Miracle-dz/UniFAR-FTUs huggingface dataset:
Climate and leaf traits, not latitude, explain variation in plant–herbivore interactions across a species' range

Spatial variation in abiotic and biotic factors creates local contexts that influence the intensity of plant–herbivore interactions. Some previous studies have accounted for the complexity of these interactions with latitudinal clines, while the absence of such clines in many other systems suggests other, often unknown, local community factors may instead explain the variation in herbivory across populations. We investigated plant–herbivore interactions across the entire range of a long‐lived tree (Quercus garryana), evaluating the relative importance of climate, latitude, population size, and insect feeding guilds in determining leaf phenotype and the extent and variation in insect herbivory. In this ecosystem, rain shadows create a nonlinear relationship between climate and latitude, allowing us to disentangle the effects of environmental factors. By performing similar analyses on trees grown in a common garden, we were able to assess the relative importance of environmental factors to leaf defence traits and herbivory. Total herbivory varied significantly among populations, and was best explained by variation in spring precipitation, leaf traits, and tree population size, but not latitude. The relative importance of each of these factors changed over the growing season and with insect feeding guild. Conversely, damage in the common garden did not vary among trees from different origins when grown in a constant environment, leading us to believe variation in damage in natural populations is more likely the result of the local environments. Leaf traits (trichome density and specific leaf area) varied significantly among populations, but neither showed an effect of latitude. Variation in both traits was best explained by tree size, and seasonal temperatures or precipitation. We found no variation in insect diversity among field populations, but abundance varied with mean summer precipitation and population size. Synthesis. Seasonal precipitation consistently explained the geographical variation in the extent of herbivory to Q. garryana, while latitude and winter temperatures, factors that are commonly associated with latitudinal gradients in the intensity of species interactions, did not. Our findings highlight the importance of local climates and functional traits in shaping biotic interactions and intraspecific variation in plant–insect interactions across large spatial scales.
GC content shapes mRNA decay and storage in human cells

The control of protein expression results from the fine tuning of mRNA synthesis, decay and translation. These processes, which are controlled by a large number of RNA binding proteins and by localization in RNP granules such as P-bodies, appear often intimately linked although the rules of this interplay are not well understood. In this study, we combined our recent P-body transcriptome with various transcriptomes after silencing broadly acting mRNA decay and repression factors. This analysis demonstrated the existence of two mRNA decay pathways in human cells, which apply to distinct mRNA subsets. It also revealed the central role of GC content in mRNA fate, in terms of mRNA decay, mRNA translation and P-body localization. Furthermore, sequence-specific RBPs and miRNAs had only modest additional effects on their bulk targets. Finally, the different GC content biases associated with the two mRNA decay pathways and with mRNA translation repression had a strong impact on codon usage and protein yield. Altogether, these results lead to an integrated view of post-transcriptional control in human cells where regulation at the level of translation is dedicated to AU-rich mRNAs, which have a limiting protein yield, whereas regulation at the level of 5’ decay is for GC-rich mRNAs, whose translation is optimal.
The Prevalence and Impact of Model Violations in Phylogenetics Analysis

In phylogenetic inference we commonly use models which assume that sequence evolution is stationary, reversible and homogeneous (SRH). Although such assumptions are often criticized, the extent of SRH violations and their effects on phylogenetic inference are not well understood. Here, we extend the matched-pairs test of symmetry to assess the scale and impact of SRH model violations on 3,572 partitions from 35 published phylogenetic datasets. We show that many partitions (39.5%) reject the SRH assumptions, and that in most datasets, phylogenies inferred from all partitions differ significantly from those inferred using the subset of partitions that do not reject the SRH assumptions. These results suggest that the extent and effects of model violation in phylogenetics may be substantial. They highlight the importance of testing for model violations and possibly excluding partitions that violate models prior to tree reconstruction. They also suggest that further effort in developing models that do not require SRH assumptions could lead to large improvements in the accuracy of phylogenomic inference. The scripts necessary to perform the analysis are available in https://github.com/roblanf/SRHtests, and the new tests we describe are available as a new option in IQ-TREE (http://www.iqtree.org).
High-fidelity Rendering of Physical Colour References for Projected-based Spatial Augmented Reality Design Applications

Spatial Augmented Reality allows users to visualise information onto physical objects by projecting digital contents on them. Product design applications could proﬁtably exploit this feature to create prototypes partially real and partially virtual (mixed prototypes) to be used for the evaluation of products during the development processes. A mixed prototype needs a high visual quality, because design decisions are taken on the base of its aspect, and projected colours should match the colour standards (e.g. Pantone, RAL, etc.) to be able to rely on the visualised colours. The current paper analyzes the eﬀect of a colour calibration method, based on the iteration of comparison and compensation phases, onto the projected images using objective measurements and subjective users’ evaluations. The procedure, whose eﬀectiveness is veriﬁed thanks to the presented results, allows to replicate any colour available inside the projector gamut by simply using a physical sample.
Parliament2: Fast Structural Variant Calling Using Optimized Combinations of Callers

Here we present Parliament2 – a structural variant caller which combines multiple best-in-class structural variant callers to create a highly accurate callset. This captures more events than the individual callers achieve independently. Parliament2 uses a call-overlap-genotype approach that is highly extensible to new methods and presents users the choice to run some or all of Breakdancer, Breakseq, CNVnator, Delly, Lumpy, and Manta to run. Parliament2 applies an additional parallelization framework to speed certain callers and executes these in parallel, taking advantage of the different resource requirements to complete structural variant calling much faster than running the programs individually. Parliament2 is available as a Docker container, which pre-installs all required dependencies. This allows users to run any caller with easy installation and execution. This Docker container can easily be deployed in cloud or local environments and is available as an app on DNAnexus.
Natural distinct inter-preference between genetic codon and protein secondary structure combinations

The central dogma of molecular biology describes the process of genetic information transferred to protein. Many studies have found that genetic codon not only influences the protein amino acid sequence, but also affects protein 3D structure, such as local protein 3D structure may be affected by synonymous codon preferred usage. Here, in addition to the effect of single codons, we furtherly considering the preferences of short codon sequences for protein secondary structures. Also, we studied the preferences of short protein secondary structures for codon sequences. We studied in six cases that how codon combinations with length of N (N -codons) affect protein secondary structure element combinations with the same length (N -secondary structures), where N = 1, . , 6. A few distinct codon combination sequences and their corresponding structure sequences were found by calculating Relative Codon Usage (RCU) and Relative Structure Usage (RSU). The preferences of many codon combinations vary for secondary structure combinations when N is different; similar preference patterns were found for protein secondary structure preference for genetic codons. This work is based on the CSandS database. In order to further confirm our conclusion, we selected seven proteins of human that are not in the CSandS to predict its secondary structures from nucleotide sequences using the statistical results. Prediction accuracy can reach 75.72%. It is sufficient to show the imprint of codons on protein structure, and it also indicates that codon usage probably is related to species.
Recurrent hybridization without homoeologous chromosome paring in the Dryopteris varia complex (Dryopteridaceae)

Controlling combining chromosomes in meiosis is necessary to maintain genome constitutions. The Dryopteirs varia complex is one of the apogamous fern groups which perform recurrent hybridization with unequal meiosis, and produce spores after meiosis of the genome doubling in spore mother cells. We analyzed five low-copy nuclear markers (AK1, EST, GapCp, G6PD, and PgiC) and three regions of plastid DNA (rbL, ndhF and trnL-F). The genetic constitution of the five nuclear markers was the same in the D. varia complex. Therefore, recurrent hybridization seemed to be occurred without homoeologous chromosome paring.
Windows of opportunity for salt marsh establishment: the importance for salt marsh restoration in the Yangtze Estuary

Restoration has been promoted as an important strategy to reverse the decline of salt marsh ecosystems. Physical and biological processes limiting the colonization of bare tidal flats by pioneer salt marsh species are commonly recognized. Recently, the window of opportunity (WoO) concept has been proposed as a framework to provide an explanation for the initial establishment of biogeomorphic ecosystems on tidal flats under high physical stress. Understanding the thresholds for early seedling establishment and colonization is critical for the successful restoration and management of this threatened ecosystem. In this study, we investigated the WoOs for the establishment and colonization of a Scirpus mariqueter salt marsh at a large-scale restoration site in the Yangtze Estuary. A set of field monitoring and measurements were conducted to identify the potential physical and biological thresholds that could provide a mechanistic insight on the establishment and colonization of this pioneer marsh. The results showed that the successful colonization and expansion of the S. mariqueter marsh on the tidal flat required passing both physical and biological thresholds to open WoOs for establishment and colonization. The concurrence of WoOs, that is, propagule availability in the early growing season at a suitable tidal flat elevation with a benign sedimentary regime together with the removal of competition from invasive species, is presumed to be essential for the success of S. mariqueter marsh establishment and colonization. In applying such ecological insights, the seed-sowing field experiment proved that by surpassing these thresholds, an S. mariqueter salt marsh can be successfully restored in a cost-effective manner. We suggest that these WoOrelated establishment and colonization thresholds as well the cost-effectiveness of using these WoOs should be considered in future large-scale restorations of salt marshes.
End-to-End Noisy Speech Recognition Using Fourier and Hilbert Spectrum Features

Despite the progress of deep neural networks over the last decade, the state-of-the-art speech recognizers in noisy environment conditions are still far from reaching satisfactory performance. Methods to improve noise robustness usually include adding components to the recognition system that often need optimization. For this reason, data augmentation of the input features derived from the Short-Time Fourier Transform (STFT) has become a popular approach. However, for many speech processing tasks, there is an evidence that the combination of STFT-based and Hilbert–Huang transform (HHT)-based features improves the overall performance. The Hilbert spectrum can be obtained using adaptive mode decomposition (AMD) techniques, which are noise-robust and suitable for non-linear and non-stationary signal analysis. In this study, we developed a DeepSpeech2-based recognition system by adding a combination of STFT and HHT spectrum-based features. We propose several ways to combine those features at different levels of the neural network. All evaluations were performed using the WSJ and CHiME-4 databases. Experimental results show that combining STFT and HHT spectra leads to a 5–7% relative improvement in noisy speech recognition.
Supertwisting Sliding Mode Algorithm Based Nonlinear MPPT Control for a Solar PV System with Artificial Neural Networks Based Reference Generation

The problem of extracting maximum power from a photovoltaic (PV) system with negligible power loss is concerned with the power generating capability of the PV array and nature of the output load. Changing weather conditions and nonlinear behavior of PV systems pose a challenge in tracking of varying maximum power point. A robust nonlinear controller is required to ensure maximum power point tracking (MPPT) by handling nonlinearities of a system and making it robust against changing environmental conditions. Sliding mode controller is robust against disturbances, model uncertainties and parametric variations. It depicts undesirable phenomenon like chattering, inherent in it causing power and heat losses. In this paper, a supertwisting sliding mode algorithm based nonlinear robust controller has been designed for MPPT of a PV system which not only removes the chattering but also enhances the overall system’s dynamic response. Moreover, supertwisting sliding mode controller is robust against changing environmental conditions like change in temperature and irradiance. Noninverting DC-DC Buck-Boost converter has been used as an interface between source and the load. The efficiency of MPPT of a PV system depends upon the accuracy of reference for peak power voltage, therefore an efficient mechanism for reference generation has also been proposed in this work. The reference for peak power voltage has been generated by using a trained artificial neural network, which is to be tracked by proposed nonlinear controllers. Sliding mode controller (SMC) and synergetic controllers have also been designed for MPPT of a PV system in order to compare them with supertwisting sliding mode controller (ST-SMC). Global asymptotic stability of the system has been ensured by using Lyapunov stability criterion. The performance of the proposed nonlinear controllers has been validated in MATLAB/Simulink ODE 45 environment. ST-SMC has also been compared with recently proposed integral backstepping controller and other conventional MPPT controllers given in the literature. The simulation results show the better performance of ST-SMC in terms of best dynamic response and robustness.
Medium pH and macronutrients content affects growth and production of secondary metabolites by Drosera plants

Carnivorous plants have always been fascinating to humans. Sundew (Drosera) has been known since middle ages as a plant with a wide application in herbal and folk medicine. The infusion or tincture was used as antitussive drug and painkiller, as well as a remedy for intimate infections and gastrointestinal diseases. Today we know that the biological activity of Drosera is mainly due to the high content of flavonoids and naphthoquinones, as well as cyanogens, proteolytic enzymes, anthocyanins and organic acids. Most of these compounds are plant secondary metabolism products. Secondary metabolites are a kind of plant’s weapon, protecting against threats (bacteria, fungi, insects) and adverse environmental conditions (unsuitable soil pH, unavailability of minerals, UV radiation). The substances of plant origin are also used in various industries as flavouring additives, dyes, natural preservatives or active ingredients of medicines. It has been shown that extracts from Drosera plants, rich in naphthoquinones, may have anti-cancer (Ahmad, Banerjee, Wang, Kong, & Sarkar, 2008) and bactericidal effects, even against multiresistant bacteria (Krolicka et al., 2009).
Genetic Algorithm 3D Trajectory Planning Based on Digital Map Pre-processing for Tilt-rotor Aircraft

Tilt-rotor aircraft is a new type of aircraft which can take off and land vertically and cruise at high speed. It can be used to perform specific tasks by special departments such as public security or fire rescue. The terrain environment and threat of tasks are complex and changeable. In order to ensure flight safety, the flight trajectory should be planned in advance. As a global optimization algorithm simulating biological evolution process, genetic algorithm is mostly used in two-dimensional flight path planning. In this paper, the three-dimensional digital map is preprocessed according to the actual mission environment and constraints of the tiltrotor aircraft. The related genetic operators and individual evaluation function of the genetic algorithm are improved to reduce the calculation of the trajectory planning and effectively avoid the partial optimal solution. The simulation results show that after preprocessing the 3D digital map, a 3D mission trajectory with the best cost in the complex mission environment can be successfully planned by the improved genetic algorithm.
Reliability Evaluation of Hinged Slab Bridge Considering Hinge Joints Damage and Member Failure Credibility

The hinged slab bridge is widely used in medium- and small-span bridges because of its simple structure and convenient construction. However, hinge joints damage is the main defect of this kind of bridge, and it is difficult to express the deterministic damage degree of hinge joints in the detection process. A system reliability evaluation method considering fuzzy detection information of hinge joints damage and member failure credibility is proposed in this paper. Firstly, the membership function is used to quantitatively express the fuzzy detection information of hinge joints, and the fuzzy variable is transformed to an equivalent random variable. Secondly, the functional relationship between the transverse distribution coefficient and hinge joints damage is constructed by the modified hinge-jointed plate method and response surface method, and the reliability of the member considering the fuzzy detection information of hinge joints damage is calculated by the first-order second-moment method (FOSM). Then, the failure credibility is introduced to represent the different possibilities of system failure caused by member failure, and a system reliability assessment method of different failure criteria considering member failure credibility is established based on copula theory. Finally, the applicability of the proposed method is verified by taking the reinforced concrete hinged slab bridge as a numerical example.
Handling the Microbial Complexity Associated to Ticks

Ticks and the pathogens they transmit constitute a growing burden for human and animal health worldwide. In the last years, high-throughput detection and sequencing technologies (HTT) have revealed that individual ticks carry a high diversity of microorganisms, including pathogenic and non-pathogenic bacteria. Despite several studies have contributed to the availability of a catalog of microorganisms associated to different tick species, major limitations and challenges remain ahead HTT studies to acquire further insights on the microbial complexity associated to ticks. Currently, using next generation sequencing (NGS), bacteria genera (or higher taxonomic levels) can be recorded; however, species identification remains problematic which in turn affects pathogen detection using NGS. Microfluidic PCR, a high-throughput detection technology, can detect up to 96 different pathogen species, and its combination with NGS might render interesting insights into pathogen-microbiota co-occurrence patterns. Microfluidic PCR, however, is also limited because detection of pathogen strains has not been implemented, and therefore, putative associations among bacterial genotypes are currently unknown. Combining NGS and microfluidic PCR data may prove challenging. Here, we review the impact of some HTT applied to tick microbiology research and propose network analysis as an integrative data analysis benchmark to unravel the structure and significance of microbial communities associated to ticks in different ecosystems.
Depth‐Scanning Algorithm: Accurate, Automatic, and Efficient Determination of Focal Depths for Local and Regional Earthquakes

Precise source depths are critical to the understanding and interpretation of many seismological and tectonic processes. However, conventional earthquake location methods based on the arrival times of direct P and S phases have far less constraint on focal depths than on epicenters. Therefore, developing a method that can systematically and efficiently estimate focal depths with high accuracy, especially for the vast number of small earthquakes that can only be observed at local and regional distances, would make significant contributions to the geoscience research community. In this study, we develop a new method, named “Depth‐Scanning Algorithm,” to efficiently identify depth phases at local and regional distances. We first construct template waveforms of possible depth phases by applying various phase shifts to the original P and S waveforms to mimic the effect of reflection(s). We then systematically scan waveforms after the P and S phases for segments that match the depth‐phase templates. The arrival times of those segments are compared to the theoretical arrival times of depth phases predicted with an assumed velocity model and focal depth. We repeat the above process for a range of assumed focal depths, and the one most consistent with the theoretical prediction is deemed the final solution. Synthetic tests and applications to real data demonstrate the merits of our method compared to conventional location methods.
Psychosocial Care Service in the Mental Health Provision

The approach of health service can be divided into a medical term and psychosocial term that are applied by the mental health professional. The mental heath services help their clients with mental illness by giving a specific treatments particularly from psychological view. The information in this essay were collected from two databases that are CINAHL and Health Science. It also included the University of Wollongong e-journal database for nursing program. Based on the internet research, it is imperative that the intervention can be delivered in the form of case management. This paper therefore will discuss the psychosocial care for mentally ill clients in terms of concept, components, interventions and benefit in the practical area. The strategies to develop the treatment more effective are also discussed in depth. Keywords. psychosocial care, medical care, mental health.
Nonlinear Control of Damping Constant by Electric Field in Ultrathin Ferromagnetic Films

ultrathin ferromagnetic films B. Rana,1 C. A. Akosa,1, 2 K. Miura,3 H. Takahashi,3 G. Tatara,1, 4 and Y. Otani1, 5 1RIKEN, CEMS, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan 2African University of Science and Technology (AUST), Km 10 Airport Road, Galadimawa, Abuja F.C. T, Nigeria 3Research and Development Group, Hitachi, Ltd., 1-280 Higashi-koigakubo, Kokubunji-shi, Tokyo 185-8601, Japan 4RIKEN Cluster for Pioneering Research (CPR), 2-1 Hirosawa, Wako, Saitama, 351-0198 Japan 5Institute for Solid State Physics, University of Tokyo, Kashiwa 277-8581, Japan