gebhart/patrepeval huggingface dataset:
Characterization of Type II Phosphatidylinositol 4-Kinase Isoforms Reveals Association of the Enzymes with Endosomal Vesicular Compartments (2002)

Phosphorylation of phosphatidylinositol (PI) to PI 4-phosphate is one of the key reactions in the production of phosphoinositides, lipid regulators of several cellular functions. This reaction is catalyzed by multiple enzymes that belong either to the type II or the type III family of PI 4-kinases. Type III enzymes are structurally similar to PI 3-kinases and are sensitive to PI 3-kinase inhibitors. In contrast, the recent cloning of the first type II PI 4-kinase enzyme defined a novel enzyme family. Here we characterize a new member of this family, the type IIbeta enzyme that has been identified in the NCBI data base based on its homology to the first-cloned type IIalpha enzyme. The type IIbeta enzyme has a primary transcript size of approximately 3.8 kb and shows wide tissue distribution. It contains an open reading frame of 1.4 kb, encoding a protein of approximately 54 kDa. Sequence comparison reveals a high degree of similarity to the type IIalpha enzyme within the C-terminal catalytic domain but significantly lower homology within the N-terminal region. Expression of both enzyme yields increased PI 4-kinase activity that is associated with the microsomal membrane fractions and is significantly lower for the type IIbeta than the type IIalpha form. Both enzymes use PI as their primary substrate and have no detectable activity on PI monophosphates. Epitope-tagged as well as green fluorescent protein-tagged forms of both enzymes localize primarily to intracellular membranes and show prominent co-localization with early endosomes and recycling endosomes but not with the Golgi. These compartments participate in the processing of both the transferrin receptor and the G protein-coupled AT(1A) angiotensin receptor. Our data indicate the existence of multiple forms of type II PI 4-kinase in mammalian cells and suggest that their functions are related to the endocytic pathway.
Design and implementation of a smartphone-based portable ultrasound pulsed-wave doppler device for blood flow measurement (2012)

Blood flow measurement using Doppler ultrasound has become a useful tool for diagnosing cardiovascular diseases and as a physiological monitor. Recently, pocket-sized ultrasound scanners have been introduced for portable diagnosis. The present paper reports the implementation of a portable ultrasound pulsed-wave (PW) Doppler flowmeter using a smartphone. A 10-MHz ultrasonic surface transducer was designed for the dynamic monitoring of blood flow velocity. The directional baseband Doppler shift signals were obtained using a portable analog circuit system. After hardware processing, the Doppler signals were fed directly to a smartphone for Doppler spectrogram analysis and display in real time. To the best of our knowledge, this is the first report of the use of this system for medical ultrasound Doppler signal processing. A Couette flow phantom, consisting of two parallel disks with a 2-mm gap, was used to evaluate and calibrate the device. Doppler spectrograms of porcine blood flow were measured using this stand-alone portable device under the pulsatile condition. Subsequently, in vivo portable system verification was performed by measuring the arterial blood flow of a rat and comparing the results with the measurement from a commercial ultrasound duplex scanner. All of the results demonstrated the potential for using a smartphone as a novel embedded system for portable medical ultrasound applications.
A methodology for workload characterization of E-commerce sites (1999)

Article Free Access Share on A methodology for workload characterization of E-commerce sites Authors: Daniel A. Menascé Dept. of Computer Science, George Mason University, Fairfax, VA Dept. of Computer Science, George Mason University, Fairfax, VAView Profile , Virgilio A. F. Almeida Dept. of Computer Science, Univ. Federal de Minas Gerais, Belo Horizonte, MG 30161, Brazil Dept. of Computer Science, Univ. Federal de Minas Gerais, Belo Horizonte, MG 30161, BrazilView Profile , Rodrigo Fonseca Dept. of Computer Science, Univ. Federal de Minas Gerais, Belo Horizonte, MG 30161, Brazil Dept. of Computer Science, Univ. Federal de Minas Gerais, Belo Horizonte, MG 30161, BrazilView Profile , Marco A. Mendes Dept. of Computer Science, Univ. Federal de Minas Gerais, Belo Horizonte, MG 30161, Brazil Dept. of Computer Science, Univ. Federal de Minas Gerais, Belo Horizonte, MG 30161, BrazilView Profile Authors Info & Claims EC '99: Proceedings of the 1st ACM conference on Electronic commerceNovember 1999 Pages 119–128https://doi.org/10.1145/336992.337024Published:01 November 1999Publication History 176citation2,293DownloadsMetricsTotal Citations176Total Downloads2,293Last 12 Months162Last 6 weeks14 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
1,4‐Thienodiazepine‐2,5‐diones via MCR (I): Synthesis, Virtual Space and p53‐Mdm2 Activity (2010)

1,4-Thienodiazepine-2,5-diones have been synthesized via the Ugi-Deprotection-Cyclization (UDC) approach starting from Gewald 2-aminothiophenes in a convergent and versatile manner. The resulting scaffold is unprecedented, cyclic, and peptidomimetic with four points of diversity introduced from readily available starting materials. In addition to eighteen synthesized and characterized compounds, a virtual compound library was generated and evaluated for chemical space distribution and drug-like properties. A small focused compound library of 1,4-thienodiazepine-2,5-diones has been screened for the activity against p53-Mdm2 interaction. Biological evaluations demonstrated that some compounds exhibited promising antagonistic activity.
Cache performance of chronological garbage collection (2002)

The paper presents the cache performance analysis of the Chronological Garbage Collection algorithm used in the LVM system. The LVM is a new Logic Virtual Machine for Prolog. It adopts one stack policy for all dynamic memory requirements and cooperates with an efficient garbage collection algorithm, Chronological Garbage Collection to recuperate space, not as deliberate garbage collection operation but as a natural activity of the LVM engine to gather useful objects. This algorithm takes advantages of the traditional copying, mark-compact, generational, and incremental garbage collection schemes. In order to determine the improvement of cache performance under our garbage collection algorithm, we developed an emulator to do the trace driven cache simulation. Direct mapped cache and set-associative cache with different cache sizes, block sizes and set associativities are simulated and measured. The objectives of this simulation are to verify and validate our experimental results, and to find important factors which influence the performance of the CGC algorithm.
SNA – a toolbox for the stoichiometric analysis of metabolic networks (2006)

Thanks to its performance and modular design, SNA is demonstrably useful in analysing genome scale metabolic networks. Further, the integration into Mathematica provides a very flexible environment for the subsequent analysis and interpretation of the results.
Molecular Adsorbent Recirculating System: clinical experience in patients with liver failure based on hepatitis B in China (2002)

The aim of this study is to evaluate the effect of treatment with the Molecular Adsorbent Recirculating System (MARS) on liver failure based on HBV. In 25 patients (median age, 36.3 years, range, 22-67 years, bilirubin level > 255 micro mol/l) admitted with liver failure based on HBV, the 6-8h MARS intermittent treatments were performed without any adverse events, A significant decrease in bilirubin, ammonia and urea levels were observed (P < 0.05). All patients achieved a remarkable neurologic recovery, particularly 2 HE-III and 3 HE-IV patients regained normal consciousness, respectively. The survival rate for the patients whose treatments kept to the MARS art strategy was 76.9% (10/13), while the others only had the survival rate of 16.7% (2/12) due to their giving up sequential MARS treatments after the first time. The rebounding rate of the bilirubin level in the patients after a single MARS treatment was significantly lower than that of patients, who underwent a single plasma-exchange treatment (P < 0.01). It is concluded that MARS method can contribute to the optimistic treatment of liver failure patients based on HBV which being the major epidemic liver disease in China.
Multivariate techniques and their application in nutrition: a metabolomics case study (2007)

The post-genomic technologies are generating vast quantities of data but many nutritional scientists are not trained or equipped to analyse it. In high-resolution NMR spectra of urine, for example, the number and complexity of spectral features mean that computational techniques are required to interrogate and display the data in a manner intelligible to the researcher. In addition, there are often multiple underlying biological factors influencing the data and it is difficult to pinpoint which are having the most significant effect. This is especially true in nutritional studies, where small variations in diet can trigger multiple changes in gene expression and metabolite concentration. One class of computational tools that are useful for analysing this highly multivariate data include the well-known 'whole spectrum' methods of principal component analysis and partial least squares. In this work, we present a nutritional case study in which NMR data generated from a human dietary Cu intervention study is analysed using multivariate methods and the advantages and disadvantages of each technique are discussed. It is concluded that an alternative approach, called feature subset selection, will be important in this type of work; here we have used a genetic algorithm to identify the small peaks (arising from metabolites of low concentration) that have been altered significantly following a dietary intervention.
Epidemiology of Spinal Osteoporosis (1997)

Approximately 30% of postmenopausal white women in the United States have osteoporosis, and 16% have osteoporosis of the lumbar spine in particular. Bone density of the spine is positively associated with greater height and weight, older age at menopause, a history of arthritis, more physical activity, moderate use of alcoholic beverages, diuretic treatment, and current estrogen replacement therapy, whereas later age at menarche and a maternal history of fracture are associated with lower levels of density. Low bone density leads to an increased risk of osteoporotic fractures. Fracture risk also increase with age. Vertebral fractures affect approximately 25% of postmenopausal women, although the exact figure depends on the definition used. Recent data show that vertebral fracture rates are as great in men as in women but, because women live longer, the lifetime risk of a vertebral fracture from age 50 onward is 16% in white women and only 5% in white men. Fracture rates are less in most nonwhite populations, but vertebral fractures are as common in Asian women as in those of European heritage. Other risk factors for vertebral fractures are less clear but include hypogonadism and secondary osteoporosis; obesity is protective of fractures as it is of bone loss. Compared with hip fractures, vertebral fractures are less disabling and less expensive, costing approximately $746 million in the United States in 1995. However, they have a substantial negative impact on the patient's function and quality of life. The adverse effects of osteoporotic fractures are likely to increase in the future with the growing number of elderly people.
Well-conditioned multiproduct Hamiltonian simulation (2019)

Product formula approximations of the time-evolution operator on quantum computers are of great interest due to their simplicity, and good scaling with system size by exploiting commutativity between Hamiltonian terms. However, product formulas exhibit poor scaling with the time $t$ and error $ε$ of simulation as the gate cost of a single step scales exponentially with the order $m$ of accuracy. We introduce well-conditioned multiproduct formulas, which are a linear combination of product formulas, where a single step has polynomial cost $\mathcal{O}(m^2\log{(m)})$ and succeeds with probability $Ω(1/\operatorname{log}^2{(m)})$. Our multiproduct formulas imply a simple and generic simulation algorithm that simultaneously exploits commutativity in arbitrary systems and has a worst-case cost $\mathcal{O}(t\log^{2}{(t/ε)})$ which is optimal up to poly-logarithmic factors. In contrast, prior Trotter and post-Trotter Hamiltonian simulation algorithms realize only one of these two desirable features. A key technical result of independent interest is our solution to a conditioning problem in previous multiproduct formulas that amplified numerical errors by $e^{Ω(m)}$ in the classical setting, and led to a vanishing success probability $e^{-Ω(m)}$ in the quantum setting.
The effect of N‐terminal acetylation on the structure of an N‐terminal tropomyosin peptide and αα‐tropomyosin (1994)

We have used a synthetic peptide consisting of the first 30 residues of striated muscle alpha-tropomyosin, with GlyCys added to the C-terminus, to investigate the effect of N-terminal acetylation on the conformation and stability of the N-terminal domain of the coiled-coil protein. In aqueous buffers at low ionic strength, the reduced, unacetylated 32mer had a very low alpha-helical content (approximately 20%) that was only slightly increased by disulfide crosslinking or N-terminal acetylation. Addition of salt (> 1 M) greatly increased the helical content of the peptide. The CD spectrum, the cooperativity of folding of the peptide, and sedimentation equilibrium ultracentrifugation studies showed that it formed a 2-chained coiled coil at high ionic strength. Disulfide crosslinking and N-terminal acetylation both greatly stabilized the coiled-coil alpha-helical conformation in high salt. Addition of ethanol or trifluoroethanol to solutions of the peptide also increased its alpha-helical content. However, the CD spectra and unfolding behavior of the peptide showed no evidence of coiled-coil formation. In the presence of the organic solvents, N-terminal acetylation had very little effect on the conformation or stability of the peptide. Our results indicate that N-terminal acetylation stabilizes coiled-coil formation in the peptide. The effect cannot be explained by interactions with the "helix-dipole" because the stabilization is observed at very high salt concentrations and is independent of pH. In contrast to the results with the peptide, N-terminal acetylation has only small effects on the overall stability of tropomyosin.
Reaction of Chlorosulfonyl Isocyanate with Fluorosubstituted Alkenes: Evidence of a Concerted Pathway (2010)

Concerted reactions are indicated for the electrophilic addition of chlorosulfonyl isocyanate with monofluoroalkenes. A vinyl fluorine atom on an alkene raises the energy of a stepwise transition state more than the energy of the competing concerted pathway. This energy shift induces CSI to react with monofluoroalkenes by a one-step process. The low reactivity of CSI with monofluoroalkenes, stereospecific reactions, the absence of 2:1 uracil products with neat fluoroalkenes, and quantum chemical calculations support a concerted pathway.
Sedna: A Memory Based Key-Value Storage System for Realtime Processing in Cloud (2012)

Comparing with the traditional disk based distributed storage system, RAM based storage has been proven to be an effective way to accelerate real time applications processing speed. In this paper, we propose a memory based distributed Cloud storage system called Sedna. Managing 'big data' across lots of commodity servers, Sedna provides high scalability, simple effective data access APIs with data consistency and persistency, and a new trigger based APIs for real time applications. To guarantee the scalability with low latency, we design and implement a hierarchical structure to manage huge size data center which is simple and effective. Except the high speed provided by memory based storage, Sedna absorbs advantages from state-of-art cloud programming frameworks, and gives programmers a new way to write massive data real time applications. These data read/write triggers APIs are necessary but are missing parts of modern distributed storage system. Experiments and examples show Sedna achieve comparable speed to widely-used distributed cache system, and provide a more efficient way to use distributed storage.
Coverage issue in sensor networks with adjustable ranges (2004)

In this paper, we study the problem of maintaining sensing coverage by keeping a small number of active sensor nodes and a small amount of energy consumption in wireless sensor networks. This paper extends a result from [21] where only uniform sensing range among all sensors is used. We adopt an approach that allows non-uniform sensing ranges for different sensors. As opposed to the uniform sensing range node scheduling model in [21], two new energy-efficient models of different sensing ranges are proposed. Our objective is to minimize the overlapped sensing area of sensor nodes, thus to reduce the overall energy consumption by sensing to prolong the whole network?s life time, and at the same time to achieve the high ratio of coverage. Extensive simulation is conducted to verify the effectiveness of our node scheduling models.
Spectroscopic measurements of temperature and plasma impurity concentration during magnetic reconnection at the Swarthmore Spheromak Experiment (2009)

Electron temperature measurements during counterhelicity spheromak merging studies at the Swarthmore Spheromak Experiment (SSX) [M. R. Brown, Phys. Plasmas 6, 1717 (1999)] are presented. VUV monochromator measurements of impurity emission lines are compared with model spectra produced by the non-LTE excitation kinematics code PRISMSPECT [J. J. MacFarlane et al., in Proceedings of the Third Conference on Inertial Fusion Science and Applications (2004)] to yield the electron temperature in the plasma with 1 μs time resolution. Average Te is seen to increase from 12 to 19 eV during spheromak merging. Average C III ion temperature, measured with a new ion Doppler spectrometer (IDS) [C. D. Cothran et al., Rev. Sci. Instrum. 77, 063504 (2006)], likewise rises during spheromak merging, peaking at ∼22 eV, but a similar increase in Ti is seen during single spheromak discharges with no merging. The VUV emission line measurements are also used to constrain the concentrations of various impurities in the SSX plasma, which are dominated by carbon, but include some oxygen and nitrogen. A burst of soft x-ray emission is seen during reconnection with a new four-channel detector (SXR). There is evidence for spectral changes in the soft x-ray emission as reconnection progresses, although our single-temperature equilibrium spectral models are not able to provide adequate fits to all the SXR data.
An efficient recycling process of glycolysis of PET in the presence of a sustainable nanocatalyst (2018)

ABSTRACT We demonstrate that the catalyst Perkalite F100 efficiently works as a nanocatalyst in the depolymerization of poly(ethylene terephthalate) (PET). After depolymerization of PET in the presence of ethylene glycol and the Perkalite nanocatalyst, the main product obtained was bis(2‐hydroxylethyl) terephthalate (BHET) with high purity, as confirmed by Fourier transform infrared spectroscopy and NMR. The BHET monomers could serve directly as starting materials in a further polymerization into PET with a virgin quality and contribute to a solution for the disposal of PET polymers. Compared with the direct glycolysis of PET, the addition of a predegradation step was shown to reduce the reaction time needed to reach the depolymerization equilibrium. The addition of the predegradation step also allowed lower reaction temperatures. Therefore, the strategy to include a predegradation step before depolymerization is suitable for increasing the efficiency of the glycolysis reaction of PET into BHET monomers. © 2018 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2018 , 135 , 46285.
Continuous axial rotation and pulmonary fluid balance in acute lung injury (2000)

Objective: To investigate the effect of continuous axial rotation (CAR) treatment on the degree of pulmonary oedema (extravascular lung water [EVLW]) and arterial oxygenation in mechanically ventilated patients with acute lung injury (ALI). Design: Prospective investigation in a 12-bed intensive care unit (ICU) of a university hospital. Patients: Sixteen patients with ALI requiring mechanical ventilation. Methods: Random allocation into two groups. In the CAR group (n =8), patients were treated in a kinetic bed for a period of 72 h. In the control group (n =8), patients were treated in a 'conventional' bed. Intrathoracic blood volume (ITBV) and EVLW were assessed by the thermal dye dilution method at baseline (T0) and at 12, 24, 48, and 72 h after baseline. Additionally, arterial oxygenation, serum albumin levels and colloid osmotic pressure values in the serum were measured. Results: After 48 h of treatment, mean EVLW was significantly lower in the CAR group (6.3 ± 1.6 ml/kg [standard deviation, SD]), compared with the control group (11.2 ± 4.9 ml/kg) (p<0.05). In the control group, EVLW tended to increase during the study period. Arterial oxygenation (PaO2/FIO2-ratio) improved continuously during axial rotation therapy and was significantly higher after 24 h of treatment compared with the control group (32 ± 7.5 kPa vs. 21.2 ± 6.6 kPa, p<0.05, respectively). Serum albumin levels, ITBV, and colloid-osmotic pressures in the serum did not show any difference between the two groups during the experimental protocol. Conclusions: Continuous axial rotation caused a reduction of EVLW in patients with ALI. This may be due to continuous changes in intrathoracic pressures during kinetic therapy.