bluuebunny/crossref_metadata_2025_split huggingface dataset:
System drift and speciation
Authors: Schiffman Josh S , Ralph Peter L 
Published: December 2017

AbstractEven if a species’ phenotype does not change over evolutionary time, the underlying mechanism may change, as distinct molecular pathways can realize identical phenotypes. Here we use linear system theory to explore the consequences of this idea, describing how a gene network underlying a conserved phenotype evolves, as the genetic drift of small changes to these molecular pathways cause a population to explore the set of mechanisms with identical phenotypes. To do this, we model an organism’s internal state as a linear system of differential equations for which the environment provides input and the phenotype is the output, in which context there exists an exact characterization of the set of all mechanisms that give the same input–output relationship. This characterization implies that selectively neutral directions in genotype space should be common and that the evolutionary exploration of these distinct but equivalent mechanisms can lead to the reproductive incompatibility of independently evolving populations. This evolutionary exploration, or system drift, is expected to proceed at a rate proportional to the amount of intrapopulation genetic variation divided by the effective population size (Ne). At biologically reasonable parameter values this could lead to substantial interpopulation incompatibility, and thus speciation, on a time scale of Ne generations. This model also naturally predicts Haldane’s rule, thus providing a concrete explanation of why heterogametic hybrids tend to be disrupted more often than homogametes during the early stages of speciation.
VlbZIP30 of grapevine functions in drought tolerance via the abscisic acid core signaling pathway
Authors: Tu Mingxing , Wang Xianhang , Zhu Yanxun , Wang Dejun , Zhang Xuechuan , Cui Ye , Li Yajuan , Gao Min , Li Zhi , Wang Xiping 
Published: December 2017

AbstractDrought stress limits the growth and development of grapevines, thereby reducing productivity, but the mechanisms by which grapevines respond to drought stress remain largely uncharacterized. Here, we characterized a group A bZIP gene from ‘Kyoho’ grapevine, VlbZIP30, which was shown to be induced by abscisic acid (ABA) and dehydration stress. Overexpression of VlbZIP30 in transgenic Arabidopsis enhanced dehydration tolerance during seed germination, and in the seedling and adult stages. Transcriptome analysis revealed that a major proportion of ABA- and/or drought-responsive genes are transcriptionally regulated by VlbZIP30 during ABA or mannitol treatment at the cotyledon greening stage. We identified an A. thaliana G-box motif (CACGTG) and a potential grapevine G-box motif (MCACGTGK) in the promoters of the 39 selected A. thaliana genes up-regulated in the transgenic plants and in the 35 grapevine homologs, respectively. Subsequently, using two grapevine-related databases, we found that 74% and 84% (a total of 27 genes) of the detected grapevine genes were significantly up-regulated by ABA and drought stress, respectively, suggesting that these 27 genes involve in ABA or dehydration stress and may be regulated by VlbZIP30 in grapevine. We propose that VlbZIP30 functions as a positive regulator of drought-responsive signaling in the ABA core signaling pathway.HighlightVlbZIP30 positively regulate plant drought tolerance through regulated the expression of 27 grapevine candidate genes via G-box cis-element (MCACGTGK) in ABA signaling pathway.
Rarefaction, alpha diversity, and statistics
Authors: Willis Amy 
Published: December 2017

AbstractUnderstanding the drivers of microbial diversity is a fundamental question in microbial ecology. Extensive literature discusses different methods for describing microbial diversity and documenting its effects on ecosystem function. However, it is widely believed that diversity depends on the number of reads that are sequenced. I discuss a statistical perspective on diversity, framing the diversity of an environment as an unknown parameter, and discussing the bias and variance of plug-in and rarefied estimates. I argue that by failing to account for both bias and variance, we invalidate analysis of alpha diversity. I describe the state of the statistical literature for addressing these problems, and suggest that measurement error modeling can address issues with variance, but bias corrections need to be utilized as well. I encourage microbial ecologists to avoid motivating their investigations with alpha diversity analyses that do not use valid statistical methodology.
Differential medial temporal lobe and default-mode network functional connectivity and morphometric changes in Alzheimer’s Disease
Authors: Grajski Kamil A. , Bressler Steven L. ,   for the Alzheimer’s Disease Neuroimaging Initiative
Published: December 2017

AbstractWe report group level differential detection of medial temporal lobe resting-state functional connectivity disruption and morphometric changes in the transition from cognitively normal to early mild cognitive impairment in an age-, education- and gender-matched 105 subjects Alzheimer’s Disease Neuroimaging Initiative dataset. In mild Alzheimer’s Disease, but not early mild cognitive impairment, characteristic brain atrophy was detected in FreeSurfer estimates of cortical thickness and subcortical and hippocampal subfield volumes. By contrast, functional connectivity analysis detected earlier significant changes. In early mild cognitive impairment these changes involved medial temporal lobe regions of transentorhinal, perirhinal and entorhinal cortices (associated with the earliest stages of neurofibrillary changes in Alzheimer’s Disease), hippocampus, parahippocampal gyrus and temporal pole, and cortical regions comprising or co-activated with the default-mode network, including rostral and medial prefrontal cortex, anterior cingulate cortex, precuneus and inferior temporal cortex. Key findings include: a) focal and bilaterally symmetric spatial organization of affected medial temporal lobe regions; b) mutual hyperconnectivity bilaterally involving ventral medial temporal lobe structures (temporal pole, uncus); and c) dorsal medial temporal lobe hypoconnectivity with anterior and posterior midline default-mode network nodes. These findings position medial temporal lobe resting state functional connectivity as a candidate biomarker of an Alzheimer’s Disease pathophysiological cascade, potentially in advance of clinical biomarkers, and coincident with biomarkers of the earliest stages of Alzheimer’s neuropathology. Our results indicate that medial temporal lobe resting-state functional connectivity should be further investigated as a potential biomarker in the diagnosis of Alzheimer’s Disease.HighlightsFunctional connectivity change seen before structural change in Alzheimer’s DiseaseMedial temporal lobes mutually hyper-connect in mild cognitive impairmentMedial temporal lobe and default mode network decouple in mild cognitive impairmentLoci of functional change in hippocampi are focal with bilaterally symmetric featuresNonmonotonic functional connectivity changes in Alzheimer’s Disease progression
Pivotal roles of PCNA loading and unloading on heterochromatin function
Authors: Janke Ryan , King Grant , Kupiec Martin , Rine Jasper 
Published: December 2017

ABSTRACTInSaccharomyces cerevisiae, heterochromatin structures required for transcriptional silencing of theHMLandHMRloci are duplicated in coordination with passing DNA replication forks. Despite major reorganization of chromatin structure, the heterochromatic, transcriptionally-silent states ofHMLandHMRare successfully maintained throughout S-phase. Mutations of specific components of the replisome diminish the capacity to maintain silencing ofHMLandHMRthrough replication. Similarly, mutations in histone chaperones involved in replication-coupled nucleosome assembly reduce gene silencing. Bridging these observations, we determined that the PCNA unloading activity of Elg1 was important for coordinating DNA replication forks with the process of replication-coupled nucleosome assembly to maintain silencing ofHMLandHMRthrough S-phase. Collectively these data identified a mechanism by which chromatin reassembly is coordinated with DNA replication to maintain silencing through S-phase.SIGNIFICANCE STATEMENTDNA replication poses a unique logistical challenge for the cell in that structural features of chromatin and their regulatory functions must be carefully coordinated with passage of replication machinery so faithful duplication of both the genome and its chromatin structures may be achieved. Nucleosome assembly is fundamental to reestablishment of chromatin in the wake of DNA replication, and here a mechanism by which nucleosome assembly is coordinated with DNA replication to maintain silenced chromatin is described.
“TRIF is a key inflammatory mediator of acute sickness behavior and cancer cachexia”
Authors: Burfeind Kevin G. , Zhu Xinxia , Levasseur Peter R. , Michaelis Katherine A. , Norgard Mason A. , Marks Daniel L. 
Published: December 2017

AbstractHypothalamic inflammation is a key component of acute sickness behavior and cachexia, yet mechanisms of inflammatory signaling in the central nervous system remain unclear. We assessed the role of TRIF signaling in acute inflammation (lipopolysaccharide (LPS) challenge) and in a chronic inflammatory state (cancer cachexia). TRIFKO mice resisted anorexia and weight loss after peripheral (intraperitoneal, IP) or central (intracerebroventricular, ICV) LPS challenge and in a model of pancreatic cancer cachexia. Compared to WT mice, TRIFKO mice showed attenuated upregulation of Il6, Ccl2, Ccl5, Cxcl1, Cxcl2, and Cxcl10 in the hypothalamus after IP LPS treatment, as well as attenuated microglial activation and neutrophil infiltration into the brain after ICV LPS treatment. Our results show that TRIF is an important inflammatory signaling mediator of sickness behavior and cachexia and presents a novel therapeutic target for these conditions.
Cell-wall synthesis and ribosome maturation are co-regulated by an RNA switch in Mycobacterium tuberculosis
Authors: Schwenk Stefan , Moores Alexandra , Nobeli Irene , McHugh Timothy D. , Arnvig Kristine B. 
Published: December 2017

AbstractThe success of Mycobacterium tuberculosis as a pathogen relies on the ability to switch between active growth and non-replicating persistence, associated with latent TB infection. Resuscitation promoting factors (Rpfs) are essential for the transition of M. tuberculosis to dormancy and for emergence from the non-replicating persistent state. But these enzymes are double-edged swords, as their ability to degrade the cell wall, is potentially lethal to the bacterium itself. Hence, Rpf expression is tightly regulated. We have identified a novel regulatory element in the 5’ untranslated region (UTR) of rpfB. We demonstrate that this element is a transcriptionally regulated RNA switch/riboswitch candidate, which is restricted to pathogenic mycobacteria, suggesting a role in virulence. Moreover, we have used translation start site mapping to re-annotate the RpfB start codon and identified and validated a ribosome binding site that is likely to be targeted by an RpfB antisense RNA. Finally, we show that rpfB is co-transcribed with downstream genes, ksgA and ispE. ksgA encodes a universally conserved methyl transferase involved in ribosome maturation and ispE encodes an essential ATP-dependent kinase involved in cell wall synthesis. This arrangement implies co-regulation of resuscitation, cell wall synthesis and ribosome maturation via the RNA switch. We propose that deregulation of this switch, associated with cell wall synthesis and ribosome function, presents a new target for anti-tuberculosis drug development.ImportanceThis work describes the identification and characterisation of a novel regulatory RNA element/attenuator that controls cell wall synthesis and ribosome function in Mycobacterium tuberculosis, the causative agent of human tuberculosis (TB). By switching between two different conformations, this RNA switch can either enable or inhibit transcription of a tri-cistronic mRNA that encodes a cell-wall remodelling enzyme crucial for activation of latent TB, an RNA methytransferase that is important for ribosome function and a protein kinase essential for early steps in cell wall synthesis. This RNA switch is only present in a subset of pathogenic mycobacteria, and by regulating the expression of three genes associated with classical antimicrobial targets we believe that it offers a novel important target for future anti-tuberculosis drugs.
An attenuated CRISPR-Cas system in Enterococcus faecalis permits DNA acquisition
Authors: Hullahalli Karthik , Rodrigues Marinelle , Nguyen Uyen Thy , Palmer Kelli 
Published: December 2017

AbstractAntibiotic resistant bacteria are critical public health concerns. Among the prime causative factors for the spread of antibiotic resistance is horizontal gene transfer (HGT). A useful model organism for investigating the relationship between HGT and antibiotic resistance is the opportunistic pathogen Enterococcus faecalis, since the species possesses highly conjugative plasmids that readily disseminate antibiotic resistance genes and virulence factors in nature. Unlike many commensal E. faecalis strains, the genomes of multidrug-resistant (MDR) E. faecalis clinical isolates are enriched for mobile genetic elements (MGEs) and lack CRISPR-Cas genome defense systems. CRISPR-Cas systems cleave foreign DNA in a programmable, sequence-specific manner and are disadvantageous for MGE-derived genome expansion. An unexplored facet of CRISPR biology in E. faecalis is that MGEs that are targeted by native CRISPR-Cas systems can be transiently maintained. Here, we investigate the basis for this “CRISPR tolerance.” We observe that E. faecalis can maintain self-targeting constructs that direct Cas9 to cleave the chromosome, but at a fitness cost. Interestingly, DNA repair genes were not up-regulated during self-targeting, but integrated prophages were strongly induced. We determined that low cas9 expression contributes to this transient non-lethality and use this knowledge to develop a robust CRISPR-assisted genome editing scheme. Our results suggest that E. faecalis has maximized the potential for DNA acquisition by attenuating its CRISPR machinery, thereby facilitating acquisition of potentially beneficial MGEs that may otherwise be restricted by genome defense.ImportanceCRISPR-Cas has provided a powerful toolkit to manipulate bacteria, resulting in improved genetic manipulations and novel antimicrobials. These powerful applications rely on the premise that CRISPR-Cas chromosome targeting, which leads to double-stranded DNA breaks, is lethal. In this study, we show that chromosomal CRISPR targeting in Enterococcus faecalis is transiently non-lethal. We uncover novel phenotypes associated with this “CRISPR tolerance” and, after determining its genetic basis, develop a genome editing platform in E. faecalis with negligible off-target effects. Our findings reveal a novel strategy exploited by a bacterial pathogen to cope with CRISPR-induced conflicts to more readily accept DNA, and our robust CRISPR editing platform will help simplify genetic modifications in this organism.
The co-movement and causality between housing and stock markets in the time and frequency domains considering inflation
Authors: Fan Jiaojiao , Li Xin , Shi Qinghua , Su Chi-Wei 
Published: December 2017

Purpose
The purpose of this paper is to examine the causal relationship between Chinese housing and stock markets. The authors discuss the three transmission mechanisms between the two markets: wealth effect, modern portfolio theory and credit-price effect. Moreover, the authors focus on the effects of inflation on the relationship between the two markets.

Design/methodology/approach
This paper uses wavelet analysis to test the housing and stock markets relationship both in the frequency domain and time domain.

Findings
The empirical results indicate that housing prices have a positive effect on stock prices, and these have the same effect on housing prices. Moreover, this positive effect means that stock prices have a wealth effect on housing prices and these have a credit-price effect on stock prices.

Research limitations/implications
These results provide information to financial institutions and individual investors in China to assist them in constructing investment portfolios within these two asset markets.

Originality/value
The authors first use wavelet analysis to analyze Chinese housing and stock markets and to provide information both on the frequency domain and time domain. Moreover, the authors take the inflation factor as a control variable in the causal relationship between the housing and stock markets.
The distinctive challenges and opportunities for creating leadership within social enterprises
Authors: Jackson Brad , Nicoll Matthew , Roy Michael J. 
Published: December 2017

PurposeThe purpose of this study is to present a systematic assessment of the distinctive challenges and opportunities associated with creating leadership within the realm of social enterprise. A modified and expanded form of Grint’s leadership lenses heuristic framework (i.e. person, position, process, performance, purpose and place) is used to examine and highlight what is particular about creating leadership in social enterprises by virtue of their distinctive missions, strategic contexts, legal forms and organisational structures and cultures. Based on this initial exploration, five research priorities are identified to better understand and then develop leadership practice in the social enterprise realm.Design/methodology/approachAn enhanced heuristic framework for systematically examining leadership within the social enterprise research literature has been applied, drawing on the leadership practice literature. The application is illustrated through six instrumental case studies.FindingsWhile there are a number of similarities between leading in the social enterprise realm and leading within the private, public and not-for-profit sectors, the levels of complexity, ambiguity and the lack of an established theoretical and practical knowledge base makes creating leadership in the social enterprise sector that much more challenging. On the positive side of the ledger, the fact that the purpose is at the core of social enterprise means that it is relatively easier to use the purpose to create a basis for common meaningful action, compared to leadership within the private and public sectors. Related to this, given the strongly local or “glocal” nature of social enterprise, a ready opportunity exists for leaders to draw upon a place as a strategic resource in mobilising followers and other stakeholders. The novel, uncertain and pioneering nature of a social enterprise is also arguably more tolerant and accommodating of a leadership mindset that focuses on posing questions regarding “wicked” problems compared to public, private for-profit and, indeed, traditional not-for-profit sector organisations.Originality/valueAs far as we can ascertain, this is the first systematic attempt to examine the distinctive challenges and opportunities associated with creating leadership within the social enterprise realm. The application of the heuristic framework leads to the identification of five key inter-related lines of empirical research into leadership practices within social enterprises.
Renegotiations of Target CEOs' Personal Benefits During Mergers and Acquisitions
Authors: Patrick Paige H. 
Published: December 2017

ABSTRACTMany view large payments following mergers or acquisitions as excessive and evidence of rent extraction. Using additional disclosures required by the SEC since 2006, I hand‐collect details of preexisting change in control (CIC) provisions in employment agreements and CIC benefits granted to target CEOs during mergers. I find that CIC benefits are renegotiated in approximately 50 percent of my sample. I then investigate whether renegotiation of CIC benefits tends to be opportunistic, or, instead, evidence of efficient contracting. The overall evidence is more consistent with efficient contracting. This contrasts prior research that focuses solely on certain components of CIC benefits, such as employment in merged firms or merger bonuses. I find that changes in CIC benefits are positively associated with the CEO's horizon, as would be predicted by efficient contracting, but only limited evidence that changes in CIC benefits are positively associated with proxies for CEO power, as would be predicted by rent extraction. Acquiring firm shareholders interpret increases in target CEOs' CIC benefits as evidence of rent extraction, although I find that the merged firm's post‐merger performance is positively associated with changes in CIC benefits. This result is more consistent with acquiring firms providing target CEOs increased CIC benefits to complete mergers and realize synergies than with value‐reducing rent extraction.
FOREWORD
Authors: ARENA VALENTINA , GÓRÁIN FIACHRA MAC 
Published: December 2017

Abstract
For we were wandering around and lost like visitors in our own city, and it was as if your books led us home, so that we could finally recognize who and where we were. You revealed the age of our homeland, the chronology of our history, you revealed the laws of the rites and the laws of the priests, you revealed our civic and military institutions, you revealed the topography of our districts and places, you revealed the names, kinds, functions, and origins of all things divine and human. Indeed you have shed a flood of light on our poets and in fact on the whole of Latin language and literature. (Cic. Acad. 1.9: editors' translation)
VARRO IN VIRGILIAN COMMENTARIES: TRANSMISSION IN FRAGMENTS
Authors: VALLAT DANIEL 
Published: December 2017

Abstract:
This paper analyses the transmission of Varro in late antique Virgil commentaries. Various problems are identified and discussed: the reliability of authors' names and titles of works in citations and testimonies; different forms of quotation; complications entailed by manuscript transmission; the delimitation of the fragments; the indirect transmission of Varro already in antiquity; the status and function of Varro in a Virgil commentary. Finally I suggest that Varro had a special if implicit status in fourth-century ideological debates, in the tacit rivalry of grammarians with Christian polemicists.
Profile of ethnicity, living arrangements and loneliness amongst older adults in Aotearoa New Zealand: A national cross‐sectional study
Authors: Jamieson Hamish A , Gibson Helen M , Abey‐Nesbit Rebecca , Ahuriri‐Driscoll Annabel , Keeling Sally , Schluter Philip J 
Published: December 2017

ObjectiveTo explore the patterns of living arrangements, ethnicity and loneliness amongst older adults (aged 65+ years) living at home.MethodsNational interRAI‐HC (International Residential Assessment Instrument‐Home Care) assessments conducted between 1 September 2012 and 31 January 2016 were analysed. Analysis focused on the associations between loneliness and both ethnic groups and living arrangements.ResultsThere were 71 859 eligible participants, with average age 82.7 years, comprising Māori (5%), Pasifika (3%), Asian (2%) and European/Other (89%) ethnic identification. Most stated that they were not lonely (79%), but those living alone were more likely to be lonely (29%) than those living with others (14%) (P < 0.05). Amongst those living alone, significant differences in the likelihood of being lonely emerged between ethnic groups (P < 0.05).ConclusionsEthnic identification and living arrangements were significantly associated with the likelihood of loneliness for those having an interRAI‐HC assessment. Efforts to reduce the negative impacts of loneliness need a nuanced approach.