Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterization of the Biosynthesis Gene Cluster for the Pyrrole Polyether Antibiotic Calcimycin (A23187) in Streptomyces chartreusis NRRL 3882

ABSTRACT The pyrrole polyether antibiotic calcimycin (A23187) is a rare ionophore that is specific for divalent cations. It is widely used as a biochemical and pharmacological tool because of its multiple, unique biological effects. Here we report on the cloning, sequencing, and mutational analysis of the 64-kb biosynthetic gene cluster from Streptomyces chartreusis NRRL 3882. Gene replacements confirmed the identity of the gene cluster, and in silico analysis of the DNA sequence revealed 27 potential genes, including 3 genes for the biosynthesis of the α-ketopyrrole moiety, 5 genes that encode modular type I polyketide synthases for the biosynthesis of the spiroketal ring, 4 genes for the biosynthesis of 3-hydroxyanthranilic acid, an N-methyltransferase tailoring gene, a resistance gene, a type II thioesterase gene, 3 regulatory genes, 4 genes with other functions, and 5 genes of unknown function. We propose a pathway for the biosynthesis of calcimycin and assign the genes to the biosynthesis steps. Our findings set the stage for producing much desired calcimycin derivatives using genetic modification instead of chemical synthesis.
Haematocrit and the risk of developing end-stage renal disease.

BACKGROUND Anaemia is common in patients with renal failure; however, it is not known whether haematocrit level in the general population is a predictor for developing end-stage renal disease (ESRD). METHODS A retrospective analysis was conducted to assess the development of ESRD within a population of 71 802 subjects (37 190 men and 34 612 women), 20-99 years, in Okinawa, Japan. Haematocrit data were collected between April 1983 and March 1984 and the subjects were followed forward to the year 2000 whether they were identified in the Okinawa Dialysis Study registry for identification of ESRD. Multivariate logistic analyses were performed to analyse the influence of haematocrit on the development of ESRD after adjusting for age, sex, blood pressure, body mass index, proteinuria and haematuria. In a subgroup of the cohort, similar analyses were repeated adjusting for estimated creatinine clearance by the method of Cockcroft and Gault. RESULTS The mean (SD) level of haematocrit at the time of screening was 45.3% (3.3%) for men and 38.8% (3.2%) for women. During the 17-year follow-up, 269 patients (171 men and 98 women) were identified with ESRD. The mean time to onset of ESRD was 130.4 (53.6) months. The adjusted odds ratio and 95% confidence interval (CI) for the influence of haematocrit (%) on the development of ESRD was 0.991 and 0.988-0.995 (P<0.0001), suggesting that the lower haematocrit, the greater was the risk of developing ESRD. This finding was repeated in the subgroup analysis that included calculated creatinine clearance (adjusted odds ratio 0.991 and 95% CI 0.984-0.997, P=0.0057). In women, the adjusted odds ratio for haematocrits of 20.0-34.9% was 3.086 (CI 1.770-5.376, P<0.0001) when compared with the reference haematocrits of 35.0-39.9%. In men, the adjusted odds ratio for haematocrits of 25.0-39.9% was 1.927 (CI 1.418-2.625, P<0.0001) when compared with the reference haematocrits of 45.0-49.9%. CONCLUSIONS Subjects with low haematocrits, <40% for men and <35% for women, have a significantly increased risk of ESRD.
T Cell Intrinsic NOD2 Is Dispensable for CD8 T Cell Immunity

NOD2 is an intracellular pattern recognition receptor that provides innate sensing of bacterial muramyl dipeptide by host cells, such as dendritic cells, macrophages and epithelial cells. While NOD2's role as an innate pathogen sensor is well established, NOD2 is also expressed at low levels in T cells and there are conflicting data as to whether NOD2 plays an intrinsic role in T cell function. Here we show that following adoptive transfer into WT hosts, NOD2−/− OT-I T cells show a small decrease in the number of OVA-specific CD8 T cells recovered at the peak of the response to respiratory influenza virus infection. On the other hand, no such defect was observed upon intranasal immunization with a replication defective adenovirus carrying the OVA epitope recognized by OT-I, or when OVA was delivered with LPS subcutaneously, or when influenza-OVA was delivered intraperitoneally. Thus we observed a selective defect in NOD2-deficient T cell responses only during a live viral infection. Moreover, there was no apparent defect when NOD2−/− OT-I T cells were stimulated in vitro. Finally, this selective defect in recovery of NOD2-deficient CD8 T cells was not observed in a non-transgenic respiratory infection model in which mixed bone marrow chimeras were used such that the NOD2−/− T cells were allowed to develop and respond in a NOD2-sufficient host. Taken together our data indicate that T cell intrinsic NOD2 is not required for CD8 T cell responses to antigen delivered under a variety of conditions in vitro and in vivo. However, CD8 T cells that have developed in the absence of NOD2 show a selective and modest impairment in their response to live respiratory influenza infection.
Transformation-based tree-to-tree alignment

Previous experiments suggest that a rule-based approach to tree alignment error correction serves to be an eective complement to statistical alignment. We show how, using relatively few features, an implementation of Brill’s Transformation-Based Learning algorithm improves the results of a high precision model of the statistical aligner Lingua-Align. Using our system to correct already tree aligned data, we achieve balanced F-scores of 80.6 on our test set and 85.2 on our development test set. Using it as a tree aligner on word aligned data, our best F-scores using the same model amount to 78.7 and 83.0 respectively. Finally, we apply a pipeline of alignment and error correction tools to create several versions of a large parallel treebank consisting of various domains for Dutch to English for use in a syntax-based MT system. We conclude that transformation-based learning is a promising approach for the large-scale creation of parallel treebanks for various NLP purposes.
Peri-atrial epicardial adipose tissue is associated with new-onset nonvalvular atrial fibrillation.

BACKGROUND Atrial fibrillation (AF) is associated with considerable morbidity and mortality in patients with coronary artery disease (CAD). Epicardial adipose tissue (EAT) is recognized as an important inflammatory tissue that may exert deleterious effects on the adjacent left atrial (LA) wall. Multidetector computed tomography (MDCT) can accurately assess EAT's volume and distribution. This study used MDCT to investigate the effect of peri-atrial EAT on new-onset nonvalvular AF. METHODS AND RESULTS The study group consisted of 279 patients (176 men; age, 65±10 years) with no history of AF who underwent MDCT examination for evaluation of CAD. EAT was automatically identified on the basis of threshold attenuation values of -30 to -250 Hounsfield units. EAT volume was calculated as the sum of EAT area and subsequently divided into peri-atrial and peri-ventricular EAT. During follow-up of 3.3±1.0 years, AF occurred in 17 (6.1%) patients. Cox proportional hazards regression analysis indicated that male sex, and the LA and peri-atrial EAT volumes (P=0.03, P<0.001, and P<0.001, respectively) were independent predictors for future AF. The sensitivity and specificity for the prediction of AF using a peri-atrial EAT volume index of ≥27 ml/m(2) were 88% and 92%, respectively. CONCLUSIONS This is the first study demonstrating that peri-atrial EAT volume estimated by MDCT excellently predicted the development of new-onset AF in patients with CAD, independent of LA enlargement.
Systematic review and meta-analysis of behavioral interventions to improve child pedestrian safety.

OBJECTIVE Pedestrian injuries represent a pediatric public health challenge. This systematic review/meta-analysis evaluated behavioral interventions to teach children pedestrian safety. METHODS Multiple strategies derived eligible manuscripts (published before April 1, 2013, randomized design, evaluated behavioral child pedestrian safety interventions). Screening 1,951 abstracts yielded 125 full-text retrievals. 25 were retained for data extraction, and 6 were later omitted due to insufficient data. In all, 19 articles reporting 25 studies were included. Risk of bias and quality of evidence were assessed. RESULTS Behavioral interventions generally improve children's pedestrian safety, both immediately after training and at follow-up several months later. Quality of the evidence was low to moderate. Available evidence suggested interventions targeting dash-out prevention, crossing at parked cars, and selecting safe routes across intersections were effective. Individualized/small-group training for children was the most effective training strategy based on available evidence. CONCLUSIONS Behaviorally based interventions improve children's pedestrian safety. Efforts should continue to develop creative, cost-efficient, and effective interventions.
A novel compound neural network for fault sources recognition

Independent component analysis (ICA) is a powerful tool for redundancy reduction and nongaussian data analysis. And, artificial neural network (ANN), especially the self-organizing map (SOM) based on unsupervised learning is a kind of excellent method for pattern clustering and recognition. By combining ICA with ANN, a novel compound neural network for fault sources recognition was proposed. First, neural ICA algorithm was applied to fusion of multi-channel measurements by sensors. Moreover, further feature extraction was made. Thus, statistical features higher than second order were captured from the measurements. Second, a typical neural classifier such as the back-propagation (BP), the radial basis function (RBF) or the SOM network was trained for the final fault sources recognition. The results from contrast experiments in fault diagnosis of rotating machines show that the proposed compound neural network with ICA based feature extraction can recognize various fault sources at considerable accuracy, and be constructed in simpler way, both of which imply its great potential in fault diagnosis.
Aloe Vera used as Inhibitor for Corrosion Protection of Beverage Containing Stainless steel

Beverage companies are used stainless steel in their manufacturing operations. Generally beverage companies make wine, beer and various types of soft drink. Their transportation and storage can be done in stainless steel containers. Beverage industries use different types of raw materials for the productions wine, beer and soft drink. They are acidic nature and their pH occur between5.5 to 6.5. Some preservatives are also added into these drinks for prevention of microorganism. These preservatives have acidic character. Wine, beer, soft drink and preservatives develop corrosion cell on the surface stainless steel thus corrosion reaction starts and harmful metal ions go into solution in this way these drinks contaminated. The contaminated drinks create several diseases. Corrosive effects are of remarkable consequence in beverage processing industry as wine, beer and soft drink contain corrosive substances, thereby causing significant impact on the degradation of constructional materials and the maintenance or replacement of products lost or contaminated as a result of corrosion reactions. For this work aloevera was taken as inhibitor. Aloevera was found to inhibit the corrosion of stainless steel in beverage. Its inhibition activities studied at different concentrations, temperatures and different intervals of times. The inhibition efficiencies and surface coverage area of aloevera increased as the concentration and temperature of aloevera increased. Inhibitive and adsorption properties of aloevera for the corrosion of stainless steel were investigated using weight loss and potentiostic methods. Test coupons dipped into drinks and the corrosion rate was determined by weight loss method. The corrosion current density absence and presence of inhibitor was studied by Potentiostic polarization technique.
Establishment and characterization of continuous cell line MTC-SK derived from a human medullary thyroid carcinoma.

Tumor cells of a human medullary thyroid carcinoma were isolated and propagated in tissue culture. Several cell lines with different morphology developed from the primary culture, among others a fibroblast-like growing cell line (MTC-F) and a cell line growing as a suspension of single cells and spherical cell clusters (MTC-SK). The MTC-SK cell line was serially propagated for 90 passages, over 3 years. When examined at different times throughout the in vitro period, MTC-SK exhibited properties characteristic of medullary thyroid carcinomas: the cells maintained their epithelioid morphology; endocrine granules were demonstrated in the cytoplasm by electron microscopy; in situ hybridization confirmed the production of calcitonin- and bombesin-mRNA (gastrin releasing peptide); the cells revealed positive immunoreactivity with antibodies to calcitonin, calcitonin gene-related peptide, and bombesin. The in vitro properties of the MTC-SK cells corresponded to the results obtained from the tissue of origin. Cytogenetic studies of the MTC-F cell line revealed a supernumerary metacentric chromosome (20? ). In the MTC-SK cell line the predominant findings were terminal chromosomal rearrangements most frequently concerning chromosome 11p, i.e., the locus of the calcitonin and calcitonin gene-related peptide genes and the H-ras oncogene, and a characteristic instability of the centromeric region of chromosome 16 and somatic pairing of the homologous chromosomes 16.
Impact of egg disinfection of hatching eggs on the eggshell microbiome and bacterial load

ABSTRACT Disinfection of hatching eggs is essential to ensure high quality production of broilers. Different protocols are followed in different hatcheries; however, only limited scientific evidence on how the disinfection procedures impact the microbiome is available. The aim of the present study was to characterize the microbiome and aerobic bacterial load of hatching eggs before disinfection and during the subsequent disinfection steps. The study included a group of visibly clean and a group of visibly dirty eggs. For dirty eggs, an initial wash in chlorine was performed, hereafter all eggs were submitted to two times fumigation and finally spray disinfection. The eggshell microbiome was characterized by sequencing of the total amount of 16S rRNA extracted from each sample, consisting of shell surface swabs of five eggs from the same group. In addition, the number of colony forming units (cfu) under aerobic conditions was established for each disinfection step. The disinfection procedure reduced the bacterial load from more than 104 cfu (initially visibly clean eggs) and 105 cfu (initially visibly dirty eggs) to less than 10 cfu per sample after disinfection for both groups of eggs. The microbiome of both initially visibly clean and initially visibly dirty eggs had the highest abundances of the phyla Firmicutes, Proteobacteria and Bacteroidetes. Within the phyla Firmicutes the relative abundances of Clostridiales decreased while Lactobacillus increased from before to after final disinfection. In conclusion, the investigated disinfection procedure is effective in reducing the bacterial load, and by adding a chlorine wash for initially visibly dirty eggs, the microbiome of initially visibly clean and initially visibly dirty eggs had a highly similar microflora after the final disinfection step.
Ab initio computational study of quantum plasmons in graphene nanoflakes

We investigate the potential merit in using nanometer-sized graphene flakes as building blocks of two-dimensional (2D) quantum metamaterials. The choice of the building blocks is crucial to the design of quantum metamaterials with desired properties, graphene nano-structures being promising candidates towards this end. Thus, they can be grown either by bottom-up chemical synthesis or top-down electron-beam patterning in various shapes, densities, topology, and size, down to the molecular scale. We show that this versatility provides a wide range of parameters to tune the optical properties of graphene-based 2D quantum metamaterials.
State of Big Data Analysis in the Cloud

Big Data is data that either is too large, grows too fast, or does not fit into traditional architectures. Within such data can be valuable information that can be discovered through data analysis. With the emergence of cloud computing services, big data processing has become a less costly task. In this paper, we examine the current trends and characteristics of Big Data, its analysis and how these are presenting challenges in data collection, storage and management in cloud computing.
Building reputation and trust using federated search and opinion mining

The term online reputation addresses trust relationships amongst agents in dynamic open systems. These can appear as ratings, recommendations, referrals and feedback. Several reputation models and rating aggregation algorithms have been proposed. However, finding a trusted entity on the web is still an issue as all reputation systems work individually. The aim of this project is to introduce a global reputation system that aggregates people's opinions from different resources (e.g. e-commerce websites, and review) with the help federated search techniques. A sentiment analysis approach is subsequently used to extract high quality opinions and inform how to increase trust in the search result.
Mesh objective damage modeling of ductile fracture at visco-plastic continuum response

Local-continuum damage models, such as the JC-dynamic failure criterion are often combined with the constitutive JC-model to represent the material behavior during machining. The major drawback is that the failure criterion exhibit a pathological mesh dependence. In literature it has been argued that a viscous regularization of the continuum material model coupled to damage via visco-plasticity may remove the mesh dependence. We present results, based on the objective enhanced element removal model derived from previous contribution, form a mesh dependence study using a extended formulation of the constitutive JC-model covering visco-plasticity. The results show that, excluding the mesh objective enhancement the pathological mesh dependence still exist if the visco-plastic formulation is used. If the mesh objective enhancement is used a relatively good convergence is obtained for a set of mesh sizes for the damage model.
The Role of Heat Shock Protein 70 in Mediating Age-Dependent Mortality in Sepsis

Sepsis is primarily a disease of the aged, with increased incidence and mortality occurring in aged hosts. Heat shock protein (HSP) 70 plays an important role in both healthy aging and the stress response to injury. The purpose of this study was to determine the role of HSP70 in mediating mortality and the host inflammatory response in aged septic hosts. Sepsis was induced in both young (6- to 12-wk-old) and aged (16- to 17-mo-old) HSP70−/− and wild-type (WT) mice to determine whether HSP70 modulated outcome in an age-dependent fashion. Young HSP70−/− and WT mice subjected to cecal ligation and puncture, Pseudomonas aeruginosa pneumonia, or Streptococcus pneumoniae pneumonia had no differences in mortality, suggesting HSP70 does not mediate survival in young septic hosts. In contrast, mortality was higher in aged HSP70−/− mice than aged WT mice subjected to cecal ligation and puncture (p = 0.01), suggesting HSP70 mediates mortality in sepsis in an age-dependent fashion. Compared with WT mice, aged septic HSP70−/− mice had increased gut epithelial apoptosis and pulmonary inflammation. In addition, HSP70−/− mice had increased systemic levels of TNF-α, IL-6, IL-10, and IL-1β compared with WT mice. These data demonstrate that HSP70 is a key determinant of mortality in aged, but not young hosts in sepsis. HSP70 may play a protective role in an age-dependent response to sepsis by preventing excessive gut apoptosis and both pulmonary and systemic inflammation.
QGRP: A Novel QoS-Geographic Routing Protocol for Multimedia Wireless Sensor Networks

Thanks to the potential they hold and the variety of their application domains, Multimedia Wireless Sensor Networks (MWSN) are forecast to become highly integrated into our daily activities. Due to the carried content nature, mainly composed of images and/or video streams with high throughput and delay constraints, Quality of Service in the context of MWSN is a crucial issue. In this paper, we propose a QoS and energy aware geographic routing protocol for MWSN: QGRP. The proposed protocol addresses bandwidth, delay and energy constraints associated with MWSN. QGRP adopts an analytical model of IEEE 802.11 Distributed Coordination Function (DCF) to estimate available bandwidth and generates loop-free routing paths.
SIMULATION OF MPC BASED SPEED CONTROL OF PERMANENT MAGNET SYNCHRONOUS MOTOR DRIVE

This paper describes the implementation of an optimal control strategy used for speed control of Permanent Magnet Synchronous Motor (PMSM) drive. Since several decades Power Electronics and Drives deals with cascaded control, which provides easy implementation and robust in operation. A serious drawback of requiring fast operating inner loop looks forward a strong candidate to eliminate the drawback. The Model Predictive Controller cost function enables a simple, flexible and improved performance controller for the drive. The basic concepts, operating principles, control diagrams, and results are used to provide a comparison between the different control strategies. Several key aspects related to this methodology are, in depth, presented and compared with conventional control technique. The performance of the motor drive with the proposed controller results is found to be prominent.
SME financing in the EU: Moving beyond one-size-fits-all

The proposal for a European Capital Markets Union (CMU) carries large potential economic benefits from enhancing the financing possibilities for Small and Medium-Sized Enterprises (SMEs). By deepening the capital markets and strengthening crossborder integration, the European Commission hopes to stimulate economic growth and boost employment. In this paper, we discuss to what extent these goals can be achieved, in light of the complex business environment of European SMEs. We outline the different types of SMEs in terms of their financing structures as well as the pervasive differences across the EU, concluding that any policy approach must take into account the diversity of the companies’ financing needs and the market realities in the Member States. We argue that the CMU is likely to have a heterogeneous impact, with some types of SMEs and certain regions gaining more than others.
Characterization of Corneal Biomechanics using Customized Atomic Force Microscopy Techniques

of a dissertation at the University of Miami. Dissertation supervised by Professor Noel Marysa Ziebarth. No. of pages in text. (183) Corneal biomechanics has become an increasingly important field within ophthalmology. Striving to establish a relationship between corneal physiological structure and function, corneal biomechanics is an objective, quantitative measure that aids in the development and improvement of diagnostic and therapeutic methods for corneal-related diseases. The goal of this project was to advance the technology of Atomic Force Microscopy (AFM) as a suitable characterization technique within the field of corneal biomechanics. The studies of this project include the development of AFM instrumentation, experimental techniques, and models to measure the elastic, viscoelastic, and poroelastic properties of the cornea in situ. Such developed instrumentation, techniques, and models were then implemented to quantify the treatment efficacy of corneal crosslinking for keratoconus, the most prevalent corneal dystrophy in the United States. In addition, age implications of the treatment efficacy of corneal crosslinking were determined using corneal biomechanics measured from the developed AFM technology.