bluuebunny/crossref_metadata_2025_split huggingface dataset:
Performance of Cervical Screening a Decade Following HPV Vaccination: The Costa Rica Vaccine Trial
Authors: Hu Shang-Ying , Kreimer Aimée R , Porras Carolina , Guillén Diego , Alfaro Mario , Darragh Teresa M , Stoler Mark H , Villegas Luis F , Ocampo Rebecca , Rodriguez Ana Cecilia , Schiffman Mark , Tsang Sabrina H , Lowy Douglas R , Schiller John T , Schussler John , Quint Wim , Gail Mitchell H , Sampson Joshua N , Hildesheim Allan , Herrero Rolando ,   the Costa Rica HPV Vaccine Trial (CVT) Group
Published: June 2022

Abstract

Background
We investigated the impact of human papillomavirus (HPV) vaccination on the performance of cytology-based and HPV-based screening for detection of cervical precancer among women vaccinated as young adults and reaching screening age.

Methods
A total of 4632 women aged 25-36 years from the Costa Rica HPV Vaccine Trial were included (2418 HPV-vaccinated as young adults and 2214 unvaccinated). We assessed the performance of cytology- and HPV-based cervical screening modalities in vaccinated and unvaccinated women to detect high-grade cervical precancers diagnosed over 4 years and the absolute risk of cumulative cervical precancers by screening results at entry.

Results
We detected 95 cervical intraepithelial neoplasia grade 3 or worse (52 in unvaccinated and 43 in vaccinated women). HPV16/18/31/33/45 was predominant (69%) among unvaccinated participants, and HPV35/52/58/39/51/56/59/66/68 predominated (65%) among vaccinated participants. Sensitivity and specificity of cervical screening approaches were comparable between women vaccinated as young adults and unvaccinated women. Colposcopy referral rates were lower in the vaccinated group for HPV-based screening modalities, but the positive predictive value was comparable between the 2 groups.

Conclusions
Among women approaching screening ages, vaccinated as young adults, and with a history of intensive screening, the expected reduction in the positive predictive value of HPV testing, associated with dropping prevalence of HPV-associated lesions, was not observed. This is likely due to the presence of high-grade lesions associated with nonvaccine HPV types, which may be less likely to progress to cancer.
High-throughput unmanned aerial vehicle-based phenotyping provides insights into the dynamic process and genetic basis of rapeseed waterlogging response in the field
Authors: Li Jijun , Xie Tianjin , Chen Yahui , Zhang Yuting , Wang Chufeng , Jiang Zhao , Yang Wanneng , Zhou Guangsheng , Guo Liang , Zhang Jian 
Published: June 2022

Abstract
Waterlogging severely affects the growth, development, and yield of crops. Accurate high-throughput phenotyping is important for exploring the dynamic crop waterlogging response in the field, and the genetic basis of waterlogging tolerance. In this study, a multi-model remote sensing phenotyping platform based on an unmanned aerial vehicle (UAV) was used to assess the genetic response of rapeseed (Brassica napus) to waterlogging, by measuring morphological traits and spectral indices over 2 years. The dynamic responses of the morphological and spectral traits indicated that the rapeseed waterlogging response was severe before the middle stage within 18 d after recovery, but it subsequently decreased partly. Genome-wide association studies identified 289 and 333 loci associated with waterlogging tolerance in 2 years. Next, 25 loci with at least nine associations with waterlogging-related traits were defined as highly reliable loci, and 13 loci were simultaneously identified by waterlogging tolerance coefficients of morphological traits, spectral indices, and common factors. Forty candidate genes were predicted in the regions of 13 overlapping loci. Our study provides insights into the understanding of the dynamic process and genetic basis of rapeseed waterlogging response in the field by a high-throughput UAV phenotyping platform. The highly reliable loci identified in this study are valuable for breeding waterlogging-tolerant rapeseed cultivars.
Phenotyping for waterlogging tolerance in crops: current trends and future prospects
Authors: Langan Patrick , Bernád Villő , Walsh Jason , Henchy Joey , Khodaeiaminjan Mortaza , Mangina Eleni , Negrão Sónia 
Published: June 2022

AbstractYield losses to waterlogging are expected to become an increasingly costly and frequent issue in some regions of the world. Despite the extensive work that has been carried out examining the molecular and physiological responses to waterlogging, phenotyping for waterlogging tolerance has proven difficult. This difficulty is largely due to the high variability of waterlogging conditions such as duration, temperature, soil type, and growth stage of the crop. In this review, we highlight use of phenotyping to assess and improve waterlogging tolerance in temperate crop species. We start by outlining the experimental methods that have been utilized to impose waterlogging stress, ranging from highly controlled conditions of hydroponic systems to large-scale screenings in the field. We also describe the phenotyping traits used to assess tolerance ranging from survival rates and visual scoring to precise photosynthetic measurements. Finally, we present an overview of the challenges faced in attempting to improve waterlogging tolerance, the trade-offs associated with phenotyping in controlled conditions, limitations of classic phenotyping methods, and future trends using plant-imaging methods. If effectively utilized to increase crop resilience to changing climates, crop phenotyping has a major role to play in global food security.
Significance of differential expression profiles of ABC transporters in azole susceptibility between Cryptococcus gattii VGI and VGII strains
Authors: Xue Xinying , Zang Xuelei , Xiao Meng , Wang Lifeng , Wu Hua , Ma Xidong , Wu Ningxin , Deng Hengyu , Zhou Meng , Pan Lei , Shen Dingxia , Wang Jianxin 
Published: June 2022

Abstract

Azoles were used as the primary antifungal agents to treat the Cryptococcus gattii infection. Evidence showed that subtypes of C. gattii respond differently to azoles, but the mechanism is largely elusive. In this study, we aimed to find the mechanisms of differences in azole drug susceptibility in different subtypes of C. gattii. Eight clinical strains of C. gattii were collected for molecular typing, multilocus sequence typing (MLST) analysis, and antifungal susceptibility testing. Based on drug susceptibility differences, the RNA sequencing data were analyzed to find candidate azole drug susceptibility genes, and qPCR validation was performed. Five VGI subtypes and three VGII subtypes were identified among the eight strains of C. gattii. The clinical isolates showed high genetic diversity, and seven sequence types (STs) were identified. The geometric mean (GM) of minimum inhibitory concentration (MIC) for fluconazole, voriconazole, and itraconazole of VGI subtype was significantly lower than that of VGII subtype, and genes related to transporter activities were differentially expressed between VGI and VGII strains. The results of the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the DEGs (differential expressed genes) were found to be enriched in multiple ABC transporters. We further performed qPCR to quantify the expression level of seven ABC transporters. We found that ABC transporters ATM1, MDR1, PDR5, PDR5-3, and PXA2 were expressed significantly higher in VGII strains than in VGI strains. Our work revealed four novel ABC transporters, ATM1, PDR5, PDR5-3, and PXA2, promising candidate targets regulating azole susceptibility in C. gattii strains.

Lay Summary
Azoles were used as the primary antifungal agents for treating Cryptococuss gattii infection. Since subtypes of C. gattii respond differently to azoles. We analyzed mRNA expression profiles of different subtypes and identified four ABC transporters that could be potential genes regulating azole sensitivity.
A cosmological distance measure using radio-loud quasars
Authors: Huang L , Chang Z X 
Published: June 2022

ABSTRACT
We use the X-ray luminosity relation of radio-loud quasars (RLQs) to measure these luminosity distances as well as estimate cosmological parameters. We adopt four parametric models of X-ray luminosity to test luminosity correlation for RLQs and radio-intermediate quasars (RIQs) and give these cosmological distances. By Bayesian information criterion (BIC), the data suggest that the luminosity relation ${L_X} \propto L_{\rm UV}^{{\gamma _{\rm uv}}}L_{\rm Radio}^{\gamma _{\rm radio}^{\prime }}$ for RLQs has a better goodness of fit, relative to other models, which can be interpreted as this relation being preferred for RLQs. Meanwhile, we compare the results from flat-spectrum radio-loud quasars (FSRLQs) and steep-spectrum radio-loud quasars (SSRLQs), which indicate that their luminosity correlations are not exactly the same. We also consider dividing the RLQ sample into various redshift bins, which can be used to check if the X-ray luminosity relation depends on the redshift. Finally, we apply a combination of RLQs and SN Ia Pantheon to verify the nature of dark energy concerning whether or not its density deviates from the constant, and give the statistical results.
How well do local relations predict gas-phase metallicity gradients? Results from SDSS-IV MaNGA
Authors: Boardman N , Zasowski G , Newman J A , Sanchez S F , Andrews B , Barrera-Ballesteros J K , Lian J , Riffel R , Riffel R A , Schaefer A , Bundy K 
Published: June 2022

ABSTRACT
Gas-phase metallicity gradients in galaxies provide important clues to those galaxies’ formation histories. Using SDSS-IV MaNGA data, we previously demonstrated that gas metallicity gradients vary systematically and significantly across the galaxy mass–size plane: at stellar masses beyond approximately $10^{10}\, \mathrm{M_\odot }$, more extended galaxies display steeper gradients (in units of dex/Re) at a given stellar mass. Here, we set out to develop a physical interpretation of these findings by examining the ability of local ∼kpc-scale relations to predict the gradient behaviour along the mass–size plane. We find that local stellar mass surface density, when combined with total stellar mass, is sufficient to reproduce the overall mass–size trend in a qualitative sense. We further find that we can improve the predictions by correcting for residual trends relating to the recent star formation histories of star-forming regions. However, we find as well that the most extended galaxies display steeper average gradients than predicted, even after correcting for residual metallicity trends with other local parameters. From these results, we argue that gas-phase metallicity gradients can largely be understood in terms of known local relations, but we also discuss some possible physical causes of discrepant gradients.
Uniform modelling of the stellar density of thirteen tidal streams within the Galactic halo
Authors: Patrick Jeffrey M , Koposov Sergey E , Walker Matthew G 
Published: June 2022

ABSTRACT
We present the results of fitting a flexible stellar stream density model to a collection of thirteen streams around the Milky Way, using photometric data from DES, DECaLS, and Pan-STARRS. We construct density maps for each stream and characterize their tracks on the sky, width, and distance modulus curves along the length of each stream. We use these measurements to compute lengths and total luminosities of streams and identify substructures. Several streams show prominent substructures, such as stream broadening, gaps, large deviations of stream tracks, and sharp changes in stream densities. Examining the group of streams as a population, as expected we find that streams with globular cluster progenitors are typically narrower than those with dwarf galaxy progenitors, with streams around 100 pc wide showing overlap between the two populations. We also note the average luminosity of globular cluster streams is significantly lower than the typical luminosity of intact globular clusters. The likely explanation is that observed globular cluster streams preferentially come from lower luminosity and lower density clusters. The stream measurements done in a uniform manner presented here will be helpful for more detailed stream studies such as identifying candidate stream members for spectroscopic follow up and stellar stream dynamical modelling.
The luminosity of cluster galaxies in the Cluster-EAGLE simulations
Authors: Negri Andrea , Dalla Vecchia Claudio , Aguerri J Alfonso L , Bahé Yannick 
Published: June 2022

ABSTRACT
We computed the luminosity of simulated galaxies of the c-eagle project, a suite of 30 high-resolution zoom-in simulations of galaxy clusters based on the eagle simulation. The AB magnitudes are derived for different spectral bands, from ultraviolet to infrared, using the simple stellar population modelling based on the E-MILES stellar spectra library. We take into account obscuration due to dust in star forming regions and diffuse interstellar medium. The g − r colour–stellar mass diagram, at z = 0.1, presents a defined red sequence, reaching g − r ≃ 0.8, 0.05 dex redder than eagle at high masses, and a well populated blue cloud, when field galaxies are included. The clusters’ inner regions are dominated by red-sequence galaxies at all masses, although a non-negligible amount of blue galaxies are still present. We adopt Bayesian inference to compute the clusters LFs, testing for statistical significance of both single and double Schechter functions. The multicolour LFs at z = 0 show a knee luminosity that peaks in the infrared and increases with the cluster’s mass. The faint-end is weakly dependent on colour and mass and shows an upturn in the optical, bounded between −1.25 and −1.39, just moderately steeper than the field. The simulations reproduce, within the observational errors, the spectroscopic LFs of the Hercules and Abell 85 clusters, including their faint end upturn. c-eagle LFs are in broad agreement with observed LFs taken from SDSS and XXL surveys, up to z = 0.67, showing a rather flat faint end when the observational constrains are taken into account.
Genetic Variation in Reproductive Investment Across an Ephemerality Gradient inDaphnia pulex
Authors: Barnard-Kubow Karen B , Becker Dörthe , Murray Connor S , Porter Robert , Gutierrez Grace , Erickson Priscilla , Nunez Joaquin C B , Voss Erin , Suryamohan Kushal , Ratan Aakrosh , Beckerman Andrew , Bergland Alan O 
Published: June 2022

AbstractSpecies across the tree of life can switch between asexual and sexual reproduction. In facultatively sexual species, the ability to switch between reproductive modes is often environmentally dependent and subject to local adaptation. However, the ecological and evolutionary factors that influence the maintenance and turnover of polymorphism associated with facultative sex remain unclear. We studied the ecological and evolutionary dynamics of reproductive investment in the facultatively sexual model species, Daphnia pulex. We found that patterns of clonal diversity, but not genetic diversity varied among ponds consistent with the predicted relationship between ephemerality and clonal structure. Reconstruction of a multi-year pedigree demonstrated the coexistence of clones that differ in their investment into male production. Mapping of quantitative variation in male production using lab-generated and field-collected individuals identified multiple putative quantitative trait loci (QTL) underlying this trait, and we identified a plausible candidate gene. The evolutionary history of these QTL suggests that they are relatively young, and male limitation in this system is a rapidly evolving trait. Our work highlights the dynamic nature of the genetic structure and composition of facultative sex across space and time and suggests that quantitative genetic variation in reproductive strategy can undergo rapid evolutionary turnover.
Recent advances in the application of metallomics in diagnosis and prognosis of human cancer
Authors: Zhang Yan , He Jie , Jin Jiao , Ren Cihan 
Published: June 2022

Abstract
Metals play a critical role in human health and diseases. In recent years, metallomics has been introduced and extensively applied to investigate the distribution, regulation, function, and crosstalk of metal(loid) ions in various physiological and pathological processes. Based on high-throughput multielemental analytical techniques and bioinformatics methods, it is possible to elucidate the correlation between the metabolism and homeostasis of diverse metals and complex diseases, in particular for cancer. This review aims to provide an overview of recent progress made in the application of metallomics in cancer research. We mainly focuses on the studies about metallomic profiling of different human biological samples for several major types of cancer, which reveal distinct and dynamic patterns of metal ion contents and the potential benefits of using such information in the detection and prognosis of these malignancies. Elevated levels of copper appear to be a significant risk factor for various cancers, and each type of cancer has a unique distribution of metals in biofluids, hair/nails, and tumor-affected tissues. Furthermore, associations between genetic variations in representative metalloprotein genes and cancer susceptibility have also been demonstrated. Overall, metallomics not only offers a better understanding of the relationship between metal dyshomeostasis and the development of cancer but also facilitates the discovery of new diagnostic and prognostic markers for cancer translational medicine.
Probing small ribosomal subunit RNA helix 45 acetylation across eukaryotic evolution
Authors: Bortolin-Cavaillé Marie-Line , Quillien Aurélie , Thalalla Gamage Supuni , Thomas Justin M , Sas-Chen Aldema , Sharma Sunny , Plisson-Chastang Célia , Vandel Laurence , Blader Patrick , Lafontaine Denis L J , Schwartz Schraga , Meier Jordan L , Cavaillé Jérôme 
Published: June 2022

Abstract
NAT10 is an essential enzyme that catalyzes N4-acetylcytidine (ac4C) in eukaryotic transfer RNA and 18S ribosomal RNA. Recent studies suggested that rRNA acetylation is dependent on SNORD13, a box C/D small nucleolar RNA predicted to base-pair with 18S rRNA via two antisense elements. However, the selectivity of SNORD13-dependent cytidine acetylation and its relationship to NAT10’s essential function remain to be defined. Here, we demonstrate that SNORD13 is required for acetylation of a single cytidine of human and zebrafish 18S rRNA. In-depth characterization revealed that SNORD13-dependent ac4C is dispensable for human cell growth, ribosome biogenesis, translation and development. This loss of function analysis inspired a cross-evolutionary survey of the eukaryotic rRNA acetylation ‘machinery’ that led to the characterization of many novel metazoan SNORD13 genes. This includes an atypical SNORD13-like RNA in Drosophila melanogaster which guides ac4C to 18S rRNA helix 45 despite lacking one of the two rRNA antisense elements. Finally, we discover that Caenorhabditis elegans 18S rRNA is not acetylated despite the presence of an essential NAT10 homolog. Our findings shed light on the molecular mechanisms underlying SNORD13-mediated rRNA acetylation across eukaryotic evolution and raise new questions regarding the biological and evolutionary relevance of this highly conserved rRNA modification.
Structural basis for interaction between CLAMP and MSL2 proteins involved in the specific recruitment of the dosage compensation complex in Drosophila
Authors: Tikhonova Evgeniya , Mariasina Sofia , Efimov Sergey , Polshakov Vladimir , Maksimenko Oksana , Georgiev Pavel , Bonchuk Artem 
Published: June 2022

Abstract
Transcriptional regulators select their targets from a large pool of similar genomic sites. The binding of the Drosophila dosage compensation complex (DCC) exclusively to the male X chromosome provides insight into binding site selectivity rules. Previous studies showed that the male-specific organizer of the complex, MSL2, and ubiquitous DNA-binding protein CLAMP directly interact and play an important role in the specificity of X chromosome binding. Here, we studied the highly specific interaction between the intrinsically disordered region of MSL2 and the N-terminal zinc-finger C2H2-type (C2H2) domain of CLAMP. We obtained the NMR structure of the CLAMP N-terminal C2H2 zinc finger, which has a classic C2H2 zinc-finger fold with a rather unusual distribution of residues typically used in DNA recognition. Substitutions of residues in this C2H2 domain had the same effect on the viability of males and females, suggesting that it plays a general role in CLAMP activity. The N-terminal C2H2 domain of CLAMP is highly conserved in insects. However, the MSL2 region involved in the interaction is conserved only within the Drosophila genus, suggesting that this interaction emerged during the evolution of a mechanism for the specific recruitment of the DCC on the male X chromosome in Drosophilidae.
Clinical Practices and Institutional Protocols on Prophylaxis, Monitoring, and Management of Selected Adverse Events Associated with Trastuzumab Deruxtecan
Authors: Bardia Aditya , Harnden Kathleen , Mauro Lauren , Pennisi Angela , Armitage Melissa , Soliman Hatem 
Published: June 2022

Abstract
The treatment of metastatic breast cancer (mBC) has evolved significantly in the past several years with the approval of new targeted agents. Trastuzumab deruxtecan (T-DXd), an antibody-drug conjugate with a topoisomerase I inhibitor payload, is a new addition to the class of therapies that target the human epidermal growth factor 2 (HER2) receptor. T-DXd was approved in the US in December 2019 for patients with HER2-positive metastatic or unresectable breast cancer who have received 2 or more prior anti-HER2–based regimens in the metastatic setting. In the DESTINY-Breast01 phase II trial (NCT03248492), T-DXd demonstrated high rates of durable responses in heavily pretreated patients with HER2-positive mBC, with a confirmed objective response rate of 62%, median duration of response of 18.2 months, and median progression-free survival of 19.4 months. In addition to efficacy, successful implementation of any new anticancer therapy includes learning how to prevent, monitor, and manage treatment-related adverse events. As T-DXd becomes more widely used, information can be gained from real-world clinical practices, institutional approaches, and the collaboration of multidisciplinary oncology teams who treat patients with T-DXd. This article reviews practical insights and management of nausea and vomiting, neutropenia, interstitial lung disease, risk of cardiotoxicity, and other adverse events associated with T-DXd administration from the perspective of health care providers who have experience utilizing T-DXd.