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At least 145 records · Page 8

COMPARING H{alpha} AND H I SURVEYS AS MEANS TO A COMPLETE LOCAL GALAXY CATALOG IN THE ADVANCED LIGO/VIRGO ERA

Identifying the electromagnetic counterparts of gravitational wave (GW) sources detected by upcoming networks of advanced ground-based interferometers will be challenging, due in part to the large number of unrelated astrophysical transients within the {approx}10-100 deg{sup 2} sky localizations. A potential way to greatly reduce the number of such false positives is to limit detailed follow-up to only those candidates near galaxies within the GW sensitivity range of {approx}200 Mpc for binary neutron star mergers. Such a strategy is currently hindered by the fact that galaxy catalogs are grossly incomplete within this volume. Here, we compare two methods for completing the local galaxy catalog: (1) a narrowband H{alpha} imaging survey and (2) an H I emission line radio survey. Using H{alpha} fluxes, stellar masses (M {sub *}), and star formation rates (SFRs) from galaxies in the Sloan Digital Sky Survey (SDSS), combined with H I data from the GALEX Arecibo SDSS Survey and the Herschel Reference Survey, we estimate that an H{alpha} survey with a luminosity sensitivity of L {sub H{alpha}} = 10{sup 40} erg s{sup -1} at 200 Mpc could achieve a completeness of f {sup H{alpha}} {sub SFR} Almost-Equal-To 75% with respect to total SFR, but only f{sub M* Star-Operator }{sup H{alpha}} approx. 33% with respect to M {sub *} (due to lack of sensitivity to early-type galaxies). These numbers are significantly lower than those achieved by an idealized spectroscopic survey due to the loss of H{alpha} flux resulting from resolving out nearby galaxies and the inability to correct for the underlying stellar continuum. An H I survey with sensitivity similar to the proposed WALLABY survey on ASKAP could achieve f{sub SFR}{sup H{sub I}} Almost-Equal-To 80% and f{sub M Star-Operator }{sup H{sub I}} Almost-Equal-To 50%, somewhat higher than that of the H{alpha} survey. Finally, both H{alpha} and H I surveys should achieve {approx}> 50% completeness with respect to the host galaxies of short-duration gamma-ray bursts, which may trace the population of binary neutron star mergers.

79 ASTRONOMY AND ASTROPHYSICS↗

Spacetime completeness of non-singular black holes in conformal gravity

We explicitly prove that the Weyl conformal symmetry solves the black hole singularity problem, otherwise unavoidable in a generally covariant local or non-local gravitational theory. Moreover, we yield explicit examples of local and non-local theories enjoying Weyl and diffeomorphism symmetry (in short co-covariant theories). Following the seminal paper by Narlikar and Kembhavi, we provide an explicit construction of singularity-free spherically symmetric and axi-symmetric exact solutions for black hole spacetimes conformally equivalent to the Schwarzschild or the Kerr spacetime. We first check the absence of divergences in the Kretschmann invariant for the rescaled metrics. Afterwords, we show that the new types of black holes are geodesically complete and linked by a Newman-Janis transformation just as in standard general relativity (based on Einstein-Hilbert action). Furthermore, we argue that no massive or massless particles can reach the former Schwarzschild singularity or touch the former Kerr ring singularity in a finite amount of their proper time or of their affine parameter. Finally, we discuss the Raychaudhuri equation in a co-covariant theory and we show that the expansion parameter for congruences of both types of geodesics (for massless and massive particles) never reaches minus infinity. Actually, the null geodesics become parallel at the r =0 point in the Schwarzschild spacetime (the origin) and the focusing of geodesics is avoided. The arguments of regularity of curvature invariants, geodesic completeness, and finiteness of geodesics' expansion parameter ensure us that we are dealing with singularity-free and geodesically-complete black hole spacetimes.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

miss-SNF: a multimodal patient similarity network integration approach to handle completely missing data sources

Abstract Motivation Precision medicine leverages patient-specific multimodal data to improve prevention, diagnosis, prognosis, and treatment of diseases. Advancing precision medicine requires the non-trivial integration of complex, heterogeneous, and potentially high-dimensional data sources, such as multi-omics and clinical data. In the literature, several approaches have been proposed to manage missing data, but are usually limited to the recovery of subsets of features for a subset of patients. A largely overlooked problem is the integration of multiple sources of data when one or more of them are completely missing for a subset of patients, a relatively common condition in clinical practice. Results We propose miss-Similarity Network Fusion (miss-SNF), a novel general-purpose data integration approach designed to manage completely missing data in the context of patient similarity networks. miss-SNF integrates incomplete unimodal patient similarity networks by leveraging a non-linear message-passing strategy borrowed from the SNF algorithm. miss-SNF is able to recover missing patient similarities and is “task agnostic”, in the sense that can integrate partial data for both unsupervised and supervised prediction tasks. Experimental analyses on nine cancer datasets from The Cancer Genome Atlas (TCGA) demonstrate that miss-SNF achieves state-of-the-art results in recovering similarities and in identifying patients subgroups enriched in clinically relevant variables and having differential survival. Moreover, amputation experiments show that miss-SNF supervised prediction of cancer clinical outcomes and Alzheimer’s disease diagnosis with completely missing data achieves results comparable to those obtained when all the data are available. Availability and implementation miss-SNF code, implemented in R, is available at https://github.com/AnacletoLAB/missSNF.

Biochemistry & Molecular Biology↗

scMicrobe PTA: near complete genomes from single bacterial cells

Microbial genomes produced by standard single-cell amplification methods are largely incomplete. Here, we show that primary template-directed amplification (PTA), a novel single-cell amplification technique, generated nearly complete genomes from three bacterial isolate species. Furthermore, taxonomically diverse genomes recovered from aquatic and soil microbiomes using PTA had a median completeness of 81%, whereas genomes from standard multiple displacement amplification-based approaches were usually <30% complete. PTA-derived genomes also included more associated viruses and biosynthetic gene clusters.

59 BASIC BIOLOGICAL SCIENCES↗

Complete prevalence of malignant primary brain tumors registry data in the United States compared with other common cancers, 2010

Complete prevalence proportions illustrate the burden of disease in a population. Here, this study estimates the 2010 complete prevalence of malignant primary brain tumors overall and by Central Brain Tumor Registry of the United States (CBTRUS) histology groups, and compares the brain tumor prevalence estimates to the complete prevalence of other common cancers as determined by the Surveillance, Epidemiology, and End Results Program (SEER) by age at prevalence (2010): children (0–14 y), adolescent and young adult (AYA) (15–39 y), and adult (40+ y).

60 APPLIED LIFE SCIENCES↗

Past-completeness of inflationary spacetimes

Here, we discuss the question of whether or not inflationary spacetimes can be geodesically complete in the infinite past. Geodesic completeness is a necessary condition for averting an initial singularity during eternal inflation. It is frequently argued that cosmological models which are expanding sufficiently fast (having average Hubble expansion rate H avg > 0) must be incomplete in null and timelike past directions. This well-known conjecture relies on specific bounds on the integral of the Hubble parameter over a past- directed timelike or null geodesic. As stated, we show this claim is an open issue. We show that the calculation of H avg yields a continuum of results for a given spacetime predicated upon the underlying topological assumptions. We present an improved definition for H avg and introduce an uncountably infinite cohort of cosmological solutions which are geodesically complete despite having H avg > 0. We discuss a standardized definition for inflationary spacetimes as well as quantum (semiclassical) cosmological concerns over physically reasonable scale factors.

79 ASTRONOMY AND ASTROPHYSICS↗

Puzzle of Complete Fusion Suppression in Weakly Bound Nuclei: A Trojan Horse Effect?

Experimental studies of nuclear collisions involving light weakly-bound nuclei show a systematic suppression of the complete fusion cross section by ~30% with respect to the expectation for tightly bound nuclei, at energies above the Coulomb barrier. Although it is widely accepted that the phenomenon is related to the weak binding of these nuclei, the origin of this suppression is not fully understood. In here, we present a novel approach that provides the complete fusion for weakly bound nuclei and relates its suppression to the competition between the different mechanisms contributing to the reaction cross section. The method is applied to the 6,7 Li+ 209 Bi reactions, where we find that the suppression of complete fusion is mostly caused by the flux associated with non-elastic breakup modes, such as the partial capture of the projectile (incomplete fusion), whereas the elastic breakup mode is found to play a minor role. Finally, we demonstrate that the large α yields observed in these reactions can be naturally explained as a consequence of a Trojan Horse mechanism.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

A complete software application for automatic registration of x-ray mammography and magnetic resonance images

Purpose: This work presents a complete and automatic software application to aid radiologists in breast cancer diagnosis. The application is a fully automated method that performs a complete registration of magnetic resonance (MR) images and x-ray (XR) images in both directions (from MR to XR and from XR to MR) and for both x-ray mammograms, craniocaudal (CC), and mediolateral oblique (MLO). This new approximation allows radiologists to mark points in the MR images and, without any manual intervention, it provides their corresponding points in both types of XR mammograms and vice versa. Methods: The application automatically segments magnetic resonance images and x-ray images using the C-Means method and the Otsu method, respectively. It compresses the magnetic resonance images in both directions, CC and MLO, using a biomechanical model of the breast that distinguishes the specific biomechanical behavior of each one of its three tissues (skin, fat, and glandular tissue) separately. It makes a projection of both compressions and registers them with the original XR images using affine transformations and nonrigid registration methods. Results: The application has been validated by two expert radiologists. This was carried out through a quantitative validation on 14 data sets in which the Euclidean distance between points marked by the radiologists and the corresponding points obtained by the application were measured. The results showed a mean error of 4.2 ± 1.9 mm for the MRI to CC registration, 4.8 ± 1.3 mm for the MRI to MLO registration, and 4.1 ± 1.3 mm for the CC and MLO to MRI registration. Conclusions: A complete software application that automatically registers XR and MR images of the breast has been implemented. The application permits radiologists to estimate the position of a lesion that is suspected of being a tumor in an imaging modality based on its position in another different modality with a clinically acceptable error. The results show that the application can accelerate the mammographic screening process for high risk populations or for dense breasts.

60 APPLIED LIFE SCIENCES↗

Mechanical and Dynamic Stability of Complete and Nonstoichiometric 3C-Si{sub x}C{sub y} from Ab Initio Calculations

The energies of formation of vacancies in the carbon and silicon sublattices, the independent elastic constants, the all-round compression, shear and Young’s moduli, and the anisotropy coefficients are determined for the complete and nonstoichiometric cubic phases of 3C-Si{sub x}C{sub y} (x, y = 1.0–0.75) by ab initio methods of the band theory. In the formalism of the density functional perturbation theory (DFPT), the phonon dispersion dependences are obtained for these phases (the comparison with the experiment is given for the complete phase). It is shown that the mechanical characteristics of the phases become strongly anisotropic upon the transition from 3C-SiC{sub 0.875} to 3C-SiC{sub 0.75}. It is established from the analysis of the phonon dispersion curves that the 3C-SiC{sub 0.875} and 3C-SiC{sub 0.75} phases, in contrast to the complete 3C-SiC phase, are dynamically unstable at T = 0 K.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Non-Wilsonian ultraviolet completion via transseries

We study some of the implications for the perturbative renormalization program when augmented with the Borel–Ecalle resummation. We show the emergence of a new kind of nonperturbative fixed point for the scalar [Formula: see text] model, representing an ultraviolet self-completion by transseries. We argue that this completion is purely non-Wilsonian and it depends on one arbitrary constant stemming from the transseries solution of the renormalization group equation. On the other hand, if no fixed points are demanded through the adjustment of this arbitrary constant, we end up with an effective theory in which the scalar mass is quadratically-sensitive to the cutoff, even working in dimensional regularization. Complete decoupling of the scalar mass to this energy scale can be used to determine a physical prescription for the Borel–Laplace resummation of the renormalons in nonasymptotically free models. We also comment on possible orthogonal scenarios available in the literature that might play a role when no fixed points exist.

Physics↗

Complete genome sequence and the expression pattern of plasmids of the model ethanologen Zymomonas mobilis ZM4 and its xylose-utilizing derivatives 8b and 2032

Zymomonas mobilis is a natural ethanologen being developed and deployed as an industrial biofuel producer. To date, eight Z. mobilis strains have been completely sequenced and found to contain 2-8 native plasmids. However, systematic verification of predicted Z. mobilis plasmid genes and their contribution to cell fitness has not been hitherto addressed. Moreover, the precise number and identities of plasmids in Z. mobilis model strain ZM4 have been unclear. The lack of functional information about plasmid genes in ZM4 impedes ongoing studies for this model biofuel-producing strain. In this study, we determined the complete chromosome and plasmid sequences of ZM4 and its engineered xylose-utilizing derivatives 2032 and 8b. Compared to previously published and revised ZM4 chromosome sequences, the ZM4 chromosome sequence reported here contains 65 nucleotide sequence variations as well as a 2400-bp insertion. Four plasmids were identified in all three strains, with 150 plasmid genes predicted in strain ZM4 and 2032, and 153 plasmid genes predicted in strain 8b due to the insertion of heterologous DNA for expanded substrate utilization. Plasmid genes were then annotated using Blast2GO, InterProScan, and systems biology data analyses, and most genes were found to have apparent orthologs in other organisms or identifiable conserved domains. To verify plasmid gene prediction, RNA-Seq was used to map transcripts and also compare relative gene expression under various growth conditions, including anaerobic and aerobic conditions, or growth in different concentrations of biomass hydrolysates. Overall, plasmid genes were more responsive to varying hydrolysate concentrations than to oxygen availability. Additionally, our results indicated that although all plasmids were present in low copy number (about 1-2 per cell), the copy number of some plasmids varied under specific growth conditions or due to heterologous gene insertion. The complete genome of ZM4 and two xylose-utilizing derivatives is reported in this study, with an emphasis on identifying and characterizing plasmid genes. Furthermore, plasmid gene annotation, validation, expression levels at growth conditions of interest, and contribution to host fitness are reported for the first time.

09 BIOMASS FUELS↗

The effects of well damage and completion designs on geoelectrical responses in mature wellbore environments

Well integrity is one of the major concerns in long-term geologic storage sites due to the potential risk of well leakage and groundwater contamination. Evaluating changes in electrical responses due to energized steel-cased wells has the potential to quantify and predict possible wellbore failures because any kind of breakage or corrosion along highly conductive well casings will have an impact on the distribution of the subsurface electrical potential. However, realistic wellbore-geoelectrical models that can fully capture fine-scale details of well completion design and the state of well damage at the field scale require extensive computational effort, or they can even be intractable to simulate. To overcome this computational burden while still keeping the model realistic, we have used the hierarchical finite-element method that represents electrical conductivity at each dimensional component (1D edges, 2D planes, and 3D cells) of a tetrahedral mesh. This allows well completion designs with real-life geometric scales and well systems with realistic, detailed, progressive corrosion and damage in our models. We have developed a comparison of possible discretization approaches of a multicasing completion design in the finite-element model. The effects of the surface casing and the coupling between concentric well casings as well as the effects of the degree and the location of well damage on the electrical responses are also examined. As a result, we analyze real surface electric field data to detect wellbore integrity failure associated with damage.

58 GEOSCIENCES↗

Robotic Extended Right Hemicolectomy with Complete Mesocolic Excision and D3 Lymph Node Dissection

Background: Recent studies have shown the benefits of complete mesocolic excision and extended lymphadenectomy (D3 lymph node dissection) in patients with colon cancer.1{sup –}3 Methods: We present the case of a 62-year-old male with hepatic flexure adenocarcinoma. No metastatic disease was identified by computed tomography. A robot-assisted extended right hemicolectomy with complete mesocolic excision, D3 lymph node dissection, and resection of the mesentery with intact visceral peritoneum was performed. Results: The trocars are placed in the right lower (8 mm), lower midline (8 mm), and left upper (12 mm) quadrants. The camera port is placed superior to the umbilicus, and the assistant port is placed in the left lower quadrant. The robotic right lower port is used to place the cecum on tension in order to outline the ileocolic pedicle. The assistant retracts the transverse colon cephalad to outline the superior mesenteric artery and vein. Using two robotic arms, the surgeon begins dissection over the superior mesenteric vein inferior to the ileocolic pedicle. Cephalad dissection along the superior mesenteric vein proceeds with reflection of the mesentery and D3 lymph nodes laterally to allow en bloc resection. The ileocolic and middle colic vessels are identified, ligated and divided at their origins. The plane is then developed between the right colon mesentery and the retroperitoneum, including Gerota’s fascia, duodenum, and head of the pancreas, in a medial-to-lateral fashion, with care taken to ensure an intact visceral peritoneum is maintained. The proximal transverse colon, hepatic flexure, and ascending colon are mobilized by taking down lateral attachments. The intervening mesentery is transected, and perfusion is assessed with indocyanine green fluorescence imaging. An intracorporeal, isoperistaltic, side-to-side anastomosis is performed using the 45-mm robotic stapler. The common enterotomy is sewn closed in two layers. Pathology showed T3N0 adenocarcinoma with all negative margins. Conclusion: Extended right hemicolectomy with complete mesocolic excision and D3 lymph node dissection is facilitated by a robotic approach, which improves visualization and instrument dexterity.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Using Stage Level Microseismic Analysis to Gain Insight into Fracture Efficiency and Completion Effectiveness

Microseismic event density heat maps at sequential time intervals during the treatment of individual completion stages have been developed to better understand fracture behavior on a stage level. Animating these heat maps through time on a single stage provides fascinating visual insights into the dynamic sequencing of populations of events, event timing and their likely genesis, providing a new way of visualizing and interpreting microseismic data sets. This technique leverages heat-map benefits from URTEC 2674376, excluding microseismic event clusters that may obscure or skew statistical analysis of the event densities, thus allowing for more accurate assessment of geologic features, stimulated rock volume, near-field concentration of events due to varying cluster spacing, fracture efficiency and stress shadowing. Far-field microseismic events prior to ramp up of treatment pressure are clearly indicated from this technique that cannot be observed with standard heat maps with certain completion designs. Unambiguous changes in microseismic event character from these far-field pre-ramp up events to those near-field events occurring at the onset of pressure are also observed. Applying a stage by stage approach on packages of wells and different locations provides robust statistical conclusions pertaining to reservoir behavior during well completion.

Wang, Iris↗

Level-2 Milestone 5213. CTS-1 Contract Award Completed

This report documents the fact that the first commodity technology (CT) system contract award, CTS-1, has been completed. The description of the milestone is: Based on Tri-Lab CTS-1 process and review, LLNL successfully awards the procurement for the next-generation Tri-Lab Linux CTS-1. The milestone completion criterion is: Signed contract. The milestone was completed on September 24th. 2015.

97 MATHEMATICS AND COMPUTING↗

Site Rehabilitation Completion Report with No Further Action Proposal for the Northeast Site

The purpose of this Site Rehabilitation Completion Report is to present the post-active-remediation monitoring results for the Northeast Site and to propose No Further Action with Controls. This document includes information required by Chapter 62-780.750(4)(d), 62-780.750(6), and 62-780.600(8)(a)27 Florida Administrative Code (F.A.C.). The Closure Monitoring Plan for the Northeast Site and 4.5 Acre Site (DOE 2009a) describes the approach for post-active-remediation monitoring. The Young - Rainey Science, Technology, and Research Center (STAR Center) is a former U.S. Department of Energy (DOE) facility constructed in the mid-1950s. The 99-acre STAR Center is located in Largo, Florida. The Northeast Site is located in the northeast corner of the STAR Center. The Northeast Site meets all the requirements for an RMO II closure—No Further Action with Controls. DOE is nearing completion of a restrictive covenant for the Northeast Site. DOE has completed post-active-remediation monitoring at the Northeast Site as of September 2012. No additional monitoring will be conducted.

54 ENVIRONMENTAL SCIENCES↗

Central Asia Seismic Hazard Assessment (Casha) "Complete" Catalog of Earthquakes

Probabilistic Seismic Hazard Assessments (PSHA) greatly benefit from reliable earthquake catalogs. Central Asia, while rich in seismic monitoring history, reports a fraction of their earthquake data to international data collection centres. Furthermore, since the collapse of Soviet Union until now, monitoring and data collection efforts in Central Asia have not been centralized, making monitoring and reporting uneven and disconnected in this time period. Lawrence Livermore National Laboratory (LLNL) has undertaken a multi-year effort to systematically work with national seismic monitoring and data centres and seismic networks in Kazakhstan, Kyrgyzstan, and Tajikistan to compile a unified seismological bulletin for Central Asia. In tandem with this effort, an earthquake catalog that is processed to be PSHA ready was also generated. The processing for this effort included further duplicate identification and removal, magnitude harmonization and catalog completeness analyses. This report describes the “complete” PSHA-ready earthquake catalog, including the completeness intervals that were applied.

58 GEOSCIENCES↗

Permutation-adapted complete and independent basis for atomic cluster expansion descriptors

In many recent applications, particularly in the field of atom-centered descriptors for interatomic potentials, tensor products of spherical harmonics have been used to characterize complex atomic environments. When coupled with a radial basis, the atomic cluster expansion (ACE) basis is obtained. However, symmetrization with respect to both rotation and permutation results in an overcomplete set of ACE descriptors with linear dependencies occurring within blocks of functions corresponding to particular generalized Wigner symbols. All practical applications of ACE employ semi-numerical constructions to generate a complete, fully independent basis. While computationally tractable, the resultant basis cannot be expressed analytically, is susceptible to numerical instability, and thus has limited reproducibility. Here we present a procedure for generating explicit analytic expressions for a complete and independent set of ACE descriptors. The procedure uses a coupling scheme that is maximally symmetric w.r.t. permutation of the atoms, exposing the permutational symmetries of the generalized Wigner symbols, and yields a permutation-adapted rotationally and permutationally invariant basis (PA-RPI ACE). Theoretical support for the approach is presented, as well as numerical evidence of completeness and independence. A summary of explicit enumeration of PA-RPI functions up to rank 6 and polynomial degree 32 is provided. The PA-RPI blocks corresponding to particular generalized Wigner symbols may be either larger or smaller than the corresponding blocks in the simpler rotationally invariant basis. Finally, we demonstrate that basis functions of high polynomial degree persist under strong regularization, indicating the importance of not restricting the maximum degree of basis functions in ACE models a priori.

74 ATOMIC AND MOLECULAR PHYSICS↗