bluuebunny/crossref_metadata_2025_split huggingface dataset:
Primary Exposure to SARS-CoV-2 via Infection or Vaccination Determines Mucosal Antibody-Dependent ACE2 Binding Inhibition
Authors: Fröberg Janeri , Koomen Vera J C H , van der Gaast-de Jongh Christa E , Philipsen Ria , GeurtsvanKessel Corine H , de Vries Rory D , Baas Marije C , van der Molen Renate G , de Jonge Marien I , Hilbrands Luuk B , Huynen Martijn A , Diavatopoulos Dimitri A 
Published: September 2023

Abstract

Background
Mucosal antibodies play a critical role in preventing SARS-CoV-2 infections or reinfections by blocking the interaction of the receptor-binding domain (RBD) with the angiotensin-converting enzyme 2 (ACE2) receptor on the cell surface. In this study, we investigated the difference between the mucosal antibody response after primary infection and vaccination.

Methods
We assessed longitudinal changes in the quantity and capacity of nasal antibodies to neutralize the interaction of RBD with the ACE2 receptor using the spike protein and RBD from ancestral SARS-CoV-2 (Wuhan-Hu-1), as well as the RBD from the Delta and Omicron variants.

Results
Significantly higher mucosal IgA concentrations were detected postinfection vs postvaccination, while vaccination induced higher IgG concentrations. However, ACE2-inhibiting activity did not differ between the cohorts. Regarding whether IgA or IgG drove ACE2 inhibition, infection-induced binding inhibition was driven by both isotypes, while postvaccination binding inhibition was mainly driven by IgG.

Conclusions
Our study provides new insights into the relationship between antibody isotypes and neutralization by using a sensitive and high-throughput ACE2 binding inhibition assay. Key differences are highlighted between vaccination and infection at the mucosal level, showing that despite differences in the response quantity, postinfection and postvaccination ACE2 binding inhibition capacity did not differ.
Green tissue-targeted expression of the Cry1Ab/c gene in transgenic maize using the Cre/loxP system as an alternative strategy against lepidopteran pests
Authors: Yuan Guangsheng , Shi Jiaxin , Shi Jiahao , He Dandan , Li Youliang , Du Juan , Zou Chaoying , Ma Langlang , Pan Guangtang , Shen Yaou 
Published: September 2023

Abstract
Genetically modified (GM) proteins in edible tissues of transgenic maize are of intense public concern. We provided a Cre/loxP-based strategy for manipulating the expression of transgenes in green tissues while locking them in nongreen tissues. First, the Cre gene was driven by the green tissue-specific promoter Zm1rbcS to generate transgenic maize KEY. Meanwhile, a gene cassette containing a Nos terminator (NosT) in front of the Cry1Ab/c gene was driven by the strong promoter ZmUbi to generate another transgenic maize LOCK. By crossing KEY and LOCK plants, the expressed Cre recombinase under the control of the Zm1rbcS promoter from KEY maize accurately removed the NosT of LOCK maize. Consequently, the expression of blocked Cry1Ab/c was enabled in specific green tissues in their hybrids. The expression level and concentration of Cry1Ab/c were observed using a strategy with high specific accumulation in green tissues (leaf and stem). Still, only a small or absent amount was observed in root and kernel tissues. Furthermore, we assessed the bioactivity of transgenic maize against 2 common lepidopteran pests, Ostrinia furnacalis and Spodoptera frugiperda, in the laboratory and field. The transgenic plants showed high plant resistance levels against the 2 pests, with mortality rates above 97.2% and damage scales below 2.2 compared with the control group. These findings are significant for exploring novel genetic engineering techniques in GM maize and providing a feasible strategy for transgenes avoiding expression in edible parts. In addition, implementing the Cre/loxP-mediated system could relieve public sentiment toward the biosafety of GM plants.
Investigation on interaction effects of multiple factors on clean gas extraction: implementation of response surface methodology
Authors: Zheng Chunshan , Wu Haifei , Jiang Bingyou , Xue Sheng , Zhao Yang 
Published: September 2023

AbstractGas-related disasters have become a major threat to mining safety of coal resources. Investigation into the optimization approach for inseam borehole gas extraction is important for improving extraction efficiency. By establishing control equations for coal seam deformation, porosity-permeability properties, and gas flow, effects of extraction time, initial gas pressure, initial coal permeability, and borehole diameter on gas flow pattern and effective extraction radius are analyzed. Based on response surface methodology and orthogonal experimental design, a regression analysis model of effective extraction radius and multiple influencing factors is established. Meanwhile, the interaction mechanism between effects of multiple factors is analyzed, thus identifying optimal parameters for gas extraction. Results show that effective extraction radius is positively correlated with initial permeability, extraction time, and borehole diameter, and negatively associated with original gas pressure. In terms of effect on effective extraction radius, those parameters could be ranked as follows: initial gas pressure, extraction time, initial coal permeability, then borehole diameter. Interaction between multiple factors could inhibit the impact of individual factors on extraction radius. An increase in initial gas pressure reduces the positive effect of permeability on extraction radius. Growing initial gas pressure inhibits the contribution of extraction time to effective drainage radius. Prolonged duration of extraction suppresses the positive effect of permeability on extraction radius. Interaction between initial gas pressure and initial permeability has the most significant influence on extraction radius. Results from orthogonal experimental design correspond to those of response surface methodology. These findings could provide guidance for dynamically adjusting drilling extraction parameters and improving gas-extraction outcomes.
DIW-based reflection full waveform inversion and its application of land seismic data
Authors: Hu Guanghui , Xu Wencai , He Binghong , He Weiguang , Du Zeyuan , Yao Jiashun 
Published: September 2023

Abstract
The exploration zone in Northwest China poses unique challenges due to its complex structures, fractured blocks, deep reservoirs, and geological anomalies. Conventional velocity modeling and migration imaging methods face difficulties in accurately imaging the underlying reservoirs beneath abnormal rock formations, resulting in poor signal-to-noise ratio and resolution. Moreover, the seismic data quality often falls short, leading to unfocused images. To address these challenges, we propose a novel approach: dynamic image warping-based reflection full waveform inversion. This method combines a model regularization strategy and structural constraints to generate high-resolution velocity models. The application in the Taha Industrial Zone demonstrates that the proposed method effectively characterizes the velocity characteristics of special geological bodies, such as deep weathering crusts, improving imaging effects and resolution, which allows for a more precise understanding of the complex geological features.
Validating a model for predicting breast cancer and nonbreast cancer death in women aged 55 years and older
Authors: Wolfson Emily A , Schonberg Mara A , Eliassen A Heather , Bertrand Kimberly A , Shvetsov Yurii B , Rosner Bernard A , Palmer Julie R , LaCroix Andrea Z , Chlebowski Rowan T , Nelson Rebecca A , Ngo Long H 
Published: September 2023

Abstract

Background
To support mammography screening decision making, we developed a competing-risk model to estimate 5-year breast cancer risk and 10-year nonbreast cancer death for women aged 55 years and older using Nurses’ Health Study data and examined model performance in the Black Women’s Health Study (BWHS). Here, we examine model performance in predicting 10-year outcomes in the BWHS, Women’s Health Initiative-Extension Study (WHI-ES), and Multiethnic Cohort (MEC) and compare model performance to existing breast cancer prediction models.

Methods
We used competing-risk regression and Royston and Altman methods for validating survival models to calculate our model’s calibration and discrimination (C index) in BWHS (n = 17 380), WHI-ES (n = 106 894), and MEC (n = 49 668). The Nurses’ Health Study development cohort (n = 48 102) regression coefficients were applied to the validation cohorts. We compared our model’s performance with breast cancer risk assessment tool (Gail) and International Breast Cancer Intervention Study (IBIS) models by computing breast cancer risk estimates and C statistics.

Results
When predicting 10-year breast cancer risk, our model’s C index was 0.569 in BWHS, 0.572 in WHI-ES, and 0.576 in MEC. The Gail model’s C statistic was 0.554 in BWHS, 0.564 in WHI-ES, and 0.551 in MEC; IBIS’s C statistic was 0.547 in BWHS, 0.552 in WHI-ES, and 0.562 in MEC. The Gail model underpredicted breast cancer risk in WHI-ES; IBIS underpredicted breast cancer risk in WHI-ES and in MEC but overpredicted breast cancer risk in BWHS. Our model calibrated well. Our model’s C index for predicting 10-year nonbreast cancer death was 0.760 in WHI-ES and 0.763 in MEC.

Conclusions
Our competing-risk model performs as well as existing breast cancer prediction models in diverse cohorts and predicts nonbreast cancer death. We are developing a website to disseminate our model.
The inefficiency of stellar feedback in driving galactic outflows in massive galaxies at high redshift
Authors: Bassini Luigi , Feldmann Robert , Gensior Jindra , Hayward Christopher C , Faucher-Giguère Claude-André , Cenci Elia , Liang Lichen , Bernardini Mauro 
Published: September 2023

ABSTRACT
Recent observations indicate that galactic outflows are ubiquitous in high-redshift (high-z) galaxies, including normal star-forming galaxies, quasar hosts, and dusty star-forming galaxies (DSFGs). However, the impact of outflows on the evolution of their hosts is still an open question. Here, we analyse the star-formation histories and galactic outflow properties of galaxies in massive haloes ($10^{12}\, {\rm M}_{\odot }\ \lt\ M_{\rm vir}\ \lt\ 5\times 10^{12}\, {\rm M}_{\odot }$) at z ≳ 5.5 in three zoom-in cosmological simulations from the MassiveFIRE suite, as part of the Feedback In Realistic Environments (FIRE) project. The simulations were run with the FIRE-2 model, which does not include feedback from active galactic nuclei. The simulated galaxies resemble z &gt; 4 DSFGs, with star-formation rates of $\sim\!{1000}\ {\rm M}_{\odot }\, \rm yr^{-1}$ and molecular gas masses of Mmol ∼ 1010 M⊙. However, the simulated galaxies are characterized by higher circular velocities than those observed in high-z DSFGs. The mass loading factors from stellar feedback are of the order of ∼0.1, implying that stellar feedback is inefficient in driving galactic outflows and gas is consumed by star formation on much shorter time-scales than it is expelled from the interstellar medium. We also find that stellar feedback is highly inefficient in self-regulating star formation in this regime, with an average integrated star formation efficiency (SFE) per dynamical time of 30 per cent. Finally, compared with FIRE-2 galaxies hosted in similarly massive haloes at lower redshift, we find lower mass loading factors and higher SFEs in the high-z sample. We argue that both effects originate from the higher total and gas surface densities that characterize high-z massive systems.
Punctuated chaos and the unpredictability of the Galactic Centre S-star orbital evolution
Authors: Portegies Zwart Simon F , Boekholt Tjarda C N , Heggie Douglas C 
Published: September 2023

ABSTRACT
We investigate the chaotic behaviour of the S-star cluster in the Galactic Centre using precise N-body calculations, free from round-off or discretization errors. Our findings reveal that chaos among the Galactic Centre S-stars arises from close encounters, particularly among pairs and near the massive central body. These encounters induce perturbations, causing sudden changes in the orbital energies of the interacting stars. Consequently, neighbouring solutions experience roughly exponential growth in separation. We propose a theory of ‘punctuated chaos’ that describes the S-star cluster’s chaotic behaviour. This phenomenon results from nearly linear growth in the separation between neighbouring orbits after repeated finite perturbations. Each participating star’s orbit experiences discrete, abrupt changes in energy due to the perturbations. The cumulative effect of these events is further amplified by the steady drift in orbital phase. In the Galactic Centre, perturbations originate from coincidental encounters occurring within a distance of ≲100 au between at least two stars (in some cases, three stars). Our model satisfactorily explains the observed exponential growth in the 27 S-stars cluster. We determine that the S-star system has a Lyapunov time-scale of approximately 462 ± 74 yr. For the coming millennium, chaos in the S-star cluster will be driven mainly by a few of the closest orbiting stars: S2, S5, S6, S8, S9, S14, S18, S31, S21, S24, S27, S29, and S38.
Discovery of compact disc galaxies with high-surface brightness in the Sloan Digital Sky Survey
Authors: Chen Cheng-Yu , Hwang Chorng-Yuan 
Published: September 2023

ABSTRACT
Compact disc galaxies (CDGs) with high-surface brightness were identified in the Sloan Digital Sky Survey data. We determined the surface profiles of the CDGs and compared them to those of normal-sized disc galaxies (NDGs). The CDGs have higher central brightness and older stellar age than the NDGs. Furthermore, the brightness profiles of the CDGs fit a Sérsic model with n ≈ 2.11 and have a zero g′ − r′ colour gradient on average. By contrast, the NDGs fit an exponential profile and have a negative colour gradient on average. These results indicate that the structure and stellar population of the CDGs and NDGs differ. We suggest that the CDGs are ancient galaxies in the quenching phase following the initial central starburst.
Formation of first star clusters under the supersonic gas flow – I. Morphology of the massive metal-free gas cloud
Authors: Hirano Shingo , Shen Youcheng , Nishijima Sho , Sakai Yusuke , Umeda Hideyuki 
Published: September 2023

ABSTRACT
We performed 42 simulations of first star formation with initial supersonic gas flows relative to the dark matter at the cosmic recombination era. Increasing the initial streaming velocities led to delayed halo formation and increased halo mass, enhancing the mass of the gravitationally shrinking gas cloud. For more massive gas clouds, the rate of temperature drop during contraction, in other words, the structure asymmetry, becomes more significant. When the maximum and minimum gas temperature ratios before and after contraction exceed ∼10, the asymmetric structure of the gas cloud prevails, inducing fragmentation into multiple dense gas clouds. We continued our simulations until 105 yr after the first dense core formation to examine the final fate of the massive star-forming gas cloud. Among the 42 models studied, we find the simultaneous formation of up to four dense gas clouds, with a total mass of about $2254\, \mathrm{ M}_\odot$. While the gas mass in the host halo increases with increasing the initial streaming velocity, the mass of the dense cores does not change significantly. The star formation efficiency decreases by more than one order of magnitude from ϵIII ∼ 10−2 to 10−4 when the initial streaming velocity, normalized by the root mean square value, increases from 0 to 3.
Interlocus Gene Conversion, Natural Selection, and Paralog Homogenization
Authors: Yang Yixuan , Xu Tanchumin , Conant Gavin , Kishino Hirohisa , Thorne Jeffrey L , Ji Xiang 
Published: September 2023

Abstract
Following a duplication, the resulting paralogs tend to diverge. While mutation and natural selection can accelerate this process, they can also slow it. Here, we quantify the paralog homogenization that is caused by point mutations and interlocus gene conversion (IGC). Among 164 duplicated teleost genes, the median percentage of postduplication codon substitutions that arise from IGC rather than point mutation is estimated to be between 7% and 8%. By differentiating between the nonsynonymous codon substitutions that homogenize the protein sequences of paralogs and the nonhomogenizing nonsynonymous substitutions, we estimate the homogenizing nonsynonymous rates to be higher for 163 of the 164 teleost data sets as well as for all 14 data sets of duplicated yeast ribosomal protein-coding genes that we consider. For all 14 yeast data sets, the estimated homogenizing nonsynonymous rates exceed the synonymous rates.
Sustained post-rituximab B-cell depletion is common in ANCA-associated vasculitis and is affected by sex and renal function
Authors: Mescia Federica , Salviani Chiara , Tonoli Mattia , Affatato Stefania , Moratto Daniele , Tedesco Martina , Guerini Alice , Gemmo Alessia , Camoni Marta , Delbarba Elisa , Zubani Roberto , Garrafa Emirena , Chiarini Marco , Gregorini Gina , Scolari Francesco , Alberici Federico 
Published: September 2023

ABSTRACTObjectiveDespite the increasing use of rituximab in anti-neutrophil cytoplasmic antibody (ANCA)-associated vasculitis (AAV), it remains unclear what the optimal dosing is, especially for maintenance of remission. A deeper understanding of post-rituximab B-cell repopulation patterns may aid better-tailored treatment.MethodsThis is a monocentric, retrospective study including ANCA-positive AAV patients receiving a single course of rituximab induction. CD19+ B cells were longitudinally monitored with flow cytometry. B-cell repopulation was defined as CD19+ &gt;10 cells/μL.ResultsSeventy-one patients were included, the majority with microscopic polyangiitis (75%), myeloperoxidase-ANCA positivity (75%) and with renal involvement (79%). During a median follow-up of 54 months since the first rituximab infusion, 44 patients (62%) repopulated B cells, with a median time to repopulation of 39 months (range 7–102). Patients experiencing B-cell depletion lasting longer than the overall median time to repopulation (39 months) exhibited a lower risk of flare and higher risk of serious infection. In multivariate Cox regression, higher estimated glomerular filtration rate (eGFR) [hazard ratio (HR) 1.84, 95% confidence interval (CI) 1.13–2.98 per 30 mL/min/1.73 m2 eGFR] and female sex (HR 2.70, 95% CI 1.37–5.31) were independent predictors of increased rate of B-cell repopulation.ConclusionA subset of AAV patients develop sustained post-rituximab B-cell depletion, which associates with reduced risk of flare and increased risk of serious infection in the long term. Preserved renal function and female sex are associated with faster B-cell repopulation. These observations further highlight the need to personalize immunosuppression to improve clinical outcomes.
N-body simulation of planetary formation through pebble accretion in a radially structured protoplanetary disk
Authors: Jinno Tenri , Saitoh Takayuki R , Ishigaki Yota , Makino Junichiro 
Published: September 2023

Abstract
In the conventional theory of planet formation, it is assumed that protoplanetary disks are axisymmetric and have a smooth radial profile. However, recent radio observations of protoplanetary disks have revealed that many of them have complex radial structures. In this study, we perform a series of N-body simulations to investigate how planets are formed in protoplanetary disks with radial structures. For this purpose, we consider the effect of continuous pebble accretion onto the discontinuity boundary within the terrestrial planet-forming region (∼0.6 au). We find that protoplanets grow efficiently at the discontinuity boundary, reaching the Earth mass within ∼104 yr. We confirm that giant collisions of protoplanets occur universally in our model. Moreover, we find that multiple planet-sized bodies form at regular intervals in the vicinity of the discontinuity boundary. These results indicate the possibility of the formation of solar system-like planetary systems in radially structured protoplanetary disks.
The paradoxical influence of the COVID-19 lockdown period on different types of preterm births in Alberta: a provincial study
Authors: Dosani Aliyah , Sikdar Khokan C , Kumaran Mahalakshmi , Kumaran Kumar , Hyderi Abbas , Benlamri Amina , Rai Baldeep , Singhal Nalini , Lodha Abhay 
Published: September 2023

Abstract

Objectives
The objective of this study was to determine if the COVID-19 pandemic impacted different types of preterm birth rates in Alberta, Canada.

Methods
A population-based, retrospective, cohort study was conducted from March 15, 2015 to December 31, 2020 using provincial data. The primary exposure was the COVID-19 lockdown period, and the primary outcome was the incidence of preterm birth (&lt;37 weeks gestational age). Multivariable analyses in the complete lockdown and overall lockdown (partial and complete lockdown) periods were performed to test the association between the year of birth and preterm birth status and were adjusted for various independent variables. Preterm birth status was adjusted for various confounding factors.

Results
Following the analysis of n = 41,187 mothers and their singleton infants, we found that the lockdown due to COVID-19 had no impact in reducing the overall preterm birth rate. However, a paradoxical influence was observed with an increase of extremely low preterm births in the overall lockdown period, and a decrease in moderate preterm births during the complete lockdown period.

Conclusions
The results of this study demonstrated that there was a decrease in moderate and increase in extremely low preterm birth rates as a result of the COVID-19 lockdown. However, the COVID-19 lockdown did not impact the very preterm and late preterm birth rate in Alberta.
Transcriptomic Analysis Reveals Novel Regulators of the Scots Pine Stilbene Pathway
Authors: Paasela Tanja , Lim Kean-Jin , Pavicic Mirko , Harju Anni , Venäläinen Martti , Paulin Lars , Auvinen Petri , Kärkkäinen Katri , Teeri Teemu H 
Published: September 2023

Abstract
Stilbenes accumulate in Scots pine heartwood where they have important roles in protecting wood from decaying fungi. They are also part of active defense responses, and their production is induced by different (a)biotic stressors. The specific transcriptional regulators as well as the enzyme responsible for activating the stilbene precursor cinnamate in the pathway are still unknown. UV-C radiation was the first discovered artificial stress activator of the pathway. Here, we describe a large-scale transcriptomic analysis of pine needles in response to UV-C and treatment with translational inhibitors, both activating the transcription of stilbene pathway genes. We used the data to identify putative candidates for the missing CoA ligase and for pathway regulators. We further showed that the pathway is transcriptionally activated by phosphatase inhibitor, ethylene and jasmonate treatments, as in grapevine, and that the stilbene synthase promoter retains its inducibility in some of the tested conditions in Arabidopsis, a species that normally does not synthesize stilbenes. Shared features between gymnosperm and angiosperm regulation and partially retained inducibility in Arabidopsis suggest that pathway regulation occurs not only via ancient stress-response pathway(s) but also via species-specific regulators. Understanding which genes control the biosynthesis of stilbenes in Scots pine aids breeding of more resistant trees.