Molecular Subtyping of Bacillus anthracis and the 2001 Bioterrorism-Associated Anthrax Outbreak, United States

Molecular subtyping of Bacillus anthracis played an important role in differentiating and identifying anthrax strains during the 2001 bioterrorism-associated outbreak. Because B. anthracis has a low level of genetic variability, only a few subtyping methods, with varying reliability, exist. We initially used multiple-locus variable-number tandem repeat analysis (MLVA) to subtype 135 B. anthracis isolates associated with the outbreak. All isolates were determined to be of genotype 62, the same as the Ames strain used in laboratories. We sequenced the protective antigen gene (pagA) from 42 representative outbreak isolates and determined they all had a pagA sequence indistinguishable from the Ames strain (PA genotype I). MLVA and pagA sequencing were also used on DNA from clinical specimens, making subtyping B. anthracis possible without an isolate. Use of high-resolution molecular subtyping determined that all outbreak isolates were indistinguishable by the methods used and probably originated from a single source. In addition, subtyping rapidly identified laboratory contaminants and non-outbreak–related isolates

Aging in One-Dimensional Coagulation-Diffusion Processes and the Fredrickson-Andersen Model

We analyse the aging dynamics of the one-dimensional Fredrickson-Andersen (FA) model in the nonequilibrium regime following a low temperature quench. Relaxation then effectively proceeds via diffusion limited pair coagulation (DLPC) of mobility excitations. By employing a familiar stochastic similarity transformation, we map exact results from the free fermion case of diffusion limited pair annihilation to DLPC. Crucially, we are able to adapt the mapping technique to averages involving multiple time quantities. This relies on knowledge of the explicit form of the evolution operators involved. Exact results are obtained for two-time correlation and response functions in the free fermion DLPC process. The corresponding long-time scaling forms apply to a wider class of DLPC processes, including the FA model. We are thus able to exactly characterise the violations of the fluctuation-dissipation theorem (FDT) in the aging regime of the FA model. We find nontrivial scaling forms for the fluctuation-dissipation ratio (FDR) X = X(tw/t), but with a negative asymptotic value X = -3*pi/(6*pi - 16) = -3.307. While this prevents a thermodynamic interpretation in terms of an effective temperature, it is a direct consequence of probing FDT with observables that couple to activated dynamics. The existence of negative FDRs should therefore be a widespread feature in non mean-field systems.Comment: 39 pages, 4 figure

A Study of Thymidylate Synthase Expression as a Biomarker for Resectable Colon Cancer: Alliance (Cancer and Leukemia Group B) 9581 and 89803.

PurposeTumor levels of thymidylate synthase (TS), a target of 5-fluorouracil (5-FU)-based chemotherapy for colorectal cancer, have been studied as a predictive or prognostic biomarker with mixed results.Patients and methodsTumor TS levels were prospectively evaluated in two adjuvant therapy trials for patients with resected stage II or III colon cancer. TS expression was determined by standard immunohistochemistry and by automated quantitative analysis. Tumor mismatch repair deficiency (MMR-D) and BRAF c.1799T > A (p.V600E) mutation status were also examined. Relationships between tumor TS, MMR-D, and BRAF mutation status, overall survival (OS), and disease-free survival (DFS) were investigated in the subset of stage III patients.ResultsPatients whose tumors demonstrated high TS expression experienced better treatment outcomes, with DFS hazard ratio (HR) = 0.67, 95% confidence interval (CI) = 0.53, 0.84; and OS HR = 0.68, 95% CI = 0.53, 0.88, for high versus low TS expression, respectively. No significant interaction between TS expression and stage was observed (DFS: interaction HR = 0.94; OS: interaction HR = 0.94). Tumors with high TS expression were more likely to demonstrate MMR-D (22.2% vs. 12.8%; p =  .0003). Patients whose tumors demonstrated both high TS and MMR-D had a 7-year DFS of 77%, compared with 58% for those whose tumors had low TS and were non-MMR-D (log-rank p =  .0006). Tumor TS expression did not predict benefit of a particular therapeutic regimen.ConclusionThis large prospective analysis showed that high tumor TS levels were associated with improved DFS and OS following adjuvant therapy for colon cancer, although tumor TS expression did not predict benefit of 5-FU-based chemotherapy. The Oncologist 2017;22:107-114Implications for Practice: This study finds that measurement of tumor levels of thymidylate synthase is not helpful in assigning specific adjuvant treatment for colorectal cancer. It also highlights the importance of using prospective analyses within treatment clinical trials as the optimal method of determining biomarker utility

Penicillin Use in Meningococcal Disease Management: Active Bacterial Core Surveillance Sites, 2009.

In 2009, in the Active Bacterial Core surveillance sites, penicillin was not commonly used to treat meningococcal disease. This is likely because of inconsistent availability of antimicrobial susceptibility testing and ease of use of third-generation cephalosporins. Consideration of current practices may inform future meningococcal disease management guidelines

Narrative skills in adolescents with a history of SLI in relation to non-verbal IQ scores

There is a debate about whether the language of children with primary language disorders and normal cognitive levels is qualitatively different from those with language impairments who have low or borderline non-verbal IQ (NVIQ). As children reach adolescence, this distinction may be even harder to ascertain, especially in naturalistic settings. Narrative may provide a useful, ecologically valid way in which to assess the language ability of adolescents with specific language impairment (SLI) who have intact or lowered NVIQ and to determine whether there is any discernable difference in every day language. Nineteen adolescents with a history of SLI completed two narrative tasks: a story telling condition and a conversational condition. Just under half the group (n = 8) had non-verbal IQs of 85. The remaining 11 had NVIQs in the normal range or above. Four areas of narrative (productivity, syntax, cohesion and performance) were assessed. There were no differences between the groups on standardized tests of language. However, the group with low NVIQ were poorer on most aspects of narrative, suggesting that cognitive level is important, even when language is the primary disorder. The groups showed similar patterns of differences between story telling and conversational narrative. It was concluded that adolescents with a history of SLI and poor cognitive levels have poorer narrative skills than those with normal range NVIQ even though these may not be detected by standardized assessment. Their difficulties present as qualitatively similar to those with normal range NVIQ and narratives appear impoverished rather than inaccurate

Relação genética entre cepas de Neisseria meningitidis sorogrupo B sorotipo 4

We compared the results obtained by serotyping of PorB epitopes using an expanded panel of monoclonal antibodies (mAb) including mAb 7 and mAb 10, with results obtained by RFLP of rRNA genes (ribotyping). The purpose of this study was to assess the correlation between phenotypic- and genotypic- methods for typing N. meningitidis. The ribotypes obtained using ClaI or EcoRV endonucleases grouped the strains in seven and two different patterns, respectively. This additional characterization of PorB epitopes improved the correlation between these two methods of typing N. meningitidis.Nós comparamos os resultados obtidos pela sorotipagem usando um painel de anticorpos monoclonais (mAb) ao qual se incluíam os mAbs 7 e 10, com os resultados obtidos pelo RFLP do gene rRNA (ribotipagem). O propósito deste estudo foi avaliar a correlação entre os métodos fenotípico e genotípico de tipagem de N. meningitidis. Os ribotipos obtidos usando as endonucleases de restrição ClaI e EcoRV foram hábeis em dividir as cepas em sete e dois diferentes perfis de restrição, respectivamente. A caracterização adicional de epítopos na proteína PorB melhorou a correlação entre os dois métodos de tipagem de N. meningitidis

Sequencing of 16S rRNA Gene: A Rapid Tool for Identification of Bacillus anthracis

In a bioterrorism event, a tool is needed to rapidly differentiate Bacillus anthracis from other closely related spore-forming Bacillus species. During the recent outbreak of bioterrorism-associated anthrax, we sequenced the 16S rRNA generom these species to evaluate the potential of 16S rRNA gene sequencing as a diagnostic tool. We found eight distinct 16S types among all 107 16S rRNA gene seqs fuences that differed from each other at 1 to 8 positions (0.06% to 0.5%). All 86 B. anthracis had an identical 16S gene sequence, designated type 6; 16S type 10 was seen in all B. thuringiensis strains; six other 16S types were found among the 10 B. cereus strains. This report describes the first demonstration of an exclusive association of a distinct 16S sequence with B. anthracis. Consequently, we were able to rapidly identify suspected isolates and to detect the B. anthracis 16S rRNA gene directly from culture-negative clinical specimens from seven patients with laboratory-confirmed anthrax

Neither Shoreditch nor Manhattan: Post-politics, 'soft austerity urbanism' and real abstraction in Glasgow North

Speirs Locks is being re-constructed as a new cultural quarter in Glasgow North, with urban boosters envisioning the unlikely, rundown and de-populated light industrial estate as a key site in the city's ongoing cultural regeneration strategy. Yet this creative place-making initiative, I argue, masks a post-political conjuncture based on urban speculation, displacement and the foreclosure of dissent. Post-politics at Speirs Locks is characterised by what I term ‘soft austerity urbanism’: seemingly progressive, instrumental small-scale urban catalyst initiatives that in reality complement rather than counter punitive hard austerity urbanism. Relating such processes of soft austerity urbanism to a wider context of state-led gentrification, this study contributes to post-political debates in several ways. Firstly, it questions demands for participation as a proper politics when it has become practically compulsory in contemporary biopolitical capitalism. Secondly, it demonstrates how an extreme economy of austerity urbanism remains the hard underside of post-political, soft austerity urbanism approaches. Thirdly, it illustrates how these approaches relate to wider processes of ‘real abstraction’ – which is no mere flattery of the mind, but instead is rooted in actually existing processes of commodity exchange. Such abstraction, epitomised in the financialisation and privatisation of land and housing, buttresses the same ongoing property dynamics that were so integral to the global financial crisis and ensuing austerity policies in the first place. If we aim to generate a proper politics that creates a genuine rupture with the destructive play of capital in the built environment, the secret of real abstraction must be critically addressed