bluuebunny/crossref_metadata_2025 huggingface dataset:
Integrated ACMG-approved genes and ICD codes for the translational research and precision medicine
Authors: Wable Raghunandan , Nair Achuth Suresh , Pappu Anirudh , Pierre-Louis Widnie , Abdelhalim Habiba , Patel Khushbu , Mendhe Dinesh , Bolla Shreyas , Mittal Sahil , Ahmed Zeeshan
Published: May 2023

A timely understanding of the biological secrets of complex diseases will ultimately benefit millions of individuals by reducing the high risks for mortality and improving the quality of life with personalized diagnoses and treatments. Due to the advancements in sequencing technologies and reduced cost, genomics data are developing at an unmatched pace and levels to foster translational research and precision medicine. Over 10 million genomics datasets have been produced and publicly shared in 2022. Diverse and high-volume genomics and clinical data have the potential to broaden the scope of biological discoveries and insights by extracting, analyzing and interpreting the hidden information. However, the current and still unresolved challenges include the integration of genomic profiles of the patients with their medical records. The definition of disease in genomics medicine is simplified, whereas in the clinical world, diseases are classified, identified and adopted with their International Classification of Diseases (ICD) codes, which are maintained by the World Health Organization. Several biological databases have been produced, which include information about human genes and related diseases. However, still, there is no database that exists, which can precisely link clinical codes with relevant genes and variants to support genomic and clinical data integration for clinical and translational medicine. In this project, we focused on the development of an annotated gene–disease–code database, which is accessible through an online, cross-platform and user-friendly application, i.e. PROMIS-APP-SUITE-Gene-Disease-Code. However, our scope is limited to the integration of ICD-9 and ICD-10 codes with the list of genes approved by the American College of Medical Genetics and Genomics. The results include over 17 000 diseases and 4000 ICD codes, and over 11 000 gene–disease–code combinations.

Database URL https://promis.rutgers.edu/pas/
The quality of paediatric asthma guidelines: evidence underpinning diagnostic test recommendations from a meta-epidemiological study
Authors: Thomas Elizabeth T , Thomas Sarah T , Perera Rafael , Gill Peter J , Moloney Susan , Heneghan Carl J
Published: May 2023

Background

Asthma is one of the most frequent reasons children visit a general practitioner (GP). The diagnosis of childhood asthma is challenging, and a variety of diagnostic tests for asthma exist. GPs may refer to clinical practice guidelines when deciding which tests, if any, are appropriate, but the quality of these guidelines is unknown.

Objectives

To determine (i) the methodological quality and reporting of paediatric guidelines for the diagnosis of childhood asthma in primary care, and (ii) the strength of evidence supporting diagnostic test recommendations.

Design

Meta-epidemiological study of English-language guidelines from the United Kingdom and other high-income countries with comparable primary care systems including diagnostic testing recommendations for childhood asthma in primary care. The AGREE-II tool was used to assess the quality and reporting of the guidelines. The quality of the evidence was assessed using GRADE.

Results

Eleven guidelines met the eligibility criteria. The methodology and reporting quality varied across the AGREE II domains (median score 4.5 out of 7, range 2–6). The quality of evidence supporting diagnostic recommendations was generally of very low quality. All guidelines recommended the use of spirometry and reversibility testing for children aged ≥5 years, however, the recommended spirometry thresholds for diagnosis differed across guidelines. There were disagreements in testing recommendations for 3 of the 7 included tests.

Conclusions

The variable quality of guidelines, lack of good quality evidence, and inconsistent recommendations for diagnostic tests may contribute to poor clinician adherence to guidelines and variation in testing for diagnosing childhood asthma.
Trolls without borders: a comparative analysis of six foreign countries’ online propaganda campaigns
Authors: Walter Dror , Ophir Yotam
Published: May 2023

Despite the existence of multiple propaganda campaigns from around the globe, most scholarly attention has been primarily given to those operated by Russia. This focus on a single country has limited the scope of propaganda research. We offer a systematic comparison of six campaigns, examining the issues they engaged with, and their deployment strategies. Using a computational analysis of more than 9.5 million tweets released by the Twitter Moderation Research Consortium, we show differences across campaigns. Some operations were massive in scale while others were modest. Some focused on US domestic affairs, while others emphasized global issues. While some campaigns showed high levels of sophistication in terms of persona crafting and account deployment, others did not participate in pre-propaganda. We conclude by discussing the practical and theoretical implications of these findings.
An Effective Criterion for Nielsen–Schreier Varieties
Authors: Dotsenko Vladimir , Umirbaev Ualbai
Published: May 2023

To the memory of V. A. Artamonov (1946–2021) All algebras of a certain type are said to form a Nielsen–Schreier variety if every subalgebra of a free algebra is free. This property has been perceived as extremely rare; in particular, only six Nielsen–Schreier varieties of algebras with one binary operation have been discovered in prior work on this topic. We propose an effective combinatorial criterion for the Nielsen–Schreier property in the case of algebras over a field of zero characteristic; in our approach, operads play a crucial role. Using this criterion, we show that the well-known varieties of all pre-Lie algebras and of all Lie-admissible algebras are Nielsen–Schreier, and, quite surprisingly, that there are already infinitely many non-equivalent Nielsen–Schreier varieties of algebras with one binary operation and identities of degree four.
Cohomology of (, Γ)-Modules Over Pseudorigid Spaces
Authors: Bellovin Rebecca
Published: May 2023

We study the cohomology of families of $(\varphi ,\Gamma )$-modules with coefficients in pseudoaffinoid algebras. We prove that they have finite cohomology, and we deduce an Euler characteristic formula and Tate local duality. We classify rank-$1$$(\varphi ,\Gamma )$-modules and deduce that triangulations of pseudorigid families of $(\varphi ,\Gamma )$-modules can be interpolated, extending a result of [29]. We then apply this to study extended eigenvarieties at the boundary of weight space, proving in particular that the eigencurve is proper at the boundary and that Galois representations attached to certain characteristic $p$ points are trianguline.
On the Average of p-Selmer Ranks in Quadratic Twist Families of Elliptic Curves Over Global Function Fields
Authors: Park Sun Woo , Wang Niudun
Published: May 2023

Let $\mathbb{F}_{q}$ be a finite field whose characteristic is relatively prime to $2$ and $3$. Let $p$ be a prime number that is coprime to $q$. Let $E$ be an elliptic curve over the global function field $K = \mathbb{F}_{q}(t)$ such that $\textrm{Gal}(K(E[p])/K)$ contains the special linear group $\textrm{SL}_{2}(\mathbb{F}_{p})$. We show that if the quadratic twist family of $E$ has an element whose Néron model has a multiplicative reduction away from $\infty $, then the average $p$-Selmer rank is $p+1$ in large $q$-limit for almost all primes $p$.
Stabilizing Authoritarian Rule: The Role of International Organizations
Authors: Cottiero Christina , Haggard Stephan
Published: May 2023

Research has demonstrated how membership in more democratic regional intergovernmental organizations (ROs) can strengthen the prospects for democracy. However, a significant number of ROs are dominated by autocratic members who have quite different preferences: to limit democratic contagion and consolidate authoritarian rule against democratic challengers. We outline a menu of mechanisms through which ROs with authoritarian memberships might have pernicious effects on the prospects for democratic rule. We use cross-national quantitative analyses to demonstrate that membership in more deeply authoritarian international organizations is associated with autocratization. We supplement the quantitative results with an analysis of twenty-nine of the most authoritarian ROs and illustrative case studies. The multi-method approach strengthens inference by showing that authoritarian international organizations do in fact engage in behaviors inimical to democratic rule.
Dominated Cosmopolitanism: Consumer Habitus Dynamics among Low-Resource Migrants
Authors: Chytkova Zuzana , Kjeldgaard Dannie
Published: May 2023

Cosmopolitanism is often cast as an elite cultural orientation and as a privileged disposition to an increasingly globalized marketplace, instigated by, and lived through, mobility. But how does cosmopolitanism evolve among consumers at intersectional subordinate positions of power? This article analyzes the emergence of cosmopolitanism through a 9 year longitudinal extended case study of female migrants with low levels of resources. Through the deployment of a Bourdieusian framework, cosmopolitanism is theorized to evolve through processes set in motion by the experience of mismatch and subsequent alignment between new social contexts and existing socialized dispositions (hysteresis). The experience of hysteresis caused by mobility can lead to a habitus with traits of cosmopolitanism. The emergence of a cosmopolitan habitus can result in a sense of emancipation, but it also engenders new subordinate positions within intersectional systems of power. The outcome of this process is labeled dominated cosmopolitanism, representing a more nuanced version of cosmopolitanism that incorporates various systems of power. The analysis has implications for acculturation studies in consumption contexts characterized by low-resource endowments and provides new insights into the processual nature of the constitution of social systems of power.
Reference genome of an iconic lizard in western North America, Blainville’s horned lizard Phrynosoma blainvillii
Authors: Richmond Jonathan Q , McGuire Jimmy A , Escalona Merly , Marimuthu Mohan P A , Nguyen Oanh , Sacco Samuel , Beraut Eric , Toffelmier Erin , Fisher Robert N , Wang Ian J , Shaffer H Bradley
Published: May 2023

Genome assemblies are increasingly being used to identify adaptive genetic variation that can help prioritize the population management of protected species. This approach may be particularly relevant to species like Blainville’s horned lizard, Phrynosoma blainvillii, due to its specialized diet on noxious harvester ants, numerous adaptative traits for avoiding predation (e.g. cranial horns, dorsoventrally compressed body, cryptic coloration, and blood squirting from the orbital sinuses), and status as Species of Special Concern in California. Rangewide decline since the early 20th century, the basis of its conservation status, has been driven mainly by habitat conversion, over-collecting, and invasion of a non-native ant that displaces its native ant prey base. Here, we report on a scaffold-level genome assembly for P. blainvillii as part of the California Conservation Genomics Project (CCGP), produced using Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technology. The de novo assembly has 78 scaffolds, a total length of ~2.21 Gb, a scaffold N50 length of ~352 Mb, and BUSCO score of 97.4%. This is the second species of Phrynosoma for which a reference genome has been assembled and represents a considerable improvement in terms of contiguity and completeness. Combined with the landscape genomics data being compiled by the CCGP, this assembly will help strategize efforts to maintain and/or restore local genetic diversity, where interventions like genetic rescue, translocation, and strategic land preservation may be the only means by which P. blainvillii and other low-vagility species can survive in the fragmented habitats of California.
Improving combination therapies: targeting A2B-adenosine receptor to modulate metabolic tumor microenvironment and immunosuppression
Authors: Evans Jason V , Suman Shankar , Goruganthu Mounika Uttam L , Tchekneva Elena E , Guan Shuxiao , Arasada Rajeswara Rao , Antonucci Anneliese , Piao Longzhu , Ilgisonis Irina , Bobko Andrey A , Driesschaert Benoit , Uzhachenko Roman V , Hoyd Rebecca , Samouilov Alexandre , Amann Joseph , Wu Ruohan , Wei Lai , Pallerla Aaditya , Ryzhov Sergey V , Feoktistov Igor , Park Kyungho P , Kikuchi Takefumi , Castro Julio , Ivanova Alla V , Kanagasabai Thanigaivelan , Owen Dwight H , Spakowicz Daniel J , Zweier Jay L , Carbone David P , Novitskiy Sergey V , Khramtsov Valery V , Shanker Anil , Dikov Mikhail M
Published: May 2023

Background

We investigated the role of A2B-adenosine receptor in regulating immunosuppressive metabolic stress in the tumor microenvironment. Novel A2B-adenosine receptor antagonist PBF-1129 was tested for antitumor activity in mice and evaluated for safety and immunologic efficacy in a phase I clinical trial of patients with non-small cell lung cancer.

Methods

The antitumor efficacy of A2B-adenosine receptor antagonists and their impact on the metabolic and immune tumor microenvironment were evaluated in lung, melanoma, colon, breast, and epidermal growth factor receptor–inducible transgenic cancer models. Employing electron paramagnetic resonance, we assessed changes in tumor microenvironment metabolic parameters, including pO2, pH, and inorganic phosphate, during tumor growth and evaluated the immunologic effects of PBF-1129, including its pharmacokinetics, safety, and toxicity, in patients with non-small cell lung cancer.

Results

Levels of metabolic stress correlated with tumor growth, metastasis, and immunosuppression. Tumor interstitial inorganic phosphate emerged as a correlative and cumulative measure of tumor microenvironment stress and immunosuppression. A2B-adenosine receptor inhibition alleviated metabolic stress, downregulated expression of adenosine-generating ectonucleotidases, increased expression of adenosine deaminase, decreased tumor growth and metastasis, increased interferon γ production, and enhanced the efficacy of antitumor therapies following combination regimens in animal models (anti–programmed cell death 1 protein vs anti–programmed cell death 1 protein plus PBF-1129 treatment hazard ratio = 11.74 [95% confidence interval = 3.35 to 41.13], n = 10, P < .001, 2-sided F test). In patients with non-small cell lung cancer, PBF-1129 was well tolerated, with no dose-limiting toxicities; demonstrated pharmacologic efficacy; modulated the adenosine generation system; and improved antitumor immunity.

Conclusions

Data identify A2B-adenosine receptor as a valuable therapeutic target to modify metabolic and immune tumor microenvironment to reduce immunosuppression, enhance the efficacy of immunotherapies, and support clinical application of PBF-1129 in combination therapies.
Professional service firms and the manufacturing of the corporate nobility
Authors: Bühlmann Felix
Published: May 2023

Global professional service firms (GPSFs) are key actors in contemporary capitalism. They (co-) produce and disseminate new business practices, linking firms, sectors, and countries, integrating them into a global system. We examine a second, less studied function of these firms: underpinning capitalism’s status hierarchies. We ask whether these firms have emerged as producers of a new corporate nobility—as an extension of elite universities, and as a stepping stone in the selection and promotion of top executives. Focusing on the US, we ask: do global professional service firms merely amplify the credentials of elite universities, or can they compensate for an absence of an elite education in the careers of US top managers? and do professional service firms equip future top managers with specific expertise or merely with symbolic capital? Based on a sample of 2,610 top executive managers from leading American firms in 2005 and 2018, we study the role law, consulting, or audit firms played in their careers. Using multinomial regression analyses, we find that the career function of GPSFs varies: consulting firms amplify existing status and enhance the symbolic capital of alumni, aiding their ascent to the most prestigious jobs in US top firms. In contrast, top managers leverage audit firm roles to compensate for a non-elite background, yet then tend to be channelled into narrow, specialist roles in top management. We relate these results to Bourdieu’s state nobility analysis and propose an augmented typology of these firms at the heart of contemporary capitalism.
Effective two-body scatterings around a massive object
Authors: Wang Yihan , Ford Saavik , Perna Rosalba , McKernan Barry , Zhu Zhaohuan , Zhang Bing
Published: May 2023

Two-body scatterings under the potential of a massive object are very common in astrophysics. If the massive body is far enough away that the two small bodies are in their own gravitational sphere of influence, the gravity of the massive body can be temporarily ignored. However, this requires the scattering process to be fast enough that the small objects do not spend too much time at distances near the surface of the sphere of influence. In this paper, we derive the validation criteria for effective two-body scattering and establish a simple analytical solution for this process, which we verify through numerical scattering experiments. We use this solution to study star–black hole scatterings in the discs of active galactic nuclei and planet–planet scatterings in planetary systems, and calculate their one-dimensional cross-section analytically. Our solution will be valuable in reducing computational time when treating two-body scatterings under the potential of a much more massive third body, provided that the problem settings are in the valid parameter space region identified by our study.
A statistical analysis of the structure of the interstellar medium in the disc of the Milky Way
Authors: Bates M L , Whitworth A P
Published: May 2023

We construct Convolutional Neural Networks (CNNs) trained on exponentiated fractional Brownian motion (xfBm) images, and use these CNNs to analyse Hi-GAL images of surface density in the Galactic Plane. The CNNs estimate the Hurst parameter, ${\cal H}$ (a measure of the power spectrum), and the scaling exponent, ${\cal S}$ (a measure of the range of surface densities), for a square patch comprising $[{\cal N}\times {\cal N}]=$ [128 × 128], [64 × 64], or [32 × 32] pixels. The resulting estimates of ${\cal H}$ are more accurate than those obtained using Δ-variance. We stress that statistical measures of structure are inevitably strongly dependent on the range of scales they actually capture, and difficult to interpret when applied to fields that conflate very different lines of sight. The CNNs developed here mitigate this issue by operating effectively on small fields (small ${\cal N}$), and we exploit this property to develop a procedure for constructing detailed maps of ${\cal H}$ and ${\cal S}$. This procedure is then applied to Hi-GAL maps generated with the ppmap procedure. There appears to be a bimodality between sightlines with higher surface density ($\gtrsim 32\, {\rm M}_{_\odot }\, {\rm pc^{-2}}$), which tend to have higher ${\cal H}\, (\gtrsim 0.8)$ and ${\cal S}\, (\gtrsim 1)$; and sightlines intercepting regions of lower surface density ($\lesssim 32\, {\rm M}_{_\odot }\, {\rm pc^{-2}}$), which tend to have lower ${\cal H}\, (\lesssim 0.8)$ and ${\cal S}\, (\lesssim 1)$; unsurprisingly the former sightlines are concentrated towards the Galactic Midplane and the Inner Galaxy. The surface density PDF takes the form dP/dΣ ∝ Σ−3 for $\Sigma \gtrsim 32\, {\rm M}_{_\odot }\, {\rm pc^{-2}}$, and on most sightlines this power-law tail is dominated by dust cooler than $\, \sim 20\, \rm {K}$, which is the median dust temperature in the Galactic Plane.
TOI-2498 b: a hot bloated super-Neptune within the Neptune desert
Authors: Frame Ginger , Armstrong David J , Cegla Heather M , Fernández Fernández Jorge , Osborn Ares , Adibekyan Vardan , Collins Karen A , Delgado Mena Elisa , Giacalone Steven , Kielkopf John F , Santos Nuno C , Sousa Sérgio G , Stassun Keivan G , Ziegler Carl , Anderson David R , Barros Susana C C , Bayliss Daniel , Briceño César , Conti Dennis M , Dressing Courtney D , Dumusque Xavier , Figueira Pedro , Fong William , Gill Samuel , Hawthorn Faith , Jenkins Jon M , Jensen Eric L N , Keniger Marcelo Aron F , Latham David W , Law Nicholas , Lissauer Jack J , Mann Andrew W , Nielsen Louise D , Osborn Hugh , Paegert Martin , Seager Sara , Schwarz Richard P , Shporer Avi , Srdoc Gregor , Strøm Paul A , Winn Joshua N , Wheatley Peter J
Published: May 2023

We present the discovery and confirmation of a transiting hot bloated super-Neptune using photometry from the Transiting Exoplanet Survey Satellite (TESS) and the Las Cumbres Observatory Global Telescope (LCOGT) and radial velocity measurements from the High Accuracy Radial velocity Planet Searcher (HARPS). The host star TOI-2498 is a V  = 11.2, G-type (Teff  = 5905 ± 12 K) solar-like star with a mass of 1.12 ± 0.02 M⊙ and a radius of 1.26 ± 0.04 R⊙. The planet, TOI-2498 b, orbits the star with a period of 3.7 d, has a radius of 6.1 ± 0.3 R⊕, and a mass of 35 ± 4 M⊕. This results in a density of 0.86 ± 0.25 g cm−3. TOI-2498 b resides on the edge of the Neptune desert; a region of mass–period parameter space in which there appears to be a dearth of planets. Therefore TOI-2498 b is an interesting case to study to further understand the origins and boundaries of the Neptune desert. Through modelling the evaporation history, we determine that over its ∼3.6 Gyr lifespan, TOI-2498 b has likely reduced from a Saturn-sized planet to its current radius through photoevaporation. Moreover, TOI-2498 b is a potential candidate for future atmospheric studies searching for species like water or sodium in the optical using high resolution spectroscopy, and for carbon-based molecules in the infrared using JWST.
The Spitzer Extragalactic Representative Volume Survey and DeepDrill extension: clustering of near-infrared galaxies
Authors: van Kampen Eelco , Lacy Mark , Farrah Duncan , Lagos Claudia del P , Jarvis Matt , Maraston Claudia , Nyland Kristina , Oliver Seb , Surace Jason , Thorne Jessica
Published: May 2023

We have measured the angular autocorrelation function of near-infrared galaxies in SERVS + DeepDrill, the Spitzer Extragalactic Representative Volume Survey and its follow-up survey of the Deep Drilling Fields, in three large fields totalling over 20 deg2 on the sky, observed in two bands centred on 3.6 and 4.5 μm. We performed this analysis on the full sample as well as on sources selected by [3.6]–[4.5] colour in order to probe clustering for different redshift regimes. We estimated the spatial correlation strength as well, using the redshift distribution from S-COSMOS with the same source selection. The strongest clustering was found for our bluest subsample, with 〈z〉 ∼ 0.7, which has the narrowest redshift distribution of all our subsamples. We compare these estimates to previous results from the literature, but also to estimates derived from mock samples, selected in the same way as the observational data, using deep light-cones generated from the SHARK semi-analytical model of galaxy formation. For all simulated (sub)samples, we find a slightly steeper slope than for the corresponding observed ones, but the spatial clustering length is comparable in most cases.
An empirical study of dust properties at the earliest epochs
Authors: Witstok Joris , Jones Gareth C , Maiolino Roberto , Smit Renske , Schneider Raffaella
Published: May 2023

We present an empirical analysis of the properties of dust-continuum emission in a sample of 17 galaxies in the early Universe (4 < z < 8) with well-sampled far-infrared spectral energy distributions (SEDs) compiled from the literature. We place our results into context by self-consistently comparing to samples of nearby star-forming galaxies, luminous infrared galaxies (LIRGs), and quasars. With the exception of two sources, we find no significant evolution in the dust emissivity index across cosmic time, measuring a consistent value of βIR = 1.8 ± 0.3 at z > 4, suggesting that the effective dust properties do not change dramatically for most galaxies. Despite having comparable stellar masses, we find the high-redshift galaxies to be similar to, or even more extreme than, LIRGs in the Herschel (U)LIRG Survey, where (U)LIRG refers to (ultra-)LIRG, sample in terms of dust temperature ($T_\text{dust} \gt 40 \, \mathrm{K}$) and infrared (IR) luminosity ($L_\text{IR} \gt 10^{11} \, \mathrm{L_\odot }$). We find that the dust temperature evolves mildly towards high redshift, though the LIRGs and quasars exhibit elevated temperatures indicating a more efficient and/or additional heating mechanism. Where available, we compare stellar mass estimates to our inferred dust masses, whose degeneracy with dust temperature can only be mitigated with a well-constrained SED. In merely half of the cases, the dust yield may be explained by supernovae alone, with four sources ($44{{\ \rm per\ cent}}$) significantly exceeding a highly optimistic yield where Mdust ≈ 0.01M*. We discuss possible explanations for this apparent inconsistency and potential observational biases in the measurements of the dust properties of high-redshift galaxies, including in the current IR-bright sample.
Partition function approach to non-Gaussian likelihoods: formalism and expansions for weakly non-Gaussian cosmological inference
Authors: Röver Lennart , Bartels Lea Carlotta , Schäfer Björn Malte
Published: May 2023

Non-Gaussian likelihoods, ubiquitous throughout cosmology, are a direct consequence of non-linearities in the physical model. Their treatment requires Monte Carlo Markov chain (MCMC) or more advanced sampling methods for the determination of confidence contours. As an alternative, we construct canonical partition functions as Laplace transforms of the Bayesian evidence, from which MCMC methods would sample microstates. Cumulants of order n of the posterior distribution follow by direct n-fold differentiation of the logarithmic partition function, recovering the classic Fisher-matrix formalism at second order. We connect this approach for weakly non-Gaussianities to the DALI and Gram−Charlier expansions and demonstrate the validity with a supernova-likelihood on the cosmological parameters Ωm and w. We comment on extensions of the canonical partition function to include kinetic energies in order to bridge to Hamilton Monte Carlo sampling, and on ensemble Markov-chain methods, as they would result from transitioning to macrocanonical partition functions depending on a chemical potential. Lastly we demonstrate the relationship of the partition function approach to the Cramér−Rao boundary and to information entropies.
SP(k) – a hydrodynamical simulation-based model for the impact of baryon physics on the non-linear matter power spectrum
Authors: Salcido Jaime , McCarthy Ian G , Kwan Juliana , Upadhye Amol , Font Andreea S
Published: May 2023

Upcoming large-scale structure surveys will measure the matter power spectrum to approximately per cent level accuracy with the aim of searching for evidence for new physics beyond the standard model of cosmology. In order to avoid biasing our conclusions, the theoretical predictions need to be at least as accurate as the measurements for a given choice of cosmological parameters. However, recent theoretical work has shown that complex physical processes associated with galaxy formation (particularly energetic feedback processes associated with stars and especially supermassive black holes) can alter the predictions by many times larger than the required accuracy. Here we present SP(k), a model for the effects of baryon physics on the non-linear matter power spectrum based on a new large suite of hydrodynamical simulations. Specifically, the ANTILLES suite consists of 400 simulations spanning a very wide range of the ‘feedback landscape’ and show that the effects of baryons on the matter power spectrum can be understood at approaching the per cent level in terms of the mean baryon fraction of haloes, at scales of up to $k \, {\lesssim } \, 10\, h$ Mpc−1 and redshifts up to z = 3. For the range of scales and redshifts that will be probed by forthcoming cosmic shear measurements, most of the effects are driven by galaxy group mass haloes (M ∼ 1013–14 M⊙). We present a simple python implementation of our model, available at https://github.com/jemme07/pyspk, which can be used to incorporate baryon effects in standard gravity-only predictions, allowing for marginalization over baryon physics within cosmological pipelines.
On the interaction of pebble accreting embryos with the gaseous disc: importance of thermal forces
Authors: Cornejo Sonia , Masset Frédéric S , Sánchez-Salcedo F J
Published: May 2023

A planetary embryo embedded in a gaseous disc can grow by pebble accretion while subjected to a gravitational force from the disc that changes its orbital elements. Usually, that force is considered to arise from the Lindblad and corotation resonances with the embryo. However, more important contributions exist for low-mass planets. Radiative thermal diffusion in the vicinity of embryos yields an additional contribution to the disc’s force that damps the eccentricity and inclination much more vigorously than the resonant interaction with the disc, and that in general induces fast inward migration. In addition, the irradiation of the disc by a hot embryo gives rise to an additional contribution that excites eccentricity and inclination, and induces outward migration. Which of the two contributions dominates depends on the embryo’s luminosity. We assess the importance of these contributions (termed thermal forces) on the dynamics and growth of a set of pebble-accreting embryos initially of Martian mass, by means of N-body simulations that include analytic expressions for the disc’s force. We find very different outcomes for the embryos subjected to thermal forces and those subjected only to resonant forces. Importantly, we find that the median final mass of the embryos subjected to thermal forces is nearly independent of the metallicity, whereas this mass roughly scales with the metallicity when they are subjected only to resonant forces. These results can be explained by the strong damping of eccentricity and inclination at low metallicity, which enhances the embryos’ accretion efficiency.
On collective nature of non-linear torsional Alfvén waves
Authors: Belov S A , Riashchikov D S , Kolotkov D Y , Vasheghani Farahani S , Molevich N E , Bezrukovs V V
Published: May 2023

Torsional Alfvén waves in coronal plasma loops are usually considered to be non-collective, i.e. consist of cylindrical surfaces evolving independently, which significantly complicates their detection in observations. This non-collective nature, however, can get modified in the non-linear regime. To address this question, the propagation of non-linear torsional Alfvén waves in straight magnetic flux tubes has been investigated numerically using the astrophysical MHD code Athena++ and analytically, to support numerical results, using the perturbation theory up to the second order. Numerical results have revealed that there is radially uniform-induced density perturbation whose uniformity does not depend on the radial structure of the mother Alfvén wave. Our analysis showed that the ponderomotive force leads to the induction of the radial and axial velocity perturbations, while the mechanism for the density perturbation is provided by a non-equal elasticity of a magnetic flux tube in the radial and axial directions. The latter can be qualitatively understood by the interplay between the Alfvén wave perturbations, external medium, and the flux tube boundary conditions. The amplitude of these non-linearly induced density perturbations is found to be determined by the amplitude of the Alfvén driver squared and the plasma parameter β. The existence of the collective and radially uniform density perturbation accompanying non-linear torsional Alfvén waves could be considered as an additional observational signature of Alfvén waves in the upper layers of the solar atmosphere.
Physical properties of NEOs derived from their phase curves
Authors: Arcoverde Plícida , Rondón Eduardo , Monteiro Filipe , Pereira Weslley , Ieva Simone , Michtchenko Tatiana , Evangelista-Santana Marçal , Michimani Jonatan , Mesquita Wesley , Corrêa Tatiane , Dotto Elisabetta , Giunta Alessio , Di Paola Andrea , Medeiros Hissa , Carvano Jorge M , Rodrigues Teresinha , Lazzaro Daniela
Published: May 2023

The observation of Near Earth objects (NEOs) allows us to study the physical properties of the smallest size bodies of our Solar System and help impose constraints on their origin and evolution. The solar phase curve is a very important tool to derive diverse physical properties of a small body so that we set up an observational campaign to derive the phase curve parameters (H, G1, G2) for a large number of NEOs. We present here the obtained phase curves for 12 NEOs, along with the rotation period for two of them and the V–R colour for four. The data was acquired mainly at the Astronomical Observatory of Sertão de Itaparica (Brazil), with some NEOs also observed at the Osservatorio di Campo Imperatore (Italy). Considering all the objects observed throughout our campaign we analysed a homogeneous dataset of 30 NEOs along with data acquired by ATLAS (Asteroid Terrestrial-impact Last Alert System telescopes survey) for MB asteroids. The behavior in the phase space G1-G2 of 21,865 MBA and 103 NEOs was analysed, separating the objects in intervals of albedos and sizes. From the large MB data set we found evidence that the distribution in the G1-G2 phase space has strong dependence not only on the albedo but also on the object’s size. This is particularly true for the smaller objects. The main result being that, on the contrary to what occurs with the MB larger objects, we are unable to estimate the albedo of a NEO from its phase curve parameters.
On the perturbative picture and the Chang–Refsdal lens approximation for planetary microlensing
Authors: Zhang Keming
Published: May 2023

Under the perturbative picture of planetary microlensing, the planet is considered to act as a uniform-shear Chang–Refsdal lens on one of the two images produced by the host star that comes close to the angular Einstein radius of the planet, leaving the other image unaffected. However, this uniform-shear approximation is only valid for isolated planetary caustics and breaks down in the resonant regime. Recently, the planetary-caustic degeneracy arising from the above formalism is found to generalize to the regime of central and resonant caustics, indicating that the perturbative picture and Chang–Refsdal lens approximation may have been underexplored in the past. Here, I introduce a new variable-shear Chang–Refsdal lens approximation, which not only supports central and resonant caustics, but also enables full magnification maps to be calculated analytically. Moreover, I introduce the generalized perturbative picture, which relaxes the required proximity between the planet and the image being perturbed in the previous work. Specifically, the planet always perturbs the image in the same half of the lens plane as the planet itself, leaving the other image largely unaffected. It is demonstrated how this new framework results in the offset degeneracy as a consequence of physical symmetry. The generalized perturbative picture also points to an approach to solve the two-body lens equation semi-analytically. The analytic and semi-analytic microlensing solutions associated with this work may allow for substantially faster light-curve calculations and modelling of observed events. A Python implementation is provided.
Spectroscopic searches for evolutionary orbital period changes in WR + OB binaries: the case of CQ Cep and CX Cep
Authors: Shaposhnikov I , Cherepashchuk A , Dodin A , Postnov K
Published: May 2023

We present the results of spectroscopic observations of two eclipsing WR + OB-type systems – CQ Cep and CX Cep – performed in 2020–2023 with a low-resolution slit spectrograph TDS (λλ = 3660–7410 Å, R = 1300–2500) on 2.5-m telescope of the SAI MSU Caucasian Mountain Observatory. For CQ Cep, the radial velocity curves of a WN6 star are constructed, the problem of visibility of spectroscopic traces of an OB star is discussed, and the components’ mass ratio q ∼ 0.6 is estimated. For CX Cep, the radial velocity curves are constructed for both the WN5 and O5 components enabling their masses and circular orbit elements to be refined. The comparison of the radial velocity curves of these systems obtained in different epochs allowed us to derive the orbital period change rate $\dot{P}$ by the spectroscopic method, which is found to be in good agreement with estimates obtained by comparing the moments of primary eclipse minima: $\dot{P} = -0.0151\pm 0.0013$ s yr−1 for CQ Cep and $\dot{P} = 0.054\pm 0.009$ s yr−1 for CX Cep. The prospects of applicability of the spectroscopic dynamical method for studying the orbital evolution of Galactic WR + OB binaries and related objects are considered. We also discuss the effect of finite sizes of stars with stellar wind mass-loss in close binary systems on their orbital evolution.
Probing z ≳ six massive black holes with gravitational waves
Authors: Chakraborty Srija , Gallerani Simona , Zana Tommaso , Sesana Alberto , Valentini Milena , Izquierdo-Villalba David , Di Mascia Fabio , Vito Fabio , Barai Paramita
Published: May 2023

We investigate the coalescence of massive black hole ($M_{\rm BH}\gtrsim 10^{6}~\rm {\rm M}_{\odot }$) binaries (MBHBs) at 6 < z < 10 by adopting a suite of cosmological hydrodynamical simulations of galaxy formation, zoomed-in on biased (>3σ) overdense regions (Mh ∼ 1012 M⊙ dark matter haloes at z = 6) of the Universe. We first analyse the impact of different resolutions and AGN feedback prescriptions on the merger rate, assuming instantaneous mergers. Then, we compute the halo bias correction factor due to the overdense simulated region. Our simulations predict merger rates that range between 3 and 15 $\rm yr^{-1}$ at z ∼6, depending on the run considered, and after correcting for a bias factor of ∼20−30. For our fiducial model, we further consider the effect of delay in the MBHB coalescence due to dynamical friction. We find that 83 per cent of MBHBs will merge within the Hubble time, and 21 per cent within 1 Gyr, namely the age of the Universe at z > 6. We finally compute the expected properties of the gravitational wave (GW) signals and find the fraction of LISA detectable events with high signal-to-noise ratio (SNR > 5) to range between 66 per cent and 69 per cent. However, identifying the electro-magnetic counterpart of these events remains challenging due to the poor LISA sky localization that, for the loudest signals ($\mathcal {M}_c\sim 10^6~{{\rm M}_{\odot }}$ at z = 6), is around 10 $\rm deg^2$.
Caecilian Genomes Reveal the Molecular Basis of Adaptation and Convergent Evolution of Limblessness in Snakes and Caecilians
Authors: Ovchinnikov Vladimir , Uliano-Silva Marcela , Wilkinson Mark , Wood Jonathan , Smith Michelle , Oliver Karen , Sims Ying , Torrance James , Suh Alexander , McCarthy Shane A , Durbin Richard , O’Connell Mary J
Published: May 2023

We present genome sequences for the caecilians Geotrypetes seraphini (3.8 Gb) and Microcaecilia unicolor (4.7 Gb), representatives of a limbless, mostly soil-dwelling amphibian clade with reduced eyes, and unique putatively chemosensory tentacles. More than 69% of both genomes are composed of repeats, with retrotransposons being the most abundant. We identify 1,150 orthogroups that are unique to caecilians and enriched for functions in olfaction and detection of chemical signals. There are 379 orthogroups with signatures of positive selection on caecilian lineages with roles in organ development and morphogenesis, sensory perception, and immunity amongst others. We discover that caecilian genomes are missing the zone of polarizing activity regulatorysequence (ZRS) enhancer of Sonic Hedgehog which is also mutated in snakes. In vivo deletions have shown ZRS is required for limb development in mice, thus, revealing a shared molecular target implicated in the independent evolution of limblessness in snakes and caecilians.
ZnT1 induces a crosstalk between T-type and L-type calcium channels through interactions with Raf-1 kinase and the calcium channel β2 subunit
Authors: Mor Merav , Beharier Ofer , Cook David I , Campbell Craig R , Gheber Levi A , Katz Amos , Moran Arie , Etzion Yoram
Published: May 2023

ZnT1 is a major zinc transporter that regulates cellular zinc homeostasis. We have previously shown that ZnT1 has additional functions that are independent of its activity as a Zn2+ extruder. These include inhibition of the L-type calcium channel (LTCC) through interaction with the auxiliary β-subunit of the LTCC and activation of the Raf-ERK signaling leading to augmented activity of the T-type calcium channel (TTCC). Our findings indicate that ZnT1 increases TTCC activity by enhancing the trafficking of the channel to the plasma membrane. LTCC and TTCC are co-expressed in many tissues and have different functions in a variety of tissues. In the current work, we investigated the effect of the voltage-gated calcium channel (VGCC) β-subunit and ZnT1 on the crosstalk between LTCC and TTCC and their functions. Our results indicate that the β-subunit inhibits the ZnT1-induced augmentation of TTCC function. This inhibition correlates with the VGCC β-subunit-dependent reduction in ZnT1-induced activation of Ras-ERK signaling. The effect of ZnT1 is specific, as the presence of the β-subunit did not change the effect of endothelin-1 (ET-1) on TTCC surface expression. These findings document a novel regulatory function of ZnT1 serving as a mediator in the crosstalk between TTCC and LTCC. Overall, we demonstrate that ZnT1 binds and regulates the activity of the β-subunit of VGCC and Raf-1 kinase and modulates surface expression of the LTCC and TTCC catalytic subunits, consequently modulating the activity of these channels.
ChemMaps.com v2.0: exploring the environmental chemical universe
Authors: Borrel Alexandre , Conway Mike , Nolte Sue Z , Unnikrishnan Aswani , Schmitt Charles P , Kleinstreuer Nicole C
Published: May 2023

Access to computationally based visualization tools to navigate chemical space has become more important due to the increasing size and diversity of publicly accessible databases, associated compendiums of high-throughput screening (HTS) results, and other descriptor and effects data. However, application of these techniques requires advanced programming skills that are beyond the capabilities of many stakeholders. Here we report the development of the second version of the ChemMaps.com webserver (https://sandbox.ntp.niehs.nih.gov/chemmaps/) focused on environmental chemical space. The chemical space of ChemMaps.com v2.0, released in 2022, now includes approximately one million environmental chemicals from the EPA Distributed Structure-Searchable Toxicity (DSSTox) inventory. ChemMaps.com v2.0 incorporates mapping of HTS assay data from the U.S. federal Tox21 research collaboration program, which includes results from around 2000 assays tested on up to 10 000 chemicals. As a case example, we showcased chemical space navigation for Perfluorooctanoic Acid (PFOA), part of the Per- and polyfluoroalkyl substances (PFAS) chemical family, which are of significant concern for their potential effects on human health and the environment.
PHASTEST: faster than PHASTER, better than PHAST
Authors: Wishart David S , Han Scott , Saha Sukanta , Oler Eponine , Peters Harrison , Grant Jason R , Stothard Paul , Gautam Vasuk
Published: May 2023

PHASTEST (PHAge Search Tool with Enhanced Sequence Translation) is the successor to the PHAST and PHASTER prophage finding web servers. PHASTEST is designed to support the rapid identification, annotation and visualization of prophage sequences within bacterial genomes and plasmids. PHASTEST also supports rapid annotation and interactive visualization of all other genes (protein coding regions, tRNA/tmRNA/rRNA sequences) in bacterial genomes. Given that bacterial genome sequencing has become so routine, the need for fast tools to comprehensively annotate bacterial genomes has become progressively more important. PHASTEST not only offers faster and more accurate prophage annotations than its predecessors, it also provides more complete whole genome annotations and much improved genome visualization capabilities. In standardized tests, we found that PHASTEST is 31% faster and 2–3% more accurate in prophage identification than PHASTER. Specifically, PHASTEST can process a typical bacterial genome in 3.2 min (raw sequence) or in 1.3 min when given a pre-annotated GenBank file. Improvements in PHASTEST’s ability to annotate bacterial genomes now make it a particularly powerful tool for whole genome annotation. In addition, PHASTEST now offers a much more modern and responsive visualization interface that allows users to generate, edit, annotate and interactively visualize (via zooming, rotating, dragging, panning, resetting), colourful, publication quality genome maps. PHASTEST continues to offer popular options such as an API for programmatic queries, a Docker image for local installations, support for multiple (metagenomic) queries and the ability to perform automated look-ups against thousands of previously PHAST-annotated bacterial genomes. PHASTEST is available online at https://phastest.ca.
Knockout of protein phosphatase 1 in Leishmania major reveals its role during RNA polymerase II transcription termination
Authors: Kieft Rudo , Zhang Yang , Yan Haidong , Schmitz Robert J , Sabatini Robert
Published: May 2023

The genomes of kinetoplastids are organized into polycistronic transcription units that are flanked by a modified DNA base (base J, beta-D-glucosyl-hydroxymethyluracil). Previous work established a role of base J in promoting RNA polymerase II (Pol II) termination in Leishmania major and Trypanosoma brucei. We recently identified a PJW/PP1 complex in Leishmania containing a J-binding protein (JBP3), PP1 phosphatase 1, PP1 interactive-regulatory protein (PNUTS) and Wdr82. Analyses suggested the complex regulates transcription termination by recruitment to termination sites via JBP3-base J interactions and dephosphorylation of proteins, including Pol II, by PP1. However, we never addressed the role of PP1, the sole catalytic component, in Pol II transcription termination. We now demonstrate that deletion of the PP1 component of the PJW/PP1 complex in L. major, PP1-8e, leads to readthrough transcription at the 3’-end of polycistronic gene arrays. We show PP1-8e has in vitro phosphatase activity that is lost upon mutation of a key catalytic residue and associates with PNUTS via the conserved RVxF motif. Additionally, purified PJW complex with associated PP1-8e, but not complex lacking PP1-8e, led to dephosphorylation of Pol II, suggesting a direct role of PNUTS/PP1 holoenzymes in regulating transcription termination via dephosphorylating Pol II in the nucleus.