bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quorum Regulated Resistance of Vibrio cholerae against Environmental Bacteriophages
Authors: Hoque M. Mozammel , Naser Iftekhar Bin , Bari S. M. Nayeemul , Zhu Jun , Mekalanos John J. , Faruque Shah M. 
Published: November 2016

AbstractPredation by bacteriophages can significantly influence the population structure of bacterial communities. Vibrio cholerae the causative agent of cholera epidemics interacts with numerous phages in the aquatic ecosystem, and in the intestine of cholera patients. Seasonal epidemics of cholera reportedly collapse due to predation of the pathogen by phages. However, it is not clear how sufficient number of the bacteria survive to seed the environment in the subsequent epidemic season. We found that bacterial cell density-dependent gene expression termed “quorum sensing” which is regulated by signal molecules called autoinducers (AIs) can protect V. cholerae against predatory phages. V. cholerae mutant strains carrying inactivated AI synthase genes were significantly more susceptible to multiple phages compared to the parent bacteria. Likewise when mixed cultures of phage and bacteria were supplemented with exogenous autoinducers CAI-1 or AI-2 produced by recombinant strains carrying cloned AI synthase genes, increased survival of V. cholerae and a decrease in phage titer was observed. Mutational analyses suggested that the observed effects of autoinducers are mediated in part through the quorum sensing-dependent production of haemaglutinin protease, and partly through downregulation of phage receptors. These results have implication in developing strategies for phage mediated control of cholera.
Chorioamnionitis appears not to be a Risk Factor for Patent Ductus Arteriosus in Preterm Infants: A Systematic Review and Meta-Analysis
Authors: Behbodi Elham , Villamor-Martínez Eduardo , Degraeuwe Pieter L. J. , Villamor Eduardo 
Published: November 2016

AbstractThe contribution of chorioamnionitis (CA) to mortality and morbidity in preterm infants is difficult to assess because observational studies frequently present significant differences in baseline characteristics of the infants exposed or non-exposed to CA. In an attempt to perform a thorough assessment of the possible association between CA and patent ductus arteriosus (PDA) in preterm infants, we conducted a meta-analysis in which adjusted odds ratios (ORs) were pooled and we analyzed the effects of potential confounders, such as gestational age (GA) or birth weight (BW). We identified 45 relevant studies (27186 patients, 7742 CA cases). Random effects meta-analysis of crude ORs showed a significant positive association between CA and PDA (OR 1.352, 95% CI 1.172 to 1.560). Adjusted ORs were reported in 11 studies (19577 infants). Meta-analysis of these studies showed a significant negative association between CA and PDA (OR 0.802, 95% CI 0.751 to 0.959). Meta-regression showed that the differences in GA or BW between the CA-exposed and non-exposed groups were significantly correlated with the effect size of the association between PDA and CA. In conclusion, our study confirms that confounders need to be taken into account when assessing the association between CA and clinical outcomes in preterm infants.
Circular RNAs are down-regulated in KRAS mutant colon cancer cells and can be transferred to exosomes
Authors: Dou Yongchao , Cha Diana J. , Franklin Jeffrey L. , Higginbotham James N. , Jeppesen Dennis K. , Weaver Alissa M. , Prasad Nripesh , Levy Shawn , Coffey Robert J. , Patton James G. , Zhang Bing 
Published: November 2016

AbstractRecent studies have shown that circular RNAs (circRNAs) are abundant, widely expressed in mammals, and can display cell-type specific expression. However, how production of circRNAs is regulated and their precise biological function remains largely unknown. To study how circRNAs might be regulated during colorectal cancer progression, we used three isogenic colon cancer cell lines that differ only in KRAS mutation status. Cellular RNAs from the parental DLD-1 cells that contain both wild-type and G13D mutant KRAS alleles and isogenically-matched derivative cell lines, DKO-1 (mutant KRAS allele only) and DKs-8 (wild-type KRAS allele only) were analyzed using RNA-Seq. We developed a bioinformatics pipeline to identify and evaluate circRNA candidates from RNA-Seq data. Hundreds of high-quality circRNA candidates were identified in each cell line. Remarkably, circRNAs were significantly down-regulated at a global level in DLD-1 and DKO-1 cells compared to DKs-8 cells, indicating a widespread effect of mutant KRAS on circRNA abundance. This finding was confirmed in two independent colon cancer cell lines HCT116 (KRAS mutant) and HKe3 (KRAS WT). In all three cell lines, circRNAs were also found in secreted extracellular-vesicles, and circRNAs were more abundant in exosomes than cells. Our results suggest that circRNAs may serve as promising cancer biomarkers.
In vivo coherent Raman imaging of the melanomagenesis-associated pigment pheomelanin
Authors: Wang Hequn , Osseiran Sam , Igras Vivien , Nichols Alexander J. , Roider Elisabeth M. , Pruessner Joachim , Tsao Hensin , Fisher David E. , Evans Conor L. 
Published: November 2016

AbstractMelanoma is the most deadly form of skin cancer with a yearly global incidence over 232,000 patients. Individuals with fair skin and red hair exhibit the highest risk for developing melanoma, with evidence suggesting the red/blond pigment known as pheomelanin may elevate melanoma risk through both UV radiation-dependent and -independent mechanisms. Although the ability to identify, characterize, and monitor pheomelanin within skin is vital for improving our understanding of the underlying biology of these lesions, no tools exist for real-time, in vivo detection of the pigment. Here we show that the distribution of pheomelanin in cells and tissues can be visually characterized non-destructively and noninvasively in vivo with coherent anti-Stokes Raman scattering (CARS) microscopy, a label-free vibrational imaging technique. We validated our CARS imaging strategy in vitro to in vivo with synthetic pheomelanin, isolated melanocytes, and the Mc1re/e, red-haired mouse model. Nests of pheomelanotic melanocytes were observed in the red-haired animals, but not in the genetically matched Mc1re/e; Tyrc/c (“albino-red-haired”) mice. Importantly, samples from human amelanotic melanomas subjected to CARS imaging exhibited strong pheomelanotic signals. This is the first time, to our knowledge, that pheomelanin has been visualized and spatially localized in melanocytes, skin, and human amelanotic melanomas.
Streptococcus pneumoniae disrupts pulmonary immune defence via elastase release following pneumolysin-dependent neutrophil lysis
Authors: Domon Hisanori , Oda Masataka , Maekawa Tomoki , Nagai Kosuke , Takeda Wataru , Terao Yutaka 
Published: November 2016

AbstractStreptococcus pneumoniae is a leading cause of bacterial pneumonia and is the principal cause of morbidity and mortality worldwide. Previous studies suggested that excessive activation of neutrophils results in the release of neutrophil elastase, which contributes to lung injury in severe pneumonia. Although both pneumococcal virulence factors and neutrophil elastase contribute to the development and progression of pneumonia, there are no studies analysing relationships between these factors. Here, we showed that pneumolysin, a pneumococcal pore-forming toxin, induced cell lysis in primary isolated human neutrophils, leading to the release of neutrophil elastase. Pneumolysin exerted minimal cytotoxicity against alveolar epithelial cells and macrophages, whereas neutrophil elastase induced detachment of alveolar epithelial cells and impaired phagocytic activity in macrophages. Additionally, activation of neutrophil elastase did not exert bactericidal activity against S. pneumoniae in vitro. P2X7 receptor, which belongs to a family of purinergic receptors, was involved in pneumolysin-induced cell lysis. These findings suggested that infiltrated neutrophils are the primary target cells of pneumolysin, and that S. pneumoniae exploits neutrophil-elastase leakage to induce the disruption of pulmonary immune defences, thereby causing lung injury.
Multi-strategy genome-wide association studies identify the DCAF16-NCAPG region as a susceptibility locus for average daily gain in cattle
Authors: Zhang Wengang , Li Junya , Guo Yong , Zhang Lupei , Xu Lingyang , Gao Xue , Zhu Bo , Gao Huijiang , Ni Hemin , Chen Yan 
Published: November 2016

AbstractAverage daily gain (ADG) is the most economically important trait in beef cattle industry. Using genome-wide association study (GWAS) approaches, previous studies have identified several causal variants within the PLAG1, NCAPG and LCORL genes for ADG in cattle. Multi-strategy GWASs were implemented in this study to improve detection and to explore the causal genes and regions. In this study, we conducted GWASs based on the genotypes of 1,173 Simmental cattle. In the SNP-based GWAS, the most significant SNPs (rs109303784 and rs110058857, P = 1.78 × 10−7) were identified in the NCAPG intron on BTA6 and explained 4.01% of the phenotypic variance, and the independent and significant SNP (rs110406669, P = 5.18 × 10−6) explained 3.32% of the phenotypic variance. Similarly, in the haplotype-based GWAS, the most significant haplotype block, Hap-6-N1416 (P = 2.56 × 10−8), spanned 12.7 kb on BTA6 and explained 4.85% of the phenotypic variance. Also, in the gene-based GWAS, seven significant genes were obtained which included DCAF16 and NCAPG. Moreover, analysis of the transcript levels confirmed that transcripts abundance of NCAPG (P = 0.046) and DCAF16 (P = 0.046) were significantly correlated with the ADG trait. Overall, our results from the multi-strategy GWASs revealed the DCAF16-NCAPG region to be a susceptibility locus for ADG in cattle.
Anthropogenic Impacts Facilitate Native Fish Hybridization in the Bonneville Basin of Western North America
Authors: Bangs Max R. , Douglas Marlis R. , Thompson Paul , Douglas Michael E. 
Published: November 2016

AbstractHabitat modification and introduced species are impacting native fishes in western North America, a situation now exacerbated by drought and anthropogenic water acquisition. One species of concern, the Bluehead Sucker Catostomus discobolus in the Bonneville basin of Utah, Idaho, and Wyoming, has experienced sharp population declines potentially augmented by hybridization with native Utah Sucker C. ardens. To evaluate this situation, we sequenced three diagnostic nuclear DNA loci and two mitochondrial genes across 81 Bluehead Suckers, 74 of which were collected in a basinwide genetic assessment and 7 from a targeted morphological evaluation. Combined, we detected 14 hybrids from the single site in the Bear River and the three sites in the Weber River that hosts the three largest remaining populations in the basin. All individuals sampled as putative hybrids were confirmed as F1 hybrids, ascertaining efficacy of field‐based morphological identifications. Hybridization may be especially problematic for the numerically reduced Bluehead Sucker because it can further depress recruitment. However, no evidence of post‐F1 backcrosses was found, suggesting in turn that hybrids are not reproducing, although the reasons for this are currently not understood. These results underscore the need to quantify the proportion of Bluehead Sucker recruitment lost to hybridization.Received January 6, 2016; accepted August 31, 2016 Published online November 28, 2016
Multi-Criteria Decision Analysis for Recreational Trout Fisheries in British Columbia, Canada: A Bayesian Network Implementation
Authors: Varkey Divya A. , McAllister Murdoch K. , Askey Paul J. , Parkinson Eric , Clarke Adrian , Godin Theresa 
Published: November 2016

Abstract
One of the key challenges in recreational fisheries management is to provide a rational basis for decisions in the face of conflicting objectives, such as improving angling opportunities, maintaining satisfaction across a diverse fishing client base, controlling costs, and conserving wild populations. We developed a multi-criteria decision analysis approach for managing recreational trout fisheries (e.g., Rainbow Trout Oncorhynchus mykiss). The approach was implemented in a Bayesian decision network. The decision support tool, called “Stock-Optim,” provides a user-friendly interface for predicting fishery performance from alternate stocking prescriptions. The tool integrates survey information on angler typology and satisfaction with previously developed models for fish biology and fishery dynamics to more fully consider the biological and social outcomes of management decisions. Specifically, the tool evaluated alternative stocking options given three performance criteria: angler effort, angler satisfaction, and the cost of the stocking program. Predicted effort was highest for fish that were released in the size range of 8–20 g and at stocking densities of 200–500 fish/ha. Effort maximization at these rates and sizes is a result of compromise between the conflicting preferences of Rainbow Trout enthusiasts and occasional anglers toward fish size and harvest. Furthermore, lowering the stocking program's costs will lead to lower stocking rates and thereby favor the enthusiasts. Currently, stocking levels in British Columbia are lower than levels that would maximize effort and are most consistent with a policy of maximizing satisfaction for Rainbow Trout enthusiasts and minimizing costs. Stock-Optim will allow managers to compare predicted outcomes from the current and alternative regimes with stated lake-specific or region-specific management objectives and regional averages and thereby more closely meet these objectives in the future. Lastly, the model was validated by comparing predicted effort with observed effort in stocked lakes.
Received February 1, 2016; accepted July 14, 2016 Published online November 28, 2016
Genetic Stock Structure of Anadromous Arctic Char in Canada's Central Arctic: Potential Implications for the Management of Canada's Largest Arctic Char Commercial Fishery
Authors: Harris Les N. , Moore Jean-Sébastien , Bajno Robert , Tallman Ross F. 
Published: November 2016

Abstract
The Arctic Char Salvelinus alpinus is widely considered the most important subsistence fish species in the Canadian Arctic. Throughout the species’ range, commercial fisheries for Arctic Char also exist, the management of which primarily follows river-specific harvest strategies. Such an approach, however, may not be appropriate if the management unit or stock does not accurately reflect a demographically independent population or if mixtures of populations are being harvested. We assayed microsatellite DNA variation among 744 Arctic Char from the Cambridge Bay region, Nunavut, where the largest commercial fishery for the species exists, in order to identify the most appropriate spatial scale at which these stocks should be managed. Our sampling design specifically mirrored that of the commercial fishery in order to describe patterns of genetic structure and genetic variation within and among the harvested component. We also included Arctic Char from more geographically distant sampling locations to provide a spatial context for genetic stock structuring in the region. Overall, we found moderate but significant structure across the entire study area. In contrast, commercially harvested stocks were weakly differentiated, especially among the stocks that are considered part of the Wellington Bay complex. We propose several hypotheses for this weak differentiation, including (1) our sampling design that mirrored the commercial harvest, (2) high rates of potential gene flow, and (3) large effective population sizes. Our results may have important implications for commercial and subsistence fisheries management, including the notion that there are several potential units of conservation below the species level.
Received September 29, 2015; accepted August 17, 2016 Published online November 28, 2016
Key Figures: North American Environmental Scientist Activists
Authors: Wohl Ellen 
Published: November 2016

Environmental scientist activist is not an established phrase. Here it designates individuals who begin their careers as professional scientists and become concerned about the loss of natural ecosystems or species, or environmental degradation and associated health effects. This concern gives rise to activism on behalf of environmental protection and enhancing public awareness of environmental issues. For some, activism takes the form of writing for a popular audience. Others become widely recognized figures who appear in documentary films or television shows. Some of the scientist activists are associated with a particular environment, such as Eugenie Clark and Sylvia Earle as advocates for protection of marine ecosystems. Others are noted for their expertise and activism in relation to a specific issue, such as Theo Colborn, Sandra Steingraber, and Devra Davis for environmental contamination or Hansen for climate change. Dian Fossey and Birutė Galdikas are associated with particular groups of animals—gorillas and chimpanzees, respectively. Others, such as Aldo Leopold and E. O. Wilson, are associated with a broader spectrum of environmental issues. Some of the individuals in this article speak out primarily based on their own research, whereas others have only a brief research career and draw from a wider base of published studies. Scientist activists are largely a 20th- and 21st-century phenomenon. Although scientifically trained individuals such as George Perkins Marsh argued for environmental preservation during the 19th century, environmental advocacy by professional scientists became more widespread during the 20th century. This likely reflects the rapid increase in the number of professional scientists since World War II, as well as widespread environmental degradation. As more scientists trained in chemistry, biology, and other environmental disciplines become aware of the threats facing ecosystems, wild organisms, and human health, the urge to communicate this awareness drives environmental activism. Two themes emerge: the fundamental reliance of humans on natural ecosystems and ecosystem services, and the shared traits of humans and other organisms. From Leopold’s articulation of the land ethic, to Wilson’s arguments for protecting biodiversity, the scientists who have become activists argue for the critical importance of protecting functional ecosystems in order to insure human survival. In addition, humans have traditionally distinguished themselves from other species based on traits such as communication, construction and use of tools, learned behavior, and distinctive personalities. As biologists including Fossey, Galdikas, and Schaller have documented the same traits in other species and raised public awareness of these traits, many people have begun to rethink the intrinsic right of other species to exist.
Thomas Wentworth Higginson
Authors: Petrulionis Sandra 
Published: November 2016

Thomas Wentworth Higginson (b. 1823–d. 1911) was a native of Cambridge, Massachusetts, and a graduate of Harvard College (1841) and Harvard Divinity School (1847). A prolific author and popular lecturer, Higginson was also a Unitarian minister, an abolitionist activist, a soldier, an editor, a women’s rights leader, and a literary critic. His reputation has largely been based on his relationship with and co-editing (with Mabel Loomis Todd) of the poet Emily Dickinson as well as on his antislavery activism and command of the First South Carolina Volunteers (later the 33rd US Colored Infantry Regiment), the first military unit composed of freed slaves during the Civil War. More recently, critical attention has focused on specific writings in Higginson’s extensive literary canon. In his wide-ranging articles, Higginson addressed topics of interest in 19th-century America—from transcendentalism, physical health, abolitionism, and women’s rights to US and transatlantic literary culture, Civil War experiences, biography, and history, in addition to, albeit fewer in number, works of fiction and poetry. His articles appeared regularly in the Atlantic Monthly, Scribner’s, Putnam’s Monthly, Independent, Century, Harper’s Monthly, and other periodicals. He also contributed hundreds of columns addressing women’s rights and other political subjects to the Nation, the Radical, and the Boston Woman’s Journal. Higginson’s best-selling work was a classroom text, Young Folks’ History of the United States (1875), while his Civil War volume, Army Life in a Black Regiment (1870), has become a staple of today’s college syllabi. His only novel, Malbone (1869), is a fairly formulaic romance, set in New England, that received little critical attention. During the antebellum era, his liberal Unitarian ministry reflected his radical abolitionism as well as the transcendentalism of Ralph Waldo Emerson and Theodore Parker. After the Civil War, Higginson settled in Newport, Rhode Island, with his first wife, Mary Channing Higginson, where he cultivated a staid postbellum literary identity frequently characterized as “genteel.” He was closely involved with the women’s rights activists who organized the American Woman Suffrage Association in 1868, and for many years he penned a column on women’s issues for this organization’s Woman’s Journal. Higginson is known for encouraging young literary aspirants, particularly women, who in addition to Dickinson, include Harriet Prescott Spofford, Helen Hunt Jackson, and Emma Lazarus. His Life of Margaret Fuller Ossoli (1884) offers a sympathetic treatment of Fuller’s genius and importance. In 1879, following the death of his first wife two years prior, Higginson married Mary Thacher Higginson; their daughter, Margaret, was born in 1881. Toward the end of his life, Higginson joined the likes of Upton Sinclair, Charlotte Perkins Gilman, Jack London, and others in his support for the newly organized Intercollegiate Socialist Society.
Genome-Wide Association Study Reveals First Locus for Anorexia Nervosa and Metabolic Correlations
Authors: Duncan E. L. , Thornton L. M. , Hinney A. , Daly M. J. , Sullivan P. F. , Zeggini E. , Breen G. , Bulik C. M. 
Published: November 2016

AbstractAnorexia nervosa (AN) is a serious eating disorder characterized by restriction of energy intake relative to requirements, resulting in abnormally low body weight. It has a lifetime prevalence of approximately 1%, disproportionately affects females1,2, and has no well replicated evidence of effective pharmacological or psychological treatments despite high morbidity and mortality2. Twin studies support a genetic basis for the observed aggregation of AN in families3, with heritability estimates of 48%-74%4. Although initial genome-wide association studies (GWASs) were underpowered5,6, evidence suggested that signals for AN would be detected with increased power5. We present a GWAS of 3,495 AN cases and 10,982 controls with one genome-wide significant locus (index variant rs4622308, p=4.3x10−9) in a region (chr12:56,372,585-56,482,185) which includes six genes. The SNP-chip heritabilityof AN from these data is 0.20 (SE=0.02), suggesting that a substantial fraction of the twin-based heritability stems from common genetic variation. Using these GWAS results, we also find significant positive genetic correlations with schizophrenia, neuroticism, educational attainment, and HDL cholesterol, and significant negative genetic correlations with body mass, insulin, glucose, and lipid phenotypes. Our results support the reconceptualization of AN as a disorder with both psychiatric and metabolic components.