Theory of radiation trapping by the accelerating solitons in optical fibers

We present a theory describing trapping of the normally dispersive radiation by the Raman solitons in optical fibers. Frequency of the radiation component is continuously blue shifting, while the soliton is red shifting. Underlying physics of the trapping effect is in the existence of the inertial gravity-like force acting on light in the accelerating frame of reference. We present analytical calculations of the rate of the opposing frequency shifts of the soliton and trapped radiation and find it to be greater than the rate of the red shift of the bare Raman soliton. Our findings are essential for understanding of the continuous shift of the high frequency edge of the supercontinuum spectra generated in photonic crystal fibers towards higher frequencies.Comment: Several misprints in text and formulas corrected. 10 pages, 9 figures, submitted to Phys. Rev.

Complete Genome Sequence and Comparative Analysis of the Wild-type Commensal Escherichia coli Strain SE11 Isolated from a Healthy Adult

We sequenced and analyzed the genome of a commensal Escherichia coli (E. coli) strain SE11 (O152:H28) recently isolated from feces of a healthy adult and classified into E. coli phylogenetic group B1. SE11 harbored a 4.8 Mb chromosome encoding 4679 protein-coding genes and six plasmids encoding 323 protein-coding genes. None of the SE11 genes had sequence similarity to known genes encoding phage- and plasmid-borne virulence factors found in pathogenic E. coli strains. The comparative genome analysis with the laboratory strain K-12 MG1655 identified 62 poorly conserved genes between these two non-pathogenic strains and 1186 genes absent in MG1655. These genes in SE11 were mostly encoded in large insertion regions on the chromosome or in the plasmids, and were notably abundant in genes of fimbriae and autotransporters, which are cell surface appendages that largely contribute to the adherence ability of bacteria to host cells and bacterial conjugation. These data suggest that SE11 may have evolved to acquire and accumulate the functions advantageous for stable colonization of intestinal cells, and that the adhesion-associated functions are important for the commensality of E. coli in human gut habitat

Model-based probe set optimization for high-performance microarrays

A major challenge in microarray design is the selection of highly specific oligonucleotide probes for all targeted genes of interest, while maintaining thermodynamic uniformity at the hybridization temperature. We introduce a novel microarray design framework (Thermodynamic Model-based Oligo Design Optimizer, TherMODO) that for the first time incorporates a number of advanced modelling features: (i) A model of position-dependent labelling effects that is quantitatively derived from experiment. (ii) Multi-state thermodynamic hybridization models of probe binding behaviour, including potential cross-hybridization reactions. (iii) A fast calibrated sequence-similarity-based heuristic for cross-hybridization prediction supporting large-scale designs. (iv) A novel compound score formulation for the integrated assessment of multiple probe design objectives. In contrast to a greedy search for probes meeting parameter thresholds, this approach permits an optimization at the probe set level and facilitates the selection of highly specific probe candidates while maintaining probe set uniformity. (v) Lastly, a flexible target grouping structure allows easy adaptation of the pipeline to a variety of microarray application scenarios. The algorithm and features are discussed and demonstrated on actual design runs. Source code is available on request

Stokes solitons in optical microcavities

Solitons are wave packets that resist dispersion through a self-induced potential well. They are studied in many fields, but are especially well known in optics on account of the relative ease of their formation and control in optical fibre waveguides. Besides their many interesting properties, solitons are important to optical continuum generation, in mode-locked lasers, and have been considered as a natural way to convey data over great distances. Recently, solitons have been realized in microcavities, thereby bringing the power of microfabrication methods to future applications. This work reports a soliton not previously observed in optical systems, the Stokes soliton. The Stokes soliton forms and regenerates by optimizing its Raman interaction in space and time within an optical potential well shared with another soliton. The Stokes and the initial soliton belong to distinct transverse mode families and benefit from a form of soliton trapping that is new to microcavities and soliton lasers in general. The discovery of a new optical soliton can impact work in other areas of photonics, including nonlinear optics and spectroscopy

Stimulation of lymphocyte anti-melanoma activity by co-cultured macrophages activated by complex homeopathic medication

<p>Abstract</p> <p>Background</p> <p>Melanoma is the most aggressive form of skin cancer, and the most rapidly expanding cancer in terms of worldwide incidence. Chemotherapeutic approaches to treat melanoma have been uniformly disappointing. A Brazilian complex homeopathic medication (CHM), used as an immune modulator, has been recommended for patients with depressed immune systems. Previous studies in mice have demonstrated that the CHM activates macrophages, induces an increase in the number of leukocytes and improves the murine response against Sarcoma-180.</p> <p>Methods</p> <p>Here we studied the interaction of mouse lymph node lymphocytes, co-cultured <it>in vitro </it>with macrophages in the presence or absence of the CHM, with B16F10 melanoma cells.</p> <p>Results</p> <p>Lymphocytes co-cultured with macrophages in the presence of the CHM had greater anti-melanoma activity, reducing melanoma cell density and increasing the number of lysed tumor cells. There was also a higher proportion of activated (CD25⁺) lymphocytes with increased viability. Overall, lymphocytes activated by treatment destroyed growing cancer cells more effectively than control lymphocytes.</p> <p>Conclusion</p> <p>Co-culture of macrophages with lymphocytes in the presence of the CHM enhanced the anti-cancer performance of lymphocytes against a very aggressive lineage of melanoma cells. These results suggest that non-toxic therapies using CHMs are a promising alternative approach to the treatment of melanomas. In addition, they are attractive combination-therapy candidates, which may enhance the efficacy of conventional medicines by improving the immune response against tumor cells.</p

Real-time observation of dissipative soliton formation in nonlinear polarization rotation mode-locked fibre lasers

Formation of coherent structures and patterns from unstable uniform state or noise is a fundamental physical phenomenon that occurs in various areas of science ranging from biology to astrophysics. Understanding of the underlying mechanisms of such processes can both improve our general interdisciplinary knowledge about complex nonlinear systems and lead to new practical engineering techniques. Modern optics with its high precision measurements offers excellent test-beds for studying complex nonlinear dynamics, though capturing transient rapid formation of optical solitons is technically challenging. Here we unveil the build-up of dissipative soliton in mode-locked fibre lasers using dispersive Fourier transform to measure spectral dynamics and employing autocorrelation analysis to investigate temporal evolution. Numerical simulations corroborate experimental observations, and indicate an underlying universality in the pulse formation. Statistical analysis identifies correlations and dependencies during the build-up phase. Our study may open up possibilities for real-time observation of various nonlinear structures in photonic systems

Coherent master equation for laser modelocking

Modelocked lasers constitute the fundamental source of optically-coherent ultrashort-pulsed radiation, with huge impact in science and technology. Their modeling largely rests on the master equation (ME) approach introduced in 1975 by Hermann A. Haus. However, that description fails when the medium dynamics is fast and, ultimately, when light-matter quantum coherence is relevant. Here we set a rigorous and general ME framework, the coherent ME (CME), that overcomes both limitations. The CME predicts strong deviations from Haus ME, which we substantiate through an amplitude-modulated semiconductor laser experiment. Accounting for coherent effects, like the Risken-Nummedal-Graham-Haken multimode instability, we envisage the usefulness of the CME for describing self-modelocking and spontaneous frequency comb formation in quantum-cascade and quantum-dot lasers. Furthermore, the CME paves the way for exploiting the rich phenomenology of coherent effects in laser design, which has been hampered so far by the lack of a coherent ME formalism

Unplanned readmission rates, length of hospital stay, mortality, and medical costs of ten common medical conditions: a retrospective analysis of Hong Kong hospital data

<p>Abstract</p> <p>Background</p> <p>Studies on readmissions attributed to particular medical conditions, especially heart failure, have generally not addressed the factors associated with readmissions and the implications for health outcomes and costs. This study aimed to investigate the factors associated with 30-day unplanned readmission for 10 common conditions and to determine the cost implications.</p> <p>Methods</p> <p>This population-based retrospective cohort study included patients admitted to all public hospitals in Hong Kong in 2007. The sample consisted of 337,694 hospitalizations in Internal Medicine. The disease-specific risk-adjusted odd ratio (OR), length of stay (LOS), mortality and attributable medical costs for the year were examined for unplanned readmissions for 10 medical conditions, namely malignant neoplasms, heart diseases, cerebrovascular diseases, pneumonia, injury and poisoning, nephritis and nephrosis, diabetes mellitus, chronic liver disease and cirrhosis, septicaemia, and aortic aneurysm.</p> <p>Results</p> <p>The overall unplanned readmission rate was 16.7%. Chronic liver disease and cirrhosis had the highest OR (1.62, 95% confidence interval (CI) 1.39-1.87). Patients with cerebrovascular disease had the longest LOS, with mean acute and rehabilitation stays of 6.9 and 3.0 days, respectively. Malignant neoplasms had the highest mortality rate (30.8%) followed by aortic aneurysm and pneumonia. The attributed medical cost of readmission was highest for heart disease (US$3 199 418, 95$2 579 443-803 393).</p> <p>Conclusions</p> <p>Our findings showed variations in readmission rates and mortality for different medical conditions which may suggest differences in the quality of care provided for various medical conditions. In-hospital care, comprehensive discharge planning, and post-discharge community support for patients need to be reviewed to improve the quality of care and patient health outcomes.</p

The Convex Geometry of Linear Inverse Problems

In applications throughout science and engineering one is often faced with the challenge of solving an ill-posed inverse problem, where the number of available measurements is smaller than the dimension of the model to be estimated. However in many practical situations of interest, models are constrained structurally so that they only have a few degrees of freedom relative to their ambient dimension. This paper provides a general framework to convert notions of simplicity into convex penalty functions, resulting in convex optimization solutions to linear, underdetermined inverse problems. The class of simple models considered are those formed as the sum of a few atoms from some (possibly infinite) elementary atomic set; examples include well-studied cases such as sparse vectors and low-rank matrices, as well as several others including sums of a few permutations matrices, low-rank tensors, orthogonal matrices, and atomic measures. The convex programming formulation is based on minimizing the norm induced by the convex hull of the atomic set; this norm is referred to as the atomic norm. The facial structure of the atomic norm ball carries a number of favorable properties that are useful for recovering simple models, and an analysis of the underlying convex geometry provides sharp estimates of the number of generic measurements required for exact and robust recovery of models from partial information. These estimates are based on computing the Gaussian widths of tangent cones to the atomic norm ball. When the atomic set has algebraic structure the resulting optimization problems can be solved or approximated via semidefinite programming. The quality of these approximations affects the number of measurements required for recovery. Thus this work extends the catalog of simple models that can be recovered from limited linear information via tractable convex programming

Immune Cell Recruitment and Cell-Based System for Cancer Therapy

Immune cells, such as cytotoxic T lymphocytes, natural killer cells, B cells, and dendritic cells, have a central role in cancer immunotherapy. Conventional studies of cancer immunotherapy have focused mainly on the search for an efficient means to prime/activate tumor-associated antigen-specific immunity. A systematic understanding of the molecular basis of the trafficking and biodistribution of immune cells, however, is important for the development of more efficacious cancer immunotherapies. It is well established that the basis and premise of immunotherapy is the accumulation of effective immune cells in tumor tissues. Therefore, it is crucial to control the distribution of immune cells to optimize cancer immunotherapy. Recent characterization of various chemokines and chemokine receptors in the immune system has increased our knowledge of the regulatory mechanisms of the immune response and tolerance based on immune cell localization. Here, we review the immune cell recruitment and cell-based systems that can potentially control the systemic pharmacokinetics of immune cells and, in particular, focus on cell migrating molecules, i.e., chemokines, and their receptors, and their use in cancer immunotherapy