gebhart/patrepeval huggingface dataset:
Comparative analysis of plant immune receptor architectures uncovers host proteins likely targeted by pathogens (2016)

We have built a robust reproducible pipeline for detecting variable domain architectures in plant immune receptors across species. We hypothesize that NLR-IDs that we revealed provide clues to the host proteins targeted by pathogens, and that this information can be deployed to discover new sources of disease resistance.
Novel diffractive feedback structures for semiconducting polymer lasers (2005)

Semiconducting conjugated polymers have recently attracted significant interest as amplifying media for solid-state lasers due to their functional photo-physical properties and simple fabrication. Distributed feedback (DFB) cavities are proving to be the most attractive for polymer lasers, since they can combine the properties of transverse optical pumping, low threshold and practical output beams. To date, in most polymer DFB lasers the feedback is provided by second order diffraction. This has the advantage of surface emission, though it also imposes extensive scattering losses. In this work, we present the use of alternative structures that attempt to reduce the threshold of polymer DFB lasers, and also achieve dual wavelength operation. The former was addressed with cavities formed by alternative symmetries of the Brillouin zone of a square lattice. Using the diagonal &#915;M symmetry first order feedback was attained. The threshold energy was thus reduced by almost an order of magnitude as compared with the more commonly used &#915;X symmetry of second order square gratings. Finally, we show that two lasing wavelengths may be set independently in a semiconducting polymer laser by using a doubly periodic (i.e. Moiré) DFB grating.
Modeling of Deterministic Output Emissions of Power Amplifiers Into Adjacent Receive Bands (2015)

This paper discusses the measurement and modeling of the deterministic components of power amplifier (PA) emissions into neighboring receive (Rx) bands caused by PA nonlinearity, and proposes ways to distinguish these components from stochastic components. A method is presented to determine the orders of nonlinearity that are the principal contributors to the Rx band emissions. A Volterra-based model for their estimation is proposed, along with considerations for estimation accuracy. A criterion based on the matrix condition number for efficient pruning of the Volterra-based models is also presented. The proposed techniques are verified with measurements. The proposed model can be used to gain a deeper understanding of the nonlinearity mechanisms responsible for PA spurious emissions, and offers the possibility of canceling the deterministic components to improve receiver sensitivity.
Relationship between streamwise and azimuthal length scales in a turbulent pipe flow (2017)

The statistical relationships among the turbulence structures of the streamwise velocity fluctuations along the streamwise and azimuthal directions in a turbulent pipe flow were examined using direct numerical simulation data at Reτ = 3008. Two-point correlations of the streamwise velocity fluctuations showed a linear relationship between the streamwise and azimuthal length scales (lx and lθ), where lθ/lx = 0.07 along the wall-normal distance, indicating the long coherent structures called very-large-scale motions (VLSMs). The one-dimensional pre-multiplied energy spectra of the streamwise velocity fluctuations showed that the streamwise and the azimuthal wavelengths (λx and λθ) grew linearly along the wall-normal distance, λx/y = 20 and λθ/y = 7, respectively. The ratio between the two linear relationships was determined to be λθ/λx = 0.35, indicative of large-scale motions (LSMs). The energetic modes obtained from a proper orthogonal decomposition (POD) analysis using the translational invariance method showed that the averaged helical angles of the wall mode (ix &amp;lt; iθ; β &amp;lt; 0.1 rad, where ix and iθ are the streamwise and azimuthal mode numbers and β is the helical angle) and lift mode (ix ≥ iθ; β ≥ 0.1 rad) were related to lθ/lx = 0.07 (VLSMs) and λθ/λx ≈ 0.35 (LSMs), respectively. The superposition of the energetic POD modes showed the superimposed X-shaped patterns. The helical angle of the wall mode in the near-wall region was similar to that in the outer region, implying the existence of the VLSMs in the entire wall-normal distance. The LSMs showed more inclined X-shaped patterns. The LSMs were concatenated with the azimuthal offsets to form meandering VLSMs. Most of the VLSMs and LSMs in the near-wall region inclined smaller and larger than 10° (0.17 rad), respectively. In the core region, VLSMs were distributed more helically along the azimuthal direction due to the space limitations of the pipe geometry.
ChemInform Abstract: Gadolinium(III) Chelates as MRI Contrast Agents: Structure, Dynamics, and Applications (1999)

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.
Hardness and approximation of Gathering in static radio networks (2006)

In this paper, we address the problem of gathering information in a central node of a radio network, where interference constraints are present. We take into account the fact that, when a node transmits, it produces interference in an area bigger than the area in which its message can actually be received. The network is modeled by a graph; a node is able to transmit one unit of information to the set of vertices at distance at most d <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">T</sub> in the graph, but when doing so it generates interference that does not allow nodes at distance up to d <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">I</sub> (d <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">I</sub> ges d <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">T</sub> ) to listen to other transmissions. Time is synchronous and divided into time-steps in each of which a round (set of non-interfering radio transmissions) is performed. We give a general lower bound on the number of rounds required to gather on any graph, and present an algorithm working on any graph, with an approximation factor of 4. We also show that the problem of finding an optimal strategy for gathering (one that uses a minimum number of time-steps) does not admit a fully polynomial time approximation scheme if d <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">I</sub> > d <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">T</sub> , unless P=NP, and in the case d <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">I</sub> = d <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">T</sub> the problem is NP-hard
Visible light‐induced photodeoxygenation of polycyclic selenophene Se‐oxides (2020)

Abstract Photodeoxygenation of dibenzothiophene S ‐oxide (DBTO) is believed to produce ground‐state atomic oxygen [O( 3 P)] in solution. Compared with other reactive oxygen species (ROS), O( 3 P) is a unique oxidant as it is potent and selective. Derivatives of DBTO have been used as O( 3 P)‐precursors to oxidize variety of molecules, including plasmid DNA, proteins, lipids, thiols, and other small organic molecules. Unfortunately, the photodeoxygenation of DBTO requires ultraviolet irradiation, which is not an ideal wavelength range for biological systems, and has a low quantum yield of approximately 0.003. In this work, benzo[ b ]naphtho[1,2‐ d ]selenophene Se ‐oxide, benzo[ b ]naphtho[2,1‐ d ]selenophene Se ‐oxide, dinaphtho[2,3‐ b :2’,3’‐ d ]selenophene Se ‐oxide, and perylo[1,12‐ b,c,d ]selenophene Se ‐oxide were synthesized, and their ability to utilize visible light for generating O( 3 P) was interrogated. Benzo[ b ]naphtho[1,2‐ d ]selenophene Se ‐oxide produces O( 3 P) upon irradiation centered at 420 nm. Additionally, benzo[ b ]naphtho[1,2‐ d ]selenophene Se ‐oxide, benzo[ b ]naphtho[2,1‐ d ]selenophene Se ‐oxide, and dinaphtho[2,3‐ b :2’,3’‐ d ]selenophene Se ‐oxide produce O( 3 P) when irradiated with UVA light and have quantum yields of photodeoxygenation ranging from 0.009 to 0.33. This work increases the utility of photodeoxygenation by extending the range of wavelengths that can be used to generate O( 3 P) in solution.
Friendscope: Exploring In-the-Moment Experience Sharing on Camera Glasses via a Shared Camera (2022)

We introduce Friendscope, an instant, in-the-moment experience sharing system for lightweight commercial camera glasses. Friendscope explores a new concept called a shared camera. This concept allows a wearer to share control of their camera with a remote friend, making it possible for both people to capture photos/videos from the camera in the moment. Through a user study with 48 participants, we found that users felt connected to each other, describing the shared camera as a more intimate form of livestreaming. Moreover, even privacy-sensitive users were able to retain their sense of privacy and control with the shared camera. Friendscope's different shared camera configurations give wearers ultimate control over who they share the camera with and what photos/videos they share. We conclude with design implications for future experience sharing systems.
Localization of the human dihydrolipoamide dehydrogenase gene (DLD) to 7q31→q32 (1991)

The gene for human dihydrolipoamide dehydrogenase (DLD) has been localized to the long arm of chromosome 7, within bands q31→q32, by gel-blot hybridization analysis with DNA from a panel of somatic cell hybrids containing various portions of human chromosome 7.
Selfish Response to Epidemic Propagation (2012)

An epidemic that spreads in a network calls for a decision on the part of the network users. They have to decide whether to protect themselves or not. Their decision depends on the tradeoff between the perceived infection and the protection cost. Aiming to help users reach an informed decision, security advisories provide periodic information about the infection level in the network. We study the best-response dynamic in a network whose users repeatedly activate or de-activate security, depending on what they learn about the infection level. Our main result is the counterintuitive fact that the equilibrium level of infection increases as the users' learning rate increases. The same is true when the users follow smooth best-response dynamics, or any other continuous response function that implies higher probability of protection when learning a higher level of infection. In both cases, we characterize the stability and the domains of attraction of the equilibrium points. Our finding also holds when the epidemic propagation is simulated on human contact traces, both when all users are of the same best-response behavior type and when they are of two distinct behavior types.
Paracrine regulation of mammalian oocyte maturation and male germ cell survival (2004)

Mammalian oocytes are arrested at the prophase of meiosis before induction of maturation by the preovulatory luteinizing hormone (LH) surge. LH also promotes the survival of meiotic male germ cells in the testis. Because LH binds somatic cells, the mechanism underlying its regulation of germ cell function is unclear. We found that LH stimulates Leydig insulin-like 3 (INSL3) transcripts in ovarian theca and testicular Leydig cells. INSL3, in turn, binds a G protein-coupled receptor, LGR8 (leucine-rich repeat-containing G protein-coupled receptor 8), expressed in germ cells to activate the inhibitory G protein, thus leading to decreases in cAMP production. Treatment with INSL3 initiates meiotic progression of arrested oocytes in preovulatory follicles in vitro and in vivo and suppresses male germ cell apoptosis in vivo, thus demonstrating the importance of the INSL3-LGR8 paracrine system in mediating gonadotropin actions.
Variants of the elongator protein 3 ( ELP3 ) gene are associated with motor neuron degeneration (2008)

Amyotrophic lateral sclerosis (ALS) is a spontaneous, relentlessly progressive motor neuron disease, usually resulting in death from respiratory failure within 3 years. Variation in the genes SOD1 and TARDBP accounts for a small percentage of cases, and other genes have shown association in both candidate gene and genome-wide studies, but the genetic causes remain largely unknown. We have performed two independent parallel studies, both implicating the RNA polymerase II component, ELP3, in axonal biology and neuronal degeneration. In the first, an association study of 1884 microsatellite markers, allelic variants of ELP3 were associated with ALS in three human populations comprising 1483 people (P=1.96 x 10(-9)). In the second, an independent mutagenesis screen in Drosophila for genes important in neuronal communication and survival identified two different loss of function mutations, both in ELP3 (R475K and R456K). Furthermore, knock down of ELP3 protein levels using antisense morpholinos in zebrafish embryos resulted in dose-dependent motor axonal abnormalities [Pearson correlation: -0.49, P=1.83 x 10(-12) (start codon morpholino) and -0.46, P=4.05 x 10(-9) (splice-site morpholino), and in humans, risk-associated ELP3 genotypes correlated with reduced brain ELP3 expression (P=0.01). These findings add to the growing body of evidence implicating the RNA processing pathway in neurodegeneration and suggest a critical role for ELP3 in neuron biology and of ELP3 variants in ALS.
The Web Is Flat (2016)

People populate the web with content relevant to their lives, content that millions of others rely on for information and guidance. However, the web is not a perfect rep- resentation of lived experience: some topics appear in greater proportion online than their true incidence in our population, while others are deflated. This paper presents a large scale data collection study of this phenomenon. We collect webpages about 21 topics of interest capturing roughly 200,000 webpages, and then compare each topic's popularity to representative national surveys as ground truth. We find that rare experiences are inflated on the web (by a median of 7x), while common experiences are deflated (by a median of 0.7x). We call this phenomenon novelty bias.
A 2-ns cycle, 3.8-ns access 512-kb CMOS ECL SRAM with a fully pipelined architecture (1991)

The authors describe a 512 K CMOS static RAM (SRAM) with emitter-coupled-logic (ECL) interfaces which has a 2-ns cycle time and a 3.8-ns access time, both of which are valid for random READ/WRITE operations. The CMOS technology and the physical organization of the chip are briefly discussed, and the pipelined architecture of the chip is described. Detailed measurements of internal chip waveforms demonstrating 2-ns cycle time operation are presented. The impact of wire RC delays on performance is discussed. Circuit examples that demonstrate the implementation of the pipelined architecture are included. Measurements of operating margins, access time, and cycle time are outlined.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Novel strategies for development of gas sensors for combustion and medical applications (2014)

Chemical gas sensors can have an enormous impact on optimizing complex processes as well as facilitate disease diagnosis. In this article, we demonstrate how sensing of gas molecules is influencing the next generation of engines for transportation applications, as well as in disease diagnosis. In such applications, the demands on sensors are quite extreme. Not only does the device have to detect the gas of interest with high sensitivity, it also has to discriminate against other species present in a complex environment, such as combustion exhaust and human breath. In addition, the sensors will need to have as small a footprint as possible in size and power requirements. With these varied requirements in mind, only electrochemical sensors have the potential to be practical. This article focuses on nitric oxide (NO x ) and ammonia (NH 3 ) sensor necessary for emission control of next generation, high efficiency, lean burn engines and nitric oxide (NO) sensor for breath analysis for diagnosis of respiratory diseases. In all of these applications, there has been significant recent commercial activity. We indicate the electrochemical principles of these commercial sensors, and the development from our research group. We present potentiometric total NO x sensors that can operate in harsh environments, and impedance-based NH 3 sensor for transportation industry. For detecting NO in human breath, we have demonstrated two strategies, the first using a resistive approach, and the second with an array of potentiometric sensors. Data from these sensors, their limitations as well as novel MEMS-based approaches for miniaturization is presented.
Software-defined Open Access for flexible and service-oriented 5G deployment (2016)

The evolution of 5G mobile radio and its complex interaction with fixed access network infrastructures poses new challenges and opportunities. In this article, a software-defined converged fixed-mobile 5G architecture is introduced using carrier-grade Ethernet as a transport platform. An active remote node (ARN) is used to connect end-users. Powered at a radio base station, the ARN aggregates the traffic of fixed and mobile radio users. Transport capacity is reduced due to statistical multiplexing, and scalability is achieved by a modular design. The ARN enables software-defined networking (SDN) via the open-networks-as-a-service (Open NaaS) control and management plane. Adopting the Open Access model, this architecture offers both, multi-technology and multi-operator features. Next generation fronthaul, resource sharing, synchronization, low latency can all be established as services to build an advanced 5G infrastructure. Key concepts of the new architecture have been realized using low-cost hardware and offer economic high-speed, fixed and mobile Internet. E.g., for wireless connectivity to macro- and small cells, mm-wave links reaching 5 Gb/s and short-range optical wireless links have been used. As data rates can be scaled up, the proposed architecture is considered future-proof for converged 5G fixed-mobile access networks.
Radiomic subtyping improves disease stratification beyond key molecular, clinical, and standard imaging characteristics in patients with glioblastoma (2017)

Our study stresses the role of integrating radiomics into a multilayer decision framework with key molecular and clinical features to improve disease stratification and to potentially advance personalized treatment of patients with glioblastoma.
A nonhierarchical rural network with decentralized control (1988)

Describes the design of the Delft Rural Telephone System (DRTS). This system was designed with special attention to its future use in rural areas in developing countries. The main characteristics of the system are the use of digital techniques (in both switching and transmission). The nonhierarchical networks structure, the application of modular switching nodes and special features for remote and/or computer assisted maintenance. The choice of digital techniques with PCM-TDM will be explained and justified with a look to the future. The advantages of a non-hierarchical network will be explained considering the special needs of developing countries with respect to expandability and reliability. The switching nodes that are used in the design are microprocessor controlled and can be configured in different ways depending on their functions. These functions are transit switching, drop-insert, and subscriber interfacing. Each configuration can be assembled using a limited amount of modular building blocks. These are constructed with modern off-the-shelf telecommunications integrated circuits. >
An ELISA Based Binding and Competition Method to Rapidly Determine Ligand-receptor Interactions (2016)

A comprehensive understanding of signaling pathways requires detailed knowledge regarding ligand-receptor interaction. This article describes two fast and reliable point-by-point protocols of enzyme-linked immunosorbent assays (ELISAs) for the investigation of ligand-receptor interactions: the direct ligand-receptor interaction assay (LRA) and the competition LRA. As a case study, the ELISA based analysis of the interaction between different lambda interferons (IFNLs) and the alpha subunit of their receptor (IL28RA) is presented: the direct LRA is used for the determination of dissociation constants (KD values) between receptor and IFN ligands, and the competition LRA for the determination of the inhibitory capacity of an oligopeptide, which was designed to compete with the IFNLs at their receptor binding site. Analytical steps to estimate KD and half maximal inhibitory concentration (IC50) values are described. Finally, the discussion highlights advantages and disadvantages of the presented method and how the results enable a better molecular understanding of ligand-receptor interactions.
Impedance spectroscopy flow cytometry: Parameters for label-free cell differentiation (2005)

This work presents label-free separation of cells in an on-chip flow cytometer based on impedance spectroscopy. The amplitude, opacity, and phase information can be used for discrimination depending on the cell types. Red blood cells, ghosts, and fixed cells are differentiated based on differences in their membrane and cytoplasm dielectric properties. Among other applications, detecting changes in cell conductivity and membrane capacitance will allow the indentification of early-stage apoptosis or cancer.
Testing telediagnostic right upper quadrant abdominal ultrasound in Peru: A new horizon in expanding access to imaging in rural and underserved areas (2021)

This asynchronous telediagnostic system allows individuals without prior ultrasound experience to effectively scan the liver, gallbladder, and right kidney with a high degree of agreement with standard of care ultrasound. This system can be deployed to improve access to diagnostic imaging in low-resource areas.
Living Carbocationic Polymerization. XXXVIII. On the Nature of the Active Species in Isobutylene and Vinyl Ether Polymerization (1991)

Abstract The nature of the species that gives rise to living carbocationic polymerization (LP+Pzn) of isobutylene (IB) coinitiated by Friedel-Crafts acids (FCA) in the presence of electron pair donors (ED) has been investigated. It is proposed that the key species responsible for mediating LC+Pzn of IB are FCA·ED complexes, formed by Lewis acid-Lewis base interaction, where FCA = BCl3 TiCl4, and ED = ethyl acetate, tetrahydrofuran, etc. Free EDs are inhibitors of IB polymerization. These findings are in sharp contrast to those of LC+Pzn of vinyl ethers coinitiated by EtAlCl2 in which excess (i.e., free) EDs are required for the living polymerizations to occur. Comparison of IB polymerizations induced by the 2-chloro-2,4,4-trimethylpentane/BCl3 and 2-acetyl-2,4,4-trimethylpentane/BCl3 systems shows that these reactions do not proceed by the same intermediate (i.e., by tert-chlorides) and that the mechanisms of BC13- and TiC14-coinitiated living polymerizations are different. Experiments with the proton trap 2,6-di-tert-butylpyridine indicate that proton scavenging by FCA·ED complexes may be responsible for the narrow molecular weight distribution (MWD) products obtained in BC13-coinitiated LC+Pzn of isobutylene. These findings also prove that Ri (rate of initiation) > R p (rate of propagation), the relation required for narrow MWD in living polymerizations.