ALBERT

Description: Modulation of neuronal activities by light [e.g., laser or light-emitting diode] using optogenetics is a powerful tool for studies on neuronal functions in a brain. Herein, flexible thin-film optical waveguide arrays based on a highly biocompatible material of parylene are reported. Parylene-C and -N thin layers with the different refractive indices form the clad and the core of the waveguide, respectively, and neural recording microelectrodes are integrated to record optical stimuli and electrical recordings simultaneously using the same alignment. Both theoretical and experimental investigations confirm that light intensities of more than 90% can propagate in a bent waveguide with a curvature radius of 〉5 mm. The proposed flexible thin-film waveguide arrays with microelectrodes can be used for numerous spherical bio-tissues, including brain and spinal cord samples.

Description: Hydroxynitrile lyase (HNL) catalyzes the degradation of cyanohydrins and causes the release of hydrogen cyanide (cyanogenesis). HNL can enantioselectively produce cyanohydrins, which are valuable building blocks for the synthesis of fine chemicals and pharmaceuticals, and is used as an important biocatalyst in industrial biotechnology. Currently, HNLs are isolated from plants...

Description: The existence of multiple subclasses of Type Ia supernovae (SNe Ia) has been the subject of great debate in the last decade. One major challenge inevitably met when trying to infer the existence of one or more subclasses is the time consuming, and subjective, process of subclass definition. In this work, we show how machine learning tools facilitate identification of subtypes of SNe Ia through the establishment of a hierarchical group structure in the continuous space of spectral diversity formed by these objects. Using deep learning, we were capable of performing such identification in a four-dimensional feature space (+1 for time evolution), while the standard principal component analysis barely achieves similar results using 15 principal components. This is evidence that the progenitor system and the explosion mechanism can be described by a small number of initial physical parameters. As a proof of concept, we show that our results are in close agreement with a previously suggested classification scheme and that our proposed method can grasp the main spectral features behind the definition of such subtypes. This allows the confirmation of the velocity of lines as a first-order effect in the determination of SN Ia subtypes, followed by 91bg-like events. Given the expected data deluge in the forthcoming years, our proposed approach is essential to allow a quick and statistically coherent identification of SNe Ia subtypes (and outliers). All tools used in this work were made publicly available in the python package Dimensionality Reduction And Clustering for Unsupervised Learning in Astronomy ( dracula ) and can be found within COINtoolbox ( https://github.com/COINtoolbox/DRACULA ).

Description: A new method to study the intrinsic colour and luminosity of Type Ia supernovae (SNe Ia) is presented. A metric space built using principal component analysis on a spectral series for SNe Ia between –12.5 and +17.5 d from the B maximum is used as a set of predictors. This metric space is built to be insensitive to reddening. Hence, it does not predict the part of the colour excess due to dust extinction. At the same time, the rich variability of SN Ia spectra is a good predictor of a large fraction of the intrinsic colour variability. Such a metric space is a good predictor of the epoch when the maximum in the B  –  V colour curve is reached. Multivariate partial least-squares regression predicts the intrinsic B -band light curve and the intrinsic B  –  V colour curve up to a month after the maximum. This allows us to study the relation between the light curves of SNe Ia and their spectra. The total-to-selective extinction ratio R V in the host galaxy of SNe Ia is found, on average, to be consistent with typical Milky Way values. This analysis shows the importance of collecting spectra to study SNe Ia, even with a large sample publicly available. Future automated surveys, such as the Large Synoptic Survey Telescope, will provide a large number of light curves. The analysis shows that observing accompanying spectra for a significant number of SNe will be important even for normal SNe Ia.

Description: To evaluate the advantages of combination of two advanced electron microscopic technologies such as serial block-face scanning electron microscopy and double-axis electron beam tomography, we analyzed the three-dimensional morphology of cellular relationships between dendritic and plasma cells in the synovial membrane from patients with rheumatoid arthritis, using the combined approach.

Description: Motivation: Sequence homology searches are used in various fields. New sequencing technologies produce huge amounts of sequence data, which continuously increase the size of sequence databases. As a result, homology searches require large amounts of computational time, especially for metagenomic analysis. Results: We developed a fast homology search method based on database subsequence clustering, and implemented it as GHOSTZ. This method clusters similar subsequences from a database to perform an efficient seed search and ungapped extension by reducing alignment candidates based on triangle inequality. The database subsequence clustering technique achieved an ~2-fold increase in speed without a large decrease in search sensitivity. When we measured with metagenomic data, GHOSTZ is ~2.2–2.8 times faster than RAPSearch and is ~185–261 times faster than BLASTX. Availability and implementation: The source code is freely available for download at http://www.bi.cs.titech.ac.jp/ghostz/ Contact: akiyama@cs.titech.ac.jp Supplementary information: Supplementary data are available at Bioinformatics online.

Description: Amphiboles have played a leading role in metamorphic petrology, from helping to define several metamorphic facies to forming the basis of geothermobarometry, if their thermodynamic mixing properties can be calibrated to the temperature and pressure of formation. Compositional variations of sodium- and sodium-calcium-amphiboles may reveal important information about paleo-subduction zones but have not been studied as much as the more common calcium-amphiboles. In this study we investigate the mixing properties of amphibole solid solutions between magnesio-hornblende and glaucophane [ B Ca 2 C (Mg 4 Al) T (AlSi 7 )O 22 (OH) 2 – B Na 2 C (Mg 3 Al 2 ) T (Si 8 )O 22 (OH) 2 ] as a binary sub-join within the ternary amphibole system tremolite–glaucophane–tschermakite where the principal substitutions are Ca for Na at the B, Al for Mg at the C, and Al for Si at the T crystallographic sites. Amphiboles were made from mixtures of reagent oxides at 10 mol% increments between magnesio-hornblende and glaucophane, formed in a piston-cylinder press at 735–860 °C and 1.3–2.5 GPa for 72–216 h giving good yields (92–100 wt%). A positive deviation is present in the volume-composition plot, even after correcting volumes for non-binary components, supporting the presence of a positive deviation in the enthalpy of mixing ( H mix ) along this join. Fourier transform infrared spectra (FTIR) were obtained in the range of 350–4000 cm –1 for the mid-infrared spectra (MIR) for the purpose of estimating the extent of short-range ordering and for autocorrelation analysis, and, in the 650–50 cm –1 , for far-infrared spectra (FIR) for autocorrelation analysis. Autocorrelation analysis gave Corr values, which further support a positive deviation in the H mix along the magnsio-hornblende–glaucophane join, although the Corr maximum did not occur at the calcium-poor (i.e., glaucophane-rich) portion of the join as expected. Synthetic end-member glaucophane and magnesio-hornblende were mixed in a molar ratio of 1:1 and allowed to equilibrate by homogenization for variable durations in the range of 600–800 °C at 2.0 GPa to determine the maximum-width of the miscibility gap. These compositional re-equilibration experiments suggested the presence of an asymmetric miscibility gap (steeper toward glaucophane) with a critical-point below 700 °C. Combining the results of this study with previously published results on the tremolite–glaucophane join allowed refinement of several asymmetric formalism mixing parameters (i.e., W Gl,Ts = 20 kJ, α Ts = 1.2) and modeling of the miscibility gap within the tremolite–glaucophane–tschermakite ternary system. The results showed that the composition of the critical point is very close to the maximum in the autocorrelation parameter Corr , as one would predict. An important implication of this study is that low-temperature immiscibility between calcium- and sodium-rich amphiboles may be more important than the role of pressure, as proposed by Brown (1977) , in accounting for the change in B-site Na contents of metamorphic amphiboles.

Description: Among the insertional mutagenesis techniques used in the current international knockout mouse project (KOMP) on the inactivation of all mouse genes in embryonic stem (ES) cells, random gene trapping has been playing a major role. Gene-targeting experiments have also been performed to individually and conditionally knockout the remaining ‘difficult-to-trap’ genes. Here, we show that transcriptionally silent genes in ES cells are severely underrepresented among the randomly trapped genes in KOMP. Our conditional poly(A)-trapping vector with a common retroviral backbone also has a strong bias to be integrated into constitutively transcribed genome loci. Most importantly, conditional gene disruption could not be successfully accomplished by using the retrovirus vector because of the frequent development of intra-vector deletions/rearrangements. We found that one of the cut and paste-type DNA transposons, Tol2 , can serve as an ideal platform for gene-trap vectors that ensures identification and conditional disruption of a broad spectrum of genes in ES cells. We also solved a long-standing problem associated with multiple vector integration into the genome of a single cell by incorporating a mixture of differentially tagged Tol2 transposons. We believe our strategy indicates a straightforward approach to mass-production of conditionally disrupted alleles for genes in the target cells.

Description: We report the longitudinal spin-Seebeck effects (LSSEs) for Pt/Fe 70 Cu 30 /BiY 2 Fe 5 O 12 (BiYIG) and Pt/BiYIG devices. The LSSE voltage was found to be enhanced by inserting an ultra-thin Fe 70 Cu 30 interlayer. This enhancement decays sharply with increasing the Fe 70 Cu 30 thickness, suggesting that it is not due to bulk phenomena, such as a superposition of conventional thermoelectric effects, but due to interface effects related to the Fe 70 Cu 30 interlayer. Combined with control experiments using Pt/Fe 70 Cu 30 devices, we conclude that the enhancement of the LSSE voltage in the Pt/Fe 70 Cu 30 /BiYIG devices is attributed to the improvement of the spin-mixing conductance at the Pt/BiYIG interfaces.

Description: Discharge of humic acid (HA) in aqueous environments is a key health and aesthetic issue. The present work investigates the use of hydrogarnet as a novel adsorbent for HA. Hydrogarnet was hydrothermally synthesized with different solvents to control the chemical composition. Hydrogarnet with three types of chemical compositions had better adsorption properties for HA than hydrogarnet with a single chemical composition. Controlling the chemical composition of hydrogarnet increased the number of hydroxyl groups and the overall binding energy of the system, leading to changes in the zeta potential. The enhancement of these adsorption properties is related to the increased numbers of hydroxyl groups on the surface and their diverse binding energies.