gebhart/patrepeval huggingface dataset:
Protection from Anthrax Toxin-Mediated Killing of Macrophages by the Combined Effects of Furin Inhibitors and Chloroquine (2005)

Cell surface proteolytic processing of anthrax protective antigen by furin or other furin-related proteases is required for its oligomerization, endocytosis, and function as a translocon for anthrax lethal and edema factors. Countering toxin lethality is essential to developing effective chemotherapies for anthrax infections that have proceeded beyond the stage at which antibiotics are effective. The primary target for toxin is the macrophage, which can be killed by lethal factor via both necrotic and apoptotic pathways. Here we show that three high-affinity inhibitors of furin efficiently blocked killing of murine J774A.1 macrophages by recombinant protective antigen plus lethal factor: RRD-eglin and RRDG-eglin, developed by engineering the protein protease inhibitor eglin c, and the peptide boronic acid inhibitor acetyl-Arg-Glu-Lys-boroArg pinanediol. Inhibition of killing was dose dependent and correlated with prevention of protective antigen processing. Previous studies have shown that weak bases, such as chloroquine, which neutralize acidic compartments, also interfere with toxin-dependent killing. Here we show that combining furin inhibitors and chloroquine strongly augments the inhibition of toxin-dependent killing, suggesting that combined use of antifurin drugs and chloroquine might provide enhanced therapeutic benefits. Reversible furin inhibitors protected against anthrax toxin killing for at least 5 h, but by 8 h, toxin-dependent killing resumed even though furin inhibitors were still active. An irreversible chloromethylketone inhibitor did not exhibit this loss of protection.
Gene expression profiling with oligonucleotide microarrays distinguishes World Health Organization grade of oligodendrogliomas. (2001)

Oligodendrogliomas are the second most common type of glial neoplasm with distinct prognostic and therapeutic implications. Although refinements have led to improved clinical stratification, current grading schemes are still limited by subjective histopathological criteria. In this report, we have used oligonucleotide array technology to perform expression profiling in morphologically classic oligodendrogliomas. Expression information from approximately 1100 genes divided tumors into two molecularly distinct groups that corresponded exactly to their previously assigned histological grades. Subsequent gene clustering identified a subset of 196 transcripts showing a common, differential expression pattern between tumor grades. A number of these genes have been associated with the maintenance of cytoarchitecture, cellular differentiation and maturation, immunogenicity, and chemotherapeutic resistance. These results demonstrate the utility of gene expression profiling as an objective, ancillary tool for grading oligodendrogliomas and a potential approach for classifying diffuse gliomas where histological assessment may be difficult or ambiguous.
Origins and Consequences of Mitochondrial Variation in Vertebrate Muscle (2003)

This review addresses the mechanisms by which mitochondrial structure and function are regulated, with a focus on vertebrate muscle. We consider the adaptive remodeling that arises during physiological transitions such as differentiation, development, and contractile activity. Parallels are drawn between such phenotypic changes and the pattern of change arising over evolutionary time, as suggested by interspecies comparisons. We address the physiological and evolutionary relationships between ATP production, thermogenesis, and superoxide generation in the context of mitochondrial function. Our discussion of mitochondrial structure focuses on the regulation of membrane composition and maintenance of the three-dimensional reticulum. Current studies of mitochondrial biogenesis strive to integrate muscle functional parameters with signal transduction and molecular genetics, providing insight into the origins of variation arising between physiological states, fiber types, and species.
Complex Formation with Plasmid DNA Increases the Cytotoxicity of Cationic Liposomes (2007)

Cationic liposomes (CL) are one of the most widely studied non-viral vectors for gene delivery. It is well-known that CL induces cytotoxicity following lipofection. However, little is known regarding the mechanism involved in the cytotoxicity. In this study, the in vitro cytotoxicity of CL and its complex with pDNA (lipoplex) was investigated, and a part of the mechanism of induction as well. While free pDNA did not show any cytotoxicity, pDNA increased the cytotoxicity of CL via the formation of lipoplex. In addition, the lipoplex-induced cytotoxicity increased in a lipoplex dose-dependent manner, irrespective of the type of pDNA, cell line and the absence or presence of serum. An assay showed that apoptosis was largely induced by treatment with the lipoplex (lipofection), but not with CL alone, in the tested range of concentration of CL and pDNA. Furthermore, following treatment with lipoplexes, the cells exhibited the morphological features of apoptosis and DNA fragmentation. A cDNA microarray study showed that the lipofection up-regulated 45 genes related to apoptosis, transcription regulation and immune response. These results clearly indicate that pDNA in the lipoplex increases the cytotoxicity of CL as a result of inducing apoptosis. The fundamental principle for gene therapy is to deliver gene-based therapeutics to target cells for specific gene targeting with minimal cytotoxicity. Our results suggest the possibility that cytotoxicity induced by lipofection, accompanied by gene changes, could intrinsically exacerbate, attenuate or even mask the desired effects of gene-based therapy.
Tolerance to Imidazolinone Herbicides in Wheat (1992)

An imidazolinone-tolerant wheat (Triticum aestivum L. em Thell) mutant in the winter wheat cultivar Fidel has been identified and characterized. The mutant was isolated from a population derived through seed mutagenesis of the variety with an aqueous solution containing sodium azide. Imidazolinone-tolerant wheat seedlings were selected from the M(2) generation of the population in the presence of imazethapyr herbicide and identified as herbicide-insensitive individuals. The trait is inherited as a single semidominant gene and confers high levels of tolerance to imazethapyr. Acetohydroxyacid synthase activity in extracts from imidazolinonetolerant plants was less inhibited by imazethapyr than the enzyme from the wild type. The herbicide-tolerant plants have a completely normal phenotype and display no negative effects on growth and yield in either the absence or presence of imazethapyr.
Photonic band structure investigation of two-dimensional Bragg reflector mirrors for semiconductor laser mode control (1993)

A theoretical study that follows the lines of previous photonic band structure investigations has been undertaken in search of a two-dimensional (2D) periodic dielectric structure that exhibits a certain type of photonic band structure for application as an external feedback mirror for laser diode arrays and broad-area devices. Instead of looking for an absolute band gap for a band of frequencies, we are particularly interested in structures that exhibit only stop bands, i.e., bands with a narrow extent in both frequency and angle. This type of reflecting structure, which can also be termed a 2D Bragg reflector, could provide improved mode control for both longitudinal and transverse characteristics of the modes for these devices. Our study, which employed photonic band structure calculational methods, showed that square lattice dielectric structures exhibit such stop bands for both TE and TM waves and could be used as photonic band structure mirrors to induce better mode control.
Rotavirus A-specific single-domain antibodies produced in baculovirus-infected insect larvae are protective in vivo (2012)

Our results open up the possibility of using insects as living biofactories (IBES® technology) for the cost-efficient production of these and other fully functional VHHs to be used for diagnostic or therapeutic purposes, thereby eliminating concerns regarding the use of bacterial or mammalian cells. To the best of our knowledge, this is the first time that insects have been used as living biofactories to produce a VHH molecule.
.pi. Complexation in ion pair bonding. Structure of benzyllithium triethylenediamine (1970)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXT.pi. Complexation in ion pair bonding. Structure of benzyllithium triethylenediamineS. P. Patterman, Isabella L. Karle, and G. D. StuckyCite this: J. Am. Chem. Soc. 1970, 92, 5, 1150–1157Publication Date (Print):March 1, 1970Publication History Published online1 May 2002Published inissue 1 March 1970https://pubs.acs.org/doi/10.1021/ja00708a008https://doi.org/10.1021/ja00708a008research-articleACS PublicationsRequest reuse permissionsArticle Views203Altmetric-Citations136LEARN 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
Quantitative Determination of Paralytic Shellfish Poisoning Toxins in Shellfish Using Prechromatographic Oxidation and Liquid Chromatography with Fluorescence Detection: Interlaboratory Study (2004)

A collaborative study was conducted for the determination of paralytic shellfish poisoning (PSP) toxins in shellfish. The method used liquid chromatography with fluorescence detection after prechromatographic oxidation of the toxins with hydrogen peroxide and periodate. The PSP toxins studied were saxitoxin (STX), neosaxitoxin (NEO), gonyautoxins 2 and 3 (GTX2,3; together), gonyautoxins 1 and 4 (GTX1,4; together), decarbamoyl saxitoxin (dcSTX), B-1 (GTX5), C-1 and C-2 (C1,2; together), and C-3 and C-4 (C3,4; together). B-2 (GTX6) toxin was also included, but for qualitative identification only. Mussels, both blank and naturally contaminated, were mixed and homogenized to provide a variety of PSP toxin mixtures and concentration levels. The same procedure was followed with clams, oysters, and scallops. Twenty-one test samples in total were sent to 21 collaborators who agreed to participate in the study. Results were obtained from 18 laboratories representing 14 different countries. It is recommended that the method be adopted First Action by AOAC INTERNATIONAL.
IRES-Mediated Translation of Utrophin A Is Enhanced by Glucocorticoid Treatment in Skeletal Muscle Cells (2008)

Glucocorticoids are currently the only drug treatment recognized to benefit Duchenne muscular dystrophy (DMD) patients. The nature of the mechanisms underlying the beneficial effects remains incompletely understood but may involve an increase in the expression of utrophin. Here, we show that treatment of myotubes with 6alpha-methylprednisolone-21 sodium succinate (PDN) results in enhanced expression of utrophin A without concomitant increases in mRNA levels thereby suggesting that translational regulation contributes to the increase. In agreement with this, we show that PDN treatment of cells transfected with monocistronic reporter constructs harbouring the utrophin A 5'UTR, causes an increase in reporter protein expression while leaving levels of reporter mRNAs unchanged. Using bicistronic reporter assays, we further demonstrate that PDN enhances activity of an Internal Ribosome Entry Site (IRES) located within the utrophin A 5'UTR. Analysis of polysomes demonstrate that PDN causes an overall reduction in polysome-associated mRNAs indicating that global translation rates are depressed under these conditions. Importantly, PDN causes an increase in the polysome association of endogenous utrophin A mRNAs and reporter mRNAs harbouring the utrophin A 5'UTR. Additional experiments identified a distinct region within the utrophin A 5'UTR that contains the inducible IRES activity. Together, these studies demonstrate that a translational regulatory mechanism involving increased IRES activation mediates, at least partially, the enhanced expression of utrophin A in muscle cells treated with glucocorticoids. Targeting the utrophin A IRES may thus offer an important and novel therapeutic avenue for developing drugs appropriate for DMD patients.
Analysis of the 3' end of the human pro-alpha 2(I) collagen gene. Utilization of multiple polyadenylation sites in cultured fibroblasts. (1983)

Three overlapping genomic clones covering 28 kilobases of the human pro-alpha 2(I) collagen gene have been isolated from a lambda phage library. The analysis of 12 introns and 12 exons in the 3' end region has shown that the human gene has a structure remarkably similar to that reported for the homologous chicken gene. One large intron, in the alpha-chain domain, contains an AluI sequence flanked by short direct repeats; a second AluI sequence is present 4 kilobases downstream from the termination codon. The analysis of the exon coding for the 3'-untranslated region has revealed that the pro-alpha 2(I) collagen gene transcribes at least four different mRNAs in cultured fibroblasts. The colinearity and exact location of the termini of these transcripts was determined by Northern blots, R-looping analysis, S1 protection, and DNA sequencing. The ends of two transcripts are closely preceded by the canonical polyadenylation signal (AAUAAA), whereas two of its variations (AUUAAA and AUUAA) precede the ends of the other two transcripts.
Tunable Delivery of siRNA from a Biodegradable Scaffold to Promote Angiogenesis In Vivo (2013)

A system is engineered for temporally controlled delivery of siRNA from biodegradable tissue regenerative scaffolds. Therapeutic application of this approach to silence PHD2 promotes expression of pro-angiogenic genes controlled by HIF1α and enhanced scaffold vascularization in vivo. This technology provides a new standard for efficient and controllable gene silencing to modulate host response within regenerative biomaterials. As a service to our authors and readers, this journal provides supporting information supplied by the authors. Such materials are peer reviewed and may be re-organized for online delivery, but are not copy-edited or typeset. Technical support issues arising from supporting information (other than missing files) should be addressed to the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
HER-2 DNA and Protein Vaccines Containing Potent Th Cell Epitopes Induce Distinct Protective and Therapeutic Antitumor Responses in HER-2 Transgenic Mice (2003)

Overexpression of the growth factor receptor HER-2 (c-erbB-2, neu) has transforming potential and occurs in approximately 20-30% of breast and ovarian cancers. HER-2 is a self Ag, but Abs and T cells specific for HER-2 have been isolated from cancer patients, suggesting HER-2 may be a good target for active immunotherapy. We constructed rat HER-2 DNA and protein vaccines containing potent Th cell epitopes derived from tetanus toxin and studied their potency in two strains of mice transgenic for the rat HER-2 molecule. Vaccination with HER-2 DNA protected nontransgenic mice from tumor challenge, but induced only moderate protection in one of the tumor models. However, vaccination with the modified HER-2 protein resulted in almost complete protection from tumor challenge in both tumor models. This protection could be mediated by Abs alone. In addition, protein vaccination efficiently eliminated pre-established tumors in both models, even when vaccination occurred 9 days after tumor implantation. These data demonstrate the potential of HER-2-based vaccines as therapeutic agents for the treatment of cancers overexpressing HER-2.
Interleukin-10: Potential Benefits and Possible Risks in Clinical Infectious Diseases (1998)

Human interleukin-10 (IL-10) is a potent anti-inflammatory cytokine that inhibits the synthesis of the major proinflammatory cytokines and chemokines. IL-10 is the principal TH2-type cytokine that upregulates humoral immune responses and attenuates cell-mediated immune reactions. This cytokine has a number of immunomodulatory properties that might be clinically useful in a variety of inflammatory and infectious disease states. Clinical trials with human recombinant IL-10 are already in progress. Carefully selected patients with inflammatory conditions may benefit from IL-10 therapy if concomitant infectious diseases are recognized and treated appropriately.
Microfluidic synthesis of monodisperse porous microspheres with size-tunable pores (2012)

We use a perfluorinated-dendrimer–dye complex that stabilizes microbubbles as a novel pore-forming agent. We use microfluidics to produce monodisperse emulsions containing a polymer matrix material, a model active, and the perfluorinated complex; upon drying, the emulsions form porous microspheres. This porosity causes the encapsulated model active to be released faster than from non-porous microspheres. Moreover, because of the fluorous features of the pores, we can also attach an additional guest molecule to the pores which is released with a profile that is distinct from that of the encapsulated active. These porous microspheres can encapsulate and controllably release multiple actives; this makes them valuable for applications such as drug delivery and imaging.
MEMS-actuated microdisk resonators with variable power coupling ratios (2005)

A novel tunable microdisk resonator with microelectromechanical-system (MEMS)-actuated deformable waveguides is demonstrated for the first time. The deformable waveguide enables us to continuously vary the power coupling ratio of the microdisks. A laterally coupled device with a quality factor of 7700 is fabricated on silicon-on-insulator substrate. An optical notch filter with variable attenuation at the resonant wavelength is successfully demonstrated, with an extinction ratio of 9 dB. The MEMS-actuated tunable microdisk is a basic building block for many dynamic wavelength-division-multiplexing circuits.
Attenuated traumatic axonal injury and improved functional outcome after traumatic brain injury in mice lackingSarm1 (2016)

Axonal degeneration is a critical, early event in many acute and chronic neurological disorders. It has been consistently observed after traumatic brain injury, but whether axon degeneration is a driver of traumatic brain injury remains unclear. Molecular pathways underlying the pathology of traumatic brain injury have not been defined, and there is no efficacious treatment for traumatic brain injury. Here we show that mice lacking the mouse Toll receptor adaptor Sarm1 (sterile α/Armadillo/Toll-Interleukin receptor homology domain protein) gene, a key mediator of Wallerian degeneration, demonstrate multiple improved traumatic brain injury-associated phenotypes after injury in a closed-head mild traumatic brain injury model. Sarm1(-/-) mice developed fewer β-amyloid precursor protein aggregates in axons of the corpus callosum after traumatic brain injury as compared to Sarm1(+/+) mice. Furthermore, mice lacking Sarm1 had reduced plasma concentrations of the phophorylated axonal neurofilament subunit H, indicating that axonal integrity is maintained after traumatic brain injury. Strikingly, whereas wild-type mice exibited a number of behavioural deficits after traumatic brain injury, we observed a strong, early preservation of neurological function in Sarm1(-/-) animals. Finally, using in vivo proton magnetic resonance spectroscopy we found tissue signatures consistent with substantially preserved neuronal energy metabolism in Sarm1(-/-) mice compared to controls immediately following traumatic brain injury. Our results indicate that the SARM1-mediated prodegenerative pathway promotes pathogenesis in traumatic brain injury and suggest that anti-SARM1 therapeutics are a viable approach for preserving neurological function after traumatic brain injury.
Development of safe and scalable continuous-flow methods for palladium-catalyzed aerobic oxidation reactions (2010)

The synthetic scope and utility of Pd-catalyzed aerobic oxidation reactions has advanced significantly over the past decade, and these reactions have potential to address important green-chemistry challenges in the pharmaceutical industry. This potential has been unrealized, however, because safety concerns and process constraints hinder large-scale applications of this chemistry. These limitations are addressed by the development of a continuous-flow tube reactor, which has been demonstrated on several scales in the aerobic oxidation of alcohols. Use of a dilute oxygen gas source (8% O(2) in N(2)) ensures that the oxygen/organic mixture never enters the explosive regime, and efficient gas-liquid mixing in the reactor minimizes decomposition of the homogeneous catalyst into inactive Pd metal. These results provide the basis for large-scale implementation of palladium-catalyzed (and other) aerobic oxidation reactions for pharmaceutical synthesis.
Improved Semantic Region Labeling Based on Scene Context (2005)

Semantic region labeling in outdoor scenes, e.g., identifying sky, grass, foliage, water, and snow, facilitates content-based image retrieval, organization, and enhancement. A major limitation of current object detectors is the significant number of misclassifications due to the similarities in color and texture characteristics of various object types and lack of context information. Building on previous work of spatial context-aware object detection, we have developed a further improved system by modeling and enforcing spatial context constraints specific to individual scene type. In particular, the scene context, in the form of factor graphs, is obtained by learning and subsequently used via MAP estimation to reduce misclassification by constraining the object detection beliefs to conform to the spatial context models. Experimental results show that the richer spatial context models improve the accuracy of object detection over the individual object detectors and the general outdoor scene model.