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1.

Background

The ability to digest lactose after weaning, namely, lactase persistence (LP), is encoded by polymorphisms in the MCM6 gene and varies widely in frequency among different human populations. Although, evolution of LP-related genetic variants was investigated in many groups of Sub-Saharan African, Middle Eastern, and European ancestry, only few studies have focused on populations from North Africa and no data are especially available from the Tunisian one. For this reason, there is an urgent need to investigate the frequency patterns at these loci in Tunisia since this adaptive trait is implicated in health.

Methods

Forty SNPs covering the LCT/MCM6 genes and including the two functional variants ??13,910 C > T and ??22,018 G > A were genotyped in 117 Tunisian individuals using the Sequenom Mass Array technology. The observed nucleotide and haplotype patterns of variation were then compared with those of several African, European, and Mediterranean human groups for which comparable data were publicly available. Admixture analysis on a 5 Mb genomic region surrounding the LCT/MCM6 loci was also performed by extracting genotypes from a previously generated genome-wide dataset in order to deepen the reconstruction of the evolutionary history of these loci.

Results

We found that lactase non-persistence (LNP)-related alleles and haplotypes were predominantly present in the examined population. A clear differentiation between Tunisian, African, and North European/North Italian samples was found, while the Tunisian population showed more genetic affinity to Central and South Italian groups.

Conclusions

Our study provided a first report of LP-associated alleles and haplotypes in the Tunisian population. We highlighted a gradient followed by LP diffusion from Europe to North Africa. Based on the rich historic background of Tunisia, we suggest that this adaptive trait was introduced in that geographic region by a relatively recent gene flow.
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2.

Background

Different strategies have been used to improve the initiation and duration of breastfeeding. Peer counsellors are reported to improve exclusive breastfeeding levels, but few studies have assessed the satisfaction of women with the support given, especially in Africa. In this paper we describe women's experiences of peer counselling for exclusive breastfeeding in an East African setting.

Methods

In the Ugandan site of PROMISE-EBF, a multi-centre community randomised trial to evaluate the effect of peer counselling for exclusive breastfeeding on infant health, 370 women in the intervention arm participated in a study exit interview. Individual peer counselling was offered to women in 12 of the 24 study clusters, scheduled as five visits: before childbirth and during weeks 1, 4, 7 and 10 after childbirth. During the visits, the women were given information and skills to help them breastfeed exclusively. After the 10-week visit, they were interviewed about their feelings and experiences related to the peer counselling.

Results

Overall, more than 95% of the women expressed satisfaction with the various aspects of peer counselling offered. Those who had received five or more visits were more likely to give positive responses about their experience with peer counselling than those who had received fewer visits. They explained their satisfaction with time spent with the peer counsellor in terms of how much she discussed with them. Most women felt their knowledge needs about breastfeeding were covered by the peer counsellors, while others expressed a desire to learn about complementary feeding and family planning. Attributes of the peer counsellors included their friendliness, being women and giving support in a familiar and relaxed way. Women were positive about the acquisition of knowledge and the benefit to their babies from the peer counselling. They preferred a peer counsellor to a health worker for support of exclusive breastfeeding because of their friendly approach.

Conclusions

Individual peer counselling to support exclusive breastfeeding was positively received by the women.

Trial Registration

clinicaltrials.gov no: NCT00397150.
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3.

Background

Diffuse alveolar hemorrhage syndrome is a life threatening condition with diverse etiologies. Sensitive prognostic markers for diffuse alveolar hemorrhage have not been well investigated. Serum KL-6 is a biomarker for various interstitial lung disease associated with disease activity and prognosis. The purpose of the present study was to evaluate the clinical utility of serum KL-6 level as a prognostic marker for diffuse alveolar hemorrhage.

Methods

We retrospectively collected 41 consecutive patients clinically diagnosed as having diffuse alveolar hemorrhage who were admitted to the Intensive Care Unit of Hiroshima University Hospital between 2004 and 2011. Correlation between prognosis and age, sex, laboratory findings including serum KL-6, radiological findings, ventilatory modes or therapeutic regimens were evaluated.

Results

Baseline and peak serum KL-6 levels were significantly higher in non-survivors compared with survivors. An increase in KL-6 levels during the initial week was associated with a subsequent deterioration of the oxygenation index. Higher baseline KL-6 levels and higher peak KL-6 levels were strongly correlated with death. With a cut-off level of 700 U/mL for peak KL-6, the sensitivity, specificity and accuracy for non-survival were 75%, 85% and 78%, respectively. In the multivariate analysis, only the peak KL-6 level ≥700 U/ml was an independent poor prognostic factor for diffuse alveolar hemorrhage.

Conclusions

Peak serum KL-6 level ≥700 U/ml may become a clinically useful marker of poor prognosis for diffuse alveolar hemorrhage.
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4.

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.
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5.

Background

The etiology of more than half of all patients with X-linked intellectual disability remains elusive, despite array-based comparative genomic hybridization, whole exome or genome sequencing. Since short read massive parallel sequencing approaches do not allow the detection of larger tandem repeat expansions, we hypothesized that such expansions could be a hidden cause of X-linked intellectual disability.

Methods

We selectively captured over 1800 tandem repeats on the X chromosome and characterized them by long read single molecule sequencing in 3 families with idiopathic X-linked intellectual disability.

Results

In male DNA samples, full tandem repeat length sequences were obtained for 88–93% of the targets and up to 99.6% of the repeats with a moderate guanine-cytosine content. Read length and analysis pipeline allow to detect cases of >?900?bp tandem repeat expansion. In one family, one repeat expansion co-occurs with down-regulation of the neighboring MIR222 gene. This gene has previously been implicated in intellectual disability and is apparently linked to FMR1 and NEFH overexpression associated with neurological disorders.

Conclusions

This study demonstrates the power of single molecule sequencing to measure tandem repeat lengths and detect expansions, and suggests that tandem repeat mutations may be a hidden cause of X-linked intellectual disability.
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6.

Background

Infection with H. pylori is important in the etiology of gastric cancer. Gastric cancer is infrequent in Africa, despite high frequencies of H. pylori infection, referred to as the African enigma. Variation in environmental and host factors influencing gastric cancer risk between different populations have been reported but little is known about the biological differences between gastric cancers from different geographic locations. We aim to study genomic instability patterns of gastric cancers obtained from patients from United Kingdom (UK) and South Africa (SA), in an attempt to support the African enigma hypothesis at the biological level.

Methods

DNA was isolated from 67 gastric adenocarcinomas, 33 UK patients, 9 Caucasian SA patients and 25 native SA patients. Microsatellite instability and chromosomal instability were analyzed by PCR and microarray comparative genomic hybridization, respectively. Data was analyzed by supervised univariate and multivariate analyses as well as unsupervised hierarchical cluster analysis.

Results

Tumors from Caucasian and native SA patients showed significantly more microsatellite instable tumors (p < 0.05). For the microsatellite stable tumors, geographical origin of the patients correlated with cluster membership, derived from unsupervised hierarchical cluster analysis (p = 0.001). Several chromosomal alterations showed significantly different frequencies in tumors from UK patients and native SA patients, but not between UK and Caucasian SA patients and between native and Caucasian SA patients.

Conclusions

Gastric cancers from SA and UK patients show differences in genetic instability patterns, indicating possible different biological mechanisms in patients from different geographical origin. This is of future clinical relevance for stratification of gastric cancer therapy.
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7.

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.
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8.

Purpose of Review

The emergence of a group of previously unknown or unrecognized dimorphic fungal species causing systemic human disease resulted in taxonomic shifts and the creation of a new genus, Emergomyces, within Onygenales. We review the morphology, taxonomy, physiology, and ecology of Emergomyces spp., and the epidemiology, clinicopathology, diagnosis, and management of disease.

Recent Findings

Emergomyces species have been reported as causes of human disease in Europe, Asia, Africa, and North America. Es. pasteurianus is most cosmopolitan, and Es. africanus, in southern Africa, causes the largest reported disease burden; in fact, emergomycosis is the most common endemic mycosis diagnosed in South Africa. The classic clinical picture is of disseminated disease, often with cutaneous involvement, in immunocompromised individuals.

Summary

Members of the genus Emergomyces are uncommon but important agents of systemic disease in immunocompromised hosts worldwide. Knowledge gaps include the biology of the fungus, and the pathophysiology and management of disease.
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9.

Introduction

The Latitudinal Gradient Hypothesis (LGH) foresees that specialized metabolites are overexpressed under low latitudes, where organisms are subjected to higher herbivory pressure. The widespread macroalga Asparagopsis taxiformis is composed of six distinct genetic lineages, some of them being introduced in many regions.

Objectives

To study (i) metabolic fingerprints of the macroalga and (ii) its bioactivity in space and time, both as proxies of its investment in defensive traits, in order to assess links between bioactivities and metabotypes with macroalgal invasiveness.

Methods

289 macroalgal individuals, from four tropical and three temperate regions, were analyzed using untargeted metabolomics and the standardized Microtox® assay.

Results

Metabotypes showed a low divergence between tropical and temperate populations, while bioactivities were higher in temperate populations. However, these phenotypes varied significantly in time, with a higher variability in tropical regions. Bioactivities were high and stable in temperate regions, whereas they were low and much variable in tropical regions. Although the introduced lineage two exhibited the highest bioactivities, this lineage could also present variable proliferation fates.

Conclusion

The metabolomic approach partly discriminates macroalgal populations from various geographic origins. The production of chemical defenses assessed by the bioactivity assay does not match the macroalgal genetic lineage and seems more driven by the environment. The higher content of chemical defenses in temperate versus tropical populations is not in accordance with the LGH and cannot be related to the invasiveness of the macroalgae.
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10.

Background

Sheeppox virus (SPPV) and goatpox virus (GTPV), members of the Capripoxvirus genus of the Poxviridae family are causative agents of sheep pox and goat pox respectively, which are important contagious diseases and endemic in central and northern Africa, the Middle and Far East, and the Indian sub-continent. Both sheep pox and goat pox can cause wool and hide damage, and reduce the production of mutton and milk, which may result in significant economic losses and threaten the stockbreeding. In this study, three SPPVs and two GTPVs were collected from China in 2009 and 2011. We described the sequence features and phylogenetic analysis of the P32 gene, GPCR gene and RPO30 gene of the SPPVs and GTPVs to reveal their genetic relatedness.

Results

Sequence and phylogenetic analysis showed that there was a close relationship among SPPV/GanS/2/2011/China, SPPV/GanS/1/2011/China and SPPV/NingX/2009/China. They were clustered on the same SPPV clade. GTPV/HuB/2009/China and GS-V1 belonged to the GTPV lineage. GS-V1 was closely related to other GTPV vaccine strains. GTPV/HuB/2009/China and GS-V1 were clustered with GTPVs from China and some southern Asian countries.

Conclusion

This study may expand the datum for spread trend research of Chinese SPPVs and GTPVs, meanwhile provide theoretical references to improve the preventive and control strategy.
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11.

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.
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12.

Background and aims

It is generally assumed that very large herbivores, such as elephants, make foraging decisions at large spatial scales, but the extent to which seasonal foraging decisions are driven by soil quality, and its link to plant nutrient levels, is uncertain.

Methods

We studied the diet selection of African elephants Loxodonta africana in Ithala Game Reserve in northern KwaZulu-Natal, South Africa, using data on elephant feeding preferences and spatial distributions from a published paper. Elephants were present in the eastern half with granite soils in the wet season, and in the western half with sedimentary soils in the dry season. The quality of these two soil types and of seven key tree species for elephants was assessed in both seasons.

Results

Soil quality was higher on the sedimentary soils in terms of total nitrogen, soil respiration, water-holding capacity, organic carbon and pH. Leaf quality was higher on the sedimentary soils in the dry season, while in the wet season there was no significant difference in leaf quality of the seven key tree species growing on the two substrates.

Conclusion

Soil quality may explain elephants’ foraging decisions in the dry season, but not in the wet season. Elephants preferred trees with higher protein and lower concentrations of fibre on both granite and sedimentary soils.
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13.

Background

Glaucoma is a leading cause of blindness in developed countries. Primary open-angle glaucoma (POAG), the most prevalent clinical subtype of glaucoma in the United States, affects African Americans at a higher rate compared with European Americans. Risk factors identified for POAG include increased age and family history, which coupled with heritability estimates, suggest this complex condition is associated with genetic and environmental factors. To date, several genome-wide studies have identified loci significantly associated with POAG risk, but most of these studies were performed in populations of European-descent.

Methods

To identify population-specific and trans-population genetic associations for POAG, we genotyped 11,521 African Americans using the Illumina Metabochip as part of the Epidemiologic Architecture for Genes Linked to Environment (EAGLE) study accessing BioVU, the Vanderbilt University Medical Center’s biorepository linked to de-identified electronic health records. Among this study population, we identified 138 cases of POAG and 1376 controls and performed Metabochip-wide tests of association. We also estimated local genetic ancestry at CDKN2B-AS1, a POAG-associated locus established in European-descent populations.

Results

Overall, we did not identify significant single SNP-POAG associations after adjusting for multiple testing. We did, however, detect a significant association between POAG risk and local African genetic ancestry at CDKN2B-AS1, where on average cases were of 90% African descent compared with controls at 58% (p?=?2?×?10??6).

Conclusions

These data suggest that CDKN2B-AS1 is an important locus for POAG risk among African Americans, warranting further investigation to identify the variants underlying this association.
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14.

Background

While continental level ancestry is relatively simple using genomic information, distinguishing between individuals from closely associated sub-populations (e.g., from the same continent) is still a difficult challenge.

Methods

We study the problem of predicting human biogeographical ancestry from genomic data under resource constraints. In particular, we focus on the case where the analysis is constrained to using single nucleotide polymorphisms (SNPs) from just one chromosome. We propose methods to construct such ancestry informative SNP panels using correlation-based and outlier-based methods.

Results

We accessed the performance of the proposed SNP panels derived from just one chromosome, using data from the 1000 Genome Project, Phase 3. For continental-level ancestry classification, we achieved an overall classification rate of 96.75% using 206 single nucleotide polymorphisms (SNPs). For sub-population level ancestry prediction, we achieved an average pairwise binary classification rates as follows: subpopulations in Europe: 76.6% (58 SNPs); Africa: 87.02% (87 SNPs); East Asia: 73.30% (68 SNPs); South Asia: 81.14% (75 SNPs); America: 85.85% (68 SNPs).

Conclusion

Our results demonstrate that one single chromosome (in particular, Chromosome 1), if carefully analyzed, could hold enough information for accurate prediction of human biogeographical ancestry. This has significant implications in terms of the computational resources required for analysis of ancestry, and in the applications of such analyses, such as in studies of genetic diseases, forensics, and soft biometrics.
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15.

Purpose

The study aimed to evaluate the environmental impacts of used lubricating oil (ULO) recovery in the largest oil consumer country in Africa, Egypt. The main questions were: What are the impacts of the different waste management strategies for the recovery of used lubricating oil and which waste management strategy is more eco-friendly?

Methods

Life cycle assessment (LCA) was employed to model the environmental impacts of the two waste management approaches for used lubricating oil recovery in Egypt: recycling by re-firing and recovery by co-firing. The model was applied to assess the impacts of one of the largest ULO recovery units in the Middle East and North Africa (MENA) region and the only operating unit in Egypt. The following impact categories were included: global warming potential (GWP), acidification potential (AP), eutrophication potential (EP), carcinogens potential (CP), ecotoxicity potential (ETP), respiratory inorganic formation potential (RIFP), respiratory organic formation potential (ROFP), radiation potential (RP), ozone layer depletion (OLD), mineral depletion (MD), land use (LU) and fossil fuel depletion (FFD).

Results and discussion

Results indicated that recycling by re-refining strategy is more environment-friendly. De-asphalting, de-aromatization and de-waxing processes are the main processes that affect the environmental impacts of lubricating oil production in both strategies, due to the use of hazard materials and toxic solvents in these processes. Fuel gas and fuel oil used as a fuel in the refinery and power units are the main contributors affecting the environmental impacts in case of recycling by re-refining strategy. The highest impacts were detected on FFD, followed by RIFP, GWP, AP, EP, ETP and CP in both strategies; no impacts were detected on RP, OLD and MD.

Conclusions

It can be concluded that recycling by re-refining of ULO is the more eco-friendly approach. This strategy is more energy conservative, saves a diminishing fossil fuel resource and reduces burdens on the environment. ULO containing high percentages of additive remnants such as viscosity index improvers and pour point depressants which represents a valuable resource and its proper management should be given the most attention.
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16.

Objective

This study examined the differences of psychological strains between Chinese and American college students and discussed how strains may influence individuals’ suicidal ideation and depression.

Participants/methods

A total of 539 college students (298 from China and 241 from the U.S.) were recruited in March 2016 to complete the survey study. Multiple linear regressions were used in data analysis.

Results

Students in America had higher scores on depression and stress than students in China, while students in China rated higher on suicidal ideation than students in America. In contrast of students in America facing more coping strains, students in China were confronting more value strains in their life.

Conclusion

The cross-cultural variations in the effect of psychological strains have been substantiated in current study, indicating that understanding the psychological strains in different cultural contexts is necessary for the early intervention and prevention in college aged populations.
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17.

Purpose

Metabolic syndrome (MS) is a clustering of cardiovascular disease risk factors that identifies individuals with the highest risk for heart disease. Two factors that may influence the MS are physical activity and aerobic fitness. This study determined if adolescent with the MS had low levels of aerobic fitness and physical activity as children.

Methods

This longitudinal, exploratory study had 389 participants: 51% girls, 84% Caucasian, 12% African American, 1% Hispanic, and 3% other races, from the State of North Carolina. Habitual physical activity (PA survey), aerobic fitness (VO2max), body mass index (BMI), blood pressure, and lipids obtained at 7–10 y of age were compared to their results obtained 7 y later at ages 14–17 y.

Results

Eighteen adolescents (4.6%) developed 3 or more characteristics of the MS. Logistic regression, adjusting for BMI percentile, blood pressure, and cholesterol levels, found that adolescents with the MS were 6.08 (95%CI = 1.18–60.08) times more likely to have low aerobic fitness as children and 5.16 (95%CI = 1.06–49.66) times more likely to have low PA levels.

Conclusion

Low levels of childhood physical activity and aerobic fitness are associated with the presence of the metabolic syndrome in adolescents. Thus, efforts need to begin early in childhood to increase exercise.
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18.

Background

Apiculture has been practiced in North Africa and the Middle-East from antiquity. Several thousand years of selective breeding have left a mosaic of Apis mellifera subspecies in the Middle-East, many uniquely adapted and survived to local environmental conditions. In this study we explore the genetic diversity of A. mellifera from Syria (n?=?1258), Lebanon (n?=?169) and Iraq (n?=?35) based on 14 short tandem repeat (STR) loci in the context of reference populations from throughout the Old World (n?=?732).

Results

Our data suggest that the Syrian honeybee Apis mellifera syriaca occurs in both Syrian and Lebanese territories, with no significant genetic variability between respective populations from Syria and Lebanon. All studied populations clustered within a new fifth independent nuclear cluster, congruent with an mtDNA Z haplotype identified in a previous study. Syrian honeybee populations are not associated with Oriental lineage O, except for sporadic introgression into some populations close to the Turkish and Iraqi borders. Southern Syrian and Lebanese populations demonstrated high levels of genetic diversity compared to the northern populations.

Conclusion

This study revealed the effects of foreign queen importations on Syrian bee populations, especially for the region of Tartus, where extensive introgression of A. m. anatolica and/or A. m. caucasica alleles were identified. The policy of creating genetic conservation centers for the Syrian subspecies should take into consideration the influence of the oriental lineage O from the northern Syrian border and the large population of genetically divergent indigenous honeybees located in southern Syria.
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19.

Purpose

The aim of the current study was to analyze the impacts of acrylic fiber manufacturing on the environment and to obtain information for assisting decision makers in improving relevant environmental protection measures for green field investments in developing countries especially in Africa and Middle East and North Africa (MENA) regions. The key research questions were as follows: what are the different impacts of acrylic fiber manufacturing on the environment and which base material has the highest impact?

Methods

The life cycle assessment (LCA) started from obtaining the raw material until the end of the production process (cradle to gate analysis). Focus was given on water consumption, energy utilization in acrylic fiber production, and generated waste from the industry. The input and output data for life cycle inventory was collected from an acrylic fiber manufacturing plant in Egypt. SimaPro software was used to calculate the inventory of twelve impact categories that were taken into consideration, including global warming potential (GWP), acidification potential (AP), eutrophication potential (EP), carcinogen potential (CP), ecotoxicity potential (ETP), respiratory inorganic formation potential (RIFP), respiratory organic formation potential (ROFP), radiation potential (RP), ozone layer depletion (OLD), mineral depletion (MD), land use (LU), and fossil fuel depletion (FFD).

Results and discussion

LCA results of acrylic fiber manufacturing on the environment show that 82.0 % of the impact is on fossil fuel depletion due to the high-energy requirement for acrylonitrile production, 15.9 % of the impact is on human health, and 2.1 % on ecosystem quality. No impacts were detected on radiation potential, ozone layer depletion, land use, mineral depletion, or human respiratory system due to organic substances.

Conclusions

Based on these study results, it is concluded that acrylic fiber manufacturing is a high-energy consumption industry with the highest impact to be found on fossil fuel depletion and human health. This study is based on modeling the environmental effects of the production of 1-kg acrylic fiber and can serve to estimate impacts of similar manufacturing facilities and accordingly use these results as an indicator for better decision-making.
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20.

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.
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