bluuebunny/crossref_metadata_2025_split huggingface dataset:
CO2 Release Driven by the Combination of Sulfide Oxidation and Carbonate Dissolution in the Upper Changjiang River: Effect of Erosion and Lithology on Chemical Weathering
Authors: Liu Jinke , Han Guilin , Wang Di 
Published: April 2023

AbstractThe positive link between weathering and orogeny suggests that the drawdown of atmospheric carbon dioxide (CO2) over the Cenozoic should be closely related to the enhanced silicate weathering caused by Cenozoic orogeny, especially the uplift of the Tibetan plateau. However, the uplift of orogens could also exhume carbonate and sulfide minerals, the coupling weathering of which can act as a source for atmospheric CO2 at the long‐term timescale and counteract the CO2 consumption by silicate weathering. In this study, the solute concentrations and isotopic ratios in the upper Changjiang River are determined to investigate the co‐weathering of silicate, carbonate, and sulfide minerals and its impact on the long‐term carbon cycle. An inverse mixing model incorporating elemental and isotopic ratios is established to quantitatively identify the sources of cations and weathering acids. The inversion of our samples reveals that carbonate weathering dominates the chemical composition of river water, even with the presence of secondary calcite precipitation. The sulfide oxidation widely occurs in the study area and the bulk of generated sulfuric acid is buffered by carbonate minerals. The erosion is decoupled from sulfide oxidation and chemical weathering, likely due to lithology and secondary calcite precipitation. Overall, we find that the CO2 release from sulfide oxidation coupled with carbonate dissolution exceeds the CO2 drawdown from silicate weathering in the Changjiang River basin, indicating the weathering will act as a source for atmospheric CO2 at the timescale between marine carbonate compensation (105 years) and sulfate reduction (<10 Ma).
Characterizing expression changes in noncoding RNAs during aging and heterochronic parabiosis across mouse tissues
Authors: Wagner Viktoria , Kern Fabian , Hahn Oliver , Schaum Nicholas , Ludwig Nicole , Fehlmann Tobias , Engel Annika , Henn Dominic , Rishik Shusruto , Isakova Alina , Tan Michelle , Sit Rene , Neff Norma , Hart Martin , Meese Eckart , Quake Steve , Wyss-Coray Tony , Keller Andreas 
Published: April 2023

AbstractMolecular mechanisms of organismal and cell aging remain incompletely understood. We, therefore, generated a body-wide map of noncoding RNA (ncRNA) expression in aging (16 organs at ten timepoints from 1 to 27 months) and rejuvenated mice. We found molecular aging trajectories are largely tissue-specific except for eight broadly deregulated microRNAs (miRNAs). Their individual abundance mirrors their presence in circulating plasma and extracellular vesicles (EVs) whereas tissue-specific ncRNAs were less present. For miR-29c-3p, we observe the largest correlation with aging in solid organs, plasma and EVs. In mice rejuvenated by heterochronic parabiosis, miR-29c-3p was the most prominent miRNA restored to similar levels found in young liver. miR-29c-3p targets the extracellular matrix and secretion pathways, known to be implicated in aging. We provide a map of organism-wide expression of ncRNAs with aging and rejuvenation and identify a set of broadly deregulated miRNAs, which may function as systemic regulators of aging via plasma and EVs.
Single duplex DNA sequencing with CODEC detects mutations with high sensitivity
Authors: Bae Jin H. , Liu Ruolin , Roberts Eugenia , Nguyen Erica , Tabrizi Shervin , Rhoades Justin , Blewett Timothy , Xiong Kan , Gydush Gregory , Shea Douglas , An Zhenyi , Patel Sahil , Cheng Ju , Sridhar Sainetra , Liu Mei Hong , Lassen Emilie , Skytte Anne-Bine , Grońska-Pęski Marta , Shoag Jonathan E. , Evrony Gilad D. , Parsons Heather A. , Mayer Erica L. , Makrigiorgos G. Mike , Golub Todd R. , Adalsteinsson Viktor A. 
Published: April 2023

AbstractDetecting mutations from single DNA molecules is crucial in many fields but challenging. Next-generation sequencing (NGS) affords tremendous throughput but cannot directly sequence double-stranded DNA molecules (‘single duplexes’) to discern the true mutations on both strands. Here we present Concatenating Original Duplex for Error Correction (CODEC), which confers single duplex resolution to NGS. CODEC affords 1,000-fold higher accuracy than NGS, using up to 100-fold fewer reads than duplex sequencing. CODEC revealed mutation frequencies of 2.72 × 10−8 in sperm of a 39-year-old individual, and somatic mutations acquired with age in blood cells. CODEC detected genome-wide, clonal hematopoiesis mutations from single DNA molecules, single mutated duplexes from tumor genomes and liquid biopsies, microsatellite instability with 10-fold greater sensitivity and mutational signatures, and specific tumor mutations with up to 100-fold fewer reads. CODEC enables more precise genetic testing and reveals biologically significant mutations, which are commonly obscured by NGS errors.
Multi-organ landscape of therapy-resistant melanoma
Authors: Liu Sixue , Dharanipragada Prashanthi , Lomeli Shirley H. , Wang Yan , Zhang Xiao , Yang Zhentao , Lim Raymond J. , Dumitras Camelia , Scumpia Philip O. , Dubinett Steve M. , Moriceau Gatien , Johnson Douglas B. , Moschos Stergios J. , Lo Roger S. 
Published: April 2023

AbstractMetastasis and failure of present-day therapies represent the most common causes of mortality in patients with cutaneous melanoma. To identify the underlying genetic and transcriptomic landscapes, in this study we analyzed multi-organ metastases and tumor-adjacent tissues from 11 rapid autopsies after treatment with MAPK inhibitor (MAPKi) and/or immune checkpoint blockade (ICB) and death due to acquired resistance. Either treatment elicits shared genetic alterations that suggest immune-evasive, cross-therapy resistance mechanisms. Large, non-clustered deletions, inversions and inter-chromosomal translocations dominate rearrangements. Analyzing data from separate melanoma cohorts including 345 therapy-naive patients and 35 patients with patient-matched pre-treatment and post-acquired resistance tumor samples, we performed cross-cohort analyses to identify MAPKi and ICB as respective contributors to gene amplifications and deletions enriched in autopsy versus therapy-naive tumors. In the autopsy cohort, private/late mutations and structural variants display shifted mutational and rearrangement signatures, with MAPKi specifically selecting for signatures of defective homologous-recombination, mismatch and base-excision repair. Transcriptomic signatures and crosstalks with tumor-adjacent macroenvironments nominated organ-specific adaptive pathways. An immune-desert, CD8+-macrophage-biased archetype, T-cell exhaustion and type-2 immunity characterized the immune contexture. This multi-organ analysis of therapy-resistant melanoma presents preliminary insights with potential to improve therapeutic strategies.
Thermodynamic determination of the equilibrium first-order phase-transition line hidden by hysteresis in a phase diagram
Authors: Matsuura Keisuke , Nishizawa Yo , Kriener Markus , Kurumaji Takashi , Oike Hiroshi , Tokura Yoshinori , Kagawa Fumitaka 
Published: April 2023

AbstractIn some materials exhibiting field-induced first-order transitions (FOTs), the equilibrium phase-transition line is hidden by the hysteresis region associated with the FOT. In general, phase diagrams form the basis for the study of material science, and the profiles of phase-transition lines separating different thermodynamic phases include comprehensive information about thermodynamic quantities, such as latent heat. However, in a field-induced FOT, the equilibrium phase-transition line cannot be precisely determined from measurements of resistivity, magnetization, etc, especially when the transition is accompanied by large hysteresis. Here, we demonstrate a thermodynamics-based method for determining the hidden equilibrium FOT line in a material exhibiting a field-induced FOT. This method is verified for the field-induced FOT between antiferromagnetic and ferrimagnetic states in magneto-electric compounds ($$\text {Fe}_{0.95}\text {Zn}_{0.05})_{2}\text {Mo}_{3}\hbox {O}_{8}$$

Fe

0.95

Zn

0.05

)

2

Mo
3

O
8

. The equilibrium FOT line determined based on the Clausius–Clapeyron equation exhibits a reasonable profile in terms of the third law of thermodynamics, and it shows marked differences from the midpoints of the hysteresis region. Our findings highlight that for a field-induced FOT exhibiting large hysteresis, care should be taken for referring to the hysteresis midpoint line when discussing field-induced latent heat or magnetocaloric effects.
Biotransformation and bioaccessibility of active ingredients from Radix Astragali by Poria cocos during solid-state fermentation and in vitro digestion and antioxidant activity evaluation
Authors: Chen Cai-Yun , Zhang Run , Zhang Li-Jie , Hu Zhi-Yong , Wang Shao-Ping , Mei Xue , Mi Wei , Zhang Jia-Yu 
Published: April 2023

AbstractRadix Astragali is one of the most famous and frequently used health food supplements and herbal medicines. Among more than 227 components of Radix Astragali, Astragaloside IV (AG IV) is famous functional compound and is commonly used as a quality marker for Radix Astragali. However, the relatively low content of AG IV in Radix Astragali (< 0.04%, w/w) severely limits its application. The purpose of this study is to improve the biotransformation of AG IV and its bioaccessibility during in vitro digestion by Poria cocos solid fermenting Radix Astragali. The optimum fermentation conditions were as follows: Inoculation amount 8 mL; fermentation time 10 d; fermentation humidity 90%. Through fermentation, the content of AG IV was increased from 384.73 to 1986.49 μg/g by 5.16-fold. After in vitro digestion, the contents of genistin, calycosin, formononetin, AG IV, Astragaloside II (AG II) and total flavonoids in fermented Radix Astragali (FRA) of enteric phase II (ENTII) were 34.52 μg/g, 207.32 μg/g, 56.76 μg/g, 2331.46 μg/g, 788.31 μg/g, 3.37 mg/g, which were 2.08-fold, 2.51-fold, 1.05-fold, 8.62-fold, 3.22-fold and 1.50-fold higher than those of control, respectively. The Scanning electron microscopy (SEM) of FRA showed rough surface and porous structure. The DPPH and ABTS radical scavenging rate of FRA were higher than those of control. These results showed that the Poria cocos solid fermentation could increase the content of the AG IV in Radix Astragali and improve the bioaccessibility and antioxidant activity of Radix Astragali, which is providing new ideas for future development and utilization of Radix Astragali.
Infection-induced extracellular vesicles evoke neuronal transcriptional and epigenetic changes
Authors: Tedford Ellen , Badya Norhidayah Binti , Laing Conor , Asaoka Nozomi , Kaneko Shuji , Filippi Beatrice Maria , McConkey Glenn Alan 
Published: April 2023

AbstractInfection with the protozoan Toxoplasma gondii induces changes in neurotransmission, neuroinflammation, and behavior, yet it remains elusive how these changes come about. In this study we investigated how norepinephrine levels are altered by infection. TINEV (Toxoplasma-induced neuronal extracellular vesicles) isolated from infected noradrenergic cells down-regulated dopamine ß-hydroxylase (DBH) gene expression in human and rodent cells. Here we report that intracerebral injection of TINEVs into the brain is sufficient to induce DBH down-regulation and distrupt catecholaminergic signalling. Further, TINEV treatment induced hypermethylation upstream of the DBH gene. An antisense lncRNA to DBH was found in purified TINEV preparations. Paracrine signalling to induce transcriptional gene silencing and DNA methylation may be a common mode to regulate neurologic function.
An AI based classifier model for lateral pillar classification of Legg–Calve–Perthes
Authors: Soydan Zafer , Saglam Yavuz , Key Sefa , Kati Yusuf Alper , Taskiran Murat , Kiymet Seyfullah , Salturk Tuba , Aydin Ahmet Serhat , Bilgili Fuat , Sen Cengiz 
Published: April 2023

AbstractWe intended to compare the doctors with a convolutional neural network (CNN) that we had trained using our own unique method for the Lateral Pillar Classification (LPC) of Legg–Calve–Perthes Disease (LCPD). Thousands of training data sets are frequently required for artificial intelligence (AI) applications in medicine. Since we did not have enough real patient radiographs to train a CNN, we devised a novel method to obtain them. We trained the CNN model with the data we created by modifying the normal hip radiographs. No real patient radiographs were ever used during the training phase. We tested the CNN model on 81 hips with LCPD. Firstly, we detected the interobserver reliability of the whole system and then the reliability of CNN alone. Second, the consensus list was used to compare the results of 11 doctors and the CNN model. Percentage agreement and interobserver analysis revealed that CNN had good reliability (ICC = 0.868). CNN has achieved a 76.54% classification performance and outperformed 9 out of 11 doctors. The CNN, which we trained with the aforementioned method, can now provide better results than doctors. In the future, as training data evolves and improves, we anticipate that AI will perform significantly better than physicians.
Energy‐efficient multipath clustering with load balancing routing protocol for wireless multimedia sensor networks
Authors: Saleem Madyen Mohammad , Alabady Salah Abdulghani 
Published: April 2023

AbstractWireless multimedia sensor networks (WMSNs) has the capability of collecting scalar information, as well as multi‐media events like moving object tracking and traffic fatalities. Because energy in WMSNs is a constrained resource, several researchers offered cluster routing approaches, and most protocols generally do not offer an average resource usage of the network that is balanced and minimised. To address this issue, this paper proposes an Energy‐Efficient Multipath Clustering with Load Balancing Routing Protocol for WMSNs (EEMCL) to prolong the network lifetime. The suggested protocol, which segments the network into layers of clusters, would be implemented using multi‐hop. Sensing data from the sensor is transmitted to the sink by the main cluster heads in each layer, cooperating with the cluster heads in the upper layers. The proposed protocol improves energy dissipation, network life‐times, and network stability according to simulation results when compared with SEP, SEP‐E, and SEPFL protocols. The last node dead for the proposed protocol is at round 5833, 4027 for SEPFL, 2828 for SEP‐E, and 2325 for SEP.
Applying a temporal systematics model to vector Apodizing Phase Plate coronagraphic data: TRAP4vAPP
Authors: Liu Pengyu , Bohn Alexander J. , Doelman David S. , Sutlieff Ben J. , Samland Matthias , Kenworthy Matthew A. , Snik Frans , Birkby Jayne L. , Biller Beth A. , Males Jared R. , Morzinski Katie M. , Close Laird M. , Otten Gilles P. P. L. 
Published: April 2023

Context. The vector Apodizing Phase Plate (vAPP) is a pupil plane coronagraph that suppresses starlight by forming a dark hole in its point spread function (PSF). The unconventional and non-axisymmetrical PSF arising from the phase modification applied by this coronagraph presents a special challenge to post-processing techniques.
Aims. We aim to implement a recently developed post-processing algorithm, temporal reference analysis of planets (TRAP) on vAPP coronagraphic data. The property of TRAP that uses non-local training pixels, combined with the unconventional PSF of vAPP, allows for more flexibility than previous spatial algorithms in selecting reference pixels to model systematic noise.
Methods. Datasets from two types of vAPPs are analysed: a double grating-vAPP (dgvAPP360) that produces a single symmetric PSF and a grating-vAPP (gvAPP180) that produces two D-shaped PSFs. We explore how to choose reference pixels to build temporal systematic noise models in TRAP for them. We then compare the performance of TRAP with previously implemented algorithms that produced the best signal-to-noise ratio (S/N) in companion detections in these datasets.
Results. We find that the systematic noise between the two D-shaped PSFs is not as temporally associated as expected. Conversely, there is still a significant number of systematic noise sources that are shared by the dark hole and the bright side in the same PSF. We should choose reference pixels from the same PSF when reducing the dgvAPP360 dataset or the gvAPP180 dataset with TRAP. In these datasets, TRAP achieves results consistent with previous best detections, with an improved S/N for the gvAPP180 dataset.
A Novel Method for Administering Epinephrine during Neonatal Resuscitation
Authors: Gu Hannah , Perl Juliana , Rhine William , Yamada Nicole K. , Sherman Jules , McMillin Alexandra , Halamek Louis P. , Wall James K. , Fuerch Janene H. 
Published: April 2023

Objective This study aimed to determine if prefilled epinephrine syringes will reduce time to epinephrine administration compared with conventional epinephrine during standardized simulated neonatal resuscitation.
Study Design Timely and accurate epinephrine administration during neonatal resuscitation is lifesaving in bradycardic infants. Current epinephrine preparation is inefficient and error-prone. For other emergency use drugs, prefilled medication syringes have decreased error and administration time. Twenty-one neonatal intensive care unit nurses were enrolled. Each subject engaged in four simulated neonatal resuscitation scenarios involving term or preterm manikins using conventional epinephrine or novel prefilled epinephrine syringes specified for patient weight and administration route. All scenarios were video-recorded. Two investigators analyzed video recordings for time to epinephrine preparation and administration. Differences between conventional and novel techniques were evaluated using the Wilcoxon Signed Rank Tests.
Results Twenty-one subjects completed 42 scenarios with conventional epinephrine and 42 scenarios with novel prefilled syringes. Epinephrine preparation was faster using novel prefilled epinephrine syringes (median = 17.0 s, interquartile range [IQR] = 13.3–22.8) compared with conventional epinephrine (median = 48.0 s, IQR = 40.5–54.9, n = 42, z = 5.64, p < 0.001). Epinephrine administration was also faster using novel prefilled epinephrine syringes (median = 26.9 s, IQR = 22.1–33.2) compared with conventional epinephrine (median = 57.6 s, IQR = 48.8–66.8, n = 42, z = 5.63, p < 0.001). In a poststudy survey, all subjects supported the clinical adoption of prefilled epinephrine syringes.
Conclusion During simulated neonatal resuscitation, epinephrine preparation and administration are faster using novel prefilled epinephrine syringes, which may hasten return of spontaneous circulation and be lifesaving for bradycardic neonates in clinical practice.
Key Points
High-performance shim coil design and engineering optimization for use in an extremely high field superconducting magnet
Authors: Zheng Yijie , Wang Yaohui , Liu Feng , Yan Ming , Wang Qiuliang 
Published: April 2023

The extremely high field has significant advantages in imaging quality and analyzing the fine structure of substances. However, its excellent performance requires the support of a higher-performance shim technique. In this paper, a novel structural design pattern of the shim coil for a 27 T extremely high field superconducting magnet is proposed. According to the contours of the stream function, we designed and optimized the shim coil pattern and engineering processing. The novel design was realized by using the contours as the centerline, and the wire spacing was controlled at 1 mm. The performance of the novel pattern was compared with those of alternative winding schemes. The results indicate that the novel design can improve coil performance, achieving higher fidelity and lower power dissipation.
2-Propanol interacting with Co3O4(001): A combined vSFS and AIMD study
Authors: Omranpoor Amir H. , Bera Anupam , Bullert Denise , Linke Matthias , Salamon Soma , Webers Samira , Wende Heiko , Hasselbrink Eckart , Spohr Eckhard , Kenmoe Stéphane 
Published: April 2023

The interaction of 2-propanol with Co3O4(001) was studied by vibrational sum frequency spectroscopy and ab initio molecular dynamics simulations of 2-propanol dissolved in a water film to gain an insight, at the molecular level, into the pathways of catalytic oxidation. The experimental study has been performed under near ambient conditions, where the presence of water vapor is unavoidable, resulting in a water film on the sample and, thereby, allowing us to mimic the solution–water interface. Both experiment and theory conclude that 2-propanol adsorbs molecularly. The lack of dissociation is attributed to the adsorption geometry of 2-propanol in which the O–H bond does not point toward the surface. Furthermore, the copresent water not only competitively adsorbs on the surface but also inhibits 2-propanol deprotonation. The calculations reveal that the presence of water deactivates the lattice oxygen, thereby reducing the surface activity. This finding sheds light on the multifaceted role of water at the interface for the electrochemical oxidation of 2-propanol in aqueous solution as recently reported [Falk et al., ChemCatChem 13, 2942–2951 (2021)]. At higher temperatures, 2-propanol remains molecularly adsorbed on Co3O4(001) until it desorbs with increasing surface temperature.
Tunability of silicon clathrate film properties by controlled guest-occupation of their cages
Authors: Vollondat Romain , Stoeffler Daniel , Preziosi Daniele , Roques Stéphane , Slaoui Abdelilah , Fix Thomas 
Published: April 2023

Type I and type II silicon clathrates are guest–host structures made of silicon polyhedral cages large enough to contain atoms that can be either inserted or evacuated with only a slight volume change of the structure. This feature is of interest not only for batteries or storage applications but also for tuning the properties of the silicon clathrate films. The thermal decomposition process can be tuned to obtain Na8Si46 and Na2&lt;x&lt;10Si136 silicon clathrate films on intrinsic and p-type c-Si (001) wafer. Here, from a unique synthesized NaxSi136 film, a range of resistivity of minimum four order of magnitude is possible by using post-synthesis treatments, switching from metallic to semiconductor behavior as the Na content is lowered. Extended exposition to sodium vapor allows us to obtain fully occupied Na24Si136 metallic films, and annealing under iodine vapor is a way to reach the guest-free Si136, a semiconducting metastable form of silicon with a 1.9 eV direct bandgap. Electrical measurements and resistance vs temperature measurements of the silicon clathrate films further discriminate the behavior of the various materials as the Na concentration is changing, additionally shouldered by density functional theory calculations for various guest occupations, further motivating the urge of an innovative pathway toward true guest-free type I and type II silicon clathrates.