Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of a novel large extrachromosomal DNA (LED) in the Trypanosomatidae

We have identified a novel 75 kbp large extrachromosomal DNA (LED) which is stably maintained during developmental conversion of Trypanosoma cruzi. It has a covalently closed circular conformation and is not derived from the kinetoplast network. In all T. cruzi strains analysed, LED contains 18S rRNA and spliced leader (sl) sequences. LED from the T. cruzi Y strain contains a minimum of 15 copies of the sl repeat arrayed in a head‐to‐tail configuration and 50 copies of a 196 bp repeat. LED is also present in Trypanosoma dionisii (subgenus Schizotrypanosoma) and in other members of the family Trypanosomatidae. LED from different T. cruzi strains and from other members of the Trypanosomatidae differ in their content of large ribosomal subunit rRNA sequences and the 196 bp repeat. The presence of LED in four evolutionarily distant trypanosomatid species suggests that it plays an important rote in the biology of these parasites.
Verification of chicken Nanog as an epiblast marker and identification of chicken PouV as Pou5f3 by newly raised antibodies

Pluripotency is an important feature of early embryonic cells of multicellular organisms. Recent advances in stem cell research have shown that Nanog and Pou5f1 (Oct3/4) play important roles in mammalian pluripotency. However, whether these molecules exert conserved functions in other species remains unknown. Although the epiblast of the early chicken embryo would provide a useful experimental model, a lack of antibodies against chicken Nanog (cNanog) and chicken PouV/Pou5f3 (cPouV) proteins has hampered intensive investigation. Here we report newly raised polyclonal antibodies that specifically recognize cNanog and cPouV proteins. The specificity and sensitivity of the antibodies were validated by both western blotting and immunostaining with transfected 293T cells and chicken embryonic tissues. Immunohistochemistry using these antibodies revealed that cNanog protein was specifically localized in epiblastic cells and germ cells. In contrast, cPouV expression was seen almost ubiquitously. We also found that chicken epiblast‐derived colony‐forming cells that morphologically resemble mouse embryonic stem cells were cNanog‐positive, implying that these colony‐forming cells possess pluripotency. The anti‐cPouV antibody further enabled us to identify a previously unknown region at the N‐terminus of the cPouV protein containing a characteristic motif that is absent in mammalian Pou5f1. Thus, the antibodies raised in this study are useful tools for studying the functions of cNanog and cPouV at the protein level and the molecular mechanisms of chicken pluripotency.
A Flying Tool for Sensing Vessel Structure Defects Using Image Contrast-Based Saliency

Vessels have to undergo regular visual inspections in order to detect the typical defective situations affecting metallic structures, such as cracks and corrosion. These inspections are nowadays performed manually by ship surveyors at a great cost. Assisting them during the inspection process by means of, e.g., a fleet of robots capable of defect detection would, without doubt, decrease the inspection cost. In this paper, a robotic sensor for visual defect detection on vessel structures is presented. Its hardware comprises a micro-aerial platform, a suite of navigation sensors, and vision cameras, to provide a close-up view of the vessel surface under inspection. The software architecture has been designed around the supervised autonomy paradigm, so that the user is introduced in the position control loop, while the platform is in charge of providing functionalities, such as collision prevention and other self-preservation issues. The inspection tool is completed with a vision-based defect detector that labels those areas that are suspicious of being affected by corrosion or cracks. Both hardware and software architectures have been assessed for the vessel inspection task with good results.
Genotypic evaluation of rickettsial isolates recovered from various species of ticks in Portugal

SUMMARY Twelve rickettsial isolates, from Rhipicephalus sanguineus, R. turanicus, Dermacentor marginatus and Hyalomma marginatus, were subjected to genotypic analysis. Amplification of specific DNA sequences, restriction endonuclease digestion of amplified DNA products, and gel electrophoresis were used to identify specific DNA fragment-banding patterns. Five patterns were resolved. Four were homologous with those of previously described rickettsial genotypes, R. conorii, R. slovaca, R. rhipicephali and R. massiliae. The fifth pattern differed by only a single altered restriction endonuclease cleavage site. For the first time in Portugal a widely distributed spectrum of spotted fever group rickettsia was found among potential vector species stressing the need to determine their potential for human and domestic animals infection.
Shift from Rh‐positive to Rh‐negative phenotype caused by a somatic mutation within the RHD gene in a patient with chronic myelocytic leukaemia

We report a female patient whose Rh phenotype shifted from RhD‐positive to RhD‐negative over a 3‐year period (1991–94), during which time she was treated with mastectomy (1992) and local irradiation for a low‐grade recurrent breast cancer. She was diagnosed with chronic myeloid leukaemia in 1994, and has since then received chemotherapy. The patient was repeatedly typed as O, RhD‐positive between 1965 and 1991 and was repeatedly found RhD‐negative after 1994. Bcr‐Abl transcripts typical of Ph1 chromosome were detected. Molecular analysis indicated that the patient was heterozygous at the RH locus, carrying one haplotype in which the RHD gene exhibited a single nucleotide deletion (G600) resulting in a frameshift and premature stop codon, and a normal RHCE gene (allele Ce). The second haplotype contained only the RHCE gene (allele ce) and was normal. Further analysis carried out on total leucocytes, purified neutrophils, EBV‐lymphoblastoid cell line and cultured erythroblasts indicated that the G600 deletion was restricted to the myeloid lineage. No modification of other blood group antigens could be detected. These findings suggest a somatic mutation which most probably occurred in a stem cell common to the myeloid lineage.
Contribution to growth. European Public Procurement. Delivering economic benefits for citizens and businesses

This study assesses the impact of recent EU public procurement legislation on strategic goals such as cross-border procurement, SME participation, and competition. Based on the assessment of the most recent TED dataset SME participation in procurement is increasing in most countries whereas cross-border contracting and competition are still areas where further improvement is needed. Therefore, we propose digital end-to-end processes, interoperability, and a one-stop shop procurement portal as well as an improved management of data quality. This document was prepared for Policy Department A on request of the Committee on the Internal Market and Consumer Protection. Contribution to Growth European Public Procurement Delivering Economic Benefits for Citizens and Businesses This document was requested by the European Parliament's Committee on the Internal Market and Consumer Protection. AUTHORS Prof. Dr. Dr. h.c. Dr. h.c. Jörg BECKER, University of Münster, ERCIS, Germany Marco NIEMANN, University of Münster, ERCIS, Germany Sebastian HALSBENNING, University of Münster, ERCIS, Germany ADMINISTRATOR RESPONSIBLE Mariusz MACIEIEWSKI EDITORIAL ASSISTANT Irene VERNACOTOLA LINGUISTIC VERSIONS Original: EN ABOUT THE EDITOR Policy departments provide in-house and external expertise to support EP committees and other parliamentary bodies in shaping legislation and exercising democratic scrutiny over EU internal policies. To contact the Policy Department or to subscribe for updates, please write to: Policy Department for Economic, Scientific and Quality of Life Policies European Parliament B-1047 Brussels Email: Poldep-Economy-Science@ep.europa.eu Manuscript completed: December 2018 Date of publication: January 2019 © European Union, 2019 This document is available on the internet at: http://www.europarl. europa.eu/supporting-analyses DISCLAIMER AND COPYRIGHT The opinions expressed in this document are the sole responsibility of the authors and do not necessarily represent the official position of the European Parliament. Reproduction and translation for non-commercial purposes are authorised, provided the source is acknowledged and the European Parliament is given prior notice and sent a copy. For citation purposes, the study should be referenced as: Becker, J. e al, Contribution to Growth. European Public Procurement. Delivering Economic Benefits for Citizens and Businesses, Study for the Committee on the Internal Market and Consumer Protection, Policy Department for Economic, Scientific and Quality of Life Policies, European Parliament, Luxembourg, 2018. t European Public Procurement. Delivering Economic Benefits for Citizens and Businesses PE 631.048 3 CONTENTS LIST OF ABBREVIATIONS 4 LIST OF FIGURES 5 LIST OF TABLES 5 EXECUTIVE SUMMARY 6
Inflation Dynamics in Brazil: The Case of a Small Open Economy*

This paper derives and estimates a structural model for inflation in an open economy. The model represents the standard new-Keynesian Phillips curve (NKPC) and the hybrid curve proposed by Woodford (2003) and Gaĺı and Gertler (1999) as special cases. We present two sets of estimates for the Brazilian economy, initially regarded as a closed economy and then as a small open economy. According to the recent literature, the model contemplates indexation to past inflation and a measure of marginal cost as relevant inflation indicators. Some of the results can be summarized as follows: (i) Brazil, when regarded as a closed economy, has a relatively higher level of nominal rigidity than that of the United States and Europe, and a high level of indexation as well; (ii) In an open economy with indexation, nominal exchange rate appreciation plus foreign inflation affects consumer inflation, and this effect becomes more intense with larger economic openness; (iii) There is a small direct impact of the variables associated with economic openness, with the sum of their coefficients being close to zero; (iv) However, the indirect impact is significant, consistently changing the weights associated with lagged inflation and the expected future inflation.
NADPH oxidase and extracellular regulated kinases 1/2 are targets of prion protein signaling in neuronal and nonneuronal cells

Putative functions of the cellular prion protein, PrPC, include resistance to oxidative stress, copper uptake, cell adhesion, and cell signaling. Here, we report NADPH oxidase-dependent reactive oxygen species (ROS) production and extracellular regulated kinases 1/2 (ERK1/2) phosphorylation on PrPC stimulation in the 1C11 neuroectodermal precursor, in its neuronal differentiated progenies, and in GT1-7 neurohypothalamic and BW5147 lymphoid cells. In neuroprogenitor, hypothalamic, and lymphoid cells, ERK1/2 activation is fully controlled by the NADPH oxidase-dependent ROS production. In 1C11-derived bioaminergic cells, ROS signaling and ERK1/2 phosphorylation are both controlled by Fyn kinase activation, introducing some specificity in PrPC transduction associated with this neuronal context. These data argue for an ubiquitous function of PrPC in cell-redox homeostasis through ROS production.
Research of Collaborative Interactive Visualization for Medical Imaging

In medical science field, a large amount of medical data needs to be shared in order to assist doctors to make a diagnosis and give treatment collaboratively. Traditional medical visualization systems lack cross-platform access and collaborative visualization mechanisms, it is difficult to achieve remote access and collaborative interaction. This paper proposes a collaborative interactive visualization systems for medical imaging. Using the collaborative medical data exchange protocol presented in this paper, only the server sends data to the single master's browser, the spectators can share the visualization scene. The experimental results show that: not only remote browsers can share a large amount of image data sets, but also our system supports real-time collaborative interaction of slice rendering and volume rendering, and has a better visualization result.
A Bacteroides ruminicola 1,4-beta-D-endoglucanase is encoded in two reading frames

Escherichia coli transformed with a plasmid containing a Bacteroides ruminicola endoglucanase (carboxymethyl cellulase [CMCase]) gene produced three immunologically cross-reacting CMCases which had molecular weights of 40,500, 84,000, and 88,000, while B. ruminicola produced CMCases with molecular weights of 82,000 and 88,000. The two B. ruminicola enzymes (purified from culture supernatants) had different N-terminal amino acid sequences, but each enzyme was encoded by the same gene (three independent clones had the same DNA sequence). The 88,000-molecular-weight CMCase (88K CMCase) gene appeared to contain two open reading frames which overlapped for 18 bp and were -1 out of frame, and each open reading frame contained several stop codons near the overlap region. The two 88K CMCase open reading frames had enough DNA to produce a protein of 106K, but the mobility of the enzyme in sodium dodecyl sulfate gels gave a value which was 20% lower. On the basis of the -1 frame shift and the large deviation in theoretical versus actual size, it appears that an unusual event (e.g., ribosomal hopping or RNA splicing) is involved in either the translation or the transcription of the 88K B. ruminicola CMCase gene. The 82K CMCase was completely encoded in the second reading frame, and its size was in agreement with the DNA sequence.
Induction and regulation of T-cell immunity by the novel tuberculosis vaccine M72/AS01 in South African adults.

RATIONALE Tuberculosis (TB) is a major cause of morbidity and mortality worldwide, thus there is an urgent need for novel TB vaccines. OBJECTIVES We investigated a novel TB vaccine candidate, M72/AS01, in a phase IIa trial of bacille Calmette-Guérin-vaccinated, HIV-uninfected, and Mycobacterium tuberculosis (Mtb)-infected and -uninfected adults in South Africa. METHODS Two doses of M72/AS01 were administered to healthy adults, with and without latent Mtb infection. Participants were monitored for 7 months after the first dose; cytokine production profiles, cell cycling, and regulatory phenotypes of vaccine-induced T cells were measured by flow cytometry. MEASUREMENTS AND MAIN RESULTS The vaccine had a clinically acceptable safety profile, and induced robust, long-lived M72-specific T-cell and antibody responses. M72-specific CD4 T cells produced multiple combinations of Th1 cytokines. Analysis of T-cell Ki67 expression showed that most vaccination-induced T cells did not express Th1 cytokines or IL-17; these cytokine-negative Ki67(+) T cells included subsets of CD4 T cells with regulatory phenotypes. PD-1, a negative regulator of activated T cells, was transiently expressed on M72-specific CD4 T cells after vaccination. Specific T-cell subsets were present at significantly higher frequencies after vaccination of Mtb-infected versus -uninfected participants. CONCLUSIONS M72/AS01 is clinically well tolerated in Mtb-infected and -uninfected adults, induces high frequencies of multifunctional T cells, and boosts distinct T-cell responses primed by natural Mtb infection. Moreover, these results provide important novel insights into how this immunity may be appropriately regulated after novel TB vaccination of Mtb-infected and -uninfected individuals. Clinical trial registered with www.clinicaltrials. gov (NCT 00600782).
Quick Ontology Mapping Algorithm for Distributed Environments

The ontology mapping appears in many application domains and its resolution is complex due to the different ways to represent the information. Our approach is based on the creation of a new structure that contains the main concepts of an ontology. These concepts define the ontology purpose and its granularity. Furthermore, we increase these terms using external resources to simplify the number of concepts to compare. Thus, the mapping algorithm compares these structures and quickly decides if there are similarities, instead of usign traditional techniques which compare most of the ontology elements one by one.
Interleukin-18 treatment options for inflammatory diseases

Several autoimmune diseases are believed to be mediated, in part, by interleukin (IL)-18. Many are those with associated elevated interferon-γ levels, such as systemic lupus erythematosus, macrophage activation syndrome, rheumatoid arthritis, Crohn’s disease, psoriasis, as well as graft-versus-host disease. Clinical and animal studies also support the concept that IL-18 is a key player in atherosclerosis, acute renal ischemia and hepatitis. IL-18 is a member of the IL-1 family; IL-1β and IL-18 are closely related, and both require the intracellular cysteine protease caspase-1 for biologic activity. The IL-18 binding protein, a naturally occurring, specific inhibitor of IL-18, neutralizes IL-18 activities and is likely to be safe in patients. Other options for reducing IL-18 activities are inhibitors of capsase-1, human monoclonal antibodies to IL-18, soluble IL-18 receptors and anti-IL-18 receptor monoclonal antibodies.
Evidence cerebral blood-flow regulation mediates exercise-cognition links in healthy young adults.

OBJECTIVE Healthy young adults are presumed to be in their cognitive prime, yet emerging evidence indicates that regular engagement in physical activity can still benefit their cognitive functioning. The mechanisms supporting these exercise-related cognitive benefits remain unclear, but recent research points to cerebral blood-flow (CBF) regulation as potentially important. The current study investigated the possibility that efficacy of CBF regulation underpins exercise-cognition links in this high functioning population. METHOD In 55 healthy young adults, cognitive control performance (inhibition and switching) was examined in relation to habitual physical activity, aerobic fitness, and CBF regulation (evidenced by blood-flow responsiveness to increases and decreases in carbon dioxide: hypercapnic reactivity, n = 43, and hypocapnic reactivity, n = 42). RESULTS Multiple regression analyses revealed that more frequent physical activity, and to some extent better aerobic fitness, predicted both better CBF regulation and better cognitive inhibitory control. CBF regulation also predicted better cognitive inhibitory control. Moreover, mediation analyses indicated that more frequent participation in physical activity may bring about improvements in cognitive inhibitory control through improved CBF regulation. CONCLUSION These results provide novel insight into the cognitive and cerebrovascular benefits that may be gained with regular engagement in physical activity, even in a high-functioning population. Moreover, they point to better CBF regulation as a specific mechanism that may drive physical activity-related cognitive benefits, which converges with recent data in older women (Brown et al., 2010).
Phylogenomic Analysis of the Giardia intestinalis Transcarboxylase Reveals Multiple Instances of Domain Fusion and Fission in the Evolution of Biotin-Dependent Enzymes

Sequencing of the gene encoding a pyruvate carboxylase-like protein from the amitochondrial eukaryote Giardiaintestinalis revealed a 1,338 aa protein composed of acetyl-CoA carboxyltransferase (ACCT), pyruvate carboxyltransferase (PycB), and biotin carboxyl carrier protein (BCCP) domains, linked in a single polypeptide chain. This particular domain combination has been previously seen only in the methylmalonyl-CoA:pyruvate transcarboxylase from Propionibacteriumfreudenreichii, where each of these domains is encoded by an individual gene and forms a separate subunit. To get an insight into the evolutionary origin and biochemical function of the G.intestinalis enzyme, we compared its domain composition to those of other biotin-dependent enzymes and performed a phylogenetic analysis of each of its domains. The results obtained indicate that: (1) evolution of the BCCP domain included several domain fusion events, leading to the ACCT-BCCP and PycB-BCCP domain combinations; (2) fusions of the PycB and BCCP domains in pyruvate carboxylases and oxaloacetate decarboxylases occurred on several independent occasions in different prokaryotic lineages, probably due to selective pressure towards co-expression of these genes, and (3) because newly sequenced biotin-dependent enzymes are often misannotated in sequence databases, their annotation as either carboxylases, decarboxylases, or transcarboxylases has to rely on detailed analysis of their domain composition, operon organization of the corresponding genes, gene content in the particular genome, and phylogenetic analysis.
A Hurdle Model Approach of Store Choice and Market Area Analysis in Grocery Retailing

Abstract Store choice models play an important role in applied geography, especially in location analysis and retail impact assessment. Econometric store choice models enable the analysis of variables influencing store choice based on observed shopping behavior. Using these models—such as the multiplicative competitive interaction model or the discrete choice model—faces several methodical and conceptual problems limiting their explanatory power and applicability. Addressing these problems, a new approach of store choice analysis is developed, based on a generalized linear model for truncated data, the hurdle model. This approach is applied to grocery stores in Karlsruhe, based on empirical data from a customer survey. Three main insights can be gained: (1) The explanatory performance of the model is superior to the common models as it allows decomposing spatial shopping behavior into a store choice and the intensity of customer–store interactions, such as shopping trips or expenditures. (2) The hurdle approach allows for dealing with a large number of empirical customer–store interactions equal to zero, which is an important statistical feature. (3) The model results confirm previous findings; for example, that spatial shopping behavior in grocery retailing is mainly affected by the accessibility and size of the stores, which proves the approach’s plausibility.
Learning Spatial Localization: From Rat Studies to Computational Models of the Hippocampus

In his landmark article, Richard Morris (1981) introduced a set of rat experiments intended “to demonstrate that rats can rapidly learn to locate an object that they can never see, hear, or smell provided it remains in a fixed spatial location relative to distal room cues” (p. 239). These experimental studies have greatly impacted our understanding of rat spatial cognition. In this article, we address a spatial cognition model primarily based on hippocampus place cell computation where we extend the prior Barrera–Weitzenfeld model (2008) intended to allow navigation in mazes containing corridors. The current work extends beyond the limitations of corridors to enable navigation in open arenas where a rat may move in any direction at any time. The extended work reproduces Morris's rat experiments through virtual rats that search for a hidden platform using visual cues in a circular open maze analogous to the Morris water maze experiments. We show results with virtual rats comparing them to Morris's original studies with rats.