Mean Fragment Size Research Articles

Dynamic fracture mechanism and fragment characteristics of sandstone specimens with asymmetrical conjugate fissures under static pre-compression

This paper systematically investigates the dynamic mechanical response and fragment characteristics of sandstone with asymmetrical conjugate fissures subjected to preexisting static stress based on the split Hopkinson pressure bar apparatus. The cross-fissured sandstone exhibits significant variations in mechanical behavior when exposed to higher dynamic strain rates under identical static pre-stress. The cross-fissured sandstone with a higher dynamic strain rate is characterized by a greater coupled strength under the same static pre-stress; for a given dynamic load, the highest coupled strength occurs under the static pre-stress of 60% UCS. The failure mode of the cross-fissured sandstone is predominantly governed by the dynamic strain rate, independent of static pre-stress variations considered in this investigation. At lower dynamic strain rates, the specimens typically exhibit a mixed tensile-shear failure mode, characterized by the dominance of larger fragments in the broken specimens. In contrast, under high dynamic impacts, the sandstone tends to fail in a shear-dominated manner, resulting in smaller fragments with a more uniform size distribution. Furthermore, the study explores how varying dynamic strain rates and static pre-stress influence the fragment characteristics of the cross-fissured sandstone. Higher dynamic strain rates and increased static pre-stress generally lead to smaller mean fragment sizes. This phenomenon is quantitatively described by fitting fragment size distributions using the Generalized Extreme Value (GEV) distribution, revealing a decrease in the location parameter (μ) and an increase in fractal dimension. These metrics indicate that higher dynamic strain rates and static pre-stress result in sandstone specimens breaking into smaller fragments with a more homogeneous size distribution. These findings contribute to a deeper understanding of rock dynamics, with potential implications for engineering applications involving similar geological configuration under dynamic loading conditions.

Optimizing Mean Fragment Size Prediction in Rock Blasting: A Synergistic Approach Combining Clustering, Hyperparameter Tuning, and Data Augmentation

Accurate estimation of the mean fragment size is crucial for optimizing open-pit mining operations. This study presents an approach that combines clustering, hyperparameter optimization, and data augmentation to enhance prediction accuracy using the Xtreme Gradient Boosting (XGBoost) regression model. A dataset of 110 blasts was divided into 97 blasts for training and testing, whereas a separate set of 13 new, unseen blasts was used to evaluate the robustness and generalization of the model. Hierarchical Agglomerative (HA) and K-means clustering algorithms were used, with HA clustering providing a higher cluster quality. To address class imbalance and improve model generalization, a synthetic minority oversampling technique for regression with Gaussian noise (SMOGN) was employed. Hyperparameter tuning was conducted using HyperOpt by comparing Random Search (RS) with the Advanced Tree-structured Parzen Estimator (ATPE). The combination of ATPE with HA clustering and SMOGN in an expanded search space produced the best results, achieving superior prediction accuracy and reliability. The proposed HAC1-SMOGN model, which integrates HA clustering, ATPE tuning, and SMOGN augmentation, achieved a mean squared error (MSE) of 0.0002 and an R2 of 0.98 on the test set. This study highlights the synergistic benefits of clustering, hyperparameter optimization, and data augmentation in enhancing machine learning models for regression tasks, particularly in scenarios with class imbalance or limited data.

Strain rate effects on fragment morphology of ceramic alumina: A synchrotron-based study

Dynamic (600–1000 s−1) and quasi-static (0.001–0.01 s−1) compression experiments are conducted on a high-purity alumina ceramic using a split Hopkinson pressure bar and a material test system, respectively. The postmortem fragments of ceramic samples at different strain rates are then characterized via synchrotron micro computed tomography (CT). The three-dimensional (3D) morphologies of fragments are quantified using the gyration tensor analysis after proper segmentation of CT images. The mean fragment size decreases in a power-law form while the mean shape indices (sphericity, elongation index and flatness index) increase in a logarithmic-linear form, with increasing strain rates. In addition, the fragment size and shape distributions are all found to follow the Weibull probability distribution. To reveal the underlying mechanisms of such strain rate effects, high-speed optical and X-ray imaging are implemented to capture the fracture process of ceramic samples under quasi-static and dynamic compression. Primary and secondary wing cracks (PWCs/SWCs) control the fracture and fragmentation of the ceramic under both loading conditions. Compared to quasi-static loading, a considerably larger number of SWCs are produced under dynamic loading, and pronounced branching and bridging occur among the PWCs, which prevent the PWCs from coalescing into axial splitting cracks. Consequently, crack networks composed of high-density wing cracks break the sample into finer and more isotropic fragments, consistent with CT characterizations. Scanning electron microscopy is utilized to analyze the micro damage modes of ceramic samples. Transgranular fracture dominates the grain-scale damage and contributes to the higher dynamic fracture resistance of the alumina under dynamic loading, as a result of more homogeneous nucleation and growth of micro cracks.

Prediction of the mean fragment size in mine blasting operations by deep learning and grey wolf optimization algorithm

Prediction of the mean fragment size in mine blasting operations by deep learning and grey wolf optimization algorithm

Dispersal of high-burnup fuel fragment surrogate particles during and after loss-of-coolant accident tests

The issue of fuel fragmentation, relocation, and dispersal is critical in the licensing and use of high-burnup (>62GWd/MTU) nuclear fuel in light water reactors (LWRs). In this work, two test series are reported that examine the fragment dispersal during a burst event and an additional dispersal following the burst due to vibrations in the rod, such as those induced by accident recovery systems. To examine dispersal during the balloon and burst portion of a Loss-of-Coolant Accident event, HfO2 fragments and yttria-stabilized zirconia pellets were filled into an as-fabricated cladding tube, which was then pressurized and subjected to loss-of-coolant accident testing in steam. Results from this test were found to be highly non-prototypic, and dispersal was both significantly more violent and significantly greater in magnitude than identified for actual fuel tests. These findings were attributed to the conservative (more dispersive) nature of the particles chosen for dispersal and to the details of the test conditions used that led to particularly wide bursts. The second set of tests examined dispersal following the burst when vibrations were induced in the rod, primarily via recovery activities such as Emergency Core Cooling System actuation leading to rapid water addition. Post-burst dispersal testing was performed by inducing sinusoidal oscillations with 2–25 nm peak-to-peak amplitude and 2–5 Hz frequencies in pre-burst rods that had been refilled with HfO2 fragments or high-burnup fragment surrogate mixture of HfO2 fragments and yttria-stabilized zirconia sands. Testing revealed that rods with large burst openings (7 mm wide in this work) led to unmitigated dispersal from above the burst zone but that smaller bursts (5 mm wide), although still much larger than the mean fragment size of 3 mm, led to effectively no dispersal because of interparticle locking. Additionally, mixture and moisture were found to impact the amount of dispersal: mixtures increased dispersal, and moisture drastically reduced it. The implications of these findings on likely dispersal from actual fuel are discussed.

Prediction of rock fragmentation in a fiery seam of an open-pit coal mine in India

Spontaneous combustion of coal increases the temperature in adjoining overburden strata of coal seams and poses a challenge when loading blastholes. This condition, known as hot-hole blasting, is dangerous due to the increased possibility of premature explosions in loaded blastholes. Thus, it is crucial to load the blastholes with an appropriate amount of explosives within a short period to avoid premature detonation caused by high temperatures of blastholes. Additionally, it will help achieve the desired fragment size. This study tried to ascertain the most influencial variables of mean fragment size and their optimum values adopted for blasting in a fiery seam. Data on blast design, rock mass, and fragmentation of 100 blasts in fiery seams of a coal mine were collected and used to develop mean fragmentation prediction models using soft computational techniques. The coefficient of determination (R2), root mean square error (RMSE), mean absolute error (MAE), mean square error (MSE), variance account for (VAF) and coefficient of efficiency in percentage (CE) were calculated to validate the results. It indicates that the random forest algorithm (RFA) outperforms the artificial neural network (ANN), response surface method (RSM), and decision tree (DT). The values of R2, RMSE, MAE, MSE, VAF, and CE for RFA are 0.94, 0.034, 0.027, 0.001, 93.58, and 93.01, respectively. Multiple parametric sensitivity analyses (MPSAs) of the input variables showed that the Schmidt hammer rebound number and spacing-to-burden ratio are the most influencial variables for the blast fragment size. The analysis was finally used to define the best blast design variables to achieve optimum fragment size from blasting. The optimum factor values for RFA of S/B, ld/B and ls/ld are 1.03, 1.85 and 0.7, respectively.

Abstract 987: Novel ALK mutations in EML4::ALK+ NSCLC resistant to TKIs identified by liquid biopsy

Abstract The identification of Anaplastic Lymphoma Kinase (ALK) chromosomal translocations led to the development of effective targeted therapies in a subset of Non-Small Cell Lung Cancer (NSCLC) patients. Several drugs are currently in clinical practice for advanced ALK+ NSCLC. However, resistance remains a challenge in these patients. The possibility to analyze circulating tumor DNA (ctDNA) with non-invasive methods can greatly improve prognostic capabilities, by allowing early detection of relapse and of drug-resistant mutations from peripheral blood. We report a series of 15 consecutive relapsed NSCLC patients (12 ALK+, 3 ROS1+) treated at the Fondazione IRCCS-San Gerardo dei Tintori (Monza, Italy) that were investigated by liquid biopsy at tyrosine kinase inhibitor (TKI) failure, through amplicon deep sequencing of the ALK/ROS1 kinase domains. Median DNA yield was 4.8 ng per ml of plasma and mean fragment size was 176 bp. Mutational hotspot coding regions of ALK and ROS1 genes were amplified by high-fidelity PCR and sequenced. Mean coverage of called variants was 24,687x. The threshold for mutation calling was set at 0.6%, after correcting for mapping quality, minimum coverage, and strand bias. Analysis of background signal on healthy control DNA identified 0.0024 mismatches per mapped base. Overall, plasma ctDNA analysis detected an ALK mutation in 7/18 relapse samples from 7/15 patients. No ROS1 mutations were found in ROS1 fusion-positive patients. Among 12 patients carrying an EML4::ALK fusion, 10 variants potentially driving resistance were found. Along with mutations that were previously identified (L1196M/G1202R, E1154K, F1174L), novel ALK variants were detected such as L1198R, T1211I, C1235R, C1237Y, L1196P. Mutations were characterized for sensitivity to ALK inhibitors in a BaF3-EML4::ALK cell model, using cell proliferation assays and western blotting to evaluate the effects on ALK phosphorylation. C1237Y and L1196P mutants appeared to resist all TKIs; hence, we further tested their sensitivity to novel investigational drugs, zotizalkib and repotrectinib. Both mutants demonstrated resistance, suggesting that these two mutations confer broad resistance to TKIs. Molecular modelling of C1237Y and L1196P mutants was run to elucidate the mechanisms of resistance. The ADP-C1237Y complex showed a much smaller root-mean-square deviation than ADP-WT, indicating a higher affinity/activity of the mutant. L1196 interacts hydrophobically with a methyl group of lorlatinib, P1196 is predicted to lose such interaction, while ATP binding is not affected. The presence of C1237Y and L1196P variants, is a relevant finding due to their resistance, even after the exposure to the fourth-generation inhibitor zotizalkib. The clonal selection of these mutations, made by second/third generation ALK TKIs may lead to a complete refractory status, which would then render TKIs useless in a sequential therapeutic strategy. Citation Format: Federica Malighetti, Matteo Villa, Elisa Sala, Geeta Sharma, Giulia Arosio, Maria Gemelli, Chiara Manfroni, Diletta Fontana, Nicoletta Cordani, Raffaella Meneveri, Alfonso Zambon, Rocco Piazza, Fabio Pagni, Diego Cortinovis, Luca Mologni. Novel ALK mutations in EML4::ALK+ NSCLC resistant to TKIs identified by liquid biopsy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 987.

Hot alkaline lysis gDNA extraction from formalin-fixed archival tissues.

Formalin fixation of natural history specimens and histopathological material has historically been viewed as an impediment to successful genomic analysis. However, the development of extraction methods specifically tailored to contend with heavily crosslinked archival tissues, re-contextualises millions of previously overlooked specimens as viable molecular assets. Here, we present an easy-to-follow protocol for screening archival wet specimens for molecular viability and subsequent genomic DNA extraction suitable for sequencing. The protocol begins with non-destructive assessment of specimen degradation and preservation media conditions to allow both museum curators and researchers to select specimens most likely to yield an acceptable proportion (20-60%) of mappable endogenous DNA during short-read DNA sequencing. The extraction protocol uses hot alkaline lysis in buffer (0.1M NaOH, 1% SDS, pH 13) to simultaneously lyse and de-crosslink the tissue. To maximise DNA recovery, phenol:chloroform extraction is coupled with a small-fragment optimised SPRI bead clean up. Applied to well-preserved archival tissues, the protocol can yield 1-2 μg DNA per 50 mg of tissue with mean fragment sizes typically ranging from 50-150 bp, which is suitable to recover genomic DNA sufficient to reconstruct complete mitochondrial genomes and achieve up to 25X nuclear genome coverage. We provide guidance for read mapping to a reference genome and discuss the limitations of relying on small fragments for SNP genotyping and de novo genome assembly. This protocol opens the door to broader-scale genetic and phylogenetic analysis of historical specimens, contributing to a deeper understanding of evolutionary trends and adaptation in response to changing environments.

Development of a Multiplication Factor for the Kuz-Ram Model to Match the Fragment Size Obtained from Wipfrag Image Analysis

The degree to which the rock is fragmented by blasting operations significantly impacts the productivity of the opencast mining operation. Over image analysis-based tools, the Kuz-Ram empirical model is preferred for determining the mean fragment size of a blasted muck pile. The fragmentation analysis results by the Kuz-Ram model are said to report the overestimation of the size of the fragments. On the other hand, while accurate, measuring the mean fragment size by image-based analysis is also time-consuming and expensive. Therefore, in the present research, the fragmentation difference index (Fdi) is introduced as a new multiplication factor to reduce the discrepancy in the results obtained using the Kuz-Ram model and the image-based analysis. The error minimization method of least squares is used to formulate the objective function of Fdi. The proposed equation is tested using data sets that weren't used in the model's development. Statistical indicators viz. the coefficient of determination (R2 ) and Root Mean Square Error (RMSE) have been used to evaluate the model's performance. These are found to be 0.80 and 0.007, respectively. The values obtained by multiplying Fdi by the Kuz-Ram results match those of the Wipfrag study, with an average error of 2.09%. Therefore, the suggested methodology will assist the field engineers in cost-effectively calculating the mean fragment size before blasting utilizing only the findings from the Fdi and Kuz-Ram models.

Glenoid rim morphology in young athletes with unstable painful shoulders: primarily painful vs. frankly unstable

To investigate the characteristics of glenoid rim morphology in young athletes (<40 yr) with unstable painful shoulder. This was a retrospective case series. The inclusion criteria were as follows: (1) shoulder pain during sports activity, (2) traumatic onset, (3) no complaint of shoulder instability, and (4) soft tissue or bony lesions confirmed on imaging examinations (computed tomography and magnetic resonance imaging). The above-mentioned painful cohort was then compared (in a 2:1 ratio) to a match-paired control group of patients with similar demographics but with frank anterior glenohumeral instability as defined by imaging and physical findings. The pain (not apprehension) was reproduced during the anterior apprehension test in supine position and relieved by relocation test in all patients. Glenoid rim morphology, bone union in shoulders with a fragment-type glenoid, glenoid defect size, bone fragment size, medial displacement of bone fragments (MDBF), and medial distance of erosion (MDE) were compared between painful shoulders and unstable shoulders. There were 79 painful shoulders and 165 unstable shoulders. The glenoid rim morphology was normal in 33 shoulders, erosion-type in 15 shoulders, and fragment-type in 31 shoulders among painful shoulders, whereas the respective shoulders were 19, 33, and 113 among unstable shoulders (P<.001). Bone union was complete in 15 shoulders, partial in 14 shoulders, and nonunion in 2 shoulders among painful shoulders, whereas the respective shoulders were 43, 31, and 39 among unstable shoulders (P=.001). The mean glenoid defect size was 6.0±7.2% and 12.7±7.4%, respectively (P<.001), and the mean bone fragment size was 5.8±6.4% and 5.4±4.6%, respectively, (P=.591). The mean MDBF was 1.4±1.5 mm and 3.0±2.2 mm, respectively (P<.001), and the mean MDE was 2.3±1.2 mm and 5.2±2.4 mm, respectively (P<.001). In shoulders with a smaller glenoid defect (<13.5%), the prevalence of shoulders with MDBF (<2 mm) and shoulders with MDE (<2 mm) was more frequent in painful shoulders. On the other hand, in shoulders with a larger glenoid defect (≥13.5%), erosion-type glenoid, nonunion in fragment-type glenoid and bone fragment smaller than 7.5% was not recognized in painful shoulders. Shoulders with MDBF (<2 mm) were significantly more frequent in painful shoulders (P=.009). In painful shoulders normal or erosion-type glenoid was predominant, and glenoid defect size was significantly smaller than unstable shoulders. On the other hand, a large bone fragment (≥7.5%) remained and united completely or partially in all shoulders with a larger glenoid defect (≥13.5%). Bone union was obtained within 2 mm from the articular surface in most of them.

Highlighting the risk of environmental lead contamination for deer management in Australia

SummaryLead‐based bullets used to shoot deer typically fragment. These toxic fragments are a threat to wildlife scavengers and human consumers of venison. Awareness of this issue is widespread internationally but limited in Australia. The aim of this research was to characterise deer carcass contamination via bullet fragmentation associated with lead‐based and lead‐free ammunition in a deer culling program conducted in Australia. We used radiography (X‐rays) to study Hog Deer (Axis porcinus) shot in a professional ground‐based shooting program in Victoria, south‐eastern Australia. Our data captured 33 deer shot with frangible lead‐based bullets in 2021, and 21 deer shot with monolithic lead‐free (copper‐based) bullets from the same rifles in 2021–2022. For lead‐based bullets, the mean number of lead fragments per carcass ranged from seven to 629 (mean ± SD = 256 ± 169), mean fragment size was 1.2 mm2 (74% of fragments were &lt;1.0 mm2) and the mean fragment coverage area (the smallest ellipse covering all fragments) was 325 cm2. Of these deer, 36% had metallic fragments in the ‘back strap’ (loin) muscles and 42% had metallic fragments in the shoulder muscles: meat cuts typically removed for human consumption. In contrast, for lead‐free bullets, the mean number of metallic fragments per carcass ranged from zero to four (0.5 ± 1.0), with only 29% of carcasses having any fragments, and no deer had metallic fragments in the loin or shoulder muscles. On the basis of these results, it is clear that lead‐based bullets used for shooting deer in Australia pose risks to wildlife scavengers, and to human consumers when used in hunting. Australian wildlife managers involved in mitigating deer impacts should strongly consider a timely transition to lead‐free bullets.

Experimental Study on the Size of Rock Fragments Ejected from Boreholes Drilled in Coal Mine Roadway Floors

Borehole drilling is required if floor heave in underground mines is to be controlled using bolts through the floor. How well the bolt is anchored depends, in part, on the borehole’s quality. A major factor that can reduce borehole quality is the difficulty of discharging rock fragments from a small-diameter borehole drilled at a downward angle. Therefore, a fuller understanding of the sizes of the rock fragments will aid attempts to achieve smooth fragment discharge. In this study, drilling experiments in the laboratory and SEM imaging were carried out to determine the size and shape of the fragments generated when drilling boreholes in three sedimentary rocks typically found in roadway floors. The results show that the size distribution of the rock fragments conformed to the three-parameter generalized extreme value distribution. The mean fragment size increased with rock density and the mean size of the fragments larger than 1.5 mm increased with the rock’s uniaxial compressive strength. The fractal dimension of the cracks in the fragments was lower for high-density rocks and the mean fragment size was larger for rocks whose cracks had a lower fractal dimension. When a drill rod drills through very dense or high-strength rock, the mean size of the fragments will increase and the discharge power should be increased to prevent fragment discharge blockages. This paper may provide a theoretical basis and a data reference for discharge power settings and discharge channel optimization.

Experimental and numerical study on the dynamic behavior of a transversely isotropic rock

The present work investigates the dynamic mechanical behavior of transversely isotropic Jhiri shale at five anisotropy angles (0°, 30°, 45°, 60°, and 90°) using a large diameter (76 mm) split Hopkinson pressure bar. Jhiri shale, a type of Vindhyan shale, is collected from the Rewa region in the Madhya Pradesh state of India. Samples are loaded at strain rates of ∼150/s, ∼230/s, and ∼320/s under compression. It is found that the strength is rate-dependent and increases as the strain rate rises. At elevated strain rates, U-type anisotropy is noted. The anisotropy ratio lowers from 3.50 to 3.37 when the strain rate changes from quasi-static to ∼320/s, indicating that the influence of bedding planes diminished at higher strain rates. All the samples subjected to dynamic compressive loading are pervasively fragmented and undergo complete pulverization. As the strain increases, the degree of fragmentation intensifies, and the mean fragment size reduces. Samples with intermediate anisotropy angles (30°, 45°, 60°) are subjected to a higher degree of fragmentation than those with 0° and 90°. The rock fragments exhibit fractal distribution, which can be described using a power-law relationship. The dynamic experiments are numerically simulated using the discrete element method. The grains of the rock are generated as randomly sized and distributed polygonal blocks using Voronoi tessellation. The initiation and propagation of micro-cracks and failure mechanisms are explored via numerical simulations. It is found that samples mainly undergo shear failure dynamically. As the strain rate increases, the number of cracks increases. For samples with intermediate anisotropy angles, shear cracks begin along the bedding planes and then spread internally. At any given strain rate, they have a higher number of cracks than 0° and 90° samples, indicating a higher degree of fragmentation, as noted experimentally.

Glenoid defect size increases but the bone fragment rarely resorbs in shoulders with recurrent anterior instability

With recurrent anterior instability the bone fragment of a bony Bankart lesion is often small compared to the glenoid defect. The purpose of the present study was to clarify the changes to both the bone fragment and glenoid defect over time in a single subject. Participants were patients who underwent computed tomography (CT) at least twice after an instability event between 2004 and 2021 and had a fragment-type glenoid at first CT. The glenoid rim width (A), glenoid defect width (B), and bone fragment width (C) were measured in millimeters. If B or C increased by 1 mm or more from the first to final CT, the change was judged as "enlarged," and if B or C decreased by 1 mm or more, it was judged as "reduced"; all other cases were judged as "similar." Then, glenoid defect size and bone fragment size were calculated as B/A×100% and C/A×100%, respectively, and the changes from the first to final CT were compared. From the first to final CT, the glenoid defect was enlarged in 30 shoulders, similar in 13shoulders, and reduced in 4 shoulders, and the bone fragment was enlarged in 18 shoulders, similar in 24 shoulders, and reduced in 5 shoulders. The mean glenoid defect size significantly increased from 10.9% to 15.3% (P<.001), and the mean bone fragment size increased from 6.4% to 7.8%, respectively (P=.005). At the final CT, in 6 shoulders a new glenoid fracture was observed at a different site from the original fracture. When they were excluded from the analyses, the mean glenoid defect size still significantly increased (from 11.2% to 15.2%; P<.001), but the mean bone fragment size did not (6.5% vs. 7.3%, respectively; P=.088). In shoulders with recurrent anterior instability, glenoid defect size appears to increase significantly over time, whereas the bone fragment size remains unchanged or increases only slightly. Bone fragment resorption is quite rare, and a bone fragment appears to be small because of an enlarged glenoid defect.

Rock factor prediction in the Kuz–Ram model and burden estimation by mean fragment size

In order to use the Kuz–Ram fragmentation model efficiently, the rock factor must be determined correctly. One of the aims of this study is to provide an approach to estimate the rock factor, which represents the blastability of the rock mass, in the Kuz–Ram fragmentation model. This proposed approach is based on previous blasting data from quarry records such as blast geometry, explosive quantities and amount of coarse fragmented material to be obtained after blasting. Using the proposed approach, if the mass of the material over a given fragment size is known, the rock factor in the Kuz–Ram model can be determined for a particular site. Another purpose of this study is to estimate the optimal burden according to the intended mean fragment size using the Kuz–Ram model. Studies were firstly carried out to find the most appropriate burden for the mean fragment size intended for a quarry where the rock factor is known. After this, generalized equations were derived for the optimal burden depending on the rock factor, the intended mean fragment size, the bench height and the density of the explosive. Finally, the obtained values from the suggested relations were compared with the actual blast rounds, considering the total cost and the coarse fragmented material ratio. It can be seen that the values obtained from the proposed relationships for burden are compatible with the most cost-effective blast pattern’s parameters that were actually obtained.

Fungal Metabarcoding Data for Two Grapevine Varieties (Regent and Vitis vinifera ‘Cabernet-Sauvignon’) Inoculated with Powdery Mildew (Erysiphe necator) Under Drought Conditions

Fungal Metabarcoding Data for Two Grapevine Varieties (Regent and <i>Vitis vinifera</i> ‘Cabernet-Sauvignon’) Inoculated with Powdery Mildew (<i>Erysiphe necator</i>) Under Drought Conditions

Whole-genome sequencing of artificial single-nucleotide variants induced by DNA degradation in biological crime scene traces

The aim of this study was to identify artificial single-nucleotide variants (SNVs) in degraded trace DNA samples. In a preliminary study, blood samples were stored for up to 120 days and whole-genome sequencing was performed using the Snakemake workflow dna-seq-gatk-variant-calling to identify positions that vary between the time point 0 sample and the aged samples. In a follow-up study on blood and saliva samples stored under humid and dry conditions, potential marker candidates for the estimation of the age of a blood stain (= time since deposition) were identified. Both studies show that a general decrease in the mean fragment size of the libraries over time was observed, presumably due to the formation of abasic sites during DNA degradation which are more susceptible to strand breaks by mechanical shearing of DNA. Unsurprisingly, an increase in the number of failed genotype calls (no coverage) was detected over time. Both studies indicated the presence of artificial SNVs with the majority of changes happening at guanine and cytosine positions. This confirms previous studies and can be explained by depurination through hydrolytic attacks which more likely deplete guanine while deamination leads to cytosine to thymine variants. Even complete genotype switches from homozygote 0/0 genotypes to the opposite 1/1 genotypes were observed. While positions with such drastic changes might provide suitable candidate markers for estimating short-term time since deposition (TsD), 11 markers were identified which show a slower gradual change of the relative abundance of the artificial variant in both blood and saliva samples, irrespective of storage conditions.

Unrecognized glenoid fracture in opposite shoulders with symptomatic anterior instability

BackgroundThe purpose of the present study was to investigate the characteristics of unrecognized glenoid fracture in opposite shoulders with symptomatic anterior instability. MethodsParticipants were 38 patients, who had complaints of instability on only one side (symptomatic shoulder) and had no complaints despite of a glenoid fracture on the other shoulder (asymptomatic shoulder) from 2011 to 2020. Factors that could influence the onset of symptoms including glenoid rim morphology were retrospectively investigated. ResultsAmong the asymptomatic shoulders, 16 had a single traumatic event and 22 had no history of trauma. The glenoid morphology was normal in 6, erosion in 12 and bony Bankart in 20 on the symptomatic side, whereas the respective shoulders were 0, 16 and 22 on the asymptomatic side. Bone union of bony Bankart was complete in 9, partial in 3 and non-union in 8 on the symptomatic side, whereas the respective shoulders were 18, 3 and 1 on the asymptomatic side. The mean glenoid defect size was 10.4% and 7.8%, and the mean bone fragment size was 5.0% and 4.5%, respectively. The mean medial displacement of bone fragments was 2.6 mm and 1.0 mm, respectively (p < 0.001). A larger glenoid defect (≥10%) was recognized in 19 symptomatic shoulders and 10 asymptomatic shoulders. Among them, erosion was solely recognized in 5 symptomatic shoulders. In shoulders with bony Bankart, all 10 asymptomatic shoulders had a completely or partially united fragment with less than 2 mm displacement. On the other hand, among 14 symptomatic shoulders, united fragment was solely recognized in 8 shoulders, in which medial displacement was less than 2 mm in 3 shoulders. ConclusionsEven if a glenoid fracture occurred, symptom such as instability or pain was not always recognized by all patients. Regardless of glenoid defect size, shoulders with a completely or partially united bone fragment and with less than 2 mm displacement were found to be asymptomatic.

Dynamic Split Tensile Strength of Basalt, Granite, Marble and Sandstone: Strain Rate Dependency and Fragmentation

The aim of this study is to understand the strength behaviour and fragment size of rocks during indirect, quasi-static and dynamic tensile tests. Four rocks with different lithological characteristics, namely: basalt, granite, sandstone, and marble were selected for this study. Brazilian disc experiments were performed over a range of strain rates from ~ 10–5 /s to 2.7 × 101 /s using a hydraulic loading frame and a split Hopkinson bar. Over the range of strain rates, our measurements of dynamic strength increase are in good agreement with the universal theoretical scaling relationship of (Kimberley et al., Acta Mater 61:3509–3521, 2013). Dynamic fragmentation during split tension mode failure has received little attention, and in the present study, we determine the fragment size distribution based on the experimentally fragmented specimens. The fragments fall into two distinct groups based on the nature of failure: coarser primary fragments, and finer secondary fragments. The degree of fragmentation is assessed in terms of characteristic strain rate and is compared with existing theoretical tensile fragmentation models. The average size of the secondary fragments has a strong strain rate dependency over the entire testing range, while the primary fragment size is less sensitive at lower strain rates. Marble and sandstone are found to generate more pulverised secondary debris when compared to basalt and granite. Furthermore, the mean fragment sizes of primary and secondary fragments are well described by a power-law function of strain rate.

Abstract 5164: cell-free DNA (cfDNA) fragment size as a potential quantitative biomarker for metastatic colorectal cancer (mCRC)

Abstract Introduction: The fragment size of cfDNA derived from tumor cells are known to be shorter than that from normal cells for not yet precisely known mechanisms. We hypothesized that the fragment size of cfDNA can be utilized to reliably estimate tumor burden in patients with mCRC undergoing palliative chemotherapy. Methods: cfDNA sequencing data from mCRC patients receiving first-line palliative chemotherapy at Seoul National University Hospital (Seoul, Korea) were used for this analysis. The patients were enrolled in a main study evaluating the dynamic changes of circulating tumor DNA mutational profiles during chemotherapy. Blood samples were obtained prior to chemotherapy and after every four cycles of chemotherapy until disease progression. cfDNA sequencing data from normal individuals were used as control data. cfDNA sequencing for both cancer patients and normal individuals were performed using AlphaLiquid® 100 target capture panel (IMBdx, Inc., Seoul, South Korea). AlphaLiquid® 100 is a tumor agnostic panel consist of 106 genes, including 10 gene fusion and MSI. Based on the panel sequencing data, the genetic alterations and the fragment size of cfDNA were calculated. The fragmentation ratio was defined by the ratio of the read fragment proportion in size range P1 (100 - 155 bp) and P2 (160 - 180 bp). Results: cfDNA sequencing data from 280 plasma samples from 62 mCRC patients and 50 healthy controls were used for analysis. Compared to cfDNA from healthy controls, the cfDNA fragment sizes from mCRC patients were significantly shorter (169.585 bp vs. 173.964 bp; p &amp;lt; 0.001). Comparing the fragment sizes by the mutational status, the fragment sizes of alleles with detected somatic mutations were significantly shorter than those with reference alleles (mean fragment size 155.853 bp in alleles with somatic mutations vs. 160.613 bp in reference alleles; p &amp;lt; 0.001), but such difference was not observed with germline mutations (mean fragment size 160.911 bp in alleles with germline mutations vs. 159.889 bp in reference alleles; p = 0.992). Further, the clonality inferred from the variant allele frequency (VAF) of somatic mutation was negatively correlated with the size of the cfDNA fragment. The read fragment proportion in size range P1 was significantly associated with the clonality (r = 0.86, p &amp;lt;0.001). We calculated the mean size of DNA fragment and the fragmentation ratio with each longitudinal sample. The fragmentation ratio was found to decrease with chemotherapy in responders and re-increase at the time of resistance to chemotherapy. Conclusions: The fragmentation ratio calculated from cfDNA in mCRC patients can represent tumor burden in dynamic samples and potentially can be used as a biomarker. Citation Format: Jun-Kyu Kang, Hwang-Phill Kim, Yoojoo Lim, Su Yeon Kim, Tae-You Kim. cell-free DNA (cfDNA) fragment size as a potential quantitative biomarker for metastatic colorectal cancer (mCRC) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5164.