Scaffolder - Software for Reproducible Genome Scaffolding.

Background: Assembly of short-read sequencing data can result in a fragmented non-contiguous series of genomic sequences. Therefore a common step in a genome project is to join neighboring sequence regions together and fill gaps in the assembly using additional sequences. This scaffolding step, however, is non-trivial and requires manually editing large blocks of nucleotide sequence. Joining these sequences together also hides the source of each region in the final genome sequence. Taken together, these considerations may make reproducing or editing an existing genome build difficult.

Methods: The software outlined here, “Scaffolder,” is implemented in the Ruby programming language and can be installed via the RubyGems software management system. Genome scaffolds are defined using YAML - a data format, which is both human and machine-readable. Command line binaries and extensive documentation are available.

Results: This software allows a genome build to be defined in terms of the constituent sequences using a relatively simple syntax to define the scaffold. This syntax further allows unknown regions to be defined, and adds additional sequences to fill gaps in the scaffold. Defining the genome construction in a file makes the scaffolding process reproducible and easier to edit compared with FASTA nucleotide sequence.

Conclusions: Scaffolder is easy-to-use genome scaffolding software. This tool promotes reproducibility and continuous development in a genome project. Scaffolder can be found at http://next.gs

ELISA detection of phenazepam, etizolam, pyrazolam, flubromazepam, diclazepam and delorazepam in blood using Immunalysis® benzodiazepine kit

Phenazepam and etizolam were the first uncontrolled benzodiazepines available for sale in the UK. Pyrazolam, flubromazepam and diclazepam are not used medicinally anywhere in the world; they are produced exclusively for the uncontrolled, recreational market. It is important to know whether potentially abused drugs like these can be detected in routine toxicological screening tests. The purpose of this study was to evaluate whether the Immunalysis® Benzodiazepines ELISA kit could detect phenazepam, etizolam, pyrazolam, flubromazepam, diclazepam and its metabolite delorazepam. Their cross-reactivity was assessed by comparing the absorbance of the drug with that of oxazepam, the reference standard. This study found that these uncontrolled benzodiazepines cross-react sufficiently to produce a positive result with the Immunalysis® Benzodiazepine ELISA kit. Cross-reactivity ranged from 79 to 107% for phenazepam, etizolam, pyrazolam, flubromazepam, diclazepam and delorazepam fortified into blood. The results show that it is possible to detect these newer benzodiazepines with traditional forensic toxicology laboratory tools and it is important to include these benzodiazepines in the confirmation tests

Modeling Supply Chain Resiliency

Engineered Resilient Systems (ERS) is a Department of Defense (DoD) program focusing on the effective and efficient design and development of complex engineered systems throughout their life cycle. There is a growing literature with qualitative definitions of resilience and quantitative models for systems with one performance measure. This paper uses a quantitative resilience framework (the Framework for ERS) that includes system design options, reliability, threats, vulnerabilities, responses, and consequences assessed in multiple system performance measures. The framework assists in establishing a model for any system to evaluate resiliency. This paper applies this framework using Multiple Objective Decision Analysis (MODA) to evaluate resiliency tradeoffs in designing supply chain and logistics networks to help decision makers increase the resilience of their supply chain networks. By using the MODA framework, decision makers can identify and evaluate multiple design options for a supply chain network

Peacebuilding and governance in a post-conflict society: a comparative analysis of Northern Ireland and Colombia

When the Government of Colombia formally ratified a peace accord in November 2016 with the left-wing guerrilla group FARC (Revolutionary Armed Forces of Colombia)it promised an end to more than 50 years of conflictwhich claimed the lives of 220,000 and displaced nearly 8 million people (Guardian, 2016). The hope for peace in Colombiawas further strengthened by promising early signs of a similar agreement forming as the National Liberation Army (ELN) called a 102 day truce in October 2017 (Al Jazeera, 2017a). If Colombian peace is to be successful in the rebuilding of a stable and cohesive society, it will take concerted political efforts towards peacebuilding and governance on both the domestic and international levels. In light of this significant peace brokerage in a protracted civil conflict, the aim of this paper is to provide a comparative analysis of the nascent Colombian peace agreement alongside the Northern Irish peace process on its 20th year anniversary, in order to identifysome of the key challenges faced and methods of peacebuilding which have proven successful in increasing social capital and structural stability. Over the last twenty years, Northern Ireland has been the focus of many international peacebuilding strategies and conflict research programmes, and as such offers opportunity for detailed comparative analysis against the conflict transformation journey which has only just started in Colombia. Protracted conflicts have a lasting impact on civil society creating division along ethnic or political lines, and this translates into low levels of support for state governance structures. Indeed, there is significant evidence to suggest that without government social integration interventions these divisions can become trans-generational conflicts. By using World Bank governance indicators to measure the changes in civil society after peace, acknowledging that positive performance against governance indicators correlates with a reduced capacity for conflict (Fearon, 2010), this paper identifiesthe challenges faced by post-conflict societies and proposes several effective frameworks for long-term development and peacebuilding. Several common themes emerge, including: the necessity of international stewardship during peace negotiation to lend legitimacy to the process, the need for development models focusing on conflict transformation, and lastly the use of spatial planning to combat development duality and as a long-term strategy towards social cohesion

Alien Registration- Warner, Hazel A. (Hampden, Penobscot County)

https://digitalmaine.com/alien_docs/11638/thumbnail.jp

Alien Registration- Wiley, Hazel A. (Monticello, Aroostook County)

https://digitalmaine.com/alien_docs/34289/thumbnail.jp

Alien Registration- Yerxa, Hazel A. (Fort Fairfield, Aroostook County)

https://digitalmaine.com/alien_docs/35905/thumbnail.jp

Understanding an Outlier: The U.S. System of Airport Governance and Economic Regulation

Unlike airports in many other countries which have been corporatized or privatized, nearly all U.S. airports continue to be operated by the public sector. They are subject to a system of economic regulation that provides little incentive to control costs or allocate capital efficiently. Yet, despite its apparent shortcomings, the current system has persisted over several decades. This Article explains the persistence of the current U.S. system of airport economic regulation based on price theory, regulatory economics, and public choice principles. It offers supporting empirical evidence for this equilibrium and identifies factors that might lead to a different outcome. Elected officials benefit from the current system because it permits them to bolster public employment, influence large contract awards, and provide financial support for local causes without relying on tax dollars. Airlines tolerate the current system, despite its inefficiencies, because airport costs are not a significant part of the airlines’ cost structure. Also, while airlines have only a limited influence on airport spending decisions at most airports, they have a greater influence on those decisions at airports that are most important to their competitive position. Airlines have more influence at airports with a high proportion of connecting passengers that the airlines can credibly threaten to re-route via other hub airports. Finally, airline executives are risk-averse and fear that the alternative they wind up with could be worse than the status quo. However, they have been willing to support alternatives when the benefits are clearly demonstrated and minimize the risks