A more detailed look at the Opacities for Enriched Carbon and Oxygen Mixtures

We have included opacity tables in our stellar evolution code that enable us to accurately model the structure of stars composed of mixtures with carbon and oxygen independently enhanced relative to solar. We present tests to demonstrate the effects of the new tables. Two of these are practical examples, the effect on the evolution of a thermally pulsing asymptotic giant branch star and a Wolf-Rayet Star. The changes are small but perceptible.Comment: 6 pages, 3 figures, 5 tables. Refereed version with corrections resubmitted to MNRA

Multiscale image analysis of calcium dynamics in cardiac myocytes

Cardiac myocytes are the muscle cells that build up heart tissue and provide the mechanical action to pump blood by synchronously contracting at every heartbeat. Heart muscle contraction is regulated by intracellular calcium concentration which exhibits a complex spatio-temporal dynamical behavior at the molecular, cellular and tissue levels. Details of such dynamical patterns are closely related to the mechanisms responsible for cardiovascular diseases , the single largest cause of death in the developed countries. The emerging field of translational cardiology focuses on the study of how such mechanisms connect and influence each other across spatial and temporal scales, eventually yielding to a certain clinical condition. To study such calcium dynamics in cardiac myocytes, we benefit from the recent advances in the field of experimental cell physiology. Fluorescence microscopy allows us to observe the distribution of calcium in the cell with a spatial resolution below one micron and a frame rate around one millisecond, thus providing a very accurate monitoring of calcium fluxes in the cell. The aim of the thesis summarized in this paper, was to develop image processing computational techniques for extracting quantitative data of physiological relevance from fluorescence confocal microscopy images at different scales. The two main subjects covered in the thesis were image segmentation and classification methods applied to fluorescence microscopy imaging of cardiac myocytes and calcium imaging. These methods were applied to a variety of problems involving different space and time scales, such as the localization of molecular receptors, the detection and characterization of spontaneous calcium-release events, and the propagation of calcium waves across a culture of cardiac cells. The following is a summary of the thesis as a consequence of having been awarded the 7th Justiniano Casas Award accessit by the Sociedad Española de Óptica.Peer ReviewedPostprint (published version

103 Atypical Progressive Bulbar Palsy presenting with Dropped Head

Introduction: Typical amyotrophic lateral sclerosis (ALS) presents on neurological examination with specific signs of upper and lower motor neuron degeneration (Brooks et al, 1995), which can account for 85% of patients with ALS (Turner and Talbot, 2013). There are different types of clinical presentations, including progressive bulbar palsy (PBP), Limb-onset ALS, progressive muscular atrophy (PMA) and upper motor neuron (UMN) predominant ALS. PBP has mainly brainstem signs. There are a few case reports of dropped head syndrome in ALS, mainly in patients with the limb involvement variant. Methods: Case report Results: A 56 year old right-handed male, presented to the clinic with four months of dysphagia to liquids and solids, neck pain and progressive neck weakness causing constant drop head. No dysarthria or other neurological symptoms, no dyspnea. Neurological examination: Cranial Nerve (CN) CN XII: Nasal voice, bilateral atrophy of the tongue with tremor and fasciculations. Motor: Diffuse atrophy and decreased tone of the sternocleidomastoid and trapezii bilaterally, strength: 2/5 in neck flexors and extensors. Sensory: Hypoesthesia of the tongue. The rest of his neurological examination was normal. Labs: Routine blood work, thyroid function tests, collagen vascular work-up, and protein electrophoresis were normal. Creatine Phosphokinase (CPK) and Acetylcholine Receptor Antibodies (AChR Ab) were negative. Brain and Spinal Cord MRI: Showed mild brainstem, cerebellar and cervical spinal atrophy. Conclusions: Patients with ALS initially present with symptoms localized to the limbs or bulbar muscles. A very small percentage 1-2% of ALS patients had neck muscle weakness with head drop (Jokelainen et al, 1977; Gourie-Devi et al, 2003). However, in all the previously reported cases, the patients had limb involvement at the time of presentation which was absent in this case, and the head drop occurred after the onset of symptoms (Lange et al, 1986; Katz et al; 1996). Dropped head syndrome can be seen in inflammatory myopathies, myasthenia gravis, facioscapulohumeral muscular dystrophy, spinal muscular atrophy, nemaline myopathy and carnitine deficiency (Umapathy et al, 2003) but ALS should also be considered in patients with atypical presentations

Optimization of Charcoal Production Process from Woody Biomass Waste: Effect of Ni-Containing Catalysts on Pyrolysis Vapors

Woody biomass waste (Pinus radiata) coming from forestry activities has been pyrolyzed with the aim of obtaining charcoal and, at the same time, a hydrogen-rich gas fraction. The pyrolysis has been carried out in a laboratory scale continuous screw reactor, where carbonization takes place, connected to a vapor treatment reactor, at which the carbonization vapors are thermo-catalytically treated. Different peak temperatures have been studied in the carbonization process (500-900 degrees C), while the presence of different Ni-containing catalysts in the vapor treatment has been analyzed. Low temperature pyrolysis produces high liquid and solid yields, however, increasing the temperature progressively up to 900 degrees C drastically increases gas yield. The amount of nickel affects the vapors treatment phase, enhancing even further the production of interesting products such as hydrogen and reducing the generated liquids to very low yields. The gases obtained at very high temperatures (700-900 degrees C) in the presence of Ni-containing catalysts are rich in H-2 and CO, which makes them valuable for energy production, as hydrogen source, producer gas or reducing agent.The authors thank the Basque Country Government (consolidated research groups funding and Programa predoctoral de formacion de personal investigador no doctor), Befesa Steel R&D company for financial assistance for this work and Biotermiak Zeberio 2009 S.L. for the supply of fresh biomass

Detection of protein interactions based on GFP fragment complementation by fluorescence microscopy and spectrofluorometry

[Abstract] We have developed a set of simple modifications of the green fluorescent protein (GFP)fragment reassembly assay in bacteria that permits: (i)fluorescent microscopy visualization of GFP reassembly only 1-2 h after induction of protein expression, thus approximating the detection of GFP reassembly to the real-time dynamics of protein complex formation in living cells; (ii) spectrofluorometric detection of reassembled GFP fluorescent signals directly in lysates from cell suspension thereby avoiding, in many cases, the need for tag-affinity isolation of protein complexes; and (iii) comparative quantification of signal intensity in numerous cell-sample lysates using a Bio-Rad IQ5 spectrofluorometric detection system (Bio-Rad Laboratories, Madrid, Spain). Collectively, the results demonstrate that the combination of microscopic and spectrofluorometric detection provides a time-saving and sensitive alternative to existing methods of fluorescence complementation analysis.Ministerio de Educación y Ciencia; SAF2004-01462Galicia. Consellería de Innovación, Industria e Comercio; PGIDIT04BTF161001P

Asteroseismic signatures of helium gradients in late F-type stars

Element diffusion is expected to occur in all kinds of stars : according to the relative effect of gravitation and radiative acceleration, they can fall or be pushed up in the atmospheres. Helium sinks in all cases, thereby creating a gradient at the bottom of the convective zones. This can have important consequences for the sound velocity, as has been proved in the sun with helioseismology. We investigate signatures of helium diffusion in late F-type stars by asteroseismology. Stellar models were computed with different physical inputs (with or without element diffusion) and iterated in order to fit close-by evolutionary tracks for each mass. The theoretical oscillation frequencies were computed and compared for pairs of models along the tracks. Various asteroseismic tests (large separations, small separations, second differences) were used and studied for the comparisons. The results show that element diffusion leads to changes in the frequencies for masses larger than 1.2 Msun. In particular the helium gradient below the convective zone should be detectable through the second differences.Comment: 8 pages, 11 figures, 2 tables Accepted for publication in Astronomy and Astrophysics. The official date of acceptance is 03/05/200

Uncertainty-Aware Annotation Protocol to Evaluate Deformable Registration Algorithms

Landmark correspondences are a widely used type of gold standard in image registration. However, the manual placement of corresponding points is subject to high inter-user variability in the chosen annotated locations and in the interpretation of visual ambiguities. In this paper, we introduce a principled strategy for the construction of a gold standard in deformable registration. Our framework: (i) iteratively suggests the most informative location to annotate next, taking into account its redundancy with previous annotations; (ii) extends traditional pointwise annotations by accounting for the spatial uncertainty of each annotation, which can either be directly specified by the user, or aggregated from pointwise annotations from multiple experts; and (iii) naturally provides a new strategy for the evaluation of deformable registration algorithms. Our approach is validated on four different registration tasks. The experimental results show the efficacy of suggesting annotations according to their informativeness, and an improved capacity to assess the quality of the outputs of registration algorithms. In addition, our approach yields, from sparse annotations only, a dense visualization of the errors made by a registration method. The source code of our approach supporting both 2D and 3D data is publicly available at https://github.com/LoicPeter/evaluation-deformable-registration

Identification of Candidate Genes Potentially Relevant to Chamber-Specific Remodeling in Postnatal Ventricular Myocardium

Molecular predisposition of postnatal ventricular myocardium to chamber-dependent (concentric or eccentric) remodeling remains largely elusive. To this end, we compared gene expression in the left (LV) versus right ventricle (RV) in newborn piglets, using a differential display reverse transcription-PCR (DDRT-PCR) technique. Out of more than 5600 DDRT-PCR bands, a total of 153 bands were identified as being differentially displayed. Of these, 96 bands were enriched in the LV, whereas the remaining 57 bands were predominant in the RV. The transcripts, displaying over twofold LV-RV expression differences, were sequenced and identified by BLAST comparison to known mRNA sequences. Among the genes, whose expression was not previously recognized as being chamber-dependent, we identified a small cohort of key regulators of muscle cell growth/proliferation (MAP3K7IP2, MSTN, PHB2, APOBEC3F) and gene expression (PTPLAD1, JMJD1C, CEP290), which may be relevant to the chamber-dependent predisposition of ventricular myocardium to respond differentially to pressure (LV) and volume (RV) overloads after birth. In addition, our data demonstrate chamber-dependent alterations in expression of as yet uncharacterized novel genes, which may also be suitable candidates for association studies in animal models of LV/RV hypertrophy

A new type of Na+-driven ATP synthase membrane rotor with a two-carboxylate ion-coupling motif

Abstract: The anaerobic bacterium Fusobacterium nucleatum uses glutamate decarboxylation to generate a transmembrane gradient of Na+. Here, we demonstrate that this ion-motive force is directly coupled to ATP synthesis, via an F1Fo-ATP synthase with a novel Na+ recognition motif, shared by other human pathogens. Molecular modeling and free-energy simulations of the rotary element of the enzyme, the c-ring, indicate Na+ specificity in physiological settings. Consistently, activity measurements showed Na+ stimulation of the enzyme, either membrane-embedded or isolated, and ATP synthesis was sensitive to the Na+ ionophore monensin. Furthermore, Na+ has a protective effect against inhibitors targeting the ion-binding sites, both in the complete ATP synthase and the isolated c-ring. Definitive evidence of Na+ coupling is provided by two identical crystal structures of the c11 ring, solved by X-ray crystallography at 2.2 and 2.6 Å resolution, at pH 5.3 and 8.7, respectively. Na+ ions occupy all binding sites, each coordinated by four amino acids and a water molecule. Intriguingly, two carboxylates instead of one mediate ion binding. Simulations and experiments demonstrate that this motif implies that a proton is concurrently bound to all sites, although Na+ alone drives the rotary mechanism. The structure thus reveals a new mode of ion coupling in ATP synthases and provides a basis for drug-design efforts against this opportunistic pathogen. Author Summary: Essential cellular processes such as biosynthesis, transport, and motility are sustained by the energy released in the hydrolysis of ATP, the universal energy carrier in living cells. Most ATP in the cell is produced by a membrane-bound enzyme, the ATP synthase, through a rotary mechanism that is coupled to the translocation of ions across the membrane. The majority of ATP synthases are energized by transmembrane electrochemical gradients of protons (proton-motive force), but a number of organisms, including some important human pathogens, use gradients of sodium ions instead (sodium-motive force). The ion specificity of ATP synthases is determined by a membrane-embedded sub-complex, the c-ring, which is the smallest known biological rotor. The functional mechanism of the rotor ring and its variations among different organisms are of wide interest, because of this enzyme's impact on metabolism and disease, and because of its potential for nanotechnology applications. Here, we characterize a previously unrecognized type of Na+-driven ATP synthase from the opportunistic human pathogen Fusobacterium nucleatum, which is implicated in periodontal diseases. We analyzed this ATP synthase and its rotor ring through a multi-disciplinary approach, combining cell-growth and biochemical assays, X-ray crystallography and computer-simulation methods. Two crystal structures of the membrane rotor were solved, at low and high pH, revealing an atypical ion-recognition motif mediated by two carboxylate side-chains. This motif is shared by other human pathogens, such as Mycobacterium tuberculosis or Streptococcus pneumonia, whose ATP synthases are targets of novel antibiotic drugs. The implications of this ion-recognition mode on the mechanism of the ATP synthase and the cellular bioenergetics of F. nucleatum were thus examined. Our results provide the basis for future pharmacological efforts against this important pathogen

On the linear fractional self-attracting diffusion

In this paper, we introduce the linear fractional self-attracting diffusion driven by a fractional Brownian motion with Hurst index 1/2<H<1, which is analogous to the linear self-attracting diffusion. For 1-dimensional process we study its convergence and the corresponding weighted local time. For 2-dimensional process, as a related problem, we show that the renormalized self-intersection local time exists in L^2 if $\frac12<H<\frac3{4}$.Comment: 14 Pages. To appear in Journal of Theoretical Probabilit