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Jan Wilhelm, Patrick Seewald, Mauro Del Ben, Juerg Hutter
We present an algorithm for computing the correlation energy in the random phase approximation (RPA) in a Gaussian basis requiring $\mathcal{O}(N^3)$ operations and $\mathcal{O}(N^2)$ memory. The method is based on the resolution of the identity (RI) with the overlap metric, a reformulation of RI-RPA in the Gaussian basis, imaginary time and imaginary frequency integration techniques and the use of sparse linear algebra. Additional memory reduction without extra computations can be achieved by an iterative scheme which overcomes the memory bottleneck of canonical RPA implementations...
October 25, 2016: Journal of Chemical Theory and Computation
Miriam Jauset-Rubio, Jonathan Sabaté Del Río, Teresa Mairal, Markéta Svobodová, Mohammad S El-Shahawi, Abdulaziz S Bashammakh, Abdulrahman O Alyoubi, Ciara K O'Sullivan
Lupin is increasingly being used in a variety of food products due to its nutritional, functional and nutraceutical properties. However, several examples of severe and even fatal food-associated anaphylaxis due to lupin inhalation or ingestion have been reported, resulting in the lupin subunit β-conglutin, being defined as the Lup an 1 allergen by the International Union of Immunological Societies (IUIS) in 2008. Here, we report an innovative method termed aptamer-recombinase polymerase amplification (Apta-RPA) exploiting the affinity and specificity of a DNA aptamer selected against the anaphylactic β-conglutin allergen termed β-conglutin binding aptamer II (β-CBA II), facilitating ultrasensitive detection via isothermal amplification...
October 20, 2016: Analytical and Bioanalytical Chemistry
Zhi-Hao Cui, Feng Wu, Hong Jiang
The relative stability of TiO2 in the rutile and anatase structure is wrongly described by density functional theory in various local, semilocal, or even hybrid functional approximations. In this work, we have found that by considering high-order correlations in the adiabatic connection fluctuation-dissipation theory with the random phase approximation (ACFDT-RPA), rutile is correctly predicted to be more stable than anatase, which can be physically attributed to different characters in the electronic band structure of rutile and anatase, including, in particular, that rutile has a smaller band gap than anatase...
October 20, 2016: Physical Chemistry Chemical Physics: PCCP
T Chen, Z-P Guo, L-X Fu, N Cao, S Qin
BACKGROUND: Tumour necrosis factor (TNF)-like weak inducer of apoptosis (TWEAK) is a pro-inflammatory cytokine, which is closely associated with the pathogenesis of various types of cutaneous vasculitis (CV). AIM: To investigate the therapeutic effects of an anti-TWEAK monoclonal antibody (mAb) in a mouse model of cutaneous reverse passive Arthus (RPA) reaction. METHODS: Cutaneous RPA reaction was induced in BALB/c mice by intradermal injection of anti-ovalbumin IgG into the left ear followed immediately by intravenous injection of chicken ovalbumin...
October 18, 2016: Clinical and Experimental Dermatology
A van Uitert, F C H d'Ancona, J Deinum, H J L M Timmers, J F Langenhuijsen
BACKGROUND: Laparoscopic adrenalectomy is an effective method for benign adrenal tumor removal. In the literature, both lateral transperitoneal (TLA) and posterior retroperitoneoscopic (RPA) approaches are described. Since 2007, the number of patients increased significantly in our center. Therefore, RPA was introduced in 2011 because of its potential advantages in operating and recovery times. The learning curve of RPA is now evaluated. METHODS: All data of patients undergoing laparoscopic adrenalectomy from 2007 until 2014 were prospectively collected...
October 17, 2016: Surgical Endoscopy
Patricia Perez-Arnaiz, Daniel L Kaplan
Mcm10 is an essential protein that functions to initiate DNA replication after the formation of the replication fork helicase. In this manuscript, we identified a budding yeast Mcm10 mutant (Mcm10-m2,3,4) that is defective in DNA binding in vitro. Moreover, this Mcm10-m2,3,4 mutant does not stimulate the phosphorylation of Mcm2 by DDK in vitro. When we expressed wild-type levels of mcm10-m2,3,4 in budding yeast cells, we observed a severe growth defect and substantially decreased DNA replication. We also observed a substantially reduced RPA-ChIP signal at origins of replication, reduced levels of DDK-phosphorylated-Mcm2 and diminished GINS association with Mcm2-7 in vivo...
October 14, 2016: Journal of Molecular Biology
Craig Waitt, Nashali M Ferrara, Henk Eshuis
The performance of the random phase approximation (RPA) is tested for ther- mochemistry and geometries of transition metal chemistry using various benchmarks obtained either computationally or experimentally. Comparison is made to popular (semi-)local, meta- and hybrid density functionals as well as to second-order Møller- Plesset perturbation theory (MP2) and its spin-component-scaled derivatives. The benchmarks sets include reaction energies, barrier heights and dissociation energies of prototype bond-activation reactions, dissociation energies for a set of large transition metal complexes, bond lengths and dissociation energies of metal hydride ions, and bond lengths and angles of a set of closed-shell first-row transition metal complexes...
October 17, 2016: Journal of Chemical Theory and Computation
Abhishek Raval, Bhavesh Thakkar, Tarun Madan, Nilesh Oswal, Rajiv Garg, Rhshikesh Umalkar, Komal Shah, Bhumika Maheriya
OBJECTIVES: We aimed to study the feasibility and outcomes of ductal stenting in patients with duct-dependent pulmonary blood flow (PBF). METHODS: Duct-dependent hypoxic patients with confluent pulmonary artery (PA) branches were enrolled for ductal stenting and followed regularly. RESULTS: Sixty patients, with a median age of 12 (1-1095) days and weight of 2.8 (2.2-8.9) kg, were enrolled. Median right PA (RPA) and left PA (LPA) Z-scores were -1...
October 13, 2016: Portuguese Journal of Cardiology: An Official Journal of the Portuguese Society of Cardiology
Zain A Husain, Tiange Chen, Christopher D Corso, Zoheng Wang, Henry Park, Benjamin Judson, Wendell Yarbrough, Hari Deshpande, Saral Mehra, Phoebe Kuo, Roy H Decker, Barbara A Burtness
Importance: The current American Joint Committee on Cancer/Union for International Cancer Control (AJCC/UICC) staging system, developed for human papillomavirus (HPV)-unrelated disease, discriminates poorly when applied to HPV-related oropharyngeal squamous cell cancer (OPSCC), leading to calls for a new staging system. Objective: To compare the prognostic ability of the AJCC/UICC seventh edition staging system; a recently proposed system, the International Collaboration on Oropharyngeal Cancer Network for Staging (ICON-S); and a novel objectively derived system for HPV-related OPSCC using a national database of patients primarily treated with either radiation or surgery...
October 13, 2016: JAMA Oncology
Yukinori Takenaka, Norihiko Takemoto, Toshimichi Yasui, Yoshifumi Yamamoto, Atsuhiko Uno, Haruka Miyabe, Naoki Ashida, Kotaro Shimizu, Susumu Nakahara, Atshushi Hanamoto, Takahito Fukusumi, Takahiro Michiba, Hironori Cho, Masashi Yamamoto, Hidenori Inohara
Various serum biomarkers have been developed for predicting head and neck squamous cell carcinoma (HNSCC) prognosis. However, none of them have been proven to be clinically significant. A recent study reported that the ratio of aspartate aminotransaminase (AST) to alanine aminotransaminase (ALT) had a prognostic effect on non-metastatic cancers. This study aimed to examine the effect of the AST/ALT ratio on the survival of patients with HNSCC. Clinical data of 356 patients with locoregionally advanced HNSCC were collected...
2016: PloS One
Yu-Tong Chen, Ze-Ping Huang, Zhi-Wei Zhou, Ming-Ming He
Previous studies of pancreatic ductal adenocarcinoma (PDAC) have demonstrated that the addition of tumor grade to the 7th American Joint Committee on Cancer (AJCC) staging can provide improved prognostication and that the recently proposed 8th edition AJCC staging exhibited superior reproducibility to the 7th edition in resectable PDAC. Thus, we aimed to combine tumor grade and 8th AJCC stage to develop a refined staging scheme for resectable PDAC. We analyzed 7719 patients with resectable PDAC from the 2004-2012 Surveillance, Epidemiology, and End Results database...
November 2016: Medical Oncology
Huimin Zhang, Yu Hua, Rui Li, Daochun Kong
Double-stranded DNA breaks (DSBs) are highly detrimental DNA lesions, which may be repaired by the homologous recombination-mediated repair pathway. The 5 prime to 3 prime direction of long-range end resection on one DNA strand, in which 3 prime-single-strand DNA overhangs are created from broken DNA ends, is an essential step in this pathway. Dna2 has been demonstrated as an essential nuclease in this event, but the molecular mechanism how Dna2 is recruited to DNA break sites in vivo is not elucidated. In this study, a novel recombination factor called Cdc24 was identified in fission yeast...
October 11, 2016: Journal of Biological Chemistry
Thomas E Bass, Jessica W Luzwick, Gina Kavanaugh, Clinton Carroll, Huzefa Dungrawala, Gloria G Glick, Michael D Feldkamp, Reid Putney, Walter J Chazin, David Cortez
The ATR checkpoint kinase coordinates cellular responses to DNA replication stress. Budding yeast contain three activators of Mec1 (the ATR orthologue); however, only TOPBP1 is known to activate ATR in vertebrates. We identified ETAA1 as a replication stress response protein in two proteomic screens. ETAA1-deficient cells accumulate double-strand breaks, sister chromatid exchanges, and other hallmarks of genome instability. They are also hypersensitive to replication stress and have increased frequencies of replication fork collapse...
October 10, 2016: Nature Cell Biology
Peter Haahr, Saskia Hoffmann, Maxim A X Tollenaere, Teresa Ho, Luis Ignacio Toledo, Matthias Mann, Simon Bekker-Jensen, Markus Räschle, Niels Mailand
Activation of the ATR kinase following perturbations to DNA replication relies on a complex mechanism involving ATR recruitment to RPA-coated single-stranded DNA via its binding partner ATRIP and stimulation of ATR kinase activity by TopBP1. Here, we discovered an independent ATR activation pathway in vertebrates, mediated by the uncharacterized protein ETAA1 (Ewing's tumour-associated antigen 1). Human ETAA1 accumulates at DNA damage sites via dual RPA-binding motifs and promotes replication fork progression and integrity, ATR signalling and cell survival after genotoxic insults...
October 10, 2016: Nature Cell Biology
Kaifeng Wang, Yue Wu, Dan Yin, Shixing Tang, Guifang Hu, Yaqing He
Coxsackievirus A6 (CV-A6) is an important pathogen causing hand, foot and mouth disease (HFMD). The aim of this study was to develop and evaluate a rapid real-time reverse transcription recombinase polymerase amplification (RT-RPA) assay for detection of CV-A6. The sensitivity of this assay was 202 copies/reaction, with 100 % specificity. Furthermore, this assay yielded consistent results comparable with a commercial qRT-PCR diagnostic kit. This assay is therefore potentially useful for surveillance of CV-A6 infections and outbreak control...
October 8, 2016: Archives of Virology
Kevin M Koo, Eugene J H Wee, Paul N Mainwaring, Yuling Wang, Matt Trau
Cancer is a heterogeneous disease which manifests as different molecular subtypes due to the complex nature of tumor initiation, progression, and metastasis. The concept of precision medicine aims to exploit this cancer heterogeneity by incorporating diagnostic technology to characterize each cancer patient's molecular subtype for tailored treatments. To characterize cancer molecular subtypes accurately, a suite of multiplexed bioassays have currently been developed to detect multiple oncogenic biomarkers. Despite the reliability of current multiplexed detection techniques, novel strategies are still needed to resolve limitations such as long assay time, complex protocols, and difficulty in interpreting broad overlapping spectral peaks of conventional fluorescence readouts...
September 26, 2016: Small
Akihiro Sasahara, Mamika Motokawa, Katsunari Terakawa, Takashi Miyamoto
We have repaired a unilateral absent pulmonary artery(UAPA) using a prosthetic graft with a ring. Case 1 was a 1-month old girl. The right pulmonary artery(RPA) was anti-anatomically reconstructed with a 4 mm ePTFE graft. In postoperative year 1, however, the graft became stenosed due to compression by the ascending aorta. We reversed the stenosis with a 6 mm stent by percutaneous transluminal angioplasty. Case 2 was 6-year old boy. His RPA was anatomically reconstructed with a ringed 5 mm ePTFE graft when he was 5-months old...
October 2016: Kyobu Geka. the Japanese Journal of Thoracic Surgery
Andrew A Kelso, Steven D Goodson, Leah E Watts, LeAnna L Ledford, Sarah M Waldvogel, J Nathaniel Diehl, Shivani B Shah, Amanda F Say, Julie D White, Michael G Sehorn
Homologous recombination (HR) is a template-driven repair pathway that mends DNA double-stranded breaks (DSBs), and thus helps to maintain genome stability. The RAD51 recombinase facilitates DNA joint formation during HR, but to accomplish this task, RAD51 must be loaded onto the single-stranded DNA. DSS1, a candidate gene for split hand/split foot syndrome, provides the ability to recognize RPA-coated ssDNA to the tumor suppressor BRCA2, which is complexed with RAD51. Together BRCA2-DSS1 displace RPA and load RAD51 onto the ssDNA...
September 30, 2016: Nucleic Acids Research
Anukana Bhattacharjee, Jason Stewart, Mary Chaiken, Carolyn M Price
Mammalian CST (CTC1-STN1-TEN1) participates in multiple aspects of telomere replication and genome-wide recovery from replication stress. CST resembles Replication Protein A (RPA) in that it binds ssDNA and STN1 and TEN1 are structurally similar to RPA2 and RPA3. Conservation between CTC1 and RPA1 is less apparent. Currently the mechanism underlying CST action is largely unknown. Here we address CST mechanism by using a DNA-binding mutant, (STN1 OB-fold mutant, STN1-OBM) to examine the relationship between DNA binding and CST function...
September 2016: PLoS Genetics
Valerie W Rusch, Kari Chansky, Hedy L Kindler, Anna K Nowak, Harvey I Pass, David C Rice, Lynn Shemanski, Françoise Galateau-Sallé, Brian C McCaughan, Takashi Nakano, Enrico Ruffini, Jan P van Meerbeeck, Masahiro Yoshimura
INTRODUCTION: The M component and TNM stage groupings for malignant pleural mesothelioma (MPM) have been empirical. The International Association for the Study of Lung Cancer developed a multinational database to propose evidence-based revisions for the eighth edition of the TNM classification of MPM. METHODS: Data from 29 centers were submitted either electronically or by transfer of existing institutional databases. The M component as it currently stands was validated by confirming sufficient discrimination (by Kaplan-Meier analysis) with respect to overall survival (OS) between the clinical M0 (cM0) and cM1 categories...
September 28, 2016: Journal of Thoracic Oncology
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