bluuebunny/crossref_metadata_2025_split huggingface dataset:
ABA control of plant macroelement membrane transport systems in response to water deficit and high salinity
Authors: Osakabe Yuriko , Yamaguchi‐Shinozaki Kazuko , Shinozaki Kazuo , Tran Lam‐Son Phan 
Published: November 2013

SummaryPlant growth and productivity are adversely affected by various abiotic stressors and plants develop a wide range of adaptive mechanisms to cope with these adverse conditions, including adjustment of growth and development brought about by changes in stomatal activity. Membrane ion transport systems are involved in the maintenance of cellular homeostasis during exposure to stress and ion transport activity is regulated by phosphorylation/dephosphorylation networks that respond to stress conditions. The phytohormone abscisic acid (ABA), which is produced rapidly in response to drought and salinity stress, plays a critical role in the regulation of stress responses and induces a series of signaling cascades. ABA signaling involves an ABA receptor complex, consisting of an ABA receptor family, phosphatases and kinases: these proteins play a central role in regulating a variety of diverse responses to drought stress, including the activities of membrane‐localized factors, such as ion transporters. In this review, recent research on signal transduction networks that regulate the function ofmembrane transport systems in response to stress, especially water deficit and high salinity, is summarized and discussed. The signal transduction networks covered in this review have central roles in mitigating the effect of stress by maintaining plant homeostasis through the control of membrane transport systems.

Contents

Summary
35

I.
Introduction
35

II.
Water deficit stress stimulates ABA biosynthesis and transport
36

III.
ABA signal transductions control ion transport for modulating stomatal aperture
39

IV.
The involvement of ion transport systems in the maintenance of ion homeostasis during abiotic stress
42

V.
Conclusion
44

Acknowledgements
44

References
45
Highly rearranged and size‐variable chloroplast genomes in conifers II clade (cupressophytes): evolution towards shorter intergenic spacers
Authors: Wu Chung‐Shien , Chaw Shu‐Miaw 
Published: November 2013

SummaryAlthough conifers are of immense ecological and economic value, bioengineering of their chloroplasts remains undeveloped. Understanding the chloroplast genomic organization of conifers can facilitate their bioengineering. Members of the conifer II clade (or cupressophytes) are highly diverse in both morphologic features and chloroplast genomic organization. We compared six cupressophyte chloroplast genomes (cpDNAs) that represent four of the five cupressophyte families, including three genomes that are first reported here (Agathis dammara, Calocedrus formosana and Nageia nagi). The six cupressophyte cpDNAs have lost a pair of large inverted repeats (IRs) and vary greatly in size, organization and tRNA copies. We demonstrate that cupressophyte cpDNAs have evolved towards reduced size, largely due to shrunken intergenic spacers. In cupressophytes, cpDNA rearrangements are capable of extending intergenic spacers, and synonymous mutations are negatively associated with the size and frequency of rearrangements. The variable cpDNA sizes of cupressophytes may have been shaped by mutational burden and genomic rearrangements. On the basis of cpDNA organization, our analyses revealed that in gymnosperms, cpDNA rearrangements are phylogenetically informative, which supports the ‘gnepines’ clade. In addition, removal of a specific IR influences the minimal rearrangements required for the gnepines and cupressophyte clades, whereby Pinaceae favours the removal of IRB but cupressophytes exclusion of IRA. This result strongly suggests that different IR copies have been lost from conifers I and II. Our data help understand the complexity and evolution of cupressophyte cpDNAs.
High‐throughput deep sequencing shows that microRNAs play important roles in switchgrass responses to drought and salinity stress
Authors: Xie Fuliang , Stewart Charles Neal , Taki Faten A. , He Qiuling , Liu Huawei , Zhang Baohong 
Published: November 2013

SummaryMicroRNAs (miRNAs) are an important class of small regulatory RNAs. The goal of this study was to analyse stress‐responsive miRNAs in switchgrass (Panicum virgatum), the emerging biofuel crop, to facilitate choosing gene targets for improving biomass and biofuel yield. After sequencing three small RNA libraries constructed from control, salt‐ and drought‐treated switchgrass using Illumina sequencing technology, we identified 670 known miRNA families from a total of more than 50 million short reads. A total of 273 miRNAs were identified with precursors: 126 conserved miRNAs and 147 novel miRNAs. Of them, 265 miRNAs were found to have their opposite sequences (miRNA*) with 2‐nt overhang on the 3′ end. Of them, 194 were detected in switchgrass transcriptome sequences generated from 31 high‐throughput RNA sequencing (RNA‐Seq) data sets in NCBI. Many miRNAs were differentially or uniquely expressed during salinity or drought stress treatment. We also discovered 11 miRNA clusters containing 29 miRNAs. These identified miRNAs potentially targeted 28 549 genes with a various function, including transcription factors, stress‐response proteins and cellulose biosynthesis‐related proteins. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the identified miRNAs and their targets were classified to 3779 GO terms including 1534 molecular functions, 1851 biological processes and 394 cellular components and were enriched to 147 KEGG pathways. Interestingly, 195 miRNA families and 450 targets were involved in the biosynthesis pathways of carbon, glucose, starch, fatty acid and lignin and in xylem formation, which could aid in designing next‐generation switchgrass for biomass and biofuel.
Teaching and Learning Guide for Cognitive Phenomenology
Authors: Smithies Declan 
Published: November 2013

AbstractCognitive phenomenology can be defined as the experience that is associated with cognitive activities, such as thinking, reasoning, and understanding. What is at issue in contemporary debates is not the existence of cognitive phenomenology, so defined, but rather its nature and theoretical significance. Debated questions about the nature of cognitive phenomenology include the following: What is the relationship between the phenomenology of cognition and the intentionality of cognition? And what is the relationship between the phenomenology of cognition and the phenomenology of perception? Debated questions about the significance of cognitive phenomenology concern its role in theories of intentionality, introspective self‐knowledge, and knowledge of the external world.
Imagining and Fiction: Some Issues
Authors: Stock Kathleen 
Published: November 2013

AbstractIn this paper, I survey in some depth three issues arising from the connection between imagination and fiction: (i) whether fiction can be defined as such in terms of its prescribing imagining; (ii) whether imagining in response to fiction isde se, orde re, or both; (iii) the phenomenon of ‘imaginative resistance’ and various explanations for it. Along the way I survey, more briefly, several other prominent issues in this area too.
Russell on Incomplete Symbols
Authors: Pickel Bryan 
Published: November 2013

AbstractRussell's notion of an incomplete symbol has become a standard against which philosophers compare their views on the relationship between language and the world. But Russell's exact characterization of incomplete symbols and the role they play in his philosophy are still disputed. In this paper, I trace the development of the notion of an incomplete symbol in Russell's philosophy. I suggest – against Kaplan, Evans, and others – that Russell's many characterizations of the notion of an incomplete symbol are compatible. To this end, I examine and reject arguments for the purported incompatibility between declaring an expression to be incomplete and incorporating that symbol into a compositional semantic theory. I then examine how Russell puts the notion of an incomplete symbol to use in metaphysics.
Luck Egalitarianism
Authors: Knight Carl 
Published: November 2013

AbstractLuck egalitarianism is a family of egalitarian theories of distributive justice that aim to counteract the distributive effects of luck. This article explains luck egalitarianism's main ideas, and the debates that have accompanied its rise to prominence. There are two main parts to the discussion. The first part sets out three key moves in the influential early statements of Dworkin, Arneson, and Cohen: the brute luck/option luck distinction, the specification of brute luck in everyday or theoretical terms and the specification of advantage as resources, welfare, or some combination of these. The second part covers three later developments: the democratic egalitarian critique of luck egalitarianism, the luck egalitarian acceptance of pluralism, and luck egalitarian doubts about the significance of the brute luck/option luck distinction.
Prevention of polymorphic light eruption by oral administration of a nutritional supplement containing lycopene, β‐carotene, and Lactobacillus johnsonii: results from a randomized, placebo‐controlled, double‐blinded study
Authors: Marini Alessandra , Jaenicke Thomas , Grether‐Beck Susanne , Le Floc'h Caroline , Cheniti Ahsène , Piccardi Nathalie , Krutmann Jean 
Published: November 2013

SummaryBackgroundPolymorphic light eruption (PLE) is the most common photodermatosis. Little is known about the efficacy of systemic photoprotection provided by nutritional supplements in PLE patients.PurposeThe purpose of this study was to assess efficacy of nutritional supplement containing lycopene, β‐carotene, and Lactobacillus johnsonii to diminish skin lesions induced by ‘photoprovocation’ testing in PLE patients.MethodsIn this randomized, placebo‐controlled, double‐blinded study, 60 PLE patients were supplemented with the nutritional supplement or placebo. For inducing skin lesions, patient skin was exposed to single daily doses of 100 J/cm2 ultraviolet A1 (UVA1) for two consecutive days. Skin lesions were evaluated using a PLE score. Skin biopsies were taken before and after supplementation from unexposed and exposed skin, and intercellular adhesion molecule 1 (ICAM‐1) mRNA expression was assessed by real‐time polymerase chain reaction.ResultsPrior to supplementation, skin lesions were induced in all patients with comparable PLE scores. After 12 weeks, intake of the supplement significantly reduced the PLE score after one exposure as compared with patients taking placebo (P < 0.001). After two exposures, these differences were no longer significant. At a molecular level, the development of skin lesions was associated with an increased expression of ICAM‐1 mRNA, which was significantly reduced after supplementation (P = 0.022), but not with placebo.ConclusionThe nutritional supplement provides protection against the development of UVA‐induced PLE lesions at clinical and molecular levels.
Strategic Planning for Support Services for Children with a Parent or Close Relative in Prison
Authors: Leeson Caroline , Morgan Julia 
Published: November 2013

AbstractIt has long been recognized that children with a parent or close relative in prison are more likely to experience educational difficulties, emotional distress, family breakdown and a substantial reduction in family income (Boswell 2002; Smith et al. 2007; Morgan et al. 2013b; Morgan and Gill 2013). Consequently, children with a parent in prison are more likely to require support from statutory services, especially education and social care. However, statutory support for this group of children is sparse, and children of prisoners tend not to be identified as a priority group. The demand on local authorities to spend their limited budgets wisely means tough decisions have to be made. These decisions are not taken in a vacuum: they are taken in a context of local need, consumer representation, central and local politics; underpinned by the values and attitudes of individual members as well as by the ethos or culture of the local authority itself. In this article we apply Axford's typology (2009) of the different cultures which underpin local authority service provision to data from a research study carried out in 2011 in one local authority which explored support provision in schools for children of prisoners. We examine the contradictions and gaps within the local authority's attempts to synergize the different modules of service delivery into a coherent pattern of provision, and we explore how changes in strategic culture might lead to improvements being made in terms of service delivery to this group of ‘vulnerable’ children.
Breast density quantification using magnetic resonance imaging (MRI) with bias field correction: A postmortem study
Authors: Ding Huanjun , Johnson Travis , Lin Muqing , Le Huy Q. , Ducote Justin L. , Su Min‐Ying , Molloi Sabee 
Published: November 2013

Purpose:Quantification of breast density based on three‐dimensional breast MRI may provide useful information for the early detection of breast cancer. However, the field inhomogeneity can severely challenge the computerized image segmentation process. In this work, the effect of the bias field in breast density quantification has been investigated with a postmortem study.Methods:T1‐weighted images of 20 pairs of postmortem breasts were acquired on a 1.5 T breast MRI scanner. Two computer‐assisted algorithms were used to quantify the volumetric breast density. First, standard fuzzy c‐means (FCM) clustering was used on raw images with the bias field present. Then, the coherent local intensity clustering (CLIC) method estimated and corrected the bias field during the iterative tissue segmentation process. Finally, FCM clustering was performed on the bias‐field‐corrected images produced by CLIC method. The left–right correlation for breasts in the same pair was studied for both segmentation algorithms to evaluate the precision of the tissue classification. Finally, the breast densities measured with the three methods were compared to the gold standard tissue compositions obtained from chemical analysis. The linear correlation coefficient, Pearsonˈsr, was used to evaluate the two image segmentation algorithms and the effect of bias field.Results:The CLIC method successfully corrected the intensity inhomogeneity induced by the bias field. In left–right comparisons, the CLIC method significantly improved the slope and the correlation coefficient of the linear fitting for the glandular volume estimation. The left–right breast density correlation was also increased from 0.93 to 0.98. When compared with the percent fibroglandular volume (%FGV) from chemical analysis, results after bias field correction from both the CLIC the FCM algorithms showed improved linear correlation. As a result, the Pearsonˈsr increased from 0.86 to 0.92 with the bias field correction.Conclusions:The investigated CLIC method significantly increased the precision and accuracy of breast density quantification using breast MRI images by effectively correcting the bias field. It is expected that a fully automated computerized algorithm for breast density quantification may have great potential in clinical MRI applications.
The Innate Growth Bistability and Fitness Landscapes of Antibiotic-Resistant Bacteria
Authors: Deris J. Barrett , Kim Minsu , Zhang Zhongge , Okano Hiroyuki , Hermsen Rutger , Groisman Alexander , Hwa Terence 
Published: November 2013

Introduction
Understanding how bacteria harboring antibiotic resistance grow in the presence of antibiotics is critical for predicting the spread and evolution of drug resistance. Because drugs inhibit cell growth and a cell’s growth state globally influences its gene expression, the expression of drug resistance is subject to an innate, growth-mediated feedback, leading to complex behaviors that affect both the characterization and the prevention of antibiotic resistance. We characterized the consequences of this feedback for the growth of antibiotic-resistant bacteria.

Methods

We studied the growth of
Escherichia coli
strains expressing resistance to translation-inhibiting antibiotics, by using both bulk and single-cell techniques. The growth of each strain was quantified in a broad range of drug concentrations by using time-lapse microscopy (to track the responses of individual cells to antibiotics inside a microfluidic chemostat) and by the enrichment of batch cultures for nongrowing cells. We formulated a quantitative phenomenological model to predict the growth rates of drug-resistant strains in the presence of drugs, based on the well-characterized biochemistry of drug and drug-resistance interactions and on bacterial growth laws that dictate relations between cell growth and gene expression. We tested the model predictions for various drugs and resistance mechanisms by constructing strains that constitutively express varying degrees of drug resistance.

Results
In strains expressing a moderate degree of drug resistance, growth rates dropped abruptly above a critical drug concentration, the minimum inhibitory concentration (MIC), whose value increased linearly with the basal level of resistance expression (see figure below, panel A). Cells exhibited growth bistability over a broad range of drug concentrations below the MIC: Isogenic cells expressing drug resistance coexisted in growing and nongrowing states in a homogeneous environment (panel B). Our model accurately predicted the range of drug concentrations in which growth bistability occurred, as well as the growth rates of the growing subpopulation, without any ad hoc fitting parameters. These findings reveal a plateau-like fitness landscape (panel A), which can be used to study the evolution of drug resistance in environments with varying drug concentrations.

Discussion
The broad occurrence of growth bistability in drug-resistant bacteria challenges the common notions and measures of drug efficacy and resistance. And because growth bistability can arise without complex regulation when gene expression is coupled to the state of cell growth, similar physiological links may underlie the growth bistability implicated in causing bacterial persistence. The availability of quantitative, predictive models will facilitate the formulation of strategies to limit the efficacy and evolvability of drug resistance.
Oral Immunization with Recombinant Lactobacillus acidophilus Expressing the Adhesin Hp0410 of Helicobacter pylori Induces Mucosal and Systemic Immune Responses
Authors: Hongying Fan , Xianbo Wu , Fang Yu , Yang Bai , Beiguo Long 
Published: November 2013

ABSTRACTHelicobacter pyloriinfection is relatively common worldwide and is closely related to gastric mucosa-associated lymphoid tissue (MALT) lymphoma, chronic gastritis, and stomach ulcers. Therefore, a safe and effective method for preventingH. pyloriinfection is urgently needed. Given that developing an effective vaccine againstH. pyloriis one of the best alternatives,H. pyloriadhesin Hp0410 was expressed in the food-grade bacteriumLactobacillus acidophilus. The recombinant live bacterial vaccine was then used to orally vaccinate mice, and the immunoprotective effects of Hp0410-producing strains were investigated.H. pyloricolonization in the stomach of mice immunized with the recombinantL. acidophiluswas significantly reduced, in comparison with that in control groups. Furthermore, mucosal secretory IgA antibodies were elicited in the mucosal tissue of mice immunized with the recombinant bacteria, and specific anti-Hp0410 IgG responses were also detected in mouse serum. There was a significant increase in the level of protection against gastricHelicobacterinfection following a challenge withH. pyloriSydney strain 1 (SS1). Our results collectively indicate that adhesin Hp0410 is a promising candidate vaccine antigen, and recombinantL. acidophilusexpressing Hp0410 is likely to constitute an effective, low-cost, live bacterial vaccine againstH. pylori.
Identification of Immunological Biomarkers Which May Differentiate Latent Tuberculosis from Exposure to Environmental Nontuberculous Mycobacteria in Children
Authors: Hur Yun-Gyoung , Crampin Amelia C. , Chisambo Christina , Kanyika James , Houben Rein , Ndhlovu Richard , Mzembe Themba , Lalor Maeve K. , Saul Jacky , Branson Keith , Stanley Carolynne , Ngwira Bagrey , French Neil , Ottenhoff Tom H. , Dockrell Hazel M. , Gorak-Stolinska Patricia 
Published: November 2013

ABSTRACT

A positive gamma interferon (IFN-γ) response to
Mycobacterium tuberculosis
early secretory antigenic target-6 (ESAT-6)/culture filtrate protein-10 (CFP-10) has been taken to indicate latent tuberculosis (TB) infection, but it may also be due to exposure to environmental nontuberculous mycobacteria in which ESAT-6 homologues are present. We assessed the immune responses to
M. tuberculosis
ESAT-6 and cross-reactive responses to ESAT-6 homologues of
Mycobacterium avium
and
Mycobacterium kansasii
. Archived culture supernatant samples from children at 3 years post-BCG vaccination were tested for cytokine/chemokine responses to
M. tuberculosis
antigens. Furthermore, the IFN-γ responses to
M. tuberculosis
antigens were followed up for 40 children at 8 years post-BCG vaccination, and 15 TB patients were recruited as a control group for the
M. tuberculosis
ESAT-6 response in Malawi. IFN-γ enzyme-linked immunosorbent assays (ELISAs) on supernatants from diluted whole-blood assays, IFN-γ enzyme-linked immunosorbent spot (ELISpot) assays, QuantiFERON TB Gold-In Tube tests, and multiplex bead assays were performed. More than 45% of the responders to
M. tuberculosis
ESAT-6 showed IFN-γ responses to
M. avium
and
M. kansasii
ESAT-6. In response to
M. tuberculosis
ESAT-6/CFP-10, interleukin 5 (IL-5), IL-9, IL-13, and IL-17 differentiated the stronger IFN-γ responders to
M. tuberculosis
ESAT-6 from those who preferentially responded to
M. kansasii
and
M. avium
ESAT-6. A cytokine/chemokine signature of IL-5, IL-9, IL-13, and IL-17 was identified as a putative immunological biosignature to differentiate latent TB infection from exposure to
M. avium
and
M. kansasii
in Malawian children, indicating that this signature might be particularly informative in areas where both TB and exposure to environmental nontuberculous mycobacteria are endemic.
Complete Genome Sequences of 63 Mycobacteriophages
Authors: Hatfull Graham F. ,   Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) Program,   KwaZulu-Natal Research Institute for Tuberculosis and HIV (K-RITH) Mycobacterial Genetics Course,   University of California—Los Angeles Research Immersion Laboratory in Virology,   Phage Hunters Integrating Research and Education (PHIRE) Program
Published: November 2013

ABSTRACT

Mycobacteriophages are viruses that infect mycobacterial hosts. The current collection of sequenced mycobacteriophages—all isolated on a single host strain,
Mycobacterium smegmatis
mc
2
155, reveals substantial genetic diversity. The complete genome sequences of 63 newly isolated mycobacteriophages expand the resolution of our understanding of phage diversity.
Complete Genome Sequence of pAP13, a Large Linear Plasmid of a
Brevibacterium
Strain Isolated from a Saline Lake at 4,200 Meters above Sea Level in Argentina
Authors: Dib Julian Rafael , Schuldes Jörg , Thürmer Andrea , Farias María E. , Daniel Rolf , Meinhardt Friedhelm 
Published: November 2013

ABSTRACT

pAP13 is an 89-kb linear plasmid hosted by
Brevibacterium
sp. strain Ap13, an actinobacterium isolated from the feces of a flamingo from an extremely high-altitude lake in Argentina. Because of the ecological importance of the genus
Brevibacterium
, the absolute lack of information concerning
Brevibacterium
linear plasmids, and the possible ecological significance of this unusual plasmid, pAP13 was completely sequenced, including the inversely oriented termini.