bluuebunny/crossref_metadata_2025_split huggingface dataset:
The mechanism study of low-pressure air plasma cleaning on large-aperture optical surface unraveled by experiment and reactive molecular dynamics simulation
Authors: LI Yuhai , BAI Qingshun , GUAN Yuheng , LIU Hao , ZHANG Peng , BATELIBIEKE Buerlike , SHEN Rongqi , LU Lihua , YUAN Xiaodong , MIAO Xinxiang , HAN Wei , YAO Caizhen 
Published: April 2022

Abstract
Low-pressure air plasma cleaning is an effective method for removing organic contaminants on large-aperture optical components in situ in the inertial confinement fusion facility. Chemical reactions play a significant role in plasma cleaning, which is a complex process involving abundant bond cleavage and species generation. In this work, experiments and reactive molecular dynamics simulations were carried out to unravel the reaction mechanism between the benchmark organic contaminants of dibutyl phthalate and air plasma. The optical emission spectroscopy was used to study the overall evolution behaviors of excited molecular species and radical signals from air plasma as a reference to simulations. Detailed reaction pathways were revealed and characterized, and specific intermediate radicals and products were analyzed during experiments and simulation. The reactive species in the air plasma, such as O, HO2 and O3 radicals, played a crucial role in cleaving organic molecular structures. Together, our findings provide an atomic-level understanding of complex reaction processes of low-pressure air plasma cleaning mechanisms and are essential for its application in industrial plasma cleaning.
Improving quantum state detection with adaptive sequential observations
Authors: Geller Shawn , Cole Daniel C , Glancy Scott , Knill Emanuel 
Published: April 2022

Abstract
For many quantum systems intended for information processing, one detects the logical state of a qubit by integrating a continuously observed quantity over time. For example, ion and atom qubits are typically measured by driving a cycling transition and counting the number of photons observed from the resulting fluorescence. Instead of recording only the total observed count in a fixed time interval, one can observe the photon arrival times and get a state detection advantage by using the temporal structure in a model such as a hidden Markov model. We study what further advantage may be achieved by applying pulses to adaptively transform the state during the observation. We give a three-state example where adaptively chosen transformations yield a clear advantage, and we compare performances on an ion example, where we see improvements in some regimes. We provide a software package that can be used for exploration of temporally resolved strategies with and without adaptively chosen transformations.
scCODE: an R package for data-specific differentially expressed gene detection on single-cell RNA-sequencing data
Authors: Zou Jiawei , Deng Fulan , Wang Miaochen , Zhang Zhen , Liu Zheqi , Zhang Xiaobin , Hua Rong , Chen Ke , Zou Xin , Hao Jie 
Published: April 2022

Abstract
Differential expression (DE) gene detection in single-cell ribonucleic acid (RNA)-sequencing (scRNA-seq) data is a key step to understand the biological question investigated. Filtering genes is suggested to improve the performance of DE methods, but the influence of filtering genes has not been demonstrated. Furthermore, the optimal methods for different scRNA-seq datasets are divergent, and different datasets should benefit from data-specific DE gene detection strategies. However, existing tools did not take gene filtering into consideration. There is a lack of metrics for evaluating the optimal method on experimental datasets. Based on two new metrics, we propose single-cell Consensus Optimization of Differentially Expressed gene detection, an R package to automatically optimize DE gene detection for each experimental scRNA-seq dataset.
Revisiting benchmark study for response to methodological critiques of ‘Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases’
Authors: Yuan Xiao , Zhang Peng 
Published: April 2022

Abstract
Evaluation of phenotype-driven gene prioritization approaches for Mendelian diseases could facilitate the software development and method selection for the workflow configuration and clinical practice. In our original article, the performance of 10 well-recognized causal-gene prioritization methods was benchmarked using 305 cases from the deciphering developmental disorders (DDD) project and 209 in-house cases via a relatively unbiased methodology. The evaluation results showed that LIRICAL and AMELIE were two of the best methods in our benchmark experiments, and the possible integrative approach of these two methods may enhance the diagnostic efficiency. However, some methodological critiques were raised by the authors of Exomiser and PhenIX, so we revisited our benchmarking studies to answer their comments in this letter.
Relative Vaccine Effectiveness of a Severe Acute Respiratory Syndrome Coronavirus 2 Messenger RNA Vaccine Booster Dose Against the Omicron Variant
Authors: Butt Adeel A , Talisa Victor B , Shaikh Obaid S , Omer Saad B , Mayr Florian B 
Published: April 2022

Abstract

Background
The current severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccines may be less effective against the Omicron variant than against earlier variants. With recent resurgence of SARS-CoV-2 cases, the role of booster doses of the vaccine needs to be highlighted.

Methods
Using a retrospective cohort study design emulating a target trial, we determined the relative vaccine effectiveness (RVE) of a homologous booster dose of a SARS-CoV-2 messenger RNA (mRNA) vaccine compared with the primary vaccine series alone in preventing infection, hospitalization, and intensive care unit admission, and death in the Department of Veterans Affairs healthcare system in the United States. Among infection-free survivors who received 2 doses of a mRNA vaccine before 30 April 2021, we identified those who received a booster between 22 September and 25 December 2021 and matched them 1:1 with individuals who did not receive a booster.

Results
Among 2 384 272 previously uninfected persons with 2 doses of an mRNA vaccine by 30 April 2021, we identified 462 950 booster recipients between 22 September and 25 December 2021, who were matched 1:1 with non–booster recipients. The RVE (95% confidence interval) was 19% (17%–22%) for confirmed infection, 52% (46%–57%) for hospitalization, and 83% (65%–92%) for intensive care unit admission or death. Recipients of the mRNA-1273 vaccine had a lower cumulative incidence of infections and hospitalizations than recipients of the BNT162b2 vaccine (log-rank P &lt;.001 for both comparisons).

Conclusions
While the RVE of SARS-CoV-2 mRNA booster vaccine dose in preventing infection against the Omicron variant is low, it is substantial in preventing hospitalization and high in preventing the most severe/critical disease.
A wealth tax on corporations’ stock
Authors: Saez Emmanuel , Zucman Gabriel 
Published: April 2022

Abstract
We propose to institute a new tax on corporations’ stock shares for all publicly listed companies and large private companies headquartered in G20 countries. Each of these companies would have to pay 0.2% of the value of its stock in taxes each year. As the G20 stock market capitalization is around 100% of world GDP, the tax would raise approximately 0.2% of world GDP in revenue. Because stock ownership is highly concentrated among the rich, this tax would be progressive. The tax could be paid in kind by corporations (by issuing new stock) so that the tax does not raise liquidity issue nor affect business operations. In today’s globalized and fast-moving world, companies can become enormously valuable once they establish market power, even before they start making large profits (e.g., Amazon and Tesla). This tax would make them start paying taxes sooner than standard income taxes.
Mortality in COVID-19 among women on hormone replacement therapy: a retrospective cohort study
Authors: Dambha-Miller Hajira , Hinton William , Wilcox Christopher R , Joy Mark , Feher Michael , de Lusignan Simon 
Published: April 2022

Abstract

Background
Limited recent observational data have suggested that there may be a protective effect of oestrogen on the severity of COVID-19 disease. Our aim was to investigate the association between hormone replacement therapy (HRT) or combined oral contraceptive pill (COCP) use and the likelihood of death in women with COVID-19.

Methods
We undertook a retrospective cohort study using routinely collected computerized medical records from the Oxford-Royal College of General Practitioners (RCGP) Research and Surveillance Centre (RSC) primary care database. We identified a cohort of 1,863,478 women over 18 years of age from 465 general practices in England. Mixed-effects logistic regression models were used to quantify the association between HRT or COCP use and all-cause mortality among women diagnosed with confirmed or suspected COVID-19 in unadjusted and adjusted models.

Results
There were 5,451 COVID-19 cases within the cohort. HRT was associated with a reduction in all-cause mortality in COVID-19 (adjusted OR 0.22, 95% CI 0.05 to 0.94). There were no reported events for all-cause mortality in women prescribed COCPs. This prevented further examination of the impact of COCP.

Conclusions
We found that HRT prescription within 6 months of a recorded diagnosis of COVID-19 infection was associated with a reduction in all-cause mortality. Further work is needed in larger cohorts to examine the association of COCP in COVID-19, and to further investigate the hypothesis that oestrogens may contribute a protective effect against COVID-19 severity.
Engineering the polyphenolic biosynthetic pathway stimulates metabolic and molecular changes during fruit ripening in “Bronze” tomato
Authors: Scarano Aurelia , Gerardi Carmela , Sommella Eduardo , Campiglia Pietro , Chieppa Marcello , Butelli Eugenio , Santino Angelo 
Published: April 2022

Abstract
The metabolic engineered Bronze tomato line is characterized by the constitutive over-expression of the VvStSy gene encoding a structural protein responsible for the stilbenoids biosynthesis and the fruit-specific over-expression of AmDel/Rosea1 and AtMYB12 genes encoding transcription factors that activate the polyphenol biosynthetic pathway. This tomato line is known for the increased levels of polyphenols in ripe fruits and for beneficial health promoting antioxidant and anti-inflammatory effects. In this study we analyzed the transcriptional and metabolic profiling in mature green, breaker, orange and ripe fruits compared to the normal tomato counterparts during ripening, to unravel the effect of regulatory and structural transgenes on metabolic fluxes of primary and secondary metabolisms. Our results showed that the shikimate synthase (SK) gene was up-regulated in the Bronze fruit, and the transcriptional activation is consistent with the metabolic changes observed throughout fruit ripening. These results paralleled with a reduced level of simple sugars and malate, highlighting the consumption of primary metabolites to favor secondary metabolites production and accumulation. Finally, carotenoids quantification revealed a change in the lycopene/β-carotene ratio in the Bronze fruit as a consequence of significant lower level of the first and higher levels of the latter. The high polyphenols and β-carotene content displayed by the Bronze fruit at the later stages of fruit ripening renders this line an interesting model to study the additive or synergic effects of these phyto-chemicals in the prevention of human pathologies.
Identification of WRKY transcription factors involved in regulating the biosynthesis of the anti-cancer drug camptothecin in Ophiorrhiza pumila
Authors: Wang Can , Hao Xiaolong , Wang Yao , Maoz Itay , Zhou Wei , Zhou Zhigang , Kai Guoyin 
Published: April 2022

Abstract
Camptothecin is a chemotherapeutic drug widely used to treat various cancers. Ophiorrhiza pumila is an ideal plant model for the study of camptothecin production, with various advantages for studying camptothecin biosynthesis and regulation. The DNA-binding WRKY transcription factors have a key regulatory role in secondary metabolite biosynthesis in plants. However, little is currently known about their involvement in camptothecin biosynthesis in O. pumila. We identified 46 OpWRKY genes unevenly distributed on the 11 chromosomes of O. pumila. Phylogenetic and multiple sequence alignment analyses divided the OpWRKY proteins into three subfamilies. Based on spatial expression and co-expression, we targeted the candidate gene OpWRKY6. Overexpression of OpWRKY6 significantly reduced the accumulation of camptothecin compared with the control. Conversely, camptothecin accumulation increased in OpWRKY6 knockout lines. Further biochemical assays showed that OpWRKY6 negatively regulates camptothecin biosynthesis from both the iridoid and shikimate pathways by directly downregulating the gene expression of OpGES, Op10HGO, Op7DLH, and OpTDC. Our data provide direct evidence for the involvement of WRKYs in the regulation of camptothecin biosynthesis and offer valuable information for enriching the production of camptothecin in plant systems.
Bladder lymphoepithelioma-like carcinoma: a case report
Authors: Rahoui Moez , Ouanes Yassine , Chaker Kays , Dali Kheireddine Mrad , Bibi Mokhtar , Sellami Ahmed , Rhouma Sami Ben , Nouira Yassine 
Published: April 2022

Abstract
Bladder lymphoepithelioma-like carcinoma is a rare entity. It represents a particular variant of urothelial carcinoma characterized by an important infiltrating power. Therapeutic management of this cancer is not codified. Surgery associated with chemotherapy seems to be the best therapeutic option. Few cases of this tumor have been reported in the literature. We report a case of bladder lymphoepithelioma-like carcinoma in a 52-year-old patient who presented with gross hematuria and discusses difficulties of diagnostic and treatment.
Delayed brain metastasis after 17-years from papillary thyroid cancer without local recurrence: case report and literature review
Authors: Knight James , Kingham Matthew , Price Sally-Ann , Bodi Istvan , Lavrador Jose Pedro 
Published: April 2022

Abstract
Papillary thyroid carcinoma (PTC) is the most common malignancy originating from the thyroid, with a good overall prognosis. However, distant metastasis of such lesions is very rare, with the brain being an incredibly uncommon site for secondary spread. The authors report a case of PTC brain metastasis 17-years after successful treatment of the primary malignancy, with no local or locoregional recurrence. Initial diagnostic uncertainty necessitated the involvement of a multidisciplinary team, and eventually the patient underwent image-guided gross surgical resection with intraoperative neuromonitoring (IOMN).
Evaluation of Prescribing Patterns Following Surgical Procedures in Opioid Naïve Patients at a Veterans Affairs Teaching Hospital
Authors: Chitwood Caleb , Haug Karlie L , Wenthur Cody , Gillis Carly , Maloney James D , Johnson Diane 
Published: April 2022

ABSTRACT

Objectives
To evaluate facility postoperative opioid prescribing patterns in comparison to published guidelines and adherence to opioid safety mandates.

Methods
This quality analysis was performed between November 2019 and March 2020. Patients were identified to have been opioid naïve prior to receiving a new opioid prescription postoperatively during the study period. Patient charts were reviewed, and patients were contacted to collect desired data. Statistical analysis was performed to evaluate distributions of morphine equivalent daily dose and opioid day supply prescribed across study subpopulations.

Results
Ninety-four of 100 prescriptions evaluated were determined to be within quantity or duration recommendations of the selected guideline. Statistical analysis found no significantly different distributions between the duration and quantity of opioid prescribed at discharge and patient-specific risk factors. Forty-eight patients did not use the entire quantity of the initial opioid prescription dispensed. Of those patients, 26 still had opioids within the home. Opioid risk review documentation was completed in 19 of 65 patients indicated for documentation.

Conclusion
Most opioid prescriptions provided within the study period aligned with recommendations from author-selected guidelines. However, a review of risk prior to opioid prescribing frequently was not performed. The number of patients utilizing less than 50% of prescribed opioids, and few refills indicate that reductions in opioids prescribed would improve safety for both patients and the surrounding community without increasing the risk for the under-treatment of postoperative pain. Improved prescribing habits and patient safety will be targeted through provider education regarding risk review documentation in opioid naïve patients.
Reliable event detection for Taylor methods in astrodynamics
Authors: Biscani Francesco , Izzo Dario 
Published: April 2022

ABSTRACT
We present a novel approach for the detection of events in systems of ordinary differential equations. The new method combines the unique features of Taylor integrators with state-of-the-art polynomial root finding techniques to yield a novel algorithm, ensuring strong event detection guarantees at a modest computational overhead. Detailed tests and benchmarks focused on problems in astrodynamics and celestial mechanics (such as collisional N-body systems, spacecraft dynamics around irregular bodies accounting for eclipses, computation of Poincaré sections, etc.) show how our approach is superior in both performance and detection accuracy to strategies commonly employed in modern numerical integration works. The new algorithm is available in our open source Taylor integration package heyoka.
The cosmic-ray staircase: the outcome of the cosmic-ray acoustic instability
Authors: Tsung Tsun Hin Navin , Oh S Peng , Jiang Yan-Fei 
Published: April 2022

ABSTRACT
Recently, cosmic rays (CRs) have emerged as a leading candidate for driving galactic winds. Small-scale processes can dramatically affect global wind properties. We run two-moment simulations of CR streaming to study how sound waves are driven unstable by phase-shifted CR forces and CR heating. We verify linear theory growth rates. As the sound waves grow non-linear, they steepen into a quasi-periodic series of propagating shocks; the density jumps at shocks create CR bottlenecks. The depth of a propagating bottleneck depends on both the density jump and its velocity; ΔPc is smaller for rapidly moving bottlenecks. A series of bottlenecks creates a CR staircase structure, which can be understood from a convex hull construction. The system reaches a steady state between growth of new perturbations, and stair mergers. CRs are decoupled at plateaus, but exert intense forces and heating at stair jumps. The absence of CR heating at plateaus leads to cooling, strong gas pressure gradients and further shocks. If bottlenecks are stationary, they can drastically modify global flows; if their propagation times are comparable to dynamical times, their effects on global momentum and energy transfer are modest. The CR acoustic instability is likely relevant in thermal interfaces between cold and hot gas, as well as galactic winds. Similar to increased opacity in radiative flows, the build-up of CR pressure due to bottlenecks can significantly increase mass outflow rates, by up to an order of magnitude. It seeds unusual forms of thermal instability, and the shocks could have distinct observational signatures, on ∼kpc scales.
Can a binary neutron star merger in the vicinity of a supermassive black hole enable a detection of a post-merger gravitational wave signal?
Authors: Vijaykumar Aditya , Kapadia Shasvath J , Ajith Parameswaran 
Published: April 2022

ABSTRACT
The post-merger gravitational-wave (GW) signal of a binary neutron star (BNS) merger is expected to contain valuable information that could shed light on the equation of state (EOS) of NSs, the properties of the matter produced during the merger, as well as the nature of any potential intermediate merger product such as hypermassive or supramassive NSs. However, the post-merger lies in the high frequency regime (≳1000 Hz) where current LIGO-Virgo detectors are insensitive. While proposed detectors such as NEMO, Cosmic Explorer and Einstein Telescope could potentially detect the post-merger for BNSs within $\mathcal {O}(10~\mathrm{Mpc})$, such events are likely to be rare. In this work, we speculate on the possibility of detecting the post-merger from BNSs coalescing in the vicinity of supermassive black holes (SMBHs). The redshift produced by the gravitational field of the SMBH, as well as the BNS’s proper motion around the SMBH, could effectively ‘stretch’ the post-merger signal into the band of the detectors. We demonstrate, using a phenomenological model, that such BNS coalescences would enable constraints on the peak of the post-merger signal that would otherwise have not been possible, provided the degree of redshifting due to the SMBH can be independently acquired. Further, using numerical simulations of binary neutron stars, we show how such mergers would improve EOS model selection using the post-merger signal. We discuss the mechanisms that might deliver such events and the limitations of this work.
Centrifugal breakout reconnection as the electron acceleration mechanism powering the radio magnetospheres of early-type stars
Authors: Owocki S P , Shultz M E , ud-Doula A , Chandra P , Das B , Leto P 
Published: April 2022

ABSTRACT
Magnetic B-stars often exhibit circularly polarized radio emission thought to arise from gyrosynchrotron emission by energetic electrons trapped in the circumstellar magnetosphere. Recent empirical analyses show that the onset and strength of the observed radio emission scale with both the magnetic field strength and the stellar rotation rate. This challenges the existing paradigm that the energetic electrons are accelerated in the current sheet between opposite-polarity field lines in the outer regions of magnetized stellar winds, which includes no role for stellar rotation. Building on recent success in explaining a similar rotation-field dependence of H α line emission in terms of a model in which magnetospheric density is regulated by centrifugal breakout (CBO), we examine here the potential role of the associated CBO-driven magnetic reconnection in accelerating the electrons that emit the observed gyrosynchrotron radio. We show in particular that the theoretical scalings for energy production by CBO reconnection match well the empirical trends for observed radio luminosity, with a suitably small, nearly constant conversion efficiency ϵ ≈ 10−8. We summarize the distinct advantages of our CBO scalings over previous associations with an electromotive force, and discuss the potential implications of CBO processes for X-rays and other observed characteristics of rotating magnetic B-stars with centrifugal magnetospheres.