Transient process of cortical activity during Necker cube perception: from local clusters to global synchrony

Background

It has been discussed that neural phase-synchrony across distant cortical areas (or global phase-synchrony) was correlated with various aspects of consciousness. The generating process of the synchrony, however, remains largely unknown. As a first step, we investigate transient process of global phase-synchrony, focusing on phase-synchronized clusters. We hypothesize that the phase-synchronized clusters are dynamically organized before global synchrony and clustering patterns depend on perceptual conditions.

Methods

In an EEG study, Kitajo reported that phase-synchrony across distant cortical areas was selectively enhanced by top-down attention around 4 Hz in Necker cube perception. Here, we further analyzed the phase-synchronized clusters using hierarchical clustering which sequentially binds up the nearest electrodes based on similarity of phase locking between the cortical signals. First, we classified dominant components of the phase-synchronized clusters over time. We then investigated how the phase-synchronized clusters change with time, focusing on their size and spatial structure.

Results

Phase-locked clusters organized a stable spatial pattern common to the perceptual conditions. In addition, the phase-locked clusters were modulated transiently depending on the perceptual conditions and the time from the perceptual switch. When top-down attention succeeded in switching perception as subjects intended, independent clusters at frontal and occipital areas grew to connect with each other around the time of the perceptual switch. However, the clusters in the occipital and left parietal areas remained divided when top-down attention failed in switching perception. When no primary biases exist, the cluster in the occipital area grew to its maximum at the time of the perceptual switch within the occipital area.

Conclusions

Our study confirmed the existence of stable phase-synchronized clusters. Furthermore, these clusters were transiently connected with each other. The connecting pattern depended on subjects’ internal states. These results suggest that subjects’ attentional states are associated with distinct spatio-temporal patterns of the phase-locked clusters.

     

Social life cycle assessment of average Irish dairy farm

Purpose

The majority of sustainability studies of dairy farms focused on environmental performance and profitability; however, social aspect has been hardly assessed. This study aims to investigate the social impacts of dairy farm via a case study using a social life cycle assessment framework.

Methods

The assessment was carried out applying the social LCA Guideline by UNEP-SETAC. Nineteen suitable social indicators were selected from four stakeholder categories of the guideline. Characterization and normalization were further developed based on data availability. National farm survey data was used as foreground data for farm activities, supplemented with background data from public database and life cycle working environment (LCWE) data by Gabi database. All indicators were divided into three groups: functional unit-related quantitative indicators, non-functional unit-related quantitative indicators and semi-quantitative indicators.

Results and discussion

Irish dairy farming has positive social impacts on value chain actors and society, predominantly positive impacts for local community and generally positive values for workers. The main negative impacts are health and safety issue, equal opportunity for workers, and safe and healthy living conditions for the local community. Possible actions to improve the social performance include introducing more efficient and robotic milk production systems; applying better handling methods and using real time decision support to operational management for emissions reduction.

Conclusions

This study is the first attempt of social LCA in Ireland. It demonstrated a possible method to carry out SLCA for Irish dairy sector. The results identified the positive and negative social hotspot of dairy farm with recommendation for future improvement.

     

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.

     

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.

     

Multi-actor multi-criteria sustainability assessment framework for energy and industrial systems in life cycle perspective under uncertainties. Part 2: improved extension theory

Purpose

The concept of sustainability and sustainable development has been widely incorporated in energy and industrial systems. This paper is the second part of a two-paper series dealing with multi-actor multi-criteria sustainability assessment of alternative energy and industrial systems in life cycle perspective under uncertainties.

Methods

The criteria system including four macroscopic aspects (environmental, safety, social and economic aspects) has been developed for sustainability assessment of energy and industrial systems. An improved extension theory which can address interval decision-making matrix has been developed for determining the sustainability degree of the energy and industrial systems.

Results and discussion

The weights of the criteria for sustainability assessment are the first part of the two-paper series. An illustrative case has been studied by the proposed multi-criteria decision-making method, and the sustainability of six alternative options for the production of a 1-t product was investigated. The sustainability degree of these six alternative options can be determined by the proposed method.

Conclusions and perspectives

A methodology for multi-actor multi-criteria sustainability assessment of energy and industrial options has been developed in this study, the traditional extension theory has been modified to deal with the uncertainty problems and the proposed method can rank the alternative energy and industrial systems with the decision-making matrix in which the data of the alternatives with respect to the evaluation criteria are intervals. In the improved extension theory, sustainability has been dived into five grades: excellent, good, satisfied, barely adequate and fail. According to the method for calculating the weights of the criteria for sustainability assessment proposed in part 1, these weights were used to calculate the integrated dependent degree which is a measure of what degree an alternative belongs to the classical fields. An optimal programming model for maximizing the satisfied degree has been developed to rank the sustainability sequence of the alternative options and determine the sustainability degree of each alternative.

     

Framework for integrating animal welfare into life cycle sustainability assessment

Purpose

This study seeks to provide a framework for integrating animal welfare as a fourth pillar into a life cycle sustainability assessment and presents three alternative animal welfare indicators.

Methods

Animal welfare is assessed during farm life and during slaughter. The indicators differ in how they value premature death. All three consider (1) the life quality of an animal such as space allowance, (2) the slaughter age either as life duration or life fraction, and (3) the number of animals affected for providing a product unit, e.g. 1 Mcal. One of the indicators additionally takes into account a moral value denoting their intelligence and self-awareness. The framework allows for comparisons across studies and products and for applications at large spatial scales. To illustrate the framework, eight products were analysed and compared: beef, pork, poultry, milk, eggs, salmon, shrimps, and, as a novel protein source, insects.

Results and discussion

Insects are granted to live longer fractions of their normal life spans, and their life quality is less compromised due to a lower assumed sentience. Still, they perform worst according to all three indicators, as their small body sizes only yield low product quantities. Therefore, we discourage from eating insects. In contrast, milk is the product that reduces animal welfare the least according to two of the three indicators and it performs relatively better than other animal products in most categories. The difference in animal welfare is mostly larger for different animal products than for different production systems of the same product. This implies that, besides less consumption of animal-based products, a shift to other animal products can significantly improve animal welfare.

Conclusions

While the animal welfare assessment is simplified, it allows for a direct integration into life cycle sustainability assessment. There is a trade-off between applicability and indicator complexity, but even a simple estimate of animal welfare is much better than ignoring the issue, as is the common practice in life cycle sustainability assessments. Future research should be directed towards elaborating the life quality criterion and extending the product coverage.

     

Dynamics of plant nutrient uptake as affected by biopore-associated root growth in arable subsoil

Background and aims

Soil microbial communities influence nutrient cycling, chemistry and structure of soil, and plant productivity. In turn, agronomic practices such as fertilization and crop rotation alter soil physical and chemical properties and consequently soil microbiomes. Understanding the long-term effects of agronomic practices on soil microbiomes is essential for improving agronomic practices to optimize these microbial communities for agricultural sustainability. We examine the composition and substrate-utilization profiles of microbial communities at the Morrow Plots in Illinois.

Methods

Microbial community composition is assessed with 16S rRNA gene sequencing and subsequent bioinformatic analyses. Community- level substrate utilization is characterized with the BIOLOG EcoPlate.

Results

Fertilizer and rotation treatments significantly affected microbial community structure, while substrate utilization was affected by fertilizer, but not crop-rotation treatments. Differences in relative abundance and occurrence of bacterial taxa found in fertilizer treatments can explain the observed differences in community level substrate utilization.

Conclusion

Long-term fertilization and crop-rotation treatments affect soil microbial community composition and physiology, specifically through chronic nutrient limitation, long-term influx of microbes and organic matter via manure application, as well as through changes in soil chemistry. Relatively greater abundance of Koribacteraceae and Solibacterales taxa in soils might prove useful as indicators of soil degradation.

     

Gastric bypass surgery reveals independency of obesity and diabetes melitus type 2

Background

Roux-en-Y gastric bypass surgery is widely applied to ameliorate morbid obesity, including diabetes in people with type 2 diabetes. The latter vanish a few days after surgery for many, but not in all patients before any weight reduction has occurred. The explanation for this change in metabolic status is poorly understood, but the observation may suggest that the fate obesity and diabetes is only partly linked after surgery.

Methods

The trajectories of weight reduction measured as reduced body mass index (BMI) in 741obese subjects with and without diabetes were evaluated. Evaluation was performed on three groups: 1) subjects that were non-diabetic before and after surgery; 2) subjects that were diabetics before surgery but non-diabetics after surgery; and 3) subjects that were diabetics before surgery and remained diabetics after surgery. The diabetic state was established at HbA1c above 48 mmol/mol.

Results

The trajectories differ significantly between groups and any sub-populations of groups, the latter identified by the distance between individual trajectories using a k-means procedure. The results suggest that different domains in the enormous genetic network governing basic metabolism are perturbed in obesity and diabetes, and in fact some of the patients are affected by two distinct diseases: obesity and diabetes mellitus type 2.

Conclusion

Although RYGB “normalized” many glycaemic parameters in some of the diabetic subjects apparently converting to a non-diabetics state, other diabetic subjects stay diabetic in the context of the new gut anatomy after surgery. Thus, the obesity part of the glycaemic derangement may have been ameliorated, but some defects of the diabetic state had not.

     

Factor XIII Val34Leu polymorphism and risk of recurrent pregnancy loss in Iranian population: a case control study

BACKGROUND

Recurrent pregnancy loss (RPL) is a heterogeneous condition and thrombophilias have been considered as a probable cause.

OBJECTIVE

The aim of this study was to investigate the prevalence of the coagulation factor XIII Val34Leu polymorphism among women with unexplained RPL.

METHODS

A total of 140 women with a history of unexplained RPL and 100 age-matched healthy fertile women were recruited. The presence of FXIII Val34Leu polymorphism among the cases and controls was investigated using PCR-RFLP method.

RESULTS

Genotype analyses of the subjects revealed that the patients had a significantly higher prevalence of V/L and L/L than the controls (P<0.05): 33.5% vs. 15%, and 9.2% vs. 2%, respectively.

CONCLUSION

These results indicate a significant association between FXIII Val34Leu polymorphism and unexplained RPL in the Iranian patient.

     

Pseudo current density maps of electrophysiological heart,nerve or brain function and their physical basis

Background

In recent years the visualization of biomagnetic measurement data by so-called pseudo current density maps or Hosaka-Cohen (HC) transformations became popular.

Methods

The physical basis of these intuitive maps is clarified by means of analytically solvable problems.

Results

Examples in magnetocardiography, magnetoencephalography and magnetoneurography demonstrate the usefulness of this method.

Conclusion

Hardware realizations of the HC-transformation and some similar transformations are discussed which could advantageously support cross-platform comparability of biomagnetic measurements.

     

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.

     

Product social impact assessment

Purpose

Whereas the business evolution of environmental sustainability metrics has advanced significantly over the past decade, social sustainability at product level is still relatively immature. Research continues to support the front runners on organisational sustainability, while workable solutions at product level have not yet been addressed sufficiently. Triggered by this imbalance, a group of experts from large companies decided to join forces, initiating the Roundtable for Product Social Metrics.

Methods

Starting in early 2013, this group of companies aimed to (i) consolidate principles for product social sustainability assessment and harmonise approaches, (ii) align with other global initiatives and share with other companies and (iii) develop solutions for cross-cutting implementation issues. In order to be able to produce a comprehensive method for social impact assessment that provides enough flexibility for individual requirements, the Roundtable developed a method based on the approaches of the participant companies and external references such as the UNEP/SETAC Guidelines for Social Life-Cycle Assessment of Products and corporate level standards. Guiding principles were defined for the development of the method.

Results and discussion

The results of the first two phases of the Roundtable for Product Social Metrics are documented in a handbook, which proposes a practical method for organisations to assess the social impacts of a product or a service along its life cycle. The handbook outlines an aligned method for social impact assessment at a product level offering two approaches: quantitative and scale based. The method was developed to allow reasoned assessment of overall performance by including social topics and performance indicators that reflect positive and negative impacts of the product on three stakeholder groups: workers, consumers and local communities. Nineteen social topics are proposed, together with their individual performance indicators, including detailed definitions. Application examples and recommendations for the communication of results are also included in the handbook.

Conclusions

The method can be applied in numerous scenarios, from understanding improvement opportunities and steering product development in different stages, to providing support for decision making and external communications. However, the method still has further potential for improvement, inter alia that the proposed indicators are not fully applicable to small farmers, SMEs and the self-employed, as well as that the indicators are mainly at inventory level. Furthermore, the proposed method is strongly dependent on the availability of data.

     

A methodology for elucidating regulatory mechanisms leading to changes in lipid profiles

Introduction

It is difficult to elucidate the metabolic and regulatory factors causing lipidome perturbations.

Objectives

This work simplifies this process.

Methods

A method has been developed to query an online holistic lipid metabolic network (of 7923 metabolites) to extract the pathways that connect the input list of lipids.

Results

The output enables pathway visualisation and the querying of other databases to identify potential regulators. When used to a study a plasma lipidome dataset of polycystic ovary syndrome, 14 enzymes were identified, of which 3 are linked to ELAVL1—an mRNA stabiliser.

Conclusion

This method provides a simplified approach to identifying potential regulators causing lipid-profile perturbations.

     

Improving benchmarking by using an explicit framework for the development of composite indicators: an example using pediatric quality of care

Background

The measurement of healthcare provider performance is becoming more widespread. Physicians have been guarded about performance measurement, in part because the methodology for comparative measurement of care quality is underdeveloped. Comprehensive quality improvement will require comprehensive measurement, implying the aggregation of multiple quality metrics into composite indicators.

Objective

To present a conceptual framework to develop comprehensive, robust, and transparent composite indicators of pediatric care quality, and to highlight aspects specific to quality measurement in children.

Methods

We reviewed the scientific literature on composite indicator development, health systems, and quality measurement in the pediatric healthcare setting. Frameworks were selected for explicitness and applicability to a hospital-based measurement system.

Results

We synthesized various frameworks into a comprehensive model for the development of composite indicators of quality of care. Among its key premises, the model proposes identifying structural, process, and outcome metrics for each of the Institute of Medicine's six domains of quality (safety, effectiveness, efficiency, patient-centeredness, timeliness, and equity) and presents a step-by-step framework for embedding the quality of care measurement model into composite indicator development.

Conclusions

The framework presented offers researchers an explicit path to composite indicator development. Without a scientifically robust and comprehensive approach to measurement of the quality of healthcare, performance measurement will ultimately fail to achieve its quality improvement goals.

     

Weight loss moderately affects the mixed meal challenge response of the plasma metabolome and transcriptome of peripheral blood mononuclear cells in abdominally obese subjects

Introduction

The response to dietary challenges has been proposed as a more accurate measure of metabolic health than static measurements performed in the fasted state. This has prompted many groups to explore the potential of dietary challenge tests for assessment of diet and lifestyle induced shifts in metabolic phenotype.

Objectives

We examined whether the response to a mixed-meal challenge could provide a readout for a weight loss (WL)-induced phenotype shift in abdominally obese male subjects. The underlying assumption of a mixed meal challenge is that it triggers all aspects of phenotypic flexibility and provokes a more prolonged insulin response, possibly allowing for better differentiation between individuals.

Methods

Abdominally obese men (n?=?29, BMI?=?30.3?±?2.4 kg/m²) received a mixed-meal challenge prior to and after an 8-week WL or no-WL control intervention. Lean subjects (n?=?15, BMI?=?23.0?±?2.0 kg/m²) only received the mixed meal challenge at baseline to have a benchmark for WL-induced phenotype shifts.

Results

Levels of several plasma metabolites were significantly different between lean and abdominally obese at baseline as well as during postprandial metabolic responses. Genes related to oxidative phosphorylation in peripheral blood mononuclear cells (PBMCs) were expressed at higher levels in abdominally obese subjects as compared to lean subjects at fasting, which was partially reverted after WL. The impact of WL on the postprandial response was modest, both at the metabolic and gene expression level in PBMCs.

Conclusion

We conclude that mixed-meal challenges are not necessarily superior to measurements in the fasted state to assess metabolic health. Furthermore, the mechanisms accounting for the observed differences between lean and abdominally obese in the fasted state are different from those underlying the dissimilarity observed during the postprandial response.

     

Serum metabolites associated with feed efficiency in black angus steers

Introduction

Improving feed utilization in cattle is required to reduce input costs, increase production, and ultimately improve sustainability of the beef cattle industry. Characterizing metabolic differences between efficient and non-efficient animals will allow stakeholders to identify more efficient cattle during backgrounding.

Objectives

This study used an untargeted metabolomics approach to determine differences in serum metabolites between animals of low and high residual feed intake.

Methods

Residual feed intake was determined for 50 purebred Angus steers and 29 steers were selected for the study steers based on low versus high feed efficiency. Blood samples were collected from steers and analyzed using untargeted metabolomics via mass spectrometry. Metabolite data was analyzed using Metaboanalyst, visualized using orthogonal partial least squares discriminant analysis, and p-values derived from permutation testing. Non-esterified fatty acids, urea nitrogen, and glucose were measured using commercially available calorimetric assay kits. Differences in metabolites measured were grouped by residual feed intake was measured using one-way analysis of variance in SAS 9.4.

Results

Four metabolites were found to be associated with differences in feed efficiency. No differences were found in other serum metabolites, including serum urea nitrogen, non-esterified fatty acids, and glucose.

Conclusions

Four metabolites that differed between low and high residual feed intake have important functions related to nutrient utilization, among other functions, in cattle. This information will allow identification of more efficient steers during backgrounding.

     

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.

     

Profiling of faecal water and urine metabolites among Papua New Guinea highlanders believed to be adapted to low protein intake

Introduction

Adequate amount of proteins from foods are normally needed to maintain muscle mass of the human body. Although protein intakes of Papua New Guinea (PNG) highlanders are less than biologically adequate, protein deficiency related disorders have rarely been reported. It has been postulated that gut microbiota play a role in such low-protein-adaptation.

Objective

To explore underlying biological mechanisms of low-protein adaptation among PNG highlanders by investigating metabolomic profiles of faecal water and urine.

Methods

We performed metabolome analysis using faecal water extracted from faecal samples of PNG highlanders, PNG non-highlanders and Japanese subjects. We paid special attention to amino acids and other metabolites produced by gut microbiota, as well as to metabolites involved in nitrogen recycling in the human gut.

Results

Our results indicated that amino acid levels were higher in faecal water from PNG highlanders than PNG non-highlanders, but amino acid levels did not differ between PNG highlanders and Japanese subjects. Among PNG highlander samples, amino acid levels tended to be higher in those who consumed less protein.

Conclusion

We speculated that a greater proportion of urea was excreted to the intestine among the PNG highlanders than other groups, and that the urea was used for nitrogen salvage. Intestinal bacteria are essential for producing ammonia from urea and also for producing amino acids from ammonia, which is a key process in low-protein adaptation. Profiling the gut microbiota of PNG highlanders is an important avenue for further research into the mechanisms of low-protein adaptation.

     

Characterizing alternative feeds for rainbow trout (<Emphasis Type="Italic">O. mykiss</Emphasis>) by <Superscript>1</Superscript>H NMR metabolomics

Introduction

Fish feed formulations are constantly evolving to improve the quality of diets for farmed fish and to ensure the sustainability of the aquaculture sector. Nowadays, insect, microalgae and yeast are feedstuff candidates for new feeds. However, the characterization of aquafeed is still based on proximate and targeted analyses which may not be sufficient to assess feed quality.

Objectives

Our aim was to highlight the soluble compounds that specifically differ between selected plant-based feeds complemented with alternative feedstuffs and discuss their origin and potential for fish nutrition.

Methods

A growth trial was carried out to evaluate growth performances and feed conversion ratios of fish fed plant-based, commercial, insect, spirulina and yeast feeds. ¹H NMR metabolomics profiling of each feed was performed using a CPMG sequence on polar extracts. Spectra were processed, and data were analyzed using multivariate and univariate analyses to compare alternative feeds to a plant-based feed.

Results

Fish fed insect or yeast feed showed the best growth performances associated with the lowest feed conversion ratios compared to plant-based feed. Soluble compound ¹H NMR profiles of insect and spirulina alternative feeds differed significantly from the plant-based one that clustered with yeast feed. In insect and spirulina feeds, specific differences compared to plant-based feed concerned glycerol and 3-hydroxybutyrate, respectively.

Conclusion

This strategy based on compositional differences between plant-based and alternative feeds can be useful for detecting compounds unsuspected until now that could impact fish metabolism.

     

Metabolomic profiling of maternal hair suggests rapid development of intrahepatic cholestasis of pregnancy

Introduction

Intrahepatic cholestasis of pregnancy (ICP) is a common maternal liver disease; development can result in devastating consequences, including sudden fetal death and stillbirth. Currently, recognition of ICP only occurs following onset of clinical symptoms.

Objective

Investigate the maternal hair metabolome for predictive biomarkers of ICP.

Methods

The maternal hair metabolome (gestational age of sampling between 17 and 41 weeks) of 38 Chinese women with ICP and 46 pregnant controls was analysed using gas chromatography–mass spectrometry.

Results

Of 105 metabolites detected in hair, none were significantly associated with ICP.

Conclusion

Hair samples represent accumulative environmental exposure over time. Samples collected at the onset of ICP did not reveal any metabolic shifts, suggesting rapid development of the disease.