bluuebunny/crossref_metadata_2025 huggingface dataset:
Kinetic Model of Translational Autoregulation
Authors: Tyng Vivian , Kellman Michael E.
Published: October 2018

We investigate dynamics of a kinetic model of inhibitory autoregulation as exemplified when a protein inhibits its own production by interfering with its messenger RNA, known in molecular biology as translational autoregulation. We first show how linear models without feedback set the stage with a nonequilibrium steady state that constitutes the target of the regulation. However, regulation in the simple linear model is far from optimal. The negative feedback mechanism whereby the protein “jams” the mRNA greatly enhances the effectiveness of the control, with response to perturbation that is targeted, rapid, and metabolically efficient. Understanding the full dynamics of the system phase space is essential to understanding the autoregulation process.
The time course of different surround suppression mechanisms
Authors: Schallmo Michael-Paul , Kale Alex M. , Murray Scott O.
Published: October 2018

What we see depends on the spatial context in which it appears. Previous work has linked the reduction of perceived stimulus contrast in the presence of surrounding stimuli to the suppression of neural responses in early visual cortex. It has also been suggested that this surround suppression depends on at least two separable neural mechanisms, one ‘low-level’ and one ‘higher-level,’ which can be differentiated by their response characteristics. In a recent study, we found evidence consistent with these two suppression mechanisms using psychophysical measurements of perceived contrast. Here, we used EEG to demonstrate for the first time that neural responses in the human occipital lobe also show evidence of two separable suppression mechanisms. Eighteen adults (10 female and 8 male) each participated in a total of 3 experimental sessions, in which they viewed visual stimuli through a mirror stereoscope. The first session was used to definitively identify the C1 component, while the second and third comprised the main experiment. ERPs were measured in response to center gratings either with no surround, or with surrounding gratings oriented parallel or orthogonal, and presented either in the same eye (monoptic) or opposite eye (dichoptic). We found that the earliest ERP component (C1; ∼60 ms) was suppressed in the presence of surrounding stimuli, but that this suppression did not depend on surround configuration, suggesting a low-level suppression mechanism which is not tuned for relative orientation. A later response component (N1; ∼160 ms) showed stronger surround suppression for parallel and monoptic stimulus configurations, consistent with our earlier psychophysical results and a higher-level, binocular, orientation-tuned suppression mechanism. We conclude that these two surround suppression mechanisms have distinct response time courses in the human visual system, which can be differentiated using electrophysiology.
View-channel-depth light-field microscopy: real-time volumetric reconstruction of biological dynamics by deep learning
Authors: Wang Zhaoqiang , Zhu Lanxin , Zhang Hao , Li Guo , Yi Chengqiang , Li Yi , Yang Yicong , Ding Yichen , Zhen Mei , Gao Shangbang , Hsiai Tzung K. , Fei Peng
Published: October 2018

Light-field microscopy has emerged as a technique of choice for high-speed volumetric imaging of fast biological processes. However, artefacts, non-uniform resolution, and a slow reconstruction speed have limited its full capabilities for in toto extraction of the dynamic spatiotemporal patterns in samples. Here, we combined a view-channel-depth (VCD) neural network with light-field microscopy to mitigate these limitations, yielding artefact-free three-dimensional image sequences with uniform spatial resolution and three-order-higher video-rate reconstruction throughput. We imaged neuronal activities across moving C. elegans and blood flow in a beating zebrafish heart at single-cell resolution with volume rates up to 200 Hz.
A novel localization based biosensor, SEDAR, visualizes spatio-temporal dynamics of activated Ras in endogenousDrosophilatissues
Authors: Changede Rishita
Published: October 2018

Chemokine signaling via growth factor receptor tyrosine kinases (RTKs) regulates development, differentiation, growth and disease implying that it is involved in a myriad of cellular processes. A single RTK, for example the Epidermal Growth Factor Receptor (EGFR), is used repeatedly for a multitude of developmental programs. Quantitative differences in magnitude and duration of RTK signaling can bring about different signaling outcomes. Understanding this complex RTK signals requires real time visualization of the signal. To visualize spatio-temporal signaling dynamics, a biosensor calledSEnsitiveDetection ofActivatedRas (SEDAR) was developed. It is a localization-based sensor that binds to activated Ras directly downstream of the endogenous activated RTKs. This binding was reversible and SEDAR expression did not cause any detectable perturbation of the endogenous signal. Using SEDAR, endogenous guidance signaling was visualized during RTK mediated chemotaxis of border cells inDrosophilaovary. SEDAR localized to both the leading and rear end of the cluster but polarized at the leading edge of the cluster. Perturbation of RTKs that led to delays in forward migration of the cluster correlated with loss of SEDAR polarization in the cluster. Gliding or tumbling behavior of border cells was a directly related to the high or low magnitude of SEDAR polarization respectively, in the leading cell showing that signal polarization at the plasma membrane provided information for the migratory behavior. Further, SEDAR localization to the plasma membrane detected EGFR mediated signaling in five distinct developmental contexts. Hence SEDAR, a novel biosensor could be used as a valuable tool to study the dynamics of endogenous Ras activation in real time downstream of RTKs, in three-dimensional tissues, at an unprecedented spatial and temporal resolution.
Impact of temperature and photoperiod on survival and biomarkers of senescence in common woodlouse
Authors: Depeux Charlotte , Samba-Louaka Ascel , Braquart-Varnier Christine , Moreau Jérôme , Lemaître Jean-François , Laverre Tiffany , Pauhlac Hélène , Dechaume-Moncharmont François-Xavier , Gaillard Jean-Michel , Beltran-Bech Sophie
Published: October 2018

Most living organisms display a decline in physiological performances when ageing, a process called senescence that is most often associated with increased mortality risk. Previous researches have shown that both the timing and the intensity of senescence vary a lot within and among species, but the role of environmental factors in this variation is still poorly understood. To fill this knowledge gap, we investigated the impact of environmental conditions on the strength of senescence using an experimental design applied to a population of common woodlouseArmadillidium vulgareintensively monitored in the lab. Cellular senescence biomarkers are available in woodlouse and are age-related. These biomarkers provide relevant biomarkers to test the impact of environmental conditions, through changes in temperature and photoperiod, on individuals of the same age maintained in different environmental conditions. We found different effects of the environmental changing: the increasing of day light modification leaded the same effect as age on our senescence biomarkers while temperature modifications leaded the opposite effect as age on the β-galactosidase activity and cell size. We also demonstrated the existence of sex-specific responses to changes in environmental conditions. By using an experimental approach and biomarkers of senescence in woodlouse, we show that environmental conditions and sex both shape the diversity observed in senescence patterns of woodlouse and underline the importance of identifying senescence biomarkers to understand how environmental conditions influence the evolution of senescence.
Behavioural and neural signatures of perceptual evidence accumulation are modulated by pupil-linked arousal
Authors: van Kempen Jochem , Loughnane Gerard M. , Newman Daniel P. , Kelly Simon P. , Thiele Alexander , O’Connell Redmond G , Bellgrove Mark A.
Published: October 2018

The timing and accuracy of perceptual decision making is exquisitely sensitive to fluctuations in arousal. Although extensive research has highlighted the role of neural evidence accumulation in forming decisions, our understanding of how arousal impacts these processes remains limited. Here we isolated electrophysiological signatures of evidence accumulation alongside signals reflecting target selection, attentional engagement and motor output and examined their modulation as a function of both tonic and phasic arousal, indexed by baseline and task-evoked pupil diameter, respectively. For both pupillometric measures, the relationship with reaction time was best described by a second-order, U-shaped, polynomial. Additionally, the two pupil measures were predictive of a unique set of EEG signatures that together represent multiple information processing steps of perceptual decision-making, including evidence accumulation. Finally, we found that behavioural variability associated with fluctuations in both tonic and phasic arousal was largely mediated by variability in evidence accumulation.
Response outcomes gate the impact of expectations on perceptual decisions
Authors: Hermoso-Mendizabal Ainhoa , Hyafil Alexandre , Rueda-Orozco Pavel E. , Jaramillo Santiago , Robbe David , de la Rocha Jaime
Published: October 2018

Perceptual decisions are not only determined by current sensory information but are also influenced by expectations based on recent experiences. Can the impact of these expectations be flexibly modulated based on the outcome of previous decisions? We trained rats in several two-alternative forced choice auditory tasks, where the probability to repeat the previous stimulus category was varied in blocks of trials. All rats capitalized on the serial correlations of the stimulus sequence by consistently exploiting atransition bias:a tendency to repeat or alternate their previous response using an internal trial-by-trial estimate of the sequence repeating probability. Surprisingly, this bias was null in trials immediately following an error. The internal estimate however was not reset and it became effective again causing a bias after the next correct response. This ability to rapidly activate and inactivate the bias was captured by a non-linear generative model of rat behavior, whereby a reward-driven modulatory signal gated the use of the latent estimate of the environment statistics on the current decision. These results demonstrate that, based on the outcome of previous choices, rats flexibly modulate how expectations influence their current decisions.
Membrane-cytoskeleton mechanical feedback mediated by myosin-I controls phagocytic efficiency
Authors: Barger Sarah R. , Reilly Nicholas S. , Shutova Maria S. , Li Qingsen , Maiuri Paolo , Mooseker Mark S. , Flavell Richard A. , Svitkina Tatyana , Oakes Patrick W. , Krendel Mira , Gauthier Nils
Published: October 2018

Phagocytosis of invading pathogens or cellular debris requires a dramatic change in cell shape driven by actin polymerization. For antibody-covered targets, phagocytosis is thought to proceed through the sequential engagement of Fc-receptors on the phagocyte with antibodies on the target surface, leading to the extension and closure of the phagocytic cup around the target. We have found that two actin-dependent molecular motors, class 1 myosins myosin 1e and myosin 1f, are specifically localized to Fc-receptor adhesions and required for efficient phagocytosis of antibody-opsonized targets. Using primary macrophages lacking both myosin 1e and myosin 1f, we found that without the actin-membrane linkage mediated by these myosins, the organization of individual adhesions is compromised, leading to excessive actin polymerization, slower adhesion turnover, and deficient phagocytic internalization. This work identifies a novel role for class 1 myosins in coordinated adhesion turnover during phagocytosis and supports a model for a membrane-tension based feedback mechanism for phagocytic cup closure.
RNA polymerases display collaborative and antagonistic group behaviors over long distances through DNA supercoiling
Authors: Kim Sangjin , Beltran Bruno , Irnov Irnov , Jacobs-Wagner Christine
Published: October 2018

Transcription by RNA polymerases (RNAPs) is essential for cellular life. Genes are often transcribed by multiple RNAPs. While the properties of individual RNAPs are well appreciated, it remains less explored whether group behaviors can emerge from co-transcribing RNAPs under most physiological levels of gene expression. Here, we provide evidence inEscherichia colithat well-separated RNAPs can exhibit collaborative and antagonistic group dynamics. Co-transcribing RNAPs translocate faster than a single RNAP, but the density of RNAPs has no significant effect on their average speed. When a promoter is inactivated, RNAPs that are far downstream from the promoter slow down and experience premature dissociation, but only in the presence of other co-transcribing RNAPs. These group behaviors depend on transcription-induced DNA supercoiling, which can also mediate inhibitory dynamics between RNAPs from neighboring divergent genes. Our findings suggest that transcription on topologically-constrained DNA, a norm across organisms, can provide an intrinsic mechanism for modulating the speed and processivity of RNAPs over long distances according to the promoter’s on/off state.
Unsupervised deep learning with variational autoencoders applied to breast tumor genome-wide DNA methylation data with biologic feature extraction
Authors: Titus Alexander J. , Wilkins Owen M. , Bobak Carly A. , Christensen Brock C.
Published: October 2018

Recent advances in deep learning, particularly unsupervised approaches, have shown promise for furthering our biological knowledge through their application to gene expression datasets, though applications to epigenomic data are lacking. Here, we employ an unsupervised deep learning framework with variational autoencoders (VAEs) to learn latent representations of the DNA methylation landscape from three independent breast tumor datasets. Through interrogation of methylation-based learned latent dimension activation values, we demonstrate the feasibility of VAEs to track representative differential methylation patterns among clinical subtypes of tumors. CpGs whose methylation was most correlated VAE latent dimension activation values were significantly enriched for CpG sparse regulatory regions of the genome including enhancer regions. In addition, through comparison with LASSO, we show the utility of the VAE approach for revealing novel information about CpG DNA methylation patterns in breast cancer.
Erythrocyte indices, anaemia levels and types in Kenyan injection and non-injection substance users
Authors: Mulaya Khazalwa Emmanuel , Were Tom , Hughes Mulama David , Budambula Valentine
Published: October 2018

The impact of injection and non-injection substance use in HIV infections is an area of great public importance especially with respect to hematologic and immune profiles. Evaluations of hematologic and immune status are critical for better disease classification and clinical management especially of HIV positive substance users. However, not much information is known about the hematologic and immune derangements in HIV infected injection and non-injection substance users. This study, therefore, aimed at determining the laboratory markers of hematologic and immune derangements in HIV infected substance users. Hematologic and immune profiles were evaluated on venous blood specimens obtained from injection substance users, ISU (HIV-infected, n=62 and -uninfected, n=213) and non-injection substance users (HIV-infected, n=33 and -uninfected, n=186); and non-substance using controls (n=56) from Mombasa, coastal town of Kenya. The prevalence of anemia was higher in HIV infected ISU (48.4%) and non-ISU (63.6%) (p<0.0001); and HIV uninfected ISUs (56.3%) compared to HIV-uninfected non-ISUs (39.2%) and non-substance using controls (28.6%; p=0.0028). Hypochromic anaemia was more prevalent in the HIV-infected ISU (50.0%) and non-ISU (61.9%), and HIV-negative ISU (63.3%) relative to the HIV-negative non-ISU (39.7%) and non-substance using controls (56.3%; p=0.0007). Mild immunodeficiency dominated in the HIV infected individuals (HIV-infected ISU, 32.3% and non-ISU, 21.2%) versus HIV-uninfected ISU (16.9%); non-ISU (12.9%); and non-substance users (14.3%) while severe immunosuppression prevailed in HIV infected substance users (ISU, 14.5% and non-ISU, 15.2%) against HIV uninfected substance users (ISU, 5.2% and non-ISU, 3.8%); thus immunosuppression in substance users is aggravated with HIV infection. Moreover, drug-induced immunosuppression is associated with a higher likelihood of anaemia in HIV-uninfected substance users; ISU (OR=3.95, CI=1.934-8.077, p<0.0001) and non-ISU (OR=3.63, CI=1.571-8.39, p=0.003). Altogether, hypochromic anaemia, normochromic anaemia and CD4+ T-helper cytopenia are the most prevalent hemocytopenias in HIV infected and uninfected injection and non-injection substance users.
Within-subject Consistency of Paired Associative Stimulation as Assessed by Linear Mixed Models
Authors: Ottenhoff Myrthe Julia , Fani Lana , Erler Nicole Stephanie , Castricum Jesminne , Obdam Imara Fedora , der Vaart Thijs van , Kushner Steven Aaron , de Wit Marie-Claire Yvette , Elgersma Ype , Tulen Joke H.M.
Published: October 2018

Paired associative stimulation (PAS) is a frequently used TMS paradigm that induces long-term potentiation in the human cortex. However, little is known about the within-subject consistency of PAS-induced effects. We determined PAS-induced effects and their consistency in healthy volunteers between two PAS sessions. Additionally, we assessed the benefit of applying linear mixed models (LMMs) to PAS data. Thirty-eight healthy volunteers underwent two identical PAS sessions with a >1 week interval. During each session, motor evoked potentials (MEPs) were assessed once before PAS induction and 3 times after at 30 min intervals. We did not detect any significant potentiation of MEP size after PAS induction. However, MEP size during PAS induction showed significant potentiation over time in both sessions (LR(1)=13.36, p<0.001). Nevertheless, there was poor within-subject consistency of PAS-induced effects both during (ICC=0.15) and after induction (ICC=0.04-0.09). Additionally, statistical model selection procedures demonstrate that a LMM with an unstructured covariance matrix better estimated PAS-induced effects than one with a conventional compound symmetry matrix (LR(34)=214.73, p<0.001). While our results are supportive of a high intra-individual variability of PAS-induced effects, the generalizability of our results is unclear, as we were only partially successful in replicating results from previous PAS studies typically showing potentiation of MEPs during and after PAS induction. We do, however, demonstrate that linear mixed models can improve the reliability of PAS-induced effects estimation.
Arrhythmia Mechanisms and Spontaneous Calcium Release: II - From Calcium Spark to Re-entry and Back
Authors: Colman Michael A.
Published: October 2018

Motivation

The role of sub-cellular spontaneous calcium release events (SCRE) in the development of arrhythmia associated with atrial and ventricular tachycardia and fibrillation has yet to be investigated in detail. SCRE may underlie the emergence of spontaneous excitation in single cells, resulting in arrhythmic triggers in tissue. Furthermore, they can promote the substrate for conduction abnormalities. However, the potential interactions with re-entrant excitation have yet to be explored. The primary aim of this study was therefore to apply a novel computational approach to understand the multi-scale coupling between re-entrant excitation and SCRE.

Methods

A general implementation of Spontaneous Release Functions - which reproduce the calcium dependent SCRE dynamics of detailed cell models at a significantly reduced computational cost - was used to reproduce SCRE in tissue models. Arrhythmic dynamics, such as rapid pacing and re-entry, were induced in the tissue models and the resulting interactions with SCRE were analysed.

Results

In homogeneous tissue, the emergence of a spontaneous beat from a single source was observed and the positive role of coupling was demonstrated. Conduction block could be promoted by SCRE by both inactivation of the fast sodium channel as well as focal pacing heterogeneity interactions. Sustained re-entrant excitation promoted calcium overload, and led to the emergence of focal excitations both after termination of re-entry and also during re-entrant excitation. These results demonstrated a purely functional mechanism of re-entry and focal activity localisation, related to the unexcited spiral wave core.

Conclusions

SCRE may interact with tissue excitation to promote and perpetuate arrhythmia through multiple mechanisms, including functional localisation and mechanism switching. These insights may be particularly relevant for successful pharmacological management of arrhythmia.
Arrhythmia Mechanisms and Spontaneous Calcium Release: I - Multi-scale Modelling Approaches
Authors: Colman Michael A.
Published: October 2018

Motivation

Spontaneous sub-cellular calcium release events (SCRE), controlled by microscopic stochastic fluctuations of the proteins responsible for intracellular calcium release, are conjectured to promote the initiation and perpetuation of rapid arrhythmia associated with conditions such as heart failure and atrial fibrillation: SCRE may underlie the emergence of spontaneous excitation in single cells, resulting in arrhythmic triggers in tissue. However, translation of single-cell data to the tissue scale is non-trivial due to complex substrate considerations. Computational modelling provides a viable approach to dissect these multi-scale mechanisms, yet there remains a significant challenge in accurately and efficiently modelling this probabilistic behaviour in large-scale tissue models. The aim of this study was to develop an approach to overcome this challenge.

Methods

The dynamics of SCRE under multiple conditions (pacing rate, beta-stimulation, disease remodelling) in a computational model of stochastic, spatio-temporal calcium handling were analysed in order to develop Spontaneous Release Functions, which capture the variability and properties of SCRE matched to the full cell model. These functions were then integrated with tissue models, comprising idealised 2D sheets as well as full reconstructions of ventricular and atrial anatomy.

Results

The Spontaneous Release Functions accurately reproduced the dynamics of SCRE and its dependence on environment variables under multiple different conditions observed in the full single-cell model. Differences between cellular models and conditions where enhanced at the tissue scale, where the emergence of a focal excitation is largely an all-or-nothing response. Generalisation of the approaches was demonstrated through integration with an independent cell model, and parameterisation to an experimental dataset.

Conclusions

A novel approach has been developed to dynamically model SCRE at the tissue scale, in-line with behaviour observed in detailed single-cell models. Such an approach allows evaluation of the potential importance of SCRE in arrhythmia in both general mechanistic and disease-specific investigation.
Comprehensive proteomic and metabolomic profiling of mcr-1 mediated colistin resistance in Escherichia coli
Authors: Li Hui , Wang Yingyu , Meng Qingshi , Wang Yang , Xia Guoliang , Xia Xi , Shen Jianzhong
Published: October 2018

The spread of mcr-1 in human and veterinary medicine has jeopardized the use of polymyxins, the last-resort antibiotics against life-threatening multidrug-resistant Gram-negative bacteria. As a lipid-modified gene, whether mcr-1 brings proteomic and metabolomic changes in the bacteria and affects the corresponding metabolic pathway is largely unknown. Herein, we used label-free quantitative proteomics and untargeted metabolomics to profile comprehensive proteome and metabolome characteristics of mcr-1-mediated colistin-resistant and -sensitive Escherichia coli and further insight the resistant mechanism of colistin. We identified large sets of differential expression proteins and metabolites that contributed to mcr-1-mediated antibiotic resistance predominantly in the different growth conditions with and without colistin. mcr-1 could cause the down-regulated expression of most proteins to adapt drug pressure. Pathway analysis showed that metabolic process was significantly affected, mainly related to glycerophospholipid metabolism, thiamine metabolism, and lipopolysaccharide biosynthesis. The substrate phosphatidylethanolamine for mcr-1 to mediate colistin resistance is accumulated in colistin-resistant E. coli. Notably, mcr-1 can not only cause the phosphoethanolamine modification of bacterial cell membrane lipid A, but also affect the biosynthesis and transport of lipoprotein in colistin resistance through disturbing the expression of efflux pump proteins involved in cationic antibacterial peptide resistance pathway. Overall, the disturbed glycerophospholipid metabolism, lipopolysaccharide biosynthesis and the accumulation of the substrate phosphatidylethanolamine is closely related with mcr-1-mediated colistin resistance and these findings can further provide valuable information to inhibit colistin resistance by blocking this metabolic process.
Schlafen 11 Restricts Flavivirus Replication
Authors: Valdez Federico , Salvador Julienne , Palermo Pedro , Mohl Jonathon E. , Hanley Kathryn A. , Watts Douglas , Llano Manuel
Published: October 2018

Schlafen 11 (Slfn11) is a ubiquitously expressed interferon stimulating gene (ISG) that controls synthesis of proteins by regulating tRNA abundance. Likely through this mechanism, Slfn11 has previously been shown to impair human immunodeficiency virus 1 (HIV-1) infection and the expression of codon-biased open reading frames. Because replication of positive-sense single-stranded RNA [(+)ssRNA viruses] requires the immediate translation of the incoming viral genome whereas negative sense, single stranded [(−)ssRNA] viruses carry at infection an RNA replicase that makes multiple translation competent copies of the incoming viral genome, we reasoned that (+)ssRNA viruses will be more sensitive to the effect of Slfn11 on protein synthesis than (−)ssRNA viruses. To evaluate this hypothesis, we tested the effects of Slfn11 on the replication of a panel of ssRNA viruses in the human glioblastoma cell line A172, which naturally expresses Slfn11. Depletion of Slfn11 in this cell line significantly increased the replication of (+)ssRNA viruses from theFlavivirus family, including West Nile (WNV), dengue (DENV), and Zika virus (ZIKV) but had no significant effect on the replication of the (−)ssRNA viruses vesicular stomatitis (VSV,Rhabdoviridae family) and Rift Valley fever (RVFV,Phenuiviridae family). Despite that WNV titers in Slfn11-deficient cells were almost 100-fold higher than in cells expressing this protein; they produced approximately two-fold less viral particles, as determined by PCR-based quantification of virion-associated WNV RNA in the cell culture supernatant. These data indicated that Slfn11 impairs WNV fitness but does not affect other steps of the viral life cycle including entry, viral RNA replication and translation, and budding. Similarly to the proposed anti-HIV-1 mechanism of Slfn11, this protein prevented WNV-induced down-regulation of a subset of tRNAs implicated in the translation of 19% of the viral polyprotein. Importantly, we provided evidence suggesting that the broad anti-viral activity of Slfn11 requires other cellular proteins, since overexpression of Slfn11 in cells that naturally lack the expression of this protein, did not impair WNV or HIV-1 infection. In summary, this study demonstrates that Slfn11 restricts flaviviruses replication by impairing viral fitness.

AUTHOR SUMMARY

The host targets mechanisms that viruses have evolved to optimize replication. We provide evidence that the cellular protein Schlafen 11 (Slf11) impairs replication of flaviviruses, including West Nile (WNV), dengue (DENV), and Zika virus (ZIKV). However, replication of single-stranded, negative RNA viruses was not affected. Specifically, Slf11 decreases the fitness of WNV potentially by preventing virus-induced modifications of the host tRNA repertoire that could lead to enhanced viral protein folding. Furthermore, we demonstrated that Slf11 is not the limiting factor of this novel broad anti-viral pathway.
Microbial dormancy improves predictability of soil respiration at the seasonal time scale
Authors: Salazar A. , Lennon J.T. , Dukes J.S
Published: October 2018

Climate change is accelerating global soil respiration, which could in turn accelerate climate change. The biological mechanisms through which soil carbon (C) responds to climate are not well understood, limiting our ability to predict future global soil respiration rates. As part of a climate manipulation experiment, we tested whether differences in soil heterotrophic respiration driven by season or climate treatment (RH) are linked to 1) relative abundances of microbes in active and dormant metabolic states, 2) net changes in microbial biomass and/or 3) changes in the relative abundances of microbial groups with different C-use strategies. We used a flow-cytometric single-cell metabolic assay to quantify the abundance of active and dormant microbes, and the phospholipid fatty acid (PLFA) method to determine microbial biomass and ratios of fungi:bacteria and Gram-positive:Gram-negative bacteria. RH did not respond to climate treatments but was greater in the warm and dry summer than in the cool and less-dry fall. These dynamics were better explained when microbial data were taken into account compared to when only physical data (temperature and moisture) were used. Overall, our results suggest that RH responses to temperature are stronger when soil contains more active microbes, and that seasonal patterns of RH can be better explained by shifts in microbial activity than by shifts in the relative abundances of fungi and Gram-positive and Gram-negative bacteria. These findings contribute to our understanding of how and under which conditions microbes influence soil C responses to climate.
Emerging countries’ dilemmas in multilateral frameworks: the case of the Japanese “miracle”
Authors: Shibata Shigeki
Published: October 2018

Purpose

Regardless of economic interdependence, there is possibility that two countries occasionally have severe international stress. This is especially true between rising and ruling countries, which is referred to as “Thucydides’s Trap.” In order to analyze how a rising country can manage its growing presence in the world, the purpose of this paper is to examine the case of Japan as a rising power in the past.

Design/methodology/approach

There seem to be similarities between the “Japan problem” and the “China problem” such as the economic ascendance of a rising country and the failures of American leadership in spite of different time periods. Thus, analyzing Japan’s experience in the past can help understand how the growing international presence of a rising country can be managed.

Findings

When Japan created international economic policies, it aimed for the following three effects: for its trade liberalization to reduce western countries’ restrictions on its export products, for its economic assistance to contribute to developing countries’ stabilization and for its trade liberalization and its economic assistance to contribute to promoting its international trade and upgrading its international status. To accommodate an emerging country into the international system smoothly, not only the country itself but also others require comprehensive measures while considering policy interactions.

Originality/value

Most previous studies that analyze the relationship between a rising and a ruling country examine conflicts between the two parties from a bilateral perspective. However, since the conflicts do not only involve the two countries, but also other countries in the world, it is important to consider how the two countries and other affected countries manage the growing presence of a rising power. Therefore, this paper aims to analyze how an emerging country integrates itself into the existing international system from a multilateral perspective based on the case of Japan.
Economy-wide impact of drought induced productivity losses
Authors: Kilimani Nicholas , van Heerden Jan , Bohlmann Heinrich , Roos Louise
Published: October 2018

Purpose

The purpose of this paper is to investigate how a drought which initially affects agricultural productivity can ultimately affect an entire economy. The study aims to assess the magnitude of the impact as well as highlight key issues that can inform the implementation of drought mitigation programmes.

Design/methodology/approach

The paper presents the literature on the economic impact of drought and uses a computable general equilibrium model where productivity shocks are applied to the agricultural industries following which the resulting impacts on the rest of the sectors of the economy are obtained.

Findings

The findings show that the key macroeconomic variables, namely, real GDP, industry output, employment, the trade balance and household consumption are negatively affected by the drought shock.

Practical implications

The results point to the fact that in the absence of drought mitigation mechanisms, the occurrence of even a short drought as modelled in this paper can impose substantial socioeconomic losses.

Originality/value

First, a general equilibrium framework which uses climate and economic data when evaluating the social-economic impacts of drought is used. Most studies employ partial equilibrium analysis in analysing drought impacts on specific sectors or crops within a limited geographical area. Others use global or multi-regional models which impose averages on the observed impacts. The current study provides valuable insights on the potential damage which droughts can impose on a single economy. This gives a basis for decision making to support drought mitigation policies and programmes.
Developing organizational capabilities to deliver lean and green project outcomes using BIM
Authors: Ahuja Ritu , Sawhney Anil , Arif Mohammed
Published: October 2018

Purpose

The purpose of this paper is to describe the process through which an organization develops organizational capabilities by tapping the technical skills and social skills of its employees in the use of Building Information Modeling (BIM) to deliver lean and green project outcomes. The resulting framework for BIM-based organizational capabilities development comprising of three hierarchical layers – technology, process and outcomes – is explained.

Design/methodology/approach

For this study, BIM has been identified as an enabler and a process for achieving lean and green outcomes on construction projects. Based on a detailed literature review, this paper identifies the organizational capabilities needed by the architecture, engineering and construction organizations to effectively implement BIM on construction projects. The study has been conducted through a sequential mixed-method approach involving semi-structured interviews, focus groups and qualitative comparative analyses.

Findings

It was discovered that to attain desired project outcomes, an organization needs to embrace an underlying BIM adoption culture not only within its project teams but also within the organization as a whole. The study also concluded that an integrated approach to BIM usage – connecting it with lean and green initiatives – on construction projects resulted in improved project outcomes, especially ones targeting lean and green aspects of improvements.

Practical implications

The proposed outline for BIM-based organizational capabilities will help the organizations focus on the “human factors” along with the technical factors while striving for successful usage within their organizations.

Originality/value

Using the organizational capabilities matrix, this paper highlights the importance of technical and social skill sets of an individual employee and their role in developing the organizational capabilities to gain the desired lean and green outcomes.
Multinational contracting and the eclectic paradigm of internationalization
Authors: Rahman Azmeri , Bridge Adrian J. , Rowlinson Steve , Hubbard Bryan , Xia Bo
Published: October 2018

Purpose

The purpose of this paper is to present a novel version of Dunning’s eclectic paradigm of internationalisation (OLI framework) to explain both inbound and outbound Foreign Direct Investment (FDI) in multinational contracting.

Design/methodology/approach

The OLI factors and hypothesis are significantly developed to address a weakness in the OLI framework in its application to settings, such as multinational contracting, with extreme heterogeneity arising from extreme location specificity.

Findings

These developments advance Dunning’s seminal contribution and bring this to life in construction research that has barely applied the framework and, when doing so, has focused only on outbound FDI by multinational contractors (MCs).

Research limitations/implications

The power of the OLI framework is increased on explaining and predicting FDI in contexts that exhibit extreme heterogeneity associated with extreme location specificity. Furthermore, the operationalisation of key theories representing the framework’s OLI factors is made far more precise.

Practical implications

Engineering, construction and architectural managers, can now more reliably apply the OLI framework both in MCs’ outbound FDI decisions and in governments’ decisions to attract new MCs – or inbound FDI.

Originality/value

A significant advance is made in the OLI framework in settings with extreme location specificity, along with the operationalisation of key theories associated with the OLI factors, including the first steps to operationalise Coase’s Nobel prize-winning transaction cost thesis.
Review of methods for evaluating adaptability of buildings
Authors: Rockow Zoraya Roldán , Ross Brandon , Black Anna K.
Published: October 2018

Purpose

The purpose of this paper is to present a review of existing models and tools for evaluating the adaptability of buildings. A baseline of the current state of the art in adaptability evaluation and adaptation decision support is established; from this baseline, gaps for future research are recommended.

Design/methodology/approach

A literature review was conducted to identify papers describing adaptability models and tools. The identified models were characterized based on their focus (new buildings, existing buildings, building life cycle), considered variables (physical and/or context features) and degree/type of validation.

Findings

Models can be grouped as those focusing on: evaluating adaptation decisions for existing buildings; the design of new buildings for future adaptation; and understanding adaptation throughout a building life cycle. Models focusing on existing building evaluation are further in development and validation than the other model types; as such, they are more suitable for use by practitioners. Another finding is that modeling of adaptability in buildings is still in its nascent stage and that data-driven quantitative modeling is a prime area for future research.

Originality/value

This paper is the first comprehensive review of models and tools for evaluating adaptability. Other works have evaluated the topic of adaptability more broadly, but this is the first paper to systematically characterize existing models and tools. Based on the review future, research topics are recommended.
Critical links detection in stochastic networks: application to the transport networks
Authors: Guettiche Mourad , Kheddouci Hamamache
Published: October 2018

Purpose

The purpose of this paper is to study a multiple-origin-multiple-destination variant of dynamic critical nodes detection problem (DCNDP) and dynamic critical links detection problem (DCLDP) in stochastic networks. DCNDP and DCLDP consist of identifying the subset of nodes and links, respectively, whose deletion maximizes the stochastic shortest paths between all origins–destinations pairs, in the graph modeling the transport network. The identification of such nodes (or links) helps to better control the road traffic and predict the necessary measures to avoid congestion.

Design/methodology/approach

A Markovian decision process is used to model the shortest path problem under dynamic traffic conditions. Effective algorithms to determine the critical nodes (links) while considering the dynamicity of the traffic network are provided. Also, sensitivity analysis toward capacity reduction for critical links is studied. Moreover, the complexity of the underlying algorithms is analyzed and the computational efficiency resulting from the decomposition operation of the network into communities is highlighted.

Findings

The numerical results demonstrate that the use of dynamic shortest path (time dependency) as a metric has a significant impact on the identification of critical nodes/links and the experiments conducted on real world networks highlight the importance of sensitive links to dynamically detect critical links and elaborate smart transport plans.

Research limitations/implications

The research in this paper also revealed several challenges, which call for future investigations. First, the authors have restricted our experimentation to a small network where the only focus is on the model behavior, in the absence of historical data. The authors intend to extend this study to very large network using real data. Second, the authors have considered only congestion to assess network’s criticality; future research on this topic may include other factors, mainly vulnerability.

Practical implications

Taking into consideration the dynamic and stochastic nature in problem modeling enables to be effective tools for real-time control of transportation networks. This leads to design optimized smart transport plans particularly in disaster management, to improve the emergency evacuation effeciency.

Originality/value

The paper provides a novel approach to solve critical nodes/links detection problems. In contrast to the majority of research works in the literature, the proposed model considers dynamicity and betweenness while taking into account the stochastic aspect of transport networks. This enables the approach to guide the traffic and analyze transport networks mainly under disaster conditions in which networks become highly dynamic.
Improving distribution and business performance through lean warehousing
Authors: Abushaikha Ismail , Salhieh Loay , Towers Neil
Published: October 2018

Purpose

Recent literature recognizes the role of warehouses in enhancing the overall logistics performance. Thus, lean thinking has recently found its way in supporting warehouse and distribution centre operations. The purpose of this paper is to examine the relationships among warehouse waste reduction practices, warehouse operational performance, distribution performance and business performance.

Design/methodology/approach

A two-stage study was conducted. First, a Delphi technique was adopted to develop a relevant questionnaire. Second, this questionnaire was used to measure the degree of waste reduction in the different warehouse activities and to test the developed research hypotheses. The authors test the hypotheses with a sample of Middle Eastern warehouse operators.

Findings

There exists a positive relationship between warehouse waste reduction level and both warehouse operational performance and distribution performance. There was no direct relationship between warehouse waste reduction level and business performance. However, results revealed that the relationship between warehouse waste reduction level and business performance was mediated by warehouse operational performance and distribution performance.

Practical implications

The developed instrument provides a guide for logistics managers as to understand how to reduce waste in each warehousing activity. The results also inform logistics managers of how distribution performance can be improved through lean warehousing. The resulting performance improvements in the distribution operations will ultimately be reflected in the logistics performance of downstream retailers.

Originality/value

The study develops an original instrument for measuring waste reduction in warehouses, and provides insights into the evolving lean warehousing research area. This is the first scholarly work to uncover the relationships among warehouse waste reduction practices, warehouse operational performance, distribution performance and business performance.
Credit unions, co-operatives, sustainability and accountability in a time of change
Authors: Kleanthous Akis , Paton Robert A. , Wilson Fiona M.
Published: October 2018

Purpose

The financial crisis of 2008 resulted in calls for change. Commentators suggested that co-operatives, in particular credit unions, could provide accountability and sustainability through their open governance and mutual status. However, such suggestions assumed that co-operative principles and practice continued to underpin the efficacy of co-operative banking, and that credit unions, one of the most prevalent forms of co-operative banking, could offer a viable financial alternative. Instead, in the case of Cyprus, the financial crisis and the associated aftershocks triggered the nationalisation and demutualisation of credit unions. This prompted the researchers to question both the viability of a co-operative banking future and the extent to which co-operative principles were shaping decision making, governance, accountability and sustainability. The paper aims to discuss these issues.

Design/methodology/approach

A case study approach was adopted to explore the degree to which co-operative principles still shaped credit union thinking and stakeholder relationships.

Findings

As is the case elsewhere within the co-operative movement, the findings point the fact that governance is weaken by the low membership participation and that the principles are no longer universally applied. Credit unions, if not co-operative banking, may not offer the financial assurances that commentators have called for. Moreover, the guiding principles may no longer be embedded within the fabric of the movement.

Practical implications

Findings are important for practitioners/supervisory body as they highlight possible impacts on co-operative’ future and especially on their governance model and level of autonomy and independence in case of state intervention.

Originality/value

The research undertaken is original as it is the first time credit unions in Cyprus were examined for adherence to co-operative principles.