Using Sequencing to Improve Operational Efficiency and Reliability

Operation of an accelerator requires the efficient and reproducible execution of many different types of procedures. Some procedures, like beam acceleration, magnet quench recovery, and species switching can be quite complex. To improve accelerator reliability and efficiency, automated execution of procedures is required. Creation of a single robust sequencing application permits the streamlining of this process and offers many benefits in sequence creation, editing, and control. In this paper, we present key features of a sequencer application commissioned at the Collider-Accelerator Department of Brookhaven National Laboratory during the 2007 run. Included is a categorization of the different types of sequences in use, a discussion of the features considered desirable in a good sequencer, and a description of the tools created to aid in sequence construction and diagnosis. Finally, highlights from our operational experience are presented, with emphasis on Operations control of the sequencer, and the alignment of sequence construction with existing operational paradigms

Aluminum tolerance association mapping in triticale

<p>Abstract</p> <p>Background</p> <p>Crop production practices and industrialization processes result in increasing acidification of arable soils. At lower pH levels (below 5.0), aluminum (Al) remains in a cationic form that is toxic to plants, reducing growth and yield. The effect of aluminum on agronomic performance is particularly important in cereals like wheat, which has promoted the development of programs directed towards selection of tolerant forms. Even in intermediately tolerant cereals (i.e., triticale), the decrease in yield may be significant. In triticale, Al tolerance seems to be influenced by both wheat and rye genomes. However, little is known about the precise chromosomal location of tolerance-related genes, and whether wheat or rye genomes are crucial for the expression of that trait in the hybrid.</p> <p>Results</p> <p>A mapping population consisting of 232 advanced breeding triticale forms was developed and phenotyped for Al tolerance using physiological tests. AFLP, SSR and DArT marker platforms were applied to obtain a sufficiently large set of molecular markers (over 3000). Associations between the markers and the trait were tested using General (GLM) and Multiple (MLM) Linear Models, as well as the Statistical Machine Learning (SML) approach. The chromosomal locations of candidate markers were verified based on known assignments of SSRs and DArTs or by using genetic maps of rye and triticale.</p> <p>Two candidate markers on chromosome 3R and 9, 15 and 11 on chromosomes 4R, 6R and 7R, respectively, were identified. The <it>r²</it>values were between 0.066 and 0.220 in most cases, indicating a good fit of the data, with better results obtained with the GML than the MLM approach. Several QTLs on rye chromosomes appeared to be involved in the phenotypic expression of the trait, suggesting that rye genome factors are predominantly responsible for Al tolerance in triticale.</p> <p>Conclusions</p> <p>The Diversity Arrays Technology was applied successfully to association mapping studies performed on triticale breeding forms. Statistical approaches allowed the identification of numerous markers associated with Al tolerance. Available rye and triticale genetic maps suggested the putative location of the markers and demonstrated that they formed several linked groups assigned to distinct chromosomes (3R, 4R, 6R and 7R). Markers associated with genomic regions under positive selection were identified and indirectly mapped in the vicinity of the Al-tolerant markers. The present findings were in agreement with prior reports.</p

The role of septal perforators and "myocardial bridging effect" in atherosclerotic plaque distribution in the coronary artery disease

The distribution of atherosclerotic plaque burden in the human coronary arteries is not uniform. Plaques are located mostly in the left anterior descending artery (LAD), then in the right coronary artery (RCA), circumflex branch (LCx) and the left main coronary artery (LM) in a decreasing order of frequency. In the LAD and LCx, plaques tend to cluster within the proximal segment, while in the RCA their distribution is more uniform. Several factors have been involved in this phenomenon, particularly flow patterns in the left and right coronary artery. Nevertheless, it does not explain the difference in lesion frequency between the LAD and the LCx as these are both parts of the left coronary artery. Branching points are considered to be the risk points of atherosclerosis. In the LCx, the number of side branches is lower than in the LAD or RCA and there are no septal perforators with intramuscular courses like in the proximal third of the LAD and the posterior descending artery (PDA). We hypothesized that septal branches generate disturbed flow in the LAD and PDA in a similar fashion to the myocardial bridge (myocardial bridging effect). This coronary architecture determines the non-uniform plaque distribution in coronary arteries and LAD predisposition to plaque formation

Spin Excitations in BaFe1.84Co0.16As2 Superconductor Observed by Inelastic Neutron Scattering

Superconductivity appears to compete against the spin-density-wave in Fe pnictides. However, optimally cobalt doped samples show a quasi-two-dimensional spin excitation centered at the (0.5, 0.5, L) wavevector, "the spin resonance peak", that is strongly tied to the onset of superconductivity. By inelastic neutron scattering on single crystals we show the similarities and differences of the spin excitations in BaFe1.84Co0.16As2, with respect to the spin excitations in the high-temperature superconducting cuprates. As in the cuprates the resonance occurs as an enhancement to a part of the spin excitation spectrum which extends to higher energy transfer and higher temperature. However, unlike in the cuprates, the resonance peak in this compound is asymmetric in energy.Comment: 12 pages, 6 figures; PACS # 74.70.-b, 74.20.Mn, 78.70.Nx, 74.25.Ha; corrected discussion of figures in tex

Predominant location of coronary artery atherosclerosis in the left anterior descending artery. The impact of septal perforators and the myocardial bridging effect

INTRODUCTION: Coronary artery atherosclerosis presents characteristic patterns of plaque distribution despite systemic exposure to risk factors. We hypothesized that local hemodynamic forces induced by the systolic compression of intramuscular septal perforators could be involved in atherosclerotic processes in the left anterior descending artery (LAD) adjacent to the septal perforators' origin. Therefore we studied the spatial distribution of atherosclerosis in coronary arteries, especially in relation to the septal perforators' origin. MATERIAL AND METHODS: 64-slice computed tomography angiography was performed in 309 consecutive patients (92 male and 217 female) with a mean age of 59.9 years. Spatial plaque distribution in the LAD was analyzed in relation to the septal perforators' origin. Additionally, plaque distribution throughout the coronary artery tree is discussed. RESULTS: The coronary calcium score (CCS) was positive in 164 patients (53.1%). In subjects with a CCS > 0, calcifications were more frequent in the LAD (n = 150, 91.5%) compared with the right coronary artery (RCA) (n = 94, 57.3%), circumflex branch (CX) (n = 76, 46.3%) or the left main stem (n = 42, 25.6%) (p < 0.001). Total CCS was higher in the LAD at 46.1 (IQR: 104.2) and RCA at 34.1 (IQR: 90.7) than in the CX at 16.8 (IQR: 61.3) (p = 0.007). In patients with calcifications restricted to a single vessel (n = 54), the most frequently affected artery was the LAD (n = 42, 77.8%). In patients with lesions limited to the LAD, the plaque was located mostly (n = 37, 88.1%) adjacent to the septal perforators' origin. CONCLUSIONS: We demonstrated that coronary calcifications are most frequently located in the LAD in proximity to the septal branch origin. A possible explanation for this phenomenon could be the dynamic compression of the tunneled septal branches, which may result in disturbed blood flow in the adjacent LAD segment (milking effect)

Monomeric PcrA helicase processively unwinds plasmid lengths of DNA in the presence of the initiator protein RepD

The helicase PcrA unwinds DNA during asymmetric replication of plasmids, acting with an initiator protein, in our case RepD. Detailed kinetics of PcrA activity were measured using bulk solution and a single-molecule imaging technique to investigate the oligomeric state of the active helicase complex, its processivity and the mechanism of unwinding. By tethering either DNA or PcrA to a microscope coverslip surface, unwinding of both linear and natural circular plasmid DNA by PcrA/RepD was followed in real-time using total internal reflection fluorescence microscopy. Visualization was achieved using a fluorescent single-stranded DNA-binding protein. The single-molecule data show that PcrA, in combination with RepD, can unwind plasmid lengths of DNA in a single run, and that PcrA is active as a monomer. Although the average rate of unwinding was similar in single-molecule and bulk solution assays, the single-molecule experiments revealed a wide distribution of unwinding speeds by different molecules. The average rate of unwinding was several-fold slower than the PcrA translocation rate on single-stranded DNA, suggesting that DNA unwinding may proceed via a partially passive mechanism. However, the fastest dsDNA unwinding rates measured in the single-molecule unwinding assays approached the PcrA translocation speed measured on ssDNA

Palpable pediatric thyroid abnormalities – diagnostic pitfalls necessitate a high index of clinical suspicion: a case report

A 12-year-old girl presented with a 4 year history of an enlarged, firm thyroid gland. On exam, her thyroid was firm and fixed and an enlarged cervical lymph node was palpable as well. Though a thyroid ultrasound prior to referral was read as thyroiditis, clinical suspicion for thyroid carcinoma mandated continued investigation. The diagnosis of papillary thyroid cancer was established and her workup revealed lymph node metastases as well as a tremendous burden of pulmonary metastases. Pediatric thyroid cancer is extremely rare, but often presents with aggressive disease. Palpable thyroid abnormalities in an individual under 20-years-old should be viewed with suspicion and should be thoroughly investigated to rule out malignancy even in the face of negative diagnostic procedures. Though pediatric papillary thyroid cancer often presents with loco-regional and even distant metastatic disease, mortality rates in follow-up for as long as 20 years are very favorable

Assessment of adipokines, adenine nucleotides and uric acid in the dynamics of coronary intervention

Introduction: The association of vaspin and visfatin, with a myocardial infarction is still not fully understood. Reduced levels of adenine nucleotides are hallmarks of chronic heart failure. There is little data concerning the relationship between these markers and their changes over time. Material/Methods: The concentration of adenine nucleotides, vaspin and visfatinwere assessed in 41 consecutive patients with acute myocardial infarction one before (day I) and four days after (day IV) percutaneous coronary intervention (PCI) and a control group. Results: Visfatin concentrations were higher before and after PCI vs. control (visfatin I: median 25.55, 20.12 - 30.69 ng/ml; visfatin IV: median 20.79, 16.89 - 25.61 ng/ml vs. control: median 14.94, 10.66 - 25.25 ng/ml; p < 0.0001). Vaspin concentrations were lower before and after PCI vs. control (vaspin I: median 0.18, 0.11 - 0.44 ng/ml; vaspin IV: median 0.24, 0.15 - 0.58 ng/ml vs. control: median 1.303, 1.13 - 2.26 ng/ml, p < 0.00001). Concentrations of visfatin, day I, correlated well to vaspin concentrations (r2 = 0.201, p = 0.011). ATP levels were significantly lower in patients vs. controls (day I: p = 0.00012; day IV: p = 0.0001). Conclusions: Changes in the analyzed visfatin and vaspin concentrations can be used as potential MI markers. Visfatin serum concentration may be considered a potential marker to differentiate MI over time