gebhart/patrepeval huggingface dataset:
DUX4 and DUX4 downstream target genes are expressed in fetal FSHD muscles (2013)

Facioscapulohumeral muscular dystrophy (FSHD) is one of the most prevalent adult muscular dystrophies. The common clinical signs usually appear during the second decade of life but when the first molecular dysregulations occur is still unknown. Our aim was to determine whether molecular dysregulations can be identified during FSHD fetal muscle development. We compared muscle biopsies derived from FSHD1 fetuses and the cells derived from some of these biopsies with biopsies and cells derived from control fetuses. We mainly focus on DUX4 isoform expression because the expression of DUX4 has been confirmed in both FSHD cells and biopsies by several laboratories. We measured DUX4 isoform expression by using qRT-PCR in fetal FSHD1 myotubes treated or not with an shRNA directed against DUX4 mRNA. We also analyzed DUX4 downstream target gene expression in myotubes and fetal or adult FSHD1 and control quadriceps biopsies. We show that both DUX4-FL isoforms are already expressed in FSHD1 myotubes. Interestingly, DUX4-FL expression level is much lower in trapezius than in quadriceps myotubes, which is confirmed by the level of expression of DUX4 downstream genes. We observed that TRIM43 and MBD3L2 are already overexpressed in FSHD1 fetal quadriceps biopsies, at similar levels to those observed in adult FSHD1 quadriceps biopsies. These results indicate that molecular markers of the disease are already expressed during fetal life, thus opening a new field of investigation for mechanisms leading to FSHD.
An Overview of the Effects of Dioxins and Dioxin-Like Compounds on Vertebrates, as Documented in Human and Ecological Epidemiology (2009)

Dioxins and dioxin-like compounds are primary examples of persistent organic pollutants that induce toxicity in both wildlife and humans. Over the past 200 years these compounds have been almost exclusively generated by human activity and have left a string of disasters in the wake of their accidental release. Most recently, the contamination of the Irish pork supply with dioxins resulted in an international recall of all Irish pork products. Epidemiologic data on human and ecological dioxin exposures have revealed a common pattern of biological response among vertebrate species, which is mediated through activation of the Aryl hydrocarbon Receptor (AhR). These AhR-mediated effects include profound consequences on the vertebrate individual exposed in early life with respect to myriad developmental endpoints including neurologic, immunologic, and reproductive parameters. Humans appear to be susceptible to these effects in a manner similar to that of the laboratory and wildlife species, which have demonstrated such outcomes. Furthermore, epidemiologic data suggest that there is little or no margin of exposure for humans with respect to these developmental effects. Given these concerns, prudent public health policy should include the continued reduction of exposures.
Artifact Trapping During Time Reversal Photoacoustic Imaging for Acoustically Heterogeneous Media (2009)

Several different reconstruction algorithms have been proposed for photoacoustic tomography, most of which presuppose that the acoustic properties of the medium are constant and homogeneous. In practice, there are often unknown spatial variations in the acoustic properties, and these algorithms give, at best, only approximate estimates of the true image. The question as to which approach is the most robust in these circumstances is therefore one of practical importance. Image reconstruction by "time reversal"-using a numerical propagation model with a time-varying boundary condition corresponding to the measured data in reversed temporal order-has been shown to be less restrictive in its assumptions than most, and therefore a good candidate for a general and practically useful algorithm. Here, it is shown that such reconstruction algorithms can "trap" time reversed scattered waves, leading to artifacts within the image region. Two ways to mitigate this effect are proposed.
Detection and Characterizationof Cellular Immune Responses Using Peptide–MHC Microarrays (2003)

The detection and characterization of antigen-specific T cell populations is critical for understanding the development and physiology of the immune system and its responses in health and disease. We have developed and tested a method that uses arrays of peptide-MHC complexes for the rapid identification, isolation, activation, and characterization of multiple antigen-specific populations of T cells. CD4(+) or CD8(+) lymphocytes can be captured in accordance with their ligand specificity using an array of peptide-MHC complexes printed on a film-coated glass surface. We have characterized the specificity and sensitivity of a peptide-MHC array using labeled lymphocytes from T cell receptor transgenic mice. In addition, we were able to use the array to detect a rare population of antigen-specific T cells following vaccination of a normal mouse. This approach should be useful for epitope discovery, as well as for characterization and analysis of multiple epitope-specific T cell populations during immune responses associated with viral and bacterial infection, cancer, autoimmunity, and vaccination.
Complement-mediated cell death induced by rituximab in B-cell lymphoproliferative disorders is mediated in vitro by a caspase-independent mechanism involving the generation of reactive oxygen species (2001)

Mechanisms involving the in vitro effect of rituximab in cells from 55 patients with B-cell lymphoproliferative disorders were investigated. No cytotoxic effect was observed when cells were incubated with rituximab alone, but in the presence of human AB serum rituximab induced complement-dependent cell death (R-CDC). A cytotoxic effect was observed in cells from 9 of 33 patients with B-cell chronic lymphocytic leukemia, 16 of 16 patients with mantle-cell lymphoma, 4 of 4 patients with follicular lymphoma, and 2 of 2 patients with hairy-cell leukemia. R-CDC was observed in cells from patients expressing more than 50 x 10(3) CD20 molecules per cell, and directly correlated with the number of CD20 molecules per cell. Preincubation with anti-CD59 increased the cytotoxic effect of rituximab and sensitized cells from nonsensitive cases. Neither cleavage of poly-ADP ribose polymerase (PARP) nor activation of caspase-3 was observed in R-CDC. In addition, no cells with a hypodiploid DNA content were detected and R-CDC was not prevented by a broad-spectrum caspase inhibitor, suggesting a caspase-independent mechanism. Incubation with rituximab in the presence of AB serum induced a rapid and intense production of reactive oxygen species (ROS). R-CDC was blocked by the incubation of cells with N-acetyl-L-cysteine (NAC) or Tiron, 2 ROS scavengers, indicating that the cytotoxic effect was due to the generation of superoxide (O) radicals. In conclusion, the results of the present study suggest that CD20, CD59, and complement have a role in the in vitro cytotoxic effect of rituximab, which is mediated by a caspase-independent process that involves ROS generation.
Characterization and Expression of Mammalian Cyclin B3, a Prepachytene Meiotic Cyclin (2002)

We report the identification and expression pattern of a full-length human cDNA and a partial mouse cDNA encoding cyclin B3. Cyclin B3 (CCNB3) is conserved from Caenorhabditis elegans to Homo sapiens and has an undefined meiotic function in female, but not male Drosophila melanogaster. We show that H. sapiens cyclin B3 interacts with cdk2, is localized to the nucleus, and is degraded during anaphase entry after the degradation of cyclin B1. Degradation is dependent on sequences conserved in a destruction box motif. Overexpression of nondegradable cyclin B3 blocks the mitotic cell cycle in late anaphase, and at higher doses it can interfere with progression through G(1) and entry into S phase. H. sapiens cyclin B3 mRNA and protein are detected readily in developing germ cells in the human testis and not in any other tissue. The mouse cDNA has allowed us to further localize cyclin B3 mRNA to leptotene and zygotene spermatocytes. The expression pattern of mammalian cyclin B3 suggests that it may be important for events occurring in early meiotic prophase I.
Europium Chelate Labels in Time-Resolved Fluorescence Immunoassays and DNA Hybridization Assays (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTEuropium Chelate Labels in Time-Resolved Fluorescence Immunoassays and DNA Hybridization AssaysEleftherios P. Diamandis and Theodore K. ChristopoulosCite this: Anal. Chem. 1990, 62, 22, 1149A–1157APublication Date (Print):November 15, 1990Publication History Published online30 May 2012Published inissue 15 November 1990https://doi.org/10.1021/ac00221a716RIGHTS & PERMISSIONSArticle Views336Altmetric-Citations152LEARN 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 InReddit PDF (5 MB) Get e-Alerts Get e-Alerts
Providing universal location services using a wireless E911 location network (1998)

This article reviews the issues associated with the development of an E911 location network in light of the desire to leverage the E911 location network to provide universal non-cellular location-based services. The key issues are illustrated with a system originally developed for locating elderly patients with Alzheimer's disease.
Optical bistability due to increasing absorption (1984)

It is shown theoretically that optical bistability will exist in a material whose optical absorption is more than linearly proportional to the degree to which the material is excited. No cavity or external feedback is required. The underlying principle of this bistability appears to be a generalization of several previous independent discussions of mirrorless bistabilities in specific physical systems. This bistability and associated differential gain are demonstrated experimentally using a thermal nonlinearity in a GaAs/GaAlAs multiple-quantum-well semiconductor. Theory and experiment show good agreement.
Pronuclear Microinjection (2001)

Last year marked the 20th anniversary of the invention of the term "transgenic" and the development of pronuclear microinjection, a straightforward technique designed to transfer genetic information from nearly any living organism to mammals. After two decades of use, pronuclear microinjection protocols have changed little from the reliable, if not efficient, method described by Gordon and Ruddle. Experience has taught us that once microinjection skills are perfected there are only a few parameters one needs to be concerned about to successfully produce transgenic animals. Those parameters will be discussed, as will some new innovations that promise to finally increase efficiency of pronuclear microinjection methodology.
Interaction of a Tyrosine Kinase from Human Sperm with the Zona Pellucida at Fertilization (1995)

A 95-kilodalton mouse sperm protein with characteristics of a protein tyrosine kinase has been identified as a receptor for ZP3, a glycoprotein in the egg's extracellular matrix. The structure of the human homolog was determined by screening an expression library from human testis; a testis-specific complementary DNA was isolated that encodes a protein similar to receptor tyrosine kinases and appears to be expressed only in testicular germ cells. Antibodies against a synthetic peptide from the intracellular domain recognized a 95-kilodalton human sperm protein that contains phosphotyrosine; human ZP3 stimulates the kinase activity of this sperm protein. Synthetic peptides corresponding to regions of the predicted extracellular domain inhibited sperm binding to human zona pellucida. Availability of the primary sequence of a receptor for ZP3 provides a rational starting point for sperm-targeted contraceptive development.
Techniques for the diagnosis of switching circuit failures (1961)

In 2.12 minutes an IBM 7090 program found four input tests (for an 8-input parity check circuit) whose outcome determines whether any one of 102 possible failures occurred. For any single-output combinational circuit, with no more than 35 input variables, the program computes the set of all inputs detecting a given failure - the essential novelty of the method. These sets, one for each failure, are then Processed to find a (small) subset of tests which detect any failure. The underlying method extends to the diagnosis of circuits with feedback.
Inductively Heated Shape Memory Polymer for the Magnetic Actuation of Medical Devices (2006)

Presently, there is interest in making medical devices such as expandable stents and intravascular microactuators from shape memory polymer (SMP). One of the key challenges in realizing SMP medical devices is the implementation of a safe and effective method of thermally actuating various device geometries in vivo. A novel scheme of actuation by Curie-thermoregulated inductive heating is presented. Prototype medical devices made from SMP loaded with nickel zinc ferrite ferromagnetic particles were actuated in air by applying an alternating magnetic field to induce heating. Dynamic mechanical thermal analysis was performed on both the particle-loaded and neat SMP materials to assess the impact of the ferrite particles on the mechanical properties of the samples. Calorimetry was used to quantify the rate of heat generation as a function of particle size and volumetric loading of ferrite particles in the SMP. These tests demonstrated the feasibility of SMP actuation by inductive heating. Rapid and uniform heating was achieved in complex device geometries and particle loading up to 10% volume content did not interfere with the shape recovery of the SMP
Proteomics analysis of bodily fluids in pancreatic cancer (2015)

Proteomics study of pancreatic cancer using bodily fluids emphasizes biomarker discovery and clinical application, presenting unique prospect and challenges. Depending on the physiological nature of the bodily fluid and its proximity to pancreatic cancer, the proteomes of bodily fluids, such as pancreatic juice, pancreatic cyst fluid, blood, bile, and urine, can be substantially different in terms of protein constitution and the dynamic range of protein concentration. Thus, a comprehensive discovery and specific detection of cancer‐associated proteins within these varied fluids is a complex task, requiring rigorous experiment design and a concerted approach. While major challenges still remain, fluid proteomics studies in pancreatic cancer to date have provided a wealth of information in revealing proteome alterations associated with pancreatic cancer in various bodily fluids.
Terminal Alkene Formation by the Thioesterase of Curacin A Biosynthesis (2011)

Curacin A is a polyketide synthase (PKS)-non-ribosomal peptide synthetase-derived natural product with potent anticancer properties generated by the marine cyanobacterium Lyngbya majuscula. Type I modular PKS assembly lines typically employ a thioesterase (TE) domain to off-load carboxylic acid or macrolactone products from an adjacent acyl carrier protein (ACP) domain. In a striking departure from this scheme the curacin A PKS employs tandem sulfotransferase and TE domains to form a terminal alkene moiety. Sulfotransferase sulfonation of β-hydroxy-acyl-ACP is followed by TE hydrolysis, decarboxylation, and sulfate elimination (Gu, L., Wang, B., Kulkarni, A., Gehret, J. J., Lloyd, K. R., Gerwick, L., Gerwick, W. H., Wipf, P., Håkansson, K., Smith, J. L., and Sherman, D. H. (2009) J. Am. Chem. Soc. 131, 16033-16035). With low sequence identity to other PKS TEs (<15%), the curacin TE represents a new thioesterase subfamily. The 1.7-Å curacin TE crystal structure reveals how the familiar α/β-hydrolase architecture is adapted to specificity for β-sulfated substrates. A Ser-His-Glu catalytic triad is centered in an open active site cleft between the core domain and a lid subdomain. Unlike TEs from other PKSs, the lid is fixed in an open conformation on one side by dimer contacts of a protruding helix and on the other side by an arginine anchor from the lid into the core. Adjacent to the catalytic triad, another arginine residue is positioned to recognize the substrate β-sulfate group. The essential features of the curacin TE are conserved in sequences of five other putative bacterial ACP-ST-TE tridomains. Formation of a sulfate leaving group as a biosynthetic strategy to facilitate acyl chain decarboxylation is of potential value as a route to hydrocarbon biofuels.
p62/SQSTM1 forms protein aggregates degraded by autophagy and has a protective effect on huntingtin-induced cell death (2005)

Autophagic degradation of ubiquitinated protein aggregates is important for cell survival, but it is not known how the autophagic machinery recognizes such aggregates. In this study, we report that polymerization of the polyubiquitin-binding protein p62/SQSTM1 yields protein bodies that either reside free in the cytosol and nucleus or occur within autophagosomes and lysosomal structures. Inhibition of autophagy led to an increase in the size and number of p62 bodies and p62 protein levels. The autophagic marker light chain 3 (LC3) colocalized with p62 bodies and coimmunoprecipitated with p62, suggesting that these two proteins participate in the same complexes. The depletion of p62 inhibited recruitment of LC3 to autophagosomes under starvation conditions. Strikingly, p62 and LC3 formed a shell surrounding aggregates of mutant huntingtin. Reduction of p62 protein levels or interference with p62 function significantly increased cell death that was induced by the expression of mutant huntingtin. We suggest that p62 may, via LC3, be involved in linking polyubiquitinated protein aggregates to the autophagy machinery.
Ability of Pseudomonas pseudomallei malleobactin to acquire transferrin-bound, lactoferrin-bound, and cell-derived iron (1993)

The ability of malleobactin to mobilize iron from transferrin and lactoferrin was examined in an equilibrium dialysis assay in the absence of bacteria. Malleobactin was capable of removing iron from both transferrin and lactoferrin at pH values of 7.4, 6.0, and 5.0. However, the levels of iron mobilization were greater for transferrin than for lactoferrin at all the pH values used in the assay. The ability of Pseudomonas pseudomallei to acquire iron from 30% iron-saturated transferrin and K562 human erythroleukemic cells was compared in parallel cultures as described previously (J. H. Brock, P. H. Williams, J. Liceaga, and K. G. Woldridge, Infect. Immun. 59:3185-3190, 1991). P. pseudomallei U7 tended to acquire iron from transferrin. In contrast, P. aeruginosa PAO and P. cepacia Pc275C acquired iron from both sources. P. cepacia H1721, which does not produce detectable siderophores, but can utilize malleobactin, pyochelin, and azurechelin as iron sources, was used in a similar experiment. Addition of malleobactin resulted in iron uptake only from transferrin, whereas pyochelin and azurechelin promoted iron uptake from both sources. When the siderophores were incubated with K562 cells alone, malleobactin was less efficient at removing iron from cells than pyochelin and azurechelin. It was also determined that malleobactin was less effective in binding to or entering cells than pyochelin and azurechelin. These results suggest that malleobactin can acquire iron more effectively from host proteins than from cellular sources. Pyochelin and azurechelin can acquire cell-derived iron in addition to iron bound to host proteins.
Seroprevalence of antibodies to Sarcocystis neurona in horses residing in a county of southeastern Pennsylvania (1997)

High seroprevalence of antibodies to S neurona and the lack of neurologic deficits among horses sampled indicate that positive results of serologic examination alone are of limited value for diagnosis of equine protozoal myeloencephalitis. Clinical signs consistent with the disease are the most important consideration in accurate diagnosis.
Effect of pmt gene overexpression on tropane alkaloid production in transformed root cultures of Datura metel and Hyoscyamus muticus (2002)

In order to increase the production of the pharmaceuticals hyoscyamine and scopolamine in hairy root cultures, a binary vector system was developed to introduce the T‐DNA of the Ri plasmid together with the tobacco pmt gene under the control of CaMV 35S promoter, into the genome of Datura metel and Hyoscyamus muticus. This gene codes for putres cine:SAM N‐methyltransferase (PMT; EC. 2.1.1.53), which catalyses the first committed step in the tropane alkaloid pathway. Hairy root cultures overexpressing the pmt gene aged faster and accumulated higher amounts of tropane alkaloids than control hairy roots. Both hyoscyamine and scopolamine production were improved in hairy root cultures of D. metel, whereas in H. muticus only hyoscyamine contents were increased by pmt gene overexpression. These roots have a high capacity to synthesize hyoscyamine, but their ability to convert it into scopolamine is very limited. The results indicate that the same biosynthetic pathway in two related plant species can be differently regulated, and overexpression of a given gene does not necessarily lead to a similar accumulation pattern of secondary metabolites.
A prospective study of the impact of nasopharyngeal cancer and radiotherapy on the psychosocial condition of Chinese patients (2007)

Different periods in treatment of NPC imposed different psychosocial demands on patients. The current results indicated that the period from diagnosis to 2-month post-RT was a high-risk period both physically and emotionally. After treatment, most patients showed resilience despite persistent side effects of RT and successfully resumed their pretreatment level of functioning by the end of the year. Despite resuming a normal or near-normal living, patients still noted a subdued fear of recurrence.
Making Deep Belief Networks effective for large vocabulary continuous speech recognition (2011)

To date, there has been limited work in applying Deep Belief Networks (DBNs) for acoustic modeling in LVCSR tasks, with past work using standard speech features. However, a typical LVCSR system makes use of both feature and model-space speaker adaptation and discriminative training. This paper explores the performance of DBNs in a state-of-the-art LVCSR system, showing improvements over Multi-Layer Perceptrons (MLPs) and GMM/HMMs across a variety of features on an English Broadcast News task. In addition, we provide a recipe for data parallelization of DBN training, showing that data parallelization can provide linear speed-up in the number of machines, without impacting WER.