| 1. |
- Klionsky, Daniel J., et al.
(author)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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In: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Research review (peer-reviewed)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 2. |
- In ’t Veld, Sjors G.J.G., et al.
(author)
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Detection and localization of early- and late-stage cancers using platelet RNA
- 2022
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In: Cancer Cell. - : Elsevier. - 1535-6108 .- 1878-3686. ; 40:9, s. 999-1009.e6
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Journal article (peer-reviewed)abstract
- Cancer patients benefit from early tumor detection since treatment outcomes are more favorable for less advanced cancers. Platelets are involved in cancer progression and are considered a promising biosource for cancer detection, as they alter their RNA content upon local and systemic cues. We show that tumor-educated platelet (TEP) RNA-based blood tests enable the detection of 18 cancer types. With 99% specificity in asymptomatic controls, thromboSeq correctly detected the presence of cancer in two-thirds of 1,096 blood samples from stage I–IV cancer patients and in half of 352 stage I–III tumors. Symptomatic controls, including inflammatory and cardiovascular diseases, and benign tumors had increased false-positive test results with an average specificity of 78%. Moreover, thromboSeq determined the tumor site of origin in five different tumor types correctly in over 80% of the cancer patients. These results highlight the potential properties of TEP-derived RNA panels to supplement current approaches for blood-based cancer screening.
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| 3. |
- Palmer, Nicholette D, et al.
(author)
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A genome-wide association search for type 2 diabetes genes in African Americans.
- 2012
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In: PloS one. - San Francisco : Public Library of Science (PLoS). - 1932-6203. ; 7:1, s. e29202-
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Journal article (peer-reviewed)abstract
- African Americans are disproportionately affected by type 2 diabetes (T2DM) yet few studies have examined T2DM using genome-wide association approaches in this ethnicity. The aim of this study was to identify genes associated with T2DM in the African American population. We performed a Genome Wide Association Study (GWAS) using the Affymetrix 6.0 array in 965 African-American cases with T2DM and end-stage renal disease (T2DM-ESRD) and 1029 population-based controls. The most significant SNPs (n = 550 independent loci) were genotyped in a replication cohort and 122 SNPs (n = 98 independent loci) were further tested through genotyping three additional validation cohorts followed by meta-analysis in all five cohorts totaling 3,132 cases and 3,317 controls. Twelve SNPs had evidence of association in the GWAS (P<0.0071), were directionally consistent in the Replication cohort and were associated with T2DM in subjects without nephropathy (P<0.05). Meta-analysis in all cases and controls revealed a single SNP reaching genome-wide significance (P<2.5×10(-8)). SNP rs7560163 (P = 7.0×10(-9), OR (95% CI) = 0.75 (0.67-0.84)) is located intergenically between RND3 and RBM43. Four additional loci (rs7542900, rs4659485, rs2722769 and rs7107217) were associated with T2DM (P<0.05) and reached more nominal levels of significance (P<2.5×10(-5)) in the overall analysis and may represent novel loci that contribute to T2DM. We have identified novel T2DM-susceptibility variants in the African-American population. Notably, T2DM risk was associated with the major allele and implies an interesting genetic architecture in this population. These results suggest that multiple loci underlie T2DM susceptibility in the African-American population and that these loci are distinct from those identified in other ethnic populations.
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| 4. |
- Sodergren, Erica, et al.
(author)
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The genome of the sea urchin Strongylocentrotus purpuratus.
- 2006
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In: Science. - : American Association for the Advancement of Science (AAAS). - 1095-9203 .- 0036-8075. ; 314:5801, s. 941-52
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Journal article (peer-reviewed)abstract
- We report the sequence and analysis of the 814-megabase genome of the sea urchin Strongylocentrotus purpuratus, a model for developmental and systems biology. The sequencing strategy combined whole-genome shotgun and bacterial artificial chromosome (BAC) sequences. This use of BAC clones, aided by a pooling strategy, overcame difficulties associated with high heterozygosity of the genome. The genome encodes about 23,300 genes, including many previously thought to be vertebrate innovations or known only outside the deuterostomes. This echinoderm genome provides an evolutionary outgroup for the chordates and yields insights into the evolution of deuterostomes.
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| 5. |
- Ai, Jiaoyu, et al.
(author)
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Bcl3 Couples Cancer Stem Cell Enrichment With Pancreatic Cancer Molecular Subtypes
- 2021
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In: Gastroenterology. - : Elsevier BV. - 0016-5085 .- 1528-0012. ; 161:1, s. 318-332
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Journal article (peer-reviewed)abstract
- Background & Aims: The existence of different subtypes of pancreatic ductal adenocarcinoma (PDAC) and their correlation with patient outcome have shifted the emphasis on patient classification for better decision-making algorithms and personalized therapy. The contribution of mechanisms regulating the cancer stem cell (CSC) population in different subtypes remains unknown.Methods: Using RNA-seq, we identified B-cell CLL/lymphoma 3 (BCL3), an atypical nf-κb signaling member, as differing in pancreatic CSCs. To determine the biological consequences of BCL3 silencing in vivo and in vitro, we generated bcl3-deficient preclinical mouse models as well as murine cell lines and correlated our findings with human cell lines, PDX models, and 2 independent patient cohorts. We assessed the correlation of bcl3 expression pattern with clinical parameters and subtypes.Results: Bcl3 was significantly down-regulated in human CSCs. Recapitulating this phenotype in preclinical mouse models of PDAC via BCL3 genetic knockout enhanced tumor burden, metastasis, epithelial to mesenchymal transition, and reduced overall survival. Fluorescence-activated cell sorting analyses, together with oxygen consumption, sphere formation, and tumorigenicity assays, all indicated that BCL3 loss resulted in CSC compartment expansion promoting cellular dedifferentiation. Overexpression of BCL3 in human PDXs diminished tumor growth by significantly reducing the CSC population and promoting differentiation. Human PDACs with low BCL3 expression correlated with increased metastasis, and BCL3-negative tumors correlated with lower survival and nonclassical subtypes.Conclusions: We demonstrate that bcl3 impacts pancreatic carcinogenesis by restraining CSC expansion and by curtailing an aggressive and metastatic tumor burden in PDAC across species. Levels of BCL3 expression are a useful stratification marker for predicting subtype characterization in PDAC, thereby allowing for personalized therapeutic approaches.
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| 6. |
- Balatsky, Alexander V., et al.
(author)
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Dynamic Quantum Matter
- 2020
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In: Annalen der Physik. - : John Wiley & Sons. - 0003-3804 .- 1521-3889. ; 532:2
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Journal article (other academic/artistic)
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| 7. |
- Beretta, Davide, et al.
(author)
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Thermoelectrics: From history, a window to the future
- 2019
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In: Materials Science and Engineering: R: Reports. - : Elsevier BV. - 0927-796X. ; 138
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Research review (peer-reviewed)abstract
- Thermoelectricity offers a sustainable path to recover and convert waste heat into readily available electric energy, and has been studied for more than two centuries. From the controversy between Galvani and Volta on the Animal Electricity, dating back to the end of the XVIII century and anticipating Seebeck's observations, the understanding of the physical mechanisms evolved along with the development of the technology. In the XIX century Ørsted clarified some of the earliest observations of the thermoelectric phenomenon and proposed the first thermoelectric pile, while it was only after the studies on thermodynamics by Thomson, and Rayleigh's suggestion to exploit the Seebeck effect for power generation, that a diverse set of thermoelectric generators was developed. From such pioneering endeavors, technology evolved from massive, and sometimes unreliable, thermopiles to very reliable devices for sophisticated niche applications in the XX century, when Radioisotope Thermoelectric Generators for space missions and nuclear batteries for cardiac pacemakers were introduced. While some of the materials adopted to realize the first thermoelectric generators are still investigated nowadays, novel concepts and improved understanding of materials growth, processing, and characterization developed during the last 30 years have provided new avenues for the enhancement of the thermoelectric conversion efficiency, for example through nanostructuration, and favored the development of new classes of thermoelectric materials. With increasing demand for sustainable energy conversion technologies, the latter aspect has become crucial for developing thermoelectrics based on abundant and non-toxic materials, which can be processed at economically viable scales, tailored for different ranges of temperature. This includes high temperature applications where a substantial amount of waste energy can be retrieved, as well as room temperature applications where small and local temperature differences offer the possibility of energy scavenging, as in micro harvesters meant for distributed electronics such as sensor networks. While large scale applications have yet to make it to the market, the richness of available and emerging thermoelectric technologies presents a scenario where thermoelectrics is poised to contribute to a future of sustainable future energy harvesting and management. This work reviews the broad field of thermoelectrics. Progress in thermoelectrics and milestones that led to the current state-of-the-art are presented by adopting an historical footprint. The review begins with an historical excursus on the major steps in the history of thermoelectrics, from the very early discovery to present technology. A panel on the theory of thermoelectric transport in the solid state reviews the transport theory in complex crystal structures and nanostructured materials. Then, the most promising thermoelectric material classes are discussed one by one in dedicated sections and subsections, carefully highlighting the technological solutions on materials growth that have represented a turning point in the research on thermoelectrics. Finally, perspectives and the future of the technology are discussed in the framework of sustainability and environmental compatibility. © 2018 Elsevier B.V.
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| 8. |
- Campbell, PJ, et al.
(author)
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Pan-cancer analysis of whole genomes
- 2020
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In: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 578:7793, s. 82-
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Journal article (peer-reviewed)abstract
- Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1–3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4–5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10–18.
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| 9. |
- Derewjanko, Dennis, et al.
(author)
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Delocalization Enhances Conductivity at High Doping Concentrations
- 2022
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In: Advanced Functional Materials. - : Wiley. - 1616-3028 .- 1616-301X. ; 32:20
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Journal article (peer-reviewed)abstract
- Many applications of organic semiconductors require high electrical conductivities and hence high doping levels. Therefore, it is indispensable for effective material design to have an accurate understanding of the underlying transport mechanisms in this regime. In this study, own and literature experimental data that reveal a power-law relation between the conductivity and charge density of strongly p-doped conjugated polymers are combined. This behavior cannot consistently be described with conventional models for charge transport in energetically disordered materials. Here, it is shown that the observations can be explained in terms of a variable range hopping model with an energy-dependent localization length. A tight-binding model is used to quantitatively estimate of the energy-dependent localization length, which is used in an analytical variable range hopping model. In the limit of low charge densities, the model reproduces the well-known Mott variable range hopping behavior, while for high charge densities, the experimentally observed superlinear increase in conductivity with charge density is reproduced. The latter behavior occurs when the Fermi level reaches partially delocalized states. This insight can be anticipated to lead to new strategies to increase the conductivity of organic semiconductors.
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| 10. |
- Dworeck, Christian, et al.
(author)
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Radial artery access is associated with lower mortality in patients undergoing primary PCI : a report from the SWEDEHEART registry
- 2020
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In: European Heart Journal. - : Sage Publications. - 2048-8726 .- 2048-8734. ; 9:4, s. 323-332
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Journal article (peer-reviewed)abstract
- Objectives: The purpose of this observational study was to evaluate the effects of radial artery access versus femoral artery access on the risk of 30-day mortality, inhospital bleeding and cardiogenic shock in patients with ST-elevation myocardial infarction undergoing primary percutaneous coronary intervention.Methods: We used data from the SWEDEHEART registry and included all patients who were treated with primary percutaneous coronary intervention in Sweden between 2005 and 2016. We compared patients who had percutaneous coronary intervention by radial access versus femoral access with regard to the primary endpoint of all-cause death within 30 days, using a multilevel propensity score adjusted logistic regression which included hospital as a random effect.Results: During the study period, 44,804 patients underwent primary percutaneous coronary intervention of whom 24,299 (54.2%) had radial access and 20,505 (45.8%) femoral access. There were 2487 (5.5%) deaths within 30 days, of which 920 (3.8%) occurred in the radial access and 1567 (7.6%) in the femoral access group. After propensity score adjustment, radial access was associated with a lower risk of death (adjusted odds ratio (OR) 0.70, 95% confidence interval (CI) 0.55-0.88,P = 0.025). We found no interaction between access site and age, gender and cardiogenic shock regarding 30-day mortality. Radial access was also associated with a lower adjusted risk of bleeding (adjusted OR 0.45, 95% CI 0.25-0.79,P = 0.006) and cardiogenic shock (adjusted OR 0.41, 95% CI 0.24-0.73,P = 0.002).Conclusions: In patients with ST-elevation myocardial infarction, primary percutaneous coronary intervention by radial access rather than femoral access was associated with an adjusted lower risk of death, bleeding and cardiogenic shock. Our findings are consistent with, and add external validity to, recent randomised trials.
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