| 1. |
- Zamora, Juan Carlos, et al.
(författare)
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Considerations and consequences of allowing DNA sequence data as types of fungal taxa
- 2018
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Ingår i: IMA Fungus. - : INT MYCOLOGICAL ASSOC. - 2210-6340 .- 2210-6359. ; 9:1, s. 167-185
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Tidskriftsartikel (refereegranskat)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. |
- Aad, G, et al.
(författare)
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- 2015
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swepub:Mat__t
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| 3. |
- Knutsson, Jesper, 1973, et al.
(författare)
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Evaluation of a passive sampler for the speciation of metals in urban runoff water
- 2013
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Ingår i: Environmental Sciences: Processes and Impacts. - : Royal Society of Chemistry (RSC). - 2050-7895 .- 2050-7887. ; 15:12, s. 2233-2239
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Tidskriftsartikel (refereegranskat)abstract
- Metals in urban runoff water need to be monitored in order to estimate fluxes and assess their impact on the aquatic environment. Passive sampling is a useful and reliable emerging tool for measuring time averaged concentrations of metals in water bodies. This paper describes the deployment of a passive sampler to measure Cu, Ni and Zn in an urban runoff water treatment facility. The concentrations derived from the passive samplers are compared to concentrations obtained from an automated water sampler which provides pooled spot water samples and to model predictions from the visualMINTEQ computer speciation code. Results show that visualMINTEQ predictions partly describe the metal speciation in non-equilibrium systems. In addition we conclude that passive samplers are useful for monitoring and characterization of metal speciation under chemodynamic conditions. © 2013 The Royal Society of Chemistry.
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| 4. |
- Arnesson, Marcus, et al.
(författare)
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Naturvärden i lövträdsmiljöer runt Värnanäs
- 2007
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- Området vid Värnanäs har tidigare pekats ut för att ha internationella naturvärden. De inventeringar som presenteras här i rapporten bekräftar detta med många och mycket ovanliga arter. Den gemensamma nämnaren för de flesta av arterna är de gamla och grova träden framför allt av ek och bok. I samband med trädinventeringen noterades 2681 värdefulla träd, både levande träd, döda liggande, döda stående och högstubbar. Det största trädet är en ek med en omkrets på 969 cm. Eken tillhör med stor sannolikhet ett av landets tio största träd. Sammanlagt finns tio träd i området med en omkrets på över 6 meter, av dessa är nio ekar och en bokhögstubbe. Hela 66 inmätta träd har en omkrets på över 5 meter. Anmärkningsvärt är även den grova sälgen vid Halltorpsån med en omkrets på 450 cm samt tallen med en omkrets 482 cm, båda tillhör de absolut största av sitt trädslag i Sverige. I trädinventeringen noterades 1227 håliga lövträd av dessa var 446 ekar och 397 bokar. Där fanns också en hel del grova högstubbar och döda stående träd. Totalt noterades 56 bokar och 97 ekar som hade en brösthöjdsdiameter >40 cm. Sätts gränsen till >99 cm blir antalet 19 bokar och 30 ekar. Grova lågor är extremt sällsynt i dagens landskap men inom det inventerade området påträffades 59 bokar och 140 ekar med en basdiameter >40 cm. Sätts gränsen till >99 cm blir antalet 5 bokar och 30 ekar. Under 2006 inventerades vedlevande skalbaggar, fjärilar, lavar och svampar och 2004 inventerades fladdermöss. Antalet funna rödlistade arter bara under 2006 var: 65 skalbaggar, 6 fjärilar, 16 svampar och 14 lavar. Undersökningarna är inte heltäckande och flera tidigare funna arter som sannolikt finns kvar i området hittades inte under 2006. Området hyser också en rad rödlistade arter ur andra organismgrupper, noterat är bland annat 3 fladdermöss, 2 grod- och kräldjur samt 19 fåglar. En förutsättning för att behålla naturvärdena är att trygga förekomsten av gamla träd i området och spara alla former av död ved. Det finns ett stort behov att röja runt äldre träd. Det är också viktigt att skötseln görs på ett sådant sätt att antalet skyddsvärda träd ökar på sikt. En annan förutsättning är att de förekommer i en mosaik av öppna och halvöppna områden. Allt detta kräver skötsel i form av röjningar och bete. På de igenväxta markerna bör restaurering med efterföljande betesdrift ske snarast för att inte naturvärden ska gå förlorade. Ett annat problem, främst i bokbestånden, är att åldersblandningen homogeniserats via gallringar. För att naturvärdena på sikt ska bestå och utvecklas måste de gamla träden få tillräckligt med utrymme och nya gammelträd kontinuerligt bildas. Detta är mycket svårt att förena med produktionsinriktad skogsskötsel. Inventeringen av skyddsvärda träd ingår i det nationella åtgärdsprogrammet för skyddsvärda träd i kulturlandskapet. Området berörs av nio olika åtgärdsprogram och utöver det ovan nämnda är följande åtgärdsprogram aktuella för området: skalbaggar i eklågor (där svart guldbagge och brunoxe ingår), hotade bokskogsarter (där bokblombock och rombjätteknäppare ingår), läderbagge, havsörn, långbensgroda, sandödla, större vattensalamander och knubbsäl (Östersjöbestånd).
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| 5. |
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| 6. |
- Donahue, Manus J, et al.
(författare)
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Consensus statement on current and emerging methods for the diagnosis and evaluation of cerebrovascular disease
- 2018
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Ingår i: Journal of cerebral blood flow and metabolism : official journal of the International Society of Cerebral Blood Flow and Metabolism. - 1559-7016. ; 38:9, s. 1391-1417
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Forskningsöversikt (refereegranskat)abstract
- Cerebrovascular disease (CVD) remains a leading cause of death and the leading cause of adult disability in most developed countries. This work summarizes state-of-the-art, and possible future, diagnostic and evaluation approaches in multiple stages of CVD, including (i) visualization of sub-clinical disease processes, (ii) acute stroke theranostics, and (iii) characterization of post-stroke recovery mechanisms. Underlying pathophysiology as it relates to large vessel steno-occlusive disease and the impact of this macrovascular disease on tissue-level viability, hemodynamics (cerebral blood flow, cerebral blood volume, and mean transit time), and metabolism (cerebral metabolic rate of oxygen consumption and pH) are also discussed in the context of emerging neuroimaging protocols with sensitivity to these factors. The overall purpose is to highlight advancements in stroke care and diagnostics and to provide a general overview of emerging research topics that have potential for reducing morbidity in multiple areas of CVD.
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| 7. |
- Durmo, Faris, et al.
(författare)
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Brain Tumor Characterization Using Multibiometric Evaluation of MRI
- 2018
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Ingår i: Tomography : a journal for imaging research. - : MDPI AG. - 2379-1381. ; 4:1, s. 14-25
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Tidskriftsartikel (refereegranskat)abstract
- The aim was to evaluate volume, diffusion, and perfusion metrics for better presurgical differentiation between high-grade gliomas (HGG), low-grade gliomas (LGG), and metastases (MET). For this retrospective study, 43 patients with histologically verified intracranial HGG (n = 18), LGG (n = 10), and MET (n = 15) were chosen. Preoperative magnetic resonance data included pre- and post-gadolinium contrast-enhanced T1-weighted fluid-attenuated inversion recover, cerebral blood flow (CBF), cerebral blood volume (CBV), fractional anisotropy, and apparent diffusion coefficient maps used for quantification of magnetic resonance biometrics by manual delineation of regions of interest. A binary logistic regression model was applied for multiparametric analysis and receiver operating characteristic (ROC) analysis. Statistically significant differences were found for normalized-ADC-tumor (nADC-T), normalized-CBF-tumor (nCBF-T), normalized-CBV-tumor (nCBV-T), and normalized-CBF-edema (nCBF-E) between LGG and HGG, and when these metrics were combined, HGG could be distinguished from LGG with a sensitivity and specificity of 100%. The only metric to distinguish HGG from MET was the normalized-ADC-E with a sensitivity of 68.8% and a specificity of 80%. LGG can be distinguished from MET by combining edema volume (Vol-E), Vol-E/tumor volume (Vol-T), nADC-T, nCBF-T, nCBV-T, and nADC-E with a sensitivity of 93.3% and a specificity of 100%. The present study confirms the usability of a multibiometric approach including volume, perfusion, and diffusion metrics in differentially diagnosing brain tumors in preoperative patients and adds to the growing body of evidence in the clinical field in need of validation and standardization.
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| 8. |
- Eklund, Anders, 1981-, et al.
(författare)
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Cluster failure revisited: Impact of first level design and physiological noise on cluster false positive rates
- 2019
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Ingår i: Human Brain Mapping. - : Wiley. - 1065-9471 .- 1097-0193. ; 40:7, s. 2017-2032
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Tidskriftsartikel (refereegranskat)abstract
- Methodological research rarely generates a broad interest, yet our work on the validity of cluster inference methods for functional magnetic resonance imaging (fMRI) created intense discussion on both the minutia of our approach and its implications for the discipline. In the present work, we take on various critiques of our work and further explore the limitations of our original work. We address issues about the particular event‐related designs we used, considering multiple event types and randomization of events between subjects. We consider the lack of validity found with one‐sample permutation (sign flipping) tests, investigating a number of approaches to improve the false positive control of this widely used procedure. We found that the combination of a two‐sided test and cleaning the data using ICA FIX resulted in nominal false positive rates for all data sets, meaning that data cleaning is not only important for resting state fMRI, but also for task fMRI. Finally, we discuss the implications of our work on the fMRI literature as a whole, estimating that at least 10% of the fMRI studies have used the most problematic cluster inference method (p = .01 cluster defining threshold), and how individual studies can be interpreted in light of our findings. These additional results underscore our original conclusions, on the importance of data sharing and thorough evaluation of statistical methods on realistic null data.
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| 9. |
- Eklund, Anders, et al.
(författare)
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Cluster failure: Why fMRI inferences for spatial extent have inflated false-positive rates
- 2016
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 113:28, s. 7900-7905
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Tidskriftsartikel (refereegranskat)abstract
- The most widely used task functional magnetic resonance imaging (fMRI) analyses use parametric statistical methods that depend on a variety of assumptions. In this work, we use real resting-state data and a total of 3 million random task group analyses to compute empirical familywise error rates for the fMRI software packages SPM, FSL, and AFNI, as well as a nonparametric permutation method. For a nominal familywise error rate of 5%, the parametric statistical methods are shown to be conservative for voxelwise inference and invalid for clusterwise inference. Our results suggest that the principal cause of the invalid cluster inferences is spatial autocorrelation functions that do not follow the assumed Gaussian shape. By comparison, the nonparametric permutation test is found to produce nominal results for voxelwise as well as clusterwise inference. These findings speak to the need of validating the statistical methods being used in the field of neuroimaging.
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| 10. |
- Eklund, Anders, et al.
(författare)
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Empirically Investigating the Statistical Validity of SPM, FSL and AFNI for Single Subject fMRI Analysis
- 2015
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Ingår i: 2015 IEEE 12th International Symposium on Biomedical Imaging (ISBI). - : IEEE conference proceedings. - 9781479923748 ; , s. 1376-1380
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Konferensbidrag (refereegranskat)abstract
- The software packages SPM, FSL and AFNI are the most widely used packages for the analysis of functional magnetic resonance imaging (fMRI) data. Despite this fact, the validity of the statistical methods has only been tested using simulated data. By analyzing resting state fMRI data (which should not contain specific forms of brain activity) from 396 healthy con- trols, we here show that all three software packages give in- flated false positive rates (4%-96% compared to the expected 5%). We isolate the sources of these problems and find that SPM mainly suffers from a too simple noise model, while FSL underestimates the spatial smoothness. These results highlight the need of validating the statistical methods being used for fMRI.
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