Rapid identification and investigation of healthcare-associated infections (HCAIs) is important for suppression of SARS-CoV-2, but the infection source for hospital onset COVID-19 infections (HOCIs) ...cannot always be readily identified based only on epidemiological data. Viral sequencing data provides additional information regarding potential transmission clusters, but the low mutation rate of SARS-CoV-2 can make interpretation using standard phylogenetic methods difficult.
We developed a novel statistical method and sequence reporting tool (SRT) that combines epidemiological and sequence data in order to provide a rapid assessment of the probability of HCAI among HOCI cases (defined as first positive test >48 hr following admission) and to identify infections that could plausibly constitute outbreak events. The method is designed for prospective use, but was validated using retrospective datasets from hospitals in Glasgow and Sheffield collected February-May 2020.
We analysed data from 326 HOCIs. Among HOCIs with time from admission ≥8 days, the SRT algorithm identified close sequence matches from the same ward for 160/244 (65.6%) and in the remainder 68/84 (81.0%) had at least one similar sequence elsewhere in the hospital, resulting in high estimated probabilities of within-ward and within-hospital transmission. For HOCIs with time from admission 3-7 days, the SRT probability of healthcare acquisition was >0.5 in 33/82 (40.2%).
The methodology developed can provide rapid feedback on HOCIs that could be useful for infection prevention and control teams, and warrants further prospective evaluation. The integration of epidemiological and sequence data is important given the low mutation rate of SARS-CoV-2 and its variable incubation period.
COG-UK HOCI funded by COG-UK consortium, supported by funding from UK Research and Innovation, National Institute of Health Research and Wellcome Sanger Institute.
We here apply the recently developed initiator density matrix quantum Monte Carlo (i-DMQMC) to a variety of atoms and molecules in vacuum. i-DMQMC samples the exact density matrix of a Hamiltonian at ...finite temperature and combines the accuracy of full configuration interaction quantum Monte Carlo (FCIQMC)full configuration interaction (FCI) or exact energies in a finite basis setwith finite temperature. In order to explore the applicability of i-DMQMC for molecular systems, we choose to study a recently developed test set by Rubenstein and co-workers: Be, H2O, and H10 at near-equilibrium and stretched geometries. We find that, for Be and H2O, i-DMQMC delivers energies with submillihartree accuracy when compared with finite temperature FCI. For H2O and both geometries of H10, we examine the difference between FT-AFQMC and i-DMQMC, which, in turn, estimates the difference in canonical versus grand canonical energies. We close with two discussions: one of simulation settings (initiator error, the interaction picture, and different basis sets), and another of energy difference calculations in the form of specific heat capacity and ionization potential calculations.
The facile production of ArCF2X and ArCX3 from ArCF3 using catalytic iron(III)halides is reported, which constitutes the first iron‐catalyzed halogen exchange for non‐aromatic C−F bonds. Theoretical ...calculations suggest direct activation of C−F bonds by iron coordination. ArCX3 and ArCF2X products of the reaction are synthetically valuable due to their diversification potential. In particular, chloro‐ and bromodifluoromethyl arenes (ArCF2Cl, ArCF2Br respectively) provide access to a myriad of difluoromethyl arene derivatives (ArCF2R). To optimize for mono‐halogen exchange, a statistical method called Design of Experiments was used. Optimized parameters were successfully applied to electron rich and electron deficient aromatic substrates, and to the late stage diversification of flufenoxuron, a commercial insecticide. These methods are highly practical, being run at convenient temperatures and using inexpensive common reagents.
The production of synthetically valuable ArCF2X and ArCX3 compounds from ArCF3 using catalytic iron(III)halides is described, which constitutes the first iron‐catalyzed halogen exchange of non‐aromatic C−F bonds. Theoretical calculations suggest direct activation of C−F bonds by iron coordination. To optimize for mono‐exchange, a statistical analysis called Design of Experiments was used. Optimized parameters were successfully applied to both electron‐rich and electron‐deficient aromatic substrates, and to the late‐stage diversification of flufenoxuron, a commercial insecticide.
The Sign Problem in Density Matrix Quantum Monte Carlo Petras, Hayley R; Van Benschoten, William Z; Ramadugu, Sai Kumar ...
Journal of chemical theory and computation,
10/2021, Letnik:
17, Številka:
10
Journal Article
Recenzirano
Odprti dostop
Density matrix quantum Monte Carlo (DMQMC) is a recently developed method for stochastically sampling the N-particle thermal density matrix to obtain exact-on-average energies for model and ab initio ...systems. We report a systematic numerical study of the sign problem in DMQMC based on simulations of atomic and molecular systems. In DMQMC, the density matrix is written in an outer product basis of Slater determinants. In principle, this means that DMQMC needs to sample a space that scales in the system size, N, as O(exp(N))2. In practice, removing the sign problem requires a total walker population that exceeds a system-dependent critical walker population (N c), imposing limitations on both storage and compute time. We establish that N c for DMQMC is the square of N c for FCIQMC. By contrast, the minimum N c in the interaction picture modification of DMQMC (IP-DMQMC) is only linearly related to the N c for FCIQMC. We find that this difference originates from the difference in propagation of IP-DMQMC versus canonical DMQMC: the former is asymmetric, whereas the latter is symmetric. When an asymmetric mode of propagation is used in DMQMC, there is a much greater stochastic error and is thus prohibitively expensive for DMQMC without the interaction picture adaptation. Finally, we find that the equivalence between IP-DMQMC and FCIQMC seems to extend to the initiator approximation, which is often required to study larger systems with large basis sets. This suggests that IP-DMQMC offers a way to ameliorate the cost of moving between a Slater determinant space and an outer product basis.
Advances in computing technology and bioinformatics mean that medical research is increasingly characterized by large international consortia of researchers that are reliant on large data sets and ...biobanks. These trends raise a number of challenges for obtaining consent, protecting participant privacy concerns and maintaining public trust. Participant-centred initiatives (PCIs) use social media technologies to address these immediate concerns, but they also provide the basis for long-term interactive partnerships. Here, we give an overview of this rapidly moving field by providing an analysis of the different PCI approaches, as well as the benefits and challenges of implementing PCIs.
Celotno besedilo
Dostopno za:
DOBA, IJS, IZUM, KILJ, NUK, PILJ, PNG, SAZU, UILJ, UKNU, UL, UM, UPUK
The southern beech (genus Fuscospora and Lophozonia) forest in New Zealand periodically has “mast” years, during which very large volumes of seeds are produced. This excessive seed production results ...in a population explosion of rodents and mustelids, which then puts pressure on native birds. To protect the birds, extra pest controls, costing in the order of NZD 20 million, are required in masting areas. To plan pest control and keep it cost-effective, it would be helpful to have a map of the masting areas. In this study, we developed a remote sensing method for the creation of a national beech flowering map. It used a temporal sequence of Sentinel-2 satellite imagery to determine areas in which a yellow index, which was based on red and green reflectance (red-green)/(red + green), was higher than normal in spring. The method was used to produce national maps of heavy beech flowering for the years 2017 to 2021. In 2018, which was a major beech masting year, of the 4.1 million ha of beech forest in New Zealand, 27.6% was observed to flower heavily. The overall classification accuracy of the map was 90.8%. The method is fully automated and could be used to help to identify areas of potentially excessive seed fall across the whole of New Zealand, several months in advance of when pest control would be required.
Here we report the synthesis and characterization of diiron complexes containing triaryl N 4 and N 2 S 2 ligands derived from o -phenylenediamine. The complexes display significant differences in ...Fe–Fe distances and magnetic properties that depend on the identity of the flanking NMe 2 and SMe donor groups.
is a large viral family, with members infecting a diverse range of hosts including, vertebrate species, arthropods, and plants. The predominant human pathogen within the family is
, the main cause of ...human rabies. While rabies is itself a neglected disease, there are other, less well studied, rhabdoviruses known to cause human infection. The increasing application of next-generation sequencing technology to clinical samples has led to the detection of several novel or rarely detected rhabdoviruses associated with febrile illness. Many of these viruses have been detected in low- and middle-income countries where the extent of human infection and the burden of disease remain largely unquantified. This review describes the rhabdoviruses other than
that have been associated with human infection. The discovery of the Bas Congo virus and Ekpoma virus is discussed, as is the re-emergence of species such as Le Dantec virus, which has recently been detected in Africa 40 years after its initial isolation. Chandipura virus and the lyssaviruses that are known to cause human rabies are also described. Given their association with human disease, the viruses described in this review should be prioritised for further study.
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