Monitoring carbohydrate 3D structure quality with the Privateer database.

The remediation of the carbohydrate data of the Protein Data Bank (PDB) has brought numerous enhancements to the findability and interpretability of deposited glycan structures, yet crucial quality indicators are either missing or hard to find on the PDB pages. Without a way to access wider glycochemical context, problematic structures may be taken as fact by keen but inexperienced scientists. The Privateer software is a validation and analysis tool that provides access to a number of metrics and links to external experimental resources, allowing users to evaluate structures using carbohydrate-specific methods. Here, we present the Privateer database, a free resource that aims to complement the growing glycan content of the PDB

Missing OH source in a suburban environment near Beijing: observed and modelled OH an HO2 concentrations in summer 2006

Measurements of ambient OH and HO₂ radicals were performed by laser induced fluorescence (LIF) during CAREBeijing2006 (Campaigns of Air Quality Research in Beijing and Surrounding Region 2006) at the suburban site Yufa in the south of Beijing in summer 2006. On most days, local air chemistry was influenced by aged air pollution that was advected by a slow, almost stagnant wind from southern regions. Observed daily maxima of OH and HO₂^* were in the range of (4–17) × 10⁶ cm^−3 and (2–24) × 10⁸ cm^−3, respectively. During daytime, OH reactivities were generally high (10–30 s^−1) and mainly contributed by VOCs and their oxidation products. The comparison of modelled and measured HO_x concentrations reveals a systematic underprediction of OH as a function of NO. A large discrepancy of a factor 2.6 is found at the lowest NO concentration encountered (0.1 ppb), whereas the discrepancy becomes insignificant above 1 ppb NO. This study extends similar observations from the Pearl-River Delta (PRD) in South China to a more urban environment. The OH discrepancy at Yufa can be resolved, if NO-independent additional OH recycling is assumed in the model. The postulated Leuven Isoprene Mechanism (LIM) has the potential to explain the gap between modelled and measured OH at Beijing taking into account conservative error estimates, but still lacks experimental confirmation. This and the hereby unresolved discrepancy at PRD suggest that other VOCs besides isoprene might be involved in the required, additional OH recycling. Fast primary production of RO_x radicals up to 7 ppb h^−1 was determined at Beijing which was dominated by the photolysis of O₃, HONO, HCHO, and dicarbonyls. For a special case, 20 August, when the plume of Beijing city was encountered, a missing primary HO_x source (≈ 3 ppb h^−1) was determined under high NO_x conditions similar to other urban areas like Mexico city. CAREBeijing2006 emphasizes the important role of OVOCs as a radical source and sink, and the need for further investigation of the chemical degradation of VOCs in order to better understand radical chemistry in VOC-rich air

Technical Note: Formal blind intercomparison of HO₂ measurements in the atmosphere simulation chamber SAPHIR during the HOxComp campaign

Hydroperoxy radical (HO₂) concentrations were measured during the formal blind intercomparison campaign HOxComp carried out in Jülich, Germany, in 2005. Three instruments detected HO₂ via chemical conversion to hydroxyl radicals (OH) and subsequent detection of the sum of OH and HO₂ by laser induced fluorescence (LIF). All instruments were based on the same detection and calibration scheme. Because measurements by a MIESR instrument failed during the campaign, no absolute reference measurement was available, so that the accuracy of individual instruments could not be addressed. Instruments sampled ambient air for three days and were attached to the atmosphere simulation chamber SAPHIR during the second part of the campaign. Six experiments of one day each were conducted in SAPHIR, where air masses are homogeneously mixed, in order to investigate the performance of instruments and to determine potential interferences of measurements under well-controlled conditions. Linear correlation coefficients (<i>R</i>²) between measurements of the LIF instruments are generally high and range from 0.82 to 0.98. However, the agreement between measurements is variable. The regression analysis of the entire data set of measurements in SAPHIR yields slopes between 0.69 to 1.26 and intercepts are smaller than typical atmospheric daytime concentrations (less than 1 pptv). The quality of fit parameters improves significantly, when data are grouped into data subsets of similar water vapor concentrations. Because measurements of LIF instruments were corrected for a well-characterized water dependence of their sensitivities, this indicates that an unknown factor related to water vapor affected measurements in SAPHIR. Measurements in ambient air are also well-correlated, but regression parameters differ from results obtained from SAPHIR experiments. This could have been caused by differences in HO₂ concentrations in the sampled air at the slightly different locations of instruments

Missing OH source in a suburban environment near Beijing: observed and modelled OH and HO2 concentrations in summer 2006

Measurements of ambient OH and HO2 radicals were performed by laser induced fluorescence (LIF) during CAREBeijing2006 (Campaigns of Air Quality Research in Beijing and Surrounding Region 2006) at the suburban site Yufa in the south of Beijing in summer 2006. On most days, local air chemistry was influenced by aged air pollution that was advected by a slow, almost stagnant wind from southern regions. Observed daily concentration maxima were in the range of (4–17) × 106 cm&minus;3 for OH and (2–24) × 108 cm&minus;3 for HO2 (including an estimated interference of 25% from RO2). During daytime, OH reactivities were generally high (10–30 s−1) and mainly contributed by observed VOCs and their calculated oxidation products. The comparison of modelled and measured HOx concentrations reveals a systematic underprediction of OH as a function of NO. A large discrepancy of a factor 2.6 is found at the lowest NO concentration encountered (0.1 ppb), whereas the discrepancy becomes insignificant above 1 ppb NO. This study extends similar observations from the Pearl-River Delta (PRD) in South China to a more urban environment. The OH discrepancy at Yufa can be resolved, if NO-independent additional OH recycling is assumed in the model. The postulated Leuven Isoprene Mechanism (LIM) has the potential to explain the gap between modelled and measured OH at Beijing taking into account conservative error estimates, but lacks experimental confirmation. This and the hereby unresolved discrepancy at PRD suggest that other VOCs besides isoprene might be involved in the required, additional OH recycling. Fast primary production of ROx radicals up to 7 ppb h&minus;1 was determined at Beijing which was dominated by the photolysis of O3, HONO, HCHO, and dicarbonyls. For a special case, 20 August, when the plume of Beijing city was encountered, a missing primary HOx source (about 3 ppb h&minus;1) was determined under high NOx conditions similar to other urban areas like Mexico City. CAREBeijing2006 emphasizes the important role of OVOCs as a radical source and sink, and the need for further investigation of the chemical degradation of VOCs in order to better understand radical chemistry in VOC-rich air

Exploring the atmospheric chemistry of nitrous acid (HONO) at a rural site in Southern China

We performed measurements of nitrous acid (HONO) during the PRIDE-PRD2006 campaign in the Pearl River Delta region 60 km north of Guangzhou, China, for 4 weeks in June 2006. HONO was measured by a LOPAP in-situ instrument which was setup in one of the campaign supersites along with a variety of instruments measuring hydroxyl radicals, trace gases, aerosols, and meteorological parameters. Maximum diurnal HONO mixing ratios of 1–5 ppb were observed during the nights. We found that the nighttime build-up of HONO can be attributed to the heterogeneous NO2 to HONO conversion on ground surfaces and the OH + NO reaction. In addition to elevated nighttime mixing ratios, measured noontime values of ≈200 ppt indicate the existence of a daytime source higher than the OH + NO→HONO reaction. Using the simultaneously recorded OH, NO, and HONO photolysis frequency, a daytime additional source strength of HONO (PM) was calculated to be 0.77 ppb h−1 on average. This value compares well to previous measurements in other environments. Our analysis of PM provides evidence that the photolysis of HNO3 adsorbed on ground surfaces contributes to the HONO formation

Online carbohydrate 3D structure validation with the Privateer web app

Owing to the difficulties associated with working with carbohydrates, validating glycan 3D structures prior to deposition into the Protein Data Bank has become a staple of the structure-solution pipeline. The Privateer software provides integrative methods for the validation, analysis, refinement and graphical representation of 3D atomic structures of glycans, both as ligands and as protein modifiers. While Privateer is free software, it requires users to install any of the structural biology software suites that support it or to build it from source code. Here, the Privateer web app is presented, which is always up to date and available to be used online (https://privateer.york.ac.uk) without installation. This self-updating tool, which runs locally on the user's machine, will allow structural biologists to simply and quickly analyse carbohydrate ligands and protein glycosylation from a web browser whilst retaining all confidential information on their devices

Sparse motion bases selection for human motion denoising

Human motion denoising is an indispensable step of data preprocessing for many motion data based applications. In this paper, we propose a data-driven based human motion denoising method that sparsely selects the most correlated subset of motion bases for clean motion reconstruction. Meanwhile, it takes the statistic property of two common noises, i.e., Gaussian noise and outliers, into account in deriving the objective functions. In particular, our method firstly divides each human pose into five partitions termed as poselets to gain a much fine-grained pose representation. Then, these poselets are reorganized into multiple overlapped poselet groups using a lagged window moving across the entire motion sequence to preserve the embedded spatial 13temporal motion patterns. Afterward, five compacted and representative motion dictionaries are constructed in parallel by means of fast K-SVD in the training phase; they are used to remove the noise and outliers from noisy motion sequences in the testing phase by solving !131-minimization problems. Extensive experiments show that our method outperforms its competitors. More importantly, compared with other data-driven based method, our method does not need to specifically choose the training data, it can be more easily applied to real-world applications

Strategies for Treating Latent Multiple-Drug Resistant Tuberculosis: A Decision Analysis

BACKGROUND: The optimal treatment for latent multiple-drug resistant tuberculosis infection remains unclear. In anticipation of future clinical trials, we modeled the expected performance of six potential regimens for treatment of latent multiple-drug resistant tuberculosis. METHODS: A computerized Markov model to analyze the total cost of treatment for six different regimens: Pyrazinamide/ethambutol, moxifloxacin monotherapy, moxifloxacin/pyrazinamide, moxifloxacin/ethambutol, moxifloxacin/ethionamide, and moxifloxacin/PA-824. Efficacy estimates were extrapolated from mouse models and examined over a wide range of assumptions. RESULTS: In the base-case, moxifloxacin monotherapy was the lowest cost strategy, but moxifloxacin/ethambutol was cost-effective at an incremental cost-effectiveness ratio of $21,252 per quality-adjusted life-year. Both pyrazinamide-containing regimens were dominated due to their toxicity. A hypothetical regimen of low toxicity and even modest efficacy was cost-effective compared to "no treatment." CONCLUSION: In our model, moxifloxacin/ethambutol was the preferred treatment strategy under a wide range of assumptions; pyrazinamide-containing regimens fared poorly because of high rates of toxicity. Although more data are needed on efficacy of treatments for latent MDR-TB infection, data on toxicity and treatment discontinuation, which are easier to obtain, could have a substantial impact on public health practice

Acute effects of intracranial hypertension and ARDS on pulmonary and neuronal damage: a randomized experimental study in pigs

Abstract PURPOSE: To determine reciprocal and synergistic effects of acute intracranial hypertension and ARDS on neuronal and pulmonary damage and to define possible mechanisms. METHODS: Twenty-eight mechanically ventilated pigs were randomized to four groups of seven each: control; acute intracranial hypertension (AICH); acute respiratory distress syndrome (ARDS); acute respiratory distress syndrome in combination with acute intracranial hypertension (ARDS + AICH). AICH was induced with an intracranial balloon catheter and the inflation volume was adjusted to keep intracranial pressure (ICP) at 30-40 cmH2O. ARDS was induced by oleic acid infusion. Respiratory function, hemodynamics, extravascular lung water index (ELWI), lung and brain computed tomography (CT) scans, as well as inflammatory mediators, S100B, and neuronal serum enolase (NSE) were measured over a 4-h period. Lung and brain tissue were collected and examined at the end of the experiment. RESULTS: In both healthy and injured lungs, AICH caused increases in NSE and TNF-alpha plasma concentrations, extravascular lung water, and lung density in CT, the extent of poorly aerated (dystelectatic) and atelectatic lung regions, and an increase in the brain tissue water content. ARDS and AICH in combination induced damage in the hippocampus and decreased density in brain CT. CONCLUSIONS: AICH induces lung injury and also exacerbates pre-existing damage. Increased extravascular lung water is an early marker. ARDS has a detrimental effect on the brain and acts synergistically with intracranial hypertension to cause histological hippocampal damage