Carbon Monoxide Oxidation on Ceria-Supported Nanoclusters.

Periodic density functional theory is used to evaluate the minimum energy pathways of CO oxidation on cerium oxide-supported platinum and palladium nanoclusters (Pt/CeO2 and Pd/CeO2). For Pt/CeO2, the oxidation process involves the participation of lattice oxygen from CeO2 at the boundary sites of the cluster-ceria interface, which exhibits an exceptionally low energy barrier. Conversely, on Pd/CeO2, oxidation predominantly occurs through oxygen species bound to the Pd cluster. Experimental analysis using the temperature-programmed reduction of the oxidized Pd/CeO2 catalyst reveals a lower CO oxidation temperature compared to Pt/CeO2. This observation aligns with the anticipated decrease in the energy barrier for CO oxidation due to the oxygen coverage of the Pd cluster.

Tailoring and Identifying Brønsted Acid Sites on Metal Oxo-Clusters of Metal-Organic Frameworks for Catalytic Transformation.

Metal-organic frameworks (MOFs) with Brønsted acidity are an alternative solid acid catalyst for many important chemical and fuel processes. However, the nature of the Brønsted acidity on the MOF's metal cluster or center is underexplored. To design and optimize the acid strength and density in these MOFs, it is important to understand the origin of their acidity at the molecular level. In the present work, isoreticular MOFs, ZrNDI and HfNDI (NDI = N,N'-bis(5-isophthalate)naphthalenediimide), were prepared as a prototypical system to unravel and compare their Brønsted and Lewis acid sites through an array of spectroscopic, computational, and catalytic characterization techniques. With the aid of solid-state nuclear magnetic resonance and density functional calculations, Hf6 oxo-clusters on HfNDI are quantitatively proved to possess a higher density Brønsted acid site, while ZrNDI-based MOFs display stronger and higher-population Lewis acidity. HfNDI-based MOFs exhibit a superior catalytic performance in activating dihydroxyacetone (DHA) and converting DHA to ethyl lactate, with 71.1% selectivity at 54.7% conversion after 6 h. The turnover frequency of BAS-dominated Hf-MOF in DHA conversion is over 50 times higher than that of ZSM-5, a strong BAS-based zeolite. It is worth noting that HfNDI is reported for the first time in the literature, which is an alternative platform catalyst for biorefining and green chemistry. The present study furthermore highlights the uniqueness of Hf-based MOFs in this important biomass-to-chemical transformation.

A Review of Terminology Used to Describe Soot Formation and Evolution under Combustion and Pyrolytic Conditions.

This review presents a glossary and review of terminology used to describe the chemical and physical processes involved in soot formation and evolution and is intended to aid in communication within the field and across disciplines. There are large gaps in our understanding of soot formation and evolution and inconsistencies in the language used to describe the associated mechanisms. These inconsistencies lead to confusion within the field and hinder progress in addressing the gaps in our understanding. This review provides a list of definitions of terms and presents a description of their historical usage. It also addresses the inconsistencies in the use of terminology in order to dispel confusion and facilitate the advancement of our understanding of soot chemistry and particle characteristics. The intended audience includes senior and junior members of the soot, black carbon, brown carbon, and carbon black scientific communities, researchers new to the field, and scientists and engineers in associated fields with an interest in carbonaceous material production via high-temperature hydrocarbon chemistry.

Validation of Fragile X Screening in the Newborn Population Using a Fit-for-Purpose FMR1 PCR Assay System.

Newborn screening is designed for presymptomatic identification of serious conditions with effective early interventions. Clinical laboratories must perform prospective pilot studies to ensure that the analytical performance and workflow for a given screening test are appropriate. We assessed the potential to screen newborns for fragile X syndrome, a monogenic neurodevelopmental disorder, by establishing a customized, high-throughput PCR and analysis software system designed to detect fragile X mental retardation 1 gene repeat expansions from dried blood spots (DBSs). Assay precision, accuracy, sensitivity, and specificity were characterized across the categorical range of repeat expansions. The assay consistently resolved genotypes within three CGG repeats of reference values up to at least 137 repeats and within six repeats for larger expansions up to 200 repeats. Accuracy testing results were concordant with reference results. Full and premutation alleles were detected from subnanogram DNA inputs eluted from DBSs and from mixtures with down to 1% relative abundance of the respective expansion. Analysis of 963 deidentified newborn DBS samples identified 957 normal and 6 premutation specimens, consistent with previously published prevalence estimates. These studies demonstrate that the assay system can support high-throughput newborn screening programs.

Atomic order, electronic structure and thermodynamic stability of nickel aluminate.

The atomic order, electronic structure and thermodynamic stability of nickel aluminate, NiAl2O4, have been analyzed using periodic density functional theory and cluster expansion. NiAl2O4 forms a tetragonal structure with P4122 space group. At temperatures below 800 K, it is an inverse spinel, with Ni occupying the octahedral sites and Al occupying both the octahedral and the tetrahedral sites. Some Niocta + Altetra ⇌ Nitetra + Alocta exchange occurs above 800 K, but the structure remains largely inverse at high temperatures, with about 95% Niocta at 1500 K. Various functionals, with and without van der Waals corrections, were used to predict the experimental formation energy, lattice parameters and electronic structure. In all cases, the NiAl2O4 is found to be ferromagnetic and a semiconductor with an indirect band gap along the Γ â†’ M symmetry points. NiAl2O4 is found to be thermodynamically stable at operating conditions of 900-1000 K and 1 atm relative to its competing oxide phases, NiO and Al2O3.

Multilaboratory Assessment of a New Reference Material for Quality Assurance of Cell-Free Tumor DNA Measurements.

We conducted a multilaboratory assessment to determine the suitability of a new commercially available reference material with 40 cancer variants in a background of wild-type DNA at four different variant allele frequencies (VAFs): 2%, 0.50%, 0.125%, and 0%. The variants include single nucleotides, insertions, deletions, and two structural variations selected for their clinical importance and to challenge the performance of next-generation sequencing (NGS) methods. Fragmented DNA was formulated to simulate the size distribution of circulating wild-type and tumor DNA in a synthetic plasma matrix. DNA was extracted from these samples and characterized with different methods and multiple laboratories. The various extraction methods had differences in yield, perhaps because of differences in chemistry. Digital PCR assays were used to measure VAFs to compare results from different NGS methods. Comparable VAFs were observed across the different NGS methods. This multilaboratory assessment demonstrates that the new reference material is an appropriate tool to determine the analytical parameters of different measurement methods and to ensure their quality assurance.

An Integrated Next-Generation Sequencing System for Analyzing DNA Mutations, Gene Fusions, and RNA Expression in Lung Cancer.

We developed and characterized a next-generation sequencing (NGS) technology for streamlined analysis of DNA and RNA using low-input, low-quality cancer specimens. A single-workflow, targeted NGS panel for non-small cell lung cancer (NSCLC) was designed covering 135 RNA and 55 DNA disease-relevant targets. This multiomic panel was used to assess 219 formalin-fixed paraffin-embedded NSCLC surgical resections and core needle biopsies. Mutations and expression phenotypes were identified consistent with previous large-scale genomic studies, including mutually exclusive DNA and RNA oncogenic driver events. Evaluation of a second cohort of low cell count fine-needle aspirate smears from the BATTLE-2 trial yielded 97% agreement with an independent, validated NGS panel that was used with matched surgical specimens. Collectively, our data indicate that broad, clinically actionable insights that previously required independent assays, workflows, and analyses to assess both DNA and RNA can be conjoined in a first-tier, highly multiplexed NGS test, thereby providing faster, simpler, and more economical results.

Design, Optimization, and Multisite Evaluation of a Targeted Next-Generation Sequencing Assay System for Chimeric RNAs from Gene Fusions and Exon-Skipping Events in Non-Small Cell Lung Cancer.

Lung cancer accounts for approximately 14% of all newly diagnosed cancers and is the leading cause of cancer-related deaths. Chimeric RNA resulting from gene fusions (RNA fusions) and other RNA splicing errors are driver events and clinically addressable targets for non-small cell lung cancer (NSCLC). The reliable assessment of these RNA markers by next-generation sequencing requires integrated reagents, protocols, and interpretive software that can harmonize procedures and ensure consistent results across laboratories. We describe the development and verification of a system for targeted RNA sequencing for the analysis of challenging, low-input solid tumor biopsies that includes reagents for nucleic acid quantification and library preparation, run controls, and companion bioinformatics software. Assay development reconciled sequence discrepancies in public databases, created predictive formalin-fixed, paraffin-embedded RNA qualification metrics, and eliminated read misidentification attributable to index hopping events on the next-generation sequencing flow cell. The optimized and standardized system was analytically verified internally and in a multiphase study conducted at five independent laboratories. The results show accurate, reproducible, and sensitive detection of RNA fusions, alternative splicing events, and other expression markers of NSCLC. This comprehensive approach, combining sample quantification, quality control, library preparation, and interpretive bioinformatics software, may accelerate the routine implementation of targeted RNA sequencing of formalin-fixed, paraffin-embedded samples relevant to NSCLC.

The effect of surface coverage on N2, NO and N2O formation over Pt(111).

The effect of surface coverage of species, θ, on the kinetic parameters of N2, NO and N2O formation in a system simulating ammonia oxidation over Pt(111) has been studied by using periodic density functional theory (DFT). The energy barriers for product formation decrease as θ increases, with the effect being more significant above 0.25 ML. The heat of surface reaction decreases as θ increases, making the dissociation of the products less favourable due to a weaker interaction of the intermediates with the surface. The effect of θ on the binding energy is stronger for N* than for either O* or NO*, but it is more apparent in the co-adsorption with O* and NO*. Similarly, the coverage of N* more strongly affects the activation energy of N2 and N2O desorption than does the coverage of O* for NO* and N2O formation.

In situ synchrotron XRD analysis of the kinetics of spodumene phase transitions.

The phase transition by thermal activation of natural α-spodumene was followed by in situ synchrotron XRD in the temperature range 896 to 940 °C. We observed both ß- and γ-spodumene as primary products in approximately equal proportions. The rate of the α-spodumene inversion is first order and highly sensitive to temperature (apparent activation energy ∼800 kJ mol-1). The γ-spodumene product is itself metastable, forming ß-spodumene, with the total product mass fraction ratio fγ/fß decreasing as the conversion of α-spodumene continues. We found the relationship between the product yields and the degree of conversion of α-spodumene to be the same at all temperatures in the range studied. A model incorporating first order kinetics of the α- and γ-phase inversions with invariant rate constant ratio describes the results accurately. Theoretical phonon analysis of the three phases indicates that the γ phase contains crystallographic instabilities, whilst the α and ß phases do not.

Congruence between patient characteristics and interventions may partly explain medication adherence intervention effectiveness: an analysis of 190 randomized controlled trials from a Cochrane systematic review.

OBJECTIVES: Due to the negative outcomes of medication nonadherence, interventions to improve adherence have been the focus of countless studies. The congruence between adherence-related patient characteristics and interventions may partly explain the variability of effectiveness in medication adherence studies. In their latest update of a Cochrane review reporting inconsistent effects of adherence interventions, the authors offered access to their database for subanalysis. We aimed to use this database to assess congruence between adherence-related patient characteristics and interventions and its association with intervention effects. STUDY DESIGN AND SETTING: We developed a congruence score consisting of six features related to inclusion criteria, patient characteristics at baseline, and intervention design. Two independent raters extracted and scored items from the 190 studies available in the Cochrane database. We correlated overall congruence score and individual features with intervention effects regarding adherence and clinical outcomes using Kruskal-Wallis rank sum test and Fisher's exact test. RESULTS: Interrater reliability for newly extracted data was almost perfect with a Cohen's Kappa of 0.92 [95% confidence interval (CI) = 0.89-0.94; P < 0.001]. Although present in only six studies, the inclusion of nonadherent patients was the single feature significantly associated with effective adherence interventions (P = 0.003). Moreover, effective adherence interventions were significantly associated with improved clinical outcomes (odds ratio = 6.0; 95% CI = 3.1-12.0; P < 0.0001). However, neither the overall congruence score nor any other individual feature (i.e., "determinants of nonadherence as inclusion criteria," "tailoring of interventions to the inclusion criteria," "reasons for nonadherence assessed at baseline," "adjustment of intervention to individual patient needs," and "theory-based interventions") was significantly associated with intervention effects. CONCLUSION: The presence of only six studies that included nonadherent patients and the interdependency of this feature with the remaining five might preclude a conclusive assessment of congruence between patient characteristics and adherence interventions. In order to obtain clinical benefits from effective adherence interventions, we encourage researchers to focus on the inclusion of nonadherent patients.

Molecular classification of thyroid lesions by combined testing for miRNA gene expression and somatic gene alterations.

Multiple molecular markers contribute to the pathogenesis of thyroid cancer and can provide valuable information to improve disease diagnosis and patient management. We performed a comprehensive evaluation of miRNA gene expression in diverse thyroid lesions (n = 534) and developed predictive models for the classification of thyroid nodules, alone or in combination with genotyping. Expression profiling by reverse transcription-quantitative polymerase chain reaction in surgical specimens (n = 257) identified specific miRNAs differentially expressed in 17 histopathological categories. Eight supervised machine learning algorithms were trained to discriminate benign from malignant lesions and evaluated for accuracy and robustness. The selected models showed invariant area under the receiver operating characteristic curve (AUC) in cross-validation (0.89), optimal AUC (0.94) in an independent set of preoperative thyroid nodule aspirates (n = 235), and classified 92% of benign lesions as low risk/negative and 92% of malignant lesions as high risk/positive. Surgical and preoperative specimens were further tested for the presence of 17 validated oncogenic gene alterations in the BRAF, RAS, RET or PAX8 genes. The miRNA-based classifiers complemented and significantly improved the diagnostic performance of the 17-mutation panel (p < 0.001 for McNemar's tests). In a subset of resected tissues (n = 54) and in an independent set of thyroid nodules with indeterminate cytology (n = 42), the optimized ThyraMIR Thyroid miRNA Classifier increased diagnostic sensitivity by 30-39% and correctly classified 100% of benign nodules negative by the 17-mutation panel. In contrast, testing with broad targeted next-generation sequencing panels decreased diagnostic specificity by detecting additional mutations of unknown clinical significance in 19-39% of benign lesions. Our results demonstrate that, independent of mutational status, miRNA expression profiles are strongly associated with altered molecular pathways underlying thyroid tumorigenesis. Combined testing for miRNA gene expression and well-established somatic gene alterations is a novel diagnostic strategy that can improve the preoperative diagnosis and surgical management of patients with indeterminate thyroid nodules.

Effect of the Local Atomic Ordering on the Stability of ß-Spodumene.

This study focuses on the relative energetic stability of ß-spodumene configurations with different atomic ordering, evaluated using electronic structure methods based on static periodic density functional theory. We found that ß-spodumene configurations with a framework containing exclusively Al-O-Si linkages are energetically the most stable, consistent with the aluminum avoidance principle. A correlation between the interstitial sites occupied by lithium and the stability of the configuration was established: highly stable configurations contain greater proportions of lithium associated with the edges of AlO4 tetrahedrons. The identified low-energy configurations have a band gap of ∼4.8 eV, and similar electronic band structures and densities of states. Both the PBE and PBEsol functionals predict small differences in the relative stabilities of the different configurations of ß-spodumene. However, only PBEsol is able to reproduce the experimentally observed stability differences between α-spodumene and ß-spodumene. ß-Spodumene is the preferred polymorph at high temperatures, with the PBEsol inversion temperature from α- to ß-spodumene predicted to occur at 1070 K.

Integration of Wet and Dry Bench Processes Optimizes Targeted Next-generation Sequencing of Low-quality and Low-quantity Tumor Biopsies.

All next-generation sequencing (NGS) procedures include assays performed at the laboratory bench ("wet bench") and data analyses conducted using bioinformatics pipelines ("dry bench"). Both elements are essential to produce accurate and reliable results, which are particularly critical for clinical laboratories. Targeted NGS technologies have increasingly found favor in oncology applications to help advance precision medicine objectives, yet the methods often involve disconnected and variable wet and dry bench workflows and uncoordinated reagent sets. In this report, we describe a method for sequencing challenging cancer specimens with a 21-gene panel as an example of a comprehensive targeted NGS system. The system integrates functional DNA quantification and qualification, single-tube multiplexed PCR enrichment, and library purification and normalization using analytically-verified, single-source reagents with a standalone bioinformatics suite. As a result, accurate variant calls from low-quality and low-quantity formalin-fixed, paraffin-embedded (FFPE) and fine-needle aspiration (FNA) tumor biopsies can be achieved. The method can routinely assess cancer-associated variants from an input of 400 amplifiable DNA copies, and is modular in design to accommodate new gene content. Two different types of analytically-defined controls provide quality assurance and help safeguard call accuracy with clinically-relevant samples. A flexible "tag" PCR step embeds platform-specific adaptors and index codes to allow sample barcoding and compatibility with common benchtop NGS instruments. Importantly, the protocol is streamlined and can produce 24 sequence-ready libraries in a single day. Finally, the approach links wet and dry bench processes by incorporating pre-analytical sample quality control results directly into the variant calling algorithms to improve mutation detection accuracy and differentiate false-negative and indeterminate calls. This targeted NGS method uses advances in both wetware and software to achieve high-depth, multiplexed sequencing and sensitive analysis of heterogeneous cancer samples for diagnostic applications.

Computational Analysis Reveals a Key Regulator of Cryptococcal Virulence and Determinant of Host Response.

UNLABELLED: Cryptococcus neoformans is a ubiquitous, opportunistic fungal pathogen that kills over 600,000 people annually. Here, we report integrated computational and experimental investigations of the role and mechanisms of transcriptional regulation in cryptococcal infection. Major cryptococcal virulence traits include melanin production and the development of a large polysaccharide capsule upon host entry; shed capsule polysaccharides also impair host defenses. We found that both transcription and translation are required for capsule growth and that Usv101 is a master regulator of pathogenesis, regulating melanin production, capsule growth, and capsule shedding. It does this by directly regulating genes encoding glycoactive enzymes and genes encoding three other transcription factors that are essential for capsule growth: GAT201, RIM101, and SP1. Murine infection with cryptococci lacking Usv101 significantly alters the kinetics and pathogenesis of disease, with extended survival and, unexpectedly, death by pneumonia rather than meningitis. Our approaches and findings will inform studies of other pathogenic microbes. IMPORTANCE: Cryptococcus neoformans causes fatal meningitis in immunocompromised individuals, mainly HIV positive, killing over 600,000 each year. A unique feature of this yeast, which makes it particularly virulent, is its polysaccharide capsule; this structure impedes host efforts to combat infection. Capsule size and structure respond to environmental conditions, such as those encountered in an infected host. We have combined computational and experimental tools to elucidate capsule regulation, which we show primarily occurs at the transcriptional level. We also demonstrate that loss of a novel transcription factor alters virulence factor expression and host cell interactions, changing the lethal condition from meningitis to pneumonia with an exacerbated host response. We further demonstrate the relevant targets of regulation and kinetically map key regulatory and host interactions. Our work elucidates mechanisms of capsule regulation, provides methods and resources to the research community, and demonstrates an altered pathogenic outcome that resembles some human conditions.

Site Isolation Leads to Stable Photocatalytic Reduction of CO2 over a Rhenium-Based Catalyst.

A porous organic polymer incorporating [(α-diimine)Re(CO)3Cl] moieties was produced and tested in the photocatalytic reduction of CO2, with NEt3 as a sacrificial donor. The catalyst generated both H2 and CO, although the Re moiety was not required for H2 generation. After an induction period, the Re-containing porous organic polymer produced CO at a stable rate, unless soluble [(bpy)Re(CO)3Cl] (bpy=2,2'-bipyridine) was added. This provides the strongest evidence to date that [(α-diimine)Re(CO)3Cl] catalysts for photocatalytic CO2 reduction decompose through a bimetallic pathway.

Model-driven mapping of transcriptional networks reveals the circuitry and dynamics of virulence regulation.

Key steps in understanding a biological process include identifying genes that are involved and determining how they are regulated. We developed a novel method for identifying transcription factors (TFs) involved in a specific process and used it to map regulation of the key virulence factor of a deadly fungus-its capsule. The map, built from expression profiles of 41 TF mutants, includes 20 TFs not previously known to regulate virulence attributes. It also reveals a hierarchy comprising executive, midlevel, and "foreman" TFs. When grouped by temporal expression pattern, these TFs explain much of the transcriptional dynamics of capsule induction. Phenotypic analysis of TF deletion mutants revealed complex relationships among virulence factors and virulence in mice. These resources and analyses provide the first integrated, systems-level view of capsule regulation and biosynthesis. Our methods dramatically improve the efficiency with which transcriptional networks can be analyzed, making genomic approaches accessible to laboratories focused on specific physiological processes.

Gaps in Medical and Device Therapy for Patients with Left Ventricular Systolic Dysfunction: The EchoGap Study.

OBJECTIVES: To assess gaps between guidelines and medicine prescription/dosing and referral for defibrillator therapy in patients with left ventricular systolic dysfunction (LVSD). METHODS: Outpatient echocardiography reports at an academic hospital centre were screened and outpatients with LVEF<40% were included. A questionnaire was mailed to the patients' physician, querying prescription/dosing of ACE-inhibitors (ACEi), angiotensin receptor blockers (ARB) and beta-blockers (BB). Patients with LVEF<30% had additional questions on implantable cardiac defibrillator (ICD) referral. RESULTS: Mean age was 69.6+/-12.2 years and mean LVEF was 29.7+/-6.5%. ACEi and/or ARB prescription rate was 260/309(84.1%) versus 256/308(83.1%) for BB (p=NS for comparison). Of patients on ACEi, 77/183(42.1%) were on target dose, compared to 7/45(15.5%) for ARB and 9/254(3.5%) for BB (p<0.01). Of 171/309 patients (55.3%) with LVEF<30%, 72/171(42.1%) had an ICD and 16/171(9.4%) were referred for one. CONCLUSION: Prescription rates of evidence-based HF medicines are relatively high in outpatients with LVSD referred for echocardiography at this Canadian academic medical centre; however, the proportion of patients at target doses was modest for ACEi and low for ARB and BB. Approximately half of patients who qualify for ICD by EF alone have one or were referred. Important reasons for patients with LVSD not on evidence-based therapy were identified.

Hydrogen from formic acid through its selective disproportionation over sodium germanate--a non-transition-metal catalysis system.

A robust catalyst for the selective dehydrogenation of formic acid to liberate hydrogen gas has been designed computationally, and also successfully demonstrated experimentally. This is the first such catalyst not based on transition metals, and it exhibits very encouraging performance. It represents an important step towards the use of renewable formic acid as a hydrogen-storage and transport vector in fuel and energy applications.