Miracle-dz/UniFAR-FTUs huggingface dataset:
A multidisciplinary approach to dissect the molecular basis of the Neotyphodium lolii/ryegrass symbiosis

Neotyphodium lolii is a fungal endophyte that lives entirely within the intercellular spaces of its grass host, perennial ryegrass (Lolium perenne L.). Infection is symptomless and the endophyte relies on the host plant for dissemination via the seed. The association is mutually beneficial since the endophyte confers a number of biotic and abiotic advantages to the host. This paper will present an overview of the multidisciplinary approach we are using at AgResearch to dissect the molecular basis of this symbiosis. Topics covered will include how we intend to link the knowledge gained from basic biology and cytology with the fields of Genomics, Transcriptomics, Proteomics and Metabolomics. To achieve this we are using isogenic ryegrass lines infected or uninfected with endophyte in combination with a suite of molecular biology tools, including Expressed Sequence Tags (ESTs), Microarray analysis, 2D-gel electrophoresis (to identify novel proteins associated with symbiosis), and metabolic profiling. To aid our proteomics approach, we have also generated both fungal genomic and fungal EST resources. By linking these approaches we hope to identify genes which are important in both the establishment and maintenance of symbiosis. In addition, by combining transcriptomic with metabolomic approaches, we intend to elucidate how endophyte infection influences host secondary metabolism. We hypothesise the latter is correlated with many of the endophyte-conferred enhancements to its host.
Complexity of Model Checking over General Linear Time

Temporal logics over general linear time allow us to capture continuous properties in applications such as distributed systems, natural language, message passing and A.I. modelling of human reasoning. Linear time structures, however, can exhibit a wide range of behaviours that are hard to reason with, or even describe finitely. Recently, a formal language of Model Expressions has been proposed to allow the convenient finite description of an adequately representative range of these generally infinite structures. Given a model described in this Model Expression language and a temporal logic formula, a model checking algorithm decides whether the formula is satisfied at some time in the model. Tools based on such algorithms would support a wide variety of tasks such as verification and counter-example investigation. A previous paper gave an exponential space algorithm for the problem of model checking Until/Since temporal formulas over linear time Model Expressions. Here we prove that the problem is actually PSPACE-complete. We present a new PSPACE algorithm and we show PSPACE-hardness by a reduction from quantified Boolean formulas.
Carbon exchange between a shelf sea and the ocean: The Hebrides Shelf, west of Scotland

Global mass balance calculations indicate the majority of particulate organic carbon (POC) exported from shelf seas is transferred via downslope exchange processes. Here we demonstrate the downslope flux of POC from the Hebrides Shelf is approximately 3-to-5-fold larger per unit length/area than the global mean. To reach this conclusion we quantified the offshore transport of particulate and dissolved carbon fractions via the “Ekman Drain”, a strong downwelling feature of the NW European Shelf circulation, and subsequently compared these fluxes to simultaneous regional air-sea CO2 fluxes and on-shore wind-driven Ekman fluxes to constrain the carbon dynamics of this shelf. Along the shelf break we estimate a mean offshelf total carbon (dissolved? +? particulate) flux of 4.2 tonnes C m? 1 d? 1 compared to an onshelf flux of 4.5 tonnes C m? 1 d? 1. Organic carbon represented 3.3% of the onshelf carbon flux but 6.4% of the offshelf flux indicating net organic carbon export. Dissolved organic carbon represented 95% and POC 5% of the exported organic carbon pool. When scaled along the shelf break the total offshelf POC flux (0.007 Tg C d? 1) was found to be three times larger than the regional air-sea CO2 ingassing flux (0.0021 Tg C d? 1), an order of magnitude larger than the particulate inorganic carbon flux (0.0003 Tg C d? 1) but far smaller than the DIC (2.03 Tg C d? 1) or DOC (0.13 Tg C d? 1) fluxes. Significant spatial heterogeneity in the Ekman drain transport confirms that offshelf carbon fluxes via this mechanism are also spatially heterogeneous. This article is protected by copyright. All rights reserved.
The focusing positions of polypeptides in immobilized pH gradients can be predicted from their amino acid sequences

The focusing positions in narrow range immobilized pH gradients of 29 polypeptides of known amino acid sequence were determined under denaturing conditions. The isoelectric points of the proteins calculated from their amino acid sequences matched with good accuracy the experimentally determined pI values. We show the advantages of being able to predict the position of a protein of known structure within a two‐dimensional gel.
Inhibition of Proteasomal Function by Curcumin Induces Apoptosis through Mitochondrial Pathway*

Curcumin is a natural polyphenolic compound having an antiproliferative property, which recent evidence suggests is due to its ability to induce apoptosis. However, the molecular mechanisms through which curcumin induces apoptosis are not fully understood. Here, we report that the curcumin-induced apoptosis is mediated through the impairment of the ubiquitin-proteasome system. Exposure of curcumin to the mouse neuro 2a cells causes a dose-dependent decrease in proteasome activity and an increase in ubiquitinated proteins. Curcumin exposure also decreases the turnover of the destabilized enhanced green fluorescence protein, a model substrate for proteasome and cellular p53 protein. Like other proteasome inhibitors, curcumin targets proliferative cells more efficiently than differentiated cells and induces apoptosis via mitochondrial pathways. Addition of curcumin to neuro 2a cells induces a rapid decrease in mitochondrial membrane potential and the release of cytochrome c into cytosol, followed by activation of caspase-9 and caspase-3.
Cell division number regulates IgG1 and IgE switching of B cells following stimulation by CD40 ligand and IL‐4

CD40 ligand (CD40L) and IL‐4 are sufficient to induce resting murine B cells to divide and switch isotypes from IgM and IgD to IgG1 and IgE. Tracking of cell division following (5‐and 6) carboxyfluorescein diacetate succinimidyl ester (CFSE) labeling revealed that B cells expressed IgG1 after three cell divisions, and IgE after five. The probability of isotype switching at each division was independent of both time after stimulation and of the dose of CD40L. IL‐4 concentration regulated the number of divisions that preceded isotype switching. Loss of surface IgM and IgD was also related to cell division and appeared to be differentially regulated. B cell proliferation was typically asynchronous with the proportion of cells in consecutive divisions being markedly affected by the concentration of CD40L and IL‐4. Simultaneous (5‐bromo)‐2 ′ ‐deoxyuridine labeling and CFSE staining revealed that B cells in each division cycle were dividing at the same rate. Therefore, division cycle asynchrony resulted from dose‐dependent variation in the time taken to enter the first division cycle. These results suggest that T‐dependent B cell expansion is linked to predictable functional changes that may, in part, explain why IgE is produced in response to prolonged antigenic stimulation.
Common Metrics for Analyzing, Developing and Managing Telecommunication Networks

The metrics play increasingly fundamental role in the design, development, deployment and operation of telecommunication systems. Despite their importance, the studies of metrics are usually limited to a narrow area or a well-defined objective. Our study aims to more broadly survey the metrics that are commonly used for analyzing, developing and managing telecommunication networks in order to facilitate understanding of the current metrics landscape. The metrics are simple abstractions of systems, and they directly influence how the systems are perceived by different stakeholders. However, defining and using metrics for telecommunication systems with ever increasing complexity is a complicated matter which has not been so far systematically and comprehensively considered in the literature. The common metrics sources are identified, and how the metrics are used and selected is discussed. The most commonly used metrics for telecommunication systems are categorized and presented as energy and power metrics, quality-of-service metrics, quality-of-experience metrics, security metrics, and reliability and resilience metrics. Finally, the research directions and recommendations how the metrics can evolve, and be defined and used more effectively are outlined.
Benchmarking RGB-D Segmentation: Toy Dataset of Complex Crowded Scenes

In this paper we present a new RGB-D dataset a captured with the Kinect sensor. The dataset is composed of typical children’s toys and contains a total of 449 RGB-D images alongside with their annotated ground truth images. Compared to existing RBG-D object segmentation datasets, the objects in our proposed dataset have more complex shapes and less texture. The images are also crowded and thus highly occluded. Three state-of-the-art segmentation methods are benchmarked using the dataset. These methods attack the problem of object segmentation from different starting points, providing a comprehensive view on the properties of the proposed dataset as well as the state-of-the-art performance. The results are mostly satisfactory but there remains plenty of room for improvement. This novel dataset thus poses the next challenge in the area of RGB-D object segmentation. aAvailable at http://robosvn.org. aalto.fi/software-and-data
Screening for tuberculosis and hepatitis B prior to the initiation of anti‐tumor necrosis therapy

Background: Since the introduction of infliximab, anti‐tumor necrosis factor alpha (anti‐TNF‐&agr;) agents have been used with increasing frequency for the treatment of inflammatory bowel disease (IBD). Reactivation of latent Mycobacterium tuberculosis (TB) soon became recognized as a complication of therapy. More recently, reactivation of hepatitis B while on anti‐TNF therapy has been documented. The aim of this study was to assess the adherence to screening for latent TB and hepatitis B by gastroenterologists prior to initiation of an anti‐TNF. Methods: This is a retrospective analysis of all patients with IBD treated with an anti‐TNF at a large urban academic hospital. In our population, 65% of patients were screened for latent TB prior to the initiation of anti‐TNF therapy, while 25% of patients were screened for hepatitis B. Results: Failure to screen for latent TB was strongly correlated with prior exposure to an anti‐TNF (odds ratio [OR]: 5.3; P < 0.0001) and initiation of treatment prior to 2006 (OR: 5.8; P < 0.0001). Failure to screen for hepatitis B was associated with lack of an abnormal alanine aminotransferase (OR: 2.6; P = 0.005) and treatment prior to 2010 (OR: 3.3; P = 0.02). Providers who had been in practice longer were less likely screen for TB or hepatitis B. Conclusions: The rate of screening for both latent TB and hepatitis B in this study was inadequate. While the rate of screening is increasing, further systems improvements and physician education is needed. (Inflamm Bowel Dis 2012;)
The Effect of Safranin on Glutathione Reductase and Glucose 6-Phosphate Dehydrogenase Enzymes

Bu çalışmanın amacı safraninin insan eritrosit glutayon redüktaz (GR) ve glukoz 6-fosfat dehidrogenaz (G6PD) üzerindeki inhibitör etkilerini değerlendirmektir. Bu amaçla, 2’,5’-ADP Sepharose 4B afinite jeli ve Sephadex G-200 jel filtrasyon kromatografisi kullanılarak insan eritrosit glutayon redüktaz 2175-kat (%31.35 verim) ve 2’,5’-ADP Sepharose 4B afinite jeli kullanılarak eritrosit glukoz 6-fosfat dehidrogenaz 8681.3-kat (%24.77 verim) ile saflaştırıldı.
Residents' support in major local events: Leeds Pride

This article examines the extent to which community participation and perceived impacts have an influence on residents' support of major events, more specifically, the Leeds Pride celebration. The research examines the perspectives of 400 Leeds permanent residents. The study tests a structural equation model, which has its theoretical basis in social exchange theory. It examines the constructs of community participation, perceived positive and negative impacts, and community support, including the actual participation of locals in the event. The findings reveal that the actual participation of locals to decision making influences their perspectives on community participation. The support is influenced by views of the perceived impacts, whereas community participation has no direct influence. Conversely, the community involvement in decision making considerably influences the perceived benefits and costs of the event, acting as a moderator, whereas the willingness of support is connected with the community's participation. Finally, the article discusses theoretical and managerial aspects for major event planning and development.
Electron Linear Accelerator for the Pion Therapy

The electron linear accelerator has been designed for the pion therapy. The accelerating structures are of Disk and Washer (DAW) type and cooled by the help of heat pipes. The energy and beam current of the accelerator, are 500 MeV and 400 ¿A, respectively, with a conventional RF system. The length of the linac is about 50 m, which is shorter than those hitherto designed for a similar purpose. Production of the pions and inevitable background radiations, mainly, neutrons and electrons, at the target are optimized. A new cooling technique of the target is suggested. Collection of the pions emitted over about 1 str. is performed by using the superconducting coils of the SMPG and axisymmetric types. About 35 rad. 1/min. is expected at the position of a patient.
Alpha-carboxy nucleoside phosphonates as universal nucleoside triphosphate mimics

Significance The polymerization of nucleotides by DNA polymerases occurs through a common mechanism based on similar highly conserved amino acid motifs and the universal role of the coordination of Mg2+ by three dNTP phosphate oxygens. Based on these universal principles, we aimed at designing a dNTP mimic that could interact with a broad variety of DNA polymerases and should consist of three major indispensable entities: a nucleobase for Watson–Crick base-pairing, an enzymatically and chemically stable triphosphate replacement that can efficiently coordinate the Mg2+ cation, and a variable linker moiety between the nucleobase and the modified phosphate. The resulting α-carboxy nucleoside phosphonates (α-CNPs) were structurally, kinetically, and biochemically investigated, and the novel dNTP mimics were successfully validated in several DNA polymerase models. Polymerases have a structurally highly conserved negatively charged amino acid motif that is strictly required for Mg2+ cation-dependent catalytic incorporation of (d)NTP nucleotides into nucleic acids. Based on these characteristics, a nucleoside monophosphonate scaffold, α-carboxy nucleoside phosphonate (α-CNP), was designed that is recognized by a variety of polymerases. Kinetic, biochemical, and crystallographic studies with HIV-1 reverse transcriptase revealed that α-CNPs mimic the dNTP binding through a carboxylate oxygen, two phosphonate oxygens, and base-pairing with the template. In particular, the carboxyl oxygen of the α-CNP acts as the potential equivalent of the α-phosphate oxygen of dNTPs and two oxygens of the phosphonate group of the α-CNP chelate Mg2+, mimicking the chelation by the β- and γ-phosphate oxygens of dNTPs. α-CNPs (i) do not require metabolic activation (phosphorylation), (ii) bind directly to the substrate-binding site, (iii) chelate one of the two active site Mg2+ ions, and (iv) reversibly inhibit the polymerase catalytic activity without being incorporated into nucleic acids. In addition, α-CNPs were also found to selectively interact with regulatory (i.e., allosteric) Mg2+-dNTP-binding sites of nucleos(t)ide-metabolizing enzymes susceptible to metabolic regulation. α-CNPs represent an entirely novel and broad technological platform for the development of specific substrate active- or regulatory-site inhibitors with therapeutic potential.
A Liver Vessel Skeleton Line Reconstruction Method Based on Linear Interpolation

The liver is one of the largest internal organs in the human body and has the most complicated vascular system. However, it is difficult to obtain very high-quality images in clinical. Meanwhile, a good understanding and observation of skeleton lines of the liver vessel system is one of the key factors to the judgment and planning of surgeries. To recover the diameter information lost both in the CT imaging and in the following segmentation and thinning stages, in this paper the linear interpolation method was first discussed as an attempt, then some improvements and approaches for a better interpolation were introduced. The result showed that our reconstruction method was practical and had good performance.
Introduction Ranjan Bandyopadhyay Th e perennial Western tourism representations of India that refuse to die

Western media represents Th ird World destinations and communities as stagnant and primitive. Scholars have argued that these representations are fundamentally related to the practices of colonization. Except for a few valuable exceptions research on tourism representations of the Th ird World is scarce. In tourism research, previous investigations have been mainly limited to analyses of visual images and texts of tourist brochures, newspaper articles, postcards and travel magazines. However, researchers have paid little attention to conduct a historical study of Western tourism representations of the Th ird World taking a larger sample of data. Th us, this study explored if there is any diff erence between the way India and Indians are represented in the nineteenth century Western travel writing, and contemporary Western travel writing. Th e results revealed that much like in the nineteenth century, contemporary Western travel writing also emphasizes the romantic image of India and Indians – timeless, poverty-stricken, exotic women and eff eminate men. Th erefore, it can be argued that colonialism is still pervasive in contemporary Western tourism representations.
User eXperience Management from Early Stages of Computer Game Development

The video game industry is becoming increasingly important due to its revenues and growing capabilities. User eXperience (UX) is an important factor which contributes to the acceptance of a video game. The UX is usually assessed at the end of the development process, and for this reason it is difficult to ensure an adequate level of interactive experience between computer game and players. Cancelation of projects or even bankruptcy of a company can be caused by bad management of UX. In this paper, we propose the game experience management (GEM), a method to evaluate, manage, measure and track the UX from early stages of computer game development. In order to compare the proposal against a method comprised by conventional approaches, teams of master degree students were formed for developing six tower defense games for teaching basic multiplication operations; surveys were conducted to compare the UX of games. In this setting, we find that games developed with GEM significantly improve UX by increasing the puppetry and consequently reducing player frustration.
Localization of Blood Coagulation Factors In Situ in Pancreatic Carcinoma

Summary Blood coagulation is activated commonly in pancreatic carcinoma but the role of the tumor cell in this activation is undefined. Immunohistochemical procedures were applied to fixed sections of 22 cases of resected adenocarcinoma of the pancreas to determine the presence of components of coagulation and fibrinolysis pathways in situ. Tumor cell bodies stained for tissue factor; prothrombin; and factors VII, VIIIc, IX, X, XII, and subunit “a” of factor XIII. Fibrinogen existed throughout the tumor stroma, and tumor cells were surrounded by fibrin. Staining for tissue factor pathway inhibitor, and plasminogen activators was minimal and inconsistent. Plasminogen activator inhibitors -1, -2, and -3 were present in the tumor stroma, and on tumor cells and vascular endothelium. Extravascular coagulation activation exists associated with pancreatic carcinoma cells in situ that is apparently unopposed by naturally occurring inhibitors or the plasminogen activator-plasmin system. We postulate that such local coagulation activation may regulate growth of this malignancy. These findings provide a rationale for testing agents that modulate the blood coagulation/fibrinolytic system (that inhibit tumor growth in other settings) in pancreatic carcinoma.
Development and validation of a novel technique for murine first-pass radionuclide angiography with a fast multiwire camera and tantalum 178

BackgroundThe use of genetically altered mice as a model system to study cardiovascular disease has created a need for accurate and quantitative assessment of murine ventricular function. To address this very challenging problem, we have developed a technique of murine firstpass radionuclide angiography using pinhole imaging and the short-lived isotope tantalum 178 (Ta-178) with a high-speed multiwire proportional camera (MPC). Methods and ResultsAn MPC was fitted with a pinhole lens of 2-mm-diameter aperture positioned 15 cm from the camera face. The short-lived isotope Ta-178 (half-life 9.3 minutes) was generated from the tungsten 178 (W-178) (half-life 21.7 days)/Ta-178 generator and concentrated on site to an injection volume of 15 to 20 µL. Mice were imaged in the supine position with the chest wall 3 mm from the camera pinhole aperture, and images were acquired at 160 frames per second after a rapid bolus injection of Ta-178. In the absence of a true gold standard, the technology was validated with measurements in control mice and mice with surgically ligated left anterior descending arteries (LADs). In addition, the effects of pharmacologic intervention with verapamil and with dobutamine were observed. Finally, peak aortic velocity measurements obtained with this technology were compared with those obtained with echocardiographic Doppler ultrasonography, the only available quantitative comparator. There was a significant decrease in the mean left ventricular ejection fraction (LVEF) between normal mice (62% ± 4.6% [mean ± SEM], n = 12) and mice with experimentally induced myocardial infarction produced by surgical LAD ligation (22% ± 2.0%, n = 41; P <.01). The LVEF decreased from 51% ± 5.8% to 37% ± 3.5% in a group of normal mice receiving verapamil (P <.05, n = 8) and increased from 34% ± 2.2% to 43% ± 2.3% in a group of LAD-ligated mice receiving dobutamine (P <.01, n = 48). Peak camera sensitivity during first pass was 25,000 cps/mCi injected. Intraobserver and interobserver variability of LVEF was studied, yielding r = 0.9639 and 0.9529 and SE of the estimate 2.6% and 3.1%, respectively. Reproducibility in serial studies was excellent (r = 0.92, SE of the estimate 5.18). ConclusionsThis study demonstrates the development and use of a promising new method that uses the short-lived radioisotope Ta-178 and MPC for noninvasive quantification of murine ventricular function, that produces accurate and highly reproducible results, and that can be applied in multiple serial studies.