Trace Profiler Research Articles

Development of a high-precision long trace profiler utilizing shear measurements.

Compensating for the pitch error in the scanning movement is a fundamental issue when conducting large-scale surface shape measurements with deflectometric profilers. This paper presents a new long trace profiler employing a shearing measurement technique. In this setup, the optical head and the mirror under test are mounted on two independent parallel movable air-bearing carriages to enable shearing and scanning movements separately. The distance between the optical head and the tested mirror remains fixed, effectively minimizing the influence of system errors resulting from imperfections in optical devices. Simulation studies show that the double shear measurement method with a low-spatial-frequency filtering process can effectively mitigate high-frequency angular measurement errors introduced by the instability of the air-bearing stage. Experimental tests conducted on flat mirrors demonstrated a precision of less than 50 nrad rms, thereby confirming the robustness of the system.

Workflow Trace Profiling and Execution Time Analysis in Quantitative Verification

Workflows orchestrate a collection of computing tasks to form a complex workflow logic. Different from the traditional monolithic workflow management systems, modern workflow systems often manifest high throughput, concurrency and scalability. As service-based systems, execution time monitoring is an important part of maintaining the performance for those systems. We developed a trace profiling approach that leverages quantitative verification (also known as probabilistic model checking) to analyse complex time metrics for workflow traces. The strength of probabilistic model checking lies in the ability of expressing various temporal properties for a stochastic system model and performing automated quantitative verification. We employ semi-Makrov chains (SMCs) as the formal model and consider the first passage times (FPT) measures in the SMCs. Our approach maintains simple mergeable data summaries of the workflow executions and computes the moment parameters for FPT efficiently. We describe an application of our approach to AWS Step Functions, a notable workflow web service. An empirical evaluation shows that our approach is efficient for computer high-order FPT moments for sizeable workflows in practice. It can compute up to the fourth moment for a large workflow model with 10,000 states within 70 s.

Concentrations and influencing factors of 17 elements in placenta, cord blood, and maternal blood of women from an e-waste recycling area

BackgroundThe effects of prenatal element exposure on mothers and fetuses have generated concern. Profiles of trace and toxic elements in biological material are urgently desired, especially for women who reside near e-waste recycling facilities. The aim of this study was to investigate elements concentrations in placenta, cord blood, and maternal blood of women and to evaluate the influencing factors. MethodsA group of 48 women from an e-waste recycling site and a group of 31 women from a non-e-waste recycling site were recruited. Basic characteristics were collected by questionnaire and the concentrations of 17 elements in placenta, cord blood, and maternal blood samples were analyzed by inductively coupled plasma mass spectrometry (ICP-MS). Finally, the generalized linear model regression analysis (GLM) was used to test the association between element concentrations and possible factors. ResultsCompared to the control group, the exposed group had significantly elevated cadmium (Cd), zinc (Zn), nickel (Ni), and antimony (Sb) in placenta, and higher lead (Pb) in maternal blood and cord blood (P<0.05). Sb concentration in maternal blood was significantly lower than in the control group (P<0.05). GLM analysis showed that element concentrations were mainly associated with maternal age [chromium (Cr), iron (Fe), selenium (Se), cobalt (Co), mercury (Hg) in placenta, copper (Cu) in maternal blood], education (Se, Sb in placenta), family income (Cu in maternal blood and Ni in placenta), passive smoking [Cu and Zn in placenta, Pb in maternal blood], and e-waste contact history (Hg in cord blood, Cu, Zn, and Cd in maternal blood). ConclusionsWomen in the e-waste recycling area had higher toxic element levels in the placenta and blood samples. More preventive measures were needed to reduce the risk of element exposure for mothers and fetuses in these areas.

Stitching interferometry for long X-ray mirrors with lateral multi-shift-based absolute calibration.

To eliminate the reference mirror (REF) error of the Fizeau interferometer for measuring X-ray mirrors, the reference calibration method of lateral multi-shift measurements at the hundreds-micrometer pixel level is presented. Because of the high aspect ratio of long X-ray mirrors, by shifting the surface under test (SUT) along the tangential direction with integer multiple pixels, we extend the calibration method by using the difference between multiple shifted measurements to build an augmented multi-matrix for extracting the two-dimensional (2D) absolute surface. The method can be applied to arbitrary measurement regions of the test optics, and the measurement for both the benchmark sub-aperture and calibration of the REF is accomplished in a single measuring process. Furthermore, by adjusting the shift to the millimeter scale, reference-subtracted sub-apertures can be stitched to obtain the absolute 2D map of the X-ray mirror. Experimental results show that all the 2D discrepancies reach sub-nanometer repeatability, and comparison results between the long trace profiler (LTP) and the proposed method have been performed. Therefore, the results demonstrated that the proposed method meets the requirements of X-ray mirror measurements.

Effect of NaCl on ammonium and nitrate uptake and transport in salt-tolerant and salt-sensitive poplars.

Nitrogen (N) plays an important role in mitigating salt stress in tree species. We investigate the genotypic differences in the uptake of ammonium (NH4+) and nitrate (NO3-) and the importance for salt tolerance in two contrasting poplars, salt-tolerant Populus euphratica Oliv. and salt-sensitive P. simonii × (P. pyramidalis ×Salix matsudana) (P. popularis cv. 35-44, P. popularis). Total N content, growth and photosynthesis were significantly reduced in P. popularis after 7days of exposure to NaCl (100mM) supplied with 1mM NH4+ and 1mM NO3-, while the salt effects were not pronounced in P. euphratica. The 15NH4+ trace and root flux profiles showed that salt-stressed poplars retained ammonium uptake, which was related to the upregulation of ammonium transporters (AMTs) in roots, as two of the four AMTs tested significantly increased in salt-stressed P. euphratica (i.e., AMT1.2, 2.1) and P. popularis (i.e., AMT1.1, 1.6). It should be noted that P. euphratica differs from salt-sensitive poplar in the maintenance of NO3- under salinity. 15NO3- tracing and root flux profiles showed that P. euphratica maintained nitrate uptake and transport, while the capacity to uptake NO3- was limited in salt-sensitive P. popularis. Salt increased the transcription of nitrate transporters (NRTs), NRT1.1, 1.2, 2.4, 3.1, in P. euphratica, while P. popularis showed a decrease in the transcripts of NRT1.1, 2.4, 3.1 after 7days of salt stress. Furthermore, salt-stimulated transcription of plasmalemma H+-ATPases (HAs), HA2, HA4 and HA11 contributed to H+-pump activation and NO3- uptake in P. euphratica. However, salt stimulation of HAs was less pronounced in P. popularis, where a decrease in HA2 transcripts was observed in the stressed roots. We conclude that the salinity-decreased transcripts of NRTs and HAs reduced the ability to uptake NO3- in P. popularis, resulting in limited nitrogen supply. In comparison, P. euphratica maintains NH4+ and NO3- supply, mitigating the negative effects of salt stress.

The Use of Artificial Intelligence (AI) is Customer Service Process in the Pharmaceutical Industry: A Case Study in Public Laboratories

The Consumer Service (SAC) is an important communication and relationship channel with the customer. This study sought automated data collection and analysis techniques to trace profiles and strategies that are part of the SAC 4.0 model in official laboratories A and B. The method consisted of document analysis of standardized procedures and database research using the keywords SAC, artificial intelligence, and pharmaceutical industry. The results showed that laboratories A and B use the SAC 2.0 model and do not apply AI techniques. Evidence shows that pharmaceutical industries in Brazil use the SAC 4.0 model. It is concluded that the AI tools in the SAC contribute to improvements and efficiency in the process.

Numerical simulation of the rheology of alumina abrasive particles applied to UHMWPE during the microabrasion test

The material used for 50 years in orthopedics for joint replacements is ultra-high molecular weight polyethylene (UHMWPE). Joint replacements are designed so that the metal is in surface contact with the polymeric material, and it is used in most degenerative joint disorders. A problem with joint replacements is the half-life of their UHMWPE components resulting from surface contact, leading to premature wear. This leads to the detachment of wear particles causing osteolysis. In the present investigation, a numerical simulation of the rheology of 5 μm size alumina abrasive particles applied to UHMWPE type GUR 1020 was performed by duplicating the microabrasion test. An analogy was proposed between the alumina particles observed in the scanning electron microscope (SEM) and the gravel stone obtaining a geometry similar to that of the alumina particles. A 3D scanner was used, obtaining different randomly selected gravel models. They were scanned and rendered to obtain the IGS files to be used in the finite element software. Using Archad’s abrasive wear theory, the volume displaced by the abrasive particles was obtained as a function of the geometry of the abrasive grains, influenced by the entry position of one or more of the different cutting edges contained in the geometry, the hardness of the softer material, the value of the normal load and the sliding distance. Individual trace profiles were obtained by 2D profilometry and wear traces were analyzed by SEM. Explicit dynamic analysis of particle motion was used to simulate the entry, transition and displacement during the abrasive wear test caused by detached particles. The experimental results of the microabrasion test were compared with finite element analysis, demonstrating that simulation can be used as a reliable tool to obtain information about the type of wear of a material.

From clean spaces to crime scenes: Exploring trace DNA recovery from titania-coated self-cleaning substrates

Titanium dioxide (titania, TiO2) is frequently used as a coating for a variety of self-cleaning products, such as antifogging vehicle mirrors, ceramic tiles, and glass windows because of its distinct physiochemical features. When exposed to light TiO2 causes photocatalytic decomposition of organic contaminants, potentially compromising DNA integrity. The impact of TiO2-coated commercial glasses, Bioclean® and SaniTise™, on trace DNA persistence, recovery, and profiling was investigated. DNA in saliva and touch samples deposited on self-cleaning glass slides exposed to indoor fluorescent light for up to seven days was more degraded than control samples indicating some degree of fluorescent light-induced photocatalytic activity of the self-cleaning surfaces. When exposed to sunlight, DNA yields from saliva and touch samples deposited on the titania-coated substrates decreased rapidly, with a corresponding increase in DNA degradation. After three days no DNA samples applied to self-cleaning glass and exposed to natural sunlight yielded STR profiles. These results suggest that the photocatalytic activation of TiO2 is the likely mechanism of action underlying the extreme DNA degradation on the Bioclean® and SaniTise™ glasses. Consequently, rapid sample collection and use may be warranted in casework scenarios involving TiO2-coated materials.

A nano-radian precision absolute local slope measurement method for X-ray reflectors.

Ultra-precise reflectors in the advanced light source facilities urgently call for local slope error measurements with nano-radian precision. However, the existing methods currently utilized in the long trace profiler systems struggle to meet the requirements. In this paper, we present a weak-value amplification enhanced absolute local slope measurement scheme, in which the surface height difference between two adjacent points can be measured directly with precision on the pico-meter level. As a result, the absolute local slope measurement reaches a record precision level of 9.7 nrad (RMS) with a small lateral separation of 0.5 mm. Comparing to the existing methods, our scheme is more disturbance-resistant, more compact and cost-effective. The local curvature measuring capability is also validated with two synchronously parallel local slope measurement paths, between which the separation is set as 2mm. A local curvature measurement is obtained with precision of 3.4 × 10-6m-1 (RMS) and its corresponding slope variation is 6.8 nrad. Our method exhibits important application prospects in the field of ultra-precise surface fabrication inspection.

X-ray mirrors with sub-nanometre figure errors obtained by differential deposition of thin WSi2 films.

Differential deposition by DC magnetron sputtering was applied to correct for figure errors of X-ray mirrors to be deployed on low-emittance synchrotron beamlines. During the deposition process, the mirrors were moved in front of a beam-defining aperture and the required velocity profile was calculated using a deconvolution algorithm. The surface figure was characterized using conventional off-line visible-light metrology instrumentation (long trace profiler and Fizeau interferometer) before and after the deposition. WSi2 was revealed to be a promising candidate material since it conserves the initial substrate surface roughness and limits the film stress to acceptable levels. On a 300 mm-long flat Si mirror the average height errors were reduced by a factor of 20 down to 0.2 nm root mean square. This result shows the suitability of WSi2 for differential deposition. Potential promising applications include the upgrade of affordable, average-quality substrates to the standards of modern synchrotron beamlines.

CLIMCAPS—A NASA Long‐Term Product for Infrared + Microwave Atmospheric Soundings

AbstractThe Community Long‐term Infrared Microwave Combined Atmospheric Product System (CLIMCAPS) spans more than two decades of soundings from infrared and microwave instrument pairs on Aqua, Suomi‐NPP, and NOAA‐20. CLIMCAPS builds on three decades of research within the National Aeronautics and Space Administration Atmospheric Infrared Sounder Science Team (AST) to retrieve profiles of atmospheric temperature, water vapor, ozone, and many other trace gases as well as cloud and surface properties. In this paper, we highlight four innovative aspects of the AST retrieval methodology that allows the CLIMCAPS record (2002 to present) to bridge technology differences, maintain global coverage and stay updated with fast reprocessing times. CLIMCAPS improves on the AST method with rigorous optimal estimation uncertainty quantification for improved understanding of the signal‐to‐noise in sounding retrievals to allow their use in scientific research.

Stitching Measurement of Line Density of Variable-Line-Spacing Gratings with Long Trace Profiler

Stitching Measurement of Line Density of Variable-Line-Spacing Gratings with Long Trace Profiler

Enhanced-spatial-resolution optical surface profiler based on focusing deflectometry.

Deflectometric slope profiler is an essential technique for accessing the surface metrology of mirrors used in synchrotron radiation beamlines. To increase the upper spatial frequency bandwidth limits of deflectometric slope profiler, reducing the beam spot size on the mirrors is necessary. In this paper, we introduce a profiler system: the focusing long trace profiler (FLTP). It contains a newly developed optical head capable of raising upper spatial frequency bandwidth limits by using a focused beam instead of a collimated beam to scan the sample. This feature has been proven in a numerical simulation experiment, where a spatial resolution of up to around 0.05 mm was reached when the sample is set at focus plane. The system is implemented and characterized in several experiments; calibration of the focusing optical head shows that it can achieve a high angular accuracy of sub-50 nrad root-mean-square (rms) and defocusing of sample under test (SUT) has no effect on the measurement results; the measurement tests also demonstrate the system's advantage in highly curved mirror profile metrology.

Ultra high precision in-vacuum long trace profiler for real time slope determination of optical surface

The development of an in-vacuum long trace profiler (IVLTP) which can provide ultra high precision real time measurements on the surface slope of optical elements is reported. The unique features of this instrument include a specifically designed ultra high repeatability linear slide, a pentamirror composed of two plane mirrors of ultra low slope error, and an ultra high vacuum (UHV) compatible complementary metal oxide semiconductor (CMOS) image sensor. The mechanical system is made of Invar 36 alloy to reduce the room temperature drift effect during data acquisitions. Each IVLTP scan completes in 120 seconds, covering a 168 mm of surface length and generating more than 5000 slope data points. The root mean square (RMS) of the difference between two consecutive scans was found to be 0.0081 μrad on average and 0.0045 μrad RMS at its best. The main application of this IVLTP is to provide the real time feedback signals needed for controlling the 25-actuator surface benders of the active mirrors and active gratings installed in the ultra high resolution soft X-ray beamlines at the Taiwan Photon Source (TPS).

Mercury and other trace elements distribution and profiling of microbial community in the surface sediments of East Siberian Sea

In this study, total mercury (THg), methylmercury (MeHg), various trace elements, and microbial communities were measured in surface sediments of the East Siberian Sea (ESS). The results showed that the average values of THg and MeHg were 58.8 ± 15.21 μg/kg and 0.50 ± 0.22 μg/kg, respectively. The notable levels of trace elements present in both surface sediment and porewater were Al, Fe, and Mn. The enrichment factor and geoaccumulation index analyses found that both natural phenomena and anthropogenic activities contributed to elevated concentrations of metals in the ESS. The redox proxy metals, pH, and SO42− were the major factors influencing the THg and MeHg distributions. Microbial profiles were substantially affected by metals and other abiotic factors. Proteobacteria and Thaumarchaeota were the most abundant phyla. Overall, the findings presented here facilitate the understanding of the current status of metal contamination, its influencing factors, and metal-microbiota-interactions in ESS.

ATOCA: an Algorithm to Treat Order Contamination. Application to the NIRISS SOSS Mode

After a successful launch, the James Webb Space Telescope is preparing to undertake one of its principal mission objectives, the characterization of the atmospheres of exoplanets. The Single Object Slitless Spectroscopy (SOSS) mode of the Near Infrared Imager and Slitless Spectrograph (NIRISS) is the only observing mode that has been specifically designed for this objective. It features a wide simultaneous spectral range (0.6–2.8 μm) through two spectral diffraction orders. However, due to mechanical constraints, these two orders overlap slightly over a short range, potentially introducing a “contamination” signal in the extracted spectrum. We show that for a typical box extraction, this contaminating signal amounts to 1% or less over the 1.6–2.8 μm range (order 1), and up to 1% over the 0.85–0.95 μm range (order 2). For observations of exoplanet atmospheres (transits, eclipses or phase curves) where only temporal variations in flux matter, the contamination signal typically biases the results by order of 1% of the planetary atmosphere spectral features strength. To address this problem, we developed the Algorithm to Treat Order ContAmination (ATOCA). By constructing a linear model of each pixel on the detector, treating the underlying incident spectrum as a free variable, ATOCA is able to perform a simultaneous extraction of both orders. We show that, given appropriate estimates of the spatial trace profiles, the throughputs, the wavelength solutions, as well as the spectral resolution kernels for each order, it is possible to obtain an extracted spectrum accurate to within 10 ppm over the full spectral range.

Nickel hyperaccumulation, elemental profiles and agromining potential of three species of Odontarrhena from the ultramafics of Western Iran

The profiles of trace and major elements in three Odontarrhena species from the ultramafics of Western Iran (O. callichroa, O. penjwinensis and O. inflata) were evaluated to provide detailed information on their soil-plant relationships and potentials for agromining. The mean concentrations of Ni in leaf dry matter of these three species were 877, 3,270 and 2,720 mg kg−1, respectively. The mean concentrations of total soil Ni at sites Mazi Ban, Kamyaran and Ghala Ga were 1,470, 2,480, 1,030 mg kg−1, respectively. The Bioconcentration Factor (BCF) for Ni was >1 in O. penjwinensis and O. inflata, but not in O. callichroa. A positive relationship between shoot Ni and soil pH was found for all three species. They display Ni hyperaccumulation in the leaves, but with pronounced variation in the Ni concentrations attained. Odontarrhena penjwinensis emerged as the most promising potential candidate for future Ni agromining. The progress made in this study will enable further consideration of the three Odontarrhena species, especially O. penjwinensis, for any future commercial Ni agromining of the serpentinic ultramafic soils in Western Iran.

Stitching method based on dual quaternion for cylindrical mirrors.

In this study, a stitching method based on dual quaternion is proposed. The application of a dual quaternion in sub-aperture stitching interferometry is analyzed in detail, and a calculation method for sub-aperture stitching based on a dual quaternion is deduced. The experimental results demonstrate the accuracy of the stitching method proposed in this study (residuals of overlapping area approximately 0.22 nm RMS). Finally, the residual differences of 0.79 nm RMS between the figure errors are acquired with a stitching by parts algorithm based on the dual quaternion and long trace profiler (FSP at HEPS). The high-accuracy and high-efficiency stitching method proposed in this study will expand its application in the metrology and manufacture of long cylindrical mirrors.

An informatics approach to distinguish RNA modifications in nanopore direct RNA sequencing

Modifications in RNA can influence their structure, function, and stability and play essential roles in gene expression and regulation. Methods to detect RNA modifications rely on biophysical techniques such as chromatography or mass spectrometry, which are low throughput, or on high throughput short-read sequencing techniques based on selectively reactive chemical probes. Recent studies have utilized nanopore-based fourth-generation sequencing methods to detect modifications by directly sequencing RNA in its native state. However, these approaches are based on modification-associated mismatch errors that are liable to be confounded by SNPs. Also, there is a need to generate matched knockout controls for reference, which is laborious. In this work, we introduce an internal comparison strategy termed “IndoC,” where features such as ‘trace’ and ‘current signal intensity’ of potentially modified sites are compared to similar sequence contexts on the same RNA molecule within the sample, alleviating the need for matched knockout controls. We first show that in an IVT model, ‘trace’ is able to distinguish between artificially generated SNPs and true pseudouridine (Ψ) modifications, both of which display highly similar mismatch profiles. We then apply IndoC on yeast and human ribosomal RNA to demonstrate that previously reported Ψ sites show marked changes in their trace and signal intensity profiles compared with their unmodified counterparts in the same dataset. Finally, we perform direct RNA sequencing of RNA containing Ψ intact with a chemical probe adduct (N-cyclohexyl-N′-β-(4-methylmorpholinium) ethylcarbodiimide [CMC]) and show that CMC reactivity also induces changes in trace and signal intensity distributions in a Ψ specific manner, allowing their separation from high mismatch sites that display SNP-like behavior.

Technical note: Performing LR calculations when loci are missing between reference and trace DNA profiles

The initial version of DNAStatistX calculated likelihood ratios (LRs) using only loci present in both the trace and reference profiles, thereby ignoring loci from the trace that are not present in the reference. Here, DNAStatistX was adapted to include all trace loci. At loci missing in the reference, an unknown contributor was invoked. Although this strategy is already incorporated in other systems, such as EuroForMix, we now explicitly study the effect on the LRs. As expected, stronger weights of evidence are achieved when all loci in the trace are included, especially when missing loci occur for a conditioned contributor.