gebhart/patrepeval huggingface dataset:
Immune Privilege and Angiogenic Privilege of the Cornea (2007)

The cornea is the transparent window of the eye and corneal transparency is essential for good vision. Inflammatory reactions within the cornea cannot only cause tissue destruction and scar formation, but are also associated with angiogenesis and lymphangiogenesis in the cornea. Both inflammation-associated processes interfere with corneal transparency and cause corneal blindness. During evolution the cornea has developed mechanisms for preventing and modulating inflammatory and angiogenic reactions. The fact that the cornea is normally devoid of both blood and lymphatic vessels and actively maintains this avascularity has been termed 'corneal angiogenic privilege'. Corneal 'immune privilege', on the other hand, indicates that the cornea is an immune-privileged site and tissue, enabling the extraordinary success of histologically incompatible corneal transplantation. Recent evidence indicates that there is considerable overlap in the molecular mechanisms maintaining corneal 'angiogenic' and 'immune privilege'.
DRTF: a database of rice transcription factors (2006)

DRTF is available at http://drtf.cbi.pku.edu.cn
Alkynes Between Main Group Elements: From Dumbbells via Rods to Squares and Tubes (2010)

ADVERTISEMENT RETURN TO ISSUEPREVReviewAlkynes Between Main Group Elements: From Dumbbells via Rods to Squares and TubesRolf Gleiter*† and Daniel B. Werz*‡View Author Information Organisch-Chemisches Institut der Universität Heidelberg, Im Neuenheimer Feld 270, D-69120 Heidelberg, Germany, and Institut für Organische und Biomolekulare Chemie der Georg-August-Universität Göttingen, Tammannstr. 2, D-37077 Göttingen, Germany* To whom correspondence should be addressed. E-mail: [email protected] (R.G.); [email protected] (D.B.W.).†Organisch-Chemisches Institut der Universität Heidelberg.‡Institut für Organische und Biomolekulare Chemie der Georg-August-Universität Göttingen.Cite this: Chem. Rev. 2010, 110, 7, 4447–4488Publication Date (Web):April 14, 2010Publication History Received11 November 2009Published online14 April 2010Published inissue 14 July 2010https://pubs.acs.org/doi/10.1021/cr9003727https://doi.org/10.1021/cr9003727review-articleACS PublicationsCopyright © 2010 American Chemical SocietyRequest reuse permissionsArticle Views3686Altmetric-Citations81LEARN 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:Elements,Energy,Hydrocarbons,Salts,Substituents Get e-Alerts
Analysis of the Structural Requirements for Lysosomal Membrane Targeting Using Transferrin Receptor Chimeras (1998)

The sorting of membrane proteins to the lysosome requires tyrosine- or dileucine-based targeting signals. Recycling receptors have similar signals, yet these proteins seldom enter the latter stages of the endocytic pathway. To determine how lysosomal and internalization signals differ, we prepared chimeric molecules consisting of the cytoplasmic tails of CD3 gamma-chain, lysosomal acid phosphatase, and lysosomal-associated membrane glycoprotein-1, each fused to the transmembrane and extracellular domains of the transferrin receptor (TR). Each chimera was expressed on the cell surface and rapidly internalized. Metabolic pulse-chase experiments showed that the CD3 gamma-chain and lysosomal acid phosphatase chimeras, unlike the lysosomal-associated membrane glycoprotein chimera, were rapidly degraded in a post-Golgi compartment following normal glycosylation. Transplantation of signals from CD3 gamma-chain and lysosomal acid phosphatase into the TR cytoplasmic tail in place of the native signal, Y20TRF23, indicated that each signal was sufficient to promote endocytosis but not lysosomal targeting of the resulting mutant. Transplantation of two CD3 signals at specific sites in the TR cytoplasmic tail or a single tyrosine-based signal in a truncated TR tail, however, was sufficient to promote lysosomal targeting. Our results therefore suggest that the relative position of the signal within the cytoplasmic tail is a critical feature that distinguishes lysosomal targeting signals from internalization signals.
PROTEOMICS Reviews 2014 (2014)

This issue of PROTEOMICS contains the 2014 collection of review articles covering various aspects of proteomics technologies and their application in the biosciences.We firmly believe that such an annual collection of review articles is an excellent way for both relative newcomers and experts to keep abreast of developments in the field and we hope that you will find this year's collection of review articles interesting and informative. BioinformaticsWith more dynamic information becoming available, attention has recently focused on the dynamic properties of protein-protein interaction networks.In their review, Jianxin Wang and colleagues discuss the construction of dynamic protein interaction networks (DPINs) using a combination of proteomic, genomic and transcriptomic analyses.They discuss applications on DPINs, including protein complexes/functional modules and network organization analysis, biomarkers detection in the progression or prognosis of the disease, and network medicine.They also highlight challenges in the construction of DPINs and suggest future directions in this research area.Machine learning is a branch of artificial intelligence that focuses on algorithms allowing computers to learn how to solve complex problems using existing data.Mass spectrometry based proteomics has no shortage of complex problems, and since publicly available data is ever growing, machine learning is fast becoming a very popular tool in the field.In their article, Lennart Martens and colleagues overview applications of machine learning in proteomics.These cover both wet-and dry-laboratory workflows, and address key bottlenecks in experimental planning and design, as well as in data processing and analysis.Modern day proteomics is generating ever more complex data, the storage and processing of which has outgrown the capacity of most desktop computers.To cope with these increased computational demands, distributed architectures have gained substantial popularity in recent years.In their review, Lennart Martens and colleagues provide an overview of current techniques for distributed computing, along with examples of how these techniques are currently being employed in proteomics.
Single-Molecule Detection of a Cyanine Dye in Silver Colloidal Solution Using Near-Infrared Surface-Enhanced Raman Scattering (1998)

Single-molecule Raman spectroscopy of a cyanine dye in aqueous silver colloidal solution with the use of surface-enhanced Raman scattering at near-infrared excitation (NIR-SERS) is reported. A characteristic Poisson distribution of SERS signals due to the Brownian motion of single dye molecule-loaded silver particles reflects the probability of finding 0, 1, or 2 1,1'-diethyl-2,2'cyanine (PIC) molecules in the probed volume during an actual measurement and is evidence that single-molecule detection by SERS has been achieved. Spectra measured in 1 s collection time with 100 mW nonresonant 830 nm excitation provide a clear “fingerprint” of a single PIC molecule by showing its typical Raman lines between 700 and 1700 cm −1 . Single-molecule Raman signals are also detected for the first time at the anti-Stokes side of the excitation laser. Effective Raman cross sections for PIC of ∼10 −16 cm 2 per molecule can be inferred from the ratio between “pumped” anti-Stokes and Stokes signals.
Interleukin-18 (IL-18) synergizes with IL-2 to enhance cytotoxicity, interferon-gamma production, and expansion of natural killer cells. (2001)

We investigated the in vitro effects of combining interleukin-18 (IL-18) and IL-2 on human lymphocytes. The combined use of these two cytokines synergistically enhanced the proliferation, cytolytic activity, and interferon-gamma production of peripheral blood mononuclear cells. Phenotypic analysis revealed a preferential expansion of CD56+CD3- cells and an up-regulation of IL-2 receptor-alpha expression on natural killer cells. Isolated natural killer cells showed a substantial increase in proliferation and cytotoxicity compared with CD4+ and CD8+ T cells. The combined use of IL-18 and IL-2 should be considered a viable strategy to induce an antitumor response in vivo.
Combined circulating tumor DNA and protein biomarker-based liquid biopsy for the earlier detection of pancreatic cancers (2017)

The earlier diagnosis of cancer is one of the keys to reducing cancer deaths in the future. Here we describe our efforts to develop a noninvasive blood test for the detection of pancreatic ductal adenocarcinoma. We combined blood tests for <i>KRAS</i> gene mutations with carefully thresholded protein biomarkers to determine whether the combination of these markers was superior to any single marker. The cohort tested included 221 patients with resectable pancreatic ductal adenocarcinomas and 182 control patients without known cancer. <i>KRAS</i> mutations were detected in the plasma of 66 patients (30%), and every mutation found in the plasma was identical to that subsequently found in the patient's primary tumor (100% concordance). The use of <i>KRAS</i> in conjunction with four thresholded protein biomarkers increased the sensitivity to 64%. Only one of the 182 plasma samples from the control cohort was positive for any of the DNA or protein biomarkers (99.5% specificity). This combinatorial approach may prove useful for the earlier detection of many cancer types.
Endothelium-Dependent and -Independent Vasodilation Involving Cyclic GMP: Relaxation Induced by Nitric Oxide, Carbon Monoxide and Light (1991)

The characteristics of carbon monoxide (CO)-induced, endothelium-independent relaxation of rabbit aorta were compared with those of nitric oxide (NO)-induced and light-induced relaxation and endothelium-dependent relaxation mediated by endothelium-dependent relaxing factor (EDRF). CO was less than one thousandth as potent as NO as a relaxant. Various findings, including an increase in cyclic GMP associated with CO-induced relaxation, led to the conclusion that CO - like NO, EDRF and light - produces relaxation as a result of its stimulation of guanylate cyclase. LY 83583, which generates superoxide, was a potent, fast-acting inhibitor of acetylcholine-induced endothelium-dependent relaxation and NO-induced relaxation, and a fairly potent, moderately fast-acting inhibitor of photorelaxation, but only a very weak inhibitor of CO-induced relaxation. The ability of LY 83583 as well as hemoglobin to inhibit photorelaxation is consistent with the hypothesis that on radiation a photo-induced relaxing factor is formed which can stimulate guanylate cyclase and which can be inactivated by superoxide and by hemoglobin.
Novel Reversible Indole-3-carboxylate Decarboxylase Catalyzing Nonoxidative Decarboxylation (2002)

After enrichment culture with indole-3-carboxylate in static culture, a novel reversible decarboxylase, indole-3-carboxylate decarboxylase, was found in Arthrobacter nicotianae FI1612 and several molds. The enzyme reaction was examined in resting-cell reactions with A. nicotianae FI1612. The enzyme activity was induced specifically by indole-3-carboxylate, but not by indole. The indole-3-carboxylate decarboxylase of A. nicotianae FI1612 catalyzed the nonoxidative decarboxylation of indole-3-carboxylate into indole, and efficiently carboxylated indole and 2-methylindole by the reverse reaction. In the presence of 1 mM dithiothreitol, 50 mM Na2 S2O3, and 20% (v/v) glycerol, indole-3-carboxylate decarboxylase was partially purified from A. nicotianae FI1612. The purified enzyme had a molecular mass of approximately 258 kDa. The enzyme did not need any cofactor for the decarboxylating and carboxylating reactions.
Elastically Stretchable Insulation and Bilevel Metallization and Its Application in a Stretchable RLC Circuit (2011)

Stretchable electronics need stretchable wiring membranes that are equivalent to printed wiring boards but with elastically stretchable insulators and multilevel metallization. We have developed technology for elastically stretchable two-level metallization on an elastomeric membrane. Two levels of conductors were separated by a photopatternable elastomeric dielectric and connected through via holes. They were evaluated at uniaxial tensile strains of up to 30% and then used to create an elastomeric resistor–inductor–capacitor (RLC) circuit, whose alternating-current (AC) response was measured at biaxial tensile strains of up to 6%. We describe the fabrication process, morphology, and electrical performance of the bilevel metallization and the RLC circuit.
Innervation and Effects of Dilatory Neuropeptides on Cerebral Vessels (1991)

The cerebral circulation is supplied with two vasodilator systems: the parasympathetic system storing vasoactive intestinal peptide, peptide histidine isoleucine, acetylcholine and in a subpopulation of nerves neuropeptide Y, and the sensory system, mainly originating in the trigeminal ganglion, storing substance P, neurokinin A and calcitonin gene-related peptide (CGRP). Recent knowledge of the innervation and effects of the dilator neuropeptides in the cerebral circulation is reviewed. Their role in the pathophysiology of subarachnoid hemorrhage and migraine has now received attention, with documentation of a clear linkage with the release of CGRP. In subarachnoid hemorrhage, other perivascular peptides are, to a lesser extent, involved.
Advances in Microfluidic Materials, Functions, Integration, and Applications (2013)

ADVERTISEMENT RETURN TO ISSUEPREVReviewNEXTAdvances in Microfluidic Materials, Functions, Integration, and ApplicationsPamela N. Nge, Chad I. Rogers, and Adam T. Woolley*View Author Information Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States*Phone: 801-422-1701. E-mail: [email protected]Cite this: Chem. Rev. 2013, 113, 4, 2550–2583Publication Date (Web):February 14, 2013Publication History Received15 August 2012Published online14 February 2013Published inissue 10 April 2013https://pubs.acs.org/doi/10.1021/cr300337xhttps://doi.org/10.1021/cr300337xreview-articleACS PublicationsCopyright © 2013 American Chemical SocietyRequest reuse permissionsArticle Views21812Altmetric-Citations719LEARN 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:Biotechnology,Fluid dynamics,Liquids,Microchips,Microfluidic devices Get e-Alerts
Interleukin-2 improves tumour response to DNP-modified autologous vaccine for the treatment of metastatic malignant melanoma (2004)

This paper is a report of response rate (RR) and survival of 34 metastatic melanoma patients who received a dinitrophenyl (DNP)-modified autologous melanoma cell vaccine. In all, 27 patients started the vaccine as a primary treatment for metastatic melanoma and seven started it as an adjuvant, with no evidence of disease at the time, but had developed new metastases. Interleukin-2 (IL-2) was administered in 24 out of the 34 patients: 19 who progressed on vaccine alone and five who had the combination from start. Interleukin-2 was administered in the intravenous, bolus high-dose regimen (seven patients) or as subcutaneous (s.c.) low-dose treatment (17). Overall response for the entire group was 35% (12 patients out of 34), 12% having a complete response (CR) and 23% a partial response (PR). However, only two patients had tumour responses while on the vaccine alone, whereas the other 10 demonstrated objective tumour regression following the combination with IL-2 (two CR, eight PR), lasting for a median duration of 6 months (range 3-50 months). Of the 12 responding patients, 11 attained strong skin reactivity to the s.c. injection of irradiated, unmodified autologous melanoma cells. None of the patients with a negative reactivity experienced any tumour response. Patients with positive skin reactions survived longer (median survival - 54 months). The results suggest enhanced RRs to the combination of IL-2 and autologous melanoma vaccine. Skin reactivity to unmodified autologous melanoma cells may be a predictor of response and improved survival, and therefore a criterion for further pursuing of immunotherapeutic strategies.
Production and stability study of a hospital parenteral nutrition solution for neonates (2018)

Standard parenteral nutrition solutions are mixtures comprising interacting components that may degrade themselves over time. The objective of this study was to investigate the physicochemical and microbiological stability of a hospital preparation for parenteral nutrition in neonatology. The analyses were performed throughout the storage of the preparations at 2-8 °C (up to 4 months). The extent of stability was based on the determination of amino acids dosage, visual and physicochemical properties (glucose and electrolytes concentrations, pH and osmolality measurements, particle counting) and microbiological analysis (sterility test). A thermal degradation of ascorbic acid was conducted to evaluate the antioxidant properties of the parenteral mixture. Physicochemical and microbiological controls were found to comply with the specifications. Amino acids showed a good stability throughout the 4months storage except for cysteine, which was progressively degraded to cystine, conferring a yellow coloration to parenteral solutions. Parenteral nutrition standards solutions remain stable for 4 months at 2-8 °C, ensuring safe administration in preterm infants.
[Hyperbaric oxygenation in neurotraumatology]. (1987)

The use of hyperbaric oxygenation (HBO) as a therapeutic measure has a favorable effect, in the postoperative period also, on traumatic affections of different levels of the nervous system (the brain, spinal cord, peripheral nerve trunks and plexuses. It allows the severity of the neurologic deficit and the degree of the patient's disability to be reduced and in some cases it prevents the growth of vital disorders. At the same time, the effect may exert a certain load on the adaptation mechanisms which are very limited in many neurosurgical patients. In view of this, the tolerance of the patient's organism to this load must be taken into account in choosing the HBO schedules. The tolerance is decisively determined by the intactness of the integral function of the central nervous system and diminishes markedly as the impairment of the consciousness of patients with primary affection of the brain gradually becomes deeper and longer in duration.
Intravitreal injection of gentamicin in rabbits. Effect of inflammation and pigmentation on half-life and ocular distribution. (1981)

Most regimens for intravitreal injection of antibiotics are based on studies in normal albino rabbits. We examined the effect of two variables, infection and pigmentation, on the ocular distribution of an intravitreal injection of 50 micrograms of gentamicin in rabbit eyes. The half-life of gentamicin in the vitreous of normal pigmented rabbits after intravitreal administration was 24 hr. Antibiotic levels in cornea and aqueous reached a peak 18 hr after injection; terminal half-lives in these sites were similar to those in vitreous. With inflammation, the half-life in the vitreous was decreased to 10 hr, and there was no accumulation of drug in anterior sites. To the extent that these data are applicable to humans, they suggest that the treatment of bacterial endophthalmitis by the intravitreal route may require more frequent injections than had been recommended on the basis of studies in normal eyes. Normal pigmented and albino rabbits showed similar levels of gentamicin in the cornea, aqueous, and vitreous; however, the drug was barely detectable in iris, choroid-retina, and sclera of pigmented animals, presumably on account of an interaction with melanin-containing tissues. This effect of pigment may explain the differences in the reported thresholds for toxicity of gentamicin with intravitreal injection.
Expression of plasmid R388-encoded type II dihydrofolate reductase as a dominant selective marker in Saccharomyces cerevisiae. (1984)

The R388 plasmid-encoded drug-resistant type II dihydrofolate reductase gene (R . dhfr) was expressed in Saccharomyces cerevisiae by fusing the R . dhfr coding sequence to the yeast TRP5 promoter. Yeast cells harboring these recombinant plasmids grew in media with 10 micrograms of methotrexate per ml and 5 mg of sulfanilamide per ml, a condition which inhibits the growth of wild-type cells. Addition of a 390-base-pair fragment from the 3'-noncoding region of TRP5 downstream from R . dhfr increased expression. Presumably, the added segment promoted termination or polyadenylation or both of the R . dhfr transcript. The activity of the plasmid-encoded dihydrofolate reductase and the copy number of the R . dhfr plasmid in cells grown in drug-selective media were higher by one order of magnitude than those grown in nutrition-selective media. Plasmid copy number, as well as the plasmid-encoded enzyme level, decreased when cells were selected for prototrophy. In drug-selective media, the plasmid-encoded enzyme level and the content of R . dhfr transcripts were nearly constant in cells harboring R . dhfr plasmids containing different yeast promoters. In contrast, the plasmid copy number and beta-lactamase activity encoded in cis by plasmids were much higher when R . dhfr was associated with the weak TRP5 promoter than when it was fused to the strong ADC1 promoter. These results indicate that plasmid copy number, i.e., gene dosage of R . dhfr, correlates inversely with the strength of the promoter associated with R . dhfr, and cells with a higher plasmid copy number were enriched in drug-selective media. The transformation efficiency of R . dhfr fused to the ADC1 promoter was almost the same on drug-selective plates as on nutrition-selective plates, indicating that R . dhfr is suitable as a dominant selective transformation marker in S. cerevisiae.