Water diffusion in rat brain in vivo as detected at very large b values is multicompartmental

The diffusion-weighted signal attenuation of water in rat brain was measured with pulsed-field gradient nuclear magnetic resonance methods in a single voxel under in vivo and global ischemic conditions. The diffusion-attenuated water signal was observed in vivo at b values of 300 ms/ mu m/sup 2/ (strength of diffusion weighting) and diffusion times up to 400 ms. A series of constant diffusion time (CT) experiments with varied gradient directions and diffusion times revealed a multiexponential decay with apparent diffusion coefficients (ADC) covering two orders of magnitude from I to 0.01 mu m/sup 2//ms. In a four-exponential fit, the observed changes during global ischemia could be fully explained by changes in the relative volume fractions only with unchanged ADCs. An anisotropy of the ADC, detected at small b values, was not observed for the ADC at large b values, but for the concomitant volume fractions. An inverse Laplace Transform of the CT curves, performed with CONTIN, resulted in continuously distributed diffusion coefficients, for which the term `diffusogram' is proposed. This approach was more appropriate than a discrete exponential model with four to six components, being related to the morphology of brain tissue and its cell size distribution. On the basis of an analytical, quantitative model, it is suggested that the measured ADC at small b values reflects mainly properties of the restricting boundaries, i.e. the relative volume fractions and the extracellular tortuosity, while the intrinsic intracellular diffusion constant and the exchange time are predicted to have minor influence

Investigation of BOLD using CARR-PURCELL T2 Weighting with SPIRAL Readout

It is demonstrated that a Carr-Purcell (CP) technique based on the fully adiabatic pulse sequence (CP-LASER) with SPIRAL readout can be used to generate zoomed images with relatively short acquisition window (at) for the investigation of the mechanisms of the BOLD effect. Based on the capability of the developed technique to refocus the dynamic dephasing, it is demonstrated that the BOLD effect is suppressed as the pulse interval cp of CP-LASER sequence decreased

How to run a brain bank. A report from the Austro-German brain bank

The sophisticated analysis of and growing information on the human brain requires that acquisition, dissection, storage and distribution of rare material are managed in a professional way. In this publication we present the concept and practice of our brain bank. Both brain tissue and information are handled by standardized procedures and flow in parallel from pathology to neuropathology and neurochemistry. Data concerning brain material are updated with clinical information gained by standardized procedures

Fluctuations of the baryonic flux-tube junction from effective string theory

In quenched QCD, where the dynamic creation of quark-antiquark pairs out of the vacuum is neglected, a confined baryonic system composed of three static quarks exhibits string-like behaviour at large interquark separation, with the formation of flux tubes characterized by the geometry of the so-called Y ansatz. We study the fluctuations of the junction of the three flux tubes, assuming the dynamics to be governed by an effective bosonic string model. We show that the asymptotic behaviour of the effective width of the junction grows logarithmically with the distance between the sources, with the coefficient depending on the number of joining strings, on the dimension of spacetime and on the string tension.Comment: 9 pages, 2 figures, RevTeX4 style, revision: style changed, references added, more explanations added, typos correcte

Water diffusion in rat brain in vivo as detected at very large b values is multicompartmental

The diffusion-weighted signal attenuation of water in rat brain was measured with pulsed-field gradient nuclear magnetic resonance methods in a single voxel under in vivo and global ischemic conditions. The diffusion- attenuated water signal was observed in vivo at b values of 300 ms/μm2 (strength of diffusion weighting) and diffusion times up to 400 ms. A series of constant diffusion time (CT) experiments with varied gradient directions and diffusion times revealed a multiexponential decay with apparent diffusion coefficients (ADC) covering two orders of magnitude from 1 to 0.01 μm2/ms. In a four-exponential fit, the observed changes during global ischemia could be fully explained by changes in the relative volume fractions only with unchanged ADCs. An anisotropy of the ADC, detected at small b values, was not observed for the ADC at large b values, but for the concomitant volume fractions. An inverse Laplace Transform of the CT curves, performed with CONTIN, resulted in continuously distributed diffusion coefficients, for which the term 'diffusogram' is proposed. This approach was more appropriate than a discrete exponential model with four to six components, being related to the morphology of brain tissue and its cell size distribution. On the basis of an analytical, quantitative model, it is suggested that the measured ADC at small b values reflects mainly properties of the restricting boundaries, i.e. the relative volume fractions and the extracellular tortuosity, while the intrinsic intracellular diffusion constant and the exchange time are predicted to have minor influence

Fast and Efficient Postsynthetic DNA Labeling in Cells by Means of Strain-Promoted Sydnone-Alkyne Cycloadditions

Fast and efficient: DNA strands, modified with the novel bioorthogonal reporters sydnones, undergo fast and efficient labeling with cyclooctynes and have the potential to become essential tools for imaging DNA and possibly RNA in cells. Sydnones are highly stable mesoionic 1,3-dipoles that react with cyclooctynes through strain-promoted sydnone-alkyne cycloaddition (SPSAC). Although sydnones have been shown to be valuable bioorthogonal chemical reporters for the labeling of proteins and complex glycans, nucleic acids have not yet been tagged by SPSAC. Evaluation of SPSAC kinetics with model substrates showed fast reactions with cyclooctyne probes (up to k=0.59 M$^{-1}$ s$^{-1}$), and two different sydnones were effectively incorporated into both 2’-deoxyuridines at position 5, and 7-deaza-2’-deoxyadenosines at position 7. These modified nucleosides were synthetically incorporated into single-stranded DNAs, which were successfully postsynthetically labeled with cyclooctyne probes both in vitro and in cells. These results show that sydnones are versatile bioorthogonal tags and have the premise to become essential tools for tracking DNA and potentially RNA in living cells

The Portable Ice Nucleation Experiment (PINE): A new online instrument for laboratory studies and automated long-term field observations of ice-nucleating particles

Atmospheric ice-nucleating particles (INPs) play an important role in determining the phase of clouds, which affects their albedo and lifetime. A lack of data on the spatial and temporal variation of INPs around the globe limits our predictive capacity and understanding of clouds containing ice. Automated instrumentation that can robustly measure INP concentrations across the full range of tropospheric temperatures is needed in order to address this knowledge gap. In this study, we demonstrate the functionality and capacity of the new Portable Ice Nucleation Experiment (PINE) to study ice nucleation processes and to measure INP concentrations under conditions pertinent for mixed-phase clouds, with temperatures from about −10 to about −40 C. PINE is a cloud expansion chamber which avoids frost formation on the cold walls and thereby omits frost fragmentation and related background ice signals during the operation. The development, working principle and treatment of data for the PINE instrument is discussed in detail. We present laboratory-based tests where PINE measurements were compared with those from the established AIDA (Aerosol Interaction and Dynamics in the Atmosphere) cloud chamber. Within experimental uncertainties, PINE agreed with AIDA for homogeneous freezing of pure water droplets and the immersion freezing activity of mineral aerosols. Results from a first field campaign conducted at the Atmospheric Radiation Measurement (ARM) Southern Great Plains (SGP) observatory in Oklahoma, USA, from 1 October to 14 November 2019 with the latest PINE design (a commercially available PINE chamber) are also shown, demonstrating PINE\u27s ability to make automated field measurements of INP concentrations at a time resolution of about 8 min with continuous temperature scans for INP measurements between −10 and −30 ∘C. During this field campaign, PINE was continuously operated for 45 d in a fully automated and semi-autonomous way, demonstrating the capability of this new instrument to also be used for longer-term field measurements and INP monitoring activities in observatories

The Quantum Spin Hall Effect: Theory and Experiment

The search for topologically non-trivial states of matter has become an important goal for condensed matter physics. Recently, a new class of topological insulators has been proposed. These topological insulators have an insulating gap in the bulk, but have topologically protected edge states due to the time reversal symmetry. In two dimensions the helical edge states give rise to the quantum spin Hall (QSH) effect, in the absence of any external magnetic field. Here we review a recent theory which predicts that the QSH state can be realized in HgTe/CdTe semiconductor quantum wells. By varying the thickness of the quantum well, the band structure changes from a normal to an "inverted" type at a critical thickness $d_c$. We present an analytical solution of the helical edge states and explicitly demonstrate their topological stability. We also review the recent experimental observation of the QSH state in HgTe/(Hg,Cd)Te quantum wells. We review both the fabrication of the sample and the experimental setup. For thin quantum wells with well width $d_{QW}< 6.3$ nm, the insulating regime shows the conventional behavior of vanishingly small conductance at low temperature. However, for thicker quantum wells ($d_{QW}> 6.3$ nm), the nominally insulating regime shows a plateau of residual conductance close to $2e^2/h$. The residual conductance is independent of the sample width, indicating that it is caused by edge states. Furthermore, the residual conductance is destroyed by a small external magnetic field. The quantum phase transition at the critical thickness, $d_c= 6.3$ nm, is also independently determined from the occurrence of a magnetic field induced insulator to metal transition.Comment: Invited review article for special issue of JPSJ, 32 pages. For higher resolution figures see official online version when publishe

The PRIDE database and related tools and resources in 2019: improving support for quantification data

The PRoteomics IDEntifications (PRIDE) database (https://www.ebi.ac.uk/pride/) is the world's largest data repository of mass spectrometry-based proteomics data, and is one of the founding members of the global ProteomeXchange (PX) consortium. In this manuscript, we summarize the developments in PRIDE resources and related tools since the previous update manuscript was published in Nucleic Acids Research in 2016. In the last 3years, public data sharing through PRIDE (as part of PX) has definitely become the norm in the field. In parallel, data re-use of public proteomics data has increased enormously, with multiple applications. We first describe the new architecture of PRIDE Archive, the archival component of PRIDE. PRIDE Archive and the related data submission framework have been further developed to support the increase in submitted data volumes and additional data types. A new scalable and fault tolerant storage backend, Application Programming Interface and web interface have been implemented, as a part of an ongoing process. Additionally, we emphasize the improved support for quantitative proteomics data through the mzTab format. At last, we outline key statistics on the current data contents and volume of downloads, and how PRIDE data are starting to be disseminated to added-value resources including Ensembl, UniProt and Expression Atlas