Thermodynamic Study of 1,4-Bis(3-methylimidazolium-1-yl)butane Bis(trifluoromethylsulfonyl)imide ([C(MIm)][NTf]) from 6 to 350 K.

The molar heat capacity of 1,4-bis(3-methylimidazolium-1-yl)butane bis(trifluoromethylsulfonyl)imide dicationic ionic compound ([C(MIm)][NTf]) has been studied over the temperature range from 6 to 350 K by adiabatic calorimetry. In the above temperature interval, this compound has been found to form crystal, liquid, and supercooled liquid. For [C(MIm)][NTf], the temperature of fusion ° = (337.

Biomedical SERS - the current state and future trends.

Surface enhanced Raman spectroscopy (SERS) is meeting the requirements in biomedical science being a highly sensitive and specific analytical tool. By employing portable Raman systems in combination with customized sample pre-treatment, point-of-care-testing (POCT) becomes feasible. Powerful SERS-active sensing surfaces with high stability and modification layers if required are available for testing and application in complex biological matrices such as body fluids, cells or tissues.

SERS as a tool for determination of structurally related compounds: The case of sulfanilamide class antibiotics.

Analysis of real objects based on surface-enhanced Raman spectroscopy (SERS) often utilizes new SERS substrates and/or complex analysis procedures, and they are optimized for only the determination of a single analyte. Moreover, analysis simplicity and selectivity are often sacrificed for maximum (sometimes unnecessary) sensitivity. Consequently, this trend limits the versatility of SERS analysis and complicates its practical implementation.

Asymmetric Cluster-Based Measures for Comparative Phylogenetics.

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Reverse-zoonoses of 2009 H1N1 pandemic influenza A viruses and evolution in United States swine results in viruses with zoonotic potential.

The 2009 H1N1 pandemic (pdm09) lineage of influenza A virus (IAV) crosses interspecies barriers with frequent human-to-swine spillovers each year. These spillovers reassort and drift within swine populations, leading to genetically and antigenically novel IAV that represent a zoonotic threat. We quantified interspecies transmission of the pdm09 lineage, persistence in swine, and identified how evolution in swine impacted zoonotic risk.

Phylogenetic diversity statistics for all clades in a phylogeny.

The classic quantitative measure of phylogenetic diversity (PD) has been used to address problems in conservation biology, microbial ecology, and evolutionary biology. PD is the minimum total length of the branches in a phylogeny required to cover a specified set of taxa on the phylogeny. A general goal in the application of PD has been identifying a set of taxa of size k that maximize PD on a given phylogeny; this has been mirrored in active research to develop efficient algorithms for the problem.

PARNAS: Objectively Selecting the Most Representative Taxa on a Phylogeny.

The use of next-generation sequencing technology has enabled phylogenetic studies with hundreds of thousands of taxa. Such large-scale phylogenies have become a critical component in genomic epidemiology in pathogens such as SARS-CoV-2 and influenza A virus. However, detailed phenotypic characterization of pathogens or generating a computationally tractable dataset for detailed phylogenetic analyses requires objective subsampling of taxa.

Cyclodextrin-assisted SERS determination of fluoroquinolone antibiotics in urine and blood plasma.

This paper describes the use of cyclodextrins (CDs) to improve the determination of fluoroquinolone antibiotics in human body fluids using surface-enhanced Raman spectroscopy (SERS). CDs were used to (i) prepare the CD-SERS substrate (synthesis and stabilization of silver nanoparticles), (ii) increase the sensitivity of the assay by enhancing the interaction between analyte molecules and the substrate, and (iii) improve the analysis accuracy by reducing the interaction between the substrate and endogenous components of body fluids. Two native CDs (α-CD and β-CD) and two of their derivatives with hydroxypropyl groups were tested, and the best results were obtained with CD-SERS substrate prepared using native β-CD.

Thermodynamic Study of Formamidinium Lead Iodide (CHNPbI) from 5 to 357 K.

In the present study, the molar heat capacity of solid formamidinium lead iodide (CHNPbI) was measured over the temperature range from 5 to 357 K using a precise automated adiabatic calorimeter. In the above temperature interval, three distinct phase transitions were found in ranges from 49 to 56 K, from 110 to 178 K, and from 264 to 277 K. The standard thermodynamic functions of the studied perovskite, namely the heat capacity °(), enthalpy [() - (0)], entropy (), and [°() - °(0)]/, were calculated for the temperature range from 0 to 345 K based on the experimental data.

RF-Net 2: fast inference of virus reassortment and hybridization networks.

Motivation: A phylogenetic network is a powerful model to represent entangled evolutionary histories with both divergent (speciation) and convergent (e.g. hybridization, reassortment, recombination) evolution.

Thermodynamic Properties of the First-Generation Hybrid Dendrimer with "Carbosilane Core/Phenylene Shell" Structure.

The molar heat capacity of the first-generation hybrid dendrimer with a "carbosilane core/phenylene shell" structure was measured for the first time in the temperature range = 6-600 K using a precise adiabatic vacuum calorimeter and DSC. In the above temperature interval, the glass transition of the studied compound was observed, and its thermodynamic characteristics were determined. The standard thermodynamic functions (the enthalpy, the entropy, and the Gibbs energy) of the hybrid dendrimer were calculated over the range from = 0 to 600 K using the experimentally determined heat capacity.

octoFLUshow: an Interactive Tool Describing Spatial and Temporal Trends in the Genetic Diversity of Influenza A Virus in U.S. Swine.

Influenza A virus (IAV) is passively surveilled in swine in the United States through a U.S. Department of Agriculture administered surveillance system.

Cyclodextrin-assisted surface-enhanced Raman spectroscopy: a critical review.

Numerous approaches have been proposed to overcome the intrinsically low selectivity of surface-enhanced Raman spectroscopy (SERS), and the modification of SERS substrates with diverse recognition molecules is one of such approaches. In contrast to the use of antibodies, aptamers, and molecularly imprinted polymers, application of cyclodextrins (CDs) is still developing with less than 100 papers since 1993. Therefore, the main goal of this review is the critical analysis of all available papers on the use of CDs in SERS analysis, including physicochemical studies of CD complexation and the effect of CD presence on the Raman enhancement.

Taming the Duplication-Loss-Coalescence Model with Integer Linear Programming.

The duplication-loss-coalescence (DLC) parsimony model is invaluable for analyzing the complex scenarios of concurrent duplication loss and deep coalescence events in the evolution of gene families. However, inferring such scenarios for already moderately sized families is prohibitive owing to the computational complexity involved. To overcome this stringent limitation, we make the first step by describing a flexible integer linear programming (ILP) formulation for inferring DLC evolutionary scenarios.

Quartet-based inference is statistically consistent under the unified duplication-loss-coalescence model.

Motivation: The classic multispecies coalescent (MSC) model provides the means for theoretical justification of incomplete lineage sorting-aware species tree inference methods. This has motivated an extensive body of work on phylogenetic methods that are statistically consistent under MSC. One such particularly popular method is ASTRAL, a quartet-based species tree inference method.

Finding orthologous gene blocks in bacteria: the computational hardness of the problem and novel methods to address it.

Motivation: The evolution of complexity is one of the most fascinating and challenging problems in modern biology, and tracing the evolution of complex traits is an open problem. In bacteria, operons and gene blocks provide a model of tractable evolutionary complexity at the genomic level. Gene blocks are structures of co-located genes with related functions, and operons are gene blocks whose genes are co-transcribed on a single mRNA molecule.

Copper nanoparticles for SERS-based determination of some cephalosporin antibiotics in spiked human urine.

Copper nanoparticles (CuNPs) were prepared through a wet chemistry method to be used as substituents for noble-metal-based materials in the determination of cephalosporin antibiotics in urine using surface-enhanced Raman spectroscopy (SERS). The synthesis of the CuNPs was optimized to maximize the analytical signal, and microwave heating was used to increase the reaction rate and improve the homogeneity of the CuNPs. Ceftriaxone (CTR), cefazolin (CZL), and cefoperazone (CPR) were used as the analytes of interest.

Exact median-tree inference for unrooted reconciliation costs.

Background: Solving median tree problems under tree reconciliation costs is a classic and well-studied approach for inferring species trees from collections of discordant gene trees. These problems are NP-hard, and therefore are, in practice, typically addressed by local search heuristics. So far, however, such heuristics lack any provable correctness or precision.

Determination of methotrexate in spiked human urine using SERS-active sorbent.

This report is dedicated to determination of anticancer drug methotrexate (MTX) in human urine using surface-enhanced Raman spectroscopy (SERS). Aluminum oxide loaded with silver nanoparticles (AO-Ag) was proposed as SERS-active sorbent and used for solid-phase extraction (SPE) of the analyte and its SERS-based determination (SPE-SERS protocol). MTX has strong SERS signal only in alkaline media that challenges its determination in urine due to strong background signal caused by creatinine.

Optical sensors for determination of biogenic amines in food.

This review presents the state-of-the-art of optical sensors for determination of biogenic amines (BAs) in food by publications covering about the last 10 years. Interest in the development of rapid and preferably on-site methods for quantification of BAs is based on their important role in implementation and regulation of various physiological processes. At the same time, BAs can develop in different kinds of food by fermentation processes or microbial activity or arise due to contamination, which induces toxicological risks and food poisoning and causes serious health issues.

Liquid-liquid extraction-assisted SERS-based determination of sulfamethoxazole in spiked human urine.

The determination of antibiotic levels in body fluids is of great importance in the field of personalized medicine and therapeutic drug monitoring. We report on the determination of sulfamethoxazole (SMX), an antibacterial drug of the sulfanilamide class, in spiked human urine. The protocol is based on the combination of surface-enhanced Raman spectroscopy (SERS) and liquid-liquid extraction (LLE-SERS analysis).

Application of Aluminum Hydroxide for Improvement of Label-Free SERS Detection of Some Cephalosporin Antibiotics in Urine.

This report is dedicated to development of surface-enhanced Raman spectroscopy (SERS) based analysis protocol for detection of antibiotics in urine. The key step of the protocol is the pretreatment of urine before the detection to minimize background signal. The pretreatment includes extraction of intrinsic urine components using aluminum hydroxide gel (AHG) and further pH adjusting of the purified sample.

SERS detection of ceftriaxone and sulfadimethoxine using copper nanoparticles temporally protected by porous calcium carbonate.

The authors describe a new composite based on SERS-active copper nanoparticles (CuNPs; 10 ± 2 nm) incorporated into calcium carbonate microspheres (CaCO-CuNPs; 3.4 ± 0.3 μm).