bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fishing for revenue: how leasing quota can be hazardous to your health
Authors: Emery Timothy J. , Hartmann Klaas , Green Bridget S. , Gardner Caleb , Tisdell John 
Published: February 2014

Abstract
Fisheries management decisions have the potential to influence the safety of fishers by affecting how and when they fish. This implies a responsibility of government agencies to consider how fishers may behave under different policies and regulations in order to reduce the incidence of undesirable operational health and safety outcomes. In the Tasmanian southern rock lobster fishery, Australia, the expansion of the quota lease market under individual transferable quota (ITQ) management coincided with a rise in the number of commercial fishing fatalities, with five between 2008 and 2012. A discrete choice model of daily participation was fitted to compare whether physical risk tolerance varied between fishers who owned the majority of their quota units (quota owners) and those who mainly leased (lease quota fishers). In general, fishers were averse to physical risk (wave height), however this was offset by increases in expected revenue. Lease quota fishers were more responsive to changes in expected revenue than quota owners, which contributed to risk tolerance levels that were significantly higher than those of quota owners in some areas. This pattern in behaviour appeared to be related to the cost of leasing quota. Although ITQs have often been considered to reduce the incentive for fishers to operate in hazardous weather conditions, this assumes fishing by quota owners. This analysis indicated that this doesn't hold true for lease quota fishers in an ITQ system, where in some instances there remains an economic incentive to fish in conditions with high levels of physical risk.
Epigenetics of Human Myometrium: DNA Methylation of Genes Encoding Contraction-Associated Proteins in Term and Preterm Labor
Authors: Mitsuya Kohzoh , Singh Natasha , Sooranna Suren R. , Johnson Mark R. , Myatt Leslie 
Published: February 2014

Abstract
Preterm birth involves the interaction of societal and environmental factors potentially modulating the length of gestation via the epigenome. An established form of epigenetic regulation is DNA methylation where promoter hypermethylation is associated with gene repression. We hypothesized we would find differences in DNA methylation in the myometrium of women with preterm labor of different phenotypes versus normal term labor. Myometrial tissue was obtained at cesarean section at term with or without labor, preterm without labor, idiopathic preterm labor, and twin gestations with labor. Genomic DNA was isolated, and samples in each group were combined and analyzed on a NimbleGen 2.1M human DNA methylation array. Differences in methylation from −8 to +3 kb of transcription start sites of 22 contraction-associated genes were determined. Cytosine methylation was not present in CpG islands of any gene but was present outside of CpG islands in shores and shelves in 19 genes. No differential methylation was found across the tissue groups for six genes (PTGES3L, PTGER2, PTGER4, PTGFRN, ESR2, and GJA1). For 13 genes, differential methylation occurred in several patterns between tissue groups. We find a correlation between hypomethylation and increased mRNA expression of PTGES/mPGES-1, indicating potential functional relevance of methylation, but no such correlation for PTGS2/COX-2, suggesting other regulatory mechanisms for PTGS2 at labor. The majority of differential DNA methylation of myometrial contraction-associated genes with different labor phenotypes occurs outside of CpG islands in gene promoters, suggesting that the entirety of DNA methylation across the genome should be considered.
Fast-spiking Cell to Pyramidal Cell Connections Are the Most Sensitive to Propofol-induced Facilitation of GABAergic Currents in Rat Insular Cortex
Authors: Koyanagi Yuko , Oi Yoshiyuki , Yamamoto Kiyofumi , Koshikawa Noriaki , Kobayashi Masayuki 
Published: February 2014

Abstract

Background:
Propofol facilitates γ-aminobutyric acid–mediated inhibitory synaptic transmission. In the cerebral cortex, γ-aminobutyric acidergic interneurons target both excitatory pyramidal cells (Pyr) and fast-spiking (FS) and non-FS interneurons. Therefore, the propofol-induced facilitation of inhibitory transmission results in a change in the balance of excitatory and inhibitory inputs to Pyr. However, it is still unknown how propofol modulates γ-aminobutyric acidergic synaptic transmission in each combination of Pyr and interneurons.

Methods:
The authors examined whether propofol differentially regulates inhibitory postsynaptic currents (IPSCs) depending on the presynaptic and postsynaptic cell subtypes using multiple whole cell patch clamp recording from γ-aminobutyric acidergic interneurons and Pyr in rat insular cortex.

Results:
Propofol (10 μM) consistently prolonged decay kinetics of unitary IPSCs (uIPSCs) in all types of inhibitory connections without changing paired-pulse ratio of the second to first uIPSC amplitude or failure rate. The FS→Pyr connections exhibited greater enhancement of uIPSC charge transfer (2.2 ± 0.5 pC, n = 36) compared with that of FS→FS/non-FS connections (0.9 ± 0.2 pC, n = 37), whereas the enhancement of charge transfer in non-FS→Pyr (0.3 ± 0.1 pC, n = 15) and non-FS→FS/non-FS connections (0.2 ± 0.1 pC, n = 36) was smaller to those in FS→Pyr/FS/non-FS. Electrical synapses between FS pairs were not affected by propofol.

Conclusions:
The principal inhibitory connections (FS→Pyr) are the most sensitive to propofol-induced facilitation of uIPSCs, which is likely mediated by postsynaptic mechanisms. This preferential uIPSC enhancement in FS→Pyr connections may result in suppressed neural activities of projection neurons, which in turn reduces excitatory outputs from cortical local circuits.
Chromatin Loops as Allosteric Modulators of Enhancer-Promoter Interactions
Authors: Doyle Boryana , Fudenberg Geoffrey , Imakaev Maxim , Mirny Leonid A. 
Published: February 2014

AbstractThe classic model of eukaryotic gene expression requires direct spatial contact between a distal enhancer and a proximal promoter. Recent Chromosome Conformation Capture (3C) studies show that enhancers and promoters are embedded in a complex network of looping interactions. Here we use a polymer model of chromatin fiber to investigate whether, and to what extent, looping interactions between elements in the vicinity of an enhancer-promoter pair can influence their contact frequency. Our equilibrium polymer simulations show that a chromatin loop, formed by elements flanking either an enhancer or a promoter, suppresses enhancer-promoter interactions, working as an insulator. A loop formed by elements located in the region between an enhancer and a promoter, on the contrary, facilitates their interactions. We find that different mechanisms underlie insulation and facilitation; insulation occurs due to steric exclusion by the loop, and is a global effect, while facilitation occurs due to an effective shortening of the enhancer-promoter genomic distance, and is a local effect. Consistently, we find that these effects manifest quite differently forin silico3C and microscopy. Our results show that looping interactions that do not directly involve an enhancer-promoter pair can nevertheless significantly modulate their interactions. This phenomenon is analogous to allosteric regulation in proteins, where a conformational change triggered by binding of a regulatory molecule to one site affects the state of another site.Author SummaryIn eukaryotes, enhancers directly contact promoters over large genomic distances to regulate gene expression. Characterizing the principles underlying these long-range enhancer-promoter contacts is crucial for a full understanding of gene expression. Recent experimental mapping of chromosomal interactions by the Hi-C method shows an intricate network of local looping interactions surrounding enhancers and promoters. We model a region of chromatin fiber as a long polymer and study how the formation of loops between certain regulatory elements can insulate or facilitate enhancer-promoter interactions. We find 2-5 fold insulation or facilitation, depending on the location of looping elements relative to an enhancer-promoter pair. These effects originate from the polymer nature of chromatin, without requiring additional mechanisms beyond the formation of a chromatin loop. Our findings suggest that loop-mediated gene regulation by elements in the vicinity of an enhancer-promoter pair can be understood as an allosteric effect. This highlights the complex effects that local chromatin organization can have on gene regulation.
The Competition between Liquid and Vapor Transport in Transpiring Leaves
Authors: Rockwell Fulton Ewing , Holbrook N. Michele , Stroock Abraham Duncan 
Published: February 2014

Abstract
In leaves, the transpirational flux of water exits the veins as liquid and travels toward the stomata in both the vapor and liquid phases before exiting the leaf as vapor. Yet, whether most of the evaporation occurs from the vascular bundles (perivascular), from the photosynthetic mesophyll cells, or within the vicinity of the stomatal pore (peristomatal) remains in dispute. Here, a one-dimensional model of the competition between liquid and vapor transport is developed from the perspective of nonisothermal coupled heat and water molecule transport in a composite medium of airspace and cells. An analytical solution to the model is found in terms of the energy and transpirational fluxes from the leaf surfaces and the absorbed solar energy load, leading to mathematical expressions for the proportions of evaporation accounted for by the vascular, mesophyll, and epidermal regions. The distribution of evaporation in a given leaf is predicted to be variable, changing with the local environment, and to range from dominantly perivascular to dominantly peristomatal depending on internal leaf architecture, with mesophyll evaporation a subordinate component. Using mature red oak (Quercus rubra) trees, we show that the model can be solved for a specific instance of a transpiring leaf by combining gas-exchange data, anatomical measurements, and hydraulic experiments. We also investigate the effect of radiation load on the control of transpiration, the potential for condensation on the inside of an epidermis, and the impact of vapor transport on the hydraulic efficiency of leaf tissue outside the xylem.
Tolerance landscapes in thermal ecology
Authors: Rezende Enrico L. , Castañeda Luis E. , Santos Mauro 
Published: February 2014

SummaryHow thermal tolerance estimated in the laboratory can be extrapolated to natural settings remains a contentious subject. Here, we argue that the general premise that a single temperature can accurately describe upper or lower tolerance limits is incorrect.Survival probability is determined by both the intensity and the duration of a thermal stress, and the association between these variables can be adequately conveyed by a thermal tolerance landscape. Employing this framework, we demonstrate that the temperature range that an organism can tolerate is expected to narrow down with the duration of the thermal challenge.Analyses suggest that a trade‐off exists between tolerances to acute and chronic exposition to thermal stress, and that changes in temperature means or extremes may result in drastically different selective pressures and subsequent evolutionary responses.After controlling for the duration of the thermal challenge, we also uncover latitudinal effects on upper lethal temperatures in insects that remained unnoticed in previous broad‐scale comparative analyses.Ultimately, critical thermal limits have been adopted in the ecological literature for logistic reasons and are inadequate descriptors of thermal tolerance on conceptual grounds. We consider that tolerance landscapes provide a more suitable framework to study temperature tolerance and its potential impact in ecological settings.
The hygroscopic biosurfactant syringafactin produced by Pseudomonas syringae enhances fitness on leaf surfaces during fluctuating humidity
Authors: Burch Adrien Y. , Zeisler Viktoria , Yokota Kenji , Schreiber Lukas , Lindow Steven E. 
Published: February 2014

SummaryBiosurfactant production by bacteria on leaf surfaces is poorly documented, and its role in this habitat has not been explored. Therefore, we investigated the production and fitness benefits of syringafactin by Pseudomonas syringae pv. syringae B728a on leaves. Syringafactin largely adsorbed to the waxy leaf cuticle both when topically applied and when produced by cells on plants. Syringafactin increased the rate of diffusion of water across isolated cuticles and attracted water to hydrophobic surfaces exposed to high relative humidity due to its hygroscopic properties. While a wild‐type and syringafactin mutant exhibited similar fitness on bean leaves incubated in static conditions, the fitness of the wild‐type strain was higher under fluctuating humidity conditions typical of field conditions. When co‐inoculated onto either the host plant bean or the non‐host plant romaine lettuce, the proportion of viable wild‐type cells recovered from plants relative to that of a mutant unable to produce syringafactin increased 10% over 10 days. The number of disease lesions incited by the wild‐type strain on bean was also significantly higher than that of the syringafactin mutant. The production of hygroscopic biosurfactants on waxy leaf surfaces apparently benefits bacteria by both attracting moisture and facilitating access to nutrients.
The Return of Historical Sociology
Authors: Smith Dennis 
Published: February 2014

The Modern World-System IV: Centrist Liberalism Triumphant 1789–1914 Immanuel Wallerstein, University of California Press, Berkeley, 2011, £47.95, paper £21.95, 377pp. Power in the 21st Century: Conversations with John A. Hall Michael Mann, Polity, Cambridge, 2011, £50.00, paper £14.99, 179pp. The Sources of Social Power, Volume 3: Global Empires and Revolution, 1890–1945 Michael Mann, Cambridge University Press, Cambridge, 2012, £62.00, paper £23.99, 516pp. The Sources of Social Power, Volume 4: Globalizations, 1945–2011 Michael Mann, Cambridge University Press, Cambridge, 2013, £60.00, paper £22.99, 496pp.
Choice of primary outcomes in randomised trials and systematic reviews evaluating interventions for preterm birth prevention: a systematic review
Authors: Meher S , Alfirevic Z 
Published: February 2014

BackgroundThe inappropriate and inconsistent selection of primary outcomes (POs) in randomised controlled trials (RCTs) and systematic reviews (SRs) can make evidence difficult to interpret, limiting its usefulness to inform clinical practice.ObjectivesTo systematically review the choice and consistency of POs in RCTs and SRs of preventative interventions for preterm birth.Search strategyCochrane Pregnancy and Childbirth Group's Specialised Register of trials and a full list of published reviews and protocols.Selection criteriaFull reports of RCTs for preterm birth prevention published after CONSORT (January 1997–January 2011), and Cochrane Reviews and protocols relevant to preterm birth prevention, for the same period.Data collection and analysisFor RCTs, the PO was the outcome used for sample size calculation. For SRs, we included all outcomes listed as ‘primary’. Two review authors selected studies and double‐checked the data for accuracy.ResultsSeventy‐two different POs were reported by 103 RCTs. The three most common POs were based on length of gestation, with preterm birth before 37 weeks of gestation being the most common (18/103, 18%). Few RCTs chose perinatal morbidity (4/103) or mortality (1/103), or their composites (5/103), as POs. In 33 Cochrane Reviews, 29 different POs were reported. The three most common POs were based on death or morbidity in the baby, with death of the baby being the most common (22/33, 67%). POs were variably defined.ConclusionsThere is a lack of consistency in the choice and definitions of POs in clinical research related to preterm birth prevention. SRs are more likely to report morbidity and mortality as POs, whereas RCTs tend to use length of gestation. Researchers are urged to review the outcomes reported in RCTs and SRs in their respective areas of interest to highlight discrepancies and facilitate the development of core outcome sets.
Application of the LUminometric Methylation Assay to ecological species: tissue quality requirements and a survey of DNA methylation levels in animals
Authors: Head Jessica A. , Mittal Krittika , Basu Niladri 
Published: February 2014

AbstractThe LUminometric Methylation Assay (LUMA) measures global DNA methylation. LUMA depends on digestion of DNA with methyl‐sensitive and methyl‐insensitive restriction enzymes, followed by pyrosequencing. Until recently, LUMA has been principally used for biomedical research. Here, we use chickens as a model to investigate sample quality issues relating to LUMA and then apply the method to ecological species. First, we assessed the effect of tissue storage conditions on DNA methylation values. This is an important consideration for ecological species because samples are not always ideally preserved and LUMA is sensitive to poor DNA quality. We found that good quality LUMA data could be obtained from chicken liver and brain tissues stored at 21 °C for at least 2 and 12 h, respectively. Longer storage times introduced nonspecific peaks to pyrograms which were associated with reduced DNA methylation. Repeatedly, freezing and thawing the tissues did not affect LUMA data. Second, we measured DNA methylation in 12 species representing five animal classes: amphibians (African and Western clawed frog), reptiles (green anole lizard), fish (yellow perch, goldfish, lake trout), mammals (American mink, polar bear, short‐beaked common dolphin, Atlantic white‐sided dolphin) and birds (chicken, Japanese quail). We saw a pattern of high DNA methylation in fish (84–87%), and intermediate levels in mammals (68–72%) and birds (52–71%). This pattern corresponds well with previous measures of DNA methylation generated by HPLC. Our data represent the first CpG methylation values to be reported in several species and provide a basis for studying patterns of epigenetic inheritance in an ecological context.
Poor Autonomic Nervous System Functioning During Sleep in Recently Detoxified Alcohol‐Dependent Men and Women
Authors: de Zambotti Massimiliano , Baker Fiona C. , Sugarbaker David S. , Nicholas Christian L. , Trinder John , Colrain Ian M. 
Published: February 2014

BackgroundAlcoholism is considered an important risk factor for cardiovascular (CV) disease. Autonomic nervous system (ANS) function is a major indicator of CV health. Sleep is a suitable model to investigate ANS activity free from wake‐related confounders. We investigated nighttime ANS functioning, and the relation between ANS activity and severity of alcohol dependence in chronic alcoholism.MethodsFourteen recently abstaining alcoholics (age: 42.0 ± 9.0 years, 7 women) and 16 age‐ and sex‐matched controls (age: 45.2 ± 9.1 years, 8 women) underwent a night of standard clinical polysomnography, including electrocardiographic recording. Time‐ and frequency‐domain spectral analysis of heart rate variability (HRV) was performed across hours of the night and during artifact‐free epochs of stable sleep and wakefulness (presleep wakefulness, rapid‐eye‐movement [REM], and non‐REM sleep).ResultsAlcoholics had a poorer subjective and objective sleep quality compared to controls. Across the night, alcoholic men and women had elevated heart rate, reduced total HRV, that is, lower standard deviation of normal‐to‐normal interbeat intervals, and reduced high frequency (HF) activity (assessed by the HF power and by the square root of the mean squared of successive heart period differences). This ANS pattern was most apparent at the beginning of the night. None of the ANS measures was associated with lifetime alcohol consumption or duration of alcohol dependence.ConclusionsOur results show that ANS functioning is disrupted during the night, even in undisturbed sleep periods, indicating poor CV functioning in recently detoxified alcohol‐dependent men and women.
Growth, governance and corporate payout policy
Authors: Bhabra Gurmeet , Luu Khanh Hien 
Published: February 2014

AbstractWe show that when growth opportunities decreased following the end of the Cold War, defence firms responded by increasing total payout. This change in policy was largely driven by increased stock buybacks as opposed to changes in cash dividends and primarily by firms that faced stronger external governance. On the other hand, firms with weaker internal governance that were more severely affected by the reduced growth chose to alter the mix of payout at the expense of repurchases. Overall, our findings (i) demonstrate a causal link where exogenous shocks to growth cause payout policy changes, (ii) support the role of internal governance in payout policy design where entrenched managers pre‐commit to higher dividends and (iii) emphasize the monitoring role of external governance in mitigating agency costs of free cash flow.
LMO2 andBCL6 are associated with improved survival in primary central nervous system lymphoma
Authors: Lossos Chen , Bayraktar Soley , Weinzierl Elizabeth , Younes Sheren F. , Hosein Peter J. , Tibshirani Robert J. , Sutton Posthumus Jocelyn , DeAngelis Lisa M. , Raizer Jeffrey , Schiff David , Abrey Lauren , Natkunam Yasodha , Lossos Izidore S. 
Published: February 2014

SummaryPrimary central nervous system lymphoma (PCNSL) is an aggressive sub‐variant of non‐Hodgkin lymphoma (NHL) with morphological similarities to diffuse large B‐cell lymphoma (DLBCL). While methotrexate (MTX)‐based therapies have improved patient survival, the disease remains incurable in most cases and its pathogenesis is poorly understood. We evaluated 69 cases ofPCNSLfor the expression ofHGAL(also known asGCSAM),LMO2andBCL6– genes associated withDLBCLprognosis and pathobiology, and analysed their correlation to survival in 49PCNSLpatients receivingMTX‐based therapy. We demonstrate thatPCNSLexpressesLMO2,HGAL(also known asGCSAM) andBCL6 proteins in 52%, 65% and 56% of tumours, respectively.BCL6 protein expression was associated with longer progression‐free survival (P = 0·006) and overall survival (OS,P = 0·05), while expression ofLMO2 protein was associated with longerOS(P = 0·027). Further research is needed to elucidate the function ofBCL6andLMO2inPCNSL.