gebhart/patrepeval huggingface dataset:
Elimination of Glycerol Production in Anaerobic Cultures of a Saccharomyces cerevisiae Strain Engineered To Use Acetic Acid as an Electron Acceptor (2009)

In anaerobic cultures of wild-type Saccharomyces cerevisiae, glycerol production is essential to reoxidize NADH produced in biosynthetic processes. Consequently, glycerol is a major by-product during anaerobic production of ethanol by S. cerevisiae, the single largest fermentation process in industrial biotechnology. The present study investigates the possibility of completely eliminating glycerol production by engineering S. cerevisiae such that it can reoxidize NADH by the reduction of acetic acid to ethanol via NADH-dependent reactions. Acetic acid is available at significant amounts in lignocellulosic hydrolysates of agricultural residues. Consistent with earlier studies, deletion of the two genes encoding NAD-dependent glycerol-3-phosphate dehydrogenase (GPD1 and GPD2) led to elimination of glycerol production and an inability to grow anaerobically. However, when the E. coli mhpF gene, encoding the acetylating NAD-dependent acetaldehyde dehydrogenase (EC 1.2.1.10; acetaldehyde+NAD++coenzyme A<-->acetyl coenzyme A+NADH+H+), was expressed in the gpd1Delta gpd2Delta strain, anaerobic growth was restored by supplementation with 2.0 g liter(-1) acetic acid. The stoichiometry of acetate consumption and growth was consistent with the complete replacement of glycerol formation by acetate reduction to ethanol as the mechanism for NADH reoxidation. This study provides a proof of principle for the potential of this metabolic engineering strategy to improve ethanol yields, eliminate glycerol production, and partially convert acetate, which is a well-known inhibitor of yeast performance in lignocellulosic hydrolysates, to ethanol. Further research should address the kinetic aspects of acetate reduction and the effect of the elimination of glycerol production on cellular robustness (e.g., osmotolerance).
The Smart Box Concept for Ubiquitous Computing Environments (2003)

A family in Taiwan is reported to have Mal de Meleda with possibly autosomal recessive inheritance among 5 of its members. The glove- and sock-like erythrokeratosis and the hyperkeratotic plaques of the knees and elbows are the common features. Erythema of the nose, cheeks, and the perioral area in 4 affected members, actinic elastosis in 2 severely affected members, and partially impaired cell-mediated immunity in vitro in both affected and unaffected members are notable findings. Tigason (etretinate) treatment was beneficial in regard to hyperkeratinization, but not to erythema.
Staphylococcal Cell Wall: Morphogenesis and Fatal Variations in the Presence of Penicillin (1998)

The primary goal of this review is to provide a compilation of the complex architectural features of staphylococcal cell walls and of some of their unusual morphogenetic traits including the utilization of murosomes and two different mechanisms of cell separation. Knowledge of these electron microscopic findings may serve as a prerequisite for a better understanding of the sophisticated events which lead to penicillin-induced death. For more than 50 years there have been controversial disputes about the mechanisms by which penicillin kills bacteria. Many hypotheses have tried to explain this fatal event biochemically and mainly via bacteriolysis. However, indications that penicillin-induced death of staphylococci results from overall biochemical defects or from a fatal attack of bacterial cell walls by bacteriolytic murein hydrolases were not been found. Rather, penicillin, claimed to trigger the activity of murein hydrolases, impaired autolytic wall enzymes of staphylococci. Electron microscopic investigations have meanwhile shown that penicillin-mediated induction of seemingly minute cross wall mistakes is the very reason for this killing. Such "morphogenetic death" taking place at predictable cross wall sites and at a predictable time is based on the initiation of normal cell separations in those staphylococci in which the completion of cross walls had been prevented by local penicillin-mediated impairment of the distribution of newly synthesized peptidoglycan; this death occurs because the high internal pressure of the protoplast abruptly kills such cells via ejection of some cytoplasm during attempted cell separation. An analogous fatal onset of cell partition is considered to take place without involvement of a detectable quantity of autolytic wall enzymes ("mechanical cell separation"). The most prominent feature of penicillin, the disintegration of bacterial cells via bacteriolysis, is shown to represent only a postmortem process resulting from shrinkage of dead cells and perturbation of the cytoplasmic membrane. Several schematic drawings have been included in this review to facilitate an understanding of the complex morphogenetic events.
An allosteric modulator of metabotropic glutamate receptors (mGluR2), (+)‐TFMPIP, inhibits restraint stress‐induced phasic glutamate release in rat prefrontal cortex (2012)

The potential anxiolytic effects of a novel positive allosteric modulator (PAM) of the metabotropic glutamate receptor subgroup 2 (mGluR₂) were investigated using a self-referencing recording technique with enzyme-based microelectrode arrays (MEAs) that reliably measures tonic and phasic changes in extracellular glutamate levels in awake rats. Studies involved glutamate measures in the rat prefrontal cortex during subcutaneous injections of the following: vehicle, a mGluR₂/₃ agonist, LY354740 (10 mg/kg), or a mGluR₂ PAM, 1-Methyl-2-((cis-(R,R)-3-methyl-4-(4-trifluoromethoxy-2-fluoro)phenyl)piperidin-1-yl)methyl)-1H-imidazo[4,5-b]pyridine ((+)-TFMPIP; 1.0 or 17.8 mg/kg). Studies assessed changes in tonic glutamate levels and the glutamatergic responses to a 5-min restraint stress. Subcutaneous injection of (+)-TFMPIP at a dose of 1.0 mg/kg (day 3: -7.1 ± 15.1 net AUC; day 5: -24.8 ± 24.9 net AUC) and 17.8 mg/kg (day 3: -46.5 ± 33.0 net AUC; day 5: 34.6 ± 36.8 net AUC) significantly attenuated the stress-evoked glutamate release compared to vehicle controls (day 3: 134.7 ± 50.6 net AUC; day 5: 286.6 ± 104.5 net AUC), whereas the mGluR₂/₃ agonist LY354740 had no effect. None of the compounds significantly affected resting glutamate levels, which we have recently shown to be extensively derived from neurons. Taken together, these data support that systemic administration of (+)-TFMPIP produces phasic rather than tonic release of glutamate that may play a major role in the effects of stress on glutamate neuronal systems in the prefrontal cortex.
Rigid, Conjugated, Fluoresceinated Thymidine Triphosphates: Syntheses and Polymerase Mediated Incorporation into DNA Analogues (2003)

Abstract Syntheses of a unique set of energy transfer dye labeled nucleoside triphosphates, compounds 1 – 3 , are described. Attempts to prepare these compounds were only successful if the triphosphorylation reaction was performed before coupling the dye to the nucleobase, and not the other way around. Compounds were prepared as both the 2′‐deoxy ( a ) and 2′,3′‐dideoxy‐ ( b ) forms. They feature progressively longer rigid conjugated linkers connecting the nucleobase and the hydroxyxanthone moiety. UV spectra of the parent nucleosides 12 – 14 show that as the length of the linker increases so does the absorption of the donor in the 320–330 nm region, but with relatively little red‐shift of the maxima. Fluorescence spectra of the same compounds show that radiation in the 320–330 nm region results in predominant emission from the fluorescein. When the linker is irradiated at 320 nm, the only significant emission observed corresponds to the hydroxyxanthone part of the molecules at 520 nm; this corresponds to an effective Stokes' shift of 200 nm. As the absorption at 320–330 nm by the linker increases with length, so does the intensity of the fluorescein emission. A gel assay was used to gauge relative incorporation efficiencies of compounds 1 – 3 , dTTP, ddTTP, and 6‐TAMRA‐ddTTP. Throughout, the thermostable polymerase Taq FS was used, as it is the one most widely applied in high throughput DNA sequencing. This assay showed that only compounds 3 were incorporated efficiently; these have the longest linkers. Of these, the 2′‐deoxy nucleoside 3 a was incorporated and did not prevent the polymerase from extending the chain further. The 2′,3′‐dideoxy nucleoside 3 b was incorporated only about 430 times less efficiently than ddTTP under the same conditions, and caused chain termination. The implications of these studies on modified sequencing protocols are discussed.
Vertical Interference Testing Across a Low-Permeability Zone (1986)

Summary Bremer et al.1 described a mathematical model for analysis of a vertical interference test across a low-permeability zone. The test configuration called for recording wellbore pressure vs. time opposite one permeable layer while fluid is produced from the second permeable layer. The two permeable layers are separated by a tight zone of low vertical permeability. This paper offers a more general interpretation technique that allows for distinct properties in the two permeable layers and includes wellbore-storage and skin effects. The purpose of the vertical interference test across a low-permeability zone is to determine the vertical permeability of the tight zone separating the two permeable strata. The results of such a test may influence well completion decisions for primary, secondary, and enhanced oil recovery. Of particular interest is the estimation of the fluid flow rate into or out of the packed-off layer. Field test data have been analyzed with the new techniques. By including wellbore-storage and skin effects, the model presented in this study provides a much better fit with the data presented by Bremer et al.1 Because this method allows for determination of formation properties in both permeable zones, simultaneous recording of the pressures in both the producing and packed-off layers is recommended. Results indicate that the wellbore- pressure difference between the flowing and packed-off zones becomes constant after sufficient time and depends only on the permeabilities in the three zones. If wellbore-storage effects can be minimized, the behavior of pressure vs. log time may exhibit two distinct slopes: the first providing for calculation of the permeability in the flowing layer, and the second allowing calculation of the permeability in the packed-off layer. Type curves are presented for analysis of both the pressure and pressure-derivative transients. The interpretation method is suitable for broader application than previous methods would allow. An important result is an estimate of the rate of crossflow between layers separated by a low-permeability zone.
An Experiment on Prediction Markets in Science (2009)

Prediction markets are powerful forecasting tools. They have the potential to aggregate private information, to generate and disseminate a consensus among the market participants, and to provide incentives for information acquisition. These market functionalities can be very valuable for scientific research. Here, we report an experiment that examines the compatibility of prediction markets with the current practice of scientific publication. We investigated three settings. In the first setting, different pieces of information were disclosed to the public during the experiment. In the second setting, participants received private information. In the third setting, each piece of information was private at first, but was subsequently disclosed to the public. An automated, subsidizing market maker provided additional incentives for trading and mitigated liquidity problems. We find that the third setting combines the advantages of the first and second settings. Market performance was as good as in the setting with public information, and better than in the setting with private information. In contrast to the first setting, participants could benefit from information advantages. Thus the publication of information does not detract from the functionality of prediction markets. We conclude that for integrating prediction markets into the practice of scientific research it is of advantage to use subsidizing market makers, and to keep markets aligned with current publication practice.
Reliable navigation using landmarks (2002)

Building a truly reliable mobile robot system-one that can navigate without failures for long periods of time (weeks or months)-requires making clear assumptions bounding uncertainty and enforcing those assumptions by appropriately engineering the robot and its workspace. Weak assumptions may result in low-cost engineering but make the navigation problem intractable. On the other hand, strict assumptions may simplify navigation but reduce the flexibility of the resulting system. The work presented in this paper investigates the tradeoff between "computational complexity" and "physical complexity" and advocates landmarks as a way of managing this tradeoff. We first define a formal navigation problem which incorporates enough assumptions to make it computationally tractable. We then use landmarks to enforce those assumptions. By implementing this system on our mobile robot we show that the assumptions are enforceable, that the engineering costs of using landmarks are acceptable, and that the resulting navigation system is both efficient and robust.
An electrochemical deamidated gliadin antibody immunosensor for celiac disease clinical diagnosis (2013)

The first electrochemical immunosensor (EI) for the detection of antibodies against deamidated gliadin peptides (DGP) is described here. A disposable nanohybrid screen-printed carbon electrode modified with DGP was employed as the transducer's sensing surface. Real serum samples were successfully assayed and the results were corroborated with an ELISA kit. The presented EI is a promising analytical tool for celiac disease diagnosis.
Severe encephalopathy with brain atrophy and hypomyelination due to adenylosuccinate lyase deficiency--MRI, clinical, biochemical and neuropathological findings of Polish patients. (2009)

Adenylosuccinate lyase (ADSL) deficiency is an autosomal recessive disorder caused by mutation in the ADSL gene. The disease was identified in 1984 by Jaeken and van der Berghe as the first inborn defect of purine biosynthesis. Affected children revealed encephalopathy with epilepsy and marked psychomotor retardation. A neurological examination showed hypotonia, followed sometimes after years by spasticity. The diagnosis is based on detection in the urine and CSF succinyladenosine (S-Ado) and succinylaminoimidazole carboxamide ribotide (SAICAr). We present brain MR examinations of seven patients with ADSL deficiency in the correlation with their clinical findings. In all cases lack of myelination or of delayed myelination of cerebral white matter was seen. Additionally cerebral and cerebellar atrophy was observed. Neuropathological findings revealed damage of all cellular elements of brain tissue and are cause of observed MR changes. Hypo/dysmyelination seemed to be secondary to damage of oligodendroglia and axons of damaged neuronal cells.
Pharmacokinetics, safety, and efficacy of combination treatment with methotrexate and leflunomide in patients with active rheumatoid arthritis (1999)

The combination of methotrexate and leflunomide has therapeutic potential in RA.
(Trifluoromethyl)cyclopentadienide: a powerful electron-withdrawing ligand for transition-metal complexes (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXT(Trifluoromethyl)cyclopentadienide: a powerful electron-withdrawing ligand for transition-metal complexesPaul G. Gassman and Charles H. WinterCite this: J. Am. Chem. Soc. 1986, 108, 14, 4228–4229Publication Date (Print):July 1, 1986Publication History Published online1 May 2002Published inissue 1 July 1986https://pubs.acs.org/doi/10.1021/ja00274a065https://doi.org/10.1021/ja00274a065research-articleACS PublicationsRequest reuse permissionsArticle Views828Altmetric-Citations80LEARN 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
pAM401-Based Shuttle Vectors That Enable Overexpression of Promoterless Genes and One-Step Purification of Tag Fusion Proteins Directly from Enterococcus faecalis (2001)

Two novel Enterococcus faecalis-Escherichia coli shuttle vectors that utilize the promoter and ribosome binding site of bacA on the E. faecalis plasmid pPD1 were constructed. The vectors were named pMGS100 and pMGS101. pMGS100 was designed to overexpress cloned genes in E. coli and E. faecalis and encodes the bacA promoter followed by a cloning site and stop codon. pMGS101 was designed for the overexpression and purification of a cloned protein fused to a Strep-tag consisting of 9 amino acids at the carboxyl terminus. The Strep-tag provides the cloned protein with an affinity to immobilized streptavidin that facilitates protein purification. We cloned a promoterless beta-galactosidase gene from E. coli and cloned the traA gene of the E. faecalis plasmid pAD1 into the vectors to test gene expression and protein purification, respectively. beta-Galactosidase was expressed in E. coli and E. faecalis at levels of 10(3) and 10 Miller units, respectively. By cloning the pAD1 traA into pMGS101, the protein could be purified directly from a crude lysate of E. faecalis or E. coli with an immobilized streptavidin matrix by one-step affinity chromatography. The ability of TraA to bind DNA was demonstrated by the DNA-associated protein tag affinity chromatography method using lysates prepared from both E. coli and E. faecalis that overexpress TraA. The results demonstrated the usefulness of the vectors for the overexpression and cis/trans analysis of regulatory genes, purification and copurification of proteins from E. faecalis, DNA binding analysis, determination of translation initiation site, and other applications that require proteins purified from E. faecalis.
Interaction of alpha-actinin with the cadherin/catenin cell-cell adhesion complex via alpha-catenin. (1995)

Cadherins are Ca(2+)-dependent, cell surface glycoproteins involved in cell-cell adhesion. Extracellularly, transmembrane cadherins such as E-, P-, and N-cadherin self-associate, while intracellularly they interact indirectly with the actin-based cytoskeleton. Several intracellular proteins termed catenins, including alpha-catenin, beta-catenin, and plakoglobin, are tightly associated with these cadherins and serve to link them to the cytoskeleton. Here, we present evidence that in fibroblasts alpha-actinin, but not vinculin, colocalizes extensively with the N-cadherin/catenin complex. This is in contrast to epithelial cells where both cytoskeletal proteins colocalize extensively with E-cadherin and catenins. We further show that alpha-actinin, but not vinculin, coimmunoprecipitates specifically with alpha- and beta-catenin from N- and E-cadherin-expressing cells, but only if alpha-catenin is present. Moreover, we show that alpha-actinin coimmunoprecipitates with the N-cadherin/catenin complex in an actin-independent manner. We therefore propose that cadherin/catenin complexes are linked to the actin cytoskeleton via a direct association between alpha-actinin and alpha-catenin.
Use of microarray hybrid capture and next-generation sequencing to identify the anatomy of a transgene (2013)

Transgenic animals are extensively used to model human disease. Typically, the transgene copy number is estimated, but the exact integration site and configuration of the foreign DNA remains uncharacterized. When transgenes have been closely examined, some unexpected configurations have been found. Here, we describe a method to recover transgene insertion sites and assess structural rearrangements of host and transgene DNA using microarray hybridization and targeted sequence capture. We used information about the transgene insertion site to develop a polymerase chain reaction genotyping assay to distinguish heterozygous from homozygous transgenic animals. Although we worked with a bacterial artificial chromosome transgenic mouse line, this method can be used to analyse the integration site and configuration of any foreign DNA in a sequenced genome.
Unscheduled activation of cyclin B1/Cdc2 kinase in human promyelocytic leukemia cell line HL60 cells undergoing apoptosis induced by DNA damage. (1995)

We have studied changes in cyclin A- and B1-dependent kinases during apoptosis induced in human promyelocytic leukemia (HL60) cells treated with the topoisomerase I inhibitor camptothecin. We found that cyclin B1/Cdc2 kinase activity transiently increases within 30 min after camptothecin treatment. This increase is followed by a rapid inactivation of the cyclin B1/Cdc2 kinase that is associated with Cdc2 tyrosine phosphorylation without any change in Cdc2 or cyclin B1 protein levels. The DNA polymerase inhibitor aphidicolin abrogates camptothecin-induced changes in cyclin B1/Cdc2 kinase activity, indicating that DNA replication-induced DNA damage is essential for both Cdc2 alterations and apoptosis activation. Apoptosis and the initial cyclin B1/Cdc2 kinase activation were amplified using synchronized S-phase cells, and cyclin A/cdk2 kinase did not change under these conditions. The same transient activation and subsequent inactivation of cyclin B1/Cdc2 kinase were observed after DNA damage by etoposide or bis-(2-chloroethyl)methylamine hydrochloride. These observations suggest that DNA damage promotes the transient and unscheduled stimulation of cyclin B1/Cdc2 kinase activity in HL60 cells prior to apoptosis.
Molecular aspects of rheumatoid arthritis: role of transcription factors (2008)

Rheumatoid arthritis is a multifactorial disease characterized by chronic inflammation of the joints. Both genetic and environmental factors are involved in the pathogenesis leading to joint destruction and ultimately disability. In the inflamed RA joint the synovium is highly infiltrated by CD4+ T cells, B cells and macrophages, and the intimal lining becomes hyperplastic owing to the increased number of macrophage-like and fibroblast-like synoviocytes. This hyperplastic intimal synovial lining forms an aggressive front, called pannus, which invades cartilage and bone structures, leading to the destruction and compromised function of affected joints. This process is mediated by a number of cytokines (tumor necrosis factor-alpha, interleukin-1, interleukin-6, interleukin-17 interferon-gamma, etc.), chemokines (monocyte chemoattractant protein-1, monocyte chemoattractant protein-4 CCL18, etc.), cell adhesion molecules (intercellular adhesion molecule-1, vascular cell adhesion molecule-1, etc.) and matrix metalloproteinases. Expression of these molecules is controlled at the transcription level and activation of a limited number of transcription factors is involved in this process.