| 1. |
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| 2. |
- Thomas, HS, et al.
(author)
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- 2019
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swepub:Mat__t
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| 3. |
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| 4. |
- 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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| 5. |
- Drake, TM, et al.
(author)
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Surgical site infection after gastrointestinal surgery in children: an international, multicentre, prospective cohort study
- 2020
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In: BMJ global health. - : BMJ. - 2059-7908. ; 5:12
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Journal article (peer-reviewed)abstract
- Surgical site infection (SSI) is one of the most common healthcare-associated infections (HAIs). However, there is a lack of data available about SSI in children worldwide, especially from low-income and middle-income countries. This study aimed to estimate the incidence of SSI in children and associations between SSI and morbidity across human development settings.MethodsA multicentre, international, prospective, validated cohort study of children aged under 16 years undergoing clean-contaminated, contaminated or dirty gastrointestinal surgery. Any hospital in the world providing paediatric surgery was eligible to contribute data between January and July 2016. The primary outcome was the incidence of SSI by 30 days. Relationships between explanatory variables and SSI were examined using multilevel logistic regression. Countries were stratified into high development, middle development and low development groups using the United Nations Human Development Index (HDI).ResultsOf 1159 children across 181 hospitals in 51 countries, 523 (45·1%) children were from high HDI, 397 (34·2%) from middle HDI and 239 (20·6%) from low HDI countries. The 30-day SSI rate was 6.3% (33/523) in high HDI, 12·8% (51/397) in middle HDI and 24·7% (59/239) in low HDI countries. SSI was associated with higher incidence of 30-day mortality, intervention, organ-space infection and other HAIs, with the highest rates seen in low HDI countries. Median length of stay in patients who had an SSI was longer (7.0 days), compared with 3.0 days in patients who did not have an SSI. Use of laparoscopy was associated with significantly lower SSI rates, even after accounting for HDI.ConclusionThe odds of SSI in children is nearly four times greater in low HDI compared with high HDI countries. Policies to reduce SSI should be prioritised as part of the wider global agenda.
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| 6. |
- 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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| 7. |
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| 8. |
- Zhao, Xu, et al.
(author)
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Wet Twisting in Spinning for Rapid and Cost-Effective Fabrication of Superior Carbon Nanotube Yarns
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In: Advanced Functional Materials. - 1616-301X.
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Journal article (peer-reviewed)abstract
- Carbon nanotubes (CNTs) are promising blocks for building advanced yarns with unique structural and functional attributes. However, the complexity of fabrication and high cost has hindered the widespread adoption of CNT yarns. In this study, a rapid and continuous twisting wet spun yarn strategy to produce highly densified CNT yarns is presented. The method involves effectively dispersing CNTs in the surfactant dispersion, swiftly removing the surfactant in the coagulation bath and twisting treatment to effectively improve the density of yarn and the orientation of CNT. Detailed characterizations on the influence of each spinning conditions reveal that twisting treatment significantly enhances the packing density of yarns, improves the orientation of CNTs, and mitigates the impact of impurities on conductivity. The resulting CNT yarns exhibit a remarkable tensile strength of 600 MPa, a Young's modulus of ≈40 GPa, and a high conductivity of 8990 S cm−1. When utilized as a yarn heater, the CNT yarn demonstrates an ultra-fast electrothermal response of over 1000 °C s−1 at a low operating voltage of 5 V. Impressively, the mechanical properties of CNT yarns show good stability during heating. This study provides a perspective of structural engineering for the large-scale preparation of high-performance CNT yarns.
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| 15. |
- Kong, Na, et al.
(author)
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Carbohydrate conjugation through microwave-assisted functionalization of single-walled carbon nanotubes using perfluorophenyl azides
- 2015
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In: Carbohydrate Research. - : Elsevier BV. - 0008-6215 .- 1873-426X. ; 405, s. 33-38
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Journal article (peer-reviewed)abstract
- Carbohydrate-functionalized single-walled carbon nanotubes (SWNTs) were synthesized using microwave-assisted reaction of perfluorophenyl azide with the nanotubes. The results showed that microwave radiation provides a rapid and effective means to covalently attach carbohydrates to SWNTs, producing carbohydrate-SWNT conjugates for biorecognition. The carbohydrate-functionalized SWNTs were furthermore shown to interact specifically with cognate carbohydrate-specific proteins (lectins), resulting in predicted recognition patterns. The carbohydrate-presenting SWNTs constitute a new platform for sensitive protein-or cell recognition, which pave the way for glycoconjugated carbon nanomaterials in biorecognition applications.
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| 18. |
- Kong, Na, et al.
(author)
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Carbohydrate Functionalization of Few-Layer Graphene through Microwave-Assisted Reaction of Perfluorophenyl Azide
- 2019
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In: ACS Applied Bio Materials. - : American Chemical Society. - 2576-6422. ; 2:1, s. 284-291
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Journal article (peer-reviewed)abstract
- The excellent physical and chemical properties of graphene make it an attractive nanomaterial and a component in high-performance nanocomposite materials. To prepare graphene-based nanocomposite materials, chemical functionalization is often necessary. Water-soluble ligands such as carbohydrates not only make the functionalized graphene compatible with aqueous media, but also introduce biorecognition, which is important for graphene to be used in biotechnology. In this study, we report the derivatization of few-layer graphene (FLG) with carbohydrates through microwave-assisted reaction of perfluorophenyl azide (PFPA). FLG was first treated with PFPA under microwave radiation. Subsequent conjugation with glycosyl amine gave carbohydrate-presenting FLG. Thermogravimetric analysis showed that microwave radiation gave a higher degree of functionalization compared to conventional heating, with higher weight losses for both PFPA and Man ligands. The carbohydrates (mannose and galactose) retained their bioactivity, as demonstrated by the lectin binding assays. Higher degree of binding toward lectins was obtained for the carbohydrate-functionalized FLG prepared by microwave radiation than the conventional heating.
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| 19. |
- Kong, Na, 1984-
(author)
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Carbohydrate-Functionalized Nanomaterials : Synthesis, Characterization and Biorecognition Studies
- 2015
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Doctoral thesis (other academic/artistic)abstract
- This thesis focuses on the development of carbohydrate coupling chemistry on nanomaterials and their biological activity studies. It is divided into two parts:In part one, two carbohydrate immobilization approaches, based on perfluorophenyl azide (PFPA)-functionalized silica nanoparticles (SNPs), are presented, where the binding affinity of the glyconanoparticles was evaluated through carbohydrate-lectin interaction. In the first approach, PFPAfunctionalized SNPs were treated with propargylated glycosides and functionalized under copper-catalyzed azide-alkyne cycloaddition (CuAAC) conditions to give glyconanoparticles. For the second approach, a metal-free coupling chemistry based on perfluorophenyl azide-aldehyde-amine cycloaddition (AAAC) was developed for carbohydrate immobilization on PFPA-functionalized SNPs using glycosyl amine and phenylacetaldehyde. Subsequently, a quantitative fluorine nuclear magnetic resonance (19F qNMR) technique was developed to determine the carbohydrate density on the glyconanoparticles. The addition of an internal standard allowed the accurate determination of carbohydrate density, which was then used to calculate the apparent dissociation constant (Kd ) of the glyconanoparticles with lectin by a ligand competition assay. The developed approaches proved general and versatile, and the carbohydrate-presenting nanoplatforms showed high binding specificity in lectin binding.In part two, microwave irradiation was used to functionalize carbon nanomaterials with PFPA followed by carbohydrate conjugation. The microwave-assisted method proved efficient for a number of carbon nanomaterials including carbon nanotubes (CNTs), graphene and fullerene. The carbohydrates on the glyconanomaterials retained their binding patterns towards cognate lectins.
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| 20. |
- Kong, Na, et al.
(author)
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Catalyst-Free Cycloaddition Reaction for the Synthesis of Glyconanoparticles
- 2016
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In: ACS Applied Materials and Interfaces. - : American Chemical Society (ACS). - 1944-8244 .- 1944-8252. ; 8:41, s. 28136-28142
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Journal article (peer-reviewed)abstract
- A new conjugation method for the immobilization of carbohydrates on nanomaterials was demonstrated simply by mixing perfluorophenyl azide-functionalized silica nanoparticles (SNPs), an amine-derivatized carbohydrate, and phenylacetaldehyde under ambient conditions without any catalyst. The density of carbohydrates on the glyconanoparticles was determined using the quantitative F-19 NMR (F-19 qNMR) technique; for example, the density of D-mannose (Man) on Man-SNPs was 2.5 +/- 0.2 x 10(-16) nmol/nm(2). The glyconanoparticles retained their binding affinity and selectivity toward cognate lectins. The apparent dissociation constant of the glyconanoparticles was measured by a fluorescence competition assay, where the binding affinity of Man-SNPs was almost 4 orders of magnitude higher than that of Man with concanavalin A. Moreover, even with a ligand density of 2.6 times lower than Man-SNPs synthesized by the copper catalyzed azide-alkyne cycloaddition, the binding affinity of Man-SNPs prepared by the current method was more than 4 times higher.
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| 21. |
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| 22. |
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| 23. |
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| 24. |
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| 25. |
- Kong, Na, et al.
(author)
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Quantitative Fluorine NMR To Determine Carbohydrate Density on Glyconanomaterials Synthesized from Perfluorophenyl Azide-Functionalized Silica Nanoparticles by Click Reaction
- 2015
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In: Analytical Chemistry. - : American Chemical Society (ACS). - 0003-2700 .- 1520-6882. ; 87:18, s. 9451-9458
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Journal article (peer-reviewed)abstract
- A quantitative fluorine NMR (F-19 qNMR) method was developed to determine the carbohydrate density on glyconanomaterials. Mannose (Man)- and galactose (Gal)-conjugated silica nanoparticles (SNPs) were synthesized from perfluorophenyl azide (PFPA)-functionalized SNPs and propargylated Man or Gal by copper-catalyzed azide-alkyne cycloaddition (click reaction). After treating PFPA-SNPs or Man-SNPs with hydrofluoric acid followed by lyophilization, the remaining residues were directly subjected to F-19 NMR analysis. The density of PFPA on PFPA-SNP was determined to be 7.7 +/- 0.2 x 10(-16) nmol/nm(2) and Man on Man-SNP to be 6.4 +/- 0.2 x 10(-16) nmol/nm(2) giving a yield of similar to 83% for the click coupling reaction. The apparent dissociation constant (K-d) of Man-SNPs with fluorescein isothiocyanate(FITC)-concanavalin A (Con A) was determined using a fluorescence competition assay to be 0.289 +/- 0.003 mu M, which represents more than 3 orders of magnitude affinity increase compared to free Man with Con A.
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| 26. |
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| 27. |
- Li, Junjie, et al.
(author)
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A Novel Dry Selective Isotropic Atomic Layer Etching of SiGe for Manufacturing Vertical Nanowire Array with Diameter Less than 20 nm
- 2020
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In: Materials. - : MDPI AG. - 1996-1944. ; 13:3
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Journal article (peer-reviewed)abstract
- Semiconductor nanowires have great application prospects in field effect transistors and sensors. In this study, the process and challenges of manufacturing vertical SiGe/Si nanowire array by using the conventional lithography and novel dry atomic layer etching technology. The final results demonstrate that vertical nanowires with a diameter less than 20 nm can be obtained. The diameter of nanowires is adjustable with an accuracy error less than 0.3 nm. This technology provides a new way for advanced 3D transistors and sensors.
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| 28. |
- Lin, Jia, et al.
(author)
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Pressure-induced semiconductor-to-metal phase transition of a charge-ordered indium halide perovskite
- 2019
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In: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 116:47, s. 23404-23409
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Journal article (peer-reviewed)abstract
- Phase transitions in halide perovskites triggered by external stimuli generate significantly different material properties, providing a great opportunity for broad applications. Here, we demonstrate an In-based, charge-ordered (In+/In3+) inorganic halide perovskite with the composition of Cs2In(I)In(III)Cl-6 in which a pressure-driven semiconductor-to-metal phase transition exists. The single crystals, synthesized via a solid-state reaction method, crystallize in a distorted perovskite structure with space group I4/m with a = 17.2604(12) angstrom, c = 11.0113(16) angstrom if both the strong reflections and superstructures are considered. The supercell was further confirmed by rotation electron diffraction measurement. The pressure-induced semiconductor-to-metal phase transition was demonstrated by high-pressure Raman and absorbance spectroscopies and was consistent with theoretical modeling. This type of charge-ordered inorganic halide perovskite with a pressure-induced semiconductor-to-metal phase transition may inspire a range of potential applications.
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| 29. |
- Murari, A., et al.
(author)
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A control oriented strategy of disruption prediction to avoid the configuration collapse of tokamak reactors
- 2024
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In: Nature Communications. - 2041-1723 .- 2041-1723. ; 15:1
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Journal article (peer-reviewed)abstract
- The objective of thermonuclear fusion consists of producing electricity from the coalescence of light nuclei in high temperature plasmas. The most promising route to fusion envisages the confinement of such plasmas with magnetic fields, whose most studied configuration is the tokamak. Disruptions are catastrophic collapses affecting all tokamak devices and one of the main potential showstoppers on the route to a commercial reactor. In this work we report how, deploying innovative analysis methods on thousands of JET experiments covering the isotopic compositions from hydrogen to full tritium and including the major D-T campaign, the nature of the various forms of collapse is investigated in all phases of the discharges. An original approach to proximity detection has been developed, which allows determining both the probability of and the time interval remaining before an incoming disruption, with adaptive, from scratch, real time compatible techniques. The results indicate that physics based prediction and control tools can be developed, to deploy realistic strategies of disruption avoidance and prevention, meeting the requirements of the next generation of devices.
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| 33. |
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| 35. |
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| 36. |
- Thompson, PM, et al.
(author)
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ENIGMA and global neuroscience: A decade of large-scale studies of the brain in health and disease across more than 40 countries
- 2020
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In: Translational psychiatry. - : Springer Science and Business Media LLC. - 2158-3188. ; 10:1, s. 100-
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Journal article (peer-reviewed)abstract
- This review summarizes the last decade of work by the ENIGMA (Enhancing NeuroImaging Genetics through Meta Analysis) Consortium, a global alliance of over 1400 scientists across 43 countries, studying the human brain in health and disease. Building on large-scale genetic studies that discovered the first robustly replicated genetic loci associated with brain metrics, ENIGMA has diversified into over 50 working groups (WGs), pooling worldwide data and expertise to answer fundamental questions in neuroscience, psychiatry, neurology, and genetics. Most ENIGMA WGs focus on specific psychiatric and neurological conditions, other WGs study normal variation due to sex and gender differences, or development and aging; still other WGs develop methodological pipelines and tools to facilitate harmonized analyses of “big data” (i.e., genetic and epigenetic data, multimodal MRI, and electroencephalography data). These international efforts have yielded the largest neuroimaging studies to date in schizophrenia, bipolar disorder, major depressive disorder, post-traumatic stress disorder, substance use disorders, obsessive-compulsive disorder, attention-deficit/hyperactivity disorder, autism spectrum disorders, epilepsy, and 22q11.2 deletion syndrome. More recent ENIGMA WGs have formed to study anxiety disorders, suicidal thoughts and behavior, sleep and insomnia, eating disorders, irritability, brain injury, antisocial personality and conduct disorder, and dissociative identity disorder. Here, we summarize the first decade of ENIGMA’s activities and ongoing projects, and describe the successes and challenges encountered along the way. We highlight the advantages of collaborative large-scale coordinated data analyses for testing reproducibility and robustness of findings, offering the opportunity to identify brain systems involved in clinical syndromes across diverse samples and associated genetic, environmental, demographic, cognitive, and psychosocial factors.
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| 37. |
- Uppalapati, Suji, et al.
(author)
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Ionization of covalent immobilized poly(4-vinylphenol) monolayers measured by ellipsometry, QCM and SPR
- 2015
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In: Applied Surface Science. - : Elsevier BV. - 0169-4332 .- 1873-5584. ; 343, s. 166-171
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Journal article (peer-reviewed)abstract
- Covalently immobilized poly(4-vinylphenol) (PVP) monolayer films were fabricated by spin coating PVP on perfluorophenyl azide (PFPA)-functionalized surfaces followed by UV irradiation. The pH-responsive behavior of these PVP ultrathin films was evaluated by ellipsometry, quartz crystal microbalance (QCM) and surface plasmon resonance (SPR). By monitoring the responses of these films to pH in situ, the ionization constant of the monolayer thin films was obtained. The apparent plc, value of these covalently immobilized PVP monolayers, 13.4 by SPR, was 3 units higher than that of the free polymer in aqueous solution.
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| 38. |
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| 39. |
- Xie, Sheng, et al.
(author)
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A versatile catalyst-free perfluoroaryl azide-aldehyde-amine conjugation reaction
- 2019
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In: Materials Chemistry Frontiers. - : Royal Society of Chemistry. - 2052-1537. ; 3:2, s. 251-256
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Journal article (peer-reviewed)abstract
- In a tri-component reaction, an electrophilically-activated perfluoroaryl azide, an enolizable aldehyde and an amine react readily at room temperature without any catalysts in solvents including aqueous conditions to yield a stable amidine conjugate. The versatility of this reaction is demonstrated in the conjugation of an amino acid without prior protection of the carboxyl group, and in the synthesis of antibiotic-nanoparticle conjugates.
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| 40. |
- Yuan, Xiaotian, et al.
(author)
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GABPA inhibits invasion/metastasis in papillary thyroid carcinoma by regulating DICER1 expression
- 2019
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In: Oncogene. - : Springer Science and Business Media LLC. - 0950-9232 .- 1476-5594. ; 38:7, s. 965-979
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Journal article (peer-reviewed)abstract
- The ETS family transcription factor GABPA is suggested as an oncogenic element, which is further supported by the recent reporting of it as the sole ETS member to activate the mutant TERT promoter in thyroid carcinomas (TC). However, it remains unclear how GABPA contributes to TC pathogenesis. The present study is designed to address this issue. TERT expression was significantly diminished in TERT promoter-mutated TC cells upon GABPA inhibition. Surprisingly, GABPA depletion led to robustly increased cellular invasion independently of TERT promoter mutations and TERT expression. DICER1, a component of the microRNA machinery, was identified as a downstream effector of GABPA. GABPA facilitated Dicer1 transcription while its depletion reduced Dicer1 expression. The mutation of the GABPA binding site in the DICER1 promoter led to diminished basal levels of DICER1 promoter activity and abolishment of GABPA-stimulated promoter activity as well. The forced DICER1 expression abrogated the invasiveness of GABPA-depleted TC cells. Consistently, the analyses of 93 patients with papillary thyroid carcinoma (PTC) revealed a positive correlation between GABPA and DICER1 expression. GABPA expression was negatively associated with TERT expression and promoter mutations, in contrast to published observations in cancer cell lines. Lower GABPA expression was associated with distant metastasis and shorter overall/disease-free survival in PTC patients. Similar results were obtained for PTC cases in the TCGA dataset. In addition, a positive correlation between GABPA and DICER1 expression was seen in multiple types of malignancies. Taken together, despite its stimulatory effect on the mutant TERT promoter and telomerase activation, GABPA may itself act as a tumor suppressor rather than an oncogenic factor to inhibit invasion/metastasis in TCs and be a useful predictor for patient outcomes.
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| 41. |
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| 42. |
- Zhou, Juan, et al.
(author)
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Trehalose-Conjugated, Photofunctionalized Mesoporous Silica Nanoparticles for Efficient Delivery of Isoniazid into Mycobacteria
- 2015
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In: ACS Biomaterials Science & Engineering. - : American Chemical Society (ACS). - 2373-9878. ; 1:12, s. 1250-1255
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Journal article (peer-reviewed)abstract
- Glyconanoparticle carriers have been synthesized and efficiently delivered into mycobacteria. Mesoporous silica nanoparticles were functionalized with a,a-trehalose through azide-mediated surface photoligation, and loaded with the antitubercular drug isoniazid. The glyconanoparticles showed high isoniazid loading capacity and higher antimicrobial activity than the free drug.
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| 43. |
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