gebhart/patrepeval huggingface dataset:
Structure searching in chemical databases by direct lookup methods (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStructure searching in chemical databases by direct lookup methodsBradley D. Christie, Burton A. Leland, and James G. NourseCite this: J. Chem. Inf. Comput. Sci. 1993, 33, 4, 545–547Publication Date (Print):July 1, 1993Publication History Published online1 May 2002Published inissue 1 July 1993https://doi.org/10.1021/ci00014a004RIGHTS & PERMISSIONSArticle Views208Altmetric-Citations26LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (281 KB) Get e-Alerts
A Network Analyzer Incorporating Two Six-Port Reflectometers (1977)

This paper outlines the theory and design of a microwave network analyzer capable of measuring the network parameters of any linear reciprocal or nonreciprocal, active or passive two port. An RF signal from one source is applied at the same time to two six-port reflectometers which measure the incident and reflected waves at the ports of the two port being measured. An experimental dual six-port network analyzer for the 2-18-GHZ range has been completed and is described briefly. Some advantages of the proposed design over existing network analyzer designs are 1) only one source is needed, 2) no phase detectors are required, 3) no flexible cables or arms are used between the reflectometers and the two port being measured, and 4) self-calibration techniques are readily applied.
Five‐Membered Heterocyclic Thiones. Part VII . 1,2,3‐ThiadiazoIe‐5‐thiolates (1978)

Abstract The synthesis of the stable potassium salts of the first known 1,2,3‐thiadiazole‐5‐thiols is described.
A Nuclease from Mung Bean Sprouts (1962)

Minnesoia, who generously supplied us with mung bean sprouts.Thev were shinned frozen and kept at -29'.No loss of activity *could be detected after 6 months-of storage. 2 The abbreviation used is: Poly AU, polymers of adenylic and uridylic acid.The abbreviations of the derivatives of nucleic acids are those used by The Journal of Biological Chemistry.HOWever, when fragments of unknown composition are dealt with, nucleosides are represented by capital letters, X, Y, and Z.
Session 16 (2008)

Abstract Chapter 18 outlines the sixteenth and final session of the group therapy program, encouraging further discussion about problems that participants have faced during the program, and suggestions for making healthy food choices and staying physically active. Participants' feelings about the group termination are addressed.
Ovine ill-thrift in Nova Scotia. 9. Production of experimental quantities of isocyanide metabolites of <i>Trichoderma hamatum</i> (1982)

Laboratory cultures of Trichoderma hamatum produce metabolites that are characterized by an isocyanide functionality. Three such metabolites predominate. One is the known compound trichoviridin (I). The other two, described here for the first time, are 3-(3-isocyano-6-oxabicyclo[3,1,0]hex-2-en-5-yl)acrylic acid (II) and a very unstable compound 3-(3-isocyanocyclopent-2-enylidene-)propionic acid (III). Production of these three metabolites by a random sample of wild isolates of the fungus has been examined. At least one of these isocyanides was isolated from all cultures in which the culture broth inhibited the growth of Micrococcus luteus. The relative amounts of the three isocyanides produced by individual isolates were not the same and cultures were found in which I, II, or III was the main product. The isocyanide III was produced by all wild isolates which had antibiotic activity in their culture broth, and it was present in the concentration range 2-40 mg X L-1.
Effect of ppGpp on <i>Escherichia coli</i> Cyclopropane Fatty Acid Synthesis Is Mediated through the RpoS Sigma Factor (ς <sup>S</sup> ) (1999)

Strains of Escherichia coli carrying mutations at the relA locus are deficient in cyclopropane fatty acid (CFA) synthesis, a phospholipid modification that occurs as cultures enter stationary phase. RelA protein catalyzes the synthesis of guanosine-3',5'-bisdiphosphate (ppGpp); therefore, ppGpp was a putative direct regulator of CFA synthesis. The nucleotide could act by increasing either the activity or the amount of CFA synthase, the enzyme catalyzing the lipid modification. We report that the effect of RelA on CFA synthesis is indirect. In vitro and in vivo experiments show no direct interaction between ppGpp and CFA synthase activity. The relA effect is due to ppGpp-engendered stimulation of the synthesis of the alternative sigma factor, RpoS, which is required for function of one of the two promoters responsible for expression of CFA synthase.
Role of Side-Chain Molecular Features in Tuning Lower Critical Solution Temperatures (LCSTs) of Oligoethylene Glycol Modified Polypeptides (2016)

A series of thermoresponsive polypeptides has been synthesized using a methodology that allowed facile adjustment of side-chain functional groups. The lower critical solution temperature (LCST) properties of these polymers in water were then evaluated relative to systematic molecular modifications in their side-chains. It was found that in addition to the number of ethylene glycol repeats in the side-chains, terminal and linker groups also have substantial and predictable effects on cloud point temperatures (Tcp). In particular, we found that the structure of these polypeptides allowed for inclusion of polar hydroxyl groups, which significantly increased their hydrophilicity and decreased the need to use long oligoethylene glycol repeats to obtain LCSTs. The thioether linkages in these polypeptides were found to provide an additional structural feature for reversible switching of both polypeptide conformation and thermoresponsive properties.
Human papillomavirus-related head and neck tumors: clinical and research implication (2009)

The increasing incidence of HPV-related HNSCC has led to the development of novel research strategies in HNSCC. This review summarizes the epidemiology, clinical presentation, molecular pathogenesis, diagnosis, and therapy of HPV-associated HNSCC; it also summarizes how a better understanding of the molecular pathogenesis of HPV-associated HNSCC is expected to change treatment.
Compacting DNA During the Interphase: Condensin Maintains rDNA Integrity (2007)

During mitosis, condensin is responsible for folding chromatin fibers into highly compact chromosomes, ensuring the faithful segregation of replicated chromosomes into daughter cells after each cell division. Our laboratory has unexpectedly found that condensin is capable of condensing DNA during the interphase: upon nutrient starvation, condensin is loaded to the rDNA array, leading to DNA condensation in this region. This subchromosomal DNA condensation appears to protect the integrity of the rDNA array. These observations provide the first microscopic evidence of DNA compaction by condensin outside mitosis. In addition, they show that condensin is also highly regulated outside mitosis.
Ammonia Inhibition in High-Solids Biogasification: An Overview and Practical Solutions (1999)

A comprehensive literature search was conducted to evaluate ammonia inhibition in biogasification. An overview of ammonia inhibition including the fundamentals of biochemical pathways of nitrogenous compounds, ammonia inhibition mechanisms and impact of free ammonia inhibition was conducted. Past studies and the experience gained with the pilot project at the University of California, Davis (UC Davis) were reviewed and discussed. Long-term experimental studies at the pilot scale revealed that ammonia inhibition in a high-solids thermophilic anaerobic digestion occurs at ammonia concentration of 1200 mg l−1. Two methods: (1) dilution of digester content with fresh water and (2) adjustment of feedstock C/N ratio were evaluated to mitigate ammonia inhibition. Both methods were found to be practical and effective.
Flocculating Agents (2000)

Abstract Flocculating agents are chemical additives that cause suspended solids to form aggregates called flocs. These agents are used in water treatment, municipal and industrial waste treatment, mineral processing, and papermaking. Flocculating agents are either inorganic salts or water‐soluble organic polymers. They act by shrinking the ionic double layer, or neutralizing the surface charge of suspended particles, or bridging between particles. The type of flocculant used depends on the type of solid‐liquid separation being performed. The physical properties and size of the flocs as well as the rate of floc formation are the critical parameters in this process. Flocculants are usually selected by the results of laboratory‐scale experiments. The manner in which the flocculating agent is mixed with the substrate can affect the results. Special analytical methods are used for some flocculating agents. Some agents or impurities in them may present toxicological or environmental problems. The general economic trend is the replacement of inorganic salts with organic polymers, which give improved performance.
Scalable compression for image browsing (1994)

We present scalable compression algorithms for image browsing. Recently, the International Standards Organization (ISO) has proposed the JPEG standard for still image compression. JPEG standard not only provides the basic feature of compression (baseline algorithm) but also provides the framework for reconstructing images in different picture qualities and sizes. These features are referred to as SNR and spatial scalability, respectively. SNR scalability and spatial scalability can be implemented using the progressive and hierarchical modes in the JPEG standard. In this paper, we implement and investigate the performance of the progressive and hierarchical coding modes of the JPEG standard and compare their performance with the baseline algorithm.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Inhibition of CK2 activity by TGF-β1 promotes IκB-α protein stabilization and apoptosis of immortalized hepatocytes (2003)

Nuclear factor κB (NF-κB) is an antiapoptotic factor involved in development, regeneration, and neoplastic progression of the liver. Previously, we have shown that stabilization of inhibitor κB (IκB)-α protein following treatment of hepatocytes with transforming growth factor (TGF)-β1 promoted NF-κB repression, which then permitted induction of AP-1/SMAD-mediated liver cell death. Because basal IκB-α protein turnover is regulated by protein kinase CK2, here we have elucidated the regulation of CK2 kinase activity and its role in control of NF-κB levels following treatment with TGF-β1. We show that both messenger RNA (mRNA) and protein levels of the CK2α catalytic subunit are down-regulated following TGF-β1 stimulation in murine hepatocyte cells. The ensuing inhibition of CK2 kinase activity promotes stabilization of IκB protein, which is followed by the shutoff of constitutive NF-κB activity and induction of apoptosis. Ectopic expression of CK2α inhibits TGF-β1-induced apoptosis through sustained activation of NF-κB. Conversely, expression of a kinase-dead mutant of CK2α potentiates TGF-β1 cell killing. Importantly, we show that hepatocellular carcinomas (HCCs) derived from TGF-β1 transgenic mice and human HCC cell lines display enhanced CK2 IκB kinase activity that contributes in part to an elevated NF-κB activity in vivo. In conclusion, inhibition of CK2 expression levels by TGF-β1 is crucial for the induction of apoptosis of hepatocytes. Circumvention of this process by up-regulation of CK2 activity in transformed cells may contribute to the promotion of TGF-β1-induced liver carcinogenesis. (Hepatology 2003;38:1540-1551.)
Routing performance in the presence of unidirectional links in multihop wireless networks (2002)

We examine two aspects concerning the influence of unidirectional links on routing performance in multihop wireless networks. In the first part of the paper we evaluate the benefit from utilizing unidirectional links for routing as opposed to using only bidirectional links. Our evaluations are based on three transmit power assignment models that reflect some realistic network scenarios with unidirectional links. Our results indicate that the marginal benefit of using a high-overhead routing protocol to utilize unidirectional links is questionable.Most common routing protocols however simply assume that all network links are bidirectional and thus may need additional protocol actions to remove unidirectional links from route computations. In the second part of the paper we investigate this issue using a well known on-demand routing protocol Ad hoc On-demand Distance Vector (AODV) as a case study. We study the performance of three techniques for AODV for efficient operation in presence of unidirectional links viz. BlackListing Hello and ReversePathSearch. While BlackListing and Hello techniques explicitly eliminate unidirectional links the ReversePathSearch technique exploits the greater network connectivity offered by the existence of multiple paths between nodes. Performance results using ns-2 simulations under varying number of unidirectional links and node speeds show that all three techniques improve performance by avoiding unidirectional links the ReversePathSearch technique being the most effective.
Real Time Animation of Realistic Fog (2002)

Fog introduces a high level of realism to computer graphics. But fog is often simulated by uniform density when real fog is always much more complex. Its variable density creates beautiful shapes of mist what can add a realistic ambience to virtual scene. We present here a new algorithm to render such complex medium in real-time and propose a mean to design non homogeneous fog using chosen functions. Then we take advantage of fog properties and of graphic hardware to achieve fast rendering. We also present a method to integrate wind effects and fog animation without expensive cost in time.
Systemic Sclerosis is a Complex Disease Associated Mainly with Immune Regulatory and Inflammatory Genes (2014)

Systemic sclerosis (SSc) is a fibrotic and autoimmune disease characterized clinically by skin and internal organ fibrosis and vascular damage, and serologically by the presence of circulating autoantibodies. Although etiopathogenesis is not yet well understood, the results of numerous genetic association studies support genetic contributions as an important factor to SSc. In this paper, the major genes of SSc are reviewed. The most recent genome-wide association studies (GWAS) are taken into account along with robust candidate gene studies. The literature search was performed on genetic association studies of SSc in PubMed between January 2000 and March 2014 while eligible studies generally had over 600 total participants with replication. A few genetic association studies with related functional changes in SSc patients were also included. A total of forty seven genes or specific genetic regions were reported to be associated with SSc, although some are controversial. These genes include HLA genes, STAT4, CD247, TBX21, PTPN22, TNFSF4, IL23R, IL2RA, IL-21, SCHIP1/IL12A, CD226, BANK1, C8orf13-BLK, PLD4, TLR-2, NLRP1, ATG5, IRF5, IRF8, TNFAIP3, IRAK1, NFKB1, TNIP1, FAS, MIF, HGF, OPN, IL-6, CXCL8, CCR6, CTGF, ITGAM, CAV1, MECP2, SOX5, JAZF1, DNASEIL3, XRCC1, XRCC4, PXK, CSK, GRB10, NOTCH4, RHOB, KIAA0319, PSD3 and PSOR1C1. These genes encode proteins mainly involved in immune regulation and inflammation, and some of them function in transcription, kinase activity, DNA cleavage and repair. The discovery of various SSc-associated genes is important in understanding the genetics of SSc and potential pathogenesis that contribute to the development of this disease.
Evolution of Kerogen and Bitumen during Thermal Maturation via Semi-Open Pyrolysis Investigated by Infrared Spectroscopy (2015)

A series of artificial maturation (anhydrous, semi-open pyrolysis) experiments on Green River oil shale have been performed to simulate the thermal maturation of type I kerogen. The goals of this program were to develop a kinetic model of petroleum generation from oil shale and to characterize the yield and composition of petroleum as a function of artificial thermal maturity. The thermal maturity level (EASY%Ro = 0.48–1.28%) is based upon the kinetic model of kerogen degradation and is equivalent to vitrinite reflectance maturity. Here, we compare the structural characteristics of kerogen and bitumen during artificial maturation of oil shale using quantitative Fourier transform infrared (IR) spectroscopy. Quantitative comparison was enabled by a novel method for the preparation of bitumen for IR spectroscopy. Bitumen can be a reaction intermediate during maturation of kerogen, and the IR data indicate that bitumen has a structure intermediate between that of kerogen and generated petroleum. Moreover, the IR data reveal that the composition of bitumen changes with maturity, with trends that are similar in some aspects to those observed previously in kerogen, but different in others. Kerogen is characterized by the early depletion of oxygenated functional groups prior to petroleum generation (EASY%Ro < 0.9%) and then a late enrichment of oxygen at higher artificial maturity (EASY%Ro > 1.2%). In contrast, bitumen shows initial enrichment of oxygenated functional groups at low artificial maturity (EASY%Ro < 0.8%) and subsequent depletion at higher maturity. Kerogen evolution follows the previously observed trend with aliphatic carbon chains that became shorter and/or more branched as kerogen is consumed during all stages of artificial maturation. Bitumen, in contrast, appears to have aliphatic carbon chains that lengthen within the same artificial maturity range as bitumen is predominantly generated from kerogen. The aliphatic carbon content of bitumen is greater than that of kerogen at all levels of artificial maturity. Both kerogen and bitumen become more aromatic in character with increasing thermal maturity, especially above artificial levels EASY%Ro > 0.9%. This similarity likely results from loss of aliphatic chains from both organic fractions during petroleum generation, suggesting that both kerogen and bitumen can be direct sources for petroleum. The loss of aliphatic carbons from aromatic centers in both kerogen and bitumen leads to protonation of the residual aromatic rings. The IR spectra of kerogen and bitumen indicate very similar degrees of protonation of those aromatic rings.
Random Amplified Polymorphic DNA Analysis of Dry Turfgrass Seed (1996)

Random amplified polymorphic DNA (RAPD) markers from leaf tissue extractions are effective for discrimination of turfgrass varieties. The usefulness of RAPD markers for turfgrass variety identification can be enhanced by use of seed rather than leaf tissue for DNA extraction. To determine whether DNA extracted from turfgrass seed was suitable for amplification, DNA was extracted from bulk samples and individual seeds of bermudagrass [ Cynodon dactylon (L.) Pers.], chewings fescue ( Festuca rubra var. commutata Gaud.), Poa annua L., Poa supina Schrad., creeping bentgrass [ Agrostis stolonifera L. var. palustrus (Huds.) Farw.], Kentucky bluegrass ( Poa pratensis L.), perennial ryegrass ( Lolium perenne L.), and tall fescue ( Festuca arundinacea Schreb.). All samples were successfully amplified using an arbitrary primer. Amplification intensity varied among species. With an almost infinite number of arbitrary primers available, it is likely that suitable primers can be found to amplify DNA from most turfgrass species. Amplification of turfgrass seed DNA, whether bulk or individual seed, is possible and should prove more useful than amplification of leaf tissue DNA for discrimination of turfgrass varieties.
HIGH EXPRESSION OF CHEMOKINE GENE AS A FAVORABLE PROGNOSTIC FACTOR IN RENAL CELL CARCINOMA (2004)

These results suggest that IP-10, MIG and MIP-1beta are expressed at high levels in tumors that rarely recur after surgery. The antitumorigenic effect of IP-10, MIG and MIP-1beta may result from the recruitment of lymphocyte infiltration and/or inhibition of angiogenesis in RCC. The amplification of chemokine expression by immunotherapy or gene therapy may be a practical and effective strategy to promote tumor regression.
ASIC package design optimization for 10 Gbps and above backplane serdes links (2012)

This paper discussed the package selection and BGA signal pin assignment consideration for high-end ASIC design with over 400 SerDes (Serializer Deserializer) pairs for >;10Gbps backplane interface. The ASIC package is using advanced high-performance organic build-up (BU) materials like GX13, GZ41 and thinner core in the stack-up to help reduce the package loss and improve the signal transmission on the highspeed SerDes links. For return loss and insertion loss studies, the main objectives are to investigate the core thickness, BU material properties, and routing configurations impact on the differential signalling. The design suggestions are then made at each area for performance and cost optimization. For crosstalk studies, various pin-out patterns for transmit to transmit or receive to receive signals, and transmit to receive signals, have been designed and studied to investigate signal coupling and PCB escape routing requirements. Both frequency and time domain simulations are performed to compare the signal isolation performance. The most optimized pin-out is then selected to achieve the overall required system performance. Lastly, various package substrate samples with different BU materials, core thicknesses and crosstalk structures are manufactured to validate package design performance using probe station technique.
PINK1-mediated phosphorylation of the Parkin ubiquitin-like domain primes mitochondrial translocation of Parkin and regulates mitophagy (2012)

Parkinson's disease genes PINK1 and parkin encode kinase and ubiquitin ligase, respectively. The gene products PINK1 and Parkin are implicated in mitochondrial autophagy, or mitophagy. Upon the loss of mitochondrial membrane potential (ΔΨm), cytosolic Parkin is recruited to the mitochondria by PINK1 through an uncharacterised mechanism - an initial step triggering sequential events in mitophagy. This study reports that Ser65 in the ubiquitin-like domain (Ubl) of Parkin is phosphorylated in a PINK1-dependent manner upon depolarisation of ΔΨm. The introduction of mutations at Ser65 suggests that phosphorylation of Ser65 is required not only for the efficient translocation of Parkin, but also for the degradation of mitochondrial proteins in mitophagy. Phosphorylation analysis of Parkin pathogenic mutants also suggests Ser65 phosphorylation is not sufficient for Parkin translocation. Our study partly uncovers the molecular mechanism underlying the PINK1-dependent mitochondrial translocation and activation of Parkin as an initial step of mitophagy.
China's policy and the Nixon visit (1972)

(1972). China's policy and the Nixon visit. Journal of Contemporary Asia: Vol. 2, No. 1, pp. 3-16.