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The nematic phase transition in electronic liquids, driven by Coulomb interactions, represents a new class of strongly correlated electronic ground states. We studied suspended samples of bilayer graphene, annealed so that it achieves very high quasiparticle mobilities (greater than 10 6 square centimers per volt-second). Bilayer graphene is a truly two-dimensional material with complex chiral electronic spectra, and the high quality of our samples allowed us to observe strong spectrum reconstructions and electron topological transitions that can be attributed to a nematic phase transition and a decrease in rotational symmetry. These results are especially surprising because no interaction effects have been observed so far in bilayer graphene in the absence of an applied magnetic field.

We describe a new algorithm for the “perfect” extraction of one-dimensional (1D) spectra from two-dimensional (2D) digital images of optical fiber spectrographs, based on accurate 2D forward modeling of the raw pixel data. The algorithm is correct for arbitrarily complicated 2D point-spread functions (PSFs), as compared to the traditional optimal extraction algorithm, which is only correct for a limited class of separable PSFs. The algorithm results in statistically independent extracted samples in the 1D spectrum, and preserves the full native resolution of the 2D spectrograph without degradation. Both the statistical errors and the 1D resolution of the extracted spectrum are accurately determined, allowing a correctχ2 χ 2 comparison of any model spectrum with the data. Using a model PSF similar to that found in the red channel of the Sloan Digital Sky Survey spectrograph, we compare the performance of our algorithm to that of cross-section based optimal extraction, and also demonstrate that our method allows coaddition and foreground estimation to be carried out as an integral part of the extraction step. This work demonstrates the feasibility of current and next-generation multifiber spectrographs for faint-galaxy surveys even in the presence of strong night-sky foregrounds. We describe the handling of subtleties arising from fiber-to-fiber cross talk, discuss some of the likely challenges in deploying our method to the analysis of a full-scale survey, and note that our algorithm could be generalized into an optimal method for the rectification and combination of astronomical imaging data.

Three‐dimensional spectroscopy of extended sources is typically performed with dedicated integral field spectrographs. We describe a method of reconstructing full spectral cubes, with two spatial and one spectral dimension, from rastered spectral mapping observations employing a single slit in a traditional slit spectrograph. When the background and image characteristics are stable, as is often achieved in space, the use of traditional long slits for integral field spectroscopy can substantially reduce instrument complexity over dedicated integral field designs, without loss of mapping efficiency—particularly compelling when a long‐slit mode for single unresolved source follow‐up is separately required. We detail a custom flux‐conserving cube reconstruction algorithm, discuss issues of extended‐source flux calibration, and describe CUBISM, a tool that implements these methods for spectral maps obtained with theSpitzer Space Telescope’s Infrared Spectrograph.

The development of diffuse optical tomography as a functional imaging modality has relied largely on the use of model-based image reconstruction. The recovery of optical parameters from boundary measurements of light propagation within tissue is inherently a difficult one, because the problem is nonlinear, ill-posed and ill-conditioned. Additionally, although the measured near-infrared signals of light transmission through tissue provide high imaging contrast, the reconstructed images suffer from poor spatial resolution due to the diffuse propagation of light in biological tissue. The application of model-based image reconstruction is reviewed in this paper, together with a numerical modelling approach to light propagation in tissue as well as generalized image reconstruction using boundary data. A comprehensive review and details of the basis for using spatial and structural prior information are also discussed, whereby the use of spectral and dual-modality systems can improve contrast and spatial resolution.

The study of metabolic responses to drugs, environmental changes, and diseases is a new promising area of metabonomic research. Metabolic fingerprints can be obtained by analytical techniques such as nuclear magnetic resonance (NMR). In principle, alterations of these fingerprints due to appearance/disappearance or concentration changes of metabolites can provide early evidences of, for example, onset of diseases. A major drawback in this approach is the strong day-to-day variability of the individual metabolic fingerprint, which should be rather called a metabolic \"snapshot.\" We show here that a thorough statistical analysis performed on NMR spectra of human urine samples reveals an invariant part characteristic of each person, which can be extracted from the analysis of multiple samples of each single subject. This finding (i) provides evidence that individual metabolic phenotypes may exist and (ii) opens new perspectives to metabonomic studies, based on the possibility of eliminating the daily \"noise\" by multiple sample collection.

BtuCD is an adenosine triphosphate-binding cassette (ABC) transporter that translocates vitamin B₁₂ from the periplasmic binding protein BtuF into the cytoplasm of Escherichia coli. The 2.6 angstrom crystal structure of a complex BtuCD-F reveals substantial conformational changes as compared with the previously reported structures of BtuCD and BtuF. The lobes of BtuF are spread apart, and B₁₂ is displaced from the binding pocket. The transmembrane BtuC subunits reveal two distinct conformations, and the translocation pathway is closed to both sides of the membrane. Electron paramagnetic resonance spectra of spin-labeled cysteine mutants reconstituted in proteoliposomes are consistent with the conformation of BtuCD-F that was observed in the crystal structure. A comparison with BtuCD and the homologous HI1470/71 protein suggests that the structure of BtuCD-F may reflect a posttranslocation intermediate.

Advances in tandem mass spectrometry (MS/MS) steadily increase the rate of generation of MS/MS spectra. As a result, the existing approaches that compare spectra against databases are already facing a bottleneck, particularly when interpreting spectra of modified peptides. Here we explore a concept that allows one to perform an MS/MS database search without ever comparing a spectrum against a database. We propose to take advantage of spectral pairs, which are pairs of spectra obtained from overlapping (often nontryptic) peptides or from unmodified and modified versions of the same peptide. Having a spectrum of a modified peptide paired with a spectrum of an unmodified peptide allows one to separate the prefix and suffix ladders, to greatly reduce the number of noise peaks, and to generate a small number of peptide reconstructions that are likely to contain the correct one. The MS/MS database search is thus reduced to extremely fast pattern-matching (rather than time-consuming matching of spectra against databases). In addition to speed, our approach provides a unique paradigm for identifying posttranslational modifications by means of spectral networks analysis.

We present a fast and portable reimplementation of Piskunov and Valenti's optimal-extraction algorithm (Piskunov & Valenti 2002) in C/C++ together with full uncertainty propagation, improved cosmic-ray removal, and an optimal background-subtraction algorithm. This reimplementation can be used with IRAF and most existing data-reduction packages and leads to signal-to-noise ratios close to the Poisson limit. The algorithm is very stable, operates on spectra from a wide range of instruments (slit spectra and fibre feeds), and has been extensively tested for VLT/UVES, ESO/CES, ESO/FEROS, NTT/EMMI, NOT/ALFOSC, STELLA/SES, SSO/WiFeS, and finally, P60/SEDM-IFU data.

The peridinin-chlorophyll a-protein (PCP) of dinoflagellates is unique among the large variety of natural photosynthetic light-harvesting systems. In contrast to other chlorophyll protein complexes, the soluble PCP is located in the thylakoid lumen, and the carotenoid pigments outnumber the chlorophylls. The structure of the PCP complex consists of two symmetric domains, each with a central chlorophyll a (Chl-a) surrounded by four peridinin molecules. The protein provides distinctive surroundings for the pigment molecules, and in PCP, the specific environment around each peridinin results in overlapping spectral line shapes, suggestive of different functions within the protein. One particular Per, Per-614, is hypothesized to show the strongest electronic interaction with the central Chl-a. We have performed an in vitro reconstitution of pigments into recombinant PCP apo-protein (RFPCP) and into a mutated protein with an altered environment near Per-614. Steady-state and transient optical spectroscopic experiments comparing the RFPCP complex with the reconstituted mutant protein identify specific amino acid-induced spectral shifts. The spectroscopic assignments are reinforced by a determination of the structures of both RFPCP and the mutant by x-ray crystallography to a resolution better than 1.5 Å. RFPCP and mutated RFPCP are unique in representing crystal structures of in vitro reconstituted light-harvesting pigment-protein complexes.

We have observed W Hya, one of the closest and best-studied oxygen-rich evolved stars, in the dust sensitive mid-IR spectral domain with the interferometric instrument MIDI. Images could be obtained for the first time with MIDI in 25 wavelengths bins with the image reconstruction software MiRA using only the modulus of the visibilities. This still remains one of the few cases in which images could be successfully recovered due to the difficulties inherent to optical/infrared interferometry concerning the sparseness of the UV-plane and the missing Fourier phase information. Different regularization terms were compared and the influence of the UV-coverage was investigated. The lack of Fourier phase information, however, still limits the interpretation of the images. W Hya appears clearly nonsymmetric and the size is wavelength dependent. The photosphere, molecular layers, and dust formation zone could be resolved with an photospheric Gaussian FWHM diameter of 42 ± 2 mas (corresponding to 4.1 AU) and a dust layer of presumably amorphous aluminum oxide (Al2O3) at around two photospheric radii. The position angle of the major axis of the elongated structure could be determined to be (15 ± 10)° with a less well defined axis ratio between 0.4 and 0.6 showing that the dust forms primarily along a N–S axis. By comparing the elongated structure seen with MIDI with the Herschel/PACS 70 μm image at much larger scales, one can conclude that the asymmetry in the mass-loss most likely originates in the very close vicinity of the star and is thus not due to an interaction with the ambient media.