Tests and applications of self-consistent cranking in the interacting boson model

The self-consistent cranking method is tested by comparing the cranking calculations in the interacting boson model with the exact results obtained from the SU(3) and O(6) dynamical symmetries and from numerical diagonalization. The method is used to study the spin dependence of shape variables in the $sd$ and $sdg$ boson models. When realistic sets of parameters are used, both models lead to similar results: axial shape is retained with increasing cranking frequency while fluctuations in the shape variable $\gamma$ are slightly reduced.Comment: 9 pages, 3 ps figures, Revte

Description of superdeformed nuclei in the interacting boson model

The interacting boson model is extended to describe the spectroscopy of superdeformed bands. Microscopic structure of the model in the second minimum is discussed and superdeformed bosons are introduced as the new building blocks. Solutions of a quadrupole Hamiltonian are implemented through the $1/N$ expansion method. Effects of the quadrupole parameters on dynamic moment of inertia and electric quadrupole transition rates are discussed and the results are used in a description of superdeformed bands in the Hg-Pb and Gd-Dy regions.Comment: 18 pages revtex, 9 figures available upon reques

Calculation of the photoionization with de-excitation cross sections of He and helium-like ions

We discuss the results of the calculation of the photoionization with de-excitation of excited He and helium-like ions Li$^{+}$ and B$^{3+}$ at high but non-relativistic photon energies $\omega$. Several lower $^{1}S$ and $^{3}S$ states are considered. We present and analyze the ratios $R_{d}^{+\ast}$ of the cross sections of photoionization with de-excitation, $\sigma_{(d)}^{+\ast}(\omega)$, and of the photo-ionization with excitation, $\sigma ^{+\ast}(\omega)$. The dependence of $R_{d}^{+\ast}$ on the excitation of the target object and the charge of its nucleus is presented. Apart to theoretical interest, results obtained can be verified using such long living excited state as $2^{3}S$ of He.Comment: 10 pages, 6 table

MethylPCA: a toolkit to control for confounders in methylome-wide association studies

Background In methylome-wide association studies (MWAS) there are many possible differences between cases and controls (e.g. related to life style, diet, and medication use) that may affect the methylome and produce false positive findings. An effective approach to control for these confounders is to first capture the major sources of variation in the methylation data and then regress out these components in the association analyses. This approach is, however, computationally very challenging due to the extremely large number of methylation sites in the human genome. Result We introduce MethylPCA that is specifically designed to control for potential confounders in studies where the number of methylation sites is extremely large. MethylPCA offers a complete and flexible data analysis including 1) an adaptive method that performs data reduction prior to PCA by empirically combining methylation data of neighboring sites, 2) an efficient algorithm that performs a principal component analysis (PCA) on the ultra high-dimensional data matrix, and 3) association tests. To accomplish this MethylPCA allows for parallel execution of tasks, uses C++ for CPU and I/O intensive calculations, and stores intermediate results to avoid computing the same statistics multiple times or keeping results in memory. Through simulations and an analysis of a real whole methylome MBD-seq study of 1,500 subjects we show that MethylPCA effectively controls for potential confounders. Conclusions MethylPCA provides users a convenient tool to perform MWAS. The software effectively handles the challenge in memory and speed to perform tasks that would be impossible to accomplish using existing software when millions of sites are interrogated with the sample sizes required for MWAS

Evaluation of Methyl-Binding Domain Based Enrichment Approaches Revisited

Methyl-binding domain (MBD) enrichment followed by deep sequencing (MBD-seq), is a robust and cost efficient approach for methylome-wide association studies (MWAS). MBD-seq has been demonstrated to be capable of identifying differentially methylated regions, detecting previously reported robust associations and producing findings that replicate with other technologies such as targeted pyrosequencing of bisulfite converted DNA. There are several kits commercially available that can be used for MBD enrichment. Our previous work has involved MethylMiner (Life Technologies, Foster City, CA, USA) that we chose after careful investigation of its properties. However, in a recent evaluation of five commercially available MBD-enrichment kits the performance of the MethylMiner was deemed poor. Given our positive experience with MethylMiner, we were surprised by this report. In an attempt to reproduce these findings we here have performed a direct comparison of MethylMiner with MethylCap (Diagenode Inc, Denville, NJ, USA), the best performing kit in that study. We find that both MethylMiner and MethylCap are two well performing MBD-enrichment kits. However, MethylMiner shows somewhat better enrichment efficiency and lower levels of background “noise”. In addition, for the purpose of MWAS where we want to investigate the majority of CpGs, we find MethylMiner to be superior as it allows tailoring the enrichment to the regions where most CpGs are located. Using targeted bisulfite sequencing we confirmed that sites where methylation was detected by either MethylMiner or by MethylCap indeed were methylated

Unconventional decay law for excited states in closed many-body systems

We study the time evolution of an initially excited many-body state in a finite system of interacting Fermi-particles in the situation when the interaction gives rise to the ``chaotic'' structure of compound states. This situation is generic for highly excited many-particle states in quantum systems, such as heavy nuclei, complex atoms, quantum dots, spin systems, and quantum computers. For a strong interaction the leading term for the return probability $W(t)$ has the form $W(t)\simeq \exp (-\Delta_E^2t^2)$ with $\Delta_E^2$ as the variance of the strength function. The conventional exponential linear dependence $W(t)=C\exp (-\Gamma t)$ formally arises for a very large time. However, the prefactor $C$ turns out to be exponentially large, thus resulting in a strong difference from the conventional estimate for $W(t)$.Comment: RevTex, 4 pages including 1 eps-figur

Clinical reports of pulmonary metastasectomy for colorectal cancer: a citation network analysis

INTRODUCTION: Pulmonary metastasectomy for colorectal cancer is a commonly performed and well-established practice of similar to 50 years standing. However, there have been no controlled studies, randomised or otherwise. We sought to investigate the evidence base that has been used in establishing its status as a standard of care.METHODS: Among 51 papers used in a recent systematic review and quantitative synthesis, a citation network analysis was performed. A total of 344 publications (the 51 index papers and a further 293 cited in them) constitute the citation network.RESULTS: The pattern of citation is that of a citation cascade. Specific analyses show the frequent use of historical or landmark papers, which add authority. Papers expressing an opposing viewpoint are rarely cited.CONCLUSIONS: The citation network for this common and well-established practice provides an example of selective citation. This pattern of citation tends to escalate belief in a clinical practice even when it lacks a high-quality evidence base and may create an impression of more authority than is warranted.British Journal of Cancer (2011) 104, 1085-1097. doi: 10.1038/sj.bjc.6606060 www.bjcancer.comPublished online 8 March 2011 (c) 2011 Cancer Research U

Neurodegeneration and Epilepsy in a Zebrafish Model of CLN3 Disease (Batten Disease)

The neuronal ceroid lipofuscinoses are a group of lysosomal storage disorders that comprise the most common, genetically heterogeneous, fatal neurodegenerative disorders of children. They are characterised by childhood onset, visual failure, epileptic seizures, psychomotor retardation and dementia. CLN3 disease, also known as Batten disease, is caused by autosomal recessive mutations in the CLN3 gene, 80–85% of which are a ~1 kb deletion. Currently no treatments exist, and after much suffering, the disease inevitably results in premature death. The aim of this study was to generate a zebrafish model of CLN3 disease using antisense morpholino injection, and characterise the pathological and functional consequences of Cln3 deficiency, thereby providing a tool for future drug discovery. The model was shown to faithfully recapitulate the pathological signs of CLN3 disease, including reduced survival, neuronal loss, retinopathy, axonopathy, loss of motor function, lysosomal storage of subunit c of mitochondrial ATP synthase, and epileptic seizures, albeit with an earlier onset and faster progression than the human disease. Our study provides proof of principle that the advantages of the zebrafish over other model systems can be utilised to further our understanding of the pathogenesis of CLN3 disease and accelerate drug discovery

Cluster Interpretation of Properties of Alternating Parity Bands in Heavy Nuclei

The properties of the states of the alternating parity bands in actinides, Ba, Ce and Nd isotopes are analyzed within a cluster model. The model is based on the assumption that cluster type shapes are produced by the collective motion of the nuclear system in the mass asymmetry coordinate. The calculated spin dependences of the parity splitting and of the electric multipole transition moments are in agreement with the experimental data.Comment: 29 pages, 10 figure

Quantum Fluctuation Theorems

Recent advances in experimental techniques allow one to measure and control systems at the level of single molecules and atoms. Here gaining information about fluctuating thermodynamic quantities is crucial for understanding nonequilibrium thermodynamic behavior of small systems. To achieve this aim, stochastic thermodynamics offers a theoretical framework, and nonequilibrium equalities such as Jarzynski equality and fluctuation theorems provide key information about the fluctuating thermodynamic quantities. We review the recent progress in quantum fluctuation theorems, including the studies of Maxwell's demon which plays a crucial role in connecting thermodynamics with information.Comment: As a chapter of: F. Binder, L. A. Correa, C. Gogolin, J. Anders, and G. Adesso (eds.), "Thermodynamics in the quantum regime - Fundamental Aspects and New Directions", (Springer International Publishing, 2018