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The Earth’s atmosphere is comprised of layers which can be defined by their temperature characteristics. These layers are the troposphere, stratosphere, mesosphere and thermosphere. The region where life exists is in the troposphere, however the study of the layers above is important as changes in these regions can directly impact, or indicate significant changes in, weather in the troposphere. The mesosphere is the least well-known region because it is the most difficult to observe. One of the best tools for observing this region is the Rayleigh-scatter lidar. It is capable of remotely observing the entirety of the mesosphere with good time and altitude resolution. Until recently, this tool was used mainly to study temperatures in the middle atmosphere. In this work we introduce a new, reliable method for obtaining the absolute densities in this region. Long term trends were studied, and are presented, in the temperature and densities int the form of climatologies. Additionally, a case study of atmospheric tides is presented which utilizes the new densities and temperatures.

An optimal estimation method (OEM) was used to obtain all-night temperature profiles from Rayleigh-scatter lidar (RSL) observations obtained by the original and updated lidar systems at Utah State University (USU). These data were used to produce annual climatologies of temperatures above USU. The climatology of temperatures from the original lidar, which operated from late 1993 through 2004, was compared with the climatology produced using the widely used Hauchecorne-Chanin method (HC). This comparison highlights the similarities at lower altitudes and differences, which start between 70 km and 80 km and extend to the top altitudes with the OEM temperatures warmer on average than those of the HC. The differences between methods are likely due to the reliance of the HC on a seeding temperature at the top altitude which likely has a large influence on the temperatures at the top 10 km. OEM and HC temperature climatologies were also produced using observations from the upgraded RSL at USU, which operated from early 2014 to early 2015. Like the original climatology, the newer climatology was seen to differ most at higher altitudes. The OEM climatologies from the original and newer data sets were compared, showing good agreement in the location of the summer mesopause but with colder temperatures in this region from the newer observations.

The Rayleigh-scatter lidar (RSL) system at the Atmospheric Lidar Observatory at Utah State University (ALO-USU) provided a rich database of absolute temperatures throughout the mesosphere from 45 km to above 90 km between 1993 and 2004. Recently, a new method for retrieving absolute temperatures from RSL observations has been developed by a group at the University of Western Ontario (UWO), Canada. The Optimal Estimation Method (OEM) uses machine learning to minimize a cost function by optimizing the temperature parameter in a forward model, in our case the lidar equation, to RSL data. This optimization provides some benefits over the existing method through a robust uncertainty budget and a quantitative determination of the cut-off altitude, or the topmost altitude in the temperature profile. Using this method also provides a slight increase in the top observable altitude and does not have a large dependence on the initial temperature. The OEM procedure was converted from MATLAB, which is used by the UWO group, into Python, which is used at ALO-USU. The temperatures were then reduced using the OEM from observations made between 1993 and 2004. Initial results obtained using the Python version of OEM were compared with those using MATLAB showing good agreement. More observations from ALO-USU were then reduced using OEM and compared with the original reduction method. The results show good agreement between the two methods until higher altitudes. These differences can be attributed to dependence on initial conditions in the original method or over-constraining from overestimating the altitude range to be used in the OEM retrieval. At higher altitudes, however, the temperatures tend to agree within the given uncertainties. Further work with this method is being done to generate a temperature climatology using ALO-USU observations and developing a method to retrieve absolute neutral densities using a modification of the forward model in the OEM.

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ObjectivesCognitive impairment is known to occur in bipolar disorder (BD), even in euthymic patients, with largest effect sizes often seen in Verbal Learning and Memory Tasks (VLT). However, comparisons between BD Type-I and Type-II have produced inconsistent results partly due to low sample sizes.MethodsThis study compared the performance of 183 BDI with 96 BDII out-patients on an adapted version of the Rey Verbal Learning Task. Gender, age, years of education, mood scores and age at onset were all used as covariates. Current medication and a variety of illness variables were also investigated for potential effects on VLT performance.ResultsBDI patients were significantly impaired relative to BDII patients on all five VLT outcome measures after controlling for the other variables [Effect Sizes=.13–.17]. The impairments seem to be unrelated to drug treatment and largely unrelated to illness variables, although age of onset affected performance on three outcome measures and number of episodes of mood elevation affected performance on one.LimitationsThis study used historical healthy controls. Analysis of potential drug effects was limited by insufficient participants not being drug free. Cross-sectional nature of the study limited the analysis of the potential effect of illness variables.ConclusionsThis study replicates earlier findings of increased verbal learning impairment in BDI patients relative to BDII in a substantially larger sample. Such performance cannot be wholly explained by medication effects or illness variables. Thus, the cognitive impairment is likely to reflect a phenotypic difference between bipolar sub-types.

This research is an analysis of absolute densities throughout the mesosphere (45 km to 90 km). Although much research has gone into the study of temperatures and their variations occurring in our atmosphere, little has been done to research the densities and their variations. Due to the remoteness of the middle atmosphere there is a high degree of difficulty in making observations in the mesosphere. There are currently three major types of ground-based instruments used to sense the mesosphere remotely. They are atmospheric radars, LIDARs and optical spectrometers. As far as measuring density in the mesosphere LIDAR is the most efficient. A Rayleigh-scatter LIDAR operated at the Atmospheric LIDAR Observatory (ALO; 41.7 ° N, 111.8 ° W), as part of CASS (Center for Atmosphere and Space Studies), on the campus of Utah State University (USU) has collected extensive data between 1993 and 2004. This LIDAR is used to measure relative densities (which can be used to derive temperatures) throughout the mesosphere. An analysis is made with the absolute densities from the atmosphere reanalysis model ERA-20C (the European Reanalysis 20th century model.) by using the model densities at 45 km to calibrate the LIDAR observations made at USU. Thereby, converting the relative densities measured by the USU LIDAR into measurements of absolute densities. These densities are used to examine the density structure of the mesosphere, how it varies with altitude and time, possible atmospheric anomalies, along with annual or semiannual atmospheric variations. Monthly averages are used to compare density variations related to altitude and season. By normalizing the relative densities from the Rayleigh LIDAR observations to the absolute densities from the reanalysis models, these differences can be observed and analyzed to better characterize the neutral atmosphere and learn how it varies during the year.

The goal of this project is to take relative densities of the mesosphere (altitude 45-90 km) from data that has been collected and convert them into absolute densities. It is then possible to look at how these densities vary with altitude and season. The data was collected using a Rayleigh-scatter LIDAR at the Atmospheric LIDAR Observatory. This is a part of the Center for Atmospheric and Space Sciences and is located on the Utah State University Campus. It spans a total of 11 years beginning in 1993 and ending in 2004. The collected data is used to create a composite year and is then normalized to a constant at an attitude of 45 km. It is then compared to an absolute density measurement at 45 km that is calculated using the European Reanalysis 20th Century (ERA-20C) model. This density is then used to convert all of the relative mesospheric densities into absolute densities.

DOI: 10.1111/brv.12256; International audience; The general dynamic model of oceanic island biogeography (GDM) has added a new dimension to theoretical island biogeography in recognizing that geological processes are key drivers of the evolutionary processes of diversification and extinction within remote islands. It provides a dynamic and essentially non-equilibrium framework generating novel predictions for emergent diversity properties of oceanic islands and archipelagos. Its publication in 2008 coincided with, and spurred on, renewed attention to the dynamics of remote islands. We review progress, both in testing the GDM's predictions and in developing and enhancing ecological-evolutionary understanding of oceanic island systems through the lens of the GDM. In particular, we focus on four main themes: (i) macroecological tests using a space-for-time rationale; (ii) extensions of theory to islands following different patterns of ontogeny; (iii) the implications of GDM dynamics for lineage diversification and trait evolution; and (iv) the potential for downscaling GDM dynamics to local-scale ecological patterns and processes within islands. We also consider the implications of the GDM for understanding patterns of non-native species diversity. We demonstrate the vitality of the field of island biogeography by identifying a range of potentially productive lines for future research. © 2016 Cambridge Philosophical Society.

The Rayleigh-scatter lidar at the Atmospheric Lidar Observatory at Utah State University (ALO-USU; 41.74° N, 111.81° W) started observations in 1993. In 2012 the original lidar system was upgraded with an array of larger mirrors and two lasers to enable observations of the upper mesosphere and lower thermosphere from 70 km to about 115 km in altitude. (Continued refinement should provide data to above 120 km.) Recently, the original system was reconfigured [Elliott et al., 2016] to again observe the lower mesosphere between 40 km and 90 km. Initial data collected by these two parts of the Rayleigh system have been “stitched” together to obtain a full temperature profile from 40 km to about 115 km. These extended profiles have been used to obtain relative neutral densities and temperatures through the entire mesosphere and well into the lower thermosphere. This extends the CEDAR goal of studying coupling between atmospheric regions. Furthermore, by normalizing the relative neutral densities between ~35 and 45 km to an advanced reanalysis model, absolute neutral densities become available from a ground-based, remote-sensing instrument all the way into the lower thermosphere. This opens that region to detailed studies for many research topics.

Supplementary data file includes Figures S1â S11, Tables S1â S12 and Notes 1â 4. (PDF 107087 kb)

The SABER instrument aboard the TIMED satellite is a multichannel radiometer and has been continuously measuring the altitude distribution of infrared airglow intensity in the mesosphere on a global basis since 2002. While the majority of these altitude distributions are Gaussian-like, a significant portion exhibit two or more local maxima, suggesting multiple airglow layers. To better understand the cause of this phenomenon, the global and temporal distributions of infrared OH andO2 scans resulting in multiple peak altitude profiles are being examined.

This thesis analyzes the continuation behavior of prior service Selected Marine Corps Reserve (SMCR) unit members in the grades of E3 to E5 and examines the effect of activation post-9/11 on 12-month continuation rates. The effect of monetary incentives is estimated and other significant predictors of continuation identified. Data were collected from the Total Force Data Warehouse (TFDW) for all Selected Reserve (SelRes) members who served between August 31, 2001 and October 31, 2009. Limited data to determine service history were collected from December 31, 1994 to July 31, 2001. Two probit regression models were estimated for the three tour lengths of 4-, 12- and 24-months. The models included explanatory variables for activation in support of a contingency operation, bonuses, economic conditions, ability, person-job fit, military experience, and demographics. Two additional models were estimated to isolate the effects of prior reserve experience in the active and Reserve Components (RC). Factors having positive effects on continuation were activation frequency, bonuses, the unemployment rate, prior RC experience, tour length, and multiple tours. Negative influencers on continuation included activation length, deploying outside the continental U.S., unexcused absence from drill, being female, being married, and being older. Outstanding Thesis US Marine Corps (USMC) author Approved for public release; distribution is unlimited.

This report follows the preliminary assessment of the potential for carbon dioxide (CO2) sequestration in geological settings in Nevada (Price et al. 2005) by more thoroughly evaluating the potentials for reaction of CO2 with naturally occurring minerals and for use of CO2 in enhanced oil recovery (EOR). The results of these two evaluations have been published by the Nevada Bureau of Mines and Geology (Sturmer et al. 2007 for the mineral-reaction work; LaPointe et al. 2007 for the EOR work). This contract report combines those two reports.

BACKGROUND: DNA methylation is an important mechanism of epigenetic gene expression control that can be passed between generations. Here, we use sodium bisulfite treatment and targeted gene enrichment to study genome-wide methylation across the three sub-genomes of allohexaploid wheat. RESULTS: While the majority of methylation is conserved across all three genomes we demonstrate that differential methylation exists between the sub-genomes in approximately equal proportions. We correlate sub-genome-specific promoter methylation with decreased expression levels and show that altered growing temperature has a small effect on methylation state, identifying a small but functionally relevant set of methylated genes. Finally, we demonstrate long-term methylation maintenance using a comparison between the D sub-genome of hexaploid wheat and its progenitor Aegilops tauschii. CONCLUSIONS: We show that tri-genome methylation is highly conserved with the diploid wheat progenitor while sub-genome-specific methylation shows more variation.

Parental exposure to pathogens can prime offspring immunity in diverse organisms. The mechanisms by which this heritable priming occurs are largely unknown. Here we report that the soil bacteria Pseudomonas vranovensis is a natural pathogen of the nematode Caenorhabditis elegans and that parental exposure of animals to P. vranovensis promotes offspring resistance to infection. Furthermore, we demonstrate a multigenerational enhancement of progeny survival when three consecutive generations of animals are exposed to P. vranovensis. By investigating the mechanisms by which animals heritably adapt to P. vranovensis infection, we found that parental infection by P. vranovensis results in increased expression of the cysteine synthases cysl-1 and cysl-2 and the regulator of hypoxia inducible factor rhy-1 in progeny, and that these three genes are required for adaptation to P. vranovensis. These observations establish a CYSL-1, CYSL-2, and RHY-1 dependent mechanism by which animals heritably adapt to infection.

PIWI-interacting RNAs (piRNAs) are genome-encoded small RNAs that regulate germ cell development and maintain germline integrity in many animals. Mature piRNAs engage Piwi Argonaute proteins to silence complementary transcripts, including transposable elements and endogenous genes. piRNA biogenesis mechanisms are diverse and remain poorly understood. Here, we identify the RNA Polymerase II (RNA Pol II) core subunit RPB-9 as required for piRNA-mediated silencing in the nematode Caenorhabditis elegans. We show that rpb-9 initiates heritable piRNA-mediated gene silencing at two DNA transposon families and at a subset of somatic genes in the germline. We provide genetic and biochemical evidence that RPB-9 is required for piRNA biogenesis by recruiting the Integrator complex at piRNA genes, hence promoting transcriptional termination. We conclude that, as a part of its rapid evolution, the piRNA pathway has co-opted an ancient machinery for high-fidelity transcription.

Funder: National Institutes of Health; FundRef: http://dx.doi.org/10.13039/100000002, Despite reports of parental exposure to stress promoting physiological adaptations in progeny in diverse organisms, there remains considerable debate over the significance and evolutionary conservation of such multigenerational effects. Here, we investigate four independent models of intergenerational adaptations to stress in Caenorhabditis elegans ��� bacterial infection, eukaryotic infection, osmotic stress, and nutrient stress ��� across multiple species. We found that all four intergenerational physiological adaptations are conserved in at least one other species, that they are stress -specific, and that they have deleterious tradeoffs in mismatched environments. By profiling the effects of parental bacterial infection and osmotic stress exposure on progeny gene expression across species, we established a core set of 587 genes that exhibited a greater than twofold intergenerational change in expression in response to stress in C. elegans and at least one other species, as well as a set of 37 highly conserved genes that exhibited a greater than twofold intergenerational change in expression in all four species tested. Furthermore, we provide evidence suggesting that presumed adaptive and deleterious intergenerational effects are molecularly related at the gene expression level. Lastly, we found that none of the effects we detected of these stresses on C. elegans F1 progeny gene expression persisted transgenerationally three generations after stress exposure. We conclude that intergenerational responses to stress play a substantial and evolutionarily conserved role in regulating animal physiology and that the vast majority of the effects of parental stress on progeny gene expression are reversible and not maintained transgenerationally.

Parental exposure to pathogens can prime offspring immunity in diverse organisms. The mechanisms by which this heritable priming occurs are largely unknown. Here we report that the soil bacteria Pseudomonas vranovensis is a natural pathogen of the nematode Caenorhabditis elegans and that parental exposure of animals to P. vranovensis promotes offspring resistance to infection. Furthermore, we demonstrate a multigenerational enhancement of progeny survival when three consecutive generations of animals are exposed to P. vranovensis. By investigating the mechanisms by which animals heritably adapt to P. vranovensis infection, we found that parental infection by P. vranovensis results in increased expression of the cysteine synthases cysl-1 and cysl-2 and the regulator of hypoxia inducible factor rhy-1 in progeny, and that these three genes are required for adaptation to P. vranovensis. These observations establish a CYSL-1, CYSL-2, and RHY-1 dependent mechanism by which animals heritably adapt to infection.

The Coronaviridae is a family of positive-strand RNA viruses that includes SARS-CoV-2, the etiologic agent of the COVID-19 pandemic. Bearing the largest single-stranded RNA genomes in nature, coronaviruses are critically dependent on long-distance RNA-RNA interactions to regulate the viral transcription and replication pathways. Here we experimentally mapped the in vivo RNA-RNA interactome of the full-length SARS-CoV-2 genome and subgenomic mRNAs. We uncovered a network of RNA-RNA interactions spanning tens of thousands of nucleotides. These interactions reveal that the viral genome and subgenomes adopt alternative topologies inside cells and engage in different interactions with host RNAs. Notably, we discovered a long-range RNA-RNA interaction, the FSE-arch, that encircles the programmed ribosomal frameshifting element. The FSE-arch is conserved in the related MERS-CoV and is under purifying selection. Our findings illuminate RNA structure-based mechanisms governing replication, discontinuous transcription, and translation of coronaviruses and will aid future efforts to develop antiviral strategies.

Despite reports of parental exposure to stress promoting physiological adaptations in progeny in diverse organisms, there remains considerable debate over the significance and evolutionary conservation of such multigenerational effects. Here, we investigate four independent models of intergenerational adaptations to stress in Caenorhabditis elegans – bacterial infection, eukaryotic infection, osmotic stress, and nutrient stress – across multiple species. We found that all four intergenerational physiological adaptations are conserved in at least one other species, that they are stress -specific, and that they have deleterious tradeoffs in mismatched environments. By profiling the effects of parental bacterial infection and osmotic stress exposure on progeny gene expression across species, we established a core set of 587 genes that exhibited a greater than twofold intergenerational change in expression in response to stress in C. elegans and at least one other species, as well as a set of 37 highly conserved genes that exhibited a greater than twofold intergenerational change in expression in all four species tested. Furthermore, we provide evidence suggesting that presumed adaptive and deleterious intergenerational effects are molecularly related at the gene expression level. Lastly, we found that none of the effects we detected of these stresses on C. elegans F1 progeny gene expression persisted transgenerationally three generations after stress exposure. We conclude that intergenerational responses to stress play a substantial and evolutionarily conserved role in regulating animal physiology and that the vast majority of the effects of parental stress on progeny gene expression are reversible and not maintained transgenerationally.

Parental exposure to pathogens can prime offspring immunity in diverse organisms. The mechanisms by which this heritable priming occurs are largely unknown. Here we report that the soil bacteria Pseudomonas vranovensis is a natural pathogen of the nematode Caenorhabditis elegans and that parental exposure of animals to P. vranovensis promotes offspring resistance to infection. Furthermore, we demonstrate a multigenerational enhancement of progeny survival when three consecutive generations of animals are exposed to P. vranovensis. By investigating the mechanisms by which animals heritably adapt to P. vranovensis infection, we found that parental infection by P. vranovensis results in increased expression of the cysteine synthases cysl-1 and cysl-2 and the regulator of hypoxia inducible factor rhy-1 in progeny, and that these three genes are required for adaptation to P. vranovensis. These observations establish a CYSL-1, CYSL-2, and RHY-1 dependent mechanism by which animals heritably adapt to infection., Caenorhabditis elegans exhibits multigenerational adaptation to bacterial infection but the mechanisms remain unclear. Here, the authors show that C. elegans parental exposure to Pseudomonas vranovensis promotes offspring resistance to infection, a process mediated by the cysteine synthases CYSL-1 and CYSL-2.

This thesis identifies the effects of mobilization on Marine Corps Reserve non-prior service (NPS) personnel continuation rates. The research evaluates the retention effects of reservists' expectations about mobilization by analyzing retention data from three separate time periods - Pre-9/11, Overlap-9/11, and Post-9/11. The analysis used monthly observations for NPS reserve enlisted personnel who have completed their initial 6-year obligated drilling contracts. This research analyzed the end of contract "waterfall" period, which describes the drastic drop in reserve continuation that takes place upon the completion of NPS reservists drilling obligation. Analysis was performed using multivariate models for each time period, which consider the effects of mobilization, as well as other explanatory variables for demographics, military performance, education benefits, unit type, geographic region, and unemployment rate. The effects of mobilization on continuation were found to differ depending on mobilization duration, frequency, and time period. Factors negatively influencing continuation were found to include general overseas deployment and longer mobilizations. However, the negative impacts on continuation were found to decrease or become statistically insignificant for those who enlisted after 9/11. Shorter mobilization durations were found to positively impact continuation rates. http://archive.org/details/patternsofmarine109455778 Approved for public release; distribution is unlimited.