gebhart/patrepeval huggingface dataset:
Bacterial inactivation by using near- and supercritical carbon dioxide (1999)

The three most common methods of sterilization in use today are ethylene oxide exposure, gamma-irradiation, and steam sterilization. Each of these methods has serious limitations for the sterilization of some materials used in medicine, especially thermally and hydrolytically sensitive polymers by themselves and in combination with proteins. In this work, we demonstrate a potential new method of sterilization by using supercritical fluid carbon dioxide. Using this method we achieve complete inactivation of a wide variety of bacterial organisms at moderate temperatures and in the absence of organic solvents or irradiation. Sterilization is a function of both the proximity to the fluid's critical point and the chemical nature of the fluid itself. When biodegradable polymers poly(lactic-co-glycolic) acid and polylactic acid were included in the sterilization process, there was no effect on the inactivation efficiency, yet no physical or chemical damage to these thermally and hydrolytically labile materials was observed.
Structure, assembly and regulation of expression of capsules in Escherichia coli (1999)

Many Escherichia coli strains are covered in a layer of surface-associated polysaccharide called the capsule. Capsular polysaccharides represent a major surface antigen, the K antigen, and more than 80 distinct K serotypes result from structural diversity in these polymers. However, not all capsules consist of K antigen. Some are due to production of an extensive layer of a polymer structurally identical to a lipopolysaccharide O antigen, but distinguished from lipopolysaccharide by the absence of terminal lipid A-core. Recent research has provided insight into the manner in which capsules are organized on the Gram-negative cell surface, the pathways used for their assembly, and the regulatory processes used to control their expression. A limited repertoire of capsule expression systems are available, despite the fact that the producing bacteria occupy a variety of ecological niches and possess diverse physiologies. All of the known capsule assembly systems seen in Gram-negative bacteria are represented in E. coli, as are the majority of the regulatory strategies. Escherichia coli therefore provides a variety of working models on which studies in other bacteria are (or can be) based. In this review, we present an overview of the current molecular and biochemical models for capsule expression in E. coli. By taking into account the organization of capsule gene clusters, details of the assembly pathway, and regulatory features that dictate capsule expression, we provide a new classification system that separates the known capsules of E. coli into four distinct groups.
Micrometer-Sized Sodium Ion-Selective Optodes Based on a “Tailed” Neutral Ionophore (1999)

The preparation and response features of a micrometer-sized sodium ion-selective fiber optode based on a liquid membrane were described. The sensing membrane is a plasticized poly(vinyl chloride)-based copolymer with a neutral sodium ionophore and an anionic dye. To fabricate a micrometer-sized fiber optode, a “micropipet fabrication method” was proposed to fix a liquid membrane-based optode on the small tip of an optical fiber probe, in which the optode size can be varied from ∼1 μm to more than 10 μm. Our first optode incorporated a 16-crown-5 derivative as the neutral sodium ionophore and a dibromofluorescein derivative as the single-emission anionic dye. The sensor response was monitored by measuring the fluorescence intensity under a time-resolved photon-counting method. At the first stage of the investigation, it was found that the ionophore including a sodium ion in its cavity leached from the membrane phase. However, we have discovered that the problem can be resolved by using a “tailed” ionophore, which is an ionophore possessing a lipophilic long alkyl chain. The “tail” of the ionophore functions as an “anchor” that prevents leaching of the ionophore from the membrane phase into the water phase. The anchor effect of the tailed ionophore was clearly demonstrated with 6-μm-sized sodium ion-selective optodes. Using a 3-μm-sized optode, the sensor response was examined and successfully explained by the response theory. The size limitation of the optode was also examined using the response features of a 1.5-μm-sized fiber optode. The second optode incorporated a tailed 16-crown-5 derivative as the neutral sodium ionophore and a coumarin derivative as the dual-emission anionic dye. The second optode is more practical than the first optode because the problem of fluorescence distortion due to photobleaching and solvent effect is resolved by ratiometric calibration where the sensor response is monitored by the spectral shift of the dual-emission fluorescence. The sensor response of an 8-μm-sized fiber optode having ratiometric calibration was examined and successfully explained by the response theory.
Isopentenyl diphosphate biosynthesis via a mevalonate-independent pathway: Isopentenyl monophosphate kinase catalyzes the terminal enzymatic step (1999)

In plants, the biosynthesis of isopentenyl diphosphate, the central precursor of all isoprenoids, proceeds via two separate pathways. The cytosolic compartment harbors the mevalonate pathway, whereas the newly discovered deoxyxylulose 5-phosphate pathway, which also operates in certain eubacteria, including Escherichia coli, is localized to plastids. Only the first two steps of the plastidial pathway, which involve the condensation of pyruvate and glyceraldehyde 3-phosphate to deoxyxylulose 5-phosphate followed by intramolecular rearrangement and reduction to 2-C-methylerythritol 4-phosphate, have been established. Here we report the cloning from peppermint (Mentha x piperita) and E. coli, and expression, of a kinase that catalyzes the phosphorylation of isopentenyl monophosphate as the last step of this biosynthetic sequence to isopentenyl diphosphate. The plant gene defines an ORF of 1,218 bp that, when the proposed plastidial targeting sequence is excluded, corresponds to approximately 308 aa with a mature size of approximately 33 kDa. The E. coli gene (ychB), which is located at 27.2 min of the chromosomal map, consists of 852 nt, encoding a deduced enzyme of 283 aa with a size of 31 kDa. These enzymes represent a conserved class of the GHMP family of kinases, which includes galactokinase, homoserine kinase, mevalonate kinase, and phosphomevalonate kinase, with homologues in plants and several eubacteria. Besides the preferred substrate isopentenyl monophosphate, the recombinant peppermint and E. coli kinases also phosphorylate isopentenol, and, much less efficiently, dimethylallyl alcohol, but dimethylallyl monophosphate does not serve as a substrate. Incubation of secretory cells isolated from peppermint glandular trichomes with isopentenyl monophosphate resulted in the rapid production of monoterpenes and sesquiterpenes, confirming that isopentenyl monophosphate is the physiologically relevant, terminal intermediate of the deoxyxylulose 5-phosphate pathway.
<title>3D image guidance in radiotherapy: a feasibility study</title> (2001)

Currently, one major research field in radiotheraphy is focused on patient setup verification and on detection of organ motion and deformation. A phantom study is performed to demonstrate the feasibility of image guidance in radiotherapy. Patient setup errors are simulated with a humanoid phantom, which is imaged using a linear accelerator and a therapy simulator to address megavoltage and kilovoltage (kV) computed tomography (CT), respectively. Projections are recorded by a flat panel imager. The various data sets of the humanoid phantom are compared by mutual information matching. The CT investigations show that the spatial resolution is better than 1.6 mm for high contrast objects. The uncertainties remaining after mutual information matching are found to be less than 1 mm for translations and 1 degree(s) for rotations. The phantom study indicates that the detection of patient setup errors as well as organ motion or deformation is possible with a high accuracy, especially if a kV X-ray tube could be attached to the linear accelerator. The presented method allows sophisticated quality assurance of beam delivery in each fraction and may even enable the use of new concepts of adaptive radiotherapy.
Virtual 2-D Gel Electrophoresis:  Visualization and Analysis of the E. coli Proteome by Mass Spectrometry (2001)

Mass spectrometric surface analysis of isoelectric focusing gels provides an ultrasensitive approach to proteome analysis. This "virtual 2-D gel" approach, in which mass spectrometry is substituted for the size-based separation of SDS-PAGE, provides advantages in mass resolution and accuracy over classical 2-D gels and can be readily automated. Protein identities can be postulated from molecular mass (+/-0.1-0.2% for proteins of <50 kDa in size) and pI (+/-0.3 pH unit) and confirmed by MALDI in-source decay of the intact protein (providing sequence spanning up to 43 residues) or by peptide mass mapping following gel-wide chemical cleavage. Additionally, posttranslational modifications such as fatty acid acylation can be detected by the mass-resolved heterogeneity of component hydrocarbon chains. Sensitivity was evaluated by comparing the number of proteins detected by this method to equivalently loaded silver-stained 2-D gels. In the 5.7-6.0 pH range, E. coli is predicted to contain 435 proteins; virtual 2-D gels found 250 proteins ranging from >2 to <120 kDa in size present at levels to tens of femtomoles, as compared to the 100 proteins found by silver-staining 2-D gels. Extrapolating this result to the total theoretical proteome suggests that this technology is capable of detecting over 2500 E. coli proteins.
The rational use of methotrexate in rheumatoid arthritis and other rheumatic diseases (1997)

Methotrexate's mechanism of action affects both the inflammatory and immunosuppressive aspects of response. Its kinetics are defined and include variable absorption, intracellular metabolism, and both renal and biliary excretion. Methotrexate is clearly effective in the treatment of rheumatoid arthritis and may be able to decrease the rate of formation of new bony erosions. It is also effective in psoriatic arthritis and is being used in a multiplicity of other rheumatic diseases. The most common toxicities ascribed to methotrexate are gastrointestinal (e.g. stomatitis) and central nervous system (e.g. headache, fatigue, malaise). Methotrexate-induced hepatic cirrhosis is less common in rheumatoid arthritis than previously thought, although its occurrence in psoriasis is probably higher than in rheumatoid arthritis. Haematological, renal and pulmonary toxicity occur, but are rare, while teratogenicity is well documented. A new and disturbing adverse event, pseudolymphomas are being reported at present.
‘The Right Answer’ (1999)

When men have looked to philosophy for wisdom, or when they have sought it in the works of great philosophers, what is it that they have been seeking?
Hydrolyzation oxidation of AlxGa1−xAs-AlAs-GaAs quantum well heterostructures and superlattices (1990)

Data are presented on the conversion (selective conversion) of high-composition (AlAs)x(GaAs)1−x layers, e.g., in AlxGa1−xAs-AlAs-GaAs quantum well heterostructures and superlattices (SLs), into dense transparent native oxide by reaction with H2O vapor (N2 carrier gas) at elevated temperatures (400 °C). Hydrolyzation oxidation of a fine-scale AlAs(LB)-GaAs(Lz) SL (LB +Lz≲100 Å), or random alloy AlxGa1−xAs (x≳0.7), is observed to proceed more slowly and uniformly than a coarse-scale ‘‘alloy’’ such as an AlAs-GaAs superlattice with LB + Lz≳200 Å.
Mouse Retinoid X Receptor Contains a Separable Ligand-Binding and Transactivation Domain in Its E Region (1995)

Steroid, thyroid, and retinoid hormones exert their biological functions by interacting with their cognate nuclear receptors. Upon binding receptors, hormones induce a protease-resistant structural change in the receptor ligand-binding domain and subsequently activate the receptors. Utilizing partial proteolysis, we have been able to delineate a region in the mouse retinoid X receptor beta (mRXR beta) required for ligand binding. A separable activation domain within the mRXR beta E region has been identified. The activation domain, which is 21 amino acids in length, is located at the extreme C terminus of mRXR beta. This domain is not required for ligand binding since removal of this sequence neither eliminates the ligand-induced, protease-resistant conformational change nor alters the ligand-enhanced DNA binding. Furthermore, deletion of this activation domain converts the receptor into a transcriptional silencer. Finally, a further truncation of 9 amino acids (for a total of 30 amino acids) from the C terminus results in a mutant which does not undergo the protease-resistant conformational change and cannot bind DNA as a homodimer. Nevertheless, this mutant is still able to form a heterodimer with the thyroid hormone receptor. Therefore, homodimerization and heterodimerization can be distinguished by this nine-amino-acid sequence.
Lipoprotein synthesis in mycobacteria (2007)

Lipoproteins are a functionally diverse class of secreted bacterial proteins characterized by an N-terminal lipid moiety. The lipid moiety serves to anchor these proteins to the cell surface. Lipoproteins are synthesized as pre-prolipoproteins and mature by post-translational modifications. The post-translational modifications are directed by the lipobox motif located within the signal peptide. Enzymes involved in lipoprotein synthesis are essential in Gram-negative bacteria but not in Gram-positive bacteria. Inactivation of genes involved in lipoprotein synthesis attenuates a variety of Gram-positive pathogens, including Mycobacterium tuberculosis. The attenuated phenotype of these mutants indicates an important role of lipoproteins and lipoprotein synthesis in bacterial virulence. M. tuberculosis, the causative agent of tuberculosis, is one of the most devastating pathogens in the world. This article reviews recent findings on the synthesis, localization and function of lipoproteins in mycobacteria.
Domain decomposition methods for the rapid electromagnetic simulation of photomask scattering (2002)

An integrated methodology has been developed for computer simulation of electromagnetic scattering from large, nonperiodic, two-dimensional layouts of advanced photomasks (masks with optical proximity correction and phase-shifting masks). The domain decomposition method consists of three steps: First, by virtue of the linearity of the Kirchhoff-Fresnel diffraction integral, the mask layout is decomposed into a set of constituent single-opening masks. Second, the rigorous electromagnetic simulation of each three-dimensional structure from the set of these single-opening masks is circumvented and, instead, the result for the scattered field is synthesized based on two two-dimensional rigorous electromagnetic simulations that model the mask geometry in two cross-sectional planes. Subsequently, compact equivalent source models are used to describe the scattered fields on a reference plane. These models are constructed in such a way as to minimize the error in the part of the diffraction spectrum that passes through the projection system, allowing accurate and efficient image simulation. The normalized mean square error of the near scattered field is typically a fraction of 1% and speed-up factors for the total simulation time in excess of 400 (compared with the rigorous mask model) are achieved. The use of a look-up table approach facilitates orders of magnitude of further speed improvement.
Biomechanics of the posterior lumbar articulating elements (2007)

The clinical success of lumbar spinal fusion varies considerably, depending on techniques and indications. Although spinal fusion generally helps to eliminate certain types of pain, it may also decrease function by limiting patient mobility. Furthermore, spinal fusion may increase stresses on adjacent nonfused motion segments, accelerating the natural degeneration process at adjacent discs. Additionally, pseudarthrosis, that is, incomplete or ineffective fusion, may result in an absence of pain relief. Finally, the recuperation time after a fusion procedure can be lengthy. The era of disc replacement is in its third decade, and this procedure has demonstrated promise in relieving back pain through preservation of motion. Total joint replacement with facet arthroplasty of the lumbar spine is a new concept in the field of spinal surgery. The devices used are intended to replace either the entire functional spinal unit (FSU) or just the facets. These devices provide dynamic stabilization for the functional spinal segment as an adjunct to disc replacement or laminectomy and facetectomy performed for neural decompression. The major role of facet replacement is to augment the instabilities created by the surgical decompression or to address chronic instability. Additionally, facet joint replacement devices can be used to replace the painful facet joints, restore stability, and/or to salvage a failed disc or nucleus prosthesis without losing motion. In this paper the authors review and discuss the role of the lumbar facet joints as part of the three-joint complex and discuss their role in intersegmental motion load transfer and multidirectional flexibility in a lumbar FSU.
Potentiation of radiation effects on two murine tumors by lonidamine. (1986)

Lonidamine is a potent inhibitor of spermatogenesis and a hyperthermic sensitizer. The principal established locus of biochemical action of lonidamine is a selective inhibitory effect of the energy metabolism either in NAD-linked reactions in germ cell mitochondria, as well as the glycolytic metabolism of a variety of tumor cell lines by means of inhibition of mitochondrially bound hexokinase. We carried out in vivo tumor experiments to determine whether lonidamine when combined with radiation could potentiate the cytotoxic effects of radiation on two murine tumors. The combined effects of single acute lonidamine (100 mg/kg) and single dose X-irradiation were evaluated on the transplanted methylcholanthrene-induced fibrosarcoma in BALB/c mice and on the radiation-induced fibrosarcoma in C3H/He mice. The radiosensitizing effect by lonidamine was maximal when lonidamine was administered immediately prior to or after X-irradiation. The dose modifying factor of lonidamine is estimated to be 1.36 for methylcholanthrene-induced fibrosarcoma tumors and 1.25 for radiation-induced fibrosarcoma tumors. There was no disproportionately enhanced skin reaction following the combined treatments. The present results of the potentiating effects of radiation may be attributed, in part, to the findings of cell culture studies that lonidamine is a potent inhibitor of repair of potentially lethal damage.
Nucleoside analogues : chemistry, biology, and medical applications (1979)

Nucleotide Conformations: Rules and Exceptions.- Nuclear Magnetic Resonance Studies of Nucleoside Conformational Properties.- Methods of Nucleoside Synthesis.- Chemical Transformations of the Sugar Moiety of Nucleosides.- Chemistry of Naturally Occurring Pyrimidine Nucleosides and Analogues.- Chemistry of the Heterocyclic Moiety of Purine Nucleosides and Some Closely Related Analogues.- The Mechanisms of Inhibition of Cellular and Viral Multiplication by Aranucleosides and Aranucleotides.- Uptake and Metabolism of Purine Nucleosides and Purine Nucleoside Analogues by Cells.- Basis for the Selective Antiviral and Antitumour Activity of Pyrimidine Nucleoside Analogues.- Development of Antiherpes Virus Agents on the Basis of Virus Induced Enzymes.- Test Systems for Evaluating the Antiviral Activity of Nucleoside Analogues.- Test Systems for Evaluating the Antitumour Activity of Nucleoside Analogues.- Success of Antiviral Therapy Involves Cooperative Immune Responses.- The Clinical Uses of Nucleoside Analogues in Malignant Disease.- Industrial Development of New Drugs.- Participants.
Purinergic Receptor Inhibition Prevents the Development of Smoke-Induced Lung Injury and Emphysema (2010)

Extracellular ATP acts as a "danger signal" and can induce inflammation by binding to purinergic receptors. Chronic obstructive pulmonary disease is one of the most common inflammatory diseases associated with cigarette smoke inhalation, but the underlying mechanisms are incompletely understood. In this study, we show that endogenous pulmonary ATP levels are increased in a mouse model of smoke-induced acute lung inflammation and emphysema. ATP neutralization or nonspecific P2R-blockade markedly reduced smoke-induced lung inflammation and emphysema. We detected an upregulation the purinergic receptors subtypes on neutrophils (e.g., P2Y2R), macrophages, and lung tissue from animals with smoke-induced lung inflammation. By using P2Y(2)R deficient ((-/-)) animals, we show that ATP induces the recruitment of blood neutrophils to the lungs via P2Y(2)R. Moreover, P2Y(2)R deficient animals had a reduced pulmonary inflammation following acute smoke-exposure. A series of experiments with P2Y(2)R(-/-) and wild type chimera animals revealed that P2Y(2)R expression on hematopoietic cell plays the pivotal role in the observed effect. We demonstrate, for the first time, that endogenous ATP contributes to smoke-induced lung inflammation and then development of emphysema via activation of the purinergic receptor subtypes, such as P2Y(2)R.
Adsorbed block copolymer of poly(2-vinylpyridine) and polystyrene studied by neutron reflectivity and surface force techniques (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAdsorbed block copolymer of poly(2-vinylpyridine) and polystyrene studied by neutron reflectivity and surface force techniquesTerence Cosgrove, John S. Phipps, Robert M. Richardson, Michael L. Hair, and David A. GuzonasCite this: Macromolecules 1993, 26, 16, 4363–4367Publication Date (Print):August 1, 1993Publication History Published online1 May 2002Published inissue 1 August 1993https://pubs.acs.org/doi/10.1021/ma00068a045https://doi.org/10.1021/ma00068a045research-articleACS PublicationsRequest reuse permissionsArticle Views139Altmetric-Citations17LEARN 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