gebhart/patrepeval huggingface dataset:
<i>In Vitro</i> and <i>In Vivo</i> Study of Amphotericin B Formulation with Quaternized Bioreducible Lipidoids (2020)

Invasive fungal infections are well-known causes of morbidity and mortality in immunocompromised patients. Amphotericin B (AmB) is a polyene fungicidal agent with excellent properties of the broad antifungal spectrum, high activity, and relatively rare drug resistance. However, significant toxicities limit the clinical application of AmB and its conventional formulation AmB deoxycholate (Fungizone). Here we investigated nanoparticle formulations of AmB using synthetic biodegradable lipidoids and evaluated their stability, <i>in vitro</i> antifungal efficacy, and <i>in vivo</i> toxicity and pharmacokinetics. We found that the AmB formulated using a mixture of quaternized lipidoid (Q78-O14B) and DSPE-PEG2000 has the size around 70-100 nm and is stable during storage. The formulation showed no hemotoxicity to red blood cells (RBCs) <i>in vitro</i>. It also possesses the highest antifungal activity (<i>in vitro</i>) and lowest toxicity (both <i>in vitro</i> and <i>in vivo</i>). These metrics are significantly superior to the commercial antifungal product Fungizone. Meanwhile, AmB/Q78-O14B-P exhibited prolonged blood circulation in comparison to Fungizone <i>in vivo.</i> In AmB/Q78-O14B-P formulation, AmB was still detectable in the liver, spleen, and lung tissues with a concentration above the minimum inhibitory concentrations 72 h after low-dose intravenous injection. Based on these results, AmB in lipidoid nanoparticle formulation may produce sustained antifungal activity against blood-borne and systemic organ infections. Moreover, the new AmB formulation showed low nephrotoxicity and hepatotoxicity in rats even at high doses, allowing a dramatically wider and safer therapeutic window than Fungizone. This method provides a means to develop much needed antifungal agents that will be more therapeutically efficacious, more affordable (than AmBisome), and less toxic (than Fungizone) for the treatment of systemic fungal infections.
A Fast-Moving Floorshow-The Space between Acting and Thinking in Dramatherapy with Offenders (2000)

This paper was originally presented at an Arts Therapies in Prisons Seminar at Home Office Headquarters in 1996. I have presented several papers subsequently but this is the only one written for an arts therapies audience and I feel that the difficulties and doubts I describe still hold true for dramatherapists beginning work in such an environment.
Intragastric Ethanol Infusion Model in Rodents (2008)

Alcohol-associated life-style disease, as exemplified by alcoholic liver disease (ALD), is multifactorial with intricate interactions among genetic and environmental factors predicating individual predisposition. To experimentally dissect the interfaces of these interactions for better understanding of the pathogenesis, it is essential to have an animal model that provides maximal control over ethanol and dietary intake and that enables a precise addition or deletion analysis for a risk or protective factor of interest. Rodent intragastric ethanol infusion (IEI) model was developed two decades ago to meet this requirement. Work conducted with the model to date demonstrates the importance of both maximal ethanol intake and secondary risk factors in ALD. Mouse IEI model proved to be particularly useful for genetic analysis of the ALD pathogenesis and has the potential of producing synergistic pathologic outcome by combination of risk factors. The model is best used by alcohol researchers through a center-supported core facility and its tissue sharing program.
CausalGAN: Learning Causal Implicit Generative Models with Adversarial Training (2017)

We propose an adversarial training procedure for learning a causal implicit generative model for a given causal graph. We show that adversarial training can be used to learn a generative model with true observational and interventional distributions if the generator architecture is consistent with the given causal graph. We consider the application of generating faces based on given binary labels where the dependency structure between the labels is preserved with a causal graph. This problem can be seen as learning a causal implicit generative model for the image and labels. We devise a two-stage procedure for this problem. First we train a causal implicit generative model over binary labels using a neural network consistent with a causal graph as the generator. We empirically show that WassersteinGAN can be used to output discrete labels. Later, we propose two new conditional GAN architectures, which we call CausalGAN and CausalBEGAN. We show that the optimal generator of the CausalGAN, given the labels, samples from the image distributions conditioned on these labels. The conditional GAN combined with a trained causal implicit generative model for the labels is then a causal implicit generative model over the labels and the generated image. We show that the proposed architectures can be used to sample from observational and interventional image distributions, even for interventions which do not naturally occur in the dataset.
A Hidden Markov Model for urban navigation based on fingerprinting and pedestrian dead reckoning (2010)

An algorithm for pedestrian navigation in indoor and urban canyon environments is presented. It considers platforms with low processing power and low-cost sensors. A combination of Wi-Fi positioning and dead reckoning, based on a Hidden Markov Model, is used. The positions of the Wi-Fi fingerprints in the database are used as hidden states. Dead reckoning is taken for state transition and a database correlation of the Wi-Fi signal strength measurements is performed in the measurement update. The dead reckoning consists of an accelerometer driven step length estimation and a magnetic field based heading calculation. Simulations and tests demonstrate that in this way ambiguities common in Wi-Fi positioning can be solved and outages can be bridged. Therefore, higher accuracy and robustness can be achieved.
Sequential 2-acetylaminofluorene — phenobarbital exposure induces a cytosolic aldehyde dehydrogenase during rat hepatocarcinogenesis (1982)

A significant change in hepatic aldehyde dehydrogenase activity has been observed in normal Sprague-Dawley rat liver during the promotion phase of hepatocarcinogenesis induced by brief feeding of 2-acetylaminofluorene (2-AAF) followed by tumor promotion using dietary phenobarbital (PB) exposure. Animals receiving only 2-AAF or PB do not possess this new aldehyde dehydrogenase activity. The phenotype is characterized by the appearance of a new cytosolic isozyme kinetically, electrophoretically and immunochemically distinct from the normal liver aldehyde dehydrogenase isozymes and from aldehyde dehydrogenases inducible in 2-AAF-induced hepatomas. The new isozyme is NAD-dependent, disulfiram-sensitive and cross-reacts with antiserum to a normal liver aldehyde dehydrogenase inducible in several lines of rats by PB. However, the population of animals used in this study has been shown previously to be non-responsive to aldehyde dehydrogenase induction by dietary PB. Since no animals receiving only PB express this new isozyme, the carcinogen must play a significant role in its induction. Moreover, that not all animals receiving carcinogen and promoter possess the phenotype suggests this carcinogen/promoter interaction has a genetic basis.
Determination and Functional Analysis of the Consensus Binding Site for TFII-I Family Member BEN, Implicated in Williams-Beuren Syndrome* (2008)

The ubiquitously expressed TFII-I family of multifunctional transcription factors is involved in gene regulation as well as signaling. Despite the fact that they share significant sequence homology, these factors exhibit varied and distinct functions. The lack of knowledge about its binding sites and physiological target genes makes it more difficult to assign a definitive function for the TFII-I-related protein, BEN. We set out to determine its optimal binding site with the notion of predicting its physiological target genes. Here we report the identification of an optimal binding sequence for BEN by SELEX (systematic evolution of ligands by exponential enrichment) and confirm the relevance of this sequence by functional assays. We further performed a data base search to assign genes that have this consensus site(s) and validate several candidate genes by quantitative PCR upon stable silencing of BEN and by chromatin immunoprecipitation assay upon stable expression of BEN. Given that haploinsufficiency in BEN is causative to Williams-Beuren syndrome, these results may further lead to the identification of a set of physiologically relevant target genes for BEN and may help identify molecular determinants of Williams-Beuren syndrome.
Preparation, Characterization, and Properties of Dy‐Doped Small‐Grained BaTiO <sub>3</sub> Ceramics (1977)

The effects of Dy doping and sintering parameters on the properties of BaTiO 3 ceramics were studied. The average grain size decreases with increasing Dy content and is controlled at ∼1.5 μ m by 0.8 at.% Dy. The Curie temperature change, associated with ≤1.2 at.% Dy, is <3°C. The dielectric constant is ∼2600 for specimens doped with 0.8 at.% Dy, calcined at 1200°C, and sintered at 1450°C. The dielectric constant variation with ambient temperature is much less than that of conventional BaTiO 3 ceramics. Lattice constant c decreases with increasing Dy concentration whereas a increases slightly. The effects of grain size on dielectric constant, lattice parameters, and linear thermal expansion coefficient are more pronounced than the chemical effects of Dy doping in the ferroelectric state, whereas in the paraelectric state, these characteristics are almost independent of grain size as well as Dy concentration. The decrease in the frequency of occurrence of 90° twins with decreasing grain size implies that internal stress, which develops when BaTiO 3 ceramics are cooled below T c , strongly influences the effects of grain size.
Multiclass classification based on a deep convolutional network for head pose estimation (2015)

Head pose estimation has been considered an important and challenging task in computer vision. In this paper we propose a novel method to estimate head pose based on a deep convolutional neural network (DCNN) for 2D face images. We design an effective and simple method to roughly crop the face from the input image, maintaining the individual-relative facial features ratio. The method can be used in various poses. Then two convolutional neural networks are set up to train the head pose classifier and then compared with each other. The simpler one has six layers. It performs well on seven yaw poses but is somewhat unsatisfactory when mixed in two pitch poses. The other has eight layers and more pixels in input layers. It has better performance on more poses and more training samples. Before training the network, two reasonable strategies including shift and zoom are executed to prepare training samples. Finally, feature extraction filters are optimized together with the weight of the classification component through training, to minimize the classification error. Our method has been evaluated on the CAS-PEAL-R1, CMU PIE, and CUBIC FacePix databases. It has better performance than state-of-the-art methods for head pose estimation.
Genre-Oriented Web Content Extraction with Deep Convolutional Neural Networks and Statistical Methods. (2018)

conference paper
Pros: Can tissue biopsy be replaced by liquid biopsy? (2016)

In the era of personalized medicine, a critical appraisal new developments and controversies are essential in order to derived tailored approaches. In addition to its educative aspect, we expect these discussions to help younger researchers to refine their own research strategies.
Ca<sup>2+</sup>-Binding Mode of the C<sub>2</sub>A-Domain of Synaptotagmin (2003)

The ability of neurons to communicate with each other lies at the center of brain function. Communication between neurons occurs primarily by synaptic transmission and is mediated by neurotransmitters that are released by synaptic vesicle exocytosis. This process is tightly regulated by a complex protein machinery and is triggered by Ca2+influx into a presynaptic terminal when an action potential causes opening of voltage-gated Ca2+-channels (). The synaptic vesicle protein synaptotagmin I is an essential component of this machinery (), acting most likely as a Ca2+sensor in neurotransmitter release (). The Ca2+-binding properties of synaptotagmin I are thus likely to be key for the mechanism of interneuronal communication.
Wireless impedance sensor nodes for functions of structural damage identification and sensor self-diagnosis (2009)

Economic and reliable online health monitoring strategies are very essential for safe operation of civil, mechanical and aerospace structures. This study presents online structural health monitoring (SHM) techniques using wireless impedance sensor nodes equipped with both functions of structural damage identification and sensor self-diagnosis. The wireless impedance sensor node incorporating a miniaturized impedance measuring chip, a microcontroller and radio-frequency (RF) telemetry is equipped with the capabilities for temperature sensing, multiplexing of several sensors, and local data analysis. The feasibility of the sensor node for structural damage identification is firstly investigated through a series of experimental studies inspecting loosened bolt damage and cut damage cases. Additionally, a temperature effects-free sensor self-diagnosis algorithm is embedded into the sensor node and its feasibility is examined from the experiments monitoring the integrity of each piezoelectric sensor on a wireless sensor network.
10-Gb/s Operation of RSOA for WDM PON Using Return-to-Zero Modulation Format (2012)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text K. Y. Cho and Y. C. Chung, "10-Gb/s Operation of RSOA for WDM PON Using Return-to-Zero Modulation Format," in Optical Fiber Communication Conference, OSA Technical Digest (Optica Publishing Group, 2012), paper OTh1F.2. Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Peroxisome Proliferator-activated Receptor γ Ligands Inhibit Retinoblastoma Phosphorylation and G1 → S Transition in Vascular Smooth Muscle Cells (2000)

Peroxisome proliferator-activated receptor gamma (PPARgamma) is a member of the nuclear receptor superfamily that is activated by binding certain fatty acids, eicosanoids, and insulin-sensitizing thiazolidinediones (TZD). The TZD troglitazone (TRO) inhibits vascular smooth muscle cell proliferation and migration both in vitro and in vivo. The precise mechanism of its antiproliferative activity, however, has not been elucidated. We report here that PPARgamma ligands inhibit rat aortic vascular smooth muscle cell proliferation by blocking the events critical for G(1) --> S progression. Flow cytometry demonstrated that both TRO and another TZD, rosiglitazone, prevented G(1) --> S progression induced by platelet-derived growth factor and insulin. Movement of cells from G(1) --> S was also inhibited by the non-TZD, natural PPARgamma ligand 15-deoxy-(12,14)Delta prostaglandin J(2) (15d-PGJ(2)), and the mitogen-activated protein kinase pathway inhibitor PD98059. Inhibition of G(1) --> S exit by these compounds was accompanied by a substantial blockade of retinoblastoma protein phosphorylation. TRO and rosiglitazone attenuated both the mitogen-induced degradation of p27(kip1) and the mitogenic induction of p21(cip1). 15d-PGJ(2) and PD98059 inhibited both the degradation of p27(kip1) and the induction of cyclin D1 in response to mitogens. These effects resulted in the inhibition of mitogenic stimulation of cyclin-dependent kinases activated by cyclins D1 and E. These data demonstrate that PPARgamma ligands are antiproliferative drugs that act by modulating cyclin-dependent kinase inhibitors; they may provide a new therapeutic approach for proliferative vascular diseases.
Evidence Suggesting That Francisella tularensis O-Antigen Capsule Contains a Lipid A-Like Molecule That Is Structurally Distinct from the More Abundant Free Lipid A (2016)

Francisella tularensis, the Gram-negative bacterium that causes tularemia, produces a high molecular weight capsule that is immunologically distinct from Francisella lipopolysaccharide but contains the same O-antigen tetrasaccharide. To pursue the possibility that the capsule of Francisella live vaccine strain (LVS) has a structurally unique lipid anchor, we have metabolically labeled Francisella with [14C]acetate to facilitate highly sensitive compositional analysis of capsule-associated lipids. Capsule was purified by two independent methods and yielded similar results. Autoradiographic and immunologic analysis confirmed that this purified material was largely devoid of low molecular weight LPS and of the copious amounts of free lipid A that the Francisellae accumulate. Chemical hydrolysis yielded [14C]-labeled free fatty acids characteristic of Francisella lipid A but with a different molar ratio of 3-OH C18:0 to 3-OH C16:0 and different composition of non-hydroxylated fatty acids (mainly C14:0 rather than C16:0) than that of free Francisella lipid A. Mild acid hydrolysis to induce selective cleavage of KDO-lipid A linkage yielded a [14C]-labeled product that partitioned during Bligh/Dyer extraction and migrated during thin-layer chromatography like lipid A. These findings suggest that the O-antigen capsule of Francisella contains a covalently linked and structurally distinct lipid A species. The presence of a discrete lipid A-like molecule associated with capsule raises the possibility that Francisella selectively exploits lipid A structural heterogeneity to regulate synthesis, transport, and stable bacterial surface association of the O-antigen capsular layer.
Cre‐mediated recombination can induce apoptosis in vivo by activating the p53 DNA damage‐induced pathway (2011)

Cre-mediated apoptosis has been observed in many contexts in mice expressing Cre-recombinase and can confound the analysis of genetically engineered conditional mutant or transgenic alleles. Several mechanisms have been proposed to explain this phenomenon. We find that the degree of apoptosis induced correlates roughly with the copy number of loxP sites present in the genome and that some level of increased apoptosis accompanies the presence of even only a few loxP sites, as occurs in conditional floxed alleles. Cre-induced apoptosis in this context is completely p53-dependent, suggesting that the apoptosis is stimulated by p53 activation in response to DNA damage incurred during the process of Cre-mediated recombination.
Characterization of the Mouse and Rat IgE Antibody Responses to Timothy Pollen by Means of Crossed Radioimmunoelectrophoresis (1982)

The IgE antibody responses to timothy pollen allergens in one rat strain and five mouse strains were investigated by means of crossed radioimmunoelectrophoresis. The rodent strains were selected for their capacity to respond with IgE antibody production. When sensitized parenterally with the antigen mixed in alum, the animals produced IgE antibodies to essentially the same antigens in timothy pollen as timothy sensitive patients have been shown to do. Thus, the allergenicity of the complex mixture of antigens in a timothy extract is similarly expressed in animals immunized parenterally with alum as in patients sensitized by inhalation.
Analysis of the rectangular waveguide slot coupled multilayer hemispherical dielectric resonator antenna (2012)

A rectangular waveguide feed to the dielectric resonator antenna (DRA) is proposed. A three-layer DRA structure is used to achieve enhanced and broadband coupling to the waveguide. The antenna topology is easy to realise and does not need additional coupling or matching elements to effectively excite the DRA. The configuration also affords ease in frequency tuning without sacrificing bandwidth or radiation performance. The full-wave Green's function approach is presented for the analysis of such multilayer structures with an arbitrary number of layers with greatly reduced computational overhead. The modes of the multilayer DRA can be identified from the analysis, which can be used to explain the broadband nature of the coupling. The double-summation representation of the homogeneous Green's function has been extended to the multilayer case, leading to a substantial reduction in computation time for the input impedance.
Distinct Effects of RGD-glycoproteins on Integrin-Mediated Adhesion and Osteogenic Differentiation of Human Mesenchymal Stem Cells (2013)

The detailed interactions of mesenchymal stem cells (MSCs) with their extracellular matrix (ECM) and the resulting effects on MSC differentiation are still largely unknown. Integrins are the main mediators of cell-ECM interaction. In this study, we investigated the adhesion of human MSCs to fibronectin, vitronectin and osteopontin, three ECM glycoproteins which contain an integrin-binding sequence, the RGD motif. We then assayed MSCs for their osteogenic commitment in the presence of the different ECM proteins. As early as 2 hours after seeding, human MSCs displayed increased adhesion when plated on fibronectin, whereas no significant difference was observed when adhering either to vitronectin or osteopontin. Over a 10-day observation period, cell proliferation was increased when cells were cultured on fibronectin and osteopontin, albeit after 5 days in culture. The adhesive role of fibronectin was further confirmed by measurements of cell area, which was significantly increased on this type of substrate. However, integrin-mediated clusters, namely focal adhesions, were larger and more mature in MSCs adhering to vitronectin and osteopontin. Adhesion to fibronectin induced elevated expression of α₅-integrin, which was further upregulated under osteogenic conditions also for vitronectin and osteopontin. In contrast, during osteogenic differentiation the expression level of β₃-integrin was decreased in MSCs adhering to the different ECM proteins. When MSCs were cultured under osteogenic conditions, their commitment to the osteoblast lineage and their ability to form a mineralized matrix in vitro was increased in presence of fibronectin and osteopontin. Taken together these results indicate a distinct role of ECM proteins in regulating cell adhesion, lineage commitment and phenotype of MSCs, which is due to the modulation of the expression of specific integrin subunits during growth or osteogenic differentiation.