bluuebunny/crossref_metadata_2025 huggingface dataset:
Ginsenoside Rh1: A Systematic Review of Its Pharmacological Properties
Authors: Tam Dao , Truong Duy , Nguyen Thi , Quynh Le , Tran Linh , Nguyen Hong , Shamandy Bahaa eldin , Le Thi , Tran Dang , Sayed Dina , Vu Van , Mizukami Shusaku , Hirayama Kenji , Huy Nguyen
Published: January 2018

Ginsenoside Rh1 is one of major bioactive compounds extracted from red ginseng, which has been increasingly used for enhancing cognition and physical health worldwide. The objective of this study was to review the pharmacological effects of ginsenoside Rh1 in a systematic manner. We performed searches on eight electronic databases including MEDLINE (Pubmed), Scopus, Google Scholar, POPLINE, Global Health Library, Virtual Health Library, the System for Information on Grey Literature in Europe, and the New York Academy of Medicine Grey Literature Report to select the original research publications reporting the biological and pharmacological effects of ginsenoside Rh1 from in vitro and in vivo studies regardless of publication language and study design. Upon applying the inclusion and exclusion criteria, we included a total of 57 studies for our systemic review. Ginsenoside Rh1 exhibited the potent characteristics of anti-inflammatory, antioxidant, immunomodulatory effects, and positive effects on the nervous system. The cytotoxic effects of ginsenoside Rh1 were dependent on different types of cell lines. Other pharmacological effects including estrogenic, enzymatic, anti-microorganism activities, and cardiovascular effects have been mentioned, but the results were considerably diverged. A higher quality of evidence on clinical trial studies is highly recommended to confirm the consistent efficacy of ginsenoside Rh1.
Ontogenetic changes in DNA and RNA content of laboratory-reared Prochilodus lineatus larvae: use of RNA/DNA ratios as indicators of nutritional condition
Authors: Diaz M. V. , Gómez M. I. , Sánchez S. , Fuentes C. M.
Published: January 2018

The aims of the present study were to describe the ontogenetic performance of DNA and RNA content, as well as to assess the nutritional condition of Prochilodus lineatus larvae reared under different feeding treatments. The experiment consisted of two parts, the first 6–14 days after hatching (DAH) and the second 15–21 DAH. In the first part of the experiment, larvae were kept under one of two feeding treatments: fed or starved. During the second part of the experiment, larvae were kept under one of four treatments: fed, fed until 14 DAH and later starved, starved until 14 DAH and fed later or starved. It is of note that the size and weight reached of larvae that were starved during early development and later received food were higher than those of than larvae in the other feeding treatments. In addition, instantaneous growth rates were higher and nutritional condition was better in larvae that were initially starved and fed later. The availability of food following a period of starvation seems to trigger larval metabolism and cellular division. Consequently, we recommend maintaining appropriate food provision in the aquaculture of P. lineatus larvae, especially in advanced developmental stages. We verified that RNA/DNA ratio is affected by the feeding condition and that it is sensitive enough to promptly reflect changes in feeding conditions of P. lineatus larvae. Thus, the RNA/DNA ratio could be used to assess nutritional condition of both wild and cultured P. lineatus larvae.
Performing gesture
Authors: Green E. Mara
Published: January 2018

This article focuses on a signed performance by a deaf Nepali man who communicates in natural sign, which is similar to home sign but with greater cross-signer conventionality. The signer skillfully employs pantomimic (“gestural”) and lexical (“linguistic”) repertoires for distinct pragmatic purposes. In the narrative frame, he uses pantomime to vividly enact his morning routine; in the metanarrative frame, he utilizes lexical signs to directly address the audience. By examining the two repertoires’ formal characteristics and their relationship to different frames, this analysis showcases the signer’s communicative competency, demonstrates the relevance of pragmatics and genre to studies of all signed communicative modes, and challenges the idea that gesture is what language leaves behind.
Polymorphism observed in mitochondrial genes of red flour beetle, Tribolium castaneum (Coleoptera: Tenebrionidae) of different origin in laboratory cultures
Authors: Yamauchi Hiromasa , Harada Masami , Miyanoshita Akihiro
Published: January 2018

Tribolium castaneum, a pest of stored grain, has a uniform morphology, preventing the visual identification of strains from different areas. Polymorphisms in the nucleotide sequences of the mitochondrial genes of this species were examined, and combined into seven haplotypes among the test insect specimens originating from Japan, Thailand, and Canada. These results suggested the potential for geographical differentiation.
A distance-based approach for testing the mediation effect of the human microbiome
Authors: Zhang Jie , Wei Zhi , Chen Jun
Published: January 2018

Motivation

Recent studies have revealed a complex interplay between environment, the human microbiome and health and disease. Mediation analysis of the human microbiome in these complex relationships could potentially provide insights into the role of the microbiome in the etiology of disease and, more importantly, lead to novel clinical interventions by modulating the microbiome. However, due to the high dimensionality, sparsity, non-normality and phylogenetic structure of microbiome data, none of the existing methods are suitable for testing such clinically important mediation effect.

Results

We propose a distance-based approach for testing the mediation effect of the human microbiome. In the framework, the nonlinear relationship between the human microbiome and independent/dependent variables is captured implicitly through the use of sample-wise ecological distances, and the phylogenetic tree information is conveniently incorporated by using phylogeny-based distance metrics. Multiple distance metrics are utilized to maximize the power to detect various types of mediation effect. Simulation studies demonstrate that our method has correct Type I error control, and is robust and powerful under various mediation models. Application to a real gut microbiome dataset revealed that the association between the dietary fiber intake and body mass index was mediated by the gut microbiome.

Availability and implementation

An R package ‘MedTest’ is freely available at https://github.com/jchen1981/MedTest.

Supplementary information

Supplementary data are available at Bioinformatics online.
VIPER: a web application for rapid expert review of variant calls
Authors: Wöste Marius , Dugas Martin
Published: January 2018

With the rapid development in next-generation sequencing, cost and time requirements for genomic sequencing are decreasing, enabling applications in many areas such as cancer research. Many tools have been developed to analyze genomic variation ranging from single nucleotide variants to whole chromosomal aberrations. As sequencing throughput increases, the number of variants called by such tools also grows. Often employed manual inspection of such calls is thus becoming a time-consuming procedure. We developed the Variant InsPector and Expert Rating tool (VIPER) to speed up this process by integrating the Integrative Genomics Viewer into a web application. Analysts can then quickly iterate through variants, apply filters and make decisions based on the generated images and variant metadata. VIPER was successfully employed in analyses with manual inspection of more than 10 000 calls.

Availability and implementation

VIPER is implemented in Java and Javascript and is freely available at https://github.com/MarWoes/viper.

Supplementary information

Supplementary data are available at Bioinformatics online.
Electoral Systems and Issue Polarization
Authors: Adams James F. , Rexford Nathan J.
Published: January 2018

This chapter reviews theoretical and empirical research pertaining to the question: How do electoral systems influence parties’ programmatic incentives, that is, the policy positions party elites present to the public? More specifically, it discusses whether electoral systems influence the diversity of party policy positions, measured via the degree of party system polarization. It emphasizes electoral laws’ permissiveness or proportionality, defined in terms of the relationship between parties’ national vote shares and their share of parliamentary seats. The review of theoretical arguments suggests that any effects of proportionality on polarization should be modest, a prediction supported by empirical studies that identify only weak and inconsistent relationships between proportionality and party polarization along the left–right ideological dimension.
Levinas on the Problem of Language
Authors: Large William
Published: January 2018

This chapter discusses the problem of language in Levinas’s philosophy regarding methodology. Ethics, for Levinas, happens in everyday speech, where the Other demands a response from me. How he describes this relation presents methodological problems for Levinas, because it is resistant to any kind of theoretical approach, including phenomenology. Any writing about ethics, including Levinas’s, would immediately be its betrayal. This chapter describes Levinas’s account of language in Totality and Infinity, the issues that remain there, which it highlights through Blanchot’s and Derrida’s discussion of Levinas’s work. It also outlines a different way of thinking about the alterity of Other that is suggested in Totality and Infinity but comes to the fore in Otherwise Than Being, which is not as an opposition between speech and the visible, but enunciation (the saying) and the sayable (the said).
Levinas Reading the Ancients
Authors: Staehler Tanja
Published: January 2018

This article will explore how Levinas reads the Ancients, with a special emphasis on Plato since Levinas deems Plato’s concept of the “Good beyond Being” as one of the most important ideas in Western philosophy. Aristotle, by contrast, lost us the Good beyond Being, whereas the Presocratics help to see how the Good is rooted in the elementals. Levinas’s Platonism leads to striking parallels in his treatment of Eros, art, and politics since all of these are areas of ambiguity in which the transcendence of the Good beyond Being is in certain ways undermined, yet still shines through. On Levinas’s reading, Plato shows us the significance of Ethics beyond Being, as well as the diverse ways in which the Good manifests itself in this world, in our souls and in our relations to each other.
Levinas and Education
Authors: Katz Claire Elise
Published: January 2018

“How does one become an ethical subject in the manner that Levinas describes?” This question reveals a central quandary in Levinas’s ethical project. Stated differently, the question asks if Levinas’s ethics describe a subject that is not yet. The question lies at the heart of a significant scholarly debate within scholarship on Levinas’s work. This essay examines Levinas’s writings on education considering in particular how Levinas’s ethical subject emerges. The first part of the essay focuses on Levinas’s claim that we are in a crisis of humanism, a crisis that calls for a new subjectivity. His claim and ensuing argument can be found in both his writings on Judaism and his philosophical writings.
You Are What You Eat, But Should You Eat What You Are? Modern Philosophical Dietetics
Authors: Garrett Aaron , Grey John
Published: January 2018

This chapter presents three different aspects of the moral relevance of diet. It begins with eating for virtue and considers some discussions in the sixteenth and seventeenth century of how diet impacts philosophy—either via its impact upon physical health or more directly via its impact upon spiritual well-being. Specifically, it considers two foundational figures of early modern philosophy, Michel de Montaigne and René Descartes, and then turns to Anne Conway, who unifies elements of their views along with elements of traditional theology to present an account of the spiritual significance of diet. The chapter then turns to eating virtuously, both via the moral consideration of animals in the eighteenth century and the political consequences of luxury and diet. It concludes by considering how Malthus posed a pressing problem to those who thought that an age of reason might be at hand if one just heeded the cry of nature.
The Ethical Basis for Veganism
Authors: McPherson Tristram
Published: January 2018

This chapter aims to clearly explain the current state of the ethical case for veganism, to orient readers to (some of) the relevant philosophical literature, and to focus attention on important outstanding questions on this topic. The chapter examines different variants of ethical veganism, and different types of reasons that can be used to support it. It then spells out the core argument for the wrongness of making animals suffer and die. The chapter then considers three ways of arguing from this conclusion to an ethical defense of the vegan lifestyle, which appeal respectively to the ethical significance of the effects of individual use of animal products, of group efficacy, and of complicity with wrongdoing. The chapter concludes by examining several neglected complications facing the ethical case for veganism.
Public Justification and the Politics of Agriculture
Authors: Shahar Danny
Published: January 2018

In recent years, food activists have condemned industrialized agricultural systems for contributing to pollution, environmental degradation, biodiversity loss, economic insecurity, and political inequality. On the basis of such concerns, they have advocated abandoning these systems in favor of more agrarian alternatives. Meanwhile, however, defenders of industrialized agriculture have argued that their favored techniques are needed to address major challenges to global food security. In their eyes, abandoning industrialized food systems would be catastrophic. Given the depths of these disagreements, one might question how any agricultural policy regime could hope to achieve legitimacy in the eyes of all citizens. This chapter explores the theories of Thomas Hobbes, John Rawls, and Gerald Gaus in order to show how these controversial issues can be resolved without abandoning a commitment to public justification.
Farming, the Virtues, and Agrarian Philosophy
Authors: Thompson Paul B.
Published: January 2018

Food production can be viewed as one among many activities that produce goods in modern industrial societies, with ethical issues analogous to those of other sectors of the economy. Contrarily, agriculture and farming have historically been thought to have unique influence on the nature of social institutions, the reinforcement of moral virtues, and the reproduction of cultural forms. Mainstream approaches in consequentialist and deontological ethics implicitly adopt the first perspective: the industrial philosophy of agriculture. The chapter summarizes alternative agrarian viewpoints, emphasizing the role of the household farm in the thought of Aristotle and Xenophon, as well as the special role accorded to agriculture in early modern debates on property and political economy. It concludes with the emergence of contemporary agrarian philosophies that see farming and food systems as uniquely significant for environmental ethics and sustainability.
Introduction
Authors: Barnhill Anne , Budolfson Mark , Doggett Tyler
Published: January 2018

Academic food ethics is vast, incorporating work from philosophy as well as anthropology, economics, environmental sciences and other natural sciences, geography, law, and sociology. Scholars from these fields, including some philosophers, have been producing work for decades on the food system, and on ethical, social, and policy issues connected to the food system. Yet in the last several years, there has been a notable increase in philosophical work on these issues—work that draws on multiple literatures within practical ethics, normative ethics, and political philosophy. This Handbook provides a sample of that philosophical work across multiple areas of food ethics: conventional agriculture and alternatives to it, animals, consumption, food justice, food politics, food workers, and food and identity. This Introduction provides a short history of food ethics, a brief overview of some core issues in food ethics, and an introduction to the essays in this Handbook.
Positive Institutions
Authors: Huang Peter H. , Brafford Anne M. , Austin Debra S. , Knudson Martha
Published: January 2018

We analyze how institutions in the form of organizations, laws, and policies can help foster human flourishing, and provide examples of the role that institutions can play by changing individual preferences and values. First, we analyze how to apply positive psychology to redesign law firm cultures to enable attorneys, clients, and communities to thrive. Second, we investigate how to empower law students, law professors, and other law school constituencies. Third, we demonstrate how to apply positive psychology to foster innovation, creativity, and entrepreneurship. Fourth, we identify some complexities of utilizing subjective well-being measures to evaluate the impacts of laws and policies. Finally, we develop implications from positive psychology about what governments and others can do to support individuals, communities, and societies to thrive. Our goal is to provoke discussion about positive psychology’s role in developing institutions in the form of organizations, laws, and policies that help individuals, communities, and societies.
Introduction to the Field and the Issues
Authors: Zucker Robert A. , Brown Sandra A.
Published: January 2018

This volume provides a comprehensive overview of the origins, development, and course of substance use as it emerges and unfolds in adolescence, a period where great change at genetic, neurobiological, behavioral, and social-environmental levels is taking place. The volume also provides reviews of clinical symptomatology and the multiple methods for intervention that have developed to address this major set of public health problems. This chapter provides a brief overview of these areas; it includes sections on epidemiology, similarities and differences among the different drugs of abuse, etiology and course, clinical symptomatology and comorbidity, intervention methods, and social policy. These summaries, covering multiple levels of analysis, provide a comprehensive description of a field that is still developing, but that has already achieved a substantial level of maturity.
Queer as Trad
Authors: Slominski Tes
Published: January 2018

This chapter demonstrates that studying the experiences of queer musicians and dancers is vital to understanding the relationships among music, selfhood, and social identities in Irish traditional music. By breaking the silence around LGBTQ performers of Irish traditional music through ethnographic interviews with queer musicians in the United States, this chapter addresses the paradox that non-normative participants experience musical performance as simultaneously liberatory and confining. This chapter explores musicians’ feelingful experiences of “the music itself” as an escape and examines the issues queer musicians face in gaining recognition in the Irish traditional music scene. More broadly, this chapter begins a conversation about nationalist assumptions around sexuality, gender, ethnicity, and race still implicit in the (re)production of sounds and bodily practices considered “Irish.”
Newton’s Regulae Philosophandi
Authors: Biener Zvi
Published: January 2018

Newton’s Regulae philosophandi—the rules for reasoning in natural philosophy—are maxims of causal reasoning and induction. This essay reviews their significance for Newton’s method of inquiry, as well as their application to particular propositions within the Principia. Two main claims emerge. First, the rules are not only interrelated, they defend various facets of the same core idea: that nature is simple and orderly by divine decree, and that, consequently, human beings can be justified in inferring universal causes from limited phenomena, if only fallibly. Second, the rules make substantive ontological assumptions on which Newton’s argument in the Principia relies.
Use of Viable Cryopreserved Placental Membrane as an Adjunct to Facial Keloid Resection
Authors: Gupta Rishi J. , Connelly Stephen T. , Silva Rebeka G. , Gwilliam Nat R.
Published: January 2018

Keloids are the physical manifestation of an exaggerated inflammatory response resulting in excess collagen deposition. The resulting fibroproliferative mass can be distressing for patients due to appearance, pruritus, and/or pain. Despite extensive research into the pathophysiology of keloid formation and the development of numerous treatments, keloids remain a challenge to treat. Even when the initial treatment is successful, a risk of recurrence remains. Basic science research into viable cryopreserved placental membranes and viable cryopreserved umbilical tissue has demonstrated their anti-inflammatory and anti-fibrotic effects, which may decrease keloid recurrence after excision. In this article, we present the first-reported case of viable cryopreserved placental membrane, with living mesenchymal stem cells, to treat a painful preauricular keloid in conjunction with surgical resection.
Peer review in scholarly publishing part B: how to do it?
Authors: Fowler Alexander J. , Koshy Kiron , Gundogan Buket , Agha Riaz A.
Published: January 2018

Peer review is a key part of the scientific process, whereby a body of experts review a manuscript and provide feedback. In this article, we discuss the steps typically undertaken in completing a peer review and key questions to be asked of the manuscript while undertaking a review. This article provides a step-by-step instructional guide in how to effectively peer review a paper.
Precision of Optic Nerve Head and Retinal Nerve Fiber Layer Parameter Measurements by Spectral-domain Optical Coherence Tomography
Authors: Schrems-Hoesl Laura M. , Schrems Wolfgang A. , Laemmer Robert , Kruse Friedrich E. , Mardin Christian Y.
Published: January 2018

Purpose:

The aim of this study was to assess the repeatability and reproducibility (R&R) of Bruch membrane opening based on minimum rim width (BMO-MRW), minimum rim area (BMO-MRA) and peripapillary retinal nerve fiber layer thickness (RNFLT) with the Spectralis optical coherence tomography (Heidelberg Engineering) for normal and glaucoma subjects. Precise measurement of these parameters can support detection of structural glaucomatous damage and progression.

Methods:

This cross-sectional study included 16 healthy controls and 16 patients with glaucoma. One eye was randomly selected and included in this study. Subjects underwent 1 baseline and 3 follow-up measurements, using 3 different Spectralis optical coherence tomography devices in randomized order, each operated by a single operator. Outcome measures were global and sectorial averages of BMO-MRW and BMO-MRA, and of peripapillary RNFLT obtained from 12/14/16-degree circle scans. Coefficients of variation (COV) were calculated and a mixed-effects analysis of variance was performed to compare R&R between devices.

Results:

COVs of global and sectorial BMO-MRW measurement under repeatability conditions ranged from 0.51% to 1.7% (normal, 0.62% to 1.3%; glaucoma, 0.64% to 2.3%). Respective COVs under reproducibility conditions ranged from 0.89% to 1.9% (normal, 0.77% to 2.8%; glaucoma, 1.1% to 2.6%). COVs of global and sectorial RNFLT measurements under repeatability conditions ranged from 0.5% to 2.8%. Respective COVs under reproducibility conditions ranged from 1.6% to 3.5%.

Conclusions:

For R&R, the COVs of measured parameters were by trend higher for glaucoma eyes compared with normal controls. The BMO-MRW measurement system has an excellent precision taking into account that major and minor corrections of segmentation have to be done by the examiner before evaluation.
Immune Responses to Booster Vaccination With Meningococcal ABCWY Vaccine After Primary Vaccination With Either Investigational or Licensed Vaccines
Authors: Szenborn Leszek , Block Stan L. , Jackowska Teresa , Konior Ryszard , D’Agostino Diego , Smolenov Igor , Toneatto Daniela , Welsch Jo Anne
Published: January 2018

Background:

Current meningococcal prime-boost vaccination schedules include separate vaccines for serogroups ACWY and B. An investigational combined serogroups ABCWY vaccine (MenABCWY) was developed to protect against clinically important Neisseria meningitidis serogroups.

Methods:

In this phase 2, randomized, observer-blind, extension study (NCT01272180), participants 10–25 years of age received 1 booster dose of MenABCWY vaccine at 24 months (M) postprimary series of MenABCWY (2 doses), 4CMenB (2 doses) or MenACWY-CRM vaccine (1 dose). Immune responses to booster dose (1M postbooster) and antibody persistence (24M, 36M postprimary series) were assessed using bactericidal assay with human complement (hSBA). Reactogenicity and safety were evaluated.

Results:

One hundred ninety participants were vaccinated. At 1M after the MenABCWY booster dose, seroresponse rates against serogroups ACWY ranged between 85% and 96%, 73% and 100% and 83% and 95% for participants previously receiving MenABCWY, 4CMenB and MenACWY-CRM, respectively. At 12M postbooster dose, ≥67% of participants across all groups had hSBA titers ≥8 for serogroups ACWY, except in 4CMenB-primed individuals for serogroup Y (45%). Across MenABCWY and 4CMenB-primed groups, hSBA titers ≥5 across serogroup B test strains were observed in 82%–100% and 29%–100% of participants at 1M and 12M postbooster, respectively. Geometric mean titers against serogroups ACWY increased from pre- to 1M postboosting with MenABCWY and persisted at 12M. The reactogenicity and safety profile of MenABCWY was similar to that of 4CMenB.

Conclusions:

MenABCWY may be suitable for prime-boost schedules against meningococcal disease, including regimens involving a primary series of either 4CMenB or MenACWY-CRM licensed vaccines.
Open Source Brain: a collaborative resource for visualizing, analyzing, simulating and developing standardized models of neurons and circuits
Authors: Gleeson Padraig , Cantarelli Matteo , Marin Boris , Quintana Adrian , Earnshaw Matt , Piasini Eugenio , Birgiolas Justas , Cannon Robert C. , Cayco-Gajic N. Alex , Crook Sharon , Davison Andrew P. , Dura-Bernal Salvador , Ecker András , Hines Michael L. , Idili Giovanni , Larson Stephen , Lytton William W. , Majumdar Amitava , McDougal Robert A. , Sivagnanam Subhashini , Solinas Sergio , Stanislovas Rokas , van Albada Sacha J. , van Geit Werner , Silver R. Angus
Published: January 2018

Computational models are powerful tools for investigating brain function in health and disease. However, biologically detailed neuronal and circuit models are complex and implemented in a range of specialized languages, making them inaccessible and opaque to many neuroscientists. This has limited critical evaluation of models by the scientific community and impeded their refinement and widespread adoption. To address this, we have combined advances in standardizing models, open source software development and web technologies to develop Open Source Brain, a platform for visualizing, simulating, disseminating and collaboratively developing standardized models of neurons and circuits from a range of brain regions. Model structure and parameters can be visualized and their dynamical properties explored through browser-controlled simulations, without writing code. Open Source Brain makes neural models transparent and accessible and facilitates testing, critical evaluation and refinement, thereby helping to improve the accuracy and reproducibility of models, and their dissemination to the wider community.
Population structure of theBrachypodiumspecies complex and genome wide association of agronomic traits in response to climate
Authors: Wilson Pip , Streich Jared , Murray Kevin , Eichten Steve , Cheng Riyan , Aitkin Niccy , Spokas Kurt , Warthmann Norman ,   Accession Contributors, Borevitz Justin
Published: January 2018

The development of model systems requires a detailed assessment of standing genetic variation across natural populations. TheBrachypodiumspecies complex has been promoted as a plant model for grass genomics with translational to small grain and biomass crops. To capture the genetic diversity within this species complex, thousands ofBrachypodiumaccessions from around the globe were collected and sequenced using genotyping by sequencing (GBS). Overall, 1,897 samples were classified into two diploid or allopolyploid species and then further grouped into distinct inbred genotypes. A core set of diverseB. distachyondiploid lines were selected for whole genome sequencing and high resolution phenotyping. Genome-wide association studies across simulated seasonal environments was used to identify candidate genes and pathways tied to key life history and agronomic traits under current and future climatic conditions. A total of 8, 22 and 47 QTLs were identified for flowering time, early vigour and energy traits, respectively. Overall, the results highlight the genomic structure of theBrachypodiumspecies complex and allow powerful complex trait dissection within this new grass model species.
Direct imaging of the circular chromosome in a live bacterium
Authors: Wu Fabai , Japaridze Aleksandre , Zheng Xuan , Kerssemakers Jacob W. J. , Dekker Cees
Published: January 2018

New assays for quantitative imaging1–6 and sequencing7–11 have yielded great progress towards understanding the organizational principles of chromosomes. Yet, even for the well-studied model bacterium Escherichia coli, many basic questions remain unresolved regarding chromosomal (sub-)structure2,11, its mechanics1,2,12 and dynamics13,14, and the link between structure and function1,15,16. Here we resolve the spatial organization of the circular chromosome of bacteria by directly imaging the chromosome in live E. coli cells with a broadened cell shape. The chromosome was observed to exhibit a torus topology with a 4.2 μm toroidal length and 0.4 μm bundle thickness. On average, the DNA density along the chromosome shows dense right and left arms that branch from a lower-density origin of replication, and are connected at the terminus of replication by an ultrathin flexible string of DNA. At the single-cell level, the DNA density along the torus is found to be strikingly heterogeneous, with blob-like Mbp-size domains that undergo major dynamic rearrangements, splitting and merging at a minute timescale. We show that prominent domain boundaries at the terminus and origin of replication are induced by MatP proteins, while weaker transient domain boundaries are facilitated by the global transcription regulators HU and Fis. These findings provide an architectural basis for the understanding of the spatial organization of bacterial genomes.
Widespread and targeted gene expression by systemic AAV vectors: Production, purification, and administration
Authors: Challis Rosemary C , Kumar Sripriya Ravindra , Chan Ken Y , Challis Collin , Jang Min J , Rajendran Pradeep S , Tompkins John D , Shivkumar Kalyanam , Deverman Benjamin E , Gradinaru Viviana
Published: January 2018

We recently developed novel AAV capsids for efficient and noninvasive gene transfer across the central and peripheral nervous systems. In this protocol, we describe how to produce and systemically administer AAV-PHP viruses to label and/or genetically manipulate cells in the mouse nervous system and organs including the heart. The procedure comprises three separate stages: AAV production, intravenous delivery, and evaluation of transgene expression. The protocol spans eight days, excluding the time required to assess gene expression, and can be readily adopted by laboratories with standard molecular and cell culture capabilities. We provide guidelines for experimental design and choosing the capsid, cargo, and viral dose appropriate for the experimental aims. The procedures outlined here are adaptable to diverse biomedical applications, from anatomical and functional mapping to gene expression, silencing, and editing.
Development and worldwide use of a non-lethal and minimal population-level impact protocols for the isolation of chytrids from amphibians
Authors: Fisher Matthew C. , Ghosh Pria , Shelton Jennifer M. G. , Bates Kieran , Brookes Lola , Wierzbicki Claudia , Rosa Gonçalo M. , Farrer Rhys A. , Aanensen David M. , Alvarado-Rybak Mario , Bataille Arnaud , Berger Lee , Böll Susanne , Bosch Jaime , Clare France C. , Courtois Elodie , Crottini Angelica , Cunningham Andrew A. , Doherty-Bone Thomas M. , Gebresenbet Fikirte , Gower David J. , Höglund Jacob , James Timothy Y. , Jenkinson Thomas S. , Kosch Tiffany A. , Lambertini Carolina , Laurila Anssi , Lin Chun-Fu , Loyau Adeline , Martel An , Meurling Sara , Miaud Claude , Minting Pete , Ndriantsoa Serge , Pasmans Frank , Rakotonanahary Tsanta , Rabemananjara Falitiana C. E. , Ribeiro Luisa P. , Schmeller Dirk S. , Schmidt Benedikt R. , Skerratt Lee , Smith Freya , Soto-Azat Claudio , Tessa Giulia , Toledo Luís Felipe , Valenzuela-Sánchez Andrés , Verster Ruhan , Vörös Judit , Waldman Bruce , Webb Rebecca J. , Weldon Che , Wombwell Emma , Zamudio Kelly R. , Longcore Joyce E. , Garner Trenton W.J.
Published: January 2018

Parasitic chytrid fungi have emerged as a significant threat to amphibian species worldwide, necessitating the development of techniques to isolate these pathogens into sterile culture for research purposes. However, early methods of isolating chytrids from their hosts relied on killing amphibians. We modified a pre-existing protocol for isolating chytrids from infected animals to use toe clips and biopsies from toe webbing rather than euthanizing hosts, and distributed the protocol to interested researchers worldwide as part of the BiodivERsA project RACE – here called the RML protocol. In tandem, we developed a lethal procedure for isolating chytrids from tadpole mouthparts. Reviewing a database of use a decade after their inception, we find that these methods have been widely applied across at least 5 continents, 23 countries and in 62 amphibian species, and have been successfully used to isolate chytrids in remote field locations. Isolation of chytrids by the non-lethal RML protocol occured in 18% of attempts with 207 fungal isolates and three species of chytrid being recovered. Isolation of chytrids from tadpoles occured in 43% of attempts with 334 fungal isolates of one species (Batrachochytrium dendrobatidis) being recovered. Together, these methods have resulted in a significant reduction and refinement of our use of threatened amphibian species and have improved our ability to work with this important group of emerging fungal pathogens.
Task-Related EEG Source Localization via Graph Regularized Low-Rank Representation Model
Authors: Liu Feng , Rosenberger Jay , Qin Jing , Lou Yifei , Wang Shouyi
Published: January 2018

To infer brain source activation patterns under different cognitive tasks is an integral step to understand how our brain works. Traditional electroencephalogram (EEG) Source Imaging (ESI) methods usually do not distinguish task-related and spurious non-task-related sources that jointly generate EEG signals, which inevitably yield misleading reconstructed activation patterns. In this research, we argue that the task-related source signal intrinsically has a low-rank property, which is exploited to to infer the true task-related EEG sources location. Although the true task-related source signal is sparse and low-rank, the contribution of spurious sources scattering over the source space with intermittent activation patterns makes the actual source space lose the low-rank property. To reconstruct a low-rank true source, we propose a novel ESI model that involves a spatial low-rank representation and a temporal Laplacian graph regularization, the latter of which guarantees the temporal smoothness of the source signal and eliminate the spurious ones. To solve the proposed model, an augmented Lagrangian objective function is formulated and an algorithm in the framework of alternating direction method of multipliers is proposed. Numerical results illustrate the effectiveness of the proposed method in terms of reconstruction accuracy with high effciency.
Reducing False Positives in CRISPR/Cas9 Screens from Copy Number Variations
Authors: Wu Alexander , Xiao Tengfei , Fei Teng , Shirley Liu X. , Li Wei
Published: January 2018

CRISPR/Cas9 knockout screens have been widely used to interrogate gene functions across a wide range of cell systems. However, the screening outcome is biased in amplified genomic regions, due to the ability of the Cas9 nuclease to induce multiple double-stranded breaks and strong DNA damage responses at these regions. We developed algorithms to correct biases associated with copy number variations (CNV), even when the CNV profiles are unknown. We demonstrated that our methods effectively reduced false positives in amplified regions while preserving signals of true positives. In addition, we developed a sliding window approach to estimate regions of high copy numbers for cases in which CNV information is not available. These copy number estimations can subsequently be used to effectively correct CNV-related biases in CRISPR screening experiments. Our approach is integrated into the existing MAGeCK/MAGeCK-VISPR analysis pipelines and provides a convenient framework to improve the precision of CRISPR screening results.
Crystal structure of 4-(pyrazin-2-yl)morpholine
Authors: Bandaru Siva Sankar Murthy , Kapdi Anant Ramakant , Schulzke Carola
Published: January 2018

The molecular structure of the title compound, C8H11N3O, is nearly planar despite the chair conformation of the morpholine moiety. In the crystal, the molecules form sheets parallel to the b axis, which are supported by non-classical hydrogen-bonding interactions between C—H functionalities and the O atom of morpholine and the 4-N atom of pyrazine, respectively. The title compound crystallizes in the monoclinic space group P21/c with four molecules in the unit cell.
Crystal structure of catena-poly[[[dichloridocopper(II)]-{μ-tert-butyl N-methyl-N-[4-(6-{[4-(pyridin-2-yl-κN)-1H-1,2,3-triazol-1-yl-κN
3]methyl}-1,3-benzothiazol-2-yl)phenyl]carbamato}] acetonitrile monosolvate]
Authors: Pocinho Alexandre , Duhayon Carine , Gras Emmanuel , Hureau Christelle
Published: January 2018

In the title coordination polymer, {[CuCl2(C27H26N6O2S)]·CH3CN}
n
, the copper(II) ion is fivefold coordinated, with an almost perfect square-pyramidal coordination sphere. In the equatorial plane, it is ligated to a pyridine N atom and an N atom of the triazole unit and to two Cl− ions, while the apical position is occupied by the carbonyl O atom of the tert-butyl carbamate group. In the crystal, the polymer chains propagate in the [11-1] direction, with the acetonitrile solvent molecules linked to the chain by C—H...N hydrogen bonds. The chains are linked by C—H...Cl hydrogen bonds forming sheets parallel to the plane (011). The crystal packing is further consolidated by C—H...π interactions and offset π–π stacking interactions [intercentroid distance = 3.6805 (15) Å], forming a three-dimensional supramolecular structure.
3,5-Dibromobenzonitrile
Authors: Noland Wayland E. , Tritch Kenneth J.
Published: January 2018

Molecules of the title compound (I), C7H3Br2N, lie on a crystallographic mirror plane that bisects the benzene ring and the cyano group. In the crystal, no C[triple-bond]N...Br or Br...Br short contacts are observed. Head-to-tail C(7) chains form based on weak hydrogen bonding between the the para H atom and the cyano N atom. Although molecules of (I) pack differently than 3,5-difluorobenzonitrile, both compounds have similarly distorted benzene rings. For (I), the endocyclic bond angles are 121.16 (16)° and 117.78 (16)° about the ipso and para C atoms, respectively.
Warfare, atrocities, and political participation: eastern Africa
Authors: Ember Carol R. , Jones Eric C. , Skoggard Ian , Adem Teferi Abate
Published: January 2018

Purpose

Ember et al. (1992) addressed whether the “democracies rarely fight each other” hypothesis held true in the anthropological record of societies of various sizes and scales around the world. They indeed found that more participatory polities had less internal warfare – or warfare between one society’s territorial units (e.g. bands, villages, districts). The purpose of this paper is to examine when political participation would have similar effects in eastern Africa, and whether more participatory polities commit fewer atrocities against each other.

Design/methodology/approach

A cross-cultural sample of 46 societies from eastern Africa was used to retest the original Ember et al. (1992) multiple regression model and revised post-hoc models. The team read ethnographies to code for levels of political participation at the local and multilocal levels. Other variables came from previous research including warfare and atrocity variables (Ember et al., 2013).

Findings

The Ember et al. (1992) model did not replicate in eastern Africa, but analysis with additional variables (degree of formal leadership, presence of state-level organization, and threat of natural disasters that destroy food supplies) suggested that greater local political participation does predict less internal warfare. Also, more participatory polities were less likely to commit atrocities in the course of internal warfare.

Originality/value

This study demonstrates regional comparisons are important because they help us evaluate the generalizability of worldwide findings. Additionally, adding atrocities to the study of democracy and warfare is new and suggests reduced atrocities as an additional benefit of political participation.
Co-production in integrated health and social care programmes: a pragmatic model
Authors: Kaehne Axel , Beacham Andrea , Feather Julie
Published: January 2018

Purpose

The purpose of this paper is to outline the current thinking on co-production in health and social care, examine the challenges in implementing genuine co-production and argue for a pragmatic version of co-production that may assist programme managers in deciding which type of co-production is most suitable for which programme.

Design/methodology/approach

A discussion paper based on the professional and academic knowledge and insights of the authors. A focus group interview schedule was used to guide discussions between authors.

Findings

The authors argue for a pragmatic approach to co-production within integrated care programmes. The authors set out the basic parameters of such an approach containing procedural rather than substantive standards for co-production activities leaving sufficient room for specific manifestations of the practice in particular contexts.

Practical implications

The authors put forward a pragmatic model of co-production that defines the essential elements of a process for ensuring services are designed to meet with the needs of patients yet allowing the process itself to be adapted to different circumstances.

Originality/value

The paper summarises the discussion on co-production in relation to integration programmes. It formulates a pragmatic model of co-production that may assist programme managers in establishing good practice co-production frameworks when designing or implementing integrated health and social care services.
Adult attachment and perceived parental style may shape leadership behaviors
Authors: Eldad Rom , Benatov Joy
Published: January 2018

Purpose

The purpose of this paper is to examine the role of both attachment and parental styles in shaping leadership behavioral patterns. Research predictions were that childhood perceived parental experiences will be associated with attachment style, and that both perceived parental and attachment styles will fulfill a significant role in shaping the individual’s leadership orientation in adulthood.

Design/methodology/approach

The authors tested the research hypotheses with a field survey data from 90 supervisors belonging to diverse industrial and service organizations. During their attendance in a leadership seminar, the managers’ attachment style was assessed using the Experiences in Close Relationship Inventory. They were also asked to report on their childhood experiences using the Parenting Style Index, and to answer questions regarding their leadership behavior, using a short version of the Multifactor Leadership Questionnaire.

Findings

Results indicated associations between parental style, attachment style, and leadership. Specifically, parental autonomy granting was negatively associated with both attachment anxiety and avoidance. Both transformational and transactional leadership styles were positively associated with parental autonomy, but only transformational leadership was also positively associated with parental involvement. In addition, transactional leadership was positively associated with attachment avoidance in close relationships.

Research limitations/implications

Testing the contributions of perceived parental style in childhood and attachment style in adulthood to the manager’s manifested leadership style helps to advance our theoretical understanding of important leadership antecedents. The findings may also help practitioners in developing leadership skills and assisting managers in finding ways to moderate their natural tendencies and better depend on, delegate, and empower subordinates.

Originality/value

This empirical study provides evidence of the important role of perceived parental style in the development of adult attachment and leadership styles. The effects found in the study also extend the existing findings by showing that not only the attachment style but also parental style play a significant role in shaping the individual’s leadership behaviors.
Future of research published in the International Journal of Selection and Assessment: Incoming editor's perspective
Authors: Dilchert Stephan
Published: January 2018

The International Journal of Selection and Assessment (IJSA) plays an important role for the scientist‐practitioner communities in the fields of personnel psychology, human resource management, and industrial‐organizational psychology. This article briefly summarizes goals of the journal and a vision for future work to be published in IJSA.
Wrench Capability of a Stewart Platform With Series Elastic Actuators
Authors: Ophaswongse Chawin , Murray Rosemarie C. , Agrawal Sunil K.
Published: January 2018

This paper proposes a novel method for analyzing linear series elastic actuators (SEAs) in a parallel-actuated Stewart platform, which has full six degrees-of-freedom (DOF) in position and orientation. SEAs can potentially provide a better human–machine interface for the user. However, in the study of parallel-actuated systems with full 6DOF, the effect of compliance in series with actuators has not been adequately studied from the perspective of wrench capabilities. We found that some parameters of the springs and the stroke lengths of the linear actuators play a major role in the actuation limits of the system. This is an important consideration when adding SEAs into a Stewart platform or other parallel-actuated robots to improve their human usage.