bluuebunny/crossref_metadata_2025 huggingface dataset:
Cardinality balanced multitarget multi‐Bernoulli filter for multipath multitarget tracking in over‐the‐horizon radar
Authors: Qin Yong , Ma Hong , Cheng Li , Li Yang , Zhou Xueqin
Published: October 2015

Conventional multitarget tracking systems presume that each target produces at most one measurement per scan. Owing to the multiple ionosphere propagation paths in over‐the‐horizon radar, this assumption is not valid. To solve this problem, a novel multitarget tracking algorithm based on the finite set statistics (FISST), called multipath cardinality balanced multitarget multi‐Bernoulli (MP‐CBMeMBer) filter, is proposed in this study. First, the authors derive the MP‐CBMeMBer filter based on the FISST, and then both the sequential Monte Carlo and Gaussian mixture (GM) method are used to implement the proposed filter. Moreover, the extended Kalman filter is implemented to deal with the problem of the non‐linear measurement models for the GM‐MP‐CBMeMBer filter. Eventually, the simulation results are presented to demonstrate the effectiveness of the proposed filter.
Correction about rear of aperture serves as sphere wall in effective area method
Authors: Chen Xiangzi , Fang Wei , Xu Shuyan , Quan Xiangqian , Xia Zhiwei , Wang Kai , Wang Yupeng
Published: October 2015

To eliminate the non‐uniformity response of integrating sphere detector, which is brought by the back surface of the measured main aperture of the solar irradiance absolute radiometer serving as a part of the integrating sphere wall in effective area method, a correction optical model is designed to tackle the issue in TracePro program. By simulations, the radiant flux responded by the integrating sphere detector is given. Then the curve of the relative change about the radiant flux is deduced and the experiment measurement data are corrected on the basis of relative change curve. Eventually, the uncorrected and the corrected main aperture areas are calculated. Within a series of repeated measurements, the relative uncertainties of the uncorrected results and the corrected results are both 7 × 10−5 (n = 7). The relative uncertainty of the differences between the raw results and corrected results is 9.65 × 10−5 which proves that the optical model can evaluate the deviation, efficiently.
Synthesis and application of silver nanoparticles loaded on modified montorillonite
Authors: Tian Li , Tuping Li , Ziwei Huang
Published: October 2015

Na+ montmorillonite (MMT) was modified with L‐cystine, polyvinylpyrrolidone or mercaptoacetic acid and then silver (Ag) was loaded on the modified MMTs via ion‐exchange reaction under microwave irradiation for 4 min, and finally the Ag ions were turned to Ag nanoparticles (Ag NPs) under the irradiation of an ultraviolet lamp. The Ag‐loaded L‐cystine‐modified MMT (Ag@AA‐MMT) with an Ag content of 10.93 wt% was the highest of all, suggesting the distinct advantage of microwave‐assisted ion‐exchange reaction on a modified MMT. X‐ray photoelectron spectroscopy confirmed the successful loading of silver and the strong interaction between sulphur and Ag. Scanning electron microscopy, transmission electron microscopy and high‐resolution transmission electron microscopy and X‐ray diffraction patterns proved the existence and formation mechanism of metallic Ag NPs. The Ag‐loaded modified MMT has shown a slow release property and good thermal stability owing to the shielding effect of the MMT layers. The Ag@AA‐MMT, showing a very excellent antibacterial property and catalytic activity, exhibited a wide range of potential applications.
Integrated microoxygen sensor based on nanostructured TiO2 thin films
Authors: Wang Hairong , Wang Jiaxin , Chen Lei , Yao Yuqing , Sun Quantao , Qunming Zhang
Published: October 2015

An integrated microoxygen sensor based on the nanostructured TiO2 thin film is presented. A pair of interdigitated electrodes was designed with the microheater around them on the same layer, which was aimed at simplifying the structure and avoiding fracture of the embedded heater. To fabricate the sensor chips, an optimisation process consisting of 14 steps was designed. The adiabatic cavity was formed by releasing the Si substrate from backside to a certain thickness at first, then a TiO2 film was prepared by the sol–gel process and patterned by the wet etching process, after that electrodes and the heater were patterned and finally the remaining silicon was thinned further. Response properties to different gases were tested, and the sensor shows a good sensitivity of 0.093 and high selectivity of 0.258 to O2 than H2, response time of 51 s and hysteresis of 2.93%. The integrated microoxygen sensor has potential applications on the occasions of miniaturised, integrated, low power and mass production.
Enhancing SO2 capture capacity by preparation of a nano‐CaO sorbent with modified structural parameters
Authors: Moshiri Hadi , Ale Ebrahim Habib , Nasernejad Bahram
Published: October 2015

The reaction of CaO with SO2 is one of the most important methods for flue gas desulphurisation. Two methods for producing high‐capacity sorbents are investigated: a nanoporous CaO and a modified sorbent by washing with acetic acid. The capturing capacities of these sorbents are compared with CaO derived from natural limestone calcination. The solid conversion at 850°C after 3 h for the natural sorbent was only 5%, while this value was improved by up to 13 and 46% for acid‐washed and nanosynthesised sorbents, respectively. The effect of various sorbent pore size distributions on SO2 capture capacity is investigated.
Silicon etching characteristics for tetramethylammonium hydroxide‐based solution with additives
Authors: Jun Ki‐Wha , Kim Byung‐Min , Kim Jung‐Sik
Published: October 2015

In this reported work, the anisotropic etching properties of single‐crystal silicon with tetramethylammonium hydroxide (TMAH) solution are examined in detail. The variations in the Si etching rate and surface morphology at different etching temperatures and TMAH concentrations are evaluated. The effect of isopropyl alcohol (IPA) additive is also examined. As the TMAH concentration (10–25 wt%) decreased, the etching rate increased from 10 to 70 μm/h at temperatures between 70 and 90°C. On the other hand, the etched surface roughness became degraded as the hillock density and corner undercut ratio increased. The additive of IPA affected the morphology of the etched surface to be flat. In addition, the IPA additive improved the etched surface significantly by decreasing the hillock density on the surface.
Silicon on insulator pressure sensor based on a thermostable electrode for high temperature applications
Authors: Liu G.D. , Cui W.P. , Hu H. , Zhang F.S. , Zhang Y.X. , Gao C.C. , Hao Y.L.
Published: October 2015

A high temperature silicon on insulator pressure sensor utilising a Ti/TiN/Pt/Au electrode is presented for improving the thermal stability of ohmic contacts, which can work stably at high temperatures of up to 500°C. To analyse the characteristics of the electrode at high temperatures, a special test structure is measured using the linear transmission line method and Auger electron spectroscopy. To solve the measurement problem, a novel calibration setup is designed to calibrate the absolute pressure sensor at extremely high temperatures. The measurement results have shown that the pressure sensor has a nonlinearity error of 0.17%FS and a sensitivity of 0.24 mV/kPa with a measurement range of 30–150 kPa at 500°C, indicating the good thermal stability of the ohmic contacts.
Wet/dry etching combined microtextured structures for high‐efficiency solar cells
Authors: Cho Chan Seob , Kong DaeYoung , Kim Bonghwan
Published: October 2015

A solar cell texturing process using a two‐step process that includes wet etching and dry etching has been developed. The surface reflectance and fill factor (FF) of the pyramid structure by general wet etching texturing process were 5.834 and 70.597%, respectively; the surface reflectance and FF of the two‐step pyramid structure by wet etching and dry etching texturing process were 3.69 and 65.013%; and the surface reflectance and FF of the two‐step pyramid structure by rounded pyramid and dry etching texturing process were 4.533 and 70.727%. The process of the two‐step pyramid structure is as follows. First, the pyramid structure formed by the wet etching process was etched again with tetramethylammonium hydroxide solution. Then, the crest and the trough of the pyramid structure was fine etched, and rounded pyramid structures with a uniform n+ layer was formed. Secondly, a pyramid structure with a high angle on the rounded pyramid structure was formed by using reactive‐ion etching with a metal mesh. The two‐step pyramid structure by the wet etching and dry etching texturing process has a lower surface reflectance and higher FF than the pyramid structure formed of the wet etching texturing process. Therefore, the etching process is suitable for producing high‐efficiency solar cells.
Charge character in the double‐barrier quantum dots in well hybrid structure
Authors: Ning Wenguo , Wang Weiwei , Jin Xiaobo , Guo Fangmin , Yue Fangyu
Published: October 2015

The charge character in the double‐barrier quantum dots (QDs) in a well hybrid structure is investigated experimentally and numerically. The capacitance hysteresis phenomenon of a double‐barrier InAs QDs and InGaAs quantum well hybrid structure is reported, as well as the carrier transport properties in the photoelectric device. Due to the coupling effect among multiple QDs, the photoelectric device's measured I –V and C –V curves show that the capacitance changes with the light intensity. When the dumping readout designed, it can enhance the sensitivity of the device at weak light illumination. This indicates that the photoelectric device has the potential to be a promising candidate both in quantum information applications and highly sensitive imaging applications.
Out‐of‐plane buckled cantilever microstructures with adjustable angular positions using thermal bimorph actuation for transducer applications
Authors: Arevalo Arpys , Conchouso David , Castro David , Diaz Marlon , Foulds Ian G.
Published: October 2015

The integration of thermal bimorph actuators and buckled cantilever structures to form an out‐of‐plane plate with adjustable angular positions is reported. This structure could be used as a platform to build other transducers such as optical micromirrors, scanning antennas, switches or low‐frequency oscillators. The electromechanical characterisation has shown that these structures can adjust their angular position by 6° when they are operated using a DC source. The thermal characterisation performed by an infrared camera showed that the heat‐affected zone reaches a maximum temperature of 125°C while the rest of the structure remains unaffected by the generated heat.
Optimization of a wall-less Hall thruster
Authors: Vaudolon Julien , Mazouffre Stéphane , Hénaux Carole , Harribey Dominique , Rossi Alberto
Published: October 2015

An experimental optimization of a Hall thruster in wall-less operation mode is performed with the PPS-Flex, a 1.5 kW class thruster capable of modifying the magnetic field topology over a broad range of configurations. The anode geometry and the magnetic topology have been modified to avoid interaction between the magnetic field lines and the anode surface, compared to the first wall-less Hall thruster prototype. The measurements of the thrust and far-field ion properties reveal that a satisfactory performance level can be obtained once the magnetic barrier is restored, and pave the way towards the development of a high-efficiency wall-less Hall thruster.
Concepts of magnetic filter fields in powerful negative ion sources for fusion
Authors: Kraus W. , Fantz U. , Heinemann B. , Wünderlich D.
Published: October 2015

The performance of large negative ion sources used in neutral beam injection systems is in long pulses mainly determined by the increase of the currents of co-extracted electrons. This is in particular a problem in deuterium and limits the ion currents which are for long pulses below the requirements for the ITER source. In the source of the ELISE test facility, the magnetic field in front of the first grid, which is essential to reduce the electron current, is generated by a current of several kA flowing through the plasma facing grid. Weakening of this field by the addition of permanent magnets placed close to the lateral walls has led to a reduction of the electron current by a factor three without loss of ion current when source was operated in volume production. If this effect can be validated for the cesiated source, it would be a large step towards achieving the ITER parameter in long pulses.
Electronic structure of a superconducting topological insulator Sr-doped Bi2Se3
Authors: Han C. Q. , Li H. , Chen W. J. , Zhu Fengfeng , Yao Meng-Yu , Li Z. J. , Wang M. , Gao Bo F. , Guan D. D. , Liu Canhua , Gao C. L. , Qian Dong , Jia Jin-Feng
Published: October 2015

Using high-resolution angle-resolved photoemission spectroscopy and scanning tunneling microscopy/spectroscopy, the atomic and low energy electronic structure of the Sr-doped superconducting topological insulators (SrxBi2Se3) was studied. Scanning tunneling microscopy shows that most of the Sr atoms are not in the van der Waals gap. After Sr doping, the Fermi level was found to move further upwards when compared with the parent compound Bi2Se3, which is consistent with the low carrier density in this system. The topological surface state was clearly observed, and the position of the Dirac point was determined in all doped samples. The surface state is well separated from the bulk conduction bands in the momentum space. The persistence of separated topological surface state combined with small Fermi energy makes this superconducting material a very promising candidate for the time reversal invariant topological superconductor.
Electrocaloric enhancement near the morphotropic phase boundary in lead-free NBT-KBT ceramics
Authors: Le Goupil Florian , Bennett James , Axelsson Anna-Karin , Valant Matjaz , Berenov Andrey , Bell Andrew J. , Comyn Tim P. , Alford Neil McN.
Published: October 2015

The electrocaloric effects (ECEs) of the morphotropic phase boundary (MPB) composition 0.82(Na0.5Bi0.5)TiO3-0.18(K0.5Bi0.5)TiO3 (NBT-18KBT) are studied by direct measurements. The maximum ECE ΔTmax = 0.73 K is measured at 160 °C under 22 kV/cm. This corresponds to an ECE responsivity (ΔT/ΔE) of 0.33 × 10−6 K m/V, which is comparable with the best reported values for lead-free ceramics. A comparison between the direct and indirect ECE measurements shows significant discrepancies. The direct measurement of both positive and negative electrocaloric effect confirms the presence of numerous polar phases near the MPB of NBT-based materials and highlights their potential for solid-state cooling based on high field-induced entropy changes.
Confocal microscopic analysis of optical crosstalk in GaN micro-pixel light-emitting diodes
Authors: Li K. H. , Cheung Y. F. , Cheung W. S. , Choi H. W.
Published: October 2015

The optical crosstalk phenomenon in GaN micro-pixel light-emitting diodes (LED) has been investigated by confocal microscopy. Depth-resolved confocal emission images indicate light channeling along the GaN and sapphire layers as the source of crosstalk. Thin-film micro-pixel devices are proposed, whereby the light-trapping sapphire layers are removed by laser lift-off. Optical crosstalk is significantly reduced but not eliminated due to the remaining GaN layer. Another design involving micro-pixels which are completely isolated is further proposed; such devices exhibited low-noise and enhanced optical performances, which are important attributes for high-density micro-pixel LED applications including micro-displays and multi-channel optical communications.
Effect of abandonment of olive orchards on soil organic carbon sequestration in Mediterranean Lebanon
Authors: Atallah T. , Sitt K. , El Asmar E. , Bitar S. , Ibrahim L. , Khatib M. N. , Darwish T.
Published: October 2015

As a result of rural exodus, terraced orchards are the first abandoned lands in Mediterranean Lebanon. The aim of the present study was to develop knowledge of the status of soil organic carbon (SOC) in abandoned olive orchards. Thirty pairs of abandoned–actively managed fields were sampled at two soil depths (0–0.1 and 0.1–0.3 m) and two positions (crown area and between trees). Mean SOC ranged between 20.9 and 29.1 g kg–1 soil, with the smallest values between trees in the 0.1–0.3 m depth. Abandoned plots showed a surface build up of SOC (SOC0–0.1 m > SOC0.1–0.3 m) and a significantly higher SOC0–0.1 m content than the control. As a result of abandonment, 80% of plots showed increased C stocks (+18.6 Mg C ha–1). Recently abandoned plots (6–12 years) had a C0–0.1 m stock of 6.2 Mg C ha–1, compared with 9.5 Mg C ha–1 for those abandoned for over two decades. Two chronosequences showed that when the initial C was high, one decade was sufficient to reach stock stability. The relative C stock increase reached 38% after two decades of abandonment. Particle size separation showed that 30% of C0–0.1 m in the abandoned fields occurred as particulate organic matter (>50 μm) compared with 20% in the actively managed plots.
Assessing the Australian Soil Classification using cladistic analysis
Authors: Miltenyi Gregory P. L. , Ebach Malte C. , Triantafilis John
Published: October 2015

The Australian Soil Classification (ASC) has its roots in both the Handbook of Australian Soils and the Factual Key. The scheme’s use of mutually exclusive characteristics has led to Soil Orders containing a diverse range of soils, such as the Dermosols. The extent of these groupings has resulted in classes of soils sharing greater relationships with soils from other classes than they do with soils in the same class. Situations such as this arise from artificial classifications and highlight the need for natural classifications. Natural classifications accurately represent what is occurring in nature and are desirable because they represent evidence of a common history, process or mechanism. This study uses cladistics, a robust biological method that uncovers natural classifications, to assess the naturalness of the ASC. The analysis has the secondary aims of identifying natural soil orders and establishing which characters and tiers require revision. Two measures commonly used in cladistics, consistency index (CI) and retention index (RI), are used along with confidence levels generated by bootstrapping. The cladistic analysis undertaken consisted of coding 113 morphological and non-morphological characters used to identify 13 of the 14 Soil Orders in ASC into binary and multi-state matrices and analysis using a parsimony cladistic algorithm. The results suggest that, because of its low CI (0.196), the ASC is not a natural classification. However, certain Soil Orders of Organosols, Podosls and Vertosols, which all registered high CI, are natural. The analysis also indicated which soil morphological characters and Soil Orders require revision in order to make the ASC more natural, namely, soil colour and characters located in the Great Groups as well as Soil Orders such as Chromosols, Ferrosols and Dermosols. We conclude that cladistics offers a new avenue in discerning relationships between soils and in assessing the accuracy of, and identifying where improvements can be made in, the classifications used to identify them.
Variable impact of late-Quaternary megafaunal extinction in causing ecological state shifts in North and South America
Authors: Barnosky Anthony D. , Lindsey Emily L. , Villavicencio Natalia A. , Bostelmann Enrique , Hadly Elizabeth A. , Wanket James , Marshall Charles R.
Published: October 2015

Significance

Removing megafauna from contemporary ecosystems changes vegetation and small mammal communities over ecological time scales. We show that similar dynamics seem to operate over millennial time scales but only if the megafaunal loss includes ecosystem engineers in settings that also contain plant species susceptible to ecological release. Under such conditions, megafauna extinction can initiate changes that quickly lead to new, lasting ecological states. This implies that should some megafauna currently at risk for extinction actually become extinct, their characteristic ecosystems—for example, mosaics of savannah and forest—would also disappear, rapidly transforming into novel systems with respect to what is considered normal in today’s world.
Virus-mimetic nanovesicles as a versatile antigen-delivery system
Authors: Zhang Pengfei , Chen Yixin , Zeng Yun , Shen Chenguang , Li Rui , Guo Zhide , Li Shaowei , Zheng Qingbing , Chu Chengchao , Wang Zhantong , Zheng Zizheng , Tian Rui , Ge Shengxiang , Zhang Xianzhong , Xia Ning-Shao , Liu Gang , Chen Xiaoyuan
Published: October 2015

Significance

The previously unidentified virus-mimetic nanovesicles (VMVs) described in this manuscript consist of phospholipid derived from mammalian cell plasma membrane, recombinant protein anchored to cell membrane via the route of signal peptide sorting, and surfactants capable of controlling the VMV size and strength, which allows the VMVs to display functional polypeptides or maintain the correct conformation of protein antigen. The protein integrated into VMV by its hydrophobic transmembrane peptide has more modifications, such as glycosylation, than proteins in conventional subunit vaccines. Moreover, many viral envelope glycoproteins can be genetically engineered onto VMV liposomal surface so as to mimic the properties and conformational epitopes of natural virus. VMV provides an effective, straightforward, and tunable approach against a wide range of emerging enveloped viruses.
Novel plasticity rule can explain the development of sensorimotor intelligence
Authors: Der Ralf , Martius Georg
Published: October 2015

Significance

To find how autonomous behavior and its development can be realized by a brain or an artificial neural network is a fundamental challenge for neuroscience and robotics. Commonly, the self-organized unfolding of behavior is explained by postulating special concepts like internal drives, curiosity, specific reward systems, or selective pressures. We propose a simple, local, and biologically plausible synaptic mechanism that enables an embodied agent to self-organize its individual sensorimotor development without recourse to such higher-level constructs. When applied to robotic systems, a rich spectrum of rhythmic behaviors emerges, ranging from locomotion patterns to spontaneous cooperation between partners. A possible utilization of our novel mechanism in nature would lead to a new understanding of the early stages of sensorimotor development and of saltations in evolution.
Airborne measurements of organic bromine compounds in the Pacific tropical tropopause layer
Authors: Navarro Maria A. , Atlas Elliot L. , Saiz-Lopez Alfonso , Rodriguez-Lloveras Xavier , Kinnison Douglas E. , Lamarque Jean-Francois , Tilmes Simone , Filus Michal , Harris Neil R. P. , Meneguz Elena , Ashfold Matthew J. , Manning Alistair J. , Cuevas Carlos A. , Schauffler Sue M. , Donets Valeria
Published: October 2015

Significance

This study reports an extensive set of in situ measurements of natural organic bromine species at the tropical tropopause. Compared with prior estimates, this study reduces the uncertainty of the contribution of reactive bromine to stratospheric ozone depletion. We compare measurements over the Eastern and Western Pacific, two regions characterized by different transport dynamics, to show the influence of convective events on the chemistry of the tropopause region. Using measurements and modeling, we describe the budget and partitioning of bromine at the tropical tropopause and evaluate the contribution of bromine to ozone destruction in the lower stratosphere.
Cryo-EM structures elucidate neutralizing mechanisms of anti-chikungunya human monoclonal antibodies with therapeutic activity
Authors: Long Feng , Fong Rachel H. , Austin Stephen K. , Chen Zhenguo , Klose Thomas , Fokine Andrei , Liu Yue , Porta Jason , Sapparapu Gopal , Akahata Wataru , Doranz Benjamin J. , Crowe James E. , Diamond Michael S. , Rossmann Michael G.
Published: October 2015

Significance

A recent outbreak of chikungunya virus in the Americas has caused more than one million infections in humans. The reemergence of this virus has become a major threat to public health due to a lack of available vaccines and antiviral drugs. We determined the cryo-EM structures of chikungunya virus particles complexed with two of the most potent human antibody fragments described in a previous study. Both antibodies neutralized the virus by stabilizing the position of the viral surface glycoproteins, which blocks the exposure of the glycoprotein fusion loops required to initiate viral entry into the cytoplasm of a target cell.
The transcription factors ZEB2 and T-bet cooperate to program cytotoxic T cell terminal differentiation in response to LCMV viral infection
Authors: Dominguez Claudia X. , Amezquita Robert A. , Guan Tianxia , Marshall Heather D. , Joshi Nikhil S. , Kleinstein Steven H. , Kaech Susan M.
Published: October 2015

The transcription factor T-bet is critical for cytotoxic T lymphocyte (CTL) differentiation, but it is unclear how it operates in a graded manner in the formation of both terminal effector and memory precursor cells during viral infection. We find that, at high concentrations, T-bet induced expression of Zeb2 mRNA, which then triggered CTLs to adopt terminally differentiated states. ZEB2 and T-bet cooperate to switch on a terminal CTL differentiation program, while simultaneously repressing genes necessary for central memory CTL development. Chromatin immunoprecipitation sequencing showed that a large proportion of these genes were bound by T-bet, and this binding was altered by ZEB2 deficiency. Furthermore, T-bet overexpression could not fully bypass ZEB2 function. Thus, the coordinated actions of T-bet and ZEB2 outline a novel genetic pathway that forces commitment of CTLs to terminal differentiation, thereby restricting their memory cell potential.
Transcriptional repressor ZEB2 promotes terminal differentiation of CD8+ effector and memory T cell populations during infection
Authors: Omilusik Kyla D. , Best J. Adam , Yu Bingfei , Goossens Steven , Weidemann Alexander , Nguyen Jessica V. , Seuntjens Eve , Stryjewska Agata , Zweier Christiane , Roychoudhuri Rahul , Gattinoni Luca , Bird Lynne M. , Higashi Yujiro , Kondoh Hisato , Huylebroeck Danny , Haigh Jody , Goldrath Ananda W.
Published: October 2015

ZEB2 is a multi-zinc-finger transcription factor known to play a significant role in early neurogenesis and in epithelial-mesenchymal transition–dependent tumor metastasis. Although the function of ZEB2 in T lymphocytes is unknown, activity of the closely related family member ZEB1 has been implicated in lymphocyte development. Here, we find that ZEB2 expression is up-regulated by activated T cells, specifically in the KLRG1hi effector CD8+ T cell subset. Loss of ZEB2 expression results in a significant loss of antigen-specific CD8+ T cells after primary and secondary infection with a severe impairment in the generation of the KLRG1hi effector memory cell population. We show that ZEB2, which can bind DNA at tandem, consensus E-box sites, regulates gene expression of several E-protein targets and may directly repress Il7r and Il2 in CD8+ T cells responding to infection. Furthermore, we find that T-bet binds to highly conserved T-box sites in the Zeb2 gene and that T-bet and ZEB2 regulate similar gene expression programs in effector T cells, suggesting that T-bet acts upstream and through regulation of ZEB2. Collectively, we place ZEB2 in a larger transcriptional network that is responsible for the balance between terminal differentiation and formation of memory CD8+ T cells.
Graphical pan-genome analysis with compressed suffix trees and the Burrows–Wheeler transform
Authors: Baier Uwe , Beller Timo , Ohlebusch Enno
Published: October 2015

Motivation: Low-cost genome sequencing gives unprecedented complete information about the genetic structure of populations, and a population graph captures the variations between many individuals of a population. Recently, Marcus et al. proposed to use a compressed de Bruijn graph for representing an entire population of genomes. They devised an O(nlogg) time algorithm called splitMEM that constructs this graph directly (i.e. without using the uncompressed de Bruijn graph) based on a suffix tree, where n is the total length of the genomes and g is the length of the longest genome. Since the applicability of their algorithm is limited to rather small datasets, there is a strong need for space-efficient construction algorithms.

Results: We present two algorithms that outperform splitMEM in theory and in practice. The first implements a novel linear-time suffix tree algorithm by means of a compressed suffix tree. The second algorithm uses the Burrows–Wheeler transform to build the compressed de Bruijn graph in O(nlogσ) time, where σ is the size of the alphabet. To demonstrate the scalability of the algorithms, we applied it to seven human genomes.

Availability and implementation:  https://www.uni-ulm.de/in/theo/research/seqana/  .

Contact:  Enno.Ohlebusch@uni-ulm.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
Public Awareness of Sepsis Is Low in Sweden
Authors: Mellhammar Lisa , Christensson Bertil , Linder Adam
Published: October 2015

Background.  Sepsis is a serious and common condition with high mortality and morbidity. The public awareness, knowledge, and perception of sepsis in Sweden are unknown.

Methods.  A survey was performed using an online interview distributed to adults, aged 18–74, between March 6 and 9, 2015.

Results.  A total of 1001 people responded to the survey. Twenty-one percent of participants had heard of sepsis, whereas more than 86% had heard of each of the other conditions listed; for example, stroke (95%), chronic obstructive pulmonary disease (COPD) (95%), and leukemia (92%). Of those who had heard of sepsis, 93% responded that it is an infection or blood poisoning in an open question. The respondents who had heard of each disease estimated its mortality. For sepsis, the mortality was estimated at an average of 30%, which was at the same level as estimated mortalities for prostate and breast cancer but lower than for stroke, COPD, and leukemia.

Conclusions.  The awareness and knowledge of sepsis is low. The mortality for sepsis is not as overestimated as for many other diseases. The lack of awareness of sepsis might be a target to improve the outcome for sepsis patients by reducing the prehospital delay and hence enable early interventions. An increased general awareness might also raise interest for funding for research in this area and for its priority in healthcare support.
Evaluation of Perioperative Medication Errors and Adverse Drug Events
Authors: Nanji Karen C. , Patel Amit , Shaikh Sofia , Seger Diane L. , Bates David W.
Published: October 2015

AbstractAbstract

This prospective observational study found that approximately 1 in 20 perioperative medication administrations, and every second operation, resulted in a medication error and/or an adverse drug event. More than one third of these errors led to observed patient harm, and the remaining two thirds had the potential for patient harm.

Background

The purpose of this study is to assess the rates of perioperative medication errors (MEs) and adverse drug events (ADEs) as percentages of medication administrations, to evaluate their root causes, and to formulate targeted solutions to prevent them.

Methods

In this prospective observational study, anesthesia-trained study staff (anesthesiologists/nurse anesthetists) observed randomly selected operations at a 1,046-bed tertiary care academic medical center to identify MEs and ADEs over 8 months. Retrospective chart abstraction was performed to flag events that were missed by observation. All events subsequently underwent review by two independent reviewers. Primary outcomes were the incidence of MEs and ADEs.

Results

A total of 277 operations were observed with 3,671 medication administrations of which 193 (5.3%; 95% CI, 4.5 to 6.0) involved a ME and/or ADE. Of these, 153 (79.3%) were preventable and 40 (20.7%) were nonpreventable. The events included 153 (79.3%) errors and 91 (47.2%) ADEs. Although 32 (20.9%) of the errors had little potential for harm, 51 (33.3%) led to an observed ADE and an additional 70 (45.8%) had the potential for patient harm. Of the 153 errors, 99 (64.7%) were serious, 51 (33.3%) were significant, and 3 (2.0%) were life-threatening.

Conclusions

One in 20 perioperative medication administrations included an ME and/or ADE. More than one third of the MEs led to observed ADEs, and the remaining two thirds had the potential for harm. These rates are markedly higher than those reported by retrospective surveys. Specific solutions exist that have the potential to decrease the incidence of perioperative MEs.
Nitrous Oxide and Serious Long-term Morbidity and Mortality in the Evaluation of Nitrous Oxide in the Gas Mixture for Anaesthesia (ENIGMA)-II Trial
Authors: Leslie Kate , Myles Paul S. , Kasza Jessica , Forbes Andrew , Peyton Philip J. , Chan Matthew T. V. , Paech Michael J. , Sessler Daniel I. , Beattie W. Scott , Devereaux P. J. , Wallace Sophie
Published: October 2015

AbstractAbstract

Nitrous oxide did not increase the risk of a composite primary outcome of death and major cardiovascular events at 1 yr in 5,844 patients with cardiovascular disease recruited to the Evaluation of Nitrous Oxide in the Gas Mixture for Anaesthesia (ENIGMA)-II trial. These results support the long-term safety of nitrous oxide administration in noncardiac surgical patients with known or suspected cardiovascular disease.

Supplemental Digital Content is available in the text.

Background

The Evaluation of Nitrous Oxide in the Gas Mixture for Anaesthesia (ENIGMA)-II trial randomly assigned 7,112 noncardiac surgery patients at risk of perioperative cardiovascular events to 70% N2O or 70% N2 groups. The aim of this follow-up study was to determine the effect of nitrous oxide on a composite primary outcome of death and major cardiovascular events at 1 yr after surgery.

Methods

One-year follow-up was conducted via a medical record review and telephone interview. Disability was defined as a Katz index of independence in activities of daily living score less than 8. Adjusted odds ratios and hazard ratios were calculated as appropriate for primary and secondary outcomes.

Results

Among 5,844 patients evaluated at 1 yr, 435 (7.4%) had died, 206 (3.5%) had disability, 514 (8.8%) had a fatal or nonfatal myocardial infarction, and 111 (1.9%) had a fatal or nonfatal stroke during the 1-yr follow-up period. Exposure to nitrous oxide did not increase the risk of the primary outcome (odds ratio, 1.08; 95% CI, 0.94 to 1.25; P = 0.27), disability or death (odds ratio, 1.07; 95% CI, 0.90 to 1.27; P = 0.44), death (hazard ratio, 1.17; 95% CI, 0.97 to 1.43; P = 0.10), myocardial infarction (odds ratio, 0.97; 95% CI, 0.81 to 1.17; P = 0.78), or stroke (odds ratio, 1.08; 95% CI, 0.74 to 1.58; P = 0.70).

Conclusion

These results support the long-term safety of nitrous oxide administration in noncardiac surgical patients with known or suspected cardiovascular disease.
Spatial metrics of tumour vascular organisation predict radiation efficacy in a computational model
Authors: Scott Jacob G. , Fletcher Alexander G. , Anderson Alexander R.A. , Maini Philip K.
Published: October 2015

Intratumoural heterogeneity is known to contribute to poor therapeutic response. Variations in oxygen tension in particular have been correlated with changes in radiation responsein vitroand at the clinical scale with overall survival. Heterogeneity at the microscopic scale in tumour blood vessel architecture has been described, and is one source of the underlying variations in oxygen tension. We endeavour to determine whether histologic scale measures of the erratic distribution of blood vessels within a tumour can be used to predict differing radiation response. Using a two-dimensional hybrid cellular automaton model of tumour growth, we evaluate the effect of vessel distribution on cell survival outcomes of simulated radiation therapy. Using the standard equations for the oxygen enhancement ratio for cell survival probability under differing oxygen tensions, we calculate average radiation effect over a range of different vessel densities and organisations. We go on to quantify the vessel distribution heterogeneity and measure spatial organization using Ripley’sLfunction, a measure designed to detect deviations from spatial homogeneity. We find that under differing regimes of vessel density the correlation coefficient between the measure of spatial organization and radiation effect changes sign. This provides not only a useful way to understand the differences seen in radiation effect for tissues based on vessel architecture, but also an alternate explanation for the vessel normalization hypothesis.

Author Summary

In this paper we use a mathematical model, called a hybrid cellular automaton, to study the effect of different vessel distributions on radiation therapy outcomes at the cellular level. We show that the correlation between radiation outcome and spatial organization of vessels changes signs between relatively low and high vessel density. Specifically, that for relatively low vessel density, radiation efficacy is decreased when vessels are more homogeneously distributed, and the opposite is true, that radiation efficacy is improved, when vessel organisation is normalised in high densities. This result suggests an alteration to the vessel normalization hypothesis which states that normalisation of vascular beds should improve radio- and chemo-therapeutic response, but has failed to be validated in clinical studies. In this alteration, we provide a metric that differentiates between vascular architectures in different density regimes in which the hypothesis holds and does not and that could be used for quantitative histologic analysis of tumours, and for radiation dose personalisation.

Author Contributions

Conceived and designed the experiments: JGS, AGF, ARAA, PKM

Performed the experiments: JGS

Analyzed the data: JGS, AGF, ARAA, PKM

Wrote the paper: JGS, AGF, ARAA, PKM
Generalized Regressive Motion: a Visual Cue to Collision
Authors: Chalupka Krzysztof , Dickinson Michael , Perona Pietro
Published: October 2015

Brains and sensory systems evolved to guide motion. Central to this task is controlling the approach to stationary obstacles and detecting moving organisms. Looming has been proposed as the main monocular visual cue for detecting the approach of other animals and avoiding collisions with stationary obstacles. Elegant neural mechanisms for looming detection have been found in the brain of insects and vertebrates. However, looming has not been analyzed in the context of collisions between two moving animals. We propose an alternative strategy,generalized regressive motion(GRM), which is consistent with recently observed behavior in fruit flies. Geometric analysis proves that GRM is a reliable cue to collision among conspecifics, whereas agent-based modeling suggests that GRM is a better cue than looming as a means to detect approach, prevent collisions and maintain mobility.
Effect of lossy compression of quality scores on variant calling
Authors: Ochoa Idoia , Hernaez Mikel , Goldfeder Rachel , Weissman Tsachy , Ashley Euan
Published: October 2015

Recent advancements in sequencing technology have led to a drastic reduction in the cost of genome sequencing. This development has generated an unprecedented amount of genomic data that must be stored, processed, and communicated. To facilitate this effort, compression of genomic files has been proposed. Specifically, lossy compression of quality scores is emerging as a natural candidate for reducing the growing costs of storage. A main goal of performing DNA sequencing in population studies and clinical settings is to identify genetic variation. Though the field agrees that smaller files are advantageous, the cost of lossy compression, in terms of variant discovery, is unclear.

Bioinformatic algorithms to identify SNPs and INDELs from next-generation DNA sequencing data use base quality score information; here, we evaluate the effect of lossy compression of quality scores on SNP and INDEL detection. We analyze several lossy compressors introduced recently in the literature. Specifically, we investigate how the output of the variant caller when using the original data (uncompressed) differs from that obtained when quality scores are replaced by those generated by a lossy compressor. Using gold standard genomic datasets such as the GIAB (Genome In A Bottle) consensus sequence for NA12878 and simulated data, we are able to analyze how accurate the output of the variant calling is, both for the original data and that previously lossily compressed. We show that lossy compression can significantly alleviate the storage while maintaining variant calling performance comparable to that with the uncompressed data. Further, in some cases lossy compression can lead to variant calling performance which is superior to that using the uncompressed file. We envisage our findings and framework serving as a benchmark in future development and analyses of lossy genomic data compressors.

TheSupplementary Datacan be found athttp://web.stanford.edu/~iochoa/supplementEffectLossy.zip.
Predicting quantitative traits from genome and phenome with near perfect accuracy
Authors: Märtens Kaspar , Hallin Johan , Warringer Jonas , Liti Gianni , Parts Leopold
Published: October 2015

In spite of decades of linkage and association studies and its potential impact on human health1, reliable prediction of an individual's risk for heritable disease remains difficult2-4. Large numbers of mapped loci do not explain substantial fractions of the heritable variation, leaving an open question of whether accurate complex trait predictions can be achieved in practice5,6. Here, we use a full genome sequenced population of 7396 yeast strains of varying relatedness, and predict growth traits from family information, effects of segregating genetic variants, and growth measurements in other environments with an average coefficient of determinationR2of 0.91. This accuracy exceeds narrow-sense heritability, approaches limits imposed by measurement repeatability, and is higher than achieved with a single replicate assay in the lab. We find that both relatedness and variant-based predictions are greatly aided by availability of closer relatives, while information from a large number of more distant relatives does not improve predictive performance when close relatives can be used. Our results prove that very accurate prediction of heritable traits is possible, and recommend prioritizing collection of deeper family-based data over large reference cohorts.
Crystal structure of 1,1,2,2-tetramethyl-1,2-bis(2,3,4,5-tetramethylcyclopenta-2,4-dien-1-yl)disilane
Authors: Godemann Christian , Spannenberg Anke , Beweries Torsten
Published: October 2015

The molecular structure of the title compound, C22H38Si2, features atransarrangement of the cyclopentadienyl rings to avoid steric strain [C—Si—Si—C torsion angle = −179.0 (5)°]. The Si—Si bond length is 2.3444 (4) Å. The most notable intermolecular interactions in the molecular packing are C—H...π contacts that lead to the formation of wave-like supramolecular chains along thebaxis.
Crystal structure ofN′-diphenylmethylidene-5-methyl-1H-pyrazole-3-carbohydrazide
Authors: Karrouchi Khalid , Ansar M'hammed , Radi Smaail , Saadi Mohamed , El Ammari Lahcen
Published: October 2015

In the title compound, C18H16N4O, the planes of the phenyl rings are approximately perpendicular to each other [dihedral angle = 78.07 (8)°] and form dihedral angles of 56.43 (8) and 24.59 (8)° with the pyrazole ring. In the crystal, molecules are linked by N—H...O hydrogen bonds to form one-dimensional chains parallel to the [010] direction.
Investigation of an integrative transverse-flux linear compressor
Authors: Lu Qinfen , Yao Yihua , Ye Yunyue
Published: October 2015

Purpose

– The purpose of this paper is propose a novel integrative transverse-flux linear compressor (TFLC), which integrates compressor into a single-phase transverse-flux linear oscillating actuator with moving magnet. Its main merit is having similar lamination as rotate motor which is easy to be stacked.

Design/methodology/approach

– The simple lumped circuit model accounting for magnetic saturation, armature reaction and axial fringing effect is proposed. Based on this model, the magnetic field in air gap is calculated, and then the optimal PM height, PM length, split ratio and pole number are found. The predicted thrust force, stroke and system resonant frequency at no load are validated by prototype measurement. The relation of system resonant frequency and load are also measured.

Findings

– In this novel TFLC, the optimal split ratio is in area of 0.54∼0.56 and pole number is 6. For designed stroke 10 mm, suitable PM height and length are 3 mm and 63 mm, respectively. By measurement, the predicted thrust force, stroke and system resonant frequency at no load are validated. The measurement also shows that the system resonant frequency can be improved from 30 Hz of no load to 39 Hz at 0.7 Mpa air load.

Originality/value

– The novel TFLC has excellent driving performance and simple structure for maintenance. It can produce enough pressure to meet the requirement of refrigerator, so it is a strong candidate for refrigerating apparatus.
Impact of the management strategy on the sizing of a collaborative system
Authors: Le Goff Latimier R. , Multon B. , Ben Ahmed H.
Published: October 2015

Purpose

– To foster the grid integration of both electric vehicles (EV) and renewable generators, the purpose of this paper is to investigate the possible synergies between these players so as to jointly improve the production predictability while ensuring a green mobility. It is here achieved by the mean of a grid commitment over the overall power produced by a collaborative system which here gathers a photovoltaic (PV) plant with an EV fleet. The scope of the present contribution is to investigate the conditions to make the most of such an association, mainly regarding to the management strategies and optimal sizing, taking into account forecast errors on PV production.

Design/methodology/approach

– To evaluate the collaboration added value, several concerns are aggregated into a primary energy criterion: the commitment compliance, the power spillage, the vehicle charging, the user mobility and the battery aging. Variations of these costs are computed over a range of EV fleet size. Moreover, the influence of the charging strategy is specifically investigated throughout the comparison of three managements: a simple rule of thumb, a perfect knowledge deterministic case and a charging strategy computed by stochastic dynamic programming. The latter is based on an original modeling of the production forecast error. This methodology is carried out to assess the collaboration added value for two operators’ points of view: a virtual power plant (VPP) and a balance responsible party (BRP).

Findings

– From the perspective of a BRP, the added value of PV-EV collaboration for the energy system has been evidenced in any situation even when the charging strategy is very simple. On the other hand, for the case of a VPP operator, the coupling between the optimal sizing and the management strategy is highlighted.

Originality/value

– A co-optimization of the sizing and the management of a PV-EV collaborative system is introduced and the influence of the management strategy on the collaboration added value has been investigated. This gave rise to the presentation and implementation of an original modeling tool of the PV production forecast error. Finally, to widen the scope of application, two different business models have been tackled and compared.