Astronomical Spectroscopy

Spectroscopy is one of the most important tools that an astronomer has for studying the universe. This chapter begins by discussing the basics, including the different types of optical spectrographs, with extension to the ultraviolet and the near-infrared. Emphasis is given to the fundamentals of how spectrographs are used, and the trade-offs involved in designing an observational experiment. It then covers observing and reduction techniques, noting that some of the standard practices of flat-fielding often actually degrade the quality of the data rather than improve it. Although the focus is on point sources, spatially resolved spectroscopy of extended sources is also briefly discussed. Discussion of differential extinction, the impact of crowding, multi-object techniques, optimal extractions, flat-fielding considerations, and determining radial velocities and velocity dispersions provide the spectroscopist with the fundamentals needed to obtain the best data. Finally the chapter combines the previous material by providing some examples of real-life observing experiences with several typical instruments.Comment: An abridged version of a chapter to appear in Planets, Stars and Stellar Systems, to be published in 2011 by Springer. Slightly revise

P-Rex1 Controls Sphingosine 1-Phosphate Receptor Signalling, Morphology, and Cell-Cycle Progression in Neuronal Cells.

P-Rex1 is a guanine-nucleotide exchange factor (GEF) that activates Rac-type small G proteins in response to the stimulation of a range of receptors, particularly G protein-coupled receptors (GPCRs), to control cytoskeletal dynamics and other Rac-dependent cell responses. P-Rex1 is mainly expressed in leukocytes and neurons. Whereas its roles in leukocytes have been studied extensively, relatively little is known about its functions in neurons. Here, we used CRISPR/Cas9-mediated P-Rex1 deficiency in neuronal PC12 cells that stably overexpress the GPCR S1PR1, a receptor for sphingosine 1-phosphate (S1P), to investigate the role of P-Rex1 in neuronal GPCR signalling and cell responses. We show that P-Rex1 is required for the S1P-stimulated activation of Rac1 and Akt, basal Rac3 activity, and constitutive cAMP production in PC12-S1PR1 cells. The constitutive cAMP production was not due to increased expression levels of major neuronal adenylyl cyclases, suggesting that P-Rex1 may regulate adenylyl cyclase activity. P-Rex1 was required for maintenance of neurite protrusions and spreading in S1P-stimulated PC12-S1PR1 cells, as well as for cell-cycle progression and proliferation. In summary, we identified novel functional roles of P-Rex1 in neuronal Rac, Akt and cAMP signalling, as well as in neuronal cell-cycle progression and proliferation

Results from the first English stool bank using faecal microbiota transplant as a medicinal product for the treatment of Clostridioides difficile infection.

BACKGROUND: Faecal Microbiota Transplant (FMT) has improved outcomes for the treatment of Clostridioides difficile infection (CDI) compared to antibiotic therapy. FMT is classified as a medicinal product in the United Kingdom, similar to the USA and Canada, limiting supply via stool banks without appropriate licencing. In the largest UK cohort to date, we describe the clinical outcomes for 124 patients receiving FMT for recurrent or refractory CDI and present a framework to produce FMT as a licenced medicinal product. METHODS: Anonymous unrelated healthy donors, screened via health assessment and microbiological testing donated stool. In aerobic conditions FMT aliquots were prepared for immediate use or frozen storage, following a production framework developed to comply with Good Manufacturing Practice. Outcome measures were clinical response to FMT defined as resolution of diarrhoea within seven days and clinical cure defined as response without diarrhoea recurrence at 90 days. FINDINGS: Clinical response was 83·9% (95% CI 76·0%-90·0%) after one treatment. Clinical cure was 78·2% (95% CI 67·4%-89·0%) across the cohort. Refractory cases appeared to have a lower initial clinical response rate compared to recurrent cases, however at day 90 there were no differences observed between these groups. INTERPRETATION: The methodology developed here enabled successful licencing of FMT by The Medicines and Healthcare products Regulatory Agency as a medicinal product. This has widened the availability of FMT in the National Health Service via a stool bank and can be applied in other centres across the world to improve access to safe and quality assured treatments

Combinatorial Bounds and Characterizations of Splitting Authentication Codes

We present several generalizations of results for splitting authentication codes by studying the aspect of multi-fold security. As the two primary results, we prove a combinatorial lower bound on the number of encoding rules and a combinatorial characterization of optimal splitting authentication codes that are multi-fold secure against spoofing attacks. The characterization is based on a new type of combinatorial designs, which we introduce and for which basic necessary conditions are given regarding their existence.Comment: 13 pages; to appear in "Cryptography and Communications

Copula Eigenfaces with Attributes: Semiparametric Principal Component Analysis for a Combined Color, Shape and Attribute Model

Principal component analysis is a ubiquitous method in parametric appearance modeling for describing dependency and variance in datasets. The method requires the observed data to be Gaussian-distributed. We show that this requirement is not fulfilled in the context of analysis and synthesis of facial appearance. The model mismatch leads to unnatural artifacts which are severe to human perception. As a remedy, we use a semiparametric Gaussian copula model, where dependency and variance are modeled separately. This model enables us to use arbitrary Gaussian and non-Gaussian marginal distributions. Moreover, facial color, shape and continuous or categorical attributes can be analyzed in an unified way. Accounting for the joint dependency between all modalities leads to a more specific face model. In practice, the proposed model can enhance performance of principal component analysis in existing pipelines: The steps for analysis and synthesis can be implemented as convenient pre- and post-processing steps

The Mechanisms of Codon Reassignments in Mitochondrial Genetic Codes

Many cases of non-standard genetic codes are known in mitochondrial genomes. We carry out analysis of phylogeny and codon usage of organisms for which the complete mitochondrial genome is available, and we determine the most likely mechanism for codon reassignment in each case. Reassignment events can be classified according to the gain-loss framework. The gain represents the appearance of a new tRNA for the reassigned codon or the change of an existing tRNA such that it gains the ability to pair with the codon. The loss represents the deletion of a tRNA or the change in a tRNA so that it no longer translates the codon. One possible mechanism is Codon Disappearance, where the codon disappears from the genome prior to the gain and loss events. In the alternative mechanisms the codon does not disappear. In the Unassigned Codon mechanism, the loss occurs first, whereas in the Ambiguous Intermediate mechanism, the gain occurs first. Codon usage analysis gives clear evidence of cases where the codon disappeared at the point of the reassignment and also cases where it did not disappear. Codon disappearance is the probable explanation for stop to sense reassignments and a small number of reassignments of sense codons. However, the majority of sense to sense reassignments cannot be explained by codon disappearance. In the latter cases, by analysis of the presence or absence of tRNAs in the genome and of the changes in tRNA sequences, it is sometimes possible to distinguish between the Unassigned Codon and Ambiguous Intermediate mechanisms. We emphasize that not all reassignments follow the same scenario and that it is necessary to consider the details of each case carefully.Comment: 53 pages (45 pages, including 4 figures + 8 pages of supplementary information). To appear in J.Mol.Evo

Multi-Way Multi-Group Segregation and Diversity Indices

Background: How can we compute a segregation or diversity index from a three-way or multi-way contingency table, where each variable can take on an arbitrary finite number of values and where the index takes values between zero and one? Previous methods only exist for two-way contingency tables or dichotomous variables. A prototypical three-way case is the segregation index of a set of industries or departments given multiple explanatory variables of both sex and race. This can be further extended to other variables, such as disability, number of years of education, and former military service. Methodology/Principal Findings: We extend existing segregation indices based on Euclidean distance (square of coefficient of variation) and Boltzmann/Shannon/Theil index from two-way to multi-way contingency tables by including multiple summations. We provide several biological applications, such as indices for age polyethism and linkage disequilibrium. We also provide a new heuristic conceptualization of entropy-based indices. Higher order association measures are often independent of lower order ones, hence an overall segregation or diversity index should be the arithmetic mean of the normalized association measures at all orders. These methods are applicable when individuals selfidentify as multiple races or even multiple sexes and when individuals work part-time in multiple industries. Conclusions/Significance: The policy implications of this work are enormous, allowing people to rigorously test whethe

Asymmetry of Chromosome Replichores Renders the DNA Translocase Activity of FtsK Essential for Cell Division and Cell Shape Maintenance in Escherichia coli

Bacterial chromosomes are organised as two replichores of opposite polarity that coincide with the replication arms from the ori to the ter region. Here, we investigated the effects of asymmetry in replichore organisation in Escherichia coli. We show that large chromosome inversions from the terminal junction of the replichores disturb the ongoing post-replicative events, resulting in inhibition of both cell division and cell elongation. This is accompanied by alterations of the segregation pattern of loci located at the inversion endpoints, particularly of the new replichore junction. None of these defects is suppressed by restoration of termination of replication opposite oriC, indicating that they are more likely due to the asymmetry of replichore polarity than to asymmetric replication. Strikingly, DNA translocation by FtsK, which processes the terminal junction of the replichores during cell division, becomes essential in inversion-carrying strains. Inactivation of the FtsK translocation activity leads to aberrant cell morphology, strongly suggesting that it controls membrane synthesis at the division septum. Our results reveal that FtsK mediates a reciprocal control between processing of the replichore polarity junction and cell division

Female Urethral Reconstruction

Female urethral strictures are rare; thus, the literature describing stricture management in women is sparse. Although urethral dilation continues to be performed at a high frequency in women despite lack of proven efficacy, this procedure is used for a variety of voiding complaints other than stricture. Hence, the long-term utility of dilation and urethrotomy for urethral stricture in women is unknown. This review describes the various urethroplasty techniques used in the management of female urethral stricture. Although grafts using a dorsal approach have been shown to be feasible in women, ventral flap techniques offer good long-term outcomes with minimal morbidity. Acute and delayed management of pelvic fracture–associated urethral distraction defects in women is also described. Unlike in men, immediate urethroplasty in women should be performed once the patient is hemodynamically stable

Condensed Mitotic Chromosome Structure at Nanometer Resolution Using PALM and EGFP- Histones

Photoactivated localization microscopy (PALM) and related fluorescent biological imaging methods are capable of providing very high spatial resolutions (up to 20 nm). Two major demands limit its widespread use on biological samples: requirements for photoactivatable/photoconvertible fluorescent molecules, which are sometimes difficult to incorporate, and high background signals from autofluorescence or fluorophores in adjacent focal planes in three-dimensional imaging which reduces PALM resolution significantly. We present here a high-resolution PALM method utilizing conventional EGFP as the photoconvertible fluorophore, improved algorithms to deal with high levels of biological background noise, and apply this to imaging higher order chromatin structure. We found that the emission wavelength of EGFP is efficiently converted from green to red when exposed to blue light in the presence of reduced riboflavin. The photon yield of red-converted EGFP using riboflavin is comparable to other bright photoconvertible fluorescent proteins that allow <20 nm resolution. We further found that image pre-processing using a combination of denoising and deconvolution of the raw PALM images substantially improved the spatial resolution of the reconstruction from noisy images. Performing PALM on Drosophila mitotic chromosomes labeled with H2AvD-EGFP, a histone H2A variant, revealed filamentous components of ∼70 nm. This is the first observation of fine chromatin filaments specific for one histone variant at a resolution approximating that of conventional electron microscope images (10–30 nm). As demonstrated by modeling and experiments on a challenging specimen, the techniques described here facilitate super-resolution fluorescent imaging with common biological samples