gebhart/patrepeval huggingface dataset:
Analysis of recombinant yeast decapping enzyme (2003)

A critical step in the turnover of yeast mRNAs is decapping. Two yeast proteins, Dcp1p and Dcp2p, are absolutely required for decapping, although their precise roles in the decapping reaction have not been established. To determine the function of both Dcp1p and Dcp2p in decapping, we purified recombinant versions of these proteins from Escherichia coli and examined their properties. These experiments demonstrate that copurification of Dcp1p and Dcp2p yields active decapping enzyme under a variety of conditions. Moreover, Dcp2p alone can have decapping activity under some biochemical conditions. This suggests that Dcp2p can be a catalytic subunit of the decapping complex, and Dcp1p may function to enhance Dcp2p activity, or as an additional active subunit. In addition, recombinant Dcp1p/Dcp2p prefers long mRNA substrates and is sensitive to inhibition by sequestration of the 5' end but not the 3' end of the substrate. This suggests that Dcp1p/Dcp2p contains an additional RNA-binding site spatially distinct from the active site. Finally, using two RNA-binding proteins that enhance decapping in vivo (Edc1p and Edc2p), we can reconstitute the activation of decapping with recombinant proteins. This indicates that the Edc1 and Edc2 proteins act directly on the decapping enzyme.
Sodium dodecyl sulfate‐polyacrylamide gel electrophoretic method for assessing the quaternary state and comparative thermostability of avidin and streptavidin (1996)

Avidin, a positively charged egg-white protein, aggregates extensively when mixed at ambient temperatures with anionic detergents, such as sodium dodecyl sulfate (SDS). The resultant aggregates fail to penetrate the stacking gel during polyacrylamide gel electrophoresis (PAGE). To prevent the formation of such aggregates, avidin was acetylated and the pI was thus reduced. Acetylated avidin was found to behave in a manner similar to that of streptavidin; under nondenaturing conditions (i.e., incubation of samples at room temperature), both proteins normally migrated mainly as tetramers with a tendency to form oligomers of the tetramer. When samples were boiled, both proteins migrated mainly as the monomer. The comparative stability properties of avidin and streptavidin were also examined using SDS-PAGE by heating samples and determining the extent of dissociation of tetramers to monomers as a function of temperature. A distinctive transition temperature could be defined for individual samples. Using this assay, it was determined that, in the absence of biotin, the quaternary structure of streptavidin is more stable than that of avidin. Biotin appears to stabilize structures of both avidin and streptavidin to a similar degree. Acetylation of avidin thus provides a simple means to analyze the quaternary structure of the molecule using SDS-PAGE.
Enteric Expression of the Integrin αvβ6 Is Essential for Nematode-Induced Mucosal Mast Cell Hyperplasia and Expression of the Granule Chymase, Mouse Mast Cell Protease-1 (2002)

The immunoregulatory cytokine transforming growth factor (TGF)-beta(1) is secreted as a biologically inactive complex with latency-associated peptide, which must be modified by local factors to expose the functionally active cytokine. The epithelial integrin alpha(v)beta(6) mediates local activation of TGF-beta(1) in the lung and beta(6)(-/-) mice exhibit exaggerated pulmonary inflammation, but their response to inflammatory stimuli in the gut has not been investigated. We found that both beta(6) and TGF-beta(1) are constitutively expressed in the jejunal epithelial compartment in uninfected mice and during infection with the intestinal nematode Nippostrongylus brasiliensis. We also present data showing that beta(6)(-/-) mice are seriously compromised in their ability to mount a mucosal mast cell response after infection, and there is a significant reduction in the expression and systemic release of the granule chymase, mouse mast cell protease-1. Because in vitro expression of this chymase is regulated by TGF-beta(1), these data indicate that in the absence of alpha(v)beta(6) epithelially expressed TGF-beta(1) may not be activated, with a consequent absence of expression of mouse mast cell protease-1 and down-regulation of the mucosal mast cell response.
Oxidation Resistance of Graphene-Coated Cu and Cu/Ni Alloy (2011)

The ability to protect refined metals from reactive environments is vital to many industrial and academic applications. Current solutions, however, typically introduce several negative effects, including increased thickness and changes in the metal physical properties. In this paper, we demonstrate for the first time the ability of graphene films grown by chemical vapor deposition to protect the surface of the metallic growth substrates of Cu and Cu/Ni alloy from air oxidation. In particular, graphene prevents the formation of any oxide on the protected metal surfaces, thus allowing pure metal surfaces only one atom away from reactive environments. SEM, Raman spectroscopy, and XPS studies show that the metal surface is well protected from oxidation even after heating at 200 °C in air for up to 4 h. Our work further shows that graphene provides effective resistance against hydrogen peroxide. This protection method offers significant advantages and can be used on any metal that catalyzes graphene growth.
Computer-assisted superimposition of magnetic resonance and high-resolution technetium-99m-HMPAO and thallium-201 SPECT images of the brain. (1991)

A method for registering three-dimensional CT, MR, and PET data sets that require no special patient immobilization or other precise positioning measures was adapted to high-resolution SPECT and MRI and was applied in 14 subjects (five normal volunteers, four patients with dementia (Alzheimer's disease), two patients with recurrent glioblastoma, and three patients with focal lesions (stroke, arachnoid cyst and head trauma]. T2-weighted axial magnetic resonance images and transaxial 99mTc-HMPAO and 201Tl images acquired with an annular gamma camera were merged using an objective registration (translation, rotation and rescaling) program. In the normal subjects and patients with dementia and focal lesions, focal areas of high uptake corresponded to gray matter structures. Focal lesions observed on MRI corresponded to perfusion defects on SPECT. In the patients who had undergone surgical resection of glioblastoma followed by interstitial brachytherapy, increased 201Tl corresponding to recurrent tumor could be localized from the superimposed images. The method was evaluated by measuring the residuals in all subjects and translational errors due to superimposition of deep structures in the 12 subjects with normal thalamic anatomy and 99mTc-HMPAO uptake. This method for superimposing magnetic resonance and high-resolution SPECT images of the brain is a useful technique for correlating regional function with brain anatomy.
Structural Studies of Recombinant Norwalk Capsids (2000)

Norwalk virus is the major cause of epidemic viral gastroenteritis in humans. Attempts to grow this human virus in laboratory cell lines have been unsuccessful; however, the Norwalk virus capsid protein, when expressed in insect cells infected with a recombinant baculovirus, spontaneously assembles into virus-like particles. The x-ray crystallographic structure of these recombinant Norwalk particles has been determined to 3.4 A, using a 22-A electron cryomicroscopy structure as a phasing model. The recombinant capsids, 380 A in diameter, exhibit a T=3 icosahedral symmetry. The capsid is formed by 90 dimers of the capsid protein, each of which forms an arch-like capsomere. The capsid protein has two distinct domains-a shell (S) and a protruding (P) domain-that are connected by a flexible hinge. Although the S domain has a classical beta-sandwich fold, the structure of the P domain is unlike any other viral protein. One of the subdomains in the P domain formed by the most variable part of the sequence is located at the exterior of the capsid.
Production of non-fucosylated antibodies by co-expression of heterologous GDP-6-deoxy-D-lyxo-4-hexulose reductase (2010)

All IgG-type antibodies are N-glycosylated in their Fc part at Asn-297. Typically, a fucose residue is attached to the first N-acetylglucosamine of these complex-type N-glycans. Antibodies lacking core fucosylation show a significantly enhanced antibody-dependent cell-mediated cytotoxicity (ADCC) and an increased efficacy of anti-tumor activity. In cases where the clinical efficacy of an antibody is to some extent mediated by its ADCC effector function, afucosylated N-glycans could help to reduce dose requirement and save manufacturing costs. Using Chinese hamster ovary (CHO) cells as a model, we demonstrate here that heterologous expression of the prokaryotic enzyme GDP-6-deoxy-d-lyxo-4-hexulose reductase within the cytosol can efficiently deflect the fucose de novo pathway. Antibody-producing CHO cells that were modified in this way secrete antibodies lacking core fucose as demonstrated by MALDI-TOF mass spectrometry and HPAEC-PAD monosaccharide analysis. Engineering of the fucose de novo pathway has led to the construction of IgGs with a strongly enhanced ADCC effector function. The method described here should have broad practical applicability for the development of next-generation therapeutic antibodies.
An EKG in your Underwear (2011)

This article discusses the use and benefits of e-Nanoflex that combines nanostructured sensors, smart phones, and cloud computing and promises a new platform for everyday medical monitoring. At the University of Arkansas, a team of surgeons, engineers, and computer scientists has developed a personal heart monitor based on e-Nanoflex nanostructured sensors. The sensors can be embedded in clothing that can be worn and washed just like any other garment. The e-Nanoflex can also monitor recovery from surgery, medical compliance, and neurological diseases, or help athletes optimize their training routines. The nanostructured sensors developed at the University of Arkansas make true portable, wearable electrocardiograph (EKG) systems possible. They consist of tiny metal nanowires growing outwards from the surface of the electrodes. Sophisticated software can monitor data from e-Nanoflex sensors about heart rate consistency and other factors to ensure that patients comply with their prescriptions. The combination of wearable nanostructured sensors, smart phones, and cloud computing makes wearable EKGs possible.
Interactive effects of aging with noise induced hearing loss. (1998)

Aging is associated with a down-regulation in metabolism, which may underlie an increased sensitivity to stress agents and a decreased repair of tissues following stress. In the auditory system this could lead to increased sensitivity to noise induced hearing loss (NIHL) with age. This study examines the effects of high intensity noise exposure (0.5-40 kHz noise at 108 dB SPL for 45 min) on young and old normal (CBA/Ca) mice and young premature presbycusis (C57BL/6) mice. Tone evoked auditory brainstem response (ABR) audiograms were obtained before and after the exposure. The animals were sacrificed and cytocochleograms were performed. The ABR threshold shifts and hair cell losses which followed noise exposure increased with increasing age in the normal (CBA/Ca) mice. Subjects which showed early presbycusis (C57BL/6) associated with vascular pathology, showed an increased sensitivity to noise induced hearing loss over normal subjects. Interestingly, in some cases the physiological loss in C57BL/6 mice was not associated with hair cell loss. These findings support the view that aging with or without hearing loss increased the sensitivity of the ear to NIHL. However, it seems that other factors may contribute to NIHL in the animals with premature presbycusis.
Effects of sample arm motion in endoscopic polarization-sensitive optical coherence tomography (2005)

Motion of the sample arm fiber in optical coherence tomography (OCT) systems can dynamically alter the polarization state of light incident on tissue during imaging, with consequences for both conventional and polarization-sensitive (PS-)OCT. Endoscopic OCT is particularly susceptible to polarization-related effects, since in most cases, the transverse scanning mechanism involves motion of the sample arm optical fiber to create an image. We investigated the effects of a scanning sample arm fiber on the polarization state of light in an OCT system, and demonstrate that by referencing the state backscattered from within a sample to the measured state at the surface, changes in polarization state due to sample fiber motion can be isolated. The technique is demonstrated by high-speed PS-OCT imaging at 1 frame per second, with both linear and rotary scanning fiber-optic probes. Measurements were made on a calibrated wave plate, and endoscopic PS-OCT images of ex-vivo human tissues are also presented, allowing comparison with features in histologic sections.
Saturn-ring defects around microspheres suspended in nematic liquid crystals: An analogy between confined geometries and magnetic fields (2002)

Particles suspended in a nematic liquid crystal exhibit characteristic dipolar and Saturn-ring configurations. Using results on the magnetic-field behavior of these configurations, we explain the recent observation of the Saturn-ring defect in confined geometries based on the idea that a confining geometry and a magnetic field generate a similar "confinement" for the nematic phase.
Two-Dimensional Simulations of Displacement Accumulation Incorporating Shear Strain (2013)

Using ultrasound images to track large tissue deformations usually requires breaking up the deformation into steps and then summing the resulting displacement estimates. The accumulated displacement estimation error therefore depends not only on the error in each step but also on the statistical relationships between estimation steps. These relationships have not been thoroughly studied. Building on previous work with one-dimensional (1-D) simulations, the work reported here measured error variance for single-step and accumulated displacement estimates using two-dimensional (2-D) numerical simulations of ultrasound echo signals, subjected to both normal and axial shear strain as well as electronic noise. Previous results from 1-D simulations were confirmed, showing that errors due to electronic noise are negatively correlated between steps and accumulate slowly, while errors due to strain are positively correlated and accumulate quickly. These properties hold for both normal and axial shear strain. An analysis of 2-D kernel size for tissue under normal and axial shear strain was also performed. Under axial shear strain, error variance tends to increase with larger lateral kernel sizes but decrease for larger axial kernel sizes; the opposite relationship holds under normal strain. A combination of these two types of strain limits the practical kernel size in both dimensions.
The LRRK2 G2019S mutation is associated with Parkinson disease and concomitant non-skin cancers (2012)

Ashkenazi Jewish patients with PD who harbor the G2019S LRRK2 mutation are more likely to have a concomitant non-skin cancer than noncarriers.
Structure of the rat pancreatic cholesterol esterase gene (1991)

The gene encoding the rat pancreatic cholesterol esterase has been isolated and characterized. Analysis of overlapping genomic clones showed that the cholesterol esterase gene spans approximately 8 kb, containing 11 exons interrupted by 10 introns. The exons ranged in size from 83 to 201 bp except for the last exon, which was 548 bp in length. A TAAATA sequence was present at -31 nucleotides from the transcriptional initiation site. A putative pancreas-specific enhancer sequence was found at -90 bp upstream from the CAP site. Although cholesterol esterase shares three domains of similarity with cholinesterase and acetylcholinesterase, these domains were found to be localized in distinct exons of the cholesterol esterase gene. The organization of the cholesterol esterase gene suggests its divergent evolution with other members of the serine esterase gene family.
RD Optimized Coding for Motion Vector Predictor Selection (2008)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> The H.264/MPEG4-AVC video coding standard has achieved a higher coding efficiency compared to its predecessors. The significant bit rate reduction is mainly obtained by efficient motion compensation tools, as variable block sizes, multiple reference frames, 1/4-pel motion accuracy and powerful prediction modes (e.g., SKIP and DIRECT). These tools have contributed to an increased proportion of the motion information in the total bit stream. To achieve the performance required by the future ITU-T challenge, namely to provide a codec with 50% bit rate reduction compared to the current H.264, the reduction of this motion information cost is essential. </para>
An integrated microfluidic chip for DNA/RNA amplification, electrophoresis separation and on‐line optical detection (2006)

This study presents an integrated microfluidic chip capable of performing DNA/RNA (deoxyribonucleic acid/ribonucleic acid) amplification, electrokinetic sample injection and separation, and on-line optical detection of nucleic acid products in an automatic mode. In the proposed device, DNA/RNA samples are first replicated using a micromachine-based PCR module or reverse transcription PCR (RT-PCR) module and then transported by a pneumatic micropump to a sample reservoir. The samples are subsequently driven electrokinetically into a microchannel, where they are separated electrophoretically and then detected optically by a buried optical fiber. The various modules of the integrated microfluidic chip are fabricated from cheap bio-compatible materials, such as PDMS, polymethylmethacrylate, and soda-lime glass. The functionality of the proposed device is demonstrated through its successful application to the DNA-based bacterial detection of Streptococcus pneumoniae and the RNA-based detection of Dengue-2 virus. It is shown that the low thermal inertia of the PCR/RT-PCR modules reduces the sample and reagent consumption and shortens the reaction time. With less human intervention, the subsequent DNA separation and detection could be performed in an automatic mode. The integrated microfluidic device proposed in this study represents a crucial contribution to the fields of molecular biology, genetic analysis, infectious disease detection, and other biomedical applications.
Inhibition of Transfer Messenger RNA Aminoacylation and trans-Translation by Aminoglycoside Antibiotics (2003)

Transfer messenger RNA (tmRNA) directs the modification of proteins of which the biosynthesis has stalled or has been interrupted. Here, we report that aminoglycosides can interfere with this quality control system in bacteria, termed trans-translation. Neomycin B is the strongest inhibitor of tmRNA aminoacylation with alanine (K(i) value of approximately 35 micro m), an essential step during trans-translation. The binding sites of neomycin B do not overlap with the identity determinants for alanylation, but the aminoglycoside perturbs the conformation of the acceptor stem that contains the aminoacylation signals. Aminoglycosides reduce the conformational freedom of the transfer RNA-like domain of tmRNA. Additional contacts between aminoglycosides and tmRNA are within the tag reading frame, probably also disturbing reprogramming of the stalled ribosomes prior protein tagging. Aminoglycosides impair tmRNA aminoacylation in the presence of all of the transfer RNAs from Escherichia coli, small protein B, and elongation factor Tu, but when both proteins are present, the inhibition constant is 1 order of magnitude higher. SmpB and elongation factor Tu have RNA chaperone activities, ensuring that tmRNA adopts an optimal conformation during aminoacylation.
Scaling the Ivory Tower: Merit and Its Limits in Academic Careers (2000)

Following in the tradition of Thorstein Veblen's Higher Learning in America, Lionel S. Lewis has amassed solid evidence to support his conclusions about what leads to success in Scaling the Ivory Tower. As background to his consideration of academic freedom, sexism, merit, tenure, and other such highly charged subjects, Lewis examines the attitudes of those in universities toward academic qualification. The modern rule of thumb has become publish or perish. According to Lewis, however, research and publication may not be such prime considerations after all. Two thought-provoking chapters are devoted to an examination of letters of recommendation as important factors in hiring and promoting in the academic world. Lewis also scrutinizes academic freedom cases from the archives of the American Association of University Professors. Other intriguing issues examined by Lewis are: how spouses and significant others factor into whether or not a professor gets a promotion; a typical day in the life, both academic and personal, of a professor; how the celebrity syndrome has spread to campus; discrimination against women; and bureaucracy as a contributing factor to campus unrest. In the new introduction, Lewis affirms that the most apparent changes in higher education since Scaling the Ivory Tower was initially published have actually made the campus less meritocratic, and less a place where quality academic work is recognized and rewarded. One contributing factor is the necessity to consider age, gender, ethnicity, and race in personnel decisions. Because many on campus are convinced that academic life can only be improved when the demographics of faculty reflect those in the larger society, departments are routinely expected to explain why they did not fill an opening with someone from an underrepresented group. While showing some irreverence toward academia, Scaling the Ivory Tower should also provoke sober consideration of where our colleges and universities are headed. This is a significant volume for university administrators, academics, and graduate students.
System islanding using minimal cutsets with minimum net flow (2005)

Slow coherency has effectively proved its capability in determining sets of generator groups among weak connections in any given power system. In this paper, we provide two comprehensive approaches to deal with islanding the actual system based on the grouping information, by using the minimal cutsets technique in graph theory. The issue of minimal cutsets has been widely discussed in areas related to network topology determination, reliability analysis, etc. The results of this paper also show potential in application to power system islanding. The verification of the islanding scheme is provided based on a WECC 179-bus, 29-generator test system.
ON THE RELATION BETWEEN THE INTERNAL STRUCTURE OF THE MOON AND THE MOONQUAKES (1981)

This paper deals with the relation between the internal structure of the Moon and the radial distribution of the focuses of moonquakes. It has been shown from lunar probes that most of the focuses of moonquakes located at the moon mantle near the possible liquid core of the Moon.We think that the radial inhomogeneity of the composition of the Moon is the essential factor of this phenomenon.In this paper we adopted the model composed of two different uniform compositions for the Moon and worked out the elastic solution with uniform surface load and uniform body forces, respectively. The results have shown that it is possible that the maximum shear stress is induced in the outer spherical shell near the inner sphere. The study of the earthquake wave theory has shown that the earthquake is induced by shear dislocation. Most of the moonquakes, therefore, occur there.
Recessive mutations in the RLBP1 gene encoding cellular retinaldehyde-binding protein in a form of retinitis punctata albescens. (1999)

Recessive mutations in the RLBP1 gene are an uncommon cause of retinal degeneration in humans. The phenotype produced by RLBP1 mutations seems to be a form of retinitis punctata albescens.