bluuebunny/crossref_metadata_2025 huggingface dataset:
Sexual Selection: A Very Short Introduction
Authors: Zuk Marlene , Simmons Leigh W.
Published: August 2018

Sexual Selection: A Very Short Introduction introduces the astounding array of behaviours and decorative traits in the animal world used for competing for mates, and considers the evolutionary logic that underpins them. It also looks at the history of our understanding of sexual selection, from Darwin’s key insights to the modern day. Considering the investment animals place on reproduction, variation in mating systems, sexual conflict, and the origin of sexual dimorphism, it discusses questions such as whether females can really choose between males on aesthetic grounds, and how sexual conflict is resolved in different species. It concludes with a consideration of the thorny question of how, and even if, sexual selection theory applies to humans.
1. Ritual and the Reformation
Authors: Cummings Brian
Published: August 2018

‘Ritual and the Reformation’ describes how liturgy—with mass at its centre—lay at the heart of medieval religion. Mass was a social rite and a public occasion. The Office of the Dead is also outlined along with the different ritual books that contained rites, prayers, hymns, and scripture, including the Books of Hours. The challenge to tradition came in the form of Martin Luther’s Reformation and his theological creativity. The English Reformation began as a political revolution with Henry VIII’s marriage to Anne Boleyn in 1533, and resulted in wholesale changes in religious and social organization. The Reformation tore up a millennium of sacred worship and brought new forms of life into being.
4. Artificial neural networks
Authors: Boden Margaret A.
Published: August 2018

Artificial neural networks (ANNs) are made up of many interconnected units, each one capable of computing only one thing. ANNs have myriad applications, from playing the stock market and monitoring currency fluctuations to recognizing speech or faces. ANNs are parallel-processing virtual machines implemented on classical computers. They are intriguing partly because they are very different from the virtual machines of symbolic AI. Sequential instructions are replaced by massive parallelism, top-down control by bottom-up processing, and logic by probability. ‘Artificial neural networks’ considers the wider implications of ANNs and discusses parallel distributed processing (PDP), learning in neural networks, back-propagation, deep learning, and hybrid systems.
Parallel clustering of single cell transcriptomic data with split-merge sampling on Dirichlet process mixtures
Authors: Duan Tiehang , Pinto José P , Xie Xiaohui
Published: August 2018

Motivation

With the development of droplet based systems, massive single cell transcriptome data has become available, which enables analysis of cellular and molecular processes at single cell resolution and is instrumental to understanding many biological processes. While state-of-the-art clustering methods have been applied to the data, they face challenges in the following aspects: (i) the clustering quality still needs to be improved; (ii) most models need prior knowledge on number of clusters, which is not always available; (iii) there is a demand for faster computational speed.

Results

We propose to tackle these challenges with Parallelized Split Merge Sampling on Dirichlet Process Mixture Model (the Para-DPMM model). Unlike classic DPMM methods that perform sampling on each single data point, the split merge mechanism samples on the cluster level, which significantly improves convergence and optimality of the result. The model is highly parallelized and can utilize the computing power of high performance computing (HPC) clusters, enabling massive inference on huge datasets. Experiment results show the model outperforms current widely used models in both clustering quality and computational speed.

Availability and implementation

Source code is publicly available on https://github.com/tiehangd/Para_DPMM/tree/master/Para_DPMM_package.

Supplementary information

Supplementary data are available at Bioinformatics online.
Characterizing protein–DNA binding event subtypes in ChIP-exo data
Authors: Yamada Naomi , Lai William K M , Farrell Nina , Pugh B Franklin , Mahony Shaun
Published: August 2018

Motivation

Regulatory proteins associate with the genome either by directly binding cognate DNA motifs or via protein–protein interactions with other regulators. Each recruitment mechanism may be associated with distinct motifs and may also result in distinct characteristic patterns in high-resolution protein–DNA binding assays. For example, the ChIP-exo protocol precisely characterizes protein–DNA crosslinking patterns by combining chromatin immunoprecipitation (ChIP) with 5′ → 3′ exonuclease digestion. Since different regulatory complexes will result in different protein–DNA crosslinking signatures, analysis of ChIP-exo tag enrichment patterns should enable detection of multiple protein–DNA binding modes for a given regulatory protein. However, current ChIP-exo analysis methods either treat all binding events as being of a uniform type or rely on motifs to cluster binding events into subtypes.

Results

To systematically detect multiple protein–DNA interaction modes in a single ChIP-exo experiment, we introduce the ChIP-exo mixture model (ChExMix). ChExMix probabilistically models the genomic locations and subtype memberships of binding events using both ChIP-exo tag distribution patterns and DNA motifs. We demonstrate that ChExMix achieves accurate detection and classification of binding event subtypes using in silico mixed ChIP-exo data. We further demonstrate the unique analysis abilities of ChExMix using a collection of ChIP-exo experiments that profile the binding of key transcription factors in MCF-7 cells. In these data, ChExMix identifies possible recruitment mechanisms of FoxA1 and ERα, thus demonstrating that ChExMix can effectively stratify ChIP-exo binding events into biologically meaningful subtypes.

Availability and implementation

ChExMix is available from https://github.com/seqcode/chexmix.

Supplementary information

Supplementary data are available at Bioinformatics online.
The Distance Precision Matrix: computing networks from non-linear relationships
Authors: Ghanbari Mahsa , Lasserre Julia , Vingron Martin
Published: August 2018

Motivation

Full-order partial correlation, a fundamental approach for network reconstruction, e.g. in the context of gene regulation, relies on the precision matrix (the inverse of the covariance matrix) as an indicator of which variables are directly associated. The precision matrix assumes Gaussian linear data and its entries are zero for pairs of variables that are independent given all other variables. However, there is still very little theory on network reconstruction under the assumption of non-linear interactions among variables.

Results

We propose Distance Precision Matrix, a network reconstruction method aimed at both linear and non-linear data. Like partial distance correlation, it builds on distance covariance, a measure of possibly non-linear association, and on the idea of full-order partial correlation, which allows to discard indirect associations. We provide evidence that the Distance Precision Matrix method can successfully compute networks from linear and non-linear data, and consistently so across different datasets, even if sample size is low. The method is fast enough to compute networks on hundreds of nodes.

Availability and implementation

An R package DPM is available at https://github.molgen.mpg.de/ghanbari/DPM.

Supplementary information

Supplementary data are available at Bioinformatics online.
PolyQTL: Bayesian multiple eQTL detection with control for population structure and sample relatedness
Authors: Zeng Biao , Gibson Greg
Published: August 2018

Motivation

Expression quantitative loci (eQTL) are being used widely to annotate and interpret GWAS hits. Recent studies have demonstrated that individual gene expression is often regulated by multiple independent cis-acting eQTL. Diverse methods, frequentist and Bayesian, have already been developed to simultaneously detect and fine-map such multiple eQTL, but most of these ignore sample relatedness and potential population structure. This can result in false positives and disrupt the accuracy of fine-mapping. Here we introduce PolyQTL software for identifying and estimating eQTL effects. The package incorporates a genetic relatedness matrix to remove the influence of population structure and sample relatedness, while utilizing a Bayesian multiple eQTL detection pipeline to identify the most plausible candidate causal variants at one or more independent loci influencing abundance of a transcript.

Results

Simulations demonstrate that our approach improves the rate of discovery of causal variants relative to methods that do not account for relatedness.

Availability and implementation

The software is written in C++, and freely available for download at https://github.com/jxzb1988/PolyQTL.
AncestryView: data-driven visualization of whole-genome local-ancestry
Authors: Zhao Yan , Ma Li , Jiang Sukun , Song George D , He Shaohua , Li Hong , Song Qing
Published: August 2018

Data visualization is a crucial tool for data exploration, analysis and interpretation. To visualize the ancestry data, we developed a new software tool, called AncestryView. We demonstrate its functionality with the data from admixed individuals.

Availability and implementation

Freely available to non-commercial users on the web at https://f001.backblazeb2.com/file/=4DGenome/AncestryView.zip.

Supplementary information

Supplementary data are available at Bioinformatics online.
Large-scale comparative analysis of microbial pan-genomes using PanOCT
Authors: Inman Jason M , Sutton Granger G , Beck Erin , Brinkac Lauren M , Clarke Thomas H , Fouts Derrick E
Published: August 2018

The JCVI pan-genome pipeline is a collection of programs to run PanOCT and tools that support and extend the capabilities of PanOCT. PanOCT (pan-genome ortholog clustering tool) is a tool for pan-genome analysis of closely related prokaryotic species or strains. The JCVI Pan-Genome Pipeline wrapper invokes command-line utilities that prepare input genomes, invoke third-party tools such as NCBI Blast+, run PanOCT, generate a consensus pan-genome, annotate features of the pan-genome, detect sets of genes of interest such as antimicrobial resistance (AMR) genes and generate figures, tables and html pages to visualize the results. The pipeline can run in a hierarchical mode, lowering the RAM and compute resources used.

Availability and implementation

Source code, demo data, and detailed documentation are freely available at https://github.com/JCVenterInstitute/PanGenomePipeline.
RepeatCraft: a meta-pipeline for repetitive element de-fragmentation and annotation
Authors: Wong Wai Yee , Simakov Oleg
Published: August 2018

Repetitive elements comprise large proportion of many genomes. They have impact on both genome evolution and regulation. Their classification and the study of evolutionary history is a major emerging field. Various software exist to-date to classify and map repeats across genomes. The major unresolved drawback, however, is the fragmented nature of many identified repeat loci. This ultimately makes the classification of novel repeats and their evolutionary analyses difficult. To improve on this, we developed a pipeline (RepeatCraft) that integrates results from several repeat element classification tools based on both sequence similarity and structural features. The pipeline de-fragments closely spaced repeat loci in the genomes, reconstructing longer copies, thus allowing for a better annotation and sequence comparisons. The pipeline also includes a user interface that can run in a web browser allowing for an easy access and exploration of the repeat data.

Availability and implementation

RepeatCraft is implemented in Python and the web application is implemented in R. Download and documentation is freely available at https://github.com/niccw/repeatCraftp.

Supplementary information

Supplementary data are available at Bioinformatics online.
Structural analysis of estrogen receptors: interaction between estrogen receptors and cav-1 within the caveolae†
Authors: Pastore Mayra B , Landeros Rosalina Villalon , Chen Dong-bao , Magness Ronald R
Published: August 2018

Pregnancy is a physiologic state of substantially elevated estrogen biosynthesis that maintains vasodilator production by uterine artery endothelial cells (P-UAECs) and thus uterine perfusion. Estrogen receptors (ER-α and ER-β; ESR1 and ESR2) stimulate nongenomic rapid vasodilatory responses partly through activation of endothelial nitric oxide synthase (eNOS). Rapid estrogenic responses are initiated by the ∼4% ESRs localized to the plasmalemma of endothelial cells. Caveolin-1 (Cav-1) interactions within the caveolae are theorized to influence estrogenic effects mediated by both ESRs. Hypothesis: Both ESR1 and ESR2 display similar spatial partitioning between the plasmalemma and nucleus of UAECs and have similar interactions with Cav-1 at the plasmalemma. Using transmission electron microscopy, we observed numerous caveolae structures in UAECs, while immunogold labeling and subcellular fractionations identified ESR1 and ESR2 in three subcellular locations: membrane, cytosol, and nucleus. Bioinformatics approaches to analyze ESR1 and ESR2 transmembrane domains identified no regions that facilitate ESR interaction with plasmalemma. However, sucrose density centrifugation and Cav-1 immunoisolation columns uniquely demonstrated very high protein–protein association only between ESR1, but not ESR2, with Cav-1. These data demonstrate (1) both ESRs localize to the plasmalemma, cytosol and nucleus; (2) neither ESR1 nor ESR2 contain a classic region that crosses the plasmalemma to facilitate attachment; and (3) ESR1, but not ESR2, can be detected in the caveolar subcellular domain demonstrating ESR1 is the only ESR bound in close proximity to Cav-1 and eNOS within this microdomain. Lack of protein–protein interaction between Cav-1 and ESR2 demonstrates a novel independent association of these proteins at the plasmalemma.
The upstrap
Authors: Crainiceanu Ciprian M , Crainiceanu Adina
Published: August 2018

The bootstrap, introduced in Efron (1979. Bootstrap methods: another look at the jackknife. The Annals of Statistics7, 1–26), is a landmark method for quantifying variability. It uses sampling with replacement with a sample size equal to that of the original data. We propose the upstrap, which samples with replacement either more or fewer samples than the original sample size. We illustrate the upstrap by solving a hard, but common, sample size calculation problem. The data and code used for the analysis in this article are available on GitHub (2018. https://github.com/ccrainic/upstrap).
Neural Correlates of Group Bias During Natural Viewing
Authors: Andrews Timothy J , Smith Ryan K , Hoggart Richard L , Ulrich Philip I N , Gouws Andre D
Published: August 2018

Individuals from different social groups interpret the world in different ways. This study explores the neural basis of these group differences using a paradigm that simulates natural viewing conditions. Our aim was to determine if group differences could be found in sensory regions involved in the perception of the world or were evident in higher-level regions that are important for the interpretation of sensory information. We measured brain responses from 2 groups of football supporters, while they watched a video of matches between their teams. The time-course of response was then compared between individuals supporting the same (within-group) or the different (between-group) team. We found high intersubject correlations in low-level and high-level regions of the visual brain. However, these regions of the brain did not show any group differences. Regions that showed higher correlations for individuals from the same group were found in a network of frontal and subcortical brain regions. The interplay between these regions suggests a range of cognitive processes from motor control to social cognition and reward are important in the establishment of social groups. These results suggest that group differences are primarily reflected in regions involved in the evaluation and interpretation of the sensory input.
Chloroquine Versus Dihydroartemisinin-Piperaquine With Standard High-dose Primaquine Given Either for 7 Days or 14 Days in Plasmodium vivax Malaria
Authors: Chu Cindy S , Phyo Aung Pyae , Turner Claudia , Win Htun Htun , Poe Naw Pet , Yotyingaphiram Widi , Thinraow Suradet , Wilairisak Pornpimon , Raksapraidee Rattanaporn , Carrara Verena I , Paw Moo Kho , Wiladphaingern Jacher , Proux Stéphane , Bancone Germana , Sriprawat Kanlaya , Lee Sue J , Jeeyapant Atthanee , Watson James , Tarning Joel , Imwong Mallika , Nosten François , White Nicholas J
Published: August 2018

Chloroquine or dihydroartemisinin-piperaquine with either 7- or 14-day primaquine regimens provided highly effective radical cure of vivax malaria on the Thailand-Myanmar border. Short course higher dose primaquine regimens for vivax malaria radical cure may improve efficacy by improving adherence.
On the Supersingular Reduction of K3 Surfaces with Complex Multiplication
Authors: Ito Kazuhiro
Published: August 2018

We study the good reduction modulo $p$ of $K3$ surfaces with complex multiplication. If a $K3$ surface with complex multiplication has good reduction, we calculate the Picard number and the height of the formal Brauer group of the reduction. Moreover, if the reduction is supersingular, we calculate its Artin invariant under some assumptions. Our results generalize some results of Shimada for $K3$ surfaces with Picard number $20$. Our methods rely on the main theorem of complex multiplication for $K3$ surfaces by Rizov, an explicit description of the Breuil–Kisin modules associated with Lubin–Tate characters due to Andreatta, Goren, Howard, and Madapusi Pera, and the integral comparison theorem recently established by Bhatt, Morrow, and Scholze.
Dopamine regulates cytokine secretion during innate and adaptive immune responses
Authors: Kawano Masaaki , Takagi Rie , Saika Kikue , Matsui Masanori , Matsushita Sho
Published: August 2018

Dopamine (DA) is synthesized by various immune cells. DA receptors (DARs), which comprise five isoforms, are expressed on the surface of these cells. Therefore, it is likely that DA plays a role in regulating innate and adaptive responses. However, the underlying molecular mechanism(s) is largely unknown. Here, we found that, during innate immune responses, DA suppressed secretion of IFN-γ, TNF-α and IL-1β, but promoted secretion of IL-10 and CXCL1 by lipopolysaccharide (LPS)-stimulated mouse splenocytes, suggesting that DA regulates cytokine secretion. Immune subset studies indicated that DA suppressed secretion of IFN-γ, TNF-α and IL-1β by NK cells, as well as secretion of TNF-α by neutrophils and monocytes; however, DA up-regulated IL-10 secretion by neutrophils, monocytes, B cells, macrophages (Mφs) and dendritic cells within the splenocyte population. In addition, DA up-regulated secretion of CXCL1 by LPS-stimulated NK cells and Mφs. Meanwhile, treatment with DAR agonists or antagonists suppressed secretion of inflammatory cytokines from LPS-stimulated splenocytes. Pre-treatment of LPS-stimulated splenocytes with the PI3K inhibitor wortmannin reversed DA-mediated suppression of IFN-γ secretion, indicating that DA regulates IFN-γ secretion via the inositol 1,4,5-trisphosphate signaling pathway in these cells. Administration of DA and LPS to mice immunized with chicken ovalbumin (OVA) increased secretion of IL-5 by mouse lung lymphocytes, suggesting that DA promotes OVA-specific Th2-mediated immune responses by these cells. Taken together, these findings indicate that DA regulates cytokine secretion during innate and adaptive immune responses.
Process in the Community, Detain Offshore or ‘Turn Back the Boats’? Predicting Australian Asylum-seeker Policy Support from False Beliefs, Prejudice and Political Ideology
Authors: Hartley Lisa K , Anderson Joel R , Pedersen Anne
Published: August 2018

Over the past few decades, there has been a progressive implementation of policies designed to deter the arrival of people seeking protection. In Australia, this has included offshore processing and towing boats of asylum seekers away from Australian waters. In a community survey of 164 Australians, this study examined the predictive role of false beliefs about asylum seekers, prejudice and political ideology in support of three policies. Multiple hierarchical regression models indicated that, although political ideology and prejudice were significant predictors of policy support, false beliefs was the strongest predictor. For the policy of processing asylum seekers in the community, less endorsement of false beliefs was a significant predictor, while, for the policy of offshore processing, more endorsement of false beliefs was a significant predictor. For the boat turn-back policy, an increase in false-belief endorsement was the strongest predictor; although increases in prejudice and a prejudice–political ideology interaction (i.e. the predictive value of prejudice was stronger for participants who identified as politically conservative) also independently predicted support. Practical implications and future research avenues are discussed.
Powerful mechanical-driven outflows in the central parsecs of the low-luminosity active galactic nucleus ESO 428-G14
Authors: May D , Rodríguez-Ardila A , Prieto M A , Fernández-Ontiveros J A , Diaz Y , Mazzalay X
Published: August 2018

Low-luminosity Active Galactic Nuclei (LLAGNs) are characterized for low-radiative efficiency, much less than one percent of their Eddington limit. Nevertheless, their main energy release may be mechanical, opposite to powerful AGN classes like Seyfert and Quasars. This work reports on the jet-driven mechanical energy and the corresponding mass outflow deposited by the jet in the central 170 parsecs of the nearby LLAGN ESO 428-G14. The jet kinetic output is traced through the coronal line [Si vi] λ19641 Å. It is shown that its radial extension, up to hundreds of parsecs, requires a combination of photoionization by the central source and shock excitation as its origin. From the energetics of the ionized gas it is found that the mass outflow rate of the coronal gas is in the range from 3–8 M⊙ yr−1, comparable to those estimated from H i gas at kiloparsec scales in powerful radio galaxies.
Working It Out together
Authors: Richardson Henry
Published: August 2018

Resisting some of the leading conceptions of joint moral reasoning prominent in the philosophical tradition, such as Kant’s kingdom of ends and Habermas’s discourse ethics, because they are too idealized to be useful in understanding joint, socially embodied reasoning, this chapter sets out from a simple understanding of reasoning, centered on the idea of responsibly conducted thinking. It does so to support the book’s account of the moral community’s moral authority, which invokes the possibility of joint, socially embodied reasoning at three distinct levels. Reconciling the idea of reasoning to that of social embodiment requires reconsideration of the relationship of reason to power or empowerment, which can be helpful to reasoning, as well as inimical to it. Generality and inclusiveness are central virtues of the socially embodied reasoning considered here, and violence, epistemic injustice, and a lack of mutually attuned, open-minded responsiveness some of its most serious vices.
Landscapes
Authors: Gamble Ruth
Published: August 2018

Chapter 4 looks at the relationship between space and the reincarnation tradition. It explains the cultural geography of Tibet and how Tibet’s sited traditions were pressed into service to aid the Karmapa lineage. It explores the importance of place and environmental imagery to Rangjung Dorje’s poetry, his songs, and his praises. It then outlines Tibet’s cultural geography: its indigenous traditions of autochthonous deities and spirits, and the way Buddhism was said to have “tamed” them. It also describes Rangjung Dorje’s non-Tibetan, lineal forebears, the Indian mahāsiddhas whose mahāmudrā tradition approached environments with a mixture of skepticism and transformation. Following in their footsteps, Rangjung Dorje’s Tibetan forebears like Milarepa had begun to reimagine the Tibetan landscape as maṇḍalas and created a series of sacred sites. The early Karmapas’ monasteries also came to be seen as their maṇḍalas and, therefore, a place to which they should return life after life.
Empire in the Heimat
Authors: Sandler Willeke
Published: August 2018

With the end of the First World War, Germany became a “postcolonial” power. The Treaty of Versailles in 1919 transformed Germany’s overseas colonies in Africa and the Pacific into League of Nations Mandates, administered by other powers. Yet a number of Germans rejected this “postcolonial” status, arguing instead that Germany was simply an interrupted colonial power and would soon reclaim these territories. With the Nazi seizure of power in 1933, irredentism seemed once again on the agenda, and these colonialist advocates actively and loudly promoted their colonial cause in the Third Reich. Examining the domestic activities of these colonialist lobbying organizations, Empire in the Heimat demonstrates the continued place of overseas colonialism in shaping German national identity after the end of formal empire. In the Third Reich, the Deutsche Kolonialgesellschaft and the Reichskolonialbund framed Germans as having a particular aptitude for colonialism and the overseas territories as a German Heimat. As such, they sought to give overseas colonialism renewed meaning for both the present and the future of Nazi Germany. They brought this message to the German public through countless publications, exhibitions, rallies, lectures, photographs, and posters. Their public activities were met with a mix of occasional support, ambivalence, or even outright opposition from some Nazi officials, who privileged the Nazi regime’s European territorial goals over colonialists’ overseas goals. Colonialists’ ability to navigate this obstruction and intervention reveals both the limitations and the spaces available in the public sphere under Nazism for such “special interest” discourses.
Introduction
Authors: McClintock Cynthia
Published: August 2018

During the third wave, like most democratizing countries worldwide, Latin American countries replaced plurality rules for presidential election with runoff rules. To date, most scholars fear the proliferation of political parties under runoff and favor plurality. I argue, however, that Latin American leaders were correct to adopt runoff. Runoff established a virtuous circle: amid lower barriers to entry, opposition parties and new parties held greater respect for the democratic process and this respect was in turn important to elites’ toleration of their entry. By contrast, plurality often facilitated political exclusion by long-standing dominant parties and exacerbated cynicism and polarization. Although the larger number of parties under runoff was problematic, and measures for the amelioration of the problem are important, the number of parties was considerable under plurality; runoff enabled democracies to cope, increasing the legitimacy of their elected presidents.
Microbial growth, biomass production, and controls
Authors: Kirchman David L.
Published: August 2018

Soon after the discovery that bacteria are abundant in natural environments, the question arose as to whether or not they were active. Although the plate count method suggested that they were dormant if not dead, other methods indicated that a large fraction of bacteria and fungi are active, as discussed in this chapter. It goes on to discuss fundamental equations for exponential growth and logistic growth, and it describes phases of growth in batch cultures, continuous cultures, and chemostats. In contrast with measuring growth in laboratory cultures, it is difficult to measure in natural environments for complex communities with co-occurring mortality. Among many methods that have been suggested over the years, the most common one for bacteria is the leucine approach, while for fungi it is the acetate-in ergosterol method. These methods indicate that the growth rate of the bulk community is on the order of days for bacteria in their natural environment. It is faster in aquatic habitats than in soils, and bacteria grow faster than fungi in soils. But bulk rates for bacteria appear to be slower than those for phytoplankton. All of these rates for natural communities are much slower than rates measured for most microbes in the laboratory. Rates in subsurface environments hundreds of meters from light-driven primary production and high organic carbon conditions are even lower. Rates vary greatly among microbial taxa, according to data on 16S rRNA. Copiotrophic bacteria grow much faster than oligotrophic bacteria, but may have low growth rates when conditions turn unfavorable. Some of the factors limiting heterotrophic bacteria and fungi include temperature and inorganic nutrients, but the supply of organic compounds is perhaps most important in most environments.
The Biblical Philology of Daniel Heinsius (1619–1640)
Authors: van Miert Dirk
Published: August 2018

Chapter 4 assesses the biblical annotations of Scaliger’s star pupil, Daniel Heinsius. Recognizing the increasing currency of biblical philology, Heinsius published two massive tomes displaying his New Testariment scholarship, his versatility in Greek, and his apparent mastering of Hebrew. Yet, the results of his studies were diffuse. Heinsius subjected himself to the control of the professors of theology of his own university, and he was reticent with his textual criticism. Instead, he concentrated on criticizing the work of Theodorus Beza and on advancing his theory that New Testament Greek was not merely koine Greek with Hebrew and Aramaic influences, but a ‘Hellenistic dialect’ spoken by the native Greek-speaking Jews. Heinsius’s annotations show that it is not useful to attempt to place biblical philology on a one-dimensional scale between orthodoxy on the one hand and radicalism on another, but also that mainstream philology was welcomed by many.
Spinoza’s Biblical Criticism
Authors: Touber Jetze
Published: August 2018

Chapter 1 homes in on Spinoza as a Bible critic. Based on existing historiography, it parses the main relevant historical contexts in which Spinoza came to articulate his analysis of the Bible: the Sephardi community of Amsterdam, freethinking philosophers, and the Reformed Church. It concludes with a detailed examination of the Tractatus theologico-politicus, Spinoza’s major work of biblical criticism. Along the way I highlight themes for which Spinoza appealed to the biblical texts themselves: the textual unity of the Bible, and the biblical concepts of prophecy, divine election, and religious laws. The focus is on the biblical arguments for these propositions, and the philological choices that Spinoza made that enabled him to appeal to those specific biblical texts. This first chapter lays the foundation for the remainder of the book, which examines issues of biblical philology and interpretation discussed among the Dutch Reformed contemporaries of Spinoza.
‘A bit of shrapnel’
Authors: Campbell Matthew
Published: August 2018

In the papers of the Irish poet Dora Sigerson (1866–1918) is an unpublished poem called ‘The Second Wife’, a satirical ballad dating from 1916 to 1918. The poem addresses the marital arrangements of Thomas and Florence Hardy, friends of Sigerson and her husband, Clement Shorter. This chapter examines the poem and the relations between the Shorters and the Hardys in relation to Anglo-Irish literary attitudes to the Irish rebellion against the British in 1916. Shorter also published Yeats, being the first to print ‘Easter, 1916’. Sigerson wrote a number of poems in her last volumes, The Sad Years, Sixteen Dead Men, and The Tricolour, about these events. The chapter considers how these poems reflect not just her anger against the lack of sympathy for the Irish cause in the liberal England in which she was based, but also her extreme imaginative projection on to the sacrifice of 1916.
Introduction
Authors: Brundin Abigail , Howard Deborah , Laven Mary
Published: August 2018

The importance of the Italian Renaissance home as a fundamental unit of society and a dynamic site of cultural activity is often acknowledged. This book turns instead to consider the religious dimensions of domestic life. The introduction discusses the pre-existing scholarship out of which The Sacred Home has grown, paying particular attention to the divergent historiographies relating to the early modern household in Protestant and Catholic Europe. Here the rationale behind the chronological and geographical framework of the book is explained, and the nature of its interdisciplinary approach is outlined. By drawing on a wide range of textual, visual, and material sources, The Sacred Home explores domestic devotion across the spectrum of Italian Renaissance society.
Density in Plutarch
Authors: Hutchinson G. O.
Published: August 2018

The next move is to show that when rhythmic phrases are more densely packed together than usual, the passage calls for heightened attention. This illustrated from the climax of Plutarch’s Adversus Colotem. Then, to avert the possibility of chance, the book looks at passages in the Lives where at least twenty rhythmic closes come closely together, with few interruptions from unrhythmic closes or longer phrases. When they are looked at as a group, they are clearly not random. They come much more frequently in the second of pairs of Lives: a point with big implications for the conception of the work. They often come at key moments in the narrative (death, disaster, responses to these, triumphant summations of achievement); they also show significant connections with philosophy, substantial speeches, and comparison—the last an aspect of the Lives which they highlight far beyond the official pairings.
Master Principles of Criminalization?
Authors: Duff R A
Published: August 2018

This chapter turns to criminalization, and the question whether we should seek a ‘master principle’ by which to guide criminalization deliberations. Different kinds of master principle are distinguished (positive/negative, responsive/preventive, pro tanto/categorical, thick/thin); familiar principles (notably harm principles) are criticized. A plausible master principle should be positive, pro tanto, at least partly preventive, and thin: it will leave most of the substantive normative work in deciding what to criminalize still to be done. A thin master principle emerges from the preceding chapters: we have good reason to criminalize a type of conduct if and only if it constitutes a public wrong; it constitutes a public wrong if and only if it violates the polity’s civil order. This leaves the questions of how the polity’s civil order is constituted, and what kinds of conduct violate it, to be decided; but it shows what kinds of argument are relevant to criminalization decisions.
The association between driving time and unhealthy lifestyles: a cross-sectional, general population study of 386 493 UK Biobank participants
Authors: Mackay A , Mackay D F , Celis-Morales C A , Lyall D M , Gray S R , Sattar N , Gill J M R , Pell J P , Anderson J J
Published: August 2018

Background

Driving is a common type of sedentary behaviour; an independent risk factor for poor health. The study explores whether driving is also associated with other unhealthy lifestyle factors.

Methods

In a cross-sectional study of UK Biobank participants, driving time was treated as an ordinal variable and other lifestyle factors dichotomized into low/high risk based on guidelines. The associations were explored using chi-square tests for trend and binary logistic regression.

Results

Of the 386 493 participants who drove, 153 717 (39.8%) drove <1 h/day; 140 140 (36.3%) 1 h/day; 60 973 (15.8%) 2 h/day; and 31 663 (8.2%) ≥3 h/day. Following adjustment for potential confounders, driving ≥3 h/day was associated with being overweight/obese (OR = 1.74, 95% CI: 1.64–1.85), smoking (OR = 1.48, 95% CI: 1.37–1.63), insufficient sleep (1.70, 95% CI: 1.61–1.80), low fruit/vegetable intake (OR = 1.26, 95% CI: 1.18–1.35) and low physical activity (OR = 1.05, 95% CI: 1.00–1.11), with dose relationships for the first three, but was not associated with higher alcohol consumption (OR = 0.94, 95% CI: 0.87–1.02).

Conclusions

Sedentary behaviour, such as driving, is known to have an independent association with adverse health outcomes. It may have additional impact mediated through its effect on other aspects of lifestyle. People with long driving times are at higher risk and might benefit from targeted interventions.
Cell Autoaggregation, Biofilm Formation, and Plant Attachment in a Sinorhizobium meliloti lpsB Mutant
Authors: Sorroche Fernando , Bogino Pablo , Russo Daniela M. , Zorreguieta Angeles , Nievas Fiorela , Morales Gustavo M. , Hirsch Ann M. , Giordano Walter
Published: August 2018

Bacterial surface molecules are crucial for the establishment of a successful rhizobia-legume symbiosis, and, in most bacteria, are also critical for adherence properties, surface colonization, and as a barrier for defense. Rhizobial mutants defective in the production of exopolysaccharides (EPSs), lipopolysaccharides (LPSs), or capsular polysaccharides are usually affected in symbiosis with their plant hosts. In the present study, we evaluated the role of the combined effects of LPS and EPS II in cell-to-cell and cell-to-surface interactions in Sinorhizobium meliloti by studying planktonic cell autoaggregation, biofilm formation, and symbiosis with the host plant Medicago sativa. The lpsB mutant, which has a defective core portion of LPS, exhibited a reduction in biofilm formation on abiotic surfaces as well as altered biofilm architecture compared with the wild-type Rm8530 strain. Atomic force microscopy and confocal laser microscopy revealed an increase in polar cell-to-cell interactions in the lpsB mutant, which might account for the biofilm deficiency. However, a certain level of biofilm development was observed in the lpsB strain compared with the EPS II-defective mutant strains. Autoaggregation experiments carried out with LPS and EPS mutant strains showed that both polysaccharides have an impact on the cell-to-cell adhesive interactions of planktonic bacteria. Although the lpsB mutation and the loss of EPS II production strongly stimulated early attachment to alfalfa roots, the number of nodules induced in M. sativa was not increased. Taken together, this work demonstrates that S. meliloti interactions with biotic and abiotic surfaces depend on the interplay between LPS and EPS II.
Dual regulatory role of CCNA2 in modulating CDK6 and MET‐mediated cell‐cycle pathway and EMT progression is blocked by miR‐381‐3p in bladder cancer
Authors: Li Jiangfeng , Ying Yufan , Xie Haiyun , Jin Ke , Yan Huaqing , Wang Song , Xu Mingjie , Xu Xin , Wang Xiao , Yang Kai , Zheng Xiangyi , Xie Liping
Published: August 2018

Emerging evidence has elucidated that microRNAs (miRNAs) transcribed from miRNA cluster at DLK‐DIO3 imprinted domain are involved in various cancers. However, as one member of this cluster, the underlying mechanisms and functions of miR‐381‐3p in bladder cancer (BCa) still remains elusive. Here we demonstrate that the hypermethylated status of upstream maternally expressed gene 3 divergent methylation region reduces the expression of miR‐381‐3p in BCa by bisulfite‐sequencing PCR. In vitro and in vivo experiments indicate that overexpression of miR‐381‐3p significantly inhibits cell proliferation via inducing G1 phase arrest and migration via down‐regulating MET and CCNA2 induced EMT progression. CDK6/CCNA2/MET are all identified as the direct targets of miR‐381‐3p by bioinformatics analysis and dual‐luciferase reporter assay. Furthermore, inhibition of CCNA2 mediated by miR‐381‐3p as the crucial biregulator not only participates in the proliferation regulation with CDK6 in cell cycle but also modulates the EMT progression via ROCK/AKT/β‐catenin/SNAIL pathway, which establishes an EMT circuit combined with miR‐381‐3p/MET/AKT/GSK‐3β/SNAIL pathway, and SNAIL is the last confocal target to induce EMT progression. To conclude, we propose 2 novel regulatory circuits mediated by miR‐381‐3p in BCa, which may assist in the development of more effective therapies against BCa in the future.—Li, J., Ying, Y., Xie, H., Jin, K., Yan, H., Wang, S., Xu, M., Xu, X., Wang, X., Yang, K., Zheng, X., Xie, L. Dual regulatory role of CCNA2 in modulating CDK6 and MET‐mediated cell‐cycle pathway and EMT progression is blocked by miR‐381‐3p in bladder cancer. FASEB J. 33, 1374–1388 (2019). www.fasebj.org
Assessing Pressure Injury Knowledge Using the Pieper-Zulkowski Pressure Ulcer Knowledge Test
Authors: Delmore Barbara , Ayello Elizabeth A. , Smart Hiske , Sibbald R. Gary
Published: August 2018

OBJECTIVE:

To determine the pressure injury knowledge of health professionals before and after providing an interactive, educational intervention.

DESIGN AND SETTING:

The research design was a quasi-experimental study using a nonrandomized pretest/posttest methodology in Manila, Philippines.

PATIENTS AND INTERVENTION:

The population for this study was healthcare professionals who participated in a 2-day Basic WoundPedia course. There were 57 participants on day 1 and 55 participants on day 2. The Pieper-Zulkowski Pressure Ulcer Knowledge Test (PZ-PUKT, version 2), a standardized, validated instrument with 72 items, was used to measure 3 domains: prevention (28 items), staging (20 items), and wounds (24 items). The test was used to determine the baseline pressure injury knowledge of the students on day 1 before the course began and on day 2 after related content was completed. The intent of this approach was to document that knowledge deficits were met, especially for future courses.

MAIN RESULTS:

There was a statistically significant increase in pressure injury knowledge scores after healthcare professionals received an interactive, educational intervention.

CONCLUSIONS:

Measuring knowledge before and after educational intervention should be considered to determine whether knowledge deficits are corrected. This methodology reinforced the adult learning theory and to help participants realize their own knowledge deficits. The PZ-PUKT may prove a valuable nonthreatening instrument for adult learners to self-identify, self-learn, and self-correct knowledge according to the best new evidence as it becomes available. These findings documented that this interactive, educational intervention did improve the percentage of correct pressure injury knowledge concepts for this group in all 3 subscales. This study also added support for the newly revised PZ-PUKT.
The Safety of Negative-Pressure Wound Therapy on Surgical Wounds: An Updated Meta-analysis of 17 Randomized Controlled Trials
Authors: Ge Dongmei
Published: August 2018

OBJECTIVE:

To assess whether negative-pressure wound therapy (NPWT) reduced complications such as wound infection, dehiscence, seroma/hematoma, skin necrosis/blistering, and bleeding compared with non-NPWT treatments.

METHODS:

This meta-analysis involved randomized clinical trials of NPWT compared with non-NPWT on surgical wound healing. The main outcome was surgical site infections; secondary outcomes were dehiscence, seroma/hematoma, skin necrosis/blistering, bleeding, and reoperation.

MAIN RESULTS:

Seventeen randomized controlled trials met the inclusion criteria, reporting on 928 NPWT and 930 non-NPWT patients. Compared with non-NPWT, NPWT was not associated with a significant reduction in wound infection (relative risk, 0.96; 95% confidence interval, 0.74–1.24). The reduction in wound dehiscence, seroma/hematoma, skin necrosis/blistering, and bleeding in the NPWT group was significant compared with that in the non-NPWT groups. Significant heterogeneity was observed in seroma/hematoma and skin necrosis/blistering between the NPWT and non-NPWT groups. No publication bias was observed.

CONCLUSIONS:

Compared with non-NPWT, NPWT significantly reduced the rates of dehiscence, seroma/hematoma, skin necrosis\blistering, and bleeding, but not surgical site infections.
Machine Learning Models for the Hearing Impairment Prediction in Workers Exposed to Complex Industrial Noise: A Pilot Study
Authors: Zhao Yanxia , Li Jingsong , Zhang Meibian , Lu Yao , Xie Hongwei , Tian Yu , Qiu Wei
Published: August 2018

Objectives:

To demonstrate the feasibility of developing machine learning models for the prediction of hearing impairment in humans exposed to complex non-Gaussian industrial noise.

Design:

Audiometric and noise exposure data were collected on a population of screened workers (N = 1,113) from 17 factories located in Zhejiang province, China. All the subjects were exposed to complex noise. Each subject was given an otologic examination to determine their pure-tone hearing threshold levels and had their personal full-shift noise recorded. For each subject, the hearing loss was evaluated according to the hearing impairment definition of the National Institute for Occupational Safety and Health. Age, exposure duration, equivalent A-weighted SPL (LAeq), and median kurtosis were used as the input for four machine learning algorithms, that is, support vector machine, neural network multilayer perceptron, random forest, and adaptive boosting. Both classification and regression models were developed to predict noise-induced hearing loss applying these four machine learning algorithms. Two indexes, area under the curve and prediction accuracy, were used to assess the performances of the classification models for predicting hearing impairment of workers. Root mean square error was used to quantify the prediction performance of the regression models.

Results:

A prediction accuracy between 78.6 and 80.1% indicated that the four classification models could be useful tools to assess noise-induced hearing impairment of workers exposed to various complex occupational noises. A comprehensive evaluation using both the area under the curve and prediction accuracy showed that the support vector machine model achieved the best score and thus should be selected as the tool with the highest potential for predicting hearing impairment from the occupational noise exposures in this study. The root mean square error performance indicated that the four regression models could be used to predict noise-induced hearing loss quantitatively and the multilayer perceptron regression model had the best performance.

Conclusions:

This pilot study demonstrated that machine learning algorithms are potential tools for the evaluation and prediction of noise-induced hearing impairment in workers exposed to diverse complex industrial noises.