Packing of Compressible Granular Materials

3D Computer simulations and experiments are employed to study random packings of compressible spherical grains under external confining stress. Of particular interest is the rigid ball limit, which we describe as a continuous transition in which the applied stress vanishes as (\phi-\phi_c)^\beta, where \phi is the (solid phase) volume density. This transition coincides with the onset of shear rigidity. The value of \phi_c depends, for example, on whether the grains interact via only normal forces (giving rise to random close packings) or by a combination of normal and friction generated transverse forces (producing random loose packings). In both cases, near the transition, the system's response is controlled by localized force chains. As the stress increases, we characterize the system's evolution in terms of (1) the participation number, (2) the average force distribution, and (3) visualization techniques.Comment: 4 pages, 7 figures, to appear in Phys. Rev. Let

Why Effective Medium Theory Fails in Granular Materials

Experimentally it is known that the bulk modulus, K, and shear modulus, \mu, of a granular assembly of elastic spheres increase with pressure, p, faster than the p^1/3 law predicted by effective medium theory (EMT) based on Hertz-Mindlin contact forces. To understand the origin of these discrepancies, we perform numerical simulations of granular aggregates under compression. We show that EMT can describe the moduli pressure dependence if one includes the increasing number of grain-grain contacts with p. Most important, the affine assumption (which underlies EMT), is found to be valid for K(p) but breakdown seriously for \mu(p). This explains why the experimental and numerical values of \mu(p) are much smaller than the EMT predictions.Comment: 4 pages, 5 figures, http://polymer.bu.edu/~hmaks

A Generalization of Chetaev's Principle for a Class of Higher Order Non-holonomic Constraints

The constraint distribution in non-holonomic mechanics has a double role. On one hand, it is a kinematic constraint, that is, it is a restriction on the motion itself. On the other hand, it is also a restriction on the allowed variations when using D'Alembert's Principle to derive the equations of motion. We will show that many systems of physical interest where D'Alembert's Principle does not apply can be conveniently modeled within the general idea of the Principle of Virtual Work by the introduction of both kinematic constraints and variational constraints as being independent entities. This includes, for example, elastic rolling bodies and pneumatic tires. Also, D'Alembert's Principle and Chetaev's Principle fall into this scheme. We emphasize the geometric point of view, avoiding the use of local coordinates, which is the appropriate setting for dealing with questions of global nature, like reduction.Comment: 27 pages. Journal of Mathematical Physics (to zappear

Geographic distribution and habitat use of Lepidoblepharis miyatai (Squamata: Sphaerodactylidae), with comments on the taxonomic status of the genus in northern Colombia

Geographic distribution and habitat use of Lepidoblepharis miyatai (Squamata: Sphaerodactylidae), with comments on the taxonomic status of the genus in northern Colombia. We present some ecological and biogeographic data on Lepidoblepharis miyatai, a small and endangered gecko endemic to the northwestern foothills of the Sierra Nevada de Santa Marta (SNSM), 31 years after its description. Based on museum specimens and feld observations, we recorded four new localities with confrmed presence of L. miyatai. We calculated the extent of occurrence and altitudinal distribution of this species reaching 21.3 km2 and from sea level to 360 m respectively. Lepidoblepharis miyatai inhabits plant formations of scrub thorn and tropical deciduous forest. Based on microhabitat data obtained from 88 individuals observed in “Las Tinajas Village” we can state a differential use of three substrates with predominant use of leaf-litter. We consider L. miyatai an endemic species of the northwestern sector of the SNSM with a distribution range limited to the south-west by the occurrence of L. sanctaemartae, and towards the east by a thus far undetermined Lepidoblepharis species (here called Lepidoblepharis cf. sanctaemartae). We do not register sympatry of L. miyatai with any other congener. Accordingly, we consider that the recent records of this species in the southeast sector of SNSM are erroneous, given that the specimens cited as L. miyatai of this zone correspond to Lepidoblepharis cf. sanctaemartae. Finally, a reevaluation of the conservation status of L. miyatai is needed, including precise information of its distribution.Distribuição geográfca e uso de hábitat de Lepidoblepharis miyatai (Squamata: Sphaerodactylidae) com comentários sobre a taxonomia do gênero no norte da Colômbia. Apresentamos alguns dados ecológicos de Lepidoblepharis miyatai, um pequeno lagarto ameaçado endêmico das encostas norteocidentais da Sierra Nevada de Santa Marta (SNSM) 31 anos após sua descrição. Com base em exemplares depositados em coleções e observações de campo, registramos quatro novas localidades com presença confrmada de L. miyatai. Calculamos a extensão de ocorrência e a distribuição altitudinal dessa espécie com as localidades apresentadas, alcançando uma área de 21.3 km2 e uma variação altitudinal do nível do mar a 360 m. Essa espécie está presente em formações de bosque espinhoso e de foresta tropical decídua. Com informações sobre o uso de micro-hábitats obtidas de 88 indivíduos registrados em “Las Tinajas”, determinamos que essa espécie apresenta uso diferencial dos três tipos de substrato que ocupa, utilizando principalmente a serapilheira. Consideramos esse lagarto como endêmico do setor norte-ocidental de SNSM, com sua distribuição limitada a sudoeste pelo contato com Lepidoblepharis sanctaemartae e a leste com uma espécie indeterminada de Lepidoblepharis (aqui denominada Lepidoblepharis cf. sanctaemartae). Não registramos simpatria de L. miyatai com nenhuma dessas espécies congêneres. Do mesmo modo, consideramos errôneos os registros recentes dessa espécie no setor sul-oriental de SNSM, já que os exemplares citados previamente como L. miyatai nessa zona correspondem a Lepidoblepharis cf. sanctaemartae. Finalmente, se faz necessária uma reavaliação do estado de conservação de L. miyatai que incluam informações mais precisas sobre sua distribuição.Distribución geográfca y uso de hábitat de Lepidoblepharis miyatai (Squamata: Sphaerodactylidae) con comentarios sobre la taxonomía del género en el norte de Colombia. Presentamos algunos datos ecológicos de Lepidoblepharis miyatai, un pequeño y amenazado gecko endémico de las estribaciones noroccidentales de la Sierra Nevada de Santa Marta (SNSM) 31 años después de su descripción. Con base a ejemplares depositados en colecciones y observaciones en campo, registramos cuatro nuevas localidades con presencia confrmada de L. miyatai. Calculamos la extensión de ocurrencia y la distribución altitudinal de esta especie con las localidades presentadas, alcanzando un área de 21.3 km2 y un rango altitudinal entre el nivel del mar y los 360 m. Esta especie está presente en formaciones de matorral espinoso y bosque seco. Con la información de microhábitat obtenida de 88 individuos registrados en “Las Tinajas”, determinamos que esta especie presenta uso diferencial de los tres tipos de sustrato que ocupa, utilizando principalmente la hojarasca. Consideramos a este lagarto como endémico del sector noroccidental de la SNSM, limitando hacia occidente con el rango de distribución de Lepidoblepharis sanctaemartae y hacia oriente con una especie de Lepidoblepharis hasta ahora no determinada (denominada aquí como Lepidoblepharis cf. sanctaemartae). No registramos simpatría de L. miyatai con alguno de estos congéneres. De igual manera, consideramos que los registros recientes de esta especie en el sector suroriental de la SNSM son erróneos, dado a que los ejemplares citados previamente como L. miyatai en esta zona corresponden con Lepidoblepharis cf. sanctaemartae. Finalmente, se hace necesaria una reevaluación del estado de conservación de L. miyatai, donde se incluya la información más precisa de su distribución

Culture-free genome-wide locus sequence typing (GLST) provides new perspectives on Trypanosoma cruzi dispersal and infection complexity

El análisis del polimorfismo genético es una poderosa herramienta para la vigilancia epidemiológica y investigar. Sin embargo, la inferencia poderosa de la variación genética del patógeno es a menudo restringido por el acceso limitado al ADN objetivo representativo, especialmente en el estudio de especies parásitas obligadas para las cuales el cultivo ex vivo requiere muchos recursos o es propenso a sesgos. Los métodos modernos de captura de secuencias permiten analizar directamente la variación genética de los patógenos del material del huésped/vector, pero a menudo son demasiado complejos y costosos para entornos de escasos recursos donde prevalecen las enfermedades infecciosas. Este estudio propone un método sencillo y rentable Herramienta de tipificación de secuencias de locus de todo el genoma (GLST) basada en la amplificación paralela masiva de puntos críticos de información en todo el genoma del patógeno objetivo. el multiplexado La reacción en cadena de la polimerasa amplifica cientos de objetivos genéticos diferentes definidos por el usuario en un único tubo de reacción y la posterior limpieza basada en gel de agarosa y código de barras completan la preparación de la biblioteca por menos de 4 USD por muestra. Nuestro estudio genera un modelo flexible Flujo de trabajo de diseño de panel de imprimación GLST para Trypanosoma cruzi, el agente parásito de Chagas enfermedad. Aplicamos con éxito nuestro panel GLST de 203 objetivos a extractos nómicos metagénicos directos y sin cultivo de vectores triatominos que contienen un mínimo de 3,69 pg/μl de ADN de T. cruzi y elaborar más sobre el rendimiento del método mediante la secuenciación de bibliotecas GLST de T. cruzi clones de referencia que representan unidades de tipificación discretas (DTU) TcI, TcIII, TcIV, TcV y TcVI. Los 780 sitios SNP que identificamos en el conjunto de muestras distinguen parásitos de forma repetitiva infectar vectores simpátricos y detectar correlaciones entre distancias genéticas y geográficas a escala regional (< 150 km), así como continental. Los marcadores también separan claramente TcI, TcIII, TcIV y TcV + TcVI y parecen distinguir infecciones multiclonales dentro de TcI. Discutimos las ventajas, limitaciones y perspectivas de nuestro método a través de un espectro de la investigación epidemiológica.Analysis of genetic polymorphism is a powerful tool for epidemiological surveillance and research. Powerful inference from pathogen genetic variation, however, is often restrained by limited access to representative target DNA, especially in the study of obli gate parasitic species for which ex vivo culture is resource-intensive or bias-prone. Mod ern sequence capture methods enable pathogen genetic variation to be analyzed directly from host/vector material but are often too complex and expensive for resource-poor set tings where infectious diseases prevail. This study proposes a simple, cost-effective ‘genome-wide locus sequence typing’ (GLST) tool based on massive parallel amplifica tion of information hotspots throughout the target pathogen genome. The multiplexed polymerase chain reaction amplifies hundreds of different, user-defined genetic targets in a single reaction tube, and subsequent agarose gel-based clean-up and barcoding com pletes library preparation at under 4 USD per sample. Our study generates a flexible GLST primer panel design workflow for Trypanosoma cruzi, the parasitic agent of Chagas disease. We successfully apply our 203-target GLST panel to direct, culture-free metage nomic extracts from triatomine vectors containing a minimum of 3.69 pg/μl T. cruzi DNA and further elaborate on method performance by sequencing GLST libraries from T. cruzi reference clones representing discrete typing units (DTUs) TcI, TcIII, TcIV, TcV and TcVI. The 780 SNP sites we identify in the sample set repeatably distinguish parasites infecting sympatric vectors and detect correlations between genetic and geographic dis tances at regional (< 150 km) as well as continental scales. The markers also clearly sep arate TcI, TcIII, TcIV and TcV + TcVI and appear to distinguish multiclonal infections within TcI. We discuss the advantages, limitations and prospects of our method across a spectrum of epidemiological research

Associations of vitamin D pathway genes with circulating 25-hydroxyvitamin-D, 1,25-dihydroxyvitamin-D, and prostate cancer:a nested case-control study

Vitamin D pathway single nucleotide polymorphisms (SNPs) are potentially useful proxies for investigating whether circulating vitamin D metabolites [total 25-hydroxyvitamin-D, 25(OH)D; 1,25-dihydroxyvitamin, 1,25(OH)2D] are causally related to prostate cancer. We investigated associations of sixteen SNPs across seven genes with prostate-specific antigen-detected prostate cancer

Field theories with anisotropic scaling in 2D, solitons and the microscopic entropy of asymptotically Lifshitz black holes

Field theories with anisotropic scaling in 1+1 dimensions are considered. It is shown that the isomorphism between Lifshitz algebras with dynamical exponents z and 1/z naturally leads to a duality between low and high temperature regimes. Assuming the existence of gap in the spectrum, this duality allows to obtain a precise formula for the asymptotic growth of the number of states with a fixed energy which depends on z and the energy of the ground state, and reduces to the Cardy formula for z=1. The holographic realization of the duality can be naturally inferred from the fact that Euclidean Lifshitz spaces in three dimensions with dynamical exponents and characteristic lengths given by z, l, and 1/z, l/z, respectively, are diffeomorphic. The semiclassical entropy of black holes with Lifshitz asymptotics can then be recovered from the generalization of Cardy formula, where the ground state corresponds to a soliton. An explicit example is provided by the existence of a purely gravitational soliton solution for BHT massive gravity, which precisely has the required energy that reproduces the entropy of the analytic asymptotically Lifshitz black hole with z=3. Remarkably, neither the asymptotic symmetries nor central charges were explicitly used in order to obtain these results.Comment: 17 pages, no figures, references corrected and update

Population genomics of the critically endangered kākāpō

Summary The kākāpō is a flightless parrot endemic to New Zealand. Once common in the archipelago, only 201 individuals remain today, most of them descending from an isolated island population. We report the first genome-wide analyses of the species, including a high-quality genome assembly for kākāpō, one of the first chromosome-level reference genomes sequenced by the Vertebrate Genomes Project (VGP). We also sequenced and analyzed 35 modern genomes from the sole surviving island population and 14 genomes from the extinct mainland population. While theory suggests that such a small population is likely to have accumulated deleterious mutations through genetic drift, our analyses on the impact of the long-term small population size in kākāpō indicate that present-day island kākāpō have a reduced number of harmful mutations compared to mainland individuals. We hypothesize that this reduced mutational load is due to the island population having been subjected to a combination of genetic drift and purging of deleterious mutations, through increased inbreeding and purifying selection, since its isolation from the mainland ∼10,000 years ago. Our results provide evidence that small populations can survive even when isolated for hundreds of generations. This work provides key insights into kākāpō breeding and recovery and more generally into the application of genetic tools in conservation efforts for endangered species

Culture-free genome-wide locus sequence typing (GLST) provides new perspectives on Trypanosoma cruzi dispersal and infection complexity.

Analysis of genetic polymorphism is a powerful tool for epidemiological surveillance and research. Powerful inference from pathogen genetic variation, however, is often restrained by limited access to representative target DNA, especially in the study of obligate parasitic species for which ex vivo culture is resource-intensive or bias-prone. Modern sequence capture methods enable pathogen genetic variation to be analyzed directly from host/vector material but are often too complex and expensive for resource-poor settings where infectious diseases prevail. This study proposes a simple, cost-effective 'genome-wide locus sequence typing' (GLST) tool based on massive parallel amplification of information hotspots throughout the target pathogen genome. The multiplexed polymerase chain reaction amplifies hundreds of different, user-defined genetic targets in a single reaction tube, and subsequent agarose gel-based clean-up and barcoding completes library preparation at under 4 USD per sample. Our study generates a flexible GLST primer panel design workflow for Trypanosoma cruzi, the parasitic agent of Chagas disease. We successfully apply our 203-target GLST panel to direct, culture-free metagenomic extracts from triatomine vectors containing a minimum of 3.69 pg/μl T. cruzi DNA and further elaborate on method performance by sequencing GLST libraries from T. cruzi reference clones representing discrete typing units (DTUs) TcI, TcIII, TcIV, TcV and TcVI. The 780 SNP sites we identify in the sample set repeatably distinguish parasites infecting sympatric vectors and detect correlations between genetic and geographic distances at regional (< 150 km) as well as continental scales. The markers also clearly separate TcI, TcIII, TcIV and TcV + TcVI and appear to distinguish multiclonal infections within TcI. We discuss the advantages, limitations and prospects of our method across a spectrum of epidemiological research