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- Ahnesjö, Ingrid, et al.
(author)
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Considering gender‑biased assumptions in evolutionary biology
- 2020
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In: Evolutionary biology. - : Springer Nature. - 0071-3260 .- 1934-2845. ; 47, s. 1-5
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Journal article (peer-reviewed)abstract
- Many organisms studied by evolutionary biologists have different sexes, and the evolution of separate sexes and sexual dimorphisms in morphology and behaviour are central questions in evolutionary biology. Considering scientists to be embedded in a social and cultural context, we are also subjected to the risk of gender-biased assumptions and stereotypical thinking to appear when working on topics related to sexual reproduction and sexual dimorphism. Here we present, for continued discussion, a set of good-practice guidelines aimed at (1) helping to improve researchers’ awareness of gender-biased assumptions underlying language use, generalizations, and interpretation of observations; and (2) providing recommendations to increase transparency, avoid problematic terminology, and improve study designs.
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| 4. |
- Bulten, Wouter, et al.
(author)
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Artificial intelligence assistance significantly improves Gleason grading of prostate biopsies by pathologists
- 2021
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In: Modern Pathology. - : NATURE PUBLISHING GROUP. - 0893-3952 .- 1530-0285. ; 34, s. 660-671
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Journal article (peer-reviewed)abstract
- The Gleason score is the most important prognostic marker for prostate cancer patients, but it suffers from significant observer variability. Artificial intelligence (AI) systems based on deep learning can achieve pathologist-level performance at Gleason grading. However, the performance of such systems can degrade in the presence of artifacts, foreign tissue, or other anomalies. Pathologists integrating their expertise with feedback from an AI system could result in a synergy that outperforms both the individual pathologist and the system. Despite the hype around AI assistance, existing literature on this topic within the pathology domain is limited. We investigated the value of AI assistance for grading prostate biopsies. A panel of 14 observers graded 160 biopsies with and without AI assistance. Using AI, the agreement of the panel with an expert reference standard increased significantly (quadratically weighted Cohens kappa, 0.799 vs. 0.872;p = 0.019). On an external validation set of 87 cases, the panel showed a significant increase in agreement with a panel of international experts in prostate pathology (quadratically weighted Cohens kappa, 0.733 vs. 0.786;p = 0.003). In both experiments, on a group-level, AI-assisted pathologists outperformed the unassisted pathologists and the standalone AI system. Our results show the potential of AI systems for Gleason grading, but more importantly, show the benefits of pathologist-AI synergy.
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| 5. |
- Chen, Zhishan, et al.
(author)
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Fine-mapping analysis including over 254 000 East Asian and European descendants identifies 136 putative colorectal cancer susceptibility genes
- 2024
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In: Nature Communications. - : Springer Nature. - 2041-1723. ; 15:1
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Journal article (peer-reviewed)abstract
- Genome-wide association studies (GWAS) have identified more than 200 common genetic variants independently associated with colorectal cancer (CRC) risk, but the causal variants and target genes are mostly unknown. We sought to fine-map all known CRC risk loci using GWAS data from 100,204 cases and 154,587 controls of East Asian and European ancestry. Our stepwise conditional analyses revealed 238 independent association signals of CRC risk, each with a set of credible causal variants (CCVs), of which 28 signals had a single CCV. Our cis-eQTL/mQTL and colocalization analyses using colorectal tissue-specific transcriptome and methylome data separately from 1299 and 321 individuals, along with functional genomic investigation, uncovered 136 putative CRC susceptibility genes, including 56 genes not previously reported. Analyses of single-cell RNA-seq data from colorectal tissues revealed 17 putative CRC susceptibility genes with distinct expression patterns in specific cell types. Analyses of whole exome sequencing data provided additional support for several target genes identified in this study as CRC susceptibility genes. Enrichment analyses of the 136 genes uncover pathways not previously linked to CRC risk. Our study substantially expanded association signals for CRC and provided additional insight into the biological mechanisms underlying CRC development.
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| 6. |
- Chiodaroli, Marco, et al.
(author)
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“Every morning I take two steps to my desk…” : students’ perspectives on distance learning during the COVID-19 pandemic
- 2024
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In: Higher Education. - : Springer Science+Business Media B.V.. - 0018-1560 .- 1573-174X.
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Journal article (peer-reviewed)abstract
- During the COVID-19 pandemic, distance learning became the predominant teaching method at most universities, exposing students and teachers alike to novel and unexpected challenges and learning opportunities. Our study is situated in the context of higher physics education at a large Swedish university and adopts a mixed-methods approach to explore how students perceive shifts to distance learning. Quantitative student survey responses comparing distance learning during the pandemic with previous in-person learning are analyzed with k-means cluster analysis and with a random-intercept multilevel linear model. Combined analyses produce a consistent picture of students who report having experienced the greatest challenges. They are on average younger, report being less autonomous in their learning, and find it harder than peers to ask questions to the instructor. They are also less likely to have access to a place where they can study without interruptions. Variation across courses is small with students being largely subjected to the same set of challenges. Qualitative data from semi-structured focus group interviews and open-ended questions supports these findings, provides a deeper understanding of the struggles, and reveals possibilities for future interventions. Students report an overall collapse of structure in their learning that takes place along multiple dimensions. Our findings highlight a fundamental role played by informal peer-to-peer and student-instructor interactions, and by the exchange of what we refer to as “structural information.” We discuss implications for teachers and institutions regarding the possibility of providing support structures, such as study spaces, as well as fostering student autonomy.
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| 7. |
- Curcio, Davide, et al.
(author)
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Ultrafast electronic linewidth broadening in the C 1s core level of graphene
- 2021
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In: Physical Review B. - : American Physical Society (APS). - 2469-9950 .- 2469-9969. ; 104:16
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Journal article (peer-reviewed)abstract
- We show that the presence of a transiently excited hot electron gas in graphene leads to a substantial broadening of the C 1s line probed by time-resolved x-ray photoemission spectroscopy. The broadening is found to be caused by an exchange of energy and momentum between the photoemitted core electron and the hot electron gas, rather than by vibrational excitations. This interpretation is supported by a quantitative line-shape analysis that accounts for the presence of the excited electrons. Fitting the spectra to this model directly yields the electronic temperature of the system, in good agreement with electronic temperature values obtained from valence band data. Furthermore, we show how the momentum change of the outgoing core electrons leads to a detectable but very small change in the time-resolved photoelectron diffraction pattern and to a nearly complete elimination of the core level binding energy variation associated with the presence of a narrow σ band in the C 1s state.
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- Fernandez-Rozadilla, Ceres, et al.
(author)
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Deciphering colorectal cancer genetics through multi-omic analysis of 100,204 cases and 154,587 controls of European and east Asian ancestries
- 2023
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In: Nature Genetics. - : Nature Publishing Group. - 1061-4036 .- 1546-1718. ; 55, s. 89-99
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Journal article (peer-reviewed)abstract
- Colorectal cancer (CRC) is a leading cause of mortality worldwide. We conducted a genome-wide association study meta-analysis of 100,204 CRC cases and 154,587 controls of European and east Asian ancestry, identifying 205 independent risk associations, of which 50 were unreported. We performed integrative genomic, transcriptomic and methylomic analyses across large bowel mucosa and other tissues. Transcriptome- and methylome-wide association studies revealed an additional 53 risk associations. We identified 155 high-confidence effector genes functionally linked to CRC risk, many of which had no previously established role in CRC. These have multiple different functions and specifically indicate that variation in normal colorectal homeostasis, proliferation, cell adhesion, migration, immunity and microbial interactions determines CRC risk. Crosstissue analyses indicated that over a third of effector genes most probably act outside the colonic mucosa. Our findings provide insights into colorectal oncogenesis and highlight potential targets across tissues for new CRC treatment and chemoprevention strategies.
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| 9. |
- Günter, Katerina Pia, 1989-, et al.
(author)
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“Biology is not an education one chooses by coincidence” : Students Identity Work in the Figured World of Higher Biology Education
- 2020
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Conference paper (peer-reviewed)abstract
- Science identity has been shown to be a central aspect influencing students’ trajectories and persistence in science (Carlone and Johnson 2007). Identity research has accelerated particularly in science disciplines such as physics, providing novel insights into students’ challenges when studying physics, and more attention needs to be paid to the specific challenges at play in other disciplines. In this study, we aim to unfold the identity work of biology students. We use Holland et al.'s (1998) concept of figured worlds to explore how students at the beginning of their biology program at a Swedish university imagine and figure the World of Higher Biology Education. What kind of discourses can be found in the students’ narratives and how do the students author themselves within the imagined world? Considering scientific knowledge to be situated and science, including biology, to be culturally shaped (Harding 1986), we identify broader cultural models and resources that the students employ in their identity work and when figuring the World of Higher Biology Education.Embedded in a figured worlds framework, we use Gee's Discourse Analysis Toolkit (2010) to analyse 55 student motivation texts that were written during the first course of the biology program. By combining Gee’s Figured World with the Identities Building Tool, we identify dominant discourses such as the straight path natural science discourse. This dominant discourse is challenged by interdisciplinary approaches to biology, where environmental matters are valued impetus for students’ motivation and aspiration. These discourses could be linked to cultural models of science that for example emphasized the “alwaysness” of being a science person that transitions from a naïve broad interest in nature to a narrow interest when starting higher education. The students recognized, accepted and used or rejected resources from those models such as interest of the child-self to author themselves in recognized or alternative ways.Our findings show that dominant cultural models of science can already be found in early undergraduate students’ narratives. The students display shared conceptions of who is and what is valued particularly within higher biology education. They thereby manifest themselves as legitimate participants in higher biology education. However, more than a third of the students in this study display knowledge about the dominant cultural models but reject drawing on all or a part of them. They thereby author alternative ways of participating in the World of Higher Biology Education and expand the boundaries of biology as a discipline.
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| 10. |
- Günter, Katerina Pia, 1989-, et al.
(author)
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‘Biology must become better at seeing the human beings behind it’ : University students’ identity work across European contexts
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Other publication (other academic/artistic)abstract
- Higher education biology, numerically female-biased at undergraduate level across national contexts, has been given little attention in exploring norms of scientific practice. This study brings into focus how university biology students negotiate identities in relation to figured worlds of higher education biology. Empirically grounded in 27 timeline interviews with students from a Swedish, a German, and a British university and using an eclectic theoretical framework of feminist science critique, science identity, and figured worlds, we identified three hegemonic imaginaries in students’ narratives: showing dedication through sacrifice, being forced to "fake it to make it", and survival of/as the fittest. We then demonstrate how these imaginaries are negotiated by three female biology students who consider themselves successful and who want to pursue a PhD in their future. We thereby make visible how the three students successfully negotiate these norms, yet disavow and challenge them. This conflict suggests that they consider themselves successful despite the pressure to engage in the “typical” practices they contest. Our findings provoke discussions on how the above-mentioned imaginaries risk contributing to a decrease of female participation in higher education biology across academic ranks.
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