SpatialWavePredict: a tutorial-based primer and toolbox for forecasting growth trajectories using the ensemble spatial wave sub-epidemic modeling framework.

BACKGROUND: Dynamical mathematical models defined by a system of differential equations are typically not easily accessible to non-experts. However, forecasts based on these types of models can help gain insights into the mechanisms driving the process and may outcompete simpler phenomenological growth models. Here we introduce a friendly toolbox, SpatialWavePredict, to characterize and forecast the spatial wave sub-epidemic model, which captures diverse wave dynamics by aggregating multiple asynchronous growth processes and has outperformed simpler phenomenological growth models in short-term forecasts of various infectious diseases outbreaks including SARS, Ebola, and the early waves of the COVID-19 pandemic in the US. RESULTS: This tutorial-based primer introduces and illustrates a user-friendly MATLAB toolbox for fitting and forecasting time-series trajectories using an ensemble spatial wave sub-epidemic model based on ordinary differential equations. Scientists, policymakers, and students can use the toolbox to conduct real-time short-term forecasts. The five-parameter epidemic wave model in the toolbox aggregates linked overlapping sub-epidemics and captures a rich spectrum of epidemic wave dynamics, including oscillatory wave behavior and plateaus. An ensemble strategy aims to improve forecasting performance by combining the resulting top-ranked models. The toolbox provides a tutorial for forecasting time-series trajectories, including the full uncertainty distribution derived through parametric bootstrapping, which is needed to construct prediction intervals and evaluate their accuracy. Functions are available to assess forecasting performance, estimation methods, error structures in the data, and forecasting horizons. The toolbox also includes functions to quantify forecasting performance using metrics that evaluate point and distributional forecasts, including the weighted interval score. CONCLUSIONS: We have developed the first comprehensive toolbox to characterize and forecast time-series data using an ensemble spatial wave sub-epidemic wave model. As an epidemic situation or contagion occurs, the tools presented in this tutorial can facilitate policymakers to guide the implementation of containment strategies and assess the impact of control interventions. We demonstrate the functionality of the toolbox with examples, including a tutorial video, and is illustrated using daily data on the COVID-19 pandemic in the USA.

An analytical model for simulating the rainfall-interception-infiltration-runoff process with non-uniform rainfall.

The rainfall runoff process is a critical factor in determining the transport of surface materials. Simulating the surface runoff process is fundamental to accurately characterize soil erosion and soil nutrient loss. This research aims to develop a comprehensive simulation model for rainfall-interception-infiltration-runoff under vegetation cover conditions. The model integrates three key components: a vegetation interception model, Philip's infiltration model, and a kinematic wave model. By combining these models, an analytical solution is derived to simulate slope runoff considering vegetation interception and infiltration during non-constant rainfall events. To validate the reliability of the analytical solution, a numerical solution was obtained using the Pressimann Box scheme method and compared with the analytical results. The comparison confirms the accuracy and robustness of the analytical solution (R2 = 0.984, RMSE = 0.0049 cm/min, NS = 0.969). Moreover, this study investigates the influence of two significant parameters, Intm and k, on the production flow process. The analysis reveals that both parameters exert a significant impact on the timing of production initiation and the magnitude of runoff. Specifically, Intm exhibits a positive correlation with runoff intensity, while k displays a negative correlation. This research introduces a novel simulation method that enhances our understanding and modeling of rainfall production and convergence under complex slope conditions. The proposed model provides valuable insights into rainfall-runoff dynamics, particularly in scenarios characterized by varying rainfall patterns and vegetation cover. Overall, this study contributes to advancing the field of hydrological modeling and offers a practical approach for quantifying soil erosion and nutrient loss under different environmental conditions.

Analyzing Transverse Momentum Spectra of Pions, Kaons and Protons in p-p, p-A and A-A Collisions via the Blast-Wave Model with Fluctuations.

The transverse momentum spectra of different types of particles, π±, K±, p and p¯, produced at mid-(pseudo)rapidity in different centrality lead-lead (Pb-Pb) collisions at 2.76 TeV; proton-lead (p-Pb) collisions at 5.02 TeV; xenon-xenon (Xe-Xe) collisions at 5.44 TeV; and proton-proton (p-p) collisions at 0.9, 2.76, 5.02, 7 and 13 TeV, were analyzed by the blast-wave model with fluctuations. With the experimental data measured by the ALICE and CMS Collaborations at the Large Hadron Collider (LHC), the kinetic freeze-out temperature, transverse flow velocity and proper time were extracted from fitting the transverse momentum spectra. In nucleus-nucleus (A-A) and proton-nucleus (p-A) collisions, the three parameters decrease with the decrease of event centrality from central to peripheral, indicating higher degrees of excitation, quicker expansion velocities and longer evolution times for central collisions. In p-p collisions, the kinetic freeze-out temperature is nearly invariant with the increase of energy, though the transverse flow velocity and proper time increase slightly, in the considered energy range.

Four Theories of the Madden-Julian Oscillation.

Studies of the Madden-Julian Oscillation (MJO) have progressed considerably during the past decades in observations, numerical modeling, and theoretical understanding. Many theoretical attempts have been made to identify the most essential processes responsible for the existence of the MJO. Criteria are proposed to separate a hypothesis from a theory (based on the first principles with quantitative and testable assumptions, able to predict quantitatively the fundamental scales and eastward propagation of the MJO). Four MJO theories are selected to be summarized and compared in this article: the skeleton theory, moisture-mode theory, gravity-wave theory, and trio-interaction theory of the MJO. These four MJO theories are distinct from each other in their key assumptions, parameterized processes, and, particularly, selection mechanisms for the zonal spatial scale, time scale, and eastward propagation of the MJO. The comparison of the four theories and more recent development in MJO dynamical approaches lead to a realization that theoretical thinking of the MJO is diverse and understanding of MJO dynamics needs to be further advanced.

A Fast Analysis Method for Blue-Green Laser Transmission through the Sea Surface.

The fast estimation of blue-green laser transmission characteristics through the fluctuating sea surface, such as refraction angles and transmittance, is very important to correct operating parameters, detection depth and anti-detection warning in airborne Light Detection and Ranging (LiDAR) applications. However, the geometry of the sea surface is changed by complex environment factors, such as wind and wave, which significantly affect the rapid acquisition of the blue-green laser transmission characteristics. To address this problem, a fast analysis method is provided to rapidly compute the blue-green laser transmittance and refraction angles through the fluctuating sea surface driven by different wind directions and speeds. In the method, a three-dimensional wave model driven by the wind was built to describe the wave spatial distribution varying with time. Using the wave model, the propagation path of the scanning laser footprint was analyzed using the proposed meshing method, thus the transmittance and refraction angles of the optical path can be fast obtained by using parallel computing. The simulation results imply that the proposed method can reduce the time consumption by 70% compared with the traditional analytical method with sequential computing. This paper provides some statistical laws of refraction angles and transmittance through the fluctuating sea surface under different wind conditions, which may serve as a basic for fast computation of airborne LiDAR transmission characteristics in complex environments.

Estimating the viscoelastic anisotropy of human skin through high-frequency ultrasound elastography.

BACKGROUND: The skin is the largest organ of the human body and serves distinct functions in protecting the body. The viscoelastic properties of the skin play a key role in supporting the skin-healing process, also it may be changed due to some skin diseases. PROPOSE: In this study, high-frequency ultrasound (HFUS) elastography based on a Lamb wave model was used to noninvasively assess the viscoelastic anisotropy of human skin. METHOD: Elastic waves were generated through an external vibrator, and the wave propagation velocity was measured through 40 MHz ultrafast HFUS imaging. Through the use of a thin-layer gelatin phantom, HFUS elastography was verified to produce highly accurate estimates of elasticity and viscosity. In a human study involving five volunteers, viscoelastic anisotropy was assessed by rotating an ultrasound transducer 360°. RESULTS: An oval-shaped pattern in the elasticity of human forearm skin was identified, indicating the high elastic anisotropy of skin; the average elastic moduli were 24.90 ± 6.63 and 13.64 ± 2.67 kPa along and across the collagen fiber orientation, respectively. The average viscosity of all the recruited volunteers was 3.23 ± 0.93 Pa·s. CONCLUSIONS: Although the examined skin exhibited elastic anisotropy, no evident viscosity anisotropy was observed.

Laboratory and non-hydrostatic modelling of focused wave group evolution over fringing reef.

This paper presents physical experiments and numerical simulations to study the propagation of focused waves group across hypothetical fringing reef profiles. A wave flume is 69 m long and 1.0 m deep, and the reef cross section is made up of a reef face, a reef flat and a vertical wall. A reef crest of 0.085 m is optionally constructed on the outside to replicate the reef crown. By focusing wave trains of the JONSWAP or constant wave amplitude spectrum, the transient wave group is generated on the reef slope. Free surface elevations and flow velocity are measured over time along the flume's centreline. The focused wave process and the development of higher harmonics as a result of the nonlinear interaction over the reef face are clearly visible in the wavelet and FFT analyses of the observed free surface elevation. Low frequency wave is increasing on the reef flat while these short-period wave motions are primarily absorbed by rapid breaking on reef edge and crest. On the flat, it is discovered that reef crest has the effect of reducing short-period wave motion and increasing long-period wave motion. A numerical multi-layer non-hydrostatic wave model is employed and its ability to describe the propagation of focused wave groups over fringing reef profiles is assessed.

Vaccines Induce Homeostatic Immunity, Generating Several Secondary Benefits.

The optimal immune response eliminates invading pathogens, restoring immune equilibrium without inflicting undue harm to the host. However, when a cascade of immunological reactions is triggered, the immune response can sometimes go into overdrive, potentially leading to harmful long-term effects or even death. The immune system is triggered mostly by infections, allergens, or medical interventions such as vaccination. This review examines how these immune triggers differ and why certain infections may dysregulate immune homeostasis, leading to inflammatory or allergic pathology and exacerbation of pre-existing conditions. However, many vaccines generate an optimal immune response and protect against the consequences of pathogen-induced immunological aggressiveness, and from a small number of unrelated pathogens and autoimmune diseases. Here, we propose an "immuno-wave" model describing a vaccine-induced "Goldilocks immunity", which leaves fine imprints of both pro-inflammatory and anti-inflammatory milieus, derived from both the innate and the adaptive arms of the immune system, in the body. The resulting balanced, 'quiet alert' state of the immune system may provide a jump-start in the defense against pathogens and any associated pathological inflammatory or allergic responses, allowing vaccines to go above and beyond their call of duty. In closing, we recommend formally investigating and reaping many of the secondary benefits of vaccines with appropriate clinical studies.

Numerical studies on shortening the duration of HIFU ablation therapy and their experimental validation.

High Intensity Focused Ultrasound (HIFU) is used in clinical practice for thermal ablation of malignant and benign solid tumors located in various organs. One of the reason limiting the wider use of this technology is the long treatment time resulting from i.a. the large difference between the size of the focal volume of the heating beam and the size of the tumor. Therefore, the treatment of large tumors requires scanning their volume with a sequence of single heating beams, the focus of which is moved in the focal plane along a specific trajectory with specific time and distance interval between sonications. To avoid an undesirable increase in the temperature of healthy tissues surrounding the tumor during scanning, the acoustic power and exposure time of each HIFU beam as well as the time intervals between sonications should be selected in such a way as to cover the entire volume of the tumor with necrosis as quickly as possible. This would reduce the costs of treatment. The aim of this study was to quantitatively evaluate the hypothesis that selecting the average acoustic power and exposure time for each individual heating beam, as well as the temporal intervals between sonications, can significantly shorten treatment time. Using 3D numerical simulations, the dependence of the duration of treatment of a tumor with a diameter of 5 mm or 9 mm (requiring multiple exposure to the HIFU beam) on the sonication parameters (acoustic power, exposure time) of each single beam capable of delivering the threshold thermal dose (CEM43 = 240 min) to the treated tissue volume was examined. The treatment duration was determined as the sum of exposure times to individual beams and time intervals between sonications. The tumor was located inside the ex vivo tissue sample at a depth of 12.6 mm. The thickness of the water layer between the HIFU transducer and the tissue was 50 mm. The sonication and scanning parameters selected using the developed algorithm shortened the duration of the ablation procedure by almost 14 times for a 5-mm tumor and 20 times for a 9-mm tumor compared to the duration of the same ablation plan when a HIFU beam was used of a constant acoustic power, constant exposure time (3 s) and constant long time intervals (120 s) between sonications. Results of calculations of the location and size of the necrotic lesion formed were experimentally verified on ex vivo pork loin samples, showing good agreement between them. In this way, it was proven that the proper selection of sonication and scanning parameters for each HIFU beam allows to significantly shorten the time of HIFU therapy.

Coastal erosion and climate change: A review on coastal-change process and modeling.

Coastal erosion is a normal process of nature. However, the rate of coastal erosion, and the frequency and intensity of coastal flooding events, are now on the rise around the world due to the changing climate. Current responses to coastal erosion are primarily determined by site-specific factors, such as coastal elevation, coastal slope, coastal features, and historical coastline change rate, without a systematic understanding of the coastal-change processes in the context of climate change, including spatiotemporal changes in sea level, regional changes in wave climate, and sea ice coverage. In the absence of a clear understanding of the coastal-change processes, most of the current coastal responses have been built upon a risky assumption (i.e., the present-day coastal change will persist) and are not resilient to future climate change. Here, we conduct a literature review to summarize the latest scientific understanding of the coastal-change processes under climate change and the potential research gaps towards the prediction of future coastal erosion. Our review suggests that a coupled coastal simulation system with a nearshore wave model (e.g., SWAN, MIKE21, etc.) can play a critical role in both the short-term and long-term coastal risk assessment and protective measure development.

Building a new reasonable atomic theory.

CONTEXT: This article is an initiation to build reasonable atomic/molecular theory to study chemicals utilized in different sectors of science including chemistry, biology, and medicine as well as the material science. It is all about opening new pathways and method-developments which need to be simple, reasonable, rational, and applicable to all chemicals and be closely consistent with the experimental data and real world. Hence, the success may simplify the process and eliminate the need to sophisticated software and heavy computations. The article first reviews the current classical atomic theory, and discusses some of its flaws. Then, it suggests a more reasonable approach through several presented simple formulas which would generate results consistent with the experimental data. Finally, the article goes through some examples, cases, and details to present the differences between the new suggested approach and the current classical atomic theory. Building new pathways would help not only with the ongoing scientific achievements but it would also help in classrooms and the education of next future generations. METHODS: All of the calculations and figures presented in this article are done by simple calculators and the use of Microsoft software including excel spreadsheet. The presented atomic theory does not need any sophisticated software and/or heavy computations. If desired, one can also use a simple personal programing technique to generate the desired results. So the key is in better understanding of the subjects and not in development of complicated computational tools and theoretical techniques. This article did not use any of the usual ab initio or DFT, or basis sets, or force field molecular-dynamics techniques. The focus of this article is mainly atomic theory which will expand to molecular theory in future articles.

A mathematical model of maternal vascular growth and remodeling and changes in maternal hemodynamics in uncomplicated pregnancy.

The maternal vasculature undergoes tremendous growth and remodeling (G&R) that enables a > 15-fold increase in blood flow through the uterine vasculature from conception to term. Hemodynamic metrics (e.g., uterine artery pulsatility index, UA-PI) are useful for the prognosis of pregnancy complications; however, improved characterization of the maternal hemodynamics is necessary to improve prognosis. The goal of this paper is to develop a mathematical framework to characterize maternal vascular G&R and hemodynamics in uncomplicated human pregnancies. A validated 1D model of the human vascular tree from the literature was adapted and inlet blood flow waveforms at the ascending aorta at 4 week increments from 0 to 40 weeks of gestation were prescribed. Peripheral resistances of each terminal vessel were adjusted to achieve target flow rates and mean arterial pressure at each gestational age. Vessel growth was governed by wall shear stress (and axial lengthening in uterine vessels), and changes in vessel distensibility were related to vessel growth. Uterine artery velocity waveforms generated from this model closely resembled ultrasound results from the literature. The literature UA-PI values changed significantly across gestation, increasing in the first month of gestation, then dramatically decreasing from 4 to 20 weeks. Our results captured well the time-course of vessel geometry, material properties, and UA-PI. This 1D fluid-G&R model captured the salient hemodynamic features across a broad range of clinical reports and across gestation for uncomplicated human pregnancy. While results capture available data well, this study highlights significant gaps in available data required to better understand vascular remodeling in pregnancy.

Effect of daily temperature fluctuations on virus lifetime.

Epidemiological studies based on statistical methods indicate inverse correlations between virus lifetime and both (i) daily mean temperature and (ii) diurnal temperature range (DTR). While thermodynamic models have been used to predict the effect of constant-temperature surroundings on virus inactivation rate, the relationship between virus lifetime and DTR has not been explained using first principles. Here, we model the inactivation of viruses based on temperature-dependent chemical kinetics with a time-varying temperature profile to account for the daily mean temperature and DTR simultaneously. The exponential Arrhenius relationship governing the rate of virus inactivation causes fluctuations above the daily mean temperature during daytime to increase the instantaneous rate of inactivation by a much greater magnitude than the corresponding decrease in inactivation rate during nighttime. This asymmetric behavior results in shorter predicted virus lifetimes when considering DTR and consequently reveals a potential physical mechanism for the inverse correlation observed between the number of cases and DTR reported in statistical epidemiological studies. In light of the ongoing COVID-19 pandemic, a case study on the effect of daily mean temperature and DTR on the lifetime of SARS-CoV-2 was performed for the five most populous cities in the United States. In Los Angeles, where mean monthly temperature fluctuations are low (DTR ≈ 7 °C), accounting for DTR decreases predicted SARS-CoV-2 lifetimes by only 10%; conversely, accounting for DTR for a similar mean temperature but larger mean monthly temperature fluctuations in Phoenix (DTR ≈ 15 °C) decreases predicted lifetimes by 50%. The modeling framework presented here provides insight into the independent effects of mean temperature and DTR on virus lifetime, and a significant impact on transmission rate is expected, especially for viruses that pose a high risk of fomite-mediated transmission.

Seasonality, mediation and comparison (SMAC) methods to identify influences on lung function decline.

This study develops a comprehensive method to assess seasonal influences on a longitudinal marker and compare estimates between cohorts. The method extends existing approaches by (i) combining a sine-cosine model of seasonality with a specialized covariance function for modeling longitudinal correlation; (ii) performing mediation analysis on a seasonality model. An example dataset and R code are provided. The bundle of methods is referred to as seasonality, mediation and comparison (SMAC). The case study described utilizes lung function as the marker observed on a cystic fibrosis cohort but SMAC can be used to evaluate other markers and in other disease contexts. Key aspects of customization are as follows.•This study introduces a novel seasonality model to fit trajectories of lung function decline and demonstrates how to compare this model to a conventional model in this context.•Steps required for mediation analyses in the seasonality model are shown.•The necessary calculations to compare seasonality models between cohorts, based on estimation coefficients, are derived in the study.

Natural dynamics overshadow anthropogenic impact on marine fauna at an urbanised coastal embayment.

Understanding vulnerabilities of coastal ecosystems facing anthropogenic use is a precondition for management decisions and development planning. This can be challenging in urbanised areas with multiple activities affecting different faunal communities. The aim of this study was to provide a holistic understanding of the relative importance of anthropogenic and natural variables for macroinfauna, epifauna and fish in a heavily modified waterbody (HMWB) designated under the EU Water Framework Directive (WFD). The study area, Swansea Bay (Wales, UK), had two regularly dredged industrial ports, three estuaries, a wastewater discharge point and a dredge-spoil disposal site. Wave and tidal current models were constructed, and environmental data were gathered by field studies. Biota were assessed by grab sampling and dredging. Modelled and empirical data were combined in a Distance-based Linear Model (DistLM) that quantified how much of the faunal variation was explained by wave exposure and tidal currents, sediment characteristics and other environmental factors, and by anthropogenic usage. Wave and tidal current parameters explained over 50% of the variation in all biota. Infauna communities were further linked with sediment properties and epibenthos with distance to estuaries. Fish and epibenthos were affected by a dredge-spoil disposal site, but none of the faunal communities was affected by the wastewater outfall. Biota were predominantly driven by the natural hydrodynamic regime while anthropogenic factors had secondary influence. The study highlighted that ecosystems driven by a strong hydrodynamic regime can be relatively resistant to human activities.

Quantitative confocal optical coherence elastography for evaluating biomechanics of optic nerve head using Lamb wave model.

The mechanosensitivity of the optic nerve head (ONH) plays a pivotal role in the pathogenesis of glaucoma. Characterizing elasticity of the ONH over changing physiological pressure may provide a better understanding of how changes in intraocular pressure (IOP) lead to changes in the mechanical environment of the ONH. Optical coherence elastography (OCE) is an emerging technique that can detect tissue biomechanics noninvasively with both high temporal and spatial resolution compared with conventional ultrasonic elastography. We describe a confocal OCE system in measuring ONH elasticity in vitro, utilizing a pressure inflation setup in which IOP is controlled precisely. We further utilize the Lamb wave model to fit the phase dispersion curve during data postprocessing. We present a reconstruction of Young's modulus of the ONH by combining our OCE system with a Lamb wave model for the first time. This approach enables the quantification of Young's modulus of the ONH, which can be fit using a piecewise polynomial to the corresponding IOP.

Fourier Transform Ultrasound Spectroscopy for the determination of wave propagation parameters.

The reported results for ultrasonic wave attenuation constant (α) in pure water show noticeable inconsistency in magnitude. A "Propagating-Wave" model analysis of the most popular pulse-echo technique indicates that this is a consequence of the inherent wave propagation characteristics in a bounded medium. In the present work Fourier Transform Ultrasound Spectroscopy (FTUS) is adopted to determine ultrasonic wave propagation parameters, the wave number (k) and attenuation constant (α) at 1MHz frequency in tri-distilled water at room temperature (25°C). Pulse-echo signals obtained under same experimental conditions regarding the exciting input signal and reflecting boundary wall of the water container for various lengths of water columns are captured. The Fast Fourier Transform (FFT) components of the echo signals are taken to compute k, α and r, the reflection constant at the boundary, using Oak Ridge and Oxford method. The results are compared with existing literature values.

A new interpretation of TCM pulse diagnosis based on quantum physical model of the human body / 数字中医药（英文）

@#Following the quantum theory-based physical model of the human body, a new interpretation of the traditional Chinese medicine (TCM) principle of “Cunkou reads viscera” is presented. Then, a Gaussian pulse wave model as a solution to the Schrodinger equation is shown to accurately describe 19 different pulse shapes, and to quantitatively capture the degree of Yin-Yang attributes of 13 pulse shapes. Furthermore, the model suggests using pulse depth and strength as leading-order quantity and pulse shape as first-order quantity, to characterize the hierarchical resonance between the human body and the environment. The future pulse informatics will focus on determining an individual’s unique quantum human equilibrium state, and diagnose its health state according to the pulse deviation from its equilibrium state, to truly achieve the high level of TCM: “knowing the normal state and reaching the change”.

Pulse-echo method cannot measure wave attenuation accurately.

A number of techniques with different degrees of accuracies have been devised for the measurement of acoustic wave attenuation in solids and liquids. Still, a wide variation is observed in the attenuation values in different materials reported in the literature. Present numerical study based on a 'propagating wave' model analysis clearly shows that the attenuation constant obtained from exponential fitting of the echo heights in pulse-echo method differs from the exact value of intrinsic attenuation in the medium, even in the ideal situation of plane wave propagation without diffraction, dispersion or scattering.

Modelling rogue waves through exact dynamical lump soliton controlled by ocean currents.

Rogue waves are extraordinarily high and steep isolated waves, which appear suddenly in a calm sea and disappear equally fast. However, though the rogue waves are localized surface waves, their theoretical models and experimental observations are available mostly in one dimension, with the majority of them admitting only limited and fixed amplitude and modular inclination of the wave. We propose two dimensions, exactly solvable nonlinear Schrödinger (NLS) equation derivable from the basic hydrodynamic equations and endowed with integrable structures. The proposed two-dimensional equation exhibits modulation instability and frequency correction induced by the nonlinear effect, with a directional preference, all of which can be determined through precise analytic result. The two-dimensional NLS equation allows also an exact lump soliton which can model a full-grown surface rogue wave with adjustable height and modular inclination. The lump soliton under the influence of an ocean current appears and disappears preceded by a hole state, with its dynamics controlled by the current term. These desirable properties make our exact model promising for describing ocean rogue waves.