gebhart/patrepeval huggingface dataset:
Leukocyte integrin Mac-1 regulates thrombosis via interaction with platelet GPIbα (2017)

Inflammation and thrombosis occur together in many diseases. The leukocyte integrin Mac-1 (also known as integrin α<sub>M</sub>β<sub>2</sub>, or CD11b/CD18) is crucial for leukocyte recruitment to the endothelium, and Mac-1 engagement of platelet GPIbα is required for injury responses in diverse disease models. However, the role of Mac-1 in thrombosis is undefined. Here we report that mice with Mac-1 deficiency (Mac-1<sup>-/-</sup>) or mutation of the Mac-1-binding site for GPIbα have delayed thrombosis after carotid artery and cremaster microvascular injury without affecting parameters of haemostasis. Adoptive wild-type leukocyte transfer rescues the thrombosis defect in Mac-1<sup>-/-</sup> mice, and Mac-1-dependent regulation of the transcription factor Foxp1 contributes to thrombosis as evidenced by delayed thrombosis in mice with monocyte-/macrophage-specific overexpression of Foxp1. Antibody and small-molecule targeting of Mac-1:GPIbα inhibits thrombosis. Our data identify a new pathway of thrombosis involving leukocyte Mac-1 and platelet GPIbα, and suggest that targeting this interaction has anti-thrombotic therapeutic potential with reduced bleeding risk.
Task routing for prediction tasks (2012)

We describe methods for routing a prediction task on a network where each participant can contribute information and route the task onwards. Routing scoring rules bring truthful contribution of information about the task and optimal routing of the task into a Perfect Bayesian Equilibrium under common knowledge about the competencies of agents. Relaxing the common knowledge assumption, we address the challenge of routing in situations where each agent's knowledge about other agents is limited to a local neighborhood. A family of local routing rules isolate in equilibrium routing decisions that depend only on this local knowledge, and are the only routing scoring rules with this property. Simulation results show that local routing rules can promote effective task routing.
Beyond biotemplating: multiscale porous inorganic materials with high catalytic efficiency (2020)

Biotemplating makes it possible to prepare materials with complex structures by taking advantage of nature's ability to generate unique morphologies. In this work, we designed and produced a multi-scale porosity (MSP) scaffold starting from sea urchin spines by adding an additional nano-porosity to its native micro-porosity. The final replica shows porosity in both length scales and is an effective high-performing photocatalytic material.
Arabidopsis late blight: infection of a nonhost plant by Albugo laibachii enables full colonization by Phytophthora infestans (2016)

The oomycete pathogen Phytophthora infestans causes potato late blight, and as a potato and tomato specialist pathogen, is seemingly poorly adapted to infect plants outside the Solanaceae. Here, we report the unexpected finding that P. infestans can infect Arabidopsis thaliana when another oomycete pathogen, Albugo laibachii, has colonized the host plant. The behaviour and speed of P. infestans infection in Arabidopsis pre-infected with A. laibachii resemble P. infestans infection of susceptible potato plants. Transcriptional profiling of P. infestans genes during infection revealed a significant overlap in the sets of secreted-protein genes that are induced in P. infestans upon colonization of potato and susceptible Arabidopsis, suggesting major similarities in P. infestans gene expression dynamics on the two plant species. Furthermore, we found haustoria of A. laibachii and P. infestans within the same Arabidopsis cells. This Arabidopsis-A. laibachii-P. infestans tripartite interaction opens up various possibilities to dissect the molecular mechanisms of P. infestans infection and the processes occurring in co-infected Arabidopsis cells.
Hyperledger Fabric: A Distributed Operating System for Permissioned Blockchains (2018)

Fabric is a modular and extensible open-source system for deploying and operating permissioned blockchains and one of the Hyperledger projects hosted by the Linux Foundation (www.hyperledger.org). Fabric is the first truly extensible blockchain system for running distributed applications. It supports modular consensus protocols, which allows the system to be tailored to particular use cases and trust models. Fabric is also the first blockchain system that runs distributed applications written in standard, general-purpose programming languages, without systemic dependency on a native cryptocurrency. This stands in sharp contrast to existing blockchain platforms that require "smart-contracts" to be written in domain-specific languages or rely on a cryptocurrency. Fabric realizes the permissioned model using a portable notion of membership, which may be integrated with industry-standard identity management. To support such flexibility, Fabric introduces an entirely novel blockchain design and revamps the way blockchains cope with non-determinism, resource exhaustion, and performance attacks. This paper describes Fabric, its architecture, the rationale behind various design decisions, its most prominent implementation aspects, as well as its distributed application programming model. We further evaluate Fabric by implementing and benchmarking a Bitcoin-inspired digital currency. We show that Fabric achieves end-to-end throughput of more than 3500 transactions per second in certain popular deployment configurations, with sub-second latency, scaling well to over 100 peers.
Marine Bio-Nanotechnology: High-Performance Materials from Sponge Silicatein (2007)

Marine sponges produce nanoscale silicon dioxide structures called spicules. In previous California Sea Grant research, UC Santa Barbara professor Daniel Morse and colleagues identified the principal protein responsible for directing spicule construction at the molecular and atomic scale.
Space-time codes with bit interleaving (2002)

We develop a new construction criterion for BSPK space-time codes. Based on this criterion, we propose a new method of improving the performance of space-time codes, namely bit interleaving. Then, we provide a computationally effective, iterative way of decoding bit interleaved space-time codes. At the end, we note the 2 dB gain due to the new approach. A proposed 16 state bit interleaved code operates close to 3 dB from the outage probability.
Spotted (2015)

Being able to react fast to exceptional events such as riots protests or disaster preventions is of paramount importance, especially when trying to ensure peoples' safety and security, or even save lives. This chapter presents a study on the use of fully anonymized and highly aggregated cellular network data, like Call Detail Records (CDRs) in order to connect people, locations and events. The goal of the study is to see if the CDR data can be used to detect exceptional spatio-temporal patterns of the collective human mobile data usage and correlate these ‘anomalies' with real-world events (e.g., parades, public concerts, soccer match, traffic congestion, riots protests etc.). These observations could be further used to develop an intelligent system that detects exceptional events in real-time from CDRs data monitoring. Such system could be used in intelligent transportation management, urban planning, emergency situations, network resource allocation and performance optimization, etc.
Equilibrium modeling and solution approaches inspired by nonconvex bilevel programming (2021)

Solution methods for generalized Nash equilibrium have been dominated by variational inequalities and complementarity problems. Since these approaches fundamentally rely on the sufficiency of first-order optimality conditions for the players' decision problems, they only apply as heuristic methods when the players are modeled by nonconvex optimization problems. In contrast, this work approaches generalized Nash equilibrium using theory and methods for the global optimization of nonconvex bilevel programs. Through this perspective, we draw precise connections between generalized Nash equilibria, feasibility for bilevel programming, the Nikaido-Isoda function, and classic arguments involving Lagrangian duality and spatial price equilibrium. Significantly, this is all in a general setting without the assumption of convexity. Along the way, we introduce the idea of minimum disequilibrium as a solution concept that reduces to traditional equilibrium when equilibrium exists. The connections with bilevel programming and related semi-infinite programming permit us to adapt global optimization methods for those classes of problems, such as constraint generation or cutting plane methods, to the problem of finding a minimum disequilibrium solution. We propose a specific algorithm and show that this method can find a pure Nash equilibrium even when the players are modeled by mixed-integer programs.
Characterization of enteropathogenicEscherichia coliof clinical origin from the pediatric population in Pakistan (2016)

Non-typeable EPEC strains were frequently observed. ESBL production in ESBL producers was found to be plasmid mediated. No significant association of antibiotic resistance profile with specific phylogroup of EPEC was found, however G. mellonella infection model differentiated representative phylotypes.
Faculty Opinions recommendation of Tandem action of the O2- and FADH2-dependent halogenases KtzQ and KtzR produce 6,7-dichlorotryptophan for kutzneride assembly. (2008)

Kutznerides are actinomycete-derived antifungal nonribosomal hexadepsipeptides which are assembled from five unsual nonproteinogenic amino acids and one hydroxy acid. Conserved in all structurally characterized kutznerides is a dichlorinated tricyclic hexahydropyrroloindole postulated to be derived from 6,7-dichlorotryptophan. In this Communication, we identify KtzQ and KtzR as tandem acting FADH2-dependent halogenases that work sequentially on free L-tryptophan to generate 6,7-dichloro-L-tryptophan. Kinetic characterization of these two enzymes has shown that KtzQ (along with the flavin reductase KtzS) acts first to chlorinate at the 7-position of L-tryptophan. KtzR, with a 120 fold preference for 7-chloro-L-tryptophan over L-tryptophan, then installs the second chlorine at the 6-position of 7-chloro-L-tryptophan to generate 6,7-dichloro-L-tryptophan. These findings provide further insights into the enzymatic logic of carbon-chloride bond formation during the biosynthesis of halogenated secondary metabolites. PMID: 18828589 Funding information This work was supported by: NIGMS NIH HHS, United States Grant ID: R01 GM020011 NIGMS NIH HHS, United States Grant ID: F32 GM083464-01 NIAID NIH HHS, United States Grant ID: R01 AI042738 NIGMS NIH HHS, United States Grant ID: F32 GM083464 NIGMS NIH HHS, United States Grant ID: 1 F32 GM083464-01 NIGMS NIH HHS, United States Grant ID: R01 GM020011-37 NIGMS NIH HHS, United States Grant ID: GM20011 NIGMS NIH HHS, United States Grant ID: F32 GM020011 More Less keyboard_arrow_down
Analysis of Rous sarcoma virus Gag protein by mass spectrometry indicates trimming by host exopeptidase (1996)

We have used electrospray ionization-mass spectrometry to investigate Gag protein structure and processing in Rous sarcoma virus, the prototype of the avian sarcoma and leukemia viruses. Molecular masses determined for the mature virion proteins MA, CA, NC, and PR agree closely with those predicted by currently accepted models for their structures. However, the data for p10 imply that only about 10% of the product has the predicted mass while the remainder is missing the C-terminal methionine residue. Molecular masses also were obtained for products generated by PR cleavage in vitro of a Gag precursor polyprotein expressed in Escherichia coli. The data confirm the predicted Gag cleavage sites for PR. Thus, carboxypeptidase activity appears to be responsible for generating the des-Met form of p10. The same activity may account for the small amount of the mature des-Met CA, as previously reported. Analysis of cleavage products generated in vitro also serves to define the PR processing site separating the p2a and p2b peptides, Asn-164-Cys-165. In conjunction with published characterizations of these two peptides processed from the segment of Gag between MA and p10, these data suggest trimming of p2b by an aminopeptidase. Finally, the molecular masses determined for the MA-related species p19f, p23, and p35 now accurately define the structures of these proteins.
swga: a primer design toolkit for selective whole genome amplification (2017)

Supplementary data are available at Bioinformatics online.
Human breath-print identification by E-nose, using information-theoretic feature selection prior to classification (2014)

The composition of bodily fluids reflects many aspects of health status of a patient. Breath is another sample that may be useful for diagnosis of infectious and other diseases. Analysis of breath has the advantage of being less invasive than analysis of other fluids such as blood and bronchial biopsy. Two recent studies, using either mass spectrometry or electronic nose (E-nose) technologies, showed there are definite "breath-prints" that characterised individuals despite temporal variation in internal metabolism and environment. In this study we demonstrate that by employing an information-theoretic feature selection method that is specific to the problem together with machine learning techniques, we can dramatically improve (cross-validated) identification of individuals through their breath using a very small selected subset of E-nose measurement features. Indeed, we demonstrate here that we can identify the 10 individuals in this study with perfect accuracy using fewer than 10 features.
İktisadi ve Siyasi Etkenlerle Osmanlı’da Dış Göç: 16. Yüzyılda Mühimme Defterlerinde (2015)

In the 16th century's Ottoman, external migration, which means winning or losing population, were questioned to originate from which factors. Gaining information about, under which factors, the migrate from the outside and migrating out of the Ottoman replaced each other, were aimed. The provisions of a limited number of Muhimmah were screened and was supported by secondary sources. After the transcription of the provisions were given, summary and main theme were given with today's Turkish. Simplification was made in some documents. It was seen to be demanded from the concerned state officials that the required measures be taken for the prevention of population movements, the population mobility in Safavid Iran in the East and on the borderland between Hungary and Austria in the West, were processed. In practice, unity, integrity, legality, justice and harmony principles were observed. The population movements were based on such reasons as economical, political, administrative, social and denominational; with the purpose of search for security; that the summer pastures and winter quarters were seized of them by the rulers to be transferred to some others for diverse reasons; the heavy burden of taxes; invited population from abroad; that those places allocated were considered to be insufficient by some administrators; the attempts of some people to join the Safavids; offering tax exemption up to three years and drawing populations from inlands. The implementation of the population policy that, encourages the population living in the place they are, providing welfare requirements, has been proposed.
Computational Complexity of Decoding Orthogonal Space-Time Block Codes (2011)

The computational complexity of optimum decoding for an orthogonal space-time block code G <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">N</sub> satisfying G <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">N</sub> <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">H</sup> G <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">N</sub> = c(Σ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">k=1</sub> <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">K</sup> |s <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">k</sub> | <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> )I <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">N</sub> where c is a positive integer is quantified. Four equivalent techniques of optimum decoding which have the same computational complexity are specified. Modifications to the basic formulation in special cases are calculated and illustrated by means of examples. This paper corrects and extends, and unifies them with the results from the literature. In addition, a number of results from the literature are extended to the case c >; 1.
Supplementary Table 1 from Lowering Bone Mineral Affinity of Bisphosphonates as a Therapeutic Strategy to Optimize Skeletal Tumor Growth Inhibition <i>In vivo</i> (2023)

Supplementary Table 1 from Lowering Bone Mineral Affinity of Bisphosphonates as a Therapeutic Strategy to Optimize Skeletal Tumor Growth Inhibition &lt;i&gt;In vivo&lt;/i&gt;
CmERF5‐CmRAP2.3 transcriptional cascade positively regulates waterlogging tolerance in Chrysanthemum morifolium (2022)

Waterlogging stress affects plant growth by limiting root respiration and reducing yield and economic value. Therefore, identifying genes involved in regulating waterlogging stress is vital. This study reports the ethylene-responsive VII transcription factor (CmRAP2.3) in the chrysanthemum. Subcellular localization and transactivation assay analyses revealed that CmRAP2.3 was localized in the nucleus and possessed transactivation activity. Overexpression of CmRAP2.3 in chrysanthemum was found to enhance waterlogging tolerance by decreasing reactive oxygen species (ROS) levels. Furthermore, we found that the transcription factor CmERF5 binds to GCC-like motifs in the CmRAP2.3 promoter region and activates CmRAP2.3 expression. Additionally, CmERF5 overexpression maintained a low ROS level and improved chrysanthemum waterlogging tolerance. Taken together, this study shows a molecular mechanism by which CmERF5 transcriptionally activates CmRAP2.3 to reduce waterlogging stress via the ROS pathway in the chrysanthemum.
Genetic heterogeneity and spectrum of mutations of the PRKAR1A gene in patients with the Carney complex (2000)

Carney complex (CNC) is an autosomal dominant multiple neoplasia syndrome, which has been linked to loci on 2p16 and 17q22-24. We recently reported that PRKAR1A, which codes for the type 1A regulatory subunit of protein kinase A (PKA), is a tumor suppressor gene on chromosome 17 that is mutated in some CNC families. To evaluate the spectrum of PRKAR1A mutations, we identified its genomic structure and screened for mutations in 54 CNC kindreds (34 families and 20 patients with sporadic disease). Fourteen families were informative for linkage analysis: four of four families that mapped to 17q had PRKAR1A mutations, whereas there were no mutations found in seven families exhibiting at least one recombination with 17q. In six of the latter, CNC mapped to 2p16. PRKAR1A mutations were also found in 12 of 20 non-informative families and 7 of 20 sporadic cases. Altogether, 15 distinct PRKAR1A mutations were identified in 22 of 54 kindreds (40.7%). In 14 mutations, the sequence change was predicted to lead to a premature stop codon; one altered the initiator ATG codon. Mutant mRNAs containing a premature stop codon were unstable, as a result of nonsense-mediated mRNA decay. Accordingly, the predicted truncated PRKAR1A protein products were absent in these cells. We conclude that (i) genetic heterogeneity exists in CNC; and (ii) all of the CNC alleles on 17q are functionally null mutations of PRKAR1A. CNC is the first human disease recognized to be caused by mutations of the PKA holoenzyme, a critical component of cellular signaling.
Reactions of 2- Amino-1,4- Naphthoquinone with Aldehydes (2003)

Reactions of 2-amino-1,4-naphthoquinone with aldehydes give 2-(N-alkenyl)amino- 1,4-naphthoquinones (7) under neutral conditions while they give substituted 1H-2,4-dihydronaphtho(2,3-d)1,3-oxazine-5,10-diones (8) using catalytic amount of trifluoroacetic acid.
Supplementary Figure Legends from <i>In Vivo</i> Detection of HSP90 Identifies Breast Cancers with Aggressive Behavior (2023)

&lt;p&gt;Figure Legends for Supplementary Figures 1-4&lt;/p&gt;
Fundamentals of Optics and Radiometry for Color Reproduction (2014)

Abstract Visual appearance of objects comes from the interpretation by the human visual system of a light signal issued from the objects. Describing or predicting appearance is, therefore, a question of light and requires notions about light propagation and measurement. In this chapter, we introduce basic laws of optics, the science of light, and radiometry, the science of light measurement, in the context of colored surfaces. We address light spectrum and illuminants, polarization, notions of reflectance and transmittance based on radiometric definitions, gloss, absorption, scattering, fluorescence, and models for light reflection and transmission by flat and rough surfaces and by slabs of nonscattering media and diffusing layers. Throughout the chapter, we present the most current methods to assess the different physical quantities by measurement.
Piezoelectric actuator array for motion-enabled reconfigurable RF circuits (2015)

This paper reports on the translation and rotation capabilities of arrays of piezoelectrically actuated MEMS cantilevers developed for a motion-enabled reconfigurable radio frequency (RF) circuit micro-factory, known as RFactory. The reported actuator surface demonstrates 2.4 to 100 times faster translational speeds than similar devices, depending on the actuation technology used for comparison. The array was driven with different waveforms, voltages, and frequencies to characterize the quality of motion of a silicon chip placed on the array. It has demonstrated instantaneous velocities of 20 mm/s, maximum average velocities of 3.5 mm/s, and rotational speeds of 31.9 rpm at sub-10 V actuation and less than 2% off-axis translational deviation. The effort has identified significant operational and design variables using the first dynamic contact model developed for micromanipulation surfaces.
Control of feedback for assistive listening devices (2014)

Acoustic feedback refers to the undesired acoustic coupling between the loudspeaker and microphone in hearing aids. This feedback channel poses limitations to the normal operation of hearing aids under varying acoustic scenarios. This work makes contributions to improve the performance of adaptive feedback cancellation techniques and speech quality in hearing aids. For this purpose a two microphone approach is proposed and analysed; and probe signal injection methods are also investigated and improved upon.
Current Management of the Axilla (2016)

Despite advances in estimating prognosis and predicting response to adjuvant systemic therapy, the status of the axillary lymph nodes remains a critical component in initial surgical planning and in determining therapeutic strategies for patients with breast cancer. Buoyed by evidence from multi-institutional randomized clinical trials, the last 2 decades have witnessed remarkable and practice-changing advances in our approach to the axilla. This review concentrates on the current best practice in axillary management for both node-negative and node-positive patients, with particular focus on the evolving management of the axilla in the era of neoadjuvant systemic therapy.