gebhart/patrepeval huggingface dataset:
Mammary tumor virus proviral DNA in normal murine tissue and non-virally induced mammary tumors (1981)

The Southern DNA filter transfer technique was used to study the involvement of the endogenous mouse mammary tumor virus (MMTV) in the development of mammary tumors of nonviral etiology. The presence of extra MMTV proviruses in the genomes of these non-virally induced mammary tumors would indicate an integration of the provirus of an activated endogenous MMTV. Acquisition of MMTV proviruses did not seem to be an absolute requirement for the development of hormone or carcinogenically induced mammary tumors in strain BALB/c nor for hormone-induced mammary tumors in mouse strains 020, C57BL, and C3Hf. In some hormone-induced mammary tumors we did observe extra MMTV proviruses in submolar quantities, indicating that reintegration may occasionally occur and that only a part of the tumor cells acquired new MMTV DNA information. Hormone-dependent and -independent primary mammary tumors of the mouse strain GR, which are controlled by the Mtv-2 mammary tumor induction gene, all acquired extra MMTV proviruses. Most of these extra MMTV proviral-DNA-containing fragments appeared present in submolar quantities, suggesting that only part of the tumor cells acquired extra MMTV proviral information. These findings indicate that the initially transformed mammary gland cells of non-virally induced mammary tumors do not necessarily acquire extra MMTV proviral DNA information, in contrast to the MMTV-induced mammary tumors, in which all tumor cells contain extra MMTV DNA information.
Understanding data survivability in archival storage systems (2012)

Preserving data for a long period of time in the face of faults, large and small, is crucial for designing reliable archival storage systems. However, the survivability of data is different from the reliability of storage because typically, data are stored in more than one storage at a given moment. Previous studies of reliability ignore the former. We present a framework for relating data survivability and storage reliability, and use the framework to gauge the impact of rare but large-scale events on data survivability. We also present a method to track all copies of data and the condition of all the online and offline media, devices and systems on which they are stored uninterruptedly over the whole lifetime of the data. With this method, the survivability of the data can be closely monitored, and potential dangers can be handled in a timely manner. A better understanding of data survivability can be used in reducing unnecessary data replicas, thus reducing the cost.
Analytical Evaluation of an Automated Immunoassay for Cardiac Troponin I: The Vidas Troponin I Assay (2003)

Cardiac troponin I (cTnI) is a sensitive and specific biochemical marker of myocardial damage. We assessed the analytical performance of the Vidas Troponin I assay (Biomerieux). Controls and serum pools were used to determine the precision, analytical sensitivity and linearity; 97.5 and 99.5 percentiles concentrations were determined from the reference population. Fifty corresponding samples of serum and plasma (lithium-heparin) were tested and the results compared. The in vitro stability of serum and plasma samples was assessed at 20 degrees C, 4 degrees C and -20 degrees C, respectively. Samples of serum were used to assess the agreement between the Vidas Troponin I method and the revised Dimension RxL cTnI method (Dade-Behring). The total imprecision (CVs) was 13.1-5.2% for concentrations ranging between 0.25 and 19.8 microg/l cTnI. The lower detection limit was <0.1 microg/l. The upper reference limit (97.5 and 99.5 percentiles) was 0.11 microg/l and 0.12 microg/l, respectively (CV > 10%). The assay was linear up to 21 microg/l. The concentrations in lithium-heparin plasma were higher compared to those of the matched serum samples. The study of the agreement between the Vidas and Dimension RxL cTnI assays showed a total concordance of 96% with a bias value of -0.042. The Vidas Troponin I test is a fast, precise and sensitive method for the determination of cTnI.
miR-132 downregulation alleviates behavioral impairment of rats exposed to single prolonged stress, reduces the level of apoptosis in PFC, and upregulates the expression of MeCP2 and BDNF (2021)

Post-traumatic stress disorder (PTSD) is usually accompanied by anxiety symptoms and decreased expression of brain-derived neurotrophic factor (BDNF), which played an important role in promoting neuronal proliferation and survival. Methyl CpG-binding protein 2 (MeCP2) is a positive mediator of BDNF and is regulated by miR-132-3p. In the present study, we explored the possible molecular mechanism of miR-132, focusing on the involvement of MeCP2 and BDNF in the formation of anxiety-like symptoms of PTSD. Single prolonged stress (SPS) was used to establish a model of PTSD in adult rats and the anxiety-like behavior was tested by the elevated plus-maze (EPM). The level of miR-132 in the prefrontal cortex (PFC) was increased and intraventricular injection of anti-miR-132 could significantly improve the anxiety-like behavior of rats exposed to SPS through MeCP2 and the subsequent upregulation of BDNF levels. Then tropomyosin-related kinase B (TrkB) and downstream signals, including MAP kinase ERK1/2 and phosphoinositol 3-kinase (PI3K)/Akt pathways, were activated by BDNF upregulation, and might participate in regulating dendritic complexity and the expression of postsynaptic density-95 (PSD95) and synapsin I in the PFC of SPS rats. Furthermore, we found that the apoptosis of cells in PFC induced by SPS procedure could be alleviated by miR-132 inhibition. Our results suggest that miR-132 might be involved in the formation of anxiety-like symptoms of adult rat PTSD models by targeting MeCP2, and this effect is related to BDNF/TrkB and its downstream ERK and Akt signaling pathways.
Prospective Study of Slip-interface Imaging in Meningioma for Brain-tumor Adhesion (2017)

Introduction: Magnetic Resonance Elastography(MRE) is a MRI-based imaging sequence utilizing mechanical waves to quantify the stiffness of tissue measured in kilopascal. More recently, an MRE form has been developed called slip-interface imaging(SII) to evaluate the plane between extra-axial brain tumors and adjacent neural structures. We report on SII in meningioma for tumor-brain adhesion.
Security is a Process, Not a Product (2001)

Picture the scene: you’re just leaving your house for work in the morning and before setting off you run a quick security check. All windows are closed, the back door is shut and the alarm set before you double lock the front door. You then place the front door key under the welcome mat with a sign saying ‘look under here’. This is what thousands of organizations are doing by failing to monitor and manage their user IDs effectively, because they are the technology equivalent of a master key to your network systems.
A secure e-Government's e-voting system (2015)

This paper proposed a reliable cost effective secure electronic voting system that can be used in cost effectively way in many development countries like Egypt. The important obstacle in any e-voting system across the world is the security issue. Election's results may be modified when delivered to the Higher Elections Committee, unauthorized voter may vote instead of the eligible voter, a vote may not be calculated; also the voter has to ensure that nobody has the possibility to know his ballot data. The proposed Voting Model System overcomes these obstacles. Security evaluation experiments are performed successfully to the proposed system proving that it satisfies privacy, accuracy, reusability, eligibility and integrity.
Medications Used for ADHD (2021)

Attention-deficit hyperactivity disorder (ADHD; see also Chapter 10, “Attention-Deficit/Hyperactivity Disorder”) is a common neuropsychiatric disorder that has an estimated worldwide prevalence of 5%–9% (Polanczyk et al. 2014). ADHD typically has an onset in childhood and often persists into adulthood. The symptoms include developmentally inappropriate motor activity, impulsivity, and difficulty maintaining and shifting attention, which result in significant and often cumulative impairments in family, academic, and social functioning. Treatment includes behavioral and educational strategies for associated problems, but the core symptoms of ADHD are typically treated with medications. Stimulant medications are the most widely used and have a long-established track record for safety and efficacy. There are also nonstimulant agents available that can be used either as monotherapy or in combination with a stimulant (Chan et al. 2016; Connor and Steingard 2004; Cortese et al. 2018; Dopheide and Pliszka 2009; Steingard et al. 2019). The most common questions asked by parents and patients focus on whether to start a medication; the effects, side effects or potential safety issues; and how long medication will be needed. After completing a diagnostic evaluation and providing psychoeducation, the prescribing clinician should discuss the course of the disorder, treatment options, and an initial treatment plan and evaluation strategy. In this chapter we focus on medication treatment for ADHD. Psychosocial and school interventions are covered in Part VI, “Psychosocial Treatments,” and Part VII, “Consultation,” in this textbook.
Rationally Designed, Polymeric, Extended Metal–Ciprofloxacin Complexes (2005)

Reactions of the antimicrobial fluoroquinolone ciprofloxacin (cfH) with metal salts in the presence of aromatic polycarboxylate ligands or under basic conditions produce fourteen new metal-cfH complexes, namely, [Ba2(cf)2(1,4-bdc)(H2O)2] x H2O (1), [Sr6(cf)6(1,4-bdc)3(H2O)6] x 2H2O (2), [M2(cfH)2(bptc)(H2O)2] x 8H2O (M = Mn3 and Cd4), [M(cfH)(1,3-bdc)] (M = Mn5, Co6, and Zn7), [Zn2(cfH)4(1,4-bdc)](1,4-bdc) x 13H2O (8), [Ca(cfH)2(1,2-Hbdc)2] x 2H2O (9) and [M(cf)2] x 2.5H2O (M = Mn10, Co11, Zn12, Cd13, and Mg14) (1,4-bdc = 1,4-benzenedicarboxylate, bptc = 3,3',4,4'-benzophenonetetracarboxylate, 1,3-bdc = 1,3-benzenedicarboxylate, 1,2-bdc = 1,2-benzenedicarboxylate). Their structures were determined by single-crystal X-ray diffraction analyses and further characterized by elemental analyses, IR spectra, and thermogravimetric analyses. The structures of 1 and 2 consist of unique two-dimensional arm-shaped layers. Compounds 3 and 4 are isostructural and feature one-dimensional structures formed from the interconnection of [M2(cfH)2(H2O)2] dimers with bptc ligands. Compounds 5-7 are isostructural and contain double-chain-like ribbons constructed from [M2(cfH)2(CO2)2] dimers and 1,3-bdc. Compound 8 consists of a pair of [Zn(cfH)2]2+ fragments bridged by a 1,4-bdc into a dinuclear dumbbell structure. Compound 9 is a neutral monomeric complex. To the best of our knowledge, compounds 1-9 are the first examples of metal-quinolone complexes that contain aromatic polycarboxylate ligands. Compounds 10-14 are isostructural and exhibit interesting two-dimensional rhombic grids featuring large cavities with dimensions of 13.6x13.6 A. Up to now, polymeric extended metal-cfH complexes have never been reported.
Cycloadditions. 41. Conversion of unsaturated alcohols into functionalized tetrahydrofurans and tetrahydropyrans via nitrile oxide dipolar cycloadditions (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCycloadditions. 41. Conversion of unsaturated alcohols into functionalized tetrahydrofurans and tetrahydropyrans via nitrile oxide dipolar cycloadditionsAlfred Hassner, K. S. K. Murthy, Albert Padwa, Ugo Chiacchio, Dennis C. Dean, and Allen M. SchoffstallCite this: J. Org. Chem. 1989, 54, 22, 5277–5286Publication Date (Print):October 1, 1989Publication History Published online1 May 2002Published inissue 1 October 1989https://pubs.acs.org/doi/10.1021/jo00283a021https://doi.org/10.1021/jo00283a021research-articleACS PublicationsRequest reuse permissionsArticle Views850Altmetric-Citations68LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
High Amplification Rates from the Association of Two Enzymes Confined within a Nanometric Layer Immobilized on an Electrode:  Modeling and Illustrating Example (2006)

Electrochemical responses (e.g., chronoamperometric) obtained with an immobilized enzyme that produces an electroactive species may be used to quantitate the amount of enzyme or the concentration of its substrate. It is shown, on theoretical and experimental bases, that product-to-substrate coupling with a second enzyme co-immobilized with the first within one or within a small number of monolayers, allows high amplification rates (higher than 1000), avoids membrane transport limitations, and lends itself to precise kinetic analyses that provide guidelines for optimization of the analytical sensitivity. Very large amplification factors, as large as several thousands, can be reached experimentally, in agreement with appropriately derived theoretical predictions, thus opening the route to the rational design of high-performance substrate sensing or affinity assays applications.
Single-shot spatial-coherence measurement of 13 nm high-order harmonic beam by a Young's double-slit measurement (2007)

The interference pattern produced by a single 13 nm high-order harmonic pulse is captured by an extreme-ultraviolet CCD camera. A beam divergence of 0.35 mrad and a high fringe visibility of 0.96 are obtained with an optimal phase-matching condition for the 13 nm harmonics. The spatial coherence length of the 13 nm harmonics selected by Mo/Si multilayer mirrors is larger than the beam diameter. This result shows that the 13 nm harmonic beam is useful for applications in interferometry, time-resolved studies of ultrafast dynamics.
microRNA Expression Levels Change in Neonatal Patients During and After Exposure to Cardiopulmonary Bypass (2022)

Background The systemic inflammation that occurs after exposure to cardiopulmonary bypass (CPB), which is especially severe in neonatal patients, is associated with poorer outcomes and is not well understood. In order to gain deeper insight into how exposure to bypass activates inflammatory responses in circulating leukocytes, we studied changes in microRNA (miRNA) expression during and after exposure to bypass. miRNAs are small noncoding RNAs that have important roles in modulating protein levels and function of cells. Methods and Results We performed miRNA-sequencing on leukocytes isolated from neonatal patients with CPB (n=5) at 7 time points during the process of CPB, including before the initiation of bypass, during bypass, and at 3 time points during the first 24 hours after weaning from bypass. We identified significant differentially expressed miRNAs using generalized linear regression models, and miRNAs were defined as statistically significant using a false discovery rate-adjusted <i>P</i><0.05. We identified gene targets of these miRNAs using the TargetScan database and identified significantly enriched biological pathways for these gene targets. We identified 54 miRNAs with differential expression during and after CPB. These miRNAs clustered into 3 groups, including miRNAs that were increased during and after CPB (3 miRNAs), miRNAs that decreased during and after CPB (10 miRNAs), and miRNAs that decreased during CPB but then increased 8 to 24 hours after CPB. A total of 38.9% of the target genes of these miRNAs were significantly differentially expressed in our previous study. miRNAs with altered expression levels are predicted to significantly modulate pathways related to inflammation and signal transduction. Conclusions The unbiased profiling of the miRNA changes that occur in the circulating leukocytes of patients with bypass provides deeper insight into the mechanisms that underpin the systemic inflammatory response that occurs in patients after exposure to CPB. These data will help the development of novel treatments and biomarkers for bypass-associated inflammation.
Elevated Root-Zone Dissolved Inorganic Carbon Alters Plant Nutrition of Lettuce and Pepper Grown Hydroponically and Aeroponically (2020)

Enhancing root-zone (RZ) dissolved inorganic carbon (DIC) levels of plants grown hydroponically and aeroponically can increase biomass accumulation but may also alter plant nutrient uptake. These experiments investigated how bicarbonate (HCO3−) added to a hydroponic nutrient solution and CO2 gas added to an aeroponic system affected biomass and nutrient concentrations of lettuce and pepper plants. Applying high RZ HCO3− concentrations (20 mM) to lettuce plants grown hydroponically decreased foliar N, P, Cu, K, Mn and Zn concentrations, concurrent with decreased biomass accumulation (50% less than control plants). On the contrary, 1 mM RZ HCO3− promoted biomass accumulation (10% more than control plants), but this could not be attributed to higher tissue nutrient concentrations. While elevated RZ CO2 did not alter biomass accumulation and nutrient concentrations in pepper grown aeroponically, it decreased foliar Mg and S concentrations in lettuce grown aeroponically even though nutrient contents (concentration x biomass) did not differ between treatments, due to 22% more biomass than control plants. In addition, elevated RZ CO2 enhanced N, P, Cu and Zn contents relative to control plants, indicating greater uptake of those elements. Nevertheless, there was no consistent relationship between plant growth promotion and altered plant nutrition, suggesting alternative mechanisms of growth regulation.
Peptidoglycan-linked protein A promotes T cell-dependent antibody expansion during Staphylococcus aureus infection (2016)

A hallmark of Staphylococcus aureus disease in humans is persistent infections without development of protective immune responses. Infected patients generate VH3 plasmablast expansions and increased VH3 idiotype Ig; however, the mechanisms for staphylococcal modification of immune responses are not known. We report here that S. aureus-infected mice generate VH3 antibody expansions via a mechanism requiring MHC-restricted antigen presentation to CD4(+) T cells and staphylococcal protein A (SpA), a cell wall-anchored surface molecule that binds Fcγ and VH3 variant heavy chains of Ig. VH3 expansion occurred with peptidoglycan-linked SpA from the bacterial envelope but not with recombinant SpA, and optimally required five tandem repeats of its Ig-binding domains. Signaling via receptor-interacting serine/threonine protein kinase 2 (RIPK2) was essential for implementing peptidoglycan-linked SpA superantigen activity. VH3 clan IgG from S. aureus-infected or SpA-treated animals was not pathogen-specific, suggesting that SpA cross-linking of VH3 idiotype B-cell receptors and activation via attached peptidoglycan are the determinants of staphylococcal escape from adaptive immune responses.
One Pot Large Scale Procedure for the Production of 2-Ethyl- and 2-Butyl-2-carboethoxycyclopentanone from Ethyl Adipate. (1997)

Abstract Abstract: Dieckman Cyclization of ethyl adipate (1) mediated by Na or K in toluene, followed by removal of the resulting ethanol, addition of t-BuOH or DMSO and addition of ethyl iodide or n-butyl bromide, led to production of the title compounds (3a and 3b), in one pot, in 50–75% isolated yield.
Phosphonate Appended Porphyrins as Versatile Chemosensors for Selective Detection of Trinitrotoluene (2015)

Fluorescent molecular probes based on phosphonate-functionalized porphyrin derivatives have been designed for selective detection of nitroaromatics. It is shown that molecular recognition is based on cooperative hydrogen bonding and π-π stacking interactions with electron-deficient molecules (nitroaromatic compounds, NACs), displaying superior detection toward trinitrotoluene (TNT). The P═O functional groups decrease the lowest unoccupied molecular orbital (LUMO) energy level of the porphyrins and, consequently, facilitate the electron inoculation to TNT through a photoinduced electron transfer (PET) process. The hydroxyl groups of the phosphonates and pyrrole -NH protons are further engaged in donor-acceptor interactions with TNT by strong intermolecular hydrogen bonding interactions (as evidenced by single crystal X-ray, NMR, and density functional theory (DFT)) showing turn off fluorescence behavior. The nonplanarity of the porphyrins induced by protonation at the central core of the porphyrin H4TPPA(2+) undergoes additional interactions, furnishing an anomalous increase in the selectivity of TNT at nanomolar levels in solution (limit of detection, LOD ∼ 5 nM). Porphyrin-doped hybrid PMMA [poly(methyl methacrylate)] polymer films demonstrate the reversibility of the fluorescence behavior and exhibit high photostability. The formation of discrete molecular aggregates on the surface of hybrid films and efficient diffusion of TNT vapors (10 ppb) displayed high selectivity in the solid state. The hybrid films are further used to demonstrate the detection of NACs in the aqueous medium, ultimately providing a platform for a practical strategy and implementation for the detection of toxic NACs.
Abstract A47: Somatic mutations in human cancer cell lines predict sorafenib response (2009)

Abstract It is now widely accepted that a spectrum of somatic alterations occur in human cancer and that particular alterations are associated with response or lack of response to anti-cancer therapies. Here, we undertook a systematic correlation analysis of somatic mutations, copy number aberrations and drug response across 300+ human cancer cell lines. We studied the RAF and VEGFR inhibitor, sorafenib, evaluating associations between sorafenib response and somatic mutations in 35 common cancer genes and high-level amplifications and homozygous deletions in more than 100 minimal common regions of gain and loss, which include many known oncogenes and tumor suppressor genes. Notably, we found that NRAS mutations, among other alterations, were significantly associated with sensitivity to sorafenib (odds ratio = 7, p-value = 0.003), whereas activating BRAF mutations were strongly associated with a lack of response (odds ratio = 4.9, p-value = 0.012). Specifically, 64% (7 of 11) of NRAS mutant cell lines were sensitive to sorafenib, while only 20% (34 of 170) of NRAS wild-type lines were sensitive. On the contrary, just 6.7% (2 of 30) of BRAF mutant lines were sensitive to sorafenib. Because NRAS mutations occur frequently in leukemia and no leukemia cell lines were included in the original analysis, we selected 5 NRAS mutant and 5 NRAS wild-type leukemia cell lines for further evaluation. Consistent with our previous observation, the four most sensitive leukemia cell lines were all NRAS mutant, each line exhibiting greater than 50% growth inhibition after 72 hours of exposure to 4uM sorafenib. These results confirm the original association and suggest that across both solid tumors and hematologic malignancies, NRAS mutations may identify a subset of cancers that are likely to respond sorafenib. In addition, this work demonstrates that systematic analysis of somatic alterations and drug response across a large collection of cancer cell lines is capable of discovering novel predictive biomarkers. Citation Information: Mol Cancer Ther 2009;8(12 Suppl):A47.