bluuebunny/crossref_metadata_2025_split huggingface dataset:
Verb echo answers and ellipsis operations: A reply to Sato and Hayashi (2018)
Authors: Tanaka Hidekazu 
Published: March 2024

AbstractRecent research suggests that verb echo answers (VEAs) to a polar question in Japanese are derived by sluicing: the V head moves to C, and the complement of C, TP, undergoes deletion, stranding the verbal complex in C. Two pieces of evidence are provided for the view: adjunct inclusive interpretation and voice mismatch, neither of which is conclusive, as shown here. One consequence of the sluicing analysis is that VEAs reverse scope. We show that the semantic shift has nothing to do with the scope reversal. Our conclusion is that VEAs are unambiguously derived by multiple applications of argument ellipsis. We also advance an alternative explanation of the obligatory wide scope for focus phrases.
On the Origin of “Rotating Instabilities”—Stability and Frequency Studies of Channel Flows
Authors: Sauer Helmut , Lange Martin 
Published: March 2024

Abstract
A group of unsteady flow phenomena in turbomachinery is often referred to as “rotating instabilities.” They occur at flow conditions with very asymmetric velocity profiles, as found downstream of blade rows in axial compressors with large rotor tip clearance in stable operating points close to compressor stall or off-design operating points in steam turbines. In the present work, it is shown that such instabilities do not depend on the blading but also occur in blading-free flow channels. The theoretical proof is carried out with the tools and computational programs of spatial stability theory and Reynolds number dependent jumps in the transverse wavelengths at characteristic perturbation frequencies of the present asymmetric turbulent channel flow are discovered. Experimental investigations in a straight flow channel confirm the calculated frequency field and other characteristics of the perturbations. In agreement to theoretical results, a very asymmetric velocity profile across the channel height was found to trigger disturbances within a limited range of frequencies and not bound to the existence of blading. The notion of rotating instability is misleading in the characterization of this disturbance.
Daily Pain Severity but Not Vertebral Fractures Is Associated With Lower Physical Activity in Postmenopausal Women With Back Pain
Authors: Montgomery Gallin , Tobias Jon H. , Paskins Zoe , Khera Tarnjit K. , Huggins Cameron J. , Allison Sarah J. , Abasolo Daniel , Clark Emma M. , Ireland Alex 
Published: March 2024

Back pain lifetime incidence is 60%–70%, while 12%–20% of older women have vertebral fractures (VFs), often with back pain. We aimed to provide objective evidence, currently lacking, regarding whether back pain and VFs affect physical activity (PA). We recruited 69 women with recent back pain (age 74.5 ± 5.4 years). Low- (0.5 < g < 1.0), medium- (1.0 ≤ g < 1.5), and high-impact (g ≥ 1.5) PA and walking time were measured (100 Hz for 7 days, hip-worn accelerometer). Linear mixed-effects models assessed associations between self-reported pain and PA, and group differences (VFs from spine radiographs/no-VF) in PA. Higher daily pain was associated with reduced low (β = −0.12, 95% confidence interval, [−0.22, −0.03], p = .013) and medium-impact PA (β = −0.11, 95% confidence interval, [−0.21, −0.01], p = .041), but not high-impact PA or walking time (p > .11). VFs were not associated with PA (all p > .2). Higher daily pain levels but not VFs were associated with reduced low- and medium-impact PA, which could increase sarcopenia and falls risk in older women with back pain.
Priorities, opportunities, and challenges for integrating microorganisms into Earth system models for climate change prediction
Authors: Lennon J. T. , Abramoff R. Z. , Allison S. D. , Burckhardt R. M. , DeAngelis K. M. , Dunne J. P. , Frey S. D. , Friedlingstein P. , Hawkes C. V. , Hungate B. A. , Khurana S. , Kivlin S. N. , Levine N. M. , Manzoni S. , Martiny A. C. , Martiny J. B. H. , Nguyen N. K. , Rawat M. , Talmy D. , Todd-Brown K. , Vogt M. , Wieder W. R. , Zakem E. J. 
Published: March 2024

ABSTRACT

Climate change jeopardizes human health, global biodiversity, and sustainability of the biosphere. To make reliable predictions about climate change, scientists use Earth system models (ESMs) that integrate physical, chemical, and biological processes occurring on land, the oceans, and the atmosphere. Although critical for catalyzing coupled biogeochemical processes, microorganisms have traditionally been left out of ESMs. Here, we generate a “top 10” list of priorities, opportunities, and challenges for the explicit integration of microorganisms into ESMs. We discuss the need for coarse-graining microbial information into functionally relevant categories, as well as the capacity for microorganisms to rapidly evolve in response to climate-change drivers. Microbiologists are uniquely positioned to collect novel and valuable information necessary for next-generation ESMs, but this requires data harmonization and transdisciplinary collaboration to effectively guide adaptation strategies and mitigation policy.
Draft genomes of three aerobic methanotrophs from a temperate eutrophic fishpond
Authors: Wutkowska Magdalena , Daebeler Anne 
Published: March 2024

ABSTRACT

Here we introduce draft genomes of three methanotrophs belonging to the
Methylococcaceae,
a family of typically fast-growing methane oxidizers.
Methylobacter
sp. Wu1,
Methylomicrobium
sp. Wu6, and
Methylobacter
sp. Wu8 were cultured from the top sediment collected from a shore of a eutrophic fishpond in the southern Czech Republic.
Genome sequence of Soos: a siphovirus of the CP cluster infecting
Gordonia rubripertincta
Authors: Adams Reese M. , Britton Holly A. , Bruce Emily D. , De La Paz Yucita , Kratz Emily N. , Pfeifer Emma J. , Priddy Daisy E. , Schotter Brooklyn I. , Stuffle Wyatt A. , Wagner Jordyn , Weiss Meredith R. , Watt Danielle K. , Connerly Pamela L. , Rueschhoff Elizabeth E. 
Published: March 2024

ABSTRACT

Novel actinobacteriophage Soos was isolated and purified from Southern Indiana soil using host
Gordonia rubripertincta
NRRL B-16540. Sequencing revealed a 57,509 bp circularly permuted genome encoding 87 predicted protein-coding genes. Soos is only the third phage in cluster CP, along with phages Clawz and Sting.
Effects of calcium channel blockers on perioperative ischemic events in hypertensive patients with intracranial aneurysms undergoing neurointervention
Authors: Peng Qichen , Zhou Yangyang , Wang Chao , Xie Xuanping , Dong Linggen , Zhang Yisen , Zhang Hongqi , Wang Jun , Li Liang , Zhang Pinyuan , Zhao Yuanli , Wang Yang , Xiao Fushun , Luo Bin , Li Wenqiang , Mu Shiqing 
Published: March 2024

BackgroundAlthough calcium channel blockers (CCBs) are useful in stroke prevention, their specific role in preventing stroke in hypertensive patients with intracranial aneurysms undergoing endovascular stent placement remains unclear.MethodsWe retrospectively examined 458 hypertensive patients with intracranial aneurysms who underwent stent treatment, drawn from a larger multicenter cohort comprising 1326 patients across eight centers. Patients were dichotomized into two groups according to use of a CCB. Propensity score matching (PSM) was performed to balance group differences in patient and aneurysm characteristics. We conducted a comparison of patient and aneurysm characteristics, ischemic complications, and clinical outcomes between the two groups.ResultsThe CCB and non-CCB groups comprised 279 and 179 patients, respectively. PSM resulted in 165 matched pairs. After PSM, the incidence of ischemic events within 1 month of the procedure (4.2% vs 10.9%; P=0.022) and proportion of patients with modified Rankin Scale score >2 at last follow-up (1.5% vs 7.8%; P=0.013) were significantly lower in the CCB group. Among patients treated with combination therapy, inclusion of a CCB was associated with a lower incidence of ischemic events (1.5% vs 13.3%; P=0.345), but the difference was not statistically significant after correction.ConclusionsCCB use in hypertensive patients undergoing endovascular stenting for treatment of intracranial aneurysms is associated with a lower incidence of ischemic events and a lower incidence of unfavorable neurological outcomes, especially when used in combination therapy.
Associations between tobacco 21 and state flavour restrictions with young adult tobacco use
Authors: Hawkins Summer Sherburne , Carey Naoka , Levine Coley Rebekah , Baum Christopher F 
Published: March 2024

BackgroundStates have recently enacted tobacco-related age and flavour restrictions in addition to federal T21 laws. Little is known about the independent effects of these policies on young adult tobacco use.MethodsLinking 2011–2022 Behavioural Risk Factor Surveillance System data on 2 696 870, 18–59 years from 50 states and DC with policy data, we conducted probit regression models to evaluate the associations between state and federal T21 laws and state flavour restrictions with cigarettes, electronic nicotine delivery system (ENDS) and smokeless tobacco use. Models were adjusted for sociodemographics, additional tobacco policies, COVID-19-related factors, year and state. We tested two-way and three-way interactions between age, state T21 and federal T21 laws.ResultsAlthough we did not find evidence that state T21 laws were associated with cigarette, smokeless tobacco or ENDS use overall, the federal T21 law was associated with lower use of all three tobacco products by 0.39–0.92 percentage points. State flavour restrictions were associated with lower use of cigarettes by 0.68 (−1.27 to –0.09) and ENDS by 0.56 (−1.11 to –0.00) percentage points, but not with smokeless tobacco. A three-way interaction revealed that state and federal T21 laws together were associated with a lower prevalence of ENDS use among 18–20 years, but there were no differences in cigarette use from both policies combined versus either alone.ConclusionState and federal T21 laws are broadly effective at reducing adult tobacco use, while state flavour restrictions specifically lower use of cigarettes and ENDS.
Prediction of large spin-valley polarization in the Janus 2H–WSSe monolayer on VN magnetic substrate
Authors: Zhang Ruoxue , Li Zefang , An Yukai 
Published: March 2024

Two-dimensional heterostructures based on transition metal dichalcogenides (TMDs) exhibit broad application prospects in valleytronics due to the space-reversal symmetry breaking and strong spin–orbit coupling. In this work, the electronic structure, magnetic anisotropy and valley polarization of 2H–WSSe/VN van der Waals heterostructure under various interlayer spacings, magnetic angle and in-plane strain are investigated in detail by first-principles calculations. The stacked configuration of Se-C2-1 with most stable structure shows the largest valley polarization of 386.5[Formula: see text]meV. By adjusting the interlayer spacing of heterostructure, the largest valley polarization of 702.7[Formula: see text]meV appears in Se-C2-1 stacked configuration with interlayer spacing of 2.24 Å. The magnetic angle [Formula: see text] exhibits significant effects on valley polarization and magnetic anisotropy of 2H–WSSe/VN heterostructures. The stability and valley polarization of 2H–WSSe/VN heterostructure decrease after the in-plane biaxial strain is applied. The large and tunable valley polarization as well as magnetic anisotropy in the 2H–WSSe/VN heterostructures make it potential applications in valleytronic devices.
Exploring plasma phenomena with the Nizhnik–Novikov–Veselov formula: Analyzing ion-acoustic waves, solitons, and shocks
Authors: Altuijri Reem , Abdel-Aty Abdel-Haleem , Nisar Kottakkaran Sooppy , Khater Mostafa M. A. 
Published: March 2024

This paper delves into the intricacies of the ([Formula: see text])-dimensional asymmetric Nizhnik–Novikov–Veselov ([Formula: see text]) model, a nonlinear partial differential equation governing ion-acoustic wave propagation in plasma. By employing advanced analytical and numerical approaches, the study explores innovative solitary wave solutions, particularly focusing on the dynamics of isochoric flow. Isochoric flow analysis is crucial for unraveling the complex behaviors exhibited by incompressible fluids like elastomers and bio-elastomers, which maintain a constant density. The derivation of the ([Formula: see text])-dimensional [Formula: see text] equation stems from fluid equations governing plasma dynamics. This model serves as a valuable tool for simulating experimental observations of plasma waves. The computational methodology applied in this research demonstrates a commendable level of precision and consistency, yielding novel solitary wave solutions previously unreported in the [Formula: see text] model. These results underscore the study’s importance and novelty. The outcomes not only contribute to our understanding of incompressible fluid dynamics, but also lay the groundwork for future investigations in this domain. The revealed solitary wave solutions have the potential to inform the development of more accurate models for predicting fluid dynamics, thereby advancing the field.
Measurement of ctDNA Tumor Fraction Identifies Informative Negative Liquid Biopsy Results and Informs Value of Tissue Confirmation
Authors: Rolfo Christian D. , Madison Russell W. , Pasquina Lincoln W. , Brown Derek W. , Huang Yanmei , Hughes Jason D. , Graf Ryon P. , Oxnard Geoffrey R. , Husain Hatim 
Published: March 2024

Abstract

Purpose:
Liquid biopsy (LBx) for tumor profiling is increasingly used, but concerns remain regarding negative results. A lack of results may truly reflect tumor genomics, or it may be a false negative that would be clarified by tissue testing. A method of distinguishing between these scenarios could help clarify when follow-on tissue testing is valuable.

Experimental Design:
Here we evaluate circulating tumor DNA (ctDNA) tumor fraction (TF), a quantification of ctDNA in LBx samples, for utility in identifying true negative results. We assessed concordance between LBx and tissue-based results, stratified by ctDNA TF, in a real-world genomic dataset of paired samples across multiple disease types. We also evaluated the frequency of tissue results identifying driver alterations in patients with lung cancer after negative LBx in a real-world clinicogenomic database.

Results:
The positive percent agreement and negative predictive value between liquid and tissue samples for driver alterations increased from 63% and 66% for all samples to 98% and 97% in samples with ctDNA TF ≥1%. Among 505 patients with lung cancer with no targetable driver alterations found by LBx who had subsequent tissue-based profiling, 37% had a driver, all of which had ctDNA TF &lt;1%.

Conclusions:
Patients with lung cancer with negative LBx and ctDNA TF ≥1% are unlikely to have a driver detected on confirmatory tissue testing; such informative negative results may benefit instead from prompt treatment initiation. Conversely, negative LBx with ctDNA TF &lt;1% will commonly have a driver identified by follow-up tissue testing and should be prioritized for reflex testing.
The ω-3 Polyunsaturated Fatty Acid Docosahexaenoic Acid Enhances NK-Cell Antitumor Effector Functions
Authors: Wu Shuting , Peng Hongyan , Li Songyang , Huang Lanlan , Wang Xiangyu , Li Yana , Liu Yongjie , Xiong Peiwen , Yang Qinglan , Tian Kunpeng , Wu Weiru , Pu Rongxi , Lu Xiulan , Xiao Zhenghui , Yang Jian , Zhong Zhaoyang , Gao Yuan , Deng Yafei , Deng Youcai 
Published: March 2024

Abstract
ω-3 polyunsaturated fatty acids (PUFA) are known to directly repress tumor development and progression. In this study, we explored whether docosahexaenoic acid (DHA), a type of ω-3 PUFA, had an immunomodulatory role in inhibiting tumor growth in immunocompetent mice. The number of natural killer (NK) cells but not the number of T or B cells was decreased by DHA supplementation in various tissues under physiologic conditions. Although the frequency and number of NK cells were comparable, IFNγ production by NK cells in both the spleen and lung was increased in DHA-supplemented mice in the mouse B16F10 melanoma tumor model. Single-cell RNA sequencing revealed that DHA promoted effector function and oxidative phosphorylation in NK cells but had no obvious effects on other immune cells. Using Rag2−/− mice and NK-cell depletion by PK136 antibody injection, we demonstrated that the suppression of B16F10 melanoma tumor growth in the lung by DHA supplementation was dependent mainly on NK cells. In vitro experiments showed that DHA directly enhanced IFNγ production, CD107a expression, and mitochondrial oxidative phosphorylation (OXPHOS) activity and slightly increased proliferator-activated receptor gamma coactivator-1α (PGC-1α) protein expression in NK cells. The PGC-1α inhibitor SR-18292 in vitro and NK cell–specific knockout of PGC-1α in mice reversed the antitumor effects of DHA. In summary, our findings broaden the current knowledge on how DHA supplementation protects against cancer growth from the perspective of immunomodulation by upregulating PGC-1α signaling–mediated mitochondrial OXPHOS activity in NK cells.
Estimating Vitamin K Antagonist Anticoagulation Benefit in People With Atrial Fibrillation Accounting for Competing Risks: Evidence From 12 Randomized Trials
Authors: Shah Sachin J. , van Walraven Carl , Jeon Sun Young , Boscardin John , Hobbs F.D. Richard , Connolly Stuart J. , Ezekowitz Michael D. , Covinsky Kenneth E. , Fang Margaret C. , Singer Daniel E. 
Published: March 2024

BACKGROUND:
Patients with atrial fibrillation have a high mortality rate that is only partially attributable to vascular outcomes. The competing risk of death may affect the expected anticoagulant benefit. We determined if competing risks materially affect the guideline-endorsed estimate of anticoagulant benefit.

METHODS:

We conducted a secondary analysis of 12 randomized controlled trials that randomized patients with atrial fibrillation to vitamin K antagonists (VKAs) or either placebo or antiplatelets. For each participant, we estimated the absolute risk reduction (ARR) of VKAs to prevent stroke or systemic embolism using 2 methods—first using a guideline-endorsed model (CHA
2
DS
2
-VASc) and then again using a competing risk model that uses the same inputs as CHA
2
DS
2
-VASc but accounts for the competing risk of death and allows for nonlinear growth in benefit. We compared the absolute and relative differences in estimated benefit and whether the differences varied by life expectancy.

RESULTS:

A total of 7933 participants (median age, 73 years, 36% women) had a median life expectancy of 8 years (interquartile range, 6–12), determined by comorbidity-adjusted life tables and 43% were randomized to VKAs. The CHA
2
DS
2
-VASc model estimated a larger ARR than the competing risk model (median ARR at 3 years, 6.9% [interquartile range, 4.7%–10.0%] versus 5.2% [interquartile range, 3.5%–7.4%];
P
<0.001). ARR differences varied by life expectancies: for those with life expectancies in the highest decile, 3-year ARR difference (CHA
2
DS
2
-VASc model – competing risk model 3-year risk) was −1.3% (95% CI, −1.3% to −1.2%); for those with life expectancies in the lowest decile, 3-year ARR difference was 4.7% (95% CI, 4.5%–5.0%).

CONCLUSIONS:

VKA anticoagulants were exceptionally effective at reducing stroke risk. However, VKA benefits were misestimated with CHA
2
DS
2
-VASc, which does not account for the competing risk of death nor decelerating treatment benefit over time. Overestimation was most pronounced when life expectancy was low and when the benefit was estimated over a multiyear horizon.
Does Thrombosis Play a Causal Role in Lacunar Stroke and Cerebral Small Vessel Disease?
Authors: Koohi Fatemeh , Harshfield Eric L. , Shatunov Alexey , Markus Hugh S. 
Published: March 2024

BACKGROUND:
The importance of thromboembolism in the pathogenesis of lacunar stroke (LS), resulting from cerebral small vessel disease (cSVD), is debated, and although antiplatelets are widely used in secondary prevention after LS, there is limited trial evidence from well-subtyped patients to support this approach. We sought to evaluate whether altered anticoagulation plays a causal role in LS and cSVD using 2-sample Mendelian randomization.

METHODS:

From a recent genome-wide association study (n=81 190), we used 119 genetic variants associated with venous thrombosis at genome-wide significance (
P
<5*10
−8
) and with a linkage disequilibrium r
2
<0.001 as instrumental variables. We also used genetic associations with stroke from the GIGASTROKE consortium (62 100 ischemic stroke cases: 10 804 cardioembolic stroke, 6399 large-artery stroke, and 6811 LS). In view of the lower specificity for LS with the CT-based phenotyping mainly used in GIGASTROKE, we also used data from patients with magnetic resonance imaging–confirmed LS (n=3199). We also investigated associations with more chronic magnetic resonance imaging features of cSVD, namely, white matter hyperintensities (n=37 355) and diffusion tensor imaging metrics (n=36 533).

RESULTS:
Mendelian randomization analyses showed that genetic predisposition to venous thrombosis was associated with an increased odds of any ischemic stroke (odds ratio [OR], 1.19 [95% CI, 1.13–1.26]), cardioembolic stroke (OR, 1.32 [95% CI, 1.21–1.45]), and large-artery stroke (OR, 1.41 [95% CI, 1.26–1.57]) but not with LS (OR, 1.07 [95% CI, 0.99–1.17]) in GIGASTROKE. Similar results were found for magnetic resonance imaging–confirmed LS (OR, 0.94 [95% CI, 0.81–1.09]). Genetically predicted risk of venous thrombosis was not associated with imaging markers of cSVD.

CONCLUSIONS:
These findings suggest that altered thrombosis plays a role in the risk of cardioembolic and large-artery stroke but is not a causal risk factor for LS or imaging markers of cSVD. This raises the possibility that antithrombotic medication may be less effective in cSVD and underscores the necessity for further trials in well-subtyped cohorts with LS to evaluate the efficacy of different antithrombotic regimens in LS.
Kuhnian Lessons for the Study of Open-Ended Evolution
Authors: Bedau Mark A. 
Published: March 2024

Abstract
Kuhnian philosophy of science implies that progress in the study of open-ended evolution (OEE) would be accelerated if the OEE science community were to agree on some examples of striking success in OEE science. This article recounts the important role of scientific paradigms and scientific exemplars in creating the productivity of what Kuhn, in The Structure of Scientific Revolutions, calls “normal” science, and it describes how the study of OEE today would benefit from exhibiting more of the hallmarks of normal science. The article concludes by describing five proposed projects that would help create a consensus in the OEE community on some good examples of the scientific study of OEE.