bluuebunny/crossref_metadata_2025_split huggingface dataset:
A data-driven model for the assessment of Tuberculosis transmission in evolving demographic structures
Authors: Arregui Sergio , Iglesias María José , Samper Sofía , Marinova Dessislava , Martín Carlos , Sanz Joaquín , Moreno Yamir 
Published: March 2017

In the case of tuberculosis (TB), the capabilities of epidemic models to produce quantitatively robust forecasts are limited by multiple hindrances. Among these, understanding the complex relationship between disease epidemiology and populations' age structure has been highlighted as one of the most relevant. TB dynamics depends on age in multiple ways, some of which are traditionally simplified in the literature. That is the case of the heterogeneities in contact intensity among different age-strata that are common to all air-borne diseases, but still typically neglected in the TB case. Furthermore, whilst demographic structures of many countries are rapidly aging, demographic dynamics is pervasively ignored when modeling TB spreading. In this work, we present a TB transmission model that incorporates country-specific demographic prospects and empirical contact data around a data-driven description of TB dynamics. Using our model, we find that the inclusion of demographic dynamics is followed by an increase in the burden levels prospected for the next decades in the areas of the world that are most hit by the disease nowadays. Similarly, we show that considering realistic patterns of contacts among individuals in different age-strata reshapes the transmission patterns reproduced by the models, a result with potential implications for the design of age-focused epidemiological interventions.Significance StatementEven though tuberculosis (TB) is acknowledged as a strongly age-dependent disease, it remains unclear how TB epidemics would react, in the following decades, to the generalized aging that human populations are experiencing worldwide. This situation is partly caused by the limitations of current transmission models at describing the relationship between demography and TB transmission. Here, we present a data-driven epidemiological model that, unlike previous approaches, explicitly contemplates relevant aspects of the coupling between agestructure and TB dynamics, such as demographic evolution and contact heterogeneities. Using our model, we identify substantial biases in epidemiological forecasts rooted in an inadequate description of these aspects, both at the level of aggregated incidence and mortality rates and their distribution across age-strata.
A Bayesian Framework for Estimating Cell Type Composition from DNA Methylation Without the Need for Methylation Reference
Authors: Rahmani Elior , Schweiger Regev , Shenhav Liat , Wingert Theodora , Hofer Ira , Gabel Eilon , Eskin Eleazar , Halperin Eran 
Published: March 2017

AbstractWe introduce a Bayesian semi-supervised method for estimating cell counts from DNA methylation by leveraging an easily obtainable prior knowledge on the cell type composition distribution of the studied tissue. We show mathematically and empirically that alternative methods which attempt to infer explicit cell counts without methylation reference can only capture linear combinations of cell counts rather than provide one component per cell type. Our approach, which allows the construction of a set of components such that each component corresponds to a single cell type, therefore provides a new opportunity to investigate cell compositions in genomic studies of tissues for which it was not possible before.
Face inversion reveals holistic processing of peripheral faces
Authors: Kovács Petra , Knakker Balázs , Hermann Petra , Kovács Gyula , Vidnyánszky Zoltán 
Published: March 2017

AbstractFace perception is accomplished by face-selective neural processes, involving holistic processing that enables highly efficient integration of facial features into a whole face representation. It has been shown that in face-selective regions of the ventral temporal cortex, neural resources involved in holistic processing are primarily dedicated to the central portion of the visual field. These findings raise the intriguing possibility that holistic processing might be the privilege of centrally presented faces and could be strongly diminished in the case of peripheral faces. We addressed this question using the face inversion effect, a well established marker of holistic face processing. The behavioral results revealed impaired identity discrimination performance for inverted peripheral faces scaled according to the V1 magnification factor, compared to upright presented faces. The size of peripheral face inversion effect (FIE) was comparable to that found for centrally displayed faces. Face inversion affected the early ERP responses to faces in two time intervals. The earliest FIE was most pronounced in the time window between 130-140 ms following stimulus presentation, for both centrally and peripherally displayed faces and in the latter case, it was present only over the contralateral hemisphere. The timing of the next component FIE corresponded closely with the temporal interval of the N170 ERP component and showed strong right hemisphere lateralization, both when faces were displayed in the left or right visual field. Furthermore, we also showed that centrally presented face masks impaired peripheral face identity discrimination performance, but did not reduce the magnitude of the FIE. These findings revealed robust behavioral and neural inversion effects for peripheral faces and thus suggest that faces are processed holistically throughout the visual field.HighlightsRobust behavioral and neural inversion effect was found for peripheral faces.P1 ERP component is modulated by inverted central and contralateral faces.N170 ERP component is modulated by centrally and peripherally presented faces.Neural face inversion effect shows strong right hemisphere lateralization.Faces are processed holistically throughout the visual field.
Functional Annotation of Chemical Libraries across Diverse Biological Processes
Authors: Piotrowski Jeff S. , Li Sheena C. , Deshpande Raamesh , Simpkins Scott W. , Nelson Justin , Yashiroda Yoko , Barber Jacqueline M. , Safizadeh Hamid , Wilson Erin , Okada Hiroki , Gebre Abraham A. , Kubo Karen , Torres Nikko P. , LeBlanc Marissa A. , Andrusiak Kerry , Okamoto Reika , Yoshimura Mami , DeRango-Adem Eva , van Leeuwen Jolanda , Shirahige Katsuhiko , Baryshnikova Anastasia , Brown Grant W. , Hirano Hiroyuki , Costanzo Michael , Andrews Brenda , Ohya Yoshikazu , Osada Hiroyuki , Yoshida Minoru , Myers Chad L. , Boone Charles 
Published: March 2017

AbstractChemical-genetic approaches offer the potential for unbiased functional annotation of chemical libraries. Mutations can alter the response of cells to a compound, revealing chemical-genetic interactions that can elucidate a compound’s mode of action. We developed a highly parallel and unbiased yeast chemical-genetic screening system involving three key components. First, in a drug-sensitive genetic background, we constructed an optimized, diagnostic mutant collection that is predictive all major yeast biological processes. Second, we implemented a multiplexed (768-plex) barcode sequencing protocol, enabling assembly of thousands of chemical-genetic profiles. Finally, based on comparison of the chemical-genetic profiles with a compendium of genome-wide genetic interaction profiles, we predicted compound functionality. Applying this high-throughput approach, we screened 7 different compound libraries and annotated their functional diversity. We further validated biological process predictions, prioritized a diverse set of compounds, and identified compounds that appear to have dual modes of action.
GMPR: A novel normalization method for microbiome sequencing data
Authors: Chen Li , Chen Jun 
Published: March 2017

ABSTRACTSummaryNormalization is the first and a critical step in microbiome sequencing (microbiome-Seq) data analysis to account for variable library sizes. Though RNA-Seq based normalization methods have been adapted for microbiome-Seq data, they fail to consider the unique characteristics of microbiome-Seq data, which contain a vast number of zeros due to the physical absence or undersampling of the microbes. Normalization methods that specifically address the zeroinflation remain largely undeveloped. Here we propose GMPR - a simple but effective normalization method - for zeroinflated sequencing data such as microbiome-Seq data. Simulation studies and analyses of 38 real gut microbiome datasets from 16S rRNA gene amplicon sequencing demonstrated the superior performance of the proposed method.Availability and Implementation‘GMPR’ is implemented in R andavailable athttps://github.com/jchen1981/GMPRSupplementary InformationSupplementary data are available at Bioinformatics online.ContactChen.Jun2@mayo.edu
Privacy-preserving recommendations in context-aware mobile environments
Authors: Polatidis Nikolaos , Georgiadis Christos K. , Pimenidis Elias , Stiakakis Emmanouil 
Published: March 2017

PurposeThis paper aims to address privacy concerns that arise from the use of mobile recommender systems when processing contextual information relating to the user. Mobile recommender systems aim to solve the information overload problem by recommending products or services to users of Web services on mobile devices, such as smartphones or tablets, at any given point in time and in any possible location. They use recommendation methods, such as collaborative filtering or content-based filtering and use a considerable amount of contextual information to provide relevant recommendations. However, because of privacy concerns, users are not willing to provide the required personal information that would allow their views to be recorded and make these systems usable.Design/methodology/approachThis work is focused on user privacy by providing a method for context privacy-preservation and privacy protection at user interface level. Thus, a set of algorithms that are part of the method has been designed with privacy protection in mind, which is done by using realistic dummy parameter creation. To demonstrate the applicability of the method, a relevant context-aware data set has been used to run performance and usability tests.FindingsThe proposed method has been experimentally evaluated using performance and usability evaluation tests and is shown that with a small decrease in terms of performance, user privacy can be protected.Originality/valueThis is a novel research paper that proposed a method for protecting the privacy of mobile recommender systems users when context parameters are used.
Does corporate ethics help investors forecast future earnings?
Authors: Lin Hsuan-Chu , Wang Chuan-San , Wu Ruei-Shian 
Published: March 2017

PurposeA firm’s ethical behavior is commonly perceived beneficial to the firm and its investors in the literature. However, activities of corporate social responsibility (CSR) are often delivered with multiple purposes, and their expenses are aggregated with other expenditures in financial statements. These two features motivate the authors to hypothesize and find that investors’ ability to predict future earnings of ethical firms may not be improved through observing the CSR activities. The study aims to suggest that CSR spending should be expressed separately from other expenses in financial reports to help investors predict the future performance of CSR firms.Design/methodology/approachThe authors use future (forward) earnings response coefficients (FERC) to testing whether current stock returns reflect correct information about future earnings. The basic specification of FERC framework, initially developed by Collinset al.(1994), is a regression of current-year stock returns on past, concurrent and future reported earnings with future stock returns as a control variable. A significantly positive FERC provides evidence that investors have rich and correct information about future earnings.FindingsThe authors find less future earnings information contained in current stock returns for firms with higher intensity of CSR activities. The association is also negative between current stock returns and future earnings reported by firms with a higher degree of CSR spending aggregated with selling, general and administrative expenses (SG&A). In additional analyses, the intensity of CSR activities is positively associated the uncertainty of benefits, measured by the standard deviation of future earnings over the next five years. This future earnings variability does not exist, even though CSR spending is aggregated with SG&A, consistent with the basic principle that accounting expenses create no future economic impacts.Originality/valueThe authors contribute to the current debate over consequences of CSR activities and accounting for CSR spending from a different angle. A common belief is that voluntary disclosure on CSR activities would aid in reducing costs of equity capital and financial reporting errors. These studies provide corporate managers with good reasons and motivations to expect beneficial consequences of voluntary disclosure. The results show that general investors are less capable of predicting future earnings when there is a higher degree of CSR spending aggregated with SG&A. It also highlights potential problems in the disclosure of general-purpose financial reporting to accounting standard setters.
Promoting a strategic business focus to balance competitive advantage and corporate social responsibility – missing elements
Authors: Fish Alan J. , Wood Jack 
Published: March 2017

Purpose
This paper aims to highlight dysfunctional multi-stakeholder relations and negative business outcomes, evidenced in lose/lose results, exacerbated by failure to acknowledge strategic business focus as a means to redress problematic business thinking and practice amongst key leadership teams associated with achieving balance between competitive advantage and corporate social responsibility.

Design/methodology/approach
The reframed strategic business focus has been developed using Eastern philosophy and Western organization theory and refers to four case examples of dysfunctional business thinking and practice.

Findings
Strategic business focus results from an interdependent and complementary positive mediating relationship between competitive advantage and corporate social responsibility, which is moderated by organization culture (organization core values, including shared value) and strategic human resource management (talent and mindset).

Research limitations/implications
Strategic business focus as proposed has not been empirically tested but seeks to address a conceptualization that competing business and stakeholder agendas are interdependent and complementary.

Practical implications
Strategic business focus seeks to redress traditional win/lose and lose/lose business outcomes, by supporting win/win results, represented by shared value amongst multi-stakeholders.

Social implications
Strategic business focus seeks to provide a means whereby corporate social responsibility, particularly the social contract, plays a key role in the decisions and practices of key leadership teams and the behaviour of corporate staff in host environments when seeking competitive advantage.

Originality/value
Eastern thinking and behaviour are usually undervalued in the western business literature, particularly in western business practice. Joint attention, however, may improve competitive advantage and corporate social responsibility agendas in support of diverse management practices, including shared value.
Microbial communities in soil chronosequences with distinct parent material: the effect of soil pH and litter quality
Authors: Alfaro Fernando D. , Manzano Marlene , Marquet Pablo A. , Gaxiola Aurora 
Published: March 2017

Summary

During soil development, bacteria and fungi can be differentially affected by changes in soil biogeochemistry. Since the chemistry of parent material affects soil pH, nutrient availability, and indirectly litter quality, we hypothesize that parent material has an important influence on microbial community patterns during long‐term soil development.

In this paper, we tested for the effect of parent material, as well as, soil and litter properties upon microbial community patterns in three c. 20 000‐year‐old semi‐arid chronosequences developed on sedimentary and volcanic (i.e. Andesitic and Dacitic) soils in the Dry Puna of Bolivia. We evaluated microbial patterns by analysing the terminal restriction fragment length polymorphism from amplified bacterial 16S rRNA genes, and the fungal internal transcribed spacer region, and quantitative real‐time polymerase chain reaction.

Soil and litter characteristics differed significantly between the Sedimentary and volcanic chronosequences. In particular, soil pH was alkaline in all stages of the Sedimentary chronosequence; whereas it changed from alkaline to near neutral across stages in both volcanic chronosequences. Composition of bacterial communities changed across volcanic chronosequences, and this change was associated with a reduction in soil pH and increases in litter quality, whereas no differences were found in the Sedimentary chronosequence. Fungal community composition, in contrast, did not change across any chronosequence.

Relative microbial abundance, expressed as the fungal:bacterial ratio, declined across stages of the Sedimentary chronosequence in association with decreases in TC and TP, whereas in the Andesitic chronosequence decreases in fungal:bacterial ratios were related with increases in litter quality and declines in soil pH.

Synthesis. Our results show the importance of parent material in affecting bacterial and fungal communities during soil development. Further, in semi‐arid chronosequences, fungal:bacterial ratios tend to decline given that soil pH in young soils is rather alkaline. Our results also are consistent with the general framework that highlights the importance of above‐ground (i.e. litter quality) and below‐ground (i.e. soil properties) in affecting microbial relative abundance and community composition during soil development.
Policy Uncertainty from a Central Bank Perspective
Authors: McDermott C. John 
Published: March 2017

AbstractIn this article, I argue that a substantial portion of macroeconomic policy uncertainty derives from the external environment, which propagates into uncertainty about actual policy. I also illustrate elements of the Reserve Bank of New Zealand's monetary policy framework that aim to mitigate uncertainty, highlighting our clear objectives, regular decision‐making cycle and active communication strategy. Lastly, I leave researchers with two questions: What measures of uncertainty should be pre‐eminently important to policy‐makers? And how should policy‐makers respond to those measurements?
An Aquatic Decomposition Scoring Method to Potentially Predict the Postmortem Submersion Interval of Bodies Recovered from the North Sea
Authors: van Daalen Marjolijn A. , de Kat Dorothée S. , Oude Grotebevelsborg Bernice F.L. , de Leeuwe Roosje , Warnaar Jeroen , Oostra Roelof Jan , M Duijst‐Heesters Wilma L.J. 
Published: March 2017

AbstractThis study aimed to develop an aquatic decomposition scoring (ADS) method and investigated the predictive value of this method in estimating the postmortem submersion interval (PMSI) of bodies recovered from the North Sea. This method, consisting of an ADS item list and a pictorial reference atlas, showed a high interobserver agreement (Krippendorff's alpha ≥ 0.93) and hence proved to be valid. This scoring method was applied to data, collected from closed cases—cases in which the postmortal submersion interval (PMSI) was known—concerning bodies recovered from the North Sea from 1990 to 2013. Thirty‐eight cases met the inclusion criteria and were scored by quantifying the observed total aquatic decomposition score (TADS). Statistical analysis demonstrated that TADS accurately predicts the PMSI (p < 0.001), confirming that the decomposition process in the North Sea is strongly correlated to time.
Comparative analysis of the Monochamus alternatus immune system
Authors: Zhou Jiao , Yu Hai‐Ying , Zhang Wei , Ahmad Faheem , Hu Song‐Nian , Zhao Li‐Lin , Zou Zhen , Sun Jiang‐Hua 
Published: March 2017

AbstractThe pine sawyer beetle, Monochamus alternatus, is regarded as a notorious forest pest in Asia, vectoring an invasive pathogenic nematode, Bursaphelenchus xylophilus, which is known to cause pine wilt disease. However, little sequence information is available for this vector beetle. This hampered the research on its immune system. Based on the transcriptome of M. alternatus, we have identified and characterized 194 immunity‐related genes in M. alternatus, and compared them with homologues molecules from other species known to exhibit immune responses against invading microbes. The lower number of putative immunity‐related genes in M. alternatus were attributed to fewer C‐type lectin, serine protease (SP) and anti‐microbial peptide (AMP) genes. Phylogenetic analysis revealed that M. alternatus had a unique recognition gene, galectin3, orthologues of which were not identified in Tribolium castaneum, Drosophila melanogastor, Anopheles gambiae and Apis mellifera. This suggested a lineage‐specific gene evolution for coleopteran insects. Our study provides the comprehensive sequence resources of the immunity‐related genes of M. alternatus, presenting valuable information for better understanding of the molecular mechanism of innate immunity processes in M. alternatus against B. xylophilus.
Heavy Prenatal Alcohol Exposure is Related to Smaller Corpus Callosum in Newborn MRI Scans
Authors: Jacobson Sandra W. , Jacobson Joseph L. , Molteno Christopher D. , Warton Christopher M.R. , Wintermark Pia , Hoyme H. Eugene , De Jong Greetje , Taylor Paul , Warton Fleur , Lindinger Nadine M. , Carter R. Colin , Dodge Neil C. , Grant Ellen , Warfield Simon K. , Zöllei Lilla , van der Kouwe André J.W. , Meintjes Ernesta M. 
Published: March 2017

BackgroundMagnetic resonance imaging (MRI) studies have consistently demonstrated disproportionately smaller corpus callosa in individuals with a history of prenatal alcohol exposure (PAE) but have not previously examined the feasibility of detecting this effect in infants. Tissue segmentation of the newborn brain is challenging because analysis techniques developed for the adult brain are not directly transferable, and segmentation for cerebral morphometry is difficult in neonates, due to the latter's incomplete myelination. This study is the first to use volumetric structural MRI to investigate PAE effects in newborns using manual tracing and to examine the cross‐sectional area of the corpus callosum (CC).MethodsForty‐three nonsedated infants born to 32 Cape Coloured heavy drinkers and 11 controls recruited prospectively during pregnancy were scanned using a custom‐designed birdcage coil for infants, which increases signal‐to‐noise ratio almost 2‐fold compared to the standard head coil. Alcohol use was ascertained prospectively during pregnancy, and fetal alcohol spectrum disorders diagnosis was conducted by expert dysmorphologists. Data were acquired using a multi‐echo FLASH protocol adapted for newborns, and a knowledge‐based procedure was used to hand‐segment the neonatal brains.ResultsCC was disproportionately smaller in alcohol‐exposed neonates than controls after controlling for intracranial volume. By contrast, CC area was unrelated to infant sex, gestational age, age at scan, or maternal smoking, marijuana, or methamphetamine use during pregnancy.ConclusionsGiven that midline craniofacial anomalies have been recognized as a hallmark of fetal alcohol syndrome in humans and animal models since this syndrome was first identified, the CC deficit identified here in newborns may support early identification of a range of midline structural impairments. Smaller CC during the newborn period may provide an early indicator of fetal alcohol‐related cognitive deficits that have been linked to this critically important brain structure in childhood and adolescence.