Abstract
Summary
pyTFA and matTFA are the first published implementations of the original TFA paper. Specifically, they include explicit formulation of Gibbs energies and metabolite concentrations, ...which enables straightforward integration of metabolite concentration measurements.
Motivation
High-throughput analytic technologies provide a wealth of omics data that can be used to perform thorough analyses for a multitude of studies in the areas of Systems Biology and Biotechnology. Nevertheless, most studies are still limited to constraint-based Flux Balance Analyses (FBA), neglecting an important physicochemical constraint: thermodynamics. Thermodynamics-based Flux Analysis (TFA) in metabolic models enables the integration of quantitative metabolomics data to study their effects on the net-flux directionality of reactions in the network. In addition, it allows us to estimate how far each reaction operates from thermodynamic equilibrium, which provides critical information for guiding metabolic engineering decisions.
Results
We present a Python package (pyTFA) and a Matlab toolbox (matTFA) that implement TFA. We show an example of application on both a reduced and a genome-scale model of E. coli., and demonstrate TFA and data integration through TFA reduce the feasible flux space with respect to FBA.
Availability and implementation
Documented implementation of TFA framework both in Python (pyTFA) and Matlab (matTFA) are available on www.github.com/EPFL-LCSB/.
Supplementary information
Supplementary data are available at Bioinformatics online.
The opportunistic behavior of parties in the supply chain leads to resource wastages. Information asymmetry and the opportunistic behavior of transacting parties in supply chains squanders the ...intended benefits of supply chain integration (SCI). Literature suggests that reducing information asymmetry between transacting organizations will curb their opportunistic behavior. This study investigates the SCI between the hauliers and the container depots. The hauliers provide the transportation of containers for the shippers and consignees to and from the depots. Transaction Cost Economics (TCE) underpins the conceptual framework. The supply environment which embodies transaction cost economics attributes is expected to affect SCI and SCI is expected to affect operational efficiency and subsequently environmental performance. Business process is anticipated to moderate the impact of SCI on operational efficiency by reducing information asymmetry and curbing opportunistic behavior. Responses from 84 haulier companies were analyzed using partial least squares, structural equation modeling. Results indicate strong support for almost all transaction cost economics propositions. However, transaction cost economics suggests that transaction attributes have a linear relationship with SCI, though findings from this study indicate that it could be curvilinear. Results confirm that strengthening of business process between hauliers and depots could strengthen the SCI positive impact on hauliers' performance and subsequently their environmental performance. Stronger SCI can reduce cost and increase revenue and at the same time, reduce the greenhouse-gas emissions of the hauliers. Findings support that economic gains and environmental protection can be complementary and can be attained by curbing the opportunistic behavior of organizations in supply chains.
•The opportunistic behavior of parties transacting in supply chain leads to resource wastages.•This study is grounded on Transaction Cost Economics propositions which are rare in supply chain integration research.•Supply environment affects supply chain integration and subsequently operational efficiency and environmental performance.•Business process moderates the SCI effects and reduces information asymmetry between transacting organizations.•Curbing the opportunistic behavior of transacting parties could protect the environment.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
The COVID-19 pandemic has an adverse impact on the global trade supply chain. Countries where the economy is driven by global trade, either as exporters or importers and are faced with the problem of ...declining imports and exports. This is due to the interruption of the main players of the global supply chain (i.e., production, logistics and transportation sector) as well as the slow-down in consumption of overseas customers. This paper presents the development of an efficiency related metric from the Coherent Data Envelopment Analysis (CoDEA) method for assessing the vulnerability (or conversely, the robustness) levels of the supply chain system of six ASEAN countries. The results reveal that Thailand is most vulnerable to international supply chain issues indicated by its lowest efficiency score. This is due to Thailand's severe disruption of logistics and transportation systems compared with its neighboring countries. In contrast, Vietnam is the most robust because of its efficiency in the exports sector. Our research reveals that trading partners with a lower risk and the ability to rapidly recover their import volume reflect their less vulnerable supply chains. This research provides the associated strategies to establish a resilient global supply chain in spite of the COVID-19 pandemic.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Redox and energy balance plays a key role in determining microbial fitness. Efforts to redirect bacterial metabolism often involve overexpression and deletion of genes surrounding key central ...metabolites, such as pyruvate and acetyl-coA. In the case of metabolic engineering of
Escherichia coli for succinate production, efforts have mainly focused on the manipulation of key pyruvate metabolizing enzymes.
E. coli AFP111 strain lacking
ldhA,
pflB and
ptsG encoded activities accumulates acetate and ethanol as well as shows poor anaerobic growth on rich and minimal media. To address these issues, we first deleted genes (
adhE,
ackA-pta) involved in byproduct formation downstream of acetyl-CoA followed by the deletion of
iclR and pdhR to activate the glyoxylate pathway. Based on data from these studies, we hypothesized that the succinate productivity was limited by the insufficient ATP generation. Genome-scale thermodynamics-based flux balance analysis indicated that overexpression of ATP-forming PEPCK from
Actinobacillus succinogenes in an
ldhA,
pflB and
ptsG triple mutant strain could result in an increase in biomass and succinate flux. Testing of this prediction confirmed that PEPCK overexpression resulted in a 60% increase in biomass and succinate formation in the
ldhA, pflB, ptsG mutant strain.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK
This research was prompted by the underutilization of public transport (PT) and a gap in the relationship between intention and behavior. A research model was developed based on the theory of ...interpersonal behavior (TIB, Triandis, 1980) to identify the predictors of drivers’ intention to switch from car driving to PT and their behavioral readiness to use PT. The sample of drivers (n = 317) was solicited from Malaysia using web based survey (SoGoSurvey). Results from the structural equation modeling of partial least square (PLS-SEM) show the significant associations between convenience, flexible service, commute impedance, and the intention to switch. Whereas, the intention to switch serves as the primary predictor of the behavioral readiness to use PT. Practical implications are discussed and pragmatic intervention programs proposed to target improvement in the drivers’ behavioral readiness to use PT.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
When driving a single-occupancy vehicle (SOV) on roads has become ubiquitous for certain drivers, it causes 23% of the global greenhouse gas emissions. The adoption of high-occupancy public bus ...transport (PT) by the SOV drivers contributes to the lower and more responsible consumption of energy. This paper predicts drivers’ implementation intention to try public buses (implementation intention) as a desirable solution to reduce carbon emissions. It builds on the renaissance of drivers’ cognitive, social, and affective factors to examine their implementation intention. An actionable model investigated their desire for services, perceived influence of referents (referents), worry to try PT (worry), intention to try PT (intention), and habit of driving every day was synthesized. This study employs 9 focus groups and solicits 653 responses from SOV drivers through web surveys. Data is analyzed using variance-based structural equation modeling of partial least squares (PLS-SEM). The empirical results indicate that their desire for comfort and convenience predicted their intention and implementation intention. Although the desire for service information and referents predicted intention, these predictors were found to have no impact on their implementation intention. The intention remains as the primary predictor of implementation intention. Strong driving habit exerts significant lower implementation intention whereas weak habit exerts higher implementation intention. On the contrary, their worry acted as an impediment to intention and implementation intention. The findings indicate that social intervention is imperative to mitigate worry and to break the habit of driving SOVs in order to promote implementation intention.
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•A proposed actionable model to predict the intentions of single-occupancy vehicle (SOV) drivers to try public buses.•Comfort and convenience are the most desired services from SOV drivers for trying public buses.•Worry to try deters drivers’ implementation intention towards cleaner travel.•The habit of everyday driving moderates the trying of sustainable transportation.•The analysis is conducted using variance-based partial least squares structural equation modeling (PLS-SEM).
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
•The influence of EU Waste and Landfill Directives has a legal-geostrategic impact on national and municipal legislations and household practices.•Human Behaviour is also a strategic domain due to ...the enduring effects of poor and good recycling habits.•This should be further investigated.
The objective of this review is to provide an overview of the substance of the Resource, Conservation and Recycling journal. The four domains of Hierarchy of Waste, Recycling, Human Behaviour and Legal Influence populate the journal. The journal articles predominantly dwell on mid-level of the hierarchy reflecting Recycling. The recycling articles are varied and are associated with biotechnology, industrial technology, and human attitudes and behaviour. The European Union’s (EU) Waste and Landfill Directives cast a considerable influence on national and municipal recycling policies and laws. This legal-geostrategic impactful research focus should be sustained because they have a deep and wide bearing at regional, national, municipal and community levels. This overview also reveals human behaviour is a strategic domain because of the enduring effects of both poor and good recycling habits. However, the success of moving waste management strategies up the hierarchy seems elusive. This journal exhibits strategic research attributes in addition to the journal’s objectives of operational recycling transformation processes. This overview suggests developing waste management habits and the DFX research mindset. It concludes with recycling dilemma.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK, ZRSKP
Foreign Direct Investment (FDI) plays an important part in the economic growth of developing Asia and logistics capability is a crucial factor in FDI location choice. Till today, research ...investigating Logistics Performance (LP) and FDI in Asia are still lacking and rather inconclusive and not standardised. Using a total of 31 Asian countries covering 2007 through 2017, the study critically investigates the impact of LP on FDI using static panel regression method. The results demonstrate that while LP significantly impact FDI, there is a threshold effect of institutional quality in the LP-FDI relationship. Specifically, this paper found that the impact of LP on FDI varies across the perceived level of institutional quality i.e., the effect is positive only before certain threshold level of institutional quality, after which the effect of LP on FDI is reversed. This finding suggests that the LP-FDI nexus is contingent on the perceived level of institutional quality, thus supporting the idea that innovations (i.e., creativity and flexibility embedded within a sound institutional framework) is potent in delivering long-run LP-FDI development in Asia.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
The resource wastage in supply chains may be reduced by proper supply chain integration (SCI). SCI may be able to provide the additional means in assuring economic growth while protecting the ...environment. The hauliers provide the primary linkage between shippers and consignees and logistics service providers in the inland container supply chain. This empirical investigation aims to ascertain the supply environment factors and information system which affect SCI and whether SCI affect operational and environmental performance. Data collected from 110 haulier companies were analysed using partial least squares, structural equation modeling (PLS-SEM) methodology. Supply environment which represents transaction attributes affects SCI which in turn positively affects operational and environmental performance. Information system reduces information asymmetry between transacting organizations and by this, moderate the effect of supply environment on SCI. Results provide evidence that SCI is dependent on the context of the supply environment. Opportunistic behavior due to information asymmetry could also be curtailed by proper information system. Therefore, practitioners and stakeholders need to align SCI to the context of supply environment to reap the maximum benefit of SCI. Concurrently, opportunistic behavior needs to be curtailed in supply chain to improve operational and environmental performance.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK, ZRSKP
Mathematical modeling is an essential tool for the comprehensive understanding of cell metabolism and its interactions with the environmental and process conditions. Recent developments in the ...construction and analysis of stoichiometric models made it possible to define limits on steady‐state metabolic behavior using flux balance analysis. However, detailed information on enzyme kinetics and enzyme regulation is needed to formulate kinetic models that can accurately capture the dynamic metabolic responses. The use of mechanistic enzyme kinetics is a difficult task due to uncertainty in the kinetic properties of enzymes. Therefore, the majority of recent works considered only mass action kinetics for reactions in metabolic networks. Herein, we applied the optimization and risk analysis of complex living entities (ORACLE) framework and constructed a large‐scale mechanistic kinetic model of optimally grown Escherichia coli. We investigated the complex interplay between stoichiometry, thermodynamics, and kinetics in determining the flexibility and capabilities of metabolism. Our results indicate that enzyme saturation is a necessary consideration in modeling metabolic networks and it extends the feasible ranges of metabolic fluxes and metabolite concentrations. Our results further suggest that enzymes in metabolic networks have evolved to function at different saturation states to ensure greater flexibility and robustness of cellular metabolism.
Using mass action kinetics in modeling metabolic processes can lead to overly conservative assessments of feasible physiological conditions of the organism. This study shows that considering the enzyme saturations as observed in biological systems consistently increases the stability of the kinetic models. This indicates that enzymes have evolved in a way to increase the flexibility and thus the viability and adaptability of the living organism. Thus, for consistent modeling of cellular metabolism enzyme saturation should be considered as an inevitable component.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
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