Miracle-dz/UniFAR-FTUs huggingface dataset:
Exploring the Mechanism of the miRNA-145/Paxillin Axis in Cell Metabolism During VEGF-A–Induced Corneal Angiogenesis

Purpose Paxillin (PXN) is a key component of focal adhesions and plays an important role in angiogenesis. The aim of the present study was to investigate the effect of PXN in vascular endothelial growth factor A (VEGF-A)–induced angiogenesis in human umbilical vein endothelial cells (HUVECs). Methods HUVECs were transfected with PXN overexpression and PXN interference vectors. Biochemical detection was used to detect adenosine triphosphate and lactic acid production. The morphology of mitochondria was observed under an electron microscope, and flow cytometry was conducted to measure mitochondrial membrane potential. Transwell experiments were used to detect the migration and tube formation ability of each group of cells. The expression of hexokinase (HK)1, HK2, glucose transporter 1 (GLUT1), phosphorylated phosphatidylinositol 3-kinase (PI3K), phosphorylated AKT, and phosphorylated mechanistic target of rapamycin (mTOR) was evaluated by western blot. Results PXN silencing reduced the levels of lactic acid and adenosine triphosphate, downregulated HK1, HK2, and GLUT1, suppressed PI3K/AKT/mTOR signaling activation, and inhibited VEGF-A–induced mitochondria injury in VEGF-A–induced HUVECs. We also determined that miR-145-5p decreased the VEGF-A–induced expression of PXN and inhibited the invasion and angiogenesis of HUVECs. Also, miR-145-5p inhibition blocked the protective effect of PXN interference on VEGF-A–induced HUVEC injury. Furthermore, PXN interference significantly decreased lactic acid and adenosine triphosphate levels, inhibited PI3K/AKT/mTOR activation, and decreased the levels of HK1, HK2, and GLUT1 in VEGF-A-treated mouse corneal. Conclusions The results indicate that PXN silencing inhibited the VEGF-A–induced invasion and angiogenesis of HUVECs via regulation of cell metabolism and mitochondrial damage, suggesting that PXN may be a potential target for antiangiogenic therapies.
Comparison of efficacy of three different mouthwashes in reducing aerosol contamination produced by ultrasonic scaler: A pilot study

Background and Objective: Aerosol produced during the procedure of scaling and root planing is a potent source of infection. Preprocedural mouthrinsing has been found effective in reducing the bacterial load of the aerosol produced during the procedure. Thus, the aim of the present study was to evaluate and compare the efficacy of three different mouthwashes containing Chlorhexidine, Essential Oils & Herbal Extracts by using them as preprocedural rinsing agent in reducing the bacterial load of the aerosol produced by ultrasonic scaler. Material and Methodology: 40 subjects age and gender matched were randomly divided into four groups on the basis of agents used for preprocedural mouthrinsing - Group I: Distilled Water (Control), Group II: Chlorhexidine (CHX), Group III: Herbal Extracts (HR) & Group IV: Essential Oils (EO). The aerosols were collected on three previously prepared and sterilised blood agar plates at three different positions in the operatory. The colony forming units were counted after incubating the plates for 48 hours. Result: At all locations, the mean CFU was highest in Group I followed by Group III, Group IV and Group II. Conclusion: In the study 0.2 % chlorhexidine was found to be most effective preprocedural mouthwash in reducing the bacterial load in the aerosol produced during ultrasonic scaling followed by essential oil and herbal mouthwash respectively.
SAR11 Cells Rely on Enzyme Multifunctionality To Metabolize a Range of Polyamine Compounds

Genome streamlining in SAR11 bacterioplankton has resulted in a small repertoire of genes, yet paradoxically, they consume a substantial fraction of primary production in the oceans. Enzyme multifunctionality, referring to enzymes that are adapted to have broader substrate and catalytic range than canonically defined, is hypothesized to be an adaptation that increases the range of organic compounds metabolized by cells in environments where selection favors genome minimization. ABSTRACT In the ocean surface layer and cell culture, the polyamine transport protein PotD of SAR11 bacteria is often one of the most abundant proteins detected. Polyamines are organic cations at seawater pH produced by all living organisms and are thought to be an important component of dissolved organic matter (DOM) produced in planktonic ecosystems. We hypothesized that SAR11 cells uptake and metabolize multiple polyamines and use them as sources of carbon and nitrogen. Metabolic footprinting and fingerprinting were used to measure the uptake of five polyamine compounds (putrescine, cadaverine, agmatine, norspermidine, and spermidine) in two SAR11 strains that represent the majority of SAR11 cells in the surface ocean environment, “Candidatus Pelagibacter” strain HTCC7211 and “Candidatus Pelagibacter ubique” strain HTCC1062. Both strains took up all five polyamines and concentrated them to micromolar or millimolar intracellular concentrations. Both strains could use most of the polyamines to meet their nitrogen requirements, but polyamines did not fully substitute for their requirements of glycine (or related compounds) or pyruvate (or related compounds). Our data suggest that potABCD transports all five polyamines and that spermidine synthase, speE, is reversible, catalyzing the breakdown of spermidine and norspermidine, in addition to its usual biosynthetic role. These findings provide support for the hypothesis that enzyme multifunctionality enables streamlined cells in planktonic ecosystems to increase the range of DOM compounds they metabolize. IMPORTANCE Genome streamlining in SAR11 bacterioplankton has resulted in a small repertoire of genes, yet paradoxically, they consume a substantial fraction of primary production in the oceans. Enzyme multifunctionality, referring to enzymes that are adapted to have broader substrate and catalytic range than canonically defined, is hypothesized to be an adaptation that increases the range of organic compounds metabolized by cells in environments where selection favors genome minimization. We provide experimental support for this hypothesis by demonstrating that SAR11 cells take up and metabolize multiple polyamine compounds and propose that a small set of multifunctional enzymes catalyze this metabolism. We report that polyamine uptake rates can exceed metabolic rates, resulting in both high intracellular concentrations of these nitrogen-rich compounds (in comparison to native polyamine levels) and an increase in cell size.
Home range variation in leopards living across the human density gradient

Home range size is a fundamental measure of animal space use, providing insight into habitat quality, animal density, and social organization. Human impacts increasingly are affecting wildlife, especially among wide-ranging species that encounter anthropogenic disturbance. Leopards (Panthera pardus) provide a useful model for studying this relationship because leopards coexist with people at high and low human densities and are sensitive to human disturbance. To compare leopard home range size across a range of human densities and other environmental conditions, we combined animal tracking data from 74 leopards in multiple studies with new analytical techniques that accommodate different sampling regimes. We predicted that home ranges would be smaller in more productive habitats and areas of higher human population density due to possible linkage with leopard prey subsidies from domestic species. We also predicted that male leopards would have larger home ranges than those of females. Home ranges varied in size from 14.5 km2 in India to 885.6 km2 in Namibia, representing a 60-fold magnitude of variation. Home range stability was evident for 95.2% of nontranslocated individuals and 38.5% of translocated individuals. Leopard home range sizes were negatively correlated with landscape productivity, and males used larger areas than females. Leopards in open habitats had a predicted negative correlation in home range size with human population density, but leopards in closed habitats used larger home ranges in areas with more people.
Gauss Stylization: Interactive Artistic Mesh Modeling based on Preferred Surface Normals

Extending the ARAP energy with a term that depends on the face normal, energy minimization becomes an effective stylization tool for shapes represented as meshes. Our approach generalizes the possibilities of Cubic Stylization: the set of preferred normals can be chosen arbitrarily from the Gauss sphere, including semi‐discrete sets to model preference for cylinder‐ or cone‐like shapes. The optimization is designed to retain, similar to ARAP, the constant linear system in the global optimization. This leads to convergence behavior that enables interactive control over the parameters of the optimization. We provide various examples demonstrating the simplicity and versatility of the approach.
Roominoes: Generating Novel 3D Floor Plans From Existing 3D Rooms

Realistic 3D indoor scene datasets have enabled significant recent progress in computer vision, scene understanding, autonomous navigation, and 3D reconstruction. But the scale, diversity, and customizability of existing datasets is limited, and it is time‐consuming and expensive to scan and annotate more. Fortunately, combinatorics is on our side: there are enough individual rooms in existing 3D scene datasets, if there was but a way to recombine them into new layouts. In this paper, we propose the task of generating novel 3D floor plans from existing 3D rooms. We identify three sub‐tasks of this problem: generation of 2D layout, retrieval of compatible 3D rooms, and deformation of 3D rooms to fit the layout. We then discuss different strategies for solving the problem, and design two representative pipelines: one uses available 2D floor plans to guide selection and deformation of 3D rooms; the other learns to retrieve a set of compatible 3D rooms and combine them into novel layouts. We design a set of metrics that evaluate the generated results with respect to each of the three subtasks and show that different methods trade off performance on these subtasks. Finally, we survey downstream tasks that benefit from generated 3D scenes and discuss strategies in selecting the methods most appropriate for the demands of these tasks.
A heterotypic assembly mechanism regulates CHIP E3 ligase activity

CHIP (C‐terminus of Hsc70‐interacting protein) and its worm ortholog CHN‐1 are E3 ubiquitin ligases that link the chaperone system with the ubiquitin‐proteasome system (UPS). CHN‐1 can cooperate with UFD‐2, another E3 ligase, to accelerate ubiquitin chain formation; however, the basis for the high processivity of this E3s set has remained obscure. Here, we studied the molecular mechanism and function of the CHN‐1–UFD‐2 complex in Caenorhabditis elegans. Our data show that UFD‐2 binding promotes the cooperation between CHN‐1 and ubiquitin‐conjugating E2 enzymes by stabilizing the CHN‐1 U‐box dimer. However, HSP70/HSP‐1 chaperone outcompetes UFD‐2 for CHN‐1 binding, thereby promoting a shift to the autoinhibited CHN‐1 state by acting on a conserved residue in its U‐box domain. The interaction with UFD‐2 enables CHN‐1 to efficiently ubiquitylate and regulate S‐adenosylhomocysteinase (AHCY‐1), a key enzyme in the S‐adenosylmethionine (SAM) regeneration cycle, which is essential for SAM‐dependent methylation. Our results define the molecular mechanism underlying the synergistic cooperation of CHN‐1 and UFD‐2 in substrate ubiquitylation.
Proteome-wide screening for mitogen-activated protein kinase docking motifs and interactors

Essential functions of mitogen-activated protein kinases (MAPKs) depend on their capacity to selectively phosphorylate a limited repertoire of substrates. MAPKs harbor a conserved groove located outside of the catalytic cleft that binds to short linear sequence motifs found in substrates and regulators. However, the weak and transient nature of these “docking” interactions poses a challenge to defining MAPK interactomes and associated sequence motifs. Here, we describe a yeast-based genetic screening pipeline to evaluate large collections of MAPK docking sequences in parallel. Using this platform we analyzed a combinatorial library based on the docking sequences from the MAPK kinases MKK6 and MKK7, defining features critical for binding to the stress-activated MAPKs JNK1 and p38α. We subsequently screened a library consisting of ~12,000 sequences from the human proteome, revealing a large number of MAPK-selective interactors, including many not conforming to previously defined docking motifs. Analysis of p38α/JNK1 exchange mutants identified specific docking groove residues mediating selective binding. Finally, we verified that docking sequences identified in the screen could function in substrate recruitment in vitro and in cultured cells. Collectively, these studies establish an approach for characterization of MAPK docking sequences and provide a resource for future investigation of signaling downstream of p38 and JNK MAP kinases.
Spinal Cord Stimulation as Treatment for Cancer and Chemotherapy-Induced Pain

Neuropathic pain is a rampant disease exacting a significant toll on patients, providers, and health care systems around the globe. Neuromodulation has been successfully employed to treat many indications including failed back surgery syndrome (FBSS), complex regional pain syndrome (CRPS), phantom limb pain (PLP), radiculopathies, and intractable pelvic pain, among many others. Recent studies have also demonstrated efficacy for cancer-related pain and chemotherapy induced neuropathy with these techniques. Spinal cord stimulation (SCS) is the most commonly employed technique and involves implantation of percutaneous or paddle leads targeting the dorsal columns of the spinal cord with the goal of disrupting the pain signals traveling to the brain. Tonic, high frequency, and burst waveforms have all been shown to reduce pain and disability in chronic pain patients. Closed-loop SCS systems that automatically adjust stimulation parameters based on feedback (such as evoked compound action potentials) are becoming increasingly used to help ease the burden placed on patients to adjust their programming to their pain and position. Additionally, dorsal root ganglion stimulation (DRGS) is a newer technique that allows for dermatomal coverage especially in patients with pain in up to two dermatomes. Regardless of the technique chosen, neuromodulation has been shown to be cost-effective and efficacious and should be given full consideration in patients with chronic pain conditions.
Spider Phobia: Neural Networks Informing Diagnosis and (Virtual/Augmented Reality-Based) Cognitive Behavioral Psychotherapy—A Narrative Review

Recent fMRI studies on specific animal phobias, particularly spider phobia (arachnophobia), have identified a large variety of specific brain regions involved in normal and disturbed fear processing. Both functional and structural brain abnormalities have been identified among phobic patients. Current research suggests that both conscious and subconscious fear processing play a crucial role in phobic disorders. Cognitive behavioral therapy has been identified as an effective treatment for specific phobias and has been associated with neuroplastic effects which can be evaluated using current neuroimaging techniques. Recent research suggests that new approaches using virtual (VR) or augmented reality (AR) tend to be similarly effective as traditional “in vivo” therapy methods and could expand treatment options for different medical or individual scenarios. This narrative review elaborates on neural structures and particularities of arachnophobia. Current treatment options are discussed and future research questions are highlighted.
Omega-3 Fatty Acids and Inflammation—You Are What You Eat!

Have you ever heard the phrase, “You are what you eat? ” Of course, if you eat a donut, you will not actually turn into a donut—but bits and pieces of what we eat do become parts of us! In this article, we will talk about how the fatty acids in our cells can help protect us from various diseases by controlling inflammation. Specifically, we will focus on food components called omega-3 polyunsaturated fatty acids, which are most abundant in seafood. We will talk about how eating foods rich in omega-3s increases the levels of omega-3s in your cell membranes and may protect against several diseases that are associated with uncontrolled inflammation.
A Polysaccharide From the Whole Plant of Plantago asiatica L. Enhances the Antitumor Activity of Dendritic Cell-Based Immunotherapy Against Breast Cancer

Dendritic cells (DCs) are the most potent professional antigen-presenting cells (APCs) that mediate T-cell immune responses. Breast cancer is one of the most commonly diagnosed diseases and its mortality rate is higher than any other cancer in both humans and canines. Plantain polysaccharide (PLP), extracted from the whole plant of Plantago asiatica L. , could promote the maturation of DCs. In this research, we found that PLP could upregulate the maturation of DCs both in vitro and in vivo. PLP-activated DCs could stimulate lymphocytes’ proliferation and differentiate naive T cells into cytotoxic T cells. Tumor antigen-specific lymphocyte responses were enhanced by PLP and CIPp canine breast tumor cells lysate-pulsed DCs, and PLP and CIPp-cell-lysate jointly stimulated DCs cocultured with lymphocytes having the great cytotoxicity on CIPp cells. In the 4T1 murine breast tumor model, PLP could control the size of breast tumors and improve immunity by recruiting DCs, macrophages, and CD4+ and CD8+ T cells in the tumor microenvironment. These results indicated that PLP could achieve immunotherapeutic effects and improve immunity in the breast tumor model.
Development of Wheat (Triticum aestivum L.) Populations for Drought Tolerance and Improved Biomass Allocation Through Ethyl Methanesulphonate Mutagenesis

The narrow genetic variation for drought adaptive traits and biomass allocation in wheat (Triticum aestivum L.) presents a major bottleneck for breeding. Induced mutagenesis creates genetic variation and complements conventional breeding for drought tolerance improvement. The aims of this study were to induce mutations in wheat genotype LM43 using three ethyl methanesulphonate (EMS) treatments, and to develop mutant populations for improving drought tolerance, biomass allocation and agronomic performance. Experiments were conducted under controlled and field conditions at the University of KwaZulu-Natal. Data on percentage germination (%G), days to 90% maturity (DTM), plant height (PH), shoot biomass (SB), root biomass (RB), root-shoot ratio (RSR), spike length (SL), spikelet count (SPS), thousand seed weight (TSW), and grain yield (GY) were collected from M1 to M4 generations. Significant (p < 0.001) differences among individuals and generations were observed for all the assessed traits and the generation × population interaction effects were significant (p < 0.01) for SB, TSW, and GY due to EMS treatments. The differences among the generations showed that the mutagenic effects were cumulative and exhibited clear segregations in subsequent generations. The new selections with unique biomass allocation, drought response and agronomic performance will be useful for wheat improvement programs.
Marine-Derived Collagen as Biomaterials for Human Health

Collagen is a kind of biocompatible protein material, which is widely used in medical tissue engineering, drug delivery, cosmetics, food and other fields. Because of its wide source, low extraction cost and good physical and chemical properties, it has attracted the attention of many researchers in recent years. However, the application of collagen derived from terrestrial organisms is limited due to the existence of diseases, religious beliefs and other problems. Therefore, exploring a wider range of sources of collagen has become one of the main topics for researchers. Marine-derived collagen (MDC) stands out because it comes from a variety of sources and avoids issues such as religion. On the one hand, this paper summarized the sources, extraction methods and characteristics of MDC, and on the other hand, it summarized the application of MDC in the above fields. And on the basis of the review, we found that MDC can not only be extracted from marine organisms, but also from the wastes of some marine organisms, such as fish scales. This makes further use of seafood resources and increases the application prospect of MDC.
NF-E2-Related Factor 2 (Nrf2) Ameliorates Radiation-Induced Skin Injury

Radiation-induced skin injury (RISI) commonly occur in cancer patients who received radiotherapy and is one of the first clinical symptoms after suffering from nuclear exposure. Oxidative damage is the major causes of RISI. Nuclear factor erythroid 2-related factor 2 (Nrf2) is considered as a key mediator of the cellular antioxidant response. However, whether Nrf2 can alleviate RISI after high-dose irradiation remains unknown. In this study, we demonstrated that Nrf2-deficient (Nrf2 -/-) mice were susceptible to high-dose irradiation and adenovirus-mediated overexpression of Nrf2 (ad-Nrf2) protected against radiation in skin cells. Overexpression of Nrf2 attenuated the severity of skin injury after high-dose electron beam irradiation. To uncover the mechanisms of Nrf2 involved in RISI, mRNA sequencing technology was performed to analyze the mRNA expression profiles of Ad-Nrf2 skin cells following radiation. The results revealed that a total of 127 genes were significantly changed, 55 genes were upregulated, and 72 genes were downregulated after Nrf2 overexpression. GSEA showed that Nrf2 was associated with positive regulation of genes involved in the reactive oxygen species pathway after radiation. Taken together, this study illustrated the role of Nrf2 in RISI and provided potentially strategies for ameliorating RISI.