gebhart/patrepeval huggingface dataset:
Reducing the signalling overhead for wireless VoIP transmission using weighted prioritisation (2009)

User scheduling in future cellular networks is a complex and much-studied problem, further complicated in the increasingly relevant scenario of delay-sensitive VoIP applications. In such cases, the full buffer model that attempts to maximise the total sum-rate of the individual users does not adequately capture the satisfaction level of the users. As a result, fairness needs to be introduced and this is done in this paper through a modification of the weighted fair queuing (WFQ) approach to resource allocation that uses buffer status reports from mobile terminals (MTs). Put another way, user rates are weighted by respective buffer fill levels. In addition to outperforming both maximum sum-rate and the ldquoconventionalrdquo proportional fair scheduling (PFS) algorithm in terms of the number of satisfied users for VoIP applications, the WFQ used is shown to be able to help reduce the signalling overhead: it is demonstrated here that the weights applied can be adapted depending on the frequency with which the resource allocation is updated. This enables the system to benefit from the reduction in signalling overhead (which arises from a reduced resource allocation update rate) at a diminished loss of performance. Results are based on practical simulation scenarios that can be applied to both LTE and W-CDMA systems and are revealing in terms of the user capacities these systems can offer under realistic levels of traffic load.
Structural Adaptation of Darunavir Analogues against Primary Mutations in HIV-1 Protease (2018)

HIV-1 protease is one of the prime targets of agents used in antiretroviral therapy against HIV. However, under selective pressure of protease inhibitors, primary mutations at the active site weaken inhibitor binding to confer resistance. Darunavir (DRV) is the most potent HIV-1 protease inhibitor in clinic; resistance is limited, as DRV fits well within the substrate envelope. Nevertheless, resistance is observed due to hydrophobic changes at residues including I50, V82, and I84 that line the S1/S1′ pocket within the active site. Through enzyme inhibition assays and a series of 12 crystal structures, we interrogated susceptibility of DRV and two potent analogues to primary S1′ mutations. The analogues had modifications at the hydrophobic P1′ moiety compared to DRV to better occupy the unexploited space in the S1′ pocket where the primary mutations were located. Considerable losses of potency were observed against protease variants with I84V and I50V mutations for all three inhibitors. The crystal structures revealed an unexpected conformational change in the flap region of I50V protease bound to the analogue with the largest P1′ moiety, indicating interdependency between the S1′ subsite and the flap region. Collective analysis of protease–inhibitor interactions in the crystal structures using principle component analysis was able to distinguish inhibitor identity and relative potency solely based on van der Waals contacts. Our results reveal the complexity of the interplay between inhibitor P1′ moiety and S1′ mutations and validate principle component analyses as a useful tool for distinguishing resistance and inhibitor potency.
Polymer surfaces and interfaces in light-emitting devices (1998)

In the context of polymer electronic devices, it is of critical importance to understand the nature of the polymer surfaces and the polymer-electrode interfaces. It has been shown that for conjugated polymers, photoelectron spectroscopy, especially in connection with quantum chemical modeling, provides a maximum amount of both chemical and electronic structural information in one type of measurement. Here are delineated some particular features of the surface electronic structure of conjugated polymers and their interfaces with certain metals and a particular semiconductor, indium-doped tin oxide.
Distributed Task Assignment Based on Gossip with Guaranteed Performance on Heterogeneous Networks (2015)

In this paper we propose a novel distributed algorithm for task assignment on heterogeneous networks. We consider a set of tasks with heterogeneous cost to be assigned to a set of nodes with heterogeneous execution speed and interconnected by a network with unknown topology represented by an undirected graph. Our objective is to minimize the execution time of the set of tasks by the networked system. We propose a local interaction rule which allows the nodes of a network to cooperatively assign tasks among themselves with a guaranteed performance with respect to the optimal assignment exploiting a gossip based randomized interaction scheme. We characterize the convergence properties of the proposed approach and provide simulation results.
Coevolution of DNA-Interacting Proteins and Genome “Dialect” (2005)

Several species-specific characteristics of genome organization that are superimposed on its coding aspects were proposed earlier, including genome signature (GS), genome accent, and compositional spectrum (CS). These notions could be considered as representatives of genome dialect (GD). We measured within the Proteobacteria some GD representatives, the relative abundance of dinucleotides or GS, the profiles of occurrence of 10 nucleotide words (CS), and the profiles of occurrence of 20 nucleotide words, using a degenerate two-letter alphabet (purine-pyrimidine compositional spectra [PPCS]). Here, we show that the evolutionary distances between DNA repair and recombination orthologous enzymes (especially those of the nucleotide excision repair system) are highly correlated with PPCS and GS distances. Orthologous proteins involved in structural or metabolic processes (control group) have significantly lower correlations of their evolutionary distances with the PPCS and GS distances. We hypothesize that the high correlation of the evolutionary distances of the DNA repair orthologous enzymes with their GD is a result of the coevolution of the DNA repair enzymes' structures and GDs. Species GDs could be substantially influenced by the function of DNA polymerase I (the bacterial major DNA repair polymerase). This might cause the correlation of species GDs differentiation with evolutionary changes of species DNA polymerase I. Simultaneously, the structures of DNA repair-recombination enzymes might be evolutionarily sensitive and responsive to changes in the structure of their substrate-the DNA (including those that are represented by GD differentiation). We further discuss the rationale and mechanisms of the hypothesized coevolution. We suggest that stress might be an important cause of changes in the repair-recombination genes and the GD and the trigger of the aforementioned coevolution process. Other triggers might be massive horizontal gene transfer and ecological selection.
Oxazolium-Derived Azomethine Ylides. External Oxazole Activation and Internal Dipole Trapping in the Synthesis of an Aziridinomitosene (2000)

Intermolecular alkylation of the aziridinyl oxazole 20 using PhSO(2)CH(2)CH(2)OTf is possible despite the presence of potentially nucleophilic aziridine nitrogen. The resulting oxazolium salt 22 reacts with BnNMe(3)(+)CN(-) to produce the azomethine ylide 24b via electrocyclic ring opening of an oxazoline 23b. Internal cycloaddition affords 26 in 66% yield. After saponification and base-induced cleavage of the N-phenylsulfonylethyl group, conventional cyclization provides access to 33. Deprotection and DDQ oxidation completes the synthesis of the aziridinomitosene derivative 9b. The starting cis-disubstituted aziridine ester 16 can be prepared by the aza-Darzens reaction of 15 with tert-butyl chloroacetate.
Mode of Action of an Antibacterial Peptide, KLKLLLLLKLK-NH21 (1995)

Previously, we reported that a synthetic undecapeptide, KLKLLLLLKLK-NH2, and its D-enantiomer have potent bactericidal activities against both Gram-positive and Gram-negative bacteria. Here we examined the mode of action of KLKLLLLLKLK-NH2 with special reference to its effect on bacterial membranes. We found that both the outer and inner membrane of Escherichia coli become permeable to low molecular mass substances when treated with this peptide. Under these conditions, the bacteria lost the ability to synthesize ATP and to transport proline, suggesting that their electrochemical membrane potential was disrupted. This peptide appears to form numerous channels in bacterial membranes that interfere with membrane functions, resulting in cell death.
Wavelet change-point prediction of transmembrane proteins (2000)

The transmembrane database, TMALN and source code are available upon request from the authors.
7.3 A 40nm low-power transceiver for LTE-A Carrier Aggregation (2017)

The demand of higher data-rates for mobile communication has driven the LTE standard to adopt methods to increase channel bandwidth by Carrier Aggregation (CA), this is known as LTE-Advanced (LTE-A). Due to regional spectrum allocation, these carriers can be inter-band, or intra-band with contiguous (CCA) or non-contiguous (NCCA) channels. The band combinations create a major challenge for an LTE-A transceiver (TRX) in dealing with the intermodulation (IM) of aggregated channels. These IM sources include fundamental and harmonics of LOs, VCOs, and the transmitter (TX) modulated signals. In addition, when multiple receivers (RXs) and synthesizers (SXs) are needed to support CA, power consumption becomes a key challenge. This work describes an adaptive RX that can adjust trade-offs between power consumption and RX performance, allowing significant power reduction under normal field conditions. Additionally several techniques are described for mitigation of CA IM spurs.
Optical fiber poling by induction (2014)

Conventional thermal poling methods require direct physical contact to internal fiber electrodes. Here, we report an indirect electrostatic induction technique using electrically floating wires inside the fiber combined with external electric fields that can allow for facile poling of complex microstructured fibers (MOFs) of arbitrarily long lengths. In combination with our unique ability to use liquid gallium electrodes, inducing second-order nonlinearities inside otherwise difficult to access multi-core or multi-hole MOFs now becomes entirely feasible and practical. The formation of a permanent second-order nonlinearity is unequivocally demonstrated by realizing quasi-phase-matched frequency doublers using periodic UV erasure methods in the induction-poled fibers. The second-order susceptibility created inside the fiber is driven by the potential difference established between the floating electrodes, which we calculate via numerical simulations.
The charged region of Hsp90 modulates the function of the N-terminal domain (1999)

Hsp90, an abundant heat shock protein that is highly expressed even under physiological conditions, is involved in the folding of key molecules of the cellular signal transduction system such as kinases and steroid receptors. It seems to contain two chaperone sites differing in substrate specificity. Binding of ATP or the antitumor drug geldanamycin alters the substrate affinity of the N-terminal chaperone site, whereas both substances show no influence on the C-terminal one. In wild-type Hsp90 the fragments containing the chaperone sites are connected by a highly charged linker of various lengths in different organisms. As this linker region represents the most striking difference between bacterial and eukaryotic Hsp90s, it may be involved in a gain of function of eukaryotic Hsp90s. Here, we have analyzed a fragment of yeast Hsp90 consisting of the N-terminal domain and the charged region (N272) in comparison with the isolated N-terminal domain (N210). We show that the charged region causes an increase in the affinity of the N-terminal domain for nonnative protein and establishes a crosstalk between peptide and ATP binding. Thus, the binding of peptide to N272 decreases its affinity for ATP and geldanamycin, whereas the ATP-binding properties of the monomeric N-terminal domain N210 are not influenced by peptide binding. We propose that the charged region connecting the two chaperone domains plays an important role in regulating chaperone function of Hsp90.
The on-line shortest path problem under partial monitoring (2007)

The on-line shortest path problem is considered under various models of partial monitoring. Given a weighted directed acyclic graph whose edge weights can change in an arbitrary (adversarial) way, a decision maker has to choose in each round of a game a path between two distinguished vertices such that the loss of the chosen path (defined as the sum of the weights of its composing edges) be as small as possible. In a setting generalizing the multi-armed bandit problem, after choosing a path, the decision maker learns only the weights of those edges that belong to the chosen path. For this problem, an algorithm is given whose average cumulative loss in n rounds exceeds that of the best path, matched off-line to the entire sequence of the edge weights, by a quantity that is proportional to 1/\sqrt{n} and depends only polynomially on the number of edges of the graph. The algorithm can be implemented with linear complexity in the number of rounds n and in the number of edges. An extension to the so-called label efficient setting is also given, in which the decision maker is informed about the weights of the edges corresponding to the chosen path at a total of m << n time instances. Another extension is shown where the decision maker competes against a time-varying path, a generalization of the problem of tracking the best expert. A version of the multi-armed bandit setting for shortest path is also discussed where the decision maker learns only the total weight of the chosen path but not the weights of the individual edges on the path. Applications to routing in packet switched networks along with simulation results are also presented.
Economics of malware: Epidemic risks model, network externalities and incentives (2009)

Malicious softwares or malwares for short have become a major security threat. While originating in criminal behavior, their impact are also influenced by the decisions of legitimate end users. Getting agents in the Internet, and in networks in general, to invest in and deploy security features and protocols is a challenge, in particular because of economic reasons arising from the presence of network externalities. Our goal in this paper is to model and quantify the impact of such externalities on the investment in security features in a network. We study a network of interconnected agents, which are subject to epidemic risks such as those caused by propagating viruses and worms. Each agent can decide whether or not to invest some amount to self-protect and deploy security solutions which decreases the probability of contagion. Borrowing ideas from random graphs theory, we solve explicitly this 'micro'-model and compute the fulfilled expectations equilibria. We are able to compute the network externalities as a function of the parameters of the epidemic. We show that the network externalities have a public part and a private one. As a result of this separation, some counter-intuitive phenomena can occur: there are situations where the incentive to invest in self-protection decreases as the fraction of the population investing in self-protection increases. In a situation where the protection is strong and ensures that the protected agent cannot be harmed by the decision of others, we show that the situation is similar to a free-rider problem. In a situation where the protection is weaker, then we show that the network can exhibit critical mass. We also look at interaction with the security supplier. In the case where security is provided by a monopolist, we show that the monopolist is taking advantage of these positive network externalities by providing a low quality protection.
Two-stage Semi-automatic Organ Segmentation Framework using Radial Basis Functions and Level Sets (2007)

Abstract. The automatic segmentation of complex anatomical structures often fails due to low-contrast or missing edges, pathologic alterations, or high noise. As an alternative, we propose a novel two-stage semi-automatic algorithm that is able to segment complex structures like the liver shape with moderate user interaction. The first stage of our algorithm is the manual delineation of cross-sections of the anatomical structure in 2-D multi-planar reconstruction views. From this set of contours, an initial 3-D surface is reconstructed using radial basis functions. In a second step, the surface is evolved using a level set algorithm incorporating a new combination of both image information and shape information, the latter being derived from the initial contours. The algorithm has been evaluated for 10 Computed Tomography scans of the liver and has shown promising results. 1
Supramolecular Reactor in an Aqueous Environment:  Aromatic Cross Suzuki Coupling Reaction at Room Temperature (2005)

[reaction: see text] We have investigated supramolecular reactors for the Suzuki coupling reactions of aryl halides with phenyl boronic acids by using self-assembly of amphiphilic rod-coil molecules in aqueous solution at room temperature. All the rod-coil molecules synthesized in this work showed to self-assemble into discrete micelles consisting of aromatic rod bundles encapsulated by hydrophilic poly(ethylene oxide) coils. We present a comparative study of rod-coil molecules' efficiency as supramolecular reactors for Suzuki coupling reaction. The closed-packed aromatic bundles play an efficient role in supramolecular reactors for the coupling reactions at room temperature. The supramolecular reactor based on hexa-p-phenylene confers unprecedented activity, allowing reactions to be performed at very low catalyst levels, without conventional heating or microwave.
Hypolipidemic Effect of Polyvinylpyrrolidone in Man (1968)

Intravenous infusion of 500 ml of 6% polyvinylpyrrolidone (PVP, average molecular weight 40,000) in isotonic saline solution daily for 2 days induced prompt and significant reductions in serum cholesterol and triglyceride concentrations in eight hyperlipidemic patients. Mean maximal decrements in serum cholesterol and triglyceride were 29% and 28% below control values, respectively, occurring 5 days after infusion of PVP. Mean values for hematocrit and total serum protein concentration were slightly decreased following PVP infusion, but there were no changes in percentage composition of serum proteins, blood sugar, serum sodium and potassium, body weight, and blood pressure. The hypolipidemic effect of PVP persisted beyond the period of plasma volume expansion, as demonstrated by measurement of the plasma volume isotopically and by long-term follow-up in five of the patients.
Nicotiana alata Defensin Chimeras Reveal Differences in the Mechanism of Fungal and Tumor Cell Killing and an Enhanced Antifungal Variant (2016)

The plant defensin NaD1 is a potent antifungal molecule that also targets tumor cells with a high efficiency. We examined the features of NaD1 that contribute to these two activities by producing a series of chimeras with NaD2, a defensin that has relatively poor activity against fungi and no activity against tumor cells. All plant defensins have a common tertiary structure known as a cysteine-stabilized α-β motif which consists of an α helix and a triple-stranded β-sheet stabilized by four disulfide bonds. The chimeras were produced by replacing loops 1 to 7, the sequences between each of the conserved cysteine residues on NaD1, with the corresponding loops from NaD2. The loop 5 swap replaced the sequence motif (SKILRR) that mediates tight binding with phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2] and is essential for the potent cytotoxic effect of NaD1 on tumor cells. Consistent with previous reports, there was a strong correlation between PI(4,5)P2 binding and the tumor cell killing activity of all of the chimeras. However, this correlation did not extend to antifungal activity. Some of the loop swap chimeras were efficient antifungal molecules, even though they bound poorly to PI(4,5)P2, suggesting that additional mechanisms operate against fungal cells. Unexpectedly, the loop 1B swap chimera was 10 times more active than NaD1 against filamentous fungi. This led to the conclusion that defensin loops have evolved as modular components that combine to make antifungal molecules with variable mechanisms of action and that artificial combinations of loops can increase antifungal activity compared to that of the natural variants.
ChemInform Abstract: Synthesis of a Chiral α‐(Aminooxy)arylacetic Ester. Part 1. A Route Through Optical Resolution of a Racemic α‐(Phthalimidooxy) arylacetic Acid. (1991)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
A high throughput belief propagation decoder architecture for polar codes (2016)

The belief propagation (BP) decoding algorithm not only is an alternative to the successive cancelation (SC) decoders of polar codes, but also provides soft outputs that are necessary for joint detection and decoding. The BP decoders with the flooding schedule achieve high throughput with excessive hardware cost especially when the block length is large. The soft-cancelation (SCAN) decoders for polar codes have reduced memory complexity compared to the BP decoders based on the flooding schedule. The simplified SC aided reduced complexity soft-cancelation (S-RCSC) decoders further reduce the computational and memory complexity of the SCAN decoders at the cost of negligible error performance degradation. Both the SCAN and S-RCSC decoders have limited throughput due to their serial decoding schedules. In this paper, we first propose an improved S-RCSC (IS-RCSC) decoding algorithm and then present a high throughput decoder architecture based on our IS-RCSC algorithm. Our IS-RCSC decoding algorithm performs the message passing on a binary tree representation of a polar code. Compared to the S-RCSC decoding algorithm, our IS-RCSC decoding algorithm accelerates the computing of the returned soft messages when certain types of nodes are activated. The corresponding hardware architecture of our IS-RCSC decoder is also proposed. In terms of area efficiency, the hardware implementation results demonstrate that our IS-RCSC decoders are 19% to 43% better than decoders in the literature.
Emerging monoclonal antibody therapies for malignant gliomas (2007)

An improved understanding of the molecular characteristics of gliomas has led to the recognition of potential antigen targets and monoclonal antibody (mAb) therapies for these challenging tumors. The design of glioma mAbs--including species, construct, immunoglobulin isotype and conjugate--affects their delivery, efficacy and toxicities. mAbs that are under study for glioma therapy include some mAbs that are currently approved for use in the treatment of other cancers, as well as novel molecules. Although the greatest experience so far is with locally administered, radiolabeled mAbs, systemic unconjugated mAbs are being studied increasingly for glioma treatment. Previous experience with mAbs in other malignancies may provide guidance for their use in the treatment of CNS malignancies.