gebhart/patrepeval huggingface dataset:
On-Die Droop Detector for Analog Sensing of Power Supply Noise (2004)

Understanding the supply fluctuations of various frequency harmonics is essential to maximizing microprocessor performance. Conventional methods used for analog validation of the power delivery system fall short in one or more of the following areas. 1) Measurement accuracy in both frequency and time domains, especially for very high-frequency noise caused by large di/dt events. The multigigahertz power supply noise attenuates very quickly away from the die. Conventional approaches of measuring the noise at the pins of the package or at the die using capacitive probes are not accurate for multigigahertz clocks. For this reason, the observability of high-frequency on-die noise has been very tricky. 2) Implementation (e.g., delivery) of analog references to multiple areas across a "noisy" die, compactness/modularity of the measurement units, restraining assumptions inherent in the measurement circuit such as periodicity of the supply noise event. 3) Automation to enable a timely volume of measurements. The efficiency of the measurements is key to correlating a particular speed path to poser supply noise. To address these issues, this paper presents an on-die droop detector (ODDD), a scalable IC solution implemented and validated on a 90-nm process, for analog sensing of differential high-bandwidth supply noise.
The antitumor histone deacetylase inhibitor suberoylanilide hydroxamic acid exhibits antiinflammatory properties via suppression of cytokines (2002)

Suberoylanilide hydroxamic acid (SAHA) is a hydroxamic acid-containing hybrid polar molecule; SAHA specifically binds to and inhibits the activity of histone deacetylase. Although SAHA, like other inhibitors of histone deacetylase, exhibits antitumor effects by increasing expression of genes regulating tumor survival, we found that SAHA reduces the production of proinflammatory cytokines in vivo and in vitro. A single oral administration of SAHA to mice dose-dependently reduced circulating TNF-alpha, IL-1-beta, IL-6, and IFN-gamma induced by lipopolysaccharide (LPS). Administration of SAHA also reduced hepatic cellular injury in mice following i.v. injection of Con A. SAHA inhibited nitric oxide release in mouse macrophages stimulated by the combination of TNF-alpha plus IFN-gamma. Human peripheral blood mononuclear cells stimulated with LPS in the presence of SAHA released less TNF-alpha, IL-1-beta, IL-12, and IFN-gamma (50% reduction at 100-200 nM). The production of IFN-gamma stimulated by IL-18 plus IL-12 was also inhibited by SAHA (85% at 200 nM). However, SAHA did not affect LPS-induced synthesis of the IL-1-beta precursor, the IL-1 receptor antagonist, or the chemokine IL-8. In addition, IFN-gamma induced by anti-CD3 was not suppressed by SAHA. Steady-state mRNA levels for LPS-induced TNF-alpha and IFN-gamma in peripheral blood mononuclear cells were markedly decreased, whereas IL-8 and IL-1-beta mRNA levels were unaffected. Because SAHA exhibits antiinflammatory properties in vivo and in vitro, inhibitors of histone deacetylase may stimulate the expression of genes that control the synthesis of cytokines and nitric oxide or hyperacetylate other targets.
Design and optimization of a digital microfluidic biochip for protein crystallization (2008)

Proteins crystallization is a commonly used technique for protein analysis and subsequent drug design. It predicts the three-dimensional arrangement of the constituent amino acids, which in turn indicates the specific biological function of a protein. Protein crystallization experiments are typically carried out manually on multi-well plates in the laboratory. These experiments are slow, expensive, and error-prone. We present the design of a multi-well plate microfluidic biochip for protein crystallization; this biochip can transfer protein samples, prepare candidate solutions, and carry out crystallization automatically. To reduce the manufacturing cost of such devices, we present an efficient algorithm to generate a pin-assignment plan for the proposed design. The resulting biochip enables control of a large number of on-chip electrodes using only a small number of pins. Based on the pin-constrained chip design, we present an efficient shuttle-passenger-like droplet manipulation method to achieve high-throughput and defect-tolerant well loading.
Third harmonic generation microscopy (1998)

Third harmonic generation microscopy is used to make dynamical images of living systems for the first time. A 100 fs excitation pulse at 1.2 aem results in a 400 nm signal which is generated directly within the specimen. Chara plant rhizoids have been imaged, showing dynamic plant activity, and non-fading image characteristics even with continuous viewing, indicating prolonged viability under these THG-imaging conditions.
Totalsynthese eines Tetrasaccharid‐Antigens von Bacillus anthracis – Basis für einen Impfstoff gegen Anthrax (2005)

Kann man Anthrax mit seinen eigenen Waffen schlagen? Der Anthrax-Erreger, Bacillus anthracis, trägt spezifische Oligosaccharide auf seiner Oberfläche, die für die erste Interaktion mit dem Wirt wahrscheinlich von großer Bedeutung sind. Ausgehend von diesen spezifischen Oligosacchariden können Impfstoffe entwickelt werden, die eine Immunantwort hervorrufen. Die Synthese eines solchen Impfstoff-Kandidaten wird vorgestellt (siehe Bild; Pent=4-Pentenyl). Hintergrundinformationen zu diesem Beitrag sind im WWW unter http://www.wiley-vch.de/contents/jc_2001/2005/z502615_s.pdf zu finden oder können beim Autor angefordert werden. 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.
Changes of the phosphorylation of membrane-associated proteins following treatment of HeLa cells with the guanine analogue, queuine. (1993)

The guanine analogue, queuine (q), is a nutrition factor for eukaryotes and occurs as a free base or as modified nucleoside queuosine (Q) inserted into the anticodon of tRNAs(GUN) in place of guanosine (G). The free q-base and the corresponding Q-deficient tRNAs accumulate in fast proliferating tumors and in embryonic cells. The present data show that treatment of Q-deficient HeLa cells with queuine resulted in reduced in vitro phosphorylation of two membrane-associated proteins, pp110 and pp18. Reduced phosphorylation of pp110 and pp18 was also observed when a membrane-containing particulate fraction from queuine starved HeLa cells was labelled with [gamma-32P]ATP in the presence of queuine. Incorporated phosphate into pp110 was alkali-stable, suggesting that this protein became phosphorylated at tyrosine residues. After stimulation of intact Q-deficient cells with epidermal growth factor, pp110 was rapidly phosphorylated at tyrosine residues. The results show that queuine as a free base influences protein tyrosine phosphorylation in intact cells, suggesting that it might interfere with protein phosphorylation involved in signal transduction pathways.
Nutrition Needs of Mammalian Cells in Tissue Culture (1955)

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A function blocking anti-mouse integrin α5β1 antibody inhibits angiogenesis and impedes tumor growth in vivo (2007)

The results herein demonstrate that 339.1, like volociximab, exhibits potent anti-alpha5beta1 activity and confirms that inhibition of integrin alpha5beta1 impedes angiogenesis and slows tumor growth in vivo.
Histones Activate the NLRP3 Inflammasome in Kupffer Cells during Sterile Inflammatory Liver Injury (2013)

Cellular processes that drive sterile inflammatory injury after hepatic ischemia/reperfusion (I/R) injury are not completely understood. Activation of the inflammasome plays a key role in response to invading intracellular pathogens, but mounting evidence suggests that it also plays a role in inflammation driven by endogenous danger-associate molecular pattern molecules released after ischemic injury. The nucleotide-binding domain, leucine-rich repeat containing protein 3 (NLRP3) inflammasome is one such process, and the mechanism by which its activation results in damage and inflammatory responses following liver I/R is unknown. In this article, we report that both NLRP3 and its downstream target caspase-1 are activated during I/R and are essential for hepatic I/R injury, because both NLRP3 and caspase-1 knockout mice are protected from injury. Furthermore, inflammasome-mediated injury is dependent on caspase-1 expression in liver nonparenchymal cells. Although upstream signals that activate the inflammasome during ischemic injury are not well characterized, we show that endogenous extracellular histones activate the NLRP3 inflammasome during liver I/R through TLR9. This occurs through TLR9-dependent generation of reactive oxygen species. This mechanism is operant in resident liver Kupffer cells, which drive innate immune responses after I/R injury by recruiting additional cell types, including neutrophils and inflammatory monocytes. These novel findings illustrate a new mechanism by which extracellular histones and activation of NLRP3 inflammasome contribute to liver damage and the activation of innate immunity during sterile inflammation.
Measurement of Matrix Metalloproteinases and Tissue Inhibitors of Metalloproteinases in Blood and Tissues: Clinical and Experimental Applications (1999)

The balance between production and activation of MMPs and their inhibition by TIMPs is a crucial aspect of cancer invasion and metastasis. On the basis of the concept that MMPs synthesized in tissues seep into the bloodstream, we have examined MMP levels in the plasma of patients with cancer. In colorectal, breast, prostate, and bladder cancer, most patients with aggressive disease have increased plasma levels of gelatinase B. In patients with advanced colorectal cancer, high levels of either gelatinase B or TIMP complex were associated with shortened survival. We propose that these assays may be clinically useful in characterizing metastatic potential in selected kinds of cancer. In rheumatoid arthritis and systemic lupus erythematosus (SLE), serum and plasma levels of stromelysin-1 were approximately 3-5-fold increased. Fluctuating serum stromelysin-1 levels in SLE did not correspond with change in disease activity. In SLE, stromelysin-1 may be a component of the chronic tissue repair process rather than being responsible for inciting tissue damage. On the basis of these observations, we conclude that measurement of plasma/serum MMP and TIMP levels may provide important data for selecting and following patients considered for treatment with drugs that interfere with MMP activity.
<title>Collaborative object sharing for multimedia operating system (COSMOS): a framework for real-time multimedia group presentation</title> (1995)

Current multimedia group presentation environments such as video conference systems, remote presentation and shared workspaces are typically developed as self-contained applications, i.e. without much support from operating systems. However, newly developed operating systems have a framework to support multimedia data processing but these are still not enough for multimedia group presentations. To resolve this problem, we present a framework for designing an extended operating system called COSMOS (Collaborative Object Sharing for Multimedia Operating System). The framework provides concurrent and distributed multimedia data processing, fine grained synchronization, real-time data flow management, presentation, session and shared object management of multimedia CSCW applications. The framework can be useful for either designing customized multimedia servers for playback machines or application developments using its API.
Cloning, genetic mapping, and expression analysis of an Arabidopsis thaliana gene that encodes 1-aminocyclopropane-1-carboxylate synthase. (1992)

A genomic clone of one member of the Arabidopsis thaliana (L.) Heynh. 1-aminocyclopropane-1-carboxylate (ACC) synthase (S-adenosyl-L-methionine methylthioadenosine-lyase, EC 4.4.1.14) gene family (AT-ACC1) was isolated and sequenced. A region of homology was found in the 5'-untranslated region with the promoter of a zucchini and a tomato ACC synthase gene. Comparison of its primary structure with other ACC synthases revealed conservation of seven peptide regions as well as similarity with 11 amino acids of the catalytic site of aminotransferases. Genomic DNA gel blotting suggested the existence of an ACC synthase multigene family in Arabidopsis, possibly with three other members, none of which is very closely related to AT-ACC1. The existence of at least one other gene was confirmed by the isolation of a cDNA (AT-ACC2) from a flower-specific cDNA library. The AT-ACC1 gene was mapped on the Arabidopsis restriction fragment length polymorphism map and is located on the top of chromosome 1. This position does not correspond to any known mutation on the genetic map. Expression of the AT-ACC1 gene was studied by reverse transcription-PCR on total RNA. Messenger accumulation was strong in young leaves and flowers. The gene was not induced by wounding of young leaves or in seedlings in the presence of auxin. Ethylene exposure of mature plants led to an induction of AT-ACC1 gene expression. It is suggested that AT-ACC1 protein has a role in developmental control of ethylene synthesis.
A panel of kallikrein markers can predict outcome of prostate biopsy following clinical work-up: an independent validation study from the European Randomized Study of Prostate Cancer screening, France (2010)

In this independent validation study, the model was highly predictive of prostate cancer in men for whom the decision to biopsy is based on both elevated PSA and clinical work-up. Use of this model would reduce a large number of biopsies while missing few cancers.
Viral Myc Oncoproteins in Infected Fibroblasts Down-modulate Thrombospondin-1, a Possible Tumor Suppressor Gene (1996)

We are interested in identifying the transcriptional targets of the Myc oncoproteins. To this end, we have fused Myc of the MC29 retrovirus with the rat glucocorticoid receptor. This chimeric protein requires dexamethasone to undergo nuclear translocation and achieve an active conformation. We employed a differential hybridization approach to identify mRNAs that are induced or repressed in infected avian fibroblasts in response to dexamethasone. This screen yielded one mRNA underrepresented in the dexamethasone-treated cells. In Myc-transformed cell clones, its level decreases 6-fold as early as 4 h and more than 30-fold after 32 h of exposure to the hormone. This mRNA was also down-regulated by recombinant Myc retroviruses in rodent fibroblasts, including those refractory to transformation. Sequence analysis revealed that it is homologous to the 3' untranslated regions of the mammalian thrombospondin-1 genes. Using an anti-thrombospondin antibody, we confirmed that rodent cells overexpressing Myc produce very small amounts of this protein. Also, they do not support efficient expression of a reporter gene driven by the thrombospondin-1 promoter. Thus, thrombospondin-1 is a bona fide target of Myc. Moreover, its silencing might pertain to the transforming activity of Myc, since in several systems thrombospondin-1 exhibits tumor suppressor properties, presumably due to its negative effect on neovascularization.
Single-Disk and Double-Disk Viscous Micropump (2004)

The development and testing of two novel micropumps called the single-disk and double-disk viscous pumps are described. A single disk and the top pump housing, or two disks are separated by a small gap that forms a fluid passage. A wiper, that is the height of this gap, is placed between the two disks, or between the single disk and top pump housing, and extends from the outer diameter of the disk(s) to the center region of the disk(s). The movement of the disk(s) induces viscous stresses on the fluid that forces the fluid through the pump area above the single disk, or between the two disks. The wiper acts to “wipe” the fluid from the disk(s) toward the outlet channel. The fluid flow through the double-disk pump is visualized using a red Rhodamine dye that is injected into the fluid passage upstream of the pumping area. Experimental flow rate for the single-disk and double-disk pumps are obtained for a disk diameter of 2.381 mm, and a gap height of 103 μm. The maximum flow rates obtained are 0.74 ml/min and 2.1 ml/min for the single-disk and double-disk pumps, respectively, for a rotational speed of 5000 rpm. Advantages of the disk pumps include simplicity of design, planar structure, continuous flow, well controlled flow rate, and mixing characteristics.
Role of competition for inorganic nutrients in the biodegradation of mixtures of substrates (1995)

A study was conducted to determine whether competition for inorganic nutrients affects the biodegradation of mixtures of substrates. Little benzylamine was mineralized by Pseudomonas putida in solutions with no added P, but the substrate was degraded if the medium contained 100 nM P. The enhancement by P addition did not occur if the medium also contained caprolactam and a caprolactam-utilizing strain of Pseudomonas aeruginosa. The suppression by the second bacterium was overcome by a higher P concentration. The rate of caprolactam utilization by P. aeruginosa was reduced if benzylamine and P. putida were also present in media with 100 nM P, but the suppression was absent if the solution contained a higher P concentration. Glutamate increased and inorganic N plus P decreased the length of the acclimation phase prior to benzylamine mineralization in lake water. We suggest that the effect of one biodegradable substrate on the metabolism of a second often results from a competition for inorganic nutrients.
DNA Binding Compounds. VI. Synthesis and Characterization of 2,5'-Disubstituted Bibenzimidazoles Related to the DNA Minor Groove Binder Hoechst-33258 (1994)

A series of compounds have been synthesized in which the basic 2-phenylbibenzimidazole structure of Hoechst 33258 has been modified to include various combinations of bromo, iodo, methoxy, amino, alkylamino and nitro groups in the terminal phenyl ring. Both sequential and convergent synthetic routes have been followed using coupling reactions of both imino ethers and aldehydes to 1,2-diamines. All these compounds were characterized by a combination of f.a.b . Mass spectrometry and 1H and 13C n.m.r. spectroscopy including inverse detection of long-range heteronuclear CH correlations (HMBC).
Purification and characterization of the human adenosine A2a receptor functionally expressed in Escherichia coli (2002)

The adenosine A(2a) receptor belongs to the seven transmembrane helix G-protein-coupled receptor family, is abundant in striatum, vasculature and platelets and is involved in several physiological processes such as blood pressure regulation and protection of cells during anoxia. For structural and biophysical studies we have expressed the human adenosine A(2a) receptor (hA2aR) at high levels inserted into the Escherichia coli inner membrane, and established a purification scheme. Expression was in fusion with the periplasmic maltose-binding protein to levels of 10-20 nmol of receptor per L of culture, as detected with the specific antagonist ligand [(3)H]ZM241385. As the receptor C-terminus was proteolyzed upon solubilization, a protease-resistant but still functional receptor was created by truncation to Ala316. Addition of the sterol, cholesteryl hemisuccinate, allowed a stable preparation of functional hA2aR solubilized in dodecylmaltoside to be obtained, and, increased the stability of the receptor solubilized in other alkylmaltosides. Purification to homogeneity was achieved in three steps, including ligand affinity chromatography based on the antagonist xanthine amine congener. The purified hA2aR fusion protein bound [(3)H]ZM241385 with a K(d) of 0.19 nm and an average B(max) of 13.7 nmol x mg(-1) that suggests 100% functionality. Agonist affinities for the purified solubilized receptor were higher than those for the membrane-bound form. Sufficient pure, functional hA2aR can now be prepared regularly for structural studies.
A novel human UDP‐N‐acetyl‐D‐galactosamine:polypeptide N‐acetylgalactosaminyltransferase, GalNAc‐T7, with specificity for partial GalNAc‐glycosylated acceptor substrates (1999)

A novel member of the human UDP-N-acetyl-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase gene family, designated GalNAc-T7, was cloned and expressed. GalNAc-T7 exhibited different properties compared to other characterized members of this gene family, in showing apparent exclusive specificity for partially GalNAc-glycosylated acceptor substrates. GalNAc-T7 showed no activity with a large panel of non-glycosylated peptides, but was selectively activated by partial GalNAc glycosylation of peptide substrates derived from the tandem repeats of human MUC2 and rat submaxillary gland mucin. The function of GalNAc-T7 is suggested to be as a follow-up enzyme in the initiation step of O-glycosylation.
Selective Acylation of 4,6-O-Benzylidene Glycopyranosides by Enzymatic Catalysis (1993)

Abstract Selective acylation of different hydroxyls is of great importance, and widespread applications are found in carbohydrate chemistry.1 Ass protecting groups, esters offer the advantage of being easily prepared and easily removed, and accordingly, partially acylated monosaccharides have been used for the preparation of other O-substituted derivatives as well as for the synthesis of oligosaccharides. For this latter purpose 4,6-O-benzylidene-D-glycopyranosides like la, once selectively modified at one of their two free hydroxy groups, are particularly suitable compounds.
Stroboscopic ultrahigh-resolution full-field optical coherence tomography (2005)

We present a new technique that produces en face tomographic images with a 10-micros acquisition time per image. The setup consists of an interference microscope with stroboscopic illumination provided by a xenon arc flash lamp (10-micros flashes at 15 Hz). The tomographic images are obtained from two phase-opposed interferometric images recorded simultaneously by two synchronized CCD cameras. Transverse resolution better than 1.0 microm is achieved by use of high-numerical-aperture microscope objectives. The short coherence length of the source yields an axial resolution of 0.9 microm. 3 x 3 pixel binning leads to a detection sensitivity of 71 dB. Our system is suitable for various applications, particularly in biology for in vivo cellular-level imaging.