gebhart/patrepeval huggingface dataset:
Molecular Beam Epitaxy of III-V Compounds: Technology and Growth Process (1981)

Molecular beam epitaxy (MBE) has now become a versatile technique for growing expitaxial thin films of semiconductors and metals by impinging thermal energy beams of atoms or molecules onto a heated substrate under ultra-high vacuum (UHV) conditions. Compared to the more established techniques of liquid phase epitaxy (LPE) and vapor phase epitaxy (VPE), the characteristic features of MBE are (a) the slow growth rate of 0.1-2.0 �m/hr that permits very precise control of layer thickness in the sub micron range; (b) the reduced growth temperature, e.g. 500600°C for GaAs, which is low enough not to disturb abrupt composi­ tional or doping profiles because of negligible bulk diffusion; ( c) the specific non equilibrium growth mechanism that is responsible for pro­ gressive smoothing of the surface for most substrate orientations; (d) the ability to abruptly cease or initiate molecular beams that produces hyperabrupt material interfaces and dopant profiles; and (e) the facility for in situ analysis to assure that the desired surface and reaction conditions are reached before commencement of growth and are main­ tained during crystal growth. Based on its potential for excellent dimensional control even over large lateral dimensions, the MBE process can uniquely tailor the electronic
Segmentation and measurement of the cortex from 3-D MR images using coupled-surfaces propagation (1999)

The cortex is the outermost thin layer of gray matter in the brain; geometric measurement of the cortex helps in understanding brain anatomy and function. In the quantitative analysis of the cortex from MR images, extracting the structure and obtaining a representation for various measurements are key steps. While manual segmentation is tedious and labor intensive, automatic reliable efficient segmentation and measurement of the cortex remain challenging problems, due to its convoluted nature. Here we present a new approach of coupled-surfaces propagation, using level set methods to address such problems. Our method is motivated by the nearly constant thickness of the cortical mantle and takes this tight coupling as an important constraint. By evolving two embedded surfaces simultaneously, each driven by its own image-derived information while maintaining the coupling, a final representation of the cortical bounding surfaces and an automatic segmentation of the cortex are achieved. Characteristics of the cortex, such as cortical surface area, surface curvature, and cortical thickness, are then evaluated. The level set implementation of surface propagation offers the advantage of easy initialization, computational efficiency, and the ability to capture deep sulcal folds. Results and validation from various experiments on both simulated and real three-dimensional (3-D) MR images are provided.
Investigation of intact protein complexes by mass spectrometry (2004)

Mass spectrometry has grown in recent years to a well-accepted and increasingly important complementary technique in structural biology. Especially electrospray ionization mass spectrometry is well suited for the detection of non-covalent protein complexes and their interactions with DNA, RNA, ligands, and cofactors. Over the last decade, significant advances have been made in the ionization and mass analysis techniques, which makes the investigation of even larger and more heterogeneous intact assemblies feasible. These technological developments have paved the way to study intact non-covalent protein-protein interactions, assembly and disassembly in real time, subunit exchange, cooperativity effects, and effects of cofactors, allowing us a better understanding of proteins in cellular processes. In this review, we describe some of the latest developments and several highlights.
Automatic Estimation of Fetal Abdominal Circumference From Ultrasound Images (2017)

Ultrasound diagnosis is routinely used in obstetrics and gynecology for fetal biometry, and owing to its time-consuming process, there has been a great demand for automatic estimation. However, the automated analysis of ultrasound images is complicated because they are patient specific, operator dependent, and machine specific. Among various types of fetal biometry, the accurate estimation of abdominal circumference (AC) is especially difficult to perform automatically because the abdomen has low contrast against surroundings, nonuniform contrast, and irregular shape compared to other parameters. We propose a method for the automatic estimation of the fetal AC from two-dimensional ultrasound data through a specially designed convolutional neural network (CNN), which takes account of doctors' decision process, anatomical structure, and the characteristics of the ultrasound image. The proposed method uses CNN to classify ultrasound images (stomach bubble, amniotic fluid, and umbilical vein) and Hough transformation for measuring AC. We test the proposed method using clinical ultrasound data acquired from 56 pregnant women. Experimental results show that, with relatively small training samples, the proposed CNN provides sufficient classification results for AC estimation through the Hough transformation. The proposed method automatically estimates AC from ultrasound images. The method is quantitatively evaluated and shows stable performance in most cases and even for ultrasound images deteriorated by shadowing artifacts. As a result of experiments for our acceptance check, the accuracies are 0.809 and 0.771 with expert 1 and expert 2, respectively, whereas the accuracy between the two experts is 0.905. However, for cases of oversized fetus, when the amniotic fluid is not observed or the abdominal area is distorted, it could not correctly estimate AC.
Auger and x-ray electron spectroscopy studies of <i>h</i>BN, <i>c</i>BN, and N+2 ion irradiation of boron and boron nitride (1990)

Boron and nitrogen KVV Auger electron spectroscopy (AES) and core level x-ray photoelectron spectroscopy (XPS) features are shown to be conspicuously different for the cubic and hexagonal phases of boron nitride, i.e., cBN and hBN, respectively. The origin and assignments of these features are discussed in terms of the valence band density of states and plasmon losses. Application of these results to the identification of the boron nitride phase formed by N+2 irradiation of boron and N+2 or Ar+ irradiation of cubic boron nitride are presented.
Rabbit muscle extracts catalyze the specific removal of N-acetylmethionine from acetylated peptides. (1986)

Rabbit muscle has been found to contain an activity that catalyzes the specific removal of Ac-Met from acetylated peptides. The activity is associated with free ribosomes and microsomes in the rabbit muscle extract but can be removed from these subcellular fractions by exposure to 0.5 M NaCl in the presence of 2 mM MgCl2; only partial removal was achieved with microsomes, but complete removal with ribosomes. A nearly 200-fold enrichment of the activity was achieved by this simple succession of differential centrifugation and salt extraction. Eighteen 14C-acetylpeptides have been tested as substrates for the partially purified activity assaying for the production of free 14C-acetylamino acid by high performance liquid chromatography. None of the peptides containing N-terminal acetylated Ala, Asp, Ser, or Gly were cleaved at a significant rate. Six of a total of eight peptides containing N-terminal Ac-Met were cleaved by the ribosomal extract at different rates. The active substrates varied in length from tri- to undecapeptides. The activity is inhibited by high concentrations of the protease inhibitor phenylmethylsulfonyl fluoride. Based on these observations, we tentatively conclude that the activity satisfy the criteria of a general N-terminal protein processing enzyme: it can remove Ac-Met from most, but not all, N-terminal sequences and appears to be inactive toward the N-terminal acetylamino acids most commonly found in eukaryotic proteins.
A Multi-Wall Carbon Nanotube Tower Electrochemical Actuator (2006)

Patterned multiwall carbon nanotube arrays up to four millimeters long were synthesized using chemical vapor deposition. Electrochemical actuation of a nanotube array tower was demonstrated in a 2 M NaCl solution at frequencies up to 10 Hz with 0.15% strain using a 2 V square wave excitation. The synthesis and electrochemical modeling approach outlined in the paper provide a foundation for the design of nanotube smart materials that actuate and are load bearing.
Molecular Cloning, Splice Variants, Expression, and Purification of Phospholipase C-δ;4 (1996)

Complementary DNAs encoding a previously unidentified phosphoinositide-specific phospholipase C (PLC) isozyme were cloned from a rat brain cDNA library by the polymerase chain reaction with degenerate oligonucleotide primers based on sequences common to three known delta-type PLC isozymes. The encoded polypeptide contains 772 amino acids (calculated molecular mass, 88,966 daltons) and is similar in primary structure to delta-type PLC isozymes, with overall sequence identities of 45% to PLC-delta 1, 72% to PLC-delta 2, and 47% to PLC-delta 3. Thus, the new PLC isozyme was named PLC-delta 4. Recombinant PLC-delta 4 was purified from extracts of HeLa cells that had been infected with vaccinia virus containing the corresponding cDNA. The purified protein exhibited an apparent molecular mass of 90 kDa on SDS-polyacrylamide gels. The specific activity of PLC-delta 4 and its dependence on Ca2+ were similar to those of PLC-delta 1. The distribution of PLC-delta 4 in 16 different rat tissues was studied by immunoblot analysis with PLC-delta 4-specific antibodies of fractions obtained after an enzyme-enrichment procedure. The 90-kDa immunoreactive protein was detected unambiguously in only eight tissues and was present at concentrations that were low compared to those of other major PLC isozymes. A 93-kDa immunoreactive protein was also prominent in testis but was not detected in the other seven positive tissues. The 93-kDa enzyme appears to be derived from a splice variant of the mRNA that encodes the 90-kDa PLC-delta 4 and contains an additional 32 amino acids between the X and Y catalytic domains. Splice variants have not previously been detected for delta-type PLC isozymes.
Tumour markers for managing men who present with metastatic prostate cancer and serum prostate‐specific antigen levels of <10 ng/mL (2005)

In this patient group, immunohistochemical assessments of PSMA and AR are potentially useful as diagnostic markers.
A 40 nm 512 kb Cross-Point 8 T Pipeline SRAM With Binary Word-Line Boosting Control, Ripple Bit-Line and Adaptive Data-Aware Write-Assist (2014)

This paper presents a cross-point 512 kb 8 T pipeline static random-access memory (SRAM). The cross-point structure eliminates write half-select disturb to facilitate bit-interleaving architecture for enhanced soft error immunity. The design employs boosted word-line (WL) for improving both read performance and write-ability. A ripple bit-line (RiBL) structure provides 30%–44% read access performance improvement and 2 <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex Notation="TeX">$\times$</tex></formula> –3.5 <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex Notation="TeX">$\times$</tex></formula> variation immunity at 0.7 V compared with the conventional hierarchical bit-line (HiBL) schemes. An adaptive data-aware write-assist (ADAWA) with VCS tracking is employed to further enhance the write-ability while ensuring adequate stability for half-selected cells on the selected bit-lines. An adaptive voltage detector (AVD) with binary boosting control is used to mitigating gate electric over-stress. The design is implemented in UMC 40 nm low-power (40LP) CMOS technology. The 512 kb test chip operates from 1.5 V to 0.65 V, with maximum operation frequency of 800 MHz@1.1 V and 200 MHz@0.65 V. The measured power consumption is 0.5 mW/MHz (active) and 4.4 mW (standby) at 1.1 V, and 0.107 mW/MHz (active) and 0.367 mW (standby) at 0.65 V.
Practical microstrip design and applications (2005)

Introduction. Overview of Strip Transmission Lines. Methods of Microstrip Analysis. Dispersion on Microstrip Line. Planar Waveguide Model. Microstrip Discontinuities. Microstrip Filter Design. Appendixes.
The phosphorylation targets of p47phox, a subunit of the respiratory burst oxidase. Functions of the individual target serines as evaluated by site-directed mutagenesis. (1995)

The respiratory burst oxidase of phagocytes and B lymphocytes catalyzes the reduction of oxygen to O2- at the expense of NADPH. Dormant in resting cells, the oxidase is activated by exposing the cells to appropriate stimuli. During activation, p47phox, a cytosolic oxidase subunit, becomes extensively phosphorylated on a number of serines located between S303 and S379. To determine whether this phosphorylation is necessary for oxidase activation, we examined phorbol-elicited oxidase activity in EBV-transformed B lymphoblasts deficient in p47phox after transfection with plasmids expressing various S-->A mutants of p47phox. The mutant containing S-->A mutations involving all serines between S303 and S379 [S(303-379)A] was not phosphorylated, did not translocate to plasma membrane during activation and was almost devoid of function. As to individual serines, S379 was of special interest because (a) p47 phox S379 was phosphorylated in phorbol-activated lymphoblasts expressing wild-type p47phox, and (b) p47phox S379A failed to translocate to the membrane, and was as functionless as p47phox S(303-379)A; other single S-->A mutations had little effect on oxidase activity. These findings suggest that the phosphorylation of S379 may be important for oxidase activation in whole cells.
Measurement of the exciton-formation time and the electron- and hole-tunneling times in a double-quantum-well structure (1991)

The bimolecular nature of exciton formation from free carriers is demonstrated experimentally in a GaAs asymmetric double-quantum-well tunneling structure. A bimolecular formation coefficient of 6\ifmmode\times\else\texttimes\fi{}${10}^{\mathrm{\ensuremath{-}}12}$ ${\mathrm{cm}}^{2}$/ps is obtained. The electron- and hole-tunneling times are determined simultaneously under the same sample conditions.
N -Acyl- <scp>l</scp> -Homoserine Lactone Autoinducers Control Production of an Extracellular Lipopeptide Biosurfactant Required for Swarming Motility of <i>Serratia liquefaciens</i> MG1 (1998)

A nonswarming Serratia liquefaciens mutant deficient in serrawettin W2 production was constructed by transposon mutagenesis. Sequence homology indicated that insertion had occurred in gene swrA, which encodes a putative peptide synthetase. Expression of swrA is controlled by quorum sensing.
TreeDock:  A Tool for Protein Docking Based on Minimizing van der Waals Energies (2002)

Predicting protein-protein and protein-ligand docking remains one of the challenging topics of structural biology. The main problems are (i) to reliably estimate the binding free energies of docked states, (ii) to enumerate possible docking orientations at a high resolution, and (iii) to consider mobility of the docking surfaces and structural rearrangements upon interaction. Here we present a novel algorithm, TreeDock, that addresses the enumeration problem in a rigid-body docking search. By representing molecules as multidimensional binary search trees and by exploring a sufficient number of docking orientations such that two chosen atoms, one from each molecule, are always in contact, TreeDock is able to explore all clash-free orientations at very fine resolution in a reasonable amount of time. Due to the speed of the program, many contact pairs can be examined to search partial or complete surface areas. The deterministic systematic search of TreeDock is in contrast to most other docking programs that use stochastic searches such as Monte Carlo or simulated annealing methods. At this point, we have used the Lennard-Jones potential as the only scoring function and show that this can predict the correct docked conformation for a number of protein-protein and protein-ligand complexes. The program is most powerful if some information is known about the location of binding faces from NMR chemical-shift perturbation studies, orientation information from residual dipolar coupling, or mutational screening. The approach has the potential to include docking-site mobility by performing molecular dynamics or other randomization methods of the docking site and docking families to families of structures. The performance of the algorithm is demonstrated by docking three complexes of immunoglobulin superfamily domains, CD2 to CD58, the V(alpha) domain of a T-cell receptor to its V(beta) domain, and a T-cell receptor to a pMHC complex as well as a small molecule inhibitor to a phosphatase.
Scatter correction for three-dimensional PET based on an analytic model dependent on source and attenuating object (1994)

Three-dimensional positron emission tomography admits a significant scatter fraction due to the large aperture of the detectors, and requires accurate scatter subtraction. A scatter-correction method, applicable to both emission and transmission imaging, calculates the projections of the single-scatter distribution, using an approximate image of the source and attenuating object. The scatter background is subtracted in projection space for transmission data and in image space for emission data, yielding corrected attenuation and emission images. The accuracy of this single-scatter distribution is validated for the authors' small imaging system by comparison with Monte Carlo simulations. The correction is demonstrated using transmission and emission data obtained from measurements on the authors' QPET imaging system using two acrylic phantoms. For the transmission data, generated with a flood source, errors of up to 24% in the linear attenuation coefficients resulted with no scatter subtraction, but the correction yielded an accurate value of mu =0.11+or-0.01 cm-1. For the emission data, the corrected images show that the scattered background has been removed to within the level of the background noise outside the source. The residual amplitude within a cold spot in one of the phantoms was reduced from 21% to 3% of the image amplitude.
Primary infection with dengue or Zika virus does not affect the severity of heterologous secondary infection in macaques (2019)

Zika virus (ZIKV) and dengue virus (DENV) are genetically and antigenically related flaviviruses that now co-circulate in much of the tropical and subtropical world. The rapid emergence of ZIKV in the Americas in 2015 and 2016, and its recent associations with Guillain-Barré syndrome, birth defects, and fetal loss have led to the hypothesis that DENV infection induces cross-reactive antibodies that influence the severity of secondary ZIKV infections. It has also been proposed that pre-existing ZIKV immunity could affect DENV pathogenesis. We examined outcomes of secondary ZIKV infections in three rhesus and fifteen cynomolgus macaques, as well as secondary DENV-2 infections in three additional rhesus macaques up to a year post-primary ZIKV infection. Although cross-binding antibodies were detected prior to secondary infection for all animals and cross-neutralizing antibodies were detected for some animals, previous DENV or ZIKV infection had no apparent effect on the clinical course of heterotypic secondary infections in these animals. All animals had asymptomatic infections and, when compared to controls, did not have significantly perturbed hematological parameters. Rhesus macaques infected with DENV-2 approximately one year after primary ZIKV infection had higher vRNA loads in plasma when compared with serum vRNA loads from ZIKV-naive animals infected with DENV-2, but a differential effect of sample type could not be ruled out. In cynomolgus macaques, the serotype of primary DENV infection did not affect the outcome of secondary ZIKV infection.
Peripheral levels of glutathione and protein oxidation as markers in the development of Alzheimer's disease from Mild Cognitive Impairment (2008)

There is a great interest in the relationship between Mild Cognitive Impairment (MCI) and the progression to Alzheimer's disease (AD). Several studies show the importance of oxidative stress in the pathogenesis of AD. The purpose of this study was the link between oxidative damage, MCI and AD. It analysed protein carbonyls and erythrocyte glutathione system plasma levels of 34 subjects with MCI, 45 subjects with AD and 28 age-matched control subjects. The results showed an increase in protein modification, a decrease in GSH levels and GSH/GSSG ratio in AD and MCI patients compared to age-matched control subjects (p<0.05). The present study shows that some peripheral markers of oxidative stress appear in MCI with a similar pattern to that observed in AD, which suggests that oxidative stress might represent a signal of the AD pathology. AD and MCI are biochemically equivalent. MCI does not necessarily need to progress to AD on a biochemical level.
Genetic and Molecular Analysis of Spontaneous Respiratory Deficient (<i>res</i><sup>−</sup>) Mutants of <i>Escherichia coli</i> K‐12 (1991)

Respiratory deficient (res-) mutants of E. coli are slow growing microcolonial, anaerobic, catalase and benzidine negative strains whose broad phenotypic alteration may result from pleiotropic mutations in genes of the hemin biosynthetic pathway. They are easily recovered from platings of sensitive cells on concentrations of gentamicin higher than the minimal inhibitory concentration. These mutants show a dramatic change in their biochemical diagnostic profile resulting primarily from deficiencies in the active transport mechanisms of the cell. Using well-marked F- and Hfr strains, 157 mutants were analyzed from 3 different parent strains; all but 2 resulted from mutations in 3 loci of the hemin biosynthetic pathway. Of these a marked skew to hemB- mutations was seen, with more than 80% mapping there. The possibility that this hot spot resulted from transpositional activity was tested by Southern hybridization of EcoRI digests of the chromosomal DNA, using as a probe, a 2.8-kb fragment containing the hemB gene. The WT and other hemB+ control strains contained a 14.6-kb fragment. Of 18 hemB strains tested, 14 showed deletion and insertion mutations which fell into four classes based on the variation in the size of the fragment or on the absence of hybridization. The latter resulted from complete deletion of the hemB gene. An increase in fragment size from 1.5-kb to 3.4-kb was observed in some of the strains.
Annual Broadleaf Control With KIH-485 in Glyphosate-Resistant Furrow-Irrigated Corn (2008)

Weed management in furrow-irrigated corn is challenging because of weed emergence associated with each irrigation event. Residual herbicides that provide extended in-season control of a broad spectrum of weeds would be beneficial to producers in this system. Field experiments were conducted in 2005 and 2006 in Yellowstone County, Montana, to evaluate KIH-485 for the control of velvetleaf, kochia, and wild buckwheat in furrow-irrigated corn. KIH-485 was applied at three rates (166, 209, and 250 g ai/ha) and two timings (PRE and POST) and compared to standard rates of S -metolachlor, acetochlor, and pendimethalin. All PRE treatments were applied alone, whereas POST treatments were combined with 1,261 g ae/ha of glyphosate. All rates of KIH-485 applied PRE controlled velvetleaf and kochia 88% or greater at 4 mo after planting (MAP). Wild buckwheat was controlled 89% or greater with the high rate of KIH-485 applied PRE, which was superior to control achieved with any other PRE herbicide treatment. Velvetleaf, kochia, and wild buckwheat were controlled 91% or greater when any herbicide treatment was combined with glyphosate. Corn treated with KIH-485 applied at 209 g ai/ha PRE produced yield that was similar to that produced by the weed-free control in both years.