bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic and phenotypic evidence for an incomplete domestication of South American grain amaranth (Amaranthus caudatus)
Authors: Stetter Markus G. , Müller Thomas , Schmid Karl J. 
Published: December 2016

AbstractThe domestication syndrome comprises phenotypic changes that differentiate crops from their wild ancestors. We compared the genomic variation and phenotypic differentiation of the two putative domestication traits seed size and seed colour of the grain amaranth Amaranthus caudatus, which is an ancient crop of South America, and its two close wild relatives and putative ancestors A. hybridus and A. quitensis. Genotyping 119 accessions of the three species from the Andean region using genotyping by sequencing (GBS) resulted in 9485 SNPs that revealed a strong genetic differentiation of cultivated A. caudatus from its two relatives. A. quitensis and A. hybridus accessions did not cluster by their species assignment but formed mixed groups according to their geographic origin in Ecuador and Peru, respectively. A. caudatus had a higher genetic diversity than its close relatives and shared a high proportion of polymorphisms with their wild relatives consistent with the absence of a strong bottleneck or a high level of recent gene flow. Genome sizes and seed sizes were not significantly different between A. caudatus and its relatives, although a genetically distinct group of A. caudatus from Bolivia had significantly larger seeds. We conclude that despite a long history of human cultivation and selection for white grain colour, A. caudatus shows a weak genomic and phenotypic domestication syndrome and proposes that it is an incompletely domesticated crop species either because of weak selection or high levels of gene flow from its sympatric close undomesticated relatives that counteracted the fixation of key domestication traits.
The escalatory Red Queen: Population extinction and replacement following arms race dynamics in poplar rust
Authors: Persoons Antoine , Hayden Katherine J. , Fabre Bénédicte , Frey Pascal , De Mita Stéphane , Tellier Aurélien , Halkett Fabien 
Published: December 2016

AbstractHost–parasite systems provide convincing examples of Red Queen co‐evolutionary dynamics. Yet, a key process underscored in Van Valen's theory – that arms race dynamics can result in extinction – has never been documented. One reason for this may be that most sampling designs lack the breadth needed to illuminate the rapid pace of adaptation by pathogen populations. In this study, we used a 25‐year temporal sampling to decipher the demographic history of a plant pathogen: the poplar rust fungus, Melampsora larici‐populina. A major adaptive event occurred in 1994 with the breakdown of R7 resistance carried by several poplar cultivars widely planted in Western Europe since 1982. The corresponding virulence rapidly spread in M. larici‐populina populations and nearly reached fixation in northern France, even on susceptible hosts. Using both temporal records of virulence profiles and temporal population genetic data, our analyses revealed that (i) R7 resistance breakdown resulted in the emergence of a unique and homogeneous genetic group, the so‐called cultivated population, which predominated in northern France for about 20 years, (ii) selection for Vir7 individuals brought with it multiple other virulence types via hitchhiking, resulting in an overall increase in the population‐wide number of virulence types and (iii) – above all – the emergence of the cultivated population superseded the initial population which predominated at the same place before R7 resistance breakdown. Our temporal analysis illustrates how antagonistic co‐evolution can lead to population extinction and replacement, hence providing direct evidence for the escalation process which is at the core of Red Queen dynamics.
Prioritization of polysaccharide utilization and control of regulator activation in Bacteroides thetaiotaomicron
Authors: Schwalm Nathan D. , Townsend Guy E. , Groisman Eduardo A. 
Published: December 2016

SummaryBacteroides thetaiotaomicron is a human gut symbiotic bacterium that utilizes a myriad of host dietary and mucosal polysaccharides. The proteins responsible for the uptake and breakdown of many of these polysaccharides are transcriptionally regulated by hybrid two‐component systems (HTCSs). These systems consist of a single polypeptide harboring the domains of sensor kinases and response regulators, and thus, are thought to autophosphorylate in response to specific signals. We now report that the HTCS BT0366 is phosphorylated in vivo when B. thetaiotaomicron experiences the BT0366 inducer arabinan but not when grown in the presence of glucose. BT0366 phosphorylation and transcription of BT0366‐activated genes requires the conserved predicted sites of phosphorylation in BT0366. When chondroitin sulfate is added to arabinan‐containing cultures, BT0366 phosphorylation and transcription of BT0366‐activated genes are inhibited and the bacterium exhibits diauxic growth. Whereas 20 additional combinations of polysaccharides also give rise to diauxic growth, other combinations result in synergistic or unaltered growth relative to bacteria experiencing a single polysaccharide. The different strategies employed by B. thetaiotaomicron when faced with multiple polysaccharides may aid its competitiveness in the mammalian gut.
The GpsB files: the truth is out there
Authors: Lewis Richard J. 
Published: December 2016

SummaryPeptidoglycan (PG), an essential stress‐bearing component of the bacterial cell wall, is synthesised by penicillin binding proteins (PBPs). PG synthesis at the cell division septum is necessary for constructing new poles of progeny cells, and cells cannot elongate without inserting new PG in the side‐wall. The cell division regulator GpsB appears to co‐ordinate PG synthesis at the septum during division and at the side‐wall during elongation in rod‐shaped and ovococcoid Gram‐positive bacteria. How the control over PG synthesis is exerted is unknown. In this issue of Molecular Microbiology, Rued et al. show that in pneumococci GpsB forms complexes with PBP2a and PBP2b, and that deletion or depletion of GpsB prevents closure of the septal ring that in itself is PBP2x‐dependent. Loss of GpsB can be suppressed by spontaneous mutations, including within the gene encoding the only PP2C Ser/Thr phosphatase in Streptococcus pneumoniae, indicating that GpsB plays a key – but unknown – role in protein phosphorylation in pneumococci. Rued et al. combine phenotypic and genotypic analyses of mutant strains that suggest discrepancies in the literature concerning GpsB might have arisen from accumulation of unidentified suppressors, highlighting the importance and power of strain validation and whole genome sequencing in this context.
Relaxation of DNA supercoiling leads to increased invasion of epithelial cells and protein secretion by Campylobacter jejuni
Authors: Scanlan Eoin , Ardill Laura , Whelan Matthew V. X. , Shortt Claire , Nally Jarlath E. , Bourke Billy , Ó Cróinín Tadhg 
Published: December 2016

SummaryInvasion of intestinal epithelial cells by Campylobacter jejuni is a critical step during infection of the intestine by this important human pathogen. In this study we investigated the role played by DNA supercoiling in the regulation of invasion of epithelial cells and the mechanism by which this could be mediated. A significant correlation between more relaxed DNA supercoiling and an increased ability of C. jejuni strains to penetrate human epithelial cells was demonstrated. Directly inducing relaxation of DNA supercoiling in C. jejuni was shown to significantly increase invasion of epithelial cells. Mutants in the fibronectin binding proteins CadF and FlpA still displayed an increased invasion after treatment with novobiocin suggesting these proteins were not essential for the observed phenotype. However, a large increase in protein secretion from multiple C. jejuni strains upon relaxation of DNA supercoiling was demonstrated. This increase in protein secretion was not mediated by outer membrane vesicles and appeared to be dependent on an intact flagellar structure. This study identifies relaxation of DNA supercoiling as playing a key role in enhancing C. jejuni pathogenesis during infection of the human intestine and identifies proteins present in a specific invasion associated secretome induced by relaxation of DNA supercoiling.
Oral swirl samples – a robust source of microRNA protected by extracellular vesicles
Authors: Yap T , Vella LJ , Seers C , Nastri A , Reynolds E , Cirillo N , McCullough M 
Published: December 2016

BackgroundMicroRNAs are small non‐coding RNAs which are dysregulated in disease states, such as oral cancer. Extracellular vesicles, a potential source of microRNA, are found in saliva.ObjectiveTo demonstrate that a quantifiable amount of microRNA can be isolated from oral swirl samples. Additionally, we hypothesized that extracellular vesicles may protect contained microRNA from degradation in these samples.MethodA polyethylene glycol‐based precipitation was used for extracellular vesicle enrichment of oral swirl samples. Comparison was made between samples treated with and without RNase. Further, samples from three subjects were exposed to a range of conditions over 7 days and assessed for presence of microRNA by reverse‐transcription quantitative PCR. Extracellular vesicles from samples were identified under transmission electron microscopy.ResultsAn adequate quantity of microRNA for qPCR analysis was extractable from samples despite exposure to conditions under which degradation of RNA would be expected.ConclusionA technique was developed to isolate an adequate quantity of microRNA for analysis from oral swirl samples. Extracellular vesicle‐associated microRNA may be protected from degradation. This technique moves towards chairside application of translational microRNA research in the field of oral cancer prognostics.
Shale oil boom and the profitability of US petroleum refiners
Authors: Walls W. D. , Zheng Xiaoli 
Published: December 2016

AbstractThis article provides a quantitative analysis of how the recent boom in US oil production—largely a result of shale oil production—has impacted the domestic petroleum refining industry. We quantify how domestic crude prices are related to refiners’ financial performance. The estimates suggest that since 2011 independent refiners’ profitability rose by 3 per cent for a domestic crude oil price decrease of 1 per cent, while they were not associated with domestic crude prices before 2011. The relation between refinery profitability and domestic oil prices is consistent with the results of pass‐through of relative domestic crude prices to relative refined product prices in the United States before and since the dramatic rise in shale oil production.
Effects of oil price on food prices in developing oil exporting countries: a panel autoregressive distributed lag analysis
Authors: Olayungbo David , Hassan Wale 
Published: December 2016

AbstractThis study focused on the relationship between oil and food prices in developing oil‐exporting countries. Annual data sets of 31 developing oil‐exporting countries were employed. The study covered a period of 13 years, spanning 2001–2013. Given the mixed stationarity processes of the variables of interest, we adopted a panel autoregressive distributed lag (ARDL) approach, proposed by Pesaran et al. (2001, Journal of Applied Econometrics, 16, 289). The bound test cointegration showed a long‐run cointegration to exist between food prices and oil price in the sample countries. The long‐run result showed positive and significant effects of oil price on food prices while the short‐run effect was also positive but insignificant. We therefore conclude that oil price has a long‐run positive effect on food price and recommend that developing oil‐exporting countries should formulate long‐term agricultural policies to insulate their economies from any global food crisis that may result from oil price changes.
(ANTI)‐Anti‐Intellectualism and the Sufficiency Thesis
Authors: Carter J. Adam , Czarnecki Bolesław 
Published: December 2016

AbstractAnti‐intellectualists about knowledge‐how insist that, when an agent S knows how to φ, it is in virtue of some ability, rather than in virtue of any propositional attitudpaes, S has. Recently, a popular strategy for attacking the anti‐intellectualist position proceeds by appealing to cases where an agent is claimed to possess a reliable ability to φ while nonetheless intuitively lacking knowledge‐how to φ. John Bengson and Marc Moffett and Carlotta Pavese have embraced precisely this strategy and have thus claimed, for different reasons, that anti‐intellectualism is defective on the grounds that possessing the ability to φ is not sufficient for knowing how to φ. We investigate this strategy of argument‐by‐counterexample to the anti‐intellectualist's sufficiency thesis and show that, at the end of the day, anti‐intellectualism remains unscathed.
Atmospheric CO2 mole fraction affects stand‐scale carbon use efficiency of sunflower by stimulating respiration in light
Authors: Gong Xiao Ying , Schäufele Rudi , Lehmeier Christoph Andreas , Tcherkez Guillaume , Schnyder Hans 
Published: December 2016

AbstractPlant carbon‐use‐efficiency (CUE), a key parameter in carbon cycle and plant growth models, quantifies the fraction of fixed carbon that is converted into net primary production rather than respired. CUE has not been directly measured, partly because of the difficulty of measuring respiration in light. Here, we explore if CUE is affected by atmospheric CO2. Sunflower stands were grown at low (200 μmol mol−1) or high CO2 (1000 μmol mol−1) in controlled environment mesocosms. CUE of stands was measured by dynamic stand‐scale 13C labelling and partitioning of photosynthesis and respiration. At the same plant age, growth at high CO2 (compared with low CO2) led to 91% higher rates of apparent photosynthesis, 97% higher respiration in the dark, yet 143% higher respiration in light. Thus, CUE was significantly lower at high (0.65) than at low CO2 (0.71). Compartmental analysis of isotopic tracer kinetics demonstrated a greater commitment of carbon reserves in stand‐scale respiratory metabolism at high CO2. Two main processes contributed to the reduction of CUE at high CO2: a reduced inhibition of leaf respiration by light and a diminished leaf mass ratio. This work highlights the relevance of measuring respiration in light and assessment of the CUE response to environment conditions.
Evaluation of tubulin β‐3 as a novel senescence‐associated gene in melanocytic malignant transformation
Authors: Orfanidis Kyriakos , Wäster Petra , Lundmark Katarzyna , Rosdahl Inger , Öllinger Karin 
Published: December 2016

SummaryMalignant melanoma might develop from melanocytic nevi in which the growth‐arrested state has been broken. We analyzed the gene expression of young and senescent human melanocytes in culture and compared the gene expression data with a dataset from nevi and melanomas. A concordant altered gene expression was identified in 84 genes when comparing the growth‐arrested samples with proliferating samples. TUBB3, which encodes the microtubule protein tubulin β‐3, showed a decreased expression in senescent melanocytes and nevi and was selected for further studies. Depletion of tubulin β‐3 caused accumulation of cells in the G2/M phase and decreased proliferation and migration. Immunohistochemical assessment of tubulin β‐3 in benign lesions revealed strong staining in the superficial part of the intradermal components, which faded with depth. In contrast, primary melanomas exhibited staining without gradient in a disordered pattern and strong staining of the invasive front. Our results describe an approach to find clinically useful diagnostic biomarkers to more precisely identify cutaneous malignant melanoma and present tubulin β‐3 as a candidate marker.
Genetic analysis of Phytophthora sojae populations in Fujian, China
Authors: Wu M. , Li B. , Liu P. , Weng Q. , Zhan J. , Chen Q. 
Published: December 2016

Phytophthora sojae is a destructive soilborne pathogen causing seedling damping‐off and root rot of soybean (Glycine max). The goal of this study was to determine the genetic structure of P. sojae populations in Fujian, China. Nine microsatellite markers were used to investigate the genetic variation in 19 P. sojae populations, sampled from Fujian Province and northeastern China (Jilin and Heilongjiang Provinces) between 2002 and 2013. Overall, a low genetic diversity, Hardy–Weinberg disequilibrium, and an index (an index of association) that was significantly different from zero were detected in populations; these results were consistent with self‐fertilization and clonal modes of reproduction for this pathogen. However, using Bayesian Markov chain Monte Carlo approach, principal component analysis and neighbour joining (NJ) algorithm, the Fujian P. sojae populations clustered into three distinct groups, one of which included most isolates of the northeast populations. What is more, significant estimates of pairwise fixation indices (FST) were detected between most populations, especially in different clusters. It is hypothesized that the cropping system used, the limited dispersal ability, and human‐mediated gene flow may account for the observed genetic structure of P. sojae populations in Fujian, China. In addition, a high virulence frequency of the pathogen on different cultivars carrying known major R genes for resistance, and a rapid increase in virulence frequency, indicated that these major R genes should not be used to manage seedling damping‐off and root rot diseases of soybean (Glycine max).
Causal Linkages among the Product Diversification of Exports, Economic Globalization and Economic Growth
Authors: Gözgör Giray , Can Muhlis 
Published: December 2016

AbstractThis paper examines causal relationships between economic globalization, the three indices for product diversification of exports (Theil index, intensive margin and extensive margin) and economic growth in the unbalanced panel data framework in 139 countries over the period 1970–2010. We also consider the subgroup of the countries related to the income levels and run the panel Granger non‐causality tests for heterogeneous panels. The empirical results indicate that there is a bidirectional causal relationship between economic globalization and economic growth. There is also a significant causal relationship that runs from all three indices for the diversification of exports to economic growth. After implementing various robustness checks, we observe that diversification of exports and economic globalization are positively related with economic growth merely in the upper middle economies.
A site selection method of DNS using the particle swarm optimization algorithm
Authors: Liao Yilan , Chen Wenwen , Wu Kaichao , Li Dongyue , Liu Xin , Geng Guanggang , Su Zheng , Zheng Zheng 
Published: December 2016

AbstractThe Domain Name System (DNS) is an essential component of the functionality of the Internet. With the growing number of domain names and Internet users, the growing rate and number of visit quantity and analytic capacity of DNS are also proportional to the Internet users' size. This study (based on the analysis of access popularity and the distribution of massive DNS log data) aims to optimize the configuration of the DNS sites, which has become an important problem. The ArcGIS software is used to show the temporal and spatial distributions of visit source of DNS logs. This study also analyzes the influence of different sites and the dependence on DNS service in different regions of the world. This information is important to further decision‐making on new DNS site selection. This article proposes new DNS site selection solutions, using particle swarm and multi‐objective particle swarm optimization algorithms for one new site and multiple sites, respectively. The results from particle swarm optimization, genetic, and simulated annealing algorithms were compared and experimental results confirmed the correctness and effectiveness of the proposed methods. The proposed methods could also be extended to solve other layout related issues, such as onsite facility layout and road network optimization.
Improved planning of leukapheresis endpoint with customized prediction algorithm: minimizing collection days, volume of blood processed, procedure time, and citrate toxicity
Authors: Leberfinger Daniel L. , Badman Kira L. , Roig Joseph M. , Loos Tamara 
Published: December 2016

BACKGROUNDIncreased emphasis on cost and productivity in apheresis centers calls for a proficient and predictable hematopoietic progenitor cell (HPC) collection. Therefore, the aim of this study was to determine the value of a customized predictive algorithm that estimates how many blood volumes are required to process for a targeted CD34 cell dose.STUDY DESIGN AND METHODSRetrospective analysis was performed on 107 HPC collections completed on the Spectra Optia MNC from January 2013 to June 2014 in 51 patients and 12 donors. In December 2014, a prediction algorithm was implemented, designed from data acquired since January 2013, by linear regression of preapheresis CD34 cell counts (pre‐CD34) versus collected CD34 cell dose per volume blood processed.RESULTSCD34 collection efficiencies (CE2) of 51.9 ± 1.7% (mean ± SEM) and 57.5 ± 3.0% were observed in autologous and allogeneic procedures, respectively. After implementation of the algorithm, the mean number of collections per patient declined from 1.97 to 1.5. Accordingly, the frequency of patients requiring single‐day collections increased from 35% to 57%. All donors were collected in single procedures, although only 12.2 ± 1.1 L blood was processed, including for National Marrow Donor Program collections. Cumulative procedure time, processed blood volume, product volume, infused anticoagulant volume, and symptomatic calcium administration decreased in patients, and overcollection was limited.CONCLUSIONA prediction algorithm can provide great value in the planning of leukapheresis, which may optimize resource utilization and capacity of the unit. In addition, predictability was facilitated by a proficient and consistent performance of the Spectra Optia MNC.