gebhart/patrepeval huggingface dataset:
Carbon Nanotube/Manganese Oxide Ultrathin Film Electrodes for Electrochemical Capacitors (2010)

Multiwall carbon nanotube (MWNT)/manganese oxide (MnO2) nanocomposite ultrathin film electrodes have been created via redox deposition of MnO2 on layer-by-layer (LbL)-assembled MWNT films. We demonstrate that these LbL-assembled MWNT (LbL-MWNT)/MnO2 thin films consist of a uniform coating of nanosized MnO2 on the MWNT network structure using SEM and TEM, which is a promising structure for electrochemical capacitor applications. LbL-MWNT/MnO2 electrodes yield a significantly higher volumetric capacitance of 246 F/cm3 with good capacity retention up to 1000 mV/s due to rapid transport of electrons and ions within the electrodes. The electrodes are generated with two simple aqueous deposition processes: the layer-by-layer assembly of MWNTs followed by redox deposition of MnO2 at ambient conditions, thus providing a straightforward approach to the fabrication of high-power and -energy electrochemical capacitors with precise control of electrode thickness at nanometer scales.
A strategy for designing inhibitors of α ‐synuclein aggregation and toxicity as a novel treatment for Parkinson's disease and related disorders (2004)

Convergent biochemical and genetic evidence suggests that the formation of alpha-synuclein (alpha-syn) protein deposits is an important and, probably, seminal step in the development of Parkinson's disease (PD), dementia with Lewy bodies (DLB) and multiple system atrophy (MSA). It has been reported that transgenic animals overexpressing human alpha-syn develop lesions similar to those found in the brain in PD, together with a progressive loss of dopaminergic cells and associated abnormalities of motor function. Inhibiting and/or reversing alpha-syn self-aggregation could, therefore, provide a novel approach to treating the underlying cause of these diseases. We synthesized a library of overlapping 7-mer peptides spanning the entire alpha-syn sequence, and identified amino acid residues 64-100 of alpha-syn as the binding region responsible for its self-association. Modified short peptides containing alpha-syn amino acid sequences from part of this binding region (residues 69-72), named alpha-syn inhibitors (ASI), were found to interact with full-length alpha-syn and block its assembly into both early oligomers and mature amyloid-like fibrils. We also developed a cell-permeable inhibitor of alpha-syn aggregation (ASID), using the polyarginine peptide delivery system. This ASID peptide was able to inhibit the DNA damage induced by Fe(II) in neuronal cells transfected with alpha-syn(A53T), a familial PD-associated mutation. ASI peptides without this delivery system did not reverse levels of Fe(II)-induced DNA damage. Furthermore, the ASID peptide increased (P<0.0005) the number of cells stained positive for Bcl-2, while significantly (P<0.05) decreasing the percentage of cells stained positive for BAX. These short peptides could serve as lead compounds for the design of peptidomimetic drugs to treat PD and related disorders.
Serotype Specificity of Adenovirus Purification Using Anion-Exchange Chromatography (2005)

Recombinant adenoviruses continue to be a leading vector choice for gene transfer applications, with growing interest in the use of less prevalent serotypes, and of chimeras. As a result, the development of scaleable purification processes for alternative serotypes is needed. Anion-exchange chromatography is routinely used for scaleable adenovirus type 5 purification; however, retention varies for other serotypes because of differences in the exposed capsid proteins. Understanding how the viral surface influences retention behavior can provide a rational basis for chromatography development and optimization. In this work, chimeric vectors were used to show that the hexon protein is responsible for retention differences in anion-exchange chromatography. Next, the relative retention of eight serotypes from three subgroups was studied. Although all serotypes bound to the anion-exchange resin, the sodium chloride required to elute the virus varied over a 2- fold range, from 270 to 490 mM. Retention was accurately correlated to the electrostatic properties of the hexon protein, with an average error in sodium chloride concentration required to elute of only 14 mM. This correlation enables preparative chromatography gradients for alternative serotypes to be established with minimal effort.
Micromixers—a review (2004)

This review reports the progress on the recent development of micromixers. The review first presents the different micromixer types and designs. Micromixers in this review are categorized as passive micromixers and active micromixers. Due to the simple fabrication technology and the easy implementation in a complex microfluidic system, passive micromixers will be the focus of this review. Next, the review discusses the operation points of the micromixers based on characteristic dimensionless numbers such as Reynolds number Re, Peclet number Pe, and in dynamic cases the Strouhal number St. The fabrication technologies for different mixer types are also analysed. Quantification techniques for evaluation of the performance of micromixers are discussed. Finally, the review addresses typical applications of micromixers.
Targeting complement in therapy (2001)

With increasing evidence that complement activation significantly contributes to the pathogenesis of a large number of inflammatory diseases, strategies that interfere with its deleterious action have become a major focus in pharmacological research. Endogenous soluble complement inhibitors (C1 inhibitor, recombinant soluble complement receptor 1, antibodies) blocking key proteins of the cascade reaction, neutralizing the action of the complement-derived anaphylatoxin C5a, or interfering with complement receptor 3 (CR3, CD18/11b)-mediated adhesion of inflammatory cells to the vascular endothelium have successfully been tested in various animal models over the past years. Promising results consequently led to clinical trials. Furthermore, incorporation of membrane-bound complement regulators (decay-accelerating factor (CD55), membrane co-factor protein (CD46), CD59) in transgenic animals has provided a major step forward in protecting xenografts from hyperacute rejection. At the same time, the poor contribution of complement to the antitumor response, which is caused by multiple resistance mechanisms that hamper the efficacy of antibody-based tumor therapy, is increasingly recognized and requires pharmacologic intervention. First attempts have now been made to interfere with the resistance mechanisms, thereby improving complement-mediated tumor cell destruction.
A time and frequency synchronization scheme for multiuser OFDM (1999)

We present a multiuser synchronization scheme for tracking the mobile's uplink time and frequency offsets. It uses the redundancy introduced by the cyclic prefix and does not need additional pilots. We show performance results of an orthogonal frequency division multiplexing (OFDM)-based radio interface based on the universal mobile telecommunication system (UMTS) parameters. For a UMTS-typical mobile channel environment, the performance of a coherent system employing the scheme is virtually indistinguishable from the performance of a perfectly synchronized system. In a differentially modulated system, synchronization errors decrease the system performance by about 0.7 dB compared to a perfectly synchronized system.
Is the Failing Heart Energy Starved? (2004)

The requirement of chemical energy in the form of ATP to support systolic and diastolic work of the heart is absolute. Because of its central role in cardiac metabolism and performance, the subject of this review on energetics in the failing heart is ATP. We briefly review the basics of myocardial ATP metabolism and describe how this changes in the failing heart. We present an analysis of what is now known about the causes and consequences of these energetic changes and conclude by commenting on unsolved problems and opportunities for future basic and clinical research.
Spoof Attacks on Multimodal Biometric Systems (2011)

Biometrics, referred as the science of recognizing an individual based on his or her physical or behavioral traits, has been widely employed as a security system in the awake of latest security issues. However, recent researches have shown that many biometric traits are vulnerable to spoof attacks. In addition, a latest results have questioned that, contrary to a common claim, multimodal systems can be cracked by spoofing only one trait. Those results were obtained using simulated spoof attacks, under the unrealistic assumption that the spoofed and genuine samples are identical, turned out to be the same outputs. We further investigate this significant security issue, focusing on behavior of fixed and trained score fusion rules, using real spoof attack samples under different spoof attack scenarios. Preliminary empirical results on real biometric systems made up of face, fingerprint and iris with twelve score fusion rules confirm that multimodal biometric systems are not intrinsically robust against spoof attacks as believed so far. In particular, most widely used fixed rules can be less robust, even if the quality of fake biometric trait is low. The false acceptance rate increases substantially under spoof attacks which means that an attacker might wrongly get authenticated by spoofing a subset of traits. In all considered spoofing scenarios, we also found that trained rules are more accurate, flexible and robust against spoof attacks as compare to fixed one.
Synthesis of Thio Analogues of Quinolone Antibacterials (2005)

A facile and rapid synthesis of thio compounds, analogues to ciprofloxacin, and norfloxacin is described.
Studies that shed new light on aging (2013)

I will first discuss how all aging models that assume that the aged cell has irreversibly lost its youthful capabilities through such mechanisms as accumulated dysfunction, accumulated damage, and/or accumulation of toxic byproducts of metabolism have been shown to be incorrect. I will then briefly discuss models of aging and propose an experiment that would distinguish between those models and provide a basis for organismic rejuvenation.
Comparison Of The Two Alternate Methods Of Wide Area Carrier Phase Positioning (2004)

In recent years new dual frequency carrier phase based real-time DGPS services have emerged to provide decimeter level positioning accuracy over wide areas. These services use geostationary satellite links to provide wide area coverage. The new positioning methods bridge the accuracy and coverage gap between meter level code based DGPS and prohibitively expensive centimeter level Real-Time Kinematic systems. In order to assure the highest level of integrity of the inherently ambiguous carrier phase positioning solution Fugro has developed two independent wide area carrier phase positioning methods. The first method uses the corrections from the multiple reference stations to mitigate the influence of the GPS satellite orbit and clock errors. The second method, instead of eliminating the orbit and clock errors along the line of sight from the reference stations, explicitly uses the satellite orbit and clock corrections without the reference stations. Both methods provide decimeter accuracy positioning. The paper reviews both carrier phase positioning methods. It describes the implementation of the methods in the operational real-time positioning services. It also presents the comparison results of the testing of the two methods. The results show better performance of the multiple reference station method. However both multiple reference station and precise orbit and clock methods achieved decimeter level positioning accuracy.
Ex Vivo Characteristics of Human Amniotic Membrane-Derived Stem Cells (2007)

Cells were isolated from four human amniotic membranes, and their biological characteristics analyzed during ex vivo expansion. Morphologically homogenous populations of fibroblast-like cells were obtained from the second or third passage. Under the appropriate culture conditions, these human amniotic membrane-derived mesenchymal cells (HAM) were shown to differentiate into adipocytes, osteocytes, chondrocytes and neuronal cells, as visualized by Oil Red O, von Kossa, alcian blue, anti-Neu N, and anti-Gal C antibody staining, respectively. Immunophenotype analysis of HAM cells revealed the presence of antigens for SSEA-3, SSEA-4, collagen type-I, -II, -III, -IV, -XII, fibronectin, alpha-SMA, vimentin, desmin, cytokeratin18 (CK18), HCAM-1, fibroblast surface protein, and human leukocyte antigen (HLA) ABC. ICAM-1 protein was weakly detectable, and proteins of TRA-1-60, VCAM-1, von Willebrand factor, PECAM-1, and HLA DR were not detected. HAM cells reached senescence after 14.5+/-0.9 passages, over a period of 146.8+/-8.9 days, and underwent an average of 36.9 4.7 population doublings. RT-PCR analysis showed that all four HAM cell lines consistently expressed genes of Oct-4, Rex-1, SCF, NCAM, nestin, BMP-4, GATA-4, HNF-4alpha, vimentin, and CK18, regardless of the passage number. The genes of Brachyury, FGF-5, Pax-6, and BMP2 were never expressed. Strikingly, alpha-fetoprotein (alphaFP), HLA ABC, and HLA DR genes were expressed in an earlier passage but not expressed in later passages. Telomerase activity of two HAM lines was discernable upon the third passage. These observations strongly suggest that HAM might be immune-privileged and, thus, advantageous as therapeutic cells.
High-power InGaN/GaN double-heterostructure violet light emitting diodes (1993)

InGaN/GaN double-heterostructure light-emitting diodes were fabricated. The output power was 90 μW and the external quantum efficiency was as high as 0.15% at a forward current of 20 mA at room temperature. The peak wavelengths of the electroluminescence (EL) varied between 411 and 420 nm with changes in the growth temperatures of an InGaN active layer between 820 and 800 °C. The full widths at half maximum of EL were between 22 and 25 nm.
The use of computerized tomography in the measurement of glenoid version. (1992)

Computerized tomography was done preoperatively on twenty shoulders (thirteen patients) in which there were severe arthritic changes, to measure glenoid version. Ten of the twenty shoulders had osteoarthrosis; eight, rheumatoid arthritis; and two, gouty arthritis. To help determine normal values, computerized tomographic scans of the chest of sixty-three patients who did not have roentgenographic evidence of disease of the shoulder were studied retrospectively for comparison as a control group. In the group of patients who had severe arthritis, the mean glenoid orientation was 11 degrees of retroversion (range, 2 degrees of anteversion to 32 degrees of retroversion). The computerized tomographic scans showed uneven wear of the glenoid surface, osteophytes, large cysts, and posterior displacement of the humeral head. In the control group, the mean orientation of the glenoid was 2 degrees of anteversion (range, 14 degrees of anteversion to 12 degrees of retroversion). The difference between the groups was significant (p less than 0.0001). Glenoid retroversion was increased in the patients who had severe arthritis, and the computerized tomographic scans accurately revealed the extent and pattern of erosion of the bone.
Conservation and divergence of methylation patterning in plants and animals (2010)

Cytosine DNA methylation is a heritable epigenetic mark present in many eukaryotic organisms. Although DNA methylation likely has a conserved role in gene silencing, the levels and patterns of DNA methylation appear to vary drastically among different organisms. Here we used shotgun genomic bisulfite sequencing (BS-Seq) to compare DNA methylation in eight diverse plant and animal genomes. We found that patterns of methylation are very similar in flowering plants with methylated cytosines detected in all sequence contexts, whereas CG methylation predominates in animals. Vertebrates have methylation throughout the genome except for CpG islands. Gene body methylation is conserved with clear preference for exons in most organisms. Furthermore, genes appear to be the major target of methylation in Ciona and honey bee. Among the eight organisms, the green alga Chlamydomonas has the most unusual pattern of methylation, having non-CG methylation enriched in exons of genes rather than in repeats and transposons. In addition, the Dnmt1 cofactor Uhrf1 has a conserved function in maintaining CG methylation in both transposons and gene bodies in the mouse, Arabidopsis, and zebrafish genomes.
Biosynthesis of isoprenoids, polyunsaturated fatty acids and flavonoids in Saccharomyces cerevisiae (2006)

Industrial biotechnology employs the controlled use of microorganisms for the production of synthetic chemicals or simple biomass that can further be used in a diverse array of applications that span the pharmaceutical, chemical and nutraceutical industries. Recent advances in metagenomics and in the incorporation of entire biosynthetic pathways into Saccharomyces cerevisiae have greatly expanded both the fitness and the repertoire of biochemicals that can be synthesized from this popular microorganism. Further, the availability of the S. cerevisiae entire genome sequence allows the application of systems biology approaches for improving its enormous biosynthetic potential. In this review, we will describe some of the efforts on using S. cerevisiae as a cell factory for the biosynthesis of high-value natural products that belong to the families of isoprenoids, flavonoids and long chain polyunsaturated fatty acids. As natural products are increasingly becoming the center of attention of the pharmaceutical and nutraceutical industries, the use of S. cerevisiae for their production is only expected to expand in the future, further allowing the biosynthesis of novel molecular structures with unique properties.
PDZK1, a novel PDZ domain-containing protein up-regulated in carcinomas and mapped to chromosome 1q21, interacts with cMOAT (MRP2), the multidrug resistance-associated protein. (1999)

We recently reported the isolation and partial characterization of two novel proteins, MAP17 and PDZK1. Using in situ hybridization, we demonstrated that MAP17 and PDZK1 mRNAs are markedly up-regulated in human carcinomas. PDZK1, originally isolated as a protein interacting with MAP17, contains four PDZ protein-interaction domains and could potentially interact with as many as four target proteins. In this paper, we confirm the overexpression of PDZK1 in human carcinomas using a specific antibody and demonstrate the localization of the PDZK1 gene to human chromosome 1q21, a region frequently altered in neoplastic conditions. Using the yeast two-hybrid system, we have also determined that PDZK1 interacts with the carboxy-terminal portion of cMOAT (MRP2), the canalicular multispecific organic anion transporter associated with multidrug resistance. This is of particular interest because proteins containing PDZ domains are involved in the clustering and signaling pathways of membrane-associated proteins, including ion channels. Therefore, the protein cluster formed by the association of cMOAT, PDZK1, and MAP17 could play an important role in the cellular mechanisms associated with multidrug resistance, and PDZK1 may represent a new target in cancer cells resistant to chemotherapeutic agents.
The complete sequence of perlecan, a basement membrane heparan sulfate proteoglycan, reveals extensive similarity with laminin A chain, low density lipoprotein-receptor, and the neural cell adhesion molecule. (1991)

A heparan sulfate proteoglycan is a component of all basement membranes. This molecule consists of three heparan sulfate side chains linked to a large core protein of approximately 400 kDa. We have isolated seven overlapping murine cDNA clones that encode the entire mRNA sequence of 12.685 kilobases of this molecule. This sequence has a single open reading frame of 3,707 amino acids that encodes for a protein of 396 kDa. Identical or near identical matchups with nine peptide sequences derived from the core protein of the molecule isolated from the Engelbreth-Holm-Swarm tumor were found with the deduced sequence. Sequence analysis and data base comparison of the deduced sequence show the protein to consist of five different domains, most of which contain internal repeats. Domain I contains a start methionine followed by a typical signal transfer sequence and a unique segment of 172 amino acids that contains the three probable sites of heparan sulfate attachment, SGD. Domain II contains four cysteine- and acidic amino acid-rich repeats that are very similar to those found in the LDL receptor and proteins such as GP330. Domain III consists of cysteine-rich and globular regions, both of which show similarity to those in the short arm of the laminin A chain. Domain IV contains 14 repeats of the immunoglobulin superfamily that are most highly similar to the immunoglobulin-like repeats in the neural cell adhesion molecule. Domain V contains three repeats with similarity to the laminin A chain G domain that are separated by epidermal growth factor-like regions not found in the laminin A chain. As the primary structural data agree with the appearance of the molecule in the electron microscope as a series of globules separated by rods, or "beads on a string," we have adopted the name perlecan for this molecule. The variety of domains in perlecan suggest multiple interactions with other molecules.
Search designs for protein crystallization based on orthogonal arrays (1994)

In protein crystallography, the initial experimental problem is the identification of physical and chemical conditions that will support nucleation and crystal growth. Ideally, experiments to search for such conditions would be based on a full-factorial structure, with variation in the temperature and solution composition. However, consideration of even a moderate number of possibilities for the composition of the system will result in factorial experiments which may be prohibitively large. In this paper it is proposed that search experiments for protein crystallization might be based on orthogonal arrays. These are subsets of full-factorial experiments which possess a great deal of symmetry, such that a uniform distribution of points throughout the experimental region is preserved. Such experiments have reasonable size, explore the proposed experimental region in a systematic fashion, and form a logical basis for a sequential approach to the search for crystallization conditions. Examples of such initial search experiments are given, and their application to some recent protein crystallization problems in this laboratory is described briefly. The relationship of this approach to other protein crystallization search procedures is also discussed.