Compost land management and soil carbon sequestration

Extensive fossil fuel burning has released carbon dioxide into the atmosphere. Under proper ecological conditions plants convert atmospheric carbon dioxide into stable soil organic matter, a natural and efficient means of mitigating climate change. In the symbiotic relationship between mycorrhizae and plants, mycorrhizae provide plants with essential nutrients in exchange for carbon sugars leaked from the plants. Mycorrhizae convert carbon sugars to an exudate called glomalin, a protein that assists in developing soil aggregates composed of sand, silt, and clay. These aggregates, called humus, store carbon for hundreds of years under healthy ecological conditions. Compost prompts soil microbes to aerobically transform organic matter into nutrients readily available to plants. Compost fosters the relationship between plants, mycorrhizae, and soil organisms to enrich the humification process. The Marin Carbon Project is an effort to augment this soil carbon sequestration process through compost application onto California rangelands. This project is being modeled on the East Campus Hillside to determine if compost boosts carbon storage within soils. The Hillside area has 1.5 acres of tallgrass prairie meadow. Eight 10 x 10 meter meadow plots were treated with compost, another eight meadow area plots served as controls, and the remaining 6 plots were located in the lawn area for comparison. Soil samples were gathered from each plot by the ISAT 320 class and analyzed by the Waypoint Laboratory. Additional samples were collected and then burned in an on-campus muffle furnace to calculate the total carbon from each sample. The data assembled from the muffle furnace was analyzed spatially and statistically to investigate correlations between the soil treatment and percentage of stable soil carbon. Across the trials executed, soil treated with compost had the highest carbon percentage. Results from this experiment will be integrated into the ongoing study of the health of the East Campus Hillside

Workers\u27 Responses to Incentives: The Case of Pending MLB Free Agents

This study examines ways in which workers respond to implicit incentives. Specifically, we examine the extent to which workers shift their effort to activities that are measured and which have been previously rewarded in the labor market. To examine this question, we examine the changes in the performance measures of professional baseball players in the season prior to the opportunity to freely negotiate their contract (free agency). We will examine different eras in baseball to examine if we can identify changes in behavior in this pivotal year based on changes to the current premium outputs for each time period

Beyond Moneyball: Changing Compensation in MLB

This study examines the changes in player compensation in Major League Baseball during the last three decades. Specifically, we examine the extent to which recently documented changes in players’ compensation structure based on certain types of productivity fits in with the longer term trends in compensation, and identify the value of specific output activities in different time periods. We examine free agent contracts in three-year periods across three decades and find changes to which players’ performance measures are significantly rewarded in free agency. We find evidence that the compensation strategies of baseball teams increased the rewards to “power” statistics like home runs and doubles in the 1990s when compared to a model that focused on successfully reaching base with a batted ball without a significant regard for the number of bases reached. Similarly, we confirm and expand upon the increased financial return to bases-on-balls in the late 2000s as found in previous research

Long-term functional recovery after facial nerve transection and repair in the rat

BACKGROUND: The rodent model is commonly used to study facial nerve injury. Because of the exceptional regenerative capacity of the rodent facial nerve, it is essential to consider the timing when studying facial nerve regeneration and functional recovery. Short-term functional recovery data following transection and repair of the facial nerve has been documented by our laboratory. However, because of the limitations of the head fixation device, there is a lack of long-term data following facial nerve injury. The objective of this study was to elucidate the long-term time course and functional deficit following facial nerve transection and repair in a rodent model. METHODS: Adult rats were divided into group 1 (controls) and group 2 (experimental). Group 1 animals underwent head fixation, followed by a facial nerve injury, and functional testing was performed from day 7 to day 70. Group 2 animals underwent facial nerve injury, followed by delayed head fixation, and then underwent functional testing from months 6 to 8. RESULTS: There was no statistical difference between the average whisking amplitudes in group 1 and group 2 animals. CONCLUSION: Functional whisking recovery 6 months after facial nerve injury is comparable to recovery within 1 to 4 months of transection and repair, thus the ideal window for evaluating facial nerve recovery falls within the 4 months after injury

The association of North Dakota skilled nursing facility characteristics with COVID-19 outbreak severity

Context: COVID-19 exerted severe challenges on skilled nursing facility (SNF) residents and staff. A combination of internal and external factors predisposed SNFs to an increased propensity of COVID-19 spread. Objective: The purpose of this paper is to examine which facility characteristics may have contributed to COVID-19 outbreaks within urban and rural North Dakota skilled nursing facilities. Methods: A 23-question survey regarding facility characteristics was developed and distributed to all 78 North Dakota skilled nursing facilities (SNF). Findings: Of the North Dakota SNF, 40 out of 78 total facilities (51.2%) participated in the survey. Of those participating, 38 of 40 (95%) were in counties with populations under 50,000, with the smallest county population being 1,876. A Spearman’s rank test suggested a relationship between the community spread of COVID-19 and the COVID-19 positivity of SNF residents. Spearman’s rank also suggested a positive association between the SNF resident COVID-19 positivity in relation to staff positivity (p-value 0.042) and county rates (p-value 0.045). Limitations: While this is a comprehensive survey with a very good response rate, two key limitations are identified. First, the survey relies on self-reported data from SNF staff. Second, it is not clear what data would have been received from non-responding SNFs. Implications: Substantial lessons have been learned, which may not only aid future pandemic preparedness but improve the quality of care for nursing home residents during a pandemic or other respiratory disease outbreaks. Proactively knowing susceptibilities and vulnerabilities ahead of time will allow local and state leaders to plan and allocate resources. Future state and local pandemic emergency plans need to be reviewed with the prioritization of skilled nursing facilities as front line facilities during a pandemic, rather than placing their “traditional” emphasis of emergency preparedness on hospitals

Genetic variation modifies risk for neurodegeneration based on biomarker status

Background: While a great deal of work has gone into understanding the relationship between CSF biomarkers, brain atrophy, and disease progression, less work has attempted to investigate how genetic variation modifies these relationships. The goal of this study was two-fold. First, we sought to identify high-risk v. low-risk individuals based on their CSF tau and Aβ load and characterize these individuals with regard to brain atrophy in an AD-relevant region of interest. Next, we sought to identify genetic variants that modified the relationship between biomarker classification and neurodegeneration.Methods: Participants were categorized based on established cut-points for biomarker positivity. Mixed model regression was used to quantify longitudinal change in the left inferior lateral ventricle. Interaction analyses between single nucleotide polymorphisms (SNPs) and biomarker group status were performed using a genome wide association study (GWAS) approach. Correction for multiple comparisons was performed using the Bonferroni procedure. Results: One intergenic SNP (rs4866650) and one SNP within the SPTLC1 gene (rs7849530) modified the association between amyloid positivity and neurodegeneration. A transcript variant of WDR11-AS1 gene (rs12261764) modified the association between tau positivity and neurodegeneration. These effects were consistent across the two sub-datasets and explained approximately 3% of variance in ventricular dilation. One additional SNP (rs6887649) modified the association between amyloid positivity and baseline ventricular volume, but was not observed consistently across the sub-datasets.Conclusions: Genetic variation modifies the association between AD biomarkers and neurodegeneration. Genes that regulate the molecular response in the brain to oxidative stress may be particularly relevant to neural vulnerability to the damaging effects of amyloid-β

Multiple Gene Variants Linked to Alzheimer\u27s-Type Clinical Dementia via GWAS are Also Associated with Non-Alzheimer\u27s Neuropathologic Entities

The classic pathologic hallmarks of Alzheimer’s disease (AD) are amyloid plaques and neurofibrillary tangles (AD neuropathologic changes, or ADNC). However, brains from individuals clinically diagnosed with “AD-type” (amnestic) dementia usually harbor heterogeneous neuropathologies in addition to, or other than, ADNC. We hypothesized that some AD-type dementia associated genetic single nucleotide variants (SNVs) identified from large genomewide association studies (GWAS) were associated with non-ADNC neuropathologies. To test this hypothesis, we analyzed data from multiple studies with available genotype and neuropathologic phenotype information. Clinical AD/dementia risk alleles of interest were derived from the very large GWAS by Bellenguez et al. (2022) who reported 83 clinical AD/dementia-linked SNVs in addition to the APOE risk alleles. To query the pathologic phenotypes associated with variation of those SNVs, National Alzheimer’s disease Coordinating Center (NACC) neuropathologic data were linked to AD Sequencing Project (ADSP) and AD Genomics Consortium (ADGC) data. Separate data were obtained from the harmonized Religious Orders Study and the Rush Memory and Aging Project (ROSMAP). A total of 4811 European participants had at least ADNC neuropathology data and also genotype data available; data were meta-analyzed across cohorts. As expected, a subset of dementia-associated SNVs were associated with ADNC risk in Europeans—e.g., BIN1, PICALM, CR1, MME, and COX7C. Other gene variants linked to (clinical) AD dementia were associated with non-ADNC pathologies. For example, the associations of GRN and TMEM106B SNVs with limbic-predominant age-related TDP-43 neuropathologic changes (LATE-NC) were replicated. In addition, SNVs in TNIP1 and WNT3 previously reported as ADrelated were instead associated with hippocampal sclerosis pathology. Some genotype/neuropathology association trends were not statistically significant at P \u3c 0.05 after correcting for multiple testing, but were intriguing. For example, variants in SORL1 and TPCN1 showed trends for association with LATE-NC whereas Lewy body pathology trended toward association with USP6NL and BIN1 gene variants. A smaller cohort of non-European subjects (n = 273, approximately one-half of whom were African-Americans) provided the basis for additional exploratory analyses. Overall, these findings were consistent with the hypothesis that some genetic variants linked to AD dementia risk exert their affect by influencing non-ADNC neuropathologies

Agile methods in biomedical software development: a multi-site experience report

BACKGROUND: Agile is an iterative approach to software development that relies on strong collaboration and automation to keep pace with dynamic environments. We have successfully used agile development approaches to create and maintain biomedical software, including software for bioinformatics. This paper reports on a qualitative study of our experiences using these methods. RESULTS: We have found that agile methods are well suited to the exploratory and iterative nature of scientific inquiry. They provide a robust framework for reproducing scientific results and for developing clinical support systems. The agile development approach also provides a model for collaboration between software engineers and researchers. We present our experience using agile methodologies in projects at six different biomedical software development organizations. The organizations include academic, commercial and government development teams, and included both bioinformatics and clinical support applications. We found that agile practices were a match for the needs of our biomedical projects and contributed to the success of our organizations. CONCLUSION: We found that the agile development approach was a good fit for our organizations, and that these practices should be applicable and valuable to other biomedical software development efforts. Although we found differences in how agile methods were used, we were also able to identify a set of core practices that were common to all of the groups, and that could be a focus for others seeking to adopt these methods

The Association of North Dakota Skilled Nursing Facility Characteristics with COVID-19 Outbreak Severity

Context: COVID-19 exerted severe challenges on skilled nursing facility (SNF) residents and staff. A combination of internal and external factors predisposed SNFs to an increased propensity of COVID-19 spread. Objective: The purpose of this paper is to examine which facility characteristics may have contributed to COVID-19 outbreaks within urban and rural North Dakota skilled nursing facilities. Methods: A 23-question survey regarding facility characteristics was developed and distributed to all 78 North Dakota skilled nursing facilities (SNF). Findings: Of the North Dakota SNF, 40 out of 78 total facilities (51.2%) participated in the survey. Of those participating, 38 of 40 (95%) were in counties with populations under 50,000, with the smallest county population being 1,876. A Spearman’s rank test suggested a relationship between the community spread of COVID-19 and the COVID-19 positivity of SNF residents. Spearman’s rank also suggested a positive association between the SNF resident COVID-19 positivity in relation to staff positivity (p-value 0.042) and county rates (p-value 0.045). Limitations: While this is a comprehensive survey with a very good response rate, two key limitations are identified. First, the survey relies on self-reported data from SNF staff. Second, it is not clear what data would have been received from non-responding SNFs. Implications: Substantial lessons have been learned, which may not only aid future pandemic preparedness but improve the quality of care for nursing home residents during a pandemic or other respiratory disease outbreaks. Proactively knowing susceptibilities and vulnerabilities ahead of time will allow local and state leaders to plan and allocate resources. Future state and local pandemic emergency plans need to be reviewed with the prioritization of skilled nursing facilities as front line facilities during a pandemic, rather than placing their “traditional” emphasis of emergency preparedness on hospitals