gebhart/patrepeval huggingface dataset:
In vitro replication of DNA containing either the SV40 or the polyoma origin (1987)

The replication of DNA containing either the polyoma or SV40 origin has been done in vitro. Each system requires its cognate large-tumour antigen (T antigen) and extracts from cells that support its replication in vivo. The host-cell source of DNA polymerase alpha - primase complex plays an important role in discriminating between polyoma T antigen and SV40 T antigen-dependent replication of their homologous DNA. The SV40 origin- and T antigen-dependent DNA replication has been reconstituted in vitro with purified protein components isolated from HeLa cells. In addition to SV40 T antigen, HeLa DNA polymerase alpha - primase complex, eukaryotic topoisomerase I and a single-strand DNA binding protein from HeLa cells are required. The latter activity, isolated solely by its ability to support SV40 DNA replication, sediments and copurifies with two major protein species of 72 and 76 kDa. Although crude fractions yielded closed circular monomer products, the purified system does not. However, the addition of crude fractions to the purified system resulted in the formation of replicative form I (RFI) products. We have separated the replication reaction with purified components into multiple steps. In an early step, T antigen in conjunction with a eukaryotic topoisomerase (or DNA gyrase) and a DNA binding protein, catalyses the conversion of a circular duplex DNA molecule containing the SV40 origin to a highly underwound covalently closed circle. This reaction requires the action of a helicase activity and the SV40 T antigen preparation contains such an activity. The T antigen associated ability to unwind DNA copurified with other activities intrinsic to T antigen (ability to support replication of SV40 DNA containing the SV40 origin, poly dT-stimulated ATPase activity and DNA helicase).
A-Ion (2016)

This document contains recommendations for terminology in mass spectrometry. Development of standard terms dates back to 1974 when the IUPAC Commission on Analytical Nomenclature issued recommendations on mass spectrometry terms and definitions. In 1978, the IUPAC Commission on Molecular Structure and Spectroscopy updated and extended the recommendations and made further recommendations regarding symbols, acronyms, and abbreviations. The IUPAC Physical Chemistry Division Commission on Molecular Structure and Spectroscopy’s Subcommittee on Mass Spectroscopy revised the recommended terms in 1991 and appended terms relating to vacuum technology. Some additional terms related to tandem mass spectrometry were added in 1993 and accelerator mass spectrometry in 1994. Owing to the rapid expansion of the field in the intervening years, particularly in mass spectrometry of biomolecules, a further revision of the recommendations has become necessary. This document contains a comprehensive revision of mass spectrometry terminology that represents the current consensus of the mass spectrometry community.
Validation of GPU‐accelerated superposition–convolution dose computations for the Small Animal Radiation Research Platform (2018)

The GPU-accelerated Superposition-Convolution dose computation method was successfully validated with EBT2 film measurements and MC calculations. The SC method offers much faster computation speed than MC and provides calculations of both dose-to-water in medium and dose-to-medium in medium.
Automated assignment of SCOP and CATH protein structure classification from FSSP scores (2001)

We present an automated procedure to assign CATH and SCOP classifications to proteins whose FSSP score is available. CATH classification is assigned down to the topology level and SCOP classification to the fold level. As the FSSP database is updated weekly, this method makes it possible to update also CATH and SCOP with the same frequency. Our predictions have a nearly perfect success rate when ambiguous cases are discarded. These ambiguous cases are intrinsic in any protein structure classification, which relies on structural information alone. Hence, we introduce the notion of ``twilight zone for structure classification''. We further suggest that in order to resolve these ambiguous cases other criteria of classification, based also on information about sequence and function, must be used.
Storage Function of Carbon Nanospaces For Molecules and Ions (2007)

Interfacial importance and nanopore structures of single wall nanocarbons such as single wall carbon nanotube (SWCNT) and single wall carbon nanohorn (SWCNH) are described in terms of intermolecular interaction theory. The relationships between the nanopore structure and nanoconfinement effect for molecules and ions are shown using examples on supercritical H2 adsorption on SWCNT, quantum molecular sieving effect of SWCNT for H2 and D2 below 77 K, water structure and hydration structure of Rb, Cs, and Sr ions in nanopores of activated carbon fiber and SWCNH, and capacitance storage of SWCNH. The SWCNT produced by laser ablation shows upward-curved adsorption isotherm of H2 at 77 K, suggesting the presence of the strong sites. The adsorption amount of D2 on this SWCNT at 77 K was clearly larger than that of H2 by about 20% at 77 K due to quantum effect. The hydration number around Cs and Sr ions in 1.1 nm slit pores of ACF reduced by more than 20 %. The capacitance depended on the opening of SWCNH and charging time for organic electrolyte (C2H5)4NBF4 in propyrene carbonate.
QoS routing protocol based on ACO in wireless multimedia sensor network (2009)

In view of the complexity,higher power consumption and other shortcomings of current wireless multimedia sensor networks(WMSN) QoS routing protocol algorithm,this paper proposes the ant colony optimization to improve the WMSN routing protocol.First of all,a routing model for multimedia sensor networks QoS was presented and then a routing algorithm—AntWMSN was brought forward,which used the network restrict condition to update the pheromone concentration.The forward ants(Fant) collects the link bandwidth,delay,packet loss rate and other parameters,along with the elite strategy for the ant system to update the local node of the network state model and the pheromone of each visited node in order to find the best routing under the conditions of multi-constrained QoS.The simulation results show that the algorithm is characterized by the distributed network routing optimization and has better convergence than the traditional QoS routing protocol and can significantly improve the network lifetime.
Monoclonal antibodies to DNA modified by 8-methoxypsoralen and ultraviolet A light (1985)

A panel of monoclonal antibodies have been developed which specifically recognize DNA modified by 8-methoxypsoralen (8-MOP) and ultraviolet A light (320-400 nm) (UVA). These antibodies have been characterized as to sensitivity and specificity by an enzyme linked immunosorbent assay (ELISA). In a competitive ELISA with the most sensitive antibody, 50% inhibition of antibody binding occurred at 17 fmole 8-MOP-DNA photo adducts. One adduct per 10(7) bases could be reliably detected. There was also some antibody cross-reactivity with DNAs modified by 4' aminomethyl-4, 5, 8-trimethylpsoralen and 4', 5-dimethylangelicin as well as DNA isolated from cells treated with 8-MOP and UVA. The primary specificity of one of the antibodies was shown to be the 4', 5' thymine monoadduct by competitive inhibition studies using HPLC fractions of an enzymatic digest of 8-MOP poly(dA-dT) . poly(dA-dT). These antibodies should allow the quantitation of adduct levels in various in vitro systems as well as humans exposed clinically to 8-MOP and UVA.
Immunogenicity of a virosomally-formulated Plasmodium falciparum GLURP-MSP3 chimeric protein-based malaria vaccine candidate in comparison to adjuvanted formulations (2011)

A virosomal formulation of the chimeric protein GMZ2 induced P. falciparum blood stage parasite cross-reactive IgG responses specific for both MSP3 and GLURP. GMZ2 thus represents a candidate component suitable for inclusion into a multi-valent virosomal malaria vaccine and influenza virosomes represent a versatile antigen delivery system suitable for adjuvant-free immunization with recombinant proteins.
Outcome of Secondary Open Surgical Procedure in Patients who Failed Primary Endopyelotomy (1993)

Endopyelotomy is an effective method for treating pelviureteric junction (PUJ) obstruction; however, up to 28% of patients fail endoscopic treatment and require a secondary open surgical procedure. Six patients underwent secondary open surgical procedures following failed endopyelotomy for primary PUJ obstruction at this institution. One patient had impaired renal function in the affected kidney prior to endopyelotomy and postoperative evaluation indicated further deterioration; nephrectomy was performed for chronic obstruction and pain. The remaining 5 patients underwent secondary open pyeloplasty. In 4 patients the operation was difficult and lengthy because of extensive periureteric fibrosis. Difficult dissection was associated with a repeat endoscopic attempt to repair the PUJ obstruction, urinoma formation or stent occlusion requiring intervention. A mean follow-up of 1.7 years demonstrated no radiographic or clinical evidence of recurrent obstruction in the 5 patients undergoing secondary open pyeloplasty; all 6 patients are currently asymptomatic.
The structure and energetics of carbon-nitrogen clusters (2001)

The structures and energies of clusters of carbon and nitrogen with up to 12 atoms have been investigated by density functional theory using the hybrid B3LYP functional and the cc-pVTZ basis set. This is the first systematic study of these clusters. Geometries are reported for the lowest energy states at this level of theory. Linear structures tend to be the global minima for clusters containing one or two nitrogen atoms, and patterns in the electronic structure of these clusters are reported. More complex branched structures lie close in energy to the linear conformations and, for clusters greater than six atoms and containing three or more nitrogen atoms, these branched structures are the minimum energy conformers. Comparisons are made with pure carbon and silicon-carbon clusters.
Impact of chronic migraine attacks and their severity on the endogenous μ-opioid neurotransmission in the limbic system (2019)

Increased endogenous μ-opioid receptor-mediated neurotransmission is seen in the limbic system of CM patients, especially in right amygdala, which is highly modulated by the attack frequency, pain severity, and sensitivity. This study demonstrates for the first time the negative impact of chronification and exacerbation of headache attacks on the endogenous μ-opioid mechanisms of migraine patients. ClinicalTrials.gov identifier: NCT03004313.
Preoperative planning in shoulder arthroplasty: what about the soft tissue? (2022)

The primary objective of this study was to obtain a reliable method of automatic segmentation of shoulder muscles. The secondary objective of this study was to define a new computed tomography (CT)-based quantitative 3-dimensional (3D) measure of muscle loss (3DML) based on the rationale of the 2-dimensional (2D) qualitative Goutallier score. 102 CT scans were manually segmented and an algorithm of automated segmentation of the muscles was created. The volume of muscle fibers without intramuscular fat was then calculated for each rotator cuff muscle and normalized to the patient's scapular volume to account for the effect of body size (NVfibers). 3D muscle mass (3DMM) was calculated by dividing the NVfibers value of a given muscle by the mean expected volume in healthy shoulders. 3D muscle loss (3DML) was defined as 1 - (3DMM). Automated segmentation of the muscles was possible with a mean Dice of 0.904 ± 0.01 for the deltoid, 0.887 ± 0.014 for the infraspinatus (ISP), 0.892 ± 0.008 for the subscapularis (SSC), 0.885 for the supraspinatus (SSP) and 0.796 ± 0.006 for the teres minor (TM). The mean values of 3DFI and 3DML were 0.9% and 5.3% for Goutallier 0, 2.9% and 25.6% for Goutallier 1, 11.4% and 49.5% for Goutallier 2, 20.7% and 59.7% for Goutallier 3, and 29.3% and 70.2% for Goutallier 4, respectively. 3DML measurements obtained automatically incorporate both atrophy and fatty infiltration, thus they could become a very reliable index for assessing shoulder muscle function which could help in the decision process in shoulder surgery
L' affare dei morti mercato funerario, politica e gestione della sepoltura a Napoli (secoli XVII - XIX) (2014)

Carnevale Diego. L’affare dei morti : mercato funerario, politica e gestione della sepoltura a Napoli (secoli XVII-XIX) Rome : École Française de Rome, 2014. 0 p. (Publications de l'École française de Rome, 496)
Excision of bilateral multiple pulmonary arteriovenous fistulas complicating Rendu-Osler-Weber disease. (1991)

Rendu-Oslar-Weber病に伴う14歳男性の両側多発性肺動静脈瘻症例に対し, 二期的両側開胸により瘻切除術を行なった.手術前の検査成績では著明な低酸素血症を認め, 右-左シャント率は29%であった.運動に伴い動脈血酸素飽和度が低下し, 耐運動能に著しい制限を認めた.左開胸による肺動静脈瘻切除のみではシャント率は25%に低下したにとどまった.一方, 両側開胸術後には動脈血酸素分圧は上昇し, シャント率は16%にまで低下した.また運動に伴う動脈血酸素飽和度の低下は軽微で, 耐運動能に飛躍的な改善が得られた.従来より両側多発性肺動静脈瘻に対する外科療法の適応はしぼしば困難とされてきた.しかし肺組織の温存を意図した瘻切除術により血行動態に十分な改善が得られることから, 両側多発性肺動静脈瘻に対しても積極的な外科治療を行なうことが肝要であると考えられた.
Watermarking JBIG2 text region for image authentication (2005)

An authentication watermarking technique (AWT) inserts hidden data into an image in order to detect any accidental or malicious alteration to the image. AWT usually computes, using a secret-key, the message authentication code (MAC) of the image, and somehow inserts MAC into the image itself. The authentication verification is performed using the same secret-key used in the insertion. JBIG2 is an international standard for lossy and lossless binary image compression. It decomposes the image into several regions (text, halftone, line-art) and encodes each one using the most appropriate method. This paper proposes a novel data-hiding technique to embed the data into the text region of a JBIG2 file. We, then, use it to create an AWT for a JBIG2-encoded image. The embedded data can be extracted from either the JBIG2 file itself or the binary image obtained by decoding the JBIG2 file.
Macrocyclic Retinoic Acid Receptor-Related Orphan Receptor C2 Inverse Agonists (2023)

Macrocyclic retinoic acid receptor-related orphan receptor C2 (RORC2) inverse agonists have been designed with favorable properties for topical administration. Inspired by the unanticipated bound conformation of an acyclic sulfonamide-based RORC2 ligand from cocrystal structure analysis, macrocyclic linker connections between the halves of the molecule were explored. Further optimization of analogues was accomplished to maximize potency and refine physiochemical properties (MW, lipophilicity) best suited for topical application. Compound <b>14</b> demonstrated potent inhibition of interleukin-17A (IL-17A) production by human Th17 cells and in vitro permeation through healthy human skin achieving high total compound concentration in both skin epidermis and dermis layers.
Nanoscience and Nanotechnology at UCLA (2019)

ADVERTISEMENT RETURN TO ISSUEEditorialNEXTNanoscience and Nanotechnology at UCLAAli KhademhosseiniAli KhademhosseiniMore by Ali Khademhosseinihttp://orcid.org/0000-0002-2692-1524, Andre E. NelAndre E. NelMore by Andre E. Nelhttp://orcid.org/0000-0002-5232-4686, Holly BunjeHolly BunjeMore by Holly Bunjehttp://orcid.org/0000-0002-3085-9890, Christopher J. DeSantisChristopher J. DeSantisMore by Christopher J. DeSantishttp://orcid.org/0000-0002-4769-7541, Anne M. AndrewsAnne M. AndrewsMore by Anne M. Andrewshttp://orcid.org/0000-0002-1961-4833, Rita A. BlaikRita A. BlaikMore by Rita A. Blaikhttp://orcid.org/0000-0003-3449-8882, Zhen GuZhen GuMore by Zhen Guhttp://orcid.org/0000-0003-2947-4456, Huan MengHuan MengMore by Huan Menghttp://orcid.org/0000-0001-8844-3938, Aydogan OzcanAydogan OzcanMore by Aydogan Ozcanhttp://orcid.org/0000-0002-0717-683X, Sarah H. TolbertSarah H. TolbertMore by Sarah H. Tolberthttp://orcid.org/0000-0001-9969-1582, Tian XiaTian XiaMore by Tian Xiahttp://orcid.org/0000-0003-0123-1305, Jeffrey I. ZinkJeffrey I. ZinkMore by Jeffrey I. Zinkhttp://orcid.org/0000-0002-9792-4976, and Paul S. Weiss*Paul S. Weiss*E-mail: [email protected]More by Paul S. Weisshttp://orcid.org/0000-0001-5527-6248Cite this: ACS Nano 2019, 13, 6, 6127–6129Publication Date (Web):June 25, 2019Publication History Published online25 June 2019Published inissue 25 June 2019https://pubs.acs.org/doi/10.1021/acsnano.9b04680https://doi.org/10.1021/acsnano.9b04680editorialACS PublicationsCopyright © 2019 American Chemical Society. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views4987Altmetric-Citations1LEARN 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 PDF (2 MB) Get e-AlertscloseSUBJECTS:Luminescence,Nanoscience,Nanotechnology,Safety,Students Get e-Alerts
Discovery of Specific Inhibitors for Intestinal E. coli  β‐Glucuronidase through In Silico Virtual Screening (2015)

Glucuronidation is a major metabolism process of detoxification for carcinogens, 4-(methylnitrosamino)-1-(3-pyridy)-1-butanone (NNK) and 1,2-dimethylhydrazine (DMH), of reactive oxygen species (ROS). However, intestinal E. coli β-glucuronidase (eβG) has been considered pivotal to colorectal carcinogenesis. Specific inhibition of eβG may prevent reactivating the glucuronide-carcinogen and protect the intestine from ROS-mediated carcinogenesis. In order to develop specific eβG inhibitors, we found that 59 candidate compounds obtained from the initial virtual screening had high inhibition specificity against eβG but not human βG. In particular, we found that compounds 7145 and 4041 with naphthalenylidene-benzenesulfonamide (NYBS) are highly effective and selective to inhibit eβG activity. Compound 4041 (IC50 = 2.8 μM) shows a higher inhibiting ability than compound 7145 (IC50 = 31.6 μM) against eβG. Furthermore, the molecular docking analysis indicates that compound 4041 has two hydrophobic contacts to residues L361 and I363 in the bacterial loop, but 7145 has one contact to L361. Only compound 4041 can bind to key residue (E413) at active site of eβG via hydrogen-bonding interactions. These novel NYBS-based eβG specific inhibitors may provide as novel candidate compounds, which specifically inhibit eβG to reduce eβG-based carcinogenesis and intestinal injury.
Modeling Oxide Formation and Reduction on Platinum (2015)

The formation and reduction of surface oxide species determine both the electrocatalytic activity of Pt towards the oxygen reduction reaction as well as the rate of corrosive Pt dissolution [1]. We perform theory and modeling work to rationalize the various stages of oxide formation and reduction at Pt and, subsequently, use it to explore mechanisms of Pt dissolution. Mechanistic models developed through this work strive to establish relations between metal phase potential and surface oxidation state that govern the transient current response of the electrode. The first part focuses on a recently developed kinetic model for oxide formation and reduction at Pt in the voltage range of 0.65–1.15 V [2]. The model is evaluated against electrochemical [3], spectroscopic [4] and computational studies [5]. The second part presents a kinetic model of oxide growth on platinum in the high voltage regime, above 1.15 V. The governing equations of the oxide growth model account for mass and charge conservation, species migration, and electric field effects. The model is expected to provide insights into different oxide growth mechanisms and to rationalize various growth laws that have been found experimentally. Results will be compared to experimental cyclic voltammetry data to extract rates of kinetic and transport processes. In an ensuing step, platinum dissolution kinetics will be incorporated and linked dynamically to oxide growth and reduction. It is thus expected that the model will be able to explain the dramatically enhanced rate of Pt dissolution that was found in recent experimental studies, when the electrode voltage was cycled through the high voltage regime [6,7,8]. The detailed mechanistic understanding of oxide growth and reduction on platinum will thus complete our theory of platinum dissolution in catalyst layers for polymer electrolyte fuel cells [9]. References [1] A. Seyeux, V. Maurice, and P. Marcus, J. Electrochem. Soc. 160 , C189 (2013). [2] S. G. Rinaldo, W. Lee, J. Stumper, and M. Eikerling, Electrocatalysis 5 , 262 (2014). [3] A.M. Gómez-Marín, J. Clavilier, J.M. Feliu, J. Electroanal. Chem. 688 , 360 (2013) [4] M. Wakisaka, H. Suzuki, S. Mitsui, H. Uchida, M. Watanabe, Langmuir 25 , 1897 (2009) [5] L. Wang, A. Roudgar, M. Eikerling, J. Phys. Chem. C 113 , 17989 (2009) [6] S. G. Rinaldo, P. Urchaga, J. Hu, W. Lee, J. Stumper, C. Rice, and M. Eikerling, Phys. Chem. Chem. Phys. , in press. [7] A. A. Topalov, S. Cherevko, A. R. Zeradjanin, J. C. Meier, I. Katsounaros, and K. J. J. Mayrhofer, Chemical Science 5 , 631 (2014). [8] L. Xing, M. A. Hossain, M. Tian, D. Beauchemin, K. T. Adjemian, and G. Jerkiewicz, Electrocatalysis 5 , 96 (2014). [9] S. G. Rinaldo, W. Lee, J. Stumper, and M. Eikerling, Physical Review E 86 , 041601 (2012).
Metal carbonyl photoassisted cis-trans isomerization of stilbene (1971)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMetal carbonyl photoassisted cis-trans isomerization of stilbeneHarry B. Gray, Mark Wrighton, and G. S. HammondCite this: J. Am. Chem. Soc. 1971, 93, 13, 3285–3287Publication Date (Print):June 1, 1971Publication History Published online1 May 2002Published inissue 1 June 1971https://pubs.acs.org/doi/10.1021/ja00742a033https://doi.org/10.1021/ja00742a033research-articleACS PublicationsRequest reuse permissionsArticle Views149Altmetric-Citations29LEARN 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