SSW Library: An SIMD Smith-Waterman C/C++ Library for Use in Genomic Applications

Summary: The Smith Waterman (SW) algorithm, which produces the optimal pairwise alignment between two sequences, is frequently used as a key component of fast heuristic read mapping and variation detection tools, but current implementations are either designed as monolithic protein database searching tools or are embedded into other tools. To facilitate easy integration of the fast Single Instruction Multiple Data (SIMD) SW algorithm into third party software, we wrote a C/C++ library, which extends Farrars Striped SW (SSW) to return alignment information in addition to the optimal SW score. Availability: SSW is available both as a C/C++ software library, as well as a stand alone alignment tool wrapping the librarys functionality at https://github.com/mengyao/Complete- Striped-Smith-Waterman-Library Contact: [email protected]: 3 pages, 2 figure

Analysis of on-orbit thermal characteristics of the 15-meter hoop/column antenna

In recent years, interest in large deployable space antennae has led to the development of the 15 meter hoop/column antenna. The thermal environment the antenna is expected to experience during orbit is examined and the temperature distributions leading to reflector surface distortion errors are determined. Two flight orientations corresponding to: (1) normal operation, and (2) use in a Shuttle-attached flight experiment are examined. A reduced element model was used to determine element temperatures at 16 orbit points for both flight orientations. The temperature ranged from a minimum of 188 K to a maximum of 326 K. Based on the element temperatures, orbit position leading to possible worst case surface distortions were determined, and the subsequent temperatures were used in a static finite element analysis to quantify surface control cord deflections. The predicted changes in the control cord lengths were in the submillimeter ranges

Employee Non-competes and Consideration: A Proposed Good Faith Standard for the 'Afterthought' Agreement"

This article proposes a good faith standard for the so-called “afterthought” agreement—a non-compete agreement given to and signed after an employee has commenced work. This issue has perplexed commentators and divided courts. The majority hold that continued employment is sufficient consideration for an existing at-will employee’s promise not to compete. A minority of courts require “independent” or “separate” consideration—such as a promotion, pay raise, or some other obligation incurred by the employer. The requirement of good faith would provide an important deterrent to employers who might otherwise seek to unfairly use their superior bargaining position to secure a mid-stream non-compete agreement, and additionally provide a significant incentive for employers to be open and transparent during all stages of the negotiation process for an afterthought agreement. At the same time, a good faith standard would permit employers the flexibility they need to protect their business assets by securing non-compete covenants as employment relationships develop and change over time. We propose a two-prong test for good faith. The substantive component would consider the business justification for an afterthought agreement, including changes in the employment relationship justifying a non-compete agreement. The process component of the good faith standard would consider the means by which the employer secured the employee’s assent to the non-compete agreement, including whether the employee was apprised of the non-compete provision during pre-hire negotiations and any coercive activity used to secure the employee’s consent

The Evolving Law of Employee Noncompete Agreements: Recent Trends and an Alternative Policy Approach

Businesses increasingly rely on employee non-compete agreements to protect their assets and forestall competition by former employees, a trend that will likely continue given the ascendancy of the information economy and the fundamental changes taking place in the post-industrial employment relationship. The proper balance between and among the competing interests of employers, employees and society implicated by post-employment restraints will continue to be an important public policy issue. This paper analyzes recent developments in the law of employee non-compete agreements and proposes an alternative framework to judge the enforceability of post-employment restraints on competition. Under our proposed policy framework, employee non-compete agreements designed to prevent the exploitation of the former employer’s customer relationships would be enforceable under a modified common law reasonableness standard. Trade secrets, however, would no longer be deemed a protectible interest justifying a covenant not to compete. Employers could prevent competition by a former employee only under the inevitable disclosure doctrine, which we contend provides a more balanced and fair resolution of the competing interests of employers and employees with regard to trade secrets and post-employment competition. By substituting a carefully framed injunction based on demonstrated necessity (inevitability) for the enforcement of a non-compete agreement based only on the potential for trade secret misappropriation, the proposed framework would support a climate of employee mobility while providing businesses an adequate level of protection for their trade secrets

Department of Homeland Security Science and Technology Directorate: Developing Technology to Protect America

In response to a congressional mandate and in consultation with Department of Homeland Security's (DHS) Science and Technology Directorate (S&T), the National Academy conducted a review of S&T's effectiveness and efficiency in addressing homeland security needs. This review included a particular focus that identified any unnecessary duplication of effort, and opportunity costs arising from an emphasis on homeland security-related research. Under the direction of the National Academy Panel, the study team reviewed a wide variety of documents related to S&T and homeland security-related research in general. The team also conducted interviews with more than 200 individuals, including S&T officials and staff, officials from other DHS component agencies, other federal agencies engaged in homeland security-related research, and experts from outside government in science policy, homeland security-related research and other scientific fields.Key FindingsThe results of this effort indicated that S&T faces a significant challenge in marshaling the resources of multiple federal agencies to work together to develop a homeland security-related strategic plan for all agencies. Yet the importance of this role should not be underestimated. The very process of working across agencies to develop and align the federal homeland security research enterprise around a forward-focused plan is critical to ensuring that future efforts support a common vision and goals, and that the metrics by which to measure national progress, and make changes as needed, are in place

Patient experience and challenges in group concept mapping for clinical research.

BACKGROUND AND OBJECTIVE: Group concept mapping (GCM) is a research method that engages stakeholders in generating, structuring and representing ideas around a specific topic or question. GCM has been used with patients to answer questions related to health and disease but little is known about the patient experience as a participant in the process. This paper explores the patient experience participating in GCM as assessed with direct observation and surveys of participants. METHODS: This is a secondary analysis performed within a larger study in which 3 GCM iterations were performed to engage patients in identifying patient-important outcomes for diabetes care. Researchers tracked the frequency and type of assistance required by each participant to complete the sorting and rating steps of GCM. In addition, a 17-question patient experience survey was administered over the telephone to the participants after they had completed the GCM process. Survey questions asked about the personal impact of participating in GCM and the ease of various steps of the GCM process. RESULTS: Researchers helped patients 92 times during the 3 GCM iterations, most commonly to address software and computer literacy issues, but also with the sorting phase itself. Of the 52 GCM participants, 40 completed the post-GCM survey. Respondents averaged 56 years of age, were 50% female and had an average hemoglobin A1c of 9.1%. Ninety-two percent (n = 37) of respondents felt that they had contributed something important to this research project and 90% (n = 36) agreed or strongly agreed that their efforts would help others with diabetes. Respondents reported that the brainstorming session was less difficult when compared with sorting and rating of statements. DISCUSSION: Our results suggest that patients find value in participating in GCM. Patients reported less comfort with the sorting step of GCM when compared with brainstorming, an observation that correlates with our observations from the GCM sessions. Researchers should consider using paper sorting methods and objective measures of sorting quality when using GCM in patient-engaged research to improve the patient experience and concept map quality

Tensile Strength of Malosma Laurina Leaves in Wet and Dry Conditions

Pepperdine University is one located in one of the most diverse places of the world. It is located in the Mediterranean which occupies less than 5% of the earth\u27s landmass and is only found in five areas which includes California. On the campus there are several canyons. One of the canyons is called Winter Canyon. The canyon contained a plant called Malosma laurina which is located in a riparian environment and a chaparral environment. The plant grows in both areas however, our hypothesis was that the dry plants\u27 leaves would demonstrate more plasticity. The soil humidity was also measured to compare the difference between the two and there was a significant difference. The average humidity for the wet soil was 43.5% and the dry was 22.5%. Our hypothesis was proven to be true after analyzing the results of the instron machine. The tensile strength was higher among dry leaves