gebhart/patrepeval huggingface dataset:
Replication of simian virus 40 origin-containing DNA in vitro with purified proteins. (1987)

Simian virus 40 (SV40) DNA replication dependent on the SV40 origin of replication and the SV40 large tumor (T) antigen has been reconstituted in vitro with purified protein components isolated from HeLa cells. In addition to SV40 T antigen, these components included the DNA polymerase alpha-primase complex, topoisomerase I, and a fraction that contained a single-stranded DNA binding protein. The latter protein, which sediments at 5.1 S on glycerol gradients and copurifies with two major protein species of 72 and 76 kDa, was isolated solely by its ability to support SV40 DNA replication. The purified system retained the species-specific DNA polymerase alpha-primase requirement previously observed with crude fractions; the complex from HeLa cells supported SV40 replication, whereas that from calf thymus and mouse cells did not. DNA containing the polyomavirus origin of replication was replicated in a system containing polyomavirus T antigen, the HeLa single-stranded DNA binding protein-containing fraction, and DNA polymerase alpha-primase complex from mouse, but not HeLa, cells. While crude fractions yielded closed circular duplex DNA, none was detected with the purified system. Nevertheless, the addition of a crude fraction to the purified system yielded closed circular monomer products.
HOMOGENIZATION OF PERIODIC OBJECTS EMBEDDED IN LAYERED MEDIA (2015)

An effective medium modeling technique is proposed to homogenize the periodic objects embedded in layered media. The homogenization is based on the same scattering coefficients. An integral equation based approach is adopted to solve the scattering problem of original structures. Our modeling results are compared with Maxwell-Garnett mixing formula and published results. Good agreements have been observed. Periodic metal patches embedding in layered dielectric structure is fabricated and measured to validate the modeling technique. The difference between experiment results and proposed modeling results is less than 3%.
Methodology to construct large realizations of perfectly hyperuniform disordered packings (2019)

Disordered hyperuniform packings (or dispersions) are unusual amorphous two-phase materials that are endowed with exotic physical properties. Such hyperuniform systems are characterized by an anomalous suppression of volume-fraction fluctuations at infinitely long-wavelengths, compared to ordinary disordered materials. While there has been growing interest in such singular states of amorphous matter, a major obstacle has been an inability to produce large samples that are perfectly hyperuniform due to practical limitations of conventional numerical and experimental methods. To overcome these limitations, we introduce a general theoretical methodology to construct perfectly hyperuniform packings in d-dimensional Euclidean space R^{d}. Specifically, beginning with an initial general tessellation of space by disjoint cells that meets a "bounded-cell" condition, hard particles of general shape are placed inside each cell such that the local-cell particle packing fractions are identical to the global packing fraction. We prove that the constructed packings with a polydispersity in size are perfectly hyperuniform in the infinite-sample-size limit, regardless of particle shapes, positions, and numbers per cell. We use this theoretical formulation to devise an efficient and tunable algorithm to generate extremely large realizations of such packings. We employ two distinct initial tessellations: Voronoi as well as sphere tessellations. Beginning with Voronoi tessellations, we show that our algorithm can remarkably convert extremely large nonhyperuniform packings into hyperuniform ones in R^{2} and R^{3}. Implementing our theoretical methodology on sphere tessellations, we establish the hyperuniformity of the classical Hashin-Shtrikman multiscale coated-spheres structures, which are known to be two-phase media microstructures that possess optimal effective transport and elastic properties. A consequence of our work is a rigorous demonstration that packings that have identical tessellations can either be nonhyperuniform or hyperuniform by simply tuning local characteristics. It is noteworthy that our computationally designed hyperuniform two-phase systems can easily be fabricated via state-of-the-art methods, such as 2D photolithographic and 3D printing technologies. In addition, the tunability of our methodology offers a route for the discovery of novel disordered hyperuniform two-phase materials.
Spatial Scalable JPEG2000 Transcoding and Tracking of Regions of Interest for Video Surveillance. (2008)

This paper presents a method for spatial scalable region of interest transcoding of JPEG2000 coded video frames for video surveillance systems. Based on a user defined ROI the method transcodes HD frames into images in moderate resolution with a ROI in HD resolution. The transcoder extracts all packets belonging to the ROI or the lower resolution levels of the background from the JPEG2000 bitstream. Non-ROI packets of higher resolution levels are replaced by empty packets. The ROI is tracked using a mean shift algorithm to guarantee that always the correct image details are extracted in high resolution. Since the transcoding is performed by extracting and replacing packets of the codestream, an expensive re-encoding of the codestream is not required. Thus, the transcoding technique is of low complexity and shows a short processing time. Combining the transcoding technique with mean shift tracking leads to a powerful video transcoding technique.
Adaptation of Plasmodium falciparum to humans involved the loss of an ape-specific erythrocyte invasion ligand (2019)

Plasmodium species are frequently host-specific, but little is currently known about the molecular factors restricting host switching. This is particularly relevant for P. falciparum, the only known human-infective species of the Laverania sub-genus, all other members of which infect African apes. Here we show that all tested P. falciparum isolates contain an inactivating mutation in an erythrocyte invasion associated gene, PfEBA165, the homologues of which are intact in all ape-infective Laverania species. Recombinant EBA165 proteins only bind ape, not human, erythrocytes, and this specificity is due to differences in erythrocyte surface sialic acids. Correction of PfEBA165 inactivating mutations by genome editing yields viable parasites, but is associated with down regulation of both PfEBA165 and an adjacent invasion ligand, which suggests that PfEBA165 expression is incompatible with parasite growth in human erythrocytes. Pseudogenization of PfEBA165 may represent a key step in the emergence and evolution of P. falciparum.
ChemInform Abstract: Segment‐Coupling Prins Cyclizations. (1999)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
ChemInform Abstract: LARGE METAL ION‐CENTERED TEMPLATE REACTIONS. CHEMICAL AND SPECTRAL STUDIES OF THE ′SUPERPHTHALOCYANINE′ DIOXOCYCLOPENTAKIS(1‐IMINOISOINDOLINATO)URANIUM(VI) AND ITS DERIVATIVES (1978)

Abstract Die Templatereaktion von wasserfreiem Uranylchlorid mit den Phthalonitrilen (I) in trockenem DMF liefert die Uranylkomplexe (II) mit erweitertem Phthalocyaninmakrocyclus.
N-Glucosyl-5-amino-4-carbamoyl- and 4-Ethoxycarbonylimidazoles as Potential Precursors of 4-Oxoimdazo[4,5-c]-1,2,6-thiadiazine 2,2-Dioxides (1986)

The syntheses of l-(tetra-~-acetyl-6-D-glucopyrano- s y l ) -5 -a m i n o -4 -e t h o x y -c a r b o n y l i m i d a z o l e and 1-(tetra-C-acetyl-a
Data from First-in-Human Study of AT13148, a Dual ROCK-AKT Inhibitor in Patients with Solid Tumors (2023)

&lt;div&gt;AbstractPurpose:&lt;p&gt;AT13148 is an oral AGC kinase inhibitor, which potently inhibits ROCK and AKT kinases. In preclinical models, AT13148 has been shown to have antimetastatic and antiproliferative activity.&lt;/p&gt;Patients and Methods:&lt;p&gt;The trial followed a rolling six design during dose escalation. An intrapatient dose escalation arm to evaluate tolerability and a biopsy cohort to study pharmacodynamic effects were later added. AT13148 was administered orally three days a week (Mon–Wed–Fri) in 28-day cycles. Pharmacokinetic profiles were assessed using mass spectrometry and pharmacodynamic studies included quantifying p-GSK3β levels in platelet-rich plasma (PRP) and p-cofilin and p-MLC2 levels in tumor biopsies.&lt;/p&gt;Results:&lt;p&gt;Fifty-one patients were treated on study. The safety of 5–300 mg of AT13148 was studied. Further, the doses of 120–180–240 mg were studied in an intrapatient dose escalation cohort. The dose-limiting toxicities included hypotension (300 mg), pneumonitis, and elevated liver enzymes (240 mg), and skin rash (180 mg). The most common side effects were fatigue, nausea, headaches, and hypotension. On the basis of tolerability, 180 mg was considered the maximally tolerated dose. At 180 mg, mean &lt;i&gt;C&lt;/i&gt;&lt;sub&gt;max&lt;/sub&gt; and AUC were 400 nmol/L and 13,000 nmol/L/hour, respectively. At 180 mg, ≥50% reduction of p-cofilin was observed in 3 of 8 posttreatment biopsies.&lt;/p&gt;Conclusions:&lt;p&gt;AT13148 was the first dual potent ROCK-AKT inhibitor to be investigated for the treatment of solid tumors. The narrow therapeutic index and the pharmacokinetic profile led to recommend not developing this compound further. There are significant lessons learned in designing and testing agents that simultaneously inhibit multiple kinases including AGC kinases in cancer.&lt;/p&gt;&lt;/div&gt;
Front Matter: Volume 7320 (2009)

This PDF file contains the front matter associated with SPIE Proceedings Volume 7320, including the Title Page, Copyright information, Table of Contents, Introduction, and the Conference Committee listing.
A novel ESD super-clamp structure for TVS applications (2008)

This paper presents a new ESD clamp structure for transient voltage suppressor (TVS) applications that combines the advantages of avalanche diode and bipolar transistor clamps. The device structure consists of a non-snapback avalanche diode triggered vertical NPN transistor. The avalanche diode provides the fast trigger and current conduction path at low currents, while the vertical NPN bipolar transistor turn-on provides alternate low resistance path for current conduction at high currents. The snapback in the IV characteristics is minimized by matching the avalanche diode breakdown voltage V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">BD</sub> and the vertical NPN transistor open base collector-emitter breakdown voltage, BV <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">CEO-</sub> Measurements on fabricated devices show consistent results with the theory. The TVS has low leakage currents (< 25 nAmps), negligible snapback in the output characteristics (<0.5 Volts) and excellent clamping voltage at high currents (13.1 Volts @ 30 Amps of TLP current). The presence of low doped base region also results in 35 % decrease in the TVS capacitance.
A Bioactive Cartilage Graft of IGF1-Transduced Adipose Mesenchymal Stem Cells Embedded in an Alginate/Bovine Cartilage Matrix Tridimensional Scaffold (2019)

Articular cartilage injuries remain as a therapeutic challenge due to the limited regeneration potential of this tissue. Cartilage engineering grafts combining chondrogenic cells, scaffold materials, and microenvironmental factors are emerging as promissory alternatives. The design of an adequate scaffold resembling the physicochemical features of natural cartilage and able to support chondrogenesis in the implants is a crucial topic to solve. This study reports the development of an implant constructed with IGF1-transduced adipose-derived mesenchymal stem cells (immunophenotypes: CD105<sup>+</sup>, CD90<sup>+</sup>, CD73<sup>+</sup>, CD14<sup>-</sup>, and CD34<sup>-</sup>) embedded in a scaffold composed of a mix of alginate/milled bovine decellularized knee material which was cultivated <i>in vitro</i> for 28 days (3CI). Histological analyses demonstrated the distribution into isogenous groups of chondrocytes surrounded by a de novo dense extracellular matrix with balanced proportions of collagens II and I and high amounts of sulfated proteoglycans which also evidenced adequate cell proliferation and differentiation. This graft also shoved mechanical properties resembling the natural knee cartilage. A modified Bern/O'Driscoll scale showed that the 3CI implants had a significantly higher score than the 2CI implants lacking cells transduced with IGF1 (16/18 vs. 14/18), representing high-quality engineering cartilage suitable for <i>in vivo</i> tests. This study suggests that this graft resembles several features of typical hyaline cartilage and will be promissory for preclinical studies for cartilage regeneration.
On the presence of bilirubin in the ocular humors of premature infants. (1976)

The yellow pigments observed in the ocular humors of premature infants were identified as the plasma pigments bilirubin and oxyhemoglobin. The blood/vitreous humor barrier to bilirubin was estimated to be (1/0.11) for total bilirubin and (1/0.25) for direct-acting bilirubin. Hall method histochemical staining for bilirubin in sections of premature infant eyes was highly positive for the vitreous humor, and suggestive of uptake of bilirubin by the neural-retinal cells.
Robust Routing in Wireless Multi-Hop Networks (2007)

This paper introduces a robust approach to stochastic multi-hop routing for wireless networks when the quality of links is modelled through a reliability matrix R. Yielding to the practical constraint that link reliabilities have to be measured, we consider that R is random with known mean and variance. Thus, network utilities are also random quantities. Robust routing algorithms are then introduced to maximize an average utility subject to a variance constraint; or, alternatively, to minimize variance subject to a minimum utility yield. We prove that both problems can be solved by convex programming techniques. We further show that the robust routing optimization problems exhibit a separable structure enabling the proposal of routing protocols based on communication with one-hop neighbors only. Although the communication cost to compute the optimal routes is thus significantly reduced, we show that there is no performance penalty with respect to optimal routes computed by a centralized algorithm.
Tests of the Weak Equivalence Principle with Trapped Antimatter (1992)

Abstract Recent developments in the trapping of ions and neutral atoms suggest that significant improvements in the precision of spectroscopic measurements on such systems can be expected. The application of these techniques to trapped antiprotons, positrons and antihydrogen atoms opens up new possibilities for precision tests of the weak equivalence principle (WEP) for antimatter. It is shown that constraints on WEP for positrons and antiprotons may be imposed by comparison of electron and positron, or proton and antiproton cyclotron frequencies, or of transition frequencies in hydrogen and antihydrogen, at the same height in a gravitational potential. The constraints that may be inferred from the results of existing particle-antiparticle cyclotron frequency comparisons are derived, and the improvements which will be possible from future, higher precision experiments are analysed.
Mechanical Control of Tissue Morphogenesis (2008)

Mechanical forces participate in morphogenesis from the level of individual cells to whole organism patterning. This article reviews recent research that has identified specific roles for mechanical forces in important developmental events. One well defined example is that dynein-driven cilia create fluid flow that determines left-right patterning in the early mammalian embryo. Fluid flow is also important for vasculogenesis, and evidence suggests that fluid shear stress rather than fluid transport is primarily required for remodeling the early vasculature. Contraction of the actin cytoskeleton, driven by nonmuscle myosins and regulated by the Rho family GTPases, is a recurring mechanism for controlling morphogenesis throughout development, from gastrulation to cardiogenesis. Finally, novel experimental approaches suggest critical roles for the actin cytoskeleton and the mechanical environment in determining differentiation of mesenchymal stem cells. Insights into the mechanisms linking mechanical forces to cell and tissue differentiation pathways are important for understanding many congenital diseases and for developing regenerative medicine strategies.
Mitochondrial acetyl-CoA reversibly regulates locus-specific histone acetylation and gene expression (2018)

Abstract The impact of mitochondria in epigenetics is emerging but our understanding of this relationship and its impact on gene expression remain incomplete. We previously showed that acute mitochondrial DNA (mtDNA) loss leads to histone hypoacetylation. It remains to be defined if these changes are maintained when mitochondrial dysfunction is chronic and, importantly, if they are sufficient to alter gene expression. To fill these gaps, we here studied both a progressive and a chronic model of mtDNA depletion using biochemical, pharmacological, genomics and genetic assays. We show that histones are hypoacetylated in both models. We link these effects to decreased histone acetyltransferase (HAT) activity independent of changes in ATP citrate lyase function, which can be reversibly modulated by altering specifically the mitochondrial pool of acetyl-CoA. Also, we determined that these changes regulate locus-specific gene expression and physiological outcomes, including the production of prostaglandins. These results may be relevant to the pathophysiology of mtDNA depletion syndromes and to understanding the effects of environmental agents, such as AZT or antibiotics, that lead to physical or functional mtDNA loss.
Circular dichroism study of microtubule protein (1972)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCircular dichroism study of microtubule proteinMarta Ventilla, Charles R. Cantor, and Michael ShelanskiCite this: Biochemistry 1972, 11, 9, 1554–1561Publication Date (Print):April 1, 1972Publication History Published online1 May 2002Published inissue 1 April 1972https://pubs.acs.org/doi/10.1021/bi00759a002https://doi.org/10.1021/bi00759a002research-articleACS PublicationsRequest reuse permissionsArticle Views149Altmetric-Citations75LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Enhancement in light extraction efficiency from GaN based LEDs with nanopores ITO p-contact grown on patterned sapphire substrate (2010)

Blue light emitting diodes (LEDs) have been fabricated with InGaN/GaN well layers (QWs) on micro-patterned sapphire substrate (PSS). Low pressure growth of GaN layer on PSS effectively reduces the density of edge dislocations. The growth of InGaN/GaN MQWs on PSS as compared to conventional sapphire substrate (CSS) improves the internal quantum efficiency (IQE) from 50 to 56%. The higher thermal barrier for luminescence thermal quenching ensures of more e–h pair recombination at the quantum wells and improves the IQE. The light extraction efficiency (ηextr) from the LEDs is enhanced with use of PSS substrate and nanopores generation on the ITO p-contact. This would be attributed to the improvement in the quality of GaN film through reduction of threading dislocations and scattering of light from the sidewalls of the patterned sapphire.
Ex vivo catheter-based imaging of coronary atherosclerosis using multimodality OCT and NIRAF excited at 633 nm (2015)

While optical coherence tomography (OCT) has been shown to be capable of imaging coronary plaque microstructure, additional chemical/molecular information may be needed in order to determine which lesions are at risk of causing an acute coronary event. In this study, we used a recently developed imaging system and double-clad fiber (DCF) catheter capable of simultaneously acquiring both OCT and red excited near-infrared autofluorescence (NIRAF) images (excitation: 633 nm, emission: 680nm to 900nm). We found that NIRAF is elevated in lesions that contain necrotic core - a feature that is critical for vulnerable plaque diagnosis and that is not readily discriminated by OCT alone. We first utilized a DCF ball lens probe and a bench top setup to acquire en face NIRAF images of aortic plaques ex vivo (n = 20). In addition, we used the OCT-NIRAF system and fully assembled catheters to acquire multimodality images from human coronary arteries (n = 15) prosected from human cadaver hearts (n = 5). Comparison of these images with corresponding histology demonstrated that necrotic core plaques exhibited significantly higher NIRAF intensity than other plaque types. These results suggest that multimodality intracoronary OCT-NIRAF imaging technology may be used in the future to provide improved characterization of coronary artery disease in human patients.
Ventilation Defect Synthesis in Hyperpolarized 129Xe Ventilation MRI to Accelerate Training of Segmentation Models (2023)

Quantification of 129 Xe MRI relies on accurate segmentation of the thoracic cavity. This segmentation could potentially be performed directly on the 129 Xe ventilation image using an automated convolutional neural network, but this task is challenging, especially in cases where peripheral ventilation defects obscure the lung boundary. Currently, overcoming this obstacle requires large, diverse training datasets created by time-consuming manual segmentation. Here, we demonstrate the use of a generative Pix2Pix model to synthesize both 129 Xe images with defects, and corresponding segmentation masks. We then test the effects of this additional training data on the performance of an existing U-net segmentation algorithm.
DQDB/sup +/-/: a fair and waste-free media access protocol for dual bus metropolitan networks (1993)

A media access protocol that achieves a fair distribution of the bandwidth in one round-trip delay is presented. The protocol is based on a unique solution to a fair and waste-free bandwidth allocation. This bandwidth allocation can be implemented in a distributed manner. A comparison of the new protocol with the DQDB (distributed queue dual bus) protocol shows considerable advantages regarding the transmission delay of messages and the time a station needs to obtain a fair portion of the available bandwidth. The advantages of the protocol become more apparent for large networks and high transmission speeds. In addition, the new protocol can perform nonuniform bandwidth allocations.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>