gebhart/patrepeval huggingface dataset:
Mass spectrometry tools and metabolite-specific databases for molecular identification in metabolomics (2009)

The chemical identification of mass spectrometric signals in metabolomic applications is important to provide conversion of analytical data to biological knowledge about metabolic pathways. The complexity of electrospray mass spectrometric data acquired from a range of samples (serum, urine, yeast intracellular extracts, yeast metabolic footprints, placental tissue metabolic footprints) has been investigated and has defined the frequency of different ion types routinely detected. Although some ion types were expected (protonated and deprotonated peaks, isotope peaks, multiply charged peaks) others were not expected (sodium formate adduct ions). In parallel, the Manchester Metabolomics Database (MMD) has been constructed with data from genome scale metabolic reconstructions, HMDB, KEGG, Lipid Maps, BioCyc and DrugBank to provide knowledge on 42,687 endogenous and exogenous metabolite species. The combination of accurate mass data for a large collection of metabolites, theoretical isotope abundance data and knowledge of the different ion types detected provided a greater number of electrospray mass spectrometric signals which were putatively identified and with greater confidence in the samples studied. To provide definitive identification metabolite-specific mass spectral libraries for UPLC-MS and GC-MS have been constructed for 1,065 commercially available authentic standards. The MMD data are available at http://dbkgroup.org/MMD/.
Adipose Tissue Leptin Production and Plasma Leptin Kinetics in Humans (1996)

Abdominal adipose tissue leptin production was determined in vivo by arteriovenous balance in 14 lean and obese men (mean BMI 27.0 +/- 1.9, range 21.4-45.2). Blood samples were taken simultaneously from an abdominal vein that drains subcutaneous adipose tissue and from a radial artery. Adipose tissue blood flow was measured by xenon washout. Abdominal vein leptin concentrations (mean 8.9 +/- 2.4 ng/ml, range 2.1-36.5 ng/ml) were consistently greater than arterial values (mean 6.6 +/- 1.9 ng/ml, range 1.7-28.2 ng/ml) (P < 0.001). The net rate of abdominal adipose tissue leptin production (mean 3.2 +/- 0.5 ng x 100 g(-1) x min(-1)) correlated directly with percentage body fat (rs = 0.59, P = 0.016). Estimated whole-body leptin production rate (797 +/- 283 ng x person(-1) x min(-1)) correlated directly with percent body fat (rs = 0.93, P < 0.0001) and with regional leptin production (rs = 0.81, P < 0.001). In contrast, the rate of leptin clearance from plasma (mean 1.50 +/- 0.23 ml x kg(-1) x min(-1)) and plasma leptin half-life (mean 24.9 +/- 4.4 min) was unrelated to adiposity (rs = 0.06, P = 0.30; rs = 0.16, P = 0.30, respectively). These results provide direct evidence that leptin is produced by adipose tissue in humans and that the rate of production is directly related to adiposity. A combination of greater leptin production per unit of body fat and increased production from expanded total body fat mass, rather than alterations in leptin clearance, account for the increase in plasma leptin concentrations observed in obese humans.
Characteristics of binding to estrogen, androgen, progestin, and glucocorticoid receptors in 7,12-dimethylbenz(a)anthracene-induced mammary tumors and their hormonal control. (1980)

Abstract In order to perform simultaneous measurement of binding of four classes of steroids and facilitate study of their mechanism of action in 7,12-dimethylbenz( a )anthracene-induced mammary tumors in the rat, we have investigated in detail the binding characteristics of 17β-[2,4,6,7,16,17- 3 H]estradiol (17β-[ 3 H]estradiol), 17,21-[6,7- 3 H]dimethyl-19-norpregna-4,9-diene-3,20-dione ([ 3 H]R5020), [ 3 H]dexamethasone (DEX), and 5α-[ 3 H]dihydrotestosterone (DHT) in cytosol prepared from these tumors. Following assessment of optimal buffer composition, separation of bound and free steroids was achieved with dextran-coated charcoal, protamine sulfate, or hydroxylapatite. Using the same buffer and the optimal method of separation for each tracer, we have found that the time course of binding of each labeled steroid was fast, the slowest rate of association being obtained with [ 3 H]DEX ( t ⋍ 100 to 150 min) at 4°. In addition, the level of specific binding of each tracer was stable for a period of at least 21 hr at 4° but decreased markedly at 23° (except with 17β-[ 3 H]estradiol). Complete exchange of the tracer from the binding component was achieved at 4° for [ 3 H]R5020 and at 23° for 17β-[ 3 H]estradiol. Although [ 3 H]DEX dissociated from its binding component at 4°, the receptor complex was unstable during long-term incubations necessary to achieve complete exchange. No significant exchange of [ 3 H]DHT binding occurred at 4°. Using six increasing concentrations of a large series of unlabeled steroids, each tracer showed a high degree of binding specificity. Sucrose gradient analysis performed in low-ionic-strength buffer revealed specific and protamine sulfate-precipitable steroid-binding components migrating in the 8 to 9S area for 17β-[ 3 H]estradiol, 7S and 4 to 5S for [ 3 H]R5020, and 7 to 8S for [ 3 H]DEX and [ 3 H]DHT. Sucrose gradient analysis in a high-ionic-strength buffer (0.4 m KCl) gave only one labeled area (3 to 5S) for each tracer. Scatchard analysis revealed K d 9s of 0.14 nm for 17β-[ 3 H]estradiol, 2.9 nm for [ 3 H]R5020, 13 nm for [ 3 H]DEX, and 0.45 nm for [ 3 H]DHT binding. In a second series of experiments, while adrenalectomy had no effect on the binding of any of the four classes of steroids, 17β-[ 3 H]estradiol, [ 3 H]R5020, and [ 3 H]DHT binding levels were decreased in 7,12-dimethylbenz( a )anthracene-induced mammary tumors after ovariectomy plus adrenalectomy or hypophysectomy, while the binding of [ 3 H]DEX remained unchanged. The present data describe the optimal conditions for simultaneous and specific measurement of binding of four classes of steroids in cytosol from 7,12-dimethylbenz( a )anthracene-induced mammary tumors in the rat. Moreover, as revealed by hypophysectomy, adrenalectomy, and ovariectomy, the levels of the progesterone and glucocorticoid receptors are under different hormonal control.
Macrocyclic Chelators with Paramagnetic Cations Are Internalized into Mammalian Cells via a HIV-Tat Derived Membrane Translocation Peptide (2000)

A major obstacle to using paramagnetic MR contrast agents for in vivo cell tracking or molecular sensing is their generally low cellular uptake. In this study, we show that a paramagnetically labeled DOTA chelator derivatized with a 13-mer HIV-tat peptide is efficiently internalized into mammalian cells. Intracellular concentrations were attained that were readily detectable by MR imaging using both gadolinium and dysprosium chelates. Using this paradigm, it should be feasible to internalize a variety of chemically different agents into mammalian cells.
Beyond DNA: Zinc Finger Domains as RNA-Binding Modules (2010)

Over the last 25 years, we have learned that many structural classes of zinc-binding domains (zinc fingers, ZFs) exist and it has become clear that the molecular functions of these domains are by no means limited to the sequence-specific recognition of double-stranded DNA. For example, ZFs can act as protein recognition or RNA-binding modules, and some domains can exhibit more than one function. In this chapter we describe the progress that has been made in understanding the role of ZF domains as RNA-recognition modules, and we speculate about both the prevalence of such functions and the prospects for creating designer ZFs that target RNA.
Fast and globally optimal single view reconstruction of curved objects (2012)

We propose a novel algorithmic solution for estimating a three-dimensional model of an object observed in a single image. Based on a minimal user input, the algorithm interactively determines the objects' silhouette and subsequently computes a silhouette-consistent 3D model which is precisely the globally minimal surface with user-specified volume. In contrast to a recently published approach to single view reconstruction, the proposed algorithm does not constrain the resolution in the depth-direction, it assures the global optimum and is faster by about an order of magnitude. Experiments demonstrate that plausible high-resolution 3D models can be generated in fractions of a second and compare favorably with other methods.
Pseudo Esters of Levulinic Acid (1948)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPseudo Esters of Levulinic AcidDavid P. Langlois and Hans WolffCite this: J. Am. Chem. Soc. 1948, 70, 8, 2624–2626Publication Date (Print):August 1, 1948Publication History Published online1 May 2002Published inissue 1 August 1948https://doi.org/10.1021/ja01188a004RIGHTS & PERMISSIONSArticle Views516Altmetric-Citations31LEARN 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 InReddit PDF (363 KB) Get e-Alerts Get e-Alerts
Suppression of Reaginic Antibodies with Modified Allergens (1981)

Our previous findings that antigens, such as ovalbumin (OA) and the extract of ragweed pollen (RAG), could be rendered nonantigenic, nonallergenic and tolerogenic by conjugation with polyethylene glycol (PEG) have been extended in the present study to the synthesis of conjugates of a variety of antigens with monofunctional monomethoxy-PEGs (mPEGS) of different molecular weights by the use of the mixed anhydride method. Thus, mPEGs with molecular weights of 2,000, 5,000, 10,000 and 20,000 were coupled to proteins such as dog serum albumin (DA), bovine pancreatic ribonuclease, OA and the constituents of pollen, helminth and bacterial allergens (RAG, Timothy grass pollen, &lt;i&gt;Ascaris suum &lt;/i&gt;and &lt;i&gt;Micropolyspora faeni&lt;/i&gt;)&lt;i&gt;. &lt;/i&gt;All these mPEG conjugates depressed markedly the ongoing IgE antibody formation in sensitized animals, in spite of additional injections of the sensitizing dose of the appropriate antigen. Moreover, the allergenicity of the proteins was either totally abolished or markedly reduced after coupling to mPEGs. Conjugates of DA and OA of varying degree of substitution (i.e. number of mPEG molecules attached per protein molecule) were prepared with mPEGs of different molecular weights and their immunological properties were assessed. It appears that, for a series of tolerogenic conjugates of the same antigen, there exists some inverse relationship between the degree of substitution and the molecular weight of mPEG, i.e. a high level of tolerogenicity with a concomitant reduction or total loss of allergenicity was achieved with a lower degree of substitution utilizing mPEGs of increasing molecular weights. On the basis of these results, it is concluded that a variety of allergens may be converted by conjugation with mPEGs to tolerogenic products with a potential for use in the therapy of patients allergic to a wide spectrum of common allergens.
Mid‐infrared (IR) – A hot topic: The potential for using mid‐IR light for non‐invasive early detection of skin cancer in vivo (2013)

Abstract magnified image After an introduction to the mid‐infrared (IR) spectral region, the tremendous significance of mid‐IR spectroscopic sensing is highlighted. The remarkable progress made towards mid‐IR spectral in vitro mapping of tissue and cancer detection is reviewed, with emphasis on diagnosis of skin cancer. The status quo of chalcogenide glass mid‐IR fibre optics and photonics for meeting opportunities for remote mid‐IR sensing in general, and in in vivo cancer detection in particular, is assessed. Raman spectroscopy is a sister technique to mid‐IR spectroscopy. The current success of Raman spectroscopy in medical diagnosis is appraised, with particular emphasis on Raman spectral imaging of tissue towards skin cancer diagnosis in vivo , based on a silica‐glass fibreoptic sensor‐head. The challenges to be met in chalcogenide glass science and technology towards facilitating analogous fibreoptic diagnostics based on mid‐IR spectroscopy are addressed.
Transluminal aortic valve placement. A feasibility study with a newly designed collapsible aortic valve. (1997)

Percutaneous stents are used in vascular applications in conjunction with angioplasty and in combination with graft material for repair of abdominal aneurysms. The authors have designed a collapsible bioprosthetic aortic valve for placement by a transluminal catheter technique. This trileaflet stent valve is composed of stainless steel and bovine pericardium. Stent valves, 23 and 29 mm, were tested in a pulse duplicator system with rigid rings from 21 to 31 mm in 2 mm increments. At a mean flow of 3.1 L/min (+/-0.7), normal systemic aortic pressure was generated with a transvalvular gradient of 14.9 +/- 7 mmHg (mean +/- SD). Regurgitation fraction ranged from 10 to 18% (mean 13.8 +/- 3%) in the best ring size. Valves with the best hemodynamic profile were used for implantation in three 70 kg pigs in an open chest model. The valve was collapsed in a 24 Fr catheter designed to allow slow, controlled release. After resection of the native leaflets, the new valve was placed in the subcoronary position. No additional sutures were used for securing the valve. Two animals were successfully weaned from cardiopulmonary bypass and maintained systemic pressures of 100/45 (+/-10) and 116/70 (+/-15) mmHg, respectively. Intraoperative color echocardiography revealed minimal regurgitation, central flow, full apposition of all leaflets, and no interference with coronary blood flow. Both animals were sacrificed after being off bypass for 2 hr. Postmortem examination revealed the valves to be securely anchored. The third animal was weaned from cardiopulmonary bypass but developed refractory ventricular fibrillation because of valve dislodgment due to structural failure. Although long term survival data are needed, development of a hemodynamically acceptable prosthetic aortic valve for transluminal placement is feasible.
Patterns Of Septic Shock In Man—a Detailed Study Of 56 Patients (1967)

MACLEAN, LLOYD D. M.D., F.R.C.S.(C); MULLIGAN, WILLIAM G. M.D.; MCLEAN, A. P. H. M.D., F.R.C.S.(C); DUFF, JOHN H. M.D., F.R.C.S.(C) Author Information
Negotiating the Barrier of Hypoglycemia in Diabetes (2002)

Hypoglycemia is the limiting factor in the glycemic management of diabetes. It is a barrier to quality of life and even survival in the short term and to true glycemic control, with its established microvascular and potential macrovascular benefits, in the long term. Although it is possible to both improve glycemic control and minimize the risk of hypoglycemia in many patients with currently available regimens—by applying the principles of aggressive therapy and practicing hypoglycemia risk reduction—people with diabetes need treatment methods that provide glucose-regulated insulin secretion or replacement if euglycemia is to be maintained safely over a lifetime of diabetes.
Cytomegalovirus MicroRNA Expression Is Tissue Specific and Is Associated with Persistence (2010)

MicroRNAs (miRNAs) are a class of small noncoding RNAs involved in posttranscriptional regulation. miRNAs are utilized in organisms ranging from plants to higher mammals, and data have shown that DNA viruses also use this method for host and viral gene regulation. Here, we report the sequencing of the small RNAs in rat cytomegalovirus (RCMV)-infected fibroblasts and persistently infected salivary glands. We identified 24 unique miRNAs that mapped to hairpin structures found within the viral genome. While most miRNAs were detected in both samples, four were detected exclusively in the infected fibroblasts and two were specific for the infected salivary glands. The RCMV miRNAs are distributed across the viral genome on both the positive and negative strands, with clusters of miRNAs at a number of locations, including near viral genes r1 and r111. The RCMV miRNAs have a genomic positional orientation similar to that of the miRNAs described for mouse cytomegalovirus, but they do not share any substantial sequence conservation. Similar to other reported miRNAs, the RCMV miRNAs had considerable variation at their 3' and 5' ends. Interestingly, we found a number of specific examples of differential isoform usage between the fibroblast and salivary gland samples. We determined by real-time PCR that expression of the RCMV miRNA miR-r111.1-2 is highly expressed in the salivary glands and that miR-R87-1 is expressed in most tissues during the acute infection phase. Our study identified the miRNAs expressed by RCMV in vitro and in vivo and demonstrated that expression is tissue specific and associated with a stage of viral infection.
Substitution in .beta.-cyclodextrin directed by basicity: preparation of 2-O- and 6-O-[(R)- and (S)-2-hydroxypropyl] derivatives (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSubstitution in .beta.-cyclodextrin directed by basicity: preparation of 2-O- and 6-O-[(R)- and (S)-2-hydroxypropyl] derivativesC. Trinadha Rao, Bengt Lindberg, Johan Lindberg, and Josef PithaCite this: J. Org. Chem. 1991, 56, 3, 1327–1329Publication Date (Print):February 1, 1991Publication History Published online1 May 2002Published inissue 1 February 1991https://pubs.acs.org/doi/10.1021/jo00003a082https://doi.org/10.1021/jo00003a082research-articleACS PublicationsRequest reuse permissionsArticle Views452Altmetric-Citations47LEARN 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
Oligonucleotidase Activity of Phosphodiesterase from the Fruit Body ofFlammulina velutipes (1990)

Journal Article Oligonucleotidase Activity of Phosphodiesterase from the Fruit Body of Flammulina velutipes Get access Shin-ichi Kurosawa, Shin-ichi Kurosawa Department of Bioscience and Biotechnology, Shinshu University, 8304 Minamiminowa, Nagano 399-45, Japan Search for other works by this author on: Oxford Academic Google Scholar Alfredo M Shimabuku T, Alfredo M Shimabuku T Department of Bioscience and Biotechnology, Shinshu University, 8304 Minamiminowa, Nagano 399-45, Japan Search for other works by this author on: Oxford Academic Google Scholar Hiroshi Ishizawa, Hiroshi Ishizawa Department of Bioscience and Biotechnology, Shinshu University, 8304 Minamiminowa, Nagano 399-45, Japan Present address: Fushimi Kamaboko Co., Ltd., Niigata 950, Japan Search for other works by this author on: Oxford Academic Google Scholar Kikuo Sen Kikuo Sen Department of Bioscience and Biotechnology, Shinshu University, 8304 Minamiminowa, Nagano 399-45, Japan Search for other works by this author on: Oxford Academic Google Scholar Agricultural and Biological Chemistry, Volume 54, Issue 3, 1 March 1990, Pages 587–592, https://doi.org/10.1080/00021369.1990.10869999 Published: 01 March 1990 Article history Received: 24 July 1989 Published: 01 March 1990
Identification of Cancer Stem-like Side Population Cells in Ovarian Cancer Cell Line OVCAR-3 (2009)

Side population (SP) cells may enrich stem-like cells in many normal and malignant tissues. However, SP method application has drawn special attention to the field of stem cell research, and the existence of SP cells in cell culture is being debated, most probably because different cell lines require different technical modifications, especially when cell staining is considered. In this study, the authors aimed to disclose whether the hoechst33342 staining required extensive optimization for identifying SP cells in the human ovarian cancer cell line OVCAR-3. After systematic evaluations, it was found that only 2.5 microg/mL hoechst33342 staining of the cells for 60 min could get an ideal SP population, which accounted for 0.9% of the whole cell population. The sorted SP cells showed significantly higher colony formation efficiency than the non-side population (NSP) cells, and only the SP cells could form holoclones. Real-time PCR disclosed that SP cells expressed higher levels of "stemness" gene Oct3/4 than the NSP cells did, indicating that the SP cells might harbor cancer stem cells in this cell line. The results highlight the necessity of SP method optimization in cell studies, and the SP cells in this cell line merit further studies when cancer stem cell identification and isolation are considered.
Pharyngeal Pressure and Flow Effects on Genioglossus Activation in Normal Subjects (2002)

Pharyngeal dilator muscles are clearly important in the pathogenesis of obstructive sleep apnea syndrome. Substantial data support the role of local mechanisms in mediating pharyngeal dilator muscle activation in normal humans during wakefulness. Using a recently reported iron lung ventilation model, we sought to determine the stimuli modulating genioglossus activity, dissociating the influences of pharyngeal negative pressure, from inspiratory airflow, resistance, and CO(2). To achieve this aim, we used two gas densities at several levels of end-tidal CO(2) and a number of intrapharyngeal negative pressures. The correlations between genioglossus electromyography (GGEMG) and epiglottic pressure across a breath remained robust under all conditions (R values range from 0.71 +/- 0.07 to 0.83 +/- 0.05). In addition, there was no significant change in the slope of this relationship despite variable gas density or CO(2) levels. Although flow also showed strong correlations with genioglossus activity, there was a significant change in the slope of the GGEMG/flow relationship with altered gas density. For the group averages across conditions (between breath analysis), the correlation with GGEMG was robust for negative pressure (R(2) = 0.98) and less strong for other variables such as flow and resistance. These data suggest that independent of central pattern generator activity, intrapharyngeal negative pressure itself modulates genioglossus activity both within breaths and between breaths.