gebhart/patrepeval huggingface dataset:
ATOMIC FORCE MICROSCOPY AND FLUORESCENCE MICROSCOPY OF MALARIAL HEPATOCYTES (2008)

Malaria is a devastating disease which kills millions of people around the world each year. The disease is caused by one of several parasites of the genus Plasmodium. The parasite enters the human host in the form of sporozoites, delivered by a mosquito bite and reaches the liver through the bloodstream. In the liver, the parasite undergoes a development and multiplication process, after which thousands of merozoites, a second form of the parasite, are released into the blood stream, where the characteristic fevers of the disease occur. Because the liver stage of infection is asymptomatic, and samples are more difficult to extract, it has been studied much less than the blood infection stage, but is vital for the lifecycle of Plasmodium, and for the progression and severity of the disease1. We have used simultaneous atomic force microscopy (AFM) and optical microscopy to study a human hepatoma cell line, Huh7, infected by Plasmodium berghei. Exposure of liver cells to the parasites causes a low percentage of infection (ca. 1%) of the cells, and so we used P. berghei genetically modified to express green fluorescence protein (GFP). This allowed fluorescence microscopy to be used to identify and locate infected cells. Having identified which cells were infected, we studied both infected and uninfected cells using AFM to
Measuring Fiber Orientation in Nonwovens (1996)

In nonwovens, fiber orientation is an important characteristic because it directly influences the properties of the material. In a series of papers, we plan to explore the viability of image analysis algorithms for characterizing fiber orientation. In the first part of this series, we present a simulation scheme to produce images to test these different algorithms. As part of the series, we will present a direct tracking method in Part II, as well as Fourier and flow field analyses in subsequent parts for characterizing fiber orientation.
Serum dopamine-beta-hydroxylase activity in parents and children. (1975)

Dopamine-beta-hydroxylase (DBH), an enxyme catalyzing the final step in the synthesis of norepinephrine, is released with norepinephrine on stimulation of the sympathetic nervous system. In this study an enzymatic colorimetric method was used to assay serum DBH activity in 196 individuals of whom 169 were either the parents or children in 29 families. We examined the association of DBH with age and with hypertension and the faamilial pattern of distribution of serum DBH activity. Serum DBH activity was highest in te groups 10 to 14, 40 to 49, and over 60 years. There was no significant difference in serum DBH activity between normal subjects and individuals with hypertension in any age group. tfurthermore, there was no significant correlation of mean blood pressure with serum DBH activity with or without correction of DBH for age differences; Highly significant correlations of serum DBH activity were found in sibling-sibling pairs and in mean parent-child pairs. No significant correlations were found for father-mother pairs. These observations suggest that the contribution of heredity is more important that shared environment in determining the familial pattern of distribution of serum DBH activity. Serum DBH activity did not have a bimodal distribution in the population. Noevidence was found for a maternal influence or for sex linkage in the transmission of this trait. Our data, derived from this study restricted to families with only two generations, are not adequate to specify with confidence the mode of inheritance of DBH activity in the general population.
<title>Best viewpoints for active vision classification and pose estimation</title> (1997)

We advance new active computer vision algorithms that classify objects and estimate their pose from intensity images. Our algorithms automatically reposition the sensor if the class or pose of an object is ambiguous in a given image and incorporate data from multiple object views in determining the final object classification. A feature space trajectory (FST) in a global eigenfeature space is used to represent 3-D distorted views of an object. Assuming that an observed feature vector consists of Gaussian noise added to a point on the FST, we derive a probability density function (PDF) for the observation conditioned on the class and pose of the object. Bayesian estimation and hypothesis testing theory are then used to derive approximations to the maximum a posteriori probability pose estimate and the minimum probability of error classifier. New confidence measures for the class and pose estimates, derived using Bayes theory, determine when additional observations are required as well as where the sensor should be positioned to provide the most useful information.
Distribution System State Estimation Via Data-Driven and Physics-Aware Deep Neural Networks (2019)

Massive integration of renewables and electric vehicles comes with unknown dynamics - what exemplifies the need for fast, accurate, and robust distribution system state estimation (DSSE). Due to limited real-time measurements however, optimization-oriented DSSE faces major challenges related to convergence, as well as multiple global/local minima. To address these challenges, this paper puts forth a novel deep neural network (DNN)-based computational framework for DSSE that consists of two modules: a deep recurrent neural network (RNN) based pseudo-measurement postulating module, and a prox-linear net-based real-time state estimation module. Both RNN and prox-linear nets learn complex nonlinear functions, and can afford efficient training by leveraging existing deep learning platforms. Numerical tests with semi-real load data demonstrate the merits of the DNN-based DSSE approach.
Passive membrane transport of lignin-related compounds (2019)

Lignin is an abundant aromatic polymer found in plant secondary cell walls. In recent years, lignin has attracted renewed interest as a feedstock for bio-based chemicals via catalytic and biological approaches and has emerged as a target for genetic engineering to improve lignocellulose digestibility by altering its composition. In lignin biosynthesis and microbial conversion, small phenolic lignin precursors or degradation products cross membrane bilayers through an unidentified translocation mechanism prior to incorporation into lignin polymers (synthesis) or catabolism (bioconversion), with both passive and transporter-assisted mechanisms postulated. To test the passive permeation potential of these phenolics, we performed molecular dynamics simulations for 69 monomeric and dimeric lignin-related phenolics with 3 model membranes to determine the membrane partitioning and permeability coefficients for each compound. The results support an accessible passive permeation mechanism for most compounds, including monolignols, dimeric phenolics, and the flavonoid, tricin. Computed lignin partition coefficients are consistent with concentration enrichment near lipid carbonyl groups, and permeability coefficients are sufficient to keep pace with cellular metabolism. Interactions between methoxy and hydroxy groups are found to reduce membrane partitioning and improve permeability. Only carboxylate-modified or glycosylated lignin phenolics are predicted to require transporters for membrane translocation. Overall, the results suggest that most lignin-related compounds can passively traverse plant and microbial membranes on timescales commensurate with required biological activities, with any potential transport regulation mechanism in lignin synthesis, catabolism, or bioconversion requiring compound functionalization.
NY-ESO-1 protein formulated With ISCOMATRIX™ adjuvant induces a broad-based immune response involving high titers of antibody, CD4+ and CD8+ T-cell responses (2003)

NY-ESO-1 is a cancer-testis (CT) antigen that is expressed in a wide variety of common cancers. We vaccinated patients with full length NY-ESO-1 protein with and without the ISCOMATRIX™ adjuvant. Immune responses were evaluated by DTH skin testing, antibody assays and cellular assays for epitope-specific CD4+ and CD8+ cells. Antibody titers and DTH reactions were significantly greater in patients who received adjuvant compared to those who received protein alone. Biopsy of DTH lesions showed CD4+ and CD8+ T-cell infiltrates. Antigen-specific T cells capable of recognizing Class I and class II NY-ESO-1 epitopes were isolated from these lesions. Circulating T-cell responses in blood were assessed with tetramers and an intracellular cytokine staining (ICS) assay for IFN-gamma to assess responses to an HLA-A2-restricted epitope NY-ESO-1157-165 (SLLMWITQC). ICS was also employed in a novel assay, which used autologous PBMCs and panels of overlapping peptides. Three of 8 patients who received 100 mg of protein with adjuvant responded to NY-ESO-1157-165. Importantly, responses to a variety of other previously described and undescribed CD4 and CD8 epitopes were seen, demonstrating a broad-based CD4+ and CD8+ cellular immune response against NY-ESO-1. In ongoing work we are defining minimal peptides, mapping these epitopes, and identifying the HLA class I and II restriction for each. Although the study was not designed to evaluate clinical outcomes, data show that those patients who received vaccine with ISCOMATRIX™ adjuvant appeared to have a longer disease-free survival than those who received protein alone or placebo. A prospective evaluation is required to determine whether immune responses to NY-ESO-1 can modify the survival of patients with tumors that express this antigen. 

This abstract was published in Cancer Immunity , a [Cancer Research Institute][1] journal that ceased publication in 2013 and is now provided online in association with Cancer Immunology Research .

 [1]: http://cancerresearch.org/
Characterization of the Methylation Patterns in Human Papillomavirus Type 16 Viral DNA in Head and Neck Cancers (2011)

Human papillomavirus (HPV) type 16 can integrate into the host genome, thereby rendering the viral coding genes susceptible to epigenetic modification. Using bisulfite genomic sequencing, we determined the methylation status of all 110 CpG sites within the viral epigenome in advanced stage III/IV HPV-16-associated head and neck cancers. We found that the viral genome was hypomethylated in the majority of head and neck cancers, in particular within the viral regulatory region, long control region (LCR), which controls transcription of the E6 and E7 oncogenes. The hypomethylation status of LCR correlated with detectable levels of E6 and E7 expression, which suggests that the tumors may still be dependent on these viral oncogenes to maintain the malignant phenotype. In addition to the methylation status of LCR, we report other potential factors which may influence intratumoral E6 and E7 expression including viral copy number and integration site. We were able to detect the viral epigenetic alterations in sampled body fluids, such as serum and saliva, which correlated with the changes observed in the primary tumors. Because viral epigenetic changes occur in the setting of viral integration into the human genome, the detection of methylated HPV genes in the serum and/or saliva may have diagnostic potential for early detection strategies of viral integration and assessment of risk for cancer development in high-risk individuals. Our findings also support continued targeting of the E6 and/or E7 antigens through various vaccine strategies against HPV-associated cancers.
Dipyridamole-Cisplatin Potentiation: Enhanced in Vivo Cytotoxicity in Xenograft Models of Human Testicular and Bladder Cancers (1990)

The antitumor efficacy and host toxicity of dipyridamole (DP), methotrexate (MTX) and cisplatin (CDDP) alone and combined were evaluated in a nude mouse supported human bladder cancer model. Single agent post treatment tumor volume growth ratio [TGR] values of DP, MTX and CDDP were 97%, 65% and 49% of control. While the MTX/DP combination produced only mild cytotoxic enhancement, CDDP/DP and CDDP/MTX/DP reduced TGR to 20% and 17%, respectively. A second multi-dose evaluation of CDDP/DP using human testicular carcinoma in this model also showed a CDDP dose-dependent response with achievable complete tumor regression. Host toxicity was not substantially increased by DP. DP would appear to be effective in vivo as a chemosensitizer of CDDP; it may enhance the therapeutic efficacy of CDDP in a variety of tumors.
Genetics of Experimental Autoimmune Encephalomyelitis (1999)

The genetic basis for susceptibility to experimental autoimmune encepha- lomyelitis (EAE) has been the subject of intense study for several decades. In spite of this long history, however, the eVort has only yielded small hints and contradictory leads to which genes influence susceptibility to this autoimmune disease. EAE is a prototypical model of autoimmunity that diVers from other autoimmune diseases since it is relatively easily induced and quickly diagnosed in a wide range of strains and species. It also typically shows what looks, at first glance, to be a simple autosomal dominant inheritance pattern, making it appear to be an ideal disease to be solved genetically. In reality, however, the underlying genetics of EAE are much more complex than they appear on the surface, and the disease itself has a complex pathology that is only just beginning to be understood. With the advent in the last few years of transgene and knockout technologies and progress on the mapping and sequencing of genomes, strides are finally being made that promise to make an understanding of the genetics of EAE susceptibility a realizable goal. EAE is well established as a model for the human disease multiple sclerosis (MS), with resemblance in both its clinical and pathological features. Unlike MS, however, which is a spontaneous disease of unknown etiology, EAE is induced by driving the immune system to attack the brain and spinal cord through an immunization with any of several well-described central nervous system (CNS) myelin proteins. The disease that ensues begins with an inflam- matory reaction in the white matter of the brain and spinal cord, causing both edema and myelin damage. As the inflammation progresses, damage to the myelin, which normally forms an insulating sheath around axons, leads to a disruption in the transmission of nerve signals along the spinal cord. This disruption typically manifests outwardly as paralysis in the tail and limbs.
Identification of GSK625433: A novel clinical candidate for the treatment of hepatitis C. (2007)

Hepatitis C is an infection of the liver caused by a pos. single-stranded RNA virus (HCV) which affects 170 million people worldwide. It is responsible for 40-60% of all liver disease and is the major cause of liver transplants in the United States. The HCV NS5B gene encodes the viral RNA-dependent RNA polymerase which is essential for HCV replication. We have previously reported the identification of acylpyrrolidines as potent inhibitors of NS5B; however their activity is attenuated against genotype 1a. The design of improved broader-spectrum compds., capable of effective inhibition of both genotypes 1b and 1a is desirable. An understanding of the binding site and genotype sequence differences was utilized to design compds. with greatly enhanced genotype 1a and 1b potency. Our studies led to the identification of GSK625433, a potent, homochiral inhibitor of these HCV genotypes in both enzyme and sub-genomic replicon cell-based assays. GSK625433 has a good pharmacokinetic profile in pre-clin. animal species, enabling progression to clin. evaluation.
Nudging for sustainable consumption of electronics (2016)

Nordic co-operation is one of the world's most extensive forms of regional collaboration, involving Denmark, Finland, Iceland, Norway, Sweden, and the Faroe Islands, Greenland, and land
The influence of waste variability on the properties and phase stability of the West Valley reference glass (1987)

A year long study of the effects of waste variability on properties and phase stability of the West Valley reference glass has been conducted. Viscosity, electrical conductivity, glass transition temperature, density, and liquidus temperature have been measured for a series of glasses where the weight fraction of Al{sub 2}0{sub 3}, Fe{sub 2}0{sub 3}, NiO, MnO{sub 2}, Cr{sub 2}O{sub 3}, and P{sub 2}0{sub 5}, was varied systematically around the reference glass composition. A computer program for predicting melt viscosity has been developed. A preliminary Time-Temperature-Transformation diagram was also determined for the reference composition. It is concluded that the system, ``Glass Formers-Zeolite-Waste Mix,`` is a forgiving one in the sense that considerable variation of waste composition can be tolerated without substantially affecting the melting and phase behavior of the reference glass.
Indirect Adaptive Feed-Forward Tracking Controllers (1989)

This paper presents a general indirect adaptive feed-forward control scheme for the purpose of tracking time varying signals. An approach which allows independent design of the adaptive identifier and the feed-forward tracking controller is given and so is the characterization of its tracking performance. When disturbances and unmodeled dynamics exist, methods such as signal filtering, dead zone and constrained parameter estimation are important for obtaining robust adaptive identifies, without which the standard approach could not be successful. Application to a hydraulic servo system, the dynamics of which are nonlinear, time varying and of infinite order, demonstrates the usefulness of the proposed adaptive scheme.
Streptococcal inhibitor of complement (SIC) modulates fibrinolysis and enhances bacterial survival within fibrin clots (2018)

Some strains of the bacterial pathogen <i>Streptococcus pyogenes</i> secrete protein SIC (streptococcal inhibitor of complement), including strains of the clinically relevant M1 serotype. SIC neutralizes the effect of a number of antimicrobial proteins/peptides and interferes with the function of the host complement system. Previous studies have shown that some <i>S. pyogenes</i> proteins bind and modulate coagulation and fibrinolysis factors, raising the possibility that SIC also may interfere with the activity of these factors. Here we show that SIC interacts with both human thrombin and plasminogen, key components of coagulation and fibrinolysis. We found that during clot formation, SIC binds fibrin through its central region and that SIC inhibits fibrinolysis by interacting with plasminogen. Flow cytometry results indicated that SIC and plasminogen bind simultaneously to <i>S. pyogenes</i> bacteria, and fluorescence microscopy revealed co-localization of the two proteins at the bacterial surface. As a consequence, SIC-expressing bacteria entrapped in clots inhibit fibrinolysis, leading to delayed bacterial escape from the clots as compared with mutant bacteria lacking SIC. Moreover, within the clots SIC-expressing bacteria were protected against killing. In an animal model of subcutaneous infection, SIC-expressing bacteria exhibited a delayed systemic spread. These results demonstrate that the bacterial protein SIC interferes with coagulation and fibrinolysis and thereby enhances bacterial survival, a finding that has significant implications for <i>S. pyogenes</i> virulence.
Platelet lipid(s) bound to albumin increases endothelial electrical resistance: mimicked by LPA (2001)

The objectives were to determine whether the permeability-decreasing activity of platelet-conditioned medium (PCM) is associated with a lipid bound to albumin and whether lysophosphatidic acid (LPA) is present in the PCM. A decrease in permeability was assessed by an increase in electrical resistance across endothelial cell monolayers derived from bovine pulmonary arteries and microvessels. The Sephacryl S-200 fraction of PCM that contained albumin, the albumin immunoprecipitate from the PCM, and the methanol extract from the albumin immunoprecipitate all increased endothelial electrical resistance. Increased electrical resistance induced by PCM was not abolished by boiling and was mimicked by 1-oleoyl-LPA and 1-palmitoyl-LPA. Analysis of a methanol-chloroform extract of one sample of PCM by electrospray mass spectrometry revealed many fatty acids, ceramide, diacylglycerol, phosphatidic acid, and palmitoyl-LPA, but analysis of a second sample of PCM and the methanol extract of its albumin immunoprecipitate revealed no LPA, only lipids. These findings indicate that a bioactive lipid(s), possibly LPA, released from platelets and subsequently bound to albumin forms an active complex that decreases endothelial permeability.
A design optimization methodology for multiband stochastic antennas (2003)

A versatile design optimization approach for miniature multiband loaded fractal dipole antennas has been developed in Werner et al. (2001). This technique combines the robustness of genetic algorithms (GAs) (Haupt and Haupt 1997; Rahmat-Samii and Michielssen 1999) with the flexibility of iterated function systems (IFSs) (Peitgen et al. 1992) to evolve optimal self-affine fractal antenna shapes as well as determine the load locations and corresponding component values required to achieve the specified multiband operation. In this paper, an alternative design methodology for achieving the same objectives is introduced. This new methodology employs a GA to evolve a class of multiband antennas, called stochastic antennas, which offer optimal performance characteristics. This method is more general than the approach outlined in Werner et al. since it is not restricted to fractal geometries and there are no loads required to achieve the desired multiband performance. The only disadvantage of the new method is the fact that the optimization procedure is not as efficient as the GA-IFS technique. Several examples of optimized stochastic antennas are presented and discussed.
Characterization of Non-Nitrocatechol Pan and Isoform Specific Catechol-O-methyltransferase Inhibitors and Substrates (2011)

Reduced dopamine neurotransmission in the prefrontal cortex has been implicated as causal for the negative symptoms and cognitive deficit associated with schizophrenia; thus, a compound which selectively enhances dopamine neurotransmission in the prefrontal cortex may have therapeutic potential. Inhibition of catechol-O-methyltransferase (COMT, EC 2.1.1.6) offers a unique advantage, since this enzyme is the primary mechanism for the elimination of dopamine in cortical areas. Since membrane bound COMT (MB-COMT) is the predominant isoform in human brain, a high throughput screen (HTS) to identify novel MB-COMT specific inhibitors was completed. Subsequent optimization led to the identification of novel, non-nitrocatechol COMT inhibitors, some of which interact specifically with MB-COMT. Compounds were characterized for in vitro efficacy versus human and rat MB and soluble (S)-COMT. Select compounds were administered to male Wistar rats, and ex vivo COMT activity, compound levels in plasma and cerebrospinal fluid (CSF), and CSF dopamine metabolite levels were determined as measures of preclinical efficacy. Finally, novel non-nitrocatechol COMT inhibitors displayed less potent uncoupling of the mitochondrial membrane potential (MMP) compared to tolcapone as well as nonhepatotoxic entacapone, thus mitigating the risk of hepatotoxicity.