gebhart/patrepeval huggingface dataset:
Chronic lung diseases (2009)

Chronic lung diseases often have high morbidity and mortality rate and have posed a serious threat to human health. The incidence of many chronic lung diseases such as asthma has been on the rise in the past decade, which causes serious economic burden. Despite many efforts which employed traditional experimental approaches to elucidate the mechanisms of the diseases have been made, little is known about the pathogenesis of complex lung diseases. Systems biology approaches which aim to integrate and analyze information gathered from multiple sources offer a great opportunity to examine complex human diseases from a new angle. Many attempts have been made using high-throughput technologies such as microarrays to study chronic lung diseases; although compared with the full-fledged systems biology approach, research strategies employed in most of these investigations still have much room to improve, promising findings have already emerged from these efforts, which demonstrates the potential of implementing systems biology in pulmonary biomedical research.
ChemInform Abstract: A Regiospecific Fluorination Strategy: Synthesis of (α‐ Fluoropropargyl)‐ and (α‐Fluoroallyl)phosphonate Esters. (1994)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Mapping and Quantification of Over 2000 O-linked Glycopeptides in Activated Human T Cells with Isotope-Targeted Glycoproteomics (Isotag) (2018)

Post-translational modifications (PTMs) on proteins often function to regulate signaling cascades, with the activation of T cells during an adaptive immune response being a classic example. Mounting evidence indicates that the modification of proteins by O-linked N-acetylglucosamine (O-GlcNAc), the only mammalian glycan found on nuclear and cytoplasmic proteins, helps regulate T cell activation. Yet, a mechanistic understanding of how O-GlcNAc functions in T cell activation remains elusive, partly because of the difficulties in mapping and quantifying O-GlcNAc sites. Thus, to advance insight into the role of O-GlcNAc in T cell activation, we performed glycosite mapping studies via direct glycopeptide measurement on resting and activated primary human T cells with a technique termed Isotope Targeted Glycoproteomics. This approach led to the identification of 2219 intact O-linked glycopeptides across 1045 glycoproteins. A significant proportion (>45%) of the identified O-GlcNAc sites lie near or coincide with a known phosphorylation site, supporting the potential for PTM crosstalk. Consistent with other studies, we find that O-GlcNAc sites in T cells lack a strict consensus sequence. To validate our results, we employed gel shift assays based on conjugating mass tags to O-GlcNAc groups. Notably, we observed that the transcription factors c-JUN and JUNB show higher levels of O-GlcNAc glycosylation and higher levels of expression in activated T cells. Overall, our findings provide a quantitative characterization of O-GlcNAc glycoproteins and their corresponding modification sites in primary human T cells, which will facilitate mechanistic studies into the function of O-GlcNAc in T cell activation.
Free-text speaker identification over long distance telephone channel using hypothesized phonetic segmentation (1992)

Experimental investigation of a free-text speaker identification method based on long-term statistics was conducted on a widely used long-distance telephone database. On a 26-speaker subset, an average correct identification of 93.3% was obtained; on the complete 51-speaker set, 67.6% correct identification is obtained. Speaker verification experiments on the database provided receiver operating characteristics (ROCs) comparable to or better than the ones available in open literature.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Technologies and Approaches to Elucidate and Model the Virulence Program of Salmonella (2011)

Salmonella is a primary cause of enteric diseases in a variety of animals. During its evolution into a pathogenic bacterium, Salmonella acquired an elaborate regulatory network that responds to multiple environmental stimuli within host animals and integrates them resulting in fine regulation of the virulence program. The coordinated action by this regulatory network involves numerous virulence regulators, necessitating genome-wide profiling analysis to assess and combine efforts from multiple regulons. In this review we discuss recent high-throughput analytic approaches used to understand the regulatory network of Salmonella that controls virulence processes. Application of high-throughput analyses have generated large amounts of data and necessitated the development of computational approaches for data integration. Therefore, we also cover computer-aided network analyses to infer regulatory networks, and demonstrate how genome-scale data can be used to construct regulatory and metabolic systems models of Salmonella pathogenesis. Genes that are coordinately controlled by multiple virulence regulators under infectious conditions are more likely to be important for pathogenesis. Thus, reconstructing the global regulatory network during infection or, at the very least, under conditions that mimic the host cellular environment not only provides a bird's eye view of Salmonella survival strategy in response to hostile host environments but also serves as an efficient means to identify novel virulence factors that are essential for Salmonella to accomplish systemic infection in the host.
Langmuir Parameters Prediction: New Insights into the Porosity of the Nanoporous Media of Organic Media of Organic-Rich Shale (2022)

Abstract Shale is a type of unconventional reservoir with a significant potential for storing natural gas attributed to its ability to host hydrocarbons as both free and sorbed phases. However, modeling this multi-physics storage capacity requires redefining some macroscopic parameters such as the porosity to capture the adsorption behavior and pore compressibility, which changes over the entire production life of the asset. Besides, a distinct confining stress phenomenon occurs in a reservoir with a different faulting system and degree of stress heterogeneity. Such mechanisms at nanoscale are complex and difficult to isolate through conventional experimental approaches. Alternatively, computational frameworks like molecular simulation can provide a proxy to accurately describe such intervening mechanisms. The study starts with recreating realistic organic matter structures from a given macromolecule kerogen unit using a molecular dynamics protocol. The created structures were subject to adsorption analysis and mechanical properties assessment while tracking the changes in porosity and pore size distribution. The analyses were used to redefine the porosity considering the adsorption behavior, mechanical properties, pore, and confining pressures. Furthermore, a correlation between stress-induced porosity and Langmuir quantities was developed to predict the Langmuir parameters. The logarithmic function-based model showed that a 33.3% change in stress-dependent kerogen porosity could result in a Langmuir amount, pressure and maximum adsorbed gas density variation of around 100%, 100%, and 50% respectively. Consequently, nanoporosity influence on Langmuir parameters should be critically understood as it plays a significant role in adsorbed gas storage and molecular transport processes in organic-rich shale.
Time-Domain Observation of the Spinmotive Force in Permalloy Nanowires (2012)

The spinmotive force associated with a moving domain wall is observed directly in Permalloy nanowires using real time voltage measurements with proper subtraction of the electromotive force. Whereas the wall velocity exhibits nonlinear dependence on magnetic field, the generated voltage increases linearly with the field. We show that the sign of the voltage reverses when the wall propagation direction is altered. Numerical simulations explain quantitatively these features of spinmotive force and indicate that it scales with the field even in a field range where the wall motion is no longer associated with periodic angular rotation of the wall magnetization.
A survey of lower layer technologies for Vehicle-to-Vehicle communication (2009)

Vehicle-to-Vehicle (V2V) communication is an evolving research field that has potential to augment safety on our roads. Safety focused V2V communication also offers convenience and commercial applications in order to enhance driving comfort and pleasure. V2V communication demonstrates unique characteristics and consequently reliable network access has become crucial to exploit a wide spectrum of applications. Development of complex networking protocols, ingenious medium access control (MAC) techniques and robust communication technology are the main challenges to reliable and pragmatic V2V communication. This paper provides survey of lower layer technologies proposed for V2V communication and concludes with analytical summary drawn from the survey.
One-step synthesis of nanocrystalline transition metal oxides on thin sheets of disordered graphitic carbon by oxidation of MXenes (2014)

Herein we show that heating 2D Ti3C2 in air results in TiO2 nanocrystals enmeshed in thin sheets of disordered graphitic carbon structures that can handle extremely high cycling rates when tested as anodes in lithium ion batteries. Oxidation of 2D Ti3C2 in either CO2 or pressurized water also resulted in TiO2-C hybrid structures. Similarly, other hybrids can be produced, as we show here for Nb2O5/C from 2D Nb2C.
Dielectric Strength of Sub-Millimeter Water Gaps Subjected to Microsecond and Sub-Microsecond Voltage Pulses (2005)

To move high energy pulsed power systems from the laboratory to practice requires the development of compact lightweight drivers. To reduce the size and weight of high voltage components, an increase in the energy density in dielectrics at high electric stress is required. Water, which has a dielectric constant of epsiv = 80 and high dielectric strength, can be used for both energy storage and for switching. To date, most of the studies of breakdown in water have been conducted for relatively wide gaps. Empirical equations for the breakdown strength under these conditions were developed by J. C. Martin [1]. In this paper, sub-millimeter water gaps were studied for applied pulses of microsecond duration and compared to gaps subjected to sub-microsecond pulses. A pin-plane electrode configuration was used. The pin electrode exhibits a hemispherical geometry with a diameter of 1.7 mm. The gap distance between the electrodes is variable but was set to 200 mum in the experiments reported in this paper. In the case of short pulses (20 ns, 50 ns, 100 ns and 200 ns) a Blumlein type pulse-forming line was used. For the longer pulses of 1 mus, 3 mus and 4.8mus, a Blumlein type pulse forming network (PFN) was employed. It was found that for sub-millimeter gaps with the pin-electrode as anode, and when the pulse width is within the microsecond range, the dielectric strength of water remained almost independent of the pulse width. However, when the pulse width was decreased to the sub- microsecond range, the dielectric strength increased as the pulse width decreased. This trend is consistent with Martin's empirical formulas except that the breakdown voltage values were about two times higher than predicted. In contrast, when the pin-electrode was used as cathode, the experimental results were in better agreement with those calculated using the empirical formulas.
dnaG (primase)-dependent origins of DNA replication. Nucleotide sequences of the negative strand initiation sites of bacteriophages St-1, phi K, and alpha 3. (1979)

The simplest known origins of DNA replication occur in the single-stranded bacteriophages. In one set of phages, negative strand synthesis is initiated by a single protein, the product of the Escherichia coli replication gene dnaG. Evidently, in these phages--G4, St-1, phi K, and alpha 3--the origin for negative strand synthesis consists of a nucleic acid element capable of direct recognition by the dnaG priming protein. We have located and sequenced the origins of negative strand synthesis in St-1, phi K, and alpha 3, and compared them with the origin sequence previously determined for G4. In each case, the point at which the negative strand is initiated can be identified at the nucleotide level. The data lead to the following conclusions: 1. In all four phages, the negative strand initiation site occurs within an intercistronic region of approximately 135 bases. While in G4, the origin lies between genes specifying the viral coat proteins F and G, the origin is shifted in St-1, phi K, and alpha 3 to a position between coat protein genes G and H. 2. Extensive nucleotide conservation exists at the negative strand origin, but does not extend into the adjacent coding regions. The conserved origin DNA occurs in two regions, 42 and 45 bases long, which are separated by 13 bases of divergent sequence. 3. Correlated with the two stretches of conserved nucleotide sequence are two regions of potential secondary structure. The start point of negative strand synthesis lies just prior to one of these hairpins. Similarities in both primary sequence and secondary structure can be found between the negative strand origins of G4, St-1, phi K, and alpha 3 and the general origin regions of bacteriophage lambda and of E. coli.
Synthesis of Cribrostatin 6 and Its Related Compounds (2006)

The synthesis of cribrostatin 6 (1), which shows good biological activity as a dark blue cancer cells growth inhibitor and a number of pathogenic bacteria and fungi, was achieved in two steps from 1-acetylaminomethyl-5,7-diethoxy-8-hydroxy-6-methylisoquinoline ( 14).The related compounds (8~11) were also synthesized, and the antimicrobial activities of 1 and its nine
Detection of the multidrug resistance of P-glycoprotein in healthy tissues: the example of the blood-brain barrier. (1996)

The blood-brain barrier is formed by the cerebral capillary endothelial cells, joined together by tight junctions. These cells express the general endothelial cell markers as well as specific markers found on endothelial cells forming physiological barriers such as gamma-glutamyltranspeptidase, the glucose transporter Glut1 and the neutral amino-acid transporter. Using the monoclonal antibodies C219 and MRK16, we have revealed by Western blot and immuno-histochemistry the expression of the multidrug resistance P-glycoprotein on isolated rat cerebral cortex capillaries. On the other hand, P-glycoprotein was not detectable in brain cortex homogenates. P-glycoprotein thus appears to be a blood-brain barrier endothelium-specific marker which could regulate brain penetration of xenobiotics and thus participate in the neuroprotection of the brain.
Towards Self-Powering Touch/Flex-Sensitive OLED Systems (2011)

In this work, we present a novel design for an organic light-emitting system integrated with a mechanical energy harvesting and energy storage polymer films (patent pending). The system is configured into multiple stacked layers to form a thin, flexible, and lightweight assembly. The thin “film-like” device can be deformed and flexed to generate energy up to 0.5 mW within 100 s with ease. This platform technology finds applications in energy harvesting displays, electronic papers, key-input-pads, novel packaging, smart-IDs, disposable lab-on-a-chip optomicrofluidic systems, and much more. Results on the energy storage characteristics of the ionic polymer-metal composite film, the performance of a polyfluorene-based organic light-emitting device, and the mechanical energy transduction of the piezoelectric polymer energy harvester are presented. The polymeric nature of this platform system further makes it suitable for roll-to-roll print manufacturing, supporting applications requiring high volume and low cost.
Characterisation of Electroless Deposited Cobalt by Hard and Soft X-ray Photoemission Spectroscopy (2018)

Electroless deposited (ELD) cobalt with palladium as a catalyst, and an underlying self-assembled monolayer (SAM) was investigated for potential use in advanced complementary metal oxide semiconductor (CMOS) applications using both hard (HAXPES) and soft (XPS) x-ray photoelectron spectroscopy. HAXPES spectra established the uniformity of the deposited Co film and the nature of the buried Co-Si interface ~20nm below the surface. The Pd is seen to diffuse through the Co following thermal annealing. While the deposited Co film is predominantly metallic, Co-silicide forms at the Co-Si interface upon deposition and decomposes with thermal anneal up to 500°C.
Functional Cross-modulation between SOCS Proteins Can Stimulate Cytokine Signaling (2006)

SOCS (suppressors of cytokine signaling) proteins are negative regulators of cytokine signaling that function primarily at the receptor level. Remarkably, in vitro and in vivo observations revealed both inhibitory and stimulatory effects of SOCS2 on growth hormone signaling, suggesting an additional regulatory level. In this study, we examined the possibility of direct cross-modulation between SOCS proteins and found that SOCS2 could interfere with the inhibitory actions of other SOCS proteins in growth hormone, interferon, and leptin signaling. This SOCS2 effect was SOCS box-dependent, required recruitment of the elongin BC complex, and coincided with degradation of target SOCS proteins. Detailed mammalian protein-protein interaction trap (MAPPIT) analysis indicated that SOCS2 can interact with all members of the SOCS family. SOCS2 may thus function as a molecular bridge between a ubiquitin-protein isopeptide ligase complex and SOCS proteins, targeting them for proteasomal turnover. We furthermore extended these observations to SOCS6 and SOCS7. Our findings point to a unique regulatory role for SOCS2, SOCS6, and SOCS7 within the SOCS family and provide an explanation for the unexpected phenotypes observed in SOCS2 and SOCS6 transgenic mice.
Power control in wireless CDMA: performance with cell site antenna arrays (2002)

To combat the near-far problem, tight power control is essential in the use of direct sequence code division multiple access (DS/CDMA) communication systems. Recently, antenna arrays and adaptive beamforming at base station were proposed for improving system performance. This paper studies the closed loop power control (CLPC) performance with antenna arrays (AA) and adaptive beamforming through a combination of analysis and discrete event simulations. Our results show that with small angle spread, adaptive beamforming with AA has little effect on the CLPC performance. However, with larger angle spread, better performance is obtained due to space diversity.
Artificial Intelligence: Research Impact on Key Industries; the Upper-Rhine Artificial Intelligence Symposium (UR-AI 2020) (2020)

The TriRhenaTech alliance presents a collection of accepted papers of the cancelled tri-national 'Upper-Rhine Artificial Inteeligence Symposium' planned for 13th May 2020 in Karlsruhe. The TriRhenaTech alliance is a network of universities in the Upper-Rhine Trinational Metropolitan Region comprising of the German universities of applied sciences in Furtwangen, Kaiserslautern, Karlsruhe, and Offenburg, the Baden-Wuerttemberg Cooperative State University Loerrach, the French university network Alsace Tech (comprised of 14 'grandes écoles' in the fields of engineering, architecture and management) and the University of Applied Sciences and Arts Northwestern Switzerland. The alliance's common goal is to reinforce the transfer of knowledge, research, and technology, as well as the cross-border mobility of students.
Measurement and Modeling of a Complete Optical Absorption and Scattering by Coherent Surface Plasmon-Polariton Excitation Using a Silver Thin-Film Grating (2012)

We demonstrate the plasmonic analogue of a coherent photonic effect known as coherent perfect absorption. A periodically nanopatterned metal film perfectly absorbs multiple coherent light beams coupling to a single surface plasmon mode. The perfect absorbing state can be switched to a nearly perfect scattering state by tuning the phase difference between the incident beams. We theoretically explain the plasmonic coherent perfect absorption by considering time-reversal symmetry of surface plasmon amplification by stimulated emission of radiation. We experimentally demonstrate coherent control of the plasmonic absorption in good agreement with a coupled-mode theory of dissipative resonances. Associated potential applications include absorption-based plasmonic switches, modulators, and light-electricity transducers.
Genuine open form of the pentameric ligand-gated ion channel GLIC (2015)

Pentameric ligand-gated ion channels (pLGICs) mediate fast chemical neurotransmission of nerve signalling in the central and peripheral nervous systems. GLIC is a bacterial homologue of eukaryotic pLGIC, the X-ray structure of which has been determined in three different conformations. GLIC is thus widely used as a model to study the activation and the allosteric transition of this family of receptors. The recently solved high-resolution structure of GLIC (2.4 Å resolution) in the active state revealed two bound acetate molecules in the extracellular domain (ECD). Here, it is shown that these two acetates exactly overlap with known sites of pharmacological importance in pLGICs, and their potential influence on the structure of the open state is studied in detail. Firstly, experimental evidence is presented for the correct assignment of these acetate molecules by using the anomalous dispersion signal of bromoacetate. Secondly, the crystal structure of GLIC in the absence of acetate was solved and it is shown that acetate binding induces local conformational changes that occur in strategic sites of the ECD. It is expected that this acetate-free structure will be useful in future computational studies of the gating transition in GLIC and other pLGICs.
Large-Scale 2D Spin-Based Quantum Processor with a Bi-Linear Architecture (2021)

Here, we propose a bi-linear 2D device architecture for the demonstration of large-scale silicon-based quantum computers. Based on extensive modeling of the structure with multiphysics techniques, we report critical dimensions, quantum gate times, fidelities, and quantum-chip resources for error correction. The design is compact, can be realized with current CMOS fabrication technology, and allows planar integration of the control lines for the quantum bits, thereby providing a straightforward route for large-scale silicon quantum computers.
Non intrusive Polynomial Chaos-based stochastic macromodeling of multiport systems (2014)

We present a novel technique to efficiently perform the variability analysis of electromagnetic systems. The proposed method calculates a Polynomial Chaos-based macromodel of the system transfer function that includes its statistical properties. The combination of a non-intrusive Polynomial Chaos approach with the Vector Fitting algorithm allows to describe the system variability features with accuracy and efficiency. The results of the variability analysis performed with the proposed method are verified by means of comparison with respect to the standard Monte Carlo analysis.