Miracle-dz/UniFAR-FTUs huggingface dataset:
Rice XA21 Binding Protein 3 Is a Ubiquitin Ligase Required for Full Xa21-Mediated Disease Resistance[W][OA]

XA21 is a receptor-like kinase protein in rice (Oryza sativa) that confers gene-for-gene resistance to specific races of the causal agent of bacterial blight disease, Xanthomonas oryzae pv oryzae. We identified XA21 binding protein 3 (XB3), an E3 ubiquitin ligase, as a substrate for the XA21 Ser and Thr kinase. The interaction between XB3 and the kinase domain of XA21 has been shown in yeast and in vitro, and the physical association between XB3 and XA21 in vivo has also been confirmed by coimmunoprecipitation assays. XB3 contains an ankyrin repeat domain and a RING finger motif that is sufficient for its interaction with the kinase domain of XA21 and for its E3 ubiquitin ligase activity, respectively. Transgenic plants with reduced expression of the Xb3 gene are compromised in resistance to the avirulent race of X. oryzae pv oryzae. Furthermore, reduced levels of Xb3 lead to decreased levels of the XA21 protein. These results indicate that Xb3 is necessary for full accumulation of the XA21 protein and for Xa21-mediated resistance.
The distinct fate of smooth and rough Mycobacterium abscessus variants inside macrophages

Mycobacterium abscessus is a pathogenic, rapidly growing mycobacterium responsible for pulmonary and cutaneous infections in immunocompetent patients and in patients with Mendelian disorders, such as cystic fibrosis (CF). Mycobacterium abscessus is known to transition from a smooth (S) morphotype with cell surface-associated glycopeptidolipids (GPL) to a rough (R) morphotype lacking GPL. Herein, we show that M. abscessus S and R variants are able to grow inside macrophages and are present in morphologically distinct phagosomes. The S forms are found mostly as single bacteria within phagosomes characterized by a tightly apposed phagosomal membrane and the presence of an electron translucent zone (ETZ) surrounding the bacilli. By contrast, infection with the R form leads to phagosomes often containing more than two bacilli, surrounded by a loose phagosomal membrane and lacking the ETZ. In contrast to the R variant, the S variant is capable of restricting intraphagosomal acidification and induces less apoptosis and autophagy. Importantly, the membrane of phagosomes enclosing the S forms showed signs of alteration, such as breaks or partial degradation. Although not frequently encountered, these events suggest that the S form is capable of provoking phagosome–cytosol communication. In conclusion, M. abscessus S exhibits traits inside macrophages that are reminiscent of slow-growing mycobacterial species.
UDP-Glucosyltransferases from Rice, Brachypodium, and Barley: Substrate Specificities and Synthesis of Type A and B Trichothecene-3-O-β-d-glucosides

Trichothecene toxins are confirmed or suspected virulence factors of various plant-pathogenic Fusarium species. Plants can detoxify these to a variable extent by glucosylation, a reaction catalyzed by UDP-glucosyltransferases (UGTs). Due to the unavailability of analytical standards for many trichothecene-glucoconjugates, information on such compounds is limited. Here, the previously identified deoxynivalenol-conjugating UGTs HvUGT13248 (barley), OsUGT79 (rice) and Bradi5g03300 (Brachypodium), were expressed in E. coli, affinity purified, and characterized towards their abilities to glucosylate the most relevant type A and B trichothecenes. HvUGT13248, which prefers nivalenol over deoxynivalenol, is also able to conjugate C-4 acetylated trichothecenes (e.g., T-2 toxin) to some degree while OsUGT79 and Bradi5g03300 are completely inactive with C-4 acetylated derivatives. The type A trichothecenes HT-2 toxin and T-2 triol are the kinetically preferred substrates in the case of HvUGT13248 and Bradi5g03300. We glucosylated several trichothecenes with OsUGT79 (HT-2 toxin, T-2 triol) and HvUGT13248 (T-2 toxin, neosolaniol, 4,15-diacetoxyscirpenol, fusarenon X) in the preparative scale. NMR analysis of the purified glucosides showed that exclusively β-d-glucosides were formed regio-selectively at position C-3-OH of the trichothecenes. These synthesized standards can be used to investigate the occurrence and toxicological properties of these modified mycotoxins.
Peripheral artery disease

In addition to specific features of peripheral artery disease (PAD) including intermittent claudication, critical limb ischemia, and acute limb ischemia, the significant increased risk of cardiovascular events in this group of patients cannot be overlooked. The ankle-brachial index (ABI) is the method of choice to screen and establish the diagnosis of PAD. Then duplex ultrasound, CT, and MR angiography or even contrast angiography and DSA are used for better evaluation of PAD diagnosis and for planing of treatment strategy with different indications. Finally, current treatment of PAD is focused mainly on cardiovascular risk modification, supervised exercise training, medical therapy, and endovascular or surgical interventions. The goals of these therapies are improving cardiovascular outcome and functional capacity in addition to preserve limb viability. Currently an endovascular-first approach is the preferred revascularization technique in most PAD patients.
Parking slot assignment games

With the proliferation of location-based services, mobile devices, and embedded wireless sensors, more and more applications are being developed to improve the efficiency of the transportation system. In particular, new applications are arising to help vehicles locate open parking spaces. Nevertheless, while engaged in driving, travelers are better suited being guided to a particular and ideal parking slot, than looking at a map and choosing which spot to go to. Then the question of how an application should choose this ideal parking spot becomes relevant. Vehicular parking can be viewed as vehicles (players) competing for parking slots (resources with different costs). Based on this competition, we present a game-theoretic framework to analyze parking situations. We introduce and analyze Parking Slot Assignment Games (Psag) in complete and incomplete information contexts. For both models we present algorithms for individual players to choose parking spaces ideally. To evaluate the more realistic incomplete information Psag, simulations were performed to test the performance of various proposed algorithms.
VE-cadherin interacts with cell polarity protein Pals1 to regulate vascular lumen formation

Blood vessel tubulogenesis requires the establishment of apicobasal polarity of endothelial cells. A novel interaction is described of the cell adhesion molecule VE-cadherin with the cell polarity protein Pals1. The activity of VE-cadherin in regulation of endothelial lumen formation depends on its interaction with both Pals1 and Par3.
Effects of a sodium chloride deicing additive on the rheological properties of asphalt mastic

This paper investigated the effects of sodium chloride deicing additive (SCDA) on the rheological properties of asphalt mastic. SCDA and mineral filler (MF) were mixed with styrene butadiene styrene modified asphalt at filler/asphalt (F/A) ratios of 0.8, 1.0 and 1.2. The viscosity of the asphalt mastic containing SCDA was greater than that containing MF at high temperatures. The corresponding mixing and compaction temperatures of the SCDA asphalt mixtures were 4°C and 4.5°C greater than those of the MF asphalt mixtures when the F/A ratio was 1.2. Furthermore, the bending beam rheometer results indicated that the SCDA mastic was more brittle at low temperatures than the MF mastic. Dynamic mechanical analysis results indicated that the SCDA asphalt mastic had the higher glass transition temperature and activation energy, which further explain that the SCDA asphalt mastic is stiffer than the MF asphalt mastic at low temperatures. The dynamic shear rheometer results indicated that the SCDA enhanced the rutting resistance of the asphalt. Finally, a shear creep test was conducted for the asphalt mastic, which showed that the SCDA improved the creep deformation resistance of the asphalt mastic.
Prototheca zopfii isolated from bovine mastitis induced oxidative stress and apoptosis in bovine mammary epithelial cells

Bovine protothecal mastitis results in considerable economic losses worldwide. However, Prototheca zopfii induced morphological alterations and oxidative stress in bovine mammary epithelial cells (bMECs) is not comprehensively studied yet. Therefore, the aim of this current study was to investigate the P. zopfii induced pathomorphological changes, oxidative stress and apoptosis in bMECs. Oxidative stress was assessed by evaluating catalase (CAT), superoxide dismutase (SOD), glutathione peroxidase (GPx), malondialdehyde (MDA) contents and lactate dehydrogenase (LDH) activity, while ROS generation and apoptosis was measured by confocal laser scanning microscopy. The results revealed that infection of P. zopfii genotype II (GTII) significantly changed bMECs morphology, increased apoptotic rate and MDA contents at 12 h (p < 0.05) and 24 h (p < 0.01) in comparison with control group, in time-dependent manner. LDH activity and ROS generation was also increased (p < 0.01) at 12 h and 24 h. However, SOD and CAT contents in bMECs infected with GTII were decreased (p < 0.05) at 12 h, while GPx (p < 0.01), SOD (p < 0.05) and CAT (p < 0.01) levels were reduced at 24 h. In case of GTI, only CAT and GPx activities were significantly decreased when the duration prolonged to 24 h but lesser than GTII. This suggested that GTII has more devastating pathogenic effects in bMECs, and the findings of this study concluded that GTII induced apoptosis and oxidative stress in bMECs via the imbalance of oxidant and antioxidant defenses as well as the production of intracellular ROS.
Case report of asthma associated with 3D printing.

Background Three-dimensional (3D) printing is being increasingly used in manufacturing and by small business entrepreneurs and home hobbyists. Exposure to airborne emissions during 3D printing raises the issue of whether there may be adverse health effects associated with these emissions. Aims We present a case of a worker who developed asthma while using 3D printers, which illustrates that respiratory problems may be associated with 3D printer emissions. Case report The patient was a 28-year-old self-employed businessman with a past history of asthma in childhood, which had resolved completely by the age of eight. He started using 10 fused deposition modelling 3D printers with acrylonitrile-butadiene-styrene filaments in a small work area of approximately 3000 cubic feet. Ten days later, he began to experience recurrent chest tightness, shortness of breath and coughing at work. After 3 months, his work environment was modified by reducing the number of printers, changing to polylactic acid filaments and using an air purifier with an high-efficiency particulate air filter and organic cartridge. His symptoms improved gradually, although he still needed periodic treatment with a salbutamol inhaler. While still symptomatic, a methacholine challenge indicated a provocation concentration causing a 20% fall in FEV1 (PC20) of 4 mg/ml, consistent with mild asthma. Eventually, his symptoms resolved completely and a second methacholine challenge after symptom resolution was normal (PC20 > 16 mg/ml). Conclusions This case indicates that workers may develop respiratory problems, including asthma when using 3D printers. Further investigation of the specific airborne emissions and health problems from 3D printing is warranted.
The ORCA Hub: Explainable Offshore Robotics through Intelligent Interfaces

We present the UK Robotics and Artificial Intelligence Hub for Offshore Robotics for Certification of Assets (ORCA Hub), a 3.5 year EPSRC funded, multi-site project. The ORCA Hub vision is to use teams of robots and autonomous intelligent systems (AIS) to work on offshore energy platforms to enable cheaper, safer and more efficient working practices. The ORCA Hub will research, integrate, validate and deploy remote AIS solutions that can operate with existing and future offshore energy assets and sensors, interacting safely in autonomous or semi-autonomous modes in complex and cluttered environments, co-operating with remote operators. The goal is that through the use of such robotic systems offshore, the need for personnel will decrease. To enable this to happen, the remote operator will need a high level of situation awareness and key to this is the transparency of what the autonomous systems are doing and why. This increased transparency will facilitate a trusting relationship, which is particularly key in high-stakes, hazardous situations.
Exposure to fermentation supernatant of Staphylococcus aureus accelerated dedifferentiation of chondrocytes and production of antimicrobial peptides

Staphylococcus aureus (S. aureus) is the most popular pathogen found in septic arthritis. Despite bacteria was eradicated from joint cavity during acute infection, destruction of articular cartilage often continues for years, leading to permanent joint damage. The mechanism responsible for this consistent catabolic reaction in septic arthritis remains unclear. Here, we found that fermentation supernatant (FS) of S. aureus accelerated dedifferentiation of chondrocytes and induced expression of catabolic factors including A Disintegrin‐like and Metalloproteinase with Thrombospondin‐1 motifs 5, NO synthase 2, matrix metalloproteinase‐3, ‐13. In response to FS of S. aureus stimulation, expression of antimicrobial peptides (AMPs) including β‐defensin‐1, ‐2, ‐3, ‐4, cathelicidin antimicrobial peptide (CAMP) in dedifferentiated chondrocytes was significantly higher than that in chondrocytes which maintained their differentiated phenotype. Among AMPs detected, expression of CAMP in dedifferentiated chondrocytes was observed to increase 170 times higher than that in differentiated ones. When exposed to FS of S. aureus, expression of interleukin (IL)‐1β, IL‐17F, and IL‐22 were remarkably increased in dedifferentiated chondrocytes. These results indicated that dedifferentiation of chondrocytes caused by exposure to S. aureus might be responsible for secondary osteoarthritis (OA) after acute S. aureus infection in joint. While, one potential benefit of dedifferentiation resulted from S. aureus exposure is that chondrocytes initiates a self‐protective responsiveness by producing more AMPs against bacterial infection. © 2017 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 36:443–451, 2018.
Bone healing in an aged murine fracture model is characterized by sustained callus inflammation and decreased cell proliferation

Geriatric fractures take longer to heal and heal with more complications than those of younger patients; however, the mechanistic basis for this difference in healing is not well understood. To improve this understanding, we investigated cell and molecular differences in fracture healing between 5‐month‐old (young adult) and 25‐month‐old (geriatric) mice healing utilizing high‐throughput analysis of gene expression. Mice underwent bilateral tibial fractures and fracture calluses were harvested at 5, 10, and 20 days post‐fracture (DPF) for analysis. Global gene expression analysis was performed using Affymetrix MoGene 1.0 ST microarrays. After normalization, data were compared using ANOVA and evaluated using Principal Component Analysis (PCA), CTen, heatmap, and Incromaps analysis. PCA and cross‐sectional heatmap analysis demonstrated that DPF followed by age had pronounced effects on changes in gene expression. Both un‐fractured and 20 DPF aged mice showed increased expression of immune‐associated genes (CXCL8, CCL8, and CCL5) and at 10 DPF, aged mice showed increased expression of matrix‐associated genes, (Matn1, Ucma, Scube1, Col9a1, and Col9a3). Cten analysis suggested an enrichment of CD8+ cells and macrophages in old mice relative to young adult mice and, conversely, a greater prevalence of mast cells in young adult mice relative to old. Finally, consistent with the PCA data, the classic bone healing pathways of BMP, Indian Hedgehog, Notch and Wnt clustered according to the time post‐fracture first and age second. Clinical Significance: Greater understanding of age‐dependent molecular changes with healing will help form a mechanistic basis for therapies to improve patient outcomes. © 2017 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 36:149–158, 2018.
Emergence of CD4+ and CD8+ Polyfunctional T Cell Responses Against Immunodominant Lytic and Latent EBV Antigens in Children With Primary EBV Infection

Long term carriers were shown to generate robust polyfunctional T cell (PFC) responses against lytic and latent antigens of Epstein-Barr virus (EBV). However, the time of emergence of PFC responses against EBV antigens, pattern of immunodominance and difference between CD4+ and CD8+ T cell responses during various stages of EBV infection are not clearly understood. A longitudinal study was performed to assess the development of antigen-specific PFC responses in children diagnosed to have primary symptomatic (infectious mononucleosis [IM]) and asymptomatic (AS) EBV infection. Evaluation of IFN-γ secreting CD8+ T cell responses upon stimulation by HLA class I-specific peptides of EBV lytic and latent proteins by ELISPOT assay followed by assessment of CD4+ and CD8+ PFC responses upon stimulation by a panel of overlapping EBV peptides for co-expression of IFN-γ, TNF-α, IL-2, perforin and CD107a by flow cytometry were performed. Cytotoxicity of T cells against autologous lymphoblastoid cell lines (LCLs) as well as EBV loads in PBMC and plasma were also determined. Both IM and AS patients had elevated PBMC and plasma viral loads which declined steadily during a 12-month period from the time of diagnosis whilst decrease in the magnitude of CD8+ T cell responses toward EBV lytic peptides in contrast to increase toward latent peptides was shown with no significant difference between those of IM and AS patients. Both lytic and latent antigen-specific CD4+ and CD8+ T cells demonstrated polyfunctionality (defined as greater or equal to three functions) concurrent with enhanced cytotoxicity against autologous LCLs and steady decrease in plasma and PBMC viral loads over time. Immunodominant peptides derived from BZLF1, BRLF1, BMLF1 and EBNA3A-C proteins induced the highest proportion of CD8+ as well as CD4+ PFC responses. Diverse functional subtypes of both CD4+ and CD8+ PFCs were shown to emerge at 6–12 months. In conclusion, EBV antigen-specific CD4+ and CD8+ PFC responses emerge during the first year of primary EBV infection, with greatest responses toward immunodominant epitopes in both lytic and latent proteins, correlating to steady decline in PBMC and plasma viral loads.
Analysis of flicker noise conversion to phase noise in CMOS differential LC oscillators

An analysis of the flicker noise conversion to close‐in phase noise in complementary metal‐oxide semiconductor (CMOS) differential inductance‐capacitance (LC)‐voltage controlled oscillator is presented. The contribution of different mechanisms responsible for flicker noise to phase noise conversion is investigated from a theoretical point of view. Impulse sensitivity function theory is exploited to quantify flicker noise to phase noise conversion process from both tail and core transistors. The impact of different parasitic capacitances inside the active core on flicker noise to phase noise conversion is investigated. Also, it is shown how different flicker noise models for core metal‐oxide semiconductor (MOS) transistors may result in different close‐in phase noise behaviors. Based on the developed analysis, design guidelines for reducing the close‐in phase noise are introduced. Copyright © 2015 John Wiley & Sons, Ltd.
Three-dimensional virtual histology enabled through cytoplasm-specific X-ray stain for microscopic and nanoscopic computed tomography

Significance Three-dimensional histology of soft-tissue samples has proven to provide crucial benefits for the understanding of tissue structure. Nevertheless, the low attenuation of soft tissue has impaired the use of computed tomography (CT) as a tool for the nondestructive and 3D visualization of external and internal structural details. We present a cytoplasm-specific staining method tailored for X-ray CT that enables a routine and efficient 3D volume screening at high resolutions. Our technique is fully compatible with conventional histology and allows further histological investigations, as demonstrated for a mouse kidney. The comparative analysis of our CT data with conventional 2D histology highlights the future applicability of the cytoplasm-specific X-ray staining method for modern histological and histopathological investigations using laboratory X-ray CT devices. Many histological methods require staining of the cytoplasm, which provides instrumental details for diagnosis. One major limitation is the production of 2D images obtained by destructive preparation of 3D tissue samples. X-ray absorption micro- and nanocomputed tomography (microCT and nanoCT) allows for a nondestructive investigation of a 3D tissue sample, and thus aids to determine regions of interest for further histological examinations. However, application of microCT and nanoCT to biological samples (e.g., biopsies) is limited by the missing contrast within soft tissue, which is important to visualize morphological details. We describe an eosin-based preparation overcoming the challenges of contrast enhancement and selectivity for certain tissues. The eosin-based staining protocol is suitable for whole-organ staining, which then enables high-resolution microCT imaging of whole organs and nanoCT imaging of smaller tissue pieces retrieved from the original sample. Our results demonstrate suitability of the eosin-based staining method for diagnostic screening of 3D tissue samples without impeding further diagnostics through histological methods.
Decrease in newly generated oligodendrocytes leads to motor dysfunctions and changed myelin structures that can be rescued by transplanted cells

NG2‐glia in the adult brain are known to proliferate and differentiate into mature and myelinating oligodendrocytes throughout lifetime. However, the role of these newly generated oligodendrocytes in the adult brain still remains little understood. Here we took advantage of the Sox10‐iCreERT2 x CAG‐eGFP x Esco2fl/fl mouse line in which we can specifically ablate proliferating NG2‐glia in adult animals. Surprisingly, we observed that the generation of new oligodendrocytes in the adult brain was severely affected, although the number of NG2‐glia remained stable due to the enhanced proliferation of non‐recombined cells. This lack of oligodendrogenesis led to the elongation of the nodes of Ranvier as well as the associated paranodes, which could be locally rescued by myelinating oligodendrocytes differentiated from transplanted NG2‐glia deriving from wildtype mice. Repetitive measurements of conduction velocity in the corpus callosum of awake animals revealed a progressive deceleration specifically in the mice lacking adult oligodendrogenesis that resulted in progressive motor deficits. In summary, here we demonstrated for the first time that axon function is not only controlled by the reliable organization of myelin, but also requires a dynamic and continuous generation of new oligodendrocytes in the adult brain. GLIA 2016;64:2201–2218