State of the art in S-LCA: integrating literature review and automatic text analysis

Purpose

Social life cycle assessment (S-LCA) method lacks of standard and code of practice. The aim of the study is to classify the wide variety of contributions on S-LCA for tracking the development of different themes and for defining and classifying the main approaches in a systematic and reproducible way.

Methods

The research addressed to study a collection of 51 articles published between January 2006 and November 2014 using statistical criteria. We used automatic text analysis (ATA) tools related to lexicon analysis to identify keywords useful in tracing the main topics covered in articles published in different periods. We conducted principal component analysis (PCA) to classify the different approaches in the literature and to outline the orientations of the various research groups.

Results and discussion

The results from lexicon analysis showed a rapid succession of different topics covered in the analyzed period. This alternation is strongly affected by the introduction of UNEP/Society of Environmental Toxicology and Chemistry (SETAC) S-LCA guidelines and methodological sheets. PCA analysis enabled to synthesize the information related to the numerous approaches. Results did not show a clear division into groups which indicates the absence of a dominant position on the subject in the literature.

Conclusions

This study attempted to map the state of art in S-LCA integrating literature review with multivariate statistical techniques. The analysis showed a highly fragmented field. These results confirm the existence of a variety of approaches that in part have already been identified by literature reviews on S-LCA. Alignment with the results in the literature confirms ATA to be a suitable instrument for the realization of reviews. Moreover, being systematic and reproducible allows ATA to be applied repeatedly, expanding the number of articles and topics analyzed.

     

Attributional and consequential LCA in the ILCD handbook

Purpose

This discussion article aims to highlight two problematic aspects in the International Reference Life Cycle Data System (ILCD) Handbook: its guidance to the choice between attributional and consequential modeling and to the choice between average and marginal data as input to the life cycle inventory (LCI) analysis.

Methods

We analyze the ILCD guidance by comparing different statements in the handbook with each other and with previous research in this area.

Results and discussion

We find that the ILCD handbook is internally inconsistent when it comes to recommendations on how to choose between attributional and consequential modeling. We also find that the handbook is inconsistent with much of previous research in this matter, and also in the recommendations on how to choose between average and marginal data in the LCI.

Conclusions

Because of the inconsistencies in the ILCD handbook, we recommend that the handbook be revised.

     

Optimization of fecal sample preparation for untargeted LC-HRMS based metabolomics

Introduction

Collecting feces is easy. It offers direct outcome to endogenous and microbial metabolites.

Objectives

In a context of lack of consensus about fecal sample preparation, especially in animal species, we developed a robust protocol allowing untargeted LC-HRMS fingerprinting.

Methods

The conditions of extraction (quantity, preparation, solvents, dilutions) were investigated in bovine feces.

Results

A rapid and simple protocol involving feces extraction with methanol (1/3, M/V) followed by centrifugation and a step filtration (10 kDa) was developed.

Conclusion

The workflow generated repeatable and informative fingerprints for robust metabolome characterization.

     

A lost opportunity for science: journals promote data sharing in metabolomics but do not enforce it

Introduction

Data sharing is being increasingly required by journals and has been heralded as a solution to the ‘replication crisis’.

Objectives

(i) Review data sharing policies of journals publishing the most metabolomics papers associated with open data and (ii) compare these journals’ policies to those that publish the most metabolomics papers.

Methods

A PubMed search was used to identify metabolomics papers. Metabolomics data repositories were manually searched for linked publications.

Results

Journals that support data sharing are not necessarily those with the most papers associated to open metabolomics data.

Conclusion

Further efforts are required to improve data sharing in metabolomics.

     

Untargeted metabolomics suffers from incomplete raw data processing

Introduction

Untargeted metabolomics is a powerful tool for biological discoveries. To analyze the complex raw data, significant advances in computational approaches have been made, yet it is not clear how exhaustive and reliable the data analysis results are.

Objectives

Assessment of the quality of raw data processing in untargeted metabolomics.

Methods

Five published untargeted metabolomics studies, were reanalyzed.

Results

Omissions of at least 50 relevant compounds from the original results as well as examples of representative mistakes were reported for each study.

Conclusion

Incomplete raw data processing shows unexplored potential of current and legacy data.

     

How the chemical features of molecules may have addressed the settlement of metabolic steps

Introduction

While the evolutionary adaptation of enzymes to their own substrates is a well assessed and rationalized field, how molecules have been originally selected in order to initiate and assemble convenient metabolic pathways is a fascinating, but still debated argument.

Objectives

Aim of the present study is to give a rationale for the preferential selection of specific molecules to generate metabolic pathways.

Methods

The comparison of structural features of molecules, through an inductive methodological approach, offer a reading key to cautiously propose a determining factor for their metabolic recruitment.

Results

Starting with some commonplaces occurring in the structural representation of relevant carbohydrates, such as glucose, fructose and ribose, arguments are presented in associating stable structural determinants of these molecules and their peculiar occurrence in metabolic pathways.

Conclusions

Among other possible factors, the reliability of the structural asset of a molecule may be relevant or its selection among structurally and, a priori, functionally similar molecules.

     

Extraction of natural products from bark of <Emphasis Type="Italic">Betula pendula</Emphasis> using ionic liquids

Introduction

Aqueous–methanol mixtures have successfully been applied to extract a broad range of metabolites from plant tissue. However, a certain amount of material remains insoluble.

Objectives

To enlarge the metabolic compendium, two ionic liquids were selected to extract the methanol insoluble part of trunk from Betula pendula.

Methods

The extracted compounds were analyzed by LC/MS and GC/MS.

Results

The results show that 1-butyl-3-methylimidazolium acetate (IL-Ac) predominantly resulted in fatty acids, whereas 1-ethyl-3-methylimidazolium tosylate (IL-Tos) mostly yielded phenolic structures. Interestingly, bark yielded more ionic liquid soluble metabolites compared to interior wood.

Conclusion

From this one can conclude that the application of ionic liquids may expand the metabolic snapshot.

     

An Italian tomato “Cuore di Bue” case study: challenges and benefits using subcategory assessment method for social life cycle assessment

Purpose

The main purpose of this study is to present an implementation of the subcategory assessment method (SAM) to the life cycle of an Italian variety of tomato called “Cuore di Bue” produced by an Italian cooperative. The case study was used to use the methodology proposed in compliance with the guidelines of social life cycle assessment (S-LCA) in order to highlight issues for the improvement of SAM. A summary of strengths and weaknesses of the methodology as well as the social performance of the considered Italian tomato is an important result of this case study.

Methods

The methodology used is based on SAM. The UNEP/SETAC guidelines of S-LCA and the complementary methodological sheets were used as main references to carry out SAM, and it was used to assess the social performances of Cuore di Bue. The focus was on the assessment of the following three out of five stakeholder groups presented in the guidelines: workers, local community and consumers. Specific questionnaires have been developed to collect the inventory data related to each stakeholder group and along the product life cycle.

Results and discussion

SAM of Cuore di Bue showed a range of values, between 2 and 3 (C-B) for consumer stakeholder group and mainly 3 (B) for the local community and worker stakeholders. Because the best performance (A) is related to a numerical value of 4, better performances were not identified, owing to no propagation of actions in the value chain. The collective bargaining, transparency, feedback mechanism and privacy are the subcategories with the worst performance, but at the same time with more potential for improvements.

Conclusions

The implementation of SAM on Cuore di Bue allowed us to demonstrate how SAM transforms qualitative data into semi-quantitative information through a score scale that can help a decision maker achieve a product overview. SAM has been implemented on Cuore di Bue; the product assessment, the strengths and weaknesses of the methodology are identified and discussed as well. It has been possible to present the best and worst performances in product life cycle, by identifying the phase or the subcategories with good or bad performance. However, in this case study, as the same company owns most of the product life cycle taken into account, the majority of social performances are identical, and this may represent a limit of the methodology or that more organisations along the life cycle must be taken into account (for example, energy, distribution).

     

Life cycle assessment-based selection of a sustainable lightweight automotive engine hood design

Purpose

This study presents a life cycle assessment (LCA)-based sustainable and lightweight automotive engine hood design and compares the life cycle energy consumption and potential environmental impacts of a steel (baseline) automotive engine hood with three types of lightweight design: advanced high strength steel (AHSS), aluminum, and carbon fiber.

Methods

A “cradle-to-grave” LCA including the production, use, and end-of-life stages is conducted in accordance with the ISO 14040/14044 standards. Onsite data collected by Chinese automotive companies in 2015 are used in the assessment. The Cumulative Energy Demand v1.09 method is applied to evaluate cumulative energy demand (CED), and the International Panel on Climate Change 2013 100a method is used to estimate global warming potential (GWP 100a).

Results and discussion

Among the different lightweight designs for the engine hood, the aluminum design is the most sustainable and has the lowest CED and GWP (100a) from a life cycle perspective, which is based on a lifetime driving distance of approximately 150,000 km. In addition, the AHSS design is also sustainable and lightweight. The carbon fiber design results in higher CED and GWP (100a) values than the steel (baseline) design during the life cycle but results in the largest CED and GWP (100a) savings through waste material recycling. The AHSS design exhibits the best break-even distance based on CED and GWP (100a) within 150,000 km.

Conclusions

Sensitivity analysis results show that the lifetime driving distance and material recycling rate have the largest impacts on the overall CEDs and GWPs of the three lightweight designs.

     

NMRProcFlow: a graphical and interactive tool dedicated to 1D spectra processing for NMR-based metabolomics

Introduction

Concerning NMR-based metabolomics, 1D spectra processing often requires an expert eye for disentangling the intertwined peaks.

Objectives

The objective of NMRProcFlow is to assist the expert in this task in the best way without requirement of programming skills.

Methods

NMRProcFlow was developed to be a graphical and interactive 1D NMR (¹H & ¹³C) spectra processing tool.

Results

NMRProcFlow (http://nmrprocflow.org), dedicated to metabolic fingerprinting and targeted metabolomics, covers all spectra processing steps including baseline correction, chemical shift calibration and alignment.

Conclusion

Biologists and NMR spectroscopists can easily interact and develop synergies by visualizing the NMR spectra along with their corresponding experimental-factor levels, thus setting a bridge between experimental design and subsequent statistical analyses.

     

Resazurin-based 96-well plate microdilution method for the determination of minimum inhibitory concentration of biosurfactants

Objectives

To develop and validate a microdilution method for measuring the minimum inhibitory concentration (MIC) of biosurfactants.

Results

A standardized microdilution method including resazurin dye has been developed for measuring the MIC of biosurfactants and its validity was established through the replication of tetracycline and gentamicin MIC determination with standard bacterial strains.

Conclusion

This new method allows the generation of accurate MIC measurements, whilst overcoming critical issues related to colour and solubility which may interfere with growth measurements for many types of biosurfactant extracts.

     

Corneal Collagen Cross-Linking for the Management of Mycotic Keratitis

Purpose

To evaluate the efficiency of corneal collagen cross-linking (CXL) in addition to topical voriconazole in cases with mycotic keratitis.

Design

Retrospective case series in a tertiary university hospital.

Participants

CXL was performed on 13 patients with mycotic keratitis who presented poor or no response to topical voriconazole treatment.

Methods

The clinical features, symptoms, treatment results and complications were recorded retrospectively. The corneal infection was graded according to the depth of infection into the stroma (from grade 1 to grade 3). The visual analogue scale was used to calculate the pain score before and 2 days after surgery.

Main Outcome Measures

Grade of the corneal infection.

Results

Mean age of 13 patients (6 female and 7 male) was 42.4 ± 17.7 years (20–74 years). Fungus was demonstrated in culture (eight patients) or cytological examination (five patients). Seven of the 13 patients (54%) were healed with topical voriconazole and CXL adjuvant treatment in 26 ± 10 days (15–40 days). The remaining six patients did not respond to CXL treatment; they initially presented with higher grade ulcers. Pre- and post-operative pain score values were 8 ± 0.8 and 3.5 ± 1, respectively (p < 0.05).

Conclusions

The current study suggests that adjunctive CXL treatment is effective in patients with small and superficial mycotic ulcers. These observations require further research by large randomized clinical trials.

     

An oncoplastic technique to reduce the formation of lateral 'dog-ears' after mastectomy

Background

Lateral skin folds or 'dog-ears' are frequent following mastectomy, particularly in patients with large body habitus.

Methods

We describe a method of modifying the mastectomy incision and suturing to eliminate these lateral 'dog-ears'.

Conclusion

This surgical technique, as compared to others described in the literature, is simple, does not require additional incisions and is cosmetically acceptable to the patient.

     

Iridoid and phenylethanoid/phenylpropanoid metabolite profiles of <Emphasis Type="Italic">Scrophularia</Emphasis> and <Emphasis Type="Italic">Verbascum</Emphasis> species used medicinally in North America

Introduction

Botanicals containing iridoid and phenylethanoid/phenylpropanoid glycosides are used worldwide for the treatment of inflammatory musculoskeletal conditions that are primary causes of human years lived with disability, such as arthritis and lower back pain.

Objectives

We report the analysis of candidate anti-inflammatory metabolites of several endemic Scrophularia species and Verbascum thapsus used medicinally by peoples of North America.

Methods

Leaves, stems, and roots were analyzed by ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) and partial least squares-discriminant analysis (PLS-DA) was performed in MetaboAnalyst 3.0 after processing the datasets in Progenesis QI.

Results

Comparison of the datasets revealed significant and differential accumulation of iridoid and phenylethanoid/phenylpropanoid glycosides in the tissues of the endemic Scrophularia species and Verbascum thapsus.

Conclusions

Our investigation identified several species of pharmacological interest as good sources for harpagoside and other important anti-inflammatory metabolites.

     

Synthesis and physicochemical characterization of the one-carbon carrier 10-formyltetrahydrofolate; a reference standard for metabolomics

Introduction

Metabolomics analysis depends on the identification and validation of specific metabolites. This task is significantly hampered by the absence of well-characterized reference standards. The one-carbon carrier 10-formyltetrahydrofolate acts as a donor of formyl groups in anabolism, where it is a substrate in formyltransferase reactions in purine biosynthesis. It has been reported as an unstable substance and is currently unavailable as a reference standard for metabolomics analysis.

Objectives

The current study was undertaken to provide the metabolomics community thoroughly characterized 10-formyltetrahydrofolate along with analytical methodology and guidelines for its storage and handling.

Methods

Anaerobic base treatment of 5,10-methenyltetrahydrofolate chloride in the presence of antioxidant was utilized to prepare 10-formyltetrahydrofolate.

Results

Pure 10-formyltetrahydrofolate has been prepared and physicochemically characterized. Conditions toward maintaining the stability of a solution of the dipotassium salt of 10-formyltetrahydrofolate have been determined.

Conclusion

This study describes the facile preparation of pure (>90%) 10-formyltetrahydrofolate, its qualitative physicochemical characterization, as well as conditions to enable its use as a reference standard in physiologic samples.

     

<Emphasis Type="Italic">massPix</Emphasis>: an R package for annotation and interpretation of mass spectrometry imaging data for lipidomics

Introduction

Mass spectrometry imaging (MSI) experiments result in complex multi-dimensional datasets, which require specialist data analysis tools.

Objectives

We have developed massPix—an R package for analysing and interpreting data from MSI of lipids in tissue.

Methods

massPix produces single ion images, performs multivariate statistics and provides putative lipid annotations based on accurate mass matching against generated lipid libraries.

Results

Classification of tissue regions with high spectral similarly can be carried out by principal components analysis (PCA) or k-means clustering.

Conclusion

massPix is an open-source tool for the analysis and statistical interpretation of MSI data, and is particularly useful for lipidomics applications.

     

Using multitask classification methods to investigate the kinase-specific phosphorylation sites

Background

Identification of phosphorylation sites by computational methods is becoming increasingly important because it reduces labor-intensive and costly experiments and can improve our understanding of the common properties and underlying mechanisms of protein phosphorylation.

Methods

A multitask learning framework for learning four kinase families simultaneously, instead of studying each kinase family of phosphorylation sites separately, is presented in the study. The framework includes two multitask classification methods: the Multi-Task Least Squares Support Vector Machines (MTLS-SVMs) and the Multi-Task Feature Selection (MT-Feat3).

Results

Using the multitask learning framework, we successfully identify 18 common features shared by four kinase families of phosphorylation sites. The reliability of selected features is demonstrated by the consistent performance in two multi-task learning methods.

Conclusions

The selected features can be used to build efficient multitask classifiers with good performance, suggesting they are important to protein phosphorylation across 4 kinase families.

     

A modeling framework to evaluate sustainability of building construction based on LCSA

Purpose

Life cycle sustainability assessment (LCSA) is a method that combines three life cycle techniques, viz. environmental life cycle assessment (LCA), life cycle costing (LCC), and social life cycle assessment (S-LCA). This study is intended to develop a LCSA framework and a case study of LCSA for building construction projects.

Methods

A LCSA framework is proposed to combine the three life cycle techniques. In the modeling phases, three life cycle models are used in the LCSA framework, namely the environmental model of construction (EMoC), cost model of construction (CMoC), and social-impact model of construction (SMoC). A residential building project is applied to the proposed LCSA framework from “cradle to the end of construction” processes to unveil the limitations and future research needs of the LCSA framework.

Results and discussion

It is found that material extraction and manufacturing account for over 90 % to the environmental impacts while they contribute to 61 % to the construction cost. In terms of social impacts, on-site construction performs better than material extraction and manufacturing, and on-site construction has larger contributions to the positive social impacts. The model outcomes are validated through interviews with local experts in Hong Kong. The result indicates that the performance of the models is generally satisfactory.

Conclusions

The case study has confirmed that LCSA is feasible. Being one of the first applications of LCSA on building construction, this study fulfills the current research gap and paves the way for future development of LCSA.

     

An effective hybrid of hill climbing and genetic algorithm for 2D triangular protein structure prediction

Background

Proteins play fundamental and crucial roles in nearly all biological processes, such as, enzymatic catalysis, signaling transduction, DNA and RNA synthesis, and embryonic development. It has been a long-standing goal in molecular biology to predict the tertiary structure of a protein from its primary amino acid sequence. From visual comparison, it was found that a 2D triangular lattice model can give a better structure modeling and prediction for proteins with short primary amino acid sequences.

Methods

This paper proposes a hybrid of hill-climbing and genetic algorithm (HHGA) based on elite-based reproduction strategy for protein structure prediction on the 2D triangular lattice.

Results

The simulation results show that the proposed HHGA can successfully deal with the protein structure prediction problems. Specifically, HHGA significantly outperforms conventional genetic algorithms and is comparable to the state-of-the-art method in terms of free energy.

Conclusions

Thanks to the enhancement of local search on the global search, the proposed HHGA achieves promising results on the 2D triangular protein structure prediction problem. The satisfactory simulation results demonstrate the effectiveness of the proposed HHGA and the utility of the 2D triangular lattice model for protein structure prediction.