gebhart/patrepeval huggingface dataset:
Probe design optimization of HLA microarray: Data cleaning of probe signals from cDNA tiling microarray: Outlier detection, noise reduction, and identification of uninformative probes in HLA typing application (2011)

Custom made tiling cDNA microarrays have been developed for high resolution HLA genotyping. The array comprises tens of thousands of sequence-specific oligonucleotide probes (SSOP) that hybridize with HLA sequences. Sophisticated methods for analyzing the multidimensional complex data are needed due to large amounts of data generated from the microarray experiments. Moreover, the inconsistencies, noise, and outliers in the probe signals add additional complexities. We proposed data cleaning methods for the identification of uninformative and misinformative probes to improve the performance of HLA typing process.
Extracellular CIRP&nbsp;Activates the IL-6Rα/STAT3/Cdk5 Pathway&nbsp;in Neurons (2021)

Abstract Extracellular cold-inducible RNA-binding protein (eCIRP) stimulates microglial inflammation causing neuronal damage during ischemic stroke and is a critical mediator of alcohol-induced cognitive impairment. However, the precise role of eCIRP in mediating neuroinflammation remains unknown. In this study, we report that eCIRP activates neurotoxic cyclin-dependent kinase-5 (Cdk5)/p25 through the induction of IL-6Rα/STAT3 pathway in neurons. Amyloid b (Aβ)-mediated neuronal stress, which is associated with Alzheimer’s disease, increased levels of eCIRP released from BV2 microglial cells. The released eCIRP levels from BV2 cells increased 3.2-fold upon stimulation with conditioned medium from Neuro-2a (N2a) cells containing Aβ compared to control N2a supernatant in a time-dependent manner. Stimulation of N2a cells and primary neurons with eCIRP upregulated the neuronal Cdk5 activator p25 expression in a dose- and time-dependent manner. eCIRP directly induced neuronal STAT3 phosphorylation and p25 increase via its novel receptor IL-6Rα. Next, we showed using surface plasmon resonance that eCIRP-derived peptide C23 inhibited the binding of eCIRP to IL-6Rα at 25 mM, with a 40-fold increase in equilibrium dissociation constant (K d ) value (from 8.08 x 10 -8 M to 3.43 x 10 -6 M), and completely abrogated the binding at 50 mM. Finally, C23 reversed the eCIRP-induced increase in neuronal STAT3 phosphorylation and p25 levels. In conclusion, the current study demonstrates that upregulation of neuronal IL-6Rα/STAT3/Cdk5 pathway is a key mechanism of eCIRP’s role in neuroinflammation and that C23 as a potent inhibitor of this pathway, has translational potential in neurodegenerative pathologies controlled by eCIRP.
An <i>HRD</i> / <i>DER</i> -independent ER quality control mechanism involves Rsp5p-dependent ubiquitination and ER-Golgi transport (2002)

We have identified a new pathway of ER-associated degradation in Saccharomyces cerevisiae that functions separately from the HRD/DER pathway comprised of Hrd1p, Hrd3p, Der1p, and Ubc7p. This pathway, termed Hrd1p independent-proteolysis (HIP), is capable of recognizing and degrading both lumenal (CPY* and PrA*), and integral membrane proteins (Sec61-2p) that misfold in the ER. CPY* overexpression likely saturates the HRD/DER pathway and activates the HIP pathway, so the slowed degradation kinetics of CPY* in a hrd1 Delta strain is restored to a wild-type rate when CPY* is overexpressed. Substrates of HIP require vesicular trafficking between the ER and Golgi apparatus before degradation by the ubiquitin-proteasome system. Ubiquitination of HIP substrates does not involve the HRD/DER pathway ubiquitin ligase Hrd1p, but instead uses another ubiquitin ligase, Rsp5p. HIP is regulated by the unfolded protein response as Ire1p is necessary for the degradation of CPY* when overexpressed, but not when CPY* is expressed at normal levels. Both the HIP and HRD/DER pathways contribute to the degradation of CPY*, and only by eliminating both is CPY* degradation completely blocked.
Antibacterial Concentrations in Prostatic Fluid 1. Nitrofurantoin (1967)

No AccessJournal of Urology1 Mar 1967Antibacterial Concentrations in Prostatic Fluid 1. Nitrofurantoin Bruce L. Dunn, and Thomas A. Stamey Bruce L. DunnBruce L. Dunn More articles by this author , and Thomas A. StameyThomas A. Stamey More articles by this author View All Author Informationhttps://doi.org/10.1016/S0022-5347(17)63069-6AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail © 1967 by The American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetailsCited ByMeares E (2018) Prostatitis Syndromes: New Perspectives About Old WoesJournal of Urology, VOL. 123, NO. 2, (141-147), Online publication date: 1-Feb-1980.Rodríguez Díaz L, Friedman A, Duarte C and Guariguata J (2018) Tissue, Blood and Urine Levels of Hetacillin in Patients with Urinary Tract InfectionJournal of Urology, VOL. 107, NO. 4, (652-654), Online publication date: 1-Apr-1972.Stamey T, Meares E and Winningham D (2018) Chronic Bacterial Prostatitis and the Diffusion of Drugs into Prostatic FluidJournal of Urology, VOL. 103, NO. 2, (187-194), Online publication date: 1-Feb-1970.Madsen P, Wolf H, Barquin O and Rhodes P (2018) The Nitrofurantoin Concentration in Prostatic Fluid of Humans and DogsJournal of Urology, VOL. 100, NO. 1, (54-56), Online publication date: 1-Jul-1968. Volume 97Issue 3March 1967Page: 505-507 Advertisement Copyright & Permissions© 1967 by The American Urological Association Education and Research, Inc.MetricsAuthor Information Bruce L. Dunn More articles by this author Thomas A. Stamey More articles by this author Expand All Advertisement Loading ...
Connection request protocol (CRP) for IP over ATM (2002)

All current protocol models for transporting IP packets over ATM require two operations across the UNI (user network interface): address resolution and connection setup. We propose combining the address resolution and setup operations into a single operation across the UNI interface thereby simplifying the end-host signaling software and improving performance. The protocol defined to support this combined scheme is called CRP (connection request protocol). The three IP over ATM models:, classical IP over ATM, LAN emulation; and routing over large clouds, are supported in the CRP scheme.
Digital image processing of hydrogen bubble lines for instantaneous velocity profiles (1992)

Boundary layer transition and turbulence have been described as being comprised of smaller structures called turbulent spots. Many researchers have obtained ensemble averaged velocity measurements in the transition region and some attempts have been made to obtain instantaneous information. Ensemble averaging can predict the overall scales of the flow field but it fails to yield information on the flow physics of the substructures within the spot. To facilitate investigation of these flow features and to establish the spot's relationship with transition or turbulence, an experimental method to obtain instantaneous full velocity profiles has been developed. The qualitative hydrogen bubble technique of flow visualization has been augmented to yield quantitative unsteady boundary layer information. The technique has been advanced by incorporating digital image processing of videotaped boundary layer flow. The method was verified by direct comparison with a laser Doppler anemometer and an analytical uncertainty analysis was performed. The technique compared well against the LDA, in both steady and unsteady flows. Recommendations were made for effective use of this technique and for further development.
Permanent Left Atrial Pacing with a Specifically Designed Coronary Sinus Lead (1997)

This article reports the original use of a specifically designed coronary sinus (CS) lead for permanent left atrial (LA) pacing. The device is characterized by its distal end shape featuring a double 45 degree angulation, which ensures very close contact with the CS upper wall. The device was successfully implanted in 39 out of 40 patients (97.5%). The tip electrode was eventually positioned in the distal CS in 9 patients, in the middle CS in 21 patients, and close to the ostium in the proximal CS in 9 patients. The mean acute pacing threshold voltage was 0.9 +/- 0.5 V with a mean impedance of 578 +/- 144 omega as measured in unipolar distal configuration at 0.5 ms pulse width (PW). The mean A wave amplitude was 3.5 +/- 2.1 mV. Early lead dislodgment occurred only once (3%) when the tip electrode was placed in the distal or middle CS, but more often (4/9 cases) when it was placed in the proximal CS. After a mean follow-up duration of 14 +/- 8.5 months, 35 of the 39 successfully implanted leads (89.7%) were still functional in terms of LA pacing and sensing. The mean chronic pacing threshold voltage was 1.5 +/- 0.8 V and the mean A wave amplitude was 2.7 +/- 1.6 mV. There were no lead related complications. In conclusion, the device proved to be safe and highly effective for permanent LA pacing, provided the distal tip could be positioned in the distal or middle part of the CS.
(Invited) Mechanism of Vfb Shift in HfO<sub>2</sub> Gate Stack by Al Diffusion from (TaC)<sub>1-x</sub>Al<sub>x</sub> Gate Electrode (2012)

We investigate Vfb behavior of (TaC)1-xAlx gated HfO2 MOS capacitors as a function of post metal annealing (PMA) temperature. The positive Vfb shift appears in PMA temperature at above 700 °C, while the negative Vfb shift occurs at below 600 °C. At below 600 °C, the effective work function (φm,eff) of gate electrode becomes lower by increasing Al atoms with a low work function. We found that the positive Vfb shift occurs dominantly due to the φm,eff change induced by Al diffusion from gate electrode at 700 and 800 °C. At above 900 °C, Al atoms reach to the HfO2/SiO2 interface and form the AlOx layers, and results in positive Vfb shift due to the bottom interface dipole. We can divide into two components of φm,eff change of gate electrode and the bottom interface dipole due to AlOx layer as a function of PMA temperature.
The history of antiretrovirals: key discoveries over the past 25 years (2009)

Within 25 years after zidovudine (3'-azido-2',3'-dideoxythymidine, AZT) was first described as an inhibitor of HIV replication, 25 anti-HIV drugs have been formally approved for clinical use in the treatment of HIV infections: seven nucleoside reverse transcriptase inhibitors (NRTIs): zidovudine, didanosine, zalcitabine, stavudine, lamivudine, abacavir and emtricitabine; one nucleotide reverse transcriptase inhibitor (NtRTI): tenofovir [in its oral prodrug form: tenofovir disoproxil fumarate (TDF)]; four non-nucleoside reverse transcriptase inhibitors (NNRTIs): nevirapine, delavirdine, efavirenz and etravirine; ten protease inhibitors (PIs): saquinavir, ritonavir, indinavir, nelfinavir, amprenavir, lopinavir, atazanavir, fosamprenavir, tipranavir and darunavir; one fusion inhibitor (FI): enfuvirtide; one co-receptor inhibitor (CRI): maraviroc and one integrase inhibitor (INI): raltegravir. These compounds are used in various drug combination (some at fixed dose) regimens so as to achieve the highest possible benefit and tolerability, and to diminish the risk of virus-drug resistance development.
Athermal emission in Yb,Er:glass (2007)

We report on the temperature dependent spectroscopic properties of Yb(3+) and Er(3+) co-doped glass gain media in the eye-safe spectral region. Measurements suggest that judicious selection of the operating wavelength can lead to a laser output with minimal dependence on the temperature of the gain medium.
1.4.4 Berührungslose Schallfeldmessung für den Einsatz in Flugzeugtriebwerken (2012)

Die Belastung der Bevlkerung durch Fluglrm weltweit zu reduzieren ist das erklrte Ziel namhafter Hersteller, Forschungseinrichtungen und Behrden im Bereich des Flugwesens [Eur01
Retention of the Radiotracers <sup>64</sup>Cu-ATSM and <sup>64</sup>Cu-PTSM in Human and Murine Tumors Is Influenced by MDR1 Protein Expression (2009)

The expression of MDR1 glycoprotein (or its equivalents in mice) affects the retention of (64)Cu-ATSM and -PTSM in the human and murine tumors tested. These results may have implications for clinical hypoxia imaging in tumors and the therapeutic efficacy of (64)Cu-ATSM.
Silicon quantum dots in a MOSFET structure: level structure (1999)

We have fabricated silicon quantum dot devices based on a dual gate technique in a silicon MOS technology. Two lateral gates deplete the inversion layer which is induced by a top gate, thus forming a quantum dot. Hence, the dot is located between the source and drain of a long channel MOSFET. Here, we report on the dependence of the charging of the dot with variation in the top gate, as well as a study of the magnetic field effect on the energy level structure.
Alteration of growth and differentiation factors response by Kirsten and Harvey sarcoma viruses in the IL-3-dependent murine hematopoietic cell line 32D C13(G). (1989)

32D C13(G) is an interleukin 3(IL3)-dependent non-tumorigenic murine hematopoietic cell line which undergoes terminal differentiation into granulocytes when exposed to granulocytic colony stimulating factor (G-CSF). Infections of 32D C13(G) cells with either Kirsten rat sarcoma virus or Balb murine sarcoma virus, both containing a v-ras oncogene, generates clones that can permanently grow in G-CSF without differentiation. 32D-Ki-ras cells show a heterogeneous morphology ranging from the promyelocytic to the myelocytic stage of differentiation, and express high levels of both myeloperoxidase (MPO) and lactoferrin (LF) mRNA. 32D-Ha-ras cells show a more immature phenotype and express MPO but no LF mRNA. The apparent differentiation block of both 32D Ki-ras and 32D Ha ras can be reversed by treatment with the chemical inducers retinoic acid, sodium butyrate or dimethylsulphoxide, which leads to terminal differentiation into granulocytes. When 32D-Ki-ras and 32D-Ha-ras cells are cultured in medium containing IL-3 they become adherent and express some monocyte-macrophage markers. Upon prolonged exposure to IL3, 32D-Ki-ras, but not 32D-Ha-ras, resume suspension growth. Both 32D-Ki-ras and 32D-Ha-ras rapidly die if grown in chemically defined medium in the absence of any growth factor and are non-tumorigenic in immunosuppressed mice. These findings indicate that ras activation may interfere with the normal response to growth and differentiation factors in cells of the granulocytic lineage. These alterations may represent a critical, although non-sufficient, step in leukemogenesis.
The Discrete Variational Conformal Technique for the Calculation of Strip Transtission-Line Parameters (1986)

This paper describes a new method of obtaining the transmission line properties of strip transmission lines whose geometrical configurations would make them difficult to analyze with other available techniques. The Discrete Variational Conformal (DVC) technique relies on conformal transformations to obtain the simplest possible representation of the Green function for the configuration of interest. This Green function is then used with an assumed charge distribution in the plane of the original configuration, and in a novel variational expression for the modal capacitance. The resulting equation is particularly well suited for numerical evaluation. Sample configurations are used to compare DVC to other techniques: Exact conformal mapping, Method of Moments, Full Wave solutions, and a Transverse Transmission Line Method. Two examples of application of DVC to asymmetric configurations are given.
Transient Modeling Synthesis: a flexible analysis/synthesis tool for transient signals (1997)

We propose a flexible analysis/synthesis model for transient signals that effectively extends the Spectral Modeling Synthesis (SMS) parameterization of signals from sinusoids+noise to sinusoids +transients+noise. The explicit handling of transients provides a more realistic and robust signal model. The model presented is a parametric model for transients that allows for a wide range of signal transformations. In addition to modeling, a transient detection scheme is also presented. 1 Introduction Transient Modeling Synthesis (TMS) is a flexible analysis/synthesis tool for transient signals. TMS is the frequency domain dual to sinusoidal modeling. Sinusoidal modeling and Spectral Modeling Synthesis (SMS) [1, 2] have enjoyed a rich history in both speech and audio. SMS is a flexible signal model that consists of sines and noise. While SMS provides a representation for sinusoidal signals that allows a wide range of transformations, TMS provides a representation for transient signals that ...
810 (2012)

Introduction: Optimal triage and time-sensitive treatment for patients at risk of critical illness requires accurate risk prediction. The initial clinical exam provides only limited information, leading to considerable interest in a plethora of candidate biomarkers. There are little data, however, on the performance criteria required of a potential biomarker to be clinically useful. Our goal was to determine such criteria through a simulation exercise using a large clinical dataset and illustrative theoretical biomarkers. Methods: We used a population-based cohort of emergency medical services records linked to hospital discharge data. We studied all adult, non-cardiac arrest, non-trauma patients transported to a hospital from 2002-2006 in King County, Washington. We simulated hypothetical biomarkers increasingly associated with critical illness during hospitalization, and determined the biomarker strength and sample size necessary to improve risk classification beyond the best-fitting model that used clinical information alone. We also evaluated study sizes necessary to document statistically significant improvements in risk classification. Results: Of 57,647 encounters, 3,121 (5.4%) were hospitalized with critical illness (cases) and 54,526 (94.6%) without critical illness (controls). The addition of a moderate strength biomarker (odds ratio=3.0 with critical illness) to a clinical triage model improved discrimination (c-statistic 0.85 vs. 0.8, p<0.01), reclassification (net reclassification improvement = 0.15, 95%CI: 0.13, 0.18), and increased the proportion of cases to the highest risk category by +8.6% (95%CI: 7.5, 10.8%). The same biomarker would change reclassification to the lowest risk category less commonly (+1.0%, 95%CI: 0.1, 2.3%). An even stronger biomarker (odds ratio=6.0 for critical illness) increased the proportion of cases deemed high risk by 20.7% (95%CI: 19, 23%) and the proportion of controls as low risk by 4.4% (95%CI: 3.4, 5.7%). Introducing moderate correlation between the biomarker and physiological variables in the clinical risk score did not modify the results. Detection of statistically significant changes in net reclassification required a sample size of at least 1000 subjects. Conclusions: Clinical models for triage of critical illness could be significantly improved, especially by incorporating biomarker measurements. Yet, substantial sample sizes and biomarker strength may be required to uncover incremental benefit from candidate biomarkers beyond best clinical predictors.
Analysis of multibeam's scalable column for complementary e-beam lithography (CEBL) (2012)

We present an analysis of the performance of an all electro-static electron-beam column designed for CEBL (Complementary Electron Beam Lithography). To meet the requirements of CEBL at advanced technology nodes (16 nm half-pitch and beyond), a beam size of < 20 nm FWHM (Full Width Half Maximum) and overlay accuracy of < 4 nm are needed. Beam current and beam energy must be optimized to achieve these specifications while meeting throughput requirements. In this paper, we present an in-depth analysis of the resolution of Multibeam's electron beam column as a function of beam energy. We focus on an analysis of beam energy below 30 keV, to avoid wafer heating and improve overlay accuracy. The beam size is analyzed with respect to aperture size and current. Spherical aberrations, chromatic aberrations and other effects at various beam energy levels are analyzed. At 7.5 or 5 keV beam energy, the 2 dominating factors in the beam spot size are the image size of the virtual source of the TFE (thermal field emitter) electron gun, chromatic and spherical aberrations. Performance of the column and process window to meet patterning requirements will be discussed.
Maximum dynamic range of clipped correlation of integrated laser speckle intensity (1988)

The relationship between the dynamic range and the clipping threshold of a double-clipped correlation of integrated laser speckle intensity signals is discussed. In particular, the maximum dynamic range of the clipped correlation is evaluated. For α = 1 (α being the number of the integrated speckles), the maximum dynamic range occurs for the clipping threshold of In 2〈I〉, and the clipping threshold approaches the mean intensity 〈I〉 as the number of integrated speckles increases. On the other hand, the maximum dynamic range does not change and has the same value of Δ = 1/4 (Δ being defined as the dynamic range of the clipping correlation normalized by that of the nonclipping correlation), even if the number of the integrated speckles varies.
Spontaneous inter-conversion of insulin fibril chirality (2011)

Amyloid fibrils are associated with many neurodegenerative diseases and are considered to be the energetically most favorable form of proteins. Here we report that a small pH change initiates spontaneous transformation of insulin fibrils from one polymorph to another. As a result, fibril supramolecular chirality overturns both accompanying morphological and structural changes.
SECRET (2002)

Developing regression models for large datasets that are both accurate and easy to interpret is a very important data mining problem. Regression trees with linear models in the leaves satisfy both these requirements, but thus far, no truly scalable regression tree algorithm is known. This paper proposes a novel regression tree construction algorithm (SECRET) that produces trees of high quality and scales to very large datasets. At every node, SECRET uses the EM algorithm for Gaussian mixtures to find two clusters in the data and to locally transform the regression problem into a classification problem based on closeness to these clusters. Goodness of split measures, like the gini gain, can then be used to determine the split variable and the split point much like in classification tree construction. Scalability of the algorithm can be achieved by employing scalable versions of the EM and classification tree construction algorithms. An experimental evaluation on real and artificial data shows that SECRET has accuracy comparable to other linear regression tree algorithms but takes orders of magnitude less computation time for large datasets.
New Developments in Gravity Applications and Instruments (2008)

Gravity meters are commonly used to map spatial changes in the earth's gravity. The application of gravity surveys to monitor change and recent improvements in gravity instrumentation will be summarized. The use of gravity to track the progress of a waterflood in Prudhoe Bay, Alaska, provides a 4D Gravity case history. Monitoring injected products using surface gravity measurements provides an effective "early warning system" for injection and sequestration projects. A borehole gravity survey in Hanford, Washington, demonstrates the ability to measure bulk densities using a borehole gravimeter. The applications include geotechnical studies, locating and monitoring thief zones in reservoirs, mineral exploration and grade control in mines. Long period movements of the earth can be recorded by gravity meters. The ground shaking in Luxembourg before and after an earthquake in Japan was recorded on a seismometer, a superconducting gravity meter and a gPhone gravity meter. The portable gPhone gravity meter provides the means to record earth movements along active faults using small earthquakes for signal sources. Airborne gravity systems have improved with better platform control, timing and GPS. Airborne gravity data acquired in the transition zones provide information for geoid mapping.