Miracle-dz/UniFAR-FTUs huggingface dataset:
Solvent-Dependent Structures of Natural Products Based on the Combined Use of DFT Calculations and 1H-NMR Chemical Shifts

Detailed solvent and temperature effects on the experimental 1H-NMR chemical shifts of the natural products chrysophanol (1), emodin (2), and physcion (3) are reported for the investigation of hydrogen bonding, solvation and conformation effects in solution. Very small chemical shift of │Δδ│ < 0.3 ppm and temperature coefficients │Δδ/ΔΤ│ ≤ 2.1 ppb/K were observed in DMSO-d6, acetone-d6 and CDCl3 for the C(1)–OH and C(8)–OH groups which demonstrate that they are involved in a strong intramolecular hydrogen bond. On the contrary, large chemical shift differences of 5.23 ppm at 298 K and Δδ/ΔΤ values in the range of −5.3 to −19.1 ppb/K between DMSO-d6 and CDCl3 were observed for the C(3)–OH group which demonstrate that the solvation state of the hydroxyl proton is a key factor in determining the value of the chemical shift. DFT calculated 1H-NMR chemical shifts, using various functionals and basis sets, the conductor-like polarizable continuum model, and discrete solute-solvent hydrogen bond interactions, were found to be in very good agreement with the experimental 1H-NMR chemical shifts even with computationally less demanding level of theory. The 1H-NMR chemical shifts of the OH groups which participate in intramolecular hydrogen bond are dependent on the conformational state of substituents and, thus, can be used as molecular sensors in conformational analysis. When the X-ray structures of chrysophanol (1), emodin (2), and physcion (3) were used as input geometries, the DFT-calculated 1H-NMR chemical shifts were shown to strongly deviate from the experimental chemical shifts and no functional dependence could be obtained. Comparison of the most important intramolecular data of the DFT calculated and the X-ray structures demonstrate significant differences for distances involving hydrogen atoms, most notably the intramolecular hydrogen bond O–H and C–H bond lengths which deviate by 0.152 tο 0.132 Å and 0.133 to 0.100 Å, respectively, in the two structural methods. Further differences were observed in the conformation of –OH, –CH3, and –OCH3 substituents.
Theory of Randomized Search Heuristics: Foundations and Recent Developments

Randomized search heuristics such as evolutionary algorithms, genetic algorithms, evolution strategies, ant colony and particle swarm optimization turn out to be highly successful for optimization in practice. The theory of randomized search heuristics, which has been growing rapidly in the last five years, also attempts to explain the success of the methods in practical applications. This book covers both classical results and the most recent theoretical developments in the field of randomized search heuristics such as runtime analysis, drift analysis and convergence. Each chapter provides an overview of a particular domain and gives insights into the proofs and proof techniques of more specialized areas. Open problems still remain widely in randomized search heuristics -- being a relatively young and vast field. These problems and directions for future research are addressed and discussed in this book. The book will be an essential source of reference for experts in the domain of randomized search heuristics and also for researchers who are involved or ready to embark in this field. As an advanced textbook, graduate students will benefit from the comprehensive coverage of topics.
Visual Information Processing Based on Spatial Filters Constrained by Biological Data.

Abstract : Visual perception was investigated using spatial filters that are constrained by biological data. This report has four major parts: (1) a theoretical background to Fourier analysis; (2) a review of the literature relating to the spatial filtering characteristics of mammalian visual systems; (3) visual information processing in terms of spatial filtering; (4) the relating of contrast sensitivity to the identification of complex objects. The common denominator to all the investigations is spatial filtering. The major goal of the dissertation was the attempt to explain certain aspects of visual perception using a single concept: filtering. (Author)
The epileptic network of Lennox-Gastaut syndrome

Objective To identify brain regions underlying interictal generalized paroxysmal fast activity (GPFA), and their causal interactions, in children and adults with Lennox-Gastaut syndrome (LGS). Methods Concurrent scalp EEG-fMRI was performed in 2 separately analyzed patient groups with LGS: 10 children (mean age 8.9 years) scanned under isoflurane-remifentanil anesthesia and 15 older patients (mean age 31.7 years) scanned without anesthesia. Whole-brain event-related analysis determined GPFA-related activation in each group. Results were used as priors in a dynamic causal modeling (DCM) analysis comparing evidence for different neuronal hypotheses describing initiation and propagation of GPFA between cortex, thalamus, and brainstem. Results A total of 1,045 GPFA events were analyzed (cumulative duration 1,433 seconds). In both pediatric and older groups, activation occurred in distributed association cortical areas, as well as the thalamus and brainstem (p < 0.05, corrected for family-wise error). Activation was similar across individual patients with structural, genetic, and unknown etiologies of epilepsy, particularly in frontoparietal cortex. In both groups, DCM revealed that GPFA was most likely driven by prefrontal cortex, with propagation occurring first to the brainstem and then from brainstem to thalamus. Conclusions We show reproducible evidence of a cortically driven process within the epileptic network of LGS. This network is present early (in children) and late (in older patients) in the course of the syndrome and across diverse etiologies of epilepsy, suggesting that LGS reflects shared “secondary network” involvement. A cortical-to-subcortical hierarchy is postulated whereby GPFA rapidly propagates from prefrontal cortex to the brainstem via extrapyramidal corticoreticular pathways, whereas the thalamus is engaged secondarily.
Drink Choice is Important: Beverages Make a Substantial Contribution to Energy, Sugar, Calcium and Vitamin C Intake among Australians

It is important to understand the role of beverages in population dietary intake in order to give relevant advice. Population estimates were derived from one-day food recall dietary data from 12,153 participants in the 2011–2012 Australian National Nutrition and Physical Activity Survey. Almost all Australians (99.9%) consumed at least one beverage on the day of the survey, accounting for 16.6% of the total energy intake for adults (aged 19 years and over) and 13.0% for children (aged 2–18 years). Similarly, beverages contributed 26–29% to calcium intake, 22–28% to vitamin C intake, and 35–36% to sugar intake. Water was consumed on the day of the survey by 84.1% of Australian adults and 90.5% of children. For adults, the greatest beverage contributors to total energy intake were alcoholic drinks (5.6%), coffee (3.1%), and soft drinks (1.9%), and for children, plain milk (3.1%), flavoured milk (2.8%), and fruit juice (2.6%). Coffee (10.6%) made the greatest contribution to calcium intake for adults; and plain milk (9.9%) and flavoured milk (7.6%) for children. The greatest contributors to vitamin C intake were fruit juice (13.4%) and alcoholic drinks (6.1%) for adults; and fruit juice (23.4%) for children. For total sugar intake, soft drinks (8.0%), coffee (8.4%), and fruit juice (5.9%) made the highest contribution for adults; and fruit juice (9.8%) and soft drinks (8.7%) for children. The type and amount of beverage consumption has considerable relevance to dietary quality for Australians.
Maytenus macrocarpa (Ruiz & Pav.) Briq.: Phytochemistry and Pharmacological Activity

Maytenus macrocarpa (Celastraceae) is a tree native to Amazonia. Its roots, leaves, bark, and combinations of these are used in traditional medicine mainly to treat rheumatism and, to a lesser extent, to heal wounds and to combat bronchitis and diarrhea. To date, mainly triterpenes and dihydro-β-agarofuran sesquiterpenes were isolated from M. macrocarpa. Extracts and selected pure compounds isolated from the leaves, roots, and stem bark showed antibacterial, antiviral, antiparasitic, anti-inflammatory, and cytotoxic activities in vitro. The aim of this review is to summarize the available ethnobotanical, phytochemical, and pharmacological information about this traditional Amazonian medicinal tree, as well as to attract the attention of phytochemists and pharmacognosists to this potentially interesting source of ethnopharmaceuticals.
Assessing dengue control in Tokyo, 2014

Background In summer 2014, an autochthonous outbreak of dengue occurred in Tokyo, Japan, in which Yoyogi Park acted as the focal area of transmission. Recognizing the outbreak, concerted efforts were made to control viral spread, which included mosquito control, public announcement of the outbreak, and a total ban on entering the park. We sought to assess the effectiveness of these control measures. Methodology/Principal findings We used a mathematical model to describe the transmission dynamics. Using dates of exposure and illness onset, we categorized cases into three groups according to the availability of these datasets. The infection process was parametrically modeled by generation, and convolution of the infection process and the incubation period was fitted to the data. By estimating the effective reproduction number, we determined that the effect of dengue risk communication together with mosquito control from 28 August 2014 was insufficiently large to lower the reproduction number to below 1. However, once Yoyogi Park was closed on 4 September, the value of the effective reproduction number began to fall below 1, and the associated relative reduction in the effective reproduction number was estimated to be 20%–60%. The mean incubation period was an estimated 5.8 days. Conclusions/Significance Regardless of the assumed number of generations of cases, the combined effect of mosquito control, risk communication, and park closure appeared to be successful in interrupting the chain of dengue transmission in Tokyo.
Unraveling the role of the secretor antigen in human rotavirus attachment to histo-blood group antigens

Rotavirus is the leading agent causing acute gastroenteritis in young children, with the P[8] genotype accounting for more than 80% of infections in humans. The molecular bases for binding of the VP8* domain from P[8] VP4 spike protein to its cellular receptor, the secretory H type-1 antigen (Fuc-α1,2-Gal-β1,3-GlcNAc; H1), and to its precursor lacto-N-biose (Gal-β1,3-GlcNAc; LNB) have been determined. The resolution of P[8] VP8* crystal structures in complex with H1 antigen and LNB and site-directed mutagenesis experiments revealed that both glycans bind to the P[8] VP8* protein through a binding pocket shared with other members of the P[II] genogroup (i.e.: P[4], P[6] and P[19]). Our results show that the L-fucose moiety from H1 only displays indirect contacts with P[8] VP8*. However, the induced conformational changes in the LNB moiety increase the ligand affinity by two-fold, as measured by surface plasmon resonance (SPR), providing a molecular explanation for the different susceptibility to rotavirus infection between secretor and non-secretor individuals. The unexpected interaction of P[8] VP8* with LNB, a building block of type-1 human milk oligosaccharides, resulted in inhibition of rotavirus infection, highlighting the role and possible application of this disaccharide as an antiviral. While key amino acids in the H1/LNB binding pocket were highly conserved in members of the P[II] genogroup, differences were found in ligand affinities among distinct P[8] genetic lineages. The variation in affinities were explained by subtle structural differences induced by amino acid changes in the vicinity of the binding pocket, providing a fine-tuning mechanism for glycan binding in P[8] rotavirus.
Instant vocabulary through prefixes and suffixes

Aims to help expand vocabulary and improve reading comprehension by modifying the reader's existing lexicon. The Power Japanese series presents a selection of guides to difficult or confusing aspects of the Japanese language. The student can find a quick reference to particles, a guide to the myriad levels of politeness, books of idioms, vocabulary builders, emotive expressions and turns of speech - all with natural examples.
New Rabies Vaccines for Use in Humans

Although vaccines are available, rabies still claims more than 55,000 human lives each year. In most cases, rabies vaccines are given to humans after their exposure to a rabid animal; pre-exposure vaccination is largely reserved for humans at high risk for contacts with the virus. Most cases of human rabies are transmitted by dogs. Dog rabies control by mass canine vaccination campaigns combined with intensive surveillance programs has led to a decline of human rabies in many countries but has been unsuccessful in others. Animal vaccination programs are also not suited to control human rabies caused by bat transmission, which is common in some Central American countries. Alternatively, or in addition, more widespread pre-exposure vaccination, especially in highly endemic remote areas, could be implemented. With the multiple dose regimens of current vaccines, pre-exposure vaccination is not cost effective for most countries and this warrants the development of new rabies vaccines, which are as safe as current vaccines, but achieve protective immunity after a single dose, and most importantly, are less costly. This chapter discusses novel rabies vaccines that are in late stage pre-clinical testing or have undergone clinical testing and their potential for replacing current vaccines.
A method to concatenate multiple short time series for evaluating dynamic behaviour during walking

Gait variability is a sensitive metric for assessing functional deficits in individuals with mobility impairments. To correctly represent the temporal evolution of gait kinematics, nonlinear measures require extended and uninterrupted time series. In this study, we present and validate a novel algorithm for concatenating multiple time-series in order to allow the nonlinear analysis of gait data from standard and unrestricted overground walking protocols. The full-body gait patterns of twenty healthy subjects were captured during five walking trials (at least 5 minutes) on a treadmill under different weight perturbation conditions. The collected time series were cut into multiple shorter time series of varying lengths and subsequently concatenated using a novel algorithm that identifies similar poses in successive time series in order to determine an optimal concatenation time point. After alignment of the datasets, the approach then concatenated the data to provide a smooth transition. Nonlinear measures to assess stability (Largest Lyapunov Exponent, LyE) and regularity (Sample Entropy, SE) were calculated in order to quantify the efficacy of the concatenation approach using intra-class correlation coefficients, standard error of measurement and paired effect sizes. Our results indicate overall good agreement between the full uninterrupted and the concatenated time series for LyE. However, SE was more sensitive to the proposed concatenation algorithm and might lead to false interpretation of physiological gait signals. This approach opens perspectives for analysis of dynamic stability of gait data from physiological overground walking protocols, but also the re-processing and estimation of nonlinear metrics from previously collected datasets.
Robust Model Predictive Control for Process Control and Supply Chain Optimization

Model Predictive Control (MPC) is traditionally designed assuming no model mismatch and tuned to provide acceptable behavior when mismatch occurs. This thesis extends the MPC design to account for explicit mismatch in the control and optimization of a wide range of uncertain dynamic systems with feedback, such as in process control and supply chain optimization. The major contribution of the thesis is the development of a new MPC method for robust performance, which offers a general framework to optimize the uncertain system behavior in the closed-loop subject to hard bounds on manipulated variables and soft bounds on controlled variables. This framework includes the explicit handling of correlated, time-varying or time-invariant, parametric uncertainty appearing externally (in demands and disturbances) and internally (in plant/model mismatch) to the control system. In addition, the uncertainty in state estimation is accounted for in the controller. For efficient and reliable real-time solution, the bilevel stochastic optimization formulation of the robust MPC method is approximated by a limited number of (convex) Second Order Cone Programming (SOCP) problems with an industry-proven heuristic and the classical chance-constrained programming technique. A closed-loop uncertainty characterization method is also developed which improves real-time tractability by performing intensive calculations off-line. The new robust MPC method is extended for process control problems by integrating a robust steady-state optimization method addressing closed-loop uncertainty. In addition, the objective function for trajectory optimization can be formulated as nominal or expected dynamic performance. Finally, the method is formulated m deviation variables to correctly estimate time-invariant uncertainty.
Increased intestinal carbonate precipitate abundance in the sea bream (Sparus aurata L.) in response to ocean acidification

Marine fish contribute to the carbon cycle by producing mineralized intestinal precipitates generated as by-products of their osmoregulation. Here we aimed at characterizing the control of epithelial bicarbonate secretion and intestinal precipitate presence in the gilthead sea bream in response to predicted near future increases of environmental CO2. Our results demonstrate that hypercapnia (950 and 1800 μatm CO2) elicits higher intestine epithelial HCO3- secretion ex vivo and a subsequent parallel increase of intestinal precipitate presence in vivo when compared to present values (440 μatm CO2). Intestinal gene expression analysis in response to environmental hypercapnia revealed the up-regulation of transporters involved in the intestinal bicarbonate secretion cascade such as the basolateral sodium bicarbonate co-transporter slc4a4, and the apical anion transporters slc26a3 and slc26a6 of sea bream. In addition, other genes involved in intestinal ion uptake linked to water absorption such as the apical nkcc2 and aquaporin 1b expression, indicating that hypercapnia influences different levels of intestinal physiology. Taken together the current results are consistent with an intestinal physiological response leading to higher bicarbonate secretion in the intestine of the sea bream paralleled by increased luminal carbonate precipitate abundance and the main related transporters in response to ocean acidification.
Network Management Architectures

i Abstract Network management is needed to control and optimize the operation of the network and to respond to changing user requirements. Management includes the initialization, monitoring and modification of the network functions. In order to perform management, special functions are needed. To distinguish these functions from the normal network functions, this thesis introduces the terms 'management functions' and 'primary functions'. Management functions may be performed explicitly by human operators, but also automatically by dedicated hard-and software modules. In case human operators are responsible for network management, most management functions will be performed from a limited number of remote locations. In case management functions are performed automatically, it is possible to distribute the hard-and software modules that implement these functions over the various systems in the network. Architectures for network management enable the designers to discuss management functions at a high level of abstraction and guide the design of management protocols and services. In this thesis it is assumed that architectures consist of: • a set of architectural concepts, • rules that tell how to use these concepts, • models that show the application of these rules and concepts to design a specific class of systems. All current management architectures, notably the ISO, ITU-T (the former CCITT) and the IETF architectures, have been developed after the design of the network functions have been completed. Such approach indicates a specific conceptual view on the role of management functions and invites to apply different architectural concepts for the design of management functions. This thesis proposes an alternative approach, in which no principle distinction is made between the management requirements and the requirements of primary functions. Both sets of requirements can be integrated into one set of requirements and elaborated in a single design process, which uses one architectural model. The thesis consists of two parts; Part I (Chapter 2-Chapter 4) analyses the state of the art in network management architectures and Part II (Chapter 5-Chapter 9) develops an alternative network management architecture. Chapter 2 analyses the ISO management architecture, which is defined in the 'Management Framework' and the 'Systems Management Overview' standards. As compared to other network management architectures, the ISO architecture received most attention within the research community. Abstract ii The management architecture of the ITU-T is known as the 'Telecommunica-tions Management Network' (TMN), and is discussed in Chapter 3. The name of this architecture already indicates that this architecture is …
Light: Toward a Transdisciplinary Science of Appearance and Atmosphere.

To understand the processes behind seeing light, we need to integrate knowledge about the incoming optical structure, its perception, and how light interacts with material, shape, and space-objectively and subjectively. To that end, we need a novel approach to the science of light, namely, a transdisciplinary science of appearance, integrating optical, perceptual, and design knowledge and methods. In this article, I review existing literature as a basis for such a synthesis, which should discuss light in its full complexity, including its spatial properties and interactions with materials, shape, and space. I propose to investigate this by representing the endless variety of light, materials, shapes, and space as canonical modes and their combinations. Expected final online publication date for the Annual Review of Vision Science Volume 5 is September 16, 2019. Please see http://www.annualreviews. org/page/journal/pubdates for revised estimates.
Process identification using a modified Elman neural net

In this paper, a modified Elman neural network (1990) is utilized to identify industrial processes. The basic structure of the Elman network is introduced and one of its modified versions is presented. A specific learning algorithm is developed which optimizes not only the feedforward but also the self-feedback connections of such partially recurrent neural networks. The identification system proposed is arranged in a parallel pattern. Numerical results for the identification of a pH neutralization process are also included. <<ETX>>