| 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. |
- Adeboye, Peter, 1982, et al.
(författare)
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Catabolism of coniferyl aldehyde, ferulic acid and p-coumaric acid by Saccharomyces cerevisiae yields less toxic products
- 2015
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Ingår i: Microbial Cell Factories. - : Springer Science and Business Media LLC. - 1475-2859. ; 14:1, s. 149-
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Tidskriftsartikel (refereegranskat)abstract
- Background: Lignocellulosic substrates and pulping process streams are of increasing relevance to biorefineries for second generation biofuels and biochemical production. They are known to be rich in sugars and inhibitors such as phenolic compounds, organic acids and furaldehydes. Phenolic compounds are a group of aromatic compounds known to be inhibitory to fermentative organisms. It is known that inhibition of Sacchromyces cerevisiae varies among phenolic compounds and the yeast is capable of in situ catabolic conversion and metabolism of some phenolic compounds. In an approach to engineer a S. cerevisiae strain with higher tolerance to phenolic inhibitors, we selectively investigated the metabolic conversion and physiological effects of coniferyl aldehyde, ferulic acid, and p-coumaric acid in Saccharomyces cerevisiae. Aerobic batch cultivations were separately performed with each of the three phenolic compounds. Conversion of each of the phenolic compounds was observed on time-based qualitative analysis of the culture broth to monitor various intermediate and final metabolites. Result: Coniferyl aldehyde was rapidly converted within the first 24 h, while ferulic acid and p-coumaric acid were more slowly converted over a period of 72 h. The conversion of the three phenolic compounds was observed to involved several transient intermediates that were concurrently formed and converted to other phenolic products. Although there were several conversion products formed from coniferyl aldehyde, ferulic acid and p-coumaric acid, the conversion products profile from the three compounds were similar. On the physiology of Saccharomyces cerevisiae, the maximum specific growth rates of the yeast was not affected in the presence of coniferyl aldehyde or ferulic acid, but it was significantly reduced in the presence of p-coumaric acid. The biomass yields on glucose were reduced to 73 and 54 % of the control in the presence of coniferyl aldehyde and ferulic acid, respectively, biomass yield increased to 127 % of the control in the presence of p-coumaric acid. Coniferyl aldehyde, ferulic acid and p-coumaric acid and their conversion products were screened for inhibition, the conversion products were less inhibitory than coniferyl aldehyde, ferulic acid and p-coumaric acid, indicating that the conversion of the three compounds by Saccharomyces cerevisiae was also a detoxification process. Conclusion: We conclude that the conversion of coniferyl aldehyde, ferulic acid and p-coumaric acid into less inhibitory compounds is a form of stress response and a detoxification process. We hypothesize that all phenolic compounds are converted by Saccharomyces cerevisiae using the same metabolic process. We suggest that the enhancement of the ability of S. cerevisiae to convert toxic phenolic compounds into less inhibitory compounds is a potent route to developing a S. cerevisiae with superior tolerance to phenolic compounds.
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| 3. |
- Adeboye, Peter, 1982, et al.
(författare)
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In situ conversion of phenolic compounds as a tool to phenolic tolerance development by S. cerevisiae
- 2015
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Phenolic compounds in hydrolysates are degradation products from the lignin component of wood. They are diverse in nature and they account for some of the inhibitory activities observed during lignocellulosic fermentation. S. cerevisiae possesses the ability to convert some phenolic compounds. We are currently studying the interaction between S. cerevisiae and selected phenolic compounds namely; coniferyl aldehyde, ferulic acid and p-coumaric acid to understand the ability of S. cerevisiae to convert the selected compounds. Preliminary results show that the three phenolic compounds are being converted into several other less inhibitory phenolic compounds common to the three compounds. We hypothesised a conversion route and engineered S. cerevisiae strains to test the hypothesis, the preliminary result shows faster conversion in an engineered strain.
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| 4. |
- Aeddula, Omsri, 1993-, et al.
(författare)
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AI-driven Ossification Assessment in Knee MRI : A Product-Service System Development for Informed Clinical Decision-Making
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Background: Traditionally, assessing the degree of ossification in the epiphyseal plate for growth plate development relies on manual evaluation, which can be inefficient due to the complexities of the distal femoral epiphysis anatomy. Existing methods lack efficient detection techniques.Method: This study proposes an AI-based decision support system, designed within a product-service system (PSS) framework, to automate ossification assessment and detection of the distal femoral epiphysis in knee magnetic resonance imaging (MRI) data. The system leverages advanced machine learning techniques, specifically two Convolutional Neural Networks (CNNs), combined with computer vision techniques. This intelligent system analyzes MRI slices to predict the optimal slice for analysis and identify variations in the degree of ossification within individual datasets.Results: The proposed method's effectiveness is demonstrated using a set of T2-weighted gradient echo grayscale knee MRI data. The system successfully detects the complex anatomy of the distal femoral epiphysis, revealing variations in the degree of ossification ranging from completely closed/open to fully open/closed regions.Conclusions: This study presents a robust and efficient AI-based method, integrated within a PSS framework, for measuring the degree of ossification in the distal femoral epiphysis. This approach automates ossification assessment, providing valuable insights for clinical decision-making by clinicians and forensic practitioners. The PSS framework ensures seamless integration of the AI technology into existing workflows.
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| 5. |
- Aeddula, Omsri, 1993-
(författare)
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Navigating Data Challenges: AI-Driven Decision Support for Product-Service System Development
- 2024
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Solution providers are transitioning from product-centric models to service-oriented solutions. This shift has led to the rise of Product-Service Systems (PSS), which offer a holistic approach by integrating physical products with associated services. However, the inherent complexity and collaborative nature of PSS development present a significant challenge: information gathering, analysis, and knowledge building. This is further amplified in the early stages of PSS development due to data challenges such as uncertainty, ambiguity, and complexity. This complicates informed decision-making, potentially leading to the risk of sub-optimal outcomes and impacting the success of final offerings.This research proposes an AI-powered data analysis approach to address these data challenges and augment the decision-making process of PSS development. The focus is on supporting early-stage decision-making, as decisions made at this stage greatly impact the success of final solutions. The research investigates how data can be utilized and visualized to extract actionable insights, ultimately facilitating informed decision-making.The presented research demonstrates that AI-powered data analysis effectively supports informed decision-making in early-stage PSS development. By extracting actionable insights from complex data, handling data limitations, and enabling informed strategic decisions, knowledge sharing, and collaboration are facilitated among stakeholders. Furthermore, integrating AI with visualization tools fosters knowledge building and a deeper understanding of system behavior, ultimately leading to more successful PSS solutions. The efficacy of AI-powered data analysis for handling diverse data types across application domains is demonstrated, potentially leading to benefits such as a deeper understanding of system behavior and proactive solution strategies. These advancements contribute to developing decision support systems specifically for PSS development.Overall, this research demonstrates the efficacy of AI-powered data analysis in overcoming data challenges and empowering decision-makers in early-stage PSS development. This translates to more informed choices, leading to the creation of successful and efficient PSS solutions.
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| 6. |
- Bardizbanyan, Alen, 1986, et al.
(författare)
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Improving Data Access Efficiency by Using a Tagless Access Buffer (TAB)
- 2013
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Ingår i: Proceedings of the 2013 IEEE/ACM International Symposium on Code Generation and Optimization, CGO 2013. - 9781467355254 ; , s. 269-279
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Konferensbidrag (refereegranskat)abstract
- The need for energy efficiency continues to grow for many classes of processors, including those for which performance remains vital. Data cache is crucial for good performance, but it also represents a significant portion of the processor's energy expenditure. We describe the implementation and use of a tagless access buffer (TAB) that greatly improves data access energy efficiency while slightly improving performance. The compiler recognizes memory reference patterns within loops and allocates these references to a TAB. This combined hardware/software approach reduces energy usage by (1) replacing many level-one data cache (L1D) accesses with accesses to the smaller, more power-efficient TAB; (2) removing the need to perform tag checks or data translation lookaside buffer (DTLB) lookups for TAB accesses; and (3) reducing DTLB lookups when transferring data between the L1D and the TAB. Accesses to the TAB occur earlier in the pipeline, and data lines are prefetched from lower memory levels, which result in asmall performance improvement. In addition, we can avoid many unnecessary block transfers between other memory hierarchy levels by characterizing how data in the TAB are used. With a combined size equal to that of a conventional 32-entry register file, a four-entry TAB eliminates 40% of L1D accesses and 42% of DTLB accesses, on average. This configuration reduces data-access related energy by 35% while simultaneously decreasing execution time by 3%.
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| 7. |
- Berglund, Åsa M. M., 1978-, et al.
(författare)
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Effects on the food-web structure and bioaccumulation patterns of organic contaminants in a climate-altered Bothnian Sea mesocosms
- 2023
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Ingår i: Frontiers in Marine Science. - : Frontiers Media S.A.. - 2296-7745. ; 10
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Tidskriftsartikel (refereegranskat)abstract
- Climate change is expected to alter global temperature and precipitation patterns resulting in complex environmental impacts. The proposed higher precipitation in northern Scandinavia would increase runoff from land, hence increase the inflow of terrestrial dissolved organic matter (tDOM) in coastal regions. This could promote heterotrophic bacterial production and shift the food web structure, by favoring the microbial food web. The altered climate is also expected to affect transport and availability of organic micropollutants (MPs), with downstream effects on exposure and accumulation in biota. This study aimed to assess climate-induced changes in a Bothnian Sea food web structure as well as bioaccumulation patterns of MPs. We performed a mesocosms-study, focusing on aquatic food webs with fish as top predator. Alongside increased temperature, mesocosm treatments included tDOM and MP addition. The tDOM addition affected nutrient availability and boosted both phytoplankton and heterotrophic bacteria in our fairly shallow mesocosms. The increased tDOM further benefitted flagellates, ciliates and mesozooplankton, while the temperature increase and MP addition had minor effect on those organism groups. Temperature, on the other hand, had a negative impact on fish growth and survival, whereas tDOM and MP addition only had minor impact on fish. Moreover, there were indications that bioaccumulation of MPs in fish either increased with tDOM addition or decreased at higher temperatures. If there was an impact on bioaccumulation, moderately lipophilic MPs (log Kow 3.6 - 4.6) were generally affected by tDOM addition and more lipophilic MPs (log Kow 3.8 to 6.4) were generally affected by increased temperature. This study suggest that both increased temperatures and addition of tDOM likely will affect bioaccumulation patterns of MPs in shallow coastal regions, albeit with counteracting effects.
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| 8. |
- Carlsson, Lena M S, 1957, et al.
(författare)
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Long-term incidence of microvascular disease after bariatric surgery or usual care in patients with obesity, stratified by baseline glycaemic status: a post-hoc analysis of participants from the Swedish Obese Subjects study.
- 2017
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Ingår i: The lancet. Diabetes & endocrinology. - 2213-8595. ; 5:4, s. 271-279
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Tidskriftsartikel (refereegranskat)abstract
- Bariatric surgery is associated with remission of diabetes and prevention of diabetic complications in patients with obesity and type 2 diabetes. Long-term effects of bariatric surgery on microvascular complications in patients with prediabetes are unknown. The aim of this study was to examine the effects of bariatric surgery on incidence of microvascular complications in patients with obesity stratified by baseline glycaemic status.Patients were recruited to the Swedish Obese Subjects (SOS) study between Sept 1, 1987, and Jan 31, 2001. Inclusion criteria were age 37-60 years and BMI of 34 kg/m(2) or greater in men and 38 kg/m(2) or greater in women. Exclusion criteria were identical in surgery and control groups and designed to exclude patients not suitable for surgery. The surgery group (n=2010) underwent gastric bypass (265 [13%]), gastric banding (376 [19%]), or vertical-banded gastroplasty (1369 [68%]). Participants in the control group (n=2037) received usual care. Bodyweight was measured and questionnaires were completed at baseline and at 0·5 years, 1 year, 2 years, 3 years, 4 years, 6 years, 8 years, 10 years, 15 years, and 20 years. Biochemical variables were measured at baseline and at 2 years, 10 years, and 15 years. We categorised participants into subgroups on the basis of baseline glycaemic status (normal [fasting blood glucose concentration <5·0 mmol/L], prediabetes [5·0-6·0 mmol/L], screen-detected diabetes [≥6·1 mmol/L at baseline visit without previous diagnosis], and established diabetes [diagnosis of diabetes before study inclusion]). We obtained data about first incidence of microvascular disease from nationwide registers and about diabetes incidence at study visits at 2 years, 10 years, and 15 years. We did the main analysis by intention to treat, and subgroup analyses after stratification by baseline glycaemic status and by diabetes status at the 15 year follow-up. The SOS study is registered with ClinicalTrials.gov, NCT01479452.4032 of the 4047 participants in the SOS study were included in this analysis. We excluded four patients with suspected type 1 diabetes, and 11 patients with unknown glycaemic status at baseline. At baseline, 2838 patients had normal blood glucose, 591 had prediabetes, 246 had screen-detected diabetes, and 357 had established diabetes. Median follow-up was 19 years (IQR 16-21). We identified 374 incident cases of microvascular disease in the control group and 224 in the surgery group (hazard ratio [HR] 0·56, 95% CI 0·48-0·66; p<0·0001). Interaction between baseline glycaemic status and effect of treatment on incidence of microvascular disease was significant (p=0·0003). Unadjusted HRs were lowest in the subgroup with prediabetes (0·18, 95% CI 0·11-0·30), followed by subgroups with screen-detected diabetes (0·39, 0·24-0·65), established diabetes (0·54, 0·40-0·72), and normoglycaemia (0·63, 0·48-0·81). Surgery was associated with reduced incidence of microvascular events in people with prediabetes regardless of whether they developed diabetes during follow-up.Bariatric surgery was associated with reduced risk of microvascular complications in all subgroups, but the greatest relative risk reduction was observed in patients with prediabetes at baseline. Our results suggest that prediabetes should be treated aggressively to prevent future microvascular events, and effective non-surgical treatments need to be developed for this purpose.US National Institutes of Health, Swedish Research Council, Sahlgrenska University Hospital Regional Agreement on Medical Education and Research, and Swedish Diabetes Foundation.
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| 9. |
- Elfwen, Ludvig, et al.
(författare)
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Direct or subacute coronary angiography in out-of-hospital cardiac arrest (DISCO)-An initial pilot-study of a randomized clinical trial
- 2019
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Ingår i: Resuscitation. - : ELSEVIER IRELAND LTD. - 0300-9572 .- 1873-1570. ; 139, s. 253-261
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Tidskriftsartikel (refereegranskat)abstract
- Background: The clinical importance of immediate coronary angiography, with potentially subsequent percutaneous coronary intervention (PCI), in out-of-hospital cardiac arrest (OHCA) patients without ST-elevation on the ECG is unclear. In this study, we assessed feasibility and safety aspects of performing immediate coronary angiography in a pre-specified pilot phase of the 'DIrect or Subacute Coronary angiography in Out-of-hospital cardiac arrest' (DISCO) randomized controlled trial (ClinicalTrials.gov ID: NCT02309151). Methods: Resuscitated bystander witnessed OHCA patients > 18 years without ST-elevation on the ECG were randomized to immediate coronary angiography versus standard of care. Event times, procedure related adverse events and safety variables within 7 days were recorded. Results: In total, 79 patients were randomized to immediate angiography (n = 39) or standard of care (n = 40). No major differences in baseline characteristics between the groups were found. There were no differences in the proportion of bleedings and renal failure. Three patients randomized to immediate angiography and six patients randomized to standard care died within 24 h. The median time from EMS arrival to coronary angiography was 135 min in the immediate angiography group. In patients randomized to immediate angiography a culprit lesion was found in 14/38 (36.8%) and PCI was performed in all these patients. In 6/40 (15%) patients randomized to standard of care, coronary angiography was performed before the stipulated 3 days. Conclusion: In this out-of-hospital cardiac arrest population without ST-elevation, randomization to a strategy to perform immediate coronary angiography was feasible although the time window of 120 min from EMS arrival at the scene of the arrest to start of coronary angiography was not achieved. No significant safety issues were reported.
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| 10. |
- Engqvist, Hanna, 1985, et al.
(författare)
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Integrative genomics approach identifies molecular features associated with early-stage ovarian carcinoma histotypes.
- 2020
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Ingår i: Scientific reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 10:1
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Tidskriftsartikel (refereegranskat)abstract
- Ovarian cancer comprises multiple subtypes (clear-cell (CCC), endometrioid (EC), high-grade serous (HGSC), low-grade serous (LGSC), and mucinous carcinomas (MC)) with differing molecular and clinical behavior. However, robust histotype-specific biomarkers for clinical use have yet to be identified. Here, we utilized a multi-omics approach to identify novel histotype-specific genetic markers associated with ovarian carcinoma histotypes (CCC, EC, HGSC, and MC) using DNA methylation, DNA copy number alteration and RNA sequencing data for 96 primary invasive early-stage (stage I and II) ovarian carcinomas. More specifically, the DNA methylation analysis revealed hypermethylation for CCC in comparison with the other histotypes. Moreover, copy number imbalances and novel chromothripsis-like rearrangements (n=64) were identified in ovarian carcinoma, with the highest number of chromothripsis-like patterns in HGSC. For the 1000 most variable transcripts, underexpression was most prominent for all histotypes in comparison with normal ovarian samples. Overall, the integrative approach identified 46 putative oncogenes (overexpressed, hypomethylated and DNA gain) and three putative tumor suppressor genes (underexpressed, hypermethylated and DNA loss) when comparing the different histotypes. In conclusion, the current study provides novel insights into molecular features associated with early-stage ovarian carcinoma that may improve patient stratification and subclassification of the histotypes.
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