gebhart/patrepeval huggingface dataset:
A novel repression module, an extensive activation domain, and a bipartite nuclear localization signal defined in the immediate-early transcription factor Egr-1. (1993)

Egr-1 is an immediate-early response gene induced transiently and ubiquitously by mitogenic stimuli and also regulated in response to signals that initiate differentiation. The Egr-1 gene product, a nuclear phosphoprotein with three zinc fingers of the Cys2His2 class, binds to the sequence CGCCCCCGC and transactivates a synthetic promoter construct 10-fold in transient-transfection assays. We have analyzed the structure and function of the Egr-1 protein in detail, delineating independent and modular activation, repression, DNA-binding, and nuclear localization activities. Deletion analysis, as well as fusions to the DNA-binding domain of GAL4, indicated that the activation potential of Egr-1 is distributed over an extensive serine/threonine-rich N-terminal domain. In addition, a novel negative regulatory function has been precisely mapped 5' of the zinc fingers: amino acids 281 to 314 are sufficient to confer the ability to repress transcription on a heterologous DNA-binding domain. Specific DNA-binding activity was shown to reside in the three zinc fingers of Egr-1, as predicted by homology to other known DNA-binding proteins. Finally, nuclear localization of Egr-1 is specified by signals in the DNA-binding domain and basic flanking sequences, as determined by subcellular fractionation and indirect immunofluorescence. Basic residues 315 to 330 confer partial nuclear localization on the bacterial protein beta-galactosidase. A bipartite signal consisting of this basic region in conjunction with either the second or third zinc finger, but not the first, suffices to target beta-galactosidase exclusively to the nucleus. Our work shows that Egr-1 is a functionally complex protein and suggests that it may play different roles in the diverse settings in which it is induced.
Integrins alpha v beta 3 and alpha v beta 5 contribute to cell attachment to vitronectin but differentially distribute on the cell surface. (1991)

We investigated the role of the integrins alpha v beta 3 and alpha v beta 5 in mediating vitronectin adhesion of three phenotypically distinct cell types. M21 human melanoma cells and H2981 lung carcinoma cells use both alpha v-containing integrins in adhering to vitronectin while UCLA-P3 lung carcinoma cells adhere exclusively with alpha v beta 5. Specifically, monoclonal antibodies directed to functional epitopes on both receptors were required to block adhesion of M21 or H2981 cells while adhesion of UCLA-P3 cells to vitronectin could be blocked with a monoclonal antibody to alpha v beta 5. Although both receptors are involved in M21 and H2981 cell adhesion to vitronectin, only alpha v beta 3 can be detected in focal contacts, colocalizing with vinculin, talin, and the ends of actin filaments, while alpha v beta 5 shows a distinct, nonfocal contact, distribution on the cell surface. These results provide the first evidence that two homologous integrins that recognize the same ligand distribute differentially on the cell surface.
Coordinate changes in heat shock element-binding activity and HSP70 gene transcription rates in human cells. (1988)

Activation of human heat shock gene transcription by heat shock, heavy metal ions, and amino acid analogs required the heat shock element (HSE) in the HSP70 promoter. Both heat shock- and metal ion-induced HSP70 gene transcription occurred independently of protein synthesis, whereas induction by amino acid analogs required protein synthesis. We identified a HSE-binding activity from control cells which was easily distinguished by a gel mobility shift assay from the stress-induced HSE-binding activity which appeared following heat shock or chemically induced stress. The kinetics of HSP70 gene transcription paralleled the rapid appearance of stress-induced HSE-binding activity. During recovery from heat shock, both the rate of HSP70 gene transcription and stress-induced HSE-binding activity levels declined and the control HSE-binding activity reappeared. The DNA contacts of the control and stress-induced HSE-binding activities deduced by methylation interference were similar but not identical. While stable complexes with HSE were formed with extracts from both control and stressed cells in vitro at 25 degrees C, only the stress-induced complex was detected when binding reactions were performed at elevated temperatures.
THE 3-ACETYLPYRIDINE ANALOG OF DPN1 (1954)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTHE 3-ACETYLPYRIDINE ANALOG OF DPN1Nathan O. Kaplan and Margaret M. CiottiCite this: J. Am. Chem. Soc. 1954, 76, 6, 1713–1714Publication Date (Print):March 1, 1954Publication History Published online1 May 2002Published inissue 1 March 1954https://pubs.acs.org/doi/10.1021/ja01635a089https://doi.org/10.1021/ja01635a089research-articleACS PublicationsRequest reuse permissionsArticle Views107Altmetric-Citations67LEARN 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
A low latency router supporting adaptivity for on-chip interconnects (2005)

The increased deployment of System-on-Chip designs has drawn attention to the limitations of on-chip interconnects. As a potential solution to these limitations, Networks-on -Chip (NoC) have been proposed. The NoC routing algorithm significantly influences the performance and energy consumption of the chip. We propose a router architecture which utilizes adaptive routing while maintaining low latency. The two-stage pipelined architecture uses look ahead routing, speculative allocation, and optimal output path selection concurrently. The routing algorithm benefits fromcongestionaware flow control, making better routing decisions. We simulate and evaluate the proposed architecture in terms of network latency and energy consumption. Our results indicate that the architecture is effective in balancing the performance and energy of NoC designs.
Evidence for a Holin-Like Protein Gene Fully Embedded Out of Frame in the Endolysin Gene of Staphylococcus aureus Bacteriophage 187 (1999)

We have cloned, sequenced, and characterized the genes encoding the lytic system of the unique Staphylococcus aureus phage 187. The endolysin gene ply187 encodes a large cell wall-lytic enzyme (71.6 kDa). The catalytic site, responsible for the hydrolysis of staphylococcal peptidoglycan, was mapped to the N-terminal domain of the protein by the expression of defined ply187 domains. This enzymatically active N terminus showed convincing amino acid sequence homology to an N-acetylmuramoyl-L-alanine amidase, whereas the C-terminal part, whose function is unknown, revealed striking relatedness to major staphylococcal autolysins. An additional reading frame was identified entirely embedded out of frame (+1) within the 5' region of ply187 and was shown to encode a small, hydrophobic protein of holin-like function. The hol187 gene features a dual-start motif, possibly enabling the synthesis of two products of different lengths (57 and 55 amino acids, respectively). Overproduction of Hol187 in Escherichia coli resulted in growth retardation, leakiness of the cytoplasmic membrane, and loss of de novo ATP synthesis. Compared to other holins identified to date, Hol187 completely lacks the highly charged C terminus. The secondary structure of the polypeptide is predicted to consist of two small, antiparallel, hydrophobic, transmembrane helices. These are supposed to be essential for integration into the membrane, since site-specific introduction of negatively charged amino acids into the first transmembrane domain (V7D G8D) completely abolished the function of the Hol187 polypeptide. With antibodies raised against a synthetic 18-mer peptide representing a central part of the protein, it was possible to detect Hol187 in the cytoplasmic membrane of phage-infected S. aureus cells. An important indication that the protein actually functions as a holin in vivo was that the gene (but not the V7D G8D mutation) was able to complement a phage lambda Sam mutation in a nonsuppressing E. coli HB101 background. Plaque formation by lambdagt11::hol187 indicated that both phage genes have analogous functions. The data presented here indicate that a putative holin is encoded on a different reading frame within the enzymatically active domain of ply187 and that the holin is synthesized during the late stage of phage infection and found in the cytoplasmic membrane, where it causes membrane lesions which are thought to enable access of Ply187 to the peptidoglycan of phage-infected Staphylococcus cells.
"Aircraft Ice Detection Method" (2007)

A method of ice detection is discussed which utilizes a combination of impedance, thermal conductivity and temperature measurements to detect the presence of glaze ice and to determine its thickness. Two supplemental means are described by which in-flight impedance data may be checked to assure that it is free of significant error. I Introduction To be alerted in real time that ice is forming on an aircraft or UAV and to be provided with the ice thickness variation with time remains a problem of interest, Ref. 1 and Ref. 2. Ice principally deposits from supercooled water droplets in the atmosphere that freeze on the vehicle at atmospheric/aircraft surface temperatures in the range from 0C to -25C and at altitudes between sea level and 22,000 ft, Ref. 3 and Ref. 4, though on occasion ice occurs outside these ranges. Two forms of ice may be encountered: glaze or rime, Ref. 3. Glaze ice is clear in appearance and weighs 0.98-0.99 g/cubic cm, while rime is white and opaque in appearance and weighs between 0.35-0.55 g/cubic cm depending on aircraft Mach number. Prior methods proposed for ice detection have included, but have not been limited to, visual identification, ice effects on vibrating structures, light reflection using fiber optics, Ref. 5, capacitive measurements, Ref. 6, and time domain reflectometry, Ref. 7. This paper discusses a method of ice detection which utilizes a combination of impedance, thermal conductivity and temperature measurements to detect the presence of ice and to provide its thickness. The method also includes supplementary ways for confirming the type of ice that is collecting and the fact that a correct measurement is being made. There are a number of general considerations that confront any aircraft ice detection approach. Not only must it operate properly during icing conditions, but it must demonstrate certain measurement values and characteristics that are unique to icing and not replicated when flying in fog or rain to avoid confusion. In addition, its use should not interfere significantly with airflow or add significant drag. Any electrical method, of which the impedance measurement approach discussed here is one, may be challenged by the dramatic variation with temperature of the electrical properties of pure glaze ice as well as rime ice in the temperature range of interest (taken here to be 0C to -40C), Ref. 8. Electrical measurements may be affected by cracks, flaws and/or voids in the ice formed over the sensor being used to make the measurement, Ref. 9 ; a situation associated more with rime ice though it may also occur with glaze ice. Acid rain present in the atmosphere and other contaminents may also have some effect on ice electrical properties of the ice that is formed. Finally, it is important
Nuclear transformation of Volvox carteri. (1994)

Stable nuclear transformation of Volvox carteri was achieved using the cloned V. carteri nitA+ gene (which encodes nitrate reductase) to complement a nitA- mutation. Following bombardment of mutant cells with plasmid-coated gold particles, putative transformants able to utilize nitrate as a nitrogen source were recovered with an efficiency of approximately 2.5 x 10(5). DNA analysis indicated that the plasmid integrated into the genome, often in multiple copies, at sites other than the nitA locus. Cotransformants were recovered with a frequency of 40-80% when cells were cobombarded with a selected and an unselected marker. Thus, V. carteri becomes one of the simplest multicellular organisms that is accessible to detailed molecular studies of genes regulating cellular differentiation and morphogenesis.
Cancer risk in humans predicted by increased levels of chromosomal aberrations in lymphocytes: Nordic study group on the health risk of chromosome damage. (1994)

Cytogenetic assays in peripheral blood lymphocytes (PBL) have been used extensively to survey the exposure of humans to genotoxic agents. The conceptual basis for this has been the hypothesis that the extent of genetic damage in PBL reflects critical events for carcinogenic processes in target tissues. Until now, no follow-up studies have been performed to assess the predictive value of these methods for subsequent cancer risk. In an ongoing Nordic cohort study of cancer incidence, 3182 subjects were examined between 1970 and 1988 for chromosomal aberrations (CA), sister chromatid exchange or micronuclei in PBL. In order to standardize for the interlaboratory variation, the results were trichotomized for each laboratory into three strata: low (1-33 percentile), medium (34-66 percentile), or high (67-100 percentile). In this second follow-up, a total of 85 cancers were diagnosed during the observation period (1970-1991). There was no significant trend in the standardized incidence ratio with the frequencies of sister chromatid exchange or micronuclei, but the data for these parameters are still too limited to allow firm conclusions. There was a statistically significant linear trend (P = 0.0009) in CA strata with regard to subsequent cancer risk. The point estimates of the standardized incidence ratio in the three CA strata were 0.9, 0.7, and 2.1, respectively. Thus, an increased level of chromosome breakage appears to be a relevant biomarker of future cancer risk.
Mechanisms involved in the inhibition of growth of a human B lymphoma cell line, B104, by anti‐MHC class II antibodies (1994)

The mechanisms involved in the inhibition of growth of a human B lymphoma cell line, B104, by anti-MHC class II antibodies (Ab) were compared with those in anti-IgM Ab-induced B104 growth inhibition. Two anti-MHC class II Ab, L227 and 2.06, inhibited the growth of B104 cells, although 2.06, but not L227, needed to be further cross-linked with a goat anti-mouse IgG Ab (GAM) to show the effect. L227 induced an increase in intracellular free Ca2+ concentration ([Ca2+]i) from the intracellular pool and little or no protein tyrosine phosphorylation, phosphatidyl inositol turnover, or expression of Egr-1 mRNA, whereas 2.06 plus GAM induced an increase in [Ca2+]i from both the intracellular and, in particular, the extracellular pools. The inhibition of B104 cell growth induced by anti-MHC class II Ab was Ca(2+)-independent and not inhibited by actinomycin D or cyclosporin A, and cell cycle arrest at the G2/M interphase was not observed. These features are very different from those observed in B104 cell death induced by anti-IgM Ab. Neither DNA fragmentation nor the morphology of apoptosis was observed. These findings demonstrate that cross-linking of MHC class II molecules transduced the negative signals through intracellular mechanisms different from those present in the cross-linking of surface IgM.
Parametric shape analysis via 3-valued logic (2002)

Shape analysis concerns the problem of determining "shape invariants" for programs that perform destructive updating on dynamically allocated storage. This article presents a parametric framework for shape analysis that can be instantiated in different ways to create different shape-analysis algorithms that provide varying degrees of efficiency and precision. A key innovation of the work is that the stores that can possibly arise during execution are represented (conservatively) using 3-valued logical structures. The framework is instantiated in different ways by varying the predicates used in the 3-valued logic. The class of programs to which a given instantiation of the framework can be applied is not limited a priori (i.e., as in some work on shape analysis, to programs that manipulate only lists, trees, DAGS, etc.); each instantiation of the framework can be applied to any program, but may produce imprecise results (albeit conservative ones) due to the set of predicates employed.
Theory of strong intrinsic mixing of particle suspensions in vortex magnetic fields (2009)

Recent experiments have shown that a type of triaxial magnetic field we call a vortex field can induce strong mixing in a magnetic particle suspension. A vortex triaxial field consists of a rotating magnetic field in a horizontal plane, with a dc field applied normal to this. The mixing torque is found to be independent of the field frequency and fluid viscosity over a broad range; scales as the square of the applied field; and is strongest for a balanced triaxial field-one in which the root-mean-square amplitudes of the three field components are equal. In this paper we show that these anomalous effects are consistent with the formation of volatile particle chains that have a precessionlike motion. Theoretical results are given for both particle chains and magnetic rods for arbitrary vortex field angles. A key conclusion is that the mixing torque is independent of particle size, making this mixing technique scale adaptive, and thus suitable for microfluidics applications.
Linguistic uses of segmental duration in English: Acoustic and perceptual evidence (1976)

The pattern of durations of individual phonetic segments and pauses conveys information about the linguistic content of an utterance. Acoustic measures of segmental timing have been used by many investigators to determine the variables that influence the durational structure of a sentence. The literature on segmental duration is reviewed and related to perceptual data on the discrimination of duration and to psychophysical data on the ability of listeners to make linguistic decisions on the basis of durational cues alone. We conclude that, in English, duration often serves as a primary perceptual cue in the distinctions between (1) inherently long verses short vowels, (2) voiced verses voiceless fricatives, (3) phrase-final verses non-final syllables, (4) voiced versus voiceless postvocalic consonants, as indicated by changes to the duration of the preceding vowel in phrase-final positions, (5) stressed verses unstressed or reduced vowels, and (6) the presence or absence of emphasis. Subject Classification: [43]70.40, [43]70.70, [43]70.20.
The Utility of Cellulose Meals for Studies on Gastrointestinal Motility in Dogs (1982)

This study evaluated the effect of a cellulose meal and a cellulose-oleic acid meal on gastroduodenal motility and gastric emptying. The cellulose meal produced a high antral motility index (100 +/- 34 V/10 min) and a high proportion (80.2%) of propulsive duodenal contractions. The oleic acid meal was associated with a significantly lower antral motility index (70 +/- 34 V/10 min), a high proportion (78.7%) of segmental duodenal contractions, and a reduced emptying rate (half time 93 +/- 18 versus 30 +/- 7 min). Results indicate that the inert cellulose meal is advantageous in studying the effects of different nutrients on gastrointestinal motility.
Comparative Immunogenicity in Rhesus Monkeys of DNA Plasmid, Recombinant Vaccinia Virus, and Replication-Defective Adenovirus Vectors Expressing a Human Immunodeficiency Virus Type 1 gag Gene (2003)

Cellular immune responses, particularly those associated with CD3(+) CD8(+) cytotoxic T lymphocytes (CTL), play a primary role in controlling viral infection, including persistent infection with human immunodeficiency virus type 1 (HIV-1). Accordingly, recent HIV-1 vaccine research efforts have focused on establishing the optimal means of eliciting such antiviral CTL immune responses. We evaluated several DNA vaccine formulations, a modified vaccinia virus Ankara vector, and a replication-defective adenovirus serotype 5 (Ad5) vector, each expressing the same codon-optimized HIV-1 gag gene for immunogenicity in rhesus monkeys. The DNA vaccines were formulated with and without one of two chemical adjuvants (aluminum phosphate and CRL1005). The Ad5-gag vector was the most effective in eliciting anti-Gag CTL. The vaccine produced both CD4(+) and CD8(+) T-cell responses, with the latter consistently being the dominant component. To determine the effect of existing antiadenovirus immunity on Ad5-gag-induced immune responses, monkeys were exposed to adenovirus subtype 5 that did not encode antigen prior to immunization with Ad5-gag. The resulting anti-Gag T-cell responses were attenuated but not abolished. Regimens that involved priming with different DNA vaccine formulations followed by boosting with the adenovirus vector were also compared. Of the formulations tested, the DNA-CRL1005 vaccine primed T-cell responses most effectively and provided the best overall immune responses after boosting with Ad5-gag. These results are suggestive of an immunization strategy for humans that are centered on use of the adenovirus vector and in which existing adenovirus immunity may be overcome by combined immunization with adjuvanted DNA and adenovirus vector boosting.
Expression, Purification, and Characterization of Recombinant HIV gp140 (2001)

Efforts to understand the molecular basis of human immunodeficiency virus (HIV) envelope glycoprotein function have been hampered by the inability to generate sufficient quantities of homogeneous material. We now report on the high level expression, purification, and characterization of soluble HIV gp140 ectodomain proteins in Chinese hamster ovary-Lec3.2.8.1 cells. Gel filtration and analytical ultracentrifugation show that the uncleaved ADA strain-derived gp140 proteins are trimeric without further modification required to maintain oligomers. These spike proteins are native as judged by soluble CD4 (sCD4) (K(D) = 1-2 nm) and monoclonal antibody binding studies using surface plasmon resonance. CD4 ligation induces conformational change in the trimer, exposing the chemokine receptor binding site as assessed by 17b monoclonal antibody reactivity. Lack of anti-cooperativity in sCD4-ADA trimer interaction distinct from that observed with sCD4-SIV mac32H implies quaternary structural differences in ground states of their respective spike proteins.
Innovations in Payment Technologies and the Emergence of Digital Currencies (2014)

Modern electronic payment systems rely on trusted, central third parties to process payments securely. Recent developments have seen the creation of digital currencies like Bitcoin, which combine new currencies with decentralised payment systems. Although the monetary aspects of digital currencies have attracted considerable attention, the distributed ledger underlying their payment systems is a significant innovation. As with money held as bank deposits, most financial assets today exist as purely digital records. This opens up the possibility for distributed ledgers to transform the financial system more generally.