Long-distance soliton transmission through ultralong fiber lasers

We present the first experimental demonstration (to our knowledge) of long-distance unperturbed fundamental optical soliton transmission in conventional single-mode optical fiber. The virtual transparency in the fiber required for soliton transmission, over 15 complete periods, was achieved by using an ultralong Raman fiber laser amplification scheme. Optical soliton pulse duration, pulse bandwidth, and peak intensity are shown to remain constant along the transmission length. Frequency-resolved optical gating spectrograms and numerical simulations confirm the observed optical soliton dynamics

Bifidobacterium breve reduces apoptotic epithelial cell shedding in an exopolysaccharide and MyD88-dependent manner

Certain members of the microbiota genus Bifidobacterium are known to positively influence host well-being. Importantly, reduced bifidobacterial levels are associated with inflammatory bowel disease (IBD) patients, who also have impaired epithelial barrier function, including elevated rates of apoptotic extrusion of small intestinal epithelial cells (IECs) from villi—a process termed ‘cell shedding’. Using a mouse model of pathological cell shedding, we show that mice receiving Bifidobacterium breve UCC2003 exhibit significantly reduced rates of small IEC shedding. Bifidobacterial-induced protection appears to be mediated by a specific bifidobacterial surface exopolysaccharide and interactions with host MyD88 resulting in downregulation of intrinsic and extrinsic apoptotic responses to protect epithelial cells under highly inflammatory conditions. Our results reveal an important and previously undescribed role for B. breve, in positively modulating epithelial cell shedding outcomes via bacterial- and host-dependent factors, supporting the notion that manipulation of the microbiota affects intestinal disease outcomes

Next generation of selenocyanate and diselenides with upgraded leishmanicidal activity

Nowadays, leishmaniasis is still treated with outdated drugs that present several obstacles related to their high toxicity, long duration, parenteral administration, high costs and drug resistance. Therefore, there is an urgent demand for safer and more effective novel drugs. Previous studies indicated that selenium compounds are promising derivatives for innovative therapy in leishmaniasis treatment. With this background, a new library of 20 selenocyanate and diselenide derivatives were designed based on structural features present in the leishmanicidal drug miltefosine. Compounds were initially screened against promastigotes of L. major and L. infantum and their cytotoxicity was evaluated in THP-1 cells. Compounds B8 and B9 were the most potent and less cytotoxic and were further screened for the intracellular back transformation assay. The results obtained revealed that B8 and B9 showed EC50 values of 7.7 µM and 5.7 µM, respectively, in L. major amastigotes, while they presented values of 6.0 µM and 7.4 µM, respectively, against L. infantum amastigotes. Furthermore, they exerted high selectivity (60 70) towards bone marrow-derived macrophages. Finally, these compounds exhibited higher TryR inhibitory activity than mepacrine (IC50 7.6 and 9.2 µM, respectively), and induced nitric oxide (NO) and reactive oxygen species (ROS) production in macrophages. These results suggest that the compounds B8 and B9 could not only exert a direct leishmanicidal activity against the parasite but also present an indirect action by activating the microbicidal arsenal of the macrophage. Overall, these new generation of diselenides could constitute promising leishmanicidal drug candidates for further studies

Materials characterisation and software tools as key enablers in Industry 5.0 and wider acceptance of new methods and products

Recently, the NMBP-35 Horizon 2020 projects -NanoMECommons, CHARISMA, and Easi-stress -organised a collaborative workshop to increase awareness of their contributions to the industry "commons" in terms of characterisation and digital transformation. They have established interoperability standards for knowledge management in characterisation and introduced new solutions for materials testing, aided by the standardisation of faster and more accurate assessment methods. The lessons learned from these projects and the discussions during the joint workshop emphasised the impact of recent developments and emerging needs in the field of characterisation. Specifically, the focus was on enhancing data quality through harmonisation and stand-ardisation, as well as making advanced technologies and instruments accessible to a broader community with the goal of fostering increased trust in new products and a more skilled society. Experts also highlighted how characterisation and the corresponding experimental data can drive future innovation agendas towards tech-nological breakthroughs. The focus of the discussion revolved around the characterisation and standardisation processes, along with the collection of modelling and characterisation tools, as well as protocols for data ex-change. The broader context of materials characterisation and modelling within the materials community was explored, drawing insights from the Materials 2030 Roadmap and the experiences gained from NMBP-35 pro-jects. This whitepaper has the objective of addressing common challenges encountered by the materials com-munity, illuminating emerging trends and evolving techniques, and presenting the industry's perspective on emerging requirements and past success stories. It accomplishes this by providing specific examples and high-lighting how these experiences can create fresh opportunities and strategies for newcomers entering the market. These advancements are anticipated to facilitate a more efficient transition from Industry 4.0 to 5.0 during the industrial revolution

Molecular architecture of the Jumonji C family histone demethylase KDM5B

Abstract The full length human histone 3 lysine 4 demethylase KDM5B (PLU-1/Jarid1B) has been studied using Hydrogen/Deuterium exchange mass spectrometry, homology modelling, sequence analysis, small angle X-ray scattering and electron microscopy. This first structure on an intact multi-domain Jumonji histone demethylase reveal that the so-called PLU region, in the central region of KDM5B, has a curved α-helical three-dimensional structure, that acts as a rigid linker between the catalytic core and a region comprising four α-helices, a loop comprising the PHD2 domain, two large intrinsically disordered loops and the PHD3 domain in close proximity. The dumbbell shaped and curved KDM5B architecture observed by electron microscopy is complementary to the nucleosome surface and has a striking overall similarity to that of the functionally related KDM1A/CoREST complex. This could suggest that there are similarities between the demethylation mechanisms employed by the two histone 3 lysine 4 demethylases at the molecular level

Particular genomic and virulence traits associated with preterm infant-derived toxigenic Clostridium perfringens strains

Clostridium perfringens is an anaerobic toxin-producing bacterium associated with intestinal diseases, particularly in neonatal humans and animals. Infant gut microbiome studies have recently indicated a link between C. perfringens and the preterm infant disease necrotizing enterocolitis (NEC), with specific NEC cases associated with overabundant C. perfringens termed C. perfringens-associated NEC (CPA-NEC). In the present study, we carried out whole-genome sequencing of 272 C. perfringens isolates from 70 infants across 5 hospitals in the United Kingdom. In this retrospective analysis, we performed in-depth genomic analyses (virulence profiling, strain tracking and plasmid analysis) and experimentally characterized pathogenic traits of 31 strains, including 4 from CPA-NEC patients. We found that the gene encoding toxin perfringolysin O, pfoA, was largely deficient in a human-derived hypovirulent lineage, as well as certain colonization factors, in contrast to typical pfoA-encoding virulent lineages. We determined that infant-associated pfoA+ strains caused significantly more cellular damage than pfoA- strains in vitro, and further confirmed this virulence trait in vivo using an oral-challenge C57BL/6 murine model. These findings suggest both the importance of pfoA+ C. perfringens as a gut pathogen in preterm infants and areas for further investigation, including potential intervention and therapeutic strategies

Streaming histogram sketching for rapid microbiome analytics

Background: The growth in publically available microbiome data in recent years has yielded an invaluable resource for genomic research, allowing for the design of new studies, augmentation of novel datasets and reanalysis of published works. This vast amount of microbiome data, as well as the widespread proliferation of microbiome research and the looming era of clinical metagenomics, means there is an urgent need to develop analytics that can process huge amounts of data in a short amount of time. To address this need, we propose a new method for the compact representation of microbiome sequencing data using similarity-preserving sketches of streaming k-mer spectra. These sketches allow for dissimilarity estimation, rapid microbiome catalogue searching and classification of microbiome samples in near real time. Results: We apply streaming histogram sketching to microbiome samples as a form of dimensionality reduction, creating a compressed ‘histosketch’ that can efficiently represent microbiome k-mer spectra. Using public microbiome datasets, we show that histosketches can be clustered by sample type using the pairwise Jaccard similarity estimation, consequently allowing for rapid microbiome similarity searches via a locality sensitive hashing indexing scheme. Furthermore, we use a ‘real life’ example to show that histosketches can train machine learning classifiers to accurately label microbiome samples. Specifically, using a collection of 108 novel microbiome samples from a cohort of premature neonates, we trained and tested a random forest classifier that could accurately predict whether the neonate had received antibiotic treatment (97% accuracy, 96% precision) and could subsequently be used to classify microbiome data streams in less than 3 s. Conclusions: Our method offers a new approach to rapidly process microbiome data streams, allowing samples to be rapidly clustered, indexed and classified. We also provide our implementation, Histosketching Using Little K-mers (HULK), which can histosketch a typical 2 GB microbiome in 50 s on a standard laptop using four cores, with the sketch occupying 3000 bytes of disk space

Top-down characterization of resource use in LCA: from problem definition of resource use to operational characterization factors for dissipation of elements to the environment

Purpose The methods for assessing the impact of using abiotic resources in life cycle assessment (LCA) have always been heavily debated. One of the main reasons for this is the lack of a common understanding of the problem related to resource use. This article reports the results of an effort to reach such common understanding between different stakeholder groups and the LCA community. For this, a top-down approach was applied. Methods To guide the process, a four-level top-down framework was used to (1) demarcate the problem that needs to be assessed, (2) translate this into a modeling concept, (3) derive mathematical equations and fill these with data necessary to calculate the characterization factors, and (4) align the system boundaries and assumptions that are made in the life cycle impact assessment (LCIA) model and the life cycle inventory (LCI) model. Results We started from the followingdefinition of the problemof using resources: the decrease of accessibility on a global level of primary and/or secondary elements over the very long term or short term due to thenetresult of compromising actions. Thesystem modeldistinguishes accessible and inaccessible stocks in both the environment and the technosphere. Human actions can compromise the accessible stock through environmental dissipation, technosphere hibernation, and occupation in use or through exploration. As abasis for impact assessment, we propose two parameters: the global change in accessible stock as a net result of the compromising actions and the global amount of the accessible stock. We propose three impact categories for the use of elements: environmental dissipation, technosphere hibernation, and occupation in use, with associated characterization equations for two different time horizons. Finally, preliminary characterization factors are derived and applied in a simple illustrative case study for environmental dissipation. Conclusions Due to data constraints, at this moment, only characterization factors for "dissipation to the environment" over a very-long-term time horizon could be elaborated. The case study shows that the calculation of impact scores might be hampered by insufficient LCI data. Most presently available LCI databases are far from complete in registering the flows necessary to assess the impacts on the accessibility of elements. While applying the framework, various choices are made that could plausibly be made differently. We invite our peers to also use this top-down framework when challenging our choices and elaborate that into a consistent set of choices and assumptions when developing LCIA methods.Industrial Ecolog