GEOSIM: A numerical model for geophysical fluid flow simulation

A numerical model which simulates geophysical fluid flow in a wide range of problems is described in detail, and comparisons of some of the model's results are made with previous experimental and numerical studies. The model is based upon the Boussinesq Navier-Stokes equations in spherical coordinates, which can be reduced to a cylindrical system when latitudinal walls are used near the pole and the ratio of latitudinal length to the radius of the sphere is small. The equations are approximated by finite differences in the meridional plane and spectral decomposition in the azimuthal direction. The user can specify a variety of boundary and initial conditions, and there are five different spectral truncation options. The results of five validation cases are presented: (1) the transition between axisymmetric flow and baroclinic wave flow in the side heated annulus; (2) the steady baroclinic wave of the side heated annulus; (3) the wave amplitude vacillation of the side heated annulus; (4) transition to baroclinic wave flow in a bottom heated annulus; and (5) the Spacelab Geophysical Fluid Flow Cell (spherical) experiment

Scalable Text and Link Analysis with Mixed-Topic Link Models

Many data sets contain rich information about objects, as well as pairwise relations between them. For instance, in networks of websites, scientific papers, and other documents, each node has content consisting of a collection of words, as well as hyperlinks or citations to other nodes. In order to perform inference on such data sets, and make predictions and recommendations, it is useful to have models that are able to capture the processes which generate the text at each node and the links between them. In this paper, we combine classic ideas in topic modeling with a variant of the mixed-membership block model recently developed in the statistical physics community. The resulting model has the advantage that its parameters, including the mixture of topics of each document and the resulting overlapping communities, can be inferred with a simple and scalable expectation-maximization algorithm. We test our model on three data sets, performing unsupervised topic classification and link prediction. For both tasks, our model outperforms several existing state-of-the-art methods, achieving higher accuracy with significantly less computation, analyzing a data set with 1.3 million words and 44 thousand links in a few minutes.Comment: 11 pages, 4 figure

The Generalized Crewther Relation in QCD and its Experimental Consequences

We use the BLM scale-fixing prescription to derive a renormalization-scheme invariant relation between the coefficient function for the Bjorken sum rule for polarized deep inelastic scattering and the $R$-ratio for the $e^+e^-$ annihilation cross section. This relation provides a generalization of the Crewther relation to non-conformally invariant gauge theories. The derived relations allow one to calculate unambiguously without renormalization scale or scheme ambiguity the effective charges of the polarized Bjorken and the Gross-Llewellen Smith sum rules from the experimental value for the effective charge associated with $R$-ratio. Present data are consistent with the generalized Crewther relations, but measurements at higher precision and energies will be needed to decisively test these fundamental relations in QCD.Comment: 16 pages, LATEX fil

Familial hypomagnesaemia, Hypercalciuria and Nephrocalcinosis associated with a novel mutation of the highly conserved leucine residue 116 of Claudin 16 in a Chinese patient with a delayed diagnosis: A case report

Background: Sixty mutations of claudin 16 coding gene have been reported in familial hypomagnesemia with hypercalciuria and nephrocalcinosis (FHHNC) patients. Recent investigations revealed that a highly conserved glycine-leucine-tryptophan (115G-L-W117) motif in the first extracellular segment (ESC1) of claudin 16 might be essential for stabilization of the appropriately folded ECS1 structure and conservation of normal claudin 16 function. However, neither missense nor nonsense mutation has ever been described in this motif. Our study aimed at identifying mutations in a Chinese patient with FHHNC and exploring the association between genotype and phenotype. Case presentation: A 33-year-old female presented with 4 years history of recurrent acute pyelonephritis without other notable past medical history. Her healthy parents, who aged 56 and 53 respectively, were second cousins, and her only sibling died from renal failure without definite cause at age 25. Renal ultrasound imaging demonstrated atrophic kidneys and bilateral nephrocalcinosis. The laboratory workup revealed impaired renal function (Stage CKD IV), hypocalcemia and mild hypomagnesemia, accompanied with marked renal loss of magnesium and hypercalciuria. During the follow-up, treatment with calcitriol and calcium but not with magnesium was difficult to achieve normal serum calcium levels, whereas her serum magnesium concentration fluctuated within normal ranges. In the end, the patient unavoidably reached ESRD at 36 years old. The clinical features and family history suggested the diagnosis of FHHNC. To make a definite diagnosis, we use whole-exome sequencing to identify the disease-causing mutations and Sanger sequencing to confirm the mutation co-segregation in the family. As a result, a novel homozygous mutation (c.346C > G, p.Leu116Val) in115G-L-W117motif of claudin 16 was identified. Her parents, grandmother and one of her cousins carried heterozygous p.Leu116Val, whereas 200 unrelated controls did not carry this mutation. Conclusions: We described a delayed diagnosis patient with FHHNC in the Chinese population and identified a novel missense mutation in the highly conserved115G-L-W117motif of claudin 16 for the first time. According to the reported data and the information deduced from 3D modeling, we speculate that this mutation probably reserve partial residual function which might be related to the slight phenotype of the patient

Tracers of chromospheric structure. I. CaII H&\&K emission distribution of 13000 F, G and K stars in SDSS DR7 spectroscopic sample

We present chromospheric activity index $S\rm_{HK}$ measurements for over 13,000 F, G and K disk stars with high signal-to-noise ratio ($>$ 60) spectra in the Sloan Digital Sky Survey (SDSS) Data Release 7 (DR7) spectroscopic sample. A parameter $\delta$S is defined as the difference between $S\rm_{HK}$ and a `zero' emission line fitted by several of the most inactive stars. The $S\rm_{HK}$ indices of subgiant stars tend to be much lower than dwarfs, which provide a way to distinguish dwarfs and giants with relatively low resolution spectra. Cooler stars are generally more active and display a larger scatter than hotter stars. Stars associated with the thick disk are in general less active than those of the thin disk. The fraction of K dwarfs that are active drops with vertical distance from the Galactic plane. Metallicity affects $S\rm_{HK}$ measurements differently among F, G and K dwarfs in this sample. Using the open clusters NGC 2420, M67 and NGC6791 as calibrations, ages of most field stars in this SDSS sample range from 3-8 Gyr.Comment: 9 pages, 11 figures, AJ, 2013, 145, 14