bluuebunny/crossref_metadata_2025_split huggingface dataset:
A unified numerical model for two-phase porous, mush and suspension flow dynamics in magmatic systems
Authors: Wong Ying-Qi , Keller Tobias 
Published: December 2022

SUMMARYMagmatic systems in the Earth’s mantle and crust contain multiple phases including solid crystals, liquid melt and low viscosity fluids. Depending on depth, tectonic setting and chemical composition, magmatic systems can range from partially molten rock at low melt fraction to magma mushes at intermediate melt fraction to magmatic suspensions at high melt fraction. However, the theories underpinning most process-based models of magmatic systems describe magma as a single-phase fluid, or as a two-phase mixture either in the porous flow regime at low melt fractions or in the suspension flow regime at high melt fractions. Connections between the two-phase end-member theories are poorly established and hinder investigations into the dynamics of mush flows at intermediate phase fractions, leaving a significant gap in bridging trans-crustal magma processing from source to surface. To address this knowledge gap and unify two-phase magma flow models, we develop a 2-D system-scale numerical model of the fluid mechanics of an n-phase system at all phase proportions, based on a recent theoretical model for multiphase flows in igneous systems. We apply the model to two-phase, solid-liquid mixtures by calibrating transport coefficients to theory and experiments on mixtures with olivine-rich rock and basaltic melt using a Bayesian parameter estimation approach. We verify the model using the method of manufactured solutions and test the scalability for high resolution modelling. We then demonstrate 1-D and 2-D numerical experiments across the porous, mush and suspension flow regimes. The experiments replicate known phenomena from end-member regimes, including rank-ordered porosity wave trains in 1-D and porosity wave breakup in 2-D in the porous flow regime, as well as particle concentration waves in 1-D and mixture convection in 2-D in the suspension flow regime. By extending self-consistently into the mush regime, the numerical experiments show that the weakening solid matrix facilitates liquid localization into liquid-rich shear bands with their orientation controlled by the solid stress distribution. Although the present model can already be used to investigate three-phase mixtures using conceptually derived transport coefficients, more rigorous calibration to experiments and end-member theories is needed to ensure accurate timescales and mechanics. With a self-consistent way to examine multiphase mixtures at any phase proportion, this new model transcends theoretical limitations of existing multiphase numerical models to enable new investigations into two-phase or higher magma mush dynamics.
Performance and limits of a shallow-water model for landslide-generated tsunamis: from laboratory experiments to simulations of flank collapses at Montagne Pelée (Martinique)
Authors: Poulain P , Friant A Le , Mangeney A , Viroulet S , Fernandez-Nieto E , Castro Diaz M , Peruzzetto M , Grandjean G , Bouchut F , Pedreros R , Komorowski J-C 
Published: December 2022

SUMMARYWe investigate the dynamics and deposits of granular flows and the amplitude of landslide-generated water waves using the HySEA depth-averaged shallow-water numerical model, both at laboratory and field scales. We evaluate the different sources of error by quantitatively comparing the simulations with (i) new laboratory experiments of granular collapses in different conditions (dry, immersed, dry flow entering water) and slope angles and (ii) numerical simulations made with the SHALTOP code that describes topography effects better than most depth-averaged landslide-tsunami models. For laboratory configurations, representing the limits of the shallow-water approximation in such models, we show that topography and non-hydrostatic effects are crucial. When topography effects are accounted for empirically—by artificially increasing the friction coefficient and performing non-hydrostatic simulations—the model is able to reproduce the granular mass deposit and the waves recorded at gauges located at a distance of more than two to three times the characteristic dimension of the slide with an error ranging from 1 to 25 per cent depending on the scenario, without any further calibration. Taking into account this error estimate, we simulate landslides that occurred on Montagne Pelée volcano, Martinique, Lesser Antilles as well as the generated waves. Multiple collapse simulations support the assumption that large flank collapses on Montagne Pelée likely occurred in several successive subevents. This result has a strong impact on the amplitude of the generated waves and thus on the associated hazards. In the context of the ongoing seismic volcanic unrest at Montagne Pelée volcano, we calculate the debris avalanche and associated tsunamis for two potential flank-collapse scenarios.
Azimuthal amplitude difference inversion constrained by azimuth velocity anisotropy
Authors: Ji Lixiang , Zong Zhaoyun , Yang Yaming 
Published: December 2022

SUMMARYAmplitude variation with incident angle and azimuth (AVAZ) inversion is usually used for estimating subsurface medium properties from azimuthal stacked seismic data for fracture prediction. And weak anisotropy parameters play an important role in the fracture prediction of shale reservoirs. However, the low contribution of the anisotropic parameters to the reflection coefficient and too many condition numbers of forward solver lead to insufficient inversion stability of the anisotropic parameters. Therefore, a new azimuthal-amplitude-difference inversion method with the azimuth-velocity-anisotropic constraints is proposed to improve the stability of inversion and obtain a reasonable estimation of anisotropic parameters. The azimuthal amplitude difference AVAZ forward solver in the anisotropic medium is initially established from a rewritten approximate reflectivity equation and variable substitution. Sensitivity analysis of estimated parameters of the rewritten approximate reflectivity indicates that our approach is sufficiently suitable for seismic inversion of anisotropic parameters. Furthermore, an azimuthal amplitude difference Bayesian AVAZ inversion approach with azimuth-velocity-anisotropic constraint is developed to improve the stability of the inversion. We add Gaussian noise to the synthetic seismic records and assume the Cauchy distributions as a prior constraint on the model parameters. The anisotropic information obtained from the azimuth-velocity-anisotropic inversion is utilized as a constraint for improving the stability of inversion. Synthetic data tests reveal that the anisotropic parameters can be estimated stably even with moderate noise. Field data tests illustrate the feasibility and reliability of the presented inversion method for estimating anisotropic parameters in a shale reservoir with vertical or near-vertical fractures.
Parkin regulates neuronal lipid homeostasis through SREBP2-lipoprotein lipase pathway—implications for Parkinson’s disease
Authors: Tang Willcyn , Thundyil John , Lim Grace Gui Yin , Tng Teddy J W , Yeow Sean Qing Zhang , Nair Aditya , Chai Chou , Yao Tso-Pang , Lim Kah-Leong 
Published: December 2022

AbstractAbnormal lipid homeostasis has been observed in the brain of Parkinson’s disease (PD) patients and experimental models, although the mechanism underlying this phenomenon is unclear. Notably, previous studies have reported that the PD-linked protein Parkin functionally interacts with important lipid regulators, including Sterol Regulatory Element-Binding Proteins (SREBPs) and cluster of differentiation 36 (CD36). Here, we demonstrate a functional relationship between Parkin and lipoprotein lipase (LPL), a triglyceride lipase that is widely expressed in the brain. Using a human neuroblastoma cell line and a Parkin knockout mouse model, we demonstrate that Parkin expression level positively correlates with neuronal LPL protein level and activity. Importantly, our study identified SREBP2, a major regulator of sterol and fatty acid synthesis, as a potential mediator between Parkin and LPL. Supporting this, SREBP2 genetic ablation abolished Parkin effect on LPL expression. We further demonstrate that Parkin-LPL pathway regulates the formation of intracellular lipid droplets, and that this pathway is upregulated upon exposure to PD-linked oxidative stress induced by rotenone. Finally, we show that inhibition of either LPL or SREBP2 exacerbates rotenone-induced cell death. Taken together, our findings reveal a novel pathway linking Parkin, SREBP2 and LPL in neuronal lipid homeostasis that may be relevant to the pathogenesis of PD.
Identification and characterization of CsSRP43, a major gene controlling leaf yellowing in cucumber
Authors: Zhang Tingting , Dong Xiangyu , Yuan Xin , Hong Yuanyuan , Zhang Lingling , Zhang Xuan , Chen Shuxia 
Published: December 2022

Abstract
Mutants are crucial to extending our understanding of genes and their functions in higher plants. In this study a spontaneous cucumber mutant, yf, showed yellow color leaves, had significant decreases in related physiological indexes of photosynthesis characteristics, and had more abnormal chloroplasts and thylakoids. Inheritance analysis indicated that the yellow color of the leaf was controlled by a recessive nuclear locus, yf. A candidate gene, CsSRP43, encoding a chloroplast signal recognition particle 43 protein, was identified through map-based cloning and whole-genome sequence analysis. Alignment of the CsSRP43 gene homologs between both parental lines revealed a 7-kb deletion mutation including the promoter region and the coding sequence in the yf mutant. In order to determine if the CsSRP43 gene was involved in the formation of leaf color, the CRISPR/Cas9-mediate system was used to modify CsSRP43 in the 9930 background; two independent transgenic lines, srp43-1 and srp43-2, were generated, and they showed yellow leaves with abnormal chloroplasts and thylakoids. Transcriptomic analysis revealed that differentially expressed genes associated with the photosynthesis-related pathway were highly enriched between srp43-1 and wild type, most of which were significantly downregulated in line srp43-1. Furthermore, yeast two-hybrid and biomolecular fluorescence complementation assays were used to confirm that CsSRP43 directly interacted with LHCP and cpSRP54 proteins. A model was established to explain the molecular mechanisms by which CsSRP43 participates in the leaf color and photosynthesis pathway, and it provides a valuable basis for understanding the molecular and genetic mechanisms of leaf color in cucumber.
Novel insights into reproductive ageing and menopause from genomics
Authors: Das Arunika , Destouni Aspasia 
Published: December 2022

ABSTRACT
The post-reproductive phase or menopause in females is triggered by a physiological timer that depends on a threshold of follicle number in the ovary. Curiously, reproductive senescence appears to be decoupled from chronological age and is instead thought to be a function of physiological ageing. Ovarian ageing is associated with a decrease in oocyte developmental competence, attributed to a concomitant increase in meiotic errors. Although many biological hallmarks of general ageing are well characterized, the precise mechanisms underlying the programmed ageing of the female reproductive system remain elusive. In particular, the molecular pathways linking the external menopause trigger to the internal oocyte chromosome segregation machinery that controls fertility outcomes is unclear. However, recent large scale genomics studies have begun to provide insights into this process. Next-generation sequencing integrated with systems biology offers the advantage of sampling large datasets to uncover molecular pathways associated with a phenotype such as ageing. In this mini-review, we discuss findings from these studies that are crucial for advancing female reproductive senescence research. Targets identified in these studies can inform future animal models for menopause. We present three potential hypotheses for how external pathways governing ovarian ageing can influence meiotic chromosome segregation, with evidence from both animal models and molecular targets revealed from genomics studies. Although still in incipient stages, we discuss the potential of genomics studies combined with epigenetic age acceleration models for providing a predictive toolkit of biomarkers controlling menopause onset in women. We also speculate on future research directions to investigate extending female reproductive lifespan, such as comparative genomics in model systems that lack menopause. Novel genomics insights from such organisms are predicted to provide clues to preserving female fertility.
Effectiveness and Duration of Protection of a Fourth Dose of Coronavirus Disease 2019 Messenger RNA Vaccine Among Long-term Care Residents in Ontario, Canada
Authors: Grewal Ramandip , Nguyen Lena , Buchan Sarah A , Wilson Sarah E , Costa Andrew P , Kwong Jeffrey C 
Published: December 2022

Abstract
We estimated the effectiveness of a fourth dose of messenger RNA coronavirus disease 2019 vaccine against Omicron infections and severe outcomes over time among long-term care residents in Ontario, Canada. Fourth doses provide additional protection against Omicron-related outcomes, but the protection wanes over time, with more waning seen against infection than severe outcomes.
Proteomic Analysis of Hepatic Fibrosis in Human Immunodeficiency Virus–Associated Nonalcoholic Fatty Liver Disease Demonstrates Up-regulation of Immune Response and Tissue Repair Pathways
Authors: Fourman Lindsay T , Stanley Takara L , Ockene Mollie W , McClure Colin M , Toribio Mabel , Corey Kathleen E , Chung Raymond T , Torriani Martin , Kleiner David E , Hadigan Colleen M , Grinspoon Steven K 
Published: December 2022

Abstract

Background
Human immunodeficiency virus (HIV)–associated nonalcoholic fatty liver disease (NAFLD) is characterized by a high prevalence of hepatic fibrosis as a strong clinical predictor of all-cause and liver-specific mortality risk.

Methods
We leveraged data from an earlier clinical trial to define the circulating proteomic signature of hepatic fibrosis in HIV-associated NAFLD. A total of 183 plasma proteins within 2 high-multiplex panels were quantified at baseline and at 12 months (Olink Cardiovascular III; Immuno-Oncology).

Results
Twenty proteins were up-regulated at baseline among participants with fibrosis stages 2–3 versus 0–1. Proteins most differentially expressed included matrix metalloproteinase 2 (P &lt; .001), insulin-like growth factor–binding protein 7 (P = .001), and collagen α1(I) chain (P = .001). Proteins were enriched within pathways including response to tumor necrosis factor and aminopeptidase activity. Key proteins correlated directly with visceral adiposity and glucose intolerance and inversely with CD4+ T-cell count. Within the placebo-treated arm, 11 proteins differentially increased among individuals with hepatic fibrosis progression over a 12-month period (P &lt; .05).

Conclusions
Among individuals with HIV-associated NAFLD, hepatic fibrosis was associated with a distinct proteomic signature involving up-regulation of tissue repair and immune response pathways. These findings enhance our understanding of potential mechanisms and biomarkers of hepatic fibrosis in HIV.
Frissons in Dance
Authors: Nanay Bence 
Published: December 2022

Abstract
Musical frissons (or chills) have been at the forefront of both philosophical and psychological research on audience responses to music. The aim of this article is to argue that frissons also play an important role in the experience of dance performances. Following Jerrold Levinson’s distinction between sound-quality frissons and sound-structure frissons, the article zooms in on the concept of conflict-induced frissons, which feature prominently in a variety of art forms besides music, from film to literature, and it is of crucial importance for understanding the audience reaction to some dance performances. A case study of Pina Bausch’s choreographies is given to illustrate this point.
Mental Imagery and Poetry
Authors: Liu Michelle 
Published: December 2022

Abstract
Poetry evokes mental imagery in its readers. But how is mental imagery precisely related to poetry? This article provides a systematic treatment. It clarifies two roles of mental imagery in relation to poetry—as an effect generated by poetry and as an efficient means for understanding and appreciating poetry. The article also relates mental imagery to the discussion on the ‘heresy of paraphrase’. It argues against the orthodox view that the imagistic effects of poetry cannot be captured by prosaic paraphrase, but points to features of poetry that can shape aspects of mental imagery that are liable to be lost in paraphrase.
Characterizing variability of electronic health record-driven phenotype definitions
Authors: Brandt Pascal S , Kho Abel , Luo Yuan , Pacheco Jennifer A , Walunas Theresa L , Hakonarson Hakon , Hripcsak George , Liu Cong , Shang Ning , Weng Chunhua , Walton Nephi , Carrell David S , Crane Paul K , Larson Eric B , Chute Christopher G , Kullo Iftikhar J , Carroll Robert , Denny Josh , Ramirez Andrea , Wei Wei-Qi , Pathak Jyoti , Wiley Laura K , Richesson Rachel , Starren Justin B , Rasmussen Luke V 
Published: December 2022

AbstractObjectiveThe aim of this study was to analyze a publicly available sample of rule-based phenotype definitions to characterize and evaluate the variability of logical constructs used.Materials and MethodsA sample of 33 preexisting phenotype definitions used in research that are represented using Fast Healthcare Interoperability Resources and Clinical Quality Language (CQL) was analyzed using automated analysis of the computable representation of the CQL libraries.ResultsMost of the phenotype definitions include narrative descriptions and flowcharts, while few provide pseudocode or executable artifacts. Most use 4 or fewer medical terminologies. The number of codes used ranges from 5 to 6865, and value sets from 1 to 19. We found that the most common expressions used were literal, data, and logical expressions. Aggregate and arithmetic expressions are the least common. Expression depth ranges from 4 to 27.DiscussionDespite the range of conditions, we found that all of the phenotype definitions consisted of logical criteria, representing both clinical and operational logic, and tabular data, consisting of codes from standard terminologies and keywords for natural language processing. The total number and variety of expressions are low, which may be to simplify implementation, or authors may limit complexity due to data availability constraints.ConclusionsThe phenotype definitions analyzed show significant variation in specific logical, arithmetic, and other operators but are all composed of the same high-level components, namely tabular data and logical expressions. A standard representation for phenotype definitions should support these formats and be modular to support localization and shared logic.
Phosphorylation of PBX2, a novel downstream target of mTORC1, is determined by GSK3 and PP1
Authors: Wada Reona , Fujinuma Shun , Nakatsumi Hirokazu , Matsumoto Masaki , Nakayama Keiichi I 
Published: December 2022

Summary
Mechanistic target of rapamycin complex 1 (mTORC1) is a serine–threonine kinase that is activated by extracellular signals, such as nutrients and growth factors. It plays a key role in the control of various biological processes, such as protein synthesis and energy metabolism by mediating or regulating the phosphorylation of multiple target molecules, some of which remain to be identified. We have here reanalysed a large-scale phosphoproteomics data set for mTORC1 target molecules and identified pre–B cell leukemia transcription factor 2 (PBX2) as such a novel target that is dephosphorylated downstream of mTORC1. We confirmed that PBX2, but not other members of the PBX family, is dephosphorylated in an mTORC1 activity–dependent manner. Furthermore, pharmacological and gene knockdown experiments revealed that glycogen synthase kinase 3 (GSK3) and protein phosphatase 1 (PP1) are responsible for the phosphorylation and dephosphorylation of PBX2, respectively. Our results thus suggest that the balance between the antagonistic actions of GSK3 and PP1 determines the phosphorylation status of PBX2 and its regulation by mTORC1.
Optimization of workpiece processing based on the orthogonal double-chain differential evolution algorithm
Authors: Huang Xin , Lv Danju , Chen Xu , Xi Rui , Zi Jiali , Gao Mingyuan , Zhang Yan 
Published: December 2022

Abstract
An orthogonal double-chain differential evolution (ODCDE) algorithm is proposed to optimize the problem’s parameters for workpiece processing. ODCDE improves the differential evolution structure by changing the parcels into the orthogonal chains in the adaptive search range of the solution, which can avoid falling into local optimum, improve the solution precision, and speed up the convergence speed. The superiority of the proposed algorithm was proved by the function performance test on three sets of bench functions, which reached the first place in the set of 23 functions with other 11 optimal algorithms, ranked the second in the CEC2017 functions with other more recent 5 algorithms, and ranked the seventh in the CEC2011 functions with other 11 algorithms including AMO, SFS, and GSK algorithms. Finally, two kinds of optimal workpiece processing, the tubular column design and the multipass milling, are studied, and the results show that our algorithm performs better than other methods.
The efficacy of a machine learning algorithm for assessing tumour components as a prognostic marker of surgically resected stage IA lung adenocarcinoma
Authors: Terada Yukihiro , Isaka Mitsuhiro , Kawata Takuya , Mizuno Kiyomichi , Muramatsu Koji , Katsumata Shinya , Konno Hayato , Nagata Toshiyuki , Mizuno Tetsuya , Serizawa Masakuni , Ono Akira , Sugino Takashi , Shimizu Kimihiro , Ohde Yasuhisa 
Published: December 2022

Abstract

Background
The importance of the stromal components in tumour progression has been discussed widely, but their prognostic role in small size tumours with lepidic components is not fully understood. Applying digital tissue image analysis to whole-slide imaging may enhance the accuracy and reproducibility of pathological assessment. This study aimed to evaluate the prognostic value of tumour components of lung adenocarcinoma by measuring the dimensions of the tumour consisting elements separately, using a machine learning algorithm.

Methods
Between September 2002 and December 2016, 317 patients with surgically resected, pathological stage IA adenocarcinoma with lepidic components were analysed. We assessed the whole tumour area, including the lepidic components, and measured the epithelium, collagen, elastin areas and alveolar air space. We analysed the prognostic impact of each tumour component.

Results
The dimensions of the epithelium and collagen areas were independent significant risk factors for recurrence-free survival (hazard ratio, 8.38; 95% confidence interval, 1.14–61.88; P = 0.037, and hazard ratio, 2.58; 95% confidence interval, 1.14–5.83; P = 0.022, respectively). According to the subgroup analysis when combining the epithelium and collagen areas as risk factors, patients with tumours consisting of both large epithelium and collagen areas showed significantly poor prognoses (P = 0.002).

Conclusions
We assessed tumour components using a machine learning algorithm to stratify the post-operative prognosis of surgically resected stage IA adenocarcinomas. This method might guide the selection of patients with a high risk of recurrence.