bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deep near-infrared survey towards the W40 and Serpens South region in the Aquila Rift: A comprehensive catalogue of young stellar objects
Authors: Sun Jia , Gutermuth Robert A , Wang Hongchi , Zhang Miaomiao , Zhang Shuinai , Ma Yuehui , Du Xinyu , Long Min 
Published: September 2022

ABSTRACT
Active star-forming regions are excellent laboratories for studying the origins and evolution of young stellar object (YSO) clustering. The W40–Serpens South region is such a region, and we compile a large near- and mid-infrared catalogue of point sources in it, based on deep near-infrared observations of Canada-France-Hawaii Telescope (CFHT) in combination with Two Micron All Sky Survey (2MASS), UKIRT Infrared Deep Sky Survey (UKIDSS), and Spitzer catalogues. From this catalogue, we identify 832 YSOs, and classify 15, 135, 647, and 35 of them to be deeply embedded sources, Class I YSOs, Class II YSOs, and transition disc sources, respectively. In general, these YSOs are well correlated with the filamentary structures of molecular clouds, especially the deeply embedded sources and the Class I YSOs. The W40 central region is dominated by Class II YSOs, but in the Serpens South region, half of the YSOs are Class I. We further generate a minimum spanning tree (MST) for all the YSOs. Around the W40 cluster, there are eight prominent MST branches that may trace the vestigial molecular gas filaments that once fed gas to the central natal gas clump. Of the eight, only two now include detectable filamentary gas in Herschel data and corresponding Class I YSOs, while the other six are populated exclusively with Class II YSOs. Four MST branches overlap with the Serpens South main filament, and where they intersect, molecular gas ‘hubs’ and more Class I YSOs are found. Our results imply a mixture of YSO distributions composed of both primordial and somewhat evolved YSOs in this star-forming region.
Hierarchical structure of YSO clusters in the W40 and Serpens South region: group extraction and comparison with fractal clusters
Authors: Sun Jia , Gutermuth Robert A , Wang Hongchi , Zhang Shuinai , Long Min 
Published: September 2022

ABSTRACT
Young stellar clusters are believed to inherit the spatial distribution like hierarchical structures of their natal molecular cloud during their formation. However, the change of the structures between the cloud and the young clusters is not well constrained observationally. We select the W40–Serpens South region (∼7 × 9 pc2) of the Aquila Rift as a testbed and investigate hierarchical properties of spatial distribution of young stellar objects (YSOs) in this region. We develop a minimum spanning tree (MST) based method to group stars into several levels by successively cutting down edges longer than an algorithmically determined critical value. A total of 832 YSOs are divided into 5 levels with 23 groups. For describing the hierarchical properties in a controlled way, we construct a set of synthetic source distributions at various fractal dimensions, and apply the same method to explore their group characters. By comparing the Q parameter and the surface density profiles of the observed and the synthetic data, we find that the YSO observation matches spatial patterns from multifractal dimensions. In the periphery region where the molecular clouds are more diffuse, the YSO structure is close to a fractal dimension of 2.0. While in the core regions, the fractal dimensions are close to 1.6 and 1.4 for the W40 and the Serpens South regions, respectively. Therefore, the YSOs may inherit the fractal pattern of the dense part of the molecular clouds, but such pattern dissipates slowly in several Myr.
Dissecting the microphysics behind the metallicity-dependence of massive stars radii
Authors: Xin Chengcheng , Renzo Mathieu , Metzger Brian D 
Published: September 2022

ABSTRACT
Understanding the radii of massive stars throughout their evolution is important to answering numerous questions about stellar physics, from binary interactions on the main sequence to the pre-supernova radii. One important factor determining a star’s radius is the fraction of its mass in elements heavier than Helium (metallicity, Z). However, the metallicity enters stellar evolution through several distinct microphysical processes, and which dominates can change throughout stellar evolution and with the overall magnitude of Z. We perform a series of numerical experiments with 15 $\, \mathrm{M}_{\odot }$mesa models computed doubling separately the metallicity entering the radiative opacity, the equation of state, and the nuclear reaction network to isolate the impact of each on stellar radii. We explore separately models centred around two metallicity values: one near solar Z = 0.02 and another sub-solar Z ∼ 10−3, and consider several key epochs from the end of the main sequence to core carbon depletion. We find that the metallicity entering the opacity dominates at most epochs for the solar metallicity models, contributing to on average ∼60–90 per cent of the total change in stellar radius. Nuclear reactions have a larger impact (∼50–70 per cent) during most epochs in the subsolar Z models. The methodology introduced here can be employed more generally to propagate known microphysics errors into uncertainties on macrophysical observables including stellar radii.
The chemical enrichment in the early Universe as probed by JWST via direct metallicity measurements at z ∼ 8
Authors: Curti Mirko , D’Eugenio Francesco , Carniani Stefano , Maiolino Roberto , Sandles Lester , Witstok Joris , Baker William M , Bennett Jake S , Piotrowska Joanna M , Tacchella Sandro , Charlot Stephane , Nakajima Kimihiko , Maheson Gabriel , Mannucci Filippo , Amiri Amirnezam , Arribas Santiago , Belfiore Francesco , Bonaventura Nina R , Bunker Andrew J , Chevallard Jacopo , Cresci Giovanni , Curtis-Lake Emma , Hayden-Pawson Connor , Jones Gareth C , Kumari Nimisha , Laseter Isaac , Looser Tobias J , Marconi Alessandro , Maseda Michael V , Scholtz Jan , Smit Renske , Übler Hannah , Wallace Imaan E B 
Published: September 2022

ABSTRACT
We analyse the chemical properties of three z∼ 8 galaxies behind the galaxy cluster SMACS J0723.3-7327, observed as part of the Early Release Observations programme of the James Webb Space Telescope. Exploiting [O iii]λ4363 auroral line detections in NIRSpec spectra, we robustly apply the direct Te  method for the very first time at such high redshift, measuring metallicities ranging from extremely metal poor (12 + log(O/H)≈ 7) to about one-third solar. We also discuss the excitation properties of these sources, and compare them with local strong-line metallicity calibrations. We find that none of the considered diagnostics match simultaneously the observed relations between metallicity and strong-line ratios for the three sources, implying that a proper re-assessment of the calibrations may be needed at these redshifts. On the mass–metallicity plane, the two galaxies at z ∼ 7.6 ($\rm log(M_*/M_{\odot }) = 8.1, 8.7$) have metallicities that are consistent with the extrapolation of the mass–metallicity relation at z∼2–3, while the least massive galaxy at z ∼ 8.5 ($\rm log(M_*/M_{\odot }) = 7.8$) shows instead a significantly lower metallicity. The three galaxies show different level of offset relative to the Fundamental Metallicity Relation, with two of them (at z∼ 7.6) being marginally consistent, while the z∼ 8.5 source deviating significantly, being probably far from the smooth equilibrium between gas flows, star formation, and metal enrichment in place at later epochs.
Non-universal stellar initial mass functions: large uncertainties in star formation rates at z ≈ 2–4 and other astrophysical probes
Authors: Ziegler Joshua J , Edwards Thomas D P , Suliga Anna M , Tamborra Irene , Horiuchi Shunsaku , Ando Shin’ichiro , Freese Katherine 
Published: September 2022

ABSTRACT
We explore the assumption, widely used in many astrophysical calculations, that the stellar initial mass function (IMF) is universal across all galaxies. By considering both a canonical broken-power-law IMF and a non-universal IMF, we are able to compare the effect of different IMFs on multiple observables and derived quantities in astrophysics. Specifically, we consider a non-universal IMF that varies as a function of the local star formation rate, and explore the effects on the star formation rate density (SFRD), the extragalactic background light, the supernova (both core-collapse and thermonuclear) rates, and the diffuse supernova neutrino background. Our most interesting result is that our adopted varying IMF leads to much greater uncertainty on the SFRD at $z \approx 2-4$ than is usually assumed. Indeed, we find an SFRD (inferred using observed galaxy luminosity distributions) that is a factor of $\gtrsim 3$ lower than canonical results obtained using a universal IMF. Secondly, the non-universal IMF we explore implies a reduction in the supernova core-collapse rate of a factor of $\sim 2$, compared against a universal IMF. The other potential tracers are only slightly affected by changes to the properties of the IMF. We find that currently available data do not provide a clear preference for universal or non-universal IMF. However, improvements to measurements of the star formation rate and core-collapse supernova rate at redshifts $z \gtrsim 2$ may offer the best prospects for discernment.
Chemical abundances of the Typhon stellar stream
Authors: Ji Alexander P , Naidu Rohan P , Brauer Kaley , Ting Yuan-Sen , Simon Joshua D 
Published: September 2022

ABSTRACT
We present the first high-resolution chemical abundances of seven stars in the recently discovered high-energy stream Typhon. Typhon stars have apocentres r ≳ 100 kpc, making this the first detailed chemical picture of the Milky Way’s very distant stellar halo. Though the sample size is limited, we find that Typhon’s chemical abundances are more like a dwarf galaxy than a globular cluster, showing a metallicity dispersion and no presence of multiple stellar populations. Typhon stars display enhanced α-element abundances and increasing r-process abundances with increasing metallicity. The high-α abundances suggest a short star formation duration for Typhon, but this is at odds with expectations for the distant Milky Way halo and the presence of delayed r-process enrichment. If the progenitor of Typhon is indeed a new dwarf galaxy, possible scenarios explaining this apparent contradiction include a dynamical interaction that increases Typhon’s orbital energy, a burst of enhanced late-time star formation that raises [α/Fe], and/or group pre-processing by another dwarf galaxy before infall into the Milky Way. Alternatively, Typhon could be the high-energy tail of a more massive disrupted dwarf galaxy that lost energy through dynamical friction. We cannot clearly identify a known low-energy progenitor of Typhon in the Milky Way, but 70 per cent of high-apocentre stars in cosmological simulations are from high-energy tails of large dwarf galaxies. Typhon’s surprising combination of kinematics and chemistry thus underscores the need to fully characterize the dynamical history and detailed abundances of known substructures before identifying the origin of new substructures.
Long-read single-molecule RNA structure sequencing using nanopore
Authors: Bizuayehu Teshome Tilahun , Labun Kornel , Jakubec Martin , Jefimov Kirill , Niazi Adnan Muhammad , Valen Eivind 
Published: September 2022

Abstract
RNA molecules can form secondary and tertiary structures that can regulate their localization and function. Using enzymatic or chemical probing together with high-throughput sequencing, secondary structure can be mapped across the entire transcriptome. However, a limiting factor is that only population averages can be obtained since each read is an independent measurement. Although long-read sequencing has recently been used to determine RNA structure, these methods still used aggregate signals across the strands to detect structure. Averaging across the population also means that only limited information about structural heterogeneity across molecules or dependencies within each molecule can be obtained. Here, we present Single-Molecule Structure sequencing (SMS-seq) that combines structural probing with native RNA sequencing to provide non-amplified, structural profiles of individual molecules with novel analysis methods. Our new approach using mutual information enabled single molecule structural interrogation. Each RNA is probed at numerous bases enabling the discovery of dependencies and heterogeneity of structural features. We also show that SMS-seq can capture tertiary interactions, dynamics of riboswitch ligand binding, and mRNA structural features.
Translational enhancement by base editing of the Kozak sequence rescues haploinsufficiency
Authors: Ambrosini Chiara , Destefanis Eliana , Kheir Eyemen , Broso Francesca , Alessandrini Federica , Longhi Sara , Battisti Nicolò , Pesce Isabella , Dassi Erik , Petris Gianluca , Cereseto Anna , Quattrone Alessandro 
Published: September 2022

AbstractA variety of single-gene human diseases are caused by haploinsufficiency, a genetic condition by which mutational inactivation of one allele leads to reduced protein levels and functional impairment. Translational enhancement of the spare allele could exert a therapeutic effect. Here we developed BOOST, a novel gene-editing approach to rescue haploinsufficiency loci by the change of specific single nucleotides in the Kozak sequence, which controls translation by regulating start codon recognition. We evaluated for translational strength 230 Kozak sequences of annotated human haploinsufficient genes and 4621 derived variants, which can be installed by base editing, by a high-throughput reporter assay. Of these variants, 149 increased the translation of 47 Kozak sequences, demonstrating that a substantial proportion of haploinsufficient genes are controlled by suboptimal Kozak sequences. Validation of 18 variants for 8 genes produced an average enhancement in an expression window compatible with the rescue of the genetic imbalance. Base editing of the NCF1 gene, whose monoallelic loss causes chronic granulomatous disease, resulted in the desired increase of NCF1 (p47phox) protein levels in a relevant cell model. We propose BOOST as a fine-tuned approach to modulate translation, applicable to the correction of dozens of haploinsufficient monogenic disorders independently of the causing mutation.
snoDB 2.0: an enhanced interactive database, specializing in human snoRNAs
Authors: Bergeron Danny , Paraqindes Hermes , Fafard-Couture Étienne , Deschamps-Francoeur Gabrielle , Faucher-Giguère Laurence , Bouchard-Bourelle Philia , Abou Elela Sherif , Catez Frédéric , Marcel Virginie , Scott Michelle S 
Published: September 2022

Abstract
snoDB is an interactive database of human small nucleolar RNAs (snoRNAs) that includes up-to-date information on snoRNA features, genomic location, conservation, host gene, snoRNA–RNA targets and snoRNA abundance and provides links to other resources. In the second edition of this database (snoDB 2.0), we added an entirely new section on ribosomal RNA (rRNA) chemical modifications guided by snoRNAs with easy navigation between the different rRNA versions used in the literature and experimentally measured levels of modification. We also included new layers of information, including snoRNA motifs, secondary structure prediction, snoRNA–protein interactions, copy annotations and low structure bias expression data in a wide panel of tissues and cell lines to bolster functional probing of snoRNA biology. Version 2.0 features updated identifiers, more links to external resources and duplicate entry resolution. As a result, snoDB 2.0, which is freely available at https://bioinfo-scottgroup.med.usherbrooke.ca/snoDB/, represents a one-stop shop for snoRNA features, rRNA modification targets, functional impact and potential regulators.
Nanopore tweezers measurements of RecQ conformational changes reveal the energy landscape of helicase motion
Authors: Craig Jonathan M , Mills Maria , Kim Hwanhee C , Huang Jesse R , Abell Sarah J , Mount Jonathan W , Gundlach Jens H , Neuman Keir C , Laszlo Andrew H 
Published: September 2022

Abstract
Helicases are essential for nearly all nucleic acid processes across the tree of life, yet detailed understanding of how they couple ATP hydrolysis to translocation and unwinding remains incomplete because their small (∼300 picometer), fast (∼1 ms) steps are difficult to resolve. Here, we use Nanopore Tweezers to observe single Escherichia coli RecQ helicases as they translocate on and unwind DNA at ultrahigh spatiotemporal resolution. Nanopore Tweezers simultaneously resolve individual steps of RecQ along the DNA and conformational changes of the helicase associated with stepping. Our data reveal the mechanochemical coupling between physical domain motions and chemical reactions that together produce directed motion of the helicase along DNA. Nanopore Tweezers measurements are performed under either assisting or opposing force applied directly on RecQ, shedding light on how RecQ responds to such forces in vivo. Determining the rates of translocation and physical conformational changes under a wide range of assisting and opposing forces reveals the underlying dynamic energy landscape that drives RecQ motion. We show that RecQ has a highly asymmetric energy landscape that enables RecQ to maintain velocity when encountering molecular roadblocks such as bound proteins and DNA secondary structures. This energy landscape also provides a mechanistic basis making RecQ an ‘active helicase,’ capable of unwinding dsDNA as fast as it translocates on ssDNA. Such an energy landscape may be a general strategy for molecular motors to maintain consistent velocity despite opposing loads or roadblocks.
PLK3 amplification and tumor immune microenvironment of metastatic tumors are linked to adjuvant treatment outcomes in uterine serous cancer
Authors: Jones Wendell , Tait David , Livasy Chad , Ganapathi Mahrukh , Ganapathi Ram 
Published: September 2022

Abstract
Uterine serous carcinoma (USC), an aggressive variant of endometrial cancer representing approximately 10% of endometrial cancer diagnoses, accounts for ∼39% of endometrial cancer-related deaths. We examined the role of genomic alterations in advanced-stage USC associated with outcome using paired primary-metastatic tumors (n = 29) treated with adjuvant platinum and taxane chemotherapy. Comparative genomic analysis of paired primary-metastatic patient tumors included whole exome sequencing and targeted gene expression. Both PLK3 amplification and the tumor immune microenvironment (TIME) in metastatic tumors were linked to time-to-recurrence (TTR) risk without any such association observed with primary tumors. TP53 loss was significantly more frequent in metastatic tumors of platinum-resistant versus platinum-sensitive patients and was also associated with increased recurrence and mortality risk. Increased levels of chr1 breakpoints in USC metastatic versus primary tumors co-occur with PLK3 amplification. PLK3 and the TIME are potential targets for improving outcomes in USC adjuvant therapy.
Systematic analysis of the underlying genomic architecture for transcriptional–translational coupling in prokaryotes
Authors: Bharti Richa , Siebert Daniel , Blombach Bastian , Grimm Dominik G 
Published: September 2022

Abstract
Transcriptional-translational coupling is accepted to be a fundamental mechanism of gene expression in prokaryotes and therefore has been analyzed in detail. However, the underlying genomic architecture of the expression machinery has not been well investigated so far. In this study, we established a bioinformatics pipeline to systematically investigated &gt;1800 bacterial genomes for the abundance of transcriptional and translational associated genes clustered in distinct gene cassettes. We identified three highly frequent cassettes containing transcriptional and translational genes, i.e. rplk-nusG (gene cassette 1; in 553 genomes), rpoA-rplQ-rpsD-rpsK-rpsM (gene cassette 2; in 656 genomes) and nusA-infB (gene cassette 3; in 877 genomes). Interestingly, each of the three cassettes harbors a gene (nusG, rpsD and nusA) encoding a protein which links transcription and translation in bacteria. The analyses suggest an enrichment of these cassettes in pathogenic bacterial phyla with &gt;70% for cassette 3 (i.e. Neisseria, Salmonella and Escherichia) and &gt;50% for cassette 1 (i.e. Treponema, Prevotella, Leptospira and Fusobacterium) and cassette 2 (i.e. Helicobacter, Campylobacter, Treponema and Prevotella). These insights form the basis to analyze the transcriptional regulatory mechanisms orchestrating transcriptional–translational coupling and might open novel avenues for future biotechnological approaches.
Obesity and its association with mental health among Mexican children and adolescents: systematic review
Authors: Godina-Flores Naara L , Gutierrez-Gómez Yareni Yunuen , García-Botello Marcela , López-Cruz Lizet , Moreno-García Carlos Francisco , Aceves-Martins Magaly 
Published: September 2022

Abstract

Context
Obesity and mental health issues increasingly affect children and adolescents, but whether obesity is a risk factor for mental health issues is unclear.

Objective
To systematically review the association between obesity and mental health issues (ie, anxiety and/or depression) among Mexican children and adolescents.

Data sourcing, extraction, and synthesis
A literature search of 13 databases and 1 search engine was conducted. Population, exposure, comparison, outcomes, and study design data were extracted, analyzed, and narratively synthesized. The JBI critical appraisal tool was used to evaluate evidence quality.

Results
A total of 16 studies with 12 103 participants between 8 and 18 years old were included. Four studies focused on anxiety outcomes, 10 on depression, and 2 on both (ie, anxiety and depression). Evidence is unclear about the association of obesity with anxiety. However, most evidence shows that Mexican children and adolescents with overweight or obesity are more likely to have depression or report a higher number of depressive symptoms than normal-weight participants. Such likelihood is greater for females.

Conclusion
Health promotion interventions to treat or prevent obesity could also consider mental health outcomes.

Systematic Review Registration
PROSPERO registration no. CRD42019154132
Diffuse idiopathic pulmonary neuroendocrine cell hyperplasia presenting as a solitary lung nodule: a rare histopathological diagnosis
Authors: Simon Natalie , Negmeldin Mostafa 
Published: September 2022

ABSTRACT
We present a case of diffuse idiopathic pulmonary neuroendocrine cell hyperplasia (DIPNECH) in a 56-year-old woman, who presented to our emergency department with a 7-day history of exertional dyspnoea. Due to profound haemodynamic compromise, pulmonary embolism (PE) was suspected, and the patient underwent emergency thrombolysis on admission. A subsequent computerized tomography pulmonary angiogram revealed extensive bilateral PE. Incidentally, a 1.3 cm lesion within the right upper lobe, associated with pleural tethering, was identified. Positron emission tomography computerized tomography and, subsequently, histopathology revealed this lesion to be primary DIPNECH, a rare pre-invasive hyperplasia of neuroendocrine cells. While studies are scarce and cohort numbers are low, somatostatin analogues and protein kinase inhibitors have been proven to reduce symptoms and increase progression-free survival in DIPNECH, respectively.