bluuebunny/crossref_metadata_2025 huggingface dataset:
The effects of training length on the perceptual learning of time-compressed speech and its generalization
Authors: Banai Karen , Lavner Yizhar
Published: October 2014

Brief exposure to time-compressed speech yields both learning and generalization. Whether such learning continues over the course of multi-session training and if so whether it is more or less specific than exposure-induced learning is not clear, because the outcomes of intensive practice with time-compressed speech have rarely been reported. The goal here was to determine whether prolonged training on time-compressed speech yields additional learning and generalization beyond that induced by brief exposure. Listeners practiced the semantic verification of time-compressed sentences for one or three training sessions. Identification of trained and untrained tokens was subsequently compared between listeners who trained for one or three sessions, listeners who were briefly exposed to 20 time-compressed sentences and naive listeners. Trained listeners outperformed the other groups of listeners on the trained condition, but only the group that was trained for three sessions outperformed the other groups when tested with untrained tokens. These findings suggest that although learning of distorted speech can occur rapidly, more stable learning and generalization might be achieved with longer, multi-session practice. It is suggested that the findings are consistent with the framework proposed by the Reverse Hierarchy Theory of perceptual learning.
Source levels of the underwater calls of a male leopard seal
Authors: Rogers Tracey L.
Published: October 2014

Leopard seals (Hydrurga leptonyx) are top predators in the Antarctic ecosystem. They produce stereotyped calls as part of a stylized underwater vocal display. Understanding of their acoustic behavior is improved by identifying the amplitude of their calls. The amplitude of five types of calls (n = 50) from a single male seal were measured as broadband source levels and ranged from 153 to 177 dB re 1 μPa at 1 m. The mean source levels differed between call types, the lower frequency calls (L, D, and O) tended to have source levels 10 dB higher than the higher frequency calls (H and M). Information on call-type source levels is important to take into account for passive acoustic studies investigating repertoire usage as calls produced with greater amplitudes are likely to have larger acoustic ranges, especially when these are also the calls with lower frequencies, such as is the case in leopard seals.
Time-frequency composition of mosquito flight tones obtained using Hilbert spectral analysis
Authors: Aldersley Andrew , Champneys Alan , Homer Martin , Robert Daniel
Published: October 2014

Techniques for estimating temporal variation in the frequency content of acoustic tones based on short-time fast Fourier transforms are fundamentally limited by an inherent time-frequency trade-off. This paper presents an alternative methodology, based on Hilbert spectral analysis, which is not affected by this weakness, and applies it to the accurate estimation of mosquito wing beat frequencies. Mosquitoes are known to communicate with one another via the sounds generated by their flapping wings. Active frequency modulation between pairs of mosquitoes is thought to take place as a precursor to courtship. Studying the acoustically-based interactions of mosquitoes therefore relies on an accurate representation of flight frequency as a time-evolving property, yet conventional Fourier spectrograms are unable to capture the rapid modulations in frequency that mosquito flight tones exhibit. The algorithms introduced in this paper are able to automatically detect and extract fully temporally resolved frequency information from audio recordings. Application of the technique to experimental recordings of single tethered mosquitoes in flight reveals corroboration with previous reported findings. The advantages of the method for animal communication studies are discussed, with particular attention given to its potential utility for studying pairwise mosquito interactions.
Impact of the irregular microgeometry of polyurethane foam on the macroscopic acoustic behavior predicted by a unit-cell model
Authors: Doutres O. , Ouisse M. , Atalla N. , Ichchou M.
Published: October 2014

This paper deals with the prediction of the macroscopic sound absorption behavior of highly porous polyurethane foams using two unit-cell microstructure-based models recently developed by Doutres, Atalla, and Dong [J. Appl. Phys. 110, 064901 (2011); J. Appl. Phys. 113, 054901 (2013)]. In these models, the porous material is idealized as a packing of a tetrakaidecahedra unit-cell representative of the disordered network that constitutes the porous frame. The non-acoustic parameters involved in the classical Johnson-Champoux-Allard model (i.e., porosity, airflow resistivity, tortuosity, etc.) are derived from characteristic properties of the unit-cell and semi-empirical relationships. A global sensitivity analysis is performed on these two models in order to investigate how the variability associated with the measured unit-cell characteristics affects the models outputs. This allows identification of the possible limitations of a unit-cell micro-macro approach due to microstructure irregularity. The sensitivity analysis mainly shows that for moderately and highly reticulated polyurethane foams, the strut length parameter is the key parameter since it greatly impacts three important non-acoustic parameters and causes large uncertainty on the sound absorption coefficient even if its measurement variability is moderate. For foams with a slight inhomogeneity and anisotropy, a micro-macro model associated to cell size measurements should be preferred.
Modeling transient sound propagation over an absorbing plane by a half-space interpolated time-domain equivalent source method
Authors: Pan Siwei , Jiang Weikang , Zhang Haibin , Xiang Shang
Published: October 2014

A half-space interpolated time-domain equivalent source method (ITDESM) is proposed to model the transient sound propagation over an absorbing plane. In this approach, a closed-form transient half-space Green's function (i.e., the impulse response function in three-dimensional space) for a pure absorbing infinite plane is introduced to develop the half-space ITDESM formulation. Instead of the free transient Green's function employed in the conventional ITDESM, such Green's function contains the reflection effect of the absorbing plane. As a numerical example, reconstructing the transient pressure fields from two monopole sources is depicted, where both monopoles are located in front of an infinite plane with absorbing impedance. Simulation results indicate that the half-space ITDESM can reconstruct the half-space transient sound fields in both the space and time domains very well. The proposed method is also investigated by taking into account the measurement noise in the reconstruction process. An experiment of an impacted steel plate above a glass wool board is presented to illustrate the validity of the proposed method under actual conditions.
Multifractal detrended fluctuation analysis to characterize phase couplings in seahorse (Hippocampus kuda) feeding clicks
Authors: Haris K. , Chakraborty Bishwajit , Menezes A. , Sreepada R. A. , Fernandes W. A.
Published: October 2014

Nonlinear phenomena in animal vocalizations fundamentally includes known features, namely, frequency jump, subharmonics, biphonation, and deterministic chaos. In the present study, the multifractal detrended fluctuation analysis (MFDFA) has been employed to characterize the phase couplings revealed in the feeding clicks of Hippocampus kuda yellow seahorse. The fluctuation function Fq(s), generalized Hurst exponent h(q), multifractal scaling exponent τ(q), and the multifractal spectrum f(α) calculated in the procedure followed were analyzed to comprehend the underlying nonlinearities in the seahorse clicks. The analyses carried out reveal long-range power-law correlation properties in the data, substantiating the multifractal behavior. The resulting h(q) spectrum exhibits a distinct characteristic pattern in relation to the seahorse sex and size, and reveals a spectral blind spot in the data that was not possible to detect by conventional spectral analyses. The corresponding multifractal spectrum related width parameter Δh(q) is well clustered, defining the individual seahorse clicks. The highest degree of multifractality is evident in the 18 cm male seahorse, signifying greater heterogeneity. A further comparison between the seahorse body size and weight (wet) with respect to the width parameter Δh(q) and the second-order Hurst exponent h(q=2) underscores the versatility of MFDFA as a robust statistical tool to analyze bioacoustic observations.
Noninvasive brain-computer interface enables communication after brainstem stroke
Authors: Sellers Eric W. , Ryan David B. , Hauser Christopher K.
Published: October 2014

An individual “locked-in” by a brainstem stroke was able to communicate using noninvasive brain-computer interface technology.
Genotype-based treatment of type 2 diabetes with an α
2A
-adrenergic receptor antagonist
Authors: Tang Yunzhao , Axelsson Annika S. , Spégel Peter , Andersson Lotta E. , Mulder Hindrik , Groop Leif C. , Renström Erik , Rosengren Anders H.
Published: October 2014

The α
2A
-adrenergic receptor antagonist yohimbine improves insulin secretion in type 2 diabetics carrying the
ADRA2A
risk variant.
Protecting the Fortress: Preventing Metastasis by Neutralizing Niche Homing
Authors: Lathia Justin D.
Published: October 2014

Multiple myeloma metastasis can be prevented by neutralizing stromal-cell–derived factor 1 to inhibit tumor cell homing to the bone marrow.
Five Years of Advancing Science, Improving Health
Authors: Kelner Katrina L. , McNutt Marcia
Published: October 2014

On its 5-year anniversary,
Science Translational Medicine
highlights its published research papers that have spurred encouraging translational progress.
An investigation into the role of alcohol in self-harm in rural Sri Lanka: a protocol for a multimethod, qualitative study
Authors: Sørensen Jane Brandt , Rheinländer Thilde , Sørensen Birgitte Refslund , Pearson Melissa , Agampodi Thilini , Siribaddana Sisira , Konradsen Flemming
Published: October 2014

Introduction

Sri Lanka has one of the highest suicide and self-harm rates in the world and although alcohol has been found to be a risk factor for self-harm in Sri Lanka, we know little about the connection between the two. This paper comprises a protocol for a qualitative study investigating alcohol's role in self-harm in rural Sri Lanka at three levels: the individual, community and policy level. The analysis will bring new understanding of the link between alcohol and self-harm in Sri Lanka, drawing on structural, cultural and social concepts. It will equip researchers, health systems and policy makers with vital information for developing strategies to address alcohol-related problems as they relate to self-harm.

Methods and analysis

To capture the complexity of the link between alcohol and self-harm in the Anuradhapura district in the North Central Province in Sri Lanka, qualitative methods will be utilised. Specifically, the data will consist of serial narrative life-story interviews with up to 20 individuals who have non-fatally self-harmed and where alcohol directly or indirectly was involved in the incidence as well as with their significant others; observations in communities and families; six focus group discussions with community members; and key-informant interviews with 15–25 stakeholders who have a stake in alcohol distribution, marketing, policies, prevention and treatment as they relate to self-harm.

Ethics and dissemination

The study has received ethical approval from the Ethical Review Committee of the Faculty of Medicine and Allied Sciences, Rajarata University of Sri Lanka. A sensitive data collection technique will be used and ethical issues will be considered throughout the study.

Results

The results will be disseminated in scientific peer-reviewed articles in collaboration with Sri Lankan and other international research partners.
Nocturnal antihypertensive treatment in patients with type 1 diabetes with autonomic neuropathy and non-dipping of blood pressure during night time: protocol for a randomised, placebo-controlled, double-blind, two-way crossover study
Authors: Hjortkær Henrik , Jensen Tonny , Kofoed Klaus , Mogensen Ulrik , Køber Lars , Hilsted Karen Lisa , Corinth Helle , Theilade Simone , Hilsted Jannik
Published: October 2014

Introduction

Cardiac autonomic neuropathy (CAN) and elevated nocturnal blood pressure are independent risk factors for cardiovascular disease in patients with diabetes. Previously, associations between CAN, non-dipping of nocturnal blood pressure and coronary artery calcification have been demonstrated. The present protocol describes a trial to test the efficacy of bedtime dosing of the ACE inhibitor enalapril on night time blood pressure and left ventricular mass in patients with type 1 diabetes.

Materials and methods

In a randomised, double-blind, two-way cross-over study, 24 normoalbuminuric patients with type 1 diabetes with CAN will be treated for 12 weeks with either morning or bedtime dosing of 20 mg enalapril, followed by 12 weeks of switched treatment regimen. During each treatment period, two 24 h ambulatory blood pressure measurements will be performed and after each treatment period left ventricular mass will be determined by multisliced CT. Primary end points will be reduction in blood pressure and reduction in left ventricular mass.

Ethics and dissemination

The study has been approved by the Danish Medicines Agency, the Scientific-Ethical Committee of the Capital Region of Denmark and the Danish Data Protection Agency. An external monitoring committee (the Good Clinical Practice Unit at Copenhagen University Hospital) will oversee the study. The results of the study will be presented at national and international scientific meetings and publications will be submitted to peer-reviewed journals.

Trial registration number

EudraCT (2012- 002136-90).
Is neuroendocrine differentiation useful to discriminate primary sinonasal intestinal-type adenocarcinomas from metastatic colorectal adenocarcinomas?
Authors: Projetti Fabrice , Serrano Elie , Vergez Sebastien , Bissainthe Anne-Charlotte , Delisle Marie-Bernadette , Uro-Coste Emmanuelle
Published: October 2014

Primary sinonasal intestinal-type adenocarcinomas (ITAC) are defined on the basis of their morphological similarities to colorectal adenocarcinomas (CRA). Thus, differential diagnosis with sinonasal metastasis of CRA could be a real challenge. Neuroendocrine differentiation has been variably described in several types of adenocarcinomas and notably in ITACs and CRAs. In a series of 25 ITACs and 25 lymph node metastasis of CRAs (nmCRA), we analysed neuroendocrine differentiation by immunohistochemistry with anti-chromogranin A and synaptophysin antibodies. Neuroendocrine differentiation (chromogranin A and/or synaptophysin positivity) was significantly different (p=0.0002) in ITACs (72%) and in nmCRAs (20%). In conclusion, presence of neuroendocrine cells seems more in favour of a sinonasal intestinal-type adenocarcinoma, than metastatic CRA. This immunohistochemical study could be useful in difficult cases and should be an interesting complement in a clinical discussion.
A glossary of policy frameworks: the many forms of ‘universalism’ and policy ‘targeting’
Authors: Carey Gemma , Crammond Brad
Published: October 2014

The recognition that certain characteristics (such as poverty, disadvantage or membership of marginalised social or cultural groups) can make individuals more susceptible to illness has reignited interest in how to combine universal programmes and policies with ones targeted at specific groups. However, ‘universalism’ and ‘targeting’ are used in different ways for different purposes. In this glossary, we define different types and approaches to universalism and targeting. We anticipate that greater clarity in relation to what is meant by ‘universalism’ and ‘targeting’ will lead to a more nuanced debate and practice in this area.
O-GlcNAc protein modification in C2C12 myoblasts exposed to oxidative stress indicates parallels with endogenous antioxidant defense
Authors: Peternelj Tina Tinkara , Marsh Susan A. , Morais Christudas , Small David M. , Dalbo Vincent J. , Tucker Patrick S. , Coombes Jeff S.
Published: October 2014

A growing body of evidence demonstrates the involvement of protein modification with O-linked β-N-acetylglucosamine (O-GlcNAc) in the stress response and its beneficial effects on cell survival. Here we investigated protein O-GlcNAcylation in skeletal muscle cells exposed to oxidative stress and the crosstalk with endogenous antioxidant system. The study focused on antioxidant enzymes superoxide dismutase 2 (SOD2), catalase (CAT), and glutathione peroxidase 1 (GPX1), and transcriptional regulators proliferator-activated receptor gamma coactivator 1-α (PGC-1α) and forkhead box protein O1 (FOXO1), which play important roles in oxidative stress response and are known to be O-GlcNAc-modified. C2C12 myoblasts were subjected to 24 h incubation with different reagents, including hydrogen peroxide, diethyl maleate, high glucose, and glucosamine, and the inhibitors of O-GlcNAc cycling enzymes. Surprisingly, O-GlcNAc levels were significantly increased only with glucosamine, whilst other treatments showed no effect. Significant changes at the mRNA level were observed with concomitant upregulation of the genes for O-GlcNAc enzymes and stress-related proteins with oxidizing agents and downregulation of these genes with agents promoting O-GlcNAcylation. Our findings suggest a role of O-GlcNAc in the stress response and indicate an inhibitory mechanism controlling O-GlcNAc levels in the muscle cells. This could represent an important homeostatic regulation of the cellular defense system.
Improving an insensitive low-energy compound, 1,3,4,6,7,9-hexaazacycl[3.3.3]azine, to be an insensitive high explosive by way of two-step structural modifications
Authors: Wu Qiong , Xiong Guolin , Liu Zhichao , Xiang Dong , Yang Chunhong , Zhu Weihua , Xiao Heming
Published: October 2014

We improved an insensitive low-energy compound, 1,3,4,6,7,9-hexaazacycl[3.3.3]azine (HAA), to be an insensitive high explosive by a useful approach of two-step structural modifications. First, the three carbon atoms in HAA are substituted by three new nitrogen atoms symmetrically to form a new energetic compound, 1,2,3,4,5,6,7,8,9-nonaazacycl[3.3.3]azine (NAA). Then, introducing three N-oxides into NAA symmetrically generates another new energetic compound, 1,2,3,4,5,6,7,8,9-nonaazacycl[3.3.3]azine-2,5,8-trioxides (NAATO). The energetic properties and sensitivity of NAATO were studied by using density functional theory. The results indicate that NAATO has higher detonation performance than RDX and comparative sensitivity to TNT, indicating that it has outstanding overall performance and may be considered as a potential candidate of insensitive high explosives. Thus, the insensitive low-energy compound HAA was successfully improved to be an insensitive high explosive by the two-step structural modifications.
Using lateral coefficient of friction to evaluate effectiveness of plowing and sanding operations
Authors: Salimi Sahar , Nassiri Somayeh , Bayat Alireza
Published: October 2014

Returning the streets to safe driving conditions during wintertime is a priority in cold regions. Using Real-Time Traction Tool (RT3)-Curve’s lateral friction measurements, the effectiveness of plowing and three rates of sanding on different road conditions was investigated. Even a low amount of sand caused a significant reduction in friction on bare dry surfaces. Plowing did not provide significant benefits on ice; though it was a critical operation for snow conditions. While low sanding did not necessarily improve friction over plowed ice and snow, medium and high sanding considerably increased friction over plowed ice and snow. Regression analysis on the collected data revealed that abrasive mixtures can quickly scatter off the road due to high-speed traffic; it also showed that the salt portion of the mixture was not able to melt the ice before it was scattered from the road; however, it was immediately effective for snow at −8 °C.
Impact of steel quick connection system on steel erection labor productivity: case studies and simulation based analyses
Authors: Shan Yongwei , Kim Jung Yeol , Goodrum Paul M. , Caldas Carlos H. , Haas Carl
Published: October 2014

Traditional steel connection systems rely on on-site welding and bolting, which are labor intensive and require skilled craft workers. Reducing welding and bolting efforts in structural steel erection presents an opportunity to improve steel structure construction productivity. A series of steel quick connection systems (SQCS) have been introduced in the market in the last few years, either through research prototypes or commercial products. However, their real benefits need to be confirmed and quantified at actual construction sites. Hence, the main goal of this study was to evaluate the impact of steel quick connection systems on construction productivity and cost. To accomplish this goal, the authors performed analyses of data from nine SQCS projects and conducted two case studies. The authors also utilized a building information modeling based simulation to compare the schedule impact of SQCS and conventional structural steel connections systems. This paper describes the details of this study and its findings.
Exponential fertilization and plant competition effects on the growth and N nutrition of trembling aspen and white spruce seedlings
Authors: Hu Ya-Lin , Hu Yue , Zeng De-Hui , Tan Xiao , Chang Scott X.
Published: October 2014

Exponential fertilization has been shown to be a useful technique for improving seedling quality during nursery production. In this study, we evaluated (i) the impact of exponential vs. conventional fertilization on trembling aspen (Populus tremuloides Michx.) and white spruce (Picea glauca (Moench) Voss) seedlings during nursery production and (ii) the growth performance and nitrogen (N) utilization of those seedlings in response to foxtail barley (Hordeum jubatum L.) competition after the transplantation of seedlings in a greenhouse experiment. Exponential fertilization with an application rate higher than the conventional fertilization increased the internal N reserve in trembling aspen and white spruce seedlings during nursery production and also increased new leaf, new stem, and old stem biomass and N retranslocation rates in trembling aspen seedlings but not in white spruce seedlings after transplantation. Foxtail barley competition decreased N concentrations in seedlings and soil N uptake by the seedlings; however, increased N retranslocation rates with foxtail barley competition were observed in white spruce seedlings but not in trembling aspen seedlings. Our results suggest that the growth performance of seedlings was improved by N loading, whereas the impact of vegetation management was species specific.
Synchronization in complex dynamical networks coupled with complex chaotic system
Authors: Wei Qiang , Xie Cheng-Jun , Wang Bo
Published: October 2014

This paper investigates synchronization in complex dynamical networks with time delay and perturbation. The node of complex dynamical networks is composed of complex chaotic system. A complex feedback controller is designed to realize different component of complex state variable synchronize up to different scaling complex function when complex dynamical networks realize synchronization. The synchronization scaling function is changed from real field to complex field. Synchronization in complex dynamical networks with constant delay and time-varying coupling delay are investigated, respectively. Numerical simulations show the effectiveness of the proposed method.
Casimir effect for massive scalar field
Authors: Mobassem S.
Published: October 2014

The energy–momentum tensor is used to introduce the Casimir force of the massive scalar field acting on a nonpenetrating surface. This expression can be used to evaluate the vacuum force by employing the appropriate field operators. To simplify our formalism, we also relate the vacuum force expression to the imaginary part of the Green function via the fluctuation–dissipation theorem and Kubo's formula. This allows one to evaluate the vacuum force without resorting to the process of field quantization. These two approaches are used to calculate the attractive force between two nonpenetrating plates. Special attention is paid to the generalization of the formalism to D+1 spacetime dimensions.
Semi-Supervised Local Fisher Discriminant Analysis Based on Reconstruction Probability Class
Authors: Wang Yintong , Wang Jiandong , Chen Haiyan , Sun Bo
Published: October 2014

Fisher discriminant analysis (FDA) is a classic supervised dimensionality reduction method in statistical pattern recognition. FDA can maximize the scatter between different classes, while minimizing the scatter within each class. As it only utilizes the labeled data and ignores the unlabeled data in the analysis process of FDA, it cannot be used to solve the unsupervised learning problems. Its performance is also very poor in dealing with semi-supervised learning problems in some cases. Recently, several semi-supervised learning methods as an extension of FDA have proposed. Most of these methods solve the semi-supervised problem by using a tradeoff parameter that evaluates the ratio of the supervised and unsupervised methods. In this paper, we propose a general semi-supervised dimensionality learning idea for the partially labeled data, namely the reconstruction probability class of labeled and unlabeled data. Based on the probability class optimizes Fisher criterion function, we propose a novel Semi-Supervised Local Fisher Discriminant Analysis (S2LFDA) method. Experimental results on real-world datasets demonstrate its effectiveness compared to the existing similar correlation methods.
Cost-Sensitive Learning of Fuzzy Rules for Imbalanced Classification Problems Using FURIA
Authors: Palacios Ana , Trawiński Krzysztof , Cordón Oscar , Sánchez Luciano
Published: October 2014

This paper is intended to verify that cost-sensitive learning is a competitive approach for learning fuzzy rules in certain imbalanced classification problems. It will be shown that there exist cost matrices whose use in combination with a suitable classifier allows for improving the results of some popular data-level techniques. The well known FURIA algorithm is extended to take advantage of this definition. A numerical study is carried out to compare the proposed cost-sensitive FURIA to other state-of-the-art classification algorithms, based on fuzzy rules and on other classical machine learning methods, on 64 different imbalanced datasets.
Migrative Property for Nullnorms
Authors: Zong Wenwen , Su Yong , Liu Hua-Wen
Published: October 2014

The α-migrativity is an important property of a binary operation, and many authors discussed this property for various operators. In this paper, the migrative property for nullnorms is investigated. All solutions of the migrativity equation for all possible combinations of nullnorms are analyzed and characterized.
IF-Bags and Knowledge Representation in Soft Decision Analysis
Authors: Chakrabarty Kankana
Published: October 2014

The concept of IF-Bags was introduced by the author as a generalization of the notion of fuzzy bags. In case of IF-Bags, each element is associated with a crisp bag drawn from the Cartesian product I×I of the unit interval I = [0, 1]. This paper introduces a method for quantitatively measuring the similarity between two IF-Bags. As a consequence, the notions of a measure of coherence and a measure of hesitancy between two IF-Bags are also introduced. It is observed that the measure of coherence and the measure of hesitancy between the IF-Bags can be regarded as crucial factors in case of scenario evaluation as well as grading that relates to knowledge representation in soft decision analysis problems.
Aligned genomic data compression via improved modeling
Authors: Ochoa Idoia , Hernaez Mikel , Weissman Tsachy
Published: October 2014

With the release of the latest Next-Generation Sequencing (NGS) machine, the HiSeq X by Illumina, the cost of sequencing the whole genome of a human is expected to drop to a mere $1000. This milestone in sequencing history marks the era of affordable sequencing of individuals and opens the doors to personalized medicine. In accord, unprecedented volumes of genomic data will require storage for processing. There will be dire need not only of compressing aligned data, but also of generating compressed files that can be fed directly to downstream applications to facilitate the analysis of and inference on the data. Several approaches to this challenge have been proposed in the literature; however, focus thus far has been on the low coverage regime and most of the suggested compressors are not based on effective modeling of the data.

We demonstrate the benefit of data modeling for compressing aligned reads. Specifically, we show that, by working with data models designed for the aligned data, we can improve considerably over the best compression ratio achieved by previously proposed algorithms. Our results indicate that the pareto-optimal barrier for compression rate and speed claimed by Bonfield and Mahoney (2013) [Bonfield JK and Mahoneys MV, Compression of FASTQ and SAM format sequencing data, PLOS ONE, 8(3):e59190, 2013.] does not apply for high coverage aligned data. Furthermore, our improved compression ratio is achieved by splitting the data in a manner conducive to operations in the compressed domain by downstream applications.
Implementing a modeling software for animated protein-complex interactions using a physics simulation library
Authors: Ueno Yutaka , Ito Shuntaro , Konagaya Akihiko
Published: October 2014

To better understand the behaviors and structural dynamics of proteins within a cell, novel software tools are being developed that can create molecular animations based on the findings of structural biology. This study proposes our method developed based on our prototypes to detect collisions and examine the soft-body dynamics of molecular models. The code was implemented with a software development toolkit for rigid-body dynamics simulation and a three-dimensional graphics library. The essential functions of the target software system included the basic molecular modeling environment, collision detection in the molecular models, and physical simulations of the movement of the model. Taking advantage of recent software technologies such as physics simulation modules and interpreted scripting language, the functions required for accurate and meaningful molecular animation were implemented efficiently.
Discovering novel protein–protein interactions by measuring the protein semantic similarity from the biomedical literature
Authors: Chiang Jung-Hsien , Ju Jiun-Huang
Published: October 2014

Protein–protein interactions (PPIs) are involved in the majority of biological processes. Identification of PPIs is therefore one of the key aims of biological research. Although there are many databases of PPIs, many other unidentified PPIs could be buried in the biomedical literature. Therefore, automated identification of PPIs from biomedical literature repositories could be used to discover otherwise hidden interactions. Search engines, such as Google, have been successfully applied to measure the relatedness among words. Inspired by such approaches, we propose a novel method to identify PPIs through semantic similarity measures among protein mentions. We define six semantic similarity measures as features based on the page counts retrieved from the MEDLINE database. A machine learning classifier, Random Forest, is trained using the above features. The proposed approach achieve an averaged micro-F of 71.28% and an averaged macro-F of 64.03% over five PPI corpora, an improvement over the results of using only the conventional co-occurrence feature (averaged micro-F of 68.79% and an averaged macro-F of 60.49%). A relation-word reinforcement further improves the averaged micro-F to 71.3% and averaged macro-F to 65.12%. Comparing the results of the current work with other studies on the AIMed corpus (ranging from 77.58% to 85.1% in micro-F, 62.18% to 76.27% in macro-F), we show that the proposed approach achieves micro-F of 81.88% and macro-F of 64.01% without the use of sophisticated feature extraction. Finally, we manually examine the newly discovered PPI pairs based on a literature review, and the results suggest that our approach could extract novel protein–protein interactions.
Decisions in Product Platform Development Projects
Authors: Harland Peter E. , Yörür Haluk
Published: October 2014

Introducing "product platforms" in companies to achieve competitive advantages, like decreased costs and increased product variety, is a widely recognized strategy in research and industry. Nevertheless, there are certain challenges involved in developing product platforms. In order to address this complexity, we focus on the decision-making perspective of platform development in this paper. Based on a systematic literature review, we identify the decisions in product platform development projects (PPDP) and categorize them. We identified 21 decisions that are made within PPDP, which represent a greater scope of decisions than presented in the literature sources reviewed. The plausibility of these platform project decisions is illustrated with a case study of a perennial platform development project within the automotive supply industry. While most of the literature sources only mention very few decisions, the case study shows the complexity and high number of decisions required for an actual PPDP. In addition, it also recognizes all of the prior reviews of the decisions identified. Unlike in the literature, the decisions in the case study were made over a certain period of time. Therefore, we propose that the dynamics of the decision-making process in PPDP have to be taken into account. The set of PPDP decisions identified will help project managers to structure future PPDPs better and support researchers in building related product platform models.
Managing Contradictory Stakeholder Demands of a Publicly Funded Research Center
Authors: Hutterer Peter , Gattringer Regina , Irschik Hans , Strehl Franz
Published: October 2014

Following the guidelines of the European Union (EU), Austria supports scientific research and technological development by publicly funding of research centers. Such centers are positioned between scientific and industrial stakeholders and have to simultaneously fulfill contradictory demands. This paper deeply analyzes the Austrian Center of Competence in Mechatronics (ACCM) and exposes why this publicly funded research center is able to effectively manage these conflicting demands. Using the theory of ambidexterity, the study highlights that appropriate structures and strategies are preliminarily needed. In particular we found that the fundamental abilities for managing contradictory demands are located on an individual level and argue that especially the autonomous, well-educated people and their competences of self-organization enable the research center to be ambidextrous.
THE RELATIONSHIP BETWEEN TOP MANAGEMENT TEAM INNOVATION ORIENTATION AND FIRM GROWTH: THE MEDIATING ROLE OF FIRM INNOVATIVENESS
Authors: KRAICZY NILS D. , HACK ANDREAS , KELLERMANNS FRANZ W.
Published: October 2014

Upper echelon theory and research on innovation have considered top management teams and their behaviour and characteristics as important factors that positively influence innovativeness and organizational outcomes. Yet, innovation research has mostly focused on individual new product projects, and their performance and impact on firm performance. Recent research has started to apply a more holistic view in terms of innovation, by considering firm-wide innovation instead of single new products. Upper echelon research has concentrated on direct relationships between top management team characteristics and organizational outcomes. But recent research calls for mediating effects of the relationship between top management team characteristics and organizational outcomes. Hence, this study introduces firm innovativeness as a mediator between top management team innovation orientation and firm growth. Focusing on small and medium-sized firms, which often represent highly innovative firms, results show that firm innovativeness fully mediates the relationship between top management team innovation orientation and firm growth. Implications and future research are discussed.
Mechanism modeling and analysis of surplus torque in aeroload simulator
Authors: Chen Yuqing , Ma Jie , Fang Yan
Published: October 2014

Aeroload simulator (ALS) is an important hardware-in-loop simulation equipment. In ALS system, surplus torque is the main cause of loading error. And the elimination of surplus torque has become research hotspot for a while, but study about cause of surplus torque has not made much progress. In this paper, a theory about the origin and mechanism modeling method of surplus torque is raised and the model is simulated based on permanent magnet synchronous motor (PMSM) system. Validity of newly launched model is proved by comparison with initial model and the source of error is analyzed afterwards. Moreover, to determine control strategy for eliminating loading error, influential factors of surplus torque are analyzed based on the mechanism model.
Modeling, Control and Locomotion Planning of an Anguilliform Robotic Fish
Authors: Niu Xuelei , Xu Jianxin
Published: October 2014

In this paper, mathematical model, control law design, different locomotion patterns, and locomotion planning are presented for an Anguilliform robotic fish. The robotic fish, consisted of links and joints, are driven by torques applied to the joints. Considering kinematic constraints, Lagrangian formulation is used to obtain the mathematical model of the robotic fish. The model reveals the relation between motion of the fish and external forces. Computed torque control method is first applied, which can provide satisfactory tracking performance for reference joint angles. To deal with parameter uncertainties, sliding model control is adopted. Three locomotion patterns — forward locomotion, backward locomotion, and turning locomotion — are realized by assigning appropriate reference angles to the joints, and the three locomotions are verified by experiments and simulations. A new form of central pattern generator (CPG) model is presented, which consists of three-dimensional coupled Andronov–Hopf oscillators, artificial neural network, and outer amplitude modulator. By using this CPG model, swimming pattern of a real Anguilliform fish is successfully applied to the robotic fish in an experiment.
Uterine Responses to the Preattachment Embryo in Domestic Ungulates: Recognition of Pregnancy and Preparation for Implantation
Authors: Bauersachs Stefan , Wolf Eckhard
Published: October 2014

The endometrium is a tissue newly evolved with the development of mammalian species. Its main function is the support of embryonic growth and development and the nutrition of the fetus. The species-specific differences in establishment and maintenance of pregnancy make the study of this tissue in various mammalian organisms particularly interesting. With the application of omics technologies to various mammalian species, many systematic studies of endometrial gene expression changes during the phase of establishment of pregnancy have been performed to obtain a global view of regulatory events associated with this biological process. This review summarizes the results of trancriptome studies of bovine, porcine, and equine endometrium. Furthermore, the results are compared between these species and to humans. Because an increasing number of studies suggest an important role of small regulatory RNAs (i.e., microRNAs), recent findings related to the regulation of endometrial functions and the development of the conceptus are presented.
Comparative Dendritic Cell Biology of Veterinary Mammals
Authors: Summerfield Artur , Auray Gael , Ricklin Meret
Published: October 2014

Dendritic cells (DC) have a main function in innate immunity in that they sense infections and environmental antigens at the skin and mucosal surfaces and thereby critically influence decisions about immune activation or tolerance. As professional antigen-presenting cells, they are essential for induction of adaptive immune responses. Consequently, knowledge on this cell type is required to understand the immune systems of veterinary mammals, including cattle, sheep, pigs, dogs, cats, and horses. Recent ontogenic studies define bona fide DC as an independent lineage of hematopoietic cells originating from a common precursor. Distinct transcription factors control the development into the two subsets of classical DC and plasmacytoid DC. These DC subsets express a distinguishable transcriptome, which differs from that of monocyte-derived DC. Using a comparative approach based on phenotype and function, this review attempts to classify DC of veterinary mammals and to describe important knowledge gaps.
The Evolution of Animal Domestication
Authors: Larson Greger , Fuller Dorian Q.
Published: October 2014

The domestication of plants and animals over the past 11,500 years has had a significant effect not just on the domesticated taxa but also on human evolution and on the biosphere as a whole. Decades of research into the geographical and chronological origins of domestic animals have led to a general understanding of the pattern and process of domestication, though a number of significant questions remain unresolved. Here, building upon recent theoretical advances regarding the different pathways animals followed to become domesticated, we present a large-scale synthesis that addresses the global pattern of animal domestication alongside a discussion of the differential evolutionary processes that have shaped domestic animal populations. More specifically, we present a framework for understanding how unconscious selection characterized the earliest steps of animal domestication and the role of introgression and the importance of relaxed and positive selection in shaping modern domestic phenotypes and genomes.
Reversible Trait Loss: The Genetic Architecture of Female Ornaments
Authors: Kraaijeveld Ken
Published: October 2014

The evolution of female ornamentation has been subject to considerable debate. Although originally thought to be by-products of selection on males, recent studies have emphasized the adaptive nature of female ornaments. Here, I review current knowledge on the genetic architecture of ornamental traits and how their expression is (or is not) restricted to one sex. Ornament development typically involves deeply conserved developmental genes. Their expression is modified by pre-existing sexually dimorphic signals, such as hormones in vertebrates or doublesex gene products in insects. Changes in dosage and binding affinities in these systems apparently allow frequent switches between sexually dimorphic and monomorphic ornament expression. However, early-developing ornaments may be difficult to modulate, as this would result in severe pleiotropic effects. Comparative studies on the molecular structure of the sex-specific modulating signals and their receptors should provide detailed insight into the mechanisms underlying the loss and gain of female ornaments.
Warmer Shorter Winters Disrupt Arctic Terrestrial Ecosystems
Authors: Cooper Elisabeth J.
Published: October 2014

The Earth is warming, especially in polar areas in which winter temperatures and precipitation are expected to increase. Despite a growing research focus on winter climatic change, the impacts on Arctic terrestrial ecosystems remain poorly understood. Snow acts as an insulator, and depth changes affect the enhancement of thermally dependent reactions, such as microbial activity, affecting soil nutrient composition, respiration, and winter gas efflux. Snow depth and spring temperatures influence snowmelt timing, determining the start of plant growth and forage availability. Delays in winter onset affect tundra carbon balance, faunal hibernation, and migration but are unlikely to lengthen the plant growing season. Mild periods in winter followed by a return to freezing have negative consequences for plants and invertebrates, and the resultant ice layers act as barriers to foraging, triggering starvation of herbivores and their predators. In summary, knock-on effects between seasons and trophic levels have important consequences for biological activity, diversity, and ecosystem function.
Using Ancient DNA to Understand Evolutionary and Ecological Processes
Authors: Orlando Ludovic , Cooper Alan
Published: October 2014

Ancient DNA provides a unique means to record genetic change through time and directly observe evolutionary and ecological processes. Although mostly based on mitochondrial DNA, the increasing availability of genomic sequences is leading to unprecedented levels of resolution. Temporal studies of population genetics have revealed dynamic patterns of change in many large vertebrates, featuring localized extinctions, migrations, and population bottlenecks. The pronounced climate cycles of the Late Pleistocene have played a key role, reducing the taxonomic and genetic diversity of many taxa and shaping modern populations. Importantly, the complex series of events revealed by ancient DNA data is seldom reflected in current biogeographic patterns. DNA preserved in ancient sediments and coprolites has been used to characterize a range of paleoenvironments and reconstruct functional relationships in paleoecological systems. In the near future, genome-level surveys of ancient populations will play an increasingly important role in revealing, calibrating, and testing evolutionary processes.
Fountains in Industry and Nature
Authors: Hunt G.R. , Burridge H.C.
Published: October 2014

Turbulent fountains arise when a localized flow, free to entrain fluid from its surroundings, is opposed by a buoyancy force. This review cites numerous examples to highlight their wide occurrence in nature and in industry. The breadth of the literature reviewed is significant, drawing from over half a century of progress, and we initially focus on axisymmetric, small–density difference fountains in uniform environments. Many aspects of their rich dynamical behavior, including that of their rise heights and fluctuations in height, are described and encapsulated within the fountain classification presented. Drawing from detailed experimental data sets, dimensional considerations, recent numerical studies, and numerous successful extensions to the original theoretical model for a fountain, we implicitly highlight the current predictive capability offered. The turbulent entrainment of ambient fluid, the effects of environmental stratification, and the role of confinement on a fountain are all discussed. Finally, we suggest future avenues of research.