Miracle-dz/UniFAR-FTUs huggingface dataset:
The “all-in-one” rol-type binary vectors as a tool for functional genomic studies using hairy roots

The hairy root culture system has several desirable features as an experimental model for functional analyses of the genes involved in root metabolism and/or physiology. We developed a binary vector set for efficient target gene overexpression and RNA interference (RNAi) in transformed (hairy) roots. The vectors, pHR-OX and pHR-RNAi, contain a cluster of rol (rooting locus) genes, together with the single GATEWAYTM conversion cassette (in pHR-OX vectors) or inverted repeats of the GATEWAYTM conversion cassette separated by an intron sequence (in pHR-RNAi vectors), flanked by a dual CaMV 35S promoter and nopaline synthase polyadenylation signal, on the same T-DNA. Transformation experiments with pHR-OX vectors using Arabidopsis, potato, and tobacco as model plants revealed that by inoculating Agrobacterium tumefaciens harboring these vectors, a large number of independently transformed roots could be induced from explants in a short period of time, and subsequent establishment of root culture lines was possible. A model experiment that focused on the sterol biosynthetic pathway in Arabidopsis validated the utility of pHR-RNAi vectors for gene functional analysis in cultured roots. Use of our vector system may facilitate identification of regulatory or biosynthetic genes for the production of valuable secondary metabolites in plant roots.
Mapping the Global Mangrove Forest Aboveground Biomass Using Multisource Remote Sensing Data

Mangrove forest ecosystems are distributed at the land–sea interface in tropical and subtropical regions and play an important role in carbon cycles and biodiversity. Accurately mapping global mangrove aboveground biomass (AGB) will help us understand how mangrove ecosystems are affected by the impacts of climatic change and human activities. Light detection and ranging (LiDAR) techniques have been proven to accurately capture the three-dimensional structure of mangroves and LiDAR can estimate forest AGB with high accuracy. In this study, we produced a global mangrove forest AGB map for 2004 at a 250-m resolution by combining ground inventory data, spaceborne LiDAR, optical imagery, climate surfaces, and topographic data with random forest, a machine learning method. From the published literature and free-access datasets of mangrove biomass, we selected 342 surface observations to train and validate the mangrove AGB estimation model. Our global mangrove AGB map showed that average global mangrove AGB density was 115.23 Mg/ha, with a standard deviation of 48.89 Mg/ha. Total global AGB storage within mangrove forests was 1.52 Pg. Cross-validation with observed data demonstrated that our mangrove AGB estimates were reliable. The adjusted coefficient of determination (R2) and root-mean-square error (RMSE) were 0.48 and 75.85 Mg/ha, respectively. Our estimated global mangrove AGB storage was similar to that predicted by previous remote sensing methods, and remote sensing approaches can overcome overestimates from climate-based models. This new biomass map provides information that can help us understand the global mangrove distribution, while also serving as a baseline to monitor trends in global mangrove biomass.
The effect of elbow position on the handgrip strength test in children: validity and reliability of TKK 5101 and DynX dynamometers

Background and Study Aim: One of the most widely applied methods to assess upper-body strength in children and adolescents is the handgrip strength test. While in adolescents it has been determined which elbow position, and which type of dynamometer are most appropriate for achieving the maximal grip strength, in children is still not clear. Therefore, the purpose of this study was to investigate whether elbow position and the type of dynamometer affect the handgrip strength in children. Material and Methods: Grip strength was measured by TKK and DynX dynamometers, and their validity and reliability were also analysed. A total of 60 children, 6 to 11 years old, participated in this study, and performed the handgrip strength test with their elbow extended and flexed at 90°. Results: While using the TKK dynamometer, grip strength was significantly higher when the test was performed with elbow extended, in contrast to those obtained with elbow flexed (14.58±3.04 kg vs 12.97±2.99 kg, p<0.001 for right, and 14.25±3.05 kg vs 12.61±2.99 kg, p<0.001 for left hand). Likewise, when using the DynX dynamometer, the difference between the two elbow positions was smaller but still significant (13.84±3.22 kg vs 13.35±3.01 kg, p=0.035 for right, and 13.35±2.95 kg vs 12.77±2.96 kg, p=0.003 for left hand). Conclusions: Both dynamometers provided sufficient results in terms of their reliability and the TKK dynamometer showed to be more valid. Performing the handgrip strength test with elbow extended appears to be the most appropriate position in order to obtain maximal results in children.
Ex Situ Conservation of the Federally Endangered Plant Species Clematis socialis Kral (Ranunculaceae)

ABSTRACT: The Center for Plant Conservation (CPC) has created sampling guidelines for the ex situ conservation of rare plant species. These guidelines estimate the number of individuals needed to maximize the genetic diversity of the collection according to population genetic theory. For many clonal plant species, knowledge of the number of unique individuals is not easily discerned and application of these guidelines must be based on molecular genetic data. In this paper, we discuss the steps taken in order to meet CPC guidelines for the conservation of a rare clonal plant, Clematis socialis. Due to limited seed availability, methods were developed for successful in vitro propagation and cryopreservation of C. socialis shoot tips. Inter-simple sequence repeat (ISSR) analysis identified fifteen unique genotypes in the ex situ in vitro collection. One genotype in this collection has been conserved from a population that is now presumed extinct. Although the initial sampling protocol managed to capture considerable genetic diversity, an additional 97 genotypes are needed to meet CPC guidelines. The information and experience gained through the initial C. socialis ex situ conservation efforts form the basis for a strategy to improve ex situ conservation activities for this endangered species. We recommend that additional in vitro collections be made from each of the five extant populations and placed in cryostorage.
Repriming of Vascular Smooth Muscle Photorelaxation is Dependent upon Endothelium-derived Nitric Oxide

Precontracted vascular smooth muscle (VSM) relaxes when irradiated with visible or UV light. Recent evidence indicates that VSM cells contain a finite store of a photosensitive precursor which is capable of releasing nitric oxide (NO) on exposure to light. Here we report that the store can be exhausted rapidly, by irradiating vessels with laser light. Regeneration of the store occurs spontaneously in the dark. The repriming process displays an absolute requirement for endothelium-derived NO. It is impaired by mechanical damage to the endothelium, and also by treatment of intact vessels with either NG monomethyl-L-arginine or oxyhaemoglobin. Pretreating vessels with ethacrynic acid, a thiol alkylating agent, also prevents repriming of the store. Conversely, bolus injections of authentic NO or S-nitroso-N-acetyl penicillamine accelerate repriming in intact vessels and restore photorelaxation in endothelium-deficient preparations. We conclude that photorelaxation is caused by the release of NO from a photose.
Dynamics and Isotropic Control of Parallel Mechanisms for Vibration Isolation

Parallel mechanisms have been employed as architectures of high-precision vibration isolation systems. However, their performances in all degrees of freedom (DOFs) are nonidentical. The conventional solution to this problem is isotropic mechanism design, which is laborious and can hardly be achieved. This article proposes a novel concept; namely, isotropic control, to solve this problem. Dynamic equations of parallel mechanisms with base excitation are established and analyzed. An isotropic control framework is then synthesized in modal space. We derive an explicit relationship between modal control force and actuation force in joint space, enabling implementation of the isotropic controller. The multi-DOF system is transformed into multiidentical single-DOF systems. Under the framework of isotropic control, parallel mechanisms obtain an identical frequency response for all modes. An identical corner frequency, active damping, and rate of low-frequency transmissibility are achieved for all modes using a combining proportional, integral, and double integral compensator as a subcontroller. A 6-UPS parallel mechanism is presented as an example to demonstrate effectiveness of the new approach.
Finite element model updating of long-span cable-stayed bridge by Kriging surrogate model

In the finite element modelling of long-span cable-stayed bridges, there are a lot of uncertainties brought about by the complex structural configuration, material behaviour, boundary conditions, structural connections, etc. In order to reduce the discrepancies between the theoretical finite element model and the actual static and dynamic behaviour, updating is indispensable after establishment of the finite element model to provide a reliable baseline version for further analysis. Traditional sensitivity-based updating methods cannot support updating based on static and dynamic measurement data at the same time. The finite element model is required in every optimization iteration which limits the efficiency greatly. A convenient but accurate Kriging surrogate model for updating of the finite element model of cable-stayed bridge is proposed. First, a simple cable-stayed bridge is used to verify the method and the updating results of Kriging model are compared with those using the response surface model. Results show that Kriging model has higher accuracy than the response surface model. Then the method is utilized to update the model of a long-span cable-stayed bridge in Hong Kong. The natural frequencies are extracted using various methods from the ambient data collected by the Wind and Structural Health Monitoring System installed on the bridge. The maximum deflection records at two specific locations in the load test form the updating objective function. Finally, the fatigue lives of the structure at two cross sections are calculated with the finite element models before and after updating considering the mean stress effect. Results are compared with those calculated from the strain gauge data for verification.
Hysteresis Voltage Prediction Control for Multilevel Converter in the Series-Form Switch-Linear Hybrid Envelope Tracking Power Supply

Switch-linear hybrid (SLH) envelope tracking (ET) power supply can achieve high efficiency and high tracking bandwidth simultaneously, and it has two typical forms, namely, series-form and parallel-form. In the series-form SLH ET power supply, the switched-mode converter is expected to output a continuous-wave voltage which can track the load voltage accurately to enhance the overall efficiency, and the buck converter with hysteresis voltage control (HVC) can be utilized. However, the output voltage of the buck converter will go over the hysteresis voltage boundaries, degrading the linearity and efficiency of the ET power supply. In this article, the hysteresis voltage prediction control (HVPC) is proposed to mitigate the problem in the HVC for buck converter. Moreover, in order to further increase the efficiency, the multilevel converter (MLC) is adopted instead of the buck converter for reducing the switching frequency and the inductor root-mean-square current, and the corresponding HVPC control strategy is also proposed. A prototype of the series-form SLH ET power supply employing the MLC with HVPC aimed at 5-MHz envelope signal is fabricated in the lab. The measured overall efficiency is 77.5%, a 12% efficiency improvement over that using step-wave switched-mode converter.
Lightweight group key distribution schemes based on pre-shared pairwise keys

In a secure communication, a one-time session key is needed to be shared among all participants. Most well-known key distribution schemes, such as Diffie–Hellman public-key key distribution scheme invented in 1976 and quantum key distribution scheme invented in 1984 (also called the BB84 scheme), can only allow two users to share a key in conventional one-to-one communications. There are many research papers in the literature to propose group key distribution schemes for multiple participants in modern group communications. In this study, the authors propose lightweight group key distributions using pre-shared pairwise keys. The authors first propose a three-party group key distribution scheme. They then extend the basic three-party scheme to establish a group key for a large size of group communications. The proposed generalised schemes can be based to any type of pairwise key distribution schemes, e.g. either quantum or non-quantum. Moreover, both generalised multi-party group key distribution schemes are lightweight. The main operations in the proposed schemes are key comparison between two or more than two keys (i.e. logic XOR operation) and the computation of key derivation functions.
Biogenesis of peroxisomes in regenerating rat liver. II: Immunoelectron microscopical investigation of catalase and acyl-CoA oxidase

Des rats subissent une ablation de deux-tiers de leur foie. Celui-ci en phase de regeneration est preleve a des temps divers. Les coupes fines sont incubees en presence de DAB (diaminobenzidine) afin de localiser l'activite peroxydasique de la catalase. La detection de l'activite de l'acyl-CoA, ne fait a l'aide d'un antiserum onvi Acyl CoA oxydase. Technique immunocytochimique prot A-or
Numbers of follicles and oocytes in mammalian ovaries and their allometric relationships

The numbers of ovarian follicles present in the reserve pool of non-growing (‘primordial’) stages at the commencement of adult life in 19 species varied allometrically with both body weight (M, in kg) and with maximum life expectation (L, in years), the mathematical expressions being 27700M0.47 and 820M1.58, respectively. These allometric relationships, which could not be accounted for by differences in reproductive behaviour patterns or ovulation rates, indicate that species differences in the size of the follicular store, perhaps accompanied by more parsimonious utilization, could be a life strategy which guarantees fecundity throughout most of the lifespan. The number of follicles in humans at menarcheal age is commensurate with body size, and follicular deficiency at menopause in mid-life may have therefore arisen adventitiously with lifespan extension.
Functional expression of an animal type-Na⁺-ATPase gene from a marine red seaweed Porphyra yezoensis increases salinity tolerance in rice plants

Despite lacking Na+-ATPase as a sodium pump in vascular plants, a gene encoding KPA (K+ P-type ATPase), a putative animal type-Na+/K+-ATPase, has been isolated from the marine red alga Porphyra yezoensis and designated PyKPA1. To characterize the properties of PyKPA1 and also to confirm its ability to confer salinity tolerance in land plants, transgenic rice plants were produced that expressed the full-length PyKPA1 cDNA under the control of cauliflower mosaic virus 35S RNA promoter. We observed transcriptional activation of the transgene, plasma membrane-localization of the gene product fused with green fluorescent protein in onion epidermal cells, and Na+-ATPase activity in the plasma membrane fraction from transgenic rice plants, indicating that PyKPA1 was functionally expressed in rice plants. Transgenic lines were examined in terms of growth in salinity stress conditions, resulting in protection from a decrease in biomass, although growth of control rice plants was repressed. These results demonstrate the utility of a red algal animal type-sodium pump for conferring salinity tolerance to land plants.
A functional evaluation of virtual climate station rainfall data

Abstract Model simulations are increasingly being used to assess farm performance and its impact on the environment. A crucial input in most of these models is daily rainfall data, which are difficult to obtain for remote areas or if the period required is long. Recently, a new long‐term daily climate dataset for all New Zealand, known as Virtual Climate Station (VCS) data, has become available from NIWA (National Institute of Water & Atmospheric Research Ltd). A reasonable agreement between the VCS and observed data has been reported; nonetheless the effect of the uncertainty in the estimated rainfall on model simulations remains an issue to be examined. In this study we investigated the differences in simulated evapotranspiration, drainage and pasture growth by two models of varying complexity when using VCS or observed rainfall data from several locations around New Zealand. The results showed a general agreement between model outputs whether using observed or VCS rainfall dataseis. Model outputs that are closely related to rainfall events, such as drainage, were more sensitive to deviations in the rainfall dataseis than the indirect outputs, such as evapotranspiration. Data aggregation and correction of bias improved agreement between observed and VCS data and this was reflected in the model outputs. Although short‐term simulations should be analysed with care, overall results were promising. The NIWA VCS rainfall data have the potential to be extensively used in conjunction with simulation models for the assessment of land use and management practices.
Natural infection of Fraxinus excelsior seeds by Chalara fraxinea.

Summary The occurrence of Chalara fraxinea, the fungus responsible for dieback of European ash (Fraxinus excelsior), was investigated in the current and previous seed years collected from symptomatic trees in Latvia and Sweden using molecular techniques (DNA extraction, ITS-PCR, Sanger sequencing). Molecular analysis of seeds revealed the presence of 30 different fungal taxa. Chalara fraxinea was detected in 8.3% of seeds tested from the current year originating from Latvia. The presence of C. fraxinea in seeds of F. excelsior is of great concern to phytosanitary protection authorities in countries outside the current zone of infestation.
Enhanced Logical Representations of a Real Network Based on an Algebraic Model

The algebraic model and logical representations of a real network are important but very challenging issues in automatic network verification. In this paper, we abstract the concrete network to its corresponding abstract graph with enhanced vertices and edges by splitting the vertices according to the protocols that they run. Based on classical routing algebra, we consider combining the interactions of different protocols and routing records and then give a newly modified algebraic structure. To apply the abstract modified algebra routing into the concrete network, we make use of the SMT solver to encode the components of algebra into logical constraints motivated by the work of Ryan Beckett et al. By encoding the network behaviors and properties into logical formulas, we can compute whether the experimental network that we configured satisfies any property, including reachability, routing loop, and so on. In the previous work, the routing algebra or the representation of the network is only applied to several network properties. However, in this paper, we extract all kinds of properties into exact logical formulas.
Spatio-temporal relationships of the macaronesian endemic flora : a relictual series or window of opportunity?

Convolvulus is represented in Macaronesia by two endemic clades. The first (Clade I) has a predominantly western Mediterranean sister group whilst the second (Clade II) is nested within a predominantly eastern Mediterranean clade. The Relictual Series Hypothesis (RSH) predicts that degree of geographical disjunction between Macaronesian groups and their sister taxa is related to time available for continental extinction to occur and this would provide a possible explanation for the observed pattern in Convolvulus if Clade I is younger than Clade II. To test this hypothesis, mean relative divergence times for the two Macaronesian Convolvulus clades are estimated using a nrITS dataset. The results do not support the age-disjunction hypothesis and indicate that the mean divergence time for Clade I predates that of Clade II, although the difference between mean divergence times is small and the standard deviations are large. The inconsistency between this result and the RSH might be explained by the stochastic nature of evolution: with continental extinction events occurring during a similar time period, there may have been inadequate time for a clear spatio-temporal pattern to develop. An alternative explanation, termed the "Colonisation Window Hypothesis" (CWH), is also presented. This hypothesis emphasises island establishment rather than continental extinction as the prime determinant of spatio-temporal relationships of Macaronesian groups and predicts that opportunities for colonisation into Macaronesia has been temporally constrained to discrete waves of colonisation. Whilst the Convolvulus results are consistent with both RSH and CWH, a framework for establishing the ability of these two hypotheses to explain the spatial relationships of the Macaronesian endemic flora is presented.
Does proximity to freshwater refuge affect the size structure of an estuarine predator (Carcharhinus leucas) in the north-western Gulf of Mexico?

The life histories of estuarine species are often adapted to the environmental variability they experience. However, estuaries are increasingly vulnerable to natural and anthropogenic changes, necessitating an understanding of how shifting conditions affect the survival, behaviour and population structure of estuarine-dependent animals. In this study we used data from fisheries-independent surveys collected across six estuaries with variable salinity regimes in Texas, USA, from 1975 to 2016 to investigate the role sources of freshwater inflow play in shaping juvenile bull shark Carcharhinus leucas size structure. High frequencies of co-occurrence with similarly sized conspecifics (59% of capture events) suggest bull sharks segregated within Texan estuaries based on body size. Bull shark sizes increased with distance to the nearest source of freshwater inflow, although effect sizes were small and access to freshwater habitats may be more important in shaping size-dependent distribution patterns. River mouths were disproportionately used by smaller juveniles ( 135cm TL). However, the use of river mouths decreased in estuaries characterised by limited freshwater inflow and greater variability in salinities at river mouths, highlighting geographic differences in the functions these habitats provide as potential environmental and predator refugia. Young-of-the-year (i.e. age-0) sharks also increased their use of river mouths throughout the 40-year study period, revealing the growing importance of river mouths as potential nursery habitats.
Experimental determination of requirements for the growth of edible Rhizopus species for use in solid substrate fermentation systems

Rhizopus oryzae and R oligosporus germinated best in a starter culture of 5% V8 juice. R oligosporus had a higher optimum temperature for germination and growth than R oryzae, R oryzae utilised starch and nitrogen-containing salts but not urea in liquid culture. Optimum mycelial growth on membranes on agar was achieved where the protein to carbohydrate ratio of substrates was between 0.4 and 0.5 R oryzae gave higher yields than R oligosporus. The results will be used to optimise solid substrate fermentation systems for these fungi.