gebhart/patrepeval huggingface dataset:
Incidence of Impact Trauma With Cranial Injuries Ascribed to Shaking (1990)

Shaking as a mechanism of severe brain injury in infants has been challenged on a theoretical basis as insufficient to explain the magnitude of observed injuries. Computed tomography and magnetic resonance imaging, developed since shaken baby syndrome was first described, are helpful in establishing whether external trauma occurred for infants thought to have been shaken. We compiled data from 24 infants initially diagnosed as having shaken baby syndrome, including physical examination, roentgenograms, computed tomography or magnetic resonance imaging, and autopsy (when applicable). Half of the patients showed no evidence of direct impact, and evidence of external trauma was not predictive of a fatal outcome. These findings indicate that shaking by itself is sufficient to cause severe or fatal intracranial injury and that the shaken baby syndrome reflects a spectrum of such child abuse injuries that may include direct trauma or only shaking.
Rapid Digestion of Cry34Ab1 and Cry35Ab1 in Simulated Gastric Fluid (2003)

Two genes were identified in Bacillus thuringiensis Berliner (Bt) that code for the proteins that comprise a Cry34Ab1/Cry35Ab1 binary insecticidal crystal protein. Maize, Zea mays L., plants have been transformed to express the Cry34Ab1/Cry35Ab1 proteins, and as a result, these plants are resistant to attack by western corn rootworm, Diabrotica virgifera virgifera LeConte, a major pest in the Midwestern corn-growing area of the U.S.A. As part of the safety assessment for the proteins, digestibility studies were conducted. Digestion experiments with both proteins demonstrated rapid degradation in simulated gastric fluid, comparable to other registered plant-incorporated protectants. Quantitative and qualitative approaches for determining digestibility are illustrated.
Transistor laser with emission wavelength at 1544nm (2008)

Data are presented demonstrating continuous wave laser operation at −185°C of an InP–InAlGaAs–InAlAs double heterojunction bipolar transistor with strained InGaAs quantum wells incorporated in the p-type base region. The laser exhibits a peak wavelength λ∼1544nm when biased in the forward active mode in the common-emitter configuration. A threshold current IB=10mA is observed.
Defining parameters for homology-tolerant database searching. (2004)

De novo interpretation of tandem mass spectrometry (MS/MS) spectra provides sequences for searching protein databases when limited sequence information is present in the database. Our objective was to define a strategy for this type of homology-tolerant database search. Homology searches, using MS-Homology software, were conducted with 20, 10, or 5 of the most abundant peptides from 9 proteins, based either on precursor trigger intensity or on total ion current, and allowing for 50%, 30%, or 10% mismatch in the search. Protein scores were corrected by subtracting a threshold score that was calculated from random peptides. The highest (p < .01) corrected protein scores (i.e., above the threshold) were obtained by submitting 20 peptides and allowing 30% mismatch. Using these criteria, protein identification based on ion mass searching using MS/MS data (i.e., Mascot) was compared with that obtained using homology search. The highest-ranking protein was the same using Mascot, homology search using the 20 most intense peptides, or homology search using all peptides, for 63.4% of 112 spots from two-dimensional polyacrylamide gel electrophoresis gels. For these proteins, the percent coverage was greatest using Mascot compared with the use of all or just the 20 most intense peptides in a homology search (25.1%, 18.3%, and 10.6%, respectively). Finally, 35% of de novo sequences completely matched the corresponding known amino acid sequence of the matching peptide. This percentage increased when the search was limited to the 20 most intense peptides (44.0%). After identifying the protein using MS-Homology, a peptide mass search may increase the percent coverage of the protein identified.
A skeletal-based solid editor (1999)

This paper explores the concept of using skeletons as the basis for constructing a solid-editing system. Skeletal data (i.e., the skeleton and the associated maximal sphere radii) offers a valid solid representation scheme, and we examine the capability of the skeletal representation to support shape editing operations. In addition to general discussion of the capabilities of skeletalbased methods, we also present concrete examples of editing operations reahzed in a recent implementation of a skeletonbased solid editor. The im lemented skeletal-based editor imports polyhedral solids or po yhedral approximations of solids) by I, p computing their s eletal data. The editor then displays the skeletal data and provides a simple interface for editing both the skeleton and the sphere radii. The edited skeleton is then "refleshed", based on the edited skeletal data, to reconstruct the edited solid. The reconstructed solid is represented as the halfspace associated with an implicit tinction, and polygonization methods can be applied to produce output that, like the input, is polyhedral. Editing operations illustrated correspond to stretching, bending, rounding, and uniform or non-uniform thickening of the solid. Discussions of the key enabling technologies including skeletonization, and polygonization are also presented.
Different Domain Interactions Are Involved in the Binding of Tissue Inhibitors of Metalloproteinases to Stromelysin-1 and Gelatinase A (1994)

The matrix metalloproteinases gelatinase A and stromelysin-1 have definable N-terminal (catalytic) and C-terminal domains. In order to analyze their interactions with the N- and C-terminal domains of the tissue inhibitors of metalloproteinases TIMP-1 and -2, mutants of both the enzymes and the inhibitors were prepared in which the C-terminal domains had been deleted. Since the Ki values for TIMP inhibition of the matrix metalloproteinases are in the picomolar range, it was not possible to measure these accurately within the sensitivity of available activity assays. Rate constants for the association of the wild-type proteins were therefore determined and systematically compared with those for the deletion mutants. It was found that TIMP-1 binds more rapidly than TIMP-2 to stromelysin-1 and that the C-terminal domain of the enzyme does not affect the rate of association of enzyme and inhibitor. This is in contrast to gelatinase A, where the C-terminal domain has been shown to play an important role in increasing the rate of complex formation with the TIMPs (Willenbrock et al., 1993). The TIMPs are also comprised of an N- and C-terminal domain. By deletion mutagenesis, we found that the C-terminal domain of both TIMPs contributed less to the rate of complex formation with stromelysin-1 than to that with gelatinase A. Hybrids of the N- and C-terminal domains of gelatinase A and stromelysin-1 were prepared and used to analyze further the differences in domain interactions with the TIMPs. They demonstrated that the interactions between the C-terminal domains of enzyme and inhibitor can occur irrespective of the nature of the N-terminal domain. We can conclude that the TIMPs have two major binding regions which associate in different ways with the domains of the enzymes gelatinase A and stromelysin-1. The N-terminal domains of the TIMPs bind to the enzyme catalytic domains to inhibit activity. The TIMP C-terminal domain acts to increase the association rate constant by binding to the N-terminal domain of stromelysin or the C-terminal domain of gelatinase A.
Formation of Zein Microphases in Ethanol−Water (2010)

Zein, a major protein of corn, is soluble in binary mixtures of ethanol and water. It has an amphiphilic character and is capable of self-assembly into nano- and microsized rods, spheres, and films upon solvent evaporation. The formation of microspheres is of particular interest for the development of delivery systems. Control over structure formation requires a better understanding of zein behavior in solution. The objective of this work was to investigate the effect of zein concentration and the effect of ethanol-water ratio on the microphase behavior of zein solutions, believed to govern the morphology of microstructures after solvent evaporation. The Flory-Huggins solution theory was applied to model boundary lines between microphases in solution. The study generated information on the zein concentration-ethanol/water ratio conditions where microspheres are formed and provided insight into the microphase behavior of zein ethanolic solutions.
Synthesis of a Dibenz(b,e)oxepin-Bovine Serum Albumin Conjugate for Radioimmunoassay of KW-4679((Z)-11-(3-(Dimethylamino)propylidene)-6,11-dihydrodibenz(b,e)oxepin-2-acetic Acid Hydrochloride). (1992)

(Z)-11-[3-(Dimethylamino)propylidene]-2-(methoxycarbonyl)methyl-6, 11- dihydrodibenz[b,e]oxepin-9-acrylic acid (5) was prepared for application to the radioimmunoassay of KW-4679 (1, (Z)-11-[3-(dimethylamino)propylidene]-6,11-dihydrodibenz[b,e ] oxepin-2-acetic acid hydrochloride). The acrylic acid moiety in the 9-position of 5 was employed for coupling with an amino group of bovine serum albumin (BSA) to provide 17. Subsequently, the conjugate 17 was treated with aqueous NaOH to hydrolyze the terminal methoxycarbonyl group in the 2-position of the BSA conjugated 5. Antiserum raised against the antigenic BSA-conjugate 4 finally obtained was specific for 1.
Efficacy of vitamin C as an adjunct to fluoxetine therapy in pediatric major depressive disorder: a randomized, double-blind, placebo-controlled pilot study (2013)

These preliminary results suggest that vitamin C may be an effective adjuvant agent in the treatment of MDD in pediatric patients.
High-Level Production of Recombinant Human Parathyroid Hormone 1-34 (1998)

Expression of the synthetic human parathyroid hormone 1-34 [hPTH(1-34)] gene by a gene fusion strategy was demonstrated. hPTH(1-34) was produced at the C terminus of the partner peptides involving amino acids 1 to 97, 1 to 117, or 1 to 139 of a modified Escherichia coli beta-galactosidase by linker peptides containing oligohistidine of different lengths. The fusion proteins in the inclusion bodies were rendered soluble with urea and subjected to site-specific cleavage with the secretory type yeast Kex2 protease. Optimal expression and enzymatic processing were achieved in the fusion protein beta G-117S4HPT, constructed from amino acids 1 to 117 of beta-galactosidase and the linker of HHHHPGGSVKKR. The fusion protein accumulated more than 20% of the E. coli total protein. The hPTH(1-34) was purified up to 99.5% with a good yield of 0.5 g/liter of culture. The purified product was identified as intact hPTH(1-34) by amino acid analysis and N-terminal sequencing.
Differential Impact of Systolic and Diastolic Blood Pressure Level on JNC-VI Staging (1999)

The sixth Report of the Joint National Committee on Prevention, Detection, Evaluation, and Treatment of High Blood Pressure classifies blood pressure into stages on the basis of both systolic (SBP) and diastolic (DBP) blood pressure levels. When a disparity exists between SBP and DBP stages, patients are classified into the higher stage ("up-staged"). We evaluated the effect of disparate levels of SBP and DBP on blood pressure staging and eligibility for therapy. We examined 4962 Framingham Heart Study subjects between 1990 and 1995 and determined blood pressure stages on the basis of SBP alone, DBP alone, or both. After the exclusion of subjects on antihypertensive therapy (n=1306), 3656 subjects (mean age 58+/-13 years; 55% women) were eligible. In this sample, 64.6% of subjects had congruent stages of SBP and DBP, 31.6% were up-staged on the basis of SBP, and 3.8% on the basis of DBP; thus, SBP alone correctly classified JNC-VI stage in approximately 96% (64.6%+31.6%) of the subjects. Among subjects >60 years of age, SBP alone correctly classified 99% of subjects; in those </=60 years old, SBP alone correctly classified 95%. Of 1488 subjects with high-normal blood pressure or hypertension, who were potentially eligible for drug therapy, 13.0% had congruent elevations of SBP and DBP, 77.7% were up-staged on the basis of SBP, and 9.3% were up-staged on the basis of DBP; SBP alone correctly classified 91%, whereas DBP alone correctly classified only 22%. SBP elevation out of proportion to DBP is common in middle-aged and older persons. SBP appears to play a greater role in the determination of JNC-VI blood pressure stage and eligibility for therapy. Given these results, combined with evidence from hypertension treatment trials, future guidelines might consider a greater role for SBP than for DBP in determining the presence of hypertension, risk of cardiovascular events, eligibility for therapy, and benefits of treatment.
Polymerlike <i>C:H</i> Thin Film Coating of Nanopowders in Capacitively Coupled RF Discharge (2003)

Abstract Nanopowders of amorphous SiO2, with typical particle sizes of 30-80 nm, were treated under non-equilibrium plasma conditions created by a capacitively coupled (CC) RF discharge in pure methane or ethane. The gas flow rate was varied between 0.02-0.06 slpm, with reactor pressures maintained between 1000 and 5000 Pa, and applied RF power inputs between 700 and 1500 W. The plasma properties were monitored through measurements of the C2 rotational and the atomic hydrogen excitation temperatures. The compositions of the gases that passed through the plasma were analyzed by mass-spectrometry. In spite of the evidence indicating the presence of CnH2n+2 and CnH2n (n=1-3) species, as well as acetylene, in the discharge, the homogeneous formation of soot was not observed. At the same time, introduced nanoparticles acted as centers for the inception and growth of C:H thin coatings in the form of polymer-like hydrocarbon layers, whose thickness lay between &lt; 5 - 30 nm. The results of TEM, IR spectroscopy, thermo-gravimetric and precision calorimetric analyses performed on the plasma treated powders provided evidence for the formation of an amorphous, high density C:H matrix on particles' surfaces.
An Efficient and User-friendly Sinhala Input Method Based on Phonetic Transcription (2007)

We propose an application-independent Sinhala character input method called Sri Shell with a principled key assignment based on phonetic transcription of Sinhala characters. A good character input method should fulfill two criteria, efficiency and user-friendliness. We have introduced several quantification methods to quantify the efficiency and user-friendliness of Sinhala character input methods. Experimental results prove the efficiency and user-friendliness of our proposed method.
Quantitative determination of the binding of epsilon-aminocaproic acid to native plasminogen. (1978)

The binding of epsilon-amino[14C]caproic acid (6-aminohexanoic acid, EACA) to native human plasminogen was determined using the ultrafiltration technique of Paulus (Paulus, H. (1969) Anal. Biochem. 32, 91-100) at free ligand concentrations ranging from 2 micrometer to 16 mM. One strong binding site (Kd = 0.009 mM) and approximately five weaker ones (Kd = 5 mM) were found. The constants were obtained by fitting the experimental points to the simple assumption of two sets of noninteracting sites. The distinct separation of the two kinds of sites allowed the correlation of the well known epsilon-aminocaproic acid-induced conformational transition in plasminogen with the saturation of the weaker group of binding sites by this ligand. The conformational transition was monitored by measurements of the sedimentation coefficient, as was done by others earlier. The midpoint of the transition occurred at approximately 3.3 mM free ligand. A dissociation constant of 0.32 mM was also obtained for L-lysine by measurements of the competition between this compound and labeled epsilon-aminocaproic acid for the strong binding site. The correlation between epsilon-aminocaproic acid binding and effects of the compound on various physical and functional properties is discussed. A discussion of the possible sources of error encountered in the technique used is also included.
PCR Detection of Polycyclic Aromatic Hydrocarbon-Degrading Mycobacteria (1995)

Polymerase chain reaction (PCR) methods based on the 16S rRNA genes of Mycobacterium sp. PYR-1 and Mycobacterium sp. PAH135, known PAH-degrading bacteria, were developed. An efficient mycobacterial cell lysis procedure was used for the PCR assay. The PCR methods were positive with the target species, but negative for the other 45 bacterial species tested including other Mycobacterium spp. The PCR sensitivity for pure cultures was 20 cells for Mycobacterium sp. PAH135 and 200 cells for Mycobacterium sp. PYR-1. The PCR with a simple sample preparation procedure was used to monitor Mycobacterium sp. PYR-1 cell concentrations in soil slurries amended with [14C]pyrene. The pyrene mineralization correlated with the Mycobacterium PYR-1 cell concentrations in the soil slurries. When the PCR titer (the maximum dilution for positive PCR results) reached 10-4−10-5 at 5−10 days incubation, approximately 50% of the [14C]pyrene had been mineralized to 14CO2. However, without inoculation with Mycobacterium PYR-1 cells, both the sterile and nonsterile soils had negative PCR results and no pyrene mineralization.
Exploring the potential of the glycerol-3-phosphate dehydrogenase 2 (GPD2) promoter for recombinant gene expression in Saccharomyces cerevisiae (2015)

A control point for keeping redox homeostasis in <i>Saccharomyces cerevisiae</i> during fermentative growth is the dynamic regulation of transcription for the glycerol-3-phosphate dehydrogenase 2 (<i>GPD2</i>) gene. In this study, the possibility to steer the activity of the <i>GPD2</i> promoter was investigated by placing it in strains with different ability to reoxidise NADH, and applying different environmental conditions. Flow cytometric analysis of reporter strains expressing green fluorescent protein (<i>GFP</i>) under the control of the <i>GPD2</i> promoter was used to determine the promoter activity at the single-cell level<i>.</i> When placed in a <i>gpd1Δgpd2Δ</i> strain background, the <i>GPD2</i> promoter displayed a 2-fold higher activity as compared to the strong constitutive glyceraldehyde-3-phosphate dehydrogenase (<i>TDH3</i>). In contrast, the <i>GPD2</i> promoter was found to be inactive when cells were cultivated in continuous mode at a growth rate of 0.3 h<sup>-1</sup> and in conditions with excess oxygen (i.e. with an aeration of 2.5 vvm, and a stirring of 800 rpm). In addition, a clear window of operation where the <i>gpd1Δgpd2Δ</i> strain can be grown with the same efficiency as wild type yeast was identified. In conclusion, the flow cytometry mapping revealed conditions where the <i>GPD2</i> promoter was either completely inactive or hyperactive, which has implications for its implementation in future biotechnological applications such as for process control of heterologous gene expression.
Solid Cancers after Bone Marrow Transplantation (1997)

Patients undergoing bone marrow transplantation have an increased risk of new solid cancers later in life. The trend toward an increased risk over time after transplantation and the greater risk among younger patients indicate the need for life-long surveillance.
Peptide- and saccharide-conjugated dendrimers for targeted drug delivery: a concise review (2012)

Dendrimers comprise a category of branched materials with diverse functions that can be constructed with defined architectural and chemical structures. When decorated with bioactive ligands made of peptides and saccharides through peripheral chemical groups, dendrimer conjugates are turned into nanomaterials possessing attractive binding properties with the cognate receptors. At the cellular level, bioactive dendrimer conjugates can interact with cells with avidity and selectivity, and this function has particularly stimulated interests in investigating the targeting potential of dendrimer materials for the design of drug delivery systems. In addition, bioactive dendrimer conjugates have so far been studied for their versatile capabilities to enhance stability, solubility and absorption of various types of therapeutics. This review presents a brief discussion on three aspects of the recent studies to use peptide- and saccharide-conjugated dendrimers for drug delivery: (i) synthesis methods, (ii) cell- and tissue-targeting properties and (iii) applications of conjugated dendrimers in drug delivery nanodevices. With more studies to elucidate the structure-function relationship of ligand-dendrimer conjugates in transporting drugs, the conjugated dendrimers hold promise to facilitate targeted delivery and improve drug efficacy for discovery and development of modern pharmaceutics.
RevMiner (2012)

Smartphones are convenient, but their small screens make searching, clicking, and reading awkward. Thus, perusing product reviews on a smartphone is difficult. In response, we introduce RevMiner - a novel smartphone interface that utilizes Natural Language Processing techniques to analyze and navigate reviews. RevMiner was run over 300K Yelp restaurant reviews extracting attribute-value pairs, where attributes represent restaurant attributes such as sushi and service, and values represent opinions about the attributes such as fresh or fast. These pairs were aggregated and used to: 1) answer queries such as "cheap Indian food", 2) concisely present information about each restaurant, and 3) identify similar restaurants. Our user studies demonstrate that on a smartphone, participants preferred RevMiner's interface to tag clouds and color bars, and that they preferred RevMiner's results to Yelp's, particularly for conjunctive queries (e.g., "great food and huge portions"). Demonstrations of RevMiner are available at revminer.com.
Large eddy simulation study of fully developed wind-turbine array boundary layers (2010)

It is well known that when wind turbines are deployed in large arrays, their efficiency decreases due to complex interactions among themselves and with the atmospheric boundary layer (ABL). For wind farms whose length exceeds the height of the ABL by over an order of magnitude, a “fully developed” flow regime can be established. In this asymptotic regime, changes in the streamwise direction can be neglected and the relevant exchanges occur in the vertical direction. Such a fully developed wind-turbine array boundary layer (WTABL) has not been studied systematically before. A suite of large eddy simulations (LES), in which wind turbines are modeled using the classical “drag disk” concept, is performed for various wind-turbine arrangements, turbine loading factors, and surface roughness values. The results are used to quantify the vertical transport of momentum and kinetic energy across the boundary layer. It is shown that the vertical fluxes of kinetic energy are of the same order of magnitude as the power extracted by the forces modeling the wind turbines. In the fully developed WTABL, the kinetic energy extracted by the wind turbines is transported into the wind-turbine region by vertical fluxes associated with turbulence. The results are also used to develop improved models for effective roughness length scales experienced by the ABL. The effective roughness scale is often used to model wind-turbine arrays in simulations of atmospheric dynamics at larger (regional and global) scales. The results from the LES are compared to several existing models for effective roughness lengths. Based on the observed trends, a modified model is proposed, showing improvement in the predicted effective roughness length.