bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optical spectroscopic characterization of Fermi blazar candidates of uncertain type with TNG and DOT: first results
Authors: Olmo-García Amanda , Paliya Vaidehi S , Álvarez Crespo Nuria , Kumar Brajesh , Domínguez Alberto , Gil de Paz Armando , Sánchez-Blázquez Patricia 
Published: September 2022

ABSTRACT
The classification of γ-ray-detected blazar candidates of uncertain type (BCU) is a relevant problem in extragalactic γ-ray astronomy. Here, we report the optical spectroscopic characterization, using two 3–4 m class telescopes, Telescopio Nazionale Galileo and Devasthal Optical Telescope, of 27 BCUs detected with the Fermi Large Area Telescope. Since the identification of emission lines is easier in broad-line blazars, which usually exhibit low frequency peaked (synchrotron peak frequency ≤1014 Hz) spectral energy distribution, we primarily target such BCUs. We found that 8 out of 27 sources exhibit broad emission lines in their optical spectra, 3 of them have redshifts &gt;1 and the farthest one is at z = 2.55. The optical spectra of 2 of the 19 remaining objects are dominated by the absorption spectra of the host galaxy, and there is a tentative detection of the Lyman-α absorption feature in one source. The spectra of the remaining 16 objects, on the other hand, are found to be featureless.
The physics of Lyman-α escape from disc-like galaxies
Authors: Smith Aaron , Kannan Rahul , Tacchella Sandro , Vogelsberger Mark , Hernquist Lars , Marinacci Federico , Sales Laura V , Torrey Paul , Li Hui , Yeh Jessica Y-C , Qi Jia 
Published: September 2022

ABSTRACT
Hydrogen emission lines can provide extensive information about star-forming galaxies in both the local and high-redshift Universe. We present a detailed Lyman continuum (LyC), Lyman-α (Lyα), and Balmer line (Hα and Hβ) radiative transfer study of a high-resolution isolated Milky Way simulation using the state-of-the-art Arepo-RT radiation hydrodynamics code with the SMUGGLE galaxy formation model. The realistic framework includes stellar feedback, non-equilibrium thermochemistry accounting for molecular hydrogen, and dust grain evolution in the interstellar medium (ISM). We extend our publicly available Cosmic Lyα Transfer (COLT) code with photoionization equilibrium Monte Carlo radiative transfer and various methodology improvements for self-consistent end-to-end (non-)resonant line predictions. Accurate LyC reprocessing to recombination emission requires modelling pre-absorption by dust ($f_\text{abs} \approx 27.5\,\rm{per\,\,cent}$), helium ionization ($f_\text{He} \approx 8.7\,\rm{per\,\,cent}$), and anisotropic escape fractions ($f_\text{esc} \approx 7.9\,\rm{per\,\,cent}$), as these reduce the available budget for hydrogen line emission ($f_\text{H} \approx 55.9\,\rm{per\,\,cent}$). We investigate the role of the multiphase dusty ISM, disc geometry, gas kinematics, and star formation activity in governing the physics of emission and escape, focusing on the time variability, gas-phase structure, and spatial spectral, and viewing angle dependence of the emergent photons. Isolated disc simulations are well-suited for comprehensive observational comparisons with local Hα surveys, but would require a proper cosmological circumgalactic medium (CGM) environment as well as less dust absorption and rotational broadening to serve as analogs for high-redshift Lyα emitting galaxies. Future applications of our framework to next-generation cosmological simulations of galaxy formation including radiation-hydrodynamics that resolve ≲10 pc multiphase ISM and ≲1 kpc CGM structures will provide crucial insights and predictions for current and upcoming Lyα observations.
Weak gravitational lensing shear estimation with metacalibration for the Roman High-Latitude Imaging Survey
Authors: Yamamoto Masaya , Troxel M A , Jarvis Mike , Mandelbaum Rachel , Hirata Christopher , Long Heyang , Choi Ami , Zhang Tianqing 
Published: September 2022

ABSTRACT
We investigate the performance of the metacalibration shear calibration framework using simulated imaging data for the Nancy Grace Roman Space Telescope (Roman) reference High-Latitude Imaging Survey (HLIS). The weak lensing programme of Roman requires the mean weak lensing shear estimate to be calibrated within about 0.03 per cent. To reach this goal, we can test our calibration process with various simulations and ultimately isolate the sources of residual shear biases in order to improve our methods. In this work, we build on the HLIS image simulation pipeline to incorporate several more realistic processing-pipeline updates. We show the first metacalibration results for 6 deg2 of the simulated reference HLIS and compare them to measurements on simpler, faster Roman-like image simulations. We neglect the impact of blending of objects. We find in the simplified simulations metacalibration can calibrate shapes to within m = (−0.01 ± 0.10) per cent. When applied to the current most-realistic version of the simulations, the precision is much lower, with estimates of m = (−0.76 ± 0.43) per cent for joint multiband multi-epoch measurements and m = (−1.13 ± 0.60) per cent for multiband coadd measurements. These results are all consistent with zero within 1–2σ, indicating we are currently limited by our simulated survey volume. Further work on testing the shear calibration methodology is necessary at the precision of the Roman requirements, in particular in the presence of blending. Current results demonstrate, however, that metacalibration can work on undersampled space-based Roman imaging data at levels comparable to requirements of current weak lensing surveys.
Primordial black holes capture by stars and induced collapse to low-mass stellar black holes
Authors: Oncins Marc , Miralda-Escudé Jordi , Gutiérrez Jordi L , Gil-Pons Pilar 
Published: September 2022

ABSTRACT
Primordial black holes in the asteroid-mass window, which might constitute all the dark matter, can be captured by stars when they traverse them at low enough velocity. After being placed on a bound orbit during star formation, they can repeatedly cross the star if the orbit happens to be highly eccentric, slow down by dynamical friction, and end up in the stellar core. The rate of these captures is highest in haloes of high dark matter density and low velocity dispersion, when the first stars form at redshift z ∼ 20. We compute this capture rate for low-metallicity stars of 0.3–$1\, {\rm M_{\odot }}$, and find that a high fraction of these stars formed in the first dwarf galaxies would capture a primordial black hole, which would then grow by accretion up to a mass that may be close to the total star mass. We show the capture rate of primordial black holes does not depend on their mass over this asteroid-mass window, and should not be much affected by external tidal perturbations. These low-mass stellar black holes could be discovered today in low-metallicity, old binary systems in the Milky Way containing a surviving low-mass main-sequence star or a white dwarf, or via gravitational waves emitted in a merger with another compact object. No mechanisms in standard stellar evolution theory are known to form black holes below the Chandrasekhar mass, so detecting a low-mass black hole would fundamentally impact our understanding of stellar evolution, dark matter, and the early Universe.
Identifying the most constraining ice observations to infer molecular binding energies
Authors: Heyl Johannes , Sellentin Elena , Holdship Jonathan , Viti Serena 
Published: September 2022

ABSTRACT
In order to understand grain-surface chemistry, one must have a good understanding of the reaction rate parameters. For diffusion-based reactions, these parameters are binding energies of the reacting species. However, attempts to estimate these values from grain-surface abundances using Bayesian inference are inhibited by a lack of enough sufficiently constraining data. In this work, we use the Massive Optimised Parameter Estimation and Data compression algorithm to determine which species should be prioritized for future ice observations to better constrain molecular binding energies. Using the results from this algorithm, we make recommendations for which species future observations should focus on.
Analysis of Gaia radial-velocity standards: stability and new substellar companion candidates
Authors: Boulkaboul A , Damerdji Y , Morel T , Frémat Y , Soubiran C , Gosset E , Abdelatif T E 
Published: September 2022

ABSTRACT
Our main aim is to test the non-variability of the radial velocity (RV) of a sample of 2351 standard stars used for wavelength calibration of the Radial Velocity Spectrometer (RVS) instrument onboard Gaia. In this paper, we present the spectroscopic analysis of these stars with the determination of their physical parameters by matching observed and synthetic spectra. We estimate the offset between different instruments after determining the shift between measured and archived RVs since the instrument pipelines use various numerical masks. Through the confirmation of the stability of the target RVs, we find 68 stars with a long-term variation having an acceleration that exceeds $10 \, \rm {m\, s^{-1}\,yr^{-1}}$. This suggests a barycentric reflex motion caused by a companion. As activity phenomena may be the source of periodic and trend-like RV variations in stars with putative planetary companions, we analysed various activity indicators in order to check their correlations to the RV changes. Among the trend stars, 18 have a trend model scatter greater than $100 \, \rm {m\, s^{-1}}$ over a time span from 10 to 12 yr. We also confirm that six stars with known substellar companions have a total model scatter, 3σ, exceeding the threshold set by Gaia, that is, $300 \, \rm {m\, s^{-1}}$. In addition, TYC8963-01543-1, an SB2 star, has data scatter $\sigma = 176.6\, \rm {m\, s^{-1}}$. Four more other stars are revealed to be variable after combining data from different instruments. Despite the presence of low-amplitude changes, a very large fraction of our sample (98.8 per cent) appears suitable as RV calibrators for Gaia RVS.
Functional Divergence in a Multi-gene Family Is a Key Evolutionary Innovation for Anaerobic Growth in Saccharomyces cerevisiae
Authors: Krause David J , Hittinger Chris Todd 
Published: September 2022

Abstract
The amplification and diversification of genes into large multi-gene families often mark key evolutionary innovations, but this process often creates genetic redundancy that hinders functional investigations. When the model budding yeast Saccharomyces cerevisiae transitions to anaerobic growth conditions, the cell massively induces the expression of seven serine/threonine-rich anaerobically-induced cell wall mannoproteins (anCWMPs): TIP1, TIR1, TIR2, TIR3, TIR4, DAN1, and DAN4. Here, we show that these genes likely derive evolutionarily from a single ancestral anCWMP locus, which was duplicated and translocated to new genomic contexts several times both prior to and following the budding yeast whole genome duplication (WGD) event. Based on synteny and their phylogeny, we separate the anCWMPs into four gene subfamilies. To resolve prior inconclusive genetic investigations of these genes, we constructed a set of combinatorial deletion mutants to determine their contributions toward anaerobic growth in S. cerevisiae. We found that two genes, TIR1 and TIR3, were together necessary and sufficient for the anCWMP contribution to anaerobic growth. Overexpressing either gene alone was insufficient for anaerobic growth, implying that they encode non-overlapping functional roles in the cell during anaerobic growth. We infer from the phylogeny of the anCWMP genes that these two important genes derive from an ancient duplication that predates the WGD event, whereas the TIR1 subfamily experienced gene family amplification after the WGD event. Taken together, the genetic and molecular evidence suggests that one key anCWMP gene duplication event, several auxiliary gene duplication events, and functional divergence underpin the evolution of anaerobic growth in budding yeasts.
Progesterone suppresses podocalyxin partly by up-regulating miR-145 and miR-199 in human endometrial epithelial cells to enhance receptivity in in vitro models
Authors: Shekibi Manizha , Heng Sophea , Wang Yao , Samarajeewa Nirukshi , Rombauts Luk , Nie Guiying 
Published: September 2022

Abstract
Establishment of endometrial surface receptivity is crucial for the initiation of embryo implantation yet the molecular mechanisms are not well understood, especially in humans. We have recently discovered that podocalyxin (PODXL) is a critical negative regulator of human endometrial surface receptivity. PODXL is highly expressed in all epithelial and endothelial cells in the non-receptive endometrium, but down-regulated specifically in the luminal epithelium at receptivity. We have further shown that PODXL inhibits embryo implantation, and that PODXL down-regulation is essential for endometrial surface receptivity. Our previous study also indicated that progesterone down-regulates PODXL; however, the exact molecular regulations are unknown. Here, we investigated whether progesterone suppresses PODXL via microRNAs (miRNAs). We first bioinformatically predicted 13 miRNAs that may potentially target human PODXL, then experimentally determined whether any of these 13 miRNAs are altered in primary human endometrial epithelial cells (HEECs) by progesterone, and whether the identified miRNAs can affect PODXL expression in Ishikawa cells without progesterone and alter receptivity to embryo implantation. Progesterone significantly up-regulated miR-145 and miR-199 while suppressing PODXL in HEECs. When these two miRNAs were transfected into Ishikawa cells, both significantly down-regulated PODXL mRNA and protein in the absence of progesterone. Moreover, both miR-145 and miR-199 significantly enhanced receptivity of the Ishikawa monolayer to embryo implantation in in vitro models. This study thus provides in vitro evidence that PODXL is down-regulated by progesterone partly via miR-145 and miR-199 during the development of human endometrial epithelial receptivity. These results also reveal the likely importance of hormonal regulation of miRNAs for embryo implantation.
QUADRatlas: the RNA G-quadruplex and RG4-binding proteins database
Authors: Bourdon Sébastien , Herviou Pauline , Dumas Leïla , Destefanis Eliana , Zen Andrea , Cammas Anne , Millevoi Stefania , Dassi Erik 
Published: September 2022

AbstractRNA G-quadruplexes (RG4s) are non-canonical, disease-associated post-transcriptional regulators of gene expression whose functions are driven by RNA-binding proteins (RBPs). Being able to explore transcriptome-wide RG4 formation and interaction with RBPs is thus paramount to understanding how they are regulated and exploiting them as potential therapeutic targets. Towards this goal, we present QUADRatlas (https://rg4db.cibio.unitn.it), a database of experimentally-derived and computationally predicted RG4s in the human transcriptome, enriched with biological function and disease associations. As RBPs are key to their function, we mined known interactions of RG4s with such proteins, complemented with an extensive RBP binding sites dataset. Users can thus intersect RG4s with their potential regulators and effectors, enabling the formulation of novel hypotheses on RG4 regulation, function and pathogenicity. To support this capability, we provide analysis tools for predicting whether an RBP can bind RG4s, RG4 enrichment in a gene set, and de novo RG4 prediction. Genome-browser and table views allow exploring, filtering, and downloading the data quickly for individual genes and in batch. QUADRatlas is a significant step forward in our ability to understand the biology of RG4s, offering unmatched data content and enabling the integrated analysis of RG4s and their interactions with RBPs.
Accuratein silicoconfirmation of rare copy number variant calls from exome sequencing data using transfer learning
Authors: Tan Renjie , Shen Yufeng 
Published: September 2022

AbstractExome sequencing is widely used in genetic studies of human diseases and clinical genetic diagnosis. Accurate detection of copy number variants (CNVs) is important to fully utilize exome sequencing data. However, exome data are noisy. None of the existing methods alone can achieve both high precision and recall rate. A common practice is to perform heuristic filtration followed by manual inspection of read depth of putative CNVs. This approach does not scale in large studies. To address this issue, we developed a transfer learning method, CNV-espresso, for in silico confirming rare CNVs from exome sequencing data. CNV-espresso encodes candidate CNVs from exome data as images and uses pretrained convolutional neural network models to classify copy number states. We trained CNV-espresso using an offspring–parents trio exome sequencing dataset, with inherited CNVs as positives and CNVs with Mendelian errors as negatives. We evaluated the performance using additional samples that have both exome and whole-genome sequencing (WGS) data. Assuming the CNVs detected from WGS data as a proxy of ground truth, CNV-espresso significantly improves precision while keeping recall almost intact, especially for CNVs that span a small number of exons. CNV-espresso can effectively replace manual inspection of CNVs in large-scale exome sequencing studies.
Hippocampal subfield morphology in regular hemodialysis patients
Authors: Chen Hui Juan , Qiu Jie , Qi Yonghui , Fu Lili , Fu Qingqing , Wu Wenyuan , Dai Ganmian , Chen Feng 
Published: September 2022

ABSTRACTBackgroundHippocampal alterations have been implicated in the pathophysiology of cognitive impairment in hemodialysis patients. The hippocampus consists of several distinct subfields, and the molecular mechanisms underlying cognition might be associated with specific hippocampal subfield volume changes. However, this has not yet been investigated in hemodialysis patients. This study aimed to explore volumetric abnormalities in hippocampal subfields in regular hemodialysis patients.MethodsHigh-resolution T1-weighted structural images were collected in 61 subjects including 36 hemodialysis patients and 25 healthy controls. A state-of-the-art hippocampal segmentation approach was adopted to segment the hippocampal subfields. Group differences in hippocampal subfield volumes were assessed in Python with a statsmodels module using an ordinary least squares regression with age and sex as nuisance effects.ResultsHemodialysis patients had significantly smaller volumes in the bilateral hippocampus (P &lt; .05/2, Bonferroni corrected), cornu ammonis 1 (CA1), CA4, granule cell and molecular layer of the dentate gyrus, hippocampus–amygdala transition area and molecular layer of the hippocampus than healthy controls (P &lt; .05/24, Bonferroni corrected). Hemodialysis patients also had lower volumes in the left hippocampal tail and right fimbria than healthy controls (P &lt; .05/24, Bonferroni corrected). Hippocampal subfield volumes were associated with neuropsychological test scores, the duration of disease and hemoglobin levels.ConclusionsWe found smaller hippocampal subfield volumes in hemodialysis patients, which were associated with impaired cognition, supporting their role in memory disturbance in the hemodialysis population. However, multiple clinical factors may have confounded the results, and therefore, the interpretation of these results needs to be cautious.
Cadmium, active smoking and renal function deterioration in patients with type 2 diabetes
Authors: Oosterwijk Milou M , Hagedoorn Ilse J M , Maatman Ronald G H J , Bakker Stephan J L , Navis Gerjan , Laverman Gozewijn D 
Published: September 2022

ABSTRACTBackgroundCadmium is an established nephrotoxin, present in cigarette smoke. We investigated the hazards of cadmium concentration and smoking status on renal function deterioration. We furthermore discerned whether the association of cadmium concentration with renal function deterioration is attributable to smoking status.MethodsProspective analyses were performed in data of 226 patients of the DIAbetes and LifEstyle Cohort Twente-1 (DIALECT). Cadmium concentrations were determined from EDTA whole-blood. Smoking status was determined via a self-administered questionnaire. Renal function deterioration was defined as need for renal replacement therapy or a persistent decline of ≥30% in estimated glomerular filtration rate from baseline for at least 3 months. Multivariable Cox regression models were performed to calculate hazard ratios (HRs) for the association between smoking status, cadmium concentration and renal function deterioration.ResultsMedian (interquartile range) whole-blood cadmium was 2.9 (1.9–5.1) nmol/L. Active smokers had significantly higher cadmium [7.4 (3.3–11.7) nmol/L] compared with never smokers [2.6 (1.6–4.2) nmol/L] and former smokers [2.8 (1.8–4.8) nmol/L]. During median follow-up for 6 (4–8) years, renal function deterioration occurred in 60 persons (27%). Both cadmium and active smoking were associated with an increased hazard for renal function deterioration [HR 1.37, 95% confidence interval (95% CI) 1.06–1.78 and 3.77, 95% CI 1.72–8.29, respectively]. In a multivariable model with both smoking status and cadmium concentration included, active smokers have an increased risk for renal function deterioration (HR 3.00, 95% CI 1.22–7.40), while the association between cadmium and renal function deterioration lost statistical significance (HR 1.16, 95% CI 0.87–1.54).ConclusionsActive smoking is associated with progressive kidney disease in type 2 diabetes. The association between cadmium concentration and renal function deterioration in large part determined by smoking status. Extensive assessment of smoking status may be useful in patients with type 2 diabetesat high risk of kidney damage.
Antiretroviral Drug Resistance in HIV Sequences From People Who Inject Drugs and Men Who Have Sex With Men Across 21 Cities in India
Authors: Clipman Steven J , Solomon Sunil S , Srikrishnan Aylur K , McFall Allison M , Gomathi Selvamurthi , Saravanan Shanmugam , Anand Santhanam , Vasudevan Canjeevaram K , Kumar Muniratnam S , Celentano David D , Mehta Shruti H , Lucas Gregory M 
Published: September 2022

Abstract

Background
Drug resistance testing is limited in public-sector human immunodeficiency virus (HIV) care in India, and there are few systematic samplings for prevalent drug resistance mutations (DRMs), particularly among men who have sex with men (MSM) and people who inject drugs (PWID).

Methods
We conducted genotypic resistance testing on 915 HIV sequences sampled from viremic self-reported antiretroviral therapy (ART) experienced and naive PWID and MSM recruited from 21 cities across India in 2016–2017. We analyzed factors associated with resistance using logistic regression and evaluated evidence for transmitted resistance using phylogenetic analyses.

Results
Of the 915 participants sequenced, median age was 31, 436 were MSM, and 191 were ART experienced. Overall, 62.8% of ART-experienced participants and 14.4% of ART-naive participants were found to have low-level resistance or higher to 1 or more classes of drugs. Prevalence of tenofovir disoproxil fumarate resistance was 25.7% in ART-experienced participants and 1.11% in ART-naive participants. The highest proportion of drug resistance was seen across nucleoside reverse transcriptase inhibitors and nonnucleoside reverse transcriptase inhibitors, and resistance was significantly more common among MSM participants than PWID. Phylogenetic analyses revealed that 54.6% of ART-naive participants with resistance who clustered had shared DRMs, suggesting transmitted resistance may have occurred.

Conclusions
Patients experiencing virologic failure on first-line therapy switched blindly to tenofovir/lamivudine/dolutegravir may effectively be receiving dolutegravir monotherapy due to resistance to tenofovir and lamivudine. While dolutegravir is expected to have full activity in the majority of patients in India, follow-up is needed to understand how resistance may affect long-term outcomes.