SciRecSys: A Recommendation System for Scientific Publication by Discovering Keyword Relationships

In this work, we propose a new approach for discovering various relationships among keywords over the scientific publications based on a Markov Chain model. It is an important problem since keywords are the basic elements for representing abstract objects such as documents, user profiles, topics and many things else. Our model is very effective since it combines four important factors in scientific publications: content, publicity, impact and randomness. Particularly, a recommendation system (called SciRecSys) has been presented to support users to efficiently find out relevant articles

Quantum theory of a micromaser operating on the atomic scattering from a resonant standing wave

Journals published by the American Physical Society can be found at http://publish.aps.org/We study the amplification of a resonant standing-wave light field due to the interaction with a beam of monovelocity two-level atoms moving in the Raman-Nath regime and in the Bragg regime. The atomic density is low so that, at most, one atom is inside the cavity at a time. This system is very similar to the well-known micromaser but it is operating in the optical region of the field frequencies. Therefore, the situation corresponds to a microlaser, Unlike the micromaser system, the momentum transfer between the atoms and photons in the microlaser essentially effects the center-of-mass motion of the atoms and the evolution of the field

Effect of an atom on a quantum guided field in a weakly driven fiber-Bragg-grating cavity

We study the interaction of an atom with a quantum guided field in a weakly driven fiber-Bragg-grating (FBG) cavity. We present an effective Hamiltonian and derive the density-matrix equations for the combined atom-cavity system. We calculate the mean photon number, the second-order photon correlation function, and the atomic excited-state population. We show that, due to the confinement of the guided cavity field in the fiber cross-section plane and in the space between the FBG mirrors, the presence of the atom in the FBG cavity can significantly affect the mean photon number and the photon statistics even though the cavity finesse is moderate, the cavity is long, and the probe field is weak.Comment: Accepted for Phys. Rev.

Force of light on a two-level atom near an ultrathin optical fiber

We study the force of light on a two-level atom near an ultrathin optical fiber using the mode function method and the Green tensor technique. We show that the total force consists of the driving-field force, the spontaneous-emission recoil force, and the fiber-induced van der Waals potential force. Due to the existence of a nonzero axial component of the field in a guided mode, the Rabi frequency and, hence, the magnitude of the force of the guided driving field may depend on the propagation direction. When the atomic dipole rotates in the meridional plane, the spontaneous-emission recoil force may arise as a result of the asymmetric spontaneous emission with respect to opposite propagation directions. The van der Waals potential for the atom in the ground state is off-resonant and opposite to the off-resonant part of the van der Waals potential for the atom in the excited state. Unlike the potential for the ground state, the potential for the excited state may oscillate depending on the distance from the atom to the fiber surface

Optical nanofibers and spectroscopy

We review our recent progress in the production and characterization of tapered optical fibers with a sub-wavelength diameter waist. Such fibers exhibit a pronounced evanescent field and are therefore a useful tool for highly sensitive evanescent wave spectroscopy of adsorbates on the fiber waist or of the medium surrounding. We use a carefully designed flame pulling process that allows us to realize preset fiber diameter profiles. In order to determine the waist diameter and to verify the fiber profile, we employ scanning electron microscope measurements and a novel accurate in situ optical method based on harmonic generation. We use our fibers for linear and non-linear absorption and fluorescence spectroscopy of surface-adsorbed organic molecules and investigate their agglomeration dynamics. Furthermore, we apply our spectroscopic method to quantum dots on the surface of the fiber waist and to caesium vapor surrounding the fiber. Finally, towards dispersive measurements, we present our first results on building and testing a single-fiber bi-modal interferometer.Comment: 13 pages, 18 figures. Accepted for publication in Applied Physics B. Changes according to referee suggestions: changed title, clarification of some points in the text, added references, replacement of Figure 13

Dark States and Interferences in Cascade Transitions of Ultra-Cold Atoms in a Cavity

We examine the competition among one- and two-photon processes in an ultra-cold, three-level atom undergoing cascade transitions as a result of its interaction with a bimodal cavity. We show parameter domains where two-photon transitions are dominant and also study the effect of two-photon emission on the mazer action in the cavity. The two-photon emission leads to the loss of detailed balance and therefore we obtain the photon statistics of the cavity field by the numerical integration of the master equation. The photon distribution in each cavity mode exhibits sub- and super- Poissonian behaviors depending on the strength of atom-field coupling. The photon distribution becomes identical to a Poisson distribution when the atom-field coupling strengths of the modes are equal.Comment: 15 pages including 7 figures in Revtex, submitted to PR

Gene expression profile of AIDS-related Kaposi's sarcoma

BACKGROUND: Kaposi's Sarcoma (KS) is a proliferation of aberrant vascular structures lined by spindle cells, and is caused by a gammaherpes virus (HHV8/KSHV). Its course is aggravated by co-infection with HIV-1, where the timing of infection with HIV-1 and HHV8 is important for the clinical outcome. METHODS: In order to better understand the pathogenesis of KS, we have analysed tissue from two AIDS-KS lesions, and from normal skin by serial analysis of gene expression (SAGE). Semi-quantitative RT-PCR was then used to validate the results. RESULTS: The expression profile of AIDS-related KS (AIDS-KS) reflects an active process in the skin. Transcripts of HHV8 were found to be very low, and HIV-1 mRNA was not detected by SAGE, although it could be found using RT-PCR. Comparing the expression profile of AIDS-KS tissue with publicly available SAGE libraries suggested that AIDS-KS mRNA levels are most similar to those in an artificially mixed library of endothelial cells and leukocytes, in line with the description of KS lesions as containing spindle cells with endothelial characteristics, and an inflammatory infiltrate. At least 64 transcripts were found to be significantly elevated, and 28 were statistically downregulated in AIDS-KS compared to normal skin. Five of the upregulated mRNAs, including Tie 1 and sialoadhesin/CD169, were confirmed by semi-quantitative PCR to be elevated in additional AIDS-KS biopsies. Antibodies to sialoadhesin/CD169, a known marker of activated macrophages, were shown to specifically label tumour macrophages. CONCLUSION: The expression profile of AIDS-KS showed 64 genes to be significantly upregulated, and 28 genes downregulated, compared with normal skin. One of the genes with increased expression was sialoadhesin (CD169). Antibodies to sialoadhesin/CD169 specifically labelled tumour-associated macrophages, suggesting that macrophages present in AIDS-KS lesions belong to a subset of human CD169+ macrophages

Genomic insights into rapid speciation within the world's largest tree genus Syzygium

Acknowledgements Y.W.L. was supported by a postgraduate scholarship research grant from the Ministry of National Development, Singapore awarded through the National Parks Board, Singapore (NParks; NParks’ Garden City Fund). Principal research funding from NParks and the School of Biological Sciences (SBS), Nanyang Technological University (NTU), Singapore, is acknowledged. We thank Peter Preiser, Associate Vice President for Biomedical and Life Sciences, for facilitating NTU support, and Kenneth Er, CEO of NParks, for facilitating research funding through that organisation. V.A.A. and C.L. were funded by SBS, NTU for a one-year research leave. V.A.A. and C.L. also acknowledge support from the United States National Science Foundation (grants 2030871 and 1854550, respectively). S.R. was supported by a postdoctoral research fellowship under the NTU Strategic Plant Programme. S.R. and N.R.W.C. acknowledge funding from NTU start-up and the Academy of Finland (decisions 318288, 319947) grants to J.S. Fieldwork conducted by Y.W.L. was supported by an Indonesian Government RISTEK research permit (Application ID: 1517217008) and an Access License from the Sabah State government [JKM/MBS.1000-2/2JLD.7(84)]. T.N.C.V. is grateful to the Assemblée de la Province Nord and Assemblée de la Province Sud (New Caledonia) for facilitating relevant collection permits. A.N. was partly supported by the Research Project Promotion Grant (Strategic Research Grant No. 17SP01302) from the University of the Ryukyus, and partly by the Environment Research and Technology Development Fund (JPMEERF20204003) from the Environmental Restoration and Conservation Agency of Japan. Fieldwork in Fiji conducted by R.B. was hosted and facilitated by Elina Nabubuniyaka-Young (The Pacific Community’s Centre for Pacific Crops and Trees, Fiji). We thank the NTU-Smithsonian Partnership for tree data obtained for the Bukit Timah Nature Reserve (BTNR) long-term forest dynamics plots. Administrative support provided by Mui Hwang Khoo-Woon and Peter Ang at the molecular laboratory of the Singapore Botanic Gardens (SBG) is acknowledged. Rosie Woods and Imalka Kahandawala (DNA and Tissue Bank, Royal Botanic Gardens, Kew) facilitated additional DNA samples. Daniel Thomas (SBG) and Yan Yu (Sichuan University) commented on biogeographical analyses. NovogeneAIT in Singapore is acknowledged for personalised sequencing service.Peer reviewedPublisher PD

Genomic insights into rapid speciation within the world's largest tree genus Syzygium

The relative importance of the mechanisms underlying species radiation remains unclear. Here, the authors combine reference genome assembly and population genetics analyses to show that neutral forces have contributed to the radiation of the most species-rich tree genus Syzygium. Species radiations, despite immense phenotypic variation, can be difficult to resolve phylogenetically when genetic change poorly matches the rapidity of diversification. Genomic potential furnished by palaeopolyploidy, and relative roles for adaptation, random drift and hybridisation in the apportionment of genetic variation, remain poorly understood factors. Here, we study these aspects in a model radiation, Syzygium, the most species-rich tree genus worldwide. Genomes of 182 distinct species and 58 unidentified taxa are compared against a chromosome-level reference genome of the sea apple, Syzygium grande. We show that while Syzygium shares an ancient genome doubling event with other Myrtales, little evidence exists for recent polyploidy events. Phylogenomics confirms that Syzygium originated in Australia-New Guinea and diversified in multiple migrations, eastward to the Pacific and westward to India and Africa, in bursts of speciation visible as poorly resolved branches on phylogenies. Furthermore, some sublineages demonstrate genomic clines that recapitulate cladogenetic events, suggesting that stepwise geographic speciation, a neutral process, has been important in Syzygium diversification.Peer reviewe