bluuebunny/crossref_metadata_2025_split huggingface dataset:
Scale dependence in the phylogenetic relatedness of alien and native taxa
Authors: McGrannachan Chris M , Horner Gillis J , McGeoch Melodie A 
Published: August 2020

AbstractAimsDarwin’s naturalization hypothesis proposes that successfully established alien species are less closely related to native species due to differences in their ecological niches. Studies have provided support both for and against this hypothesis. One reason for this is the tendency for phylogenetic clustering between aliens and natives at broad spatial scales with overdispersion at fine scales. However, little is known about how the phylogenetic relatedness of alien species alters the phylogenetic structure of the communities they invade, and at which spatial scales effects may manifest. Here, we examine if invaded understorey plant communities, i.e. containing both native and alien taxa, are phylogenetically clustered or overdispersed, how relatedness changes with spatial scale and how aliens affect phylogenetic patterns in understorey communities.MethodsField surveys were conducted in dry forest understorey communities in south-east Australia at five spatial scales (1, 20, 500, 1500 and 4500 m2). Standardized effect sizes of two metrics were used to quantify phylogenetic relatedness between communities and their alien and native subcommunities, and to examine how phylogenetic patterns change with spatial scale: (i) mean pairwise distance and (ii) mean nearest taxon distance (MNTD).Important FindingsAliens were closely related to each other, and this relatedness tended to increase with scale. Native species and the full community exhibited either no clear pattern of relatedness with increasing spatial scale or were no different from random. At intermediate spatial scales (20–500 m2), the whole community tended towards random whereas the natives were strongly overdispersed and the alien subcommunity strongly clustered. This suggests that invasion by closely related aliens shifts community phylogenetic structure from overdispersed towards random. Aliens and natives were distantly related across spatial scales, supporting Darwin’s naturalization hypothesis, but only when phylogenetic distance was quantified as MNTD. Phylogenetic dissimilarity between aliens and natives increased with spatial scale, counter to expected patterns. Our findings suggest that the strong phylogenetic clustering of aliens is driven by human-mediated introductions involving closely related taxa that can establish and spread successfully. Unexpected scale-dependent patterns of phylogenetic relatedness may result from stochastic processes such as fire and dispersal events and suggest that competition and habitat filtering do not exclusively dominate phylogenetic relationships at fine and coarse spatial scales, respectively. Distinguishing between metrics that focus on different evolutionary depths is important, as different metrics can exhibit different scale-dependent patterns.
Analyses of local control and survival after stereotactic body radiotherapy for pulmonary oligometastases from colorectal adenocarcinoma
Authors: Yamamoto Takaya , Niibe Yuzuru , Matsumoto Yasuo , Onishi Hiroshi , Aoki Masahiko , Nishikawa Atsushi , Oh Ryoong-Jin , Shintani Takashi , Yahara Katsuya , Ozaki Masatoki , Manabe Yoshihiko , Jingu Keiichi 
Published: August 2020

Abstract
This study is a subset analysis of a retrospective multicenter study performed in Japan and its purpose was to investigate the effectiveness of stereotactic body radiotherapy (SBRT) for pulmonary oligometastases from colorectal cancer. Local control (LC), freedom from further metastases, relapse-free survival and overall survival (OS) after SBRT were retrospectively analyzed. The Kaplan–Meier method was used to estimate lifetime data and the log-rank test was performed as univariate analyses. The Cox proportional hazards model was applied in multivariate analyses. Data for 330 patients with 371 tumors were used for analyses. The median follow-up period was 25.0 months. The 3-year LC, freedom from further metastases, relapse-free survival and OS rates were 64.9, 34.9, 24.9 and 63.4%, respectively. The results of multivariate analyses showed that a higher LC rate was associated with no history of local therapy for oligometastases (P = 0.01), SBRT without concurrent chemotherapy (P &lt; 0.01), type B calculation algorithm (P &lt; 0.01) and higher biological effective radiation doses (≥115 Gy, P = 0.04). A longer OS was associated with no history of local therapy for oligometastases (P = 0.04), a more recent period of SBRT (2010–15, P = 0.02), tumor located in the upper or middle lobe (P &lt; 0.01) and higher biological effective radiation doses (≥115 Gy, P = 0.01). In conclusion, OS after SBRT was good, but LC rate was relatively low. The use of high biological effective radiation doses can improve both LC and OS outcomes.
Building on a Sequential Mixed-Mode Research Design in the Monitoring the Future Study
Authors: Patrick Megan E , Couper Mick P , Jang Bohyun Joy , Laetz Virginia , Schulenberg John E , O’Malley Patrick M , Bachman Jerald , Johnston Lloyd D 
Published: August 2020

AbstractGiven the promise of the web push plus e-mail survey design for providing cost-effective and high-quality data (Patrick et al. 2018, 2019) as an alternative to a paper-and-pencil mailed survey design for the longitudinal Monitoring the Future (MTF) study, the current study sought to further enhance the web push condition. The MTF sample is based on US nationally representative samples of 12th grade students surveyed annually. The MTF control group for the current study included participants who completed the in-school baseline survey in the 12th grade and were selected to participate in their first follow-up survey in 2017 via mailed surveys (N = 1,222). A supplementary sample (N = ∼2,450) was assigned to one of the two sequential mixed-mode conditions. Those in condition 1 (N = 1,198), or mail push, were invited to complete mailed surveys and later given a web survey option. Those in condition 2 (N = 1,173), or enhanced web push, were invited to complete a web survey (the same as in the 2014 study, but with the addition of text messages and quick response (QR) codes and the web survey was optimized for mobile devices) and then later given a mailed survey option. Research aims were to examine response rates across conditions, as well as how responses were distributed across mode (paper, web), devices (computer, smartphone, table), and method of accessing the web survey (hand-entered URL, QR code, e-mail link, SMS link). Response rates differed significantly: the MTF control group was 34.2 percent, mail push was 35.4 percent, and enhanced web push was 42.05 percent. The higher response rate in the enhanced web push condition suggests that the additional strategies were effective at bringing in more respondents. Key estimates produced by the enhanced web push condition did not differ from those of the MTF control group.
Extended X-ray emission from the z = 4.26 radio galaxy 4C 63.20
Authors: Napier Kate , Foord Adi , Gallo Elena , Ghisellini Gabriele , Hodges-Kluck Edmund , Wu Jianfeng , Haardt Francesco , Ciardi Benedetta 
Published: August 2020

ABSTRACT
We report on deep Chandra X-ray Telescope imaging observations of 4C 63.20, one of the few known radio galaxies at z &gt; 3.5. The X-ray counterpart is resolved into a core plus two off-nuclear sources that (combined) account for close to 30 per cent of the total X-ray flux. Their morphology and orientation are consistent with a diffuse, lobe-like nature, albeit compact hotspots cannot be ruled out. The broad-band spectral energy distribution of 4C 63.20 can be reproduced with a jet model where the majority of the radio flux can be ascribed to synchrotron emission from the hotspots, whereas the (non-nuclear) X-ray emission is produced via inverse Compton (IC) off of cosmic microwave background (CMB) photons within the extended lobes. This scenario is broadly consistent with the expectation from highly magnetized lobes in a hotter CMB, and supports the view that IC/CMB may quench less extreme radio lobes at high redshifts.
Census and classification of low-surface-brightness structures in nearby early-type galaxies from the MATLAS survey
Authors: Bílek Michal , Duc Pierre-Alain , Cuillandre Jean-Charles , Gwyn Stephen , Cappellari Michele , Bekaert David V , Bonfini Paolo , Bitsakis Theodoros , Paudel Sanjaya , Krajnović Davor , Durrell Patrick R , Marleau Francine 
Published: August 2020

ABSTRACT
The morphology of galaxies gives essential constraints on the models of galaxy evolution. The morphology of the features in the low-surface-brightness (LSB) regions of galaxies has not been fully explored yet because of observational difficulties. Here we present the results of our visual inspections of very deep images of a large volume-limited sample of 177 nearby massive early-type galaxies from the MATLAS survey. The images reach a surface-brightness limit of 28.5–29 mag arcsec−2 in the g′ band. Using a dedicated navigation tool and questionnaire, we looked for structures at the outskirts of the galaxies such as tidal shells, streams, tails, disturbed outer isophotes, or peripheral star-forming discs, and simultaneously noted the presence of contaminating sources, such as Galactic cirrus. We also inspected internal substructures such as bars and dust lanes. We discuss the reliability of this visual classification investigating the variety of answers made by the participants. We present the incidence of these structures and the trends of the incidence with the mass of the host galaxy and the density of its environment. We find an incidence of shells, stream, and tails of approximately 15 per cent, about the same for each category. For galaxies with masses over 1011 M⊙, the incidence of shells and streams increases about 1.7 times. We also note a strong unexpected anticorrelation of the incidence of Galactic cirrus with the environment density of the target galaxy. Correlations with other properties of the galaxies, and comparisons to model predictions, will be presented in future papers.
Mapping the ionized gas of the metal-poor H ii galaxy PHL 293B with MEGARA
Authors: Kehrig C , Iglesias-Páramo J , Vílchez J M , Gil de Paz A , Duarte Puertas S , Pérez-Montero E , Díaz A I , Gallego J , Carrasco E , Cardiel N , García-Vargas M L , Castillo-Morales A , Cedazo R , Gómez-Álvarez P , Martínez-Delgado I , Pascual S , Pérez-Calpena A 
Published: August 2020

ABSTRACT
Here we report the first spatially resolved spectroscopic study for the galaxy PHL 293B using the high-resolution GTC/MEGARA integral field unit (IFU). PHL 293B is a local, extremely metal-poor, high ionization galaxy. This makes PHL 293B an excellent analogue for galaxies in the early Universe. The MEGARA aperture (∼ 12.5 arcsec × 11.3 arcsec) covers the entire PHL 293B main body and its far-reaching ionized gas. We created and discussed maps of all relevant emission lines, line ratios, and physical–chemical properties of the ionized ISM. The narrow emission gas appears to be ionized mainly by massive stars according to the observed diagnostic line ratios, regardless of the position across the MEGARA aperture. We detected low intensity broad emission components and blueshifted absorptions in the Balmer lines (H α,H β) which are located in the brightest zone of the galaxy ISM. A chemically homogeneity, across hundreds of parsecs, is observed in O/H. We take the oxygen abundance 12+log (O/H) = 7.64 ± 0.06 derived from the PHL 293B integrated spectrum as the representative metallicity for the galaxy. Our IFU data reveal for the first time that the nebular He iiλ4686 emission from PHL 293B is spatially extended and coincident with the ionizing stellar cluster, and allow us to compute its absolute He ii ionizing photon flux. Wolf-Rayet bumps are not detected excluding therefore Wolf-Rayet stars as the main He ii excitation source. The origin of the nebular He iiλ4686 is discussed.
CCCP and MENeaCS: (updated) weak-lensing masses for 100 galaxy clusters
Authors: Herbonnet Ricardo , Sifón Cristóbal , Hoekstra Henk , Bahé Yannick , van der Burg Remco F J , Melin Jean-Baptiste , von der Linden Anja , Sand David , Kay Scott , Barnes David 
Published: August 2020

ABSTRACT
Large area surveys continue to increase the samples of galaxy clusters that can be used to constrain cosmological parameters, provided that the masses of the clusters are measured robustly. To improve the calibration of cluster masses using weak gravitational lensing we present new results for 48 clusters at 0.05 &lt; z &lt; 0.15, observed as part of the Multi Epoch Nearby Cluster Survey, and re-evaluate the mass estimates for 52 clusters from the Canadian Cluster Comparison Project. Updated high-fidelity photometric redshift catalogues of reference deep fields are used in combination with advances in shape measurements and state-of-the-art cluster simulations, yielding an average systematic uncertainty in the lensing signal below 5 per cent, similar to the statistical uncertainty for our cluster sample. We derive a scaling relation with Planck measurements for the full sample and find a bias in the Planck masses of 1 − b = 0.84 ± 0.04 (stat) ±0.05 (syst). We find no statistically significant trend of the mass bias with redshift or cluster mass, but find that different selections could change the bias by up to 0.07. We find a gas fraction of 0.139 ± 0.014 (stat) for eight relaxed clusters in our sample, which can also be used to infer cosmological parameters.
Transcriptional signatures in histologic structures within glioblastoma tumors may predict personalized drug sensitivity and survival
Authors: Kersch Cymon N , Claunch Cheryl J , Ambady Prakash , Bucher Elmar , Schwartz Daniel L , Barajas Ramon F , Iliff Jeffrey J , Risom Tyler , Heiser Laura , Muldoon Leslie L , Korkola James E , Gray Joe W , Neuwelt Edward A 
Published: August 2020

Abstract

Background
Glioblastoma is a rapidly fatal brain cancer that exhibits extensive intra- and intertumoral heterogeneity. Improving survival will require the development of personalized treatment strategies that can stratify tumors into subtypes that differ in therapeutic vulnerability and outcomes. Glioblastoma stratification has been hampered by intratumoral heterogeneity, limiting our ability to compare tumors in a consistent manner. Here, we develop methods that mitigate the impact of intratumoral heterogeneity on transcriptomic-based patient stratification.

Methods
We accessed open-source transcriptional profiles of histological structures from 34 human glioblastomas from the Ivy Glioblastoma Atlas Project. Principal component and correlation network analyses were performed to assess sample inter-relationships. Gene set enrichment analysis was used to identify enriched biological processes and classify glioblastoma subtype. For survival models, Cox proportional hazards regression was utilized. Transcriptional profiles from 156 human glioblastomas were accessed from The Cancer Genome Atlas to externally validate the survival model.

Results
We showed that intratumoral histologic architecture influences tumor classification when assessing established subtyping and prognostic gene signatures, and that indiscriminate sampling can produce misleading results. We identified the cellular tumor as a glioblastoma structure that can be targeted for transcriptional analysis to more accurately stratify patients by subtype and prognosis. Based on expression from cellular tumor, we created an improved risk stratification gene signature.

Conclusions
Our results highlight that biomarker performance for diagnostics, prognostics, and prediction of therapeutic response can be improved by analyzing transcriptional profiles in pure cellular tumor, which is a critical step toward developing personalized treatment for glioblastoma.
Telemedicine in rheumatology: a reliable approach beyond the pandemic
Authors: Cavagna Lorenzo , Zanframundo Giovanni , Codullo Veronica , Pisu Maria Grazia , Caporali Roberto , Montecucco Carlomaurizio 
Published: August 2020

Abstract

Objectives
The SARS-CoV-2 outbreak has imposed considerable restrictions on people’s mobility, which affects the referral of chronically ill patients to health care structures. The emerging need for alternative ways to follow these patients up is leading to a wide adoption of telemedicine. We aimed to evaluate the feasibility of this approach for our cohort of patients with CTDs, investigating their attitude to adopting telemedicine, even after the pandemic.

Methods
We conducted a telephonic survey among consecutive patients referred to our CTD outpatients’ clinic, evaluating their capability and propensity for adopting telemedicine and whether they would prefer it over face-to-face evaluation. Demographical and occupational factors were also collected, and their influence on the answers has been evaluated by a multivariate analysis.

Results
A total of 175 patients answered our survey (M/F = 28/147), with a median age of 62.5 years [interquartile range (IQR) 53–73]. About 80% of patients owned a device allowing video-calls, and 86% would be able to perform a tele-visit, either alone (50%) or with the help of a relative (36%). Telemedicine was considered acceptable by 78% of patients and 61% would prefer it. Distance from the hospital and patient’s educational level were the strongest predictive factors for the acceptance of telemedicine (P &lt; 0.05), whereas age only affected the mastering of required skills (P &lt; 0.001).

Conclusion
Telemedicine is a viable approach to be considered for routine follow-up of chronic patients, even beyond the pandemic. Our data showed that older patients would be willing to use this approach, although a proper guide for them would be required.
Genome-wide association studies of callus differentiation for the desert tree,Populus euphratica
Authors: Zhang Qianru , Su Zhifang , Guo Yunqian , Zhang Shilong , Jiang Libo , Wu Rongling 
Published: August 2020

AbstractCallus differentiation is a key developmental process in plant regeneration from cells. A better understanding of the genetic architecture of callus differentiation timing can help improve tissue transformation and the efficiency of artificial propagation. In this study, we investigated genotypic variation in callus differentiation capacity among 297 diverse P. euphratica trees sampled from a natural population. We employed a genome-wide association study (GWAS) of binary and growth-based parameters to identify loci and characterize the genetic architecture and genetic network underlying regulation of callus differentiation in P. euphratica. The results of this GWAS experiment suggested potential associations controlling whether the callus could differentiate and the process of callus differentiation. We identified multiple significant quantitative trait loci (QTLs), including the genes LOG1 and LOG7 and a locus containing WOX1. We reconstructed a genetic network that visualizes how each QTL interacts uniquely with other variants, and several core QTLs were detected that are involved in the degree of callus differentiation, providing potential targets for selection. This study represents one of the first to identify genetic variants affecting callus differentiation in a forest tree. Our results suggest that callus differentiation may be a typical qualitative-quantitative trait controlled by a major gene as well as polygenes across the genome of P. euphratica. This GWAS will help to design more complex and specific molecular tools for systematically manipulating organ regeneration.
Point-of-Care Lung Ultrasound for Detecting Severe Presentations of Coronavirus Disease 2019 in the Emergency Department: A Retrospective Analysis
Authors: Favot Mark , Malik Adrienne , Rowland Jonathan , Haber Brian , Ehrman Robert , Harrison Nicholas 
Published: August 2020

Objectives:
Analyze the diagnostic test characteristics of point-of-care lung ultrasound for patients suspected to have novel coronavirus disease 2019.

Design:
Retrospective cohort.

Setting:
Two emergency departments in Detroit, Michigan, United States, during a local coronavirus disease 2019 outbreak (March 2020 to April 2020).

Patients:
Emergency department patients receiving lung ultrasound for clinical suspicion of coronavirus disease 2019 during the study period.

Interventions:
None, observational analysis only.

Measurements and Main Results:
By a reference standard of serial reverse transcriptase-polymerase chain reactions, 42 patients were coronavirus disease 2019 positive, 16 negative, and eight untested (test results lost, died prior to testing, and/or did not meet hospital guidelines for rationing of reverse transcriptase-polymerase chain reaction tests). Thirty-three percent, 44%, 38%, and 17% had mortality, ICU admission, intubation, and venous or arterial thromboembolism, respectively. Receiver operating characteristics, area under the curve, sensitivity, and specificity with 95% CIs were calculated for five lung ultrasound patterns coded by a blinded reviewer and chest radiograph. Chest radiograph had area under the curve = 0.66 (95% CI, 0.54–0.79), 74% sensitivity (95% CI, 48–93%), and 53% specificity (95% CI, 32–75%). Two lung ultrasound patterns had a statistically significant area under the curve: symmetric bilateral pulmonary edema (area under the curve, 0.57; 95% CI, 0.50–0.64), and a nondependent bilateral pulmonary edema pattern (edema in superior lung ≥ inferior lung and no pleural effusion; area under the curve, 0.73; 95% CI, 0.68–0.90). Chest radiograph plus the nondependent bilateral pulmonary edema pattern showed a statistically improved area under the curve (0.80; 95% CI, 0.68–0.90) compared to either alone, but at the ideal cutoff had sensitivity and specificity equivalent to nondependent bilateral pulmonary edema only (69% and 77%, respectively). The strongest combination of clinical, chest radiograph, and lung ultrasound factors for diagnosis was nondependent bilateral pulmonary edema pattern with temperature and oxygen saturation (area under the curve, 0.86; 95% CI, 0.76–0.94; sensitivity = 77% [58–93%]; specificity = 76% [53–94%] at the ideal cutoff), which was superior to chest radiograph alone.

Conclusions:
Lung ultrasound diagnosed severe presentations of coronavirus disease 2019 with similar sensitivity to chest radiograph, CT, and reverse transcriptase-polymerase chain reaction (on first testing) and improved specificity compared to chest radiograph. Diagnostically useful lung ultrasound patterns differed from those hypothesized by previous, nonanalytical, reports (case series and expert opinion), and should be evaluated in a rigorous prospective study.