Experimental procedures in GIGCAS The chemical abrasion mineral dissolution

Experimental procedures in GIGCAS
The chemical abrasion, mineral-dissolution and isotope dilution technique, also termed “conventional”, which requires a high degree of control on many parameters to ensure highest data quality (Schaltegger et al., 2015). A multi-step procedure described as follows were performed at the State Key Laboratory of Isotope Geochemistry (SKLIG), GIGCAS.


Conclusions and future work
Minimization of laboratory blanks ensures high-precision U–Pb zircon analysis at GIGCAS. The total procedural blanks hcv protease inhibitors maintained at ∼ 1 pg in the Guangzhou laboratory, suitable for the CA-ID-TIMS pretreatment and operation. The 206Pb/238U dates obtain at GIGCAS for standard zircons (R33) and 500 Ma solution are 419.88 ± 0.94 Ma (n = 7; MSWD = 6.8) and 500.50 ± 0.19 Ma (n = 9; MSWD = 0.84), respectively, in excellent agreement with the recommended values. Thus we are now able to measure the zircon standards and reference solution within 0.5% precision. Comprehensive procedures of CA-ID-TIMS technique therefore have been established at GIGCAS.

Xin Li and Wen Zeng are thanked for their assistance in the clean laboratory. We gratefully acknowledge an anonymous reviewer for the constructive comments which helped to improve the manuscript. This research was supported by CAS technique R&D program and State Key Laboratory of Isotope Geochemistry (SKLIG-JY-14-03) to YTZ, and CAS Strategic Priority Research Program B (XDB18000000) to YGX. RM\’s visit to GIGCAS was supported by the CAS visiting professorship (2013T1Z0005). This is Nick translation contribution no. IS-2370 from GIGCAS.

Caffeine crosses the placental barrier easily

Caffeine crosses the placental barrier easily, where it can directly affect the fetus in several different aspects. The half-life of caffeine is greatly increased in pregnancy, as it cannot be metabolized by the fetus or the placenta (Aldridge et al., 1981). In the first trimester the half life is about ten hours, while it increases up to 18h during the third trimester, as the hcv protease inhibitors in the human liver do not exist until the eight month of life (Grosso and Bracken, 2005). Several previous studies focused primarily on the associations between caffeine intake during pregnancy and birth weight showed inconsistency (Linn et al., 1982; Martin and Bracken, 1987; Larroque et al., 1993; Shu et al., 1995; Bech et al., 2007). Based on the dose-conversion correlation between humans and mice (Wang, 2005), the low dose of caffeine used in the present study (2mg/100g per day for mice is 0.36-fold that of average caffeine intake during pregnancy in Europe or 0.2-fold that of average caffeine intake during pregnancy in the US (Barone and Roberts, 1996). According to a previous study conducted by Butt and Sultan (2011) a standard cup of coffee contains, on average, between 100 and 150mg caffeine; thus, the aforementioned dose in the present study (2mg/100g daily) of caffeine exposure is equivalent to approximately a cup of coffee daily consumed in pregnant women. In this context, it has been reported that in women who consume more than 300mg caffeine daily, the conception of a primigravida is reduced by 27% (Bolúmar et al., 1997). Furthermore, the risks of spontaneous abortion and low-weight fetuses increase significantly when the intake of caffeine during pregnancy is >150mg/day (Valsamakis et al., 2006). Moreover, as early as 1980, the US Food and Drug Administration (FDA) proposed that caffeine should be taken cautiously during pregnancy (Fernandes et al., 1998). We showed that caffeine intake at low dose (2mg/100g b.w) per day during pregnancy might be associated with skeletal related fetal growth characteristics that seemed to be most consistently affected from the second trimester onwards on the basis of TGFβ2 downregulation in the perichondrium as the site of chondrocyte proliferation. Further follow up studies are needed focused on the effects of fetal caffeine exposure on postnatal skeletal and bone measurements.
Furthermore, it is well known that retinoids are essential for adequate embryo development. They hcv protease inhibitors are important signaling molecules for the regulation of cell differentiation, proliferation and morphogenesis. Inadequate levels of these compounds (excess or deficiency) results in a set of defects denoted by retinoic acid embryopathy including neural crest, limbs and skeleton differentiation (Zile, 1998; Mulder et al., 2000; Ross et al., 2000; Ali-khan and Hales, 2006; Maden, 2006). Other types of anomalies such as omphalocele, gastroschisis, limb and rib alterations and tail regression were noted in pregnant mice in early developmental stages of conception at doses less than 60mg/kg while doses of 80mg/kg or higher provoked many reabsorptions (Quemelo et al., 2007). In the present study, however, a small dose of retinoic acid did not initiate such overmentioned teratogenicity. Dose-dependent alterations of chondrocytes were observed with concomitant downregulation of TGFβ2 expression in the perichondrium at the 14th day of gestation. These alterations were manifested at 18th day embryos in which a minor defects of phalanges were observed. Specificity of exogenous trans-retinoic acid (RA) effects during embryogenesis, especially on developing and regenerating limbs in different vertebrates were recorded in either systemic or locally applied (Bryant and Gardiner, 1992; Mohanty-Hejmadi et al., 1992; Maden, 1993), unlike in chickens and amphibians, in which RA was applied locally to developing or regenerating limbs or to amputated tails. In mice, RA injections of pregnant females 4.5–5.5days after mating were found to be effective in inducing the duplication effects on lower body including limbs at higher doses (Quemelo et al., 2007).

The situation becomes more complex if different phases at

The situation becomes more complex if different phases at the tip surface hcv protease inhibitors in their respective field evaporation probabilities. The threshold fields for the onset of evaporation, can differ by a factor of two or more. In response to this heterogeneity, the tip surface develops a variation of local curvature that balances the evaporation rate per surface area via an adjustment of the local surface field. Hence, the apex shape in APT experiments often deviates from the assumed hemisphere, and so significant trajectory aberrations can be observed [5,6]. In addition, the shape develops dynamically during measurement. As a consequence, imaging properties of the microscope are subject to continuous change [7], which further increases the complexity of the volume reconstruction.
Established APT reconstruction protocols are based on two premises. First, the validity of a simple ion projection law and second, the negligence of possible trajectory aberrations induced by a non-conforming tip-shape. The standard approach has been introduced by Bas et al. [8] in 1995. Except for some improvements for a wide field of view [9], this method still notably represents the accepted state of the art and is widely used by scientists working with APT [10,11]. The purely geometric approach is based on a point projection that links the impact position at the detector to the original position at the tip surface with a straight line. It is assumed that the emitter apex maintains a hemispherical shape during the entire reconstruction process. Only the curvature radius is allowed to change according to a presumed evolution during the measurement. The centre of the point projection is considered to lie between a stereographic and a gnomonic projection. Assuming a self-similar evolution of the emitter shape, important reconstruction parameters, the field factor and the image compression, are treated as constants, although it is well known that these reconstruction parameters undergo a characteristic variation throughout the measurement. Consequently, a variant of the standard reconstruction protocol has already been proposed to describe the reconstruction parameters as functions of the curvature radius in order to improve the quality of reconstruction in this respect [12].
The described geometric reconstruction approach is adversely affected by characteristic limitations. At interfaces between materials of strongly contrasting evaporation thresholds, densified or depleted regions as well as distortions in the geometric appearance of particles or thin films are produced [13–16]. In extreme cases, aberrations may even lead to an overlap of the trajectories of nearby atoms [17–19]. As a result, artificial zones of erroneous mixing are reconstructed. The limitations of the geometric point projection become particularly obvious in these situations.
In this work, we suggest an alternative concept for the volume reconstruction. Enabled by a recently published APT simulation package (‘TAPSim’ [20,21]), which is based on a flexible Delaunay tessellation, the proposed concept relies on the calculation of realistic and physically sound ion trajectories between the emitter apex and the detector entrance. To allow such an accurate calculation, the atomic order of the reconstruction must be reversed. The atoms detected last are the first to be reconstructed. The aim of this article is to outline the concept and to demonstrate its principle functionality using relatively small numeric model calculations. Before scaling the approach up to the data size of practical measurements, restrictions in computing efficiency must be overcome and the robustness of the approach against incomplete experimental data sets has to be further improved.

Principle of the new reconstruction approach
Imagine the arbitrary atomic geometry of the tip to be known exactly at a given moment, as illustrated by Fig. 1. It is then a straight-forward task to calculate the realistic field distribution around the tip, if a sufficiently flexible numeric algorithm is at hand, e.g. as it has been introduced by the TAPSim package [20]. TAPSim was originally developed to simulate the evaporation of APT emitters of arbitrary structure and shape. In this study, we make use of it to maintain a realistic electrostatic model of the tip, the detector, and the field in between. In other words, TAPSim is used to refine the geometric point projection by calculation of realistic trajectories.

hcv protease inhibitors Cord oacute n et al proposed a

Cordón et al. [12] proposed a Multi-objective GA (MOGA) based FS technique and a Fuzzy Rule Based Classification System (FRBCS), but their work lacked extensive simulations. Spolaor et al. [52] developed an MOGA based method for FS. They used combinations of different measures like class correlation, inconsistent example pairs, entropy, etc., as their objective functions and optimized them to yield the optimal feature vectors. However, the classification accuracy offered by the different pairs of measures were not consistent over different datasets and the authors were unable to propose a single combination of measure, which would yield the best results for a wide range of datasets. Xue et al. [59] proposed a new multi-objective approach based on PSO for FS. They simultaneously maximized classification accuracy and minimized the cardinality of the feature subset. But their results reflect that they hcv protease inhibitors were unable to achieve a set of non-dominating solutions. This can be inferred from the fact that classification accuracy and number of features selected are not monotonically conflicting, that is if one of them decreases, the other does not increase monotonically. Instead, an optimal number of features are required to obtain maximum accuracy in classification for most datasets. A very similar work was done by the Cervante et al. [7], where they used binary PSO scheme to optimize the classification performance and number of features selected. Recently, Xue et al. [60] proposed a Multi Objective Differential Evolution based FS (DEMOFS) technique, which minimizes the classification error rate and the number of features selected. Instead of presenting a single feature subset, their algorithm offers a set of solutions with varying number of features and classification accuracy. Other multi-objective optimization based FS techniques have been proposed in [20], [41] and [17].
Optimizing inter- and intra-class distance measures is a common underlying technique for several FS as well as classification algorithms. However, use of this idea in the framework of a multi-objective evolutionary optimization algorithm with formulations similar to our algorithm is unknown till date, to the best of our knowledge. For example, among the commonly used classifiers, Linear Discriminant Analysis (LDA) uses the concept of inter- and intra-class distances. James et al. [23] optimized the area of overlap between the feature-wise inter- and intra-class distances for efficient selection of features. Liu et al. [31] used a similar concept and formulated their problem as a constrained Linear Programming (LP), but solved it by using a gradient descent approach, whose major drawback is trapping at local optima. Michael et al. [38] used intra- and inter-class distance ratio, as one of the criteria for iterative feature selection.
In this paper, a simultaneous feature selection and weighting method is proposed. Most feature selection algorithms focus only on selection rather than selection and weighting, where the later has the potential to further enhance the classifier performance [47]. Here, the formulated inter-class and intra-class distance measures are maximized and minimized simultaneously by using a Multi-Objective Evolutionary Algorithm based on Decomposition (MOEA/D). Currently MOEA/D appears as one of the most competitive algorithms for multi-objective optimization. The population of MOEA/D comprises of vectors containing the candidate feature weights, which are varied according to the algorithm to optimize the inter-class and intra-class distance measures discussed subsequently. A repair mechanism is used to increase the probability of choosing lesser number of features. Also a penalty function is augmented with the fitness functions to reduce the number of features selected. After convergence to optima using MOEA/D, a fuzzy membership based technique [1] is incorporated to choose only a single feature subset (representing the best compromise solution) out of the Pareto optimal solution set. Finally it is shown that by using the k-NN classifier on the optimal feature subset, it is possible to produce higher classification accuracy than some of the state-of-art algorithms for FS.

Our recent pilot study showed

Our recent pilot study showed some success in using an onco-proteogenomic approach to compare biomarkers from tissues and urine of HCC patients and normal controls [55]. The current study used an optimized shotgun-based quantitative proteomic strategy to analyze urinary proteins in each of 44 pairs of HCC patients and normal controls. Further cross-analyses of these proteomic results with genomic and transcriptomic data (Figure 1) revealed urinary HCC biomarkers with potential use individually or in combination with other biomarkers. As Figure 2 shows, two major protein biomarker candidates were identified with high confidence levels in quantitative proteomic analysis of differentially expressed proteins in urine samples from HCC patients.
Figure 1
Potential urinary biomarkers for HCC were identified by an onco-proteogenomic approach. Urine samples from patients diagnosed with HCC and from normal controls (n = 44) were analyzed by quantitative proteomics. Identified candidates were further analyzed and selected using genomic/transcriptomic approaches. HCC = hepatocellular carcinoma.
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Figure 2
Flow-chart and experimental schemes of the procedures used for quantitative proteomics. Upon enzymatic digestion, hcv protease inhibitors were differentially stable isotope dimethyl-labeled and combined prior to desalting and fractionation. The quantitative shotgun analysis of proteome changes in clinical samples of urine from hepatocellular carcinoma patients and normal controls was performed by hydrophilic interaction liquid chromatography (HILIC)-C18 peptide separation and nano-liquid chromatography–tandem mass spectrometry coupled with stable isotope dimethyl labeling.
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Quantitative proteomic analysis of differentially expressed proteins in urine samples from HCC patients by a shotgun approach
Figure 2 shows that urinary proteins were characterized and compared between the disease and control groups (n = 44) by using gel-free shotgun proteomic analysis coupled with stable isotope dimethyl labeling [23] and [44] and nanoLC-MS/MS [46]. Differentially released proteins were identified by dimethyl labeling, enzyme digestion, and peptide mass fingerprinting followed by comparison of urinary-peptide quantification ratios (D/H) between HCC patients (deuterium labeling) and normal controls (hydrogen labeling). Approximately 1000 proteins were systematically mapped in the 44 pairs of urine samples. Figure 3 shows that expression levels of 91 identified proteins significantly differed (p < 0.05). Of these, 83 were upregulated (red shaded areas), and eight were downregulated (green shaded areas) proteins. Cluster analysis of D/H ratios further revealed two subgroups of the 44 patients: a subgroup that had numerous upregulated proteins (34 patients) and a subgroup that had relatively more separate and distinct expression profiles (10 patients). These differences suggest that, for early diagnosis, multiple biomarkers may provide better prediction accuracy compared to individual biomarkers.

Material and experimental details A titanium

2. Material and experimental details
A titanium aluminide rod with the diameter of 58 mm and nominal composition of Ti48Al2Cr2Nb at.% was selected. Disk shaped samples with 5 mm in thickness and 58 mm in diameter were prepared by electro-discharge machining. All specimens were normalized at 1385 ± 10 °C in 伪 phase domain for 15 min (holding time) with the cooling rate of 30 °C/min. Surface oxides were eliminated by subsequent grinding followed by polishing using SiC emery papers up to 3000 grits, while the roughness (Ra) of 0.2 渭m was reached. Prior to the nitriding process, TiAl disks were cleaned ultrasonically in acetone for 10 min to remove any eventual contamination.
2.2. Plasma nitriding procedure
Plasma nitriding processes were carried out using a semi-industrial pulse-DC plasma nitriding unit. Schematic sketch of CPN and ACN processes is demonstrated in Fig. 1. The apparatus was equipped with a heating system in order to increase the temperature up to 900 °C by radiation. The samples were placed on the main Ti 6Al 4 V cathode stage (D = 150 mm & h = 20 mm) in both methods. A Ti 6Al 4 V disk (D = 150 mm & h = 10 mm) was placed as an auxiliary cathode in distance of 15 mm from the main cathode in the ACN process. The process temperature was measured by a NiCr (type K) thermocouple which was connected to the hcv protease inhibitors cathode surface.
Fig. 1. Schematic sketch of conventional plasma nitriding (CPN) and auxiliary plasma nitriding (ACN) processes.Figure optionsDownload full-size imageDownload high-quality image (426 K)Download as PowerPoint slide
At the first stage of nitriding process, the pressure vessel was evacuated to a vacuum of about 5 × 10?3 Torr before purging the process gases. The purity of nitrogen, hydrogen and argon gases used in this study was 99.999 volume percent. Sputter cleaning was accomplished at Ar/H2 ratio of 2 and temperature of 100 °C for duration of 2 h. All processing conditions were adjusted using a programmable logic controller (PLC) system. The temperature was controlled by continually varying the voltage of plasma and the assisting heating system. As the temperature was reached to 800 °C, the atmosphere was switched to a ratio of H2/N2 = 1 and nitriding cycle began.
The plasma nitriding processes were performed for the durations of 10, 20 and 30 h for CPN and 3, 6 and 9 h for the ACN processes. The durations of CPN processes were based on the previous researches [4] and [15]. The ACN durations were reduced hcv protease inhibitors to about one third of the CPN processes times because of the higher plasma intensity of hallow cathode discharge processes. The voltage of 600 V, current of 5 A, total working pressure of about 5 Torr, duty cycle of 70% and frequency of 8 kHz were selected for all processes.
2.3. Characterizations
For microstructural observation, specimens were electrically copper plated, mounted, ground and mechanically polished down. All polished surfaces were etched by a reagent solution consisting of 50 ml glycerin, 25 ml nitric acid, 2 ml hydrofluoric acid and 25 ml distilled water [16]. Microstructures were studied by field emission scanning electron microscope (FESEM-TESCAN MIRA 3 LMU).