gebhart/patrepeval huggingface dataset:
Characterization of a cyclic AMP-resistant Chinese hamster ovary cell mutant containing both wild-type and mutant species of type I regulatory subunit of cyclic AMP-dependent protein kinase. (1985)

We have characterized a cyclic AMP-resistant Chinese hamster ovary (CHO) cell mutant in which one of two major species of type I regulatory subunit (RI) of cyclic AMP-dependent protein kinase is altered. Wild-type CHO cell extracts contain two cyclic AMP-dependent protein kinase activities. As shown by DEAE-cellulose chromatography, there is a peak of type I protein kinase activity in mutant extracts, but the type II protein kinase activity is considerably reduced even though free type II regulatory subunit (RII) is present. The type I kinase from the mutant has an altered RI (RI*) whose KD for the binding of 8-N3[32P] cAMP (KD = 1.3 X 10(-5) M) is increased by more than 200-fold compared to RI from the wild-type enzyme (KD = 5.5 X 10(-8) M). No differences were found between the catalytic subunits from the wild-type and mutant type I kinases. A large portion of RI in mutant and wild-type extracts is present in the free form. The RI* derived from mutant type I protein kinase shows altered labeling by 8-N3[32P]cAMP (KD = 1.3 X 10(-5) M) whereas the free RI from the mutant is labeled normally by the photoaffinity label (KD = 7.2 X 10(-8) M), suggesting that the RI* which binds to the catalytic subunit is functionally different from the free form of RI. The decreased amount of type II kinase activity in the mutant appears to be due to competition of RI* with RII for binding to the catalytic subunit. Translation of mRNA from wild-type CHO cells results in the synthesis of two different charge forms of RI, providing biochemical confirmation of two different species of RI in CHO cells. Additional biochemical evidence based on isoelectric focusing behavior of 8-N3[32P]cAMP-labeled RI species and [35S]methionine-labeled RI from mutant and wild-type extracts confirms the charge heterogeneity of RI species in CHO cells. These genetic and biochemical data taken together are consistent with the conclusion that there are at least two different species of RI present in CHO cells and that one of these species is altered in the mutant analyzed in this work.
Discovery of new methylation markers to improve screening for cervical intraepithelial neoplasia grade 2/3 (2016)

We identified new CIN2/3-specific methylation markers using genome-wide DNA methylation analysis. The diagnostic performance of our new methylation panel shows higher specificity, which should result in prevention of unnecessary colposcopies for women referred with abnormal cytology. In addition, these newly found markers might be applied as a triage test in hrHPV-positive women from population-based screening. The next step before implementation in primary screening programs will be validation in population-based cohorts.
Engineering a substrate‐specific cold‐adapted subtilisin (2004)

One region predicted to be highly flexible for a psychrophilic enzyme, TA39 subtilisin (S39), was transferred in silico to the mesophilic subtilisin, savinase (EC 3.4.21.62), from Bacillus lentus (clausii). The engineered hybrid and savinase were initially investigated by molecular dynamic simulations at 300 K to show binding region and global flexibility. The predicted S39 region consists of 12 residues, which due to homology between the subtilisins, results in a total change of eight residues. By site-directed modifications, the region was transferred to the binding region of savinase, thus a savinase-S39 hybrid, named H5, was constructed. The designed hybrid showed the same temperature optimum and pH profile as savinase, but H5 had higher specific activity on the synthetic substrate N-succinyl-L-Ala-L-Ala-L-Pro-L-Phe-p-nitroanilide (AAPF) at all temperatures measured and, at the same time, H5 showed a decrease in thermostability. The H5 hybrid showed broader substrate specificity, measured at room temperature, due to an increase in catalytic efficiency on AAPF, AAPA and FAAF compared with savinase (N-succinyl-XXXX-pNA; XXXX = AAPF, AAPA and FAAF). The H5 hybrid showed increased activity at low temperature, increased binding region and global flexibility, as investigated by molecular dynamic simulations, and global destabilization from differential scanning calorimetry measurements. These psychrophilic characteristics indicated an increase in binding site flexibility, probably due to the modifications P129S, S130G, P131E, and thus we show that it is possible to increase low temperature activity and global flexibility by engineered flexibility in the binding region.
Low-cost YBCO coated conductor technology (2000)

Deformation-textured, non-silver substrates, and solution-based deposition of buffer and superconductor layers offer routes to a low-cost YBCO coated-conductor technology for high-temperature superconducting wire. Several significant steps towards such a technology are reported here: a solution-based Gd2O3 seed buffer layer was deposited by a web-coating technique over a metre-length tape of deformation-textured nickel with excellent texture and uniformity. Also, short full-stack samples with YBCO performance up to 0.8 MA cm-2 at 77 K were prepared at Oak Ridge National Laboratory (ORNL) and American Superconductor (ASC) using a CeO2/YSZ/CeO2 buffer sequence on textured nickel and a trifluoroacetate (TFA) precursor YBCO process; in this case the buffers are deposited by e-beam and magnetron sputtering.
Hydrogen diffusion simulation model considering thermal and stress changes in sport welds. (2019)

High-strength steel sheets have been developed for both reducing automobile weight and keeping passengers’ safety. Delayed fracture due to diffusible hydrogen is known as one of the problems in arc welds of high-strength steel plates, which is often prevented by applying pre/post-heating processes. However, there is little reported regarding hydrogen diffusion behaviour during rapid temperature change in resistance spot welds of steel sheets. Hydrogen diffusion behaviour is affected by thermal and stress ﬁelds. Therefore, the effect of rapid change in these ﬁelds needs to be properly considered for the elucidation of hydrogen diffusion behaviour in resistance spot welds. This study aims to clarify the delayed fracture mechanism of resistance spot welds. The hydrogen diffusion simulation model considering the effects of thermal and stress changes during welding is constructed. It is assumed in the model that hydrogen solubility and diffusivity in the nugget are larger than those of base metal. A change in fracture pattern dependent on hydrogen environment can be well explained using this model. The numerical simulation predicts that high residual stress leads to hydrogen concentration at the edge of the nugget after welding. This concentration would be the main factor of the delayed fracture in the nugget when the nugget diameter is small. In this situation, hydrogen is introduced from antirust oil, water and contamination on sheet surfaces to the nugget during welding. The numerical simulation assumed in actual use is also performed, in which the hydrogen is introduced from the sheet surfaces. Hydrogen concentrates at the edge of the nugget in a relatively mild hydrogen environment, whereas in the severe environment it highly concentrates in the heat-affected zone around the nugget before concentrating in the nugget. These calculated results can well explain the transition of the fracture pattern from the nugget to theheat-affected zone in the experiment.
RESULTS OF SURGICAL REPAIR OF FULL-THICKNESS TEARS OF THE ROTATOR CUFF (1997)

Shoulder pain is often caused by pathologic conditions of the rotator cuff. Many investigators have studied the factors that influence the outcome after rotator cuff repair. This article reviews the different factors and the various methods of reporting outcome after shoulder surgery.
Mechanism of Carrier Mobility Degradation Induced by Crystallization of HfO2Gate Dielectrics (2009)

We have experimentally shown that crystallization of HfO2 and the subsequent formation of fixed charges localized at the HfO2/SiO2 interface bring about a degradation of electron mobility. Systematic analyses of valence-band photoemission and transmission electron microscopy indicate that the oxygen transfer from the HfO2 layer to the Si substrate is promoted upon the crystallization of HfO2 and the fixed charges are generated during the process. These findings highlight the importance of controlling the crystallinity of HfO2 for realizing high performance metal gate high-κ field-effect transistors.
Primary care clinician adherence with asthma guidelines: the National Asthma Survey of Physicians (2019)

<i>Background and objectives</i><b>:</b> Although primary care clinicians provide >60% of U.S. asthma care, no nationally representative study has examined variation in adherence among primary care groups to four cornerstone domains of the Expert Panel Report-3 asthma guidelines: assessment/monitoring, patient education, environmental assessment, and medications. We used the 2012 National Asthma Survey of Physicians: National Ambulatory Medical Care Survey to compare adherence by family/general medicine practitioners (FM/GM), internists, pediatricians and Community Health Center mid-level clinicians (CHC). <i>Methods:</i> Adherence was self-reported (<i>n</i> = 1355 clinicians). Adjusted odds of almost always adhering to each recommendation (≥75% of the time) were estimated controlling for clinician/practice characteristics, and agreement and self-efficacy with guideline recommendations. <i>Results:</i> A higher percentage of pediatricians adhered to most assessment/monitoring recommendations compared to FM/GM and other groups (e.g. 71.6% [SE 4.0] almost always assessed daytime symptoms versus 50.6% [SE 5.1]-51.1% [SE 5.8], <i>t</i>-test <i>p</i> < 0.05) but low percentages from all groups almost always performed spirometry (6.8% [SE 2.0]-16.8% [SE 4.7]). Pediatricians were more likely to provide asthma action/treatment plans than FM/GM and internists. Internists were more likely to assess school/work triggers than pediatricians and CHC (environmental assessment). All groups prescribed inhaled corticosteroids for daily control (84.0% [SE 3.7]-90.7% [SE 2.5]) (medications). In adjusted analyses, pediatric specialty, high self-efficacy and frequent specialist referral were associated with high adherence. <i>Conclusions:</i> Pediatricians were more likely to report high adherence than other clinicians. Self- efficacy and frequent referral were also associated with adherence. Adherence was higher for history-taking recommendations and lower for recommendations involving patient education, equipment and expertise.
Supplementary Figure Legend from Human Monoclonal Antibodies Targeting Nonoverlapping Epitopes on Insulin-like Growth Factor II as a Novel Type of Candidate Cancer Therapeutics (2023)

&lt;p&gt;PDF file, 62KB.&lt;/p&gt;
Identification of Francisella tularensis by Whole-Cell Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry: Fast, Reliable, Robust, and Cost-Effective Differentiation on Species and Subspecies Levels (2010)

Francisella tularensis, the causative agent of tularemia, is a potential agent of bioterrorism. The phenotypic discrimination of closely related, but differently virulent, Francisella tularensis subspecies with phenotyping methods is difficult and time-consuming, often producing ambiguous results. As a fast and simple alternative, matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) was applied to 50 different strains of the genus Francisella to assess its ability to identify and discriminate between strains according to their designated species and subspecies. Reference spectra from five representative strains of Francisella philomiragia, Francisella tularensis subsp. tularensis, Francisella tularensis subsp. holarctica, Francisella tularensis subsp. mediasiatica, and Francisella tularensis subsp. novicida were established and evaluated for their capability to correctly identify Francisella species and subspecies by matching a collection of spectra from 45 blind-coded Francisella strains against a database containing the five reference spectra and 3,287 spectra from other microorganisms. As a reference method for identification of strains from the genus Francisella, 23S rRNA gene sequencing was used. All strains were correctly identified, with both methods showing perfect agreement at the species level as well as at the subspecies level. The identification of Francisella strains by MALDI-TOF MS and subsequent database matching was reproducible using biological replicates, different culture media, different cultivation times, different serial in vitro passages of the same strain, different preparation protocols, and different mass spectrometers.
A neural network-based estimator for the mixture ratio of the Space Shuttle Main Engine (1992)

In order to properly utilize the available fuel and oxidizer of a liquid propellant rocket engine, the mixture ratio is closed loop controlled during main stage (65 percent - 109 percent power) operation. However, because of the lack of flight-capable instrumentation for measuring mixture ratio, the value of mixture ratio in the control loop is estimated using available sensor measurements such as the combustion chamber pressure and the volumetric flow, and the temperature and pressure at the exit duct on the low pressure fuel pump. This estimation scheme has two limitations. First, the estimation formula is based on an empirical curve fitting which is accurate only within a narrow operating range. Second, the mixture ratio estimate relies on a few sensor measurements and loss of any of these measurements will make the estimate invalid. In this paper, we propose a neural network-based estimator for the mixture ratio of the Space Shuttle Main Engine. The estimator is an extension of a previously developed neural network based sensor failure detection and recovery algorithm (sensor validation). This neural network uses an auto associative structure which utilizes the redundant information of dissimilar sensors to detect inconsistent measurements. Two approaches have been identified for synthesizing mixture ratio from measurement data using a neural network. The first approach uses an auto associative neural network for sensor validation which is modified to include the mixture ratio as an additional output. The second uses a new network for the mixture ratio estimation in addition to the sensor validation network. Although mixture ratio is not directly measured in flight, it is generally available in simulation and in test bed firing data from facility measurements of fuel and oxidizer volumetric flows. The pros and cons of these two approaches will be discussed in terms of robustness to sensor failures and accuracy of the estimate during typical transients using simulation data.
1,550-nm uncooled EA-modulator and EA/DFB for 10/40-Gbit/s low-power-consumption transceivers (2005)

New uncooled 1,550-nm InGaAlAs electroabsorption-modulators and their laser-integration technologies were developed for 10/40-Gbit/s small-form-factor modules. For the first time, 10-Gbit/s 40-km SMF transmission and 40-Gbit/s operation were achieved up to 85/spl deg/C.
Effects of Subchronic Treatment With the Long-Acting Glucose-Dependent Insulinotropic Polypeptide Receptor Agonist, N-AcGIP, on Glucose Homeostasis in Streptozotocin-Induced Diabetes (2007)

These data indicate that subchronic treatment with the long-acting glucose-dependent insulinotropic polypeptide receptor agonist, N-AcGIP, does not have beneficial effects in insulin-deficient STZ-diabetic mice. This supports the primary antidiabetic action of this analogue in type 2 diabetes as stimulation of beta-cell function and insulin secretion.
Fast block motion estimation by edge based partial distortion search (2009)

In order to reduce the computations of motion estimation, this paper proposes a novel edge based partial distortion search (EPDS) algorithm in which the entire macroblock (MB) is divided into different sub-blocks and the calculation order of partial distortion is determined based on the edge strength of sub-blocks. In the proposed method, only selected numbers of search points are considered for candidate motion vectors. An efficient early termination method, which is based on the dynamic threshold, is also proposed to decide whether a search point has met the distortion criterion. Simulation results show that the proposed method is 108 times faster than Full Search (FS), 10 times faster than Normalized Partial Distortion search (NPDS) and 2 times faster than the dual halfway stop NPDS (DHS-NPDS) on an average. PSNR degradation of the proposed algorithm is negligible and in the region of 0.01 dB.
Supplementary Table Legends, Figure Legends, Figures S1 - S6 from Systematic Functional Interrogation of Rare Cancer Variants Identifies Oncogenic Alleles (2023)

&lt;p&gt;Supplementary Figure S1. Distribution of barcode read representation in pre-expansion and pre-injection samples. Supplementary Figure S2. Tumor composition of in vivo pooled screen, excluding the pools shown in Figure 2. Supplementary Figure S3. Gene expression differentiates functional alleles. Supplementary Figure S4. Validation of rare oncogenic alleles, excluding the ones shown in Figure 4. Supplementary Figure S5. Gene expression signatures of NFE2L2 wild type and gain-offunction mutants are correlated. Supplementary Figure S6. Comparison to in silico methods.&lt;/p&gt;
Effects of ACL reconstruction surgery on muscle activity of the lower limb during a jump‐cut maneuver in males and females (2013)

We compared muscle activity of the quadriceps, hamstring, and gastrocnemius muscles when ACL-intact (ACL(INT)) and ACL-reconstructed (ACL(REC)) male and female subjects performed a jump-cut task. Surface electromyography sensors were used to evaluate time to peak muscle activity and muscle activity ratios. Rectus femoris (RF) and vastus medialis (VM) peak timing was 71 and 78 ms earlier in ACL(INT) than in ACL(REC) subjects, respectively. Biceps femoris (BF) peak timing was 90 ms earlier in ACL(INT) than in ACL(REC) subjects and 75 ms earlier in females than in males. Medial gastrocnemius (MG) muscle peak timing was 77 ms earlier in ACL(INT) than in ACL(REC) subjects. Lateral gastrocnemius (LG) and MG muscle peak times were 106 ms and 87 ms earlier in females than in males, respectively. The RF, VM, BF, and MG peaked later in ACL(REC) than in ACL(INT) subjects. There was evidence suggesting that the loading phase quadriceps:hamstring (quad:ham) muscle activity ratio was greater in ACL(REC) than in ACL(INT) subjects. Finally, the injury risk phase quad:ham muscle activity ratio was 4.8 times greater in females than in males. In conclusion, differences exist in muscle activity related to ACL status and sex that could potentially help explain graft failure risk and the sex bias.
Quantitative Analytical Method for the Determination of Biotinidase Activity in Dried Blood Spot Samples (2015)

Biotinidase activity assay is included in most newborn screening protocols, and the positive results are confirmed by quantitative enzyme activity measurements. In our study, we describe a new quantitative analytical method for the determination of biotinidase activity using the blood sample deposited onto filter paper as the assay medium, by predepositing N-biotinyl-p-aminobenzoic acid onto the standard sample collection paper. The analysis of the assay mixture requires a simple extraction step from a dried blood spot followed by the quantification of product by LC-MS. The method provides a simple and reliable enzyme assay method that enables the rapid diagnosis of biotinidase deficiency (BD). Out of the measured 36 samples, 13 were healthy with lower enzyme activities, 16 were patients with partial BD, and 7 were patients with profound BD with residual activity below 10%. Expression of enzyme activity in percentage of mean activity of negative controls allows comparison of the different techniques. The obtained results are in good agreement with activity data determined from both dried blood spots and serum samples, giving an informative diagnostic value.
Spectroscopic analysis of different types of single-wall carbon nanotubes (1998)

The Raman response of the radial breathing mode in single-wall carbon nanotubes was analyzed for excitation with 10 different laser lines. The line shape was fitted with 14 Voigtian oscillators which could be correlated to tubes of different helicity. The strongest lines were observed between 172 and 199 cm−1. For an assignment frequencies evaluated from a density functional calculation and scattering intensities for the resonance transitions were used. The 5 strongest lines observed are consistent with scattering from tubes with 11 different helicities. From the evaluation of the scattering intensities the nearest-neighbor integral between two carbon atoms on the curved sheet was found to be 2.6 ± 0.5 eV.
Cell-Based Therapies for Myocardial Repair: Emerging Role for Bone Marrow-Derived Mesenchymal Stem Cells (MSCs) in the Treatment of the Chronically Injured Heart (2013)

Accumulating data support the use of bone marrow (BM)-derived MSCs in animal models (e.g., swine) to restore cardiac function and tissue perfusion in chronic cardiac injury. Based on results obtained in swine, we are currently conducting phase I/II clinical trials to address the safety, cell type, cell dose, delivery technique, and efficacy of MSCs in patients with chronic heart failure. MSCs for these trials are isolated from harvested BM and then processed and expanded for intracardiac injection. The BM-MSCs in use for the clinical trials are of clinical grade having been processed successfully in an FDA-approved cGMP facility.
High fidelity reconstruction of three-dimensional objects by FINCH fluorescence microscopy (2012)

FINCH holography produces super-resolved images above and below the focal plane of the microscope objective but with different magnifications. A method is presented to faithfully reconstruct 3D objects with dimensional fidelity.
Wavelength-tunable CW optical parametric oscillator for calibration of Si and InGaAs phododiodes (2007)

We present a CW optical parametric oscillator (OPO) based on quasi-phase-matching. Pumped at 532 nm, the OPO provides coherent radiation from 800 nm to 900 nm and from 1300 nm to 1600 nm for signal and idler, respectively. Application for calibrating the spectral responsivity of Si and InGaAs photodiodes is demonstrated.
A genome-wide association study of outcome from traumatic brain injury (2022)

A full list of funding bodies that contributed to this study can be found in the Acknowledgements section.