SIFTER search: a web server for accurate phylogeny-based protein function prediction.

We are awash in proteins discovered through high-throughput sequencing projects. As only a minuscule fraction of these have been experimentally characterized, computational methods are widely used for automated annotation. Here, we introduce a user-friendly web interface for accurate protein function prediction using the SIFTER algorithm. SIFTER is a state-of-the-art sequence-based gene molecular function prediction algorithm that uses a statistical model of function evolution to incorporate annotations throughout the phylogenetic tree. Due to the resources needed by the SIFTER algorithm, running SIFTER locally is not trivial for most users, especially for large-scale problems. The SIFTER web server thus provides access to precomputed predictions on 16 863 537 proteins from 232 403 species. Users can explore SIFTER predictions with queries for proteins, species, functions, and homologs of sequences not in the precomputed prediction set. The SIFTER web server is accessible at http://sifter.berkeley.edu/ and the source code can be downloaded

The effect of variability in other objects’ sizes on the extent to which people rely on retinal image size as a cue for judging distance

Retinal image size can be used to judge objects’ distances because for any object one can assume that some sizes are more likely than others. It has been shown that an increased variability in the size of otherwise identical target objects over trials reduces the weight given to retinal image size as a distance cue. Here, we examined whether an increased variability in the size of objects of a different color, orientation, or shape reduces the weight given to retinal image size when judging distance. Subjects had to indicate the 3D position of a simulated target object. Retinal image size was given significantly less weight as a cue for judging the target cube’s distance when differently colored and differently oriented target objects appeared in many simulated sizes but not when differently shaped objects had many simulated sizes. We also examined whether increasing the variability in the size of cubes in the surroundings reduces the weight given to retinal image size when judging distance. It does not. We conclude that variability in surrounding or dissimilar objects’ sizes has a negligible influence on the extent to which people rely on retinal image size as a cue for judging distance

Judging an unfamiliar object’s distance from its retinal image size

How do we know how far an object is? If an object's size is known, its retinal image size can be used to judge its distance. To some extent, the retinal image size of an unfamiliar object can also be used to judge its distance, because some object sizes are more likely than others. To examine whether assumptions about object size are used to judge distance, we had subjects indicate the distance of virtual cubes in complete darkness. In separate sessions, the simulated cube size either varied slightly or considerably across presentations. Most subjects indicated a further distance when the simulated cube was smaller, showing that they used retinal image size to judge distance. The cube size that was considered to be most likely depended on the simulated cubes on previous trials. Moreover, subjects relied twice as strongly on retinal image size when the range of simulated cube sizes was small. We conclude that the variability in the perceived cube sizes on previous trials influences the range of sizes that are considered to be likely. © ARVO

Does size matter?

For isolated objects in complete darkness, retinal image size contributes to distance judgments even if the true object size is unknown. Here we show that the same is true under more natural conditions. On a wide beach we positioned a red cube at 10–20 m distance and then asked subjects to walk to it while blindfolded. Subjects never had a close view of the cube and were unaware that on separate trials cubes with sides of 15 cm and 20 cm were positioned at the same locations. On average, subjects walked 1 m further after seeing the 15 cm cube than after seeing the 20 cm cube

The influence of previously seen objects' sizes in distance judgments

An object's retinal image size is determined by a combination of its physical size and its distance, so judgments of an object's size and distance from its retinal image size are coupled. Since one does not have direct access to information about the object's physical size, people may make assumptions about how large it is likely to be. Here we investigated whether the sizes of similar, previously encountered objects influence the assumptions about the physical size of an object and therefore the interpretation of its retinal image size in terms of its distance. Subjects moved their unseen index finger to the positions of binocular simulations of red cubes. For identical target cubes at the same position, they indicated a nearer position of the cube when the preceding cube was small than when it was big. This is in agreement with a tendency to expect the cube to be the same size as that on the previous trial. However, if the expectation were simply adjusted slightly on each trial, the cube would be judged to be nearer when preceded by two consecutive smaller cubes than when preceded by only one smaller cube. It was not, so there must be a more direct influence of the size in the previous trial on distance judgments

Encapsulation of phosphorus dopants in silicon for the fabrication of a quantum computer

The incorporation of phosphorus in silicon is studied by analyzing phosphorus delta-doped layers using a combination of scanning tunneling microscopy, secondary ion mass spectrometry and Hall effect measurements. The samples are prepared by phosphine saturation dosing of a Si(100) surface at room temperature, a critical annealing step to incorporate phosphorus atoms, and subsequent epitaxial silicon overgrowth. We observe minimal dopant segregation (5 nm), complete electrical activation at a silicon growth temperature of 250 degrees C and a high two-dimensional electron mobility of 100 cm2/Vs at a temperature of 4.2 K. These results, along with preliminary studies aimed at further minimizing dopant diffusion, bode well for the fabrication of atomically precise dopant arrays in silicon such as those found in recent solid-state quantum computer architectures.Comment: 3 pages, 4 figure

Curved Graphene Nanoribbons: Structure and Dynamics of Carbon Nanobelts

Carbon nanoribbons (CNRs) are graphene (planar) structures with large aspect ratio. Carbon nanobelts (CNBs) are small graphene nanoribbons rolled up into spiral-like structures, i. e., carbon nanoscrolls (CNSs) with large aspect ratio. In this work we investigated the energetics and dynamical aspects of CNBs formed from rolling up CNRs. We have carried out molecular dynamics simulations using reactive empirical bond-order potentials. Our results show that similarly to CNSs, CNBs formation is dominated by two major energy contribution, the increase in the elastic energy due to the bending of the initial planar configuration (decreasing structural stability) and the energetic gain due to van der Waals interactions of the overlapping surface of the rolled layers (increasing structural stability). Beyond a critical diameter value these scrolled structures can be even more stable (in terms of energy) than their equivalent planar configurations. In contrast to CNSs that require energy assisted processes (sonication, chemical reactions, etc.) to be formed, CNBs can be spontaneously formed from low temperature driven processes. Long CNBs (length of $\sim$ 30.0 nm) tend to exhibit self-folded racket-like conformations with formation dynamics very similar to the one observed for long carbon nanotubes. Shorter CNBs will be more likely to form perfect scrolled structures. Possible synthetic routes to fabricate CNBs from graphene membranes are also addressed

An unappreciated role for RNA surveillance

BACKGROUND: Nonsense-mediated mRNA decay (NMD) is a eukaryotic mRNA surveillance mechanism that detects and degrades mRNAs with premature termination codons (PTC(+ )mRNAs). In mammals, a termination codon is recognized as premature if it lies more than about 50 nucleotides upstream of the final intron position. More than a third of reliably inferred alternative splicing events in humans have been shown to result in PTC(+ )mRNA isoforms. As the mechanistic details of NMD have only recently been elucidated, we hypothesized that many PTC(+ )isoforms may have been cloned, characterized and deposited in the public databases, even though they would be targeted for degradation in vivo. RESULTS: We analyzed the human alternative protein isoforms described in the SWISS-PROT database and found that 144 (5.8% of 2,483) isoform sequences amenable to analysis, from 107 (7.9% of 1,363) SWISS-PROT entries, derive from PTC(+ )mRNA. CONCLUSIONS: For several of the PTC(+ )isoforms we identified, existing experimental evidence can be reinterpreted and is consistent with the action of NMD to degrade the transcripts. Several genes with mRNA isoforms that we identified as PTC(+ )- calpain-10, the CDC-like kinases (CLKs) and LARD - show how previous experimental results may be understood in light of NMD

Are people adapted to their own glasses?

Negative lenses, either in the form of glasses or contact lenses, can correct nearsightedness. Unlike contact lenses, glasses do not only correct, but also induce optic distortions. In the scientific literature, it has often been assumed that people who wear corrective glasses instantaneously account for these distortions when they put their glasses on. We tested this assumption and found that, when people switched between their contact lenses and their glasses, they made the errors that one would predict based on the optics.This shows that people are not immediately adapted to their own glasses when they put them on