| 1. |
- Zamora, Juan Carlos, et al.
(author)
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Considerations and consequences of allowing DNA sequence data as types of fungal taxa
- 2018
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In: IMA Fungus. - : INT MYCOLOGICAL ASSOC. - 2210-6340 .- 2210-6359. ; 9:1, s. 167-185
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Journal article (peer-reviewed)abstract
- Nomenclatural type definitions are one of the most important concepts in biological nomenclature. Being physical objects that can be re-studied by other researchers, types permanently link taxonomy (an artificial agreement to classify biological diversity) with nomenclature (an artificial agreement to name biological diversity). Two proposals to amend the International Code of Nomenclature for algae, fungi, and plants (ICN), allowing DNA sequences alone (of any region and extent) to serve as types of taxon names for voucherless fungi (mainly putative taxa from environmental DNA sequences), have been submitted to be voted on at the 11th International Mycological Congress (Puerto Rico, July 2018). We consider various genetic processes affecting the distribution of alleles among taxa and find that alleles may not consistently and uniquely represent the species within which they are contained. Should the proposals be accepted, the meaning of nomenclatural types would change in a fundamental way from physical objects as sources of data to the data themselves. Such changes are conducive to irreproducible science, the potential typification on artefactual data, and massive creation of names with low information content, ultimately causing nomenclatural instability and unnecessary work for future researchers that would stall future explorations of fungal diversity. We conclude that the acceptance of DNA sequences alone as types of names of taxa, under the terms used in the current proposals, is unnecessary and would not solve the problem of naming putative taxa known only from DNA sequences in a scientifically defensible way. As an alternative, we highlight the use of formulas for naming putative taxa (candidate taxa) that do not require any modification of the ICN.
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| 2. |
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- 2019
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Journal article (peer-reviewed)
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| 3. |
- Barone, Giovanni Davide, et al.
(author)
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Harnessing photosynthetic microorganisms for enhanced bioremediation of microplastics : A comprehensive review
- 2024
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In: ENVIRONMENTAL SCIENCE AND ECOTECHNOLOGY. - : Elsevier. - 2666-4984. ; 20
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Research review (peer-reviewed)abstract
- Mismanaged plastics, upon entering the environment, undergo degradation through physicochemical and/or biological processes. This process often results in the formation of microplastics (MPs), the most prevalent form of plastic debris (<1 mm). MPs pose severe threats to aquatic and terrestrial ecosystems, necessitating innovative strategies for effective remediation. Some photosynthetic microorganisms can degrade MPs but there lacks a comprehensive review. Here we examine the specific role of photoautotrophic microorganisms in water and soil environments for the biodegradation of plastics, focussing on their unique ability to grow persistently on diverse polymers under sunlight. Notably, these cells utilise light and CO2 to produce valuable compounds such as carbohydrates, lipids, and proteins, showcasing their multifaceted environmental benefits. We address key scientific questions surrounding the utilisation of photosynthetic microorganisms for MPs and nanoplastics (NPs) bioremediation, discussing potential engineering strategies for enhanced efficacy. Our review highlights the significance of alternative biomaterials and the exploration of strains expressing enzymes, such as polyethylene terephthalate (PET) hydrolases, in conjunction with microalgal and/or cyanobacterial metabolisms. Furthermore, we delve into the promising potential of photo-biocatalytic approaches, emphasising the coupling of plastic debris degradation with sunlight exposure. The integration of microalgal-bacterial consortia is explored for biotechnological applications against MPs and NPs pollution, showcasing the synergistic effects in wastewater treatment through the absorption of nitrogen, heavy metals, phosphorous, and carbon. In conclusion, this review provides a comprehensive overview of the current state of research on the use of photoautotrophic cells for plastic bioremediation. It underscores the need for continued investigation into the engineering of these microorganisms and the development of innovative approaches to tackle the global issue of plastic pollution in aquatic and terrestrial ecosystems. (c) 2024 The Authors. Published by Elsevier B.V. on behalf of Chinese Society for Environmental Sciences, Harbin Institute of Technology, Chinese Research Academy of Environmental Sciences.
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| 4. |
- Emmert, Kirsten, et al.
(author)
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Meta-analysis of real-time fMRI neurofeedback studies using individual participant data : How is brain regulation mediated?
- 2016
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In: NeuroImage. - : Elsevier BV. - 1053-8119 .- 1095-9572. ; 124:Part A, s. 806-812
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Journal article (peer-reviewed)abstract
- An increasing number of studies using real-time fMRI neurofeedback have demonstrated that successful regulation of neural activity is possible in various brain regions. Since these studies focused on the regulated region(s), little is known about the target-independent mechanisms associated with neurofeedback-guided control of brain activation, i.e. the regulating network. While the specificity of the activation during self-regulation is an important factor, no study has effectively determined the network involved in self-regulation in general. In an effort to detect regions that are responsible for the act of brain regulation, we performed a post-hoc analysis of data involving different target regions based on studies from different research groups. We included twelve suitable studies that examined nine different target regions amounting to a total of 175 subjects and 899 neurofeedback runs. Data analysis included a standard first-(single subject, extracting main paradigm) and second-level (single subject, all runs) general linear model (GLM) analysis of all participants taking into account the individual timing. Subsequently, at the third level, a random effects model GLM included all subjects of all studies, resulting in an overall mixed effects model. Since four of the twelve studies had a reduced field of view (FoV), we repeated the same analysis in a subsample of eight studies that had a well-overlapping FoV to obtain a more global picture of self-regulation. The GLM analysis revealed that the anterior insula as well as the basal ganglia, notably the striatum, were consistently active during the regulation of brain activation across the studies. The anterior insula has been implicated in interoceptive awareness of the body and cognitive control. Basal ganglia are involved in procedural learning, visuomotor integration and other higher cognitive processes including motivation. The larger FoV analysis yielded additional activations in the anterior cingulate cortex, the dorsolateral and ventrolateral prefrontal cortex, the temporo-parietal area and the visual association areas including the temporo-occipital junction. In conclusion, we demonstrate that several key regions, such as the anterior insula and the basal ganglia, are consistently activated during self-regulation in real-time fMRI neurofeedback independent of the targeted region-ofinterest. Our results imply that if the real-time fMRI neurofeedback studies target regions of this regulation network, such as the anterior insula, care should be given whether activation changes are related to successful regulation, or related to the regulation process per se. Furthermore, future research is needed to determine how activation within this regulation network is related to neurofeedback success.
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| 5. |
- Escott-Price, Valentina, et al.
(author)
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Gene-Wide Analysis Detects Two New Susceptibility Genes for Alzheimer's Disease
- 2014
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In: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 9:6, s. e94661-
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Journal article (peer-reviewed)abstract
- Background: Alzheimer's disease is a common debilitating dementia with known heritability, for which 20 late onset susceptibility loci have been identified, but more remain to be discovered. This study sought to identify new susceptibility genes, using an alternative gene-wide analytical approach which tests for patterns of association within genes, in the powerful genome-wide association dataset of the International Genomics of Alzheimer's Project Consortium, comprising over 7 m genotypes from 25,580 Alzheimer's cases and 48,466 controls. Principal Findings: In addition to earlier reported genes, we detected genome-wide significant loci on chromosomes 8 (TP53INP1, p = 1.4x10(-6)) and 14 (IGHV1-67 p = 7.9x10(-8)) which indexed novel susceptibility loci. Significance: The additional genes identified in this study, have an array of functions previously implicated in Alzheimer's disease, including aspects of energy metabolism, protein degradation and the immune system and add further weight to these pathways as potential therapeutic targets in Alzheimer's disease.
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| 6. |
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| 7. |
- Johnston, Wesley, et al.
(author)
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Scientific muddling : Decision making through a Lindblomian lens
- 2012
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In: Journal of Business Research. - : Elsevier BV. - 0148-2963 .- 1873-7978. ; 65:6, s. 717-719
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Journal article (peer-reviewed)abstract
- This introduction reviews the history and core principles of Charles Lindblom's concept of muddling and its application across a wide array of business decisions. The approach recognizes certain decisions as sequential. strategic practices and thus finds applications in a wide variety of business decisions. This article provides a brief summary of the 15 contributions that follow and take up on this theme. The authors extend a note of appreciation to the reviewers of the papers in the issue and to the editor of Joumal of Business Research, Arch Woodside. (C) 2011 Elsevier Inc. All rights reserved.
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| 8. |
- Jones, Lesley, et al.
(author)
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Convergent genetic and expression data implicate immunity in Alzheimer's disease
- 2015
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In: Alzheimer's & Dementia. - : Wiley. - 1552-5260 .- 1552-5279. ; 11:6, s. 658-671
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Journal article (peer-reviewed)abstract
- Background: Late-onset Alzheimer's disease (AD) is heritable with 20 genes showing genome-wide association in the International Genomics of Alzheimer's Project (IGAP). To identify the biology underlying the disease, we extended these genetic data in a pathway analysis. Methods: The ALIGATOR and GSEA algorithms were used in the IGAP data to identify associated functional pathways and correlated gene expression networks in human brain. Results: ALIGATOR identified an excess of curated biological pathways showing enrichment of association. Enriched areas of biology included the immune response (P = 3.27 X 10(-12) after multiple testing correction for pathways), regulation of endocytosis (P = 1.31 X 10(-11)), cholesterol transport (P = 2.96 X 10(-9)), and proteasome-ubiquitin activity (P = 1.34 X 10(-6)). Correlated gene expression analysis identified four significant network modules, all related to the immune response (corrected P = .002-.05). Conclusions: The immime response, regulation of endocytosis, cholesterol transport, and protein ubiquitination represent prime targets for AD therapeutics.
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| 9. |
- Nene, Vishvanath, et al.
(author)
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Genome sequence of Aedes aegypti, a major arbovirus vector.
- 2007
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In: Science (New York, N.Y.). - : American Association for the Advancement of Science (AAAS). - 1095-9203 .- 0036-8075. ; 316:5832, s. 1718-23
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Journal article (peer-reviewed)abstract
- We present a draft sequence of the genome of Aedes aegypti, the primary vector for yellow fever and dengue fever, which at approximately 1376 million base pairs is about 5 times the size of the genome of the malaria vector Anopheles gambiae. Nearly 50% of the Ae. aegypti genome consists of transposable elements. These contribute to a factor of approximately 4 to 6 increase in average gene length and in sizes of intergenic regions relative to An. gambiae and Drosophila melanogaster. Nonetheless, chromosomal synteny is generally maintained among all three insects, although conservation of orthologous gene order is higher (by a factor of approximately 2) between the mosquito species than between either of them and the fruit fly. An increase in genes encoding odorant binding, cytochrome P450, and cuticle domains relative to An. gambiae suggests that members of these protein families underpin some of the biological differences between the two mosquito species.
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| 10. |
- Olsson, Rolf, et al.
(author)
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Combined videomanometric identification of abnormalities related to pharyngeal retention
- 1997
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In: Academic Radiology. - 1878-4046. ; 4:5, s. 349-354
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Journal article (peer-reviewed)abstract
- RATIONALE AND OBJECTIVES: The authors determined the usefulness of performing videoradiography and pharyngeal solid-state manometry during barium swallow in dysphagic patients with pharyngeal retention. METHODS: Results were retrospectively analyzed of simultaneous videoradiography and manometry examinations in 14 patients with retention of barium in the pharynx. Twelve age-matched patients without retention served as a control group. RESULTS: Patients with retention regularly had less opening of the upper esophageal sphincter than patients without retention (7.6 vs 10.3 mm, respectively; P = .003). In patients with retention, the laryngeal elevation was lower (17.1 vs 23.8 mm, respectively; P = .001), and the resting pressure of the upper esophageal sphincter was significantly lower (42.4 vs 54.0 mm Hg, respectively; P = .04). The duration of upper esophageal sphincter relaxation was also shorter in patients with retention (374 vs 603 msec, respectively; P = .003). The peak pharyngeal contraction pressure was not significantly different. CONCLUSION: The constrictors play a minor role in the conveyance of the bolus through the pharynx. Pharyngeal shortening could be the most important mechanism in bolus transport.
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