Automated Software Architecture Extraction Using Graph-based Clustering

As the size and complexity of software grows developers have an ever-increasing need to understand software in a modular way. Most complex software systems can be divided into smaller modules if the developer has domain knowledge of the code or up-to-date documentation. If neither of these exist discovery of code modules can be a tedious, manual process. This research hypothesizes that graph-based clustering can be used effectively for automated software architecture extraction. We propose methods of representing relationships between program artifacts as graphs and then propose new partitional algorithms to extract software modules from those graphs. To validate our hypothesis and the partitional algorithms a new set of tools, including a software data miner, cluster builder, graph viewer, and cluster score calculator, were created. This toolset was used to implement partitional algorithms and analyze their performance in extracting modules. The Xinu operating system was used as a case study because it has defined modules that can be compared to the results of the partitional algorithm

Automated Software Architecture Extraction Using Graph-based Clustering

As the size and complexity of software grows developers have an ever-increasing need to understand software in a modular way. Most complex software systems can be divided into smaller modules if the developer has domain knowledge of the code or up-to-date documentation. If neither of these exist discovery of code modules can be a tedious, manual process. This research hypothesizes that graph-based clustering can be used effectively for automated software architecture extraction. We propose methods of representing relationships between program artifacts as graphs and then propose new partitional algorithms to extract software modules from those graphs. To validate our hypothesis and the partitional algorithms a new set of tools, including a software data miner, cluster builder, graph viewer, and cluster score calculator, were created. This toolset was used to implement partitional algorithms and analyze their performance in extracting modules. The Xinu operating system was used as a case study because it has defined modules that can be compared to the results of the partitional algorithm.</p

Korean red ginseng extract prevents bone loss in an oral model of glucocorticoid induced osteoporosis in mice

The gut microbiota and barrier function play important roles in bone health. We previously demonstrated that chronic glucocorticoid (GC)-induced bone loss in mice is associated with significant shifts in gut microbiota composition and impaired gut barrier function. Korean Red Ginseng (KRG, Panax Ginseng Meyer, Araliaceae) extract has been shown to prevent glucocorticoid-induced osteoporosis (GIO) in a subcutaneous pellet model in mice, but its effect on gut microbiota and barrier function in this context is not known. The overall goal of this study was to test the effect of KRG extract in a clinically relevant, oral model of GIO and further investigate its role in modulating the gut-bone axis. Growing male mice (CD-1, 8 weeks) were treated with 75 μg/mL corticosterone (∼9 mg/kg/day) or 0.4% ethanol vehicle in the drinking water for 4 weeks. During this 4-week period, mice were treated daily with 500 mg/kg/day KRG extract dissolved in sterile water or an equal amount of sterile water via oral gastric gavage. After 4 weeks of treatment, we assessed bone volume, microbiota composition, gut barrier integrity, and immune cells in the bone marrow (BM) and mesenteric lymph nodes (MLNs). 4 weeks of oral GC treatment caused significant distal femur trabecular bone loss, and this was associated with changes in gut microbiota composition, impaired gut barrier function and altered immune cell composition. Importantly, KRG extract prevented distal femur trabecular bone loss and caused significant alterations in gut microbiota composition but had only modest effects on gut barrier function and immune cell populations. Taken together, these results demonstrate that KRG extract significantly modulates the gut microbiota-bone axis and prevents glucocorticoid-induced bone loss in mice

On the Move: Correlation of Impaired Mobility with Spatial Navigation Ability in Persons with Multiple Sclerosis

Spatial navigation ability is essential for independent living, and it relies on complex cognitive and motor processes that are vulnerable to decline in persons with multiple sclerosis (pwMS). The role of mobility in the physical act of navigation has been well documented; however, its association with cognitive processing that supports efficient navigation and recall of the environment is unknown. This study examined the relation between clinical mobility function and spatial navigation ability in pwMS. In a clinical sample of 43 individuals with relapsing-remitting MS (MPDDS = 2; age 25–67 years), we assessed spatial navigation ability in a virtual Morris water maze that allowed for active search by controlling a joystick while seated at a computer, and subsequent free recall of environment details. Individuals with worse mobility (measured by slower forward and backward walking) traveled less efficient virtual navigation routes to the goal location and recalled fewer accurate details of the environment. A stratified analysis by disability revealed moderate–strong correlations for those with a low level of disability, and effects were attenuated in individuals with a high level of disability. Given that the virtual navigation task was performed while seated, evidence of any correlation with mobility suggests differences in navigation ability that cannot be ascribed to general walking impairment, and instead suggests a role for mobility impairment to modify cognitive processing supporting navigation in pwMS

Lactobacillus Reuteri 6475 Prevents Bone Loss in a Clinically Relevant Oral Model of Glucocorticoid‐Induced Osteoporosis in Male CD‐1 Mice

ABSTRACT Glucocorticoids (GCs) are commonly used anti‐inflammatory medications with significant side effects, including glucocorticoid‐induced osteoporosis (GIO). We have previously demonstrated that chronic subcutaneous GC treatment in mice leads to gut barrier dysfunction and trabecular bone loss. We further showed that treating with probiotics or barrier enhancers improves gut barrier function and prevents GIO. The overall goal of this study was to test if probiotics could prevent GC‐induced gut barrier dysfunction and bone loss in a clinically relevant oral‐GC model of GIO. Eight‐week‐old male CD‐1 mice were treated with vehicle or corticosterone in the drinking water for 4 weeks and administered probiotics Lactobacillus reuteri ATCC 6475 (LR 6475) or VSL#3 thrice weekly via oral gavage. As expected, GC treatment led to significant gut barrier dysfunction (assessed by measuring serum endotoxin levels) and bone loss after 4 weeks. Serum endotoxin levels significantly and negatively correlated with bone volume. Importantly, LR 6475 treatment effectively prevented both GC‐induced increase in serum endotoxin and trabecular bone loss. VSL#3 had intermediate results, not differing from either control or GC‐treated animals. GC‐induced reductions in femur length, cortical thickness, and cortical area were not affected by probiotic treatment. Taken together, these results are the first to demonstrate that LR 6475 effectively prevents the detrimental effects of GC treatment on gut barrier, which correlates with enhanced trabecular bone health in an oral mouse model of GIO. © 2023 The Authors. JBMR Plus published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research

Keel bone damage assessment: consistency in enriched colony laying hens

Damage to the keel bone is a major issue in the laying hen industry. The goal of this study was to compare palpation results of live laying hens to digital computed tomography (CT) images, to assess changes in palpation reliability as training and familiarity increased, and to examine keel bone morphology over time. The longitudinal study consisted of 2 trials of 3 observation periods using 40 different (n = 120) W-36 hens housed in enriched colony cages. The first trial began when hens were 52 to 58 wk of age repeating the trial when the same birds were 74 to 81 wk of age. At 52 wk of age, each hen's keel bone was palpated by a single individual for keel bone caudal tip fractures (Tip), sagittal deviations (Evenness), and transverse deviations (Straightness). After palpation, each hen was placed in a motion limiting restraint and scanned using CT. The hens spent the next 21 d in their cages and on day 21, the hens were collected, palpated, and CT scanned again. The CT scans were imported into Mimics analysis software, 3D models of each keel bone were constructed and evaluated. Each bone and 3D model was scored (0, 1, 2) on the measurement of transverse deviation based on 1.0 cm total deviation, respectively. Analysis of data using Proc Freq and Means in SAS 9.3 revealed minimal to moderate kappa values and moderate agreement percentages between palpators and digital analysis. The computer generated 3D models of individual keel bones were compared to palpation scores for Tip, Evenness, and Straightness at the beginning and end of each trial. The visual observations of the 3D models were qualitative, performed by a single individual. Overall, we found CT scanning to be a useful tool in observing changes to the keel bone, we observed changes in palpation accuracy as training/familiarity increased, and examined changes in keel morphology, specifically in the tip, after 52 wk of age