bluuebunny/crossref_metadata_2025_split huggingface dataset:
Vertical Transmission of Hepatitis C Virus Among Women With a History of Injection Opioid Use
Authors: Cafardi John M , Lin Hong T , Lange Lana , Kelley Lacey , Lemon Kelly , Odegard Elizabeth A , Meeds Heidi L , Blackard Jason T , Feinberg Judith 
Published: April 2024

Abstract
We evaluated vertical transmission and linkage to care in women with hepatitis C virus (HCV) and history of injection drug use employing co-localized testing and treatment. Transmission occurred in 1 of 23 infants, with mother-infant genetic distance of 1.26%. Rates for infant testing, maternal linkage, and cure were 77%, 52%, and 100%, respectively.
Enhanced pan-genomic resources at the maize genetics and genomics database
Authors: Cannon Ethalinda K , Portwood John L , Hayford Rita K , Haley Olivia C , Gardiner Jack M , Andorf Carson M , Woodhouse Margaret R 
Published: April 2024

Abstract
Pan-genomes, encompassing the entirety of genetic sequences found in a collection of genomes within a clade, are more useful than single reference genomes for studying species diversity. This is especially true for a species like Zea mays, which has a particularly diverse and complex genome. Presenting pan-genome data, analyses, and visualization is challenging, especially for a diverse species, but more so when pan-genomic data is linked to extensive gene model and gene data, including classical gene information, markers, insertions, expression and proteomic data, and protein structures as is the case at MaizeGDB. Here, we describe MaizeGDB's expansion to include the genic subset of the Zea pan-genome in a pan-gene data center featuring the maize genomes hosted at MaizeGDB, and the outgroup teosinte Zea genomes from the Pan-Andropoganeae project. The new data center offers a variety of browsing and visualization tools, including sequence alignment visualization, gene trees and other tools, to explore pan-genes in Zea that were calculated by the pipeline Pandagma. Combined, these data will help maize researchers study the complexity and diversity of Zea, and to use the comparative functions to validate pan-gene relationships for a selected gene model.
Social Connectedness of Older Adults During the COVID-19 Pandemic: Evidence by Survey Mode and Respondent Dementia
Authors: Cornwell Benjamin , Qu Tianyao , York Cornwell Erin 
Published: April 2024

Abstract

Objectives
The coronavirus disease-2019 (COVID-19) pandemic has affected many aspects of social life, especially among older adults who may face cognitive impairments. Concerning this combination of circumstances, the study evaluates the degree to which data collection on social connectedness among older adults might be affected by the social complexities of the COVID-19 pandemic.

Methods
We use data from the National Social Life, Health and Aging Project, a nationally representative study of community-dwelling older adults in the United States, which conducted a special multi-mode COVID study between September 2020 and January 2021, in part to examine social impacts of the COVID-19 pandemic and to assess how alternative survey modes performed during the pandemic. Our final sample includes 2,251 older adults, aged 55 and older.

Results
Older adults’ social connectedness was adversely affected by the pandemic. People reported a tendency to move toward electronic communication and away from in-person contact. Concomitantly, there is some evidence of survey mode effects that are related to electronic communication. Those who elected to participate on the phone or the internet disproportionately reported using those means of communication with their social network members. Notably, this pattern was stronger among those who did not suffer from dementia, suggesting cognition effects on survey completion.

Discussion
Researchers should remain cognizant of how data on social connections were collected during the COVID-19 pandemic. These findings may indicate the role dementia plays in preventing people from adapting to new social networking realities with alternative means of communication during the pandemic.
Bayesian variational time-lapse full waveform inversion
Authors: Zhang Xin , Curtis Andrew 
Published: April 2024

SUMMARY
Time-lapse seismic full-waveform inversion (FWI) provides estimates of dynamic changes in the Earth’s subsurface by performing multiple seismic surveys at different times. Since FWI problems are highly non-linear and non-unique, it is important to quantify uncertainties in such estimates to allow robust decision making based on the results. Markov chain Monte Carlo (McMC) methods have been used for this purpose, but due to their high computational cost, those studies often require a pre-existing accurate baseline model and estimates of the locations of potential velocity changes, and neglect uncertainty in the baseline velocity model. Such detailed and accurate prior information is not always available in practice. In this study we use an efficient optimization method called stochastic Stein variational gradient descent (sSVGD) to solve time-lapse FWI problems without assuming such prior knowledge, and to estimate uncertainty both in the baseline velocity model and the velocity change over time. We test two Bayesian strategies: separate Bayesian inversions for each seismic survey, and a single joint inversion for baseline and repeat surveys, and compare the methods with standard linearized double difference inversion. The results demonstrate that all three methods can produce accurate velocity change estimates in the case of having fixed (exactly repeatable) acquisition geometries. However, the two Bayesian methods generate significantly more accurate results when acquisition geometries changes between surveys. Furthermore, joint inversion provides the most accurate velocity change and uncertainty estimates in all cases tested. We therefore conclude that Bayesian time-lapse inversion using a joint inversion strategy may be useful to image and monitor subsurface changes, in particular where variations in the results would lead to different consequent decisions.
Multi-omic dissection of the cold resistance traits of white water lily
Authors: Qiu Penghe , Liu Tong , Xu Yingchun , Ye Chunxiu , Zhang Ran , Wang Yanjie , Jin Qijiang 
Published: April 2024

Abstract
The white water lily (Nymphaea candida), exemplifying nature’s resilience, thrives in the high-altitude terrains of Xinjiang, China, serving as an ideal model for investigating cold adaptation mechanisms in aquatic plants. This study meticulously elucidates the complex cold adaptation mechanisms of the white water lily through a comprehensive and integrated methodological approach. We discovered that the water lily undergoes ecodormancy in winter, retaining high cellular viability and growth potential. During overwintering, the white water lily demonstrates effective resource reallocation, a process facilitated by morphological adjustments, thereby strengthening its resistance to cold temperatures. This enhancement is achieved particularly through the compartmentalization of large vacuoles, the accumulation of osmoregulatory substances, and an increased antioxidant capacity. We established the first exhaustive full-length transcriptome for the white water lily. A subsequent comprehensive analysis of the transcriptome, phytohormones, and metabolome uncovered a multifaceted regulatory network orchestrating cold adaptation. Our research spotlights phytohormone signaling, amino acid metabolism, and circadian rhythms as key elements in the water lily’s defense against cold. The results emphasize the critical role of nitrogen metabolism, especially amino acid-related pathways, during cold stress. Metabolite profiling revealed the importance of compounds like myo-inositol and L-proline in enhancing cold tolerance. Remarkably, our study demonstrates that the white water lily notably diminishes the utilization of unsaturated fatty acids in its temperature regulation strategies. In conclusion, this research substantially enriches our understanding of the white water lily’s intricate cold adaptation mechanisms, offering new perspectives on the adaptive strategies of aquatic plants and potential applications in agricultural advancement.
Slope Boundedness and Equidistribution Theorem
Authors: Luo Wenbin 
Published: April 2024

Abstract
In this article, we prove the boundedness of minimal slopes of adelic line bundles over function fields of characteristic $0$. This can be applied to prove the equidistribution of generic and small points with respect to a big and semipositive adelic line bundle. Our methods can be applied to the finite places of number fields as well. We also show the continuity of $\chi $-volumes over function fields.
Biological Variation Estimates for Plasma Copeptin and Clinical Implications
Authors: Choy Kay Weng , Carobene Anna , Loh Tze Ping , Chiang Cherie , Wijeratne Nilika , Locatelli Massimo , Coskun Abdurrahman , Cavusoglu Coskun , Unsal Ibrahim 
Published: April 2024

Abstract

Background
Plasma copeptin measurement is useful for the differential diagnoses of polyuria-polydipsia syndrome. It has also been proposed as a prognostic marker for cardiovascular diseases. However, limited information is available about the within- (CVI) and between-subject (CVG) biological variation (BV). This study presents BV estimates for copeptin in healthy individuals.

Methods
Samples were collected weekly from 41 healthy subjects over 5 weeks and analyzed using the BRAHMS Copeptin proAVP KRYPTOR assay after at least 8 h of food and fluid abstinence. Outlier detection, variance homogeneity, and trend analysis were performed followed by CV-ANOVA for BV and analytical variation (CVA) estimation with 95% confidence intervals. Reference change values (RCVs), index of individuality (II), and analytical performance specification (APS) were also calculated.

Results
The analysis included 178 results from 20 males and 202 values from 21 females. Copeptin concentrations were significantly higher in males than in females (mean 8.5 vs 5.2 pmol/L, P &lt; 0.0001). CVI estimates were 18.0% (95% CI, 15.4%–21.6%) and 19.0% (95% CI, 16.4%–22.6%), for males and females, respectively; RCVs were −35% (decreasing value) and 54% (increasing value). There was marked individuality for copeptin. No result exceeded the diagnostic threshold (&gt;21.4 pmol/L) for arginine vasopressin resistance.

Conclusions
The availability of BV data allows for refined APS and associated II, and RCVs applicable as aids in the serial monitoring of patients with specific diseases such as heart failure. The BV estimates are only applicable in subjects who abstained from oral intake due to the rapid and marked effects of fluids on copeptin physiology.
Aberration Correction for Large-Angle Illumination Scanning Transmission Electron Microscopy by Using Iterative Electron Ptychography Algorithms
Authors: Ma Yinhang , Shi Jinan , Guzman Roger , Li Ang , Zhou Wu 
Published: April 2024

Abstract
Modern aberration correctors in the scanning transmission electron microscope (STEM) have dramatically improved the attainable spatial resolution and enabled atomical structure and spectroscopic analysis even at low acceleration voltages (≤80 kV). For a large-angle illumination, achieving successful aberration correction to high angles is challenging with an aberration corrector, which limits further improvements in applications such as super-resolution, three-dimensional atomic depth resolution, or atomic surface morphology analyses. Electron ptychography based on four-dimensional STEM can provide a postprocessing strategy to overcome the current technological limitations. In this work, we have demonstrated that aberration correction for large-angle illumination is feasible by pushing the capabilities of regularized ptychographic iterative engine algorithms to reconstruct 4D data sets acquired using a relatively low-efficiency complementary metal oxide semiconductor camera. We report super resolution (0.71 Å) with large-angle illumination (50–60 mrad) and under 60 kV accelerating voltage.
Looking for timing variations in the transits of 16 exoplanets
Authors: Yalçınkaya S , Esmer E M , Baştürk Ö , Muhaymin A , Kutluay A C , Silistre D İ , Akar F , Southworth J , Mancini L , Davoudi F , Karamanlı E , Tezcan F , Demir E , Yılmaz D , Güleroğlu E , Tekin M , Taşkın İ , Aladağ Y , Sertkan E , Kurt U Y , Fişek S , Kaptan S , Aliş S , Aksaker N , Yelkenci F K , Tezcan C T , Kaya A , Oğlakkaya D , Aydın Z S , Yeşilyaprak C 
Published: April 2024

ABSTRACT
We update the ephemerides of 16 transiting exoplanets using our ground-based observations, new Transiting Exoplanet Survey Satellite data, and previously published observations including those of amateur astronomers. All these light curves were modelled by making use of a set of quantitative criteria with the exofast code to obtain mid-transit times. We searched for statistically significant secular and/or periodic trends in the mid-transit times. We found that the timing data are well modelled by a linear ephemeris for all systems except for XO-2 b, for which we detect an orbital decay with the rate of −12.95 ± 1.85 ms yr−1 that can be confirmed with future observations. We also detect a hint of potential periodic variations in the transit timing variation data of HAT-P-13 b, which also requires confirmation with further precise observations.
Chandra X-ray analysis of Herbig Ae/Be stars
Authors: Anilkumar Hema , Mathew Blesson , Jithesh V , Kartha Sreeja S , Manoj P , Narang Mayank , Chavali Mahathi 
Published: April 2024

ABSTRACT
Herbig Ae/Be (HAeBe) stars are intermediate-mass pre-main-sequence stars, characterized by infrared (IR) excess and emission lines. They are observed to emit X-rays, whose origin is a matter of discussion and not settled yet. X-ray emission is not expected in HAeBe stars, as they lack the subsurface convective zone. In this study, we retrieved observations from the Chandra archive for 62 HAeBe stars, among which 44 sources (detection fraction ∼71 per cent) were detected in X-rays, with 7 being new detections. We use this sample as a test bed to conduct a comparative analysis of the X-ray properties of HAeBe stars and their low-mass counterparts, T Tauri stars (TTSs). Further, we compare the X-ray properties of HAeBe stars and TTSs with optical and IR properties to constrain the X-ray emission mechanism in HAeBe stars. We found no correlation between X-ray emission and disc properties of HAeBe stars, confirming that X-rays are not related to accretion shocks. About 56 per cent of HAeBe stars without any known subarcsec companions have lower plasma temperatures (kT ≤ 2 keV). We observe flaring/variability in HAeBe stars with confirmed low-mass companions. These stars show plasma temperatures &gt; 2 keV, similar to TTSs. Guided by this information, we discuss the role of a T Tauri companion for X-ray emission seen in our sample of HAeBe stars. From the results obtained in this paper, we suggest that X-ray emission from HAeBe stars may not be related to accretion shocks or hidden TTS, but rather can be due to magnetically driven coronal emission.
Towards quantifying the impact of triaxiality on optical signatures of galaxy clusters: weak lensing and galaxy distributions
Authors: Fu Shenming , Zhang Yuanyuan , Avestruz Camille , Coronel Ruben 
Published: April 2024

ABSTRACT
We present observational evidence of the impact of triaxiality on radial profiles that extend to 40 Mpc from galaxy cluster centres in optical measurements. We perform a stacked profile analysis from a sample of thousands of nearly relaxed galaxy clusters from public data releases of the Dark Energy Survey and the Dark Energy Camera Legacy Survey. Using the central galaxy elliptical orientation angle as a proxy for galaxy cluster orientation, we measure cluster weak lensing and excess galaxy density axis-aligned profiles, extracted along the central galaxy’s major or minor axes on the plane of the sky. Our measurements show a ≳ 2σ–3σ difference per radial bin between the normalized axis-aligned profiles. The profile difference between each axis-aligned profile and the azimuthally averaged profile ($\sim \pm 10\,\rm per\ cent-20~{{\ \rm per\ cent}}$ along major/minor axis) appears inside the clusters (∼0.4 Mpc) and extends to the large-scale structure regime (∼10–20 Mpc). The magnitude of the difference appears to be relatively insensitive to cluster richness and redshift, and extends further out in the weak lensing surface mass density than in the galaxy overdensity. Looking forward, this measurement can easily be applied to other observational or simulation data sets and can inform the systematics in cluster mass modelling related to triaxiality. We expect imminent upcoming wide-area deep surveys, such as the Vera C. Rubin Observatory’s Legacy Survey of Space and Time, to improve our quantification of optical signatures of cluster triaxiality.
Formation of long-period radio pulsars
Authors: Zhou Xia , Huang Hai-Tao , Cheng Quan , Zheng Xiao-Ping 
Published: April 2024

ABSTRACT
This study investigates the influence of different braking mechanisms on the formation of three long-period radio pulsars (PSRs J0250+5854, J2251−3711, and J0901−4046): plasma-filled magnetosphere in combination with magnetic field decay, fall-back disc, and r-mode instability. These braking mechanisms can also affect the thermal evolution of pulsars. By comparing the model-predicted values with observational data such as spin periods, period derivatives, and upper limits of the bolometric luminosity of these pulsars, we find that these three braking mechanisms can reasonably explain the spin period and the period derivative within a certain range of parameters for these sources. The model-predicted bolometric luminosity associated with magnetic field dissipation exceeds the upper limit for PSR J0901−4046 but falls below the upper limits for PSR J0250+5854 and PSR J2251−3711. The model-predicted bolometric luminosity within the fall-back disc model exceeds the observed results, whereas the luminosity within the r-mode instability falls below the observed upper limit for these three pulsars. However, a conflict arises when we consider the pulsar radio activity and the accretion phases within the fall-back disc model simultaneously. By combining data from radio and X-ray observations, along with precise measurements of surface thermal emissions, we can enhance our understanding of the braking mechanisms involved in the formation of long-period radio pulsars or constrain key model parameters. Finding more long-period pulsars in the future and conducting multiband observations will enhance our understanding of the formation and nature of long-period radio pulsars.
Fast radio bursts in the discs of active galactic nuclei
Authors: Zhao Z Y , Chen K , Wang F Y , Dai Zi-Gao 
Published: April 2024

ABSTRACT
Fast radio bursts (FRBs) are luminous millisecond-duration radio pulses with extragalactic origin, which were discovered more than a decade ago. Despite the numerous samples, the physical origin of FRBs remains poorly understood. FRBs have been thought to originate from young magnetars or accreting compact objects (COs). Massive stars or COs are predicted to be embedded in the accretion discs of active galactic nuclei (AGNs). The dense disc absorbs FRBs severely, making them difficult to observe. However, progenitors’ ejecta or outflow feedback from the accreting COs interact with the disc material to form a cavity. The existence of the cavity can reduce the absorption by the dense disc materials, making FRBs escape. Here, we investigate the production and propagation of FRBs in AGN discs and find that the AGN environments lead to the following unique observational properties, which can be verified in future observation. First, the dense material in the disc can cause large dispersion measure (DM) and rotation measure (RM). Secondly, the toroidal magnetic field in the AGN disc can cause Faraday conversion. Thirdly, during the shock breakout, DM and RM show non-power-law evolution patterns over time. Fourthly, for accreting-powered models, higher accretion rates lead to more bright bursts in AGN discs, accounting for up to 1 per cent of total bright repeating FRBs.
Gut-derived trimethylamine N-oxide promotes CCR2-mediated macrophage infiltration in acute kidney injury
Authors: Ren Yuan , Wang Zuoyuan , You Li , Zhou Jie , Huang Haowen , Chang Sansi , Wu Yuanhao , Xue Jun 
Published: April 2024

ABSTRACT

Background
Inflammation is crucial in the development of acute kidney injury (AKI) and subsequent chronic kidney disease (CKD) following renal ischaemia–reperfusion (IR) injury. Gut microbiota metabolites trigger inflammation and affect IR-induced renal damage. Yet the driving factors and mechanisms are unclear. Trimethylamine N-oxide (TMAO), a gut-derived choline metabolite, is a strong pro-inflammatory factor that increases in patients with AKI and CKD. We hypothesized that TMAO can promote renal injury caused by IR.

Methods
Mice subjected to unilateral renal IR to induce AKI and CKD were fed a high-choline diet to observe the effects of TMAO on kidney inflammation, fibrosis and macrophage dynamics.

Results
A choline-rich diet altered the gut microbiota and elevated TMAO levels, exacerbating IR-induced AKI and subsequent CKD. Single-cell analysis identified a distinct subset of CCR2+ macrophages derived from monocytes as key responders to TMAO, intensifying immune cell interactions and worsening renal injury. TMAO promoted sustained CCR2 expression after IR, increasing macrophage infiltration. CCR2 deletion and antagonist RS-102895 improved TMAO-induced inflammation and fibrosis and alleviated renal injury induced by IR.

Conclusions
Our study provides valuable insights into the link between TMAO and IR-induced renal inflammation and fibrosis, emphasizing the critical role of TMAO-mediated macrophage infiltration via CCR2 as a key therapeutic target in the acute and chronic phases after IR.