Trivial, Strongly Minimal Theories Are Model Complete After Naming Constants

We prove that if M is any model of a trivial, strongly minimal theory, then the elementary diagram Th(MM) is a model complete LM-theory. We conclude that all countable models of a trivial, strongly minimal theory with at least one computable model are 0 -decidable, and that the spectrum of computable models of any trivial, strongly minimal theory is Σ05

Composites of Heavy Rain Producing Elevated Thunderstorms in the Central United States

Composite analyses of the atmosphere over the central United States during elevated thunderstorms producing heavy rainfall are presented. Composites were created for five National Weather Service County Warning Areas (CWAs) in the region. Events studied occurred during the warm season (April–September) during 1979–2012. These CWAs encompass the region determined previously to experience the greatest frequency of elevated thunderstorms in the United States. Composited events produced rainfall of \u3e50 mm 24 hr−1 within the selected CWA. Composites were generated for the 0–3 hr period prior to the heaviest rainfall, 6–9 hours prior to it, and 12–15 hours prior to it. This paper focuses on the Pleasant Hill, Missouri (EAX) composites, as all CWA results were similar; also these analyses focus on the period 0–3 hours prior to event occurrence. These findings corroborate the findings of previous authors. What is offered here that is unique is (1) a measure of the interquartile range within the composite mean fields, allowing for discrimination between variable fields that provided a strong reliable signal, from those that may appear strong but possess large variability, and (2) composite soundings of two subclasses of elevated thunderstorms. Also, a null case (one that fits the composite but failed to produce significant rainfall) is also examined for comparison

Generation and analysis of a mouse intestinal metatranscriptome through Illumina based RNA-sequencing

With the advent of high through-put sequencing (HTS), the emerging science of metagenomics is transforming our understanding of the relationships of microbial communities with their environments. While metagenomics aims to catalogue the genes present in a sample through assessing which genes are actively expressed, metatranscriptomics can provide a mechanistic understanding of community inter-relationships. To achieve these goals, several challenges need to be addressed from sample preparation to sequence processing, statistical analysis and functional annotation. Here we use an inbred non-obese diabetic (NOD) mouse model in which germ-free animals were colonized with a defined mixture of eight commensal bacteria, to explore methods of RNA extraction and to develop a pipeline for the generation and analysis of metatranscriptomic data. Applying the Illumina HTS platform, we sequenced 12 NOD cecal samples prepared using multiple RNA-extraction protocols. The absence of a complete set of reference genomes necessitated a peptide-based search strategy. Up to 16% of sequence reads could be matched to a known bacterial gene. Phylogenetic analysis of the mapped ORFs revealed a distribution consistent with ribosomal RNA, the majority from Bacteroides or Clostridium species. To place these HTS data within a systems context, we mapped the relative abundance of corresponding Escherichia coli homologs onto metabolic and protein-protein interaction networks. These maps identified bacterial processes with components that were well-represented in the datasets. In summary this study highlights the potential of exploiting the economy of HTS platforms for metatranscriptomics

A gp41 MPER-specific llama VHH requires a hydrophobic CDR3 for neutralization but not for antigen recognition

The membrane proximal external region (MPER) of the HIV-1 glycoprotein gp41 is targeted by the broadly neutralizing antibodies 2F5 and 4E10. To date, no immunization regimen in animals or humans has produced HIV-1 neutralizing MPER-specific antibodies. We immunized llamas with gp41-MPER proteoliposomes and selected a MPER-specific single chain antibody (VHH), 2H10, whose epitope overlaps with that of mAb 2F5. Bi-2H10, a bivalent form of 2H10, which displayed an approximately 20-fold increased affinity compared to the monovalent 2H10, neutralized various sensitive and resistant HIV-1 strains, as well as SHIV strains in TZM-bl cells. X-ray and NMR analyses combined with mutagenesis and modeling revealed that 2H10 recognizes its gp41 epitope in a helical conformation. Notably, tryptophan 100 at the tip of the long CDR3 is not required for gp41 interaction but essential for neutralization. Thus bi-2H10 is an anti-MPER antibody generated by immunization that requires hydrophobic CDR3 determinants in addition to epitope recognition for neutralization similar to the mode of neutralization employed by mAbs 2F5 and 4E10

Residence time distributions in surface transient storage zones in streams : estimation via signal deconvolution

Author Posting. © American Geophysical Union, 2011. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Water Resources Research 47 (2011): W05509, doi:10.1029/2010WR009959.Little is known about the impact of surface transient storage (STS) zones on reach-scale transport and the fate of dissolved nutrients in streams. Exchange with these locations may influence the rates of nutrient cycling often observed in whole-stream tracer experiments, particularly because they are sites of organic matter collection and lower flow velocities than those observed in the thalweg. We performed a conservative stream tracer experiment (slug of dissolved NaCl) in the Ipswich River in northeastern Massachusetts and collected solute tracer data both in the thalweg and adjacent STS zones at three locations in a fifth-order reach. Tracer time series observed in STS zones are an aggregate of residence time distributions (RTDs) of the upstream transport to that point (RTDTHAL) and that of the temporary storage within these zones (RTDSTS). Here we demonstrate the separation of these two RTDs to determine the RTDSTS specifically. Total residence times for these individual STS zones range from 4.5 to 7.5 h, suggesting that these zones have the potential to host important biogeochemical transformations in stream systems. All of the RTDSTS show substantial deviations from the ideal prescribed by the two-state (mobile/immobile) mass transfer equations. The deviations indicate a model mismatch and that parameter estimation based on the mass transfer equations will yield misleading values.This research was funded by the National Science Foundation, grants DEB 06-14350 and EAR 07- 49035, and DOE grant DE-FG02-07ER15841

Overview of the CCP4 suite and current developments.

The CCP4 (Collaborative Computational Project, Number 4) software suite is a collection of programs and associated data and software libraries which can be used for macromolecular structure determination by X-ray crystallography. The suite is designed to be flexible, allowing users a number of methods of achieving their aims. The programs are from a wide variety of sources but are connected by a common infrastructure provided by standard file formats, data objects and graphical interfaces. Structure solution by macromolecular crystallography is becoming increasingly automated and the CCP4 suite includes several automation pipelines. After giving a brief description of the evolution of CCP4 over the last 30 years, an overview of the current suite is given. While detailed descriptions are given in the accompanying articles, here it is shown how the individual programs contribute to a complete software package

A treatment evaluator tool to monitor the real-world effectiveness of inhaled aztreonam lysine in cystic fibrosis

Background: Studies are required that evaluate real-world outcomes of inhaled aztreonam lysine in patients with cystic fibrosis (CF). Methods: Our treatment-evaluator tool assessed the effectiveness of inhaled aztreonam in routine practice in 117 CF patients across four time periods (6–12 (P2) and 0–6 months (P1) pre-initiation, and 0–6 (T1) and 6–12 months (T2) post-initiation). Outcomes were: changes in %-predicted forced expiratory volume in 1 s (FEV1), body-mass index (BMI), hospitalisation days and intravenous antibiotic usage. Results: Median FEV1% predicted for each 6-month period was 38.9%, 34.6%, 37.1% and 36.5%; median change was − 2.0% between P2 and P1, increasing to + 0.6% (p < 0.001) between P1 and T1. Annualised hospital bed-days was reduced (p = 0.05) post-initiation, as was intravenous antibiotics days (p = 0.001). BMI increased over 6 months post-initiation (p ≤ 0.001). Conclusions: In patients with CF in routine practice, inhaled aztreonam lysine is associated with improved lung function and weight, and reduced hospitalisation and intravenous antibiotic use

A Role for TLR4 in Clostridium difficile Infection and the Recognition of Surface Layer Proteins

Clostridium difficile is the etiological agent of antibiotic-associated diarrhoea (AAD) and pseudomembranous colitis in humans. The role of the surface layer proteins (SLPs) in this disease has not yet been fully explored. The aim of this study was to investigate a role for SLPs in the recognition of C. difficile and the subsequent activation of the immune system. Bone marrow derived dendritic cells (DCs) exposed to SLPs were assessed for production of inflammatory cytokines, expression of cell surface markers and their ability to generate T helper (Th) cell responses. DCs isolated from C3H/HeN and C3H/HeJ mice were used in order to examine whether SLPs are recognised by TLR4. The role of TLR4 in infection was examined in TLR4-deficient mice. SLPs induced maturation of DCs characterised by production of IL-12, TNFα and IL-10 and expression of MHC class II, CD40, CD80 and CD86. Furthermore, SLP-activated DCs generated Th cells producing IFNγ and IL-17. SLPs were unable to activate DCs isolated from TLR4-mutant C3H/HeJ mice and failed to induce a subsequent Th cell response. TLR4−/− and Myd88−/−, but not TRIF−/− mice were more susceptible than wild-type mice to C. difficile infection. Furthermore, SLPs activated NFκB, but not IRF3, downstream of TLR4. Our results indicate that SLPs isolated from C. difficile can activate innate and adaptive immunity and that these effects are mediated by TLR4, with TLR4 having a functional role in experimental C. difficile infection. This suggests an important role for SLPs in the recognition of C. difficile by the immune system