Effects of memory on the shapes of simple outbreak trees

Genomic tools, including phylogenetic trees derived from sequence data, are increasingly used to understand outbreaks of infectious diseases. One challenge is to link phylogenetic trees to patterns of transmission. Particularly in bacteria that cause chronic infections, this inference is affected by variable infectious periods and infectivity over time. It is known that non-exponential infectious periods can have substantial effects on pathogens’ transmission dynamics. Here we ask how this non-Markovian nature of an outbreak process affects the branching trees describing that process, with particular focus on tree shapes. We simulate Crump-Mode-Jagers branching processes and compare different patterns of infectivity over time. We find that memory (non-Markovian-ness) in the process can have a pronounced effect on the shapes of the outbreak’s branching pattern. However, memory also has a pronounced effect on the sizes of the trees, even when the duration of the simulation is fixed. When the sizes of the trees are constrained to a constant value, memory in our processes has little direct effect on tree shapes, but can bias inference of the birth rate from trees. We compare simulated branching trees to phylogenetic trees from an outbreak of tuberculosis in Canada, and discuss the relevance of memory to this dataset

Radiosensitization of noradrenaline transporter-expressing tumour cells by proteasome inhibitors and the role of reactive oxygen species

Background The radiopharmaceutical 131I-metaiodobenzylguanidine (131I-MIBG) is used for the targeted radiotherapy of noradrenaline transporter (NAT)-expressing neuroblastoma. Enhancement of 131I-MIBG's efficacy is achieved by combination with the topoisomerase I inhibitor topotecan - currently being evaluated clinically. Proteasome activity affords resistance of tumour cells to radiation and topoisomerase inhibitors. Therefore, the proteasome inhibitor bortezomib was evaluated with respect to its cytotoxic potency as a single agent and in combination with 131I-MIBG and topotecan. Since elevated levels of reactive oxygen species (ROS) are induced by bortezomib, the role of ROS in tumour cell kill was determined following treatment with bortezomib or the alternative proteasome inhibitor, MG132.<p></p> Methods Clonogenic assay and growth of tumour xenografts were used to investigate the effects of proteasome inhibitors alone or in combination with radiation treatment. Synergistic interactions in vitro were evaluated by combination index analysis. The dependency of proteasome inhibitor-induced clonogenic kill on ROS generation was assessed using antioxidants.<p></p> Results Bortezomib, in the dose range 1 to 30 nM, decreased clonogenic survival of both SK-N-BE(2c) and UVW/NAT cells, and this was prevented by antioxidants. It also acted as a sensitizer in vitro when administered with X-radiation, with 131I-MIBG, or with 131I-MIBG and topotecan. Moreover, bortezomib enhanced the delay of the growth of human tumour xenografts in athymic mice when administered in combination with 131I-MIBG and topotecan. MG132 and bortezomib had similar radiosensitizing potency, but only bortezomib-induced cytotoxicity was ROS-dependent.<p></p> Conclusions Proteasome inhibition shows promise for the treatment of neuroblastoma in combination with 131I-MIBG and topotecan. Since the cytotoxicity of MG132, unlike that of bortezomib, was not ROS-dependent, the latter proteasome inhibitor may have a favourable toxicity profile in normal tissues.<p></p&gt

A multiplex PCR assay for differentiating economically important gastrointestinal nematodes of cattle

A multiplex polymerase chain reaction (PCR) test was developed for identifying gastrointestinal (GI) nematodes that commonly infect cattle. This assay was developed using adult-derived genomic DNA and shown capable of discriminating parasite eggs from the feces of experimentally-infected animals at both the species and genus levels. Sequence data from internal (ITS) and external (ETS) transcribed spacers of the ribosomal DNA (rDNA) repeats as well as the 3′-end of the small subunit rDNA and 5′-end of the large subunit rDNA were used to generate five primer sets which, when used simultaneously in a multiplex PCR, produce a unique electrophoretic DNA banding pattern charac- terized by a single DNA fragment for Ostertagia ostertagi (257 bp), Haemonchus placei (176 bp),Oesophagostomum radiatum (329 bp), Trichostrongylus colubriformis (243 bp) and Cooperia on- cophora (151 bp). In a similar manner, the constructed primer sets amplified DNA from Ostertagia lyrata, Haemonchus contortus, Trichostrongylus axei, Cooperia surnabada and Cooperia punctata. With respect to H. contortus, a closely migrating doublet was generated suggesting size heterogene- ity in the ETS which is consistent with multiple rDNA repeat units within this species. PCR analyses using mixtures of monospecifically-purified nematode eggs indicated a sensitivity of less than 0.5 egg-DNA equivalent per species. Although, not designed as a quantitative technique, relative PCR signal intensities corresponded to relative egg burdens within the DNA samples from mixed species of eggs. Published by Elsevier Science B.V

Raman gain against a background of non-thermal ion fluctuations in a plasma

A complex stimulated Raman scattering event against a background of non-thermal ion acoustic waves in an inhomogeneous plasma is described. We obtain analytic forms for the Raman gain due to a five-wave interaction consisting of conventional three-wave Raman scattering followed by the decay of the Raman Langmuir wave into a second Langmuir wave (or a second scattered light wave) and an ion acoustic wave. Very modest levels of ion waves produce a. significant effect on Raman convective gain. A combination of plasma inhomogeneity and suprathermal ion fluctuations may offer a means for the control of Raman gain

Bounds on Heavy-to-Heavy Mesonic Form Factors

We provide upper and lower bounds on the form factors for B -> D, D^* by utilizing inclusive heavy quark effective theory sum rules. These bounds are calculated to leading order in Lambda_QCD/m_Q and alpha_s. The O(alpha_s^2 beta_0) corrections to the bounds at zero recoil are also presented. We compare our bounds with some of the form factor models used in the literature. All the models we investigated failed to fall within the bounds for the combination of form factors (omega^2 - 1)/(4 omega)|omega h_{A2}+h_{A3}|^2.Comment: 27 pages, 10 figure

Haploinsufficiency of the Myc regulator Mtbp extends survival and delays tumor development in aging mice.

Alterations of specific genes can modulate aging. Myc, a transcription factor that regulates the expression of many genes involved in critical cellular functions was shown to have a role in controlling longevity. Decreased expression of Myc inhibited many of the deleterious effects of aging and increased lifespan in mice. Without altering Myc expression, reduced levels of Mtbp, a recently identified regulator of Myc, limit Myc transcriptional activity and proliferation, while increased levels promote Myc-mediated effects. To determine the contribution of Mtbp to the effects of Myc on aging, we studied a large cohort of Mtbp heterozygous mice and littermate matched wild-type controls. Mtbp haploinsufficiency significantly increased longevity and maximal survival in mice. Reduced levels of Mtbp did not alter locomotor activity, litter size, or body size, but Mtbp heterozygous mice did exhibit elevated markers of metabolism, particularly in the liver. Mtbp(+/-) mice also had a significant delay in spontaneous cancer development, which was most prominent in the hematopoietic system, and an altered tumor spectrum compared to Mtbp(+/+) mice. Therefore, the data suggest Mtbp is a regulator of longevity in mice that mimics some, but not all, of the properties of Myc in aging

Scanning Tunneling Spectroscopic Studies of the Effects of Dielectrics and Metallic Substrates on the Local Electronic Characteristics of Graphene

Atomically resolved imaging and spectroscopic characteristics of graphene grown by chemical vapor deposition (CVD) on copper foils are investigated and compared with those of mechanical exfoliated graphene on SiO_2. For exfoliated graphene, the local spectral deviations from ideal behavior may be attributed to strain induced by the SiO_2 substrate. For CVD grown graphene, the lattice structure appears strongly distorted by the underlying copper, with regions in direct contact with copper showing nearly square lattices whereas suspended regions from thermal relaxation exhibiting nearly honeycomb or hexagonal lattice structures. The electronic density of states (DOS) correlates closely with the atomic arrangements of carbon, showing excess zero-bias tunneling conductance and nearly energy-independent DOS for strongly distorted graphene, in contrast to the linearly dispersive DOS for suspended graphene. These results suggest that graphene can interact strongly with both metallic and dielectric materials in close proximity, leading to non-negligible modifications to the electronic properties

Religious leaders\u27 perceptions of advance care planning: a secondary analysis of interviews with Buddhist, Christian, Hindu, Islamic, Jewish, Sikh and Bahai leaders

Background: International guidance for advance care planning (ACP) supports the integration of spiritual and religious aspects of care within the planning process. Religious leaders’ perspectives could improve how ACP programs respect patients’ faith backgrounds. This study aimed to examine: (i) how religious leaders understand and consider ACP and its implications, including (ii) how religion affects followers’ approaches to end-of-life care and ACP, and (iii) their implications for healthcare. Methods: Interview transcripts from a primary qualitative study conducted with religious leaders to inform an ACP website, ACPTalk, were used as data in this study. ACPTalk aims to assist health professionals conduct sensitive conversations with people from different religious backgrounds. A qualitative secondary analysis conducted on the interview transcripts focussed on religious leaders’ statements related to this study’s aims. Interview transcripts were thematically analysed using an inductive, comparative, and cyclical procedure informed by grounded theory. Results: Thirty-five religious leaders (26 male; mean 58.6-years-old), from eight Christian and six non-Christian (Jewish, Buddhist, Islamic, Hindu, Sikh, Bahá’í) backgrounds were included. Three themes emerged which focussed on: religious leaders’ ACP understanding and experiences; explanations for religious followers’ approaches towards end-of-life care; and health professionals’ need to enquire about how religion matters. Most leaders had some understanding of ACP and, once fully comprehended, most held ACP in positive regard. Religious followers’ preferences for end-of-life care reflected family and geographical origins, cultural traditions, personal attitudes, and religiosity and faith interpretations. Implications for healthcare included the importance of avoiding generalisations and openness to individualised and/ or standardised religious expressions of one’s religion. Conclusions: Knowledge of religious beliefs and values around death and dying could be useful in preparing health professionals for ACP with patients from different religions but equally important is avoidance of assumptions. Community-based initiatives, programs and faith settin