Prediction of line shape parameters and their temperature dependences for CO2-N2 using molecular dynamics simulations.

We show in this paper that requantized classical molecular dynamics simulations (rCMDSs) are capable of predicting various refined spectral-shape parameters of absorption lines of CO2 broadened by N2 with high precision. Combining CMDSs and a requantization procedure, we computed the auto-correlation function of the CO2 dipole moment responsible for the absorption transition. Its Fourier-Laplace transform directly yields the spectrum. Calculations were made for two temperatures, 200 and 296 K, at 1 atm and for a large range of Doppler widths, from the near-Doppler to the collision-dominant regimes. For each temperature and each line, the spectra calculated for various Doppler widths were simultaneously fit with the Hartmann-Tran (HT) profile. This refined profile, which takes into account the effects of the speed dependent collisional line broadening, the Dicke narrowing, and the collisional line mixing, was recommended as a reference model to be used in high-resolution spectroscopy (instead of the simplified Voigt model). The HT parameters retrieved from the rCMDS-calculated spectra were then directly compared with those deduced from high-precision measurements [J. S. Wilzewski et al., J. Quant. Spectrosc. Radiat. Transfer 206, 296-305 (2018)]. The results show a very good agreement, even for those parameters whose influence on the spectra is very small. Good agreement is also obtained between measured and predicted temperature dependences of these parameters. This demonstrates that rCMDS is an excellent tool, highly competitive with respect to high quality measurements for precise line-shape studies.

The effects of transboundary air pollution following major events in China on air quality in the U.S.: Evidence from Chinese New Year and sandstorms.

Transboundary air pollution is a global environmental and public health problem including in the U.S., where pollution emissions from China, the largest emitter of anthropogenic air pollution in the world, can travel across the Pacific Ocean and reach places like California and Oregon. We examine the effects of transboundary air pollution following major events in China, specifically sandstorms, a natural-occurring source of air pollution, and Chinese New Year, a major 7-day holiday, on background air quality in the U.S. We focus on high elevation sites on the west coast between 2000 and 2013. We use regression analysis and a natural experiment to exploit the variation in the timing of these events in China, which are plausibly uncorrelated to other factors that affect air quality in China and the U.S. We find that sandstorms are associated with statistically significant increases in background coarse and fine particulate matter (PM) in the U.S., representing between 16 and 39% of average weekly PM levels. We also find Chinese New Year is associated with modest reductions in background air quality in the U.S., representing between 0.4 and 2.5% of PM levels. Findings are robust to different models and falsification tests. These results suggest that regression analysis could be a powerful tool to complement other, more widely used techniques in the environmental sciences that study this problem. This also has important implications for policymakers, who could track major sandstorms in China and prepare for possible increased foreign pollution emissions in the U.S.

Why participation matters for air quality studies: risk perceptions, understandings of air pollution and mobilization in a poor neighborhood in Nairobi, Kenya.

OBJECTIVES: With high urbanization rates, Sub-Saharan Africa is facing growing problems of poor air quality in its cities. We make a case for participatory approaches in air quality studies especially including those living in poor neighborhoods who may be particularly at risk from this trend. STUDY DESIGN: We used collaboration with a community based organization, interviews, focus group discussions and a community forum. METHODS: We conducted a pilot study to assess health risk perceptions of air pollution for civic-minded residents in Mathare, an informal settlement in Nairobi, Kenya. Simultaneously, we involved Mathare residents in measuring levels of PM2.5 and later presented these data at a community forum with the participants of the monitoring study and the focus group discussions. RESULTS: We found that participation in conducting and interpreting air quality studies helped residents improve their understanding of air pollution and also helped them develop responses to it. Initially, participants associated air pollution with a bad odor or discomfort rather than their health, but once the connection to health was made through participation, they sought more information about air quality data and its hazards. Some residents also came up with strategies for coping with their environment and its risks. CONCLUSIONS: These results point to the potential of including participation in air quality monitoring as a way to increase awareness and support local action to address it. Discussion and sharing of results at the local level as well as at a wider policy level will be critical for advocacy to improve air quality.

Safety, tolerability, pharmacokinetics and pharmacodynamics of AZP-531, a first-in-class analogue of unacylated ghrelin, in healthy and overweight/obese subjects and subjects with type 2 diabetes.

AIM: To explore the safety, pharmacokinetics and pharmacodynamics in humans of the unacylated ghrelin analogue AZP-531, designed to improve glycaemic control and reduce weight. METHODS: Assessments, including glucose measurements, were performed in a three-part randomized study. In Part A, healthy subjects [n = 44, age 18-50 years, body mass index (BMI) 20-28 kg/m(2) ] received a single subcutaneous dose of 0.3, 3, 15, 30, 60 or 120 µg/kg AZP-531 or placebo. In Part B, overweight/obese subjects (n = 32, age 18-65 years, BMI 28-38 kg/m(2) ) and in Part C, patients with type 2 diabetes [T2D; n = 36, age 18-65 years, BMI 20-40 kg/m(2) , glycated haemoglobin (HbA1c) 7-10%] received AZP-531 or placebo for 14 days (daily doses of 3, 15, 30 or 60 µg/kg and 15, 2 × 30 or 60 µg/kg, respectively). RESULTS: AZP-531 was well tolerated. Single- and multiple-dose pharmokinetic variables were similar. Maximum AZP-531 concentrations were typically reached at 1 h post-dose. Observed maximum concentration (Cmax ) and area under the curve were dose-proportional. The mean terminal half-life (t1/2 ) was 2-3 h. In Part B, AZP-531 doses of ≥15 µg/kg significantly improved glucose concentrations, without increasing insulin levels, suggesting an insulin-sensitizing effect. AZP-531 decreased mean body weight by 2.6 kg (vs 0.8 kg for placebo). In Part C, glucose variables improved in all groups, including placebo, suggesting a study effect in uncontrolled patients at baseline. Notwithstanding, AZP-531 60 µg/kg reduced HbA1c by 0.4% (vs 0.2% for placebo) and body weight by 2.1 kg (vs 1.3 kg for placebo). CONCLUSIONS: AZP-531 was well tolerated in this first-in-human study. Its pharmacokinetic profile, suitable for once-daily dosing, and metabolic effects support further clinical development for T2D.

Structural essentials for ß-N-acetylhexosaminidase inhibition by amides of prolines, pipecolic and azetidine carboxylic acids.

This paper explores the computer modelling aided design and synthesis of ß-N-acetylhexosaminidase inhibitors along with their applicability to human disease treatment through biological evaluation in both an enzymatic and cellular setting. We investigated the importance of individual stereocenters, variations in structure-activity relationships along with factors influencing cell penetration. To achieve these goals we modified nitrogen heterocycles in terms of ring size, side chains present and ring nitrogen derivatization. By reducing the inhibitor interactions with the active site down to the essentials we were able to determine that besides the established 2S,3R trans-relationship, the presence and stereochemistry of the CH2OH side chain is of crucial importance for activity. In terms of cellular penetration, N-butyl side chains favour cellar uptake, while hydroxy- and carboxy-group bearing sidechains on the ring nitrogen retarded cellular penetration. Furthermore we show an early proof of principle study that ß-N-acetylhexosaminidase inhibitors can be applicable to use in a potential anti-invasive anti-cancer strategy.

Human plasmacytoid dendritic cells sense lymphocytic choriomeningitis virus-infected cells in vitro.

We previously reported that exosomal transfer of hepatitis C virus (HCV) positive-strand RNA from human Huh-7 hepatoma cells to human plasmacytoid dendritic cells (pDCs) triggers pDC alpha/beta interferon (IFN-α/ß) production in a Toll-like receptor 7 (TLR7)-dependent, virus-independent manner. Here we show that human pDCs are also activated by a TLR7-dependent, virus-independent, exosomal RNA transfer mechanism by human and mouse hepatoma and nonhepatoma cells that replicate the negative-strand lymphocytic choriomeningitis virus (LCMV).

An expression signature of the angiogenic response in gastrointestinal neuroendocrine tumours: correlation with tumour phenotype and survival outcomes.

BACKGROUND: Gastroenteropancreatic neuroendocrine tumours (GEP-NETs) are heterogeneous with respect to biological behaviour and prognosis. As angiogenesis is a renowned pathogenic hallmark as well as a therapeutic target, we aimed to investigate the prognostic and clinico-pathological role of tissue markers of hypoxia and angiogenesis in GEP-NETs. METHODS: Tissue microarray (TMA) blocks were constructed with 86 tumours diagnosed from 1988 to 2010. Tissue microarray sections were immunostained for hypoxia inducible factor 1α (Hif-1α), vascular endothelial growth factor-A (VEGF-A), carbonic anhydrase IX (Ca-IX) and somatostatin receptors (SSTR) 1-5, Ki-67 and CD31. Biomarker expression was correlated with clinico-pathological variables and tested for survival prediction using Kaplan-Meier and Cox regression methods. RESULTS: Eighty-six consecutive cases were included: 51% male, median age 51 (range 16-82), 68% presenting with a pancreatic primary, 95% well differentiated, 51% metastatic. Higher grading (P=0.03), advanced stage (P<0.001), high Hif-1α and low SSTR-2 expression (P=0.03) predicted for shorter overall survival (OS) on univariate analyses. Stage, SSTR-2 and Hif-1α expression were confirmed as multivariate predictors of OS. Median OS for patients with SSTR-2+/Hif-1α-tumours was not reached after median follow up of 8.8 years, whereas SSTR-2-/Hif-1α+ GEP-NETs had a median survival of only 4.2 years (P=0.006). CONCLUSION: We have identified a coherent expression signature by immunohistochemistry that can be used for patient stratification and to optimise treatment decisions in GEP-NETs independently from stage and grading. Tumours with preserved SSTR-2 and low Hif-1α expression have an indolent phenotype and may be offered less aggressive management and less stringent follow up.

Immunohistochemical markers of the hypoxic response can identify malignancy in phaeochromocytomas and paragangliomas and optimize the detection of tumours with VHL germline mutations.

BACKGROUND: There are no reliable markers of malignancy in phaeochromocytomas (PCC) and paragangliomas (PGL). We investigated the relevance of the mammalian target of rapamycin (mTOR)/AKT and hypoxic pathways as novel immunohistochemical markers of malignancy. METHODS: Tissue microarray blocks were constructed with a total of 100 tumours (10 metastatic) and 20 normal adrenomedullary samples. Sections were immunostained for hypoxia-inducible factor 1α (Hif-1α), vascular endothelial growth factor A (VEGF-A), mTOR, carbonic anhydrase IX (CaIX) and AKT. The predictive performance of these markers was studied using univariate, multivariate and receiver operating characteristic analyses. RESULTS: In all, 100 consecutive patients, 64% PCC, 29% familial with a median tumour size of 4.7 cm (range 1-14) were included. Univariate analyses showed Hif-1α overexpression, tumour necrosis, size >5 cm, capsular and vascular invasion to be predictors of metastasis. In multivariate analysis, Hif-1α, necrosis and vascular invasion remained as independent predictors of metastasis. Hif-1α was the most discriminatory biomarker for the presence of metastatic diffusion. Strong membranous CaIX expression was seen in von Hippel-Lindau (VHL) PCC as opposed to other subtypes. CONCLUSION: Lack of vascular invasion, tumour necrosis and low Hif-1α expression identify tumours with lower risk of malignancy. We propose membranous CaIX expression as a potential marker for VHL disease in patients presenting with PCC.

Velocity effects on the shape of pure H2O isolated lines: complementary tests of the partially correlated speed-dependent Keilson-Storer model.

Complementary tests of the partially correlated speed-dependent Keilson-Storer (pCSDKS) model for the shape of isolated transition of pure water vapor [N. H. Ngo et al., J. Chem. Phys. 136, 154310 (2012)] are made using new measurements. The latter have been recorded using a high sensitivity cavity ring down spectrometer, for seven self-broadened H(2)O lines in the 1.6 µm region at room temperature and for pressures from 0.5 to 15 Torr. Furthermore, the H(2) (18)O spectra of [M. D. De Vizia et al., Phys. Rev. A 83, 052506 (2011)] in the 1.38 µm region, measured at 273.15 K and for pressures from 0.3 to 3.75 Torr have also been used for comparison with the model. Recall that the pCSDKS model takes into account the collision-induced velocity changes, the speed dependences of the broadening and shifting coefficients as well as the partial correlation between velocity and rotational-state changes. All parameters of the model have been fixed at values previously determined, except for a scaling factor applied to the input speed-dependent line broadening. Comparisons between predictions and experiments have been made by looking at the results obtained when fitting the calculated and measured spectra by Voigt profiles. The good agreement obtained for all considered lines, at different temperature and pressure conditions, confirms the consistency and the robustness of the model. Limiting cases of the model have been then derived, showing the influence of different contributions to the line shape.

A pure H2O isolated line-shape model based on classical molecular dynamics simulations of velocity changes and semi-classical calculations of speed-dependent collisional parameters.

It is well known that the Voigt profile does not well describe the (measured) shapes of isolated lines. This is due to the neglect of the intermolecular collision-induced velocity changes and of the speed dependence of the collisional parameters. In this paper, we present a new line profile model for pure H(2)O which takes both of these effects into account. The speed dependence of the collisional parameters has been calculated by a semi-classical method. The velocity changes have been modeled by using the Keilson-Storer collision kernel with two characteristic parameters. The latter have been deduced from classical molecular dynamics simulations which also indicate that, for pure H(2)O, the correlation between velocity-changing and state-changing collisions is not negligible, a result confirmed by the analysis of measured spectra. A partially correlated speed-dependent Keilson-Storer model has thus been adopted to describe the line-shape. Comparisons between simulated spectra and measurements for four self-broadened lines in the near-infrared at various pressures show excellent agreements.

Influence of velocity effects on the shape of N2 (and air) broadened H2O lines revisited with classical molecular dynamics simulations.

The modeling of the shape of H(2)O lines perturbed by N(2) (and air) using the Keilson-Storer (KS) kernel for collision-induced velocity changes is revisited with classical molecular dynamics simulations (CMDS). The latter have been performed for a large number of molecules starting from intermolecular-potential surfaces. Contrary to the assumption made in a previous study [H. Tran, D. Bermejo, J.-L. Domenech, P. Joubert, R. R. Gamache, and J.-M. Hartmann, J. Quant. Spectrosc. Radiat. Transf. 108, 126 (2007)], the results of these CMDS show that the velocity-orientation and -modulus changes statistically occur at the same time scale. This validates the use of a single memory parameter in the Keilson-Storer kernel to describe both the velocity-orientation and -modulus changes. The CMDS results also show that velocity- and rotational state-changing collisions are statistically partially correlated. A partially correlated speed-dependent Keilson-Storer model has thus been used to describe the line-shape. For this, the velocity changes KS kernel parameters have been directly determined from CMDS, while the speed-dependent broadening and shifting coefficients have been calculated with a semi-classical approach. Comparisons between calculated spectra and measurements of several lines of H(2)O broadened by N(2) (and air) in the ν(3) and 2ν(1) + ν(2) + ν(3) bands for a wide range of pressure show very satisfactory agreement. The evolution of non-Voigt effects from Doppler to collisional regimes is also presented and discussed.

Weak anti-HIV CD8(+) T-cell effector activity in HIV primary infection.

HIV-specific CD8(+) T cells play a major role in the control of virus during HIV primary infection (PI) but do not completely prevent viral replication. We used IFN-gamma enzyme-linked immunospot assay and intracellular staining to characterize the ex vivo CD8(+) T-cell responses to a large variety of HIV epitopic peptides in 24 subjects with early HIV PI. We observed HIV-specific responses in 71% of subjects. Gag and Nef peptides were more frequently recognized than Env and Pol peptides. The number of peptides recognized was low (median 2, range 0-6). In contrast, a much broader response was observed in 30 asymptomatic subjects with chronic infection: all were responders with a median of 5 peptides recognized (range 1-13). The frequency of HIV-specific CD8(+) T cells among PBMC for a given peptide was of the same order of magnitude in both groups. The proportion of HIV-specific CD8(+)CD28(-) terminally differentiated T cells was much lower in PI than at the chronic stage of infection. The weakness of the immune response during HIV PI could partially account for the failure to control HIV. These findings have potential importance for defining immunotherapeutic strategies and establishing the goals for effective vaccination.

Single-Cell Profiling of an In Vitro Model of Human Interneuron Development Reveals Temporal Dynamics of Cell Type Production and Maturation.

GABAergic interneurons are essential for neural circuit function, and their loss or dysfunction is implicated in human neuropsychiatric disease. In vitro methods for interneuron generation hold promise for studying human cellular and functional properties and, ultimately, for therapeutic cell replacement. Here we describe a protocol for generating cortical interneurons from hESCs and analyze the properties and maturation time course of cell types using single-cell RNA-seq. We find that the cell types produced mimic in vivo temporal patterns of neuron and glial production, with immature progenitors and neurons observed early and mature cortical neurons and glial cell types produced late. By comparing the transcriptomes of immature interneurons to those of more mature neurons, we identified genes important for human interneuron differentiation. Many of these genes were previously implicated in neurodevelopmental and neuropsychiatric disorders.

A Single-Cell Roadmap of Lineage Bifurcation in Human ESC Models of Embryonic Brain Development.

During human brain development, multiple signaling pathways generate diverse cell types with varied regional identities. Here, we integrate single-cell RNA sequencing and clonal analyses to reveal lineage trees and molecular signals underlying early forebrain and mid/hindbrain cell differentiation from human embryonic stem cells (hESCs). Clustering single-cell transcriptomic data identified 41 distinct populations of progenitor, neuronal, and non-neural cells across our differentiation time course. Comparisons with primary mouse and human gene expression data demonstrated rostral and caudal progenitor and neuronal identities from early brain development. Bayesian analyses inferred a unified cell-type lineage tree that bifurcates between cortical and mid/hindbrain cell types. Two methods of clonal analyses confirmed these findings and further revealed the importance of Wnt/ß-catenin signaling in controlling this lineage decision. Together, these findings provide a rich transcriptome-based lineage map for studying human brain development and modeling developmental disorders.

Down modulation of TNF-alpha mRNA placental expression by AZT used for the prevention of HIV-1 mother-to-child transmission.

Mechanisms of HIV-1 in utero mother-to-child transmission (MTCT) protection provided by AZT are not completely understood. The placental cytokine network is involved in the control of HIV-1 in utero transmission but the effect of AZT on this network is unknown. To evaluate the effects of AZT on placental cytokine expression, the chorionic villi from HIV-1 uninfected women term placentae were cultured with 0, 100, and 2,000 ng/ml AZT. Tissue fragments were harvested at days 1, 4, and 7 to determine the level of cytokine mRNA by real-time RT-PCR. The viability and morphology of the placental histocultures were monitored by the expression of beta-human chorionic gonadotropin (beta-hCG) gene, lipopolysaccharide (LPS) activation, and microscopic examination. AZT at 2,000 ng/ml significantly down-regulated TNF-alpha mRNA expression at day 1 and day 4, but had no effect on beta-hCG, stromal cell-derived factor 1 (SDF-1), and IL-10 gene expression. AZT did not induce any deleterious impact on placental tissue structure. Furthermore, activation of chorionic villi by LPS for 24 h up-regulated IL-10 and TNF-alpha mRNA expression. Down-regulation of TNF-alpha mRNA could represent a mechanism through which AZT can decrease the risk of HIV-1 MTCT, in addition to its direct effect on HIV-1 replication.

Multiwavelength Raman fiber laser with a continuously-tunable spacing.

A spacing-tunable multiwavelength Raman fiber laser with an independently-adjustable channel number is proposed and demonstrated. It uses a novel free-spectral-range (FSR)-tunable comb filter based on a superimposed chirped-fiber Bragg grating (CFBG) and a linear cavity formed by a bandwidth-tunable CFBG reflector, a pumped highly-nonlinear fiber for Raman gain, and an optical circulator based loop mirror. Multiwavelength laser operations with spacing tuning from 0.3 to 0.6 nm and channel number adjustment from 2 to 10 have been achieved.

Optical functions of (x)GeO2:(1-x)SiO2 films determined by multi-sample and multi-angle spectroscopic ellipsometry.

Thin films of (x)GeO2:(1-x)SiO2, 0

No evidence for proliferation in the blood CD4+ T-cell pool during HIV-1 infection and triple combination therapy.

OBJECTIVE: To evaluate the role of cell proliferation in peripheral blood lymphocyte (PBL) dynamics during HIV infection and potent antiretroviral therapy including protease inhibitors. DESIGN: Transverse study of 150 patients at different stages of infection. Longitudinal study of 50 patients on triple combination antiretroviral therapy with 9-month follow-up. METHODS: Ex vivo incubation of fresh PBL with the DNA biosynthetic marker bromodeoxyuridine (BrdU). Flow cytometric analysis of cell phenotypes and BrdU incorporation. Parallel determination of plasma virus load and CD4+ cell counts. RESULTS: Percentages of BrdU+ B and T lymphocytes found in patients with asymptomatic HIV infection were not different from the low values found in HIV-seronegative controls, and were not correlated with the CD4+ cell count. DNA synthesis increased significantly only during acute opportunistic infections occurring in patients with high plasma viral load and fewer than 100 x 10(6) CD4+ cells/l. Triple combination therapy induced a decrease of plasma virus load and a rise of CD4+ cell counts, whereas BrdU incorporation remained low or decreased. CONCLUSION: Proliferation of peripheral blood T cells observed at late stages of HIV infection corresponds to a response to opportunistic infections. Apart from these particular cases, proliferation in this compartment does not appear as a critical parameter of CD4+ cell kinetics during chronic HIV infection and potent therapy.

Fast Hankel transform and its application for studying the propagation of cylindrical electromagnetic fields.

We present a fast Hankel transform (FHTn) method for direct numerical evaluation of electromagnetic (EM) field propagation through an axially symmetric system. Comparing with the vector-based plane-wave spectrum (VPWS) method, we present an alternative approach to implement the fast Hankel transform which does not require an additional coordinate transformation for Fourier transform. The proposed FHTn method is an efficient approach for numerical evaluation of an arbitrary integer order of the Hankel transform (HT). As an example to demonstrate the effectiveness of the proposed method, we apply the FHTn technique to the analysis of cylindrical EM field propagation through a diffractive microlens.

Cost-effective fabrication of microlenses on hybrid sol-gel glass with a high-energy beam-sensitive gray-scale mask.

A negative-tone inorganic-organic hybrid SiO(2):TiO(2) glass is investigated for fabrication of refractive microlenses. This sol-gel material enjoys an advantage over materials used in conventional photoresist-based fabrication techniques in that it lends itself to a single-step etching-free process. The application of a high-energy beam-sensitive (HEBS) mask provides a reliable and simple method for fabrication of three-dimensional micro-optical elements with a single UV exposure. The technique of using the sol-gel material with the HEBS gray-scale mask has considerable potential for low-cost mass production of continuous-phase-level diffractive optical elements and micro-optical structures.