Miracle-dz/UniFAR-FTUs huggingface dataset:
The rhg1‐a (Rhg1 low‐copy) nematode resistance source harbors a copia‐family retrotransposon within the Rhg1‐encoded α‐SNAP gene

Soybean growers widely use the Resistance to Heterodera glycines 1 (Rhg1) locus to reduce yield losses caused by soybean cyst nematode (SCN). Rhg1 is a tandemly repeated four gene block. Two classes of SCN resistance-conferring Rhg1 haplotypes are recognized: rhg1-a (“Peking-type”, low copy number, 3 or fewer Rhg1 repeats) and rhg1-b (“PI 88788-type”, high copy number, 4 or more Rhg1 repeats). The rhg1-a and rhg1-b haplotypes encode α-SNAP (alpha-Soluble NSF Attachment Protein) variants α-SNAPRhg1LC and α-SNAPRhg1HC respectively, with differing atypical C-terminal domains, that contribute to SCN-resistance. Here we report that rhg1-a soybean accessions harbor a copia retrotransposon within their Rhg1 Glyma.18G022500 (α-SNAP-encoding) gene. We termed this retrotransposon “RAC”, for Rhg1 alpha-SNAP copia. Soybean carries multiple RAC-like retrotransposon sequences. The Rhg1 RAC insertion is in the Glyma.18G022500 genes of all true rhg1-a haplotypes we tested and was not detected in any examined rhg1-b or Rhg1WT (single-copy) soybeans. RAC is an intact element residing within intron 1, anti-sense to the rhg1-a α-SNAP open reading frame. RAC has intrinsic promoter activities, but overt impacts of RAC on transgenic α-SNAPRhg1LC mRNA and protein abundance were not detected. From the native rhg1-a RAC+ genomic context, elevated α-SNAPRhg1LC protein abundance was observed in syncytium cells, as was previously observed for α-SNAPRhg1HC (whose rhg1-b does not carry RAC). Using a SoySNP50K SNP corresponding with RAC presence, just ∼42% of USDA accessions bearing previously identified rhg1-a SoySNP50K SNP signatures harbor the RAC insertion. Subsequent analysis of several of these putative rhg1-a accessions lacking RAC revealed that none encoded α-SNAPRhg1LC, and thus they are not rhg1-a. rhg1-a haplotypes are of rising interest, with Rhg4, for combating SCN populations that exhibit increased virulence against the widely used rhg1-b resistance. The present study reveals another unexpected structural feature of many Rhg1 loci, and a selectable feature that is predictive of rhg1-a haplotypes.
Identification of guanine nucleotide exchange factors that increase Cdc42 activity in primary human endothelial cells

ABSTRACT The Rho GTPase family is involved in actin dynamics and regulates the barrier function of the endothelium. One of the main barrier-promoting Rho GTPases is Cdc42, also known as cell division control protein 42 homolog. Currently, regulation of Cdc42-based signalling networks in endothelial cells (ECs) lack molecular details. To examine these, we focused on a subset of 15 Rho guanine nucleotide exchange factors (GEFs), which are expressed in the endothelium. By performing single cell FRET measurements with Rho GTPase biosensors in primary human ECs, we monitored GEF efficiency towards Cdc42 and Rac1. A new, single cell-based analysis was developed and used to enable the quantitative comparison of cellular activities of the overexpressed full-length GEFs. Our data reveal GEF dependent activation of Cdc42, with the most efficient Cdc42 activation induced by PLEKHG2, FGD1, PLEKHG1 and PREX1 and the highest selectivity for FGD1. Additionally, we generated truncated GEF constructs that comprise only the catalytic dbl homology (DH) domain or together with the adjacent pleckstrin homology domain (DHPH). The DH domain by itself did not activate Cdc42, whereas the DHPH domain of ITSN1, ITSN2 and PLEKHG1 showed activity towards Cdc42. Together, our study characterized endothelial GEFs that may directly or indirectly activate Cdc42, which will be of great value for the field of vascular biology.
Impact of nanoparticle surface charge and phosphate on the uptake of coexisting cerium oxide nanoparticles and cadmium by soybean (Glycine max. (L.) merr.)

Abstract Engineered nanoparticles (ENPs) often interact closely with coexisting environmental pollutants; however, the effect of their surface properties on such interactions in a plant system has not been examined. This study investigated the roles of ENP surface charge and growth media chemistry on the mutual effects of cerium oxide nanoparticles (CeO2NPs) and cadmium (Cd) on their plant uptake and accumulation in a hydroponic system. Soybean seedlings were exposed to five nanoparticle/Cd treatments including: 100 mg L−1 CeO2NPs(+); 100 mg L−1 CeO2NPs(−); 100 mg L−1 CeO2NPs(+) + 1 mg L−1 Cd; 100 mg L−1 CeO2NPs(−) + 1 mg L−1 Cd; and 1 mg L−1 Cd only, in the presence or absence of 15 mg L−1 phosphorous in the form of phosphate. After 4 days of exposure, concentrations of Cd and Ce in plant tissues were quantified by inductively coupled plasma-mass spectrometry. Roots exposed to CeO2NPs(+) contained 87% higher Ce than plants exposed to CeO2NPs(−). Phosphate significantly increased the root concentration of Ce by 61% and 66% exposed to CeO2NPs(+) and CeO2NPs(−), respectively. The mutual effect of CeO2NPs and Cd was also affected by phosphate, and the net effect of phosphate depended upon the surface charge of CeO2NPs.
Benchmarking optimization methods for parameter estimation in large kinetic models

Motivation Mechanistic kinetic models usually contain unknown parameters, which need to be estimated by optimizing the fit of the model to experimental data. This task can be computationally challenging due to the presence of local optima and ill-conditioning. While a variety of optimization methods have been suggested to surmount these issues, it is not obvious how to choose the best one for a given problem a priori, since many factors can influence their performance. A systematic comparison of methods that are suited to parameter estimation problems of sizes ranging from tens to hundreds of optimization variables is currently missing, and smaller studies indeed provided contradictory findings. Results Here, we use a collection of benchmark problems to evaluate the performance of two families of optimization methods: (i) a multi-start of deterministic local searches; and (ii) a hybrid metaheuristic combining stochastic global search with deterministic local searches. A fair comparison is ensured through a collaborative evaluation, involving researchers applying each method on a daily basis, and a consideration of multiple performance metrics capturing the trade-off between computational efficiency and robustness. Our results show that, thanks to recent advances in the calculation of parametric sensitivities, a multi-start of gradient-based local methods is often a successful strategy, but a better performance can be obtained with a hybrid metaheuristic. The best performer is a combination of a global scatter search metaheuristic with an interior point local method, provided with gradients estimated with adjoint-based sensitivities. We provide an implementation of this novel method in an open-source software toolbox to render it available to the scientific community. Availability and Implementation The code to reproduce the results is available at Zenodo https://doi.org/10.5281/zenodo.1160343 Contact jan.hasenauer@helmholtz-muenchen.de, julio@iim.csic. es
A “fitness” Theme May Mitigate Regional Prevalence of Overweight and Obesity: Evidence from Google Search and Tweets

Taking ecological perspectives to overweight and obesity, the current study applies data mining approach to examine the association between information and social environments and regional prevalence of overweight and obesity. In particular, we focus on online search and social media data since the increasing popularity of location-based geo-targeting could be an influential source of regional differences in health information and social environment. In Study 1, we calculated the correlation between regional overweight and obesity rates with regional Google searches for a time period of 12 years (2004 to 2016). The findings showed that in regions with high overweight and obesity rates, people were looking for and obtaining information on weight-loss and diet;, but in regions with low overweight and obesity rates, people were looking for and obtaining information on fitness services and facilities. In Study 2, we analyzed and compared 4010 tweets from Houston, a city with a high overweight and obesity rate, and 3281 tweets from San Diego, a city with a low overweight and obesity rate. The tweets were collected from August 2015 to August of 2016. We analyzed the textual content of tweets by word frequency analysis and topic modeling. The findings suggest that San Diego has a social environment that focuses on fitness and combining exercising with dieting. In contrast, Houston’s social environment emphasizes dieting. The implication of these findings is that health practitioners should push a paradigm shift to a stronger focus on “healthy life” (combining exercising and dieting) in regions with high overweight and obesity rates.
Diagnostic reference levels for paediatric CT in Jordan

This study aimed to investigate the current status of Diagnostic Reference Levels (DRLs) in paediatric CT across Jordan. The dose data for four main CT examinations (brain, chest, abdominopelvic, and chest, abdomen and pelvis (CAP)) in hospitals and imaging centres (n = 4) were measured. The volume CT dose index (CTDIvol) and Dose Length Product (DLP) values were compared within the different hospitals and age groups (<1 year, 1–4 years, 5–10 years and 11–18 years). DRLs in Jordan were compared to international DRLs. The paediatric population consisted of 1818 children; 61.4% of them were male. There were significant variations between the DRLs for each CT scanner with an up to four-fold difference in dose between hospitals. There were apparent significant differences between Jordan and other countries with the DLPs in Jordan being relatively high. However, for CTDIvol, the values in Jordan were close to those of other countries. This study confirmed variations in the CTDIvol and DLP values of paediatric CT scans in Jordan. These variations were attributed to the different protocols and equipment used. There is a need to optimise paediatric CT examinations doses in Jordan.
Low intensity pulsed ultrasound promotes the migration of bone marrow- derived mesenchymal stem cells via activating FAK-ERK1/2 signalling pathway

Abstract To investigate the promoting effects and mechanisms of low intensity pulsed ultrasound (LIPUS) on the migration of bone marrow-derived mesenchymal stem cells (BMSCs). The BMSCs migration was researched from cell and animal experiments. In the cell experiment, the BMSCs was treated using LIPUS (30 mW/cm2, 20 min/day, 2 days), and the wound healing and transwell migration were observed. In the animal experiment, the BMSCs labelled with green fluorescent protein (GFP) were injected into rats with femoral defects via the tail vein (1 × 106/mL). The healing of bone was detected using x-ray and sampled for hematoxylin & eosin (H&E) staining and fluorescence microscopy. About the mechanisms, the cellular F-actin of cytoskeleton was stained with FITC-phalloidin. The changes of BMSCs genes after LIPUS treatment were screened using microarray assay and verified using quantitative real-time polymerase chain reaction (qRT-PCR). The biological processes of those genes were predicted by KEGG analysis. The protein expression levels of FAK, ERK1/2 and myosin II related migration were detected using western blotting. The results showed LIPUS promoted the BMSCs migration (p < .05) without significant temperature changes (p > .05) in vitro and in vivo than control group (p < .05). The cytoskeletal rearrangement was carried out, and the ITGA8 gene related with cell migration was found with high expression after LIPUS treatment (p < .05). FAK inhibitor (PF-573228) and ERK1/2 inhibitor (U0126) were proved, in turn, decreased the BMSCs migration induced using LIPUS (p < .05). LIPUS can promote the BMSCs migration in vitro and in vivo, one mechanism may be related to the activation of FAK-ERK1/2 signalling pathways using LIPUS. GRAPHICAL ABSTRACT Experiments in vivo and in vitro were designed to explore the migration and mechanisms of BMSCs treated using LIPUS.
Developing a fully automated evidence synthesis tool for identifying, assessing and collating the evidence

Evidence synthesis is a key element of evidence-based medicine. However, it is currently hampered by being labour intensive meaning that many trials are not incorporated into robust evidence syntheses and that many are out of date. To overcome this, a variety of techniques are being explored, including using automation technology. Here, we describe a fully automated evidence synthesis system for intervention studies, one that identifies all the relevant evidence, assesses the evidence for reliability and collates it to estimate the relative effectiveness of an intervention. Techniques used include machine learning, natural language processing and rule-based systems. Results are visualised using modern visualisation techniques. We believe this to be the first, publicly available, automated evidence synthesis system: an evidence mapping tool that synthesises evidence on the fly.
Nearly Complete Genome Sequence of a Novel Phlebovirus-Like Virus Detected in a Human Plasma Sample by High-Throughput Sequencing

Here, we report a novel phlebovirus-like virus sequence detected in a plasma sample from a febrile adult patient collected in the United Republic of Tanzania in 2014. A nearly complete RNA sequence was generated by high-throughput sequencing on a HiSeq 2500 instrument and further confirmed after repeating the analysis, starting from the initial sample. ABSTRACT Here, we report a novel phlebovirus-like virus sequence detected in a plasma sample from a febrile adult patient collected in the United Republic of Tanzania in 2014. A nearly complete RNA sequence was generated by high-throughput sequencing on a HiSeq 2500 instrument and further confirmed after repeating the analysis, starting from the initial sample.
Sulfonamide-based diffusible signal factor analogs interfere with quorum sensing in Stenotrophomonas maltophilia and Burkholderia cepacia.

Aim: Stenotrophomonas maltophilia (Sm) and Burkholderia cepacia complex (BCC) are Gram-negative bacterial pathogens, which are typically multidrug resistant and excellent biofilm producers. These phenotypes are controlled by quorum sensing (QS) systems from the diffusible signal factor (DSF) family. We aim to interfere with this QS system as an alternative approach in combatting such difficult-to-treat infections. Materials & methods: A library of sulfonamide-based DSF bioisosteres was synthesized and tested against the major phenotypes regulated by QS. Results & conclusion: Several analogs display significant antibiofilm activity while the majority increase the action of the last-resort antibiotic colistin against Sm and BCC. Most compounds inhibit DSF synthesis in the Sm K279a strain. Our results support the strategy of interfering with QS communications to combat multidrug resistance.
Genome‐wide expression quantitative trait locus analysis in a recombinant inbred line population for trait dissection in peanut

Summary The transcriptome connects genome to the gene function and ultimate phenome in biology. So far, transcriptomic approach was not used in peanut for performing trait mapping in bi‐parental populations. In this research, we sequenced the whole transcriptome in immature seeds in a peanut recombinant inbred line (RIL) population and explored thoroughly the landscape of transcriptomic variations and its genetic basis. The comprehensive analysis identified total 49 691 genes in RIL population, of which 92 genes followed a paramutation‐like expression pattern. Expression quantitative trait locus (eQTL) analysis identified 1207 local eQTLs and 15 837 distant eQTLs contributing to the whole‐genome transcriptomic variation in peanut. There were 94 eQTL hot spot regions detected across the genome with the dominance of distant eQTL. By integrating transcriptomic profile and annotation analyses, we unveiled a putative candidate gene and developed a linked marker InDel02 underlying a major QTL responsible for purple testa colour in peanut. Our result provided a first understanding of genetic basis of whole‐genome transcriptomic variation in peanut and illustrates the potential of the transcriptome‐aid approach in dissecting important traits in non‐model plants.
Extracorporeal shock wave therapy improves short-term limb use after canine tibial plateau leveling osteotomy.

OBJECTIVE To determine the influence of postoperative extracorporeal shock wave therapy (ESWT) on hind limb use after tibial plateau leveling osteotomy (TPLO). STUDY DESIGN Randomized, prospective clinical trial. ANIMALS Sixteen client-owned dogs, 2 to 10 years old weighing 18 to 75 kg. METHODS Dogs were randomly assigned to treatment cohorts, TPLO with ESWT (ESWT, n = 9) or TPLO without ESWT (control, n = 7). Treatment consisted of 1000 pulses at 0.15 mJ/mm2 immediately and 2 weeks after surgery. Subjective pain, stifle goniometry, stifle circumference, peak vertical force (PVF) and vertical impulse (VI) were measured before surgery, prior to ESWT, and 2 and 8 weeks after surgery. Measures were compared between treatments at each time point and among time points for each treatment (P < .05). RESULTS The PVF (5.5 ± 1.0 N/kg, mean ± SD) and VI (0.67 ± 0.14 N-s/kg) of surgically treated limbs in the ESWT cohort were higher 8 weeks after surgery compared with preoperative (3.8 ± 1.1 N/kg, P < .0001 and 0.47 ± 0.21 N-s/kg, P = .0012, respectively) values. In the control cohort, PVF (2.9 ± 1.3 N/kg, P = .0001) and VI (0.33 ± 0.20 N-s/kg, P = .0003) 2 weeks after surgery and VI (0.42 ± 0.2 N-s/kg, P = .0012) 8 weeks after surgery were lower (4.59 ± 2.33 N/kg and 0.592 ± 0.35 N-s/kg, respectively) than before surgery. Other parameters did not differ between groups. CONCLUSION Weight bearing increased faster after TPLO in dogs treated with postoperative ESWT. CLINICAL SIGNIFICANCE This study provides evidence to consider adjunct ESWT after TPLO.
Social Inequalities in Exposure to Ambient Air Pollution: A Systematic Review in the WHO European Region

Ambient air pollution is a long-standing and significant public health issue. The aim of this review is to systematically examine the peer-reviewed evidence on social inequalities and ambient air pollution in the World Health Organization European Region. Articles published between 2010 and 2017 were analyzed in the review. In total 31 articles were included in the review. There is good evidence from ecological studies that higher deprivation indices and low economic position are usually linked with higher levels of pollutants such as particulate matter (particulate matter under 2.5 and 10 microns in diameter, PM2.5, PM10) and oxides of nitrogen (e.g., NO2, and NOx). There is also evidence that ethnic minorities experience a mixed exposure in comparison to the majority population being sometimes higher and sometimes lower depending on the ethnic minority under consideration. The studies using data at the individual level in this review are mainly focused on pregnant women or new mothers, in these studies deprivation and ethnicity are more likely to be linked to higher exposures of poor air quality. Therefore, there is evidence in this review that the burden of higher pollutants falls disproportionally on different social groups.
Biocompatibility of Cyclopropylamine-Based Plasma Polymers Deposited at Sub-Atmospheric Pressure on Poly (ε-caprolactone) Nanofiber Meshes

In this work, cyclopropylamine (CPA) monomer was plasma-polymerized on poly (ε-caprolactone) nanofiber meshes using various deposition durations to obtain amine-rich surfaces in an effort to improve the cellular response of the meshes. Scanning electron microscopy and X-ray photoelectron spectroscopy (XPS) were used to investigate the surface morphology and surface chemical composition of the PCL samples, respectively. The measured coating thickness was found to linearly increase with deposition duration at a deposition rate of 0.465 nm/s. XPS analysis revealed that plasma exposure time had a considerable effect on the surface N/C and O/C ratio as well as on amino grafting efficiency and amino selectivity. In addition, cell studies showed that cell adhesion and proliferation significantly improved for all coated samples.
Adaptive Special Strategies Resampling for Inertial-based Mobile Indoor Positioning Systems : An Initial Proposal

The phenomenon of sample impoverishment during particle filtering always contribute computation burden to the inertial-based mobile IPS systems. This is due to the factor of noise measurement and number of particle. Usually, the special strategies resampling algorithms was used. However, these algorithms just can fit in certain environment. This needs an adaptation of noise measurement and number of particle in a algorithm in order to make resampling with more intelligence, reliability and robust. In tbis paper, we will propose an adaptive special strategies resampling by adapting noise and particle measurement. These adaptation is used to determine the most suitable algorithm of special strategies resampling, that can be switched for resampling purpose. Finally, we illustrate our proposed solution our for indoor environment setup.
Amazon fires clearly linked to deforestation, scientists say.

Brazil9s government claims its policies aren9t to blame for the fires ravaging the Amazon rainforest. But scientists in Brazil and elsewhere disagree. Satellite data show the rise in blazes is linked to a recent rise in deforestation, which is at least partly the result of government policies, they argue. Most of the fires occur in municipalities with the highest rate of deforestation this year. Many are active for several days, burning with intense heat and producing tall, thick, smoke pillars—all indicators that trees are on fire, not overgrown pastures, crop residues, or roadside vegetation.
Affect regulation training reduces symptom severity in depression – A randomized controlled trial

Deficits in general emotion regulation skills have been shown to be associated with various mental disorders. Thus, general affect-regulation training has been proposed as promising transdiagnostic approach to the treatment of psychopathology. In the present study, we aimed to evaluate the efficacy of a general affect-regulation as a stand-alone, group-based treatment for depression. For this purpose, we randomly assigned 218 individuals who met criteria for major depressive disorder (MDD) to the Affect Regulation Training (ART), to a waitlist control condition (WLC), or to a condition controlling for common factors (CFC). The primary outcome was the course of depressive symptom severity as assessed with the Hamilton Rating Scale for Depression and the Beck Depression Inventory. Multi-level analyses indicated that participation in ART was associated with a greater reduction of depressive symptom severity than was participation in WLC (d = 0.56), whereas the slight superiority of ART over CFC (d = 0.25) was not statistically significant. Mediation analyses indicated that changes in emotion regulation skills mediated the differences between ART/CFC and WLC. Thus, the findings provide evidence for enhancing emotion regulation skills as a common mechanism of change in psychological treatments for depression. The study was registered with ClinicalTrials.gov (NCT01330485) and was supported by grants from the German Research Association (DFG; BE 4510/3-1; HI 456/6-2). Future research should compare the (cost-) efficacy of ART with that of disorder-specific interventions.