Comparison Log
2026-04-12 08:19:08.400410
mwtab Python Library Version: 2.0.0
Source:      https://www.metabolomicsworkbench.org/rest/study/analysis_id/AN006349/mwtab/...
Study ID:    ST003863
Analysis ID: AN006349
Status:      Inconsistent

Sections "COLLECTION" contain missmatched items: {'COLLECTION_SUMMARY': ['This study obtained ethical approval from both the University of Northumbria Ethics Committee (Ref. 11623) and the University of Central Lancashire Ethics Committee (Ref. SCIENCE 0223). De-fleshed pig mandibles (N = 12) were purchased from a local butcher and were considered "fresh" with a PMI effectively set to zero despite the animals\' actual time of death. The mandibles were kept refrigerated at +4 °C for one day before the experiment began. Each mandible was sectioned into four quadrants by performing both longitudinal and transversal cuts using a manual saw to limit bone molecular decay due to heating, producing four fragments that could be considered as biological replicates from a molecular point of view. To confirm the suitability of these fragments as replicates, preliminary proteomics and metabolomics tests were conducted on a separate test mandible from the same supplier. The results (data not shown) confirmed the biomolecular profile similarity among the four fragments, indicating no significant differences between each mandible portion.', "This study obtained ethical approval from both the University of Northumbria Ethics Committee (Ref. 11623) and the University of Central Lancashire Ethics Committee (Ref. SCIENCE 0223). De-fleshed pig mandibles (N = 12) were purchased from a local butcher and were considered fresh with a PMI effectively set to zero despite the animals'' actual time of death. The mandibles were kept refrigerated at +4 °C for one day before the experiment began. Each mandible was sectioned into four quadrants by performing both longitudinal and transversal cuts using a manual saw to limit bone molecular decay due to heating, producing four fragments that could be considered as biological replicates from a molecular point of view. To confirm the suitability of these fragments as replicates, preliminary proteomics and metabolomics tests were conducted on a separate test mandible from the same supplier. The results (data not shown) confirmed the biomolecular profile similarity among the four fragments, indicating no significant differences between each mandible portion."]}
Sections "SAMPLEPREP" contain missmatched items: {'SAMPLEPREP_SUMMARY': ["Bone sub-samples from each quadrant were taken by cutting a small bone fragment (approximately 0.5 cm³) using a manual saw. Control samples (time 0) were collected from each mandible at the start of the experiment (n = 12 control samples in total). Additional samples were collected from each quadrant at the end of each selected time point in the experiment. All samples were stored at -20°C until the experiment's completion, after which they underwent metabolomic extraction. The quadrants from PM4 buried at 10 cm, from PM8 buried at 10 cm and from PM12 buried at 30 cm and 50 cm were not recovered, likely due to scavenging activity or for other unforeseen reasons and were therefore not available for subsequent -omics analyses. The small bone samples collected from each mandible (n = 56 including the 12 controls collected at time 0) were reduced in powder with a 6775 Freezer/Mill® Cryogenic Grinder (SPEX® Sample Prep, Metuchen, NJ) under the following conditions: samples were pre-cooled for 2 minutes in liquid nitrogen before being subjected to two grinding cycles. Each cycle consisted of a 2-minute run at a rate of 7 cycles per second (cps), with 2 minutes of intermediate cooling time. The samples were placed in appropriate milling vials and submerged in liquid nitrogen to ensure cryogenic temperatures throughout the process. After grinding, the resulting bone powder was carefully collected for subsequent analysis. The extraction followed the protocol by Bonicelli et al.(https://doi.org/10.1039/D4MO00015C) with minimal amendments. Specifically, 50 mg of bone powder were added to 2 mL pre-filled bead mill tube containing ceramic beads (1.4 mm in diameter), and 950 μL of an 8:2 (% v/v) methanol-water solution was added. The samples were vortexed for 30 seconds and then homogenized using a Precellys Evolution Touch Homogenizer with four 20-second bursts at 5854 g, with a 2-minute pause between bursts. The homogenization tube was then centrifuged at 18,213 g at 4 °C for 10 minutes, and 900 μL of the supernatant was transferred to a new tube. An additional 750 μL of the methanol-water solution was added to the original tube, and the homogenization process was repeated. After centrifugation at 18,213 g at 4 °C for 10 minutes, another 700 μL of supernatant was transferred to the same collection tube. This combined extract was centrifuged once more at 18,213 g at 4 °C for 10 minutes, after which 1.2 mL of the supernatant was transferred to a fresh tube and dried under a nitrogen flow. The dried extracts were then stored at −80 °C until further testing. Bone extracts were resuspended in 50 µL of methoxamine hydrochloride solution in pyridine (Sigma-Aldrich: TS45950) and incubated in a Thermomixer (Thermo Scientific) at 60 °C with shaking at 400 rpm for 15 minutes. After incubation, the samples were removed from the Thermomixer and left to cool. Subsequently, 50 µL of BSTFA + 1% TMCS (Supelco: B-023) was added, and the mixture was incubated again at 60 °C with shaking at 400 rpm for another 15 minutes. Negative controls consisting of methoxamine hydrochloride solution and BSTFA alone were prepared as blanks.", "Bone sub-samples from each quadrant were taken by cutting a small bone fragment (approximately 0.5 cm³) using a manual saw. Control samples (time 0) were collected from each mandible at the start of the experiment (n = 12 control samples in total). Additional samples were collected from each quadrant at the end of each selected time point in the experiment. All samples were stored at -20°C until the experiment''s completion, after which they underwent metabolomic extraction. The quadrants from PM4 buried at 10 cm, from PM8 buried at 10 cm and from PM12 buried at 30 cm and 50 cm were not recovered, likely due to scavenging activity or for other unforeseen reasons and were therefore not available for subsequent -omics analyses. The small bone samples collected from each mandible (n = 56 including the 12 controls collected at time 0) were reduced in powder with a 6775 Freezer/Mill® Cryogenic Grinder (SPEX® Sample Prep, Metuchen, NJ) under the following conditions: samples were pre-cooled for 2 minutes in liquid nitrogen before being subjected to two grinding cycles. Each cycle consisted of a 2-minute run at a rate of 7 cycles per second (cps), with 2 minutes of intermediate cooling time. The samples were placed in appropriate milling vials and submerged in liquid nitrogen to ensure cryogenic temperatures throughout the process. After grinding, the resulting bone powder was carefully collected for subsequent analysis. The extraction followed the protocol by Bonicelli et al.(https://doi.org/10.1039/D4MO00015C) with minimal amendments. Specifically, 50 mg of bone powder were added to 2 mL pre-filled bead mill tube containing ceramic beads (1.4 mm in diameter), and 950 μL of an 8:2 (% v/v) methanol-water solution was added. The samples were vortexed for 30 seconds and then homogenized using a Precellys Evolution Touch Homogenizer with four 20-second bursts at 5854 g, with a 2-minute pause between bursts. The homogenization tube was then centrifuged at 18,213 g at 4 °C for 10 minutes, and 900 μL of the supernatant was transferred to a new tube. An additional 750 μL of the methanol-water solution was added to the original tube, and the homogenization process was repeated. After centrifugation at 18,213 g at 4 °C for 10 minutes, another 700 μL of supernatant was transferred to the same collection tube. This combined extract was centrifuged once more at 18,213 g at 4 °C for 10 minutes, after which 1.2 mL of the supernatant was transferred to a fresh tube and dried under a nitrogen flow. The dried extracts were then stored at −80 °C until further testing. Bone extracts were resuspended in 50 µL of methoxamine hydrochloride solution in pyridine (Sigma-Aldrich: TS45950) and incubated in a Thermomixer (Thermo Scientific) at 60 °C with shaking at 400 rpm for 15 minutes. After incubation, the samples were removed from the Thermomixer and left to cool. Subsequently, 50 µL of BSTFA + 1% TMCS (Supelco: B-023) was added, and the mixture was incubated again at 60 °C with shaking at 400 rpm for another 15 minutes. Negative controls consisting of methoxamine hydrochloride solution and BSTFA alone were prepared as blanks."]}
Sections "TREATMENT" contain missmatched items: {'TREATMENT_SUMMARY': ["The taphonomy experiment was conducted at the Taphonomic Research in Anthropology: Centre for Experimental Studies (TRACES) research site at the University of Central Lancashire. A 7.7 x 4.3 m area of grassland at 290 m altitude was selected for the experiment. This area had never been used for taphonomic experiments before and is located at the highest point in the research site, minimizing the risk of soil contamination from the percolation and flowing of decomposition fluids. The burial depths selected were 0 cm (surface), 10 cm, 30 cm, and 50 cm, to simulate forensic scenarios where shallow burials tend to be most frequently encountered, with post-mortem intervals ranging from zero to six months. The plot was divided into smaller 70 cm² squares, each designated for a specific soil depth and post-mortem interval. Specifically, moving from south to north, squares were allocated to the surface experiments, followed by those at 10 cm, 30 cm, and 50 cm depths, respectively. Moving from west to east, squares were designated for post-mortem intervals from one to six months. After digging holes to the required depth, the removed soil was replaced to cover the bone completely (except for surface experiments). Marking flags indicated the location of each buried quadrant were used. A 70 cm buffer zone was maintained between squares in the west-to-east direction and a 50 cm buffer zone in the south-to-north direction, to minimize potential soil contamination considering the area's expected water flow direction. The entire area was covered with cages to prevent scavenger interference as much as possible.", "The taphonomy experiment was conducted at the Taphonomic Research in Anthropology: Centre for Experimental Studies (TRACES) research site at the University of Central Lancashire. A 7.7 x 4.3 m area of grassland at 290 m altitude was selected for the experiment. This area had never been used for taphonomic experiments before and is located at the highest point in the research site, minimizing the risk of soil contamination from the percolation and flowing of decomposition fluids. The burial depths selected were 0 cm (surface), 10 cm, 30 cm, and 50 cm, to simulate forensic scenarios where shallow burials tend to be most frequently encountered, with post-mortem intervals ranging from zero to six months. The plot was divided into smaller 70 cm² squares, each designated for a specific soil depth and post-mortem interval. Specifically, moving from south to north, squares were allocated to the surface experiments, followed by those at 10 cm, 30 cm, and 50 cm depths, respectively. Moving from west to east, squares were designated for post-mortem intervals from one to six months. After digging holes to the required depth, the removed soil was replaced to cover the bone completely (except for surface experiments). Marking flags indicated the location of each buried quadrant were used. A 70 cm buffer zone was maintained between squares in the west-to-east direction and a 50 cm buffer zone in the south-to-north direction, to minimize potential soil contamination considering the area''s expected water flow direction. The entire area was covered with cages to prevent scavenger interference as much as possible."]}