Miracle-dz/UniFAR-FTUs huggingface dataset:
Monitoring the Spatiotemporal Difference in Glacier Elevation on Bogda Mountain from 2000 to 2017

The difference in glacier surface elevation is a sensitive indicator of climate change and is also important for disaster warning and water supply. In this paper, 25 glaciers on Bogda Mountain, in the eastern Tianshan Mountains, are selected as the study object as they are typical of glaciers in arid or semi-arid areas with importance for water supply. The Repeat Orbit Interferometry (ROI) method is used to survey the surface elevation of these glaciers using Sentinel-1A Radar data from 2017. Using data from the Shuttle Radar Topography Mission (SRTM) and a Digital Elevation Model (DEM), the difference in the glacier surface elevation between 2000 and 2017 is obtained. A scheme to evaluate the accuracy of estimated variations in glacier surface elevation is proposed in this article. By considering the surfaces of lakes in the study region as ideal horizontal planes, the average standard deviation (SD) value of the lake elevation is taken as the error caused by the radar sensor and observing conditions. The SD of the lake elevation is used as an index to evaluate the error in the estimated variation of the glacier surface elevation, and the obtained SD values indicate that the result obtained using the ROI method is reliable. Additionally, the glacier surface elevation variation pattern and a Logarithmic Fitting Model (LFM) are used to reduce the error in high-altitude glacial accumulation areas to improve the estimation of the difference in the glacier surface elevation obtained using ROI. The average SD of the elevation of the 12 lakes is ±2.87 m, which shows that the obtained glacier surface elevations are reliable. This article concludes that, between 2000 and 2017, the surface elevation of glaciers on Bogda Mountain decreased by an average of 11.6 ± 1.3 m, corresponding to an average decrease rate of 0.68 m/a, and glaciers volume decreased by an average of 0.504 km3. Meanwhile, the surface elevations of the lakes increased by an average of 8.16 m. The decrease of glacier surface elevation leads to the expansion of glacial lakes. From the north slope clockwise to the south slope, the glacier elevation variation showed a decreasing trend, and the elevation variation gradually increased from the south slope to the north slope. With the increase of glacier altitude, the variation of glacier surface elevation gradually changed from negative to positive. The findings of this article suggest that the rate of glacier retreat on Bogda Mountain increased from 2000 to 2017.
Role of Photobiomodulation Therapy in Modulating Oxidative Stress in Temporomandibular Disorders. A Systematic Review and Meta-Analysis of Human Randomised Controlled Trials

This systematic review and meta-analysis (PROSPERO registration; ref CRD 42020198921) aimed to govern photobiomodulation therapy (PBMT) efficacy in temporomandibular disorder (TMD). PRISMA guidelines and Cochrane Collaboration recommendations were followed. Differences in pain reduction assessment by qualitative measurement with visual analogue scale (VAS), pain pressure threshold (PPT) and maximum mouth opening (MMO) were calculated with 95% confidence intervals and pooled in a random effects model with a subgroup analysis, evaluating the role of follow-up duration. Heterogeneity was analysed using Q and I2 tests. Publication bias was assessed by visual examination of funnel plot symmetry. Qualitative analysis revealed 46% of the 44 included studies showed a high risk of bias. Meta-analysis on 32 out of 44 studies revealed statistically significant intergroup differences (SSID) for VAS (SMD = −0.55; 95% CI = −0.82 to −0.27; Z = 3.90 (p < 0.001)), PPT (SMD = −0.45; 95% CI = −0.89 to 0.00; Z = 1.97 (p = 0.05)) and MMO (SMD = −0.45; 95% CI = −0.89 to 0.00; Z = 1.97 (p = 0.05)), favouring PBMT compared to control treatment strategies. Sensitivity analysis revealed SSID (SMD = −0.53; 95% CI = −0.73 to −0.32; Z = 5.02 (p < 0.0001)) with low heterogeneity (Τ2 = 0.02; χ2 = 16.03 (p = 0.31); I2 = 13%). Hence, this review, for first time, proposed suggested recommendations for PBMT protocols and methodology for future extensive TMD research.
3D Collagen Hydrogel Promotes In Vitro Langerhans Islets Vascularization through ad-MVFs Angiogenic Activity

Adipose derived microvascular fragments (ad-MVFs) consist of effective vascularization units able to reassemble into efficient microvascular networks. Because of their content in stem cells and related angiogenic activity, ad-MVFs represent an interesting tool for applications in regenerative medicine. Here we show that gentle dissociation of rat adipose tissue provides a mixture of ad-MVFs with a length distribution ranging from 33–955 μm that are able to maintain their original morphology. The isolated units of ad-MVFs that resulted were able to activate transcriptional switching toward angiogenesis, forming tubes, branches, and entire capillary networks when cultured in 3D collagen type-I hydrogel. The proper involvement of metalloproteases (MMP2/MMP9) and serine proteases in basal lamina and extracellular matrix ECM degradation during the angiogenesis were concurrently assessed by the evaluation of alpha-smooth muscle actin (αSMA) expression. These results suggest that collagen type-I hydrogel provides an adequate 3D environment supporting the activation of the vascularization process. As a proof of concept, we exploited 3D collagen hydrogel for the setting of ad-MVF–islet of Langerhans coculture to improve the islets vascularization. Our results suggest potential employment of the proposed in vitro system for regenerative medicine applications, such as the improving of the islet of Langerhans engraftment before transplantation.
Genetic variation of BnaA3.NIP5;1 expressing in the lateral root cap contributes to boron deficiency tolerance in Brassica napus

Boron (B) is essential for vascular plants. Rapeseed (Brassica napus) is the second leading crop source for vegetable oil worldwide, but its production is critically dependent on B supplies. BnaA3.NIP5;1 was identified as a B-efficient candidate gene in B. napus in our previous QTL fine mapping. However, the molecular mechanism through which this gene improves low-B tolerance remains elusive. Here, we report genetic variation in BnaA3.NIP5;1 gene, which encodes a boric acid channel, is a key determinant of low-B tolerance in B. napus. Transgenic lines with increased BnaA3.NIP5;1 expression exhibited improved low-B tolerance in both the seedling and maturity stages. BnaA3.NIP5;1 is preferentially polar-localized in the distal plasma membrane of lateral root cap (LRC) cells and transports B into the root tips to promote root growth under B-deficiency conditions. Further analysis revealed that a CTTTC tandem repeat in the 5’UTR of BnaA3.NIP5;1 altered the expression level of the gene, which is tightly associated with plant growth and seed yield. Field tests with natural populations and near-isogenic lines (NILs) confirmed that the varieties carried BnaA3.NIP5;1Q allele significantly improved seed yield. Taken together, our results provide novel insights into the low-B tolerance of B. napus, and the elite allele of BnaA3.NIP5;1 could serve as a direct target for breeding low-B-tolerant cultivars.
The Roles of the IGF Axis in the Regulation of the Metabolism: Interaction and Difference between Insulin Receptor Signaling and IGF-I Receptor Signaling

It has been well established that insulin-like growth factors (IGFs) mainly mediate long-term actions in cell fates, whereas insulin predominantly exerts its role on metabolic activity. Indeed, insulin mediates multiple anabolic biological activities in glucose and amino acid transport, lipid and protein synthesis, the induction of glycogen, the inhibition of gluconeogenesis, lipolysis, and protein degradation. The interactions and differences between insulin receptor signaling and IGF-I receptor signaling in the metabolism and the cell fates are quite complicated. Because of the overlapping actions of IGF-I singling with insulin signaling, it has been difficult to distinguish the role of both signaling mechanisms on the metabolism. Furthermore, comprehensive information on the IGF-I function in respective tissues remains insufficient. Therefore, we need to clarify the precise roles of IGF-I signaling on the metabolism separate from those of insulin signaling. This review focuses on the metabolic roles of IGFs in the respective tissues, especially in terms of comparison with those of insulin, by overviewing the metabolic phenotypes of tissue-specific IGF-I and insulin receptor knockout mice, as well as those in mice treated with the dual insulin receptor/IGF-I receptor inhibitor OSI-906.
Genome-Wide Analysis of the YABBY Transcription Factor Family in Rapeseed (Brassica napus L.)

The YABBY family of plant-specific transcription factors play important regulatory roles during the development of leaves and floral organs, but their functions in Brassica species are incompletely understood. Here, we identified 79 YABBY genes from Arabidopsis thaliana and five Brassica species (B. rapa, B. nigra, B. oleracea, B. juncea, and B. napus). A phylogenetic analysis of YABBY proteins separated them into five clusters (YAB1–YAB5) with representatives from all five Brassica species, suggesting a high degree of conservation and similar functions within each subfamily. We determined the gene structure, chromosomal location, and expression patterns of the 21 BnaYAB genes identified, revealing extensive duplication events and gene loss following polyploidization. Changes in exon–intron structure during evolution may have driven differentiation in expression patterns and functions, combined with purifying selection, as evidenced by Ka/Ks values below 1. Based on transcriptome sequencing data, we selected nine genes with high expression at the flowering stage. qRT-PCR analysis further indicated that most BnaYAB family members are tissue-specific and exhibit different expression patterns in various tissues and organs of B. napus. This preliminary study of the characteristics of the YABBY gene family in the Brassica napus genome provides theoretical support and reference for the later functional identification of the family genes.
The Influence of the Grapevine Bacterial and Fungal Endophytes on Biomass Accumulation and Stilbene Production by the In Vitro Cultivated Cells of Vitis amurensis Rupr.

Plant endophytes are known to alter the profile of secondary metabolites in plant hosts. In this study, we identified the main bacterial and fungal representatives of the wild grape Vitis amurensis Rupr. microbiome and investigated a cocultivation effect of the 14 endophytes and the V. amurensis cell suspension on biomass accumulation and stilbene biosynthesis. The cocultivation of the V. amurensis cell culture with the bacteria Agrobacterium sp. , Bacillus sp. , and Curtobacterium sp. for 2 weeks did not significantly affect the accumulation of cell culture fresh biomass. However, it was significantly inhibited by the bacteria Erwinia sp. , Pantoea sp. , Pseudomonas sp. , and Xanthomonas sp. and fungi Alternaria sp. , Biscogniauxia sp. , Cladosporium sp. , Didymella sp. 2, and Fusarium sp. Cocultivation of the grapevine cell suspension with the fungi Didymella sp. 1 and Trichoderma sp. resulted in cell death. The addition of endophytic bacteria increased the total stilbene content by 2.2–5.3 times, while the addition of endophytic fungi was more effective in inducing stilbene accumulation by 2.6–16.3 times. The highest content of stilbenes in the grapevine cells cocultured with endophytic fungi was 13.63 and 13.76 mg/g of the cell dry weight (DW) after cultivation with Biscogniauxia sp. and Didymella sp. 2, respectively. The highest content of stilbenes in the grapevine cells cocultured with endophytic bacteria was 4.49 mg/g DW after cultivation with Xanthomonas sp. The increase in stilbene production was due to a significant activation of phenylalanine ammonia lyase (PAL) and stilbene synthase (STS) gene expression. We also analyzed the sensitivity of the selected endophytes to eight antibiotics, fluconazole, and trans-resveratrol. The endophytic bacteria were sensitive to gentamicin and kanamycin, while all selected fungal strains were resistant to fluconazole with the exception of Cladosporium sp. All endophytes were tolerant of trans-resveratrol. This study showed that grape endophytes stimulate the production of stilbenes in grape cell suspension, which could further contribute to the generation of a new stimulator of stilbene biosynthesis in grapevine or grape cell cultures.
Targeting the Angiotensin II Type 1 Receptor in Cerebrovascular Diseases: Biased Signaling Raises New Hopes

The physiological and pathophysiological relevance of the angiotensin II type 1 (AT1) G protein-coupled receptor no longer needs to be proven in the cardiovascular system. The renin–angiotensin system and the AT1 receptor are the targets of several classes of therapeutics (such as angiotensin converting enzyme inhibitors or angiotensin receptor blockers, ARBs) used as first-line treatments in cardiovascular diseases. The importance of AT1 in the regulation of the cerebrovascular system is also acknowledged. However, despite numerous beneficial effects in preclinical experiments, ARBs do not induce satisfactory curative results in clinical stroke studies. A better understanding of AT1 signaling and the development of biased AT1 agonists, able to selectively activate the β-arrestin transduction pathway rather than the Gq pathway, have led to new therapeutic strategies to target detrimental effects of AT1 activation. In this paper, we review the involvement of AT1 in cerebrovascular diseases as well as recent advances in the understanding of its molecular dynamics and biased or non-biased signaling. We also describe why these alternative signaling pathways induced by β-arrestin biased AT1 agonists could be considered as new therapeutic avenues for cerebrovascular diseases.
Antimicrobial and Antibiofilm Activity of the Probiotic Strain Streptococcus salivarius K12 against Oral Potential Pathogens

Oral probiotics are increasingly used in the harmonization of the oral microbiota in the prevention or therapy of various oral diseases. Investigation of the antimicrobial activity of the bacteriocinogenic strain Streptococcus salivarius K12 against oral pathogens shows promising results, not only in suppressing growth, but also in eliminating biofilm formation. Based on these findings, we decided to investigate the antimicrobial and antibiofilm activity of the neutralized cell-free supernatant (nCFS) of S. salivarius K12 at various concentrations against selected potential oral pathogens under in vitro conditions on polystyrene microtiter plates. The nCFS of S. salivarius K12 significantly reduced growth (p < 0.01) in Streptococcus mutans Clarke with increasing concentration from 15 to 60 mg/mL and also in Staphylococcus hominis 41/6 at a concentration of 60 mg/mL (p < 0.001). Biofilm formation significantly decreased (p < 0.001) in Schaalia odontolytica P10 at nCFS concentrations of 60 and 30 mg/mL. Biofilm inhibition (p < 0.001) was also observed in Enterobacter cloacae 4/2 at a concentration of 60 mg/mL. In Schaalia odontolytica P10 and Enterobacter cloacae 4/2, the nCFS had no effect on their growth.
The Effectiveness of Interventions Delivered Using Digital Food Environments to Encourage Healthy Food Choices: A Systematic Review and Meta-Analysis

Digital food environments are now commonplace across many food service and retail settings, influencing how the population orders and accesses foods. As such, digital food environments represent a novel platform to deliver strategies to improve public health nutrition. The purpose of this review was to explore the impact of dietary interventions embedded within online food ordering systems, on user selection and purchase of healthier foods and beverages. A systematic search of eight electronic databases and grey literature sources was conducted up to October 2020. Eligible studies were randomized controlled trials and controlled trials, designed to encourage the selection and purchase of healthier products and/or discourage the selection and purchase of less-healthy products using strategies delivered via real-world online food ordering systems. A total of 9441 articles underwent title and abstract screening, 140 full-text articles were assessed for eligibility, and 11 articles were included in the review. Meta-analysis of seven studies indicated that interventions delivered via online food ordering systems are effective in reducing the energy content of online food purchases (standardized mean difference (SMD): −0.34, p = 0.01). Meta-analyses including three studies each suggest that these interventions may also be effective in reducing the fat (SMD: −0.83, p = 0.04), saturated fat (SMD: −0.7, p = 0.008) and sodium content (SMD: −0.43, p = 0.01) of online food purchases. Given the ongoing growth in the use of online food ordering systems, future research to determine how we can best utilize these systems to support public health nutrition is warranted.
Protein Denaturation Through the Use of Magnetic Molecularly Imprinted Polymer Nanoparticles

The inhibition of the protein function for therapeutic applications remains challenging despite progress these past years. While the targeting application of molecularly imprinted polymer are in their infancy, no use was ever made of their magnetic hyperthermia properties to damage proteins when they are coupled to magnetic nanoparticles. Therefore, we have developed a facile and effective method to synthesize magnetic molecularly imprinted polymer nanoparticles using the green fluorescent protein (GFP) as the template, a bulk imprinting of proteins combined with a grafting approach onto maghemite nanoparticles. The hybrid material exhibits very high adsorption capacities and very strong affinity constants towards GFP. We show that the heat generated locally upon alternative magnetic field is responsible of the decrease of fluorescence intensity.
Linear functional organization of the omic embedding space

Abstract Motivation We are increasingly accumulating complex omics data that capture different aspects of cellular functioning. A key challenge is to untangle their complexity and effectively mine them for new biomedical information. To decipher this new information, we introduce algorithms based on network embeddings. Such algorithms represent biological macromolecules as vectors in d-dimensional space, in which topologically similar molecules are embedded close in space and knowledge is extracted directly by vector operations. Recently, it has been shown that neural networks used to obtain vectorial representations (embeddings) are implicitly factorizing a mutual information matrix, called Positive Pointwise Mutual Information (PPMI) matrix. Thus, we propose the use of the PPMI matrix to represent the human protein–protein interaction (PPI) network and also introduce the graphlet degree vector PPMI matrix of the PPI network to capture different topological (structural) similarities of the nodes in the molecular network. Results We generate the embeddings by decomposing these matrices with Nonnegative Matrix Tri-Factorization. We demonstrate that genes that are embedded close in these spaces have similar biological functions, so we can extract new biomedical knowledge directly by doing linear operations on their embedding vector representations. We exploit this property to predict new genes participating in protein complexes and to identify new cancer-related genes based on the cosine similarities between the vector representations of the genes. We validate 80% of our novel cancer-related gene predictions in the literature and also by patient survival curves that demonstrating that 93.3% of them have a potential clinical relevance as biomarkers of cancer. Availability and implementation Code and data are available online at https://gitlab.bsc. es/axenos/embedded-omics-data-geometry/. Supplementary information Supplementary data are available at Bioinformatics online.
Novel High-Quality Sonographic Methods to Diagnose Muscle Wasting in Long-Stay Critically Ill Patients: Shear Wave Elastography, Superb Microvascular Imaging and Contrast-Enhanced Ultrasound

Novel ultrasound (US) methods are required to assess qualitative changes in the quadriceps rectus femoris (QRF) muscle when evaluating mechanically ventilated, long-stay ICU patients with suspected neuromuscular acquired weakness (ICUAW). Our aim was to analyze novel US muscle assessment methods in these patients versus healthy controls by carrying out a prospective observational study. Shear wave elastography (SWE) showed, with a receiver operating characteristic (ROC) curve of 0.972 (95% confidence interval (CI) = 0.916–1.000), that patients increased muscle stiffness associated with muscle fibrosis when diagnosed with ICUAW. We also performed, for the first time, superb microvascular imaging (SMI), which is an innovative US technique designed for imaging microvascularization unseen with color Doppler US, and observed that 53.8% of cases had significantly lower QRF muscle microvascular angiogenic activity than controls (p < 0.001). Finally, we used contrast-enhanced ultrasound (CEUS) to analyze maximum and minimum QRF muscle perfusion and obtained a ROC curve of 0.8, but when used as markers for SMI, their diagnostic capacity increased to 0.988 (CI = 0.965–1) and 0.932 (CI = 0.858–1), respectively. These findings show, for the first time, that these novel sonographic muscle methods should be used for their diagnostic capacity when assessing sarcopenic processes associated with this group of critically ill patients.