is missing for all naturally occurring archaeal DNA polymerases, provides a framework for engineering new TNA polymerase variants.
Manufacturing modeling methods: USE of GI/G/1 queuing approximations to set tactical parameters for the simulation of MRP systems (2002)

There is a lack of prescriptive methods for setting lot sizes and planned lead times effectively in MRP systems. Recent research has suggested the application of queuing relationships. This study experimentally investigates the use of GI/G/1 relationships for lot size selection along with the use of exponentially smoothed feedback for dynamic planned lead time setting. Results show that assumptions regarding lot interarrival time variability have a large effect on lot sizes and performance.
Cortical network functional connectivity in the descent to sleep (2009)

Descent into sleep is accompanied by disengagement of the conscious brain from the external world. It follows that this process should be associated with reduced neural activity in regions of the brain known to mediate interaction with the environment. We examined blood oxygen dependent (BOLD) signal functional connectivity using conventional seed-based analyses in 3 primary sensory and 3 association networks as normal young adults transitioned from wakefulness to light sleep while lying immobile in the bore of a magnetic resonance imaging scanner. Functional connectivity was maintained in each network throughout all examined states of arousal. Indeed, correlations within the dorsal attention network modestly but significantly increased during light sleep compared to wakefulness. Moreover, our data suggest that neuronally mediated BOLD signal variance generally increases in light sleep. These results do not support the view that ongoing BOLD fluctuations primarily reflect unconstrained cognition. Rather, accumulating evidence supports the hypothesis that spontaneous BOLD fluctuations reflect processes that maintain the integrity of functional systems in the brain.
A Catalytic Microwave Process for Superfast Preparation of High‐Quality Reduced Graphene Oxide (2017)

Herein we report that a small amount of graphite can unexpectedly act as the catalyst to greatly promote the microwave exfoliation and reduction of graphite oxide in ambient air. The reaction can be finished in a few seconds in contrast to more than ten minutes without catalyst. The catalytic microwave exfoliated graphite oxide (CMEGO) is of higher quality than the traditional microwave exfoliated graphite oxide, including a much higher exfoliation degree with thinner graphene sheets and higher specific surface area (886 m<sup>2</sup> g<sup>-1</sup> vs. 466 m<sup>2</sup> g<sup>-1</sup> ), a much larger C/O ratio (19.4 vs. 6.3) and a higher lattice crystallinity, as well as significantly improved electrical conductivity (53180 S m<sup>-1</sup> vs. 5140 S m<sup>-1</sup> ). The CMEGO is used as anode for lithium-ion battery (LIB) and sodium-ion battery (SIB), and delivers ultrahigh reversible capacities, remarkable rate capabilities, and superior cycling stabilities in both LIB and SIB.
The ubiquitin‐specific protease UBP14 is essential for early embryo development in <i>Arabidopsis thaliana</i> (2001)

The ubiquitin/26S proteasome pathway is a major route for selectively degrading cytoplasmic and nuclear proteins in eukaryotes. In this pathway, chains of ubiquitins become attached to short-lived proteins, signalling recognition and breakdown of the modified protein by the 26S proteasome. During or following target degradation, the attached multi-ubiquitin chains are released and subsequently disassembled by ubiquitin-specific proteases (UBPs) to regenerate free ubiquitin monomers for re-use. Here, we describe Arabidopsis thaliana UBP14 that may participate in this recycling process. Its amino acid sequence is most similar to yeast UBP14 and its orthologues, human IsoT1-3 and Dictyostelium UbpA, and it can functionally replace yeast UBP14 in a ubp14Delta mutant. Like its orthologues, AtUBP14 can disassemble multi-ubiquitin chains linked internally via epsilon-amino isopeptide bonds using Lys48 and can process some, but not all, translational fusions of ubiquitin linked via alpha-amino peptide bonds. However, unlike its yeast and Dictyostelium orthologues, AtUBP14 is essential in Arabidopsis. T-DNA insertion mutations in the single gene that encodes AtUBP14 cause an embryonic lethal phenotype, with the homozygous embryos arresting at the globular stage. The arrested seeds have substantially increased levels of multi-ubiquitin chains, indicative of a defect in ubiquitin recycling. Taken together, the data demonstrate an essential role for the ubiquitin/26S proteasome pathway in general and for AtUBP14 in particular during early plant development.
Opportunities and challenges with net zero energy buildings (2011)

Buildings represent around 41% of the total energy consumption in the US followed closely by industry (31%) and transportation (28%). One of the milestones set by the US Department of Energy is the development and deployment of net zero energy buildings defined as buildings that on a yearly average spend as much energy as they generate using renewable energy sources. Realization of net zero energy buildings require a wide ranges of technologies, systems and solutions with varying degrees of complexity and sophistication depending upon the location and surrounding environmental conditions. Lighting is a dominant load in buildings followed by heating, cooling, ventilation and various plug loads. This paper will address the roles of different technologies, devices and control strategies being developed for low energy buildings leading to net zero energy buildings. These include high efficiency lighting, daylight integration, DC power bus, solar power integration; closed loop integrated control, smart grid interface as well as emerging approaches such as chilled beams and active facades. All of these involve power conversion and controls in one form or the other where high voltage or high power integrated solutions are key to commercial viability. In addition to this, the role of whole building modeling and simulation in the development and deployment of the solutions will be addressed.
Reconstruction of Microtia (2009)

The reconstruction of microtia continues to represent one of the more challenging plastic surgery procedures. The limitations of the reconstruction are partly inherent in the soft-tissue deficiencies present in increasing degrees from large conchal remnant microtia, to lobular microtia, to the displaced remnant in auricular dystopia, and partly because of the high level of technical expertise required. After a brief review of the history of ear reconstruction in general and microtia specifically, issues related to the transition in the popularity from techniques involving three or more stages (Tanzer and Brent) to the current popularity of two-stage procedures (Nagata, Firmin, and Park) are discussed in detail. Each of the popular procedures is viewed in relation to timing of the reconstruction, procedure planning, and how both the soft tissues and framework construction are handled, in each of the stages. The most significant differences include whether the autogenous cartilage framework is constructed with or without the tragal construct (for the lobular-type microtia), whether or not the lobule is rotated in the first-stage reconstruction, whether an additional cartilage block is placed behind the framework for added ear projection, and how that added block is covered (choice of fascia flap and skin graft). Each of the techniques has to be varied in reconstruction of auricular dystopia in light of the associated skeletal and soft-tissue hypoplasia. In this article, the author demonstrates that although there may be significant advantages to the two-stage reconstructions of Nagata and Firmin, some may feel that the larger amount of cartilage harvested, the later optimal age for beginning the reconstruction, the additional scalp scars engendered by using the temporoparietal fascia flap in the second-stage elevation of the framework, and even the exchange of lobule tissue (and ability to later pierce ears) to obtain better coverage of the concha and tragus are unacceptable. Having gained experience with each of the varied approaches and having modified them when unusual variations in deformities have required it, the author discusses his current preferences. Clearly, this author feels that there may be significant advantages to delaying the reconstruction to age 10 years or older, yet experience gained over the past 25 years would seem to indicate that as in all other aspects of plastic and reconstructive surgery one must never be wed to a single approach, and experience and flexibility are essential in obtaining the optimal outcome in all variations of the deformity.
Roles of nuclear cardiology, cardiac computed tomography, and cardiac magnetic resonance: assessment of patients with suspected coronary artery disease. (2006)

Noninvasive cardiac imaging is now central to the diagnosis and management of patients with known or suspected chronic coronary artery disease (CAD). Although rest echocardiography has become the most common of the techniques, nuclear cardiology and more recently cardiac computed tomography (CCT) and cardiac magnetic resonance (CMR) play important roles in this regard. This review examines the current applications and interactions of noninvasive cardiac imaging approaches for the assessment of patients with suspected CAD. In addition to considering the strengths and weaknesses of each technique, this review attempts to provide a guide to the selection of a test (or tests) that is based on the question being asked and the ability of each test to answer this question. In patients with suspected CAD, the pretest likelihood of disease, a clinical assessment, becomes the most important determinant of the initial test. If the likelihood is very low, no testing is needed. However, if the likelihood is low, recent data suggest that assessment of early atherosclerosis is likely to be the most useful and cost-effective test. In patients who have an intermediate likelihood of CAD, nuclear cardiology with myocardial perfusion SPECT (MPS) becomes highly valuable; however, coronary CT angiography (CTA), with fast 16-slice or greater scanners, may emerge as the initial test of choice. MPS would then be used if the CTA is inconclusive or if there is a need to assess the functional significance of a stenosis defined by CTA. Coronary CTA, however, is not yet widely available and is limited in patients with dense coronary calcification. In older patients with a high likelihood of CAD, MPS may be the initial test of choice, since a high proportion of these patients have too much coronary calcium to allow accurate assessment of the presence of coronary stenoses. PET/CT or SPECT/CT could emerge as important modalities combining the advantages of each modality. While CMR has great promise as a radiation-free and contrast-free "one-stop" shop, it currently lags behind CTA for noninvasive coronary angiography. Nonetheless, CMR clearly has the potential for this application and has already emerged as a highly effective method for assessing ventricular function, myocardial mass, and myocardial viability, and there is increasing use of this approach for clinical rest and stress perfusion measurements. CMR is particularly valuable in distinguishing ischemic from nonischemic cardiomyopathy. While CT and CMR are likely to grow considerably in diagnostic evaluation over the next several years, MPS and PET will continue to be very valuable techniques for this purpose.
Large piezoelectric response of quarternary wurtzite nitride alloys and its physical origin from first principles (2015)

The potential of quarternary wurtzite ${\mathrm{TM}}_{x/2}{\mathrm{M}}_{x/2}{\mathrm{Al}}_{1\ensuremath{-}x}\mathrm{N}$ ($\mathrm{TM}=\text{Ti}$, Zr, Hf; $\mathrm{M}=\text{Mg}$, Ca, Zn) alloys for piezoelectric applications is investigated using first-principles calculations. All considered alloys show increased piezoelectric response compared to pure AlN, and competing with the best ternary system proven to date: ScAlN. ${(\text{Zr},\text{Hf})}_{x/2}{(\text{Mg},\text{Ca})}_{x/2}{\mathrm{Al}}_{1\ensuremath{-}x}\mathrm{N}$ alloys are particularly promising. Calculations reveal positive mixing enthalpies indicative for phase separating systems; their values are smaller compared to related nitride alloys, which still can be grown as metastable thin films. The wurtzite phase of the alloys is lowest in energy at least up to $x=0.5$ and for ${\mathrm{Ti}}_{x/2}{\mathrm{Zn}}_{x/2}{\mathrm{Al}}_{1\ensuremath{-}x}\mathrm{N}$ in the full composition range. Moreover, calculations reveal that wurtzite ${\mathrm{TM}}_{0.5}{\mathrm{Zn}}_{0.5}\mathrm{N}$ ($\mathrm{TM}=\text{Ti}$, Zr, Hf) are piezoelectric alloys with ${d}_{33,f}=19.95$, 29.89, and 24.65 pC/N respectively, up to six times that of AlN. Finally, we discuss the physical origin behind the increased piezoelectric response and show that the energy difference between tetrahedrally coordinated zinc-blende (B3) and the layered hexagonal $({B}_{k})$ phases of the ${\mathrm{TM}}_{0.5}{\mathrm{M}}_{0.5}\mathrm{N}$ alloy can be used as a descriptor in a high-throughput search for complex wurtzite alloys with high piezoelectric response.
Transcriptional regulation of proline biosynthesis in <i>Medicago truncatula</i> reveals developmental and environmental specific features (2004)

The model legume plant Medicago truncatula accumulates free proline in response to hyperosmotic stress as do many other organisms. In order to analyse the transcriptional regulation of proline biosynthesis in M. truncatula, three cDNAs encoding Delta(1)-pyrroline-5-carboxylate synthetase (P5CS1, P5CS2; EC not assigned) and ornithine delta-aminotransferase (OAT; EC 2.6.1.13) were isolated. The cDNAs shared high homologies with the other plant sequences and genomic organization analysis indicated the presence of two P5CS and two putative OAT genes. The two P5CS genes showed differing transcript level regulation according to organs and in response to osmotic stress. MtP5CS1 steady-state transcript levels in the different plant organs were correlated with proline levels but transcript abundance was unaffected by osmotic stresses. MtP5CS2 transcripts were poorly detected in all organs but were strongly accumulated in shoots of salt-stressed plants. We suggest a specific of MtP5CS1 and MtP5CS2 as a housekeeping product and as a stress specific isoform, respectively. MtOAT transcripts were predominantly detected in roots and shoots of unstressed plants. Salt-stress treatment induced the accumulation of MtOAT transcripts in the whole plant whatever the developmental stage. In salt-stressed roots, a positive correlation was found between proline and MtOAT transcript accumulation. These results suggest that both ornithine and glutamate biosynthesis pathways contribute to the osmotic stress-induced proline accumulation in M. truncatula.