Core and penumbra estimation using deep learning-based AIF in association with clinical measures in computed tomography perfusion

Objectives: To investigate whether utilizing a convolutional neural network (CNN)-based arterial input function (AIF) improves the volumetric estimation of core and penumbra in association with clinical measures in stroke patients. Methods: The study included 160 acute ischemic stroke patients (male = 87, female = 73, median age = 73 years) with approval from the institutional review board. The patients had undergone CTP imaging, NIHSS and ASPECTS grading. convolutional neural network (CNN) model was trained to fit a raw AIF curve to a gamma variate function. CNN AIF was utilized to estimate the core and penumbra volumes which were further validated with clinical scores. Results: Penumbra estimated by CNN AIF correlated positively with the NIHSS score (r = 0.69; p  20) and lower ASPECT score ( 10 s, Tmax > 10 s volumes were statistically significantly higher (p < .05). Conclusions: With inclusion of the CNN AIF in perfusion imaging pipeline, penumbra and core estimations are more reliable as they correlate with scores representing neurological deficits in stroke. Critical relevance statement: With CNN AIF perfusion imaging pipeline, penumbra and core estimations are more reliable as they correlate with scores representing neurological deficits in stroke

Star Formation Rate Indicators in Wide-Field Infrared Survey Preliminary Release

With the goal of investigating the degree to which theMIR luminosity in theWidefield Infrared Survey Explorer (WISE) traces the SFR, we analyze 3.4, 4.6, 12 and 22 {\mu}m data in a sample of {\guillemotright} 140,000 star-forming galaxies or star-forming regions covering a wide range in metallicity 7.66 < 12 + log(O/H) < 9.46, with redshift z < 0.4. These star-forming galaxies or star-forming regions are selected by matching the WISE Preliminary Release Catalog with the star-forming galaxy Catalog in SDSS DR8 provided by JHU/MPA 1.We study the relationship between the luminosity at 3.4, 4.6, 12 and 22 {\mu}m from WISE and H\alpha luminosity in SDSS DR8. From these comparisons, we derive reference SFR indicators for use in our analysis. Linear correlations between SFR and the 3.4, 4.6, 12 and 22 {\mu}m luminosity are found, and calibrations of SFRs based on L(3.4), L(4.6), L(12) and L(22) are proposed. The calibrations hold for galaxies with verified spectral observations. The dispersion in the relation between 3.4, 4.6, 12 and 22 {\mu}m luminosity and SFR relates to the galaxy's properties, such as 4000 {\deg}A break and galaxy color.Comment: 10 pages, 3 figure

The Evolution of Bat Vestibular Systems in the Face of Potential Antagonistic Selection Pressures for Flight and Echolocation

PMCID: PMC3634842This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited

Gene expression and splicing alterations analyzed by high throughput RNA sequencing of chronic lymphocytic leukemia specimens.

BackgroundTo determine differentially expressed and spliced RNA transcripts in chronic lymphocytic leukemia specimens a high throughput RNA-sequencing (HTS RNA-seq) analysis was performed.MethodsTen CLL specimens and five normal peripheral blood CD19+ B cells were analyzed by HTS RNA-seq. The library preparation was performed with Illumina TrueSeq RNA kit and analyzed by Illumina HiSeq 2000 sequencing system.ResultsAn average of 48.5 million reads for B cells, and 50.6 million reads for CLL specimens were obtained with 10396 and 10448 assembled transcripts for normal B cells and primary CLL specimens respectively. With the Cuffdiff analysis, 2091 differentially expressed genes (DEG) between B cells and CLL specimens based on FPKM (fragments per kilobase of transcript per million reads and false discovery rate, FDR q &lt; 0.05, fold change &gt;2) were identified. Expression of selected DEGs (n = 32) with up regulated and down regulated expression in CLL from RNA-seq data were also analyzed by qRT-PCR in a test cohort of CLL specimens. Even though there was a variation in fold expression of DEG genes between RNA-seq and qRT-PCR; more than 90 % of analyzed genes were validated by qRT-PCR analysis. Analysis of RNA-seq data for splicing alterations in CLL and B cells was performed by Multivariate Analysis of Transcript Splicing (MATS analysis). Skipped exon was the most frequent splicing alteration in CLL specimens with 128 significant events (P-value &lt;0.05, minimum inclusion level difference &gt;0.1).ConclusionThe RNA-seq analysis of CLL specimens identifies novel DEG and alternatively spliced genes that are potential prognostic markers and therapeutic targets. High level of validation by qRT-PCR for a number of DEG genes supports the accuracy of this analysis. Global comparison of transcriptomes of B cells, IGVH non-mutated CLL (U-CLL) and mutated CLL specimens (M-CLL) with multidimensional scaling analysis was able to segregate CLL and B cell transcriptomes but the M-CLL and U-CLL transcriptomes were indistinguishable. The analysis of HTS RNA-seq data to identify alternative splicing events and other genetic abnormalities specific to CLL is an added advantage of RNA-seq that is not feasible with other genome wide analysis

Small Polarons in Transition Metal Oxides

The formation of polarons is a pervasive phenomenon in transition metal oxide compounds, with a strong impact on the physical properties and functionalities of the hosting materials. In its original formulation the polaron problem considers a single charge carrier in a polar crystal interacting with its surrounding lattice. Depending on the spatial extension of the polaron quasiparticle, originating from the coupling between the excess charge and the phonon field, one speaks of small or large polarons. This chapter discusses the modeling of small polarons in real materials, with a particular focus on the archetypal polaron material TiO2. After an introductory part, surveying the fundamental theoretical and experimental aspects of the physics of polarons, the chapter examines how to model small polarons using first principles schemes in order to predict, understand and interpret a variety of polaron properties in bulk phases and surfaces. Following the spirit of this handbook, different types of computational procedures and prescriptions are presented with specific instructions on the setup required to model polaron effects.Comment: 36 pages, 12 figure

Experimental Demonstration of Five-photon Entanglement and Open-destination Teleportation

Universal quantum error-correction requires the ability of manipulating entanglement of five or more particles. Although entanglement of three or four particles has been experimentally demonstrated and used to obtain the extreme contradiction between quantum mechanics and local realism, the realization of five-particle entanglement remains an experimental challenge. Meanwhile, a crucial experimental challenge in multi-party quantum communication and computation is the so-called open-destination teleportation. During open-destination teleportation, an unknown quantum state of a single particle is first teleported onto a N-particle coherent superposition to perform distributed quantum information processing. At a later stage this teleported state can be readout at any of the N particles for further applications by performing a projection measurement on the remaining N-1 particles. Here, we report a proof-of-principle demonstration of five-photon entanglement and open-destination teleportation. In the experiment, we use two entangled photon pairs to generate a four-photon entangled state, which is then combined with a single photon state to achieve the experimental goals. The methods developed in our experiment would have various applications e.g. in quantum secret sharing and measurement-based quantum computation.Comment: 19 pages, 4 figures, submitted for publication on 15 October, 200

Classical conformal blocks from TBA for the elliptic Calogero-Moser system

The so-called Poghossian identities connecting the toric and spherical blocks, the AGT relation on the torus and the Nekrasov-Shatashvili formula for the elliptic Calogero-Moser Yang's (eCMY) functional are used to derive certain expressions for the classical 4-point block on the sphere. The main motivation for this line of research is the longstanding open problem of uniformization of the 4-punctured Riemann sphere, where the 4-point classical block plays a crucial role. It is found that the obtained representation for certain 4-point classical blocks implies the relation between the accessory parameter of the Fuchsian uniformization of the 4-punctured sphere and the eCMY functional. Additionally, a relation between the 4-point classical block and the $N_f=4$, ${\sf SU(2)}$ twisted superpotential is found and further used to re-derive the instanton sector of the Seiberg-Witten prepotential of the $N_f=4$, ${\sf SU(2)}$ supersymmetric gauge theory from the classical block.Comment: 25 pages, no figures, latex+JHEP3, published versio

Exploring 4D Quantum Hall Physics with a 2D Topological Charge Pump

The discovery of topological states of matter has profoundly augmented our understanding of phase transitions in physical systems. Instead of local order parameters, topological phases are described by global topological invariants and are therefore robust against perturbations. A prominent example thereof is the two-dimensional integer quantum Hall effect. It is characterized by the first Chern number which manifests in the quantized Hall response induced by an external electric field. Generalizing the quantum Hall effect to four-dimensional systems leads to the appearance of a novel non-linear Hall response that is quantized as well, but described by a 4D topological invariant - the second Chern number. Here, we report on the first observation of a bulk response with intrinsic 4D topology and the measurement of the associated second Chern number. By implementing a 2D topological charge pump with ultracold bosonic atoms in an angled optical superlattice, we realize a dynamical version of the 4D integer quantum Hall effect. Using a small atom cloud as a local probe, we fully characterize the non-linear response of the system by in-situ imaging and site-resolved band mapping. Our findings pave the way to experimentally probe higher-dimensional quantum Hall systems, where new topological phases with exotic excitations are predicted

Different genes interact with particulate matter and tobacco smoke exposure in affecting lung function decline in the general population

BACKGROUND: Oxidative stress related genes modify the effects of ambient air pollution or tobacco smoking on lung function decline. The impact of interactions might be substantial, but previous studies mostly focused on main effects of single genes. OBJECTIVES: We studied the interaction of both exposures with a broad set of oxidative-stress related candidate genes and pathways on lung function decline and contrasted interactions between exposures. METHODS: For 12679 single nucleotide polymorphisms (SNPs), change in forced expiratory volume in one second (FEV(1)), FEV(1) over forced vital capacity (FEV(1)/FVC), and mean forced expiratory flow between 25 and 75% of the FVC (FEF(25-75)) was regressed on interval exposure to particulate matter >10 microm in diameter (PM10) or packyears smoked (a), additive SNP effects (b), and interaction terms between (a) and (b) in 669 adults with GWAS data. Interaction p-values for 152 genes and 14 pathways were calculated by the adaptive rank truncation product (ARTP) method, and compared between exposures. Interaction effect sizes were contrasted for the strongest SNPs of nominally significant genes (p(interaction)>0.05). Replication was attempted for SNPs with MAF<10% in 3320 SAPALDIA participants without GWAS. RESULTS: On the SNP-level, rs2035268 in gene SNCA accelerated FEV(1)/FVC decline by 3.8% (p(interaction) = 2.5x10(-6)), and rs12190800 in PARK2 attenuated FEV1 decline by 95.1 ml p(interaction) = 9.7x10(-8)) over 11 years, while interacting with PM10. Genes and pathways nominally interacting with PM10 and packyears exposure differed substantially. Gene CRISP2 presented a significant interaction with PM10 (p(interaction) = 3.0x10(-4)) on FEV(1)/FVC decline. Pathway interactions were weak. Replications for the strongest SNPs in PARK2 and CRISP2 were not successful. CONCLUSIONS: Consistent with a stratified response to increasing oxidative stress, different genes and pathways potentially mediate PM10 and tobac smoke effects on lung function decline. Ignoring environmental exposures would miss these patterns, but achieving sufficient sample size and comparability across study samples is challengin