gebhart/patrepeval huggingface dataset:
Definition of the minimal simian virus 40 large T antigen- and adenovirus E1A-binding domain in the retinoblastoma gene product. (1990)

It has previously been demonstrated that the simian virus 40 large T antigen and adenovirus E1A proteins can form complexes with the retinoblastoma susceptibility gene product (RB). We studied the ability of these proteins to bind to mutant RB proteins in vitro. A region of RB spanning residues 379 to 792 was found to be both necessary and sufficient for binding to T or E1A. Furthermore, this region of RB contains sufficient structural information to mimic wild-type RB in its ability to distinguish between wild-type T and the transformation-defective T mutant K1. The results of competition experiments with peptide analogs of the RB-binding sequence in T suggest that this region of RB makes direct contact with a short colinear region of T, i.e., residues 102 to 115, previously implicated in both transformation and RB binding.
Fabrication of a carbon nanotube-based gas sensor using dielectrophoresis and its application for ammonia detection by impedance spectroscopy (2003)

This paper describes a new method for fabricating a gas sensor composed of multi-wall carbon nanotubes (MWCNTs) using dielectrophoresis (DEP). MWCNTs dispersed in ethanol were trapped and enriched in an interdigitated microelectrode gap under the action of a positive DEP force that drove the MWCNTs to a higher electric field region. During the trapping of MWCNTs, the electrode impedance varied as the number of MWCNTs bridging the electrode gap increased. After the DEP process, the ethanol was evaporated and the microelectrode retaining the MWCNTs was exposed to ammonia (NH3) gas while the electrode impedance was monitored. It was found that the electrode impedance was altered by ppm-levels of ammonia at room temperature. The ammonia exposure decreased the sensor conductance, while the capacitance increased. The sensor showed a reversible response with a time constant of a few minutes. The conductance change was proportional to ammonia concentration below 10 ppm and then gradually saturated at higher concentrations. Effects of the number of trapped MWCNTs on sensor response were also discussed.
Only UCP1 can mediate adaptive nonshivering thermogenesis in the cold (2001)

Adaptive nonshivering thermogenesis may have profound effects on energy balance and is therefore therefore is a potential mechanism for counteracting the development of obesity. The molecular basis for adaptive nonshivering thermogenesis has remained a challenge that sparked acute interest with the identification of proteins (UCP2, UCP3, etc.) with high-sequence similarity to the original uncoupling protein-1 (UCP1), which is localized only in brown adipose tissue. Using UCP1-ablated mice, we examined whether any adaptive nonshivering thermogenesis could be recruited by acclimation to cold. Remarkably, by successive acclimation, the UCP1-ablated mice could be made to subsist for several weeks at 4C during which they had to constantly produce heat at four times their resting levels. Despite these extreme requirements for adaptive nonshivering thermogenesis, however, no substitution of shivering by any adaptive nonshivering thermogenic process occurred. Thus, although the existence of, for example, muscular mechanisms for adaptive nonshivering thermogenesis has recurrently been implied, we did not find any indication of such thermogenesis. Not even during prolonged and enhanced demand for extra heat production was any endogenous hormone or neurotransmitter able to recruit any UCP1-independent adaptive nonshivering thermogenic process in muscle or in any other organ, and no proteins other than UCP1-not even UCP2 or UCP3-therefore have the ability to mediate adaptive nonshivering thermogenesis in the cold.
Unforced translocation of a polymer chain through a nanopore: The solvent effect (2007)

The authors have performed the Langevin dynamics simulation to investigate the unforced polymer translocation through a narrow nanopore in an impermeable membrane. The effects of solvent quality controlled by the attraction strength lambda of the Lennard-Jones cosine potential between polymer beads and beads on two sides of the membrane on the translocation processes are extensively examined. For polymer translocation under the same solvent quality on both sides of the membrane, the two-dimensional and three-dimensional simulations confirm the scaling law of tautrans approximately N1+2upsilon for the translocation in the good solvent, where tautrans is the translocation time, N is the chain length, and upsilon is the Flory exponent. For the three-dimensional polymer translocation under different solvent qualities on two sides of the membrane, the translocation efficiency may be notably improved. The scaling law between tautrans and N varies from tautrans approximately N1+2upsilon to tautrans approximately N with the increase of the difference of solvent qualities, and the crossover occurs at the theta temperature point, where a scaling law of tautrans approximately N1.27 is found. The simulation results here also show that the translocation time changes from a wide and asymmetric distribution with a long tail to a narrow and symmetric distribution with the increase of the difference of the solvent qualities.
A new Genotype of Japanese Encephalitis Virus from Indonesia (1992)

Primer-extension sequencing of the RNA template of polio, dengue, Rift Valley fever, and Japanese encephalitis (JE) viruses has provided new information on their geographic distribution, origin, and evolution. In a previous study of 46 diverse JE virus strains, we demonstrated the existence of three distinct JE genotypes in Asia. We now report the occurrence of a fourth genotype. In the present study, 19 JE virus isolates, representing various geographic regions of Asia and a 50-year time span, were compared with each other and with Murray Valley encephalitis, West Nile, and Kunjin viruses. Twelve of the JE strains from the Indonesian Archipelago and the Philippines had not been previously examined; the remainder were representatives of the three previously identified genotypes. Two hundred forty nucleotides from the pre-M gene region of the virus were used in these comparisons. Using 12% divergence as a cut-off point, the 19 JE strains fell into four distinct genotypic groups; maximum divergence across the comparison region was 21%. The newly recognized fourth genotype was comprised of five Indonesian isolates that were 7% divergent from the rest of the JE viruses.
Intraoperative cell salvage is associated with reduced postoperative blood loss and transfusion requirements in cardiac surgery: a cohort study (2013)

The use of cell salvage throughout the entire procedure reduces postoperative blood loss and allogeneic RBC transfusion. These findings advocate implementation of cell salvage in all patients undergoing on-pump cardiac surgery, irrespective of anticipated surgery-related blood loss.
A Large Scale Analysis of cDNA in Arabidopsis thaliana: Generation of 12,028 Non-redundant Expressed Sequence Tags from Normalized and Size-selected cDNA Libraries (2000)

For comprehensive analysis of genes expressed in the model dicotyledonous plant, Arabidopsis thaliana, expressed sequence tags (ESTs) were accumulated. Normalized and size-selected cDNA libraries were constructed from aboveground organs, flower buds, roots, green siliques and liquid-cultured seedlings, respectively, and a total of 14,026 5'-end ESTs and 39,207 3'-end ESTs were obtained. The 3'-end ESTs could be clustered into 12,028 non-redundant groups. Similarity search of the non-redundant ESTs against the public non-redundant protein database indicated that 4816 groups show similarity to genes of known function, 1864 to hypothetical genes, and the remaining 5348 are novel sequences. Gene coverage by the non-redundant ESTs was analyzed using the annotated genomic sequences of approximately 10 Mb on chromosomes 3 and 5. A total of 923 regions were hit by at least one EST, among which only 499 regions were hit by the ESTs deposited in the public database. The result indicates that the EST source generated in this project complements the EST data in the public database and facilitates new gene discovery.
Protection against ischaemic neuronal damage by drugs acting on excitatory neurotransmission. (1990)

An excitotoxic action of glutamate and aspartate contributes to the pathological outcome after transient global cerebral ischaemia, focal ischaemia, neonatal hypoxia/ischaemia, and secondary ischaemia following brain trauma. This provides a therapeutic approach utilising drugs acting on (i) glutamate release, (ii) postsynaptic glutamate receptors, and (iii) the secondary events following receptor activation (including the arachidonic acid cascade). Both NMDA and non-NMDA receptors are involved in the excitotoxic effects of glutamate and aspartate. The availability of competitive and noncompetitive antagonists acting at the NMDA receptor has permitted the demonstration of cerebroprotective effects of these compounds in animal models of global, focal, neonatal, and secondary cerebral ischaemia. Protection is seen with antagonist administration prior to and after the onset of ischaemia. The postischaemic therapeutic time window is not fully defined for the different models but is in the range of 0-20 min for incomplete global ischaemia and 1-3 h for focal ischaemia. The clinical usefulness of this approach remains to be established.
Experimental infection with Chlamydia pneumoniae in nonhuman primates (1990)

To serially examine the immunopathogenesis and histopathology of infection with Chlamydia pneumoniae, we inoculated two cynomolgus monkeys in the conjunctival sac, nose, and nasopharynx with C. pneumoniae TWAR. After inoculation, C. pneumoniae was isolated from the inoculation sites and the rectums of both monkeys for a period of 5 weeks. After a second inoculation, C. pneumoniae was recovered from the inoculation sites and the rectums of both monkeys for 20 weeks. A third inoculation with C. pneumoniae caused very little productive infection at any site. Prior C. pneumoniae infection did not prevent subsequent C. trachomatis serovar E (Bour strain) infection. Clinical and histopathologic ocular responses to C. pneumoniae infection were mild compared with those to infection with C. trachomatis serovar E. Rectal infection, demonstrated by culture isolation and immunohistopathology, occurred without direct experimental inoculation. Both immunofluorescent staining of mucosal smears with monoclonal antibodies and tissue culture were able to detect C. pneumoniae infection. Experimental nonhuman primate infection with C. pneumoniae appears to be clinically and histopathologically mild and can occur at extrapulmonary sites.
EcoCyc: Enyclopedia of Escherichia coli Genes and Metabolism (1997)

The Encyclopedia of Genes and Metabolism (EcoCyc) is a database that combines information about the genome and the intermediary metabolism of Escherichia coli. It describes 2970 genes of E.coli, 547 enzymes encoded by these genes, 702 metabolic reactions that occur in E.coli and the organization of these reactions into 107 metabolic pathways. The EcoCyc graphical user interface allows scientists to query and explore the EcoCyc database using visualization tools such as genomic-map browsers and automatic layouts of metabolic pathways. EcoCyc spans the space from sequence to function to allow scientists to investigate an unusually broad range of questions. EcoCyc can be thought of as both an electronic review article because of its copious references to the primary literature, and as an in silicio model of E.coli metabolism that can be probed and analyzed through computational means.
Enrichment for enhanced competitive plant root tip colonizers selects for a new class of biocontrol bacteria (2005)

Our group studies tomato foot and root rot, a plant disease caused by the fungus Forl (Fusarium oxysporum f.sp. radicis-lycopersici ). Several bacteria have been described to be able to control the disease, using different mechanisms. Here we describe a method that enables us to select, after application of a crude rhizobacterial mixture on a sterile seedling, those strains that reach the root tip faster than our best tomato root colonizer tested so far, the Pseudomonas fluorescens biocontrol strain WCS365. Of the five tested new isolates, four appeared to be able to reduce the number of diseased plants. Analysis of one of these strains, P. fluorescens PCL1751, suggests that it controls the disease through the mechanism 'competition for nutrients and niches', a mechanism novel for biocontrol bacteria. Moreover, this is the first report describing a method to enrich for biocontrol strains from a crude mixture of rhizobacteria. Another advantage of the method is that four out of five strains do not produce antifungal metabolites, which is preferential for registration as a commercial product.
Antisense strategy shows that Mcl-1 rather than Bcl-2 or Bcl-xL is an essential survival protein of human myeloma cells (2002)

Multiple myeloma (MM) is a plasma cell malignancy that occurs mainly in bone marrow. As MM cells proliferate slowly, it would seem essential to find means of preventing their growth and accumulation inside bone marrow. The present study used an antisense strategy to elucidate the respective roles of Bcl-2, Bcl-x(L), and Mcl-1 proteins in myeloma cell survival. Each antisense oligonucleotide (ASO; Bcl-2, Bcl-x(L), or Mcl-1 ASO) introduced into human myeloma cell lines by electroporation induced a marked reduction in the level of the corresponding protein. Mcl-1 ASO triggers an important decrease of viability in all myeloma cell lines tested and in 2 primary myeloma cells, whereas neither Bcl-2 nor Bcl-x(L) ASO affected the viability of myeloma cells. The decrease of cell viability induced by Mcl-1 ASO treatment was associated with an induction of apoptosis that occurred through the disruption of mitochondrial membrane potential Delta Psi m and the activation of executioner caspase-3. Furthermore, we have shown that interleukin 6 cannot prevent the Mcl-1 ASO-induced apoptosis. Finally, although Bcl-2 ASO treatment alone has no effect, it can sensitize myeloma cell lines to dexamethasone (Dex), whereas Bcl-x(L) ASO in combination with Dex still had no effect. As MM remains an incurable disease despite intensive chemotherapy, these results suggest that Mcl-1 antisense strategy rather than Bcl-2 antisense strategy could be of considerable importance in the treatment of MM.
Use of an Electromagnetic Seepage Meter to Investigate Temporal Variability in Lake Seepage (2004)

A commercially available electromagnetic flowmeter is attached to a seepage cylinder to create an electromagnetic seepage meter (ESM) for automating measurement of fluxes across the sediment/water interface between ground water and surface water. The ESM is evaluated through its application at two lakes in New England, one where water seeps into the lake and one where water seeps out of the lake. The electromagnetic flowmeter replaces the seepage-meter bag and provides a continuous series of measurements from which temporal seepage processes can be investigated. It provides flow measurements over a range of three orders of magnitude, and contains no protruding components or moving parts. The ESM was used to evaluate duration of seepage disturbance following meter installation and indicated natural seepage rates resumed approximately one hour following meter insertion in a sandy lakebed. Lakebed seepage also varied considerably in response to lakebed disturbances, near-shore waves, and rainfalls, indicating hydrologic processes are occurring in shallow lakebed settings at time scales that have largely gone unobserved.
A multicenter Phase I safety study of intratumoral photoactivation of talaporfin sodium in patients with refractory solid tumors (2003)

Photoactivation of talaporfin sodium using intratumoral nonlaser light was found to be safe in the patient population of the current study at all light dose levels tested.
Design, Synthesis, and Characterization of Potent, Slow-binding Inhibitors That Are Selective for Gelatinases (2002)

Gelatinases have been shown to play a key role in angiogenesis and tumor metastasis. Small molecular weight synthetic inhibitors for these enzymes are highly sought for potential use as anti-metastatic agents. Virtually all of the known inhibitors of matrix metalloproteinases (MMPs) are broad spectrum. We report herein the synthesis and kinetic characterization of two compounds, 4-(4-phenoxyphenylsulfonyl)butane-1,2-dithiol (compound 1) and 5-(4-phenoxyphenylsulfonyl)pentane-1,2-dithiol (compound 2), that are potent and selective gelatinase inhibitors. These compounds are slow, tight-binding inhibitors of gelatinases (MMP-2 and MMP-9) with K(i) values in the nanomolar range. In contrast, competitive inhibition of the catalytic domain of membrane-type 1 metalloproteinase (MMP-14(cat)) with comparable K(i) values (K(i) approximately 200 nm) was observed. Binding to stromelysin (MMP-3) was substantially weaker, with K(i) values in the micromolar range (K(i) approximately 10 microm). No binding to matrilysin (MMP-7) and collagenase 1 (MMP-1) was detected at inhibitor concentrations up to 60 microm. We have previously shown that synthetic MMP inhibitors work synergistically with TIMP-2 in the promotion of pro-MMP-2 activation by MT1-MMP in a process that depends on the affinity of the inhibitor toward MT1-MMP. It is shown herein that the dithiols are significantly less efficient (>100-fold) than marimastat, a broad-spectrum MMP inhibitor, in enhancing pro-MMP-2 activation in cells infected to express MT1-MMP, consistent with the lower affinity of the dithiols toward MT1-MMP. Thus, in contrast to broad-spectrum MMP inhibitors, the dithiols are less likely to promote MT1-MMP-dependent pro-MMP-2 activation in the presence of TIMP-2, while maintaining their ability to inhibit active MMP-2 effectively.
ChemInform Abstract: Preparation of Na1+xFe4P12 Whiskers by Hydrothermal Reduction Alloying Synthesis Method. (2001)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Swelling behavior of submicron gel particles (1998)

We prepared submicron Poly(N-isopropylacrylamide) gel particles. Their swelling behavior was investigated by a photon correlation spectroscopy (PCS) technique. The swelling behavior of submicron gel particles showed a continuous volume phase transition for various temperatures. We combined the extended Flory-Huggins model for mixing solvent and network with a modified Flory-Rehner theory for the elastic contribution. The proposed model agreed very well with swelling behaviors of both submicron gel particles and bulk gels. A continuous volume phase transition behavior of submicron gel particles was predicted successfully by the proposed model. © 1998 John Wiley & Sons, Inc. J Appl Polym Sci 69: 109–114, 1998
Proliferation: the Most Prominent Predictor of Clinical Outcome in Breast Cancer (2006)

We recently identified a gene expression cassette of 97 unique genes that were consistently differentially expressed between low and high grade breast carcinomas. The majority of these genes were overexpressed in high grade tumors and, as expected, they were associated with cell cycle progression and proliferation. Interestingly, by applying this gene expression cassette to several datasets, we demonstrated that intermediate grade tumors were composed of a mixture of well- and poorly- differentiated tumors with statistically distinct clinical outcome similar to those of low and high grade carcinomas. Furthermore, these proliferation-related genes appear to be a common denominator of several existing prognostic gene expression signatures. This recapitulates their prognostic power far beyond the estrogen receptor (ER) status and highlights the importance of proliferation genes in breast cancer biology. Importantly, their weight seems to be far more important in ER-positive than in ER-negative disease.
Polymerized surfactant vesicles. Determinations of rates and degrees of polymerization in vesicles prepared from styrene-containing surfactants (1985)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPolymerized surfactant vesicles. Determinations of rates and degrees of polymerization in vesicles prepared from styrene-containing surfactantsJuan Serrano, Sergio Mucino, Sonia Millan, Rocio Reynoso, Luz Alicia Fucugauchi, Wayne Reed, Faruk Nome, Pietro Tundo, and Janos H. FendlerCite this: Macromolecules 1985, 18, 10, 1999–2005Publication Date (Print):October 1, 1985Publication History Published online1 May 2002Published inissue 1 October 1985https://pubs.acs.org/doi/10.1021/ma00152a034https://doi.org/10.1021/ma00152a034research-articleACS PublicationsRequest reuse permissionsArticle Views94Altmetric-Citations13LEARN 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
Selective Bromination of Perylene Diimides under Mild Conditions (2007)

A novel method for the bromination of perylene diimides, PDI (1), under mild conditions is reported. Variation of the reaction conditions allows mono- and dibromination of PDIs to afford 2 and 3 (these can be separated through standard procedures) or exclusive dibromination to afford 3. Pure 1,7 regioisomers are obtained through repetitive crystallization. The structure of 1,7-3b was elucidated by a single-crystal X-ray analysis. The facility of the bromination reaction, which decreases in the order 1a > 1b > 1c, depends on PDI aggregation propensities. Monobrominated PDIs were utilized for the syntheses of novel unsymmetrical piperidinyl (4a and 4b) and trimethylsilylethynyl derivatives (5a and 5b). Computational studies (DFT) on imide substituent rotation in PDIs reveal that in the case of bulky groups there is a restricted rotation leading to isomers, in agreement with our experimental results. An aromatic core twist in PDIs bearing one and two bromine substituents was also investigated by DFT.
Analysis of the Morphology of Oral Structures from 3-D Co-Ordinate Data (2000)

A non-intrusive method is described which can be used to determine the forms of oral structures. It is based on the digitising of standard replicas with a co-ordinate-measuring machine. Supporting software permits a mathematical model of the surface to be reconstructed and visualised from captured three-dimensional co-ordinates. A series of surface data sets can be superposed into a common reference frame without the use of extrinsic markers, allowing changes in the shapes of oral structures to be quantified accurately over an extended period of time. The system has found numerous applications.