bluuebunny/crossref_metadata_2025_split huggingface dataset:
Towards fast and reliable simultaneous EEG-fMRI analysis of epilepsy with automatic spike detection
Authors: Omidvamia Amir , Kowalczyk Magdalena A. , Pedersen Mangor , Jackson Graeme D. 
Published: July 2018

AbstractObjectiveThe process of manually marking up epileptic spikes for simultaneous electroencephalogram (EEG) and resting state functional MRI (rsfMRI) analysis in epilepsy studies is a tedious and subjective task for a human expert. The aim of this study was to evaluate whether automatic EEG spike detection can facilitate EEG-rsfMRI analysis, and to assess its potential as a clinical tool in epilepsy.MethodsWe implemented a fast algorithm for detection of uniform interictal epileptiform discharges (IEDs) in one-hour scalp EEG recordings of 19 refractory focal epilepsy datasets (from 16 patients) who underwent a simultaneous EEG-rsfMRI recording. Our method was based on matched filtering of an IED template (derived from human markup) used to automatically detect other ‘similar’ EEG events. We comprehensively compared simultaneous EEG-rsfMRI results between automatic IED detection and standard analysis with human EEG markup only.ResultsIn contrast to human markup, automatic IED detection takes a much shorter time to detect IEDs and export an output text file containing spike timings. In 13/19 focal epilepsy cases, statistical EEG-rsfMRI maps based on automatic spike detection method were comparable with human markup, and in 6/19 focal epilepsy cases it revealed additional brain regions not seen with human EEG markup. Additional events detected by our automated method independently revealed similar patterns of activation to a human markup. Overall, automatic IED detection provides greater statistical power in EEG-rsfMRI analysis compared to human markup in a short timeframe.ConclusionsAutomatic spike detection is a simple and fast method that can reproduce comparable and, in some cases, even superior results compared to the common practice of manual EEG markup in EEG-rsfMRI analysis of epilepsy.SignificanceOur study shows that IED detection algorithms can be effectively used in epilepsy clinical settings. This work further helps in translating EEG-rsfMRI research into a fast, reliable and easy-to-use clinical tool for epileptologists. Our IED detection approach will be publicly available as a MATLAB package at: https://github.com/omidvarnia/Automatic_focal_spike_detection.HighlightsAutomatic spike detection increases the number of detected uniform epileptic interictal discharges and enhances statistical power of EEG-rsfMRI inter-subject variability maps,Automatic spike detection can identify additional activated brain regions with presumed epileptogenic focus not seen in standard analysis based on human markup,Automatic spike detection can shorten the IED identification process.
Dynamic Distribution Decomposition for Single-Cell Snapshot Time Series Identifies Subpopulations and Trajectories during iPSC Reprogramming
Authors: Taylor-King Jake P. , Riseth Asbjørn N. , Claassen Manfred 
Published: July 2018

AbstractRecent high-dimensional single-cell technologies such as mass cytometry are enabling time series experiments to monitor the temporal evolution of cell state distributions and to identify dynamically important cell states, such as fate decision states in differentiation. However, these technologies are destructive, and require analysis approaches that temporally map between cell state distributions across time points. Current approaches to approximate the single-cell time series as a dynamical system suffer from too restrictive assumptions about the type of kinetics, or link together pairs of sequential measurements in a discontinuous fashion.We propose Dynamic Distribution Decomposition (DDD), an operator approximation approach to infer a continuous distribution map between time points. On the basis of single-cell snapshot time series data, DDD approximates the continuous time Perron-Frobenius operator by means of a finite set of basis functions. This procedure can be interpreted as a continuous time Markov chain over a continuum of states. By only assuming a memoryless Markov (autonomous) process, the types of dynamics represented are more general than those represented by other common models, e.g., chemical reaction networks, stochastic differential equations. Additionally, the continuity assumption ensures that the same dynamical system maps between all time points, not arbitrarily changing at each time point. We demonstrate the ability of DDD to reconstruct dynamically important cell states and their transitions both on synthetic data, as well as on mass cytometry time series of iPSC reprogramming of a fibroblast system. We use DDD to find previously identified subpopulations of cells and to visualize differentiation trajectories.Dynamic Distribution Decomposition allows interpreting high-dimensional snapshot time series data as a low-dimensional Markov process, thereby enabling an interpretable dynamics analysis for a variety of biological processes by means of identifying their dynamically important cell states.Author summaryHigh-dimensional single-cell snapshot measurements are now increasingly utilized to study dynamic processes. Such measurements enable us to evaluate cell population distributions and their evolution over time. However, it is not trivial to map these distribution across time and to identify dynamically important cell states, i.e. bottleneck regions of state space exhibiting a high degree of change. We present Dynamic Distribution Decomposition (DDD) achieving this task by encoding single-cell measurements as linear combination of basis function distributions and evolving these as a linear system. We demonstrate reconstruction of dynamically important states for synthetic data of a bifurcated diffusion process and mass cytometry data for iPSC reprogramming.
Application of clinical genomic sequencing among Chinese advanced cancer patients to guide precision medicine decisions
Authors: Jiao Shunchang , Bai Yuxian , Dai Chun , Xu Xiaoman , Cai Xin , Wang Guan , Wei Jinwang , Wu Bing , Sun Wending , Xu Qiang 
Published: July 2018

AbstractPurposeA number of studies have suggested that high-throughput genomic analyses might improve the outcomes of cancer patients. However, whether integrative information about genomic sequencing and related clinical interpretation may benefit Chinese cancer patients with stage IV disease to date has not investigated.MethodsTargeted gene panel and whole exome of tumor/blood samples in > 1,000 Chinese cancer patients were sequenced. Then we provided patients and their oncologists with the sequencing results and a clinical recommendation roadmap based on evidence-based medicine, defined as CWES. Only patients with stage IV disease who failed the previous treatment upon receiving the CWES reports were included for analyzing the impact of CWES on clinical outcomes in 1-year follow-ups.ResultsWe identified the mutational signatures of 953 Chinese cancer patients, with some being unique. Approximately 88.6% of patients had clinically actionable somatic genomic alterations. We successfully followed up 22 stage IV patients. Of these, 11 patients treatment followed the CWES reports defined as group A. Eleven patients received the next treatment, but did not follow the CWES suggestions, and are defined as group B. The types of therapies before CWES were similar in the two groups. The median PFS of group A was 12 months and 45% patients failed this round of therapy. The median PFS of group B was 4 months and 91% of patients failed the treatment.ConclusionThe current study suggested that CWES has the potential to help explore the clinical benefits in multiple line therapies among advanced stage tumor patients.
The draft genome sequence of mandrill (Mandrillus sphinx)
Authors: Yin Ye , Yang Ting , Liu Huan , Huang Ziheng , Zhang Yaolei , Song Yue , Wang Wenliang , Kristiansen Karsten 
Published: July 2018

AbstractBackgroundMandrill (Mandrillus sphinx) is a primate species which belong to Old World monkey (Cercopithecidae) family. It is closely related to human, serving as model for some human diseases researches. However, genetic researches and genomic resources of mandrill were limited, especially comparing to other primate species.FindingsHere we sequenced 284 Gb data, providing 96-fold coverage (considering the estimate genome size of 2.9 Gb), to construct a reference genome for mandrill. The assembled draft genome was 2.79 Gb with contig N50 of 20.48 Kb and scaffold N50 of 3.56 Mb. We annotated the mandrill genome to find 43.83% repeat elements, as well as 21,906 protein coding genes. We found good quality of the draft genome and gene annotation by BUSCO analysis which revealed 98% coverage of the BUSCOs.ConclusionsWe established the first draft genome sequence of mandrill, which is valuable resource for future evolutionary and human diseases studies.
Coxiella burnetiiblocks intracellular IL-17 signaling in macrophages
Authors: Clemente Tatiana M. , Mulye Minal , Justis Anna V. , Nallandhighal Srinivas , Tran Tuan M. , Gilk Stacey D. 
Published: July 2018

AbstractCoxiella burnetiiis an obligate intracellular bacterium and the etiological agent of Q fever. Successful host cell infection requires theCoxiellaType IVB Secretion System (T4BSS), which translocates bacterial effector proteins across the vacuole membrane into the host cytoplasm, where they manipulate a variety of cell processes. To identify host cell targets ofCoxiellaT4BSS effector proteins, we determined the transcriptome of murine alveolar macrophages infected with aCoxiellaT4BSS effector mutant. We identified a set of inflammatory genes that are significantly upregulated in T4BSS mutant-infected cells compared to mock-infected cells or cells infected with wild type (WT) bacteria, suggestingCoxiellaT4BSS effector proteins downregulate expression of these genes. In addition, the IL-17 signaling pathway was identified as one of the top pathways affected by the bacteria. While previous studies demonstrated that IL-17 plays a protective role against several pathogens, the role of IL-17 duringCoxiellainfection is unknown. We found that IL-17 kills intracellularCoxiellain a dose-dependent manner, with the T4BSS mutant exhibiting significantly more sensitivity to IL-17 than WT bacteria. In addition, quantitative PCR confirmed increased expression of IL-17 downstream signaling genes in T4BSS mutant-infected cells compared to WT or mock-infected cells, including the pro-inflammatory cytokinesI11a, Il1bandTnfa, the chemokinesCxcl2andCcl5, and the antimicrobial proteinLcn2. We further confirmed that theCoxiellaT4BSS downregulates macrophage CXCL2/MIP-2 and CCL5/RANTES protein levels following IL-17 stimulation. Together, these data suggest thatCoxielladownregulates IL-17 signaling in a T4BSS-dependent manner in order to escape the macrophage immune response.
Noninvasive Vagus Nerve Stimulation Alters the Neural and Physiological Response to Noxious Thermal Challenge
Authors: Lerman Imanuel , Davis Bryan , Huang Mingxiong , Huang Charles , Sorkin Linda , Proudfoot James , Zhong Edward , Kimball Donald , Rao Ramesh , Simon Bruce , Spadoni Andrea , Strigo Irina , Baker Dewleen G , Simmons Alan N 
Published: July 2018

AbstractThe mechanisms by which noninvasive vagal nerve stimulation (nVNS) affect central and peripheral neural circuits that subserve pain and autonomic physiology are not clear, and thus remain an area of intense investigation. Effects of nVNS vs sham stimulation on subject responses to five noxious thermal stimuli (applied to left lower extremity), were measured in 30 healthy subjects (n=15 sham and n=15 nVNS), with fMRI and physiological galvanic skin response (GSR). With repeated noxious thermal stimuli a group × time analysis showed a significantly (p < .001) decreased response with nVNS in bilateral primary and secondary somatosensory cortices (SI and SII), left dorsoposterior insular cortex, bilateral paracentral lobule, bilateral medial dorsal thalamus, right anterior cingulate cortex, and right orbitofrontal cortex. A group × time × GSR analysis showed a significantly decreased response in nVNS group (p < .0005) in bilaterally in SI, lower and mid medullary brainstem, and inferior occipital cortex. Finally, nVNS treatment showed decreased activity in pronociceptive brainstem nuclei (e.g. the reticular nucleus and rostral ventromedial medulla) and key autonomic integration nuclei (e.g. the rostroventrolateral medulla, nucleus ambiguous, and dorsal motor nucleus of the vagus nerve). In aggregate, noninvasive vagal nerve stimulation reduced the physiological response to noxious thermal stimuli and impacted neural circuits important for pain processing and autonomic output.
Dynamics of the p53 response to ionizing and ultraviolet radiation
Authors: Fedak Elizabeth A. , Adler Frederick R. , Young Erin L. , Abegglen Lisa M. , Schiffman Joshua D. 
Published: July 2018

AbstractThe tumor suppressor protein p53 compiles information about cellular stressors to make decisions on whether the cell should survive or undergo apoptosis. However, the p53 response depends on the source of damage, displaying a ‘digital’ oscillatory response after ionizing radiation (IR) damage and a proportional non-oscillatory response following UV damage. We propose a mathematical model that qualitatively replicates this observed behavior. The difference in p53 dynamics in the model results from two mechanisms: IR damage is fully detected minutes after exposure while UV damage is detected over several hours; and the p53-controlled transcriptional response is dominated by inactive p53 following UV damage. In particular, we hypothesize that an unidentified positive feedback loop controlled by inactive p53 is required to maintain the qualitative high p53 response to UV damage. This work proposes an explanation for two distinct responses of p53 to DNA damage and how each response can lead to cell cycle arrest or apoptosis.Author summaryWe propose a mathematical model hypothesizing how the tumor suppressor protein p53 produces two contrasting dynamical responses in response to different types of DNA damage. In particular, we predict the existence of a positive feedback loop controlled by the inactive form of p53, which allows the cell to respond to slowly detected damage. The existence of differing dynamic responses by p53 has implications for our understanding of tumor development and possibly p53-related therapeutic strategies.
Posttranscriptional regulation of intestinal epithelial cell repair by RNA binding protein IMP1
Authors: Chatterji Priya , Whelan Kelly A. , Andres Sarah F. , Samper Fernando C. , Simon Lauren A. , Mizuno Rei , Lundsmith Emma T. , Lee David S.M. , Liang Shun , Wijeratne H.R. Sagara , Marti Stefanie , Chau Lillian , Williams Patrick A. , Giroux Veronique , Wilkins Benjamin J. , Wu Gary D. , Shah Premal , Tartaglia Gian G. , Hamilton Kathryn E. 
Published: July 2018

AbstractRNA binding proteins, such as IMP1, are emerging as essential regulators of intestinal development and cancer. IMP1 hypomorphic mice exhibit severe intestinal growth defects, yet it’s role in adult intestinal epithelium is unclear. We employed ribosome profiling to test the effect of IMP1 loss on the “translatome” in colon cancer cell lines. In parallel, we evaluated mice with intestinal epithelial-specific Imp1 deletion (Imp1ΔIEC) following irradiation or colitis models. Ribosome-profiling revealed translation efficiency changes for multiple pathways important for intestinal homeostasis, including autophagy, in IMP1 knockout cells. We found increased autophagy flux in Imp1ΔIEC mice, reinforced through in silico and biochemical analyses revealing direct binding of IMP1 to autophagy transcripts MAP1LC3B and ATG3. We found that Imp1ΔIEC mice exhibit enhanced recovery following irradiation, which is attenuated with genetic deletion of autophagy gene Atg7. Finally, we demonstrated that IMP1 is upregulated in Crohn’s disease patients and Imp1 loss lessened colitis severity in mice. These studies demonstrate that IMP1 acts as a posttranscriptional regulator of gut epithelial repair post-irradiation and colitis, in part through modulation of autophagy.
Price-based quality inferences for insects as food
Authors: Berger Sebastian , Christandl Fabian , Schmidt Christina , Baertsch Christian 
Published: July 2018

Purpose
Entomophagy (i.e. human insect consumption) is seen as one promising route to substantially reduce food-related carbon footprints as insects can be produced at a fraction of the carbon emitted by traditional Western meat production (e.g. beef, pork, poultry). In this light, the purpose of this paper is to address how prices may affect preferences for insects as food.

Design/methodology/approach
Drawing on consumer research on “positive” functions of prices (e.g. the widely held belief that price and quality are positively correlated), the authors present two behavioural experiments that manipulated price cues to estimate the effect on expectations, eating behaviour and willingness-to-pay as central preference indicators.

Findings
Consistent with the predictions, high prices as initial anchors positively affect food preferences. Furthermore, they incur a positive spill-over effect to subsequent consumption of insects that are unprocessed (i.e. truffles in which mealworms are visible in their entity) and for which no price information is available. Additionally, the authors show that the positive effects of high prices on preferences are muted if prices are artificially lowered (e.g. by means of government subsidies, Experiment 2).

Practical implications
Taken together, the authors show that preferences for novel foods such as insects can be promoted by systematically taking into account behavioural economic theories. This suggests that behavioural theory can be used to reap environmental benefits of entomophagy.

Originality/value
This research links behavioural economics with the actual consumption of insects and therefore complements survey research on behavioural intentions.
Customer influence on supply chain management strategies
Authors: Brun Alessandro , Karaosman Hakan 
Published: July 2018

PurposeCustomers influence companies’ operational strategies and supply chain (SC) processes. In this vein, signals coming from the market must be translated into proper strategies in terms of production and supply. The purpose of this paper is to provide an understanding on how to transform customers’ expectations into SC decisions. The yacht industry, encompassing both technical and emotional peculiarities, becomes this study’s driven focus to interrogate the interrelationship between supply and demand.Design/methodology/approachThe study explores the luxury yacht industry through exploratory case studies conducted with eight companies operating in Italy.FindingsIt was found that a wide range of factors influenced customers. That is to say, brand reputation, other brands’ involvement in the final product and emotional appeal were the most distinguishing characteristics identifying emotion-oriented customers. In this sense, companies serving such customers adjusted their SC strategies to channel a direct emotional impact. It was noticed that personalization was pivotal and companies were increasingly required to customize and create unique products to attract and further satisfy the customers. Thus, multiple sourcing strategies were often employed with an increasing number of suppliers to ensure that increasing material supply need would be met. As for performance-oriented companies, cost, quality and innovation capabilities emerged as key signals to be embedded in operations management. Companies serving performance-oriented customers were characterized by low product value and medium level of customization, and kept their core activities, including design and architecture, vertically integrated. In order to generate cost advantages without compromising product quality, single sourcing strategy was largely implemented. What the findings suggested is that the customization level and the product value were positively correlated. To illustrate, companies having more exclusive products were found allowing their customization and customer involvement in higher degrees.Originality/valueDue to a relatively unexplored nature of the phenomenon, this study opted for a method by which individual and collective reconstructions were explored in a not well-investigated area, that is, the luxury yacht industry.
The effects of soybean trade policies on domestic soybean market in China during the food crisis
Authors: Sun Lin , Qi Mingxian , Reed Michael R. 
Published: July 2018

PurposeMany grain exporting/importing countries implement temporary trade policies to intervene in grain trade volume during food crises. The purpose of this paper is to analyze the effects of Chinese soybean trade policies on the domestic soybean market during the food crisis.Design/methodology/approachA Markov switching error correction model is constructed for the empirical analysis. Market integration, market equilibrium and market stability are compared among three regimes: the normal state, crisis state and post-crisis state. In order to reduce the disturbance from external markets factors on the results, the US soybean market is selected as a control group in that it did not use any soybean intervention trade policies during the food crisis.FindingsThe empirical results indicate that China’s temporary soybean trade policies lead to a decrease in market integration between domestic and international soybean markets and a reduction in domestic soybean market stability.Originality/valueIt is the first time that China’s soybean market is selected as a sample and case on this issue. The regime shifting non-linear model could be more applicable because there exists a non-linear transmission relationship between grains markets during food crises. The results imply that China’s temporary soybean trade policies do not improve market integration and stability. China should reconsider implementing soybean trade intervening policies to protect the domestic market and safeguard food security.
Job satisfaction and union participation in China
Authors: Hu Enhua , Zhang Maolong , Shan Hongmei , Zhang Long , Yue Yaqing 
Published: July 2018

PurposeThe purpose of this paper is to offer empirical evidence on whether and how the work experiences of employees in China influence their union-related attitudes and behaviours.Design/methodology/approachThe authors developed a mediated moderation model to examine how job satisfaction and labour relations climate interactively affect union participation and whether union commitment mediates the interactive effects. A total of 585 employees from enterprises in Jiangsu, Zhejiang, Anhui, Jiangxi and Fujian province of China were surveyed to verify the model.FindingsJob satisfaction was negatively related to union participation and union commitment. Labour relations climate moderated the relationship between job satisfaction and union participation; the relationship was negative and stronger when employees perceived an adverse, rather than a favourable, labour relations climate. Further, the interactive effect of job satisfaction and labour relations climate on union participation was partly mediated by union commitment.Originality/valueBy empirically examining employees’ attitudes and behaviours towards unions in the Chinese context, this study confirms that unions could provide employees with alternative work resources to cope with job dissatisfaction, even in a country where unions play a “transmission belt” role between employees and employers. This study adds value to the existing base of knowledge on union practice and labour relations construction, both inside and outside of China.