Cooking shapes the structure and function of the gut microbiome

Diet is a critical determinant of variation in gut microbial structure and function, outweighing even host genetics1-3. Numerous microbiome studies have compared diets with divergent ingredients1-5, but the everyday practice of cooking remains understudied. Here, we show that a plant diet served raw versus cooked reshapes the murine gut microbiome, with effects attributable to improvements in starch digestibility and degradation of plant-derived compounds. Shifts in the gut microbiota modulated host energy status, applied across multiple starch-rich plants, and were detectable in humans. Thus, diet-driven host-microbial interactions depend on the food as well as its form. Because cooking is human-specific, ubiquitous and ancient6,7, our results prompt the hypothesis that humans and our microbiomes co-evolved under unique cooking-related pressures

Letter from E. Turnbaugh

Letter concerning a copy of the catalogue for Utah Agricultural College

“My Bruises Are Inward:” A Study of Mental Trauma in the American Civil War

War is traumatic. Since the American Psychiatric Association first recognized post-traumatic stress disorder (PTSD) in 1980, living veterans of combat have been diagnosed at an alarmingly high rate. However, mental trauma related diagnoses have existed for centuries, including several that were identified around the time of the American Civil War. This thesis argues that Civil War soldiers experienced mental trauma related to their military service. It does so through three lenses. Focused on the mental trauma among Northern veterans, this study investigates in particular the relationship between mental trauma and socioeconomic status. It analyzes the experiences of both white and African-American soldiers with mental trauma resulting from combat, and it examines the public’s perception of veterans and their mental trauma accrued during the war. This work is grounded in a rich secondary literature and contemporary personal correspondence, diaries, newspapers, periodicals, military pensions, asylum records, and medical documents. These primary sources offer an intimate examination of the struggles of Civil War soldiers to overcome the psychological impact of war. An in-depth study of the emotional suffering of Civil War combatants results in a better understanding of mental trauma as it relates to military history

The financing of education in homestead areas

Some explanation is necessary of the method of procedure in compiling material for this thesis. The first step was really taken seven years ago. At that time the writer interviewed state officials at Sacramento, California, in the hope of obtaining state aid for educational finance in the Tule Lake section of the Klamath Irrigation Project. The Governor, the department of education, and the finance department were all consulted, but no legal way was discovered of using state money for the erection of school buildings in the district mentioned. Some county money was available for payment of teachers’ salary, but none for building purposes. Chapter V will relate in some detail how that particular problem was solved. The main study began in the fall of 1934 and was carried on up to mid-summer, 1935, Letters of inquiry were sent to all states that had or still have homestead lands. These letters contained a statement of the financial problem peculiar to homestead areas during the period of “proving up” on homestead entries. They requested information as to whether any study of similar nature had ever been completed in the United States. They also requested a list of sources of information. Without exception, replies to these letters indicated that no such study had been made. While some replies contained suggestions as to sources of information, none gave any direct solution to the problem, or pointed to any source that did. These letters of inquiry were sent to state departments of education, to state universities, to historical societies, to the Department of the Interior, Bureau of Reclamation, and Office of Education, and to individuals noted as specialists in school finance. WHile awaiting these letters, the writer searched general histories, stories of pioneering in the West, histories of education, and periodicals of magazine articles relating to homesteads. In this research the librarians of the College of the Pacific and of the State Library at Sacramento gave all the assistance possible. At no time, however, during the whole years’ study did the writer obtain any information dealing absolutely and directly with the problem at hand. It seemed best, therefore, to obtain as accurately as possible a general picture of methods of financing education in homestead states during those periods most likely to have been affected by lack of finances for a building program. IN addition to this general study, a specific study was made of homestead areas now going through those five difficult years. This was done by means of personal visitation, by assistance of pamphlets and letters from superintendents of irrigation projects, and from educators now struggling with the perplexing difficulties of financing education in homestead areas. It was from these school men and from the writer’s own experience that information was received dealing directly with this special problem. The writer regrets that he could not visit the great homestead states east of the Rockies to obtain first hand a more direct knowledge of how the problem was handled there forty to sixty years ago. It is likely that pioneers still living could tell how the problem was solved, or was not solved, as the case might be. Also private letters, school minutes preserved, and similar unpublished documents might give valuable information. It is to be hoped that this research may be made and the material found summarized before available sources have passed out of existence

A Hybrid Templated-Based Composite Classification System

An automatic target classification system contains a classifier which reads a feature as an input and outputs a class label. Typically, the feature is a vector of real numbers. Other features can be non-numeric, such as a string of symbols or alphabets. One method of improving the performance of an automatic classification system is through combining two or more independent classifiers that are complementary in nature. Complementary classifiers are observed by finding an optimal method for partitioning the problem space. For example, the individual classifiers may operate to identify specific objects. Another method may be to use classifiers that operate on different features. We propose a design for a hybrid composite classification system, which exploits both real-numbered and non-numeric features with a template matching classification scheme. This composite classification system is made up of two independent classification systems.These two independent classification systems, which receive input from two separate sensors are then combined over various fusion methods for the purpose of target identification. By using these two separate classifiers, we explore conditions that allow the two techniques to be complementary in nature, thus improving the overall performance of the classification system. We examine various fusion techniques, in search of the technique that generates the best results. We investigate different parameter spaces and fusion rules on example problems to demonstrate our classification system. Our examples consider various application areas to help further demonstrate the utility of our classifier. Optimal classifier performance is obtained using a mathematical framework, which takes into account decision variables based on decision-maker preferences and/or engineering specifications, depending upon the classification problem at hand

Making It Last: Storage Time and Temperature Have Differential Impacts on Metabolite Profiles of Airway Samples from Cystic Fibrosis Patients.

Metabolites of human or microbial origin have the potential to be important biomarkers of the disease state in cystic fibrosis (CF). Clinical sample collection and storage conditions may impact metabolite abundances with clinical relevance. We measured the change in metabolite composition based on untargeted gas chromatography-mass spectrometry (GC-MS) when CF sputum samples were stored at 4°C, -20°C, or -80°C with one or two freeze-thaw cycles. Daily measurements were taken for 1 week and then weekly for 4 weeks (4°C) and 8 weeks (-20°C). The metabolites in samples stored at -20°C maintained abundances similar to those found at-80°C over the course of 8 weeks (average change in Bray-Curtis distance, 0.06 ± 0.04) and were also stable after one or two freeze-thaw cycles. However, the metabolite profiles of samples stored at 4°C shifted after 1 day and continued to change over the course of 4 weeks (average change in Bray-Curtis distance, 0.31 ± 0.12). The abundances of several amino acids and other metabolites increased with time of storage at 4°C but remained constant at -20°C. Storage temperature was a significant factor driving the metabolite composition (permutational multivariate analysis of variance: r2 = 0.32 to 0.49, P < 0.001). CF sputum samples stored at -20°C at the time of sampling maintain a relatively stable untargeted GC-MS profile. Samples should be frozen on the day of collection, as more than 1 day at 4°C impacts the global composition of the metabolites in the sample. IMPORTANCE Metabolomics has great potential for uncovering biomarkers of the disease state in CF and many other contexts. However, sample storage timing and temperature may alter the abundance of clinically relevant metabolites. To assess whether existing samples are stable and to direct future study design, we conducted untargeted GC-MS metabolomic analysis of CF sputum samples after one or two freeze-thaw cycles and storage at 4°C and -20°C for 4 to 8 weeks. Overall, storage at -20°C and freeze-thaw cycles had little impact on metabolite profiles; however, storage at 4°C shifted metabolite abundances significantly. GC-MS profiling will aid in our understanding of the CF lung, but care should be taken in studies using sputum samples to ensure that samples are properly stored

Factors Associated with the Diversification of the Gut Microbial Communities within Chimpanzees from Gombe National Park.

The gastrointestinal tract harbors large and diverse populations of bacteria that vary among individuals and within individuals over time. Numerous internal and external factors can influence the contents of these microbial communities, including diet, geography, physiology, and the extent of contact among hosts. To investigate the contributions of such factors to the variation and changes in gut microbial communities, we analyzed the distal gut microbiota of individual chimpanzees from two communities in Gombe National Park, Tanzania. These samples, which were derived from 35 chimpanzees, many of whom have been monitored for multiple years, provide an unusually comprehensive longitudinal depth for individuals of known genetic relationships. Although the composition of the great-ape microbiota has been shown to codiversify with host species, indicating that host genetics and phylogeny have played a major role in its differentiation over evolutionary timescales, the geneaological relationships of individual chimpanzees did not coincide with the similarity in their gut microbial communities. However, the inhabitants from adjacent chimpanzee communities could be distinguished based on the contents of their gut microbiota. Despite the broad similarity of community members, as would be expected from shared diet or interactions, long-term immigrants to a community often harbored the most distinctive gut microbiota, suggesting that individuals retain hallmarks of their previous gut microbial communities for extended periods. This pattern was reinforced in several chimpanzees sampled over long temporal scales, in which the major constituents of the gut microbiota were maintained for nearly a decade