Miracle-dz/UniFAR-FTUs huggingface dataset:
Production of tailored hydroxylated prodiginine showing combinatorial activity with rhamnolipids against plant-parasitic nematodes

Bacterial secondary metabolites exhibit diverse remarkable bioactivities and are thus the subject of study for different applications. Recently, the individual effectiveness of tripyrrolic prodiginines and rhamnolipids against the plant-parasitic nematode Heterodera schachtii, which causes tremendous losses in crop plants, was described. Notably, rhamnolipid production in engineered Pseudomonas putida strains has already reached industrial implementation. However, the non-natural hydroxyl-decorated prodiginines, which are of particular interest in this study due to a previously described particularly good plant compatibility and low toxicity, are not as readily accessible. In the present study, a new effective hybrid synthetic route was established. This included the engineering of a novel P. putida strain to provide enhanced levels of a bipyrrole precursor and an optimization of mutasynthesis, i.e., the conversion of chemically synthesized and supplemented monopyrroles to tripyrrolic compounds. Subsequent semisynthesis provided the hydroxylated prodiginine. The prodiginines caused reduced infectiousness of H. schachtii for Arabidopsis thaliana plants resulting from impaired motility and stylet thrusting, providing the first insights on the mode of action in this context. Furthermore, the combined application with rhamnolipids was assessed for the first time and found to be more effective against nematode parasitism than the individual compounds. To obtain, for instance, 50% nematode control, it was sufficient to apply 7.8 μM hydroxylated prodiginine together with 0.7 μg/ml (~ 1.1 μM) di-rhamnolipids, which corresponded to ca. ¼ of the individual EC50 values. In summary, a hybrid synthetic route toward a hydroxylated prodiginine was established and its effects and combinatorial activity with rhamnolipids on plant-parasitic nematode H. schachtii are presented, demonstrating potential application as antinematodal agents. Graphical Abstract
Characteristics and a comparison of the gut microbiota in two frog species at the beginning and end of hibernation

Season has been suggested to contribute to variation in the gut microbiota of animals. The complicated relationships between amphibians and their gut microbiota and how they change throughout the year require more research. Short-term and long-term hypothermic fasting of amphibians may affect gut microbiota differently; however, these changes have not been explored. In this study, the composition and characteristics of the gut microbiota of Rana amurensis and Rana dybowskii during summer, autumn (short-term fasting) and winter (long-term fasting) were studied by high-throughput Illumina sequencing. Both frog species had higher gut microbiota alpha diversity in summer than autumn and winter, but no significant variations between autumn and spring. The summer, autumn, and spring gut microbiotas of both species differed, as did the autumn and winter microbiomes. In summer, autumn and winter, the dominant phyla in the gut microbiota of both species were Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria. All animals have 10 OTUs (>90% of all 52 frogs). Both species had 23 OTUs (>90% of all 28 frogs) in winter, accounting for 47.49 ± 3.84% and 63.17 ± 3.69% of their relative abundance, respectively. PICRUSt2 analysis showed that the predominant functions of the gut microbiota in these two Rana were focused on carbohydrate metabolism, Global and overview maps, Glycan biosynthesis metabolism, membrane transport, and replication and repair, translation. The BugBase analysis estimated that among the seasons in the R. amurensis group, Facultatively_Anaerobic, Forms_Biofilms, Gram_Negative, Gram_Positive, Potentially_Pathogenic were significantly different. However, there was no difference for R. dybowskii. The research will reveal how the gut microbiota of amphibians adapts to environmental changes during hibernation, aid in the conservation of endangered amphibians, particularly those that hibernate, and advance microbiota research by elucidating the role of microbiota under various physiological states and environmental conditions.
Performance and physiological quality of Escallonia resinosa seeds: prospects for their use in reforestation and restoration

In the Andes, many native forest species are not used in reforestation or restoration programs mainly due to a lack of information about their propagation. In this study, we evaluated the performance of the seeds of Escallonia resinosa by analyzing fruit and seed productivity and characteristics, seed physiological quality, and the germination rate of seeds collected at different stages of fruit physiological maturity, using tetrazolium and standard germination tests. Our results show an estimated production (mean ± SD) of 34,252.5 ± 25,900 fruits per tree and 26.5 ± 20 million seeds per tree. Seed length was 1.0 ± 0.13 mm and seed weight was 12.4 ± 1 μg. We recognized two different morphological types of seeds: Type I seeds (lacking testa) were unviable, whereas all Type II seeds (with testa) germinated. Seed viability and germination rates were 10.5 and 48.6%, respectively; therefore, the viability test underestimated the actual germination rate. Morphological or microsite variables of the parent tree did not influence seed viability or germination. Germination rates were highest (41.8 ± 2.5%) for the seeds of fruits harvested at the initial maturity stage (green fruits). Our results show that E. resinosa is a species with potential for reforestation and restoration projects in the Andes: it has high seed production and good germination performance, and seeds can be harvested from fruits collected at different stages of physiological maturity.
The CMC-MRB Global Environmental Multiscale (GEM) Model. Part III: Nonhydrostatic Formulation

Abstract An integrated forecasting and data assimilation system has been and is continuing to be developed by the Meteorological Research Branch (MRB) in partnership with the Canadian Meteorological Centre (CMC) of Environment Canada. Part III of this series of papers presents the nonhydrostatic formulation and some sample results. The nonhydrostatic formulation uses Laprise's hydrostatic pressure as the basis for its vertical coordinate. This allows the departure from the hydrostatic formulation to be incorporated in an efficient switch-controlled perturbative manner. The time discretization of the model dynamics is (almost) fully implicit semi-Lagrangian, where all terms including the nonlinear terms are (quasi-) centered in time. The spatial discretization for the adjustment step employs a staggered Arakawa C grid that is spatially offset by half a mesh length in the meridional direction with respect to that employed in previous model formulations. It is accurate to second order, whereas the interpolat.
Homogenization of the Poisson Equation in a Thick Periodic Junction

A convergence theorem and asymptotic estimates as C 0 are proved for a solution to a mixed boundary-value problem for the Poisson equation in a junction Q, of a domain o and a large number N 2 of c-periodically situated thin cylinders with thickness of order e = °(*) For this junction, we construct an extension operator and study its properties.
Nonlinear Least Squares

In the first three examples,m (x, β) is (generically) differentiable in the parameters β. In the final example, m (·) is not differentiable with respect to β3. Nonlinear regression is frequently adopted because the functional form m (x, β) is suggested by an economic model. In other cases, it is adopted as a flexible approximation to an unknown regression function. This document provides a brief introduction to the nonlinear least squares problem and is organized as follows: Section 2 presents the nonlinear least squares (NLLS) estimator. Section 3 discusses issues related to numerical methods that can be used to obtain it. Section 4 addresses the issue of inference in the NLLS context. Section 5 generalizes the NLLS estimator when homoskedasticity and/or autocorrelation are present. Finally, Section 6 presents a particular class of nonlinear models denominated artificial neural networks (ANN).
Introduction to Sensitivity Analysis

Sensitivity analysis provides users of mathematical and simulation models with tools to appreciate the dependency of the model output from model input and to investigate how important is each model input in determining its output. All application areas are concerned, from theoretical physics to engineering and socio-economics. This introductory paper provides the sensitivity analysis aims and objectives in order to explain the composition of the overall “Sensitivity Analysis” chapter of the Springer Handbook. It also describes the basic principles of sensitivity analysis, some classification grids to understand the application B. Iooss ( ) Industrial Risk Management Department, EDF RD biooss@yahoo.fr A. Saltelli Centre for the Study of the Sciences and the Humanities (SVT), University of Bergen (UIB), Bergen, Norway Institut de Ciencia i Tecnologia Ambientals (ICTA), Universitat Autonoma de Barcelona (UAB), Barcelona, Spain e-mail: andrea.saltelli@svt.uib. no; andrea.saltelli@jrc.ec. europa.eu © Springer International Publishing Switzerland 2015 R. Ghanem et al. (eds.), Handbook of Uncertainty Quantification, DOI 10.1007/978-3-319-11259-6_31-1 1 2 B. Iooss and A. Saltelli ranges of each method, a useful software package, and the notations used in the chapter papers. This section also offers a succinct description of sensitivity auditing, a new discipline that tests the entire inferential chain including model development, implicit assumptions, and normative issues and which is recommended when the inference provided by the model needs to feed into a regulatory or policy process. For the “Sensitivity Analysis” chapter, in addition to this introduction, eight papers have been written by around twenty practitioners from different fields of application. They cover the most widely used methods for this subject: the deterministic methods as the local sensitivity analysis, the experimental design strategies, the sampling-based and variance-based methods developed from the 1980s, and the new importance measures and metamodelbased techniques established and studied since the 2000s. In each paper, toy examples or industrial applications illustrate their relevance and usefulness.
The total waiting time in a busy period of a stable single-server queue, II

This paper is a continuation of Daley (1969), referred to as (I), whose notation and numbering is continued here. We shall indicate various approaches to the study of the total waiting time in a busy period2 of a stable single-server queue with a Poisson arrival process at rate λ, and service times independently distributed with common distribution function (d.f.) B(·). Let X'i denote3 the total waiting time in a busy period which starts at an epoch when there are i (≧ 1) customers in the system (to be precise, the service of one customer is just starting and the remaining i − 1 customers are waiting for service). We shall find the first two moments of X'i, prove its asymptotic normality for i → ∞ when B(·) has finite second moment, and exhibit the Laplace-Stieltjes transform of X'i in M/M/1 as the ratio of two Bessel functions.
General variational solution for seismic and static active earth pressure on rigid walls considering soil tensile strength cut-off

目 的 传统的主动土压力计算方法在考虑土体抗拉强度时的假设不合理, 具有明显的局限性. 本文考虑土体剪切屈服和拉伸破坏准则, 不假设滑裂面形态, 并基于墙后填土主动极限平衡条件与变分极值原理, 提出刚性挡土墙的地震和静态主动土压力的一般解析解, 确定相应于墙体可能运动模式的主动土压力合力值及其作用点的变化范围. 创新点 1. 采用变分法, 建立同时考虑土体剪切和拉伸破坏的刚性挡土墙地震和静态主动土压力的紧凑解析解; 2. 确立相应于墙体平动和转动复合运动模式的刚性挡土墙主动土压力的可能变化范围, 以及其合力作用点的合理范围; 3. 揭示13个基本参数对主动土压力的影响规律, 并定量确定剪切-拉裂复合模式的滑裂面形态以及作用于滑裂面上的法向应力. 方 法 1. 基于刚性挡土墙后侧土体的主动极限平衡状态, 通过拟静力法引入等效地震力, 并根据拉格朗日乘子法和变分极值原理, 建立考虑土体剪切与拉裂破坏的地震 (含静态) 主动土压力的隐式求解方程; 2. 运用 MATLAB 中的 fsolve 函数, 通过叠代计算与精度控制, 得到主动土压力的计算结果. 结 论 1. 所提方法算得的地震和静态主动土压力, 与试验及理论结果具有较好的一致性, 且本方法的适用性更为广泛; 2. 同一刚性挡土墙在不同的运动模式下, 墙后主动土压力有所不同, 但其总是在有限范围内变化; 3. 随着土压力合力作用点在其合理变化范围内逐渐升高, 滑裂面剪切段的形态逐渐由平面向曲面发展; 4. 墙后土体表层的张拉裂隙深度受竖向地震系数、 条形荷载分布宽度及其距墙顶水平距离的影响均很小, 但受其余 10 个参数的影响较大. According to the limit equilibrium state of soils behind rigid walls and the pseudo-static approach, a general closed-form solution to seismic and static active earth pressure on the walls, which considers shear and tension failure of the retained soil, is put forward using a variational calculus method. The application point of the active resultant force specified in the proposed method is explained with a clear physical meaning related to possible movement modes of the walls. In respect of the derived nine dependent equations reflecting the functional characteristics of the earth pressure, the proposed method can be performed easily via an implicit strategy. There are 13 basic factors related to the retained soils, walls, and external loads to be involved in the proposed method. The tension crack segment of the slip surface is obviously influenced by these parameters, apart from vertical seismic coefficient and geometric bounds of the surcharge, but the shear slip segment maintains an approximately planar shape almost uninfluenced by these parameters. Noticeably, the proposed method quantitatively reflects that the resultant of the active earth pressure is always within a limited range under different possible movements of the same wall.
Humoral Immune Response after COVID-19 mRNA Vaccination in Patients with Liver Cirrhosis: A Prospective Real-Life Single Center Study

Coronavirus-disease-2019 (COVID-19) mRNA vaccination effectively reduces mortality and morbidity in cirrhotic patients, but the immunogenicity and safety of vaccination have been partially characterized. The study aimed to evaluate humoral response, predictive factors, and safety of mRNA-COVID-19 vaccination in cirrhotic patients compared to healthy subjects. A prospective, single-center, observational study enrolled consecutive cirrhotic patients who underwent mRNA-COVID-19 vaccination from April to May 2021. Anti-spike-protein (anti-S) and nucleocapsid-protein (anti-N) antibodies were evaluated before the first (T0) and the second (T1) doses and 15 days after completing the vaccination. An age and sex-matched healthy reference group was included. The incidence of adverse events (AEs) was assessed. In total, 162 cirrhotic patients were enrolled, 13 were excluded due to previous SARS-CoV-2 infection; therefore, 149 patients and 149 Health Care Workers (HCWs) were included in the analysis. The seroconversion rate was similar in cirrhotic patients and HCWs at T1 (92.5% vs. 95.3%, p = 0.44) and T2 (100% in both groups). At T2, anti-S-titres were significantly higher in cirrhotic patients compared to HCWs (2776.6 vs. 1756 BAU/mL, p < 0.001]. Male sex (β = −0.32 [−0.64, −0.04], p = 0.027) and past-HCV-infection (β = −0.31 [−0.59, −0.04], p = 0.029) were independent predictors of lower anti-S-titres on multiple-gamma-regression-analysis. No severe AEs occurred. The COVID-19-mRNA vaccination induces a high immunization rate and anti-S-titres in cirrhotic patients. Male sex and past-HCV infection are associated with lower anti-S-titres. The COVID-19-mRNA vaccination is safe.
Deeply Virtual Compton Scattering on Neon

The measurement of Deeply Virtual Compton Scattering (DVCS) provides access to the spin structure of nucleons. Its description within the theoretical framework of generalized parton distributions offers a possibility to determine the total angular momentum carried by the quarks in the nucleon. In this thesis a cross section asymmetry with respect to the beam-helicity has been measured for hard exclusive electroproduction of photons from a neon target. The resulting asymmetry appears in the distribution of the produced photon in the azimuthal angle φ around the virtual-photon direction. Attributed to the interference between the BetheHeitler process and the DVCS process, the asymmetry gives access to the latter at the amplitude level. The DVCS reaction on nuclei proceeds through two different processes the coherent process that involves the nucleus as a whole and the incoherent process as the reaction on a single nucleon. The beam-helicity asymmetry and its dependences are studied for the coherent and incoherent sample, separately. The data presented has been accumulated by the HERMES experiment at DESY, scattering the HERA 27.6 GeV polarized positron beam off an unpolarized neon target.
Honeydew Is a Food Source and a Contact Kairomone for Aphelinus mali

Simple Summary Natural enemies of major pests such as parasitoids require sugar-rich food for development and reproduction. In agricultural fields, honeydew excreted by aphids is often the predominant sugar source that parasitoids can consume. Moreover, honeydew can constitute a cue used by parasitoid females to find their aphid host. However, in some species, such as the woolly apple aphid (Eriosoma lanigerum), honeydew is coated with a thin layer of wax, which could make its consumption harder and prevent the emission of attractive odors for parasitoids. In the present study, we evaluated the benefits in terms of longevity and host searching that could provide honeydew to the main parasitoid of the woolly apple aphid, Aphelinus mali, and infer parasitoid feeding patterns in apple orchards. Results suggested that A. mali is able to consume honeydew in laboratory and field conditions and to benefit from honeydew, as it increased its longevity when honeydew was provided with water. Although no olfactory preference was observed, honeydew also stimulated oviposition by A. mali. The contribution of honeydew to increase the efficiency of A. mali as a biological control agent is discussed. Abstract Many parasitoids need to feed on sugar sources at the adult stage. Although nectar has been proven to be a source of higher nutritional quality compared to honeydew excreted by phloem feeders, the latter can provide the necessary carbohydrates for parasitoids and increase their longevity, fecundity and host searching time. Honeydew is not only a trophic resource for parasitoids, but it can also constitute an olfactory stimulus involved in host searching. In this study, we combined longevity measurements in the laboratory, olfactometry and feeding history inference of individuals caught in the field to test the hypothesis that honeydew excreted by the aphid Eriosoma lanigerum could serve as a trophic resource for its parasitoid Aphelinus mali as well as a kairomone used by the parasitoid to discover its hosts. Results indicate that honeydew increased longevity of A. mali females if water was provided. Water could be necessary to feed on this food source because of its viscosity and its coating by wax. The presence of honeydew allowed longer stinging events by A. mali on E. lanigerum. However, no preference towards honeydew was observed, when given the choice. The role of honeydew excreted by E. lanigerum on A. mali feeding and searching behavior to increase its efficiency as a biological control agent is discussed.
Spatial Channel Attention based Change Detection in Synthetic Aperture Radar Images

Change Detection (CD) in Synthetic Aperture Radar (SAR) images is a key research field in remote sensing. Recently, CD in SAR images has received more attention due to the availability of SAR images, irrespective of weather conditions. However, it is difficult to exploit the changed information from SAR images, as these are subject to speckle noise. In this work, a Spatial Channel Attention (SCA) based CD network (SCACDNet) has been proposed. The SCACDNet is designed by integrating convolution neural network with the SCA module. Initially, the two SAR images are preprocessed and then, difference image is produced using the Log-Ratio operator. Then, the hierarchical fuzzy c-means clustering is used to classify the pixels into unchanged, changed and fuzzy classes. Now, image patches around highly probable unchanged and changed pixels are fed as an input to the network. After training, the pixels belong to fuzzy class are classified by the SCACDNet to produce a change map. The quantitative and qualitative results obtained for three SAR datasets demonstrate the superior performance of the proposed model.
Interpretation of Ambulatory Blood Pressure Monitoring for Risk Stratification in Hypertensive Patients: The ‘Ambulatory Does Prediction Valid (ADPV)’ Approach

Several outcome-based prospective investigations have provided solid data which support the prognostic value of 24 h ambulatory blood pressure over and beyond cardiovascular traditional risk factors. Average 24 h, daytime, and nighttime blood pressures are the principal components of the ambulatory blood pressure profile that have improved cardiovascular risk stratification beyond traditional risk factors. Furthermore, several additional ambulatory blood pressure measures have been investigated. The correct interpretation in clinical practice of ambulatory blood pressure monitoring needs a standardization of methods. Several algorithms for its clinical use have been proposed. Implementation of the results of ambulatory blood pressure monitoring in the management of individual subjects with the aim of improving risk stratification is challenging. We suggest that clinicians should focus attention on ambulatory blood pressure components which have been proven to act as the main independent predictors of outcome (average 24 h, daytime, and nighttime blood pressure, pulse pressure, dipping status, BP variability).
Data Assimilation with Model Error from Unresolved Scales

In this note, we provide an overview of two important competing data assimilation schemes that were developed in the past two-decade, discuss the current methods that are operationally used in weather forecasting applications, and point out one major challenge in data assimilation community: utilize these existing schemes in the presence of model error from unresolved scales. The main goal of this note is to discuss a simple mathematical analysis to understand why this problem is difficult and to provide a mathematically justifiable stochastic parameterization to mitigate this type of model error in practical multiscale filtering problems. This is a prototypical situation in many applications due to limited ability in resolving the smaller scale processes as well as the difficulty to model the interaction across scales. We will present simple examples to point out the importance of accounting for model error when the separation of scales are not apparent. These examples also elucidate the necessity of treating model error as a stochastic process in a nontrivial fashion for optimal filtering. In general, it is difficult to guess the appropriate stochastic models to represent model error and/or even to estimate higher order statistics. For practical consideration, we only discuss “optimality” in the sense that the first two moments are as accurate as those of the true filter. Although this is just a necessary (and not sufficient) condition for optimal nonlinear filtering, we shall see that many of the existing approaches do not even meet this minimum criteria. Several classical approaches to estimate model error statistics are briefly reviewed and reassessed, and several recent developments are overviewed, including important open problems/questions. We hope that this review note can make this important issue accessible to inspire more applied mathematicians to work on this exciting open problem. More importantly, we hope that the theoretical results reviewed ∗The bibliography is far from complete. If one is interested to discuss this research topic, please don’t hesitate to contact me at: jharlim@psu.edu.