Miracle-dz/UniFAR-FTUs huggingface dataset:
Persistence of Protective Immunity to Malaria Induced by DNA Priming and Poxvirus Boosting: Characterization of Effector and Memory CD8+-T-Cell Populations

ABSTRACT The persistence of immunity to malaria induced in mice by a heterologous DNA priming and poxvirus boosting regimen was characterized. Mice were immunized by priming with DNA vaccine plasmids encoding the Plasmodium yoelii circumsporozoite protein (PyCSP) and murine granulocyte-macrophage colony-stimulating factor and boosting with recombinant vaccinia encoding PyCSP. BALB/c mice immunized with either high-dose (100 μg of p PyCSP plus 30 μg of pGM-CSF) or low-dose (1 μg of p PyCSP plus 1 μg of pGM-CSF DNA) priming were protected against challenge with 50 P. yoelii sporozoites. Protection 2 weeks after immunization was 70 to 100%, persisted at this level for at least 20 weeks, and declined to 30 to 40% by 28 weeks. Eight of eight mice protected at 20 weeks were still protected when rechallenged at 40 weeks. The antigen (Ag)-specific effector CD8+-T-cell population present 2 weeks after boosting had ex vivo Ag-specific cytolytic activity, expressed both gamma interferon (IFN-γ) and tumor necrosis factor alpha, and constituted 12 to 20% of splenic CD8+ T cells. In contrast, the memory CD8+-Ag-specific-cell population at 28 weeks lacked cytolytic activity and constituted only 6% of splenic CD8+ T cells, but at the single-cell level it produced significantly higher levels of IFN-γ than the effectors. High levels of Ag- or parasite-specific antibodies present 2 weeks after boosting had declined three- to sevenfold by 28 weeks. Low-dose priming was similarly immunogenic and as protective as high-dose priming against a 50-, but not a 250-, sporozoite challenge. These results demonstrate that a heterologous priming and boosting vaccination can provide lasting protection against malaria in this model system.
QUANTIFYING SPATIO-TEMPORAL CHAOS IN RAYLEIGH BÉNARD CONVECTION

In this project Rayleigh Bénard convection (RBC) in a cylindrical domain with experimentally realistic boundaries was investigated numerically. The results were obtained using large-scale parallel calculations. The flow field was determined as well as its linearized solutions in order to obtain Lyapunov diagnostics. The emphasis is on the effects that the domain size Γ has on the system dynamics (Γ = radius/depth for a cylindrical domain). Temperature fields were viewed for different Γ’s and a transition to spiral defect chaos was observed for large Γ’s. The temperature and thermal perturbation fields were inspected for Γ = 10 and large perturbations were found to be very localized and caused by small defects in the temperature field. The azimuthal average of thermal perturbations indicate that the perturbations are largest at the boundaries for small domains and largest at the center for large domains. This suggests that small to intermediate aspect ratio RBC should not be thought of as a set of weakly correlated regions in space. The leading order Lyapunov exponent was positive over a range of conditions indicating that the system is truly chaotic. The fractal dimension was calculated for several domain sizes and the system was found to be extensive even though the system dynamics change significantly.
Immune Modulation by Schistosoma mansoni Antigens in NOD Mice: Effects on Both Innate and Adaptive Immune Systems

We have shown that Schistosoma mansoni egg soluble antigen (SEA) prevents diabetes in the nonobese diabetic (NOD) mouse inducing functional changes in antigen presenting cells (APCs) and expanding T helper (Th) 2 and regulatory T cell (Treg) responses. A Th2 response to S. mansoni infection or its antigens is key to both the establishment of tolerance and successfully reproduction in the host. More recently we demonstrated that SEA treatment upregulates bioactive TGFβ on T cells with consequent expansion of Foxp3+ Tregs, and these cells might be important in SEA-mediated diabetes prevention together with Th2 cells. In this study we profile further the phenotypic changes that SEA induces on APCs, with particular attention to cytokine expression and markers of macrophage alternative activation. Our studies suggest that TGFβ from T cells is important not just for Treg expansion but also for the successful Th2 response to SEA, and therefore, for diabetes prevention in the NOD mouse.
A Pilot Trial of a Telecommunications System in Sleep Apnea Management

Background:Continuous positive airway pressure (CPAP) is an effective therapy for obstructive sleep apnea syndrome (OSAS), although many patients have difficulty adhering to this therapy. The purpose of this study was to investigate the effectiveness of totally automated telephone technology in improving adherence to prescribed CPAP therapy. Research Design:This pilot study was a randomized clinical trial in 30 patients being started on CPAP therapy for OSAS. Patients were randomly assigned to use of a computer telephone system designed to improve CPAP adherence (telephone-linked communications for CPAP [TLC-CPAP]) in addition to usual care (n = 15) or to usual care alone (n = 15) for a period of 2 months. TLC-CPAP is a computer-based system that monitors patients’ self-reported behavior and provides education and reinforcement through a structured dialogue. Measures:A sleep symptoms checklist and the Functional Outcomes of Sleep Questionnaire were administered at study entry and at 2-month follow up. Hours of CPAP use at effective mask pressure were measured by the CPAP device, stored in its memory, and retrieved at the 2-month visit. Results:At 2 months, patients randomized to TLC-CPAP had fewer reported sleep-related symptoms (9.4 vs. 13.4, P = 0.047) than those receiving usual care. The average nightly CPAP use in the TLC-CPAP group was 4.4 hours compared with 2.9 hours (P = 0.076) in the usual-care group. Conclusions:This pilot study suggests that patients with OSAS started on CPAP and a concurrently administered automated education and counseling system had better CPAP adherence and better control of OSAS symptoms.
On the Expressive Power of Deep Neural Networks

We propose a new approach to the problem of neural network expressivity, which seeks to characterize how structural properties of a neural network family affect the functions it is able to compute. Our approach is based on an interrelated set of measures of expressivity, unified by the novel notion of trajectory length, which measures how the output of a network changes as the input sweeps along a one-dimensional path. Our findings can be summarized as follows: (1) The complexity of the computed function grows exponentially with depth. (2) All weights are not equal: trained networks are more sensitive to their lower (initial) layer weights. (3) Regularizing on trajectory length (trajectory regularization) is a simpler alternative to batch normalization, with the same performance.
Chemopreventive effects of wild carrot oil against 7,12-dimethyl benz(a)anthracene-induced squamous cell carcinoma in mice

Context: Daucus carota L. ssp. carota (Apiacea) is widely distributed throughout the world and has many uses in traditional medicine. Objective: The present study investigates the chemopreventive effects of oil extract of D. carota umbels on 7,12-dimethyl benz(a)anthracene (DMBA)-induced skin cancer in mice. Materials and methods: D. carota oil extract (DCOE) was prepared by extracting the dried umbels with 50:50 acetone:methanol. Skin papilloma were initiated by DMBA and promoted by 12-O-tetradecanoyl phorobol-13-acetate (TPA). The extract was administered to animals via gavage (0.02 mL of 100% oil), intraperitoneal (0.3 mL of 2% oil), and topical (0.2 mL of 5, 50, and 100% oil) routes for 20 weeks. Tumor appearance, incidence, yield, and volume were compared with those of a non-treated control group. Results: Topical 100% treatment delayed tumor appearance, and inhibited tumor incidence and yield by 40 and 89%, respectively. Topical 50% treatment inhibited tumor incidence and yield by 30 and 83%, respectively, whereas the 5% treatment inhibited tumor yield by 36%. Tumor volume was decreased by 99, 91, and 70% following topical treatments with 100, 50, and 5% oil, respectively. Intraperitoneal treatment inhibited tumor yield by 43%, and decreased tumor volume by 85%, whereas gavage treatment showed minimal effects on both. Intraperitoneal and topical treatment decreased infiltration and hyperplasia with an increase in the level of hyperkeratosis. Conclusion: These findings demonstrate that DCOE has remarkable antitumor activity against DMBA-induced skin cancer compared with non-treated animals paving the ground for further investigations.
PEP-FOLD: an online resource for de novo peptide structure prediction

Rational peptide design and large-scale prediction of peptide structure from sequence remain a challenge for chemical biologists. We present PEP-FOLD, an online service, aimed at de novo modelling of 3D conformations for peptides between 9 and 25 amino acids in aqueous solution. Using a hidden Markov model-derived structural alphabet (SA) of 27 four-residue letters, PEP-FOLD first predicts the SA letter profiles from the amino acid sequence and then assembles the predicted fragments by a greedy procedure driven by a modified version of the OPEP coarse-grained force field. Starting from an amino acid sequence, PEP-FOLD performs series of 50 simulations and returns the most representative conformations identified in terms of energy and population. Using a benchmark of 25 peptides with 9–23 amino acids, and considering the reproducibility of the runs, we find that, on average, PEP-FOLD locates lowest energy conformations differing by 2.6 Å Cα root mean square deviation from the full NMR structures. PEP-FOLD can be accessed at http://bioserv.rpbs. univ-paris-diderot.fr/PEP-FOLD
Biological Stoichiometry: An Ecological Perspective on Tumor Dynamics

Abstract Biological stoichiometry is the study of the balance of energy and multiple chemical elements in biological systems. A key idea in biological stoichiometry is the growth rate hypothesis, which states that variation in the carbon:nitrogen:phosphorus stoichiometry of living things is associated with growth rate because of the elevated demands for phosphorus-rich ribosomal RNA, a requirement for rapid growth. In this article, we synthesize studies in the cancer literature to test the growth rate hypothesis; consistent with its predictions, rapidly growing tumors have elevated ribosome content, key oncogenes are closely affiliated with regulation of ribosome biogenesis, and tumor development has physiological impacts on patient phosphate metabolism. We also describe a new eco-evolutionary model of tumor dynamics that incorporates stoichiometric mechanisms. Since biological stoichiometry is fundamental in its approach, other areas of biology in which multiple key resources are involved in generating important tradeoffs may also benefit from the new tools provided by stoichiometric theory.
Human Polymorphonuclear Leukocytes Inhibit Aspergillus fumigatus Conidial Growth by Lactoferrin-Mediated Iron Depletion1

Aspergillus fumigatus, a common mold, rarely infects humans, except during prolonged neutropenia or in cases of chronic granulomatous disease (CGD), a primary immunodeficiency caused by mutations in the NADPH oxidase that normally produces fungicidal reactive oxygen species. Filamentous hyphae of Aspergillus are killed by normal, but not CGD polymorphonuclear leukocytes (PMN); however, the few studies on PMN-mediated host defenses against infectious conidia (spores) of this organism have yielded conflicting results, some showing that PMN do not inhibit conidial growth, with others showing that they do, most likely using reactive oxygen species. Given that CGD patients are exposed daily to hundreds of viable A. fumigatus conidia, yet considerable numbers of them survive years without infection, we reasoned that PMN use ROS-independent mechanisms to combat Aspergillus. We show that human PMN from both normal controls and CGD patients are equipotent at arresting the growth of Aspergillus conidia in vitro, indicating the presence of a reactive oxygen species-independent factor(s). Cell-free supernatants of degranulated normal and CGD neutrophils both suppressed fungal growth and were found to be rich in lactoferrin, an abundant PMN secondary granule protein. Purified iron-poor lactoferrin at concentrations occurring in PMN supernatants (and reported in human mucosal secretions in vivo) decreased fungal growth, whereas saturation of lactoferrin or PMN supernatants with iron, or testing in the presence of excess iron in the form of ferritin, completely abolished activity against conidia. These results demonstrate that PMN lactoferrin sequestration of iron is important for host defense against Aspergillus.
Identification of IL-7–Producing Cells in Primary and Secondary Lymphoid Organs Using IL-7–GFP Knock-In Mice

IL-7 is a cytokine crucial for development and maintenance of lymphocytes and other hematopoietic cells. However, how IL-7–expressing cells are distributed in lymphoid organs is not well known. To address this question, we established and analyzed IL-7–GFP knock-in mice. Thymic epithelial cells (TECs) expressed high GFP levels in the cortex and medulla, as detected with an anti-GFP Ab. Thymic mesenchymal cells also expressed GFP. Flow cytometry analysis suggested that cortical TECs expressed higher GFP levels than did medullary TECs. In bone marrow, immunohistochemistry indicated high levels of GFP in many VCAM-1+ mesenchymal stromal cells and in some VCAM-1− cells. Additionally, half of the VCAM-1+CD31− stromal cells and some platelet-derived growth factor receptor α+ stromal cells were GFP+, as detected by flow cytometry. Moreover, we detected GFP expression in fibroblastic reticular cells in the T cell zone and cortical ridge of lymph nodes. Remarkably, lymphatic endothelial cells (LECs) expressed GFP at high levels within the lymph node medulla, skin epidermis, and intestinal tissues. Additionally, we detected abundant IL-7 transcripts in isolated LECs, suggesting that LECs produce IL-7, a heretofore unknown finding. Furthermore, GFP is expressed in a subpopulation of intestinal epithelial cells, and that expression was markedly upregulated in a dextran sulfate sodium-induced acute colitis model. Overall, IL-7–GFP knock-in mice serve as a unique and powerful tool to examine the identity and distribution of IL-7–expressing cells in vivo.
The biocontrol endophytic bacterium Pseudomonas fluorescens PICF7 induces systemic defense responses in aerial tissues upon colonization of olive roots

Pseudomonas fluorescens PICF7, a native olive root endophyte and effective biocontrol agent (BCA) against Verticillium wilt of olive, is able to trigger a broad range of defense responses in root tissues of this woody plant. In order to elucidate whether strain PICF7 also induces systemic defense responses in above-ground organs, aerial tissues of olive plants grown under non-gnotobiotic conditions were collected at different time points after root bacterization with this endophytic BCA. A suppression subtractive hybridization (SSH) cDNA library, enriched in up-regulated genes, was generated. This strategy enabled the identification of 376 ESTs (99 contigs and 277 singlets), many of them related to response to different stresses. Five ESTs, involved in defense responses, were selected to carry out time-course quantitative real-time PCR (qRT-PCR) experiments aiming to: (1) validate the induction of these genes, and (2) shed light on their expression pattern along time (from 1 to 15 days). Induction of olive genes potentially coding for lipoxygenase 2, catalase, 1-aminocyclopropane-1-carboxylate oxidase, and phenylananine ammonia-lyase was thus confirmed at some time points. Computational analysis also revealed that different transcription factors were up-regulated in olive aerial tissues (i.e., JERF, bHLH, WRKY), as previously reported for roots. Results confirmed that root colonization by this endophytic bacterium does not only trigger defense responses in this organ but also mounts a wide array of systemic defense responses in distant tissues (stems, leaves). This sheds light on how olive plants respond to the “non-hostile” colonization by a bacterial endophyte and how induced defense response can contribute to the biocontrol activity of strain PICF7.
Characterization of Ultra High Temperature Ceramics via Transmission Electron Microscopy. Part 2: UHTCs sintered with addition of TaSi2

Abstract : Zirconium and hafnium diborides and carbides belong to the class of materials defined UHTCs (Ultra-High-Temperature-Ceramics). These materials are of particular interest because of the excellent and unique combination of properties which make them attractive candidates for high temperature applications where corrosion-wear-oxidation resistance are demanded. So far, the effort of the scientific community has been mainly directed to the study of processing procedures to improve the densification of these compounds. As very refractory compounds, these materials are very difficult to sinter to full density and temperatures as high as 2000-2400 degrees C and pressure-assisted techniques are required to achieve dense materials. The addition of sintering aids has represented a strategy to overcome the intrinsic low sinterability of these highly refractory compounds. However the reaction between sintering additives, the matrix and its oxides (ZrO2, HfO2, B2O3.) during the high temperature stage leads to formation of intergranular phases and/or solid solutions, which, in turn affect the high temperature properties. The control of secondary phases composition is therefore of paramount importance for tailoring the performance of these materials. As there is still lack of knowledge on these microstructural aspects, the main aim of this work was to characterize Ultra-High-Temperature-Ceramics via electron microscopy techniques.
Compositional Morphology for Word Representations and Language Modelling

This paper presents a scalable method for integrating compositional morphological representations into a vector-based probabilistic language model. Our approach is evaluated in the context of log-bilinear language models, rendered suitably efficient for implementation inside a machine translation decoder by factoring the vocabulary. We perform both intrinsic and extrinsic evaluations, presenting results on a range of languages which demonstrate that our model learns morphological representations that both perform well on word similarity tasks and lead to substantial reductions in perplexity. When used for translation into morphologically rich languages with large vocabularies, our models obtain improvements of up to 1.2 BLEU points relative to a baseline system using back-off n-gram models.
Impact of Friction on the Plough Body Draft Resistance

By using analytical correlations derived as a result of theoretical research, a computer algorithm has been worked out for simulating the functions of the plough body and the forces exerted by soil upon the operating parts, as well as its draft resistance. These correlations allow to determine the draft resistance of the plough depending on the parameters of its body, as well as to evaluate the impact of the physical and mechanical properties of soil, such as friction upon it. The greatest influence upon the draft resistance is exerted by soil hardness, density and slip resistance along the surfaces of the operating parts. The latter is also affected by soil adhesion, which particularly manifests itself in wet clay soils at lower temperatures. It has been clarified that the friction resistance constitutes 46 – 62 % of the total draft resistance of the plough body. The main ways of lowering the friction resistance and the total draft resistance of the plough are the introduction of a more rational design of its body having optimum parameters, decreasing the resistance of the share-mouldboard surface and the values of reactions of the supporting surfaces, as well as the application of antifriction materials and better modes of joining with tractors.
PET/CT in the management of thyroid cancers.

OBJECTIVE Thyroid cancer is the most common endocrine cancer. This review evaluates the established use of (18)F-FDG PET/CT in papillary, follicular, Hürthle cell, anaplastic, and medullary thyroid cancers. The significance of incidental diffuse and focal thyroid FDG uptake is discussed. The evolving value of non-FDG radiotracers, including (124)I, (18)F-dihydroxyphenylalanine, and (68)Ga somatostatin analogs, is summarized. CONCLUSION PET/CT is a valuable imaging test, in the appropriate clinical context, for the management of thyroid cancers.
Results of the ISDB-T system tests, as part of digital TV study carried out in Brazil

Since the year 2000, Mackenzie Presbyterian University has been carrying out lab and field tests to evaluate the performance of current DTV systems, with the aim of providing backing for the Brazilian Government's decision on the standard to be adopted. This paper presents the results of tests using the Japanese DTV system ISDB-T. Initially, the tests were done using a first generation prototype of the ISDB-T DTV set-top box. When DTV transmissions began in Japan in November 2003, the Brazilian tests were repeated using several new commercial set-top boxes. The main tests accomplished in 2000 were: measurement of the C/N ratio, behavior of the signal with multipath, Doppler effect and immunity to impulse noise. In 2003/2004, these tests were repeated using new receivers to analyze the evolution of the system. Furthermore, two new tests were introduced: resilience to phase noise and simultaneous transmission of two types of modulation in the same TV channel, in order to evaluate the band segmentation. Also, a one-segment DTV receiver (1STV) in a portable handset was tested in the laboratory.
Impact of solid-state fault current limiters on protection equipment in transmission and distribution systems

Solid-state fault current limiters (SSFCLs) offer a number of benefits when incorporated within transmission and distribution systems. SSFCLs can limit the magnitude of a fault current seen by a system using different methods, such as inserting a large impedance in the current path or controlling the voltage applied to the fault. However, these two methods can introduce a few problems when SSFCLs are used in a system along with other protection equipment such as protective relays and sensors. An experiment was designed and implemented to evaluate the behavior of the protective relays in a mimic distribution system with a SSFCL. This paper introduces the details of the experiment and the result shows that the distorted current and voltage waveforms resulting from the action of the SSFCL disturb the protective equipment.