gebhart/patrepeval huggingface dataset:
Down-regulation of the novel gene melastatin correlates with potential for melanoma metastasis. (1998)

We have used differential cDNA display to search for genes whose expression correlates with an aggressive phenotype in variants of the B16 murine melanoma line, B16-F1 and B16-F10. This analysis identified a novel gene, termed melastatin, that is expressed at high levels in poorly metastatic variants of B16 melanoma and at much reduced levels in highly metastatic B16 variants. Melastatin was also found to be differentially expressed in tissue sections of human melanocytic neoplasms. Benign nevi express high levels of melastatin, whereas primary melanomas showed variable melastatin expression. Melastatin transcripts were not detected in melanoma metastases. Within the set of human primary cutaneous melanomas examined, melastatin expression appeared to correlate inversely with tumor thickness. The expression pattern observed suggests that loss of melastatin expression is an indicator of melanoma aggressiveness.
Selection of Antibiotic‐Resistant Bacterial Mutants: Allelic Diversity among Fluoroquinolone‐Resistant Mutations (2000)

To obtain a general framework for understanding selection of antibiotic-resistant mutants, allelic diversity was examined with about 600 fluoroquinolone-resistant mutants of mycobacteria. Selection at low fluoroquinolone concentration produced many low-level resistance mutants. Some of these contained mutations that conferred unselected antibiotic resistance; none contained alterations in the quinolone-resistance-determining region of the GyrA protein, the principal drug target. As selection pressure increased, a variety of GyrA variants became prevalent. High concentrations of antibiotic reduced the variety to a few types, and eventually a concentration was reached at which no mutant was recovered. That concentration defined a threshold for preventing the selection of resistance. The pattern of variants selected, which was also strongly influenced by antibiotic structure, readily explained the variants present in clinical isolates. Thus, resistance arises from selection of mutants whose identity depends on drug concentration and structure, both of which can be manipulated to restrict selection.
Rapid and Efficient Gene Delivery into Plant Cells Using Designed Peptide Carriers (2012)

To develop a new easy and quick gene delivery system for any types of plants, we prepared ionic complexes of plasmid DNA with designed peptide carriers, each of which combined a cell-penetrating peptide (Bp100 or Tat(2)) with a polycation (nona-arginine or a copolymer of histidine and lysine). The present system via the designed peptides demonstrated rapid and efficient transient transfections into intact leaf cells of Nicotiana benthamiana and Arabidopsis thaliana without protoplast preparations. The designed peptides demonstrated significantly higher transfection efficiency in comparison to the nonfusion peptides (Bp100, Tat2, nona-arginine, and copolymer of histidine and lysine), indicating that the combination of functional peptides was a key to develop an efficient peptide-based gene delivery system. On the basis of the results, we exhibited the versatility of the designed peptide-based gene delivery system, which will explore the application of plant biotechnology.
Mechanism of Constitutive Phosphoinositide 3-Kinase Activation by Oncogenic Mutants of the p85 Regulatory Subunit (2005)

p85/p110 phosphoinositide 3-kinases regulate multiple cell functions and are frequently mutated in human cancer. The p85 regulatory subunit stabilizes and inhibits the p110 catalytic subunit. The minimal fragment of p85 capable of regulating p110 is the N-terminal SH2 domain linked to the coiled-coil iSH2 domain (referred to as p85ni). We have previously proposed that the conformationally rigid iSH2 domain tethers p110 to p85, facilitating regulatory interactions between p110 and the p85 nSH2 domain. In an oncogenic mutant of murine p85, truncation at residue 571 leads to constitutively increased phosphoinositide 3-kinase activity, which has been proposed to result from either loss of an inhibitory Ser-608 autophosphorylation site or altered interactions with cellular regulatory factors. We have examined this mutant (referred to as p65) in vitro and find that p65 binds but does not inhibit p110, leading to constitutive p110 activity. This activated phenotype is observed with recombinant proteins in the absence of cellular factors. Importantly, this effect is also produced by truncating p85ni at residue 571. Thus, the phenotype is not because of loss of the Ser-608 inhibitory autophosphorylation site, which is not present in p85ni. To determine the structural basis for the phenotype of p65, we used a broadly applicable spin label/NMR approach to define the positioning of the nSH2 domain relative to the iSH2 domain. We found that one face of the nSH2 domain packs against the 581-593 region of the iSH2 domain. The loss of this interaction in the truncated p65 would remove the orienting constraints on the nSH2 domain, leading to a loss of p110 regulation by the nSH2. Based on these findings, we propose a general model for oncogenic mutants of p85 and p110 in which disruption of nSH2-p110 regulatory contacts leads to constitutive p110 activity.
Controlling Molecular Orientation in Solid Films via Self-Organization in the Liquid-Crystalline Phase (2002)

We report the control of molecular orientation in solid films through self-organization and induced-orientation processes. We synthesized water-soluble cationic 3,4,9,10-perylene diimide (1) and studied its self-organization in aqueous solution. By UV−vis spectroscopy, H-aggregates of 1 were observed forming in solutions with concentrations as low as 10-7 M. At concentrations above approximately 0.1 M (7% w/w), these solutions were observed with polarized microscopy to form a chromonic N phase (a nematic lyotropic liquid crystalline phase) at room temperature. Upon induced alignment (by shearing) of the chromonic N phase on a glass substrate and removal of solvent, anisotropic solid films of the dichroic dye were produced. These films have dichroic ratio values that routinely exceed 25 and in some cases 30, making them excellent polarizers over the blue and green region. By use of a combination of polarized UV−vis and FT-IR spectroscopies, the orientation of the average molecular plane in these films was determined to be perpendicular to both the shearing direction and the substrate plane. Small-angle X-ray diffraction studies indicate that the molecules in the solid film possess a high degree of order.
CanGEM: mining gene copy number changes in cancer (2007)

The use of genome-wide and high-throughput screening methods on large sample sizes is a well-grounded approach when studying a process as complex and heterogeneous as tumorigenesis. Gene copy number changes are one of the main mechanisms causing cancerous alterations in gene expression and can be detected using array comparative genomic hybridization (aCGH). Microarrays are well suited for the integrative systems biology approach, but none of the existing microarray databases is focusing on copy number changes. We present here CanGEM (Cancer GEnome Mine), which is a public, web-based database for storing quantitative microarray data and relevant metadata about the measurements and samples. CanGEM supports the MIAME standard and in addition, stores clinical information using standardized controlled vocabularies whenever possible. Microarray probes are re-annotated with their physical coordinates in the human genome and aCGH data is analyzed to yield gene-specific copy numbers. Users can build custom datasets by querying for specific clinical sample characteristics or copy number changes of individual genes. Aberration frequencies can be calculated for these datasets, and the data can be visualized on the human genome map with gene annotations. Furthermore, the original data files are available for more detailed analysis. The CanGEM database can be accessed at http://www.cangem.org/.
Total Synthesis of Baccatin III and Taxol (1996)

An intramolecular Heck reaction (90 → 91) serves as the key step in the total synthesis of the titled compounds. The synthetic route is based on utilizing the Wieland−Miescher ketone (5) as a matrix to provide the C and D rings of the targets and to provide functionality implements for joining this sector to an A ring precursor (6). Catalytically induced enantiotopic control and early emplacement of the oxetane are other features of the route.
Study of features based on nonlinear dynamical modeling in ECG arrhythmia detection and classification (2002)

We present a study of the nonlinear dynamics of electrocardiogram (ECG) signals for arrhythmia characterization. The correlation dimension and largest Lyapunov exponent are used to model the chaotic nature of five different classes of ECG signals. The model parameters are evaluated for a large number of real ECG signals within each class and the results are reported. The presented algorithms allow automatic calculation of the features. The statistical analysis of the calculated features indicates that they differ significantly between normal heart rhythm and the different arrhythmia types and, hence, can be rather useful in ECG arrhythmia detection. On the other hand, the results indicate that the discrimination between different arrhythmia types is difficult using such features. The results of this work are supported by statistical analysis that provides a clear outline for the potential uses and limitations of these features.
Decreased protein level of nicotinic receptor α7 subunit in the frontal cortex from schizophrenic brain (1999)

The alpha7 subunit of nicotinic receptor (nAChR) was investigated in post-mortem brain tissue from eight schizophrenics and eight age-matched controls by Western blot. Using anti-alpha7 antibodies a single band with a mol. wt of 42 kDa was detected in human post-mortem brain, which was smaller in size than the single band (52 kDa) detected in SH-SY5Y and PC12 cells. The smaller band specifically bound to [125I]alpha-bungarotoxin, confirming the specificity of the detection in the human brain samples. A significant decrease in the level of alpha7 subunit protein was observed with the same method in the frontal cortex of schizophrenics compared with controls, while no difference was found in the parietal cortex. These findings suggest that a deficit of nAChR alpha7 subunit in the frontal cortex might be involved in the pathophysiology of schizophrenia.
Integrating signals from IFN-gamma and IL-4 by B cells: positive and negative effects on CD40 ligand-induced proliferation, survival, and division-linked isotype switching to IgG1, IgE, and IgG2a. (1999)

IL-4 and IFN-gamma each have potent effects on B cell responses as well as strong mutual antagonism. Here we have examined the quantitative effects of these cytokines on CD40 ligand-induced B cell proliferation, cell survival, and division-linked isotype switching. Both IL-4 (strongly) and IFN-gamma (weakly) enhanced the number of B cells found in culture by reducing the average time cells take to enter the first division cycle and by promoting B cell survival. When added in combination, the net effect of IL-4 and IFN-gamma on time to division and survival was a response intermediate between that of the two cytokines alone, indicating a partial antagonism of IL-4 by IFN-gamma. By modulating both time to division and cell survival, these small effects of IFN-gamma are amplified and give rise to large reductions in cell number in the presence of IL-4. At higher concentrations, IFN-gamma had minor inhibitory effects on IL-4-induced isotype switching to IgG1 and greater effects on IgE. A reciprocal relation was observed between the ability to inhibit IgE at late cell divisions vs induction of IgG2a. In contrast, IL-4 did not prevent switching to IgG2a induced by IFN-gamma alone. Therefore, antagonism between IFN-gamma and IL-4 is observed at multiple levels and over different concentration ranges, resulting in complex net outcomes. The evolutionary significance of this complexity is discussed.
l-Proline Functionalized Polymers Prepared by RAFT Polymerization and Their Assemblies as Supported Organocatalysts (2011)

We have prepared a range of well-defined copolymers of styrene and L-proline functionalized styrene (5-11 kDa) using reversible addition-fragmentation chain transfer (RAFT) polymerization techniques and explored their use in supported catalysis. Upon deprotection of the L-proline functionalities, the solution self-assembly of these copolymers was investigated in mixed solvent systems. The resulting assemblies were characterized by dynamic light scattering, transmission electron microscopy (on graphene oxide substrates, along with cryo-TEM and tomography), and scanning electron microscopy. The application of these functional assemblies as supported catalysts for the aldol condensation reaction was explored using cyclohexanone and 4-nitrobenzaldehyde. The rate and selectivity of solution catalysis in our self-assembled system were comparable to those of L-proline, and a significant advantage of our system was that the polymer support could be utilized at lower catalyst loadings with comparable activity and also could be recycled a number of times while maintaining activity and selectivity.
Synthesis of Mustards from Putrescine, Cadaverine, and 1,3-Diaminopropane1 (1963)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis of Mustards from Putrescine, Cadaverine, and 1,3-Diaminopropane1William W. Lee, Bernard J. Berridge Jr., Leonard O. Ross, and Leon GoodmanCite this: J. Med. Chem. 1963, 6, 5, 567–569Publication Date (Print):September 1, 1963Publication History Published online1 May 2002Published inissue 1 September 1963https://doi.org/10.1021/jm00341a023Request reuse permissions Article Views264Altmetric-Citations7LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (379 KB) Get e-Alertsclose Get e-Alerts
Shedding of GD2 ganglioside by human neuroblastoma (1987)

Substantial concentrations of the cell-surface glycosphingolipid, the disialoganglioside GD2, are uniformly present in human neuroblastoma tumors. This ganglioside can also be detected in the plasma of patients with neuroblastoma by direct thin-layer chromatographic analysis. Among 32 neuroblastoma patients in all clinical stages studied prior to the initiation of treatment, 27 (84%) showed measurably elevated plasma concentrations of GD2 (greater than or equal to 50 pmol/ml). The mean level (545 +/- 108 pmol/ml) was more than 50 times the normal plasma GD2 concentration of less than or equal to 10 pmol/ml. Circulating GD2 was not detected in the plasma of patients with the related, more differentiated tumors, ganglioneuroblastoma and ganglioneuroma, indicating an association of the shedding of this ganglioside with the undifferentiated phenotype. Circulating GD2 diminished in patients in response to therapy, and reappeared in patients whose disease recurred. The results suggest that the sequential determination of circulating GD2 will be of value in monitoring individual patients with neuroblastoma.
Reconciling high server utilization and sub-millisecond quality-of-service (2014)

The simplest strategy to guarantee good quality of service (QoS) for a latency-sensitive workload with sub-millisecond latency in a shared cluster environment is to never run other workloads concurrently with it on the same server. Unfortunately, this inevitably leads to low server utilization, reducing both the capability and cost effectiveness of the cluster.
Amyloid-β-Induced Ion Flux in Artificial Lipid Bilayers and Neuronal Cells: Resolving a Controversy (2009)

Understanding the pathogenicity of amyloid-beta (Abeta) peptides constitutes a major goal in research on Alzheimer's disease (AD). One hypothesis entails that Abeta peptides induce uncontrolled, neurotoxic ion flux through cellular membranes. The exact biophysical mechanism of this ion flux is, however, a subject of an ongoing controversy which has attenuated progress toward understanding the importance of Abeta-induced ion flux in AD. The work presented here addresses two prevalent controversies regarding the nature of transmembrane ion flux induced by Alphabeta peptides. First, the results clarify that Alphabeta can induce stepwise ion flux across planar lipid bilayers as opposed to a gradual increase in transmembrane current; they show that the previously reported gradual thinning of membranes with concomitant increase in transmembrane current arises from residues of the solvent hexafluoroisopropanol, which is commonly used for the preparation of amyloid samples. Second, the results provide additional evidence suggesting that Abeta peptides can induce ion channel-like ion flux in cellular membranes that is independent from the postulated ability of Alphabeta to modulate intrinsic cellular ion channels or transporter proteins.
Semisynthesis of axial-ligand (position 80) mutants of cytochrome c (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSemisynthesis of axial-ligand (position 80) mutants of cytochrome cAdrienne L. Raphael and Harry B. GrayCite this: J. Am. Chem. Soc. 1991, 113, 3, 1038–1040Publication Date (Print):January 1, 1991Publication History Published online1 May 2002Published inissue 1 January 1991https://pubs.acs.org/doi/10.1021/ja00003a045https://doi.org/10.1021/ja00003a045research-articleACS PublicationsRequest reuse permissionsArticle Views431Altmetric-Citations131LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Vehicle Applications of Controller Area Network (2005)

The Controller Area Network (CAN) is a serial bus communications protocol developed by Bosch in the early 1980s. It defines a standard for efficient and reliable communication between sensor, actuator, controller, and other nodes in real-time applications. CAN is the de facto standard in a large variety of networked embedded control systems. The early CAN development was mainly supported by the vehicle industry: CAN is found in a variety of passenger cars, trucks, boats, spacecraft, and other types of vehicles. The protocol is also widely used today in industrial automation and other areas of networked embedded control, with applications in diverse products such as production machinery, medical equipment, building automation, weaving machines, and wheelchairs. The purpose of this chapter is to give an introduction to CAN and some of its vehicle applications. The outline is as follows. Section 2 describes the CAN protocol, including its message formats and error handling. The section is concluded by a brief history of CAN. Examples of vehicle application architectures based on CAN are given in Section 3. A few specific control loops closed over CAN buses are discussed in Section 4. The paper is concluded with some perspectives in Section 5, where current research issues such as x-by-wire and standardized software architectures are considered. The examples are described in more detail in [14]. A detailed description of CAN is given in the textbook [6]. Another good resource for further information is the homepage of the organization CAN-in-Automation (CiA) [3]. The use of CAN as a basis for distributed control systems is discussed in [13].
Measurements of alloy composition and strain in thin GexSi1−x layers (1994)

The utility of Raman spectroscopy for the simultaneous determination of composition and strain in thin GexSi1−x layers has been investigated. Using data from the literature and new data for the strain shift of the Si-Si phonon mode presented here, we show how Raman spectra provide several different means of measuring composition and strain in samples as thin as 200 Å. We demonstrate that for largely relaxed layers with compositions near x=0.30, Raman scattering can measure the composition, x, with an accuracy of ±0.015 and the strain, ε, with an accuracy ±0.0025. The accuracy of the alloy composition obtained from Raman spectra is comparable or, in the case of very thin layers, superior to that measured by other techniques such as x-ray diffraction, electron microprobe, and Auger electron spectroscopy.
Risk Factors for Cardiovascular Disease in Homeless Adults (2005)

Cardiovascular risk factor modification is suboptimal among homeless adults in Toronto, despite universal health insurance. Multiple risk factor equations may underestimate true risk in this population because of inadequate accounting for factors such as cocaine use and heavy smoking.
An adaptive de-interlacing algorithm based on motion morphologic detection (2010)

De-interlacing is a key technology in digital video processing and standard conversion. This paper proposes a motion adaptive spatial-temporal de-interlacing algorithm based on motion morphologic detection. In the proposed algorithm, a motion morphologic detector is presented to determine where the missing pixels belong to moving or static region. If the missing pixel belongs to the static region, the field copy method is adopted; otherwise, an adaptive spatial -temporal -wise interpolation is applied according to the texture complexity. Furthermore, a modified five direction interpolation method is proposed to improve the performance. Experimental results show that the proposed algorithm can improve the subjective qualities and the interlaced artifacts are eliminated.