Simulations of the infrared, Raman, and 2D-IR photon echo spectra of water in nanoscale silica pores

Vibrational spectroscopy is frequently used to characterize nanoconfined liquids and probe the effect of the confining framework on the liquid structure and dynamics relative to the corresponding bulk fluid. However, it is still unclear what molecular-level information can be obtained from such measurements. In this paper, we address this question by using molecular dynamics (MD) simulations to reproduce the linear infrared (IR), Raman, and two-dimensional IR (2D-IR) photon echo spectra for water confined within hydrophilic (hydroxyl-terminated) silica mesopores. To simplify the spectra the OH stretching region of isotopically dilute HOD in D2O is considered. An empirical mapping approach is used to obtain the OH vibrational frequencies, transition dipoles, and transition polarizabilities from the MD simulations. The simulated linear IR and Raman spectra are in good general agreement with measured spectra of water in mesoporous silica reported in the literature. The key effect of confinement on the water spectrum is a vibrational blueshift for OH groups that are closest to the pore interface. The blueshift can be attributed to the weaker hydrogen bonds (H-bonds) formed between the OH groups and silica oxygen acceptors. Non-Condon effects greatly diminish the contribution of these OH moieties to the linear IR spectrum, but these weaker H-bonds are readily apparent in the Raman spectrum. The 2D-IR spectra have not yet been measured and thus the present results represent a prediction. The simulated spectra indicates that it should be possible to probe the slower spectral diffusion of confined water compared to the bulk liquid by analysis of the 2D-IR spectra

Meta-analyses of chemotherapy for locally advanced and metastatic pancreatic cancer: results of secondary end points analyses

In advanced pancreatic cancer, level one evidence has established a significant survival advantage with chemotherapy, compared to best supportive care. The treatment-associated toxicity needs to be evaluated. This study examines the secondary outcome measures for chemotherapy in advanced pancreatic cancer using meta-analyses. A systematic review was undertaken employing Cochrane methodology, with search of databases, conference proceedings and trial registers. The secondary end points were progression-free survival (PFS)/time to progression (TTP) (summarised using the hazard ratio (HR)), response rate and toxicity (summarised using relative risk). There was no significant advantage of 5FU combinations vs 5FU alone for TTP (HR=1.02; 95% CI=0.85–1.23) and toxicity. Progression-free survival (HR 0.78; CI 0.70–0.88), TTP (HR=0.85; 95% CI=0.72–0.99) and overall response rate (RR=0.56; 95% CI=0.46–0.68) were significantly better for gemcitabine combination chemotherapy, but offset by the greater grade 3/4 toxicity thrombocytopenia (RR=1.94; 95% CI=1.32–2.84), leucopenia (RR=1.46; 95% CI=1.15–1.86), neutropenia (RR=1.48; 95% CI=1.07–2.05), nausea (RR=1.77; 95% CI=1.37–2.29), vomiting (RR=1.64; 95% CI=1.24–2.16) and diarrhoea (RR=2.73; 95% CI=1.87–3.98). There is no significant advantage on secondary end point analyses for administering 5FU in combination over 5FU alone. There is improved PFS/TTP and response rate, with gemcitabine-based combinations, although this comes with greater toxicity

Strategies to Integrate Genomic Medicine into Clinical Care: Evidence from the IGNITE Network

The complexity of genomic medicine can be streamlined by implementing some form of clinical decision support (CDS) to guide clinicians in how to use and interpret personalized data; however, it is not yet clear which strategies are best suited for this purpose. In this study, we used implementation science to identify common strategies for applying provider-based CDS interventions across six genomic medicine clinical research projects funded by an NIH consortium. Each project’s strategies were elicited via a structured survey derived from a typology of implementation strategies, the Expert Recommendations for Implementing Change (ERIC), and follow-up interviews guided by both implementation strategy reporting criteria and a planning framework, RE-AIM, to obtain more detail about implementation strategies and desired outcomes. We found that, on average, the three pharmacogenomics implementation projects used more strategies than the disease-focused projects. Overall, projects had four implementation strategies in common; however, operationalization of each differed in accordance with each study’s implementation outcomes. These four common strategies may be important for precision medicine program implementation, and pharmacogenomics may require more integration into clinical care. Understanding how and why these strategies were successfully employed could be useful for others implementing genomic or precision medicine programs in different contexts

The Light Responsive Transcriptome of the Zebrafish: Function and Regulation

Most organisms possess circadian clocks that are able to anticipate the day/night cycle and are reset or “entrained” by the ambient light. In the zebrafish, many organs and even cultured cell lines are directly light responsive, allowing for direct entrainment of the clock by light. Here, we have characterized light induced gene transcription in the zebrafish at several organizational levels. Larvae, heart organ cultures and cell cultures were exposed to 1- or 3-hour light pulses, and changes in gene expression were compared with controls kept in the dark. We identified 117 light regulated genes, with the majority being induced and some repressed by light. Cluster analysis groups the genes into five major classes that show regulation at all levels of organization or in different subset combinations. The regulated genes cover a variety of functions, and the analysis of gene ontology categories reveals an enrichment of genes involved in circadian rhythms, stress response and DNA repair, consistent with the exposure to visible wavelengths of light priming cells for UV-induced damage repair. Promoter analysis of the induced genes shows an enrichment of various short sequence motifs, including E- and D-box enhancers that have previously been implicated in light regulation of the zebrafish period2 gene. Heterologous reporter constructs with sequences matching these motifs reveal light regulation of D-box elements in both cells and larvae. Morpholino-mediated knock-down studies of two homologues of the D-box binding factor Tef indicate that these are differentially involved in the cell autonomous light induction in a gene-specific manner. These findings suggest that the mechanisms involved in period2 regulation might represent a more general pathway leading to light induced gene expression

Total and CO-reactive heme content of actinorhizal nodules and the roots of some non-nodulated plants

The concentration of total and CO-reactive heme was measured in actinorhizal nodules from six different genera. This gave the upper limit to hemoglobin concentration in these nodules. Quantitative extraction of CO-reactive heme was achieved under anaerobic conditions in a buffer equilibrated with CO and containing Triton X-100. The concentration of CO-reactive heme in nodules of Casuarina and Myrica was approximately half of that found in legume nodules, whereas in Comptonia, Alnus and Ceanothus the concentrations of heme were about 10 times lower than in legume nodules. There was no detectable CO-reactive heme in Datisca nodules, but low concentrations were detected in roots of all non-nodulating plants examined, including Zea mays . Difference spectra of CO treated minus dithionite-reduced extracts displayed similar wavelengths of maximal and minimal light absorption for all extracts, and were consistent with those of a hemoglobin. The concentration of CO-reactive heme was not correlated to the degree to which CO inhibited nitrogenase activity nor was it affected by reducing the oxygen concentration in the rooting zone. However, there was a positive correlation between heme concentration and suberization or lignification of the walls of infected host cells. These observations demonstrate that, unlike legume nodules, high concentrations of heme or hemoglobin are not needed for active nitrogen fixation in most actinorhizal nodules. Nonetheless, a significant amount of CO-reactive heme is found in the nodules of Alnus, Comptonia, and Ceanothus, and in the roots of Zea mays . The identity and function of this heme is unknown.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/43460/1/11104_2006_Article_BF02370943.pd

Establishing the value of genomics in medicine: the IGNITE Pragmatic Trials Network.

PURPOSE: A critical gap in the adoption of genomic medicine into medical practice is the need for the rigorous evaluation of the utility of genomic medicine interventions. METHODS: The Implementing Genomics in Practice Pragmatic Trials Network (IGNITE PTN) was formed in 2018 to measure the clinical utility and cost-effectiveness of genomic medicine interventions, to assess approaches for real-world application of genomic medicine in diverse clinical settings, and to produce generalizable knowledge on clinical trials using genomic interventions. Five clinical sites and a coordinating center evaluated trial proposals and developed working groups to enable their implementation. RESULTS: Two pragmatic clinical trials (PCTs) have been initiated, one evaluating genetic risk APOL1 variants in African Americans in the management of their hypertension, and the other to evaluate the use of pharmacogenetic testing for medications to manage acute and chronic pain as well as depression. CONCLUSION: IGNITE PTN is a network that carries out PCTs in genomic medicine; it is focused on diversity and inclusion of underrepresented minority trial participants; it uses electronic health records and clinical decision support to deliver the interventions. IGNITE PTN will develop the evidence to support (or oppose) the adoption of genomic medicine interventions by patients, providers, and payers

In the interest of food safety: a qualitative study investigating communication and trust between food regulators and food industry in the UK, Australia and New Zealand

Background Food regulatory bodies play an important role in public health, and in reducing the costs of food borne illness that are absorbed by both industry and government. Regulation in the food industry involves a relationship between regulators and members of the industry, and it is imperative that these relationships are built on trust. Research has shown in a variety of contexts that businesses find the most success when there are high levels of trust between them and their key stakeholders. An evidence-based understanding of the barriers to communication and trust is imperative if we are to put forward recommendations for facilitating the (re)building of trusting and communicative relationships. Methods We present data from 72 interviews with regulators and industry representatives regarding their trust in and communication with one another. Interviews were conducted in the UK, New Zealand, and Australia in 2013. Results Data identify a variety of factors that shape the dynamic and complex relationships between regulators and industry, as well as barriers to communication and trust between the two parties. Novel in our approach is our emphasis on identifying solutions to these barriers from the voices of industry and regulators. Conclusions We provide recommendations (e.g., development of industry advisory boards) to facilitate the (re)building of trusting and communicative relationships between the two parties