gebhart/patrepeval huggingface dataset:
Novel protein folds and their nonsequential structural analogs (2008)

Newly determined protein structures are classified to belong to a new fold, if the structures are sufficiently dissimilar from all other so far known protein structures. To analyze structural similarities of proteins, structure alignment tools are used. We demonstrate that the usage of nonsequential structure alignment tools, which neglect the polypeptide chain connectivity, can yield structure alignments with significant similarities between proteins of known three-dimensional structure and newly determined protein structures that possess a new fold. The recently introduced protein structure alignment tool, GANGSTA, is specialized to perform nonsequential alignments with proper assignment of the secondary structure types by focusing on helices and strands only. In the new version, GANGSTA+, the underlying algorithms were completely redesigned, yielding enhanced quality of structure alignments, offering alignment against a larger database of protein structures, and being more efficient. We applied DaliLite, TM-align, and GANGSTA+ on three protein crystal structures considered to be novel folds. Applying GANGSTA+ to these novel folds, we find proteins in the ASTRAL40 database, which possess significant structural similarities, albeit the alignments are nonsequential and in some cases involve secondary structure elements aligned in reverse orientation. A web server is available at http://agknapp.chemie.fu-berlin.de/gplus for pairwise alignment, visualization, and database comparison.
Physico-chemical Characteristics of Nanovesicle−Carbohydrate Complexes in Grape Juice Concentrate (2008)

It is generally assumed that polyphenols, such as anthocyanins in fruit juice, exist in a free soluble state and are readily available for absorption in the gastro-intestinal tract. In the present study, we have investigated the interaction of polyphenols with soluble carbohydrate polymers, such as pectin and lipid nanovesicles, that are generated during homogenization of the fruit tissue during juice extraction. A commercially available grape juice concentrate contained nearly 25% of polyphenol fraction bound to macromolecules that were nondialyzable. Treatment of dialyzed juice with cellulase, pectinase, and beta-galactosidase did not cause the release of bound polyphenols; however, treatment with triton X-100 caused an increased release of bound polyphenols. The dialyzate contained relatively more -3-O glucosides and -3-O-acetoyl glucosides in comparison to the bound fraction which was enriched in -3-O-coumaroyl glucosides, suggesting qualitative differences in the bound and the free anthocyanin composition. Electron microscopic analysis of the juice fractions revealed the presence of electron-dense nanovesicle-fiber complexes ranging from 10 to 200 nm in diameter. Such complexes were absent in the dialyzate fraction. Cellulase treatment did not change the morphology of the complexes; however, treatment with pectinase and beta-galactosidase disrupted the complexes, releasing vesicular structures, suggestive of the pectin nature of the fibrous matrix. The dialyzed and the dialyzate fractions also showed differences in their 1H NMR and fluorescence spectral characteristics. The dialyzed fraction containing polyphenol-pectin complexes showed no superoxide scavenging capacity, reduced hydroxyl radical scavenging activity, and high 2,2-diphenyl-1-picrylhydrazyl radical scavenging activity, indicating potential changes in functionality because of the complex formation.
In vitro activities of the lichen secondary metabolites vulpinic acid, (+)-usnic acid, and (-)-usnic acid against aerobic and anaerobic microorganisms (1995)

Secondary metabolites of different species of lichen were tested for their activities against a variety of microbial species. While gram-negative rods and fungi were not inhibited by these compounds, Staphylococcus aureus, Enterococcus faecalis, Enterococcus faecium, and some anaerobic species (Bacteroides and Clostridium species) were susceptible at the concentrations tested. Vulpinic acid generally was less active than usnic acid, regardless of its stereochemistry. The susceptibility to usnic acid was not impaired in clinical isolates of S. aureus resistant to methicillin and/or mupirocin.
Localization of a Minimal Binding Domain and Activation Regions in Yeast Regulatory Protein ADR1 (1989)

ADR1 is a transcription factor required for activation of the glucose-repressible alcohol dehydrogenase 2 (ADH2) gene in Saccharomyces cerevisiae. ADR1 has two zinc finger domains between amino acids 102 and 159, and it binds to an upstream activation sequence (UAS1) in the ADH2 promoter. A functional dissection of ADR1 was performed by using a series of amino- and carboxy-terminal deletion mutants of ADR1, most of which were fused to the Escherichia coli beta-galactosidase. These deletion mutants were assayed for binding to UAS1 in vitro, for the ability to activate ADH2 transcription in vivo, and for level of expression. Deletion of ADR1 amino acids 150 to 172 and 76 to 98 eliminated DNA binding in vitro, which accounted for the loss of transcriptional activation in vivo. Results with the former deletion mutant indicated that both of the ADR1 zinc fingers are necessary for sequence-specific DNA binding. Results with the latter deletion mutant suggested that at least part of the sequence between amino acids 76 to 98, in addition to the two finger domains, is required for high-affinity DNA binding. The smallest fusion protein able to activate ADH2 transcription, containing ADR1 amino acids 76 to 172, was much less active in vivo than was the longest fusion protein containing amino acids 1 to 642 of ADR1. In addition, multiple regions of the ADR1 polypeptide (including amino acids 40 to 76, 260 to 302, and 302 to 505), which are required for full activation of ADH2, were identified. An ADR1-beta-galactosidase fusion protein containing only the amino-terminal 16 amino acids of ADR1 was present at a much higher level than were larger fusion proteins, which suggested that the sequences within ADR1 influence the expression of the gene fusion.
Non-Terminal DNS Name Redirection (1999)

This document defines a new DNS Resource Record called DNAME, which
provides the capability to map an entire subtree of the DNS name space
to another domain. [STANDARDS-TRACK]
Reversal of the direction of internal carotid artery blood flow by occlusion of the common and external carotid arteries in a swine model (2003)

In a swine model, blood flow direction [antegrade (+) and retrograde (-)] and velocity were defined within the common (CCA), internal (ICA), and external (ECA) carotid arteries during CCA occlusion with and without ECA occlusion and blood aspiration. In seven anesthetized swine, Doppler recordings of blood flow direction and velocity were performed in the CCA, ICA, and ECA, before and after vessel(s) occlusion, and after passively and actively induced reversal of blood flow direction. Baseline ICA and ECA blood flow direction and velocities were 92 +/- 4 and 90 +/- 3 cm/sec; and, with CCA occlusion, the ICA velocity decreased to 30 +/- 2 cm/sec (P < 0.001). No flow (zero velocity) occurred with CCA and ECA occlusion. An artificial femoral arteriovenous fistula's continuous gradient passively reversed ICA blood flow direction (-), with the recorded blood's velocity (-24 +/- 4 cm/sec) increasing with continuous active aspiration to -90 +/- 6 cm/sec. Occlusion of the CCA occlusion alone was unable completely to halt ICA antegrade blood flow direction, while CCA and ECA occlusion completely stopped ICA antegrade flow. CCA and ECA occlusion, when coupled with an arteriovenous fistula arteriovenous and/or aspiration, resulted in ICA blood flow direction reversal, whose velocity could be actively augmented.
Mesenchymal stem cell secreted vesicles provide novel opportunities in (stem) cell-free therapy (2012)

Mesenchymal stem cells (MSCs) are adult multipotent cells that give rise to various cell types of the mesodermal germ layer. MSCs are of great interest in the field of regenerative medicine and cancer therapy because of their unique ability to home to damaged and cancerous tissue. These cells also regulate the immune response and contribute to reparative processes in different pathological conditions, including musculoskeletal and cardiovascular diseases. The use of MSCs for tissue repair was initially based on the hypothesis that these cells home to and differentiate within the injured tissue into specialized cells. However, it now appears that only a small proportion of transplanted MSCs actually integrate and survive in host tissues. Thus, the predominant mechanism by which MSCs participate in tissue repair seems to be related to their paracrine activity. Indeed, MSCs provide the microenvironment with a multitude of trophic and survival signals including growth factors and cytokines. Recent discoveries suggest that lipid microvesicles released by MSCs may also be important in the physiological function of these cells. Over the past few years the biological relevance of micro- and nano-vesicles released by cells in intercellular communication has been established. Alongside the conventional mediators of cell secretome, these sophisticated nanovesicles transfer proteins, lipids and, most importantly, various forms of RNAs to neighboring cells, thereby mediating a variety of biological responses. The physiological role of MSC-derived vesicles (MSC-MVs) is currently not well understood. Nevertheless, encouraging results indicate that MSC-MVs have similar protective and reparative properties as their cellular counterparts in tissue repair and possibly anti-cancer therapy. Thus, MSC-MVs represent a promising opportunity to develop novel cell-free therapy approaches that might overcome the obstacles and risks associated with the use of native or engineered stem cells.
Metabolism of Methanol in Plant Cells. Carbon-13 Nuclear Magnetic Resonance Studies (2000)

Using (13)C-NMR, we demonstrate that [(13)C]methanol readily entered sycamore (Acer pseudoplatanus L.) cells to be slowly metabolized to [3-(13)C]serine, [(13)CH(3)]methionine, and [(13)CH(3)]phosphatidylcholine. We conclude that the assimilation of [(13)C]methanol occurs through the formation of (13)CH(3)H(4)Pte-glutamate (Glu)(n) and S-adenosyl-methionine, because feeding plant cells with [3-(13)CH(3)]serine, the direct precursor of (13)CH(2)H(4)Pte-Glu(n), can perfectly mimic [(13)CH(3)]methanol for folate-mediated single-carbon metabolism. On the other hand, the metabolism of [(13)C]methanol in plant cells revealed assimilation of label into a new cellular product that was identified as [(13)CH(3)]methyl-beta-D-glucopyranoside. The de novo synthesis of methyl-beta-D-glucopyranoside induced by methanol did not require the formation of (13)CH(3)H(4)Pte-Glu(n) and was very likely catalyzed by a "transglycosylation" process.
I n s i t u observation of lamp zone melting of Si films on patterned SiO2 (1986)

Using video recording equipment we are able to visualize and study both the melting and freezing interfaces in lamp zone melting recrystallization of silicon on insulator (SOI) films. A so-called ‘‘explosive’’ melting has been observed, corresponding to a noncontinuous advance of the front. We also show the effectiveness of an etched pattern in the underlying SiO2 on the modulation of the solidification front. We thereby confirm the entrainment effect of this pattern. We observe then the effect of the scan speed on the liquid/solid interface morphology together with the entrainment efficiency.
Editorial (1994)

Amid all the brouhaha about care in the community for people with serious mental illness, it is easy to forget one simple fact. As far as primary' care professionals are concerned, mental health care is not generally about services for people with psychosis. It is about depression, the most common mental illness seen in primary' care.
Nanowire Transistor Performance Limits and Applications (2008)

Semiconductor nanowires represent unique materials for exploring phenomena at the nanoscale. Developments in nanowire growth have led to the demonstration of a wide range of nanowire materials with precise control of composition, morphology, and electrical properties, and it is believed that this excellent control together with small channel size could yield device performance exceeding that obtained using top-down techniques. Here, we review advances in chemically synthesized semiconductor nanowires as nanoelectronic devices. We first introduce basic nanowire field-effect transistor structures and review results obtained from both p- and n-channel homogeneous composition nanowires. Second, we describe nanowire heterostructures, show that by using nanowire heterostructures, several limiting factors in homogeneous nanowire devices can be mitigated, and demonstrate that nanowire transistor performance can reach the ballistic limit and exceed state-of-the-art planar devices. Third, we discuss basic methods for organization of nanowires necessary for fabricating arrays of device and circuits. Fourth, we introduce the concept of crossbar nanowire circuits, discuss results for both transistor and nonvolatile switch devices, and describe unique approaches for multiplexing/demultiplexing enabled by synthetically coded nanowire. Fifth, we discuss the unique application of thin-film nanowire transistor arrays on low-cost substrates and illustrate this with results for relatively high-frequency ring oscillators and completely transparent device arrays. Finally, we describe 3-D heterogeneous integration that is uniquely enabled by multifunctional nanowires within a bottom-up approach.
Reaction of 3-amino-2-alkenimines with alkali metals: unexpected synthesis of substituted 4-(arylamino)quinolines (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTReaction of 3-amino-2-alkenimines with alkali metals: unexpected synthesis of substituted 4-(arylamino)quinolinesJose Barluenga, Enrique Aguilar, Jesus Joglar, Bernardo Olano, and Santos FusteroCite this: J. Org. Chem. 1989, 54, 11, 2596–2598Publication Date (Print):May 1, 1989Publication History Published online1 May 2002Published inissue 1 May 1989https://pubs.acs.org/doi/10.1021/jo00272a026https://doi.org/10.1021/jo00272a026research-articleACS PublicationsRequest reuse permissionsArticle Views73Altmetric-Citations10LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Democracy, eLiteracy and the internet (2005)

Purpose Argues that the internet has an important contribution to make to the improvement of the democratic process, but that this contribution can only be effective with advocacy and support from information professionals and educators; the cultivation of eLiteracy by such information professionals and educators is vital in delivering the democratic potential of the internet. Design/methodology/approach An opinion piece based on current and recent trends in thinking about digital citizenship, the internet and democracy. Findings Hopeful initial visions of the impact of internet technologies on democracy have been shown to be in some ways too optimistic. Many of the most notable social impacts of the internet on our collective well‐being have been harmful. The cultivation of eLiteracy as a democratic attribute of citizenship should enable us to make the most of the social beneficent potential of the networks. Research limitations/implications Purely an expression of belief about what may prove to be the likely social and political benefits of promoting eLiteracy as an aspect of enhanced citizenship. Offers potential for exploration via more in‐depth research. Practical implications Opens up an optimistic social and political purpose to the cultivation of eLiteracy in a broad mass of citizens. Originality/value Affirms an optimistic view of the democratic potential of the internet, but makes it clear that this potential will not emerge of its own accord. Citizens must engage intelligently with the social and political issues raised by the internet, in particular with the issue of how the new media enable the electorate to conduct dialogue with government. Information professionals have a particular civic duty to be aware of the democratic significance of their promotion of information literacy and, more specifically, of eLiteracy.
Binding of NCK to SOS and Activation of ras -Dependent Gene Expression (1995)

NCK, an SH2- and SH3 domain-containing protein, becomes phosphorylated and associated with tyrosine kinase receptors upon growth factor stimulation. The sequence of NCK suggests that NCK functions as a linker between receptors and a downstream signaling molecule. To determine if NCK can mediate growth factor-stimulated responses, we measured the ability of NCK to activate the fos promoter. We found that in NIH 3T3 cells, NCK strongly activates this promoter. The effect of NCK on the fos promoter is enhanced by c-ras and blocked by dominant negative ras. We also found that NCK binds directly to the guanine nucleotide exchange factor SOS. This interaction is mediated by the SH3 domains of NCK. These findings suggest that NCK can regulate p21ras-dependent gene transcription through interaction with SOS protein.
Toward the Validation of RDC Schizoaffective Disorder (1980)

• The Research Diagnostic Criteria (RDC) for schizoaffective disorder were applied to a clinic population of 71 patients with bipolar I disorder. Twenty-five patients were found to meet RDC criteria for schizoaffective disorder. The RDC-positive group were found to be the most psychotic patients and had a younger age at onset and admission to the clinic than the RDC-negative group. They had also had their conditions diagnosed more frequently as schizophrenic by referring physicians. There was no difference, however, between the two groups on many other variables, including clinical, family history, drug response, and laboratory studies. We conclude that our bipolar I population cannot be further subdivided into meaningful clinical entities using the RDC criteria for schizoaffective disorder.
Three-dimensional photonic crystal structures achieved with two-photon-absorption photopolymerization of resin (1999)

Three-dimensional photonic crystal structures were fabricated with laser microfabrication techniques through two-photon-absorption photopolymerization of resin. Significant band-gap effects in the infrared wavelength region were observed from “layer-by-layer” structures.
Melatonin Shifts Human Orcadian Rhythms According to a Phase-Response Curve (1992)

A physiological dose of orally administered melatonin shifts circadian rhythms in humans according to a phase-response curve (PRC) that is nearly opposite in phase with the PRCs for light exposure: melatonin delays circadian rhythms when administered in the morning and advances them when administered in the afternoon or early evening. The human melatonin PRC provides critical information for using melatonin to treat circadian phase sleep and mood disorders, as well as maladaptation to shift work and transmeridional air travel. The human melatonin PRC also provides the strongest evidence to date for a function of endogenous melatonin and its suppression by light in augmenting entrainment of circadian rhythms by the light-dark cycle.
Scan testing of asynchronous sequential circuits (2002)

A method to design and test asynchronous sequential circuits (ASCs) based on the micropipeline design style is presented in this paper. According to the proposed scan test approach the combinational block is tested separately by scanning the test vectors in and shifting the responses out of the state registers. This provides for the detection of all single stuck-at and delay faults in the ASC under test. The complexity of the test procedure of such a testable ASC is reduced to that of the combinational circuit. Tests for the combinational circuit and state holding elements can be derived using standard test generation techniques.
Discovery of Chromone‐Based Inhibitors of the Transcription Factor STAT5 (2008)

Obstacles overcome: Gene-specific transcription factors are emerging therapeutic targets, but their direct inhibition is considered to be difficult because of the absence of enzymatic activities. This manuscript describes the discovery of chromone-based inhibitors of the protein–protein interactions required for activity of the transcription factor STAT5, a therapeutic target for the treatment of human cancers. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2268/2008/z700701_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Implementation of a robust coded structured light technique for dynamic 3D measurements (2004)

This paper presents the implementation details of a coded structured light system for rapid shape acquisition of unknown surfaces. Such techniques are based on the projection of patterns onto a measuring surface and grabbing images of every projection with a camera. Analyzing the pattern deformations that appear in the images, 3D information of the surface can be calculated. The implemented technique projects a unique pattern so that it can be used to measure moving surfaces. The structure of the pattern is a grid where the color of the slits are selected using a De Bruijn sequence. Moreover, since both axis of the pattern are coded, the cross points of the grid have two codewords (which permits to reconstruct them very precisely), while pixels belonging to horizontal and vertical slits have also a codeword. Different sets of colors are used for horizontal and vertical slits, so the resulting pattern is invariant to rotation. Therefore, the alignment constraint between camera and projector considered by a lot of authors is not necessary.
Exciplex-triplet energy transfer: A new method to achieve extremely efficient organic light-emitting diode with external quantum efficiency over 30% and drive voltage below 3 V (2014)

A novel approach to enhance the power efficiency of an organic light-emitting diode (OLED) by employing energy transfer from an exciplex to a phosphorescent emitter is reported. It was found that excitation energy of an exciplex formed between an electron-transporting material with a π-deficient quinoxaline moiety and a hole-transporting material with aromatic amine structure can be effectively transferred to a phosphorescent iridium complex in an emission layer of a phosphorescent OLED. Moreover, such an exciplex formation increases quantum efficiency and reduces drive voltage. A highly efficient, low-voltage, and long-life OLED based on this energy transfer is also demonstrated. This OLED device exhibited extremely high external quantum efficiency of 31% even without any attempt to enhance light outcoupling and also achieved a low drive voltage of 2.8 V and a long lifetime of approximately 1,000,000 h at a luminance of 1,000 cd/m 2 .