Comparison of regression methods for biomass estimation of sagebrush and bunchgrass

Regression analyses for plant biomass estimation from physical measurements of individual plant dimensions that are nonlinear have generally used some form of the allometric equation. Use of this equation has most often involved logarithmic transformation of the variables (power regression). Transformation, however, introduces systematic bias into the analyses. Power regression was compared with a bias correction technique and with nonlinear regression for the prediction of the total foliage biomass (phytomass). Crown volumes of one sagebrush and one perennial grass species were used for these evaluations. The bias correction factor was uniformly applied to all the predicted values from power regression. Nonlinear regression avoided this bias by not requiring logarithmic transformation. It was also consistently less variable than either power regression or the correction factor method in estimating actual total phytomass by the allometric equation and equivalent or better in accuracy. The correction factor technique consistently gave the poorest predictions of the methods evaluated. Standard linear regression worked as well for the bunchgrass as the best method based on the allometric equation. Predictions were generally better when sample sizes used to derive the regression equations represented the range of plant size and variability in the data for which the phytomass was estimated.     

A comparison of the spherical densiometer and ocular methods of estimating canopy cover

Percent tree canopy cover in a ponderosa pine ( Pinus ponderosa ) forest of northeastern California was estimated by the point intercept spherical densiometer and ocular methods. Estimates derived by the two methods were similar (P > .05). The ocular method is recommended when understory vegetation is tall or clumped instead of randomly distributed, or if available field time limits sample size.     

Graphene and boron nitride lateral heterostructures for atomically thin circuitry

Precise spatial control over the electrical properties of thin films is the key capability enabling the production of modern integrated circuitry. Although recent advances in chemical vapour deposition methods have enabled the large-scale production of both intrinsic and doped graphene, as well as hexagonal boron nitride (h-BN), controlled fabrication of lateral heterostructures in these truly atomically thin systems has not been achieved. Graphene/h-BN interfaces are of particular interest, because it is known that areas of different atomic compositions may coexist within continuous atomically thin films and that, with proper control, the bandgap and magnetic properties can be precisely engineered. However, previously reported approaches for controlling these interfaces have fundamental limitations and cannot be easily integrated with conventional lithography. Here we report a versatile and scalable process, which we call 'patterned regrowth', that allows for the spatially controlled synthesis of lateral junctions between electrically conductive graphene and insulating h-BN, as well as between intrinsic and substitutionally doped graphene. We demonstrate that the resulting films form mechanically continuous sheets across these heterojunctions. Conductance measurements confirm laterally insulating behaviour for h-BN regions, while the electrical behaviour of both doped and undoped graphene sheets maintain excellent properties, with low sheet resistances and high carrier mobilities. Our results represent an important step towards developing atomically thin integrated circuitry and enable the fabrication of electrically isolated active and passive elements embedded in continuous, one-atom-thick sheets, which could be manipulated and stacked to form complex devices at the ultimate thickness limit.     

Global landscape of protein complexes in the yeast Saccharomyces cerevisiae

Identification of protein-protein interactions often provides insight into protein function, and many cellular processes are performed by stable protein complexes. We used tandem affinity purification to process 4,562 different tagged proteins of the yeast Saccharomyces cerevisiae. Each preparation was analysed by both matrix-assisted laser desorption/ionization-time of flight mass spectrometry and liquid chromatography tandem mass spectrometry to increase coverage and accuracy. Machine learning was used to integrate the mass spectrometry scores and assign probabilities to the protein-protein interactions. Among 4,087 different proteins identified with high confidence by mass spectrometry from 2,357 successful purifications, our core data set (median precision of 0.69) comprises 7,123 protein-protein interactions involving 2,708 proteins. A Markov clustering algorithm organized these interactions into 547 protein complexes averaging 4.9 subunits per complex, about half of them absent from the MIPS database, as well as 429 additional interactions between pairs of complexes. The data (all of which are available online) will help future studies on individual proteins as well as functional genomics and systems biology.     

‘Conservative prejudice’ in the debate over disjunctively distributed life forms

During the thirties and forties, and early fifties, Wegener's ideas were generally rejected as a fantasy—fascinating but false. ‘Ein Machen, a pipe dream, a beautiful fairy story’ chanted the American bandwagon. During these decades of repudiation, arguments which denied continental dispersion passed without scrutiny or test. They were correct a priori because everybody knew that continental drift was wrong.     

Origin and fate of Lake Vostok water frozen to the base of the East Antarctic ice sheet

The subglacial Lake Vostok may be a unique reservoir of genetic material and it may contain organisms with distinct adaptations, but it has yet to be explored directly. The lake and the overlying ice sheet are closely linked, as the ice-sheet thickness drives the lake circulation, while melting and freezing at the ice-sheet base will control the flux of water, biota and sediment through the lake. Here we present a reconstruction of the ice flow trajectories for the Vostok core site, using ice-penetrating radar data and Global Positioning System (GPS) measurements of surface ice velocity. We find that the ice sheet has a significant along-lake flow component, persistent since the Last Glacial Maximum. The rates at which ice is frozen (accreted) to the base of the ice sheet are greatest at the shorelines, and the accreted ice layer is subsequently transported out of the lake. Using these new flow field and velocity measurements, we estimate the time for ice to traverse Lake Vostok to be 16,000-20,000 years. We infer that most Vostok ice analysed to date was accreted to the ice sheet close to the western shoreline, and is therefore not representative of open lake conditions. From the amount of accreted lake water we estimate to be exported along the southern shoreline, the lake water residence time is about 13,300 years.     

Ecological and immunological determinants of influenza evolution

In pandemic and epidemic forms, influenza causes substantial, sometimes catastrophic, morbidity and mortality. Intense selection from the host immune system drives antigenic change in influenza A and B, resulting in continuous replacement of circulating strains with new variants able to re-infect hosts immune to earlier types. This 'antigenic drift' often requires a new vaccine to be formulated before each annual epidemic. However, given the high transmissibility and mutation rate of influenza, the constancy of genetic diversity within lineages over time is paradoxical. Another enigma is the replacement of existing strains during a global pandemic caused by 'antigenic shift'--the introduction of a new avian influenza A subtype into the human population. Here we explore ecological and immunological factors underlying these patterns using a mathematical model capturing both realistic epidemiological dynamics and viral evolution at the sequence level. By matching model output to phylogenetic patterns seen in sequence data collected through global surveillance, we find that short-lived strain-transcending immunity is essential to restrict viral diversity in the host population and thus to explain key aspects of drift and shift dynamics.     

Fraser syndrome and mouse blebbed phenotype caused by mutations in FRAS1/Fras1 encoding a putative extracellular matrix protein

Fraser syndrome (OMIM 219000) is a multisystem malformation usually comprising cryptophthalmos, syndactyly and renal defects. Here we report autozygosity mapping and show that the locus FS1 at chromosome 4q21 is associated with Fraser syndrome, although the condition is genetically heterogeneous. Mutation analysis identified five frameshift mutations in FRAS1, which encodes one member of a family of novel proteins related to an extracellular matrix (ECM) blastocoelar protein found in sea urchin. The FRAS1 protein contains a series of N-terminal cysteine-rich repeat motifs previously implicated in BMP metabolism, suggesting that it has a role in both structure and signal propagation in the ECM. It has been speculated that Fraser syndrome is a human equivalent of the blebbed phenotype in the mouse, which has been associated with mutations in at least five loci including bl. As mapping data were consistent with homology of FRAS1 and bl, we screened DNA from bl/bl mice and identified a premature termination of mouse Fras1. Thus, the bl mouse is a model for Fraser syndrome in humans, a disorder caused by disrupted epithelial integrity in utero.