bluuebunny/crossref_metadata_2025_split huggingface dataset:
Moran’s I quantifies spatio-temporal pattern formation in neural imaging data
Authors: Schmal Christoph , Myung Jihwan , Herzel Hanspeter , Bordyugov Grigory 
Published: May 2017

Abstract

Motivation
Neural activities of the brain occur through the formation of spatio-temporal patterns. In recent years, macroscopic neural imaging techniques have produced a large body of data on these patterned activities, yet a numerical measure of spatio-temporal coherence has often been reduced to the global order parameter, which does not uncover the degree of spatial correlation. Here, we propose to use the spatial autocorrelation measure Moran’s I, which can be applied to capture dynamic signatures of spatial organization. We demonstrate the application of this technique to collective cellular circadian clock activities measured in the small network of the suprachiasmatic nucleus (SCN) in the hypothalamus.

Results
We found that Moran’s I is a practical quantitative measure of the degree of spatial coherence in neural imaging data. Initially developed with a geographical context in mind, Moran’s I accounts for the spatial organization of any interacting units. Moran’s I can be modified in accordance with the characteristic length scale of a neural activity pattern. It allows a quantification of statistical significance levels for the observed patterns. We describe the technique applied to synthetic datasets and various experimental imaging time-series from cultured SCN explants. It is demonstrated that major characteristics of the collective state can be described by Moran’s I and the traditional Kuramoto order parameter R in a complementary fashion.

Availability and implementation
Python 2.7 code of illustrative examples can be found in the Supplementary Material.

Supplementary information
Supplementary data are available at Bioinformatics online.
‘Like a Raging Lion’: Richard the Lionheart’s Anger during the Third Crusade in Medieval and Modern Historiography
Authors: Spencer Stephen J 
Published: May 2017

Abstract
Historians have almost universally characterised King Richard I of England, otherwise known as ‘the Lionheart’, as an intemperate hothead, whose anger was both uncontrollable and socially dysfunctional. This article seeks to test the evidential foundations of this longstanding view, and to explain its genesis, by analysing descriptions of Richard I’s anger in the narratives of the Third Crusade—narratives which have been foundational in formulating such assessments. It does not argue that Richard was a meek or tranquil king, or even that he was always in control of his passions. Rather, it contends that there exists a disparity between how most medieval chroniclers perceived Richard’s wrath and the evaluations of modern historians. The main conclusion reached is that the nature of the source material, which was not only polarised between the king’s supporters and detractors but also witnessed the incorporation of legendary material from an early stage, curtails any attempt to reconstruct the ‘reality’ of Richard’s temperament. After mapping the evolution of attitudes towards anger in the Middle Ages and scrutinising the twelfth- and thirteenth-century narrative accounts of the Lionheart’s wrath, the article seeks to explain why scholars have persisted in casting Richard as an individual who was unusually susceptible to irrational fits of rage and, in so doing, calls for greater sensitivity to the role of memory in future studies of medieval emotions.
Complications of Head Immobilization Devices in Children: Contact Mechanics, and Analysis of a Single Institutional Experience
Authors: Zaazoue Mohamed A , Bedewy Mostafa , Goumnerova Liliana C 
Published: May 2017

Abstract

BACKGROUND
Head immobilization devices (HIDs) are a staple of neurosurgical procedures, including in the intraoperative magnetic resonance imaging (iMRI) operating rooms (ORs) where material modifications were necessary for compatibility with the magnets utilized.

OBJECTIVE
To present the experience in this OR environment and discuss the multifactorial nature of the observed adverse events.

METHODS
A retrospective chart review was performed, utilizing the Department of Neurosurgery and iMRI OR databases to identify patients who suffered complications related to HIDs between November 2007 and March 2016. A literature review was also done to identify the magnitude of the problem and the availability of safety guidelines.

RESULTS
Nine hundred and forty patients underwent surgery in the iMRI OR requiring head immobilization. Seven (0.7%) suffered complications related to the HID—depressed skull fractures (n = 7) and epidural hematomas (n = 6). Age at surgery ranged from 1.6 to 10.3 yr. All patients had posterior fossa neoplasms and associated obstructive hydrocephalus. Four patients (57%) suffered permanent neurological deficits. Six patients (86%) underwent a surgical procedure to evacuate the epidural hematomas and repair the depressed skull fracture. In contrast, 1 out of 445 patient (0.2%) suffered HID-related adverse events in the conventional ORs, aged 10.2 yr.

CONCLUSION
HIDs are important to provide stability and support during neurosurgical procedures. Modifications in the material or the shape of the pins can significantly change the pressure exerted. Most of these complications are preventable if certain precautionary measures are taken especially in certain high-risk patients, and the overall benefits of HIDs continue to outweigh the risks. There is a need for consensus on guidelines for the safe use of these devices.
SOHO comets: 20 years and 3000 objects later
Authors: Battams Karl , Knight Matthew M. 
Published: May 2017

We present a summary of the more than 3000 sungrazing and near-Sun comets discovered in coronagraph images returned by the Solar and Heliospheric Observatory (SOHO), since its launch in December 1995. We address each of the four main populations of objects observed by SOHO: Kreutz (sungrazing) group, Meyer group, Marsden and Kracht (96P-family) group and non-group comets. Discussions for each group include basic properties, discovery statistics and morphological appearance. In addition to updating the community on the status of the discoveries by SOHO, we also show that the rate of discovery of Kreutz sungrazers has probably remained static since approximately 2003 and we report on the first likely fragmentation pair observed within the Meyer group.
This article is part of the themed issue ‘Cometary science after Rosetta’.
The abrogation of condensin function provides independent evidence for defining the self-renewing population of pluripotent stem cells
Authors: Lai Alvina G. , Kosaka Nobuyoshi , Abnave Prasad , Sahu Sounak , Aboobaker A. Aziz 
Published: May 2017

AbstractHeterogeneity of planarian neoblast stem cells has been categorised on the basis of single cell expression analyses and subsequent experiments to demonstrate lineage relationships. Some data suggest that despite gene expression heterogeneity amongst cells in the cell cycle, in fact only one sub-population, known assigmaneoblasts, can self-renew. Without the tools to perform livein vivolineage analysis, we instead took an alternative approach to provide independent evidence for defining the self-renewing stem cell population. We exploited the role of highly conserved condensin proteins to functionally assay neoblast self-renewal properties. Condensins are involved in forming properly condensed chromosomes to allow cell division to proceed during mitosis, and their abrogation inhibits mitosis and can lead to repeated endoreplication of the genome in cells that make repeated attempts to divide. We find that planarians possess only the condensin I complex, and that this is required for normal stem cell function. Abrogation of condensin function led to rapid stem cell depletion accompanied by the appearance of giant cells with increased DNA content. Using previously discovered markers of heterogeneity we show that enlarged cells are always from thesigma-class of the neoblast population and we never observe evidence for endoreplication for the other neoblast subclasses. Overall, our data establish that condensins are essential for stem cell maintenance and provide independent evidence that onlysigma-neoblasts are capable of multiple rounds of cell division and hence self-renewal.
Theory on the rate equation of Michaelis-Menten type single-substrate enzyme catalyzed reactions
Authors: Murugan Rajamanickam 
Published: May 2017

AbstractAnalytical solution to the Michaelis-Menten (MM) rate equations for single-substrate enzyme catalysed reaction is not known. Here we introduce an effective scaling scheme and identify the critical parameters which can completely characterize the entire dynamics of single substrate MM enzymes. Using this scaling framework, we reformulate the differential rate equations of MM enzymes over velocity-substrate, velocity-product, substrate-product and velocity-substrate-product spaces and obtain various approximations for both pre- and post-steady state dynamical regimes. Using this framework, under certain limiting conditions we successfully compute the timescales corresponding to steady state, pre- and post-steady states and also compute the approximate steady state values of velocity, substrate and product. We further define the dynamical efficiency of MM enzymes as the ratio between the reaction path length in the velocity-substrate-product space and the average reaction time required to convert the entire substrate into product. Here dynamical efficiency characterizes the phase-space dynamics and it would tell us how fast an enzyme can clear a harmful substrate from the environment. We finally perform a detailed error level analysis over various pre- and post-steady state approximations along with the already existing quasi steady state approximations and progress curve models and discuss the positive and negative points corresponding to various steady state and progress curve models.
Inoculation of biocontrol bacteria alleviatedPanax ginsengreplanting problem
Authors: Dong Linlin , Xu Jiang , Zhang Lianjuan , Wei Guangfei , Su He , Yang Juan , Qian Jun , Xu Ran , Liao Baosheng , Shen Liang , Wu Mingli , Cheng Ruiyang , Chen Shilin 
Published: May 2017

AbstractReplanting problem is a common and serious issue hindering the continuous cultivation ofPanaxplants. Changes in soil microbial community driven by plant species of different ages and developmental stages are speculated to cause this problem. Inoculation of microbial antagonists is proposed to alleviate replanting issues efficiently.High-throughput sequencing revealed that bacterial diversity evidently decreased, and fungal diversity markedly increased in soils of adult ginseng plants in the root growth stage. Relatively few beneficial microbe agents, such asLuteolibacter, Cytophagaceae,Luteibacter, Sphingomonas, Sphingomonadaceae, and Zygomycota, were observed. On the contrary, the relative abundance of harmful microorganism agents, namely, Brevundimonas, Enterobacteriaceae,Pandoraea, Cantharellales,Dendryphion, Fusarium, and Chytridiomycota, increased with pant age. Furthermore,Bacillus subtilis50-1 was isolated and served as microbial antagonists against pathogenicFusarium oxysporumof ginseng root-rot, and its biocontrol efficacy was 67.8% using a dual culture assay. The ginseng death rate and relative abundance ofFusariumdecreased by 63.3% and 46.1%, respectively, after inoculation with 50-1 in replanting soils. Data revealed that changes in the diversity and composition of rhizospheric microbial communities driven by ginseng of different ages and developmental stages could cause microecological degradation. Biocontrol using microbial antagonists was an effective method for alleviating the replanting problem.HighlightChanges in rhizospheric microbial communities driven by ginseng plants 13 of different ages and developmental stages could cause microecological degradation. 14 Biocontrol using microbial antagonists effectively alleviated the replanting problem.
Back-translating a rodent measure of negative bias into humans: the impact of induced anxiety and unmedicated mood and anxiety disorders
Authors: Aylward Jessica , Hales Claire , Robinson Emma , Robinson Oliver J 
Published: May 2017

AbstractBackgroundMood and anxiety disorders are ubiquitous but current treatment options are ineffective for large numbers of sufferers. Moreover, recent years have seen a number of promising pre-clinical interventions fail to translate into clinical efficacy in humans. Improved treatments are unlikely without better animal-human translational pipelines. Here, we directly adapt–i.e. back-translate - a rodent measure of negative affective bias into humans, and explore its relationship with a)pathological mood and anxiety symptoms (study one) and b)transient induced anxiety (study two).MethodParticipants who met criteria for mood or anxiety disorder symptomatology according to a face-to-face neuropsychiatric interview were included in the symptomatic group. N = 77(47 asymptomatic; Female = 21; 30 symptomatic; Female = 25) participants completed study one and N = 47 asymptomatic participants (25 female) completed study two. Outcome measures were choice ratios, reaction times and parameters recovered from a computational model of reaction time; the drift diffusion model (DDM).ResultsSymptomatic individuals demonstrated increased negative affective bias relative to asymptomatic individuals (proportion high reward = 0.42(SD = 0.14), and 0.53(SD = 0.17), respectively) as well as reduced DDM drift rate (p = 0.004). No significant effects were observed for the within-subjects anxiety-induction in study 2.ConclusionHumans with pathological anxiety symptoms directly mimic rodents undergoing anxiogenic manipulation. The lack of sensitivity to transient anxiety suggests the paradigm may, moreover, be primarily sensitive to clinically relevant symptoms. Our results establish a direct translational pipeline (and candidate therapeutics screen) from negative affective bias in rodents to pathological mood and anxiety symptoms in humans, and link it to a computational model of reaction time.
Early and Late Components of EEG Delay Activity Correlate Differently with Scene Working Memory Performance
Authors: Ellmore Timothy M. , Ng Kenneth , Reichert Chelsea P. 
Published: May 2017

AbstractSustained and elevated activity during the working memory delay period has long been considered the primary neural correlate for maintaining information over short time intervals. This idea has recently been reinterpreted in light of findings generated from multiple neural recording modalities and levels of analysis. To further investigate the sustained or transient nature of activity, the temporal-spectral evolution (TSE) of delay period activity was examined in humans with high density EEG during performance of a Sternberg working memory paradigm with a relatively long six second delay and with novel scenes as stimuli. Multiple analyses were conducted using different trial window durations and different baseline periods for TSE computation. Sensor level analyses revealed transient rather than sustained activity during delay periods. Specifically, the consistent finding among the analyses was that high amplitude activity encompassing the theta range was found early in the first three seconds of the delay period. These increases in activity early in the delay period correlated positively with subsequent ability to distinguish new from old probe scenes. Source level signal estimation implicated a right parietal region of transient early delay activity that correlated positively with working memory ability. This pattern of results adds to recent evidence that transient rather than sustained delay period activity supports visual working memory performance. The findings are discussed in relation to synchronous and desynchronous intra- and inter-regional neural transmission, and choosing an optimal baseline for expressing temporal-spectral delay activity change.
Mitigating mitochondrial genome erosion without recombination
Authors: Radzvilavicius Arunas L , Kokko Hanna , Christie Joshua 
Published: May 2017

AbstractMitochondria are ATP-producing organelles of bacterial ancestry that played a key role in the origin and early evolution of complex eukaryotic cells. Most modern eukaryotes transmit mitochondrial genes uniparentally, often without recombination among genetically divergent organelles. While this asymmetric inheritance maintains the efficacy of purifying selection at the level of the cell, the absence of recombination could also make the genome susceptible to Muller’s ratchet. How mitochondria escape this irreversible defect accumulation is a fundamental unsolved question. Occasional paternal leakage could in principle promote recombination, but it would also compromise the purifying-selection benefits of uniparental inheritance. We assess this tradeoff using a stochastic population-genetic model. In the absence of recombination, uniparental inheritance of freely segregating genomes mitigates mutational erosion, while paternal leakage exacerbates the ratchet effect. Mitochondrial fusion-fission cycles ensure independent genome segregation, improving purifying selection. Paternal leakage provides opportunity for recombination to slow down the mutation accumulation, but always at a cost of increased steady-state mutation load. Our findings indicate that random segregation of mitochondrial genomes under uniparental inheritance can effectively combat the mutational meltdown, and that homologous recombination under paternal leakage might not be needed.
Meiotic crossover patterning in the absence of ATR: Loss of interference and assurance but not the centromere effect
Authors: Brady Morgan M. , McMahan Susan , Sekelsky Jeff 
Published: May 2017

ABSTRACTMeiotic crossovers must be properly patterned to ensure accurate disjunction of homologous chromosomes during meiosis I. Disruption of the spatial distribution of crossovers can lead to nondisjunction, aneuploidy, gamete dysfunction, miscarriage, or birth defects. One of the earliest identified genes in involved proper crossover patterning is textitDrosophila mei-41, which encodes the ortholog of the checkpoint kinase ATR. Analysis of hypomorphic mutants suggested the existence of crossover patterning defects, but it was not possible to assess this in null mutants because of maternal-effect embryonic lethality. To overcome this lethality, we constructedmei-41null mutants in which we expressed wild-type Mei-41 in the germline after completion of meiotic recombination, allowing progeny to survive. We find that crossovers are decreased to about one third of wild-type levels, but the reduction is not uniform, being less severe in the proximal regions of2Lthan in medial or distal2Lor on theXchromosome. None of the crossovers formed in the absence of Mei-41 require Mei-9, the presumptive meiotic resolvase, suggesting that Mei-41 functions everywhere, despite the differential effects on crossover frequency. Interference appears to be significantly reduced or absent inmei-41mutants, but the reduction in crossover density in centromere-proximal regions is largely intact. We propose that crossover patterning is achieved in a stepwise manner, with the crossover suppression related to proximity to the centromere occurring prior to and independently of crossover designation and enforcement of interference. In this model, Mei-41 has an essential after the centromere effect is established but before crossover designation and interference occur.
Integrating over uncertainty in spatial scale of response within multispecies occupancy models yields more accurate assessments of community composition
Authors: Frishkoff Luke Owen , Mahler D. Luke , Fortin Marie-Josée 
Published: May 2017

AbstractSpecies abundance and community composition are affected not only by the local environment, but also by broader landscape and regional context. Yet determining the spatial scale at which landscapes affect species remains a persistent challenge that hinders ecologists’ abilities to understand how environmental gradients influence species presence and shape entire communities, especially in the face of data deficient species and imperfect species detection.Here we present a Bayesian framework that allows uncertainty surrounding the ‘true’ spatial scale of species’ responses (i.e.,changes in presence/absence) to be integrated directly into a community hierarchical model.This scale selecting multi-species occupancy model (ssMSOM) estimates the scale of response, and shows high accuracy and correct type I error rates across a broad range of simulation conditions. In contrast, ensembles of single species GLMs frequently fail to detect the correct spatial scale of response, and are often falsely confident in favoring the incorrect spatial scale, especially as species’ detection probabilities deviate from perfect.Integrating spatial scale selection directly into hierarchical community models provides a means of formally testing hypotheses regarding spatial scales of response, and more accurately determining the environmental drivers that shape communities.
Agricultural aircraft wing slat tolerance for bird strike
Authors: Deskiewicz Adam , Perz Rafał 
Published: May 2017

Purpose
The aim of this study is to assess and describe possible consequences of a bird strike on a Polish-designed PZL-106 Kruk agricultural aircraft. Due to its susceptibility to such events, a wing slat has been chosen for analysis.

Design/methodology/approach
Smooth particle hydrodynamics (SPH) formulation has been used for generation of the bird finite element model. The simulations were performed by the LS-Dyna explicit finite element analysis software. Several test cases have been analysed with differing parameters such as impact velocity, initial velocity vector direction, place of impact and bird mass.

Findings
Results of this study reveal that the structure remains safe after an impact at the velocity of 25 m/s. The influence of bird mass on slat damage is clearly observable when the impact velocity rises to 60 m/s. Another important finding was that in each case where the part did not withstand the applied load, it was the lug where first failure occurred. Some of the analysed cases indicated the possibility a consequent wing box damage.

Practical implications
This finding provides the manufacturer an important insight into the behaviour of the slat and suggests that more detailed analysis of the current lug design might improve the safety of the structure.

Originality/value
Even though similar analyses have been performed, they tended to focus on large transport aircraft components. This investigation will enhance our understanding of structural response of small, low-speed aircraft to a bird impact, which is a realistic scenario for the chosen case of an agricultural plane.