bluuebunny/crossref_metadata_2025 huggingface dataset:
X-chromosome inactivation and its implications for human disease
Authors: Gribnau Joost , Stefan Barakat Tahsin
Published: March 2017

In humans and other mammals, female cells carry two X-chromosomes, whereas male cells carry a single X and Y-chromosome. To achieve an equal expression level of X-linked genes in both sexes, a dosage compensation mechanism evolved, which results in transcriptional silencing of one X-chromosome in females. X chromosome inactivation (XCI) is random with respect to the parental origin of the X, occurs early during embryonic development, and is then stably maintained through a near infinite number of cell divisions. As a result of this, every female individual consists of a mosaic of two different cell populations, in which either the maternally or paternally derived X-chromosome is inactivated. As the X-chromosome harbors more than a thousand genes, of which many are implicated in human disease when mutated, this mosaicism has important disease implications. Whereas X-linked disorders are usually more severe in hemizygous males harboring a single X-chromosome, a more variable phenotype is observed in females. This variability is a direct consequence of the XCI-mosaicism, and is affected by the randomness of the XCI process. Here we review the latest insights into the regulation of this important female specific process, and discuss mechanisms that influence mosaicism in females, with a focus on the clinical consequences related to X-linked diseases in females.
Association of pre-pregnancy body mass index with future offspring metabolic profile: findings from three independent European birth cohorts
Authors: Santos Ferreira Diana L. , Williams Dylan M. , Kangas Antti J. , Soininen Pasi , Ala-Korpela Mika , Smith George Davey , Jarvelin Marjo-Riitta , Lawlor Debbie A.
Published: March 2017

Background

A high proportion of women start pregnancy overweight/obese. According to the developmental overnutrition hypothesis, this could lead offspring to have metabolic disruption throughout their lives, and, thus perpetuate the obesity epidemic across generations. Concerns about this hypothesis are influencing antenatal care. However, it is unknown whether maternal pregnancy adiposity is associated with long-term risk of adverse metabolic profiles in offspring, and if so, whether this association is causal, via intrauterine mechanisms, or explained by shared familial (genetic, lifestyle, socioeconomic) characteristics. We aimed to determine if associations between maternal body mass index (BMI) with offspring systemic metabolite profile are causal via intrauterine mechanisms or familial factors.

Methods and Findings

We used one and two-stage individual participant data (IPD) metaanalysis, and a negative-control (paternal BMI) to examine the association between maternal prepregnancy BMI and offspring serum metabolome from three European birth cohorts (offspring age at metabolite assessment 16, 17 and 31 years). Circulating metabolites were quantified by high-throughput nuclear magnetic resonance metabolomics. Results from one-stage IPD meta-analysis (N=5327 to 5377 mother-father-offspring trios) showed that increasing maternal and paternal BMI was associated with an adverse cardio-metabolic profile in offspring. We observed strong positive associations with VLDL-lipoproteins, VLDL-C, VLDL-triglycerides, VLDL-diameter, branched/aromatic amino acids, glycoprotein acetyls, and triglycerides, and strong negative associations with HDL-lipoprotein, HDL-diameter, HDL-C, HDL2-C and HDL3-C (all P<0.003). Stronger magnitudes of associations were present for maternal compared with paternal BMI across these associations, however there was no strong statistical evidence for heterogeneity between them (all bootstrap P >0.003, equivalent to 0.05 after accounting for multiple testing). Results were similar in each individual cohort, and in the two-stage analysis. Offspring BMI showed similar patterns of crosssectional association with metabolic profiles as for parental pre-pregnancy BMI associations, but with greater magnitudes. Adjustment of the parent BMI-offspring metabolite associations for offspring BMI suggested the parental associations were largely due to the association of parental BMI measures with offspring BMI.

Conclusion

Our findings suggest that maternal BMI-offspring metabolome associations are likely to be largely due to shared genetic or familial lifestyle confounding, rather than intrauterine programming mechanisms. They do not support the introduction of measures to reduce maternal BMI in order to prevent adverse offspring cardio-metabolic health.
Scaling up DNA data storage and random access retrieval
Authors: Organick Lee , Ang Siena Dumas , Chen Yuan-Jyue , Lopez Randolph , Yekhanin Sergey , Makarychev Konstantin , Racz Miklos Z. , Kamath Govinda , Gopalan Parikshit , Nguyen Bichlien , Takahashi Christopher , Newman Sharon , Parker Hsing-Yeh , Rashtchian Cyrus , Stewart Kendall , Gupta Gagan , Carlson Robert , Mulligan John , Carmean Douglas , Seelig Georg , Ceze Luis , Strauss Karin
Published: March 2017

Current storage technologies can no longer keep pace with exponentially growing amounts of data.1Synthetic DNA offers an attractive alternative due to its potential information density of ~ 1018B/mm3, 107times denser than magnetic tape, and potential durability of thousands of years.2Recent advances in DNA data storage have highlighted technical challenges, in particular, coding and random access, but have stored only modest amounts of data in synthetic DNA.3,4,5This paper demonstrates an end-to-end approach toward the viability of DNA data storage with large-scale random access. We encoded and stored 35 distinct files, totaling 200MB of data, in more than 13 million DNA oligonucleotides (about 2 billion nucleotides in total) and fully recovered the data with no bit errors, representing an advance of almost an order of magnitude compared to prior work.6Our data curation focused on technologically advanced data types and historical relevance, including the Universal Declaration of Human Rights in over 100 languages,7a high-definition music video of the band OK Go,8and a CropTrust database of the seeds stored in the Svalbard Global Seed Vault.9We developed a random access methodology based on selective amplification, for which we designed and validated a large library of primers, and successfully retrieved arbitrarily chosen items from a subset of our pool containing 10.3 million DNA sequences. Moreover, we developed a novel coding scheme that dramatically reduces the physical redundancy (sequencing read coverage) required for error-free decoding to a median of 5x, while maintaining levels of logical redundancy comparable to the best prior codes. We further stress-tested our coding approach by successfully decoding a file using the more error-prone nanopore-based sequencing. We provide a detailed analysis of errors in the process of writing, storing, and reading data from synthetic DNA at a large scale, which helps characterize DNA as a storage medium and justify our coding approach. Thus, we have demonstrated a significant improvement in data volume, random access, and encoding/decoding schemes that contribute to a whole-system vision for DNA data storage.
A powerful approach to estimating annotation-stratified genetic covariance using GWAS summary statistics
Authors: Lu Qiongshi , Li Boyang , Ou Derek , Erlendsdottir Margret , Powles Ryan L. , Jiang Tony , Hu Yiming , Chang David , Jin Chentian , Dai Wei , He Qidu , Liu Zefeng , Mukherjee Shubhabrata , Crane Paul K. , Zhao Hongyu
Published: March 2017

Despite the success of large-scale genome-wide association studies (GWASs) on complex traits, our understanding of their genetic architecture is far from complete. Jointly modeling multiple traits’ genetic profiles has provided insights into the shared genetic basis of many complex traits. However, large-scale inference sets a high bar for both statistical power and biological interpretability. Here we introduce a principled framework to estimate annotation-stratified genetic covariance between traits using GWAS summary statistics. Through theoretical and numerical analyses we demonstrate that our method provides accurate covariance estimates, thus enabling researchers to dissect both the shared and distinct genetic architecture across traits to better understand their etiologies. Among 50 complex traits with publicly accessible GWAS summary statistics (Ntotal≈ 4.5 million), we identified more than 170 pairs with statistically significant genetic covariance. In particular, we found strong genetic covariance between late-onset Alzheimer’s disease (LOAD) and amyotrophic lateral sclerosis (ALS), two major neurodegenerative diseases, in single-nucleotide polymorphisms (SNPs) with high minor allele frequencies and in SNPs located in the predicted functional genome. Joint analysis of LOAD, ALS, and other traits highlights LOAD’s correlation with cognitive traits and hints at an autoimmune component for ALS.
Soft sweeps and beyond: Understanding the patterns and probabilities of selection footprints under rapid adaptation
Authors: Hermisson Joachim , Pennings Pleuni S
Published: March 2017

The tempo and mode of adaptive evolution determine how natural selection shapes patterns of genetic diversity in DNA polymorphism data. While slow mutation-limited adaptation leads to classical footprints of “hard” selective sweeps, these patterns are different when adaptation responds quickly to a novel selection pressure, acting either on standing genetic variation or on recurrent new mutation. In the past decade, corresponding footprints of “soft” selective sweeps have been described both in theoretical models and in empirical data.

Here, we summarize the key theoretical concepts and contrast model predictions with observed patterns inDrosophila,humans, and microbes.

Evidence in all cases shows that “soft” patterns of rapid adaptation are frequent. However, theory and data also point to a role of complex adaptive histories in rapid evolution.

While existing theory allows for important implications on the tempo and mode of the adaptive process, complex footprints observed in data are, as yet, insufficiently covered by models. They call for in-depth empirical study and further model development.
An epigenome-wide association study of educational attainment (n= 10,767)
Authors: Karlsson Linnér Richard , Marioni Riccardo E , Rietveld Cornelius A , Simpkin Andrew , Davies Neil M , Watanabe Kyoko , Armstrong Nicola J , Auro Kirsi , Baumbach Clemens , Bonder Marc Jan , Buchwald Jadwiga , Fiorito Giovanni , Ismail Khadeeja , Iurato Stella , Joensuu Anni , Karell Pauliina , Kasela Silva , Lahti Jari , McRae Allan F , Mandaviya Pooja R , Seppälä Ilkka , Wang Yunzhang , Baglietto Laura , Binder Elisabeth B , Harris Sarah E , Hodge Allison M , Horvath Steve , Hurme Mikko , Johannesson Magnus , Latvala Antti , Mather Karen A , Medland Sarah E , Metspalu Andres , Milani Lili , Milne Roger L , Pattie Alison , Pedersen Nancy L , Peters Annette , Polidoro Silvia , Räikkönen Katri , Severi Gianluca , Starr John M , Stolk Lisette , Waldenberger Melanie ,   BIOS Consortium, Eriksson Johan G , Esko Tõnu , Franke Lude , Gieger Christian , Giles Graham G , Hägg Sara , Jousilahti Pekka , Kaprio Jaakko , Kähönen Mika , Lehtimäki Terho , Martin Nicholas G , van Meurs Joyce B. C , Ollikainen Miina , Perola Markus , Posthuma Danielle , Raitakari Olli T , Sachdev Perminder S , Taskesen Erdogan , Uitterlinden André G , Vineis Paolo , Wijmenga Cisca , Wright Margaret J , Relton Caroline , Davey Smith George , Deary Ian J , Koellinger Philipp D , Benjamin Daniel J
Published: March 2017

The epigenome has been shown to be influenced by biological factors, such as disease status, and environmental factors, such as smoking, alcohol consumption, and body mass index. Although there is a widespread perception that environmental influences on the epigenome are pervasive and profound, there has been little evidence to date in humans with respect to environmental factors that are biologically distal. Here, we provide evidence on the associations between epigenetic modifications—in our case, CpG methylation—and educational attainment (EA), a biologically distal environmental factor that is arguably among of the most important life-shaping experiences for individuals. Specifically, we report the results of an epigenome-wide association study meta-analysis of EA based on data from 27 cohort studies with a total of 10,767 individuals. While we find that 9 CpG probes are significantly associated with EA, only two remain associated when we restrict the sample to never-smokers. These two are known to be strongly associated with maternal smoking during pregnancy, and thus their association with EA could be due to correlation between EA and maternal smoking. Moreover, their effect sizes on EA are far smaller than the known associations between CpG probes and biologically proximal environmental factors. Two analyses that combine the effects of many probes—polygenic methylation score and epigenetic-clock analyses—both suggest small associations with EA. If our findings regarding EA can be generalized to other biologically distal environmental factors, then they cast doubt on the hypothesis that such factors have large effects on the epigenome.
A DNA demethylase overexpression promotes early apical bud maturation in poplar through the biosynthesis and accumulation of flavonoids
Authors: Conde Daniel , Moreno-Cortés Alicia , Dervinis Christopher , Ramos-Sánchez José M. , Kirst Matias , Perales Mariano , González-Melendi Pablo , Allona Isabel
Published: March 2017

ASBTRACT

The transition from active growth to dormancy is critical for the survival of perennial plants. We identified aDEMETER-like(CsDML) cDNA from a winter-enriched cDNA subtractive library in chestnut(Castanea sativaMill.), an economically and ecologically important species. Next, we characterized this DNA demethylase and its putative orthologue in the more experimentally tractable hybrid poplar(Populus tremula × alba),under the signals that trigger bud dormancy in trees. We performed phylogenetic and protein sequence analysis, gene expression profiling and 5mC immunodetection studies to evaluate the role of CsDML and its homologue in poplar, PtaDML6. Transgenic hybrid poplars overexpressingCsDMLwere produced and analyzed. Short days (SD) and cold temperatures inducedCsDMLandPtaDML6.Overexpression ofCsDMLaccelerated SD-induced bud formation, specifically from stage 1 to 0. Bud acquired a red-brown coloration earlier than wild type (WT) plants, alongside with the upregulation of flavonoid biosynthesis enzymes and accumulation of flavonoids in the SAM and bud scales. Our data shows that theCsDMLgene induces bud formation needed for the survival of the apical meristem under the harsh conditions of winter. This study providesin plantaevidence implicating chromatin remodeling by DNA demethylation during SD induction of bud maturation through the induction of flavonoids biosynthesis.
The genome sizes of ostracod crustaceans correlate with body size and phylogeny
Authors: Jeffery Nicholas W. , Ellis Emily A. , Oakley Todd H. , Gregory T. Ryan
Published: March 2017

Within animals a positive correlation between genome size and body size has been detected in several taxa but not in others, such that it remains unknown how pervasive this pattern may be. Here we provide another example of a positive relationship, in a group of crustaceans whose genome sizes have not previously been investigated. We analyze genome size estimates for 46 species across Class Ostracoda, including 29 new estimates made using Feulgen image analysis densitometry and flow cytometry. Genome sizes in this group range ~80-fold, a level of variability that is otherwise not seen in crustaceans with the exception of some malacostracan orders. We find a strong positive correlation between genome size and body size across all species, including after phylogenetic correction. We additionally detect evidence of XX/XO sex determination in all three species of myodocopids where male and female genome sizes were estimated. On average, genome sizes are larger but less variable in myodocopids than in podocopids, and marine ostracods have larger genomes than freshwater species, but this appears to be explained by phylogenetic inertia. The relationship between phylogeny, genome size, body size, and habitat is complex in this system, and will benefit from additional data collection across various habitats and ostracod taxa.
The theoretical molecular weight of NaYF4:RE upconversion nanoparticles
Authors: Mackenzie Lewis E. , Goode Jack A. , Vakurov Alexandre , Nampi Padmaja P. , Saha Sikha , Jose Gin , Millner Paul A.
Published: March 2017

Upconversion nanoparticles (UCNPs) are utilized extensively for biomedical imaging, sensing, and therapeutic applications, yet the molecular weight of UCNPs has not previously been reported. We present a theory based upon the crystal structure of UCNPs to estimate the molecular weight of UCNPs: enabling insight into UCNP molecular weight for the first time. We estimate the theoretical molecular weight of various UCNPs reported in the literature, predicting that spherical NaYF4 UCNPs ~ 10 nm in diameter will be ~1 MDa (i.e. 106g/mol), whereas UCNPs ~ 45 nm in diameter will be ~100 MDa (i.e. 108g/mol). We also predict that hexagonal crystal phase UCNPs will be of greater molecular weight than cubic crystal phase UCNPs. Additionally we find that a Gaussian UCNP diameter distribution will correspond to a lognormal UCNP molecular weight distribution. Our approach could potentially be generalised to predict the molecular weight of other arbitrary crystalline nanoparticles: as such, we provide standalone graphic user interfaces to calculate the molecular weight both UCNPs and arbitrary crystalline nanoparticles. We expect knowledge of UCNP molecular weight to be of wide utility in biomedical applications where reporting UCNP quantity in absolute numbers or molarity will be beneficial for inter-study comparison and repeatability.
Organizational Hierarchy and Structural Diversity of Microvascular Pericytes in Adult Mouse Cortex
Authors: Grant Roger I. , Hartmann David A. , Underly Robert G. , Berthiaume Andrée-Anne , Bhat Narayan R. , Shih Andy Y.
Published: March 2017

Smooth muscle cells and pericytes, together called mural cells, coordinate many distinct vascular functions. Smooth muscle cells are ring-shaped and cover arterioles with circumferential processes, whereas pericytes extend thin processes that run longitudinally along capillaries. In between these canonical mural cell types are cells with mixed phenotype of both smooth muscle cells and pericytes. Recent studies suggest that these transitional cells are critical for controlling blood flow to the capillary bed during health and disease, but there remains confusion on how to identify them and where they are located in the brain microvasculature. To address this issue, we measured the morphology, vascular territory, and α-smooth muscle actin content of structurally diverse mural cells in adult mouse cortex. We first imaged intact 3-D vascular networks to establish the locations of major gradations in mural cell appearance as arterioles branched into capillaries. We then imaged individual mural cells occupying the regions within these gradations. This revealed two transitional cells that were often similar in appearance, but with sharply contrasting levels of α-smooth muscle actin. Our findings highlight the diversity of mural cell morphologies in brain microvasculature, and provide guidance for identification and categorization of mural cell types.
Bayesian and likelihood phylogenetic reconstructions of morphological traits are not discordant when taking uncertainty into consideration. A comment on Putticket al
Authors: Brown Joseph W. , Parins-Fukuchi Caroline , Stull Gregory W. , Vargas Oscar M. , Smith Stephen A.
Published: March 2017

Putticket al.[1] performed a simulation study to compare accuracy among methods of inferring phylogeny from discrete morphological characters. They report that a Bayesian implementation of the Mk model [2] was most accurate (but with low resolution), while a maximum likelihood (ML) implementation of the same model was least accurate. They conclude by strongly advocating that Bayesian implementations of the Mk model should be the default method of analysis for such data. While we appreciate the authors’ attempt to investigate the accuracy of alternative methods of analysis, their conclusion is based on an inappropriate comparison of the ML point estimate, which does not consider confidence, with the Bayesian consensus, which incorporates estimation credibility into the summary tree. Using simulation, we demonstrate that ML and Bayesian estimates are concordant when confidence and credibility are comparably reflected in summary trees, a result expected from statistical theory. We therefore disagree with the conclusions of PEA and consider their prescription of any default method to be poorly founded. Instead, we recommend caution and thoughtful consideration of the model or method being applied to a morphological dataset.
Prophage genomics reveals patterns in phage genome organization and replication
Authors: Kang Han Suh , McNair Katelyn , Cuevas Daniel A. , Bailey Barbara A. , Segall Anca M. , Edwards Robert A.
Published: March 2017

Temperate phage genomes are highly variable mosaic collections of genes that infect a bacterial host, integrate into the host’s genome or replicate as low copy number plasmids, and are regulated to switch from the lysogenic to lytic cycles to generate new virions and escape their host. Genomes from most Bacterial phyla contain at least one or more prophages. We updated our PhiSpy algorithm to improve detection of prophages and to provide a web-based framework for PhiSpy. We have used this algorithm to identify 36,488 prophage regions from 11,941 bacterial genomes, including almost 600 prophages with no known homology to any proteins. Transfer RNA genes were abundant in the prophages, many of which alleviate the limits of translation efficiency due to host codon bias and presumably enable phages to surpass the normal capacity of the hosts’ translation machinery. We identified integrase genes in 15,765 prophages (43% of the prophages). The integrase was routinely located at either end of the integrated phage genome, and was used to orient and align prophage genomes to reveal their underlying organization. The conserved genome alignments of phages recapitulate early, middle, and late gene order in transcriptional control of phage genes, and demonstrate that gene order, presumably selected by transcription timing and/or coordination among functional modules has been stably conserved throughout phage evolution.
Position Effects Influencing Intrachromosomal Repair of a Double-Strand Break in Budding Yeast
Authors: Wang Ruoxi W. , Lee Cheng-Sheng , Haber James E.
Published: March 2017

Repair of a double-strand break (DSB) by an ectopic homologous donor sequence is subject to the three-dimensional arrangement of chromosomes in the nucleus of haploid budding yeast. The data for interchromosomal recombination suggest that searching for homology is accomplished by a random collision process, strongly influenced by the contact probability of the donor and recipient sequences. Here we explore how recombination occurs on the same chromosome and whether there are additional constraints imposed on repair. Specifically, we examined how intrachromosomal repair is affected by the location of the donor sequence along the 812-kb chromosome 2 (Chr2), with a site-specific DSB created on the right arm (position 625kb). Repair correlates well with contact frequencies determined by chromosome conformation capture-based studies (r= 0.85). Moreover, there is a profound constraint imposed by the anchoring of the centromere (CEN2,position 238kb) to the spindle pole body. Sequences at the same distance on either side ofCEN2are equivalently constrained in recombining with a DSB located more distally on one arm, suggesting that sequences on the opposite arm from the DSB are not otherwise constrained in their interaction with the DSB. The centromere constraint can be partially relieved by inducing transcription through the centromere to inactivateCEN2tethering. In diploid cells, repair of a DSB via its allelic donor is strongly influenced by the presence and the position of an ectopic intrachromosomal donor.

Author Summary

A double-strand break (DSB) on a chromosome can be repaired by recombining with an ectopic homologous donor sequence. Interchromosomal ectopic recombination is strongly influenced by the three-dimensional arrangement of chromosomes in the nucleus of haploid budding yeast, that is strongly influenced by the probability of chemical cross-linking of the donor and recipient sequences. Here we explore how recombination occurs on the same chromosome. We examined how intrachromosomal repair is affected by the location of the donor sequence along the 812-kb chromosome 2 (Chr2), with a site-specific DSB created on the right arm (position 625kb). Repair correlates well with contact frequencies determined by chromosome conformation capture-based studies (r= 0.85). Moreover, there is a profound constraint imposed by the anchoring of the centromere (CEN2, position 238kb) to the spindle pole body. Sequences at the same distance on either side ofCEN2are equivalently accessible in recombining with a DSB located more distally on one arm, suggesting that sequences on the opposite arm from the DSB are not otherwise constrained in their interaction with the DSB. The centromere constraint can be partially relieved by inducing transcription through the centromere to inactivateCEN2tethering. In diploid cells, repair of a DSB via its allelic donor is strongly influenced by the presence and the position of an ectopic intrachromosomal donor.
Polymorphic dynamics of ribosomal proteins gene expression during somatic cell reprogramming and their differentiation in to specialized cells-types
Authors: Guthikonda Prashanth Kumar , Bharathan Sumitha Prameela , Rayabaram Janakiram , Sornapudi Trinadha Rao , Yellaboina Sailu , Velayudhan Shaji Ramachandran , Kurukuti Sreenivasulu
Published: March 2017

Factor induced pluripotent stem cells (iPSCs) offer great promise in regenerative medicine. However, accumulating evidence suggests that iPSCs are heterogeneous in comparison with embryonic stem cells (ESCs), and that is attributed to various genetic and epigenetic states of donor cells. In the light of the discovery of cell-type specialized ribosomal protein composition, its role as the cells transit through different stages of reprogramming and when iPSCs differentiate into specialized cell-types has not been explored to understand its influence in the reprogramming and differentiation process and outcome. By re-analyzing the publicly available gene expression datasets among ESCs, various sources of iPSCs and somatic cells and by studying the ribosomal protein gene expression during different stages of reprogramming of somatic cells and different passages of established iPSCs we found distinct patterns of their expression across multiple cell-types. We experimentally validated these results on the cells undergoing reprogramming from human dermal fibroblasts. Finally, by comparing publicly available data from iPSCs, iPSCs derived specialized cells and it’sin vivocounterparts, we show alterations in ribosomal gene expression during differentiation of specialized cells from iPSCs which may have Implications in the context of ribosomopathies. Our results provide an informatics framework for researchers in efficient generation of iPSCs that are equivalent to ESCs.
Improper Localization of the OmcS Cytochrome May Explain the Inability of thexapD-Deficient Mutant ofGeobacter sulfurreducensto Reduce Fe(III) Oxide
Authors: Flanagan Kelly A. , Leang Ching , Ward Joy E. , Lovley Derek R.
Published: March 2017

Extracellular electron transfer through a redox-active exopolysaccharide matrix has been proposed as a strategy for extracellular electron transfer to Fe(III) oxide byGeobacter sulfurreducens,based on the phenotype of axapD-deficient strain. Central to this model was the assertion that thexapD-deficient strain produced pili decorated with the multi-hemec-type cytochrome OmcS in manner similar to the wild-type strain. Further examination of thexapD-deficient strain with immunogold labeling of OmcS and transmission electron microscopy revealed that OmcS was associated with the outer cell surface rather than pili. PilA, the pilus monomer, could not be detected in thexapD-deficient strain under conditions in which it was readily detected in the wild-type strain. Multiple lines of evidence in previous studies have suggested that long-range electron transport to Fe(III) oxides proceeds through electrically conductive pili and that OmcS associated with the pili is necessary for electron transfer from the pili to Fe(III) oxides. Therefore, an alternative explanation for the Fe(III) oxide reduction phenotype of thexapD-deficientstrain is that the pili-OmcS route for extracellular electron transport to Fe(III) oxide has been disrupted in thexapD-deficient strain.
Molybdenum-based diazotrophy in aSphagnumpeatland in northern Minnesota
Authors: Warren Melissa J. , Lin Xueju , Gaby John C. , Kretz Cecilia B. , Kolton Max , Morton Peter L. , Pett-Ridge Jennifer , Weston David J. , Schadt Christopher W. , Kostka Joel E. , Glass Jennifer B.
Published: March 2017

Microbial N2fixation (diazotrophy) represents an important nitrogen source to oligotrophic peatland ecosystems, which are important sinks for atmospheric CO2and susceptible to changing climate. The objectives of this study were: (i) to determine the active microbial group and type of nitrogenase mediating diazotrophy in a ombrotrophicSphagnum-dominated peat bog (the S1 peat bog, Marcell Experimental Forest, Minnesota, USA); and (ii) to determine the effect of environmental parameters (light, O2, CO2, CH4) on potential rates of diazotrophy measured by acetylene (C2H2) reduction and15N2incorporation. Molecular analysis of metabolically active microbial communities suggested that diazotrophy in surface peat was primarily mediated byAlphaproteobacteria(BradyrhizobiaceaeandBeijerinckiaceae). Despite higher dissolved vanadium (V; 11 nM) than molybdenum (Mo; 3 nM) in surface peat, a combination of metagenomic, amplicon sequencing and activity measurements indicated that Mo-containing nitrogenases dominate over the V-containing form. Acetylene reduction was only detected in surface peat exposed to light, with the highest rates observed in peat collected from hollows with the highest water content. Incorporation of15N2was suppressed 90% by O2and 55% by C2H2, and was unaffected by CH4and CO2amendments. These results suggest that peatland diazotrophy is mediated by a combination of C2H2- sensitive and C2H2- insensitive microbes that are more active at low O2and show similar activity at high and low CH4.

Importance

Previous studies indicate that diazotrophy provides an important nitrogen source and is linked to methanotrophy inSphagnum-dominated peatlands. However, the environmental controls and enzymatic pathways of peatland diazotrophy, as well as the metabolically active microbial populations that catalyze this process remain in question. Our findings indicate that oxygen levels and photosynthetic activity override low nutrient availability in limiting diazotrophy, and that members of theAlphaproteobacteria(Rhizobiales) catalyze this process at the bog surface using the molybdenum - based form of the nitrogenase enzyme.
A new stochastic multi source approach to improve the accuracy of the sales forecasts
Authors: Cassettari Lucia , Bendato Ilaria , Mosca Marco , Mosca Roberto
Published: March 2017

Purpose

The aim of this paper is to suggest a new approach to the problem of sales forecasting for improving forecast accuracy. The proposed method is capable of combining, by means of appropriate weights, both the responses supplied by the best-performing conventional algorithms, which base their output on historical data, and the insights of company’s forecasters which should take account future events that are impossible to predict with traditional mathematical methods.

Design/methodology/approach

The authors propose a six-step methodology using multiple forecasting sources. Each of these forecasts, to consider the uncertainty of the variables involved, is expressed in the form of suitable probability density function. A proper use of the Monte Carlo Simulation allows obtaining the best fit among these different sources and to obtain a value of forecast accompanied by a probability of error known a priori.

Findings

The proposed approach allows the company’s demand forecasters to provide timely response to market dynamics and make a choice of weights, gradually ever more accurate, triggering a continuous process of forecast improvement. The application on a real business case proves the validity and the practical utilization of the methodology.

Originality/value

Forecast definition is normally entrusted to the company’s demand forecasters who often may radically modify the information suggested by the conventional prediction algorithms or, contrarily, can be too influenced by their output. This issue is the origin of the methodological approach proposed that aims to improve the forecast accuracy merging, with appropriate weights and taking into account the stochasticity involved, the outputs of sales forecast algorithms with the contributions of the company’s forecasters.
Wildcards – natural and artificial: the combination of a panel of experts and Fuzzy TOPSIS
Authors: Mohammadi Mohsen , Eivazi Mohammad Rahim , Sajjadi Jafar
Published: March 2017

Purpose

The purpose of this paper is threefold: to classify wildcards into three particular types sharing similar characteristics; use the Fuzzy TOPSIS as a new method in foresight to turn qualitative ideas into quantitative ones; and apply a combination of Fuzzy TOPSIS and a panel of experts to prioritize weak signals.

Design/methodology/approach

In this paper, the authors classify wildcards into three particular types which share similar character: natural wildcards, artificial wildcards (Degree 1) and artificial wildcards (Degree 2). Wildcards point to unexpected and surprising events including important results that can form watershed in the development of a specific trend. In addition, the authors present a Fuzzy TOPSIS model which can be used in various cases to prioritize a number of weak signals and put them in order, so that the most important ones are likely to yield the wildcard in the future

Findings

The authors presented a classification of wildcards with the same characteristics being natural wildcards, artificial wildcards (Degree 1) and artificial wildcards (Degree 2). The authors also prioritized the weak signals to deal with the most important ones and take appropriate action in advance so as to minimize possible damages and maximize the benefits of potential wildcards in an uncertain environment.

Originality/value

In this paper, the authors report on the prioritizing of weak signals by applying Fuzzy TOPSIS and classify wildcards. This is significant because, by identifying the most important weak signals, appropriate actions can be taken in the future if necessary. The paper should be of interest to readers in the area of participatory foresight.
Optimal number of ports and implications for Korea’s port policy
Authors: Lee Sanghack , Cho Jungran
Published: March 2017

Purpose

Many governments around the world have strategically privatized their ports. The privatized ports try to maximize profits by setting higher charges for port services and attracting transship cargos. This paper shows that such privatization of ports can be complemented by adjusting the number of ports. Specifically, the purpose of this paper is to derive the optimal number of ports in cases in which ports serve transship and domestic cargos.

Design/methodology/approach

This paper constructs a theoretical model in which ports compete with each other for transship and domestic cargos. In the first stage, the government determines the number of ports. In the second stage, the ports compete with each other in quantity to maximize profits. The authors have derived the optimal number of ports that maximizes national welfare.

Findings

The optimal number of ports is expressed as a function of the slope of the demand curve, the slope of the supply curve, and the share of domestic demand relative to total demand for port services. It is shown that the optimal number of ports tends to increase as the share of domestic cargo increases. The optimal number of ports, n*, is given as n*=1/(1−θ), where θ denotes the share of domestic demand in total demand for port services, when the unit cost of port services is constant.

Research limitations/implications

The analysis in the present paper is confined to the case of unilateral intervention by the government of the domestic country. Analyzing interaction among governments via competition policy would offer valuable policy implications.

Practical implications

The results of the current research offer important implications for Korean port policy in the context of maritime industrial changes, in particular, China’s New Silk Road initiative. In particular, the findings of this study suggest that Korea’s investment in ports should be concentrated on ports with competitive advantages.

Originality/value

Relatively scant attention has been paid to the possibility, or need, of strategic privatization being complemented by governmental competition policy. Filling this knowledge gap, the authors have shown that the government can mitigate the negative effects of privatization on domestic consumer surplus by introducing competition in the supply of port services.
Attitudes toward mobile search ads: a study among Mexican millennials
Authors: Murillo Enrique
Published: March 2017

Purpose

The purpose of this study is to conduct a survey of Mexican millennials to measure the extent of negative bias and perceived advertising value they experienced toward the ads they encountered while performing a search for local products and services from their smartphones.

Design/methodology/approach

Using a paper survey with a scenario question, responses were collected from 1,215 millennial smartphone owners about the strategies they used for scanning mobile search organic and sponsored results and quickly reaching the information they needed when performing a mobile search. The 315 participants who reported clicking on ads were further surveyed on their perceptions of ad informativeness, entertainment, irritation and credibility. These constructs were used as the predictors of advertising value in a structural equations model which was estimated with partial least squares.

Findings

A substantial bias against sponsored results was found, with two-thirds of respondents skipping the ads when performing a mobile search from their smartphones. However, 28.2 per cent reported clicking on the most relevant result without regard to it being organic or sponsored, and an additional 5.6 per cent reported clicking on an ad as their first strategy. In the structural model, all four hypothesized antecedents of advertising value were significant, and some gender differences were detected.

Practical implications

With the increasing penetration of smartphones, and rapid growth of mobile search, these results are particularly relevant for local merchants, who can use mobile search ads to leverage their location and communicate with searching consumers at the precise moment when they are most receptive to timely and relevant advertising.

Originality/value

This study is the first to measure the extent of consumer bias against sponsored results in a mobile search, and the first empirical estimation of the advertising value of mobile-sponsored results.
Effective customer selection for marketing campaigns based on net scores
Authors: Michel René , Schnakenburg Igor , von Martens Tobias
Published: March 2017

Purpose

This paper aims to address the effective selection of customers for direct marketing campaigns. It introduces a new method to forecast campaign-related uplifts (also known as incremental response modeling or net scoring). By means of these uplifts, only the most responsive customers are targeted by a campaign. This paper also aims at calculating the financial impact of the new approach compared to the classical (gross) scoring methods.

Design/methodology/approach

First, gross and net scoring approaches to customer selection for direct marketing campaigns are compared. After that, it is shown how net scoring can be applied in practice with regard to different strategical objectives. Then, a new statistic for net scoring based on decision trees is developed. Finally, a business case based on real data from the financial sector is calculated to compare gross and net scoring approaches.

Findings

Whereas gross scoring focuses on customers with a high probability of purchase, regardless of being targeted by a campaign, net scoring identifies those customers who are most responsive to campaigns. A common scoring procedure – decision trees – can be enhanced by the new statistic to forecast those campaign-related uplifts. The business case shows that the selected scoring method has a relevant impact on economical indicators.

Practical implications

The contribution of net scoring to campaign effectiveness and efficiency is shown by the business case. Furthermore, this paper suggests a framework for customer selection, given strategical objectives, e.g. minimizing costs or maximizing (gross or lift)-added value, and presents a new statistic that can be applied to common scoring procedures.

Originality/value

Despite its lever on the effectiveness of marketing campaigns, only few contributions address net scores up to now. The new χ2-statistic is a straightforward approach to the enhancement of decision trees for net scoring. Furthermore, this paper is the first to the application of net scoring with regard to different strategical objectives.
Home‐field advantages of litter decomposition increase with increasing N deposition rates: a litter and soil perspective
Authors: Li Ying‐Bin , Li Qi , Yang Jun‐Jie , Lü Xiao‐Tao , Liang Wen‐Ju , Han Xing‐Guo , Martijn Bezemer T.
Published: March 2017

Differences in litter quality and in soil microbial community composition can influence the litter decomposition and ‘home‐field advantage’ (HFA). However, our knowledge about the relative role of litter and soil characteristics on litter decomposition andHFAeffects is still limited, especially under long‐term N deposition.

We collected soil and two types of litter (monospecific and mixed species litter) from five replicate plots from a long‐term N deposition field experiment with seven N addition treatments (0, 2, 5, 10, 15, 20, 50 g N m−2 year−1). We examined the effects of N addition on litter quality and soil characteristics. We then carried out a three‐pronged microcosm decomposition experiment with (i) litter from different N addition treatments decomposed on a standard field soil; (ii) standard litter decomposed on soils from the different N addition treatments; and (iii) litter decomposed on soil from the same N addition treatment plot.

Decomposition of litter on standard soil was influenced strongly by the N addition treatment, but did not consistently decrease or increase with increasing N addition rates. Instead, decomposition of standard litter on soils collected from different N addition treatments decreased with increasing rates of N addition. Decomposition of litter on soil collected from the same plot increased with increasing N addition rates. Soil characteristics explained more of the variation in litter decomposition than litter characteristics.

There was a clearHFAeffect for litter decomposition, both from a litter and from a soil perspective.HFAeffects increased when the dissimilarity in litter quality (N content and C : N ratio) increase among the different N addition treatments and the soil effect was strongest at high N addition rates.

N addition influenced litter decomposition by changing both litter and soil characteristics. Importantly, N addition decreased the capability of soils to decompose litter and it increased the HFA effect indicating that soils decomposed local litter better than other litter, due to specialization in soil communities. Nitrogen deposition is an important threat to ecosystems worldwide and our study emphasizes that ecosystem functions such as decomposition can be greatly influenced by these global changes.

Alay summaryis available for this article.
‘It's like taking a bit of masculinity away from you’: towards a theoretical understanding of men's experiences of infertility
Authors: Dolan Alan , Lomas Tim , Ghobara Tarek , Hartshorne Geraldine
Published: March 2017

In theUK, nearly half of all cases of infertility involve a ‘male‐factor’. Yet, little empirical work has explored how men as men negotiate this terrain. Three interrelated concepts; ‘hegemonic masculinity’, ‘embodied masculinity’ and the linkages between ‘masculinities’ and male help‐seeking, provide the theoretical framework that guided a qualitative study conducted with 22 men experiencing infertility. The paper explores men's propensity to delay their help‐seeking in relation to infertility despite their desire for children. It also demonstrates how, in the context of infertility, the male body can be defined as both a failed entity in itself (unable to father a child) and a subordinated social entity (unable to measure up to hegemonic ideals) that characterises men's masculine identities. The paper also illustrates how men appear willing to accept responsibility for their infertility and adopt aspects of hitherto subordinate masculine practice. This does not, however, constitute the total unravelling of well understood and accepted expressions of masculinity. Finally, the paper demonstrates how infertility is perceived as having the potential to fracture current and even future relationships. Moreover, regardless of how well men measured up to other hegemonic ideals, ultimately they can do little to counteract the threat of other (fertile) men.
Have we seen the geneticisation of society? Expectations and evidence
Authors: Weiner Kate , Martin Paul , Richards Martin , Tutton Richard
Published: March 2017

Abby Lippman's geneticisation thesis, of the early 1990s, argued and anticipated that with the rise of genetics, increasing areas of social and health related activities would come to be understood and defined in genetic terms leading to major changes in society, medicine and health care. We review the considerable literature on geneticisation and consider how the concept stands both theoretically and empirically across scientific, clinical, popular and lay discourse and practice. Social science scholarship indicates that relatively little of the original claim of the geneticisation thesis has been realised, highlighting the development of more complex and dynamic accounts of disease in scientific discourse and the complexity of relationships between bioscientific, clinical and lay understandings. This scholarship represents a shift in social science understandings of the processes of sociotechnical change, which have moved from rather simplistic linear models to an appreciation of disease categories as multiply understood. Despite these shifts, we argue that a genetic imaginary persists, which plays a performative role in driving investments in new gene‐based developments. Understanding the enduring power of this genetic imaginary and its consequences remains a key task for the social sciences, one which treats ongoing genetic expectations and predictions in a sceptical yet open way.