gebhart/patrepeval huggingface dataset:
Integrated RNA and DNA sequencing improves mutation detection in low purity tumors (2014)

Identifying somatic mutations is critical for cancer genome characterization and for prioritizing patient treatment. DNA whole exome sequencing (DNA-WES) is currently the most popular technology; however, this yields low sensitivity in low purity tumors. RNA sequencing (RNA-seq) covers the expressed exome with depth proportional to expression. We hypothesized that integrating DNA-WES and RNA-seq would enable superior mutation detection versus DNA-WES alone. We developed a first-of-its-kind method, called UNCeqR, that detects somatic mutations by integrating patient-matched RNA-seq and DNA-WES. In simulation, the integrated DNA and RNA model outperformed the DNA-WES only model. Validation by patient-matched whole genome sequencing demonstrated superior performance of the integrated model over DNA-WES only models, including a published method and published mutation profiles. Genome-wide mutational analysis of breast and lung cancer cohorts (n = 871) revealed remarkable tumor genomics properties. Low purity tumors experienced the largest gains in mutation detection by integrating RNA-seq and DNA-WES. RNA provided greater mutation signal than DNA in expressed mutations. Compared to earlier studies on this cohort, UNCeqR increased mutation rates of driver and therapeutically targeted genes (e.g. PIK3CA, ERBB2 and FGFR2). In summary, integrating RNA-seq with DNA-WES increases mutation detection performance, especially for low purity tumors.
American Society of Plastic Surgeons: What???s in a Name Change? (2000)

Dallas, Texas Rod J. Rohrich, M.D. Co-Editor, Plastic and Reconstructive Surgery University of Texas Southwestern Medical Center Department of Plastic Surgery 5323 Harry Hines Blvd., Suite E7-210 Dallas, Texas 75235-9132 [email protected]
The health care cost of intravenous iron treatment in IBD patients depends on the economic evaluation perspective (2010)

Both the Cost Effective Analysis and the Cost Benefit Analysis showed clearly that iron carboxymaltose is a more cost effective way of giving intravenous iron than iron sucrose in IBD patients. Only the Budget Impact Analysis showed that intravenous iron sucrose was the cheapest choice if only direct cost was included in the analysis.
RETRACTED: Ligand‐induced differentiation of glucocorticoid receptor (GR) trans‐repression and transactivation: preferential targetting of NF‐ κ B and lack of I‐ κ B involvement (1999)

1. Glucocorticoids are highly effective in controlling chronic inflammatory diseases, such as asthma and rheumatoid arthritis, but the exact molecular mechanism of their anti-inflammatory action remains uncertain. They act by binding to a cytosolic receptor (GR) resulting in activation or repression of gene expression. This may occur via direct binding of the GR to DNA (transactivation) or by inhibition of the activity of transcription factors such as AP-1 and NF-kappaB (transrepression). 2. The topically active steroids fluticasone propionate (EC50= 1.8 x 10(-11) M) and budesonide (EC50=5.0 x 10(-11) M) were more potent in inhibiting GM-CSF release from A549 cells than tipredane (EC50 = 8.3 x 10(-10)) M), butixicort (EC50 = 3.7 x 10(-8) M) and dexamethasone (EC50 = 2.2 x 10(-9) M). The anti-glucocorticoid RU486 also inhibited GM-CSF release in these cells (IC50= 1.8 x 10(-10) M). 3. The concentration-dependent ability of fluticasone propionate (EC50 = 9.8 x 10(-10) M), budesonide (EC50= 1.1 x 10(-9) M) and dexamethasone (EC50 = 3.6 x 10(-8) M) to induce transcription of the beta2-receptor was found to correlate with GR DNA binding and occurred at 10-100 fold higher concentrations than the inhibition of GM-CSF release. No induction of the endogenous inhibitors of NF-kappaB, IkappaBalpha or I-kappaBbeta, was seen at 24 h and the ability of IL-1beta to degrade and subsequently induce IkappaBalpha was not altered by glucocorticoids. 4. The ability of fluticasone propionate (IC50=0.5 x 10(-11) M), budesonide (IC50=2.7 x 10(-11) M), dexamethasone (IC50=0.5 x 10(-9) M) and RU486 (IC50=2.7 x 10(-11) M) to inhibit a 3 x kappaB was associated with inhibition of GM-CSF release. 5. These data suggest that the anti-inflammatory properties of a range of glucocorticoids relate to their ability to transrepress rather than transactivate genes.
Polymerase Chain Reaction: Basic Protocol Plus Troubleshooting and Optimization Strategies (2012)

In the biological sciences there have been technological advances that catapult the discipline into golden ages of discovery. For example, the field of microbiology was transformed with the advent of Anton van Leeuwenhoek's microscope, which allowed scientists to visualize prokaryotes for the first time. The development of the polymerase chain reaction (PCR) is one of those innovations that changed the course of molecular science with its impact spanning countless subdisciplines in biology. The theoretical process was outlined by Keppe and coworkers in 1971; however, it was another 14 years until the complete PCR procedure was described and experimentally applied by Kary Mullis while at Cetus Corporation in 1985. Automation and refinement of this technique progressed with the introduction of a thermal stable DNA polymerase from the bacterium Thermus aquaticus, consequently the name Taq DNA polymerase. PCR is a powerful amplification technique that can generate an ample supply of a specific segment of DNA (i.e., an amplicon) from only a small amount of starting material (i.e., DNA template or target sequence). While straightforward and generally trouble-free, there are pitfalls that complicate the reaction producing spurious results. When PCR fails it can lead to many non-specific DNA products of varying sizes that appear as a ladder or smear of bands on agarose gels. Sometimes no products form at all. Another potential problem occurs when mutations are unintentionally introduced in the amplicons, resulting in a heterogeneous population of PCR products. PCR failures can become frustrating unless patience and careful troubleshooting are employed to sort out and solve the problem(s). This protocol outlines the basic principles of PCR, provides a methodology that will result in amplification of most target sequences, and presents strategies for optimizing a reaction. By following this PCR guide, students should be able to: • Set up reactions and thermal cycling conditions for a conventional PCR experiment • Understand the function of various reaction components and their overall effect on a PCR experiment • Design and optimize a PCR experiment for any DNA template • Troubleshoot failed PCR experiments.
The biological degradation of cellulose (1994)

Cellulolytic microorganisms play an important role in the biosphere by recycling cellulose, the most abundant carbohydrate produced by plants. Cellulose is a simple polymer, but it forms insoluble, crystalline microfibrils, which are highly resistant to enzymatic hydrolysis. All organisms known to degrade cellulose efficiently produce a battery of enzymes with different specificities, which act together in synergism. The study of cellulolytic enzymes at the molecular level has revealed some of the features that contribute to their activity. In spite of a considerable diversity, sequence comparisons show that the catalytic cores of cellulases belong to a restricted number of families. Within each family, available data suggest that the various enzymes share a common folding pattern, the same catalytic residues, and the same reaction mechanism, i.e. either single substitution with inversion of configuration or double substitution resulting in retention of the beta-configuration at the anomeric carbon. An increasing number of three-dimensional structures is becoming available for cellulases and xylanases belonging to different families, which will provide paradigms for molecular modeling of related enzymes. In addition to catalytic domains, many cellulolytic enzymes contain domains not involved in catalysis, but participating in substrate binding, multi-enzyme complex formation, or possibly attachment to the cell surface. Presumably, these domains assist in the degradation of crystalline cellulose by preventing the enzymes from being washed off from the surface of the substrate, by focusing hydrolysis on restricted areas in which the substrate is synergistically destabilized by multiple cutting events, and by facilitating recovery of the soluble degradation products by the cellulolytic organism. In most cellulolytic organisms, cellulase synthesis is repressed in the presence of easily metabolized, soluble carbon sources and induced in the presence of cellulose. Induction of cellulases appears to be effected by soluble products generated from cellulose by cellulolytic enzymes synthesized constitutively at a low level. These products are presumably converted into true inducers by transglycosylation reactions. Several applications of cellulases or hemicellulases are being developed for textile, food, and paper pulp processing. These applications are based on the modification of cellulose and hemicellulose by partial hydrolysis. Total hydrolysis of cellulose into glucose, which could be fermented into ethanol, isopropanol or butanol, is not yet economically feasible. However, the need to reduce emissions of greenhouse gases provides an added incentive for the development of processes generating fuels from cellulose, a major renewable carbon source.
Fixed polarizer ellipsometry for simple and sensitive detection of thin films generated by specific molecular interactions: applications in immunoassays and DNA sequence detection (1998)

Biological thin films may form on a surface by specific molecular interactions. The fixed polarizer ellipsometer (FPE) is a sensitive instrument that detects biological thin films either qualitatively or quantitatively. The design is simple and inexpensive. The assays are formatted on an optical surface, and the FPE detection is based on the phase shift of linearly polarized light after reflection through a thin film. We have constructed mathematical models of the FPE response to reflection through single-layer and two-layer films that agree closely with experimental data. Several biological assays have been measured with the FPE to demonstrate the application of this technology to clinical targets, including ultrasensitive immunoassays for hepatitis B surface antigen (0.1 ng/mL) and alpha-fetoprotein (0.01 ng/ mL) and DNA hybridization (0.5 fmol/microL target probe). A clinical study for detection of group A streptococcus from patient throat swabs demonstrated the qualitative application of the FPE to infectious disease targets. The flexibility and sensitivity of the FPE makes this technology suitable for numerous target analytes and applications.
Complex Formation between Junctin, Triadin, Calsequestrin, and the Ryanodine Receptor (1997)

Several key proteins have been localized to junctional sarcoplasmic reticulum which are important for Ca2+ release. These include the ryanodine receptor, triadin, and calsequestrin, which may associate into a stable complex at the junctional membrane. We recently purified and cloned a fourth component of this complex, junctin, which exhibits homology with triadin and is the major 125I-calsequestrin-binding protein detected in cardiac sarcoplasmic reticulum vesicles (Jones, L. R., Zhang, L., Sanborn, K., Jorgensen, A. O., and Kelley, J. (1995) J. Biol. Chem. 270, 30787-30796). In the present study, we have examined the binding interactions between the cardiac forms of these four proteins with emphasis placed on the role of junctin. By a combination of approaches including calsequestrin-affinity chromatography, filter overlay, immunoprecipitation assays, and fusion protein binding analyses, we find that junctin binds directly to calsequestrin, triadin, and the ryanodine receptor. This binding interaction is localized to the lumenal domain of junctin, which is highly enriched in charged amino acids organized into "KEKE" motifs. KEKE repeats are also found in the common lumenal domain of triadin, which likewise is capable of binding to calsequestrin and the ryanodine receptor (Guo, W., and Campbell, K. P. (1995) J. Biol. Chem. 270, 9027-9030). It appears that junctin and triadin interact directly in the junctional sarcoplasmic reticulum membrane and stabilize a complex that anchors calsequestrin to the ryanodine receptor. Taken together, these results suggest that junctin, calsequestrin, triadin, and the ryanodine receptor form a quaternary complex that may be required for normal operation of Ca2+ release.
Two homologous genes, originated by duplication, encode the human hnRNP proteins A2 and A1 (1994)

Heterogeneous nuclear ribonucleoprotein (hnRNP) A2 belongs, with A1, B1 and B2, to the basic protein subset of the hnRNP complex in mammalian cells. All these proteins share a modular structure consisting of two conserved RNA binding domains linked to less conserved Gly-rich domains (2xRBD-Gly). In the framework of our studies on the genetic basis of hnRNP proteins structure and diversity we have isolated and sequenced the A2 gene and compared it to the previously described A1 gene. The A2 gene, which exists in a single copy on Ch. 7 band p15, is split in 12 exons including an alternatively spliced 36 nt mini exon specific for the human hnRNP protein B1. In this work we show that the intron/exon organisation of the A2 gene is identical to that of the A1 gene over the entire length, indicating a common origin by gene duplication. Moreover the comparison of corresponding exons evidences significant conservation also in the apparently divergent Gly-rich domains that could define previously unenvisaged structural and/or functional motifs. The A2 gene promoter is also analysed in comparison to that of the A1 gene.
Enzymatic signal amplification of molecular beacons for sensitive DNA detection (2008)

Molecular beacons represent a new family of fluorescent probes for nucleic acids, and have found broad applications in recent years due to their unique advantages over traditional probes. Detection of nucleic acids using molecular beacons has been based on hybridization between target molecules and molecular beacons in a 1:1 stoichiometric ratio. The stoichiometric hybridization, however, puts an intrinsic limitation on detection sensitivity, because one target molecule converts only one beacon molecule to its fluorescent form. To increase the detection sensitivity, a conventional strategy has been target amplification through polymerase chain reaction. Instead of target amplification, here we introduce a scheme of signal amplification, nicking enzyme signal amplification, to increase the detection sensitivity of molecular beacons. The mechanism of the signal amplification lies in target-dependent cleavage of molecular beacons by a DNA nicking enzyme, through which one target DNA can open many beacon molecules, giving rise to amplification of fluorescent signal. Our results indicate that one target DNA leads to cleavage of hundreds of beacon molecules, increasing detection sensitivity by nearly three orders of magnitude. We designed two versions of signal amplification. The basic version, though simple, requires that nicking enzyme recognition sequence be present in the target DNA. The extended version allows detection of target of any sequence by incorporating rolling circle amplification. Moreover, the extended version provides one additional level of signal amplification, bringing the detection limit down to tens of femtomolar, nearly five orders of magnitude lower than that of conventional hybridization assay.
High‐mobility oxide TFT for circuit integration of AMOLEDs (2011)

Abstract— A high‐mobility and high‐reliability oxide thin‐film transistor (TFT) that uses In‐Sn‐Zn‐O (ITZO) as a channel material has been developed. The mobility was 30.9 cm 2 /V‐sec and the threshold voltage shift after 20,000 sec of a bias‐temperature‐stress (BTS) test (with a stress condition of Vg = 15 V, Vd = 15 V, and T = 50°C) was smaller than 0.1 V. In addition, a method of obtaining a stable enhancement‐type TFT, which realizes circuit integration for active‐matrix organic light‐emitting diode (AMOLED) displays has been developed.
Odysseus: A High-Performance ORDBMS Tightly-Coupled with IR Features (2005)

We propose the notion of tight-coupling [K. Whang et al., (1999)] to add new data types into the DBMS engine. In this paper, we introduce the Odysseus ORDBMS and present its tightly-coupled IR features (US patented). We demonstrate a Web search engine capable of managing 20 million Web pages in a non-parallel configuration using Odysseus.
Primary biliary cirrhosis: seeking the silent partner of autoimmunity (2002)

Primary biliary cirrhosis is a disorder characterised by an intense inflammatory response in the septal and interlobular bile ducts and is considered to be an autoimmune disease. Evidence to suggest that chronic viral infection could be a crucial element in the development of biliary epithelial cell damage and activation of the associated autoimmune response is reviewed
Mitigating Damage to Hybrid Perovskites Using Pulsed-Beam TEM (2020)

Using a pulsed-beam transmission electron microscope, we discover a reduction in damage to methylammonium lead iodide (MAPbI<sub>3</sub>) as compared to conventional beams delivered at the same dose rates. For rates as low as 0.001 e·Å<sup>-2</sup>·s<sup>-1</sup>, we find up to a 17% reduction in damage at a total dose of 10 e·Å<sup>-2</sup>. We systematically study the effects of number of electrons in each pulse and the duration between pulse arrival. Damage increases for both, though the number of electrons per pulse has a larger effect. A crossover is identified, where a pulsed beam causes more damage than a conventional one. Although qualitatively similar to previous findings, the degree to which damage is reduced in MAPbI<sub>3</sub> is less than that observed for other materials (<i>e.g.</i>, C<sub>36</sub>H<sub>74</sub>), supporting the hypothesis that the effects are material- and damage-mechanism-dependent. Despite this, the observation here of damage reduction for relatively large electron packets (up to 200 electrons per pulse) suggests that MAPbI<sub>3</sub> is in fact less susceptible to irradiation than C<sub>36</sub>H<sub>74</sub>, which may be related to reported self-healing effects. This work provides insights into damage processes and durability in hybrid perovskites and also illustrates the viability of using pulsed-beam TEM to explore the associated molecular-level routes to degradation, analogous to laser-accelerated energetic pulsed electron beams and the study of damage to biomolecules, cells, and tissues in radiobiology.
Dication disulfides by reaction of thioureas and related compounds with trifluoromethanesulfonic anhydride. The role of triflic anhydride as an oxidizing agent (1981)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDication disulfides by reaction of thioureas and related compounds with trifluoromethanesulfonic anhydride. The role of triflic anhydride as an oxidizing agentGerhard Maas and Peter J. StangCite this: J. Org. Chem. 1981, 46, 8, 1606–1610Publication Date (Print):April 1, 1981Publication History Published online1 May 2002Published inissue 1 April 1981https://pubs.acs.org/doi/10.1021/jo00321a015https://doi.org/10.1021/jo00321a015research-articleACS PublicationsRequest reuse permissionsArticle Views722Altmetric-Citations28LEARN 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
Synthesis of 3S-Pyrrolidinol from L-Glutamic Acid (1986)

Abstract A practical synthesis of 3S-pyrrolidinol and derivatives from L-glutamic acid is described.
Thrombus precursor protein (TpP): marker of thrombosis early in the pathogenesis of myocardial infarction. (1996)

We have developed an enzyme-linked immunosorbent immunoassay for quantifying the immediate precursor proteins to intravascular thrombi. This thrombus precursor protein (TpP) assay identifies active thrombosis in several clinical conditions, including early myocardial infarction (MI). In a study of patients recruited for the GUSTO intervention study, MI patients had concentrations of TpP 4-20-fold that of controls; patients diagnosed without MI had concentrations similar to the control subjects. In a separate study of subjects presenting at the emergency room with chest pain, MI patients who presented early after the onset of chest pain had TpP concentrations significantly (P <0.01) higher than controls. Patients presenting late or diagnosed with other chest pain had concentrations within the reference range. The potential utility of the TpP assay as an aid for the diagnosis of thrombotic MI and other thrombotic conditions is described.
Differential syncytium-inducing capacity of human immunodeficiency virus isolates: frequent detection of syncytium-inducing isolates in patients with acquired immunodeficiency syndrome (AIDS) and AIDS-related complex (1988)

Human immunodeficiency virus isolates were studied with respect to syncytium-inducing capacity, replicative properties, and host range. Five of 10 isolates from patients with acquired immunodeficiency syndrome (AIDS) and AIDS-related complex were able to induce syncytia in cultures of peripheral blood mononuclear cells (MNC). In contrast, only 2 of 12 isolates from asymptomatic individuals had syncytium-inducing capacity. Syncytium-inducing isolates were reproducibly obtained from the same MNC sample in over 90% of the cases, independent of the donor MNC used for propagation. Syncytium-inducing capacity was shown to be a stable property of an isolate, independent of viral replication rates. Evidence was obtained that the high replication rate of syncytium-inducing isolates observed during primary isolation may be due to higher infectivity of these isolates. The finding that only syncytium-inducing isolates could be transmitted to the H9 cell line is compatible with this higher infectivity. The frequent isolation of syncytium-inducing isolates from individuals with AIDS-related complex or AIDS and the apparent higher in vitro infectivity of these isolates suggest that syncytium-inducing isolates may unfavorably influence the course of human immunodeficiency virus infection.