gebhart/patrepeval huggingface dataset:
Rapid evolution of the DNA-binding site in LAGLIDADG homing endonucleases (2001)

Sequence analysis of chloroplast and mitochondrial large subunit rRNA genes from over 75 green algae disclosed 28 new group I intron-encoded proteins carrying a single LAGLIDADG motif. These putative homing endonucleases form four subfamilies of homologous enzymes, with the members of each subfamily being encoded by introns sharing the same insertion site. We showed that four divergent endonucleases from the I-CreI subfamily cleave the same DNA substrates. Mapping of the 66 amino acids that are conserved among the members of this subfamily on the 3-dimensional structure of I-CreI bound to its recognition sequence revealed that these residues participate in protein folding, homodimerization, DNA recognition and catalysis. Surprisingly, only seven of the 21 I-CreI amino acids interacting with DNA are conserved, suggesting that I-CreI and its homologs use different subsets of residues to recognize the same DNA sequence. Our sequence comparison of all 45 single-LAGLIDADG proteins identified so far suggests that these proteins share related structures and that there is a weak pressure in each subfamily to maintain identical protein-DNA contacts. The high sequence variability we observed in the DNA-binding site of homologous LAGLIDADG endonucleases provides insight into how these proteins evolve new DNA specificity.
Multi-scale visualization and characterization of lignocellulosic plant cell wall deconstruction during thermochemical pretreatment (2011)

Deconstruction of lignocellulosic plant cell walls to fermentable sugars by thermochemical and/or biological means is impeded by several poorly understood ultrastructural and chemical barriers. A promising thermochemical pretreatment called ammonia fiber expansion (AFEX) overcomes the native recalcitrance of cell walls through subtle morphological and physicochemical changes that enhance cellulase accessibility without extracting lignin and hemicelluloses into separate liquid streams. Multi-scale visualization and characterization of Zea mays (i.e., corn stover) cell walls were carried out by laser scanning confocal fluorescence microscopy (LSCM), Raman spectroscopy, atomic force microscopy (AFM), electron microscopy (SEM, TEM), nuclear magnetic resonance (NMR), and electron spectroscopy for chemical analysis (ESCA) to elucidate the mechanism of AFEX pretreatment. AFEX first dissolves, then extracts and, as the ammonia evaporates, redeposits cell wall decomposition products (e.g., amides, arabinoxylan oligomers, lignin-based phenolics) on outer cell wall surfaces. As a result, nanoporous tunnel-like networks, as visualized by 3D-electron tomography, are formed within the cell walls. We propose that this highly porous structure greatly enhances enzyme accessibility to embedded cellulosic microfibrils. The shape, size (10 to 1000 nm), and spatial distribution of the pores depended on their location within the cell wall and the pretreatment conditions used. Exposed pore surface area per unit AFEX pretreated cell wall volume, estimated via TEM-tomogram image analysis, ranged between 0.005 and 0.05 nm2 per nm3. AFEX results in ultrastructural and physicochemical modifications within the cell wall that enhance enzymatic hydrolysis yield by 4–5 fold over that of untreated cell walls.
Design and development of a rapid data collection methodology (1998)

This paper presents research work undertaken on input data modelling for the simulation of batch manufacturing systems. It describes the development of a data reference model using IDEFIX data modelling language and a step-by-step approach to identify and collect required data quickly. The purpose of this reference model is to describe the interaction between various data groups relating to items such as parts, resources and some aspects of system logic. This model has been developed and refined using data collected from real industrial situations. The model encapsulates the major entities (data groups) with their attributes and relationships. This model was then translated into a normalised relational database. Having developed the data model, a step-by-step approach was devised to support simulation practitioners. The reference model has been annotated with the sources of real data, so that practitioners could identify the most suitable source of data for their requirements.
Crystallization of diaminopimelate decarboxylase fromEscherichia coli, a stereospecificD-amino-acid decarboxylase (2002)

The final step in lysine biosynthesis in bacteria, the conversion of meso-diaminopimelate to L-lysine, is catalyzed by the only known D-amino-acid decarboxylase, diaminopimelate decarboxylase (DDC). The Escherichia coli DDC has been cloned, overexpressed in E. coli with a carboxy-terminal polyhistidine purification tag and crystallized from lithium sulfate. The protein is intensely yellow, owing to the pyridoxal-5'-phosphate cofactor, and is enzymatically active. Large well ordered crystals, belonging to space group P6(1)22 with unit-cell parameters a = b = 98.6, c = 177 A, make high-resolution X-ray diffraction studies possible to characterize the residues important in stereospecific decarboxylation and reprotonation during catalytic turnover.
Mouse, but not Human STING, Binds and Signals in Response to the Vascular Disrupting Agent 5,6-Dimethylxanthenone-4-Acetic Acid (2013)

Vascular disrupting agents such as 5,6-dimethylxanthenone-4-acetic acid (DMXAA) represent a novel approach for cancer treatment. DMXAA has potent antitumor activity in mice and, despite significant preclinical promise, failed human clinical trials. The antitumor activity of DMXAA has been linked to its ability to induce type I IFNs in macrophages, although the molecular mechanisms involved are poorly understood. In this study, we identify stimulator of IFN gene (STING) as a direct receptor for DMXAA leading to TANK-binding kinase 1 and IFN regulatory factor 3 signaling. Remarkably, the ability to sense DMXAA was restricted to murine STING. Human STING failed to bind to or signal in response to DMXAA. Human STING also failed to signal in response to cyclic dinucleotides, conserved bacterial second messengers known to bind and activate murine STING signaling. Collectively, these findings detail an unexpected species-specific role for STING as a receptor for an anticancer drug and uncover important insights that may explain the failure of DMXAA in clinical trials for human cancer.
Nanopore-Based Single-Molecule Mass Spectrometry on a Lipid Membrane Microarray (2011)

We report on parallel high-resolution electrical single-molecule analysis on a chip-based nanopore microarray. Lipid bilayers of <20 μm diameter containing single alpha-hemolysin pores were formed on arrays of subpicoliter cavities containing individual microelectrodes (microelectrode cavity array, MECA), and ion conductance-based single molecule mass spectrometry was performed on mixtures of poly(ethylene glycol) molecules of different length. We thereby demonstrate the function of the MECA device as a chip-based platform for array-format nanopore recordings with a resolution at least equal to that of established single microbilayer supports. We conclude that devices based on MECAs may enable more widespread analytical use of nanopores by providing the high throughput and ease of operation of a high-density array format while maintaining or exceeding the precision of state-of-the-art microbilayer recordings.
Corrosion-Resistant Zeolite Coatings (2008)

As a promising, environmentally friendly alternative for the toxic and carcinogenic chromate conversion surface finishing, zeolite coatings on various metal alloys have shown excellent corrosion resistance, strong adhesion to substrates, and extraordinary thermal and mechanical properties. This review summarizes recent technological advances of zeolite corrosion-resistant coatings from the conventional hydrothermal in situ synthesis method to the newly developed ambient pressure deposition process. The topic of zeolites as smart inhibitor pigments is also discussed. Future perspectives of zeolite corrosion-resistant coatings are envisaged at the end of this review.
Vector field SLAM (2010)

Localization in unknown environments using low-cost sensors remains a challenge. This paper presents a new localization approach that learns the spatial variation of an observed continuous signal. We model the signal as a piece-wise linear function and estimate its parameters using a simultaneous localization and mapping (SLAM) approach. We apply our framework to a sensor measuring bearing to active beacons where measurements are systematically distorted due to occlusion and signal reflections of walls and other objects present in the environment. Experimental results from running GraphSLAM and EKF-SLAM on manually collected sensor measurements as well as on data recorded on a vacuum-cleaner robot validate our model.
Adoptive transfer of immature dendritic cells with autologous or allogeneic tumor cells generates systemic antitumor immunity. (1999)

Dendritic cells (DCs) are potent antigen-presenting cells that are capable of priming systemic antitumor immune responses in animal tumor models. However, many of the model tumor systems tested need definition of the specific tumor antigens involved. To use DCs in situations that are more relevant to the majority of human cancers, where the antigens are unknown, we have tested the adoptive transfer of immature DCs in mouse colorectal and melanoma models of varying immunogenicity but with undefined antigens. When DCs admixed with a syngeneic primary tumor inoculum were seeded s.c., the growth of the primary tumor was unchanged; however, if the primary tumor was then surgically excised and the animal was rechallenged with the same tumor, significant protection (75%) was generated when DCs were present in the original primary inoculum of a moderately immunogenic colorectal model (CMT93tk). This effect was not observed when a nonimmunogenic melanoma (B16) was tested in an identical protocol. Next, DCs were injected directly into 6-9-mm established tumors; again, protection (55%) was achieved against a secondary tumor challenge following excision of the primary, but only in the CMT93tk model of moderate immunogenicity. To increase the clinical relevance of this approach still further, we tested irradiated allogeneic K1735 melanoma cells mixed with syngeneic DCs as a vaccine against subsequent challenge with the poorly immunogenic syngeneic melanoma B16. The allogeneic vaccine alone was ineffective, but when admixed with DCs, a significant number of animals rejected a subsequent B16 challenge, suggesting that DCs are able to prime an immune response against melanoma antigens shared between K1735 and B16. The generation of systemic antitumor immunity by adoptive transfer of DCs has significant clinical potential because it is technically straightforward and does not require the definition of specific tumor antigens.
A potent enhancer made of clustered liver-specific elements in the transcription control sequences of human alpha 1-microglobulin/bikunin gene. (1992)

alpha 1-Microglobulin (A1M) and bikunin are plasma proteins which are present both as free molecules and as complexes with either IgA heavy chains for A1M or the H1, H2, and H3 heavy chains of the inter-alpha-inhibitor family for bikunin. Mature A1M and bikunin originate from the cleavage of an A1M/bikunin precursor (ABP) synthesized from a single gene with liver-specific expression. Five kilobases of the 5'-flanking region of the human ABP gene were sequenced. Deletion mutants of this region subcloned upstream of a CAT reporter gene were transfected into HepG2 hepatoma cells. A segment covering the -2.7- to -2.8-kb area is required for full activity of the ABP gene. This segment contains a cluster of six elements (boxes 1-6, 5' to 3') which are potential binding sites for the liver-enriched trans-acting factors HNF-1, HNF-4, HNF-3, HNF-1, HNF-3, and HNF-4, respectively. This cluster enhances the activity of heterologous minimal promoters in a position- and distance-independent fashion in HepG2 cells. This enhancer activity is restricted to liver cells as the cluster is unable to activate promoters in Chinese hamster ovary (CHO) or HeLa cells. By band-shift experiments we have shown that the liver-enriched transcription factors HNF-1, or HNF-3, do bind to boxes 1 and 4, or 3, respectively. The combination of a weak promoter and a strong distant and liver-specific enhancer distinguishes the ABP gene from most other plasma protein genes expressed in hepatocytes.
Presence of RNA in the nucleoprotein complex spontaneously released by human lymphocytes and frog auricles in culture. (1978)

Cell systems as different as normal human blood lymphocytes and frog auricles release spontaneously a nucleoprotein complex in their culture medium. This release seems to be an active mechanism that is unrelated to cell death. The presence of RNA in this complex is demonstrated. The amount of extracellular RNA is regulated by the same homeostatic mechanism that has previously been shown to govern DNA release in the same cell systems. This extracellular RNA is linked by hydrogen bonds to the extracellular DNA and cannot be extracted by a usual phenol procedure, due perhaps to the presence of a glycoprotein. Further purifications by chloroform, sodium perchlorate, and hydroxyapatite are necessary to obtain an RNA molecule that is acid precipitable, RNase and KOH sensitive, and orcinol positive. The extracellular RNA sediments between 2.5 and 4S and is not a transfer RNA. It is more highly methylated than the 28S, 18S, and 4 to 5S cellular RNA. It activates DNA synthesis in vitro.
Synthesis of inositol phosphates (1988)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis of inositol phosphatesJames L. Meek, Fred. Davidson, and Frank W. HobbsCite this: J. Am. Chem. Soc. 1988, 110, 7, 2317–2318Publication Date (Print):March 1, 1988Publication History Published online1 May 2002Published inissue 1 March 1988https://pubs.acs.org/doi/10.1021/ja00215a061https://doi.org/10.1021/ja00215a061research-articleACS PublicationsRequest reuse permissionsArticle Views619Altmetric-Citations46LEARN 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
Regional Localization ofERG, the Channel Protein Responsible for the Rapid Component of the Delayed Rectifier, K+Current in the Ferret Heart (1997)

Repolarization of the cardiac action potential varies widely throughout the heart. This could be due to the differential distribution of ion channels responsible for repolarization, especially the K+ channels. We have therefore studied the cardiac localization of ERG, a channel protein known to play an important role in generation of the rapid component of the delayed rectifier K+ current (IKr), an important determinant of the repolarization waveform, Cryosections of the ferret atrium and ventricle were prepared to determine the localization of ERG by fluorescence in situ hybridization (FISH) and immunofluorescence. We found that in the ferret, ERG transcript and protein expression was most abundant in the epicardial cell layers throughout most of the ventricle, except at the base. In the atrium, we found that ERG is most abundant in the medial right atrium, especially in the trabeculae and the crista terminalis of the right atrial appendage. It also is present in areas within the sinoatrial node. In all regions studied, FISH and immunofluorescence showed concordant localization patterns. These data suggest that repolarization mediated by IKr is not uniform throughout the ferret heart and provide a molecular explanation for heterogeneity in action potential repolarization throughout the mammalian heart.
In Vivo Visualization of Oxyradical-Dependent Photoemission during Endothelium-Granulocyte Interaction in Microvascular Beds Treated with Platelet-Activating Factor1 (1989)

Oxyradical-dependent chemiluminescence from granulocytes sticking to venular endothelium was successfully visualized in rat mesenteric microvascular beds treated with platelet-activating factor (PAF). Intravital photonic image intensifier microscopy revealed that topical application of PAF-acether (100 nM) caused remarkable granulocyte adherence on endothelial walls and the subsequent activation of a luminol-dependent photonic burst. Chemilumigenic sites clearly corresponded to the spatial distribution of sticking cells in post-capillary venules. The present findings thus serve as the first demonstration of an intravital oxidative burst of granulocytes on venular endothelium in PAF-induced microcirculatory disturbances.
Bladder cancer discovered by ovarian metastasis: Cytokeratin expression is useful when making differential diagnosis (2005)

A 49-year-old woman underwent hysterectomy and bilateral adnexectomy after the diagnosis of a right ovarian tumor with paraaortic and pelvic lymph node metastases. The pathological diagnosis was undifferentiated carcinoma of the ovary. After the operation, a bladder tumor was discovered during the evaluation for microscopic hematuria. The bladder tumor was pathologically diagnosed as transitional cell carcinoma, pT1b, G3. Although the pathological findings of the bladder cancer and ovarian cancer were very similar, we could diagnose primary bladder cancer with ovary and lymph node metastases according to the immunohistochemical staining pattern of cytokeratins 7 and 20. Herein, the clinical usefulness of immunohistochemical staining using cytokeratins for making a differential diagnosis of the origin of a tumor in the pelvic cavity is demonstrated.
Preparation and properties of water-soluble, poly(styrenesulfonic acid)-doped polyaniline (1994)

K. Shannon and J. E. Fernandez, J. Chem. Soc., Chem. Commun., 1994, 643 DOI: 10.1039/C39940000643
Liposomes as Possible Carriers for Lactoferrin in the Local Treatment of Inflammatory Diseases (2001)

Liposomes prepared from naturally occurring biodegradable and nontoxic lipids are good candidates for local delivery of therapeutic agents. Treatment of arthritis by intra-articular administration of anti-inflammatory drugs encapsulated in liposomes prolongs the residence time of the drug in the joint. We have previously shown that intra-articular injection of human lactoferrin (hLf), a glycoprotein that possesses anti-inflammatory and antimicrobial activities, into mice with collagen-induced arthritis reduces inflammation. We have now investigated the possibility of using liposome-entrapped hLf as a delivery system to prolong hLf retention at sites of local inflammation such as the rheumatoid joint. Entrapment of hLf in negatively charged liposomes enhanced its accumulation in cultured human synovial fibroblasts from rheumatoid arthritis (RA) patients, compared with positively charged formulations or free protein. However, in the presence of synovial fluid, positively charged liposomes with entrapped hLf were more stable than the negatively charged formulations. In vivo experiments in mice with collagen-induced arthritis showed that the positive liposomes were more efficient in prolonging the residence time of hLf in the inflamed joint as compared with other liposomes. Thus, the amount of hLf retained in the joint after 2 hr was 60% of the injected dose in the case of positive liposomes and only 16% for negative pH-sensitive liposomes. The results suggest that entrapment of hLf in positively charged liposomes may modify its pharmacodynamic profile and be of therapeutic benefit in the treatment of RA and other local inflammatory conditions.
New Method of Superheterodyne Light Beating Spectroscopy for Brillouin Scattering Using Frequency-Tunable Lasers (1995)

We have developed a new optical superheterodyne method for light scattering using frequencytunable lasers and succeeded in measuring Brillouin spectra of simple liquids in a wide frequency range, 10 MHz to 3 GHz. Its frequency resolution (\ensuremath{\sim}300 kHz) is determined by the short-time coherency between the two lasers. A great advantage of our method over conventional optical beating methods is that the speed of the photodetector and electric circuits never limits the upper frequency bound. This is realized by the continuous tunability of the laser frequency. The method has a high potential for studying the dynamics in a wide class of condensed matters.
Stability of ivermectin in rumen fluids (1996)

To determine whether ivermectin is metabolized in the rumen, in vitro studies were conducted with the tritium-labelled H2B1a component of ivermectin in rumen fluid from sheep and cattle. No detectable metabolism occurred over 24 h in in vitro incubations at 38 degrees C. The viability of the microbes in the rumen fluids was demonstrated by the conversion of 17% and 11% of [14C]cellulose to 14CO2 in 24 h in the incubations with sheep and steer rumen fluids respectively. The results indicate that ivermectin is not metabolized in the rumen. Based on the lack of in vitro metabolism of ivermectin in rumen fluid, the similarity of in vitro liver microsomal metabolism with in vivo metabolism of the avermectins and the physicochemical properties of the avermectins, any disappearance of ivermectin in vitro from rumen fluid is probably a result of binding to solids or surfaces. Apparent discrimination by dung beetles, where observed, between control faeces and faeces from cattle or sheep treated with ivermectin or abamectin therefore must be attributable to chance, to factors unrelated to treatment or to factors such as changes in amino acid composition rather than the production of volatile metabolites of ivermectin.
Residue-specific structures and membrane locations of pH-low insertion peptide by solid-state nuclear magnetic resonance (2015)

The pH-low insertion peptide (pHLIP) binds to a membrane at pH 7.4 unstructured but folds across the bilayer as a transmembrane helix at pH∼6. Despite their promising applications as imaging probes and drug carriers that target cancer cells for cytoplasmic cargo delivery, the mechanism of pH modulation on pHLIP-membrane interactions has not been completely understood. Here, we show the first study on membrane-associated pHLIP using solid-state NMR spectroscopy. Data on residue-specific conformation and membrane location describe pHLIP in various surface-bound and membrane-inserted states at pH 7.4, 6.4 and 5.3. The critical membrane-adsorbed state is more complex than previously envisioned. At pH 6.4, for the major unstructured population, the peptide sinks deeper into the membrane in a state II' that is distinct from the adsorbed state II observed at pH 7.4, which may enable pHLIP to sense slight change in acidity even before insertion.