gebhart/patrepeval huggingface dataset:
Identification of recognition residues for ligation-based detection and quantitation of pseudouridine and N6 -methyladenosine (2007)

Over 100 chemical types of RNA modifications have been identified in thousands of sites in all three domains of life. Recent data suggest that modifications function synergistically to mediate biological function, and that cells may coordinately modulate modification levels for regulatory purposes. However, this area of RNA biology remains largely unexplored due to the lack of robust, high-throughput methods to quantify the extent of modification at specific sites. Recently, we developed a facile enzymatic ligation-based method for detection and quantitation of methylated 2'-hydroxyl groups within RNA. Here we exploit the principles of molecular recognition and nucleic acid chemistry to establish the experimental parameters for ligation-based detection and quantitation of pseudouridine (Psi) and N6-methyladenosine (m6A), two abundant modifications in eukaryotic rRNA/tRNA and mRNA, respectively. Detection of pseudouridylation at several sites in the large subunit rRNA derived from yeast demonstrates the feasibility of the approach for analysis of pseudouridylation in biological RNA samples.
Clustering data streams (2002)

We study clustering under the data stream model of computation where: given a sequence of points, the objective is to maintain a consistently good clustering of the sequence observed so far, using a small amount of memory and time. The data stream model is relevant to new classes of applications involving massive data sets, such as Web click stream analysis and multimedia data analysis. We give constant-factor approximation algorithms for the k-median problem in the data stream model of computation in a single pass. We also show negative results implying that our algorithms cannot be improved in a certain sense.
Investigation of Cross-Contamination and Misidentification of 278 Widely Used Tumor Cell Lines (2017)

In recent years, biological research involving human cell lines has been rapidly developing in China. However, some of the cell lines are not authenticated before use. Therefore, misidentified and/or cross-contaminated cell lines are unfortunately commonplace. In this study, we present a comprehensive investigation of cross-contamination and misidentification for a panel of 278 cell lines from 28 institutes in China by using short tandem repeat profiling method. By comparing the DNA profiles with the cell bank databases of ATCC and DSMZ, a total of 46.0% (128/278) cases with cross-contamination/misidentification were uncovered coming from 22 institutes. Notably, 73.2% (52 out of 71) of the cell lines established by the Chinese researchers were misidentified and accounted for 40.6% of total misidentification (52/128). Further, 67.3% (35/52) of the misidentified cell lines established in laboratories of China were HeLa cells or a possible hybrid of HeLa with another kind of cell line. Furthermore, the bile duct cancer cell line HCCC-9810 and degenerative lung cancer Calu-6 exhibited 88.9% match in the ATCC database (9-loci), indicating that they were from the same origin. However, when we used 21-loci to compare these two cell lines with the same algorithm, the percent match was only 48.2%, indicating that these two cell lines were different. The SNP profiles of HCCC-9810 and Calu-6 also revealed that they were different cell lines. 150 cell lines with unique profiles demonstrated a wide range of in vitro phenotypes. This panel of 150 genomically validated cancer cell lines represents a valuable resource for the cancer research community and will advance our understanding of the disease by providing a standard reference for cell lines that can be used for biological as well as preclinical studies.
MOLTEN CARBONATE FUEL CELL PRODUCT DESIGN IMPROVEMENT (2002)

No abstract prepared.
Plasma cholecystokinin in obese patients before and after jejunoileal bypass with 3:1 or 1:3 jejunoileal ratio--no role in the increased risk of gallstone formation. (1994)

Postoperative changes in plasma CCK levels neither explain the increased risk of gallstone formation after bypass surgery nor the higher incidence with a long compared to a short ileum left in continuity in the bypass.
Metastable solid solutions with quartz-type structures on the join SiO2–MgAl2O4 (1961)

Various members of a series of metastable solid solutions with a quartz-type structure and with compositions between SiO 2 and MgAl 2 O 4 have been synthesized from glass. Increasing amounts of Mg +2 and Al +3 in the quartz structure cause a gradual contraction parallel to, and a gradual expansion perpendicular to, the c axis. Siliceous members of the series are optically positive and less siliceous ones are negative; for a member with about 73 weight percent SiO 2 the birefringence is zero. The refractive indices of the solid solutions increase with decreasing SiO 2 content. Members with less than about 92 weight percent SiO 2 exhibit high-quartz structures even at room temperature, whereas more siliceous members go through an inversion to a low-quartz structure when quenched to room temperature. The temperature of this inversion is lower than that of pure quartz (SiO 2 ) as a result of the presence of Mg +2 and Al +3 in the structure.
Biomechanical and neuroautonomic adaptation to acute blood volume displacement in ischemic dilated cardiomyopathy: the predictive value of the CD25 test (2020)

We aimed to examine biomechanical and neuroautonomic adaptation to blood volume displacement induced by tilt test in patients with previous inferoapical/inferolateral (IA-IL) or basal/apical septal (BS-AS) myocardial infarction (MI). Twenty-four patients with heart failure (HF) and previous IA-IL MI and 30 patients with HF and previous BS-AS MI were enrolled. All patients underwent head-up tilt test, radionuclide ventricular function monitoring (VEST), sympathovagal balance evaluation, and chronotropic 25-dose isoproterenol infusion test (CD<sub>25</sub>). Physiopathological reactions to stress-tests were assessed in both groups. Follow-up lasted 36 mo. IA-IL patients showed lower stroke volume (SV), cardiac output (CO), and left ventricle ejection fraction (LVEF) compared with BS-AS. End-diastolic volume decreased in IA-IL group (<i>F</i> = 3.1, <i>P</i> = 0.043) more than in BS-AS group during tilt test. The time trend of end-systolic volume, SV, CO, LVEF, and peak filling rate were similar in the two groups. Norepinephrine (IA-IL supine→tilting 499.5 (SD:28.8)→719.3 (SD:41.5) pg/mL vs. BS-AS supine→tilting 533.9 (SD:33.3)→768.8 (SD:47.9) pg/mL; <i>P</i> < 0.001) and epinephrine plasma concentrations (IA-IL supine→ tilting 125.7 (SD:9.8)→193.7 (SD:9.6) pg/mL vs. BS-AS supine→ tilting 118.8 (SD:8.9)→191.7 (SD:10.2) pg/mL; <i>P</i> < 0.001) increased in both groups. Low-to-high frequencies ratio significantly increased in IA-IL and decreased in BS-AS patients. CD25 was similar in IA-IL and BS-AS patients (IA-IL = 4.6 (SD:0.94), BS-AS = 5.0 (SD:1.06) µg; <i>P</i> = 0.79). CD<sub>25</sub> predicted all-cause mortality (hazard ratio 1.48, 95% confidence interval 1.32-1.67; <i>P</i> < 0.0001) after adjusting for age/heart rate. In conclusion, patients with ischemic HF show abnormal biomechanical adaptation to volume displacement and compensatory sympathetic overdrive. The association of reduced β-adrenergic sensitivity and sympathetic denervation in such patients warrants for careful therapeutic choices.<b>NEW & NOTEWORTHY</b> The adaptation to volume displacement induced by tilt test was assessed in patients with heart failure and previous inferoapical/inferolateral or basal/apical septal myocardial infarction. The responsiveness of cardiac muscle to sympathetic nervous system stimulation predicts the mortality in patients with ischemic heart failure and may represent a useful tool for clinicians in the general assessment of this kind of patients.
Evaluation of pigtail termination of STP cable using modal equivalent circuit of four-conductor transmission systems (2013)

For investigating mode conversion in four-conductor transmission systems we have developed a modal-equivalent-circuit expressed by an imbalance factor of transmission line, a current division factor, in the same way as we developed the one in three-conductor transmission systems. The modal equivalent circuit consists of three modal equivalent circuits of normal mode, primary-common mode, and secondary-common mode. In this paper, the influence of mode conversion by the pigtail termination of a shielded-twisted-pair (STP) cable was analyzed using the modal equivalent circuit and mixed-mode S parameters with respect to normal mode and primary-common mode. As a result, it was found that mode conversion depends on the imbalance factor and that the modal equivalent circuit helps to explain mode conversion that occurs in terminating STP cables with pigtail.
Multistage Viscous Micropumps (2004)

The viscous micropump consists of a cylinder placed eccentrically inside a microchannel, where the rotor axis is perpendicular to the channel axis. When the cylinder rotates, a net force is transferred to the fluid due to the unequal shear stresses on the upper and lower surfaces of the rotor. Consequently, this causes the surrounding fluid in the channel to displace towards the microchannel outlet. The simplicity of the viscous micropump renders it ideal for micro pumping, however, previous studies have shown that its performance is still less than what is required for various applications. The performance of the viscous micropump, in terms of flow rate, pressure head and efficiency, may be enhanced by implementing more than one rotor into the configuration. The present study will numerically investigate the performance of various configurations of the viscous micropumps with multiple rotors, namely the dual-horizontal rotor, the triple-horizontal rotor, the symmetrical-dual-vertical rotor, and the 8-shaped dual-vertical rotor. The development of drag force with time, as well as the viscous resisting torque on the cylinders were studied. In addition, the corresponding drag and moment coefficients were calculated. Results show that the symmetrical-dual-vertical rotor configuration yields the best efficiency, and generates the highest flow rate. The steady state performance of the single-stage micropump was compared with the available experimental and numerical data, and was found to be in very good agreement. This work provides a foundation for future research on the subject of fluid phenomena in viscous micropumps.
Death by Gun Violence—A Public Health Crisis (2017)

The shooting in Las Vegas, Nevada, that left 59 people dead, 10 times that number wounded, and thousands of people with the psychological distress from being present at the scene during and after the massacre has once again raised the issue of what we as a nation can and should do about guns. The solution lies in not just focusing on Las Vegas and the hundreds of other mass shootings that have occurred in the United States in the last 14 months, but rather to underscore that on average almost 100 people die each day in the United States from gun violence. The 36 252 deaths from firearms in the United States in 2015 1 exceeded the number of deaths from motor vehicle traffic crashes that year (36 161). 1 That same year, the US Centers for Disease Control and Prevention reported that 5 people died from terrorism. Since 1968, more individuals in the United States have died from gun violence than in battle during all the wars the country has fought since its inception. uns do not make individuals, their families, or homes safer and they result in far more deaths to loved ones than to an intruder intending to cause harm. Often forgotten is that 60.7% of the gun deaths in 2015 in the United States were suicides. 1 Means used to attempt suicide matter; guns will result in suicidal deaths well over 90% of the time, whereas ingestion of pills or wrist cutting will be unsuccessful more than 90% of the time. The majority of people who try to commit suicide but survive the attempt will not go on to die from suicide 4 ; if the attempt is with a gun, there will be no second chance at life.
A field test of eye tracking systems with one and three cameras (2011)

Driver state monitoring by eye tracking is an increasingly used method to assess driver distraction and sleepiness. The aim of this study is to compare a 1-camera eye tracking system with a 3-camera system in a field setting and evaluate how the choice of eye tracker impacts (a) the quality of the recordings and (b) behavioural performance indicators. Eighteen drivers drove an instrumented vehicle on a motorway for about 90 minutes while their gaze patterns were recorded with the two systems in parallel. The results show that neither quality nor performance indicators deteriorate over time. Tracking is available for 96 ± 6 % of the time for the 3-camera system and 77 ± 22 % for the 1- camera system, and both the frequency and the duration of lapses are considerably higher in the 1- camera system. The 3-camera system provides better vertical accuracy and increased horizontal availability. These properties cause performance indicators calculated from the two systems to deviate. For example glance durations are 0.76o ± 0.34o for the 3-camera system and 0.60o ± 0.48o for the 1-camera system. When comparing the output from the systems, it becomes clear that not all differences can be explained by the larger coverage of multiple cameras. In conclusion, the 3-camera system shows better performance with respect to data availability, working environment and accuracy. In many applications it is sufficient to use one camera, but special focus on the handling of lapses is essential.
EVIDENCE OF PROTON TUNNELING IN THE ROTATIONAL SPECTRUM OF THE PROPIOLIC ACID-FORMIC ACID HYDROGEN BONDED COMPLEX (2004)

Author Institution: Department of Chemistry, University of Virginia
A remote collaboration system design and construction (2011)

Remote Desktop Protocol (RDP) provides the remote login and desktop control capabilities that a client can fully control and access a remote server. It is implemented by Microsoft Corporation based on ITU-T T.120 family protocols. The major advantage of RDP distinguishing from other remote desktop schemes such as the frame-buffer approach is based on sending graphics device interface (GDI) information from the server as possible, instead of full bitmap images. This paper proposes a remote collaboration system which is based, designed and implemented on the RDP architecture. The proposed system consisting of cross control scheme with bus re-encryption architecture provides the full capabilities of all remote collaborations, such as remote control, applications access and sharing between all RDP clients.
Frontispiece: Triazine‐Based Graphitic Carbon Nitride: a Two‐Dimensional Semiconductor (2014)

Graphitic Carbon Nitride In their Communication on page 7450 ff., A. I. Cooper, M. J. Bojdys, et al. report crystalline thin films of triazine-based graphitic carbon nitride (TGCN). TGCN is structurally similar to graphite but it is a semiconductor, and the thin films display a direct bandgap between 1.6 and 2.0 eV.
The Entner-Doudoroff Pathway Is an Essential Metabolic Route for Methylotuvimicrobium buryatense 5GB1C (2020)

<i>Methylotuvimicrobium buryatense</i> 5GB1C, a fast-growing gammaproteobacterial methanotroph, is equipped with two glycolytic pathways, the Entner-Doudoroff (ED) pathway and the Embden-Meyerhof-Parnas (EMP) pathway. Metabolic flux analysis and <sup>13</sup>C-labeling experiments have shown the EMP pathway is the principal glycolytic route in <i>M. buryatense</i> 5GB1C, while the ED pathway appears to be metabolically and energetically insignificant. However, it has not been possible to obtain a null mutant in the <i>edd</i>-<i>eda</i> genes encoding the two unique enzymatic reactions in the ED pathway, suggesting the ED pathway may be essential for <i>M. buryatense</i> 5GB1C growth. In this study, the inducible P <i><sub>BAD</sub></i> promoter was used to manipulate gene expression of <i>edd-eda</i>, and in addition, the expression of these two genes was separated from that of a downstream <i>gltA</i> gene. The resulting strain shows arabinose-dependent growth that correlates with ED pathway activity, with normal growth achieved in the presence of ∼0.1 g/liter arabinose. Flux balance analysis shows that <i>M. buryatense</i> 5GB1C with a strong ED pathway has a reduced energy budget, thereby limiting the mutant growth at a high concentration of arabinose. Collectively, our study demonstrates that the ED pathway is essential for <i>M. buryatense</i> 5GB1C. However, no known mechanism can directly explain the essentiality of the ED pathway, and thus, it may have a yet unknown regulatory role required for sustaining a healthy and functional metabolism in this bacterium.<b>IMPORTANCE</b> The gammaproteobacterial methanotrophs possess a unique central metabolic architecture where methane and other reduced C<sub>1</sub> carbon sources are assimilated through the ribulose monophosphate cycle. Although efforts have been made to better understand methanotrophic metabolism in these bacteria via experimental and computational approaches, many questions remain unanswered. One of these is the essentiality of the ED pathway for <i>M. buryatense</i> 5GB1C, as current results appear contradictory. By creating a construct with <i>edd-eda</i> and <i>gltA</i> genes controlled by P <i><sub>BAD</sub></i> and P <i><sub>J23101</sub></i> , respectively, we demonstrated the essentiality of the ED pathway for this obligate methanotroph. It is also demonstrated that these genetic tools are applicable to <i>M. buryatense</i> 5GB1C and that expression of the target genes can be tightly controlled across an extensive range. Our study adds to the expanding knowledge of methanotrophic metabolism and practical approaches to genetic manipulation for obligate methanotrophs.
Synthesis of ring-oxidized retinoids as substrates of mouse class I alcohol dehydrogenase (ADH1) (2004)

Ring-oxidized retinoids have been synthesized stereoselectively using the Stille cross-coupling reaction. Kinetic constants of mouse class I alcohol dehydrogenase (ADH1) with these retinoids were determined.
Synthesis, Characterization, and Enzymatic Degradation Studies on Novel Network Aliphatic Polyesters (1998)

Network polyesters were prepared from1,1,1-trimethylolethane (Ye), 1,1,1-trimethylolpropane (Yp), 1,2,3,4-butanetetrol (Xe), and d-glucitol (Zs) with aliphatic dicarboxylic acids containing different numbers of methylene groups (HOOC(CH2)n-2COOH, n =4, 6−14, 16, and 20). Prepolymers prepared by melt polycondensation were cast from dimethylformamide solution and postpolymerized at 230 °C for 4 h to form a network. The resultant films were transparent, flexible, and insoluble in organic solvents. The network polyesters obtained were characterized by infrared absorption spectra, wide-angle X-ray diffraction analysis, density measurement, thermomechanical analysis, differential scanning calorimetry, and tensile test. The enzymatic degradation was estimated by the weight loss of the network polyester films in a buffer solution with lipase enzymes at 37 °C. The enzymatic degradation for Yen films was compared with that for the network polyester films of glycerol (Yg) or pentaerithritol (Xp) with various aliphatic dicarboxylic acids reported earlier.11,12 After the incubation in Rhizopus delemar lipase solution for 2 days, the weight loss was hardly observed for Ye4−7, while it increased drastically for Ye8−13 (13−15 g/m2) and then decreased gradually for Ye14−20. Other lipases of porcine pancreas and Psedomonas cepacia hardly degraded Yen films. The degradation rate for 10 series films was decreased as follows:Yg10 >Ye10 > Yp10 = Xe10 > Xp10 > Zs10, corresponding to the increase in the number of hydroxyl groups in the polyhydric alcohols.
Enantioselective Palladium(II)-Catalyzed Formal [3,3]-Sigmatropic Rearrangement of 2-Allyloxypyridines and Related Heterocycles (2009)

Enantioselective palladium(II)-catalyzed formal [3,3]-sigmatropic rearrangement of (E)- and (Z)-allyloxy substituted N-heterocycles generates N-allyl N-heterocyclic amides in good yields and high enantioselectivities (up to 96% ee). The chiral palladacycle COP-Cl (5 mol %) is used as a catalyst with silver(I) trifluoroacetate (10 mol %) at 35-45 degrees C. Examples of heterocycles synthesized include 2-pyridones, quinolin-2(1H)-ones, and isoquinolin-1(2H)-ones.
On the Capacity of Noncoherent Network Coding (2011)

We consider the problem of multicasting information from a source to a set of receivers over a network where intermediate network nodes perform randomized linear network coding operations on the source packets. We propose a channel model for the noncoherent network coding introduced by Koetter and Kschischang in , that captures the essence of such a network operation, and calculate the capacity as a function of network parameters. We prove that use of subspace coding is optimal, and show that, in some cases, the capacity-achieving distribution uses subspaces of several dimensions, where the employed dimensions depend on the packet length. This model and the results also allow us to give guidelines on when subspace coding is beneficial for the proposed model and by how much, in comparison to a coding vector approach, from a capacity viewpoint. We extend our results to the case of multiple source multicast that creates a virtual multiple access channel.
Novel hydroxyl naphthoquinones with potent Cdc25 antagonizing and growth inhibitory properties (2005)

Cdc25 phosphatases are important in cell cycle control and activate cyclin-dependent kinases (Cdk). Efforts are currently under way to synthesize specific small-molecule Cdc25 inhibitors that might have anticancer properties. NSC 95397, a protein tyrosine phosphatase antagonist from the National Cancer Institute library, was reported to be a potent Cdc25 inhibitor. We have synthesized two hydroxyl derivatives of NSC 95397, monohydroxyl-NSC 95397 and dihydroxyl-NSC 95397, which both have enhanced activity for inhibiting Cdc25s. The new analogues, especially dihydroxyl-NSC 95397, potently inhibited the growth of human hepatoma and breast cancer cells in vitro. They influenced two signaling pathways. The dual phosphorylation of extracellular signal-regulated kinase 1/2 (ERK1/2) was induced, likely due to inhibition of the ERK phosphatase activity in Hep 3B cell lysate but not the dual specificity ERK phosphatase MKP-1. They also inhibited Cdc25 enzymatic activities and induced tyrosine phosphorylation of the Cdc25 target Cdks. Addition of hydroxyl groups to the naphthoquinone ring thus enhanced the potency of NSC 95397. These two new compounds may be useful probes for the biological functions of Cdc25s and have the potential for disrupting the cell cycle of growing tumor cells.
Input current harmonics in a regenerative multi-cell inverter with single-phase active rectifiers (2003)

Harmonics are a very important issue in the design and operation of medium voltage inverter drives due to restrictions imposed by regulations. This paper studies the harmonics generated in a three-phase cascaded multi-cell inverter with single-phase active front end (AFE) at the input side of each cell. This study identifies accurately the origin of the harmonics present in the DC link voltage and in the input currents and discusses methods to reduce and, in some cases, eliminate them. It has been established that the low-frequency harmonics in the primary input current can be cancelled by an appropriate interconnection of the cells and of the input transformer.