gebhart/patrepeval huggingface dataset:
Inhibition of calcineurin by a novel FK-506-binding protein. (1994)

FK-506, a potent immunosuppressive drug, acts during the commitment phase of T-lymphocyte activation to block a subset of calcium-associated events necessary for transcription of certain early lymphokine genes. The drug binds to an abundant, cytosolic 11.8-kDa protein termed the FK-506-binding protein (FKBP12). The FKBP12.FK-506 complex inhibits calcineurin, a calcium-dependent phosphatase that is a component of the signal transduction pathway leading to early lymphokine gene transcription. FKBP12 is one member of a growing gene family. Prior to this report, all other FKBP family members had been irrelevant to the mechanism of action of FK-506 because no other FKBP.FK-506 complexes were able to bind and inhibit calcineurin. Here, we report the purification and characterization of a novel FK-506-binding protein, FKBP12.6. Having 85% amino acid sequence identity to FKBP12, FKBP12.6 is, among the FKBPs, most closely related to FKBP12. When complexed with FK-506, FKBP12.6 binds to and inhibits calcineurin, making it only the second FKBP discovered thus far to do so. The ability to inhibit calcineurin establishes the potential relevance of FKBP12.6 to the immunosuppressive or toxic side effects of FK-506.
A scheduling framework for adaptive video delivery over cellular networks (2013)

As the growth of mobile video traffic outpaces that of cellular network speed, industry is adopting HTTP-based adaptive video streaming technology which enables dynamic adaptation of video bit-rates to match changing network conditions. However, recent measurement studies have observed problems in fairness, stability, and efficiency of resource utilization when multiple adaptive video flows compete for bandwidth on a shared wired link. Through experiments and simulations, we confirm that such undesirable behavior manifests itself in cellular networks as well. To overcome these problems, we design an in-network resource management framework, AVIS, that schedules HTTP-based adaptive video flows on cellular networks. AVIS effectively manages the resources of a cellular base station across adaptive video flows. AVIS also provides a framework for mobile operators to achieve a desired balance between optimal resource allocation and user quality of experience. AVIS has three key differentiating features: (1) It optimally computes the bit-rate allocation for each user, (2) It includes a scheduler and per-flow shapers to enforce bit-rate stability of each flow and (3) It leverages the resource virtualization technique to separate resource management of adaptive video flows from regular video flows. We implement a prototype system of AVIS and evaluate it on both a WiMAX network testbed and a LTE system simulator to show its efficacy and scalability.
Conditions for Facile, Controlled RAFT Polymerization of Acrylamide in Water (2003)

ADVERTISEMENT RETURN TO ISSUEPREVCommunication to the...Communication to the EditorNEXTConditions for Facile, Controlled RAFT Polymerization of Acrylamide in Water†David B. Thomas, Brent S. Sumerlin, Andrew B. Lowe, and Charles L. McCormickView Author Information Department of Polymer Science, University of Southern Mississippi, Hattiesburg, Mississippi 39406-0076, and Department of Chemistry and Biochemistry, University of Southern Mississippi, Hattiesburg, Mississippi 39406-5043 Cite this: Macromolecules 2003, 36, 5, 1436–1439Publication Date (Web):February 14, 2003Publication History Received12 December 2002Revised17 January 2003Published online14 February 2003Published inissue 1 March 2003https://pubs.acs.org/doi/10.1021/ma025960fhttps://doi.org/10.1021/ma025960frapid-communicationACS PublicationsCopyright © 2003 American Chemical SocietyRequest reuse permissionsArticle Views3938Altmetric-Citations106LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Amides,Monomers,Polymerization,Radical polymerization,RAFT polymerization Get e-Alerts
Methods and Applications of Deoxygenation for the Conversion of Biomass to Petrochemical Products (2013)

© 2013 Gunawardena and Fernando, licensee InTech. This is an open access chapter distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Methods and Applications of Deoxygenation for the Conversion of Biomass to Petrochemical Products
A Machine Learning Approach for Computation of Fractional Flow Reserve from Coronary Computed Tomography (2016)

Fractional Flow Reserve (FFR) is a functional index quantifying the severity of coronary artery lesions, and is clinically obtained using an invasive, catheter-based measurement. Recently, physics-...
Behavioural and physiological assessments of dimethyl trisulfide treatment for acute oral sodium cyanide poisoning (2019)

Sodium cyanide (NaCN) is a commonly and widely used industrial and laboratory chemical that is highly toxic. Its availability and rapid harmful/lethal effects combine to make cyanide a potential foodborne/waterborne intentional-poisoning hazard. Effective antidotes to cyanide poisoning are currently approved only for intravenous administration. Therefore, an effective cyanide antidote that can be administered intramuscularly in pre-hospital and/or mass-casualty settings is needed. Dimethyl trisulfide (DMTS) is a naturally occurring substance used as a flavour enhancer in foods. DMTS has shown antidotal efficacy in cyanide poisoning and is thought to act as both a sulphur donor and partial methaemoglobin inducer. In this study, an intramuscular injection of DMTS (6.25-200 mg/kg) was given to rats 1 minute after an oral dose of NaCN (98.2 mg/kg; twice the median lethal dose) to test the antidotal efficacy and safety of DMTS treatment. Toxic signs and survival were examined along with behavioural function (up to 30 hour after ingestion) using a previously established operant behavioural model. A large range of DMTS doses (6.25-100 mg/kg) increased survival after oral cyanide poisoning, and the lower DMTS doses (6.25-25 mg/kg) also proved to be behaviourally and physiologically safe. Larger DMTS doses (50-200 mg/kg) produced side effects (ie, inflammation and limping) that were more severe and protracted than those observed at lower DMTS doses. The 25 mg/kg DMTS proved to be the most efficacious (increasing survival from 20% to 75%) and also produced minimal side effects (eg, inflammation) that resolved within 24-72 hour. Thus, DMTS shows promise as an intramuscularly administered cyanide antidote useful for prompt pre-hospital or mass-casualty emergency medical treatment.
Off-topic essay detection using short prompt texts (2010)

Our work addresses the problem of predicting whether an essay is off-topic to a given prompt or question without any previouslyseen essays as training data. Prior work has used similarity between essay vocabulary and prompt words to estimate the degree of ontopic content. In our corpus of opinion essays, prompts are very short, and using similarity with such prompts to detect off-topic essays yields error rates of about 10%. We propose two methods to enable better comparison of prompt and essay text. We automatically expand short prompts before comparison, with words likely to appear in an essay to that prompt. We also apply spelling correction to the essay texts. Both methods reduce the error rates during off-topic essay detection and turn out to be complementary, leading to even better performance when used in unison. 1
Insulins with built-in glucose sensors for glucose responsive insulin release (2004)

Derivatization of insulin with phenylboronic acids is described, thereby equipping insulin with novel glucose sensing ability. It is furthermore demonstrated that such insulins are useful in glucose-responsive polymer-based release systems. The preferred phenylboronic acids are sulfonamide derivatives, which, contrary to naïve boronic acids, ensure glucose binding at physiological pH, and simultaneously operate as handles for insulin derivatization at LysB29. The glucose affinities of the novel insulins were evaluated by glucose titration in a competitive assay with alizarin. The affinities were in the range 15-31 mM (K(d)), which match physiological glucose fluctuations. The dose-responsive glucose-mediated release of the novel insulins was demonstrated using glucamine-derived polyethylene glycol polyacrylamide (PEGA) as a model, and it was shown that Zn(II) hexamer formulation of the boronated insulins resulted in steeper glucose sensitivity relative to monomeric insulin formulation. Notably, two of the boronated insulins displayed enhanced insulin receptor affinity relative to native insulin (113%-122%) which is unusual for insulin LysB29 derivatives.
Measurement of Asphaltenes Using Optical Spectroscopy on a Microfluidic Platform (2013)

We present a microfluidic apparatus and method for the measurement of asphaltene content in crude-oil samples. The measurement is based on an optical absorption technique, where it was established that asphaltene coloration correlated linearly with asphaltene weight content. The initial absorbance of the oil is measured, and asphaltenes are removed from the oil by the addition of n-alkane, leading to flocculation and subsequent filtration. The absorbance of the deasphalted oil (maltenes) is then measured, and the initial asphaltene content is revealed by the change in absorbance. The asphaltene optical densities correlated linearly with conventional weight measurement results (e.g., ASTM D6560) for 38 crude-oil samples from around the world. Sample measurement repeatability was shown to be within ±2% over several months. Other aspects influencing performance of the system were evaluated, including plug dispersion, flocculation kinetics, membrane degradation, and channel clogging. The microfluidic approach described here permits asphaltene content measurement in less than 30 min as opposed to days required with traditional gravimetric techniques. This many-fold reduction in measurement time will enable more frequent characterization of crude oil samples.
Frequency Up-Conversion of Electromagnetic Radiation with Use of an Overdense Plasma (1988)

We investigate the effects of quickly creating a plasma around a monochromatic electromagnetic source wave, on time scales on the order of a cycle of the wave. It is found that this results in an upward shifting of the wave frequency, which can be varied by changing of the plasma density. It is also found that a substantial fraction of the magnetic field associated with the initial wave can be sustained in the plasma as a time-independent magnetic field. Computer simulations have been used to study this process in detail, including the effects of finite ionization time. For long ionization times, strong plasma heating results.
Discovery of 1-[2-Fluoro-4-(1<i>H</i>-pyrazol-1-yl)phenyl]-5-methoxy-3-(1-phenyl-1<i>H</i>-pyrazol-5-yl)pyridazin-4(1<i>H</i>)-one (TAK-063), a Highly Potent, Selective, and Orally Active Phosphodiesterase 10A (PDE10A) Inhibitor (2014)

A novel series of pyridazinone-based phosphodiesterase 10A (PDE10A) inhibitors were synthesized. Our optimization efforts using structure-based drug design (SBDD) techniques on the basis of the X-ray crystal structure of PDE10A in complex with hit compound 1 (IC50 = 23 nM; 110-fold selectivity over other PDEs) led to the identification of 1-[2-fluoro-4-(1H-pyrazol-1-yl)phenyl]-5-methoxy-3-(1-phenyl-1H-pyrazol-5-yl)pyridazin-4(1H)-one (27h). Compound 27h has potent inhibitory activity (IC50 = 0.30 nM), excellent selectivity (>15000-fold selectivity over other PDEs), and favorable pharmacokinetics, including high brain penetration, in mice. Oral administration of compound 27h to mice elevated striatal 3',5'-cyclic adenosine monophosphate (cAMP) and 3',5'-cyclic guanosine monophosphate (cGMP) levels at 0.3 mg/kg and showed potent suppression of phencyclidine (PCP)-induced hyperlocomotion at a minimum effective dose (MED) of 0.3 mg/kg. Compound 27h (TAK-063) is currently being evaluated in clinical trials for the treatment of schizophrenia.
Proteinase inhibition regulates the anti-tumor activity of PAI-1 towards lung and prostate cancer cells (2011)

Plasminogen activator inhibitor type 1 (PAI-1) plays an important role in tumor growth and metastasis formation, directly via specific urokinase complexing or indirectly due to its affinity to vitronectin. The aim of this study was to analyze the impact of the mutant forms of PAI-1: very long half-life (VLHL PAI-1) or devoid of affinity towards vitronectin (Vn neg PAI-1) and wild form (wPAI -1) on proliferation of lung cancer (A549 and H1299) and prostate cancer (LNCaP and DU145) cells characterized by different proteinase (urokinase) production. The dose- and time-dependent inhibition of cell proliferation in the presence of VLHL PAI-1 was evident in A549 and LNCaP cultures. In H1299 cells inhibitory effect was only dose-depended (p<0.001), while in DU145 only 100 μg/ml of VLHL PAI-1 in 72 hrs cultures suppresed prostate cancer cells proliferative activity (p <0.001). No significant effect of Vn neg PAI-1 on the proliferation of A549 and H1299 was observed while in prostate cancer lines (DU145, LNCaP) only the inhibitory effect of the highest Vn neg PAI-1 concentration (100μg/ml) was evident (p <0.001) but not time-dependent. wPAI-1 did't affect A549 and LNCaP proliferation while in highest concentration it had the stimulating effect on H1299 and Du145 (24,48 hrs cultures). PAI-1 is a negative regulator of cancer cells proliferation due to its anti-proteinase activity. Its biological effect on lung cancer cells is time and dosage-dependent.
The Lung Image Database Consortium (LIDC): pulmonary nodule measurements, the variation, and the difference between different size metrics (2007)

Size is an important metric for pulmonary nodule characterization. Furthermore, it is an important parameter in measuring the performance of computer aided detection systems since they are always qualified with respect to a given size range of nodules. The first 120 whole-lung CT scans documented by the Lung Image Database Consortium using their protocol for nodule evaluation were used in this study. For documentation, each inspected lesion was reviewed independently by four expert radiologists and, when a lesion was considered to be a nodule larger than 3 mm, the radiologist provided boundary markings in each image in which the nodule was contained. Three size metrics were considered: a uni-dimensional and a bi-dimensional measure on a single image slice and a volumetric measurement based on all the image slices. In this study we analyzed the boundary markings of these nodules in the context of these three size metrics to characterize the inter-radiologist variation and to examine the difference between these metrics. A data set of 63 nodules each having four observations was analyzed for inter-observer variation and an extended set of 252 nodules each having at least one observation was analyzed for the difference between the metrics. A very high inter-observer variation was observed for all these metrics and also a very large difference among the metrics was observed.
Engineering cellular redox balance in <i>Saccharomyces cerevisiae</i> for improved production of L‐lactic acid (2014)

Owing to the growing market for the biodegradable and renewable polymer, polylactic acid, world demand for lactic acid is rapidly increasing. However, the very high concentrations desired for industrial production of the free lactic acid create toxicity and low pH concerns for manufacturers. Saccharomyces cerevisiae is the most well characterized eukaryote, a preferred microbial cell factory for the largest industrial biotechnology product (bioethanol), and a robust, commercially compatible workhorse to be exploited for the production of diverse chemicals. S. cerevisiae has also been explored as a host for lactic acid production because of its high acid tolerance. Here, we constructed an L-lactic acid-overproducing S. cerevisiae by redirecting cellular metabolic fluxes to the production of L-lactic acid. To this end, we deleted the S. cerevisiae genes encoding pyruvate decarboxylase 1 (PDC1), L-lactate cytochrome-c oxidoreductase (CYB2), and glycerol-3-phosphate dehydrogenase (GPD1), replacing them with a heterologous L-lactate dehydrogenase (LDH) gene. Two new target genes encoding isoenzymes of the external NADH dehydrogenase (NDE1 and NDE2), were also deleted from the genome to re-engineer the intracellular redox balance. The resulting strain was found to produce L-lactic acid more efficiently (32.6% increase in final L-lactic acid titer). When tested in a bioreactor in fed-batch mode, this engineered strain produced 117 g/L of L-lactic acid under low pH conditions. This result demonstrates that the redox balance engineering should be coupled with the metabolic engineering in the construction of L-lactic acid-overproducing S. cerevisiae.
Development and Validation of a Time-Lag Correction for Vaisala Radiosonde Humidity Measurements (2004)

This study presents a method of improving the accuracy of relative humidity (RH) measurements from Vaisala RS80 and RS90 radiosondes by applying sensor-based corrections for well-understood sources of measurement error. Laboratory measurements of the sensor time constant as a function of temperature are used to develop a correction for a time-lag error that results from slow sensor response at low temperatures. The time-lag correction is a numerical inversion algorithm that calculates the ambient (''true'') humidity profile from the measured humidity and temperature profiles, based on the sensor time constant. Existing corrections for two sources of dry bias error in RS80 humidity measurements are also included in the correction procedure: inaccuracy in the sensor calibration at low temperatures, and chemical contamination of sensors manufactured before June 2000 by nonwater molecules from the radiosonde packaging material.
Abstract 169: Erythropoietin Enhances Left Ventricular Cytochrome c Oxidase Activity During Cardiac Resuscitation (2010)

In most organisms, the whole genome is maintained throughout the life span. However, exceptions occur in some species where the genome is reduced during development through a process known as programmed DNA elimination (PDE). In the human and pig parasite Ascaris, PDE occurs during the 4 to 16 cell stages of embryogenesis, when germline chromosomes are fragmented and specific DNA sequences are reproducibly lost in all somatic cells. PDE was identified in Ascaris over 120 years ago, but little was known about its molecular details until recently. Genome sequencing revealed that approximately 1,000 germline-expressed genes are eliminated in Ascaris, suggesting PDE is a gene silencing mechanism. All germline chromosome ends are removed and remodeled during PDE. In addition, PDE increases the number of chromosomes in the somatic genome by splitting many germline chromosomes. Comparative genomics indicates that these germline chromosomes arose from fusion events. PDE separates these chromosomes at the fusion sites. These observations indicate that PDE plays a role in chromosome karyotype and evolution. Furthermore, comparative analysis of PDE in other parasitic and free-living nematodes illustrates conserved features of PDE, suggesting it has important biological significance. We summarize what is known about PDE in Ascaris and its relatives. We also discuss other potential functions, mechanisms, and the evolution of PDE in these parasites of humans and animals of veterinary importance.
A clock distribution network for microprocessors (2002)

A global clock distribution strategy implemented on several microprocessor chips is described. The clock network consists of buffered, tunable tree networks, with the final trees all driving a common grid. This topology combines advantages of both trees and grids. A new tuning method was required to efficiently tune a single interconnect network with 6 m of wire and 50,000 resistors, capacitors, and inductors. Global clock skew as low as 22 ps was measured for large microprocessor chips.
Fluorescence lifetime imaging with measurements of photon migration: theory, simulation, and experiment (2002)

Frequency-domain measurements of photon migration are coupled with a model of fluorescence generation and propagation in order to develop a method for reconstructing maps of fluorescent properties within interior tissue volumes from exterior measurements at the air-tissue interface. Simulated results confirm the feasibility of optical imaging through the use of exogenously administered contrast agents on the basis of fluorophore decay kinetics and yield. Experimental measurements using single-pixel and multi-pixel devices illustrate that the contrast from exogenous fluorescence exceeds that owing to absorption or scattering caused by endogenous chromophores or tissue structure and owing to absorption caused by exogenous contrast agents. The prognosis for fluorescence lifetime imaging as a prognostic imaging modality is discussed.
Resolution enhancement in synthetic aperture digital holographic microscopy (2014)

This study presents a resolution enhancement technique in synthetic aperture digital holographic microscopy based on nonlinear scanning mechanism. Experimental results show the frequency coverage and phase sensitivity of the synthesized reconstructed image are improved simultaneously.
Automated partitioning design in parallel database systems (2011)

In recent years, Massively Parallel Processors (MPPs) have gained ground enabling vast amounts of data processing. In such environments, data is partitioned across multiple compute nodes, which results in dramatic performance improvements during parallel query execution. To evaluate certain relational operators in a query correctly, data sometimes needs to be re-partitioned (i.e., moved) across compute nodes. Since data movement operations are much more expensive than relational operations, it is crucial to design a suitable data partitioning strategy that minimizes the cost of such expensive data transfers. A good partitioning strategy strongly depends on how the parallel system would be used. In this paper we present a partitioning advisor that recommends the best partitioning design for an expected workload. Our tool recommends which tables should be replicated (i.e., copied into every compute node) and which ones should be distributed according to specific column(s) so that the cost of evaluating similar workloads is minimized. In contrast to previous work, our techniques are deeply integrated with the underlying parallel query optimizer, which results in more accurate recommendations in a shorter amount of time. Our experimental evaluation using a real MPP system, Microsoft SQL Server 2008 Parallel Data Warehouse, with both real and synthetic workloads shows the effectiveness of the proposed techniques and the importance of deep integration of the partitioning advisor with the underlying query optimizer.