Regularization independent of the noise level: an analysis of quasi-optimality

The quasi-optimality criterion chooses the regularization parameter in inverse problems without taking into account the noise level. This rule works remarkably well in practice, although Bakushinskii has shown that there are always counterexamples with very poor performance. We propose an average case analysis of quasi-optimality for spectral cut-off estimators and we prove that the quasi-optimality criterion determines estimators which are rate-optimal {\em on average}. Its practical performance is illustrated with a calibration problem from mathematical finance.Comment: 18 pages, 3 figure

Correlations between resonances in a statistical scattering model

The distortion of the regular motion in a quantum system by its coupling to the continuum of decay channels is investigated. The regular motion is described by means of a Poissonian ensemble. We focus on the case of only few channels K < 10. The coupling to the continuum induces two main effects, due to which the distorted system differs from a chaotic system (described by a Gaussian ensemble): 1. The width distribution for large coupling becomes broader than the corresponding Χ2K distribution in the GOE case. 2. Due to the coupling to the continuum, correlations are induced not only between the positions of the resonances but also between positions and widths. These correlations remain even in the strong coupling limit. In order to explain these results, an asymptotic expression for the width distribution is derived for the one channel case. It relates the width of a trapped resonance state to the distance between its two neighboring levels

A distinct structural region of the prokaryotic ubiquitin-like protein (Pup) is recognized by the N-terminal domain of the proteasomal ATPase Mpa

AbstractThe mycobacterial ubiquitin-like protein Pup is coupled to proteins, thereby rendering them as substrates for proteasome-mediated degradation. The Pup-tagged proteins are recruited by the proteasomal ATPase Mpa (also called ARC). Using a combination of biochemical and NMR methods, we characterize the structural determinants of Pup and its interaction with Mpa, demonstrating that Pup adopts a range of extended conformations with a short helical stretch in its C-terminal portion. We show that the N-terminal coiled-coil domain of Mpa makes extensive contacts along the central region of Pup leaving its N-terminus unconstrained and available for other functional interactions.Structured summaryMINT-7262427: pup (uniprotkb:B6DAC1) binds (MI:0407) to mpa (uniprotkb:Q0G9Y7) by pull down (MI:0096) MINT-7262440: mpa (uniprotkb:Q0G9Y7) and pup (uniprotkb:B6DAC1) bind (MI:0407) by isothermal titration calorimetry (MI:0065

Graphene: Piecing it together

Graphene has a multitude of striking properties that make it an exceedingly attractive material for various applications, many of which will emerge over the next decade. However, one of the most promising applications lie in exploiting its peculiar electronic properties which are governed by its electrons obeying a linear dispersion relation. This leads to the observation of half integer quantum hall effect and the absence of localization. The latter is attractive for graphene-based field effect transistors. However, if graphene is to be the material for future electronics, then significant hurdles need to be surmounted, namely, it needs to be mass produced in an economically viable manner and be of high crystalline quality with no or virtually no defects or grains boundaries. Moreover, it will need to be processable with atomic precision. Hence, the future of graphene as a material for electronic based devices will depend heavily on our ability to piece graphene together as a single crystal and define its edges with atomic precision. In this progress report, the properties of graphene that make it so attractive as a material for electronics is introduced to the reader. The focus then centers on current synthesis strategies for graphene and their weaknesses in terms of electronics applications are highlighted.Comment: Advanced Materials (2011

Epigenetic regulation of corneal epithelial differentiation by TET2

Epigenetic DNA modification by 5-hydroxymethylcytosine (5hmC), generated by the Ten-eleven translocation (TET) dioxygenases, regulates diverse biological functions in many organ tissues, including the mammalian eye. For example, 5hmC has been shown to be involved in epigenetic regulation of retinal gene expression. However, a functional role of 5hmC in corneal differentiation has not been investigated to date. Here, we examined 5hmC and TET function in the human cornea. We found 5hmC highly expressed in MUC16-positive terminally differentiated cells that also co-expressed the 5hmC-generating enzyme TET2. TET2 knockdown (KD) in cultured corneal epithelial cells led to significant reductions of 5hmC peak distributions and resulted in transcriptional repression of molecular pathways involved in corneal differentiation, as evidenced by downregulation of MUC4, MUC16, and Keratin 12. Additionally, integrated TET2 KD RNA-seq and genome-wide Reduced Representation Hydroxymethylation Profiling revealed novel epigenetically regulated genes expressed by terminally differentiated cells, including KRT78, MYEOV, and MAL. In aggregate, our findings reveal a novel function of TET2 in the epigenetic regulation of corneal epithelial gene expression and identify novel TET2-controlled genes expressed in differentiated corneal epithelial cells. These results point to potential roles for TET2 induction strategies to enhance treatment of corneal diseases associated with abnormal epithelial maturation

Consecutive dosing of UVB irradiation induces loss of ABCB5 expression and activation of EMT and fibrosis proteins in limbal epithelial cells similar to pterygium epithelium

Pterygium pathogenesis is often attributed to a population of altered limbal stem cells, which initiate corneal invasion and drive the hyperproliferation and fibrosis associated with the disease. These cells are thought to undergo epithelial to mesenchymal transition (EMT) and to contribute to subepithelial stromal fibrosis. In this study, the presence of the novel limbal stem cell marker ABCB5 in clusters of basal epithelial pterygium cells co-expressing with P63α and P40 is reported. ABCB5-positive pterygium cells also express EMT-associated fibrosis markers including vimentin and α-SMA while their β-catenin expression is reduced. By using a novel in vitro model of two-dose UV-induced EMT activation on limbal epithelial cells, we could observe the dysregulation of EMT-related proteins including an increase of vimentin and α-SMA as well as downregulation of β-catenin in epithelial cells correlating to downregulation of ABCB5. The sequential irradiation of limbal fibroblasts also induced an increase in vimentin and α-SMA. Taken together, these data demonstrate for the first time the expression of ABCB5 in pterygium stem cell activity and EMT-related events while the involvement of limbal stem cells in pterygium pathogenesis is exhibited via sequential irradiation of limbal epithelial cells. The later in vitro approach can be used to further study the involvement of limbal epithelium UV-induced EMT in pterygium pathogenesis and help identify novel treatments against pterygium growth and recurrence

Detection of mobile genetic elements associated with antibiotic resistance in Salmonella enterica using a newly developed web tool: MobileElementFinder

Objectives - Antimicrobial resistance (AMR) in clinically relevant bacteria is a growing threat to public health globally. In these bacteria, antimicrobial resistance genes are often associated with mobile genetic elements (MGEs), which promote their mobility, enabling them to rapidly spread throughout a bacterial community. Methods - The tool MobileElementFinder was developed to enable rapid detection of MGEs and their genetic context in assembled sequence data. MGEs are detected based on sequence similarity to a database of 4452 known elements augmented with annotation of resistance genes, virulence factors and detection of plasmids. Results - MobileElementFinder was applied to analyse the mobilome of 1725 sequenced Salmonella enterica isolates of animal origin from Denmark, Germany and the USA. We found that the MGEs were seemingly conserved according to multilocus ST and not restricted to either the host or the country of origin. Moreover, we identified putative translocatable units for specific aminoglycoside, sulphonamide and tetracycline genes. Several putative composite transposons were predicted that could mobilize, among others, AMR, metal resistance and phosphodiesterase genes associated with macrophage survivability. This is, to our knowledge, the first time the phosphodiesterase-like pdeL has been found to be potentially mobilized into S. enterica. Conclusions - MobileElementFinder is a powerful tool to study the epidemiology of MGEs in a large number of genome sequences and to determine the potential for genomic plasticity of bacteria. This web service provides a convenient method of detecting MGEs in assembled sequence data. MobileElementFinder can be accessed at https://cge.cbs.dtu.dk/services/MobileElementFinder/

Drug regulatory-compliant validation of a qPCR assay for bioanalysis studies of a cell therapy product with a special focus on matrix interferences in a wide range of organ tissues

Quantitative polymerase chain reaction (qPCR) has emerged as an important bioanalytical method for assessing the pharmacokinetics of human-cell-based medicinal products after xenotransplantation into immunodeficient mice. A particular challenge in bioanalytical qPCR studies is that the different tissues of the host organism can affect amplification efficiency and amplicon detection to varying degrees, and ignoring these matrix effects can easily cause a significant underestimation of the true number of target cells in a sample. Here, we describe the development and drug regulatory-compliant validation of a TaqMan qPCR assay for the quantification of mesenchymal stromal cells in the range of 125 to 20,000 cells/200 L lysate via the amplification of a human-specific, highly repetitive α-satellite DNA sequence of the chromosome 17 centromere region HSSATA17. An assessment of matrix effects in 14 different mouse tissues and blood revealed a wide range of spike recovery rates across the different tissue types, from 11 to 174%. Based on these observations, we propose performing systematic spike-and-recovery experiments during assay validation and correcting for the effects of the different tissue matrices on cell quantification in subsequent bioanalytical studies by multiplying the back-calculated cell number by tissue-specific factors derived from the inverse of the validated percent recovery rate

ABCB5+ mesenchymal stromal cells facilitate complete and durable wound closure in recessive dystrophic epidermolysis bullosa

Background and aims: Recessive dystrophic epidermolysis bullosa (RDEB) is a hereditary, rare, devastating and life-threatening skin fragility disorder with a high unmet medical need. In a recent international, single-arm clinical trial, treatment of 16 patients (aged 6–36 years) with three intravenous infusions of 2 × 106 immunomodulatory ABCB5+ dermal mesenchymal stromal cells (MSCs)/kg on days 0, 17 and 35 reduced disease activity, itch and pain. A post-hoc analysis was undertaken to assess the potential effects of treatment with ABCB5+ MSCs on the overall skin wound healing in patients suffering from RDEB. Methods: Documentary photographs of the affected body regions taken on days 0, 17, 35 and at 12 weeks were evaluated regarding proportion, temporal course and durability of wound closure as well as development of new wounds. Results: Of 168 baseline wounds in 14 patients, 109 (64.9%) wounds had closed at week 12, of which 63.3% (69 wounds) had closed already by day 35 or day 17. Conversely, 74.2% of the baseline wounds that had closed by day 17 or day 35 remained closed until week 12. First-closure ratio within 12 weeks was 75.6%. The median rate of newly developing wounds decreased significantly (P = 0.001) by 79.3%. Conclusions: Comparison of the findings with published data from placebo arms and vehicle-treated wounds in controlled clinical trials suggests potential capability of ABCB5+ MSCs to facilitate wound closure, prolongate wound recurrence and decelerate formation of new wounds in RDEB. Beyond suggesting therapeutic efficacy for ABCB5+ MSCs, the analysis might stimulate researchers who develop therapies for RDEB and other skin fragility disorders to not only assess closure of preselected target wounds but pay attention to the patients’ dynamic and diverse overall wound presentation as well as to the durability of achieved wound closure and the development of new wounds. Trial registration: Clinicaltrials.gov NCT03529877; EudraCT 2018-001009-98

The impact of oceanic near-inertial waves on climate

Author Posting. © American Meteorological Society, 2013. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Climate 26 (2013): 2833–2844, doi:10.1175/JCLI-D-12-00181.1.The Community Climate System Model, version 4 (CCSM4) is used to assess the climate impact of wind-generated near-inertial waves (NIWs). Even with high-frequency coupling, CCSM4 underestimates the strength of NIWs, so that a parameterization for NIWs is developed and included into CCSM4. Numerous assumptions enter this parameterization, the core of which is that the NIW velocity signal is detected during the model integration, and amplified in the shear computation of the ocean surface boundary layer module. It is found that NIWs deepen the ocean mixed layer by up to 30%, but they contribute little to the ventilation and mixing of the ocean below the thermocline. However, the deepening of the tropical mixed layer by NIWs leads to a change in tropical sea surface temperature and precipitation. Atmospheric teleconnections then change the global sea level pressure fields so that the midlatitude westerlies become weaker. Unfortunately, the magnitude of the real air-sea flux of NIW energy is poorly constrained by observations; this makes the quantitative assessment of their climate impact rather uncertain. Thus, a major result of the present study is that because of its importance for global climate the uncertainty in the observed tropical NIW energy has to be reduced.This research was funded as part of the Climate Process Team on internal wave-driven mixing with NSF Grant Nr E0968771 at NCAR.2013-11-0