| 1. |
- Alvez, Maria Bueno, et al.
(författare)
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Next generation pan-cancer blood proteome profiling using proximity extension assay
- 2023
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Ingår i: Nature Communications. - : Springer Nature. - 2041-1723. ; 14:1
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Tidskriftsartikel (refereegranskat)abstract
- A comprehensive characterization of blood proteome profiles in cancer patients can contribute to a better understanding of the disease etiology, resulting in earlier diagnosis, risk stratification and better monitoring of the different cancer subtypes. Here, we describe the use of next generation protein profiling to explore the proteome signature in blood across patients representing many of the major cancer types. Plasma profiles of 1463 proteins from more than 1400 cancer patients are measured in minute amounts of blood collected at the time of diagnosis and before treatment. An open access Disease Blood Atlas resource allows the exploration of the individual protein profiles in blood collected from the individual cancer patients. We also present studies in which classification models based on machine learning have been used for the identification of a set of proteins associated with each of the analyzed cancers. The implication for cancer precision medicine of next generation plasma profiling is discussed.
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| 2. |
- Andersson, Urban, 1965, et al.
(författare)
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Research.chalmers.se : building the next generation research information infrastructure at Chalmers University of Technology
- 2016
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- research.chalmers.se is the new research infrastructure - repository platform and CRIS - that is currently being developed by the library at Chalmers University of Technology, Sweden.With the aim of eventually becoming the place for all relevant research information at the university, and built in accordance with the principles of UX (User eXperience) and agile development (SCRUM) and with a steady focus on value and continuous deliveries, research.chalmers.se is set to replace most of the current research information infrastructure at the university. It will provide new services for collecting, curating and providing quality data, as well as tools for analysis, sharing and promotion of research output by new and up-to-date means.research.chalmers.se is (or will be)- creating and preserving values - research output and data repository with qualitativedata, researcher profiles, open access.- promoting open access publishing, by proving the value of knowledge sharing, visibilityand impact as a researcher.- collecting and curating all kinds of research information, including publications,research data and information about research projects and other research activities.- built with responsive design that is adapted to current user needs. - using current standards for validity and sustainability, such as ORCID, DOI andFundRef IDs.- providing new ways of exploring and analyzing data, such as altmetrics, open APIs andvisualization tools.In the first phase (starting in 2014) a complete system for handling research project and grant information has been developed, together with integration of the local HR system for persistent and structured data about staff and organisation.In the current phase (2016-) repository services are being developed, such as a new publication database and a new digital repository, along with services for sharing and collecting data.The next phase(s) will include handling of research data, research activities, learning objects and tools for bibliometric analysis.This poster will show some of the current and future features and the principles of UX and agile development, as well as the experiences of moving out of the comfort zone and dealing with new, non-publication related data, while sustaining and enhancing existing data and current services. It will discuss the challenges and possible solutions, when handling different kinds of research information for use and re-use, in the long run enabling the comprehension of the big picture of research at Chalmers University of Technology.
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| 3. |
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| 4. |
- Axelsson, Emma L., et al.
(författare)
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Napping and toddlers' memory for fast-mapped words
- 2018
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Ingår i: First language. - : SAGE Publications. - 0142-7237 .- 1740-2344. ; 38:6, s. 582-595
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Tidskriftsartikel (refereegranskat)abstract
- When toddlers hear a novel word, they quickly and independently link it with a novel object rather than known-name objects. However, they are less proficient in retaining multiple novel words. Sleep and even short naps can enhance declarative memory in adults and children and this study investigates the effect of napping on children’s memory for novel words. Forty two-and-a-half-year-old children were presented with referent selection trials for four novel nouns. Children’s retention of the words was tested immediately after referent selection, four hours later in the afternoon, and the following morning. Half of the toddlers napped prior to the afternoon retention test. Amongst the toddlers who napped, retention scores remained steady four hours after exposure and the following morning. In contrast, for the wake group, there was a steady decline in retention scores by the following morning and significantly lower retention scores compared to the nap group. Napping following exposure to novel word–object associations could help in maintaining memories and limiting decay. Nap duration was also associated with better retention scores, but there were no effects of sleep quality, habitual napping, or sleepiness. The findings have implications for the role of napping in children’s language acquisition.
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| 5. |
- Axelsson, Emma L., et al.
(författare)
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Near or far: The effect of spatial distance and vocabulary knowledge on word learning
- 2016
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Ingår i: Acta Psychologica. - : Elsevier BV. - 0001-6918 .- 1873-6297. ; 163, s. 81-87
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Tidskriftsartikel (refereegranskat)abstract
- The current study investigated the role of spatial distance in word learning. Two-year-old children saw three novel objects named while the objects were either in close proximity to each other or spatially separated. Children were then tested on their retention for the name-object associations. Keeping the objects spatially separated from each other during naming was associated with increased retention for children with larger vocabularies. Children with a lower vocabulary size demonstrated better retention if they saw objects in close proximity to each other during naming. This demonstrates that keeping a clear view of objects during naming improves word learning for children who have already learned many words, but keeping objects within close proximal range is better for children at earlier stages of vocabulary acquisition. The effect of distance is therefore not equal across varying vocabulary sizes. The influences of visual crowding, cognitive load, and vocabulary size on word learning are discussed.
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| 6. |
- Axelsson, Emma L., et al.
(författare)
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Testing a word is not a test of word learning
- 2013
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Ingår i: Acta Psychologica. - : Elsevier BV. - 0001-6918 .- 1873-6297. ; 144, s. 264-268
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Tidskriftsartikel (refereegranskat)abstract
- Although vocabulary acquisition requires children learn names for multiple things, many investigations of word learning mechanisms teach children the name for only one of the objects presented. This is problematic because it is unclear whether children’s performance reflects recall of the correct name-object association or simply selection of the only object that was singled out by being the only object named. Children introduced to one novel name may perform at ceiling as they are not required to discriminate on the basis of the name per se, and appear to rapidly learn words following minimal exposure to a single word. We introduced children to four novel objects. For half the children, only one of the objects was named and for the other children, all four objects were named. Only children introduced to one word reliably selected the target object at test. This demonstration highlights the over-simplicity of one-word learning paradigms and the need for a shift in word learning paradigms where more than one word is taught to ensure children disambiguate objects on the basis of their names rather than their degree of salience. ?? 2013.
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| 7. |
- Axelsson, Emma L., et al.
(författare)
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The Effect of Sleep on Children’s Word Retention and Generalization
- 2016
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Ingår i: Frontiers in Psychology. - : Frontiers Media SA. - 1664-1078. ; 7, s. 1-9
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Tidskriftsartikel (refereegranskat)abstract
- In the first few years of life children spend a good proportion of time sleeping as well as acquiring the meanings of hundreds of words. There is now ample evidence of the effects of sleep on memory in adults and the number of studies demonstrating the effects of napping and nocturnal sleep in children is also mounting. In particular, sleep appears to benefit children’s memory for recently-encountered novel words. The effect of sleep on children’s generalization of novel words across multiple items, however, is less clear. Given that sleep is polyphasic in the early years, made up of multiple episodes, and children’s word learning is gradual and strengthened slowly over time, it is highly plausible that sleep is a strong candidate in supporting children’s memory for novel words. Importantly, it appears that when children sleep shortly after exposure to novel word-object pairs retention is better than if sleep is delayed, suggesting that napping plays a vital role in long-term word retention for young children. Word learning is a complex, challenging, and important part of development, thus the role that sleep plays in children’s retention of novel words is worthy of attention. As such, ensuring children get sufficient good quality sleep and regular opportunities to nap may be critical for language acquisition.
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| 8. |
- Axelsson, Emma L., et al.
(författare)
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The Right Thing at the Right Time: Why Ostensive Naming Facilitates Word Learning
- 2012
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Ingår i: Frontiers in Psychology. - : Frontiers Media SA. - 1664-1078. ; 3
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Tidskriftsartikel (refereegranskat)abstract
- The current study examines how focusing children’s attention immediately after fast mapping improves their ability to retain novel names. Previous research suggests that young children can only retain novel names presented via referent selection if ostensive naming is provided and that such explicit naming works by increasing children’s attention to the target and decreasing their attention to the competitor objects (Horst and Samuelson, 2008). This explanation of the function of ostensive naming after referent selection trials was tested by drawing 24-month-old children’s attention to the target either by illuminating the target, covering the competitors, or both. A control group was given a social pragmatic cue (pointing). Children given social pragmatic cue support did not demonstrate retention. However, children demonstrated retention if the target object was illuminated, and also when it was illuminated and the competitors simultaneously dampened. This suggests that drawing children’s attention to the target object in a manner that helps focus children’s attention is critical for word learning via referent selection. Directing attention away from competitors while also directing attention toward a target also aids in the retention of novel words.
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| 9. |
- Axelsson, Ulrik, et al.
(författare)
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Strukturerad miljödatahantering inom järn- och stålindustri
- 2002
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- Efterfrågan på miljöinformation i olika former förväntas öka under de kommande åren. Det gäller såväl internt inom företaget som externt till kunder, ägare, övriga finansiärer, myndigheter m.fl. För att kunna möta de förväntade kraven har företagen inom järn- och stålindustrin identifierat ett behov av att åstadkomma en strukturerad miljödatahantering (lagring, bearbetning och dokumentation), som möjliggör att ett och samma dataunderlag så långt som möjligt kan utnyttjas och relativt enkelt omformas till olika former av kommunikationsprodukter. Projektets mål är därför att ta fram en branschgemensam struktur för miljödatahantering inom järn- och stålindustrin
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| 10. |
- Foox, Jonathan, et al.
(författare)
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The SEQC2 epigenomics quality control (EpiQC) study
- 2021
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Ingår i: Genome Biology. - : BioMed Central (BMC). - 1465-6906 .- 1474-760X. ; 22:1
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Tidskriftsartikel (refereegranskat)abstract
- BackgroundCytosine modifications in DNA such as 5-methylcytosine (5mC) underlie a broad range of developmental processes, maintain cellular lineage specification, and can define or stratify types of cancer and other diseases. However, the wide variety of approaches available to interrogate these modifications has created a need for harmonized materials, methods, and rigorous benchmarking to improve genome-wide methylome sequencing applications in clinical and basic research. Here, we present a multi-platform assessment and cross-validated resource for epigenetics research from the FDA’s Epigenomics Quality Control Group.ResultsEach sample is processed in multiple replicates by three whole-genome bisulfite sequencing (WGBS) protocols (TruSeq DNA methylation, Accel-NGS MethylSeq, and SPLAT), oxidative bisulfite sequencing (TrueMethyl), enzymatic deamination method (EMSeq), targeted methylation sequencing (Illumina Methyl Capture EPIC), single-molecule long-read nanopore sequencing from Oxford Nanopore Technologies, and 850k Illumina methylation arrays. After rigorous quality assessment and comparison to Illumina EPIC methylation microarrays and testing on a range of algorithms (Bismark, BitmapperBS, bwa-meth, and BitMapperBS), we find overall high concordance between assays, but also differences in efficiency of read mapping, CpG capture, coverage, and platform performance, and variable performance across 26 microarray normalization algorithms.ConclusionsThe data provided herein can guide the use of these DNA reference materials in epigenomics research, as well as provide best practices for experimental design in future studies. By leveraging seven human cell lines that are designated as publicly available reference materials, these data can be used as a baseline to advance epigenomics research.
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