bluuebunny/crossref_metadata_2025_split huggingface dataset:
MouseMove: an open source program for semi-automated analysis of movement and cognitive testing in rodents
Authors: Samson Andre L. , Ju Lining , Ah Kim Hyun , Zhang Shenpeng R. , Lee Jessica A. A. , Sturgeon Sharelle A. , Sobey Christopher G. , Jackson Shaun P. , Schoenwaelder Simone M. 
Published: November 2015

AbstractThe Open Field (OF) test is one of the most commonly used assays for assessing exploratory behaviour and generalised locomotor activity in rodents. Nevertheless, the vast majority of researchers still rely upon costly commercial systems for recording and analysing OF test results. Consequently, our aim was to design a freely available program for analysing the OF test and to provide an accompanying protocol that was minimally invasive, rapid, unbiased, without the need for specialised equipment or training. Similar to commercial systems, we show that our software—called MouseMove—accurately quantifies numerous parameters of movement including travel distance, speed, turning and curvature. To assess its utility, we used MouseMove to quantify unilateral locomotor deficits in mice following the filament-induced middle cerebral artery occlusion model of acute ischemic stroke. MouseMove can also monitor movement within defined regions-of-interest and is therefore suitable for analysing the Novel Object Recognition test and other field-related cognitive tests. To the best of our knowledge, MouseMove is the first open source software capable of providing qualitative and quantitative information on mouse locomotion in a semi-automated and high-throughput fashion and hence MouseMove represents a sound alternative to commercial movement analysis systems.
Lats1 suppresses centrosome overduplication by modulating the stability of Cdc25B
Authors: Mukai Satomi , Yabuta Norikazu , Yoshida Kaori , Okamoto Ayumi , Miura Daisaku , Furuta Yasuhide , Abe Takaya , Nojima Hiroshi 
Published: November 2015

AbstractNumerical aberration of the centrosome results in chromosome missegregation, eventually leading to chromosomal instability, a hallmark of human tumor malignancy. Large tumor suppressors 1 and 2 (Lats1 and Lats2) are central kinases in the Hippo pathway and regulate development and tumorigenesis by coordinating the balance between cell proliferation and apoptosis. Importantly, Lats1 and Lats2 also play pivotal roles in cell cycle checkpoint and mitosis. The Lats proteins localize at centrosomes, but their centrosomal functions remain elusive. Here, we generated Lats1-null knockout (Lats1−/−) mice and established Lats1-null mouse embryonic fibroblasts (MEFs). In Lats1−/− MEFs, centrosomes were markedly overduplicated, leading to severe mitotic defects such as chromosome missegregation and cytokinesis failure. We also found that Lats1 physically interacts with Cdc25B phosphatase that localizes both at the centrosome and in the nucleus and regulates the linkage between the centrosome cycle and mitotic progression. Although Lats1 did not phosphorylate Cdc25B, loss of Lats1 in MEFs caused abnormal accumulation of Cdc25B protein and hyperactivation of Cdk2 toward nucleophosmin (NPM/B23), one of the licensing factors involved in centriole duplication. Taken together, these data suggest that Lats1 regulates Cdc25B protein level and subsequent Cdk2 activity, thereby suppressing centrosome overduplication during interphase.
Tilt engineering of exchange coupling at G-type SrMnO3/(La,Sr)MnO3 interfaces
Authors: Li F. , Song C. , Wang Y. Y. , Cui B. , Mao H. J. , Peng J. J. , Li S. N. , Wang G. Y. , Pan F. 
Published: November 2015

AbstractWith the recent realization of hybrid improper ferroelectricity and room-temperature multiferroic by tilt engineering, “functional” octahedral tilting has become a novel concept in multifunctional perovskite oxides, showing great potential for property manipulation and device design. However, the control of magnetism by octahedral tilting has remained a challenging issue. Here a qualitative and quantitative tilt engineering of exchange coupling, one of the magnetic properties, is demonstrated at compensated G-type antiferromagnetic/ferromagnetic (SrMnO3/La2/3Sr1/3MnO3) interfaces. According to interfacial Hamiltonian, exchange bias (EB) in this system originates from an in-plane antiphase rotation (a−) in G-type antiferromagnetic layer. Based on first-principles calculation, tilt patterns in SrMnO3 are artificially designed in experiment with different epitaxial strain and a much stronger EB is attained in the tensile heterostructure than the compressive counterpart. By controlling the magnitude of octahedral tilting, the manipulation of exchange coupling is even performed in a quantitative manner, as expected in the theoretical estimation. This work realized the combination of tilt engineering and exchange coupling, which might be significant for the development of multifunctional materials and antiferromagnetic spintronics.
All-fibre photonic signal generator for attosecond timing and ultralow-noise microwave
Authors: Jung Kwangyun , Kim Jungwon 
Published: November 2015

AbstractHigh-impact frequency comb applications that are critically dependent on precise pulse timing (i.e., repetition rate) have recently emerged and include the synchronization of X-ray free-electron lasers, photonic analogue-to-digital conversion and photonic radar systems. These applications have used attosecond-level timing jitter of free-running mode-locked lasers on a fast time scale within ~100 μs. Maintaining attosecond-level absolute jitter over a significantly longer time scale can dramatically improve many high-precision comb applications. To date, ultrahigh quality-factor (Q) optical resonators have been used to achieve the highest-level repetition-rate stabilization of mode-locked lasers. However, ultrahigh-Q optical-resonator-based methods are often fragile, alignment sensitive and complex, which limits their widespread use. Here we demonstrate a fibre-delay line-based repetition-rate stabilization method that enables the all-fibre photonic generation of optical pulse trains with 980-as (20-fs) absolute r.m.s. timing jitter accumulated over 0.01 s (1 s). This simple approach is based on standard off-the-shelf fibre components and can therefore be readily used in various comb applications that require ultra-stable microwave frequency and attosecond optical timing.
Functional Near-Infrared Spectroscopy Brain Imaging Investigation of Phonological Awareness and Passage Comprehension Abilities in Adult Recipients of Cochlear Implants
Authors: Bisconti Silvia , Shulkin Masha , Hu Xiaosu , Basura Gregory J. , Kileny Paul R. , Kovelman Ioulia 
Published: November 2015

Purpose
The aim of this study was to examine how the brains of individuals with cochlear implants (CIs) respond to spoken language tasks that underlie successful language acquisition and processing.

Method

During functional near-infrared spectroscopy imaging, CI recipients with hearing impairment (
n
= 10, mean age: 52.7 ± 17.3 years) and controls with normal hearing (
n
= 10, mean age: 50.6 ± 17.2 years) completed auditory tasks—phonological awareness and passage comprehension—commonly used to investigate neurodevelopmental disorders of language and literacy.

Results
The 2 groups had similar reaction time and performance on experimental tasks, although participants with CIs had lower accuracy than controls. Overall, both CI recipients and controls exhibited similar patterns of brain activation during the tasks.

Conclusions
The results demonstrate that CI recipients show an overall neurotypical pattern of activation during auditory language tasks on which individuals with neurodevelopmental language learning impairments (e.g., dyslexia) tend to show atypical brain activation. These findings suggest that advancements in functional near-infrared spectroscopy neuroimaging with CI recipients may help shed new light on how varying types of difficulties in language processing affect brain organization for language.
The Role of Somatosensory Information in Speech Perception: Imitation Improves Recognition of Disordered Speech
Authors: Borrie Stephanie A. , Schäfer Martina C. M. 
Published: November 2015

Purpose
Perceptual learning paradigms involving written feedback appear to be a viable clinical tool to reduce the intelligibility burden of dysarthria. The underlying theoretical assumption is that pairing the degraded acoustics with the intended lexical targets facilitates a remapping of existing mental representations in the lexicon. This study investigated whether ties to mental representations can be strengthened by way of a somatosensory motor trace.

Method
Following an intelligibility pretest, 100 participants were assigned to 1 of 5 experimental groups. The control group received no training, but the other 4 groups received training with dysarthric speech under conditions involving a unique combination of auditory targets, written feedback, and/or a vocal imitation task. All participants then completed an intelligibility posttest.

Results
Training improved intelligibility of dysarthric speech, with the largest improvements observed when the auditory targets were accompanied by both written feedback and an imitation task. Further, a significant relationship between intelligibility improvement and imitation accuracy was identified.

Conclusions
This study suggests that somatosensory information can strengthen the activation of speech sound maps of dysarthric speech. The findings, therefore, implicate a bidirectional relationship between speech perception and speech production as well as advance our understanding of the mechanisms that underlie perceptual learning of degraded speech.
Measurements and modelling of three‐ and five‐limb transformer behaviour during large voltage and frequency disturbances
Authors: Persson Mattias , Baig Waqas , Thiringer Torbjörn 
Published: November 2015

This study presents the modelling of transformers for voltage disturbances. The focus in this study is on the security of the power supply for sensitive loads, for instance, the auxiliary systems for a nuclear power station feeding, for instance, pumps for emergency systems. Both steady‐state operation as well as transient conditions have been analysed. A five‐limb as well as a three‐limb 4 kVA transformer was designed in order to verify theoretical assumptions with experimental results. The results show that the theoretical models provided results in conformity to the actual experiments with an average discrepancy of 3%. Moreover, it is shown that a five‐limb transformer gives lower inrush currents, especially in the highly saturated region. In addition, it was demonstrated that an inductive load gives much higher inrush currents compared with a resistive load. A final observation was that the current drawn by the two transformers in their saturated state differ severely depending on the topology of the core.
Does affective forecasting change motivation for disaster preparedness? Motivation one month after a hypothetical earthquake / ¿Influye la predicción afectiva en la motivación para la preparación ante las catástrofes? La motivación un mes después de un terremoto hipotético
Authors: Noda Masayo 
Published: November 2015

The present study examined how disaster preparedness would change after people predicted their affective reactions in the event of a major earthquake. In Study 1, participants ( N = 255) completed an assessment of disaster preparedness. One week later, participants predicted their thoughts and feelings if a major earthquake were to strike, and then responded to the motivation measure. Study 2 ( N = 129) examined the status of participants’ motivation after one month. The results showed that greater motivation was only seen immediately after affective forecasting, and the same level of motivation was not maintained after one month. When people imagine a potential earthquake the expected negative affective reactions are overestimated. Disaster preparedness allows people to mitigate their future negative affective reactions. In order to avoid these affective reactions, affective forecasters had greater motivation for disaster preparedness.
Effect of Salinity on the Survival and Growth of the Larvae and Juveniles of Japanese Grenadier Anchovy Coilia nasus
Authors: Xu Jiabo , Deng PingPing , Shi Yonghai , Zhang Genyu , Zhang Haiming , Yan Yinlong , Lu Genhai , Liu Yongshi , Wang Yang 
Published: November 2015

Abstract
The anadromous Japanese Grenadier Anchovy Coilia nasus is a commercially important fish that is mainly distributed in the Yangtze River and its estuarine area. Two trials were performed to determine the effect of acute salinity stress on the survival of early C. nasus larvae at 0 d posthatch (DPH) and 2 DPH. The salinity treatments for these two trials were 0.4, 5, 10, 15, 20, and 25‰. A third trial compared the growth of juveniles in 3, 6, 9, 12, 15, and 18‰ salinity. Larvae could only tolerate a limited range of salinity (&lt;5‰). Salinity challenge significantly affected the survival of early C. nasus larvae. When salinity was changed, even a low concentration of 2.5‰ could adversely affect early C. nasus larvae. The growth of juveniles was also influenced by salinity. High salinity (&gt;12‰) caused low survival, and low salinity (&lt;6‰) caused poor growth. The optimum salinity for the survival and growth of C. nasus juveniles ranges from 6‰ to 12‰.
No Promoter Left Behind (NPLB): learn de novo promoter architectures from genome-wide transcription start sites
Authors: Mitra Sneha , Narlikar Leelavati 
Published: November 2015

Abstract
Summary: Promoters have diverse regulatory architectures and thus activate genes differently. For example, some have a TATA-box, many others do not. Even the ones with it can differ in its position relative to the transcription start site (TSS). No Promoter Left Behind (NPLB) is an efficient, organism-independent method for characterizing such diverse architectures directly from experimentally identified genome-wide TSSs, without relying on known promoter elements. As a test case, we show its application in identifying novel architectures in the fly genome.
Availability and implementation: Web-server at http://nplb.ncl.res.in. Standalone also at https://github.com/computationalBiology/NPLB/ (Mac OSX/Linux).
Contact: l.narlikar@ncl.res.in
Supplementary information: Supplementary data are available at Bioinformatics online.
The economic and social impacts of environmental change on fishing towns and coastal communities: a historical case study of Geraldton, Western Australia
Authors: Tull M. , Metcalf S. J. , Gray H. 
Published: November 2015

Abstract
For decades, many Australian coastal communities have been changing, in varying degrees, from traditional “fishing towns” to “mining”, “tourism”, or “retirement” towns. However, environmental changes, such as climate change, have increased the vulnerability of these communities and their capacity to continue to successfully adapt is unknown. A framework for the assessment of socio-ecological vulnerability is used to provide information on the response to change in Geraldton, Western Australia. Geraldton has traditionally been a port and fishing town and has recently become a hub for the expanding mining industry. An innovative historical assessment of adaptive capacity using sustainable livelihoods analysis with indicators of social, economic, human, financial, physical, and natural capital is used to calculate socio-ecological vulnerability over time. The framework integrates adaptive capacity with environmental change, resource dependence, and the socio-economic importance of the fished species during four census years: 1921, 1954, 1981, and 2011. The earlier years are characterized by high adaptive capacity and low socio-ecological vulnerability in keeping with strong economic growth and low unemployment rates following the First and Second World Wars. The years 1981 and 2011 showed markedly higher socio-ecological vulnerability and lower adaptive capacities. This result was due to progressively greater exposure to climate change and the high socio-economic importance of fished species, as well as relatively poor physical, social, and natural capital. With continuing environmental and economic change, the fishing industry and the broader Geraldton population is likely to become increasingly vulnerable. Proactive rather than passive adaptation may speed the recovery and reduce a decline in the fishing industry and local economies. The paper briefly discusses potential adaptation in Geraldton which may be useful as a guideline for other coastal communities.
Effects of high CO2 and warming on a Baltic Sea microzooplankton community
Authors: Horn Henriette G. , Boersma Maarten , Garzke Jessica , Löder Martin G. J. , Sommer Ulrich , Aberle Nicole 
Published: November 2015

Abstract
Global warming and ocean acidification are among the most important stressors for aquatic ecosystems in the future. To investigate their direct and indirect effects on a near-natural plankton community, a multiple-stressor approach is needed. Hence, we set up mesocosms in a full-factorial design to study the effects of both warming and high CO2 on a Baltic Sea autumn plankton community, concentrating on the impacts on microzooplankton (MZP). MZP abundance, biomass, and species composition were analysed over the course of the experiment. We observed that warming led to a reduced time-lag between the phytoplankton bloom and an MZP biomass maximum. MZP showed a significantly higher growth rate and an earlier biomass peak in the warm treatments while the biomass maximum was not affected. Increased pCO2 did not result in any significant effects on MZP biomass, growth rate, or species composition irrespective of the temperature, nor did we observe any significant interactions between CO2 and temperature. We attribute this to the high tolerance of this estuarine plankton community to fluctuations in pCO2, often resulting in CO2 concentrations higher than the predicted end-of-century concentration for open oceans. In contrast, warming can be expected to directly affect MZP and strengthen its coupling with phytoplankton by enhancing its grazing pressure.
A Virtual Clinic Improves Pneumococcal Vaccination for Asplenic Veterans at High Risk for Pneumococcal Disease
Authors: Jump Robin L. , Banks Richard , Wilson Brigid , Montpetite Michelle M. , Carter Rebecca , Phillips Susan , Perez Federico 
Published: November 2015

Abstract
We developed a “virtual clinic” to improve pneumococcal vaccination among asplenic adults. Using an electronic medical record, we identified patients, assessed their vaccination status, entered orders, and notified patients and providers. Within 180 days, 38 of 76 patients (50%) received a pneumococcal vaccination. A virtual clinic may optimize vaccinations among high-risk patients.
Intracarotid Etomidate Decreases the Interhemispheric Synchronization in Electroencephalogram (EEG) During the Wada Test
Authors: Shahaf Dana B. , Shahaf Goded , Mehta Jigesh , Venkatraghavan Lashmi 
Published: November 2015

Background:
The Wada test is a diagnostic method to anesthetize 1 cerebral hemisphere and assess the language and memory functions of awake contralateral hemisphere before temporal lobectomy in patients with epilepsy. The effects of an ipsilateral injection of etomidate on the functional properties of contralateral hemisphere are not known. Our aim was to characterize the electroencephalographic (EEG) effects after intracarotid injection of etomidate and to determine the changes in synchronization between the ipsilateral and contralateral hemispheres.

Materials and Methods:
We retrospectively analyzed EEG data from 15 patients who underwent Wada test with etomidate. Continuous EEG data from 4 electrodes (2 anterior [F3, F4] and 2 posterior [P3, P4]) were analyzed. After artifact rejection, we measured the amplitudes of delta (1 to 4 Hz) and alpha (7 to 13 Hz) waves and the changes in the interhemispheric synchronization before, during, and after etomidate injection.

Results:
Ipsilateral injection of etomidate causes EEG changes in both hemispheres with increased amplitude of delta waves anteriorly and the alpha waves posteriorly. However this effect of etomidate is not uniform. Although there was a decrease in the interhemispheric synchronization of delta waves, there was no change in the synchronization of the alpha waves.

Conclusions:
Our study showed that the EEG effects of intracarotid ipsilateral injection of etomidate is not uniform in both hemispheres. Decrease in the interhemispheric synchronization of delta waves might serve as an indicator of ipsilateral effect of etomidate on the brain. Additional studies are needed to confirm our findings.
Beyond the Markovian assumption: response–excitation probabilistic solution to random nonlinear differential equations in the long time
Authors: Athanassoulis G. A. , Tsantili I. C. , Kapelonis Z. G. 
Published: November 2015

Uncertainty quantification for dynamical systems under non-white excitation is a difficult problem encountered across many scientific and engineering disciplines. Difficulties originate from the lack of Markovian character of system responses. The response–excitation (RE) theory, recently introduced by Sapsis & Athanassoulis (Sapsis & Athanassoulis 2008
Probabilistic Eng. Mech.
23, 289–306 (
doi:10.1016/j.probengmech.2007.12.028
)) and further studied by Venturi
et al.
(Venturi
et al.
2012
Proc. R. Soc. A
468, 759–783 (
doi:10.1098/rspa.2011.0186
)), is a new approach, based on a simple differential constraint which is exact but non-closed. The evolution equation obtained for the RE probability density function (pdf) has the form of a generalized Liouville equation, with the excitation time frozen in the time-derivative term. In this work, the missing information of the RE differential constraint is identified and a closure scheme is developed for the long-time, stationary, limit-state of scalar nonlinear random differential equations (RDEs) under coloured excitation. The closure scheme does not alter the RE evolution equation, but collects the missing information through the solution of local statistically linearized versions of the nonlinear RDE, and interposes it into the solution scheme. Numerical results are presented for two examples, and compared with Monte Carlo simulations.
GBStools: A Unified Approach for Reduced Representation Sequencing and Genotyping
Authors: Cooke Thomas F , Yee Muh-Ching , Muzzio Marina , Sockell Alexandra , Bell Ryan , Cornejo Omar E , Kelley Joanna L. , Bailliet Graciela , Bravi Claudio M. , Bustamante Carlos D , Kenny Eimear E 
Published: November 2015

AbstractReduced representation sequencing methods such as genotyping-by-sequencing (GBS) enable low-cost measurement of genetic variation without the need for a reference genome assembly. These methods are widely used in genetic mapping and population genetics studies, especially with non-model organisms. Variant calling error rates, however, are higher in GBS than in standard sequencing, in particular due to restriction site polymorphisms, and few computational tools exist that specifically model and correct these errors. We developed a statistical method to remove errors caused by restriction site polymorphisms, implemented in the software package GBStools. We evaluated it in several simulated data sets, varying in number of samples, mean coverage and population mutation rate, and in two empirical human data sets (N = 8 and N = 63 samples). In our simulations, GBStools improved genotype accuracy more than commonly used filters such as Hardy-Weinberg equilibrium p-values. GBStools is most effective at removing genotype errors in data sets over 100 samples when coverage is 40X or higher, and the improvement is most pronounced in species with high genomic diversity. We also demonstrate the utility of GBS and GBStools for human population genetic inference in Argentine populations and reveal widely varying individual ancestry proportions and an excess of singletons, consistent with recent population growth.