The Adult Mouse Anatomical Dictionary: a tool for annotating and integrating data

We have developed an ontology to provide standardized nomenclature for anatomical terms in the postnatal mouse. The Adult Mouse Anatomical Dictionary is structured as a directed acyclic graph, and is organized hierarchically both spatially and functionally. The ontology will be used to annotate and integrate different types of data pertinent to anatomy, such as gene expression patterns and phenotype information, which will contribute to an integrated description of biological phenomena in the mouse

Negative plant–soil feedback predicts tree-species relative abundance in a tropical forest

The accumulation of species-specific enemies around adults is hypothesized to maintain plant diversity by limiting the recruitment of conspecific seedlings relative to heterospecific seedlings1,2,3,4,5,6. Although previous studies in forested ecosystems have documented patterns consistent with the process of negative feedback7,8,9,10,11,12,13,14,15,16, these studies are unable to address which classes of enemies (for example, pathogens, invertebrates, mammals) exhibit species-specific effects strong enough to generate negative feedback17, and whether negative feedback at the level of the individual tree is sufficient to influence community-wide forest composition. Here we use fully reciprocal shade-house and field experiments to test whether the performance of conspecific tree seedlings (relative to heterospecific seedlings) is reduced when grown in the presence of enemies associated with adult trees. Both experiments provide strong evidence for negative plant–soil feedback mediated by soil biota. In contrast, above-ground enemies (mammals, foliar herbivores and foliar pathogens) contributed little to negative feedback observed in the field. In both experiments, we found that tree species that showed stronger negative feedback were less common as adults in the forest community, indicating that susceptibility to soil biota may determine species relative abundance in these tropical forests. Finally, our simulation models confirm that the strength of local negative feedback that we measured is sufficient to produce the observed community-wide patterns in tree-species relative abundance. Our findings indicate that plant–soil feedback is an important mechanism that can maintain species diversity and explain patterns of tree-species relative abundance in tropical forests

Resource‐based habitat associations in a neotropical liana community

Summary 1. Lianas are a conspicuous element of many tropical forests, accounting for up to 40% of woody stem density and 20% of species richness in seasonal forests. However, lianas have seldom been surveyed at sufficiently large spatial scales to allow an assessment of the importance of habitat variables in structuring liana communities. 2. We compare the association patterns of 82 liana species and an equivalent sample of tree species on the 50 ha Forest Dynamics Project plot on Barro Colorado Island, Panama, with topographic habitat variables (high and low plateau, slope, swamp and streamside), and thirteen mapped soil chemical variables. In addition, we test for liana species associations with canopy disturbance using a canopy height map of the plot generated using light detection and ranging. 3. For all liana species combined, densities differed among topographic habitat types in the plot, with significantly higher densities on the seasonally drier lower plateau habitat (1044 individuals ha−1) than the moister slope habitat (729 individuals ha−1). Lianas were also significantly more abundant than expected in areas with low canopy height. 4. The proportion of liana species associated with one or more topographic habitat variables (44%) was significantly lower than that for trees (66%). Similarly, liana species were significantly less frequently associated with PC axes derived from soil chemical variables (21%) than trees (52%). The majority of liana species (63%) were significantly associated with areas of the plot with low canopy height reflecting an affinity for treefall gaps. 5. Synthesis. The habitat associations detected here suggest that liana density is associated primarily with canopy disturbance, and to a lesser extent with topography and soil chemistry. Relative to trees, few liana species were associated with local variation in topography and soil chemistry, suggesting that nutrient availability exerts only weak effects on liana community composition compared to trees. Results from this study support the contention that increases in forest disturbance rates are a driver of recently observed increases in liana abundance and biomass in neotropical forests

Acute Cholecystitis Is a Common Complication after Allogeneic Stem Cell Transplantation and Is Associated with the Use of Total Parenteral Nutrition

AbstractThe incidence and risk factors for acute cholecystitis after allogeneic hematopoietic stem cell transplantation (HSCT) are not well defined. Of 644 consecutive adult transplants performed at our institution between 2001 and 2011, acute cholecystitis occurred in the first year of transplant in 32 patients (5.0%). We conducted 2 retrospective case-control studies of this population to determine risk factors for cholecystitis after HSCT and to evaluate the performance of different methods of imaging to diagnosis cholecystitis in patients undergoing HSCT compared with non-HSCT patients. In the HSCT population, development of cholecystitis was associated with an increased 1-year overall mortality rate (62.5% versus 19.8%, P < .001). The risk of developing cholecystitis was higher in patients who received total parenteral nutrition (TPN) (adjusted odds ratio, 3.41; P = .009). There was a trend toward more equivocal abdominal ultrasound findings in HSCT recipients with acute cholecystitis compared with nontransplant patients (50.0% versus 30.6%, P = .06). However, hepatobiliary iminodiacetic acid (HIDA) scans were definitively positive for acute cholecystitis in most patients in both populations (80.0% of HSCT recipients versus 77.4% of control subjects, P = .82). In conclusion, acute cholecystitis is a common early complication of HSCT, the risk is increased in patients who receive TPN, and it is associated with high 1-year mortality. In HSCT recipients with findings suggestive of acute cholecystitis, especially those receiving TPN, early use of HIDA scan may be considered over ultrasound

Liana Abundance, Diversity, and Distribution on Barro Colorado Island, Panama

Lianas are a key component of tropical forests; however, most surveys are too small to accurately quantify liana community composition, diversity, abundance, and spatial distribution – critical components for measuring the contribution of lianas to forest processes. In 2007, we tagged, mapped, measured the diameter, and identified all lianas ≥1 cm rooted in a 50-ha plot on Barro Colorado Island, Panama (BCI). We calculated liana density, basal area, and species richness for both independently rooted lianas and all rooted liana stems (genets plus clones). We compared spatial aggregation patterns of liana and tree species, and among liana species that varied in the amount of clonal reproduction. We also tested whether liana and tree densities have increased on BCI compared to surveys conducted 30-years earlier. This study represents the most comprehensive spatially contiguous sampling of lianas ever conducted and, over the 50 ha area, we found 67,447 rooted liana stems comprising 162 species. Rooted lianas composed nearly 25% of the woody stems (trees and lianas), 35% of woody species richness, and 3% of woody basal area. Lianas were spatially aggregated within the 50-ha plot and the liana species with the highest proportion of clonal stems more spatially aggregated than the least clonal species, possibly indicating clonal stem recruitment following canopy disturbance. Over the past 30 years, liana density increased by 75% for stems ≥1 cm diameter and nearly 140% for stems ≥5 cm diameter, while tree density on BCI decreased 11.5%; a finding consistent with other neotropical forests. Our data confirm that lianas contribute substantially to tropical forest stem density and diversity, they have highly clumped distributions that appear to be driven by clonal stem recruitment into treefall gaps, and they are increasing relative to trees, thus indicating that lianas will play a greater role in the future dynamics of BCI and other neotropical forests

Lifespan extension and the doctrine of double effect

Recent developments in biogerontology—the study of the biology of ageing—suggest that it may eventually be possible to intervene in the human ageing process. This, in turn, offers the prospect of significantly postponing the onset of age-related diseases. The biogerontological project, however, has met with strong resistance, especially by deontologists. They consider the act of intervening in the ageing process impermissible on the grounds that it would (most probably) bring about an extended maximum lifespan—a state of affairs that they deem intrinsically bad. In a bid to convince their deontological opponents of the permissibility of this act, proponents of biogerontology invoke an argument which is grounded in the doctrine of double effect. Surprisingly, their argument, which we refer to as the ‘double effect argument’, has gone unnoticed. This article exposes and critically evaluates this ‘double effect argument’. To this end, we first review a series of excerpts from the ethical debate on biogerontology in order to substantiate the presence of double effect reasoning. Next, we attempt to determine the role that the ‘double effect argument’ is meant to fulfil within this debate. Finally, we assess whether the act of intervening in ageing actually can be justified using double effect reasoning

The GABBR1 locus and the G1465A variant is not associated with temporal lobe epilepsy preceded by febrile seizures

BACKGROUND: Polymorphism G1465A in the GABBR1 gene has been suggested as a risk factor for non-lesional temporal lobe epilepsy (TLE); however, this genetic association study has not been independently replicated. We attempted to replicate this study in our cohort of patients with TLE. Furthermore, we also analyzed the coding sequence of this gene and searched for disease-causing mutations. METHODS: We included 120 unrelated individuals with TLE that was preceded by febrile seizures (FS) who did not have any evidence of structural lesions suggesting secondary epilepsy. 66 individuals had positive family history of TLE epilepsy and 54 were sporadic. Each patient was genotyped for the presence of G1465A polymorphism. All exons of the GABBR1 gene were screened by single strand confirmation polymorphism method. Genotypes were compared with two independent matched control groups. RESULTS: We detected two A alleles of the G1465A polymorphism in one homozygous control subject (0.87% of all alleles) and one A allele in a patient with TLE (0.45%, not significant). Other detected polymorphisms in coding regions had similar frequencies in epilepsy patients and control groups. No disease causing mutations in the GABBR1 gene were detected in patients with sporadic or familial TLE. CONCLUSION: Our results indicate that TLE preceded by FS is not associated with the polymorphisms or mutations in the GABBR1 gene, including the G1465A polymorphism. The proportion of TLE patients with FS in the original study, reporting this positive association, did not differ between allele A negative and positive cases. Thus, our failure to reproduce this result is likely applicable to all non-lesional TLE epilepsies

Helium release and microstructural changes in Er(D,T)2-x3Hex films).

Er(D,T){sub 2-x} {sup 3}He{sub x}, erbium di-tritide, films of thicknesses 500 nm, 400 nm, 300 nm, 200 nm, and 100 nm were grown and analyzed by Transmission Electron Microscopy, X-Ray Diffraction, and Ion Beam Analysis to determine variations in film microstructure as a function of film thickness and age, due to the time-dependent build-up of {sup 3}He in the film from the radioactive decay of tritium. Several interesting features were observed: One, the amount of helium released as a function of film thickness is relatively constant. This suggests that the helium is being released only from the near surface region and that the helium is not diffusing to the surface from the bulk of the film. Two, lenticular helium bubbles are observed as a result of the radioactive decay of tritium into {sup 3}He. These bubbles grow along the [111] crystallographic direction. Three, a helium bubble free zone, or 'denuded zone' is observed near the surface. The size of this region is independent of film thickness. Four, an analysis of secondary diffraction spots in the Transmission Electron Microscopy study indicate that small erbium oxide precipitates, 5-10 nm in size, exist throughout the film. Further, all of the films had large erbium oxide inclusions, in many cases these inclusions span the depth of the film

LDRD final report on continuous wave intersubband terahertz sources.

There is a general lack of compact electromagnetic radiation sources between 1 and 10 terahertz (THz). This a challenging spectral region lying between optical devices at high frequencies and electronic devices at low frequencies. While technologically very underdeveloped the THz region has the promise to be of significant technological importance, yet demonstrating its relevance has proven difficult due to the immaturity of the area. While the last decade has seen much experimental work in ultra-short pulsed terahertz sources, many applications will require continuous wave (cw) sources, which are just beginning to demonstrate adequate performance for application use. In this project, we proposed examination of two potential THz sources based on intersubband semiconductor transitions, which were as yet unproven. In particular we wished to explore quantum cascade lasers based sources and electronic based harmonic generators. Shortly after the beginning of the project, we shifted our emphasis to the quantum cascade lasers due to two events; the publication of the first THz quantum cascade laser by another group thereby proving feasibility, and the temporary shut down of the UC Santa Barbara free-electron lasers which were to be used as the pump source for the harmonic generation. The development efforts focused on two separate cascade laser thrusts. The ultimate goal of the first thrust was for a quantum cascade laser to simultaneously emit two mid-infrared frequencies differing by a few THz and to use these to pump a non-linear optical material to generate THz radiation via parametric interactions in a specifically engineered intersubband transition. While the final goal was not realized by the end of the project, many of the completed steps leading to the goal will be described in the report. The second thrust was to develop direct THz QC lasers operating at terahertz frequencies. This is simpler than a mixing approach, and has now been demonstrated by a few groups with wavelengths spanning 65-150 microns. We developed and refined the MBE growth for THz for both internally and externally designed QC lasers. Processing related issues continued to plague many of our demonstration efforts and will also be addressed in this report

Fiber-Based Laser Transmitter at 1.57 Micrometers for Remote Sensing of Atmospheric Carbon Dioxide from Satellites

Over the past 20 years, NASA Goddard has successfully developed space-based lidar for remote sensing studies of the Earth and planets. The lidar in all missions to date have used diode pumped Nd:YAG laser transmitters. Recently we have been concentrating work on developing integrated path differential absorption (IPDA) lidar to measure greenhouse gases, with the goal of measurements from space. Due to the absorption spectrum of CO2 a fiber-based master oscillator power amplifier (MOPA) laser with a tunable seed source is an attractive laser choice. Fiber-based lasers offer a number of potential advantages for space, but since they are relatively new, challenges exist in developing them. In order to reduce risks for new missions using fiber-based lasers, we developed a 30- month plan to mature the technology of a candidate laser transmitter for space-based CO2 measurements to TRL-6. This work is also intended to reduce development time and costs and increase confidence in future mission success