Retrospectively collected medical data has the opportunity to improve patient care through knowledge discovery and algorithm development. Broad reuse of medical data is desirable for the greatest public good, but data sharing must be done in a manner which protects patient privacy. Here we present Medical Information Mart for Intensive Care (MIMIC)-IV, a large deidentified dataset of patients admitted to the emergency department or an intensive care unit at the Beth Israel Deaconess Medical Center in Boston, MA. MIMIC-IV contains data for over 65,000 patients admitted to an ICU and over 200,000 patients admitted to the emergency department. MIMIC-IV incorporates contemporary data and adopts a modular approach to data organization, highlighting data provenance and facilitating both individual and combined use of disparate data sources. MIMIC-IV is intended to carry on the success of MIMIC-III and support a broad set of applications within healthcare.

Fast Healthcare Interoperability Resources (FHIR) has emerged as a robust standard for healthcare data exchange. To explore the use of FHIR for the process of data harmonization, we converted the Medical Information Mart for Intensive Care IV (MIMIC-IV) and MIMIC-IV Emergency Department (MIMIC-IV-ED) databases into FHIR. We extended base FHIR to encode information in MIMIC-IV and aimed to retain the data in FHIR with minimal additional processing, aligning to US Core v4.0.0 where possible. A total of 24 profiles were created for MIMIC-IV data, and an additional 6 profiles were created for MIMIC-IV-ED data. Code systems and value sets were created from MIMIC terminology. We hope MIMIC-IV in FHIR provides a useful restructuring of the data to support applications around data harmonization, interoperability, and other areas of research.

This entry represents hypothetical proteins such as HI1450, which is believed to act as a putative dsDNA mimic. HI1450 is an acidic protein with a core structure consisting of α(2)-β(4), where the α-helices are packed against the side of an anti-parallel 4-stranded β meander. As such, it has some similarity to the dsDNA mimics uracil-DNA glycosylase inhibitor and nuclease A inhibitor (NuiA), including the distribution of surface charges and the position of the hydrophobic cavity . DNA mimics act to inhibit or regulate dsDNA-binding proteins.

Average performance results over test sets on MIMIC-CXR dataset using NLP validation metrics.

maser surveys have shown that many potential oh/ir stars have no oh masers in their cs envelopes, despite modest requirements which should be implicitly met by iras colourselected candidates. it is probable that these oh/ir colour mimics are related to symbiotic stars and have a degenerate companion (hidden in the optical and nearir by circumstellar dust) which disrupts the masing action. here we propose to compare farir line emission from colour mimics with that from symbiotic stars. the circumstellar dust shells will be much less opaque in the farir and, since a hot companion would inevitably stimulate line emission, our spectra will constitute a simple and effective test of whether hot stars are present. line intensities and ratios for symbiotics (and mimics, if lines are detected) will be used to analyse abundances and ionization conditions. the temperature of any colour mimic companions will help to tie down the mechanism (be it radiative or gravitational) by which masers are suppressed in symbiotic miras. our sample contains examples of colour mimics with a range of iras colours and lrs types, as well as symbiotics with agb giants and firstascent giants. these have been chosen to avoid duplication of the symbiotic and oh/ir stars in the core programme. truncated!, Please see actual data for full text [truncated!, Please see actual data for full text]

Research data supporting the publication: Loynachan C. N., et al., 2017, ACS Nano, DOI: http://dx.doi.org/10.1021/acsnano.7b06229.

Context

This is a Python package for manipulating 2-dimensional tabular data structures (aka data frames). It is close in spirit to pandas or SFrame; however we put specific emphasis on speed and big data support. As the name suggests, the package is closely related to R's data.table and attempts to mimic its core algorithms and API.

Content

The wheel file for installing datatable v0.11.0

Installation

!pip install ../input/python-datatable/datatable-0.11.0-cp37-cp37m-manylinux2010_x86_64.whl > /dev/null

Using

import datatable as dt
data = dt.fread("filename").to_pandas()

Acknowledgements

https://github.com/h2oai/datatable

Documentation

https://datatable.readthedocs.io/en/latest/index.html

License

https://github.com/h2oai/datatable/blob/main/LICENSE

Data for permeability assays across the bacterial-like phospholipid mimic. (XLSX)

Cartesian coordinates for the optimized molecular structures of [FeFe] hydrogenase mimics 1-11. Supplementary material for "Quantum chemical topological analysis of [2Fe2S] core in novel [FeFe]-hydrogenase mimics"

Data for permeability assays across the archaeal-like phospholipid mimic. (XLSX)

The synthesis of a new family of phosphorus dendrimers built from an octasubstituted metal-free phthalocyanine core is described up to generation 5. This core is used as a sensor and a probe for analyzing the properties of the internal structure and the influence of each structural part (core, branches, surface) upon the whole structure. UV−visible spectra show both a hyperchromic and bathochromic effect on the Q-bands with increasing generation, indicating that the chromophore is more isolated, and that the dendritic shell mimics a highly polar solvent. There is no evidence for aggregation, except for generation 0, showing again the isolation of the core. However, the dendritic shell is permeable to aqueous acids and bases, as demonstrated by the reversible splitting of the Q-band in an acidic medium (neutral form of the phthalocyanine) and the single Q-band in a basic medium (dianionic form), even for generation 4. The fluorescence quantum yield for the neutral form increases with increasing generation. The dianionic form of generation 0 is poorly fluorescent, whereas generations 3 and 4 (G3 and G4) exhibit better fluorescence. The cores of G3 and G4 are highly sensitive optical sensors for H3O+ and OH-. These experiments are carried out in THF/water mixtures, and the influence of water on the structure has been checked. The hydrodynamic radius of generation 4 is measured by NMR diffusion (pulse gradient spin−echo) experiments. RH varies from 35.4 Å at 4 mol % of water to 32.5 Å at 64 mol % of water in THF, indicating the hydrophobic nature of these dendrimers.

Chromophores with a benzylidene imidazolidinone core define the emission profile of commonly used biomarkers such as the green fluorescent protein (GFP) and its analogues. In this communication, artificially engineered porous scaffolds have been shown to mimic the protein β-barrel structure, maintaining green fluorescence response and conformational rigidity of GFP-like chromophores. In particular, we demonstrated that the emission maximum in our artificial scaffolds is similar to those observed in the spectra of the natural GFP-based systems. To correlate the fluorescence response with a structure and perform a comprehensive analysis of the prepared photoluminescent scaffolds, 13C cross-polarization magic angle spinning solid-state (CP-MAS) NMR spectroscopy, powder and single-crystal X-ray diffraction, and time-resolved fluorescence spectroscopy were employed. Quadrupolar spin–echo solid-state 2H NMR spectroscopy, in combination with theoretical calculations, was implemented to probe low-frequency vibrational dynamics of the confined chromophores, demonstrating conformational restrictions imposed on the coordinatively trapped chromophores. Because of possible tunability of the introduced scaffolds, these studies could foreshadow utilization of the presented approach toward directing a fluorescence response in artificial GFP mimics, modulating a protein microenvironment, and controlling nonradiative pathways through chromophore dynamics.

Data for permeability assays across the hybrid phospholipid mimic. (XLSX)

Pulmonary fibrosis is characterized by excessive extracellular matrix (ECM) accumulation caused by detrimental stimuli. The progressive impairment in lung functions is chronic and highly fatal, presenting itself as a global health challenge. Because of the lack of efficacious treatments, the underlying mechanism should be investigated. The progression of fibrosis involves transforming growth factor-beta 1 (TGF-β1), which accelerates ECM production via epithelial–mesenchymal transition and cell invasion. As microRNAs (miRNAs) serve as regulators of disease development and progression, this study aimed to investigate the interaction of miRNAs and target genes that could contribute to pulmonary fibrosis when exposed to TGF-β1. Differentially expressed mRNA and miRNA were identified in respiratory epithelial cells via transcriptome analysis by using the constructed TGF-β1-induced fibrosis model. Our results revealed a significant increase in the expression of thrombospondin 1 (THBS1), which participates in TGF-β1 activation, where THBS1 was identified as a core gene in protein interactions analyzed through bioinformatics. The expression of miR-335-3p, which targets 3ʹ-UTR of THBS1, substantially decreased upon TGF-β1 treatment. The TGF-β1 downstream signal was suppressed by inhibiting the interaction between TGF-β1 and THBS1, consequently alleviating fibrosis. When the miR-335-3p mimic was transfected in TGF-β1-treated respiratory epithelial cells, THBS1 and fibrosis markers were downregulated, while the introduction of miR-335-3p inhibitor exhibited a reverse phenomenon. Our findings demonstrated that TGF-β1 exposure to respiratory epithelial cells led to a decrease in miR-335-3p expression, resulting in the upregulation of THBS1 and ultimately exacerbating fibrosis. This study provides insights into TGF-β1-induced pulmonary fibrosis, suggesting new therapeutic targets and mechanisms.

The marine pathogen Vibrio alginolyticus employs its type III secretion system (T3SS), a syringe-like secretion apparatus, to kill eukaryotic cells. Although the cascade regulation of the ExsACDE operon has been described in detail for the V. alginolyticus T3SS, little is known about the signals and signaling pathways that regulate the operon. Herein we determined that the hybrid sensor kinase ArcB forms a signaling cascade with core members of the quorum sensing (QS) system (LuxU and LuxO) to regulate the expression of the V. alginolyticus T3SS. We further show that ArcB initiates the cascade by functioning as a sensor protein for bacterial autoinducer-2 (AI-2), a signaling molecule used for inter-species communication. In addition, we demonstrate that host cells produce an AI-2 mimic during the infection stage, which can also be sensed by ArcB and can activate the gene expression of T3SS.

Enantiopure alkaloid mimics are synthesized via high yielding intramolecular cycloadditions of photogenerated azaxylylenes tethered to pyrroles, with further growth of molecular complexity via post-photochemical transformations of primary photoproducts. This expeditious access to structurally unprecedented polyheterocyclic cores is being developed in the context of diversity-oriented synthesis, as the modular design allows for rapid “pre-assembly” of diverse photoprecursors from simple building blocks/diversity inputs.

The replacement of one chemical motif with another that is broadly similar is a common method in medicinal chemistry to modulate the physical and biological properties of a molecule (i.e., bioisosterism). In recent years, bioisosteres such as cubane and bicyclo[1.1.1]pentane (BCP) have been used as highly effective phenyl mimics. Herein, we show the successful incorporation of a range of phenyl bioisosteres during the open-source optimization of an antimalarial series. Cubane (19) and closo-carborane (23) analogues exhibited improved in vitro potency against Plasmodium falciparum compared to the parent phenyl compound; however, these changes resulted in a reduction in metabolic stability; unusually, enzyme-mediated oxidation was found to take place on the cubane core. A BCP analogue (22) was found to be equipotent to its parent phenyl compound and showed significantly improved metabolic properties. While these results demonstrate the utility of these atypical bioisosteres when used in a medicinal chemistry program, the search to find a suitable bioisostere may well require the preparation of many candidates, in our case, 32 compounds.

Multidrug resistance (MDR) bacteria pose a serious threat to human health, and the development of effective antimicrobial drugs is urgent. Herein, we used alkyl chain engineering to design and synthesize two series of antimicrobial peptide mimics with distinct cores: triphenylamine quaternary ammonium derivatives (TPQs) and diphenylethene quaternary ammonium derivatives (BPQs), and we investigated the effect of varying the alkyl chain lengths on antibacterial activity. We found that the introduction of a triphenylamine group significantly enhances the antibacterial activity of short-chain dimethyl quaternary ammonium derivatives while maintaining their excellent biocompatibility. Most notably, TPQ-1 exhibited negligible invasiveness toward living cells and possesses good antimicrobial activities, with good efficacy against biofilms and persisters. Moreover, TPQ-1 exhibited good antimicrobial effects in vivo and significantly accelerated the healing process of methicillin-resistant Staphylococcus aureus-infected wounds. This work promotes the practical application of antimicrobial peptide mimics and triphenylamine derivatives.

Two new angular trinuclear copper(II) complexes of formulation Cu3(HL)LL‘, where L‘ is imidazole (Him, 1) or 1-methylimidazole (1-MeIm, 2) and H3L is a Schiff base obtained from the condensation of salicylaldehyde and 1,3-diaminopropan-2-ol (2:1 mole ratio), are prepared from a reaction of [Cu2L(μ-Br)] and [Cu(HL)] in the presence of L‘ and isolated as perchlorate salts. The crystal structures of 1 and 2 consist of a trinuclear copper(II) unit formed by the covalent linkage of monomeric type-2 mimic and dimeric type-3 mimic precursor complexes to give an angular arrangement of the metal atoms in the core which is a model for the active site structure of blue multicopper oxidases. In 1 and 2, the coordination geometry of two terminal copper atoms is distorted square-planar. The central copper has a distorted square-pyramidal (4 + 1) geometry. The mean Cu···Cu distance is ∼3.3 Å. The complex has a diphenoxo-bridged dicopper(II) unit with the phenoxo oxygen atoms showing a planar geometry. In addition, the complex has an endogenous alkoxo-bridged dicopper(II) unit showing a pyramidal geometry for the oxygen atom. The 1:1 electrolytic complexes show a d−d band at 607 nm. Cyclic voltammetry of the complexes in MeCN containing 0.1 M TBAP using a glassy carbon working electrode displays a Cu3(II)/Cu2(II)Cu(I) couple near −1.0 V (vs SCE). The variable temperature magnetic susceptibility measurements in the range 300−18 K show antiferromagnetic coupling in the complexes giving magnetic moments of ∼3.0 μB at 300 K and ∼2.1 μB at 18 K for the tricopper(II) unit. The experimental susceptibility data are theoretically fitted using a model with Heisenberg spin-1/2 Hamiltonian for a trimer of spin-1/2 copper(II) ions having two exchange parameters involving the alkoxo-bridged dicopper(II) (J1) and the diphenoxo-bridged dicopper(II) (J2) units, giving J1 and J2 values of −82.7, −73 cm-1 for 1 and −98.3, −46.1 cm-1 for 2, respectively. The structural features indicate a higher magnitude of anitiferromagnetic coupling in the alkoxo-bridged unit based on the greater value of the Cu−O−Cu angle in comparison to the diphenoxo-bridged unit. The core structures of 1 and 2 compare well with the first generation model complexes for the active site structure of multicopper oxidases in the oxidized form. The crystal structure of 1 exhibits a lamellar structure with a gap of ∼7 Å containing water molecules in the interlamellar space. Complex 2 forms a hexanuclear species due to intermolecular hydrogen bonding interactions involving two trimeric units. The crystal packing diagram of 2 displays formation of a three-dimensional framework with cavities containing the perchlorate anions.

Attachment of the redox-active C60(H)PPh2 group modulates the electronic structure of the Fe2 core in [(μ-bdt)Fe2(CO)5(C60(H)PPh2)]. The neutral complex is characterized by X-ray crystallography, IR, NMR spectroscopy, and cyclic voltammetry. When it is reduced by one electron, the spectroscopic and density functional theory results indicate that the Fe2 core is partially spin-populated. In the doubly reduced species, extensive electron communication occurs between the reduced fullerene unit and the Fe2 centers as displayed in the spin-density plot. The results suggest that the [4Fe4S] cluster within the H cluster provides an essential role in terms of the electronic factor.