bluuebunny/crossref_metadata_2025 huggingface dataset:
The length scale of multivalent interactions is evolutionarily conserved in fungal and vertebrate phase-separating proteins
Authors: Dasmeh Pouria , Doronin Roman , Wagner Andreas
Published: October 2021

One key feature of proteins that form liquid droplets by phase separation inside a cell is multivalency—the presence of multiple sites that mediate interactions with other proteins. We know little about the variation of multivalency on evolutionary time scales. Here, we investigated the long-term evolution (∼600 million years) of multivalency in fungal mRNA decapping subunit 2 protein (Dcp2), and in the FET (FUS, EWS and TAF15) protein family. We found that multivalency varies substantially among the orthologs of these proteins. However, evolution has maintained the length scale at which sequence motifs that enable protein–protein interactions occur. That is, the total number of such motifs per hundred amino acids is higher and less variable than expected by neutral evolution. To help explain this evolutionary conservation, we developed a conformation classifier using machine-learning algorithms. This classifier demonstrates that disordered segments in Dcp2 and FET proteins tend to adopt compact conformations, which is necessary for phase separation. Thus, the evolutionary conservation we detected may help proteins preserve the ability to undergo phase separation. Altogether, our study reveals that the length scale of multivalent interactions is an evolutionarily conserved feature of two classes of phase-separating proteins in fungi and vertebrates.
Bridge Employment and Longevity: Evidence From a 10-Year Follow-Up Cohort Study in 0.16 Million Chinese
Authors: Yin Ruoyu , Xin Yiqian , Bhura Maria , Wang Zhicheng , Tang Kun
Published: October 2021

Objectives

Bridge employment has been encouraged by many countries worldwide as societies age rapidly. However, the health impact on bridge employment is not consistent in previous studies. This study aims to explore the association between bridge employment and long-term health outcome among the Chinese population.

Methods

In this prospective cohort study, we used a subset of the China Kadoorie Biobank study, in which 163,619 participants who reached the statutory age of retirement at baseline (2004–2008) were included in this study. Mortality statistics were obtained from death registries in the Death Surveillance Points system annually. We used a Cox proportional hazard model to analyze the association between bridge employment and all-cause mortality.

Results

Overall, we found that compared to retired/nonemployed men and women, hazards of all-cause mortality were lower in older people with bridge employment (men: 0.82, 95% confidence interval [CI]: 0.77–0.88; women: 0.79, 95% CI: 0.74–0.94) in healthy populations. The protective effect of bridge employment was stronger among older adults living in rural areas and among those from a relatively low socioeconomic status.

Discussion

The lower risk of all-cause mortality associated with bridge employment was consistently observed among older men and women. Our findings may provide important insights from the health dimension on the retirement policy-making in China as a hyper-aging society.
Wavefield-based evaluation of DAS instrument response and array design
Authors: Muir Jack B , Zhan Zhongwen
Published: October 2021

Distributed acoustic sensing (DAS) networks promise to revolutionize observational seismology by providing cost-effective, highly dense spatial sampling of the seismic wavefield, especially by utilizing pre-deployed telecomm fibre in urban settings for which dense seismic network deployments are difficult to construct. However, each DAS channel is sensitive only to one projection of the horizontal strain tensor and therefore gives an incomplete picture of the horizontal seismic wavefield, limiting our ability to make a holistic analysis of instrument response. This analysis has therefore been largely restricted to pointwise comparisons where a fortuitious coincidence of reference three-component seismometers and colocated DAS cable allows. We evaluate DAS instrument response by comparing DAS measurements from the PoroTomo experiment with strain-rate wavefield reconstructed from the nodal seismic array deployed in the same experiment, allowing us to treat the entire DAS array in a systematic fashion irrespective of cable geometry relative to the location of nodes. We found that, while the phase differences are in general small, the amplitude differences between predicted and observed DAS strain rates average a factor of 2 across the array and correlate with near-surface geology, suggesting that careful assessment of DAS deployments is essential for applications that require reliable assessments of amplitude. We further discuss strategies for empirical gain corrections and optimal placement of point sensor deployments to generate the best combined sensitivity with an already deployed DAS cable, from a wavefield reconstruction perspective.
Full waveform inversion based on the non-parametric estimate of the probability distribution of the residuals
Authors: Carvalho P T C , da Silva S L E F , Duarte E F , Brossier R , Corso G , de Araújo J M
Published: October 2021

In an attempt to overcome the difficulties of the full waveform inversion (FWI), several alternative objective functions have been proposed over the last few years. Many of them are based on the assumption that the residuals (differences between modelled and observed seismic data) follow specific probability distributions when, in fact, the true probability distribution is unknown. This leads FWI to converge to an incorrect probability distribution if the assumed probability distribution is different from the real one and, consequently it may lead the FWI to achieve biased models of the subsurface. In this work, we propose an objective function which does not force the residuals to follow a specific probability distribution. Instead, we propose to use the non-parametric kernel density estimation technique (KDE) (which imposes the least possible assumptions about the residuals) to explore the probability distribution that may be more suitable. As evidenced by the results obtained in a synthetic model and in a typical P-wave velocity model of the Brazilian pre-salt fields, the proposed FWI reveals a greater potential to overcome more adverse situations (such as cycle-skipping) and also a lower sensitivity to noise in the observed data than conventional L2- and L1-norm objective functions and thus making it possible to obtain more accurate models of the subsurface. This greater potential is also illustrated by the smoother and less sinuous shape of the proposed objective function with fewer local minima compared with the conventional objective functions.
Finite-difference modelling of 2-D wave propagation in the vicinity of dipping interfaces: a comparison of anti-aliasing and equivalent medium approaches
Authors: Koene Erik F M , Wittsten Jens , Robertsson Johan O A
Published: October 2021

Finite-difference (FD) modelling of seismic waves in the vicinity of dipping interfaces gives rise to artefacts. Examples are phase and amplitude errors, as well as staircase diffractions. Such errors can be reduced in two general ways. In the first approach, the interface can be anti-aliased (i.e. with an anti-aliased step-function, or a lowpass filter). Alternatively, the interface may be replaced with an equivalent medium (i.e. using Schoenberg & Muir (SM) calculus or orthorhombic averaging). We test these strategies in acoustic, elastic isotropic, and elastic anisotropic settings. Computed FD solutions are compared to analytical solutions. We find that in acoustic media, anti-aliasing methods lead to the smallest errors. Conversely, in elastic media, the SM calculus provides the best accuracy. The downside of the SM calculus is that it requires an anisotropic FD solver even to model an interface between two isotropic materials. As a result, the computational cost increases compared to when using isotropic FD solvers. However, since coarser grid spacings can be used to represent the dipping interfaces, the two effects (an expensive FD solver on a coarser FD grid) equal out. Hence, the SM calculus can provide an efficient means to reduce errors, also in elastic isotropic media.
Investigating the effects of random data errors on the waveform-based moment tensor inversion
Authors: Moghtased-Azar K , Zeynal-Kheiri H , Hallo M
Published: October 2021

The linear Gauss–Markov model for waveform-based moment tensor inversion often relies on the overdetermined least-squares method. It needs a proper stochastic model of the observables for accurate and precise estimates of the unknown parameters. Furthermore, estimating the level and distribution of random errors in the observed waveforms is challenging due to assessing the minimum-variance unbiased estimator (MVUE). Hence, according to the considerable effects of random data errors in assessing the uncertainty of the moment tensor components, this paper aims to describe an MVUE of the data covariance matrix and its application on uncertainty quantification of the moment tensor. The used mathematical prescription allows us to use the covariance matrix for the three-component noise records at every station and all possible cross-correlations among the recorded noise wavefield. To illustrate the proposed method’s performance, we conducted tests with synthetic data using configuration of the 2018 Mw 6.8 Zakynthos (Ionian Sea, Greece) earthquake. Both uncorrelated and correlated random noise traces were added to the synthetic waveform data in amounts between 5 and 20 per cent of the maximum amplitude. In order to test the efficiency of the method, we considered three different structures of covariance matrix: (i) diagonal matrix (contains a variance of individual measurements at seismic stations), (ii) block-diagonal matrix (considering cross-covariance among three components at each station), and (iii) full covariance matrix. Test results are presented by comparison of the moment tensor inversion outcomes with known noise levels of generated synthetic data and with synthetic focal mechanisms, the ability of the estimated full covariance matrix in illustrating the minimum variance of parameters (namely, minimum posterior uncertainties), unbiased of the parameters, and values of the cross-correlations between the components of each station and also among stations. Finally, we applied the method to the real waveforms of the Zakynthos earthquake having inferred focal mechanism of strike/dip/rake angles 13/40/171 (deg) with 33 per cent double couple (DC) and −61 per cent compensated linear vector dipole component (CLVD). The focal mechanism solution has strike/dip/rake angles 19/34/177 (deg) with 69 per cent DC and −23 per cent CLVD when using our estimated full covariance matrix.
Participant engagement with a short, wordless, animated video on COVID-19 prevention: a multi-site randomized trial
Authors: Favaretti Caterina , Adam Maya , Greuel Merlin , Hachaturyan Violetta , Gates Jennifer , Bärnighausen Till , Vandormael Alain
Published: October 2021

COVID-19 misinformation has spread rapidly across social media. To counter misinformation, we designed a short, wordless and animated video (called the CoVideo) to deliver scientifically informed and emotionally compelling information about preventive COVID-19 behaviours. After 15 163 online participants were recruited from Germany, Mexico, Spain, the UK and the USA, we offered participants in the attention placebo control (APC) and do-nothing arms the option to watch the CoVideo (without additional compensation) as post-trial access to treatment. The objective of our study was to evaluate participant engagement by quantifying (i) the proportion of participants opting to watch the CoVideo and (ii) the duration of time spent watching the CoVideo. We quantified the CoVideo opt-in and view time by experimental arm, age, gender, educational status, country of residence and COVID-19 prevention knowledge. Overall engagement with the CoVideo was high: 72% of the participants [CI: 71.1%; 73.0%] opted to watch the CoVideo with an average view time of 138.9 out of 144.0 s [CI: 138.4; 139.4], with no statistically significant differences by arm. Older participants (35–59 years) and participants with higher COVID-19 prevention knowledge had higher view times than their counterparts. Spanish participants had the highest opt-in percentage whereas Germans exhibited the shortest view times of the five countries. Short, wordless and animated storytelling videos, optimized for ‘viral spread’ on social media, can enhance global engagement with COVID-19 prevention messages by transcending cultural, language and literary barriers.
Effectiveness of theory-based Multimedia Messaging Service (MMS) on exercise benefits and barriers among patients with type 2 diabetes
Authors: Al-Sheyab Nihaya A , Alyahya Mohammad S , Alqudah Jumana A
Published: October 2021

The current study aimed to examine the effectiveness of multimedia messaging service (MMS) education on exercise benefits and barriers in patients with type 2 diabetes. A quasi-experimental, pretest–post-test design recruited 98 patients with type 2 diabetes. The intervention group received MMS education to improve perceived exercise benefits and decrease exercise barriers over two months, and the control group received routine care. All patients completed a survey at three time points (baseline, 4 and 8 weeks post-intervention). The results showed that there was an improvement in both perceived life enhancement and physical performance domains in the intervention group. The exercise context barriers decreased after the first follow-up but increased during the second follow-up in the intervention group. Cohen’s d values indicated a medium effect size in life enhancement (0.502) and physical performance (0.525) subscales. A small effect size was found in psychological outlook (0.196) and exercise context (0.132) subscales. However, there was no significant effect of the intervention in time expenditure (−0.244) and physical exertion (−0.119) subscales. In conclusion, theoretically based MMS health education targeting perceived exercise benefits and barriers was feasible and cost-effective in changing patients with diabetes’ perceptions and intended behaviors about regular physical activity.
‘I say I must for I am the kings Shrieve’: magistrates invoking the monarch’s name in 1 Henry VI (1592) and The Downfall of Robert Earl of Huntingdon (1598)
Authors: Clarke Lucy J S
Published: October 2021

This article examines the presentation of magistrates invoking the king’s name in two 1590s plays from the popular theatres. It examines what these moments of invoking the king’s name suggest about the state and its structure in these plays, linking the drama to recent historiography on the manifestation of the state in arrests and other magisterial interventions, conceptualizing the state as an entity that was performed into reality. It argues that both plays engage with anxiety over the succession, with little hope that a state without a strong monarch can function properly.
The Jun-dependent axon regeneration gene program: Jun promotes regeneration over plasticity
Authors: Mason Matthew R J , van Erp Susan , Wolzak Kim , Behrens Axel , Raivich Gennadij , Verhaagen Joost
Published: October 2021

The regeneration-associated gene (RAG) expression program is activated in injured peripheral neurons after axotomy and enables long-distance axon re-growth. Over 1000 genes are regulated, and many transcription factors are upregulated or activated as part of this response. However, a detailed picture of how RAG expression is regulated is lacking. In particular, the transcriptional targets and specific functions of the various transcription factors are unclear. Jun was the first-regeneration-associated transcription factor identified and the first shown to be functionally important. Here we fully define the role of Jun in the RAG expression program in regenerating facial motor neurons. At 1, 4 and 14 days after axotomy, Jun upregulates 11, 23 and 44% of the RAG program, respectively. Jun functions relevant to regeneration include cytoskeleton production, metabolic functions and cell activation, and the downregulation of neurotransmission machinery. In silico analysis of promoter regions of Jun targets identifies stronger over-representation of AP1-like sites than CRE-like sites, although CRE sites were also over-represented in regions flanking AP1 sites. Strikingly, in motor neurons lacking Jun, an alternative SRF-dependent gene expression program is initiated after axotomy. The promoters of these newly expressed genes exhibit over-representation of CRE sites in regions near to SRF target sites. This alternative gene expression program includes plasticity-associated transcription factors and leads to an aberrant early increase in synapse density on motor neurons. Jun thus has the important function in the early phase after axotomy of pushing the injured neuron away from a plasticity response and towards a regenerative phenotype.
Weight-for-height is associated with an overestimation of thinness burden in comparison to BMI-for-age in under-5 populations with high stunting prevalence
Authors: Naga Rajeev L , Saini Monika , Kumar Ashish , Sinha Sikha , Osmond Clive , Sachdev Harshpal Singh
Published: October 2021

Background

Thinness at <5 years of age, also known as wasting, is used to assess the nutritional status of populations for programmatic purposes. Thinness may be defined when either weight-for-height or body-mass-index-for-age (BMI-for-age) are below –2 SD of the respective World Health Organization standards. These definitions were compared for quantifying the burden of thinness.

Methods

Theoretical consequences of ignoring age were evaluated by comparing, at varying height-for-age z-scores, the age- and sex-specific cut-offs of BMI that would define thinness with these two metrics. Thinness prevalence was then compared in simulated populations (short, intermediate and tall) and real-life data sets from research and the National Family Health Survey-4 (NFHS-4) in India.

Results

In short (–2 SD) children, the BMI cut-offs with weight-for-height criteria were higher in comparison to BMI-for-age after 1 year of age but lower at earlier ages. In Indian research and NFHS-4 data sets (short populations), thinness prevalence with weight-for-height was lower from 0.5 to 1 years but higher at subsequent ages. The absolute difference (weight-for-height – BMI-for-age) for 0.5–5 years was 4.6% (15.9–11.3%) and 2.2% (19.2–17.0%), respectively; this attenuated in the 0–5 years age group. The discrepancy was higher in boys and maximal for stunted children, reducing with increasing stature. In simulated data sets from intermediate and tall populations, there were no meaningful differences.

Conclusions

The two definitions produce cut-offs, and hence estimates of thinness, that differ with the age, sex and height of children. The relative invariance, with age and stature, of the BMI-for-age thinness definition favours its use as the preferred index for programmatic purposes.
MR1, an immunological periscope of cellular metabolism
Authors: Chancellor Andrew , Vacchini Alessandro , De Libero Gennaro
Published: October 2021

The discovery that major histocompatibility complex (MHC) class I-related molecule 1 (MR1) presents microbial antigens to mucosal-associated invariant T (MAIT) cells was a significant scientific milestone in the last decade. Surveillance for foreign metabolically derived antigens added a new class of target structures for immune recognition. The recent identification of a second family of MR1-restricted T cells, called MR1T cells, which show self-reactivity suggests the microbial antigens characterized so far may only represent a handful of the potential structures presented by MR1. Furthermore, the reactivity of MR1T cells towards tumours and not healthy cells indicates tight regulation in the generation of self-antigens and in MR1 expression and antigen loading. These novel and exciting observations invite consideration of new perspectives of MR1-restricted antigen presentation and its wider role within immunity and disease.
Standard ganciclovir dosing results in slow decline of cytomegalovirus viral loads
Authors: Märtson Anne-Grete , Sturkenboom Marieke G. G. , Knoester Marjolein , van der Werf Tjip S. , Alffenaar Jan-Willem C. , Hope William ,   GATEWAY-1 Study Consortium, Edwina Angela E. , Burgerhof Johannes G. M. , Berger Stefan P. , de Joode Anoek , Damman Kevin , Verschuuren Erik A. M. , Blokzijl Hans , Bakker Martijn , Touw Daan J. , rtson Anne-Grete Mä , Sturkenboom Marieke G. G. , Knoester Marjolein , van der Werf Tjip S. , Alffenaar Jan-Willem C.
Published: October 2021

Background

Cytomegalovirus (CMV) can cause severe disease, including rejection in transplant recipients. Ganciclovir and its oral prodrug valganciclovir have been used as first-line therapy for CMV disease in transplant recipients. The exposure targets of ganciclovir are not exactly known, and toxicity and resistance have interfered with ganciclovir therapy.

Objectives

To evaluate the pharmacokinetics (PK) and pharmacodynamics (PD) of ganciclovir in transplant recipients.

Methods

We used patient data from a previous observational study on ganciclovir therapeutic drug monitoring (TDM) in prophylaxis and therapy. The ganciclovir concentrations and CMV viral loads were determined during routine clinical care. The PK/PD population modelling and simulations were done with non-parametric methodology using the Pmetrics program.

Results

Eighty-five patients were included in the PK modelling. The final PK model was a two-compartment model with first-order absorption and elimination. A subset of 17 patients on CMV therapy were included in the PD modelling. A median of 4 (range 2–8) viral loads were obtained per patient. A simulation of 10 000 patients showed that an approximately 1 log10 reduction of CMV viral load will be observed after 12.5 days at the current recommended dose.

Conclusions

The developed linked PK/PD population model and subsequent PD simulations showed slow decline of CMV viral load and it appears that dosing of (val)ganciclovir in this study might have been inadequate to achieve fast reduction of viral load. It is clear that further studies are needed to specify the PD effects of ganciclovir by performing systematic measurements of both ganciclovir concentrations and CMV viral loads.
Patient Safety Culture in Burn Care Units from the Perspectives of Healthcare Providers: A Cross-sectional Study
Authors: Moghimian Maryam , Farzi Sedigheh , Farzi Kolsoum , Tarrahi Mohammad Javad , Ghasemi Hossein , Jafari Fatemeh , Bighamian Safoura
Published: October 2021

Creating a positive patient safety culture is a key step in the improvement of patient safety in healthcare settings. Patient safety culture (PSC) is a set of shared attitudes, beliefs, and perceptions about patient safety (PS) among healthcare providers. This study aimed to assess PSC in burn care units from the perspectives of healthcare providers. This cross-sectional descriptive study was conducted in 2020 in the units of a specialty burn center. Participants were 213 healthcare providers recruited to the study through a census. A demographic questionnaire and the Hospital Survey on Patient Safety Culture were used for data collection. Data were managed using the SPSS16 software and were summarized using the measures of descriptive statistics. The mean of positive responses to PSC items was 51.22%, denoting a moderate-level PSC. The lowest and the highest dimensional mean scores were related to the no punitive response to error dimension (mean: 12.36%) and the teamwork within departments dimension (mean: 73.25%), respectively. Almost half of the participants (49.3%) reported acceptable PS level in their workplace and 69.5% of them had not reported any error during the past 12 months before the study. Given the great vulnerability of patients with burn injuries in clinical settings, improving PSC, particularly in the no punitive response to error dimension, is essential to encourage healthcare providers for reporting their errors and thereby, to enhance PS. For quality care delivery, healthcare providers in burn care units need a safe workplace, adequate managerial support, a blame-free PSC, and an incentive error reporting system to readily report their errors.
Gender Equality in the Decision-Making Processes of Post-War Societies: Evidence from Iraqi Kurdistan
Authors: Bagheri Saeed
Published: October 2021

During the war with Islamic State in northern Iraq (2014–17), a notable number of Kurdish women joined the Peshmerga (Iraqi-Kurdish fighters), the military forces of the Kurdish Regional Government (KRG) in an effort to prevent Islamic State’s advance into the oil-rich city of Kirkuk. Besides causing international resonance, the presence of women fighters was publicized by the KRG as a sign of modernity and gender equality. However, once the war ended, in the peace negotiations between the KRG and the Iraqi central government, the role of Kurdish women was drastically reduced. By examining the events that took place in Kirkuk before and after Islamic State and the diplomatic follow-up, this article analyses the role of women in a war to peace transition, focusing specifically on the power-sharing process to ensure that their effective and equal participation in decision-making is respected. The article provides an insight into respect for international human rights law, management of gender equality and the role of women in legal and political systems against the backdrop of the clash over Kirkuk and a complex power-sharing process in post-war Iraq.
Two new species ofPeromyscus(Cricetidae: Neotominae) from the Transverse Volcanic Belt of Mexico
Authors: Bradley Robert D , Ordóñez-Garza Nicté , Thompson Cody W , Wright Emily A , Ceballos Gerardo , Kilpatrick C William , Schmidly David J
Published: October 2021

Specimens of the Peromyscus boylii species group distributed in the western and northeastern montane regions of Michoacán, México, historically have been assigned to P. levipes. Previous studies indicated that these specimens possessed mitochondrial DNA haplotypes that were distinct from both P. levipes and P. kilpatricki, a recently named species in the P. boylii species group from northeastern Michoacán and western Morelos. Herein karyotypic, DNA sequence, and morphological data were analyzed from those populations to evaluate their taxonomic affinity. Karyotypic data indicated that individuals from western Michoacán (Dos Aguas and Aguililla) and from a newly discovered population in northeastern Michoacán (Zinapécuaro) were chromosomally similar to P. carletoni (FN = 68) but distinct from other taxa assigned to the P. boylii species group. Analyses of cranial characteristics indicated that, relative to other species in the P. boylii species group, two morphologically distinct groups were present that corresponded to the Dos Aguas/Aguililla and Zinapécuaro populations, respectively. The latter population, although represented by a small sample size (n = 5 specimens), appeared to exhibit some trenchant morphological distinctions compared with other cryptic species in the P. boylii group. Phylogenetic analyses (parsimony, Bayesian, and likelihood) of DNA sequences obtained from the mitochondrial cytochrome-b gene indicated that although the individuals from Dos Aguas/Aguililla and Zinapécuaro formed a sister group relationship, they formed monophyletic clades that differed genetically (2.54%)—a level approaching that seen between other sister species of Peromyscus. Further, the Dos Aguas/Aguililla and Zinapécuaro clade was more closely aligned with a clade containing representatives of P. carletoni and P. levipes instead of with those from closer geographic proximities (P. kilpatricki) located in eastern Michoacán. Together, these results indicated that these two populations seemingly represent two undescribed species in the P. boylii species group for which we propose the names Peromyscus greenbaumi for populations in western Michoacán (circa Dos Aguas and Aguililla) and Peromyscus ensinki for populations in northeastern Michoacán (circa Zinapécuaro).
Future Applications of Metagenomic Next-Generation Sequencing for Infectious Diseases Diagnostics
Authors: Haslam David B
Published: October 2021

Metagenomic next-generation sequencing (mNGS) has the theoretical capacity to detect any microbe present in a host. mNGS also has the potential to infer a pathogen’s phenotypic characteristics, including the ability to colonize humans, cause disease, and resist treatment. Concurrent host nucleic acid sequencing can assess the infected individual’s physiological state, including characterization and appropriateness of the immune response. When the pathogen cannot be identified, host RNA sequencing may help infer the organism’s nature. While the full promise of mNGS remains far from realization, the potential ability to identify all microbes in a complex clinical sample, assess each organism’s virulence and antibiotic susceptibility traits, and simultaneously characterize the host’s response to infection provide opportunities for mNGS to supplant existing technologies and become the primary method of infectious diseases diagnostics.
Needle insufflation into the liver as a cause of massive gas embolus and CVA
Authors: McIntosh Pamela G , Andrew Chris G
Published: October 2021

Laparoscopy is being applied more frequently and in broader applications. Complications of this technique are infrequent, and rare among them are gas emboli due to insufflation. This paper describes a 65-year-old obese female presenting for elective laparoscopic cholecystectomy who suffered a cerebral vascular accident after Veress needle insertion into undiagnosed severe fatty liver led to a massive gas embolus. Our patient experienced immediate cardiac compromise and acute monoparesis. Intra-operative transesophageal echocardiogram revealed copious air in the right atria and ventricle. A needle track within the liver was visible on a post-operative computerized tomography scan. The patient made a full recovery, but this acts as a reminder to be vigilant for potential complications of laparoscopy and highlights challenges of laparoscopic entry in the severely obese.
Finding our way home: A theory and pedagogy of anti-colonial Q-mapping
Authors: Gairola Rahul K
Published: October 2021

This brief-report details my experiences teaching critical theory at the intersection of race/ class/ gender/ sexuality/ nationality through analogue mapping exercises from my tutorial room at Murdoch University in Western Australia to a group mapping project at the 2018 Digital Humanities Summer Institute (DHSI) at the University of Victoria, Canada (UVic). Given the proximity of both countries to the history of the British Empire and current affiliation of both with the Commonwealth, my report details teaching efforts to mediate against a “pedagogy of the digitally oppressed.” In drawing on the formative concept offered by Brazilian educator-theorist Paulo Freire, I juxtapose the analogue mapping exercises through interposed lens of postcolonial, race, and queer theory. Recognizing the dominant ideologies encoded within technology, I narrate the process in which team members and I from the QDH: Queer Digital Humanities seminar produced participatory, de-centralized maps as counter sites of identity to the colonialist spaces and insignias on the UVic campus. I conclude with collective queer of colour principles which undergird the DHSI exercise, which is a modality of what might best be described as “anti-colonial Q-mapping.”
The impact of metallicity on nova populations
Authors: Kemp Alex J , Karakas Amanda I , Casey Andrew R , Kobayashi Chiaki , Izzard Robert G
Published: October 2021

The metallicity of a star affects its evolution in a variety of ways, changing stellar radii, luminosities, lifetimes, and remnant properties. In this work, we use the population synthesis code binary_c to study how metallicity affects novae in the context of binary stellar evolution. We compute a 16-point grid of metallicities ranging from Z = 10−4 to 0.03, presenting distributions of nova white dwarf masses, accretion rates, delay-times, and initial system properties at the two extremes of our 16-point metallicity grid. We find a clear anticorrelation between metallicity and the number of novae produced, with the number of novae at Z = 0.03 roughly half that at Z = 10−4. The white dwarf mass distribution has a strong systematic variation with metallicity, while the shape of the accretion rate distribution is relatively insensitive. We compute a current nova rate of approximately 33 novae per year for the Milky Way, a result consistent with observational estimates relying on extra-Galactic novae but an under-prediction relative to observational estimates relying on Galactic novae. However, the shape of our predicted Galactic white dwarf mass distribution differs significantly to existing observationally derived distributions, likely due to our underlying physical assumptions. In M31, we compute a current nova rate of approximately 36 novae per year, under-predicting the most recent observational estimate of $65^{+15}_{-16}$. Finally, we conclude that when making predictions about currently observable nova rates in spiral galaxies, or stellar environments where star formation has ceased in the distant past, metallicity can likely be considered of secondary importance compared to uncertainties in binary stellar evolution.
Five per cent measurements of the growth rate from simulation-based modelling of redshift-space clustering in BOSS LOWZ
Authors: Lange Johannes U , Hearin Andrew P , Leauthaud Alexie , van den Bosch Frank C , Guo Hong , DeRose Joseph
Published: October 2021

We use a simulation-based modelling approach to analyse the anisotropic clustering of the BOSS LOWZ sample over the radial range $0.4 \, h^{-1} \, \mathrm{Mpc}$ to $63 \, h^{-1} \, \mathrm{Mpc}$, significantly extending what is possible with a purely analytic modelling framework. Our full-scale analysis yields constraints on the growth of structure that are a factor of two more stringent than any other study on large scales at similar redshifts. We infer fσ8 = 0.471 ± 0.024 at $z$ ≈ 0.25, and fσ8 = 0.430 ± 0.025 at $z$ ≈ 0.40; the corresponding ΛCDM predictions of the Planck cosmic microwave background (CMB) analysis are 0.470 ± 0.006 and 0.476 ± 0.005, respectively. Our results are thus consistent with Planck, but also follow the trend seen in previous low-redshift measurements of fσ8 falling slightly below the ΛCDM + CMB prediction. We find that small- and large-radial scales yield mutually consistent values of fσ8, but there are 1−2.5σ hints of small scales ($\lt 10 \, h^{-1} \, \mathrm{Mpc}$) preferring lower values for fσ8 relative to larger scales. We analyse the constraining power of the full range of radial scales, finding that most of the multipole information about fσ8 is contained in the scales $2 \, h^{-1} \, \mathrm{Mpc}\lesssim s \lesssim 20 \, h^{-1} \, \mathrm{Mpc}$. Evidently, once the cosmological information of the quasi-to-nonlinear regime has been harvested, large-scale modes contain only modest additional information about structure growth. Finally, we compare predictions for the galaxy–galaxy lensing amplitude of the two samples against measurements from SDSS and assess the lensing-is-low effect in light of our findings.
Multifidelity emulation for the matter power spectrum using Gaussian processes
Authors: Ho Ming-Feng , Bird Simeon , Shelton Christian R
Published: October 2021

We present methods for emulating the matter power spectrum by combining information from cosmological N-body simulations at different resolutions. An emulator allows estimation of simulation output by interpolating across the parameter space of a limited number of simulations. We present the first implementation in cosmology of multifidelity emulation, where many low-resolution simulations are combined with a few high-resolution simulations to achieve an increased emulation accuracy. The power spectrum’s dependence on cosmology is learned from the low-resolution simulations, which are in turn calibrated using high-resolution simulations. We show that our multifidelity emulator predicts high-fidelity (HF) counterparts to percent-level relative accuracy when using only three HF simulations and outperforms a single-fidelity emulator that uses 11 simulations, although we do not attempt to produce a converged emulator with high absolute accuracy. With a fixed number of HF training simulations, we show that our multifidelity emulator is ≃100 times better than a single-fidelity emulator at $k \le 2 \, h\textrm {Mpc}{^{-1}}$, and ≃20 times better at $3 \le k \lt 6.4 \, h\textrm {Mpc}{^{-1}}$. Multifidelity emulation is fast to train, using only a simple modification to standard Gaussian processes. Our proposed emulator shows a new way to predict non-linear scales by fusing simulations from different fidelities.
On the detection of multiple shock fronts in A1914 using deep Chandra X-ray observations
Authors: Rahaman Majidul , Raja Ramij , Datta Abhirup
Published: October 2021

Here, we report the new detection of three shock fronts using archival Chandra X-ray observations in Abell 1914, which also hosts a radio halo, a radio phoenix, and a head–tail galaxy. In this study, we report the X-ray shock front at the position of the radio phoenix, which further strengthens the scenario that radio phoenix traces old plasma that gets lit up when compressed by shock passage. We further analyse the thermodynamic structure of the cluster in detail. We create temperature maps of A1914 using three different techniques, namely adaptive circular binning, weighted Voronoi tessellations, and contour binning method. These thermodynamic maps, along with the pseudo-pressure and the pseudo-entropy maps for the cluster, are evidence of disturbed morphology produced by multiple merger events. These merger events create cluster-wide turbulence, which may reaccelerate the relativistic particles and result in a radio halo within the cluster. Further, comparing X-ray and radio images reveals that the radio halo is contained within two X-ray shock fronts. Our analysis suggests that A1914 has both equatorial shock and axial shock within the cluster’s intracluster medium. We proposed a dual merging scenario based on the shock position and analysis of the thermodynamic maps obtained from the deeper Chandra X-ray observations.
Population Genomics of Wall Lizards Reflects the Dynamic History of the Mediterranean Basin
Authors: Yang Weizhao , Feiner Nathalie , Salvi Daniele , Laakkonen Hanna , Jablonski Daniel , Pinho Catarina , Carretero Miguel A , Sacchi Roberto , Zuffi Marco A L , Scali Stefano , Plavos Konstantinos , Pafilis Panayiotis , Poulakakis Nikos , Lymberakis Petros , Jandzik David , Schulte Ulrich , Aubret Fabien , Badiane Arnaud , Perez i de Lanuza Guillem , Abalos Javier , While Geoffrey M , Uller Tobias
Published: October 2021

The Mediterranean Basin has experienced extensive change in geology and climate over the past six million years. Yet, the relative importance of key geological events for the distribution and genetic structure of the Mediterranean fauna remains poorly understood. Here, we use population genomic and phylogenomic analyses to establish the evolutionary history and genetic structure of common wall lizards (Podarcis muralis). This species is particularly informative because, in contrast to other Mediterranean lizards, it is widespread across the Iberian, Italian, and Balkan Peninsulas, and in extra-Mediterranean regions. We found strong support for six major lineages within P. muralis, which were largely discordant with the phylogenetic relationship of mitochondrial DNA. The most recent common ancestor of extant P. muralis was likely distributed in the Italian Peninsula, and experienced an “Out-of-Italy” expansion following the Messinian salinity crisis (∼5 Mya), resulting in the differentiation into the extant lineages on the Iberian, Italian, and Balkan Peninsulas. Introgression analysis revealed that both inter- and intraspecific gene flows have been pervasive throughout the evolutionary history of P. muralis. For example, the Southern Italy lineage has a hybrid origin, formed through admixture between the Central Italy lineage and an ancient lineage that was the sister to all other P. muralis. More recent genetic differentiation is associated with the onset of the Quaternary glaciations, which influenced population dynamics and genetic diversity of contemporary lineages. These results demonstrate the pervasive role of Mediterranean geology and climate for the evolutionary history and population genetic structure of extant species.
Mast cells can produce transforming growth factor β1 and promote tissue fibrosis during the development of Sjögren’s syndrome-related sialadenitis
Authors: Kaieda Shinjiro , Fujimoto Kyoko , Todoroki Keita , Abe Yushi , Kusukawa Jingo , Hoshino Tomoaki , Ida Hiroaki
Published: October 2021

Objectives

This study investigated the associations of mast cells with immune-mediated inflammation and fibrosis in patients with primary Sjögren’s syndrome (pSS); it also explored the underlying pathophysiology of pSS-related sialadenitis.

Methods

Twenty-two patients with pSS and 10 patients with sicca (control individuals) underwent labial salivary gland biopsies. Sections were subjected to staining and immunofluorescence analyses. HMC-1 human mast cells were cocultured with fibroblasts in vitro; fibroblasts were also grown in HMC-1 conditioned medium. mRNA levels of collagen Type I (Col1a) and transforming growth factor (TGF)β1 were analysed in cultured cells.

Results

Mast cell numbers in labial salivary glands were significantly greater in patients with pSS than in control individuals. In salivary glands from patients with pSS, mast cell number was significantly correlated with fibrosis extent; moreover, mast cells were located near fibrous tissue and expressed TGFβ1. Col1a and TGFβ1 mRNAs were upregulated in cocultured fibroblasts and HMC-1 cells, respectively. Fibroblasts cultured in HMC-1 conditioned medium exhibited upregulation of Col1a mRNA; this was abrogated by TGFβ1 neutralizing antibodies.

Conclusions

Mast cell numbers were elevated in patients with pSS-related sialadenitis; these cells were located near fibroblasts and expressed TGFβ1. TGFβ1 could induce collagen synthesis in fibroblasts, which might contribute to fibrosis.
A set of accessible enhancers enables the initial response of breast cancer cells to physiological progestin concentrations
Authors: Zaurin Roser , Ferrari Roberto , Nacht Ana Silvina , Carbonell Jose , Le Dily Francois , Font-Mateu Jofre , de Llobet Cucalon Lara Isabel , Vidal Enrique , Lioutas Antonios , Beato Miguel , Vicent Guillermo P
Published: October 2021

Here, we report that in T47D breast cancer cells 50 pM progestin is sufficient to activate cell cycle entry and the progesterone gene expression program. At this concentration, equivalent to the progesterone blood levels found around the menopause, progesterone receptor (PR) binds only to 2800 genomic sites, which are accessible to ATAC cleavage prior to hormone exposure. These highly accessible sites (HAs) are surrounded by well-organized nucleosomes and exhibit breast enhancer features, including estrogen receptor alpha (ERα), higher FOXA1 and BRD4 (bromodomain containing 4) occupancy. Although HAs are enriched in RAD21 and CTCF, PR binding is the driving force for the most robust interactions with hormone-regulated genes. HAs show higher frequency of 3D contacts among themselves than with other PR binding sites, indicating colocalization in similar compartments. Gene regulation via HAs is independent of classical coregulators and ATP-activated remodelers, relying mainly on MAP kinase activation that enables PR nuclear engagement. HAs are also preferentially occupied by PR and ERα in breast cancer xenografts derived from MCF-7 cells as well as from patients, indicating their potential usefulness as targets for therapeutic intervention.
Phospho-Ku70 induced by DNA damage interacts with RNA Pol II and promotes the formation of phospho-53BP1 foci to ensure optimal cNHEJ
Authors: Schellenbauer Amelie , Guilly Marie-Noelle , Grall Romain , Le Bars Romain , Paget Vincent , Kortulewski Thierry , Sutcu Haser , Mathé Cécile , Hullo Marie , Biard Denis , Leteurtre François , Barroca Vilma , Corre Youenn , Irbah Lamya , Rass Emilie , Theze Benoit , Bertrand Pascale , Demmers Jeroen A A , Guirouilh-Barbat Josée , Lopez Bernard S , Chevillard Sylvie , Delic Jozo
Published: October 2021

Canonical non-homologous end-joining (cNHEJ) is the prominent mammalian DNA double-strand breaks (DSBs) repair pathway operative throughout the cell cycle. Phosphorylation of Ku70 at ser27-ser33 (pKu70) is induced by DNA DSBs and has been shown to regulate cNHEJ activity, but the underlying mechanism remained unknown. Here, we established that following DNA damage induction, Ku70 moves from nucleoli to the sites of damage, and once linked to DNA, it is phosphorylated. Notably, the novel emanating functions of pKu70 are evidenced through the recruitment of RNA Pol II and concomitant formation of phospho-53BP1 foci. Phosphorylation is also a prerequisite for the dynamic release of Ku70 from the repair complex through neddylation-dependent ubiquitylation. Although the non-phosphorylable ala-Ku70 form does not compromise the formation of the NHEJ core complex per se, cells expressing this form displayed constitutive and stress-inducible chromosomal instability. Consistently, upon targeted induction of DSBs by the I-SceI meganuclease into an intrachromosomal reporter substrate, cells expressing pKu70, rather than ala-Ku70, are protected against the joining of distal DNA ends. Collectively, our results underpin the essential role of pKu70 in the orchestration of DNA repair execution in living cells and substantiated the way it paves the maintenance of genome stability.
Real-time tracking of ER turnover during ERLAD by a rhenium complex via lifetime imaging
Authors: Hao Liang , Ling Yu-Yi , Huang Zhi-Xin , Pan Zheng-Yin , Tan Cai-Ping , Mao Zong-Wan
Published: October 2021

Endoplasmic reticulum (ER) degradation by autophagy (ER-phagy) is a recently revealed selective autophagy pathway that plays important roles in organelle turnover and protein degradation, but the biological functions of ER-phagy are largely unknown. Here, we present an ER-targeting Re(I) tricarbonyl complex (Re-ERLAD) that can accumulate in the ER, induce ER-to-lysosome-associated degradation (ERLAD) upon visible light irradiation, and label ER buds and track their morphological alterations during ER-phagy. The emission of Re-ERLAD is sensitive to viscosity, which is a key parameter reflecting the amount of unfolded protein in the ER. Quantitative detection using two-photon fluorescence lifetime imaging microscopy shows that ER viscosity initially increases and then decreases during ERLAD, which reveals that ERLAD is a pathway for alleviating ER stress caused by unfolded proteins. In conclusion, our work presents the first specific photoinducer and tracker of ERLAD, which can be used in studying the regulatory mechanism and function of this process.
A Better Way to Measure Climate Footprints
Authors: Gordon Deborah
Published: October 2021

Chapter 3 presents the Oil Climate Index plus Gas (OCI+), the first open-source tool that assesses and compares the different climate effects of the wide range of oils produced around the world, taking into account upstream, midstream, and downstream emissions. The chapter walks through the motivation behind creating the OCI+ with collaborators from Stanford University and the University of Calgary. The underlying models composing the OCI+ are discussed and visualized in detail. Model data and uncertainty are fleshed out. The chapter discusses methods for evaluating OCI+ emissions using remote sensing, satellites that spot flares from space, and an expanding array of methane measurement instruments. Possible avenues to build out the OCI+ to include other air pollutants are presented. The chapter concludes by laying out estimated ranges of currently modeled emissions intensities of global oil and gas supplies.