bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluating intraspecific genetic diversity of a fish population using environmental DNA: An approach to distinguish true haplotypes from erroneous sequences
Authors: Tsuji Satsuki , Miya Masaki , Ushio Masayuki , Sato Hirotoshi , Minamoto Toshifumi , Yamanaka Hiroki 
Published: September 2018

AbstractRecent advances in environmental DNA (eDNA) analysis using high-throughput sequencing (HTS) provide a non-invasive way to evaluate the intraspecific genetic diversity of aquatic macroorganisms. However, erroneous sequences present in HTS data can result in false positive haplotypes; therefore, reliable strategies are necessary to eliminate such erroneous sequences when evaluating intraspecific genetic diversity using eDNA metabarcoding. In this study, we propose an approach combining denoising using amplicon sequence variant (ASV) method and the removal of haplotypes with low detection rates. A mixture of rearing water of Ayu (Plecoglossus altivelis altivelis) was used as an eDNA sample. In total, nine haplotypes of Ayu mitochondrial D-loop region were contained in the sample and amplified by two-step tailed PCR. The 15 PCR replicates indexed different tags were prepared from the eDNA sample to compare the detection rates between true haplotypes and false positive haplotypes. All PCR replications were sequenced by HTS, and the total number of detected true haplotypes and false positive haplotypes were compared with and without denoising using the two types of ASV methods, Divisive Amplicon Denoising Algorithm 2 (DADA2) and UNOISE3. The use of both ASV methods considerably reduced the number of false positive haplotypes. Moreover, all true haplotypes were detected in all 15 PCR, whereas false positive haplotypes had detection rates varying from 1/15 to 15/15. Thus, by removing haplotypes with lower detection rates than 15/15, the number of false positive haplotypes were further reduced. The approach proposed in this study successfully eliminated most of false positive haplotypes in the HTS data obtained from eDNA samples, which allowed us to improve the detection accuracy for evaluating intraspecific genetic diversity using eDNA analysis.
Autoamplification and competition drive symmetry breaking: Initiation of centriole duplication by the PLK4-STIL network
Authors: Leda Marcin , Holland Andrew J. , Goryachev Andrew B. 
Published: September 2018

SummarySymmetry breaking, a central principle of physics, has been hailed as the driver of self-organization in biological systems in general and biogenesis of cellular organelles in particular, but the molecular mechanisms of symmetry breaking only begin to become understood. Centrioles, the structural cores of centrosomes and cilia, must duplicate every cell cycle to ensure their faithful inheritance through cellular divisions. Work in model organisms identified conserved proteins required for centriole duplication and found that altering their abundance affects centriole number. However, the biophysical principles that ensure that, under physiological conditions, only a single procentriole is produced on each mother centriole remain enigmatic. Here we propose a mechanistic biophysical model for the initiation of procentriole formation in mammalian cells. We posit that interactions between the master regulatory kinase PLK4 and its activator-substrate STIL form the basis of the procentriole initiation network. The model faithfully recapitulates the experimentally observed transition from PLK4 uniformly distributed around the mother centriole, the “ring”, to a unique PLK4 focus, the “spot”, that triggers the assembly of a new procentriole. This symmetry breaking requires a dual positive feedback based on autocatalytic activation of PLK4 and enhanced centriolar anchoring of PLK4-STIL complexes by phosphorylated STIL. We find that, contrary to previous proposals,in situdegradation of active PLK4 is insufficient to break symmetry. Instead, the model predicts that competition between transient PLK4 activity maxima for PLK4-STIL complexes explains both the instability of the PLK4 ring and formation of the unique PLK4 spot. In the model, strong competition at physiologically normal parameters robustly produces a single procentriole, while increasing overexpression of PLK4 and STIL weakens the competition and causes progressive addition of procentrioles in agreement with experimental observations.
Nasal respiration entrains neocortical long-range gamma coherence during wakefulness
Authors: Cavelli Matías , Castro-Zaballa Santiago , Gonzalez Joaquín , Rojas-Líbano Daniel , Rubido Nicolas , Velásquez Noelia , Torterolo Pablo 
Published: September 2018

AbstractRecent studies have shown that slow cortical potentials in archi-, paleo- and neocortex, can phase-lock with nasal respiration. In some of these areas, gamma activity (γ: 30-100 Hz) is also coupled to the animal’s respiration. It has been hypothesized that this interaction plays a role in coordinating distributed neural activity. In a similar way, inter-cortical interactions at γ frequency has been also associated as a binding mechanism by which the brain generates temporary opportunities necessary for implementing cognitive functions. The aim of the present study is to explore if nasal respiration entrains inter-cortical interactions at γ frequency.Six adult cats chronically prepared for electrographic recordings were employed in this study. Our results show that slow cortical respiratory potentials are present in several areas of the neocortex and olfactory bulb during wakefulness. Also, we found cross-frequency coupling between the respiratory phase and the amplitude of γ activity in all recorded areas. These oscillatory entrainments are independent of muscular activity, because are maintained during cataplexy induced by carbachol microinjection into the nucleus pontis oralis. Importantly, we observed that respiratory phase modulates the inter-cortical gamma coherence between neocortical pairs of electrodes during wakefulness. However, during NREM and REM sleep, breathing was unable to entrain the oscillatory activity, neither in the olfactory bulb nor in the neocortex. These results suggest a single unified phenomenon involving cross frequency coupling and long-range γ coherence across the neocortex. This fact could be related to a temporal binding process necessary for cognitive functions during wakefulness.
Identification of novel inhibitors of DLK palmitoylation by High Content Screening
Authors: Martin Dale D.O. , Kanuparthi Prasad S. , Holland Sabrina M. , Sanders Shaun S. , Jeong Hey-Kyeong , Einarson Marget B. , Jacobson Marlene , Thomas Gareth M. 
Published: September 2018

AbstractAfter axonal insult and injury, Dual leucine-zipper kinase (DLK) conveys retrograde pro-degenerative signals to neuronal cell bodies via its downstream target c-Jun N-terminal kinase (JNK). We recently reported that such signals critically require modification of DLK by the fatty acid palmitate, via a process called palmitoylation. Compounds that inhibit DLK palmitoylation could thus reduce neurodegeneration, but identifying such inhibitors requires a suitable assay. Here we report that DLK subcellular localization in non-neuronal cells is highly palmitoylation-dependent and can be used as a proxy readout to identify inhibitors of DLK palmitoylation by High Content Screening (HCS). We exploited this highly specific localization of DLK-GFP as the basis for a screen of the Prestwick Compound Library™. We found that ketoconazole, a Prestwick Library compound that most dramatically affected DLK subcellular localization in our primary screen, inhibited DLK palmitoylation in a dose-dependent manner in follow-up biochemical assays. Moeroever, ketoconazole significantly blunted phosphorylation of c-Jun in primary sensory neurons subjected to Trophic Deprivation, a well known model of DLK-dependent pro-degenerative signaling. These findings suggest that our HCS platform is capable of identifying novel inhibitors of DLK palmitoylation and signalling that may have considerable therapeutic potential.
An oxide transport chain essential for balanced insulin signaling
Authors: Wu Xiangdong , Chen Keyang , Williams Kevin Jon 
Published: September 2018

SummaryPatients with overnutrition, obesity, the atherometabolic syndrome, and type 2 diabetes mellitus exhibitimbalanced insulin action, also called pathway-selective insulin resistance. To control glycemia, they require hyperinsulinemia that then overdrives ERK and hepatic de-novo lipogenesis. We recently reported that NADPH oxidase-4 regulates balanced insulin action. Here, we show that NADPH oxidase-4 is part of a new limb of insulin signaling that we abbreviate “NSAPP” after its five major proteins. The NSAPP pathway is an oxide transport chain that begins when insulin stimulates NADPH oxidase-4 to generate. NADPH oxidase-4 handsto superoxide dismutase-3 for conversion into H2O2. The pathway ends when aquaporin-3 channels H2O2across the membrane to inactivate PTEN. Disruption of any component of the NSAPP chain, from NADPH oxidase-4 up to PTEN, leaves PTEN persistently active, thereby producing the same deadly pattern of imbalanced insulin action seen clinically. Unraveling the molecular basis for NSAPP dysfunction in overnutrition has now become a top priority.
Conserved mechanism of nucleoporin regulation of the Kcnq1ot1 imprinted domain with divergence in embryonic and trophoblast stem cells
Authors: Sachani Saqib S. , MacDonald William A. , Foulkrod Ashley M. , White Carlee R. , Zhang Liyue , Mann Mellissa R. W. 
Published: September 2018

AbstractGenomic imprinting is an epigenetic phenomenon, whereby dual chromatin states lead to expression of one, and silencing of the other parental allele. Recently, we identified a nucleoporin-mediated mechanism of Kcnq1ot1 imprinted domain regulation in extraembryonic endoderm stem cells by nucleoporins NUP107, NUP62 and NUP153. Here, we investigate their role in Kcnq1ot1 imprinted domain regulation in embryonic and trophoblast stem cells. Nucleoporin depletion in both lineages reduced Kcnq1ot1 noncoding RNA expression and volume, reduced Kcnq1ot1 paternal domain positioning at the nuclear periphery, and altered histone modifications along with histone modifier enrichment at the imprinting control region. However, while CTCF and cohesin were enriched at nucleoporin binding sites in the imprinting control region in embryonic stem cells, with reduction upon nucleoporin depletion, neither CTCF or cohesin occupied these sites in trophoblast stem cells. Finally, different subsets of silent paternal alleles were reactivated via altered histone modification upon nucleoporin depletion in embryonic and trophoblast stem cells. These results demonstrate a conserved mechanism with divergent regulation of the Kcnq1ot1 imprinted domain by NUP107, NUP62 and NUP153 in embryonic and extraembryonic lineages.Summary StatementInvestigation of nucleoporins, NUP107, NUP62, and NUP153, revealed a conserved nucleoporin-dependent mechanism that mediates Kcnq1ot1 imprinted domain regulation in ES and TS cells, although notable lineage-specific divergence was also observed.
Dynamic network partnerships and social contagion drive cooperation
Authors: Dakin Roslyn , Ryder T. Brandt 
Published: September 2018

ABSTRACTBoth reciprocity and positive assortment (like with like) are predicted to promote the evolution of cooperation, yet how partners influence each other’s behavior within dynamic networks is not well understood. One way to test this question is to partition phenotypic variation into differences among individuals in the expression of cooperative behavior (the “direct effect”), and plasticity within individuals in response to the social environment (the “indirect effect”). A positive correlation between these two sources of variation, such that more cooperative individuals elicit others to cooperate, is predicted to facilitate social contagion and selection on cooperative behavior. Testing this hypothesis is challenging, however, because it requires repeated measures of behavior across a dynamic social landscape. Here, we use an automated data-logging system to quantify the behavior of 179 wire-tailed manakins, birds that form cooperative male-male coalitions, and we use multiple-membership models to test the hypothesis that dynamic network partnerships shape within-individual variation in cooperative behavior. Our results show strong positive correlations between a bird’s own sociality and his estimated effect on his partners, consistent with the hypothesis that cooperation begets cooperation. These findings support the hypothesis that social contagion can facilitate selection for cooperative behavior within social networks.
High content analysis methods enable high throughput nematode discovery screening for viability and movement behavior in a multiplex sample in response to natural product treatment
Authors: Petitte Jennifer M. , Lewis Mary H. , Witsil Tucker K. , Huang Xiang , Rice John W. 
Published: October 2018

AbstractMonitoring nematode parasite movement and mortality in response to various treatment samples usually involves tedious manual microscopic analysis. High Content Analysis instrumentation enables rapid and high throughput collecting of large numbers of treatment data on huge numbers of individual worms. These large sample sizes and increased sample diversity result in robust, reliable results with increased statistical significance. These methods would be applicable to relevant human, crop, or animal worm parasites.
Sequence data from the internal and external transcribed spacers of nuclear ribosomal DNA of Cyclamen purpurascens allow geographic mapping
Authors: Jaag Hannah Miriam 
Published: October 2018

AbstractCyclamen purpurascens (Alpine, European or purple cyclamen) is native to central Europe. Since decades it is discussed wether the occurrences of C. purpurascens north of the alps is native or if it was introduced. Here the nuclear ribosomal DNAs (rDNA) are sequenced in oder to obtain a phylogenetic geographic pattern. Phylogenetic analyses of ITS and NTS/ETS sequences distinguish three main clades coinciding with geographical distribution: Eastern alps (Austria), southern alps (Switzerland, Italy) and western Alps (France). The paper presents interspecific relationship of C. purpurascens based on geographic sequences of rDNA. The observed variations suggest that some plants were introduced via Benedictine gardens and the plants from Monastery gardens seem to origin from Lower Austria.
Corporate governance structures and firm performance in large agriculture companies in New Zealand
Authors: Roudaki Jamal 
Published: October 2018

PurposeThis study aims to explore the role of corporate governance (CG) characteristics on the financial performance of large agricultural companies in New Zealand. External auditor remuneration and board characteristics, such as board ownership, board compensation, board independence and board gender diversity, are addressed in the context of New Zealand’s agricultural companies by applying agency theory.Design/methodology/approachThis paper uses a balanced panel data generalised least square regression analysis on 80 firm-years of observations over the period from 2012 to 2015.FindingsEmpirical analysis revealed that external auditors’ remuneration and board characteristics, such as board compensation and board independence, except for board ownership and board gender diversity, held no association with the agricultural companies’ performance. While board ownership and board gender diversity were negatively, but significantly, associated with firm performance, these results were pronounced in the listed agricultural companies rather than in the non-listed companies.Research limitations/implicationsThis study encountered limitations commonly associated with the majority of industry-specific studies, i.e. small sample size and lack of published financial information from databases. Therefore, for generalisation, these limitations were considered relevant.Practical implicationsThe results of this research project are beneficial for authorities and agricultural company directors in implementing CG principles and guidelines to empower such companies in international competition. Encouraging agricultural companies to maintain a high level of transparency in financial reporting is of central interest for the government’s economic development, and stock market investors achieve a high level of transparency in non-financial disclosures, the chief objective of this study. Finally, the results of this paper may encourage auditors to scrutinise CG disclosures by agricultural companies in more detail, looking for undisclosed information.Social implicationsThe results of this paper may encourage managerial transparency by providing appropriate disclosures for the public benefit. Investors may benefit from the disclosure provided in their economic decision-making and the public may expand on the information disclosed in facilitating development through exports, expansion of foreign investments and the indigenous economy.Originality/valueThe findings contribute to the literature by providing novel and original insights into using a sample of listed and non-listed agricultural companies to extend the current understanding of the governance-performance nexus.
Influence of temperature and magnetic field on the oblique stagnation-point flow for a nanofluid past a vertical stretching/shrinking sheet
Authors: Borrelli Alessandra , Giantesio Giulia , Patria Maria Cristina , Roşca Natalia C. , Roşca Alin V. , Pop Ioan 
Published: October 2018

Purpose
This paper aims to consider the influence of the temperature and of an external magnetic field on the steady oblique stagnation-point flow for a Boussinesquian nanofluid past a stretching or shrinking sheet.

Design/methodology/approach
The flow is reduced through similarity transformations to an ordinary boundary value problem, which is solved numerically in MATLAB using the bvp4c function. The behavior of the solution is discussed physically, and some analytical considerations concerning existence of the solution and the occurrence of dual solutions are drawn.

Findings
The study of the influence of an external magnetic field on the oblique stagnation-point flow of a Buongiorno's Boussinesquian nanofluid is carried out. The fluid clashes on a vertical stretching or shrinking sheet. Dual solutions appear for suitable values of the parameters.

Originality/value
The present results are new and original.
Forecasting performance of time series models on electricity spot markets
Authors: Gürtler Marc , Paulsen Thomas 
Published: October 2018

PurposeStudy conditions of empirical publications on time series modeling and forecasting of electricity prices vary widely, making it difficult to generalize results. The key purpose of the present study is to offer a comparison of different model types and modeling conditions regarding their forecasting performance.Design/methodology/approachThe authors analyze the forecasting performance of AR (autoregressive), MA (moving average), ARMA (autoregressive moving average) and GARCH (generalized autoregressive moving average) models with and without the explanatory variables, that is, power consumption and power generation from wind and solar. Additionally, the authors vary the detailed model specifications (choice of lag-terms) and transformations (using differenced time series or log-prices) of data and, thereby, obtain individual results from various perspectives. All analyses are conducted on rolling calibrating and testing time horizons between 2010 and 2014 on the German/Austrian electricity spot market.FindingsThe main result is that the best forecasts are generated by ARMAX models after spike preprocessing and differencing the data.Originality/valueThe present study extends the existing literature on electricity price forecasting by conducting a comprehensive analysis of the forecasting performance of different time series models under varying market conditions. The results of this study, in general, support the decision-making of electricity spot price modelers or forecasting tools regarding the choice of data transformation, segmentation and the specific model selection.
Facilitating affective experiences to stimulate women’s entrepreneurship in rural India
Authors: Katre Aparna 
Published: October 2018

Purpose
This paper aims to understand the nature of affective experiences that can help women to overcome perceived socio-cultural constraints and stimulate entrepreneurship. The paper focuses on rural poor women in India as they represent cultural contexts rich with impediments while also presenting an opportunity for socio-economic development.

Design/methodology/approach
A qualitative study with interpretative phenomenological analysis was conducted with participants from women-owned and -managed crafts-based cooperative entrepreneurial ventures from the state of Bihar in India.

Findings
Cooperative form of entrepreneurship and sisterhood among its members provides an environment for repeated affective experiences that inspire women to change the status quo. Sisterhood facilitates interactions with role models, mentee-driven mentoring and vicarious incentives, each producing positive affect, whereas cooperatives provide a work environment that fosters equality and helps women find their unique voice, generating affect. Together, the affect allows women to overcome fears associated with deviating from age-old traditions while engaging in entrepreneurial behaviors and sustaining them.

Research limitations/implications
The paper advances knowledge on women entrepreneurship for non-Western cultural contexts, particularly the environments and experiences that stimulate entrepreneurship. The values of cooperative form of entrepreneurship and the homophily among sisters creates an environment which is relaxed and comfortable, where affective experiences can be naturally embedded in daily routines in contrast to those created through formal-structured training programmes. The paper findings are limited to cultural contexts of rural women in eastern states of India with high levels of poverty.

Practical implications
Policies for cooperative entrepreneurship and grassroots support to facilitate an environment to foster cooperatives’ values, and sisterhood can lead to affective experiences necessary for change that endures.

Originality/value
Entrepreneurship for pervasive social change, such as alleviating rural women from poverty, needs theory development, particularly a better understanding of the influence of macro socio-cultural contexts on women’s ability to be entrepreneurial. This paper provides an understanding of contextually relevant affective experiences conducive for rural women entrepreneurship.