bluuebunny/crossref_metadata_2025 huggingface dataset:
Nach is a novel ancestral subfamily ofthe CNC-bZIP transcription factors selected during evolution from the marine bacteria to human
Authors: Zhu Yuping , Wang Meng , Xiang Yuancai , Qiu Lu , Hu Shaofan , Zhang Zhengwen , Mattjus Peter , Zhang Yiguo
Published: March 2018

All living organisms have undergone the evolutionary selection under the changing natural environments to survive as diverse life forms. All life processes including normal homeostatic development and growth into organismic bodies with distinct cellular identifications, as well as their adaptive responses to various intracellular and environmental stresses, are tightly controlled by signaling of transcriptional networks towards regulation of cognate genes by many different transcription factors. Amongst them, one of the most conserved is the basic-region leucine zipper (bZIP) family. They play vital roles essential for cell proliferation, differentiation and maintenance in complex multicellular organisms. Notably, an unresolved divergence on the evolution of bZIP proteins is addressed here. By a combination of bioinformatics with genomics and molecular biology, we have demonstrated that two of the most ancestral family members classified into BATF and Jun subgroups are originated from viruses, albeit expansion and diversification of the bZIP superfamily occur in different vertebrates. Interestingly, a specific ancestral subfamily of bZIP proteins is identified and also designated Nach (Nrf and CNC homology) on account of their highly conservativity with NF-E2 p45 subunit-related factors Nrf1/2. Further experimental evidence reveals that Nach1/2 from the marine bacteria exerts distinctive functions from Nrf1/2 in the transcriptional ability to regulate antioxidant response element (ARE)-driven cytoprotective genes. Collectively, an insight into Nach/CNC-bZIP proteins provides a better understanding of distinct biological functions between these factors selected during evolution from the marine bacteria to human.

Significance

We identified the novel ancestral subfamily (i.e. Nach) of CNC-bZIP transcription factors with highly conservativity from marine bacteria to human. Combination of bioinformatics with genomics and molecular biology demonstrated that two of the most ancestral family members classified into BATF and Jun subgroups are originated from viruses. The Jun and CNC subfamilies also share a common origin of these bZIP proteins. Further experimental evidence reveals that Nach1/2 from the marine bacteria exerts nuance functions from human Nrf1/2 in the transcriptional ability to regulate antioxidant response element (ARE)-driven genes, responsible for the host cytoprotection against inflammation and cancer. Overall, this study is of multidisciplinary interests to provide a better understanding of distinct biological functions between Nach/CNC-bZIPs selected during evolution.
The Origins and Consequences of Localized and Global Somatic Hypermutation
Authors: Yousif Fouad , Prokopec Stephenie D. , Sun Ren X. , Fan Fan , Lalansingh Christopher M. , Park David H. , Szyca Lesia ,   PCAWG Network, Boutros Paul C.
Published: March 2018

Cancer is a disease of the genome, but the dramatic inter-patient variability in mutation number is poorly understood. Tumours of the same type can differ by orders of magnitude in their mutation rate. To understand potential drivers and consequences of the underlying heterogeneity in mutation rate across tumours, we evaluated both local and global measures of mutation density: both single-stranded and double-stranded DNA breaks in 2,460 tumours of 38 cancer types. We find that SCNAs in thousands of genes are associated with elevated rates of point-mutations, while similarly point-mutation patterns in dozens of genes are associated with specific patterns of DNA double-stranded breaks. These candidate drivers of mutation density are enriched for known cancer drivers, and preferentially occur early in tumour evolution, appearing clonally in all cells of a tumour. To supplement this understanding of global mutation density, we developed and validated a tool called SeqKat to identify localized “rainstorms” of point-mutations (kataegis). We show that rates of kataegis differ by four orders of magnitude across tumour types, with malignant lymphomas showing the highest. Tumours withTP53mutations were 2.6-times more likely to harbour a kataegic event than those without, and 239 SCNAs were associated with elevated rates of kataegis, including loss of the tumour-suppressorCDKN2A. We identify novel subtypes of kataegic events not associated with aberrant APOBEC activity, and find that these are localized to specific cellular regions, enriched for MYC-target genes. Kataegic events were associated with patient survival in some, but not all tumour types, highlighting a combination of global and tumour-type specific effects. Taken together, we reveal a landscape of genes driving localized and tumour-specific hyper-mutation, and reveal novel mutational processes at play in specific tumour types.
Transcriptional read-through of the long non-coding RNA SVALKA governs plant cold acclimation
Authors: Kindgren Peter , Ard Ryan , Ivanov Maxim , Marquardt Sebastian
Published: March 2018

Most DNA in the genomes of higher organisms does not encode proteins, but is transcribed by RNA polymerase II (RNAPII) into long non-coding RNA (lncRNA). The biological significance of most lncRNA is largely unclear. Here, we identify a lncRNA (SVALKA) in a cold-sensitive region of the Arabidopsis genome. Mutations in SVALKA affect the timing of maximal CBF1 expression and freezing tolerance. RNAPII read-through transcription of SVALKA results in a cryptic lncRNA overlapping CBF1 on the antisense strand, termed asCBF1. asCBF1 transcription is anti-correlated with CBF1 expression. Our molecular dissection reveals that CBF1 is suppressed by RNAPII collision stemming from the SVALKA-asCBF1 lncRNA cascade. The SVK-asCBF1 cascade provides a mechanism to tightly control CBF1 expression and timing that could be exploited to maximize freezing tolerance with mitigated fitness costs. Inversion of the transcriptional direction of a lncRNA cascade relative to the genes in a co-regulated cluster provides an elegant inbuilt negative feedback for cluster expression. Our results provide a compelling example of local gene regulation by lncRNA transcription having a profound impact on the ability of plants to appropriately acclimate to suboptimal environmental conditions.
TETyper: a bioinformatic pipeline for classifying variation and genetic contexts of transposable elements from short-read whole-genome sequencing data
Authors: Sheppard Anna E , Stoesser Nicole , German-Mesner Ian , Vegesana Kasi , Walker A Sarah , Crook Derrick W , Mathers Amy J
Published: March 2018

Much of the worldwide dissemination of antibiotic resistance has been driven by resistance gene associations with mobile genetic elements (MGEs), such as plasmids and transposons. Although increasing, our understanding of resistance spread remains relatively limited, as methods for tracking mobile resistance genes through multiple species, strains and plasmids are lacking. We have developed a bioinformatic pipeline for tracking variation within, and mobility of, specific transposable elements (TEs), such as transposons carrying antibiotic resistance genes. TETyper takes short-read whole-genome sequencing data as input and identifies single-nucleotide mutations and deletions within the TE of interest, to enable tracking of specific sequence variants, as well as the surrounding genetic context(s), to enable identification of transposition events. To investigate global dissemination ofKlebsiella pneumoniaecarbapenemase (KPC) and its associated transposon Tn4401, we applied TETyper to a collection of >3000 publicly available Illumina datasets containingblaKPC. This revealed surprising diversity, with >200 distinct flanking genetic contexts for Tn4401, indicating high levels of transposition. Integration of sample metadata revealed insights into associations between geographic locations, host species, Tn4401sequence variants and flanking genetic contexts. To demonstrate the ability of TETyper to cope with high copy number TEs and to track specific short-term evolutionary changes, we also applied it to the insertion sequence IS26within a definedK. pneumoniaeoutbreak. TETyper is implemented in python and is freely available athttps://github.com/aesheppard/TETyper.
Intracranial interictal functional networks predict the effect of subacute cortical stimulation in focal epilepsy
Authors: Wang Yujiang , Taylor Peter Neal , Diaz-Diaz Judith , Selway Richard P , Valentin Antonio , Alarcon Gonzalo , Jimenez-Jimenez Diego
Published: March 2018

Background: Electric neurostimulation is being developed as an alternative treatment for drug-resistant epilepsy patients. A major challenge is to identify, among all possible combinations of stimulation parameters, the most effective stimulation protocol to achieve seizure control for each patient.

Objective: To estimate the value of interictal intracranial EEG recordings in identifying the most effective stimulation protocol in order to decrease number of seizures during intracranial subacute cortical stimulation (SCS).

Methods: Five patients undergoing SCS were included in this retrospective study. Bivariate correlation measures were applied to baseline interictal intracranial EEG recordings to infer functional correlation networks. The node strength of these networks was calculated for each recording electrode (indicating the overall correlation between activity from one electrode with the activity from all other electrodes). The relationship between node strength and the change in seizure rate associated with SCS was studied for the electrodes used for stimulation.

Results: Across all five patients, node strength was negatively correlated with seizure rate ratio (ratio of seizure rate during SCS relative to during baseline) for all frequency bands tested (delta, theta, alpha, beta, gamma, and high gamma), and both the common reference and the common average montage.

Conclusion: Interictal functional correlation networks contain information that correlates with the effect of SCS on the rate of epileptic seizures, suggesting that stimulation of those regions with higher node strength (derived from correlation networks) is more effective in reducing number of seizures.
Genome sequencing and assessment of plant growth-promoting properties of a Serratia marcescens strain isolated from vermicompost
Authors: Matteoli Filipe P. , Passarelli-Araujo Hemanoel , A. Reis Régis Josué , da Rocha Letícia O. , de Souza Emanuel M. , Aravind L. , Olivares Fabio L. , Venancio Thiago M.
Published: March 2018

Plant-bacteria associations have been extensively studied for their potential in increasing crop productivity in a sustainable manner. Serratia marcescens is a Gram-negative species found in a wide range of environments, including soil. Here we describe the genome sequencing and assessment of plant-growth promoting abilities of S. marcescens UENF-22GI (SMU), a strain isolated from mature cattle manure vermicompost. In vitro, SMU is able to solubilize P and Zn, to produce indole compounds (likely IAA), to colonize hyphae and counter the growth of two phytopathogenic fungi. Inoculation of maize with SMU remarkably increased seedling growth and biomass under greenhouse conditions. The SMU genome has 5 Mb, assembled in 17 scaffolds comprising 4,662 genes (4,528 are protein-coding). No plasmids were identified. SMU is phylogenetically placed within a clade comprised almost exclusively of environmental strains. We were able to find the genes and operons that are likely responsible for all the interesting plant-growth promoting features that were experimentally described. Genes involved other interesting properties that were not experimentally tested (e.g. tolerance against metal contamination) were also identified. The SMU genome harbors a horizontally-transferred genomic island involved in antibiotic production, antibiotic resistance, and anti-phage defense via a novel ADP-ribosyltransferase-like protein and possible modification of DNA by a deazapurine base, which likely contributes to the SMU competitiveness against other bacteria. Collectively, our results suggest that S. marcescens UENF-22GI is a strong candidate to be used in the enrichment of substrates for plant growth promotion or as part of bioinoculants for Agriculture.
AmpUMI: Design and analysis of unique molecular identifiers for deep amplicon sequencing
Authors: Clement Kendell , Farouni Rick , Bauer Daniel E. , Pinello Luca
Published: March 2018

Motivation

Unique molecular identifiers (UMIs) are added to DNA fragments before PCR amplification to discriminate between alleles arising from the same genomic locus and sequencing reads produced by PCR amplification. While computational methods have been developed to take into account UMI information in genome-wide and single-cell sequencing studies, they are not designed for modern amplicon based sequencing experiments, especially in cases of high allelic diversity. Importantly, no guidelines are provided for the design of optimal UMI length for amplicon-based sequencing experiments.

Results

Based on the total number of DNA fragments and the distribution of allele frequencies, we present a model for the determination of the minimum UMI length required to prevent UMI collisions and reduce allelic distortion. We also introduce a user-friendly software tool called AmpUMI to assist in the design and the analysis of UMI-based amplicon sequencing studies. AmpUMI provides quality control metrics on frequency and quality of UMIs, and trims and deduplicates amplicon sequences with user specified parameters for use in downstream analysis. AmpUMI is open-source and freely available at http://github.com/pinellolab/AmpUMI.

Contact

Ipinello@mgh.harvard.edu
Redetermination of nickel(II) formate dihydrate
Authors: Weil Matthias
Published: March 2018

In comparison with the previous structure determination of poly[diaquadi-μ-formato-nickel(II)], [Ni(HCOO)2(H2O)2]n, based on Weissenberg film data [Krogmann & Mattes (1963).Z. Kristallogr.118, 291–302], the current redetermination from modern CCD data revealed the positions of the H atoms, thus making a detailed description of the hydrogen-bonding pattern possible. Both Ni2+cations in the crystal structure are located on inversion centres and are octahedrally coordinated. One Ni2+cation is bound to six O atoms of six formate anions whereas the other Ni2+cation is bound to four O atoms of water molecules and to two formate O atoms. In this way, the formate anions bridge the two types of Ni2+cations into a three-dimensional framework. O—H...O hydrogen bonds of medium strength between water molecules and formate O atoms consolidate the packing.
4-(4-Bromophenyl)-2-(3-(4-bromophenyl)-5-{3-[5-methyl-1-(4-methylphenyl)-1H-1,2,3-triazol-4-yl]-1-phenyl-1H-pyrazol-4-yl}-4,5-dihydro-1H-pyrazol-1-yl)-1,3-thiazole
Authors: El-Hiti Gamal A. , Abdel-Wahab Bakr F. , Khidre Rizk E. , Mostafa Mohamed S. , Hegazy Amany S. , Kariuki Benson M.
Published: March 2018

In the title compound, C37H28Br2N8S, the dihedral angles between the planes of tolyl–triazolyl–pyrazolyl–phenyl rings are 47.5 (1), 11.4 (2) and 22.4 (2)°, respectively, and the angles between the bromophenyl–thiazolyl–dihydropyrazolyl–bromophenyl rings are 16.0 (2), 5.1 (2) and 0.8 (2)°, respectively. The dihedral angle between the planes of the pyrazolyl and dihydropyrazolyl rings is 67.7 (1)°. In the crystal, weak C—H...Br interactions form chains of molecules propagating in the [010] direction.
N-[(1R,2S)-1-(4-Bromophenyl)-2-fluoro-3-(2-methylphenyl)-3-oxopropyl]-4-nitrobenzamide
Authors: Luo Yu-hang , Feng Yan , Zhang Xin-ran , Zhang Jin-rong , Chen Yi-Yang , Li Ya
Published: March 2018

The title compound, C23H18BrFN2O4, contains two chiral carbon centres and the absolute configuration has been confirmed as (1R,2S). The dihedral angles between the three phenyl rings are 12.4 (4), 34.2 (4) and 44.5 (4)°. In the crystal, molecules are linked by N—H...O hydrogen bonds into chains, which which are further connected by C—H...O interactions, generating a three dimensional network structure.
The ethic of care: an HR strategy to address obesity in the workplace
Authors: Prieto Leon C. , Mathur-Helm Babita , Dawson Kasey N.
Published: March 2018

Purpose

This paper aims to highlight an ethic of care approach human resource (HR) departments can use to address obesity in the workplace.

Design/methodology/approach

This paper is prepared by experts who add their unbiased views to a very pertinent topic.

Findings

This paper focused on an ethic of care approach to addressing obesity in the workplace and provides advice that HR departments can adopt to address this issue.

Originality/value

This paper addresses a pertinent topic in a succinct manner that saves time for practitioners and scholars alike. This paper addresses the topic of obesity in the workplace which is of a growing concern worldwide.
Machine criticality based maintenance prioritization
Authors: Gopalakrishnan Maheshwaran , Skoogh Anders
Published: March 2018

Purpose

The purpose of this paper is to identify the productivity improvement potentials from maintenance planning practices in manufacturing companies. In particular, the paper aims at understanding the connection between machine criticality assessment and maintenance prioritization in industrial practice, as well as providing the improvement potentials.

Design/methodology/approach

An explanatory mixed method research design was used in this study. Data from literature analysis, a web-based questionnaire survey, and semi-structured interviews were gathered and triangulated. Additionally, simulation experimentation was used to evaluate the productivity potential.

Findings

The connection between machine criticality and maintenance prioritization is assessed in an industrial set-up. The empirical findings show that maintenance prioritization is not based on machine criticality, as criticality assessment is non-factual, static, and lacks system view. It is with respect to these finding that the ways to increase system productivity and future directions are charted.

Originality/value

In addition to the empirical results showing productivity improvement potentials, the paper emphasizes on the need for a systems view for solving maintenance problems, i.e. solving maintenance problems for the whole factory. This contribution is equally important for both industry and academics, as the maintenance organization needs to solve this problem with the help of the right decision support.
Cold chains, interrupted
Authors: Comes Tina , Bergtora Sandvik Kristin , Van de Walle Bartel
Published: March 2018

Purpose

The purpose of this paper is to analyze how far technology and information enable, facilitate or support the planning and implementation decisions in humanitarian vaccine cold chains for vaccination campaigns. The authors specifically focus on three emerging technologies that have the potential to create more flexible conditions in the field, and identify the need to further explore the link between uncertainty, information and irreversibility.

Design/methodology/approach

The authors present a basic structure for the analysis of cold chain disruptions in terms of three distinct yet connected layers of deficient infrastructure and capacity, information gaps and failures in decision making. The authors then review three humanitarian technologies and their impact on vaccine campaigns along these layers. From there, a research agenda is developed to address research gaps this review brought forward.

Findings

Three critical research gaps in the areas of technology innovation for humanitarian vaccine cold chain management are presented. The authors argue that technology to improve capacity, information and decisions need to be aligned, and that the areas of uncertainty, information and irreversibility require further investigation to achieve this alignment. In this way, the paper contributes to setting the research agenda on vaccine cold chains and connects humanitarian logistics to technology, information management and decision making.

Originality/value

This paper presents the humanitarian vaccine cold chain problem from an original angle by illuminating the implications of technology and information on the decisions made during the planning and implementation phases of a vaccine campaign. The authors develop an agenda to provide researchers and humanitarians with a perspective to improve cold chain planning and implementation at the intersection of technology, information and decisions.
Publication trends in a high impact journal: the case of World Psychiatry
Authors: Elango Bakthavachalam , Hartley James
Published: March 2018

Purpose

The purpose of this paper is to examine the bibliometric characteristics of papers published in a high impact journal World Psychiatry during the period 2006-2015.

Design/methodology/approach

The data for this study were obtained from Thompson Reuters’ “Web of Science”. Publication details were extracted for the journal title “World Psychiatry”. This study covers authorship patterns, annual growth, impact factors, document types, top contributors, international collaborations, highly cited papers and keyword analyses. Software programs such as “Histcite”, “intcoll.exe”, “Pajek” and “Leximancer” were used to analyze the publications.

Findings

More than half of the publications were by editorial materials and number of publications from low and middle income countries is very low when compared to proportion of editorial board members. Almost 40 per cent of papers came from the USA and editorial board members had considerable number of papers. Kings College London led the institutions.

Originality/value

Analysis of high impact journals in the field of psychiatry has been carried out in a very few. Hence, the results of this study will be useful to compare with other journals.
Trichoscopy of alopecia areata: An update
Authors: Waśkiel Anna , Rakowska Adriana , Sikora Mariusz , Olszewska Małgorzata , Rudnicka Lidia
Published: March 2018

The diagnosis of alopecia areata is usually based on clinical manifestations. However, there are several hair and scalp disorders that share similar clinical features with alopecia areata, such as tinea capitis, trichotillomania or traction alopecia. Trichoscopy as a fast, non‐invasive and easy‐to‐perform technique may help to identify subtle details and establish the correct diagnosis. The aim of this review is to present the spectrum of trichoscopic findings in alopecia areata. A systematic review of the published work was performed by searching the PubMed, Scopus and EBSCO databases, complemented by a thorough hand search of reference lists. Of 427 articles retrieved, 30 studies were eligible for quantitative analysis. The reported features of alopecia areata were: yellow dots (6–100% patients), short vellus hairs (34–100%), black dots (0–84%), broken hairs (0–71%) and exclamation mark hairs (12–71%). Tapered hairs (5–81%) were reported in few studies, but a relatively high frequency of this finding in alopecia areata may indicate their important role in the differential diagnosis of hair loss. Rarely reported features, which include upright regrowing hairs (11–96%), pigtail (circle) hairs (4–61%) and Pohl‐Pinkus constrictions (2–10%), may also be helpful in the diagnosis of alopecia areata. There is no pathognomonic trichoscopic marker for alopecia areata and the most common trichoscopic features are not the most specific. Therefore, the diagnosis should be based on the coexistence of several trichoscopic findings, not on the presence of a single feature.
Guselkumab, a human interleukin‐23 monoclonal antibody in Japanese patients with generalized pustular psoriasis and erythrodermic psoriasis: Efficacy and safety analyses of a 52‐week, phase 3, multicenter, open‐label study
Authors: Sano Shigetoshi , Kubo Hiroshi , Morishima Hitomi , Goto Ryosuke , Zheng Richuan , Nakagawa Hidemi
Published: March 2018

Generalized pustular psoriasis (GPP) and erythrodermic psoriasis (EP) are the rare and severe subtypes of psoriasis, which are often difficult to treat. The aim of this phase 3, open‐label study was to evaluate efficacy and safety of guselkumab, a human interleukin‐23 monoclonal antibody, in Japanese patients with GPP and EP. Guselkumab 50 mg was administrated to GPP (n = 10) and EP (n = 11) patients at weeks 0, 4 and thereafter every 8 weeks (q8w). Beginning at week 20, patients were escalated to 100 mg q8w if they met the dose escalation criteria. The primary end‐point was the proportion of patients achieving treatment success (Clinical Global Impression score of “very much improved”, “much improved” or “minimally improved”) at week 16. Safety evaluations included assessment of treatment‐emergent adverse events (TEAE) through week 52. At week 16, the proportions of GPP and EP patients achieving treatment success were 77.8% (7/9) and 90.9% (10/11), respectively. Furthermore, guselkumab treatment consistently showed improvement in responses of secondary end‐points such as Psoriasis Area and Severity Index, Investigator's Global Assessment, Japanese Dermatological Association severity index and improvement in body surface area involvement. Improvements in quality of life, as assessed by the Dermatology Life Quality Index, were also observed through week 52. The most commonly reported TEAE was nasopharyngitis (28.6%, 6/21). Safety findings were consistent with those observed previously in other studies. In conclusion, guselkumab treatment demonstrated efficacy and showed no safety concerns in Japanese patients with GPP and EP through week 52.
miR‐376b‐3p attenuates mitochondrial fission and cardiac hypertrophy by targeting mitochondrial fission factor
Authors: Sun Yong Le , Li Shao Hua , Yang Le , Wang Yong
Published: March 2018

Mitochondrial dysfunction contributes to the pathogenesis of cardiac hypertrophy. The disequilibrium of mitochondrial dynamic, which refers to mitochondrial fusion and fission, leads to mitochondrial morphology alteration and dysfunction. Enhanced understanding of the molecular mechanisms in depth may shed light on the therapy of the disease. In this study, we show that mitochondrial fission factor (MFF) is up‐regulated upon hypertrophic agonist noradrenaline (NA) treatment. Knockdown of MFF attenuated NA induced mitochondrial fission and cardiac hypertrophy. Mitochondrial fission factor is a direct target of miR‐376b‐3p, which attenuated expression enhanced MFF expression through binding to its 3′UTR. Expression of miR‐376b‐3p weakened the fragmentation of mitochondria as well as decreased hypertrophic response through regulating MFF in NA treated neonatal rat ventricular cells (NRVCs). This study suggested that miR‐376b‐3p is a novel modulator affecting mitochondrial morphology through targeting MFF.
Farm machinery use, off‐farm employment and farm performance in China
Authors: Ma Wanglin , Renwick Alan , Grafton Quentin
Published: March 2018

We analyse the joint impacts of farm machinery use and off‐farm employment on maize yields and agrochemical expenses from a household survey of 493 farmers in China. Our findings are obtained from an innovative two‐stage econometric procedure that combines a bivariate ordered probit model with an endogeneity‐corrected ordinary least square regression model. The results show that farmers are jointly making decisions to use farm machines and to work off the farm and that these two household activities affect maize yields and agrochemical expenses in different ways. We show that farm machinery use significantly increases both maize yields and agrochemical expenses, while off‐farm employment significantly decreases agrochemical expenses. Our findings highlight the importance of additional machinery use in increasing farm production; the need to account for possible endogeneity in estimation; and the statistical significance of key household characteristics (gender, education, and household size) on overall farm production.
State of the field: What can political ethnography tell us about anti‐politics and democratic disaffection?
Authors: BOSWELL JOHN , CORBETT JACK , DOMMETT KATE , JENNINGS WILL , FLINDERS MATTHEW , RHODES R.A.W. , WOOD MATTHEW
Published: March 2018

This article adopts and reinvents the ethnographic approach to uncover what governing elites do, and how they respond to public disaffection. Although there is significant work on the citizens’ attitudes to the governing elite (the demand side) there is little work on how elites interpret and respond to public disaffection (the supply side). It is argued here that ethnography is the best available research method for collecting data on the supply side. The article tackles longstanding stereotypes in political science about the ethnographic method and what it is good for, and highlights how the innovative and varied practices of contemporary ethnography are ideally suited to shedding light into the ‘black box’ of elite politics. The potential pay‐off is demonstrated with reference to important examples of elite ethnography from the margins of political science scholarship. The implications from these rich studies suggest a reorientation of how one understands the drivers of public disaffection and the role that political elites play in exacerbating cynicism and disappointment. The article concludes by pointing to the benefits to the discipline in embracing elite ethnography both to diversify the methodological toolkit in explaining the complex dynamics of disaffection, and to better enable engagement in renewed public debate about the political establishment.
Evaluation of the potential exposure of butterflies to genetically modified maize pollen in protected areas in Italy
Authors: Arpaia Salvatore , Baldacchino Ferdinando , Bosi Sara , Burgio Giovanni , Errico Simona , Magarelli Rosaria Alessandra , Masetti Antonio , Santorsola Salvatore
Published: March 2018

Environmental impacts of genetically modified crops are mandatorily assessed during their premarket phase. One of the areas of concern is the possible impact on nontarget organisms. Crops expressing Cry toxins might affect Lepidoptera larvae living outside cultivated fields, through pollen deposition on wild plants, which constitute their food source. While pollen toxicity varies among different events, possible exposure of nontarget species depends on the agro‐environmental conditions. This study was conducted in two protected areas in Italy, characterized by different climatic conditions, where many Lepidoptera species thrive in proximity to maize cultivations. To estimate the possible exposure in absence of the actual stressor (e.g., Cry1‐expressing maize plants), we conducted a two‐year field survey of butterflies and weeds. Indicator species were selected—Aglais (Inachis) io in the Northern site and Vanessa cardui in the Southern site—and their phenology was investigated. Pollen dispersal from maize fields was measured by collection in Petri dishes. Duration and frequency of exposure was defined by the overlap between pollen emission and presence of larvae on host plants. Different risk scenarios are expected in the two regions: highest exposure is foreseen for A. io in the Northern site, while minimal exposure is estimated for V. cardui in the Southern site. In the latter case, locally grown maize cultivars flower in mid‐summer in coincidence with an aestivation period for several butterfly species due to hot and dry conditions. Moreover, host plants of V. cardui are at the end of their life cycle thus limiting food availability.
Whole‐genome sequencing of north African honey bee Apis mellifera intermissa to assess its beneficial traits
Authors: Haddad Nizar Jamal , Adjlane Noureddine , Saini Deepti , Menon Athul , Krishnamurthy Venkatesh , Jonklaas Devan , Tomkins J. Paul , Loucif‐Ayad Wahida , Horth Lisa
Published: March 2018

Apis mellifera intermissa is the native honey bee subspecies of Algeria, and approximates a position among bee races between tropical African and European breeds. This bee is very aggressive, nervous, and produces many broods with many queen cells. It is prone to swarming and exhibits defensive behavior and an abundant use of propolis. In the present study, pure line samples of A. m. intermissa collected from Blida (Algeria; 36°31′N, 2°58′E) with preferable Varroa resistance confirmed their through hygienic cleaning behavior and high temperature adaptation, were selected as a reference sample for full‐genome sequencing. Array comparative genomic hybridization (aCGH) was also performed on the same samples to validate genomic variations. These analyses will be an important source of information for the honey bee research community worldwide. The 240‐Mb genome was annotated with 26 355 transcripts and analyzed. Analysis of 133 pathways indicated an abundance of pathways related to metabolic processes, the biosynthesis of secondary metabolites, and biodegradation of xenobiotics . In addition to simple sequence repeat markers, variant analysis for beneficial trait genes, transposons, and phylogeny was performed. The mitochondrial genome and genes involved in immunity and chemoreception were identified and compared with those from other sequenced insect models. The indels obtained by sequencing were validated by aCGH. The genome sequence, annotation, and analysis of A. m. intermissa provides new understanding of the function of bee genes, and comparison with the genome of other A. mellifera subspecies promises to yield insights into the evolution of the adaptations to high temperature and resistance to Varroa parasite infestation.
Effects of habitat fragmentation on genetic diversity and gene flow among the Homidia socia (Collembola: Entomobryidae) populations in the Thousand Island Lake
Authors: Wang Wei , Lv Kun , Wang Ji‐Rui , Zhou Jing , Gu Jian‐Qiang , Zhou Guo‐Xin , Xu Zhi‐Hong
Published: March 2018

In the present study, partial sequences of the mitochondrial cytochrome oxidase subunit I (COI) gene of 22 island populations of the springtail Homidia socia in the Thousand Island Lake were sequenced. Across all sequences, 37 haplotypes were identified for the 510‐bp mitochondrial (mt) DNA COI gene. Haplotype 2 was the most common, and was distributed in the most of the 22 island populations. Haplotype diversity ranged from 0.065 to 0.733, and the total genetic diversity was 0.56216. The genetic characteristics of the 22 island populations were analyzed using the fixation index and gene flow, with values of 0.00043–0.94900 and 0.02703–703.72540, respectively. Comparison between (island area and isolations) with population genetic diversity revealed that there were no significant correlations between them, except for a significant correlation between the number of haplotypes and island area. Mantel tests showed that there was no significant correlation between geographic distance and genetic distance among various groups. All the results indicated that there were no obvious relationships between island characteristics and the genetic diversity of the springtails. We consider that the low dispersal capacity of springtails and the island patches surrounded by water in the Thousand Island Lake are the major factors affecting the genetic diversity of H. socia.
Morphological and ultrastructural characterization of the alimentary canal in larvae of Streltzoviella insularis (Staudinger) (Lepidoptera: Cossidae)
Authors: Wang Xiuji , Lu Hao , Shao Yuying , Zong Shixiang
Published: March 2018

Streltzoviella insularis (Staudinger) is an important tree‐boring pest, that primarily damages Sophora japonica (Linnaeus) and Ginkgo biloba (Linnaeus), as well as other common species, at great economic cost to the urban landscape construction industry in China. In the present study, the alimentary canal morphology of S. insularis was observed using light microscopy, and its ultrastructure was investigated by scanning and transmission electron microscopy. The foregut of S. insularis can be divided into the pharynx, esophagus, crop, proventriculus, and cardiac valve. The well‐developed crop forms the longest section of the foregut. It is able to store large amounts of food and is lined with a monolayer of epithelial cells. Many sclerotized microspines occur on the surface of the anterior intima and there are dense spines on the posterior intima of the proventriculus. Epithelial cells of the midgut include columnar cells, goblet cells, and regenerative cells, but endocrine cells are absent. The hindgut consists of the pyloric valve, ileum, and rectum. There is no clear distinction between the ileum and colon. The intima surface of the pyloric valve carries many microspines, whereas the intestinal wall of the rectum is thin with well‐developed rectal pads. The rectal epithelial cells form a squamous monolayer. A cryptonephric excretory system is located in the hindgut. There are six spiral Malpighian tubules, in which a cellular layer on a basement membrane encloses a lumen. These results will provide the basis for further studies of the structure and function in S. insularis larvae.
Morphology and distribution of antennal, maxillary palp and labial palp sensilla of the adult bruchid beetles,Callosobruchus chinensis(L.) (Coleoptera: Bruchidae)
Authors: Wang Hongmin , Zheng Haixia , Zhang Yaowen , Zhang Xianhong
Published: March 2018

Callosobruchus chinensis(Coleoptera: Bruchidae) is the main pest of mungbean (Vigna radiata) especially during seed storage. To provide background information for chemical ecology studies, we examined the externalmorphology of the antennal, maxillary palp and labial palp sensilla of this insect with scanning electron microscopy. The antennae of adultC. chinensisexhibited sexual dimorphism. The female have serrated antenna and the male have pectinate morphology. Eight sensillum types have been observed on the antennae of both sexes: Böhm bristles, sensilla chaetica, sensilla trichodea, sensilla basiconica, sensilla styloconicum, sensilla coeloconica, sensillum campaniformia, sensilla cavity. There are no differences on the morphology of maxillary palp and labial palp between female and male. Four different types of sensilla are present on the labial and maxillary palps of both sexes ofC. chinensis: sensilla chaetica, sensilla twig basiconica, sensilla basiconica, sensilla digitiformia.
An automated barcode tracking system for behavioural studies in birds
Authors: Alarcón‐Nieto Gustavo , Graving Jacob M. , Klarevas‐Irby James A. , Maldonado‐Chaparro Adriana A. , Mueller Inge , Farine Damien R.
Published: March 2018

Recent advances in technology allow researchers to automate the measurement of animal behaviour. These methods have multiple advantages over direct observations and manual data input as they reduce bias related to human perception and fatigue, and deliver more extensive and complete datasets that enhance statistical power. One major challenge that automation can overcome is the observation of many individuals at once, enabling whole‐group or whole‐population tracking.

We provide a detailed description of an automated system for tracking birds. Our system uses printed, machine‐readable codes mounted on backpacks. This simple, yet robust, tagging system can be used simultaneously on multiple individuals to provide data on bird identity, position and directionality. Furthermore, because the backpacks are printed on paper, they are very lightweight. We show that our method is reliable, relatively easy to implement and monitor, and with proper handling, has proved to be safe for the birds over long periods of time.

We describe the deployment procedure of this system for a captive population of songbirds. We test different camera options, and discuss their advantages and disadvantages. In particular, we highlight how using single‐board computers to control the frequency and duration of image capture makes this system affordable and adaptable to a range of study systems and research questions.

The ability to automate the measurement of individual positions has the potential to significantly increase the power of both observational and experimental studies. The system can capture both detailed interactions (using video recordings) and repeated observations (e.g. once per second for the entire day) of individuals over long timescales (months or potentially years). This approach opens the door to tracking life‐long relationships among individuals, while also capturing fine‐scale differences in behaviour.
Heparin‐binding protein as a biomarker of post‐injury sepsis in trauma patients
Authors: Halldorsdottir H. D. , Eriksson J. , Persson B. P. , Herwald H. , Lindbom L. , Weitzberg E. , Oldner A.
Published: March 2018

Background

Heparin‐binding protein (HBP) is a neutrophil‐derived protein advocated as a biomarker in sepsis. We evaluated plasma HBP as a predictor of post‐injury sepsis in trauma patients.

Methods

Ninety‐seven trauma patients were studied during the first week of intensive care. Injury‐related data were collected and clinical parameters registered daily. Plasma HBP was sampled on day 1, 3 and 5 after trauma and evaluated for associations with injury‐related parameters and sepsis. The predictive properties of HBP were compared to C‐reactive protein (CRP) and white blood cell count (WBC).

Results

Median Injury Severity Score was 33, one‐third of the trauma patients received massive transfusion and a quarter was in shock on arrival. Overall 30‐day mortality was 8%. Plasma HBP was significantly higher in severely injured patients and associated with shock on arrival, massive transfusions and organ failure. Septic patients had higher levels of HBP only on day 5. When evaluated for prediction of onset of sepsis during the two following days after plasma sampling by receiver operating characteristic (ROC) analyses, areas under the curves were non‐significant for all time points. Similar patterns were seen for CRP and WBC.

Conclusion

In trauma patients, HBP levels are related to severity of injury and organ dysfunction. Heparin‐binding protein was weakly associated with sepsis and only at the later stage of the observation period of 1 week. Moreover, HBP showed poor discriminatory properties as an early biomarker of post‐injury sepsis. Trauma‐induced inflammation during the post‐injury phase may blunt the sepsis‐predictive performance of HBP.
Fish oil treatment reduces chronic alcohol exposure induced synaptic changes
Authors: Shi Zhe , Xie Youna , Ren Huixia , He Baixuan , Wang Meng , Wan Jian‐Bo , Yuan Ti‐Fei , Yao Xiaoli , Su Huanxing
Published: March 2018

Alcohol addiction is a chronic neuropsychiatric disorder that represents one of the most serious global public health problems. Yet, currently there still lacks an effective pharmacotherapy. Omega‐3 polyunsaturated fatty acids (N‐3 PUFAs) have exhibited beneficial effects in a variety of neurological disorders, particularly in reversing behavioral deficits and neurotoxicity induced by prenatal alcohol exposure and binge drinking. In the present study, we investigated if fish oil, which is rich in N‐3 PUFAs, had beneficial effects on preventing relapse and alleviating withdrawal symptoms after chronic alcohol exposure. Our results demonstrated that fish oil significantly reduced the chronic alcohol exposure‐induced aberrant dendritic morphologic changes of the medium‐sized spiny neurons in the core and the shell of nucleus accumbens. This inhibited the expression of AMPAR2‐lacking AMPARs and their accumulation on the post synaptic membranes of medium‐sized spiny neurons and eventually alleviated withdrawal symptoms and alcohol dependence. Our study therefore suggests that N‐3 PUFAs are promising for treating withdrawal symptoms and alcohol dependence.
Remarkable genetic diversity detected at river buffalo prolactin receptor (PRLR) gene and association studies with milk fatty acid composition
Authors: Cosenza G. , Iannaccone M. , Auzino B. , Macciotta N. P. P. , Kovitvadhi A. , Nicolae I. , Pauciullo A.
Published: March 2018

Prolactin is an anterior pituitary peptide hormone involved in many different endocrine activities and is essential for reproductive performance. This action is mediated by its receptor, the prolactin receptor, encoded by the PRLR gene. In this study, we sequenced and characterized the Mediterranean river buffalo PRLR gene (from exon 3 to 10), and we found remarkable genetic diversity. In particular, we found 24 intronic polymorphisms and 13 exonic SNPs, seven of which were non‐synonymous. Furthermore, the polymorphisms identified in the 3′‐UTR were investigated to establish their possible influence on microRNA binding sites. Considering all the amino acid changes and the observed allelic combinations, it is possible to deduce at least six different translations of the buffalo prolactin receptor and, consequently, the presence at the PRLR gene of at least six alleles. Furthermore, we identified a deletion of a CACTACC heptamer between nucleotides 1102 and 1103 of exon 10 (3′‐UTR), and we developed an allele‐specific PCR to identify the carriers of this genetic marker. Finally, the SNP g.11188A>G, detected in exon 10 and responsible for the amino acid replacement p.His328Arg, was genotyped in 308 Italian Mediterranean river buffaloes, and an association study with milk fat traits was carried out. The statistical analysis showed a tendency that approached significance for the AA genotype with higher contents of odd branched‐chain fatty acids. Thus, our results suggest that the PRLR gene is a good candidate for gene association studies with qualitative traits related to buffalo milk production.
The association of peri‐operative scores, including frailty, with outcomes after unscheduled surgery
Authors: McGuckin D. G. , Mufti S. , Turner D. J. , Bond C. , Moonesinghe S. R.
Published: March 2018

Postoperative hospital stay is longer for frail, older patients, who are more likely to experience prolonged postoperative morbidity and reduced long‐term survival. We recorded in‐hospital mortality, morbidity and length of stay for 164 patients aged at least 65 years after unscheduled surgery. We evaluated pre‐operative frailty with the 7‐point Clinical Frailty Scale: 81 patients were ‘not vulnerable’ (frailty score 1–3) and 83 were ‘vulnerable or frail’ (frailty score 4), with mean (SD) ages of 74.7 (7.5) years vs. 79.4 (8.3) years, respectively, p < 0.001. Within 30 postoperative days 8/164 (5%) patients died, all with frailty scores 4, p = 0.007. Postoperative morbidity was less frequent in patients categorised as ‘not vulnerable’ on four out of the six days it was measured (days 3, 5, 8, 14, 23, 28). Median (IQR [range]) postoperative stay was 9 (6–18 [2–221]) days for patients with frailty scores 1–3, and 22 (12–33 [2–270]) days for patients with score 4, p < 0.001. Four variables independently associated with hospital discharge, hazard ratio (95%CI): E‐POSSUM, 0.74 (0.60–0.92), p = 0.007; ASA 2, 0.35 (0.13–0.98), p = 0.046, ASA 3, 0.17 (0.06–0.47), p = 0.001 and ASA 4/5, 0.08 (0.02–0.28), p < 0.001; operative severity ‘major +’, 0.69 (0.41–1.08), p = 0.10 and the Surgical Outcome Risk Tool, 7.75 (0.81–74.40), p = 0.08.