Miracle-dz/UniFAR-FTUs huggingface dataset:
Multi-year molecular quantification and ‘omics analysis of Planktothrix-specific cyanophage sequences from Sandusky Bay, Lake Erie

Introduction Planktothrix agardhii is a microcystin-producing cyanobacterium found in Sandusky Bay, a shallow and turbid embayment of Lake Erie. Previous work in other systems has indicated that cyanophages are an important natural control factor of harmful algal blooms. Currently, there are few cyanophages that are known to infect P. agardhii, with the best-known being PaV-LD, a tail-less cyanophage isolated from Lake Donghu, China. Presented here is a molecular characterization of Planktothrix specific cyanophages in Sandusky Bay. Methods and Results Putative Planktothrix-specific viral sequences from metagenomic data from the bay in 2013, 2018, and 2019 were identified by two approaches: homology to known phage PaV-LD, or through matching CRISPR spacer sequences with Planktothrix host genomes. Several contigs were identified as having viral signatures, either related to PaV-LD or potentially novel sequences. Transcriptomic data from 2015, 2018, and 2019 were also employed for the further identification of cyanophages, as well as gene expression of select viral sequences. Finally, viral quantification was tested using qPCR in 2015–2019 for PaV-LD like cyanophages to identify the relationship between presence and gene expression of these cyanophages. Notably, while PaV-LD like cyanophages were in high abundance over the course of multiple years (qPCR), transcriptomic analysis revealed only low levels of viral gene expression. Discussion This work aims to provide a broader understanding of Planktothrix cyanophage diversity with the goals of teasing apart the role of cyanophages in the control and regulation of harmful algal blooms and designing monitoring methodology for potential toxin-releasing lysis events.
Stokes shift spectroscopy for breast cancer diagnosis

The objective of this study is to assess the diagnostic potential of stokes shift (SS) spectroscopy (SSS) for normal and different pathological breast tissues such as fibroadenoma and infiltrating ductal carcinoma. The SS spectra is measured by simultaneously scanning both the excitation and emission wavelengths while keeping a fixed wavelength interval Δλ=20 nm between them. Characteristic, highly resolved peaks and significant spectral differences between normal and different pathological breast tissues were observed. The SS spectra of normal and different pathological breast tissues shows the distinct peaks around 300, 350, 450, 500 and 600 nm may be attributed to tryptophan, collagen, NADH, flavin and porphyrin respectively. Using SSS technique one can obtain all the key fluorophores in a single scan and hence they can be targeted as a tumor markers in this study. In order to quantify the altered spectral differences between normal and different pathological breast tissues are verified by different ratio parameters.
Modeling ion-ion interaction in proteins: A molecular dynamics free energy calculation of the guanidinium-acetate association

The twin nitrogen–twin oxygen, C2v association of guanidinium and acetate in water is examined by means of molecular dynamics free energy calculations, using three approaches for handling Coulomb electrostatic interactions: (i) an Ewald lattice summation, (ii) a generalized reaction field correction, and, (iii) a smoothed spherical truncation. The potential of mean force obtained from the Ewald simulation exhibits the expected minima characteristic of a contact and a solvent-separated ion pair. In contrast, the repulsive and, therefore, physically unrealistic profile resulting from a spherical truncation of the electrostatic interactions at 12 A calls into question the validity of such a protocol for simulating charged proteins. The introduction of a generalized reaction field improves the description of the solution significantly, in spite of an artifactual behavior towards the edge of the cutoff sphere. Whereas this approach, compared to a conventional spherical truncation, implies virtually no addition.
Synthesis and characterization of biocompatible ZnO nanoparticles

ZnO nanoparticles are among the most promising emerging fluorescent labels for cellular imaging. However, there are only a few reports on the successful application of ZnO nanoparticles in biolabeling so far. The major problem of ZnO nanoparticles arises from their poor stability in water. In this work, two new facile synthesis methods were developed for fabricating water-stable ZnO nanoparticles, which have blue and yellow fluorescence and are expected to be of use for labeling different cellular structures simultaneously. Transmission electron microscopy (TEM), X-ray diffraction (XRD), Fourier transform infrared spectrometry (FT-IR), UV-vis, and fluorescence spectrophotometry (PL) were employed to investigate the structures and properties of ZnO nanoparticles. The mechanisms for the formation of the ZnO nanoparticles of both samples are analyzed. Furthermore, hemolysis assay was performed to evaluate the biocompatibility of these ZnO nanoparticlesin vitro. The biocompatibility of the ZnO nanoparticles, even at very high doses, ensures their potential in biomedical applications.
The high-pressure chemistry of butadiene crystal

FTIR spectroscopy was applied to the study of the high-pressure reactivity of solid butadiene. The chemical transformation from the ordered phase I was observed to occur only above 270 K. The existence of a threshold temperature for the reaction reveals the central role of the lattice phonons in the activation of the transformation. Below 4.0 GPa only dimerization to 4-vinylcyclohexene occurs, while above this pressure an increasing amount of polymer forms with rising pressure. Room temperature kinetic studies have been performed at different pressures, from 2.1 up to 6.6 GPa, and the sign of the activation volume for the dimerization has been obtained. The dimerization reaction is found to follow a first-order mechanism. A reaction pathway for this process is proposed where the internal rearrangement of a diradical intermediate specie is identified as the rate limiting step. An acceleration of the dimerization process is observed above 4.0 GPa and is ascribed to the simultaneous polymer formation. This effect causes the laser assisted reaction, where a large amount of polymer is produced at any pressure, to be not as selective on polymerization as it is in the liquid phase, since also the dimerization rate is enhanced.
Cost-effectiveness analysis of trastuzumab deruxtecan in patients with HER2-low advanced breast cancer based on DESTINY-Breast04

Background and purpose Breast cancer is a rapidly raising healthcare problem worldwide. DESTINY-Breast04 demonstrated that trastuzumab deruxtecan (T-Dxd) had a survival advantage comparing to the physician's choice of chemotherapy for patients with HER2-low metastatic breast cancer. But at the same time, this expensive novel treatment also brought an economic burden. This study assessed the cost-effectiveness of T-Dxd based on results of DESTINY-Breast04 from the perspective of Chinese healthcare system. Materials and methods A three-state partitioned-survival model [progression-free survival (PFS), progressive disease (PD) and death] based on data from DESTINY-Breast04 and Chinese healthcare system was used to estimate the incremental cost-effectiveness ratio (ICER) of T-Dxd vs. the physician's choice of chemotherapy for HER2-low metastatic breast cancer. Costs, quality-adjusted life-years (QALYs) and the ICER in terms of 2022 US$ per QALY gained were calculated for both hormone receptor–positive cohort and all patients. One-way and probabilistic sensitivity analyses were performed to assess the model robustness. Results Compared with the physician's choice of chemotherapy, T-Dxd increased costs by $104,168.30, while gaining 0.31 QALYs, resulting in an ICER of $336,026.77 per QALY in all patients. The costs of T-Dxd and the utility of PFS were the crucial factors in determining the ICER. In the hormone receptor–positive cohort, the ICER was lower than that in all patients, with the ICER of $274,905.72 per QALY. The ICER was much higher than the commonly accepted willingness-to-pay threshold ($357,96.83 per QALY). Conclusion T-Dxd as second- or subsequent-line treatment is not a cost-effective treatment option for HER2-low metastatic breast cancer from the perspective of the Chinese healthcare system.
In situ short-term carbon and nitrogen dynamics in relation to microbial dynamics after a simulated rainfall in croplands of different soil texture in Thailand

Abstract The wetting—drying cycles of soil primarily drive carbon (C) and nitrogen (N) dynamics in tropical monsoon climates. We evaluated the in situ short-term C and N dynamics and the effect of soil texture during a wetting—drying cycle in relation to hourly microbial dynamics. Two croplands of differing soil textures (clay [THc] and sand [THs]) in Thailand were used for the experiment. Hourly measurements of soil CO2 efflux and inorganic nitrogen (Inorg-N) were conducted and we determined fluctuations in the in situ microbial biomass (In-situ-MB) and in situ microbial activity (In-situ-qCO2) after the application of a simulated rainfall (W plot) and a rainfall/glucose (WG plot) treatment. The rewetting of dry soil led to a C flush, which finished within 50–120 h because of rapid soil drying at both sites. Comparing the microbial dynamics in the THc-W and THs-W plots, it is clear that the rainfall treatment predominantly increased In-situ-qCO2 in the THc-W plot, whereas it increased In-situ-MB in the THs-W plot. These different microbial dynamics resulted in different C and N dynamics; that is, the cumulative soil CO2 efflux for the first 100 h after the treatment was effectively greater in the THs-W plot (3.4 g Cm−2) than in the THc-W plot (2.8 g Cm−2). In addition, distinct N-mineralization associated with a decreasing In-situ- MB was observed only in the THs-Wplot, although this was not the case in the THc-W plot. Hence, we concluded that rainfall events should play a more important role in the C and N dynamics in sandy soils compared with clayey soils because of different microbial dynamics after rewetting of a dry soil.
Isolation and identification of antifungal compounds from Amboyna wood

In continuation of our research into biologically active compounds from trees and their production by tissue culture (Tachibana and Sumimoto 1989; Tachibana et al. 1994; Miyata et al. 1998; Muranaka et al. 1998; Premjet et al. 2002; Yoshida et al. 2002), antifungal compounds were isolated from Amboyna wood. Plants are a rich source of chemical substances, with over 100,000 plant products described to date (Vicente et al. 2003), and play an important role in the production of biologically active secondary metabolites. Many secondary metabolites such as flavonoids, stilbenes, lignans and sesquiterpenoids have antifungal activities (ReyesChilpa et al. 1998; Celimene et al. 1999; Chang et al. 2000; Kawamura et al. 2004). Amboyna, Pterocarpus indicus Willd. (Leguminosae), is an important tropical tree, known as angsana and sena in Malaysia and Indonesia or narra in the Philippines, which mainly grows in Southeast Asia. Its natural distribution seems to cover the southern part of Burma, Java and New Guinea (Ogata 1985). Amboyna wood has been used for high-quality furniture and cabinets, decorative veneers, interior wall paneling, boat building and specialized joinery (Eddowes 1977). Extracts of leaves, stem and bark of Amboyna were reported to be active against several bacteria and protozoan (Khan and Omoloso 2003), while a polyphenolic compound isolated from young bark was reported to be a plasmin activity inhibitor (Takeuchi et al. 1986). In the present paper, we report the ability of Amboyna wood to inhibit the growth of wood-rotting fungi and the isolation of active compounds that play a role in the defense system of the wood. Materials and methods
Competitive Adsorption of Nickel and Cadmium on Sheep Manure Wastes: Experimental and Prediction Studies

Sheep manure wastes (SMW) previously have been shown to be very efficient in removing nickel and cadmium from single-component, dilute aqueous solutions. Simultaneous removal of nickel and cadmium ions from aqueous solutions using SMW has been investigated in this study. The experimental results showed that the SMW has a relatively higher affinity for cadmium binding than that for nickel. Different multicomponent-isotherm models; extended Langmuir, modified Langmuir, extended Redlich–Peterson, and extended Sips isotherm models, were used to predict the removal of either ions using single metal isotherm data.
Lipase-catalyzed regioselective acylation of sugar in microreactors

The highly regioselective synthesis of sugar 6-monoesters with sugar and vinyl carboxylate in a flow microreactor using Lipozyme TL IM from Thermomyces lanuginosus as a catalyst has been developed. The important features of this method include mild reaction conditions, short reaction times (30 min), high yields and high regioselectivities.
Variable Coherence Microscopy: a Rich Source of Structural Information from Disordered Materials

Variable coherence microscopy, a tool for quantitative analysis of structural fluctuations in disordered materials, is introduced. The method involves transmission electron microscopy of thin films and uses hollow-cone illumination. Experiments were performed on annealed evaporated amorphous germanium. Although many aspects of the data agree with the continuous random network model, there is experimental evidence for additional medium-range structure on the 10–20 A scale.
Photochemistry of cis-3-Diazo-5,6-dimethyl-1,4-oxathian-2-one S-oxide in argon matrices

The photochemistry of the α-diazo sulfoxide 7 has been investigated in solid argon at 10 K by IR spectroscopy. The sulfinyl carbene was not detected directly but instead underwent photochemically induced hetero-Wolff rearrangement to the sulfine 8 which could be detected and characterized following irradiation at 248 nm. Further photochemical reaction of this intermediate led to the oxathiirane 9 which was most readily detected on irradiation of 7 at 308 nm. The matrix-isolated species were identified by comparison of experimental and calculated IR spectra. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006)
Perceived Social Support and Severity of Chronic Pain in Fire Fighters of Tehran City

: Objectives: The main goal of the study was to investigating the relation between perceived social supports with severity of chronic pain in fire fighters of Tehran city. Method: this was a descriptive and correlational study. Accordingly, 400 fire fighters were selected through cluster random sampling. All subjects filled chronic pain questionnaire and multidimensional scale of perceived social support (MSPSS). Data was analyzed through Pearson correlation coefficient and linear regression. Results: results showed that there is significant and negative relationship (p<0/0001) between severity of chronic pain with perceived social support and its' aspects (supports from family, friends and important persons). Conclusion: findings of this study again demonstrated the important role of socio-psychological factors in predicting severity of chronic pain.
PHOTORESPONSIVE POLYMERS - PHOTOMODULATION OF THE MACROMOLECULAR STRUCTURE IN POLY(L-LYSINE) CONTAINING SPIROPYRAN UNITS

Poly(L-lysine) was reacted with spiropyran reagents to give polypeptides containing 46 and 25 mol % spiropyran units in the side chains. The resulting modified polymers were soluble in hexafluoro-2-propanol (HFP), where they exhibited reverse photochromism. In pure HFP, the photochromic polymers were random coils and the structure was not affected by the photoisomerization of the side chains. When appropriate amounts of cosolvents such as triethylamine or methanol were added to the HFP solutions, exposure to visible light (500 nm) or to sunlight for a few seconds produced the coil→ α-helix transitions of the macromolecular chains. The back-reaction in the dark was accompanied by the progressive decrease of the α-helix content and recovery of the original disordered conformation. CD measurements showed that the photoisomerization of the photochromic side chains was able to trigger the coil→helix transition of the macromolecules only in a very narrow range of HFP/NEt 3 or HFP/MeOH solvent composition; therefore, spiropyran-modified poly(L-lysine) can be considered a typical example of photoresponsive systems having a gated photoresponse
Removal of copper and zinc from aqueous solutions and industrial effluents using emulsion liquid membrane technique

Copper and zinc were removed from dilute aqueous solutions together with recovery of copper from electroplating wastewater containing copper ions by emulsion liquid membrane (ELM) technique. The effects of surfactant concentration, carrier concentration, emulsification speed, emulsification time, internal phase stripping agent concentration, and aqueous-to-organic phase (A/O) volume ratio on the emulsion stability and breakup have been studied in detail and reported. A mixture of kerosene as diluent, span 80 as surfactant, di-(2-ethylhexyl) phosphate as carrier was used. An experimental study was performed to optimize the pH of the aqueous external phase based on distribution coefficient of solute between aqueous external phase and organic (membrane) phase. The batch extraction was carried out under various experimental conditions such as agitation time, agitation speed, membrane-to-external phase (M/E) ratio, solute concentration in the feed phase and carrier concentration in membrane phase on the percentage recovery of zinc and copper ions in their respective feed streams and the operating parameters have been optimized for maximum recovery. It was found that 84% of copper and 86% of zinc were removed from aqueous solution with a concentration factor of 5. It was also found that ELM extraction of copper from wastewater was around 8–17% less than that of the synthetic solution. Copyright © 2008 Curtin University of Technology and John Wiley & Sons, Ltd.
Sila-Trifluperidol, a Silicon Analogue of the Dopamine (D2) Receptor Antagonist Trifluperidol: Synthesis and Pharmacological Characterization

Trifluperidol (2a) is a dopamine (D2) receptor antagonist of the butyrophenone type. Carbon/silicon exchange (sila-substitution) in the 4-position of the piperidine ring of 2a (R3COH → R3SiOH) results in sila-trifluperidol (2b). The silanol 2b was synthesized in a multistep synthesis, starting from triethoxy(vinyl)silane, and was isolated as the hydrochloride 2b·HCl. Compound 2b·HCl was structurally characterized by single-crystal X-ray diffraction and solution NMR spectroscopy, and the stability of the silanol 2b in aqueous solutions at different pH values was studied by ESI-MS experiments. In addition, the pharmacological profiles of the C/Si analogues trifluperidol (2a) and sila-trifluperidol (2b) and of the related compounds haloperidol (1a) and sila-haloperidol (1b) were studied in functional receptor assays at human dopamine D1 and D2 receptors. Sila-substitution of 1a (→ 1b) and 2a (→ 2b) affects the pharmacological properties significantly.
The secondary passive film to Type 304 stainless steel in 0.5 M HSO

An examination has been carried out of the secondary passive film on Type 304 stainless steel in 0.5 M H2SO4. The characterization techniques used were electrochemical (potentiodynamic; potentiostatic, and film reduction experiments) and surface analytical. A bilayer model for the secondary passive film is proposed. It appears that next to the metal, there is a modified passive film which controls the electrochemical response; i.e., governs the current for any applied potential. On top of this modified passive film, the experimental data are consistent with a ''porous'' corrosion-product film which adds to the total film thickness but has little influence on the electrochemical response. The composition of the secondary passive film corresponds most probably to a mixed Fe/Cr oxide/hydroxide enriched in Cr3+, With a composition similar to a primary passive film.
Coexpression of MmpS5 and MmpL5 Contributes to Both Efflux Transporter MmpL5 Trimerization and Drug Resistance in Mycobacterium tuberculosis

It has been reported that mycobacterial membrane protein large 5 (MmpL5), a resistance-nodulation-division (RND)-type inner membrane transporter in Mycobacterium tuberculosis (Mtb), is involved in the transport of antimycobacterial drugs. However, the functional roles of the membrane fusion protein mycobacterial membrane protein small 5 (MmpS5), organized as an operon with MmpL5, are unclear. ABSTRACT The increasing occurrence of multidrug-resistant Mycobacterium tuberculosis (Mtb) is a serious threat to global public health. Among the many mechanisms of drug resistance, only resistance-nodulation-division (RND)-type multidrug efflux systems can simultaneously render bacteria tolerant to numerous toxic compounds, including antibiotics. The elevated expression of RND-type xenobiotic efflux transporter complexes, which consist of an inner membrane transporter, membrane fusion protein, and outer membrane channel, plays a major role in multidrug resistance. Among the 14 mycobacterial membrane protein large (MmpL) proteins identified as inner membrane transporters of Mtb, MmpL5 is known to participate in the acquisition of resistance to bedaquiline and clofazimine. MmpL5 exports these drugs by forming a complex with the membrane fusion protein mycobacterial membrane protein small 5 (MmpS5). However, the role of MmpS5 in the efflux of antituberculous drugs by MmpL5 remains unclear. In this study, we focused on the in vivo dynamics of MmpL5 using green fluorescent protein (GFP). Single-molecule observations of MmpL5 showed substantial lateral displacements of MmpL5-GFP without the expression of MmpS5. Nondiffusing MmpL5-GFP foci typically showed three-step photobleaching, suggesting that MmpL5 formed a homotrimeric functional complex on the inner membrane in the presence of MmpS5. These results suggest that the expression of MmpS5 facilitates the assembly of monomeric MmpL5 into a homotrimer that is anchored to the inner membrane to transport various antimycobacterial drugs. IMPORTANCE It has been reported that mycobacterial membrane protein large 5 (MmpL5), a resistance-nodulation-division (RND)-type inner membrane transporter in Mycobacterium tuberculosis (Mtb), is involved in the transport of antimycobacterial drugs. However, the functional roles of the membrane fusion protein mycobacterial membrane protein small 5 (MmpS5), organized as an operon with MmpL5, are unclear. Via the single-molecule imaging of MmpL5, we uncovered the maintenance of the functional trimeric complex structure of MmpL5 in the presence of MmpS5. These findings demonstrate that the assembly mechanisms of mycobacterial RND efflux systems are the dynamically regulated process through interactions among the components. This represents the first report of the single-molecule observation of Mtb efflux transporters, which may enhance our understanding of innate antibiotic resistance.