gebhart/patrepeval huggingface dataset:
Automated Identification of Amino Acid Sequence Variations in Proteins by HPLC/Microspray Tandem Mass Spectrometry (2000)

Amino acid sequence variations resulting from single-nucleotide polymorphisms (SNPs) were identified using a novel mass spectrometric method. This method obtains 99+% protein sequence coverage for human hemoglobin in a single LC-microspray tandem mass spectrometry (microLC-MS/MS) experiment. Tandem mass spectrometry data was analyzed using a modified version of the computer program SEQUEST to identify the sequence variations. Conditions of sample preparation, chromatographic separation, and data collection were optimized to correctly identify amino acid changes in six variants of human hemoglobin (Hb C, Hb E, Hb D-Los Angeles, Hb G-Philadelphia, Hb Hope, and Hb S). Hemoglobin proteins were isolated and purified, dehemed, (S)-carboxyami-domethylated, and then subjected to a combination proteolytic digestion to obtain a complex peptide mixture with multiple overlaps in sequence. Reversed-phase chromatographic separation of peptides was achieved on-line with MS utilizing a robust fritless microelectrospray interface. Tandem mass spectrometry was performed on an ion trap mass spectrometer using automated data-dependent MS/MS procedures. Tandem mass spectra were collected from the five most abundant ions in each scan using dynamic and isotopic exclusion to minimize redundancy. The spectra were analyzed by a version of the SEQUEST algorithm modified to identify amino acid substations resulting from SNPs.
Aquitalea magnusonii gen. nov., sp. nov., a novel Gram-negative bacterium isolated from a humic lake (2006)

A Gram-negative, rod-shaped, non-spore-forming betaproteobacterium (TRO-001DR8T) was isolated from humic-lake samples collected from northern Wisconsin, USA. On the basis of 16S rRNA gene sequence analysis, strain TRO-001DR8T belonged to the family Neisseriaceae, and the phylogenetic distance from its closest relative, Chromobacterium violaceum, was 95 %. Strain TRO-001DR8T lacked the violet pigmentation of C. violaceum and shared only 26 % DNA-DNA relatedness with C. violaceum. The DNA G+C content of strain TRO-001DR8T was 59 mol%. The predominant fatty acids were C(16 : 1)omega7c + C(16 : 1)omega7c 2-OH iso (52.5 %), C(16 : 0) (21.7 %), C(18 : 1)omega7c (8.0 %) and C(12 : 0) (5.1 %). Strain TRO-001DR8T grew optimally at 35 degrees C and pH 6.0, did not utilize sucrose, but did use glucose, some organic acids and most protein amino acids. Biochemical, physiological, chemotaxonomic and phylogenetic analyses showed that strain TRO-001DR8T could not be assigned to any known genus of the Betaproteobacteria. Therefore, the isolate represents a novel genus and species, for which the name Aquitalea magnusonii gen. nov., sp. nov. is proposed. The type strain is TRO-001DR8T (=ATCC BAA-1216T = BCCM/LMG 23054T).
Oxygen-dependent mutagenesis in Escherichia coli lacking superoxide dismutase. (1986)

Escherichia coli double mutants (sodA sodB) completely lacking superoxide dismutase (SOD) have greatly enhanced mutation rates during aerobic growth. Single mutants lacking manganese SOD (MnSOD) but possessing iron SOD (FeSOD) have a smaller increase, and single mutants lacking FeSOD but possessing MnSOD do not show such an increase. The enhancement of mutagenesis is completely dependent on the presence of oxygen, and treatments that increase the flux of superoxide radicals produce even higher levels of mutagenesis. The presence of a plasmid overproducing either form of SOD reduces the level of mutagenesis to that of wild type, showing that the O2-dependent enhancement results from a lack of SOD. The enhancement of mutagenesis is RecA-independent, and a complete lack of SOD does not induce the SOS response during aerobic growth. However, the enhanced mutagenesis in aerobically grown sodA sodB mutants is largely dependent on functional exonuclease III, suggesting that the increased flux of superoxide radicals results in DNA lesions that can be acted on by this enzyme, leading to mutations.
Significantly Enhanced Reactivities of the Nucleophilic Substitution Reactions in Ionic Liquid (2003)

We have investigated the reactivities of various metal fluorides in the nucleophilic fluorination of 2-(3-methanesulfonyloxypropyl)naphthalene (1) as a model compound in the presence of 1-n-butyl-3-methylimidazolium tetrafluoroborate ([bmim][BF(4)]). The higher periodic alkali metal fluorides demonstrate greater reactivity. The fluorination using CsF among the alkali metal fluorides was completed in 20 min, affording the desired product 2-(3-fluoropropyl)naphthalene (2a, 95%) without any byproducts. However, the fluorinations using alkali earth, transition, and low periodic alkali metal fluorides under the same conditions occurred rarely or not at all. We have also carried out the various facile nucleophilic substitutions such as halogenations, acetoxylation, nitrilation, and alkoxylations of mesyloxyalkane 1 and 2-(3-bromopropyl)naphthalene (6) at the primary aliphatic position using the potassium halides, acetate, cyanide, and alkoxides, respectively, in the presence of ionic liquids. These reactions provided the desired products, such as 2-(3-halopropyl)naphthalenes 5-7 (95% for Cl, 96% for Br, and 93% for I), 2-(3-acetoxypropyl)naphthalene (8, 95%), 2-(3-cyanopropyl)naphthalene (9, 93%), and 2-(3-methoxypropyl)naphthalene (10, 92%).
In Vitro Cytotoxic Activities of 2-Alkyl-4,6-diheteroalkyl-1,3,5-triazines:  New Molecules in Anticancer Research (2004)

The cytotoxic activities of new 2-alkyl-4,6-dihetero(N,O)alkyl-1,3,5-triazines toward selected tumor cell lines have been evaluated, and for the first time, the potential of 2-alkyl-4,6-dialkoxy-1,3,5-triazines has been shown.
Localization of Pectic Galactan in Tomato Cell Walls Using a Monoclonal Antibody Specific to (1[-&gt;]4)-β-D-Galactan (1997)

To develop antibody probes for the neutral side chains of pectins, antisera were generated to a pectic galactan isolated from tomato (Lycopersicon esculentum) pericarp cell walls and to a (1[->]4)-[beta]-galactotetraose-bovine serum albumin neoglycoprotein. The use of these two antisera in immunochemical assays and immunolocalization studies indicated that they had very similar specificities. A monoclonal antibody (LM5) was isolated and characterized subsequent to immunization with the neoglycoprotein. Hapten inhibition studies revealed that the antibody specifically recognized more than three contiguous units of (1[->]4)-[beta]-galactosyl residues. The antigalactan antibody was used to immunolocalize the galactan side chains of pectin in tomato fruit pericarp and tomato petiole cell walls. Although the LM5 epitope occurs in most cell walls of the tomato fruit, it was absent from both the locular gel and the epidermal and subepidermal cells. Furthermore, in contrast to other anti-pectin antibodies, LM5 did not label the cell wall thickenings of tomato petiole collenchyma.
CONSIDERACIONES GENERALES A CERCA DE LOS CONFLICTOS ARMADOS AFRICANOS Y SU TRATAMIENTO A LA LUZ DEL DERECHO INTERNACIONAL PÚBLICO. EL EJEMPLO DE LA COMUNIDAD ECONÓMICA DE LOS ESTADOS DE ÁFRICA OCCIDENTAL (CEDEAO) (2006)

SUMARIO: Introducción PRIMERA PARTE La comunidad Económica de los Estados de África Occidental y la gestión de los conflictos armados de tipo regional. Antecedentes y origen de la creación de la CEDEAO Objetivos y estructura de la CEDEAO Antecedentes de la cooperación militar entre los Estados de África Occidental África Occidental y las crisis de los años 90 La Guerra Civil de Liberia La crisis de Sierra Leona Guinea Bissau y la rebelión del General Mane La crisis de Costa de Marfil La segunda intervención de la CEDEAO en Liberia SEGUNDA PARTE Principales instrumentos jurídicos de diplomacia preventiva de la CEDEAO. Listas de los principales instrumentos en materia de seguridad colectiva Estructura y funcionamiento del Mecanismo de Prevención y Solución de los Conflictos adoptado por la CEDEAO el 10 de Diciembre 1999. Sus objetivos Sus Instituciones Funciones del Secretario Ejecutivo en el mismo Los órganos de apoyo al mecanismo de Prevención y solución de los conflictos armados Conclusiones Bibliografía
Permeability Valves. Permeability of Gases and Vapors through Composite Membranes (1957)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPermeability Valves. Permeability of Gases and Vapors through Composite MembranesC. E. Rogers, Vivian. Stannett, and Michael. SzwarcCite this: Ind. Eng. Chem. 1957, 49, 11, 1933–1936Publication Date (Print):November 1, 1957Publication History Published online1 May 2002Published inissue 1 November 1957https://pubs.acs.org/doi/10.1021/ie50575a046https://doi.org/10.1021/ie50575a046research-articleACS PublicationsRequest reuse permissionsArticle Views197Altmetric-Citations73LEARN 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 options Get e-Alerts
Intestinal Motor Function in Irritable Bowel Syndrome (1994)

Irritable bowel syndrome is widely considered to be associated with disordered gastro-intestinal motility. The evidence for a motor disorder in the colon and small intestine of patients with irritable bowel syndrome is reviewed. Results of myoelectric, motility and transit studies in both the colon and small intestine are inconsistent. Difficulties in interpreting colonic motility have led investigators to address the small intestine as a possible site of dysmotility. An increase in the number of clustered contractions in the proximal small intestine has been reported by some, but not all investigators. Methodological differences as well as patient selection, symptom severity and fluctuation may all contribute to discrepancies between the results of different studies. Motility disturbances may be present which are currently unrecognised due to an inadequate understanding of the propagation of colonic contractions, and of small intestinal contractions during phase II and postprandially. Whether the reported motor disturbances arise locally in the gut or originate from higher centres in the central nervous system has not been established.
Praat: Doing Phonetics by Computer (2011)

Ear and Hearing: March 2011 - Volume 32 - Issue 2 - p 266 doi: 10.1097/AUD.0b013e31821473f7
Apoptotic Vascular Endothelial Cells Become Procoagulant (1997)

Whereas unperturbed endothelial cells provide potent anticoagulant properties, exposure to inflammatory and atherogenic stimuli can rapidly lead to a procoagulant behavior. Because recent studies provide evidence that apoptosis of vascular cells may occur under conditions such as atherosclerosis and inflammation, we investigated whether apoptotic endothelial cells may contribute to the development of a prothrombotic state. In this report, it is shown that both adherent and detached apoptotic human umbilical vein endothelial cells (HUVECs) become procoagulant. Apoptosis was induced by staurosporine, a nonspecific protein kinase inhibitor, or by culture in suspension with serum deprivation. Both methods resulted in similar findings. As assessed by flow cytometric determination of annexin V binding, HUVECs undergoing cell death exhibited typically a more rapid exposure of membrane phosphatidylserine (PS) than DNA fragmentation. Depending on the stage of apoptosis, this redistribution of phospholipids was found to induce an increase of the activity of the intrinsic tenase complex by 25% to 60%. Although apoptotic cells did not show antigenic or functional tissue factor (TF) activity, when preactivated with lipopolysaccharide, TF procoagulant activity increased by 50% to 70%. At 8 hours after apoptosis induction, antigenic thrombomodulin, heparan sulfates, and TF pathway inhibitor decreased by about 83%, 80%, and 59%, respectively. The functional activity of these components was reduced by about 36%, 52%, and 39%, respectively. Moreover, the presence of apoptotic HUVECs led to a significant increase of thrombin formation in recalcified citrated plasma. In conclusion, apoptotic HUVECs, either adherent or in suspension, become procoagulant by increased expression of PS and the loss of anticoagulant membrane components.
EIN4 and ERS2 Are Members of the Putative Ethylene Receptor Gene Family in Arabidopsis (1998)

The Arabidopsis ethylene receptor gene ETR1 and two related genes, ERS1 and ETR2, were identified previously. These three genes encode proteins homologous to the two-component regulators that are widely used for environment sensing in bacteria. Mutations in these genes confer ethylene insensitivity to wild-type plants. Here, we identified two Arabidopsis genes, EIN4 and ERS2, by cross-hybridizing them with ETR2. Sequence analysis showed that they are more closely related to ETR2 than they are to ETR1 or ERS1. EIN4 previously was isolated as a dominant ethylene-insensitive mutant. ERS2 also conferred dominant ethylene insensitivity when certain mutations were introduced into it. Double mutant analysis indicated that ERS2, similar to ETR1, ETR2, ERS1, and EIN4, acts upstream of CTR1. Therefore, EIN4 and ERS2, along with ETR1, ETR2, and ERS1, are members of the ethylene receptor-related gene family of Arabidopsis. RNA expression patterns of members of this gene family suggest that they might have distinct as well as redundant functions in ethylene perception.
Interleukin-13 receptor alpha chain: a novel tumor-associated transmembrane protein in primary explants of human malignant gliomas. (2000)

Human malignant glioma cell lines express high levels of interleukin-13 receptor (IL-13R). However, the subunit structure of this receptor in primary brain tumor cells is not known. Herein, we examined the subunit composition of IL-13R by analyzing the expression of four different putative subunits of IL-13R complex in 25 primary explants of malignant brain tumors. Reverse transcription-PCR (RT-PCR) of RNA from these tumor cells, normal astrocytes, and normal brain tissue showed that transcripts of IL-13R alpha chain were present in greater abundance in malignant glioma cells compared with normal astrocytes or normal brain tissues. The transcripts for two other chains (e.g., IL-13Ralpha' and IL-4Rbeta), on the other hand, yielded similar PCR positivity in brain tumors as well as in normal samples, whereas transcripts for gammac chain were absent in all brain tumor cells and normal tissues. The specificity of RT-PCR products for these genes was confirmed by oligo liquid hybridization analysis using a radiolabeled sequence-specific internal probe. Indirect immunofluorescence studies for different receptor chains confirmed the RT-PCR results and demonstrated a striking difference in the level of expression of IL-13Ralpha protein between normal astrocytes and malignant astrocytoma cells. These studies establish the IL-13Ralpha subunit as a novel tumor-specific protein that may be useful as a tumor marker, a target for cytotoxin/immunotoxin, or alternatively, a tumor-associated antigen for active, specific immunotherapy.
The “HyTime ” (1991)

he computer and telecommunications industries have made enormous progress in communications technology standardization in recent years. One effect of good communications technology is that people can concentrate on the information being communicated. More and more people are realizing, however, that being able to send and receive files containing information is not enough.
Neurturin Exerts Potent Actions on Survival and Function of Midbrain Dopaminergic Neurons (1998)

Glial cell line-derived neurotrophic factor (GDNF) exhibits potent effects on survival and function of midbrain dopaminergic (DA) neurons in a variety of models. Although other growth factors expressed in the vicinity of developing DA neurons have been reported to support survival of DA neurons in vitro, to date none of these factors duplicate the potent and selective actions of GDNF in vivo. We report here that neurturin (NTN), a homolog of GDNF, is expressed in the nigrostriatal system, and that NTN exerts potent effects on survival and function of midbrain DA neurons. Our findings indicate that NTN mRNA is sequentially expressed in the ventral midbrain and striatum during development and that NTN exhibits survival-promoting actions on both developing and mature DA neurons. In vitro, NTN supports survival of embryonic DA neurons, and in vivo, direct injection of NTN into the substantia nigra protects mature DA neurons from cell death induced by 6-OHDA. Furthermore, administration of NTN into the striatum of intact adult animals induces behavioral and biochemical changes associated with functional upregulation of nigral DA neurons. The similarity in potency and efficacy of NTN and GDNF on DA neurons in several paradigms stands in contrast to the differential distribution of the receptor components GDNF Family Receptor alpha1 (GFRalpha1) and GFRalpha2 within the ventral mesencephalon. These results suggest that NTN is an endogenous trophic factor for midbrain DA neurons and point to the possibility that GDNF and NTN may exert redundant trophic influences on nigral DA neurons acting via a receptor complex that includes GFRalpha1.
Electrochemical Cyclization of Dipeptides toward Novel Bicyclic, Reverse-Turn Peptidomimetics. 1. Synthesis and Conformational Analysis of 7,5-Bicyclic Systems (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTElectrochemical Cyclization of Dipeptides toward Novel Bicyclic, Reverse-Turn Peptidomimetics. 1. Synthesis and Conformational Analysis of 7,5-Bicyclic SystemsFabrice Cornille, Urszula Slomczynska, Mark L. Smythe, Denise D. Beusen, Kevin D. Moeller, and Garland R. MarshallCite this: J. Am. Chem. Soc. 1995, 117, 3, 909–917Publication Date (Print):January 1, 1995Publication History Published online1 May 2002Published inissue 1 January 1995https://pubs.acs.org/doi/10.1021/ja00108a007https://doi.org/10.1021/ja00108a007research-articleACS PublicationsRequest reuse permissionsArticle Views356Altmetric-Citations56LEARN 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 (2)»Supporting Information Supporting Information Get e-Alerts
Synthese 5′‐modifizierter Adenosinderivate (1968)

Abstract Es werden neue und einfache Verfahren zur Synthese von Adenosin‐5′‐carbonsäure ( 2 ), 5′‐ O ‐Tosyl‐adenosin ( 3 ), 5′‐ O ‐Tosyl‐adenosin‐5′.5′‐d 2 ( 11 ) und 5′‐Amino‐5′‐desoxy‐adenosin ( 4 ) ausgehend von 2′.3′‐ O ‐Isopropyliden‐adenosin beschrieben.
Hyaluronic acid‐based polymers as cell carriers for tissue‐engineered repair of bone and cartilage (1999)

Culture-expanded bone marrow-derived mesenchymal progenitor cells differentiate into chondrocytes or osteoblasts when implanted subcutaneously in vivo in combination with an appropriate delivery vehicle. This in vivo implantation technique is used to test new materials as putative delivery vehicles in skeletal tissue-engineering models. HYAFF 11 and ACP sponges, two biomaterials based on hyaluronic acid modified by esterification of the carboxyl groups of the glucuronic acid, were tested as osteogenic or chondrogenic delivery vehicles for rabbit mesenchymal progenitor cells and compared with a well characterized porous calcium phosphate ceramic delivery vehicle. The implant materials were examined by scanning electron microscopy for differences in pore structure or cellular interactions, were quantified for their ability to bind and retain mesenchymal progenitor cells, and were examined histologically for their ability to support osteogenesis and chondrogenesis after subcutaneous implantation into nude mice. The ACP sponge bound the same number of cells as fibronectin-coated ceramic, whereas the HYAFF 11 sponge bound 90% more. When coated with fibronectin, ACP and HYAFF 11 bound, respectively, 100 and 130% more cells than the coated ceramics. HYAFF 11 sponge composites retained their integrity after the 3 or 6-week incubation period in the animals and were processed for histomorphometric analysis. As a result of rapid degradation or resorption in vivo, ACP sponges could not be recovered after implantation and could not be analyzed. HYAFF 11 sponges presented more area available for cell attachment and more available volume for newly formed tissue. Following loading with mesenchymal progenitor cells and implantation, the pores of the sponges contained more bone and cartilage than the pores of ceramic cubes at either time point. Thus, relative to ceramic, HYAFF 11 sponges allow incorporation of twice as many cells and produce a 30% increase in the relative amount of bone and cartilage per unit area. Hence, the hyaluronic acid-based delivery vehicles are superior to porous calcium phosphate ceramic with respect to the number of cells loaded per unit volume of implant, and HYAFF 11 sponges are superior to the ceramics with regard to the amount of bone and cartilage formed. Additionally, hyaluronic acid-based vehicles have the advantage of degradation/resorption characteristics that allow complete replacement of the implant with newly formed tissue.
Small molecule modulation of a redox-sensitive stress granule protein dissolves stress granules with beneficial outcomes for familial amyotrophic lateral sclerosis models (2019)

Abstract Neurodegeneràve diseases such as amyotrophic lateral sclerosis (ALS) are oten associated with mutàons in proteins that are associated with stress granules. Stress granules are condensates formed by liquid-liquid phase separàon which, when aberrant, can lead to altered condensàon behaviours and disease phenotypes. Here, we identified lipoamide, a small molecule which specifically prevents cytoplasmic condensàon of stress granule proteins. Thermal proteome profiling showed that lipoamide preferentially stabilises intrinsically disordered domain-containing proteins. These include SRSF1 and SFPQ, stress granule proteins necessary for lipoamide activity. The redox state of SFPQ correlates with its condensate-dissolving behaviour, in concordance with the importance of the dithiolane ring for lipoamide activity. In animals, lipoamide ameliorates aging-associated aggregàon of a stress granule reporter, improves neuronal morphology, and recovers motor defects caused by expression of ALS-associated FUS and TDP-43 mutants. In conclusion, lipoamide is a well-tolerated small molecule modulator of stress granule condensàon and dissection of its molecular mechanism identified a cellular pathway for redox regulàon of stress granule formàon.