gebhart/patrepeval huggingface dataset:
Water Bridging Dynamics of Polymerase Chain Reaction in the Gauge Theory Paradigm of Quantum Fields (2017)

We discuss the role of water bridging the DNA-enzyme interaction by resorting to recent 1 results showing that London dispersion forces between delocalized electrons of base pairs of DNA 2 are responsible for the formation of dipole modes that can be recognized by Taq polymerase. 3 We describe the dynamical origin of the high efficiency and precise targeting of Taq activity in 4 PCR. The spatiotemporal distribution of interaction couplings, frequencies, amplitudes, and phase 5 modulations comprise a pattern of fields instantiating the electromagnetic image of DNA in its 6 water environment, which is what the polymerase enzyme actually recognizes at long range. The 7 experimental realization of PCR amplification, achieved through replacement of the DNA template 8 by the treatment of pure water with electromagnetic signals recorded from viral and bacterial DNA 9 solutions, is found consistent with the gauge theory paradigm of quantum fields.
17-Cyclopropylmethyl-3,14β-dihydroxy-4,5α-epoxy-6β-(4′-pyridylcarboxamido)morphinan (NAP) Modulating the Mu Opioid Receptor in a Biased Fashion (2015)

Mounting evidence has suggested that G protein-coupled receptors can be stabilized in multiple conformations in response to distinct ligands, which exert discrete functions through selective activation of various downstream signaling events. In accordance with this concept, we report biased signaling of one C6-heterocyclic substituted naltrexamine derivative, namely, 17-cyclopropylmethyl-3,14β-dihydroxy-4,5α-epoxy-6β-(4'-pyridylcarboxamido)morphinan (NAP) at the mu opioid receptor (MOR). NAP acted as a low efficacy MOR partial agonist in the G protein-mediated [(35)S]GTPγS binding assay, whereas it did not significantly induce calcium flux or β-arrestin2 recruitment. In contrast, it potently blocked MOR full agonist-induced β-arrestin2 recruitment and translocation. Additionally, NAP dose-dependently antagonized MOR full agonist-induced intracellular calcium flux and β-arrestin2 recruitment. Further results in an isolated organ bath preparation confirmed that NAP reversed the morphine-induced reduction in colon motility. Ligand docking and dynamics simulation studies of NAP at the MOR provided more supporting evidence for biased signaling of NAP at an atomic level. Due to the fact that NAP is MOR selective and preferentially distributed peripherally upon systemic administration while β-arrestin2 is reportedly required for impairment of intestinal motility by morphine, biased antagonism of β-arrestin2 recruitment by NAP further supports its utility as a treatment for opioid-induced constipation.
Peptide ligand screening of α-synuclein aggregation modulators by in silico panning (2007)

We demonstrated that it is possible to screen alpha-synuclein-binding peptides by in silico panning. The screened peptides bind to alpha-synuclein, thus affecting the aggregation of alpha-synuclein.
Stress-Related Immune Response and Selenium Status in Autoimmune Thyroid Disease Patients (2023)

Autoimmune thyroid disease (AITD), including Graves' disease (GD) or Hashimoto's thyroiditis (HT), occurs due to genetic susceptibility and environmental factors, among which the role of stressful events remains controversial. This study investigated the relationship between the number and impact of stressful life events in AITD patients with selenium status, and the Th1/Th2/Th17 immune response. The study population included three groups: HT (<i>n</i> = 47), GD (<i>n</i> = 13), and a control group (<i>n</i> = 49). Thyroid function parameters, autoantibody levels, and the plasma levels of cytokines, selenium, selenoprotein P (SeP), and glutathione peroxidase 3 (GPx) activity were measured. Participants filled out the Life Experiences Survey. No significant differences in the number of stressful life events were found among the patients with HT, GD, and the controls. A higher (median (interquartile range)) negative stress level (8 (4-12)) than a positive stress level (3 (1-9)) was found in the HT group. The HT group showed a correlation between SeP and the positive stress level: r<sub>s</sub> = -0.296, <i>p</i> = 0.048, and the GD group between GPx and the negative stress level (r<sub>s</sub> = -0.702, <i>p</i> = 0.011). Significant positive correlations between thyroid peroxidase antibody level and the total number of major life events (<i>p</i> = 0.023), the number of major life events in the last 7-12 months, and the number of major life events with no impact and a negative stress level were found. We suggest that the measurements of Th2-related cytokines and selenoproteins could be used as biomarkers for the development of AITD in cases where stress is considered a component cause of the pathogenic mechanism of the disease.
Estimation of fractal signals from noisy measurements using wavelets (1992)

The role of the wavelet transformation as a whitening filter for 1/f processes is exploited to address problems of parameter and signal estimations for 1/f processes embedded in white background noise. Robust, computationally efficient, and consistent iterative parameter estimation algorithms are derived based on the method of maximum likelihood, and Cramer-Rao bounds are obtained. Included among these algorithms are optimal fractal dimension estimators for noisy data. Algorithms for obtaining Bayesian minimum-mean-square signal estimates are also derived together with an explicit formula for the resulting error. These smoothing algorithms find application in signal enhancement and restoration. The parameter estimation algorithms find application in signal enhancement and restoration. The parameter estimation algorithms, in addition to solving the spectrum estimation problem and to providing parameters for the smoothing process, are useful in problems of signal detection and classification. Results from simulations are presented to demonstrated the viability of the algorithms.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
High performance germanium n-MOSFET with antimony dopant activation beyond 1&#x00D7;10<sup>20</sup> cm<sup>&#x2212;3</sup> (2010)

For the first time, high performance Ge nMOSFET is fabricated using laser annealing of ion-implanted antimony (Sb) dopants which provides donor activation beyond 1×10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">20</sup> cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-3</sup> in germanium. Record I <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">on</sub> /I <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">off</sub> >; 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">5</sup> is demonstrated for n <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> /p junctions combined with significant reduction of contact resistance to 7×10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-7</sup> Ω-cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> . Performance projections for ITRS HP 22nm technology node are also discussed.
Robust manipulator control method considering limit values of torque and controller output (2002)

The robust manipulator control method based on a robust acceleration controller is effective for an accurate and guide manipulator motion control. However, as this method does not consider the limit values of torque and controller output, it often has an oscillated response or a windup phenomena caused by the saturation effect due to these limit values. This paper proposes the two new types of adjusting algorithm for manipulator control, which consider the limit values of torque and controller output. The robust manipulator motion control method using these adjusting algorithms well regulates the position and the path tracking smoothly and accurately, and its response does not cross over these limit values.
Causal Inference for a Single Group of Causally-Connected Units Under Stratified Interference (2017)

The assumption that no subject's exposure affects another subject's outcome, known as the assumption of no interference, has long held a foundational position in the study of causal inference. However, this assumption may be violated in many settings, and in recent years has been relaxed considerably. Often this has been achieved with either the aid of knowledge of an underlying network, or the assumption that the population can be partitioned into separate groups, between which there is no interference, and within which each subject's outcome may be affected by all the other subjects in the group, but only as a function of the total number of subjects exposed (the stratified interference assumption). In this paper, we consider a setting in which we can rely on neither of these aids, as each subject affects every other subject's outcome. In particular, we consider settings in which the stratified interference assumption is reasonable for a single group consisting of the entire sample, i.e., a subject's outcome is affected by all other subjects' exposures, but only via the total number of subjects exposed. This can occur when the exposure is a shared resource whose efficacy is modified by the number of subjects among whom it is shared. We present a doubly-robust estimator that allows for incorporation of machine learning, and tools for inference for a class of causal parameters that includes direct effects and overall effects under certain interventions. We conduct a simulation study, and present results from a data application where we study the effect of a nurse-based triage system on the outcomes of patients receiving HIV care in Kenyan health clinics.
Abstract 3100: MicroRNA profiling reveals miR-205 upregulation is associated with head and neck squamous cell carcinoma and modulates E2F1 signaling. (2013)

Abstract Introduction: Based on our previous screen of miRNAs in head and neck squamous cell carcinoma (HNSCC), we sought to functionally evaluate candidate transcripts that could modify Rb/E2F signaling. Thus, we chose to investigate miR-205 as a putative HNSCC oncogene and regulator of E2F1 protein expression. Methods: miRNAs were isolated from 29 newly diagnosed HNSCC tumors (HPV-positive: 14, HPV-negative: 15) and 4 normal mucosa samples using the PureLink RNA Isolation Kit (Invitrogen). miRNA was analyzed using the ABI Megaplex protocol without pre-amplification (Applied Biosystems). Reactions were run using the miRNA Reverse Transcription Kit and Megaplex RT Human Pool A primers, then analyzed by TaqMan Low-Density Array (TLDA) cards. miRNA data was normalized to MammU6 expression, with undetectable transcripts assigned a Ct value of 40. Empirical Bayes moderated t-statistics were used to assess miRNA differential expression and the Benjamini- Hotchberg correction was applied to these p-values to account for multiple hypothesis testing. miR-205 expression was then transiently modified (Dharmacon) in an HPV-positive and -negative HNSCC cell line. These cells were characterized by Western blot and assayed for changes in proliferation utilizing two- and three-dimensional growth assays. Results: HNSCC miRNA expression was characterized by a general upregulation of individual transcripts and miRNA families compared to normal mucosa. This difference in expression was independent of HPV-status, with only two miRNAs demonstrating differential expression between HPV-positive and -negative tumors: miR-449a and miR-129-3p. miR-205, a transcript upregulated in both subtypes, was able to modulate proliferation and E2F1 expression levels in 93VU147T (HPV+), but not UM-SCC-15 (HPV-). Further Western blot analysis concluded modulations in Rb-phosphorylation status and apoptotic signaling factors may explain these E2F1-mediated effects. Conclusions: While significant differences are evident in the miRNA profiles of HNSCC compared to normal mucosa, a striking degree of similarity exists between HPV-positive and -negative miRNA deregulation. A functional evaluation of miR-205 determined this transcript is capable of modulating HNSCC growth in the genetic context of p16 expression and proapoptotic signaling. Citation Format: Jason D. Howard, Haixia Cheng, Elena Ratner, Elana J. Fertig, Jimena Perez, Harry Quon, Michael Considine, Michael Ochs, Joanne Weidhaas, Christine H. Chung. MicroRNA profiling reveals miR-205 upregulation is associated with head and neck squamous cell carcinoma and modulates E2F1 signaling. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3100. doi:10.1158/1538-7445.AM2013-3100
<title>Sensitive imaging of spectrally overlapping flourochromes using the LSM 510 META</title> (2002)

Multi-color fluorescence microscopy has become a popular way to discriminate between multiple proteins, organelles or functions in a single cell or animal and can be used to approximate the physical relationships between individual proteins within the cell, for instance, by using Fluorescence Resonance Energy Transfer (FRET). However, as researchers attempt to gain more information from single samples by using multiple dyes or fluorescent proteins (FPs), spectral overlap between emission signals can obscure the data. Signal separation using glass filters is often impractical for many dye combinations. In cases where there is extensive overlap between fluorochromes, separation is often physically impossible or can only be achieved by sacrificing signal intensity. Here we test the performance of a new, integrated laser scanning system for multispectral imaging, the Zeiss LSM 510 META. This system consists of a sensitive multispectral imager and online linear unmixing functions integrated into the system software. Below we describe the design of the META device and show results from tests of the linear unmixing experiments using fluorochromes with overlapping emission spectra. These studies show that it is possible to expand the number of dyes used in multicolor applications.
Abstract A066: Role of the NRF2 signaling pathway in sustaining chemoresistance in medulloblastoma (2019)

Abstract Nrf2, a key orchestrator of cell defense mechanisms against oxidative stress and xenobiotic insults, has been linked to chemotherapy resistance and recurrence in many human cancers. Through the establishment of an in vitro model of chemoresistance, we investigated the role of Nrf2 in sustaining resistance to chemotherapy in medulloblastoma (MB), a highly aggressive pediatric brain tumor intrinsically characterized by fast growth, high invasiveness and resistance to treatments. MB DAOY cells were weekly exposed to a cocktail of drugs commonly used in MB treatment, vincristine, etoposide, cisplatin and cyclophosphamide (VECC) inducing the emergence of a resistant phenotype. After 5 cycles of VECC treatment we obtained a culture of cells resistant to subsequent chemotherapy treatments. We observed increased Nrf2 levels and activity in therapy-exposed cells already from the first received dose of VECC. Nrf2 levels remained high throughout all the rest of chemotherapy cycles and interestingly, its transcriptional activity spiked up when resistance to chemotherapy emerged, as demonstrated by the increase of antioxidant response element (ARE)-driven luciferase activity and the expression of target genes. The knock down of Nrf2 in resistant cells, by the use of specific siRNA, was able to restore chemosensitivity, suggesting a role of Nrf2 signaling pathway in the onset of chemotherapy resistance in MB cells. Resistant cells showed a higher ROS (reactive oxygen species) scavenging capacity after stimulation with hydrogen peroxide. Nrf2 silencing partially reverts the ability of resistant cells to manage oxidative stress, supporting the hypothesis of Nrf2 involvement in the ROS scavenging potential of VECC resistant MB cells. In addition to directly regulate ROS-scavenging enzymes, Nrf2 has been described to control cell metabolism that maintain redox homeostasis in cancer stem cells. Among the Nrf2 target genes upregulated in DAOY resistant cells we found the upregulation of PFKFB-3, G6PD and TKT. The increased expression of this enzymes suggests a metabolic reprogramming in resistant cells. Our data support the involvement of Nrf2 pathway in MB response to VECC treatment and show that the upregulation of this detoxifying system sustains MB resistance to chemotherapy. Citation Format: Fatlum Rruga, Elena Mariotto, Luca Persano, Elena Rampazzo, Alessandra Luchini, Lance A Liotta, Giampietro Viola, Roberta Bortolozzi. Role of the NRF2 signaling pathway in sustaining chemoresistance in medulloblastoma [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics; 2019 Oct 26-30; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2019;18(12 Suppl):Abstract nr A066. doi:10.1158/1535-7163.TARG-19-A066
Comparison of three C4 cereals for transpirational sensitivity to elevated evaporative demand (2017)

Maize, sorghum and pearl-millet are leading C4 cereals for tropical&#13;\nregions where evaporative demand is high. The transpiration&#13;\nresponse to high VPD and leaf area of plants grown under different&#13;\nVPD conditions was compared among species to assess&#13;\nthe degree of water conservation of these crops and then their&#13;\npotential fitness to different stress scenarios. Ten genotypes of&#13;\neach species were grown under moderate (2.2-2.8kPa) and high&#13;\nVPD (3.9-4.5kPa) conditions till early vegetative (V5-V7) stage&#13;\nwith no water-limitation. At that stage transpiration was measured&#13;\nunder elevating VPD (0.9-4.1kPa) in controlled conditions.&#13;\nAll three species grown under moderate VPD conditions showed&#13;\na variation in transpiration restriction above 3.0kPa, although the&#13;\ndecrease in transpiration above 3.0kPa was high in the case of&#13;\nmaize. Sorghum and pearl-millet grown under high VPD conditions&#13;\nshowed significant reduction in leaf area whereas maize&#13;\nshowed trivial differences in leaf area across VPD conditions.&#13;\nTherefore, under high evaporative demand when soil water was&#13;\nnot limiting, maize saved water only by restricting water use&#13;\nduring pre-flowering stages whereas sorghum and pearl millet&#13;\nbothreduced canopy sizeand transpiration under high VPD.&#13;\nThe soil moisture thresholds where transpiration declined upon&#13;\nprogressive water stress imposition did not differ significantly,&#13;\nregardless of different VPD in the growing conditions. Maize had&#13;\nalso higher TE than sorghum and millet in the high VPD conditions.&#13;\nTherefore, water conserved in maize by restricted transpiration&#13;\nin high VPD condition, probably leading to higher TE, was&#13;\nsufficiently rewarded to sustain biomass accumulation in water&#13;\nstress period.
PDN impedance analysis of TSV-decoupling capacitor embedded Silicon interposer for 3D-integrated CMOS image sensor system (2012)

We have proposed to use the electrostatic capacitance of through-silicon-vias (TSV) in the silicon interposer as the decoupling capacitor. Because the electrostatic capacity of the TSV acts as a decoupling capacitor, it is enabled to decrease the power distribution network (PDN) impedance. Therefore, the dependency to the PDN impedance in the effect of the layout and the shape of the TSV capacitor was analyzed. By introducing the 3-D electromagnetic field simulator, precise PDN impedance analysis was carried out. As a result, TSV functions enough as a decoupling capacitor. PDN impedance of the silicon inter-poser with TSV-decoupling capacitor decrease compared with that of the silicon interposer without TSV. Especially, PDN impedance of the silicon interposer with 200-micrometer pitch TSVs shows PDN impedance without the resonance peak from the low-frequency region to the high frequency area.
Coexistence of superconductivity and antiferromagnetic ordering in the layered superconductor SmFePO (2008)

Superconductivity and magnetic transition in SmFePO were examined by electric, magnetic, $^{57}\text{F}\text{e}$ M\"ossbauer, and $^{149}\text{S}\text{m}$ nuclear resonant forward-scattering (NRFS) measurements. Zero resistivity and negative magnetic susceptibility were observed in an undoped SmFePO, indicating superconducting transition temperature $({T}_{c})$ of $\ensuremath{\sim}3\text{ }\text{K}$. ${T}_{c}$ in undoped SmFePO appears in a narrow region of lattice constants with an optimum conductivity. Furthermore, in relation to magnetic susceptibility, NRFS spectra verify that magnetic moments of ${\text{Sm}}^{3+}$ ions order antiferromagnetically below magnetic transition $\ensuremath{\sim}5\text{ }\text{K}$, accompanying a discontinuous drop in electrical resistivity, whereas $^{57}\text{F}\text{e}$ M\"ossbauer spectra show that magnetic moments of Fe are quenched. These results indicate the coexistence of superconductivity and magnetic ordering in a crystallographic unit cell of SmFePO.
An Omnibus Nonparametric Test of Equality in Distribution for Unknown\n Functions (2015)

We present a novel family of nonparametric omnibus tests of the hypothesis\nthat two unknown but estimable functions are equal in distribution when applied\nto the observed data structure. We developed these tests, which represent a\ngeneralization of the maximum mean discrepancy tests described in Gretton et\nal. [2006], using recent developments from the higher-order pathwise\ndifferentiability literature. Despite their complex derivation, the associated\ntest statistics can be expressed rather simply as U-statistics. We study the\nasymptotic behavior of the proposed tests under the null hypothesis and under\nboth fixed and local alternatives. We provide examples to which our tests can\nbe applied and show that they perform well in a simulation study. As an\nimportant special case, our proposed tests can be used to determine whether an\nunknown function, such as the conditional average treatment effect, is equal to\nzero almost surely.\n
Stråling fra Mobilmaster - et teknisk responsum (2004)

Siden opstillingen af sendemaster til det nye 3. generationsnet til mobiltelefoner (UMTS) blev påbegyndt, har der været en omfattende debat omkring den mulige strålingsrisiko for personer, der bor eller bevæger sig i nærheden af masterne.<br/>Denne debat har primært været båret af forskellige interessegrupper som udbydere, producenter, forbrugere og NGO’er. Da Aalborg Universitet er blandt de førende i verden indenfor mobilkommunikationsområdet, herunder udbredelsen af stråling fra antennemaster, har fakultetet følt en særlig forpligtigelse til at yde vores bidrag til en afklaring af den tekniske side af spørgsmålet på baggrund af den uafhængige position, som et universitet indtager.
Calf Muscles Imaged at BOLD MR: Correlation with TcPo2and Flowmetry Measurements during Ischemia and Reactive Hyperemia—Initial Experience (2006)

BOLD MR imaging of calf muscles-depending on underlying key parameters-has moderate to good correlation with LDF and TcPo2 measurements during ischemia and reactive hyperemia.