bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modeling the Dynamics of Energetic Protons in Earth's Inner Magnetosphere
Authors: Lyu Xingzhi , Tu Weichao 
Published: March 2022

AbstractRecently, Van Allen Probes data have revealed the interesting energy‐dependent dynamics of energetic protons in Earth's inner magnetosphere. To quantify the role of radial diffusion and charge exchange to the observed energy‐dependent dynamics of ring current protons, a 1D radial diffusion model with charge exchange loss is implemented. The observed proton flux over the long‐term period of November 2012 to September 2013 is first converted to phase space densities, which are then simulated by our model driven by an outer boundary condition at L* = 5.5 derived from the data. The simulation results show that our model generally captures the transport and acceleration of energetic protons at μ = 30, 50, and 80 MeV/G and K = 0.11 G1/2 RE, suggesting that radial diffusion is the dominant source mechanism for >75 keV protons at L* = 3.5–5.5. In addition, the observed fast decay of protons at lower μ and slow decay at higher μ are well captured by the model, demonstrating the dominant role of charge exchange in explaining the observed energy‐dependent proton decay. For higher μ protons, prompt losses of protons on the time scale of hours are observed over a wide range of L*, which is too fast to be explained by charge exchange. Some of the prompt losses at high L* regions are reproduced by the model with outward radial diffusion to the outer boundary. However, many prompt losses observed at lower L* regions are not captured by the model, which could be due to other loss mechanisms including electromagnetic ion cyclotron wave scattering and field line curvature scattering.
Statistical Analysis of Convective Updrafts in Tropical Cyclone Rainbands Observed by Airborne Doppler Radar
Authors: Barron Nicholas R. , Didlake Anthony C. , Reasor Paul D. 
Published: March 2022

AbstractTen years of airborne Doppler radar observations are used to study convective updrafts' kinematic and reflectivity structures in tropical cyclone (TC) rainbands. An automated algorithm is developed to identify the strongest rainband updrafts across 12 hurricane‐strength TCs. The selected updrafts are then collectively analyzed by their frequency, radius, azimuthal location (relative to the 200–850 hPa environmental wind shear), structural characteristics, and secondary circulation (radial/vertical) flow pattern. Rainband updrafts become deeper and stronger with increasing radius. A wavenumber‐1 asymmetry arises, showing that in the downshear (upshear) quadrants of the TC, updrafts are more (less) frequent and deeper (shallower). In the downshear quadrants, updrafts primarily have in‐up‐out or in‐up‐in secondary circulation patterns. The in‐up‐out circulation is the most frequent pattern and has the deepest updraft and reflectivity tower. Upshear, the updrafts generally have out‐up‐in or in‐up‐in patterns. The radial flow of the updraft circulations largely follows the vortex‐scale radial flow shear‐induced asymmetry, being increased low‐level inflow (outflow) and midlevel outflow (inflow) in the downshear (upshear) quadrants. It is hypothesized that the convective‐scale circulations are significantly influenced by the vortex‐scale radial flow at the updraft base and top altitudes. Other processes of the convective life cycle, such as bottom‐up decay of aging convective updrafts due to increased low‐level downdrafts, can influence the base altitude and, thus, the base radial flow of the updraft circulation. The findings presented in this study support previous literature regarding convective‐scale patterns of organized rainband convection in a mature, sheared TC.
Multiplicative Non‐Gaussian Model Error Estimation in Data Assimilation
Authors: Pathiraja S. , van Leeuwen P. J. 
Published: March 2022

AbstractModel uncertainty quantification is an essential component of effective data assimilation. Model errors associated with sub‐grid scale processes are often represented through stochastic parameterizations of the unresolved process. Many existing Stochastic Parameterization schemes are only applicable when knowledge of the true sub‐grid scale process or full observations of the coarse scale process are available, which is typically not the case in real applications. We present a methodology for estimating the statistics of sub‐grid scale processes for the more realistic case that only partial observations of the coarse scale process are available. Model error realizations are estimated over a training period by minimizing their conditional sum of squared deviations given some informative covariates (e.g., state of the system), constrained by available observations and assuming that the observation errors are smaller than the model errors. From these realizations a conditional probability distribution of additive model errors given these covariates is obtained, allowing for complex non‐Gaussian error structures. Random draws from this density are then used in actual ensemble data assimilation experiments. We demonstrate the efficacy of the approach through numerical experiments with the multi‐scale Lorenz 96 system using both small and large time scale separations between slow (coarse scale) and fast (fine scale) variables. The resulting error estimates and forecasts obtained with this new method are superior to those from two existing methods.
Sub‐Annual to Interannual Arabian Sea Upwelling, Sea Surface Temperature, and Indian Monsoon Rainfall Reconstructed Using Congruent Micrometer‐Scale Climate Proxies
Authors: Napier Tiffany J. , Wörmer Lars , Wendt Jenny , Lückge Andreas , Rohlfs Nina , Hinrichs Kai‐Uwe 
Published: March 2022

AbstractThe Indian monsoon system impacts over 1 billion people, and rainfall from its southwest monsoon is critical for agriculture. Cool sea surface temperatures (SSTs) in the Arabian Sea have been associated with reduced monsoon rainfall and vice versa, although this relationship is difficult to examine due to scarce and short instrumental records. We utilize laminated Pakistan Margin sediments to reconstruct southwest monsoon rainfall and Arabian Sea SSTs at sub‐annual to multi‐annual resolution for the twentieth century. We applied paired sub‐mm mapping techniques to intact sediment core surfaces to measure elemental abundances and lipid biomarkers. The first principal component of the elemental results (PC1) explains 47% of the elemental variance and is driven by detrital lithogenic elements K, Ti, and Fe. PC1 is positively correlated with homogeneous India June‐September rainfall departures from 1903 to 1928 and 1949–1970 on a multi‐annual scale. Correlations in the remaining timespans are either negative or absent, likely driven by a combination of dam and barrage construction on the Hub and Indus Rivers and negative rainfall departures. We propose PC1 as a proxy for southwest monsoon rainfall on multi‐annual timescales prior to ∼1930. A dampened annual SST cycle is resolved with the alkenone paleothermometer, which also captures the interannual‐decadal trends of twentieth century Arabian Sea SSTs. We propose the crenarchaeol‐caldarchaeol tetraether index, sourced from planktonic Thaumarchaeota, as a delayed upwelling proxy for the western Arabian Sea. Our reconstructions corroborate the established relationship of reduced Arabian Sea upwelling leading to warmer SSTs and increased monsoon rainfall, and vice versa.
An Exploration of Bayesian Identification of Dominant Hydrological Mechanisms in Ungauged Catchments
Authors: Prieto Cristina , Le Vine Nataliya , Kavetski Dmitri , Fenicia Fabrizio , Scheidegger Andreas , Vitolo Claudia 
Published: March 2022

AbstractHydrological modeling of ungauged catchments, which lack observed streamflow data, is an important practical goal in hydrological sciences. A major challenge is to identify a model structure that reflects the hydrological processes relevant to the catchment of interest. This study contributes a Bayesian framework for identifying individual model mechanisms (process representations) from flow indices regionalized to the catchment of interest. We extend a method previously introduced for mechanism identification in gauged basins, by formulating the inference equations in the space of (regionalized) flow indices and by accounting for posterior parameter uncertainty. A flexible hydrological model is used to generate candidate mechanisms and model structures, followed by statistical hypothesis testing to identify “dominant” (more a posterior probable) model mechanisms. The proposed method is illustrated using real data and synthetic experiments based on 92 catchments from northern Spain, from which 16 catchments are treated as ungauged. 624 hydrological model structures from the flexible framework FUSE are employed. In real data experiments, the method identifies a dominant mechanism in 27% of 112 trials (processes and catchments). The most identifiable process is routing, whereas the least identifiable processes are percolation and unsaturated zone processes. In synthetic experiments, where “true” mechanisms are known, the reliability of method varies from 60% to 95% depending on the combined regionalization and hydrological error; the probability of making an identification remains stable at around 25%. More broadly, the study contributes perspectives on hydrological mechanism identification under data‐scarce conditions; limitations and opportunities for improvement are outlined.
Probabilistic Flood Hazard Mapping Considering Multiple Levee Breaches
Authors: Maranzoni A. , D’Oria M. , Mazzoleni M. 
Published: March 2022

AbstractProbabilistic methods are widely adopted for residual flood hazard assessment in flood‐prone areas protected by levees. Such methods can consider various sources of uncertainty, including breach location and flood event characteristics, and allow for the quantification of the result confidence. However, the possible occurrence of multiple levee breaches during the same flood event is usually disregarded. This paper presents a probabilistic method based on levee fragility functions and basic probability rules to estimate the probability of selected breach scenarios, including multiple breaching events. The flood hazard classification is based on inundation variables calculated for flood events of different return periods. A combined 1D‐2D hydrodynamic model is used for flood simulations. Probabilistic inundation extent maps and probabilistic flood hazard level maps are then created. Finally, probabilistic flood hazard estimates are summarized in a map of a suitable central tendency of the hazard level, coupled with a map of the Shannon entropy as an uncertainty indicator. This pair of statistical maps provides concise and effective information on a reference flood hazard along with the associated uncertainty. The method was applied to a region located along the middle reach of the Po River (northern Italy). Comparable central flood hazard estimates are obtained for the two sets of breaching events including or not including multiple breaches, with higher uncertainty if multiple breaches are considered. This result highlights the importance of considering multiple breaching events in flood risk management.
Microenvironmental stiffness mediates cytoskeleton re-organization in chondrocytes through laminin-FAK mechanotransduction
Authors: Zhou Chenchen , Duan Mengmeng , Guo Daimo , Du Xinmei , Zhang Demao , Xie Jing 
Published: March 2022

AbstractMicroenvironmental biophysical factors play a fundamental role in controlling cell behaviors including cell morphology, proliferation, adhesion and differentiation, and even determining the cell fate. Cells are able to actively sense the surrounding mechanical microenvironment and change their cellular morphology to adapt to it. Although cell morphological changes have been considered to be the first and most important step in the interaction between cells and their mechanical microenvironment, their regulatory network is not completely clear. In the current study, we generated silicon-based elastomer polydimethylsiloxane (PDMS) substrates with stiff (15:1, PDMS elastomer vs. curing agent) and soft (45:1) stiffnesses, which showed the Young’s moduli of ~450 kPa and 46 kPa, respectively, and elucidated a new path in cytoskeleton re-organization in chondrocytes in response to changed substrate stiffnesses by characterizing the axis shift from the secreted extracellular protein laminin β1, focal adhesion complex protein FAK to microfilament bundling. We first showed the cellular cytoskeleton changes in chondrocytes by characterizing the cell spreading area and cellular synapses. We then found the changes of secreted extracellular linkage protein, laminin β1, and focal adhesion complex protein, FAK, in chondrocytes in response to different substrate stiffnesses. These two proteins were shown to be directly interacted by Co-IP and colocalization. We next showed that impact of FAK on the cytoskeleton organization by showing the changes of microfilament bundles and found the potential intermediate regulators. Taking together, this modulation axis of laminin β1-FAK-microfilament could enlarge our understanding about the interdependence among mechanosensing, mechanotransduction, and cytoskeleton re-organization.
Intrauterine inflammation exacerbates maladaptive remodeling of the immature myocardium after preterm birth in lambs
Authors: Vrselja Amanda , Pillow J. Jane , Bensley Jonathan G. , Ellery Stacey J. , Ahmadi-Noorbakhsh Siavash , Moss Timothy J. , Black M. Jane 
Published: March 2022

AbstractBackgroundAntenatal conditions that are linked with preterm birth, such as intrauterine inflammation, can influence fetal cardiac development thereby rendering the heart more vulnerable to the effects of prematurity. We aimed to investigate the effect of intrauterine inflammation, consequent to lipopolysaccharide exposure, on postnatal cardiac growth and maturation in preterm lambs.MethodsPreterm lambs (~129 days gestational age) exposed antenatally to lipopolysaccharide or saline were managed according to contemporary neonatal care and studied at postnatal day 7. Age-matched fetal controls were studied at ~136 days gestational age. Cardiac tissue was sampled for molecular analyses and assessment of cardiac structure and cardiomyocyte maturation.ResultsLambs delivered preterm showed distinct ventricular differences in cardiomyocyte growth and maturation trajectories as well as remodeling of the left ventricular myocardium compared to fetal controls. Antenatal exposure to lipopolysaccharide resulted in further collagen deposition in the left ventricle and a greater presence of immune cells in the preterm heart.ConclusionsAdverse impacts of preterm birth on cardiac structure and cardiomyocyte growth kinetics within the first week of postnatal life are exacerbated by intrauterine inflammation. The maladaptive remodeling of the cardiac structure and perturbed cardiomyocyte growth likely contribute to the increased vulnerability to cardiac dysfunction following preterm birth.ImpactPreterm birth induces maladaptive cardiac remodeling and adversely impacts cardiomyocyte growth kinetics within the first week of life in sheep.These effects of prematurity on the heart are exacerbated when preterm birth is preceded by exposure to intrauterine inflammation, a common antecedent of preterm birth.Inflammatory injury to the fetal heart coupled with preterm birth consequently alters neonatal cardiac growth and maturation and thus, may potentially influence long-term cardiac function and health.
Efficacy of transcutaneous electrical nerve stimulation in people with pain after spinal cord injury: a meta-analysis
Authors: Yang Ye , Tang Yun , Qin Huiqing , Xu Jianwen 
Published: March 2022

AbstractStudy DesignMeta-analysis.ObjectivesThis study aimed to evaluate the effect of transcutaneous electrical nerve stimulation in people with pain after spinal cord injury by meta-analysis.MethodsReviewed PubMed, Embase, Cochrane library, as well as China National Knowledge Infrastructure (CNKI), Wanfang, and Vip databases to search the randomized controlled trials of pain after spinal cord injury through transcutaneous electrical nerve stimulation from the beginning of the library to March 2021, and analyze the literature with RevMan 5.3 software and the bias in the literature with STATA 12.0 software.ResultsThere are six randomized controlled trials in the study with 165 cases. 83 cases in the test group were given transcutaneous electrical nerve stimulation, and 82 cases in the control group used sham stimulation or other treatments. Meta-analysis results showed the experimental group’s visual analog scale (MD = −1.52, 95%CI, −2.44 to −0.60,P = 0.001) and short-form McGill pain questionnaire scores (MD = −0.70, 95% CI, −1.03 to −0.25,P = 0.002) were lower than those of the control group.ConclusionsTranscutaneous electrical nerve stimulation has some clinical therapeutic effects on persons with pain after spinal cord injury, but due to the lack of literature, the sample size is not large, and clinical trials need to be further improved later.
Morpholino-driven blockade of Dkk-1 in osteosarcoma inhibits bone damage and tumour expansion by multiple mechanisms
Authors: Pan Simin , Cesarek Michael , Godoy Carla , Co Cynthia M. , Schindler Catherine , Padilla Kelbi , Haskell Andrew , Barreda Heather , Story Christopher , Poole Roy , Dabney Alan , Gregory Carl A. 
Published: March 2022

AbstractBackgroundOsteosarcoma (OS) is the most common primary bone malignancy. Chemotherapy plays an essential role in OS treatment, potentially doubling 5-year event-free survival if tumour necrosis can be stimulated. The canonical Wnt inhibitor Dickkopf-1 (Dkk-1) enhances OS survival in part through upregulation of aldehyde-dehydrogenase-1A1 which neutralises reactive oxygen species originating from nutritional stress and chemotherapeutic challenge.MethodsA vivo morpholino (DkkMo) was employed to block the expression of Dkk-1 in OS cells. Cell mitosis, gene expression and bone destruction were measured in vitro and in vivo in the presence and absence of doxorubicin (DRB).ResultsDkkMo reduced the expression of Dkk-1 and Aldh1a1, reduced expansion of OS tumours, preserved bone volume and architecture and stimulated tumour necrosis. This was observed in the presence or absence of DRB.ConclusionThese results indicate that administration of DkkMo with or without chemotherapeutics can substantially improve OS outcome with respect to tumour expansion and osteolytic corruption of bone in experimental OS model.
GSDMD enhances cisplatin-induced apoptosis by promoting the phosphorylation of eIF2α and activating the ER-stress response
Authors: Zhang Qianyu , Huang Zixian , Rui Xi , Wang Yan , Wang Yongqiang , Zhou Yuwei , Chen Rui , Chen Yongju , Wang Yuepeng , Li Shihao , Li Haigang , Shen Ximing , Liang Yancan , Zhang Yin , Huang Zhiquan 
Published: March 2022

AbstractGSDMD is the key effector of pyroptosis, but its non-pyroptosis-related functions have seldom been reported. Here, we report that GSDMD is overexpressed in different types of tumours, including head and neck squamous-cell carcinoma, and it promotes the sensitivity of tumour cells to cisplatin. Unexpectedly, the enhanced cisplatin sensitivity is mediated by apoptosis but not pyroptosis, the well-known function of GSDMD. Furthermore, we found that GSDMD can activate the unfolded protein response by promoting the phosphorylation of eIF2α. Mechanistically, we demonstrated that GSDMD can directly bind to eIF2α and enhance the interaction between eIF2α and its upstream kinase PERK, leading to eIF2α phosphorylation. Consequently, the protein levels of ATF-4 were upregulated, downstream apoptosis-related proteins such as CHOP were activated, and apoptosis was induced. Remarkably, activation of endoplasmic-reticulum (ER) stress induced by GSDMD promotes cell apoptosis during cisplatin chemotherapy, thereby increasing the treatment sensitivity of tumours. Therefore, for the first time, our work reveals an unreported nonpyroptotic function of the classic pyroptosis protein GSDMD: it promotes cell apoptosis during cisplatin chemotherapy by inducing eIF2α phosphorylation and ER stress, which are related to the drug sensitivity of tumours. Our study also indicated that GSDMD might serve as a biomarker for cisplatin sensitivity.
Preferences for return of germline genome sequencing results for cancer patients and their genetic relatives in a research setting
Authors: Best Megan C. , Butow Phyllis , Savard Jacqueline , Jacobs Chris , Bartley Nicole , Davies Grace , Napier Christine E. , Ballinger Mandy L. , Thomas David M. , Biesecker Barbara , Tucker Katherine M. , Juraskova Ilona , Meiser Bettina , Schlub Timothy , Newson Ainsley J. 
Published: March 2022

AbstractGermline genome sequencing (GS) holds great promise for cancer prevention by identifying cancer risk and guiding prevention strategies, however research evidence is mixed regarding patient preferences for receiving GS results. The aim of this study was to discern preferences for return of results by cancer patients who have actually undergone GS. We conducted a mixed methods study with a cohort of cancer probands (n = 335) and their genetic relatives (n = 199) undergoing GS in a research setting. Both groups completed surveys when giving consent. A subset of participants (n = 40) completed semi-structured interviews. A significantly higher percentage of probands thought people would like to be informed about genetic conditions for which there is prevention or treatment that can change cancer risk compared to conditions for which there is no prevention or treatment (93% [311] versus 65% [216]; p < 0.001). Similar results were obtained for relatives (91% [180] versus 61% [121]; p < 0.001). Themes identified in the analysis of interviews were: (1) Recognised benefits of GS, (2) Balancing benefits with risks, (3) Uncertain results are perceived as unhelpful and (4) Competing obligations. While utility was an important discriminator in what was seen as valuable for this cohort, there was a variety of responses. In view of varied participant preferences regarding return of results, it is important to ensure patient understanding of test validity and identify individual choices at the time of consent to GS. The nature and value of the information, and a contextual understanding of researcher obligations should guide result return.
Population genetic differentiation and genomic signatures of adaptation to climate in an abundant lizard
Authors: Ruiz Miñano Maravillas , While Geoffrey M. , Yang Weizhao , Burridge Christopher P. , Salvi Daniele , Uller Tobias 
Published: March 2022

AbstractSpecies distributed across climatic gradients will typically experience spatial variation in selection, but gene flow can prevent such selection from causing population genetic differentiation and local adaptation. Here, we studied genomic variation of 415 individuals across 34 populations of the common wall lizard (Podarcis muralis) in central Italy. This species is highly abundant throughout this region and populations belong to a single genetic lineage, yet there is extensive phenotypic variation across climatic regimes. We used redundancy analysis to, first, quantify the effect of climate and geography on population genomic variation in this region and, second, to test if climate consistently sorts specific alleles across the landscape. Climate explained 5% of the population genomic variation across the landscape, about half of which was collinear with geography. Linear models and redundancy analyses identified loci that were significantly differentiated across climatic regimes. These loci were distributed across the genome and physically associated with genes putatively involved in thermal tolerance, regulation of temperature-dependent metabolism and reproductive activity, and body colouration. Together, these findings suggest that climate can exercise sufficient selection in lizards to promote genetic differentiation across the landscape in spite of high gene flow.