Pandemic (H1N1) 2009 Surveillance and Prevalence of Seasonal Influenza, Singapore

On April 25, 2009, Singapore implemented strict containment measures for pandemic (H1N1) 2009 with enhanced surveillance and hospital isolation. In the first month, seasonal influenza, predominantly virus subtype H3N2, was diagnosed for 32% of patients with acute febrile respiratory illness. Our findings underscore the high prevalence of seasonal influenza in Singapore

Author Correction: Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Correction to this paper has been published: https://doi.org/10.1038/s41467-020-20128-w

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Author Correction:Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples (Nature Communications, (2020), 11, 1, (4748), 10.1038/s41467-020-18151-y)

The original version of this Article omitted from the author list the 9th author Yize Li, who is from the ‘The McDonnell Genome Institute at Washington University, St. Louis, MO 63108, USA and Department of Medicine, Division of Oncology, Washington University School of Medicine, St. Louis, MO 63108, USA’. This has been corrected in both the PDF and HTML versions of the Article

Free-standing graphene oxide and carbon nanotube hybrid papers with enhanced electrical and mechanic performance and their synergy in polymer laminates

Hybrid nanomaterials fabricated by the heterogeneous integration of 1D (carbon nanotubes) and 2D (graphene oxide) nanomaterials showed synergy in electrical and mechanical properties. Here, we reported the infiltration of carboxylic functionalized single-walled carbon nanotubes (C-SWNT) into free-standing graphene oxide (GO) paper for better electrical and mechanical properties than native GO. The stacking arrangement of GO sheets and its alteration in the presence of C-SWNT were comprehensively explored through scanning electron microscopy, X-ray photoelectron spectroscopy (XPS) and X-ray diffraction. The C-SWNTs bridges between different GO sheets produce a pathway for the flow of electrical charges and provide a tougher hybrid system. The nanoscopic surface potential map reveals a higher work function of the individual functionalised SWNTs than surrounded GO sheets showing efficient charge exchange. We observed the enhanced conductivity up to 50 times and capacitance up to 3.5 times of the hybrid structure than the GO-paper. The laminate of polystyrene composites provided higher elastic modulus and mechanical strength when hybrid paper is used, thus paving the way for the exploitation of hybrid filler formulation in designing polymer composites

Comparison of Pandemic (H1N1) 2009 and Seasonal Influenza, Western Australia, 2009

TOC summary: Infections were similar in terms of symptoms, risk factors, and proportion of patients hospitalized

Unraveling the functional dark matter through global metagenomics

30 pages, 4 figures, 1 table, supplementary information https://doi.org/10.1038/s41586-023-06583-7.-- Data availability: All of the analysed datasets along with their corresponding sequences are available from the IMG system (http://img.jgi.doe.gov/). A list of the datasets used in this study is provided in Supplementary Data 8. All data from the protein clusters, including sequences, multiple alignments, HMM profiles, 3D structure models, and taxonomic and ecosystem annotation, are available through NMPFamsDB, publicly accessible at www.nmpfamsdb.org. The 3D models are also available at ModelArchive under accession code ma-nmpfamsdb.-- Code availability: Sequence analysis was performed using Tantan (https://gitlab.com/mcfrith/tantan), BLAST (https://blast.ncbi.nlm.nih.gov/Blast.cgi), LAST (https://gitlab.com/mcfrith/last), HMMER (http://hmmer.org/) and HH-suite3 (https://github.com/soedinglab/hh-suite). Clustering was performed using HipMCL (https://bitbucket.org/azadcse/hipmcl/src/master/). Additional taxonomic annotation was performed using Whokaryote (https://github.com/LottePronk/whokaryote), EukRep (https://github.com/patrickwest/EukRep), DeepVirFinder (https://github.com/jessieren/DeepVirFinder) and MMseqs2 (https://github.com/soedinglab/MMseqs2). 3D modelling was performed using AlphaFold2 (https://github.com/deepmind/alphafold) and TrRosetta2 (https://github.com/RosettaCommons/trRosetta2). Structural alignments were performed using TMalign (https://zhanggroup.org/TM-align/) and MMalign (https://zhanggroup.org/MM-align/). All custom scripts used for the generation and analysis of the data are available at Zenodo (https://doi.org/10.5281/zenodo.8097349)Metagenomes encode an enormous diversity of proteins, reflecting a multiplicity of functions and activities1,2. Exploration of this vast sequence space has been limited to a comparative analysis against reference microbial genomes and protein families derived from those genomes. Here, to examine the scale of yet untapped functional diversity beyond what is currently possible through the lens of reference genomes, we develop a computational approach to generate reference-free protein families from the sequence space in metagenomes. We analyse 26,931 metagenomes and identify 1.17 billion protein sequences longer than 35 amino acids with no similarity to any sequences from 102,491 reference genomes or the Pfam database3. Using massively parallel graph-based clustering, we group these proteins into 106,198 novel sequence clusters with more than 100 members, doubling the number of protein families obtained from the reference genomes clustered using the same approach. We annotate these families on the basis of their taxonomic, habitat, geographical and gene neighbourhood distributions and, where sufficient sequence diversity is available, predict protein three-dimensional models, revealing novel structures. Overall, our results uncover an enormously diverse functional space, highlighting the importance of further exploring the microbial functional dark matterWith the institutional support of the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S)Peer reviewe

Mechanical and physical characterization of graphene composites

During my PhD activities, I studied the introduction of carbon-based nanofillers in materials at different scales, while focusing primarily on fibres and fibrillar materials. Several production techniques were exploited. Little is known about the interaction of graphene with electrospun polymeric fibres. Manufacturing composite fibres is complex since fillers have lateral sizes nearing that of the embedding fibre. Indeed, graphene has a direct effect in both the assembly of the electrospun composite fibres and their mechanical performance. Moreover, the tensile behaviour of hollow micrometric electrospun fibres was compared with macroscopic hollow structures such as drinking straws. The acquired insights helped to explain the toughening mechanisms at the micro-scale and develop a model capable of predicting the stress-strain response of such structures. Among natural materials, wood has the most relevant structural applications even at large scales. Its main structural component is cellulose that has a high resistance and a low light absorption. Several structural modifications of wood derived materials were recently investigated in order to enhance the mechanical and optical properties of cellulose. These enhancements can take place after the internal structure is chemically modified with the removal of lignin and after a structural densification. Potentially, any type of wood-like materials, such as giant reed (that is a fast-growing and invasive species), can be turned into a strong structural composite. Such modifications lead to an open and interconnected internal structure that is the ideal scaffold for nanoparticle intercalation. Graphene oxide and silicon carbide nanoparticles were intercalated into densified reed. They produced an even stiffer, stronger and tougher composite compared to the best up-to-date process available. Moreover, its capabilities to resist fire and water-absorption were tested. Finally, the previous process was further developed on wood to achieve a combination of improved transparency and electrical conductivity. Graphene and carbon nanotubes were introduced into the structure of wood to foster conductivity and explore the viability of its application as a self-strain sensor

Research by Fondazione Bruno Kessler on Strategies to Improve the Yield in Plasma Focused Ion Beam Circuit Editing

This contribution explores the potential of PFIB for the post-production circuit editing of custom ASICs. The reworking of integrated circuits with ion beam is an effective tool for testing design modifications rapidly, and in small-volume productions, it proves to be a valuable substitute for the microfabrication of chips with a revised layout, thus reducing the cost and lead time. In the case study in this work, the PFIB intervention resulted in the recovery of ~90% of defective channels in a multichannel ASIC design by disconnecting some parts of the internal circuit. This contribution describes several implemented optimization strategies and their statistical effectiveness