gebhart/patrepeval huggingface dataset:
Possible involvement of cAMP in aerial mycelium formation and secondary metabolism in Streptomyces griseus (1999)

In Streptomyces griseus, A-factor (2-isocapryloyl-3R-hydroxymethyl-gamma-butyrolactone) triggers secondary metabolism and morphogenesis by binding a repressor protein (ArpA) and dissociating it from DNA. UV-mutagenesis of the A-factor-deficient mutant HH1 generated strain HO2, defective in the synthesis of ArpA and therefore able to form aerial mycelium, spores and streptomycin. Shotgun cloning of chromosomal DNA from wild-type S. griseus in strain HO2 yielded a gene that suppressed aerial mycelium formation and streptomycin production. Nucleotide sequencing and subcloning revealed that the gene encoded a eukaryotic-type adenylate cyclase (CyaA). In mutant HO2 production of cAMP was growth-dependent until the middle of the exponential growth stage; the production profile was the same as in the wild-type strain. However, the amount of cAMP produced was five times larger when mutant HO2 harboured cyaA on the high-copy-number plasmid pIJ486. Consistent with this, supplying cAMP exogenously at a high concentration to mutant HO2 suppressed formation of both aerial mycelium and streptomycin. On the other hand, some lower concentrations of cAMP stimulated or accelerated aerial mycelium formation. No effects of exogenous cAMP on morphogenesis and secondary metabolism were apparent in the wild-type strain. In addition, disruption of the chromosomal cyaA gene in the wild-type strain had almost no effect. Introducing cyaA cloned in either a low- or a high-copy-number plasmid suppressed morphogenesis and secondary metabolism not only in mutant HO2 but also in other arpA mutants, implying that the effects of cAMP became apparent in the arpA-defective background. When mutant HO2 carried cyaA on a plasmid, synthesis of the stringent response factor ppGpp was greatly reduced; this may account for the observed suppression by cAMP of morphogenesis and secondary metabolism. cAMP also affected protein tyrosine phosphorylation, as determined with antiphosphotyrosine antibody.
Accurate and compact large vocabulary speech recognition on mobile devices (2013)

In this paper we describe the development of an accurate, smallfootprint, large vocabulary speech recognizer for mobile devices. To achieve the best recognition accuracy, state-of-the-art deep neural networks (DNNs) are adopted as acoustic models. A variety of speedup techniques for DNN score computation are used to enable real-time operation on mobile devices. To reduce the memory and disk usage, on-the-fly language model (LM) rescoring is performed with a compressed n-gram LM. We were able to build an accurate and compact system that runs well below real-time on a Nexus 4 Android phone. Index Terms: Deep neural networks, embedded speech recognition, SIMD, LM compression.
Robust Occlusion Handling in Object Tracking (2007)

In object tracking, occlusions significantly undermine the performance of tracking algorithms. Unlike the existing methods that solely depend on the observed target appearance to detect occluders, we propose an algorithm that progressively analyzes the occlusion situation by exploiting the spatiotemporal context information, which is further double checked by the reference target and motion constraints. This strategy enables our proposed algorithm to make a clearer distinction between the target and occluders than existing approaches. To further improve the tracking performance, we rectify the occlusion-interfered erroneous target location by employing a variant-mask template matching operation. As a result, correct target location can always be obtained regardless of the occlusion situation. Using these techniques, the robustness of tracking under occlusions is significantly promoted. Experimental results have confirmed the effectiveness of our proposed algorithm.
Dynamic Metabolic Adjustments and Genome Plasticity Are Implicated in the Heat Shock Response of the Extremely Thermoacidophilic ArchaeonSulfolobus solfataricus (2006)

Approximately one-third of the open reading frames encoded in the Sulfolobus solfataricus genome were differentially expressed within 5 min following an 80 to 90 degrees C temperature shift at pH 4.0. This included many toxin-antitoxin loci and insertion elements, implicating a connection between genome plasticity and metabolic regulation in the early stages of stress response.
Lipopolysaccharide activation of the MEK-ERK1/2 pathway in human monocytic cells mediates tissue factor and tumor necrosis factor α expression by inducing Elk-1 phosphorylation and Egr-1 expression (2001)

Lipopolysaccharide (LPS) induces human monocytes to express many proinflammatory mediators, including the procoagulant molecule tissue factor (TF) and the cytokine tumor necrosis factor alpha (TNF-alpha). The TF and TNF-alpha genes are regulated by various transcription factors, including nuclear factor (NF)-kappaB/Rel proteins and Egr-1. In this study, the role of the MEK-ERK1/2 mitogen-activated protein kinase (MAPK) pathway in LPS induction of TF and TNF-alpha gene expression in human monocytic cells was investigated. The MAPK kinase (MEK)1 inhibitor PD98059 reduced LPS induction of TF and TNF-alpha expression in a dose-dependent manner. PD98059 did not affect LPS-induced nuclear translocation of NF-kappaB/Rel proteins and minimally affected LPS induction of kappaB-dependent transcription. In contrast, PD98059 and dominant-negative mutants of the Ras-Raf1-MEK-ERK (extacellular signal-regulated kinase) pathway strongly inhibited LPS induction of Egr-1 expression. In kinetic experiments LPS induction of Egr-1 expression preceded induction of TF expression. In addition, mutation of the Egr-1 sites in the TF and TNF-alpha promoters reduced expression of these proinflammatory genes. It was demonstrated that LPS induction of the Egr-1 promoter was mediated by 3 SRE sites, which bound an LPS-inducible complex containing serum response factor and Elk-1. LPS stimulation transiently induced phosphorylation of Elk-1 and increased the functional activity of a GAL4-Elk-1TA chimeric protein via the MEK-ERK1/2 pathway. The data indicate that LPS induction of Egr-1 gene expression is required for maximal induction of the TNF-alpha and TF genes in human monocytic cells.
An Integrated Chip for the High‐Throughput Synthesis of Transcription Activator‐like Effectors (2012)

A TALE of two assays: Transcription activator-like effectors (TALEs) are programmable proteins that can specifically recognize a DNA sequence. Previous strategies for the synthesis of TALEs were complicated and time-consuming. The solid-phase synthesis strategy demonstrated here allows quick and simple purification of the ligation product.
Analytical Performance Modeling for Null Message-Based Parallel Discrete Event Simulation (2011)

This paper presents a new analytical performance analysis for null message-based parallel discrete event simulation(PDES). Our analysis builds upon the key operation of selecting simulation events for processing in the null message algorithms. The results not only explain the well-known facts of how the look ahead capability of individual simulation processes (called logical processes, or LPs) affect the simulation performance, but also reveals quantitatively how the look ahead, the communication topology, the computation and communication delays, and the flow control mechanism affect the simulation performance. We first show that all of the LPs in a strongly connected component in the communication topology asymptotically progress at the same speed, regardless of their individual characteristics and their share of computation resource. Second, we derive an analytical upper bound on the simulation performance. The derivation shows that the ratio between the sum of the look ahead and the sum of the event processing and communication delays of LPs in a cycle bounds the simulation speed from the above, and the cycle of LPs imposes the tightest upper bound becomes the bottleneck of the simulation. We conduct a series of simulation experiments to empirically validate our findings. Moreover, we show that by using the derived upper bound as an optimization guidance, we improve the partitioning of a simple parallel simulation example and achieve a four times speedup against the same simulation based on a classic min-cut partitioning strategy.
Imino Diels−Alder-Based Construction of a Piperidine A-Ring Unit for Total Synthesis of the Marine Hepatotoxin Cylindrospermopsin (1996)

The synthesis of a piperidine A-ring precursor to the alkaloid cylindrospermopsin (1) is described. The initial approach to the A-ring precursor focused on the imino Diels-Alder reaction of diene 8 with ethyl (N-tosylimino)acetate (9) to form the cycloadduct 10 as a single stereoisomer. However, all attempts to convert ester 10 to a requisite diene such as 5 were unsuccessful. An alternative strategy involved the Diels-Alder cycloaddition of N-tosylimine 9 with oxygenated diene 19 under either thermal or Lewis acid-catalyzed conditions to produce a mixture of cis and trans enones 20 and 21. Although the undesired cis-enone 20 was the major product under all reaction conditions, it could be converted to the desired trans enone 21 by acid-catalyzed isomerization. Copper-mediated conjugate addition of vinylmagnesium bromide to cis-enone 20 followed by stereoselective ketone reduction with L-Selectride produced alcohol 23, whose structure was confirmed by X-ray crystallography. Similarly, trans-enone 21 was converted to alcohol 25 whose structure and stereochemistry were also established by X-ray analysis. Alcohol 25 was then protected as the silyl ether 26, which was hydroborated at the terminal olefin to produce primary alcohol ester 28having the stereochemistry and functionality needed for cylindrospermopsin.
Localization of Individual Lysine‐Binding Regions in Human Plasminogen and Investigations on Their Complex‐Forming Properties (1980)

After partial digestion of human plasminogen with elastase, followed by chymotryptic cleavage of one of the fragments produced, two polypeptides with molecular weights of approximately 10 000 and with lysine-binding sites still intact were isolated by means of affinity chromatography and gel filtration. One fragment, which was completely sequenced (88 residues), was identified as the fourth kringle, whereas the other, according to partial sequence analysis represented the first kringle. Equilibrium dialysis against 6-aminohexanoic and yielded for the first kringle one high-affinity binding site (Ka = 60 mM-1) and for the fourth kringle one single low-affinity binding site (Ka = 28 mM-1). Moreover, interactions were detected between the first kringle and the N-terminal CNBr fragment of plasminogen and also fibrin. In these cases an additional lysine-binding site, though of low affinity, appears to be involved. Thus, the first kringle seems to play important roles, structurally by contributing to the maintenance of a compact structure of plasminogen through an intramolecular interaction with its N-terminal polypeptide region, and functionally by increasing the fibrin affinity of Lys-plasminogen (plasminogen lacking the first 76 residues) and plasmin.
Irreversible enzyme inhibitors. CXXXIV. Effect of ring substitution on the selective irreversible inhibition of dihydrofolic reductase from L1210 mouse leukemia and liver by 2,4-diamino-5-(3,4-dichlorophenyl)-6-[p-(m-fluorosulfonylphenylureido)phenoxymethyl]pyrimidine (1969)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTIrreversible enzyme inhibitors. CXXXIV. Effect of ring substitution on the selective irreversible inhibition of dihydrofolic reductase from L1210 mouse leukemia and liver by 2,4-diamino-5-(3,4-dichlorophenyl)-6-[p-(m-fluorosulfonylphenylureido)phenoxymethyl]pyrimidineBernard Randall Baker and Nicolaas Vermeulen M. J.Cite this: J. Med. Chem. 1969, 12, 1, 74–78Publication Date (Print):January 1, 1969Publication History Published online1 May 2002Published inissue 1 January 1969https://pubs.acs.org/doi/10.1021/jm00301a019https://doi.org/10.1021/jm00301a019research-articleACS PublicationsRequest reuse permissionsArticle Views49Altmetric-Citations2LEARN 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
Expression of the protein kinase PKR in modulated by IRF-1 and is reduced in 5q- associated leukemias. (1996)

The transcription factor IRF-1 (interferon regulatory factor 1) is an activator of type I interferon and interferon-inducible genes. IRF-1 manifests tumor suppressor activity. Its overexpression results in inhibition of cell growth, and deletions of the IRF-1 gene were demonstrated in a number of human leukemias and myelodysplasias. Although the mechanism by which IRF-1 affects cell growth is unknown, it is believed that IRF-1 activates a set of genes that negatively regulate cell growth. The double-stranded RNA-dependent protein kinase (PKR), which is an interferon-inducible gene, contains a promoter element for the binding of IRF-1 and exhibits antiproliferative properties. Consequently, we investigated the role of IRF-1 in PKR expression. Here, we show that in IRF-1-deficient embryonic fibroblasts, PKR expression is reduced relative to wild-type cells. This result predicts diminished expression of PKR as a potential consequence of deletion of the IRF-1 gene in human leukemias. We show that cells of the human leukemic U937 cell line contain a deletion of one IRF-1 gene and express low levels of PKR. We demonstrate that upregulation of IRF-1 expression in U937 cells by transfection is sufficient to induce PKR expression. We also found a marked reduction in the expression of PKR in blood samples from two patients with myelodysplasias, carrying a deletion of chromosome 5q, a locus to which IRF-1 was mapped. These results show that IRF-1 activates PKR expression and suggest that loss of one allele of the IRF-1 gene is sufficient to affect PKR expression. Therefore, PKR is a strong candidate for a mediator of the tumor suppressor activity of IRF-1.
A Uniform Architecture Design for Accelerating 2D and 3D CNNs on FPGAs (2019)

Three-dimensional convolutional neural networks (3D CNNs) have gained popularity in many complicated computer vision applications. Many customized accelerators based on FPGAs are proposed for 2D CNNs, while very few are for 3D CNNs. Three-D CNNs are far more computationally intensive and the design space for 3D CNN acceleration has been further expanded since one more dimension is introduced, making it a big challenge to accelerate 3D CNNs on FPGAs. Motivated by the finding that the computation patterns of 2D and 3D CNNs are very similar, we propose a uniform architecture design for accelerating both 2D and 3D CNNs in this paper. The uniform architecture is based on the idea of mapping convolutions to matrix multiplications. A customized mapping module is developed to generate the feature matrix tilings with no need to store the entire enlarged feature matrix on-chip or off-chip, a splitting strategy is adopted to reconstruct a convolutional layer to adapt to the on-chip memory capacity, and a 2D multiply-and-accumulate (MAC) array is adopted to compute matrix multiplications efficiently. For demonstration, we implement an accelerator prototype with a high-level synthesis (HLS) methodology on a Xilinx VC709 board and test the accelerator on three typical CNN models: AlexNet, VGG16, and C3D. Experimental results show that the accelerator achieves state-of-the-art throughput performance on both 2D and 3D CNNs, with much better energy efficiency than the CPU and GPU.
Listeria monocytogenes can grow in macrophages without the aid of proteins induced by environmental stresses (1995)

Listeria monocytogenes is a facultative intracellular pathogen which is able to survive and grow within phagocytic cells. Some facultative intracellular bacteria have been shown to respond to the hostile environment within phagocytic cells by producing a set of stress proteins. Since L. monocytogenes has a mechanism for intracellular survival that is distinct from those of other bacteria, we studied the phenotypic response of the bacterium to phagocytosis by macrophages. After phagocytosis of L. monocytogenes EGD by J774-1 macrophage cells, the microorganism rapidly increased in numbers about 20-fold during an incubation period of 5 h. In this phase of phagocytosis, the selective induction of 32 proteins was observed by two-dimensional gel electrophoresis. The responses to the environmental stresses of heat and hydrogen peroxide were also studied, and it was found that 14 heat shock proteins and 13 oxidative stress proteins were induced. Five of the induced proteins were common to both heat and oxidative stresses. By amino acid sequencing analysis, homologs of DnaK and GroEL were confirmed among the heat shock proteins. A comparison of the autoradiograms of the two-dimensional gels revealed that none of these stress proteins were among the proteins induced by L. monocytogenes within the macrophages. This behavior is entirely different from that shown by other facultative intracellular pathogens. Stress proteins known to be induced by environmental stresses were absent in intracellularly grown L. monocytogenes in the present study. This absence could be due to the mechanism by which the microorganisms rapidly escape from this stressful environment at a very early phase of phagocytosis.
Conditional Loss of Nkx3.1 in Adult Mice Induces Prostatic Intraepithelial Neoplasia (2002)

The homeodomain-containing transcription factor NKX3.1 is a putative prostate tumor suppressor that is expressed in a largely prostate-specific and androgen-regulated manner. Loss of NKX3.1 protein expression is common in human prostate carcinomas and prostatic intraepithelial neoplasia (PIN) lesions and correlates with tumor progression. Disruption of the murine Nkx3.1 gene results in defects in prostate branching morphogenesis, secretions, and growth. To more closely mimic the pattern of NKX3.1 loss that occurs in human prostate tumors, we have used Cre- and loxP-mediated recombination to delete the Nkx3.1 gene in the prostates of adult transgenic mice. Conditional deletion of one or both alleles of Nkx3.1 leads to the development of preinvasive lesions that resemble PIN. The pattern of expression of several biomarkers (Ki-67, E-cadherin, and high-molecular-weight cytokeratins) in these PIN lesions resembled that observed in human cases of PIN. Furthermore, PIN foci in mice with conditional deletion of a single Nkx3.1 allele lose expression of the wild-type allele. Our results support the role of NKX3.1 as a prostate tumor suppressor and indicate a role for this gene in tumor initiation.
Importance of catalase in the adaptive response to hydrogen peroxide: analysis of acatalasaemic Saccharomyces cerevisiae (1996)

Controversy about the importance of catalase in the detoxification of H2O2 in human erythrocytes continues. It has been suggested that catalase has no role in the clearance of H2O2 in erythrocytes. In the present study we investigated the role of catalase in the defence mechanism against oxidative stress using Saccharomyces cerevisiae. S. cerevisiae has two catalases, catalase A and catalase T. We constructed a double mutant (acatalasaemic mutant) unable to produce either catalase A or catalase T, and compared it with wild-type and single-mutant cells. The acatalasaemic mutant cells showed a similar growth rate to wild-type cells under non-oxidative stress conditions, and showed a similar susceptibility to H2O2 stress in the exponential growth phase. The acatalasaemic mutant cells at stationary phase were, however, much more sensitive to H2O2 stress than wild-type and single-mutant cells. Moreover, the ability of acatalasaemic and single-mutant cells to show adaptation to 2 mM H2O2 was distinctly inferior to that of wild-type cells. These results suggest that catalase is not essential for yeast cells under normal conditions, but plays an important role in the acquisition of tolerance to oxidative stress in the adaptive response of these cells.
The yes-related cellular gene lyn encodes a possible tyrosine kinase similar to p56lck. (1987)

With v-yes DNA as the probe, a human cDNA library made from placental RNA was screened under relaxed conditions, and DNA clones derived from a novel genetic locus, termed lyn, were obtained. Nucleotide sequencing revealed that lyn could encode a novel tyrosine kinase that was very similar to mouse T-lymphocyte-specific tyrosine kinase p56lck and the v-yes protein as well as to the gene products of v-fgr and v-src. Northern hybridization analysis revealed that a 3.2-kilobase lyn mRNA was expressed in a variety of tissues of the human fetus. The pattern of lyn mRNA expression was different from those of related genes, such as yes and syn. Hybridization analysis of DNA from sorted chromosomes showed that the lyn gene is located on human chromosome 8 q13-qter.
A new measurement microphone based on MEMS technology (2003)

This paper presents a new type of measurement microphone that is based on MEMS technology. The silicon chip design and fabrication are discussed, as well as the specially developed packaging technology. The microphones are tested on a number of key parameters for measurement microphones: sensitivity, noise level, frequency response, and immunity to disturbing environmental parameters, such as temperature changes, humidity, static pressure variations, and vibration. A sensitivity of 22 mV/Pa (-33 dB re. 1 V/Pa), and a noise level of 23 dB(A) were measured. The noise level is 7 dB lower than state-of-the-art 1/4-inch measurement microphones. A good uniformity on sensitivity and frequency response has been measured. The sensitivity to temperature changes, humidity, static pressure variations and vibrations is fully comparable to the traditional measurement microphones. This paper shows that high-quality measurement microphones can be made using MEMS technology, with a superior noise performance.
PURLs: consider this option for heavy menstrual bleeding. (2011)

Women who fail to respond to--or are unable to tolerate--other treatments for heavy menstrual blood loss now have another choice.
Cardiovascular effects of human insular cortex stimulation (1992)

Recent investigations indicate a site of cardiac representation within the left insular cortex of the rat. Moreover, the results of lesion studies suggest left-sided insular dominance for sympathetic cardiovascular effects. It is unclear whether similar representation exists within the human insular cortex. Five epileptic patients underwent intraoperative insular stimulation prior to temporal lobectomy for seizure control. On stimulation of the left insular cortex, bradycardia and depressor responses were more frequently produced than tachycardia and pressor effects (p less than 0.005). The converse applied for the right insular cortex. We believe this to be the first demonstration of cardiovascular changes elicitable during insular stimulation in humans, and of lateralization of such responses for a cortical site. In humans, unlike the rat, there appears to be right-sided dominance for sympathetic effects. These findings may be of relevance in predicting the autonomic effects of stroke in humans and in the explanation of sudden unexpected epileptic death.