The effect of SU-8 patterned surfaces on the response of the quartz crystal microbalance

In this work we present data showing the effect of patterning layers of SU-8 photoresist on a quartz crystal microbalance (QCM) and subsequent chemical treatment to increase their hydrophobicity. Patterns with 5 mu m diameter pillars spaced every 10 mu m have been fabricated with heights of 3, 5 and 10 mu m in addition to equivalent thickness flat layers. Contact angle measurements have been made before and after the hydrophobic chemical treatment. The change in resonant frequency of the QCM has been investigated as the surfaces were submerged in solutions of water/PEG with changing viscosity-density product

Detection and classification of peaks in 5' cap RNA sequencing data

Background The large-scale sequencing of 5' cap enriched cDNA promises to reveal the diversity of transcription initiation across entire genomes. The process of transcription is noisy, and there is often no single, exact start site. This creates the need for a fast and simple method of identifying transcription start peaks based on this type of data. Due to both biological and technical noise, many of the peaks seen are not real transcription initiation events. Classification of the observed peaks is an essential filtering step in the discovery of genuine initiation locations. Results We develop a two-stage approach consisting of a fast and simple algorithm based on a sliding window with Poisson null distribution for detecting the genomic locations of peaks, followed by a linear support vector machine classifier to distinguish between peaks which represent the initiation of transcription and peaks that do not. Comparison of classification performance to the best existing method based on whole genome segmentation showed comparable precision and improved recall. Internal features, which are intrinsic to the data and require no further experiments, had high precision and recall rates. Addition of pooled external data or matched RNA sequencing data resulted in gains of recall with equivalent precision. Conclusions The Poisson sliding window model is an effective and fast way of taking the peak neighbourhood into account, and finding statistically significant peaks over a range of transcript expression values. It is orders of magnitude faster than doing whole genome segmentation. The support vector classification scheme has better precision and recall than existing methods. Integrating additional datasets is shown to provide minor gains in recall, in comparison to using only the cap-sequencing data

Correction: Detection and classification of peaks in 5' cap RNA sequencing data

[No abstract available

Magnetization process of the spin-1/2 XXZ models on square and cubic lattices

The magnetization process of the spin-1/2 antiferromagnetic XXZ model with Ising-like anisotropy in the ground state is investigated. We show numerically that the Ising-like XXZ models on square and cubic lattices show a first-order phase transition at some critical magnetic field. We estimate the value of the critical field and the magnetization jump on the basis of the Maxwell construction. The magnetization jump in the Ising-limit is investigated by means of perturbation theory. Based on our numerical results, we briefly discuss the phase diagram of the extended Bose-Hubbard model in the hard-core limit.Comment: 13 pages, RevTex, 7 PostScript figures, to appear in Phys.Rev.

Route of Immunization with Peptide-pulsed Dendritic Cells Controls the Distribution of Memory and Effector T Cells in Lymphoid Tissues and Determines the Pattern of Regional Tumor Control

We have established that the route of immunization with peptide-pulsed, activated DC leads to memory CD8+ T cells with distinct distributions in lymphoid tissues, which determines the ability to control tumors growing in different body sites. Both intravenous (i.v.) and subcutaneous (s.c.) immunization induced memory T cells in spleen and control of metastatic-like lung tumors. s.c. immunization also induced memory T cells in lymph nodes (LNs), imparting protection against subcutaneously growing tumors. In contrast, i.v. immunization-induced memory was restricted to spleen and failed to impart protective immunity against subcutaneously growing tumors. Memory cell distribution and tumor control were both linked to injection route–dependent localization of DCs in lymphoid compartments. Using peripheral LN–ablated mice, these LNs were shown to be essential for control of subcutaneously growing tumors but not lung metastases; in contrast, using immunized asplenic mice, we found that the spleen is necessary and sufficient for control of lung tumors, but unnecessary for control of subcutaneously growing tumors. These data demonstrate the existence of a previously undescribed population of splenic-resident memory CD8 T cells that are essential for the control of lung metastases. Thus, regional immunity based on memory T cell residence patterns is an important factor in DC-based tumor immunotherapy

Decay of the metastable phase in d=1 and d=2 Ising models

We calculate perturbatively the tunneling decay rate $\Gamma$ of the metastable phase in the quantum d=1 Ising model in a skew magnetic field near the coexistence line $0<h_{x}<1, h_{z}\to -0$ at T=0. It is shown that $\Gamma$ oscillates in the magnetic field $h_{z}$ due to discreteness of the excitation energy spectrum. After mapping of the obtained results onto the extreme anisotropic d=2 Ising model at $T<T_c$, we verify in the latter model the droplet theory predictions for the free energy analytically continued to the metastable phase. We find also evidence for the discrete-lattice corrections in this metastable phase free energy.Comment: 4 pages, REVTe

A connection between stress and development in the multicelular prokaryote Streptomyces coelicolor

Morphological changes leading to aerial mycelium formation and sporulation in the mycelial bacterium Streptomyces coelicolor rely on establishing distinct patterns of gene expression in separate regions of the colony. sH was identified previously as one of three paralogous sigma factors associated with stress responses in S. coelicolor. Here, we show that sigH and the upstream gene prsH (encoding a putative antisigma factor of sH) form an operon transcribed from two developmentally regulated promoters, sigHp1 and sigHp2. While sigHp1 activity is confined to the early phase of growth, transcription of sigHp2 is dramatically induced at the time of aerial hyphae formation. Localization of sigHp2 activity using a transcriptional fusion to the green fluorescent protein reporter gene (sigHp2–egfp) showed that sigHp2 transcription is spatially restricted to sporulating aerial hyphae in wild-type S. coelicolor. However, analysis of mutants unable to form aerial hyphae (bld mutants) showed that sigHp2 transcription and sH protein levels are dramatically upregulated in a bldD mutant, and that the sigHp2–egfp fusion was expressed ectopically in the substrate mycelium in the bldD background. Finally, a protein possessing sigHp2 promoter-binding activity was purified to homogeneity from crude mycelial extracts of S. coelicolor and shown to be BldD. The BldD binding site in the sigHp2 promoter was defined by DNase I footprinting. These data show that expression of sH is subject to temporal and spatial regulation during colony development, that this tissue-specific regulation is mediated directly by the developmental transcription factor BldD and suggest that stress and developmental programmes may be intimately connected in Streptomyces morphogenesis

Developing hierarchically porous MnO_<em>x</em>/NC hybrid nanorods for oxygen reduction and evolution catalysis

Electrochemical oxygen reduction and evolution reactions (ORR and OER) play a vital role in the field of energy conversion and storage. The problem is that both processes are sluggish, requiring precious-metal catalysts. Here, starting from abundant precursors and using a simple synthesis approach, we report the preparation of a good bifunctional oxygen electro-catalyst: a composite nanorod of manganese oxides and nitrogen-doped carbon. This material has hierarchical porosity, facilitating the mass transfer within the electrode. The nitrogen-doped carbon forms contiguous 3D network, connecting the isolated MnOx nanoparticles and ensuring superior electrical conductivity. Importantly, the MnOx particles contain manganese of mixed oxidation states; aligned with the nitrogen-doped carbon, this hybrid is among the best non-noble-metal ORR/OER catalysts in alkaline media, outperforming even Pt and RuO2 catalysts.Peer reviewed: YesNRC publication: Ye

The role of interparticle heterogeneities in the selenization pathway of Cu Zn Sn S nanoparticle thin films a real time study

Real time energy dispersive X ray diffraction EDXRD analysis has been utilized to observe the selenization of Cu Zn Sn S nanoparticle films coated from three nanoparticle populations Cu and Sn rich particles roughly 5 nm in size, Zn rich nanoparticles ranging from 10 to 20 nm in diameter, and a mixture of both types of nanoparticles roughly 1 1 by mass , which corresponds to a synthesis recipe yielding CZTSSe solar cells with reported total area efficiencies as high as 7.9 . The EDXRD studies presented herein show that the formation of copper selenide intermediates during the selenization of mixed particle films can be primarily attributed to the small, Cu and Sn rich particles. Moreover, the formation of these copper selenide phases represents the first stage of the CZTSSe grain growth mechanism. The large, Zn rich particles subsequently contribute their composition to form micrometer sized CZTSSe grains. These findings enable further development of a previously proposed selenization pathway to account for the roles of interparticle heterogeneities, which in turn provides a valuable guide for future optimization of processes to synthesize high quality CZTSSe absorber layer