Modeling And Economic Analysis Of A Crop-Livestock Production System Incorporating Cereal Rye As A Forage

This thesis consists of two chapters using agent-based modeling for a crop-livestock production system incorporating human labor. The first chapter examines the principles used to develop a fundamental simulation pertaining to grazing cereal rye (Secale cereal L.) with calves. Within the software guidelines, the base model has the ability to capture diverse system interactions between livestock/plants and land management with human labor efficiency. AnyLogic incorporates agent-based modeling while combining with discrete event modeling and system dynamics. The purpose of the model was to find the economic returns of grazing cover crops relative to the area of Mead, Nebraska. In our simulation model, we used data from the University of Nebraska-Lincoln Climate Center. The model was developed to create more in depth case studies to help further the understanding of crop and livestock interactions through simulation. AnyLogic is a complex tool that has the capabilities of discovering the interactions between crops, livestock, land, and humans. In the second chapter, we examined the economic returns of grazing cereal rye with calves versus mechanically removing the cover crop. This analysis evaluated production risks due to weather variability and cattle market risk to determine the theoretical best outcome using existing weather and market data. Working with the University of Nebraska-Lincoln’s agronomy and animal science departments, we modified a cereal rye growth production model first proposed by Feyereisen et al. (2006) to match recent on-farm production trial experience in Mead, Nebraska. Based on simulation results over multiple years, it was determined that mechanically harvesting cereal rye is a better option as a long term fixed strategy than grazing cereal rye. This is largely due to cattle market risk during the spring grazing period. The costs associated with mechanically removing the crop depend on farm size and equipment used. Both chapters utilize a model simulating the grazing of cover crops developed using the AnyLogic software while the analysis on mechanically removing the forage was completed with the use of a University of Nebraska-Lincoln cover crop budget. Through bridging the gap between production and economic information, this study sought to develop a financial comparison between the two cover crop strategies for eastern Nebraska farmers. Advisor: Jay Parson

Reflections On Service-Learning, Critical Thinking, And Cultural Competence

In today’s increasingly multicultural society, students need to be prepared for the work world they will encounter. Well-developed critical thinking skills appear essential to needed cultural competence. With its focus on community involvement, deep reflection and civic engagement, the possibility that Service-Learning (SL) could improve students’ critical thinking abilities, and thus contribute to students’ intellectual development and cultural competence, was explored. The critical thinking abilities of a group of 4th and 5th year university students were measured before and after 12 weeks of community-based experiences. The 4th year students were involved in an integrated SL course. The 5th year students had completed the SL course the previous year. There was a significant difference between the two groups with the 5th year students better able to think critically, particularly in deducing conclusions and evaluating arguments. Both quantitative and qualitative data from the two groups revealed a non-linear developmental trajectory of skills that provide insights for professionals in higher education

Community-acquired pneumonia in children: cell-free plasma sequencing for diagnosis and management.

Community-acquired pneumonia (CAP) is a common cause of pediatric hospital admission. Empiric antibiotic therapy for hospitalized children with serious CAP now targets the most likely pathogen(s), including those that may demonstrate significant antibiotic resistance. Cell-free plasma next-generation sequencing (CFPNGS) was first made available for Pediatric Infectious Diseases physicians in June 1, 2017, to supplement standard-of-care diagnostic techniques. A retrospective chart review was performed for children hospitalized with CAP between June 1, 2017, and January 22, 2018, to evaluate the impact of CFPNGS. We identified 15 hospitalized children with CAP without other underlying medical conditions for whom CFPNGS was performed. CFPNGS identified a pathogen in 13 of 15 (86%) children compared with 47% for those using standard culture and PCR-based methods alone. Changes in antibiotic management were made in 7 of 15 (47%) of children as a result of CFPNGS

Peer Review: The Importance Of Education For Best Practice

The effectiveness of teaching is expected by an increasingly skeptical public that wants those in higher education to contain costs, increase access, and teach in ways that make sure students learn. An integral and under-used component of documenting teaching effectiveness is peer review. A framework for best practice to ensure a systematic and comprehensive approach to any peer review has been developed and a foundational aspect of this framework is education about the process and its implementation. In the current pilot study, administrators and non-administrators involved in university teaching were surveyed about their knowledge of, and experiences with, peer review. A striking finding was the notable degree of uncertainty about many components of the process on the part of non-administrators. Results verify the critical importance of education prior to and following any peer review, particularly for instructors in non-administrative positions

Alternative Splicing Events Identified in Human Embryonic Stem Cells and Neural Progenitors

Human embryonic stem cells (hESCs) and neural progenitor (NP) cells are excellent models for recapitulating early neuronal development in vitro, and are key to establishing strategies for the treatment of degenerative disorders. While much effort had been undertaken to analyze transcriptional and epigenetic differences during the transition of hESC to NP, very little work has been performed to understand post-transcriptional changes during neuronal differentiation. Alternative RNA splicing (AS), a major form of post-transcriptional gene regulation, is important in mammalian development and neuronal function. Human ESC, hESC-derived NP, and human central nervous system stem cells were compared using Affymetrix exon arrays. We introduced an outlier detection approach, REAP (Regression-based Exon Array Protocol), to identify 1,737 internal exons that are predicted to undergo AS in NP compared to hESC. Experimental validation of REAP-predicted AS events indicated a threshold-dependent sensitivity ranging from 56% to 69%, at a specificity of 77% to 96%. REAP predictions significantly overlapped sets of alternative events identified using expressed sequence tags and evolutionarily conserved AS events. Our results also reveal that focusing on differentially expressed genes between hESC and NP will overlook 14% of potential AS genes. In addition, we found that REAP predictions are enriched in genes encoding serine/threonine kinase and helicase activities. An example is a REAP-predicted alternative exon in the SLK (serine/threonine kinase 2) gene that is differentially included in hESC, but skipped in NP as well as in other differentiated tissues. Lastly, comparative sequence analysis revealed conserved intronic cis-regulatory elements such as the FOX1/2 binding site GCAUG as being proximal to candidate AS exons, suggesting that FOX1/2 may participate in the regulation of AS in NP and hESC. In summary, a new methodology for exon array analysis was introduced, leading to new insights into the complexity of AS in human embryonic stem cells and their transition to neural stem cells

Quantum Holographic Encoding in a Two-dimensional Electron Gas

The advent of bottom-up atomic manipulation heralded a new horizon for attainable information density, as it allowed a bit of information to be represented by a single atom. The discrete spacing between atoms in condensed matter has thus set a rigid limit on the maximum possible information density. While modern technologies are still far from this scale, all theoretical downscaling of devices terminates at this spatial limit. Here, however, we break this barrier with electronic quantum encoding scaled to subatomic densities. We use atomic manipulation to first construct open nanostructures--"molecular holograms"--which in turn concentrate information into a medium free of lattice constraints: the quantum states of a two-dimensional degenerate Fermi gas of electrons. The information embedded in the holograms is transcoded at even smaller length scales into an atomically uniform area of a copper surface, where it is densely projected into both two spatial degrees of freedom and a third holographic dimension mapped to energy. In analogy to optical volume holography, this requires precise amplitude and phase engineering of electron wavefunctions to assemble pages of information volumetrically. This data is read out by mapping the energy-resolved electron density of states with a scanning tunnelling microscope. As the projection and readout are both extremely near-field, and because we use native quantum states rather than an external beam, we are not limited by lensing or collimation and can create electronically projected objects with features as small as ~0.3 nm. These techniques reach unprecedented densities exceeding 20 bits/nm2 and place tens of bits into a single fermionic state.Comment: Published online 25 January 2009 in Nature Nanotechnology; 12 page manuscript (including 4 figures) + 2 page supplement (including 1 figure); supplementary movie available at http://mota.stanford.ed

SALL1 enforces microglia-specific DNA binding and function of SMADs to establish microglia identity

Spalt-like transcription factor 1 (SALL1) is a critical regulator of organogenesis and microglia identity. Here we demonstrate that disruption of a conserved microglia-specific super-enhancer interacting with the Sall1 promoter results in complete and specific loss of Sall1 expression in microglia. By determining the genomic binding sites of SALL1 and leveraging Sall1 enhancer knockout mice, we provide evidence for functional interactions between SALL1 and SMAD4 required for microglia-specific gene expression. SMAD4 binds directly to the Sall1 super-enhancer and is required for Sall1 expression, consistent with an evolutionarily conserved requirement of the TGFβ and SMAD homologs Dpp and Mad for cell-specific expression of Spalt in the Drosophila wing. Unexpectedly, SALL1 in turn promotes binding and function of SMAD4 at microglia-specific enhancers while simultaneously suppressing binding of SMAD4 to enhancers of genes that become inappropriately activated in enhancer knockout microglia, thereby enforcing microglia-specific functions of the TGFβ–SMAD signaling axis.</p