Dynamic modulation of photonic crystal nanocavities using gigahertz acoustic phonons

Photonic crystal membranes (PCM) provide a versatile planar platform for on-chip implementations of photonic quantum circuits. One prominent quantum element is a coupled system consisting of a nanocavity and a single quantum dot (QD) which forms a fundamental building block for elaborate quantum information networks and a cavity quantum electrodynamic (cQED) system controlled by single photons. So far no fast tuning mechanism is available to achieve control within the system coherence time. Here we demonstrate dynamic tuning by monochromatic coherent acoustic phonons formed by a surface acoustic wave (SAW) with frequencies exceeding 1.7 gigahertz, one order of magnitude faster than alternative approaches. We resolve a periodic modulation of the optical mode exceeding eight times its linewidth, preserving both the spatial mode profile and a high quality factor. Since PCMs confine photonic and phononic excitations, coupling optical to acoustic frequencies, our technique opens ways towards coherent acoustic control of optomechanical crystals.Comment: 11 pages 4 figure

Simulation of Heavily Irradiated Silicon Pixel Sensors and Comparison with Test Beam Measurements

Charge collection measurements performed on heavily irradiated p-spray DOFZ pixel sensors with a grazing angle hadron beam provide a sensitive determination of the electric field within the detectors. The data are compared with a complete charge transport simulation of the sensor which includes signal trapping and charge induction effects. A linearly varying electric field based upon the standard picture of a constant type-inverted effective doping density is inconsistent with the data. A two-trap double junction model implemented in the ISE TCAD software can be tuned to produce a doubly-peaked electric field which describes the data reasonably well. The modeled field differs somewhat from previous determinations based upon the transient current technique. The model can also account for the level of charge trapping observed in the data.Comment: 8 pages, 11 figures. Talk presented at the 2004 IEEE Nuclear Science Symposium, October 18-21, Rome, Italy. Submitted to IEEE Transactions on Nuclear Scienc

Adaptation of Hansenula polymorpha to methanol: a transcriptome analysis

Background: Methylotrophic yeast species (e.g. Hansenula polymorpha, Pichia pastoris) can grow on methanol as sole source of carbon and energy. These organisms are important cell factories for the production of recombinant proteins, but are also used in fundamental research as model organisms to study peroxisome biology. During exponential growth on glucose, cells of H. polymorpha typically contain a single, small peroxisome that is redundant for growth while on methanol multiple, enlarged peroxisomes are present. These organelles are crucial to support growth on methanol, as they contain key enzymes of methanol metabolism. In this study, changes in the transcriptional profiles during adaptation of H. polymorpha cells from glucose- to methanol-containing media were investigated using DNA-microarray analyses. Results: Two hours after the shift of cells from glucose to methanol nearly 20% (1184 genes) of the approximately 6000 annotated H. polymorpha genes were significantly upregulated with at least a two-fold differential expression. Highest upregulation (> 300-fold) was observed for the genes encoding the transcription factor Mpp1 and formate dehydrogenase, an enzyme of the methanol dissimilation pathway. Upregulated genes also included genes encoding other enzymes of methanol metabolism as well as of peroxisomal b-oxidation. A moderate increase in transcriptional levels (up to 4-fold) was observed for several PEX genes, which are involved in peroxisome biogenesis. Only PEX11 and PEX32 were higher upregulated. In addition, an increase was observed in expression of the several ATG genes, which encode proteins involved in autophagy and autophagy processes. The strongest upregulation was observed for ATG8 and ATG11. Approximately 20% (1246 genes) of the genes were downregulated. These included glycolytic genes as well as genes involved in transcription and translation. Conclusion: Transcriptional profiling of H. polymorpha cells shifted from glucose to methanol showed the expected downregulation of glycolytic genes together with upregulation of the methanol utilisation pathway. This serves as a confirmation and validation of the array data obtained. Consistent with this, also various PEX genes were upregulated. The strong upregulation of ATG genes is possibly due to induction of autophagy processes related to remodeling of the cell architecture required to support growth on methanol. These processes may also be responsible for the enhanced peroxisomal b oxidation, as autophagy leads to recycling of membrane lipids. The prominent downregulation of transcription and translation may be explained by the reduced growth rate on methanol (td glucose 1 h vs td methanol 4.5 h).Applied Science

A comparison of three methods for estimating call densities of migrating bowhead whales using passive acoustic monitoring

TAM thanks partial support by Centro de Estatistica e Aplicações, Universidade de Lisboa (funded by FCT—Fundação para a Ciência e a Tecnologia, Portugal, through the project UID/MAT/00006/2013).Various methods for estimating animal density from visual data, including distance sampling (DS) and spatially explicit capture-recapture (SECR), have recently been adapted for estimating call density using passive acoustic monitoring (PAM) data, e.g., recordings of animal calls. Here we summarize three methods available for passive acoustic density estimation: plot sampling, DS, and SECR. The first two require distances from the sensors to calling animals (which are obtained by triangulating calls matched among sensors), but SECR only requires matching (not localizing) calls among sensors. We compare via simulation what biases can arise when assumptions underlying these methods are violated. We use insights gleaned from the simulation to compare the performance of the methods when applied to a case study: bowhead whale call data collected from arrays of directional acoustic sensors at five sites in the Beaufort Sea during the fall migration 2007–2014. Call detections were manually extracted from the recordings by human observers simultaneously scanning spectrograms of recordings from a given site. The large discrepancies between estimates derived using SECR and the other two methods were likely caused primarily by the manual detection procedure leading to non-independent detections among sensors, while errors in estimated distances between detected calls and sensors also contributed to the observed patterns. Our study is among the first to provide a direct comparison of the three methods applied to PAM data and highlights the importance that all assumptions of an analysis method need to be met for correct inference.Publisher PDFPeer reviewe

Altered miRNA processing disrupts brown/white adipocyte determination and associates with lipodystrophy

miRNAs are important regulators of biological processes in many tissues, including the differentiation and function of brown and white adipocytes. the endoribonuclease dicer is a major component of the miRNA-processing pathway, and in adipose tissue, levels of dicer have been shown to decrease with age, increase with caloric restriction, and influence stress resistance. Here, we demonstrated that mice with a fat-specific KO of dicer develop a form of lipodystrophy that is characterized by loss of intra-abdominal and subcutaneous white fat, severe insulin resistance, and enlargement and whitening of interscapular brown fat. Additionally, KO of dicer in cultured brown preadipocytes promoted a white adipocyte-like phenotype and reduced expression of several miRNAs. Brown preadipocyte whitening was partially reversed by expression of miR-365, a miRNA known to promote brown fat differentiation; however, introduction of other miRNAs, including miR-346 and miR-362, also contributed to reversal of the loss of the dicer phenotype. Interestingly, fat samples from patients with HIV-related lipodystrophy exhibited a substantial downregulation of dicer mRNA expression. Together, these findings indicate the importance of miRNA processing in white and brown adipose tissue determination and provide a potential link between this process and HIV-related lipodystrophy.NIHEllison FoundationJoslin Diabetes and Endocrinology Research Center coresMary K. Iacocca ProfessorshipAcademy of FinlandSigrid Juselius FoundationFundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Harvard Univ, Sch Med, Joslin Diabet Ctr, Sect Integrat Physiol & Metab, Boston, MA 02115 USAUniversidade Federal de São Paulo, Dept Biophys, São Paulo, BrazilUniversidade Federal de São Paulo, Program Mol Biol, São Paulo, BrazilAstraZeneca R&D, Cardiovasc & Metab Dis iMed, Molndal, SwedenUniv Helsinki, Dept Med, Helsinki, FinlandMinerva Fdn, Inst Med Res, Helsinki, FinlandUniv Massachusetts, Sch Med, Program Mol Med, Worcester, MA USAMassachusetts Gen Hosp, Program Nutr Metab, Boston, MA 02114 USAHarvard Univ, Sch Med, Boston, MA USAUniversidade Federal de São Paulo, Dept Biophys, São Paulo, BrazilUniversidade Federal de São Paulo, Program Mol Biol, São Paulo, BrazilNIH: DK082659NIH: DK033201NIH: AI060354NIH: DK040561NIH: U24-DK093000Joslin Diabetes and Endocrinology Research Center cores: DK036836FAPESP: 2010/52557-0Web of Scienc

An Aesthetic Factor Priority List of the Female Breast in Scandinavian Subjects

Background: There is little consensus about the relative determinative value of each individual factor in female breast aesthetics. When performing breast surgery with an aesthetic goal, certain factors will be more important than others. The purpose of this study was to make an aesthetic factor rank list to determine the relative contributions to overall breast aesthetics. Method: Volunteers were scanned using the 3-dimensional Vectra system. Ten Scandinavian plastic surgeons rated 37 subjects, using a validated scoring system with 49 scoring items. The correlation between specific aesthetic factors and overall breast aesthetic scores of the subjects were calculated using Pearson's r, Spearman's rho, and Kendall's tau. Results: A very strong correlation was found between overall breast aesthetic score and lower pole shape (0.876, P <0.0001). This was also true for upper pole shape (0.826, P <0.0001) and breast height (0.821, P <0.0001). A strong correlation was found between overall breast aesthetic score and nipple position (0.733, P <0.0001), breast size (0.644, P <0.0001), and breast width (0.632, P <0.0001). Factors that were only moderately correlated with aesthetic score were intermammary distance (0.496, P = 0.002), nipple size and projection (0.588, P <0.0001), areolar diameter (0.484, P <0.0001), and areolar shape (0.403, P <0.0001). Perceived symmetry was a weak factor (0.363, P = 0.027). Conclusions: Aesthetic factors of the female breast can be ranked in a priority list. Shape of the lower pole and upper pole and breast height are primary factors of female breast aesthetics. These should be prioritized in any aesthetic breast surgery. Vertical dimensional factors seem to be more determinative than horizontal factors.Peer reviewe

Generic boundaries in subtribe Saussureinae (Compositae: Cardueae): Insights from Hyb-Seq data

The subtribe Saussureinae is a highly speciose group with more than 600 species distributed in the Northern Hemisphere and is particularly species-rich at the high mountains of central and eastern Asia. Saussurea and Jurinea are the two main genera described within the subtribe. However, up to 15 satellite genera are recognized in some recent taxonomic treatments with an analytical viewpoint. For the first time, we carried out a complete sampling to clarify generic boundaries based on a well-resolved phylogeny of Saussureinae. We employed a Hyb-Seq technique that targets 1061 nuclear conserved ortholog loci designed for Compositae. After a filtering of potential paralogs, 588 loci were retained to infer phylogenetic trees under concatenation and coalescence approaches. High branch support resolution was recovered at the generic level, but a non-monophyletic pattern was detected for most of the genera as they are currently circumscribed. Accordingly, we propose a new generic delimitation based on the three main clades recovered in the backbone tree, which are also in agreement with morphological evidence: Dolomiaea, Saussurea, and Jurinea. Following this classification into three genera, 18 new combinations are proposed. This new genus delineation will be used as a basis for future evolutionary studies in the Saussureinae.Financial support from the Ministerio de Ciencia e Innovación (Project CGL2015-66703-P MINECO/FEDER, UE and Ph.D. grant to Sonia Herrando-Moraira) and the Catalan government (“Ajuts a grups consolidats” 2017-SGR1116) is also greatly acknowledged. This study has been performed under the Ph.D. program “Plant Biology and Biotechnology” of the Autonomous University of Barcelona (UAB)INTRODUCTION MATERIALS AND METHODS RESULTS DISCUSSION TAXONOMIC IMPLICATIONS NOTE ADDED IN PROOF AUTHOR CONTRIBUTIONS ACKNOWLEDGMENT

Occurrence, function and evolutionary origins of ‘2A-like’ sequences in virus genomes

2A is an oligopeptide sequence mediating a ribosome ‘skipping’ effect, producing an apparent ‘cleavage’ of polyproteins. First identified and characterized in picornaviruses, ‘2A-like’ sequences are found in other mammalian viruses and a wide range of insect viruses. Databases were analysed using a motif conserved amongst 2A/2A-like sequences. The newly identified 2A-like sequences (30 aa) were inserted into a reporter polyprotein to determine their cleavage activity. Our analyses showed that these sequences fall into two categories. The majority mediated very high (complete) cleavage to separate proteins and a few sequences mediated cleavage with lower efficiency, generating appreciable levels of the uncleaved form. Phylogenetic analyses of 2A-like sequences and RNA-dependent RNA polymerases (RdRps) indicated multiple, independent, acquisitions of these sequences at different stages during virus evolution. Within a virus family, 2A sequences are (probably) homologous, but diverge due to other evolutionary pressures. Amongst different families, however, 2A/2A-like sequences appear to be homoplasic

Loss of the lupus autoantigen Ro52/Trim21 induces tissue inflammation and systemic autoimmunity by disregulating the IL-23-Th17 pathway.

Ro52/Trim21 is targeted as an autoantigen in systemic lupus erythematosus and Sjögren\u27s syndrome. Polymorphisms in the Ro52 gene have been linked to these autoimmune conditions, but the molecular mechanism by which Ro52 may promote development of systemic autoimmune diseases has not been explored. To address this issue, we generated Ro52-null mice (Ro52(-/-)), which appear phenotypically normal if left unmanipulated. However, Ro52(-/-) mice develop severe dermatitis extending from the site of tissue injury induced by ear tags. The affected mice further develop several signs of systemic lupus with hypergammaglobulinemia, autoantibodies to DNA, proteinuria, and kidney pathology. Ro52, which was recently identified as an E3 ligase, mediates ubiquitination of several members of the interferon regulatory factor (IRF) family, and the Ro52-deficient mice have an enhanced production of proinflammatory cytokines that are regulated by the IRF transcription factors, including cytokines involved in the Th17 pathway (interleukin [IL] 6, IL-12/IL-23p40, and IL-17). Loss of IL-23/IL-17 by genetic deletion of IL-23/p19 in the Ro52(-/-) mice conferred protection from skin disease and systemic autoimmunity. These data reveal that the lupus-associated Ro52 protein is an important negative regulator of proinflammatory cytokine production, and they provide a mechanism by which a defective Ro52 function can lead to tissue inflammation and systemic autoimmunity through the IL-23-Th17 pathway