gebhart/patrepeval huggingface dataset:
Distributions of NO, NO<sub><i>x</i></sub>, and NO<sub><i>y</i></sub> in the upper troposphere and lower stratosphere between 28° and 61°N during POLINAT 2 (2000)

During the Pollution From Aircraft Emissions in the North Atlantic Flight Corridor 2 (POLINAT 2) field campaign the distribution of NO, NO x , and NO y in the upper troposphere and lowermost stratosphere over the eastern North Atlantic was measured using the Deutsches Zentrum für Luft‐und Raumfahrt research aircraft Falcon. Based from Shannon Airport in Ireland, 14 flights were carried out between September 19 and October 25, 1997. The measurements were performed in and out of the North Atlantic flight corridor covering latitudes between 28°N and 61°N. A marked latitudinal gradient in NO, NO x , and NO y , the sum of all reactive nitrogen compounds, was observed. Mean NO volume mixing ratios in the upper troposphere increased from about 50 parts per trillion by volume (pptv) at 28°N to about 180 pptv at 59°N. A similar latitude dependence was also found for NO x and NO y . In the northern part of the POLINAT 2 measuring area, NO and NO x volume mixing ratios increased significantly with increasing altitude with maximum values around the tropopause, while in the southern part of the measuring area no strong altitude gradient was observed. NO and NO x did not show a substantial gradient across the tropopause. NO/NO y and NO y /O 3 ratios showed maximum values of about 0.30 ppbv/ppbv and 0.012 ppbv/ppbv, respectively, around the tropopause. The POLINAT 2 observations suggest that aircraft emissions are an important source of NO x and NO y in the region studied. Also, the present measurements contribute to the data set obtained in the North Atlantic flight corridor during the last few years and help to establish a NO x climatology around the tropopause for this region.
Biosynthesis and Secretion of Pituitary Hormones: Dynamics and Regulation (2002)

Production and secretion of hormones by the pituitary involve highly orchestrated intracellular transport and sorting steps. Hormone precursors are routed through a series of compartments before being packaged in secretory granules. These highly dynamic carriers play crucial roles in both prohormone processing and peptide exocytosis. We have employed the ACTH-secreting AtT-20 cell line to study the membrane sorting events that confer functionality (prohormone activation and regulated exocytosis) to these secretory carriers. The unique ability of granules to promote prohormone processing is attributed to their acidic interior. Using a novel avidin-targeted fluorescence ratio imaging technique, we have found that the trans-Golgi of live AtT-20 cells maintains a mildly acidic (approximately pH 6.2) interior. Budding of secretory granules causes the lumen to acidify to <pH 6.0, which is both necessary and sufficient to trigger SPC3-mediated proteolytic conversion of proopiomelanocortin to ACTH. Investigation of the pH regulatory mechanism indicates that the trans-Golgi and secretory granules maintain different pH values by distinct sorting of key membrane transporters. Mathematical modeling of our data suggests that the decreasing pH values of organelles of the regulated secretory pathway is established by gradually increasing the density of active H+ pumps from the ER to Golgi while concomitantly decreasing the H+ permeability from ER to Golgi to secretory granules. An in vitro assay was developed to study the formation of processing-competent secretory granules from their processing-incompetent precursor trans-Golgi compartment. Our data suggest that ARF1-mediated sorting of proton pumps and leaks during early stages of granule formation confers processing competency to the resulting organelle. Once formed, these young granules continue to undergo membrane remodeling which results in dynamic changes in their exocytotic behavior. Two SNAREs, VAMP4 and synaptotagmin IV, enter newly formed granules but are removed from the maturing granule membrane by vesicle budding. Sorting of these proteins is correlated with the acquisition of Ca2+-triggered exocytosis and a decrease in unregulated exocytotic rate. Thus, biosynthesis and secretion of pituitary hormones are dynamically regulated by intracellular sorting events that govern the functions of their secretory carriers.
Outer Membrane Proteins as a Carrier for Detoxified Lipooligosaccharide Conjugate Vaccines for Nontypeable<i>Haemophilus influenzae</i> (1999)

Nontypeable Haemophilus influenzae (NTHi) is a common cause of otitis media and respiratory tract infections. Outer membrane proteins (OMP) and lipooligosaccharide (LOS) are major surface antigens of NTHi and potential vaccine candidates. De-O-acylated LOS (dLOS) or oligosaccharide (OS) was coupled to total OMP to form dLOS-OMP and OS-OMP conjugates, while a dLOS-tetanus toxoid (TT) was synthesized for comparison. These conjugates were evaluated in mice and rabbits for immunogenicity. dLOS-OMP elicited a better boostable antibody response against LOS than did dLOS-TT, while OS-OMP was not immunogenic. Formulation of the conjugates with Ribi adjuvant significantly enhanced the immunogenicity of dLOS-OMP and dLOS-TT but not that of OS-OMP. In addition, rabbit antisera elicited by dLOS-OMP but not dLOS-TT (or OMP alone) demonstrated bactericidal activity against 40% of the NTHi strains tested. These results indicate that dLOS is a better derivative of LOS than OS and that OMP is a good carrier for NTHi LOS-based conjugate vaccines.
<title>Practical range camera calibration</title> (1993)

This paper presents a calibration procedure adapted to a range camera intended for space applications. The range camera, which is based upon an auto-synchronized triangulation scheme, can measure objects from about 0.5 m to 100 m. The field of view is 30 degree(s) X 30 degree(s). Objects situated at distances beyond 10 m can be measured with the help of cooperative targets. Such a large volume of measurement presents significant challenges to a precise calibration. A two-step methodology is proposed. In the first step, the close-range volume (from 0.5 m to 1.5 m) is calibrated using an array of targets positioned at known locations in the field of view of the range camera. A large number of targets are evenly spaced in that field of view because this is the region of highest precision. In the second step, several targets are positioned at distances greater than 1.5 m with the help of an accurate theodolite and electronic distance measuring device. This second step will not be discussed fully here. The internal and external parameters of a model of the range camera are extracted with an iterative nonlinear simultaneous least-squares adjustment method. Experimental results obtained for a close-range calibration suggest a precision along the x, y and z axes of 200 micrometers , 200 micrometers , and 250 micrometers , respectively, and a bias of less than 100 micrometers in all directions.
Electrochemical Oxidations of<i>p</i>-Doped Semiconducting Single-Walled Carbon Nanotubes (2016)

Two oxidation peaks at 0.99, 1.48 V versus Fc/Fc + appear in the cyclic voltammograms of a series of defect-site functionalized SWNTs in methylene chloride solution in the presence of ferrocenes. These two peaks are demonstrated to be the electrochemical responses to the independent oxidation of v 1 and v 2 valence bands of<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" id="M1"><mml:mrow><mml:mi>p</mml:mi></mml:mrow></mml:math>-doped semiconducting SWNTs.
Controlling biofouling of reverse osmosis membranes through surface modification via grafting patterned polymer brushes (2015)

Thin film composite (TFC) polyamide membranes are extensively used as selective barriers in reverse osmosis processes. The major challenge faced with TFC membranes is significant fouling on the surface, which restricts the overall purification performance. To address the fouling problem, we developed novel fouling-resistant surface coatings via polyelectrolyte [poly(allylamine hydrochloride)/poly(styrene sulfonate)] layer-by-layer self-assembly, functionalized with patterned antimicrobial and antifouling/fouling-release polymer brushes. Two types of different polymer brushes, among antimicrobial poly(quaternary ammonium), antifouling poly(sulfobetaine) and fouling-release poly(dimethylsiloxane) (PDMS), were selected and grafted in a checkerboard pattern, with a square feature of 2 µm. The successful patterning and incorporation of different polymer brushes on the membrane was confirmed through X-ray photoelectron spectroscopy analysis. Grafting with sulfobetaine and PDMS significantly increased the hydrophilicity and lowered the surface energy of the membrane, respectively. The fouling-resistant property of the modified membrane was evaluated via static protein (bovine serum albumin) deposition and bacterial (Escherichia coli) cell adhesion tests. Surface modifications proved to diminish protein adhesion and exhibited 70–93% reduction in bacterial cell attachment. This observation suggests that the modified membranes have strong antifouling properties that inhibit the irreversible adhesion of organic and bio-foulants on the membrane surface.
Half-Sandwich Iridium Complexes for Homogeneous Water-Oxidation Catalysis (2010)

Iridium half-sandwich complexes of the types Cp*Ir(N-C)X, [Cp*Ir(N-N)X]X, and [CpIr(N-N)X]X are catalyst precursors for the homogeneous oxidation of water to dioxygen. Kinetic studies with cerium(IV) ammonium nitrate as primary oxidant show that oxygen evolution is rapid and continues over many hours. In addition, [Cp*Ir(H(2)O)(3)]SO(4) and [(Cp*Ir)(2)(μ-OH)(3)]OH can show even higher turnover frequencies (up to 20 min(-1) at pH 0.89). Aqueous electrochemical studies on the cationic complexes having chelate ligands show catalytic oxidation at pH > 7; conversely, at low pH, there are no oxidation waves up to 1.5 V vs NHE for the complexes. H(2)(18)O isotope incorporation studies demonstrate that water is the source of oxygen atoms during cerium(IV)-driven catalysis. DFT calculations and kinetic experiments, including kinetic-isotope-effect studies, suggest a mechanism for homogeneous iridium-catalyzed water oxidation and contribute to the determination of the rate-determining step. The kinetic experiments also help distinguish the active homogeneous catalyst from heterogeneous nanoparticulate iridium dioxide.
3′,4′‐Dihydroxyflavonol reduces infarct size and injury associated with myocardial ischaemia and reperfusion in sheep (2004)

1 The antioxidant properties of flavonols in vivo and their potential benefits in myocardial ischaemia/reperfusion (I/R) injury have been little investigated. We evaluated the ability of a synthetic flavonol, 3',4'-dihydroxyflavonol (DiOHF) to scavenge superoxide in post-I/R myocardium and to prevent myocardial I/R injury. 2 Anaesthetized sheep were studied in four groups (n=5-6): control, ischaemic preconditioning (IPC), vehicle and DiOHF (before reperfusion, 5 mg kg(-1), i.v.). The left anterior descending coronary artery was occluded distal to the second diagonal branch for 1 h followed by 2 h of reperfusion. Infarct size, myocardial function, NADPH-activated superoxide generation and biochemical markers of injury were measured. 3 DiOHF (10(-8)-10(-4) m) incubated in vitro with post-I/R myocardium from the vehicle group suppressed superoxide production dose-dependently. 4 DiOHF administered in vivo also significantly reduced superoxide generation in vitro. DiOHF and IPC markedly reduced infarct size, which was 73+/-2% of the area at risk in vehicle, 50+/-4% in DiOHF, 75+/-5% in control and 44+/-4% in IPC. Post-I/R segment shortening within the ischaemic zone was greater in DiOHF (2.3+/-0.7%; P<0.01) and IPC (1.7+/-0.5%; P<0.01) than those in corresponding controls (-1.7+/-0.4; -2.1+/-0.4%). 5 DiOHF and IPC improved coronary blood flow to the ischaemic area and preserved higher levels of nitric oxide metabolites in the venous outflow from the ischaemic zone. 6 DiOHF attenuated superoxide production in post-I/R myocardium, and significantly reduced infarct size and injury following I/R in anaesthetized sheep. The extent of protection by DiOHF is comparable to that afforded by IPC. Thus, DiOHF has clinical potential for improving recovery from acute myocardial infarction and other ischaemic syndromes.
Supporting Lists in a Data Model (A Timely Approach) (1992)

This paper considers the problem of adding list as a type constructor to an object-oriented data model. In particular, we are concerned with how lists in a database can be constructed and how they can be queried. We propose that operators from a discrete, linear-time temporal logic provide a natural basis for making assertions about the ordering of elements in a list. We then show how such assertions may be incor-porated into a query algebra by extending the Melam-pus Data Model (MDM) with a list type constructor and by allowing temporal assertions as predicates on lists. The extended algebra allows the expression of a significantly larger class of queries than previously possible. Furthermore, temporal operators provide a basis for creating new lists that satisfy desired order-ing properties. For example, sorting is shown to fall out as a special case. This paper also describes a new framework based on Boolean circuits for evaluating the truth of an assertion on a given list. This framework provides many opportunities for optimization and par-allelism, and it lends insight to the meaning and com-plexity of a temporal formula.
Asparagine residue in the rho Gene Product Is the Modification Site for Botulinum ADP-ribosyltransferase (1989)

We reported previously that the ADP-ribosyltransferase in C1 and D botulinum toxins specifically catalyzes ADP-ribosylation of an Mr 22,000 guanine nucleotide-binding protein and that this substrate named Gb (b = botulinum) has an amino acid sequence homologous to that deduced from the rho gene (Narumiya, S., Sekine, A., and Fujiwara, M. (1988) J. Biol. Chem. 263, 17255-17257). In this study we have determined the amino acid sequence at its ADP-ribosylation site. Purified substrate was [32P]ADP-ribosylated by C1 botulinum toxin and digested with trypsin. The radioactive peptides were isolated by reversed-phase high performance liquid chromatography and digested further either with protease V8, with proteases V8 and thermolysin, or with proline endopeptidase and thermolysin. By this procedure three radioactive peptides were obtained, and their amino acid sequences were X-Tyr-Val-Ala-Asp-Ile-Glu, X-Tyr, and Val-Phe-Glu-X-Tyr in which no amino acid peak was found in X. During the sequencing the radioactivity quantitatively adhered to the sequencing filter and was not eluted with either of the identified amino acid residues. Analysis of the protein without the ADP-ribosylation yielded the corresponding sequence as Thr-Val-Phe-Glu-Asn-Tyr which corresponds to Thr37-Tyr42 in the amino acid sequence deduced from the Aplysia rho gene. These results strongly suggest that the asparagine residue is the ADP-ribosylation site in the rho gene product. This ADP-ribose protein bond was stable in 0.5 M hydroxylamine at pH 7.5 at 37 degrees C for at least 5 h. The ADP-ribosylation of this protein affected neither its GTPase- nor its [35S]guanosine 5'-O-thiotriphosphate-binding activity.
Development of a planar immunoFET which detects protein analyte in high salt environments (2010)

Electrochemical detection of protein binding at physiological salt concentration by planar field effect transistor (FET) platforms has yet to be documented convincingly.In fact, use of immunologically modified FET sensors (immunoFETs) for in vivo detection of proteins has been dismissed as infeasible due to a classical analysis carried out nearly 20 years ago.Despite numerous conceptual flaws, this model has taken hold as dogma in the FET sensing field and stalled the development of FET-based sensing platforms for in vivo protein detection.In this work, the flaws in this classical analysis, approaches for addressing this model and demonstrating feasibility of immunoFET sensing in physiologic environments are first discussed and proposed.Successful love you and will be eternally grateful for all you"ve done for me.To my brother Savesh who in such a short time gave me a lifetime"s worth of lessons that I still am learning from today.To all my uncles and aunts in Dayton for all the love, endless food, and support you"ve given me since I"ve been in Ohio.A special thanks to Chachaji and Chachiji for giving me a place to call home whenever I wanted to.To all my cousins for being there for me these last few years, especially to Kapish, Anju, Puja, Vicky, Maneesh, Kamna, Angela, Anu and Ashish.Thank you to my wife, Sneha, for saying "yes" three years ago and joining me at Ohio State.I couldn"t have asked for a more supportive and loving partner to go through grad school with.Thank you to Rajam Ammai for raising such a beautiful person, and welcoming me into your family
The KaffeOS Java runtime system (2005)

Single-language runtime systems, in the form of Java virtual machines, are widely deployed platforms for executing untrusted mobile code. These runtimes provide some of the features that operating systems provide: interapplication memory protection and basic system services. They do not, however, provide the ability to isolate applications from each other. Neither do they provide the ability to limit the resource consumption of applications. Consequently, the performance of current systems degrades severely in the presence of malicious or buggy code that exhibits ill-behaved resource usage. We show that Java runtime systems can be extended to support processes , and that processes can provide robust and efficient support for untrusted applications.We have designed and built KaffeOS, a Java runtime system that provides support for processes. KaffeOS isolates processes and manages the physical resources available to them: CPU and memory. Unlike existing Java virtual machines, KaffeOS can safely terminate processes without adversely affecting the integrity of the system, and it can fully reclaim a terminated process's resources. Finally, KaffeOS requires no changes to the Java language. The novel aspects of the KaffeOS architecture include the application of a user/kernel boundary as a structuring principle for runtime systems, the employment of garbage collection techniques for resource management and isolation, and a model for direct sharing of objects between untrusted applications. The difficulty in designing KaffeOS lay in balancing the goals of isolation and resource management against the goal of allowing direct sharing of objects.For the SpecJVM benchmarks, the overhead that our KaffeOS prototype incurs ranges from 0% to 25%, when compared to the open-source JVM on which it is based. We consider this overhead acceptable for the safety that KaffeOS provides. In addition, our KaffeOS prototype can scale to run more applications than running multiple JVMs. Finally, in the presence of malicious or buggy code that engages in a denial-of-service attack, KaffeOS can contain the attack, remove resources from the attacked applications, and continue to provide robust service to other clients.
Rhinovirus induces an anabolic reprogramming in host cell metabolism essential for viral replication (2018)

Rhinoviruses (RVs) are responsible for the majority of upper airway infections; despite their high prevalence and the resulting economic burden, effective treatment is lacking. We report here that RV induces metabolic alterations in host cells, which offer an efficient target for antiviral intervention. We show that RV-infected cells rapidly up-regulate glucose uptake in a PI3K-dependent manner. In parallel, infected cells enhance the expression of the PI3K-regulated glucose transporter GLUT1. In-depth metabolomic analysis of RV-infected cells revealed a critical role of glucose mobilization from extracellular and intracellular pools via glycogenolysis for viral replication. Infection resulted in a highly anabolic state, including enhanced nucleotide synthesis and lipogenesis. Consistently, we observed that glucose deprivation from medium and via glycolysis inhibition by 2-deoxyglucose (2-DG) potently impairs viral replication. Metabolomic analysis showed that 2-DG specifically reverts the RV-induced anabolic reprogramming. In addition, treatment with 2-DG inhibited RV infection and inflammation in a murine model. Thus, we demonstrate that the specific metabolic fingerprint of RV infection can be used to identify new targets for therapeutic intervention.
Linear Pulse Propagation in an Absorbing Medium (1982)

The pulse velocity in the linear regime in samples of GaP: N with a laser tuned to the bound $A$-exciton line is measured with use of a picosecond time-of-flight technique. The pulse is seen to propagate through the material with little pulse-shape distortion, and with an envelope velocity given by the group velocity even when the group velocity exceeds 3\ifmmode\times\else\texttimes\fi{}${10}^{10}$ cm/sec, $\mathrm{equals}\ifmmode\pm\else\textpm\fi{}\ensuremath{\infty}$, or becomes negative. The results verify the predictions of Garrett and McCumber.
PseudoBase: structural information on RNA pseudoknots (2001)

PseudoBase is a database containing structural, functional and sequence data related to RNA pseudo-knots. It can be reached at http://wwwbio.LeidenUniv.nl/ approximately Batenburg/PKB.html. For each pseudoknot, thirteen items are stored, for example the relevant sequence, the stem positions of the pseudoknot, the EMBL accession number of the sequence and the support that can be given regarding the reliability of the pseudo-knot. Since the last publication, information on sizes of the stems and the loops in the pseudoknots has been added. Also added are alternative entries that produce surveys of where the pseudoknots are, sorted according to stem size or loop size.
From Smart to Cognitive Phones (2012)

As smartphones get smarter by pushing intelligence to the phone and computing cloud, they'll start to understand our life patterns, reason about our health and wellbeing, help us navigate our day, and intervene on our behalf. Here, the authors present various smartphone sensing systems that they've built, arguing that, eventually, these smartphones will evolve into cognitive phones.