Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterization of the Human ABCG1 Gene

The human ABCG1 gene encodes a member of the ATP-binding cassette (ABC) superfamily of transporter proteins and is highly induced when macrophages are incubated with oxysterols. Using mRNA from oxysterol-treated human THP-1 cells together with 5′-rapid amplification of cDNA ends and polymerase chain reaction, we identified a novel ABCG1 transcript that encodes a putative protein of 786 residues containing a new amino terminus of 203 amino acids. Characterization of the genomic organization and structure of the human ABCG1 gene demonstrates that: (i) the gene consists of 23 exons spanning 98 kilobase pairs (kb) on chromosome 21q22.3, (ii) the 203 amino acids are encoded on three previously unidentified exons, 8–10, and (iii) a promoter, containing a TATA box and two liver X receptor (LXR) α response elements (LXREs), is located upstream of exon 8. Northern analysis using exon-specific probes confirms that oxysterol treatment results in >10-fold induction of ABCG1 transcripts that are derived from either exons 8–23 or exons 5, 7, and 11–23. Electromobility shift assays demonstrate that LXRα and retinoid X receptor α bind to the two LXREs in intron 7. Cells were transiently transfected with reporter luciferase constructs under the control of either (i) 9 kb of genomic DNA corresponding to intron 7 and part of exon 8 and containing either wild-type or mutant LXREs or (ii) two copies of the wild-type or mutant LXRE. In all cases, the wild-type construct was regulated in an LXR- and oxysterol-dependent manner, and this regulation was attenuated when the LXREs were mutated. In conclusion, the human ABCG1 gene contains multiple promoters, spans more than 98 kb and comprises 23 exons that give rise to alternative transcripts encoding proteins with different amino-terminal sequences. Elucidation of the various roles of different ABCG1 isoforms will be important for our understanding of mammalian cholesterol homeostasis.
Advanced Glycation End Products Induce Human Corneal Epithelial Cells Apoptosis through Generation of Reactive Oxygen Species and Activation of JNK and p38 MAPK Pathways

Advanced Glycation End Products (AGEs) has been implicated in the progression of diabetic keratopathy. However, details regarding their function are not well understood. In the present study, we investigated the effects of intracellular reactive oxygen species (ROS) and JNK, p38 MAPK on AGE-modified bovine serum albumin (BSA) induced Human telomerase-immortalized corneal epithelial cells (HUCLs) apoptosis. We found that AGE-BSA induced HUCLs apoptosis and increased Bax protein expression, decreased Bcl-2 protein expression. AGE-BSA also induced the expression of receptor for advanced glycation end product (RAGE). AGE-BSA-RAGE interaction induced intracellular ROS generation through activated NADPH oxidase and increased the phosphorylation of p47phox. AGE-BSA induced HUCLs apoptosis was inhibited by pretreatment with NADPH oxidase inhibitors, ROS quencher N-acetylcysteine (NAC) or neutralizing anti-RAGE antibodies. We also found that AGE-BSA induced JNK and p38 MAPK phosphorylation. JNK and p38 MAPK inhibitor effectively blocked AGE-BSA-induced HUCLs apoptosis. In addition, NAC completely blocked phosphorylation of JNK and p38 MAPK induced by AGE-BSA. Our results indicate that AGE-BSA induced HUCLs apoptosis through generation of intracellular ROS and activation of JNK and p38 MAPK pathways.
Structural and magnetic investigations of magnetic nanoparticles and core-shell colloids

The main interest of this thesis relies on the structural and magnetic investigation of magnetic particles with dimensions in the nano-and micrometer range. Three types of particles have been investigated, namely: aqueous-based Fe3O4 nanoparticles, with an average diameter of 12±3 nm, as well as, core-shell particles and composite particles, both with diameters ranging from 680 nm to 1000 nm. The Fe3O4 nanoparticles are negatively charged and tetrabutylammonium hydroxide-stabilized. The core-shell particles consist of an anionic polystyrene core, with a diameter of 640 nm coated with multilayers of Fe3O4 nanoparticles and polyelectrolytes. The composite particles have the same polystyrene core coated with Fe3O4 nanoparticles, polyelectrolytes and silica-encapsulated gold nanoparticles with a diameter of 15 nm. The core-shell and composite particles were prepared by using a recently developed method, called layer-by-layer technique. The uniformity and regularity of the coating has been confirmed by Transmission Electron Microscopy and Atomic Force Microscopy measurements. The structure of the Fe3O4 nanoparticles has been investigated by High Resolution Transmission Electron Microscopy, X-ray Diffraction, X-ray Absorption Spectroscopy and X-ray Photoelectron Spectroscopy. The pattern formation of the core-shell and composite particles in water solution under applied magnetic field has been studied. An in-plane magnetic field arranged the microspheres into a chain-like structure. Chains up to 2 mm in length have been observed. The motion of the magnetic colloids in an aqueous solution when a magnetic field is applied has been visualized in real-time by Optical Microscopy. Ferromagnetic Resonance, SQUID-magnetometry and Magnetic Force Microscopy have been used to investigate the magnetic properties of the nano-and micrometer-size particles. The polar angular dependence of ferromagnetic resonance for Fe3O4 nanoparticles reveals an effective anisotropy field of 0.12 T and a negative out-of-plane anisotropy constant at 300 K. The magnetic measurements on the core-shell particles aligned into a chain-like structure confirm a long-range dipolar order at room temperature, an in-plane easy axis of the magnetization along the chains and a reduction of the magnetic moment of Fe3O4.
Sexually Dimorphic and Sex-Independent Left-Right Asymmetries in Chicken Embryonic Gonads

Female birds develop asymmetric gonads: a functional ovary develops on the left, whereas the right gonad regresses. In males, however, testes develop on both sides. We examined the distribution of germ cells using Vasa/Cvh as a marker. Expression is asymmetric in both sexes: at stage 35 the left gonad contains significantly more germ cells than the right. A similar expression pattern is seen for expression of ERNI (Ens1), a gene expressed in chick embryonic stem cells while they self-renew, but downregulated upon differentiation. Other pluripotency-associated markers (PouV/Oct3/4, Nanog and Sox2) also show asymmetric expression (more expressing cells on the left) in both sexes, but this asymmetry is at least partly due to expression in stromal cells of the developing gonad, and the pattern is different for all the genes. Therefore germ cell and pluripotency-associated genes show both sex-dependent and independent left-right asymmetry and a complex pattern of expression.
Porcine aortic valve bioprostheses: morphologic and functional considerations.

Porcine aortic valve (PAV) xenografts are the most frequently used type of bioprosthetic (BP) valve for the replacement of damaged or diseased heart valves. Xenograft tissues are routinely crosslinked during manufacturing using low concentrations (i.e., less than 1%) of glutaraldehyde. Crosslinking of xenograft tissue reduces the antigenicity, the rate of in vivo enzymatic degradation, and results in the loss of cell viability. The purpose of this review is to provide an overview of the morphologic and functional properties of the native aortic valve and the effects of tissue harvesting, fixation, anticalcification treatments, and mounting on PAV structure and function. Although efforts have been undertaken to design bioprostheses having increased durability, primary tissue failure still limits the long-term performance of xenograft replacement heart valves.
Controllability and reachability of 2-D positive systems: a graph theoretic approach

When dealing with two-dimensional (2-D) discrete state-space models, controllability properties are introduced in two different forms: a local form, which refers to single local states, and a global form, which instead pertains the infinite set of local states lying on a separation set. In this paper, these concepts are investigated in the context of 2-D positive systems by means of a graph theoretic approach. For all these properties, necessary and sufficient conditions, which refer to the structure of the digraph, are provided. While the global reachability index is bounded by the system dimension n, the local reachability index may far exceed the system dimension. Upper bounds on the local reachability index for some special classes of positive systems are finally derived.
Detection of a prfA-independent promoter responsible for listeriolysin gene expression in mutant Listeria monocytogenes strains lacking the PrfA regulator

Expression of listeriolysin, a major virulence factor of pathogenic Listeria monocytogenes, is positively regulated by the pleiotropic virulence regulator PrfA. In this study, we demonstrate that L. monocytogenes strains lacking the prfA regulator gene produce listeriolysin in small, albeit detectable, amounts when analyzed in a hemolysin assay and by immunoblots with listeriolysin-specific monoclonal antibodies. Transcriptional analysis revealed the existence of a PrfA-independent promoter that was responsible for the hemolytic activity expressed by these strains.
Comparative Study of the Behavioral and Neuropsychologic Characteristics of Tic Disorder With or Without Attention-Deficit Hyperactivity Disorder (ADHD)

To study the nature of the comorbidity of tic disorder and attention-deficit hyperactivity disorder (ADHD), patients with tic disorder with or without ADHD were compared on the basis of clinical ratings and neuropsychologic tests. Seventy-eight children were involved in this study: 16 with tic disorder, 19 with comorbid tic disorder and ADHD, 21 with ADHD, and 22 normal controls. Rating scales for ADHD, the Child Behavior Checklist and the Yale Global Tic Severity Scale, were completed in clinical groups. To identify differences in neuropsychologic function among the four groups, the results of seven neuropsychologic tests of global cognitive abilities, attention, information-processing capacity, and fine motor skill were compared. On most behavioral and neuropsychologic tests, the tic disorder with ADHD and the ADHD groups demonstrated similar performance patterns and marked deficits compared with the tic disorder and the control groups, whereas in most of the attention tests, the ADHD group made more commission errors than the tic disorder with ADHD group. These findings suggest that the tic disorder with ADHD group has marked cognitive deficits and behavioral disturbance similar to the ADHD group, whereas the tic disorder group is more similar to the controls. The tic disorder with ADHD group might represent a true comorbidity of the two disorders. (J Child Neurol 2001;16:719-726).
Approximate EM Algorithms for Parameter and State Estimation in Nonlinear Stochastic Models

Due to the availability of rapidly improving computer speeds, industry is increasingly using nonlinear process models in calculations that appear further down the control hierarchy. Indeed, nonlinear models are now frequently used for real-time control calculations. This trend means that there is growing interest in the availability of high speed state and parameter estimation algorithms for nonlinear models. One family of algorithms that can be used for this purpose is based on the, so called, Expectation Maximization Scheme. Unfortunately, in its basic form, this algorithm requires large computational resources. In this paper we review the EM algorithm and propose several approximate schemes aimed at retaining the essential flavour of this class of algorithm whilst ensuring that the computations are tractable. We will also compare the EM algorithm with several simpler schemes via a number of examples and comment on the trade-offs that occur.
Temozolomide downregulates P-glycoprotein expression in glioblastoma stem cells by interfering with the Wnt3a/glycogen synthase-3 kinase/β-catenin pathway.

BACKGROUND Glioblastoma multiforme stem cells display a highly chemoresistant phenotype, whose molecular basis is poorly known. We aim to clarify this issue and to investigate the effects of temozolomide on chemoresistant stem cells. METHODS A panel of human glioblastoma cultures, grown as stem cells (neurospheres) and adherent cells, was used. RESULTS Neurospheres had a multidrug resistant phenotype compared with adherent cells. Such chemoresistance was overcome by apparently noncytotoxic doses of temozolomide, which chemosensitized glioblastoma cells to doxorubicin, vinblastine, and etoposide. This effect was selective for P-glycoprotein (Pgp) substrates and for stem cells, leading to an investigation of whether there was a correlation between the expression of Pgp and the activity of typical stemness pathways. We found that Wnt3a and ABCB1, which encodes for Pgp, were both highly expressed in glioblastoma stem cells and reduced by temozolomide. Temozolomide-treated cells had increased methylation of the cytosine-phosphate-guanine islands in the Wnt3a gene promoter, decreased expression of Wnt3a, disrupted glycogen synthase-3 kinase/β-catenin axis, reduced transcriptional activation of ABCB1, and a lower amount and activity of Pgp. Wnt3a overexpression was sufficient to transform adherent cells into neurospheres and to simultaneously increase proliferation and ABCB1 expression. On the contrary, glioblastoma stem cells silenced for Wnt3a lost the ability to form neurospheres and reduced at the same time the proliferation rate and ABCB1 levels. CONCLUSIONS Our work suggests that Wnt3a is an autocrine mediator of stemness, proliferation, and chemoresistance in human glioblastoma and that temozolomide may chemosensitize the stem cell population by downregulating Wnt3a signaling.
University of Pennsylvania Working Papers in Linguistics Revisiting Incomplete Neutralization: the Case of Puerto Rican Spanish Revisiting Incomplete Neutralization: the Case of Puerto Rican Spanish Revisiting Incomplete Neutralization: the Case of Puerto Rican Spanish

Recent advances in phonetic analysis have led researchers to reexamine sounds that were previously assumed to be contextually neutralized, or merged into a single pronunciation. By using fine-grained spectrographic analysis, linguists have discovered that in many cases where neutralization was assumed, sounds are actually incompletely neutralized. That is, there are small differences in the articulation of these sounds such that they are in fact not merged, even though impressionistic descriptions report them as such. However, many researchers argue that the differences in pronunciation found in linguistic experiments are the result of hyperarticulation induced by the formality of the laboratory setting. In order to test whether or not incomplete neutralization exists in spontaneous speech, this study utilizes sociolinguistic interview data to examine coda liquid neutralization in Puerto Rican Spanish. The results from this study provide evidence that incomplete neutralization occurs outside of the laboratory context shows that the degree of neutralization and distinction between coda and in this dialect is conditioned by social and linguistic factors.
Axis I and Axis II disorders in alcoholics and drug addicts: fact or artifact?

OBJECTIVE It has been argued that Axis I and Axis II disorders diagnosed in substance users refer to substance-induced conditions rather than to independent psychiatric conditions; this argument will be referred to as the substance-related artifact hypothesis. Furthermore, Axis II symptoms co-occurring with Axis I disorders have been attributed to the contamination of personality assessment by mood and/or anxiety state effects (the trait-state artifact hypothesis). The present study is the first to prospectively examine the validity of these two hypothesized "artifacts" in substance users. METHOD In 276 individuals (57.6% female) applying for substance use treatment, current substance use disorders, mood/anxiety disorders and Axis II disorders were diagnosed using semistructured interviews both at baseline and at 1-year follow-up. The substance-related artifact hypothesis is tested by examining the covariation between recovery from substance use disorders on the one hand and recovery from and/or improvement of mood/anxiety and Axis II disorders on the other hand. The trait-state artifact hypothesis is tested by examining the covariation between recovery from mood/anxiety disorders on the one hand and recovery from and/or improvement of Axis II disorders on the other hand. RESULTS Recovery from substance use disorders covaried with recovery from and improvement of mood/anxiety disorders, but not with recovery from or improvement of Axis II pathology. Furthermore, recovery from mood/anxiety disorders covaried with recovery from and improvement of personality disorders, in particular Cluster C disorders. CONCLUSIONS Results from this study suggest that mood/anxiety disorders, but not personality disorders, diagnosed among people with substance use disorder may partly reflect substance-related artifacts. Furthermore, this study provides evidence for the contention that semistructured interview assessment of Axis II, at least without inquiry on an item-by-item basis, is susceptible to contamination by mood/anxiety state effects.
On the behaviour of porcine adipose and skeletal muscle tissues under shock compression

Abstract : The response of porcine adipose and skeletal muscle tissues to shock compression has been investigated using the plate-impact technique in conjunction with manganin foil pressure gauge diagnostics. This approach has allowed for measurement of the levels of uniaxial stress imparted to both skeletal muscle and rendered adipose tissue by the shock. In addition, the lateral stress component generated within adipose tissue during shock loading has also been investigated. The techniques employed in this study have allowed for equation-of-state relationships to be established for the investigated materials, highlighting non-hydrodynamic behaviour in each type of tissue over the range of investigated impact conditions. While the adipose tissue selected in this work has been shown to strengthen with impact stress in a manner similar to that seen to occur in polymeric materials, the skeletal muscle tissues exhibited a ow strength, or resistance to compression, that was independent of impact stress. Both the response of the adipose material and tested skeletal muscle tissues lie in contrast with the shock response of ballistic gelatin, which has previously been shown to exhibit hydrodynamic behaviour under equivalent loading conditions.
Uppers and downers: Understanding sleep regulation using small molecules in Drosophila

Sleep is an important physiological state, but its function and regulation remain elusive. In Drosophila melanogaster, a useful model organism for studying sleep, forward genetic screens have identified important sleep-modulating genes and pathways; however, the results of such screens may be limited by developmental abnormalities or lethality associated with mutation of certain genes. To circumvent these limitations, we screened 1280 small molecules for effects on sleep in adult Drosophila. We used genetic and molecular approaches to elucidate the mechanisms by which two of these drugs altered sleep behavior. We found that administration of reserpine, a small molecule inhibitor of the vesicular monoamine transporter (VMAT) that repackages monoamines into presynaptic vesicles, resulted in an increase in sleep. We found that VMAT-null mutants, like reserpine-fed flies, have an increased sleep phenotype, as well as an increased arousal threshold and resistance to the effects of reserpine. However, although the VMAT mutants are consistently resistant to reserpine, other aspects of their sleep phenotype are dependent on genetic background. Thus, they may not have been detected in a classical forward genetic screen, further attesting to the utility of a small molecule screen. Mutations affecting single monoamine pathways did not affect reserpine sensitivity, suggesting that effects of VMAT/reserpine on sleep are mediated by multiple monoamines. We also studied the mode of action of caffeine, a common wake-promoting compound. Caffeine is thought to promote wake by inhibiting adenosine receptors, however previous work demonstrated that the wakepromoting effects of caffeine are independent of the adenosine receptor in the fly. We show that dopamine is required for the wake-promoting effect of caffeine in the fly, and that caffeine likely acts presynaptically to increase dopamine signaling. We identify a cluster of neurons, the paired anterior medial (PAM) cluster of dopaminergic neurons, which are essential for the caffeine response and which show increased activity following caffeine administration. Overall, we find that small molecule screens can be used effectively to identify regulators of adult behavior. The results of our screen and follow-up experiments demonstrate that presynaptic modulation of monoamine signaling may be a major source of sleep regulation. Degree Type Dissertation Degree Name Doctor of Philosophy (PhD) Graduate Group Cell & Molecular Biology First Advisor Amita Sehgal This dissertation is available at ScholarlyCommons: http://repository.upenn. edu/edissertations/1384 Second Advisor David Raizen
Alteration of cytosolic free calcium homeostasis by SIN‐1: high sensitivity of L‐type Ca2+ channels to extracellular oxidative/nitrosative stress in cerebellar granule cells

Exposure of cerebellar granule neurones in 25 mm KCl HEPES‐containing Locke's buffer (pH 7.4) to 50–100 µm SIN‐1 during 2 h decreased the steady‐state free cytosolic Ca2+ concentration ([Ca2+]i) from 168 ± 33 nm to 60 ± 10 nm, whereas exposure to ≥ 0.3 mm SIN‐1 produced biphasic kinetics: (i) decrease of [Ca2+]i during the first 30 min, reaching a limiting value of 75 ± 10 nm (due to inactivation of L‐type Ca2+ channels) and (ii) a delayed increase of [Ca2+]i at longer exposures, which correlated with SIN‐1‐induced necrotic cell death. Both effects of SIN‐1 on [Ca2+]i are blocked by superoxide dismutase plus catalase and by Mn(III)tetrakis(4‐benzoic acid)porphyrin chloride. Supplementation of Locke's buffer with catalase before addition of 0.5–1 mm SIN‐1 had no effect on the decrease of [Ca2+]i but further delayed and attenuated the increase of [Ca2+]i observed after 60–120 min exposure to SIN‐1 and also protected against SIN‐1‐induced necrotic cell death. α‐Tocopherol, the potent NMDA receptor antagonist (+)‐MK‐801 and the N‐ and P‐type Ca2+ channels blocker ω‐conotoxin MVIIC had no effect on the alterations of [Ca2+]i upon exposure to SIN‐1. However, inhibition of the plasma membrane Ca2+ ATPase can account for the increase of [Ca2+]i observed after 60–120 min exposure to 0.5–1 mm SIN‐1. It is concluded that L‐type Ca2+ channels are a primary target of SIN‐1‐induced extracellular nitrosative/oxidative stress, being inactivated by chronic exposure to fluxes of peroxynitrite of 0.5–1 μm/min, while higher concentrations of peroxynitrite and hydrogen peroxide are required for the inhibition of the plasma membrane Ca2+ ATPase and induction of necrotic cell death, respectively.