gebhart/patrepeval huggingface dataset:
MDS1, a dosage suppressor of an mck1 mutant, encodes a putative yeast homolog of glycogen synthase kinase 3. (1994)

The yeast gene MCK1 encodes a serine/threonine protein kinase that is thought to function in regulating kinetochore activity and entry into meiosis. Disruption of MCK1 confers a cold-sensitive phenotype, a temperature-sensitive phenotype, and sensitivity to the microtubule-destabilizing drug benomyl and leads to loss of chromosomes during growth on benomyl. A dosage suppression selection was used to identify genes that, when present at high copy number, could suppress the cold-sensitive phenotype of mck1::HIS3 mutant cells. Several unique classes of clones were identified, and one of these, designated MDS1, has been characterized in some detail. Nucleotide sequence data reveal that MDS1 encodes a serine/threonine protein kinase that is highly homologous to the shaggy/zw3 kinase in Drosophila melanogaster and its functional homolog, glycogen synthase kinase 3, in rats. The presence of MDS1 in high copy number rescues both the cold-sensitive and the temperature-sensitive phenotypes, but not the benomyl-sensitive phenotype, associated with the disruption of MCK1. Analysis of strains harboring an mds1 null mutation demonstrates that MDS1 is not essential during normal vegetative growth but appears to be required for meiosis. Finally, in vitro experiments indicate that the proteins encoded by both MCK1 and MDS1 possess protein kinase activity with substrate specificity similar to that of mammalian glycogen synthase kinase 3.
Summarizing video using non-negative similarity matrix factorization (2004)

We present a novel approach to automatically extracting summary excerpts from audio video and video. Our approach is to maximize the average similarity between the excerpt and the source. We first calculate a similarity matrix by comparing each pair of time samples using a quantitative similarity measure. To determine the segment with highest average similarity, we maximize the summation of the self-similarity matrix over the support of the segment. To select multiple excerpts while avoiding redundancy, we compute the non-negative matrix factorization (NMF) of the similarity matrix into its essential structural components. We then build a summary comprised of excerpts from the main components, selecting the excerpts for maximum average similarity within each component. Variations integrating segmentation and other information are also discussed, and experimental results are presented.
Axonal Glycoproteins with Immunoglobulin‐ and Fibronectin Type III‐Related Domains in Vertebrates: Structural Features, Binding Activities, and Signal Transduction (1993)

The L1- and F11-like axonal glycoproteins, implicated in neurite outgrowth and fasciculation, are members of the Ig superfamily comprising multiple fibronectin type III-like domains. Their Ig-like and fibronectin type III-related domains are likely to be composed of seven beta-strands arranged in two opposing beta-sheets of highly similar topology. Whereas the F11-like molecules lack a transmembrane sequence and are anchored in the plasma membrane by a glycosylphosphatidylinositol, the L1-like molecules comprise cytoplasmic domains with highly conserved sequence motifs. Most of the latter proteins occur in different isoforms generated by alternative pre-mRNA splicing, which has not been documented for molecules of the F11 subgroup. L1-like proteins undergo heterophilic as well as homophilic interactions, whereas only the former mode of binding was observed for F11-like proteins. Evidence is accumulating that these Ig superfamily molecules with fibronectin type III-like domains are interacting in a complex manner with each other and molecules of the extracellular matrix. Investigations assigning structure to function reveal that their individual extracellular domains serve distinct binding activities. Recent studies also suggest that L1 and NCAM are implicated in the transduction of transmembrane signals.
Investigation of the Crystallization Process in 2 nm CdSe Quantum Dots (2005)

Investigation of the growth of CdSe nanocrystals ( approximately 160 atoms) to the uniquely stable size of 2 nm allows the monitoring of the crystallization process in semiconductor quantum dots. By using a combination of optical techniques, high-resolution transmission electron microscopy (HRTEM), and powder X-ray diffractometry (XRD), new phenomena were explored during the CdSe nanocrystal growth process, which involved significant morphological reconstruction and crystallization of the initially formed amorphous nanoparticles. During the crystallization, the absorption onset of the CdSe quantum dots blue shifted toward higher energies at 3 eV (414 nm), while the photoluminescence red shifted to lower energies. Furthermore, an apparent increasing Stokes shift was observed during the formation of small CdSe nanoparticles. On the other hand, the photoluminescence excitation spectra showed constant features over the reaction time. Additionally, results from HRTEM and XRD studies show that the CdSe nanoparticles were amorphous at early reaction stages and became better crystallized after longer reaction times, while the particle size remained the same during the crystallization process. These observations demonstrate the important role of the surface on the optical properties of small CdSe quantum dots and facilitated the spectroscopic monitoring of the crystallization process in quantum dots.
A SUBBAND HYBRID BEAMFORMING FOR IN-CAR SPEECH ENHANCEMENT (2012)

International audience
An improved cost function for static partitioning of parallel circuit simulations using a conservative synchronization protocol (1995)

Distributing computation among multiple processors is one approach to reducing simulation time for large VLSI circuit designs. However, parallel simulation introduces the problem of how to partition the logic gates and system behaviors of the circuit among the available processors in order to obtain maximum speedup. A complicating factor that is often ignored is the effect of the time-synchronization protocol (conservative [1] or optimistic [2]). Inherent in the partitioning problem is the question of how to effectively measure the relative quality of a partition. This paper describes an objective cost function for measuring the relative quality of a task partition that includes a synchronization factor for a conservative NULL-message protocol. A graph-based partitioning tool based on this cost function is used to perform the static task allocation for parallel simulation of a structural VHDL circuit. Results for two 1000 – 4000 gate circuits demonstrate that the additional consideration of the synchronization protocol in the cost function generates partitions that exhibit improved speedup.
Genetic Algorithms in Search, Optimization and Machine Learning (1988)

David Goldberg's Genetic Algorithms in Search, Optimization and Machine Learning is by far the bestselling introduction to genetic algorithms. Goldberg is one of the preeminent researchers in the field--he has published over 100 research articles on genetic algorithms and is a student of John Holland, the father of genetic algorithms--and his deep understanding of the material shines through. The book contains a complete listing of a simple genetic algorithm in Pascal, which C programmers can easily understand. The book covers all of the important topics in the field, including crossover, mutation, classifier systems, and fitness scaling, giving a novice with a computer science background enough information to implement a genetic algorithm and describe genetic algorithms to a friend.
Cooperative Diversity in Wireless Networks: Efficient Protocols and Outage Behavior (2004)

We develop and analyze low-complexity cooperative diversity protocols that combat fading induced by multipath propagation in wireless networks. The underlying techniques exploit space diversity available through cooperating terminals' relaying signals for one another. We outline several strategies employed by the cooperating radios, including fixed relaying schemes such as amplify-and-forward and decode-and-forward, selection relaying schemes that adapt based upon channel measurements between the cooperating terminals, and incremental relaying schemes that adapt based upon limited feedback from the destination terminal. We develop performance characterizations in terms of outage events and associated outage probabilities, which measure robustness of the transmissions to fading, focusing on the high signal-to-noise ratio (SNR) regime. Except for fixed decode-and-forward, all of our cooperative diversity protocols are efficient in the sense that they achieve full diversity (i.e., second-order diversity in the case of two terminals), and, moreover, are close to optimum (within 1.5 dB) in certain regimes. Thus, using distributed antennas, we can provide the powerful benefits of space diversity without need for physical arrays, though at a loss of spectral efficiency due to half-duplex operation and possibly at the cost of additional receive hardware. Applicable to any wireless setting, including cellular or ad hoc networks-wherever space constraints preclude the use of physical arrays-the performance characterizations reveal that large power or energy savings result from the use of these protocols.
ChemInform Abstract: HETEROCYCLIC SEVEN‐MEMBERED RING COMPOUNDS, XXVIII. 5‐ACETOXY‐ AND 5‐METHOXY‐1‐BENZOTHIEPINS AND ANALOGOUS 1‐BENZOXEPINS (1985)

Abstract Aus den Ketonen (I) werden über die Silylenolether (II) die ungesättigten Ketone (III) hergestellt, die in die Derivate (IV) und (V) übergeführt werden.
No evidence of platelet activation during atrial pacing in subjects with stable angina. (1989)

Platelet behaviour (activation) in ischemic heart disease (stable angina) during pacing-induced tachycardia was studied. ECG was recorded during the trial. Ischemic heart disease (IHD) subjects had 75% or more narrowing of the luminal diameter of a coronary artery, demonstrated by coronary angiography. Eight subjects needing cardiac catheterism because of supraventricular rhythm disturbances with no evidence of IHD were studied as controls. Beta-thromboglobulin (beta-tg) and platelet factor 4 (PF4) were studied as platelet activation markers; beta-tg and PF4 were evaluated before atrial pacing in peripheral venous blood and, by catheterism, before and at maximum pacing rate in coronary venous sinus (CVS) and in ascending aorta (AA). Catheterism and blood withdrawals were performed in order to reduce platelet activation in vivo. No significant difference in platelet activation between IHD patients and control group in peripheral venous blood were found. No trans-myocardial gradient neither in IHD subjects nor in controls were observed. In conclusion, no platelet activation in IHD patients during pacing-induced tachycardia could be observed.
Direct association between caspase 3 and α5β1 integrin and its role during anoikis of rat fibroblasts (2006)

We have demonstrated a direct association between alpha5beta1 integrin and caspase 3, both pro- and mature enzyme, in various sub-cellular compartments of rat fibroblasts undergoing anoikis. Integrin associated caspase 3 showed high activity in the plasma membranes, whereas in the cytosol and microsomal fraction it showed little or no activity. Our results suggest a possible role for recycled un-ligated alpha5beta1 integrin molecules between cytosol and plasma membrane, in regulation of caspase-3 activity and induction of cell death in adhesion-deprived cells.
Three Residues Predicted by Molecular Modeling To Interact with the Purine Moiety Alter Ligand Binding and Channel Gating in Cyclic Nucleotide-Gated Channels (1998)

Cytoplasmic cAMP and cGMP are soluble cellular messengers that directly activate cyclic nucleotide-gated (CNG) channels. These channels mediate sensory transduction in photoreceptors and olfactory neurons. The closely related CNG channels in these cell types have different nucleotide activation profiles, and we have investigated the molecular basis of their nucleotide selectivity properties. Previously, we predicted that the purine moiety of the nucleotide interacts with residues F533, K596, and D604 (bovine rod alpha CNG channel subunit sequences) of the nucleotide binding domain. In this study, we replaced these three residues with the corresponding residues of the bovine olfactory CNG channel. Mutations at each position altered the nucleotide activation of the rod CNG channels. In a mutant where K596 was replaced with arginine, cAMP-activated currents were enhanced 8-12-fold, suggesting that residue 596 influences channel gating. Thermodynamic cycle analysis of the data showed that (1) the residues are energetically coupled and (2) energetic coupling exists between the potentiating effects of Ni2+ and the replacement of F533 with tyrosine. These data suggest that changes in one of the residues alter the purine contacts with the other residues and that F533 communicates with the C-linker region of the channel involved in Ni2+ potentiation.
Butanol production from agricultural residues: Impact of degradation products on Clostridium beijerinckii growth and butanol fermentation (2007)

During pretreatment and hydrolysis of fiber-rich agricultural biomass, compounds such as salts, furfural, hydroxymethyl furfural (HMF), acetic, ferulic, glucuronic, rho-coumaric acids, and phenolic compounds are produced. Clostridium beijerinckii BA101 can utilize the individual sugars present in lignocellulosic [e.g., corn fiber, distillers dry grain solubles (DDGS), etc] hydrolysates such as cellobiose, glucose, mannose, arabinose, and xylose. In these studies we investigated the effect of some of the lignocellulosic hydrolysate inhibitors associated with C. beijerinckii BA101 growth and acetone-butanol-ethanol (ABE) production. When 0.3 g/L rho-coumaric and ferulic acids were introduced into the fermentation medium, growth and ABE production by C. beijerinckii BA101 decreased significantly. Furfural and HMF are not inhibitory to C. beijerinckii BA101; rather they have stimulatory effect on the growth of the microorganism and ABE production.
Molecular characterization of circulating tumor cells (CTCs) of patients with neuroendocrine prostate cancer (NEPC). (2014)

177 Background: Neuroendocrine prostate cancer (NEPC) is an aggressive variant of prostate cancer that commonly arises in later stages of castration resistant prostate cancer (CRPC), especially with visceral metastases in the setting of a low prostate-specific antigen (PSA). The genes AURKA and MYCNare frequently amplified. There are no reliable serum markers to identify patients that are transforming to NEPC and incidence of circulating tumor cells (CTCs) in these patients is unknown. Detection of NEPC has clinical implications as these patients are often treated with platinum chemotherapy rather than with androgen receptor (AR) targeted therapies. Methods: Ten men with metastatic NEPC underwent metastatic tumor biopsy and blood collection for CTC analysis utilizing the Epic Sciences platform. Clinical characteristics, pathologic and molecular features including exome sequencing of metastatic tumors, serum PSA and neuroendocrine (NE) markers, CTC count by CellSearch were obtained on all patients. AURKA and MYCNamplification were assessed by FISH in both tumors and Epic CTCs. Results: Sites of metastases included liver (6 out of 10), bone (9 out of 10), lymph nodes (8 out of 10), pleura (1 out of 10), and lungs (2 out of 10). Serum PSA, CellSearch CTCs, and serum NE markers were variable including 4 out of 10 patients with PSA less than 1 ng/ml (range 0.02-9.39) and 3 out of 5 evaluated patients with CTC count of zero (range 0 to 94). Four out of 7 evaluated tumors displayed amplification of AURKA and MYCN. Epic CTCs demonstrated frequent clusters, dim/low cytokeratin suggesting epithelial plasticity, and low AR expression. Patients were subsequently treated with platinum (4 out of 10), AURKAinhibitor (4 out of 10), or hormonal therapy (2 out of 10). Conclusions: PSA, serum NE markers, and CTC count by CellSearch may not be reliable in identifying patients with CRPC that have NE features. Epithelial plasticity potentially arising from epithelial-mesenchymal transition may explain lack of detection using conventional CTC assays. The Epic Sciences CTC platform is capable of detecting CTCs from patients with NEPC and CTCs are molecularly similar to metastatic biopsies. Epic CTCs may be useful in the earlier detection of NEPC and inform patient selection for therapy.
DURATION AND SELECTIVITY OF BLOOD-BRAIN BARRIER BREAKDOWN IN CHRONIC RELAPSING EXPERIMENTAL ALLERGIC ENCEPHALOMYELITIS STUDIED BY GADOLINIUM-DTPA AND PROTEIN MARKERS (1990)

Gadolinium-DTPA (Gd-DTPA) enhancement seen with magnetic resonance imaging in chronic relapsing experimental allergic encephalomyelitis (CREAE) corresponded with sites of blood-brain barrier breakdown judged by traditional markers in areas of inflammatory demyelination. Duration of Gd-DTPA leakage for individual lesions in CREAE varied from 5 days to more than 5 wks. By contrast, in acute EAE leakage was of shorter duration (always less than 5 days). Selective enhancement was observed in CREAE lesions using Gd-protein markers. Gd-albumin enhancement was not always seen in areas of leakage of the smaller molecular weight compound Gd-DTPA. The addition of immunoglobulin to the gadolinium complex led to enhancement of lesions not seen with Gd-albumin alone. From the similarities between the histology and the patterns of Gd-enhancement in CREAE and multiple sclerosis, it is probable that Gd-enhancement reflects active inflammation (with or without demyelination) in the human disease.
Immunohistochemical Detection of c-erbB-2 and p53 in Benign Breast Disease and Breast Cancer Risk (1998)

p53 protein accumulation, but not c-erbB-2 protein overexpression, appears to be associated with an increased risk of progression to breast cancer in women with benign breast disease.
Superconductivity above liquid nitrogen temperature: preparation and properties of a family of perovskite-based superconductors (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSuperconductivity above liquid nitrogen temperature: preparation and properties of a family of perovskite-based superconductorsE. M. Engler, V. Y. Lee, A. I. Nazzal, R. B. Beyers, G. Lim, P. M. Grant, S. S. P. Parkin, M. L. Ramirez, J. E. Vazquez, and R. J. SavoyCite this: J. Am. Chem. Soc. 1987, 109, 9, 2848–2849Publication Date (Print):April 1, 1987Publication History Published online1 May 2002Published inissue 1 April 1987https://pubs.acs.org/doi/10.1021/ja00243a061https://doi.org/10.1021/ja00243a061research-articleACS PublicationsRequest reuse permissionsArticle Views297Altmetric-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
Duplex Stabilization of DNA: Oligonucleotides containing 7‐substituted 7‐deazaadenines (1995)

Abstract The oligonucleotide building blocks 4b–d derived from 7‐bromo‐, 7‐chloro‐, and 7‐methyl‐substituted 7‐deaza‐2′‐deoxyadenosines 3b–d were prepared. They were employed in the solid‐phase synthesis of the oligonucleotides 7–25 . The dA residues of the homomer d(A 12 ), the alternating d[(A‐T) 6 ], and the palindromic d(G‐T‐A‐G‐A‐A‐T‐T‐C‐T‐A‐C) were replaced by 3b–d as well as by the parent 7‐deaza‐2′‐deoxyadenosine ( 3a ). The melting profiles and CD spectra of oligonucleotide duplexes, showing this major groove modification, were measured, and the T m values as well as the thermodynamic data were determined. It was found that small substituents such as Br, Cl, or Me introduced in the 7‐position of a 7‐deazaadenine residue increase the duplex stability compared to oligonucleotides containing adenine.
Development of Halogenase Enzymes for Use in Synthesis (2017)

Nature has evolved halogenase enzymes to regioselectively halogenate a diverse range of biosynthetic precursors, with the halogens introduced often having a profound effect on the biological activity of the resulting natural products. Synthetic endeavors to create non-natural bioactive small molecules for pharmaceutical and agrochemical applications have also arrived at a similar conclusion: halogens can dramatically improve the properties of organic molecules for selective modulation of biological targets in vivo. Consequently, a high proportion of pharmaceuticals and agrochemicals on the market today possess halogens. Halogenated organic compounds are also common intermediates in synthesis and are particularly valuable in metal-catalyzed cross-coupling reactions. Despite the potential utility of organohalogens, traditional nonenzymatic halogenation chemistry utilizes deleterious reagents and often lacks regiocontrol. Reliable, facile, and cleaner methods for the regioselective halogenation of organic compounds are therefore essential in the development of economical and environmentally friendly industrial processes. A potential avenue toward such methods is the use of halogenase enzymes, responsible for the biosynthesis of halogenated natural products, as biocatalysts. This Review will discuss advances in developing halogenases for biocatalysis, potential untapped sources of such biocatalysts and how further optimization of these enzymes is required to achieve the goal of industrial scale biohalogenation.