bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phage–bacteria interaction network in human oral microbiome
Authors: Wang Jinfeng , Gao Yuan , Zhao Fangqing 
Published: June 2015

SummaryAlthough increasing knowledge suggests that bacteriophages play important roles in regulating microbial ecosystems, phage–bacteria interaction in human oral cavities remains less understood. Here we performed a metagenomic analysis to explore the composition and variation of oral dsDNA phage populations and potential phage–bacteria interaction. A total of 1,711 contigs assembled with more than 100 Gb shotgun sequencing data were annotated to 104 phages based on their best BLAST matches against the NR database. Bray–Curtis dissimilarities demonstrated that both phage and bacterial composition are highly diverse between periodontally healthy samples but show a trend towards homogenization in diseased gingivae samples. Significantly, according to the CRISPR arrays that record infection relationship between bacteria and phage, we found certain oral phages were able to invade other bacteria besides their putative bacterial hosts. These cross‐infective phages were positively correlated with commensal bacteria while were negatively correlated with major periodontal pathogens, suggesting possible connection between these phages and microbial community structure in oral cavities. By characterizing phage–bacteria interaction as networks rather than exclusively pairwise predator–prey relationships, our study provides the first insight into the participation of cross‐infective phages in forming human oral microbiota.
The core root microbiome of sugarcanes cultivated under varying nitrogen fertilizer application
Authors: Yeoh Yun Kit , Paungfoo‐Lonhienne Chanyarat , Dennis Paul G. , Robinson Nicole , Ragan Mark A. , Schmidt Susanne , Hugenholtz Philip 
Published: June 2015

SummaryDiazotrophic bacteria potentially supply substantial amounts of biologically fixed nitrogen to crops, but their occurrence may be suppressed by high nitrogen fertilizer application. Here, we explored the impact of high nitrogen fertilizer rates on the presence of diazotrophs in field‐grown sugarcane with industry‐standard or reduced nitrogen fertilizer application. Despite large differences in soil microbial communities between test sites, a core sugarcane root microbiome was identified. The sugarcane root‐enriched core taxa overlap with those of Arabidopsis thaliana raising the possibility that certain bacterial families have had long association with plants. Reduced nitrogen fertilizer application had remarkably little effect on the core root microbiome and did not increase the relative abundance of root‐associated diazotrophs or nif gene counts. Correspondingly, low nitrogen fertilizer crops had lower biomass and nitrogen content, reflecting a lack of major input of biologically fixed nitrogen, indicating that manipulating nitrogen fertilizer rates does not improve sugarcane yields by enriching diazotrophic populations under the test conditions. Standard nitrogen fertilizer crops had improved biomass and nitrogen content, and corresponding soils had higher abundances of nitrification and denitrification genes. These findings highlight that achieving a balance in maximizing crop yields and minimizing nutrient pollution associated with nitrogen fertilizer application requires understanding of how microbial communities respond to fertilizer use.
Variable phosphorus uptake rates and allocation across microbial groups in the oligotrophic Gulf of Mexico
Authors: Popendorf Kimberly J. , Duhamel Solange 
Published: June 2015

SummaryMicrobial uptake of dissolved phosphorus (P) is an important lever in controlling both microbial production and the fate and cycling of marine P. We investigated the relative role of heterotrophic bacteria and phytoplankton in P cycling by measuring the P uptake rates of individual microbial groups (heterotrophic bacteria and the phytoplankton groups Synechococcus, Prochlorococcus and picoeukaryotic phytoplankton) in the P‐depleted Gulf of Mexico. Phosphorus uptake rates were measured using incubations with radiolabelled phosphate and adenosine triphosphate coupled with cell sorting flow cytometry. We found that heterotrophic bacteria were the dominant consumers of P on both a biomass basis and a population basis. Biovolume normalized heterotrophic bacteria P uptake rate per cell (amol P μm−3 h−1) was roughly an order of magnitude greater than phytoplankton uptake rates, and heterotrophic bacteria were responsible for generally greater than 50% of total picoplankton P uptake. We hypothesized that this variation in uptake rates reflects variation in cellular P allocation strategies, and found that, indeed, the fraction of cellular P uptake utilized for phospholipid production was significantly higher in heterotrophic bacteria compared with cyanobacterial phytoplankton. These findings indicate that heterotrophic bacteria have a uniquely P‐oriented physiology and play a dominant role in cycling dissolved P.
Bioreactor microbial ecosystems for thiocyanate and cyanide degradation unravelled with genome‐resolved metagenomics
Authors: Kantor Rose S. , van Zyl A. Wynand , van Hille Robert P. , Thomas Brian C. , Harrison Susan T. L. , Banfield Jillian F. 
Published: June 2015

SummaryGold ore processing uses cyanide (CN−), which often results in large volumes of thiocyanate‐ (SCN−) contaminated wastewater requiring treatment. Microbial communities can degrade SCN− and CN−, but little is known about their membership and metabolic potential. Microbial‐based remediation strategies will benefit from an ecological understanding of organisms involved in the breakdown of SCN− and CN− into sulfur, carbon and nitrogen compounds. We performed metagenomic analysis of samples from two laboratory‐scale bioreactors used to study SCN− and CN− degradation. Community analysis revealed the dominance of Thiobacillus spp., whose genomes harbour a previously unreported operon for SCN− degradation. Genome‐based metabolic predictions suggest that a large portion of each bioreactor community is autotrophic, relying not on molasses in reactor feed but using energy gained from oxidation of sulfur compounds produced during SCN− degradation. Heterotrophs, including a bacterium from a previously uncharacterized phylum, compose a smaller portion of the reactor community. Predation by phage and eukaryotes is predicted to affect community dynamics. Genes for ammonium oxidation and denitrification were detected, indicating the potential for nitrogen removal, as required for complete remediation of wastewater. These findings suggest optimization strategies for reactor design, such as improved aerobic/anaerobic partitioning and elimination of organic carbon from reactor feed.
Escherichia coli diversity in the lower intestinal tract of humans
Authors: Gordon David M. , O'Brien Claire L. , Pavli Paul 
Published: June 2015

SummaryPrevious studies examining the clonal diversity of Escherichia coli populations within humans have been based on faecal isolates. In this study E. coli were isolated from biopsies taken from the terminal ileum, ascending, transverse and descending colon, and rectum of 69 individuals. Multiple isolates from each biopsy were characterized using Rep‐PCR. An average of 3.5 genotypes were recovered per host, and in hosts with two or more strains, the phylogroup membership of the second most abundant strain was significantly more likely to be the same as the dominant strain. There was no indication of a non‐random distribution of E. coli phylogroups among the regions of the lower intestine. In hosts with multiple genotypes, as defined by Repetitive extragenic palindromic‐PCR, genotypes were non‐randomly distributed among gut regions in over half the individuals. The phylogroup membership of an individual's numerically dominant strain explained some of the variation in the extent to which strains within an individual were heterogeneously distributed, with most heterogeneity observed when the numerically dominant strain belonged to phylogroups E or F, and the least when the dominant strain belonged to phylogroup B2. The results of this study support previous studies on pigs that demonstrated faecal sampling underestimates the genotype diversity present within a host.
Linking the occurrence of cutaneous opportunistic fungal invaders with elemental concentrations in false killer whale (Pseudorca crassidens) skin
Authors: Mouton Marnel , Przybylowicz Wojciech , Mesjasz‐Przybylowicz Jolanta , Postma Ferdinand , Thornton Meredith , Archer Edward , Botha Alfred 
Published: June 2015

SummaryCetaceans, occupying the top levels in marine food chains, are vulnerable to elevated levels of potentially toxic trace elements, such as aluminium (Al), mercury (Hg) and nickel (Ni). Negative effects associated with these toxic metals include infection by opportunistic microbial invaders. To corroborate the link between the presence of cutaneous fungal invaders and trace element levels, skin samples from 40 stranded false killer whales (FKWs) were analysed using culture techniques and inductively coupled plasma‐mass spectroscopy. Twenty‐two skin samples yielded 18 clinically relevant fungal species. While evidence for bioaccumulation ofHg in the skin of theFKWswas observed, a strong link was found to exist between the occurrence of opportunistic fungal invaders and higherAl : Se andAl : Zn ratios. This study provides indications that elevated levels of some toxic metals, such asAl, contribute to immunotoxicity renderingFKWssusceptible to colonization by cutaneous opportunistic fungal invaders.
Inverse relationship between sleep duration and myopia
Authors: Jee Donghyun , Morgan Ian G. , Kim Eun chul 
Published: June 2015

AbstractPurposesTo investigate the association between sleep duration and myopia.MethodsThis population‐based, cross‐sectional study using a nationwide, systemic, stratified, multistage, clustered sampling method included a total of 3625 subjects aged 12–19 years who participated in the Korean National Health and Nutrition Examination Survey 2008–2012. All participants underwent ophthalmic examination and a standardized interview including average sleep duration (hr/day), education, physical activity and economic status (annual household income). Refractive error was measured by autorefraction without cycloplegia. Myopia and high myopia were defined as ≤−0.50 dioptres (D) and ≤−6.0 D, respectively. Sleep durations were classified into 5 categories: <5, 6, 7, 8 and >9 hr.ResultsThe overall prevalence of myopia and high myopia were 77.8% and 9.4%, respectively, and the overall sleep duration was 7.1 hr/day. The refractive error increased by 0.10 D per 1 hr increase in sleep after adjusting for potential confounders including sex, age, height, education level, economic status and physical activity. The adjusted odds ratio (OR) for refractive error was 0.90 (95% confidence interval [CI], 0.83–0.97) per 1 hr increase in sleep. The adjusted OR for myopia was decreased in those with >9 hr of sleep (OR, 0.59; 95% CI, 0.38–0.93; p for trend = 0.006) than in those with <5 hr of sleep. However, high myopia was not associated with sleep duration.ConclusionsThis study provides the population‐based, epidemiologic evidence for an inverse relationship between sleep duration and myopia in a representative population of Korean adolescents.
Navigating the Life Cycle of Trust in Developing Economies: One‐size Solutions Do Not Fit All
Authors: Hartman Laura Pincus , Gedro Julie , Masterson Courtney 
Published: June 2015

AbstractTrust is critical to the development and maintenance of collaborative and cohesive relationships in societies, broadly, and in organizations, specifically. At the same time, trust is highly dependent on the social context in which it occurs. Unfortunately, existing research involving trust remains somewhat limited to a particular set of developed economies, providing a window to explore a culture's stage of economic development as a key contextual determinant of trust within organizations. In this article, we review the state of the scholarship on trust and identify those qualities of trust that are common in organizations at similar stages of economic development, referred to as its etic aspects. We then also distinguish those elements of trust that are, to the contrary, culturally specific or emic in nature. We structure our discussion around the “life cycle of trust” (i.e., the creation, maintenance, and postfracture repair of trust) and consider unique factors in its application to developing economies. In doing so, we ground our examination in expository examples through field experience in Haiti. We conclude with the proposal of a framework for future research oriented toward the resolution of remaining theoretical and empirical queries as they relate to trust in developing economies.
Equator Principles: Bridging the Gap between Economics and Ethics?
Authors: Wörsdörfer Manuel 
Published: June 2015

AbstractThe hypothetical conflict between self‐interest, corporate interest, and the common good is one of the hottest debated issues in business ethics. This article focuses on a particular corporate social responsibility approach within the field of sustainable (project) finance, which has the potential—given that certain reform measures are adopted—to overcome the alleged trade‐off between self‐interest and the common good. The approach is labeled as the Equator Principles (EPs) framework, which celebrated its tenth anniversary and the formal launch of the third generation of the EPs (EP III) in 2013. The article shows how companies can theoretically be both profitable and socio‐environmentally responsible by adhering to the EPs. The article proceeds as follows: Before moving on to the EPs, section 2 defines the key terms self‐interest and common good. Section 3 then analyzes the EPs from a business ethics perspective. Section 4 shows how the EPs can help in solving the potential trade‐off between self‐interest and the common good—provided that the EPs are substantially revised. These required reform steps are discussed in section 5. The article ends with a summary of the main findings.
Corporate Social Responsibility through Cross‐sector Partnerships: Implications for Civil Society, the State, and the Corporate Sector in India
Authors: Hede Skagerlind Helena , Westman Moa , Berglund Henrik 
Published: June 2015

AbstractCorporations are increasingly forced to widen their agendas to include social and environmental concerns, or corporate social responsibility (CSR). This development has been recorded in the current academic debate, and the views regarding its implications for business, the state, and civil society diverge. However, there is agreement within the CSR and corporate governance literatures that there is a lack of thorough empirical studies of these effects. Based on a case study of the multinational wind energy company Suzlon Energy's CSR projects in rural India, this article contends that CSR projects implemented through cross‐sector partnerships can help to build the capacities of civil society organizations (CSOs). Although the risk of corporate steering of the civil society agenda is reduced when CSR prioritizes community needs over business imperatives, CSOs tend to bear the highest costs in partnerships, through credibility losses and insecurity concerning project terms and funding, reinforcing the importance of critical cooperation and complementary core competencies in cross‐sector partnerships. The results have implications for the strategies of corporations, CSOs, and governments as well as for the planning of national and international development aid.
Do Business Leaders Have Role‐Model Obligations to Be Good Political Actors?
Authors: Spurgin Earl 
Published: June 2015

AbstractThis article raises an issue about corporate political activity that is different from those typically addressed by business ethicists. It examines the role‐model status and obligations of the business leaders who direct such activity. This approach has two potential benefits. First, since ethicists often appeal to role‐model obligations and many are concerned about corporate political activity, business ethics literature would benefit from expanding the examination of role‐model status and obligations to encompass the business leaders who direct political activity. Second, it will help ethicists determine what we should demand from business leaders who direct such activity. This is important given the U.S. Supreme Court's Citizens United decision in 2010 that guarantees corporations the free‐speech right to make political expenditures in support of political causes. I seek to demonstrate that we should hold business leaders morally accountable for how they direct political activity because of their role‐model status that arises from their greater fame, authority, or power than ordinary persons possess.
Operational Best Practices in Business Ethics: A Practical and Systematic Benchmarking Tool
Authors: Collins Denis 
Published: June 2015

AbstractThis article describes a benchmarking tool managers can use to determine operational policies and processes that could enhance an organization's social and ethical performance. The benchmarking tool consists of a 13‐dimension, 110‐item survey based on an Optimal Ethics Systems Model. These best practices in business ethics are derived from an analysis and assessment of seven institutional infrastructures and accountability standards developed to help managers improve organizational social and ethical performance.
Additive gamma frailty models with applications to competing risks in related individuals
Authors: Eriksson Frank , Scheike Thomas 
Published: June 2015

SummaryEpidemiological studies of related individuals are often complicated by the fact that follow‐up on the event type of interest is incomplete due to the occurrence of other events. We suggest a class of frailty models with cause‐specific hazards for correlated competing events in related individuals. The frailties are based on sums of gamma distributed variables and offer closed form expressions for the observed intensities. An inference procedure with a recursive baseline estimator is proposed, and its large sample properties are established. The estimator readily handles cluster left‐truncation as occurring in the Nordic twin registers. The performance in finite samples is investigated by simulations and an example on prostate cancer in twins is provided for illustration.
Development of extramedullary myeloma in the era of novel agents: no evidence of increased risk with lenalidomide–bortezomib combinations
Authors: Varga Cindy , Xie Wanling , Laubach Jacob , Ghobrial Irene M. , O'Donnell Elizabeth K. , Weinstock Matthew , Paba‐Prada Claudia , Warren Diane , Maglio Michelle E. , Schlossman Robert , Munshi Nikhil C. , Raje Noopur , Weller Edie , Anderson Kenneth C. , Mitsiades Constantine S. , Richardson Paul G. 
Published: June 2015

SummaryProteasome inhibitors (PI) and immunomodulatory agents (IMIDs) have improved the overall survival (OS) of patients with multiple myeloma (MM), but concerns have been raised about increased incidence of extramedullary disease (EMD) after the combined use of PIs and IMIDs for upfront therapy. We evaluated whether the addition of lenalidomide to bortezomib‐based front‐line regimens precipitated earlier development of EMD. We reviewed the charts of 117 MM patients (median follow‐up from diagnosis 6·1 years; range 0·1–10·2 years) enrolled in eight clinical trials of first‐line treatment with bortezomib‐based regimens, with or without lenalidomide. We assessed development of EMD as extraosseous (distant from bone) or osseous (originating from bone) plasmacytomas. The primary endpoint was time from diagnosis until development of EMD, based on imaging, biopsy and/or physical examination. Any form of EMD at progression was observed in 40 (34·2%) patients, including 21 (18%) osseous, 8 (7%) extraosseous and 11 (9%) both osseous and extraosseous. Median OS was 0·9 years (range 0·1–4·8 years) after extraosseous EMD development. Sensitivity analyses with follow‐up times truncated at 5 years detected no statistically significant difference in rates of any EMD form between the two groups (P > 0·2 for each comparison). Therefore, we observed no evidence that bortezomib–lenalidomide‐based front‐line therapy precipitates earlier EMD.
Bioenergetic analysis of human peripheral blood mononuclear cells
Authors: Jones N , Piasecka J , Bryant A H , Jones R H , Skibinski D O F , Francis Nigel J , Thornton C A 
Published: June 2015

SummaryLeucocytes respond rapidly to pathogenic and other insults, with responses ranging from cytokine production to migration and phagocytosis. These are bioenergetically expensive, and increased glycolytic flux provides adenosine triphosphate (ATP) rapidly to support these essential functions. However, much of this work is from animal studies. To understand more clearly the relative role of glycolysis and oxidative phosphorylation in human leucocytes, especially their utility in a translational research setting, we undertook a study of human peripheral blood mononuclear cells (MNCs) bioenergetics. Glycolysis was essential during lipopolysaccharide (LPS)-mediated interleukin (IL)−1β, IL-6 and tumour necrosis factor (TNF)-α production, as 2-deoxy-D-glucose decreased significantly the output of all three cytokines. After optimizing cell numbers and the concentrations of all activators and inhibitors, oxidative phosphorylation and glycolysis profiles of fresh and cryopreserved/resuscitated MNCs were determined to explore the utility of MNCs for determining the bioenergetics health profile in multiple clinical settings. While the LPS-induced cytokine response did not differ significantly between fresh and resuscitated cells from the same donors, cryopreservation/resuscitation significantly affected mainly some measures of oxidative phosphorylation, but also glycolysis. Bioenergetics analysis of human MNCs provides a quick, effective means to measure the bioenergetics health index of many individuals, but cryopreserved cells are not suitable for such an analysis. The translational utility of this approach was tested by comparing MNCs of pregnant and non-pregnant women to reveal increased bioenergetics health index with pregnancy but significantly reduced basal glycolysis and glycolytic capacity. More detailed analysis of discrete leucocyte populations would be required to understand the relative roles of glycolysis and oxidative phosphorylation during inflammation and other immune responses.
Propagation of Pathology through Brain Networks in Neurodegenerative Diseases: From Molecules to Clinical Phenotypes
Authors: Agosta Federica , Weiler Marina , Filippi Massimo 
Published: June 2015

SummaryThe cellular mechanisms underlying the stereotypical progression of pathology in neurodegenerative diseases are incompletely understood, but increasing evidence indicates that misfolded protein aggregates can spread by a self‐perpetuating neuron‐to‐neuron transmission. Novel neuroimaging techniques can help elucidating how these disorders spread across brain networks. Recent knowledge from structural and functional connectivity studies suggests that the relation between neurodegenerative diseases and distinct brain networks is likely to be a strict consequence of diffuse network dynamics. Diffusion tensor magnetic resonance imaging also showed that measurement of white matter tract involvement can be a valid surrogate to assess the in vivo spreading of pathological proteins in these conditions. This review will introduce briefly the main molecular and pathological substrates of the most frequent neurodegenerative diseases and provide a comprehensive overview of neuroimaging findings that support the “network‐based neurodegeneration” hypothesis in these disorders. Characterizing network breakdown in neurodegenerative diseases will help anticipate and perhaps prevent the devastating impact of these conditions.