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https://www.readbyqxmd.com/read/28541628/high-risk-human-papillomavirus-genotype-distribution-and-attribution-to-cervical-cancer-and-precancerous-lesions-in-a-rural-chinese-population
#1
Xue Lian Zhao, Shang Ying Hu, Qian Zhang, Li Dong, Rui Mei Feng, Ross Han, Fang Hui Zhao
OBJECTIVE: To explore the genotype distribution of high-risk human papillomavirus (HR-HPV) and its attribution to different grades of cervical lesions in rural China, which will contribute to type-specific HPV screening tests and the development of new polyvalent HPV vaccines among the Chinese population. METHODS: One thousand two hundred ninety-two subjects were followed based on the Shanxi Province Cervical Cancer Screening Study I (SPOCCS-I), and screened by HPV DNA testing (hybrid capture® 2 [HC2]), liquid-based cytology (LBC), and if necessary, directed or random colposcopy-guided quadrant biopsies...
July 2017: Journal of Gynecologic Oncology
https://www.readbyqxmd.com/read/28540698/introduction-on-using-the-fastpcr-software-and-the-related-java-web-tools-for-pcr-and-oligonucleotide-assembly-and-analysis
#2
Ruslan Kalendar, Timofey V Tselykh, Bekbolat Khassenov, Erlan M Ramanculov
This chapter introduces the FastPCR software as an integrated tool environment for PCR primer and probe design, which predicts properties of oligonucleotides based on experimental studies of the PCR efficiency. The software provides comprehensive facilities for designing primers for most PCR applications and their combinations. These include the standard PCR as well as the multiplex, long-distance, inverse, real-time, group-specific, unique, overlap extension PCR for multi-fragments assembling cloning and loop-mediated isothermal amplification (LAMP)...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28535348/coarse-grained-modeling-of-polyethylene-melts-effect-on-dynamics
#3
Brandon L Peters, K Michael Salerno, Anupriya Agrawal, Dvora Perahia, Gary S Grest
The distinctive viscoelastic behavior of polymers results from a coupled interplay of motion on multiple length and time scales. Capturing the broad time and length scales of polymer motion remains a challenge. Using polyethylene (PE) as a model macromolecule, we construct coarse-grained (CG) models of PE with 3-6 methyl groups per CG bead and probe two critical aspects of the technique: pressure corrections required after iterative Boltzmann inversion (IBI) to generate CG potentials that match the pressure of reference fully-atomistic melt simulations and the transferability of CG potentials across temperatures...
May 23, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28534623/young-s-modulus-of-wurtzite-and-zinc-blende-inp-nanowires
#4
Mikhail Dunaevskiy, Pavel Geydt, Erkki Lähderanta, Prokhor Alekseev, Tuomas Haggrén, Joona-Pekko Kakko, Hua Jiang, Harri Lipsanen
The Young's modulus of thin conical InP nanowires with either wurtzite or mixed "zinc blende/wurtzite" structures was measured. It has been shown that the value of Young's modulus obtained for wurtzite InP nanowires (E[0001] = 130 ± 30 GPa) was similar to the theoretically predicted value for the wurtzite InP material (E[0001] = 120 ± 10 GPa). The Young's modulus of mixed "zinc blende/wurtzite" InP nanowires (E[111] = 65 ± 10 GPa) appeared to be 40% less than the theoretically predicted value for the zinc blende InP material (E[111] = 110 GPa)...
May 26, 2017: Nano Letters
https://www.readbyqxmd.com/read/28533481/massively-parallel-sequencing-and-genome-wide-copy-number-analysis-revealed-a-clonal-relationship-in-benign-metastasizing-leiomyoma
#5
Ren-Chin Wu, An-Shine Chao, Li-Yu Lee, Gigin Lin, Shu-Jen Chen, Yen-Jung Lu, Huei-Jean Huang, Chi-Feng Yen, Chien Min Han, Yun-Shien Lee, Tzu-Hao Wang, Angel Chao
Benign metastasizing leiomyoma (BML) is a rare disease entity typically presenting as multiple extrauterine leiomyomas associated with a uterine leiomyoma. It has been hypothesized that the extrauterine leiomyomata represent distant metastasis of the uterine leiomyoma. To date, the only molecular evidence supporting this hypothesis was derived from clonality analyses based on X-chromosome inactivation assays. Here, we sought to address this issue by examining paired specimens of synchronous pulmonary and uterine leiomyomata from three patients using targeted massively parallel sequencing and molecular inversion probe array analysis for detecting somatic mutations and copy number aberrations...
May 9, 2017: Oncotarget
https://www.readbyqxmd.com/read/28530829/highly-oriented-atomically-thin-ambipolar-mose2-grown-by-molecular-beam-epitaxy
#6
Ming-Wei Chen, Dmitry Ovchinnikov, Sorin Lazar, Michele Pizzochero, Michael Brian Whitwick, Alessandro Surrente, Michal Baranowski, Oriol Lopez Sanchez, Philippe Gillet, Paulina Plochocka, Oleg V Yazyev, Andras Kis
Transition metal dichalcogenides (TMDCs), together with other two-dimensional (2D) materials have attracted great interest due to the unique optical and electrical properties of atomically thin layers. In order to fulfill their potential, developing large-area growth and understanding the properties of TMDCs have become crucial. Here, we used molecular beam epitaxy (MBE) to grow atomically thin MoSe2 on GaAs(111)B. No intermediate compounds were detected at the interface of as-grown films. Careful optimization of the growth temperature can result in the growth of highly aligned films with only two possible crystalline orientations due to broken inversion symmetry...
May 22, 2017: ACS Nano
https://www.readbyqxmd.com/read/28529996/multiplexed-sub-doppler-spectroscopy-with-an-optical-frequency-comb
#7
D A Long, A J Fleisher, D F Plusquellic, J T Hodges
An optical frequency comb generated with an electro-optic phase modulator and a chirped radiofrequency waveform is used to perform pump-probe spectroscopy on the D1 and D2 transitions of atomic potassium at 770.1 nm and 766.7 nm, respectively. With a comb tooth spacing of 200 kHz and an optical bandwidth of 2 GHz the hyperfine transitions can be simultaneously observed. Interferograms are recorded in as little as 5 μs (a timescale corresponding to the inverse of the comb tooth spacing). Importantly, the sub-Doppler features can be measured as long as the laser carrier frequency lies within the Doppler profile, thus removing the need for slow scanning or a priori knowledge of the frequencies of the sub-Doppler features...
December 2016: Physical Review. A
https://www.readbyqxmd.com/read/28527094/circulating-tumor-dna-measurement-by-picoliter-droplet-based-digital-pcr-and-vemurafenib-plasma-concentrations-in-patients-with-advanced-braf-mutated-melanoma
#8
Fanny Garlan, Benoit Blanchet, Nora Kramkimel, Alicja Puszkiel, Jean-Louis Golmard, Gaelle Noe, Nicolas Dupin, Pierre Laurent-Puig, Michel Vidal, Valerie Taly, Audrey Thomas-Schoemann
BACKGROUND: Circulating tumor DNA (ctDNA) has been reported as a prognostic marker in melanoma. In BRAF V600-mutant melanoma, a plasma under-exposure to vemurafenib could favor emerging resistance but no biological data are available to support this hypothesis. OBJECTIVE: We aimed to investigate the relationship between vemurafenib plasma concentrations and the ctDNA plasma concentration during follow-up of BRAF-mutated melanoma patients. PATIENTS AND METHODS: Eleven patients treated with single-agent vemurafenib for advanced BRAF V600-mutant melanoma were analyzed in an exploratory monocentric study...
May 19, 2017: Targeted Oncology
https://www.readbyqxmd.com/read/28522346/seeing-in-the-dark-phosphene-thresholds-with-eyes-open-versus-closed-in-the-absence-of-visual-inputs
#9
T A de Graaf, F Duecker, Y Stankevich, S Ten Oever, A T Sack
BACKGROUND: Voluntarily opening or closing our eyes results in fundamentally different input patterns and expectancies. Yet it remains unclear how our brains and visual systems adapt to these ocular states. OBJECTIVE/HYPOTHESIS: We here used transcranial magnetic stimulation (TMS) to probe the excitability of the human visual system with eyes open or closed, in the complete absence of visual inputs. METHODS: Combining Bayesian staircase procedures with computer control of TMS pulse intensity allowed interleaved determination of phosphene thresholds (PT) in both conditions...
May 3, 2017: Brain Stimulation
https://www.readbyqxmd.com/read/28513746/structure-functionality-relationship-and-pharmacological-profiles-of-pseudomonas-aeruginosa-alkylquinolone-quorum-sensing-modulators
#10
Ahmed A M Kamal, Lucia Petrera, Jens Eberhard, Rolf W Hartmann
An important paradigm in anti-infective research is the antivirulence concept. Pathoblockers are compounds which disarm bacteria of their arsenal of virulence factors. PqsR is a transcriptional regulator controlling the production of such factors in Pseudomonas aeruginosa, most prominently pyocyanin. In this work, a series of tool compounds based on the structure of the natural ligand 2-heptyl-4-quinolone (HHQ) were used for probing the structure-functionality relationship. Four different profiles are identified namely agonists, antagonists, inverse agonists and biphasic modulators...
May 17, 2017: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/28506874/impact-of-acquisition-and-analysis-strategies-on-cortical-depth-dependent-fmri
#11
Sriranga Kashyap, Dimo Ivanov, Martin Havlicek, Benedikt A Poser, Kâmil Uludağ
Functional MRI at ultra-high magnetic fields (≥ 7T) provides the opportunity to probe columnar and laminar processing in the human brain in vivo at submillimeter spatial scales. However, fMRI data only indirectly reflects the neuronal laminar profile, due to a bias to ascending and pial veins inherent in gradient- and spin-echo BOLD fMRI. In addition, accurate delineation of the cortical depths is difficult, due to the relatively large voxel sizes and lack of sufficient tissue contrast in the functional images...
May 12, 2017: NeuroImage
https://www.readbyqxmd.com/read/28504553/aavs1-targeted-plasmid-integration-in-aav-producer-cell-lines
#12
Yuxia Luo, Amy Frederick, John M Martin, Abraham Scaria, Seng H Cheng, Donna Armentano, Samuel C Wadsworth, Karen A Vincent
Adeno-associated virus (AAV) producer cell lines are created via transfection of HeLaS3 cells with a single plasmid containing three components (the vector sequence, the AAV rep and cap genes, and a selectable marker gene). As this plasmid contains both the cis (Rep binding sites) and trans (Rep protein encoded by the rep gene) elements required for site-specific integration, it was predicted that plasmid integration might occur within the AAVS1 locus on human chromosome 19 (chr19). The objective of this study was to investigate whether integration in AAVS1 might be correlated with vector yield...
April 14, 2017: Human Gene Therapy Methods
https://www.readbyqxmd.com/read/28501862/chromosome-painting-in-trogon-s-surrucura-aves-trogoniformes-reveals-a-karyotype-derived-by-chromosomal-fissions-fusions-and-inversions
#13
Tiago M Degrandi, Analía Del Valle Garnero, Patricia C M O'Brien, Malcolm A Ferguson-Smith, Rafael Kretschmer, Edivaldo H C de Oliveira, Ricardo J Gunski
Trogons are forest birds with a wide distribution, being found in Africa, Asia, and America, and are included in the order Trogoniformes, family Trogonidae. Phylogenetic studies using molecular data have not been able to determine the phylogenetic relationship among the different genera of trogons. So far, no cytogenetic data for these birds exist. Hence, the aim of this study was to characterize the karyotype of Trogon surrucura surrucura by means of classical and molecular cytogenetics. We found a diploid chromosome number of 2n = 82, similar to most birds, with several derived features compared to chicken and the putative ancestral avian karyotype...
May 13, 2017: Cytogenetic and Genome Research
https://www.readbyqxmd.com/read/28485937/characterization-of-kcne1-inside-lipodisq-nanoparticles-for-epr-spectroscopic-studies-of-membrane-proteins
#14
Indra D Sahu, Rongfu Zhang, Megan M Dunagan, Andrew F Craig, Gary A Lorigan
EPR spectroscopic studies of membrane proteins in a physiologically relevant native membrane-bound state are extremely challenging due to the complexity observed in inhomogeneity sample preparation and dynamic motion of the spin-label. Traditionally, detergent micelles are the most widely used membrane mimetics for membrane proteins due to their smaller size and homogeneity, providing high-resolution structure analysis by solution NMR spectroscopy. However, it is often difficult to examine whether the protein structure in a micelle environment is the same as that of the respective membrane-bound state...
May 23, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28474677/quantification-of-differential-gene-expression-by-multiplexed-targeted-resequencing-of-cdna
#15
Peer Arts, Jori van der Raadt, Sebastianus H C van Gestel, Marloes Steehouwer, Jay Shendure, Alexander Hoischen, Cornelis A Albers
Whole-transcriptome or RNA sequencing (RNA-Seq) is a powerful and versatile tool for functional analysis of different types of RNA molecules, but sample reagent and sequencing cost can be prohibitive for hypothesis-driven studies where the aim is to quantify differential expression of a limited number of genes. Here we present an approach for quantification of differential mRNA expression by targeted resequencing of complementary DNA using single-molecule molecular inversion probes (cDNA-smMIPs) that enable highly multiplexed resequencing of cDNA target regions of ∼100 nucleotides and counting of individual molecules...
May 5, 2017: Nature Communications
https://www.readbyqxmd.com/read/28472459/resolving-rapid-radiations-within-angiosperm-families-using-anchored-phylogenomics
#16
Étienne Léveillé-Bourret, Julian R Starr, Bruce A Ford, Emily Moriarty Lemmon, Alan R Lemmon
Despite the promise that molecular data would provide a seemingly unlimited source of independent characters, many plant phylogenetic studies are still based on only two regions, the plastid genome and nuclear ribosomal DNA (nrDNA). Their popularity can be explained by high copy numbers and universal PCR primers that make their sequences easily amplified and converted into parallel datasets. Unfortunately, their utility is limited by linked loci and limited characters resulting in low confidence in the accuracy of phylogenetic estimates, especially when rapid radiations occur...
May 4, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28470866/cho-cells-engineered-for-fluorescence-read-out-of-cell-cycle-and-growth-rate-in-real-time
#17
Grischa Fuge, Yaeseong Hong, Kristoffer Riecken, An-Ping Zeng, Uwe Jandt
For efficient production of recombinant proteins by mammalian cells in a bioreactor, optimal growth rates are required and represent the most important process parameter. We present the first successful attempt to monitor the growth behavior and cell cycle state of a mammalian production relevant cell line under bioreactor cultivation conditions up to 1.2 l, utilizing a fluorescent read-out without the need of additional staining or marking. For this purpose, we developed two new production relevant cell line derivatives (CHO-K1 FUCCI CM & CHO-K1 FUCCI CN) and corresponding analytical methods...
May 4, 2017: Biotechnology Progress
https://www.readbyqxmd.com/read/28463247/nonscanning-moir%C3%A3-deflectometry-for-measurement-of-nonlinear-refractive-index-and-absorption-coefficient-of-liquids
#18
Shahrzad Shahrabi Farahani, Khosro Madanipour, Ata Koohian
In this work, a nonscanning measurement technique is presented for determining the nonlinear refractive index and absorption coefficient of liquid media based on Moiré deflectometry. In the proposed method two lasers are used: a low power, wide beam as probe and a high power with specific wavelength as a pump. Interaction of the pump laser beam with the nonlinear sample changes the refractive index, which leads to change in convergence/divergence of the collimated incident probe laser beam. The induced deflection is monitored by Moiré deflectometry...
May 1, 2017: Applied Optics
https://www.readbyqxmd.com/read/28459701/mecom-evi1-rearrangements-a-review-and-case-report-of-two-mds-patients-with-complex-3q-inversion-deletions
#19
Helen Lawce, Elina Szabo, Yumi Torimaru, Craig Davis, Karin Osterberg, Susan Olson, Steve Moore
Acute myelogeneous leukemia (AML) with inv(3)/t(3;3)(q13q25) is associated with aberrant expression of the stem-cell regulator MECOM (aka EVI1). Two bone marrow samples received in the OHSU Knight Diagnostic Laboratories (KDL) Cytogenetics Laboratory for chromosomes and FISH for a question of progression of myelodysplastic syndrome (MDS) to AML showed complex abnormalities including a deletion of chromosome 3q, one with del(3)(q13q25) and the other with del(3)(q22q25). In light of the prognostic importance of the activation of the MECOM oncogene and the concurrent inactivation of the GATA2 tumor suppressor that occurs with the classic inversion of chromosome 3q, fluorescence in situ hybridization (FISH) was performed using two different probe designs to better define the 3q deletions in the two cases...
2017: Journal of the Association of Genetic Technologists
https://www.readbyqxmd.com/read/28451202/specific-protein-labeling-with-caged-fluorophores-for-dual-color-imaging-and-super-resolution-microscopy-in-living-cells
#20
Sebastian Hauke, Alexander von Appen, Tooba Quidwai, Jonas Ries, Richard Wombacher
We present new fluorophore-conjugates for dual-color photoactivation and super-resolution imaging inside live mammalian cells. These custom-designed, photo-caged Q-rhodamines and fluoresceins are cell-permeable, bright and localize specifically to intracellular targets. We utilized established orthogonal protein labeling strategies to precisely attach the photoactivatable fluorophores to proteins with subsequent activation of fluorescence by irradiation with UV light. That way, diffusive cytosolic proteins, histone proteins as well as filigree mitochondrial networks and focal adhesion proteins were visualized inside living cells...
January 1, 2017: Chemical Science
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