Computation of generalized inverses using Php/MySql environment

The main aim of this paper is to develop a client/server-based model for computing the weighted Moore-Penrose inverse using the partitioning method as well as for storage of generated results. The web application is developed in the PHP/MySQL environment. The source code is open and free for testing by using a web browser. Influence of different matrix representations and storage systems on the computational time is investigated. The CPU time for searching the previously stored pseudo-inverses is compared with the CPU time spent for new computation of the same inverses.Comment: International Journal of Computer Mathematics, Volume 88, Issue 11, 201

Carbonaceous material export from Siberian permafrost tracked across the Arctic Shelf using Raman spectroscopy

Warming-induced erosion of permafrost from Eastern Siberia mobilises large amounts of organic carbon and delivers it to the East Siberian Arctic Shelf (ESAS). In this study Raman spectroscopy of Carbonaceous Material (CM) was used to characterise, identify and track the most recalcitrant fraction of the organic load. 1463 spectra were obtained from surface sediments collected across the ESAS and automatically analysed for their Raman peaks. Spectra were classified by their peak areas and widths into Disordered, Intermediate, Mildly Graphitised and Highly Graphitised groups, and the distribution of these classes was investigated across the shelf. Disordered CM was most prevalent in a permafrost core from Kurungnakh Island, and from areas known to have high rates of coastal erosion. Sediments from outflows of the Indigirka and Kolyma rivers were generally enriched in Intermediate CM. These different sediment sources were identified and distinguished along an E-W transect using their Raman spectra, showing that sediment is not homogenised on the ESAS. Distal samples, from the ESAS slope, contained greater amounts of Highly Graphitised CM compared to the rest of the shelf, attributable to degradation or, more likely, winnowing processes offshore. The presence of all four spectral classes in distal sediments demonstrates that CM degrades much slower than lipid biomarkers and other traditional tracers of terrestrial organic matter, and shows that alongside degradation of the more labile organic matter component there is also conservative transport of carbon across the shelf toward the deep ocean. Thus, carbon cycle calculations must consider the nature as well as the amount of carbon liberated from thawing permafrost and other erosional settings

Macromolecular composition of terrestrial and marine organic matter in sediments across the East Siberian Arctic Shelf

Mobilisation of terrestrial organic carbon (terrOC) from permafrost environments in Eastern Siberia has the potential to deliver significant amounts of carbon to the Arctic Ocean, via both fluvial and coastal erosion. Eroded terrOC can be degraded during offshore transport, or deposited across the wide East Siberian Arctic Shelf (ESAS). Most studies of terrOC on the ESAS have concentrated on solvent-extractable organic matter, but this represents only a small proportion of the total terrOC load. In this study we have used pyrolysis gas chromatography mass spectrometry (py-GCMS) to study all major groups of macromolecular components of the terrOC; this is the first time that this technique has been applied to the ESAS. This has shown that there is a strong offshore trend from terrestrial Phenols, Aromatics, Cyclopentenones to marine Pyridines. There is good agreement between proportion Phenols measured using py-GCMS and independent quantification of lignin phenol concentrations (r2 = 0.67, p < 0.01, n = 24). Furfurals, thought to represent carbohydrates, show no offshore trend and are likely found in both marine and terrestrial organic matter. We have also collected new radiocarbon data for bulk OC (14COC) which, when coupled with previous measurements, allows us to produce the most comprehensive 14COC map of the ESAS to date. Combining the 14COC and py-GCMS data suggests that the Aromatics group of compounds is likely sourced from old, aged terrOC in contrast to the Phenols group, which is likely sourced from modern woody material. We propose that an index of the relative proportions of Phenols and Pyridines can be used as a novel terrestrial vs. marine proxy measurement for macromolecular organic matter. Principal component analysis found that various terrestrial vs. marine proxies show different patterns across the ESAS, and shows that multiple river-ocean transects of surface sediments transition from river-dominated to coastal erosion-dominated to marine-dominated signatures

Systematic Parameterization, Storage, and Representation of Volumetric DICOM Data

Tomographic medical imaging systems produce hundreds to thousands of slices, enabling three-dimensional (3D) analysis. Radiologists process these images through various tools and techniques in order to generate 3D renderings for various applications, such as surgical planning, medical education, and volumetric measurements. To save and store these visualizations, current systems use snapshots or video exporting, which prevents further optimizations and requires the storage of significant additional data. The Grayscale Softcopy Presentation State extension of the Digital Imaging and Communications in Medicine (DICOM) standard resolves this issue for two-dimensional (2D) data by introducing an extensive set of parameters, namely 2D Presentation States (2DPR), that describe how an image should be displayed. 2DPR allows storing these parameters instead of storing parameter applied images, which cause unnecessary duplication of the image data. Since there is currently no corresponding extension for 3D data, in this study, a DICOM-compliant object called 3D presentation states (3DPR) is proposed for the parameterization and storage of 3D medical volumes. To accomplish this, the 3D medical visualization process is divided into four tasks, namely pre-processing, segmentation, post-processing, and rendering. The important parameters of each task are determined. Special focus is given to the compression of segmented data, parameterization of the rendering process, and DICOM-compliant implementation of the 3DPR object. The use of 3DPR was tested in a radiology department on three clinical cases, which require multiple segmentations and visualizations during the workflow of radiologists. The results show that 3DPR can effectively simplify the workload of physicians by directly regenerating 3D renderings without repeating intermediate tasks, increase efficiency by preserving all user interactions, and provide efficient storage as well as transfer of visualized data. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s40846-015-0097-5) contains supplementary material, which is available to authorized users

Source, transport and fate of soil organic matter inferred from microbial biomarker lipids on the East Siberian Arctic Shelf

The Siberian Arctic contains a globally significant pool of organic carbon (OC) vulnerable to enhanced warming and subsequent release by both fluvial and coastal erosion processes. However, the rate of release, its behaviour in the Arctic Ocean and vulnerability to remineralisation is poorly understood. Here we combine new measurements of microbial biohopanoids including adenosylhopane, a lipid associated with soil microbial communities, with published glycerol dialkyl glycerol tetraether (GDGTs) and bulk δ13C 5 measurements to improve knowledge of the fate of OC transported to the East Siberian Arctic Shelf (ESAS). The microbial hopanoid-based soil OC proxy R'soil ranges from 0.0 to 0.8 across the ESAS, with highest values near shore and decreases offshore. Across the shelf R'soil displays a negative linear correlation with bulk δ13C measurements (r2 = −0.73, p = < 0.001). When compared to the GDGT based OC proxy, the Branched and Isoprenoid tetraether (BIT) index, a decoupled (non-linear) behaviour on the shelf was observed, particularly in the Buor-Khaya Bay where the R'soil shows limited 10 variation, whereas the BIT index shows a rapid decline moving away from the Lena River outflow channels. This reflects a balance between delivery and removal of OC from different sources. The good correlation between the hopanoid and bulk terrestrial signal suggests a broad range of hopanoid sources, both fluvial and via coastal erosion whilst GDGTs appear to be primarily sourced via fluvial transport. Analysis of ice complex deposits (ICDs) revealed an average R'soil of 0.5 for the Lena delta, equivalent to that of the Buor-Khaya Bay sediments, whilst ICDs from further East showed higher values (0.6–0.85). Al15 though R'soil correlates more closely with bulk OC than the BIT, our understanding of the endmembers of this system is clearly still incomplete with east-west variations potentially reflecting differences in environmental conditions (e.g. temperature, pH) but other physiological controls on microbial BHP production under psychrophilic conditions are as yet unknown

An interlaboratory study of TEX86 and BIT analysis of sediments, extracts and standard mixtures.

Two commonly used proxies based on the distribution of glycerol dialkyl glycerol tetraethers (GDGTs) are the TEX86 (TetraEther indeX of 86 carbon atoms) paleothermometer for sea surface temperature reconstructions and the BIT (Branched Isoprenoid Tetraether) index for reconstructing soil organic matter input to the ocean. An initial round-robin study of two sediment extracts, in which 15 laboratories participated, showed relatively consistent TEX86 values (reproducibility ±3-4°C when translated to temperature) but a large spread in BIT measurements (reproducibility ±0.41 on a scale of 0-1). Here we report results of a second round-robin study with 35 laboratories in which three sediments, one sediment extract, and two mixtures of pure, isolated GDGTs were analyzed. The results for TEX86 and BIT index showed improvement compared to the previous round-robin study. The reproducibility, indicating interlaboratory variation, of TEX86 values ranged from 1.3 to 3.0°C when translated to temperature. These results are similar to those of other temperature proxies used in paleoceanography. Comparison of the results obtained from one of the three sediments showed that TEX86 and BIT indices are not significantly affected by interlaboratory differences in sediment extraction techniques. BIT values of the sediments and extracts were at the extremes of the index with values close to 0 or 1, and showed good reproducibility (ranging from 0.013 to 0.042). However, the measured BIT values for the two GDGT mixtures, with known molar ratios of crenarchaeol and branched GDGTs, had intermediate BIT values and showed poor reproducibility and a large overestimation of the "true" (i.e., molar-based) BIT index. The latter is likely due to, among other factors, the higher mass spectrometric response of branched GDGTs compared to crenarchaeol, which also varies among mass spectrometers. Correction for this different mass spectrometric response showed a considerable improvement in the reproducibility of BIT index measurements among laboratories, as well as a substantially improved estimation of molar-based BIT values. This suggests that standard mixtures should be used in order to obtain consistent, and molar-based, BIT values

Effect of angiotensin-converting enzyme inhibitor and angiotensin receptor blocker initiation on organ support-free days in patients hospitalized with COVID-19

IMPORTANCE Overactivation of the renin-angiotensin system (RAS) may contribute to poor clinical outcomes in patients with COVID-19. Objective To determine whether angiotensin-converting enzyme (ACE) inhibitor or angiotensin receptor blocker (ARB) initiation improves outcomes in patients hospitalized for COVID-19. DESIGN, SETTING, AND PARTICIPANTS In an ongoing, adaptive platform randomized clinical trial, 721 critically ill and 58 non–critically ill hospitalized adults were randomized to receive an RAS inhibitor or control between March 16, 2021, and February 25, 2022, at 69 sites in 7 countries (final follow-up on June 1, 2022). INTERVENTIONS Patients were randomized to receive open-label initiation of an ACE inhibitor (n = 257), ARB (n = 248), ARB in combination with DMX-200 (a chemokine receptor-2 inhibitor; n = 10), or no RAS inhibitor (control; n = 264) for up to 10 days. MAIN OUTCOMES AND MEASURES The primary outcome was organ support–free days, a composite of hospital survival and days alive without cardiovascular or respiratory organ support through 21 days. The primary analysis was a bayesian cumulative logistic model. Odds ratios (ORs) greater than 1 represent improved outcomes. RESULTS On February 25, 2022, enrollment was discontinued due to safety concerns. Among 679 critically ill patients with available primary outcome data, the median age was 56 years and 239 participants (35.2%) were women. Median (IQR) organ support–free days among critically ill patients was 10 (–1 to 16) in the ACE inhibitor group (n = 231), 8 (–1 to 17) in the ARB group (n = 217), and 12 (0 to 17) in the control group (n = 231) (median adjusted odds ratios of 0.77 [95% bayesian credible interval, 0.58-1.06] for improvement for ACE inhibitor and 0.76 [95% credible interval, 0.56-1.05] for ARB compared with control). The posterior probabilities that ACE inhibitors and ARBs worsened organ support–free days compared with control were 94.9% and 95.4%, respectively. Hospital survival occurred in 166 of 231 critically ill participants (71.9%) in the ACE inhibitor group, 152 of 217 (70.0%) in the ARB group, and 182 of 231 (78.8%) in the control group (posterior probabilities that ACE inhibitor and ARB worsened hospital survival compared with control were 95.3% and 98.1%, respectively). CONCLUSIONS AND RELEVANCE In this trial, among critically ill adults with COVID-19, initiation of an ACE inhibitor or ARB did not improve, and likely worsened, clinical outcomes. TRIAL REGISTRATION ClinicalTrials.gov Identifier: NCT0273570

Analysis on the use of Multi-Sequence MRI Series for Segmentation of Abdominal Organs

Segmentation of abdominal organs from MRI data sets is a challenging task due to various limitations and artefacts. During the routine clinical practice, radiologists use multiple MR sequences in order to analyze different anatomical properties. These sequences have different characteristics in terms of acquisition parameters (such as contrast mechanisms and pulse sequence designs) and image properties (such as pixel spacing, slice thicknesses and dynamic range). For a complete understanding of the data, computational techniques should combine the information coming from these various MRI sequences. These sequences are not acquired in parallel but in a sequential manner (one after another). Therefore, patient movements and respiratory motions change the position and shape of the abdominal organs. In this study, the amount of these effects is measured using three different symmetric surface distance metrics performed to three dimensional data acquired from various MRI sequences. The results are compared to intra and inter observer differences and discussions on using multiple MRI sequences for segmentation and the necessities for registration are presented

Camera Based Driver Support System for Rail Extraction using 2-D Gabor Wavelet Decompositions and Morphological Analysis

Determining the position and the alignment of the rails ahead of a train is an essential element of camera based driver support systems, which aim to detect the obstacles around the railway. Effective extraction of the rails through a camera faces many challenges that cause poor visibility due to several factors including but not limited to bad weather conditions, inverse illumination, shadows, rust, and clustered rails. Moreover, the process should be completed almost in real time without using any explicit knowledge about the train speed or the camera parameters. This study presents a robust approach that partitions a video frame into four regions, each of which is filtered by two-dimensional Gabor wavelets at different scales. Considering the size and the orientation range of the rails at each partition, responses of the Gabor wavelets, which are tuned to specific frequencies, enable rail edge enhancement together with noise filtering. The proposed approach has been applied to several different scenarios and the results indicate that an effective method is developed