Application of regulatory sequence analysis and metabolic network analysis to the interpretation of gene expression data

We present two complementary approaches for the interpretation of clusters of co-regulated genes, such as those obtained from DNA chips and related methods. Starting from a cluster of genes with similar expression profiles, two basic questions can be asked: 1. Which mechanism is responsible for the coordinated transcriptional response of the genes? This question is approached by extracting motifs that are shared between the upstream sequences of these genes. The motifs extracted are putative cis-acting regulatory elements. 2. What is the physiological meaning for the cell to express together these genes? One way to answer the question is to search for potential metabolic pathways that could be catalyzed by the products of the genes. This can be done by selecting the genes from the cluster that code for enzymes, and trying to assemble the catalyzed reactions to form metabolic pathways. We present tools to answer these two questions, and we illustrate their use with selected examples in the yeast Saccharomyces cerevisiae. The tools are available on the web (http://ucmb.ulb.ac.be/bioinformatics/rsa-tools/; http://www.ebi.ac.uk/research/pfbp/; http://www.soi.city.ac.uk/~msch/)

Verified modeling of a low pressure hydrogen plasma generated by electron cyclotron resonance

A self-consistent fluid model has been successfully developed and employed to model an electron cyclotron resonance driven hydrogen plasma at low pressure. This model has enabled key insights to be made on the mutual interaction of microwave propagation, power density, plasma generation, and species transport at conditions where the critical plasma density is exceeded. The model has been verified by two experimental methods. Good agreement with the ion current density and floating potential—as measured by a retarding energy field analyzer—and excellent agreement with the atomic hydrogen density—as measured by two-photon absorption laser induced fluorescence—enables a high level of confidence in the validity of the simulation

Spectroscopic study of plasma nitrocarburizing processes with an industrial-scale carbon active screen

The active screen plasma nitrocarburizing technology is an improvement of conventional plasma nitrocarburizing by providing a homogeneous temperature distribution within the workload and reducing soot formation. In this study, an industrial-scale active screen (AS) made of carbon-fibre-reinforced carbon serves as the cathode as well as the carbon source for the plasma-chemical processes taking place. The pulsed dc discharge was maintained at a few mbar of pressure while simultaneously being fed with a mixed gas flow of hydrogen and nitrogen ranging from 10 to 100 slh. Using in situ infrared laser absorption spectroscopy with lead salt tuneable diode lasers and external-cavity quantum cascade lasers, the temperatures and concentrations of HCN, NH3, CH4, C2H2, and CO have been monitored as a function of pressure and total gas flow. To simulate industrial treatment conditions the temperature of the sample workload in the centre of the reactor volume was kept at 773 K by varying the plasma power at the AS between 6 and 8.5 kW. The resulting spectroscopically measured temperatures in the plasma agreed well with this value. Concentrations of the various species ranged from 6 × 1013 to 1 × 1016 cm−3 with HCN being the most abundant species

Terahertz quantum-cascade lasers for high-resolution absorption spectroscopy of atoms and ions in plasmas

We report on terahertz (THz) quantum-cascade lasers (QCLs) based on GaAs/AlAs heterostructures, which exhibit single-mode emission at 3.360, 3.921, and 4.745 THz. These frequencies are in close correspondence to fine-structure transitions of Al atoms, N+ ions, and O atoms, respectively. Due to the low electrical pump power of these THz QCLs, they can be operated in a mechanical cryocooler in continuous-wave mode, while a sufficient intrinsic tuning range of more than 5 GHz is maintained. The single-mode operation and the intrinsic tuning range of these THz QCLs allow for the application of these lasers as radiation sources for high-resolution absorption spectroscopy to determine the absolute densities of Al atoms, N+ ions, and O atoms in plasmas

Terahertz quantum-cascade lasers for high-resolution absorption spectroscopy of atoms and ions in plasmas

We report on terahertz (THz) quantum-cascade lasers (QCLs) based on GaAs/AlAs heterostructures, which exhibit single-mode emission at 3.360, 3.921, and 4.745 THz. These frequencies are in close correspondence to fine-structure transitions of Al atoms, N+ ions, and O atoms, respectively. Due to the low electrical pump power of these THz QCLs, they can be operated in a mechanical cryocooler in continuous-wave mode, while a sufficient intrinsic tuning range of more than 5 GHz is maintained. The single-mode operation and the intrinsic tuning range of these THz QCLs allow for the application of these lasers as radiation sources for high-resolution absorption spectroscopy to determine the absolute densities of Al atoms, N+ ions, and O atoms in plasmas

Terahertz absorption spectroscopy for measuring atomic oxygen densities in plasmas

This paper describes the first implementation of terahertz (THz) quantum cascade lasers for high-resolution absorption spectroscopy on plasmas. Absolute densities of ground state atomic oxygen were directly obtained by using the fine structure transition at approximately 4.75 THz. Measurements were performed on a low-pressure capacitively coupled radio frequency oxygen discharge. The detection limit in this arrangement was found to be 2 × 10 13 cm−3, while the measurement accuracy was within 5%, as demonstrated by reference measurements of a well-defined ammonia transition. The results show that the presented method is well suited to measure atomic oxygen densities, and it closes the THz gap for quantitative atomic density measurements in harsh environments such as plasmas

Terahertz quantum-cascade lasers for high-resolution absorption spectroscopy of atoms and ions in plasmas

We report on terahertz (THz) quantum-cascade lasers (QCLs) based on GaAs/AlAs heterostructures, which exhibit single-mode emission at 3.360, 3.921, and 4.745 THz. These frequencies are in close correspondence to fine-structure transitions of Al atoms, N+ ions, and O atoms, respectively. Due to the low electrical pump power of these THz QCLs, they can be operated in a mechanical cryocooler in continuous-wave mode, while a sufficient intrinsic tuning range of more than 5 GHz is maintained. The single-mode operation and the intrinsic tuning range of these THz QCLs allow for the application of these lasers as radiation sources for high-resolution absorption spectroscopy to determine the absolute densities of Al atoms, N+ ions, and O atoms in plasmas

Initial and Residual 3D Fracture Displacement Is Predictive for Patient-Reported Functional Outcome at Mid-Term Follow-Up in Surgically Treated Tibial Plateau Fractures

Background: Conventional measures of fracture displacement have low interobserver reliability. This study introduced a novel 3D method to measure tibial plateau fracture displacement and its impact on functional outcome. Methods: A multicentre study was conducted on patients who had tibial plateau fracture surgery between 2003 and 2018. Eligible patients had a preoperative CT scan (slice thickness ≤ 1 mm) and received a Knee Injury and Osteoarthritis Outcome Score (KOOS) questionnaire. A total of 362 patients responded (57%), and assessment of initial and residual fracture displacement was performed via measurement using the 3D gap area (mm2). Patients were divided into four groups based on the 3D gap area size. Differences in functional outcome between these groups were assessed using analysis of variance (ANOVA). Multiple linear regression was used to determine the association between fracture displacement and patient-reported outcome. Results: Functional outcome appeared significantly worse when initial or residual fracture displacement increased. Multivariate linear regression showed that initial 3D gap area (per 100 mm2) was significantly negatively associated with all KOOS subscales: symptoms (−0.9, p &lt; 0.001), pain (−0.0, p &lt; 0.001), ADL (−0.8, p = 0.002), sport (−1.4, p &lt; 0.001), and QoL (−1.1, p &lt; 0.001). In addition, residual gap area was significantly negatively associated with the subscales symptoms (−2.2, p = 0.011), ADL (−2.2, p = 0.014), sport (−2.6, p = 0.033), and QoL (−2.4, p = 0.023). Conclusion: A novel 3D measurement method was applied to quantify initial and residual displacement. This is the first study which can reliably classify the degree of displacement and indicates that increasing displacement results in poorer patient-reported functional outcomes.</p

Initial and Residual 3D Fracture Displacement Is Predictive for Patient-Reported Functional Outcome at Mid-Term Follow-Up in Surgically Treated Tibial Plateau Fractures

Background: Conventional measures of fracture displacement have low interobserver reliability. This study introduced a novel 3D method to measure tibial plateau fracture displacement and its impact on functional outcome. Methods: A multicentre study was conducted on patients who had tibial plateau fracture surgery between 2003 and 2018. Eligible patients had a preoperative CT scan (slice thickness ≤ 1 mm) and received a Knee Injury and Osteoarthritis Outcome Score (KOOS) questionnaire. A total of 362 patients responded (57%), and assessment of initial and residual fracture displacement was performed via measurement using the 3D gap area (mm2). Patients were divided into four groups based on the 3D gap area size. Differences in functional outcome between these groups were assessed using analysis of variance (ANOVA). Multiple linear regression was used to determine the association between fracture displacement and patient-reported outcome. Results: Functional outcome appeared significantly worse when initial or residual fracture displacement increased. Multivariate linear regression showed that initial 3D gap area (per 100 mm2) was significantly negatively associated with all KOOS subscales: symptoms (−0.9, p &lt; 0.001), pain (−0.0, p &lt; 0.001), ADL (−0.8, p = 0.002), sport (−1.4, p &lt; 0.001), and QoL (−1.1, p &lt; 0.001). In addition, residual gap area was significantly negatively associated with the subscales symptoms (−2.2, p = 0.011), ADL (−2.2, p = 0.014), sport (−2.6, p = 0.033), and QoL (−2.4, p = 0.023). Conclusion: A novel 3D measurement method was applied to quantify initial and residual displacement. This is the first study which can reliably classify the degree of displacement and indicates that increasing displacement results in poorer patient-reported functional outcomes.</p