gebhart/patrepeval huggingface dataset:
Photoelectrochemical Ion Pumping with Dye-Functionalized Polymer Membranes (2015)

Artificial photosynthesis could be a cost-effective and sustainable means of converting sunlight energy into usable energy. Most artificial photosynthetic systems mimic nature’s properties of light absorption, electronic charge separation, and electronic charge collection, where ultimately electrons make and break chemical bonds. However, nature also transduces photon energy into proton gradients whose electric potential also drives chemical-bond formation. In my presentation I will report on my research group’s progress toward mimicking nature in function, by using light to drive endergonic proton transfer, ultimately converting photon energy into ionic current. The applicability and practicality of this material as a membrane in solar fuels devices and as a separate ionic photoelectrochemical device will also be discussed. My research group’s near-term goal is to provide a proof-of-concept demonstration of an artificial proton pump where light-driven ion transport results in photovoltaic action. For an initial model system we utilized a conical nanopore etched in a polyethylene terephthalate plastic sheet. This pore was formed via swift heavy ion bombardment followed by alkaline chemical etching which resulted in a pore lined with fixed anionic functional groups. Then, using peptide coupling chemistries, the pore was asymmetrically functionalized with novel photoacids to generate a region containing fixed cationic dyes. This ordered distribution of interfacial charge was intended to mimic a solid-state semiconductor pn-junction and be used to separate photogenerated charges. We demonstrated that under visible-light illumination and a small reverse bias, excitation of the photoacid molecules resulted in an ionic photocurrent. We are currently expanding this initial research and successful demonstration of an artificial light-driven ion pump to other polymeric materials with hopes of generating ionic power through sunlight absorption and incorporating these materials as ion-exchange membranes in solar fuels devices.
Chromosome Fragile Sites (2007)

Chromosomal fragile sites are specific loci that preferentially exhibit gaps and breaks on metaphase chromosomes following partial inhibition of DNA synthesis. Their discovery has led to novel findings spanning a number of areas of genetics. Rare fragile sites are seen in a small proportion of individuals and are inherited in a Mendelian manner. Some, such as FRAXA in the FMR1 gene, are associated with human genetic disorders, and their study led to the identification of nucleotide-repeat expansion as a frequent mutational mechanism in humans. In contrast, common fragile sites are present in all individuals and represent the largest class of fragile sites. Long considered an intriguing component of chromosome structure, common fragile sites have taken on novel significance as regions of the genome that are particularly sensitive to replication stress and that are frequently rearranged in tumor cells. In recent years, much progress has been made toward understanding the genomic features of common fragile sites and the cellular processes that monitor and influence their stability. Their study has merged with that of cell cycle checkpoints and DNA repair, and common fragile sites have provided insight into understanding the consequences of replication stress on DNA damage and genome instability in cancer cells.
Angiotensin II Stimulates Renin in Inner Medullary Collecting Duct Cells via Protein Kinase C and Independent of Epithelial Sodium Channel and Mineralocorticoid Receptor Activity (2011)

Collecting duct (CD) renin is stimulated by angiotensin (Ang) II, providing a pathway for Ang I generation and further conversion to Ang II. Ang II stimulates the epithelial sodium channel via the Ang II type 1 receptor and increases mineralocorticoid receptor activity attributed to increased aldosterone release. Our objective was to determine whether CD renin augmentation is mediated directly by Ang II type 1 receptor or via the epithelial sodium channel and mineralocorticoid receptor. In vivo studies examined the effects of epithelial sodium channel blockade (amiloride; 5 mg/kg per day) on CD renin expression and urinary renin content in Ang II-infused rats (80 ng/min, 2 weeks). Ang II infusion increased systolic blood pressure, medullary renin mRNA, urinary renin content, and intrarenal Ang II levels. Amiloride cotreatment did not alter these responses despite a reduction in the rate of progression of systolic blood pressure. In primary cultures of inner medullary CD cells, renin mRNA and (pro)renin protein levels increased with Ang II (100 nmol/L), and candesartan (Ang II type 1 receptor antagonist) prevented this effect. Aldosterone (10(-10) to 10(-7) mol/L) with or without amiloride did not modify the upregulation of renin mRNA in Ang II-treated cells. However, inhibition of protein kinase C with calphostin C prevented the Ang II-mediated increases in renin mRNA and (pro)renin protein levels. Furthermore, protein kinase C activation with phorbol 12-myristate 13-acetate increased renin expression to the same extent as Ang II. These data indicate that an Ang II type 1 receptor-mediated increase in CD renin is induced directly by Ang II via the protein kinase C pathway and that this regulation is independent of mineralocorticoid receptor activation or epithelial sodium channel activity.
Philip Levine Award Lecture: Chromosome Translocations and Oncogenes in Human Lymphoid Tumors (1990)

Chromosome studies are helping to identify oncogenes, both known and previously unknown, involved in the pathogenesis of human lymphocytic tumors; and mechanisms by which the function of these genes is critically altered. Most extensively studied have been the chromosome translocations involving the myc gene in Burkitt's lymphomas and the bcl-2 gene in low-grade lymphomas, where "activation" of the oncogene results from association with a transcriptionally active immunoglobulin gene. Other putative oncogenes, similarly involved in translocations with immunoglobulin genes (in B-cell tumors) or T-cell receptor genes (in T-cell tumors), are currently being investigated, as well as alternative mechanisms of myc gene activation in these neoplasms. Limited clinical applications of these studies have already been forthcoming, and they should eventually lead to improvements in diagnosis, prognosis, and even therapy.
CD28-dependent Rac1 activation is the molecular target of azathioprine in primary human CD4+ T lymphocytes (2003)

Azathioprine and its metabolite 6-mercaptopurine (6-MP) are immunosuppressive drugs that are used in organ transplantation and autoimmune and chronic inflammatory diseases such as Crohn disease. However, their molecular mechanism of action is unknown. In the present study, we have identified a unique and unexpected role for azathioprine and its metabolites in the control of T cell apoptosis by modulation of Rac1 activation upon CD28 costimulation. We found that azathioprine and its metabolites induced apoptosis of T cells from patients with Crohn disease and control patients. Apoptosis induction required costimulation with CD28 and was mediated by specific blockade of Rac1 activation through binding of azathioprine-generated 6-thioguanine triphosphate (6-Thio-GTP) to Rac1 instead of GTP. The activation of Rac1 target genes such as mitogen-activated protein kinase kinase (MEK), NF-kappaB, and bcl-x(L) was suppressed by azathioprine, leading to a mitochondrial pathway of apoptosis. Azathioprine thus converts a costimulatory signal into an apoptotic signal by modulating Rac1 activity. These findings explain the immunosuppressive effects of azathioprine and suggest that 6-Thio-GTP derivates may be useful as potent immunosuppressive agents in autoimmune diseases and organ transplantation.
Biomaterial-Associated Infection: Locating the Finish Line in the Race for the Surface (2012)

Biomaterial-associated infections occur on both permanent implants and temporary devices for restoration or support of human functions. Despite increasing use of biomaterials in an aging society, comparatively few biomaterials have been designed that effectively reduce the incidence of biomaterial-associated infections. This review provides design guidelines for infection-reducing strategies based on the concept that the fate of biomaterial implants or devices is a competition between host tissue cell integration and bacterial colonization at their surfaces.
Enrichment of Single-Walled Carbon Nanotubes by Diameter in Density Gradients (2005)

The bulk enrichment and separation of single-walled carbon nanotubes (SWNTs) by diameter has been achieved through ultracentrifugation of DNA-wrapped SWNTs in aqueous density gradients. The separation is identified by the visual formation of colored bands of SWNTs in the density range of 1.11-1.17 g cm(-3). The optical absorbance spectra of the separated SWNTs indicate that SWNTs of decreasing diameter are increasingly more buoyant. This nondestructive and scalable separation strategy is expected to impact the fields of molecular electronics, optoelectronics, and sensing where SWNTs of a monodisperse band gap are essential.
Comprehensive Investigation of Hydroxypropyl Methylcellulose, Propylene Glycol, Polysorbate 80, and Hydroxypropyl-Beta-Cyclodextrin for use in General Toxicology Studies (2010)

This study was conducted to assess the safety and tolerability of the alternative formulation vehicles polysorbate 80 (PS80), propylene glycol (PG), and hydroxypropyl-beta-cyclodextrin (HPβCD) in general toxicology studies in the mouse, rat, dog, and monkey. Twenty (20) mg/kg of hydroxypropyl methylcellulose (MC, control), 10 mg/kg PS80, 1000 mg/kg PG, 500 mg/kg HPβCD, or 1000 mg/kg HPβCD were administered by oral gavage to mice, rats, dogs, and cynomolgus monkeys for approximately 90 days. The effects of these formulations on clinical observations, body weight and food consumption parameters, clinical pathology, and histopathology were evaluated across all species. The suitability of formulations containing up to 20 mg/kg MC, 10 mg/kg PS80, and 1000 mg/kg PG for use in preclinical safety studies was confirmed by a lack of effects on all parameters examined. However, formulations containing HPβCD produced elevated transaminase (aspartate and alanine aminotransferase) levels in rats and mice and fecal changes (loose and soft stool) in large animals. Although the etiology and toxicological significance of the transaminase elevations in rats and mice is uncertain, this finding could represent a significant liability for a preclinical formulation because of the critical importance of these biomarkers in the risk assessment of novel therapeutic agents. Based on these data, PS80 and PG are considered to be practical alternatives to MC in preclinical toxicology studies. However, formulations containing HPβCD should be used with caution because of the elevations in rodent transaminase levels.
Significant reduction of the antiatherogenic effect of estrogen by long-term inhibition of nitric oxide synthesis in cholesterol-clamped rabbits. (1997)

The purpose of this study was to investigate whether endothelium-derived nitric oxide (NO) is involved in the plasma lipid-independent antiatherogenic effect of estrogen and levormeloxifene, a partial estrogen receptor agonist. 85 rabbits were ovariectomized and balloon-injured in the middle thoracic aorta. The rabbits were fed a cholesterol-enriched diet supplemented with 17beta-estradiol, levormeloxifene, or placebo, either alone, or together with 160 microg/ml NG-nitro- -arginine methyl ester (-NAME), an NO synthase inhibitor, in their drinking water for 12 wk. Plasma cholesterol was maintained at 25-30 mmol/liter by individualized cholesterol feeding. In the undamaged aorta, the extent of atherosclerosis in the estrogen group was only one-third that in the placebo group. Simultaneous administration of -NAME, however, significantly reduced the antiatherogenic effect of estrogen (P < 0.01). There was no significant difference between the placebo group given -NAME and the group treated with placebo alone. At the previously endothelium-denuded site, estrogen had no effect on atherosclerosis development, whereas -NAME combined with estrogen significantly increased atherogenesis (P < 0.05). The effects of levormeloxifene were almost similar to those of estrogen. Active vascular concentrations of -NAME were demonstrated in an additional study, in which maximal aortic/coronary endothelium-dependent relaxation was significantly inhibited in rabbits given -NAME. Thus, in this study a considerable part of the plasma lipid-independent antiatherogenic effect of estrogen was mediated through its effect on endothelial NO in cholesterol-fed rabbits. The results for levormeloxifene suggest a common mechanism of action for estrogen and partial estrogen receptor agonists on atherogenesis.
Protective Role of Toll-like Receptor 4 during the Initiation Stage of Cutaneous Chemical Carcinogenesis (2008)

Toll-like receptors (TLR) activate multiple steps in inflammatory reactions in innate immune responses. They also activate signals that are critically involved in the initiation of adaptive immune responses. Many tumorigenic chemicals have been associated with endotoxin hypersensitivity mediated through TLR4. To determine the role of TLR4 in cutaneous skin carcinogenesis, we treated TLR4-deficient C3H/HeJ mice and the TLR4-normal C3H/HeN mice with the carcinogenic polyaromatic hydrocarbon 7,12-dimethylbenz(a)anthracene (DMBA). TLR4-deficient C3H/HeJ mice developed more tumors relative to the TLR4-normal C3H/HeN mice. Both C3H/HeN and C3H/HeJ mice developed a T-cell-mediated immune response to topically applied DMBA. Interestingly, the cell-mediated immune response was mediated by IFN-gamma in C3H/HeN mice and by interleukin (IL)-17 in C3H/HeJ mice. Moreover, C3H/HeN mice had elevated circulating levels of IFN-gamma following topical application of DMBA, whereas IL-17 was elevated in C3H/HeJ mice. The results of this study indicate that TLR4 plays an important role in the prevention of DMBA skin tumorigenesis and that this is associated with differences in the T-cell subtype activated. Efforts to divert the cell-mediated immune response from one that is IL-17 mediated to one that is IFN-gamma mediated may prove to be beneficial in the prevention of DMBA-induced cutaneous tumors.
Eine neue Synthese von Derivaten des Pyrrols (1960)

Der durch Kondensation des Dihydromucon-dinitrils mit Oxalester zugangliche 1.6-Dihydroxy-2.5-dicyan-hexatrien-(1.3trans.5)-dicarbonsaure-(1.6)-diathylester (IV) lieferte mit Anilin in sied. Toluol vorzugl. Ausbeute den 1-Phenyl-3-cyan-pyrrol-carbonsaure-(2)-ester (XIII), dessen Konstitution durch zahlreiche Umwandlungen gesichert wurde. Entsprechende Pyrrolabkommlinge wurden aus IV mit 11 aromatischen und 12 aliphatischen primaren Aminen sowie mit Ammoniak erhalten. Der Chemismus wird mit der Bildung eines Enamins, dessen intramolekulare Addition an ein Michael-System und Aromatisierung unter Abgabe von Cyanbrenztraubenester gedeutet.
Vaccine candidate MSP-1 from Plasmodium falciparum: a redesigned 4917 bp polynucleotide enables synthesis and isolation of full-length protein from Escherichia coli and mammalian cells (1999)

The Plasmodium falciparum malaria parasite is the causative agent of malaria tropica. Merozoites, one of the extracellular developmental stages of this parasite, expose at their surface the merozoite surface protein-1 complex (MSP-1), which results from the proteolytic processing of a 190-200 kDa precursor. MSP-1 is highly immunogenic in humans and numerous studies suggest that this protein is an effective target for a protective immune response. Although its function is unknown, there are indications that it may play a role during invasion of erythrocytes by merozoites. The parasite-derived msp-1 gene, which is approximately 5000 bp long, contains 74% AT. This high AT content has prevented stable cloning of the full-size gene in Escherichia coli and consequently its expression in heterologous systems. Here, we describe the synthesis of a 4917 bp gene encoding MSP-1 from the FCB-1 strain of P. falciparum adjusted for human codon preferences. The synthetic msp-1 gene (55% AT) was cloned, maintained and expressed in its entirety in E.coli as well as in CHO and HeLa cells. The purified protein is soluble and appears to possess native conformation because it reacts with a panel of mAbs specific for conformational epitopes. The strategy we used for synthesizing the full-length msp-1 gene was toassemble it from DNA fragments encoding all of the major proteolytic fragments normally generated at the parasite's surface. Thus, after subcloning we also obtained each of these MSP-1 processing products as hexahistidine fusion proteins in E.coli and isolated them by affinity chromatography on Ni2+agarose. The availability of defined preparations of MSP-1 and its major processing products open up new possibilities for in-depth studies at the structural and functional level of this important protein, including the exploration of MSP-1-based experimental vaccines.
Synthesis of some dihydroxamic acid siderophores (1984)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis of some dihydroxamic acid siderophoresM. K. Das, P. Bose, and N. RoyCite this: J. Chem. Eng. Data 1984, 29, 3, 345–348Publication Date (Print):July 1, 1984Publication History Published online1 May 2002Published inissue 1 July 1984https://pubs.acs.org/doi/10.1021/je00037a036https://doi.org/10.1021/je00037a036research-articleACS PublicationsRequest reuse permissionsArticle Views223Altmetric-Citations14LEARN 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
Boolean operations in solid modeling: Boundary evaluation and merging algorithms (1985)

Solid modeling plays a key role in electromechanical CAD/CAM, three-dimensional computer graphics, computer vision, robotics, and other disciplines and activities that deal with spatial phenomena. Almost all contemporary solid modeling systems support Boolean operations akin to set intersection, union, and difference on solids. Boundary representations (face/edge/vertex structures) for solids defined through Boolean operations are generated in these modelers by using so-called boundary evaluation and boundary merging procedures. These are the most complex and delicate software modules in a solid modeler. This paper describes boundary evaluation algorithms used by the PADL solid modeling systems developed at the University of Rochester, and discusses other known approaches in terms of concepts that emerged from the PADL work, notably set membership classification and neighborhood manipulation.
The Abi Proteins and Their Involvement in Bacteriocin Self-Immunity (2010)

The Abi protein family consists of putative membrane-bound metalloproteases. While they are involved in membrane anchoring of proteins in eukaryotes, little is known about their function in prokaryotes. In some known bacteriocin loci, Abi genes have been found downstream of bacteriocin structural genes (e.g., pln locus from Lactobacillus plantarum and sag locus from Streptococcus pyogenes), where they probably are involved in self-immunity. By modifying the profile hidden Markov model used to select Abi proteins in the Pfam protein family database, we show that this family is larger than presently recognized. Using bacteriocin-associated Abi genes as a means to search for novel bacteriocins in sequenced genomes, seven new bacteriocin-like loci were identified in Gram-positive bacteria. One such locus, from Lactobacillus sakei 23K, was selected for further experimental study, and it was confirmed that the bacteriocin-like genes (skkAB) exhibited antimicrobial activity when expressed in a heterologous host and that the associated Abi gene (skkI) conferred immunity against the cognate bacteriocin. Similar investigation of the Abi gene plnI and the Abi-like gene plnL from L. plantarum also confirmed their involvement in immunity to their cognate bacteriocins (PlnEF and PlnJK, respectively). Interestingly, the immunity genes from these three systems conferred a high degree of cross-immunity against each other's bacteriocins, suggesting the recognition of a common receptor. Site-directed mutagenesis demonstrated that the conserved motifs constituting the putative proteolytic active site of the Abi proteins are essential for the immunity function of SkkI, and to our knowledge, this represents a new concept in self-immunity.
Bootstrapping Confidence Intervals for Clinical Input Variable Effects in a Network Trained to Identify the Presence of Acute Myocardial Infarction (1995)

May 01 1995 Bootstrapping Confidence Intervals for Clinical Input Variable Effects in a Network Trained to Identify the Presence of Acute Myocardial Infarction In Special Collection: CogNet William G. Baxt, William G. Baxt Department of Emergency Medicine and Medicine, University of California, San Diego Medical Center, San Diego, CA USA 92093 *Present address: Department of Emergency Medicine, Hospital of the University of Pennsylvania, 3400 Spruce Street, Philadelphia, PA 19104 USA. Search for other works by this author on: This Site Google Scholar Halbert White Halbert White Department of Economics and Institute for Neural Compilation, University of California, San Diego, San Diego, CA USA 92093 Search for other works by this author on: This Site Google Scholar Author and Article Information William G. Baxt Department of Emergency Medicine and Medicine, University of California, San Diego Medical Center, San Diego, CA USA 92093 Halbert White Department of Economics and Institute for Neural Compilation, University of California, San Diego, San Diego, CA USA 92093 *Present address: Department of Emergency Medicine, Hospital of the University of Pennsylvania, 3400 Spruce Street, Philadelphia, PA 19104 USA. Received: April 21 1994 Accepted: July 22 1994 Online ISSN: 1530-888X Print ISSN: 0899-7667 © 1995 Massachusetts Institute of Technology1995 Neural Computation (1995) 7 (3): 624–638. https://doi.org/10.1162/neco.1995.7.3.624 Article history Received: April 21 1994 Accepted: July 22 1994 Cite Icon Cite Permissions Share Icon Share Facebook Twitter LinkedIn Email Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Search Site Citation William G. Baxt, Halbert White; Bootstrapping Confidence Intervals for Clinical Input Variable Effects in a Network Trained to Identify the Presence of Acute Myocardial Infarction. Neural Comput 1995; 7 (3): 624–638. doi: https://doi.org/10.1162/neco.1995.7.3.624 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsNeural Computation Search Advanced Search This content is only available as a PDF. © 1995 Massachusetts Institute of Technology1995 Article PDF first page preview Close Modal You do not currently have access to this content.