Miracle-dz/UniFAR-FTUs huggingface dataset:
Glycosylation of a Capsule-Like Complex (CLC) by Francisella novicida Is Required for Virulence and Partial Protective Immunity in Mice

Francisella tularensis is a Gram-negative bacterium and the etiologic agent of tularemia. F. tularensis may appear encapsulated when examined by transmission electron microscopy (TEM), which is due to production of an extracellular capsule-like complex (CLC) when the bacterium is grown under specific environmental conditions. Deletion of two glycosylation genes in the live vaccine strain (LVS) results in loss of apparent CLC and attenuation of LVS in mice. In contrast, F. novicida, which is also highly virulent for mice, is reported to be non-encapsulated. However, the F. novicida genome contains a putative polysaccharide locus with homology to the CLC glycosylation locus in F. tularensis. Following daily subculture of F. novicida in Chamberlain's defined medium, an electron dense material surrounding F. novicida, similar to the F. tularensis CLC, was evident. Extraction with urea effectively removed the CLC, and compositional analysis indicated the extract contained galactose, glucose, mannose, and multiple proteins, similar to those found in the F. tularensis CLC. The same glycosylation genes deleted in LVS were targeted for deletion in F. novicida by allelic exchange using the same mutagenesis vector used for mutagenesis of LVS. In contrast, this mutation also resulted in the loss of five additional genes immediately upstream of the targeted mutation (all within the glycosylation locus), resulting in strain F. novicida Δ1212–1218. The subcultured mutant F. novicida Δ1212–1218 was CLC-deficient and the CLC contained significantly less carbohydrate than the subcultured parent strain. The mutant was severely attenuated in BALB/c mice inoculated intranasally, as determined by the lower number of F. novicida Δ1212–1218 recovered in tissues compared to the parent, and by clearance of the mutant by 10–14 days post-challenge. Mice immunized intranasally with F. novicida Δ1212–1218 were partially protected against challenge with the parent, produced significantly reduced levels of inflammatory cytokines, and their spleens contained only areas of lymphoid hyperplasia, whereas control mice challenged with the parent exhibited hypercytokinemia and splenic necrosis. Therefore, F. novicida is capable of producing a CLC similar to that of F. tularensis, and glycosylation of the CLC contributed to F. novicida virulence and immunoprotection.
Mapping ecological risks with a portfolio‐based technique: incorporating uncertainty and decision‐making preferences

Geographic mapping of risks is a useful analytical step in ecological risk assessments and in particular, in analyses aimed to estimate risks associated with introductions of invasive organisms. In this paper, we approach invasive species risk mapping as a portfolio allocation problem and apply techniques from decision theory to build an invasion risk map that combines risk and uncertainty in a single map product.
The 6 th International Conference on Ambient Systems , Networks and Technologies ( ANT 2015 ) WSN in Monitoring Oil Pipelines Using ACO and GA

Wireless Sensor Networks (WSNs) are one of the most important technologies in the fields of wireless networking today. WSNs have a vast amount of applications including sensors embedded in the outer surface of pipeline or mounted along the supporting structure of bridges, robotics and health care. In this paper, we study the issues of linear sensor placement to monitor oil pipelines. We address the problem of optimal number of sensors to be deployed given initial energy of each sensor node and message buffering limitations. The objectives of the deployment process are: 1) maximizing the coverage of the pipe, 2) producing a connected network, and 3) prolonging the overall network lifetime. The paper utilizes two of the evolutionary algorithms to solve the deployment problem which are Genetic Algorithms (GA) and Ant Colony Optimization (ACO). Extensive set of experiments are performed for performance evaluation. © 2015 The Authors. Published by Elsevier B.V. Peer-review under responsibility of the Conference Program Chairs.
The Dominating Role of N-Deacetylase/N-Sulfotransferase 1 in Forming Domain Structures in Heparan Sulfate*

Heparan sulfate (HS) is a highly sulfated polysaccharide participated in essential physiological functions from regulating cell growth to blood coagulation. HS contains sulfated domains known as N-S domains and low sulfate domains known as N-Ac domains. The distribution of the domain structures is likely governed by the action of glucosaminyl N-deacetylase/N-sulfotransferase (NDST). Here, we sought to determine the substrate specificity of NDST using model substrates and recombinant NDST protein. We discovered that NDST-1 carries out the modification in a highly ordered fashion. The enzyme sulfates the substrate from the nonreducing end toward the reducing end consecutively, leading to the product with a cluster of N-sulfo glucosamine residues. Furthermore, a preexisting N-sulfo glucosamine residue prevents the action of NDST-1 at the residues immediately located at the nonreducing end, allowing the formation of an N-Ac domain. Our results provide the long sought evidence for understanding the formation of sulfated versus nonsulfated domains in the HS isolated from cells and tissues. The study demonstrates the regulating role of NDST-1 in mapping the sulfation patterns of HS.
Assessment of the performance of SPM analysis in PET neuroactivation studies : A Monte Carlo investigation

Statistical parametric mapping (SPM) is now considered the gold standard both in clinical and research neuroimaging investigations. We investigate the feasibility of Monte Carlo simulations-based assessment of the sensitivity and specificity of SPM analysis in Positron Emission Tomography (PET) neuroactivation studies with respect to design parameters such as study size, activation/lesion localisation, intensity and size. Fifteen data sets were generated for different foci activation levels, and localizations using five spheres located within the digital Hoffman 3D brain phantom with diameters corresponding to 6 and 8 mm, close to the resolution limit of the ECAT ART PET scanner (CTI/Siemens). The five foci were defined in the thalamus (T), putamen (P), cingulate gyrus (CG), right frontal cortex (RFC) and the right supramarginal gyrus (RSG) covering different structures of particular interest in cognitive neuroscience. In addition, we carried out a coordinate search of the resulting maximum cluster, which was found to be close to 10 mm around the true value on the Talairach atlas.
A Generator for Description Logic Formulas

We introduce a schema for generating random formulas for different description logics, which extends an existing pattern for modal logics. Using the DL reasoners FaCT and Racer, we test the difficulty of these formulas, and it turns out that the properties that make a formula in an expressive DL hard are quite different from those known for ALC formulas.
Urban-rural differences in the occurrence of female depressive disorder in Europe--evidence from the ODIN study.

BACKGROUND In an earlier paper of the European multi-centre ODIN study (Ayuso-Mateos et al. 2001) we found remarkable urban preponderance in comparison to the corresponding rural site in the female prevalence of depressive disorder in the UK and Ireland. The aim of this paper is to analyse the possible reasons for this finding. METHOD A representative sample of 12,702 people aged between 18 and 64 residing in specified urban and rural areas were screened by the Beck Depression Inventory (BDI) for depressive disorder in four European countries (Finland, Ireland, Norway and the UK). Those over cut-off (BDI score < 12) and a 5 % random sample of those under cut-off underwent diagnostic interview including the SCAN version 2.0, and completed a battery of additional research instruments. RESULTS The estimated 1-month prevalence of depressive disorder according to ICD-10 was 9 % in the total ODIN sample. A large between-country variation was found in female urban prevalence, with Ireland (Dublin) and the UK (Liverpool) having a remarkably high rate. The women in these same countries showed a significant urban/rural difference, whereas in men and in the total sample this difference was non-significant. Logistic regression analysis including some selected risk factors of depression showed still higher risk of depressive disorder both in Dublin and Liverpool compared with the Finnish urban site (Turku), which had the lowest urban prevalence. In addition, also such factors as lack of confidant and having difficulties in getting practical help from neighbours were important predictors of depressive disorder. Similarly, when analysing the different countries separately, the significance of the urban/rural difference in women remained for Ireland and the UK, indicating that the other risk factors studied could not totally explain the difference. CONCLUSIONS ODIN is the first European study on occurrence of depressive disorder in both urban and rural settings allowing closer analysis of the urban/rural differences. The most striking result was the large urban/rural difference in women in the two countries from the British Isles which could not be totally explained by the socio-demographic factors included in this study.
Fundamentals of grain and interphase boundary diffusion

Analytical Models of Grain Boundary Diffusion. Diffusion Along Dislocations and Small-Angle Grain Boundaries. Grain Boundary Diffusion in Thin Films. Diffusion Along Migrating Grain Boundaries. Structural Effects on and Mechanisms of Grain Boundary Diffusion. Experimental Methods for Determination of Grain Boundary Diffusion Data. Index.
Digital subtraction angiography abnormalities in sudden unilateral profound hearing loss

Conclusion. The reduced caliber of the anterior inferior cerebellar artery (AICA) on the affected side in patients with sudden unilateral profound hearing loss (SUPHL) may reflect a perfusion deficit which, combined to a lesser degree with anatomic abnormalities in the vertebrobasilar system, would be implicated in the pathogenesis of SUPHL. Objective. To identify existing hemodynamic disturbances and anatomic abnormalities in patients with SUPHL using digital subtraction angiography. Material and methods. Ten patients aged 18–66 years and a control group of 25 subjects were included in the study. Both vertebral arteries (VAs) were selectively catheterized in all the patients. Results. In 7/10 patients (70%) the AICA on the side affected by SUPHL was smaller in caliber than the contralateral one after injection of contrast medium into the VA on the affected side. The situation was significantly different in the control group, whose angiography results demonstrated similarly sized AICAs in 84% of cases. Tortuosity of the VA on the affected side was encountered in two patients and important VA asymmetry in one.
Adaptive sampling in two-phase designs: a biomarker study for progression in arthritis

Response‐dependent two‐phase designs are used increasingly often in epidemiological studies to ensure sampling strategies offer good statistical efficiency while working within resource constraints. Optimal response‐dependent two‐phase designs are difficult to implement, however, as they require specification of unknown parameters. We propose adaptive two‐phase designs that exploit information from an internal pilot study to approximate the optimal sampling scheme for an analysis based on mean score estimating equations. The frequency properties of estimators arising from this design are assessed through simulation, and they are shown to be similar to those from optimal designs. The design procedure is then illustrated through application to a motivating biomarker study in an ongoing rheumatology research program. Copyright © 2015 © 2015 The Authors. Statistics in Medicine Published by John Wiley & Sons Ltd.
F-actin reorganization by V-ATPase inhibition in prostate cancer

ABSTRACT The vacuolar ATPase (V-ATPase) proton pump sustains cellular pH homeostasis, and its inhibition triggers numerous stress responses. However, the cellular mechanisms involved remain largely elusive in cancer cells. We studied V-ATPase in the prostate cancer (PCa) cell line PC-3, which has characteristics of highly metastatic PCa. V-ATPase inhibitors impaired endo-lysosomal pH, vesicle trafficking, migration, and invasion. V-ATPase accrual in the Golgi and recycling endosomes suggests that traffic of internalized membrane vesicles back to the plasma membrane was particularly impaired. Directed movement provoked co-localization of V-ATPase containing vesicles with F-actin near the leading edge of migrating cells. V-ATPase inhibition prompted prominent F-actin cytoskeleton reorganization. Filopodial projections were reduced, which related to reduced migration velocity. F-actin formed novel cytoplasmic rings. F-actin rings increased with extended exposure to sublethal concentrations of V-ATPase inhibitors, from 24 to 48 h, as the amount of alkalinized endo-lysosomal vesicles increased. Studies with chloroquine indicated that F-actin rings formation was pH-dependent. We hypothesize that these novel F-actin rings assemble to overcome widespread traffic defects caused by V-ATPase inhibition, similar to F-actin rings on the surface of exocytic organelles. Summary: V-ATPase activates multiple stress responses. In prostate cancer, sub-lethal concentrations of V-ATPase inhibitors trigger widespread traffic defects. F-actin assembles into rings that mimic those seen during regulated exocytosis.
Associations of work ability with frequent and long-term sickness absence.

BACKGROUND Reduced work ability is related to long-term sickness absence. The relationship between work ability and frequent sickness absence has not previously been investigated. It is important to distinguish between frequent and long-term sickness absence as they are outcomes of different processes. AIMS To investigate the associations of work ability with frequent short-term (three or more episodes lasting <2 weeks in the past year), long-term (one or more episodes lasting at least 2 weeks in the past year) and combined (frequent and long-term) sickness absence. METHODS In 2010-12, we invited employees working in different economic sectors to complete a postal questionnaire measuring work ability using the work ability index (WAI). We compared the WAI scores in employees with frequent, long-term and combined sickness absence with the scores in employees without such sickness absence by multinomial regression analysis. RESULTS Of 6682 invited employees, 3660 (55%) completed the questionnaire. Mean (standard deviation) WAI scores were 41.2 (3.4), 39.4 (3.9), 37.2 (5.2) and 43.2 (2.7) in employees with frequent, long-term, combined sickness absence and neither frequent nor long-term sickness absence, respectively. WAI scores were negatively related to frequent (odds ratio [OR] = 0.85; 95% confidence interval [CI] 0.82-0.88), long-term (OR = 0.79; 95% CI 0.75-0.82) and combined sickness absence (OR = 0.74; 95% CI 0.71-0.77). CONCLUSIONS Self-reported reduced work ability is associated with both frequent and long-term sickness absence, suggesting that frequent sickness absence is not only driven by motivational processes.
The impact of systemic and copper pesticide applications on the phyllosphere microflora of tomatoes

Background Contamination of tomatoes by Salmonella can occur in agricultural settings. Little is currently understood about how agricultural inputs such as pesticide applications may impact epiphytic crop microflora and potentially play a role in contamination events. We examined the impact of two materials commonly used in Virginia tomato agriculture: acibenzolar-S-methyl (crop protectant) and copper oxychloride (pesticide) to identify the effects these materials may exert on baseline tomato microflora and on the incidence of three specific genera; Salmonella, Xanthomonas and Paenibacillus. Results Approximately 186 441 16S rRNA gene and 39 381 18S rRNA gene sequences per independent replicate were used to analyze the impact of the pesticide applications on tomato microflora. An average of 3 346 677 (634 892 974 bases) shotgun sequences per replicate were used for metagenomic analyses. Conclusion A significant decrease in the presence of Gammaproteobacteria was observed between controls and copper-treated plants, suggesting that copper is effective at suppressing growth of certain taxa in this class. A higher mean abundance of Salmonella and Paenibacillus in control samples compared to treatments may suggest that both systemic and copper applications diminish the presence of these genera in the phyllosphere; however, owing to the lack of statistical significance, this could also be due to other factors. The most distinctive separation of shared membership was observed in shotgun data between the two different sampling time-points (not between treatments), potentially supporting the hypothesis that environmental pressures may exert more selective pressures on epiphytic microflora than do certain agricultural management practices. © 2014 The Authors. Journal of the Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
Towards the Wide Spread Use of Type-2 Fuzzy Logic Systems in Real World Applications

Real world applications are characterized by high levels of linguistic and numerical uncertainties. Since the inception of Fuzzy Logic Systems (FLSs), they have been applied with great success to numerous real world applications. The vast majority of FLSs so far have been traditional type-1 FLSs. However, type-1 FLSs cannot fully handle the high levels of uncertainties available in the vast majority of real world applications. This is because type-1 FLSs employ crisp and precise type-1 fuzzy sets. A type-2 FLS can handle higher uncertainty levels to produce improved performance. This paper follows on [1] to show how type-2 FLSs are starting to find their way into a variety of real world applications, promising a continuous growth both in number and variety of type-2 FLS applications in the next decade.
Do current indications for surgery of primary gastric lymphoma exist?

OBJECTIVE To analyze the results of our series in order to assess whether surgical excision is still a valid therapeutic option in case the patient needs surgery. Secondarily, to analyze Helicobacter pylori infection rate. PATIENTS AND METHOD A retrospective study of 69 consecutive patients having stage IE-IIE primary gastric lymphoma; of these, 65 were treated by gastrectomy between 1974 and 1999. Mean age: 62.6 years (28-85). New staining of paraffin-embedded samples from the surgical specimen were carried out (hematoxiline-eosine, Giemsa, immunohistochemistry) and reviewed. The histological classification was performed according to Isaacson's criteria. The statistical analysis was done by Chi-squared and Fisher's exact tests, as well as Kaplan-Meier and Log-Rank tests. RESULTS Mortality was 9.2%. There were non-fatal complications in 10.8%. Helicobacter pylori was identified in 62.7%. Seven patients (11.9%) suffered a relapse. The 5-year survival probability was 87%. The statistical analysis did not show any influences of Ann Arbor stage, gastric wall invasion, Helicobacter pylori infection, histological type, or margin resection involvement on survival. CONCLUSIONS Surgical excision provides a high rate of complete remissions and excellent long-term survival with acceptable mortality. Therefore it appears to be a valid treatment in case of emergency surgery, incidental finding, or lack of histological diagnosis.
Observer variability and sensitivity of radiographic diagnosis of canine medial coronoid disease

Summary Objective: Medial coronoid disease (MCD) is a very common form of elbow joint disease and it’s radiographic diagnosis can be challenging since it is frequently based on the detection of rather subtle primary or secondary changes than on a large primary lesion. We hypothesized that accuracy of radiographic diagnosis of MCD is highly dependent on training and experience level. Methods: Radiographs of 102 canine elbows were evaluated for MCD by four observers with different levels of training and experience. All elbows underwent CT scans and arthroscopy. Sensitivity and specificity of radiographic and CT interpretation was determined using arthroscopy as a gold standard. Interobserver and intraobserver agreement (reliability and repeatability) were assessed by using Cohen’s Kappa (κ) statistic. Results: The sensitivity (92.4–96.7%) of the two experienced observers was almost comparable to that of CT (100%) and significantly higher than that of the two less experienced observers (77.2–80.4%). Reliability of the radiographic diagnosis of MCD was better between observers with higher experience level (κ = 0.74) than between observers of lower or different experience levels (κ =0.07–0.42). Repeatability was better in experienced (κ = 0.73–0.88) than in less experienced observers (κ = 0.31–0.42). Conclusion: Our results confirm that training and experience play important roles in reaching high sensitivity, reliability and repeatability for the radiographic diagnosis of MCD. Clinical relevance: Although radiography is inferior to CT in imaging of the medial coronoid process itself, sensitivity of radiographic diagnosis MCD can be significantly improved with observer experience almost reaching that of CT. Therefore, it is advised that radiographic screening for MCD should be performed by specialists experienced in the radiographic evaluation of elbow joint disease.
Forisome dispersion in Vicia faba is triggered by Ca2+ hotspots created by concerted action of diverse Ca2+ channels in sieve element

Remote-controlled Ca2+ influx, elicited by electropotential waves, triggers local signaling cascades in sieve elements and companion cells along the phloem of Vicia faba plants. The stimulus strength seems to be communicated by the rate and duration of Ca2+ influx into SEs. The cooperative recruitment of Ca2+ channels results in a graded responses of forisome responses culminating in full sieve-tube occlusion. Several lines of evidence are integrated into a model that links the mode and strength of the EPWs with forisome dispersion, mediated by transiently enhanced levels of local Ca2+ release dependent on both plasma membrane and ER Ca2+ channels.
Dietary Hydrogenated Fat Increases High-Density Lipoprotein apoA-I Catabolism and Decreases Low-Density Lipoprotein apoB-100 Catabolism in Hypercholesterolemic Women

Objective—To determine mechanisms contributing to decreased high-density lipoprotein cholesterol (HDL-C) and increased low-density lipoprotein cholesterol (LDL-C) concentrations associated with hydrogenated fat intake, kinetic studies of apoA-I, apoB-100, and apoB-48 were conducted using stable isotopes. Methods and Results—Eight postmenopausal hypercholesterolemic women were provided in random order with 3 diets for 5-week periods. Two-thirds of the fat was soybean oil (unsaturated fat), stick margarine (hydrogenated fat), or butter (saturated fat). Total and LDL-C levels were highest after the saturated diet (P< 0.05; saturated versus unsaturated) whereas HDL-C levels were lowest after the hydrogenated diet (P< 0.05; hydrogenated versus saturated). Plasma apoA-I levels and pool size (PS) were lower, whereas apoA-I fractional catabolic rate (FCR) was higher after the hydrogenated relative to the saturated diet (P< 0.05). LDL apoB-100 levels and PS were significantly higher, whereas LDL apoB-100 FCR was lower with the saturated and hydrogenated relative to the unsaturated diet. There was no significant difference among diets in apoA-I or B-100 production rates or apoB-48 kinetic parameters. HDL-C concentrations were negatively associated with apoA-I FCR (r=−0.56, P=0.03) and LDL-C concentrations were negatively correlated with LDL apoB-100 FCR (r=−0.48, P=0.05). Conclusions—The mechanism for the adverse lipoprotein profile observed with hydrogenated fat intake is determined in part by increased apoA-I and decreased LDL apoB-100 catabolism.