High-Q exterior whispering gallery modes in a metal-coated microresonator

We propose a kind of plasmonic whispering gallery modes highly localized on the exterior surface of a metal-coated microresonator. This exterior (EX) surface mode possesses high quality factors at room temperature, and can be efficiently excited by a tapered fiber. The EX mode can couple to an interior (IN) mode and this coupling produces a strong anti-crossing behavior, which not only allows conversion of IN to EX modes, but also forms a long-lived anti-symmetric mode. As a potential application, the EX mode could be used for a biosensor with a sensitivity high up to 500 nm per refraction index unit, a large figure of merit, and a wide detection range

A new regularized least squares support vector regression for gene selection

<p>Abstract</p> <p>Background</p> <p>Selection of influential genes with microarray data often faces the difficulties of a large number of genes and a relatively small group of subjects. In addition to the curse of dimensionality, many gene selection methods weight the contribution from each individual subject equally. This equal-contribution assumption cannot account for the possible dependence among subjects who associate similarly to the disease, and may restrict the selection of influential genes.</p> <p>Results</p> <p>A novel approach to gene selection is proposed based on kernel similarities and kernel weights. We do not assume uniformity for subject contribution. Weights are calculated via regularized least squares support vector regression (RLS-SVR) of class levels on kernel similarities and are used to weight subject contribution. The cumulative sum of weighted expression levels are next ranked to select responsible genes. These procedures also work for multiclass classification. We demonstrate this algorithm on acute leukemia, colon cancer, small, round blue cell tumors of childhood, breast cancer, and lung cancer studies, using kernel Fisher discriminant analysis and support vector machines as classifiers. Other procedures are compared as well.</p> <p>Conclusion</p> <p>This approach is easy to implement and fast in computation for both binary and multiclass problems. The gene set provided by the RLS-SVR weight-based approach contains a less number of genes, and achieves a higher accuracy than other procedures.</p

Resonant spin Hall conductance in quantum Hall systems lacking bulk and structural inversion symmetry

Following a previous work [Shen, Ma, Xie and Zhang, Phys. Rev. Lett. 92, 256603 (2004)] on the resonant spin Hall effect, we present detailed calculations of the spin Hall conductance in two-dimensional quantum wells in a strong perpendicular magnetic field. The Rashba coupling, generated by spin-orbit interaction in wells lacking bulk inversion symmetry, introduces a degeneracy of Zeeman-split Landau levels at certain magnetic fields. This degeneracy, if occuring at the Fermi energy, will induce a resonance in the spin Hall conductance below a characteristic temperature of order of the Zeeman energy. At very low temperatures, the spin Hall current is highly non-ohmic. The Dresselhaus coupling due to the lack of structure inversion symmetry partially or completely suppresses the spin Hall resonance. The condition for the resonant spin Hall conductance in the presence of both Rashba and Dresselhaus couplings is derived using a perturbation method. In the presence of disorder, we argue that the resonant spin Hall conductance occurs when the two Zeeman split extended states near the Fermi level becomes degenerate due to the Rashba coupling and that the the quantized charge Hall conductance changes by 2e^2/h instead of e^2/h as the magnetic field changes through the resonant field.Comment: 9 pages, 7 figures. This is a sequel to Physical Review Letters 90, 256603 (2004

Discovering Chromatin Motifs using FAIRE Sequencing and the Human Diploid Genome

Background: Specific chromatin structures are associated with active or inactive gene transcription. The gene regulatory elements are intrinsically dynamic and alternate between inactive and active states through the recruitment of DNA binding proteins, such as chromatin-remodeling proteins. Results: We developed a unique genome-wide method to discover DNA motifs associated with chromatin accessibility using formaldehyde-assisted isolation of regulatory elements with high-throughput sequencing (FAIRE-seq). We aligned the FAIRE-seq reads to the GM12878 diploid genome and subsequently identified differential chromatin-state regions (DCSRs) using heterozygous SNPs. The DCSR pairs represent the locations of imbalances of chromatin accessibility between alleles and are ideal to reveal chromatin motifs that may directly modulate chromatin accessibility. In this study, we used DNA 6-10mer sequences to interrogate all DCSRs, and subsequently discovered conserved chromatin motifs with significant changes in the occurrence frequency. To investigate their likely roles in biology, we studied the annotated protein associated with each of the top ten chromatin motifs genome-wide, in the intergenic regions and in genes, respectively. As a result, we found that most of these annotated motifs are associated with chromatin remodeling, reflecting their significance in biology. Conclusions: Our method is the first one using fully phased diploid genome and FAIRE-seq to discover motifs associated with chromatin accessibility. Our results were collected to construct the first chromatin motif database (CMD), providing the potential DNA motifs recognized by chromatin-remodeling proteins and is freely available at http://syslab.nchu.edu.tw/chromatin

Impact of preoperative therapy on patterns of recurrence in pancreatic cancer

AbstractBackgroundA theoretical advantage of preoperative therapy in pancreatic adenocarcinoma is that it facilitates the early treatment of micrometastases and reduces postoperative systemic recurrence.MethodsMedical records of 309 consecutive patients undergoing resection of adenocarcinoma in the head of the pancreas were reviewed. Survival was calculated using the Kaplan–Meier method. Associations between preoperative therapy and patterns of recurrence were determined using chi-squared analysis.ResultsPreoperative therapy was administered to 108 patients and upfront surgery was performed in 201 patients. Preoperative therapy was associated with a significantly longer median disease-free survival of 14 months compared with 12 months in patients submitted to upfront surgery (P = 0.035). The rate of local disease as a component of first site of recurrence was significantly lower with preoperative therapy (11.3%) than with upfront surgery (22.9%) (P = 0.016). Preoperative therapy was associated with a lower rate of hepatic metastasis (21.7%) than upfront surgery (34.3%) (P = 0.026). Preoperative therapy did not affect rates of peritoneal or pulmonary metastasis.ConclusionsPreoperative therapy for pancreatic cancer was associated with longer disease-free survival and lower rates of local and hepatic recurrences. These data support the use of preoperative therapy to reduce systemic and local failures after resection

Coupling of a Single Diamond Nanocrystal to a Whispering-Gallery Microcavity: Photon Transportation Benefitting from Rayleigh Scattering

We study the Rayleigh scattering induced by a diamond nanocrystal in a whispering-gallery-microcavity--waveguide coupling system, and find that it plays a significant role in the photon transportation. On one hand, this study provides a new insight into future solid-state cavity quantum electrodynamics toward strong coupling physics. On the other hand, benefitting from this Rayleigh scattering, novel photon transportation such as dipole induced transparency and strong photon antibunching can occur simultaneously. As potential applications, this system can function as high-efficiency photon turnstiles. In contrast to [B. Dayan \textit{et al.}, \textrm{Science} \textbf{319},1062 (2008)], the photon turnstiles proposed here are highly immune to nanocrystal's azimuthal position.Comment: 4 pages, 4 figure

Discovery of Stable and Selective Antibody Mimetics from Combinatorial Libraries of Polyvalent, Loop-Functionalized Peptoid Nanosheets.

The ability of antibodies to bind a wide variety of analytes with high specificity and high affinity makes them ideal candidates for therapeutic and diagnostic applications. However, the poor stability and high production cost of antibodies have prompted exploration of a variety of synthetic materials capable of specific molecular recognition. Unfortunately, it remains a fundamental challenge to create a chemically diverse population of protein-like, folded synthetic nanostructures with defined molecular conformations in water. Here we report the synthesis and screening of combinatorial libraries of sequence-defined peptoid polymers engineered to fold into ordered, supramolecular nanosheets displaying a high spatial density of diverse, conformationally constrained peptoid loops on their surface. These polyvalent, loop-functionalized nanosheets were screened using a homogeneous Förster resonance energy transfer (FRET) assay for binding to a variety of protein targets. Peptoid sequences were identified that bound to the heptameric protein, anthrax protective antigen, with high avidity and selectivity. These nanosheets were shown to be resistant to proteolytic degradation, and the binding was shown to be dependent on the loop display density. This work demonstrates that key aspects of antibody structure and function-the creation of multivalent, combinatorial chemical diversity within a well-defined folded structure-can be realized with completely synthetic materials. This approach enables the rapid discovery of biomimetic affinity reagents that combine the durability of synthetic materials with the specificity of biomolecular materials

PYCR1 and PYCR2 Interact and Collaborate with RRM2B to Protect Cells from Overt Oxidative Stress

Ribonucleotide reductase small subunit B (RRM2B) is a stress response protein that protects normal human fibroblasts from oxidative stress. However, the underlying mechanism that governs this function is not entirely understood. To identify factors that interact with RRM2B and mediate anti-oxidation function, large-scale purification of human Flag-tagged RRM2B complexes was performed. Pyrroline-5-carboxylate reductase 1 and 2 (PYCR1, PYCR2) were identified by mass spectrometry analysis as components of RRM2B complexes. Silencing of both PYCR1 and PYCR2 by expressing short hairpin RNAs induced defects in cell proliferation, partial fragmentation of the mitochondrial network, and hypersensitivity to oxidative stress in hTERT-immortalized human foreskin fibroblasts (HFF-hTERT). Moderate overexpression of RRM2B, comparable to stress-induced level, protected cells from oxidative stress. Silencing of both PYCR1 and PYCR2 completely abolished anti-oxidation activity of RRM2B, demonstrating a functional collaboration of these metabolic enzymes in response to oxidative stress