bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractPutticket 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

AbstractTemperate 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

AbstractRepair 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 SummaryA 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

AbstractFactor 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

AbstractExtracellular 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

AbstractMicrobial 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.ImportancePrevious 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.