bluuebunny/crossref_metadata_2025 huggingface dataset:
Optical imaging provides rapid verification of static small beams, radiosurgery, and VMAT plans with millimeter resolution
Authors: Ashraf Muhammad Ramish , Bruza Petr , Pogue Brian W. , Nelson Nathan , Williams Benjamin B. , Jarvis Lesley A. , Gladstone David J.
Published: August 2019

Purpose

We demonstrate the feasibility of optical imaging as a quality assurance tool for static small beamlets, and pretreatment verification tool for radiosurgery and volumetric‐modulated arc therapy (VMAT) plans.

Methods

Small static beams and clinical VMAT plans were simulated in a treatment planning system (TPS) and delivered to a cylindrical tank filled with water‐based liquid scintillator. Emission was imaged using a blue‐sensitive, intensified CMOS camera time‐gated to the linac pulses. For static beams, percentage depth and cross beam profiles of projected intensity distribution were compared to TPS data. Two‐dimensional (2D) gamma analysis was performed on all clinical plans, and the technique was tested for sensitivity against common errors (multileaf collimator position, gantry angle) by inducing deliberate errors in the VMAT plans control points. The technique’s detection limits for spatial resolution and the smallest number of control points that could be imaged reliably were also tested. The sensitivity to common delivery errors was also compared against a commercial 2.5D diode array dosimeter.

Results

A spatial resolution of 1 mm was achieved with our imaging setup. The optical projected percentage depth intensity profiles agreed to within 2% relative to the TPS data for small static square beams (5, 10, and 50 mm2). For projected cross beam profiles, a gamma pass rate >99% was achieved for a 3%/1 mm criteria. All clinical plans passed the 3%/3 mm criteria with >95% passing rate. A static 5 mm beam with 20 Monitor Units could be measured with an average percent difference of 5.5 ± 3% relative to the TPS. The technique was sensitive to multileaf collimator errors down to 1 mm and gantry angle errors of 1°.

Conclusions

Optical imaging provides ample spatial resolution for imaging small beams. The ability to faithfully image down to 20 MU of 5 mm, 6 MV beamlets prove the ability to perform quality assurance for each control point within dynamic plans. The technique is sensitive to small offset errors in gantry angles and multileaf collimator (MLC) leaf positions, and at certain scenario, it exhibits higher sensitivity than a commercial 2.5D diode array.
Fabrication and characterization of PLA/PP/ABS ternary blend
Authors: Chaudry Umer M. , Hamad Kotiba
Published: August 2019

In this study, we fabricated and studied properties of ternary polymer blends containing polylactic acid (PLA), polypropylene (PP), and acrylonitrile‐butadiene‐styrene (ABS). The melt rheology experiments showed that the present combination (PLA/PP/ABS) exhibited a melt process‐ability, which is comparable to those of individual components. The ternary blends prepared in this work can be exploited to fabricate hierarchically porous PLA materials for biomedical applications. POLYM. ENG. SCI., 59:2273–2278, 2019. © 2019 Society of Plastics Engineers
Network Reconstruction and Significant Pathway Extraction Using Phosphoproteomic Data from Cancer Cells
Authors: Buffard Marion , Naldi Aurélien , Radulescu Ovidiu , Coopman Peter J. , Larive Romain M. , Freiss Gilles
Published: August 2019

Protein phosphorylation acts as an efficient switch controlling deregulated key signaling pathway in cancer. Computational biology aims to address the complexity of reconstructed networks but overrepresents well‐known proteins and lacks information on less‐studied proteins. A bioinformatic tool to reconstruct and select relatively small networks that connect signaling proteins to their targets in specific contexts is developed. It enables to propose and validate new signaling axes of the Syk kinase. To validate the potency of the tool, it is applied to two phosphoproteomic studies on oncogenic mutants of the well‐known phosphatidyl‐inositol 3‐kinase (PIK3CA) and the unfamiliar Src‐related tyrosine kinase lacking C‐terminal regulatory tyrosine and N‐terminal myristoylation sites (SRMS) kinase. By combining network reconstruction and signal propagation, comprehensive signaling networks from large‐scale experimental data are built and multiple molecular paths from these kinases to their targets are extracted. Specific paths from two distinct PIK3CA mutants are retrieved, and their differential impact on the HER3 receptor kinase is explained. In addition, to address the missing connectivities of the SRMS kinase to its targets in interaction pathway databases, phospho‐tyrosine and phospho‐serine/threonine proteomic data are integrated. The resulting SRMS‐signaling network comprises casein kinase 2, thereby validating its currently suggested role downstream of SRMS. The computational pipeline is publicly available, and contains a user‐friendly graphical interface (http://doi.org/10.5281/zenodo.3333687).
Solvent and Spinning Speed Effects on CH3NH3PbI3 Films Deposited by Spin Coating
Authors: Belaidi Itidal , Khelfaoui Fatima , Attaf Nadhir , Azzizi Assia , Aida Mohammed Salah
Published: August 2019

Herein, methylammonium lead triode (CH3NH3PbI3) perovskite thin films are prepared by the one‐step deposition spin‐coating process on glass substrates. The effects of solvent nature and speed centrifugation on films' morphology and structure are investigated. Two solvents are used: N,N‐dimethyl formamide (DMF) and a mixture of dimethyl sulfoxide (DMSO) with DMF. The spinning speed varies in the range 700–2000 rpm. Scanning electron microscopy (SEM) observations reveal that the prepared films are not continuous with variable morphologies; the films are formed with elongated fibers. X‐ray diffraction (XRD) analysis confirms the tetragonal structure of the prepared perovskite. The film structure is also investigated by Raman spectroscopy. The film's optical properties are studied using UV spectroscopy. The results indicate that solvent nature and spinning velocity alter film morphology. With increasing spinning velocity, the films' porosity increases. The films' formation is controlled by the competition between the radial force due to spinning velocity and resistive force due to solution viscosity.
Growth of InGaAs Solar Cells on InP(001) Miscut Substrates Using Solid‐Source Molecular Beam Epitaxy
Authors: Oshima Ryuji , Ishitsuka Yuki , Okano Yoshinobu , Sugaya Takeyoshi
Published: August 2019

Herein, the effects of both the growth temperature and the substrate miscut on the properties of lattice‐matched InGaAs solar cells grown on InP substrates via solid‐source molecular beam epitaxy are investigated. The growth temperature is varied from 420 to 490 °C. InP(001) miscut by 2° toward (111)A and (111)B denoted by 2°A and 2°B, respectively, and exactly‐cut substrates are used. Material quality is evaluated by photoluminescence (PL) and atomic force microscopy (AFM) measurements. At room temperature, the PL emissions become more intense at higher growth temperatures and with miscut substrates, indicating less nonradiative recombination. AFM results show a streaky surface with step structures along the direction for cell grown at 490 °C on 2°A, suggesting that the substrate promotes step‐flow growth. Consequently, the highest conversion efficiency (12.3%) for the cell grown at 490 °C on 2°A is obtained. Especially, the open‐circuit voltage (VOC) increases from the baseline of 0.350 V (for the cell grown at 420 °C on an exact substrate) to 0.374 V. The Eg−VOC deficit, where , of 369 mV is obtained, which is a standard benchmark for high‐material‐quality solar cells.
A Magneto‐Reflectivity Study of CuInTe2 Single Crystals
Authors: Yakushev Michael V. , Faugeras Clement , Mudryi Alexander V. , Martin Robert W.
Published: August 2019

CuInTe2 single crystals are studied using optical magneto‐reflectance (MR) in magnetic fields B up to 20 T at 4.2 K. The spectra exhibit the A and B free excitons' blue shifting at increasing magnetic fields. Fitting quadratic functions to the experimental dependencies of the exciton spectral energy on B assuming a low field limit allow the determination of diamagnetic shift rates of 8.2 × 10−5 and 8.5 × 10−5 eV T−2 for the A and B free excitons, respectively. The excitons' reduced masses of 0.0575m0 and 0.0568m0 (m0 is the free electron mass), Rydbergs of 6.2 and 6.1 meV, and Bohr radii of 10.4 and 10.5 nm are then estimated. An electron effective mass of 0.062m0 and B sub‐band effective hole mass of 0.70m0 are determined using a literature value of the A valence sub‐band hole of 0.78m0.
Exact correlation functions in conformal fishnet theory
Authors: Gromov Nikolay , Kazakov Vladimir , Korchemsky Gregory
Published: August 2019

Abstract

We compute exactly various 4−point correlation functions of shortest scalar operators in bi-scalar planar four-dimensional “fishnet” CFT. We apply the OPE to extract from these functions the exact expressions for the scaling dimensions and the structure constants of all exchanged operators with an arbitrary Lorentz spin. In particular, we determine the conformal data of the simplest unprotected two-magnon operator analogous to the Konishi operator, as well as of the one-magnon operator. We show that at weak coupling 4−point correlation functions can be systematically expanded in terms of harmonic polylogarithm functions and verify our results by explicit calculation of Feynman graphs at a few orders in the coupling. At strong coupling we obtain that the correlation functions exhibit the scaling behaviour typical for semiclassical description hinting at the existence of the holographic dual.
From static to cosmological solutions of $$ \mathcal{N} $$ = 2 supergravity
Authors: Gutowski J. , Mohaupt T. , Pope G.
Published: August 2019

Abstract

We obtain cosmological solutions with Kasner-like asymptotics in

$$ \mathcal{N} $$

N

= 2 gauged and ungauged supergravity by maximal analytic continuation of planar versions of non-extremal black hole solutions. Initially, we construct static solutions with planar symmetry by solving the time-reduced field equations. Upon lifting back to four dimensions, the resulting static regions are incomplete and bounded by a curvature singularity on one side and a Killing horizon on the other. Analytic continuation reveals the existence of dynamic patches in the past and future, with Kasner-like asymptotics. For the ungauged STU-model, our solutions contain previously known solutions with the same conformal diagram as a subset. We find explicit lifts to five, six, ten and eleven dimensions which show that in the extremal limit, the underlying brane configuration is the same as for STU black holes. The extremal limit of the six-dimensional lift is shown to be BPS for special choices of the integration constants. We argue that there is a universal correspondence between spherically symmetric black hole solutions and planar cosmological solutions which can be illustrated using the Reissner-Nordström solution of Einstein-Maxwell theory.
Hyperbolic geometry and closed bosonic string field theory. Part II. The rules for evaluating the quantum BV master action
Authors: Moosavian Seyed Faroogh , Pius Roji
Published: August 2019

Abstract

The quantum Batalian-Vilkovisky master action for closed string field theory consists of kinetic term and infinite number of interaction terms. The interaction strengths (coupling constants) are given by integrating the off-shell string measure over the distinct string diagrams describing the elementary interactions of the closed strings. In the first paper of this series, it was shown that the string diagrams describing the elementary interactions can be characterized using the Riemann surfaces endowed with the hyperbolic metric with constant curvature −1. In this paper, we construct the off-shell bosonic-string measure as a function of the Fenchel-Nielsen coordinates of the Teichmüller space of hyperbolic Riemann surfaces. We also describe an explicit procedure for integrating the off-shell string measure over the region inside the moduli space corresponding to the elementary interactions of the closed strings.
The infinite epistemic regress problem has no unique solution
Authors: Meester Ronald , Kerkvliet Timber
Published: August 2019

In this article we analyze the claim that a probabilistic interpretation of the infinite epistemic regress problem leads to a unique solution, the so called “completion” of the regress. This claim is implicitly based on the assumption that the standard Kolmogorov axioms of probability theory are suitable for describing epistemic probability. This assumption, however, has been challenged in the literature, by various authors. One of the alternatives that have been suggested to replace the Kolmogorov axioms in case of an epistemic interpretation of probability, are belief functions, introduced by Shafer in 1976. We show that when one uses belief functions to describe the infinite epistemic regress problem, it is no longer the case that the solution is unique. We also argue that this complies with common sense.
Applying the hydrodynamic model to optimize the production for crystalline basement reservoir, X field, Cuu Long Basin, Vietnam
Authors: Thai Ba Ngoc , Vo Thanh Hung , Sugai Yuichi , Sasaki Kyuro , Nguele Ronald , Phi Hoang Quang Trung , Luong Bao Minh , Le Nguyen Hai Nam
Published: August 2019

Weathered and fractured crystalline basement is known as the important unconventional reservoir in the Cuu Long Basin. Naturally fractured reservoir plays a crucial role in oil exploration to contribute for hydrocarbon production in Vietnam. However, the complexity and heterogeneity of the fractures system in the basement reservoir are challenges for oil and gas production. They require the realistic simulation scenarios to estimate the hydrocarbon potential as well as field development plan of these reservoirs. Thus, this paper aims to propose the feasibility development scenarios to improve oil recovery factor for crystalline basement reservoir, X field, Cuu Long Basin, Vietnam. First, history matching process is validated for the model to fit the actual production data (reservoir pressure, pressure, water cut in each well) in order to approach closer the fluid flow behavior through the reservoir. The manual matching was selected to adjust the actual aquifer size and permeability distribution with limit simulation runs. Next, the highest reliability matching model which approximately reflects the actual fluid flow behavior can be used as the base case to forecast the future reservoir performance through the field development plan. The most potential scenario is to add six new infill production wells, two side track wells and two water injection wells. The forecasted results indicate that this scenario yields 8% more oil recovery factor compared to the natural drive with thirteen producers. This result suggests that the precise field development plan is to increase the efficiency of the production process by increasing the displacement parameters of residual oil and reservoir sweep efficiency by stimulation. The major contribution of this paper demonstrates the merits of the field development plan in fractured basement reservoir. The findings of this study can help better understand the fluid flow behavior using the production history profiles and field development scenarios of crystalline basement reservoir of Cuu Long Basin.
Evaluating Climate Change Impacts on Soil Moisture and Groundwater Resources Within a Lake‐Affected Region
Authors: Erler Andre R. , Frey Steven K. , Khader Omar , d'Orgeville Marc , Park Young‐Jin , Hwang Hyoun‐Tae , Lapen David R. , Peltier W. Richard , Sudicky Edward A.
Published: August 2019

The impact of climate change on surface water resources is reasonably well studied. However, the impact on groundwater resources has only been considered by a few studies worldwide. Here we present an analysis of climate change impacts on groundwater resources in a well‐instrumented 6,800‐km2 watershed in the Laurentian Great Lakes Basin. We employ a physics‐based modeling pipeline consisting of an ensemble of high‐resolution regional climate model projections based on the Weather Research and Forecasting model and the fully integrated three‐dimensional hydrologic model HydroGeoSphere. The Weather Research and Forecasting model is run at a resolution as fine as 10 km using two different physics configurations, while HydroGeoSphere simulates the terrestrial hydrosphere at subkilometer scale, from deep groundwater to surface water, including surface water‐groundwater interactions. The two Weather Research and Forecasting model physics configurations exhibit opposite climate change responses in summer precipitation. The hydrologic simulations follow the climate forcing, but due to the memory of the subsurface, differences in summer affect the entire seasonal cycle. In the drier climate scenario groundwater levels and recharge decline, while in the wetter scenario groundwater levels rise (recharge remains unchanged). Soil moisture changes accordingly, but primarily in late summer. It is also shown that the magnitude of climate change impacts on groundwater is strongly modulated by local physiographic features. In particular, regions where the groundwater table is deep (below 2 m; 15% of the area) show a high sensitivity to changes in climate forcing. Furthermore, changes in groundwater levels, recharge, and soil moisture typically occur in the same regions, suggesting potentially compounding impacts.
A New Approach to New Worlds
Authors: Goss Heather
Published: August 2019

This month we look around our solar system—and much farther—as we celebrate AGU’s Centennial.
Great Pacific Garbage Patch Swim Nears Conclusion
Authors: Showstack Randy
Published: August 2019

Long-distance swimmer Ben Lecomte seeks to raise awareness about plastic pollution in the ocean.
Estimation of Field‐Scale Variability in Soil Saturated Hydraulic Conductivity From Rainfall‐Runoff experiments
Authors: Goyal Abhishek , Morbidelli Renato , Flammini Alessia , Corradini Corrado , Govindaraju Rao S.
Published: August 2019

Saturated hydraulic conductivity (Ks) is among the important soil properties that influence the partitioning of rainfall into surface and subsurface waters. Point estimates of Ks are difficult to determine and exhibit large spatial variability in fields. Often, data from field‐scale rainfall‐runoff experiments are utilized to assess the properties of the Ks random field that are required in the use of field‐scale infiltration models. Standard methods of calibration are confounded by nonuniqueness and identifiability problems associated with experimental data. In this study, a new method that employed a field‐averaged infiltration model and Monte Carlo simulations was used to obtain the possible range of distributions of Ks that would describe experimental observations over a field for a rainfall event. A Shannon information‐theoretic approach was subsequently adopted to consolidate the ranges of Ks distributions over multiple rainfall events to yield the best range of Ks distributions. The method was applied to data from several rainfall‐runoff events observed under natural conditions over an experimental field characterized by a silty loam soil and a small surface slope. Results suggest the existence of numerous parameter combinations that could satisfy the experimental observations over a single rainfall event, and high variability of these combinations among different events, thereby providing insights regarding the identifiable space of Ks distributions from individual rainfall experiments. Validation results showed that the method provides a realistic estimate of our ability to quantify the spatial variability of Ks in natural fields from rainfall‐runoff experiments.
Quantifying Uncertainties in Snow Depth Mapping From Structure From Motion Photogrammetry in an Alpine Area
Authors: Goetz Jason , Brenning Alexander
Published: August 2019

Mapping snow conditions in alpine areas is crucial for monitoring local hydrology to support water resource management decisions. Recently, the use of structure‐from‐motion multiview stereo 3‐D reconstruction (or SFM photogrammetry) to derive high‐resolution digital elevation models (DEMs) has become popular for mapping snow depth in alpine areas. In this study, methods for communicating spatial uncertainties in snow depth calculated from SFM‐derived DEMs are presented using a case study in the French Alps. A spatially varying snow depth precision estimate was determined using an error propagation model based on the precision of the acquired SFM DEMs, which was obtained from repeated unmanned aerial vehicle flights. Spatially varying snow depth detection limits were determined using Student'stdistribution. It was found that snow depths as shallow as 1 to 5 cm could be detected with high confidence for most of the study area. Areas of high uncertainties were generally related to where the extent of the ground control coverage did not match in the snow‐on and snow‐off surveys and in areas with higher surface roughness. A map of the snow depth detection threshold was found to be useful for identifying areas with high uncertainties and potential biases in the SFM snow depths, such as errors due to changes in topography between DEM acquisition dates and poor SFM reconstruction.
Amplification of 9p24.1 in diffuse large B-cell lymphoma identifies a unique subset of cases that resemble primary mediastinal large B-cell lymphoma
Authors: Wang Yucai , Wenzl Kerstin , Manske Michelle K. , Asmann Yan W. , Sarangi Vivekananda , Greipp Patricia T. , Krull Jordan E. , Hartert Keenan , He Rong , Feldman Andrew L. , Maurer Matthew J. , Slager Susan L. , Nowakowski Grzegorz S. , Habermann Thomas M. , Witzig Thomas E. , Link Brian K. , Ansell Stephen M. , Cerhan James R. , Novak Anne J.
Published: August 2019

Copy number alterations (CNAs) of 9p24.1 occur frequently in Hodgkin lymphoma, primary mediastinal large B-cell lymphoma (PMBCL), primary central nervous system lymphoma, and primary testicular lymphoma, resulting in overexpression of PD-L1 and sensitivity to PD-1 blockade-based immunotherapy. While 9p24.1 CNA was also reported in diffuse large B-cell lymphoma (DLBCL), little is known about its molecular or clinical significance. In this study, we analyzed the prevalence of 9p24.1 CNA in newly diagnosed DLBCL and examined its association with PD-L1, PD-L2, and JAK2 expression, clinical characteristics, and outcome. We found that 10% of DLBCL cases had CNA of 9p24.1, with 6.5% gains, and 3.5% amplifications. Only the cases with a 9p24.1 amplification had high levels of PD-L1, PD-L2, and JAK2 expression. Gains or amplifications of 9p24.1 were associated with a younger age and the ABC/non-GCB subtype. Compared with DLBCL cases without 9p24.1 CNA, the cases with a 9p24.1 amplification had a trend of better event-free survival. Furthermore, the amplification cases had a gene expression and mutation profile similar to those of PMBCL. Our data suggest that amplification of 9p24.1 identifies a unique subset of DLBCL with clinical and molecular features resembling PMBCL that may be amenable to PD-1 blockade-based immunotherapy.
Therapeutic Effect of pHLIP-mediated CEACAM6 Gene Silencing in Lung Adenocarcinoma
Authors: Son Seung-Myoung , Yun Jieun , Lee Sung-Hoon , Han Hye Sook , Lim Young Hyun , Woo Chang Gok , Lee Ho-Chang , Song Hyung Geun , Gu Young-Mi , Lee Hyun-Jun , Lee Ok-Jun
Published: September 2019

Carcinoembryonic antigen-related cell adhesion molecule 6 (CEACAM6) plays an important role in lung cancer progression. Here, we examined the therapeutic efficacy of CEACAM6 gene silencing using an siRNA delivery platform targeting the acidic tumour microenvironment in a lung adenocarcinoma xenograft mouse model. An siRNA delivery vector was constructed by tethering the peptide nucleic acid form of an siRNA targeting CEACAM6 (siCEACAM6) to a peptide with a low pH-induced transmembrane structure (pHLIP) to transport siRNAs across the plasma membrane. Specific binding of the pHLIP-siCEACAM6 conjugate to A549 lung adenocarcinoma cells at low pH was demonstrated by flow cytometry. A549 cells incubated with pHLIP-siCEACAM6 at an acidic pH showed downregulated expression of endogenous CEACAM6 protein and reduced cell viability. The in vivo tumour-suppressing effects of pHLIP-siCEACAM6 in lung adenocarcinoma were assessed in a xenograft model generated by injecting BALB/c nude mice with A549 cells. pHLIP-siCEACAM6 treatment alone resulted in tumour growth inhibition of up to 35.5%. When combined with cisplatin treatment, pHLIP-siCEACAM6 markedly enhanced tumour growth inhibition by up to 47%. In conclusion, the delivery of siCEACAM6 to lung adenocarcinoma using the pHLIP peptide has therapeutic potential as a unique cancer treatment approach.
Thermal C–O coupling reactions of Ta methylene clusters [TanCH2]+ (n = 1, 4) with O2
Authors: Masubuchi T. , Eckhard J. F. , Goddard G. , Tschurl M. , Heiz U.
Published: August 2019

Cationic tantalum carbenes [TaCH2]+ and [Ta4CH2]+, products of methane dehydrogenation, are reacted with dioxygen in an ion trap. Detected products suggest a formation of value-added molecules originating from C–O coupling reactions.
Room temperature, near-quantitative conversion of glucose into formic acid
Authors: Wang Can , Chen Xi , Qi Man , Wu Jianeng , Gözaydın Gökalp , Yan Ning , Zhong Heng , Jin Fangming
Published: August 2019

Herein, a facile and efficient method was developed to selectively transform glucose into formic acid at room temperature.
Design considerations, modelling, and control of dual‐active full bridge for electric vehicles charging applications
Authors: Jarraya Fatma , Khan Ahmad , Gastli Adel , Ben‐Brahim Lazhar , Hamila Ridha
Published: August 2019

The dual active full bridge (DAFB) is one of the promising isolated DC/DC converter topologies that will play a significant role in the future of electric vehicle (EV) integration in smart grids (SGs). This is due to its inherent soft switching and control simplicity. Therefore, this study presents first the latest developments related to the design of DAFB converter in EV charging technology. It provides a brief discussion of the crucial recommendations regarding the reliability, efficiency, system configuration, EV charger control scheme, battery lifetime, and system materials. Then, it presents a step‐by‐step modelling approach for a non‐ideal DAFB for the purpose of designing its controller. In addition, the model provided by this study includes all non‐idealities due to the high‐frequency (HF) transformer, semiconductor switches, passive components, and digital system delays. Eventually, the proposed system design and analysis was validated by implementing a 6.1 kW prototype on Simulink and Typhoon‐HIL real‐time simulator.
Polycomb proteins as organizers of 3D genome architecture in embryonic stem cells
Authors: Pachano Tomas , Crispatzu Giuliano , Rada-Iglesias Alvaro
Published: August 2019

Polycomb group proteins (PcGs) control the epigenetic and transcriptional state of developmental genes and regulatory elements during mammalian embryogenesis. Moreover, PcGs can also contribute to 3D genome organization, adding an additional layer of complexity to their regulatory functions. Understanding the mechanistic basis and the dynamics of PcG-dependent chromatin structures will help us untangle the full complexity of PcG function during development. Since most studies concerning the 3D organization of PcG-bound chromatin in mammals have been performed in embryonic stem cells (ESCs), here we will focus on this cell type characterized by its unique self-renewal and pluripotency properties. More specifically, we will highlight recent findings and discuss open questions regarding how PcG-dependent changes in 3D chromatin architecture control gene expression, cellular identity and differentiation potential in ESCs. We believe that this can serve to illustrate the diverse regulatory mechanisms by which PcG proteins control the proper execution of gene expression programs during mammalian embryogenesis.
Phylogenetic tree-based microbiome association test
Authors: Kim Kang Jin , Park Jaehyun , Park Sang-Chul , Won Sungho
Published: September 2019

Motivation

Ecological patterns of the human microbiota exhibit high inter-subject variation, with few operational taxonomic units (OTUs) shared across individuals. To overcome these issues, non-parametric approaches, such as the Mann–Whitney U-test and Wilcoxon rank-sum test, have often been used to identify OTUs associated with host diseases. However, these approaches only use the ranks of observed relative abundances, leading to information loss, and are associated with high false-negative rates. In this study, we propose a phylogenetic tree-based microbiome association test (TMAT) to analyze the associations between microbiome OTU abundances and disease phenotypes. Phylogenetic trees illustrate patterns of similarity among different OTUs, and TMAT provides an efficient method for utilizing such information for association analyses. The proposed TMAT provides test statistics for each node, which are combined to identify mutations associated with host diseases.

Results

Power estimates of TMAT were compared with existing methods using extensive simulations based on real absolute abundances. Simulation studies showed that TMAT preserves the nominal type-1 error rate, and estimates of its statistical power generally outperformed existing methods in the considered scenarios. Furthermore, TMAT can be used to detect phylogenetic mutations associated with host diseases, providing more in-depth insight into bacterial pathology.

Availability and implementation

The 16S rRNA amplicon sequencing metagenomics datasets for colorectal carcinoma and myalgic encephalomyelitis/chronic fatigue syndrome are available from the European Nucleotide Archive (ENA) database under project accession number PRJEB6070 and PRJEB13092, respectively. TMAT was implemented in the R package. Detailed information is available at http://healthstat.snu.ac.kr/software/tmat.

Supplementary information

Supplementary data are available at Bioinformatics online.
Self-reported Neurocognitive Impairment in People Living With Human Immunodeficiency Virus (HIV): Characterizing Clusters of Patients With Similar Changes in Self-reported Neurocognitive Impairment, 2013–2017, in the Swiss HIV Cohort Study
Authors: Kusejko Katharina , Salazar-Vizcaya Luisa , Braun Dominique L , Tarr Philip E , Bernasconi Enos , Doco-Lecompte Thanh , Cavassini Matthias , Schmid Patrick , Du Pasquier Renaud , Hauser Christoph , Günthard Huldrych F , Kouyos Roger D
Published: September 2019

Background

Self-reported neurocognitive impairment (SRNI) in people living with human immunodeficiency virus type 1 (HIV-1) infection is frequent. We use longitudinal information on SRNI in the Swiss HIV Cohort Study (SHCS) to identify and characterize groups of patients with persisting SRNI over time.

Methods

We included all SHCS patients who were assessed for SRNI during at least 5 visits spanning at least 2.5 years in 2013–2017. We first compared patients with SRNI to those without SRNI over the whole study period. Second, we used a hierarchical cluster algorithm to identify groups of patients with similar changes of SRNI over time. In both analyses, we studied clinical and demographic factors potentially influencing SRNI.

Results

In total, 79 683 questionnaires of 11 029 patients contained information about SRNI, and 8545 of 11 029 (77.5%) patients had longitudinal information. The overall percentage of patients with SRNI decreased from 19.6% in 2013 to 10.7% in 2017. Compared to patients in the cluster with low-level SRNI over time, patients in the cluster with high-level persisting SRNI more often had a prior opportunistic infection of the central nervous system (CNS) (odds ratio [OR], 3.7; P < .001), imperfect adherence to antiretroviral therapy (ART) (OR, 2.8; P < .001), and depression (OR, 1.9; P < .001).

Conclusions

Although overall SRNI is decreasing in the SHCS, there is a group of patients with persisting SRNI over time. Past opportunistic infections of the CNS, imperfect adherence to ART, and depression were associated most with persisting SRNI. Patients with these characteristics should be preferentially tested for neurocognitive impairment.

Although overall self-reported neurocognitive impairment (SRNI) is decreasing in the Swiss HIV Cohort Study, there is a group of patients with persisting SRNI over time, characterized by more past opportunistic infections of the central nervous system, imperfect adherence to antiretroviral therapy, and depression.
Emerging Evidence for Infectious Causes of Cancer in the United States
Authors: Brown Heidi E , Dennis Leslie K , Lauro Priscilla , Jain Purva , Pelley Erin , Oren Eyal
Published: August 2019

Worldwide, infectious agents currently contribute to an estimated 15% of new cancer cases. Most of these (92%, or 2 million new cancer cases) are attributable to 4 infectious agents: Helicobacter pylori, human papillomavirus, and hepatitis B and C viruses. A better understanding of how infectious agents relate to the US cancer burden may assist new diagnostic and treatment efforts. We review US-specific crude mortality rates from infection-associated cancers and describe temporal and spatial trends since 1999. We review the US-specific evidence for infection-cancer associations by reporting available estimates for attributable fractions for the infection-cancer associations. Death due to cancers with established infectious associations varies geographically, but estimates for the US attributable fraction are limited to a few observational studies. To describe the burden of infection-associated cancer in the United States, additional observational studies are necessary to estimate the prevalence of infection nationally and within subpopulations. As infectious associations emerge to explain cancer etiologies, new opportunities and challenges to reducing the burden arise. Improved estimates for the United States would help target interventions to higher-risk subpopulations.
International Commissions of Inquiry in a Networked World: Unveiling the Roles of Diasporas through an Eritrean Case Study
Authors: van den Herik Larissa , van Reisen Mirjam
Published: September 2019

International Commissions of Inquiry (COIs) have become important components of the human rights fact-finding, accountability and transitional justice architecture. The core task of COIs is to investigate international crises and construe what happened on the ground. The increasing tendency of states under scrutiny to refuse territorial access frustrates COI performance. It leaves COIs with no option but to operate from outside the state. COIs have developed various strategies to overcome the impediment of the uncooperative state, including the use of satellite imagery, conducting extraterritorial public hearings, interviewing individuals in the territory through Skype and other media as well as collecting accounts from individuals in the diaspora. This article focuses on the engagement of COIs with the diaspora. It presents diasporas as actors that may have considerable significance for COIs in a variety of ways, beyond sharing information. The article unveils the distinct roles that diasporic actors may entertain vis-à-vis international inquiries, as subjects in need of protection, information providers, and audience and mobilization forces. Looking at the COI for Eritrea, the article tests how these different roles play out in practice and how they interrelate. It thus sheds light on the capacity of COIs to make a difference extraterritorially for individuals in the diaspora, and on the capacity of diasporic actors to influence COI findings and shape follow up. The Eritrean COI experience illustrates that a purely instrumental approach towards diasporas – one which only regards diasporas as sources of information and which fails to protect extraterritorially or tap into the greater potential of diaspora mobilization – lessens COI effectivity for broader human rights and transitional justice purposes.
Cooperative action of APJ and α1A-adrenergic receptor in vascular smooth muscle cells induces vasoconstriction
Authors: Nagano Katsumasa , Kwon Chulwon , Ishida Junji , Hashimoto Tatsuo , Kim Jun-Dal , Kishikawa Nana , Murao Mei , Kimura Kenjiro , Kasuya Yoshitoshi , Kimura Sadao , Chen Yi-Ching , Tsuchimochi Hirotsugu , Shirai Mikiyasu , Pearson James T , Fukamizu Akiyoshi
Published: September 2019

The apelin receptor (APJ), a receptor for apelin and elabela/apela, induces vasodilation and vasoconstriction in blood vessels. However, the prolonged effects of increased APJ-mediated signalling, involving vasoconstriction, in smooth muscle cells have not been fully characterized. Here, we investigated the vasoactive effects of APJ gain of function under the control of the smooth muscle actin (SMA) gene promoter in mice. Transgenic overexpression of APJ (SMA-APJ) conferred sensitivity to blood pressure and vascular contraction induced by apelin administration in vivo. Interestingly, ex vivo experiments showed that apelin markedly increased the vasoconstriction of isolated aorta induced by noradrenaline (NA), an agonist for α- and β-adrenergic receptors, or phenylephrine, a specific agonist for α1-adrenergic receptor (α1-AR). In addition, intracellular calcium influx was augmented by apelin with NA in HEK293T cells expressing APJ and α1A-AR. To examine the cooperative action of APJ and α1A-AR in the regulation of vasoconstriction, we developed α1A-AR deficient mice using a genome-editing technique, and then established SMA-APJ/α1A-AR-KO mice. In the latter mouse line, aortic vasoconstriction induced by a specific agonist for α1A-AR, A-61603, were significantly less than in SMA-APJ mice. These results suggest that the APJ-enhanced response requires α1A-AR to contract vessels coordinately.
Effects of Five Host Plant Species on the Life History and Population Growth Parameters of Myzus persicae (Hemiptera: Aphididae)
Authors: Hong Feng , Han Hong-Liang , Pu Po , Wei Dong , Wang Jia , Liu Yinghong
Published: September 2019

The green peach aphid, Myzus persicae Sulzer (Hemiptera: Aphididae), is an important agricultural pest with a wide range of host plants. To study effects of host species on the life history traits of M. persicae, aphids were individually reared on five host plants: Brassica campestris L. (Brassicales: Brassicaceae), Capsicum annuum L. (Tubiflorae: Solanaceae), Nicotiana tabacum L. (Tubiflorae: Solanaceae), Raphanus sativus L. (Brassicales: Brassicaceae), and Vicia faba L. (Rosales: Leguminosae). TWOSEX-MSchart software was used for the statistical analysis according to the age-stage, two-sex life table theory. The results showed that the shortest preadult stage and adult/total prereproductive period of M. persicae were 6.48, 0.19, and 6.67 d on V. faba, respectively. While the adult and total longevity of M. persicae on R. sativus (25.00 and 31.62 d) and N. tabacum (24.40 and 30.56 d) were significantly longer than that on the other three hosts, as was the reproductive period. The fecundity of M. persicae on R. sativus (80.83 nymphs per female), N. tabacum (71.72 nymphs per female), and V. faba (70.39 nymphs per female) was also greater than that on B. campestris and C. annuum. It was demonstrated that V. faba, R. sativus, and N. tabacum were more suitable plants for the growth of M. persicae exhibiting a shorter preadult stage, longer longevity, and greater fecundity than the remaining two species, as confirmed by the higher intrinsic rate of increase and net reproductive rate.
A Process for Decomposing Total Survey Error in Probability and Nonprobability Surveys: A Case Study Comparing Health Statistics in US Internet Panels
Authors: Unangst Jennifer , Amaya Ashley E , Sanders Herschel L , Howard Jennifer , Ferrell Abigail , Karon Sarita , Dever Jill A
Published: August 2019

As survey methods evolve, researchers require a comprehensive understanding of the error sources in their data. Comparative studies, which assess differences between the estimates from emerging survey methods and those from traditional surveys, are a popular tool for evaluating total error; however, they do not provide insight on the contributing error sources themselves. The Total Survey Error (TSE) framework is a natural fit for evaluations that examine survey error components across multiple data sources. In this article, we present a case study that demonstrates how the TSE framework can support both qualitative and quantitative evaluations comparing probability and nonprobability surveys. Our case study focuses on five internet panels that are intended to represent the US population and are used to measure health statistics. For these panels, we analyze the total survey error in two ways: (1) using a qualitative assessment that describes how panel construction and management methods may introduce error and (2) using a quantitative assessment that estimates and partitions the total error for two probability-based panels into coverage error and nonresponse error. This work can serve as a “proof of concept” for how the TSE framework may be applied to understand and compare the error structure of probability and nonprobability surveys. For those working specifically with internet panels, our findings will further provide an example of how researchers may choose the panel option best suited to their study aims and help vendors prioritize areas of improvement.
GBTrans: a commensal search for radio pulses with the Green Bank 20-m telescope
Authors: Golpayegani Golnoosh , Lorimer Duncan R , Ellingson Steven W , Agarwal Devansh , Young Olivia , Ghigo Frank , Prestage Richard , Rajwade Kaustubh , McLaughlin Maura A , Mingyar Michael
Published: September 2019

We describe GBTrans, a real-time search system designed to find fast radio bursts (FRBs) using the 20-m radio telescope at the Green Bank Observatory. The telescope has been part of the Skynet educational programme since 2015. We give details of the observing system and report on the non-detection of FRBs from a total observing time of 503 d. Single pulses from four known pulsars were detected as part of the commensal observing. The system is sensitive enough to detect approximately half of all currently known FRBs and we estimate that our survey probed redshifts out to about 0.3 corresponding to an effective survey volume of around 124 000 Mpc3. Modelling the FRB rate as a function of fluence, ${\cal F}$, as a power law with ${\cal F}^{-\alpha }$, we constrain the index α < 2.5 at the 90 per cent confidence level. We discuss the implications of this result in the context of constraints from other FRB surveys.
Ingredients for solar-like systems: protostar IRAS 16293-2422 B versus comet 67P/Churyumov–Gerasimenko
Authors: Drozdovskaya Maria N , van Dishoeck Ewine F , Rubin Martin , Jørgensen Jes K , Altwegg Kathrin
Published: September 2019

Our modern day Solar System has 4.6 × 109 yr of evolution behind it with just a few relics of its birth conditions remaining. Comets are thought to be some of the most pristine tracers of the initial ingredients that were combined to produce the Earth and the other planets. Other low-mass protostars may be analogous to our proto-Sun and hence, could be used to study the building blocks necessary to form Solar-like systems. This study tests this idea on the basis of new high sensitivity, high spatial resolution ALMA data on the protoplanetary disc-scales (∼70 au) of IRAS 16293-2422 and the bulk composition of comet 67P/Churyumov-Gerasimenko, as determined for the first time with the unique in situ monitoring carried out by Rosetta. The comparative analysis of the observations from the Protostellar Interferometric Line Survey (PILS) and the measurements made with Rosetta Orbiter Spectrometer for Ion and Neutral Analysis (ROSINA) shows that the relative abundances of CHO-, N-, and S-bearing molecules correlate, with some scatter, between protostellar and cometary data. A tentative correlation is seen for the first time for P- and Cl-bearing compounds. The results imply that the volatile composition of cometesimals and planetesimals is partially inherited from the pre- and protostellar phases of evolution.
A resting-state network comparison of combat-related PTSD with combat-exposed and civilian controls
Authors: Vanasse Thomas J , Franklin Crystal , Salinas Felipe S , Ramage Amy E , Calhoun Vince D , Robinson Paul C , Kok Mitchell , Peterson Alan L , Mintz Jim , Litz Brett T , Young-McCaughan Stacey , Resick Patricia A , Fox Peter T ,   STRONG STAR Consortium
Published: August 2019

Resting-state functional connectivity (rsFC) is an emerging means of understanding the neurobiology of combat-related post-traumatic stress disorder (PTSD). However, most rsFC studies to date have limited focus to cognitively related intrinsic connectivity networks (ICNs), have not applied data-driven methodologies or have disregarded the effect of combat exposure. In this study, we predicted that group independent component analysis (GICA) would reveal group-wise differences in rsFC across 50 active duty service members with PTSD, 28 combat-exposed controls (CEC), and 25 civilian controls without trauma exposure (CC). Intranetwork connectivity differences were identified across 11 ICNs, yet combat-exposed groups were indistinguishable in PTSD vs CEC contrasts. Both PTSD and CEC demonstrated anatomically diffuse differences in the Auditory Vigilance and Sensorimotor networks compared to CC. However, intranetwork connectivity in a subset of three regions was associated with PTSD symptom severity among executive (left insula; ventral anterior cingulate) and right Fronto-Parietal (perigenual cingulate) networks. Furthermore, we found that increased temporal synchronization among visuospatial and sensorimotor networks was associated with worse avoidance symptoms in PTSD. Longitudinal neuroimaging studies in combat-exposed cohorts can further parse PTSD-related, combat stress-related or adaptive rsFC changes ensuing from combat.
A phylogenomic framework for Vetigastropoda (Mollusca)
Authors: Cunha Tauana Junqueira , Giribet Gonzalo
Published: August 2019

Abalones, turban snails, top snails, keyhole limpets and slit shells are just some of the diverse marine Vetigastropoda. With major lineages having ancient divergences in the Paleozoic Era, basal nodes in the phylogeny have been largely unresolved. Here we present the first genomic-scale dataset focused on vetigastropods, including a comprehensive sampling of taxa with all superfamilies and about half of the extant families (41 new transcriptomes, 49 total ingroup terminals). Our recovered topology is congruent among inference methods for the majority of nodes, and differs from previous studies, in which long branch attraction artifacts seem to be pervasive. The first three divergences sequentially separate Pleurotomarioidea, Seguenzioidea and Haliotoidea from remaining vetigastropods. Fissurelloidea is sister group to Scissurelloidea, Lepetodriloidea and Lepetelloidea, which all together are the sister group to Trochoidea. A methodological discordance exists in the position of Haliotidae and Fissurellidae, possibly due to a compounded effect of small sample bias derived from gene-wide partitioning. Dense sampling of trochoids and fissurellids also provides a backbone for family and subfamily-level relationships, with Tegulidae not monophyletic.