Electronic Structure in Gapped Graphene with Coulomb Potential

In this paper, we numerically study the bound electron states induced by long range Coulomb impurity in gapped graphene and the quasi-bound states in supercritical region based on the lattice model. We present a detailed comparison between our numerical simulations and the prediction of the continuum model which is described by the Dirac equation in (2+1)-dimensional Quantum Electrodynamics (QED). We also use the Fano's formalism to investigate the quasi-bound state development and design an accessible experiments to test the decay of the supercritical vacuum in the gapped graphene.Comment: 5 page, 4 figure

Cluster Persistence: a Discriminating Probe of Soap Froth Dynamics

The persistent decay of bubble clusters in coarsening two-dimensional soap froths is measured experimentally as a function of cluster volume fraction. Dramatically stronger decay is observed in comparison to soap froth models and to measurements and calculations of persistence in other systems. The fraction of individual bubbles that contain any persistent area also decays, implying significant bubble motion and suggesting that T1 processes play an important role in froth persistence.Comment: 5 pages, revtex, 4 eps figures. To appear in Europhys. Let

Topological correlations in soap froths

Correlation in two-dimensional soap froth is analysed with an effective potential for the first time. Cells with equal number of sides repel (with linear correlation) while cells with different number of sides attract (with NON-bilinear) for nearest neighbours, which cannot be explained by the maximum entropy argument. Also, the analysis indicates that froth is correlated up to the third shell neighbours at least, contradicting the conventional ideas that froth is not strongly correlated.Comment: 10 Pages LaTeX, 6 Postscript figure

Topological model of soap froth evolution with deterministic T2-processes

We introduce a topological model for the evolution of 2d soap froth. The topological rearrangements (T2 processes) are deterministic (unlike the standard stochastic model): the final topology depends on the areas of the neighboring cells. The new model gives agreement with experiments in the transient regime, where the previous models failed qualitatively, and also improves agreement in the scaling state.Comment: latex, 12 pages, 2 figure

The concerns and experiences of patients with lumbar spinal stenosis regarding prehabilitation and recovery after spine surgery: A qualitative study

Objectives To improve our understanding of patients’ perspectives regarding: (1) the decision making and prehabilitation before lumbar spinal stenosis (LSS) surgery; and (2) their postoperative experiences. Design Qualitative research with semi-structured interviews. Setting General community Participants Individuals received (n=10) and did not receive (n=15) prehabilitation before LSS surgery were recruited at the 6-month postoperative follow-up (8 females; average age: 67.7±6.7 years) by purposive sampling. Additionally, one participant invited her daughter to accompany her in an interview. Interventions Not applicable Main outcome measures Concerns and experiences of patients with LSS regarding prehabilitation and recovery after spine surgery. Results Thematic analysis was conducted to identify four themes inductively: (1) sources of information about LSS surgery; (2) factors affecting the surgical decision making; (3) attitudes toward prehabilitation; and (4) postoperative recovery. All participants desired to have more preoperative education to inform their surgical decision making. There were mixed opinions regarding the perceived benefits of prehabilitation because some individuals hesitated to participate in prehabilitaiotn due to their symptoms, or the cost or time of travelling. Many participants expected some or even complete relief of LSS-related symptoms after surgery. However, not all participants experienced the expected postoperative improvements. Some participants only experienced temporary symptomatic relief, while others experienced new postoperative symptoms. Patients generally found that postoperative exercises taught by physiotherapists were useful although their compliance decreased over time. Conclusions Our study highlights the need for better preoperative LSS education. Since face-to-face prehabilitation or postoperative rehabilitation may not be feasible for all patients, future studies should explore whether online-based prehabilitation or postoperative rehabilitation may benefit certain patient subgroups

Protein Pattern Formation

Protein pattern formation is essential for the spatial organization of many intracellular processes like cell division, flagellum positioning, and chemotaxis. A prominent example of intracellular patterns are the oscillatory pole-to-pole oscillations of Min proteins in \textit{E. coli} whose biological function is to ensure precise cell division. Cell polarization, a prerequisite for processes such as stem cell differentiation and cell polarity in yeast, is also mediated by a diffusion-reaction process. More generally, these functional modules of cells serve as model systems for self-organization, one of the core principles of life. Under which conditions spatio-temporal patterns emerge, and how these patterns are regulated by biochemical and geometrical factors are major aspects of current research. Here we review recent theoretical and experimental advances in the field of intracellular pattern formation, focusing on general design principles and fundamental physical mechanisms.Comment: 17 pages, 14 figures, review articl

Phosphorylation of centromeric histone H3 variant regulates chromosome segregation in S. cerevisiae

The centromeric histone H3 variant (CenH3) is essential for chromosome segregation in eukaryotes. We have identified posttranslational modifications of S. cerevisiae CenH3, Cse4. Functional characterization of cse4 phosphorylation mutants showed growth and chromosome segregation defects when combined with kinetochore mutants okp1 and ame1. Using a phosphoserine-specific antibody we showed that the association of phosphorylated Cse4 with centromeres is increased in response to defective microtubule attachment or reduced cohesion. We determined that evolutionarily conserved Ipl1/Aurora B contributes to phosphorylation of Cse4, as levels of phosphorylated Cse4 were reduced at centromeres in ipl1 strains in vivo and in vitro assays showed phosphorylation of Cse4 by Ipl1. Consistent with these results we observed that a phosphomimetic cse4-4SD mutant suppressed the temperature sensitive growth of ipl1-2 and Ipl1 substrate mutants dam1 spc34 and ndc80 that are defective for chromosome biorientation. Furthermore, cell biology approaches using a GFP labeled chromosome showed that cse4-4SD suppressed chromosome segregation defects in dam1 spc34 strains. Based these results we propose that phosphorylation of Cse4 destabilizes defective kinetochores to promote biorientation and ensure faithful chromosome segregation. Taken together, our study provides a detailed analysis, in vivo and in vitro, of Cse4 phosphorylation and its role in promoting faithful chromosome segregation

Contribution of the first K-homology domain of poly(C)-binding protein 1 to its affinity and specificity for C-rich oligonucleotides

Poly-C-binding proteins are triple KH (hnRNP K homology) domain proteins with specificity for single stranded C-rich RNA and DNA. They play diverse roles in the regulation of protein expression at both transcriptional and translational levels. Here, we analyse the contributions of individual αCP1 KH domains to binding C-rich oligonucleotides using biophysical and structural methods. Using surface plasmon resonance (SPR), we demonstrate that KH1 makes the most stable interactions with both RNA and DNA, KH3 binds with intermediate affinity and KH2 only interacts detectibly with DNA. The crystal structure of KH1 bound to a 5′-CCCTCCCT-3′ DNA sequence shows a 2:1 protein:DNA stoichiometry and demonstrates a molecular arrangement of KH domains bound to immediately adjacent oligonucleotide target sites. SPR experiments, with a series of poly-C-sequences reveals that cytosine is preferred at all four positions in the oligonucleotide binding cleft and that a C-tetrad binds KH1 with 10 times higher affinity than a C-triplet. The basis for this high affinity interaction is finally detailed with the structure determination of a KH1.W.C54S mutant bound to 5′-ACCCCA-3′ DNA sequence. Together, these data establish the lead role of KH1 in oligonucleotide binding by αCP1 and reveal the molecular basis of its specificity for a C-rich tetrad

Human neutrophil clearance of bacterial pathogens triggers anti-microbial gamma delta T cell responses in early infection

Human blood Vc9/Vd2 T cells, monocytes and neutrophils share a responsiveness toward inflammatory chemokines and are rapidly recruited to sites of infection. Studying their interaction in vitro and relating these findings to in vivo observations in patients may therefore provide crucial insight into inflammatory events. Our present data demonstrate that Vc9/Vd2 T cells provide potent survival signals resulting in neutrophil activation and the release of the neutrophil chemoattractant CXCL8 (IL-8). In turn, Vc9/Vd2 T cells readily respond to neutrophils harboring phagocytosed bacteria, as evidenced by expression of CD69, interferon (IFN)-c and tumor necrosis factor (TNF)-a. This response is dependent on the ability of these bacteria to produce the microbial metabolite (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate (HMB-PP), requires cell-cell contact of Vc9/Vd2 T cells with accessory monocytes through lymphocyte function-associated antigen-1 (LFA-1), and results in a TNF-a dependent proliferation of Vc9/Vd2 T cells. The antibiotic fosmidomycin, which targets the HMB-PP biosynthesis pathway, not only has a direct antibacterial effect on most HMB-PP producing bacteria but also possesses rapid anti-inflammatory properties by inhibiting cd T cell responses in vitro. Patients with acute peritoneal-dialysis (PD)-associated bacterial peritonitis – characterized by an excessive influx of neutrophils and monocytes into the peritoneal cavity – show a selective activation of local Vc9/Vd2 T cells by HMB-PP producing but not by HMB-PP deficient bacterial pathogens. The cd T celldriven perpetuation of inflammatory responses during acute peritonitis is associated with elevated peritoneal levels of cd T cells and TNF-a and detrimental clinical outcomes in infections caused by HMB-PP positive microorganisms. Taken together, our findings indicate a direct link between invading pathogens, neutrophils, monocytes and microbe-responsive cd T cells in early infection and suggest novel diagnostic and therapeutic approaches.Martin S. Davey, Chan-Yu Lin, Gareth W. Roberts, Sinéad Heuston, Amanda C. Brown, James A. Chess, Mark A. Toleman, Cormac G.M. Gahan, Colin Hill, Tanya Parish, John D. Williams, Simon J. Davies, David W. Johnson, Nicholas Topley, Bernhard Moser and Matthias Eber

Toxicity of Sediment-Associated Pesticides to Chironomus dilutus and Hyalella azteca

Two hundred sediment samples were collected and their toxicity evaluated to aquatic species in a previous study in the agriculturally dominated Central Valley of California, United States. Pyrethroid insecticides were the main contributors to the observed toxicity. However, mortality in approximately one third of the toxic samples could not be explained solely by the presence of pyrethroids in the matrices. Hundreds of pesticides are currently used in the Central Valley of California, but only a few dozen are analyzed in standard environmental monitoring. A significant amount of unexplained sediment toxicity may be due to pesticides that are in widespread use that but have not been routinely monitored in the environment, and even if some of them were, the concentrations harmful to aquatic organisms are unknown. In this study, toxicity thresholds for nine sediment-associated pesticides including abamectin, diazinon, dicofol, fenpropathrin, indoxacarb, methyl parathion, oxyfluorfen, propargite, and pyraclostrobin were established for two aquatic species, the midge Chironomus dilutus and the amphipod Hyalella azteca. For midges, the median lethal concentration (LC50) of the pesticides ranged from 0.18 to 964 μg/g organic carbon (OC), with abamectin being the most toxic and propargite being the least toxic pesticide. A sublethal growth endpoint using average individual ash-free dry mass was also measured for the midges. The no–observable effect concentration values for growth ranged from 0.10 to 633 μg/g OC for the nine pesticides. For the amphipods, fenpropathrin was the most toxic, with an LC50 of 1–2 μg/g OC. Abamectin, diazinon, and methyl parathion were all moderately toxic (LC50s 2.8–26 μg/g OC). Dicofol, indoxacarb, oxyfluorfen, propargite, and pyraclostrobin were all relatively nontoxic, with LC50s greater than the highest concentrations tested. The toxicity information collected in the present study will be helpful in decreasing the frequency of unexplained sediment toxicity in agricultural waterways