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David L Steward, Sally E Carty, Rebecca S Sippel, Samantha Peiling Yang, Julie A Sosa, Jennifer A Sipos, James J Figge, Susan Mandel, Bryan R Haugen, Kenneth D Burman, Zubair W Baloch, Ricardo V Lloyd, Raja R Seethala, William E Gooding, Simion I Chiosea, Cristiane Gomes-Lima, Robert L Ferris, Jessica M Folek, Raheela A Khawaja, Priya Kundra, Kwok Seng Loh, Carrie B Marshall, Sarah Mayson, Kelly L McCoy, Min En Nga, Kee Yuan Ngiam, Marina N Nikiforova, Jennifer L Poehls, Matthew D Ringel, Huaitao Yang, Linwah Yip, Yuri E Nikiforov
Importance: Approximately 20% of fine-needle aspirations (FNA) of thyroid nodules have indeterminate cytology, most frequently Bethesda category III or IV. Diagnostic surgeries can be avoided for these patients if the nodules are reliably diagnosed as benign without surgery. Objective: To determine the diagnostic accuracy of a multigene classifier (GC) test (ThyroSeq v3) for cytologically indeterminate thyroid nodules. Design, Setting, and Participants: Prospective, blinded cohort study conducted at 10 medical centers, with 782 patients with 1013 nodules enrolled...
November 8, 2018: JAMA Oncology
Aaron Dickenson, Nikolay Britun, Anton Nikiforov, Christophe Leys, Mohammad I Hasan, James L Walsh
The reactive chemical species generated by non-equilibrium plasma under atmospheric pressure conditions are key enablers for many emerging applications spanning the fields of biomedicine, manufacturing and agriculture. Despite showing great application potential, insight in to the underpinning reactive species generation and transport mechanisms remains scarce. This contribution focuses on the spatiotemporal behaviour of reactive nitrogen species (RNS) created and transported by an atmospheric pressure air surface barrier discharge (SBD) using both laser induced fluorescence and particle imaging velocimetry measurements combined with experimentally validated numerical modelling...
November 21, 2018: Physical Chemistry Chemical Physics: PCCP
A Kostic, R Dux, K Crombé, A Nikiforov, R Ochoukov, I Shesterikov, E H Martin, J-M Noterdaeme
IShTAR, Ion cyclotron Sheath Test ARrangement, is a linear device dedicated to the investigation of the edge plasma-ICRF (Ion Cyclotron Range of Frequencies) antenna interactions in tokamak edge-like conditions and serves as a platform for a diagnostic development for measuring the electric fields in the vicinity of ICRF antennas. We present here our progress in the development of an optical emission spectroscopy method for measuring the electric fields which concentrates on the changes in the helium spectral line profiles introduced by the external electrical field, i...
October 2018: Review of Scientific Instruments
Jens Bitzer, Thomas Henkel, Andrey I Nikiforov, Marisa O Rihner, C M Verspeek-Rip, Birol Usta, Michèle van den Wijngaard
A series of in vitro studies were conducted to assess the genetic toxicity of jelly mushroom glycolipids from Dacryopinax spathularia (herein referred to as "AM-1"). In the bacterial reverse mutation assay (Ames test), there was no evidence of mutagenic activity in any Salmonella typhimurium strains tested or in Escherichia coli strain WP2uvrA, at dose levels up to 5000 μg/plate. In the micronucleus (MN) test using human lymphocytes, AM-1 did not show a statistically significant increase in the number of binucleated cells containing micronuclei when compared to concurrent control cultures at all time points and at any of the concentrations analyzed (up to 900 μg/ml of culture medium)...
October 25, 2018: Food and Chemical Toxicology
Emily E Fink, Sudha Moparthy, Archis Bagati, Anna Bianchi-Smiraglia, Brittany C Lipchick, David W Wolff, Matthew V Roll, Jianmin Wang, Song Liu, Andrei V Bakin, Eugene S Kandel, Ann-Hwee Lee, Mikhail A Nikiforov
Transcription factor XBP1s, activated by endoplasmic reticulum (ER) stress in a dose-dependent manner, plays a central role in adaptive unfolded protein response (UPR) via direct activation of multiple genes controlling protein refolding. Here, we report that elevation of ER stress above a critical threshold causes accumulation of XBP1s protein sufficient for binding to the promoter and activation of a gene encoding a transcription factor KLF9. In comparison to other XBP1s targets, KLF9 promoter contains an evolutionary conserved lower-affinity binding site that requires higher amounts of XBP1s for activation...
October 2, 2018: Cell Reports
Niels Wardenier, Patrick Vanraes, Anton Nikiforov, Stijn W H Van Hulle, Christophe Leys
The emergence of micropollutants into our aquatic resources is regarded as an issue of increasing environmental concern. To protect the aquatic environment against further contamination with micropollutants, treatment with advanced oxidation processes (AOPs) is put forward as a promising technique. In this work, an innovative AOP based on electrical discharges in a continuous-flow pulsed dielectric barrier discharge (DBD) reactor with falling water film over activated carbon textile is examined for its potential application in water treatment...
January 15, 2019: Journal of Hazardous Materials
Juan Ignacio García, Meritxell Sabidó, Mikhail Nikiforov, Adriana Smith, Gabriela Hernández, Rudy Ortiz, Luis Ardani, Alba Cajas, Elsy Camey, Jordi B Torrelles, Shu-Hua Wang, Colin N J Campbell, Cinta Folch, Jordi Casabona
OBJECTIVE: To describe and compare trends in prevalence, sexual behaviour and HIV transmission knowledge data related to sexually transmitted infections (STI) and HIV in patients attending three STI clinics over an 8-year period in Escuintla Department, Guatemala. METHODS: STI clinic attendees were classified into transmission groups as follows: female sex workers (FSW), men who have sex with men (MSM) and 'high-risk heterosexuals' (HRH). Annual cross-sectional analysis and multivariable Poisson regression adjusted for sociodemographic variables were used for prevalence comparisons and adjusted prevalence trends for HIV/STI outcomes and used for adjusted trends in proportions in sexual behaviour and HIV transmission knowledge outcomes...
September 19, 2018: BMJ Open
Anna Bianchi-Smiraglia, Archis Bagati, Emily E Fink, Hayley C Affronti, Brittany C Lipchick, Sudha Moparthy, Mark D Long, Spencer R Rosario, Shivana M Lightman, Kalyana Moparthy, David W Wolff, Dong Hyun Yun, Zhannan Han, Anthony Polechetti, Matthew V Roll, Ilya I Gitlin, Katerina I Leonova, Aryn M Rowsam, Eugene S Kandel, Andrei V Gudkov, P Leif Bergsagel, Kelvin P Lee, Dominic J Smiraglia, Mikhail A Nikiforov
Polyamine inhibition for cancer therapy is, conceptually, an attractive approach but has yet to meet success in the clinical setting. The aryl hydrocarbon receptor (AHR) is the central transcriptional regulator of the xenobiotic response. Our study revealed that AHR also positively regulates intracellular polyamine production via direct transcriptional activation of 2 genes, ODC1 and AZIN1, which are involved in polyamine biosynthesis and control, respectively. In patients with multiple myeloma (MM), AHR levels were inversely correlated with survival, suggesting that AHR inhibition may be beneficial for the treatment of this disease...
October 1, 2018: Journal of Clinical Investigation
S V Nikiforov, I G Avdyushin, D V Ananchenko, A N Kiryakov, A F Nikiforov
New Al2 O3 -BeO ceramics were synthesized from alumina nanopowder in BeO crucibles by high-temperature treatment in reducing conditions. It was found that the TL curve of these ceramics is characterized by a dosimetric peak at 520-530 K for a heating rate of 2 K/s. The integrated TL of the peak is not influenced by the heating rate of the samples, unlike that in anion-defective alumina and beryllia crystals. The presence of an energy distribution of the traps which cause dosimetric TL peak is verified by Tm-Tstop and initial rise methods...
November 2018: Applied Radiation and Isotopes
Alyaksandr V Nikitski, Susan L Rominski, Mamta Wankhede, Lindsey M Kelly, Federica Panebianco, Guillermo Barila, Daniel L Altschuler, Yuri E Nikiforov
Chromosomal rearrangements of the ALK gene, which lead to constitutive activation of ALK tyrosine kinase, are found in various cancers. In thyroid cancers, ALK fusions, most commonly the STRN-ALK fusion, are detected in papillary thyroid cancer and with higher frequency in poorly differentiated and anaplastic thyroid cancers. Our aim was to establish a mouse model of thyroid-specific expression of STRN-ALK and to test whether this fusion drives the development of thyroid cancer with a propensity for dedifferentiation...
November 2018: American Journal of Pathology
Alexander N Orekhov, Tatiana Pushkarsky, Yumiko Oishi, Nikita G Nikiforov, Andrey V Zhelankin, Larisa Dubrovsky, Vsevolod J Makeev, Kathy Foxx, Xueting Jin, Howard S Kruth, Igor A Sobenin, Vasily N Sukhorukov, Emile R Zakiev, Anatol Kontush, Wilfried Le Goff, Michael Bukrinsky
High density lipoproteins (HDL) are key components of reverse cholesterol transport pathway. HDL removes excessive cholesterol from peripheral cells, including macrophages, providing protection from cholesterol accumulation and conversion into foam cells, which is a key event in pathogenesis of atherosclerosis. The mechanism of cellular cholesterol efflux stimulation by HDL involves interaction with the ABCA1 lipid transporter and ensuing transfer of cholesterol to HDL particles. In this study, we looked for additional proteins contributing to HDL-dependent cholesterol efflux...
October 2018: Experimental and Molecular Pathology
Ian Ganly, Vladimir Makarov, Shyamprasad Deraje, YiYu Dong, Ed Reznik, Venkatraman Seshan, Gouri Nanjangud, Stephanie Eng, Promita Bose, Fengshen Kuo, Luc G T Morris, Inigo Landa, Pedro Blecua Carrillo Albornoz, Nadeem Riaz, Yuri E Nikiforov, Kepal Patel, Christopher Umbricht, Martha Zeiger, Electron Kebebew, Eric Sherman, Ronald Ghossein, James A Fagin, Timothy A Chan
The molecular foundations of Hürthle cell carcinoma (HCC) are poorly understood. Here we describe a comprehensive genomic characterization of 56 primary HCC tumors that span the spectrum of tumor behavior. We elucidate the mutational profile and driver mutations and show that these tumors exhibit a wide range of recurrent mutations. Notably, we report a high number of disruptive mutations to both protein-coding and tRNA-encoding regions of the mitochondrial genome. We reveal unique chromosomal landscapes that involve whole-chromosomal duplications of chromosomes 5 and 7 and widespread loss of heterozygosity arising from haploidization and copy-number-neutral uniparental disomy...
August 13, 2018: Cancer Cell
Sarah Pearlstein, Arash H Lahouti, Elana Opher, Yuri E Nikiforov, Daniel B Kuriloff
Hürthle cell predominant thyroid nodules often confound the diagnostic utility of fine needle aspiration biopsy (FNAB) with cytology often interpreted as a Hürthle cell lesion with an indeterminate risk of malignancy, Bethesda category (BC) III or IV. Molecular diagnostics for Hürthle cell predominant nodules has also been disappointing in further defining the risk of malignancy. We present a case of a slowly enlarging nodule within a goiter initially reported as benign on FNAB, BC II but on subsequent FNAB suspicious for a Hürthle cell neoplasm, BC IV...
2018: Case Reports in Endocrinology
Cristiane J Gomes-Lima, Yuri E Nikiforov, Wen Lee, Kenneth D Burman
Struma ovarii is a rare ovarian teratoma predominantly composed of thyroid tissue. The simultaneous presence of thyroid carcinoma in the struma ovarii and the thyroid gland is extremely rare. It remains unclear if these carcinomas represent independent primary tumors and whether the molecular mechanisms of the tumors developing in the thyroid and ovarian tissues are similar. We present the case of a patient with two independent papillary thyroid carcinomas (PTCs) in struma ovarii and the thyroid gland that are driven by different RAS mutations...
August 1, 2018: Journal of the Endocrine Society
Dmitry Nikiforov, Valentina Russo, Delia Nardinocchi, Nicola Bernabò, Mauro Mattioli, Barbara Barboni
BACKGROUND: In recent years, autotransplantation of cryopreserved ovarian tissue became a promising approach to preserve female fertility. The slow freezing is the most effective technique which resulted in greater live birth incidence so far. Despite that, interest to vitrification of the ovarian tissue is swiftly growing, thereby undermining the necessity for further improvements in the technique. In present study, we evaluated possibilities to increase follicle survival rates adopting innovative multi-protectoral vitrification protocols, applied to the slivers of ovarian cortex or isolated early-antral follicles, frozen individually...
August 7, 2018: Journal of Ovarian Research
Patrick Vanraes, Anton Nikiforov, Annemie Bogaerts, Christophe Leys
In the last decades, AC powered atmospheric dielectric barrier discharges (DBDs) in air with a liquid electrode have been proposed as a promising plasma technology with versatile applicability in medicine, agriculture and water treatment. The fundamental features of the micro-discharge filaments that make up this type of plasma have, however, not been studied yet in sufficient detail. In order to address this need, we investigated a single DBD micro-discharge filament over a water film in a sphere-to-sphere electrode configuration, by means of ICCD imaging and optical emission spectroscopy...
July 19, 2018: Scientific Reports
Jens Bitzer, Thomas Henkel, Andrey I Nikiforov, Marisa O Rihner, Mark T Herberth
The developmental and reproduction toxicity potential of jelly mushroom glycolipids from Dacryopinax spathularia was studied in Crl:CD (SD) rats by daily oral gavage administration at doses of 150, 500 or 1000 mg/kg/day. Pregnant female rats in the developmental study received the test article from Gestation Days 6-19. F0 and F1 parental animals in the 2-generation reproduction toxicity study were dosed for a minimum of 70 days prior to mating and throughout mating, gestation, and lactation, until the day prior to euthanasia (following weaning of litters on postnatal day 21)...
July 27, 2018: Food and Chemical Toxicology
Robert L Ferris, Yuri Nikiforov, Davis Terris, Raja R Seethala, J Andrew Ridge, Peter Angelos, Quan-Yang Duh, Richard Wong, Mona M Sabra, James A Fagin, Bryan McIver, Victor J Bernet, R Mack Harrell, Naifa Busaidy, Edmund S Cibas, William C Faquin, Peter Sadow, Zubair Baloch, Maisie Shindo, Lisa Orloff, Louise Davies, Gregory W Randolph
The newly introduced pathologic diagnosis of noninvasive follicular thyroid neoplasm with papillary-like nuclear features (NIFTP) will result in less bilateral thyroid surgery as well as deescalation in T4 suppressive and radioactive iodine treatment. Although, NIFTP is a nonmalignant lesion that has nuclear features of some papillary malignancies, the challenge for the surgeon is to identify a lesion as possibly NIFTP before the pathologic diagnosis. NIFTP, due to its reduction of overall rates of malignancy, will result in the initial surgical pendulum swinging toward lobectomy instead of initial total thyroidectomy...
September 2018: Head & Neck
Keith M Callenberg, Lucas Santana-Santos, Liang Chen, Wayne L Ernst, Michelle B De Moura, Yuri E Nikiforov, Marina N Nikiforova, Somak Roy
Human Genome Variation Society (HGVS) nomenclature is a de facto clinical standard for reporting DNA sequence variants. With increasing use of high-throughput sequencing, manual generation of HGVS nomenclatures for all variants is impractical and error-prone. It is therefore beneficial to include one or more HGVS generator tools in next-generation sequencing (NGS) bioinformatics pipelines to enable automated, consistent, and accurate generation of HGVS nomenclature after appropriate validation. The authors implemented an HGVS nomenclature tool, the hgvs package, by integrating it into their custom-developed NGS variant management and reporting software...
September 2018: Journal of Molecular Diagnostics: JMD
Yuri E Nikiforov, Zubair W Baloch, Steven P Hodak, Thomas J Giordano, Ricardo V Lloyd, Raja R Seethala, Bruce M Wenig
No abstract text is available yet for this article.
August 1, 2018: JAMA Oncology
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