Miracle-dz/UniFAR-FTUs huggingface dataset:
WRKY Genes Improve Drought Tolerance in Arachis duranensis

WRKY transcription factor participates in plant growth and development and response to biotic and abiotic stresses. Arachis duranensis, a turfgrass, has high drought tolerance, yet little is known about AdWRKYs response to drought stress in A. duranensis. In this study, RNA-seq identified five AdWRKYs, including AdWRKY18, AdWRKY40, AdWRKY42, AdWRKY56, and AdWRKY64, which were upregulated under drought stress. Orthologous relationships between AdWRKYs and Arabidopsis WRKY were determined to predict the regulatory networks of the five AdWRKYs based on AtWRKYs. Additionally, protein–protein interactions were predicted using differentially expressed proteins from RNA-seq. The quantitative real-time PCR (qRT-PCR) results showed that AdWRKY40 was upregulated, while AdWRKY42, AdWRKY56, and AdWRKY64 were downregulated at different time-points under drought stress. The predicted regulatory networks showed that AdWRKY40 activates COR47, RD21, and RD29A expression under drought stress. Besides, AdWRKY56 regulated CesA8 under drought stress. Aradu.YIQ80 (NAC019) interacted with AdWRKY40, AdWRKY42, AdWRKY56, and AdWRKY64, while Aradu.Z5H58 (NAC055) interacted with AdWRKY42 and AdWRKY64 under drought stress. This study used Arabidopsis to assess AdWRKYs function and regulatory networks, providing a basis for understanding drought tolerance in A. duranensis.
Revisiting the Biological Behavior of Salmonella enterica in Hydric Resources: A Meta-Analysis Study Addressing the Critical Role of Environmental Water on Food Safety and Public Health

The increasing number of studies reporting the presence of Salmonella in environmental water sources suggests that it is beyond incidental findings originated from sparse fecal contamination events. However, there is no consensus on the occurrence of Salmonella as its relative serovar representation across non-recycled water sources. We conducted a meta-analysis of proportions by fitting a random-effects model using the restricted maximum-likelihood estimator to obtain the weighted average proportion and between-study variance associated with the occurrence of Salmonella in water sources. Moreover, meta-regression and non-parametric supervised machine learning method were performed to predict the effect of moderators on the frequency of Salmonella in non-recycled water sources. Three sequential steps (identification of information sources, screening and eligibility) were performed to obtain a preliminary selection from identified abstracts and article titles. Questions related to the frequency of Salmonella in aquatic environments, as well as putative differences in the relative frequencies of the reported Salmonella serovars and the role of potential variable moderators (sample source, country, and sample volume) were formulated according to the population, intervention, comparison, and outcome method (PICO). The results were reported according to the Preferred Reporting Items for Systematic Review and Meta-Analyzes statement (PRISMA). A total of 26 eligible papers reporting 148 different Salmonella serovars were retrieved. According to our model, the Salmonella frequency in non-recycled water sources was 0.19 [CI: 0.14; 0.25]. The source of water was identified as the most import variable affecting the frequency of Salmonella, estimated as 0.31 and 0.17% for surface and groundwater, respectively. There was a higher frequency of Salmonella in countries with lower human development index (HDI). Small volume samples of surface water resulted in lower detectable Salmonella frequencies both in high and low HDI regions. Relative frequencies of the 148 serovars were significantly affected only by HDI and volume. Considering that serovars representation can also be affected by water sample volume, efforts toward the standardization of water samplings for monitoring purposes should be considered. Further approaches such as metagenomics could provide more comprehensive insights about the microbial ecology of fresh water and its importance for the quality and safety of agricultural products.
On Gravitational Fields in Superconductors

DeWitt’s theory on superconductors in gravitational fields is re-derived in the low velocity limit and linear gravity from the Klein-Gordon equation for an ensemble of charged spinless bosons. The solution has a phase singularity that gives rise to boson condensation and enables the description of type-II superconductors in the presence of gravity.
A Scalar Poincaré Map for Anti-phase Bursting in Coupled Inhibitory Neurons With Synaptic Depression

Short-term synaptic plasticity is found in many areas of the central nervous system. In the inhibitory half-center central pattern generators involved in locomotion, synaptic depression is believed to act as a burst termination mechanism, allowing networks to generate anti-phase bursting patterns of varying periods. To better understand burst generation in these central pattern generators, we study a minimal network of two neurons coupled through depressing synapses. Depending on the strength of the synaptic conductance between the two neurons, this network can produce symmetric n : n anti-phase bursts, where neurons fire n spikes in alternation, with the period of such solutions increasing with the strength of the synaptic conductance. Relying on the timescale disparity in the model, we reduce the eight-dimensional network equations to a fully-explicit scalar Poincaré burst map. This map tracks the state of synaptic depression from one burst to the next and captures the complex bursting dynamics of the network. Fixed points of this map are associated with stable burst solutions of the full network model, and are created through fold bifurcations of maps. We derive conditions that predict the bifurcations between n : n and (n + 1) : (n + 1) solutions, producing a full bifurcation diagram of the burst cycle period. Predictions of the Poincaré map fit excellently with numerical simulations of the full network model and allow the study of parameter sensitivity for rhythm generation.
Automated segmentation of the articular space in MR images of the hip joint

Segmentation of the cartilages in the hip joint is important in diagnosis of hip diseases. Automatic localization of the hip joint articular space is a major step for finding the central line of this space in this regard. In this study, we propose an automatic technique for segmentation the articular space using clinically obtained multi-slice TI-weighted MR data. To perform an isotropic dataset, we resampled data sets with a modified sine interpolation technique which reduces the effect of unwanted Gibbs ringing. By assuming a spherical shape for the femur, we estimated the center of the femoral head by a Hough transform. Radial derivative filters were then performed to enhance the edges of the cartilages, articular spaces and pelvic bones in the data sets. We localized the articular space by customizing a Canny edge detector to the problem. Finally, we refined the articular space edges by estimating and discarding the bony edges by an Otsu adaptive thresholding technique. We implemented the techniques in C++ and Matlab programming languages. The feasibility of the proposed techniques was successfully evaluated in the presence of 40 hips including 1200 MR images.
A Prospective Study to Evaluate the Impact of Golimumab Therapy on Work Productivity and Activity, and Quality of Life in Patients With Rheumatoid Arthritis, Psoriasis Arthritis and Axial Spondyloarthritis in a Real Life Setting in AUSTRIA. The GO-ACTIVE Study

Objective To analyze real-world evidence on work productivity and daily activity impairment (WPAI) and health-related quality of life (HRQoL) in rheumatoid arthritis (RA), psoriatic arthritis (PsA), and axial spondyloarthritis (axSpA) patients treated with golimumab in Austria. Methods This was a prospective, non-interventional, multi-center study conducted in RA, PsA and axSpA patients initiating golimumab between April 2016 and May 2020 in 40 centers in Austria. WPAI, HRQoL (RAQoL, ankylosing spondylitis (AS)QoL and PsAQoL) questionnaires and disease activity (Clinical Disease Activity Index, CDAI, in RA and PsA; Bath Ankylosing Spondylitis Disease Activity Index, BASDAI, in axSpA) were assessed at baseline and months 3, 6, 12, 18, and 24. Association between WPAI and disease activity was tested using linear regression. Results We enrolled 233 patients (RA, n = 95; axSpA, n = 69; PsA, n = 69), 110 patients were followed up to month 24. Mean age was 50.2 ± 14.2 years; 64% were female. Disease activity decreased from baseline to month 24 (RA: CDAI −24.3 ± 13.5; axSpA: BASDAI −4.4 ± 2.1, and PsA: CDAI −21.7 ± 8.5, p < 0.0001, each). Total work productivity impairment (TWPI), activity impairment and presenteeism subscores continuously decreased throughout month 24 in all indications: RA (−58.3 ± 23%, −62.6 ± 23.8% and −61.7 ± 23.3%, respectively as compared to baseline; p < 0.0001, each), axSpA (−34.4 ± 38.3%, p = 0.0117; −60.9 ± 25.9%, and −43.8 ± 26.6%, respectively, p ≤ 0.0001 both) and PsA (−35.8 ± 43.7%, p = 0.0186; −52.3 ± 25.4%, p < 0.0001; and −43.3 ± 33.5%, p = 0.0007, respectively). Absenteeism scores decreased only in RA patients (−9.2 ± 24.9%, p = 0.0234). HRQoL improved between baseline and month 24 (RAQoL: −12.6 ± 7.5; ASQoL: −8.0 ± 4.3; PsAQoL; −8.3 ± 6.4, p < 0.0001, each). TWPI, presenteeism and activity impairment strongly associated with disease activity throughout the study. Conclusions This real-world study confirms the benefit of golimumab on work productivity/daily activity impairment in Austrian RA, PsA, and axSpA patients.
Chloroplast Genomic Resources and Genetic Divergence of Endangered Species Bretschneidera sinensis (Bretschneideraceae)

Bretschneidera sinensis is an endangered woody species found in East and South China. Comprehensive intraspecies chloroplast genome studies have demonstrated novel genetic resources to assess the genetic variation and diversity of this species. Using genome skimming method, we assembled the whole chloroplast genome of 12 genotypes of B. sinensis from different geographical locations, covering most wild populations. The B. sinensis chloroplast genome size ranged from 158,959 to 159,045 base pairs (bp) and displayed a typical circular quadripartite structure. Comparative analyses of 12 B. sinensis chloroplast genome revealed 33 polymorphic simple sequence repeats (SSRs), 105 polymorphic single nucleotide polymorphisms (SNPs), and 55 indels. Phylogenetic analysis showed that the 12 genotypes were grouped into 2 branches, which is consistent with the geographical distribution (Eastern clade and Western clade). Divergence time estimates showed that the two clades were divergent from 0.6 Ma in the late Pleistocene. Ex situ conservation is essential for this species. In this study, we identified SNPs, indels, and microsatellites of B. sinensis by comparative analyses of chloroplast genomes and determined genetic variation between populations using these genomic markers. Chloroplast genomic resources are also important for further domestication, population genetic, and phylogenetic analysis, possibly in combination with molecular markers of mitochondrial and/or nuclear genomes.
From the Field to the Lab: Physiological and Behavioural Consequences of Environmental Salinity in a Coastal Frog

Environmental salinization is recognized as a global threat affecting biodiversity, particularly in coastal ecosystems (affected by sea level rise and increased frequency and severity of storms), and the consequent osmoregulatory challenges can negatively affect wildlife. In order to assess whether coastal species can respond to changes in environmental salinity, it remains essential to investigate the consequences of exposure to salinity in an environmentally-relevant context. In this study, we assessed the consequences of exposure to environmental salinity in coastal frogs (Pelophylax sp., N = 156) both in the field and experimentally, using a comprehensive combination of markers of physiology, behaviour and ecology. Exposure to salinity in the field negatively affected physiological parameters (osmolality, monocytes and eosinophils counts), as well as body condition and locomotor performance, and influenced size- and sex-specific habitat selection. Further, we demonstrated in a controlled experiment that short-term exposure to salinity strongly affected physiological parameters (salt influxes, water effluxes, immunity-related stress markers) and locomotor performance. Most of these effects were transient (water and salt fluxes, locomotor performance) once optimal conditions resumed (i.e., freshwater). Taken together, our results highlight the need to investigate whether exposure to environmental salinity can ultimately affect individual fitness and population persistence across taxa.
Exogenous Melatonin Directly and Indirectly Influences Sheep Oocytes

Understanding whether and how melatonin (MT) may impact sheep oocyte development competence is central to our ability to predict how sheep oocytes will respond to artificially regulated estrus. Implanting MT can make sheep enter estrus during the non-breeding season. One study found that the blastocyst rate increased under MT treatment, while another found that the blastocyst rate decreased. Therefore, we conducted a meta-analysis of MT directly and indirectly influencing sheep oocytes. A total of 433 articles were collected from which 20 articles and 34 treatments were finally selected. A method for estimating the default value was established for the litter size analysis. We found that exogenous MT add into in vitro maturation medium was positively related to the blastocyst rate in the lab. However, subcutaneous implanting MT did not affect the in vivo ovulation rate, fertilization rate, blastocyst rate, or pregnancy rate at farm. MT did not affect the in vitro cleavage rate. However, MT improved the in vivo cleavage rate. We hypothesized that implanted MT could increase the concentration of MT in oviduct fluid in vivo, and also that in vitro MT could increase the early cleavage rate of sheep zygotes without affecting the total cleavage rate. In the analysis of oocyte apoptosis caused by injury, the results suggested that pyroptosis would be more suitable for further research. MT produces responses in all body organs, and thus implanting of MT during non-breeding seasons should consider the effect on animal welfare.
Mutations of the SARS-CoV-2 Spike Glycoprotein Detected in Cats and Their Effect on Its Structure and Function

The high frequency of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) mutations and homology of the Angiotensin-Converting Enzyme-2 (ACE2) cell receptors in various hosts help the virus transcend species barriers. In this study, we investigated the mutations of the SARS-CoV-2 spike glycoprotein detected in cats and their effect on its structure and function. Interestingly, some of these mutations are reported here in cats for the first time. Structural analysis showed seven residue substitutions in the spike glycoprotein. Four of the detected mutations are located on the spike surface, which are critical interaction points for neutralizing antibodies. Furthermore, three of the reported mutations could facilitate viral binding to the ACE2 host receptor, influence S1/S2 cleavage, destabilize the β-hairpin structure of the S2 and enhance viral infectivity. Structural modeling and phylogenic analysis of the ACE2 receptor provided an indication of the binding capacity of the virus to the specific cell receptors of different species and hosts. The presented work highlights the effects of the residue substitutions on viral evasion, infectivity and possibility of SARS-CoV-2 spillover between humans and cats. In addition, the work paves the way for in-depth molecular investigation into the relationship between SARS-CoV-2 receptor binding and host susceptibility.
Molecular Mechanisms of Plant Trichome Development

Plant trichomes, protrusions formed from specialized aboveground epidermal cells, provide protection against various biotic and abiotic stresses. Trichomes can be unicellular, bicellular or multicellular, with multiple branches or no branches at all. Unicellular trichomes are generally not secretory, whereas multicellular trichomes include both secretory and non-secretory hairs. The secretory trichomes release secondary metabolites such as artemisinin, which is valuable as an antimalarial agent. Cotton trichomes, also known as cotton fibers, are an important natural product for the textile industry. In recent years, much progress has been made in unraveling the molecular mechanisms of trichome formation in Arabidopsis thaliana, Gossypium hirsutum, Oryza sativa, Cucumis sativus, Solanum lycopersicum, Nicotiana tabacum, and Artemisia annua. Here, we review current knowledge of the molecular mechanisms underlying fate determination and initiation, elongation, and maturation of unicellular, bicellular and multicellular trichomes in several representative plants. We emphasize the regulatory roles of plant hormones, transcription factors, the cell cycle and epigenetic modifications in different stages of trichome development. Finally, we identify the obstacles and key points for future research on plant trichome development, and speculated the development relationship between the salt glands of halophytes and the trichomes of non-halophytes, which provides a reference for future studying the development of plant epidermal cells.
Prevalence and Prognostic Significance of Liver Fibrosis in Patients With Aneurysmal Subarachnoid Hemorrhage

Objectives To report the prevalence, clinical associations, and prognostic consequences of liver fibrosis in patients with aneurysmal subarachnoid hemorrhage (aSAH). Methods In a retrospective study of patients with aSAH, we evaluated three validated liver fibrosis indices and modeled them as continuous-exposure variables, including the aspartate aminotransferase/platelet ratio index (APRI), the fibrosis-4 (FIB-4) index, and the Forns index. The primary outcome was mortality at 90 days. We compared the addition of fibrosis indices to the predictors of the full Subarachnoid Hemorrhage International Trialists model. Results A total of 3,722 patients with aSAH were included in the study. According to the APRI, FIB-4 index, and Forns index, 21.7, 17.7, and 11.4% of patients had liver fibrosis. After adjusting for potential confounding factors, liver fibrosis indices were associated with increased 90-day mortality, with odds ratios of 1.35 (95% CI 1.02–1.77) for the FIB-4 index, 1.39 (95% CI.08–1.78) for APRI, and 1.53 (95% CI 1.11–2.12) for the Forns index. Similarly, high liver fibrosis indices were associated with an increased risk of rebleeding. However, the Forns index was not significantly associated with mortality and rebleeding. The addition of FIB-4 indices and APRI into the standard model improved the mortality prediction. Conclusions Liver fibrosis is common in patients with aSAH, and high liver fibrosis indices are associated with mortality and rebleeding. The addition of liver fibrosis indices to a standard clinical model significantly improves risk stratification.
A Cyclic Disulfide Diastereomer From Bioactive Fraction of Bruguiera gymnorhiza Shows Anti–Pseudomonas aeruginosa Activity

Pseudomonas aeruginosa is an opportunistic pathogen that commonly causes hospital-acquired infection and is of great concern in immunocompromised patients. The quorum sensing (QS) mechanism of P. aeruginosa is well studied and known to be responsible for pathogenicity and virulence. The QS inhibitor derived from the natural product can be an important therapeutic agent for pathogen control. The present study reports the role of Bruguiera gymnorhiza purified fraction (BG138) in inhibiting virulence factor production, biofilm formation, quorum sensing molecules, and expression of QS-related genes of P. aeruginosa. Structural characterization of BG138 by high resolution mass spectrometry, Fourier transform infrared spectroscopy, 1D (1H and 13C NMR) and 2D NMR reveals that the fraction is a mixture of already known cyclic disulfide diastereomer, namely, brugierol and isobrugierol. The minimum inhibitory concentration (MIC) of BG138 against P. aeruginosa was 32 μg/ml. Biofilm formation was significantly reduced at sub-MIC concentrations of BG138. Scanning electron microscopy analysis reports the concentration-dependent biofilm inhibition and morphological changes of P. aeruginosa. Flow cytometry–based cell viability assay showed that P. aeruginosa cells exhibit increased propidium iodide uptake on treatment with 32 and 64 μg/ml of BG138. At sub-MIC concentrations, BG138 exhibited significant inhibition of virulence factors and reduced swimming and swarming motility of P. aeruginosa. Furthermore, the effect of BG138 on the expression of QS-related genes was investigated by qRT-PCR. Taken together, our study reports the isolation and structural characterization of bioactive fraction BG138 from B. gymnorhiza and its anti-biofilm, anti-virulence, anti-quorum sensing, and cell-damaging activities against P. aeruginosa.
Detection of Genus and Three Important Species of Cronobacter Using Novel Genus- and Species-Specific Genes Identified by Large-Scale Comparative Genomic Analysis

The genus Cronobacter includes seven species; however, the strains of Cronobacter sakazakii, Cronobacter malonaticus, and Cronobacter turicensis were highly correlated with clinical infections. Rapid and reliable identification of these three species of Cronobacter is important in monitoring and controlling diseases caused by these bacteria. Here, we identified four pairs of novel marker genes for the Cronobacter genus, C. sakazakii, C. malonaticus, and C. turicensis based on large-scale comparative genomic analysis from 799 Cronobacter and 136,146 non-Cronobacter genomes, including 10 Franconibacter and eight Siccibacter, which are close relatives of Cronobacter. Duplex and multiplex PCR methods were established based on these newly identified marker genes. The reliability of duplex and multiplex PCR methods was validated with 74 Cronobacter and 90 non-Cronobacter strains. Strains of C. sakazakii, C. malonaticus, and C. turicensis could be detected accurately at both the genus and species level. Moreover, the newly developed methods enable us to detect 2.5 × 103 CFU/ml in pure culture. These data indicate that the accurate and sensitive established methods for Cronobacter can serve as valuable tools for the identification of these strains recovered from food, environmental, and clinical samples.