bluuebunny/crossref_metadata_2025 huggingface dataset:
Rovibrational energy transfer and dissociation in O2–O collisions
Authors: Andrienko Daniil A. , Boyd Iain D.
Published: March 2016

A set of state-specific transition rates for each rovibrational level is generated for the O2(X3Σg−)–O3P system using the quasi-classical trajectory method at temperatures observed in hypersonic flows. A system of master equations describes the relaxation of the rovibrational ensemble to thermal equilibrium under ideal heat bath conditions at a constant translational temperature. Vibrational and rotational relaxation times, obtained from the average internal energies, exhibit a pattern inherent in a chemically reactive collisional pair. An intrinsic feature of the O3 molecular system with a large attractive potential is a weak temperature dependence of the rovibrational transition rates. For this reason, the quasi-steady vibrational and rotational temperatures experience a maximum at increasing translational temperature. The energy rate coefficients, that characterize the average loss of internal energy due to dissociation, quickly diminish at high temperatures, compared to other molecular systems.
Infrared spectroscopic studies on the cluster size dependence of charge carrier structure in nitrous oxide cluster anions
Authors: Thompson Michael C. , Weber J. Mathias
Published: March 2016

We report infrared photodissociation spectra of nitrous oxide cluster anions of the form (N2O)nO− (n = 1–12) and (N2O)n− (n = 7–15) in the region 800–1600 cm−1. The charge carriers in these ions are NNO2− and O− for (N2O)nO− clusters with a solvation induced core ion switch, and N2O− for (N2O)n− clusters. The N–N and N–O stretching vibrations of N2O− (solvated by N2O) are reported for the first time, and they are found at (1595 ± 3) cm−1 and (894 ± 5) cm−1, respectively. We interpret our infrared spectra by comparison with the existing photoelectron spectroscopy data and with computational data in the framework of density functional theory.
High vacuum tip-enhanced Raman spectroscope based on a scanning tunneling microscope
Authors: Fang Yurui , Zhang Zhenglong , Sun Mengtao
Published: March 2016

In this paper, we present the construction of a high-vacuum tip-enhanced Raman spectroscopy (HV-TERS) system that allows in situ sample preparation and measurement. A detailed description of the prototype instrument is presented with experimental validation of its use and novel ex situ experimental results using the HV-TERS system. The HV-TERS system includes three chambers held under a 10−7 Pa vacuum. The three chambers are an analysis chamber, a sample preparation chamber, and a fast loading chamber. The analysis chamber is the core chamber and contains a scanning tunneling microscope (STM) and a Raman detector coupled with a 50 × 0.5 numerical aperture objective. The sample preparation chamber is used to produce single-crystalline metal and sub-monolayer molecular films by molecular beam epitaxy. The fast loading chamber allows ex situ preparation of samples for HV-TERS analysis. Atomic resolution can be achieved by the STM on highly ordered pyrolytic graphite. We demonstrate the measurement of localized temperature using the Stokes and anti-Stokes TERS signals from a monolayer of 1,2-benzenedithiol on a gold film using a gold tip. Additionally, plasmonic catalysis can be monitored label-free at the nanoscale using our device. Moreover, the HV-TERS experiments show simultaneously activated infrared and Raman vibrational modes, Fermi resonance, and some other non-linear effects that are not observed in atmospheric TERS experiments. The high spatial and spectral resolution and pure environment of high vacuum are beneficial for basic surface studies.
Sugarcane tops as a substitute for sugarcane in high-concentrate diets for beef bulls
Authors: Couto Julião R. L. , Villela Severino D. J. , Mourthé Mário H. F. , Lobo-Jr Adalfredo R. , Santos Roseli A. , Martins Paulo G. M. A.
Published: March 2016

Our objective was to evaluate the productive and economic performances of bulls fed increasing levels of sugarcane tops, as a substitute for sugarcane. Sixteen, 24-month-old, Nellore bulls (initial bodyweight = 360 ± 14.7 kg) were kept in a feedlot for 84 days, receiving a high-concentrate diet (80 : 20 concentrate : roughage ratio). Four levels of substitution were evaluated: T0 = no addition of sugarcane tops; T33 = 33% substitution; T66 = 66% substitution; and T100 = total substitution of sugarcane by sugarcane tops. Dry matter, organic matter, crude protein and neutral detergent fibre intake, bodyweight gain, feed conversion and feed efficiency were evaluated as productive performance parameters, and as economic indicators, total revenue, total operating expenses, gross margin, and net margin. No effect (P ≥ 0.66) of diet was found for the studied variables. Average values of total bodyweight gain, average daily gain, feed conversion, and feed efficiency were 102 ± 10.0 kg/animal, 1.2 ± 0.12 kg/day, 8.6 ± 0.72 and 0.12 ± 0.010, respectively. Unlike other treatments, the T100 net margin was positive, because of the lower cost of acquiring sugarcane tops compared with sugarcane. Partial or total substitution of sugarcane by sugarcane tops in high-concentrate diets did not affect performance of feedlot bulls, but total substitution reduced production costs, with positive net margin. We conclude that sugarcane tops can be utilised as a low-cost roughage source in diets for beef bulls.
Increased frequency of chromosome congression defects and aneuploidy in mouse oocytes cultured at lower temperature
Authors: Danadova Jitka , Matijescukova Natalie , Danylevska Anna Mac Gillavry , Anger Martin
Published: March 2016

Optimal culture conditions are essential for successful IVM of mammalian oocytes and for their further development into an embryo. In the present study we used live cell imaging microscopy to assess the effects of suboptimal culture temperature on various aspects of IVM, including duration of meiosis I, dynamics of polar body extrusion, chromosome congression, anaphase-promoting complex/cyclosome (APC/C) activation and aneuploidy. The data showed that even a small deviation from the optimal incubation temperature causes marked changes in the duration and synchronicity of meiosis, APC/C activity and the frequency of chromosome congression and segregation errors. In vitro manipulation and maturation of germ cells is widely used in both human and animal artificial reproduction techniques. Mammalian oocytes are naturally prone to chromosomal segregation errors, which are responsible for severe mental and developmental disorders. The data presented herein demonstrate that exposure of mouse oocytes to suboptimal temperature during manipulation and maturation could further increase the frequency of chromosome segregation defects in these cells.
Quantum communication complexity advantage implies violation of a Bell inequality
Authors: Buhrman Harry , Czekaj Łukasz , Grudka Andrzej , Horodecki Michał , Horodecki Paweł , Markiewicz Marcin , Speelman Florian , Strelchuk Sergii
Published: March 2016

Significance

For many communication complexity problems the quantum strategies, distinguished by using Bell nonlocal correlations, provide exponential advantage over the best possible classical strategies. Conversely, for any Bell nonlocal correlations there exists a communication complexity problem that is solved more efficiently using the former. Despite many efforts, there were only two problems for which one could certify that any strategy that outperforms the classical one must harbor Bell nonlocal correlations. We prove that any large advantage over the best known classical strategy makes use of Bell nonlocal correlations. Thus, we provide the missing link to the fundamental equivalence between Bell nonlocality and quantum advantage.
Deciphering ocean carbon in a changing world
Authors: Moran Mary Ann , Kujawinski Elizabeth B. , Stubbins Aron , Fatland Rob , Aluwihare Lihini I. , Buchan Alison , Crump Byron C. , Dorrestein Pieter C. , Dyhrman Sonya T. , Hess Nancy J. , Howe Bill , Longnecker Krista , Medeiros Patricia M. , Niggemann Jutta , Obernosterer Ingrid , Repeta Daniel J. , Waldbauer Jacob R.
Published: March 2016

Dissolved organic matter (DOM) in the oceans is one of the largest pools of reduced carbon on Earth, comparable in size to the atmospheric CO
2
reservoir. A vast number of compounds are present in DOM, and they play important roles in all major element cycles, contribute to the storage of atmospheric CO
2
in the ocean, support marine ecosystems, and facilitate interactions between organisms. At the heart of the DOM cycle lie molecular-level relationships between the individual compounds in DOM and the members of the ocean microbiome that produce and consume them. In the past, these connections have eluded clear definition because of the sheer numerical complexity of both DOM molecules and microorganisms. Emerging tools in analytical chemistry, microbiology, and informatics are breaking down the barriers to a fuller appreciation of these connections. Here we highlight questions being addressed using recent methodological and technological developments in those fields and consider how these advances are transforming our understanding of some of the most important reactions of the marine carbon cycle.
Three-dimensional bioprinting of thick vascularized tissues
Authors: Kolesky David B. , Homan Kimberly A. , Skylar-Scott Mark A. , Lewis Jennifer A.
Published: March 2016

Significance

Current tissue manufacturing methods fail to recapitulate the geometry, complexity, and longevity of human tissues. We report a multimaterial 3D bioprinting method that enables the creation of thick human tissues (>1 cm) replete with an engineered extracellular matrix, embedded vasculature, and multiple cell types. These 3D vascularized tissues can be actively perfused with growth factors for long durations (>6 wk) to promote differentiation of human mesenchymal stem cells toward an osteogenic lineage in situ. The ability to construct and perfuse 3D tissues that integrate parenchyma, stroma, and endothelium is a foundational step toward creating human tissues for ex vivo and in vivo applications.
Models for the a subunits of the
Thermus thermophilus
V/A-ATPase and
Saccharomyces cerevisiae
V-ATPase enzymes by cryo-EM and evolutionary covariance
Authors: Schep Daniel G. , Zhao Jianhua , Rubinstein John L.
Published: March 2016

Significance

In cells, chemical energy is interconverted with electrochemical ion gradients across membranes for numerous processes. Three of the most significant enzymes that carry out this conversion are known as rotary ATPases because ion translocation is coupled to the synthesis or hydrolysis of ATP by rotation of part of the enzyme. These protein assemblies are the closely related eukaryotic V-ATPases and bacterial or archaeal V/A-ATPases, and the more distantly related F-type ATP synthases. Understanding of rotary ATPases has been limited by not knowing the structure of the subunit that couples ion translocation to rotation. Here, we determine the structure of this subunit for two of the three types of rotary ATPases, identifying a conserved architecture and mechanism in all three enzymes.
Conformational dynamics of a membrane protein chaperone enables spatially regulated substrate capture and release
Authors: Liang Fu-Cheng , Kroon Gerard , McAvoy Camille Z. , Chi Chris , Wright Peter E. , Shan Shu-ou
Published: March 2016

Significance

Molecular chaperones play key roles in maintaining protein homeostasis within cells. Membrane protein chaperones face particular challenges, as they not only protect highly aggregation-prone membrane protein substrates, but also need to achieve tight spatiotemporal coordination of their chaperone cycle. In this work, biochemical and NMR analyses address these questions and for the first time, to our knowledge, define the complete chaperone cycle for cpSRP43, an ATP-independent chaperone dedicated to integral membrane proteins. The study reveals that cpSRP43’s substrate binding domain samples at least three distinct conformations. This property enables it to be readily switched on by positive regulators in the soluble phase to ensure tight substrate binding and be switched off by the translocase at the membrane to ensure facile and productive substrate release.
Use of the Fluidigm C1 platform for RNA sequencing of single mouse pancreatic islet cells
Authors: Xin Yurong , Kim Jinrang , Ni Min , Wei Yi , Okamoto Haruka , Lee Joseph , Adler Christina , Cavino Katie , Murphy Andrew J. , Yancopoulos George D. , Lin Hsin Chieh , Gromada Jesper
Published: March 2016

Significance

Pancreatic islets are complex structures composed of four cell types whose primary function is to maintain glucose homeostasis. Owing to the scarcity and heterogeneity of the islet cell types, little is known about their individual gene expression profiles. Here we used the Fluidigm C1 platform to obtain high-quality gene expression profiles of each islet cell type from mice. We identified cell-type–specific transcription factors and pathways providing previously unrecognized insights into genes characterizing islet cells. Unexpectedly, our data uncover technical limitations with the C1 Fluidigm cell capture process, which should be considered when analyzing single-cell transcriptomics data.
The unfinished business of perestroika: Latvia's memory politics and its quest for acknowledgment of victimhood in Europe
Authors: Wezel Katja
Published: March 2016

In the 25 years since the re-establishment of Baltic independence from the Soviet Union, there has been no conclusive public conversation, or “coming to terms with the past” with respect to crimes against Latvian and other persecuted groups under Communism. This paper examines how national politicians, members of the European Parliament in Brussels, representatives of Latvia's Russian-speaking minority, and the Russian government have engaged in a difficult, long-overdue conversation. Conflicting historical narratives about victimhood are at the heart of these disagreements. Special emphasis is given to Latvia's historical narrative, its development over the past 25 years, and the way it challenges Russia's interpretation of history. I argue that Latvian memory politics at the European level are a continuation of Latvia's quest for acknowledgment of its victimhood, thereby trying to finish the process started in the late 1980s when Balts first demanded acknowledgment of human rights violations they had suffered under the Soviet regime. Latvia's methods of transitional justice are examined, arguing that its memory politics at the European level are an extension of steps taken at the national level to come to terms with the past and to increase its negotiating power against Russia's neo-Soviet historical narrative.
Effects of elevated pCO2 on the survival, growth, and moulting of the Pacific krill species, Euphausia pacifica
Authors: Cooper Helen L. , Potts Donald C. , Paytan Adina
Published: March 2016

While ocean acidification (OA) is expected to have wide-ranging negative effects on marine species, organisms currently living in variable pH environments that expose them intermittently to pH values approaching those predicted for the future, may be better adapted to tolerate prolonged exposure to high pCO2 levels caused by OA. Seasonal upwelling brings low pH water to the surface along the Pacific Coast of North America. In Monterey Bay, California Euphausia pacifica, a key species supporting a diverse multi-trophic-level ecosystem, currently experiences broad pCO2 and pH ranges due to both diel vertical migrations and seasonal upwelling. We determined tolerances of E. pacifica to prolonged exposure to pH levels predicted for 2100 by maintaining adults at two pCO2 levels (380 and 1200 µatm) for 2 months. Rates of survival and moulting were the same at both pCO2 levels. High pCO2 slowed growth in all size classes. In additional experiments to determine pCO2 threshold levels above which E. pacifica is adversely affected, survival was not affected down to pH 6.96 (6050 µatm), but declined rapidly at pH 6.92 (7228 µatm) and lower, with 100% mortality within 10 d at pH 6.89.
The proper motion of HV2112: a TŻO candidate in the SMC
Authors: Worley C. Clare , Irwin Mike. J. , Tout Christopher A. , Żytkow Anna N. , Fraser Morgan , Izzard Robert G.
Published: March 2016

The candidate Thorne–Żytkow object (TŻO), HV2112, is becoming a well-studied if enigmatic object. A key point of its candidacy as a TŻO is whether or not it resides in the Small Magellanic Cloud (SMC). HV2112 has detections in a series of photometric catalogues which have resulted in contradictory estimates of its proper motion and, therefore, its membership within the SMC. This letter seeks to resolve the issue of the SMC membership of HV2112 through a reanalysis of extant photometric data. We also demonstrate the difficulties and downfalls inherent in considering a range of catalogue proper motions. We conclude that the proper motion, and associated ancillary radial velocity, positional and photometric properties, are fully consistent with HV2112 being within the SMC and thus it remains a candidate TŻO.
Revised wavelength and spectral response calibrations for AKARI near-infrared grism spectroscopy: Cryogenic phase
Authors: Baba Shunsuke , Nakagawa Takao , Shirahata Mai , Isobe Naoki , Usui Fumihiko , Ohyama Youichi , Onaka Takashi , Yano Kenichi , Kochi Chihiro
Published: March 2016

We perform revised spectral calibrations for the AKARI near-infrared grism to correct quantitatively for the effect of the wavelength-dependent refractive index. The near-infrared grism covering the wavelength range of 2.5–5.0 μm, with a spectral resolving power of 120 at 3.6 μm, is found to be contaminated by second-order light at wavelengths longer than 4.9 μm, which is especially serious for red objects. First, we present the wavelength calibration considering the refractive index of the grism as a function of the wavelength for the first time. We find that the previous solution is positively shifted by up to 0.01 μm compared with the revised wavelengths at 2.5–5.0 μm. In addition, we demonstrate that second-order contamination occurs even with a perfect order-sorting filter owing to the wavelength dependence of the refractive index. Secondly, the spectral responses of the system from the first- and second-order light are simultaneously obtained from two types of standard objects with different colors. The response from the second-order light suggests leakage of the order-sorting filter below 2.5 μm. The relations between the output of the detector and the intensities of the first- and second-order light are formalized by a matrix equation that combines the two orders. The removal of the contaminating second-order light can be achieved by solving the matrix equation. The new calibration extends the available spectral coverage of the grism mode from 4.9 μm up to 5.0 μm. The revision can be used to study spectral features falling in these extended wavelengths, e.g., the carbon monoxide fundamental ro-vibrational absorption within nearby active galactic nuclei.
Transabdominal Cerclage
Authors: SUMNERS JAMES E. , KUPER SPENCER G. , FOSTER TODD L.
Published: March 2016

The transabdominal cerclage procedure was first introduced 50 years ago as an approach in those patients who had failed transvaginal cerclage. We review the history, indications, surgical technique, complications, and reported outcomes of the procedure. The procedure has evolved over time in its application and risks appear to be less than previously perceived. Physicians have found additional patient situations in which the procedure may be beneficial outside the indications defined 50 years ago. This is a valuable surgical technique which is likely underused.
The HeartMate II Risk Score: An Adjusted Score for Evaluation of All Continuous-Flow Left Ventricular Assist Devices
Authors: Cowger Jennifer Ann , Castle Lindsay , Aaronson Keith David , Slaughter Mark S. , Moainie Sina , Walsh Mary , Salerno Christopher
Published: March 2016

The aim of this study was to evaluate the performance of an adjusted HeartMate II risk score (HMRS) in Interagency Registry for Mechanically Assisted Circulatory Support (INTERMACS; n = 9,733) and in HeartWare Ventricular Assist Device (HVAD) bridge to transplant (BTT) trial patients (n = 360). Interagency Registry for Mechanically Assisted Circulatory Support data were used to calculate an adjusted HMRS, omitting center volume, for all patients on continuous-flow left ventricular assist device (LVAD) support. Ninety day mortality was then evaluated in INTERMACS and HVAD-BTT patients. Four risk groups were identified based on INTERMACS patient-adjusted HMRS: very low (<5%, 90 day mortality; score <0.20), low (5–10%, 90 day mortality; score 0.20–1.97), medium (10–20%, 90 day mortality; score 1.98–4.48), and high risk (>20%, 90 day mortality; score >4.48). Within INTERMACS, there were significant differences in survival between all-adjusted HMRS risk groups (p < 0.001 in pairwise comparisons). Controlling for known mortality correlates, the adjusted HMRS mortality hazard ratio was 1.19 (1.25–1.23) per unit HMRS increase. The HVAD cohort was a low-risk cohort with 90 day survivals for very low-, low-, and medium-risk patients of 100%, 97 ± 1.1%, and 90 ± 3.6%, respectively (p = 0.007). Patients in the very low- and low-risk group had significantly improved survival compared with medium-risk patients, respectively (both p < 0.05). The adjusted HMRS appropriately risk stratified a large cohort of INTERMACS patients and was predictive of survival in HeartWare-supported patients.
Gastrointestinal Congestion Dilates the Hepatic Artery Through the P38 MAPK Signal Transduction Pathway During Liver Transplantation
Authors: Cao Zhongping , Tang Xiaowen , Hou Shike
Published: March 2016

During the neohepatic stage of liver transplantation, hemodynamics change markedly. The current study aimed to investigate whether gastrointestinal congestion caused by inferior vena cava and hepatic portal vein clamping can dilate the hepatic artery and to determine the associated mechanisms. Ring segments of the hepatic artery were treated with the plasma from gastrointestinal congestion or the superior vena cava. The fractions in gastrointestinal congestion and the superior vena cava plasma were tested, and the effect of these fractions on the tone of the hepatic artery ring was examined. Different signal transduction blockers and different inhibitors were then used to determine the exact signal transduction pathway involved. In addition, endothelial cell structure was observed by transmission electron microscopy after treatment with the gastrointestinal congestion plasma or the superior vena cava plasma. Gastrointestinal congestion plasma contained more inflammatory cytokines than superior vena cava plasma, and these cytokines could cause hepatic artery ring dilatation. A P38 mitogen-activated protein kinase (P38 MAPK) signal transduction pathway blocker and nitric oxide (NO), prostaglandin (PGI2), nuclear factor-κB (NF-κB), and adenosine triphosphate (ATP)-sensitive K+ (KATP) channel inhibitors were able to significantly reverse the ring tension caused by gastrointestinal congestion plasma. The normal endothelium was also injured by treatment with gastrointestinal congestion plasma. The inflammatory cytokines in gastrointestinal congestion can cause hepatic artery ring dilatation through the P38 MAPK signal transduction pathway, and this phenomenon is also associated with NO, PGI2, NF-κB, and the KATP channel. These inflammatory cytokines can injure endothelial cells in the hepatic artery.
“Debriefing-on-Demand”
Authors: McMullen Michael , Wilson Rosemary , Fleming Melinda , Mark David , Sydor Devin , Wang Louie , Zamora Jorge , Phelan Rachel , Burjorjee Jessica E.
Published: March 2016

Introduction

Simulation is an effective tool in medical education with debriefing as the cardinal educational component. Alternate debriefing strategies might further enhance the educational value of simulation. Here, we pilot a novel strategy that allows trainees to initiate debriefing at any point during the scenario, when they consider it necessary.

Methods

With ethics approval, 8 postgraduate year 1 anesthesia residents (with no previous exposure to high-fidelity simulation) were randomly assigned to lead 2 of 8 scenarios with 2 debriefing strategies. With “debriefing-on-demand,” residents had the option to initiate debriefing at any point in the scenario by activation of a “pause button”—in addition to undergoing conventional debriefing at the end of the scenario. Those randomized to “conventional debriefing” were debriefed only at the end of the scenario. All were allocated as team leader with both debriefing strategies and as a participant in remaining scenarios. Residents provided feedback regarding each method using Likert scales and completion of open-ended statements.

Results

Debriefing-on-demand was easily integrated into all scenarios, and most learners (88%) supported its use in future simulation sessions. The following 4 themes emerged from qualitative analyses: (1) improvements in the clarification and integration of knowledge, (2) reductions in stress/anxiety, (3) facilitated reflection on action, and (4) maintained realism comparable with conventional debriefing.

Conclusions

Debriefing-on-demand was easily integrated into all scenarios and well received by these trainees new to simulation. Larger trials that use validated tools are needed to determine the absolute impact of debriefing-on-demand on stress levels and the overall learning value of simulation for trainees at different levels of training.
Extracting a shape function for a signal with intra-wave frequency modulation
Authors: Hou Thomas Y. , Shi Zuoqiang
Published: March 2016

In this paper, we develop an effective and robust adaptive time-frequency analysis method for signals with intra-wave frequency modulation. To handle this kind of signals effectively, we generalize our data-driven time-frequency analysis by using a shape function to describe the intra-wave frequency modulation. The idea of using a shape function in time-frequency analysis was first proposed by Wu (Wu 2013Appl. Comput. Harmon. Anal. 35, 181–199. (doi:10.1016/j.acha.2012.08.008)). A shape function could be any smooth 2π-periodic function. Based on this model, we propose to solve an optimization problem to extract the shape function. By exploring the fact that the shape function is a periodic function with respect to its phase function, we can identify certain low-rank structure of the signal. This low-rank structure enables us to extract the shape function from the signal. Once the shape function is obtained, the instantaneous frequency with intra-wave modulation can be recovered from the shape function. We demonstrate the robustness and efficiency of our method by applying it to several synthetic and real signals. One important observation is that this approach is very stable to noise perturbation. By using the shape function approach, we can capture the intra-wave frequency modulation very well even for noise-polluted signals. In comparison, existing methods such as empirical mode decomposition/ensemble empirical mode decomposition seem to have difficulty in capturing the intra-wave modulation when the signal is polluted by noise.
On Holo-Hilbert spectral analysis: a full informational spectral representation for nonlinear and non-stationary data
Authors: Huang Norden E. , Hu Kun , Yang Albert C. C. , Chang Hsing-Chih , Jia Deng , Liang Wei-Kuang , Yeh Jia Rong , Kao Chu-Lan , Juan Chi-Hung , Peng Chung Kang , Meijer Johanna H. , Wang Yung-Hung , Long Steven R. , Wu Zhauhua
Published: March 2016

The Holo-Hilbert spectral analysis (HHSA) method is introduced to cure the deficiencies of traditional spectral analysis and to give a full informational representation of nonlinear and non-stationary data. It uses a nested empirical mode decomposition and Hilbert–Huang transform (HHT) approach to identify intrinsic amplitude and frequency modulations often present in nonlinear systems. Comparisons are first made with traditional spectrum analysis, which usually achieved its results through convolutional integral transforms based on additive expansions of ana prioridetermined basis, mostly under linear and stationary assumptions. Thus, for non-stationary processes, the best one could do historically was to use the time–frequency representations, in which the amplitude (or energy density) variation is still represented in terms of time. For nonlinear processes, the data can have both amplitude and frequency modulations (intra-mode and inter-mode) generated by two different mechanisms: linear additive or nonlinear multiplicative processes. As all existing spectral analysis methods are based on additive expansions, eithera priorior adaptive, none of them could possibly represent the multiplicative processes. While the earlier adaptive HHT spectral analysis approach could accommodate the intra-wave nonlinearity quite remarkably, it remained that any inter-wave nonlinear multiplicative mechanisms that include cross-scale coupling and phase-lock modulations were left untreated. To resolve the multiplicative processes issue, additional dimensions in the spectrum result are needed to account for the variations in both the amplitude and frequency modulations simultaneously. HHSA accommodates all the processes: additive and multiplicative, intra-mode and inter-mode, stationary and non-stationary, linear and nonlinear interactions. TheHoloprefix in HHSA denotes a multiple dimensional representation with both additive and multiplicative capabilities.
Symmetric assembly and disassembly processes in an ecological network
Authors: Tylianakis Jason M. , Martínez-García Laura B. , Richardson Sarah J. , Peltzer Duane A. , Dickie Ian A.
Published: March 2016

The processes whereby ecological networks emerge, persist and decay throughout ecosystem development are largely unknown. Here we study networks of plant and arbuscular mycorrhizal fungal (AMF) communities along a 120,000 yr soil chronosequence, as they undergo assembly (progression) and then disassembly (retrogression). We found that network assembly and disassembly were symmetrical, self-reinforcing processes that together were capable of generating key attributes of network architecture. Plant and AMF species that had short indirect paths to others in the community (i.e. high centrality), rather than many direct interaction partners (i.e. high degree), were best able to attract new interaction partners and in the case of AMF species, also to retain existing interactions with plants during retrogression. We then show using simulations that these non-random patterns of attachment and detachment promote nestedness of the network. These results have implications for predicting extinction sequences, identifying focal points for invasions, and suggesting trajectories for restoration.
mLDM: a new hierarchical Bayesian statistical model for sparse microbioal association discovery
Authors: Yang Yuqing , Chen Ning , Chen Ting
Published: March 2016

Interpretive analysis of metagenomic data depends on an understanding of the underlying associations among microbes from metagenomic samples. Although several statistical tools have been developed for metage-nomic association studies, they suffer from compositional bias or fail to take into account environmental factors that directly affect the composition of a given microbial community. In this paper, we proposemetagenomicLognormal-Dirichlet-Multinomial (mLDM), a hierarchical Bayesian model with sparsity constraints to bypass compositional bias and discover new associations among microbes and between microbes and environmental factors. The mLD-M model can 1) infer both conditionally dependent associations among microbes and direct associations between microbes and environmental factors; 2) consider both compositional bias and variance of metagenomic data; and 3) estimate absolute abundance for microbes. Thus, conditionally dependent association can capture direct relationship underlying microbial pairs and remove the indirect connections induced from other common factors. Empirical studies show the effectiveness of the mLDM model, using both synthetic data and the TARA Oceans eukaryotic data by comparing it with several state-of-the-art methodologies. Finally, mLDM is applied to western English Channel data and finds some interesting associations.
AnnoLnc: a web server for systematically annotating novel human lncRNAs
Authors: Hou Mei , Tang Xing , Tian Feng , Shi Fangyuan , Liu Fenglin , Gao Ge
Published: March 2016

Although the repertoire of human lncRNAs has rapidly expanded, their biological function and regulation remain largely elusive. Here, we present AnnoLnc (http://annolnc.cbi.pku.edu.cn), an online portal for systematically annotating newly identified human lncRNAs. AnnoLnc offers a full spectrum of annotations covering genomic location, RNA secondary structure, expression, transcriptional regulation, miRNA interaction, protein interaction, genetic association and evolution, as well as an abstraction-based text summary and various intuitive figures to help biologists quickly grasp the essentials. In addition to an intuitive and mobile-friendly Web interactive design, AnnoLnc supports batch analysis and provides JSON-based Web Service APIs for programmatic analysis. To the best of our knowledge, AnnoLnc is the first web server to provide on-the-fly and systematic annotation for newly identified human lncRNAs. Some case studies have shown the power of AnnoLnc to inspire novel hypotheses.
Drought responsive gene expression regulatory divergence between upland and lowland ecotypes of a perennial C4grass
Authors: Lovell John T. , Schwartz Scott , Lowry David B. , Shakirov Eugene V. , Bonnette Jason E. , Weng Xiaoyu , Wang Mei , Johnson Jenifer , Sreedasyam Avinash , Plott Christopher , Jenkins Jerry , Schmutz Jeremy , Juenger Thomas E.
Published: March 2016

Climatic adaptation is an example of a genotype-by-environment interaction (G×E) of fitness. Selection upon gene expression regulatory variation can contribute to adaptive phenotypic diversity; however, surprisingly few studies have examined how genome-wide patterns of gene expression G×E are manifested in response to environmental stress and other selective agents that cause climatic adaptation. Here, we characterize drought-responsive expression divergence between upland (drought-adapted) and lowland (mesic) ecotypes of the perennial C4grass,Panicum hallii, in natural field conditions. Overall, we find thatcis-regulatory elements contributed to gene expression divergence across 47% of genes, 7.2% of which exhibit drought-responsive G×E. While less well-represented, we observe 1294 genes (7.8%) withtranseffects.Trans-by-environment interactions are weaker and much less common thancisG×E, occurring in only 0.7% oftrans-regulated genes. Finally, gene expression heterosis is highly enriched in expression phenotypes with significant G×E. As such, modes of inheritance that drive heterosis, such as dominance or overdominance, may be common among G×E genes. Interestingly, motifs specific to drought-responsive transcription factors are highly enriched in the promoters of genes exhibiting G×E andtransregulation, indicating that expression G×E and heterosis may result from the evolution of transcription factors or their binding sites.P. halliiserves as the genomic model for its close relative and emerging biofuel crop, switchgrass (Panicum virgatum). Accordingly, the results here not only aid in the discovery of the genetic mechanisms that underlie local adaptation but also provide a foundation to improve switchgrass yield under water-limited conditions.
Crystal structure and crystallographic characteristics of martensite in Ni50Mn38Sb12 alloys
Authors: Zhang Chunyang , Yan Haile , Zhang Yudong , Esling Claude , Zhao Xiang , Zuo Liang
Published: March 2016

For Ni–Mn–Sb ferromagnetic multifunctional alloys, the crystal structures of martensite variants and the orientation relationships between them are decisive factors for their magnetic field-induced behaviours and are hence of importance. Such information has rarely been reported in the literature. In the present work, the crystal structure, microstructure and orientation relationships of Ni–Mn–Sb martensite were thoroughly investigated by X-ray diffraction (XRD) and electron backscatter diffraction (EBSD). Through XRD analyses, the crystal structure of the martensite, including the crystal system, the space group, the lattice parameters and the atomic coordinates, was fully resolved. The structure is orthorhombic and can be represented with a 4O superstructure. EBSD analyses show that the Ni–Mn–Sb martensite has a lamellar form. One martensite lamella corresponds to one orientation variant. The lamellae are organized in long plate-shaped colonies. Within each colony, four distinct orientation variants (A, B, C and D) appear repeatedly and extend in roughly the same direction. The four variants are twin related to one another, with variants A and C (or variants B and D) forming a type I twin, variants A and B (or C and D) a type II twin, and variants A and D (or B and C) a compound twin. The complete twinning elements for each twin relation were thus fully determined. The interfaces between the variants were identified to be their corresponding twinning planes. All these results provide fundamental information for Ni–Mn–Sb alloys that is useful for interpreting their magnetic and mechanical characteristics.
The field of accounting
Authors: Yapa Prem W. Senarath , Jacobs Kerry , Huot Bopta Chan
Published: March 2016

Purpose

– The purpose of this paper is to explore the field of accounting as a nexus between the rise of industrial societies, strategies of elites to preserve and reproduce privilege, practices of state control and the external forces of colonisation and globalisation. The authors explore this field in the context of Cambodia which embodies a particularly diverse range of internal and external influences.

Design/methodology/approach

– A qualitative research approach is employed. The research methods were an analysis of secondary sources and interviews with key officials former Head of State and academics. An effort was made to interview Khmer Rouge survivors about the nature of the accounting practices, class and state control.

Findings

– During the pre-colonial and the period of French colonial influence, there was relatively accounting practice or distinctive professional bodies. Under the Khmer Rouge there was both a clear rejection of individuals with accounting skills while there were some attempts to use of elements of accounting as tools of central control. This use of accounting as a tool of control was further normalised under Vietnamese rule and socialism. Following the restoration of independence there was some French influence on the growth of institutional and practices of accounting. However, these institutions and practices have been modified and refined by recent growth of international accounting firms and the Association of Chartered Certified Accountants.

Research limitations/implications

– This paper has significant implications for understanding the nature and development of the accounting in developing countries, recognising both national and internal influences.

Practical implications

– This paper has practical implications for understanding the nature and changes associated with the accounting profession in a global context.

Originality/value

– This paper adds new literature on accounting which recognises the nexus of interests, practices and institutions associated with the field of accounting.
Public sector budgeting: a European review of accounting and public management journals
Authors: Anessi-Pessina Eugenio , Barbera Carmela , Sicilia Mariafrancesca , Steccolini Ileana
Published: March 2016

Purpose

– Budgeting is central in public organizations. From a research viewpoint, it is an extremely multifaceted and potentially rich field to investigate and develop. The changing institutional and socio-economic landscape, moreover, requires a profound reassessment of its roles and features in accounting studies. The purpose of this paper is to review the existing European literature on public budgeting, looking at how public administration, public management, and accounting contribute to current budgeting theories and practices and to advance a proposal on how they can individually and jointly contribute in the future.

Design/methodology/approach

– The authors collect and analyze all the papers on public budgeting in the European context that were published in all the issues of 15 major accounting and public-management journals since 1980.

Findings

– Budgeting has so far played a rather marginal role in European public management and accounting research. Among the existing papers, most focus on the Anglo-Saxon context, look at the intra-organizational aspects of budgeting, emphasize its managerial and allocative functions, either adopt an interpretive theoretical framework or make no explicit reference to theory, and rely on qualitative analyses. Public budgeting lies at the intersections between different disciplines and professions, but this multifacetedness has been largely neglected by the existing literature. These intersections thus offer significant opportunities for future research. Building on the distinction between the intra- and inter-organizational foci of budgeting, between its different functions (i.e. allocative, managerial, external accountability), and between the accounting and the public administration and management perspectives, the authors propose possible future research topics.

Originality/value

– Budgeting plays a central role in public organizations and is used to allocate a large share of national incomes. This paper explores the existing literature and puts forward some potentially fruitful avenues for future research.
An “adhocracy” of stakeholders, the case of ADSA in France (Essonne)
Authors: Naszalyi Phillipe , Slama-Royer Arnaud
Published: March 2016

Purpose

– The purpose of this paper is to analyze the structural problems emerging in the course of managing and safeguarding a French association for home care to a thousand elderly or disabled people between 2007 and 2012, employing 150

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190 people and on the verge of bankruptcy. In France, small local businesses not only compete with major capital outlets in this sector but also with associations of varying size and origin. Free market rules apply, under the legislation of 2003, to what is, in part, “competition free”, being “in the public interest” and within the framework of local and national public funding.

Design/methodology/approach

– This paper analyses those pragmatic solutions put in place to meet the aim of shared governance and in the context of a generalized financial crisis.

Findings

– Borrowing from cooperatives and associations, the non-profit-based management structure the authors arrived at, including worker participation in the decision-making processes, raises questions for researchers as to the advisability of any short-term models and the validity of present social and supportive economic models.

Originality/value

– The hybrid management of this paper is offered as a working model in what the authors have termed an “adhocracy of stakeholders”.
Boys’ bands in children’s homes: a fragment of history
Authors: Parker Roy
Published: March 2016

Purpose

– The purposes of this paper are threefold. First, to draw attention to an overlooked feature of children’s institutions in the nineteenth and early twentieth centuries; namely, the widespread existence of boys’ brass bands. The second purpose is to explain why these were created and the third is to consider what implications membership of a band had for a boy’s subsequent life.

Design/methodology/approach

– The paper relies upon archival and secondary sources.

Findings

– The study traces the influences that led to the formation of so many boys’ bands. These included the background of brass bands in popular culture; the belief in the power of music as an agent of social reform; the money-spinning value of a band that gave public performances, and the opportunity for a band-boy to join a military band, thereby securing a foothold in the juvenile labour market. Over and above these findings is the fact that so many boys from deprived backgrounds could be taught to play a musical instrument to a competent standard.

Originality/value

– As far as the author knows this is the only study of children’s homes’ bands. Its value lies in emphasising the fact that some of the most disadvantaged children are likely to have latent aptitudes and talents that can be discovered and developed. That is the message for today.
Understanding and mitigating cynicism in the workplace
Authors: Scott Kristyn A. , Zweig David
Published: March 2016

Purpose

– Organizational cynicism is on the increase. The purpose of this paper is to explore how dispositions promote cynical attitudes and how to mitigate the negative impact of organizational cynicism for employees.

Design/methodology/approach

– The data consisted of two samples (n=312 andn=529) of employed adults. All participants completed online surveys containing the variables of interest. The hypothesized model was tested using structural equation modeling.

Findings

– Low levels of core self-evaluation (CSE) predict organizational cynicism which, in turn, mediates the relations between CSE and job attitudes. Importantly, the authors find that supervisory support moderates both the relations between CSE and organizational cynicism and organizational cynicism and job satisfaction.

Originality/value

– Little research has directly assessed the role of dispositions in the development of organizational cynicism. The authors suggest that CSE contributes to the development of cynical attitudes. Further, the authors demonstrate that a supportive supervisor can serve as a buffer to mitigate the expression and effects of organizational cynicism on workplace outcomes.
Prosocial motive and helping behavior: examining helping efficacy and instrumentality
Authors: Choi Byoung Kwon , Moon Hyoung Koo
Published: March 2016

Purpose

– Building on trait activation theory, theory of other orientation, and self-perception theory, the purpose of this paper is to examine how employees’ perceptions of helping efficacy and instrumentality influence the relationship between their prosocial motive and helping behavior.

Design/methodology/approach

– Data from 304 supervisor-subordinate dyads in South Korea were analyzed. Hypotheses were tested using hierarchical multiple regression.

Findings

– The results show that prosocial motive had a stronger positive influence on helping behavior among employees with high levels of helping efficacy. However, contrary to our expectation, prosocial motive was more positively related to helping behavior when employees had high levels of helping instrumentality.

Practical implications

– Organizations need to present employees with effective, standardized work procedures to make them feel efficacy in helping others. It is also necessary for organizations to consider helping behavior an important factor in performance evaluation and to signify to employees that helping behavior will be rewarded.

Social implications

– Helping behavior is critical for the effectiveness of both organizations and society at large; voluntarily helping people can enhance various kinds of performance at the societal level and can contribute to people’s welfare. Thus, it is necessary to teach people how to help others and to recognize helping behavior.

Originality/value

– This study contributes to the understanding of when the influence of prosocial motive on helping is more strongly activated by incorporating employees’ perceptions of the contexts in which helping behavior operates – efficacy and instrumentality.