gebhart/patrepeval huggingface dataset:
Mutational analysis of the adeno-associated virus Rep68 protein: identification of critical residues necessary for site-specific endonuclease activity (1997)

The Rep68 and Rep78 proteins of adeno-associated virus type 2 (AAV) are multifunctional proteins which contain overlapping amino acid sequences. They are required for viral replication and preferential integration of the AAV genome into a region of human chromosome 19. During the terminal resolution process of AAV DNA replication, these proteins make a site-specific and strand-specific endonuclease cut within the AAV inverted terminal repeat DNA. The Rep68 and Rep78 proteins also have helicase and DNA-binding activities. The endonuclease activity is believed to involve the covalent attachment of Rep68 or Rep78 at the cut site via a phosphotyrosine linkage. In an attempt to identify the active-site tyrosine residue of Rep78 and Rep68, tyrosine residues were site specifically mutated to phenylalanines by overlap extension PCR, and the resulting PCR fragments were cloned into a maltose binding protein-Rep68 fusion (MBP-Rep68delta) expression vector. The mutant MBP-Rep68delta proteins were expressed in Escherichia coli cells, purified with amylose resin, and assayed in vitro for Rep68-specific activities. Although several of the mutations disrupted the endonuclease activity, only the mutation of tyrosine 152 abrogated the endonuclease activity with no discernible effect on the helicase or DNA-binding activities. Our data therefore suggest that there are distinct active sites for the helicase and endonuclease activities.
Regulation of PTEN activity by p38δ-PKD1 signaling in neutrophils confers inflammatory responses in the lung (2012)

Despite their role in resolving inflammatory insults, neutrophils trigger inflammation-induced acute lung injury (ALI), culminating in acute respiratory distress syndrome (ARDS), a frequent complication with high mortality in humans. Molecular mechanisms underlying recruitment of neutrophils to sites of inflammation remain poorly understood. Here, we show that p38 MAP kinase p38δ is required for recruitment of neutrophils into inflammatory sites. Global and myeloid-restricted deletion of p38δ in mice results in decreased alveolar neutrophil accumulation and attenuation of ALI. p38δ counteracts the activity of its downstream target protein kinase D1 (PKD1) in neutrophils and myeloid-restricted inactivation of PKD1 leads to exacerbated lung inflammation. Importantly, p38δ and PKD1 conversely regulate PTEN activity in neutrophils, thereby controlling their extravasation and chemotaxis. PKD1 phosphorylates p85α to enhance its interaction with PTEN, leading to polarized PTEN activity, thereby regulating neutrophil migration. Thus, aberrant p38δ-PKD1 signaling in neutrophils may underlie development of ALI and life-threatening ARDS in humans.
Respiratory Syncytial Virus Load Predicts Disease Severity in Previously Healthy Infants (2005)

In previously healthy infants, higher RSV loads measured at capturable time points after symptom onset predict clinically relevant measures of increased disease severity.
<title>External factor influence on the optical activity of chiral liquid crystals</title> (1996)

Due to its diffractive nature the light polarization plane rotation in cholesterical liquid crystals (CLC) is highly dependent on the parameters of a selective reflection (SR) band of liquid crystal matrix and possesses a number of qualitative peculiarities in contrast to usual liquids, solutions or crystals. The aim of the present work is to study the influence of such parameters as cell thickness, temperature and dye-doping on the optical activity of CLC. A method of precise calculation of the cell gyrotropy and elliptisity of light passed through CLC film is described. The square dependence of polarization plane rotation upon CLC film thickness was established. Abnormally strong light absorption of dye-doped CLC in the 'red' edge of SR band was observed for small dopant concentrations resulting in an asymmetry of polarization plain rotation with respect to the maximum of SR band. On the base of experimental data the possibility to create an electrically controlled two-color CLC light indicator with high color contrast is discussed.
Catalytic Rearrangement of Xanthates to Dithiolcarbonates (1973)

During a research of the Friedel-Crafts'reaction using xanthate, it was found thatxanthates rearrange to dithiolcarbonates by the catalysis of aluminum chloride in carbondisulfide. This rearrangement needs at least a molar equivalent of aluminum chlorideto xanthates and proceeds even at room temperature. With respect to solvent, carbon disulfide can be replaced by chloroform without essential effect on the product distribution. It was presumed from a study of crossover reaction that this rearrangement might have the nature of intermolecular reaction.
Decoding of QR codes printed on spheres (2016)

In this paper, we deal with the situation wherein QR codes are printed on spheres. When an image is obtained from such a QR code, it can be seriously distorted. A scheme based on conic segmentation (CS) is proposed to rectify the distorted QR images.
Sandwich-cultured hepatocytes: an <i>in vitro</i> model to evaluate hepatobiliary transporter-based drug interactions and hepatotoxicity (2010)

Sandwich-cultured hepatocytes (SCH) are a powerful in vitro tool that can be utilized to study hepatobiliary drug transport, species differences in drug transport, transport protein regulation, drug-drug interactions, and hepatotoxicity. This review provides an up-to-date summary of the SCH model, including a brief history of, and introduction to, the use of SCH, as well as methodology to evaluate hepatobiliary drug disposition. A summary of the literature that has utilized this model to examine the interplay between drug-metabolizing enzymes and transport proteins, drug-drug interactions at the transport level, and hepatotoxicity as a result of altered hepatic transport also is provided.
Omnidirectional narrow bandpass filter based on metal-dielectric thin films (2008)

We show that a metal-dielectric Fabry-Perot (FP) structure can exhibit an omnidirectional transmission for p-polarized light, which means a passband is independent of the incidence angle of light. The omnidirectional passband occurs when the sum of the reflection phase shift at the metal-spacer interface and the propagation shift in the spacer region is almost 2pi for every incidence angle. We numerically and experimentally demonstrate such an omnidirectional narrow bandpass filter in an air/Ag/ZnS/Ag/glass structure. Moreover, we introduce an antireflection coating on both sides of the metal-dielectric FP structure. The transmittance will increase obviously, while the omnidirectional property remains the same.
High performance low temperature polysilicon thin film transistor using ECR plasma thermal oxide as gate insulator (1994)

Electron cyclotron resonance (ECR) plasma thermal oxide has been investigated as a gate insulator for low temperature (/spl les/600/spl deg/C) polysilicon thin-film transistors based on solid phase crystallization (SPC) method. The ECR plasma thermal oxide films grown on a polysilicon film has a relatively smooth interface with the polysilicon film when compared with the conventional thermal oxide and it shows good electrical characteristics. The fabricated poly-Si TFT's without plasma hydrogenation exhibit field-effect mobilities of 80 (60) cm/sup 2//V/spl middot/s for n-channel and 69 (48) cm/sup 2//V/spl middot/s for p-channel respectively when using Si/sub 2/H/sub 6/(SiH/sub 4/) source gas for the deposition of active poly-Si films.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Thrombin inhibitor perfluorocarbon nanoparticles for treatment and 19F tracking of acute thrombosis (2010)

DOAJ is a unique and extensive index of diverse open access journals from around the world, driven by a growing community, committed to ensuring quality content is freely available online for everyone.
Additive Friction Stir Manufacturing of 7055 Aluminum Alloy (2016)

The objective of the report is to investigate the feasibility and reliability of additive friction stir manufacturing of 7055 aluminum alloy. This is a technique in which multiple lap welds are performed to create a three-dimensional part out of relatively thin plate aluminum. To accomplish this, a four inch stack of 7055 aluminum alloy lap welds must be created. The solid weld nugget is then machined out of the center of the welded stack to create ASTM approved subsize tensile coupons. Rockwell hardness, yield strength, ultimate tensile strength, and percent elongation information is gathered from the tensile coupons to investigate the effectiveness of the additive friction stir manufacturing process. The data shows that the additive manufactured material experiences a significant reduction in strength and percent elongation while not showing any significant response to heat treatment. Suggestions are made regarding possible changes to the weld schedule that could improve the material properties of the additive manufactured aluminum.
The tow classes of genes for the major potato tuber protein, patatin, are differentially expressed in tubers and roots (1987)

The major potato tuber protein, patatin, is a family of 40kd glycoproteins that constitutes forty per cent of the soluble protein in tubers but is generally undetectable in other tissues. Fused rocket immunoelectro-phoresis was used to detect in roots patatin that is immunologically different from tuber patatin. Western blots of SDS-polyacrylamide gels show root patatin to have a different molecular weight distribution than tuber patatin isoforms, but immunoprecipitation of in vitro translation products shows the patatin precursors to be of similar molecular weight in both tissues. This suggests that post-translational processing may differ in tubers and roots. Northern blots show that tuber and root patatin mRNAs are of similar size, but tuber transcripts are about 100-fold more abundant. 5' S1 nuclease and primer extension mapping suggests the class of patatin transcripts expressed in roots (class II transcripts) to be a subset of patatin transcripts expressed in tubers (classes I and II). Class II patatin mRNAs differ from class I transcripts by the presence of a 22 nucleotide insertion just upstream of the initiation codon. These data demonstrate that expression of the patatin multigene family is differentially regulated in tubers and roots.
Enhanced spontaneous emission rate in annular plasmonic nanocavities (2009)

The spontaneous emission rate of erbium ions is enhanced by coupling to localized plasmonic resonances in subwavelength annular apertures in a Au film. The Er3+ ions, embedded in SiO2, are selectively located inside the apertures. The annular apertures act as nanocavities, enhancing the local density of optical states at the Er emission wavelength of 1.54 μm when the cavities are tuned to that wavelength. We show that this leads to an eightfold increase of the photoluminescence intensity, in conjunction with a 2.4-fold enhancement of the spontaneous emission rate.
Fiber optic cables : fundamentals, cable design, systems planning (2001)

Physics and chemistry of optical waveguides optical waveguide profiles optical fibre parameters and measurement methods optical fibre design manufacturing of optical fibres optical fibre buffers fibre optic cable design environmental tests on fibre optic cables cable plant design splices connectors and closures network configurations - ISDN, FITL, LAN, FTTD electro-optic signal conversion fibre optic modules and components systems for fibre optic transmission.
A dose-finding pharmacokinetic study of IT-101, the first de novo designed nanoparticle therapeutic, in refractory solid tumors (2008)

14538 Background: IT-101 is the first de novo designed experimental nanoparticle therapeutic for cancer and is comprised of a cyclodextrin-based polymer conjugate of camptothecin (CPT) that self-assembles into nanoparticles with diameter of ca. 40 nm and near neutral surface charge. The nanoparticle properties have been designed to accomplish extended circulation, tumor penetration, and slow intracellular drug release to enhance the mechanism of action of the CPT. Methods: Patients with refractory solid tumors received IT-101 by 90 minute IV infusions on days 1, 8, and 15 of a 28 day cycle over a dose range of 6 mg/m2/wk to 18 mg/m2/wk. Dose escalation was conducted with a Simon’s design. Dose limiting toxicity (DLT) was determined over the first cycle. Progressive disease (PD) was defined by RECIST (CT) results. Pharmacokinetics of free and total CPT in blood and urine were collected over after the 1st dose. Patients completing 6 cycles with stable disease (SD) or better were eligible to receive compassionate IT-101 at the same dose level every other week (QOW). Results: Twelve patients [6 (6 mg/m2), 3 (12 mg/m2), and 3 (18 mg/m2)] were enrolled. 4 of 12 (33%) had PD by CT. 8 of 12 (66%) did not have PD. (6-SD and 2 clinical deterioration (CD). Hematologic toxicity was the DLT. The MTD was < 30 mg/m2/mo. In patients receiving > 2 cycles, SD was observed at cumulative doses of 18 mg/m2/mo to 27 mg/m2/mo. Three patients (pancreatic, renal cell, NSCLC) completed 6 cycles and received treatment QOW with a PFS of ≥18, 14, and 11 months, respectively. Over 7 days, the mean plasma total CPT and free CPT t½ β were 39 ± 1.1 and 51 ± 1.5 hrs, respectively. The AUC of free and total CPT were linear with 9.9 ± 4.0 % of the CPT dose free. Urinary excretion averaged 16 ± 9.1% of the total CPT dose in the first 48 hrs. Conclusions: These data appear to demonstrate that IT-101 is safe, tolerable, and is associated with acceptable toxicity at the MTD. SD was maintained in patients treated beyond 6 cycles QOW at doses of 6 to 9 mg/m2/wk. In addition, twice monthly regimens maintained SD with minimal drug-related toxicity. A QOW schedule (allowing for 99% elimination of CPT) is warranted in future clinical trial. Author Disclosure Employment or Leadership Consultant or Advisory Role Stock Ownership Honoraria Research Expert Testimony Other Remuneration Insert Therapeutics Insert Therapeutics Insert Therapeutics
Shape‐Selective Synthesis of Palladium Nanoparticles Stabilized by Highly Branched Amphiphilic Polymers (2004)

Abstract Despite the current broad interest in such materials, the synthesis of defined structures in the size range of 10 nm to ca. 1 μm (“mesoscopic”) is challenging. Few routes shape‐selectively afford geometrically regular structures, other than the typical spherical metal particles of 1 to 10 nm. Moreover, these few routes are largely restricted to aqueous systems, however, for catalysis and other applications dispersions in organic solvents are desirable. Carbon monoxide reduction of a palladium( II ) compound in combination with stabilization by (readily available) amphiphilic hyperbranched polymers surprisingly affords dispersions of hexagonal platelets selectively with average sizes of thirty to several hundred nanometers in toluene. The size can be controlled by the polymer composition. Transmission electron microscopy (TEM), electron diffraction, and extended X‐ray absorption fine structure (EXAFS) spectroscopy demonstrate these palladium( 0 ) platelets to be extremely thin (1–2 nm). Despite this high aspect ratio, the platelets prove quite shear resistant.
The N-terminus of fission yeast DNA polymerase alpha contains a basic pentapeptide that acts in vivo as a nuclear localization signal. (1995)

The N-terminal sequence of the catalytic subunit of fission yeast DNA polymerase alpha (pol alpha) contains two putative nuclear localization signals (NLS). To check the functionality of these signals in vivo, the N-terminal sequence was experimentally divided into three amino acid blocks, two of which contain a distinct presumptive NLS. Each block was deleted, either individually or in combination with one of the two others. The deleted gene products were expressed in fission yeast, and assayed by indirect immunofluorescence for their aptitude to localize to the cell nucleus. Block II, which contains the putative NLS pentapeptide 97RKRKK, was both necessary and sufficient to promote nuclear import of pol alpha, as well as of a pyruvate kinase fusion protein. Precise excision of the NLS pentapeptide from block II inhibited the nuclear import of pol alpha, thus confirming the role of this sequence as the functional NLS of the fission yeast enzyme.
Clinical Verification of the Performance of the Pathwork Tissue of Origin Test (2011)

Gene expression-based assays have been introduced into the clinical arena to assist in the diagnosis of poorly differentiated or undifferentiated tumors. The US Food and Drug Administration has cleared the microarray-based Pathwork Tissue of Origin (TOO) Test (Pathwork Diagnostics, Sunnyvale, CA) for the molecular characterization of such challenging specimens. We aimed at verifying the analytic and clinical performance of this test on 43 poorly differentiated and undifferentiated tumor samples, including 6 off-panel cases and 7 cancers of unknown primary (CUP). Our results showed 97% (95% confidence interval, 80.4%-99.8%) agreement between the Pathwork TOO Test result and the complete diagnosis, which included clinical correlations and immunohistochemical staining, after the original diagnosis. We concluded that for off-panel and CUP samples, the tissue type and the cell type may be confounded by the Pathwork TOO Test and that careful clinicopathologic assessment is needed when interpreting results from this helpful ancillary tool for pathologists.
Stress, Neuropeptides, and Feeding Behavior: A Comparative Perspective (2002)

Stress inhibits feeding behavior in all vertebrates. Data from mammals suggest an important role for hypothalamic neuropeptides, in particular the melanocortins and corticotropin-releasing hormone (CRH)-like peptides, in mediating stress-induced inhibition of feeding. The effects of CRH on food intake are evolutionarily ancient, as this peptide inhibits feeding in fishes, birds, and mammals. The effects of melanocortins on food intake have not been as extensively studied, but available evidence suggests that the anorexic role of neuronal melanocortins has been conserved. Although there is evidence that CRH and the melanocortins influence hypothalamic circuitry controlling food intake, these peptides may have a more primitive role in modulating visuomotor pathways involved in the recognition and acquisition of food. Stress rapidly reduces visually guided prey-catching behavior in toads, an effect that can be mimicked by administration of CRH, while corticosterone and isoproterenol are without effect. Melanocortins also reduce prey-oriented turning movements and, in addition, facilitate the acquisition of habituation to a moving prey item. The effects of these neuropeptides are rapid, occurring within 30 min after administration. Thus, changes in neuroendocrine status during stress may dramatically influence the efficacy with which visual stimuli release feeding behavior. By modulating visuomotor processing these neuropeptides may help animals make appropriate behavioral decisions during stress.
Neutral Gold(I) Complexes with Mixed Phosphorus Ligands (1997)

Abstract The reaction of compounds (R 3 P) AuMe with diphenylphosphinous acid Ph 2 P(O)H affords methane and neutral complexes of the type (R 3 P(O)Ph 2 ( 1a : R = Me; 1b : R = Ph, lc : R = o‐Tol). 1a , b are obtained in high yield, but the yield of lc is lower owing to a side‐reaction which leads to a different product: Ph 2 P(OH)–Au–P(O)Ph 2 ( 2 ). The crystal structure of 1a was determined by a single‐crystal X‐ray diffraction study. The compounds is a monomer with a linear P–Au–P′ axis and the phosphane and phosphinite ligands in a staggered conformation. In solution (CHCl 3 , CH 2 Cl 2/ ) compounds 1a – c undergo a ligand redistribution, establishing equilibria that involve ionic isomers of the type [R 3 P) 2 Au] + [Au‐(P(O)Ph 2 ) 2 ] − , which are readily identified through their NMR data. The analogous reaction of (R 3 P)b AuMe with dimethylphosphite (MeO) 2 P(O)H gives methane and the corresponding dimethylphosphites of the type (R 3 P)AuP(O)(OMe) 2 ( 3a : R = Me; 3b : R = Ph; 3c : R= o‐Tol). The crystal structure of 3b has also been determined. It features a linear structure with an eclipsed conformation of the ligands. In polar solvents (CHCl 3 , methanol) there is again an eqilibrium between neutral and ionic isomers, the latter comprising bis(phosphane)gold cations [(R 3 P) 2 Au] + and {Au[P(O)‐(OMe) 2 ] 2 ) − anions, as confirmed by NMR spectroscopy and mass spectrometry.
Isolation of Chromaffin Granules (2010)

Adrenal medullary chromaffin granules (dense core secretory vesicles) have been a valuable model system for the study of the proteins and membrane components involved in the process of exocytosis. Because of the abundance of chromaffin granules in a readily available tissue source, bovine adrenal medullae, and their unique sedimentation properties, it is possible to obtain large quantities of highly purified granules and granule membranes in a short period of time. Two protocols are presented here for the isolation of chromaffin granules: a basic protocol based on differential centrifugation in an iso-osmotic medium that yields intact chromaffin granules, and an alternate protocol based on sedimentation through a density step gradient that provides a greater yield of more highly purified chromaffin granules. Since in the latter case the granules cannot be returned to a medium of physiological osmolarity without lysis after purification on the step gradient, the alternate protocol is more useful to obtain the granule membranes or contents for further study.