bluuebunny/crossref_metadata_2025 huggingface dataset:
Phenotypical and functional alteration of unconventional T cells in severe COVID-19 patients
Authors: Jouan Youenn , Guillon Antoine , Gonzalez Loïc , Perez Yonatan , Boisseau Chloé , Ehrmann Stephan , Ferreira Marion , Daix Thomas , Jeannet Robin , François Bruno , Dequin Pierre-François , Si-Tahar Mustapha , Baranek Thomas , Paget Christophe
Published: September 2020

COVID-19 includes lung infection ranging from mild pneumonia to life-threatening acute respiratory distress syndrome (ARDS). Dysregulated host immune response in the lung is a key feature in ARDS pathophysiology. However, cellular actors involved in COVID-19–driven ARDS are poorly understood. Here, in blood and airways of severe COVID-19 patients, we serially analyzed unconventional T cells, a heterogeneous class of T lymphocytes (MAIT, γδT, and iNKT cells) with potent antimicrobial and regulatory functions. Circulating unconventional T cells of COVID-19 patients presented with a profound and persistent phenotypic alteration. In the airways, highly activated unconventional T cells were detected, suggesting a potential contribution in the regulation of local inflammation. Finally, expression of the CD69 activation marker on blood iNKT and MAIT cells of COVID-19 patients on admission was predictive of clinical course and disease severity. Thus, COVID-19 patients present with an altered unconventional T cell biology, and further investigations will be required to precisely assess their functions during SARS–CoV-2–driven ARDS.
Deep learning for 2D passive source detection in presence of complex cargo
Authors: Baines W , Kuchment P , Ragusa J
Published: September 2020

Methods for source detection in high noise environments are important for single-photon emission computed tomography medical imaging and especially crucial for homeland security applications, which is our main interest. In the latter case, one deals with passively detecting the presence of low emission nuclear sources with significant background noise (with signal to noise ratio 1% or less). In passive emission problems, direction sensitive detectors are needed, to match the dimensionalities of the image and the data. Collimation, used for that purpose in standard Anger γ-cameras, is not an option. Instead, Compton γ-cameras (and their analogs for other types of radiation) can be utilized. Backprojection methods suggested before by two of the authors and their collaborators enable detection in the presence of a random uniform background. In most practical applications, however, cargo packing in shipping containers and trucks creates regions of strong absorption and scattering, while leaving some streaming gaps open. In such cases backprojection methods prove ineffective and lose their detection ability. Nonetheless, visual perception of the backprojection pictures suggested that some indications of presence of a source might still be in the data. To learn such features (if they do exist), a deep neural network approach is implemented in 2D, which indeed exhibits higher sensitivity and specificity than the backprojection techniques in a low scattering case and works well when presence of complex cargo makes backprojection fail completely.
Thornber–Feynman carrier-optical-phonon scattering rates in wurtzite crystals
Authors: Singh Ramji , Dutta Mitra , Stroscio Michael A
Published: September 2020

It is well known that the carrier-optical-phonon scattering rates dominate the carrier-acoustic-phonon scattering rates in many polar materials of interest in electronic and optoelectronic applications. Furthermore, it is known that the Fröhlich coupling constants for carrier-optical-phonon in many materials is close to or great than unity, calling into question the validity of scattering rates based on the Fermi golden rule. In a celebrated paper by Thornber and Feynman it was shown that that the large Fröhlich coupling constant in polar materials does indeed lead to substantial corrections to the Fermi golden rule scattering rates. These large corrections are due to the fact that for strong coupling constants, the first-order perturbative approach underlying the Fermi golden rule does not take into account the presence of many phonons interacting simultaneous with the carrier. In this paper, the Thornber–Feymnan scattering rates for carrier-optical-phonon interactions are derived for several technologically important wurtzite semiconductors—BN, ZnO, CdS, CdSe, ZnS, InN, and SiC- and it is shown that the commonly used Fermi golden rule scattering rates must be corrected by factors ranging up to an order-of-magnitude. The corrections to the Fermi golden rule reported herein have widespread impact on carrier transport for materials with large Fröhlich coupling constants.
Study of H-mode pedestal predictive model on EAST tokamak
Authors: Li K , Li G Q , Zang Q , Zhang T , Liu H Q , Xiang H M , Li Y Y , Wu M F , Wu M Q , Jian X , Li G S , Li H , Snyder P B
Published: September 2020

The pedestal structure of the high-confinement mode (H-mode) operation strongly impacts global confinement and fusion performance in tokamak devices. Studies of the pedestal structure also play an important role in better understanding the characterization of H-mode plasma discharges with type-I edge localized modes on the Experimental Advanced Superconducting Tokamak (EAST). The EPED model has been widely validated to predict the pedestal structure of several tokamak devices. The mean pedestal width

Δ

ψ

correlates with the square root of the poloidal pedestal beta

β

p
,
p
e
d

1

/

2

and is in good agreement with

Δ

ψ

=
0.12

β

p
,
p
e
d

1

/

2

from experimental observations. It is also found that the scaling coefficients of

Δ

ψ

and

β

p
,
p
e
d

1

/

2

may have no dependence on the heating schemes. The comparison of predictions with measurements indicates that the REPED model could be used to predict the pedestal height for a range of experimental pedestal pressures (

1.7
<

p

p
e
d

<
2.6

 kPa

) on EAST.
Neural Responses to the Implicit Processing of Emotional Facial Expressions in Binge Drinking
Authors: Lannoy Séverine , Dricot Laurence , Benzerouk Farid , Portefaix Christophe , Barrière Sarah , Quaglino Véronique , Naassila Mickaël , Kaladjian Arthur , Gierski Fabien
Published: September 2020

Aims

Emotional processing is a crucial ability in human and impairments in the processing of emotions are considered as transdiagnostic processes in psychopathology. In alcohol use disorder, numerous studies have investigated emotional processing and showed emotional deficits related to the perpetuation of alcohol use. Recent studies have also explored this topic in binge drinking, but few studies are available. In this paper, we explored whether emotional difficulties in binge drinking may be extended to implicit emotion processing.

Methods

We compared 39 binge drinkers (BD) and 40 non-binge drinkers who performed a gender categorization task while faces represented emotional expressions of anger, fear, happiness and sadness. Emotional brain responses were assessed thanks to functional magnetic resonance imaging. Emotional versus non-emotional conditions were first contrasted in the whole sample and groups were then compared.

Results

Emotional condition led to differential activations than non-emotional condition, supporting the validity of the paradigm. Regarding group comparisons, BD exhibited higher activations in the left posterior cerebellum (anger processing) and the right anterior cingulate (fear processing) as well as lower activations in the left insula (happiness), the right post-central gyrus, the right cingulate gyrus and the right medial frontal gyrus (sadness processing).

Conclusions

Beyond emotional identification, BD presented differential brain responses following the implicit processing of emotions. Emotional difficulties in binge drinking might be related to a more automatic/unconscious processing of emotions.
AFid: a tool for automated identification and exclusion of autofluorescent objects from microscopy images
Authors: Baharlou Heeva , Canete Nicolas P , Bertram Kirstie M , Sandgren Kerrie J , Cunningham Anthony L , Harman Andrew N , Patrick Ellis
Published: September 2020

Motivation

Autofluorescence is a long-standing problem that has hindered the analysis of images of tissues acquired by fluorescence microscopy. Current approaches to mitigate autofluorescence in tissue are lab-based and involve either chemical treatment of sections or specialized instrumentation and software to ‘unmix’ autofluorescent signals. Importantly, these approaches are pre-emptive and there are currently no methods to deal with autofluorescence in acquired fluorescence microscopy images.

Results

To address this, we developed Autofluorescence Identifier (AFid). AFid identifies autofluorescent pixels as discrete objects in multi-channel images post-acquisition. These objects can then be tagged for exclusion from downstream analysis. We validated AFid using images of FFPE human colorectal tissue stained for common immune markers. Further, we demonstrate its utility for image analysis where its implementation allows the accurate measurement of HIV–Dendritic cell interactions in a colorectal explant model of HIV transmission. Therefore, AFid represents a major leap forward in the extraction of useful data from images plagued by autofluorescence by offering an approach that is easily incorporated into existing workflows and that can be used with various samples, staining panels and image acquisition methods. We have implemented AFid in ImageJ, Matlab and R to accommodate the diverse image analysis community.

Availability and implementation

AFid software is available at https://ellispatrick.github.io/AFid.

Supplementary information

Supplementary data are available at Bioinformatics online.
Resistance and reproduction: an arts-based investigation into young people’s emotional responses to crime
Authors: Dodsley Thomas , Gray Emily
Published: September 2020

This paper reports on a qualitative study of young people’s emotional responses to crime, underpinned by cultural criminology and interpretive phenomenology. It uses alternative approaches to explore young people’s ‘fears’ of crime via the use of arts-based methods, specifically performative drama and focus groups. The rationale is rooted in young people’s voices being largely absent from fear of crime research and the increased movement towards a more creative and less prescriptive criminology. The findings point towards the value of such approaches and argue that young people’s emotions about crime become highly gendered and age-relevant in youth and have multiple, overlapping spheres that are culturally constructed, resisted and reproduced.
Social Workers’ Encounters with Elder Abuse and Neglect: Giving Meaning to Their Experiences
Authors: Band-Winterstein Tova , Goldblatt Hadass , Alon Sara
Published: September 2020

This article examines Israeli social workers’ experiences of their encounters with elder abuse survivors and its impact on professional and personal aspects in the social workers’ lives. Participants were seventeen experienced women social workers, who intervened with elder abuse and neglect. Data were collected via in-depth semi-structured interviews. Data analysis revealed three main themes: (i) ‘Sensing the Pain’: Exposure to the Complexity of Clients’ Life-Long Suffering; (ii) Taking Home the Pain: Social Workers Dwelling with the Sensitivity of the Encounter with Elder Abuse and (iii) ‘Caring for Them, and Letting Them Be Part of My World’: The Encounter as Resonating in Social Workers’ Professional and Personal Life Domains. Social workers’ experiences of complex, sensitive encounters with elder abuse survivors appear to be a multidimensional challenge, involving both burden and growth. This notion can leverage the client–helping professional relationship, thus enriching and shaping social workers’ personal and professional worlds.
GREB1 regulates PI3K/Akt signaling to control hormone-sensitive breast cancer proliferation
Authors: Haines Corinne N , Klingensmith Hope D , Komara Makanko , Burd Craig J
Published: September 2020

Over 70% of breast cancers express the estrogen receptor (ER) and depend on ER activity for survival and proliferation. While hormone therapies that target receptor activity are initially effective, patients invariably develop resistance which is often associated with activation of the phosphoinositide 3-kinase (PI3K)/Akt/mammalian target of rapamycin (mTOR) pathway. While the mechanism by which estrogen regulates proliferation is not fully understood, one gene target of ER, growth regulation by estrogen in breast cancer 1 (GREB1), is required for hormone-dependent proliferation. However, the molecular function by which GREB1 regulates proliferation is unknown. Herein, we validate that knockdown of GREB1 results in growth arrest and that exogenous GREB1 expression initiates senescence, suggesting that an optimal level of GREB1 expression is necessary for proliferation of breast cancer cells. Under both of these conditions, GREB1 is able to regulate signaling through the PI3K/Akt/mTOR pathway. GREB1 acts intrinsically through PI3K to regulate phosphatidylinositol (3,4,5)-triphosphate levels and Akt activity. Critically, growth suppression of estrogen-dependent breast cancer cells by GREB1 knockdown is rescued by expression of constitutively activated Akt. Together, these data identify a novel molecular function by which GREB1 regulates breast cancer proliferation through Akt activation and provides a mechanistic link between estrogen signaling and the PI3K pathway.
Structural and Functional Brain Parameters Related to Cognitive Performance Across Development: Replication and Extension of the Parieto-Frontal Integration Theory in a Single Sample
Authors: Gur Ruben C , Butler Ellyn R , Moore Tyler M , Rosen Adon F G , Ruparel Kosha , Satterthwaite Theodore D , Roalf David R , Gennatas Efstathios D , Bilker Warren B , Shinohara Russell T , Port Allison , Elliott Mark A , Verma Ragini , Davatzikos Christos , Wolf Daniel H , Detre John A , Gur Raquel E
Published: September 2020

The parieto-frontal integration theory (PFIT) identified a fronto-parietal network of regions where individual differences in brain parameters most strongly relate to cognitive performance. PFIT was supported and extended in adult samples, but not in youths or within single-scanner well-powered multimodal studies. We performed multimodal neuroimaging in 1601 youths age 8–22 on the same 3-Tesla scanner with contemporaneous neurocognitive assessment, measuring volume, gray matter density (GMD), mean diffusivity (MD), cerebral blood flow (CBF), resting-state functional magnetic resonance imaging measures of the amplitude of low frequency fluctuations (ALFFs) and regional homogeneity (ReHo), and activation to a working memory and a social cognition task. Across age and sex groups, better performance was associated with higher volumes, greater GMD, lower MD, lower CBF, higher ALFF and ReHo, and greater activation for the working memory task in PFIT regions. However, additional cortical, striatal, limbic, and cerebellar regions showed comparable effects, hence PFIT needs expansion into an extended PFIT (ExtPFIT) network incorporating nodes that support motivation and affect. Associations of brain parameters became stronger with advancing age group from childhood to adolescence to young adulthood, effects occurring earlier in females. This ExtPFIT network is developmentally fine-tuned, optimizing abundance and integrity of neural tissue while maintaining a low resting energy state.
Coronavirus Disease 2019 (COVID-19) and HIV Spotlight the United States Imperative for Permanent Affordable Housing
Authors: Riley Elise D , Hickey Matthew D , Imbert Elizabeth , Clemenzi-Allen Angelo A , Gandhi Monica
Published: September 2020

Job loss and evictions tied to the Coronavirus Disease 2019 (COVID-19) pandemic are expected to increase homelessness significantly in the coming months. Reciprocally, homelessness and the many vulnerabilities that inevitably accompany it are driving COVID-19 outbreaks in US shelters and other congregate living situations. Unless we intervene to address homelessness, these co-existing and synergistic situations will make the current public health crisis even worse. Preventing homelessness and providing permanent affordable housing has reduced the ravages of the HIV epidemic. We must take the lessons learned in 40 years of fighting HIV to respond effectively to the COVID-19 crisis. Housing is an investment that will curb the spread of COVID-19 and help protect all of us from future pandemics.
Comparison of A(H3N2) Neutralizing Antibody Responses Elicited by 2018–2019 Season Quadrivalent Influenza Vaccines Derived from Eggs, Cells, and Recombinant Hemagglutinin
Authors: Wang Wei , Alvarado-Facundo Esmeralda , Vassell Russell , Collins Limone , Colombo Rhonda E , Ganesan Anuradha , Geaney Casey , Hrncir David , Lalani Tahaniyat , Markelz Ana Elizabeth , Maves Ryan C , McClenathan Bruce , Mende Katrin , Richard Stephanie A , Schofield Christina , Seshadri Srihari , Spooner Christina , Utz Gregory C , Warkentien Tyler E , Levine Min , Coles Christian L , Burgess Timothy H , Eichelberger Maryna , Weiss Carol D
Published: September 2020

Background

Low vaccine effectiveness against A(H3N2) influenza in seasons with little antigenic drift has been attributed to substitutions in hemagglutinin (HA) acquired during vaccine virus propagation in eggs. Clinical trials comparing recombinant HA vaccine (rHA) and cell-derived inactivated influenza vaccine (IIV) to egg-derived IIVs provide opportunities to assess how egg-adaptive substitutions influence HA immunogenicity.

Methods

Neutralization titers in pre- and postimmunization sera from 133 adults immunized with 1 of 3 types of influenza vaccines in a randomized, open-label trial during the 2018–2019 influenza season were measured against egg- and cell-derived A/Singapore/INFIMH-16-0019/2016-like and circulating A(H3N2) influenza viruses using HA pseudoviruses.

Results

All vaccines elicited neutralizing antibodies to all H3 vaccine antigens, but the rHA vaccine elicited the highest titers and seroconversion rates against all strains tested. Egg- and cell-derived IIVs elicited responses similar to each other. Preimmunization titers against H3 HA pseudoviruses containing egg-adaptive substitutions T160K and L194P were high, but lower against H3 HA pseudoviruses without those substitutions. All vaccines boosted neutralization titers against HA pseudoviruses with egg-adaptive substitutions, but poorly neutralized wild-type 2019–2020 A/Kansas/14/2017 (H3N2) HA pseudoviruses.

Conclusion

Egg- and cell-derived 2018–2019 season influenza vaccines elicited similar neutralization titers and response rates, indicating that the cell-derived vaccine did not improve immunogenicity against the A(H3N2) viruses. The higher responses after rHA vaccination may be due to its higher HA content. All vaccines boosted titers to HA with egg-adaptive substitutions, suggesting boosting from past antigens or better exposure of HA epitopes. Studies comparing immunogenicity and effectiveness of different influenza vaccines across many seasons are needed.
Multi-catheter cryotherapy compared with radiofrequency ablation in long-standing persistent atrial fibrillation: a randomized clinical trial
Authors: Gallagher Mark M , Yi Gang , Gonna Hanney , Leung Lisa W M , Harding Idris , Evranos Banu , Bastiaenen Rachel , Sharma Rajan , Wright Sue , Norman Mark , Zuberi Zia , Camm A John
Published: September 2020

Aims

Restoring sinus rhythm (SR) by ablation alone is an endpoint used in radiofrequency (RF) ablation for long-standing persistent atrial fibrillation (AF) but not with cryotherapy. The simultaneous use of two cryotherapy catheters can improve ablation efficiency; we compared this with RF ablation in chronic persistent AF aiming for termination to SR by ablation alone.

Methods and results

Consecutive patients undergoing their first ablation for persistent AF of >6 months duration were screened. A total of 100 participants were randomized 1:1 to multi-catheter cryotherapy or RF. For cryotherapy, a 28-mm Arctic Front Advance was used in tandem with focal cryoablation catheters. Open-irrigated, non-force sensing catheters were used in the RF group with a 3D mapping system. Pulmonary vein (PV) isolation and non-PV triggers were targeted. Participants were followed up at 6 and 12 months, then yearly. Acute PVI was achieved in all cases. More patients in the multi-catheter cryotherapy group were restored to SR by ablation alone, with a shorter procedure duration. Sinus rhythm continued to the last available follow-up in 16/49 patients (33%) in the multi-catheter at 3.0 ± 1.6 years post-ablation and in 12/50 patients (24%) in the RF group at 4.0 ± 1.2 years post-ablation. The yearly rate of arrhythmia recurrence was similar.

Conclusion

Multi-catheter cryotherapy can restore SR by ablation alone in more cases and more quickly than RF ablation. Long-term success is difficult to achieve by either methods and is similar with both.
Inpainting of local wavefront attributes using artificial intelligence for enhancement of massive 3-D pre-stack seismic data
Authors: Gadylshin Kirill , Silvestrov Ilya , Bakulin Andrey
Published: September 2020

We propose an advanced version of non-linear beamforming assisted by artificial intelligence (NLBF-AI) that includes additional steps of encoding and interpolating of wavefront attributes using inpainting with deep neural network (DNN). Inpainting can efficiently and accurately fill the holes in waveform attributes caused by acquisition geometry gaps and data quality issues. Inpainting with DNN delivers excellent quality of interpolation with the negligible computational effort and performs particularly well for a challenging case of irregular holes where other interpolation methods struggle. Since conventional brute-force attribute estimation is very costly, we can further intentionally create additional holes or masks to restrict expensive conventional estimation to a smaller subvolume and obtain missing attributes with cost-effective inpainting. Using a marine seismic data set with ocean bottom nodes, we show that inpainting can reliably recover wavefront attributes even with masked areas reaching 50–75 per cent. We validate the quality of the results by comparing attributes and enhanced data from NLBF-AI and conventional NLBF using full-density data without decimation.
Seismological evidence of a dehydration reaction in the subducting oceanic crust beneath western Shikoku in southwest Japan
Authors: Shiomi Katsuhiko , Takeda Tetsuya , Ueno Tomotake
Published: September 2020

The Philippine Sea plate (PHS) is subducting beneath southwest Japan from the Nankai Trough. In this region, deep low-frequency earthquakes/tremors (LFEs) are active and their epicentres are distributed along the downdip of the source region of M8-class earthquakes that have occurred every 100–150 yr. The LFE activity may potentially be strongly related to the occurrence of great earthquakes between tectonic plates. To investigate the structural features around the LFEs, we applied teleseismic receiver function (RF) analysis to the seismograms observed at permanent and temporal seismograph stations in western Shikoku and we detected seismological evidence of a slab dehydration reaction linked to LFE activity. Based on the first-order harmonic decomposition of RFs, we first estimated the average plunge azimuth of the PHS beneath western Shikoku. Considering the backazimuth dependence of converted phase amplitude, we constructed the cross-section of the radial component RFs, excluding the incoming waveform data from the updip directions of the dipping slab. In this profile, the parallel negative and positive P-to-S converted phase alignment within a distance of 10 km were imaged. These phase alignments corresponded to the top of the slab and the slab Moho discontinuity, respectively. At the northern side of the profile, the landward (continental) Moho was also detected. In the region where LFEs were actively distributed, both the landward Moho and slab surface were unclear. The second-order harmonic decomposition of RFs for several kilometres above the slab Moho indicated that the anisotropic symmetry axes suddenly changed at the southern limit of the LFE active region; the fast axes in the region were normal to the trench though axes in the southern area were parallel. According to the thermal and pressure condition, a phase transition with a dehydration reaction can occur in the oceanic crust near the southern edge of the LFE active region. Once the dehydration process advances, released water causes the serpentinization of the mantle material near the slab surface and the corresponding seismic velocity decreases. The impedance contrast decreases at the boundary between the lower crust and the mantle wedge, as well as that between the mantle wedge and oceanic crust; therefore, the amplitudes of the converted phases at these boundaries also become small. Considering that serpentinite ordinarily has strong anisotropy with a seismic fast axis direct to the shear direction, all features observed are evidence of the dehydration process in the flat slab.
Measuring the impacts of labor in the platform economy: new work created, old work reorganized, and value creation reconfigured
Authors: Bearson Dafna , Kenney Martin , Zysman John
Published: September 2020

Though economists have examined labor displacement due to digitization, few have considered the new work and value created. Unlike employment relations that brought workers together on the assembly line or in an office in a previous era, platforms enable a greater, more dispersed, and complex division of labor. New and reconfigured types of labor enabled by platforms create identification and measurement challenges. Previous studies of platforms invariably focused on specific organizational forms such as sharing or gigs. They built taxonomies based on the platform's organization – few considered the scope and scale of platform-enabled value creation. To better understand changing labor arrangements in the 21st century, this article introduces a taxonomy to systematically understand work, employment, and value creation in the platform economy. We consider all of the platform-enabled value creation activities including old work displaced or reorganized to new work created. We provide suggestive evidence for the utility of our framework through case studies of Etsy and Amazon Self-Publishing in the United States.
Dimensions of Two-Valued Sets via Imaginary Chaos
Authors: Schoug Lukas , Sepúlveda Avelio , Viklund Fredrik
Published: September 2020

Two-valued sets are local sets of the 2D Gaussian free field (GFF) that can be thought of as representing all points of the domain that may be connected to the boundary by a curve on which the GFF takes values only in $[-a,b]$. Two-valued sets exist whenever $a+b\geq 2\lambda ,$ where $\lambda$ depends explicitly on the normalization of the GFF. We prove that the almost sure Hausdorff dimension of the two-valued set ${\mathbb{A}}_{-a,b}$ equals $d=2-2\lambda ^2/(a+b)^2$. For the key two-point estimate needed to give the lower bound on dimension, we use the real part of a “vertex field” built from the purely imaginary Gaussian multiplicative chaos. We also construct a non-trivial $d$-dimensional measure supported on ${\mathbb{A}}_{-a,b}$ and discuss its relation with the $d$-dimensional conformal Minkowski content of ${\mathbb{A}}_{-a,b}$.
In vitro cross-resistance to doravirine in a panel of HIV-1 clones harbouring multiple NNRTI resistance mutations
Authors: Saladini Francesco , Giammarino Federica , Hosseini Behnaz A , Giannini Alessia , Boccuto Adele , Dragoni Filippo , Vicenti Ilaria , Shafer Robert W , Zazzi Maurizio
Published: September 2020

Objectives

Doravirine is a recently licensed HIV-1 NNRTI with improved efficacy, pharmacokinetics and safety profile compared with efavirenz and limited cross-resistance with rilpivirine and etravirine. In this in vitro study, cross-resistance to doravirine was analysed in a representative panel of NNRTI-resistant clones.

Methods

In vitro phenotypic susceptibility to doravirine was assessed in 10 clinically derived infectious clones with intermediate- to high-level resistance to rilpivirine, etravirine, efavirenz and nevirapine, and in NL4-3 site-directed mutants harbouring K103N, Y181C, M230L or K103N/Y181C NNRTI mutations.

Results

Although none of the infectious clones harboured any of the major doravirine resistance-associated mutations (RAMs) included in the IAS-USA reference list, doravirine fold change (FC) values were comparable to or higher than those calculated for other NNRTIs, particularly etravirine and rilpivirine. As expected, single NNRTI mutations K103N and Y181C did not impair doravirine susceptibility (FC 1.4 and 1.8, respectively), while reduced activity was observed with the single M230L or double K103N/Y181C mutations (FC 7.6 and 4.9, respectively). Median FC values increased significantly with increasing numbers of NNRTI RAMs (P = 0.005) and were >10 in 4/4 and 1/4 clones harbouring four and three NNRTI RAMs, respectively. FC values correlated well with predicted susceptibility as inferred by Stanford HIV Drug Resistance Database (HIVdb) and ANRS algorithms (both P < 0.001).

Conclusions

Substantial cross-resistance to doravirine was detected in NNRTI-resistant viruses harbouring complex mutational patterns, even in the absence of major IAS-USA doravirine RAMs. Therefore, based on the simple IAS-USA reference list, doravirine resistance may be underestimated in viruses harbouring multiple NNRTI mutations.
The Opposites and Unity: A Study of Chinese Taoist Thought Found in Hermann Hesse’s The Glass Bead Game
Authors: Tang Xianyun , Zheng Boren
Published: September 2020

Hermann Hesse was keenly aware of the spiritual and social crises of war-torn Europe. He explored possible solutions to these problems in his writing and was interested in drawing on the resources of oriental philosophies. Of particular importance was the thought of Chinese Taoism. Hesse frequently mentioned his understanding of the Taoist philosophies of Laozi (老子) and Zhuangzi (庄子) in letters to his friends, and Taoist ideas such as ‘Tao’ (道) or ‘One’ and ‘polar opposites and unity’ recur across his work. This article will trace Hesse’s understanding of the Taoist thought of Laozi and Zhuangzi, and analyse the influence of Chinese Taoism on Hesse’s masterpiece, The Glass Bead Game (1943).
The use of the t-test in Shakespeare scholarship
Authors: Rizvi Pervez
Published: September 2020

In a recent article, the New Oxford Shakespeare scholar Hugh Craig used the t-test in statistics to compare the uses of one hundred function words across plays, authors, genres, characters, and periods in Shakespeare’s era. Craig drew some strong conclusions; for example, that authorship is a greater differentiator between plays than genre. Using both theoretical arguments and the results of further experiments, this note challenges Craig’s analysis, showing that he applied the t-test even when it is not clear that its premises are satisfied, failed to apply necessary controls, and, moreover, that his reasoning contains a fundamental error which invalidates his interpretation of the results.
Be X-ray binaries in the SMC as indicators of mass-transfer efficiency
Authors: Vinciguerra Serena , Neijssel Coenraad J , Vigna-Gómez Alejandro , Mandel Ilya , Podsiadlowski Philipp , Maccarone Thomas J , Nicholl Matt , Kingdon Samuel , Perry Alice , Salemi Francesco
Published: September 2020

Be X-ray binaries (BeXRBs) consist of rapidly rotating Be stars with neutron star (NS) companions accreting from the circumstellar emission disc. We compare the observed population of BeXRBs in the Small Magellanic Cloud (SMC) with simulated populations of BeXRB-like systems produced with the compas population synthesis code. We focus on the apparently higher minimal mass of Be stars in BeXRBs than in the Be population at large. Assuming that BeXRBs experienced only dynamically stable mass transfer, their mass distribution suggests that at least $\sim 30{{\ \rm per\ cent}}$ of the mass donated by the progenitor of the NS is typically accreted by the B-star companion. We expect these results to affect predictions for the population of double compact object mergers. A convolution of the simulated BeXRB population with the star formation history of the SMC shows that the excess of BeXRBs is most likely explained by this galaxy’s burst of star formation ∼20–40 Myr ago.
Active gas features in three HSC-SSP CAMIRA clusters revealed by high angular resolution analysis of MUSTANG-2 SZE and XXL X-ray observations
Authors: Okabe Nobuhiro , Dicker Simon , Eckert Dominique , Mroczkowski Tony , Gastaldello Fabio , Lin Yen-Ting , Devlin Mark , Romero Charles E , Birkinshaw Mark , Sarazin Craig , Horellou Cathy , Kitayama Tetsu , Umetsu Keiichi , Sereno Mauro , Mason Brian S , ZuHone John A , Honda Ayaka , Akamatsu Hiroki , Chiu I-Non , Kohno Kotaro , Lin Kai-Yang , Medezinski Elinor , Miyazaki Satoshi , Mitsuishi Ikuyuki , Nishizawa Atsushi J , Oguri Masamune , Ota Naomi , Pacaud Florian , Pierre Marguerite , Sievers Jonathan , Smolčić Vernesa , Stanchfield Sara , Tanaka Keigo , Yamamoto Ryoichi , Yang Chong , Yoshida Atsushi
Published: September 2020

We present results from simultaneous modelling of high angular resolution GBT/MUSTANG-2 90 GHz Sunyaev–Zel’dovich effect (SZE) measurements and XMM-XXL X-ray images of three rich galaxy clusters selected from the HSC-SSP Survey. The combination of high angular resolution SZE and X-ray imaging enables a spatially resolved multicomponent analysis, which is crucial to understand complex distributions of cluster gas properties. The targeted clusters have similar optical richnesses and redshifts, but exhibit different dynamical states in their member galaxy distributions: a single-peaked cluster, a double-peaked cluster, and a cluster belonging to a supercluster. A large-scale residual pattern in both regular Compton-parameter y and X-ray surface brightness distributions is found in the single-peaked cluster, indicating a sloshing mode. The double-peaked cluster shows an X-ray remnant cool core between two SZE peaks associated with galaxy concentrations. The temperatures of the two peaks reach ∼20–30 keV in contrast to the cool core component of ∼2 keV, indicating a violent merger. The main SZE signal for the supercluster is elongated along a direction perpendicular to the major axis of the X-ray core, suggesting a minor merger before core passage. The SX and y distributions are thus perturbed at some level, regardless of the optical properties. We find that the integrated Compton y parameter and the temperature for the major merger are boosted from those expected by the weak-lensing mass and those for the other two clusters show no significant deviations, which is consistent with predictions of numerical simulations.
Overdensity of SMGs in fields containing z ∼ 0.3 galaxies: magnification bias and the implications for studies of galaxy evolution
Authors: Dunne L , Bonavera L , Gonzalez-Nuevo J , Maddox S J , Vlahakis C
Published: September 2020

We report a remarkable overdensity of high-redshift submillimetre galaxies (SMG), 4–7 times the background, around a statistically complete sample of twelve 250 μm selected galaxies at z = 0.35, which were targeted by ALMA in a study of gas tracers. This overdensity is consistent with the effect of lensing by the haloes hosting the target z = 0.35 galaxies. The angular cross-correlation in this sample is consistent with statistical measures of this effect made using larger sub-mm samples. The magnitude of the overdensity as a function of radial separation is consistent with intermediate scale lensing by haloes of the order of $7\times 10^{13}\mbox{ $\rm M_{\odot }$ }$, which should host one or possibly two bright galaxies and several smaller satellites. This is supported by observational evidence of interaction with satellites in four out of the six fields with SMG, and membership of a spectroscopically defined group for a fifth. We also investigate the impact of these SMG on the reported Herschel fluxes of the z = 0.35 galaxies, as they produce significant contamination in the 350 and 500 μm Herschel bands. The higher than random incidence of these boosting events implies a significantly larger bias in the sub-mm colours of Herschel sources associated with z < 0.7 galaxies than has previously been assumed, with fboost = 1.13, 1.26, 1.44 at 250, 350, and 500 μm . This could have implications for studies of spectral energy distributions, source counts, and luminosity functions based on Herschel samples at z = 0.2–0.7.
Turbulence-induced deviation between baryonic field and dark matter field in the spatial distribution of the Universe
Authors: Yang Hua-Yu , He Ping , Zhu Weishan , Feng Long-Long
Published: September 2020

The cosmic baryonic fluid at low redshifts is similar to a fully developed turbulence. In this work, we use simulation samples produced by the hybrid cosmological hydrodynamical/N-body code, to investigate on what scale the deviation of spatial distributions between baryons and dark matter is caused by turbulence. For this purpose, we do not include the physical processes such as star formation, supernovae (SNe), and active galactic nucleus (AGN) feedback into our code, so that the effect of turbulence heating for IGM can be exhibited to the most extent. By computing cross-correlation functions rm(k) for the density field and rv(k) for the velocity field of both baryons and dark matter, we find that deviations between the two matter components for both density field and velocity field, as expected, are scale-dependent. That is, the deviations are the most significant at small scales and gradually diminish on larger and larger scales. Also, the deviations are time-dependent, i.e. they become larger and larger with increasing cosmic time. The most emphasized result is that the spatial deviations between baryons and dark matter revealed by velocity field are more significant than that by density field. At z = 0, at the $1{{\ \rm per\ cent}}$ level of deviation, the deviation scale is about $3.7\, {h^{-1} {\rm Mpc}}$ for density field, while as large as $23\, {h^{-1} {\rm Mpc}}$ for velocity field, a scale that falls within the weakly non-linear regime for the structure formation paradigm. Our results indicate that the effect of turbulence heating is indeed comparable to that of these processes such as SN and AGN feedback.
On the first δ Sct–roAp hybrid pulsator and the stability of p and g modes in chemically peculiar A/F stars
Authors: Murphy Simon J , Saio Hideyuki , Takada-Hidai Masahide , Kurtz Donald W , Shibahashi Hiromoto , Takata Masao , Hey Daniel R
Published: September 2020

Strong magnetic fields in chemically peculiar A-type (Ap) stars typically suppress low-overtone pressure modes (p modes) but allow high-overtone p modes to be driven. KIC 11296437 is the first star to show both. We obtained and analysed a Subaru spectrum, from which we show that KIC 11296437 has abundances similar to other magnetic Ap stars, and we estimate a mean magnetic field modulus of 2.8 ± 0.5 kG. The same spectrum rules out a double-lined spectroscopic binary, and we use other techniques to rule out binarity over a wide parameter space, so the two pulsation types originate in one δ Sct–roAp hybrid pulsator. We construct stellar models depleted in helium and demonstrate that helium settling is second to magnetic damping in suppressing low-overtone p modes in Ap stars. We compute the magnetic damping effect for selected p and g modes, and find that modes with frequencies similar to the fundamental mode are driven for polar field strengths ≲4 kG, while other low-overtone p modes are driven for polar field strengths up to ∼1.5 kG. We find that the high-order g modes commonly observed in γ Dor stars are heavily damped by polar fields stronger than 1–4 kG, with the damping being stronger for higher radial orders. We therefore explain the observation that no magnetic Ap stars have been observed as γ Dor stars. We use our helium-depleted models to calculate the δ Sct instability strip for metallic-lined A (Am) stars, and find that driving from a Rosseland mean opacity bump at ∼5 × 104 K caused by the discontinuous H-ionization edge in bound-free opacity explains the observation of δ Sct pulsations in Am stars.
Physical conditions of five O vi absorption systems towards PG 1522+101
Authors: Sankar Sriram , Narayanan Anand , Savage Blair D , Khaire Vikram , Rosenwasser Benjamin E , Charlton Jane , Wakker Bart P
Published: September 2020

We present the analysis of five O vi absorbers identified across a redshift path of z ∼ (0.6−1.3) towards the background quasar PG 1522+101 with information on five consecutive ionization stages of oxygen from O ii to O vi. The combined HST and Keck spectra cover UV, redshifted extreme-UV, and optical transitions from a multitude of ions spanning ionization energies in the range of ∼(13−300) eV. Low-ionization (C ii, O ii, Si ii, Mg ii) and very high-ionization species (Ne viii, Mg x) are non-detections in all the absorbers. Three of the absorbers have coverage of He i, in one of which it is a >3σ detection. The kinematic structures of these absorbers are extracted from C iv detected in HIRES spectra. The farthest absorber in our sample also contains the detections of Ne v and Ne vi. Assuming co-spatial absorbing components, the ionization models show the medium to be multiphased with small-scale density–temperature inhomogeneities that are sometimes kinematically unresolved. In two of the absorbers, there is an explicit indication of the presence of a warm gas phase (T ≳ 105 K) traced by O vi. In the remaining absorbers, the column densities of the ions are consistent with a non-uniform photoionized medium. The subsolar [C/O] relative abundances inferred for the absorbers point at enrichment from massive Type II supernovae. Despite metal enrichment, the inferred wide range for [O/H] ∼ [−2.1, +0.2] amongst the absorbers along with their anticorrelation with the observed H i suggest poor small-scale mixing of metals with hydrogen in the regions surrounding galaxies and the IGM.
Joint galaxy–galaxy lensing and clustering constraints on galaxy formation
Authors: Renneby Malin , Henriques Bruno M B , Hilbert Stefan , Nelson Dylan , Vogelsberger Mark , Angulo Raúl E , Springel Volker , Hernquist Lars
Published: September 2020

We compare predictions for galaxy–galaxy lensing profiles and clustering from the Henriques et al. public version of the Munich semi-analytical model (SAM) of galaxy formation and the IllustrisTNG suite, primarily TNG300, with observations from KiDS + GAMA and SDSS-DR7 using four different selection functions for the lenses (stellar mass, stellar mass and group membership, stellar mass and isolation criteria, and stellar mass and colour). We find that this version of the SAM does not agree well with the current data for stellar mass-only lenses with $M_\ast \gt 10^{11}\, \mathrm{ M}_\odot$. By decreasing the merger time for satellite galaxies as well as reducing the radio-mode active galactic nucleus accretion efficiency in the SAM, we obtain better agreement, both for the lensing and the clustering, at the high-mass end. We show that the new model is consistent with the signals for central galaxies presented in Velliscig et al. Turning to the hydrodynamical simulation, TNG300 produces good lensing predictions, both for stellar mass-only (χ2 = 1.81 compared to χ2 = 7.79 for the SAM) and locally brightest galaxy samples (χ2 = 3.80 compared to χ2 = 5.01). With added dust corrections to the colours it matches the SDSS clustering signal well for red low-mass galaxies. We find that both the SAMs and TNG300 predict $\sim 50\, {{\ \rm per\ cent}}$ excessive lensing signals for intermediate-mass red galaxies with 10.2 < log10M*[M⊙] < 11.2 at $r \approx 0.6\, h^{-1}\, \text{Mpc}$, which require further theoretical development.
A revision of the vdB 130 cluster stellar content based on Gaia DR2 data: interstellar extinction toward the Cyg OB1 supershell
Authors: Sitnik T G , Rastorguev A S , Tatarnikova A A , Tatarnikov A M , Egorov O V , Tatarnikov A A
Published: September 2020

Two star-forming regions are studied: the young embedded open cluster vdB 130 and the protocluster neighbourhood observed in the head and tail of the cometary molecular cloud located in the wall of the expanding supershell surrounding the Cyg OB1 association. The Gaia DR2 catalogue is employed to verify the stellar composition of the vdB 130 cluster whose members were earlier selected using the UCAC4 catalogue. The new sample of vdB 130 members contains 68 stars with close proper motions (within 1 mas yr−1) and close trigonometric parallaxes (ranging from 0.50–0.70 mas). The relative parallax error is shown to increase with distance to objects and depend on their magnitude. At a distance of 1.5–2 kpc it is of about 3–7 per cent and 20–30 per cent for bright and faint stars, respectively. The cluster is not older than ∼10 Myr. New spectroscopic and photometric observations carried out on Russian telescopes are combined with Gaia DR2 to search for optical components in the protocluster region – a new starburst. An analysis of 20 stars in the vicinity of the protocluster revealed no concentration of either proper motions or parallaxes. According to spectroscopic, photometric and trigonometric estimates, the distances to these stars range from 0.4–2.5 kpc, and colour excess is shown to increase with a distance D (kpc) in accordance with the law E(B − V) ≃ 0.6 × D mag.
Morphometric analysis of brightest cluster galaxies
Authors: Cougo J , Rembold S B , Ferrari F , Kaipper A L P
Published: September 2020

We study the build-up of the stellar mass of brightest cluster galaxies (BCGs) at z < 0.1 as a function of their morphological type. Morphometric parameters for 1216 BCGs were obtained from the SDSS DR12 r-band images with the code morfometryka. We show that the morphometric parameters are efficient to separate BCGs into cD galaxies, conventional ellipticals, disc-dominated BCGs, and merging objects. We propose a simple classification scheme using two concentration indices, C1 and C2, and the spirality σψ. We then investigate how the stellar masses of BCGs and the velocity dispersions of their parent haloes relate to their morphological properties. We find that BCGs with larger envelope contributions are more massive than BCGs in other classes and more common in massive clusters. The stellar mass and the halo velocity dispersion correlate for all classes, suggesting that environmental effects are important for BCGs of any morphology. At fixed parent halo mass, we detect a continuous mass excess up to $\sim 60{{\ \rm per\ cent}}$ from pure E galaxies to extreme cD galaxies, while the inner regions of such cDs present only $\sim 40{{\ \rm per\ cent}}$ of the mass of an E galaxy. We interpret our findings in a scenario where different BCGs have developed their mass through an asymmetric combination of distinct processes, so that present-time cD galaxies have grown in mass mainly through minor merging and tidal stripping from satellite galaxies, while elliptical BCGs evolve mainly through processes like major merging.