| 1. |
|
|
| 2. |
- Danko, David, et al.
(författare)
-
A global metagenomic map of urban microbiomes and antimicrobial resistance
- 2021
-
Ingår i: Cell. - : Elsevier BV. - 0092-8674 .- 1097-4172. ; 184:13, s. 3376-3393
-
Tidskriftsartikel (refereegranskat)abstract
- We present a global atlas of 4,728 metagenomic samples from mass-transit systems in 60 cities over 3 years, representing the first systematic, worldwide catalog of the urban microbial ecosystem. This atlas provides an annotated, geospatial profile of microbial strains, functional characteristics, antimicrobial resistance (AMR) markers, and genetic elements, including 10,928 viruses, 1,302 bacteria, 2 archaea, and 838,532 CRISPR arrays not found in reference databases. We identified 4,246 known species of urban microorganisms and a consistent set of 31 species found in 97% of samples that were distinct from human commensal organisms. Profiles of AMR genes varied widely in type and density across cities. Cities showed distinct microbial taxonomic signatures that were driven by climate and geographic differences. These results constitute a high-resolution global metagenomic atlas that enables discovery of organisms and genes, highlights potential public health and forensic applications, and provides a culture-independent view of AMR burden in cities.
|
|
| 3. |
- Humphries, Matthew P., et al.
(författare)
-
A case-matched gender comparison transcriptomic screen identifies eIF4E and eIF5 as potential prognostic markers in male breast cancer
- 2017
-
Ingår i: Clinical Cancer Research. - 1078-0432 .- 1557-3265. ; 23:10, s. 2575-2583
-
Tidskriftsartikel (refereegranskat)abstract
- Purpose: Breast cancer affects both genders, but is understudied in men. Although still rare, male breast cancer (MBC) is being diagnosed more frequently. Treatments are wholly informed by clinical studies conducted in women, based on assumptions that underlying biology is similar. Experimental Design: A transcriptomic investigation of male and female breast cancer was performed, confirming transcriptomic data in silico. Biomarkers were immunohistochemically assessed in 697 MBCs (n = 477, training; n = 220, validation set) and quantified in pre- and posttreatment samples from an MBC patient receiving everolimus and PI3K/mTOR inhibitor. Results: Gender-specific gene expression patterns were identified. eIF transcripts were upregulated in MBC. eIF4E and eIF5 were negatively prognostic for overall survival alone (log-rank P = 0.013; HR = 1.77, 1.12-2.8 and P = 0.035; HR = 1.68, 1.03-2.74, respectively), or when coexpressed (P = 0.01; HR = 2.66, 1.26-5.63), confirmed in the validation set. This remained upon multivariate Cox regression analysis [eIF4E P = 0.016; HR = 2.38 (1.18-4.8), eIF5 P = 0.022; HR = 2.55 (1.14-5.7); coexpression P = 0.001; HR = 7.04 (2.22-22.26)]. Marked reduction in eIF4E and eIF5 expression was seen post BEZ235/everolimus, with extended survival. Conclusions: Translational initiation pathway inhibition could be of clinical utility in MBC patients overexpressing eIF4E and eIF5. With mTOR inhibitors that target this pathway now in the clinic, these biomarkers may represent new targets for therapeutic intervention, although further independent validation is required.
|
|
| 4. |
- Madin, Joshua S., et al.
(författare)
-
A synthesis of bacterial and archaeal phenotypic trait data
- 2020
-
Ingår i: Scientific data. - : Springer Science and Business Media LLC. - 2052-4463. ; 7:1
-
Tidskriftsartikel (refereegranskat)abstract
- A synthesis of phenotypic and quantitative genomic traits is provided for bacteria and archaea, in the form of a scripted, reproducible workflow that standardizes and merges 26 sources. The resulting unified dataset covers 14 phenotypic traits, 5 quantitative genomic traits, and 4 environmental characteristics for approximately 170,000 strain-level and 15,000 species-aggregated records. It spans all habitats including soils, marine and fresh waters and sediments, host-associated and thermal. Trait data can find use in clarifying major dimensions of ecological strategy variation across species. They can also be used in conjunction with species and abundance sampling to characterize trait mixtures in communities and responses of traits along environmental gradients.
|
|
| 5. |
- Bartels, S. L., et al.
(författare)
-
Impact of the COVID-19 pandemic on early career dementia researchers: A global online survey
- 2022
-
Ingår i: Plos One. - : Public Library of Science (PLoS). - 1932-6203. ; 17
-
Tidskriftsartikel (refereegranskat)abstract
- Introduction The World Health Organization recognizes dementia as a public health priority and highlights research as an action to respond to the consequences, with early career dementia researchers (ECDRs) representing the key driving force. Due to the COVID-19 pandemic, however, biomedical and psychosocial dementia research was strained worldwide. The aim of this study was to understand the impact of the pandemic on ECDRs. Methods In autumn 2021, the Alzheimer's Association International Society to Advance Alzheimer's Research and Treatment (ISTAART) Professional Interest Area to Elevate Early Career Researchers (PEERs) and University College London conducted an online survey querying ECDRs' experiences during the COVID-19 pandemic. The survey was shared through the ISTAART network, social media, podcasts, and emailing lists. Data were analyzed using descriptive and inferential statistics. Results Survey data from n = 321 ECDRs from 34 countries were analyzed (67.6% women; 78.8% working in academia). Overall, 77.8% of ECDRs surveyed indicated research delays, 53.9% made project adjustments, 37.9% required additional or extended funding, and 41.8% reported a negative impact on career progression. Moreover, 19.9% felt unsupported by their institutions and employers (33% felt well supported, 42.7% somewhat supported). ECDR's conference attendance remained the same (26.5%) or increased (More: 28.6%; a lot more: 5.6%) since the start of the pandemic. Continental differences were visible, while the impact of the pandemic did not differ greatly based on ECDRs' sociodemographic characteristics. Conclusions The COVID-19 pandemic had a substantial impact on ECDRs worldwide and institutions, employers, and funding bodies are urged to consider the implications and lessons-learned when working with, managing, and promoting ECDRs. Strategies related to the pandemic and general career support to improve ECDRs career progression are discussed, including social media training, digital networking, and benefits of hybrid events. Global resources specific for ECDRs are highlighted.
|
|
| 6. |
- Chng, Kern Rei, et al.
(författare)
-
Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment
- 2020
-
Ingår i: Nature Medicine. - : Springer Science and Business Media LLC. - 1078-8956 .- 1546-170X. ; 26, s. 941-951
-
Tidskriftsartikel (refereegranskat)abstract
- Although disinfection is key to infection control, the colonization patterns and resistomes of hospital-environment microbes remain underexplored. We report the first extensive genomic characterization of microbiomes, pathogens and antibiotic resistance cassettes in a tertiary-care hospital, from repeated sampling (up to 1.5 years apart) of 179 sites associated with 45 beds. Deep shotgun metagenomics unveiled distinct ecological niches of microbes and antibiotic resistance genes characterized by biofilm-forming and human-microbiome-influenced environments with corresponding patterns of spatiotemporal divergence. Quasi-metagenomics with nanopore sequencing provided thousands of high-contiguity genomes, phage and plasmid sequences (>60% novel), enabling characterization of resistome and mobilome diversity and dynamic architectures in hospital environments. Phylogenetics identified multidrug-resistant strains as being widely distributed and stably colonizing across sites. Comparisons with clinical isolates indicated that such microbes can persist in hospitals for extended periods (>8 years), to opportunistically infect patients. These findings highlight the importance of characterizing antibiotic resistance reservoirs in hospitals and establish the feasibility of systematic surveys to target resources for preventing infections. Spatiotemporal characterization of microbial diversity and antibiotic resistance in a tertiary-care hospital reveals broad distribution and persistence of antibiotic-resistant organisms that could cause opportunistic infections in a healthcare setting.
|
|
| 7. |
- Mushtaq, Afshan, et al.
(författare)
-
Catalytic oxidative desulfurization of thio-compounds by employing χ-Anderson-type polyoxometalates-porphyrin covalent organic framework (COF)
- 2023
-
Ingår i: Tetrahedron. - : Elsevier. - 0040-4020 .- 1464-5416. ; 144
-
Tidskriftsartikel (refereegranskat)abstract
- Severe environmental sulfur contents due to the consumption of fuels in automobiles and industries resulted in serious health hazards and pollution because of it, desulfurization of diesel become inevitable. Targeting the profound desulfurization of diesel, we performed experiments to deeply desulphurized the thio-compounds by catalytic-oxidative desulfurization technique. We synthesized new metalloporphyrin (C52H36N4O8Sn)4MeO-SnPor which after conversion into (C64H64N8O16Sn)4Tris-SnTP leading towards the synthesis of covalent organic framework [(N(C4H9)4]12[HNC(CH2O)3]4[(CO)4C44H24N4Sn] [NiMo6O18]4(SnTP@NiAdCOF). SnTP@NiAd COF showed the outstanding catalytic property for deep desulfurization of thio-compounds above than 96% of thiobenzoic acid (TB) and 99% of 2-aminothiophenol (2-ATP) sulfur contents were oxides after 100 min of reaction using H2O2 as an oxidant at room temperature with constant stirring. During desulfurization percentage desulfurization efficiency was checked for different time intervals by TLC and further confirmed by reverse phase high-performance liquid chromatography (RP-HPLC). Reverse-phase high-performance liquid chromatograms indicated that the peak area and peak height of thio-compounds decrease gradually with the passage of reaction time which confirmed the removal of thio-compounds from the reaction mixture. Sulfur contents removed up to 5 ppmw showed excellent catalytic characteristics of synthesized SnTP@NiAdCOF. The exceptional catalytic efficiency of prepared catalyst SnTP@NiAdCOF was because of the existence of active oxidizing centers of χ-NiAd and metalloporphyrin that are MoO and [(Por)SnII], respectively. The potential mechanism appeared to be the formation of Mo(O2) and [(Por)SnII–OOH] from MoO and [(Por)SnII], respectively that act as active oxidizing centers and efficiently converted the thio-group into oxides and sulfones. Effective removal of sulfur grants the desulfurization of fuels by using SnTP@NiAdCOF catalyst to lessen the energy expenditure and also to enhance the production of environmentally-safe fuels.
|
|
| 8. |
|
|
| 9. |
|
|
| 10. |
- Adel, Amany, et al.
(författare)
-
Genetic Variations among Different Variants of G1-like Avian Influenza H9N2 Viruses and Their Pathogenicity in Chickens
- 2022
-
Ingår i: Viruses. - : MDPI AG. - 1999-4915. ; 14:5
-
Tidskriftsartikel (refereegranskat)abstract
- Since it was first discovered, the low pathogenic avian influenza (LPAI) H9N2 subtype has established linages infecting the poultry population globally and has become one of the most prevalent influenza subtypes in domestic poultry. Several different variants and genotypes of LPAI H9N2 viruses have been reported in Egypt, but little is known about their pathogenicity and how they have evolved. In this study, four different Egyptian LPAI H9N2 viruses were genetically and antigenically characterized and compared to representative H9N2 viruses from G1 lineage. Furthermore, the pathogenicity of three genetically distinct Egyptian LPAI H9N2 viruses was assessed by experimental infection in chickens. Whole-genome sequencing revealed that the H9N2 virus of the Egy-2 G1-B lineage (pigeon-like) has become the dominant circulating H9N2 genotype in Egypt since 2016. Considerable variation in virus shedding at day 7 post-infections was detected in infected chickens, but no significant difference in pathogenicity was found between the infected groups. The rapid spread and emergence of new genotypes of the influenza viruses pinpoint the importance of continuous surveillance for the detection of novel reassortant viruses, as well as monitoring the viral evolution.
|
|
