Clinical Case Registries: simultaneous local and national disease registries for population quality management

The Department of Veterans Affairs (VA) has a system-wide, patient-centric electronic medical record system (EMR) within which the authors developed the Clinical Case Registries (CCR) to support population-centric delivery and evaluation of VA medical care. To date, the authors have applied the CCR to populations with human immunodeficiency virus (HIV) and hepatitis C virus (HCV). Local components use diagnosis codes and laboratory test results to identify patients who may have HIV or HCV and support queries on local care delivery with customizable reports. For each patient in a local registry, key EMR data are transferred via HL7 messaging to a single national registry. From 128 local registry systems, over 60,000 and 320,000 veterans in VA care have been identified as having HIV and HCV, respectively, and entered in the national database. Local and national reports covering demographics, resource usage, quality of care metrics and medication safety issues have been generated.

Comparative Metagenomics of Eight Geographically Remote Terrestrial Hot Springs

Hot springs are natural habitats for thermophilic Archaea and Bacteria. In this paper, we present the metagenomic analysis of eight globally distributed terrestrial hot springs from China, Iceland, Italy, Russia, and the USA with a temperature range between 61 and 92 (∘)C and pH between 1.8 and 7. A comparison of the biodiversity and community composition generally showed a decrease in biodiversity with increasing temperature and decreasing pH. Another important factor shaping microbial diversity of the studied sites was the abundance of organic substrates. Several species of the Crenarchaeal order Thermoprotei were detected, whereas no single bacterial species was found in all samples, suggesting a better adaptation of certain archaeal species to different thermophilic environments. Two hot springs show high abundance of Acidithiobacillus, supporting the idea of a true thermophilic Acidithiobacillus species that can thrive in hyperthermophilic environments. Depending on the sample, up to 58 % of sequencing reads could not be assigned to a known phylum, reinforcing the fact that a large number of microorganisms in nature, including those thriving in hot environments remain to be isolated and characterized.

Metagenomic mining for thermostable esterolytic enzymes uncovers a new family of bacterial esterases

Biocatalysts exerting activity against ester bonds have a broad range of applications in modern biotechnology. Here, we have identified a new esterolytic enzyme by screening a metagenomic sample collected from a hot spring in Kamchatka, Russia. Biochemical characterization of the new esterase, termed EstDZ2, revealed that it is highly active against medium chain fatty acid esters at temperatures between 25 and 60 °C and at pH values 7-8. The new enzyme is moderately thermostable with a half-life of more than six hours at 60 °C, but exhibits exquisite stability against high concentrations of organic solvents. Phylogenetic analysis indicated that EstDZ2 is likely an Acetothermia enzyme that belongs to a new family of bacterial esterases, for which we propose the index XV. One distinctive feature of this new family, is the presence of a conserved GHSAG catalytic motif. Multiple sequence alignment, coupled with computational modelling of the three-dimensional structure of EstDZ2, revealed that the enzyme lacks the largest part of the "cap" domain, whose extended structure is characteristic for the closely related Family IV esterases. Thus, EstDZ2 appears to be distinct from known related esterolytic enzymes, both in terms of sequence characteristics, as well as in terms of three-dimensional structure.

Oxygen–iron interaction in liquid lead–bismuth eutectic alloy

Iron released in steel corrosion is a key impurity in reactions with dissolved oxygen in liquid lead–bismuth eutectic alloys.

Respiratory Pathways Reconstructed by Multi-Omics Analysis in Melioribacter roseus, Residing in a Deep Thermal Aquifer of the West-Siberian Megabasin

Melioribacter roseus, a representative of recently proposed Ignavibacteriae phylum, is a metabolically versatile thermophilic bacterium, inhabiting subsurface biosphere of the West-Siberian megabasin and capable of growing on various substrates and electron acceptors. Genomic analysis followed by inhibitor studies and membrane potential measurements of aerobically grown M. roseus cells revealed the activity of aerobic respiratory electron transfer chain comprised of respiratory complexes I and IV, and an alternative complex III. Phylogeny reconstruction revealed that oxygen reductases belonged to atypical cc(o/b)o₃-type and canonical cbb₃–type cytochrome oxidases. Also, two molybdoenzymes of M. roseus were affiliated either with Ttr or Psr/Phs clades, but not with typical respiratory arsenate reductases of the Arr clade. Expression profiling, both at transcripts and protein level, allowed us to assign the role of the terminal respiratory oxidase under atmospheric oxygen concentration for the cc(o/b)o₃ cytochrome oxidase, previously proposed to serve for oxygen detoxification only. Transcriptomic analysis revealed the involvement of both molybdoenzymes of M. roseus in As(V) respiration, yet differences in the genomic context of their gene clusters allow to hypothesize about their distinct roles in arsenate metabolism with the ‘Psr/Phs’-type molybdoenzyme being the most probable candidate respiratory arsenate reductase. Basing on multi-omics data, the pathways for aerobic and arsenate respiration were proposed. Our results start to bridge the vigorously increasing gap between homology-based predictions and experimentally verified metabolic processes, what is especially important for understudied microorganisms of novel lineages from deep subsurface environments of Eurasia, which remained separated from the rest of the biosphere for several geological periods.

Influence of Illumination on Porous Silicon Formed by Photo-Assisted Etching of p-Type Si with a Different Doping Level

The influence of illumination intensity and p-type silicon doping level on the dissolution rate of Si and total current by photo-assisted etching was studied. The impact of etching duration, illumination intensity, and wafer doping level on the etching process was investigated using scanning electron microscopy (SEM), atomic force microscopy (AFM), and Ultraviolet-Visible Spectroscopy (UV–Vis–NIR). The silicon dissolution rate was found to be directly proportional to the illumination intensity and inversely proportional to the wafer resistivity. High light intensity during etching treatment led to increased total current on the Si surface. It was shown that porous silicon of different thicknesses, pore diameters, and porosities can be effectively fabricated by photo-assisted etching on a Si surface without external bias or metals.

Spore-Forming Thermophilic Bacterium within Artificial Meteorite Survives Entry into the Earth's Atmosphere on FOTON-M4 Satellite Landing Module

One of the key conditions of the lithopanspermia hypothesis is that microorganisms situated within meteorites could survive hypervelocity entry from space through the Earth's atmosphere. So far, all experimental proof of this possibility has been based on tests with sounding rockets which do not reach the transit velocities of natural meteorites. We explored the survival of the spore-forming thermophilic anaerobic bacterium, Thermoanaerobacter siderophilus, placed within 1.4-cm thick basalt discs fixed on the exterior of a space capsule (the METEORITE experiment on the FOTON-M4 satellite). After 45 days of orbital flight, the landing module of the space vehicle returned to Earth. The temperature during the atmospheric transit was high enough to melt the surface of basalt. T. siderophilus survived the entry; viable cells were recovered from 4 of 24 wells loaded with this microorganism. The identity of the strain was confirmed by 16S rRNA gene sequence and physiological tests. This is the first report on the survival of a lifeform within an artificial meteorite after entry from space orbit through Earth's atmosphere at a velocity that closely approached the velocities of natural meteorites. The characteristics of the artificial meteorite and the living object applied in this study can serve as positive controls in further experiments on testing of different organisms and conditions of interplanetary transport.

Longitudinal Tumor Size and Neutrophil-to-Lymphocyte Ratio Are Prognostic Biomarkers for Overall Survival in Patients With Advanced Non-Small Cell Lung Cancer Treated With Durvalumab

Therapy optimization remains an important challenge in the treatment of advanced non-small cell lung cancer (NSCLC). We investigated tumor size (sum of the longest diameters (SLD) of target lesions) and neutrophil-to-lymphocyte ratio (NLR) as longitudinal biomarkers for survival prediction. Data sets from 335 patients with NSCLC from study NCT02087423 and 202 patients with NSCLC from study NCT01693562 of durvalumab were used for model qualification and validation, respectively. Nonlinear Bayesian joint models were designed to assess the impact of longitudinal measurements of SLD and NLR on patient subgrouping (by Response Evaluation Criteria in Solid Tumors 1.1 criteria at 3 months after therapy start), long-term survival, and precision of survival predictions. Various validation scenarios were investigated. We determined a more distinct patient subgrouping and a substantial increase in the precision of survival estimates after the incorporation of longitudinal measurements. The highest performance was achieved using a multivariate SLD and NLR model, which enabled predictions of NSCLC clinical outcomes.

Anodic TiO2nanotube arrays for photocatalytic CO2conversion: comparative photocatalysis and EPR study

Titania (TiO₂) is a widely used semiconductor for the photocatalytic decomposition of organic impurities in air, water and the conversion of CO₂into hydrocarbon fuel precursors. TiO₂in the form of nanotubes arrays is the most attractive for practical use because of the morphological advantages providing more favorable diffusion of photocatalytic reaction products and a low recombination rate of photogenerated electrons and holes. We have carried out a comparative study of the photocatalytic activity of gas-phase conversion of CO₂to hydrocarbon products and the defect properties of multi-walled and single-walled arrays of TiO₂nanotubes. Methanol and methane have been detected in the CO₂photoreduction process. The photocatalytic evolution rate of multi-walled TiO₂nanotubes is twice as fast for methane as for single-walled TiO₂nanotubes after four hours of irradiation and four times faster for methanol. The type and features of the structural defects have been investigated by EPR spectroscopy. For the first time, it has been shown that Ti³⁺/oxygen vacancy centers are mainly located inside the outer layer of nanotubes, while carbon dangling bonds have been observed directly on the surface of the inner layer. Carbon defects have been found to be the centers of adsorption and accumulation of photoinduced charge carriers. The results are entirely new; they clarify the role of different types of defects in the photocatalytic conversion of CO₂to hydrocarbon compounds and show good prospects for applying TiO₂nanotube arrays.

Investigation of the Pd Nanoparticles-Assisted Chemical Etching of Silicon for Ethanol Solution Electrooxidation

The formation of porous silicon by Pd nanoparticles-assisted chemical etching of single-crystal Si with resistivity ρ = 0.01 Ω·cm at 25 °C, 50 °C and 75 °C in HF/H2O2/H2O solution was studied. Porous layers of silicon were studied by optical and scanning electron microscopy, and gravimetric analysis. It is shown that por-Si, formed by Pd nanoparticles-assisted chemical etching, has the property of ethanol electrooxidation. The chromatographic analysis of ethanol electrooxidation products on por-Si/Pd shows that the main products are CO2, CH4, H2, CO, O2, acetaldehyde (CHO)+, methanol and water vapor. The mass activity of the por-Si/Pd system was investigated by measuring the short-circuit current in ethanol solutions. The influence of the thickness of porous silicon and wafer on the mass activity and the charge measured during ethanol electrooxidation was established. Additionally, the mechanism of charge transport during ethanol electrooxidation was established.

Peculiarities of Low-Temperature Behavior of Liquids Confined in Nanostructured Silicon-Based Material

This study is devoted to the confinement effects on freezing and melting in electrochemical systems containing nanomaterial electrodes and liquid electrolytes. The melting of nanoparticles formed upon freezing of liquids confined in pores of disordered nanostructured n-type silicon has been studied by low-temperature differential scanning calorimetry. Experimental results obtained for deionized water, an aqueous solution of potassium sulfate, and n-decane are presented. A model is proposed for predicting the melting point of nanoparticles formed during freezing of liquids inside the pores of a disordered nanostructured material. The model is based on the classical thermodynamic concept of the phase transition temperature dependence on the particle size. It takes into account the issues arising when a liquid is dispersed in a matrix of another material: the effect of mechanical stress resulted from the difference in the thermal linear expansion coefficients at a temperature gradient, the effect of the volumetric liquid content in the matrix, the presence of a nonfreezing liquid layer inside the pores, and the effect of wettability of the matrix with the liquid. Model calculations for water and n-decane confined in nanostructured silicon matrix have been carried out considering the volumetric liquid content. The results obtained have been compared with the differential scanning calorimetry data.

Mössbauer, Nuclear Forward Scattering, and Raman Spectroscopic Approaches in the Investigation of Bioinduced Transformations of Mixed-Valence Antimony Oxide

Mössbauer spectroscopy, nuclear forward scattering, and Raman spectroscopy were applied to study redox transformations of the synthesized mixed-valence (III/V) antimony oxide. The transformations were induced by a culture of a hyperthermophilic archaeon of the genus Pyrobaculum. The applied methods allowed us to reveal the minor decrease of ca. 11.0 ± 1.2% of the antimony(V) content of the mixed-valence oxide with the concomitant increase of antimony(III). The method sensitivities for the quantitative assessment of the Sb(III/V) ratio have been considered.

Characterization of Mesoporous Silicon Using DSC Thermoporometry

The thermal behavior of water confined in mesopores of silicon membrane was evaluated by differential scanning calorimetry. The results showed strong supercooling of water inside the pores which allowed us to estimate the content of freezable pore water and nonfreezable pore water in the analyzed membranes.

A workflow for the joint modeling of longitudinal and event data in the development of therapeutics: Tools, statistical methods, and diagnostics

Clinical trials investigate treatment endpoints that usually include measurements of pharmacodynamic and efficacy biomarkers in early-phase studies and patient-reported outcomes as well as event risks or rates in late-phase studies. In recent years, a systematic trend in clinical trial data analytics and modeling has been observed, where retrospective data are integrated into a quantitative framework to prospectively support analyses of interim data and design of ongoing and future studies of novel therapeutics. Joint modeling is an advanced statistical methodology that allows for the investigation of clinical trial outcomes by quantifying the association between baseline and/or longitudinal biomarkers and event risk. Using an exemplar data set from non-small cell lung cancer studies, we propose and test a workflow for joint modeling. It allows a modeling scientist to comprehensively explore the data, build survival models, investigate goodness-of-fit, and subsequently perform outcome predictions using interim biomarker data from an ongoing study. The workflow illustrates a full process, from data exploration to predictive simulations, for selected multivariate linear and nonlinear mixed-effects models and software tools in an integrative and exhaustive manner.

Longitudinal tumor size and NLR as predictive factors of individual survival compared to their baseline values in patients with non-small cell lung cancer treated with durvalumab

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Background: Our ability to accurately predict survival of patients with non-small cell lung cancer (NSCLC) while on treatment is limited. Prognostic markers such as stage and tumor size are well established, while neutrophil-to-lymphocytes ratio (NLR) and other hemogram measurements have recently been studied. Gain in prognostic accuracy of these markers when measured longitudinally has not been established. Methods: There were 679 NSCLC patients (Stage 3 or 4, ECOG PS 0 or 1) from clinical studies of durvalumab 10 mg/kg every two weeks (NCT02087423 and NCT01693562). We developed three models of overall survival (OS) all with ECOG as covariate: a Cox proportional hazards model with baseline tumor sum-of-longest-diameters (SLD) and NLR as covariates (COX); a joint model of OS and longitudinal SLD and baseline NLR (JM SLD); and a joint model of OS and longitudinal SLD and NLR (JM SLD&NLR). We compared prognostic accuracy of these markers measured longitudinally vs. at baseline, using predicted probability of OS at 12 months after start of durvalumab as a prognostic score. We evaluated predictive performance of the models using area under the receiver-operating characteristic curve (ROC AUC) describing trade-off between true and false positives (i.e., survival past 12 months). The AUCs were calculated for patients in the dataset using longitudinal data up to different cut-offs. Results: The AUC for all patients starting durvalumab using baseline ECOG, SLD and NLR was 0.73, while it decreased to 0.64 for patients surviving to 6 months, compared to 0.50 for noninformative models. The AUC using longitudinal information for SLD and NLR was larger the more longitudinal data was used for prediction and was 0.81 using 6 months’ worth of data. Conclusions: Using longitudinal information for SLD and NLR increased individual predictive performance of these markers compared to only baseline information in NSCLC patients. [Table: see text]

Tailoring porous/filament silicon using the two-step Au-assisted chemical etching of p-type silicon for forming an ethanol electro-oxidation layer

In this paper, we are reporting on the fabrication of a porous silicon/Au and silicon filament/Au using the two-step Au-assisted chemical etching of p-type Si with a specific resistivity of 0.01, 1, and 12 Ω·cm when varying the Au deposition times. The structure analysis results show that with an increasing Au deposition time of up to 7 min, the thickness of the porous Si layer increases for the same etching duration (60 min), and the morphology of the layer changes from porous to filamentary. This paper shows that the uniform macro-porous layers with a thickness of 125.5-171.2μm and a specific surface area of the mesopore sidewalls of 142.5-182 m²·g^-1are formed on the Si with a specific resistivity of 0.01 Ω·cm. The gradient macro-porous layers with a thickness of 220-260μm and 210-290μm, the specific surface area of the mesopore sidewalls of 3.7-21.7 m²·g^-1and 17-29 m²·g^-1are formed on the silicon with a specific resistivity of 1 and 12 Ω·cm, respectively. The por-Si/Au has excellent low-temperature electro oxidation performance with ethanol, the activity of ethanol oxidation is mainly due to the synergistic effect of the Au nanoparticles and porous Si. The formation mechanism of the uniform and gradient macro-porous layers and ethanol electro-oxidation on the porous/filament silicon, decorated with Au nanoparticles, was established. The por-Si/Au structures with perpendicularly oriented pores, a high por-Si layer thickness, and a low mono-Si layer thickness (with a specific resistivity of 1 Ω·cm) are optimal for an effective ethanol electro-oxidation, which has been confirmed with chronoamperometry measurements.

Fast-growing Arctic Fe-Mn deposits from the Kara Sea as the refuges for cosmopolitan marine microorganisms

The impact of biomineralization and redox processes on the formation and growth of ferromanganese deposits in the World Ocean remains understudied. This problem is particularly relevant for the Arctic marine environment where sharp seasonal variations of temperature, redox conditions, and organic matter inflow significantly impact the biogenic and abiotic pathways of ferromanganese deposits formation. The microbial communities of the fast-growing Arctic Fe-Mn deposits have not been reported so far. Here, we describe the microbial diversity, structure and chemical composition of nodules, crust and their underlying sediments collected from three different sites of the Kara Sea. Scanning electron microscopy revealed a high abundance of microfossils and biofilm-like structures within the nodules. Phylogenetic profiling together with redundancy and correlation analyses revealed a positive selection for putative metal-reducers (Thermodesulfobacteriota), iron oxidizers (Hyphomicrobiaceae and Scalinduaceae), and Fe-scavenging Nitrosopumilaceae or Magnetospiraceae in the microenvironments of the Fe-Mn deposits from their surrounding benthic microbial populations. We hypothesize that in the Kara Sea, the nodules provide unique redox-stable microniches for cosmopolitan benthic marine metal-cycling microorganisms in an unsteady environment, thus focusing the overall geochemical activity of nodule-associated microbial communities and accelerating processes of ferromanganese deposits formation to uniquely high rates.