bluuebunny/crossref_metadata_2025_split huggingface dataset:
Debris Flows, Boulders and Constrictions: A Simple Framework for Modeling Jamming, and Its Consequences on Outflow
Authors: Piton Guillaume , Goodwin Saoirse Robin , Mark Emily , Strouth Alex 
Published: April 2022

AbstractLarge boulders can jam in constrictions, both in canyons and man‐made structures (e.g., slit‐dams). Boulder jamming occurs stochastically, and partially governs the outflow rate of debris flow material. Explicit hydro‐mechanical models of boulder‐laden flows are too computationally demanding to study this stochasticity. This study presents a new framework implemented into a numerical program. This program encapsulates basic hydraulic equations and criteria predicting boulder blockage at narrow sections, along with a simple statistical way to compute boulder sizes and numbers. The program applies empirical estimates by experts of the average number of boulders in a deposit to evaluate how equivalent multi‐phase flows would interact with a constriction. The model stochastically generates boulders that can obstruct the constriction(s). The program outputs simple descriptions of the upstream flow level over time, as well as the downstream outlet discharge rate and volume. The model is fast (5–30 s per run), allowing uncertainty propagation analyses of interactions between flows, boulders and constrictions. Interaction between both low‐ and high‐risk flows can be quickly evaluated for different scenarios. For uncertainty propagation, we use possibility theory, which accommodates uncertainties relevant to debris flows. The framework gives practitioners a much‐needed generalized approach for understanding the long‐term behavior of boulder‐laden flows through canyons, or for designing engineered structures. Finally, we apply the model to a field case – the design of a proposed North American slit‐dam – thence elucidating the design requirements for effective flow control. We found that horizontal bars are necessary for dependably controlling outflow from this structure.
Enhance the delivery of light energy ultra-deep into turbid medium by controlling multiple scattering photons to travel in open channels
Authors: Cao Jing , Yang Qiang , Miao Yusi , Li Yan , Qiu Saijun , Zhu Zhikai , Wang Pinghe , Chen Zhongping 
Published: April 2022

AbstractMultiple light scattering is considered as the major limitation for deep imaging and focusing in turbid media. In this paper, we present an innovative method to overcome this limitation and enhance the delivery of light energy ultra-deep into turbid media with significant improvement in focusing. Our method is based on a wide-field reflection matrix optical coherence tomography (RM-OCT). The time-reversal decomposition of the RM is calibrated with the Tikhonov regularization parameter in order to get more accurate reversal results deep inside the scattering sample. We propose a concept named model energy matrix, which provides a direct mapping of light energy distribution inside the scattering sample. To the best of our knowledge, it is the first time that a method to measure and quantify the distribution of beam intensity inside a scattering sample is demonstrated. By employing the inversion of RM to find the matched wavefront and shaping with a phase-only spatial light modulator, we succeeded in both focusing a beam deep (~9.6 times of scattering mean free path, SMFP) inside the sample and increasing the delivery of light energy by an order of magnitude at an ultra-deep (~14.4 SMFP) position. This technique provides a powerful tool to understand the propagation of photon in a scattering medium and opens a new way to focus light inside biological tissues.
NUPR1 promotes the proliferation and metastasis of oral squamous cell carcinoma cells by activating TFE3-dependent autophagy
Authors: Fan Tengfei , Wang Xiaoning , Zhang Sheng , Deng Ping , Jiang Yi , Liang Yidan , Jie Sheng , Wang Qing , Li Chuwen , Tian Guocai , Zhang Zhen , Ren Zhenhu , Li Bo , Chen Yanrong , He Zhijing , Luo Yan , Chen Mingliang , Wu Hanjiang , Yu Zhengping , Pi Huifeng , Zhou Zhou , Zhang Zhiyuan 
Published: April 2022

AbstractOral squamous cell carcinoma (OSCC) is the most common type of oral malignancy, and metastasis accounts for the poor prognosis of OSCC. Autophagy is considered to facilitate OSCC development by mitigating various cellular stresses; nevertheless, the mechanisms of autophagy in OSCC cell proliferation and metastasis remain unknown. In our study, high-sensitivity label-free quantitative proteomics analysis revealed nuclear protein 1 (NUPR1) as the most significantly upregulated protein in formalin-fixed paraffin-embedded tumour samples derived from OSCC patients with or without lymphatic metastasis. Moreover, NUPR1 is aberrantly expressed in the OSCC tissues and predicts low overall survival rates for OSCC patients. Notably, based on tandem mass tag-based quantitative proteomic analysis between stable NUPR1 knockdown OSCC cells and scrambled control OSCC cells, we confirmed that NUPR1 maintained autophagic flux and lysosomal functions by directly increasing transcription factor E3 (TFE3) activity, which promoted OSCC cell proliferation and metastasis in vitro and in vivo. Collectively, our data revealed that the NUPR1–TFE3 axis is a critical regulator of the autophagic machinery in OSCC progression, and this study may provide a potential therapeutic target for the treatment of OSCC.
Genetic and geographical delineation of zoonotic vector-borne helminths of canids
Authors: Laidoudi Younes , Bedjaoui Samia , Latrofa Maria Stefania , Fanelli Angela , Dantas-Torres Filipe , Otranto Domenico 
Published: April 2022

AbstractSeveral zoonotic vector-borne helminths (VBHs) infesting canids cause serious veterinary and medical diseases worldwide. Increasing the knowledge about their genetic structures is pivotal to identify them and therefore to settle effective surveillance and control measures. To overcome the limitation due to the heterogeneity of large DNA sequence-datasets used for their genetic characterization, available cytochrome c oxidase subunit 1 (cox1) (n = 546) and the 12S rRNA (n = 280) sequences were examined using combined bioinformatic approach (i.e., distance-clustering, maximum likelihood phylogeny and phylogenetic evolutionary placement). Out of the 826 DNA available sequences from GenBank, 94.7% were characterized at the haplotype level regardless sequence size, completeness and/or their position. A total of 89 different haplotypes were delineated either by cox1 (n = 35), 12S rRNA (n = 21) or by both genes (n = 33), for 14 VBHs (e.g., Acanthocheilonema reconditum, Brugia spp., Dirofilaria immitis, Dirofilaria repens, Onchocerca lupi and Thelazia spp.). Overall, the present approach could be useful for studying global genetic diversity and phylogeography of VBHs. However, as barcoding sequences were restricted to two mitochondrial loci (cox1 and 12S rRNA), the haplotype delineation proposed herein should be confirmed by the characterization of other nuclear loci also to overcome potential limitations caused by the heteroplasmy phenomenon within the mitogenome of VBHs.
Quantum versus classical correlations in a double cavity optomechanical system
Authors: Lakhfif Abderrahim , Hidki Abdelkader , El Qars Jamal , Nassik Mostafa 
Published: April 2022

Abstract
In a bipartite quantum state, where the total correlations can be divided into classical and quantum parts, Henderson and Vedral (2001 J. Phys. A: Math. Gen.
34 6899) have conjectured that classical correlations should not be less than quantum ones. Here, we consider two symmetrical states of two driven optomechanical cavities coupled to a squeezed photon source and exposed to Markovian noise and damping. The total and quantum correlations are systematically quantified by quantum mutual information and quantum discord respectively. Interestingly, we analytically demonstrate that classical correlations in the considered two-mode Gaussian states are always superior to quantum ones, whatever the physical and environmental parameters are. Moreover, using experimentally accessible parameters, we show numerically the existence of a domination of classical correlations over quantum ones under various circumstances. Finally, we found that quantum, as well as classical correlations, have similar behaviors under the effect of thermal decoherence, squeezing and optomechanical coupling. Yet, classical correlations are more strong and robust.
Controlled engineering of a vortex-bright soliton dynamics using a constant driving force
Authors: Wang Wenlong 
Published: April 2022

Abstract
A vortex-bright (VB) soliton can precess around a fixed point. Here, we find numerically that the fixed point and the associated precessional orbits can be shifted by applying a constant driving force on the bright component, the displacement is proportional to the force with a minus sign. This robust dynamics is then discussed theoretically by treating the VB soliton as an effective point particle. By appropriately tuning the force, the VB soliton can be guided following an arbitrary trajectory with very weak density modulations, including that it can be repeatedly pinned and released at will. This finding opens a highly flexible and controllable approach of engineering the dynamics of vortical structures in Bose–Einstein condensates.
Spatial and spectral variations of high-order harmonics generated in noble gases
Authors: Iqbal M , Boltaev G S , Abbasi N , Ganeev R A , Alnaser A S 
Published: April 2022

Abstract
We report on the spatial and spectral variation of high-order harmonics generation from noble gases when driven by high-repetition rate femtosecond laser with different peak intensity and polarization states. Ar, Xe, and Kr were chosen for the generation of coherent extreme ultraviolet radiation. We observe that increasing the intensity of the driving pulses (DPs) leads to disappearance of harmonics yield in the on-axis part of the spatial distribution of the harmonics in Xe target, contrary to Ar and Kr. This observation is attributed to the higher ionization potential of the latter gases. Spectral depletion of harmonics generated in Ar and Xe using radially and azimuthally polarized Gaussian–Laguerre two-color DPs is also observed. The significant depletion in the spectral distribution of harmonics is obtained when two-color pump (TCP) scheme is applied. We demonstrate how TCP scheme with azimuthally polarized DPs can be used as a tool to control the spectral distribution of harmonics generated from gas atoms during strong field by utilizing the presence of second harmonic electromagnetic field.
Highly linear capacitive tactile sensor with elastic dome-shaped electrodes
Authors: Ye Jinhua , Chen Kaixuan , Chen Liting , You Zhaoming , Jiang Jinchao , Wu Haibin 
Published: April 2022

Abstract
Capacitive tactile sensors have been widely used for electronic skins and human-machine interfaces due to their high sensitivity, low power consumption, and fast response. Despite great advances in improving the sensitivity of the sensors through structural design or advanced material selection, achieving linear response over a broad detection range for pressure sensing is still a great challenge. Herein, a capacitive tactile sensor with elastic dome-shaped electrode is reported. We find that the elastic dome-shaped electrode can significantly enhance the linear relationship between the effective electrode area of the capacitor and the applied force over a wide range, which endowed the prepared sensor exhibiting excellent linearity (R
2 = 0.999) up to 120 kPa. In addition, the fabricated sensor sample has good stability, quick response, satisfied sensitivity of 0.115 kPa−1 (0–120 kPa), and can be further expanded with a wider sensing range up to 500 kPa. Based on the proposed model, the sensitivity and linear sensing range of the sensor can be designed flexibly for different application. It can provide a simple but powerful strategy to construct high performance flexible pressure sensors in the future.
A graph network model for neural connection prediction and connection strength estimation
Authors: Yuan Ye , Liu Jian , Zhao Peng , Wang Wei , Gu Xiao , Rong Yi , Lai Tinggeng , Chen Yuze , Xin Kuankuan , Niu Xin , Xiang Fengtao , Huo Hong , Li Zhaoyu , Fang Tao 
Published: April 2022

Abstract

Objective. Reconstruction of connectomes at the cellular scale is a prerequisite for understanding the principles of neural circuits. However, due to methodological limits, scientists have reconstructed the connectomes of only a few organisms such as C. elegans, and estimated synaptic strength indirectly according to their size and number. Approach. Here, we propose a graph network model to predict synaptic connections and estimate synaptic strength by using the calcium activity data from C. elegans. Main results. The results show that this model can reliably predict synaptic connections in the neural circuits of C. elegans, and estimate their synaptic strength, which is an intricate and comprehensive reflection of multiple factors such as synaptic type and size, neurotransmitter and receptor type, and even activity dependence. In addition, the excitability or inhibition of synapses can be identified by this model. We also found that chemical synaptic strength is almost linearly positively correlated to electrical synaptic strength, and the influence of one neuron on another is non-linearly correlated with the number between them. This reflects the intrinsic interaction between electrical and chemical synapses. Significance. Our model is expected to provide a more accessible quantitative and data-driven approach for the reconstruction of connectomes in more complex nervous systems, as well as a promising method for accurately estimating synaptic strength.
Tunable multi-bands in twisted double bilayer graphene
Authors: Zhu Yujian , Chen Yiwei , Li Qingxin , Chen Yongdao , Huang Yan , Zhu Wang , An Dongdong , Song Junwei , Gan Qikang , Wang Kaiyuan , Wei Lingnan , Zong Qijun , Watanabe Kenji , Taniguchi Takashi , Wang Haolin , Huang Li , Xian Lede , Sun Liang , Yu Geliang , Wang Lei 
Published: April 2022

Abstract
The bandstructure of a material, playing an important role in its electron transport property, is usually governed by the lattice configuration. Materials with a field-effect tunable band, such as bilayer [1] and rhombohedral trilayer graphene [2, 3], are more flexible for electronic applications. Here, on dual-gated twisted double bilayer graphene (TDBG) samples with small twist angle around 1∘, we observe vertical electric-field-tunable bandstructures at multiple moiré fillings with bandgap values continuously varying from zero to tens of mili-electron volts. Moreover, within the first moiré filling on both electron and hole sides, the carrier transport deviates from Fermi liquid behavior, with measured resistivity exhibiting linear temperature dependence between 1.5 K and 50 K. Furthermore, under a vertical magnetic field, the coupling between the two bilayer graphene layers can also be turned on and off by a displacement field. Our results suggest TDBG with small twist angle is a platform for studying the evolution of multiple electric field tunable moiré bands and the resulting emergent correlated electronic phases.
Robust fingerprinting of genomic databases
Authors: Ji Tianxi , Ayday Erman , Yilmaz Emre , Li Pan 
Published: April 2022

AbstractMotivationDatabase fingerprinting has been widely used to discourage unauthorized redistribution of data by providing means to identify the source of data leakages. However, there is no fingerprinting scheme aiming at achieving liability guarantees when sharing genomic databases. Thus, we are motivated to fill in this gap by devising a vanilla fingerprinting scheme specifically for genomic databases. Moreover, since malicious genomic database recipients may compromise the embedded fingerprint (distort the steganographic marks, i.e. the embedded fingerprint bit-string) by launching effective correlation attacks, which leverage the intrinsic correlations among genomic data (e.g. Mendel’s law and linkage disequilibrium), we also augment the vanilla scheme by developing mitigation techniques to achieve robust fingerprinting of genomic databases against correlation attacks.ResultsVia experiments using a real-world genomic database, we first show that correlation attacks against fingerprinting schemes for genomic databases are very powerful. In particular, the correlation attacks can distort more than half of the fingerprint bits by causing a small utility loss (e.g. database accuracy and consistency of SNP–phenotype associations measured via P-values). Next, we experimentally show that the correlation attacks can be effectively mitigated by our proposed mitigation techniques. We validate that the attacker can hardly compromise a large portion of the fingerprint bits even if it pays a higher cost in terms of degradation of the database utility. For example, with around 24% loss in accuracy and 20% loss in the consistency of SNP–phenotype associations, the attacker can only distort about 30% fingerprint bits, which is insufficient for it to avoid being accused. We also show that the proposed mitigation techniques also preserve the utility of the shared genomic databases, e.g. the mitigation techniques only lead to around 3% loss in accuracy.Availability and implementationhttps://github.com/xiutianxi/robust-genomic-fp-github.
Early diagnosis of anastomotic leakage after colorectal cancer surgery using an inflammatory factors-based score system
Authors: Shi Jinyao , Wu Zhouqiao , Wu Xiaolong , Shan Fei , Zhang Yan , Ying Xiangji , Li Ziyu , Ji Jiafu 
Published: April 2022

AbstractBackgroundAnastomotic leakage (AL) is a severe complication after colorectal surgery. This study aimed to investigate a method for the early diagnosis of AL after surgical resection by analysing inflammatory factors (IFs) in peritoneal drainage fluid.MethodsAbdominal drainage fluid of patients with colorectal cancer who underwent resection between April 2017 and April 2018, were prospectively collected in the postoperative interval. Six IFs, including interleukin (IL)-1β, IL-6, IL-10, tumour necrosis factor (TNF)-α, matrix metalloproteinase (MMP)2, and MMP9, in drainage were determined by multiplex immunoassay to investigate AL (in patients undergoing resection and anastomosis) and pelvic collection (in patients undergoing abdominoperineal resection). Sparreboom and colleagues’ prediction model was first evaluated for AL/pelvic collection, followed by a new IF-based score system (AScore) that was developed by a least absolute shrinkage and selection operator (LASSO) regression, for the same outcomes. The model performance was tested for the area under the curve (AUC), sensitivity, specificity, negative predictive value (NPV), and positive predictive value (PPV).ResultsOut of 123 patients eligible, 119 patients were selected, including 12 patients with AL/pelvic collection. Sparreboom and colleagues’ prediction model was documented with the best diagnostic efficacy on postoperative day 3 (POD3), with an AUC of 0.77. After optimization, AScore on POD3 increased the AUC to 0.83 and on POD1 showed the best diagnostic efficiency, with an AUC of 0.88. Based on the Youden index, the cut-off value of AScore on POD1 was set as −2.46 to stratify patients into low-risk and high-risk groups for AL/pelvic collection. The model showed 90.0 per cent sensitivity, 69.7 per cent specificity, 98.4 per cent NPV, and 25.0 per cent PPV.ConclusionsThe early determination of IFs in abdominal drainage fluid of patients undergoing colorectal surgery could be useful to predict AL or pelvic collection.
Small interfering RNAs in the management of human rheumatoid arthritis
Authors: Gargano Giuseppe , Oliva Francesco , Oliviero Antonio , Maffulli Nicola 
Published: April 2022

Abstract

Background
Rheumatoid arthritis (RA) has unclear pathogenesis, but the molecules that feed its inflammatory state are known. Small interfering RNAs (siRNAs) are useful to identify molecular targets and evaluate the efficacy of specific drugs, and can themselves be used for therapeutic purposes.

Sources of data
A systematic search of different databases to March 2022 was performed to define the role of siRNAs in RA therapy. Twenty suitable studies were identified.

Areas of agreement
Small interfering RNAs can be useful in the study of inflammatory processes in RA, and identify possible therapeutic targets and drug therapies.

Areas of controversy
Many genes and cytokines participate in the inflammatory process of RA and can be regulated with siRNA. However, it is difficult to determine whether the responses to siRNAs and other drugs studied in human cells in vitro are similar to the responses in vivo.

Growing points
Inflammatory processes can be affected by the gene dysregulation of siRNAs on inflammatory cytokines.

Areas timely for developing research
To date, it is not possible to determine whether the pharmacological response of siRNAs on cells in vitro would be similar to what takes place in vivo for the diseases studied so far.
Theory and Method for Studying How Media Messages Prompt Shared Brain Responses Along the Sensation-to-Cognition Continuum
Authors: Schmälzle Ralf 
Published: April 2022

Abstract
When members of an audience are exposed to the same messages, their brains will, to a certain degree, exhibit similar responses. These similar, and thus shared audience responses constitute the recruitment of sensory, perceptual, and higher-level neurocognitive processes, which occur separately in the brain of each individual, but in a collectively shared fashion across the audience. A method called inter-subject-correlation (ISC) analysis allows to reveal these shared responses. This manuscript introduces a theoretical model of brain function that explains why shared brain responses occur and how they emerge along a gradient from sensation to cognition as individuals process the same message content. This model makes results from ISC-based studies more interpretable from a communication perspective, helps organize the results from existing studies across different subfields, and generates testable predictions. The article discusses how research at the nexus of media, audience research, and neuroscience contributes to and advances communication theory.
The structure–function relationship ofPseudomonas aeruginosain infections and its influence on the microenvironment
Authors: Lichtenberg Mads , Jakobsen Tim Holm , Kühl Michael , Kolpen Mette , Jensen Peter Østrup , Bjarnsholt Thomas 
Published: April 2022

AbstractPseudomonas aeruginosa is a human pathogen associated with both acute and chronic infections. While intensively studied, the basic mechanisms enabling the long-term survival of P. aeruginosa in the host, despite massive immune system attack and heavy antimicrobial treatment, remain to be identified. We argue that such infections may represent niche invasions by P. aeruginosa that influence the microenvironment by depleting host-derived substrate and activating the immune response. Bacteria embedded in cell aggregates establish a microenvironmental niche, where they endure the initial host response by slowing down their metabolism. This provides stable, lasting growth conditions with a constant, albeit slow supply of substrate and electron acceptors. Under such stable conditions, P. aeruginosa exhibits distinct adaptive traits, where its gene expression pattern reflects a life exposed to continuous attack by the host immune system and antimicrobials. Here, we review fundamental microenvironmental aspects of chronic P. aeruginosa infections and examine how their structural organization influences their in vivo microenvironment, which in turn affects the interaction of P. aeruginosa biofilm aggregates with the host immune system. We discuss how improving our knowledge about the microenvironmental ecology of P. aeruginosa in chronic infections can be used to combat persistent, hard-to-treat bacterial infections.