The Immense Journey: Loess Hills Cultural Resources Study, 2011

Known as one of North America’s natural treasures, the Loess Hills is also one of our country’s archaeological gems. This unique landscape harbors hundreds of well-preserved earth lodge dwellings and palisades villages built by ancestral Plains Indians. The descendants of these early Iowa farmers were first described in the journals and accounts of 18th- and 19th-century travelers and explorers. Celebrated artists, such as Karl Bodmer and George Catlin, forever fixed the vibrant life ways of these people in our mind’s eye. The historical legacy of the Loess Hills lies in a rich archaeological record.

Impact of Cryptosporidium spp. interaction with co-occurring microorganisms on moderate-to-severe diarrhea in the developing world

Diarrheal illness is responsible for over a quarter of all deaths in children under 5 years of age in sub-Saharan Africa and South Asia. Recent findings have identified the parasite Cryptosporidium as a contributor to enteric disease. We examined 9,348 cases and 13,128 controls from the Global Enteric Multicenter Study to assess whether Cryptosporidium interacted with co-occurring pathogens based on adjusted odds of moderate-to-severe diarrhea (MSD). Cryptosporidium was found to interact negatively with Shigella spp., with multiplicative interaction score of 0.16 (95% CI: 0.07 to 0.37, p-value=0.000), and an additive interaction score of -9.81 (95% CI: -13.61 to -6.01, p-value=0.000). Cryptosporidium also interacted negatively with Aeromonas spp., Adenovirus, Norovirus, and Astrovirus with marginal significance. Odds of MSD for Cryptosporidium co-infection with Shigella spp., Aeromonas spp., Adenovirus, Norovirus, or Astrovirus are lower than odds of MSD with either organism alone. This may reduce the efficacy of intervention strategies targeted at Cryptosporidium.

Rice-Infecting Pseudomonas Genomes Are Highly Accessorized and Harbor Multiple Putative Virulence Mechanisms to Cause Sheath Brown Rot

Sheath rot complex and seed discoloration in rice involve a number of pathogenic bacteria that cannot be associated with distinctive symptoms. These pathogens can easily travel on asymptomatic seeds and therefore represent a threat to rice cropping systems. Among the rice-infecting Pseudomonas, P. fuscovaginae has been associated with sheath brown rot disease in several rice growing areas around the world. The appearance of a similar Pseudomonas population, which here we named P. fuscovaginae-like, represents a perfect opportunity to understand common genomic features that can explain the infection mechanism in rice. We showed that the novel population is indeed closely related to P. fuscovaginae. A comparative genomics approach on eight rice-infecting Pseudomonas revealed heterogeneous genomes and a high number of strain-specific genes. The genomes of P. fuscovaginae-like harbor four secretion systems (Type I, II, III, and VI) and other important pathogenicity machinery that could probably facilitate rice colonization. We identified 123 core secreted proteins, most of which have strong signatures of positive selection suggesting functional adaptation. Transcript accumulation of putative pathogenicity-related genes during rice colonization revealed a concerted virulence mechanism. The study suggests that rice-infecting Pseudomonas causing sheath brown rot are intrinsically diverse and maintain a variable set of metabolic capabilities as a potential strategy to occupy a range of environments.

Filling in gaps of Drosophila melanogaster urate degradation metabolic pathway using metabolomics approaches: towards the core metabolome of the fruit fly

The primary goal of systems biology is to integrate complex omics data, and data obtained from traditional experimental studies in order to provide a holistic understanding of organismal function. One way of achieving this aim is to generate genome-scale metabolic models (GEMs), which contain information on all metabolites, enzyme-coding genes, and biochemical reactions in a biological system. Drosophila melanogaster GEM has not been reconstructed to date. Constraint-free genome-wide metabolic model of the fruit fly has been reconstructed in our lab, identifying gaps, where no enzyme was identified and metabolites were either only produced or consume. The main focus of the work presented in this thesis was to develop a pipeline for efficient gap filling using metabolomics approaches combined with standard reverse genetics methods, using 5-hydroxyisourate hydrolase (5-HIUH) as an example. 5-HIUH plays a role in urate degradation pathway. Inability to degrade urate can lead to inborn errors of metabolism (IEMs) in humans, including hyperuricemia. Based on sequence analysis Drosophila CG30016 gene was hypothesised to encode 5- HIUH. CG30016 knockout flies were examined to identify Malpighian tubules phenotype, and shortened lifespan might reflect kidney disorders in hyperuricemia in humans. Moreover, LC-MS analysis of mutant tubules revealed that CG30016 is involved in purine metabolism, and specifically urate degradation pathway. However, the exact role of the gene has not been identified, and the complete method for gap filling has not been developed. Nevertheless, thanks to the work presented here, we are a step closer towards the development of a gap-filling pipeline in Drosophila melanogaster GEM. Importantly, the areas that require further optimisation were identified and are the focus of future research. Moreover, LC-MS analysis confirmed that tubules rather than the whole fly were more suitable for metabolomics analysis of purine metabolism. Previously, Dow/Davies lab has generated the most complete tissue-specific transcriptomic atlas for Drosophila – FlyAtlas.org, which provides data on gene expression across multiple tissues of adult fly and larva. FlyAtlas revealed that transcripts of many genes are enriched in specific Drosophila tissues, and that it is possible to deduce the functions of individual tissues within the fly. Based on FlyAtlas data, it has become clear that the fly (like other metazoan species) must be considered as a set of tissues, each 2 with its own distinct transcriptional and functional profile. Moreover, it revealed that for about 30% of the genome, reverse genetic methods (i.e. mutation in an unknown gene followed by observation of phenotype) are only useful if specific tissues are investigated. Based on the FlyAtlas findings, we aimed to build a primary tissue-specific metabolome of the fruit fly, in order to establish whether different Drosophila tissues have different metabolomes and if they correspond to tissue-specific transcriptome of the fruit fly (FlyAtlas.org). Different fly tissues have been dissected and their metabolome elucidated using LC-MS. The results confirmed that tissue metabolomes differ significantly from each other and from the whole fly, and that some of these differences can be correlated to the tissue function. The results illustrate the need to study individual tissues as well as the whole organism. It is clear that some metabolites that play an important role in a given tissue might not be detected in the whole fly sample because their abundance is much lower in comparison to other metabolites present in all tissues, which prevent the detection of the tissue-specific compound.

Insights into the Fallback Path of Best-Effort Hardware Transactional Memory Systems

Current industry proposals for Hardware Transactional Memory (HTM) focus on best-effort solutions (BE-HTM) where hardware limits are imposed on transactions. These designs may show a significant performance degradation due to high contention scenarios and different hardware and operating system limitations that abort transactions, e.g. cache overflows, hardware and software exceptions, etc. To deal with these events and to ensure forward progress, BE-HTM systems usually provide a software fallback path to execute a lock-based version of the code. In this paper, we propose a hardware implementation of an irrevocability mechanism as an alternative to the software fallback path to gain insight into the hardware improvements that could enhance the execution of such a fallback. Our mechanism anticipates the abort that causes the transaction serialization, and stalls other transactions in the system so that transactional work loss is mini- mized. In addition, we evaluate the main software fallback path approaches and propose the use of ticket locks that hold precise information of the number of transactions waiting to enter the fallback. Thus, the separation of transactional and fallback execution can be achieved in a precise manner. The evaluation is carried out using the Simics/GEMS simulator and the complete range of STAMP transactional suite benchmarks. We obtain significant performance benefits of around twice the speedup and an abort reduction of 50% over the software fallback path for a number of benchmarks.

Irrevocabilidad Relajada para Memoria Transaccional Hardware

Los sistemas comerciales que ofrecen memoria transaccional (TM) implementan un sistema hardware best-effort (BE-HTM) con limitaciones. Es necesario programar un fallback software basado en cerrojos para asegurar el progreso de la aplicación. En este artículo se propone un nuevo tipo de irrevocabilidad hardware (un modo transaccional que marca las transacciones como no abortables) para hacer frente a las limitaciones de los sistemas BE-HTM de una manera mas eficiente, y para liberar a al usuario de tener que programar un fallback. Se basa en el concepto de suscripción relajada utilizada o en el contexto de la programación de fallbacks basada o en cerrojos, donde la transacción se suscribe al cerrojo al final de la misma en lugar de al principio. El mecanismo de irrevocabilidad relajada hardware no involucra cambios en el protocolo de coherencia y se compara con su homólogo software, que proponemos como un fallback con suscripción relajada de espera escapada. También proponemos la irrevocabilidad relajada con anticipación, un mecanismo que no se puede implementar en software, y que mejora el rendimiento de las aplicaciones con múltiples reemplazos de bloques transaccionales de caché. La evaluación de las propuestas se lleva a cabo con el simulador Simics/GEMS junto con la suite de benchmarks STAMP, y se obtiene una mejora de rendimiento sobre el fallback del 14% al 28% para algunos benchmarks.

Validación de criterio concurrente del sistema de observación de tiempo de instrucción de condición física – SOFIT- para la medición de la actividad física durante las clases de educación física en escolares de 1º A 9º de Bogotá, Colombia

Determinar la validez concurrente del Sistema de Observación de Tiempo de Instrucción de Condición Física (SOFIT) a través de acelerometría, como método para medir los niveles de actividad física (AF) de los escolares de 1º a 9º durante la clase de educación física en tres colegios públicos de Bogotá, Colombia. Estudio transversal entre Octubre de 2014 y Marzo de 2015. La medición se realizó en tres colegios públicos de Bogotá. Participaron 48 estudiantes (25 niñas; 23 niños), entre 5 y 17 años, seleccionados de acuerdo al protocolo de SOFIT. El resultado se categoriza en porcentaje de tiempo en comportamiento sedentario, AF moderada, AF vigorosa, y AF moderada a vigorosa. Se validó utilizando como patrón de oro la acelerometría en las mismas categorías. Se realizó diferencia de medias, regresión lineal y modelo de efectos fijos. La correlación entre SOFIT y acelerometría fue buena para AF moderada (rho=,958; p=0,000), AF vigorosa (rho=,937; p=0,000) y AF de moderada a vigorosa (rho=0,962; p=0,000). Al igual que utilizando un modelo de efectos fijos, AF moderada (β1=0,92; p=0,00), vigorosa (β1=0,94; p=0,00) y AF de moderada a vigorosa (β1=0,95; p=0,00), mostrando ausencia de diferencias significativas entre los dos métodos para la medición de los niveles de AF. El comportamiento sedentario correlacionó positivamente en Spearman (rho=,0965; p=0,000), El sistema SOFIT demostró ser válido para medir niveles de AF en clases de educación física, tras buena correlación y concordancia con acelerometría. SOFIT es un instrumento de fácil acceso y de bajo costo para la medición de la AF durante las clases de educación física en el contexto escolar y se recomienda su uso en futuros estudios.