gebhart/patrepeval huggingface dataset:
Averaging measurement strategies for identifying single nucleotide polymorphisms from redundant data sets (2011)

Single nucleotide polymorphisms (SNPs) studies have been an active topic of research in the life sciences in recent years. Because SNPs are abundant, stable and sometimes can be related to specific diseases, they have been widely selected as biomarkers for multi-purpose research. As traditional methods for identifying SNPs are time-consuming and expensive, discovering SNPs from expressed sequence tags (ESTs) has became an alternative efficient way. As most EST databases do not store quality/trace files together with EST reads, several methods, like Phard, which requires corresponding sequences quality files, will not be suitable for further research purpose. Thus, computational methods that are able to obtain reliable SNPs without the need for trace/quality information are still essential. We have developed a pipeline framework, called PFSNP, to reveal reliable SNPs from EST data sets without the association of trace/quality files. PFSNP deploys several strategies, like modified neighborhood quality standard measurement and fuzzy logic, in this framework. Also, it automatically adjusts the slide window to efficiently fit different conditions of data sets. PFSNP is demonstrated by identifying SNPs from two subgroups of Oryza sativa with two different strategies as well as zebrafish. Based on our experimental results, PFSNP can obtain higher reliable results when compared to existing methods.
Characterization of anti-peptide antibodies directed against an extracellular immunogenic epitope on the human α1-adrenergic receptor (1994)

A synthetic peptide corresponding to amino acids 192-218 of the second extracellular loop of the human alpha 1A-adrenergic receptor was used to raise antibodies in rabbits. Affinity-purified antibodies specifically recognized main bands with a molecular weight of about 68, 40 and 37 kD on the electrotransferred membrane proteins of rat ventricle membranes. The incubation of these antibodies with rat myocardial membranes resulted in a decrease in the number of binding sites for the specific radiolabelled alpha 1-antagonist prazosin. These antibodies were also able to mimic the effects of agonist stimulation as demonstrated by a positive chronotropic effect on cultured cardiomyocytes. These results constitute the first immunochemical evidence of the presence of both the A and B subtypes of the alpha 1-adrenergic receptor in the heart. They also confirm that the second extracellular loop of the alpha 1-adrenergic receptors is an immunologically and functionally important domain.
Discovery-based brain proteomics to understand disparities in Alzheimer’s disease (2018)

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Lake Wobegon Dice (2012)

SummaryWe introduce Lake Wobegon dice, where each die is “better than the set average.” Specifically, these dice have the paradoxical property that on every roll, each die is more likely to roll greater than the set average on the roll, than less than this set average. We also show how to construct minimal optimal Lake Wobegon sets for all n ≥ 3.
Clinical Significance of Hepatitis C Virus Genotypes (2000)

SUMMARY On the basis of phylogenetic analysis of nucleotide sequences, multiple genotypes and subtypes of hepatitis C virus (HCV) have been identified. Characterization of these genetic groups is likely to facilitate and contribute to the development of an effective vaccine against infection with HCV. Differences among HCV genotypes in geographic distributions have provided investigators with an epidemiologic marker that can be used to trace the source of HCV infection in a given population. HCV genotype 1 may represent a more aggressive strain and one that is less likely to respond to interferon treatment than HCV genotype 2 or 3. However, these observations require confirmation before HCV genotyping can be used in clinical settings.
The Role of External Defects in Chemical Sensing of Graphene Field-Effect Transistors (2013)

A fundamental understanding of chemical sensing mechanisms in graphene-based chemical field-effect transistors (chemFETs) is essential for the development of next generation chemical sensors. Here we explore the hidden sensing modalities responsible for tailoring the gas detection ability of pristine graphene sensors by exposing graphene chemFETs to electron donor and acceptor trace gas vapors. We uncover that the sensitivity (in terms of modulation in electrical conductivity) of pristine graphene chemFETs is not necessarily intrinsic to graphene, but rather it is facilitated by external defects in the insulating substrate, which can modulate the electronic properties of graphene. We disclose a mixing effect caused by partial overlap of the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) of adsorbed gas molecules to explain graphene's ability to detect adsorbed molecules. Our results open a new design space, suggesting that control of external defects in supporting substrates can lead to tunable graphene chemical sensors, which could be developed without compromising the intrinsic electrical and structural properties of graphene.
Counting statistics of microwave photons in circuit QED (2020)

In superconducting circuit architectures for quantum computing, microwave resonators are often used both to isolate qubits from the electromagnetic environment and to facilitate qubit state readout. We analyze the full counting statistics of photons emitted from such driven readout resonators both in and beyond the dispersive approximation. We calculate the overlap between emitted-photon distributions for the two qubit states and explore strategies for its minimization with the purpose of increasing fidelity of intensity-sensitive readout techniques. In the dispersive approximation and at negligible qubit relaxation, both distributions are Poissonian, and the overlap between them can be easily made arbitrarily small. Nondispersive terms of the Hamiltonian generate squeezing and the Purcell decay with the latter effect giving the dominant contribution to the overlap between two distributions.
Discrimination Between Phenylephrine-Triggered Contractile Events by Atrial Natriuretic Factor in Rat Aorta (1988)

The effects of atrial natriuretic factor (ANF) on contractile events triggered by phenylephrine (PE) were investigated in rat aorta. Isometric contraction of endothelium-free rat aorta rings was recorded in Ca2+-free medium containing 1 mM EGTA. PE (1 microM) induced a phasic contraction and a sustained contraction following addition of Ca2+ (2.5 mM) to the medium. The phasic contraction was due to intracellular Ca2+ release whereas the sustained one was dependent on extracellular Ca2+ influx. ANF (1-3 nM) and prazosin (3-10 nM) both reduced the two types of contraction. However, during the sustained contraction, a rhythmic activity was observed when ANF, but not prazosin, was used as an inhibitory agent. The calcium antagonist diltiazem (0.1-1 microM) abolished this rhythmic activity, which was attributed to a Ca2+ influx through potential-dependent channels. The results indicate that ANF, unlike prazosin, may discriminate between PE-triggered contractile events in the rat aorta.
Flurbiprofen inhibits heme induced NLRP3 inflammasome in Berkeley sickle cell disease mice (2023)

Sickle cell disease (SCD) is accompanied by several complications, which emanate from the sickling of erythrocytes due to a point mutation in the <i>β</i>-globin chain of hemoglobin. Sickled erythrocytes are unable to move smoothly through small blood capillaries and therefore, cause vaso occlusion and severe pain. Apart from pain, continuous lysis of fragile sickled erythrocytes leads to the release of heme, which is a strong activator of the NLRP3 inflammasome, thus producing chronic inflammation in sickle cell disease. In this study, we identified flurbiprofen among other COX-2 inhibitors to be a potent inhibitor of heme-induced NLRP3 inflammasome. We found that apart from being a nociceptive agent, flurbiprofen exerts a strong anti-inflammatory effect by suppressing NF-κB signaling, which was evidenced by reduced levels of TNF-<i>α</i> and IL-6 in wild-type and sickle cell disease Berkeley mice models. Our data further demonstrated the protective effect of flurbiprofen on liver, lungs, and spleen in Berkeley mice. The current sickle cell disease pain management regime relies mainly on opiate drugs, which is accompanied by several side effects without modifying the sickle cell disease-related pathology. Considering the potent role of flurbiprofen in inhibiting NLRP3 inflammasome and other inflammatory cytokines in sickle cell disease, our data suggests that it can be explored further for better sickle cell disease pain management along with the possibility of disease modification.
Learning from Observing: Vision and POIROT - Using Metareasoning for Self Adaptation (2010)

We present a cognitive architecture that heavily utilizes metareasoning for self adaptation. The architecture is derived in part from neuroscience data and theories about the operation of the human vision system. We also discuss how this architecture is applied in the POIROT system, which learns web services workflow from “observing” a small number of expert examples.
Contraintes de croissance dans la zircone par diffraction des rayons X in situ et RAMAN (2017)

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Synthesis and biological screening of 2-(4-methylpiperazin-1-yl methyl)-1-(arylsulfonyl)-1H-indole derivatives as 5-HT6 receptor ligands: Part II (2012)

As a part of our ongoing research to develop novel and selective 5-HT6 receptor antagonists, a new series of 2-(4- methylpiperazin-1-yl methyl)-1-(arylsulfonyl)-1H-indole derivatives were designed to study the effect of two ionisable basic centers on the 5-HT6 receptor binding affinity. The synthesis and their in-vitro affinity towards the 5- HT6 receptor is the subject matter of this communication.
Design and Fabrication of Thick Film Sensors (1987)

This paper describes the stages in the construction of sensors implemented in thick film technology. The use of CAD facilities greatly reduces the time required for development, and automatic design rule checking minimises errors. Steps in the fabrication from layout to finished mask(s) are detailed and specific examples given. Strain gauges using piezoresistive properties of thick film resistor inks with various sheet resistivities (Du Pont HS80 series) printed on insulated stainless steel substrates were examined under strains ranging from 0 to ±1000 microstrain. Results show gauge factors to be dependent on the ink's sheet resistivity and range from 2 to 12. The temperature coefficients of resistance were determined over temperatures of +20°C to +140°C, revealing good tracking and reproducibility.
Design Technology Co-Optimization for Back-End-of-Line Nonvolatile NEM Switch Arrays (2021)

Design tradeoffs for vertically oriented nonvolatile (NV) nano-electro-mechanical (NEM) switches implemented using multiple interconnect layers in a 5-nm-generation CMOS back-end-of-line (BEOL) process are investigated via 3-D device simulation. Programming pulse voltage and width operating windows are identified for avoiding catastrophic pull-in. The simulation results indicate that sub-20-ns programming delay is possible with programming voltages compatible with standard input-output (I/O) CMOS circuitry, and that the write energy of an NV-NEM bit-cell will be less than 5 aJ. A crossbar array architecture operated with a half-select row/column bit-cell programming scheme is found to be effective for avoiding the issue of write disturbance.
Complex Processes and 3D Printing (2013)

A process which converts 2D evolving cellular automata into 3D printed objects was designed. The<br>process takes into account the limitations inherent to 3D printing processes and materials and bypasses the use of CAD software and manual part design. Alongside the process itself, a software which automates the greater part of this process was developed. A physical model of a cellular automaton was successfully printed and suggests that in the future a process similar to the one developed in this project may be used to convert<br>physics models into 3D objects.
Electrostatic Properties of PE and PTFE Subjected to Atmospheric Pressure Plasma Treatment; Correlation of Experimental Results with Atomistic Modeling (2006)

The use of an atmospheric pressure glow discharge (APGD) plasma was used at KSC to increase the hydrophilicity of spaceport materials to enhance their surface charge dissipation and prevent possible ESD in spaceport operations. Significant decreases in charge decay times were observed after tribocharging the materials using the standard KSC tribocharging test. The polarity and amount of charge transferred was dependent upon the effective work function differences between the respective materials. In this study, polyethylene (PE) and polytetrafluoroethylene (PTFE) were exposed to a He+O2 APGD. The pre and post treatment surface chemistry was analyzed by X-ray photoelectron spectroscopy and contact angle measurements. Semi-empirical and ab initio calculations were performed to correlate the experimental results with some plausible molecular and electronic structure features of the oxidation process. For the PE, significant surface oxidation was observed, as indicated by XPS showing C-O, C=O, and O-C=O bonding, and a decrease in the surface contact angle from 98.9 deg to 61.2 deg. For the PTFE, no C-O bonding appeared and the surface contact angle increased indicating the APGD only succeeded in cleaning the PTFE surface without affecting the surface structure. The calculations using the PM3 and DFT methods were performed on single and multiple oligomers to simulate a wide variety of oxidation scenarios. Calculated work function results suggest that regardless of oxidation mechanism, e.g. -OH, =0 or a combination thereof, the experimentally observed levels of surface oxidation are unlikely to lead to a significant change in the electronic structure of PE and that its increased hydrophilic properties are the primary reason for the observed changes in its electrostatic behavior. The calculations for PTFE argue strongly against significant oxidation of that material, as confirmed by the XPS results.
Microstructure and Chemistry of the Oxide Scale and Pt-containing Coatings Deposited on Superalloy N5 (2012)

Extended abstract of a paper presented at Microscopy and Microanalysis 2012 in Phoenix, Arizona, USA, July 29 – August 2, 2012.
Size of Elementary Clusters and Process Period in Silver Nanoparticle Formation (2011)

The time dependence of small-angle X-ray scattering (SAXS) curves for silver nanoparticle formation was followed in situ at a time resolution of 0.18 ms, which is 3 orders of magnitude higher than that used in previous reports (ca. 100 ms). The starting materials were silver nitrate solutions that were reacted with reducing solutions containing trisodium citrate. The SAXS analyses showed that silver nanoparticles were formed in three distinct periods from a peak diameter of ca. 0.7 nm (corresponding to the size of a Ag(13) cluster) during the nucleation and the early growth period. The Ag(13) clusters are most likely elementary clusters that agglomerate to form silver nanoparticles.
The Role of Dangling Bonds in H<sub>2</sub>O-Induced Oxidation of Si(100)-2 × 1 (2008)

The stability of the water-terminated Si(100)-2 × 1 surface in the 300−550 K temperature range is investigated with ultrahigh vacuum scanning tunneling microscopy experiments and density functional theory calculations. For temperatures below 450 K the surface is found to be stable from hydroxyl decomposition and surface oxidation. In the range of 450−550 K, new surface features associated with oxygen insertion into the silicon dimer bond are observed. It is found that the rate of hydroxyl decomposition and oxygen insertion does not follow simple first order kinetics with respect to the surface hydroxyl groups. Density functional theory calculations of oxygen insertion pathways point toward a catalytic effect of the dangling bonds and suggest that in the 450−550 K range the insertion events should predominantly occur next to unoccupied surface sites. A model is proposed where the dangling bonds diffuse along the dimer rows and promote hydroxyl decomposition. Kinetic Monte-Carlo simulations are used to compare the model with both experiments and density functional theory calculations, and an insertion activation barrier of 1.8 eV is found to give a good fit to the experimental data. On the basis of the findings, a strategy to increase hydroxyl group stability is demonstrated using water termination at cryogenic temperatures.
Control of non-homeostatic feeding in sated mice using associative learning of contextual food cues (2018)

ABSTRACT Feeding is a complex motivated behavior controlled by a distributed neural network that processes sensory information to generate adaptive behavioral responses. Accordingly, studies using appetitive Pavlovian conditioning confirm that environmental cues that are associated with food availability can induce feeding even in satiated subjects. However, in mice, appetitive conditioning generally requires intensive training and thus can impede molecular studies that often require large numbers of animals. To address this, we developed and validated a simple and rapid context-induced feeding (ctx-IF) task in which cues associated with food availability can later lead to increased food consumption in sated mice. We show that the associated increase in food consumption is driven by both positive and negative reinforcement and that spaced training is more effective than massed training. Ctx-IF can be completed in ∼1 week and provides an opportunity to study the molecular mechanisms and circuitry underlying non-homeostatic eating. We have used this paradigm to map brain regions that are activated during Ctx-IF with cFos immunohistochemistry and found that the insular cortex, and other regions, are activated following exposure to cues denoting the availability of food. Finally, we show that inhibition of the insular cortex using GABA agonists impairs performance of the task. Our findings provide a novel assay in mice for defining the functional neuroanatomy of appetitive conditioning and identify specific brain regions that are activated during the development of learned behaviors that impact food consumption.
Expression of epidermal and nerve growth factor receptors and soft agar growth factor production by human lung cancer cells. (1981)

Seventeen well-characterized human lung cancer cell lines were examined for the presence of specific membrane receptors for epidermal growth factor (EGF) and nerve growth factor (NGF) as well as for the production of diffusible factors capable of stimulating soft agar growth. These cell lines represented all four major histological types of human lung cancer including small cell carcinoma of the lung (SCCL) and the three types of non-SCCL (epidermoid, large cell, and adenocarcinoma). The SCCL lines included three lines referred to as "converters" because they had lost SCCL morphological and biochemical properties during prolonged passage in vitro. Specific receptors for EGF and NGF were detected by measuring the binding of 125I-radiolabeled growth factor to the cell surface. These assays revealed that EGF receptors are found on five of six non-SCCL cell lines and are not found on any of the SCCL lines. In contract, NGF binding was detected at low levels on three of eight SCCL lines and on all three SCCL converters but was not observed for non-SCCL lines. Thus, SCCL and SCCL converter cell lines are distinguished from non-SCCL by the pattern of membrane receptors for EGF and NGF. Such differences may ultimately prove useful as biological markers for the different histological types of lung cancer. Moreover, the majority of SCCL cells and all of the non-SCCL cells tested were found to produce diffusible growth factors which can stimulate soft agar growth of nontransformed normal rat kidney fibroblasts. Although some correlation between soft agar growth factor production and the absence of EGF receptors may exist for SCCL cells, the production of transforming growth factors appears to be a general property of human lung cancer cells in vitro and is independent of EGF receptor expression.
Measuring the impact of slow user motion on packet loss and delay over IEEE 802.11b wireless links (2004)

IEEE 802.11b compliant WLAN technology is increasingly used for cordless telephone services. Often, a WLAN phone is moved during a call. In the present paper we explore to what extent slow user motion influences the wireless link quality. We conducted extensive measurements with speech over commercial WLAN equipment using an experimental environment enforcing controlled motion. Our experiments show that - in contrast to the common assumption - an increase of motion speed can result in a better link quality: The packet loss rate and variance, measured after link-layer retransmissions, decreases. In addition, our measurements demonstrate that the modulation type, the maximal number of retransmissions, the experimental setting, and even the quality of power supply are the dominant influences on link quality.
Reconstruction filter suitable for lowpass delta-sigma RF transmitters (2013)

This paper proposes a highly selective bandpass filter suitable for lowpass delta-sigma RF transmitters. The proposed filter is characterized by a low insertion loss, high selectivity and a transfer function tailored for filtering the close-up out-of-band noise of lowpass delta-sigma transmitters. The circuit design is based on a modified stub-loaded ring resonator structure. The proposed filter has been implemented and the measurements show good agreement with simulation. The proposed filter provides a fractional 3-dB bandwidth of 14.6 %, an insertion loss of less than 1.3 dB, a suppression of more than 15 dB on both sides of desired band, and a sharp cut-off frequency response.
Enabling Cellular Communication for Aerial Vehicles: Providing Reliability for Future Applications (2020)

Due to safety concerns, a reliable radio communication link is a key component in the future application of unmanned aerial vehicles (UAVs), as it will enable beyond visual line-of-sight (BVLOS) operations. In terms of cost and deployment time, radio communication for aerial vehicles will greatly benefit from the ready-to-market infrastructure and ubiquitous coverage of cellular networks. However, these are optimized for terrestrial users, and the different propagation environment experienced by aerial vehicles poses some interference challenges. In this article, field measurements and system-level simulations are used to assess interferencemitigation solutions that can improve aerial-link reliability. We then discuss how 5 G New Radio (NR) favors the integration of UAVs into cellular networks, as its flexible air interface and beamforming-suited frequencies facilitate the deployment of interference-management solutions.
Effect of Flow Properties on Drillpipe Neutral Point (1989)

ABSTRACT For the past half century drilling engineers have been computing the required length of drill collars based upon a formula which assumes that the bouyed weight below the neutral point is equal to the weight-on-the-bit (WOB). However, a theory developed in 1950 indicates that the neutral point changes in tubulars when the pressure on the inside wall is different from the outside pressure. Using this theory, this paper proves that the neutral point in drill pipe always moves up the drill string when the mud pump is turned on and it can even move up into the drill pipe. The worst conditions occur in shallow wells, with low WOB, high pump pressure using max jet impact force hydraulics.