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inversion probes

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, En Marjolijn J L Ligtenberg
With the recent introduction of Poly(ADP-ribose) polymerase (PARP) inhibitors, a promising novel therapy has become available for ovarian carcinoma patients with inactivating BRCA1 or BRCA2 mutations in their tumour. To select patients who may benefit from these treatments, assessment of the mutation status of BRCA1 and BRCA2 in the tumour 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
Paolo Mongillo, Elisa Pitteri, Pamela Sambugaro, Paolo Carnier, Lieta Marinelli
Dogs enrolled in a previous study were assessed two years later for reliability of their local/global preference in a discrimination test with the same hierarchical stimuli used in the previous study (Experiment 1) and with a novel stimulus (Experiment 2). In Experiment 1, dogs easily re-learned to discriminate the positive stimulus; their individual global/local choices were stable compared to the previous study; and an overall clear global bias was found. In Experiment 2, dogs were slower in acquiring the initial discrimination task; the overall global bias disappeared; and, individually, dogs tended to make inverse choices compared to the original study...
October 13, 2016: Animal Cognition
Jose Maria Bastida Bermeja, Jose Ramon González-Porras, Cristina Jiménez, Rocio Benito, Gonzalo R Ordoñez, Maria Teresa Álvarez-Román, M Elena Fontecha, Kamila Janusz, David Castillo, Rosa María Fisac, Luis Javier García-Frade, Carlos Aguilar, María Paz Martínez, Nuria Bermejo, Sonia Herrero, Ana Balanzategui, Jose Manuel Martin-Antorán, Rafael Ramos, Maria Jose Cebeiro, Emilia Pardal, Carmen Aguilera, Belen Pérez-Gutierrez, Manuel Prieto, Susana Riesco, Maria Carmen Mendoza, Ana Benito, Ana Hortal Benito-Sendin, Víctor Jiménez-Yuste, Jesus Maria Hernández-Rivas, Ramon García-Sanz, Marcos González-Díaz, Maria Eugenia Sarasquete
Currently, molecular diagnosis of haemophilia A and B (HA and HB) highlights the excess risk-inhibitor development associated with specific mutations, and enables carrier testing of female relatives and prenatal or preimplantation genetic diagnosis. Molecular testing for HA also helps distinguish it from von Willebrand disease (VWD). Next-generation sequencing (NGS) allows simultaneous investigation of several complete genes, even though they may span very extensive regions. This study aimed to evaluate the usefulness of a molecular algorithm employing an NGS approach for sequencing the complete F8, F9 and VWF genes...
October 13, 2016: Thrombosis and Haemostasis
Jingjing Sherry Wu, Eric D Young, Elisabeth Glowatzki
: Auditory nerve fibers (ANFs) exhibit a range of spontaneous firing rates (SRs) that are inversely correlated with threshold for sounds. To probe the underlying mechanisms and time course of SR differentiation during cochlear maturation, loose-patch extracellular recordings were made from ANF dendrites using acutely excised rat cochlear preparations of different ages after hearing onset. Diversification of SRs occurred mostly between the second and the third postnatal week. Statistical properties of ANF spike trains showed developmental changes that approach adult-like features in older preparations...
October 12, 2016: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
Jorin Hoogenboom, Nathalja Berghuis, Dario Cramer, Rene Geurts, Han Zuilhof, Tom Wennekes
BACKGROUND: Carbohydrates, also called glycans, play a crucial but not fully understood role in plant health and development. The non-template driven formation of glycans makes it impossible to image them in vivo with genetically encoded fluorescent tags and related molecular biology approaches. A solution to this problem is the use of tailor-made glycan analogs that are metabolically incorporated by the plant into its glycans. These metabolically incorporated probes can be visualized, but techniques documented so far use toxic copper-catalyzed labeling...
October 10, 2016: BMC Plant Biology
Yuu Sasaki, Yuka Horikawa, Takashi Tokushima, Kazumasa Okada, Masaki Oura, Misako Aida
The hydration structure of trimethylamine N-oxide (TMAO) in aqueous solutions has been investigated by means of soft X-ray spectroscopy and chemometric analysis. Soft X-ray absorption spectra in the O 1s region have a concentration-dependent shoulder at 533 eV, which is assigned to the 6a1 resonance of TMAO. Soft X-ray emission spectra acquired at this resonance comprise both TMAO and water components, with a prominent peak at 525.6 eV which is assigned to the emission caused by the 5e to O 1s transition. An apparent inverse concentration dependence of around 523 eV suggests that the electronic structure of water is modified by the strong interaction with TMAO...
October 5, 2016: Physical Chemistry Chemical Physics: PCCP
Matthias Christgen, Jana L van Luttikhuizen, Mieke Raap, Peter Braubach, Lars Schmidt, Danny Jonigk, Friedrich Feuerhake, Ulrich Lehmann, Brigitte Schlegelberger, Hans H Kreipe, Doris Steinemann
HER2/ERBB2 amplification/overexpression determines the eligibility of breast cancer patients to HER2-targeted therapy. This study evaluates the agreement between ERBB2 copy number assessment by fluorescence in situ hybridization, a standard method recommended by the American Society of Clinical Oncology/College of American Pathologists (ASCO/CAP), and newly available DNA extraction-based methods. A series of n=29 formalin-fixed paraffin-embedded breast cancers were subjected to ERBB2 copy number assessment by fluorescence in situ hybridization (FISH, Vysis, Abbott)...
October 3, 2016: Oncotarget
VanTuong Pham, Laurent Vila, Gilles Zahnd, Alain Marty, Williams Savero Torres, Matthieu Jamet, Jean-Philippe Attané
Spin-orbitronics is based on the ability of spin-orbit interactions to achieve the conversion between charge currents and pure spin currents. As the precise evaluation of the conversion efficiency becomes a crucial issue, the need for straightforward ways to observe this conversion has emerged as one of the main challenges in spintronics. Here, we propose a simple device, akin to the ferromagnetic/nonmagnetic bilayers used in most spin-orbit torques experiments, and consisting of a spin Hall effect wire connected to two transverse ferromagnetic electrodes...
October 7, 2016: Nano Letters
Rui-Ning Wang, Guo-Yi Dong, Shu-Fang Wang, Guang-Sheng Fu, Jiang-Long Wang
This study is built on density functional calculations in combination with the non-equilibrium Green's function, and we probe the thermoelectric transport mechanisms through C60 molecules anchored to Al nano-electrodes in three different ways, such as, the planar, pyramidal, and asymmetric surfaces. When the electrode is switched from the planar and pyramidal surfaces, the electrical conductance (σ) and electron's thermal conductance (κel) decrease almost two orders of magnitude due to the reduction of the molecule-electrode contact coupling, whereas the Seebeck coefficients (S) are reduced by ∼55%...
October 12, 2016: Physical Chemistry Chemical Physics: PCCP
Anouk S Lubbe, Jos C M Kistemaker, Esther J Smits, Ben L Feringa
As molecular machines move to exciting applications in various environments, the study of medium effects becomes increasingly relevant. It is difficult to predict how, for example, the large apolar structure of a light-driven rotary molecular motor is affected by a biological setting or surface proximity, while for future nanotechnology precise fine tuning and full understanding of the isomerization process are of the utmost importance. Previous investigations into solvent effects have mainly focused on the relatively large solvent-solute interaction of hydrogen bonding or polarization induced by the isomerization process...
September 29, 2016: Physical Chemistry Chemical Physics: PCCP
Juan Du, Dalong Liu, Emad S Ebbini
A nonlinear filtering approach to imaging the dynamics of microbubble ultrasound contrast agents (UCA) in microvessels is presented. The approach is based on the adaptive third-order Volterra filter (TVF), which separates the linear, quadratic, and cubic components from beamformed pulse-echo ultrasound data. The TVF captures polynomial nonlinearities utilizing the full spectral components of the echo data and not from prespecified bands, e.g. second or third harmonics. This allows for imaging using broadband pulse transmission to preserve the axial resolution and the SNR...
September 29, 2016: IEEE Transactions on Ultrasonics, Ferroelectrics, and Frequency Control
Peter H Adler, Hiroyuki Takaoka, Mohd Sofian-Azirun, Van Lun Low, Zubaidah Ya'cob, Chee Dhang Chen, Koon Weng Lau, Xuan Da Pham
The increasing attention on Vietnam as a biodiversity hotspot prompted an investigation of the potential for cryptic diversity in black flies, a group well known elsewhere for its high frequency of isomorphic species. We analyzed the banding structure of the larval polytene chromosomes in the Simulium tuberosum species group to probe for diversity beyond the morphological level. Among 272 larvae, 88 different chromosomal rearrangements, primarily paracentric inversions, were discovered in addition to 25 already known in the basic sequences of the group in Asia...
2016: PloS One
Seyed R Tabaei, Jurriaan J J Gillissen, Nam-Joon Cho
Particle tracking is used to measure the diffusional motion of nanosized (≈100 nm), lipid vesicles that are electrostatically adsorbed onto a solid supported lipid bilayer. It is found that the motion of membrane-adhering vesicles is Brownian and depends inversely on the vesicle size, but is insensitive to the vesicle surface charge. The measured diffusivity agrees well with the Evans-Sackmann model for the diffusion of inclusions in supported, fluidic membranes. The agreement implies that the vesicle motion is coupled to that of a nanoscopic lipid cluster in the upper leaflet, which slides over the lower leaflet...
September 30, 2016: Small
Thomas N Hooper, Ross Inglis, Giulia Lorusso, Jakub Ujma, Perdita E Barran, Dusan Uhrin, Jürgen Schnack, Stergios Piligkos, Marco Evangelisti, Euan K Brechin
The family of compounds of general formula [Ln(III)4TM(II)8(OH)8(L)8(O2CR)8(MeOH)y](ClO4)4 {[Gd4Zn8(OH)8(hmp)8(O2C(i)Pr)8](ClO4)4 (1a); [Y4Zn8(OH)8(hmp)8(O2C(i)Pr)8](ClO4)4 (1b); [Gd4Cu8(OH)8(hmp)8(O2C(i)Pr)8](ClO4)4 (2a); [Y4Cu8(OH)8(hmp)8(O2C(i)Pr)8](ClO4)4 (2b); [Gd4Cu8(OH)8(hep)8(O2C(i)Pr)8](ClO4)4 (3a); [Gd4Cu8(OH)8(Hpdm)8(O2C(t)Bu)8](ClO4)4 (4a); [Gd4Cu8(OH)8(ea)8(O2CMe)8](ClO4)4 (5a); [Gd4Ni8(OH)8(hmp)8(O2CEt)8(MeOH)6](ClO4)4 (6a); [Y4Ni8(OH)8(hmp)8(O2CEt)8(MeOH)6](ClO4)4 (6b); [Gd4Co8(OH)8(hmp)8(O2CEt)8(MeOH)6](ClO4)4 (7a); [Y4Co8(OH)8(hmp)8(O2CEt)8(MeOH)6](ClO4)4 (7b)} can be formed very simply and in high yields from the reaction of Ln(NO3)3·6H2O and TM(ClO4)2·6H2O and the appropriate ligand blend in a mixture of CH2Cl2 and MeOH in the presence of a suitable base...
October 17, 2016: Inorganic Chemistry
Maria Stancescu, Tatiana A Fedotova, Jef Hooyberghs, Alexander Balaeff, Dmitry M Kolpashchikov
Detection of point mutations and single nucleotide polymorphisms in DNA and RNA has a growing importance in biology, biotechnology, and medicine. For the application at hand, hybridization assays are often used. Traditionally, they differentiate point mutations only at elevated temperatures (>40 °C) and in narrow intervals (ΔT = 1-10 °C). The current study demonstrates that a specially designed multistranded DNA probe can differentiate point mutations in the range of 5-40 °C. This unprecedentedly broad ambient-temperature range is enabled by a controlled combination of (i) nonequilibrium hybridization conditions and (ii) a mismatch-induced increase of equilibration time in respect to that of a fully matched complex, which we dub "kinetic inversion"...
October 4, 2016: Journal of the American Chemical Society
Merih Cibis, Wouter V Potters, Frank J Gijsen, Henk Marquering, Pim van Ooij, Ed vanBavel, Jolanda J Wentzel, Aart J Nederveen
INTRODUCTION: Wall shear stress (WSS) and oscillatory shear index (OSI) are associated with atherosclerotic disease. Both parameters are derived from blood velocities, which can be measured with phase-contrast MRI (PC-MRI). Limitations in spatiotemporal resolution of PC-MRI are known to affect these measurements. Our aim was to investigate the effect of spatiotemporal resolution using a carotid artery phantom. METHODS: A carotid artery phantom was connected to a flow set-up supplying pulsatile flow...
2016: PloS One
Christian Hundt, Andreas Hildebrandt, Bertil Schmidt
BACKGROUND: Gene Set Enrichment Analysis (GSEA) is a popular method to reveal significant dependencies between predefined sets of gene symbols and observed phenotypes by evaluating the deviation of gene expression values between cases and controls. An established measure of inter-class deviation, the enrichment score, is usually computed using a weighted running sum statistic over the whole set of gene symbols. Due to the lack of analytic expressions the significance of enrichment scores is determined using a non-parametric estimation of their null distribution by permuting the phenotype labels of the probed patients...
2016: BMC Bioinformatics
Heidi J Larson, Alexandre de Figueiredo, Zhao Xiahong, William S Schulz, Pierre Verger, Iain G Johnston, Alex R Cook, Nick S Jones
BACKGROUND: Public trust in immunization is an increasingly important global health issue. Losses in confidence in vaccines and immunization programmes can lead to vaccine reluctance and refusal, risking disease outbreaks and challenging immunization goals in high- and low-income settings. National and international immunization stakeholders have called for better monitoring of vaccine confidence to identify emerging concerns before they evolve into vaccine confidence crises. METHODS: We perform a large-scale, data-driven study on worldwide attitudes to immunizations...
September 13, 2016: EBioMedicine
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