gebhart/patrepeval huggingface dataset:
Solution of a Protein Crystal Structure with a Model Obtained from NMR Interproton Distance Restraints (1987)

Model calculations were performed to test the possibility of solving crystal structures of proteins by Patterson search techniques with three-dimensional structures obtained from nuclear magnetic resonance (NMR) interproton distance restraints. Structures for crambin obtained from simulated NMR data were used as the test system; the root-mean-square deviations of the NMR structures from the x-ray structure were 1.5 to 2.2 A for backbone atoms and 2.0 to 2.8 A for side-chain atoms. Patterson searches were made to determine the orientation and position of the NMR structures in the unit cell. The correct solution was obtained by comparing the rotation function results of several of the NMR structures and the average structure derived from them. Conventional refinement techniques reduced the R factor from 0.43 at 4 A resolution to 0.27 at 2 A resolution without inclusion of water molecules. The partially refined structure has root-mean-square backbone and side-chain atom deviations from the x-ray structure of 0.5 and 1.3 A, respectively.
Illustrated techniques for performing the Cox-Maze IV procedure through a right mini-thoracotomy. (2014)

The Cox-Maze IV procedure has replaced the "cut-and-sew" technique of the original Cox-Maze operation with lines of ablation created using bipolar radiofrequency (RF) and cryothermal energy devices. In select patients, this procedure can be performed through a right mini-thoracotomy. This illustrated review is the first to detail the complete steps of the Cox-Maze IV procedure performed through a right mini-thoracotomy with careful attention paid to operative anatomy and advice. Pre- and post-operative management and outcomes are also discussed. This should be a practical guide for the practicing cardiac surgeon.
Cbl-dependent Ubiquitination Is Required for Progression of EGF Receptors into Clathrin-coated Pits (2004)

Ligand binding causes the EGF receptor (EGFR) to become ubiquitinated by Cbl upon association with the adaptor protein Grb2. We have investigated the role of ubiquitin and Grb2 in ligand-induced endocytosis of the EGFR. Incubation of cells with EGF on ice caused translocation of Grb2 and Cbl from the cytosol to the rim of coated pits. Grb2 with point mutations in both SH3 domains inhibited recruitment of the EGFR to clathrin-coated pits, in a Ras-independent manner. On overexpression of the Cbl-binding protein Sprouty, ubiquitination of the EGFR was inhibited, the EGFR was recruited only to the rim of coated pits, and endocytosis of the EGFR was inhibited. Conjugation-defective ubiquitin similarly inhibited recruitment of EGF-EGFR to clathrin-coated pits. Even though this does not prove that cargo must be ubiquitinated, this indicates the importance of interaction of ubiquitinated protein(s) with proteins harboring ubiquitin-interacting domains. We propose that Grb2 mediates transient anchoring of the EGFR to an Eps15-containing molecular complex at the rim of coated pits and that Cbl-induced ubiquitination of the EGFR allows relocation of EGFR from the rim to the center of clathrin-coated pits.
Accurate SUV determination for small solitary pulmonary nodules using CT-based lesion volume estimates (2005)

Evaluation and follow up of small pulmonary nodules has become commonplace with advancing PET and CT technology. Limits in system resolution, recovery coefficient estimations and transaxial ROI determinations often make obtaining useful SUV data difficult. We demonstrate a method which may be more accurate for making these determinations. It is assumed that the nodule can be distinguished clearly on CT and that it resides in a region of homogenous background PET uptake. By integrating the PET activity over a large region including the small nodule and determining the volume of the lesion (V/sub lesion/) from thin slice CT images the activity concentration in the lesion (AC/sub lesion/) can be determined if the background activity concentration (AC/sub background/) is determined away from the lesion. The total integrated activity (IA) in the ROI is: IA=AC/sub lesion//spl middot/V/sub lesion/+AC/sub background/$ 8SV/sub background/. Alternatively the ratio of the activity concentration in the lesion to the background is: [(IA/AC/sub background/)-V/sub background/]/V/sub l /e/sub sion/. Results for activity ratios using a hollow spheres phantom indicate this method gives the correct value for the smallest sphere (activity volume=0.6cc) whereas the ratio using usual SUV determinations is spuriously low by a factor of up to /spl sim/2. Clinical results for a 1cc volume SPN indicate a tumor to background ratio of /spl sim/20 compared with a ratio of 15 using the maximum SUV, similar to the behavior seen in phantom measurements.
Duplicate isochorismate synthase genes of Bacillus subtilis: regulation and involvement in the biosyntheses of menaquinone and 2,3-dihydroxybenzoate (1996)

Bacillus subtilis has duplicate isochorismate synthase genes, menF and dhbC. Isochorismate synthase is involved in the biosynthesis of both the respiratory chain component menaquinone (MK) and the siderophore 2,3-dihydroxybenzoate (DHB). Several menF and dhbC deletion mutants were constructed to identify the contribution made by each gene product to MK and DHB biosynthesis. menF deletion mutants were able to produce wild-type levels of MK and DHB, suggesting that the dhbC gene product is able to compensate for the lack of MenF. However, a dhbC deletion mutant produced wild-type levels of MK but was DHB deficient, indicating that MenF is unable to compensate for the lack of DhbC. A menF dhbC double-deletion mutant was both MK and DHB deficient. Transcription analysis showed that expression of dhbC, but not of menF, is regulated by iron concentration. A dhbA'::lacZ fusion strain was constructed to examine the effects of mutations to the iron box sequence within the dhb promoter region. These mutations abolished the iron-regulated transcription of the dhb genes, suggesting that a Fur-like repressor protein exists in B. subtilis.
Production of Stevioside and Rubusoside Derivatives by Transfructosylation of<i>β</i>-Fructofuranosidase (1990)

Transfructosylated derivatives of the steviol glycosides stevioside and rubusoside were synthesized by β-fructofuranosidase from Arthrobacter sp. K-1. The enzyme transferred a fructosyl residue regioselectively to the glucosyl moiety at the 19-carboxyl group of these steviol glycosides by β-2,6-linkage. Evaluation of the sweetness of these fructosylated derivatives, in comparison with starting materials, found a great improvement in the quality of taste. Especially, the quality of taste of fructosyl-stevioside was superior to that of rebaudioside A, which is the best sweet principle in natural steviol glycosides in the intensity of sweetness as well as quality of the taste, being comparable to that of aspartame.
Cell Migration in the Vertebrate Embryo: Role of Cell Adhesion and Tissue Environment in Pattern Formation (1985)

Cells organize many of their biochemical reactions in non-membrane compartments. Recent evidence has shown that many of these compartments are liquids that form by phase separation from the cytoplasm. Here we discuss the basic physical concepts necessary ...Read More
Equilibrium Studies of a Fluorescent Paclitaxel Derivative Binding to Microtubules (1999)

A fluorescent derivative of paclitaxel, 3'-N-m-aminobenzamido-3'-N-debenzamidopaclitaxel (N-AB-PT), has been prepared in order to probe paclitaxel-microtubule interactions. Fluorescence spectroscopy was used to quantitatively assess the association of N-AB-PT with microtubules. N-AB-PT was found equipotent with paclitaxel in promoting microtubule polymerization. Paclitaxel and N-AB-PT underwent rapid exchange with each other on microtubules assembled from GTP-, GDP-, and GMPCPP-tubulin. The equilibrium binding parameters for N-AB-PT to microtubules assembled from GTP-tubulin were derived through fluorescence titration. N-AB-PT bound to two types of sites on microtubules (K(d1) = 61 +/- 7.0 nM and K(d2) = 3.3 +/- 0.54 microM). The stoichiometry of each site was less than one ligand per tubulin dimer in the microtubule (n(1) = 0.81 +/- 0.03 and n(2) = 0.44 +/- 0.02). The binding experiments were repeated after exchanging the GTP for GDP or for GMPCPP. It was found that N-AB-PT bound to a single site on microtubules assembled from GDP-tubulin with a dissociation constant of 2.5 +/- 0.29 microM, and that N-AB-PT bound to a single site on microtubules assembled from GMPCPP-tubulin with a dissociation constant of 15 +/- 4.0 nM. It therefore appears that microtubules contain two types of binding sites for paclitaxel and that the binding site affinity for paclitaxel depends on the nucleotide content of tubulin. It has been established that paclitaxel binding does not inhibit GTP hydrolysis and microtubules assembled from GTP-tubulin in the presence of paclitaxel contain almost exclusively GDP at the E-site. We propose that although all the subunits of the microtubule at steady state are the same "GDP-tubulin-paclitaxel", they are formed through two paths: paclitaxel binding to a tubulin subunit before its E-site GTP hydrolysis is of high affinity, and paclitaxel binding to a tubulin subunit containing hydrolyzed GDP at its E-site is of low affinity.
Sialochemistry in juvenile idiopathic arthritis (2002)

This data would suggest that there is both a reduced resting salivary flow and a reduced response to stimulation in JIA patients, which may contribute to a previously reported higher caries prevalence.
Nd: YAG capsulotomy for posterior capsule opacification after combined clear corneal phacoemulsification and vitrectomy (2009)

In our study, the most remarkable observation is that no complication occurred after the YAG capsulotomy, possibly because the eyes were vitrectomized and vitreous seems to play an important role in the occurrence of post-Nd:YAG complications. In addition we noted that PCO seems to occur earlier in the eyes undergoing combined surgery for cataract and ERM when compared with those where combined phacoemulsification and vitrectomy are performed for cataract and MH.
Sulfatide, a Specific Sugar Ligand for L-Selectin, Blocks CCI<sub>4</sub>-induced Liver Inflammation in Rats (1995)

The effects of sulfatide, which is a specific sugar ligand for L-selectin (LECAM-1), on CCl4-induced liver inflammation was studied in rats. Intramuscular pretreatment with sulfatide suppressed the levels of serum glutamic oxaloacetic transaminase (GOT) and glutamic pyruvic transaminase (GPT) that were increased by CCl4 injection, but galactosylceramide, a desulfated form of sulfatide, did not. A light-microscopic analysis found that the extent and the severity of lesions of the liver cells induced by CCl4 injection were significantly less in the rats treated with sulfatide. These results show that sulfatide suppresses the CCl4-induced liver inflammation by inhibiting the attachment of L-selectin expressing lymphocytes to their native sugar ligands.
Extraction Equilibria of Acetic and Propionic Acids from Dilute Aqueous Solution by Several Solvents (1992)

Abstract Extraction equilibria of acetic acid and propionic acid with hexane solutions of trioctyl amine, trioctyl phosphine oxide, and tributyl phosphate were studied. The species formed in the systems were estimated, and the distribution coefficients and the equilibrium constants for these species were evaluated.
The effect of hydroxychloroquine on glucose control and insulin resistance in the prediabetes condition (2016)

The use of hydroxychloroquine may increase the serum insulin level in patients with prediabetic states who are at risk of developing diabetes mellitus.
β,β‐Dimethylglutaric acid (2003)

Abstract β,β‐Dimethylglutaric acid product: β,β‐dimethylglutaric acid
Metal/Al2O3: A new class of x-ray mirrors (1996)

We have examined sputtered metal/Al2O3 multilayers (metal: Co, Pt, W) with respect to their suitability as x-ray mirrors in high temperature environments. The rf-sputtering technique leads to layered structures with interface roughnesses of only 0.2 nm as confirmed by x-ray scattering and transmission electron microscopy. In situ resistance measurements characterize the percolation process and indicate the lower thickness limits for the chosen materials which lead to minimum modulation periods of ≊2 nm. The samples were characterized after stepwise annealing up to 1000 °C. Reflectivity values of nearly 100% at the first satellite-reflection were found in the case of Pt and W (for λ=0.15418 nm). The most stable W/Al2O3 multilayer reflects 70% of the primary beam even after annealing at 900 °C.
USCG NDGPS Accuracy and Spatial Decorrelation Assessment (2012)

The United States Coast Guard (USCG) is a military, multi-mission, maritime service within the Department of Homeland Security (DHS). Its core roles are to protect the public, the environment, and U.S. economic and security interests in any maritime region in which those interests may be at risk. The USCG has become increasingly dependent on Global Navigation Satellite Systems (GNSS), especially the US Global Positioning Service (GPS), in order to conduct its missions more efficiently and effectively. The USCG has operated Nationwide Differential GPS (NDGPS) through a network of 85+ remote broadcast sites since 1999 to enhance user receiver position accuracy and integrity. Significant investments were made in recent years to enhance that system by replacing aging reference stations, integrity monitors, and transmitters with state of the art equipment. Results of preliminary and informal studies indicate increases in performance, specifically accuracy and availability, suggesting the need for a more formal review. The current performance standard for NDGPS dates back to the April 1993 Broadcast Standard, which requires a 10-meter (m) 2drms system over the coverage areas. This also is the basis for the US agreeing to Harbor and Harbor Approach requirements found in IALA R-121 and IMO Resolution A.953(23). The specification was derived based on spatial decorrelation, or the degradation of the accuracy of the DGPS correction over increasing baselines between the reference station and rover, as well as in the Horizontal Dilution of Precision (HDOP). The 10m standard also accounted for Selective Availability (S/A), an intentional degradation of the GPS signal applied in order to provide the intended military user with more precise accuracies than was available to civilian users. S/A was turned off by direction of a Presidential Order in 2000. The present GPS L1 Standard Positioning Service (SPS) performance specification is error ≤ 7.8m (2drms) for single frequency Course Acquisition (C/A) code, global average User Range Error (URE) during normal operations. The combination of this current GPS performance statement, preliminary studies of positioning performance following recent NDGPS recapitalization, and the disabling of S/A, together necessitate a detailed re-evaluation of the performance of the current NDGPS system and refinement of the spatial decorrelation model. The primary objectives of this study are to determine the accuracy of the NDGPS for the typical user and the development of an updated spatial decorrelation model for performance as a function of distance from the NDPGS reference site (the current model from the 1993 Broadcast Standard, is 2 meters plus 1 meter per 150 km from the beacon site). Simulation, software processing of existing GPS data sets (available from the Continuously Operating Reference Station or CORS, network) at a collection of spatially dispersed sites with the same NDGPS corrections, and actual field measurements at selected sites provides data for these objectives. This current paper provides results from all testing to date.
Development of LS-LDS combined process and material enabling simultaneous activation during additive manufacturing process (2018)

Integration of laser sintering of plastic powder and laser direct structuring using CO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> laser for the both of laser sintering and laser activation is discussed. Feasibility of activation by CO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> laser is investigated, and chromium copper oxide can be used as an agent for the integrated system. Activation can be enhanced by adding active carbon. It is revealed that surface of a part is melted on activation, and flow of the melt affects the activation quality while high flowability of the melt preferable for improvement of relative density.
An Animated Guide©: SAS Editor Regular Expressions (2008)

The SAS® editor has implemented regular expression search and replace in the replace window. Clicking on the arrow to the right of the find text box causes the editor to display the drop down box of regular expression hints that can be seen below. If one knows the syntax of regular expressions, one can type the expression in without using the drop down menu. While this could have been very useful in helping SAS users learn regular expressions, not all PERL expressions have been implemented. This paper discusses the features that were, and were not implemented in the Enhanced Editor and compares the feature list to REGEXP coding.
Hot electron emission lithography (1998)

We have developed an electron lithography method, hot electron emission lithography, which is capable of printing integrated circuits with an exposure time of only a few seconds. The basic design and fabrication of the patterned electron emitting mask made by standard metal–oxide–semiconductor technology will be discussed, and its applicability in a simple 1:1 e-beam stepper will be demonstrated. Patterns with a minimum feature size of 160 nm have been printed successfully. Further improvements in resolution to 50 nm appear to be possible.
Extinctive prescription and construction claims : the law (2013)

Extinctive refers to the extinction of a right or claim due to a time lapse. The notion of extinctive prescription encourages claimants to pursue claims with due expedition and in a manner that does not unduly prejudice a defendant in its defence.
A 100 nm CMOS technology with "sidewall-notched" 40 nm transistors and SiC-capped Cu/VLK interconnects for high performance microprocessor applications (2003)

A 40 nm CMOS transistor, an ultra high density 6T SRAM cell, and 10-level Cu interconnects and very-low-k (VLK) dielectrics for high performance microprocessor applications are presented. Key process features are the following: (1) High-NA 193 nm photolithography with phase shift mask and optical proximity correction (OPC) allows 40 nm gate length and the smallest 6T SRAM cell (<1 /spl mu/m/sup 2/). (2) A unique transistor feature which is referred to as "sidewall-notched gate" enables an optimal pocket implant placement and suppresses variations of the notch width much better than poly-notched gate structure. (3) 1.1 nm nitrided oxide (1.9 nm inversion T/sub ox/) is used to achieve high drive current, and the thermal budget is reduced to suppress the boron penetration. (4) SiC-capped Cu/SiLK structure in 0.28 /spl mu/m pitch metal 1-4 layers realizes k/sub eff/ of 3.0.
A Life-Threatening Complication of Percutaneous Central Venous Catheters in Neonates (1992)

Sir .—The modern Neonatal Intensive Care Unit cares for increasing numbers of premature infants with birth weights below 1000 g. These infants usually require prolonged parenteral nutrition for survival. Increasingly, percutaneously inserted, small-diameter Silastic catheters are being used as alternatives to surgically placed central lines in high-risk neonates. Use of these intravascular lines is, however, not without hazard. This report describes a preterm infant who developed cardiac tamponade with a fatal outcome while receiving total parenteral nutrition via a Silastic central venous catheter. Patient Report .—A 580-g preterm infant of 24 weeks' gestation was delivered to a 30-year-old woman with a hitherto normal pregnancy. Cesarean section was necessitated by severe antepartum hemorrhage. Exogenous bovine surfactant administered at birth reduced the fraction of inspired oxygen to 0.23 within a few hours of birth. A dopamine hydrochloride infusion was required during the first 36 hours of life to maintain a satisfactory blood
Synthesis of<i>C</i>‐Aryl‐flavonoid Derivatives via Suzuki‐Miyaura Coupling Reaction<sup>†</sup> (2006)

Abstract A variety of 4′‐ and 3‐ C ‐aryl‐quercetin derivatives were conveniently synthesized via Suzuki‐Miyaura coupling of the corresponding quercetin‐ O ‐triflates with aryl boronic acids or boronates.
Interferon-stimulated transcription and innate antiviral immunity require deacetylase activity and histone deacetylase 1 (2003)

The use of histone deacetylase (HDAC) inhibitors has revealed an essential role for deacetylation in transcription of IFN-responsive genes. The HDAC1 protein associates with both signal transducer and activator of transcription (STAT) 1 and STAT2, and IFN-alpha stimulation induces deacetylation of histone H4. Inhibition of HDAC1 by small interfering RNA (siRNA) decreases IFN-alpha responsiveness whereas expression of HDAC1 augments the IFN-alpha response, demonstrating that HDAC1 modulates IFN-alpha-induced transcription. Importantly, the innate antiviral response is inhibited in the absence of deacetylase activity. The requirement for deacetylase is shared by IFN-gamma transcription response and may represent a general requirement for STAT-dependent gene expression.
Pitch dependent phone modelling for HMM based speech recognition (1992)

The authors propose a novel method of incorporating pitch information into a hidden Markov model (HMM) phoneme recognizer by exploiting the correlation between pitch and spectral parameters, e.g. cepstrum. Pitch patterns are not used explicitly; instead, spectral parameters are normalized framewise according to the pitch value. Evidence is given to show that the use of pitch information consistently improves the recognition performance. Experiments with 24 phoneme labels showed that the phoneme error rate for fast continuous speech could be improved by about 10%.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Novel switching phenomena in ferroelectric Langmuir–Blodgett films (1995)

We have established ferroelectric switching and observed a novel conductance switching phenomenon in ferroelectric polymer films fabricated by the Langmuir–Blodgett technique. The films consist of 10–30 monolayers (ML) of a copolymer of vinylidene fluoride (70%) and trifluoroethylene (30%), exhibiting a first-order ferroelectric phase transition at 70 °C and nearly rectangular ferroelectric and conductance hysteresis at 24 °C. Ferroelectric switching is accompanied by switching of the conductance by three orders of magnitude. A model describing this switching phenomenon is proposed.
Adenoviruses as gene/vaccine delivery vectors: promises and pitfalls (2014)

Decades of efforts have resulted in understanding various aspects of human Ad 5 biology as well as the in vivo behavior of vectors derived from this serotype. While this vector has shown great potential, some of the limitations highlighted in recent studies have reinforced the quest for an ideal vector derived from novel Ads. Combinatorial approaches to address the various limitations of the existing vectors must be pursued to develop novel vectors with enhanced clinical potential.