gebhart/patrepeval huggingface dataset:
TRPV2 Is a Component of Osmotically Sensitive Cation Channels in Murine Aortic Myocytes (2003)

Changes in membrane tension resulting from membrane stretch represent one of the key elements in blood flow regulation in vascular smooth muscle. However, the molecular mechanisms involved in the regulation of membrane stretch remain unclear. In this study, we provide evidence that a vanilloid receptor (TRPV) homologue, TRPV2 is expressed in vascular smooth muscle cells, and demonstrate that it can be activated by membrane stretch. Cell swelling caused by hypotonic solutions activated a nonselective cation channel current (NSCC) and elevated intracellular Ca2+ ([Ca2+]i) in freshly isolated cells from mouse aorta. Both of these signals were blocked by ruthenium red, an effective blocker of TRPVs. The absence of external Ca2+ abolished this increase in [Ca2+]i caused by the hypotonic stimulation and reduced the activation of NSCC. Significant immunoreactivity to mouse TRPV2 protein was detected in single mouse aortic myocytes. Moreover, the expression of TRPV2 was found in mesenteric and basilar arterial myocytes. Treatment of mouse aorta with TRPV2 antisense oligonucleotides resulted in suppression of hypotonic stimulation-induced activation of NSCC and elevation of [Ca2+]i as well as marked inhibition of TRPV2 protein expression. In Chinese hamster ovary K1 (CHO) cells transfected with TRPV2 cDNA (TRPV2-CHO), application of membrane stretch through the recording pipette and hypotonic stimulation consistently activated single NSCC. Moreover, stretch of TRPV2-CHO cells cultured on an elastic silicon membrane significantly elevated [Ca2+]i. These results provide a strong basis for our purpose that endogenous TRPV2 in mouse vascular myocytes functions as a novel and important stretch sensor in vascular smooth muscles.
Imagining Home at a Snail's Pace in Shani Mootoo's Cereus Blooms at Night. (2014)

In her novel Cereus Blooms at Night (1996), Sharni Mootoo creates characters that simultaneously inhabit both the center and margins of her text. As colonized people, the characters in Mootoo's novel find themselves dispossessed and marginalized upon their native soil. When the character, Chandin, takes on the role of an abusive colonizer in his native land, his daughter Mala is rendered doubly homeless as a result. Because the reality of home does not exist for her either culturally or personally, she must imagine and create it in alternative ways. When Chandin is killed and his narrative accordingly silenced, Mala slowly redefines what home means to her, first by moving its focus into the garden spaces and ultimately by relocating it within her own imagination and memory. Furthermore, because Mala no longer has the ability to tell her own story at the novel's end, she must rely on others to tell it for her. Thus, in the same way her home is decentralized, so too is her story, for it is the interweaving of her story, along with several others, that creates a narrative that not only lacks 'a center' but ultimately defies it.
Defining the role of glucocorticoids in inflammation (2018)

An established body of knowledge and clinical practice has argued in favor of the use of glucocorticoids in various chronic inflammatory and autoimmune diseases. However, the very well-known adverse effects associated with their treatment hampers continuation of therapy with glucocorticoids. Analyses of the molecular mechanisms underlying the actions of glucocorticoids have led to the discovery of several mediators that add complexity and diversity to the puzzling world of these hormones and anti-inflammatory drugs. Such mediators hold great promise as alternative pharmacologic tools to be used as anti-inflammatory drugs with the same properties as glucocorticoids, but avoiding their metabolic side effects. This review summarizes findings about the molecular targets and mediators of glucocorticoid function.
Molecular cloning of rat JAK3, a novel member of the JAK family of protein tyrosine kinases (1994)

We have cloned and sequenced a cDNA (JAK3) encoding a novel member of the JAK family of protein tyrosine kinases. JAK3 was identified by RT-PCR of rat mesangial cells using degenerate oligonucleotide primers, and a full-length clone was isolated from a rat spleen cDNA library. The primary structure of JAK3 showed cDNA with an open reading frame of 1,100 amino acids which comprises the PTK catalytic domain and a second kinase-related domain characteristic for JAK kinase. JAK3 was phylogenetically shown to be most closely related to JAK2 among the previously known JAK family members, JAK1, JAK2 and Tyk2. Southern analysis revealed that JAK3 is a single copy gene and well conserved in the vertebral genome. Northern analysis indicated that the 4.0 kb mRNA was transcribed in a variety of tissues including spleen, lung, kidney and intestine.
Differential Gene Expression in the Gastrula of Xenopus laevis (1983)

A modified cloning method designed to produce differential complementary DNA libraries permits the isolation of sequences that are present in the RNA population of any developmental stage or tissue, but are not present or are much less abundant in another stage or tissue. Selective complementary DNA cloning is especially useful when the differentially expressed RNA's are of low to moderate abundance in the cells in which they occur. A class of cytoplasmic polyadenylated RNA's differentially expressed in gastrula embryos of Xenopus laevis (DG RNA's) has been isolated. These DG RNA's occur very rarely or not at all in unfertilized eggs and blastulae, accumulate as the result of transcription before and during gastrulation, and, with some exceptions, decline in abundance as development proceeds. Many of these RNA molecules appear to be translated at the gastrula stage. Thus, DG RNA's may encode proteins that are important in the process of gastrulation.
The Role of the Amino Terminus in the Kinetics and Assembly of α-Hemolysin of Staphylococcus aureus (1997)

The nature of the involvement of an intact NH2 terminus in the assembly of alpha-hemolysin of Staphylococcus aureus was reinvestigated. For the first time, a deletion of the first four amino acids at the NH2 terminus of alpha-hemolysin yielded a novel mutant that undergoes all of the conformational changes to form a lytic pore. The experimental evidence shows unequivocally that the mutant toxin forms heat- and sodium dodecyl sulfate-stable heptameric oligomers. The concentration required to achieve 50% lysis of red blood cells is around 58-116 ng/ml, and the time taken to achieve lysis to the same extent as that of intact toxin is considerably longer. Transmission electron microscopic studies also suggest that the pores formed by this deletion mutant are similar to those by the full-length toxin. This is in contrast to the previously reported 2- and 11-amino acid deletions that failed to proceed further from a presumed prefinal nonlytic pore to a lytic pore. Studies on the kinetics of assembly indicate that this mutant can form heat- and sodium dodecyl sulfate-stable oligomers as fast as full-length alpha-hemolysin but that pore opening is slowed down. The data strongly suggest that these amino acids (Ala-Asp-Ser-Asp) are involved in the final stages of assembly of alpha-hemolysin in target membranes.
Cancer cell‐targeted drug delivery utilizing oligopeptide transport activity (2000)

To study the drug delivery to tumor by utilization of an oligopeptide transport activity, we examined the accumulation of dipeptides and the peptide-mimetic anti-cancer drug, bestatin, a substrate of oligopeptide transporter PepT1. Firstly, we established HeLa cells stably expressing human peptide transporter (hPepT1) (HeLa-hPepT1). Secondly, we constructed an experimental model by inoculation of HeLa-hPepT1 cells subcutaneously into Balb/c nu/nu mice to demonstrate the contribution of PepT1 to the tissue-selective drug delivery. The accumulations of a hydrolysis-resistant dipeptide [3H]carnosine and bestatin in solid tumors formed by HeLa-hPepT1 or HeLa-pcDNA3, which are transfected with vector DNA (pcDNA3) were measured. After I.V. administration, tissue-to-plasma concentration ratios (Kp) of both compounds, in HeLa-hPepT1 tumor was significantly greater than that of [14C]inulin, a marker for extracellular fluid space, those of dipeptides in muscle, or those in HeLa-pcDNA3 tumor. Furthermore, bestatin exhibited growth inhibition of HeLa-hPepT1 in vitro. In vivo, repeated oral administration of bestatin for 28 days suppressed the growth of HeLa-hPepT1 tumor specifically. When HT-1080 cells, which may naturally express oligopeptide transport activity, were transplanted, Kp of [3H]carnosine was significantly increased in comparison with that in muscle. In addition, oligopeptide transport activities among various human cell lines were examined. These results provide the first demonstration for the selective delivery of oligopeptides to tumors by specific oligopeptide transport activity. Int. J. Cancer 88:274–280, 2000. © 2000 Wiley-Liss, Inc.
Factorizing complex predicates in queries to exploit indexes (2003)

Decision-support applications generate queries with complex predicates. We show how the factorization of complex query expressions exposes significant opportunities for exploiting available indexes. We also present a novel idea of relaxing predicates in a complex condition to create possibilities for factoring. Our algorithms are designed for easy integration with existing query optimizers and support multiple optimization levels, providing different trade-offs between plan complexity and optimization time.
Detecting Subtle Sequence Signals: a Gibbs Sampling Strategy for Multiple Alignment (1993)

A wealth of protein and DNA sequence data is being generated by genome projects and other sequencing efforts. A crucial barrier to deciphering these sequences and understanding the relations among them is the difficulty of detecting subtle local residue patterns common to multiple sequences. Such patterns frequently reflect similar molecular structures and biological properties. A mathematical definition of this "local multiple alignment" problem suitable for full computer automation has been used to develop a new and sensitive algorithm, based on the statistical method of iterative sampling. This algorithm finds an optimized local alignment model for N sequences in N-linear time, requiring only seconds on current workstations, and allows the simultaneous detection and optimization of multiple patterns and pattern repeats. The method is illustrated as applied to helix-turn-helix proteins, lipocalins, and prenyltransferases.
Oxidative stress and pathology in muscular dystrophies: focus on protein thiol oxidation and dysferlinopathies (2013)

The muscular dystrophies comprise more than 30 clinical disorders that are characterized by progressive skeletal muscle wasting and degeneration. Although the genetic basis for many of these disorders has been identified, the exact mechanism for pathogenesis generally remains unknown. It is considered that disturbed levels of reactive oxygen species (ROS) contribute to the pathology of many muscular dystrophies. Reactive oxygen species and oxidative stress may cause cellular damage by directly and irreversibly damaging macromolecules such as proteins, membrane lipids and DNA; another major cellular consequence of reactive oxygen species is the reversible modification of protein thiol side chains that may affect many aspects of molecular function. Irreversible oxidative damage of protein and lipids has been widely studied in Duchenne muscular dystrophy, and we have recently identified increased protein thiol oxidation in dystrophic muscles of the mdx mouse model for Duchenne muscular dystrophy. This review evaluates the role of elevated oxidative stress in Duchenne muscular dystrophy and other forms of muscular dystrophies, and presents new data that show significantly increased protein thiol oxidation and high levels of lipofuscin (a measure of cumulative oxidative damage) in dysferlin-deficient muscles of A/J mice at various ages. The significance of this elevated oxidative stress and high levels of reversible thiol oxidation, but minimal myofibre necrosis, is discussed in the context of the disease mechanism for dysferlinopathies, and compared with the situation for dystrophin-deficient mdx mice.
Exploiting sparseness in deep neural networks for large vocabulary speech recognition (2012)

Recently, we developed context-dependent deep neural network (DNN) hidden Markov models for large vocabulary speech recognition. While reducing errors by 33% compared to its discriminatively trained Gaussian-mixture counterpart on the switchboard benchmark task, DNN requires much more parameters. In this paper, we report our recent work on DNN for improved generalization, model size, and computation speed by exploiting parameter sparseness. We formulate the goal of enforcing sparseness as soft regularization and convex constraint optimization problems, and propose solutions under the stochastic gradient ascent setting. We also propose novel data structures to exploit the random sparseness patterns to reduce model size and computation time. The proposed solutions have been evaluated on the voice-search and switchboard datasets. They have decreased the number of nonzero connections to one third while reducing the error rate by 0.2-0.3% over the fully connected model on both datasets. The nonzero connections have been further reduced to only 12% and 19% on the two respective datasets without sacrificing speech recognition performance. Under these conditions we can reduce the model size to 18% and 29%, and computation to 14% and 23%, respectively, on these two datasets.
Flavonoids Attenuate Cardiovascular Disease, Inhibit Phosphodiesterase, and Modulate Lipid Homeostasis in Adipose Tissue and Liver (2006)

Plant flavonoids are widely distributed polyphenolic compounds of the human diet. They consist of six major classes based on specific structural differences: flavonols, flavones, flavanones, catechins, anthocyanidins, and isoflavones. All of the major classes of flavonoids are comprised of three six-membered rings: an aromatic A-ring fused to a heterocyclic C-ring that is attached through a single carbon-carbon bond to an aromatic B-ring. Population studies have shown that flavonoid intake is inversely correlated with mortality from cardiovascular disease, and numerous flavonoids of dietary significance have been shown to beneficially impact parameters associated with atherosclerosis, including lipoprotein oxidation, blood platelet aggregation, and vascular reactivity. Therapeutic effects of flavonoids on platelet aggregability and blood pressure have been attributed to competitive inhibition of cyclic nucleotide phosphodiesterase (PDE), an elevation in cAMP level, and subsequent activation of protein kinase A (cAMP-dependent protein kinase). In addition, flavonoids may Induce neutral lipid hydrolysis from lipid stores through PDE inhibition in adipose tissue and liver. Indeed, the three-dimensional structure of many flavonoids is sterically and electrostatically compatible with the catalytic site of cAMP PDE3 and PDE4. Flavonoids have also been reported to suppress pathways of lipid biosynthesis and of very low-density lipoprotein production in cultured hepatocytes. Continued studies of the biochemical mechanisms underlying the biological effects of plant flavonoids may uncover new strategies for the treatment of cardiovascular disease, as well as associated conditions such as obesity, hepatic steatosis, and Type 2 diabetes.
The use of riboflavin for the inactivation of pathogens in blood products. (2000)

The use of Riboflavin in a photochemical decontamination process for blood components shows promise.
Charts for Counting Bacterial Colonies (1947)

Charts for Counting Bacterial Colonies J. Howard Brown CopyRight https://doi.org/10.2105/AJPH.37.2.206 Published Online: August 29, 2011
Reduction of radiation exposure to the cardiologist during coronary angiography by the use of a remotely controlled mechanical pump for injection of contrast medium (1992)

Selective coronary cineangiography was carried out in 103 consecutive patients. In half the examinations (53) injection of contrast medium was performed by hand using a syringe, with the cardiologist standing in the usual position next to the X-ray table. In the other half (50) contrast medium was injected by a remotely controlled mechanical pump whilst the cardiologist stood well away from the X-ray source. Radiation dose to the lens of the cardiologists eye was estimated for the two groups by measurement of head badge dosimetry. In the first group (hand injection) total radiation dose was 1.30 mSv; in the second group (mechanical injection) it was reduced five-fold, to 0.25 mSv. This technique therefore represents an important means of achieving substantial reductions in radiation exposure to cardiologists.
Probing the Interior of Peptide Amphiphile Supramolecular Aggregates (2005)

We present a study of the aqueous solvation within self-assembled structures formed from peptide amphiphiles. We have placed tryptophan and pyrene chromophores onto the peptide backbone to enable spectroscopic examinations of the interior of the resulting supramolecular objects. Self-assembly constrains the chromophores to a defined location within an aggregate, and they experience differing degrees of quencher penetration reflective of their depth within the nanostructure. Tryptophan fluorescence indicates that the interiors remain well-solvated, suggesting that the supramolecular aggregates maintain high degrees of free volume. The Stern-Volmer quenching constants and the fractional accessibility (of covalently bound pyrene) progressively increase as the chromophore is placed closer to the aggregate exterior. Furthermore, these aggregates encourage chromophore uptake from aqueous solution as evidenced by the solubilization of free pyrene chromophores. Our findings demonstrate that covalently bound fluorophores within an aggregate can interact with the external environment. Studies with small molecular probes indicate that these self-assembled architectures may represent viable vehicles to sequester hydrophobic, insoluble organic molecules (within the interior) and to present signaling protein epitopes to cells (on the periphery).
A randomized study of chemotherapy with cisplatin plus etoposide versus chemoendocrine therapy with cisplatin, etoposide and the pineal hormone melatonin as a first‐line treatment of advanced non‐small cell lung cancer patients in a poor clinical state (1997)

Recent studies suggest that the pineal hormone melatonin may reduce chemotherapy-induced immune and bone marrow damage. In addition, melatonin may exert potential oncostatic effects either by stimulating host anticancer immune defenses or by inhibiting tumor growth factor production. On this basis, we have performed a randomized study of chemotherapy alone vs. chemotherapy plus melatonin in advanced non-small cell lung cancer patients (NSCLC) with poor clinical status. The study included 70 consecutive advanced NSCLC patients who were randomized to receive chemotherapy alone with cisplatin (20 mg/m2/day i.v. for 3 days) and etoposide (100 mg/m2/day i.v. for 3 days) or chemotherapy plus melatonin (20 mg/day orally in the evening). Cycles were repeated at 21-day intervals. Clinical response and toxicity were evaluated according to World Health Organization criteria. A complete response (CR) was achieved in 1/34 patients concomitantly treated with melatonin and in none of the patients receiving chemotherapy alone. Partial response (PR) occurred in 10/34 and in 6/36 patients treated with or without melatonin, respectively. Thus, the tumor response rate was higher in patients receiving melatonin (11/34 vs. 6/35), without, however, statistically significant differences. The percent of 1-year survival was significantly higher in patients treated with melatonin plus chemotherapy than in those who received chemotherapy alone (15/34 vs. 7/36, P < 0.05). Finally, chemotherapy was well tolerated in patients receiving melatonin, and in particular the frequency of myelosuppression, neuropathy, and cachexia was significantly lower in the melatonin group. This study shows that the concomitant administration of melatonin may improve the efficacy of chemotherapy, mainly in terms of survival time, and reduce chemotherapeutic toxicity in advanced NSCLC, at least in patients in poor clinical condition.
Singlet Oxygen as a Reactive Intermediate in the Photodegradation of an Electroluminescent Polymer (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSinglet Oxygen as a Reactive Intermediate in the Photodegradation of an Electroluminescent PolymerRodger D. Scurlock, Bojie Wang, Peter R. Ogilby, James R. Sheats, and Roger L. CloughCite this: J. Am. Chem. Soc. 1995, 117, 41, 10194–10202Publication Date (Print):October 1, 1995Publication History Published online1 May 2002Published inissue 1 October 1995https://pubs.acs.org/doi/10.1021/ja00146a004https://doi.org/10.1021/ja00146a004research-articleACS PublicationsRequest reuse permissionsArticle Views1641Altmetric-Citations319LEARN 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 Get e-Alerts
Endoscopic imaging using surface-enhanced Raman scattering (2017)

Abstract In this review, we assessed endoscopic imaging using surface-enhanced Raman scattering (SERS). As white-light endoscopy, the current standard for gastrointestinal endoscopy, is limited to morphology, Raman endoscopy using surface-enhanced Raman scattering nanoparticles (SERS endoscopy) was introduced as one of the novel functional modalities. SERS endoscopy has multiplex capability and high sensitivity with low autofluorescence and photobleaching. As a result, multiple molecular characteristics of the lesion can be accurately evaluated in real time while performing endoscopy using SERS probes and appropriate instrumentation. Especially, recently developed dual modality of fluorescence and SERS endoscopy offers easy localization with identification of multiple target molecules. For clinical use of SERS endoscopy in the future, problems of limited field of view and cytotoxicity should be addressed by fusion imaging, topical administration, and non-toxic coating of nanoparticles. We expect SERS endoscopic imaging would be an essential endoscopic technique for diagnosis of cancerous lesions, assessment of resection margins and evaluation of therapeutic responses.