Miracle-dz/UniFAR-FTUs huggingface dataset:
[A pathological study on pulmonary fibrosis caused by chronic obstructive pulmonary disease].

OBJECTIVE To estimate the morphologic characteristics of chronic obstructive pulmonary disease (COPD) induced pulmonary fibrosis. METHODS 41 autopsy cases of COPD were chosen as the study group and other 10 autopsy cases died from non-respiratory diseases as control group. Histochemical stain and image quantitative analysis were used to identify the type of collagen. RESULTS In 36 cases (88%) of study group, fibrosis proliferation could be seen in peri-bronchial area, especially in the bronchi under grade VI. Respiratory bronchiole and alveoli were also involved in 11 cases. The main component of collagen in fibrosis area was identified as type III collagen by sirius red stain, reticular fiber could also be seen by Gomori stain. The type III collagen in alveoli distributed interruptedly. Image quantitative analysis showed: the integral optical density (A) of type III collagen was much higher than that of type I collagen in peri-bronchial area (P < 0.01); Both A of type III and type I collagen in peri-bronchial area were higher than that in alveolar area (P < 0.01). Mucous purulent plugs, interrupted elastic fibers in bronchial wall and chronic inflammation accompanied with lymphocytes infiltration in fibrosis area could also be seen. CONCLUSIONS COPD induced pulmonary fibrosis distributed mainly in peri-bronchial area, especially in the bronchi under grade VI. The main component of proliferative collagen was type III collagen. The genesis of pulmonary fibrosis might be associated with chronic inflammation accompanied with lymphocytes. Peri-bronchial fibrosis, interrupt of elastic fibers in bronchial wall caused the bronchial lumen narrowed or collapsed making both airway obstruction and ventilation insufficiency deteriorated.
How slow is the k-means method?

The <b>k-means</b> method is an old but popular clustering algorithm known for its observed speed and its simplicity. Until recently, however, no meaningful theoretical bounds were known on its running time. In this paper, we demonstrate that the worst-case running time of <b>k-means</b> is <i>superpolynomial</i> by improving the best known lower bound from Ω<i>(n)</i> iterations to 2<sup>Ω(√<i>n</i>)</sup>.
Performance of BD Max StaphSR for Screening of Methicillin-Resistant Staphylococcus aureus Isolates among a Contemporary and Diverse Collection from 146 Institutions Located in Nine U.S. Census Regions: Prevalence of mecA Dropout Mutants

ABSTRACT This study determined the performance of BD Max StaphSR and the rate of methicillin-resistant Staphylococcus aureus (MRSA) with an unrecognized staphylococcal cassette chromosome mec (SCCmec) right-extremity junction (MREJ) region among 907 methicillin-resistant S. aureus (MRSA) and 900 methicillin-susceptible S. aureus (MSSA) isolates. The rate of mecA/mecC dropout mutants was also evaluated. Only three MRSA isolates (99.7% sensitivity; 904/907) were classified as MSSA by the BD Max StaphSR assay, due to negative results for MREJ. Eight MSSA isolates (99.1% sensitivity; 892/900) were assigned as MRSA. However, six of these MSSA isolates had the mecA gene confirmed by PCR and sequencing (99.8% sensitivity; 898/900). Overall, 7.1% (64/900) of MSSA isolates showed results compatible with a mecA dropout genotype.
A Study of Irradiation Stability of Carbon Nanotubes

We report preliminary results on studying the radiation stability of carbon nanotubes (CNs). Three different combinations of radiation and in situ characterization are used. Experiments include 30 keV electron bombardment with in situ characterization using a scanning electron microscope (SEM), 30 keV Ga ion bombardment with in situ SEM characterization, and 2 MeV proton irradiation with in situ electric resistance measurements. The study shows the degradation of CNs with dimensional shrinkage upon radiation, and the existence of a quasi steady state of defect creation and annealing.
Orthoptera, a new order of pollinator.

BACKGROUND AND AIMS Pollinator-mediated selection and evolution of floral traits have long fascinated evolutionary ecologists. No other plant family shows as wide a range of pollinator-linked floral forms as Orchidaceae. In spite of the large size of this model family and a long history of orchid pollination biology, the identity and specificity of most orchid pollinators remains inadequately studied, especially in the tropics where the family has undergone extensive diversification. Angraecum (Vandeae, Epidendroideae), a large genus of tropical Old World orchids renowned for their floral morphology specialized for hawkmoth pollination, has been a model system since the time of Darwin. METHODS The pollination biology of A. cadetii, an endemic species of the islands of Mauritius and Reunion (Mascarene Islands, Indian Ocean) displaying atypical flowers for the genus (white and medium-size, but short-spurred) was investigated. Natural pollinators were observed by means of hard-disk camcorders. Pollinator-linked floral traits, namely spur length, nectar volume and concentration and scent production were also investigated. Pollinator efficiency (pollen removal and deposition) and reproductive success (fruit set) were quantified in natural field conditions weekly during the 2003, 2004 and 2005 flowering seasons (January to March). KEY RESULTS Angraecum cadetii is self-compatible but requires a pollinator to achieve fruit set. Only one pollinator species was observed, an undescribed species of raspy cricket (Gryllacrididae, Orthoptera). These crickets, which are nocturnal foragers, reached flowers by climbing up leaves of the orchid or jumping across from neighbouring plants and probed the most 'fresh-looking' flowers on each plant. Visits to flowers were relatively long (if compared with the behaviour of birds or hawkmoths), averaging 16.5 s with a maximum of 41.0 s. At the study site of La Plaine des Palmistes (Pandanus forest), 46.5 % of flowers had pollen removed and 27.5 % had pollinia deposited on stigmas. The proportion of flowers that set fruit ranged from 11.9 % to 43.4 %, depending of the sites sampled across the island. CONCLUSIONS Although orthopterans are well known for herbivory, this represents the first clearly supported case of orthopteran-mediated pollination in flowering plants.
Glutamate synthesis has to be matched by its degradation – where do all the carbons go?

The central process in energy production is the oxidation of acetyl‐CoA to CO2 by the tricarboxylic acid (TCA, Krebs, citric acid) cycle. However, this cycle functions also as a biosynthetic pathway from which intermediates leave to be converted primarily to glutamate, GABA, glutamine and aspartate and to a smaller extent to glucose derivatives and fatty acids in the brain. When TCA cycle ketoacids are removed, they must be replaced to permit the continued function of this essential pathway, by a process termed anaplerosis. Since the TCA cycle cannot act as a carbon sink, anaplerosis must be coupled with cataplerosis; the exit of intermediates from the TCA cycle. The role of anaplerotic reactions for cellular metabolism in the brain has been studied extensively. However, the coupling of this process with cataplerosis and the roles that both pathways play in the regulation of amino acid, glucose, and fatty acid homeostasis have not been emphasized. The concept of a linkage between anaplerosis and cataplerosis should be underscored, because the balance between these two processes is essential. The hypothesis that cataplerosis in the brain is achieved by exporting the lactate generated from the TCA cycle intermediates into the blood and perivascular area is presented. This shifts the generally accepted paradigm of lactate generation as simply derived from glycolysis to that of oxidation and might present an alternative explanation for aerobic glycolysis.
Lessons learned: game design for large public displays

This paper presents the design and deployment of Polar Defence, an interactive game for a large public display. We designed this display based on a model of "users" and their interactions with large public displays in public spaces, which we derived from prior work. We conducted a four-day user study of this system in a public space to evaluate the game and its impact on the surrounding environment. Our analysis showed that the installation successfully encouraged participation among strangers, and that its design and deployment addressed many of the challenges described by prior research literature. Finally, we reflect on this deployment to provide design guidance to other researchers building large interactive public displays for public spaces.
The Glyceraldehyde-3-Phosphate Dehydrogenase and the Small GTPase Rab 2 Are Crucial for Brucella Replication

The intracellular pathogen Brucella abortus survives and replicates inside host cells within an endoplasmic reticulum (ER)-derived replicative organelle named the “Brucella-containing vacuole” (BCV). Here, we developed a subcellular fractionation method to isolate BCVs and characterize for the first time the protein composition of its replicative niche. After identification of BCV membrane proteins by 2 dimensional (2D) gel electrophoresis and mass spectrometry, we focused on two eukaryotic proteins: the glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and the small GTPase Rab 2 recruited to the vacuolar membrane of Brucella. These proteins were previously described to localize on vesicular and tubular clusters (VTC) and to regulate the VTC membrane traffic between the endoplasmic reticulum (ER) and the Golgi. Inhibition of either GAPDH or Rab 2 expression by small interfering RNA strongly inhibited B. abortus replication. Consistent with this result, inhibition of other partners of GAPDH and Rab 2, such as COPI and PKC ι, reduced B. abortus replication. Furthermore, blockage of Rab 2 GTPase in a GDP-locked form also inhibited B. abortus replication. Bacteria did not fuse with the ER and instead remained in lysosomal-associated membrane vacuoles. These results reveal an essential role for GAPDH and the small GTPase Rab 2 in B. abortus virulence within host cells.
Characterization of plasmids that encode for the K88 colonization antigen

K88 antigen, and important virulence factor in porcine enteropathogenic Escherichia coli (EEC), can be transferred along with the ability to ferment the trisaccharide raffinose (Raf). The plasmids from a number of EEC strains that encode these two properties were isolated and characterized. In most strains the K88 and Raf genes were found on a single nonconjugative plasmid approximately 50 x 10(6) daltons in size. This plasmid core was conserved with only slight variation among the strains tested. In some transconjugants, larger conjugative plasmids were observed that were apparently recombinants between the Raf/K88 plasmid and a transfer fa(tor. Occasionally plasmids carrying only the raffinose fermentation genes arose by deletion of a deoxyribonucleic acid segment of about 20 x 10(6) daltons that included the K88 antigen gene(s).
Maternal plasma levels of vascular endothelial growth factor in normotensive pregnancies and in pregnancies complicated by pre‐eclampsia

We have measured the level of vascular endothelial growth factor (VEGF) in maternal plasma during normotensive pregnancy and in pregnancies complicated by pre‐eclampsia. VEGF was measured using a competitive enzyme immunoassay. Plasma VEGF was significantly elevated (P<0.0001) in the pre‐eclamptic group (median value 32.7 ng mL−1, range 10.3–64.0), compared with the normotensive group (median value 11.7 ng mL−1, range 6.3–24.3). VEGF is a potent regulator of endothelial cell function. The increased level found in women with pre‐eclampsia indicates that VEGF may be involved in the maternal endothelial cell dysfunction associated with this condition. An increase in VEGF, a potent regulator of microvascular permeability, may also contribute to the extravasation of plasma proteins and the subsequent development of proteinuria, both characteristic features of pre‐eclampsia.
A novel twist on molecular interactions between thioredoxin and nicotinamide adenine dinucleotide phosphate‐dependent thioredoxin reductase

The ubiquitous disulfide reductase thioredoxin (Trx) regulates several important biological processes such as seed germination in plants. Oxidized cytosolic Trx is regenerated by nicotinamide adenine dinucleotide phosphate (NADPH)‐dependent thioredoxin reductase (NTR) in a multistep transfer of reducing equivalents from NADPH to Trx via a tightly NTR‐bound flavin. Here, interactions between NTR and Trx are predicted by molecular modelling of the barley NTR:Trx complex (HvNTR2:HvTrxh2) and probed by site directed mutagenesis. Enzyme kinetics analysis reveals mutants in a loop of the flavin adenine dinucleotide (FAD)‐binding domain of HvNTR2 to strongly affect the interaction with Trx. In particular, Trp42 and Met43 play key roles for recognition of the endogenous HvTrxh2. Trx from Arabidopsis thaliana is also efficiently recycled by HvNTR2 but turnover in this case appears to be less dependent on these two residues, suggesting a distinct mode for NTR:Trx recognition. Comparison between the HvNTR2:HvTrxh2 model and the crystal structure of the Escherichia coli NTR:Trx complex reveals major differences in interactions involving the FAD‐ and NADPH‐binding domains as supported by our experiments. Overall, the findings suggest that NTR:Trx interactions in different biological systems are fine‐tuned by multiple intermolecular contacts. Proteins 2014; 82:607–619. © 2013 Wiley Periodicals, Inc.
Structural Changes in the Carboxyl Terminus of the Gap Junction Protein Connexin43 Indicates Signaling between Binding Domains for c-Src and Zonula Occludens-1*

Regulation of cell-cell communication by the gap junction protein connexin43 can be modulated by a variety of connexin-associating proteins. In particular, c-Src can disrupt the connexin43 (Cx43)-zonula occludens-1 (ZO-1) interaction, leading to down-regulation of gap junction intercellular communication. The binding sites for ZO-1 and c-Src correspond to widely separated Cx43 domains (∼100 residues apart); however, little is known about the structural modifications that may allow information to be transferred over this distance. Here, we have characterized the structure of the connexin43 carboxyl-terminal domain (Cx43CT) to assess its ability to interact with domains from ZO-1 and c-Src. NMR data indicate that the Cx43CT exists primarily as an elongated random coil, with two regions of α-helical structure. NMR titration experiments determined that the ZO-1 PDZ-2 domain affected the last 19 Cx43CT residues, a region larger than that reported to be required for Cx43CT-ZO-1 binding. The c-Src SH3 domain affected Cx43CT residues Lys-264–Lys-287, Ser-306–Glu-316, His-331–Phe-337, Leu-356–Val-359, and Ala-367–Ser-372. Only region Lys-264–Lys-287 contains the residues previously reported to act as an SH3 binding domain. The specificity of these interactions was verified by peptide competition experiments. Finally, we demonstrated that the SH3 domain could partially displace the Cx43CT-PDZ-2 complex. These studies represent the first structural characterization of a connexin domain when integrated in a multimolecular complex. Furthermore, we demonstrate that the structural characteristics of a disordered Cx43CT are advantageous for signaling between different binding partners that may be important in describing the mechanism of channel closure or internalization in response to pathophysiological stimuli.
Languages of Styles : Ontology , Representation and Reasoning about Aesthetics in a Computational Framework

Having spent a century or more focused primarily on other goal-solving manufacturing problems, lowering costs, making goods and services widely available [. ] we are increasingly engaged in making our world special. We are demanding and creating an enticing, stimulating, diverse, and beautiful world. We want our vacuum cleaners and mobile phones to sparkle, our bathroom faucets and desk accessories to express our personalities. [. ] We demand trees in our parking lots, peaked roofs and decorative facades on our supermarkets, auto dealerships as swoopy and stylish as the cars they sell.
Factors Affecting Catalase Expression in Pseudomonas aeruginosa Biofilms and Planktonic Cells

ABSTRACT Previous work with Pseudomonas aeruginosa showed that catalase activity in biofilms was significantly reduced relative to that in planktonic cells. To better understand biofilm physiology, we examined possible explanations for the differential expression of catalase in cells cultured in these two different conditions. For maximal catalase activity, biofilm cells required significantly more iron (25 μM as FeCl3) in the medium, whereas planktonic cultures required no addition of iron. However, iron-stimulated catalase activity in biofilms was still only about one-third that in planktonic cells. Oxygen effects on catalase activity were also investigated. Nitrate-respiring planktonic cultures produced approximately twice as much catalase activity as aerobic cultures grown in the presence of nitrate; the nitrate stimulation effect could also be demonstrated in biofilms. Cultures fermenting arginine had reduced catalase levels; however, catalase repression was also observed in aerobic cultures grown in the presence of arginine. It was concluded that iron availability, but not oxygen availability, is a major factor affecting catalase expression in biofilms.
Peptide-based optical contrast agents for targeting of intestinal malignancies

Intestinal tumors exhibit cell surface properties that differ from neighboring healthy epithelia and thus allow tumor cell-specific molecular targeting. Ganglioside GM1 is such a discriminatory target. Although expressed in the apical membrane of all intestinal epithelial cells it is accessible for particle conjugated ligands on tumor cells only. In order to exploit this phenomenon we want to develop a nanoparticulate optical contrast agent equipped with a peptidic GM1 binding ligand. For identification of ligand peptides a novel screening platform was devised where potential ganglioside GM1-binding peptides are generated on glass capillary plates using microfluidic non-contact arraying techniques and screened in situ for binding of fluorophor-labeled GM1. These three-dimensional supports are easy to handle and show better sensitivity than either flat glass or membrane supports because of their large inner surface and low interference with readout systems. A custom fluorescence reader was designed to comply with the specific optical behaviour of peptide arrays synthesized on microcapillary plates. This reader uses a small numerical aperture for excitation and a large numerical aperture for detection in epifluorescence-mode. Background noise from fluorescence and Raman scattering is reduced by time gated photon counting. Peptides showing affinity to ganglioside GM1 will be conjugated to a nano-particulate carrier bearing a fluorescent dye. The resulting optical contrast agent shall be used for fluorescence endoscopic intestinal tumor screening.
Angiotensin Converting Enzyme Regulates Cell Proliferation and Migration

Background The angiotensin-I converting enzyme (ACE) plays a central role in the renin-angiotensin system, acting by converting the hormone angiotensin-I to the active peptide angiotensin-II (Ang-II). More recently, ACE was shown to act as a receptor for Ang-II, and its expression level was demonstrated to be higher in melanoma cells compared to their normal counterparts. However, the function that ACE plays as an Ang-II receptor in melanoma cells has not been defined yet. Aim Therefore, our aim was to examine the role of ACE in tumor cell proliferation and migration. Results We found that upon binding to ACE, Ang-II internalizes with a faster onset compared to the binding of Ang-II to its classical AT1 receptor. We also found that the complex Ang-II/ACE translocates to the nucleus, through a clathrin-mediated process, triggering a transient nuclear Ca2+ signal. In silico studies revealed a possible interaction site between ACE and phospholipase C (PLC), and experimental results in CHO cells, demonstrated that the β3 isoform of PLC is the one involved in the Ca2+ signals induced by Ang-II/ACE interaction. Further studies in melanoma cells (TM-5) showed that Ang-II induced cell proliferation through ACE activation, an event that could be inhibited either by ACE inhibitor (Lisinopril) or by the silencing of ACE. In addition, we found that stimulation of ACE by Ang-II caused the melanoma cells to migrate, at least in part due to decreased vinculin expression, a focal adhesion structural protein. Conclusion ACE activation regulates melanoma cell proliferation and migration.
Respiratory infection in noncystic fibrosis bronchiectasis

Purpose of review We highlight some of the main developments in the investigation and management of bronchiectasis, a condition causing susceptibility to airway infections and in more severe cases chronic bronchial suppuration. Recent findings Chronic infection with Pseudomonas aeruginosa and poor lung function adversely influence long-term prognosis. Investigation of the underlying cause of bronchiectasis leads to additional therapy in a higher proportion of patients than previously thought. Based on current data, inhaled corticosteroid cannot be recommended for routine use in patients with bronchiectasis. Nontuberculous mycobacterial infections have been associated with both aspergillus and gastrooesophageal reflux. There is new evidence supporting the practice of regular chest physiotherapy. Summary Despite some improvement in the evidence-based guide to management in noncystic fibrosis bronchiectasis, there remains a serious lack of randomized controlled trials directing therapy.
Patterns of Hsp gene expression in ectothermic marine organisms on small to large biogeographic scales1

Abstract The goal of my research program is to employ biochemical and molecular techniques to gain ecological insight into the role of temperature in setting species' distribution patterns in the marine environment. Our central focus is the study of the environmental regulation of gene expression, where we are particularly interested in a set of inducible molecular chaperones, the heat-shock proteins (Hsps), and how the expression of these genes varies with the thermal history of organisms in natural populations. The primary study organisms are intertidal invertebrates and marine fish that experience dramatic changes in body temperature on varying temporal and spatial scales. In this review, I present studies that address the variable expression of Hsps, how these genes are differentially regulated in ectothermic animals in response to ecologically relevant temperature conditions, and how such plasticity in gene expression contributes to physiological plasticity in the environment.
A beam current density monitor for intense electron beams

Abstract : The authors describe a new type of electric probe for mapping the radial current density profile of high-energy, high current electron beams. The idea of developing an electrically sensitive probe for these conditions was originally suggested to one of the authors during a year's visit to the Lawrence Livermore National Laboratory. The resulting probe is intended for use on the Experimental Test Accelerator (ETA) and the Advanced Test Accelerator at that laboratory. This report discusses in detail: the mechanical design, the electrical response, and temperature effects, as they pertain to the electric probe, and describe the first experimental results obtained using this probe on ETA.