gebhart/patrepeval huggingface dataset:
Intracellular signaling activity of synthetic (14R)-, (14S)-, and (14RS)-14-hydroxy-4,14-retro-retinol (1994)

14-Hydroxy-4,14-retro-retinol (14-HRR), first isolated from cultures of lymphoblastoid 5/2 and HeLa cells and characterized by NMR, UV, and CD, is a metabolite of retinol which promotes growth of B lymphocytes in culture and activation of T lymphocytes by antigen receptor-mediated signals. It is also produced by various tested cell lines: fibroblasts, leukemia, and Drosophila cells. 14-HRR is the first bioactive retro-retinoid to be discovered and, after retinal and retinoic acid, is the third intracellular messenger molecule derived from retinol. Physical properties and intracellular signaling activities of synthetic (14R)-HRR, (14S)-HRR, and racemic 14-HRR are described. CD spectra indicate that natural 14-HRR isolated previously was a mixture of enantiomers. B-cell survival and T-cell activation assays performed in the optimal range of (7-1.6) x 10(-7) M surprisingly showed that all 14-HRR compounds exhibit similar activity, with the 14R enantiomer exhibiting slightly higher activity in comparison to the 14S enantiomer. However, because of the semiquantitative nature of the assays, the conclusion as to which enantiomer is more active and which is the true ligand for the target receptor must await characterization of this protein.
Survivable Virtual Infrastructure Mapping With Dedicated Protection in Transport Software-Defined Networks [Invited] (2014)

Efficiently mapping multiple virtual infrastructures (VIs) onto the same physical substrate with survivability is one of the fundamental challenges related to network virtualization in transport software-defined networks (T-SDNs). In this paper, we study the survivable VI mapping problem in T-SDNs with the objective of minimizing the VI request blocking probability. In particular, we address the subproblems of modulation selection and spectrum allocation in the process of provisioning optical channels to support virtual links, taking into consideration the optical layer constraints such as the transmission reach constraint and the spectral continuity constraint. We propose an auxiliary-graph-based algorithm, namely, parallel VI mapping (PAR), to offer dedicated protection against any single physical node or link failure. More specifically, the PAR algorithm can jointly optimize the assignments of mapping the primary and backup VIs by adopting the modified Suurballe algorithm to find the shortest pair of node-disjoint paths for each virtual link. Through extensive simulations, we demonstrate that the PAR algorithm can significantly reduce the VI request blocking probability and improve the traffic-carrying capacity of the networks, compared to the baseline sequential VI mapping approaches.
Learning volume control for hearing aids (2007)

A Learning Volume Control (LVC) for hearing aids has been developed, tested and introduced in the market. It has the look and feel of a normal VC, the extra feature is that it gradually learns a more optimal VC setting during regular use of the hearing aid. It does so by combining features of the current input sound with past user behavior (past VC operation stored in the aid’s memory). The aimed effect is that users, over time, will need less VC adjustments when being exposed to changing acoustical environments. Like a normal VC, the LVC will always and instantly change the volume when operated, so the user will stay in immediate control of volume at all times, thus always being able to cope with wanted exceptions to the learned pattern. Our LVC concept has been tested in a number of patient trials (Chicago, Copenhagen, and Oldenburg) with very comparable results. Aver- age learning amounted to 2.4 dB from the default, with very large individual differences. We also found a large variability in learned volume, per patient, over different environments. This clearly shows the benefit of environmental steering in the personalization of volume. We conclude that automatic adaptation of volume by a learning algorithm is well appreciated by users, both with respect to environmental steering and personalization.
Practical high-resolution detection method for laser-induced breakdown spectroscopy (2012)

A Fabry-Perot etalon was coupled to a Czerny-Turner spectrometer to acquire high-resolution measurements in laser-induced breakdown spectroscopy (LIBS). The spectrometer was built using an inexpensive etalon coupled to a standard 0.5 m imaging spectrometer. The Hg emission doublet at 313.2 nm was used to evaluate instrument performance because it has a splitting of 29 pm. The 313.2 nm doublet was chosen due to the similar splitting seen in isotope splitting from uranium at 424.437 nm, which is 25 pm. The Hg doublet was easily resolved from a continuous-source Hg lamp with a 2 s acquisition. The doublet was also resolved in LIBS spectra of cinnabar (HgS) from the accumulation of 600 laser shots at rate of 10 Hz, or 1 min, under a helium atmosphere. In addition to the observed splitting of the 313.2 nm Hg doublet, the FWHM of the 313.1844 nm line from the doublet is reported at varying helium atmospheric pressures. The high performance, low cost, and compact footprint make this system highly competitive with 2 m double-pass Czerny-Turner spectrometers.
Side-Chain Engineering of Nonfullerene Acceptors for Near-Infrared Organic Photodetectors and Photovoltaics (2019)

Narrow bandgap n-type molecular semiconductors are relevant as key materials components for the fabrication near-infrared organic solar cells (OSCs) and organic photodetectors (OPDs). We thus designed nearly isostructural nonfullerene electron acceptors, except for the choice of solubilizing units, which absorb from 600 to 1100 nm. Specific molecules include CTIC-4F, CO1-4F, and COTIC-4F, whose optical bandgaps are 1.3, 1.2, and 1.1 eV, respectively. Modulation of intramolecular charge transfer characteristics was achieved by replacing alkoxy groups with alkyl groups on thiophene spacers that connect an electron-rich cyclopentadithiophene core to peripheral electron-poor fragments. OSCs incorporating CTIC-4F and CO1-4F with PTB7-Th achieve power conversion efficiencies of over 10% with short-circuit current densities as high as ∼25 mA·cm–2. The same blends achieve OPD responsivities of 0.52 A·W–1 at ∼920 nm. These findings highlight outstanding opportunities to tune further molecular design so that OPDs may ultimately compete with their silicon counterparts.
New Real-Time Approaches for Video-Genre-Classification Using High-Level Descriptors and a Set of Classifiers (2008)

In this paper we describe in detail the recent publications related to video-genre-classification and present our improved new approaches for classifying video sequences in real-time as 'cartoon', 'commercial', 'music', 'news' or 'sport' by analyzing the content with new high-level audio-visual descriptors and classification methods. Such applications have also been discussed in the context of MPEG-7. The results demonstrate identification rates of more than 90% based on a large representative collection of 100 videos gathered from free digital TV and Internet.
2,3‐Dihydro‐1‐Benzofuran Derivatives as a Series of Potent Selective Cannabinoid Receptor 2 Agonists: Design, Synthesis, and Binding Mode Prediction through Ligand‐Steered Modeling (2009)

We recently discovered and reported a series of N-alkyl-isatin acylhydrazone derivatives that are potent cannabinoid receptor 2 (CB(2)) agonists. In an effort to improve the druglike properties of these compounds and to better understand and improve the treatment of neuropathic pain, we designed and synthesized a new series of 2,3-dihydro-1-benzofuran derivatives bearing an asymmetric carbon atom that behave as potent selective CB(2) agonists. We used a multidisciplinary medicinal chemistry approach with binding mode prediction through ligand-steered modeling. Enantiomer separation and configuration assignment were carried out for the racemic mixture for the most selective compound, MDA7 (compound 18). It appeared that the S enantiomer, compound MDA104 (compound 33), was the active enantiomer. Compounds MDA42 (compound 19) and MDA39 (compound 30) were the most potent at CB(2). MDA42 was tested in a model of neuropathic pain and exhibited activity in the same range as that of MDA7. Preliminary ADMET studies for MDA7 were performed and did not reveal any problems.
Abstract 3067: PIK3CA hotspot mutations are present at a relatively high frequency in CTCs of operable and metastatic breast cancer patients (2014)

Abstract Introduction: Molecular characterization of CTC is crucial for the investigation of molecular targeted therapies. PIK3CA somatic mutations play a crucial role in response to molecular targeted therapies. We detected PIK3CA mutations at a high frequency in CTC after developing and validating an ultra-sensitive methodology, based on a combination of allele-specific, asymmetric rapid PCR and melting analysis. Patient and Methods: After optimizing and validating our assay in terms of sensitivity, specificity and robustness, we detected PIK3CA hotspot mutations in EpCAM positive CTCs from 57 metastatic and 118 early breast cancer patients, 26 healthy individuals and 76 corresponding primary tumors. Rapid Real-PCR and melting were performed in triplicate for all samples in the LightScanner32 (Idaho USA), in the presence of LC-Green Plus saturating dye. Results: The assay could detect 0.05% of mutated dsDNA in the presence of 99.95% wtDNA for both exons and was highly specific (0/26 healthy). We identified PIK3CA mutations in EpCAM positive CTC in 20/57(35.1%) metastatic and in 23/118(19.5%) operable breast cancer patients. In corresponding primary tumors, 45/76(59.2%) samples were positive. Patients with verified metastasis carrying PIK3CA mutations on CTC had significant shorter OS than those without. Conclusions: We report for the first time that PIK3CA hotspot mutations are present at a relatively high frequency in CTC both in metastatic and operable breast cancer. The presence of PIK3CA mutations in CTC is associated with worse survival in patients with verified metastasis. Evaluation of PIK3CA mutational status on CTCs is a strategy with potential clinical application. Citation Format: Athina N. Markou, Sofia Farkona, Christina Schiza, Antonia Eftathiou, Nikolaos Malamos, Vassilis Georgoulias, Evi Lianidou. PIK3CA hotspot mutations are present at a relatively high frequency in CTCs of operable and metastatic breast cancer patients. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3067. doi:10.1158/1538-7445.AM2014-3067
FlashStore (2010)

We present FlashStore, a high throughput persistent key-value store, that uses flash memory as a non-volatile cache between RAM and hard disk. FlashStore is designed to store the working set of key-value pairs on flash and use one flash read per key lookup. As the working set changes over time, space is made for the current working set by destaging recently unused key-value pairs to hard disk and recycling pages in the flash store. FlashStore organizes key-value pairs in a log-structure on flash to exploit faster sequential write performance. It uses an in-memory hash table to index them, with hash collisions resolved by a variant of cuckoo hashing. The in-memory hash table stores compact key signatures instead of full keys so as to strike tradeoffs between RAM usage and false flash read operations. FlashStore can be used as a high throughput persistent key-value storage layer for a broad range of server class applications. We compare FlashStore with BerkeleyDB, an embedded key-value store application, running on hard disk and flash separately, so as to bring out the performance gain of FlashStore in not only using flash as a cache above hard disk but also in its use of flash aware algorithms. We use real-world data traces from two data center applications, namely, Xbox LIVE Primetime online multi-player game and inline storage deduplication, to drive and evaluate the design of FlashStore on traditional and low power server platforms. FlashStore outperforms BerkeleyDB by up to 60x on throughput (ops/sec), up to 50x on energy efficiency (ops/Joule), and up to 85x on cost efficiency (ops/sec/dollar) on the evaluated datasets.
Round-Based Public Transit Routing (2014)

We study the problem of computing all Pareto-optimal journeys in a dynamic public transit network for multiple criteria, such as arrival time and number of transfers. Existing algorithms consider this as a graph problem and solve it using various graph search algorithms. Unfortunately, this leads to either high query times or suboptimal solutions. We take a different approach. We introduce RAPTOR, our novel round-based public transit router. Unlike previous algorithms, it is not Dijkstra-based, looks at each route (such as a bus line) in the network at most once per round, and can be made even faster with simple pruning rules and parallelization using multiple cores. Because it does not rely on preprocessing, RAPTOR works in fully dynamic scenarios. Starting from arrival time and number of transfers as criteria, it can be easily extended to handle flexible departure times or arbitrary additional criteria. As practical examples we consider fare zones and reliability of transfers. When run on complex public transportation networks (such as London), RAPTOR computes all Pareto-optimal journeys between two random locations an order of magnitude faster than previous approaches, which easily enables interactive applications.
The weakest failure detector for solving consensus (1992)

We determine what information about failures is necessary and sufficient to solve Consensus in asynchronous distributed systems subject to crash failures. In [CT91], we proved that OVV, a failure detector that provides surprisingly little information about which processes have crashed, is sufficient to solve Consensus in asynchronous systems with a majority of correct processes. In this paper, we prove that to solve Consensus, any failure detector has to provide at least as much information as OVV. Thus, OVV is indeed the weakest failure detector for solving Consensus in asynchronous systems with a majority of correct processes.
QoS Performance Based Admission Control in Cellular Networks (2010)

In this paper. we consider an admission control algorithm for cellular networks. It is based on direct/dynamic monitoring of the QoS performances - the delay tail of the admitted users. The main purpose of the direct monitoring of QoS performances is to guarantee the required QoS provision more precisely. The system delay tail is effectively computed by the proposed delay tail estimation algorithm. With the estimated delay tails, each base station determines the admission or rejection for a new user to the system. By doing so, the admission control algorithm becomes more robust against time-varying fading channel environment. Simulation results in OFDMA cellular system shows that the proposed algorithm can provide substantial capacity gains in offering QoS. We also use a general Neyman-Pearson-like framework in evaluating various admission control mechanisms.
Standards compliant CoMP scheduling over LTE heterogeneous wireless networks (2015)

We analyze Coordinated Multi-Point (CoMP) transmission and reception over heterogeneous wireless networks (HetNets). Our focus is on the design of a practical algorithm for joint resource allocation (joint scheduling) in each HetNet cluster. We present one such algorithm together with its detailed analysis and evaluation under two different approaches for obtaining and utilizing channel feedback from the users. The considered approaches as well as the evaluation methodology are fully compliant with the 3GPP LTE standard. Our evaluations reveal several important insights that are essential to achieve significant CoMP gains over HetNets.
Stable Positively Charged Liposome during Long-Term Storage. (1993)

The effect of taurine, as an isotonic solute, and of benzalkonium chloride (BZC), as a positive membrane component, on the long-term stability of liposomal suspensions was investigated by measuring surface potential. The surface potential, which introduced electrostatic repulsion to liposomes against aggregation, increased dose-dependently with the addition of BZC, which gave a positive charge. However, a further addition of BZC caused unexpected aggregation during storage, so the optimum addition of BZC was defined. On the other hand, taurine, which forms a zwitter ion in an aqueous solution, did not reduce the surface potential, suggesting that taurine is of possible utility as an isotonic solute. As the result of stability testing, the liposomal system using taurine and BZC was stable against aggregation during 6 months at 40 degrees C. We were successful in developing a stable, positively charged liposomal system during long-term storage, and our liposomal system is believed to be of wide utility as a drug carrier for therapeutic drugs applied topically to negatively charged mucosal tissues. We applied the Derjaguin-Landau-Verwey-Overbeek (DLVO) theory to estimate the colloidal stability of liposomes. As a result of stability testing, positively charged liposomes had a good correlation between maximum total repulsive energy (VT(max)/kT) between two liposome particles and colloidal stability, suggesting that the VT(max)/kT value is useful for estimating stability and for designing liposomal preparations containing some ionic substances.
On-Line Detection of Dc Arc Faults Using Hurst Exponents for Hybrid-Electric Vehicles (2020)

Series arc faults are a severe safety hazard in modern pure electric and hybrid electric vehicles, as well as dc electrical distribution systems. A new method utilizing Hurst Exponents was recently proposed that is strongly resistant to switching harmonics, load profiles, and high frequency noise. In this paper, further analysis and implementation of the Hurst based detection is performed. A method of filtering out signal noise is presented, and an on-line operation prototype is constructed using common hardware. The on-line prototype is demonstrated to successfully detect series arc faults in under 50 ms. A statistical analysis of the method effectiveness is performed to determine the success rate of the on-line prototype, which is expressed through the metrics of Precision and Recall.
Fully Automated Operational Modal Identification Using Continuously Monitoring Data of Bridge Structures (2021)

Structural modal identification for providing dynamic properties, including frequencies, damping ratios, and mode shapes, plays an important role in structural health monitoring and safety assessment. Automated modal parameter identification techniques have become increasingly important to process continuously monitored data. In this study, an improved frequency-domain method for automated modal identification of bridge structures is proposed by enhancing frequency-domain decomposition through time-related modal assurance criterion and free-decaying segment determination. First, a method using ratios in the frequency domain for determination of the cutoff frequency is proposed to reduce the computational cost and improve the accuracy. Second, time-related modal assurance criterion is proposed to select physical modes. Third, damping ratios are estimated by combining the continuous wavelet transform and free-decaying segment selection to improve the accuracy of damping ratio estimation, especially for closely spaced modes. The results of the numerical studies show that the proposed method is robust to noise and efficient for identification of closely spaced modes. Moreover, the results for the practical bridge demonstrate the effectiveness and feasibility of the proposed method for performing automated modal identification in practical bridge structures.
Magnetic Guidance of Cochlear Implants: Proof-of-Concept and Initial Feasibility Study (2012)

Cochlear implants have become a standard treatment for many with severe to profound sensorineural hearing loss. However, delicate cochlear structures can be damaged during surgical insertion, which can lead to loss of residual hearing and decreased implant effectiveness. We propose a magnetic guidance concept in which a magnetically tipped cochlear implant is guided as it is inserted into the cochlea. In a scaled in vitro experimental study, we record insertion forces for nonguided and magnetically guided insertion experiments and compare the results. Results indicate that magnetic guidance reduced insertion forces by approximately 50%. Using first principles, we discuss the effects of scaling down our in vitro experiments, and account for realistic clinical dimensions. We conclude that scale–down effects are negligible, but to produce the same field strength as in our experiments and provide sufficient clearance between the patient and the manipulator, the magnet dimensions should be increased by approximately four times.
Parallel lookahead algorithms for pruned interleavers (2009)

In this letter, the design of efficient parallel pruned channel and turbo interleavers for Ultra Mobile Broadband (UMB) physical layer standard [1] is addressed. Channel interleaving is based on a bit-reversal algorithm in which addresses are mapped from linear order into bit-reversed order. Turbo interleaving is based on filling a 2D array row by row, interleaving each row independently using a linear congruential sequence (LCS), bit-reversing the order of the rows, and then reading the interleaved addresses column by column. To accommodate for flexible codeword lengths L, interleaving is done using a mother interleaver of length M = 2 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">n</sup> , where n is the smallest integer such that L ⩽ M, such that outlier interleaved addresses greater than L - 1 get pruned away. This pruning operation creates a serial bottleneck since the interleaved address of a linear address χ is now a function of the interleaving operation as well as the number of pruned addresses up to χ. A generic parallel lookahead pruned interleaving scheme that breaks this dependency is proposed. The efficiency of the proposed scheme is demonstrated in the context of both UMB interleavers. An iterative pruned bit-reversal algorithm that interleaves any address in O(log L) steps is presented. Moreover, an iterative pruned turbo interleaving algorithm based on LCSs that interleaves any address in O(log <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> L) steps is presented.
Reconstructing biological networks using conditional correlation analysis (2004)

Errors arise from correlation between nodes connected through intermediate nodes (false positives) and when the correlation between two directly connected nodes is obscured by noise, non-linearity or multiple inputs to the target node (false negatives). Two critical components of the method are as follows: (1) the choice of an optimal correlation threshold for predicting connections and (2) the reduction of errors arising from indirect connections (for which a novel algorithm is proposed). With these improvements, we can reconstruct networks with the topology of the transcriptional regulatory network in Escherichia coli with a reasonably low error rate.