Analysis of the Hydrologic Cycle in the Community Atmosphere Model

Studying the movement of water through the atmosphere has been an area of both interest and challenge. Climate models have been trying to recreate the dynamic processes of the atmospheric hydrologic cycle in attempt to better understand past, current, and future climate. However, this has proved to be quite difficult as the hydrologic cycle is not fully understood nor simple to simulate. It is shown though that climate models such as the Community Atmosphere Model are able to capture and recreate most of the patterns and paths of water as it moves through the atmosphere. Though, many of the long-standing biases in climate models are still found to be present in current versions of the model. This study will compare model output from the Community Atmosphere Version 5 with observational data. The variables that were compared were radiative surface temperature, evaporation minus precipitation, precipitation rate, precipitable water, total cloud fraction, and cloud liquid water path. The model tends to capture the zonal patterns of moisture across the Earth with only a few discrepancies near the mid-latitudes and with total cloud fraction. The model also tends to be accurate with the magnitude of the variables though there is a major discrepancy with cloud liquid water path. As a whole, the results suggest that current climate models are able to be an effective tool in trying to better understand both the hydrologic cycle and past climates

Early Successional Microhabitats Allow the Persistence of Endangered Plants in Coastal Sand Dunes

Many species are adapted to disturbance and occur within dynamic, mosaic landscapes that contain early and late successional microhabitats. Human modification of disturbance regimes alters the availability of microhabitats and may affect the viability of species in these ecosystems. Because restoring historical disturbance regimes is typically expensive and requires action at large spatial scales, such restoration projects must be justified by linking the persistence of species with successional microhabitats. Coastal sand dune ecosystems worldwide are characterized by their endemic biodiversity and frequent disturbance. Dune-stabilizing invasive plants alter successional dynamics and may threaten species in these ecosystems. We examined the distribution and population dynamics of two federally endangered plant species, the annual Layia carnosa and the perennial Lupinus tidestromii, within a dune ecosystem in northern California, USA. We parameterized a matrix population model for L. tidestromii and examined the magnitude by which the successional stage of the habitat (early or late) influenced population dynamics. Both species had higher frequencies and L. tidestromii had higher frequency of seedlings in early successional habitats. Lupinus tidestromii plants in early successional microhabitats had higher projected rates of population growth than those associated with stabilized, late successional habitats, due primarily to higher rates of recruitment in early successional microhabitats. These results support the idea that restoration of disturbance is critical in historically dynamic landscapes. Our results suggest that large-scale restorations are necessary to allow persistence of the endemic plant species that characterize these ecosystems

Thematic Dimensions of Grandparent Caregiving: A Focus Group Approach

The present study involved 75 grandparent caregivers (M age = 59) who participated in focus groups targeting their needs and concerns relevant to raising their grandchildren. Based upon a qualitative analysis of group session notes reliably cross referenced across 3 observers, the following themes emerged: 1) Isolation, disenfranchisement, and marginalization with regard to others, 2) Difficulty in dealing with and frustration with the adult child whose child one is raising, 3) The need to be able to cope with one’s own emotions and life situation, 4) Difficulties in coping with the emotional, interpersonal, or behavioral problems of the grandchild, 5) Getting competent, trustworthy, and affordable child (day) care/respite care, 6) Frustration with service providers, 7) Ignorance of what social, medical, psychological, and legal services are available or difficulty in affording or accessing such services, 8) Challenges in managing other life stresses that are superimposed upon or consequences of the demands of raising a grandchild, 9) A lack of legal standing as the grandchild’s caregiver, and 10) A lack of parenting skills and knowledge about child development. Discussed here is the fact that these thematic concerns expressed by grandparent caregivers have a number of implications for grandfamilies’ mental and physical health, access to services, the lessening of isolation and stigmatization among such persons, and the design and implementation of interventions for them

Local adaptation constrains drought tolerance in a tropical foundation tree

Plant species with broad climatic ranges might be more vulnerable to climate change than previously appreciated due to intraspecific variation in climatic stress tolerance. In tropical forests, drought is increasingly frequent and severe, causing widespread declines and altering community dynamics. Yet, little is known about whether foundation tropical trees vary in drought tolerance throughout their distributions, and how intraspecific variation in drought tolerance might contribute to their vulnerability to climate changE. We tested for local adaptation in seedling emergence and establishment with a full-factorial reciprocal transplant experiment including 27 populations and 109,350 seeds along a 3,500 mm precipitation gradient for a widespread tropical foundation tree, Metrosideros polymorpha, in Hawaii. To more precisely relate seedling performance to soil moisture, we conducted a complementary greenhouse experiment to test responses of the same focal populations to simulated drought. In the reciprocal transplant experiment, we observed significant variation among populations and sites in germination and seedling establishment rates. Overall, there was a significant link between historical rainfall of populations and their performance under current rainfall at the study sites consistent with local adaptation. In particular, populations from historically wet sites demonstrated lower germination rates in currently dry sites compared to wet field sites, while populations from historically dry sites germinated well across all sites, with particularly high germination in dry sites. In the greenhouse, seedlings from wet populations survived fewer days without water, and succumbed at wetter soil conditions than populations from historically dry sites, corroborating results from the field experiment. Synthesis. While climate change models project the greatest drying trends for historically dry areas in Hawaii, even moderate drying of wet sites could significantly reduce Metrosideros polymorpha recruitment given the sensitivity of seedlings to very slight changes in water regimes. Thus, although M. polymorpha demonstrates high seedling drought tolerance in some populations, providing evidence of resilience at the species-scale, there are nonetheless vulnerable populations that will likely decline under climate change. Our approach demonstrates that even trees with high dispersal abilities can show significant clines in drought tolerance, and suggests that similar intraspecific variation might be an important consideration for other tropical foundational tree species

Glyoxal Formation and Its Role in Endogenous Oxalate Synthesis

Calcium oxalate kidney stones are a common condition affecting many people in the United States. The concentration of oxalate in urine is a major risk factor for stone formation. There is evidence that glyoxal metabolism may be an important contributor to urinary oxalate excretion. Endogenous sources of glyoxal include the catabolism of carbohydrates, proteins, and fats. Here, we review all the known sources of glyoxal as well as its relationship to oxalate synthesis and crystal formation

Expanded safety experience with lenalidomide plus dexamethasone in relapsed or refractory multiple myeloma

Lenalidomide gained Food and Drug Administration (FDA) approval for treatment of patients with relapsed or refractory multiple myeloma (MM) in combination with dexamethasone in June 2006. In April 2005, the FDA and patient advocacy groups requested an expanded access programme to both provide lenalidomide to patients likely to benefit and obtain additional safety information. Relapsed/refractory MM patients received lenalidomide 25 mg/d (days 1–21) and dexamethasone 40 mg/d (days 1–4, 9–12, and 17–20 of cycles 1–4; days 1–4 only from cycle 5 onwards), in 4-week cycles until disease progression, study drug discontinuation, or lenalidomide approval. Of the 1438 patients enrolled, ∼60% were male, median age was 64 years, and 61·7% had Durie-Salmon stage III disease. Median time on study was 15·4 weeks (range: 0·1–49·1) and median dose was 25 mg. The most common adverse events (AEs) were haematological (49%), gastrointestinal (59%), and fatigue (55%). The most common grade ≥3 AEs were haematological (45%), fatigue (10%), and pneumonia (7%). The most common serious AEs were pneumonia (8%), pyrexia (4%), and deep-vein thrombosis (3%). Primary cause of death was disease progression (10%). Safety data confirmed known AEs of lenalidomide plus dexamethasone therapy in patients with relapsed/refractory MM

Normalization and microbial differential abundance strategies depend upon data characteristics

BackgroundData from 16S ribosomal RNA (rRNA) amplicon sequencing present challenges to ecological and statistical interpretation. In particular, library sizes often vary over several ranges of magnitude, and the data contains many zeros. Although we are typically interested in comparing relative abundance of taxa in the ecosystem of two or more groups, we can only measure the taxon relative abundance in specimens obtained from the ecosystems. Because the comparison of taxon relative abundance in the specimen is not equivalent to the comparison of taxon relative abundance in the ecosystems, this presents a special challenge. Second, because the relative abundance of taxa in the specimen (as well as in the ecosystem) sum to 1, these are compositional data. Because the compositional data are constrained by the simplex (sum to 1) and are not unconstrained in the Euclidean space, many standard methods of analysis are not applicable. Here, we evaluate how these challenges impact the performance of existing normalization methods and differential abundance analyses.ResultsEffects on normalization: Most normalization methods enable successful clustering of samples according to biological origin when the groups differ substantially in their overall microbial composition. Rarefying more clearly clusters samples according to biological origin than other normalization techniques do for ordination metrics based on presence or absence. Alternate normalization measures are potentially vulnerable to artifacts due to library size. Effects on differential abundance testing: We build on a previous work to evaluate seven proposed statistical methods using rarefied as well as raw data. Our simulation studies suggest that the false discovery rates of many differential abundance-testing methods are not increased by rarefying itself, although of course rarefying results in a loss of sensitivity due to elimination of a portion of available data. For groups with large (~10×) differences in the average library size, rarefying lowers the false discovery rate. DESeq2, without addition of a constant, increased sensitivity on smaller datasets (<20 samples per group) but tends towards a higher false discovery rate with more samples, very uneven (~10×) library sizes, and/or compositional effects. For drawing inferences regarding taxon abundance in the ecosystem, analysis of composition of microbiomes (ANCOM) is not only very sensitive (for >20 samples per group) but also critically the only method tested that has a good control of false discovery rate.ConclusionsThese findings guide which normalization and differential abundance techniques to use based on the data characteristics of a given study

Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags

Intense interest centers on the role of the human gut microbiome in health and disease, but optimal methods for analysis are still under development. Here we present a study of methods for surveying bacterial communities in human feces using 454/Roche pyrosequencing of 16S rRNA gene tags. We analyzed fecal samples from 10 individuals and compared methods for storage, DNA purification and sequence acquisition. To assess reproducibility, we compared samples one cm apart on a single stool specimen for each individual. To analyze storage methods, we compared 1) immediate freezing at -80°C, 2) storage on ice for 24 or 3) 48 hours. For DNA purification methods, we tested three commercial kits and bead beating in hot phenol. Variations due to the different methodologies were compared to variation among individuals using two approaches--one based on presence-absence information for bacterial taxa (unweighted UniFrac) and the other taking into account their relative abundance (weighted UniFrac). In the unweighted analysis relatively little variation was associated with the different analytical procedures, and variation between individuals predominated. In the weighted analysis considerable variation was associated with the purification methods. Particularly notable was improved recovery of Firmicutes sequences using the hot phenol method. We also carried out surveys of the effects of different 454 sequencing methods (FLX versus Titanium) and amplification of different 16S rRNA variable gene segments. Based on our findings we present recommendations for protocols to collect, process and sequence bacterial 16S rDNA from fecal samples--some major points are 1) if feasible, bead-beating in hot phenol or use of the PSP kit improves recovery; 2) storage methods can be adjusted based on experimental convenience; 3) unweighted (presence-absence) comparisons are less affected by lysis method

Skunk River Review Fall 2004, vol 16

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