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Table S1. Synthetic DNA oligomers, PCR primers

Supplementary Fig. S1. Nedd9 and Aurkb seed match sequences in mucAB and umuDC.Supplementary Fig. S2. Selection of cells expressing Tet-repressor protein.Supplementary Fig. S3. Microarray analysis of deregulated oncogenes.Supplementary Fig. S4. Suppression of cellular transformation with anti-mucAB shRNA.Supplementary Fig. S5. Confirmation of interaction of miR-145 with anti-miR-145.Supplementary Fig. S6. Microcolony formation over time.Supplementary Fig. S7. Comparison of tumor incidence rates between males and females, and between presence and absence of Zn.

The basic materials of Berry's phase and chiral anomalies are presented to appreciate the phenomena related to those notions. As for Berry's phase, a general survey of the subject is presented using both Lagrangian and Hamiltonian formalisms. The canonical Hamiltonian formalism of the Born-Oppenheimer approximation, when applied to the anomalous Hall effect, can incorporate the gauge symmetry of Berry's connection but unable to incorporate the electromagnetic vector potential simultaneously. Transformed to the Lagrangian formalism with a time-derivative term allowed, the Born-Oppenheimer approximation can incorporate the electromagnetic vector potential simultaneously with Berry's connection, but the consistent canonical property is lost and thus becomes classical. The Lagrangian formalism can thus incorporate both gauge symmetries simultaneously but spoils the basic quantum symmetries, and thus results in classical anomalous Poisson brackets and the classical Nernst effect as in the conventional formalism. As for chiral anomalies, we present basic materials by the path integral formulation with an emphasis on fermions on the lattice. A chiral fermion defined by $\gamma_{5}$ on the lattice does not contain the chiral anomaly for the non-vanishing lattice spacing $a\neq0$. The idea of a spectral flow on the lattice does not lead to an anomaly for each species doubler separately but rather to a pair production in a general sense. We also mention that a specific construction called the Ginsparg-Wilson fermion, which is free of species doublers, may practically be useful. We discuss the representative applications of Berry's phase and chiral anomalies in nuclear physics and related fields to illustrate the use of these two basic notions., Comment: 126 pages. 10 figures. Corrected typos and a poorly organized page in Appendix B, together with a new reference

The mechanism of cancer induction involves an aberrant expression of oncogenes whose functions can be controlled by RNAi with miRNA. Even foreign bacterial RNA may interfere with the expression of oncogenes. Here we show that bacterial plasmid mucAB and its Escherichia coli genomic homolog umuDC, carrying homologies that match the mouse anti-miR-145, sequestered the miR-145 function in mouse BALB 3T3 cells in a tetracycline (Tet)-inducible manner, activated oncogene Nedd9 and its downstream Aurkb, and further enhanced microcolony formation and cellular transformation as well as the short fragments of the bacterial gene containing the anti-miR-145 sequence. Furthermore, mucAB transgenic mice showed a 1.7-fold elevated tumor incidence compared with wild-type mice after treatments with 3-methylcolanthrene. However, the mutation frequency in intestinal stem cells of the mucAB transgenic mice was unchanged after treatment with X-rays or ethyl-nitrosourea, indicating that the target of mucAB/umuDC is the promotion stage in carcinogenesis. Implications: Foreign bacterial genes can exert oncogenic activity via RNAi, if endogenously expressed. Visual Overview: http://mcr.aacrjournals.org/content/molcanres/18/9/1271/F1.large.jpg.

Berry's phase, which is associated with the slow cyclic motion with a finite period, looks like a Dirac monopole when seen from far away but smoothly changes to a dipole near the level crossing point in the parameter space in an exactly solvable model. This topology change of Berry's phase is visualized as a result of lensing effect; the monopole supposed to be located at the level crossing point appears at the displaced point when the variables of the model deviate from the precisely adiabatic movement. The effective magnetic field generated by Berry's phase is determined by a simple geometrical consideration of the magnetic flux coming from the displaced Dirac monopole., 14 pages, 4 figures. The agreement of Berry's phase with the solid angle drawn by a spin vector in the case of a two-component spinor is explained in connection with the lensing effect. This version is going to appear in Phys. Rev. D

The parity transformation law of the fermion field $\psi(x)$ is usually defined by the "$\gamma^{0}$-parity" $\psi^{p}(t,-\vec{x}) = \gamma^{0}\psi(t,-\vec{x})$ with eigenvalues $\pm 1$, while the "$i\gamma^{0}$-parity" $\psi^{p}(t,-\vec{x})=i\gamma^{0}\psi(t,-\vec{x})$ is required for the Majorana fermion. The compatibility issues of these two parity laws arise in generic fermion number violating theories where a general class of Majorana fermions appear. In the case of Majorana neutrinos constructed from chiral neutrinos in an extension of the Standard Model, the Majorana neutrinos can be characterized by CP symmetry although C and P are separately broken. It is then shown that either choice of the parity operation, $\gamma^{0}$ or $i\gamma^{0}$, in the level of the starting fermions gives rise to the consistent and physically equivalent descriptions of emergent Majorana neutrinos both for Weinberg's model of neutrinos and for a general class of seesaw models. The mechanism of this equivalence is that the Majorana neutrino constructed from a chiral neutrino, which satisfies the classical Majorana condition $\psi(x)=C\overline{\psi(x)}^{T}$, allows the phase freedom $\psi(x)=e^{i\alpha}\nu_{L}(x) + e^{-i\alpha}C\overline{\nu_{L}(x)}^{T}$ with $\alpha=0\ {\rm or}\ \pi/4$ that accounts for the phase coming from the different definitions of parity for $\nu_{L}(x)$ and ensures the consistent definitions of CP symmetry $({\cal CP})\psi(x)({\cal CP})^{\dagger}= \pm i\gamma^{0}\psi(t,-\vec{x})$., Comment: 24 pages. Substantially modified including title and abstract. Added an extensive appendix. This version is to appear in Phys. Rev. D

In the analysis of neutron-antineutron oscillations, it has been recently argued in the literature that the use of the $i\gamma^{0}$ parity $n^{p}(t,-\vec{x})=i\gamma^{0}n(t,-\vec{x})$ which is consistent with the Majorana condition is mandatory and that the ordinary parity transformation of the neutron field $n^{p}(t,-\vec{x}) = \gamma^{0}n(t,-\vec{x})$ has a difficulty. We show that a careful treatment of the ordinary parity transformation of the neutron works in the analysis of neutron-antineutron oscillations. Technically, the CP symmetry in the mass diagonalization procedure is important and the two parity transformations, $i\gamma^{0}$ parity and $\gamma^{0}$ parity, are compensated for by the Pauli-G\"ursey transformation. Our analysis shows that either choice of the parity gives the correct results of neutron-antineutron oscillations if carefully treated., Comment: 19 pages. Some modifications in Appendix B were made. This version is going to be published in Phys. Rev. D

The mechanism of cancer induction involves an aberrant expression of oncogenes whose functions can be controlled by RNAi with miRNA. Even foreign bacterial RNA may interfere with the expression of oncogenes. Here we show that bacterial plasmid

The Majorana neutrino $\psi_{M}(x)$ when constructed as a superposition of chiral fermions such as $\nu_{L} + C\overline{\nu_{L}}^{T}$ is characterized by $ ({\cal C}{\cal P}) \psi_{M}(x)({\cal C}{\cal P})^{\dagger} =i\gamma^{0}\psi_{M}(t,-\vec{x})$, and the CP symmetry describes the entire physics contents of Majorana neutrinos. Further specifications of C and P separately could lead to difficulties depending on the choice of C and P. The conventional $ {\cal C} \psi_{M}(x) {\cal C}^{\dagger} = \psi_{M}(x)$ with well-defined P is naturally defined when one constructs the Majorana neutrino from the Dirac-type fermion. In the seesaw model of Type I or Type I+II where the same number of left- and right-handed chiral fermions appear, it is possible to use the generalized Pauli-Gursey transformation to rewrite the seesaw Lagrangian in terms of Dirac-type fermions only; the conventional C symmetry then works to define Majorana neutrinos. In contrast, the "pseudo C-symmetry" $\nu_{L,R}(x)\rightarrow C\overline{\nu_{L,R}(x)}^{T}$ (and associated "pseudo P-symmetry"), that has been often used in both the seesaw model and Weinberg's model to describe Majorana neutrinos, attempts to assign a nontrivial charge conjugation transformation rule to each chiral fermion separately. But this common construction is known to be operatorially ill-defined and, for example, the amplitude of the neutrinoless double beta decay vanishes if the vacuum is assumed to be invariant under the pseudo C-symmetry., Comment: 25 pages. Substantially expanded to explain the subject in more detail. This version is to be published in European Physical Journal C

The gamma-ray energy spectrum of the Kinki University Reactor (UTR-KINKI) was estimated from Ge detector measurements combined with Monte Carlo N-particle transport criticality calculations. The gamma rays mainly originated from prompt fission components, although small amounts of gamma rays from (n,γ) reactions, fission product gamma rays, and activation gamma rays were detected. The averaged gamma-ray tissue kerma rate in the irradiation port during UTR-KINKI operation at 1W was calculated as 10.5cGy/h based on the estimated gamma-ray energy spectrum. This value is consistent with a previous measurement with paired ionization chambers and a tissue equivalent gas proportional counter. This result demonstrates the reliability of the estimated gamma-ray energy spectrum.

The monopole-like singularity of Berry's adiabatic phase in momentum space and associated anomalous Poisson brackets have been recently discussed in various fields. With the help of the results of an exactly solvable version of Berry's model, we show that Berry's phase does not lead to the deformation of the principle of quantum mechanics in the sense of anomalous canonical commutators. If one should assume Berry's phase of genuine Dirac monopole-type, which is assumed to hold not only in the adiabatic limit but also in the non-adiabatic limit, the deformation of the principle of quantum mechanics could take place. But Berry's phase of the genuine Dirac monopole-type is not supported by the exactly solvable version of Berry's model nor by a generic model of Berry's phase. Besides, the monopole-like Berry's phase in momentum space has a magnetic charge $e_{M}=2\pi\hbar$, for which the possible anomalous term in the canonical commutator $[x_{k},x_{l}]=i\hbar\Omega_{kl}$ would become of the order $O(\hbar^{2})$., Comment: 29 pages and 3 figures. Substantially expanded and a detailed account of the absence of no anomalous cononical commutators induced by Berry's phase is given. The title has also been changed accordingly. This version is to be published in Ann. of Phys

A new approach to the classical limit of Grover's algorithm is discussed by assuming a very rapid dephasing of a system between consecutive Grover's unitary operations, which drives pure quantum states to decohered mixed states. One can identify a specific element among $N$ unsorted elements by a probability of the order of unity after $k\sim N$ steps of classical amplification, which is realized by a combination of Grover's unitary operation and rapid dephasing, in contrast to $k\sim \pi \sqrt{N}/4$ steps in quantum mechanical amplification. The initial two-state system with enormously unbalanced existence probabilities, which is realized by a chosen specific state and a superposition of all the rest of states among $N$ unsorted states, is crucial in the present analysis of classical amplification. This analysis illustrates Grover's algorithm in extremely noisy circumstances. A similar increase from $k\sim \sqrt{N}$ to $k\sim N$ steps due to the loss of quantum coherence takes place in the {\em analog} model of Farhi and Gutmann where the entanglement does not play an obvious role. This supports a view that entanglement is crucial in quantum computation to describe quantum states by a set of qubits, but the actual speedup of the quantum computation is based on quantum coherence., Comment: 15 pages. Substantially modified with an additional author and the change of the title. This version is going to be published in Mod. Phys. Lett. A

The idea that the Majorana neutrino should be identified as a Bogoliubov quasiparticle is applied to the seesaw mechanism for the three generations of neutrinos in the Standard Model. A relativistic analogue of the Bogoliubov transformation in the present context is a CP-preserving canonical transformation but modifies charge conjugation properties in such a way that the C-noninvariant fermion number violating term (condensate) is converted to a Dirac mass term. Puzzling aspects associated with the charge conjugation of chiral Weyl fermions are clarified. By invoking the Coleman--Weinberg mechanism in the framework of dimensional regularization, it is also noted that seesaw models become unnatural in some parameter regions which induce the hierarchy problems in the bosonic sector., Comment: 20 pages

The possible neutron-antineutron oscillation is described by an effective quadratic Lagrangian analogous to the BCS theory. It is shown that the conventional equal-time anti-commutation relations of the neutron variable $n(t,\vec{x})$ are modified by the baryon number violating terms. This is established by the Bjorken--Johnson--Low prescription and also by the canonical quantization combined with equations of motion. This novel canonical behavior can give rise to an important physical effect, which is illustrated by analyzing the Lagrangian that violates the baryon number but gives rise to the degenerate effective Majorana fermions and thus no neutron-antineutron oscillation. Technically, this model is neatly treated using a relativistic analogue of the Bogoliubov transformation., Comment: 14 pages

We discuss a generalization of the Pauli-Gursey transformation, which is motivated by the Autonne-Takagi factorization, to an arbitrary $n$ number of generations of neutrinos using $U(2n)$ that defines general canonical transformations and diagonalizes symmetric complex Majorana mass matrices in special cases. The Pauli-Gursey transformation mixes particles and antiparticles and thus changes the definition of the vacuum and C. We define C, P and CP symmetries at each Pauli frame specified by a generalized Pauli-Gursey transformation. The Majorana neutrinos in the C and P violating seesaw model are then naturally defined by a suitable choice of the Pauli frame, where only Dirac-type fermions appear with well-defined C, P and CP, and thus the C symmetry for Majorana neutrinos agrees with the C symmetry for Dirac-type fermions. This fully symmetric setting corresponds to the idea of Majorana neutrinos as Bogoliubov quasi-particles. In contrast, the conventional direct construction of Majorana neutrinos in the seesaw model, where CP is well-defined but C and P are violated, encounters the mismatch of C symmetry for Majorana neutrinos and C symmetry for chiral fermions; this mismatch is recognized as the inevitable appearance of the singlet (trivial) representation of C symmetry for chiral fermions., Comment: 15 pages. Slightly expanded with some explanatory paragraphs added. This version is going to appear in Phys.Lett. B

It is shown that the specific "charge conjugation" transformation used to define the Majorana fermions in the conventional seesaw mechanism, namely $(\nu_{R})^{C}=C\bar{\nu_{R}}^{T}$ for a chiral fermion $\nu_{R}$ (and similarly for $\nu_{L}$), is a hidden symmetry associated with CP symmetry, and thus it formally holds independently of the P- and C-violating terms in the CP invariant Lagrangian and it is in principle applicable to charged leptons and quarks as well. This hidden symmetry, however, is not supported by a consistent unitary operator and thus it leads to mathematical (operatorial) ambiguities. When carefully examined, it also fails as a classical transformation law in a Lorentz invariant field theory. To distinguish it from the standard charge conjugation symmetry, we suggest for it the name of pseudo C-symmetry. The pseudo C-symmetry is effective to identify Majorana neutrinos analogously to the classical Majorana condition. The analysis of CP breaking in weak interactions is performed using the conventional CP transformation, which is defined independently of the pseudo C-transformation, in the seesaw model after mass diagonalization. A way to ensure an operatorially consistent formulation of C-conjugation is to formulate the seesaw scheme by invoking a relativistic analogue of the Bogoliubov transformation., Comment: 16 pages. Some modifications in Abstract and in the body of the manuscript. This version is going to appear in European Physical Journal C

In view of the recent applications of chiral anomaly to various fields beyond particle physics, we discuss some basic aspects of chiral anomaly which may help deepen our understanding of chiral anomaly in particle physics also. It is first shown that Berry's phase (and its generalization) for the Weyl model $H =v_{F} \vec{\sigma}\cdot \vec{p}(t)$ assumes a monopole form at the exact adiabatic limit but deviates from it off the adiabatic limit and vanishes in the high frequency limit of the Fourier transform of $\vec{p}(t)$ for bounded $|\vec{p}(t)|$. An effective action, which is consistent with the non-adiabatic limit of Berry's phase, combined with the Bjorken-Johnson-Low prescription gives normal equal-time space-time commutators and no chiral anomaly. In contrast, an effective action with a monopole at the origin of the momentum space, which describes Berry's phase in the precise adiabatic limit but fails off the adiabatic limit, gives anomalous space-time commutators and a covariant anomaly to the gauge current. We regard this anomaly as an artifact of the postulated monopole and not a consequence of Berry's phase. As for the recent application of the chiral anomaly to the description of effective Weyl fermions in condensed matter and nuclear physics, which is closely related to the formulation of lattice chiral fermions, we point out that the chiral anomaly for each species doubler separately vanishes for a finite lattice spacing, contrary to the common assumption. Instead a general form of pair creation associated with the spectral flow for the Dirac sea with finite depth takes place. This view is supported by the Ginsparg-Wilson fermion, which defines a single Weyl fermion without doublers on the lattice and gives a well-defined index (anomaly) even for a finite lattice spacing., Comment: 14 pages. Some explanations are added. This version is to be published in PRD

Medaka fish (Oryzias latipes) were whole-bodily treated with various doses of mitomycin C (MMC), ethylmethanesulfonate (EMS), cyclophosphamide (CP), diethylnitrosamine (DEN), or colchicine (COL) for 24 h, and the frequency of micronucleated cells (MNCs) was measured in the gills at 24 and 48 h after treatment. In the present experiments, MMC, CP, and DEN were recorded as efficient inducers of micronuclei at both sampling times, and none of the MNC frequencies recorded with these agents at 24 h significantly exceeded the corresponding frequency at 48 h. For EMS and COL, positive responses were recorded only 48 h after treatment. By comparison with the time-course data reported for radiation-induced MNCs in the same MN assay system, the clear responses observed at the 48-h time point for all the chemicals used were regarded as evidence of their delayed effects on micronucleus (MN) formation. The mean sizes of micronuclei induced after exposure to COL was significantly larger by a factor 2 as compared with that induced by X-irradiation, whereas those determined for the other four chemicals were almost equal to that induced by X-irradiation. These results demonstrate that the medaka gill-cell MN assay can detect chemically-induced chromosome damage, either directly or after metabolic activation, and spindle malfunction, and provide a basis for further development of the present assay system for testing cytogenetic activities of chemical agents.

We present a parity-doublet theorem for the representation of the intrinsic parity of Majorana fermions, which is expected to be useful also in condensed matter physics, and it is illustrated to provide a criterion of neutron-antineutron oscillation in a BCS-like effective theory with $\Delta B=2$ baryon number violating terms. The CP violation in the present effective theory causes no direct CP violating effects in the oscillation itself, which is demonstrated by the exact solution, although it influences the neutron electric dipole moment in the leading order of small $\Delta B=2$ parameters. An analogue of Bogoliubov transformation, which preserves P and CP, is crucial in the analysis., Comment: 13 pages

An attempt is made to incorporate the electromagnetic interaction in a Lorentz invariant but CPT violating non-local model with particle-antiparticle mass-splitting, which is regarded as a modified QED. The gauge invariance is maintained by the Schwinger non-integrable phase factor but the electromagnetic interaction breaks C, CP and CPT symmetries. Implications of the present CPT breaking scheme on the electromagnetic transitions and particle-antiparticle pair creation are discussed. The CPT violation such as the one suggested here may open a new path to the analysis of baryon asymmetry since some of the Sakharov constraints are expected to be modified., 12 pages, some remarks added; version to appear in Phys. Lett. B

We present an alternative perspective on the see-saw mechanism for the neutrino mass, according to which the small neutrino mass is given as a difference of two large masses. This view emerges when an analogue of the Bogoliubov transformation is used to describe Majorana neutrinos in the Lagrangian of the see-saw mechanism, which is analogous to the BCS theory. The Bogoliubov transformation clarifies the natural appearance of Majorana fermions when C is strongly violated by the right-handed neutrino mass term with good CP in the single flavor model. Analyzing typical models with $m_{R}$= $10^{4}$ to $10^{15}$ GeV, it is shown that a hitherto unrecognized fine tuning of the order $m_{\nu}/m_{R}=10^{-15}$ to $10^{-26}$ is required to make the commonly perceived see-saw mechanism work in a natural setting, namely, when none of dimensionless coupling constants are very small., Comment: 14 pages; version published in Phys. Lett. B

If one modifies the Dirac equation in momentum space to $[\gamma^{\mu}p_{\mu}-m-\Delta m(\theta(p_{0})-\theta(-p_{0})) \theta(p_{\mu}^{2})]\psi(p)=0$, the symmetry of positive and negative energy eigenvalues is lifted by $m\pm \Delta m$ for a small $\Delta m$. The mass degeneracy of the particle and antiparticle is thus lifted in a Lorentz invariant manner since the combinations $\theta(\pm p_{0})\theta(p_{\mu}^{2})$ with step functions are manifestly Lorentz invariant. We explain an explicit construction of this CPT breaking term in coordinate space, which is Lorentz invariant but non-local at a distance scale of the Planck length. The application of this Lorentz invariant CPT breaking mechanism to the possible mass splitting of the neutrino and antineutrino in the Standard Model is briefly discussed., Comment: Talk given at the Memorial Meeting for Abdus Salam's 90th Birthday, Nanyang Technological University, Singapore, January 25-28, 2016 (to appear in the Proceedings)

The absence of the quadratic divergence in the Higgs sector of the Standard Model in the dimensional regularization is usually regarded to be an exceptional property of a specific regularization. To understand what is going on in the dimensional regularization, we illustrate how to reproduce the results of the dimensional regularization for the $\lambda\phi^{4}$ theory in the more conventional regularization such as the higher derivative regularization; the basic postulate involved is that the quadratically divergent induced mass, which is independent of the scale change of the physical mass, is kinematical and unphysical. This is consistent with the derivation of the Callan-Symanzik equation, which is a comparison of two theories with slightly different masses, for the $\lambda\phi^{4}$ theory without encountering the quadratic divergence. We thus suggest that the dimensional regularization is generic in a bottom-up approach starting with a successful low-energy theory. We also define a modified version of the mass independent renormalization for a scalar field which leads to the homogeneous renormalization group equation. Implications of the present analysis on the Standard Model at high energies and the presence or absence of SUSY at LHC energies are briefly discussed., Comment: 20 pages. To be published in the Proceedings of Conference on New Physics at the Large Hadron Collider, Nanyang Technological University, Singapore, 29 February to 4 March, 2016

The Yang–Mills gauge field theory, which was proposed 60 years ago, is extremely successful in describing the basic interactions of fundamental particles. The Yang–Mills theory in the course of its developments also stimulated many important field theoretical machinery. In this brief review I discuss the path integral techniques, in particular, the fermionic path integrals which were developed together with the successful applications of quantized Yang–Mills field theory. I start with the Faddeev–Popov path integral formula with emphasis on the treatment of fermionic ghosts as an application of Grassmann numbers. I then discuss the ordinary fermionic path integrals and the general treatment of quantum anomalies. The contents of this review are mostly pedagogical except for a recent analysis of path integral bosonization.

The noncontextual hidden variables models in $d=2$, such as the ones constructed by Bell and by Kochen and Specker, have difficulties in accounting for the conditional measurement of two non-orthogonal projectors. An idea of branching in the hidden variables space, which provides a means to realize the notion of reduction effectively and describe the state preparation, is suggested as a way to resolve the difficulties associated with the conditional measurement., 11 pages. Progress of Theoretical Physics (in press). arXiv admin note: text overlap with arXiv:1201.4421

The uncertainty relation and the probability interpretation of quantum mechanics are intrinsically connected, as is evidenced by the evaluation of standard deviations. It is thus natural to ask if one can associate a very small uncertainty product of suitably sampled events with a very small probability. We have shown elsewhere that some examples of the evasion of the uncertainty relation noted in the past are in fact understood in this way. We here numerically illustrate that a very small uncertainty product is realized if one performs a suitable sampling of measured data which occur with a very small probability. It is also shown that our analysis is consistent with the Landau-Pollak type uncertainty relation. It is suggested that the present analysis may help reconcile the contradicting views about the "standard quantum limit" in the detection of gravitational waves., 27 pages, 4 figures. To appear in Progress of Theoretical Physics (kyoto)

The Kennard-type uncertainty relation $\Delta x\Delta p >\frac{\hbar}{2}$ is formulated for a free particle with given momentum < \hat{p}>$ inside a box with periodic boundary conditions in the large box limit. Our construction of a free particle state is analogous to that of the Bloch wave in a periodic potential. A simple Robertson-type relation, which minimizes the effect of the box boundary and may be useful in some practical applications, is also presented., Comment: 17 pages, to appear in Prog. Theor. Phys. (kyoto)