Algorithms to automatically quantify the geometric similarity of anatomical surfaces

We describe new approaches for distances between pairs of 2-dimensional surfaces (embedded in 3-dimensional space) that use local structures and global information contained in inter-structure geometric relationships. We present algorithms to automatically determine these distances as well as geometric correspondences. This is motivated by the aspiration of students of natural science to understand the continuity of form that unites the diversity of life. At present, scientists using physical traits to study evolutionary relationships among living and extinct animals analyze data extracted from carefully defined anatomical correspondence points (landmarks). Identifying and recording these landmarks is time consuming and can be done accurately only by trained morphologists. This renders these studies inaccessible to non-morphologists, and causes phenomics to lag behind genomics in elucidating evolutionary patterns. Unlike other algorithms presented for morphological correspondences our approach does not require any preliminary marking of special features or landmarks by the user. It also differs from other seminal work in computational geometry in that our algorithms are polynomial in nature and thus faster, making pairwise comparisons feasible for significantly larger numbers of digitized surfaces. We illustrate our approach using three datasets representing teeth and different bones of primates and humans, and show that it leads to highly accurate results.Comment: Changes with respect to v1, v2: an Erratum was added, correcting the references for one of the three datasets. Note that the datasets and code for this paper can be obtained from the Data Conservancy (see Download column on v1, v2

A scaling law for the cosmological constant from a stochastic model for cosmic structures

A set of scaling laws, based on the stochastic motions of the granular components of astronomical systems, is applied to a cosmological model with a positive cosmological constant. It follows that the mass of the dominant particle in the observable universe must be proportional to the sixth root of the cosmological constant and of the order of the nucleon mass, which is consistent with the Zeldovich scaling law. The approach is a natural way to solve the cosmic coincidence problem. On the other hand, the observed value of the cosmological constant emerges as the result of a scaling law induced by the stochastic mechanism which gives rise to the gravitationally bound systems.Comment: 7 pages, 2 figure

Text2Shape: Generating Shapes from Natural Language by Learning Joint Embeddings

We present a method for generating colored 3D shapes from natural language. To this end, we first learn joint embeddings of freeform text descriptions and colored 3D shapes. Our model combines and extends learning by association and metric learning approaches to learn implicit cross-modal connections, and produces a joint representation that captures the many-to-many relations between language and physical properties of 3D shapes such as color and shape. To evaluate our approach, we collect a large dataset of natural language descriptions for physical 3D objects in the ShapeNet dataset. With this learned joint embedding we demonstrate text-to-shape retrieval that outperforms baseline approaches. Using our embeddings with a novel conditional Wasserstein GAN framework, we generate colored 3D shapes from text. Our method is the first to connect natural language text with realistic 3D objects exhibiting rich variations in color, texture, and shape detail. See video at https://youtu.be/zraPvRdl13

Comparative Investigations of Social Context-Dependent Dominance in Captive Chimpanzees (Pan troglodytes) and Wild Tibetan Macaques (Macaca thibetana)

Theoretical definitions of dominance, how dominance is structured and organized in nature, and how dominance is measured have varied as investigators seek to classify and organize social systems in gregarious species. Given the variability in behavioral measures and statistical methods used to derive dominance rankings, we conducted a comparative analysis of dominance using existing statistical techniques to analyze dominance ranks, social context-dependent dominance structures, the reliability of statistical analyses, and rank predictability of dominance structures on other social behaviors. We investigated these topics using behavioral data from captive chimpanzees (Pan troglodytes) and wild Tibetan macaques (Macaca thibetana). We used a combination of all-occurrence, focal-animal, and instantaneous scan sampling to collect social, agonistic, and associative data from both species. We analyzed our data to derive dominance ranks, test rank reliability, and assess cross-context predictability using various statistical analyses. Our results indicate context-dependent dominance and individual social roles in the captive chimpanzee group, one broadly defined dominance structure in the Tibetan macaque group, and high within-context analysis reliability but little cross-context predictability. Overall, we suggest this approach is preferable over investigations of dominance where only a few behavioral metrics and statistical analyses are utilized with little consideration of rank reliability or cross-context predictability

A stem-cell-derived platform enables complete Cryptosporidium development in vitro and genetic tractability

Despite being a frequent cause of severe diarrheal disease in infants and an opportunistic infection in immunocompromised patients, Cryptosporidium research has lagged due to a lack of facile experimental methods. Here, we describe a platform for complete life cycle development and long-term growth of C. parvum in vitro using air-liquid interface (ALI) cultures derived from intestinal epithelial stem cells. Transcriptomic profiling revealed that differentiating epithelial cells grown under ALI conditions undergo profound changes in metabolism and development that enable completion of the parasite life cycle in vitro. ALI cultures support parasite expansion \u3e 100-fold and generate viable oocysts that are transmissible in vitro and to mice, causing infection and animal death. Transgenic parasite lines created using CRISPR/Cas9 were used to complete a genetic cross in vitro, demonstrating Mendelian segregation of chromosomes during meiosis. ALI culture provides an accessible model that will enable innovative studies into Cryptosporidium biology and host interactions

The thermodynamic evolution of the cosmological event horizon

By manipulating the integral expression for the proper radius $R_e$ of the cosmological event horizon (CEH) in a Friedmann-Robertson-Walker (FRW) universe, we obtain an analytical expression for the change \dd R_e in response to a uniform fluctuation \dd\rho in the average cosmic background density $\rho$. We stipulate that the fluctuation arises within a vanishing interval of proper time, during which the CEH is approximately stationary, and evolves subsequently such that \dd\rho/\rho is constant. The respective variations 2\pi R_e \dd R_e and \dd E_e in the horizon entropy $S_e$ and enclosed energy $E_e$ should be therefore related through the cosmological Clausius relation. In that manner we find that the temperature $T_e$ of the CEH at an arbitrary time in a flat FRW universe is $E_e/S_e$, which recovers asymptotically the usual static de Sitter temperature. Furthermore, it is proven that during radiation-dominance and in late times the CEH conforms to the fully dynamical First Law T_e \drv S_e = P\drv V_e - \drv E_e, where $V_e$ is the enclosed volume and $P$ is the average cosmic pressure.Comment: 6 page

Low-threshold analysis of CDMS shallow-site data

Data taken during the final shallow-site run of the first tower of the Cryogenic Dark Matter Search (CDMS II) detectors have been reanalyzed with improved sensitivity to small energy depositions. Four ~224 g germanium and two ~105 g silicon detectors were operated at the Stanford Underground Facility (SUF) between December 2001 and June 2002, yielding 118 live days of raw exposure. Three of the germanium and both silicon detectors were analyzed with a new low-threshold technique, making it possible to lower the germanium and silicon analysis thresholds down to the actual trigger thresholds of ~1 keV and ~2 keV, respectively. Limits on the spin-independent cross section for weakly interacting massive particles (WIMPs) to elastically scatter from nuclei based on these data exclude interesting parameter space for WIMPs with masses below 9 GeV/c^2. Under standard halo assumptions, these data partially exclude parameter space favored by interpretations of the DAMA/LIBRA and CoGeNT experiments' data as WIMP signals, and exclude new parameter space for WIMP masses between 3 GeV/c^2 and 4 GeV/c^2.Comment: 18 pages, 12 figures, 5 table

Exclusion Limits on the WIMP-Nucleon Cross-Section from the First Run of the Cryogenic Dark Matter Search in the Soudan Underground Lab

The Cryogenic Dark Matter Search (CDMS-II) employs low-temperature Ge and Si detectors to seek Weakly Interacting Massive Particles (WIMPs) via their elastic scattering interactions with nuclei. Simultaneous measurements of both ionization and phonon energy provide discrimination against interactions of background particles. For recoil energies above 10 keV, events due to background photons are rejected with >99.99% efficiency. Electromagnetic events very near the detector surface can mimic nuclear recoils because of reduced charge collection, but these surface events are rejected with >96% efficiency by using additional information from the phonon pulse shape. Efficient use of active and passive shielding, combined with the the 2090 m.w.e. overburden at the experimental site in the Soudan mine, makes the background from neutrons negligible for this first exposure. All cuts are determined in a blind manner from in situ calibrations with external radioactive sources without any prior knowledge of the event distribution in the signal region. Resulting efficiencies are known to ~10%. A single event with a recoil of 64 keV passes all of the cuts and is consistent with the expected misidentification rate of surface-electron recoils. Under the assumptions for a standard dark matter halo, these data exclude previously unexplored parameter space for both spin-independent and spin-dependent WIMP-nucleon elastic scattering. The resulting limit on the spin-independent WIMP-nucleon elastic-scattering cross-section has a minimum of 4x10^-43 cm^2 at a WIMP mass of 60 GeV/c^2. The minimum of the limit for the spin-dependent WIMP-neutron elastic-scattering cross-section is 2x10^-37 cm^2 at a WIMP mass of 50 GeV/c^2.Comment: 37 pages, 42 figure

Exclusion limits on the WIMP-nucleon cross-section from the Cryogenic Dark Matter Search

The Cryogenic Dark Matter Search (CDMS) employs low-temperature Ge and Si detectors to search for Weakly Interacting Massive Particles (WIMPs) via their elastic-scattering interactions with nuclei while discriminating against interactions of background particles. For recoil energies above 10 keV, events due to background photons are rejected with >99.9% efficiency, and surface events are rejected with >95% efficiency. The estimate of the background due to neutrons is based primarily on the observation of multiple-scatter events that should all be neutrons. Data selection is determined primarily by examining calibration data and vetoed events. Resulting efficiencies should be accurate to about 10%. Results of CDMS data from 1998 and 1999 with a relaxed fiducial-volume cut (resulting in 15.8 kg-days exposure on Ge) are consistent with an earlier analysis with a more restrictive fiducial-volume cut. Twenty-three WIMP candidate events are observed, but these events are consistent with a background from neutrons in all ways tested. Resulting limits on the spin-independent WIMP-nucleon elastic-scattering cross-section exclude unexplored parameter space for WIMPs with masses between 10-70 GeV c^{-2}. These limits border, but do not exclude, parameter space allowed by supersymmetry models and accelerator constraints. Results are compatible with some regions reported as allowed at 3-sigma by the annual-modulation measurement of the DAMA collaboration. However, under the assumptions of standard WIMP interactions and a standard halo, the results are incompatible with the DAMA most likely value at >99.9% CL, and are incompatible with the model-independent annual-modulation signal of DAMA at 99.99% CL in the asymptotic limit.Comment: 40 pages, 49 figures (4 in color), submitted to Phys. Rev. D; v.2:clarified conclusions, added content and references based on referee's and readers' comments; v.3: clarified introductory sections, added figure based on referee's comment