bluuebunny/crossref_metadata_2025_split huggingface dataset:
Seismic reflection waveform inversion based on Gauss–Newton optimization
Authors: Xu Wencai , Hu Guanghui , He Binghong , Du Zeyuan 
Published: August 2022

Abstract
Owing to the lack of long-offset signals and effective low-frequency components, it is extremely difficult for classical full-waveform inversion (FWI) to obtain the long-wavelength components of medium and deep elastic parameter models. Considering ray theory, reflection traveltime tomography is restricted by resolution, and the reflection waveform inversion (RWI) method of the wave equation, and its practicability, has received greater attention. However, previous studies into RWI have primarily used first-order optimization methods, in which convergence and resolution still need substantial improvement. Based on the second-order optimization inversion theory, we deduced the reflection wave-sensitive kernel, objective function gradient and Hessian operator of background and perturbation model. Additionally, we revealed the de-fuzzification effect of the Hessian matrix on the gradient of inversion and the working mechanism of background velocity updating on direction optimization and inversion resolution improvement. Experiments on the SEG/EAGE overthrust model showed that an RWI with the Gauss–Newton method using an approximate Hessian matrix significantly improved convergence and wide-spectrum modeling capability compared with the conjugate gradient method. On the streamer seismic data of the East China Sea, the second-order optimization RWI method surpassed the commonly used reflection traveltime tomography based on pre-stack depth migration. In addition, the RTM of inversion model can depict the complex fault system in the Changjiang sag with a high resolution, which improves the imaging quality of the deep basement.
Combined multi-branch selective kernel hybrid-pooling skip connection residual network for seismic random noise attenuation
Authors: Zeng Meng , Zhang Gulan , Li Yong , Luo Yiliang , Hu Guanghui , Huang Yanlin , Liang Chenxi 
Published: August 2022

Abstract
To improve the generalization ability of the single pooling (average or maximum pooling) skip connection residual network (SSN) for seismic random noise attenuation, we present a hybrid-pooling skip connection residual network (HSN). In HSN, the hybrid pooling consists of average and maximum pooling and aims to simultaneously capture the local and global features well, ultimately improving the detail recovery capability of HSN. To further improve the network performance and denoising ability of HSN, we propose a combined multi-branch selective kernel (CSK) hybrid-pooling skip connection residual network, which is referred to as CHSN. In CHSN, CSK consists of a three-branch selective kernel (TSK) and our suggested four-branch selective kernel (FSK), and aims to adaptively capture feature maps for high-accuracy effective information recovery. The superior random noise attenuation ability of CHSN is demonstrated in both synthetic three- and actual two-dimensional seismic data.
The Success of Oral Appliance Therapy Based on Symptom-Driven Titration
Authors: Kang Cpt Ryan S , Knowles Shelley , Dekow Matthew 
Published: August 2022

ABSTRACT

Study Objective
Obstructive sleep apnea (OSA) is a chronic condition that could lead to debilitating and sometimes life-threatening consequences. Oral appliance therapy (OAT) is effective in providing a conservative, nonsurgical treatment option for patients diagnosed with mild-to-moderate OSA. The primary goal of this study is to describe a symptom-based titration protocol and determine if the patients can be effectively managed with oral appliances (OAs).

Method
A retrospective chart review of patients who were treated with OAs was analyzed for the management of OSA. Patients were self-titrated for symptomatic improvement before posttreatment titration sleep studies were conducted.

Results
Our study has found that 87.5% of the test population was successfully managed with OAs after overnight titration. Seventy-five percentage of the patients were titrated to Apnea–Hypopnea Index (AHI) &lt; 5 with an average of 79.6% reduction from the baseline. Statistical studies showed that patients’ body mass index and age at baseline polysomnogram studies significantly influenced the reduction in AHI achieved, whereas the baseline AHI did not show any significant correlation.

Conclusion
Oral appliance therapy (OAT) can be a reliable treatment modality to treat OSA, and performing a separate overnight posttreatment titration study further ensures its effectiveness. Furthermore, OAT can be an effective treatment modality even for moderate-to-severe OSA with posttreatment titration.
The impact of cosmic rays on dynamical balance and disc–halo interaction in L⋆ disc galaxies
Authors: Chan T K , Kereš Dušan , Gurvich Alexander B , Hopkins Philip F , Trapp Cameron , Ji Suoqing , Faucher-Giguère Claude-André 
Published: August 2022

ABSTRACT
Cosmic rays (CRs) are an important component in the interstellar medium, but their effect on the dynamics of the disc–halo interface (&lt;10 kpc from the disc) is still unclear. We study the influence of CRs on the gas above the disc with high-resolution FIRE-2 cosmological simulations of late-type L⋆ galaxies at redshift z ∼ 0. We compare runs with and without CR feedback (with constant anisotropic diffusion κ∥ ∼ 3 × 1029 cm2 s−1 and streaming). Our simulations capture the relevant disc–halo interactions, including outflows, inflows, and galactic fountains. Extra-planar gas in all of the runs satisfies dynamical balance, where total pressure balances the weight of the overlying gas. While the kinetic pressure from non-uniform motion (≳1 kpc scale) dominates in the mid-plane, thermal and bulk pressures (or CR pressure if included) take over at large heights. We find that with CR feedback, (1) the warm (∼104 K) gas is slowly accelerated by CRs; (2) the hot (&gt;5 × 105 K) gas scale height is suppressed; (3) the warm-hot (2 × 104–5 × 105 K) medium becomes the most volume-filling phase in the disc–halo interface. We develop a novel conceptual model of the near-disc gas dynamics in low-redshift L⋆ galaxies: with CRs, the disc–halo interface is filled with CR-driven warm winds and hot superbubbles that are propagating into the circumgalactic medium with a small fraction falling back to the disc. Without CRs, most outflows from hot superbubbles are trapped by the existing hot halo and gravity, so typically they form galactic fountains.
Sub-percentage measure of distances to redshift of 0.1 by a new cosmic ruler
Authors: Shi Yong , Chen Yanmei , Mao Shude , Gu Qiusheng , Wang Tao , Xia Xiaoyang , Zhang. Zhi-Yu 
Published: August 2022

ABSTRACT
Distance-redshift diagrams probe expansion history of the Universe. We show that the stellar mass-binding energy (massE) relation of galaxies proposed in our previous study offers a new distance ruler at cosmic scales. By using elliptical galaxies in the main galaxy sample of the Sloan Digital Sky Survey Data Release 7, we construct a distance-redshift diagram over the redshift range from 0.05 to 0.2 with the massE ruler. The best-fit dark energy density is 0.675 ± 0.079  for flat Λ-cold dark matter (ΛCDM) model, consistent with those by other probes. At the median redshift of 0.11, the median distance is estimated to have a fractional error of 0.34 per cent, much lower than those by supernova (SN) Ia and baryonic acoustic oscillation (BAO) and even exceeding their future capability at this redshift. The above low-$\mathit{ z}$ measurement is useful for probing dark energy that dominates at the late Universe. For a flat dark energy equation of state model (flat wCDM), the massE alone constrains w to an error that is only a factor of 2.2, 1.7, and 1.3 times larger than those by BAO, SN Ia, and cosmic microwave background (CMB), respectively.
Patterns of failure after radiation therapy in primary spinal high-grade gliomas: A single institutional analysis
Authors: Upadhyay Rituraj , Khose Swapnil , Pokhylevych Halyna , Paulino Arnold C , McAleer Mary Frances , Ghia Amol , Li Jing , Yeboa Debra Nana , Loghin Monica , Harrison Rebecca , O’Brien Barbara , Kamiya-Matsuoka Carlos , De Groot John , Puduvalli Vinay K , Tatsui Claudio , Alvarez-Breckenridge Christopher , Prabhu Sujit , Rhines Larry , Zaky Wafik , Lin Frank , Weinberg Jeffery S , Fuller Gregory , Sandberg David I , Johnson Jason Michael , McGovern Susan L 
Published: August 2022

Abstract

Background
Primary spinal high-grade gliomas (S-HGG) are rare aggressive tumors; radiation therapy (RT) often plays a dominant role in management. We conducted a single-institution retrospective review to study the clinicopathological features and management of S-HGGs.

Methods
Patients with biopsy-proven S-HGG who received RT from 2001 to 2020 were analyzed for patient, tumor, and treatment characteristics. Kaplan–Meier estimates were used for survival analyses.

Results
Twenty-nine patients were identified with a median age of 25.9 years (range 1–74 y). Four patients had GTR while 25 underwent subtotal resection or biopsy. All patients were IDH wildtype and MGMT-promoter unmethylated, where available. H3K27M mutation was present in 5 out of 10 patients tested, while one patient harbored p53 mutation. Median RT dose was 50.4 Gy (range 39.6–54 Gy) and 65% received concurrent chemotherapy, most commonly temozolomide. Twenty-three (79%) of patients had documented recurrence. Overall, 16 patients relapsed locally, 10 relapsed in the brain and 8 developed leptomeningeal disease; only 8 had isolated local relapse. Median OS from diagnosis was 21.3 months and median PFS was 9.7 months. On univariate analysis, age, gender, GTR, grade, RT modality, RT dose and concurrent chemotherapy did not predict for survival. Patients with H3K27M mutation had a poorer PFS compared to those without mutation (10.1 m vs 45.1 m) but the difference did not reach statistical significance (P = .26).

Conclusions
The prognosis of patients with spinal HGGs remains poor with two-thirds of the patients developing distant recurrence despite chemoradiation. Survival outcomes were similar in patients ≤ 29 years compared to adults &gt; 29 years. A better understanding of the molecular drivers of spinal HGGs is needed to develop more effective treatment options.
Impact of Innate Immunity, Endothelial Damage, and Metabolic Biomarkers on COVID-19 Severity and Mortality
Authors: Rocco Joseph M , Laghetti Paola , Di Stefano Mariantonietta , Sereti Irini , Ortega-Villa Ana , Wang Jing , Rupert Adam , Chironna Maria , Ye Peiying , Liu Xiangdong , Anderson Megan V , Burbelo Peter B , Fiore Jose Ramon , Saracino Annalisa , Lisco Andrea 
Published: August 2022

Abstract
In this study, abnormal levels of myeloid activation, endothelial damage, and innate immune markers were associated with severe coronavirus disease 2019 (COVID-19), while higher levels of metabolic biomarkers (irisin, leptin) demonstrated a protective effect. These data support a model for COVID-19 immunopathogenesis linking robust inflammation and endothelial damage in metabolically predisposed individuals.
Myometrial progesterone receptor determines a transcription program for uterine remodeling and contractions during pregnancy
Authors: Wu San-Pin , Wang Tianyuan , Yao Zheng-Chen , Peavey Mary C , Li Xilong , Zhou Lecong , Larina Irina V , DeMayo Francesco J 
Published: August 2022

AbstractThe uterine myometrium expands and maintains contractile quiescence before parturition. While the steroid hormone progesterone blocks labor, the role of progesterone signaling in myometrial expansion remains elusive. This study investigated the myometrial functions of the progesterone receptor, PGR. Pgr ablation in mouse smooth muscle leads to subfertility, oviductal embryo retention, and impaired myometrial adaptation to pregnancy. While gross morphology between mutant and control uteri are comparable, mutant uteri manifest a decrease of 76.6% oxytocin-stimulated contractility in a pseudopregnant context with a reduced expression of intracellular calcium homeostasis genes including Pde5a and Plcb4. At mid-pregnancy, the mutant myometrium exhibits discontinuous myofibers and disarrayed extracellular matrix at the conceptus site. Transcriptome of the mutant mid-pregnant uterine wall manifests altered muscle and extracellular matrix profiles and resembles that of late-pregnancy control tissues. A survey of PGR occupancy, H3K27ac histone marks, and chromatin looping annotates cis-acting elements that may direct gene expression of mid-pregnancy uteri for uterine remodeling. Further analyses suggest that major muscle and matrix regulators Myocd and Ccn2 and smooth muscle building block genes are PGR direct downstream targets. Cataloging enhancers that are topologically associated with progesterone downstream genes reveals distinctive patterns of transcription factor binding motifs in groups of enhancers and identifies potential regulatory partners of PGR outside its occupying sites. Finally, conserved correlations are found between estimated PGR activities and RNA abundance of downstream muscle and matrix genes in human myometrial tissues. In summary, PGR is pivotal to direct the molecular program for the uterus to remodel and support pregnancy.
Containing novel SARS-CoV-2 variants at source is possible with high-intensity sequencing
Authors: Brett Tobias S , Rohani Pejman 
Published: August 2022

AbstractThroughout the COVID-19 pandemic, control of transmission has been repeatedly thwarted by the emergence of variants of concern (VOC) and their geographic spread. Key questions remain regarding effective means of minimizing the impact of VOC, in particular the feasibility of containing them at source, in light of global interconnectedness. By analysing a stochastic transmission model of COVID-19, we identify the appropriate monitoring requirements that make containment at source feasible. Specifically, precise risk assessment informed primarily by epidemiological indicators (e.g. accumulated hospitalization or mortality reports), is unlikely prior to VOC escape. Consequently, decision makers will need to make containment decisions without confident severity estimates. In contrast, successfully identifying and containing variants via genomic surveillance is realistic, provided sequence processing and dissemination is prompt.
SECANT: a biology-guided semi-supervised method for clustering, classification, and annotation of single-cell multi-omics
Authors: Wang Xinjun , Xu Zhongli , Hu Haoran , Zhou Xueping , Zhang Yanfu , Lafyatis Robert , Chen Kong , Huang Heng , Ding Ying , Duerr Richard H , Chen Wei 
Published: August 2022

Abstract
The recent advance of single cell sequencing (scRNA-seq) technology such as Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq) allows researchers to quantify cell surface protein abundance and RNA expression simultaneously at single cell resolution. Although CITE-seq and other similar technologies have gained enormous popularity, novel methods for analyzing this type of single cell multi-omics data are in urgent need. A limited number of available tools utilize data-driven approach, which may undermine the biological importance of surface protein data. In this study, we developed SECANT, a biology-guided SEmi-supervised method for Clustering, classification, and ANnoTation of single-cell multi-omics. SECANT is used to analyze CITE-seq data, or jointly analyze CITE-seq and scRNA-seq data. The novelties of SECANT include (1) using confident cell type label identified from surface protein data as guidance for cell clustering, (2) providing general annotation of confident cell types for each cell cluster, (3) utilizing cells with uncertain or missing cell type label to increase performance, and (4) accurate prediction of confident cell types for scRNA-seq data. Besides, as a model-based approach, SECANT can quantify the uncertainty of the results through easily interpretable posterior probability, and our framework can be potentially extended to handle other types of multi-omics data. We successfully demonstrated the validity and advantages of SECANT via simulation studies and analysis of public and in-house datasets from multiple tissues. We believe this new method will be complementary to existing tools for characterizing novel cell types and make new biological discoveries using single-cell multi-omics data.
A computational approach to study the gap and barriers between science and policy
Authors: Li Nancy , Luczak-Roesch Markus , Donadelli Flavia 
Published: August 2022

AbstractResearch on the gap between science and policymaking and the barriers to utilizing science in policy remains controversial, since previous research methods have dominated data collection with perceived participant responses. This approach makes research findings applicable to particular contexts, particular participants, and particular times but cannot be generalized. We used a computational model to analyse linguistic text data from two communities and compared the results with self-reported research findings. The outcomes support that scientists and policymakers have their own linguistic characteristics, with scientists in the medical field preferring jargon and policymakers’ language containing public satisfaction pressures. Language representation also validates the existence of barriers in the use of science.
A Population-Based Study of Associations Among Child Screen Media Use, Social-Contextual Factors, and School Readiness
Authors: Griffith Shayl F. , Qiu Yuxi 
Published: August 2022

ABSTRACT:

Objective:
Results of studies examining relations between child media use and school readiness have been inconsistent. Importantly, studies often focus on a single outcome domain (e.g., academic, social, or behavioral), making the comparison of relative importance difficult; fail to account for confounding variables; and fail to investigate social-contextual moderators. This study investigated relations among child media use exposure, social-contextual factors, and multiple domains of school readiness in preschool-aged children.

Methods:
Multivariate regression analyses were used to examine relations between child media use and 3 domains of school readiness (early learning, social-emotional skills, and self-regulation), controlling for demographic and social-contextual factors, and to investigate differential susceptibility by examining family income and 4 social-contextual factors (sleep, exposure to adverse childhood events, frequency of shared reading, and parent stress) as moderators in a large US population–based sample (N = 9323) of 3 to 5 year olds.

Results:
After controlling for confounding variables, higher screentime was negatively related to children's social-emotional skills and self-regulation, but less so for early learning. Effect sizes were small. The relation between screentime and self-regulation was significantly moderated by family income, such that the relation was stronger for children from low-income backgrounds. No other evidence of significant moderation was found.

Conclusion:
Results add to evidence that the relation between screen media use and outcomes in young children is likely complex. Future work should prioritize examining impacts of screen media use on social and behavioral functioning to further inform the evaluation of relative benefits and costs of child screen media use.
Molecular mechanism of dynein-dynactin activation by JIP3 and LIS1
Authors: Singh Kashish , Lau Clinton K. , Manigrasso Giulia , Gama José B. , Gassmann Reto , Carter Andrew P. 
Published: August 2022

AbstractMicrotubule motors, like cytoplasmic dynein-1, are tightly regulated to prevent inappropriate activity in cells. Dynein functions as a ∼4 MDa complex containing its cofactor dynactin and a cargo-specific coiled-coil adaptor. However, how dynein and dynactin recognise diverse adaptors, how they interact with each other during complex formation, and the role of critical regulators such as LIS1 remain unclear. To address this, we determine the cryo-EM structure of dynein-dynactin on microtubules with LIS1 and the lysosomal adaptor JIP3. We show how JIP3 specifies complex formation despite a shorter coiled coil and lack of identifiable motifs compared to typical adaptors. We find LIS1 directly binds dynactin’s p150 subunit, closely tethering it to dynein. This interaction is necessary for dynein’s cellular andin vitroactivity. We also show how dynein’s intermediate chain relieves p150’s autoinhibition to enable LIS1 binding. Together, our data suggest LIS1 and p150 constrain dynein-dynactin to ensure efficient complex formation.
Recently evolved combination of unique sulfatase and amidase genes enables bacterial degradation of the wastewater micropollutant acesulfame worldwide
Authors: Bonatelli Maria L. , Rohwerder Thore , Popp Denny , Liu Yu , Akay Caglar , Schultz Carolyn , Liao Kuan-Po , Ding Chang , Reemtsma Thorsten , Adrian Lorenz , Kleinsteuber Sabine 
Published: August 2022

ABSTRACTXenobiotics often challenge the principle of microbial infallibility. One example is acesulfame introduced in the 1980s as zero-calorie sweetener, which was recalcitrant in wastewater treatment plants until the early 2010s. Then, efficient removal has been reported with increasing frequency. By studying acesulfame metabolism in alphaproteobacterial degraders of the genera Bosea and Chelatococcus, we experimentally confirmed the previously postulated route of two subsequent hydrolysis steps via acetoacetamide-N-sulfonate (ANSA) to acetoacetate and sulfamate. Genome comparison of wildtype Bosea sp. 100-5 and a spontaneous acesulfame degradation-defective mutant revealed the involvement of two plasmid-borne gene clusters. The acesulfame-hydrolyzing sulfatase is strictly manganese-dependent and belongs to the metallo beta-lactamase family. In all degraders analyzed, it is encoded on a highly conserved gene cluster embedded in a composite transposon. The ANSA hydrolase, on the other hand, is an amidase signature domain enzyme encoded in another gene cluster showing variable length among degrading strains. Transposition of the sulfatase gene cluster between chromosome and plasmid explains how the two catabolic gene clusters recently combined for the degradation of acesulfame. Searching available genomes and metagenomes for the two hydrolases and associated genes indicates that the acesulfame plasmid evolved and spread worldwide in short time. While the sulfatase is unprecedented and unique for acesulfame degraders, the amidase occurs in different genetic environments and might have evolved for the degradation of other substrates. Evolution of the acesulfame degradation pathway might have been supported by the presence of structurally related natural and anthropogenic compounds, such as aminoacyl sulfamate ribonucleotide or sulfonamide antibiotics.