CERN openlab Whitepaper on Future IT Challenges in Scientific Research

This whitepaper describes the major IT challenges in scientific research at CERN and several other European and international research laboratories and projects. Each challenge is exemplified through a set of concrete use cases drawn from the requirements of large-scale scientific programs. The paper is based on contributions from many researchers and IT experts of the participating laboratories and also input from the existing CERN openlab industrial sponsors. The views expressed in this document are those of the individual contributors and do not necessarily reflect the view of their organisations and/or affiliates

The Synthesis of the Macrolide Antibiotic (+/-)-Pyrenophorin

The synthesis of the macrolide antibiotic (+/-)-pyrenophorin (1) is described. The molecular sieve promoted cyclisation of the hydroxy methyl ester (135) failed in our hands but the hydroxy-acid (190) was successfully converted to the dithioacetal of (1) using N,N'-carbonyldiimidazole (207) and 1,5-diazabicyclo(4,3,0)-non-5-ene (147). A novel method of removing p-toluenesulphonylethyl esters (166) is reported as is a new simple technique of hydroxyl alkyl-ation involving molecular sieves and sodium hydrogen carbonate

Assessing the Value of South Carolina’s Coastal and Timber Resources

South Carolina is blessed with abundant natural resources that span from the southern edge of the Blue Ridge Mountains, across the Piedmont, and into the coastal plain that borders the Atlantic Ocean. These resources are known to hold tremendous value to the state but are often understudied, leaving little documentation to support the claim of their value. The purpose of this thesis is to identify South Carolina’s coastal natural resources, estimate the economic value of these coastal resources by individual habitat components, and to estimate the effect of timber tax on property inheritance in South Carolina. By doing so, these results will provide valuable information that can be used to influence planners, policy makers, and the general public on these key topics. In-depth geospatial analysis along with current literature was used to identify and measure South Carolina’s coastal habitats and the growing challenges that they face. To estimate these coastal habitats’ value, a value-transfer method was used to analyze the literature regarding prior economic valuations of these resources conducted in South Carolina and surrounding states that share similar habitat composition. This study provides estimates for ecosystem services such as storm buffering and flood protection, carbon sequestration, outdoor recreation, shoreline stabilization, and water quality enhancement. Taxes have a significant effect on the sale of timber at final harvest, specifically capital gains tax given timber’s appreciating nature. Using a stepped-up tax basis, a landowner can delay final harvesting and pass on standing timber to the property’s heirs, avoiding the steep capital gains taxation that is innate to timber growing. The results indicate that final harvest can be delayed between four and ten years given the site index of the stand and the discount rate assumed

What mediates psychopathology in stalking victims? The role of individual-vulnerability and stalking-related factors

Stalking victims report significant psychiatric morbidity, which often persists long after the stalking itself has ceased. Elucidating predictors of psychopathology in victims is critical to informing the clinical management of this population. This study examined demographic, individual-vulnerability and stalking-related predictors of general psychopathology and post-traumatic stress in a community sample of victims (n = 236). Regression analyses showed that both general psychopathology and post-traumatic stress were influenced by individual-vulnerability factors, particularly the use of avoidance coping, and stalking-related factors, most notably being subjected to threats. This study provides the most comprehensive analysis to date of factors that mediate psychiatric morbidity among stalking victims, and highlights the utility of clinicians focussing on modifying dynamic risk factors such as maladaptive avoidance behaviours to help alleviate victims\u27 psychological distress

NCBI-BLAST programs optimization on XSEDE resources for sustainable aquaculture

The development of genomic resources of non-model organisms is now becoming commonplace as the cost of sequencing continues to decrease. The Genome Informatics Facility in collaboration with the Southwest Fisheries Science Center (SWFSC), NOAA is creating these resources for sustainable aquaculture in Seriola lalandi. Gene prediction and annotation are common steps in the pipeline to generate genomic resources, which are computationally intense and time consuming. In our steps to create genomic resources for Seriola lalandi, we found BLAST to be one of our most rate limiting steps. Therefore, we took advantage of our XSEDE Extended Collaborative Support Services (ECSS) to reduce the amount of time required to process our transcriptome data by 300 percent. In this paper, we describe an optimized method for the BLAST tool on the Stampede cluster, which works with any existing datasets or database, without any modification. At modest core counts, our results are similar to the MPI-enabled BLAST algorithm (mpiBLAST), but also allow the much needed and improved flexibility of output formats that the latest versions of BLAST provide. Reducing this time-consuming bottleneck in BLAST will be broadly applicable to the annotation of large sequencing datasets for any organism

The Immitigable Nature of Assembly Bias: The Impact of Halo Definition on Assembly Bias

Dark matter halo clustering depends not only on halo mass, but also on other properties such as concentration and shape. This phenomenon is known broadly as assembly bias. We explore the dependence of assembly bias on halo definition, parametrized by spherical overdensity parameter, $\Delta$. We summarize the strength of concentration-, shape-, and spin-dependent halo clustering as a function of halo mass and halo definition. Concentration-dependent clustering depends strongly on mass at all $\Delta$. For conventional halo definitions ($\Delta \sim 200\mathrm{m}-600\mathrm{m}$), concentration-dependent clustering at low mass is driven by a population of haloes that is altered through interactions with neighbouring haloes. Concentration-dependent clustering can be greatly reduced through a mass-dependent halo definition with $\Delta \sim 20\mathrm{m}-40\mathrm{m}$ for haloes with $M_{200\mathrm{m}} \lesssim 10^{12}\, h^{-1}\mathrm{M}_{\odot}$. Smaller $\Delta$ implies larger radii and mitigates assembly bias at low mass by subsuming altered, so-called backsplash haloes into now larger host haloes. At higher masses ($M_{200\mathrm{m}} \gtrsim 10^{13}\, h^{-1}\mathrm{M}_{\odot}$) larger overdensities, $\Delta \gtrsim 600\mathrm{m}$, are necessary. Shape- and spin-dependent clustering are significant for all halo definitions that we explore and exhibit a relatively weaker mass dependence. Generally, both the strength and the sense of assembly bias depend on halo definition, varying significantly even among common definitions. We identify no halo definition that mitigates all manifestations of assembly bias. A halo definition that mitigates assembly bias based on one halo property (e.g., concentration) must be mass dependent. The halo definitions that best mitigate concentration-dependent halo clustering do not coincide with the expected average splashback radii at fixed halo mass.Comment: 19 pages, 13 figures. Updated to published version. Main result summarized in Figure 1

Endoscopic Posterior Cricoid Split with Costal Cartilage Graft: A Fifteen‐Year Experience

Objective To evaluate outcomes of the endoscopic posterior cricoid split with rib graft (EPCS/RG) procedure in the treatment of subglottic stenosis (SGS), posterior glottic stenosis (PGS), and bilateral vocal fold immobility (BVFI). Study Design Retrospective chart review. Methods Chart review of all patients who underwent EPCS/RG at a single tertiary-care facility between 1999 and 2014. Patients were grouped based on the primary indication for the procedure. Decannulation was the primary endpoint. Secondary endpoints were the number of subsequent airway procedures and length of hospitalization. Results Thirty-three patients were identified; 32 had tracheotomy. Overall decannulation rate was 65.6%. Subgroup analysis demonstrated the following decannulation rates: 53.8% for SGS, 100% for PGS, and 28.6% for BVFI. Fisher exact test found a significant difference in overall decannulation rates between groups (P = 0.002). Operation-specific decannulation rates for patients who never required an open procedure were 23% for SGS, 91.6% for PGS, and 28.6% for BVFI. This difference was also statistically significant (P = 0.001). Multivariate logistic regression analysis found prematurity had a positive correlation with decannulation that approached statistical significance (P < 0.051; odds ratio 6.1; 95% confidence interval 0.99, 37.6). The percentage of patients who underwent repeat airway procedures for the groups was 61.5% for SGS, 16.6 % for PGS, and 14.3% for BVFI. The median length of hospitalization after EPCS/RG was 3 days. Conclusion This represents the largest series of patients who have undergone EPCS/RG and demonstrates that the majority of patients can be decannulated after this procedure. Patients with PGS had the highest operation-specific decannulation rates