bluuebunny/crossref_metadata_2025_split huggingface dataset:
Distinguishing between photoionized and collisionally ionized gas in the circumgalactic medium
Authors: Strawn Clayton , Roca-Fàbrega Santi , Primack Joel 
Published: December 2022

ABSTRACT
Most studies of highly ionized plasmas have historically assumed that ions are either in photoionization equilibrium (PIE) or in collisional ionization equilibrium (CIE), sometimes including multiple phases with different relevant mechanisms. Simulation analysis packages, on the other hand, tend to use pre-computed ion fraction tables that include both mechanisms, among others. Focusing on the low-density, high-temperature phase space likely to be most relevant in the circumgalactic medium, in this work we show that most ions can be classified as ‘PI’ or ‘CI’ on an ion-by-ion basis. This means that for a cloud at a particular point in phase space, some ions will be created primarily by PI and others by CI, with other mechanisms playing only very minor roles. Specifically, we show that ions are generally CI if the thermal energy per particle is greater than ∼6 per cent of their ionization energy, and PI otherwise. We analyse the accuracy of this ansatz compared to usual PIE/CIE calculations, and show the surprisingly minor dependence of this conclusion on redshift and ionizing background.
Comparing weak lensing peak counts in baryonic correction models to hydrodynamical simulations
Authors: Lee Max E , Lu Tianhuan , Haiman Zoltán , Liu Jia , Osato Ken 
Published: December 2022

ABSTRACT
Next-generation weak lensing (WL) surveys, such as by the Vera Rubin Observatory, the Roman Space Telescope, and the Euclid space mission, will supply vast amounts of data probing small, highly non-linear scales. Extracting information from these scales requires higher-order statistics and the controlling of related systematics such as baryonic effects. To account for baryonic effects in cosmological analyses at reduced computational cost, semi-analytic baryonic correction models (BCMs) have been proposed. Here, we study the accuracy of a particular BCM (the A20-BCM) for WL peak counts, a well-studied, simple, and effective higher-order statistic. We compare WL peak counts generated from the full hydrodynamical simulation IllustrisTNG and a baryon-corrected version of the corresponding dark matter-only simulation IllustrisTNG-Dark. We apply galaxy shape noise matching depths reached by DES, KiDS, HSC, LSST, Roman, and Euclid. We find that peak counts from the A20-BCM are (i) accurate at per cent level for peaks with S/N &lt; 4, (ii) statistically indistinguishable from IllustrisTNG in most current and ongoing surveys, but (iii) insufficient for deep future surveys covering the largest solid angles, such as LSST and Euclid. We find that the BCM matches individual peaks accurately, but underpredicts the amplitude of the highest peaks. We conclude that the A20-BCM is a viable substitute for full hydrodynamical simulations in cosmological parameter estimation from beyond-Gaussian statistics for ongoing and future surveys with modest solid angles. For the largest surveys, the A20-BCM must be refined to provide a more accurate match, especially to the highest peaks.
Measuring cosmic filament spin with the kinetic Sunyaev–Zel’dovich effect
Authors: Zheng Yi , Cai Yan-Chuan , Zhu Weishan , Neyrinck Mark , Wang Peng , Li Shaohong 
Published: December 2022

ABSTRACT
The spin of intergalactic filaments has been predicted from simulations, and supported by tentative evidence from redshift-space filament shapes in a galaxy redshift survey: generally, a filament is redshifted on one side of its axis, and blueshifted on the other. Here, we investigate whether filament spins could have a measurable kinetic Sunyaev–Zel’dovich (kSZ) signal, from cosmic microwave background (CMB) photons being scattered by moving ionized gas; this pure velocity information is complementary to filament redshift-space shapes. We propose to measure the kSZ dipole by combining galaxy redshift surveys with CMB experiments. We base our signal-to-noise ratio analyses first on an existing filament catalogue, and its combination with Planck data. We then investigate the detectability of the kSZ dipole using the combination of DESI or SKA-2 with next-stage CMB experiments. We find that the gas haloes of filament galaxies co-rotating with filaments induce a stronger kSZ dipole signal than that from the diffuse filamentary gas, but both signals seem too small to be detected in near-term surveys such as DESI+future CMB experiments. But the combination of SKA-2 with future CMB experiments could give a more than 10σ detection. The gain comes mainly from an increased area overlap and an increased number of filaments, but also the low noise and high resolution in future CMB experiments are important to capture signals from filaments small on the sky. Successful detection of the signals may help to find the gravitomagnetic effect in large-scale structure and advance our understanding of baryons in the cosmic web.
Secondary GeV-TeV emission from ultra-high-energy cosmic rays accelerated by GRB 221009A
Authors: Mirabal N 
Published: December 2022

ABSTRACT
The origin of ultra-high-energy cosmic rays (UHECRs) remains elusive. Gamma-ray bursts (GRBs) are among the best candidates able to meet the stringent energy requirements needed for particle acceleration to such high energies. If UHECRs were accelerated by the central engine of GRB 221009A, it might be possible to detect secondary photons and neutrinos as the UHECRs travel from the source to the Earth. Here, we attempt to interpret some of the early publicly available data connected to this burst. If the reported early GeV-TeV detection was produced by secondary emission from UHECRs, it probably indicates that UHECRs reached energies &gt;1021 eV and that GRB 221009A exploded inside a magnetic void with intergalactic magnetic field (IGMF) strength B ≤ 3 × 10−16 G. In order to understand the entire energy deposition mechanism, we propose to search existing and future Fermi-LAT data for secondary emission arriving over larger spatial scales and longer time-scales. This strategy might help clarify the origin of UHECRs, constrain the IGMF strength along this line of sight, and start to quantify the fraction of magnetic voids around GRBs.
The conserved domain database in 2023
Authors: Wang Jiyao , Chitsaz Farideh , Derbyshire Myra K , Gonzales Noreen R , Gwadz Marc , Lu Shennan , Marchler Gabriele H , Song James S , Thanki Narmada , Yamashita Roxanne A , Yang Mingzhang , Zhang Dachuan , Zheng Chanjuan , Lanczycki Christopher J , Marchler-Bauer Aron 
Published: December 2022

Abstract
NLM’s conserved domain database (CDD) is a collection of protein domain and protein family models constructed as multiple sequence alignments. Its main purpose is to provide annotation for protein and translated nucleotide sequences with the location of domain footprints and associated functional sites, and to define protein domain architecture as a basis for assigning gene product names and putative/predicted function. CDD has been available publicly for over 20 years and has grown substantially during that time. Maintaining an archive of pre-computed annotation continues to be a challenge and has slowed down the cadence of CDD releases. CDD curation staff builds hierarchical classifications of large protein domain families, adds models for novel domain families via surveillance of the protein ‘dark matter’ that currently lacks annotation, and now spends considerable effort on providing names and attribution for conserved domain architectures. CDD can be accessed at https://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml.
Crystal structure of a pre-chemistry viral RNA-dependent RNA polymerase suggests participation of two basic residues in catalysis
Authors: Li Rui , Wang Meihua , Gong Peng 
Published: December 2022

Abstract
The nucleic acid polymerase-catalyzed nucleotidyl transfer reaction associated with polymerase active site closure is a key step in the nucleotide addition cycle (NAC). Two proton transfer events can occur in such a nucleotidyl transfer: deprotonation of the priming nucleotide 3′-hydroxyl nucleophile and protonation of the pyrophosphate (PPi) leaving group. In viral RNA-dependent RNA polymerases (RdRPs), whether and how active site residues participate in this two-proton transfer reaction remained to be clarified. Here we report a 2.5 Å resolution crystal structure of enterovirus 71 (EV71) RdRP in a catalytically closed pre-chemistry conformation, with a proposed proton donor candidate K360 in close contact with the NTP γ-phosphate. Enzymology data reveal that K360 mutations not only reduce RdRP catalytic efficiency but also alter pH dependency profiles in both elongation and pre-elongation synthesis modes. Interestingly, mutations at R174, an RdRP-invariant residue in motif F, had similar effects with additional impact on the Michaelis constant of NTP (KM,NTP). However, direct participation in protonation was not evident for K360 or R174. Our data suggest that both K360 and R174 participate in nucleotidyl transfer, while their possible roles in acid–base or positional catalysis are discussed in comparison with other classes of nucleic acid polymerases.
Translation-complex profiling of fission yeast cells reveals dynamic rearrangements of scanning ribosomal subunits upon nutritional stress
Authors: Duncan Caia Deborah Suzanne , Mata Juan 
Published: December 2022

Abstract
Control of mRNA translation is key for stress responses. Translation initiation is usually rate-limiting and, in eukaryotes, involves mRNA scanning by the small ribosomal subunit. Despite its importance, many aspects of translation in vivo have not been explored fully, especially at the transcriptome-wide level. A recent method termed translation-complex profiling (TCP-seq) allows transcriptome-wide views of scanning ribosomal subunits. We applied TCP-seq to nutritional stress in the fission yeast Schizosaccharomyces pombe. At initiation sites, we observed multiple complexes resembling those of mammals, and consistent with queuing of scanning subunits. In 5′ UTRs, small subunit accumulations were common and may reflect impediments to scanning. A key mediator of stress responses in S. pombe is the Fil1 transcription factor, which is regulated translationally by a poorly-understood mechanism involving upstream Open Reading Frames (uORFs). TCP-seq data of fil1 shows that stress allows scanning subunits to by-pass specific uORFs and reach the fil1 coding sequence. The integration of these observations with reporter assays revealed that fil1 translational control is mediated by a combination of scanning reinitiation-repressive and permissive uORFs, and establishes fil1 as a model for uORF-mediated translational control. Altogether, our transcriptome-wide study reveals general and gene-specific features of translation in a model eukaryote.
Long COVID and return to work: a qualitative study
Authors: Kohn L , Dauvrin M , Detollenaere J , Primus-de Jong C , Maertens de Noordhout C , Castanares-Zapatero D , Cleemput I , Van den Heede K 
Published: December 2022

Abstract

Background
The COVID-19 pandemic has given rise to an increasing number of patients with ‘long COVID’. Long COVID is the persistence of symptoms for weeks or months after an infection by SARS-CoV-2. It often impacts on the professional life of affected people.

Aims
The aim of this study is to understand the experiences and needs of people with long COVID in relation to their return to work.

Methods
A qualitative study, combining individual interviews and online forum discussions, was performed early 2021, as part of a larger mixed method study on the needs of long COVID patients in Belgium.

Results
One hundred and thirty-four people participated in the study. Participants described various clinical symptoms precluding their return to work. They also face sceptical reactions from employers and colleagues and a lack of support from the social welfare system to facilitate their return to work. These barriers have various impacts, including psychological ones, likely to compromise the professional future of long COVID patients.

Conclusions
While the analysis of patients’ experiences shows variation in long COVID patients’ experiences with return to work, it may help occupational physicians and healthcare practitioners to better take up their crucial role in the return to work of long COVID patients, including raising employers’ and colleagues’ awareness of the specific difficulties related to long COVID.
Beyond transcription: compelling open questions in plant RNA biology
Authors: Manavella Pablo A , Godoy Herz Micaela A , Kornblihtt Alberto R , Sorenson Reed , Sieburth Leslie E , Nakaminami Kentaro , Seki Motoaki , Ding Yiliang , Sun Qianwen , Kang Hunseung , Ariel Federico D , Crespi Martin , Giudicatti Axel J , Cai Qiang , Jin Hailing , Feng Xiaoqi , Qi Yijun , Pikaard Craig S 
Published: December 2022

AbstractThe study of RNAs has become one of the most influential research fields in contemporary biology and biomedicine. In the last few years, new sequencing technologies have produced an explosion of new and exciting discoveries in the field but have also given rise to many open questions. Defining these questions, together with old, long-standing gaps in our knowledge, is the spirit of this article. The breadth of topics within RNA biology research is vast, and every aspect of the biology of these molecules contains countless exciting open questions. Here, we asked 12 groups to discuss their most compelling question among some plant RNA biology topics. The following vignettes cover RNA alternative splicing; RNA dynamics; RNA translation; RNA structures; R-loops; epitranscriptomics; long non-coding RNAs; small RNA production and their functions in crops; small RNAs during gametogenesis and in cross-kingdom RNA interference; and RNA-directed DNA methylation. In each section, we will present the current state-of-the-art in plant RNA biology research before asking the questions that will surely motivate future discoveries in the field. We hope this article will spark a debate about the future perspective on RNA biology and provoke novel reflections in the reader.
Analyses of Cullin1 homologs reveal functional redundancy in S-RNase-based self-incompatibility and evolutionary relationships in eudicots
Authors: Sun Linhan , Cao Shiyun , Zheng Ning , Kao Teh-hui 
Published: December 2022

Abstract
In Petunia (Solanaceae family), self-incompatibility (SI) is regulated by the polymorphic S-locus, which contains the pistil-specific S-RNase and multiple pollen-specific S-Locus F-box (SLF) genes. SLFs assemble into E3 ubiquitin ligase complexes known as Skp1–Cullin1–F-box complexes (SCFSLF). In pollen tubes, these complexes collectively mediate ubiquitination and degradation of all nonself S-RNases, but not self S-RNase, resulting in cross-compatible, but self-incompatible, pollination. Using Petunia inflata, we show that two pollen-expressed Cullin1 (CUL1) proteins, PiCUL1-P and PiCUL1-B, function redundantly in SI. This redundancy is lost in Petunia hybrida, not because of the inability of PhCUL1-B to interact with SSK1, but due to a reduction in the PhCUL1-B transcript level. This is possibly caused by the presence of a DNA transposon in the PhCUL1-B promoter region, which was inherited from Petunia axillaris, one of the parental species of Pe. hybrida. Phylogenetic and syntenic analyses of Cullin genes in various eudicots show that three Solanaceae-specific CUL1 genes share a common origin, with CUL1-P dedicated to S-RNase-related reproductive processes. However, CUL1-B is a dispersed duplicate of CUL1-P present only in Petunia, and not in the other species of the Solanaceae family examined. We suggest that the CUL1s involved (or potentially involved) in the SI response in eudicots share a common origin.
Guidance on research integrity provided by pan-European discipline-specific learned societies: A scoping review
Authors: Hastings Rosie , Labib Krishma , Lechner Iris , Bouter Lex , Widdershoven Guy , Evans Natalie 
Published: December 2022

AbstractThere is little research on the content of research integrity (RI)–related guidance provided by pan-European discipline-specific learned societies, or how this guidance compares with recommendations made in the European Code of Conduct for Research Integrity (ALLEA code). Therefore, we aimed to (1) assess the availability of RI guidance from these learned societies, (2) compare learned societies’ guidance with the ALLEA code, and (3) explore similarities and differences in guidance between learned societies of different disciplines. Using a scoping review, we identified 245 learned societies, from which we identified and conducted a content analysis of fifty-eight guideline documents, developed by forty-six of these learned societies. Less than 25 per cent of learned societies in any discipline provide guidance, and there are notable disciplinary differences. Recommendations made by learned societies, which are not reflected in the ALLEA code, relate primarily to research culture and environment. Medical and Health Sciences societies often focus on regulatory and procedural aspects of research, whereas Natural Sciences societies emphasize the importance of accurate and appropriate dissemination of results. Humanities and Social Sciences societies’ recommendations are more heterogeneous and closely related to the nature of specific subdisciplines. Our results reflect differences in epistemological approaches as well as the specific roles and responsibilities of learned societies. We recommend that learned societies develop, or endorse, appropriate RI guidance.
Causal associations of obstructive sleep apnea with cardiovascular disease: a Mendelian randomization study
Authors: Li Ye , Miao Yuyang , Zhang Qiang 
Published: December 2022

AbstractStudy ObjectivesObstructive sleep apnea (OSA) had been associated with various cardiovascular diseases (CVDs) in observational studies, but causal inferences have not been confirmed. We used the Mendelian randomization (MR) study to explore the potential causal association between OSA with CVDs in the general population.MethodsWe performed a two-sample MR analysis using five gene-wide significant single-nucleotide polymorphisms associated with OSA at genome-wide significance from the FinnGen study (N = 217 955) and 12 cardiovascular diseases from the UK Biobank and the genetic consortia. The inverse-variance weight was chosen as the primary analysis and was complemented by various sensitivity analyses. The study design applied univariable MR, multivariable MR, and mediation analysis.ResultsMR analyses provide evidence of genetically predicted OSA on the risk of heart failure (odds ratio [OR],1.26; 95% confidence interval [CI],1.08 to 1.47), hypertension (OR,1.24; 95%CI, 1.11 to 1.39) and atrial fibrillation (OR,1.21; 95%CI,1.12 to 1.31). Multivariable MR indicated the adverse effect of OSA on heart failure persisted after adjusting BMI, smoking, drinking, and education (IVW OR,1.13; 95%CI, 1.01 to 1.27). However, the significance of hypertension and atrial fibrillation was dampened. Mediation analyses suggest that the causal association between OSA and heart failure is mediated in part by Apolipoprotein B, with a mediated portion of 9%.ConclusionsThis study suggested that genetically predicted OSA is a potential causal risk factor for heart failure based on a large-scale population. Nevertheless, further studies regarding ancestral diversity are needed to confirm the causal association between OSA and CVDs.
Epidemiological patterns related to deaths caused by visceral leishmaniasis in the southern Amazon region of Brazil
Authors: Carvalho Amanda G , Kuhn André Luiz M , Dias João Victor L , Luz João Gabriel G 
Published: December 2022

ABSTRACT

Background
We analysed the spatial and spatiotemporal patterns of visceral leishmaniasis (VL) mortality at the municipality level in an endemic state in the southern Amazon region of Brazil. Individual-level factors associated with death due to VL were also investigated.

Methods
All VL cases and deaths reported between 2007 and 2018 were included. The global and local bivariate Moran's index assessed the space–time autocorrelation of smoothed triennial VL mortality. Kulldorff's scan statistics investigated spatial and spatiotemporal clusters. A multivariable logistic regression explored sociodemographic, diagnostic and clinical variables associated with death due to VL.

Results
We observed an overall VL mortality and lethality of 0.14 cases/100 000 inhabitants and 11.2%, respectively. A total of 14% of the municipalities registered at least one VL-related death. In the southeastern mesoregion of the state, we detected high-risk spatial (relative risk [RR] 14.14; p&lt;0.001) and spatiotemporal (RR 15.91; p&lt;0.001) clusters for VL mortality. Bivariate Moran's analysis suggested a high space–time autocorrelation of VL mortality. Death by VL was associated with age ≥48 y (odds ratio [OR] 7.2 [95% confidence interval {CI} 3.4 to 15.3]), displacement for notification (OR 3.3 [95% CI 1.5 to 7.2]) and occurrence of oedema (OR 2.8 [95% CI 1.3 to 6.1]) and bleeding (OR 5.8 [95% CI 2.6 to 12.8]).

Conclusions
VL mortality has a heterogeneous spatiotemporal distribution. The death-related factors suggest late diagnosis as an underlying cause of mortality.
Method Matters: The Underreporting of Intimate Partner Violence
Authors: Cullen Claire 
Published: December 2022

AbstractThis paper analyzes the magnitude and predictors of misreporting on intimate partner violence. Women in Nigeria were randomly assigned to answer questions using either an indirect method (list experiment) that gives respondents anonymity, or the standard, direct face-to-face method. Intimate partner violence rates were up to 35 percent greater when measured using the list method than the direct method. Misreporting was associated with indicators often targeted in empowerment and development programs, such as education and vulnerability. These results suggest that standard survey methods may generate significant underestimates of the prevalence of intimate partner violence, and biased correlations and treatment effect estimates.