gebhart/patrepeval huggingface dataset:
Kinetics of deposition of colloidal particles in porous media (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTKinetics of deposition of colloidal particles in porous mediaMenachem Elimelech and Charles R. O'MeliaCite this: Environ. Sci. Technol. 1990, 24, 10, 1528–1536Publication Date (Print):October 1, 1990Publication History Published online1 May 2002Published inissue 1 October 1990https://pubs.acs.org/doi/10.1021/es00080a012https://doi.org/10.1021/es00080a012research-articleACS PublicationsRequest reuse permissionsArticle Views2217Altmetric-Citations441LEARN 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
Role of Methionine 184 of Human Immunodeficiency Virus Type-1 Reverse Transcriptase in the Polymerase Function and Fidelity of DNA Synthesis (1996)

Methionine 184 of HIV-1 RT is a constituent of the catalytically crucial and highly conserved YXDD motif in the reverse transcriptase class of enzymes. We investigated the role of this residue by substituting it with Ala and Val by site-directed mutagenesis followed by extensive characterization of the two mutant enzymes. The kinetic parameters governing DNA synthesis directed by RNA and DNA templates indicated that both M184A and M184V mutants are catalytically as efficient as the wild type enzyme. Photoaffinity labeling of both the mutant and the wild type enzyme exhibited an identical affinity for RNA-DNA and DNA-DNA template primers. We further demonstrate that M-->V substitution at 184 position significantly increases the fidelity of DNA synthesis while M-->A substitution results in a highly error-prone enzyme without having compromised its efficiency of DNA synthesis. The M184V mutant exhibited a 25-45-fold increase in mismatch selectivity (ratio of k(cat)/K(m) of correct versus incorrect nucleotides) as compared to the WT enzyme. This pattern of error-prone synthesis is also confirmed by examining the abilities of the enzyme-(template-primer) covalent complexes to incorporate correct versus incorrect nucleotide onto the immobilized template-primer. The nature of error-prone synthesis by the M184A mutant shows an increase in both the mismatch synthesis and extension of the mismatched primer termini. Using a three-dimensional molecular model of the ternary complex of HIV-1 RT, template-primer, and dNTP, we observe that the strategic location of M184 may allow it to interact with the sugar moiety of either the primer nucleotide or the dNTP substrate.
Ultra high speed optical transmission using subcarrier-multiplexed four-dimensional LDPC-coded modulation (2010)

We propose a subcarrier-multiplexed four-dimensional LDPC bit-interleaved coded modulation scheme that is capable of achieving beyond 480 Gb/s single-channel transmission rate over optical channels. Subcarrier-multiplexed four-dimensional LDPC coded modulation scheme outperforms the corresponding dual polarization schemes by up to 4.6 dB in OSNR at BER 10(-8).
Towards Understandable Explanations for Document Analysis Systems (2012)

smartFIX is a product portfolio for knowledge based extraction of data from any document format. The system automatically determines the document type and extracts all relevant data for the respective business process. Data that is unreliably recognized is forwarded to a verification workplace for manual checking. In general, users have no difficulties to interpret the document data and wonder why the system needs additional input. For that reason, we implemented an explanation component that is used to justify extraction results, thus, increasing confidence of users. The component is using a semantic log making it possible to provide understandable explanations. We illustrate the benefits of that kind of technology in contrast to the current smartFIX Log Viewer by means of a preliminary user experiment.
ChemInform Abstract: In situ Neutralization in Boc‐Chemistry ‐ Solid Phase Peptide Synthesis. (1993)

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.
Patient-Specific Embryonic Stem Cells Derived from Human SCNT Blastocysts (2005)

Patient-specific, immune-matched human embryonic stem cells (hESCs) are anticipated to be of great biomedical importance for studies of disease and development and to advance clinical deliberations regarding stem cell transplantation. Eleven hESC lines were established by somatic cell nuclear transfer (SCNT) of skin cells from patients with disease or injury into donated oocytes. These lines, nuclear transfer (NT)-hESCs, grown on human feeders from the same NT donor or from genetically unrelated individuals, were established at high rates, regardless of NT donor sex or age. NT-hESCs were pluripotent, chromosomally normal, and matched the NT patient's DNA. The major histocompatibility complex identity of each NT-hESC when compared to the patient's own showed immunological compatibility, which is important for eventual transplantation. With the generation of these NT-hESCs, evaluations of genetic and epigenetic stability can be made. Additional work remains to be done regarding the development of reliable directed differentiation and the elimination of remaining animal components. Before clinical use of these cells can occur, preclinical evidence is required to prove that transplantation of differentiated NT-hESCs can be safe, effective, and tolerated.
Loss of Bcl-2 During the Senescence Exacerbates the Impaired Angiogenic Functions in Endothelial Cells by Deteriorating the Mitochondrial Redox State (2011)

Ageing is an important risk factor for ischemic cardiovascular diseases, although its underlying molecular mechanisms remain to be elucidated. Here, we report a crucial role of Bcl-2 in the impaired angiogenic functions in senescent endothelial cells (ECs) by modulating the mitochondrial redox state. Cellular senescence impaired angiogenic functions in ECs without attenuating the mitogen-activated protein kinase or Akt signaling, and vascular endothelial growth factor receptor 2 or Tie-2 expressions. We identified that Bcl-2 expression was markedly reduced in 3 independent models for senescent ECs, and pharmacological inhibition, as well as small interfering RNA-mediated gene silencing of Bcl-2, significantly impaired the angiogenic functions in young ECs. Bcl-2 has an antioxidative role by locating the glutathione at mitochondria, and we found that mitochondrial oxidative stress was significantly augmented in senescent ECs, in association with reduced mitochondria-associated glutathione. Transfection of Bcl-2 in senescent ECs significantly reduced the mitochondrial oxidative stress, restored the mitochondrial membrane potential, and improved the angiogenic capacity. Furthermore, gene transfer of Bcl-2 using adenovirus significantly improved the in vivo angiogenesis in the Matrigel plugs implanted into aged mice, whereas the Bcl-2 inhibitor reduced the angiogenesis in the Matrigel plugs implanted into young mice. Together, Bcl-2 plays a crucial role in the regulation of the mitochondrial redox state in ECs, and, thus, loss of Bcl-2 during the senescence exacerbates the impaired angiogenesis by augmenting the mitochondrial oxidative stress.
Biodegradation of aromatic carboxylic acids by Pseudomonas mira (1993)

Biodegradation of aromatic acids (ferulic, vanillic and sipapinic acids) by the soil bacterium Pseudomonas mira was studied by high-pressure liquid chromatography. The presence of glucose in the culture medium slowed down the degradation process but did not affect its mechanism. In addition to vanillic acid and hydroquinone, the products of degradation were found to include acetophenone derivatives. Probably, a mechanism capable of shortening the side chain by spontaneous decarboxylation of unstable 3-keto-3-phenylpropionic acid was present, in addition to the elimination of acetic acid via degradation of the cinnamic acid-type compounds.
Overexpression of a bacterial 1-deoxy-D-xylulose 5-phosphate synthase gene in potato tubers perturbs the isoprenoid metabolic network: implications for the control of the tuber life cycle (2006)

Potato tubers were engineered to express a bacterial gene encoding 1-deoxy-D-xylulose 5-phosphate synthase (DXS) in order to investigate the effects of perturbation of isoprenoid biosynthesis. Twenty-four independent transgenic lines out of 38 generated produced tubers with significantly elongated shape that also exhibited an early tuber sprouting phenotype. Expression analysis of nine transgenic lines (four exhibiting the phenotype and five showing a wild-type phenotype) demonstrated that the phenotype was strongly associated with dxs expression. At harvest, apical bud growth had already commenced in dxs-expressing tubers whereas in control lines no bud growth was evident until dormancy was released after 56-70 d of storage. The initial phase of bud growth in dxs tubers was followed by a lag period of approximately 56 d, before further elongation of the developing sprouts could be detected. Thus dxs expression results in the separation of distinct phases in the dormancy and sprouting processes. In order to account for the sprouting phenotype, the levels of plastid-derived isoprenoid growth regulators were measured in transgenic and control tubers. The major difference measured was an increase in the level of trans-zeatin riboside in tubers at harvest expressing dxs. Additionally, compared with controls, in some dxs-expressing lines, tuber carotenoid content increased approximately 2-fold, with most of the increase accounted for by a 6-7-fold increase in phytoene.
A Novel Putrescine Utilization Pathway Involves γ-Glutamylated Intermediates of Escherichia coli K-12 (2004)

A novel bacterial putrescine utilization pathway was discovered. Seven genes, the functions of whose products were not known, are involved in this novel pathway. Five of them encode enzymes that catabolize putrescine; one encodes a putrescine importer, and the other encodes a transcriptional regulator. This novel pathway involves six sequential steps as follows: 1) import of putrescine; 2) ATP-dependent gamma-glutamylation of putrescine; 3) oxidization of gamma-glutamylputrescine; 4) dehydrogenation of gamma-glutamyl-gamma-aminobutyraldehyde; 5) hydrolysis of the gamma-glutamyl linkage of gamma-glutamyl-gamma-aminobutyrate; and 6) transamination of gamma-aminobutyrate to form the final product of this pathway, succinate semialdehyde, which is the precursor of succinate.
Duplex Stability of Oligonucleotides Containing 7-Substituted 7-Deaza- and 8-Aza-7-Deazapurine Nucleosides (1997)

Abstract The synthesis of 7-substituted 7-deaza- and 8-aza-7-deazapurine 2′-deoxyribonucleosides, their incorporation into oligonucleotides, and the stability of corresponding duplexes is described.
Nanobodies in therapeutic applications. (2007)

Over the years, many antibodies have been successfully generated to treat patients with life-threatening diseases, most notably cancer. While the first generation of antibodies, originating from mice, caused severe side effects and were relatively inefficient, technological advances have made it possible to obtain fully human antibodies for therapeutic use. 'Heavy-chain only' antibodies have recently been discovered in the blood of camelids. Because of their size, the antigen-binding units of these antibodies comprising only a single Ig fold are called Nanobodies. These antibody fragments have several remarkable features that make them ideal candidates as next-generation cancer therapeutics. Particularly appealing is their ability to simultaneously inhibit various crucial growth factor receptors or their ligands with a single molecule. In addition, they are easy to clone and express on the tip of filamentous phage, which opens the possibility to select for Nanobodies inducing particular biological effects. Nanobodies have potential to become important cancer therapeutics in the near future, displaying unequalled and unprecedented efficacies in treatment.
Products of enzymatic reduction of benzoyl‐CoA, a key reaction in anaerobic aromatic metabolism (1993)

Benzoyl-coenzyme A is the most common central intermediate of anaerobic aromatic metabolism. Studies with whole cells of different bacteria and in vitro had shown that benzoyl-CoA is reduced to alicyclic compounds, possibly via cyclohexadiene intermediates. This reaction is considered a 'biological Birch reduction'. We have elucidated by NMR techniques the structures of six products of [ring-13C6]benzoate reduction. The reaction is catalyzed by extracts from cells of a denitrifying Pseudomonas strain K172 anaerobically grown with benzoate and nitrate as sole carbon and energy sources. The assay mixture contained [ring-13C6]benzoate plus traces of [U-14C]benzoate, Mg2+, ATP, coenzyme A (CoA), and Ti(III) as reductant. The use of the multiply 13C-labelled precursor increases the sensitivity of NMR detection and allows the analysis of crude product mixtures by two-dimensional coherence transfer procedures such as total correlation 13C-NMR spectroscopy and 13C-filtered 1H-NMR spectroscopy. The time course of product formation is consistent with the following order of events. Benzoyl-CoA is formed from benzoate via benzoate-CoA ligase. The first ring reduction product observed is cyclohex-1,5-diene-1-carboxyl-CoA. The next intermediate is 6-hydroxycyclohex-1-ene-1-carboxyl-CoA which is derived from the diene by addition of water. Part of the diene seems to be reduced to cyclohex-1-ene-1-carboxyl-CoA which becomes hydrated to trans-2-hydroxycyclohexane-1-carboxyl-CoA; these two intermediates may be side products in vitro. The first non-cyclic intermediate formed by beta-oxidation is 3-hydroxypimelyl-CoA. This aliphatic C7 dicarboxylic acid is proposed to be oxidized via glutaryl-CoA and crotonyl-CoA to three molecules of acetyl-CoA and one molecule of CO2. A similar product pattern was observed in the benzoate-degrading phototrophic bacterium Rhodopseudomonas palustris. This indicates that the enzymatic reduction of benzoyl-CoA may be mechanistically similar in different anaerobes.
Force fluctuations and polymerization dynamics of intracellular microtubules (2007)

Microtubules are highly dynamic biopolymer filaments involved in a wide variety of biological processes including cell division, migration, and intracellular transport. Microtubules are very rigid and form a stiff structural scaffold that resists deformation. However, despite their rigidity, inside of cells they typically exhibit significant bends on all length scales. Here, we investigate the origin of these bends using a Fourier analysis approach to quantify their length and time dependence. We show that, in cultured animal cells, bending is suppressed by the surrounding elastic cytoskeleton, and even large intracellular forces only cause significant bending fluctuations on short length scales. However, these lateral bending fluctuations also naturally cause fluctuations in the orientation of the microtubule tip. During growth, these tip fluctuations lead to microtubule bends that are frozen-in by the surrounding elastic network. This results in a persistent random walk of the microtubule, with a small apparent persistence length of approximately 30 microm, approximately 100 times smaller than that resulting from thermal fluctuations alone. Thus, large nonthermal forces govern the growth of microtubules and can explain the highly curved shapes observed in the microtubule cytoskeleton of living cells.
Effect of Topiramate on the Anticonvulsant Activity of Conventional Antiepileptic Drugs in Two Models of Experimental Epilepsy (2003)

The experimental data indicate that except for PHT, the combinations of TPM with conventional AEDs are beneficial against amygdala-kindled seizures in rats. In the pentylenetetrazol test, this novel AED potentiated only the protection offered by ESM.
Chemoenzymatic Synthesis of HIV-1 V3 Glycopeptides Carrying Two N-Glycans and Effects of Glycosylation on the Peptide Domain (2005)

[structure: see text] A highly efficient chemoenzymatic synthesis of HIV-1 V3 domain glycopeptides carrying two N-linked core tri- and pentasaccharides was achieved. The synthesis consisted of two key steps: a solid-phase synthesis of the cyclic, 47-mer V3 domain peptide containing two GlcNAc residues and a novel endoglycosidase-catalyzed transglycosylation that simultaneously added two N-glycan moieties to the peptide precursor from the oligosaccharide oxazoline donor substrates. The availability of the synthetic glycopeptides allowed the probing of the effects of glycosylation on the HIV-1 V3 domain. It was demonstrated that glycosylation influenced the global conformations of the V3 domain and provided protection of the V3 domain against protease digestion.
Zidovudine induces molecular, biochemical, and ultrastructural changes in rat skeletal muscle mitochondria. (1992)

Zidovudine (AZT) inhibits HIV-1 replication in AIDS. A limiting side effect is AZT-induced toxic myopathy. Molecular changes in a rat model of AZT-induced toxic myopathy in vivo helped define pathogenetic molecular, biochemical, and ultrastructural toxic events in skeletal muscle and supported clinical and in vitro findings. After 35 d of AZT treatment, selective changes in rat striated muscle were localized ultrastructurally to mitochondria, and included swelling, cristae disruption, and myelin figures. Decreased muscle mitochondrial (mt) DNA, mtRNA, and decreased mitochondrial polypeptide synthesis in vitro were found in parallel. Mitochondrial molecular changes occurred in absence of altered abundance of cytosolic glyceraldehyde-3-phosphate dehydrogenase, or sarcomeric mitochondrial creatine kinase mRNAs. Quadriceps mitochondrial DNA polymerase gamma activity was similar in both AZT-treated and control rats. In vivo findings with rats support the hypothesis that AZT-induced inhibition of mtDNA replication has an effect of depressing the abundance of striated muscle mtDNA, mtRNA, and mitochondrial polypeptide synthesis. This experimental approach may be useful to examine mitochondrial or toxic myopathies.
Application of phage display to high throughput antibody generation and characterization (2007)

We have created a high quality phage display library containing over 1010 human antibodies and describe its use in the generation of antibodies on an unprecedented scale. We have selected, screened and sequenced over 38,000 recombinant antibodies to 292 antigens, yielding over 7,200 unique clones. 4,400 antibodies were characterized by specificity testing and detailed sequence analysis and the data/clones are available online. Sensitive detection was demonstrated in a bead based flow cytometry assay. Furthermore, positive staining by immunohistochemistry on tissue microarrays was found for 37% (143/381) of antibodies. Thus, we have demonstrated the potential of and illuminated the issues associated with genome-wide monoclonal antibody generation.
Epithelial transglutaminase 2 is needed for T cell interleukin-17 production and subsequent pulmonary inflammation and fibrosis in bleomycin-treated mice (2011)

Pulmonary fibrosis is a potentially life-threatening disease that may be caused by overt or asymptomatic inflammatory responses. However, the precise mechanisms by which tissue injury is translated into inflammation and consequent fibrosis remain to be established. Here, we show that in a lung injury model, bleomycin induced the secretion of IL-6 by epithelial cells in a transglutaminase 2 (TG2)-dependent manner. This response represents a key step in the differentiation of IL-17-producing T cells and subsequent inflammatory amplification in the lung. The essential role of epithelial cells, but not inflammatory cells, TG2 was confirmed in bone marrow chimeras; chimeras made in TG2-deficient recipients showed reduced inflammation and fibrosis, compared with those in wild-type mice, regardless of the bone marrow cell phenotype. Epithelial TG2 thus appears to be a critical inducer of inflammation after noninfectious pulmonary injury. We further demonstrated that fibroblast-derived TG2, acting downstream of transforming growth factor-β, is also important in the effector phase of fibrogenesis. Therefore, TG2 represents an interesting potential target for therapeutic intervention.
Neuroscience: Breaking Down Scientific Barriers to the Study of Brain and Mind (2000)

In this month's essay, Eric R. Kandel and Larry R. Squire chronicle how brain research has migrated from the peripheries of biology and psychology to assume a central position within those disciplines. The multidiscipline of neuroscience that emerged from this process now ranges from genes to cognition, from molecules to minds.
Preparation of Next-Generation Sequencing Libraries Using Nextera™ Technology: Simultaneous DNA Fragmentation and Adaptor Tagging by In Vitro Transposition (2011)

DNA library preparation is a common entry point and bottleneck for next-generation sequencing. Current methods generally consist of distinct steps that often involve significant sample loss and hands-on time: DNA fragmentation, end-polishing, and adaptor-ligation. In vitro transposition with Nextera™ Transposomes simultaneously fragments and covalently tags the target DNA, thereby combining these three distinct steps into a single reaction. Platform-specific sequencing adaptors can be added, and the sample can be enriched and bar-coded using limited-cycle PCR to prepare di-tagged DNA fragment libraries. Nextera technology offers a streamlined, efficient, and high-throughput method for generating bar-coded libraries compatible with multiple next-generation sequencing platforms.
Absorbing Stone Impact to Enable Separation from Potatoes (1986)

ABSTRACT Anew technique which enables separation of both stones and soil clods from pototates, after mechanical harvesting, was investigated. The general concept was to modify a commercial clod separator which incorporates bouncing of the potatoes and the clods on a cylindrical drum, where the difference in the restitution coefficient, e^, between the two products was 0.4. Stones were not separated well by this unit because they presented e^ similar to that of the potatoes. Ways to reduce the e^ of firm bodiessuch as stones, without affecting soft bodiessuch as potatoes or clods, were investigated. A technique based upon the energy absorption of a colliding body by dynamic bending of an elastic plate was proposed and later evaluated analytically and experimentally. A plate configuration which enables reduction of e^ for the stones without a noticable change for the potatoes and clods was obtained.