bluuebunny/crossref_metadata_2025 huggingface dataset:
Understanding the emergence of bacterial pathogens in novel hosts
Authors: Bonneaud Camille , Weinert Lucy A. , Kuijper Bram
Published: August 2019

Our understanding of the ecological and evolutionary context of novel infections is largely based on viral diseases, even though bacterial pathogens may display key differences in the processes underlying their emergence. For instance, host-shift speciation, in which the jump of a pathogen into a novel host species is followed by the specialization on that host and the loss of infectivity of previous host(s), is commonly observed in viruses, but less often in bacteria. Here, we suggest that the extent to which pathogens evolve host generalism or specialism following a jump into a novel host will depend on their level of adaptation to dealing with different environments, their rates of molecular evolution and their ability to recombine. We then explore these hypotheses using a formal model and show that the high levels of phenotypic plasticity, low rates of evolution and the ability to recombine typical of bacterial pathogens should reduce their propensity to specialize on novel hosts. Novel bacterial infections may therefore be more likely to result in transient spillovers or increased host ranges than in host shifts. Finally, consistent with our predictions, we show that, in two unusual cases of contemporary bacterial host shifts, the bacterial pathogens both have small genomes and rapid rates of substitution. Further tests are required across a greater number of emerging pathogens to assess the validity of our hypotheses.

This article is part of the theme issue ‘Dynamic and integrative approaches to understanding pathogen spillover’.
Percolation models of pathogen spillover
Authors: Washburne Alex D. , Crowley Daniel E. , Becker Daniel J. , Manlove Kezia R. , Childs Marissa L. , Plowright Raina K.
Published: August 2019

Predicting pathogen spillover requires counting spillover events and aligning such counts with process-related covariates for each spillover event. How can we connect our analysis of spillover counts to simple, mechanistic models of pathogens jumping from reservoir hosts to recipient hosts? We illustrate how the pathways to pathogen spillover can be represented as a directed graph connecting reservoir hosts and recipient hosts and the number of spillover events modelled as a percolation of infectious units along that graph. Percolation models of pathogen spillover formalize popular intuition and management concepts for pathogen spillover, such as the inextricably multilevel nature of cross-species transmission, the impact of covariance between processes such as pathogen shedding and human susceptibility on spillover risk, and the assumptions under which the effect of a management intervention targeting one process, such as persistence of vectors, will translate to an equal effect on the overall spillover risk. Percolation models also link statistical analysis of spillover event datasets with a mechanistic model of spillover. Linear models, one might construct for process-specific parameters, such as the log-rate of shedding from one of several alternative reservoirs, yield a nonlinear model of the log-rate of spillover. The resulting nonlinearity is approximately piecewise linear with major impacts on statistical inferences of the importance of process-specific covariates such as vector density. We recommend that statistical analysis of spillover datasets use piecewise linear models, such as generalized additive models, regression clustering or ensembles of linear models, to capture the piecewise linearity expected from percolation models. We discuss the implications of our findings for predictions of spillover risk beyond the range of observed covariates, a major challenge of forecasting spillover risk in the Anthropocene.

This article is part of the theme issue ‘Dynamic and integrative approaches to understanding pathogen spillover’.
Spatial and temporal transcriptomics reveal microglia-astroglia crosstalk in the amyloid-β plaque cell niche of Alzheimer’s disease
Authors: Chen Wei-Ting , Lu Ashley , Craessaerts Katleen , Pavie Benjamin , Sala Frigerio Carlo , Mancuso Renzo , Qian Xiaoyan , Lalakova Jana , Kühnemund Malte , Voytyuk Iryna , Wolfs Leen , Snellinx An , Munck Sebastian , Jurek Aleksandra , Fernandez Navarro Jose , Saido Takaomi C , Lundeberg Joakim , Fiers Mark , De Strooper Bart
Published: August 2019

The linear cause-consequence relationship linking amyloid-β peptide (Aβ) accumulation to neuronal dysfunction in Alzheimer disease (AD) is gradually replaced by the concept that Aβ initiates complex inflammatory-like cellular alterations that progressively become Aβ independent and lead to brain dyshomeostasis. Little is known about the pathophysiology of this cellular phase of AD. We use here two orthogonal technologies, Spatial Transcriptomics and in situ sequencing, to analyse the transcriptome changes in cells in the amyloid-β plaque niche in a knock-in mouse model for AD. We identify a multicellular co-expressed gene network of 57 Plaque-Induced Genes (PIGs) that define a series of co-ordinated and spatially restricted microglia, astroglia and oligodendrocyte responses to progressing amyloid plaques encompassing complement, oxidative stress and inflammation. A separate oligodendrocyte network suggests abnormal myelination. Spatial Transcriptomics provides an unprecedented approach to untangle the dysregulated cellular network in the vicinity of pathogenic hallmarks of AD and other brain diseases.
Molecular responses to freshwater limitation in the mangrove tree Avicennia germinans (Acanthaceae)
Authors: Cruz Mariana Vargas , Mori Gustavo Maruyama , Oh Dong-Ha , Dassanayake Maheshi , Zucchi Maria Imaculada , Oliveira Rafael Silva , de Souza Anete Pereira
Published: August 2019

Environmental variation along the geographical space can shape populations by natural selection. In the context of global warming, accompanied by substantial changes in precipitation regimes, it is crucial to understand the role of environmental heterogeneity in tropical trees adaptation, given their disproportional contribution to water and carbon biogeochemical cycles. Here we investigated how heterogeneity in freshwater availability along tropical wetlands has influenced molecular variations of the Black-Mangrove (Avicennia germinans). Fifty-seven trees were sampled in seven sites differing markedly on precipitation regime and riverine freshwater inputs. Using 2,297 genome-wide single nucleotide polymorphic markers, we found signatures of natural selection by the genotype association with the precipitation of the warmest quarter and the annual precipitation. We also found candidate loci for selection, based on statistical deviations from neutral expectations of interpopulation differentiation. Most candidate loci present within coding sequences were functionally associated with central aspects of drought-tolerance or plant response to drought. Complementarily, our results suggest the occurrence of rapid evolution of a population, likely in response to sudden and persistent limitation in plant access to soil water, following a road construction in 1974. Observations supporting rapid evolution included reduction in tree size and changes in allele frequencies and in transcripts expression levels associated with increased drought-tolerance, through accumulation of osmoprotectants and antioxidants, biosynthesis of plant cuticle, protection against stress-induced proteins degradation, stomatal closure, photorespiration and photosynthesis. We describe a major role of spatial heterogeneity in freshwater availability in the specialization of this typically tropical tree.
Single-Cell RNA-Seq Reveals Naïve B cells Associated with Better Prognosis of HCC
Authors: He Jian , Lin Yingxin , Su Xianbin , Luo Qing , Ghazanfar Shila , Yang Jean Y H , Han Ze-guang
Published: August 2019

Hepatocellular Carcinoma (HCC) is a type of malignant solid tumor, causing high morbidity and mortality around the world and the major portion of HCC patients is from China. Cancer immunotherapies have shown some clinical responses in treating some types of cancer but did not shown significant efficiency in HCC treatment. This in part due to the impact of immune cells in the tumor microenvironment. It is commonly believed that HCC is a heterogeneous solid tumor and the microenvironment of HCC plays an important role in tumorgenesis and development. Currently, the residents of the microenvironment of HCC is not well-defined and clarification, especially the immune cells, which we believe that paly pivotal roles in tumorgenesis and development. To depict the landscape of the composition, lineage and functional states of the immune cells in HCC, we performed single-cell RNA sequencing on Diethylnitrosamine (DEN)-induced mouse HCC model. We observed heterogeneity within the immune and hepatocytes both in the precancerous condition of tumorigenesis and cancerous condition of HCC. In this study we found that the disease-associated changes appeared early in pathological progression and were highly cell-type specific. Specific subsets of T and B cells preferentially enriched in HCC, and we identified signature genes for each subset. Additionally, we mapped this group of specific cells to the human TCGA database. We found a cluster of naïve B cells characterized by high expression of CD38 associated with better prognosis of human HCC. Our study demonstrates signaling interaction map based on receptor-ligand bonding on the single-cell level could broaden our comprehending of cellular networks in varies status. Our finding provides a new approach for patient stratification and will help further understand the functional states, dynamics and signaling interaction of B cells in hepatocellular carcinoma, and may provide a novel insight and therapeutics for the HCC.
Automated and rapid self-report of nociception in transgenic mice
Authors: Black Christopher J. , Allawala Anusha B. , Bloye Kiernan , Vanent Kevin N. , Edhi Muhammad M. , Saab Carl Y. , Borton David A.
Published: August 2019

A time-resolved, conscious report of detected nociceptive stimuli in mice offers an opportunity to examine the relationship between higher order neural circuits and pain perception. We have developed a detection behavior in transgenic mice that leverages temporally precise and cell-specific stimulation to elicit self-reports of nociception. Conscious reporting of peripheral nociceptive input may help identify neural mechanisms that generate pain perception.
Identification of 15 new bypassable essential genes of fission yeast
Authors: Takeda Aoi , Saitoh Shigeaki , Ohkura Hiroyuki , Sawin Kenneth E. , Goshima Gohta
Published: August 2019

Every organism has a different set of genes essential for its viability. This indicates that an organism can become tolerant to the loss of an essential gene under certain circumstances during evolution, via the manifestation of ‘masked’ alternative mechanisms. In our quest to systematically uncover masked mechanisms in eukaryotic cells, we developed an extragenic suppressor screening method using haploid spores deleted of an essential gene in the fission yeastSchizosaccharomyces pombe. We screened for the ‘bypass’ suppressors of lethality of 92 randomly selected genes that are essential for viability in standard laboratory culture conditions. Remarkably, extragenic mutations bypassed the essentiality of as many as 20 genes (22%), 15 of which have not been previously reported. Half of the bypass-suppressible genes were involved in mitochondria function; we also identified multiple genes regulating RNA processing. 18 suppressible genes were conserved in the budding yeastSaccharomyces cerevisiae, but 13 of them were non-essential in that species. These trends are consistent with a recent independent bypass-of-essentiality (BOE) screening of 142 fission yeast genes conducted with more elaborate methodology (Liet al., 2019). Thus, our study reinforces the emerging view that BOE is not a rare event and that each organism may be endowed with secondary or backup mechanisms that can substitute for primary mechanisms in various biological processes. Furthermore, the robustness of our simple spore-based methodology paves the way for genome-scale BOE screening.
Fungal traits important for soil aggregation
Authors: Lehmann Anika , Zheng Weishuang , Ryo Masahiro , Soutschek Katharina , Rongstock Rebecca , Maaß Stefanie , Rillig Matthias C.
Published: August 2019

Soil health and sustainability is essential for ecosystem functioning and human well-being. Soil structure, the complex arrangement of soil into aggregates and pore spaces, is a key feature of soils under the influence of soil life. Soil biota, and among them filamentous saprobic fungi, have well-documented effects on soil aggregation. However, it is unclear what fungal properties, or traits, contribute to the overall positive effect on soil aggregation. So far, we lack a systematic investigation of a broad suite of fungal species for their trait expression and the relation of these traits to their soil aggregation capability.

Here, we apply a trait-based approach to a set of 15 traits measured under standardized conditions on 31 fungal strains including Ascomycota, Basidiomycota and Mucoromycota, all isolated from the same soil.

We found a spectrum of soil aggregate formation capability ranging from neutral to positive and large differences in trait expression among strains. We identified biomass density (positive effects), leucine aminopeptidase activity (negative effects) and phylogeny as important modulators of fungal aggregate formation capability. Our results point to a typical suite of traits characterizing fungi that are good soil aggregators; this could inform screening for fungi to be used in biotechnological applications, and illustrates the power of employing a trait-based approach to unravel biological mechanisms of soil aggregation, which could now be extended to other organism groups.
A single TRPV1 amino acid controls species sensitivity to capsaicin
Authors: Chu Ying , Cohen Bruce E. , Chuang Huai-hu
Published: August 2019

Chili peppers produce capsaicin, the principle chemical that accounts for the culinary sensations of heat. Capsaicin activates the transient receptor potential cation channel subfamily V member 1 (TRPV1) on sensory neurons to alter the membrane potential to induce pain. While structural studies have identified residues important for the binding of capsaicin to rat TRPV1, there is still no clear understanding of differential capsaicin sensitivity of TRPV1 between birds and mammals. To determine the residues dictating relative capsaicin sensitivity among species, we have used intracellular Ca2+imaging to characterize chimeras composed of capsaicin-sensitive rat TRPV1 (rTRPV1) and capsaicin-insensitive chicken TRPV1 (cTRPV1) with a series of capsaicinoids. We find that chimeras containing rat E570-V686 swapped into chicken receptors displays capsaicin sensitivity, and that a single amino acid substitution in the S4-S5 helix, changing the alanine at position 578 in the chick receptor to a glutamate, is sufficient to endow micromolar capsaicin sensitivity. Moreover, introduction of lysine, glutamine or proline at A578 also install capsaicin sensitivity in cTRPV1. Comparing the derivatives Cap-EA and Cap-EMA with capsaicin, these two compounds with the hydrophilic vanilloid-like moiety affect the protein-ligand interaction. The ability of 10 μM Cap-EA to activate cTRPV1-A578E and the differential response of mutants to the analogs suggests that chick A578 may participate in vanilloid binding, as does the corresponding rTRPV1 site. The hydrophilic vanilloid agonist zingerone 500 μM failed to activate any A578 mutants that retained capsaicin sensitivity, suggesting that the vanilloid group alone is not sufficient for receptor activation. Replacing the rTRPV1-E570 residue with K, Q shows a similar tendency to maintain the receptor capsaicin sensitivity. Our study demonstrates a subtle modification on different species TRPV1 globally alter their capsaicin response.
X-ray reflecto-interferometer based on compound refractive lenses
Authors: Lyatun S. , Zverev D. , Ershov P. , Lyatun I. , Konovalov O. , Snigireva I. , Snigirev A.
Published: August 2019

An X-ray amplitude-splitting interferometer based on compound refractive lenses, which operates in the reflection mode, is proposed and realized. The idea of a reflecto-interferometer is to use a very simplified experimental setup where a focused X-ray beam reflected from parallel flat surfaces creates an interference pattern in a wide angular range. The functional capabilities of the interferometer were experimentally tested at the European Synchrotron Radiation Facility (ESRF) ID06 beamline in the X-ray energy range from 10 keV to 15 keV. The main features of the proposed approach, high spatial and temporal resolution, were demonstrated experimentally. The reflections from free-standing Si3N4 membranes, gold and resist layers were studied. Experimentally recorded interferograms are in good agreement with our simulations. The main advantages and future possible applications of the reflecto-interferometer are discussed.
Generating three-color pulses in high-gain harmonic-generation free-electron lasers with a tilted electron bunch
Authors: Zhao Zhouyu , Li Heting , Li Weiwei , Jia Qika , Jiang Shimin , Wang Lin
Published: August 2019

A multi-color light source is a significant tool for nonlinear optics experiments, pump–dump/repump–probe experiments and in other fields. Here, a novel method is proposed to create three-color pulses based on a high-gain harmonic-generation (HGHG) free-electron laser with a tilted electron bunch. In this method, the initial bunch tilt is created by transverse wakefields after the bunch passes through a corrugated structure with an off-axis orbit, and is further enlarged in a following drift section. Then the tilted bunch experiences the off-axis field of a quadrupole magnet to cool down the large transverse velocity induced before. After that, it enters an HGHG configuration adopting a transverse gradient undulator (TGU) as the radiator, where only three separated fractions of the tilted bunch will resonate at three adjacent harmonics of the seed wavelength and are enabled to emit three-color pulses simultaneously. In addition, the use of the natural transverse gradient of a normal planar undulator instead of the TGU radiator to emit three-color pulses is also studied in detail. Numerical simulations including the generation of the tilted bunch and the free-electron laser radiation confirm the validity and feasibility of this scheme both for the TGU radiator and the natural gradient in the extreme-ultraviolet waveband.
Relativistic quantum crystallography of diphenyl- and dicyanomercury. Theoretical structure factors and Hirshfeld atom refinement
Authors: Bučinský Lukáš , Jayatilaka Dylan , Grabowsky Simon
Published: August 2019

Quantum crystallographic refinement of heavy-element-containing compounds is a challenge, because many physical effects have to be accounted for adequately. Here, the impact and magnitude of relativistic effects are compared with those of electron correlation, polarization through the environment, choice of basis set and treatment of thermal motion effects on the structure factors of diphenylmercury(II) [Hg(Ph)2] and dicyanomercury(II) [Hg(CN)2]. Furthermore, the individual atomic contributions to the structure factors are explored in detail (using Mulliken population analysis and the exponential decay of atomic displacement parameters) to compare the contributions of lighter atoms, especially hydrogen atoms, against mercury. Subsequently, relativistic Hirshfeld atom refinement (HAR) is validated against theoretical structure factors of Hg(Ph)2and Hg(CN)2, starting from perturbed geometries, to test if the relativistic variant of HAR leads to multiple solutions. Generally, relativistic HAR is successful, leading to a perfect match with the reference geometries, but some limitations are pointed out.
Anomalous X-ray diffraction from ω nanoparticles in β-Ti(Mo) single crystals
Authors: Šmilauerová Jana , Harcuba Petr , Cieslar Miroslav , Janeček Miloš , Holý Václav
Published: August 2019

Anomalous X-ray diffraction (AXRD) is a technique which makes use of effects occurring near the energy of an absorption edge of an element present in the studied sample. The intensity of the diffracted radiation exhibits an anomalous decrease when the primary beam energy matches the energy needed to excite an electron from an atomic orbital. The characteristics of this step are sensitive to the concentration of the `anomalous' element and its spatial distribution in the sample. In the present investigation, AXRD was employed to study ω particles in a metastable β titanium alloy Ti–15Mo (in wt%). The experiments were done in an energy range around the MoKedge at 20.0 keV, allowing investigation of the distribution of Mo in the material, which is rejected from the volume of ω particles during their diffusion-driven growth. This paper deals with diffuse scattering patterns around the (006)βdiffraction maximum. It was observed that different regions of the diffuse scattering exhibited different variations of diffracted intensity with the incident photon energy near the absorption edge. Numerical simulations of diffuse scattering patterns as well as of energy dependences of the scattered intensity were performed. It was found that the observed patterns and their dependence on the primary beam energy can be explained by taking into account (a) elastic deformation of the β matrix arising from the presence of slightly misfitting ω particles and (b) the presence of a `cloud' of a higher Mo concentration around ω particles.
Effectiveness of bilateral and multilateral concessional debts on economic growth in Africa
Authors: Ezeaku Hillary Chijindu , Egbo Obiamaka P. , Nwakoby Ifeoma , Onwumere Josaphat U.J.
Published: August 2019

Purpose

The purpose of this paper is to assess the relative effectiveness of bilateral and multilateral concessional debts on economic growth in 32 sub-Saharan African (SSA) countries over the period 1985–2016.

Design/methodology/approach

The recently developed dynamic panel autoregressive distributed lag models which comprise three different estimators, the mean group, pooled mean group (PMG) estimator and dynamic fixed effect, were applied to estimate the model. Following these estimators, the Hausman test was employed to determine the efficient and consistent estimator.

Findings

The results showed that bilateral concessional debts had a negative impact on growth. From the findings, a 1 percent increase in bilateral concessional debts induced economic growth to decline by 38.1 percent points in the short run, and by 7.1 percent points in the long run; convergence to long-run equilibrium adjusted at the speed of 90 percent on an annual basis. Multilateral concessional debts were found to have a positive impact on growth both in the short and long run. The coefficient of the error term was negatively signed and indicates that deviations from the long-run equilibrium path were being corrected at the speed of 89.4 percent annually.

Originality/value

To the authors’ best knowledge, empirical studies that specifically seek to examine how bilateral and multilateral concessional debts impacted on growth are yet to attract the attention of researchers. As a result, this study will complement related extant growth studies, especially in the case of SSA.
Public libraries as public sphere institutions
Authors: Audunson Ragnar , Aabø Svanhild , Blomgren Roger , Hobohm Hans-Christoph , Jochumsen Henrik , Khosrowjerdi Mahmood , Mumenthaler Rudolf , Schuldt Karsten , Rasmussen Casper Hvenegaard , Rydbeck Kerstin , Tóth Máté , Vårheim Andreas
Published: August 2019

Purpose

The purpose of this paper is to analyze the role of public libraries as institutions underpinning a democratic public sphere as reasons legitimizing libraries compared to reasons that are more traditional and the actual use of libraries as public sphere arenas.

Design/methodology/approach

A survey of representative samples of the adult population in six countries – Denmark, Sweden, Norway, Germany, Hungary and Switzerland – was undertaken.

Findings

Legitimations related to the libraries role as a meeting place and arena for public debate are ranked as the 3 least important out of 12 possible legitimations for upholding a public library service. Libraries are, however, used extensively by the users to access citizenship information and to participate in public sphere relevant meetings.

Originality/value

Few studies have empirically analyzed the role of libraries in upholding a democratic and sustainable public sphere. This study contributes in filling that gap.
Using the fuzzy multicriteria decision making approach to evaluate brand equity: a study of privatized firms
Authors: Dinçer Hasan , Bozaykut-Buk Tuba , Emir Şenol , Yuksel Serhat , Ashill Nicholas
Published: August 2019

Purpose

The purpose of this paper is to present a multidimensional evaluation of brand equity performance incorporating dimensions adopted from the balance scorecard (BSC) approach to business performance.

Design/methodology/approach

In this study, text mining is used for automatic extraction of valuable information from textual data such as the financial reports of firms. Instead of expert opinions, linguistic scales built upon outcomes of text mining are used as inputs for decision-making. The proposed model combines fuzzy DEMATEL (FDEMATEL), fuzzy ANP (FANP), fuzzy TOPSIS (FTOPSIS) and fuzzy VIKOR (FVIKOR) methods for weighting criteria and ranking alternatives.

Findings

Using data from five privatized firms in Turkey, the study’s findings demonstrate that the customer is the most important dimension of brand equity performance evaluation. Cash flow and brand loyalty are identified as the most important criteria in the measurement of brand equity performance.

Practical implications

Findings highlight the importance of firms taking action to increase consumer perceptions, attitudes and behaviors in the privatization processes. For this purpose, privatized firms need to understand the expectations of customers to increase customer satisfaction and loyalty and therefore improve brand equity.

Originality/value

The paper contributes to literature in several important ways. First, by adopting the BSC approach, it proposes a holistic and a multidimensional model for measuring brand equity performance. Second, the study offers a novel methodology using a hybrid multi-criteria decision-making model designed for the fuzzy environment. Third, the study uses the knowledge extraction tool of text mining in the fuzzy decision-making process. Finally, the study evaluates the brand equity performance of privatized firms in an emerging country context.
On the evolution of carry‐over effects
Authors: Moore Michael P. , Martin Ryan A.
Published: August 2019

The environment experienced early in life often affects the traits that are developed after an individual has transitioned into new life stages and environments. Because the phenotypes induced by earlier environments are then screened by later ones, these ‘carry‐over effects’ influence fitness outcomes across the entire life cycle.

While the last two decades have witnessed an explosion of studies documenting the occurrence of carry‐over effects, little attention has been given to how they adapt and diversify. To aid future research in this area, we present a framework for the evolution of carry‐over effects.

Carry‐over effects can evolve in two ways. First, the expression of traits later in life may become more or less dependent on the developmental processes of earlier stages (e.g., ‘adaptive decoupling’). Genetic correlations between life stages then either strengthen or weaken. Alternatively, those influential developmental processes that begin early in life may become more or less sensitive to that earlier environment. Here, plasticity changes in all the traits that share those developmental pathways across the whole life cycle.

Adaptive evolution of a carry‐over effect is governed by selection on the induced phenotypes in the later stage, and also by selection on any developmentally linked traits in the earlier life stage. When these selective pressures conflict, the evolution of the carry‐over effect will be biased towards maximizing performance in the life stage with stronger selection. Because life stages often contribute unequally to total fitness, the strength of selection in any one stage depends on: (a) the relationship between the traits and the stage‐specific fitness components (e.g., juvenile survival, adult mating success), and (b) the reproductive value of the life stage.

Considering the evolution of carry‐over effects reveals several intriguing features of the evolution of life histories and phenotypic plasticity more generally. For instance, carry‐over effects that manifest as maladaptive plasticity in one life stage may represent an adaptive strategy for maximizing fitness in stages with stronger selection. Additionally, adaptation to novel environments encountered early in the life cycle may be faster in the presence of carry‐over effects that influence sexually selected traits.
Minireview: demystifying microbial reaction energetics
Authors: Amend Jan P. , LaRowe Douglas E.
Published: August 2019

The biology literature is rife with misleading information on how to quantify catabolic reaction energetics. The principal misconception is that the sign and value of the standard Gibbs energy () define the direction and energy yield of a reaction; they do not. is one part of the actual Gibbs energy of a reaction (ΔGr), with a second part accounting for deviations from the standard composition. It is also frequently assumed that applies only to 25 °C and 1 bar; it does not. is a function of temperature and pressure. Here, we review how to determine ΔGr as a function of temperature, pressure and chemical composition for microbial catabolic reactions, including a discussion of the effects of ionic strength on ΔGr and highlighting the large effects when multi‐valent ions are part of the reaction. We also calculate ΔGr for five example catabolisms at specific environmental conditions: aerobic respiration of glucose in freshwater, anaerobic respiration of acetate in marine sediment, hydrogenotrophic methanogenesis in a laboratory batch reactor, anaerobic ammonia oxidation in a wastewater reactor and aerobic pyrite oxidation in acid mine drainage. These examples serve as templates to determine the energy yields of other catabolic reactions at environmentally relevant conditions.
Everyday self‐defence: Hollaback narratives, habitus and resisting street harassment
Authors: Fleetwood Jennifer
Published: August 2019

Street harassment is recognized as an ‘everyday’ form of violence against women. Influenced by contemporary sociologies of everyday life, this article examines women responses to street harassment, drawing on over 500 first person narratives submitted to the website of Hollaback London. The narrative structure highlights women’s actions, which (like street harassment) have generally been considered inconsequential. Quantitative content analysis reveals the extent and variety of strategies employed by women, including speaking back, calling on others for help, physically fighting back, walking away and an array of ‘small’, everyday actions and gestures that aim to resist harassment. I argue that these responses comprise everyday self‐defence practice. Furthermore, the notion of narrative habitus is employed to argue that Hollaback narratives do not just describe harassment, but that reading narratives can generate dispositions for self‐defence. Narrative analysis reveals the way that satire is employed to make space for women’s successful self‐defence. I argue that Hollaback narratives do not just offer storylines or scripts for resisting street harassment but foster a style for doing so. Analysis considers the limits to narratively motivated self‐defence. This research demonstrates that, in order to ‘see’ women’s resistance, we need to pay close attention to the everyday as the site of both oppression and moments of liberation.
Homicidal Ideation and Forensic Psychopathology: Evidence From the 2016 Nationwide Emergency Department Sample (NEDS)
Authors: Carbone Jason T. , Holzer Katherine J. , Vaughn Michael G. , DeLisi Matthew
Published: August 2019

Homicide is the most serious and costly criminal offense and better forensic and criminological understanding of homicidal ideation as a potential psychobehavioral precursor to homicidal conduct is critical. Using data from the 2016 Nationwide Emergency Department Sample (NEDS) from the Healthcare Cost and Utilization Project (HCUP) distributed by the Agency for Healthcare Research and Quality (AHRQ), we found 64,910 cases of homicidal ideation among a sample of 25.6 + million—a prevalence of 0.25%. Numerous conditions conferred increased substantially the likelihood of homicidal ideation including antisocial personality disorder (2406%), schizoaffective disorder (1821%), borderline personality disorder (1557%), paranoid personality disorder (1,504%), schizophrenia (1,143%), obsessive–compulsive personality disorder (921%), brief psychotic disorder (771%), unspecified psychosis (737%), avoidant personality disorder (596%), and schizoid personality disorder (571%), delusional disorder (546%), and other psychotic disorder (504%). Homicidal ideation is comorbid with serious psychiatric and behavioral problems and has important implications for offender typologies and homicidality.
Encapsulation of Lutein in Nanoemulsions Stabilized by Resveratrol and Maillard Conjugates
Authors: Steiner Benjamin M. , Shukla Viral , McClements David Julian , Li Yao Olive , Sancho‐Madriz Martin , Davidov‐Pardo Gabriel
Published: August 2019

Lutein is incorporated into foods as a natural yellow pigment and nutraceutical. The introduction of lutein into many foods and beverages, however, is problematic because of its strong hydrophobicity and poor chemical stability. In this research, lutein‐loaded nanoemulsions were prepared to overcome this problem. Casein‐dextran Maillard conjugates or physical complexes were utilized as emulsifiers, while either medium chain triglycerides (MCT) or grape seed oil (GSO) were used as carrier oils. The impact of resveratrol addition on nanoemulsion stability was also examined. The influence of storage temperature, pH, and CaCl2 concentration on the chemical and physical stability of the nanoemulsions was measured. The casein‐dextran conjugates were highly effective at improving the physical resistance of the nanoemulsions to environmental stresses, but had a detrimental effect on their color stability. Conversely, nanoemulsions prepared from casein‐dextran physical complexes were unstable around the protein's isoelectric point (pH 4.6), as well as upon addition of CaCl2. Incorporation of resveratrol and GSO into the nanoemulsions decreased lutein degradation and color fading at all temperatures. This study shows that casein‐dextran conjugates are highly effective at improving the physical stability of lutein‐loaded nanoemulsions, while resveratrol and GSO are effective at improving their chemical stability.

Practical Application

Lutein can be used by the food industry to create “clean label” and functional food products. The major challenges in incorporating lutein in foods are its poor chemical stability and its high hydrophobicity, which makes it difficult to incorporate. Emulsion‐based delivery systems assembled from natural ingredients may address these challenges. In this study, the impact of Maillard conjugates fabricated from caseinate and dextran, as well as resveratrol addition, on the formation and stability of lutein‐enriched nanoemulsions was determined. The information obtained from this study will help the formulation of more effective functional foods and beverage products.
Systemic Administration of the Cyclin‐Dependent Kinase Inhibitor (S)‐CR8 Selectively Reduces Escalated Ethanol Intake in Dependent Rats
Authors: Goulding Scott P. , de Guglielmo Giordano , Carrette Lieselot L.G. , George Olivier , Contet Candice
Published: August 2019

Background

Chronic exposure to ethanol (EtOH) and other drugs of abuse can alter the expression and activity of cyclin‐dependent kinase 5 (CDK5) and its cofactor p35, but the functional implication of CDK5 signaling in the regulation of EtOH‐related behaviors remains unknown. In the present study, we sought to determine whether CDK5 activity plays a role in the escalation of EtOH self‐administration triggered by dependence.

Methods

We tested the effect of systemically administered (S)‐CR8, a nonselective CDK inhibitor, on operant responding for EtOH or saccharin, a highly palatable reinforcer, in adult male Wistar rats. Half of the rats were made EtOH‐dependent via chronic intermittent EtOH inhalation (CIE). We then sought to identify a possible neuroanatomical locus for the behavioral effect of (S)‐CR8 by quantifying protein levels of CDK5 and p35 in subregions of the extended amygdala and prefrontal cortex from EtOH‐naïve, nondependent, and dependent rats at the expected time of EtOH self‐administration. We also analyzed the phosphorylation of 4 CDK5 substrates and of the CDK substrate consensus motif.

Results

(S)‐CR8 dose‐dependently reduced EtOH self‐administration in dependent rats. It had no effect on water or saccharin self‐administration, nor in nondependent rats. The abundance of CDK5 or p35 was not altered in any of the brain regions analyzed. In the bed nucleus of the stria terminalis, CDK5 abundance was negatively correlated with intoxication levels during EtOH vapor exposure but there was no effect of dependence on the phosphorylation ratio of CDK5 substrates. In contrast, EtOH dependence increased the phosphorylation of low‐molecular‐weight CDK substrates in the basolateral amygdala (BLA).

Conclusions

The selective effect of (S)‐CR8 on excessive EtOH intake has potential therapeutic value for the treatment of alcohol use disorders. Our data do not support the hypothesis that this effect would be mediated by the inhibition of up‐regulated CDK5 activity in the extended amygdala nor prefrontal cortex. However, increased activity of CDKs other than CDK5 in the BLA may contribute to excessive EtOH consumption in alcohol dependence. Other (S)‐CR8 targets may also be implicated.
Driving the Downward Spiral: Alcohol‐Induced Dysregulation of Extended Amygdala Circuits and Negative Affect
Authors: Centanni Samuel W. , Bedse Gaurav , Patel Sachin , Winder Danny G.
Published: August 2019

Alcohol use disorder (AUD) afflicts a large number of individuals, families, and communities globally. Affective disturbances, including stress, depression, and anxiety, are highly comorbid with AUD, contributing in some cases to initial alcohol use and continued use. Negative affect has a particularly strong influence on the withdrawal/abstinence stage of addiction as individuals with AUD frequently report stressful events, depression, and anxiety as key factors for relapse. Treatment options for negative affect associated with AUD are limited and often ineffective, highlighting the pressing need for preclinical studies examining the underlying neural circuitry driving AUD‐associated negative affect. The extended amygdala (EA) is a set of brain areas collectively involved in generating and regulating affect, and extensive research has defined a critical role for the EA in all facets of substance use disorder. Here, we review the expansive historical literature examining the effects of ethanol exposure on the EA, with an emphasis on the complex EA neural circuitry driving negative affect in all phases of the alcohol addiction cycle. Specifically, this review focuses on the effects of alcohol exposure on the neural circuitry in 2 key components of the EA, the central nucleus of the amygdala and the bed nucleus of the stria terminalis. Additionally, future directions are proposed to advance our understanding of the relationship between AUD‐associated negative affect and neural circuitry in the EA, with the long‐term goal of developing better diagnostic tools and new pharmacological targets aimed at treating negative affect in AUD. The concepts detailed here will serve as the foundation for a companion review focusing on the potential for the endogenous cannabinoid system in the EA as a novel target for treating the stress, anxiety, and negative emotional state driving AUD.
Aggravation of asthmatic inflammation by chlorine exposure via innate lymphoid cells and CD11cintermediate macrophages
Authors: Shim Ji‐Su , Lee Hyun‐Seung , Park Da‐Eun , Won Lee Ji , Bae Boram , Chang Yuna , Kim Jihyun , Kim Hye Young , Kang Hye‐Ryun
Published: August 2019

Background

Chlorine is widely used in daily life as disinfectant. However, chronic exposure to chlorine products aggravates allergic TH2 inflammation and airway hyperresponsiveness (AHR). Innate lymphoid cells (ILCs) in airways contribute to the inception of asthma in association with virus infection, pollution, and excess of nutrient, but it is not known whether chronic chlorine exposure can activate innate immune cells. The aim of this study was to evaluate the impact of chlorine inhalation on the innate immunity such as ILCs and macrophages in relation with the development of asthma by using murine ovalbumin (OVA) sensitization/challenge model.

Methods

Six‐week‐old female BALB/c mice were sensitized and challenged with OVA in the presence and absence of chronic low‐dose chlorine exposure by inhalation of naturally vaporized gas of 5% sodium hypochlorite solution. AHR, airway inflammatory cells, from BALF and the population of ILCs and macrophages in the lung were evaluated.

Results

The mice exposed to chlorine with OVA (Cl + OVA group) showed enhanced AHR and eosinophilic inflammation compared to OVA‐treated mice (OVA group). The population of TH2 cells, ILC2s, and ILC3s increased in Cl + OVA group compared with OVA group. CD11cint macrophages also remarkably increased in Cl + OVA group compared with OVA group. The deletion of macrophages by clodronate resulted in reduction of ILC2s and ILC3s population which was restored by adoptive transfer of CD11cint macrophages.

Conclusions

Chronic chlorine inhalation contributes to the exacerbation of airway inflammation in asthmatic airway by mobilizing pro‐inflammatory macrophage into the lung as well as stimulating group 2 and 3 ILCs.
HIGH‐RISK HPV testing as the primary screening method in an organized regional screening program for cervical cancer: the value of HPV16 and HPV18 genotyping?
Authors: Kares Saara , Veijalainen Olga , Kholová Ivana , Tirkkonen Mika , Vuento Risto , Huhtala Heini , Tuimala Veronica , Mäenpää Johanna , Kujala Paula
Published: August 2019

Since 2012, testing high‐risk (HR)HPV has been used as the primary screening test for women ≥35 years attending the organized cervical cancer screening program in the city of Tampere. We evaluated the contribution of HPV16/18 genotyping. Data from 2012 and 2013, and the follow‐up samples in 2013 and 2014, respectively, were analyzed. Abbott RealTime High‐Risk HPV test detecting 14 HRHPV genotypes combined with concurrent genotyping for HPV16 and HPV18 was used. HPV was positive in 794 samples out of 11 346 HPV tested women (7%). HPV16/18 was represented in 22% of HPV‐positive cases. Negative cervical cytology (NILM) was reported in 51% of HPV‐positive samples. HPV16/18 genotype was accompanied with 50% of HSIL/ASC‐H cases. The predominance of HPV16/18 in higher grade lesions was even more evident in cervical biopsies as 57% of CIN3 cases were associated with HPV16/18, and only 20% of carcinomas were associated with nonspecified high‐risk (NSHR) genotypes. In agreement with previous studies HPV16/18 genotypes caused higher grade cytological and histological changes/pathologies than NSHR genotypes in primary screening. Nevertheless, the majority of HRHPV genotypes detected in the screened population were nonHPV16/18, and especially within persistent infections, precancerous lesions were found also among women with NSHR genotypes.
Feature Preserving Octree‐Based Hexahedral Meshing
Authors: Gao Xifeng , Shen Hanxiao , Panozzo Daniele
Published: August 2019

We propose an octree‐based algorithm to tessellate the interior of a closed surface with hexahedral cells. The generated hexahedral mesh (1) explicitly preserves sharp features of the original input, (2) has a maximal, user‐controlled distance deviation from the input surface, (3) is composed of elements with only positive scaled jacobians (measured by the eight corners of a hex [SEK*07]), and (4) does not have self‐intersections.

We attempt to achieve these goals by proposing a novel pipeline to create an initial pure hexahedral mesh from an octree structure, taking advantage of recent developments in the generation of locally injective 3D parametrizations to warp the octree boundary to conform to the input surface. Sharp features in the input are bijectively mapped to poly‐lines in the output and preserved by the deformation, which takes advantage of a scaffold mesh to prevent local and global intersections.

The robustness of our technique is experimentally validated by batch processing a large collection of organic and CAD models, without any manual cleanup or parameter tuning. All results including mesh data and statistics in the paper are provided in the additional material. The open‐source implementation will be made available online to foster further research in this direction.
Novel mouthpiece for reducing the gag reflex during esophagogastroduodenoscopy
Authors: Fujiwara Kazunori , Matsumoto Kazuya , Ueda Naoki , Ueki Masaru , Fukuhara Takahiro , Ikebuchi Yuichiro , Isomoto Hajime , Takeuchi Hiromi
Published: August 2019

Background and Aim

Discomfort associated with the gag reflex during transoral endoscopy can be troublesome. To overcome this problem during esophagogastroduodenoscopy (EGD), we recently developed a novel mouthpiece. The aim of the present study was to compare acceptance and tolerability of transoral EGD with conventional and new mouthpieces in unsedated patients and analyze the effects of the new mouthpiece.

Methods

This study consisted of two phases of cephalometric and EGD examinations to analyze the effects of the new mouthpiece. Cephalometry was carried out in six subjects to evaluate differences in the size of the pharynx (anteroposterior diameter of the oropharynx and longitudinal diameter of the oral cavity) when subjects held the conventional mouthpiece (MAJ674) or the new mouthpiece in their mouths. EGD was done in 10 subjects using the conventional or new mouthpiece to evaluate the number of times the gag reflex occurred, examinee discomfort, and endoscope operability during EGD using a visual analogue scale (VAS).

Results

Anteroposterior diameter of the oropharynx and longitudinal diameter of the oral cavity were significantly larger with the new mouthpiece than with the conventional mouthpiece (oropharynx: P = 0.03; oral cavity: P = 0.03). With the new mouthpiece during EGD, subjects had significantly fewer instances of the gag reflex (P = 0.01); VAS score for discomfort was significantly lower (P < 0.01) and score for endoscope operability was significantly higher (P = 0.04).

Conclusion

The new mouthpiece we developed reduced the gag reflex during EGD by extending the pharynx, thus decreasing examinee discomfort and increasing endoscopic operability.