sj-docx-1-wmr-10.1177_0734242X231167078 – Supplemental material for Optimisation of process parameters of a thermal digester for the rapid conversion of food waste into value-added soil conditioner

Supplemental material, sj-docx-1-wmr-10.1177_0734242X231167078 for Optimisation of process parameters of a thermal digester for the rapid conversion of food waste into value-added soil conditioner by Nitin Kumar, Sunil Kumar Gupta and Brahmdeo Yadav in Waste Management & Research</p

The flowchart of arrayMap data collection and analysis procedures.

<p>Publicly available raw data or segmented data was collected from the respective data sources. Files were re-processed by distinct procedures, according to the different data types. Probe coordinates were remapped to the most commonly encountered human reference genome assembly (NCBI Build 36/hg18). All probe specific ratios were converted to log2 values. Thresholds for genomic gain and loss were obtained from the original publications or series annotations; if not available, empirical thresholds were assigned. A minimum of 2 probes was required for calling a CNA segment, with higher values used on high-density arrays and/or in cases of excessive probe level noise. Processed probe and segment information was converted to uniform formats and stored in per-sample text files, which are accessed through the arrayMap web applications.</p

Distribution of resolutions and techniques of GEO platforms.

<p>Each point represents a genomic array. The Y axis is labeled with probe number in log scale. The X axis denotes the time sequence of array data generation. From left to right are years from 2001 to 2011.</p

Copy number profiling of glioblastoma.

<p>(A) Chromosomal ideogram and histogram showing frequency of copy number aberrations. Percentage values corresponding to gains (yellow) and losses (blue) identified over the whole dataset. The most frequent imbalances include gain of chromosome 7 and loss of chromosome 10, 9p21.3. (B) Matrix plot of 1478 glioblastoma cases. The Y axis represents individual samples. The distribution of genomic copy number imbalances reveals the individual aberration patterns of glioblastoma. (C) Heatmap of regional CNA frequencies for 1478 arrays. The intensity of green and red color components correlates to the relative gain and loss frequencies, respectively. If dataset contains cancer subtypes, cancers with similar CNA frequency profiles will be clustered together, such that differences between subtypes will be revealed (e.g. see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036944#pone.0036944.s004" target="_blank">Figure S4H</a>).</p

aCGH data integrated in arrayMap.

<p>Data up to 29 April, 2011.</p>*<p>Due to lack of publication information, there may be a small amount of duplicate data in GEO.</p>**<p>Array number may be higher than case number since reported results per case occasionally may be based on more than one array. The number does not include data presented both in publication supplements as well as GEO.</p

Prominent online resources of genomic data.

<p>Data up to 29 April, 2011.</p>*<p>excluding data both in GEO and ArrayExpress.</p>**<p>statistical information only including CGH, SNP and cDNA data.</p>***<p>International system for human cytogenetic nomenclature.</p

Water Adsorption and Insertion in MOF‑5

The high surface areas and tunable properties of metal–organic frameworks (MOFs) make them attractive materials for applications in catalysis and the capture, storage, and separation of gases. Nevertheless, the limited stability of some MOFs under humid conditions remains a point of concern. Understanding the atomic-scale mechanisms associated with MOF hydrolysis will aid in the design of new compounds that are stable against water and other reactive species. Toward revealing these mechanisms, the present study employs van der Waals-augmented density functional theory, transition-state finding techniques, and thermodynamic integration to predict the thermodynamics and kinetics of water adsorption/insertion into the prototype compound, MOF-5. Adsorption and insertion energetics were evaluated as a function of water coverage, while accounting for the full periodicity of the MOF-5 crystal structure, that is, without resorting to cluster approximations or structural simplifications. The calculations suggest that the thermodynamics of MOF hydrolysis are coverage-dependent: water insertion into the framework becomes exothermic only after a sufficient number of H₂O molecules are coadsorbed in close proximity on a Zn–O cluster. Above this coverage threshold, the adsorbed water clusters facilitate facile water insertion via breaking of Zn–O bonds: the calculated free-energy barrier for insertion is very low, 0.17 eV at 0 K and 0.04 eV at 300 K. Our calculations provide a highly realistic description of the mechanisms underlying the hydrolysis of MOFs under humid working conditions

Percentage of remapped probes according to platform types.

<p>Percentage of remapped probes according to platform types.</p

The overall cancer copy number aberration profile consisted of 29137 arrays.

<p>This plot represents 177 cancer types according to ICD-O 3 code. Percentage values in Y axis corresponding to numbers of gains (green) and losses (red) account for the whole dataset.</p

Examples for non-neutral CNA regions.

<p>a) Heatmap of CNA profiles on genomic regions (same clustering as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0043689#pone-0043689-g002" target="_blank">Figure 2</a>). Genomic locations are represented with orange color when considering duplications/gains, and in blue when considering deletions/losses. Color intensity shows relative CNA frequencies; the most-affected region in each row is arbitrarily set the to brightest color (1.0) for display purposes. b) Small regions (black rectangles on the heatmap) are zoomed in to show how non-neutral CNAs can differentiate between cancer types. The example shows that 7q is preferentially gained in brain tumors (red labels) whereas it is preferentially lost in germ cell (black labels), myeloid and myeloproliferative cancer types (blue labels). c) Small regions (red rectangles on the heatmap) are zoomed in to show how 8q is preferentially lost in medullublastomas (green labels) and is preferentially gained in epithelial tumors (pink labels). Some chromosomes consist entirely of non-neutral regions (such as chromosomes 18 and 7). Note that the spatial resolution of the CNA data on the chromosome is limited (roughly corresponding to cytogenetic band resolution).</p