gebhart/patrepeval huggingface dataset:
Memory effects in nematics with quenched disorder (2006)

We present a combined experimental and Monte Carlo study of a nematic phase in the presence of quenched disorder. The turbidity of a nematic liquid crystal embedded in a porous polymer membrane is measured under different applied field conditions for field-cooled and zero-field-cooled samples. We find that a significant permanent alignment of the nematic can be induced by fields as low as 0.1 V/microm applied during the isotropic to nematic transition. An analogous effect and dependence on sample history is found by studying the order parameter of a sprinkled disorder Lebwohl-Lasher spin model, indicating that dilute quenched randomness is sufficient to produce memory effects in nematics. The large memory induced by field cooling appears to be written in the system during the transition as a result of the field action on freely oriented nematic nuclei. At lower temperature the nuclei consolidate into permanent nematic textures developed from the interaction with quenched disorder.
Cost-Effective and Rapid Presumptive Identification of Gram-Negative Bacilli in Routine Urine, Pus, and Stool Cultures: Evaluation of the Use of CHROMagar Orientation Medium in Conjunction with Simple Biochemical Tests (2000)

The algorithm for a new identification system was designed on the basis of colony color and morphology on CHROMagar Orientation medium in conjunction with simple biochemical tests such as indole (IND), lysine decarboxylase (LDC), and ornithine decarboxylase (ODC) utilization tests with gram-negative bacilli isolated from urine samples as well as pus, stool, and other clinical specimens by the following colony characteristics, biochemical reactions, and serological results: pinkish to red, IND positive (IND(+)), Escherichia coli; metallic blue, IND(+), LDC(+), and ODC negative (ODC(-)), Klebsiella oxytoca; IND(+), LDC(-), and ODC(+), Citrobacter diversus; IND(+) or IND(-), LDC(-), and ODC(-), Citrobacter freundii; IND(-), LDC(+), and ODC(+), Enterobacter aerogenes; IND(-), LDC(-), and ODC(+), Enterobacter cloacae; IND(-), LDC(+), and ODC(-), Klebsiella pneumoniae; diffuse brown and IND(+), Morganella morganii; IND(-), Proteus mirabilis; aqua blue, Serratia marcescens; bluish green and IND(+), Proteus vulgaris; transparent yellow-green, serology positive, Pseudomonas aeruginosa; clear and serology positive, Salmonella sp.; other colors and reactions, the organism was identified by the full identification methods. The accuracy and cost-effectiveness of this new system were prospectively evaluated. During an 8-month period, a total of 345 specimens yielded one or more gram-negative bacilli. A total of 472 gram-negative bacillus isolates were detected on CHROMagar Orientation medium. For 466 of the isolates (98.7%), no discrepancies in the results were obtained on the basis of the identification algorithm. The cost of identification of gram-negative bacilli during this period was reduced by about 70%. The results of this trial for the differentiation of the most commonly encountered gram-negative pathogens in clinical specimens with the new algorithm were favourable in that it permitted reliable detection and presumptive identification. In addition, this rapid identification system not only significantly reduced costs but it also improved the daily work flow within the clinical microbiology laboratory.
Integrated Genomic and Proteomic Analyses of Gene Expression in Mammalian Cells (2004)

Using DNA microarrays together with quantitative proteomic techniques (ICAT reagents, two-dimensional DIGE, and MS), we evaluated the correlation of mRNA and protein levels in two hematopoietic cell lines representing distinct stages of myeloid differentiation, as well as in the livers of mice treated for different periods of time with three different peroxisome proliferative activated receptor agonists. We observe that the differential expression of mRNA (up or down) can capture at most 40% of the variation of protein expression. Although the overall pattern of protein expression is similar to that of mRNA expression, the incongruent expression between mRNAs and proteins emphasize the importance of posttranscriptional regulatory mechanisms in cellular development or perturbation that can be unveiled only through integrated analyses of both proteins and mRNAs.
Molecular Epidemiology of Community- and Health Care-Associated Methicillin-Resistant Staphylococcus aureus in Manitoba, Canada (2005)

Recently, acquisition of methicillin-resistant Staphylococcus aureus (MRSA) has been increasingly seen in community settings. Beginning in 1995, we have routinely conducted pulsed-field gel electrophoresis (PFGE) of MRSA isolates received at Cadham Provincial Laboratory (CPL) in Manitoba, Canada. Our diverse collection of isolates coupled with molecular subtype information allowed us to assess the extent to which MRSA isolates in general were associated with community acquisition and whether specific PFGE types were more likely to be found in community settings. Forty percent of the MRSA isolates in our analysis were designated community associated (CA), with two of the six most common PFGE types showing a greater likelihood to be CA-MRSA. Overall, CA-MRSA were more likely to show multiple sensitivity to antibiotics and to be associated with younger age groups. Mapping of specific CA-MRSA types over successive 5-year periods showed rapid temporal shifts in prevalence in different parts of the province.
Integration of paper-based microfluidic devices with commercial electrochemical readers (2010)

The combination of simple Electrochemical Micro-Paper-based Analytical Devices (EµPADs) with commercially available glucometers allows rapid, quantitative electrochemical analysis of a number of compounds relevant to human health (e.g., glucose, cholesterol, lactate, and alcohol) in blood or urine.
Synthesis by a Solvothermal Route and Characterization of CuInSe2 Nanowhiskers and Nanoparticles (1999)

CuInSe2 is a leading material for high-efficiency and radiation-hard solar cell applications. The device properties of CuInSe2-based solar cells are known to be critically influenced by their stoichiometric compositions, defect chemistry, and structure; however, with the current methods of synthesis high temperature and pressure are needed to maintain satisfactory stoichiometry. Reported here is a solvothermal route to chalcopyrite CuInSe2 nanocrystals using alkylamines as a solvent. High-quality CuInSe2 nanowhiskers and spherical nanoparticles with stoichiometric composition were produced at a greatly reduced temperature.
PRIMITIVE NEUROECTODERMAL TUMOR (NEUROEPITHELIOMA) OF SPINAL NERVE ROOT–Report of an Adult Case and Establishment of a Cell Line– (1979)

A case of primitive neuroectodermal tumor arising in the cervical nerve root of a 28-year-old man is presented. Histologically, the tumor was characterised by proliferation of primitive neuroectodermal cells and formation of numerous Homer-Wright type rosettes. A cell line (Nagai line) was established from the tumor. Electron microscopic examination of Nagai cells revealed numerous microrosette formation with microvilli-like cytoplasmic processes projecting into the central lumina. Neurosecretory granules appeared in the cytoplasmic processes when Nagai cells were treated with dibutyryl cyclic AMP. Primitive satellite cells which completely surrounded other tumor cells with their tongue-like slender cytoplasmic processes were also found. Histogenesis of this unique tumor was discussed comparing with the neuroblastoma of sympathetic nervous system, medulloblastoma of the central nervous system, and with the tumors induced by Adenovirus type 12 in animals. It was concluded that the tumor was neuroepithelioma derived from a primitive stem cell of neural crest origin which possesses the bipotency to differentiate toward either neuroblastic or neurilemmal line.
Treatment of a newly established transgenic model of chronic arthritis with nondepleting anti-CD4 monoclonal antibody (1997)

We established a novel animal model for rheumatoid arthritis (RA) by following backcrossing to DBA/1 of (SWR/J x DBA/1)F1 TCR-beta Tg mice, previously reported to be highly susceptible to collagen-induced arthritis. These mice evolved, upon collagen type II immunization, into a chronic arthritis that histopathologically resembles RA. The availability of such a model prompted us to study the role of CD4+ T cells throughout the evolution of disease. Here, we show that administration of nondepleting anti-CD4 not only prevented the evolution of disease but also treated established arthritis. Moreover, functional analyses of T cells isolated from anti-CD4-treated mice demonstrated that the mechanism of protection is not achieved by suppression of the Th1 population but is mediated by induction of collagen type II-specific T cell anergy. Our study suggests that: 1) CD4+ T cells have a fundamental role both in the induction and in the perpetuation of disease; 2) targeting T cells may be an appropriate therapeutic option; and 3) a suitable and well-balanced anti-CD4 treatment may be a valid approach to the control of RA.
Self in Time: Imagined Self-Location Influences Neural Activity Related to Mental Time Travel (2008)

Conscious awareness of the self as continuous through time is attributed to the human ability to remember the past and to predict the future, a cogitation that has been called "mental time travel" (MTT). MTT allows one to re-experience one's own past by subjectively "locating" the self to a previously experienced place and time, or to pre-experience an event by locating the self into the future. Here, we used a novel behavioral paradigm in combination with evoked potential mapping and electrical neuroimaging, revealing that MTT is composed of two different cognitive processes: absolute MTT, which is the location of the self to different points in time (past, present, or future), and relative MTT, which is the location of one's self with respect to the experienced event (relative past and relative future). These processes recruit a network of brain areas in distinct time periods including the occipitotemporal, temporoparietal, and anteromedial temporal cortices. Our findings suggest that in addition to autobiographical memory processes, the cognitive mechanisms of MTT also involve mental imagery and self-location, and that relative MTT, but not absolute MTT, is more strongly directed to future prediction than to past recollection.
Detecting and dealing with hovering maneuvers in vision-aided inertial navigation systems (2013)

In this paper, we study the problem of hovering (i.e., absence of translational motion) detection and compensation in Vision-aided Inertial Navigation Systems (VINS). We examine the system's unobservable directions for two common hovering conditions (with and without rotational motion) and propose a robust motion-classification algorithm, based on both visual and inertial measurements. By leveraging our observability analysis and the proposed motion classifier, we modify existing state-of-the-art filtering algorithms, so as to ensure that the number of the system's unobservable directions is minimized. Finally, we validate experimentally the proposed modified sliding window filter, by demonstrating its robustness on a quadrotor with rapid transitions between hovering and forward motions, within an indoor environment.
Epigenetic Up-regulation of C-C Chemokine Receptor 7 and C-X-C Chemokine Receptor 4 Expression in Melanoma Cells (2005)

Histone deacetylation and DNA methylation establish epigenetic modifications, which through chromatin remodeling may result in gene silencing. We hypothesized that chemokine receptors C-C chemokine receptor 7 (CCR7) and C-X-C chemokine receptor 4 (CXCR4) on melanoma cells undergo epigenetic regulation. We investigated whether a histone deacetylase inhibitor and a demethylating agent influence CCR7 and CXCR4 expression on melanoma cells. Initially, microarray analysis was done to screen changes in chemokine receptor expression on melanoma cells after treatment with trichostatin A (TSA) and 5-Aza-2-deoxycytidine (5-Aza). CCR7 and CXCR4 mRNA expression were uniformly altered and selected for further investigation. Quantitative real-time reverse transcription-PCR assay, immunohistochemistry, and Western blot analysis were used to assess changes in mRNA and protein expression induced by TSA and 5-Aza in melanoma lines. Cell migration assays were conducted to assess the effects of altered CCR7 and CXCR4 expression on cell function. Treatment with TSA or 5-Aza increased gene expression of both CCR7 and CXCR4 in melanoma lines. TSA was the strongest enhancer. With combined treatment, CCR7 and CXCR4 mRNA expression was also up-regulated. Immunohistochemistry after combined treatment showed enhanced staining of both CCR7 and CXCR4 compared with control cells. Melanoma cell migration in TSA- and 5-Aza-treated cells was 7- and 2-fold higher than control cells for CCR7 and CXCR4, respectively. In summary, a histone deacetylase inhibitor and a demethylating agent up-regulated CCR7 and CXCR4 expression on melanoma cells. This increase in chemokine receptor expression correlated with functional activity. Most importantly, we have identified an epigenetic mechanism that may endogenously regulate chemokine receptor expression on melanoma cells.
Urban Street Lighting Infrastructure Monitoring Using a Mobile Sensor Platform (2016)

We present a system for collecting and analyzing information on street lighting infrastructure. We develop a car-mounted sensor platform that enables collection and logging of data on street lights during night-time drive-bys. We address several signal processing problems that are key to mapping street illumination levels, identifying street lamps, estimating their heights, and geotagging them. Specifically, we highlight an image recognition algorithm to identify street lamps from the video data collected by the sensor platform and its subsequent use in estimating the heights of street lamps. We also outline a framework to improve vehicle location estimates by combining sensor observations in an extended Kalman filter framework. Our eventual goal is to develop a semi-live virtual 3-D street lighting model at urban scale that enables citizens and decision makers to assess and optimize performance of nighttime street lighting.
Squalestatin Cures Prion-infected Neurons and Protects Against Prion Neurotoxicity (2004)

A key feature of prion diseases is the conversion of the normal, cellular prion protein (PrP(C)) into beta-sheet-rich disease-related isoforms (PrP(Sc)), the deposition of which is thought to lead to neurodegeneration. In the present study, the squalene synthase inhibitor squalestatin reduced the cholesterol content of cells and prevented the accumulation of PrP(Sc) in three prion-infected cell lines (ScN2a, SMB, and ScGT1 cells). ScN2a cells treated with squalestatin were also protected against microglia-mediated killing. Treatment of neurons with squalestatin resulted in a redistribution of PrP(C) away from Triton X-100 insoluble lipid rafts. These effects of squalestatin were dose-dependent, were evident at nanomolar concentrations, and were partially reversed by cholesterol. In addition, uninfected neurons treated with squalestatin became resistant to the otherwise toxic effect of PrP peptides, a synthetic miniprion (sPrP106) or partially purified prion preparations. The protective effect of squalestatin, which was reversed by the addition of water-soluble cholesterol, correlated with a reduction in prostaglandin E(2) production that is associated with neuronal injury in prion disease. These studies indicate a pivotal role for cholesterol-sensitive processes in controlling PrP(Sc) formation, and in the activation of signaling pathways associated with PrP-induced neuronal death.
Structure of the Bcr-Abl oncoprotein oligomerization domain. (2002)

The Bcr-Abl oncoprotein is responsible for a wide range of human leukemias, including most cases of Philadelphia chromosome-positive chronic myelogenous leukemia. Oligomerization of Bcr-Abl is essential for oncogenicity. We determined the crystal structure of the N-terminal oligomerization domain of Bcr-Abl (residues 1-72 or Bcr1-72) and found a novel mode of oligomer formation. Two N-shaped monomers dimerize by swapping N-terminal helices and by forming an antiparallel coiled coil between C-terminal helices. Two dimers then stack onto each other to form a tetramer. The Bcr1-72 structure provides a basis for the design of inhibitors of Bcr-Abl transforming activity by disrupting Bcr-Abl oligomerization.
Pathogenic Vibrio Activate NLRP3 Inflammasome via Cytotoxins and TLR/Nucleotide-Binding Oligomerization Domain-Mediated NF-κB Signaling (2010)

Vibrio vulnificus and Vibrio cholerae are Gram-negative pathogens that cause serious infectious disease in humans. The beta form of pro-IL-1 is thought to be involved in inflammatory responses and disease development during infection with these pathogens, but the mechanism of beta form of pro-IL-1 production remains poorly defined. In this study, we demonstrate that infection of mouse macrophages with two pathogenic Vibrio triggers the activation of caspase-1 via the NLRP3 inflammasome. Activation of the NLRP3 inflammasome was mediated by hemolysins and multifunctional repeat-in-toxins produced by the pathogenic bacteria. NLRP3 activation in response to V. vulnificus infection required NF-kappaB activation, which was mediated via TLR signaling. V. cholerae-induced NLRP3 activation also required NF-kappaB activation but was independent of TLR stimulation. Studies with purified V. cholerae hemolysin revealed that toxin-stimulated NLRP3 activation was induced by TLR and nucleotide-binding oligomerization domain 1/2 ligand-mediated NF-kappaB activation. Our results identify the NLRP3 inflammasome as a sensor of Vibrio infections through the action of bacterial cytotoxins and differential activation of innate signaling pathways acting upstream of NF-kappaB.
Safety and Pharmacokinetics of Amprenavir (141W94), a Human Immunodeficiency Virus (HIV) Type 1 Protease Inhibitor, following Oral Administration of Single Doses to HIV-Infected Adults (1999)

We conducted a double-blind, placebo-controlled, parallel, dose-escalation trial to evaluate the pharmacokinetics and safety of single, oral doses of amprenavir (141W94; formerly VX-478), a potent inhibitor of human immunodeficiency virus (HIV) type 1 protease, administered as hard gelatin capsules in 12 HIV-infected subjects. The doses of amprenavir evaluated were 150, 300, 600, 900, and 1,200 mg. Amprenavir was rapidly absorbed, with the time to maximum concentration occurring within 1 to 2 h after dosing. On the basis of power model analysis, the increase in the maximum concentration of amprenavir in plasma (Cmax) was less than dose proportional, and the increase in the area under the concentration-time curve from time zero to infinity (AUC0-infinity) was greater than dose proportional; mean slopes (with 90% confidence intervals) were 1.25 (1.16 to 1.35) and 0.78 (0.78 to 0.86) for AUC0-infinity and Cmax, respectively. Amprenavir was eliminated slowly, with a terminal-phase half-life of 8 h. A second study was conducted to determine the bioavailability of the hard gelatin capsule relative to that of a subsequently developed soft gelatin capsule. The capsules were bioequivalent in terms of AUC0-infinity but not in terms of Cmax; geometric-least-squares means ratios (with 90% confidence intervals) were 1.03 (0.92 to 1.14) and 1.25 (1.03 to 1. 53) for AUC0-infinity and Cmax, respectively. Administration of soft gelatin capsules of amprenavir with a high-fat breakfast resulted in a 14% decrease in the mean AUC0-infinity (from 9.58 to 8.26 microg. h/ml), which is not likely to be clinically significant. The most common adverse events related to amprenavir were headache, nausea, and hypesthesia. Amprenavir appears to be safe and well tolerated over the dose range of 150 to 1200 mg. On the basis of the present single-dose studies, amprenavir is an HIV protease inhibitor with favorable absorption and clearance pharmacokinetics that are only minimally affected by administration with food.
The cell cycle control gene ZAC/PLAGL1 is imprinted--a strong candidate gene for transient neonatal diabetes (2000)

We describe a screen for new imprinted human genes, and the identification in this way of ZAC (zinc finger protein which regulates apoptosis and cell cycle arrest)/ PLAGL1 (pleomorphicadenoma of the salivary gland gene like 1) as a strong candidate gene for transient neonatal diabetes mellitus (TNDM). To screen for imprinted genes, we compared parthenogenetic DNA from the chimeric patient FD and androgenetic DNA from hydatidiform mole, using restriction landmark genome scanning for methylation. This resulted in identification of two novel imprinted loci, one of which (NV149) we mapped to the TNDM region of 6q24. From analysis of the corresponding genomic region, it was determined that NV149 lies approximately 60 kb upstream of the ZAC / PLAGL1 gene. RT-PCR analysis was used to confirm that this ZAC / PLAGL1 is expressed only from the paternal allele in a variety of tissues. TNDM is known to result from upregulation of a paternally expressed gene on chromosome 6q24. The paternal expression, map position and known biological properties of ZAC / PLAGL1 make it highly likely that it is the TNDM gene. In particular, ZAC / PLAGL1 is a transcriptional regulator of the type 1 receptor for pituitary adenylate cyclase-activating polypeptide, which is the most potent known insulin secretagog and an important mediator of autocrine control of insulin secretion in the pancreatic islet.
Anti-cancer potential of traditional Chinese herbal medicines and microbial fermentation products (2005)

The uses of traditional Chinese herbal medicines (TCHM) in forms of extracts for anti-cancer purpose have been practiced in China since 3,000 B.C. However, most of the TCHMs that have been claimed to possess anti-cancer potential are still not experimentally proved and/or the underlying mechanistic actions were not defined. Recently, we have reported the principal mechanisms involved in the anomalous fruit extract of Gleditsia sinensis Lam (GSE) induced cancer cell death. Furthermore, we also continued our study on three other TCHMs including the fresh juice of Scutellaria barbata (SBJ) and warmed water extract of Radix Sophorae Tonkinensis (RSTE) (Sophora subprostrata C. et T. C) and Brucea javanica (BJE) (Fructus bruceae). On the other hand, we have also investigated the possible use of microbial fermentation products in the forms of either dried biomass (Phaffia rhodozyma) or fermented extract (effective micro-organism fermentation extract, EM-X). Taken together, we believe that the accumulation of experimental and clinical evidences could further sustain the scientific base for the clinical use of both TCHMs and microbial fermentation products in the foreseeing future.