Miracle-dz/UniFAR-FTUs huggingface dataset:
Automatic Calibration and Predictive Uncertainty Analysis of a Semidistributed Watershed Model

Semidistributed models are commonly calibrated manually, but software for automatic calibration is now available. We present a two‐stage routine for automatic calibration of the semidistributed watershed model Soil and Water Assessment Tool (SWAT) that finds the best values for the model parameters, preserves spatial variability in essential parameters, and leads to a measure of the model prediction uncertainty. In the first stage, a modified global Shuffled Complex Evolution (SCE‐UA) method was employed to find the “best” values for the lumped model parameters. In the second stage, the spatial variability of the original model parameters was restored and a local search method (a variant of Levenberg–Marquart method) was used to find a more distributed set of parameters using the results of the previous stage as starting values. A method called “regularization” was adopted to prevent the parameters from taking extreme values. In addition, we applied a nonlinear calibration‐constrained method to develop confidence intervals for annual and 7‐d average flow predictions. We calibrated stream flow in the Etowah River measured at Canton, GA (a watershed area of 1580 km2) for the years 1983 to 1992 and used the years 1993 to 2001 for validation. The Parameter Estimator (PEST) software was used to conduct the two‐stage automatic calibration and prediction uncertainty analysis. Calibration for daily and monthly flow produced a very good fit to the measured data. Nash‐Sutcliffe coefficients for daily and monthly flow over the calibration period were 0.60 and 0.86, respectively. They were 0.61 and 0.87, respectively, for the validation period. The nonlinear prediction uncertainty analysis worked well for long‐term (annual) flow in that our prediction confidence intervals included or were very near to the observed flow for most years. It did not work well for short‐term (7‐d average) flows in that the prediction confidence intervals did not include the observed flow, especially for low and high flow conditions.
Identification of Replication Origins in Prokaryotic Genomes

The availability of hundreds of complete bacterial genomes has created new challenges and simultaneously opportunities for bioinformatics. In the area of statistical analysis of genomic sequences, the studies of nucleotide composi-tional bias and gene bias between strands and replichores paved way to the development of tools for prediction of bacterial replication origins. Only a few (about 20) origin regions for eubacteria and archaea have been proven experimentally. One reason for that may be that this is now considered as an essentially bioinformatics problem, where predictions are sufficiently reliable not to run labor-intensive experiments, unless specifically needed. Here we describe the main existing approaches to the identification of replication origin (oriC) and termination (terC) loci in prokaryotic chromosomes and characterize a number of computational tools based on various skew types and other types of evidence. We also classify the eubacterial and archaeal chromosomes by predictability of their replication origins using skew plots. Finally, we discuss possible combined approaches to the identification of the oriC sites that may be used to improve the prediction tools, in particular, the analysis of DnaA binding sites using the comparative genomic methods. OVERVIEW The replication of genomic DNA is arguably the most important task performed by a cell. Prokaryotic genomes contain one or several chromosomes [1], most of which are circular [2]. The chromosomes consist of two anti-parallel DNA strands, and are supposed to have a single origin of replication (eubacteria) [3] or may have single or multiple origins (archaea) [4]. In eubacteria, the origin locus, oriC, is relatively short, from 100 to 1000 bp [5]. The replication starts there and then proceeds bi-directionally, carried out by two replication forks that copy the chromosome in two arcs called replichores and (in circular chromosomes) meet at the replication terminus (terC) [6, 7]. The DNA replication in archaea is described in [8]. Semi-conservative DNA synthesis implies that polymerization of a new strand in a replichore involves using each of the old strands as a template. Since elongation is possible only in the 5 0 ! 3 0 direction, the new strands are synthesized using different mechanisms: the leading strand is replicated continuously, while the lagging strand is replicated in a fragmented manner, through the assembly of the Okazaki fragments [3, 9]. The first Chargaff parity rule, experimentally established about 60 years ago, says that, in a two-stranded DNA molecule, %A ¼ %T and %C ¼ %G [10]. Later, …
Kafnets: kernel-based non-parametric activation functions for neural networks

Neural networks are generally built by interleaving (adaptable) linear layers with (fixed) nonlinear activation functions. To increase their flexibility, several authors have proposed methods for adapting the activation functions themselves, endowing them with varying degrees of flexibility. None of these approaches, however, have gained wide acceptance in practice, and research in this topic remains open. In this paper, we introduce a novel family of flexible activation functions that are based on an inexpensive kernel expansion at every neuron. Leveraging over several properties of kernel-based models, we propose multiple variations for designing and initializing these kernel activation functions (KAFs), including a multidimensional scheme allowing to nonlinearly combine information from different paths in the network. The resulting KAFs can approximate any mapping defined over a subset of the real line, either convex or nonconvex. Furthermore, they are smooth over their entire domain, linear in their parameters, and they can be regularized using any known scheme, including the use of $\ell_1$ penalties to enforce sparseness. To the best of our knowledge, no other known model satisfies all these properties simultaneously. In addition, we provide a relatively complete overview on alternative techniques for adapting the activation functions, which is currently lacking in the literature. A large set of experiments validates our proposal.
Reflection and transmission of waves at a fluid/porous‐medium interface

We study the wave properties at a fluid/porous‐medium interface by using newly derived closed‐form expressions for the reflection and transmission coefficients. We illustrate the usefulness of these relatively simple expressions by applying them to a water/porous‐medium interface (with open‐pore or sealed‐pore boundary conditions), where the porous medium consists of (1) a water‐saturated clay/silt layer, (2) a water‐saturated sand layer, (3) an air‐filled clay/silt layer, or (4) an air‐filled sand layer. We observe in the frequency range 5 Hz–20 kHz that the fast P‐wave and S‐wave velocities in the four porous materials are indistinguishable from the corresponding frequency‐independent ones calculated using Gassmann relations. Consequently, for these frequencies we would expect the reflection and transmission coefficients for the four water/porous‐medium interfaces to be similar to the ones for corresponding interfaces between water and effective elastic media (described by Gassmann wave velocities). Thi.
Title : Distinct networks coupled with parietal cortex for spatial representations 1 inside and outside the visual field 2

Title: Distinct networks coupled with parietal cortex for spatial representations 1 inside and outside the visual field 2 Authors: Bo Zhang 1, 3, 4, Fan Wang 7,8,9, Qi Zhang 1, 10, Naya Yuji 1, 2, 5, 6, * 3 Affiliations: 4 1 School of Psychological and Cognitive Sciences, Peking University, No. 52, Haidian Road, 5 Haidian District, Beijing 100805, China 6 2 IDG/McGovern Institute for Brain Research at Peking University, No. 52, Haidian Road, 7 Haidian District, Beijing 100805, China 8 3 Beijing Academy of Artificial Intelligence, Beijing, 100084, China 9 4 Tsinghua Laboratory of Brain and Intelligence, 160 Chengfu Rd., SanCaiTang Building, 10 Haidian District, Beijing, 100084, China 11 5 Center for Life Sciences, Peking University, No. 52, Haidian Road, Haidian District, Beijing 12 100805, China 13 6 Beijing Key Laboratory of Behavior and Mental Health, Peking University, No. 52, Haidian 14 Road, Haidian District, Beijing 100805, China 15 7 State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese 16 Academy of Sciences, 15 Datun Road, Beijing 100101, China 17 8 CAS Center for Excellence in Brain Science and Intelligence Technology 18 9 University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China 19 10 Fujian Key Laboratory of Applied Cognition and Personality, School of Educational 20 Science, Minnan Normal University, 36 Xianqianzhi Street, Zhangzhou 363000, China 21
Precipitation charge and size measurements inside a New Mexico mountain thunderstorm

We measured the charge and size of precipitation particles with an instrumented free balloon in a convective mountain thunderstorm over Langmuir Laboratory in central New Mexico. Using an instrument that measured precipitation charge from 2 to 220 pC and equivalent particle diameters from 0.6 to 3.8 mm, we deduced that (1) the charge of the main positive charge region is carried by cloud particles, the charge of the main negative charge region is carried by a mixture of negative charge bearing cloud particles and precipitation particles, and the charge of the lower positive charge region is carried almost entirely by precipitation; (2) there was a mixture of both polarities of precipitation charge at nearly all altitudes; (3) there was no relationship between precipitation charge and size; (4) our charge data appear to support the noninductive ice-ice collisional charging mechanism; and (5) the sign of charge carried by the precipitation reverses with ambient temperature. In comparing these data to previous measurements that were collected in New Mexico mountain thunderstorms with different instrumentation, we found that in most ways our precipitation charge data are similar to the previous measurements. In comparing these data with data that we previously collected in the trailing stratiform regions of mesoscale convective systems, we found that there are substantial differences in the precipitation charge data between these different cloud types.
Sugars and health – risk assessment to risk management

Public health nutrition research is dominated by studies of assessment and analysis of diet-related health outcomes and estimates of food and nutrient intakes. Single studies provide clues, but it is the totality of evidence from wellcrafted investigations that enable a full risk assessment to be undertaken. The process and interpretation of review-level evidence has become increasingly complex as the quantity of evidence grows and techniques for quality control develop. The emergence of the GRADE (Grading of Recommendations Assessment, Development and Evaluation) system for evaluating the quality of evidence represents a useful way forward in the decisionmaking process for recommendations and developing dietary guidelines. The WHO draft guideline on sugars intake for adults and children is an example of how the GRADE system can be used to assess the burgeoning evidence on sugar consumption, dental caries and excess body weight in order to assist the process of informing recommendations for food policy and dietary practices. The strength of large, heterogeneous cohort studies of participants followed from early years to later life, and appropriately powered randomized controlled trials (RCT), provide rich insight to the impact of sugar consumption on two major, globally relevant diet-related health problems: dental caries and excess weight gain. Ecological studies, including repeated historical observations, are often ignored in favour of RCT, but in cases where RCT are not practically possible these studies provide a useful lens on the diet–disease relationship.
Researching Volunteered Geographic Information: Spatial Data, Geographic Research, and New Social Practice

The convergence of newly interactive Web-based technologies with growing practices of user-generated content disseminated on the Internet is generating a remarkable new form of geographic information. Citizens are using handheld devices to collect geographic information and contribute it to crowd-sourced data sets, using Web-based mapping interfaces to mark and annotate geographic features, or adding geographic location to photographs, text, and other media shared online. These phenomena, which generate what we refer to collectively as volunteered geographic information (VGI), represent a paradigmatic shift in how geographic information is created and shared and by whom, as well as its content and characteristics. This article, which draws on our recently completed inventory of VGI initiatives, is intended to frame the crucial dimensions of VGI for geography and geographers, with an eye toward identifying its potential in our field, as well as the most pressing research needed to realize this potential. Drawing on our ongoing research, we examine the content and characteristics of VGI, the technical and social processes through which it is produced, appropriate methods for synthesizing and using these data in research, and emerging social and political concerns related to this new form of information.
Aerosol effects on stratocumulus water paths in a PDF‐based parameterization

Successful simulation of aerosol indirect effects in climate models requires parameterizations that capture the full range of cloud‐aerosol interactions, including positive and negative liquid water path (LWP) responses to increasing aerosol concentrations, as suggested by large eddy simulations (LESs). A parameterization based on multi‐variate probability density functions with dynamics (MVD PDFs) has been incorporated into the single‐column version of GFDL AM3, extended to treat aerosol activation, and coupled with a two‐moment microphysics scheme. We use it to explore cloud‐aerosol interactions. In agreement with LESs, our single‐column simulations produce both positive and negative LWP responses to increasing aerosol concentrations, depending on precipitation and free atmosphere relative humidity. We have conducted sensitivity tests to vertical resolution and droplet sedimentation parameterization. The dependence of sedimentation on cloud droplet size is essential to capture the full LWP responses to aerosols. Further analyses reveal that the MVD PDFs are able to represent changes in buoyancy profiles induced by sedimentation as well as enhanced entrainment efficiency with aerosols comparable to LESs.
Numerical Modeling of Shear Bands and Dynamic Fracture in Metals

Numerical Modeling of Shear Bands and Dynamic Fracture in Metals Colin James McAuliffe Understanding the failure of metals at high strain rate is of utmost importance in the design of a broad range of engineering systems. Numerical methods offer the ability to analyze such complex physics and aid the design of structural systems. The objective of this research will be to develop reliable finite element models for high strain rate failure modelling, incorporating shear bands and fracture. Shear band modelling is explored first, and the subsequent developments are extended to incorporate fracture. Mesh sensitivity, the spurious dependence of failure on the discretization, is a well known hurdle in achieving reliable numerical results for shear bands and fracture, or any other strain softening model. Mesh sensitivity is overcome by regularization, and while details of regularization techniques may differ, all are similar in that a length scale is introduced which serves as a localization limiter. This dissertation contains two main contributions, the first of which presents several developments in shear band modeling. The importance of using a monolithic nonlinear solver in combination with a PDE model accounting for thermal diffusion is demonstrated. In contrast, excluding one or both of these components leads to unreliable numerical results. The Pian-Sumihara stress interpolants are also employed in small and finite deformation and shown to significantly improve the computational cost of shear band modelling. This is partly due to the fact that fewer unknowns than an irreducible discretization result from the same mesh, and more significantly, the fact that convergence of numerical results upon mesh refinement is improved drastically. This means coarser meshes are adequate to resolve shear bands, alleviating some of the computational cost of numerical modelling, which are notoriously significant. Since extremely large deformations are present during shear banding, a mesh to mesh transfer algorithm is presented for the Pian Sumihara element and used as part of a remeshing strategy. A practical application of the numerical formulation developed is modelling the shear band failure of a friction stir welded aluminum joint under high rate loading. The energy absorption capacity of these joints are subsequently analyzed and found to be significantly weaker than untreated aluminum due to the nonhomogeneous material properties of the joint. The second contribution is extending the shear band model described previously to account for fracture by way of the phase field method. The phase field method is modified to account for the contribution of inelastic deformation to the creation of fracture surfaces, which results in a rate and temperature dependent theory for fracture, due to the rate and temperature dependence of plasticity. The combined fracture and shear band model is shown to be capable of representing a wider spectrum of strain rates than either the phase field model or the shear band model alone.
Correlation between the spatio-temporal distributions of aerosols, sulphur dioxide, and formaldehyde using MODIS and SCIAMACHY satellite data for China

The spatial and temporal relationship between fine-mode aerosol optical depth (AOD) observed by the Moderate Resolution Imaging Spectroradiometer (MODIS) and tropospheric columns of SO2 and formaldehyde (HCHO) from the Scanning Imaging Absorption Chartography (SCIAMACHY) are used to infer information on the variability of sulphate aerosol, which is a major determinant of fine-mode AOD (AODf) in east China. When averaging the satellite data over specific regions of China and for longer time periods (from 2005 to 2011), we find obvious similar trends between AODf and SO2, HCHO columns for southern and eastern China. The results of satellite observations show the high spatial and temporal correlation between AODf and SO2 over the Yangtze River Delta (R2), the Pearl River Delta (R3), and the Chongqing–Chengdu region (R4), with the coefficients of determination (R2) of 0.376, 0.438, and 0.837, respectively. These regions are performing with the huge amount of anthropogenic SO2 emissions by traffic, industry, and domestic heating. The trend is consistent with fine-mode aerosol and SO2 appearing in summer because AODf is often correlated with enhanced HCHO concentrations, reflecting the importance of secondary aerosol formation over industrialized regions in that season. Over the North China Plain, distinct maximum values of AODf and HCHO were observed and the minimum value for SO2 was observed in summer. The decrease in the mean SO2 column was 35.5%, which has been attributed to the strict security measures by the government during the 2008 Olympic Games period while there was a decrease of 46% in AODf at the same time. As sulphate aerosol occurs seasonally in the North China Plain, the strong correlation between anomalies of AODf and SO2 can be used to estimate and analyse the distribution of sulphate aerosol. Singular value decomposition (SVD) analysis showed the same variation between AODf and SO2 over eastern China and Sichuan Province, and a distinct negative value of SVD variables over comparably industrialized regions in southern and eastern China and Sichuan Province. The results for SO4 from the Model for Ozone and Related chemical Tracers model for southern and eastern China and the Sichuan regions suggest much stronger sulphate contributions to aerosol formation than for other areas of China. We propose that the SVD variables between AODf and SO2, which can be inferred from the satellite data, can be used as indicators for regional pollution control.
Advanced Materials for Energy Storage

Popularization of portable electronics and electric vehicles worldwide stimulates the development of energy storage devices, such as batteries and supercapacitors, toward higher power density and energy density, which significantly depends upon the advancement of new materials used in these devices. Moreover, energy storage materials play a key role in efficient, clean, and versatile use of energy, and are crucial for the exploitation of renewable energy. Therefore, energy storage materials cover a wide range of materials and have been receiving intensive attention from research and development to industrialization. In this Review, firstly a general introduction is given to several typical energy storage systems, including thermal, mechanical, electromagnetic, hydrogen, and electrochemical energy storage. Then the current status of high‐performance hydrogen storage materials for on‐board applications and electrochemical energy storage materials for lithium‐ion batteries and supercapacitors is introduced in detail. The strategies for developing these advanced energy storage materials, including nanostructuring, nano‐/microcombination, hybridization, pore‐structure control, configuration design, surface modification, and composition optimization, are discussed. Finally, the future trends and prospects in the development of advanced energy storage materials are highlighted.
Atmospheric parameters retrieved from CRISTA measurements in the upper mesosphere and lower thermosphere

During its two missions of about one week duration each in November 1994 and in August 1997 the Cryogenic Infrared Spectrometers and Telescopes for the Atmosphere (CRISTA) experiment observed spectrally resolved mid- and far- infrared emissions from the earth limb in the altitude regime from the troposphere to the lower thermosphere. The measurements concentrated on high spatial resolution in all three dimensions in the lower part of the height range. At upper mesosphere/lower thermosphere altitudes global ozone concentrations during day and night, daytime carbon-dioxide densities, and atmospheric temperatures were derived using a comprehensive non-LTE model. The derived parameters compare well with other experimental data. Pronounced horizontal structures in latitude as well as in longitude are found in all parameters showing that dynamical influences are of importance also in the upper mesosphere/lower thermosphere. Carbon dioxide mixing ratios start to depart from their tropospheric values at altitudes as low as 70 - 80 km. Atmospheric temperatures of 140 K and below were retrieved near the mesopause at high northern latitudes in August. These data are supported by the simultaneous observation of polar mesospheric clouds.