gebhart/patrepeval huggingface dataset:
Lysosomal Turnover, but Not a Cellular Level, of Endogenous LC3 is a Marker for Autophagy (2005)

During starvation-induced autophagy in mammals, autophagosomes form and fuse with lysosomes, leading to the degradation of the intra-autophagosomal contents by lysosomal proteases. During the formation of autophagosomes, LC3 is lipidated, and this LC3-phospholipid conjugate (LC3-II) is localized on autophagosomes and autolysosomes. While intra-autophagosomal LC3-II may be degraded by lysosomal hydrolases, recent studies have regarded LC3-II accumulation as marker of autophagy. The effect of lysosomal turnover of endogenous LC3-II in this process, however, has not been considered. We therefore investigated the lysosomal turnover of endogenous LC3-II during starvation-induced autophagy using E64d and pepstatin A, which inhibit lysosomal proteases, including cathepsins B, D and L. We found that endogenous LC3-II significantly accumulated in the presence of E64d and pepstatin A under starvation conditions, increasing about 3.5 fold in HEK293 cells and about 6.7 fold in HeLa cells compared with that in their absence, whereas the amount of LC3-II in their absence is cell-line dependent. Morphological analyses indicated that endogenous LC3-positive puncta and autolysosomes increased in HeLa cells under starvation conditions in the presence of these inhibitors. These results indicate that endogenous LC3-II is considerably degraded by lysosomal hydrolases after formation of autolysosomes, and suggest that lysosomal turnover, not a transient amount, of this protein reflects starvation-induced autophagic activity.
Drug resistance, serotypes, and phylogenetic groups among uropathogenic Escherichia coli including O25-ST131 in Mexico City (2011)

This is the first report that establishes the presence in Mexico of the O25-ST131 clonal group of E. coli, which has been associated with multidrug-resistance and with high virulence potential. The spread of this clone in Mexico should be monitored closely. We found a correlation between serotype O25:H4 and multidrug resistance in UPEC strains. Our results indicate that the use of ampicillin, fluoroquinolones, and TMP/SMX should be reviewed when selecting empirical therapy for UTIs.
The ATP binding cassette (ABC) transport systems ofMycobacterium tuberculosis (2000)

We have undertaken the inventory and assembly of the typical subunits of the ABC transporters encoded by the complete genome of Mycobacterium tuberculosis. These subunits, i.e. the nucleotide binding domains (NBDs), the membrane-spanning domains (MSDs) and the substrate binding proteins (SBPs), were identified on the basis of their characteristic stretches of amino acids and/or conserved structure. A total of 45 NBDs present in 38 proteins, of 47 MSDs present in 44 proteins and of 15 SBPs were found to be encoded by M. tuberculosis. Analysis of transcriptional clusters and searches of homology between the identified subunits of the transporters and proteins characterized in other organisms allowed the reconstitution of at least 26 complete (including at least one NBD and one MSD) and 11 incomplete ABC transporters. Sixteen of them were unambiguously classified as importers whereas 21 were presumed to be exporters. By searches of homology with already known transporters from other organisms, potential substrates (peptides, macrolides, carbohydrates, multidrugs, antibiotics, iron, anions) could be attributed to 30 of the ABC transporters identified in M. tuberculosis. The ABC transporters have been further classified in nine different sub-families according to a tree obtained from the clustering of their NBDs. Contrary to Escherichia coli and similarly to Bacillus subtilis, there is an equal representation of extruders and importers. Many exporters were found to be potentially implicated in the transport of drugs, probably contributing to the resistance of M. tuberculosis to many antibiotics. Interestingly, a transporter (absent in E. coli and in B. subtilis) potentially implicated in the export of a factor required for the bacterial attachment to the eukaryotic host cells was also identified. In comparison to E. coli and B. subtilis, there is an under-representation of the importers (with the exception of the phosphate importers) in M. tuberculosis. This may reflect the capacity of this bacterium to synthesize many essential compounds and to grow in the presence of few external nutrients. The genes encoding the ABC transporters occupy about 2.5% of the genome of M. tuberculosis.
Instability of dicentric plasmids in yeast. (1983)

Dicentric plasmids containing either two copies of centromere 4 or one copy of centromere 4 and one copy of centromere 3 in the yeast plasmid vector YRp17 were constructed in vitro and introduced into yeast cells by DNA transformation. The resulting colonies were heterogeneous for a mixed population of rearranged plasmids. The rearrangements always involved deletion of one or both centromere sequences originally present on the plasmid. Heterogeneity was due to the continued production of deleted plasmids from a pool of unrearranged dicentric plasmids maintained within some of the yeast cells in the colony. The RAD52 gene product is known to be required for the repair of DNA double-strand breaks in yeast. Transformation of rad52 mutant yeast cells with dicentric plasmids gave rearranged plasmids similar to those observed with RAD+ yeast cells, but the transformation frequency was only 5-10% compared to transformation with monocentric plasmids. Also, the ratio of unrearranged dicentric plasmid to deleted plasmids was greatly reduced in the rad52-transformed cells. These observations are consistent with a model in which centromeric DNA sequences can interact independently with the yeast cell spindle apparatus. Occasional movement of centromeres to opposite poles may result in mechanical breakage of plasmid sequences. Plasmids deleted for one or both centromere sequences can be obtained from these broken molecules and are resistant to further rearrangement.
Advances in refractory ulcerative colitis treatment: A new therapeutic target, Annexin A2 (2015)

Medical treatment has progressed significantly over the past decade towards achieving and maintaining clinical remission in patients with refractory ulcerative colitis (UC). Proposed mediators of inflammation in UC include pro-inflammatory cytokines such as tumor necrosis factor-α (TNF-α) and interleukin-2, and the cell-surface adhesive molecule integrin α4β7. Conventional therapeutics for active UC include 5-aminosalicylic acid, corticosteroids and purine analogues (azathioprine and 6-mercaptopurine). Patients who fail to respond to conventional therapy are treated with agents such as the calicineurin inhibitors cyclosporine and tacrolimus, the TNF-α inhibitors infliximab or adalimumab, or a neutralizing antibody (vedolizumab) directed against integrin α4β7. These therapeutic agents are of benefit for patients with refractory UC, but are not universally effective. Our recent research on TNF-α shedding demonstrated that inhibition of annexin (ANX) A2 may be a new therapeutic strategy for the prevention of TNF-α shedding during inflammatory bowel disease (IBD) inflammation. In this review, we provide an overview of therapeutic treatments that are effective and currently available for UC patients, as well as some that are likely to be available in the near future. We also propose the potential of ANX A2 as a new molecular target for IBD treatment.
A 2.5-10-GHz clock multiplier unit with 0.22-ps RMS jitter in standard 0.18-/spl mu/m CMOS (2004)

This paper demonstrates a low-jitter clock multiplier unit that generates a 10-GHz output clock from a 2.5-GHz reference clock. An integrated 10-GHz LC oscillator is locked to the input clock, using a simple and fast phase detector circuit that overcomes the speed limitation of a conventional tri-state phase frequency detector due to the lack of an internal feedback loop. A frequency detector guarantees PLL locking without degenerating jitter performance. The clock multiplier is implemented in a standard 0.18-/spl mu/m CMOS process and achieves a jitter generation of 0.22 ps while consuming 100 mW power from a 1.8-V supply.
Modified Head Shake Computerized Dynamic Posturography (2009)

The head shake modification showed a trend in increasing the separation of normal individuals across age and eliminated the limitations addressed in earlier research. Future research will investigate the head shake modification for identifying vestibular peripheral system asymmetries.
Metal substitution of Neurospora copper metallothionein (1984)

The binding of diamagnetic Zn(II), Cd(II), and Hg(II) and paramagnetic Co(II) and Ni(II) ions to the apo form of Neurospora metallothionein (MT) was investigated by various spectroscopic techniques. In contrast to native copper MT, which was shown to bind 6 mol of Cu(I)/mol of protein (Lerch, 1980), all substituted forms reveal an overall metal to protein stoichiometry of 3. The charge-transfer (CT) transitions of the complexes containing diamagnetic metal ions as well as the d-d transitions of those with paramagnetic metal ions are indicative of a distorted Td coordination. Electron paramagnetic resonance and absorption measurements of the Co(II) derivative are in agreement with the presence of a metal-thiolate cluster in this protein. Metal titration studies of the apoprotein reveal characteristic spectral features for the derivatives containing two metal equivalents as compared to those with a full complement of three metal ions. The former features are indicative of an exclusive Td type of metal-sulfur coordination whereas the latter suggest that the third metal ion is coordinated in a different fashion. This finding is in agreement with the presence of only seven cysteine residues in Neurospora MT as opposed to nine cysteine residues in the three-metal cluster of the mammalian MT's [Winge, D.R., & Miklossy, K.-A. (1982) J. Biol. Chem. 257, 3471].
Tumor oxygenation predicts for the likelihood of distant metastases in human soft tissue sarcoma. (1996)

This study was performed to explore the relationship between tumor oxygenation and treatment outcome in human soft tissue sarcoma. Twenty-two patients with nonmestastatic, high-grade, soft tissue sarcomas underwent preoperative irradiation and hyperthermia and pretreatment measurement of tumor oxygenation. The 18-month actuarial disease-free survival was 70% for patients with tumor median oxygen pressure (pO2) values of >10 mm Hg but only 35% for those with median pO2 values of <10 mm Hg (P=0.01). There were eight treatment failures; the first site of recurrence was lung in all patients. Median pO2 was 7.5 mm Hg for metastasizing tumors versus 20 mm Hg for nonmetastasizing tumors (P=0.03). Potential mechanisms and implications for clinical trial design are discussed.
Cutaneous Reactions to Injection of Progesterone Solutions into the Skin (1952)

areas.Such infants may die if the cyanosis is attributed to congenital heart disease and treatment is not given.My thanks are due to Mr. D. W. Neill for carrying out the spectroscopic examination of the blood and for estimating the nitrate content of the water.
A Plant-Produced Pfs25 VLP Malaria Vaccine Candidate Induces Persistent Transmission Blocking Antibodies against Plasmodium falciparum in Immunized Mice (2013)

Malaria transmission blocking vaccines (TBVs) are considered an effective means to control and eventually eliminate malaria. The Pfs25 protein, expressed predominantly on the surface of the sexual and sporogonic stages of Plasmodium falciparum including gametes, zygotes and ookinetes, is one of the primary targets for TBV. It has been demonstrated that plants are an effective, highly scalable system for the production of recombinant proteins, including virus-like particles (VLPs). We engineered VLPs (Pfs25-CP VLP) comprising Pfs25 fused to the Alfalfa mosaic virus coat protein (CP) and produced these non-enveloped hybrid VLPs in Nicotiana benthamiana plants using a Tobacco mosaic virus-based 'launch' vector. Purified Pfs25-CP VLPs were highly consistent in size (19.3±2.4 nm in diameter) with an estimated 20-30% incorporation of Pfs25 onto the VLP surface. Immunization of mice with one or two doses of Pfs25-CP VLPs plus Alhydrogel® induced serum antibodies with complete transmission blocking activity through the 6 month study period. These results support the evaluation of Pfs25-CP VLP as a potential TBV candidate and the feasibility of the 'launch' vector technology for the production of VLP-based recombinant vaccines against infectious diseases.
Subsurface Imaging of Living Skin with Optical Coherence Microscopy (1995)

The results of this study suggest that an optical coherence microscope may have value as a diagnostic tool for cases in which visualization of subcellular details is not required. The resolution, contrast and scanning speed of the microscope need to be improved.
Unraveling the Chemistry of Chemokine Receptor Ligands (2003)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTUnraveling the Chemistry of Chemokine Receptor LigandsZhongli Gao and William A. MetzView Author Information Medicinal Chemistry, Aventis Pharmaceuticals, Route 202-206, Bridgewater, New Jersey 08807-0800 Cite this: Chem. Rev. 2003, 103, 9, 3733–3752Publication Date (Web):August 6, 2003Publication History Received26 November 2002Published online6 August 2003Published inissue 1 September 2003https://pubs.acs.org/doi/10.1021/cr020474bhttps://doi.org/10.1021/cr020474bresearch-articleACS PublicationsCopyright © 2003 American Chemical SocietyRequest reuse permissionsArticle Views894Altmetric-Citations36LEARN 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:Antagonists,Assays,Chemical structure,Ligands,Receptors Get e-Alerts
Cinnamic acid derivatives as matrices for ultraviolet laser desorption mass spectrometry of proteins (1989)

The paper reports the discovery of three new matrices for the matrix-assisted laser desorption of proteins. These new matrices (sinapinic, ferulic and caffeic acids) are cinnamic acid derivatives that have several practical advantages over the nicotinic acid matrices previously used. These materials form much less intense photochemically generated adduct peaks in the protein quasimolecular ion signal and the adduct peaks that are present are easier to resolve. These matrices produce intense protonated-molecule ions from all of the proteins (over 50) so far examined. These new matrices are also very stable in a vacuum, allowing for their convenient use in very high vacuum applications (e.g., Fourier transform ion cyclotron resonance mass spectrometry).
Biodegradable Nanoparticle-Entrapped Vaccine Induces Cross-Protective Immune Response against a Virulent Heterologous Respiratory Viral Infection in Pigs (2012)

Biodegradable nanoparticle-based vaccine development research is unexplored in large animals and humans. In this study, we illustrated the efficacy of nanoparticle-entrapped UV-killed virus vaccine against an economically important respiratory viral disease of pigs called porcine reproductive and respiratory syndrome virus (PRRSV). We entrapped PLGA [poly (lactide-co-glycolides)] nanoparticles with killed PRRSV antigens (Nano-KAg) and detected its phagocytosis by pig alveolar macrophages. Single doses of Nano-KAg vaccine administered intranasally to pigs upregulated innate and PRRSV specific adaptive responses. In a virulent heterologous PRRSV challenge study, Nano-KAg vaccine significantly reduced the lung pathology and viremia, and the viral load in the lungs. Immunologically, enhanced innate and adaptive immune cell population and associated cytokines with decreased secretion of immunosuppressive mediators were observed at both mucosal sites and blood. In summary, we demonstrated the benefits of intranasal delivery of nanoparticle-based viral vaccine in eliciting cross-protective immune response in pigs, a potential large animal model.
Glutathione-<I>S</I>-Transferase–Fusion Based Assays for Studying Protein–Protein Interactions (2004)

Glutathione-S-transferase (GST)-fusion proteins have become an effective reagent to use in the study of protein-protein interactions. GST-fusion proteins can be produced in bacterial and mammalian cells in large quantities and purified rapidly. GST can be coupled to a glutathione matrix, which permits its use as an effective affinity column to study interactions in vitro or to purify protein complexes in cells expressing the GST-fusion protein. Here, we provide a technical description of the utilization of GST-fusion proteins as both a tool to study protein-protein interactions and also as a means to purify interacting proteins.
Prospects for developing an effective particle-mediated DNA vaccine against influenza (2009)

Vaccine strategies capable of conferring broad protection against both seasonal and pandemic strains of influenza are urgently needed. DNA vaccines are an attractive choice owing to their capacity to induce robust humoral and cellular immune responses at low doses and because they can be developed and manufactured rapidly to more effectively meet the threat of an influenza epidemic or pandemic. Particle-mediated epidermal delivery (PMED), or the gene gun, is a DNA vaccine delivery technology shown to induce protective levels of antibody and T-cell responses in animals and humans against a wide variety of diseases, including influenza. This review focuses on current advances toward the development of an effective PMED DNA vaccine against influenza, including strategies to enhance vaccine immunogenicity, the potential for PMED-based DNA vaccines to improve protection in the vulnerable elderly population, and the prospects for a vaccine capable of providing cross-protection against both seasonal and pandemic strains of influenza.
Impedance Spectroscopic Analysis of Lead Iodide Perovskite-Sensitized Solid-State Solar Cells (2013)

Mesoscopic solid-state solar cells based on the inorganic-organic hybrid perovskite CH3NH3PbI3 in conjunction with the amorphous organic semiconductor spiro-MeOTAD as a hole transport material (HTM) are investigated using impedance spectroscopy (IS). A model to interpret the frequency response of these devices is established by expanding and elaborating on the existing models used for the liquid and solid-state dye-sensitized solar cells. Furthermore, the influence of changing the additive concentrations of tert-butylpyridine and LiTFSI in the HTM and varying the HTM overlayer thickness on top of the sub-micrometer thick TiO2 on the extracted IS parameters is investigated. The internal electrical processes of such devices are studied and correlated with the overall device performance. In particular, the features in the IS responses that are attributed to the ionic and electronic transport properties of the perovskite material and manifest as a slow response at low frequency and an additional RC element at intermediate frequency, respectively, are explored.
Randomized Phase II Study of Docetaxel and Prednisone With or Without OGX-011 in Patients With Metastatic Castration-Resistant Prostate Cancer (2010)

Treatment with OGX-011 and docetaxel was well tolerated with evidence of biologic effect and was associated with improved survival. Further evaluation is warranted.
Broadcast delivery (1988)

The architecture and performance of systems that use a broadcast channel to deliver information to a community of users are discussed. Information is organized into units called pages, and at any instant of time, two or more users may request the same page. Broadcast delivery is attractive for such an environment because a single transmission of a page will satisfy all pending requests for that page. Three alternative architectures for broadcast information delivery systems are considered. They are one-way broadcast, two-way interaction, and hybrid one-way broadcast/two-way interaction. An important design issue is the scheduling of page transmissions such that the user response time is minimized. For each architecture, existing scheduling algorithms are described, and their mean-response-time performance evaluated. Properties of scheduling algorithms that yield optimal mean response time are discussed. A comparative discussion of the performance differences of the three architectures is also provided.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Application of IgG-Derived Natural Treg Epitopes (IgG Tregitopes) to Antigen-Specific Tolerance Induction in a Murine Model of Type 1 Diabetes (2013)

HLA class II-restricted regulatory T cell (Treg) epitopes in IgG (also called "Tregitopes") have been reported to suppress immune responses to coadministered antigens by stimulating the expansion of natural Tregs (nTregs). Here we evaluate their impact on human immune responses to islet cell antigens ex vivo and on the modulation of type 1 diabetes (T1D) in a murine model in vivo. Co-administration of Tregitopes and T1D antigens delayed development of hyperglycemia and reduced the incidence of diabetes in NOD mice. Suppression of diabetes could be observed even following onset of disease. To measure the impact of Tregitope treatment on T cell responses, we evaluated the effect of Tregitope treatment in DO11.10 mice. Upregulation of FoxP3 in KJ1-26-stained OVA-specific CD4(+) T cells was observed following treatment of DO11.10 mice with Tregitopes, along with reductions in anti-OVA Ig and T effector responses. In ex vivo studies of human T cells, peripheral blood mononuclear cells' (PBMC) responses to GAD65 epitopes in the presence and absence of Tregitope were variable. Suppression of immune responses to GAD65 epitopes ex vivo by Tregitope appeared to be more effective in assays using PBMC from a newly diagnosed diabetic subject than for other more established diabetic subjects, and correlation of the degree of suppression with predicted HLA restriction of the Tregitopes was confirmed. Implementation of these defined regulatory T cell epitopes for therapy of T1D and other autoimmune diseases may lead to a paradigm shift in disease management.
Bjerknes forces on bubbles in a stationary sound field (1975)

This paper concerns the translational forces exerted on pulsating air bubbles in a stationary sound field. These forces, normally called Bjerknes forces, are derived by simple arguments and classified as to their origin. Measurements have been made of the relative velocity of appoach of two bubbles undergoing a mutual Bjerknes force. The measurements were made in a rigid glass container oscillated in a vertical direction at 60 Hz by a shaker table. The ambient pressure above the liquid was reduced in order to obtain large pulsations, and the attracting bubbles were photographed with a movie camera. Oberved and calculated values for the velocity of approach are in agreement provided a drag law assuming interfacial slippage is used. Subject Classification: 25.60.