Site-specific metal and ligand substitutions in a microporous Mn(2+)-based metal-organic framework

First published online 16 Feb 2016The precise tuning of the structural and chem. features of microporous metal-org. frameworks (MOFs) is a crucial endeavour for developing materials with properties that are suitable for specific applications. In recent times, techniques for prepg. frameworks consisting of mixed-metal or ligand compns. have emerged. However, controlled spatial organization of the components within these structures at the mol. scale is a difficult challenge, particularly when species possessing similar geometries or chem. properties are used. Here, we describe the synthesis of mixed-metal and ligand variants possessing the Mn3L3 (Mn-MOF-1; H2L = bis(4-(4'-carboxyphenyl)-3,5-dimethylpyrazolyl)methane) structure type. In the case of mixed-ligand synthesis using a mixt. of L and its trifluoromethyl-functionalised deriv. (H2L' = bis(4-(4'-carboxyphenyl)-3,5-di(trifluoromethyl)pyrazolyl)methane), a mixed-ligand product in which the L' species predominanantly occupies the pillar sites lining the pores is obtained. Meanwhile, post-synthetic metal exchange of the parent Mn3L3 compd. using Fe2+ or Fe3+ ions results in cation exchange at the carboxylate clusters and metalation at the pillar bispyrazolate sites. The results demonstrate the versatility of the Mn3L3 structure type toward both metal and ligand substitutions, and the potential utility of site-specific functionalisations in achieving even greater precision in the tuning of MOFs. [on SciFinder(R)]Michael Huxley, Campbell J. Coghlan, Alexandre Burgun, Andrew Tarzia, Kenji Sumida, Christopher J. Sumby, and Christian J. Doona

Production of cascade hypernuclei via the (K-,K+) reaction within a quark-meson coupling model

We study the production of bound cascade hypernuclei via the (K-,K+) reaction on 12C and 28Si targets within a covariant effective Lagrangian model, employing the cascade bound state spinors derived from the latest quark-meson coupling model as well as Dirac single particle wave functions. The K+-cascade production vertex is described by excitation, propagation and decay of Lambda and Sigma resonance states in the initial collision of a K- meson with a target proton in the incident channel. The parameters of the resonance vertices are fixed by describing the available data on total and differential cross sections for the cascade production in elementary (K-,K+) reaction. We find that both the elementary and hypernuclear production cross sections are dominated by the contributions from the Lambda(1520) intermediate resonant state. The 0 degree differential cross sections for the formation of simple s-state cascade particle-hole states peak at a beam momentum around 1.0 GeV/c, with a value in excess of 1 mub.Comment: 17 pages, 8 figures, version accepted for publication in Nucl. Phys.

Measurements of KL Branching Fractions and the CP Violation Parameter |eta+-|

We present new measurements of the six largest branching fractions of the KL using data collected in 1997 by the KTeV experiment (E832) at Fermilab. The results are B(KL -> pi e nu) = 0.4067 +- 0.0011 B(KL -> pi mu nu) = 0.2701 +- 0.0009 B(KL -> pi+ pi- pi0) = 0.1252 +- 0.0007 B(KL -> pi0 pi0 pi0) = 0.1945 +- 0.0018 B(KL -> pi+ pi-) = (1.975 +- 0.012)E-3, and B(KL -> pi0 pi0) = (0.865 +- 0.010)E-3, where statistical and systematic errors have been summed in quadrature. We also determine the CP violation parameter |eta+-| to be (2.228 +- 0.010)E-3. Several of these results are not in good agreement with averages of previous measurements.Comment: Submitted to Phys. Rev. D; 20 pages, 22 figure

Phenomenological model for the Kbar N --> K Xi reaction

A phenomenological model for the Kbar N --> K Xi reaction is suggested. The model includes s and u channel exchanges by Lambda, Sigma, Sigma(1385), and Lambda(1520) and s channel exchanges by above-threshold hyperonic resonances. Explicit expression for the propagator for a particle with spin 7/2 is presented. High-mass and high-spin resonances play a significant role in the process. We deal with the whole set of existing experimental data on the cross sections and polarizations in the energy range from the threshold to 2.8 GeV in the center-of-mass system and reach a good agreement with experiments. Applications of the model to other elementary reactions of Xi production and to Xi hypernuclear spectroscopy are briefly discussed.Comment: Published version; minor change

TargetMine, an Integrated Data Warehouse for Candidate Gene Prioritisation and Target Discovery

Prioritising candidate genes for further experimental characterisation is a non-trivial challenge in drug discovery and biomedical research in general. An integrated approach that combines results from multiple data types is best suited for optimal target selection. We developed TargetMine, a data warehouse for efficient target prioritisation. TargetMine utilises the InterMine framework, with new data models such as protein-DNA interactions integrated in a novel way. It enables complicated searches that are difficult to perform with existing tools and it also offers integration of custom annotations and in-house experimental data. We proposed an objective protocol for target prioritisation using TargetMine and set up a benchmarking procedure to evaluate its performance. The results show that the protocol can identify known disease-associated genes with high precision and coverage. A demonstration version of TargetMine is available at http://targetmine.nibio.go.jp/

International comparisons of laboratory values from the 4CE collaborative to predict COVID-19 mortality

Given the growing number of prediction algorithms developed to predict COVID-19 mortality, we evaluated the transportability of a mortality prediction algorithm using a multi-national network of healthcare systems. We predicted COVID-19 mortality using baseline commonly measured laboratory values and standard demographic and clinical covariates across healthcare systems, countries, and continents. Specifically, we trained a Cox regression model with nine measured laboratory test values, standard demographics at admission, and comorbidity burden pre-admission. These models were compared at site, country, and continent level. Of the 39,969 hospitalized patients with COVID-19 (68.6% male), 5717 (14.3%) died. In the Cox model, age, albumin, AST, creatine, CRP, and white blood cell count are most predictive of mortality. The baseline covariates are more predictive of mortality during the early days of COVID-19 hospitalization. Models trained at healthcare systems with larger cohort size largely retain good transportability performance when porting to different sites. The combination of routine laboratory test values at admission along with basic demographic features can predict mortality in patients hospitalized with COVID-19. Importantly, this potentially deployable model differs from prior work by demonstrating not only consistent performance but also reliable transportability across healthcare systems in the US and Europe, highlighting the generalizability of this model and the overall approach

Long-term kidney function recovery and mortality after COVID-19-associated acute kidney injury: An international multi-centre observational cohort study

Background: While acute kidney injury (AKI) is a common complication in COVID-19, data on post-AKI kidney function recovery and the clinical factors associated with poor kidney function recovery is lacking. Methods: A retrospective multi-centre observational cohort study comprising 12,891 hospitalized patients aged 18 years or older with a diagnosis of SARS-CoV-2 infection confirmed by polymerase chain reaction from 1 January 2020 to 10 September 2020, and with at least one serum creatinine value 1–365 days prior to admission. Mortality and serum creatinine values were obtained up to 10 September 2021. Findings: Advanced age (HR 2.77, 95%CI 2.53–3.04, p < 0.0001), severe COVID-19 (HR 2.91, 95%CI 2.03–4.17, p < 0.0001), severe AKI (KDIGO stage 3: HR 4.22, 95%CI 3.55–5.00, p < 0.0001), and ischemic heart disease (HR 1.26, 95%CI 1.14–1.39, p < 0.0001) were associated with worse mortality outcomes. AKI severity (KDIGO stage 3: HR 0.41, 95%CI 0.37–0.46, p < 0.0001) was associated with worse kidney function recovery, whereas remdesivir use (HR 1.34, 95%CI 1.17–1.54, p < 0.0001) was associated with better kidney function recovery. In a subset of patients without chronic kidney disease, advanced age (HR 1.38, 95%CI 1.20–1.58, p < 0.0001), male sex (HR 1.67, 95%CI 1.45–1.93, p < 0.0001), severe AKI (KDIGO stage 3: HR 11.68, 95%CI 9.80–13.91, p < 0.0001), and hypertension (HR 1.22, 95%CI 1.10–1.36, p = 0.0002) were associated with post-AKI kidney function impairment. Furthermore, patients with COVID-19-associated AKI had significant and persistent elevations of baseline serum creatinine 125% or more at 180 days (RR 1.49, 95%CI 1.32–1.67) and 365 days (RR 1.54, 95%CI 1.21–1.96) compared to COVID-19 patients with no AKI. Interpretation: COVID-19-associated AKI was associated with higher mortality, and severe COVID-19-associated AKI was associated with worse long-term post-AKI kidney function recovery. Funding: Authors are supported by various funders, with full details stated in the acknowledgement section

Synthesis, isomerisation and biological properties of mononuclear ruthenium complexes containing the bis[4(4 '-methyl-2,2 '-bipyridyl)]-1,7-heptane ligand

A series of mononuclear ruthenium(II) complexes containing the tetradentate ligand bis[4(4’-methyl-2,2’- bipyridyl)]-1,7-heptane have been synthesised and their biological properties examined. In the synthesis of the [Ru(phen’)(bb7)]2+ complexes (where phen’ = 1,10-phenanthroline and its 5-nitro-, 4,7-dimethyland 3,4,7,8-tetramethyl- derivatives), both the symmetric cis-α and non-symmetric cis-β isomers were formed. However, upon standing for a number of days (or more quickly under harsh conditions) the cis-β isomer converted to the more thermodynamically stable cis-α isomer. The minimum inhibitory concentrations (MIC) and the minimum bactericidal concentrations (MBC) of the ruthenium(II) complexes were determined against six strains of bacteria: Gram-positive Staphylococcus aureus (S. aureus) and methicillin-resistant S. aureus (MRSA); and the Gram-negative Escherichia coli (E. coli) strains MG1655, APEC, UPEC and Pseudomonas aeruginosa (P. aeruginosa). The results showed that the [Ru(5-NO2phen)- (bb7)]2+ complex had little or no activity against any of the bacterial strains. By contrast, for the other cisα-[Ru(phen’)(bb7)]2+ complexes, the antimicrobial activity increased with the degree of methylation. In particular, the cis-α-[Ru(Me4phen)(bb7)]2+ complex showed excellent and uniform MIC activity against all bacteria. By contrast, the MBC values for the cis-α-[Ru(Me4phen)(bb7)]2+ complex varied considerably across the bacteria and even within S. aureus and E. coli strains. In order to gain an understanding of the relative antimicrobial activities, the DNA-binding affinity, cellular accumulation and water–octanol partition coefficients (log P) of the ruthenium complexes were determined. Interestingly, all the [Ru(phen’)- (bb7)]2+ complexes exhibited stronger DNA binding affinity (Ka ≈ 1 × 107 M−1 ) than the well-known DNAintercalating complex [Ru(phen)2(dppz)]2+ (where dppz = dipyrido[3,2-a:2’,3’-c]phenazine)

Biomedical informatics and translational medicine

Biomedical informatics involves a core set of methodologies that can provide a foundation for crossing the "translational barriers" associated with translational medicine. To this end, the fundamental aspects of biomedical informatics (e.g., bioinformatics, imaging informatics, clinical informatics, and public health informatics) may be essential in helping improve the ability to bring basic research findings to the bedside, evaluate the efficacy of interventions across communities, and enable the assessment of the eventual impact of translational medicine innovations on health policies. Here, a brief description is provided for a selection of key biomedical informatics topics (Decision Support, Natural Language Processing, Standards, Information Retrieval, and Electronic Health Records) and their relevance to translational medicine. Based on contributions and advancements in each of these topic areas, the article proposes that biomedical informatics practitioners ("biomedical informaticians") can be essential members of translational medicine teams