bluuebunny/crossref_metadata_2025_split huggingface dataset:
A learnable parallel processing architecture towards unity of memory and computing
Authors: Li H. , Gao B. , Chen Z. , Zhao Y. , Huang P. , Ye H. , Liu L. , Liu X. , Kang J. 
Published: August 2015

AbstractDeveloping energy-efficient parallel information processing systems beyond von Neumann architecture is a long-standing goal of modern information technologies. The widely used von Neumann computer architecture separates memory and computing units, which leads to energy-hungry data movement when computers work. In order to meet the need of efficient information processing for the data-driven applications such as big data and Internet of Things, an energy-efficient processing architecture beyond von Neumann is critical for the information society. Here we show a non-von Neumann architecture built of resistive switching (RS) devices named “iMemComp”, where memory and logic are unified with single-type devices. Leveraging nonvolatile nature and structural parallelism of crossbar RS arrays, we have equipped “iMemComp” with capabilities of computing in parallel and learning user-defined logic functions for large-scale information processing tasks. Such architecture eliminates the energy-hungry data movement in von Neumann computers. Compared with contemporary silicon technology, adder circuits based on “iMemComp” can improve the speed by 76.8% and the power dissipation by 60.3%, together with a 700 times aggressive reduction in the circuit area.
N-terminal-mediated oligomerization of DnaA drives the occupancy-dependent rejuvenation of the protein on the membrane
Authors: Aranovich Alexander , Braier-Marcovitz Shani , Ansbacher Esti , Granek Rony , Parola Abraham H. , Fishov Itzhak 
Published: August 2015

DnaA, the initiator of chromosome replication in most known eubacteria species, is activated once per cell division cycle. Its overall activity cycle is driven by ATP hydrolysis and ADP–ATP exchange. The latter can be promoted by binding to specific sequences on the chromosome and/or to acidic phospholipids in the membrane. We have previously shown that the transition into an active form (rejuvenation) is strongly co-operative with respect to DnaA membrane occupancy. Only at low membrane occupancy is DnaA reactivation efficiently catalysed by the acidic phospholipids. The present study was aimed at unravelling the molecular mechanism underlying the occupancy-dependent DnaA rejuvenation. We found that truncation of the DnaA N-terminal completely abolishes the co-operative transformation between the high and low occupancy states (I and II respectively) without affecting the membrane binding. The environmentally sensitive fluorophore specifically attached to the N-terminal cysteines of DnaA reported on occupancy-correlated changes in its vicinity. Cross-linking of DnaA with a short homobifunctional reagent revealed that state II of the protein on the membrane corresponds to a distinct oligomeric form of DnaA. The kinetic transition of DnaA on the membrane surface is described in the present study by a generalized 2D condensation phase transition model, confirming the existence of two states of DnaA on the membrane and pointing to the possibility that membrane protein density serves as an on-off switch in vivo. We conclude that the DnaA conformation attained at low surface density drives its N-terminal-mediated oligomerization, which is presumably a pre-requisite for facilitated nt exchange.
Induced voltages on overhead transmission lines because of nearby included lightning channel
Authors: Abouzeid Said I. , Shabib Gaber , Mohamed Adel Zein El Dein 
Published: August 2015

The power system networks can be adversely affected by indirect coupling with the cloud‐to‐ground lightning return stroke. In most computations of lightning‐induced voltages on overhead transmission lines, the overhead transmission lines are considered as straight lines and the return stroke channel is assumed to be a straight and a vertical channel. However, in reality, the line is not straight and is not parallel to the ground level because of the sag produced by its weight. In addition, the lightning channel is most often inclined. This study studies the effect of conductors’ sag as well as the inclination angle of the lightning channel on the lightning‐induced voltage on the three‐phase power lines because of inclined lightning channel. This study has been evolved, formulated and applied on Egyptian 500 kV three‐phase transmission line. Moreover, the effect of the ground conductivity on induced overvoltages in case of sagged transmission lines is considered. It can be observed that, taking into account the effects of the ground conductivity, the presence of the ground wire and the sag of the transmission lines reduce the values of the calculated induced voltages.
Analytical approximate calculation of losses for modular multilevel converters
Authors: Wang Haitian , Tang Guangfu , He Zhiyuan , Cao Junzheng , Zhang Xiaoping 
Published: August 2015

The voltages of the upper and lower arms per phase unit in a modular multilevel converter (MMC) are analysed. In addition, the enabled probabilities of each submodule (SM) in the upper and lower arms are proposed on the basis of the relationship between the arm voltage and the number of enabled SMs. Analytical models of the currents in the switches can be obtained from the current path and sign. Then, the average or root mean square (RMS) current can be obtained from the corresponding model. Therefore, the conduction and essential switching losses can be expressed by analytical formulas. In the inverter and rectifier modes, the two losses of the corresponding upper and lower switches of the SM are compared, and the sums of the two losses of the upper and lower switches are compared with the analytical method. Simulation studies are performed on a 1000 MW 320 kV MMC‐high‐voltage direct current system under typical operating conditions. The magnitudes of the compared losses are validated by the simulation results. Both the relative errors of the total conduction and essential switching losses are within ±2.5 and ±7%, respectively, and the comparison results demonstrate the effectiveness of the analytical method.
Influence of altitude on radio interference level of AC power lines based on corona cage
Authors: He Wang‐ling , He Jun‐jia , Wan Bao‐quan , Chen Yu‐chao , Pei Chun‐ming , Chen Yu‐long 
Published: August 2015

To investigate the effect of altitude on radio interference (RI) of AC power lines, a corona cage test system was used to measure the RI excitation function values of different bundle conductors in different altitude locations, such as Wuhan 23 m, Jingyuan 1408 m, Xining 2261 m, Gonghe 2943 m and Yangbajain 4300 m. Then, the RI curves with different altitudes, bundle numbers and subconductor diameters were obtained. The analysis and comparison show that the actual RI altitude correction values fall in between the range of 1 dB/300 m and 40(1 − σ/σ0) when the altitude below 3200 m, which is widely used as Italian correction term and Westinghouse correction term, respectively. Above this altitude, they are not applicable to predict the correction values. In this study, an RI correction term is proposed from the test results, which are fitted well for different altitude regions <4300 m.
Formation of silver nanoparticles induced by ultrasonically treated sodium dodecyl benzene sulphonate
Authors: Zhang Shun , Yang Keli , Liu Quansheng 
Published: August 2015

A simple and novel method for the synthesis of silver nanoparticles (AgNPs) was investigated, using only ultrasonically treated aqueous solutions of sodium dodecyl benzene sulphonate (UT‐SDBS) as both reducing and stabilizing agents at 100°C. The obtained AgNPs were characterised by their size and morphology. The results have shown that well‐dispersed AgNPs were produced with a narrow size distribution of about 3–9 and 2–13 nm using AgAc and AgNO3 as precursors, respectively. The intermediates generated in the UT‐SDBS solution served as the reducing radicals. The reduction ability of intermediates was determined by the ultrasonic time of SDBS. Most of the intermediates were produced in the first 1 h of ultrasonic irradiation, the reduction ability of UT‐SDBS‐1h was sufficient at this stage. However, by increasing the ultrasonic time to 8 h resulted in further decomposition of intermediates and in the decrease of its reduction ability.
motifbreakR: an R/Bioconductor package for predicting variant effects at transcription factor binding sites
Authors: Coetzee Simon G. , Coetzee Gerhard A. , Hazelett Dennis J. 
Published: August 2015

Abstract
Summary: Functional annotation represents a key step toward the understanding and interpretation of germline and somatic variation as revealed by genome-wide association studies (GWAS) and The Cancer Genome Atlas (TCGA), respectively. GWAS have revealed numerous genetic risk variants residing in non-coding DNA associated with complex diseases. For sequences that lie within enhancers or promoters of transcription, it is not straightforward to assess the effects of variants on likely transcription factor binding sites. Consequently we introduce motifbreakR, which allows the biologist to judge whether the sequence surrounding a polymorphism or mutation is a good match, and how much information is gained or lost in one allele of the polymorphism or mutation relative to the other. MotifbreakR is flexible, giving a choice of algorithms for interrogation of genomes with motifs from many public sources that users can choose from. MotifbreakR can predict effects for novel or previously described variants in public databases, making it suitable for tasks beyond the scope of its original design. Lastly, it can be used to interrogate any genome curated within bioconductor.
Availability and implementation: https://github.com/Simon-Coetzee/MotifBreakR, www.bioconductor.org.
Contact: dennis.hazelett@cshs.org
OVA: integrating molecular and physical phenotype data from multiple biomedical domain ontologies with variant filtering for enhanced variant prioritization
Authors: Antanaviciute Agne , Watson Christopher M. , Harrison Sally M. , Lascelles Carolina , Crinnion Laura , Markham Alexander F. , Bonthron David T. , Carr Ian M. 
Published: August 2015

Abstract
Motivation: Exome sequencing has become a de facto standard method for Mendelian disease gene discovery in recent years, yet identifying disease-causing mutations among thousands of candidate variants remains a non-trivial task.
Results: Here we describe a new variant prioritization tool, OVA (ontology variant analysis), in which user-provided phenotypic information is exploited to infer deeper biological context. OVA combines a knowledge-based approach with a variant-filtering framework. It reduces the number of candidate variants by considering genotype and predicted effect on protein sequence, and scores the remainder on biological relevance to the query phenotype.
We take advantage of several ontologies in order to bridge knowledge across multiple biomedical domains and facilitate computational analysis of annotations pertaining to genes, diseases, phenotypes, tissues and pathways. In this way, OVA combines information regarding molecular and physical phenotypes and integrates both human and model organism data to effectively prioritize variants. By assessing performance on both known and novel disease mutations, we show that OVA performs biologically meaningful candidate variant prioritization and can be more accurate than another recently published candidate variant prioritization tool.
Availability and implementation: OVA is freely accessible at http://dna2.leeds.ac.uk:8080/OVA/index.jsp
Supplementary information: Supplementary data are available at Bioinformatics online.
Contact: umaan@leeds.ac.uk
Methods that remove batch effects while retaining group differences may lead to exaggerated confidence in downstream analyses
Authors: Nygaard Vegard , Rødland Einar Andreas , Hovig Eivind 
Published: August 2015

Abstract
Removal of, or adjustment for, batch effects or center differences is generally required when such effects are present in data. In particular, when preparing microarray gene expression data from multiple cohorts, array platforms, or batches for later analyses, batch effects can have confounding effects, inducing spurious differences between study groups. Many methods and tools exist for removing batch effects from data. However, when study groups are not evenly distributed across batches, actual group differences may induce apparent batch differences, in which case batch adjustments may bias, usually deflate, group differences. Some tools therefore have the option of preserving the difference between study groups, e.g. using a two-way ANOVA model to simultaneously estimate both group and batch effects. Unfortunately, this approach may systematically induce incorrect group differences in downstream analyses when groups are distributed between the batches in an unbalanced manner. The scientific community seems to be largely unaware of how this approach may lead to false discoveries.
Effects of clam rake harvesting on the intertidal Ruditapes habitat of the English Channel
Authors: Beck Florence , Pezy Jean-Philippe , Baffreau Alexandrine , Dauvin Jean-Claude 
Published: August 2015

Abstract
Recreational and professional clam fishing was an important activity on the extensive intertidal zone of the western Cotentin coast (western English Channel). A variety of fishing gear was used to harvest the target species: the European clam Ruditapes decussatus (Linnaeus, 1758) and the introduced Manila clam R. philippinarum (Adams and Reeve, 1850). In this study, we studied the effect of rake harvesting during the spring tides of February–March 2014, following an experimental design with a control station and three stations impacted by rake harvesting in three sediment types: sandy, gravelly, and mixed gravelly rocky habitats. No significant sediment and macrofauna changes occurred at the three sites after rake harvesting. Nevertheless, the number of clams decreased significantly after raking on the gravelly habitat, whereas in the other two habitats, sediment transport in this high-energy hydrodynamic environment was able to transfer clams and other macrofauna species across the fishing sites, thus minimizing the effects of rake harvesting. Therefore, although the effect of rake harvesting appeared limited during winter, the regional impact (high fishing pressure along 60 km of coast) and increase of recreational fishers during summer needed to be studied in the future.
Historical discarding in Mediterranean fisheries: a fishers' perception
Authors: Damalas Dimitrios , Maravelias Christos D. , Osio Giacomo C. , Maynou Francesc , Sbrana Mario , Sartor Paolo , Casey John 
Published: August 2015

AbstractDiscarding of commercially important fish species in the bottom trawl fisheries in the northern Mediterranean Sea was investigated by soliciting the long-term recollections of fishers engaged or formerly engaged in such fisheries. The main aim of our investigation was to describe the prevalence of discarding and its evolution over the past 70 years using information gathered through individual questionnaire-based interviews with fishers from ports in Spain, Italy, and Greece, following a standardized sampling protocol. Although it proved impossible to derive absolute estimates of the volume of discarded catches over the period investigated, we conclude that over the past 70 years, discarding as a practice has gradually increased in the northern Mediterranean trawl fisheries and has been accompanied by a shift in the species composition of the discarded catch. While discarding can occur for a number of reasons, our investigations indicate that discarding in the past was mostly driven by market demand, but recent legal and regulatory constraints have led to changes in fishing strategies and became a significant reason for discards.
Rotation-induced deep crustal heating of millisecond pulsars
Authors: Gusakov M. E. , Kantor E. M. , Reisenegger A. 
Published: August 2015

Abstract
The spin-down of a neutron star, e.g. due to magneto-dipole losses, results in compression of the stellar matter and induces nuclear reactions at phase transitions between different nuclear species in the crust. We show that this mechanism is effective in heating recycled pulsars, in which the previous accretion process has already been compressing the crust, so it is not in nuclear equilibrium. We calculate the corresponding emissivity and confront it with available observations, showing that it might account for the likely thermal ultraviolet emission of PSR J0437−4715.
A Phase 1, Dose-escalation, Double-blind, Block-randomized, Controlled Trial of Safety and Efficacy of Neosaxitoxin Alone and in Combination with 0.2% Bupivacaine, with and without Epinephrine, for Cutaneous Anesthesia
Authors: Lobo Kimberly , Donado Carolina , Cornelissen Laura , Kim Joseph , Ortiz Rebeca , Peake Roy W. A. , Kellogg Mark , Alexander Mark E. , Zurakowski David , Kurgansky Katherine E. , Peyton James , Bilge Aykut , Boretsky Karen , McCann Mary Ellen , Berde Charles B. , Cravero Joseph 
Published: August 2015

AbstractAbstract
In a first-in-human Food and Drug Administration–regulated phase 1 safety study in 84 male volunteers, subcutaneous infiltration of Neosaxitoxin with bupivacaine produced long-lasting anesthesia but no serious adverse events although perioral numbness and tingling were noted at high doses. Addition of epinephrine reduced circulating Neosaxitoxin concentrations and perioral tingling and numbness and further prolonged sensory block.
Supplemental Digital Content is available in the text.

Background:
Neosaxitoxin (NeoSTX) is a site-1 sodium channel blocker that produces prolonged local anesthesia in animals and humans. Under a Food and Drug Administration–approved phase 1 Investigational New Drug trial, the authors evaluated safety and efficacy of NeoSTX alone and combined with 0.2% bupivacaine (Bup) with and without epinephrine.

Methods:
The authors conducted a double-blind, randomized, controlled trial involving healthy male volunteers aged 18 to 35 yr receiving two 10-ml subcutaneous injections. Control sites received Bup. In part 1, active sites received (1) 5 to 40 μg NeoSTX+Saline (NeoSTX-Saline), (2) 5 to 40 μg NeoSTX+Bup (NeoSTX-Bup), or (3) placebo (Saline). In part 2, active sites received 10 or 30 μg NeoSTX+Bup+Epinephrine (NeoSTX-Bup-Epi) or placebo. Primary outcome measures were safety and adverse events associated with NeoSTX. Secondary outcomes included clinical biochemistry, NeoSTX pharmacokinetics, and cutaneous hypoesthesia.

Results:
A total of 84 subjects were randomized and completed the two-part trial with no serious adverse events or clinically significant physiologic impairments. Perioral numbness and tingling increased with NeoSTX dose for NeoSTX-Saline and NeoSTX-Bup. All symptoms resolved without intervention. NeoSTX-Bup-Epi dramatically reduced symptoms compared with other NeoSTX combinations (tingling: 0 vs. 70%, P = 0.004; numbness: 0 vs. 60%, P = 0.013) at the same dose. Mean peak plasma NeoSTX concentration for NeoSTX-Bup-Epi was reduced at least two-fold compared with NeoSTX-Saline and NeoSTX-Bup (67 ± 14, 134 ± 63, and 164 ± 81 pg/ml, respectively; P = 0.016). NeoSTX-Bup showed prolonged cutaneous block duration compared with Bup, NeoSTX-Saline, or placebo, at all doses. Median time to near-complete recovery for 10 μg NeoSTX-Bup-Epi was almost five-fold longer compared with Bup (50 vs. 10 h, P = 0.007).

Conclusion:
NeoSTX combinations have a tolerable side effect profile and appear promising for prolonged local anesthesia.
Neosaxitoxin in Rat Sciatic Block
Authors: Templin Jay S. , Wylie Matthew C. , Kim Joseph D. , Kurgansky Katherine E. , Gorski Grzegorz , Kheir John , Zurakowski David , Corfas Gabriel , Berde Charles 
Published: August 2015

AbstractAbstract
In rats, combination of Neosaxitoxin with bupivacaine for sciatic nerve block resulted in motor and sensory block, which was longer than either agent alone, and was up to 48 h when epinephrine was added. Histologic examination showed no evidence of neural toxicity, and intravenous injection of Neosaxitoxin resulted in cardiotoxicity with longer delays than bupivacaine.

Background:
Neosaxitoxin (NeoSTX) is a site-1 sodium channel blocker undergoing clinical trials as a prolonged-duration local anesthetic. Rat sciatic block and intravenous infusion models were used to assess efficacy and local and systemic toxicities for NeoSTX in saline (NeoSTX-Saline), bupivacaine (Bup), and their combination (NeoSTX-Bup). Exploratory studies evaluated the effects of addition of epinephrine to NeoSTX-Bup (NeoSTX-Bup-Epi).

Methods:
Rats received percutaneous sciatic blocks with escalating doses of NeoSTX-Saline or NeoSTX-Bup. Sensory-nocifensive block was assessed using modified hotplate and Von Frey filaments. Motor-proprioceptive function was assessed by extensor postural thrust. Nerves were examined histologically after 7 days and scored on the Estebe–Myers scale. Median lethal dose was estimated for NeoSTX-Saline and in combinations. Accidental intravenous overdose was simulated in isoflurane-anesthetized, spontaneously breathing rats receiving NeoSTX-Saline (n = 6), Bup (n = 7), or NeoSTX-Bup (n = 13), with respiratory, hemodynamic, and electrocardiographic endpoints. Additional groups received blocks with NeoSTX-Bup-Epi (n = 80). Investigators were blinded for behavioral and histologic studies.

Results:

NeoSTX-Bup produced more prolonged sensory and motor block compared with NeoSTX-Saline or Bup. NeoSTX-Bup-Epi further prolonged median time to near-complete recovery for 3 μg/kg NeoSTX-Bup (hotplate: 48 vs. 6 h, P < 0.001). With sciatic injections, addition of Bup did not worsen the systemic toxicity (median lethal dose) compared with NeoSTX-Saline. Intravenous NeoSTX-Saline infusion had significantly longer times to apnea, first arrhythmia, and asystole compared with Bup (P < 0.001 for each). Histologic injury scores overall were low for all groups, with median scores of 0 (interquartile range, 0 to 0) on a 5-point scale.

Conclusion:

NeoSTX-Bup and NeoSTX-Bup-Epi hold promise for prolonged-duration local anesthesia.
Clinical Electroencephalography for Anesthesiologists
Authors: Purdon Patrick L. , Sampson Aaron , Pavone Kara J. , Brown Emery N. 
Published: August 2015

AbstractAbstract
The widely used electroencephalogram-based indices for depth-of-anesthesia monitoring assume that the same index value defines the same level of unconsciousness for all anesthetics. In contrast, we show that different anesthetics act at different molecular targets and neural circuits to produce distinct brain states that are readily visible in the electroencephalogram. We present a two-part review to educate anesthesiologists on use of the unprocessed electroencephalogram and its spectrogram to track the brain states of patients receiving anesthesia care. Here in part I, we review the biophysics of the electroencephalogram and the neurophysiology of the electroencephalogram signatures of three intravenous anesthetics: propofol, dexmedetomidine, and ketamine, and four inhaled anesthetics: sevoflurane, isoflurane, desflurane, and nitrous oxide. Later in part II, we discuss patient management using these electroencephalogram signatures. Use of these electroencephalogram signatures suggests a neurophysiologically based paradigm for brain state monitoring of patients receiving anesthesia care.
The authors review the neurophysiology of the electroencephalogram signatures of the anesthetics: propofol, dexmedetomidine, ketamine, sevoflurane, isoflurane, desflurane, and nitrous oxide. These signatures provide a neurophysiologically based paradigm for brain state monitoring of patients receiving anesthesia care.