gebhart/patrepeval huggingface dataset:
Opening and tuning of band gap by the formation of diamond superlattices in twisted bilayer graphene (2012)

We report results of first-principles density functional theory calculations, which introduce a new class of carbon nanostructures formed due to creation of covalent interlayer C-C bonds in twisted bilayer graphene (TBG). This interlayer bonding becomes possible by hydrogenation of the graphene layers according to certain hydrogenation patterns. The resulting relaxed configurations consist of two-dimensional (2D) superlattices of diamondlike nanocrystals embedded within the graphene layers, with the same periodicity as that of the Moir\'e pattern corresponding to the rotational layer stacking in TBG. The 2D diamond nanodomains resemble the cubic or the hexagonal diamond phase. The detailed structure of these superlattice configurations is determined by parameters that include the twist angle, ranging from 0\ifmmode^\circ\else\textdegree\fi{} to \ensuremath{\sim}15\ifmmode^\circ\else\textdegree\fi{}, and the number of interlayer C-C bonds formed per unit cell of the superlattice. We demonstrate that formation of such interlayer-bonded finite domains causes the opening of a band gap in the electronic band structure of TBG, which depends on the density and spatial distribution of interlayer C-C bonds. We have predicted band gaps as wide as 1.2 eV and found that the band gap increases monotonically with increasing size of the embedded diamond nanodomain in the unit cell of the superlattice. Such nanostructure formation constitutes a promising approach for opening a precisely tunable band gap in bilayer graphene.
Light‐sensitive Intelligent Drug Delivery Systems<sup>†</sup> (2009)

Drug delivery systems (DDS) capable of releasing an active molecule at the appropriate site and at a rate that adjusts in response to the progression of the disease or to certain functions/biorhythms of the organism are particularly appealing. Biocompatible materials sensitive to certain physiological variables or external physicochemical stimuli (intelligent materials) can be used for achieving this aim. Light-responsiveness is receiving increasing attention owing to the possibility of developing materials sensitive to innocuous electromagnetic radiation (mainly in the UV, visible and near-infrared range), which can be applied on demand at well delimited sites of the body. Some light-responsive DDS are of a single use (i.e. the light triggers an irreversible structural change that provokes the delivery of the entire dose) while others able to undergo reversible structural changes when cycles of light/dark are applied, behave as multi-switchable carriers (releasing the drug in a pulsatile manner). In this review, the mechanisms used to develop polymeric micelles, gels, liposomes and nanocomposites with light-sensitiveness are analyzed. Examples of the capability of some polymeric, lipidic and inorganic structures to regulate the release of small solutes and biomacromolecules are presented and the potential of light-sensitive carriers as functional components of intelligent DDS is discussed.
C-reactive Protein and Atrial Fibrillation Is inflammation a consequence or a cause of atrial fibrillation? (2004)

To clarify whether inflammation is a cause or consequence of atrial fibrillation (AF), we measured high-sensitivity C-reactive protein (hs-CRP), interleukin-6 (IL-6), and tumor necrosis factor alpha (TNF-alpha) before and after pharmacological cardioversion in 15 patients with paroxysmal AF. Levels of hs-CRP, IL-6, and TNF-alpha after cardioversion were significantly higher than those in controls (P < 0.05). Furthermore, the levels of these indices did not differ significantly even at 24 hours and 2 weeks after cardioversion. These results suggest that inflammation is a causative agent of paroxymal AF.
The Role of Pneumolysin in Ocular Infections with<i>Streptococcus Pneumoniae</i> (1990)

Pneumolysin, a cytolytic protein produced by Streptococcus pneumoniae, has many properties which suggest it may be an important virulence factor in pneumococcal ocular infections. To directly test this possibility, we have constructed pneumolysin-negative strains of S. pneumoniae and compared their virulence with that of the wild type in a rabbit model of intracorneal infection. A pneumolysin-negative strain produced by chemical mutagenesis (probably a point mutant) was found to be no less virulent than the parent strain. However, a strain bearing a deletion in the pneumolysin gene showed greatly reduced virulence. This strain produced less pathology while showing significantly higher bacterial counts. These results suggest that a property of the pneumolysin molecule other than its cytolytic (hemolytic) activity may be involved in its pathogenic mechanism of action. This property may be the ability to activate complement, known to be a function of pneumolysin, which results in influx of PMNs, reducing the bacterial counts but also producing tissue damage.
On the design of multi-site microelectrodes for neuronal recordings (2000)

We therefore conclude that NTCP models, at least in some cases, are definitely tools not toys. However, like any good tool, they can be abused and in fact could lead to injury with misuse. In particular, we have pointed out that it is risky indeed to apply NTCP models to dose distributions which are very dissimilar to the dose distributions for which the NTCP model has been validated. While this warning is somewhat fuzzy, it is clear that more research needs to be done in this area. We believe that ultimately for NTCP models to be used routinely in treatment planning in a safe and effective way, the actual application will need to be closely related to the characteristics of the data sets and the uncertainties of the treatment parameters in the models under consideration. Another sign that NTCP models are becoming tools rather than toys is that there is often good agreement as to what constitutes a correct direction of improving the reduced risk for that particular complication endpoint. Thus, for example, mean dose to normal lung almost always comes out as being the most predictive or nearly most predictive factor in the analysis of radiation pneumonitis.
Sequential change‐point detection based on direct density‐ratio estimation (2011)

Abstract Change‐point detection is the problem of discovering time points at which properties of time‐series data change. This covers a broad range of real‐world problems and has been actively discussed in the community of statistics and data mining. In this paper, we present a novel nonparametric approach to detecting the change of probability distributions of sequence data. Our key idea is to estimate the ratio of probability densities, not the probability densities themselves. This formulation allows us to avoid nonparametric density estimation, which is known to be a difficult problem. We provide a change‐point detection algorithm based on direct density‐ratio estimation that can be computed very efficiently in an online manner. The usefulness of the proposed method is demonstrated through experiments using artificial and real‐world datasets. © 2011 Wiley Periodicals, Inc. Statistical Analysis and Data Mining 2011
Malignant lymphomas: cell surface markers and advances in classification. (1981)

Identification of cell surface markers permits detailed analysis and classification of the cells involved in the immune response. Application of these techniques to the study of malignant lymphomas has led to our understanding of these tumors as neoplasms of specific elements of the immune system. This approach, which emphasizes functional characteristics of the neoplastic cells, promises to revolutionize the diagnosis and classification of the lymphomas and replace classifications based solely on morphology.
<i>Chlamydia pneumoniae</i> , Herpes Simplex Virus Type 1, and Cytomegalovirus and Incident Myocardial Infarction and Coronary Heart Disease Death in Older Adults (2000)

Background —Whether serological evidence of prior infection with Chlamydia pneumoniae , herpes simplex virus type 1 (HSV-1), and cytomegalovirus (CMV) is associated with myocardial infarction (MI) and coronary heart disease (CHD) death remains a source of controversy. Methods and Results —We conducted a nested case-control study among participants in the Cardiovascular Health Study, a cohort study of persons aged ≥65 years. Cases experienced an incident MI and CHD death (n=213). Control subjects were matched to cases by age, sex, clinic, year of enrollment, and month of blood draw (n=405). Serum was analyzed for IgG antibodies to C pneumoniae , HSV-1, and CMV. After adjustment for other risk factors, the risk of MI and CHD death was associated with the presence of IgG antibodies to HSV-1 (odds ratio [OR] 2.0, 95% CI 1.1 to 3.6) but was not associated with the presence of IgG antibodies to either C pneumoniae (OR 1.1, 95% CI 0.7 to 1.8) or CMV (OR 1.2, 95% CI 0.7 to 1.9). Although there was little association with low to moderate C pneumoniae antibody titers (≤1:512), high-titer (1:1024) C pneumoniae antibody was associated with an increased risk (OR 2.2, 95% CI 1.1 to 4.4). Conclusions —Among older adults, the presence of IgG antibodies to HSV-1 was associated with a 2-fold increase in the risk of incident MI and CHD death. For C pneumoniae , only high-titer IgG antibodies were associated with an increased risk of MI and CHD death. The presence of IgG antibodies to CMV was not associated with risk among the elderly.
Novel Feature Extraction, Selection and Fusion for Effective Malware Family Classification (2015)

Modern malware is designed with mutation characteristics, namely polymorphism and metamorphism, which causes an enormous growth in the number of variants of malware samples. Categorization of malware samples on the basis of their behaviors is essential for the computer security community, because they receive huge number of malware everyday, and the signature extraction process is usually based on malicious parts characterizing malware families. Microsoft released a malware classification challenge in 2015 with a huge dataset of near 0.5 terabytes of data, containing more than 20K malware samples. The analysis of this dataset inspired the development of a novel paradigm that is effective in categorizing malware variants into their actual family groups. This paradigm is presented and discussed in the present paper, where emphasis has been given to the phases related to the extraction, and selection of a set of novel features for the effective representation of malware samples. Features can be grouped according to different characteristics of malware behavior, and their fusion is performed according to a per-class weighting paradigm. The proposed method achieved a very high accuracy ($\approx$ 0.998) on the Microsoft Malware Challenge dataset.
Optimizing resource utilization and testability using hot potato techniques (1994)

Article Optimizing resource utilization and testability using hot potato techniques Share on Authors: Miodrag Potkonjak C&C Research Laboratories, NEC, Princeton, NJ C&C Research Laboratories, NEC, Princeton, NJView Profile , Sujit Dey C&C Research Laboratories, NEC, Princeton, NJ C&C Research Laboratories, NEC, Princeton, NJView Profile Authors Info & Claims DAC '94: Proceedings of the 31st annual Design Automation ConferenceJune 1994 Pages 201–205https://doi.org/10.1145/196244.196350Published:06 June 1994 11citation361DownloadsMetricsTotal Citations11Total Downloads361Last 12 Months2Last 6 weeks0 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
Targeting <i>Staphylococcus aureus</i> Quorum Sensing with Nonpeptidic Small Molecule Inhibitors (2014)

A series of 3-oxo-C12-HSL, tetramic acid, and tetronic acid analogues were synthesized to gain insights into the structural requirements for quorum sensing inhibition in Staphylococcus aureus. Compounds active against agr were noncompetitive inhibitors of the autoinducing peptide (AIP) activated AgrC receptor, by altering the activation efficacy of the cognate AIP-1. They appeared to act as negative allosteric modulators and are exemplified by 3-tetradecanoyltetronic acid 17, which reduced nasal cell colonization and arthritis in a murine infection model.
Incremental mapping compilation in an object-to-relational mapping system (2013)

In an object-to-relational mapping system (ORM), mapping expressions explain how to expose relational data as objects and how to store objects in tables. If mappings are sufficiently expressive, then it is possible to define lossy mappings. If a user updates an object, stores it in the database based on a lossy mapping, and then retrieves the object from the database, the user might get a different result than the updated state of the object; that is, the mapping might not "roundtrip." To avoid this, the ORM should validate that user-defined mappings roundtrip the data. However, this problem is NP-hard, so mapping validation can be very slow for large or complex mappings.
Allyl Glycidyl Ether-Based Polymer Electrolytes for Room Temperature Lithium Batteries (2013)

A new family of polymer electrolytes based on a poly(allyl glycidyl ether) (PAGE) platform has been developed that overcomes many of the limitations of poly(ethylene oxide) (PEO) for battery electrolyte applications. PAGE was shown to have peak conductivities at [O]/[Li] = 16, with σ > 3 × 10–5 S/cm at 25 °C and σ > 5 × 10–4 S/cm at 80 °C. Below 60 °C, PAGE has a conductivity that is 10–100 times higher than that of PEO at equivalent salt concentrations with this disparity in conductivities between PAGE and PEO increasing with decreasing temperature. In addition, the synthetic versatility of allyl glycidyl ether as a building block is demonstrated by the preparation and evaluation of various AGE–EO macromolecular architectures that show superior performance to both PAGE and PEO.
<i>In planta</i> ORFeome analysis by large‐scale over‐expression of GATEWAY<sup>®</sup>‐compatible cDNA clones: screening of ERF transcription factors involved in abiotic stress defense (2007)

Genomic approaches have generated large Arabidopsis thaliana open reading frame (ORF) collections. However, tools are required to functionally characterize this ORFeome. Here we describe a batch procedure to simultaneously recombine a population of GATEWAY-tagged full-length cDNAs into a plant expression vector. A pool of agrobacteria carrying these constructs has been used in flower-dip transformation experiments to obtain a collection of transgenic lines that over-express HA-tagged ORFs. This AtTORF-Ex library can be used in various screening approaches to identify particular gene family members involved in plant development or stress responses. The feasibility of the approach was studied using a near-complete collection of the Arabidopsis ethylene response factor (ERF) transcription factor (TF) family. Quality control performed at each step of the procedure revealed that the complexity of the population is maintained, and that almost all members of the ORF collection are covered by the plant library. The frequency of multiple transformation events has been determined as approximately 4%. Significant transgene expression was detected at the RNA and protein level in more than 60% and 30% of the transgenic plants, respectively. Striking phenotypic alterations were observed in approximately 4% of the plants. Many ERF TFs have been shown to participate in plant stress responses. As a proof of principle, the AtTORF-Ex library has been used in a selection procedure to isolate TFs involved in enhanced abiotic stress tolerance. The corresponding TF gene can be easily polymerase chain reaction-amplified using GATEWAY att site-specific primers. In summary, we describe here a method that can be generally applied for functional analysis of ORFeomes in planta.
Reversible Inhibition of Calcium Oxalate Monohydrate Growth by an Osteopontin Phosphopeptide (2013)

Calcium oxalate, primarily as calcium oxalate monohydrate (COM), is the primary constituent of most kidney stones. Certain proteins, such as osteopontin (OPN), inhibit stone formation. The complexity of stone formation and the effects of urinary proteins at various stages of the process make it hard to predict the exact physiological roles of these proteins in growth inhibition. The inhibition of crystallization due to adsorbed impurities is usually explained in terms of a model proposed in 1958 by Cabrera and Vermilyea. In this model, impurities adsorb to growth faces and pin growth steps, forcing them to curve, thus impeding their progress via the Gibbs-Thomson effect. To determine the role of OPN in the biomineralization of kidney stones, crystal growth on the {010} face of COM was examined in real time with atomic force microscopy in the presence of a synthetic peptide corresponding to amino acids 65-80 (hereafter referred to as pOPAR) of rat bone OPN. We observed clear changes in the morphology of the growth-step structure and a decrease in step velocity upon addition of pOPAR, which suggest adsorption of inhibitors on the {010} growth hillocks. Experiments in which pOPAR was replaced in the growth cell by a supersaturated solution showed that COM hillocks are able to fully recover to their preinhibited state. Our results suggest that recovery occurs through incorporation of the peptide into the growing crystal, rather than by, e.g., desorption from the growth face. This work provides new insights into the mechanism by which crystal growth is inhibited by adsorbants, with important implications for the design of therapeutic agents for kidney stone disease and other forms of pathological calcification.
DPDPE-UK14,304 synergy is retained in mu opioid receptor knockout mice (2003)

When agonists to alpha(2)adrenergic receptor (AR) and delta opioid receptor (DOR) are co-administered, they act synergistically to inhibit nociceptive elicited behavior. Some previous studies of synergism have used the DOR-selective agonist [D-Pen(2),D-Pen(5)]-enkehphalin (DPDPE), however, DPDPE has been shown to be less potent in mu opioid receptor-knockout (MOR-KO) mice. It is possible, therefore, that MOR contributes to the synergism of DPDPE with the alpha(2)AR agonists. We compared the interactions of spinally administered DPDPE with an alpha(2)AR-adrenergic agonist in MOR-KO and MOR-wildtype (WT) mice. In these mice, morphine is ineffective and the potency of spinally administered DOR agonists, deltorphin II (DELT II) and DPDPE decreased 16- and 250-fold, respectively. Antagonism studies using the MOR-selective antagonist, D-Phe-Cys-Tyr-D-Trp-Orn-Thr-Phe-Thr-NH(2) (CTOP) and the DOR-selective antagonist, naltrindole HCl (naltrindole) demonstrated that while DOR mediates DPDPE-induced antinociception in MOR-KO, both MOR and DOR participate in DPDPE antinociception in WT mice, suggesting that DPDPE is less selective for DOR than previously observed in binding studies when given in vivo. The potency of the alpha(2)AR agonist UK14,304 was equivalent in WT and MOR-KO, demonstrating that the loss of opioid-mediated antinociception in the MOR-KO was not due to generalized impairment of antinociceptive processing. Interestingly, isobolographic analysis showed that, despite substantial loss of DPDPE potency in MOR-KO, DPDPE-UK14,304 synergism is fully retained. Collectively, these experiments demonstrate that although MOR participates in DELT II- and DPDPE-mediated spinal antinociception, DOR independently participates in synergistic antinociception with alpha(2)AR. Resolution of the roles of the opioid receptor subtypes in opioid agonist-induced effects may require comparison of the effects of multiple selective agonists in knockout animals.
[Chemically induced (streptozotocin-alloxan) diabetes mellitus in dogs]. (2000)

To evaluate the efficiency and toxic and side effect of the combined chemical inducer for Type I diabetes mellitus, Type I diabetes in 9 adult dogs were induced with alloxan(50 mg.kg-1) and streptozotocin (30 mg.kg-1) with vein injection. After 7-14 days, the blood glucose of 5 male dogs was kept on high levels [mean value was (22.7 +/- 3.2) mmol.L-1], exogenous insulin was (21.4 +/- 2.4) U.day-1. Three female dogs died in 7 days after they had been injected with the combined inducers. Alloxan-streptozotocin combination administration reduced the dosage of each drug, and decreased the toxic and side effect of each drug. The results suggest that this method has a high rate of success to induce Type I diabetes male dogs.
Improved speech modification method (2005)

A speech modification method presented by Griffin and Lim [1] involves modifying the Short-Time Fourier Transform Magnitude function of the original speech, and using it as a reference to iteratively approximate a modified waveform. This method has been successfully applied to time-scale modification and noise reduction of speech [1-3]. In this paper, we discuss our experiments in applying the algorithm to the independent modification of formant and pitch information.
Street social capital in the liquid city (2012)

This article reflects on the lives of a group of young men on Ireland’s socio-economic periphery, focusing on how exclusion shapes their cultural orientation and orders their spatial practices. Whilst populist imaginaries and certain academic understandings of young, disadvantaged, urban males tend to cast them in the role of claiming and violently defending territories, their relationships to space may be considerably more transient and fluid. Within the late-modern ‘liquid city’ exclusion has cast the young men researched here into migratory practices, where they must negotiate relationships with potentially hostile peers in various parts of the urban environment. Adopting street cultural norms of rugged masculinity, crimino-entrepreneurialism and the recourse to violence can result in the accumulation of ‘street social capital’. This can allow disadvantaged young people to secure a sense of existential security, pleasurable experiences, disposable income and a culturally mediated notion of dignity, despite their spatial and socio-economic exclusion.
Effect of Dehydroepiandrosterone on Atherosclerosis in Apolipoprotein E-Deficient Mice (2009)

DHEA might be an effective agent for clinical management of atherosclerosis, but a larger controlled trial is necessary for confirmation.
Triphenylphosphine-assisted highly sensitive fluorescent chemosensor for ratiometric detection of palladium in solution and living cells (2015)

A triphenylphosphine-assisted highly sensitive fluorescent chemosensor for ratiometric detection of palladium in solution and living cells was developed.