bluuebunny/crossref_metadata_2025 huggingface dataset:
Metagenomic screening of global microbiomes identifies pathogen-enriched environments
Authors: Li Xiaofang
Published: July 2018

Background

Human pathogens are widespread in the environment, and examination of pathogen-enriched environments in a rapid and high-throughput fashion is important for development of pathogen-risk precautionary measures.

Methods

In this study, a Local BLASTP procedure for metagenomic screening of pathogens in the environment was developed using a toxin-centered database. A total of 27 microbiomes derived from ocean water, freshwater, soil, feces, and wastewater were screened using the Local BLASTP procedure. Bioinformatic analysis and Canonical Correspondence Analysis were conducted to examine whether the toxins included in the database were taxonomically associated.

Results

The specificity of the Local BLASTP method was tested with known and unknown toxin sequences. Bioinformatic analysis indicated that most toxins were phylum-specific but not genus-specific. Canonical Correspondence Analysis implied that almost all of the toxins were associated with the phyla ofProteobacteria,NitrospiraeandFirmicutes. Local BLASTP screening of the global microbiomes showed that pore-forming RTX toxin and adenylate cyclase Cya were most prevalent globally in terms of relative abundance, while polluted water and feces samples were the most pathogen-enriched.

Conclusions

A Local BLASTP procedure was established for rapid detection of toxins in environmental samples. Screening of global microbiomes in this study provided a quantitative estimate of the most prevalent toxins and most pathogen-enriched environment.
High-density extracellular probes reveal dendritic backpropagation and facilitate neuron classification
Authors: Jia Xiaoxuan , Siegle Josh , Bennett Corbett , Gale Sam , Denman Daniel R , Koch Christof , Olsen Shawn R.
Published: July 2018

Different neuron types serve distinct roles in neural processing. Extracellular electrical recordings are extensively used to study brain function but are typically blind to cell identity. Morpho-electric properties of neurons measured on spatially dense electrode arrays might be useful for distinguishing neuron types. Here we used Neuropixels probes to record from cortical and subcortical regions of the mouse brain. Extracellular waveforms of each neuron were detected across many channels and showed distinct spatiotemporal profiles among brain regions. Classification of neurons by brain region was improved with multi-channel compared to single-channel waveforms. In visual cortex, waveform clustering identified the canonical regular spiking (RS) and fast spiking (FS) classes, but also uncovered a subclass of RS units with unidirectional backpropagating action potentials (BAPs). Moreover, BAPs were observed in many hippocampal RS cells. Overall, waveform analysis of spikes from high-density probes aids neuron identification and can reveal dendritic backpropagation.
Genetics & the Geography of Health, Behavior, and Attainment
Authors: Belsky Daniel W , Caspi Avshalom , Arseneault Louise , Corcoran David L , Domingue Benjamin W , Harris Kathleen Mullan , Houts Renate M , Mill Jonathan S , Moffitt Terrie E , Prinz Joseph , Sugden Karen , Wertz Jasmin , Williams Benjamin , Odgers Candice L
Published: July 2018

People’s life chances can be predicted by their neighborhoods. This observation is driving efforts to improve lives by changing neighborhoods. Some neighborhood effects may be causal, supporting neighborhood-level interventions. Other neighborhood effects may reflect selection of families with different characteristics into different neighborhoods, supporting interventions that target families/individuals directly. To test how selection affects different neighborhood-linked problems, we linked neighborhood data with genetic, health, and social-outcome data for >7,000 European-descent UK and US young people in the E-Risk and Add Health Studies. We tested selection/concentration of genetic risks for obesity, schizophrenia, teen-pregnancy, and poor educational outcomes in high-risk neighborhoods, including genetic analysis of neighborhood mobility. Findings argue against genetic selection/concentration as an explanation for neighborhood gradients in obesity and mental-health problems, suggesting neighborhoods may be causal. In contrast, modest genetic selection/concentration was evident for teen-pregnancy and poor educational outcomes, suggesting neighborhood effects for these outcomes should be interpreted with care.
PhISCS - A Combinatorial Approach for Sub-perfect Tumor Phylogeny Reconstruction via Integrative use of Single Cell and Bulk Sequencing Data
Authors: Malikic Salem , Ciccolella Simone , Mehrabadi Farid Rashidi , Ricketts Camir , Rahman Khaledur , Haghshenas Ehsan , Seidman Daniel , Hach Faraz , Hajirasouliha Iman , Cenk Sahinalp S.
Published: July 2018

Recent technological advances in single cell sequencing (SCS) provide high resolution data for studying intra-tumor heterogeneity and tumor evolution. Available computational methods for tumor phylogeny inference via SCS typically aim to identify the most likelyperfect phylogeny treesatisfyinginfinite sites assumption(ISA). However limitations of SCS technologies such as frequent allele dropout or highly variable sequence coverage, commonly result in mutational call errors and prohibit a perfect phylogeny. In addition, ISA violations are commonly observed in tumor phylogenies due to the loss of heterozygosity, deletions and convergent evolution. In order to address such limitations, we, for the first time, introduce a new combinatorial formulation that integrates single cell sequencing data with matching bulk sequencing data, with the objective of minimizing a linear combination of (i) potential false negatives (due to e.g. allele dropout or variance in sequence coverage) and (ii) potential false positives (due to e.g. read errors) among mutation calls, as well as (iii) the number of mutations that violate ISA - to define theoptimal sub-perfect phylogeny.Our formulation ensures that several lineage constraints imposed by the use of variant allele frequencies (VAFs, derived from bulk sequence data) are satisfied. We express our formulation both in the form of an integer linear program (ILP) and - for the first time in the context of tumor phylogeny reconstruction - a boolean constraint satisfaction problem (CSP) and solve them by leveraging state-of-the-art ILP/CSP solvers. The resulting method, which we name PhISCS, is the first to integrate SCS and bulk sequencing data under the finite sites model. Using several simulated and real SCS data sets, we demonstrate that PhISCS is not only more general but also more accurate than the alternative tumor phylogeny inference tools. PhISCS is very fast especially when its CSP based variant is used returns the optimal solution, except in rare instances for which it provides an optimality gap. PhISCS is available athttps://github.com/haghshenas/PhISCS.
M3C: Monte Carlo reference-based consensus clustering
Authors: John Christopher R. , Watson David , Russ Dominic , Goldmann Katriona , Ehrenstein Michael , Pitzalis Costantino , Lewis Myles , Barnes Michael
Published: July 2018

Genome-wide data is used to stratify patients into classes for precision medicine using clustering algorithms. A common problem in this area is selection of the number of clusters (K). The Monti consensus clustering algorithm is a widely used method which uses stability selection to estimate K. However, the method has bias towards higher values of K and yields high numbers of false positives. As a solution, we developed Monte Carlo reference-based consensus clustering (M3C), which is based on this algorithm. M3C simulates null distributions of stability scores for a range of K values thus enabling a comparison with real data to remove bias and statistically test for the presence of structure. M3C corrects the inherent bias of consensus clustering as demonstrated on simulated and real expression data from The Cancer Genome Atlas (TCGA). For testing M3C, we developed clusterlab, a new method for simulating multivariate Gaussian clusters.
Platypus Induced Pluripotent Stem Cells: the Unique Pluripotency Signature of a Monotreme
Authors: Whitworth DJ , Limnios IJ , Gauthier M-E , Weeratunga P , Ovchinnikov DA , Baillie G , Grimmond SM , Marshall Graves JA , Wolvetang EJ
Published: July 2018

Summary Statement

The generation and transcriptome analysis of the first induced pluripotent stem cells from the platypus reveals SOX2 has been a key driver of the expanded pluripotency regulatory network in placental mammals.

The mechanisms by which pluripotency has evolved remain unclear. To gain insight into the evolution of mammalian pluripotency we have generated induced pluripotent stem cells (piPSCs) from the platypus. Deep sequencing of the piPSC transcriptome revealed that piPSCs robustly express the core eutherian pluripotency factorsOCT4, SOX2andNANOG. Given the more extensive role ofSOX3overSOX2in avian pluripotency, our data indicate that between 315 million years and 166 million years ago primitive mammals replaced the role ofSOX3in the vertebrate pluripotency network withSOX2. DAX1/NR0B1is not expressed in piPSCs and an analysis of the platypusDAX1promoter revealed the absence of a proximal SOX2-binding DNA motif known to be critical forDAX1expression in eutherian pluripotent stem cells, suggesting that the acquisition of SOX2 responsiveness byDAX1has facilitated its recruitment into the pluripotency network of eutherians. We further show that the expression ratio of X chromosomes to autosomes (X1-5X1-5:AA) is approximately equal to 1 indicating that there is no upregulation of X-linked genes and that there is no preference for silencing of maternal or paternal alleles (ie imprinting).
Regulation of T cell expansion by antigen presentation dynamics
Authors: Mayer Andreas , Zhang Yaojun , Perelson Alan S. , Wingreen Ned S.
Published: July 2018

An essential feature of the adaptive immune system is the proliferation of antigen-specific lymphocytes during an immune reaction to form a large pool of effector cells. This proliferation must be regulated to ensure an effective response to infection while avoiding immunopathology. Recent experiments in mice have demonstrated that the expansion of a specific clone of T cells in response to cognate antigen obeys a striking inverse power law with respect to the initial number of T cells. Here, we show that such a relationship arises naturally from a model in which T cell expansion is limited by decaying levels of presented antigen. The same model also accounts for the observed dependence of T cell expansion on affinity for antigen and on the kinetics of antigen administration. Extending the model to address expansion of multiple T cell clones competing for antigen, we find that higher affinity clones can suppress the proliferation of lower affinity clones, thereby promoting the specificity of the response. Employing the model to derive optimal vaccination protocols, we find that exponentially increasing antigen doses can achieve a nearly optimized response. We thus conclude that the dynamics of presented antigen is a key regulator of both the size and specificity of the adaptive immune response.
A robust image registration interface for large volume brain atlas
Authors: Ni Hong , Tan Chaozhen , Feng Zhao , Chen Shangbin , Zhang Zoutao , Li Wenwei , Guan Yue , Gong Hui , Luo Qingming , Li Anan
Published: July 2018

Mapping the brain structures in three-dimensional accurately is critical for an in-depth understanding of the brain functions. By using the brain atlas as a hub, mapping detected datasets into a standard brain space enables efficiently use of various datasets. However, because of the heterogeneous and non-uniform characteristics of the brain structures at cellular level brought with the recently developed high-resolution whole-brain microscopes, traditional registration methods are difficult to apply to the robust mapping of various large volume datasets. Here, we proposed a robust Brain Spatial Mapping Interface (BrainsMapi) to address the registration of large volume datasets at cellular level by introducing the extract regional features of the anatomically invariant method and a strategy of parameter acquisition and large volume transformation. By performing validation on model data and biological images, BrainsMapi can not only achieve robust registration on sample tearing and streak image datasets, different individual and modality datasets accurately, but also are able to complete the registration of large volume dataset at cellular level which dataset size reaches 20 TB. Besides, it can also complete the registration of historical vectorized dataset. BrainsMapi would facilitate the comparison, reuse and integration of a variety of brain datasets.
Effects of endophyte infected tall fescue seed and red clover isoflavones on rumen microbial populations, fiber fermentation, and volatile fatty acidsin vitro
Authors: Melchior Emily A. , Mulliniks J. Travis , Smith Jason K. , Bates Gary E. , Schneider Liesel G. , McFarlane Zachary D. , Flythe Michael D. , Klotz James L. , Goodman Jack P. , Ji Huihua , Myer Phillip R.
Published: July 2018

Negative impacts of endophyte-infectedLolium arundinaceum (Darbyshire)(tall fescue) are responsible for over $2 billion in losses to livestock producers annually. While the influence of endophyte-infected tall fescue has been studied for decades, mitigation methods have not been clearly elucidated. Isoflavones found inTrifolium pretense(red clover) have been the subject of recent research regarding tall fescue toxicosis mitigation. Therefore, the aim of this study was to determine the effect of ergovaline and red clover isoflavones on rumen microbial populations, fiber degradation, and volatile fatty acids (VFA) in anin vitrosystem. Using a dose of 1.10 mg × L−1, endophyte-infected or endophyte-free tall fescue seed was added to ANKOM fiber bags with or without 2.19 mg of isoflavones in the form of a control, powder, or pulverized tablet, resulting in a 2 × 3 factorial arrangements of treatments. Measurements of pH, VFA, bacterial taxa, as well as the disappearance of neutral detergent fiber (aNDF), acid detergent fiber (ADF), and crude protein (CP) were taken after 48 h of incubation. aNDF disappearance values were significantly altered by seed type(P= 0.003) and isoflavone treatment (P= 0.005), and ADF disappearance values were significantly different in a seed x isoflavone treatment interaction (P≤ 0.05). A seed x isoflavone treatment interaction was also observed with respect to CP disappearance (P≤ 0.05). Seventeen bacterial taxa were significantly altered by seed x isoflavone treatment interaction groups (P≤ 0.05), six bacterial taxa were increased by isoflavones (P≤ 0.05), and eleven bacterial taxa were altered by seed type (P≤ 0.05). Due to the beneficial effect of isoflavones on tall fescue seed fiber degradation, these compounds may be viable options for mitigating fescue toxicosis. Further research should be conducted to determine physiological implications as well as microbiological changesin vivo.
Compensatory mechanisms render Tcf7l1a dispensable for eye formation despite its cell-autonomous requirement in eye field specification
Authors: Young Rodrigo M. , Cavodeassi Florencia , Hawkins Thomas A. , Stickney Heather L. , Schwarz Quenten , Lawrence Lisa M. , Wierzbicki Claudia , Gestri Gaia , Ambrosio Elizabeth , Klosner Allison , Rowell Jasmine , Bianco Isaac H. , Allende Miguel L. , Wilson Stephen W.
Published: July 2018

The vertebrate eye originates from the eyefield, a domain of cells specified by a small number of transcription factors. In this study, we show that Tcf7la is one such transcription factor that acts cell-autonomously to specify the eye field in zebrafish. Despite the much reduced eyefield intcf7l1amutants, these fish develop normal eyes revealing a striking ability of the eye to recover from a severe early phenotype. This robustness is not mediated through compensation by paralogous genes; instead, the smaller optic vesicle oftcf7l1amutants shows delayed neurogenesis and continues to grow until it achieves approximately normal size. Although the developing eye is robust to the lack of Tcf7l1a function, it is sensitised to the effects of additional mutations. In support of this, a forward genetic screen identified mutations inhesx1, cct5andgdf6a, which give synthetically enhanced eye specification or growth phenotypes when in combination with thetcf7l1amutation.
Substantia nigra dopamine neurons evoke a delayed excitation in lateral dorsal striatal cholinergic interneurons via glutamate cotransmission
Authors: Chuhma Nao , Mingote Susana , Yetnikoff Leora , Kalmbach Abigail , Ma Thong , Ztaou Samira , Siena Anna-Claire , Tepler Sophia , Poulin Jean-Francois , Ansorge Mark , Awatramani Rajeshwar , Kang Un Jung , Rayport Stephen
Published: July 2018

Dopamine neurons have different synaptic actions in the ventral and dorsal striatum (dStr), but whether this heterogeneity extends to dStr subregions has not been addressed. We have found that optogenetic activation of dStr dopamine neuron terminals in mouse brain slices pauses the firing of cholinergic interneurons in both the medial and lateral subregions, while in the lateral subregion the pause is shorter due to a subsequent excitation. This excitation is mediated mainly by metabotropic glutamate receptor 1 (mGluR1) and partially by dopamine D1-like receptors coupled to transient receptor potential channel 3 and 7. DA neurons do not signal to spiny projection neurons in the medial dStr, while they elicit ionotropic glutamate responses in the lateral dStr. The DA neurons mediating these excitatory signals are in the substantia nigra (SN). Thus, SN dopamine neurons engage different receptors in different postsynaptic neurons in different dStr subregions to convey strikingly different signals.
Fundamental and realized feeding niche breadths of sexual and asexual stick-insects
Authors: Chloé Larose , Parker Darren J. , Tanja Schwander
Published: July 2018

The factors contributing to the maintenance of sex over asexuality in natural populations remain largely unknown. Ecological divergences between lineages with different reproductive modes could help to maintain reproductive polymorphisms, at least transiently, but there is little empirical information on the consequences of asexuality for the evolution of ecological niches. Here, we investigated how niche breadths evolve following transitions from sexual reproduction to asexuality. We estimated and compared the realized feeding niche breadths of five independently derived asexual Timema stick insect species and their sexual relatives. We found that asexual species had a systematically narrower realized niche than sexual species. To investigate how the narrower realized niches of asexual versus sexual species come about, we quantified the breadth of their fundamental niches but found no systematic differences between reproductive modes. The narrow realized niches found in asexuals are therefore likely a consequence of biotic interactions that constrain realized niche size in asexuals more strongly than in sexuals. Interestingly, the fundamental niche was broader in the oldest asexual species compared to its sexual relative. This broad ecological tolerance may help explain how this species has persisted over more than a million years in absence of sex.
PDEδ inhibition impedes the proliferation and survival of human colorectal cancer cell lines harboring oncogenic KRas
Authors: Klein Christian H. , Truxius Dina C. , Vogel Holger A. , Harizanova Jana , Murarka Sandip , Martín-Gago Pablo , Bastiaens Philippe I. H.
Published: July 2018

Novelty and Impact

The ‘undruggable’ KRas is a prevalent oncogene in CRC with poor prognosis. In hPDAC cells pharmacological targeting of PDEδ affects oncogenic KRas signaling, but it remained unclear whether this approach is transferable to other cancer cells. Here, we show that genetic and pharmacologic PDEδ inhibition also impedes the proliferation of oncogenic, but not wild-type KRas bearing CRC cells indicating that PDEδ inhibition is a specific tool for targeting growth of oncogenic KRas bearing CRC.

Ras proteins, most notably KRas, are prevalent oncogenes in human cancer. Plasma membrane localization and thereby signaling of KRas is regulated by the prenyl-binding protein PDEδ. Recently, we have reported the specific anti-proliferative effects of PDEδ inhibition in KRas-dependent human pancreatic ductal adenocarcinoma cell lines. Here, we investigated the proliferative dependence on the solubilizing activity of PDEδ of human colorectal cancer (CRC) cell lines with or without oncogenic KRas mutations. Our results show that genetic and pharmacologic interference with PDEδ specifically inhibits proliferation and survival of CRC cell lines harboring oncogenic KRas mutations whereas isogenic cell lines in which the KRas oncogene has been removed, or cell lines with oncogenic BRaf mutations or EGFR overexpression are not dependent on PDEδ. Pharmacological PDEδ inhibition is therefore a possible new avenue to target oncogenic KRas bearing CRC.
Subdivision of ancestral scale genetic program underlies origin of feathers and avian scutate scales
Authors: Musser Jacob M. , Wagner Günter P. , Liang Cong , Stabile Frank A. , Cloutier Alison , Baker Allan J. , Prum Richard O.
Published: July 2018

Birds and other reptiles possess a diversity of feather and scale-like skin appendages. Feathers are commonly assumed to have originated from ancestral scales in theropod dinosaurs. However, most birds also have scaled feet, indicating birds evolved the capacity to grow both ancestral and derived morphologies. This suggests a more complex evolutionary history than a simple linear transition between feathers and scales. We set out to investigate the evolution of feathers via the comparison of transcriptomes assembled from diverse skin appendages in chicken, emu, and alligator. Our data reveal that feathers and the overlapping ‘scutate’ scales of birds share more similar gene expression to each other, and to two types of alligator scales, than they do to the tuberculate ‘reticulate’ scales on bird footpads. Accordingly, we propose a history of skin appendage diversification, in which feathers and bird scutate scales arose from ancestral archosaur body scales, whereas reticulate scales arose earlier in tetrapod evolution. We also show that many “feather-specific genes” are also expressed in alligator scales. In-situ hybridization results in feather buds suggest that these genes represent ancestral scale genes that acquired novel roles in feather morphogenesis and were repressed in bird scales. Our findings suggest that the differential reuse, in feathers, and suppression, in bird scales, of genes ancestrally expressed in archosaur scales has been a key factor in the origin of feathers – and may represent an important mechanism for the origin of evolutionary novelties.
Neural Circuit Mechanism of Decision Uncertainty and Change-of-Mind
Authors: Atiya Nadim A A , Rañó Iñaki , Prasad Girijesh , Wong-Lin KongFatt
Published: July 2018

Decision-making is often accompanied by a degree of confidence on whether a choice is correct. Decision uncertainty, or lack in confidence, may lead to change-of-mind. Studies have identified the behavioural characteristics associated with decision confidence or change-of-mind, and their neural correlates. Although several theoretical accounts have been proposed, there is no neural model that can compute decision uncertainty and explain its effects on change-of-mind. We propose a neuronal circuit model that computes decision uncertainty while accounting for a variety of behavioural and neural data of decision confidence and change-of-mind, including testable model predictions. Our theoretical analysis suggests that change-of-mind occurs due to the presence of a transient uncertainty-induced choice-neutral stable steady state and noisy fluctuation within the neuronal network. Our distributed network model indicates that the neural basis of change-of-mind is more distinctively identified in motor-based neurons. Overall, our model provides a framework that unifies decision confidence and change-of-mind.
Interaction modifications lead to greater robustness than pairwise non-trophic effects in food webs
Authors: Terry J. Christopher D. , Morris Rebecca J. , Bonsall Michael B.
Published: July 2018

Considerable emphasis has been placed recently on the importance of incorporating non-trophic effects in to our understanding of ecological networks. Interaction modifications are well established as generating strong non-trophic impacts by modulating the strength of inter-specific interactions.

For simplicity and comparison with direct interactions within a network context, the consequences of interaction modifications have often been described as direct pairwise interactions. The consequences of this assumption have not been examined in non-equilibrium settings where unexpected consequences of interaction modifications are most likely.

To test the distinct dynamic nature of these ‘higher-order’ effects we directly compare, using dynamic simulations, the robustness to extinctions under perturbation of systems where interaction modifications are either explicitly modelled or represented by corresponding equivalent pairwise non-trophic interactions.

Full, multi-species representations of interaction modifications resulted in a greater robustness to extinctions compared to equivalent pairwise effects. Explanations for this increased stability despite apparent greater dynamic complexity can be found in additional routes for dynamic feedbacks. Furthermore, interaction modifications changed the relative vulnerability of species to extinction from those trophically connected close to the perturbed species towards those receiving a large number of modifications.

Future empirical and theoretical research into non-trophic effects should distinguish interaction modifications from direct pairwise effects in order to maximise information about the system dynamics. Interaction modifications have the potential to shift expectations of species vulnerability based exclusively on trophic networks.
PABA Release from Chitosan-PCL with Induced Electric Current
Authors: Miller Jennifer M. , de Guzman Roche C.
Published: July 2018

Controlled drug delivery systems such as the stimulation-based biomaterial scaffolds for sequestration and release of drugs offer safety and regulated therapeutic approach. In this study, the drug:para-aminobenzoic acid (PABA) was absorbed into a crosslinked chitosan and poly(caprolactone) (PCL) hydrogel and its release kinetics quantified under different conditions. It was experimentally-observed that the higher the pH (or the more basic the pH), the slower the PABA saturation release trended over time. At the acidic environment of pH 4, PABA was released the fastest, and enhanced by the degradation of chitosan-PCL gel. When a constant electric current of 0.6 mA sa applied, PABA release was induced at pH 10. However, at pH 7, PABA was stably-bound to the chitosan-PCL matrix, with or without the external current. The selective sequestration of PABA at basic pH and its stimulated release via electric current application can be further explored for clinical translatability.
Estimating DNA-DNA interaction frequency from Hi-C data at restriction-fragment resolution
Authors: Cameron Christopher JF , Dostie Josée , Blanchette Mathieu
Published: July 2018

Hi-C is a popular technique to map three-dimensional chromosome conformation. In principle, Hi-C’s resolution is only limited by the size of restriction fragments. However, insufficient sequencing depth forces researchers to artificially reduce the resolution of Hi-C matrices at a loss of biological interpretability. We present the Hi-C Interaction Frequency Inference (HIFI) algorithms that accurately estimate restriction-fragment resolution Hi-C matrices by exploiting dependencies between neighboring fragments. Cross-validation experiments and comparisons to 5C data and known regulatory interactions demonstrate HIFI’s superiority to existing approaches. In addition, HIFI’s restriction-fragment resolution reveals a new role for active regulatory regions in structuring topologically associating domains.

Availability:https://github.com/BlanchetteLab/HIFI
Exchange catalysis during anaerobic methanotrophy revealed by12CH2D2&13CH3D in methane
Authors: Ash Jeanine L. , Egger Matthias , Treude Tina , Kohl Issaku , Cragg Barry , John Parkes R. , Slomp Caroline P. , Sherwood Lollar Barbara , Young Edward D.
Published: July 2018

The anaerobic oxidation of methane (AOM) is a crucial component of the methane cycle, but its enzymatic versatility under environmental conditions remains poorly understood. We use sediment samples collected during IODP Expedition 347 to the Baltic Sea to show that relative abundances of12CH2D2and13CH3D molecules in methane gas trace the reversibility of methyl-coenzyme M reductase during AOM by driving methane towards internal, thermodynamic isotopic equilibrium. These data suggest that12CH2D2and13CH3D together can identify the influence of methanotrophy in environments where conventional bulk isotope ratios are ambiguous, and these findings may lead to new insights regarding the global significance of enzymatic back-flux in the methane cycle.
Distinct timescales of RNA regulators enable the construction of a genetic pulse generator
Authors: Westbrook Alexandra , Tang Xun , Marshall Ryan , Maxwell Colin S. , Chappell James , Agrawal Deepak K. , Dunlop Mary J. , Noireaux Vincent , Beisel Chase L. , Lucks Julius , Franco Elisa
Published: July 2018

To build complex genetic networks with predictable behaviours, synthetic biologists use libraries of modular parts that can be characterized in isolation and assembled together to create programmable higher-order functions. Characterization experiments and computational models for gene regulatory parts operating in isolation are routinely employed to predict the dynamics of interconnected parts and guide the construction of new synthetic devices. Here, we individually characterize two modes of RNA-based transcriptional regulation, using small transcription activating RNAs (STARs) and CRISPR interference (CRISPRi), and show how their distinct regulatory timescales can be used to engineer a composed feedforward loop that creates a pulse of gene expression. We use a cell-free transcription-translation system (TXTL) to rapidly characterize the system, and we apply Bayesian inference to extract kinetic parameters for an ODE-based mechanistic model. We then demonstrate in simulation and verify with TXTL experiments that the simultaneous regulation of a single gene target with STARs and CRISPRi leads to a pulse of gene expression. Our results suggest the modularity of the two regulators in an integrated genetic circuit, and we anticipate that construction and modeling frameworks that can leverage this modularity will become increasingly important as synthetic circuits increase in complexity.
Assessing sub-cellular resolution in spatial proteomics experiments
Authors: Gatto Laurent , Breckels Lisa M. , Lilley Kathryn S.
Published: July 2018

The sub-cellular localisation of a protein is vital in defining its function, and a protein’s mis-localisation is known to lead to adverse effect. As a result, numerous experimental techniques and datasets have been published, with the aim of deciphering the localisation of proteins at various scales and resolutions, including high profile mass spectrometry-based efforts. Here, we present a meta-analysis assessing and comparing the sub-cellular resolution of 29 such mass spectrometry-based spatial proteomics experiments using a newly developed tool termed QSep. Our goal is to provide a simple quantitative report of how well spatial proteomics resolve the sub-cellular niches they describe to inform and guide developers and users of such methods.
Real exchange rate undervaluation and sectoral growth in South Africa
Authors: Mazorodze Brian Tavonga , Tewari Dev D.
Published: July 2018

Purpose

The purpose of this paper is to establish the empirical link between real exchange rate (RER) undervaluation and sectoral growth in South Africa between 1984 and 2014.

Design/methodology/approach

The study employs a dynamic panel data approach estimated by the system generalised method of moments technique in a bid to control for endogeneity.

Findings

The authors find a significant positive impact of undervaluation on sectoral growth which increases with capital accumulation. Also, the authors confirm that undervaluation promotes sectoral growth up to a point where further increases in undervaluation retards growth.

Practical implications

The results confirm the importance of policies that keep the domestic currency weaker to foster sectoral growth.

Originality/value

The originality of this paper lies in establishing the impact of exchange rate undervaluation on growth at a sector level in the context of South Africa using a dynamic panel data approach.
Decomposition of efficiency using DEA window analysis
Authors: Shawtari Fekri Ali , Abdelnabi Salem Milad , Bakhit Izzeldin
Published: July 2018

Purpose

The purpose of this paper is to examine empirically the efficiency types of Islamic and conventional banks. It seeks to show whether the efficiency level of conventional and Islamic banks significantly differs from each other. In addition, it investigates the influential factors on each type of efficiency.

Design/methodology/approach

The paper utilises the data envelopment analysis in its windows version to estimate the efficiency scores reflecting the time variance and compares between banking models. The paper uses pure technical efficiency (TE) and scale efficiency to achieve the objective of the study. In addition, the panel data technique is adopted to assess the determinants of the efficiency of the banks econometrically.

Findings

The findings of panel regression initially indicate that the pure TE is higher for conventional banks compared to Islamic banks. However, the Islamic banks are more scale efficient than their conventional counterpart. Macro and micro indicators have different impacts on the both types of efficiency. However, the unique factors that show consistent influence on the efficiency types were loans/finance, non-interest income/finance/liquidity and GDP. Furthermore, the determinants are shaped differently for Islamic and conventional banks when the banking model is controlled for.

Originality/value

This paper examines the efficiency types using a unique window analysis approach to examine the types of efficiency with a longitudinal set of data from 1996 to 2011.
Developing a safety climate factor model in construction research and practice
Authors: Newaz Mohammad Tanvi , Davis Peter Rex , Jefferies Marcus , Pillay Manikam
Published: July 2018

Purpose

Safety climate and its impact on safety performance is well established; however, researchers in this field suggest that the absence of a common assessment framework is a reflection of the state of development of this concept. The purpose of this paper is to propose a five-factor model that can be used to diagnose and measure safety climate in construction safety research and practice.

Design/methodology/approach

A systematic review was adopted, and following Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines, 574 articles were selected at the start of the study based on a developed review protocol for investigating safety climate factors. While examining the factor analysis of different studies, data reliability and data validity of the individual research findings were considered and frequency of factors uploaded was used to determine the significance as a quantitative measure to develop the ranking of safety climate factors.

Findings

The review identified that, from the established measures of safety climate in construction, there is little uniformity on factor importance. However, management commitment safety system role of the supervisor; workers’ involvement and group safety climate were found to be the most common across the studies reviewed. It is proposed these factors are used to inform a five-factor model for investigating safety climate in the construction industry.

Originality/value

The findings of this study will motivate researchers and practitioners in safety to use the five-factor safety climate model presented in this paper and test it to develop a common factor structure for the construction industry. The fact that the model is comprised of five factors makes it easier to be used and implemented by small-to medium-sized construction companies, therefore enhancing its potential use.
Measuring efficiency, effectiveness and overall performance in the Chinese construction industry
Authors: Hu Xiancun , Liu Chunlu
Published: July 2018

Purpose

The purpose of this paper is to develop a simultaneous measurement of overall performance and its two dimensions of efficiency and effectiveness in the case of Chinese construction industry.

Design/methodology/approach

A relational two-stage data envelopment analysis (DEA) method, which builds a relationship between component stages and can effectively identify inefficient stages, is developed and applied in order to measure overall performance, efficiency and effectiveness.

Findings

The construction industry of the Eastern region in China demonstrated the best results for overall performance, efficiency and effectiveness. The gaps between regions were primarily reflected in differences of pure technical efficiency. Performance indicators in the whole construction industry improved steadily and but could be improved more effectively. The coefficients of variation became smaller and more well-balanced across the whole industry.

Practical implications

Improving overall performance should focus on promoting construction efficiency at the project level and increasing management effectiveness at the company level. Sustainable development policies, which may include large investment and preferential policies, can narrow performance differences among the regions’ construction industries, and ultimately promote overall performance for the whole industry.

Originality/value

The relational two-stage DEA model is further developed in a variable returns-to-scale condition. The developed approach is generic and can provide a pathway for simultaneously measuring performance, efficiency and effectiveness and to recognise competitive advantages for promoting sustainable development.
Platform-based service innovation and system design: research opportunities
Authors: Fu Wenhui , Wang Qiang , Zhao Xiande
Published: July 2018

Purpose

The purpose of this paper is to explore research opportunities for service innovation and system design in network platforms by investigating representative case examples in an emerging market, China.

Design/methodology/approach

The authors provide four case examples to illustrate the manner in which network platforms facilitate and lead to service innovation and effective system design. Then, the authors propose nine research directions that present significant research opportunities, and the authors make theoretical and methodological suggestions.

Findings

The results indicate that research opportunities exist mainly in three areas: ecosystem design and evolution, including role design, coherence and sustainability issues; leader–participant collaboration, including governance, co-opetition and innovation stimulation issues; and transformation of traditional industries, including process informatization, modularization and standardization issues.

Originality/value

This study extends the platform-related literature by showing new platform features represented by case evidence from emerging economies, and provides recommendations to guide and direct management practices and efforts in platform-based service innovation and system design.
Portfolio Diversification Strategy Via Tail‐Dependence Clustering and ARMA‐GARCH Vine Copula Approach
Authors: Ji Hao , Wang Hao , Liseo Brunero
Published: July 2018

This study proposes a diversified portfolio construction method based on the tail dependence between the financial assets and adopting both market prior information and the exports’ subject views. In this paper, tail‐dependence clustering was applied to divide candidate assets into different groups according to their tail dependence during the crisis period and the ARMA‐GARCH vine copula‐opinion pooling approach was applied to select the minimum Conditional Value‐at‐Risk portfolio according to the clustering results. The daily closed prices of the components of DAX 20 from 3 January 2006 to 20 December 2014 were studied to illustrate the methodology. The results reveal that more than 90% of 450 possible portfolios are modelled by D‐vine structure and Student's t‐copula dominates almost all the cases for pair copula selection. As Student's t‐copula captures the symmetric tail dependence, the 450 possible portfolios do not show stronger lower tail dependence than upper tail dependence. This study contributes by combining cluster analysis with portfolios selection. It uses vine copula to capture the dependence structure among assets. Finally, it offers a flexible method to describe market and offers a strategy to construct diversified portfolios by adding the investors’ information into portfolio selection procedure at the 1‐day forecast horizon.
What is the relationship between reading prosody and reading comprehension in European Portuguese? Evidence from grades 2 to 5
Authors: Fernandes Sandra , Querido Luís , Verhaeghe Arlette , Araújo Luísa
Published: July 2018

The relevance of reading prosody on reading comprehension has been theoretically proposed and empirically recognised. The present study aimed to investigate longitudinal and concurrent relationships between reading prosody and reading comprehension processes, beyond decoding and word reading efficiency. Two cohorts of Portuguese children, ranging different grade levels (grades 2 to 3 and 4 to 5), were tested. Reading prosody was assessed through a rating scale, and text reading comprehension and context fluency effect were used to measure effortful and effortless reading comprehension processes, respectively. Results showed no bidirectional longitudinal effects between reading prosody and reading comprehension processes. In contrast, they revealed a concurrent contribution of reading prosody to the measure that mainly captures the effortless processes of reading comprehension from grades 2 to 5 but not for effortful ones. Results also highlighted the key role of decoding and word reading efficiency in the relationship between reading prosody and reading comprehension.
Coastal Urban Planning in The ‘Green Republic’: Tourism Development and the Nature–Infrastructure Paradox in Costa Rica
Authors: Irazábal Clara
Published: July 2018

This article examines coastal urban planning in Costa Rica vis‐à‐vis the country's values in the areas of sustainable tourism and community development, focusing on the city of Jacó. I argue that an anti‐urban tourism development strategy, swift coastal urban development and weak planning have nurtured a nature–infrastructure paradox: when people are brought closer to nature without proper urban and governmental infrastructure, this causes social and environmental damage. To assess this paradox and understand local perceptions of development, I analyzed lengthy semi‐structured interviews and survey responses in San José and Jacó in this study. Research methods also encompassed analysis of current tourism planning institutions and regulations, tourism media coverage and reports, real estate data, participant observation of planning and community meetings and activities, and observations of the built and natural environmental conditions in Jacó and its surroundings. The findings show jurisdictional fragmentation, regulatory weaknesses, complexity, poor coordination, slow action, and incoherent planning and development, leading to environmental degradation and socio‐spatial inequities. A more balanced approach to planning and development would seek to improve environmental health and socio‐spatial equity in tandem, by nurturing and advancing both nature and infrastructure development. Lessons from Jacó have global resonance, given the expansion of the worldwide tourism and second‐home/retirement‐housing industries, their recent concentration in urban coastal destinations of developing countries, and the fragility of these socio‐ecological systems.
Enforcing Compulsory Schooling through Credible Coercion: Lessons from Australia's Northern Territory Intervention
Authors: Justman Moshe , Peyton Kyle
Published: July 2018

Australia's Northern Territory Emergency Response and subsequent School Enrolment and Attendance Measure (SEAM) credibly threatened to remove welfare benefits from Indigenous families if their children failed to attend school regularly. A difference‐in‐difference analysis of participation rates in the National Assessment Program – Literacy and Numeracy shows a substantial increase in participation rates the year afterSEAMwas implemented. However, administrators rarely carried out the threatened sanctions, and these initial gains largely dissipated in subsequent years. This unique episode illustrates the limited scope for promoting Indigenous school participation through conditional cash penalties.
Is the Yellow Knight Mushroom Edible or Not? A Systematic Review and Critical Viewpoints on the Toxicity of Tricholoma equestre
Authors: Rzymski Piotr , Klimaszyk Piotr
Published: July 2018

There is no scientific consensus regarding the safety of the Yellow Knight mushroom Tricholoma equestre (L.) P.Kumm. Following reports of cases of intoxication involving effects such as rhabdomyolysis, and supportive observations from in vivo experimental models, T. equestre is considered as a poisonous mushroom in some countries while in others it is still widely collected from the wild and consumed every year. In this paper, we review all the available information on T. equestre including its morphological and molecular characterization, nutritional value, levels of contaminants observed in fruiting bodies, the possibility of mistake with species that are morphologically similar, and the in vivo data on safety and cases of human intoxication. Based on available data, it is suggested that T. equestre cannot be considered as a toxic species and does not appear to exhibit any greater health threat than other mushroom species currently considered as edible. More care should be taken when reporting cases of human poisoning to fully identify T. equestre as the causative agent and to exclude a number of interfering factors. Specific guidelines for reporting future cases of poisoning with T. equestre are outlined in this paper. Any future research involving T. equestre should present the results of molecular phylogenetic analyses.
An Unplanned Complex Suicide by Multiple Blank Cartridge Gunshots and Cutting
Authors: Kučerová Štěpánka , Zátopková Lenka , Vojtíšek Tomáš , Ublová Michaela , Hejna Petr
Published: July 2018

Blank firing guns are readily accessible in most countries due to an absence of legal regulations. These weapons are capable of causing lethal injuries. We report a rare case of secondary (unplanned) complex suicide committed with a knife and blank cartridge pistol. A 59‐year‐old man was found dead with three superficial incisions in his neck and a gunshot wound to the chest. The external examination revealed an entrance wound in the left chest region consistent with contact shooting. The appearance of a muzzle imprint suggested two discharges. The autopsy showed a slightly hemorrhaged but otherwise intact pericardium, blood in the pericardial sac, and a channel‐like defect in the anterior wall of the left cardiac ventricle. The cause of death was attributed to cardiac tamponade. To the best of our knowledge, this is the first reported case of unplanned complex suicide involving an unmodified blank firing gun.