bluuebunny/crossref_metadata_2025_split huggingface dataset:
Large scale chromosome folding is stable against local changes in chromatin structure
Authors: Florescu Ana-Maria , Therizols Pierre , Rosa Angelo 
Published: May 2016

AbstractCharacterizing the link between small-scale chromatin structure and large-scale chromosome folding during interphase is a prerequisite for understanding transcription. Yet, this link remains poorly investigated. Here, we introduce a simple biophysical model where interphase chromosomes are described in terms of the folding of chromatin sequences composed of alternating blocks of fibers with different thicknesses and flexibilities, and we use it to study the influence of sequence disorder on chromosome behaviors in space and time. By employing extensive computer simulations,we thus demonstrate that chromosomes undergo noticeable conformational changes only on length-scales smaller than 105basepairs and time-scales shorter than a few seconds, and we suggest there might exist effective upper bounds to the detection of chromosome reorganization in eukaryotes. We prove the relevance of our framework by modeling recent experimental FISH data on murine chromosomes.Author SummaryA key determining factor in many important cellular processes as DNA transcription, for instance, the specific composition of the chromatin fiber sequence has a major influence on chromosome folding during interphase. Yet, how this is achieved in detail remains largely elusive. In this work, we explore this link by means of a novel quantitative computational polymer model for interphase chromosomes where the associated chromatin filaments are composed of mixtures of fibers with heterogeneous physical properties. Our work suggests a scenario where chromosomes undergo only limited reorganization, namely on length-scales below 105basepairs and time-scales shorter than a few seconds. Our conclusions are supported by recent FISH data on murine chromosomes.
Vascular Cell Induction Culture System Using Arabidopsis Leaves (VISUAL) Reveals the Sequential Differentiation of Sieve Element-Like Cells
Authors: Kondo Yuki , Nurani Alif Meem , Saito Chieko , Ichihashi Yasunori , Saito Masato , Yamazaki Kyoko , Mitsuda Nobutaka , Ohme-Takagi Masaru , Fukuda Hiroo 
Published: May 2016

Abstract
Cell differentiation is a complex process involving multiple steps, from initial cell fate specification to final differentiation. Procambial/cambial cells, which act as vascular stem cells, differentiate into both xylem and phloem cells during vascular development. Recent studies have identified regulatory cascades for xylem differentiation. However, the molecular mechanism underlying phloem differentiation is largely unexplored due to technical challenges. Here, we established an ectopic induction system for phloem differentiation named Vascular Cell Induction Culture System Using Arabidopsis Leaves (VISUAL). Our results verified similarities between VISUAL-induced Arabidopsis thaliana phloem cells and in vivo sieve elements. We performed network analysis using transcriptome data with VISUAL to dissect the processes underlying phloem differentiation, eventually identifying a factor involved in the regulation of the master transcription factor gene APL. Thus, our culture system opens up new avenues not only for genetic studies of phloem differentiation, but also for future investigations of multidirectional differentiation from vascular stem cells.
Examining the effects of doing business on Iran and MENA countries’ economic growth
Authors: Mehrabani Fatemeh , Basirat Mehdi , Abdollahi Fereshte 
Published: May 2016

Purpose
The purposes of this paper are: reviewing economic growth in Iran, investigating and comparing Iran doing business (DB) with those of Middle East and North Africa (MENA) countries and evaluating the relation between DB and economic growth for a selected sample during 2006-2012.

Design/methodology/approach
The paper uses the panel data model and takes a comparative approach.

Findings
The main findings of our investigation are: first, economic growth in Iran has decreased in recent years due the lack of proper business environment. Second, studying Iran DB indicators and comparing them with those of the MENA countries show that they are low and Iran’s ranking is undesirable. Third, the results show a robust support for the claim that the improvement in DB indicators will lead to an increase in economic growth.

Researchlimitations/implications
MENA countries’ experience shows that they are promoting their economic growth by improving their business environment, so the key element for increasing Iran’ economic growth is by improving the business environment.

Originality/value
This study contributes to the literature in at least two aspects. First is the comparative analysis of Iran’s DB with MENA countries, and second is considering the effect of DB on Iran’s and selected countries’ economic growth.
Does a retailer’s charisma matter? A study of frontline employee perceptions of charisma in the retail setting
Authors: Lindblom Arto , Kajalo Sami , Mitronen Lasse 
Published: May 2016

PurposeIn today’s retail environment, retailers’ leadership skills can make the difference between the success and failure of their retail stores. Despite the acknowledgment that retailers’ leadership skills and behaviour are important, treatment of the topic within the retail marketing and management literatures is still very limited. Against this backdrop, this paper aims to focus on the relationship between the retailers’ charismatic leadership and frontline employee outcomes.Design/methodology/approachFor the purpose of this study, the authors develop hypotheses about the influence of the retailers’ charismatic leadership on frontline employee job satisfaction, self-efficacy, organizational identification and turnover intentions. Using structural equation modelling, hypotheses are tested using a sample of 208 frontline employees from the Finnish retail industry.FindingsAs a first main contribution, the findings of this study indicate that charismatic leadership has a very strong positive impact on job satisfaction. As a second contribution, this study shows that there is strong positive link between charismatic leadership and the self-efficacy of frontline employees. As a third contribution, this study indicates that charismatic leadership is positively related to organizational identification. And finally, this study indicates that charismatic leadership has a very strong negative impact on employee turnover intentions.Originality/valueThis study contributes to retail management and services marketing literature by broadening the current understanding of the leadership behaviour of retailers and its effectiveness and demonstrating how frontline employees respond to charismatic leadership in the retail setting.
Foregrounding Justice in Nuclear Disarmament: A Practitioner Commentary
Authors: Acheson Ray 
Published: May 2016

AbstractInjustice and inequity are fundamental to the possession of nuclear weapons. But these concepts have not been at the forefront of mainstream discourse surrounding these weapons, which has instead focused on concepts of ‘deterrence’, ‘strategic stability’, and ‘national security’. The Humanitarian Initiative (see the introductory essay in this Special Section for background) recaptures ground in terms of how nuclear weapons are discussed and perceived internationally. The reemergence of a focus on the physical effects of a nuclear weapon detonation has initiated a process of stigmatising these weapons. But this changing discourse, in order to effectively lead to the elimination of nuclear weapons, also requires the recognition that nuclear weapons represent an elite threat of terror and perpetuate inequity between countries, with broader implications for humanity. Arguments about injustice help unmask additional aspects of the unacceptability of nuclear weapons. Within this broader critique, gender analysis is crucial, helping to illuminate and challenge structures of power that sustain nuclear weapons. This is not a theoretical exercise. It has practical implications for pursuing the prohibition and elimination of nuclear weapons. A gender perspective challenges governments and people to act on moral, ethical, humanitarian, legal, political, and economic grounds without waiting for those benefiting from the status quo.
Systematic review with meta‐analysis: the effect of tobacco smoking on the natural history of ulcerative colitis
Authors: To N. , Ford A. C. , Gracie D. J. 
Published: May 2016

SummaryBackgroundTobacco smoking is associated with a reduced risk of developing ulcerative colitis (UC). A high proportion of UC patients perceive a benefit in disease outcomes secondary to smoking. However, the effects of smoking on the natural history of UC are uncertain.AimTo conduct a systematic review and meta‐analysis of the effects of tobacco smoking on the natural history of UC.MethodsA search of MEDLINE, EMBASE and EMBASE classic was carried out (up to December 2015) to identify observational studies reporting data on smoking and rates of colectomy, flare of disease activity, proximal disease extension, and development of pouchitis following panproctocolectomy and ileal pouch‐anal anastomosis in patients with UC. Dichotomous data were pooled to obtain odds ratios (ORs), with 95% confidence intervals (CIs).ResultsThe search identified 16 eligible studies: five (2615 patients) studying colectomy; four (620 patients) reporting on flare of disease activity; four (687 patients) examining proximal disease extension and three (355 patients) assessing development of pouchitis. Compared with nonsmokers, the odds of colectomy (OR = 0.89; 95% CI 0.62–1.26), flare of disease activity (OR = 1.26; 95% CI 0.65–2.44), proximal extension of disease (OR = 0.57; 95% CI 0.20–1.66) or the development of pouchitis (OR = 0.57; 95% CI 0.21–1.53) were not significantly lower in smokers.ConclusionsSmoking may not improve the natural history of ulcerative colitis. Given the health benefits of smoking cessation and the lack of clear benefit in ulcerative colitis, smoking cessation advice should be incorporated into guidance on the management of ulcerative colitis.
Cell surface glycans in the human stratum corneum: distribution and depth‐related changes
Authors: Abdayem Rawad , Formanek Florian , Minondo Anne Marie , Potter Anne , Haftek Marek 
Published: May 2016

AbstractDuring the formation of the stratum corneum (SC) barrier, the extracellular spaces of viable epidermis, rich in glycans, are filled with a highly organized lipid matrix and the plasma membranes of keratinocytes are replaced by cornified lipid envelopes. These structures comprise cross‐linked proteins, including transmembrane glycoproteins and proteoglycans, covalently bound to a monolayer of cell surface ceramides. Little is known about the presence and distribution of glycans on the SC corneocytes despite their possible involvement in SC hydration, cohesion and desquamation. In this work, we visualized ultrastructurally and quantified the distribution of glycans on the surface of native and delipidated corneocytes. The cells were harvested at different depths of the SC, allowing us to define the relationship between the distribution of various glycans, proteoglycans and glycoproteins, and other changes occurring in SC. At the cell periphery, we found a correlation between the depth‐related alterations of corneodesmosome glycoproteins and α‐d‐mannosyl and N‐acetyl‐d‐glucosamine‐labelling patterns. Elimination of the terminal sugars, α‐linked fucose and α‐(2,3) linked sialic acid, was less abrupt, but also the initial extent of their peripheral distribution was overall lower than that of concanavalin A and wheat germ agglutinin lectin‐detected glycans. Diffuse labelling of heparan sulphate glycosaminoglycans disappeared completely from the outermost corneocytes, whereas that of several simple carbohydrates could be detected at all SC levels. Our results suggest that specific glycan distribution may participate in the progressive changes of SC, as it evolves from the SC compactum to the SC disjunctum, towards desquamation.
Feeding behavior in freshwater bryozoans: function, form, and flow
Authors: Tamberg Yuta , Shunatova Natalia 
Published: May 2016

AbstractBryozoans are impressively active suspension feeders, with diverse feeding behaviors. These have been studied extensively in marine bryozoans, but less so in their freshwater counterparts. Here we identified 16 distinct behaviors in three phylactolaemate species and classified them into behaviors involving separate tentacles, groups of tentacles, lophophore arms, the introvert, or multiple zooids. We examined (1) the repertoire of behaviors in each species, and each behavior's (2) absolute frequency, (3) relative frequency and (4) duration in each of the three species, at two flow velocities (0 and 0.2 cm s−1). Nine feeding behaviors were shared by all three species, but the occurrence of other behaviors in a given species was limited by its morphology. Behaviors involved in particle capture were the most frequent, and were often faster than the reactions involved in particle rejection. By contrast, the absolute frequency of behaviors varied widely among species without clear associations with species form, or function of the behavior. Flow velocity had only minor effects on the feeding behaviors exhibited by a species, or their frequencies or durations. Our results show that phylactolaemates have the same key feeding behaviors of the individual polypides (especially involving separate tentacles) as previously described in gymnolaemate and stenolaemate bryozoans, although their behaviors tend to be carried out more slowly than those of stenolaemates or gymnolaemates. Feeding behaviors involving multiple zooids were nearly absent in the studied phylactolaemates, but are common in gymnolaemates. Freshwater bryozoans appear to be intermediate between stenolaemate and gymnolaemate bryozoans in terms of richness of the repertoire of feeding behaviors.
Can Robert Adams Survive Moral Twin Earth?
Authors: Taylor Luke 
Published: May 2016

AbstractRichard Boyd and Robert Adams have both developed semantic accounts of moral terms based on Hilary Putnam's causal regulation theory for natural kind terms, according to which the terms in question refer to the properties which predominantly causally regulated the terms. However, Terence Horgan and Mark Timmons have mounted an objection to Boyd's semantics—their Moral Twin Earth argument. If this argument is successful against Boyd then it might be thought that it should also be successful against Adams, given the similarity between their semantic accounts. I will argue in this essay that Adams's semantics is sufficiently different from Boyd's to enable him to survive Moral Twin Earth, but that he is vulnerable to a modified version of Moral Twin Earth that I describe.
Law, Ethics, and the Needs of History: Mendelssohn, Krochmal, and Moral Philosophy
Authors: Sacks Elias 
Published: May 2016

AbstractAlthough the role of ethics in modern Jewish thought has been widely explored, major works by foundational philosophers remain largely absent from such discussions. This essay contributes to the recovery of these voices, focusing on the Hebrew writings of Moses Mendelssohn (1729–1786) and Nachman Krochmal (1785–1840). I argue that these texts reveal the existence of a shared ethical project animating these founding philosophical voices of Jewish modernity, and that reconstructing their claims contributes to broader conversations about the relationship between ethics and law. Mendelssohn and Krochmal present Jewish law as addressing needs emerging from the history of moral philosophy—from the modern histories of Platonic and Aristotelian ethics. Moreover, my reading highlights these thinkers’ ongoing relevance, suggesting that their work illuminates the role of law in ethical cultivation.
Sebacinales – one thousand and one interactions with land plants
Authors: Weiß Michael , Waller Frank , Zuccaro Alga , Selosse Marc‐André 
Published: May 2016

SummaryRoot endophytism and mycorrhizal associations are complex derived traits in fungi that shape plant physiology. Sebacinales (Agaricomycetes, Basidiomycota) display highly diverse interactions with plants. Although early‐diverging Sebacinales lineages are root endophytes and/or have saprotrophic abilities, several more derived clades harbour obligate biotrophs forming mycorrhizal associations. Sebacinales thus display transitions from saprotrophy to endophytism and to mycorrhizal nutrition within one fungal order. This review discusses the genomic traits possibly associated with these transitions. We also show how molecular ecology revealed the hyperdiversity of Sebacinales and their evolutionary diversification into two sister families: Sebacinaceae encompasses mainly ectomycorrhizal and early‐diverging saprotrophic species; the second family includes endophytes and lineages that repeatedly evolved ericoid, orchid and ectomycorrhizal abilities. We propose the name Serendipitaceae for this family and, within it, we transfer to the genus Serendipita the endophytic cultivable species Piriformospora indica and P. williamsii. Such cultivable Serendipitaceae species provide excellent models for root endophytism, especially because of available genomes, genetic tractability, and broad host plant range including important crop plants and the model plant Arabidopsis thaliana. We review insights gained with endophytic Serendipitaceae species into the molecular mechanisms of endophytism and of beneficial effects on host plants, including enhanced resistance to abiotic and pathogen stress.

Contents

Summary
20

I.
Introduction
21

II.
Phylogeny and systematics of Sebacinales
21

III.
Ecology and diversity of Sebacinales interactions with plants
23

IV.
Endophytism in Serendipitaceae: changing phenotype of the host plants
29

V.
Endophytism in Serendipitaceae: a fungal adaptation to biotrophy
33

VI.
Conclusion and future directions
35

Acknowledgements
36

Author contributions
36

References
36
Immunoglobulin M for Acute Infection: True or False?
Authors: Landry Marie Louise 
Published: May 2016

ABSTRACT
Immunoglobulin M (IgM) tests have clear clinical utility but also suffer disproportionately from false-positive results, which in turn can lead to misdiagnoses, inappropriate therapy, and premature closure of a diagnostic workup. Despite numerous reports in the literature, many clinicians and laboratorians remain unaware of this issue. In this brief review, a series of virology case examples is presented. However, a false-positive IgM can occur with any pathogen. Thus, when an accurate diagnosis is essential for therapy, prognosis, infection control, or public health, when the patient is sick enough to be hospitalized, or when the clinical or epidemiologic findings do not fit, IgM detection should not be accepted as a stand-alone test. Rather, whenever possible, the diagnosis should be confirmed by other means, including testing of serial samples and the application of additional test methods.
A New Genomics-Driven Taxonomy of Bacteria and Archaea: Are We There Yet?
Authors: Garrity George M. 
Published: May 2016

ABSTRACT
Taxonomy is often criticized for being too conservative and too slow and having limited relevance because it has not taken into consideration the latest methods and findings. Yet the cumulative work product of its practitioners underpins contemporary microbiology and serves as a principal means of shaping and referencing knowledge. Using methods drawn from the field of exploratory data analysis, this minireview examines the current state of the field as it transitions from a taxonomy based on 16S rRNA gene sequences to one based on whole-genome sequences and tests the validity of some commonly held beliefs.
Multicenter Evaluation of Meridian Bioscience HSV 1&2 Molecular Assay for Detection of Herpes Simplex Virus 1 and 2 from Clinical Cutaneous and Mucocutaneous Specimens
Authors: Faron Matthew L. , Ledeboer Nathan A. , Patel Anami , Beqa Safedin H. , Yen-Lieberman Belinda , Kohn Debra , Leber Amy L. , Mayne Donna , Northern William I. , Buchan Blake W. 
Published: May 2016

ABSTRACT

Herpes simplex virus (HSV) causes acute and relapsing symptoms characterized by ulcerative lesions. Laboratory diagnosis of HSV in cutaneous or mucocutaneous lesions has historically been performed with the use of viral cell culture systems; however, these tests are laborious and suffer decreased sensitivity for advanced-stage lesions. The recent availability of FDA-cleared moderately complex assays has resulted in the increased use of molecular diagnostics for the routine detection of HSV in superficial swab specimens. We performed a clinical evaluation of the recently FDA-cleared
illumi
gene HSV 1&2 loop-mediated isothermal amplification (LAMP) assay (Meridian Bioscience, Cincinnati OH) for the detection and differentiation of HSV-1 and HSV-2 in cutaneous and mucocutaneous swab specimens. A total of 1,153 clinical swab specimens were collected and tested at 7 different clinical centers. Each specimen was tested for the presence of HSV-1 and HSV-2 using the
illumi
gene assay, and results were compared to those of the enzyme-linked virus-inducible system (ELVIS) as the reference method. Overall, the
illumi
gene assay demonstrated a sensitivity and specificity of 94.8% and 95.5%, respectively, for the detection of HSV-1. Detection of HSV-2 was similar, with a sensitivity of 98.9% and a specificity of 95.5%. Discrepant analysis was performed using an alternative molecular test (AmpliVue HSV1+2 assay; Quidel Molecular, San Diego, CA) on 91/99 specimens that were recorded as false positive (FP) or false negative (FN) compared to the reference method. In total, 57/78 (73%) FP and 9/13 (69%) FN
illumi
gene results were supported by the AmpliVue result. The
illumi
gene HSV 1&2 assay demonstrated high sensitivity and specificity to detect and differentiate HSV in clinical specimens and identified 57 additional specimens that were positive for HSV compared to culture. The use of LAMP eliminates the need for the cycling of temperatures and provides results in less than 60 min, with approximately 2 min of hands-on time per specimen.
Treponema pallidum Strain Types and Association with Macrolide Resistance in Sydney, Australia: New TP0548 Gene Types Identified
Authors: Read Phillip , Tagg Kaitlin A. , Jeoffreys Neisha , Guy Rebecca J. , Gilbert Gwendolyn L. , Donovan Basil 
Published: May 2016

ABSTRACT

Strain typing of
Treponema pallidum
, using the three-target enhanced classification scheme, was performed with 191 samples obtained between 2004 and 2011 in Sydney, Australia. The most common strain type was 14d/g (92/191 samples [48%]). Two new TP0548 gene types were detected (m and n). Strain type was associated with macrolide resistance and possible acquisition outside Australia.