gebhart/patrepeval huggingface dataset:
Energetics of glutamate receptor ligand binding domain dimer assembly are modulated by allosteric ions (2009)

The activity of many ligand-gated ion channels and cell surface receptors is modulated by small molecules and ions, but an understanding of the underlying molecular mechanisms is scarce. For kainate, but not AMPA subtype glutamate receptors, the binding of Na(+) and Cl(-) ions to discrete, electrostatically coupled sites in the extracellular ligand binding domain (LBD) dimer assembly regulates the rate of entry into the desensitized state, which occurs when the dimer interface ruptures and the channel closes. Studies on glutamate receptors have defined the LBD dimer assembly as a key functional unit that controls activation and desensitization. Here we use analytical ultracentrifugation to probe the energetic effects of allosteric ions on kainate receptor dimer stability in solution, using a GluR6 mutant that desensitizes slowly. Our results show that sodium and chloride ions modulate kainate receptor dimer affinity as much as 50-fold, and that removal of either Cl(-) or Na(+) disrupts the dimer. The applicability of a similar allosteric mechanism for modulation of delta2 glutamate receptors by Ca(2+) was also tested. Our results indicate that ions can contribute substantial free energy to active state stabilization in both these receptors, and provide quantitative measurements of the energetic consequences of allosteric ion binding to a ligand-gated ion channel.
Survival Trees for Analyzing Clinical Outcome in Lung Adenocarcinomas Based on Gene Expression Profiles: Identification of Neogenin and Diacylglycerol Kinase α Expression as Critical Factors (2005)

We present survival trees as an exploratory tool for revealing new insights into gene expression profiles in combination with clinical patient data. Survival trees partition the patient data studied into groups with similar survival outcomes and identify characteristic genetic profiles within these groups. We demonstrate the application of survival trees in a study involving the expression profiles of 3,588 genes in 211 lung adenocarcinoma patients. The survival tree identified a group of early-stage cancer patients with relatively low survival rates and another group of advanced-stage patients with remarkably good survival outcome. For both groups, the tree identified characteristic expression profiles of genes that might play a role in cancerogenesis and disease progression, notably the genes for the netrin receptor neogenin and the Ras/Rho kinase modulator diacylglycerol kinase alpha.
Clinical feasibility of Raman spectroscopy for quantitative blood glucose measurement (2011)

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2011.
Beneficial effects of SK&F 105809, a novel cytokine-suppressive agent, in murine models of endotoxin shock. (1992)

SK&F 105809 is a structurally novel dual inhibitor of lipoxygenase and cyclooxygenase-mediated arachidonic acid (AA) metabolism, which has demonstrated antiinflammatory activity in rodent models of inflammation. In addition, the active metabolite of this compound, SK&F 105561, has been shown in vitro to inhibit the production of the inflammatory cytokine interleukin-1 (IL-1) in human monocytes stimulated with lipopolysaccharide (LPS). We report here that in vitro SK&F 105561 also blocks the production of tumor necrosis factor (TNF) from human monocytes (IC50 0.8-3 microM). Furthermore, in a murine model of endotoxin shock in which animals are injected with LPS in combination with D-galactosamine (D-gal), SK&F 105809 (10, 30, and 100 mg/kg p.o.), delivered 30 min prior to LPS/D-gal, caused a dramatic reduction in serum TNF (40-90%) and protected the animals from the lethal effects of this treatment. Similar results were obtained in a second model of endotoxin shock in which mice were sensitized with Propionibacterium acnes 10 days prior to LPS injection. In this system 100-fold higher levels of serum TNF are elicited than with the LPS/D-gal model. Treatment with SK&F 105809 (30 and 100 mg/kg p.o.) delivered 30 min prior to LPS resulted in 90-100% inhibition of serum TNF. Protection from the lethal effects of LPS was observed at these doses in the P. acnes/LPS model.
The Chemistry of the Benzimidazoles. (1951)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe Chemistry of the Benzimidazoles.John B. WrightCite this: Chem. Rev. 1951, 48, 3, 397–541Publication Date (Print):June 1, 1951Publication History Published online1 May 2002Published inissue 1 June 1951https://pubs.acs.org/doi/10.1021/cr60151a002https://doi.org/10.1021/cr60151a002research-articleACS PublicationsRequest reuse permissionsArticle Views6830Altmetric-Citations393LEARN 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
Two X-Chromosome STR Loci DXS6 803 and XS6793 Frequency Data in Chinese Population (2004)

Abstract 90 unrelated females and 90 unrelated males volunteer donors, Southwest China
Human purine nucleoside phosphorylase and adenosine deaminase: gene transfer into cultured cells and murine hematopoietic stem cells by using recombinant amphotropic retroviruses. (1987)

Cell lines were established which produced high titers (approximately 10(6) infectious units per ml) of amphotropic, replication-defective recombinant retroviruses which transduced sequences encoding either human purine nucleoside phosphorylase (PNP) or adenosine deaminase (ADA). These viruses also contained a human hypoxanthine phosphoribosyltransferase gene as a selectable marker and a mouse metallothionein promoter (MMP) sequence just upstream from the PNP or ADA genes. Virus structure was maintained through the replication cycle if a short (216-base pair) MMP sequence was used. However, the use of a longer (1,834-base pair) MMP sequence resulted in the deletion of a significant portion of the recombinant virus genome, including the transcriptional regulatory elements of the MMP sequence. Northern analysis indicated a predominance of genome length transcripts in cells infected with deleted virus. The demonstration of substantial human PNP or ADA activity in virus-infected mouse fibroblasts by isozyme analysis suggested that active gene product was translated from either spliced or bicistronic message. The deleted ADA and PNP viruses were introduced into mouse hematopoietic stem cells by cocultivating freshly explanted bone marrow with virus producer cells. The infected marrow cells were injected into irradiated, syngeneic recipient mice, and the presence of integrated ADA or PNP proviral sequences was demonstrated in the DNA of spleen colonies by Southern analysis. Failure of these integrated proviral sequences to express active, human isozyme in spleen colony tissue indicated the existence of some regulatory constraint not active in cultured mouse cells.
Double Entendre Headlines (1984)

While I was calmly reading the newspaper the other day, this headline near the bottom of the page caught my eye: JOHNNY, JUNE CASH ARE HIT IN HUNGARY. Had they been pelted with rotten tomatoes by a restive audience, or with bricks by protestors in the streets? (A modern civilized population has various ways of expressing its feelings.) Or had they been bashed by a car on the highway, or beaned by a meteorite? When I read the article, it was a surprise (and no small relief) to learn that their concerts in Hungary had been a big success.
Chemical control of nanotube electronics (2000)

The possibility of modifying the electronic properties of nanotubes using gas molecule adsorption is investigated using the first-principles total energy density functional calculations. Detailed analysis of the electronic structures and energetics is performed for the semiconducting (10,0) single-walled carbon nanotube interacting with several representative gas molecules (NO2, NH3, CO, O2, and H2O). The results elucidate the mechanisms of the adsorption-induced nanotube doping and illustrate an example of the simulation-based design characterization of nanoelectronic components.
Genetic Analysis of the isc Operon in Escherichia coli Involved in the Biogenesis of Cellular Iron-Sulfur Proteins (2001)

Journal Article Genetic Analysis of the isc Operon in Escherichia coli Involved in the Biogenesis of Cellular Iron-Sulfur Proteins Get access Umechiyo Tokumoto, Umechiyo Tokumoto Department of Biology, Graduate School of Science, Osaka University1-1 Machikaneyama, Toyonaka, Osaka 560-0043 Search for other works by this author on: Oxford Academic PubMed Google Scholar Yasuhiro Takahashi Yasuhiro Takahashi 2 Department of Biology, Graduate School of Science, Osaka University1-1 Machikaneyama, Toyonaka, Osaka 560-0043 2 To whom correspondence should be addressed.Tel: +81-6-6850-5423, Fax: +81-6-6850-5425, E-mail: ytaka@bio.sci.osaka-u.ac.jp Search for other works by this author on: Oxford Academic PubMed Google Scholar The Journal of Biochemistry, Volume 130, Issue 1, July 2001, Pages 63–71, https://doi.org/10.1093/oxfordjournals.jbchem.a002963 Published: 01 July 2001 Article history Received: 26 March 2001 Accepted: 12 April 2001 Published: 01 July 2001
A vector-locked loop for power amplifier linearization (2004)

This paper describes a power amplifier linearization technique called the vector-locked loop (VLL), where the amplitude- and phase-modulated output RF signal is composed of two constant-envelope phase-modulated signals. This enables the use of non-linear high-efficient PAs in the chain. The theoretical background and limitations behind the VLL concept are discussed in the paper. A prototype has been designed for the 2.11-2.17-GHz band using off-the-shelf components. Experimental results show that the concept itself is functional and complex modulations can be reconstructed. The real-time feedback operation and the utilized components limit the achievable linearization bandwidth to less than 1 MHz and allow relatively shallow modulations only, such as OQPSK or PI/4-DQPSK. Problems related to the realization can be solved by full-custom component design if modest bandwidths are targeted.
miR-9 functions as a tumor suppressor in ovarian serous carcinoma by targeting TLN1 (2013)

microRNAs (miRNAs) are important regulators of gene expression during tumorigenesis. The downregulation of microRNA-9 (miR-9) has been reported in ovarian serous carcinoma (OSC), indicating a role for miR-9 in this type of cancer. In this study, we investigated the biological significance of miR-9 in OSC in vitro. Using 3 OSC cell lines, SKOV3, CAOV3 and OVCAR3, which underexpresss miR-9, we demonstrate that the exogenous miR-9 transfection inhibits OSC cell proliferation, migration and invasion. In addition, we demonstrate that the focal adhesion protein, talin 1 (TLN1), whose expression has been associated with OSC development and progression to metastasis, is a direct target of miR-9. TLN1 knockdown mimicked the effects of miR-9 overexpression. Moreover, the activation of the TLN1-modulated FAK/AKT pathway was inhibited by the increased miR-9 levels. These results suggest that miR-9 plays a role as a tumor suppressor in OSC by suppressing TLN1 expression.
Theoretical Demonstration of Efficiency Enhancement of Dye-Sensitized Solar Cells with Double-Inverse Opal as Mirrors (2010)

Herein we describe the employment of double-inverse opal (DIO) as a novel optical element and present a theoretical analysis of the efficiency enhancement of the designed DSSCs. We find that, compared to inverse opal (IO) as the optical element, the presence of small spheres in IO (i.e., DIO structure) produces a great light-scattering effect and broader reflection region, leading to considerable enhancement of the photocurrent efficiency of cells. Dye-sensitized solar cells (DSSCs) with one DIO layer as a mirror has a photocurrent efficiency enhancement up to 47%, which is a large improvement compared to that of the IO-coupled one (28%). More remarkably, double DIO layers as a scattering layer lead to efficient enhancement of the absorptances of DSSCs in the whole visible spectrum range (400−800 nm) and a distinct increment of about 80% of photocurrent efficiency with respect to standard ones. In this work, the optimum structural parameters of such DIO optical elements needed to achieve an efficient photocurrent efficiency enhancement are provided.
Analysis of steroid conversion in vitro by testicular tissue as a means of selection of infertile males for gonadotrophic substitution therapy (1983)

Testicular biopsy specimens from 11 infertile men were incubated in vitro with [3H]progesterone before and during long term gonadotrophic treatment. The main metabolites along the delta-4 metabolic pathway and 20 alpha-dihydro-progesterone were determined and the ratio between 20 alpha-dihydro-progesterone and 17 alpha-hydroxyprogesterone formed in vitro was calculated. In 5 patients with originally high ratios (indicating gonadotrophic understimulation), steroid metabolism changed significantly towards a more stimulated pattern. Three of these patients also showed a significant increase in sperm output and 2 of them fathered children. In 6 patients with an originally low ratio (indicating adequate gonadotrophic stimulation) no change in steroid metabolism in vitro or spermatogenesis was seen during therapy. Thus, this ratio between formed 20 alpha-dihydro-progesterone and 17 alpha-hydroxyprogesterone in vitro seems to be of value in predicting whether gonadotrophic treatment will be of clinical benefit.
Single‐cell genomics reveals potential for magnetite and greigite biomineralization in an uncultivated multicellular magnetotactic prokaryote (2014)

For magnetic orientation, magnetotactic bacteria biosynthesize magnetosomes, which consist of membrane-enveloped magnetic nanocrystals of either magnetite (Fe3 O4 ) or greigite (Fe3 S4 ). While magnetite formation is increasingly well understood, much less is known about the genetic control of greigite biomineralization. Recently, two related yet distinct sets of magnetosome genes were discovered in a cultivated magnetotactic deltaproteobacterium capable of synthesizing either magnetite or greigite, or both minerals. This led to the conclusion that greigite and magnetite magnetosomes are synthesized by separate biomineralization pathways. Although magnetosomes of both mineral types co-occurred in uncultured multicellular magnetotactic prokaryotes (MMPs), so far only one type of magnetosome genes could be identified in the available genome data. The MMP Candidatus Magnetomorum strain HK-1 from coastal tidal sand flats of the North Sea (Germany) was analysed by a targeted single-cell approach. The draft genome assembly resulted in a size of 14.3 Mb and an estimated completeness of 95%. In addition to genomic features consistent with a sulfate-reducing lifestyle, we identified numerous genes putatively involved in magnetosome biosynthesis. Remarkably, most mam orthologues were present in two paralogous copies with highest similarity to either magnetite or greigite type magnetosome genes, supporting the ability to synthesize magnetite and greigite magnetosomes.
FMRFamides exert a unique modulation of rodent pancreatic polypeptide sensitive neuropeptide Y (NPY) receptors (2000)

FMRFamide and related peptides (RFamides) were found to inhibit the association binding of iodinated human pancreatic polypeptide ([125I]hPP) to Y5-like neuropeptide Y (NPY) receptor in rodent tissues. An allosteric regulation of the activity of the rodent kidney PP-sensitive neuropeptide Y (NPY) receptor by RFamides was indicated by potency decrease with particle concentration in the inhibition of the association binding of 125I-labeled human pancreatic polypeptide (hPP) by RFamides at rabbit kidney membranes. The competition by C-terminal hexapeptide of hPP (LTRPRY.NH2) did not show such affinity change. The steady-state binding of hPP showed little sensitivity to any of the RFamides tested. The Y1-selective binding of [125I][Leu31,Pro34]hPYY (at 2 nM hPP) was much less sensitive to RFamides than the binding of [125I]hPP, albeit with some differences across tissue or cell types. The binding of Y2-selective agonist 125I-labeled human peptide YY (3-36) was quite insensitive to RFamides. The presence of a unique component in the inhibition of hPP binding by RFamides was further indicated by a degree of antagonism with phospholipase C inhibitor U-73122, and by an only limited cooperation with a N5-amiloride compound, and with alkylator chloroethylclonidine. Change of the chirality of individual residues in the FMRFamide molecule produced a significant reduction of inhibitory potency only with D-Phe in the C-terminal position. Substitution of the (C-3) L-Met by L-Leu greatly increased the inhibitory potency of RFamides relative to otherwise identical congeners. RFamides could act both as ligands of membrane neighbors of the PP receptor, and as competitors of Y5-like NPY receptor epitopes that accommodate the C-terminal aspects of agonist peptides.
Accuracy of MR Imaging for Revealing Residual Breast Cancer in Patients Who Have Undergone Neoadjuvant Chemotherapy (2002)

The high correlation between measurements of residual disease obtained on MR images and those obtained at pathology validates the sensitivity of MR imaging of the breast after chemotherapy.
Synthesis, characterization, and star polymer assembly of boronic acid end‐functionalized polycaprolactone (2010)

Abstract Boronic acid end‐functionalized polycaprolactone (PCL) polymers were synthesized by ring‐opening polymerization using a pinacol boronate ester‐containing (Bpin) initiator. The polymerization provides access to boron‐terminated polymers (i.e. Bpin‐PCL‐OH) with narrow molecular weight distributions (PDI = 1.09). Postsynthetic manipulation of the polymer's terminal hydroxyl group by copper‐catalyzed azide‐alkyne cycloaddition chemistry provides a series of bis end‐functionalized polymers with significant structural diversity at the termini. Deprotection of the boronate ester end group was accomplished with an acidic solid phase DOWEX resin. The boronate ester deprotection methodology does not result in hydrolysis of the polymeric backbone. The boronic acid‐tipped polymers were converted into star polymer assemblies using thermal dehydration and ligand‐facilitated trimerization. Thermal dehydration of (HO) 2 B‐PCL‐OAc to the corresponding boroxine‐based star polymer assembly was inefficient and lead to degradation products. Ligand‐facilitated trimerization using either pyridine or 7‐azaindole as the Lewis base was efficient and mild. © 2010 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2010
Extensive Neuronal Differentiation of Human Neural Stem Cell Grafts in Adult Rat Spinal Cord (2007)

NSC grafts can show substantial neuronal differentiation in the normal and injured adult spinal cord with good potential of integration into host neural circuits. In view of recent similar findings from other laboratories, the extent of neuronal differentiation observed here disputes the notion of a spinal cord that is constitutively unfavorable to neuronal repair. Restoration of spinal cord circuitry in traumatic and degenerative diseases may be more realistic than previously thought, although major challenges remain, especially with respect to the establishment of neuromuscular connections.
Alkylation of amino acids without loss of the optical activity: preparation of .alpha.-substituted proline derivatives. A case of self-reproduction of chirality (1983)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAlkylation of amino acids without loss of the optical activity: preparation of .alpha.-substituted proline derivatives. A case of self-reproduction of chiralityDieter Seebach, Michael Boes, Reto Naef, and W. Bernd SchweizerCite this: J. Am. Chem. Soc. 1983, 105, 16, 5390–5398Publication Date (Print):August 1, 1983Publication History Published online1 May 2002Published inissue 1 August 1983https://pubs.acs.org/doi/10.1021/ja00354a034https://doi.org/10.1021/ja00354a034research-articleACS PublicationsRequest reuse permissionsArticle Views6289Altmetric-Citations353LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Analysis of the query logs of a Web site search engine (2005)

Abstract A large number of studies have investigated the transaction log of general‐purpose search engines such as Excite and AltaVista, but few studies have reported on the analysis of search logs for search engines that are limited to particular Web sites, namely, Web site search engines. In this article, we report our research on analyzing the search logs of the search engine of the Utah state government Web site. Our results show that some statistics, such as the number of search terms per query, of Web users are the same for general‐purpose search engines and Web site search engines, but others, such as the search topics and the terms used, are considerably different. Possible reasons for the differences include the focused domain of Web site search engines and users' different information needs. The findings are useful for Web site developers to improve the performance of their services provided on the Web and for researchers to conduct further research in this area. The analysis also can be applied in e‐government research by investigating how information should be delivered to users in government Web sites.
Plasmid-Assisted Molecular Breeding: New Technique for Enhanced Biodegradation of Persistent Toxic Chemicals (1981)

The persistence of synthetic herbicides such as 2,4,5-trichlorophenoxyacetic acid (2,4,5-T) and its release in massive amounts as a herbicide (Agent Orange) have created toxicological problems in many countries. In nature, 2,4,5-T is slowly degraded by cooxidation and is not utilized as a sole source of carbon and energy. The technique of plasmid-assisted molecular breeding has led to the development of bacterial strains capable of totally degrading 2,4,5-T by using it as their sole source of carbon at high concentrations (greater than 1 mg/ml). Spectrophotometry and gas chromatography reveal various intermediates during growth of the culture with 2,4,5-T.