gebhart/patrepeval huggingface dataset:
Advancements in Top-Down Proteomics (2011)

ADVERTISEMENT RETURN TO ISSUEPREVReviewNEXTAdvancements in Top-Down ProteomicsHu Zhou†‡, Zhibing Ning†, Amanda E. Starr†, Mohamed Abu-Farha§, and Daniel Figeys*†View Author Information† Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1H8M5‡ Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China 201203§ Biochemistry and Molecular Biology Unit, Dasman Diabetes Institute, Dasman 15462, Kuwait*Phone: 613-562-5800 ext. 8674. Fax: 613-562-5655. E-mail: [email protected]Cite this: Anal. Chem. 2012, 84, 2, 720–734Publication Date (Web):November 2, 2011Publication History Published online15 November 2011Published inissue 17 January 2012https://pubs.acs.org/doi/10.1021/ac202882yhttps://doi.org/10.1021/ac202882yreview-articleACS PublicationsCopyright © 2011 American Chemical SocietyRequest reuse permissionsArticle Views4396Altmetric-Citations74LEARN 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 SUBJECTS:Ions,Mass spectrometry,Peptides and proteins,Protein identification,Proteomics Get e-Alerts
The Amyloid β Protein Gene Is Not Duplicated in Brains from Patients with Alzheimer's Disease (1987)

Complementary DNAs (cDNAs) encoding portions of the amyloid beta protein were used to investigate possible amyloid gene duplication in sporadic Alzheimer's disease. A strategy employing two Eco RI restriction fragment length polymorphisms (RFLPs) detected by the amyloid cDNAs was used. RFLPs allow the detection of a 2:1 gene dosage in the DNA of any individual who is heterozygous for a particular RFLP. The amyloid gene regions homologous to the cDNAs used were not duplicated in the DNA from brains of individuals with sporadic Alzheimer's disease. Similar results were also obtained with a strategy employing a test for 3:2 gene dosage.
Therapy-Resistant Complex Regional Pain Syndrome Type I: To Amputate or Not? (2011)

The previously published studies regarding CRPS-I as a reason for amputation all represent Level-IV evidence, and they do not clearly delineate the beneficial and adverse affects of an amputation performed for this diagnosis. Whether to amputate or not in order to treat long-standing, therapy-resistant CRPS-I remains an unanswered question.
PLANTAR FAT PAD ATROPHY AFTER CORTICOSTEROID INJECTION FOR AN INTERDIGITAL NEUROMA (1999)

A case of bilateral interdigital (Morton's) neuroma treated with steroid injection therapy developed plantar fat pad atrophy, shown on magnetic resonance imaging. Some pathologic changes at the site of injection (such as subcutaneous fat atrophy, depigmentation of the skin, and telangiectasias) are well known disadvantages of local steroid injection for the treatment of the Morton's neuroma. Scientific literature reports these problems (mainly as an aesthetic problem) in the dorsal aspect of the foot. In this work, the authors describe a case in which the steroid injection therapy has caused some changes in the plantar aspect of the feet, with serious functional problems. Fat pad atrophy is a serious problem in the foot and can cause a painful metatarsal syndrome with some important effects on the gait.
A strategy for optimizing the monodispersity of fusion proteins: application to purification of recombinant HPV E6 oncoprotein (2001)

Recombinant production of HPV oncoprotein E6 is notoriously difficult. The unfused sequence is produced in inclusion bodies. By contrast, fusions of E6 to the C-terminus of carrier proteins such as maltose-binding protein or glutathione-S-transferase are produced soluble. However, it has not yet been possible to purify E6 protein from such fusion constructs. Here, we show that this was due to the biophysical heterogeneity of the fusion preparations. We find that soluble MBP-E6 preparations contain two subpopulations. A major fraction is aggregated and contains exclusively misfolded E6 moieties ('soluble inclusion bodies'). A minor fraction is monodisperse and contains the properly folded E6 moieties. Using monodispersity as a screening criterion, we optimized the expression conditions, the purification process and the sequence of E6, finally obtaining stable monodisperse MBP-E6 preparations. In contrast to aggregated MBP-E6, these preparations yielded fully soluble E6 after proteolytic removal of MBP. Once purified, these E6 proteins are stable, folded and biologically active. The first biophysical measurements on pure E6 were performed. This work shows that solubility is not a sufficient criterion to check that the passenger protein in a fusion construct is properly folded and active. By contrast, monodispersity appears as a better quality criterion. The monodispersity-based strategy presented here constitutes a general method to prepare fusion proteins with optimized folding and biological activity.
Microdeformational Wound Therapy (2006)

The vacuum-assisted closure (VAC) device causes microdeformations of the wound surface in contact with the foam. Because angiogenesis and matrix metalloproteinase (MMP) activity are altered in chronic wounds, we hypothesized that microdeformations stimulate capillary formation and affect MMP activity. A VAC device was used to deliver microdeformational wound therapy (MDWT) to the chronic wounds of 3 debilitated patients. Debrided tissue was obtained from wound areas with and without foam contact. Microvessel density and MMP activity were determined by immunohistochemistry and zymography, respectively. Microvessel density of MDWT-treated wounds was 4.5% (+/-0.8) compared with areas not covered by foam [1.6% (+/-0.1)] (P = 0.05) during the first week of treatment and 2.7% (+/-0.3) compared with untreated tissue [1.3% (+/-0.1)] (P = 0.03) during the second treatment week. Wounds subjected to MDWT had greater microvessel density compared with the same wound prior to treatment [1.5% (+/-0.3)] (P = 0.02). MMP-9/NGAL (neutrophil gelatinase-associated lipocalin), MMP-9, latent MMP-2, and active MMP-2 were reduced by 15%-76% in MDWT-treated wounds. MDWT provides a favorable wound-healing environment by increasing angiogenesis and decreasing MMP activity in chronic wounds.
Chloroquine myopathy and myasthenia‐like syndrome (1988)

A young woman on chronic corticosteroid treatment for systemic lupus erythematosus developed a myasthenia-like syndrome 7 weeks after starting chloroquine therapy. Discontinuation of chloroquine allowed symptomatic and immunological remission within 6 months. Ocular symptoms reappeared following a second short course of chloroquine. A motor-point biopsy revealed a vacuolar myopathy with membranous bodies in intramuscular nerves. We discuss the possible role of chloroquine in the pathogenesis of a myasthenia-like syndrome.
Efficacy and safety of oral cyclosporin A (CyA; SandimmunR) for long-term treatment of chronic severe plaque psoriasis (1994)

The value of oral cyclosporin A (CyA; Sandimmun) in the treatment of chronic severe plaque psoriasis has already been established. Many controlled studies have addressed the issues of efficacy and safety, mostly in studies of several months duration. Patients treated for up to several years have been reported, but never in multicentre controlled studies. Guidelines have established the maximum dose permissible to reduce the risk of side-effects. However, the efficacy and safety of therapy of longer duration remain under investigation. The results of a multicentre prospective randomized clinical study (251 patients) to evaluate the efficacy, safety and tolerability of two dose levels of CyA (2.5 or 5 mg/kg/day) for inducing remission, and for use in long-term maintenance therapy for up to 21 months, are presented. An assessment of relapse as the dose was tapered (during the last 3 months of treatment), and the reversibility of CyA-induced side-effects, is also presented (follow-up phase of 3 months). Efficacy was evaluated by means of the psoriasis area and severity index (PASI). Safety was assessed by using the results of vital signs, physical examination, laboratory tests and physician and patient evaluation of adverse events. During the induction of remission phase of therapy, a total of 184 patients (73%) were treated successfully. The percentage of patients classified as successes at the end-point was significantly higher in the group on 5.0 mg/kg/day (92%) than in that on 2.5 mg/kg/day (52%; P < 0.001). A total of 215 (86%) patients reported at least one adverse event during the study. In 136 patients (54%) the reported adverse event was judged by the investigator as being related to CyA. Nineteen patients (8%) reported events that were judged as severe, and related to treatment with CyA. A total of 45 patients (18%) discontinued treatment due to adverse events. Hypertension was one of the reasons, or the reason, for discontinuation in 16 patients (6%). The occurrence of hypertension appeared unrelated to CyA dose. One hundred and sixteen patients (46%) experienced a maximum increase in serum creatinine > 30% above baseline values on at least one occasion. This increase in serum creatinine was often transient, and was one of the reasons, or the reason, for discontinuation in 24 patients (10%). An increase in serum creatinine > 30% above baseline was dose-related. The results of this study show that 5.0 mg/kg/day of CyA is significantly more effective than 2.5 mg/kg/day in the treatment of chronic plaque psoriasis.(ABSTRACT TRUNCATED AT 400 WORDS)
Don't Scrap It, Wrap It! A Wrapper Architecture for Legacy Data Sources (1997)

Garlic is a middleware system that provides an integrated view of a variety of legacy data sources, without changing how or where data is stored. In this paper, we describe our architecture for wrappers, key components of Garlic that encapsulate data sources and mediate between them and the middleware. Garlic wrappers model legacy data as objects, participate in query planning, and provide standard interfaces for method invocation and query execution. To date, we have built wrappers for 10 data sources. Our experience shows that Garlic wrappers can be written quickly and that our architecture is flexible enough to accommodate data sources with a variety of data models and a broad range of traditional and non-traditional query processing capabilities.
Microbial degradation of oxalate in the gastrointestinal tracts of rats (1987)

Rates of oxalate degradation by mixed bacterial populations in cecal contents from wild rats ranged from 2.5 to 20.6 mumol/g (dry weight) per h. The oxalate-degrading activity in cecal contents from three strains of laboratory rats (Long-Evans, Wistar, and Sprague-Dawley) from four commercial breeders was generally lower, ranging from 1.8 to 3.5 mumol/g (dry weight) of cecal contents per h. This activity did not increase when diets were supplemented with oxalate. When Sprague-Dawley rats from a fifth commercial breeder were fed an oxalate diet, rates of oxalate degradation in cecal contents increased from 2.0 to 23.1 mumol/g (dry weight) per h. Obligately anaerobic, oxalate-degrading bacteria, similar to ruminal strains of Oxalobacter formigenes, were isolated from the latter group of laboratory rats and from wild rats. Viable counts of these bacteria were as high as 10(8)/g (dry weight) of cecal contents, which was less than 0.1% of the total viable population. This report presents the first evidence for the presence of anaerobic oxalate-degrading bacteria in the cecal contents of rats and represents the first direct measurement of the concentration of these bacteria in the large bowel of monogastric animals. We propose that methods used for the maintenance of most commercial rat colonies often preclude the intestinal colonization of laboratory rats with anaerobic oxalate-degrading bacteria.
Expression of Chlamydia pneumoniae Polymorphic Membrane Protein Family Genes (2001)

The genome of the obligate intracellular bacterium Chlamydia pneumoniae CWL029 encodes a family of 21 proteins with predicted outer membrane localization. These polymorphic membrane proteins (Pmps) are heterogeneous in both amino acid sequence and predicted size but are unified by the conserved amino acid motifs GGAI and FXXN repeated in the N-terminal half of each protein. Reverse transcriptase PCR analysis showed that all pmp genes are transcribed. To determine whether all proteins are expressed, specific antisera were generated by immunization with mutually exclusive synthetic peptides representing each of the 21 predicted Pmps. Each antiserum reacted with, and was typically immunospecific for, the corresponding peptide immunogen by enzyme-linked immunosorbent assay. Western blot analyses of purified elementary bodies showed that 11 of the 21 Pmps were detectable. Attempts to demonstrate by Sarykosyl fractionation that the Pmps were localized to the outer membrane revealed that several of the Pmps were unstable and readily degraded. Analyses of additional C. pneumoniae strains showed that although some Pmps are conserved, others vary between strains, in both molecular weight and level of expression.
A comparison of merging strategies for translation of German compounds (2009)

In this article, compound processing for translation into German in a factored statistical MT system is investigated. Compounds are handled by splitting them prior to training, and merging the parts after translation. I have explored eight merging strategies using different combinations of external knowledge sources, such as word lists, and internal sources that are carried through the translation process, such as symbols or parts-of-speech. I show that for merging to be successful, some internal knowledge source is needed. I also show that an extra sequence model for part-of-speech is useful in order to improve the order of compound parts in the output. The best merging results are achieved by a matching scheme for part-of-speech tags.
Berenil [1,3-Bis(4'-amidinophenyl)triazene] Binding to DNA Duplexes and to a RNA Duplex: Evidence for Both Intercalative and Minor Groove Binding Properties (1995)

Berenil is an antitrypanosomal agent that binds to nucleic acid duplexes. The generally accepted mode of berenil binding is via complexation into the minor groove of AT-rich domains of DNA double helices. We find that berenil can bind to RNA as well as DNA duplexes, while exhibiting properties characteristic of both intercalation as well as minor groove binding. More specifically, we use spectroscopic, calorimetric, and hydrodynamic techniques to characterize berenil binding to four DNA duplexes and to one RNA duplex. Our results reveal the following features: (i) Berenil binding to the poly[d(A-T)]2, poly(dA).poly(dT), poly[d(I-C)]2, poly[d(G-C)]2, and poly(rA).poly(rU) duplexes exhibits intercalative as well as minor groove binding characteristics. (ii) The apparent "site sizes" associated with berenil binding to these five duplexes range from 1 to 13 base pairs per bound berenil and depend, in part, on the host duplex. One of the site sizes common to all five duplexes is consistent with berenil binding to the minor groove. (iii) The apparent berenil binding affinity follows the hierarchy: poly(dA).poly(dT) > poly-[d(A-T)]2 approximately poly[d(I-C)]2 >> poly(rA).poly(rU) > poly[d(G-C)]2. (iv) Viscometric data reveal properties characteristic of a significant contribution from an intercalative mode of binding when berenil interacts with the poly[d(A-T)]2, poly[d(I-C)]2, poly[d(G-C)]2, and poly(rA).poly(rU) duplexes, while revealing an apparent nonintercalative mode when the drug binds to the poly(dA).poly(dT) duplex. (v) Berenil binding unwinds negative supercoils in the pBR322 plasmid, an observation consistent with an intercalative mode of binding to duplex DNA. (vi) Salt-dependent melting data suggest that both positively charged amidino groups of berenil participate in the complexation of the drug to the poly[d(I-C)]2, poly[d(A-T)]2, poly(dA).poly(dT), and poly(rA).poly(rU) duplexes, while also suggesting that the binding event is site-specific. In the aggregate, our results suggest that, in contrast to the conventional wisdom, berenil can exhibit intercalative as well as minor groove binding properties when it binds to both DNA and RNA duplexes, while also exhibiting a preference for DNA duplexes with unobstructed minor grooves. We comment on the potential correlation between drugs, such as berenil, that exhibit "mixed" binding motifs and those that express anticancer activity via inhibition of topoisomerase I activity.
A micro membrane pump with electrostatic actuation (1992)

A bulk micromachined membrane pump with outer dimensions of 7 mm*7 mm*2 mm and electrostatic actuation is presented. The micropump consists of four silicon chips, which form two passive check valves, a pump membrane and a counterelectrode for electrostatic actuation. Direct electrostatic forces are used for the deflection of the pump membrane, which has an area of 4 mm*4 mm and a thickness of 25 mu m. The liquid to be pumped is not subjected to any electrical field. The separation between the movable membrane and the electrically isolated stator is 4 mu m.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Protection of turkeys against Chlamydophila psittaci challenge by parenteral and mucosal inoculations and the effect of turkey interferon‐γ on genetic immunization (2001)

Plasmid DNA (pcDNA1::MOMP A) expressing the major outer membrane protein of an avian Chlamydophila psittaci serovar A strain was tested for its ability to induce protective immunity against challenge with the same C. psittaci serovar. A combined parenteral (intramuscular injection) and mucosal route (DNA drops administered to the nares) of DNA inoculation was compared to three other, different routes of administration (intramuscular inoculation, DNA drops administered to the nares and aerosol immunization). In addition, the effect of turkey interferon gamma (tIFN-gamma) on intramuscular immunization was evaluated by co-expressing pCIneo::tIFN-gamma. A significant level of protection was observed in turkeys immunized via the combined parenteral/mucosal route, the intramuscular route or by aerosol. Severe clinical signs and lesions were observed in the non-vaccinated control groups, in 80% of turkeys inoculated with a mixture of pcDNA1::MOMP A and pCIneo::tIFN-gamma, and in 60% of turkeys vaccinated with DNA drops administered to the nares. The use of MOMP-based DNA vaccination as a means of preventing severe clinical signs and lesions in a turkey model of C. psittaci infection was demonstrated, as was down-regulation of the immune response by co-expression of tIFN-gamma.
Capacitative Ca2+ Entry Is Closely Linked to the Filling State of Internal Ca2+ Stores: A Study Using Simultaneous Measurements of ICRAC and Intraluminal [Ca2+] (1998)

ICRAC (the best characterized Ca2+ current activated by store depletion) was monitored concurrently for the first time with [Ca2+] changes in internal stores. To establish the quantitative and kinetic relationship between these two parameters, we have developed a novel means to clamp [Ca2+] within stores of intact cells at any level. The advantage of this approach, which is based on the membrane-permeant low-affinity Ca2+ chelator N,N,N',N'-tetrakis (2-pyridylmethyl)ethylene diamine (TPEN), is that [Ca2+] within the ER can be lowered and restored to its original level within 10-15 s without modifications of Ca2+ pumps or release channels. Using these new tools, we demonstrate here that Ca2+ release-activated Ca2+ current (ICRAC) is activated (a) solely by reduction of free [Ca2+] within the ER and (b) by any measurable decrease in [Ca2+]ER. We also demonstrate that the intrinsic kinetics of inactivation are relatively slow and possibly dependent on soluble factors that are lost during the whole-cell recording.
FcγRIIIa Expression on Monocytes in Rheumatoid Arthritis: Role in Immune-Complex Stimulated TNF Production and Non-Response to Methotrexate Therapy (2012)

Increased FcγRIIIa/CD16 expression on CD14++ monocytes in RA may result in a cell that has increased responsiveness to IC-stimulation. This monocyte subset may contribute to non-response to methotrexate therapy.
Synthesis of many different types of organic small molecules using one automated process (2015)

Small-molecule synthesis usually relies on procedures that are highly customized for each target. A broadly applicable automated process could greatly increase the accessibility of this class of compounds to enable investigations of their practical potential. Here we report the synthesis of 14 distinct classes of small molecules using the same fully automated process. This was achieved by strategically expanding the scope of a building block-based synthesis platform to include even C(sp3)-rich polycyclic natural product frameworks and discovering a catch-and-release chromatographic purification protocol applicable to all of the corresponding intermediates. With thousands of compatible building blocks already commercially available, many small molecules are now accessible with this platform. More broadly, these findings illuminate an actionable roadmap to a more general and automated approach for small-molecule synthesis.
Reconstitution, Identification, and Purification of the Rat Liver Golgi Membrane GDP-fucose Transporter (1999)

Glycosylation of glycoproteins, proteoglycans, and glycolipids occurring in the Golgi apparatus requires the translocation of nucleotide sugars from the cytosol into the lumen of the Golgi. Translocation is mediated by specific nucleotide sugar transporters, integral Golgi membrane proteins that regulate the above glycosylation reactions. A defect in GDP-fucose transport into the lumen of the Golgi apparatus has been recently identified in a patient affected by leukocyte adhesion deficiency type II syndrome (Lubke, T., Marquardt, T., von Figura, K., and Korner, C. (1999) J. Biol. Chem. 274, 25986-25989). We have now identified and purified the rat liver Golgi membrane GDP-fucose transporter, a protein with an apparent molecular mass of 39 kDa, by a combination of column chromatography, native functional size determination on a glycerol gradient, and photoaffinity labeling with 8-azidoguanosine-5'-[alpha-(32)P] triphosphate, an analog of GDP-fucose. The purified transporter appears to exist as a homodimer within the Golgi membrane. When reconstituted into phosphatidylcholine liposomes, it was active in GDP-fucose transport and was specifically photolabeled with 8-azidoguanosine-5'-[alpha-(32)P]triphosphate. Transport was also stimulated 2-3-fold after preloading proteoliposomes with GMP, the putative antiporter.
Extermely sensitive diagnostic assay based on the exponential amplification of binary hybridization probes by Qb replicase (1996)

Extermely sensitive diagnostic assay based on the exponential amplification of binary hybridization probes by Qb replicase