From Passive to Active Community Conservation: A Study of Forest Governance in a Region of the Sierra Norte of Oaxaca, Mexico

This thesis investigates how seven communities in a subregion of the Sierra Norte of Oaxaca are conserving high forest cover in the absence of national protected areas. To conduct this study I relied on archival research and the review of community documents, focus group interviews and land use transects to explore historical and current land use. I found that communities have conserved 88.34% of the subregion as forest cover, or 58,596 hectares out of a total territory of 66,264 hectares. Analysis suggests that the communities have undergone a historical transition from more passive conservation to more active, conscious conservation particularly in the last decade. This thesis further contends that communities deserve additional financial compensation for this active conservation of globally important forests for biodiversity conservation and that exercises in systematic conservation planning ignore the reality that existing biodiversity conservation in the subregion is associated with community ownership

Direct, biomimetic synthesis of (+)-artemone via a stereoselective, organocatalytic cyclization

We present a four-step synthesis of (+)-artemone from (–)- linalool, featuring iminium organocatalysis of a doubly diastereoselective conjugate addition reaction. The strategy follows a proposed biosynthetic pathway, rapidly generates stereochemical complexity, uses no protecting groups, and minimizes redox manipulations

Comparison of RNA-Seq and Microarray Gene Expression Platforms for the Toxicogenomic Evaluation of Liver From Short-Term Rat Toxicity Studies

Gene expression profiling is a useful tool to predict and interrogate mechanisms of toxicity. RNA-Seq technology has emerged as an attractive alternative to traditional microarray platforms for conducting transcriptional profiling. The objective of this work was to compare both transcriptomic platforms to determine whether RNA-Seq offered significant advantages over microarrays for toxicogenomic studies. RNA samples from the livers of rats treated for 5 days with five tool hepatotoxicants (α-naphthylisothiocyanate/ANIT, carbon tetrachloride/CCl4, methylenedianiline/MDA, acetaminophen/APAP, and diclofenac/DCLF) were analyzed with both gene expression platforms (RNA-Seq and microarray). Data were compared to determine any potential added scientific (i.e., better biological or toxicological insight) value offered by RNA-Seq compared to microarrays. RNA-Seq identified more differentially expressed protein-coding genes and provided a wider quantitative range of expression level changes when compared to microarrays. Both platforms identified a larger number of differentially expressed genes (DEGs) in livers of rats treated with ANIT, MDA, and CCl4 compared to APAP and DCLF, in agreement with the severity of histopathological findings. Approximately 78% of DEGs identified with microarrays overlapped with RNA-Seq data, with a Spearman’s correlation of 0.7 to 0.83. Consistent with the mechanisms of toxicity of ANIT, APAP, MDA and CCl4, both platforms identified dysregulation of liver relevant pathways such as Nrf2, cholesterol biosynthesis, eiF2, hepatic cholestasis, glutathione and LPS/IL-1 mediated RXR inhibition. RNA-Seq data showed additional DEGs that not only significantly enriched these pathways, but also suggested modulation of additional liver relevant pathways. In addition, RNA-Seq enabled the identification of non-coding DEGs that offer a potential for improved mechanistic clarity. Overall, these results indicate that RNA-Seq is an acceptable alternative platform to microarrays for rat toxicogenomic studies with several advantages. Because of its wider dynamic range as well as its ability to identify a larger number of DEGs, RNA-Seq may generate more insight into mechanisms of toxicity. However, more extensive reference data will be necessary to fully leverage these additional RNA-Seq data, especially for non-coding sequences

Preclinical species gene expression database: Development and meta-analysis

The evaluation of toxicity in preclinical species is important for identifying potential safety liabilities of experimental medicines. Toxicology studies provide translational insight into potential adverse clinical findings, but data interpretation may be limited due to our understanding of cross-species biological differences. With the recent technological advances in sequencing and analyzing omics data, gene expression data can be used to predict cross species biological differences and improve experimental design and toxicology data interpretation. However, interpreting the translational significance of toxicogenomics analyses can pose a challenge due to the lack of comprehensive preclinical gene expression datasets. In this work, we performed RNA-sequencing across four preclinical species/strains widely used for safety assessment (CD1 mouse, Sprague Dawley rat, Beagle dog, and Cynomolgus monkey) in ∼50 relevant tissues/organs to establish a comprehensive preclinical gene expression body atlas for both males and females. In addition, we performed a meta-analysis across the large dataset to highlight species and tissue differences that may be relevant for drug safety analyses. Further, we made these databases available to the scientific community. This multi-species, tissue-, and sex-specific transcriptomic database should serve as a valuable resource to enable informed safety decision-making not only during drug development, but also in a variety of disciplines that use these preclinical species

French Truffles and Forest Transitions

Truffle production in France has declined by more than 90% over the last 100 years. Commonly cited causes include a massive rural exodus that led to more open canopy forests becoming less intensively managed and reverting to closed canopy forests, the latter which do not favor truffle production. Scholars have labeled such a process as a forest transition, when a location goes from previously losing forest cover to regrowth and net gains in forest cover. Scholars have single out France as a place with a marked forest transition. Commonly these increases in forest cover are assumed to be a beneficial public good. Here, I question if it is accurate to view forest transitions as being universally beneficial, especially considering that this changing ecology has had strongly deleterious impacts on truffle production and those who rely on it for revenue. In this study I will use remote sensed images to examine if a forest transition did in fact occur in the department of Lot, France and what are the impacts forest trends have had on truffle cultivation. I will further estimates potential losses of revenue from truffle production which has resulted from any existing forest transition

Truffles Have Never Been Modern: An Actor-Network Theorization of 150 Years of French Trufficulture

Contemporary scholars seeking to increase Tuber Melanosporum truffle production rely almost exclusively on technological advancements to increase yields, while failing to place the cultivation of truffles, trufficulture, in its historical or local landscape contexts. In this dissertation, I describe how truffle scholars’ conceptualization of trufficulture and landscapes has changed over 150 years in France, while focusing on the French département of Lot. I examine changing relations between humans and nonhumans and how they impact truffle harvests. I analyzed the history of French trufficulture through a close reading of historic truffle manuals, archival research and the classification of remotely sensed images. Shifting from the past to the present, from July 2014-August 2016, I conducted semi-structured survey interviews with working truffle-growers (trufficulteurs) and participant observation at meetings of trufficulteurs, truffle hunts and truffle markets. I utilize actor-network theory (ANT) as both a theory and methodology. Actor-network theory allowed me to follow the impacts made by both humans and nonhumans on trufficulture. I found that truffle harvests in the 1880s dropped by 90%. Highly populated, intensively worked landscapes of viticulture, silvopastoralism and cereal cultivation created conditions suitable to truffles. By the 1870s the phylloxera aphid ravaged grapevines, which made trufficulture an important source of revenue. These advantageous conditions would not last. Post-WWI, yields fell for decades because of an ongoing rural population exodus and consequent agricultural abandonment, which promoted reforestation and closed canopy forests in Lot, France. By the 1960s, French trufficulteurs organized associations to share knowledge and promote local truffle markets to revive production. Trufficulteurs’ utilization of tractors, ‘inoculated’ plants and irrigation systems produced a new form of “modern” trufficulture. State subsidies helped trufficulteurs adopt “modern” practices, in hopes of increasing yields. “Modern” trufficulture has not dramatically increased yields. A few highly-capitalized trufficulteurs dominate production in Lot. Many others practice trufficulture as a hobby. Instead of relying on “modern” technological fixes, my findings suggest that trufficulteurs, farmers and states should reinvigorate extensive polyculture farming practices that maintain open canopy forests, which were beneficial to trufficulture in the past. Actor-network theory allowed me to rethink human and nonhuman relations, and to propose alternatives to “modern” trufficulture

Pursuing the Performance Potential of Dynamic Cache Line Sizes *

In this paper we examine the application of offline algorithms for determining the optimal sequence of loads and superloads (a load of multiple consecutive cache lines) for direct-mapped caches. We evaluate potential gains in terms of miss rate and bandwidth and find that in many cases optimal superloading can noticeably reduce the miss rate without appreciably increasing bandwidth. Then we examine how this performance potential might be realized. We examine the effectiveness of a dynamic online algorithm and of static analysis (profiling) for superloading and compare these to next-line prefetching. Experimental results show improvements comparable to those of the optimal algorithm in terms of miss rates

On the Performance Potential of Dynamic Cache Line Sizes

In this paper we present offline algorithms for determining the optimal sequence of loads, superloads and bypasses for direct-mapped caches. We evaluate potential gains in terms of miss rate and bandwidth and find that in many cases optimal superloading can noticeably reduce the miss rate without appreciably increasing bandwidth. We also present an online algorithm for determining the sequence of loads and superloads. This algorithm operates by monitoring the reuse and conflicts of cache lines. Experimental results show comparable improvements to the optimal algorithm in terms of miss rates. 1 Introduction Since their introduction over thirty years ago, caches have become ubiquitous as components of the memory hierarchy. All modern microprocessors have on-chip, or level one, instruction and data caches and a large majority of these level one caches are backed up by second level caches. Caches have been successful because programs exhibit locality: spatial locality, i.e., the tendency ..