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inversion probes

Olga L Gladkikh, Svetlana A Romanenko, Natalya A Lemskaya, Natalya A Serdyukova, Patricia C M O'Brien, Julia M Kovalskaya, Antonina V Smorkatcheva, Feodor N Golenishchev, Polina L Perelman, Vladimir A Trifonov, Malcolm A Ferguson-Smith, Fengtang Yang, Alexander S Graphodatsky
The generic status of Lasiopodomys and its division into subgenera Lasiopodomys (L. mandarinus, L. brandtii) and Stenocranius (L. gregalis, L. raddei) are not generally accepted because of contradictions between the morphological and molecular data. To obtain cytogenetic evidence for the Lasiopodomys genus and its subgenera and to test the autosome to sex chromosome translocation hypothesis of sex chromosome complex origin in L. mandarinus proposed previously, we hybridized chromosome painting probes from the field vole (Microtus agrestis, MAG) and the Arctic lemming (Dicrostonyx torquatus, DTO) onto the metaphases of a female Mandarin vole (L...
2016: PloS One
Bayard Wilson, Erik Curtis, Brian Hirshman, Ahmet Oygar, Karen Chen, Brandon C Gabel, Florin Vaida, David W Allison, Joseph D Ciacci
OBJECTIVE Normative data exists for stimulus-evoked pedicle screw electromyography (EMG) current thresholds in the lumbar spine, and is routinely referenced during spine surgeries to detect a screw breach, prevent injury of neural elements, and ensure the most biomechanically sound instrumentation construct. To date, similar normative data for cervical lateral mass screws is limited, thus the utility of lateral mass screw testing remains unclear. To address this disparity, in this study the authors describe cumulative lateral mass screw stimulation threshold data in patients undergoing posterior cervical instrumentation with lateral mass screws...
December 9, 2016: Journal of Neurosurgery. Spine
Jingui Yu, Mingchao Wang, Shangchao Lin
Although organic-inorganic hybrid perovskites have been extensively investigated for promising applications in energy-related devices, their mechanical properties, which restrict their practical deployment as flexible and wearable devices, have been largely unexplored at the atomistic level. Toward this level of understanding, we predict the elastic constant matrix and various elastic properties of CH3NH3PbI3 (MAPbI3) using atomistic simulations. We find that single-crystalline MAPbI3 is much stiffer and exhibits higher ultimate tensile strength than polycrystalline samples, but the latter exhibit unexpected, greatly enhanced nanoductility and fracture toughness, resulting from the extensive amorphization during the yielding process...
December 9, 2016: ACS Nano
Robert J Buszek, Claron J Ridge, Samuel B Emery, C Michael Lindsay, Jerry A Boatz
In a recently reported helium droplet-mediated deposition experiment to produce copper-coated magnesium core-shell nanoclusters, structural inversion was observed, which resulted in copper in the nanocluster interior, surrounded by oxidized magnesium on the copper surface. This study utilizes density functional theory methods to model the migration of copper atoms into the interior of a magnesium nanocluster to probe the energetics of this process and to compare it to the complementary process of magnesium atom migration into the interior of a copper nanocluster...
December 8, 2016: Journal of Physical Chemistry. A
Ilya Belopolski, Daniel S Sanchez, Yukiaki Ishida, Xingchen Pan, Peng Yu, Su-Yang Xu, Guoqing Chang, Tay-Rong Chang, Hao Zheng, Nasser Alidoust, Guang Bian, Madhab Neupane, Shin-Ming Huang, Chi-Cheng Lee, You Song, Haijun Bu, Guanghou Wang, Shisheng Li, Goki Eda, Horng-Tay Jeng, Takeshi Kondo, Hsin Lin, Zheng Liu, Fengqi Song, Shik Shin, M Zahid Hasan
The recent discovery of a Weyl semimetal in TaAs offers the first Weyl fermion observed in nature and dramatically broadens the classification of topological phases. However, in TaAs it has proven challenging to study the rich transport phenomena arising from emergent Weyl fermions. The series MoxW1-xTe2 are inversion-breaking, layered, tunable semimetals already under study as a promising platform for new electronics and recently proposed to host Type II, or strongly Lorentz-violating, Weyl fermions. Here we report the discovery of a Weyl semimetal in MoxW1-xTe2 at x=25%...
December 5, 2016: Nature Communications
Joshua Yablon, Zifan Zhou, Minchuan Zhou, Ye Wang, S Tseng, M S Shahriar
We have demonstrated experimentally a Diode-Pumped Alkali Laser (DPAL) with a Raman resonance induced dip in the center of the gain profile, in order to produce an anomalous dispersion, necessary for making the laser superluminal. Numerical calculations match closely with experimental results, and indicate that the laser is operating superluminally, with the group index far below unity (~0.00526) at the center of the dip. The estimated factor of enhancement in the sensitivity to cavity length perturbation is ~190, approximately equaling the inverse of the group index...
November 28, 2016: Optics Express
Takaya Sato, Yusuke Sato, Seiichi Nishizawa
A series of triplex-forming PNA probes carrying a thiazole orange (TO) base surrogate through an alkyl linker was synthesized, and the interactions between these so-called tFIT probes and purine-rich sequences within double-stranded RNA (dsRNA) were examined. We found the TO base surrogate linker significantly affected both the binding affinity and the fluorescence response upon triplex formation with the target dsRNA. Among the probes examined, the TO base surrogate connected through the propyl linker in the tFIT probes increased the binding affinity by a factor of ten while maintaining its function as the fluorescent universal base...
November 29, 2016: Chemistry: a European Journal
Tanjina Kader, David L Goode, Stephen Q Wong, Jacquie Connaughton, Simone M Rowley, Lisa Devereux, David Byrne, Stephen B Fox, Gisela Mir Arnau, Richard W Tothill, Ian G Campbell, Kylie L Gorringe
Unlocking clinically translatable genomic information, including copy number alterations (CNA), from formalin-fixed paraffin-embedded (FFPE) tissue is challenging due to low yields and degraded DNA. We describe a robust, cost-effective low-coverage whole genome sequencing (LC WGS) method for CNA detection using 5 ng of FFPE-derived DNA. CN profiles using 100 ng or 5 ng input DNA were highly concordant and comparable with molecular inversion probe (MIP) array profiles. LC WGS improved CN profiles of samples that performed poorly using MIP arrays...
November 15, 2016: Genome Medicine
Sara M Hashmi, Sid Senthilnathan, Abbas Firoozabadi
Thermodiffusion in liquid mixtures may explain some counter-intuitive but naturally occurring phenomena such as hydrocarbon reservoirs with heavier component(s) stratified on top of lighter ones. However, beyond benchmark systems, systematic measurements of thermodiffusion in binary organic mixtures are lacking. We use an optical beam deflection apparatus to simultaneously probe Fickian and thermal diffusion in binary solution mixtures of polycyclic aromatic hydrocarbons dissolved in alkanes, and measure both Fickian diffusion D and the Soret coefficient ST, and then obtain the thermodiffusion coefficient DT...
November 14, 2016: Journal of Chemical Physics
Derek Frydel
The present work focuses on the structure of a double-layer of overscreened charged surfaces by smeared-out charges and probes the link between the structure of a double-layer and the bulk properties of an electrolyte with special view to the role of the Kirkwood crossover. Just as the Kirkwood line divides a bulk solution into a fluid with monotonic and oscillatory decaying correlations, it similarly separates charge inversion into two broad domains, with and without oscillating charge density profile. As initially oscillations may appear like a far-field occurrence, eventually they develop into a full fledged layering of a charge density...
November 14, 2016: Journal of Chemical Physics
K D Khandelwal, N Ishorst, H Zhou, K U Ludwig, H Venselaar, C Gilissen, M Thonissen, I A L M van Rooij, K Dreesen, M Steehouwer, M van de Vorst, M Bloemen, E van Beusekom, J Roosenboom, W Borstlap, R Admiraal, T Dormaar, J Schoenaers, V Vander Poorten, G Hens, A Verdonck, S Bergé, N Roeleveldt, G Vriend, K Devriendt, H G Brunner, E Mangold, A Hoischen, H van Bokhoven, C E L Carels
Common variants in interferon regulatory factor 6 (IRF6) have been associated with nonsyndromic cleft lip with or without cleft palate (NSCL/P) as well as with tooth agenesis (TA). These variants contribute a small risk towards the 2 congenital conditions and explain only a small percentage of heritability. On the other hand, many IRF6 mutations are known to be a monogenic cause of disease for syndromic orofacial clefting (OFC). We hypothesize that IRF6 mutations in some rare instances could also cause nonsyndromic OFC...
November 9, 2016: Journal of Dental Research
Jian Wu, Dao Xiang, Ghazal Hajisalem, Fan-Cheng Lin, Jer-Shing Huang, Chun-Hong Kuo, Reuven Gordon
We probe the acoustic vibrations of silver nanoprisms and gold nano-octahedrons in aqueous solution with four-wave mixing. The nonlinear optical response shows two acoustic vibrational modes: an in-plane mode of nanoprisms with vertexial expansion and contraction; an extensional mode of nano-octahedrons with longitudinal expansion and transverse contraction. The particles were also analyzed with electron microscopy and the acoustic resonance frequencies were then calculated by the finite element analysis, showing good agreement with experimental observations...
October 17, 2016: Optics Express
Fabrice Marquet, Pierre Bour, Fanny Vaillant, Sana Amraoui, Rémi Dubois, Philippe Ritter, Michel Haïssaguerre, Mélèze Hocini, Olivier Bernus, Bruno Quesson
Currently, no non-invasive cardiac pacing device acceptable for prolonged use in conscious patients exists. High Intensity Focused Ultrasound (HIFU) can be used to perform remote pacing using reversibility of electromechanical coupling of cardiomyocytes. Here we described an extracorporeal cardiac stimulation device and study its efficacy and safety. We conducted experiments ex vivo and in vivo in a large animal model (pig) to evaluate clinical potential of such a technique. The stimulation threshold was determined in 10 different ex vivo hearts and different clinically relevant electrical effects such as consecutive stimulations of different heart chambers with a single ultrasonic probe, continuous pacing or the inducibility of ventricular tachycardia were shown...
November 9, 2016: Scientific Reports
J E Bach, J Oldenburg, C R Müller, S Rost
: Haemophilia A (HA) is caused by a broad spectrum of different mutation types in the factor VIII gene (F8). In our patient cohort of more than 2600 HA patients as well as in other published studies, the most frequent cause are missense mutations in different F8 exons or the recurrent intron 22 inversion. Some exons and several specific nucleotide positions represent hot spots for point mutations in the examined cohort. About 4 % of cases remain without mutation after routine HA diagnostic methods including inversion PCRs, Sanger sequencing and multiplex ligation-dependent probe amplification (MLPA)...
November 8, 2016: Hämostaseologie
Stuart Cantsilieris, Holly A Stessman, Jay Shendure, Evan E Eichler
Molecular inversion probes (MIPs) in combination with massively parallel DNA sequencing represent a versatile, yet economical tool for targeted sequencing of genomic DNA. Several thousand genomic targets can be selectively captured using long oligonucleotides containing unique targeting arms and universal linkers. The ability to append sequencing adaptors and sample-specific barcodes allows large-scale pooling and subsequent high-throughput sequencing at relatively low cost per sample. Here, we describe a "wet bench" protocol detailing the capture and subsequent sequencing of >2000 genomic targets from 192 samples, representative of a single lane on the Illumina HiSeq 2000 platform...
2017: Methods in Molecular Biology
Aline Grein-Iankovski, Izabel C Riegel-Vidotti, Fernanda F Simas-Tosin, Suresh Narayanan, Robert L Leheny, Alec R Sandy
We report a study connecting the nanoscale and macroscale structure and dynamics of Acacia mearnsii gum as probed by small-angle X-ray scattering (SAXS), X-ray photon correlation spectroscopy (XPCS) and rheology. Acacia gum, in general, is a complex polysaccharide used extensively in industry. Over the analyzed concentration range (15 to 30 wt%) the A. mearnsii gum is found to have a gel-like linear rheology and to exhibit shear thinning flow behavior under steady shear. The gum solutions exhibited a steadily increasing elastic modulus with increasing time after they were prepared and also the emergence of shear thickening events within the shear thinning behavior, characteristic of associative polymers...
November 2, 2016: Soft Matter
Barbara Bennani-Baiti, Pascal A Baltzer
Purpose To assess the use of magnetic resonance (MR) imaging for diagnosis of malignancy in lesions that manifest as microcalcifications at mammography. Materials and Methods Two independent readers performed a systematic review of the literature published as of February 1, 2016, by using predefined search terms. All studies in which contrast material-enhanced MR imaging was used for assessment of mammographic microcalcifications that were assigned Breast Imaging Reporting and Data System (BI-RADS) scores of 3-5 were deemed eligible...
October 27, 2016: Radiology
Gerald D Dodd, Anthony C Lanctot, Kimberly E Lind
Purpose To investigate the effect of change in portal vein flow rates on the size and shape of ablations created by a bipolar radiofrequency (RF) ablation device. Materials and Methods This study was exempt from institutional animal care and use committee review. An in vitro bovine liver model perfused with autologous blood via the portal vein at three flow rates (60, 80, 100 mL/min per 100 g of liver) was used. Four ablations, two bipolar and two monopolar (control probe), were made in each of five livers perfused at each flow rate...
October 19, 2016: Radiology
Beomsue Kim, Suihan Feng, Seong-Wook Yun, Cheryl Leong, Rudrakanta Satapathy, Si Yan Diana Wan, Young-Tae Chang
Selection of a specific neural stem/progenitor cells (NSPCs) has attracted broad attention in regenerative medicine for neurological disorders. Here, we report a fluorescent probe, CDg13, and its application for isolating strong neurogenic NSPCs. In comparison to the NSPCs isolated by other biomarkers, CDg13-stained NSPCs showed higher capability to differentiate into neurons. Target identification revealed that the fluorescence intensity of the probe within cells is inversely proportional to the expression levels of mouse and human Abcg2 transporters...
October 26, 2016: Chembiochem: a European Journal of Chemical Biology
Robbert D A Weren, Arjen R Mensenkamp, Michiel Simons, Astrid Eijkelenboom, Aisha S Sie, Hicham Ouchene, Monique van Asseldonk, Encarna B Gomez-Garcia, Marinus J Blok, Joanne A de Hullu, Marcel R Nelen, Alexander Hoischen, Johan Bulten, Bastiaan B J Tops, Nicoline Hoogerbrugge, Marjolijn J L Ligtenberg
With the recent introduction of Poly(ADP-ribose) polymerase inhibitors, a promising novel therapy has become available for ovarian carcinoma (OC) patients with inactivating BRCA1 or BRCA2 mutations in their tumor. To select patients who may benefit from these treatments, assessment of the mutation status of BRCA1 and BRCA2 in the tumor is required. For reliable evaluation of germline and somatic mutations in these genes in DNA derived from formalin-fixed, paraffin-embedded (FFPE) tissue, we have developed a single-molecule molecular inversion probe (smMIP)-based targeted next-generation sequencing (NGS) approach...
October 21, 2016: Human Mutation
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