gebhart/patrepeval huggingface dataset:
Direct addition of BimL to mitochondria does not lead to cytochrome c release (2002)

Pro‐apoptotic members of the Bcl‐2 family can be subdivided in two classes according to their structure: a group including Bax, Bak, and Bok that display Bcl‐2 homology (BH) 1, BH2 and BH3 domains and a second group including Bid (BH3 interacting domain death agonist), Bad, Bim (Bcl‐2 interacting mediator of cell death) and several others that contain only a BH3 domain, the BH3‐only proteins. The BH3‐only proteins have been proposed to activate pro‐apoptotic members of the Bax subfamily to trigger a mitochondrial pathway that leads to the release of cytochrome c and other apoptogenic factors. Here we report that the mechanism of action of Bim is different from that of Bid. Although overexpression of Bid or Bim in cells leads to cytochrome c release, only Bid is able to trigger the release of cytochrome c through Bax activation when added directly to isolated mitochondria. Bim L , although unable to activate Bax, can directly inhibit Bcl‐2 or Bcl‐x L . Our data suggest two functional classes of BH3‐only proteins: those such as Bid which directly activate Bax‐like proteins leading to mitochondrial membrane permeability and apoptosis and those such as Bim which inhibit anti‐apoptotic proteins and render the cells more susceptible to apoptogenic stimuli.
LipidXplorer: A Software for Consensual Cross-Platform Lipidomics (2012)

LipidXplorer is the open source software that supports the quantitative characterization of complex lipidomes by interpreting large datasets of shotgun mass spectra. LipidXplorer processes spectra acquired on any type of tandem mass spectrometers; it identifies and quantifies molecular species of any ionizable lipid class by considering any known or assumed molecular fragmentation pathway independently of any resource of reference mass spectra. It also supports any shotgun profiling routine, from high throughput top-down screening for molecular diagnostic and biomarker discovery to the targeted absolute quantification of low abundant lipid species. Full documentation on installation and operation of LipidXplorer, including tutorial, collection of spectra interpretation scripts, FAQ and user forum are available through the wiki site at: https://wiki.mpi-cbg.de/wiki/lipidx/index.php/Main_Page.
Molecular cloning and characterization of p64, a chloride channel protein from kidney microsomes (1993)

Chloride channels were previously purified from bovine kidney cortex membranes using a drug affinity column. Reconstitution of the purified proteins into artificial liposomes and planar bilayers yielded chloride channels. A 64-kDa protein, p64, identified as a component of this chloride channel was used to generate antibodies which depleted solubilized kidney membranes of all chloride channel activity. This antibody has now been used to identify a clone, H2B, from a kidney cDNA library. Antibodies, affinity-purified against the fusion protein of H2B also depleted solubilized kidney cortex from all chloride channel activity. The predicted amino acid sequence of p64 shows that it contains two and possibly four putative transmembrane domains and potential phosphorylation sites by protein kinase A, protein kinase C, and casein kinase II. There was no significant homology to other protein (or DNA) sequences in the data base. The protein is expressed in all cells tested. Expression of its mRNA in Xenopus laevis oocytes led to the insertion of a protein with the appropriate molecular mass in microsomes but not in the plasma membrane. It is likely that p64 represents the chloride channel of intracellular organelles.
Contribution of Bone Marrow-Derived Stem Cells to Endometrium and Endometriosis (2007)

Bone marrow-derived cells (BMDCs) can differentiate into nonhematopoietic cells, suggesting that BMDCs may contribute to the maintenance of multiple tissues. Donor-derived bone marrow cells have been identified in human uterine endometrium. Here, two murine models were used to investigate the contribution of nonendometrial stem cells to endometrium. We investigate whether BMDCs can localize to uterine endometrium and to endometriosis. After bone marrow transplantation, male donor-derived bone marrow cells were found in the uterine endometrium of female mice. Although uncommon (<0.01%), these cells can differentiate into epithelial cells. After generation of experimental endometriosis by ectopic endometrial implantation in the peritoneal cavity, bone marrow from LacZ transgenic mice was used for transplantation. LacZ expressing cells were found in the wild-type ectopic endometrium implanted in the peritoneal cavity of hysterectomized LacZ transgenic mice. The repopulation of endometrium with bone marrow-derived stem cells may be important to normal endometrial physiology and also may help to explain the cellular basis for the high long-term failure of conservative alternatives to hysterectomy. The examination of a sexually dimorphic organ such as the uterus demonstrates the ability of male bone marrow, which cannot harbor circulating endometrial cells, to generate endometrium de novo and proves their mesenchymal stem cell origin. Finding Y chromosome bearing endometrial cells demonstrates the potential to recapitulate embryonic developmental pathways that were never activated in males; BMDCs may have vast regenerative capacity. Additionally, the ability of stem cells to engraft endometriosis has implications for the origin and progression of this disease. Ectopic differentiation of stem cells may be a novel mechanism of disease. Disclosure of potential conflicts of interest is found at the end of this article.
Electromagnetic suspension and levitation (1981)

Deals with the physics and engineering aspects of the four principal contenders for advanced ground transportation systems using 'maglev' and describes the most up-to-date developments in Germany, Japan, USA and the UK in this field. Some of the very recent challenging developments in the application of electromagnetic suspension and levitation techniques to contactless bearings are also described.
Evolution of technologies in endovascular grafting (1995)

The safety, efficacy and utility of inserting a vascular prosthesis through the femoral artery and attaching it to a native artery with stents to treat abdominal aortic aneurysms are under various stages of testing around the world. The potential of these endovascular techniques to reduce the morbidity and cost of care is enormous. Many advances in imaging, catheter techniques, delivery systems and the knowledge about aneurysm morphology are responsible for the progress to date. The requirements of an endoprosthesis include a small and flexible delivery system that allows retrograde insertion through the iliofemoral arterial system, secure attachments to normal arterial wall, and a fabric which meets Food and Drugs Administration criteria for strength and durability. Application of this technique to large numbers of patients with aneurysms will probably require the development of a bifurcated prosthesis. The long-term behavior of the aneurysm wall after endoprosthesis insertion will not be known until clinical trials are completed. The development of these techniques will undoubtedly fuel the 'turf battle' between vascular surgeons and interventionalists. Although each group will lay claim to the technology, a cooperative effort to maximize patient benefit seems to be the most appropriate way to insure that the interests of the patients are best served.
Mechanisms of pulmonary edema induced by tumor necrosis factor-alpha. (1990)

We tested the hypothesis that human recombinant tumor necrosis factor-alpha (TNF) promotes pulmonary edema by neutrophil-dependent effects on the pulmonary vasculature. The isolated guinea pig lung was perfused with phosphate-buffered Ringer's solution with or without human neutrophils. The infusion of neutrophils (9 x 10(6) total) into lungs isolated after the in vivo administration of TNF (3.2 x 10(5) units/kg) resulted in weight gain (+1.951 +/- 0.311 g versus -0.053 +/- 0.053 g in control) and an increase in the lung (wet-dry)-to-dry weight ratio (8.3 +/- 0.5 versus 6.0 +/- 0.2 in control), indicating the formation of pulmonary edema. The neutrophil-dependent pulmonary edema induced by TNF was associated with a combination of increased capillary permeability (capillary filtration coefficient [Kf,c], 0.170 +/- 0.048 g/min/cm H2O/g at 30 minutes versus 0.118 +/- 0.008 g/min/cm H2O/g at baseline) and increased pulmonary capillary pressure (Ppc, 12.8 +/- 0.8 cm H2O at 60 minutes versus 6.0 +/- 0.3 cm H2O at baseline). The Ppc increase was mediated by thromboxane A2 (TXA2) because the TXA2 synthetase inhibitor Dazoxiben (0.5 mM) prevented the effect (Ppc, 6.7 +/- 0.6 cm H2O at 60 minutes with Dazoxiben), and thromboxane B2 (TXB2) levels were increased in the pulmonary venous effluent (5,244 +/- 599 pg/ml at 60 minutes versus 60 +/- 13 pg/ml at baseline). Studies using WEB-2086 (37 microM), a platelet activating factor (PAF) receptor antagonist, indicated that PAF mediated the increased vascular permeability (Kf,c, 0.107 +/- 0.014 g/min/cm H2O/g at 30 minutes using WEB-2086) and, in part, the increased Ppc (Ppc, 8.4 +/- 0.7 cm H2O at 60 minutes using WEB-2086). In addition, alterations of endothelial peripheral actin bands were noted after TNF administration. The data indicate that TNF induces neutrophil-dependent pulmonary edema associated with increased Ppc (mediated by TXA2 and PAF), increased Kf,c (mediated by PAF), and changes in endothelial peripheral actin bands.
Molecular stratification model for prognosis in cytogenetically normal acute myeloid leukemia (2009)

We have evaluated 9 new molecular markers (ERG, EVI1, MLL-PTD, MN1, PRAME, RHAMM, and WT1 gene-expression levels plus FLT3 and NPM1 mutations) in 121 de novo cytogenetically normal acute myeloblastic leukemias. In the multivariate analysis, high ERG or EVI1 and low PRAME expressions were associated with a shorter relapse-free survival (RFS) and overall survival (OS). A 0 to 3 score was given by assigning a value of 0 to favorable parameters (low ERG, low EVI1, and high PRAME) and 1 to adverse parameters. This model distinguished 4 subsets of patients with different OS (2-year OS of 79%, 65%, 46%, and 27%; P = .001) and RFS (2-year RFS of 92%, 65%, 49%, and 43%; P = .005). Furthermore, this score identified patients with different OS (P = .001) and RFS (P = .013), even within the FLT3/NPM1 intermediate-risk/high-risk subgroups. Here we propose a new molecular score for cytogenetically normal acute myeloblastic leukemias, which could improve patient risk-stratification.
New Bivalent PKC Ligands Linked by a Carbon Spacer:  Enhancement in Binding Affinity (2003)

Protein kinase C (PKC) is known to play an important role in many signal transduction pathways involved in hormone release, mitogenesis, and tumor promotion. In continuation of our efforts to find highly potent activators of PKC for possible use as Alzheimer's disease therapeutics, we designed and synthesized molecules containing two binding moieties (amides of benzolactams or esters of naphthylpyrrolidones) connected by a flexible spacer chain, which could theoretically bind to both the C1a and C1b activator binding domains of the catalytic region or to the C1 domains of two adjacent PKC molecules. The dimers 2a-g of benzolactam showed a 200-fold increase in affinity to PKCalpha and -delta as the spacer length increased from 4 to 20 carbon atoms. Replacement of the oligomethylene chain with an oligoethylene glycol unit (compounds 2h, 2i) showed a 4000- to 7000-fold decrease in affinity to PKCalpha. The dimers of naphthylpyrrolidones 4a-g did not show any marked improvement in binding affinities to PKC in comparison to the monomers synthesized earlier. The dimer of benzolactam 2e did not show much selectivity for PKCalpha, -betaIota, -delta, -epsilon, and -gamma. The high binding affinity of compounds 2d-g to PKCs gives us the impetus to design additional molecules that would retain this enhanced activity and would also show selectivity for the PKC isoforms.
Onset and Persistence of Childhood Asthma: Predictors From Infancy (2001)

This study of the natural history of childhood asthma focused on the development of asthma into the school-age years in a genetically at-risk group of children. The relationships between biological and psychosocial variables in the first year and school-age asthma support the formulation of asthma as beginning early in life, with the developing immune system interacting with environmental influences. The data provide support for the possible contribution of psychosocial factors to asthma onset and persistence into childhood.
Representative feature descriptor sets for robust handheld camera localization (2012)

We present a method to automatically determine a set of feature descriptors that describes an object such that it can be localized under a variety of viewpoints. Based on a set of synthetically generated views, local image features are detected, described and aggregated in a database. Our proposed method evaluates matches between these database features to eventually find a set of the most representative descriptors from the database. Using this scalable offline process, the localization success rate is significantly increased without adding computational load to the runtime method. Moreover, if camera localization is performed with respect to objects at a known gravity orientation, we propose to create multiple reference descriptor sets for different angles between the camera's principal axis and the gravity vector. This approach is particularly suited for handheld devices with built-in inertial sensors and enables matching against a reference dataset only containing the information relevant for camera poses that are consistent with the measured gravity. Comprehensive evaluations of the proposed methods using a large quantity of real camera images, a variety of objects, different cameras and different kinds of feature descriptors confirm that our approaches outperform standard feature descriptor-based methods.
Immune Profiling Suggests an IGH Signaling-Dependent Subtype of Aggressive B-ALL (2012)

Abstract Abstract 1428 The majority of B-cell acute lymphocytic leukemias (ALL) in childhood are derived from precursor B cells. In order to more precisely define the stage in cellular differentiation of the B-cell that gave rise to the tumor, we applied high-throughput sequencing techniques to profile the IGH repertoire in marrow at the time of diagnosis in a set of nine B-ALL patients who ultimately received a bone marrow transplant. These pediatric patients were enrolled on the Children's Oncology Group ASCT0431 trial, a phase 3, randomized trial stem cell transplantation for high risk ALL. In eight of these patients we identified a dominant IGH VDJ clone accounting for 45%-99% of all sequences, consistent with the oncogenic transformation event occurring in a cell no longer capable of further IGH rearrangement. In the ninth patient, no single VDJ clone dominated, but we observed a highly recurrent rearrangement of a specific pair of IGH diversity-joining segments (D7–27 and J4) which also conserved a four base pair non-templated sequence at the N2 junction between D and J. We observed at least 143 rearrangements sharing this D-N2-J sequence, accounting for 22% of total sequences from the patient. These sequences recombined a variety of V-N1 sequences with the common D-N2-J sequence, consistent with a primary tumor that had initially rearranged the D-J segments but continued to express the RAG recombinases, allowing for full for V-DJ recombination. Of note, 140 out of 143 of these sequences were in frame, significantly more frequently than the one in three expected. This suggests that in this specific patient, the primary tumor bearing the common D-J rearrangement was relatively indolent, and signaling through a subsequently, successfully rearranged and expressed IGH protein was an important event contributing to to the malignancy. The rearranged IGH sequences show little evidence of somatic hypermutation, so the expansion signal being received through the IGH protein appears to be coinsistent with normal positive selection during pro-B cell development, rather than an antigen-specific signal. This is consistent with the signal delivered by the pre-B receptor at the pro to pre-B stage of B cell development. We are investigating additional samples to assess the frequency of this subtype of B-ALL (a single clonal rearrangement of D-J, followed by many subclones expressing different, in frame full V-DJ rearrangements), by sequencing patients at diagnosis, relapse pre-transplant, and relapse post-transplant. Our ongoing analysis of patients enrolled on this trial at various stages of relapse will allow us to determine the prevalence of this subtype among high-risk cases, and whether differential outcomes are observed in similar cases. Disclosures: Carlson: Adaptive Biotechnologies: Consultancy, Equity Ownership. Sherwood:Adaptive Biotechnologies: Employment. Robins:Adaptive Biotechnologies: Consultancy, Equity Ownership. Kalos:University of Pennsylvania: Employment, Patents &amp; Royalties.
Functions of purified E1A protein microinjected into mammalian cells. (1984)

We have purified the human type C adenovirus E1A 13S mRNA gene product, expressed in Escherichia coli, and demonstrate that the protein exhibits genuine viral functions upon microinjection into mammalian cells. We show that the E1A protein activates expression of the adenovirus E2A gene and induces expression from the major late transcription unit of the adenovirus E1A deletion mutant, H5dl312. We use this functional assay to examine the stability of E1A protein microinjected into cells and find that E1A exhibits full function for at least 18 hours after its injection. In addition, the purified E1A protein was used to generate a high-titer monospecific rabbit antiserum. This antiserum was used to detect and localize E1A proteins within adenovirus-infected cells as well as within microinjected cells. The E1A protein is found to rapidly and quantitatively localize to the cell nucleus following microinjection into the cell cytoplasm. Thus, nuclear localization is an intrinsic property of the E1A polypeptide. The ability of the E1A protein to localize to the cell nucleus and to induce expression from the H5dl312 major late transcription unit is shown to be highly heat stable.
Glycation and Carboxymethyllysine Levels in Skin Collagen Predict the Risk of Future 10-Year Progression of Diabetic Retinopathy and Nephropathy in the Diabetes Control and Complications Trial and Epidemiology of Diabetes Interventions and Complications Participants With Type 1 Diabetes (2005)

Several mechanistic pathways linking hyperglycemia to diabetes complications, including glycation of proteins and formation of advanced glycation end products (AGEs), have been proposed. We investigated the hypothesis that skin collagen glycation and AGEs predict the risk of progression of microvascular disease. We measured glycation products in the skin collagen of 211 Diabetes Control and Complications Trial (DCCT) volunteers in 1992 who continued to be followed in the Epidemiology of Diabetes Interventions and Complications study for 10 years. We determined whether the earlier measurements of glycated collagen and AGE levels correlated with the risk of progression of retinopathy and nephropathy from the end of the DCCT to 10 years later. In multivariate analyses, the combination of furosine (glycated collagen) and carboxymethyllysine (CML) predicted the progression of retinopathy (chi2 = 59.4, P < 0.0001) and nephropathy (chi2 = 18.2, P = 0.0001), even after adjustment for mean HbA(1c) (A1C) (chi2 = 32.7, P < 0.0001 for retinopathy) and (chi2 = 12.8, P = 0.0016 for nephropathy). The predictive effect of A1C vanished after adjustment for furosine and CML (chi2 = 0.0002, P = 0.987 for retinopathy and chi2 = 0.0002, P = 0.964 for nephropathy). Furosine explained more of the variation in the 10-year progression of retinopathy and nephropathy than did CML. These results strengthen the role of glycation of proteins and AGE formation in the pathogenesis of retinopathy and nephropathy. Glycation and subsequent AGE formation may explain the risk of these complications associated with prior A1C and provide a rational basis for the phenomenon of "metabolic memory" in the pathogenesis of these diabetes complications.
Highlighting Directional Reflectance Properties of Retinal Substructures From D-OCT Images (2019)

Optical coherence tomography (OCT), which is routinely used in ophthalmology, enables transverse optical imaging of the retina and, hence, the identification of the different neuronal layers. Directional OCT (D-OCT) extends this technology by acquiring sets of images at different incidence angles of the light beam. In this way, reflectance properties of photoreceptor substructures are highlighted, enabling physicians to study their orientation, which is potentially an interesting biomarker for retinal diseases. Nevertheless, commercial OCT devices equipped to automate D-OCT acquisition do not yet exist, meaning that physicians manually deviate the light beam to acquire a set of D-OCT images sequentially. Therefore, the intensities in the stack of images are not directly comparable, and a normalization step is required before differential analysis. In this paper, we present advanced image processing methods to perform differential analysis of a set of D-OCT images and extract the angle-dependent retinal substructures. Our approach relies on a robust and accurate normalization algorithm followed by a classification that is spatially regularized. We also propose a robust color representation that facilitates interpretation of D-OCT data in general, by detecting and highlighting angle-dependent structures in healthy and diseased eyes. Experimental results show evidence of photoreceptor disarray in a variety of retinal diseases, demonstrating the potential medical interest of the approach.
Selective Oxidation of Toluene to Benzaldehyde by O2 with Visible Light in Barium(2+)- and Calcium(2+)-Exchanged Zeolite Y (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSelective Oxidation of Toluene to Benzaldehyde by O2 with Visible Light in Barium(2+)- and Calcium(2+)-Exchanged Zeolite YHai Sun, Fritz Blatter, and Heinz FreiCite this: J. Am. Chem. Soc. 1994, 116, 17, 7951–7952Publication Date (Print):August 1, 1994Publication History Published online1 May 2002Published inissue 1 August 1994https://pubs.acs.org/doi/10.1021/ja00096a084https://doi.org/10.1021/ja00096a084research-articleACS PublicationsRequest reuse permissionsArticle Views763Altmetric-Citations64LEARN 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