bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Impact of Cylinder Diameter Distribution on Longitudinal and Transverse Dispersion Within Random Cylinder Arrays
Authors: Stovin V. R. , Sonnenwald F. , Golzar M. , Guymer I. 
Published: March 2022

AbstractNumerous studies focus on flow and mixing within cylinder arrays because of their similarity to vegetated flows. Randomly distributed cylinders are considered to be a closer representation of the natural distribution of vegetation stems compared with regularly distributed arrays. This study builds on previous work based on a single, fixed, cylinder diameter to consider non‐uniform cylinder diameter distributions. The flow fields associated with arrays of randomly distributed cylinders are modeled in two dimensions using the ANSYS Fluent Computational Fluid Dynamics software with Reynolds Stress Model turbulence closure. A transient scalar transport model is used to characterize longitudinal and transverse mixing (DxandDy) within each geometry. The modeling approach is validated against independent laboratory data, and the dispersion coefficients are shown to be comparable with previous experimental studies. Eight different cylinder diameter configurations (six uniform and two non‐uniform) are considered, each at 20 different solid volume fractions and with seven different transverse positions for the injection location. The new dispersion data cover a broad range of solid volume fractions, for which simultaneous estimates ofDxandDyhave not been available previously. There are no systematic differences in non‐dimensionalDxandDybetween uniform and non‐uniform cylinder diameter distributions. When non‐dimensionalized by cylinder diameter, both dispersion coefficients are independent of solid volume fraction. When non‐dimensionalized by cylinder spacing, both longitudinal and transverse dispersion can be described as linear functions of the ratio of cylinder diameter to cylinder spacing.
Probabilistic Characterization of Sweep and Ejection Events in Turbulent Flows and Its Implications on Sediment Transport
Authors: Wu Kuan‐Ting , Tsai Christina W. , Wu Meng‐Jie 
Published: March 2022

AbstractTurbulent boundary layers are populated by a hierarchy of recurrent structures normally referred to as “coherent structures.” Among others, ejection and sweep events are critical coherent structures responsible for sediment transport. This study focuses on gaining a better understanding of the spatial‐–temporal probabilistic characteristics of sweep and ejection events. The existence of uniform momentum zones (UMZs) is demonstrated to affect the spatial distribution of large‐scale motions (LSMs), and the ejection and sweep events tend to present near UMZ edges where interfacial layers of high shears exist. In this study, UMZ detection is employed to identify coherent structures. The conditional velocity decomposition is then applied to the available direct numerical simulation (DNS) flow data after UMZ edges were determined. Based on the integrated criterion for distinguishing ejection and sweep events, one can determine the probabilistic characteristics of coherent structures such as the center point, wall‐normal length, and streamwise length. Physical insights such as joint probability density functions of wall‐normal length and streamwise length can be established. The attached and detached features of the sweeps and ejections can then be classified and characterized, respectively. Durations of sweep and ejection events are demonstrated to follow a lognormal distribution in this study. The occurrence ratio of sweep events in the (LSMs) is quantified from the DNS data. The implications of the results on sediment transport are discussed. The contributions of coherent structures with respect to wall‐normal height and the intermittency and geometrical properties of the coherent structures are presented.
Debris‐Flood Hazard Assessments in Steep Streams
Authors: Jakob Matthias , Davidson Sarah , Bullard Gemma , Busslinger Matthias , Collier‐Pandya Beatrice , Grover Patrick , Lau Carie‐Ann 
Published: March 2022

AbstractDebris floods most commonly occur in steep mountain channels and on their alluvial fans but can also occur on small gravel bed rivers with watershed areas up to several hundred square kilometers. This became obvious during July 2021 and November 2021 debris floods in northwestern Germany and southwestern British Columbia, Canada. We subdivide debris floods into three categories: those triggered by a supra‐critical bed shear stress ratio, form by dilution from debris flows, and resulting from outbreak floods. This trichotomy challenges traditional hazard assessments; debris floods classify as a fluvial process, yet their destructive mechanics are difficult to characterize. Key hazards interact spatially and temporally in debris floods: inundation, scour, sediment transport and deposition and bank erosion. We describe approaches to quantify hazards by systematically accounting for these processes and introduce a novel approach for hazard quantification and mapping in which flow velocity, depth, and presumed fluid density are combined with the annual event frequency for all event scenarios. The derivative “composite hazard maps” are equally valid for debris floods and debris flows. Isolines of bank erosion based on a probabilistic analysis of a physically based model are added to capture the potential of debris floods to abruptly widen their channels. Substantial challenges remain, specifically in the reliable prediction of sediment transport and progressive bank erosion. Our intention is to homogenize debris‐flood hazard assessments and especially mapping methodologies. This could allow for systematic integration with landuse policies assuring consistency among approaches executed by practitioners acting in this field.
Correction of River Bathymetry Parameters Using the Stage–Discharge Rating Curve
Authors: Zhou Xudong , Revel Menaka , Modi Prakat , Shiozawa Takuto , Yamazaki Dai 
Published: March 2022

AbstractRiver bathymetry is an important parameter for hydrodynamic modeling; however, it is associated with large bias because direct large‐scale measurements are impractical. Recent studies adjusted river bathymetry data based on assessment of the difference between modeled and observed water surface elevation (WSE); however, model uncertainties in river discharge can lead to unintended errors in correcting river bathymetry. In this study, we propose a simple but robust and rational correction method of river bathymetry using the bias between stage–discharge rating curves rather than WSE time series data. The rating curve represents the internal characteristics of the river section, and is not sensitive to the instantaneous simulated discharge errors. Our results showed that the corrected river bathymetry are robust to bias in runoff as they converged among experiments driven by noise‐corrupted or multimodel runoff forcing. Evaluation with the corrected river bathymetry against virtual truth demonstrated that the new method reduced 0.85–1.12 m of the absolute bias than the result from the conventional method. The deviation among the results reduced by more than 70% particularly in river sections with no backwater effects. Evaluation of the corrected river model output also showed the advantage of rating‐curve bias correction, as the simulated WSE is reasonably better only with better runoff and it does not conceal errors in runoff inputs. Given the difficulty of eliminating discharge errors and bias in runoff, a method for correcting river bathymetry that is free from discharge and runoff errors is important for improving hydrodynamic modeling.
The Role of Global Data Sets for Riverine Flood Risk Management at National Scales
Authors: Bernhofen Mark V. , Cooper Sarah , Trigg Mark , Mdee Anna , Carr Andrew , Bhave Ajay , Solano‐Correa Yady Tatiana , Pencue‐Fierro Edgar Leonairo , Teferi Ermias , Haile Alemseged Tamiru , Yusop Zulkifli , Alias Nor Eliza , Sa'adi Zulfaqar , Bin Ramzan Muhamad Anwar , Dhanya C. T. , Shukla Prabhakar 
Published: March 2022

AbstractOver the last two decades, several data sets have been developed to assess flood risk at the global scale. In recent years, some of these data sets have become detailed enough to be informative at national scales. The use of these data sets nationally could have enormous benefits in areas lacking existing flood risk information and allow better flood management decisions and disaster response. In this study, we evaluate the usefulness of global data for assessing flood risk in five countries: Colombia, England, Ethiopia, India, and Malaysia. National flood risk assessments are carried out for each of the five countries using six data sets of global flood hazard, seven data sets of global population, and three different methods for calculating vulnerability. We also conduct interviews with key water experts in each country to explore what capacity there is to use these global data sets nationally. We find that the data sets differ substantially at the national level, and this is reflected in the national flood risk estimates. While some global data sets could be of significant value for national flood risk management, others are either not detailed enough, or too outdated to be relevant at this scale. For the relevant global data sets to be used most effectively for national flood risk management, a country needs a functioning, institutional framework with capability to support their use and implementation.
Molecular functions and therapeutic applications of exosomal noncoding RNAs in cancer
Authors: Liu Qin-Wen , He Yan , Xu Wen Wen 
Published: March 2022

AbstractCancer is one of the most difficult diseases in human society. Therefore, it is urgent for us to understand its pathogenesis and improve the cure rate. Exosomes are nanoscale membrane vesicles formed by a variety of cells through endocytosis. As a new means of intercellular information exchange, exosomes have attracted much attention. Noncoding RNAs exist in various cell compartments and participate in a variety of cellular reactions; in particular, they can be detected in exosomes bound to lipoproteins and free circulating molecules. Increasing evidence has suggested the potential roles of exosomal noncoding RNAs in the progression of tumors. Herein, we present a comprehensive update on the biological functions of exosomal noncoding RNAs in the development of cancer. Specifically, we mainly focus on the effects of exosomal noncoding RNAs, including microRNAs, circular RNAs, long noncoding RNAs, small nuclear RNAs, and small nucleolar RNAs, on tumor growth, metastasis, angiogenesis, and chemoresistance. Moreover, we outline the current clinical implications concerning exosomal noncoding RNAs in cancer treatment.
Characteristics of solar-irradiance spectra from measurements, modeling, and theoretical approach
Authors: Thuillier Gerard , Zhu Ping , Snow Martin , Zhang Peng , Ye Xin 
Published: March 2022

AbstractAn accurate solar-irradiance spectrum is needed as an input to any planetary atmosphere or climate model. Depending on the spectral characteristics of the chosen model, uncertainties in the irradiance may introduce significant differences in atmospheric and climate predictions. This is why several solar spectral-irradiance data sets have been published during the last decade. They have been obtained by different methods: either measurements from a single instrument or a composite of different spectra, or they are theoretical or semi-empirical solar models. In this paper, these spectral datasets will be compared in terms of irradiance, power per spectral interval, their derived solar-atmosphere brightness temperature, and time series. Whatever the different sources of these spectra are, they generally agree to within their quoted accuracy. The solar-rotation effect simultaneously observed by SORCE and PREMOS–PICARD is accurately measured. The 11-year long-term variability remains a difficult task, given the weak activity of solar cycle 24 and long-term instrument aging.
Chiral carbon dots: synthesis, optical properties, and emerging applications
Authors: Döring Aaron , Ushakova Elena , Rogach Andrey L. 
Published: March 2022

AbstractCarbon dots are luminescent carbonaceous nanoparticles that can be endowed with chiral properties, making them particularly interesting for biomedical applications due to their low cytotoxicity and facile synthesis. In recent years, synthetic efforts leading to chiral carbon dots with other attractive optical properties such as two-photon absorption and circularly polarized light emission have flourished. We start this review by introducing examples of molecular chirality and its origins and providing a summary of chiroptical spectroscopy used for its characterization. Then approaches used to induce chirality in nanomaterials are reviewed. In the main part of this review we focus on chiral carbon dots, introducing their fabrication techniques such as bottom-up and top-down chemical syntheses, their morphology, and optical/chiroptical properties. We then consider emerging applications of chiral carbon dots in sensing, bioimaging, and catalysis, and conclude this review with a summary and future challenges.
Enabling robust and hour-level organic long persistent luminescence from carbon dots by covalent fixation
Authors: Jiang Kai , Wang Yuci , Lin Cunjian , Zheng Licheng , Du Jiaren , Zhuang Yixi , Xie Rongjun , Li Zhongjun , Lin Hengwei 
Published: March 2022

AbstractThe first carbon dot (CD)-based organic long persistent luminescence (OLPL) system exhibiting more than 1 h of duration was developed. In contrast to the established OLPL systems, herein, the reported CDs-based system (named m-CDs@CA) can be facilely and effectively fabricated using a household microwave oven, and more impressively, its LPL can be observed under ambient conditions and even in aqueous media. XRD and TEM characterizations, afterglow decay, time-resolved spectroscopy, and ESR analysis were performed, showing the successful composition of CDs and CA, the formation of exciplexes and long-lived charged-separated states. Further studies suggest that the production of covalent bonds between CA and CDs plays pivotal roles in activating LPL and preventing its quenching from oxygen and water. To the best of our knowledge, this is a very rare example of an OLPL system that exhibits hour-level afterglow under ambient conditions. Finally, applications of m-CDs@CA in glow-in-the-dark paints for emergency signs and multicolored luminous pearls were preliminarily demonstrated. This work may provide new insights for the development of rare-earth-free and robust OLPL materials.
Deep learning autofluorescence-harmonic microscopy
Authors: Shen Binglin , Liu Shaowen , Li Yanping , Pan Ying , Lu Yuan , Hu Rui , Qu Junle , Liu Liwei 
Published: March 2022

AbstractLaser scanning microscopy has inherent tradeoffs between imaging speed, field of view (FOV), and spatial resolution due to the limitations of sophisticated mechanical and optical setups, and deep learning networks have emerged to overcome these limitations without changing the system. Here, we demonstrate deep learning autofluorescence-harmonic microscopy (DLAM) based on self-alignment attention-guided residual-in-residual dense generative adversarial networks to close the gap between speed, FOV, and quality. Using the framework, we demonstrate label-free large-field multimodal imaging of clinicopathological tissues with enhanced spatial resolution and running time advantages. Statistical quality assessments show that the attention-guided residual dense connections minimize the persistent noise, distortions, and scanning fringes that degrade the autofluorescence-harmonic images and avoid reconstruction artifacts in the output images. With the advantages of high contrast, high fidelity, and high speed in image reconstruction, DLAM can act as a powerful tool for the noninvasive evaluation of diseases, neural activity, and embryogenesis.
Apolipoprotein E Isoform-specific changes related to stress and trauma exposure
Authors: Torres Eileen Ruth S. , Luo Jenny , Boehnlein James K. , Towns Daniel , Kinzie J. David , DeBarber Andrea E. , Raber Jacob 
Published: March 2022

AbstractPost-Traumatic Stress Disorder (PTSD) is a highly prevalent mental health disorder. Due to the high level of variability in susceptibility and severity, PTSD therapies are still insufficient. In addition to environmental exposures, genetic risks play a prominent role and one such factor is apolipoprotein E. The protein (apoE) is functionally involved in cholesterol transport and metabolism and exists as 3 major isoforms in humans: E2, E3, and E4. To model the role of apolipoprotein E isoform in stress-related changes in behavior and cognition, female and male mice (3–5 months of age) expressing E2, E3, or E4 were used. Mice were either placed into control groups or exposed to chronic variable stress (CVS), which has been shown to induce PTSD-like behavioral and neuroendocrine changes. E2 mice showed a unique response to CVS compared to E3 and E4 mice that included impaired spatial learning and memory, increased adrenal gland weight, and no increase in glucocorticoid receptor protein levels (normalized to apoE levels). In addition, the cholesterol metabolite 7-ketocholesterol was elevated in the cortex after CVS in E3 and E4, but not E2 female mice. E2 confers unique changes in behavioral, cognitive, and biomarker profiles after stress exposure and identify 7-ketocholesterol as a possible novel biomarker of the traumatic stress response. We further explored the relationship between E2 and PTSD in an understudied population by genotyping 102 patients of Cambodian and Vietnamese ethnicity. E2 carriers demonstrated a higher odds ratio of having a PTSD diagnosis compared to E3/E3 carriers, supporting that the E2 genotype is associated with PTSD diagnosis after trauma exposure in this population.
Effects of APOE4 allelic dosage on lipidomic signatures in the entorhinal cortex of aged mice
Authors: Miranda André Miguel , Ashok Archana , Chan Robin Barry , Zhou Bowen , Xu Yimeng , McIntire Laura Beth , Area-Gomez Estela , Di Paolo Gilbert , Duff Karen E. , Oliveira Tiago Gil , Nuriel Tal 
Published: March 2022

AbstractApolipoprotein E ε4 (APOE4) is the primary genetic risk factor for the late-onset form of Alzheimer’s disease (AD). Although the reason for this association is not completely understood, researchers have uncovered numerous effects of APOE4 expression on AD-relevant brain processes, including amyloid beta (Aβ) accumulation, lipid metabolism, endosomal-lysosomal trafficking, and bioenergetics. In this study, we aimed to determine the effect of APOE4 allelic dosage on regional brain lipid composition in aged mice, as well as in cultured neurons. We performed a targeted lipidomic analysis on an AD-vulnerable brain region (entorhinal cortex; EC) and an AD-resistant brain region (primary visual cortex; PVC) from 14–15 month-old APOE3/3, APOE3/4, and APOE4/4 targeted replacement mice, as well as on neurons cultured with conditioned media from APOE3/3 or APOE4/4 astrocytes. Our results reveal that the EC possesses increased susceptibility to APOE4-associated lipid alterations compared to the PVC. In the EC, APOE4 expression showed a dominant effect in decreasing diacylglycerol (DAG) levels, and a semi-dominant, additive effect in the upregulation of multiple ceramide, glycosylated sphingolipid, and bis(monoacylglycerol)phosphate (BMP) species, lipids known to accumulate as a result of endosomal-lysosomal dysfunction. Neurons treated with conditioned media from APOE4/4 vs. APOE3/3 astrocytes showed similar alterations of DAG and BMP species to those observed in the mouse EC. Our results suggest that APOE4 expression differentially modulates regional neuronal lipid signatures, which may underlie the increased susceptibility of EC-localized neurons to AD pathology.
Arsenic alters nitric oxide signaling similar to autism spectrum disorder and Alzheimer’s disease-associated mutations
Authors: Tripathi Manish Kumar , Kartawy Maryam , Ginzburg Shelly , Amal Haitham 
Published: March 2022

AbstractEpidemiological studies have proven that exposure to Arsenic (AS) leads to the development of many neurological disorders. However, few studies have investigated its molecular mechanisms in the brain. Our previous work has revealed nitric oxide (NO)-mediated apoptosis and SNO reprogramming in the cortex following arsenic treatment, yet the role of NO and S-nitrosylation (SNO) in AS-mediated neurotoxicity has not been investigated. Therefore, we have conducted a multidisciplinary in-vivo study in mice with two different doses of Sodium Arsenite (SA) (0.1 ppm and 1 ppm) in drinking water. We used the novel SNOTRAP-based mass spectrometry method followed by the bioinformatics analysis, Western blot validation, and five different behavioral tests. Bioinformatics analysis of SA-treated mice showed significant SNO-enrichment of processes involved in mitochondrial respiratory function, endogenous antioxidant systems, transcriptional regulation, cytoskeleton maintenance, and regulation of apoptosis. Western blotting showed increased levels of cleaved PARP-1 and cleaved caspase-3 in SA-treated mice consistent with SA-induced apoptosis. Behavioral studies showed significant cognitive dysfunctions similar to those of Autism spectrum disorder (ASD) and Alzheimer’s disease (AD). A comparative analysis of the SNO-proteome of SA-treated mice with two transgenic mouse strains, models of ASD and AD, showed molecular convergence of SA environmental neurotoxicity and the genetic mutations causing ASD and AD. This is the first study to show the effects of AS on SNO-signaling in the striatum and hippocampus and its effects on behavioral characteristics. Finally, further investigation of the NO-dependent mechanisms of AS-mediated neurotoxicity may reveal new drug targets for its prevention.
Molecular rhythm alterations in prefrontal cortex and nucleus accumbens associated with opioid use disorder
Authors: Xue Xiangning , Zong Wei , Glausier Jill R. , Kim Sam-Moon , Shelton Micah A. , Phan BaDoi N. , Srinivasan Chaitanya , Pfenning Andreas R. , Tseng George C. , Lewis David A. , Seney Marianne L. , Logan Ryan W. 
Published: March 2022

AbstractSevere and persistent disruptions to sleep and circadian rhythms are common in people with opioid use disorder (OUD). Preclinical evidence suggests altered molecular rhythms in the brain modulate opioid reward and relapse. However, whether molecular rhythms are disrupted in the brains of people with OUD remained an open question, critical to understanding the role of circadian rhythms in opioid addiction. Using subjects’ times of death as a marker of time of day, we investigated transcriptional rhythms in the brains of subjects with OUD compared to unaffected comparison subjects. We discovered rhythmic transcripts in both the dorsolateral prefrontal cortex (DLPFC) and nucleus accumbens (NAc), key brain areas involved in OUD, that were largely distinct between OUD and unaffected subjects. Fewer rhythmic transcripts were identified in DLPFC of subjects with OUD compared to unaffected subjects, whereas in the NAc, nearly double the number of rhythmic transcripts was identified in subjects with OUD. In NAc of subjects with OUD, rhythmic transcripts peaked either in the evening or near sunrise, and were associated with an opioid, dopamine, and GABAergic neurotransmission. Associations with altered neurotransmission in NAc were further supported by co-expression network analysis which identified OUD-specific modules enriched for transcripts involved in dopamine, GABA, and glutamatergic synaptic functions. Additionally, rhythmic transcripts in DLPFC and NAc of subjects with OUD were enriched for genomic loci associated with sleep-related GWAS traits, including sleep duration and insomnia. Collectively, our findings connect transcriptional rhythm changes in opioidergic, dopaminergic, GABAergic signaling in the human brain to sleep-related traits in opioid addiction.