gebhart/patrepeval huggingface dataset:
Cellular recovery of dividing and confluent C3H10T1/2 cells from N-methyl-N′-nitro-N-nitrosoguanidine in the presence of ADP ribosylation inhibitors (1985)

The relationship between treatment with 3-methoxy-benzamide (MBA), a potent inhibitor of ADP-ribosylation reactions, and the response of C3H10T1/2 cells to N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) has been examined. Quiescent cells effected potentially lethal damage repair (PLDR) over a 48-h period following MNNG and the repair was coincident with the removal of DNA strand breaks. MBA had no effect on PLDR but was very co-cytotoxic with MNNG in dividing cells. The presence of MBA caused the appearance of an additional number of DNA strand breaks following MNNG in both quiescent and dividing cells. These results suggest that ADP-ribosylation is required for normal cell cycle progression following DNA damage in dividing cells.
Dissociable neural responses to facial expressions of sadness and anger (1999)

Previous neuroimaging and neuropsychological studies have investigated the neural substrates which mediate responses to fearful, disgusted and happy expressions. No previous studies have investigated the neural substrates which mediate responses to sad and angry expressions. Using functional neuroimaging, we tested two hypotheses. First, we tested whether the amygdala has a neural response to sad and/or angry facial expressions. Secondly, we tested whether the orbitofrontal cortex has a specific neural response to angry facial expressions. Volunteer subjects were scanned, using PET, while they performed a sex discrimination task involving static grey-scale images of faces expressing varying degrees of sadness and anger. We found that increasing intensity of sad facial expression was associated with enhanced activity in the left amygdala and right temporal pole. In addition, we found that increasing intensity of angry facial expression was associated with enhanced activity in the orbitofrontal and anterior cingulate cortex. We found no support for the suggestion that angry expressions generate a signal in the amygdala. The results provide evidence for dissociable, but interlocking, systems for the processing of distinct categories of negative facial expression.
Release of dissolved organic matter by coastal diatoms (2007)

Dissolved organic matter (DOM) production was examined in axenic batch cultures of five coastal diatom species. For Chaetoceros decipiens , dissolved organic carbon (DOC) accumulated beginning in late exponential growth as a result of increased cell density. For Cylindrotheca closterium , DOC actually decreased in late exponential growth and reached zero by the end of the experiment. This coincided with continued particulate organic carbon (POC) production and a threefold increase in the per‐cell concentration of transparent exopolymer particles after nutrients were depleted. DOC release rates varied between species but were significantly higher for all five species in exponential or transition growth than during stationary growth. On average, 5% of the total fixed C was released as DOC for four of the diatoms, whereas C. decipiens released ~21% of its fixed C as DOC. The percentage of fixed C released as DOC varied little with nutrient availability or diatom growth stage. The DOM produced by some diatom species adheres to filters and is measured in the particulate organic matter (POM) fraction when cells are separated from the medium by filtration. This may be an important problem when diatom species with known benthic life histories are prevalent. In contrast, for species like Chaetoceros that have no benthic life history, DOM release rates estimated by bulk measurements or 14 C appear to be accurate. Overall, these results indicate that the species composition of phytoplankton blooms has the potential to influence the relative importance of POM and DOM production and can complicate interpretation of those measurements.
Structural evidence that propofol stabilizes different GABA(A) receptor states at potentiating and activating concentrations. (2002)

The GABA(A) receptor is a target of many general anesthetics, such as propofol. General anesthetic binding sites are distinct from the GABA binding sites. At low concentrations, the anesthetics potentiate the currents induced by submaximal GABA concentrations. At higher concentrations the anesthetics directly activate GABA(A) receptors. In contrast, benzodiazepines, such as diazepam, only potentiate currents induced by submaximal GABA concentrations. Channel kinetic studies suggest that these drugs stabilize different receptor states. We previously showed that the accessibility of the anionic sulfhydryl reagent p-chloromercuribenzenesulfonate (pCMBS(-)) applied extracellularly to cysteines substituted for residues in the GABA(A) alpha1 subunit M3 membrane-spanning segment was state-dependent. The subset of pCMBS(-)-accessible, M3 segment cysteine mutants acts as a reporter for receptor conformation. Here we show that pCMBS(-), applied in the presence of a potentiating concentration of propofol, reacts with a subset of alpha1 subunit, M3 segment, cysteine-substitution mutants (Y294C, V297C, I302C, F304C). In the presence of a directly activating concentration of propofol pCMBS(-) reacts with a different subset of the M3 cysteine-substitution mutants (Y294C, S299C, I302C, E303C, A305C). These subsets are distinct from the subsets of M3 cysteine-substitution mutants that are reactive with pCMBS(-) in the absence and presence of GABA and in the presence of diazepam. We hypothesize that distinct subsets of reactive residues represent distinct conformations or ensembles of conformations of the receptor. These results provide structural evidence for at least five distinct receptor states, three nonconducting states, resting, diazepam-bound and potentiating propofol-bound, and two conducting-desensitized states, the activating propofol-bound and GABA-bound states.
Experience in black-box OSPF measurement (2001)

OSPF (Open Shortest Path First) is a widely used intra-domain routing protocol in IP networks. Internal processing delays in OSPF implementations impact the speed at which updates propagate in the network, the load on individual routers, and the time needed for both intra-domain and inter-domain routing to reconverge following an internal topology or a configuration change. An OSPF user, such as an Internet Service Provider, typically has no access to the software implementation, and no way to estimate these delays directly. In this paper, we present black-box methods (i.e., measurements that rely only on external observations) for estimating and trending delays for key internal tasks in OSPF: processing Link State Advertisements (LSAs), performing Shortest Path First calculations, updating the Forwarding Information Base, and flooding LSAs. Corresponding measurements are reported for production routers from Cisco Systems. To help validate the methodology, black-box and white-box (i.e., measurements that rely on internal instrumentation) are reported for a open source OSPF implementation, GateD.
Fluorescence Quenching as an Indirect Detection Method for Nitrated Explosives (2001)

A novel approach based on fluorescence quenching is presented for the analysis of nitrated explosives. Seventeen common explosives and their degradation products are shown to be potent quenchers of pyrene, having Stern-Volmer constants that generally increase with the degree of nitration. Aromatic explosives such as 2,4,6-trinitrotoluene (2,4,6-TNT) are more effective quenchers than aliphatic or nitramine explosives. In addition, nitroaromatic explosives are found to have unique interactions with pyrene that lead to a wavelength dependence of their Stern-Volmer constants. This phenomenon allows for their differentiation from other nitrated explosives. The fluorescence quenching method is then applied to the determination of hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX), octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazine(HMX), 2,4,6-TNT, nitromethane, and ammonium nitrate in various commercial explosive samples. The samples are separated by capillary liquid chromatography with post-column addition of the pyrene solution and detection by laser-induced fluorescence. The indirect fluorescence quenching method shows increased sensitivity and selectivity over traditional UV-visible absorbance as well as the ability to detect a wider range of organic and inorganic nitrated compounds.
Funnel metadynamics as accurate binding free-energy method (2013)

A detailed description of the events ruling ligand/protein interaction and an accurate estimation of the drug affinity to its target is of great help in speeding drug discovery strategies. We have developed a metadynamics-based approach, named funnel metadynamics, that allows the ligand to enhance the sampling of the target binding sites and its solvated states. This method leads to an efficient characterization of the binding free-energy surface and an accurate calculation of the absolute protein-ligand binding free energy. We illustrate our protocol in two systems, benzamidine/trypsin and SC-558/cyclooxygenase 2. In both cases, the X-ray conformation has been found as the lowest free-energy pose, and the computed protein-ligand binding free energy in good agreement with experiments. Furthermore, funnel metadynamics unveils important information about the binding process, such as the presence of alternative binding modes and the role of waters. The results achieved at an affordable computational cost make funnel metadynamics a valuable method for drug discovery and for dealing with a variety of problems in chemistry, physics, and material science.
Using Highly Discriminative Keys for Indexing in a Peer-to-Peer Full Text Retrieval System (2005)

Abstract. Excessive network bandwidth consumption, caused by the transmission of long posting lists, was identified as one of the major bottlenecks for implementing distributed full-text retrieval in a Peer-to-Peer (P2P) architecture. To address this problem we introduce a novel approach to indexing using highly discriminative terms and term sets, which leads to short posting lists and therefore reduces the network traffic by almost one order of magnitude. In addition, we show that retrieval based on discriminative term sets provides a retrieval quality comparable to standard full-text retrieval using TF-IDF ranking. Our indexing scheme is an important improvement towards realistic P2P retrieval systems that opens the opportunity to virtually unlimited scalability well beyond the capacity of today’s best centralized Web search engines. Keywords:distributed information retrieval, peer-to-peer (P2P), highly discriminative keys, distributional semantics 1 Introduction and
Extensive Antibody Cross-reactivity among Infectious Gram-negative Bacteria Revealed by Proteome Microarray Analysis (2008)

Antibodies provide a sensitive indicator of proteins displayed by bacteria during sepsis. Because signals produced by infection are naturally amplified during the antibody response, host immunity can be used to identify biomarkers for proteins that are present at levels currently below detectable limits. We developed a microarray comprising approximately 70% of the 4066 proteins contained within the Yersinia pestis proteome to identify antibody biomarkers distinguishing plague from infections caused by other bacterial pathogens that may initially present similar clinical symptoms. We first examined rabbit antibodies produced against proteomes extracted from Y. pestis, Burkholderia mallei, Burkholderia cepecia, Burkholderia pseudomallei, Pseudomonas aeruginosa, Salmonella typhimurium, Shigella flexneri, and Escherichia coli, all pathogenic Gram-negative bacteria. These antibodies enabled detection of shared cross-reactive proteins, fingerprint proteins common for two or more bacteria, and signature proteins specific to each pathogen. Recognition by rabbit and non-human primate antibodies involved less than 100 of the thousands of proteins present within the Y. pestis proteome. Further antigen binding patterns were revealed that could distinguish plague from anthrax, caused by the Gram-positive bacterium Bacillus anthracis, using sera from acutely infected or convalescent primates. Thus, our results demonstrate potential biomarkers that are either specific to one strain or common to several species of pathogenic bacteria.
Introduction (2007)

Le 2 décembre 2004, une journée d’études sur "Médias, censure et territoire" a été organisée par Brigitte Dumortier. Elle a permis à des chercheurs de confronter leur réflexion sur les médias et de dialoguer avec des journalistes. Bien au-delà des questions classiques de diffusion, il s’agissait de cerner les paramètres d’une géographie des médias dans une mondialisation dont ceux-ci sont l’un des principaux moteurs et de montrer comment l’information construit des territoires. Les financemen...
Effect of family role on response to disaster (1993)

This study hypothesized that family role (marital and parental status) would moderate the effect of disaster exposure on the mental health of victims. The study included St. Louis residents exposed to floods and dioxin, as well as Puerto Rican respondents exposed to floods and mudslides. In St. Louis, worst outcomes were found for single and married parents exposed to disaster, substantially exceeding the symptomatology of all unexposed respondents except non-victim single parents. In Puerto Rico, victims without families had higher levels of alcohol abuse symptoms than did any other subgroup. Perceived emotional support was found to be an important moderator of disaster's effect on psychiatric distress in this site, generally overriding the effect of family role. Single parents in both sites who were exposed to disaster had substantially reduced levels of emotional support available to them, as compared to unexposed single parents, suggesting that single parents are at particularly high risk for losing access to emotional support following a disaster. This study suggests that both single and married parents constitute important high-risk victim groups. The findings also suggest that those perceiving they lack adequate emotional support, regardless of family role, may be in special need of services.
A compiler-directed cache coherence scheme with improved intertask locality (1994)

We introduce a compiler directed coherence scheme which can exploit most of the temporal and spatial locality across task boundaries. It requires only an extended tag field per cache word, one modified memory access instruction, and a counter called the epoch counter in each processor. By using the epoch counter as a system wide version number, the scheme simplifies the cache hardware of previous version control (Hoichi Cheong and A.V. Veidenbaum, 1989) or timestamp based schemes (S.L. Min and J.-L. Baer, 1989), but still exploits most of the temporal and spatial locality across task boundaries. We present a compiler algorithm to generate the appropriate memory access instructions for the proposed scheme. The algorithm is based on a data flow analysis technique. It identifies potential stale references by examining memory reference patterns in a source program. >
An Overview of Anatomical Considerations of Infants and Children in the Adult World of Automobile Safety Design (1998)

The infant and child differ structurally from the adult in a number of ways which are critical to the design for protection against impact forces and for adequate occupant restraint systems. The purpose of this paper is to bring together a profile of the anatomy, anthropometry, growth and development of the infant and child. Age differences related to the proper design of child restraint systems are emphasized. Problems discussed include child--adult structural differences, center of gravity of the body, the head mass in relation to the neck and general body proportions, positions of key organs, and biomechanical properties of tissues.
Spatially Dependent Lattice Deformations for Dislocations at the Edges of Graphene (2014)

We show that dislocations located at the edge of graphene cause different lattice deformations to those located in the bulk lattice. When a dislocation is located near an edge, a decrease in the rippling and increase of the in-plane rotation occurs relative to the dislocations in the bulk. The increased in-plane rotation near the edge causes bond rotations at the edge of graphene to reduce the overall strain in the system. Dislocations were highly stable and remained fixed in their position even when located within a few lattice spacings from the edge of graphene. We study this behavior at the atomic level using aberration-corrected transmission electron microscopy. These results show detailed information about the behavior of dislocations in 2D materials and the strain properties that result.
Survey of the issues surrounding network traffic monitoring (2015)

As networks are continuously growing, their operation and management are becoming more and more complex. In consequence, current network monitoring systems generate a huge volume of measurement data which represents one of the most critical issues in the management of computer networks. This paper is dedicated to the challenges in network traffic monitoring. It provides a brief overview of several issues that arise during traffic measurements. We inspect the issues from three viewpoints: (1) the impact on the inter-networking devices, (2) resource asymmetry and (3) real-time data evaluation. To quantify the volume of measurement data and its cost we also performed two experiments. They were focused (1) on the estimation of the average volume of data that must be processed during monitoring along with its impact on system resources and (2) on the cost of interpretation of the measurement data. The paper is concluded by some remarks on the directions at which should the research and development be aimed as well as with a brief introduction of our idea for addressing the described issues.
Optimizing data sharing and address translation for the Cell BE Heterogeneous Chip Multiprocessor (2008)

Heterogeneous Chip Multiprocessors (HMPs), such as the Cell Broadband Engine, offer a new design optimization opportunity by allowing designers to provide accelerators for application specific domains. Data sharing between CPUs and accelerators, and memory access mechanisms and protocols are crucial decisions in the design of an HMP. In this article, we analyze the choices between hardware and software managed coherence between CPU and accelerators for DMA-based data sharing, and find that hardware-coherent DMA shows a performance benefit of up to 3x, even for simple workloads.We explore memory address translation architecture choices for DMA-based data sharing. In multiprogramming environments, address translation is commonly used to separate processes. For efficiency, direct access to system memory requires address translation capabilities in the accelerator. We find that hardware managed address translation shows a performance benefit of up to 5x, even for simple workloads, by avoiding the costs of accelerator/CPU communication and supervisor management of the translation context and the introduction of a serial bottleneck on the CPU.
Correlating Pyrene Excimer Formation with Polymer Chain Dynamics in Solution. Possibilities and Limitations (2007)

Four types of pyrene-labeled polystyrene samples (Py−PS) were prepared and the process of excimer formation between the pyrene labels was characterized by steady-state and time-resolved fluorescence to assess the effect the mode of pyrene incorporation into a polymer has on the kinetics of excimer formation. The pyrene label was incorporated into the PS backbone by either (1) reacting 1-pyrenemethoxide with a chloromethylated polystyrene backbone to yield the GrE−PS series, (2) copolymerizing styrene with 4-(1-pyrenyl)methoxymethylstyrene to yield the CoE−PS series, (3) copolymerizing styrene with N-(1-pyrenylmethyl)acrylamide to yield the CoA−PS series, or (4) polymerizing α,ω-dicarboxyl end-capped polystyrenes with l-lysine-1-pyrenemethylamide dihydrochloride to yield the ES−PS series. Steady-state and time-resolved fluorescence experiments demonstrated that the long and flexible linker of GrE−PS and CoE−PS enabled more efficient excimer formation than the short and rigid linker of CoA−PS, and that spacing the pyrene pendants in ES−PS led to a strong reduction in excimer formation. The fluorescence blob model (FBM) was applied to analyze quantitatively the monomer and excimer fluorescence decays of the four Py−PSs. The FBM analysis confirmed that the longer ether linker of GrE−PS and CoE−PS enabled the excited pyrene label to probe a larger volume inside the polymer coil. The level of clustering of the pyrene pendants was found to be minimal for ES−PS, as expected from its structural design. Interestingly, the pyrene pendants were twice more clustered for GrE−PS than for CoE−PS, despite both polymers having an identical chemical structure. The results for the GrE−PS and CoE−PS series suggest that reacting groups distribute themselves differently in a copolymer whether they are incorporated by a grafting onto reaction or copolymerization.
One-chip integrated resonance circuit with a capacitive pressure sensor (1997)

This paper describes the design, realization and measurement results of an integrated resonance circuit, suggested for pressure measurements. The circuit consists of a variable capacitor and a flat coil, i.e. a passive LC resonator. Changes in capacitance are created by pressure changes. The resonance frequency is changed in the resonance circuit. The circuit as a passive resonance circuit is designed for contactless pressure measurement and wireless information transmission in medical and other applications. The circuit was realized as a monolith integrated sensor on silicon. The dimensions are approximately . Several variants were realized with different layouts and values. The resonance frequency and the frequency dependence of the quality factor Q have been measured.
On the “degrees of freedom” of the lasso (2007)

We study the effective degrees of freedom of the lasso in the framework of Stein’s unbiased risk estimation (SURE). We show that the number of nonzero coefficients is an unbiased estimate for the degrees of freedom of the lasso—a conclusion that requires no special assumption on the predictors. In addition, the unbiased estimator is shown to be asymptotically consistent. With these results on hand, various model selection criteria—Cp, AIC and BIC—are available, which, along with the LARS algorithm, provide a principled and efficient approach to obtaining the optimal lasso fit with the computational effort of a single ordinary least-squares fit.
Contact electrification across metal-dielectric and dielectric-dielectric interfaces (1957)

An apparatus is described by means of which a spherical dielectric surface can be compressed under various loads against either a plane metal disk or a plane dielectric disk. A transfer of electric charge across the interface is recorded when the surfaces are separated. The polarity of charging between any two materials depends upon the relative positions of those materials in an electrostatic series; a metal surface does not always assume a positive charge as found for impact electrification. For two given materials the amount of charge is proportional to the contact area between the surfaces and provided that one of the surfaces has a resistivity above a critical value (5 × 1011 Ωcm) then the charge density for various combinations of materials is approximately proportional to the lower dielectric constant in each combination. This result suggests that the charging may be limited by electrical back-discharge between the separating surfaces. It is considered to be unlikely that the electrification originates from a difference in the contact potentials of the two surfaces involved.