Miracle-dz/UniFAR-FTUs huggingface dataset:
Pertussis toxin activates platelets through an interaction with platelet glycoprotein Ib

Platelets present a unique model to study the B-oligomer effects of pertussis toxin because they become activated in response to the B oligomer but are not susceptible to ADP-ribosylation by the holotoxin. In these studies, the B oligomer of pertussis toxin caused concentration-dependent platelet activation, as determined by increases in intracellular calcium concentration, dense granule secretion, and platelet aggregation. Stirring was required for pertussis toxin to increase intracellular calcium. A monoclonal antibody against platelet glycoprotein Ib abolished increases in intracellular calcium concentration and increased the latency and reduced the slope of the aggregation response elicited by the B oligomer. Pertussis toxin also evoked [14C]serotonin release from platelets, and this effect was inhibited, though not eliminated, by an antibody against platelet glycoprotein Ib. Binding of pertussis toxin to glycoprotein Ib was observed after nonreducing sodium dodecyl sulfate-polyacrylamide gel electrophoresis. These data suggest that the B oligomer of pertussis toxin induces platelet activation mediated, at least in part, by an interaction with platelet glycoprotein Ib.
Fast Digital Simulation of Spiking Neural Networks and Neuromorphic Integration with Spikelab

We present a simulation environment called SPIKELAB which incorporates a simulator that is able to simulate large networks of spiking neurons using a distributed event driven simulation. Contrary to a time driven simulation, which is usually used to simulate spiking neural networks, our simulation needs less computational resources because of the low average activity of typical networks. The paper addresses the speed up using an event driven versus a time driven simulation and how large networks can be simulated by a distribution of the simulation using already available computing resources. It also presents a solution for the integration of digital or analogue neuromorphic circuits into the simulation process.
THE ACTIVITY OF URIDINE DIPHOSPHATE GLUCOSE-GLYCOGEN SYNTHETASE IN SOME EMBRYONIC TISSUES

Uridine diphosphate glucose (UDPG)-glycogen synthetase has been studied using chemical and histochemical methods. Activity was demonstrated in whole egg and in homogenates of whole 3-day old chick embryos, in the heart and skeletal muscle from the 5th day and in the liver from the 7th day of incubation onwards. The activity increases with age until the 16th day at which time a sharp fall was noted in all tissues studied. Enzyme activity was demonstrated also in heart, liver, skeletal muscle and brain of rat embryos from the 14th day onwards. In these tissues the activity increases with age until birth. The appearance of UDPG-glycogen synthetase in the tissues of the chick embryo coincides with the time at which, according to previously published data, glycogen begins to appear. In the liver of the rat embryo, the enzyme appears before glycogen formation starts. This is contrary to the behavior of phosphorylase which appears later, at least in skeletal muscle. These findings are in agreement with the view that, in vivo, glycogen synthesis occurs via the UDPG, rather than the phosphorylase, pathway.
Multiple Actions of Pituitary Adenylyl Cyclase Activating Peptide in Nervous System Development and Regeneration

Pituitary adenylyl cyclase activating peptide (PACAP) is widely expressed in the embryonic brain at the onset of neurogenesis, and is strongly upregulated in several models of nerve injury. Moreover, high-affinity PACAP receptors are expressed in proliferative zones in the embryonic and postnatal nervous system suggesting that PACAP regulates the development of both neuronal and glial precursors. Tissue culture studies indicate that PACAP exerts a variety of growth factor-like actions that depend on the origin of the cell population and developmental stage. These effects include regulation of proliferation, survival, maturation, neurite outgrowth, and expression of trophic factors, cytokines and trk receptors. The presence of other growth factors can also markedly affect these actions of PACAP, for example, reversing PACAP’s effect from proliferative to antiproliferative. In vivo models now provide additional evidence that PACAP acts in neural development and regeneration.
Structure of Sputnik, a virophage, at 3.5-Å resolution

“Sputnik” is a dsDNA virus, referred to as a virophage, that is coassembled with Mimivirus in the host amoeba. We have used cryo-EM to produce an electron density map of the icosahedral Sputnik virus at 3.5-Å resolution, sufficient to verify the identity of most amino acids in the capsid proteins and to establish the identity of the pentameric protein forming the fivefold vertices. It was also shown that the virus lacks an internal membrane. The capsid is organized into a T = 27 lattice in which there are 260 trimeric capsomers and 12 pentameric capsomers. The trimeric capsomers consist of three double “jelly-roll” major capsid proteins creating pseudohexameric capsomer symmetry. The pentameric capsomers consist of five single jelly-roll proteins. The release of the genome by displacing one or more of the pentameric capsomers may be the result of a low-pH environment. These results suggest a mechanism of Sputnik DNA ejection that probably also occurs in other big icosahedral double jelly-roll viruses such as Adenovirus. In this study, the near-atomic resolution structure of a virus has been established where crystallization for X-ray crystallography was not feasible.
An empirical comparison of ensemble classification algorithms with support vector machines

An ensemble classifier often has better performance than any of the single learned classifiers in the ensemble. In this paper, the trained support vector machine (SVM) classifiers are used as basic classifiers. The ensemble methods for creating ensemble classifier, such as bagging and boosting, etc., are evaluated on two data sets. Some conclusions are obtained. Bagging with SVM can stably improve classification accuracy, while the improvement obtained by boosting with SVM is not obvious. These two methods largely increase space complexity and time complexity. Comparatively, the multiple SVM decision model, training individual SVM classifiers using training subsets obtained by partitioning the original training set, has a better trade-off between the classification accuracy and efficiency.
Towards optimizing prostate tissue retrieval following holmium laser enucleation of the prostate (HoLEP): Assessment of two morcellators and review of literature.

INTRODUCTION We assess different approaches to retrieve the enucleated adenoma after transurethral enucleation of the prostate, particularly using the holmium laser. METHODS A retrospective review through our prospectively maintained database was performed looking for safety and efficacy of two morcellators. The enucleation phase of the holmium laser enucleation of the prostate (HoLEP) was classically performed followed by retrieval of the intravesical adenoma using either the Piranha (Wolf Inc., Knittlingen, Germany) or VersaCut (Lumenis) morcellator. A PubMed-MEDLINE search was conducted for all transurethral enucleation procedures and relevant data regarding methods of prostate tissue retrieval were extracted. RESULTS Strictly limiting the study to 3 reusable blades with each morcellator, we performed 67 and 55 consecutive procedures with Piranha and VersaCut, respectively. There was no significant difference between the two morcellators regarding perioperative complications, apart from 5 bladder mucosal injuries with the VersaCut (9%). Furthermore, there were similar retrieved tissue weight, mechanical problems-rate, catheter-time and hospital-stay in both morcellators. However, the Piranha morcellator needed significantly less morcellation-time, needed to use cold loop to remove non-morcellated pieces and to score the adenoma by laser for better bite of the adenoma, and had a higher median morcellation-rate 6.2 (rate: 2.8-12) g/min. Despite little reporting on morcellation, we had data on the tissue retrieval rate (2.6 to 6.5 g/min with Piranha and 1.9 to 11 g/min with VersaCut. Furthermore, bladder mucosal injury was reported in 1.4% and 0.7 to 5.7% with Piranha and VersaCut, respectively; bladder perforation with VersaCut was experienced in about 0.1 to 1.5% of patients. Our study is limited by its non-randomization. CONCLUSION The Piranha morcellator was the most efficient and safe way to retrieve tissue after a transurethral enucleation of a prostate adenoma.
Preferential Attachment and Vertex Arrival Times

We study preferential attachment mechanisms in random graphs that are parameterized by (i) a constant bias affecting the degree-biased distribution on the vertex set and (ii) the distribution of times at which new vertices are created by the model. The class of random graphs so defined admits a representation theorem reminiscent of residual allocation, or "stick-breaking" schemes. We characterize how the vertex arrival times affect the asymptotic degree distribution, and relate the latter to neutral-to-the-left processes. Our random graphs generate edges "one end at a time", which sets up a one-to-one correspondence between random graphs and random partitions of natural numbers; via this map, our representation induces a result on (not necessarily exchangeable) random partitions that generalizes a theorem of Griffiths and Spano. A number of examples clarify how the class intersects with several known random graph models.
Flow Cytometric Assessment of Viability of Lactic Acid Bacteria

ABSTRACT The viability of lactic acid bacteria is crucial for their applications as dairy starters and as probiotics. We investigated the usefulness of flow cytometry (FCM) for viability assessment of lactic acid bacteria. The esterase substrate carboxyfluorescein diacetate (cFDA) and the dye exclusion DNA binding probes propidium iodide (PI) and TOTO-1 were tested for live/dead discrimination using aLactococcus, a Streptococcus, threeLactobacillus, two Leuconostoc, anEnterococcus, and a Pediococcus species. Plate count experiments were performed to validate the results of the FCM assays. The results showed that cFDA was an accurate stain for live cells; in exponential-phase cultures almost all cells were labeled, while 70°C heat-killed cultures were left unstained. PI did not give clear live/dead discrimination for some of the species. TOTO-1, on the other hand, gave clear discrimination between live and dead cells. The combination of cFDA and TOTO-1 gave the best results. Well-separated subpopulations of live and dead cells could be detected with FCM. Cell sorting of the subpopulations and subsequent plating on agar medium provided direct evidence that cFDA labels the culturable subpopulation and that TOTO-1 labels the nonculturable subpopulation. Applied to cultures exposed to deconjugated bile salts or to acid, cFDA and TOTO-1 proved to be accurate indicators of culturability. Our experiments with lactic acid bacteria demonstrated that the combination of cFDA and TOTO-1 makes an excellent live/dead assay with versatile applications.
Antidiabetic thiazolidinediones induce ductal differentiation but not apoptosis in pancreatic cancer cells.

AIM Thiazolidinediones (TZD) are a new class of oral antidiabetic drugs that have been shown to inhibit growth of same epithelial cancer cells. Although TZD were found to be ligands for peroxisome proliferator-activated receptor gamma (PPARgamma), the mechanism by which TZD exert their anticancer effect is presently unclear. In this study, we analyzed the mechanism by which TZD inhibit growth of human pancreatic carcinoma cell lines in order to evaluate the potential therapeutic use of these drugs in pancreatic adenocarcinoma. METHODS The effects of TZD in pancreatic cancer cells were assessed in anchorage-independent growth assay. Expression of PPARgamma was measured by reverse-transcription polymerase chain reaction and confirmed by Western blot analysis. PPARgamma activity was evaluated by transient reporter gene assay. Flow cytometry and DNA fragmentation assay were used to determine the effect of TZD on cell cycle progression and apoptosis respectively. The effect of TZD on ductal differentiation markers was performed by Western blot. RESULTS Exposure to TZD inhibited colony formation in a PPARgamma-dependent manner. Growth inhibition was linked to G1 phase cell cycle arrest through induction of the ductal differentiation program without any increase of the apoptotic rate. CONCLUSION TZD treatment in pancreatic cancer cells has potent inhibitory effects on growth by a PPAR-dependent induction of pancreatic ductal differentiation.
Association of Depressive Symptoms and School Adolescents' Smoking: A Cross-Lagged Analysis

This study examined the association of depressive symptoms of adolescents and their smoking behavior. A national cohort sample of school adolescents (N = 5,855) who participated in the 1989 and 1993 Teenage Attitudes and Practices Survey was obtained. The information from this survey included measures of smoking behavior and a series of factors related to depressive symptoms during a 3-yr. span. A cross-lagged analysis with Kendall tau b correlations was used. Judging from the magnitude of the cross-lagged correlations, the direction of causation cannot be ascertained. Rather, a reciprocal relationship between depression and smoking may be suggested.
A computational platform for robotized fluorescence microscopy (I): High‐content image‐based cell‐cycle analysis

Hardware automation and software development have allowed a dramatic increase of throughput in both acquisition and analysis of images by associating an optimized statistical significance with fluorescence microscopy. Despite the numerous common points between fluorescence microscopy and flow cytometry (FCM), the enormous amount of applications developed for the latter have found relatively low space among the modern high‐resolution imaging techniques. With the aim to fulfill this gap, we developed a novel computational platform named A.M.I.CO. (Automated Microscopy for Image‐Cytometry) for the quantitative analysis of images from widefield and confocal robotized microscopes. Thanks to the setting up of both staining protocols and analysis procedures, we were able to recapitulate many FCM assays. In particular, we focused on the measurement of DNA content and the reconstruction of cell‐cycle profiles with optimal parameters. Standard automated microscopes were employed at the highest optical resolution (200 nm), and white‐light sources made it possible to perform an efficient multiparameter analysis. DNA‐ and protein‐content measurements were complemented with image‐derived information on their intracellular spatial distribution. Notably, the developed tools create a direct link between image‐analysis and acquisition. It is therefore possible to isolate target populations according to a definite quantitative profile, and to relocate physically them for diffraction‐limited data acquisition. Thanks to its flexibility and analysis‐driven acquisition, A.M.I.CO. can integrate flow, image‐stream and laser‐scanning cytometry analysis, providing high‐resolution intracellular analysis with a previously unreached statistical relevance. © 2013 International Society for Advancement of Cytometry © 2012 International Society for Advancement of Cytometry
Adenovirus Serotype 5-Specific Neutralizing Antibodies Target Multiple Hexon Hypervariable Regions

ABSTRACT The immunogenicity of adenovirus serotype 5 (Ad5) vectors has been shown to be suppressed by neutralizing antibodies (NAbs) directed primarily against the hexon hypervariable regions (HVRs). We previously reported that replacing all seven HVRs with those from the rare serotype virus Ad48 resulted in a chimeric Ad5HVR48(1-7) vector that largely evaded preexisting Ad5 immunity in mice and rhesus monkeys. In this study, we evaluated the extent to which Ad5-specific NAbs are directed against various HVRs. We constructed partial HVR-chimeric Ad5 vectors with only a subset of HVRs exchanged, and we utilized these vectors in both NAb assays and murine immunogenicity studies with and without baseline Ad5 immunity. Our results demonstrate that Ad5-specific NAbs target multiple HVRs, suggesting that replacing all HVRs is required to optimize evasion of anti-Ad5 immunity. These data have important implications for the development of novel vectors for both vaccines and gene therapy.
Expression and induction of CYP1A1/1A2, CYP2A6 and CYP3A4 in primary cultures of human hepatocytes: a 10-year follow-up

1. The aims were to refine experimental conditions (using 76 human hepatocyte preparations) in terms of the selection of enzyme inducers and their optimal concentration, the treatment duration with inducers and the choice of specific cytochrome P450 isoform(s) probes to optimize the use of primary hepatocytes for predicting the potential induction by new chemical entities of cytochrome P450 isoforms in vivo
European experience with the retrograde approach for the recanalisation of coronary artery chronic total occlusions. A report on behalf of the euroCTO club.

AIMS Recanalisation rates of coronary chronic total occlusions (CTO) remain sub-optimal. The retrograde technique was recently introduced to improve success rates. METHODS AND RESULTS From February 2005 until December 2007, 175 patients were treated with this technique in seven European centres by highly experienced operators: in 84 (48%) as primary strategy, in 41 (23.5%) immediately after antegrade failure and in 50 (28.5%) as a repeat procedure after previous antegrade failure. Baseline characteristics revealed a mean age 61.4 +/- 10.8 years with 29.5% and 39% of patients having diabetes and a prior history of MI, respectively. The mean occlusion duration was 50.8 months (determined in 32% of patients). The target vessel was: LAD 21%, LCX 6.3%, RCA 71.4%. Epicardial collaterals were accessed in 20.6% and septal in 79.4% of the patients. Overall success rate was 83.4%. In 80.6% a wire crossed the collaterals and successfully delivered distal to the occlusion; success rate in this group was 91.5%. The technique implemented in the retrograde facilitated successful recanalisation was: retrograde wire/balloon crossing in 28%, CART in 34% and marker wire/"knuckle" technique in 48%. There was a great diversity between centres referring to the retrograde technique used. According to the initial strategy success rates were: primary 89.3%, immediately after antegrade failure 65.9% and repeat procedure after antegrade failure in 88%. In patients with failure to cross the collaterals success rate was 50%. Septal rupture/haematoma occurred in 6.9% of the patients, periprocedural myocardial infarction (CK-MB rise) in 4% and TIA in 0.6% and wire entrapment in 0.6%. Mean fluoroscopy time was 59.3 mn and the mean contrast used was 420.9 ml. Drug eluting stents were implanted in all successfully recanalised vessels. CONCLUSIONS There is great diversity amongst European centres with respect to how the retrograde strategy has been adopted and adapted. The retrograde approach was used with high degree of success and safety and can thus be regarded as a valid contributor to the armamentarium of the modern day interventional cardiologist.
Particulate matter speciation profiles for light-duty gasoline vehicles in the United States

Representative profiles for particulate matter particles less than or equal to 2.5 µm (PM2.5) are developed from the Kansas City Light-Duty Vehicle Emissions Study for use in the U.S. Environmental Protection Agency (EPA) vehicle emission model, the Motor Vehicle Emission Simulator (MOVES), and for inclusion in the EPA SPECIATE database for speciation profiles. The profiles are compatible with the inputs of current photochemical air quality models, including the Community Multiscale Air Quality Aerosol Module Version 6 (AE6). The composition of light-duty gasoline PM2.5 emissions differs significantly between cold start and hot stabilized running emissions, and between older and newer vehicles, reflecting both impacts of aging/deterioration and changes in vehicle technology. Fleet-average PM2.5 profiles are estimated for cold start and hot stabilized running emission processes. Fleet-average profiles are calculated to include emissions from deteriorated high-emitting vehicles that are expected to continue to contribute disproportionately to the fleet-wide PM2.5 emissions into the future. The profiles are calculated using a weighted average of the PM2.5 composition according to the contribution of PM2.5 emissions from each class of vehicles in the on-road gasoline fleet in the Kansas City Metropolitan Statistical Area. The paper introduces methods to exclude insignificant measurements, correct for organic carbon positive artifact, and control for contamination from the testing infrastructure in developing speciation profiles. The uncertainty of the PM2.5 species fraction in each profile is quantified using sampling survey analysis methods. The primary use of the profiles is to develop PM2.5 emissions inventories for the United States, but the profiles may also be used in source apportionment, atmospheric modeling, and exposure assessment, and as a basis for light-duty gasoline emission profiles for countries with limited data. Implications: PM2.5 speciation profiles were developed from a large sample of light-duty gasoline vehicles tested in the Kansas City area. Separate PM2.5 profiles represent cold start and hot stabilized running emission processes to distinguish important differences in chemical composition. Statistical analysis was used to construct profiles that represent PM2.5 emissions from the U.S. vehicle fleet based on vehicles tested from the 2005 calendar year Kansas City metropolitan area. The profiles have been incorporated into the EPA MOVES emissions model, as well as the EPA SPECIATE database, to improve emission inventories and provide the PM2.5 chemical characterization needed by CMAQv5.0 for atmospheric chemistry modeling.
van der Waals interactions between excited-state atoms and dispersive dielectric surfaces.

van der Waals interactions between atoms and dielectric surfaces are reinvestigated. To describe the nonretarded interaction potential between a dispersive dielectric surface and an atom in an arbitrary internal energy state, we derive a general expression in terms of an integral, over real frequency, of the combined atom and surface polarizabilities. It is shown that, for excited atoms, the expression is equivalent to the one obtained by Wylie and Sipe [Phys. Rev. A 32, 2030 (1985)]. We thus demonstrate how to extend this approach to excited atoms interacting with birefringent dielectrics. For isotropic dielectrics, a method of integration in closed form allows us to derive an approximate formula for the van der Waals interaction constant in terms of resonance frequencies and oscillator strengths of both the atom and the dielectric. Frequency-dependent ``dielectric reflection'' coefficients are introduced for virtual atomic dipole couplings either in absorption or in emission. In absorption, the reflection coefficient is always positive and smaller than unity. In emission, it may take arbitrary values, positive or negative (corresponding to van der Waals repulsion). Such a behavior is shown to be related to resonant excitation exchange between the atomic system and the dielectric medium, when an atomic transition frequency gets in resonance with a dielectric absorption band. Numerical calculations performed for the cesium-sapphire system are shown to be in good agreement with data obtained by selective-reflection spectroscopy. Finally, experimental tests of the birefringent character of the sapphire response are discussed.