A generalization of the injectivity condition for Projected Entangled Pair States

We introduce a family of tensor network states that we term semi-injective Projected Entangled-Pair States (PEPS). They extend the class of injective PEPS and include other states, like the ground states of the AKLT and the CZX models in square lattices. We construct parent Hamiltonians for which semi-injective PEPS are unique ground states. We also determine the necessary and sufficient conditions for two tensors to generate the same family of such states in two spatial dimensions. Using this result, we show that the third cohomology labeling of Symmetry Protected Topological phases extends to semi-injective PEPS.Comment: 63 page

Entropy Bound and Causality Violation in Higher Curvature Gravity

In any quantum theory of gravity we do expect corrections to Einstein gravity to occur. Yet, at fundamental level, it is not apparent what the most relevant corrections are. We argue that the generic curvature square corrections present in lower dimensional actions of various compactified string theories provide a natural passage between the classical and quantum realms of gravity. The Gauss-Bonnet and $({\rm Riemann})^2$ gravities, in particular, provide concrete examples in which inconsistency of a theory, such as, a violation of microcausality, and a classical limit on black hole entropy are correlated. In such theories the ratio of the shear viscosity to the entropy density, $\eta/s$, can be smaller than for a boundary conformal field theory with Einstein gravity dual. This result is interesting from the viewpoint that the nuclear matter or quark-gluon plasma produced (such as at RHIC) under extreme densities and temperatures may violate the conjectured bound $\eta/s\ge 1/4\pi$, {\it albeit} marginally so.Comment: 23 pages, several eps figures; minor changes, references added, published versio

Phase Transitions and the Perfectness of Fluids

We calculate the ratio eta/s, the shear viscosity (eta) to entropy density (s), which characterizes how perfect a fluid is, in weakly coupled real scalar field theories with different types of phase transitions. The mean-field results of the eta/s behaviors agree with the empirical observations in atomic and molecular systems such as water, He, N, and all the matters with data available in the NIST database. These behaviors are expected to be the same in N component scalar theories with an O(N) symmetry. We speculate these eta/s behaviors are general properties of fluid shared by QCD and cold atoms. Finally, we clarify some issues regarding counterexamples of the conjectured universal eta/s bound found in Refs.[16,17].Comment: 5 pages, 2 figures; Fig. 2 changed; journal versio

Revisiting the association between altitude and mortality in dialysis patients.

It was recently reported that residential altitude is inversely associated with all-cause mortality among incident dialysis patients; however, no adjustment was made for key case-mix and laboratory variables. We re-examined this question in a contemporary patient database with comprehensive clinical and laboratory data. In a contemporary 8-year cohort of 144,892 maintenance dialysis patients from a large dialysis organization, we examined the relationship between residential altitude and all-cause mortality. Using data from the US Geological Survey, the average residential altitudes per approximately 43,000 US zip codes were compiled and linked to the residential zip codes of each patient. Mortality risks for these patients were estimated by Cox proportional hazard ratios. The study population's mean ± standard deviation age was 61 ± 15 years. Forty-five percent of patients were women, and 57% of patients had diabetes. In fully adjusted analysis, those residing in the highest altitude strata (≥ 6000 ft) had a lower all-cause mortality risk in fully adjusted analyses: death hazard ratio: 0.92 (95% confidence interval, 0.86-0.99), as compared with patients in the reference group (<250 ft). Residential altitude is inversely associated in all-cause mortality risk in maintenance dialysis patients notwithstanding the unknown and unmeasured confounders

The growth of northeastern Tibet and its relevance to large-scale continental geodynamics: A review of recent studies

Recent studies of the northeastern part of the Tibetan Plateau have called attention to two emerging views of how the Tibetan Plateau has grown. First, deformation in northern Tibet began essentially at the time of collision with India, not 10–20 Myr later as might be expected if the locus of activity migrated northward as India penetrated the rest of Eurasia. Thus, the north-south dimensions of the Tibetan Plateau were set mainly by differences in lithospheric strength, with strong lithosphere beneath India and the Tarim and Qaidam basins steadily encroaching on one another as the region between them, the present-day Tibetan Plateau, deformed, and its north-south dimension became narrower. Second, abundant evidence calls for acceleration of deformation, including the formation of new faults, in northeastern Tibet since ~15 Ma and a less precisely dated change in orientation of crustal shortening since ~20 Ma. This reorientation of crustal shortening and roughly concurrent outward growth of high terrain, which swings from NNE-SSW in northern Tibet to more NE-SW and even ENE-WSW in the easternmost part of northeastern Tibet, are likely to be, in part, a consequence of crustal thickening within the high Tibetan Plateau reaching a limit, and the locus of continued shortening then migrating to the northeastern and eastern flanks. These changes in rates and orientation also could result from removal of some or all mantle lithosphere and increased gravitational potential energy per unit area and from a weakening of crustal material so that it could flow in response to pressure gradients set by evolving differences in elevation

Why ‘the uplift of the Tibetan Plateau’ is a myth?

The often-used phrase ‘the uplift of the Tibetan Plateau’ implies a flat-surfaced Tibet rose as a coherent entity, and that uplift was driven entirely by the collision and northward movement of India. Here, we argue that these are misconceptions derived in large part from simplistic geodynamic and climate modeling, as well as proxy misinterpretation. The growth of Tibet was a complex process involving mostly Mesozoic collisions of several Gondwanan terranes with Asia, thickening the crust and generating complex relief before the arrival of India. In this review, Earth system modeling, paleoaltimetry proxies and fossil finds contribute to a new synthetic view of the topographic evolution of Tibet. A notable feature overlooked in previous models of plateau formation was the persistence through much of the Cenozoic of a wide east–west orientated deep central valley, and the formation of a plateau occurred only in the late Neogene through compression and internal sedimentation

A Combination of Compositional Index and Genetic Algorithm for Predicting Transmembrane Helical Segments

Transmembrane helix (TMH) topology prediction is becoming a focal problem in bioinformatics because the structure of TM proteins is difficult to determine using experimental methods. Therefore, methods that can computationally predict the topology of helical membrane proteins are highly desirable. In this paper we introduce TMHindex, a method for detecting TMH segments using only the amino acid sequence information. Each amino acid in a protein sequence is represented by a Compositional Index, which is deduced from a combination of the difference in amino acid occurrences in TMH and non-TMH segments in training protein sequences and the amino acid composition information. Furthermore, a genetic algorithm was employed to find the optimal threshold value for the separation of TMH segments from non-TMH segments. The method successfully predicted 376 out of the 378 TMH segments in a dataset consisting of 70 test protein sequences. The sensitivity and specificity for classifying each amino acid in every protein sequence in the dataset was 0.901 and 0.865, respectively. To assess the generality of TMHindex, we also tested the approach on another standard 73-protein 3D helix dataset. TMHindex correctly predicted 91.8% of proteins based on TM segments. The level of the accuracy achieved using TMHindex in comparison to other recent approaches for predicting the topology of TM proteins is a strong argument in favor of our proposed method. Availability: The datasets, software together with supplementary materials are available at: http://faculty.uaeu.ac.ae/nzaki/TMHindex.htm

Frequency of single nucleotide polymorphisms in NOD1 gene of ulcerative colitis patients: a case-control study in the Indian population

<p>Abstract</p> <p>Background</p> <p>Epidemiological studies have provided enough evidence that genetic factors have an important role in determining susceptibility to IBD. The most significant finding in the IBD research has been identification of mutations in the gene that encodes Nod2 (nucleotide-binding oligomerization domain 2) protein in a subgroup of patients with Crohn's disease. However, a very similar gene encoding Nod1 protein still has not been well documented for its association with Ulcerative colitis patients. Detection of polymorphism in <it>NOD1 </it>gene using SNP analysis has been attempted in the present study. We evaluated frequency and significance of mutations present in the nucleotide-binding domain (NBD) of <it>NOD1 </it>gene in context to Indian population.</p> <p>Methods</p> <p>A total of 95 patients with ulcerative colitis and 102 controls enrolled in the Gastroenterology department of All India Institute of Medical Sciences, New Delhi were screened for SNPs by DHPLC and RFLP techniques. Exon 6 locus in the NBD domain of <it>NOD1 </it>gene was amplified and sequenced. Genotype and allele frequencies of the patients and controls were calculated by the Pearson's χ²test, Fisher's exact test and ANOVA with Bonferroni's correction using SPSS software version 12.</p> <p>Results</p> <p>We have demonstrated DHPLC screening technique to show the presence of SNPs in Exon 6 locus of NBD domain of <it>NOD1 </it>gene. The DHPLC analysis has proven suitable for rapid detection of base pair changes. The data was validated by sequencing of clones and subsequently by RFLP analysis. Analyses of SNP data revealed 3 significant mutations (W219R, <it>p </it>= 0.002; L349P, <it>p </it>= 0.002 and L370R, <it>p </it>= 0.039) out of 5 in the Exon 6 locus of NBD domain of the gene that encompasses ATP and Mg²⁺binding sites. No significant association was observed within different sub phenotypes.</p> <p>Conclusion</p> <p>We propose that the location of mutations in the Exon 6 spanning the ATP and Mg²⁺binding site of NBD in <it>NOD1 </it>gene may affect the process of oligomerization and subsequent function of the LRR domain. Further studies are been conducted at the protein level to prove this possibility.</p

Role of the Drosophila Non-Visual ß-Arrestin Kurtz in Hedgehog Signalling

The non-visual ß-arrestins are cytosolic proteins highly conserved across species that participate in a variety of signalling events, including plasma membrane receptor degradation, recycling, and signalling, and that can also act as scaffolding for kinases such as MAPK and Akt/PI3K. In Drosophila melanogaster, there is only a single non-visual ß-arrestin, encoded by kurtz, whose function is essential for neuronal activity. We have addressed the participation of Kurtz in signalling during the development of the imaginal discs, epithelial tissues requiring the activity of the Hedgehog, Wingless, EGFR, Notch, Insulin, and TGFβ pathways. Surprisingly, we found that the complete elimination of kurtz by genetic techniques has no major consequences in imaginal cells. In contrast, the over-expression of Kurtz in the wing disc causes a phenotype identical to the loss of Hedgehog signalling and prevents the expression of Hedgehog targets in the corresponding wing discs. The mechanism by which Kurtz antagonises Hedgehog signalling is to promote Smoothened internalization and degradation in a clathrin- and proteosomal-dependent manner. Intriguingly, the effects of Kurtz on Smoothened are independent of Gprk2 activity and of the activation state of the receptor. Our results suggest fundamental differences in the molecular mechanisms regulating receptor turnover and signalling in vertebrates and invertebrates, and they could provide important insights into divergent evolution of Hedgehog signalling in these organisms

Diagnostic criteria patterns of U.S. children with Metabolic Syndrome: NHANES 1999–2002

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