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Double robustness

Niels Vandenberk, Anders Barth, Doortje Borrenberghs, Johan Hofkens, Jelle Hendrix
Förster resonance energy transfer (FRET) is a powerful tool to probe molecular interactions, activity, analytes, forces and structure. Single-molecule (sm) FRET additionally allows real-time quantifications of conformation and conformational dynamics. SmFRET robustness critically depends on the employed dyes, yet a systematic comparison of different dye pairs is lacking. Here, we evaluated blue (Atto488 and Alexa488) and far-red (Atto647N, Alexa647, StarRed and Atto655) dyes using confocal smFRET spectroscopy on freely diffusing dsDNA molecules...
March 15, 2018: Journal of Physical Chemistry. B
Xin Mu, Emily Greenwald, Sadeem Ahmad, Sun Hur
The emergence of RNA-based therapeutics demands robust and economical methods to produce RNA with few byproducts from aberrant activity. While in vitro transcription using the bacteriophage T7 RNA polymerase is one such popular method, its transcripts are known to display an immune-stimulatory activity that is often undesirable and uncontrollable. We here showed that the immune-stimulatory activity of T7 transcript is contributed by its aberrant activity to initiate transcription from a promoter-less DNA end...
March 9, 2018: Nucleic Acids Research
Gamal Badr, Halise Inci Gul, Cem Yamali, Amal A M Mohamed, Badr M Badr, Mustafa Gul, Ahmad Abo Markeb, Nagwa Abo El-Maali
Recent developments in the literature have demonstrated that curcumin exhibit antioxidant properties supporting its anti-inflammatory, chemopreventive and antitumoral activities against aggressive and recurrent cancers. Despite the valuable findings of curcumin against different cancer cells, the clinical use of curcumin in cancer treatment is limited due to its extremely low aqueous solubility and instability, which lead to poor in vivo bioavailability and limited therapeutic effects. We therefore focused in the present study to evaluate the anti-tumor potential of curcumin analogues on the human breast carcinoma cell lines MDA-MB-231 and MCF-7, as well as their effects on non-tumorigenic normal breast epithelial cells (MCF-10)...
March 7, 2018: Bioorganic Chemistry
Chandu V V Muralee Gopi, Saurabh Singh, Araveeti Eswar Reddy, Hee-Je Kim
This paper reports an efficient and simple strategy for the synthesis of molybdenum copper selenide (MoCuSe) nanoparticles decorated with a combination of a carbon nanotube (CNT) network and reduced graphene oxide (rGO) nanosheets to form an integrated hybrid architecture (CNT@rGO@MoCuSe) using a two-step hydrothermal approach. The synthesized hybrid CNT@rGO@MoCuSe material onto the Ni foam substrate is applied successfully as an effective counter electrode (CE) in quantum dot-sensitized solar cells (QDSSCs)...
March 13, 2018: ACS Applied Materials & Interfaces
Dirk Bauwens, Katja Claus, Joachim Mergeay
Capture-mark-recapture procedures are a basic tool in population studies and require that individual animals are correctly identified throughout their lifetime. A method that has become more and more popular uses photographic records of natural markings, such as pigmentation pattern and scalation configuration. As with any other marking tool, the validity of the photographic identification technique should be evaluated thoroughly. Here, we report on a large-scale double-marking study in which European adders ( Vipera berus ) were identified by both microsatellite genetic markers and by the pattern of head scalation...
March 2018: Ecology and Evolution
Sherri Rose
OBJECTIVE: To propose nonparametric double robust machine learning in variable importance analyses of medical conditions for health spending. DATA SOURCES: 2011-2012 Truven MarketScan database. STUDY DESIGN: I evaluate how much more, on average, commercially insured enrollees with each of 26 of the most prevalent medical conditions cost per year after controlling for demographics and other medical conditions. This is accomplished within the nonparametric targeted learning framework, which incorporates ensemble machine learning...
March 11, 2018: Health Services Research
Zhiqiang Li, John P Karis, James G Pipe
PURPOSE: 2D turbo-spin-echo (TSE) is widely used in the clinic for neuroimaging. However, the long refocusing radiofrequency pulse train leads to high specific absorption rate (SAR) and alters the contrast compared to conventional spin-echo. The purpose of this work is to develop a robust 2D spiral TSE technique for fast T2 -weighted imaging with low SAR and improved contrast. METHODS: A spiral-in/out readout is incorporated into 2D TSE to fully take advantage of the acquisition efficiency of spiral sampling while avoiding potential off-resonance-related artifacts compared to a typical spiral-out readout...
March 9, 2018: Magnetic Resonance in Medicine: Official Journal of the Society of Magnetic Resonance in Medicine
Alexander J Brown, Aneesa T Al-Soodani, Miles Saul, Stephanie Her, Juan C Garcia, Dale A Ramsden, Chengtao Her, Steven A Roberts
The mechanistic understanding of how DNA double-strand breaks (DSB) are repaired is rapidly advancing in part due to the advent of inducible site-specific break model systems as well as the employment of next-generation sequencing (NGS) technologies to sequence repair junctions at high depth. Unfortunately, the sheer volume of data produced by these methods makes it difficult to analyze the structure of repair junctions manually or with other general-purpose software. Here, we describe methods to produce amplicon libraries of DSB repair junctions for sequencing, to map the sequencing reads, and then to use a robust, custom python script, Hi-FiBR, to analyze the sequence structure of mapped reads...
2018: Methods in Enzymology
Dana E Rathkopf, Tomasz M Beer, Yohann Loriot, Celestia S Higano, Andrew J Armstrong, Cora N Sternberg, Johann S de Bono, Bertrand Tombal, Teresa Parli, Suman Bhattacharya, De Phung, Andrew Krivoshik, Howard I Scher, Michael J Morris
Importance: Drug development for metastatic castration-resistant prostate cancer has been limited by a lack of clinically relevant trial end points short of overall survival (OS). Radiographic progression-free survival (rPFS) as defined by the Prostate Cancer Clinical Trials Working Group 2 (PCWG2) is a candidate end point that represents a clinically meaningful benefit to patients. Objective: To demonstrate the robustness of the PCWG2 definition and to examine the relationship between rPFS and OS...
March 8, 2018: JAMA Oncology
Jing Zhu, Pei Zhang, Dongxu Chen, Ruifeng Liu, Yingnan Zhou, Jinwen Wang, Hong Gao, Fuli Li
Precisely determining the topological charge (TC) of both integral Bessel beams (IBB) and fractional Bessel beams (FBB) is a key issue for their applications. However, most of the common methods could not probe both the IBB and FBB precisely and robustly. In this paper, we present a robust method to probe the topological charge of a Bessel beam by dynamic angular double slits (ADSs). We find that when a Bessel beam vertically illuminates on a dynamic ADS, the information of the TC can be retrieved from its Fourier transform patterns near the optical axis...
March 1, 2018: Applied Optics
Bahram Javidi, Adam Markman, Siddharth Rawat
We investigate the use of compact, lensless, single random phase encoding (SRPE) and double random phase encoding (DRPE) systems for automatic cell identification when multiple cells, either of the same or mixed classes, are in the field of view. A microscope glass slide containing the sample is inputted into the single or double random phase encoding system, which is then illuminated by a coherent or partially coherent light source generating a unique opto-biological signature (OBS) that is captured by an image sensor...
March 1, 2018: Applied Optics
P V Kumar, S K Sharma, N Rishi, D K Ghosh, V K Baranwal
Management of viral diseases relies on definite and sensitive detection methods. Citrus yellow mosaic virus (CYMV), a double stranded DNA virus of the genus Badnavirus, causes yellow mosaic disease in citrus plants. CYMV is transmitted through budwood and requires a robust and simplified indexing protocol for budwood certification programme. The present study reports development and standardization of an isothermal based recombinase polymerase amplification (RPA) assay for a sensitive, rapid, easy, and cost-effective method for detection and diagnosis of CYMV...
2018: Acta Virologica
Rajia Bahri, Adnan Custovic, Peter Korosec, Marina Tsoumani, Martin Barron, Jiakai Wu, Rebekah Sayers, Alf Weimann, Monica Ruiz-Garcia, Nandinee Patel, Abigail Robb, Mohamed H Shamji, Sara Fontanella, Mira Silar, E N Clare Mills, Angela Simpson, Paul J Turner, Silvia Bulfone-Paus
BACKGROUND: Food allergy is an increasing public health issue and the commonest cause of life-threatening anaphylactic reactions. Conventional allergy tests assess for the presence of allergen-specific IgE, significantly overestimating the rate of true clinical allergy resulting in over-diagnosis and adverse impact on health-related quality of life. OBJECTIVE: To undertake initial validation and assessment of a novel diagnostic tool, the mast cell activation test (MAT)...
March 5, 2018: Journal of Allergy and Clinical Immunology
Jessica C Petrov, Masayuki Wada, Kevin G Pinz, Lulu E Yan, Kevin H Chen, Xiao Shuai, Hua Liu, Xi Chen, Lai-Han Leung, Huda Salman, Nabil Hagag, Fang Liu, Xun Jiang, Yupo Ma
Acute myeloid leukemia (AML) bears heterogeneous cells that can consequently offset killing by single-CAR-based therapy, which results in disease relapse. Leukemic stem cells (LSCs) associated with CD123 expression comprise a rare population that also plays an important role in disease progression and relapse. Here, we report on the robust anti-tumor activity of a compound CAR (cCAR) T-cell possessing discrete scFv domains targeting two different AML antigens, CD123, and CD33, simultaneously. We determined that the resulting cCAR T-cells possessed consistent, potent, and directed cytotoxicity against each target antigen population...
February 25, 2018: Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
Sandra E Juul, Bryan A Comstock, Patrick J Heagerty, Dennis E Mayock, Amy M Goodman, Stephanie Hauge, Fernando Gonzalez, Yvonne W Wu
BACKGROUND: Hypoxic-ischemic encephalopathy (HIE) remains an important cause of neonatal death and frequently leads to significant long-term disability in survivors. Therapeutic hypothermia, while beneficial, still leaves many treated infants with lifelong disabilities. Adjunctive therapies are needed, and erythropoietin (Epo) has the potential to provide additional neuroprotection. OBJECTIVES: The aim of this study was to review the current incidence, mechanism of injury, and sequelae of HIE, and to describe a new phase III randomized, placebo-controlled trial of Epo neuroprotection in term and near-term infants with moderate to severe HIE treated with therapeutic hypothermia...
March 7, 2018: Neonatology
Chi-Ping Chan, Chun-Kit Yuen, Pak-Hin Hinson Cheung, Sin-Yee Fung, Pak-Yin Lui, Honglin Chen, Kin-Hang Kok, Dong-Yan Jin
PACT is a double-stranded RNA-binding protein that has been implicated in host-influenza A virus (IAV) interaction. PACT facilitates the action of RIG-I in the activation of the type I IFN response, which is suppressed by the viral nonstructural protein NS1. PACT is also known to interact with the IAV RNA polymerase subunit PA. Exactly how PACT exerts its antiviral activity during IAV infection remains to be elucidated. In the current study, we demonstrated the interplay between PACT and IAV polymerase. Induction of IFN-β by the IAV RNP complex was most robust when both RIG-I and PACT were expressed...
March 7, 2018: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
Alisa Dewan, Mengtan Xing, Marie Benner Lundbæk, Raquel Gago-Fuentes, Carole Beck, Per Arne Aas, Nina-Beate Liabakk, Siri Sæterstad, Khac Thanh Phong Chau, Bodil Merete Kavli, Valentyn Oksenych
To ensure genome stability, mammalian cells employ several DNA repair pathways. Nonhomologous DNA end joining (NHEJ) is the DNA repair process that fixes double-strand breaks throughout the cell cycle. NHEJ is involved in the development of B and T lymphocytes through its function in V(D)J recombination and class switch recombination (CSR). NHEJ consists of several core and accessory factors, including Ku70, Ku80, XRCC4, DNA ligase 4, DNA-PKcs, Artemis, and XLF. Paralog of XRCC4 and XLF (PAXX) is the recently described accessory NHEJ factor that structurally resembles XRCC4 and XLF and interacts with Ku70/Ku80...
March 2018: FEBS Open Bio
Valerie S Forsyth, Chelsie E Armbruster, Sara N Smith, Ali Pirani, A Cody Springman, Matthew S Walters, Greta R Nielubowicz, Stephanie D Himpsl, Evan S Snitkin, Harry L T Mobley
Uropathogenic Escherichia coli (UPEC) strains cause most uncomplicated urinary tract infections (UTIs). These strains are a subgroup of extraintestinal pathogenic E. coli (ExPEC) strains that infect extraintestinal sites, including urinary tract, meninges, bloodstream, lungs, and surgical sites. Here, we hypothesize that UPEC isolates adapt to and grow more rapidly within the urinary tract than other E. coli isolates and survive in that niche. To date, there has not been a reliable method available to measure their growth rate in vivo Here we used two methods: segregation of nonreplicating plasmid pGTR902, and peak-to-trough ratio (PTR), a sequencing-based method that enumerates bacterial chromosomal replication forks present during cell division...
March 6, 2018: MBio
Xuewen Zhang, Chunjun Liang, Mengjie Sun, Huimin Zhang, Chao Ji, Zebang Guo, Yajun Xu, Fulin Sun, Qi Song, Zhiqun He
Planar perovskite solar cells (PSCs) have gained great interest due to their low-temperature solution preparation and simple process. In inverted planar PSCs, an additional buffer layer is usually needed on the top of the PCBM electron-transport layer (ETL) to enhance the device performance. In this work, we used a new buffer layer, zirconium acetate (Zr(Ac)4 ). The inclusion of the Zr(Ac)4 buffer layer leads to the increase of FF from ∼68% to ∼79% and PCE from ∼14% to ∼17% in the planar PSCs. The UPS measurement indicates that the Zr(Ac)4 layer has a low HOMO level of -8...
March 6, 2018: Physical Chemistry Chemical Physics: PCCP
Michael J Minzenberg, Jong H Yoon, Steffan K Soosman, Cameron S Carter
Candidate pro-cognitive drugs for schizophrenia targeting several neurochemical systems have consistently failed to demonstrate robust efficacy. It remains untested whether concurrent antipsychotic medications exert pharmacodynamic interactions that mitigate pro-cognitive action in patients. We used functional MRI (fMRI) in a randomized, double-blind, placebo-controlled within-subject crossover test of single-dose modafinil effects in 27 medicated schizophrenia patients, interrogating brainstem regions where catecholamine systems arise to innervate the cortex, to link cellular and systems-level models of cognitive control...
March 6, 2018: Translational Psychiatry
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