Iterative graph cuts for image segmentation with a nonlinear statistical shape prior

Shape-based regularization has proven to be a useful method for delineating objects within noisy images where one has prior knowledge of the shape of the targeted object. When a collection of possible shapes is available, the specification of a shape prior using kernel density estimation is a natural technique. Unfortunately, energy functionals arising from kernel density estimation are of a form that makes them impossible to directly minimize using efficient optimization algorithms such as graph cuts. Our main contribution is to show how one may recast the energy functional into a form that is minimizable iteratively and efficiently using graph cuts.Comment: Revision submitted to JMIV (02/24/13

Photoreversible interconversion of a phytochrome photosensory module in the crystalline state.

A major barrier to defining the structural intermediates that arise during the reversible photointerconversion of phytochromes between their biologically inactive and active states has been the lack of crystals that faithfully undergo this transition within the crystal lattice. Here, we describe a crystalline form of the cyclic GMP phosphodiesterases/adenylyl cyclase/FhlA (GAF) domain from the cyanobacteriochrome PixJ in Thermosynechococcus elongatus assembled with phycocyanobilin that permits reversible photoconversion between the blue light-absorbing Pb and green light-absorbing Pg states, as well as thermal reversion of Pg back to Pb. The X-ray crystallographic structure of Pb matches previous models, including autocatalytic conversion of phycocyanobilin to phycoviolobilin upon binding and its tandem thioether linkage to the GAF domain. Cryocrystallography at 150 K, which compared diffraction data from a single crystal as Pb or after irradiation with blue light, detected photoconversion product(s) based on Fobs - Fobs difference maps that were consistent with rotation of the bonds connecting pyrrole rings C and D. Further spectroscopic analyses showed that phycoviolobilin is susceptible to X-ray radiation damage, especially as Pg, during single-crystal X-ray diffraction analyses, which could complicate fine mapping of the various intermediate states. Fortunately, we found that PixJ crystals are amenable to serial femtosecond crystallography (SFX) analyses using X-ray free-electron lasers (XFELs). As proof of principle, we solved by room temperature SFX the GAF domain structure of Pb to 1.55-Å resolution, which was strongly congruent with synchrotron-based models. Analysis of these crystals by SFX should now enable structural characterization of the early events that drive phytochrome photoconversion

Dispersion tuning and route reconfiguration of acoustic waves in valley topological phononic crystals

The valley degree of freedom in crystals offers great potential for manipulating classical waves, however, few studies have investigated valley states with complex wavenumbers, valley states in graded systems, or dispersion tuning for valley states. Here, we present tunable valley phononic crystals (PCs) composed of hybrid channel-cavity cells with three tunable parameters. Our PCs support valley states and Dirac cones with complex wavenumbers. They can be configured to form chirped valley PCs in which edge modes are slowed to zero group velocity states, where the energy at different frequencies accumulates at different designated locations. They enable multiple functionalities, including tuning of dispersion relations for valley states, robust routing of surface acoustic waves, and spatial modulation of group velocities. This work may spark future investigations of topological states with complex wavenumbers in other classical systems, further study of topological states in graded materials, and the development of acoustic devices

The BLAST View of the Star Forming Region in Aquila (ell=45deg,b=0deg)

We have carried out the first general submillimeter analysis of the field towards GRSMC 45.46+0.05, a massive star forming region in Aquila. The deconvolved 6 deg^2 (3\degree X 2\degree) maps provided by BLAST in 2005 at 250, 350, and 500 micron were used to perform a preliminary characterization of the clump population previously investigated in the infrared, radio, and molecular maps. Interferometric CORNISH data at 4.8 GHz have also been used to characterize the Ultracompact HII regions (UCHIIRs) within the main clumps. By means of the BLAST maps we have produced an initial census of the submillimeter structures that will be observed by Herschel, several of which are known Infrared Dark Clouds (IRDCs). Our spectral energy distributions of the main clumps in the field, located at ~7 kpc, reveal an active population with temperatures of T~35-40 K and masses of ~10^3 Msun for a dust emissivity index beta=1.5. The clump evolutionary stages range from evolved sources, with extended HII regions and prominent IR stellar population, to massive young stellar objects, prior to the formation of an UCHIIR.The CORNISH data have revealed the details of the stellar content and structure of the UCHIIRs. In most cases, the ionizing stars corresponding to the brightest radio detections are capable of accounting for the clump bolometric luminosity, in most cases powered by embedded OB stellar clusters

The Balloon-Borne Large Aperture Submillimeter Telescope (BLAST) 2005: A 10 deg^2 Survey of Star Formation in Cygnus X

We present Cygnus X in a new multi-wavelength perspective based on an unbiased BLAST survey at 250, 350, and 500 micron, combined with rich datasets for this well-studied region. Our primary goal is to investigate the early stages of high mass star formation. We have detected 184 compact sources in various stages of evolution across all three BLAST bands. From their well-constrained spectral energy distributions, we obtain the physical properties mass, surface density, bolometric luminosity, and dust temperature. Some of the bright sources reaching 40 K contain well-known compact H II regions. We relate these to other sources at earlier stages of evolution via the energetics as deduced from their position in the luminosity-mass (L-M) diagram. The BLAST spectral coverage, near the peak of the spectral energy distribution of the dust, reveals fainter sources too cool (~ 10 K) to be seen by earlier shorter-wavelength surveys like IRAS. We detect thermal emission from infrared dark clouds and investigate the phenomenon of cold ``starless cores" more generally. Spitzer images of these cold sources often show stellar nurseries, but these potential sites for massive star formation are ``starless" in the sense that to date there is no massive protostar in a vigorous accretion phase. We discuss evolution in the context of the L-M diagram. Theory raises some interesting possibilities: some cold massive compact sources might never form a cluster containing massive stars; and clusters with massive stars might not have an identifiable compact cold massive precursor.Comment: 42 pages, 31 Figures, 6 table

A Student\u27s Guide to giant Viruses Infecting Small Eukaryotes: From Acanthamoeba to Zooxanthellae

The discovery of infectious particles that challenge conventional thoughts concerning “what is a virus” has led to the evolution a new field of study in the past decade. Here, we review knowledge and information concerning “giant viruses”, with a focus not only on some of the best studied systems, but also provide an effort to illuminate systems yet to be better resolved. We conclude by demonstrating that there is an abundance of new host–virus systems that fall into this “giant” category, demonstrating that this field of inquiry presents great opportunities for future research

The Future of Fundamental Science Led by Generative Closed-Loop Artificial Intelligence

Recent advances in machine learning and AI, including Generative AI and LLMs, are disrupting technological innovation, product development, and society as a whole. AI's contribution to technology can come from multiple approaches that require access to large training data sets and clear performance evaluation criteria, ranging from pattern recognition and classification to generative models. Yet, AI has contributed less to fundamental science in part because large data sets of high-quality data for scientific practice and model discovery are more difficult to access. Generative AI, in general, and Large Language Models in particular, may represent an opportunity to augment and accelerate the scientific discovery of fundamental deep science with quantitative models. Here we explore and investigate aspects of an AI-driven, automated, closed-loop approach to scientific discovery, including self-driven hypothesis generation and open-ended autonomous exploration of the hypothesis space. Integrating AI-driven automation into the practice of science would mitigate current problems, including the replication of findings, systematic production of data, and ultimately democratisation of the scientific process. Realising these possibilities requires a vision for augmented AI coupled with a diversity of AI approaches able to deal with fundamental aspects of causality analysis and model discovery while enabling unbiased search across the space of putative explanations. These advances hold the promise to unleash AI's potential for searching and discovering the fundamental structure of our world beyond what human scientists have been able to achieve. Such a vision would push the boundaries of new fundamental science rather than automatize current workflows and instead open doors for technological innovation to tackle some of the greatest challenges facing humanity today.Comment: 35 pages, first draft of the final report from the Alan Turing Institute on AI for Scientific Discover

Gene content evolution in the arthropods

Arthropods comprise the largest and most diverse phylum on Earth and play vital roles in nearly every ecosystem. Their diversity stems in part from variations on a conserved body plan, resulting from and recorded in adaptive changes in the genome. Dissection of the genomic record of sequence change enables broad questions regarding genome evolution to be addressed, even across hyper-diverse taxa within arthropods. Using 76 whole genome sequences representing 21 orders spanning more than 500 million years of arthropod evolution, we document changes in gene and protein domain content and provide temporal and phylogenetic context for interpreting these innovations. We identify many novel gene families that arose early in the evolution of arthropods and during the diversification of insects into modern orders. We reveal unexpected variation in patterns of DNA methylation across arthropods and examples of gene family and protein domain evolution coincident with the appearance of notable phenotypic and physiological adaptations such as flight, metamorphosis, sociality, and chemoperception. These analyses demonstrate how large-scale comparative genomics can provide broad new insights into the genotype to phenotype map and generate testable hypotheses about the evolution of animal diversity

Masses, radii, and orbits of small Kepler planets : The transition from gaseous to rocky planets

We report on the masses, sizes, and orbits of the planets orbiting 22 Kepler stars. There are 49 planet candidates around these stars, including 42 detected through transits and 7 revealed by precise Doppler measurements of the host stars. Based on an analysis of the Kepler brightness measurements, along with high-resolution imaging and spectroscopy, Doppler spectroscopy, and (for 11 stars) asteroseismology, we establish low false-positive probabilities (FPPs) for all of the transiting planets (41 of 42 have an FPP under 1%), and we constrain their sizes and masses. Most of the transiting planets are smaller than three times the size of Earth. For 16 planets, the Doppler signal was securely detected, providing a direct measurement of the planet's mass. For the other 26 planets we provide either marginal mass measurements or upper limits to their masses and densities; in many cases we can rule out a rocky composition. We identify six planets with densities above 5 g cm-3, suggesting a mostly rocky interior for them. Indeed, the only planets that are compatible with a purely rocky composition are smaller than 2 R ⊕. Larger planets evidently contain a larger fraction of low-density material (H, He, and H2O).Peer reviewedFinal Accepted Versio

Hundreds of variants clustered in genomic loci and biological pathways affect human height

Most common human traits and diseases have a polygenic pattern of inheritance: DNA sequence variants at many genetic loci influence the phenotype. Genome-wide association (GWA) studies have identified more than 600 variants associated with human traits, but these typically explain small fractions of phenotypic variation, raising questions about the use of further studies. Here, using 183,727 individuals, we show that hundreds of genetic variants, in at least 180 loci, influence adult height, a highly heritable and classic polygenic trait. The large number of loci reveals patterns with important implications for genetic studies of common human diseases and traits. First, the 180 loci are not random, but instead are enriched for genes that are connected in biological pathways (P = 0.016) and that underlie skeletal growth defects (P < 0.001). Second, the likely causal gene is often located near the most strongly associated variant: in 13 of 21 loci containing a known skeletal growth gene, that gene was closest to the associated variant. Third, at least 19 loci have multiple independently associated variants, suggesting that allelic heterogeneity is a frequent feature of polygenic traits, that comprehensive explorations of already-discovered loci should discover additional variants and that an appreciable fraction of associated loci may have been identified. Fourth, associated variants are enriched for likely functional effects on genes, being over-represented among variants that alter amino-acid structure of proteins and expression levels of nearby genes. Our data explain approximately 10% of the phenotypic variation in height, and we estimate that unidentified common variants of similar effect sizes would increase this figure to approximately 16% of phenotypic variation (approximately 20% of heritable variation). Although additional approaches are needed to dissect the genetic architecture of polygenic human traits fully, our findings indicate that GWA studies can identify large numbers of loci that implicate biologically relevant genes and pathways.