gebhart/patrepeval huggingface dataset:
Space-Time Coding Schemes for Optical MIMO (2011)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text Y. Chen, L. Schmalen, H. Bülow, A. Leven, and S. t. Brink, "Space-Time Coding Schemes for Optical MIMO," in 37th European Conference and Exposition on Optical Communications, OSA Technical Digest (CD) (Optica Publishing Group, 2011), paper Tu.6.A.1. Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Pair Collaboration in End-User Debugging (2006)

The problem of dependability in end-user programming is an emerging area of interest. Pair collaboration in end-user software development may offer a way for end users to debug their programs more effectively. While pair programming studies - primarily of computer science students and professionals - report positive outcomes in terms of overall program quality, little is known about specific activities that pairs engage in that lead to those outcomes, or of how the previous results may pertain to end-user programmers. In this paper we analyze protocols of end-user pairs debugging spreadsheets. The results suggest that end-user pairs can achieve rich reasoning, effective planning, and systematic evaluation. Furthermore, end-user pairs provide specific types of mutual support that facilitate the accomplishment of their goals
Oedipus - detective and psychoanalyst? (2009)

This article analyzes the Prologue of Oedipus Rex, highlighting not only the plot of the self-recognition of Oedipus (in search of himself). What is at stake objectively speaking in this play? Is there not a realistic level of meaning on which Oedipus' subtle ears detect unsettling signs of real plotting in the behavior of the other characters of the play (Creon and Jocasta mainly)? In this perspective, the oracle my be considered by Oedipus as a means of investigating Creon's thoughts, memories and deductions - rather than as a revelation of divine truth. This first scene introduces the reader into the discovery of a real detective story, which is part of the famous tragedy.
Molecular Modeling Studies of the DNA−Topoisomerase I Ternary Cleavable Complex with Camptothecin (1998)

The present studies provide a three-dimensional model for the postulated ternary cleavable complex of topoisomerase I (top1), DNA, and camptothecin (CPT). Molecular simulations were done using the AMBER force field. The results suggest that a ternary cleavable complex might be stabilized by several hydrogen bonds in the binding site. In this proposed "drug-stacking" model, CPT is pseudointercalated in the top1-linked DNA cleavage site and interacts with the protein near its catalytic tyrosine through hydrogen bonding and stacking. The structural model is consistent with the following experimental observations: (i) the N3 position of the 5' terminal purine of the cleaved DNA strand is readily alkylated by 7-chloromethyl 10,11-methylenedioxy CPT; (ii) CPT generally tolerates substituents at positions 7, 9, and 10 but is inactivated by additions at position 12; (iii) 10,11-methylenedioxy (MDO) CPT is much more potent than 10,11-dimethoxy (DMO) CPT; (iv) the lactone portion of CPT is essential for top1 inhibitory activity; (v) 20S derivatives of CPT are much more potent than the 20R analogues; (vi) a catalytic tyrosine hydroxyl in top1 covalently links to the 3' terminal base, T, of the cleaved DNA strand; and (vii) top1 mutation Asn722Ser leads to CPT resistance. A total of 18 camptothecin derivatives with different DNA cleavage potencies were docked into the hypothetical cleavable complex binding site to test and refine the model. These studies provide insight into a possible mechanism of top1 inhibition by CPT derivatives and suggest rational approaches for the design of new CPT derivatives.
An AUTOSAR-Compliant Automotive Platform for Meeting Reliability and Timing Constraints (2011)

<div class="section abstract"><div class="htmlview paragraph">High demands on advanced safety and driving functions, such as active safety and lane departure warnings, increase a vehicle's dependency on automotive electrical/electronic architectures. Hard real-time requirements and high reliability constraints must be satisfied for the correct functioning of these safety-critical features, which can be achieved by using the AUTOSAR (Automotive Open System Architecture) standard. The AUTOSAR standard was introduced to simplify automotive system design while offering inter-operability, scalability, extensibility, and flexibility. The current version of AUTOSAR does not assist in the replication of tasks for recovering from task failures. Instead, the standard assumes that architecture designers will introduce custom extensions to meet such reliability needs. The introduction of affordable techniques with predictable properties for meeting reliability requirements will prove to be very valuable in future versions of AUTOSAR.</div><div class="htmlview paragraph">In this paper, we propose a new Software-Component (SW-C) allocation algorithm called R-FLOW (Reliable application-FLOW-aware SW-C partitioning algorithm) for fail-stop processors to support fault-tolerance with bounded recovery times, and we integrate the R-FLOW algorithm into AUTOSAR. R-FLOW leverages different types of replication schemes to satisfy reliability and timing constraints, while offering a high degree of resource utilization and flexibility. Specifically, R-FLOW classifies real-time periodic tasks into <i>Hard Recovery</i> tasks, <i>Soft Recovery</i> tasks, and <i>Best-Effort Recovery</i> tasks. <i>Hot Standbys</i> are used for recovering from failures of hard recovery tasks, whereas <i>Cold Standbys</i> are utilized for recovering from failures of soft recovery and best-effort recovery tasks. With this goal in mind, we design and implement our proposed architecture within the guidelines of the current AUTOSAR framework. We have built an at-scale prototyping platform, comprising of Freescale HCS12X processing boards, a dual-channel FlexRay bus, and a CAN network. Our proposed architecture is evaluated on this platform using reliability and timeliness metrics in the context of different fault scenarios.</div></div>
Encapsulation of triphenyltin hydroxide (1986)

Triphenyltin hydroxide was encapsulated to prolong its fungicidal activity and to decrease its phytotoxicity in peanut fields. The envelopes found to be adequate for this purpose were polyureas and ethyl cellulose, as was demonstrated by biological tests.
Glioma cell integrin expression and their interactions with integrin antagonists: Research Article. (2005)

A panel of human glioma cell explants was screened for integrin expression by flow cytometry using α(ν)β-specific antibodies. A lower percentage of the glioma cells were positive for the α(ν)β3 (mean % positive = 20.8%) integrin, whereas higher percentages were positive for the ανβ5 (mean % positive = 72.7%), VLA5α (mean % positive = 87%) and VLAβ1 (mean % positive = 41.7%) integrins. A series of RGD peptides was designed, synthesized and tested for binding to integrin receptors. Based on the results of the binding to the isolated integrin receptors and the expression of integrins on glioma cell lines, a peptide that binds potently to the α(ν)β3, α(ν)β5 and α(5)β(1) was selected for further investigations with regards to its effect on glioma cells. The peptide, Ac-c[(Pen)-Tyr(Me)-Ala-Arg-Gly-Asp-Asn-Tic-Cys]NH(2) (RGD peptide), exhibited high potential for use in clinical intracranial administration since it had good stability in rat brain cell homogenates placed into artificial cerebrospinal fluid. Using an HPLC method for quantification of peptides in rat brain cell homogenates, we could demonstrate the half-life of the RGD peptide approximated 20 hr. Relative to a scrambled peptide control (non-RGD sequence, same amino acids), the experimental RGD peptide significantly decreased glioma cell proliferation of the entire panel of rat and human glioma cells tested. Adhesion of recently passaged glioma cells to glioma-derived extracellular matrix protein-coated plates was inhibited significantly by the RGD peptide. The peptide also reversed attachment of plated glioma cells. The RGD peptide caused some, but not substantial, glioma cell injury, as evidenced by a quantitative in vitro nuclear DNA morphologic assay and by a flow cytometric assay employing 7-amino actinomycin D (7AAD). We histologically monitored for toxicity caused by various doses of the RGD peptide infused repeatedly into normal cannulated rat brain. At safe doses, the experimental RGD peptide-treated brains did not show significant differences from those infused with scrambled peptide or buffer-treated controls. In tumor-bearing brains, slightly smaller tumor areas were measured with a higher necrotic-to-tumor index in the RGD peptide treated relative to the scrambled peptide-treated controls. This was obtained with intracranial peptide administrations or combined intracranial and intraperitoneal injections. From this in vitro work, we conclude that the anti-glioma effects of the RGD peptide tested resulted from lowered glioma proliferation and adhesion/mobility, rather than from significant glioma cell injury in the timeframe analyzed. Although other mechanisms not discerned from our limited histopathological observations may be operational, from our in vivo work, we conclude that repeated administration of RGD peptide into brain is safe but that better delivery of the peptides to infiltrating tumor cells is necessary.
Selective Targeting of MAPKs to the ETS Domain Transcription Factor SAP-1 (2001)

MAPK pathways play important roles in regulating the key cellular processes of proliferation, differentiation, and apoptosis. There are multiple MAPK pathways, which are subject to different regulatory cues. It is important that these pathways maintain specificity in signaling to elicit the activation of a specific program of gene expression. MAPK-docking domains in several transcription factors have been shown to play important roles in determining the specificity and efficiency of their phosphorylation by MAPKs. Here we investigate the mechanisms by which MAPKs are targeted to the ETS domain transcription factor SAP-1. We demonstrate that SAP-1 contains two different domains that are required for its efficient phosphorylation in vitro and activation in vivo by ERK2 and a subset of p38 MAPKs. The D-domain is closely related to other MAPK-docking domains, but exhibits a novel specificity and serves to promote selective targeting of ERK2, p38alpha, and p38beta(2) to SAP-1. A second important region, the FXF motif, also plays an important role in directing MAPKs to phosphorylate SAP-1. The FXF motif promotes targeting by ERK2 and, to a lesser extent, p38alpha, but not p38beta(2). Our data therefore demonstrate that a modular system of motifs is responsible for directing specific MAPK subtypes to SAP-1, but also point to important distinctions in the mechanism of action of the D-domain and FXF motif.
An efficient and scalable synthesis of potent TLR2 agonistic PAM<sub>2</sub>CSK<sub>4</sub> (2018)

Diacylated PAM<sub>2</sub>CSK<sub>4</sub>, a highly expensive lipopeptide with desirable aqueous solubility and a broad spectrum of cytokine/chemokine induction is a most potent dual (human and murine) Toll-Like Receptor-2 (TLR2) agonist. Besides such thrilling characteristics, its synthetic process is not reported in the literature. The present report describes an efficient and scalable 20 step synthesis of PAM<sub>2</sub>CSK<sub>4</sub> in good yield (all steps > 60%) along with a clear description of the hindrances and easy solutions adopted in each step. Overall, a convergent synthetic approach was adopted involving synthesis of appropriately protected starting materials, synthesis of a key backbone skeleton PAM<sub>2</sub>CS, synthesis of a tetralysine fragment and the final coupling to yield PAM<sub>2</sub>CSK<sub>4</sub>. Tedious column chromatography was avoided on a large scale in many steps.
IL‐1β increases necrotic neuronal cell death in the developing rat hippocampus after status epilepticus by activating type I IL‐1 receptor (IL‐1RI) (2014)

Interleukin-1β (IL-1β) is associated with seizure-induced neuronal cell death in the adult brain. The contribution of IL-1β to neuronal injury induced by status epilepticus (SE) in the immature brain remains unclear. In the present study, we investigated the effects of IL-1β administration on hippocampal neuronal cell death associated with SE in the immature brain, and the role of the type I receptor of IL-1β (IL-1RI). SE was induced with lithium-pilocarpine in 14-days-old (P14) rat pups. Six hours after SE onset, pups were i.c.v. injected in the right ventricle with IL-1β (0, 0.3, 3, 30, or 300 ng), 30 ng of IL-1RI antagonist (IL-1Ra) alone, or 30 ng of IL-1Ra plus 3ng of IL-1β. As control groups, pups without seizures were injected with 3 ng of IL-1β or vehicle. Twenty-four hours after SE onset, neuronal cell death in the CA1 field of dorsal hippocampus was assessed by hematoxylin-eosin, Fluoro-Jade B and in vivo propidium iodide (PI) staining; expression of active caspase-3 (aCas-3) was also determined, using immunohistochemistry. The concentration-response curve of IL-1β showed a bell-shape. Only pups injected with 3 ng of IL-1β after SE showed a significant increase in the number of cells with eosinophilic cytoplasm and pyknotic nuclei, as well as F-JB positive cells with respect to the vehicle group. This effect was prevented when IL-1β was injected with IL-1Ra. Injection of 3 ng of IL-1β increased the number of PI-positive cells in CA1 area after SE. Injection of 3 ng of IL-1β did not produce hippocampal cell death in rats without seizures. Active caspase-3 expression was not observed after treatments in hippocampus. The activation of the IL-1β/IL-1RI system increases necrotic neuronal cell death caused by SE in rat pups.
Molecular basis of resistance to acetolactate synthase-inhibiting herbicides inSisymbrium orientale andBrassica tournefortii (1999)

Three Australian Sisymbrium orientale and one Brassica tournefortii biotypes are resistant to acetolactate synthase (ALS)-inhibiting herbicides due to their possession of an ALS enzyme with decreased sensitivity to these herbicides. Enzyme kinetic studies revealed no interbiotypic differences within species in Km (pyruvate) (the substrate concentration at which the reaction rate is half maximal) but a greater Vmax (the rate when the enzyme is fully saturated with substrate) for two of the resistant S orientale biotypes over susceptible levels. F1 hybrids from reciprocal crosses between resistant and susceptible biotypes of S orientale showed an intermediate response to chlorsulfuron compared to the parental plants. ALS herbicide resistance in S orientale segregated in a 3:1 (resistant:susceptible) ratio in F2 plants with a single rate of chlorsulfuron, indicating that resistance is inherited as a single, incompletely dominant nuclear gene. Two regions of the ALS structural gene known to vary in ALS-resistant biotypes were amplified and sequenced. Resistant S orientale biotypes NS01 and SS03 contained a single nucleotide substitution in Domain B, predicting a Trp (in susceptible) to Leu (in resistant) amino acid change. Two adjacent nucleotide substitutions (CCT to ATT) predicting a Pro (in susceptible) to Ile (in resistant) change in the primary amino acid sequence were identified in Domain A of resistant S orientale biotype SS01. Likewise, a single nucleotide substitution at the same site in the resistant B tournefortii biotype predicts a Pro (in susceptible) to Ala (in resistant) substitution. No other interbiotypic nucleotide differences predicted amino acid changes in the sequenced regions, suggesting that the amino acid substitutions reported above are responsible for resistance to ALS-inhibiting herbicides in the respective biotypes. © 1999 Society of Chemical Industry
Progressive Data Analysis and Visualization (Dagstuhl Seminar 18411) (2019)

We live in an era where data is abundant and growing rapidly; databases storing big data sprawl past memory and computation limits, and across distributed systems. New hardware and software systems have been built to sustain this growth in terms of storage management and predictive computation. However, these infrastructures, while good for data at scale, do not well support exploratory data analysis (EDA) as, for instance, commonly used in Visual Analytics. EDA allows human users to make sense of data with little or no known model on this data and is essential in many application domains, from network security and fraud detection to epidemiology and preventive medicine. Data exploration is done through an iterative loop where analysts interact with data through computations that return results, usually shown with visualizations, which in turn are interacted with by the analyst again. Due to human cognitive constraints, exploration needs highly responsive system response times: at 500 ms, users change their querying behavior; past five or ten seconds, users abandon tasks or lose attention. As datasets grow and computations become more complex, response time suffers. To address this problem, a new computation paradigm has emerged in the last decade under several names: online aggregation in the database community; progressive, incremental, or iterative visualization in other communities. It consists of splitting long computations into a series of approximate results improving with time; in this process, partial or approximate results are then rapidly returned to the user and can be interacted with in a fluent and iterative fashion. With the increasing growth in data, such progressive data analysis approaches will become one of the leading paradigms for data exploration systems, but it also will require major changes in the algorithms, data structures, and visualization tools. This Dagstuhl Seminar was set out to discuss and address these challenges, by bringing together researchers from the different involved research communities: database, visualization, and machine learning. Thus far, these communities have often been divided by a gap hindering joint efforts in dealing with forthcoming challenges in progressive data analysis and visualization. The seminar gave a platform for these researchers and practitioners to exchange their ideas, experience, and visions, jointly develop strategies to deal with challenges, and create a deeper awareness of the implications of this paradigm shift. The implications are technical, but also human--both perceptual and cognitive--and the seminar provided a holistic view of the problem by gathering specialists from all the communities.
Timestamping performance analysis of IEEE 802.15.4a systems based on SDR platforms (2012)

An increasing number of distributed measurement and control applications requires that network nodes are able to estimate the position and the time measured by other devices on a common spatio-temporal reference frame. Accurate packet timestamping is a necessary condition to achieve this goal. However, in the case of wireless networks, timestamping accuracy is generally quite poor due to the combination of multiple uncertainty sources (e.g., variable signal attenuation and interferences) affecting wireless message propagation. Various communication schemes have been proposed to improve performance. One of the most recent and promising is the Chirp Spread Spectrum (CSS) modulation. In this paper, the timestamping accuracy of CSS signals similar to those defined in the standard IEEE 802.15.4a is analyzed experimentally using two different platforms based on a Software Defined Radio (SDR). Some results confirm that CSS can be successfully employed for accurate time synchronization and ranging.
TSSPlant: a new tool for prediction of plant Pol II promoters (2017)

Our current knowledge of eukaryotic promoters indicates their complex architecture that is often composed of numerous functional motifs. Most of known promoters include multiple and in some cases mutually exclusive transcription start sites (TSSs). Moreover, TSS selection depends on cell/tissue, development stage and environmental conditions. Such complex promoter structures make their computational identification notoriously difficult. Here, we present TSSPlant, a novel tool that predicts both TATA and TATA-less promoters in sequences of a wide spectrum of plant genomes. The tool was developed by using large promoter collections from ppdb and PlantProm DB. It utilizes eighteen significant compositional and signal features of plant promoter sequences selected in this study, that feed the artificial neural network-based model trained by the backpropagation algorithm. TSSPlant achieves significantly higher accuracy compared to the next best promoter prediction program for both TATA promoters (MCC≃0.84 and F1-score≃0.91 versus MCC≃0.51 and F1-score≃0.71) and TATA-less promoters (MCC≃0.80, F1-score≃0.89 versus MCC≃0.29 and F1-score≃0.50). TSSPlant is available to download as a standalone program at http://www.cbrc.kaust.edu.sa/download/.
Therapeutic Options for Hydrating Airway Mucus in Cystic Fibrosis (2015)

Rehydrating mucus increases MCC. Mucus hydration can be achieved by direct hydration (administering osmotic agents to set up an osmotic gradient), using CFTR modulators to correct dysfunctional CFTR, or it can be achieved pharmacologically (targeting other ion channels on airway epithelial cells). Key Messages: The molecular mechanisms of several therapies are discussed in the context of pre-clinical and clinical trial studies. Currently, only the osmotic agent 7% hypertonic saline and the CFTR 'potentiator' VX-770 (ivacaftor) are used clinically to hydrate mucus. Emerging therapies include the osmotic agent mannitol (Bronchitol), the intracellular Ca(2+)-raising agent Moli1901/lancovutide, the CFTR potentiator sildenafil [phosphodiesterase type 5 (PDE5) inhibitor] and the CFTR 'corrector' VX-809 (lumacaftor). Other CFTR correctors (e.g. 'chemical chaperones') are also showing pre-clinical promise.
Rethinking Table Parsing using Graph Neural Networks (2019)

Document structure analysis, such as zone segmentation and table parsing, is a complex problem in document processing and is an active area of research. The recent success of deep learning in solving various computer vision and machine learning problems has not been reflected in document structure analysis since conventional neural networks are not well suited to the input structure of the problem. In this paper, we propose an architecture based on graph networks as a better alternative to standard neural networks for table parsing. We argue that graph networks are a more natural choice for these problems, and explore two gradient-based graph neural networks. Our proposed architecture combines the benefits of convolutional neural networks for visual feature extraction and graph networks for dealing with the problem structure. We empirically demonstrate that our method outperforms the baseline by a significant margin. In addition, we identify the lack of large scale datasets as a major hindrance for deep learning research for structure analysis, and present a new large scale synthetic dataset for the problem of table parsing. Finally, we open-source our implementation of dataset generation and the training framework of our graph networks to promote reproducible research in this direction.