Aperiodic String Transducers

Regular string-to-string functions enjoy a nice triple characterization through deterministic two-way transducers (2DFT), streaming string transducers (SST) and MSO definable functions. This result has recently been lifted to FO definable functions, with equivalent representations by means of aperiodic 2DFT and aperiodic 1-bounded SST, extending a well-known result on regular languages. In this paper, we give three direct transformations: i) from 1-bounded SST to 2DFT, ii) from 2DFT to copyless SST, and iii) from k-bounded to 1-bounded SST. We give the complexity of each construction and also prove that they preserve the aperiodicity of transducers. As corollaries, we obtain that FO definable string-to-string functions are equivalent to SST whose transition monoid is finite and aperiodic, and to aperiodic copyless SST

Ukraine should double down on reform in 2018. Why tough love from international partners and pressure from Ukrainian society is necessary. EPC Commentary, 17 January 2018

Ukraine has come a long way since the Revolution of Dignity (Maidan) in 2013-14. The country is going through a long-term transformation under difficult circumstances, fighting a war on two fronts. First, the conflict in Eastern Ukraine, and second the fight against those both inside and outside government that strongly resist change, not least the deeply embedded oligarchic interests in the country. Significant pressure needs to come from both Ukrainian society and Ukraine’s international partners to sustain the reform momentum

On the origin of the marine zinc–silicon correlation

The close linear correlation between the distributions of dissolved zinc (Zn) and silicon (Si) in seawater has puzzled chemical oceanographers since its discovery almost forty years ago, due to the apparent lack of a mechanism for coupling these two nutrient elements. Recent research has shown that such a correlation can be produced in an ocean model without any explicit coupling between Zn and Si, via the export of Zn-rich biogenic particles in the Southern Ocean, consistent with the observation of elevated Zn quotas in Southern Ocean diatoms. Here, we investigate the physical and biological mechanisms by which Southern Ocean uptake and export control the large-scale marine Zn distribution, using suites of sensitivity simulations in an ocean general circulation model (OGCM) and a box-model ensemble. These simulations focus on the sensitivity of the Zn distribution to the stoichiometry of Zn uptake relative to phosphate (PO4), drawing directly on observations in culture. Our analysis reveals that OGCM model variants that produce a well-defined step between relatively constant, high Zn:PO4 uptake ratios in the Southern Ocean and low Zn:PO4 ratios at lower latitudes fare best in reproducing the marine Zn–Si correlation at both the global and the regional Southern Ocean scale, suggesting the presence of distinct Zn-biogeochemical regimes in the high- and low-latitude oceans that may relate to differences in physiology, ecology or (micro-)nutrient status. Furthermore, a study of the systematics of both the box model and the OGCM reveals that regional Southern Ocean Zn uptake exerts control over the global Zn distribution via its modulation of the biogeochemical characteristics of the surface Southern Ocean. Specifically, model variants with elevated Southern Ocean Zn:PO4 uptake ratios produce near-complete Zn depletion in the Si-poor surface Subantarctic Zone, where upper-ocean water masses with key roles in the global oceanic circulation are formed. By setting the main preformed covariation trend within the ocean interior, the subduction of these Zn- and Si-poor water masses produces a close correlation between the Zn and Si distributions that is barely altered by their differential remineralisation during low-latitude cycling. We speculate that analogous processes in the high-latitude oceans may operate for other trace metal micronutrients as well, splitting the ocean into two fundamentally different biogeochemical, and thus biogeographic, regimes

Actually Sparse Variational Gaussian Processes

Gaussian processes (GPs) are typically criticised for their unfavourable scaling in both computational and memory requirements. For large datasets, sparse GPs reduce these demands by conditioning on a small set of inducing variables designed to summarise the data. In practice however, for large datasets requiring many inducing variables, such as low-lengthscale spatial data, even sparse GPs can become computationally expensive, limited by the number of inducing variables one can use. In this work, we propose a new class of inter-domain variational GP, constructed by projecting a GP onto a set of compactly supported B-spline basis functions. The key benefit of our approach is that the compact support of the B-spline basis functions admits the use of sparse linear algebra to significantly speed up matrix operations and drastically reduce the memory footprint. This allows us to very efficiently model fast-varying spatial phenomena with tens of thousands of inducing variables, where previous approaches failed

Shotgun Mass Spectrometry Workflow Combining IEF and LC-MALDI-TOF/TOF

We present a high throughput shotgun mass spectrometry workflow using a bidimensional peptide fractionation procedure consisting of isoelectric focusing and RP-HPLC prior to mass spectrometric analysis, with the aim of optimizing peptide separation and protein identification. As part of the workflow we used the ‘Isotope-Coded Protein Labeling’ (ICPL) method for accurate relative quantitation of protein expression. Such workflow was successfully applied to a comparative proteome analysis of schizophrenia versus healthy control brain tissues and can be an alternative to proteome researches

Riboflavin:A multifunctional vitamin.

Riboflavin, a component of the B-2 vitaminic complex, plays important roles in biochemistry, especially in redox reactions, due to the ability to participate in both one- and two-electron transfers as well as acting as a photosensitizer. Accordingly, low intakes of this vitamin have been associated with different diseases, including cancer and cardiovascular diseases. Riboflavin is thought to contribute to oxidative stress through its capacity to produce superoxide but, interestingly, it can also promote the reduction of hydroperoxides. This peculiar and multifunctional behavior allows riboflavin to take part in various biochemical pathways as a nucleophile and an electrophile, turning it into a versatile and important biological compound

Evaluation of the influence of kyphosis and scoliosis on intervertebral disc extrusion in French bulldogs

Although thoracic vertebral malformations with kyphosis and scoliosis are often considered incidental findings on diagnostic imaging studies of screw-tailed brachycephalic breeds, they have been suggested to interfere with spinal biomechanics and intervertebral disc degeneration. It is however unknown if an abnormal spinal curvature also predisposes dogs to develop clinically relevant intervertebral disc herniations. The aim of this study was to evaluate if the occurrence of thoracic vertebral malformations, kyphosis or scoliosis would be associated with a higher prevalence of cervical or thoracolumbar intervertebral disc extrusion in French bulldogs

Identification and functional characterization of a novel arginine/ornithine transporter, a member of a cationic amino acid transporter subfamily in the Trypanosoma cruzi genome

Background: Trypanosoma cruzi, the etiological agent of Chagas disease, is auxotrophic for arginine. It obtains this amino acid from the host through transporters expressed on the plasma membrane and on the membranes of intracellular compartments. A few cationic amino acid transporters have been characterized at the molecular level, such as the novel intracellular arginine/ornithine transporter, TcCAT1.1, a member of the TcCAT subfamily that is composed of four almost identical open reading frames in the T. cruzi genome. Methods: The functional characterization of the TcCAT1.1 isoform was performed in two heterologous expression systems. TcCAT subfamily expression was evaluated by real-time PCR in polysomal RNA fractions, and the cellular localization of TcCAT1.1 fused to EGFP was performed by confocal and immunoelectron microscopy. Results: In the S. cerevisiae expression system, TcCAT1.1 showed high affinity for arginine (Km = 0.085 ± 0.04 mM) and low affinity for ornithine (Km = 1.7 ± 0.2 mM). Xenopus laevis oocytes expressing TcCAT1.1 showed a 7-fold increase in arginine uptake when they were pre-loaded with arginine, indicating that transport is enhanced by substrates on the trans side of the membrane (trans-stimulation). Oocytes that were pre-loaded with [3H]-arginine displayed a 16-fold higher efflux of [3H]-arginine compared with that of the control. Analysis of polysomal RNA fractions demonstrated that the expression of members of the arginine transporter TcCAT subfamily is upregulated under nutritional stress and that this upregulation precedes metacyclogenesis. To investigate the cellular localization of the transporter, EGFP was fused to TcCAT1.1, and fluorescence microscopy and immunocytochemistry revealed the intracellular labeling of vesicles in the anterior region, in a network of tubules and vesicles. Conclusions: TcCAT1.1 is a novel arginine/ornithine transporter, an exchanger expressed in intracellular compartments that is physiologically involved in arginine homeostasis throughout the T. cruzi life cycle. The properties and estimated kinetic parameters of TcCAT1.1 can be extended to other members of the TcCAT subfamily

Mindfulness-based interventions in epilepsy: a systematic review

Mindfulness based interventions (MBIs) are increasingly used to help patients cope with physical and mental long-term conditions (LTCs). Epilepsy is associated with a range of mental and physical comorbidities that have a detrimental effect on quality of life (QOL), but it is not clear whether MBIs can help. We systematically reviewed the literature to determine the effectiveness of MBIs in people with epilepsy. Medline, Cochrane Central Register of Controlled Trials, EMBASE, CINAHL, Allied and Complimentary Medicine Database, and PsychInfo were searched in March 2016. These databases were searched using a combination of subject headings where available and keywords in the title and abstracts. We also searched the reference lists of related reviews. Study quality was assessed using the Cochrane Collaboration risk of bias tool. Three randomised controlled trials (RCTs) with a total of 231 participants were included. The interventions were tested in the USA (n = 171) and China (Hong Kong) (n = 60). Significant improvements were reported in depression symptoms, quality of life, anxiety, and depression knowledge and skills. Two of the included studies were assessed as being at unclear/high risk of bias - with randomisation and allocation procedures, as well as adverse events and reasons for drop-outs poorly reported. There was no reporting on intervention costs/benefits or how they affected health service utilisation. This systematic review found limited evidence for the effectiveness of MBIs in epilepsy, however preliminary evidence suggests it may lead to some improvement in anxiety, depression and quality of life. Further trials with larger sample sizes, active control groups and longer follow-ups are needed before the evidence for MBIs in epilepsy can be conclusively determined