gebhart/patrepeval huggingface dataset:
Solution Conformation of the<i>N</i>-(Deoxyguanosin-8-yl)-1-aminopyrene ([AP]dG) Adduct Opposite dC in a DNA Duplex (1996)

Combined NMR-molecular mechanics computational studies were undertaken on the C8-deoxyguanosine adduct formed by the carcinogen 1-nitropyrene embedded in the d(C5-[AP]G6-C7).d(G16-C17-G18) sequence context in a 11-mer duplex, with dC opposite the modified deoxyguanosine. The exchangeable and nonexchangeable protons of the aminopyrene moiety and the nucleic acid were assigned following analysis of two-dimensional NMR data sets in H2O and D2O solution. There was a general broadening of several proton resonances for the three nucleotide d(G16-C17-G18) segment positioned opposite the [AP]dG6 lesion site resulting in weaker NOEs involving these protons in the adduct duplex. The solution conformation of the [AP]dG.dC 11-mer duplex has been determined by incorporating intramolecular and intermolecular proton-proton distances defined by upper and lower bounds deduced from NOESY spectra as restraints in molecular mechanics computations in torsion angle space. The aminopyrene ring of [AP]dG6 is intercalated into the DNA helix between intact Watson-Crick dC5.dG18 and dC7.dG16 base pairs. The modified deoxyguanosine ring of [AP]dG6 is displaced into the major groove and stacks with the major groove edge of dC5 in the adduct duplex. Both carbon and proton chemical shift data for the sugar resonances of the modified deoxyguanosine residue are consistent with a syn glycosidic torsion angle for the [AP]dG6 residue. The dC17 base on the partner strand is displaced from the center of the helix toward the major groove as a consequence of the aminopyrene ring intercalation into the helix. This base-displaced intercalative structure of the [AP]dG.dC 11-mer duplex exhibits several unusually shifted proton resonances which can be accounted for by the ring current contributions of the deoxyguanosinyl and pyrenyl rings of the [AP]dG6 adduct. In summary, intercalation of the aminopyrene moiety is accompanied by displacement of both [AP]dG6 and the partner dC17 into the major groove in the [AP]dG.dC 11-mer duplex.
Ultraweak simultaneous signal detection with theoretical phase calculation approaches (2015)

This paper presents applications of a generalized theoretical analysis of Tsui's phase measurement approach to detection of N - 1 ultraweak signals. A closed-form analytical expression is obtained for one application. A detection approach is presented for real-time estimation of the slope and curvature of sampled data of the instantaneous frequency. This approach provides the capability for early simultaneous signal detection and extraction of signal parameters. The capability for N = 4 simultaneous signals is desired for electronic warfare (EW) receivers.
Selective induction of an embryonic fibronectin isoform in the rat aorta in vitro. (1993)

The temporal changes in the expression of fibronectin and other extracellular matrix genes were studied in rat aortic rings incubated in vitro in a serum-free medium. Changes in all forms of fibronectin mRNA increased progressively during the 24-hour incubation period, although an increase in the alternatively spliced form of fibronectin designated EIIIA was most pronounced. Both collagen and elastin mRNA levels decreased markedly during the 24-hour interval, as did alpha-actin mRNA. The increase in the relative amount of the EIIIA isoform after a 24-hour incubation was also shown using ribonuclease protection assays. In situ hybridization showed the distribution of the induced fibronectin mRNA to be within all cell types, including endothelial cells, medial smooth muscle cells, and adventitial fibroblasts. Localization in the media was not uniform and was clearly identified mainly in clusters of cells distributed throughout the media. The early induction of fibronectin mRNA was inhibited by genistein, implicating tyrosine kinase activation as a causative factor in fibronectin expression. The in vitro changes reported may reflect a phenotypic change in vascular cell types that is both similar to and different from the changes reported in vivo under conditions in which vascular injury and repair occur.
ADAM17 is regulated by a rapid and reversible mechanism that controls access to its catalytic site (2010)

Protein ectodomain shedding is crucial for cell-cell interactions because it controls the bioavailability of soluble tumor necrosis factor-α (TNFα) and ligands of the epidermal growth factor (EGF) receptor, and the release of many other membrane proteins. Various stimuli can rapidly trigger ectodomain shedding, yet much remains to be learned about the identity of the enzymes that respond to these stimuli and the mechanisms underlying their activation. Here, we demonstrate that the membrane-anchored metalloproteinase ADAM17, but not ADAM10, is the sheddase that rapidly responds to the physiological signaling pathways stimulated by thrombin, EGF, lysophosphatidic acid and TNFα. Stimulation of ADAM17 is swift and quickly reversible, and does not depend on removal of its inhibitory pro-domain by pro-protein convertases, or on dissociation of an endogenous inhibitor, TIMP3. Moreover, activation of ADAM17 by physiological stimuli requires its transmembrane domain, but not its cytoplasmic domain, arguing against inside-out signaling via cytoplasmic phosphorylation as the underlying mechanism. Finally, experiments with the tight binding hydroxamate inhibitor DPC333, used here to probe the accessibility of the active site of ADAM17, demonstrate that this inhibitor can quickly bind to ADAM17 in stimulated, but not quiescent cells. These findings support the concept that activation of ADAM17 involves a rapid and reversible exposure of its catalytic site.
ChemInform Abstract: FeCl<sub>3</sub>‐Mediated Arylation of α‐Hydroxyphosphonates with Unactivated Arenes: Pseudo‐Umpolung in Allylic Phosphonates. (2013)

Abstract A simple and mild protocol for the synthesis of phosphonates from readily accessible starting materials is presented.
Top Most Surface Studies by Total Reflection Positron Diffraction (2003)

In this article, we detail the development and application of reflection high-energy positron diffraction (RHEPD). A fine positron beam with a coherence length of approximately 170 Å was obtained by the electrostatic lens system. The beam quality is good enough to observe the RHEPD patterns from a clean Si(111)7×7 and SiC(0001) surfaces. The rocking curve associated with the Si(111)7×7 surface revealed the fact that the vertical position of the adatom layer relative to the first layer is sufficiently relaxed towards the vacuum region than that expected from the electron diffraction experiments. After the high temperature hydrogen etching, the SiC surface became atomically smooth. It was found that Si face is somewhat unstable to the oxygen adsorption as compared to C face. The rocking curves were reproduced assuming the attachment of oxygen atoms at T1 site with a bond length of 1.88Å. Heating the SiC surface in the ultra-high vacuum after the sacrificial oxidation and hydrofluoric etching, an atomically flat carbon rich surface appeared.[DOI: 10.1380/ejssnt.2003.152]
The Dataware manifesto (2011)

In this paper we concern ourselves with Service-Oriented Architectures (SOA) in the “business to consumer” (B2C) arena. In particular we consider the services required to enable consumers to combine data they possess with data held about them by businesses and government. We introduce the concept of Dataware as the logical federation of data sources containing “my data” and discuss an SOA to deliver new and compelling services and applications able to reap the benefits of value-in-use for consumers.
Development of Endocrine Therapy of Breast Cancer 1896 - 2006 (2008)

Obwohl die Vorstellung, dass die Mamma durch die Hormone der Ovarien beeinflusst wird, noch wesentlich älter ist, wurden die ersten klinischen Experimente zur Ovarektomie, die zur Regression eines Mammakarzinoms führten, 1896 veröffentlicht. Seit dieser Zeit sind bei prämenopausalen Frauen die Suppression der Ovarialfunktion und bei postmenopausalen Frauen die Aromatasehemmer eine Standardbehandlung zur Reduktion der Östrogenspiegel geworden. Ein anderer entscheidender Ansatz der endokrinen Therapie ist die Blockierung des Östrogenrezeptors mit hohen Dosen Östrogen, erstmals berichtet im Jahr 1944, und der Einsatz von selektiven Östrogenrezeptormodulatoren oder reiner Antagonisten wie Tamoxifen und Fulvestrant. Die Entwickung dieser Pfeiler der endokrinen Therapie wurde vor allem im Europa geleistet und die German Adjuvant Breast Cancer Group (GABG) ist hier seit Jahren in der ersten Reihe.
Transgenic mice expressing constitutively active Akt in oral epithelium validate KLFA as a potential biomarker of head and neck squamous cell carcinoma. (2009)

These data support the notion that KLF4 is potentially a reliable marker of HNSCC, and that myrAkt transgenic mice are valuable tools for preclinical research of HNSCC.
Fatigue life improvement of threaded connections by cold rolling (2005)

Failures in drillstring threaded connections continue to afflict the oil industry at a cost of millions of dollars per year. In an attempt to reduce these failures the industry has generally adopted the fatigue-life-enhancing technique of cold rolling the threaded connections which act as stress concentrations. However, this beneficial process is only specified as optional in the industry standards, and where it is performed there is very little detail provided about this important process. This paper describes full-scale fatigue tests that investigate the cold-rolling process. From the development of cold-rolling equipment and the gathering of fatigue experimental data, several key factors have been identified that influence the operational lifetime of drillstring threaded connections.
An update on the discrepancy between calculated and measured neutron-induced radioactivity levels in Hiroshima (2002)

The thermal neutron activation measurements carried out over many years in Hiroshima and Nagasaki have been the subject of ongoing debate in recent years because they indicate that current DS86 neutron doses may have been significantly underestimated in Hiroshima. Long-lived neutron activation products, 60Co, 152Eu, 154Eu and 36Cl, which are still detectable today using modern analytical techniques, appear to indicate that DS86 calculated thermal neutron activation products decrease with distance more rapidly than the measured values. The latest thermal neutron activation measurements have been collated and a new relationship for the measured to calculated (M/C) ratio of induced activity has been derived as a function of slant range. This indicates a stronger dependence of M/C on slant range than previously derived by Straume et al (1992 Health Phys. 63 421-6) and emphasises even more the discrepancy between measured and calculated (DS86) neutron doses at distances beyond 1 km. While the main body of thermal neutron activation data appears to support a significant increase in the DS86 neutron dose component in Hiroshima, there are some thermal neutron activation measurements and some very recent fast neutron activation measurements which suggest that the discrepancy may not be so great. The extent of the required revision to the neutron component of the DS86 dosimetry remains the subject of ongoing new neutron activation measurements and re-analysis of existing published measurements. A companion paper considers the impact on radiation risk estimates of possible modifications to the DS86 dosimetry system on the basis of a broad range of interpretations of the neutron activation data.
Pathways to school completion for young mothers: Are we winning the fight? (2018)

Background. Policy initiatives in South Africa are directed at promoting the educational and developmental outcomes of girls and young women (age 15 - 24 years). These include decreasing the incidence of HIV infection, teenage pregnancy and gender-based violence, and increasing school attendance and economic empowerment. This article explores the contexts of pregnancy, motherhood and schooling in a sample of young mothers in an urban area in Johannesburg, South Africa. Methods. This ethnographic study, based in a poor urban area in Johannesburg, South Africa, recruited 30 young mothers aged 18 - 20 years with whom open-ended interviews were conducted. Each mother was contacted 3 months after the first interview, and again 3 months later. In addition to the first round of 30 interviews, 9 young mothers were interviewed in the second round, and 6 young mothers in a third round. A total of 45 interviews were conducted. Results. The findings illustrate how young mothers mediate constraints and challenges to continue and complete their schooling when confronted with a mistimed and unintended pregnancy. A combination of factors converge to facilitate or impede school continuation and completion. Key barriers include school policy and discrimination against pregnant learners, limited options for childcare, and high levels of poverty and unemployment that strain existing scarce family resources. Conclusions. The pathway to school completion is complex and non-linear. Three particular interventions that support school attendance and completion for young mothers have value: the child support grant, the availability of crèches in the community, and a school policy that upholds the principle of inclusivity for pregnant learners and young mothers.
The structure of complete test sets for programmable logic arrays (2002)

A new approach to complete testing of a PLA without any auxiliary facilities is presented. PLA testability is provided by the exact minimization of the PLA in the number of product lines. A theorem about the structure of a complete test set detecting all testable single and multiple crosspoint faults in such a minimal PLA is presented. It formulates the three conditions to which the complete test set satisfies. A technique for constructing complete test sets is discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Fibronectin production by cultured human trabecular meshwork cells. (1982)

Postmortem explants of human trabecular meshwork from 23 eyebank eyes had a growth rate of 32% (71/160) cultures, with 8% (12) showing abundant cellular spread. One hundred percent confluency was achieved with eyes from donors of 11 to 40 years of age. One of the cultures grew profusely and we were able to study it through eight passages in culture. This culture had the morphologic characteristics described by Polansky et al. for cultured human trabecular meshwork cells. A sensitive radioimmunoassay for fibronectin in tissue culture supernatant showed an increase in fibronectin secretion over a 96 hr period, with a characteristic shift-down response occurring between 24 and 48 hr postmedia change. Three of four cultures showed the presence of laminin, a basement membrane protein, establishing that the cells are not fibroblasts.
Prevalence of Diabetes and Impaired Glucose Tolerance in 64-Year-Old Swedish Women (2006)

Among these women, the prevalence of undetected diabetes was high and repeated OGTTs were needed to identify and not misclassify a considerable proportion of patients. The degree of glucose tolerance impairment and the number of abnormal OGTTs were directly associated with occurrence of components of the metabolic syndrome.
An SNR estimation based adaptive hierarchical modulation classification method to recognize M-ary QAM and M-ary PSK signals (2015)

Robust automatic modulation recognition techniques are in demand for software defined radios and cognitive radio receivers in general and Communication Intelligence (COMINT) applications such as signal interception for mobile communication, defense, civil authority and surveillance in particular. It is also the key for threat analysis. Many algorithms have been proposed and studied in the literature to distinguish digitally modulated signals. The approach presented in this paper gives a robust method for recognizing a subclass of digital modulation methods using SNR estimation and higher order cumulants. We have proposed a new feature to extend the hierarchical modulation classification proposed in the literature to include QPSK and 8PSK separation. Using higher order statistic based SNR estimation method at the receiver end we have given an SNR based adaptive thresholding technique which is capable of differentiating 16QAM, 32QAM, 64QAM, BPSK, QPSK, 8PSK signals with better false alarm rates compared to fixed threshold based recognition. Simulation results demonstrate that our approach is robust for all SNRs which can be estimated well at the receiver end.
Cytochrome P-450 Monooxygenase Systems in Aquatic Species: Carcinogen Metabolism and Biomarkers for Carcinogen and Pollutant Exposure (1991)

John J. Stegeman, John J. Lech, Cytochrome P-450 Monooxygenase Systems in Aquatic Species: Carcinogen Metabolism and Biomarkers for Carcinogen and Pollutant Exposure, Environmental Health Perspectives, Vol. 90 (Jan., 1991), pp. 101-109
Comprehensive genetic diagnosis of acute myeloid leukemia by next-generation sequencing (2018)

Differential induction therapy of all subtypes of acute myeloid leukemia other than acute promyelocytic leukemia is impeded by the long time required to complete complex and diverse cytogenetic and molecular genetic analyses for risk stratification or targeted treatment decisions. Here, we describe a reliable, rapid and sensitive diagnostic approach that combines karyotyping and mutational screening in a single, integrated, next-generation sequencing assay. Numerical karyotyping was performed by low coverage whole genome sequencing followed by copy number variation analysis using a novel algorithm based on <i>in silico</i>-generated reference karyotypes. Translocations and DNA variants were examined by targeted resequencing of fusion transcripts and mutational hotspot regions using commercially available kits and analysis pipelines. For the identification of <i>FLT3</i> internal tandem duplications and <i>KMT2A</i> partial tandem duplications, we adapted previously described tools. In a validation cohort including 22 primary patients' samples, 9/9 numerically normal karyotypes were classified correctly and 30/31 (97%) copy number variations reported by classical cytogenetics and fluorescence <i>in situ</i> hybridization analysis were uncovered by our next-generation sequencing karyotyping approach. Predesigned fusion and mutation panels were validated exemplarily on leukemia cell lines and a subset of patients' samples and identified all expected genomic alterations. Finally, blinded analysis of eight additional patients' samples using our comprehensive assay accurately reproduced reference results. Therefore, calculated karyotyping by low coverage whole genome sequencing enables fast and reliable detection of numerical chromosomal changes and, in combination with panel-based fusion-and mutation screening, will greatly facilitate implementation of subtype-specific induction therapies in acute myeloid leukemia.
Role of Nitric Oxide and Mitochondria in Control of Firefly Flash (2004)

In light-producing cells (photocytes) of the firefly light organ, mitochondria are clustered in the cell periphery, positioned between the tracheolar air supply and the oxygen-requiring bioluminescent reactants which are sequestered in more centrally-localized peroxisomes. This relative positioning suggests that mitochondria could control oxygen availability for the light reaction. We hypothesized that active cellular respiration would make the interior regions of the photocytes relatively hypoxic, and that the "on" signal for production of bioluminescence might depend on inhibition of mitochondrial oxygen consumption, which would allow delivered oxygen to pass through the peripheral mitochondrial zone to reach peroxisomes deep in the cell interior. We published recently that exogenous NO induces bioluminescence in the intact firefly; that NO mediates octopamine-induced bioluminescence in the dissected lantern, and that nitric oxide synthase is abundant in cells of the tracheolar system of the light organ. Additional experiments showed that nitric oxide gas (NO) inhibits respiration in isolated lantern mitochondria. Inhibition is reversed by bright light, and this inhibition is relieved when the light is turned off. Altogether, the results support the idea that NO triggers light production by reversible inhibition of mitochondrial respiration in lantern cells, and probably in tracheolar cells as well. The data also suggest that the light of bioluminescence itself relieves NO inhibition thus contributing to rapid on/off switching. While other mechanisms may be in play, NO production that is directly related to neural input appears to have a key role in the oxygen gating that controls flash communication signals.
An Integrated Geologic and Engineering Reservoir Characterization of the North Robertson (Clearfork) Unit: A Case Study, Part 1 (1995)

BRIEF SUMMARY Infill drilling of wells on a uniform spacing, without regard to reservoir performance and characterization, must become a process of the past. Such efforts do not optimize reservoir development as they fail to account for the complex nature of reservoir heterogeneities present in many low permeability carbonate reservoirs. These reservoirs arc typically characterized by: Large, discontinuous pay intervals Vertical and lateral changes in reservoir properties Low reservoir energy High residual oil saturation Low recovery efficiency The operational problems we encounter in these types of reservoirs include: Poor or inadequate completions and stimulations Early water breakthrough Poor reservoir sweep efficiency in contacting oil throughout the reservoir as well as in the near-well regions Channeling of injected fluids due to preferential fracturing caused by excessive injection rates Limited data availability and poor data quality Infill drilling operations only need target areas of the reservoir which will be economically successful. If the most productive areas of a reservoir can be accurately identified by combining the results of geologic, petrophysical, reservoir performance, and pressure transient analyses, then this "integrated" approach can be used to optimize reservoir performance during secondary and tertiary recovery operations without resorting to "blanket" infill drilling methods. New and emerging technologies such as cross-borehole tomography, gcostatistical modeling, and rigorous decline type curve analysis can be used to quantify reservoir quality and the degree of interwell communication. These results can be used to develop a 3-D simulation model for prediction of infill locations. In this work, we will demonstrate the application of reservoir surveillance techniques to identify additional reservoir "pay" zones, and to monitor pressure and preferential fluid movement in the reservoir. These techniques are: long-term production and injection data analysis, pressure transient analysis, and advanced open and cased hole well log analysis. The major contribution of this paper is our summary of cost effective reservoir characterization and management tools that will be helpful to both independent and major operators for the optimal development of heterogeneous, low permeability carbonate reservoirs such as the North Robertson (Clearfork) Unit.