bluuebunny/crossref_metadata_2025 huggingface dataset:
Creation and Salvation
Authors: McDade John
Published: April 2018

This chapter offers an overview of Catholic teaching on the relationship between creation and salvation. It begins by affirming the centrality to Christian theology of a fully Trinitarian vision of creation. Such a vision also involves a clearly articulated account of God’s non-competitive relation to the world. The same account governs both an account of the Creator–creation relation and the relationship between the two natures of Christ. Catholic accounts of Christ’s work and the nature of salvation are steeped in the ritualistic and symbolic imagery of second-temple Judaism, and sustain—in the face of the sheer mystery of divine action—a multiplicity of metaphorical languages. The chapter ends by comparing the approaches of Hans Urs von Balthasar and Karl Rahner as symptomatic of key debates in recent Catholic soteriology.
Machine Learning
Authors: Mooney Raymond J.
Published: April 2018

This chapter introduces symbolic machine learning in which decision trees, rules, or case-based classifiers are induced from supervised training examples. It describes the representation of knowledge assumed by each of these approaches and reviews basic algorithms for inducing such representations from annotated training examples and using the acquired knowledge to classify future instances. It also briefly reviews unsupervised learning, in which new concepts are formed from unannotated examples by clustering them into coherent groups. These techniques can be applied to learn knowledge required for a variety of problems in computational linguistics ranging from part-of-speech tagging and syntactic parsing to word sense disambiguation and anaphora resolution. Applications to a variety of these problems are reviewed.
Material Evidence
Authors: Morris Sarah P.
Published: April 2018

Unlike in the study of Roman slavery (Joshel and Peterson 2014), the analysis of archaeological evidence for Greek slavery is far more challenging (I. Morris 2011), if we hope to be able to identify slaves, their labour, and their living spaces, in the ancient material record. Rather than trying to identify figures in Greek art as unfree in status, locating their place of work and living quarters in excavated structures, or distinguishing slave burials in ancient Greek necropoleis, this essay proposes that we should look rather for the wider effects of their labour on changes in health, wealth, settlement and landscapes.
Liturgy
Authors: Tucker Karen B. Westerfield
Published: April 2018

From their emergence early in the twentieth century, the liturgical movement and the ecumenical movement, the latter particularly represented by the deliberations of the Faith and Order Commission of the World Council of Churches, both called for and shaped ecumenical discourse on the nature of worship, the content and shape (ordo) of liturgy, sacraments and sacramentality, the practices of worship, and liturgical leadership and participation. This chapter highlights the history and contributions of both of these movements and notes the confluence of the two streams in the recognition of the centrality of worship for Christian life and mission. Attention also focuses on the ecumenical sharing of liturgical music, common liturgical texts, and lectionaries, and the ongoing question of ecumenical worship.
The Unity We Seek
Authors: Bordeianu Radu
Published: April 2018

Orthodox theologians such as Bulgakov, Florovsky, Afanasiev, Staniloae, and Zizioulas consider eucharistic communion to be the sign of ecclesial unity, but their understandings of the boundaries of the church and unity in love, teaching, episcopacy, and Eucharist (including intercommunion) are varied. This chapter analyses Orthodox understandings of the relationship between the Orthodox Church and the Una Sancta of the creed, considers the ecclesial status of other Christians, and assesses various models of unity, such as ‘all in each place’ (New Delhi, 1961). Unity is conditioned theologically: Christians need to confess the same faith, though uniformity is not the goal. Churches should enjoy unity in love, common service at the altar of the poor (in ‘the liturgy after the liturgy’), synodal decision-making, and communion among local churches represented by their bishops. These forms of unity do not represent successive stages, but they mutually condition each other.
Islamic Law and Gender
Authors: Yacoob Saadia
Published: April 2018

This article examines the category of gender as it is employed in the study of Islamic law. It first considers how gender scholars turned to legal practice and challenged orientalist narratives using a social historical approach. It then analyses feminist critique of legal discourse, focusing on scholarship that addresses the development of pre-modern substantive law (fiqh) and legal theory, as well as the gendered construction of legal subjecthood. It also discusses three different modes of feminist engagements with Islamic law that developed from the 1990s onwards. The first approach develops a narrative about the patriarchal nature of Islamic law and the increasing decline of women’s rights throughout Islamic history. The second approach takes a constructive approach to Islamic law and the third approach interrogates the foundational assumptions and internal logic of substantive law.
Creativity
Authors: Baer John
Published: April 2018

This article reviews research and theory dealing with the psychology of creativity. It begins with a discussion of the most influential and widely known theory of creativity, which is based on the structure of the intellect model. It then considers four aspects of divergent thinking that are frequently mentioned in the literature, along with two models for classifying creativity: the “four P” model and the four C model. The article describes other theories of creativity, including the chance configuration theory, the propulsion model, and the five-factor theory of personality. Finally, it examines other important issues in creativity research, such as mental illness, gender differences, birth order, and IQ. It also looks at some of the approaches used in the assessment of creativity, including the Torrance Tests of Creative Thinking and the consensual assessment technique. Finally, it explores the issue of teaching creativity.
Modern Zen Thinkers
Authors: Tetsurō Mori , Hitoshi Minobe , Heine Steven
Published: April 2018

This chapter consists of three parts, each of which presents the philosophical contributions of an influential modern Japanese thinker closely affiliated with Rinzai Zen Buddhism: D. T. Suzuki (Jp. Suzuki Daisetsu), Hisamatsu Shin’ichi, and Masao Abe (Jp. Abe Masao). The first part focuses on the kernel of Suzuki’s “Zen thought,” namely the “logic of is/not” that he sees as underlying Zen koāns and teachings. The second part focuses on the key themes of Hisamatsu’s thought: his understanding of the “true self” in terms of a formless and thus completely unobjectifiable “absolute nothingness” and his claim that this true self is “absolute autonomous.” The third part provides an overview of Abe’s contributions to the philosophical analyses of Zen texts and teachings as well as to intrafaith (especially between Zen and Pure Land schools of Japanese Buddhism) and interfaith dialogue (especially between Mahayana Buddhism and Christianity).
Nishida Kitarō’s Philosophy
Authors: Maraldo John C.
Published: April 2018

This chapter’s content centers on the question “Is there an ultimate context for conceptualizing everything, every being in the world, and even the world itself?” This question, a central concern of Nishida Kitarō in the mature stage of his philosophy, led him to develop a novel alternative to the ways that philosophers distinguish self and world and seek ultimate grounds for them. Nishida’s alternative was the notion of “the place of absolute nothingness” that underlies all distinctions and contextualizes all grounds. This article explores the significance of Nishida’s alternative and points to the positive role that obscurity and context play in making distinctions.
Japanese Ethics
Authors: Carter Robert E.
Published: April 2018

Ethics in Japan consists of a demand to show compassion (fellow-feeling or human-heartedness) in one’s dealings with others and with the world of nature. A key approach for the teaching of human-heartedness is through the “Japanese arts,” such as the ways of tea, flowers, calligraphy, landscape design, and the indigenous martial art called aikidō. While the ultimate aim of these “ways” (dō) is enlightenment, the more immediate fruit is a genuine expression of compassion. Ideally, the expression of human-heartedness should arise spontaneously and without calculation, as an effortless revelation of one’s true nature. An ethical person will likely have a passion for acting well, for not causing undue pain to others, and for nurturing and protecting the environment at large. This passion arises out of the realization that we are all interconnected, that we are one with others and with nature.
Prince Shōtoku’s Constitution and the Synthetic Nature of Japanese Thought
Authors: Kasulis Thomas P.
Published: April 2018

Throughout its history Japan has shown a talent for using synthesis and syncretism to inspire philosophical innovation. Rather than refuting or rejecting the new or foreign, Japanese thinkers have more often aimed for assimilation, employing a rhetoric based in strategies of allocation, hybridization, or relegation. This article begins with a description of those strategies, citing examples from across the history of Japan’s philosophical tradition. Then it focuses on the Seventeen-Article Constitution, traditionally said to have been authored by Prince Shōtoku in 604 c.e. It is arguably the first extant example of a Japanese philosophical attempt to draw on multiple traditions: Confucianism, Buddhism, and early Shintō myth. The purpose of the Constitution was to create a coherent polity grounded in moral principles. As such, it has been upheld throughout history as a founding document of the Japanese nation.
Cannabis for the treatment of paediatric epilepsy? An update for Canadian paediatricians
Authors: Huntsman Richard James , Tang-Wai Richard , Acton Bryan , Alcorn Jane , Lyon Andrew William , Mousseau Darrell David , Seifert Blair , Laprairie Robert , Prosser-Loose Erin , Hanuš Lumir Ondrej
Published: April 2018

The plant Cannabis sativa produces over 140 known cannabinoids. These chemicals generate considerable interest in the medical research community for their possible application to several intractable disease conditions. Recent reports have prompted parents to strongly consider Cannabis products to treat their children with drug resistant epilepsy. Physicians, though, are reluctant to prescribe Cannabis products due to confusion about their regulatory status and limited clinical data supporting their use. We provide the general paediatrician with a brief review of cannabinoid biology, the literature regarding their use in children with drug resistant epilepsy, the current Health Canada and Canadian Paediatric Society recommendations and also the regulations from the physician regulatory bodies for each province and territory. Given the complexities of conducting research on Cannabis products for children with epilepsy, we also discuss outstanding research objectives that must be addressed to support Cannabis products as an accepted treatment option for children with refractory epilepsy.
Spontaneous activity emerging from an inferred network model captures complex spatio-temporal dynamics of spike data
Authors: Capone Cristiano , Gigante Guido , Giudice Paolo De
Published: April 2018

Inference methods are widely used to recover effective models from observed data. However, few studies attempted to investigate the dynamics of inferred models in neuroscience, and none, to our knowledge, at the network level. We introduce a principled modification of a widely used generalized linear model (GLM), and learn its structural and dynamic parameters from in-vitro spike data. The spontaneous activity of the new model captures prominent features of the non-stationary and non-linear dynamics displayed by the biological network, where the reference GLM largely fails, and also reflects fine-grained spatio-temporal dynamical features. Two ingredients were key for success. The first is a saturating transfer function: beyond its biological plausibility, it limits the neurons information transfer, improving robustness against endogenous and external noise. The second is a super-Poisson spikes generative mechanism; it accounts for the undersampling of the network, and allows the model neuron to flexibly incorporate the observed activity fluctuations.
Accurate functional classification of thousands of BRCA1 variants with saturation genome editing
Authors: Findlay Gregory M. , Daza Riza M. , Martin Beth , Zhang Melissa D. , Leith Anh P. , Gasperini Molly , Janizek Joseph D. , Huang Xingfan , Starita Lea M. , Shendure Jay
Published: April 2018

Variants of uncertain significance (VUS) fundamentally limit the utility of genetic information in a clinical setting. The challenge of VUS is epitomized by BRCA1, a tumor suppressor gene integral to DNA repair and genomic stability. Germline BRCA1 loss-of-function (LOF) variants predispose women to early-onset breast and ovarian cancers. Although BRCA1 has been sequenced in millions of women, the risk associated with most newly observed variants cannot be definitively assigned. Data sharing attenuates this problem but it is unlikely to solve it, as most newly observed variants are exceedingly rare. In lieu of genetic evidence, experimental approaches can be used to functionally characterize VUS. However, to date, functional studies of BRCA1 VUS have been conducted in a post hoc, piecemeal fashion. Here we employ saturation genome editing to assay 96.5% of all possible single nucleotide variants (SNVs) in 13 exons that encode functionally critical domains of BRCA1. Our assay measures cellular fitness in a haploid human cell line whose survival is dependent on intact BRCA1 function. The resulting function scores for nearly 4,000 SNVs are bimodally distributed and almost perfectly concordant with established assessments of pathogenicity. Sequence-function maps enhanced by parallel measurements of variant effects on mRNA levels reveal mechanisms by which loss-of-function SNVs arise. Hundreds of missense SNVs critical for protein function are identified, as well as dozens of exonic and intronic SNVs that compromise BRCA1 function by disrupting splicing or transcript stability. We predict that these function scores will be directly useful for the clinical interpretation of cancer risk based on BRCA1 sequencing. Furthermore, we propose that this paradigm can be extended to overcome the challenge of VUS in other genes in which genetic variation is clinically actionable.
Population dynamics of Escherichia coli in the gastrointestinal tracts of Tanzanian children
Authors: Richter Taylor K. S. , Hazen Tracy H. , Lam Diana , Coles Christian L. , Seidman Jessica C. , You Yaqi , Silbergeld Ellen K. , Fraser Claire M. , Rasko David A.
Published: April 2018

The stability of the Escherichia coli populations in the human gastrointestinal tract are not fully appreciated, and represent a significant knowledge gap regarding gastrointestinal community structure, as well as resistance to incoming pathogenic bacterial species and antibiotic treatment. The current study examines the genomic content of 240 Escherichia coli isolates from children 2 to 35 months old in Tanzania. The E. coli strains were isolated from three time points spanning a six month time period, with or without antibiotic treatment. The resulting isolates were sequenced, and the genomes compared. The findings in this study highlight the transient nature of E. coli strains in the gastrointestinal tract of children, as during a six-month interval, no one individual contained phylogenomically related isolates at all three time points. While the majority of the isolates at any one time point were phylogenomically similar, most individuals did not contain phylogenomically similar isolates at more than two time points. Examination of global genome content, canonical E. coli virulence factors, multilocus sequence type, serotype, and antimicrobial resistance genes identified diversity even among phylogenomically similar strains. There was no apparent increase in the antimicrobial resistance gene content after antibiotic treatment. The examination of the E. coli from longitudinal samples from multiple children in Tanzania provides insight into the genomic diversity and population variability of resident E. coli within the rapidly changing environment of the gastrointestinal tract.

Importance

This study increases the number of resident Escherichia coli genome sequences, and explores E. coli diversity through longitudinal sampling. We investigate the genomes of E. coli isolated from human gastrointestinal tracts as part of an antibiotic treatment program among rural Tanzanian children. Phylogenomics demonstrates that resident E. coli are diverse, even within a single host. Though the E. coli isolates of the gastrointestinal community tend to be phylogenomically similar at a given time, they differed across the interrogated time points, demonstrating the variability of the members of the E. coli community. Exposure to antibiotic treatment did not have an apparent impact on the E. coli community or the presence of resistance and virulence genes within E. coli genomes. The findings of this study highlight the variable nature of bacterial members of the human gastrointestinal tract.
Adaptive periodicity in the infectivity of malaria gametocytes to mosquitoes
Authors: Schneider Petra , Rund Samuel S. C. , Smith Natasha L. , Prior Kimberley F. , O’Donnell Aidan J. , Reece Sarah E.
Published: April 2018

That periodicity in the biting activity of mosquito vectors explains why malaria parasites have evolved rhythms in cycles of asexual replication in the host’s blood was proposed almost 50 years ago. Yet, tests of this hypothesis have proved inconclusive. Using the rodent malaria Plasmodium chabaudi, we examine rhythms in the density and infectivity of transmission forms (gametocytes) in the host’s blood, parasite development inside mosquitoes, and onwards transmission.Moreover, we control for the confounding effects of rhythms in mosquito susceptibility. We reveal that at night, gametocytes are twice as infective to mosquitoes, despite being less numerous in the blood. This enhanced infectiousness at night interacts with mosquito rhythms to increase sporozoite burdens by almost four-fold when mosquitoes feed during their day. Thus, daytime blood-feeding (e.g. driven by the use of bed nets) may render gametocytes less infective, but this is compensated for by the greater susceptibility of mosquitoes.
Benchmarking optimization methods for parameter estimation in large kinetic models
Authors: Villaverde Alejandro F. , Fröhlich Fabian , Weindl Daniel , Hasenauer Jan , Banga Julio R.
Published: April 2018

Motivation

Mechanistic kinetic models usually contain unknown parameters, which need to be estimated by optimizing the fit of the model to experimental data. This task can be computationally challenging due to the presence of local optima and ill-conditioning. While a variety of optimization methods have been suggested to surmount these issues, it is not obvious how to choose the best one for a given problem a priori, since many factors can influence their performance. A systematic comparison of methods that are suited to parameter estimation problems of sizes ranging from tens to hundreds of optimization variables is currently missing, and smaller studies indeed provided contradictory findings.

Results

Here, we use a collection of benchmark problems to evaluate the performance of two families of optimization methods: (i) a multi-start of deterministic local searches; and (ii) a hybrid metaheuristic combining stochastic global search with deterministic local searches. A fair comparison is ensured through a collaborative evaluation, involving researchers applying each method on a daily basis, and a consideration of multiple performance metrics capturing the trade-off between computational efficiency and robustness. Our results show that, thanks to recent advances in the calculation of parametric sensitivities, a multi-start of gradient-based local methods is often a successful strategy, but a better performance can be obtained with a hybrid metaheuristic. The best performer is a combination of a global scatter search metaheuristic with an interior point local method, provided with gradients estimated with adjoint-based sensitivities. We provide an implementation of this novel method in an open-source software toolbox to render it available to the scientific community.

Availability and Implementation

The code to reproduce the results is available at Zenodo https://doi.org/10.5281/zenodo.1160343

Contact

jan.hasenauer@helmholtz-muenchen.de, julio@iim.csic.es
Spatial Self-Organization Resolves Conflicts Between Individuality and Collective Migration
Authors: Fu X. , Kato S. , Long J. , Mattingly H.H. , He C. , Vural D.C. , Zucker S.W. , Emonet T.
Published: April 2018

Collective behavior can spontaneously emerge when individuals follow common rules of interaction. However, the behavior of each individual will differ due to existing genetic and non-genetic variation within the population. It remains unclear how this individuality is managed to achieve collective behavior. We quantified individuality in bands of clonalEscherichia colicells that migrate collectively along a channel by following a self-generated gradient of attractant. We discovered that despite substantial differences in individual chemotactic abilities, the cells are able to migrate as a coherent group by spontaneously sorting themselves within the moving band. This sorting mechanism ensures that differences between individual chemotactic abilities are compensated by differences in the local steepness of the traveling gradient each individual must navigate, and determines the minimum performance required to travel with the band. By resolving conflicts between individuality and collective migration, this mechanism enables populations to maintain advantageous diversity while on the move.
Cdt1 variants reveal unanticipated aspects of interactions with Cyclin/CDK and MCM important for normal genome replication
Authors: Pozo Pedro N. , Matson Jacob P. , Cole Yasemin , Kedziora Katarzyna M. , Grant Gavin D. , Temple Brenda , Cook Jeanette Gowen
Published: April 2018

The earliest step in DNA replication is origin licensing which is the DNA loading of MCM helicase complexes. The Cdt1 protein is essential for MCM loading during G1 phase of the cell cycle, yet the mechanism of Cdt1 function is still incompletely understood. We examined a collection of rare Cdt1 variants that cause a form of primordial dwarfism (Meier-Gorlin syndrome) plus one hypomorphicDrosophilaallele to shed light on Cdt1 function. Three hypomorphic variants load MCM less efficiently than WT Cdt1, and their lower activity correlates with impaired MCM binding. A structural homology model of the human Cdt1-MCM complex position the altered Cdt1 residues at two distinct interfaces rather than the previously described single MCM interaction domain. Surprisingly, one dwarfism allele (Cdt1-A66T) is more active than WT Cdt1. This hypermorphic variant binds both Cyclin A and SCFSkp2poorly relative to WT Cdt1. Detailed quantitative live cell imaging analysis demonstrated no change in stability of this variant however. Instead, we propose that Cyclin A/CDK inhibits Cdt1 licensing function independently of the creation of the SCFSkp2phosphodegron. Together, these findings identify key Cdt1 interactions required for both efficient origin licensing and tight Cdt1 regulation to ensure normal cell proliferation and genome stability.
Temporal Evolution of Cortical Ensembles Promoting Remote Memory Retrieval
Authors: DeNardo Laura A. , Liu Cindy D. , Allen William E. , Adams Eliza L. , Friedmann Drew , Dadgar-Kiani Ehsan , Fu Lisa , Guenthner Casey J. , Lee Jin Hyung , Tessier-Lavigne Marc , Luo Liqun
Published: April 2018

Studies of amnesic patients and animal models support a systems consolidation model, which posits that explicit memories formed in hippocampus are transferred to cortex over time1–6. Prelimbic cortex (PL), a subregion of the medial prefrontal cortex, is required for the expression of learned fear memories from hours after learning until weeks later7–12. While some studies suggested that prefrontal cortical neurons active during learning are required for memory retrieval13–15, others provided evidence for ongoing cortical circuit reorganization during memory consolidation10,16,17. It has been difficult to causally relate the activity of cortical neurons during learning or recent memory retrieval to their function in remote memory, in part due to a lack of tools18. Here we show that a new version of ‘targeted recombination in active populations’, TRAP2, has enhanced efficiency over the past version, providing brain-wide access to neurons activated by a particular experience. Using TRAP2, we accessed PL neurons activated during fear conditioning or 1-, 7-, or 14-day memory retrieval, and assessed their contributions to 28-day remote memory. We found that PL neurons TRAPed at later retrieval times were more likely to be reactivated during remote memory retrieval, and more effectively promoted remote memory retrieval. Furthermore, reducing PL activity during learning blunted the ability of TRAPed PL neurons to promote remote memory retrieval. Finally, a series of whole-brain analyses identified a set of cortical regions that were densely innervated by memory-TRAPed PL neurons and preferentially activated by PL neurons TRAPed during 14-day retrieval, and whose activity co-varied with PL and correlated with memory specificity. These findings support a model in which PL ensembles underlying remote memory undergo dynamic changes during the first two weeks after learning, which manifest as increased functional recruitment of cortical targets.
Enhanced super-resolution microscopy by extreme value based emitter recovery
Authors: Ma Hongqiang , Jiang Wei , Xu Jianquan , Liu Yang
Published: April 2018

Super-resolution localization microscopy allows visualization of biological structure at nanoscale resolution. However, the presence of heterogeneous background can degrade the nanoscale resolution by tens of nanometers and introduce significant image artifacts. Here we develop a new approach, referred to as extreme value based emitter recovery (EVER), to accurately recover the distorted fluorescent emitters from heterogeneous background. Through numerical simulation and biological experiments, we demonstrate that EVER significantly improves the accuracy and fidelity of the reconstructed super-resolution image for a wide variety of imaging characteristics. EVER requires no manual adjustment of parameters and is implemented as an easy-to-use ImageJ plugin that can immediately enhance the quality of super-resolution images. Our method paves the way for accurate nanoscale imaging of samples with heterogeneous background fluorescence, such as thicker tissue and cells.
Peptide-binding groove contraction linked to the lack of T-cell response: Using complex structure and energy to identify neoantigens
Authors: Pang Yuan-Ping , Elsbernd Laura R. , Block Matthew S. , Markovic Svetomir N.
Published: April 2018

Using personalized peptide vaccines (PPVs) to target tumor-specific non-self antigens (neoantigens) is a promising approach to cancer treatment. However, the development of PPVs is hindered by the challenge of identifying tumor-specific neoantigens, in part because current in silico methods for identifying such neoantigens have limited effectiveness. Here we report the results of molecular dynamics simulations of 12 oligopeptides bound with a human leukocyte antigen (HLA), revealing a previously unrecognized association between the inability of an oligopeptide to elicit a T-cell response and the contraction of the peptide-binding groove upon binding of the oligopeptide to the HLA. Our conformational analysis showed that this association was due to incompatibility at the interface between the contracted groove and its αβ–T-cell antigen receptor (TCR). This structural demonstration that having the capability to bind HLA does not guarantee immunogenicity prompted us to develop an atom-based methodto predict immunogenicity through using the structure and energy of a peptide•HLA complex to assess the propensity of the complex for forming a ternary complex with its TCR. In predicting the immunogenicities of the 12 oligopeptides,achieved a 100% success rate compared with success rates of 25–50% for 11 publicly available residue-based methods including NetMHC-4.0.While further validation and refinements ofare required, our results suggest a need to develop in silico methods that assess peptide characteristics beyond their capability to form stable binary complexes with HLAs to help remove hurdles in using the patient tumor DNA information to develop PPVs for personalized cancer immunotherapy.
Earthworms and Cadmium - heavy metal resistant gut bacteria as indicators for heavy metal pollution in soils?
Authors: Šrut Maja , Menke Sebastian , Höckner Martina , Sommer Simone
Published: April 2018

Preservation of the soil resources stability is of paramount importance for the ecosystem, particularly in the current era of environmental change, which presents a severe pollution burden (e.g. by heavy metals) to soil ecosystems and its fauna. Gut microbiomes are becoming recognized as important players in organism health, with comprehension of their perturbations in the polluted environment offering new insights into the nature and extent of heavy metal effects on the health of soil biota. Our aim was therefore to evaluate the effect of environmentally relevant heavy metal concentrations of cadmium (Cd) on the earthworm gut microbiota. Cd exposure led to perturbations of several heavy metal resistant taxa as well as taxa able to bind heavy metals, revealing the potential of the earthworm-microbiota system in overcoming humancaused heavy metal pollution. An ‘indicator species analysis’ linked bacterial generaPaenibacillusandFlavobacterium, and members of the order Actinomycetales with Cd treatment, suggesting the possible use of these bacterial taxa as biomarkers of exposure for Cd stressed soils. The results of this study will be essential to understanding of the soil fauna health, under anthropogenic disturbance, and will have implications for environmental monitoring and protection of soil resources.

Importance

Soil heavy metal pollution presents a severe burden for soil invertebrates and can have impact on their health, which in turn reflects on the health of the entire ecosystem. Gut microbiome is recognized as a central driver of the host health and its shifts can have severe consequences for the host. In this study we investigated the impact of cadmium (Cd) on earthworm gut microbiota, in a controlled experiment using cutting edge next generation sequencing and state of the art bioinformatics tools. The significance of this study is in identifying the gut bacterial taxa which are indicators for Cd treatment and are potential biomarkers of exposure to Cd. Therefore, this study contributes to develop efficient measures to qualify environmental pollution and to protect fragile soil resources and ultimately human health.
Diverse progenitor cells preserve salivary gland ductal architecture after radiation induced damage
Authors: May Alison J. , Cruz-Pacheco Noel , Emmerson Elaine , Seidel Kerstin , Nathan Sara , Muench Marcus O. , Klein Ophir , Knox Sarah M.
Published: April 2018

The ductal system of the salivary gland has long been postulated to be resistant to radiation-induced damage, a common outcome incurred by head and neck cancer patients receiving radiotherapy. Yet, whether the ducts are capable of regenerating after genotoxic injury, or if damage to ductal cells induces lineage plasticity, as has been reported in other organ systems, remains unknown. Here, we show that two ductal progenitor populations marked by KRT14 and KIT exclusively maintain non-overlapping ductal compartments after radiation exposure but do so through distinct cellular mechanisms. KRT14+ progenitor cells are fast cycling cells that proliferate in response to radiation-induced damage in a sustained manner and divide asymmetrically to produce differentiated cells of the larger granulated ducts. Conversely, KIT+ cells are long lived progenitors for the intercalated ducts that undergo few cell divisions either during homeostasis or after gamma radiation, thus maintaining ductal architecture in the near absence of cell turnover. Together, these data illustrate the regenerative capacity of the salivary ducts and highlight the heterogeneity in the damage responses used by salivary progenitor cells to maintain tissue architecture.

Summary Statement

The salivary gland ductal network is maintained during homeostasis and after genotoxic injury by diverse progenitors that respond differentially to radiation induced damage.
Design Principles for Autonomous Illumination Control in Localization Microscopy
Authors: Štefko Marcel , Ottino Baptiste , Douglass Kyle M. , Manley Suliana
Published: April 2018

Super-resolution fluorescence microscopy improves spatial resolution, but this comes at a loss of image throughput and presents unique challenges in identifying optimal acquisition parameters. Microscope automation routines can offset these drawbacks, but thus far have required user inputs that presume a priori knowledge about the sample. Here, we develop a flexible illumination control system for localization microscopy comprised of two interacting components that require no sample-specific inputs: a self-tuning controller and a deep learning molecule density estimator that is accurate over an extended range. This system obviates the need to fine-tune parameters and demonstrates the design of modular illumination control for localization microscopy.
Active presynaptic ribosomes in mammalian brain nerve terminals, and increased transmitter release after protein synthesis inhibition
Authors: Scarnati Matthew S. , Kataria Rahul , Biswas Mohana , Paradiso Kenneth G.
Published: April 2018

Presynaptic neuronal activity requires the localization of thousands of proteins that are typically synthesized in the soma and transported to nerve terminals. Local translation for some dendritic proteins occurs, but local translation in mammalian presynaptic nerve terminals is difficult to demonstrate. Here, we present evidence for local presynaptic protein synthesis in the mammalian brain at a glutamatergic nerve terminal. We show an essential ribosomal component, 5.8s rRNA, in terminals. We also show active translation in nerve terminals, in situ, in brain slices demonstrating ongoing presynaptic protein synthesis. After inhibiting translation for ~1 hour, the presynaptic terminal exhibits increased spontaneous release, and increased evoked release with an increase in vesicle recycling during stimulation trains. Postsynaptic response, shape and amplitude were not affected. We conclude that ongoing protein synthesis limits vesicle release at the nerve terminal which reduces the need for presynaptic vesicle replenishment, thus conserving energy required for maintaining synaptic transmission.
Development of the MAM model of schizophrenia in mice: Sex similarities and differences of hippocampal and prefrontal cortical function
Authors: Chalkiadaki Kleanthi , Velli Aggeliki , Kyriazidis Evangelos , Stavroulaki Vasiliky , Vouvoutsis Vasilis , Chatzaki Ekaterini , Aivaliotis Michalis , Sidiropoulou Kyriaki
Published: April 2018

Schizophrenia is a debilitating disorder with complex and unclarified etiological factors. Sex differences have been observed in humans but animal models have only focused on male subjects. In this study, we report the establishment of the neurodevelopmental MAM model of schizophrenia in mice and compare the schizotypic-like characteristics and cognitive function in both sexes. Pregnant mice were injected with 26mg/kg(i.p.) of Methylazoxy-methanol acetate (MAM) or saline (5ml/kg) on gestational day (GD) 16 (MAM-16) or 17 (MAM-17). Behavioral, histological and electrophysiological and mass spectrometry-based comparative proteomic techniques were employed to assess the schizotypic-like characteristics and cognitive function of adult male and female offspring (MAM- or saline-treated). Female MAM-16, but not MAM-17 treated mice exhibited enhanced hyperlocomotion after acute administration of the NMDA receptor antagonist, MK-801, compared to saline treated mice. Male MAM-16, but not MAM-17 treated mice showed decreased pre-pulse inhibition of the acoustic startle reflex. Both male and female MAM-16 and MAM-17 treated mice exhibited reduced hippocampal (HPC) size and thinning of the prefrontal cortex (PFC), but only male MAM-16 treated mice showed decreased parvalbumin expression in HPC and PFC. Similarly, both male and female MAM-16 treated mice displayed impaired contextual fear memory, while only male MAM-16 treated mice exhibited deficits in the delayed alternation task. The neurophysiological mechanisms that underlie these cognitive functions were further investigated. Both male and female MAM-16 treated mice had significantly reduced long-term potentiation (LTP) in the HPC CA1 synapses, while only male MAM-16 treated mice exhibited decreased LTP in the PFC. Proteomic analyses of PFC lysates further showed significant MAM- and sex-dependent differences in regulation of protein expression. Our results demonstrate that while both male and female mice, prenatally exposed to MAM on GD16, display several core schizophrenia-like deficits and impairments in the hippocampus, only male MAM-treated mice have PFC-dependent cognitive deficits.
MEST induces epithelial-mesenchymal transition through IL-6/JAK/STAT3 signaling in breast cancers
Authors: Kim Min Soo , Lee Hyun Sook , Kim Yun Jae , Kang Sung Gyun , Lee Do Yup , Jin Wook
Published: April 2018

The loss of imprinting of MEST has been linked to certain types of cancer by promoter switching. However, MEST-mediated regulation of tumorigenicity and metastasis are yet to be understood. Herein, we reported that MEST is a key regulator of IL-6/JAK/STAT3/Twist-1 signal pathway-mediated tumor metastasis. Enhanced MEST expression is significantly associated with pathogenesis of breast cancer patients. Also, MEST induces metastatic potential of breast cancer through induction of the EMT-TFs-mediated EMT program. Moreover, MEST leads to Twist-1 induction by STAT3 activation and subsequently enables the induction of activation of the EMT program via the induction of STAT3 nuclear translocation. Furthermore, the c-terminal region of MEST was essential for STAT3 activation via the induction of JAK2/STAT3 complex formation. Finally, MEST significantly increases the breast cancer’s ability to metastasize from the mammary gland to the lung. These observations suggest that MEST is a promising target for intervention to prevent tumor metastasis.
Equitable Thresholding and Clustering (ETAC): A novel method for FMRI clustering in AFNI
Authors: Cox Robert W.
Published: April 2018

This paper describes a hybrid method to threshold FMRI group statistical maps derived from voxelwise second-level statistical analyses. The proposed “Equitable Thresholding and Clustering” (ETAC) approach seeks to reduce the dependence of clustering results on arbitrary parameter values by using multiple sub-tests, each equivalent to a standard FMRI clustering analysis, to make decisions about which groups of voxels are potentially significant. The union of these sub-test results decides which voxels are accepted. The approach adjusts the cluster-thresholding parameter of each sub-test in an equitable way, so that the individual false positive rates (FPRs) are balanced across sub-tests to achieve a desired final FPR (e.g., 5%). ETAC utilizes resampling methods to estimate the FPR, and thus does not rely on parametric assumptions about the spatial correlation of FMRI noise. The approach was validated with pseudo-task timings in resting state brain data. Additionally, a task FMRI data collection was used to compare ETAC’s true positive detection power vs. a standard cluster detection method, demonstrating that ETAC is able to detect true results and control false positives while reducing reliance on arbitrary analysis parameters.
CCL3 promotes germinal center B cells sampling by follicular regulatory T cells
Authors: Benet Zachary L. , Marthi Matangi , Wu Rita , Turner Jackson S. , Gabayre Jahan B. , Ivanitskiy Michael I. , Sethi Sahil S. , Grigorova Irina L.
Published: April 2018

Previous studies and our findings suggest upregulated expression of proinflammatory chemokines CCL3/4 in germinal center (GC) centrocytes. However, the role of CCL3/4 for centrocyte interactions with follicular T cells and regulation of humoral immunity is poorly understood. We found that CCL3 promotes chemotaxis of Tfr cellsex vivo. In vivoCCL3 is not required for Tfr cells recruitment of into the GC light zone. However, B cells-intrinsic production of CCL3 promotes their direct interactions and negative regulation by follicular regulatory T cells (Tfr) within GCs.
The fractional Fourier transform as a simulation tool for lens-based X-ray microscopy
Authors: Pedersen Anders Filsøe , Simons Hugh , Detlefs Carsten , Poulsen Henning Friis
Published: April 2018

The fractional Fourier transform (FrFT) is introduced as a tool for numerical simulations of X-ray wavefront propagation. By removing the strict sampling requirements encountered in typical Fourier optics, simulations using the FrFT can be carried out with much decreased detail, allowing, for example, on-line simulation during experiments. Moreover, the additive index property of the FrFT allows the propagation through multiple optical components to be simulated in a single step, which is particularly useful for compound refractive lenses (CRLs). It is shown that it is possible to model the attenuation from the entire CRL using one or two effective apertures without loss of accuracy, greatly accelerating simulations involving CRLs. To demonstrate the applicability and accuracy of the FrFT, the imaging resolution of a CRL-based imaging system is estimated, and the FrFT approach is shown to be significantly more precise than comparable approaches using geometrical optics. Secondly, it is shown that extensive FrFT simulations of complex systems involving coherence and/or non-monochromatic sources can be carried out in minutes. Specifically, the chromatic aberrations as a function of source bandwidth are estimated, and it is found that the geometric optics greatly overestimates the aberration for energy bandwidths of around 1%.
Teacher support for career development: an integrative review and research agenda
Authors: Zhang Jiahong , Yuen Mantak , Chen Gaowei
Published: April 2018

Purpose

The purpose of this paper is to review identified key features of teacher support and its influence on students’ career decision making and development. It also examines the types of research approaches to data collection and analysis in order to provide a more in-depth evaluation of this field of study.

Design/methodology/approach

The review examined 18 studies, the majority being quantitative in design. Cross-sectional and longitudinal effects of teacher support were investigated, and differences in teacher support relative to grade level and gender were considered.

Findings

Results indicated that since 2000, there has been an increase in the number of empirical studies of teacher support in the career development field, the majority involving middle and high school students. The most commonly cited frameworks that underpin the studies are the social cognitive career theory, the career construction theory and Super’s career development theory. The most frequently used instrument for data collection was the teacher support scale (Metheny et al., 2008).

Originality/value

The review will be beneficial to researchers, teachers and policy makers seeking to optimize support systems for students’ career development. The findings contribute to further theory development and have practical implications for the career guidance field. Recommendations for future research and practice are suggested.
Ownership structure, board gender diversity and charitable donation
Authors: Lin Ting-Ling , Liu Heng-Yih , Huang Chi-Jui , Chen Yu-Chiung
Published: April 2018

Purpose

This paper aims to examine the effect of ownership structure and board gender diversity on charitable donations for a group of listed electronics companies in Taiwan.

Design/methodology/approach

Using linear regression analysis, this paper analyses the ownership structure, board gender diversity and charitable donations of 380 Taiwanese electronics companies (2011-2013).

Findings

While domestic institutional investors, such as domestic mutual funds and corporate investors, take more of agency logic view, it negatively impacts on charitable donations. However, the empirical findings of this paper indicate that board gender diversity with the critical number of female directors was positively related to charitable donation. Thus, it is clear that female directors reaching critical numbers were taking more of a stakeholder view of institutional logic, emphasizing the balance of interests of internal and external stakeholders.

Research limitations/implications

This paper is limited to selected Taiwanese electronics companies over a two-year time frame, and charitable donations are the only proxy of corporate social responsibility (CSR) activity. The paper suggests that, as predicted by stakeholder theory and critical mass theory, companies with boards composed of at least three female directors make higher charitable donations.

Practical implications

This paper indicates that female directors on the board should have more voices on the board regarding the necessity and importance of CSR.

Originality/value

The paper contributes to existing literature by looking into the effects of ownership structure and board gender diversity on charitable donations.
Predicting the impacts of climate change on groundwater recharge in an arid environment using modeling approach
Authors: Ghazavi Reza , Ebrahimi Haidar
Published: April 2018

Purpose

Groundwater is an important source of water supply in arid and semi-arid areas. The purpose of this study is to predict the impact of climate change on groundwater recharge in an arid environment in Ilam Province, west of Iran.

Design/methodology/approach

A three-dimensional transient groundwater flow model (modular finite difference groundwater FLOW model: MODFLOW) was used to simulate the impacts of three climate scenarios (i.e. an average of a long-term rainfall, predicted rainfall in 2015-2030 and three years moving average rainfall) on groundwater recharge and groundwater levels. Various climate scenarios in Long Ashton Research Station Weather Generator were applied to predict weather data.

Findings

HadCM3 climatic model and A2 emission scenario were selected as the best methods for weather data generation. Based on the results of these models, annual precipitation will decrease by 3 per cent during 2015-2030. For three emission scenarios, i.e. an average of a long-term rainfall, predicted rainfall in 2015-2030 and three years moving average rainfall, precipitation in 2030 is estimated to be 265, 257 and 247 mm, respectively. For the studied aquifer, predicted recharge will decrease compared to recharge calculated based on the average of long-term rainfall.

Originality/value

The decline of groundwater level in the study area was 11.45 m during the past 24 years or 0.48 m/year. Annual groundwater depletion should increase to 0.75 m in the coming 16 years via climate change. Climate change adaptation policies in the basin should include changing the crop type, as well as water productivity and irrigation efficiency enhancement at the farm and regional scales.