bluuebunny/crossref_metadata_2025_split huggingface dataset:
The variability of brightest cluster galaxies at high radio frequencies
Authors: Rose Tom , Edge Alastair , Kiehlmann Sebastian , Baek Junhyun , Chung Aeree , Jung Tae-Hyun , Kim Jae-Woo , Readhead Anthony C S , Sedgewick Aidan 
Published: November 2021

ABSTRACT
Variability of a galaxy’s core radio source can be a significant consequence of active galactic nucleus accretion. However, this variability has not been well studied, particularly at high radio frequencies. As such, we report on a campaign monitoring the high radio frequency variability of 20 nearby, cool-core brightest cluster galaxies. From our representative sample, we show that most vary significantly on time-scales of approximately 1 yr and longer. Our highest cadence observations are at 15 GHz and are from the Owens Valley Radio Observatory. They have a median time interval of 7 d and mostly span between 8 and 13 yr. We apply a range of variability detection techniques to the sources’ light curves to analyse changes on week to decade long time-scales. Most notably, at least half of the sources show 20 per cent peak to trough variability on 3 yr time-scales, while at least a third vary by 60 per cent on 6 yr time-scales. Significant variability, which is important to studies of the Sunyaev–Zel’dovich Effect in the radio/sub-mm, is therefore a common feature of these sources. We also show how the variability relates to spectral properties at frequencies of up to 353 GHz using data from the Korean VLBI network, the NIKA2 instrument of the IRAM 30-m telescope, and the SCUBA-2 instrument of the James Clerk Maxwell Telescope.
Quenched, bulge-dominated, but dynamically cold galaxies in IllustrisTNG and their real-world counterparts
Authors: Lu Shengdong , Xu Dandan , Wang Sen , Wang Yunchong , Mao Shude , Xia Xiaoyang , Vogelsberger Mark , Hernquist Lars 
Published: November 2021

ABSTRACT
Galaxy morphologies, kinematics, and stellar populations are thought to be linked to each other. However, both simulations and observations have pointed out mismatches therein. In this work, we study the nature and origin of the present-day quenched, bulge-dominated, but dynamically cold galaxies within a stellar mass range of $10.3\, \leqslant \, \log \, M_{\ast }/\mathrm{M_{\odot }}\, \leqslant \, 11.2$ in the IllustrisTNG-100 Simulation. We compare these galaxies with a population of normal star-forming dynamically cold disc galaxies and a population of normal quenched dynamically hot elliptical galaxies within the same mass range. The populations of the present-day quenched and bulge-dominated galaxies (both being dynamically cold and hot) used to have significantly higher star formation rates and flatter morphologies at redshift of z ∼ 2. They have experienced more frequent larger mass-ratio mergers below z ∼ 0.7 in comparison to their star-forming disc counterparts, which is responsible for the formation of their bulge-dominated morphologies. The dynamically cold populations (both being star forming and quenched) have experienced more frequent prograde and tangential mergers especially below z ∼ 1, in contrast to the dynamically hot ellipticals, which have had more retrograde and radial mergers. Such different merging histories can well explain the differences on the cold and hot dynamical status among these galaxies. We point out that the real-world counterparts of these dynamically cold and hot bulge-dominated quenched populations are the fast- and slow-rotating early-type galaxies, respectively, as seen in observations and hence reveal the different evolution paths of these two distinct populations of early-type galaxies.
Lifting weak lensing degeneracies with a field-based likelihood
Authors: Porqueres Natalia , Heavens Alan , Mortlock Daniel , Lavaux Guilhem 
Published: November 2021

ABSTRACT
We present a field-based approach to the analysis of cosmic shear data to infer jointly cosmological parameters and the dark matter distribution. This forward modelling approach samples the cosmological parameters and the initial matter fluctuations, using a physical gravity model to link the primordial fluctuations to the non-linear matter distribution. Cosmological parameters are sampled and updated consistently through the forward model, varying (1) the initial matter power spectrum, (2) the geometry through the distance-redshift relationship, and (3) the growth of structure and light-cone effects. Our approach extracts more information from the data than methods based on two-point statistics. We find that this field-based approach lifts the strong degeneracy between the cosmological matter density, Ωm, and the fluctuation amplitude, σ8, providing tight constraints on these parameters from weak lensing data alone. In the simulated four-bin tomographic experiment we consider, the field-based likelihood yields marginal uncertainties on σ8 and Ωm that are, respectively, a factor of 3 and 5 smaller than those from a two-point power spectrum analysis applied to the same underlying data.
Dark Energy Camera photometry reveals extra-tidal stars around the Milky Way globular cluster NGC 6864 (M75)
Authors: Piatti Andrés E 
Published: November 2021

ABSTRACT
Globular clusters are prone to lose stars while moving around the Milky Way. These stars escape the clusters and are distributed throughout extended envelopes or tidal tails. However, such extra-tidal structures are not observed in all globular clusters, and yet there are no structural or dynamical parameters that can predict their presence or absence. NGC 6864 is an outer halo globular cluster with reported no observed tidal tails. We used Dark Energy Camera photometry reaching ∼4 mag underneath its main-sequence turnoff to confidently detect an extra-tidal envelope, and stellar debris spread across the cluster outskirts. These features emerged once robust field star filtering techniques were applied to the fainter end of the observed cluster main sequence. NGC 6864 is associated to the Gaia-Enceladus dwarf galaxy, among others 28 globular clusters. Up-to-date, nearly 64${{\ \rm per\,cent}}$ of them have been targeted looking for tidal tails and most of them have been confirmed to exhibit tidal tails. Thus, the present outcomes allow us to speculate on the possibility that Gaia-Enceladus globular clusters share a common pattern of mass loss by tidal disruption.
A deep radio view of the evolution of the cosmic star formation rate density from a stellar-mass-selected sample in VLA-COSMOS
Authors: Malefahlo Eliab D , Jarvis Matt J , Santos Mario G , White Sarah V , Adams Nathan J , Bowler Rebecca A A 
Published: November 2021

ABSTRACT
We present the 1.4 GHz radio luminosity functions (RLFs) of galaxies in the Cosmic Evolution Survey (COSMOS) field, measured above and below the 5σ detection threshold, using a Bayesian model-fitting technique. The radio flux densities from Very Large Array (VLA)-COSMOS 3-GHz data are extracted at the position of stellar-mass-selected galaxies. We fit a local RLF model, which is a combination of active galactic nuclei and star-forming galaxies (SFGs), in 10 redshift bins with a pure luminosity evolution model. Our RLF exceeds previous determinations at low radio luminosities at z &lt; 1.6 with the same radio data, due to our ability to directly constrain the knee and faint-end slope of the RLF. Beyond z ∼ 2, we find that the SFG part of the RLF exhibits a negative evolution (L* moves to lower luminosities) due to the decrease in low stellar-mass galaxies in our sample at high redshifts. From the RLF for SFGs, we determine the evolution in the cosmic star formation rate density (SFRD), which we find to be consistent with the established behaviour up to z ∼ 1 using far-infrared data, but exceeds that from the previous radio-based work for the reasons highlighted above. Beyond z ∼ 1.5 the cosmic SFRD declines. We note that the relation between radio luminosity and star formation rate is crucial in measuring the cosmic SFRD from radio data at z &gt; 1.5. We investigate the effects of stellar mass on the total RLF by splitting our sample into low (108.5 ≤ M/M⊙ ≤ 1010) and high ($M\gt 10^{10}\, \mathrm{M}_{\odot }$) stellar-mass subsets. We find that the SFRD is dominated by sources in the high stellar masses bin, at all redshifts.
Histone H3K27 Methylation Perturbs Transcriptional Robustness and Underpins Dispensability of Highly Conserved Genes in Fungi
Authors: Moser Tralamazza Sabina , Nanchira Abraham Leen , Reyes-Avila Claudia Sarai , Corrêa Benedito , Croll Daniel 
Published: November 2021

AbstractEpigenetic modifications are key regulators of gene expression and underpin genome integrity. Yet, how epigenetic changes affect the evolution and transcriptional robustness of genes remains largely unknown. Here, we show how the repressive histone mark H3K27me3 underpins the trajectory of highly conserved genes in fungi. We first performed transcriptomic profiling on closely related species of the plant pathogen Fusarium graminearum species complex. We determined transcriptional responsiveness of genes across environmental conditions to determine expression robustness. To infer evolutionary conservation, we used a framework of 23 species across the Fusarium genus including three species covered with histone methylation data. Gene expression variation is negatively correlated with gene conservation confirming that highly conserved genes show higher expression robustness. In contrast, genes marked by H3K27me3 do not show such associations. Furthermore, highly conserved genes marked by H3K27me3 encode smaller proteins, exhibit weaker codon usage bias, higher levels of hydrophobicity, show lower intrinsically disordered regions, and are enriched for functions related to regulation and membrane transport. The evolutionary age of conserved genes with H3K27me3 histone marks falls typically within the origins of the Fusarium genus. We show that highly conserved genes marked by H3K27me3 are more likely to be dispensable for survival during host infection. Lastly, we show that conserved genes exposed to repressive H3K27me3 marks across distantly related Fusarium fungi are associated with transcriptional perturbation at the microevolutionary scale. In conclusion, we show how repressive histone marks are entangled in the evolutionary fate of highly conserved genes across evolutionary timescales.
45S rDNA Repeats of Turtles and Crocodiles Harbor a Functional 5S rRNA Gene Specifically Expressed in Oocytes
Authors: Davidian Asya G , Dyomin Alexander G , Galkina Svetlana A , Makarova Nadezhda E , Dmitriev Sergey E , Gaginskaya Elena R 
Published: November 2021

Abstract
In most eukaryotic genomes, tandemly repeated copies of 5S rRNA genes are clustered outside the nucleolus organizer region (NOR), which normally encodes three other major rRNAs: 18S, 5.8S, and 28S. Our analysis of turtle rDNA sequences has revealed a 5S rDNA insertion into the NOR intergenic spacer in antisense orientation. The insertion (hereafter called NOR-5S rRNA gene) has a length of 119 bp and coexists with the canonical 5S rDNA clusters outside the NOR. Despite the ∼20% nucleotide difference between the two 5S gene sequences, their internal control regions for RNA polymerase III are similar. Using the turtle Trachemys scripta as a model species, we showed the NOR-5S rDNA specific expression in oocytes. This expression is concurrent with the NOR rDNA amplification during oocyte growth. We show that in vitellogenic oocytes, the NOR-5S rRNA prevails over the canonical 5S rRNA in the ribosomes, suggesting a role of modified ribosomes in oocyte-specific translation. The orders Testudines and Crocodilia seem to be the only taxa of vertebrates with such a peculiar rDNA organization. We speculate that the amplification of the 5S rRNA genes as a part of the NOR DNA during oogenesis provides a dosage balance between transcription of all the four ribosomal RNAs while producing a maternal pool of extra ribosomes. We further hypothesize that the NOR-5S rDNA insertion appeared in the Archelosauria clade during the Permian period and was lost later in the ancestors of Aves.
IID 2021: towards context-specific protein interaction analyses by increased coverage, enhanced annotation and enrichment analysis
Authors: Kotlyar Max , Pastrello Chiara , Ahmed Zuhaib , Chee Justin , Varyova Zofia , Jurisica Igor 
Published: November 2021

Abstract
Improved bioassays have significantly increased the rate of identifying new protein-protein interactions (PPIs), and the number of detected human PPIs has greatly exceeded early estimates of human interactome size. These new PPIs provide a more complete view of disease mechanisms but precise understanding of how PPIs affect phenotype remains a challenge. It requires knowledge of PPI context (e.g. tissues, subcellular localizations), and functional roles, especially within pathways and protein complexes. The previous IID release focused on PPI context, providing networks with comprehensive tissue, disease, cellular localization, and druggability annotations. The current update adds developmental stages to the available contexts, and provides a way of assigning context to PPIs that could not be previously annotated due to insufficient data or incompatibility with available context categories (e.g. interactions between membrane and cytoplasmic proteins). This update also annotates PPIs with conservation across species, directionality in pathways, membership in large complexes, interaction stability (i.e. stable or transient), and mutation effects. Enrichment analysis is now available for all annotations, and includes multiple options; for example, context annotations can be analyzed with respect to PPIs or network proteins. In addition to tabular view or download, IID provides online network visualization. This update is available at http://ophid.utoronto.ca/iid.
SwissBioisostere 2021: updated structural, bioactivity and physicochemical data delivered by a reshaped web interface
Authors: Cuozzo Alessandro , Daina Antoine , Perez Marta A S , Michielin Olivier , Zoete Vincent 
Published: November 2021

Abstract
At several stages of drug discovery, bioisosteric replacement is a common and efficient practice to find new bioactive chemotypes or to optimize series of molecules toward drug candidates. The critical steps consisting in selecting which molecular moiety should be replaced by which other chemical fragment is often relying on the expertise of specialists. Nowadays, valuable support can be obtained through the wealth of dedicated structural and knowledge data. The present article details the update of SwissBioisostere, a database of &gt;25 millions of unique molecular replacements with data on bioactivity, physicochemistry, chemical and biological contexts extracted from the literature and related resources. The content of the database together with analysis and visualization capacities is freely available at www.swissbioisostere.ch.
ConsensusPathDB 2022: molecular interactions update as a resource for network biology
Authors: Kamburov Atanas , Herwig Ralf 
Published: November 2021

Abstract
Molecular interactions are key drivers of biological function. Providing interaction resources to the research community is important since they allow functional interpretation and network-based analysis of molecular data. ConsensusPathDB (http://consensuspathdb.org) is a meta-database combining interactions of diverse types from 31 public resources for humans, 16 for mice and 14 for yeasts. Using ConsensusPathDB, researchers commonly evaluate lists of genes, proteins and metabolites against sets of molecular interactions defined by pathways, Gene Ontology and network neighborhoods and retrieve complex molecular neighborhoods formed by heterogeneous interaction types. Furthermore, the integrated protein–protein interaction network is used as a basis for propagation methods. Here, we present the 2022 update of ConsensusPathDB, highlighting content growth, additional functionality and improved database stability. For example, the number of human molecular interactions increased to 859 848 connecting 200 499 unique physical entities such as genes/proteins, metabolites and drugs. Furthermore, we integrated regulatory datasets in the form of transcription factor–, microRNA– and enhancer–gene target interactions, thus providing novel functionality in the context of overrepresentation and enrichment analyses. We specifically emphasize the use of the integrated protein–protein interaction network as a scaffold for network inferences, present topological characteristics of the network and discuss strengths and shortcomings of such approaches.
Cellular heterogeneity in DNA alkylation repair increases population genetic plasticity
Authors: Vincent Maxence S , Uphoff Stephan 
Published: November 2021

Abstract
DNA repair mechanisms fulfil a dual role, as they are essential for cell survival and genome maintenance. Here, we studied how cells regulate the interplay between DNA repair and mutation. We focused on the adaptive response that increases the resistance of Escherichia coli cells to DNA alkylation damage. Combination of single-molecule imaging and microfluidic-based single-cell microscopy showed that noise in the gene activation timing of the master regulator Ada is accurately propagated to generate a distinct subpopulation of cells in which all proteins of the adaptive response are essentially absent. Whereas genetic deletion of these proteins causes extreme sensitivity to alkylation stress, a temporary lack of expression is tolerated and increases genetic plasticity of the whole population. We demonstrated this by monitoring the dynamics of nascent DNA mismatches during alkylation stress as well as the frequency of fixed mutations that are generated by the distinct subpopulations of the adaptive response. We propose that stochastic modulation of DNA repair capacity by the adaptive response creates a viable hypermutable subpopulation of cells that acts as a source of genetic diversity in a clonal population.
Constrained peptides mimic a viral suppressor of RNA silencing
Authors: Kuepper Arne , McLoughlin Niall M , Neubacher Saskia , Yeste-Vázquez Alejandro , Collado Camps Estel , Nithin Chandran , Mukherjee Sunandan , Bethge Lucas , Bujnicki Janusz M , Brock Roland , Heinrichs Stefan , Grossmann Tom N 
Published: November 2021

AbstractThe design of high-affinity, RNA-binding ligands has proven very challenging. This is due to the unique structural properties of RNA, often characterized by polar surfaces and high flexibility. In addition, the frequent lack of well-defined binding pockets complicates the development of small molecule binders. This has triggered the search for alternative scaffolds of intermediate size. Among these, peptide-derived molecules represent appealing entities as they can mimic structural features also present in RNA-binding proteins. However, the application of peptidic RNA-targeting ligands is hampered by a lack of design principles and their inherently low bio-stability. Here, the structure-based design of constrained α-helical peptides derived from the viral suppressor of RNA silencing, TAV2b, is described. We observe that the introduction of two inter-side chain crosslinks provides peptides with increased α-helicity and protease stability. One of these modified peptides (B3) shows high affinity for double-stranded RNA structures including a palindromic siRNA as well as microRNA-21 and its precursor pre-miR-21. Notably, B3 binding to pre-miR-21 inhibits Dicer processing in a biochemical assay. As a further characteristic this peptide also exhibits cellular entry. Our findings show that constrained peptides can efficiently mimic RNA-binding proteins rendering them potentially useful for the design of bioactive RNA-targeting ligands.
Trophic niche partitioning of three larval Sciaenidae species in the north-western Gulf of Mexico
Authors: Mcaskill Shannan , Paxton Stormy , Geist Simon J 
Published: November 2021

AbstractThe ability of larval fish to find prey items in sufficient quantities plays an important role in determining survivorship. To understand trophic niche partitioning and the potential for competition, we analyzed morphology and digestive tract content in larvae of three co-occurring, sciaenid fish species: Cynoscion nothus, Larimus fasciatus and Micropogonias undulatus. Larvae were collected in the north-western Gulf of Mexico off Galveston, TX, at seven stations in October/November 2017. Intra- and interspecific diet composition was analyzed between three ontogenetic development stages and two sampling zones (nearshore vs mid-shelf). M. undulatus had a significantly smaller mouth size than the other two species and consumed smaller prey items compared with C. nothus. Copepoda dominated all larval diets. The highly abundant M. undulatus primarily ate Calanoida following typical Sciaenidae feeding preferences. The less abundant C. nothus and L. fasciatus shared Cyclopoida as a primary diet item but differed in the consumption of less important prey taxa (i.e. Ostracoda, Chaetognatha). Ontogenetic dietary shifts (ODSs) were observed for all species, with the timing and number of ODS differing for C. nothus between sampling zones. The inclusion of alternative food sources such as Cyclopoida and non-copepod prey taxa likely alleviated potential interspecific competition allowing for larval co-occurrence.
The perception of stakeholders on the applicability of nurse-led clinics in the management of rheumatoid arthritis
Authors: Doumen Michaël , Westhovens René , Vandeputte Maryline , Van Melder Rani , Van der Elst Kristien , Pazmino Sofia , Bertrand Delphine , Stouten Veerle , Van Laeken Els , Creten Nelly , Neys Claudia , Verschueren Patrick , De Cock Diederik 
Published: November 2021

Abstract

Objectives
RA should be treated to target in a process of shared decision-making with patients. Person-centred care is essential to meeting specific patient needs. Nurse-led clinics, where a nurse is responsible for care, have demonstrated added value in some countries but are still not implemented widely. This study aimed to explore stakeholders’ perceptions of advantages, disadvantages and conditions for the implementation of nurse-led clinics for RA in Belgium.

Methods
We performed a cross-sectional qualitative study consisting of five semi-structured focus group interviews. Rheumatology nurses, patients with RA and rheumatologists were interviewed as stakeholders. The analysis was carried out by three researchers according to the Qualitative Analysis Guide of Leuven (QUAGOL), formulating a conceptual framework of overarching themes and deconstructing this into perceived advantages, disadvantages and conditions.

Results
Two focus groups with nurses (total n = 16), two with patients (n = 17) and one with rheumatologists (n = 9) were conducted. The interview synthesis resulted in five overarching themes across stakeholders: efficiency of care, disease management, legal and organizational requirements, the conventional role of the nurse and the extended role of the nurse. All stakeholders perceived additional education for nurses as essential, but rheumatologists debated nurses’ abilities to lead a rheumatology clinic. Furthermore, patients preferred care protocols to guide nurses, and care providers approached this reluctantly. Generally, patients with a well-controlled disease were perceived as the ideal candidates for nurse-led care.

Conclusion
Nurse-led clinics could provide many benefits but require additional nurse education and a legal and organizational framework before being implemented widely and successfully.