Transmission Properties of the oscillating delta-function potential

We derive an exact expression for the transmission amplitude of a particle moving through a harmonically driven delta-function potential by using the method of continued-fractions within the framework of Floquet theory. We prove that the transmission through this potential as a function of the incident energy presents at most two real zeros, that its poles occur at energies $n\hbar\omega+\varepsilon^*$ ($0<Re(\varepsilon^*)<\hbar\omega$), and that the poles and zeros in the transmission amplitude come in pairs with the distance between the zeros and the poles (and their residue) decreasing with increasing energy of the incident particle. We also show the existence of non-resonant "bands" in the transmission amplitude as a function of the strength of the potential and the driving frequency.Comment: 21 pages, 12 figures, 1 tabl

Robustness of onion-like correlated networks against targeted attacks

Recently, it was found by Schneider et al. [Proc. Natl. Acad. Sci. USA, 108, 3838 (2011)], using simulations, that scale-free networks with "onion structure" are very robust against targeted high degree attacks. The onion structure is a network where nodes with almost the same degree are connected. Motivated by this work, we propose and analyze, based on analytical considerations, an onion-like candidate for a nearly optimal structure against simultaneous random and targeted high degree node attacks. The nearly optimal structure can be viewed as a hierarchically interconnected random regular graphs, the degrees and populations of which are specified by the degree distribution. This network structure exhibits an extremely assortative degree-degree correlation and has a close relationship to the "onion structure." After deriving a set of exact expressions that enable us to calculate the critical percolation threshold and the giant component of a correlated network for an arbitrary type of node removal, we apply the theory to the cases of random scale-free networks that are highly vulnerable against targeted high degree node removal. Our results show that this vulnerability can be significantly reduced by implementing this onion-like type of degree-degree correlation without much undermining the almost complete robustness against random node removal. We also investigate in detail the robustness enhancement due to assortative degree-degree correlation by introducing a joint degree-degree probability matrix that interpolates between an uncorrelated network structure and the onion-like structure proposed here by tuning a single control parameter. The optimal values of the control parameter that maximize the robustness against simultaneous random and targeted attacks are also determined. Our analytical calculations are supported by numerical simulations.Comment: 12 pages, 8 figure

Scaling of the buckling transition of ridges in thin sheets

When a thin elastic sheet crumples, the elastic energy condenses into a network of folding lines and point vertices. These folds and vertices have elastic energy densities much greater than the surrounding areas, and most of the work required to crumple the sheet is consumed in breaking the folding lines or ``ridges''. To understand crumpling it is then necessary to understand the strength of ridges. In this work, we consider the buckling of a single ridge under the action of inward forcing applied at its ends. We demonstrate a simple scaling relation for the response of the ridge to the force prior to buckling. We also show that the buckling instability depends only on the ratio of strain along the ridge to curvature across it. Numerically, we find for a wide range of boundary conditions that ridges buckle when our forcing has increased their elastic energy by 20% over their resting state value. We also observe a correlation between neighbor interactions and the location of initial buckling. Analytic arguments and numerical simulations are employed to prove these results. Implications for the strength of ridges as structural elements are discussed.Comment: 42 pages, latex, doctoral dissertation, to be submitted to Phys Rev

On the assessment of statistical significance of three-dimensional colocalization of sets of genomic elements

A growing body of experimental evidence supports the hypothesis that the 3D structure of chromatin in the nucleus is closely linked to important functional processes, including DNA replication and gene regulation. In support of this hypothesis, several research groups have examined sets of functionally associated genomic loci, with the aim of determining whether those loci are statistically significantly colocalized. This work presents a critical assessment of two previously reported analyses, both of which used genome-wide DNA–DNA interaction data from the yeast Saccharomyces cerevisiae, and both of which rely upon a simple notion of the statistical significance of colocalization. We show that these previous analyses rely upon a faulty assumption, and we propose a correct non-parametric resampling approach to the same problem. Applying this approach to the same data set does not support the hypothesis that transcriptionally coregulated genes tend to colocalize, but strongly supports the colocalization of centromeres, and provides some evidence of colocalization of origins of early DNA replication, chromosomal breakpoints and transfer RNAs

Cytogenetic studies of Brazilian pediatric myelodysplastic syndrome cases: challenges and difficulties in a large and emerging country

Myelodysplastic syndromes (MDS) and juvenile myelomonocytic leukemia (JMML) are rare hematopoietic stem cell diseases affecting children. Cytogenetics plays an important role in the diagnosis of these diseases. We report here the experience of the Cytogenetic Subcommittee of the Brazilian Cooperative Group on Pediatric Myelodysplastic Syndromes (BCG-MDS-PED). We analyzed 168 cytogenetic studies performed in 23 different cytogenetic centers; 84 of these studies were performed in patients with confirmed MDS (primary MDS, secondary MDS, JMML, and acute myeloid leukemia/MDS+Down syndrome). Clonal abnormalities were found in 36.9% of the MDS cases and cytogenetic studies were important for the detection of constitutional diseases and for differential diagnosis with other myeloid neoplasms. These data show the importance of the Cooperative Group for continuing education in order to avoid a late or wrong diagnosis.Univ São Paulo, Fac Med, Dept Hematol, São Paulo, BrazilUniversidade Federal de São Paulo, Dept Hematol, São Paulo, BrazilUniv São Paulo, Fac Med, Dept Hematol, Lab Citogenet, São Paulo, BrazilUniversidade Federal de São Paulo, Inst Oncol Pediat, São Paulo, BrazilUniv Estadual Paulista, Fac Med Botucatu, Dept Clin Med, Botucatu, SP, BrazilHosp Canc Barretos, Barretos, SP, BrazilCtr Tratamento Fabiana Macedo de Morais, Grp Assistencia Crianca Canc, Grp Cooperat Brasileiro Sindrome Mielodisplas Ped, Sao Jose Dos Campos, SP, BrazilUniversidade Federal de São Paulo, Dept Hematol, São Paulo, BrazilUniversidade Federal de São Paulo, Inst Oncol Pediat, São Paulo, BrazilWeb of Scienc

The Importance of Biologically Active Vitamin D for Mineralization by Osteocytes After Parathyroidectomy for Renal Hyperparathyroidism

Hypomineralized matrix is a factor determining bone mineral density. Increased perilacunar hypomineralized bone area is caused by reduced mineralization by osteocytes. The importance of vitamin D in the mineralization by osteocytes was investigated in hemodialysis patients who underwent total parathyroidectomy (PTX) with immediate autotransplantation of diffuse hyperplastic parathyroid tissue. No previous reports on this subject exist. The study was conducted in 19 patients with renal hyperparathyroidism treated with PTX. In 15 patients, the serum calcium levels were maintained by subsequent administration of alfacalcidol (2.0 μg/day), i.v. calcium gluconate, and oral calcium carbonate for 4 weeks after PTX (group I). This was followed in a subset of 4 patients in group I by a reduced dose of 0.5 μg/day until 1 year following PTX; this was defined as group II. In the remaining 4 patients, who were not in group I, the serum calcium (Ca) levels were maintained without subsequent administration of alfacalcidol (group III). Transiliac bone biopsy specimens were obtained in all groups before and 3 or 4 weeks after PTX to evaluate the change of the hypomineralized bone area. In addition, patients from group II underwent a third bone biopsy 1 year following PTX. A significant decrease of perilacunar hypomineralized bone area was observed 3 or 4 weeks after PTX in all group I and II patients. The area was increased again in the group II patients 1 year following PTX. In group III patients, an increase of the hypomineralized bone area was observed 4 weeks after PTX. The maintenance of a proper dose of vitamin D is necessary for mineralization by osteocytes, which is important to increase bone mineral density after PTX for renal hyperparathyroidism

Annotation of two large contiguous regions from the Haemonchus contortus genome using RNA-seq and comparative analysis with Caenorhabditis elegans

The genomes of numerous parasitic nematodes are currently being sequenced, but their complexity and size, together with high levels of intra-specific sequence variation and a lack of reference genomes, makes their assembly and annotation a challenging task. Haemonchus contortus is an economically significant parasite of livestock that is widely used for basic research as well as for vaccine development and drug discovery. It is one of many medically and economically important parasites within the strongylid nematode group. This group of parasites has the closest phylogenetic relationship with the model organism Caenorhabditis elegans, making comparative analysis a potentially powerful tool for genome annotation and functional studies. To investigate this hypothesis, we sequenced two contiguous fragments from the H. contortus genome and undertook detailed annotation and comparative analysis with C. elegans. The adult H. contortus transcriptome was sequenced using an Illumina platform and RNA-seq was used to annotate a 409 kb overlapping BAC tiling path relating to the X chromosome and a 181 kb BAC insert relating to chromosome I. In total, 40 genes and 12 putative transposable elements were identified. 97.5% of the annotated genes had detectable homologues in C. elegans of which 60% had putative orthologues, significantly higher than previous analyses based on EST analysis. Gene density appears to be less in H. contortus than in C. elegans, with annotated H. contortus genes being an average of two-to-three times larger than their putative C. elegans orthologues due to a greater intron number and size. Synteny appears high but gene order is generally poorly conserved, although areas of conserved microsynteny are apparent. C. elegans operons appear to be partially conserved in H. contortus. Our findings suggest that a combination of RNA-seq and comparative analysis with C. elegans is a powerful approach for the annotation and analysis of strongylid nematode genomes

DOC2B: A Novel Syntaxin-4 Binding Protein Mediating Insulin-Regulated GLUT4 Vesicle Fusion in Adipocytes

OBJECTIVE— Insulin stimulates glucose uptake in skeletal muscle and adipose tissues primarily by stimulating the translocation of vesicles containing a facilitative glucose transporter, GLUT4, from intracellular compartments to the plasma membrane. The formation of stable soluble N-ethyl-maleimide–sensitive fusion protein [NSF] attachment protein receptor (SNARE) complexes between vesicle-associated membrane protein-2 (VAMP-2) and syntaxin-4 initiates GLUT4 vesicle docking and fusion processes. Additional factors such as munc18c and tomosyn were reported to be negative regulators of the SNARE complex assembly involved in GLUT4 vesicle fusion. However, despite numerous investigations, the positive regulators have not been adequately clarified