Dieter Schwarzenbach (1936-2024).

Obituary for Dieter Schwarzenbach.

Interactive data exploration websites for large-scale electrophysiology.

Methodological advances in neuroscience have enabled the collection of massive datasets which demand innovative approaches for scientific communication. Existing platforms for data storage lack intuitive tools for data exploration, limiting our ability to interact effectively with these brain-wide datasets. We introduce two public websites: (Data and Atlas) developed for the International Brain Laboratory which provide access to millions of behavioral trials and hundreds of thousands of individual neurons.

A modular architecture for organizing, processing and sharing neurophysiology data.

We describe an architecture for organizing, integrating and sharing neurophysiology data within a single laboratory or across a group of collaborators. It comprises a database linking data files to metadata and electronic laboratory notes; a module collecting data from multiple laboratories into one location; a protocol for searching and sharing data and a module for automatic analyses that populates a website. These modules can be used together or individually, by single laboratories or worldwide collaborations.

Standardized and reproducible measurement of decision-making in mice.

Progress in science requires standardized assays whose results can be readily shared, compared, and reproduced across laboratories. Reproducibility, however, has been a concern in neuroscience, particularly for measurements of mouse behavior. Here, we show that a standardized task to probe decision-making in mice produces reproducible results across multiple laboratories.

Producing highly complicated materials. Nature does it better.

Through the years, mineralogical studies have produced a tremendous amount of data on the atomic arrangement and mineral properties. Quite often, structural analysis has led to elucidate the role played by minor components, giving interesting insights into the physico-chemical conditions of mineral crystallization and allowing the description of unpredictable structures that represented a body of knowledge critical for assessing their technological potentialities. Using such a rich database, containing many basic acquisitions, further steps became appropriate and possible, into the directions of more advanced knowledge frontiers.

ON-OFF receptive fields in auditory cortex diverge during development and contribute to directional sweep selectivity.

Neurons in the auditory cortex exhibit distinct frequency tuning to the onset and offset of sounds, but the cause and significance of ON and OFF receptive field (RF) organisation are not understood. Here we demonstrate that distinct ON and OFF frequency tuning is largely absent in immature mouse auditory cortex and is thus a consequence of cortical development. Simulations using a novel implementation of a standard Hebbian plasticity model show that the natural alternation of sound onset and offset is sufficient for the formation of non-overlapping adjacent ON and OFF RFs in cortical neurons.

Incommensurate atomic density waves in the high-pressure IVb phase of barium.

The host-guest structures of elements at high pressure discovered a decade ago still leave many open questions due to the lack of precise models based on full exploitation of the diffraction data. This concerns in particular Ba IV, which is stable in the range 12-45 GPa. With the example of phase Ba IVb, which is characterized here for the first time, a systematic analysis is presented of possible host-guest structure models based on high-quality single-crystal diffraction data obtained with synchrotron radiation at six different pressures between 16.

Graphics processing unit-accelerated quantitative trait Loci detection.

Mapping quantitative trait loci (QTL) using genetic marker information is a time-consuming analysis that has interested the mapping community in recent decades. The increasing amount of genetic marker data allows one to consider ever more precise QTL analyses while increasing the demand for computation. Part of the difficulty of detecting QTLs resides in finding appropriate critical values or threshold values, above which a QTL effect is considered significant.

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species.

Background: The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly tools are available, but they differ greatly in terms of their performance (speed, scalability, hardware requirements, acceptance of newer read technologies) and in their final output (composition of assembled sequence).

Assemblathon 1: a competitive assessment of de novo short read assembly methods.

Low-cost short read sequencing technology has revolutionized genomics, though it is only just becoming practical for the high-quality de novo assembly of a novel large genome. We describe the Assemblathon 1 competition, which aimed to comprehensively assess the state of the art in de novo assembly methods when applied to current sequencing technologies. In a collaborative effort, teams were asked to assemble a simulated Illumina HiSeq data set of an unknown, simulated diploid genome.

The role of the tangent bundle for symmetry operations and modulated structures.

An equivalence relation on the tangent bundle of a manifold is defined in order to extend a structure (modulated or not) onto it. This extension affords a representation of a structure in any tangent space and that in another tangent space can easily be derived. Euclidean symmetry operations associated with the tangent bundle are generalized and their usefulness for the determination of the intrinsic translation part in helicoidal axes and glide planes is illustrated.

Crystal structure and optical and magnetic properties of Pr(2)(MoO(4))(3).

Praseodymium molybdate Pr(2)(MoO(4))(3) was synthesized using the standard ceramic route. The crystal structure of the material has been successfully solved in superspace group I2/b(alphabeta0)00 with lattice constants a = 5.30284(4), b = 5.

Differential geometry: a natural tool for describing symmetry operations.

Differential geometry provides a useful mathematical framework for describing the fundamental concepts in crystallography. The notions of point and associated vector spaces correspond to those of manifold and tangent space at a given point. A space-group operation is a one-to-one map acting on the manifold, whereas a point-group operation is a linear map acting between two tangent spaces of the manifold.

Molecular dynamics study of tryptophylglycine: a dipeptide nanotube with confined water.

To investigate the mechanism of structural changes of a peptide nanotube and water confined inside the channel, the helical peptide tryptophylglycine monohydrate (WG.H2O) was studied by molecular dynamics (MD) simulations using the three-dimension parallel MD program ddgmq (software package) and a consistent force field. Simulations were performed on both the water-containing system and a model system without water molecules.

KSm(MoO(4))(2), an incommensurately modulated and partially disordered scheelite-like structure.

The incommensurately modulated scheelite-like KSm(MoO(4))(2) structure has been refined in the monoclinic superspace group I2/b(alphabeta0)00 by the Rietveld method on the basis of synchrotron radiation powder diffraction data. The systematic broadening of satellite reflections has been accounted for by applying anisotropic microstrain line-broadening. The microstructure has been studied by transmission electron microscopy (TEM).

Capabilities and limitations of a (3 + d)-dimensional incommensurately modulated structure as a model for the derivation of an extended family of compounds: example of the scheelite-like structures.

The previously reported incommensurately modulated scheelite-like structure KNd(MoO(4))(2) has been exploited as a natural (3 + 1)-dimensional superspace model to generate the scheelite-like three-dimensional structure family. Although each member differs in its space-group symmetry, unit-cell parameters and compositions, in (3 + 1)-dimensional space, they share a common superspace group, a common number of building units in the basic unit cell occupying Wyckoff sites with specific coordinates (x, y, z) and specific basic unit-cell axial ratios (c/a, a/b, b/c) and angles. Variations of the modulation vector q, occupation functions and t(0) are exploited for the derivation.

Hexagonal ferrites: a unified model of the (TS)nT series in superspace.

Hexagonal ferrites represent an extensive family of mixed-layer magnetic materials with periods up to 1500 A along the stacking direction, probably constituting the largest unit cells in the inorganic realm. The (TS)(n)T subfamily includes P3m1 and R3m structures that can be derived from Y ferrite Ba(2)M(2)Fe(12)O(22) (M = Zn, Fe, Co, Mg, Mn) by introducing stacking faults. A unified (3 + 1)-dimensional superspace model is proposed for all members of the (TS)(n)T family.

Barrett's esophagus: participation of the esophageal wall.

The modern inhibitors of gastric acid secretion reduce very efficiently the aggressiveness of gastroesophageal reflux but they appear to modify the pathophysiological situation in a way that favours the development of Barrett's esophagus (BE). During the last two decades, the prevalence of BE in the population submitted to endoscopy has clearly increased while the peptic stricture of the esophagus is fast disappearing. With a reduced tendency to stricture and fibrosis, the esophagus seems more prone to the columnar metaplasia.

Potassium gallium hydrogenphosphate fluoride, K(2)Ga[H(HPO(4))(2)]F(2).

Hydrothermally synthesized dipotassium gallium {hydrogen bis[hydrogenphosphate(V)]} difluoride, K(2)Ga[H(HPO(4))(2)]F(2), is isotypic with K(2)Fe[H(HPO(4))(2)]F(2). The main features of the structure are ([Ga{H(HPO(4))(2)}F(2)](2-))(n) columns consisting of centrosymmetric Ga(F(2)O(4)) octahedra [average Ga-O = 1.966 (3) Angstrom and Ga-F = 1.

Growth-induced incommensurability observed in the organic co-crystal hexamethylenetetramine resorcinol.

Co-crystals of hexamethylenetetramine and resorcinol were investigated by X-ray diffraction. The structure was refined in the superspace group Xmcm(0beta0)s0s, X=(1/2 1/2 0 1/2). In the average structure the resorcinol molecules are disordered between two orientations.