On the p,qp,q-binomial distribution and the Ising model

A completely new approach to the Ising model in 1 to 5 dimensions is developed. We employ $p,q$-binomial coefficients, a generalisation of the binomial coefficients, to describe the magnetisation distributions of the Ising model. For the complete graph this distribution corresponds exactly to the limit case $p=q$. We take our investigation to the simple $d$-dimensional lattices for $d=1,2,3,4,5$ and fit $p,q$-binomial distributions to our data, some of which are exact but most are sampled. For $d=1$ and $d=5$ the magnetisation distributions are remarkably well-fitted by $p,q$-binomial distributions. For $d=4$ we are only slightly less successful, while for $d=2,3$ we see some deviations (with exceptions!) between the $p,q$-binomial and the Ising distribution. We begin the paper by giving results on the behaviour of the $p,q$-distribution and its moment growth exponents given a certain parameterization of $p,q$. Since the moment exponents are known for the Ising model (or at least approximately for $d=3$) we can predict how $p,q$ should behave and compare this to our measured $p,q$. The results speak in favour of the $p,q$-binomial distribution's correctness regarding their general behaviour in comparison to the Ising model. The full extent to which they correctly model the Ising distribution is not settled though.Comment: 51 pages, 23 figures, submitted to PRB on Oct 23 200

The chemistry of quartz in granitic pegmatites of southern Norway: Petrogenetic and economic implications

This is the author accepted manuscript. The final version is available from Society of Economic Geologists via the DOI in this record.Trace element concentrations in quartz from 188 granitic pegmatites in the Froland and Evje-Iveland pegmatite fields, southern Norway, have been determined to establish exploration targets for high-purity quartz and to gain a better understanding of the genesis of pegmatites hosting these deposits. Both pegmatite fields were formed during the Sveconorwegian (Grenvillian) orogeny (1145-900 Ma) at the western margin of the Fennoscandian Shield. In situ raster analyses within single quartz crystals were undertaken by laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS); spot size 75 μm) to assess levels of lattice-bound impurities, rather than mineral and fluid inclusions that are relatively easily removed during high-purity quartz processing. Quartz in the Froland pegmatites has relatively pure and homogeneous compositions containing 46 ± 24 μgg-1Al, 8 ± 3 μgg-1Ti, 1.4 ± 0.8 μgg-1Ge, and 11 ± 7 μgg-1Li. The Ti-in-quartz geothermobarometer gives an average pegmatite crystallization temperature of 537° ± 39°C. Temperature estimates are highest along the northwestern margin of the pegmatite field (>550°C), whereas the most differentiated pegmatites occur toward the northeast. The area of greatest economic potential for high-purity quartz lies just north of the central part of the field where individual pegmatites contain >1 million metric tons (Mt) quartz with low average trace element contents of 67 ± 11 μgg-1. From mineral-chemical criteria, and a range of other geologic factors, we propose that pegmatite melts in the Froland field were generated by fluid-present crustal melting at about 1060 Ma, in zones of localized high-strain deformation during progressive thrusting along the Porsgrunn-Kristiansand fault zone. Quartz in the Evje-Iveland pegmatites has more variable compositions with 69 ± 57 μgg-1Al, 19 ± 11 μgg-1Ti, 2.3 ± 1.8 μgg-1Ge, and 7 ± 5 μgg-1Li. From its Ti content, it crystallized at temperatures of 613° ± 70°C. The regional spatial distribution of Ti-in-quartz temperatures appears irregular mainly due to the scattered distributions of chemical evolved pegmatites with "amazonite"-"cleavelandite" replacement zones, which show crystallization temperatures down to 442°C. Quartz from the Evje-Iveland pegmatites is unlikely to be of current economic interest due to its moderate to high trace element contents, heterogeneous chemistry, and low volume. The Evje-Iveland pegmatites show no apparent genetic link to a granite intrusion; instead they probably formed as a result of partial melting at the depth of their amphibolite country rocks at around 910 Ma. This is related to a regional low-pressure/high-temperature metamorphic event at about 930 to 920 Ma.Geological Survey of Norway in Trondhei

Combining Experiments and Simulations Using the Maximum Entropy Principle

A key component of computational biology is to compare the results of computer modelling with experimental measurements. Despite substantial progress in the models and algorithms used in many areas of computational biology, such comparisons sometimes reveal that the computations are not in quantitative agreement with experimental data. The principle of maximum entropy is a general procedure for constructing probability distributions in the light of new data, making it a natural tool in cases when an initial model provides results that are at odds with experiments. The number of maximum entropy applications in our field has grown steadily in recent years, in areas as diverse as sequence analysis, structural modelling, and neurobiology. In this Perspectives article, we give a broad introduction to the method, in an attempt to encourage its further adoption. The general procedure is explained in the context of a simple example, after which we proceed with a real-world application in the field of molecular simulations, where the maximum entropy procedure has recently provided new insight. Given the limited accuracy of force fields, macromolecular simulations sometimes produce results that are at not in complete and quantitative accordance with experiments. A common solution to this problem is to explicitly ensure agreement between the two by perturbing the potential energy function towards the experimental data. So far, a general consensus for how such perturbations should be implemented has been lacking. Three very recent papers have explored this problem using the maximum entropy approach, providing both new theoretical and practical insights to the problem. We highlight each of these contributions in turn and conclude with a discussion on remaining challenges

Cone Photoreceptor Structure in Patients With X-Linked Cone Dysfunction and Red-Green Color Vision Deficiency

Purpose: Mutations in the coding sequence of the L and M opsin genes are often associated with X-linked cone dysfunction (such as Bornholm Eye Disease, BED), though the exact color vision phenotype associated with these disorders is variable. We examined individuals with L/M opsin gene mutations to clarify the link between color vision deficiency and cone dysfunction. Methods: We recruited 17 males for imaging. The thickness and integrity of the photoreceptor layers were evaluated using spectral-domain optical coherence tomography. Cone density was measured using high-resolution images of the cone mosaic obtained with adaptive optics scanning light ophthalmoscopy. The L/M opsin gene array was characterized in 16 subjects, including at least one subject from each family. Results: There were six subjects with the LVAVA haplotype encoded by exon 3, seven with LIAVA, two with the Cys203Arg mutation encoded by exon 4, and two with a novel insertion in exon 2. Foveal cone structure and retinal thickness was disrupted to a variable degree, even among related individuals with the same L/M array. Conclusions: Our findings provide a direct link between disruption of the cone mosaic and L/M opsin variants. We hypothesize that, in addition to large phenotypic differences between different L/M opsin variants, the ratio of expression of first versus downstream genes in the L/M array contributes to phenotypic diversity. While the L/M opsin mutations underlie the cone dysfunction in all of the subjects tested, the color vision defect can be caused either by the same mutation or a gene rearrangement at the same locus

Star forming dwarf galaxies

Star forming dwarf galaxies (SFDGs) have a high gas content and low metallicities, reminiscent of the basic entities in hierarchical galaxy formation scenarios. In the young universe they probably also played a major role in the cosmic reionization. Their abundant presence in the local volume and their youthful character make them ideal objects for detailed studies of the initial stellar mass function (IMF), fundamental star formation processes and its feedback to the interstellar medium. Occasionally we witness SFDGs involved in extreme starbursts, giving rise to strongly elevated production of super star clusters and global superwinds, mechanisms yet to be explored in more detail. SFDGs is the initial state of all dwarf galaxies and the relation to the environment provides us with a key to how different types of dwarf galaxies are emerging. In this review we will put the emphasis on the exotic starburst phase, as it seems less important for present day galaxy evolution but perhaps fundamental in the initial phase of galaxy formation.Comment: To appear in JENAM Symposium "Dwarf Galaxies: Keys to Galaxy Formation and Evolution", P. Papaderos, G. Hensler, S. Recchi (eds.). Lisbon, September 2010, Springer Verlag, in pres

The Escherichia coli transcriptome mostly consists of independently regulated modules

Underlying cellular responses is a transcriptional regulatory network (TRN) that modulates gene expression. A useful description of the TRN would decompose the transcriptome into targeted effects of individual transcriptional regulators. Here, we apply unsupervised machine learning to a diverse compendium of over 250 high-quality Escherichia coli RNA-seq datasets to identify 92 statistically independent signals that modulate the expression of specific gene sets. We show that 61 of these transcriptomic signals represent the effects of currently characterized transcriptional regulators. Condition-specific activation of signals is validated by exposure of E. coli to new environmental conditions. The resulting decomposition of the transcriptome provides: a mechanistic, systems-level, network-based explanation of responses to environmental and genetic perturbations; a guide to gene and regulator function discovery; and a basis for characterizing transcriptomic differences in multiple strains. Taken together, our results show that signal summation describes the composition of a model prokaryotic transcriptome

Cold gas accretion in galaxies

Evidence for the accretion of cold gas in galaxies has been rapidly accumulating in the past years. HI observations of galaxies and their environment have brought to light new facts and phenomena which are evidence of ongoing or recent accretion: 1) A large number of galaxies are accompanied by gas-rich dwarfs or are surrounded by HI cloud complexes, tails and filaments. It may be regarded as direct evidence of cold gas accretion in the local universe. It is probably the same kind of phenomenon of material infall as the stellar streams observed in the halos of our galaxy and M31. 2) Considerable amounts of extra-planar HI have been found in nearby spiral galaxies. While a large fraction of this gas is produced by galactic fountains, it is likely that a part of it is of extragalactic origin. 3) Spirals are known to have extended and warped outer layers of HI. It is not clear how these have formed, and how and for how long the warps can be sustained. Gas infall has been proposed as the origin. 4) The majority of galactic disks are lopsided in their morphology as well as in their kinematics. Also here recent accretion has been advocated as a possible cause. In our view, accretion takes place both through the arrival and merging of gas-rich satellites and through gas infall from the intergalactic medium (IGM). The infall may have observable effects on the disk such as bursts of star formation and lopsidedness. We infer a mean ``visible'' accretion rate of cold gas in galaxies of at least 0.2 Msol/yr. In order to reach the accretion rates needed to sustain the observed star formation (~1 Msol/yr), additional infall of large amounts of gas from the IGM seems to be required.Comment: To appear in Astronomy & Astrophysics Reviews. 34 pages. Full-resolution version available at http://www.astron.nl/~oosterlo/accretionRevie

Male reproductive health and environmental xenoestrogens

EHP is a publication of the U.S. government. Publication of EHP lies in the public domain and is therefore without copyright. Research articles from EHP may be used freely; however, articles from the News section of EHP may contain photographs or figures copyrighted by other commercial organizations and individuals that may not be used without obtaining prior approval from both the EHP editors and the holder of the copyright. Use of any materials published in EHP should be acknowledged (for example, "Reproduced with permission from Environmental Health Perspectives") and a reference provided for the article from which the material was reproduced.Male reproductive health has deteriorated in many countries during the last few decades. In the 1990s, declining semen quality has been reported from Belgium, Denmark, France, and Great Britain. The incidence of testicular cancer has increased during the same time incidences of hypospadias and cryptorchidism also appear to be increasing. Similar reproductive problems occur in many wildlife species. There are marked geographic differences in the prevalence of male reproductive disorders. While the reasons for these differences are currently unknown, both clinical and laboratory research suggest that the adverse changes may be inter-related and have a common origin in fetal life or childhood. Exposure of the male fetus to supranormal levels of estrogens, such as diethlylstilbestrol, can result in the above-mentioned reproductive defects. The growing number of reports demonstrating that common environmental contaminants and natural factors possess estrogenic activity presents the working hypothesis that the adverse trends in male reproductive health may be, at least in part, associated with exposure to estrogenic or other hormonally active (e.g., antiandrogenic) environmental chemicals during fetal and childhood development. An extensive research program is needed to understand the extent of the problem, its underlying etiology, and the development of a strategy for prevention and intervention.Supported by EU Contract BMH4-CT96-0314