bluuebunny/crossref_metadata_2025 huggingface dataset:
Feasibility of energy-resolved dose imaging technique in pencil beam scanning mode
Authors: Alaka B G , Bentefour El H , Chirvase Cezarina , Samuel Deepak , Teo Boon-Keng Kevin
Published: September 2020

Purpose: Proton energy-resolved dose imaging (pERDI) is a recently proposed technique to generate water equivalent path length (WEPL) images using a single detector. Owing to its simplicity in instrumentation, analysis and the possibility of using the in-room x-ray flat panels as detectors, this technique offers a promising avenue towards a clinically usable imaging system for proton therapy using scanned beams. The purpose of this study is to estimate the achievable accuracy in WEPL and Relative Stopping Power (RSP) using the pERDI technique and to assess the minimum dose required to achieve such accuracy. The novelty of this study is the first demonstration of the feasibility of pERDI technique in the pencil beam scanning (PBS) mode. Methods: A solid water wedge was placed in front of a 2D detector (Lynx). A library of energy-resolved dose functions (ERDF) was generated from the dose deposited in the detector by 50 PBS layers of energy varying from 100 MeV to 225 MeV. This set-up is further used to image the following configurations using the pERDI technique: stair-case shaped solid water phantom (configuration 1), electron density phantom (configuration 2) and head phantom (configuration 3). The result from configuration 1 was used to determine the achievable WEPL accuracy. The result from configuration 2 was used to estimate the relative uncertainty in RSP. Configuration 3 was used to evaluate the effect of range mixing on the WEPL. In all three cases, the variation of the accuracy with respect to dose, by varying the number of scanning layers, was also studied. Results: An accuracy of 1 mm in WEPL was achieved using the Lynx detector with an imaging field of 10 PBS layers or more, which is equivalent to a total dose of 5 cGy. The RSP is measured with a precision better than 2% for all homogeneous inserts of tissue surrogates. The pERDI technique failed for tissues surrogates with total WEPL outside the calibration window (WEPL < 70 mm) like in the case of lung exhale and lung inhale. The imaging of an anthropomorphic head phantom, in the same condition, produced a WEPL radiograph and compared to the WEPL derived from CT using gamma index analysis. The gamma index failed in the heterogeneous areas due to range mixing. Conclusions: The pERDI technique is a promising clinically usable imaging modality for reducing range uncertainties and set-up errors in proton therapy. The first results have demonstrated that WEPL and RSP can be estimated with clinically acceptable accuracy using the Lynx detector. Similar accuracy is also expected with in-room flat-panel detectors but at significantly reduced imaging dose. Though the issue of range mixing is still to be addressed, we expect that a statistical moment analysis of the ERDFs can be implemented to filter out the regions with high gradient of range mixing.
The oxygen reduction reaction in solid oxide fuel cells: from kinetic parameters measurements to electrode design
Authors: Ascolani-Yael Julián , Montenegro-Hernández Alejandra , Garcés Diana , Liu Quinyuan , Wang Hongqian , Yakal-Kremski Kyle , Barnett Scott , Mogni Liliana
Published: September 2020

The research and development of new Solid Oxide Fuel Cell cathode materials is an area of intense activity. The kinetic coefficients describing the O2-reduction mechanism are the O-ion diffusion (
D

chem
) and the O-surface exchange coefficients (
k

chem
). These parameters are strongly dependent on the nature of the material, both on its bulk and surface atomic and electronic structures. This review discusses the method for obtaining the kinetic coefficients through the combination of electrochemical impedance spectroscopy with focused ion-beam 3D tomography measurements on porous electrodes (3DT-EIS). The data, together with oxygen non-stoichiometry thermodynamic data, is analysed using the Adler-Lane-Steele model for macro-homogeneous porous electrodes. The results for different families of oxides are compared: single- and double-layered perovskites with O-vacancies defects, based on La-Sr cobalt ferrites (La0.6Sr0.4Co1-xFexO3-δ
, x = 0.2 and 0.8) and La/Pr-Ba cobaltites (La0.5-xPrxBa0.5CoO3-δ
, x = 0.0, 0.2 and 0.5), as well as Ruddlesden-Popper nickelates (Nd2NiO4 +δ
) with O-interstitial defects. The analysis of the evolution of molar surface exchange rates with oxygen partial pressure provides information about the mechanisms limiting the O2-surface reaction, which generally is dissociative adsorption or dissociation-limited. At 700 °C in air, the La-Ba cobaltite structures, La0.5-xPrxBa0.5CoO3-δ
, feature the most active surfaces (
k

chem
≃0.5–1 10−2 cm.s−1), followed by the nickelate Nd2NiO4 +δ
and the La-Sr cobalt ferrites, with
k

chem
≃1–5 10−5 cm.s−1. The diffusion coefficients
D

chem
are higher for cubic perovskites than for the layered ones. For La0.6Sr0.4Co0.8Fe0.2O3-δ
and La0.6Sr0.4Co0.2Fe0.8O3-δ
,
D

chem
is 2.6 10−6 cm2.s−1 and 5.4 10−7 cm2.s−1, respectively. These values are comparable to
D

chem
= 1.2 10−6 cm2.s−1, observed for La0.5Ba0.5CoO3-δ
. The layered structure drastically reduces the O-ion bulk diffusion, e.g.
D

chem
= 1.3 10−8 cm2.s−1 for the Pr0.5Ba0.5CoO3-δ
double perovskite and
D

chem
≃2 10−7cm2.s−1 for Nd2NiO4 +δ
. Finally, the analysis of the time evolution of the electrodes shows that the surface cation segregation affects both the O-ion bulk diffusion and the surface exchange rates.
Analyzing the requirements of high-speed camera parameters for enhanced laser speckle sensing of flow dynamics
Authors: Golberg Mark , Califa Ran , Garcia Javier , Zalevsky Zeev
Published: September 2020

A novel method for optimizing fast camera parameters to sense flow dynamics is presented. A wide-field statistic of the temporal auto-correlation intensity function from sample back-scattered laser light can be obtained from the high-end fast cameras that have come on to the market in recent years. Although these statistics can reveal flow dynamics within different sample regions, these cameras can be very costly. Here we investigated the impact of several key camera features such as camera frame rate, sensor exposure time, etc, on the output data (auto-correlation decay time and function fit models). The post-processing algorithm steps are described in detail, followed by the findings from in-vitro and in-vivo experiments investigating ways to re-leaf the camera parameters. The experimental results define fast-camera minimum specification requirements for the correct monitoring of normal blood flow conditions. These findings thus contribute to a better understanding of the impact of each parameter on speckle statistics and can contribute to customizing cheaper hardware to specific needs without compromising on accuracy.
Capacity building for whole genome sequencing of Mycobacterium tuberculosis and bioinformatics in high TB burden countries
Authors: Rivière Emmanuel , Heupink Tim H , Ismail Nabila , Dippenaar Anzaan , Clarke Charlene , Abebe Gemeda , Heusden Peter , Warren Rob , Meehan Conor J , Van Rie Annelies
Published: September 2020

Background

Whole genome sequencing (WGS) is increasingly used for Mycobacterium tuberculosis (Mtb) research. Countries with the highest tuberculosis (TB) burden face important challenges to integrate WGS into surveillance and research.

Methods

We assessed the global status of Mtb WGS and developed a 3-week training course coupled with long-term mentoring and WGS infrastructure building. Training focused on genome sequencing, bioinformatics and development of a locally relevant WGS research project. The aim of the long-term mentoring was to support trainees in project implementation and funding acquisition. The focus of WGS infrastructure building was on the DNA extraction process and bioinformatics.

Findings

Compared to their TB burden, Asia and Africa are grossly underrepresented in Mtb WGS research. Challenges faced resulted in adaptations to the training, mentoring and infrastructure building. Out-of-date laptop hardware and operating systems were overcome by using online tools and a Galaxy WGS analysis pipeline. A case studies approach created a safe atmosphere for students to formulate and defend opinions. Because quality DNA extraction is paramount for WGS, a biosafety level 3 and general laboratory skill training session were added, use of commercial DNA extraction kits was introduced and a 2-week training in a highly equipped laboratory was combined with a 1-week training in the local setting.

Interpretation

By developing and sharing the components of and experiences with a sequencing and bioinformatics training program, we hope to stimulate capacity building programs for Mtb WGS and empower high-burden countries to play an important role in WGS-based TB surveillance and research.
PCAmatchR: a flexible R package for optimal case–control matching using weighted principal components
Authors: Brown Derek W , Myers Timothy A , Machiela Mitchell J
Published: September 2020

A concern when conducting genome-wide association studies (GWAS) is the potential for population stratification, i.e. ancestry-based genetic differences between cases and controls, that if not properly accounted for, could lead to biased association results. We developed PCAmatchR as an open source R package for performing optimal case–control matching using principal component analysis (PCA) to aid in selecting controls that are well matched by ancestry to cases. PCAmatchR takes user supplied PCA outputs and selects matching controls for cases by utilizing a weighted Mahalanobis distance metric which weights each principal component by the percentage of genetic variation explained. Results from the 1000 Genomes Project data demonstrate both the functionality and performance of PCAmatchR for selecting matching controls for case populations as well as reducing inflation of association test statistics. PCAmatchR improves genomic similarity between matched cases and controls, which minimizes the effects of population stratification in GWAS analyses.

Availability and implementation

PCAmatchR is freely available for download on GitHub (https://github.com/machiela-lab/PCAmatchR) or through CRAN (https://CRAN.R-project.org/package=PCAmatchR).

Supplementary information

Supplementary data are available at Bioinformatics online.
Association between SARS-CoV-2 Neutralizing Antibodies and Commercial Serological Assays
Authors: Tang Mei San , Case James Brett , Franks Caroline E , Chen Rita E , Anderson Neil W , Henderson Jeffrey P , Diamond Michael S , Gronowski Ann M , Farnsworth Christopher W
Published: September 2020

Background

Commercially available SARS-CoV-2 serological assays based on different viral antigens have been approved for the qualitative determination of anti-SARS-CoV-2 antibodies. However, there are limited published data associating the results from commercial assays with neutralizing antibodies.

Methods

Sixty-six specimens from 48 patients with PCR-confirmed COVID-19 and a positive result by the Roche Elecsys Anti-SARS-CoV-2, Abbott SARS-CoV-2 IgG, or EUROIMMUN SARS-CoV-2 IgG assays and 5 control specimens were analyzed for the presence of neutralizing antibodies to SARS-CoV-2. Correlation, concordance, positive percent agreement (PPA), and negative percent agreement (NPA) were calculated at several cutoffs. Results were compared in patients categorized by clinical outcomes.

Results

The correlation between SARS-CoV-2 neutralizing titer (EC50) and the Roche, Abbott, and EUROIMMUN assays was 0.29, 0.47, and 0.46, respectively. At an EC50 of 1:32, the concordance kappa with Roche was 0.49 (95% CI; 0.23–0.75), with Abbott was 0.52 (0.28–0.77), and with EUROIMMUN was 0.61 (0.4–0.82). At the same neutralizing titer, the PPA and NPA for the Roche was 100% (94–100) and 56% (30–80); Abbott was 96% (88–99) and 69% (44–86); and EUROIMMUN was 91% (80–96) and 81% (57–93) for distinguishing neutralizing antibodies. Patients who were intubated, had cardiac injury, or acute kidney injury from COVID-19 infection had higher neutralizing titers relative to those with mild symptoms.

Conclusions

COVID-19 patients generate an antibody response to multiple viral proteins such that the calibrator ratios on the Roche, Abbott, and EUROIMMUN assays are all associated with SARS-CoV-2 neutralization. Nevertheless, commercial serological assays have poor NPA for SARS-CoV-2 neutralization, making them imperfect proxies for neutralization.
Olfactory receptor gene evolution is unusually rapid across Tetrapoda and outpaces chemosensory phenotypic change
Authors: Yohe Laurel R , Fabbri Matteo , Hanson Michael , Bhullar Bhart-Anjan S
Published: September 2020

Chemosensation is the most ubiquitous sense in animals, enacted by the products of complex gene families that detect environmental chemical cues and larger-scale sensory structures that process these cues. While there is a general conception that olfactory receptor (OR) genes evolve rapidly, the universality of this phenomenon across vertebrates, and its magnitude, are unclear. The supposed correlation between molecular rates of chemosensory evolution and phenotypic diversity of chemosensory systems is largely untested. We combine comparative genomics and sensory morphology to test whether OR genes and olfactory phenotypic traits evolve at faster rates than other genes or traits. Using published genomes, we identified ORs in 21 tetrapods, including amphibians, reptiles, birds, and mammals and compared their rates of evolution to those of orthologous non-OR protein-coding genes. We found that, for all clades investigated, most OR genes evolve nearly an order of magnitude faster than other protein-coding genes, with many OR genes showing signatures of diversifying selection across nearly all taxa in this study. This rapid rate of evolution suggests that chemoreceptor genes are in “evolutionary overdrive,” perhaps evolving in response to the ever-changing chemical space of the environment. To obtain complementary morphological data, we stained whole fixed specimens with iodine, µCT-scanned the specimens, and digitally segmented chemosensory and nonchemosensory brain regions. We then estimated phenotypic variation within traits and among tetrapods. While we found considerable variation in chemosensory structures, they were no more diverse than nonchemosensory regions. We suggest chemoreceptor genes evolve quickly in reflection of an ever-changing chemical space, whereas chemosensory phenotypes and processing regions are more conserved because they use a standardized or constrained architecture to receive and process a range of chemical cues.
Cognitive Interference in the Context of Daily Stressors, Daily Awareness of Age-Related Change, and General Aging Attitudes
Authors: O’Brien Erica L , Torres Genesis E , Neupert Shevaun D
Published: September 2020

Objectives

Previous diary work indicates that older people experience more intrusive and unwanted thoughts (i.e., cognitive interference) on days with stressors. We examined additional predictors of daily cognitive interference to enhance understanding of the psychological context surrounding this link. We specifically focused on factors related to subjective experiences of aging based on studies that have related higher stress and impairments in cognition such as executive control processes (working memory) to negative age stereotypes. Consistent with these findings, we generally expected stronger stress effects on cognitive interference when daily self-perceptions of aging (i.e., within-person fluctuations in awareness of age-related losses [AARC losses]) and general aging attitudes (i.e., individual differences in attitudes toward own aging [ATOA]) were more negative.

Methods

Participants (n = 91; aged 60–80) on Amazon’s Mechanical Turk completed surveys on 9 consecutive days, reporting on their ATOA (Day 1) as well as their stressors, AARC losses, and cognitive interference (Days 2–9).

Results

Multilevel models showed that people reported more cognitive interference on days with more AARC losses. Individuals with positive ATOA also experienced less cognitive interference on days with more stressors, whereas those with negative ATOA experienced more.

Discussion

Both individual differences and fluctuating daily perceptions of aging appear to be important for older adults’ cognitive interference. Consistent with other work, positive ATOA protected against daily stressor effects. Further elucidating these relationships can increase understanding of and facilitate efforts to improve (daily) cognitive experiences in older adults.
Frequency derivative of Rayleigh wave phase velocity for fundamental mode dispersion inversion: parametric study and experimental application
Authors: Wang A , Leparoux D , Abraham O , Le Feuvre M
Published: September 2020

Monitoring the small variations of a medium is increasingly important in subsurface geophysics due to climate change. Classical seismic surface wave dispersion methods are limited to quantitative estimations of these small variations when the variation ratio is smaller than 10 per cent, especially in the case of variations in deep media. Based on these findings, we propose to study the contributions of the Rayleigh wave phase velocity derivative with respect to frequency. More precisely, in the first step of assessing its feasibility, we analyse the effects of the phase velocity derivative on the inversion of the fundamental mode in the simple case of a two-layer model. The behaviour of the phase velocity derivative is first analysed qualitatively: the dispersion curves of phase velocity, group velocity and the phase velocity derivative are calculated theoretically for several series of media with small variations. It is shown that the phase velocity derivatives are more sensitive to variations of a medium. The sensitivity curves are then calculated for the phase velocity, the group velocity and the phase velocity derivative to perform quantitative analyses. Compared to the phase and group velocities, the phase velocity derivative is sensitive to variations of the shallow layer and the deep layer shear wave velocity in the same wavelength (frequency) range. Numerical data are used and processed to obtain dispersion curves to test the feasibility of the phase velocity derivative in the inversion. The inversion results of the phase velocity derivative are compared with those of phase and group velocities and show improved estimations for small variations (variation ratio less than 5 per cent) of deep layer shear wave velocities. The study is focused on laboratory experiments using two reduced-scale resin-epoxy models. The differences of these two-layer models are in the deep layer in which the variation ratio is estimated as 16.4 ± 1.1 per cent for the phase velocity inversion and 17.1 ± 0.3 per cent for the phase velocity derivative. The latter is closer to the reference value 17 per cent, with a smaller error.
Serum IgG4 Subclass Deficiency Defines a Distinct, Commonly Encountered, Severe Inflammatory Bowel Disease Subtype
Authors: Koutroumpakis Filippos , Phillips Anna Evans , Yadav Dhiraj , Machicado Jorge D , Ahsan Maaz , Ramos Rivers Claudia , Tan Xiaoqing , Schwartz Marc , Proksell Siobhan , Johnston Elyse , Dueker Jeffrey , Hashash Jana G , Barrie Arthur , Harrison Janet , Dunn Michael A , Konnikova Liza , Hartman Douglas J , Din Hasieb , Babichenko Dmitriy , Tang Gong , Binion David G
Published: September 2020

Background

Immunoglobulin G subclass 4 (IgG4) is hypothesized to play an immunomodulatory role, downregulating humoral immune responses. The role of this anti-inflammatory molecule in inflammatory bowel disease (IBD) has not been fully characterized. We sought to define alterations in serum IgG4 in patients with IBD and their association with multiyear disease severity.

Methods

We analyzed metadata derived from curated electronic health records from consented patients with IBD prospectively followed at a tertiary center over a 10-year time period. Patients with IBD with IgG4 serum levels available formed the study population. Demographics and multiyear clinical data were collected and analyzed. We stratified patients with IBD with low, normal, or high serum IgG4 levels.

Results

We found IgG4 characterized in 1193 patients with IBD and low IgG4 levels in 233 patients (20%) and elevated IgG4 levels in 61 patients (5%). An IgG4 deficiency did not significantly correlate with other antibody deficiencies. In a multiple Poisson regression analysis, low IgG4 was associated with more years on biologic agents (P = 0.002) and steroids (P = 0.049) and more hospital admissions (P < 0.001), clinic visits (P = 0.010), outpatient antibiotic prescriptions (P < 0.001), and CD-related surgeries (P = 0.011) during the study period after controlling for certain confounders. Elevated IgG4 was only associated with primary sclerosing cholangitis (P = 0.011). A cohort of patients with IgG4-deficient severe IBD received intravenous Ig replacement therapy, which benefited and was continued in 10 out of 11 individuals.

Conclusions

An IgG4 subclass deficiency, distinct from other antibody deficiencies, occurred commonly in a referral IBD population and was associated with multiple markers of disease severity. This is the first association of IgG4 subclass deficiency with an inflammatory disease process. Further work is needed to define the mechanistic role of IgG4 deficiency in this severe IBD subgroup.
Swimming Through Parameter Subspaces of a Simple Anguilliform Swimmer
Authors: Battista Nicholas A
Published: September 2020

Synopsis

Computational scientists have investigated swimming performance across a multitude of different systems for decades. Most models depend on numerous model input parameters and performance is sensitive to those parameters. In this article, parameter subspaces are qualitatively identified in which there exists enhanced swimming performance for an idealized, simple swimming model that resembles a Caenorhabditis elegans, an organism that exhibits an anguilliform mode of locomotion. The computational model uses the immersed boundary method to solve the fluid-interaction system. The 1D swimmer propagates itself forward by dynamically changing its preferred body curvature. Observations indicate that the swimmer’s performance appears more sensitive to fluid scale and stroke frequency, rather than variations in the velocity and acceleration of either its upstroke or downstroke as a whole. Pareto-like optimal fronts were also identified within the data for the cost of transport and swimming speed. While this methodology allows one to locate robust parameter subspaces for desired performance in a straight-forward manner, it comes at the cost of simulating orders of magnitude more simulations than traditional fluid–structure interaction studies.
Raman spectroscopic analysis of the composition of the clam-shrimp carapace (Branchiopoda: Laevicaudata, Spinicaudata, Cyclestherida): a dual calcium phosphate-calcium carbonate composition
Authors: Hegna Thomas A , Czaja Andrew D , Rogers D Christopher
Published: September 2020

Clam shrimps constitute a paraphyletic group of bivalved branchiopod crustaceans that includes orders Laevicaudata, Spinicaudata, and Cyclestherida. The unique mineral content of the carapace, formed by molt retention in Spinicaudata and Cyclestherida, has been variously ascribed to calcium carbonate or calcium phosphate. We analyzed the composition of modern carapaces from one laevicaudatan species, thirteen spinicaudatan species (including cyzicids, leptestheriids, and limnadiids), one cyclestherid species, and two species of the notostracan TriopsSchrank, 1803 (as an outgroup comparison within Branchiopoda) via Raman spectroscopy. The results were surprisingly variable. The outgroup Triops species varied in either having no mineral content to having a slight amount of calcium phosphate. The laevicaudatans likewise had a minor calcium phosphate peak; the leptestheriid spinicaudatan had strong calcium phosphate and calcium carbonate peaks; the limnadiid spinicaudatans were variable, varying from no mineral content to strong dual calcium carbonate and calcium phosphate peaks; the cyzicid spinicaudatans tended to have strong calcium phosphate peaks with some amount of calcium carbonate; and the cyclestherid had no mineral content. The results support the conclusion that spinicaudatans primitively have a dual mineralization system in their carapace that utilizes both calcium phosphate and calcium carbonate, with the calcium phosphate ability being basal. This suggestion of a dual mineralization system is novel in branchiopods and warrants study from material scientists. Better understanding of the distribution of phosphate versus carbonate among modern spinicaudatans will help us understand the evolution of biomineralization in the group. This, in turn, will shed light on the fossilization potential of different fossil clam-shrimp lineages.
Alternative to the Existing Rule of Attribution for Use of Force by Non-State Actors in an Armed Conflict
Authors: Khaitan Bulbul
Published: September 2020

There is considerable literature to suggest that non-state actors in armed conflicts often function independently and form strategic partnerships with external (or third) states with common goals in return for material benefits such as procurement of arms and training. This article seeks to make an empirical analysis of the existing armed conflicts to ascertain the kind of relationship that armed non-state actors have formed with externally supporting states. The existing rule of attribution of ‘effective control’ would be inappropriate if it can be established that the relationship between the non-state actors and the externally supporting states is not that of a principal and an agent. If non-state actors are independent in their functioning and approach in an armed conflict, it is important to directly regulate their conduct under the law.
A HRM Assay for Rapid Identification of Members of the Seedcorn Maggot Complex (Delia florilegaandD. platura) (Diptera: Anthomyiidae) and Evidence of Variation in Temporal Patterns of Larval Occurrence
Authors: Van der Heyden Hervé , Fortier Anne-Marie , Savage Jade
Published: September 2020

The seedcorn maggot Delia platura (Meigen), and the bean seed maggot Delia florilega (Zetterstedt) can cause considerable feeding damage to a wide range of cultivated crops. The recent discovery of two distinct genetic lines of D. platura, each with a unique distribution pattern overlapping only in eastern Canada, suggests the presence of a new cryptic species for the group. The reliable identification of the three species/lines in the seedcorn maggot complex is crucial to our understanding of their distribution, phenology, and respective contribution to crop damage as well as to the development of specific integrated pest management approaches. As these taxa are morphologically indistinguishable in the immature stages, we developed a high-resolution melting PCR (HRM) assay using primers amplifying a variable 96-bp PCR product in the CO1 mitochondrial gene for rapid and economical identification of specimens. The three species/lines exhibited distinguishable melting profiles based on their different Tm values (between 0.4 and 0.9°C) and identification results based on HRM and DNA sequencing were congruent for all specimens in the validation data set (n = 100). We then used the new, highly sensitive HRM assay to identify survey specimens from the seedcorn maggot complex collected in Quebec, Canada, between 2017 and 2019. Progress curves developed to document the temporal occurrence patterns of each species/lines indicate differences between taxa, with the N-line (BOLD:AAA3453) of D. platura appearing approximately 17 d before D. florilega (BOLD:ACR4394) and the H-line (BOLD:AAG2511) of D. platura.
The Modulation of Trehalose Metabolism by 20-Hydroxyecdysone in Antheraea pernyi (Lepidoptera: Saturniidae) During its Diapause Termination and Post-Termination Period
Authors: Li Ya-Na , Liu Yu-Bo , Xie Xue-Qin , Zhang Jia-Ning , Li Wen-Li
Published: September 2020

Trehalose plays a crucial role in the diapause process of many insects, serving as an energy source and a stress protectant. Trehalose accumulation has been reported in diapause pupae of Antheraea pernyi; however, trehalose metabolic regulatory mechanisms associated with diapause termination remain unclear. Here, we showed that the enhanced trehalose catabolism was associated with an increase in endogenous 20-hydroxyecdysone (20E) in hemolymph of A. pernyi pupae during their diapause termination and posttermination period. Injection of 20E increased the mRNA level of trehalase 1A (ApTre-1A) and trehalase 2 (ApTre-2) of A. pernyi diapause pupae in a dose-dependent manner but did not affect the mRNA level of trehalase 1B (ApTre-1B). Meanwhile, exogenous 20E increased the enzyme activities of soluble and membrane-bound trehalase, leading to a decline in hemolymph trehalose. Conversely, the expression of ApTre-1A and ApTre-2 were down-regulated after the ecdysone receptor gene (ApEcRB1) was silenced by RNA interference or by injection of an ecdysone receptor antagonist cucurbitacin B (CucB), which inhibits the 20E pathway. Moreover, CucB treatment delayed adult emergence, which suggests that ApEcRB1 might be involved in regulating pupal-adult development of A. pernyi by mediating ApTre-1A and ApTre-2 expressions. This study provides an overview of the changes in the expression and activity of different trehalase enzymes in A. pernyi in response to 20E, confirming the important role of 20E in controlling trehalose catabolism during A. pernyi diapause termination and posttermination period.
Adaptations of the red fox (Vulpes vulpes) to urban environments in Sydney, Australia
Authors: Gil-Fernández Margarita , Harcourt Robert , Newsome Thomas , Towerton Alison , Carthey Alexandra
Published: September 2020

With urban encroachment on wild landscapes accelerating globally, there is an urgent need to understand how wildlife is adapting to anthropogenic change. We compared the behaviour of the invasive red fox (Vulpes vulpes) at eight urban and eight peri-urban areas of Sydney, Australia. We observed fox behaviour around a lure and compared fox activity patterns to those of potential prey and to two domestic predators (dogs—Canis lupus familiaris and cats—Felis catus). We assessed the influence of site type, vegetation cover, and distance from habitation on fox behaviour, and compared the temporal activity patterns of urban and peri-urban red foxes. Urban red foxes were marginally more nocturnal than those in peri-urban areas (88% activity overlap). There was greater overlap of red fox activity patterns with introduced mammalian prey in urban areas compared with peri-urban areas (90% urban vs 84% peri-urban). Red fox temporal activity overlapped 78% with cats, but only 20% with dogs, across both site types. The high degree of overlap with cats and introduced mammalian prey is most likely explained by the nocturnal behaviour of these species, while pet dogs are generally kept in yards or indoors at night. The behavioural differences we documented by urban red foxes suggest they may adapt to human modifications and presence, by being more nocturnal and/or more confident in urban areas.
Stephen Mitchell’s Version of the Tao Te Ching: A Spiritual Interpretation
Authors: Fan Penghua , Yu Senlin
Published: September 2020

This article analyses Stephen Mitchell’s interpretation of the Taoist classic Tao Te Ching. With his adoption of the concepts from Zen Buddhism and his borrowing of ideas from Christianity, Mitchell’s version of the Tao Te Ching is not a scholarly faithful translation but rather a spiritual interpretation that is heavily improvised. The importance of this spiritual interpretation lies in the way Mitchell fuses the horizon of Chinese Taoism with his own Zen practice and the English-speaking reader's horizon of Christianity. However, this contribution is offset by the limitation of Mitchell’s work. His version of the Tao Te Ching risks estranging itself from the sociocultural context of the Chinese original, misleading English-speaking readers, and displacing Taoist thought with Buddhist and Christian teachings.
Positive feedback at the disc–halo interface
Authors: Hobbs Alexander , Feldmann Robert
Published: September 2020

The flat star formation (SF) history of the Milky Way (MW) requires gas in the Galactic disc to be replenished, most likely from a reservoir outside the Galaxy. Such a replenishment may be achieved by a form of ‘positive’ feedback, whereby SF feedback creates a Galactic fountain cycle that collects and cools additional gas from the hot halo surrounding the Galaxy. In this paper, we present a model of this process for the MW. A section of the Galactic disc is allowed to form stars that subsequently explode as supernovae and send gas out into the hot halo. The gas that is sent out is colder than the hot halo gas and, as it mixes, the halo gas is cooled, providing fuel for further SF as the mixture falls back on to the Galactic disc. We find that this process can be sufficient to maintain a roughly constant cold gas mass in the MW over at least 3 Gyr. Our results further suggest that there is a positive feedback trend whereby increasing SF leads to an increase in the cold gas budget at average SF rates below $0.5 {\, {\rm M}_\odot}$ yr−1 and a negative feedback trend above this where further increasing the star formation rate leads to a decrease in the cold gas budget. We have constructed an analytical model for this that reproduces the data well and could have profound implications for galaxy evolution in feedback-dominated regimes.
Unsupervised machine learning for transient discovery in deeper, wider, faster light curves
Authors: Webb Sara , Lochner Michelle , Muthukrishna Daniel , Cooke Jeff , Flynn Chris , Mahabal Ashish , Goode Simon , Andreoni Igor , Pritchard Tyler , Abbott Timothy M C
Published: September 2020

Identification of anomalous light curves within time-domain surveys is often challenging. In addition, with the growing number of wide-field surveys and the volume of data produced exceeding astronomers’ ability for manual evaluation, outlier and anomaly detection is becoming vital for transient science. We present an unsupervised method for transient discovery using a clustering technique and the astronomaly package. As proof of concept, we evaluate 85 553 min-cadenced light curves collected over two ∼1.5 h periods as part of the Deeper, Wider, Faster program, using two different telescope dithering strategies. By combining the clustering technique HDBSCAN with the isolation forest anomaly detection algorithm via the visual interface of astronomaly, we are able to rapidly isolate anomalous sources for further analysis. We successfully recover the known variable sources, across a range of catalogues from within the fields, and find a further seven uncatalogued variables and two stellar flare events, including a rarely observed ultrafast flare (∼5 min) from a likely M-dwarf.
mocca-survey Database I: Binary black hole mergers from globular clusters with intermediate mass black holes
Authors: Hong Jongsuk , Askar Abbas , Giersz Mirek , Hypki Arkadiusz , Yoon Suk-Jin
Published: September 2020

The dynamical formation of black hole binaries in globular clusters that merge due to gravitational waves occurs more frequently in higher stellar density. Meanwhile, the probability to form intermediate mass black holes (IMBHs) also increases with the density. To explore the impact of the formation and growth of IMBHs on the population of stellar mass black hole binaries from globular clusters, we analyse the existing large survey of Monte Carlo globular cluster simulation data (mocca-survey Database I). We show that the number of binary black hole mergers agrees with the prediction based on clusters’ initial properties when the IMBH mass is not massive enough or the IMBH seed forms at a later time. However, binary black hole formation and subsequent merger events are significantly reduced compared to the prediction when the present-day IMBH mass is more massive than ${\sim}10^4\, \rm M_{\odot }$ or the present-day IMBH mass exceeds about 1 per cent of cluster’s initial total mass. By examining the maximum black hole mass in the system at the moment of black hole binary escaping, we find that ∼90 per cent of the merging binary black holes escape before the formation and growth of the IMBH. Furthermore, large fraction of stellar mass black holes are merged into the IMBH or escape as single black holes from globular clusters in cases of massive IMBHs, which can lead to the significant underpopulation of binary black holes merging with gravitational waves by a factor of 2 depending on the clusters’ initial distributions.
Myxosporea (Myxozoa, Cnidaria) Lack DNA Cytosine Methylation
Authors: Kyger Ryan , Luzuriaga-Neira Agusto , Layman Thomas , Milkewitz Sandberg Tatiana Orli , Singh Devika , Huchon Dorothée , Peri Sateesh , Atkinson Stephen D , Bartholomew Jerri L , Yi Soojin V , Alvarez-Ponce David
Published: September 2020

DNA cytosine methylation is central to many biological processes, including regulation of gene expression, cellular differentiation, and development. This DNA modification is conserved across animals, having been found in representatives of sponges, ctenophores, cnidarians, and bilaterians, and with very few known instances of secondary loss in animals. Myxozoans are a group of microscopic, obligate endoparasitic cnidarians that have lost many genes over the course of their evolution from free-living ancestors. Here, we investigated the evolution of the key enzymes involved in DNA cytosine methylation in 29 cnidarians and found that these enzymes were lost in an ancestor of Myxosporea (the most speciose class of Myxozoa). Additionally, using whole-genome bisulfite sequencing, we confirmed that the genomes of two distant species of myxosporeans, Ceratonova shasta and Henneguya salminicola, completely lack DNA cytosine methylation. Our results add a notable and novel taxonomic group, the Myxosporea, to the very short list of animal taxa lacking DNA cytosine methylation, further illuminating the complex evolutionary history of this epigenetic regulatory mechanism.
Gut microbiota–associated trimethylamineN-oxide and increased cardiometabolic risk in adults: a systematic review and dose-response meta-analysis
Authors: Abbasalizad Farhangi Mahdieh , Vajdi Mahdi
Published: September 2020

Context

Several studies suggest a relationship between trimethylamine N-oxide (TMAO) concentrations and increased cardiometabolic risk, but findings are controversial.

Objective

The aim of this systematic review and meta-analysis was to summarize evidence of the relationship between circulating TMAO levels and risk of hypertension and increased serum lipids in a dose-response and 2-class meta-analysis of discrete and continuous variables.

Data Sources

PubMed, Scopus, Cochrane, and ProQuest databases were searched.

Study Selection

Observational studies that reported disease status of participants (≥ 18 years), type of sample in which TMAO was measured (serum or plasma), and results based on at least 2 categories of TMAO concentrations, including relative risks, hazard ratios, or odds ratios with 95%CIs for cardiometabolic risk factors in association with circulating TMAO levels were selected. Papers were reviewed independently by both authors. The Newcastle-Ottawa Scale was used to assess the quality of included studies.

Data Extraction

The following data were extracted: first author’s name, publication year, study design, study location, demographic information of participants, and concentrations of circulating TMAO.

Results

Eighteen studies were included in the meta-analysis. There was a dose-response relationship between circulating TMAO and increased odds of hypertension in cohort studies (P  for nonlinearity = 0.049), in plasma-derived TMAO samples (P  for nonlinearity = 0.043), in patients with cardiovascular disease (P  for nonlinearity = 0.048), and in apparently healthy individuals from community-based studies (P  for nonlinearity = 0.005). Moreover, the highest category of TMAO concentrations was associated with a 2.36 mmHg increase in systolic blood pressure when compared with the lowest category. The dose-response meta-analysis of continuous variables revealed that an increase in TMAO is associated with reduced high-density lipoprotein cholesterol in apparently healthy individuals and reduced high-density lipoprotein cholesterol and increased total cholesterol in patients with cardiovascular disease.

Conclusions

Circulating TMAO is positively associated with an increased risk of hypertension and other cardiometabolic disorders in adults.

Systematic Review Registration

PROSPERO identification number CRD42019138296.
Short-term Adverse Events With BIC/FTC/TAF: Postmarketing Study
Authors: Hayes Edwin , Derrick Caroline , Smalls Danielle , Smith Hilary , Kremer Nicole , Weissman Sharon
Published: September 2020

Bictegravir (BIC)/emtricitabine (FTC)/tenofovir alafenamide (TAF) was Food and Drug Administration approved in February 2018. The paucity of real-world data prompted this retrospective, observational evaluation of discontinuation rates, adverse effects, and virologic control. In a Southern US, predominantly African American overweight population, we found optimal virologic control and low discontinuation rates, with 4% discontinuing BIC/FTC/TAF due to rash, low platelets, loss of appetite, and insomnia.
Multi-wavelength photometry during the 2018 superoutburst of the WZ Sge-type dwarf nova EG Cancri
Authors: Kimura Mariko , Isogai Keisuke , Kato Taichi , Kojiguchi Naoto , Wakamatsu Yasuyuki , Ohnishi Ryuhei , Sugiura Yuki , Matsumoto Hanami , Sumiya Sho , Ito Daiki , Nikai Kengo , Matsumoto Katsura , Shugarov Sergey Yu , Katysheva Natalia , Itoh Hiroshi , Dubovsky Pavol A , Kudzej Igor , Akitaya Hiroshi , Oide Kohei , Kanai Takahiro , Ishioka Chihiro , Uzawa Yoshinori , Oasa Yumiko , Vanmunster Tonny , Oksanen Arto , Tordai Tamás , Murata Katsuhiro L , Shiraishi Kazuki , Adachi Ryo , Oeda Motoki , Tachibana Yutaro , Kiyota Seiichiro , Pavlenko Elena P , Antonyuk Kirill , Antonyuk Oksana , Pit Nikolai , Sosnovskij Aleksei , Babina Julia , Baklanov Alex , Kawabata Koji S , Kawabata Miho , Nakaoka Tatsuya , Yamanaka Masayuki , Kasai Kiyoshi , Miller Ian , Brincat Stephen M , Liu Wei , Sasada Mahito , Nogami Daisaku
Published: September 2020

We report on the multi-wavelength photometry of the 2018 superoutburst in EG Cnc. We have detected stage A superhumps and long-lasting late-stage superhumps via the optical photometry and have constrained the binary mass ratio and its possible range. The median value of the mass ratio is 0.048 and the upper limit is 0.057, which still implies that EG Cnc is one of the possible candidates for period bouncers. This object also showed multiple rebrightenings in this superoutburst which are the same as those in its previous superoutburst in 1996–1997, despite the difference in the main superoutburst. This would represent that the rebrightening type is inherent to each object and is independent of the initial disk mass at the beginning of superoutbursts. We also found that B − I and J − Ks colors were unusually red just before the rebrightening phase and became bluer during the quiescence between rebrightenings, which would mean that the low-temperature mass reservoir at the outermost disk accreted with time after the main superoutburst. Also, the ultraviolet flux was sensitive to rebrightenings as well as the optical flux, and the U − B color became redder during the rebrightening phase, which would indicate that the inner disk became cooler when this object repeated rebrightenings. Our results thus basically support the idea that the cool mass reservoir in the outermost disk is responsible for rebrightenings.
Screening, Brief Intervention, and Referral to Treatment for Pain Management for Veterans Seeking Service-Connection Payments for Musculoskeletal Disorders: SBIRT-PM Study Protocol
Authors: Martino Steve , Lazar Christina , Sellinger John , Gilstad-Hayden Kathryn , Fenton Brenda , Barnett Paul G , Brummett Brad R , Higgins Diana M , Holtzheimer Paul , Mattocks Kristin , Ngo Tu , Reznik Thomas E , Semiatin Alicia M , Stapley Todd , Rosen Marc I
Published: September 2020

Background

Veterans with significant chronic pain from musculoskeletal disorders are at risk of substance misuse. Veterans whose condition is the result of military service may be eligible for a disability pension. Department of Veterans Affairs compensation examinations, which determine the degree of disability and whether it was connected to military service, represent an opportunity to engage Veterans in pain management and substance use treatments. A multisite randomized clinical trial is testing the effectiveness and cost-effectiveness of Screening, Brief Intervention, and Referral to Treatment for Pain Management (SBIRT-PM) for Veterans seeking compensation for musculoskeletal disorders. This telephone-based intervention is delivered through a hub-and-spoke configuration.

Design

This study is a two-arm, parallel-group, 36-week, multisite randomized controlled single-blind trial. It will randomize 1,100 Veterans experiencing pain and seeking service-connection for musculoskeletal disorders to either SBIRT-PM or usual care across eight New England VA medical centers. The study balances pragmatic with explanatory methodological features. Primary outcomes are pain severity and number of substances misused. Nonpharmacological pain management and substance use services utilization are tracked in the trial.

Early trial enrollment targets were met across sites. SBIRT-PM could help Veterans, at the time of their compensation claims, use multimodal pain treatments and reduce existing substance misuse. Strategies to address COVID-19 pandemic impacts on the SBIRT-PM protocol have been developed to maintain its pragmatic and exploratory integrity.
The posterior crus II cerebellum is specialized for social mentalizing and emotional self-experiences: a meta-analysis
Authors: Van Overwalle Frank , Ma Qianying , Heleven Elien
Published: September 2020

This meta-analysis explores the role of the posterior cerebellum Crus I/II in social mentalizing. We identified over 200 functional magnetic resonance imaging (fMRI) studies via NeuroSynth that met our inclusion criteria and fell within bilateral Crus II areas related to ‘sequencing’ during mentalizing (coordinates ±24 −76 −40; from earlier studies) and mere social ‘mentalizing’ or self-related emotional cognition (coordinates ±26 −84 −34; from NeuroSynth), located in the cerebellar mentalizing network. A large majority of these studies (74%) involved mentalizing or self-related emotional cognition. Other functions formed small minorities. This high incidence in Crus II compares very favorably against the lower base rate for mentalizing and self-related emotions (around 35%) across the whole brain as revealed in NeuroSynth. In contrast, there was much less support for a similar role of Crus I (coordinates −40 −70 −40 from earlier ‘sequencing’ studies) as only 35% of the studies were related to mentalizing or self-related emotions. The present findings show that a domain-specific social mentalizing functionality is supported in the cerebellar Crus II. This has important implications for theories of the social cerebellum focusing on sequencing of social actions, and for cerebellar neurostimulation treatments.