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/)

Evidence of the dominant production mechanism of ammonia in a hydrogen plasma with parts per million of nitrogen

Absolute ground state atomic hydrogen densities were measured, by the utilization of two-photon absorption laser induced fluorescence, in a low-pressure electron cyclotron resonance plasma as a function of nitrogen admixtures - 0 to 5000 ppm. At nitrogen admixtures of 1500 ppm and higher, the spectral distribution of the fluorescence changes from a single Gaussian to a double Gaussian distribution; this is due to a separate, nascent contribution arising from the photolysis of an ammonia molecule. At nitrogen admixtures of 5000 ppm, the nascent contribution becomes the dominant contribution at all investigated pressures. Thermal loading experiments were conducted by heating the chamber walls to different temperatures; this showed a decrease in the nascent contributions with increasing temperature. This is explained by considering how the temperature influences recombination coefficients, and from which, it can be stated that the Langmuir-Hinshelwood recombination mechanism is dominant over the Eley-Rideal mechanism

Automated Method for the Determination of 5′-Nucleotidase in Serum by Continuous Flow Analysis

Peer Reviewe

Revision of Laparoscopic Adjustable Gastric Banding: Success or Failure?

BACKGROUND: Laparoscopic adjustable gastric banding (LAGB) is a safe and frequently performed bariatric procedure. Unfortunately, re-operations are often necessary. Reports on the success of revisional procedures are scarce and show variable results, either supporting or declining the idea of revising LAGB. This study describes a large cohort of re-operations after failed LAGB to determine the success of revision. METHODS: By use of a prospective cohort, all LAGB revisions performed between 1996 and 2008 were identified. From 301 primary LAGB procedures in our centre, 43 patients (14.3%) required a band revision. In addition, 51 patients were referred from other centres. Our analysis included in total 94 patients with a mean follow-up period of 38 months after revision. RESULTS: Revision was mainly necessary due to anterior slippage (46%) and symmetrical pouch dilatation (36%), which could be resolved by replacing (70%) or refixating the band (27%). Weight loss significantly increased after revision (excess BMI loss (EBMIL), 37.2 +/- 36.3% versus 47.5 +/- 30.4%, P < 0.05). After revision, 23 patients (24%) needed a second re-operation. Patients converted to other procedures (16%) during the second re-operation showed larger weight loss than the revised group (EBMIL, 64.3 +/- 28.1% versus 44.3 +/- 28.7%, P < 0.05). CONCLUSIONS: We report on a large cohort of LAGB revisions with 38 months of follow-up. Revision of failed LAGB by either refixation or replacement of the band is successful and further increases weight loss

N, NH, and NH2 radical densities in a remote Ar-NH3-SiH4 plasma and their role in silicon nitride deposition

The densities of N, NH, and NH2 radicals in a remote Ar-NH3-SiH4 plasma used for high-rate silicon nitride deposition were investigated for different gas mixts. and plasma settings using cavity ringdown absorption spectroscopy and threshold ionization mass spectrometry. For typical deposition conditions, the N, NH, and NH2 radical densities are on the order of 1012 cm-3 and the trends with NH3 flow, SiH4 flow, and plasma source current are reported. We present a feasible reaction pathway for the prodn. and loss of the NHx radicals that is consistent with the exptl. results. Furthermore, mass spectrometry revealed that the consumption of NH3 was typically 40%, while it was over 80% for SiH4. On the basis of the measured N densities we deduced the recombination and sticking coeff. for N radicals on a silicon nitride film. Using this sticking coeff. and reported surface reaction probabilities of NH and NH2 radicals, we conclude that N and NH2 radicals are mainly responsible for the N incorporation in the silicon nitride film, while Si atoms are most likely brought to the surface in the form of SiHx radicals. [on SciFinder (R)

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

The spatial density distribution of H2O2 in the effluent of the COST-Jet and the kINPen-sci operated with a humidified helium feed gas

Cold atmospheric plasma jets operated with a helium feed gas containing small admixtures of water vapour are excellent sources of H2O2 for direct biomedical applications. However, H2O2 is typically distributed non-uniformly throughout the effluent region, meaning the dosage received by a patient or substrate is dependent on their positioning relative to the plasma source. This study presents the spatial distribution of absolute H2O2 number densities in the effluent of two popular plasma jets, the COST-Jet and the kINPen-sci plasma jet, when operated with a humidified helium feed gas. The measurements were performed using continuous wave cavity ring-down spectroscopy with a tunable, mid-infrared laser. The H2O2 number density measured close to the jet nozzle is 2.3 × 1014 cm−3 for the kINPen-sci plasma jet and 1.4 × 1014 cm−3 for the COST-Jet. The average number density of H2O2 in the effluent of the kINPen-sci plasma jet is a factor of two higher than in the effluent of the COST-Jet. The distribution of H2O2 in the COST-Jet effluent is initially highly uniform and suggests negligible mixing of H2O2 with the ambient air up to 15 mm from the jet nozzle, although it is rapidly diluted at further distances. In the case of the kINPen-sci plasma jet, the number density of H2O2 has a more pronounced radial distribution close to the nozzle, while the mixing with the ambient air is more gradual at further distances from the nozzle. It is evident that a detailed understanding of the H2O2 production in the plasma source, as well as of the transport of H2O2 to the substrate through the effluent, is required in order to optimise the intended effects. This work serves to highlight the difference of the distinct spatial distribution of H2O2 in the effluent of both types of plasma jets when considering their direct application in biomedicine

What is the long-term clinical outcome after fragility fractures of the pelvis? - A CT-based cross-sectional study

Background: Recently, Rommens and Hoffman introduced a CT-based classification system for fragility fractures of the pelvis (FFP). Although fracture characteristics have been described, the relationship with clinical outcome is lacking. The purpose of this study was to get insight into the type of treatment and subsequent clinical outcome after all types of FFP. Methods: A cross-sectional cohort study was performed including all elderly patients (≥ 65 years) with a CT-diagnosed FFP, between 2007-2019 in two level 1 trauma centers. Data regarding treatment, mortality and clinical outcome was gathered from the electronic patient files. Patients were asked to complete patient-reported outcome measures (PROMs) regarding physical functioning (SMFA) and quality of life (EQ-5D). Additionally, a standardized multidisciplinary treatment algorithm was constructed. Results: A total of 187 patients were diagnosed with an FFP of whom 117 patients were available for follow-up analysis and 58 patients responded. FFP type I was most common (60%), followed by type II (27%), type III (8%) and type IV (5%). Almost all injuries were treated non-operatively (98%). Mobility at six weeks ranged from 50% (type III) to 80% type II). Mortality at 1 year was respectively 16% (type I and II), 47% (type III) and 13% (type IV). Physical functioning (SMFA function index) ranged from 62 (type III and IV) to 69 (type II) and was significantly decreased (P=<0.001) compared to the age-matched general population. Quality of life was also significantly decreased, ranging from 0.26 (type III) to 0.69 (type IV). Conclusions: FFP type I and II are most common. Treatment is mainly non-operative, resulting in good mobility after six weeks, especially for patients with FFP type I and II. Mortality rates at one year were substantial in all patients. Physical functioning and quality of life was about 20-30% decreased compared to the general population

Are sarcopenia and myosteatosis in elderly patients with pelvic ring injury related to mortality, physical functioning and quality of life?

The purpose of this study was to evaluate the prevalence of sarcopenia and/or myosteatosis in elderly patients with pelvic ring injuries and their influence on mortality, patient-perceived physical functioning and quality of life (QoL). A multicenter retrospective cohort study was conducted including elderly patients aged ≥ 65 treated for a pelvic ring injury. Cross-sectional computed tomography (CT) muscle measurements were obtained to determine the presence of sarcopenia and/or myosteatosis. Kaplan–Meier analysis was used for survival analysis, and Cox proportional hazards regression analysis was used to determine risk factors for mortality. Patient-reported outcome measures for physical functioning (SMFA) and QoL (EQ-5D) were used. Multivariable linear regression analyses were used to determine the effect of sarcopenia and myosteatosis on patient-perceived physical functioning and QoL. Data to determine sarcopenia and myosteatosis were available for 199 patients, with a mean follow-up of 2.4 ± 2.2 years: 66 patients (33%) were diagnosed with sarcopenia and 65 (32%) with myosteatosis, while 30 of them (15%) had both. Mortality rates in patients at 1 and 3 years without sarcopenia and myosteatosis were 13% and 21%, compared to 11% and 36% in patients with sarcopenia, 17% and 31% in patients with myosteatosis and 27% and 43% in patients with both. Higher age at the time of injury and a higher Charlson Comorbidity Index (CCI) were independent risk factors for mortality. Patient-reported mental and emotional problems were significantly increased in patients with sarcopenia