Miracle-dz/UniFAR-FTUs huggingface dataset:
Mycobacterium tuberculosis-Reactive CD8+ T Lymphocytes: The Relative Contribution of Classical Versus Nonclassical HLA Restriction1

Previous studies in mice and humans models have suggested an important role for CD8+ T cells in host defense to Mycobacterium tuberculosis (Mtb). In humans, CD8+ Mtb-reactive T cells have been described that are HLA-A2-, B52-, as well as CD1-restricted. Recently, we have described Mtb-specific CD8+ T cells that are neither HLA-A-, B-, or C- nor group 1 CD1-restricted. At present, little is known about the relative contribution of each of these restriction specificities to the overall CD8+ response to Mtb. An IFN-γ enzyme-linked immunospot assay was used to determine the frequency of Mtb-reactive CD8+ T cells directly from PBMC. The effector cell frequency among five healthy purified protein derivative-positive subjects was 1/7,600 ± 4,300 compared with 1/16,000 ± 7,000 in six purified protein derivative-negative controls. To determine the frequencies of classically, CD1-, and nonclassically restricted cells, a limiting dilution analysis was performed. In one purified protein derivative-positive subject, 192 clones were generated using Mtb-infected dendritic cells (DC). Clones were assessed for reactivity against control autologous DC, Mtb-infected autologous DC, and HLA-mismatched CD1+ targets (DC), as well as HLA-mismatched CD1− targets (macrophages). Of the 96 Mtb-reactive CD8+ T cell clones, four (4%) were classically restricted and 92 (96%) were nonclassically restricted. CD1-restricted cells were not detected. Of the classically restricted cells, two were HLA-B44 restricted and one was HLA-B14 restricted. These results suggest that while classically restricted CD8+ lymphocytes can be detected, they comprise a relatively small component of the overall CD8+ T cell response to Mtb. Further definition of the nonclassical response may aid development of an effective vaccine against tuberculosis.
Visual Monocular 3D Reconstruction and Component Identification for Small Spacecraft

A monocular vision pose estimation and identification algorithm used on a small 1 spacecraft for future orbital servicing is studied in this paper. A tracker spacecraft equipped with 2 a short-range vision system is proposed to recover the 3D structural model of a space target in 3 orbit and automatically identify its solar panels and main body using only visual information from 4 an onboard camera. The proposed reconstruction and identification framework is tested using 5 structure-from-motion and point cloud identification methods. The Efficient Perspective-n-Points 6 (EPnP) descriptor is used for pose estimation. Triangulated points are used for component 7 segmentation by means of orientation histogram descriptors. Experimental results based on 8 laboratory images of a spacecraft model show the effectiveness and robustness of our approach. 9
Streptococcus pyogenes and Lactobacillus rhamnosus differentially induce maturation and production of Th1‐type cytokines and chemokines in human monocyte‐derived dendritic cells

Dendritic cells (DCs) are the most efficient antigen‐presenting cells and thus, have a major role in regulating host immune responses. In the present study, we have analyzed the ability of Gram‐positie, pathogenic Streptococcus pyogenes and nonpathogenic Lactobacillus rhamnosus to induce the maturation of human monocyte‐derived DCs. Stimulation of DCs with S. pyogenes resulted in strong expression of DC costimulatory molecules CD80, CD83, and CD86 accompanied with a T helper cell type 1 (Th1) cytokine and chemokine response. S. pyogenes also induced interleukin (IL)‐2 and IL‐12 production at mRNA and protein levels. In addition, IL‐23 and IL‐27 subunits p40, p19, p28, and EBI3 were induced at mRNA level. In contrast, L. rhamnosus‐stimulated DCs showed only moderate expression of costimulatory molecules and produced low levels of cytokines and chemokines. Furthermore, no production of IL‐2 or IL‐12 family cytokines was detected. Bacteria‐induced DC maturation and especially cytokine and chemokine production were reduced when bacteria were heat‐inactivated. Our results show that human monocyte‐derived DCs respond differently to different Gram‐positive bacteria. Although pathogenic S. pyogenes induced a strong Th1‐type response, stimulation with nonpathogenic L. rhamnosus resulted in development of semi‐mature DCs characterized by moderate expression of costimulatory molecules and low cytokine production.
Periodically poled KTiOAsO4 for second harmonic generation in the green region

We present high-quality room temperature periodic poling of KTiOAsO<sub>4</sub> with a period of 8.49 μm. The crystals are evaluated for SHG at 533 nm, and show d<sub>eff</sub> = 10.5 pm/V and η<sub>norm</sub> = 1.19%/Wcm.
Misfolded proinsulin accumulates in expanded pre‐Golgi intermediates and endoplasmic reticulum subdomains in pancreatic beta cells of Akita mice

A missense mutation of the insulin 2 gene (Cys96Tyr) in Akita mice disrupting one of the two interchain disulfide bonds results in intracellular accumulation of misfolded proinsulin. We analyzed the secretory pathway of pancreatic β cells by electron microscopy and morphometry and identified sites of proinsulin accumulation by quantitative immunogold electron microscopy in this protein‐folding disease. In Akita mice β cells, the volume density of dilated endoplasmic reticulum subdomains was increased by 2.9‐fold, resulting in a 1.7‐fold increased volume density of the entire rough endoplasmic reticulum. The volume density of pre‐Golgi intermediates was increased by 4.9‐fold, and that of the Golgi apparatus was increase by 3.4‐fold. The relative labeling intensity for proinsulin was 2.1‐fold higher in dilated endoplasmic reticulum subdomains and 2.9‐fold higher in pre‐Golgi intermediates as compared with narrow endoplasmic reticulum, resulting in a significantly different distribution pattern between Akita and control mice β cells (X2= 29.97, P<0.001). The numerical density of insulin secretory granules was equal in Akita and control mice β cells. However, their volume density and average volume were reduced to 20% and their average diameter to 58% in Akita mice. Together, these data demonstrate that misfolded proinsulin accumulates mainly in pre‐Golgi intermediates and to a lesser extent in dilated endoplasmic reticulum subdomains, providing evidence for the importance of pre‐Golgi intermediates in a protein folding disease.
Heritability and genetic correlations of obesity-related phenotypes among Roma people

Background: The Roma people are particularly vulnerable to developing obesity and related diseases, due to their social and ethnic backgrounds. However, little is known about the genetic and/or environmental factors affecting the variability of obesity-related traits among the Roma population. Aim: The aim of the present study was to estimate heritabilities and common genetic and environmental influences of obesity-related phenotypes in a sample of Roma people living in the Greater Bilbao region (Basque Country; Spain). Subjects and methods: Three hundred and seventy-two individuals from 50 large, extended and highly consanguineous pedigrees were phenotyped for anthropometric traits related to obesity. Heritability estimates were assessed for all quantitative traits and bivariate analyses were conducted to assess the phenotypic, genetic and environmental correlations among these traits. Results: Significant heritable components (p < 0.01) ranging from 0.25–0.68 exist for the studied phenotypes. Heritability for WHR (h2 = 0.60) considerably surpasses the usual heritability estimates on family-based studies ( < 0.30). Measures of overall fatness (BMI, CF and SF) show stronger correlations with each other than body fat distribution traits (WHR, CI and TER). Conclusions: The study concluded that the Greater Bilbao Roma population is genetically predisposed to abdominal fat distribution. Variation in body mass is highly associated with variation in adiposity. However, overall fatness and adiposity distribution does not seem to share major common genetic factors, although common environmental factors operate between them.
Using Qualitative Inquiry and Participatory Research Approaches to Develop Prevention Research: Validating a Life Course Perspective

Application of life course theory (LCT) holds promise for advancing knowledge toward the elimination of health disparities. This article validates the usefulness of employing a life course perspective when conducting health disparities research. We provide an overview of LCT as it applies to our research program in prevention of human immunodeficiency virus (HIV) among Latino teen parents. We illustrate the goodness-of-fit of our research with the basic premises of LCT. Though early adverse life experiences impact health over the lifespan, strength-based HIV prevention programs designed for Latino teen parents that recognize the reality of their lives may alter their health trajectory.
Sequential Effects in a Two-Choice Serial Reaction Task

Twenty-four subjects performed a symbolic two-choice serial reaction task under four conditions. These were with a delay from previous response to onset of next stimulus of 100 millisec, 600 millisec. , 2 sec. , and a fourth condition of 2 sec. delay with verbal prediction of the next stimulus. A positive recency or repetition effect occurred at 100 millisec. delay where RTs to repeated stimuli were faster than RTs to alternate stimuli. At 600 millisec. this effect was still present, though much reduced. The 2 sec. delay gave a negative recency effect where RTs were slower to repeated than to alternate stimuli. This effect increased significantly with simultaneous prediction of the next stimulus. The verbal predictions themselves displayed negative recency. Run analysis of the four conditions revealed striking differences. These results emphasize the need for analysing the microstructure of choice RT situations and reveal deficiencies in present models.
Polymeric quantum mechanics and the zeros of the Riemann zeta function

We analize the Berry-Keating model and the Sierra and Rodriguez-Laguna Hamiltonian within the polymeric quantization formalism. By using the polymer representation, we obtain for both models, the associated polymeric quantum Hamiltonians and the corresponding stationary wave functions. The self-adjointness condition provide a proper domain for the Hamiltonian operator and the energy spectrum, which turned out to be dependent on an introduced scale parameter. By performing a counting of semiclassical states, we prove that the polymer representation reproduces the smooth part of the Riemann-von Mangoldt formula, and introduces a correction depending on the energy and the scale parameter, which resembles the fluctuation behavior of the Riemann zeros.
Factors defining a pacemaker region for synchrony in the hippocampus

Synchronous activities of neuronal populations are often initiated in a pacemaker region and spread to recruit other regions. Here we examine factors that define a pacemaker site. The CA3a region acts as the pacemaker for disinhibition induced synchrony in guinea pig hippocampal slices and CA3b is a follower region. We found CA3a pyramidal cells were more excitable and fired in bursts more frequently than CA3b cells. CA3a cells had more complex dendritic arbors than CA3b cells especially in zones targetted by recurrent synapses. The product of the density of pyramidal cell axon terminals and dendritic lengths in innervated zones predicted a higher recurrent synaptic connectivity in the CA3a than in the CA3b region. We show that some CA3a cells but few CA3b cells behave as pacemaker cells by firing early during population events and by recruiting follower cells to fire. With a greater excitability and enhanced synaptic connectivity these CA3a cells may also possess initiating functions for other hippocampal ensemble activities initiated in this region.
Generation of Folded Terrains from Simple Vector Maps

While several terrain generation methods focused on plausible watersheds, the fact that most mountains should not be isolated but rather be part of wider scale mountain ranges was seldom considered. In this work, we present the first procedural method that generates folded terrains from simple user input, in the form of some sparse peak distribution on a vector map. The key idea is to infer possible continental plates from this distribution and to use simplified plate tectonics to generate relevant terrain folds. The resulting terrain with large-scale folds, computed in real-time, can be further refined using standard erosion simulation. This leads to detailed terrains with plausible mountain ranges that match the peak distributions and main rivers specified on simple vector maps.
Immune surveillance of mouse brain perivascular spaces by blood‐borne macrophages

Virchow–Robin's perivascular spaces lie between the basement membrane around pericytes and the basement membrane at the surface of the glia limitans of the brain vessels. They are directly connected to the subpial space and harbour a population of cells distinct from pericytes, perivascular microglia and other cells within perivascular spaces (e.g. T cells and mast cells) in their ability to quickly phagocytose particles from the cerebrospinal fluid (CSF). Morphology, function, and cell surface proteins of these perivascular cells suggest an origin from the monocyte/macrophage lineage. It is currently unclear to what extent these brain perivascular cells represent a resident population of histiocytes or undergo continuous supplementation from blood monocytes. Using transplants of green‐fluorescent‐protein (GFP)‐transfected bone marrow cells, we therefore investigated the replacement of perivascular cells by blood‐borne macrophages in adult mice. GFP‐positive cells in the perivascular spaces were found as early as 2 weeks post transplantation. The substitution of host perivascular cells by donor‐derived macrophages was then evaluated using immunocytochemistry and intraventricular injection of hydrophilic rhodamine‐fluorescent tracers. Such tracers diffuse along perivascular spaces and are subsequently phagocytosed by perivascular cells leading to stable phagocytosis‐dependent labelling. Thus, the population of newly immigrated macrophages could be related to the total number of perivascular macrophages. This approach revealed a continuous increase of donor‐derived perivascular cells. At 14 weeks post transplantation, all perivascular cells were donor‐derived. These data show that brain perivascular cells are a population of migratory macrophages and not resident histiocytes.
Mechanism of extraction of chymotrypsin into isooctane at very low concentrations of aerosol OT in the absence of reversed micelles

Chymotrypsin is easily extracted from an aqueous solution into isooctane containing the anionic surfactant aerosol OT (AOT). The concentration of AOT needed to efficiently extract 0.5 mg/mL CMT is as low as 1 mM and as low as 0.2 mM AOT was sufficient to extract the protein into isooctane. The extraction process was unaffected by 10% (v/v) ethyl acetate in the isooctane phase. Moreover, spectroscopic analysis by electron paramagnetic resonance indicated that CMT did not exist inside a discreet water pool of a reversed micelle. Calculations of the number of AOT molecules associated per extracted CMT molecule indicate that only ca. 30 surfactant molecules interact with the protein, a value too low for reversed micellar incorporation of the protein in isooctane. These studies suggested that reversed micelles do not need to be involved in the actual transfer of the protein from the aqueous to the organic phase and protein solubilization in the organic phase is possible in the absence of reversed micelles. Based on these findings, a new mechanism has been proposed herein for protein extraction via the phase transfer method involving ionic surfactants. The central theme of this mechanism is the formation of an electrostatic complex between CMT and AOT at the aqueous/organic interface between AOT and CMT, thereby leading to the formation of a hydrophobic species that partitions into the organic phase. Consistent with this mechanism, the efficiency of extraction is dependent on the interfacial mass transfer, the concentrations of CMT and AOT in the aqueous and organic phases, respectively; the ionic strength of the aqueous phase; and the presence of various cosolvents. © 1994 John Wiley & Sons, Inc.
Function and expression of the epithelial Ca2+ channel family: comparison of mammalian ECaC1 and 2

1 The epithelial Ca2+ channel (ECaC) family represents a unique group of Ca2+‐selective channels that share limited homology to the ligand‐gated capsaicin receptors, the osmolarity‐sensitive channel OTRPC4, as well as the transient receptor potential family. Southern blot analysis demonstrated that this family is restricted to two members, ECaC1 and ECaC2 (also named CaT1). 2 RT‐PCR analysis demonstrated that the two channels are co‐expressed in calbindin‐D‐containing epithelia, including small intestine, pancreas and placenta, whereas kidney and brain only express ECaC1 and stomach solely ECaC2. 3 From an electrophysiological point of view, ECaC1 and ECaC2 are highly similar channels. Differences concern divalent cation permeability, the kinetics of Ca2+‐dependent inactivation and recovery from inactivation. 4 Ruthenium red is a potent blocker of ECaC activity. Interestingly, ECaC2 has a 100‐fold lower affinity for ruthenium red (IC50 9 ± 1 μm) than ECaC1 (IC50 121 ± 13 nm). 5 ECaCs are modulated by intracellular Mg2+ and ATP. ECaC1 and ECaC2 activity rapidly decay in the absence of intracellular ATP. This effect is further accelerated at higher intracellular Mg2+ concentrations. 6 In conclusion, ECaC1 and ECaC2 are homologous channels, with an almost identical pore region. They can be discriminated by their sensitivity for ruthenium red and show differences in Ca2+‐dependent regulation.
Cell wall deformation and Staphylococcus aureus surface sensing

Bacterial contaminations are one of the major causes for implant failure and cause significant reduction in patient’s quality of life. Therefore, understanding the underlying factors that contribute to bacteria-biomaterial interactions are of utmost importance for researchers and health care professionals who develop biomaterials and new anti-bacterials. In this context, the aim of this thesis was to evaluate the role of adhesion forces in the response of bacteria to their adhering state. To this end, we used a model pathogen Staphylococcus aureus, common in biomaterial associated infections and several of its isogenic mutants and applied Atomic Force Microscopy (AFM) and Surface Enhanced Fluorescence (SEF) to quantify adhesion forces and cell wall deformation, respectively. Bacterial response was evaluated in terms of gene expression on different biomaterials commonly used in orthopedic implants. Our findings show that S. aureus experiences adhesion forces in the range 1.0 – 5.0 nN on the three biomaterials Stainless Steel (SS), Poly-Methylmethacrylate (PMMA) and Polyethylene (PE) and provide proof of concept that adhesion forces induce cell wall deformation upon adhesion to SS using SEF. At the molecular level we show that, as adhesion forces increase between the bacteria and the substratum, icaA gene expression and the expression of matrix components (Poly-N-acethyglocosamine and eDNA) decreases, suggesting a direct impact of adhesion forces on gene expression. Furthermore, presence of chemical stress nisin (antibiotic) in combination with mechanical stress (adhesion forces), increases the expression of the two-component system nisin-associated-sensitivity-response-regulator (NsaRS) and its downstream transporter NsaAB involved in pumping out nisin. Finally, our results confirm that adhesion forces and subsequent cell wall deformation upon surface adhesion determine the adaptability of S. aureus to the surface it adheres.
formation to epigenetic regulation and transcription termination GC skew at the 5 ' and 3 ' ends of human genes links R-loop

P<P Published online July 18, 2013 in advance of the print journal. Preprint Accepted likely to differ from the final, published version. Peer-reviewed and accepted for publication but not copyedited or typeset; preprint is License Commons Creative . http://creativecommons.org/licenses/by-nc/3.0/ described at a Creative Commons License (Attribution-NonCommercial 3.0 Unported), as ). After six months, it is available under http://genome.cshlp. org/site/misc/terms.xhtml first six months after the full-issue publication date (see This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the
Tomotherapy after Pleurectomy/Decortication or Biopsy for Malignant Pleural Mesothelioma Allows the Delivery of High Dose of Radiation in Patients with Intact Lung

Introduction: This study aimed to assess the safety of high doses of radiation delivered with tomotherapy to the intact lung after radical pleurectomy/decortication or biopsy for malignant pleural mesothelioma (MPM). Methods: Twenty-eight patients were enrolled in this prospective study and underwent adjuvant or definitive tomotherapy after radical pleurectomy/decortication (n = 20) or pleural biopsy (n = 8) for MPM. The dose prescribed to the planning target volume, defined as the entire hemithorax, including chest-wall incisions and drain sites and excluding the intact lung, was 50 Gy delivered in 25 fractions. All patients underwent fluorodeoxyglucose-positron emission tomography for staging after surgery. Any fluorodeoxyglucose-avid areas or regions of particular concern for residual disease were given a simultaneous boost of radiotherapy to 60 Gy. Specific lung dosimetric parameters were reported. Toxicity was graded using the modified Common Toxicity Criteria version 3.0. Results: The median follow-up was of 19 months (range, 6–29 months). Five patients (17.8%) experienced severe respiratory symptoms corresponding to grade 2 pneumonitis in three cases, and grade 3 pneumonitis in two cases. No fatal respiratory toxicity was reported. Controlateral lung V5 was strongly correlated with the risk of pneumonitis. Patients who developed grade 2 and 3 pneumonitis had a higher controlateral lung V5 (mean V5=32%) than those without pneumonitis (mean V5=17%) (p=0.002). Other two grade 3 toxicities were registered: one severe pain to the chest wall, and one severe thrombocytopenia. Conclusions: Tomotherapy allows the safe delivery of high dose of radiation to the hemithorax of MPM patients with intact lung.
Model Reduction for Switched Linear Discrete-Time Systems with polytopic uncertainties and arbitrary switching

Abstract In this paper, the problem of H1 model reduction for switched linear discrete-time systems with polytopic uncertainties is investigated. A reduced-order switched model is constructed for a given robustly stable switched system, which has the same structural polytopic uncertainties as the original system such that the resulting error system is robustly asymptotically stable and an H1 error performance is guaranteed. A sufficient condition for the existence of the desired reduced-order model is derived and formulated in terms of a set of linear matrix inequalities. By solving the corresponding convex optimization problem in such existence condition, the vertex system of reduced-order model can be obtained, which also provides a suboptimal H1 gain for the error system between the original system and the reduced-order model. A numerical example is given to show the effectiveness and the potential of the proposed techniques.