gebhart/patrepeval huggingface dataset:
Nucleotide sequence and transcriptional activity of the caprine arthritis-encephalitis virus long terminal repeat (1986)

Caprine arthritis-encephalitis virus (CAEV) and visna virus are pathogenic lentiviruses of goats and sheep which share morphologic features and sequence homology with human T-cell lymphotropic virus type III (HTLV-III), the etiologic agent of the acquired immune deficiency syndrome. The nucleotide sequence of the CAEV long terminal repeat (LTR) was determined, and it was found to be 450 base pairs long, with U3, R, and U5 regions of 287, 85, and 78 base pairs, respectively. Portions of the CAEV LTR are closely homologous to analogous regions of visna virus. The CAEV LTR is not significantly homologous with the HTLV-III LTR; however, like HTLV-III, visna virus, and equine infectious anemia virus, CAEV uses tRNA lysine as a primer for reverse transcription. The transcriptional activity of the CAEV and visna virus LTRs was measured by a chloramphenicol acetyltransferase assay, and the activity of the visna virus LTR was generally higher in a variety of uninfected cell types. Infection of cells with visna virus markedly increased gene expression directed by either the CAEV or visna virus LTR, but in contrast, infection of cells with CAEV had little effect on the activity of either LTR. The lack of trans-activation by CAEV, a virus which causes debilitating arthritis and encephalitis in goats, suggests that trans-activation may not be a general property of pathogenic lentiviruses.
A Mutational Analysis of the Yeast Proliferating Cell Nuclear Antigen Indicates Distinct Roles in DNA Replication and DNA Repair (1995)

The saccharomyces cerevisiae proliferating cell nuclear antigen (PCNA), encoded by the POL30 gene, is essential for DNA replication and DNA repair processes. Twenty-one site-directed mutations were constructed in the POL30 gene, each mutation changing two adjacently located charged amino acids to alanines. Although none of the mutant strains containing these double-alanine mutations as the sole source of PCNA were temperature sensitive or cold sensitive for growth, about a third of the mutants showed sensitivity to UV light. Some of those UV-sensitive mutants had elevated spontaneous mutation rates. In addition, several mutants suppressed a cold-sensitive mutation in the CDC44 gene, which encodes the large subunit of replication factor C. A cold-sensitive mutant, which was isolated by random mutagenesis, showed a terminal phenotype at the restrictive temperature consistent with a defect in DNA replication. Several mutant PCNAs were expressed and purified from Escherichia coli, and their in vitro properties were determined. The cold-sensitive mutant (pol30-52, S115P) was a monomer, rather than a trimer, in solution. This mutant was deficient for DNA synthesis in vitro. Partial restoration of DNA polymerase delta holoenzyme activity was achieved at 37 degrees C but not at 14 degrees C by inclusion of the macromolecular crowding agent polyethylene glycol in the assay. The only other mutant (pol30-6, DD41,42AA) that showed a growth defect was partially defective for interaction with replication factor C and DNA polymerase delta but completely defective for interaction with DNA polymerase epsilon. Two other mutants sensitive to DNA damage showed no defect in vitro. These results indicate that the latter mutants are specifically impaired in one or more DNA repair processes whereas pol30-6 and pol30-52 mutants show their primary defects in the basic DNA replication machinery with probable associated defects in DNA repair. Therefore, DNA repair requires interactions between repair-specific protein(s) and PCNA, which are distinct from those required for DNA replication.
Synthesis and characterization of styrene butadiene rubber—Bentonite clay nanocomposites (2009)

Abstract In the present study, naturally occurring unfractionated bentonite clay was used to prepare styrene butadiene rubber/bentonite clay nanocomposite by latex stage blending. The bentonite clay was organo‐modified by in situ resol formation by the reaction of resorcinol and formaldehyde. The latex clay mixture was co‐coagulated with acid. The resulting clay masterbatch was compounded and evaluated by Fourier Transform Infrared spectroscopy, X‐ray diffraction (XRD), Transmission Electron Microscopy (TEM), Energy Dispersive X‐ray spectroscopy (EDS), Scanning Electron Microscopy, Thermogravimetric analysis, and Differential Scanning Calorimetry. XRD showed that the interplanar distance of the in situ resol‐modified bentonite clay increased from 1.23 to 1.41 nm for the unmodified bentonite. TEM analysis indicated partial exfoliation and/or intercalation. EDS (Si and Al mapping) of the clay revealed the nature of the dispersion in the nanocomposites vis‐à‐vis the conventional styrene‐butadiene rubber (SBR)/bentonite clay composite. Thermogravimetric analysis was used to compare the decomposition trends of the SBR/clay nanocomposites with the SBR/clay composite. The glass transition temperature of SBR/clay nanocomposites increased as compared with that of neat SBR. Substantial improvement in most of the other mechanical properties was also observed in case of the nanocomposites. POLYM. ENG. SCI., 2009. © 2009 Society of Plastics Engineers
Circulatory Support by a Left Ventricular Balloon Pump (1971)

The ability of a left ventricular balloon pump to provide support of the circulation when myocardial function had been severely impaired was examined in six dogs. When the unassisted damaged left ventricle could not maintain systemic blood flows adequate for survival, left ventricular balloon pumping resulted in peripheral blood flows which ranged from 37 to 77 ml/min/kg. These balloon-generated blood flows have been maintained for periods up to three hours. Assist of the circulation by balloon pumping was accompanied by an increase in systemic arterial blood pressure and a decrease in left atrial end-diastolic pressure. The effectiveness of left ventricular balloon pumping was reduced in hypovolemia and in the presence of ventricular extrasystolic beats. Left ventricular balloon pumping was not effective in generating a sustained peripheral flow of blood when the heart was fibrillating.
Single image deblurring with adaptive dictionary learning (2010)

We propose a motion deblurring algorithm that exploits sparsity constraints of image patches using one single frame. In our formulation, each image patch is encoded with sparse coefficients using an over-complete dictionary. The sparsity constraints facilitate recovering the latent image without solving an ill-posed deconvolution problem. In addition, the dictionary is learned and updated directly from one single frame without using additional images. The proposed method iteratively utilizes sparsity constraints to recover latent image, estimates the deblur kernel, and updates the dictionary directly from one single image. The final deblurred image is then recovered once the deblur kernel is estimated using our method. Experiments show that the proposed algorithm achieves favorable results against the state-of-the-art methods.
Laparoscopic closure for perforation of the sigmoid colon by endoscopic linear stapler. (1996)

Immediate open surgery has been recommended for the management of perforation during colonoscopic examination. Laparoscopic closure for perforation of the sigmoid colon caused by diagnostic colonoscopy is described. The perforation site was identified in the antimesenteric border of the sigmoid colon by laparoscopic survey, and four ports were inserted in the lower abdomen. The margin of the perforation was lifted by two graspers, and the defect was completely closed using an endoscopic linear stapler. The patient recovered quickly without any associated complications. Postoperative barium enema showed no stenosis or leakage. This method is less invasive and allows earlier recovery of patients with colonic perforation.
Supramolekulare Chemie von Gasen (2004)

Abstract Die molekulare Erkennung von Gasen ist ein neu aufkommendes Forschungsgebiet. Anhand von Prinzipien der supramolekularen Chemie können wir verstehen, wie Gase mit biologischen Molekülen wechselwirken, und Einzelheiten zum Mechanimus ihrer physiologischen Aktivität erfahren. Das Konzept der molekularen Erkennung wurde zur Gassensorik genutzt, wobei grundlegende Kenntnisse zur Struktur und Dynamik von Rezeptor‐Analyt‐Komplexen erhalten wurden. In diesem Zusammenhang gelang die Entwicklung neuer Gassensoren und Gasspeicherungselemente, für die sich auch in der Natur zahlreiche Beispiele finden lassen. Konzepte der supramolekularen Chemie liefern die Basis zur Umwandlung von Gasen in synthetisch nützliche Reagentien. Das rationale Design neuartiger Katalysatoren für Reaktionen mit Gasen und von Einlagerungskomplexen mit Gasen liefert ausgezeichnete Perspektiven für die präparative synthetische Chemie.
Interobserver Agreement Among Sleep Scorers From Different Centers in a Large Dataset (2000)

The level of agreement in sleep stage assignment varies between scorers, by diagnosis, and by record. The level of agreement between laboratories is lower than what can be maintained between scorers within the same laboratory. This warrants caution when comparing data scored in separate laboratories. The lower agreement in SDB patients supports the generally held view that sleep fragmentation makes application of the R&K rules less reliable.
Generation of Large Chromosomal Deletions in Koji Molds <i>Aspergillus oryzae</i> and <i>Aspergillus sojae</i> via a Loop-Out Recombination (2008)

We established a technique for efficiently generating large chromosomal deletions in the koji molds Aspergillus oryzae and A. sojae by using a ku70-deficient strain and a bidirectional marker. The approach allowed deletion of 200-kb and 100-kb sections of A. oryzae and A. sojae, respectively. The deleted regions contained putative aflatoxin biosynthetic gene clusters. The large genomic deletions generated by a loop-out deletion method (resolution-type recombination) enabled us to construct multiple deletions in the koji molds by marker recycling. No additional sequence remained in the resultant deletion strains, a feature of considerable value for breeding of food-grade microorganisms. Frequencies of chromosomal deletions tended to decrease in proportion to the length of the deletion range. Deletion efficiency was also affected by the location of the deleted region. Further, comparative genome hybridization analysis showed that no unintended deletion or chromosomal rearrangement occurred in the deletion strain. Strains with large deletions that were previously extremely laborious to construct in the wild-type ku70(+) strain due to the low frequency of homologous recombination were efficiently obtained from Delta ku70 strains in this study. The technique described here may be broadly applicable for the genomic engineering and molecular breeding of filamentous fungi.
In silico modeling of the effects of alpha-synuclein oligomerization on dopaminergic neuronal homeostasis (2014)

The mathematical model presented here successfully simulates the dynamic phenomena of ASYN overexpression and oligomerization and predicts the biological system's behavior in a number of scenarios not used for model calibration. It allows, for the first time, to qualitatively estimate the protein levels that are capable of deregulating proteolytic homeostasis. In addition, it can help form new hypotheses for intervention that could be tested experimentally.
General Synthesis of a Mesoporous Composite of Metal Oxide and Silicate Nanoparticles from a Metal Salt and Laponite Suspension for Catalysis (2006)

A general approach is proposed for the synthesis of thermally stable and highly porous composite structures of metal oxide and silicate nanoparticles from aqueous solution of a metal salt and a suspension of Laponite clay. The formation of the mesoporous structure involves coupled processes: acid leaching of the Laponite clay sheets by acidic aqueous solution of the metal salt and polymerization of the metal hydrate species due to the high pH of the Laponite suspension. The extent of the acid leaching varies with the acidity of the metal salt solution. Moreover, introducing poly(ethylene oxide) surfactants in the synthesis significantly increases surface areas and porosity of the products. The nanocomposites obtained possess large porosity, large accessible surface area of metal oxide nanocrystals, and ion exchange capacity. They can be readily granulated, and metals can be loaded onto the solids by ion exchange and exist in highly dispersed metal nanocrystals. They have been found to be superior photocatalysts or supports for metal catalysts. The reaction mechanism of the synthesis is distinctly different from that for the synthesis of conventional pillared intercalated layered clays. This synthesis approach is an effective approach for constructing nanocomposites with a large porosity and structure and surface chemistry that can be tailored.
Synthesis and Molecular Structures of Neutral Nickel Complexes. Catalytic Activity of (Benzamidinato)(acetylacetonato)nickel for the Addition Polymerization of Norbornene, the Oligomerization of Ethylene, and the Dimerization of Propylene (2005)

The new neutral nickel complexes PhC(NSiMe3)2Ni(acac) (3), PhC(NSiMe3)2Ni(acac)(TMEDA) (4), [PhC(NSiMe3)2]2Ni2 (5), [PhC(NSiMe3)2]2Ni·Li2Br2(TMEDA)2 (6), (TMEDA)2Ni (7), p-MePhC(NSiMe3)2Ni(acac) (8), p-MePhC(NSiMe3)2Ni(acac)(TMEDA) (9), [p-MePhC(NSiMe3)2]2Ni (10), NiMe2Py2 (11) and [p-MePhC(NSiMe3)]2Ni(Py) (14) have been synthesized and characterized. The solid-state molecular structures of all complexes have been confirmed by low-temperature X-ray diffraction analysis. The methyl complex p-MePhC(NSiMe3)2Ni(Me)(Py) (13) is not stable and rapidly decomposes, forming the complex [p-MePhC(NSiMe3)]2Ni(Py) (14). Complex 3 activated with MAO has been shown to be an efficient catalytic system for the norbornene vinyl-type polymerization. The activity of the catalyst and the molecular weights of the resulting polynorbornenes were found to be dependent on the reaction time, the MAO/precatalyst ratio, and the reaction temperature. In addition, this catalytic system has been found to dimerize propylene to a mixture of hexenes with a high turnover frequency of η = 9040 h-1 and oligomerize ethylene to either a mixture of C4−C6 or/and C4−C14 products, depending on the temperature and the solvent, extremely rapidly (η = 83 500 h-1).
Potential Role of NK Cells in the Pathogenesis of Inflammatory Bowel Disease (2011)

NK cells are a major component of the innate immune system and play an important role in the tissue inflammation associated with autoimmune diseases such as inflammatory bowel disease (IBD). NK cells are unique in bearing both stimulatory and inhibitory receptors specific for MHC class I molecules, and their function is regulated by a series of inhibiting or activating signals. The delicate balance between activation and inhibition that decides NK cell final action provides an opportunity for their possible modulatory effect on specific therapeutic settings. Intestinal NK cells are phenotypically distinct from their counterparts in the blood and resemble "helper" NK cells, which have potentially important functions both in promoting antipathogen responses and in the maintenance of intestinal epithelial homeostasis. NK cell activities have been found to be significantly below normal levels in both remissive and active stages of IBD patients. However, some proinflammatory cytokines (e.g., IL-15, IL-21, and IL-23) could potently induce NK cell activation to secret high levels of proinflammatory cytokines (e.g., IFN-γ and TNF) and promote the cytolytic activities against the target cells. This paper provides the characteristics of intestinal NK cells and their potential role in the pathogenesis of IBD.
In vitro and in vivo studies on triclosan/PVM/MA copolymer/NaF combination as an anti-plaque agent. (1989)

A combination of triclosan, copolymer of PVM/MA and NaF has been optimized in vitro and in vivo for plaque effect. Triclosan (2, 4, 4' trichloro-2'-hydroxydiphenyl ether), a non-cationic antibacterial, was compatible with anionic surfactant, NaF and PVM/MA copolymer as evaluated by in vitro antibacterial tests. The in vitro uptake of triclosan on the saliva-coated hydroxyapatite disks, extracted human teeth and oral buccal epithelial cells was enhanced two fold in the presence of PVM/MA copolymer when compared to the uptake in the absence of the copolymer. The combination consisting of 0.3% triclosan/2% PVM/MA copolymer/1100 ppm NaF was found to be highly effective on reducing smooth and fissure caries, and plaque extent compared to to 1100 ppm/NaF by itself in rats when applied topically. The combination also showed significantly more fluoride uptake and reduction in enamel solubility than 1100 ppm/NaF. The results of these studies indicated that this optimized combination was an effective antiplaque/anticaries agent in vitro and in vivo.
Plasmon Hybridization and Field Confinement in Multilayer Metal–Dielectric Nanocups (2013)

Large-area arrays of dispersed multilayer gold–dielectric nanocups were fabricated by colloidal lithography and studied by extinction spectroscopy. Hybridization of the elemental plasmons of the individual nanocups gave rise to new resonance peaks in the visible and near-infrared regions of the extinction spectrum. Transmission electron microscopy was used to confirm the fabricated structure geometry, and the optical properties of the arrays were studied by UV–vis–NIR spectroscopy and finite-difference time-domain (FDTD) simulations. The nature of the resonances was elucidated from E-field plots and charge plots showing clear hybridized modes. We observe a dominant hybridized dipolar mode combining a bonding and antibonding mode at the two caps. A high-energy antibonding (antisymmetric) quadrupolar mode of an individual nanocup is revealed through hybridization with an elemental mode on the second nanocup. A low-energy tunable cavity mode with a very small mode volume is observed in the near-IR range.
Derivation of the low-<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mi>T</mml:mi></mml:math>phase diagram of<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msub><mml:mrow><mml:mtext>LiHo</mml:mtext></mml:mrow><mml:mi>x</mml:mi></mml:msub><mml:msub><mml:mtext>Y</mml:mtext><mml:mrow><mml:mn>1</mml:mn><mml:mo>−</mml:mo><mml:mi>x</mml:mi></mml:mrow></mml:msub><mml:msub><mml:mtext>F</mml:mtext><mml:mn>4</mml:mn></mml:msub></mml:mrow></mml:math>: A dipolar quantum Ising magnet (2008)

The ${\text{LiHo}}_{x}{\text{Y}}_{1\ensuremath{-}x}{\text{F}}_{4}$ compound is widely considered to be the archetypal dipolar quantum Ising system, with longitudinal dipolar interactions ${V}_{ij}^{zz}$ between Ho spins ${i,j}$ competing with transverse field--induced tunneling, to give a $T=0$ quantum phase transition. By varying the Ho concentration $x$, the typical strength ${V}_{0}$ of ${V}_{ij}^{zz}$ can be varied over many orders of magnitude, and so can the transverse field ${H}_{\ensuremath{\perp}}$. A new effective Hamiltonian is derived, starting from the electronuclear degrees of freedom, which is valid at low and intermediate temperatures. For any such dipolar quantum Ising system, the hyperfine interaction will dominate the physics at low temperatures, even if its strength ${A}_{0}<{V}_{0}$: One must therefore go beyond an electronic transverse field quantum Ising model. We derive the full phase diagram of this system, including all nuclear levels, as a function of transverse field ${H}_{\ensuremath{\perp}}$, temperature $T$, and dipole concentration $x$. For ${\text{LiHo}}_{x}{\text{Y}}_{1\ensuremath{-}x}{\text{F}}_{4}$ we predict a re-entrant critical field as a function of $x$. We also predict the phase diagram for $x=0.045$ and the behavior of the system in magnetic-resonance and muon-spin-relaxation experiments.
Microencapsulation of a Model Oil in Wall System Consisting of Wheat Proteins Isolate (WHPI) and Lactose (2018)

Microencapsulation allows for the entrapment, protection, and delivery of sensitive and/or active desired nutrients and ingredients as well as biologically-active agents. The microencapsulating properties of wall solutions (WS) containing 2.5–10% (w/w) wheat proteins isolate (WHPI) and 17.5–10% (w/w) lactose were investigated. Core-in-wall-emulsions (CIWEs) consisting of the WS and soy oil were prepared at a wall-to-core (W:C) ratio ranging from 25:75 to 75:25 (w/w). Microcapsules were prepared by spray-drying the CIWEs. The CIWEs had a mean particle diameter smaller than 0.5 µm and surface excess that ranged from 1.59 to 5.32 mg/m2. In all cases, microcapsules with smooth outer surfaces that exhibited only limited surface indentation were obtained. The core, in the form of protein-coated lipid droplets, was embedded throughout the wall matrices. In all but one case, core retention was higher than 83%, and in 50% of the cases, it was higher than 90%. Core retention was significantly influenced the composition of the WS and by W:C ratio (p < 0.05). Except for two cases, microcapsules exhibited very limited core extractability. The microencapsulation efficiency was >90% and was influenced, to a certain degree, by the composition of the CIWEs. Results indicated the potential for utilizing wall systems consisting of WHPI and lactose as effective and highly functional microencapsulating agents in food and related applications.
Direct observation of the principal deep level (EL2) in undoped semi-insulating GaAs (1983)

A high spatial resolution, near infrared absorption method has been used to determine [EL2] concentrations in semi-insulating undoped Czochralski liquid encapsulated (LEC) GaAs. Fine structure superimposed on the well-known ‘‘W’’ distribution across 〈110〉 diameters of {001} wafers has been detected. Fine structure has also been directly observed in {110} sections of ingots grown along 〈001〉 using a CCTV vidicon system to observe transmitted infrared radiation. The structure consists of narrow bands of increased absorption which correspond with high densities of dislocations in the same specimens.