Addressing accuracy and precision issues in iTRAQ quantitation

iTRAQ (isobaric tags for relative or absolute quantitation) is a mass spectrometry technology that allows quantitative comparison of protein abundance by measuring peak intensities of reporter ions released from iTRAQ-tagged peptides by fragmentation during MS/MS. However, current data analysis techniques for iTRAQ struggle to report reliable relative protein abundance estimates and suffer with problems of precision and accuracy. The precision of the data is affected by variance heterogeneity: low signal data have higher relative variability; however, low abundance peptides dominate data sets. Accuracy is compromised as ratios are compressed toward 1, leading to underestimation of the ratio. This study investigated both issues and proposed a methodology that combines the peptide measurements to give a robust protein estimate even when the data for the protein are sparse or at low intensity. Our data indicated that ratio compression arises from contamination during precursor ion selection, which occurs at a consistent proportion within an experiment and thus results in a linear relationship between expected and observed ratios. We proposed that a correction factor can be calculated from spiked proteins at known ratios. Then we demonstrated that variance heterogeneity is present in iTRAQ data sets irrespective of the analytical packages, LC-MS/MS instrumentation, and iTRAQ labeling kit (4-plex or 8-plex) used. We proposed using an additive-multiplicative error model for peak intensities in MS/MS quantitation and demonstrated that a variance-stabilizing normalization is able to address the error structure and stabilize the variance across the entire intensity range. The resulting uniform variance structure simplifies the downstream analysis. Heterogeneity of variance consistent with an additive-multiplicative model has been reported in other MS-based quantitation including fields outside of proteomics; consequently the variance-stabilizing normalization methodology has the potential to increase the capabilities of MS in quantitation across diverse areas of biology and chemistry.

A vibrational spectroscopic study of the phosphate mineral minyulite KAl2(OH,F)(PO4)2⋅4(H2O) and in comparison with wardite

Vibrational spectroscopy enables subtle details of the molecular structure of minyulite KAl2(OH,F)(PO4)2⋅4(H2O). Single crystals of a pure phase from a Brazilian pegmatite were used. Minyulite belongs to the orthorhombic crystal system. This indicates that it has three axes of unequal length, yet all are perpendicular to each other. The infrared and Raman spectroscopy were applied to compare the structure of minyulite with wardite. The reason for the comparison is that both are Al containing phosphate minerals. The Raman spectrum of minyulite shows an intense band at 1012 cm−1 assigned to the ν1PO43- symmetric stretching vibrations. A series of low intensity Raman bands at 1047, 1077, 1091 and 1105 cm−1 are assigned to the ν3PO43- antisymmetric stretching modes. The Raman bands at 1136, 1155, 1176 and 1190 cm−1 are assigned to AlOH deformation modes. The infrared band at 1014 cm−1 is ascribed to the PO43- ν1 symmetric stretching vibrational mode. The infrared bands at 1049, 1071, 1091 and 1123 cm−1 are attributed to the PO43- ν3 antisymmetric stretching vibrations. The infrared bands at 1123, 1146 and 1157 cm−1 are attributed to AlOH deformation modes. Raman bands at 575, 592, 606 and 628 cm−1 are assigned to the ν4 out of plane bending modes of the PO43- unit. In the 2600–3800 cm−1 spectral range, Raman bands for minyulite are found at 3661, 3669 and 3692 cm−1 are assigned to AlOH/AlF stretching vibrations. Broad infrared bands are also found at 2904, 3105, 3307, 3453 and 3523 cm−1. Raman bands at 3225, 3324 cm−1 are assigned to water stretching vibrations. A comparison is made with the vibrational spectra of wardite. Raman spectroscopy complimented with infrared spectroscopy has enabled aspects of the structure of minyulite to be ascertained and compared with that of other phosphate minerals.

A vibrational spectroscopic study of the phosphate mineral whiteite CaMn++Mg2Al2(PO4)4(OH)2·8(H2O)

Vibrational spectroscopy enables subtle details of the molecular structure of whiteite to be determined. Single crystals of a pure phase from a Brazilian pegmatite were used. The infrared and Raman spectroscopy were applied to compare the molecular structure of whiteite with that of other phosphate minerals. The Raman spectrum of whiteite shows an intense band at 972 cm-1 assigned to the m1 PO3- 4 symmetric stretching vibrations. The low intensity Raman bands at 1076 and 1173 cm-1 are assigned to the m3 PO3- 4 antisymmetric stretching modes. The Raman bands at 1266, 1334 and 1368 cm-1 are assigned to AlOH deformation modes. The infrared band at 967 cm-1 is ascribed to the PO3- 4 m1 symmetric stretching vibrational mode. The infrared bands at 1024, 1072, 1089 and 1126 cm-1 are attributed to the PO3-4 m3 antisymmetric stretching vibrations. Raman bands at 553, 571 and 586 cm-1 are assigned to the m4 out of plane bending modes of the PO3- 4 unit. Raman bands at 432, 457, 479 and 500 cm-1 are attributed to the m2 PO4 and H2PO4 bending modes. In the 2600 to 3800 cm-1 spectral range, Raman bands for whiteite are found 3426, 3496 and 3552 cm-1 are assigned to AlOH stretching vibrations. Broad infrared bands are also found at 3186 cm-1. Raman bands at 2939 and 3220 cm-1 are assigned to water stretching vibrations. Raman spectroscopy complimented with infrared spectroscopy has enabled aspects of the structure of whiteite to be ascertained and compared with that of other phosphate minerals.

The molecular structure of the vanadate mineral mottramite [PbCu(VO4)(OH)] from Tsumeb, Namibia – a vibrational spectroscopic study

We have studied a mineral sample of mottramite PbCu(VO4)(OH) from Tsumeb, Namibia using a combination of scanning electron microscopy with EDX, Raman and infrared spectroscopy. Chemical analysis shows principally the elements V, Pb and Cu. Ca occurs as partial substitution of Pb as well as P and As in substitution to V. Minor amounts of Si and Cr were also observed. The Raman band of mottramite at 829 cm-1, is assigned to the ν1 symmetric (VO-4) ) stretching mode. The complexity of the spectra is attributed to the chemical composition of the Tsumeb mottramite. The ν3 antisymmetric vibrational mode of mottramite is observed as very low intensity bands at 716 and 747 cm-1. The series of Raman bands at 411, 439, 451 cm-1 and probably also the band at 500 cm-1 are assigned to the (VO-4) ν2 bending mode. The series of Raman bands at 293, 333 and 366 cm-1 are attributed to the (VO-4) ) ν4 bending modes. The ν3, ν3 and ν4 regions are complex for both minerals and this is attributed to symmetry reduction of the vanadate unit from Td to Cs.

Vibrational spectroscopic study of the sulphate mineral glaucocerinite (Zn,Cu)10Al6(SO4)3(OH)32⋅18H2O – a natural layered double hydroxide

We have studied the molecular structure of the mineral glaucocerinite (Zn,Cu)5Al3(SO4)1.5(OH)16�9(H2O) using a combination of Raman and infrared spectroscopy. The mineral is one of the hydrotalcite supergroup of natural layered double hydroxides. The Raman spectrum is characterised by an intense Raman band at 982 cm�1 with a low intensity band at 1083 cm�1. These bands are attributed to the sulphate symmetric and antisymmetric stretching mode. The infrared spectrum is quite broad with a peak at 1020 cm�1. A series of Raman bands at 546, 584, 602, 625 and 651 cm�1 are assigned to the m4 (SO4)2� bending modes. The observation of multiple bands provides evidence for the reduction in symmetry of the sulphate anion from Td to C2v or even lower symmetry. The Raman band at 762 cm�1 is attributed to a hydroxyl deformation mode associated with AlOH units. Vibrational spectroscopy enables aspects of the molecular structure of glaucocerinite to be determined.

Molecular structural studies of the amorphous mineral pitticite Fe, AsO4, SO4, H2O

Some minerals are colloidal and show no X-ray diffraction patterns. Vibrational spectroscopy offers one of the few methods for the assessment of the structure of these types of mineral. Among this group of minerals is pitticite simply described as Fe, AsO4, SO4, H2O. The objective of this research is to determine the molecular structure of the mineral pitticite using vibrational spectroscopy. Raman microscopy offers a useful method for the analysis of such colloidal minerals. Raman and infrared bands are attributed to the , and water stretching vibrations. The Raman spectrum is dominated by a very intense sharp band at 983 cm−1 assigned to the symmetric stretching mode. A strong Raman band at 1041 cm−1 is observed and is assigned to the antisymmetric stretching mode. Low intensity Raman bands at 757 and 808 cm−1 may be assigned to the antisymmetric and symmetric stretching modes. Raman bands observed at 432 and 465 cm−1 are attributable to the doubly degenerate ν2(SO4)2- bending mode.

Exercise alters the profile of phospholipid molecular species in rat skeletal muscle

We have determined the effect of two exercise-training intensities on the phospholipid profile of both glycolytic and oxidative muscle fibers of female Sprague-Dawley rats using electrospray-ionization mass spectrometry. Animals were randomly divided into three training groups: control, which performed no exercise training; low-intensity (8 m/min) treadmill running; or high-intensity (28 m/min) treadmill running. All exercise-trained rats ran 1,000 m/session for 4 days/wk for 4 wk and were killed 48 h after the last training bout. Exercise training was found to produce no novel phospholipid species but was associated with significant alterations in the relative abundance of a number of phospholipid molecular species. These changes were more prominent in glycolytic (white vastus lateralis) than in oxidative (red vastus lateralis) muscle fibers. The largest observed change was a decrease of ∼20% in the abundance of 1-stearoyl-2-docosahexaenoyl-phosphatidylethanolamine [PE(18:0/22:6); P < 0.001] ions in both the low- and high-intensity training regimes in glycolytic fibers. Increases in the abundance of 1-oleoyl-2-linoleoyl phopshatidic acid [PA(18:1/18:2); P < 0.001] and 1-alkenylpalmitoyl-2-linoleoyl phosphatidylethanolamine [plasmenyl PE (16:0/18:2); P < 0.005] ions were also observed for both training regimes in glycolytic fibers. We conclude that exercise training results in a remodeling of phospholipids in rat skeletal muscle. Even though little is known about the physiological or pathophysiological role of specific phospholipid molecular species in skeletal muscle, it is likely that this remodeling will have an impact on a range of cellular functions.

Effect of a single session of exercise on lipoprotein(a)

Lipoprotein(a) (Lp(a)) is bound to apolipoprotein B-100 by disulfide linkage and is associated in the upper density range of low density lipoprotein cholesterol. Persons with elevated concentrations of Lp(a) are regarded as having an increased risk for premature coronary artery disease. Although many studies exist evaluating the effects of a single session of exercise on lipids and lipoproteins, little information is available concerning the effects of exercise on Lp(a). Therefore, the purpose of this study was to determine the effects of a single exercise session on plasma Lp(a). Twelve physically active men completed two 30-min submaximal treadmill exercise sessions: low intensity (LI, 50% VO2max) and high intensity (HI, 80% VO2max). Blood samples were obtained immediately before and after exercise. Total cholesterol (LI: before 4.22 +/- 0.26, after 4.24 +/- 0.28; HI: before 4.24 +/- 0.31, after 4.11 +/- 0.28 mmol . l(-1), mean +/- SE) and triglyceride (LI: before 1.14 +/- 0.16, after 1.06 +/- 0.16; HI: before 1.12 +/- 0.19, after 1.21 +/- 0.19 mmol . l(-1)) concentrations did not differ immediately after either exercise session, nor did Lp(a) concentrations differ immediately after either exercise session (LI: before 4.1 +/- 2.2, after 4.0 +/- 2.1; HI: before 3.9 +/- 2.2, after 3.7 +/- 2.0 mg . dl(-1)). These results suggest that neither a low nor a high intensity exercise session lasting 30 min in duration has an immediate effect on plasma Lp(a).

Are mothers of young children really inactive?

Australian surveys have found that only 43% of women meet the current recommendation for regular moderate physical activity, and that women who are mothers of young children are even less likely to be adequately active for health benefit. These women spend a significant proportion of their day in occupational, household and care-giving activities, which may not be ‘captured’ in conventional physical activity surveys. The purpose of this study was to compare physical activity in young mothers and age-matched controls using three different measures of physical activity. 35 women (16 mothers of young children, M) and 19 age-matched comparison women (NM) completed a survey which asked about walking to and from places, and about moderate and vigorous activity in leisure time and at work (paid and unpaid). They also kept a detailed diary of all their activities for two week-days and two week-end days, and wore a pedometer (Yamax digiwalker) on these days. Each activity in the diary was assigned an energy expenditure (EE) score based on it's intensity (Compendium of Physical Activity) and time spent in that activity. There were no differences between M and NM for pedometer steps (M: 9270 sd 2947; NM: 9768 sd 3051) or for daily energy expenditure (EE) calculated from the diaries (M: 2029 sd 189; NM: 2015 sd 169 METS.mins) or survey (M: 2079 sd 448; NM: 1495 sd 325). There was a significant correlation between pedometer steps and daily METs.mins estimated from the diaries (r = 0.35, p = 0.04); however no relationship was observed between pedometer steps and EE from the survey (r = .09, p = .56). Further analysis of the individual survey items found pedometer steps to be related to EE from walking to and from places (r = .34) and leisure time (r = .31), but not work related activity (r = -.08). There were no significant relationships between EE computed from the diaries and any of the survey questions. The three activity measures indicate that the physical activity levels of the young mothers in our sample were comparable to age-matched non-mothers. The results of the correlation analyses highlight the difficulty of assessing low-intensity work-related physical activity via self-report. Supported by Australian Commonwealth Department of Health and Aged Care.

Systematic integration of human factors in the specification of requirements for new railway technologies

Engineering design processes are necessary to attain the requisite standards of integrity for high-assurance safety-related systems. Additionally, human factors design initiatives can provide critical insights that parameterise their development. Unfortunately, the popular perception of human factors as a “forced marriage” between engineering and psychology often provokes views where the ‘human factor’ is perceived as a threat to systems design. Some popular performance-based standards for developing safety-related systems advocate identifying and managing human factors throughout the system lifecycle. However, they also have a tendency to fall short in their guidance on the application of human factors methods and tools, let alone how the outputs generated can be integrated in to various stages of the design process. This case study describes a project that converged engineering with human factors to develop a safety argument for new low-cost railway level crossing technology for system-wide implementation in Australia. The paper enjoins the perspectives of a software engineer and cognitive psychologist and their involvement in the project over two years of collaborative work to develop a safety argument for low-cost level crossing technology. Safety and reliability requirements were informed by applying human factors analytical tools that supported the evaluation and quantification of human reliability where users interfaced with the technology. The project team was confronted with significant challenges in cross-disciplinary engagement, particularly with the complexities of dealing with incongruences in disciplinary language. They were also encouraged to think ‘outside the box’ as to how users of a system interpreted system states and ehaviour. Importantly, some of these states, while considered safe within the boundary of the constituent systems that implemented safety-related functions, could actually lead the users to engage in deviant behaviour. Psychology explained how user compliance could be eroded to levels that effectively undermined levels of risk reduction afforded by systems. Linking the engineering and psychology disciplines intuitively, overall safety performance was improved by introducing technical requirements and making design decisions that minimized the system states and behaviours that led to user deviancy. As a commentary on the utility of transdisciplinary collaboration for technical specification, the processes used to bridge the two disciplines are conceptualised in a graphical model.

A vibrational spectroscopic study of the silicate mineral analcime – Na2(Al4SiO4O12)·2H2O : a natural zeolite

We have studied the mineral analcime using a combination of scanning electron microscopy with energy dispersive spectroscopy and vibrational spectroscopy. The mineral analcime Na2(Al4SiO4O12)·2H2O is a crystalline sodium silicate. Chemical analysis shows the mineral contains a range of elements including Na, Al, Fe2+ and Si. The mineral is characterized by intense Raman bands observed at 1052, 1096 and 1125 cm−1. The infrared bands are broad; nevertheless bands may be resolved at 1006 and 1119 cm−1. These bands are assigned to SiO stretching vibrational modes. Intense Raman band at 484 cm−1 is attributed to OSiO bending modes. Raman bands observed at 2501, 3542, 3558 and 3600 cm−1 are assigned to the stretching vibrations of water. Low intensity infrared bands are noted at 3373, 3529 and 3608 cm−1. The observation of multiple water bands indicate that water is involved in the structure of analcime with differing hydrogen bond strengths. This concept is supported by the number of bands in the water bending region. Vibrational spectroscopy assists with the characterization of the mineral analcime.

Facial motion engages predictive visual mechanisms

We employed a novel cuing paradigm to assess whether dynamically versus statically presented facial expressions differentially engaged predictive visual mechanisms. Participants were presented with a cueing stimulus that was either the static depiction of a low intensity expressed emotion; or a dynamic sequence evolving from a neutral expression to the low intensity expressed emotion. Following this cue and a backwards mask, participants were presented with a probe face that displayed either the same emotion (congruent) or a different emotion (incongruent) with respect to that displayed by the cue although expressed at a high intensity. The probe face had either the same or different identity from the cued face. The participants' task was to indicate whether or not the probe face showed the same emotion as the cue. Dynamic cues and same identity cues both led to a greater tendency towards congruent responding, although these factors did not interact. Facial motion also led to faster responding when the probe face was emotionally congruent to the cue. We interpret these results as indicating that dynamic facial displays preferentially invoke predictive visual mechanisms, and suggest that motoric simulation may provide an important basis for the generation of predictions in the visual system.

Cold water immersion enhances recovery of submaximal muscle function after resistance exercise

We investigated the effect of cold water immersion (CWI) on the recovery of muscle function and physiological responses following high-intensity resistance exercise. Using a randomized, cross-over design, 10 physically active men performed high-intensity resistance exercise, followed by one of two recovery interventions: 10 min of cold water immersion at 10°C, or 10 min active recovery (low-intensity cycling). After the recovery interventions, maximal muscle function was assessed after 2 h and 4 h by measuring jump height and isometric squat strength. Submaximal muscle function was assessed after 6 h by measuring the average load lifted during six sets of 10 squats at 80% 1RM. Intramuscular temperature (1 cm) was also recorded, and venous blood samples were analyzed for markers of metabolism, vasoconstriction and muscle damage. CWI did not enhance recovery of maximal muscle function. However, during the final three sets of the submaximal muscle function test, the participants lifted a greater load (p<0.05; 38%; Cohen’s d 1.3) following CWI compared with active recovery. During CWI, muscle temperature decreased 6°C below post-exercise values, and remained below pre-exercise values for another 35 min. Venous blood O2 saturation decreased below pre-exercise values for 1.5 h after CWI. Serum endothelin-1 concentration did not change after CWI, whereas it decreased after active recovery. Plasma myoglobin concentration was lower, whereas plasma interleukin-6 concentration was higher after CWI compared with active recovery. These results suggest that cold water immersion after resistance exercise allow athletes to complete more work during subsequent training sessions, which could enhance long-term training adaptations.

Wing morphology, echolocation calls, diet and emergence time of black-bearded tomb bats (Taphozous melanopogon, Emballonuridae) from southwest China

We studied the wing morphology, echolocation calls, diet and emergence time of the black-bearded tomb bat (Taphozous melanopogon) from May to October 2006 in Guangxi Province, southwest China. Taphozous melanopogon has wings with high aspect ratio, high loading and pointed wing-tip shape-characteristics associated with fast flight in open space. This species usually produces low-intensity, low frequency, and frequency-modulated (FM) calls usually containing up to four harmonics, with most energy in the second (or sometimes third) harmonic. The diet of this species consists mostly of Lepidoptera and Hemiptera. Timing of evening emergence is correlated with the time of sunset. This is the first study to describe the flight and echolocation behavior of this species in China, and opens the way for future studies of its biology.

Assessment of the molecular structure of an intermediate member of the triplite-zwieselite mineral series: A raman and infrared study

The mineral series triplite-zwieselite with theoretical formula (Mn2+)2(PO4)(F)-(Fe2+)2(PO4)(F) from the El Criolo granitic pegmatite, located in the Eastern Pampean Ranges of Córdoba Province, was studied using electron microprobe, thermogravimetry, and Raman and infrared spectroscopy. The analysis of the mineral provided a formula of (Fe1.00, Mn0.85, Ca0.08, Mg0.06)∑2.00(PO4)1.00(F0.80, OH0.20)∑1.00. An intense Raman band at 981 cm−1 with a shoulder at 977 cm−1 is assigned to the ν1 symmetric stretching mode. The observation of two bands for the phosphate symmetric stretching mode offers support for the concept that the phosphate units in the structure of triplite-zwieselite are not equivalent. Low-intensity Raman bands at 1012, 1036, 1071, 1087, and 1127 cm−1 are assigned to the ν3 antisymmetric stretching modes. A set of Raman bands at 572, 604, 639, and 684 cm−1 are attributed to the ν4 out-of-plane bending modes. A single intense Raman band is found at 3508 cm−1 and is assigned to the stretching vibration of hydroxyl units. Infrared bands are observed at 3018, 3125, and 3358 cm−1 and are attributed to water stretching vibrations. Supplemental materials are available for this article. Go to the publisher's online edition of Spectroscopy Letters to view the supplemental file.