Miracle-dz/UniFAR-FTUs huggingface dataset:
Construction of a high-density, high-resolution genetic map and its integration with BAC-based physical map in channel cat ﬁ sh

Construction of genetic linkage map is essential for genetic and genomic studies. Recent advances in sequencing and genotyping technologies made it possible to generate high-density and high-reso-lution genetic linkage maps, especially for the organisms lacking extensive genomic resources. In the present work, we constructed a high-density and high-resolution genetic map for channel cat ﬁ sh with three large resource families genotyped using the cat ﬁ sh 250K single-nucleotide polymorphism (SNP) array. A total of 54,342 SNPs were placed on the linkage map, which to our knowledge had the highest marker density among aquaculture species. The estimated genetic size was 3,505.4 cM with a resolution of 0.22 cM for sex-averaged genetic map. The sex-speci ﬁ c linkage maps spanned a total of 4,495.1 cM in females and 2,593.7 cM in males, presenting a ratio of 1.7 : 1 between female and male in recombination fraction. After integration with the previously established physical map, over 87% of physical map contigs were anchored to the linkage groups that covered a physical length of 867 Mb, accounting for ∼ 90% of the cat ﬁ sh genome. The integrated map provides a valuable tool for validating and improving the cat ﬁ sh whole-genome assembly and facilitates ﬁ ne-scale QTL mapping and positional cloning of genes responsible for economically important traits.
Charged current inclusive measurements in MINERνA

MINERvA is a neutrino scattering experiment stationed in the high intensity NuMI beam line at Fermilab, designed to measure neutrino cross sections, final states and nuclear effects on a variety of targets in the few-GeV region to reduce systematic uncertainties in oscillation experiments and provide new understanding of the nucleus. Here we present the current MINERvA results for inclusive charged current neutrino and anti-neutrino scattering in the active region of the detector and different neutrino cross section ratios with different nuclear targets.
An American Sleep Disorders Association Review The Indications for Polysomnography and Related Procedures

This paper is a review of the literature on the use of polysomnography in the diagnosis of sleep disorders in the adult. It is based on a search of MEDLINE from January 1966 through April 1996. It has been reviewed and approved by the Board of Directors of the American Sleep Disorders Association and provides the background for the accompanying ASDA Standards of Practice Committee's Parameters for the Practice of Sleep Medicine in North America. The diagnostic categories reviewed are: sleep-related breathing disorders; other respiratory disorders; narcolepsy; parasomnias and sleep-related epilepsy; restless legs syndrome and periodic limb movement disorders; insomnia; and circadian rhythm sleep disorders, Where appropriate, previously published practice parameters papers are cited and discussed, The relevant published peer-reviewed literature used as the basis for critical decisions was compiled into accompanying evidence tables and is analyzed in the text. In the section on the assessment of sleep apnea syndrome, options for estimating pretest probability to select high risk patients are also reviewed, Sleep-testing procedures other than standard polysomnography are also addressed (daytime polysomnography, split-night studies, oximetry, limited full respiratory recordings, and less-than-full respiratory recording) and treatment-related fulluw-up studies are discussed.
Low-pass ﬁltering, a new method of fractal analysis: application to PET images of pulmonary blood ﬂow

Low-pass ﬁltering, a new method of fractal analysis: application to PET images of pulmonary blood ﬂow. J Appl Physiol 88: 1365– 1373, 2000. —The pattern of a spatial structure that repeats itself independently of the scale of magniﬁcation or resolution is often characterized by a fractal dimension ( D ). Two-dimensional low-pass ﬁltering, which may serve as a method to assess D , was applied to functional images of pulmonary perfusion measured by positron emission tomography. The corner frequency of a low-pass ﬁlter is inversely proportional to the resolution scale. The method was applied to three types of images: random noise images, synthetic fractal images, and positron emission tomographic images of pulmonary perfusion. Images were processed with two-dimensional low-pass ﬁlters of decreasing corner frequencies, and a spatial heterogeneity index, the coefficient of variation, was calculated for each low-pass-ﬁltered image. The natural logarithm of the coefficient of variation scaled linearly with the natural logarithm of the resolution scale for the PET images studied (average R 2 5 0.99). D ranged from 1.25 to 1.36 for the residual distribution of pulmonary perfusion after vertical gradients were removed by linear regression. D of the same data without removal of vertical gradients ranged from 1.11 to 1.14, but the fractal plots had systematic de-viations from linearity and a lower linear correlation coefficient ( R 2 5 0.96). The method includes all data in the lung ﬁeld and is insensitive to the effects of misregistration. We conclude that low-pass ﬁltering offers new insights into the interpretation of D of two-dimensional functional images as a measure of the frequency content of spatial heterogeneity.
Drug-Induced Conformational Changes in Multidrug Efﬂux Transporter AcrB from Haemophilus inﬂuenzae (cid:1)

In gram-negative bacteria, transporters belonging to the resistance-nodulation-cell division (RND) super- family of proteins are responsible for intrinsic multidrug resistance. Haemophilus inﬂuenzae , a gram-negative pathogen causing respiratory diseases in humans and animals, constitutively produces the multidrug efﬂux transporter AcrB (AcrB HI ). Similar to other RND transporters AcrB HI associates with AcrA HI , the periplasmic membrane fusion protein, and the outer membrane channel TolC HI . Here, we report that AcrAB HI confers multidrug resistance when expressed in Escherichia coli and requires for its activity the E. coli TolC (TolC EC ) protein. To investigate the intracellular dynamics of AcrAB HI , single cysteine mutations were constructed in AcrB HI in positions previously identiﬁed as important for substrate recognition. The accessibility of these strategically positioned cysteines to the hydrophilic thiol-reactive ﬂuorophore ﬂuorescein-5-maleimide (FM) was studied in vivo in the presence of various substrates of AcrAB HI and in the presence or absence of AcrA HI and TolC EC . We report that the reactivity of speciﬁc cysteines with FM is affected by the presence of some but not all substrates. Our results suggest that substrates induce conformational changes in AcrB HI . Multidrug
Institutional Knowledge at Singapore Management University Counterparty Responses to Managerial Overconfidence

Existing research links CEO overconfidence to a number of corporate decisions including overinvestment, external acquisitions, and earnings management. These findings raise the question of whether counterparties distinguish between differences in CEOs, and how they respond to it. We focus on two key counterparties – auditors and credit rating agencies – and examine whether audit fees and credit ratings are affected by CEO overconfidence. We find a positive association between audit fees and CEO overconfidence, suggesting that auditors exert more effort or increase the risk premium associated with auditing firms with more overconfident CEOs. We also find a significant negative association between CEO overconfidence and credit ratings, suggesting that overconfident CEOs are associated with higher agency costs of debt and higher credit risk. (1) and examine these two components separately both are associated with audit fees in the predicted direction (β 1 =1.349, p value =0.000 for OVER_CON and β 1 =-0.814, p value = 0.111 for CONSERVATIVE_CON ). This result suggests the observed association between our measure of overconfidence and audit fees is because firms with less overconfident CEOs are charged lower audit fees and firms with more overconfident CEOs are charged higher audit fees.
REPORTS ON THERAPY A Randomized Placebo-Controlled Trial of Combined Early Intravenous Captopril and Recombinant Tissue-Type Plasminogen Activator Therapy in Acute Myocardial Infarction

The adjunctive use of intravenous captopril with tissue plasmino gen activator early during acute myocardial infarction oilers theoretic advantages of diminishing left ventricular volume, pre venting ventricular dilation and improving patient survival. To test the safety and efficacy of combined early administration of intravenous captopril and recombiriant tissile-iype plasminogen activator (rt-PA), 38 patients treated with rt-PA 3 ± 0.3 h (mean ± SE) after the onset of myocardial infarction were randomized to intravenous followed by oral captopril or placebo therapy. They underwent cardiac catheterization with measurement of hemody namic variables and left ventricular function and determination of serum renin, angiotensin and aldosterone levels on days 1 and 7. Oral administration of the selected agent was continued for 3 m(jnths along with other antianginal medications, including nonangiotensin-converting enzyme inhibitor vasodilators. Repeat measurements of left ventricular function were obtained before hospital discharge and at 3 months. There
The Matrix Protein of Vesicular Stomatitis Virus Binds Dynamin for Efﬁcient Viral Assembly (cid:1)

Matrix proteins (M) direct the process of assembly and budding of viruses belonging to the Mononegavirales order. Using the two-hybrid system, the amino-terminal part of vesicular stomatitis virus (VSV) M was shown to interact with dynamin pleckstrin homology domain. This interaction was conﬁrmed by coimmunoprecipi-tation of both proteins in cells transfected by a plasmid encoding a c-myc-tagged dynamin and infected by VSV. A role for dynamin in the viral cycle (in addition to its role in virion endocytosis) was suggested by the fact that a late stage of the viral cycle was sensitive to dynasore. By alanine scanning, we identiﬁed a single mutation of M protein that abolished this interaction and reduced virus yield. The adaptation of mutant virus (M.L4A) occurred rapidly, allowing the isolation of revertants, among which the M protein, despite having an amino acid sequence distinct from that of the wild type, recovered a signiﬁcant level of interaction with dynamin. This proved that the mutant phenotype was due to the loss of interaction between M and dynamin. The infectious cycle of the mutant virus M.L4A was blocked at a late stage, resulting in a quasi-absence of bullet-shaped viruses in the process of budding at the cell membrane. This was associated with an accumulation of nucleocapsids at the periphery of the cell and a different pattern of VSV glycoprotein localization. Finally, we showed that M-dynamin interaction affects clathrin-dependent endocytosis. Our study suggests that hijacking the endocytic pathway might be an important feature for enveloped virus assembly and budding at the plasma membrane.
Class I Presentation of Antigen Intercellular Spreading and Enhanced MHC Improving Vaccine Potency Through

The potency of naked DNA vaccines is limited by their inability to amplify and spread in vivo. VP22, a HSV-1 protein, has demonstrated the remarkable property of intercellular transport and may thus provide a unique approach for enhancing vaccine potency. Therefore, we created a novel fusion of VP22 with a model Ag, human papillomavirus type 16 E7, in a DNA vaccine that generated enhanced spreading and MHC class I presentation of Ag. These properties led to a dramatic increase in the number of E7-speciﬁc CD8 1 T cell precursors in vaccinated mice (around 50-fold) and converted a less effective DNA vaccine into one with signiﬁcant potency against E7-expressing tumors. In comparison, nonspreading VP22 1–267 mutants failed to enhance vaccine potency. Our data indicated that the potency of DNA vaccines may be dramatically improved through intercellular spreading and enhanced MHC class I presentation of Ag. The Journal of Immunology, 2001, 166: 5733–5740. However, one limitation DNA vaccines is potency, they do not the intrinsic ability to amplify and spread in vivo replicating viral vaccine vectors reasoned the spread of Ag may signiﬁcantly the potency of naked DNA vaccines.
A FORWARD APPROACH

Variational data assimilation problems are concerned with computing unknown initial values for the simulation and prediction of natural phenomena, most notably in weather prediction, and are usually solved via an ill-posed optimal control problem for the initial state at the time of the ﬁrst available measurements. An alternative “forward” approach focuses on computation of the ﬁnal state after this interval—which is just as suitable for prediction purposes—and is well-posed without additional regularization. Speciﬁcally, it is possible to compute projections of the unknown ﬁnal state on all elements of an orthonormal basis, which theoretically allows for the complete reconstruction of the ﬁnal state. In this paper, an eﬃcient numerical method for linear evolution equations of diﬀusive type is presented, and convergence of the numerical approximation based on a discontinuous Galerkin discretization is proved. The key of this method is the computation of an adaptively ordered orthonormal basis using proper orthogonal decomposition. Numerical examples for a scalar convection-diﬀusion equation in two and three dimensions show the eﬀectiveness of the method.
Dear Editor Thank you for the feedback on our revised manuscript. The reviewer comments were as follows (with our response in BLOCK CAPITALS)

The key component of a microstructural diffusion MRI 'superscanner' is a dedicated high-strength gradient system that enables stronger diffusion weightings per unit time compared to conventional gradient designs. This can, in turn, drastically shorten the time needed for diffusion encoding, increase the signal-to-noise ratio, and facilitate measurements at shorter diffusion times. This review, written from the perspective of the National Facility for In Vivo MR Imaging of Human Tissue Microstructure, an initiative to establish a shared 300 mT/m-gradient facility amongst the microstructural imaging community, describes ten advantages of ultra-strong gradients for microstructural imaging. Specifically, we will discuss how the increase of the accessible measurement space compared to a lower-gradient systems (in terms of ∆, bvalue, and TE) can accelerate developments in the areas of 1) axon diameter distribution mapping; 2) microstructural parameter estimation; 3) mapping microvs macroscopic anisotropy features with gradient waveforms beyond a single pair of pulsed-gradients; 4) multi-contrast experiments, e.g. diffusion-relaxometry; 5) tractography and highresolution imaging in vivo and 6) post mortem; 7) diffusion-weighted spectroscopy of metabolites other than water; 8) tumour characterisation; 9) functional diffusion MRI; and 10) quality enhancement of images acquired on lower-gradient systems. We finally discuss practical barriers in the use of ultra-strong gradients, and provide an outlook on the next generation of 'super-scanners'.
Entanglement Entropy of the N = 4 SYM spin chain

We present a detailed study of the Entanglement Entropy (EE) of excited states in all closed rank one subsectors of N = 4 SYM, namely SU(2), SU(1|1) and SL(2). Exploiting the techniques of the Coordinate and the Algebraic Bethe Ansatz we obtain the EE for spin chains with up to seven magnons, at leading order in the coupling expansion but exact in the length of the spin chain and of the part of it that we cut. Focusing on the superconformal primary operator with two magnons in the BMN limit, we derive analytic and exact, in the coupling λ′, expressions for the Renyi and the EE. The interpolating functions for the Renyi and the EE monotonically increase as the coupling increases from the weak coupling λ′ → 0 regime to the strong coupling λ′ →∞ regime. This results to a violation of a certain bound for the EE that is present at weak coupling and confirms the physical intuition that entanglement increases when the coupling increases. ar X iv :1 60 3. 05 92 9v 2 [ he pth ] 2 9 A ug 2 01 6
RRU_A_233979 519..527

1Department of Urology, University Hospital Southampton NHS Trust, Southampton, UK; 2Manipal Academy of Higher Education, Manipal, India Abstract: Laser technology is widely used in urological surgery, from lithotripsy, prostate surgery to en-bloc resection of tumours. While Holmium:YAG has been widely employed over the last two decades, in recent years, there has been a surge of interest in Thulium Fiber Laser (TFL), which offers theoretical advantages of better water absorption and lower stone ablation thresholds. A systematic review was conducted to assess the evidence from clinical research on TFL’s application for lithotripsy and prostate surgery. It identified 357 articles and 8 (1506 patients) were selected, of which 4 clinical studies each investigated TFL enucleation of prostate (ThuFLEP) and TFL lithotripsy. For flexible ureteroscopic lithotripsy (FURSL), stone ablation settings ranged from 0.1–4 J, and 7–300 Hz, mean operative time ranged from 23.4–39.8 minutes and lasing time ranged from 1.2–10 minutes. For stone dusting in percutaneous nephrolithotomy (PCNL), settings of 0.2 J and 125–200 Hz were found to be optimal. For ThuFLEP, all studies showed a significant improvement in IPSS (International Prostate Symptom Score), urinary flow rate (Qmax), quality of life measures, and post-void residual volume, with mean operative time ranging from 67–104.5 minutes. Our review shows that there is limited evidence on the use and clinical outcomes of TFL. ThuFLEP might suggest equivalence to the widely used HoLEP in the available evidence so far. TFL lithotripsy shows promising results but further prospective, randomized trials are required to properly assess its usability, clinical effectiveness and standardisation of the settings for successful adoption of the technology.
Modelling the propagation and scattering of elastic waves in inhomogeneous anisotropic media

A finite-difference numerical model for studying the propagation and scattering of elastic waves in three-dimensional inhomogeneous and anisotropic media of arbitrary symmetry is presented. The model takes account of short pulses and finite-width beams and incorporates mode conversion at boundaries. The model, called SWAM3D (scattering of elastic waves in inhomogeneous anisotropic media in 3D), can handle a region of size equivalent to 250*250*250 nodes, that is a cube of side 25 shear wavelengths. It runs on a CRAY-2 supercomputer and represents a significant advance in the numerical treatment of wave propagation and scattering in inhomogeneous and anisotropic materials. As an indication of the power of the model, it is applied to the scattering of elastic waves of different polarisations from a cylindrical hole in a homogeneous transversely isotropic material. The propagation and scattering of elastic wave in inhomogeneous materials is an important problem in ultrasonic inspection of welds in liquid-metal-cooled fast reactors. A-scans and differential scattering cross sections are presented. They are used to explain some experimental results in the ultrasonic inspection of austenitic welds. The present results confirm the validity and applicability of the model.
Resolving Ambiguities in Monocular 3D Reconstruction of Deformable Surfaces

In this thesis, we focus on the problem of recovering 3D shapes of deformable surfaces from a single camera. This problem is known to be ill-posed as for a given 2D input image there exist many 3D shapes that give visually identical projections. We present three methods which make headway towards resolving these ambiguities. We believe that our work represents a significant step towards making surface reconstruction methods of practical use. First, we propose a surface reconstruction method that overcomes the limitations of the state-of-the-art template-based and non-rigid structure from motion methods. We neither track points over many frames, nor require a sophisticated deformation model, or depend on a reference image. In our method, we establish correspondences between pairs of frames in which the shape is different and unknown. We then estimate homographies between corresponding local planar patches in both images. These yield approximate 3D reconstructions of points within each patch up to a scale factor. Since we consider overlapping patches, we can enforce them to be consistent over the whole surface. Finally, a local deformation model is used to fit a triangulated mesh to the 3D point cloud, which makes the reconstruction robust to both noise and outliers in the image data. Second, we propose a novel approach to recovering the 3D shape of a deformable surface from a monocular input by taking advantage of shading information in more generic contexts than conventional Shape-from-Shading (SfS) methods. This includes surfaces that may be fully or partially textured and lit by arbitrarily many light sources. To this end, given a lighting model, we learn the relationship between a shading pattern and the corresponding local surface shape. At run time, we first use this knowledge to recover the shape of surface patches and then enforce spatial consistency between the patches to produce a global 3D shape. Instead of treating texture as noise as in many SfS approaches, we exploit it as an additional source of information. We validate our approach quantitatively and qualitatively using both synthetic and real data. Third, we introduce a constrained latent variable model that inherently accounts for geometric constraints such as inextensibility defined on the mesh model. To this end, we learn a non-linear mapping from the latent space to the output space, which corresponds to vertex positions of a mesh model, such that the generated outputs comply with equality and inequality constraints expressed in terms of the problem variables. Since its output is encouraged to satisfy such constraints inherently, using our model removes the need for computationally expensive methods that enforce these constraints at run time. In addition, our approach is completely generic and could be used in many other different contexts as well, such as image classification to impose separation of the classes, and articulated tracking to constrain the space of possible poses.