A Brief History of BioPerl

Large-scale open-source projects face a litany of pitfalls and difficulties. Problems of contribution quality, credit for contributions, project coordination, funding, and mission-creep are ever-present. Of these, long-term funding and project coordination can interact to form a particularly difficult problem for open-source projects in an academic environment. BioPerl was chosen as an example of a successful academic open-source project. Several of the roadblocks and hurdles encountered and overcome in the development of BioPerl are examined through the telling of the history of the project. Along the way, key points of open-source law are explained, such as license choice and copyright. The BioPerl project current status is then analyzed, and four different strategies typically employed by traditional open-source projects at this stage are analyzed as future directions. Strategies such as soliciting donations, securing grants, providing dual-licenses to enhance commercial interest, and the paid provision of support have all been employed in various traditional open-source projects with success, but each has drawbacks when applied to the academy. Finally, the construction of a successful long-term strategy for BioPerl, and other academic open-source projects, is proposed so that such projects can navigate the difficulties

Pathways Across the Valley of Death: Novel Intellectual Property Strategies for Accelerated Drug Discovery

Drug discovery is stagnating. Government agencies, industry analysts, and industry scientists have all noted that, despite significant increases in pharmaceutical R&D funding, the production of fundamentally new drugs - particularly drugs that work on new biological pathways and proteins - remains disappointingly low. To some extent, pharmaceutical firms are already embracing the prescription of new, more collaborative R&D organizational models suggested by industry analysts. In this Article, we build on collaborative strategies that firms are already employing by proposing a novel public-private collaboration that would help move upstream academic research across the valley of death that separates upstream research from downstream drug candidates. By exchanging trade secrecy for contract-based collaboration, our proposal would both protect intellectual property rights and enable many more researchers to search for potential drug candidates

An Air-Filter Sensor for Home-Used Air Conditioners

This paper presents a successful senior project of instrumentation developed in a Mechanical Engineering Technology senior capstone course. Students were encouraged to approach the problem of designing an air-filter sensor and to propose an optimum and practical solution for the problem. Work includes conceptual design and analysis, implementation, tests and modifications. When an air filter is used in a home air conditioner, inhabitants often forget when to replace it until the cooling or heating capacity is obviously reduced. If the filter remains in service, the efficiency of the cooling/heating system will continue decreasing while the electricity bill will significantly increase. In some worst cases, the air quality will also be affected. This paper presents an idea of designing and fabricating an air-filter sensor to alleviate this problem. The sensor will send a warning signal when the filter collects a specific amount of dust in the air filter. It can be easily installed and only consumes a negligible amount of electricity. A photo sensor with an infrared LED emitter and receiver is used in this design. As the infrared LED can transmit through most of the home-used air filter to its receiver, a signal will be sent out when a specified amount of dust is collected in the filter and the light is blocked from the emitter to the receiver. The emitter and receiver are mounted on a simple fixture and can be easily fitted on an air filter. In addition, cost analysis of using the sensor show that it can save a significant amount on an electricity bill, when filters are replaced properly

Pathways Across the Valley of Death: Novel Intellectual Property Strategies for Accelerated Drug Discovery

Most therapeutic interventions produced by pharmaceutical firms take the form of small molecule drugs, which are mass produced at low marginal cost and ingested orally. Drug therapies typically work by affecting the activity of human proteins, known in the industry as targets, that have been implicated in disease pathways. Thus far, medical science has identified safe and effective therapies for only a few hundred of the estimated 3000 protein targets in the human genome that are potentially susceptible to a drug. Moreover, pharmaceutical firms have encountered major obstacles in producing fundamentally new small molecule drugs, especially those that work against new targets. According to one report, an average of only three drugs that act on novel targets have reached the market annually in recent years. This highly visible problem has attracted commentary in scholarly articles, government white papers, and the popular press. Government agencies, such as the National Institutes of Health, and industry insiders, have also recognized that one of the most serious pitfalls involves the difficulty of moving across the so-called valley of death that separates upstream research on promising genes, proteins, and biological pathways from downstream drug candidates. For example, an upstream finding that a given protein is differentially expressed in individuals with a particular disease may suggest that the protein merits further investigation. However, much more work (especially medicinal chemistry) is necessary to determine how good a target the protein really is and whether a marketable drug candidate that affects the activity of the protein is likely to be developed

Promoting Faculty Development with ASEE/NASA Fellowship Programs- Parametric Study of Laser Beam Cutting (LBC) processes- A Case Study

American Society for Engineering Education (ASEE) and National Aeronautics and Space Administration (NASA) offer a joint program for faculty and research development. This program known as ASEE/NASA Faculty Fellowship program offers opportunities for professional development for Engineering Technology faculty. This paper discusses one such experience involving applied research at NASA Langley Research Center, which resulted in professional development of the faculty member while enhancing the undergraduate curriculum in Engineering Technology

Design and Analysis of an Air Filter Sensor for a Residential Heating and Cooling System

This is a design project of an air-filter sensor to be used in home heating and cooling system. The project includes conceptual design, analysis, implementation, tests and modifications. First, the air quality and power consumption between a clean air filter and a dirty air filter is studied. Then, a photo sensor circuit with an ultra high brightness LED emitter and a phototransistor receiver is used to detect dust particles. A red warning LED lights up when a specified amount of dust is collected on the filter and blocks the light beam between the emitter and the receiver. The emitter and receiver are mounted on a simple fixture and can be easily fitted on any air filter. In addition, the cost analysis shows that this design can significantly reduce the electricity bill if the filters are properly replaced

Wave equations for the perturbations of a charged black hole

A pair of simple wave equations is presented for the symmetric gravitational and electromagnetic perturbations of a charged black hole. One of the equations is uncoupled, and the other has a source term given by the solution of the first equation. The derivation is presented in full detail for either axially symmetric or stationary perturbations, and is quite straightforward. This result is expected to have important applications in astrophysical models.Comment: 4 page

Drought: Understanding and reducing vulnerability through monitoring and early warning systems. Report of the DrIVER workshop, 17 March 2015.

As part of the Belmont Forum funded international DRIVER research project on linking indicators to impacts to improve drought monitoring and early warning systems (MEWs), a stakeholder workshop was held on 17th March 2015 in Wallingford, UK. The workshop was attended by representatives of various UK organisations with an interest in drought and MEWs and DRIVER researchers from the Centre for Ecology and Hydrology (UK), Open University (UK), University of Freiburg (Germany), National Drought Mitigation Center (USA) and CSIRO (Australia). The aims of the workshop were to introduce participants to the DRIVER project and recent RCUK drought projects; engage with stakeholders’ experiences, understandings and needs in relation to droughts; and identify needs for future MEWs. The design of the workshop was based on a commitment to social learning. It comprised a mix of presentations and interactive sessions using innovative techniques to develop collective insights, enabling participants to learn from others and contribute their experiences and ideas and concerns in relation to drought and MEWs. Themes emerging findings from the workshop were wide-ranging, but point to a range of issues, concerns and suggestions for improving drought management and MEWs centred on: recognition of different types of drought; uncertainties and risks relating to indicators; forecasting; impacts; politics of drought; public communication; role of stakeholders; and resilience strategies. The workshop suggests different ways of thinking and acting are required about drought and MEWs in particular. The discussions and presentations also suggest the complexity of droughts requires a more systemic understanding of drought policy, processes and practices in order to determine the role of MEWs and how these can be improved by linking indicators to impacts. The output of the workshop constitute a key source for informing and shaping ongoing DRIVER research activities and other events convened by RCUK drought research projects

Deletion in chromosome 6 spanning alpha-synuclein and multimerin1 loci in the Rab27a/b double knockout mouse

© The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Pattanayak, R., Underwood, R., Crowley, M. R., Crossman, D. K., Morgan, J. R., & Yacoubian, T. A. Deletion in chromosome 6 spanning alpha-synuclein and multimerin1 loci in the Rab27a/b double knockout mouse. Scientific Reports, 12(1), (2022): 9837, https://doi.org/10.1038/s41598-022-13557-8.We report an incidental 358.5 kb deletion spanning the region encoding for alpha-synuclein (αsyn) and multimerin1 (Mmrn1) in the Rab27a/Rab27b double knockout (DKO) mouse line previously developed by Tolmachova and colleagues in 2007. Western blot and RT-PCR studies revealed lack of αsyn expression at either the mRNA or protein level in Rab27a/b DKO mice. PCR of genomic DNA from Rab27a/b DKO mice demonstrated at least partial deletion of the Snca locus using primers targeted to exon 4 and exon 6. Most genes located in proximity to the Snca locus, including Atoh1, Atoh2, Gm5570, Gm4410, Gm43894, and Grid2, were shown not to be deleted by PCR except for Mmrn1. Using whole genomic sequencing, the complete deletion was mapped to chromosome 6 (60,678,870–61,037,354), a slightly smaller deletion region than that previously reported in the C57BL/6J substrain maintained by Envigo. Electron microscopy of cortex from these mice demonstrates abnormally enlarged synaptic terminals with reduced synaptic vesicle density, suggesting potential interplay between Rab27 isoforms and αsyn, which are all highly expressed at the synaptic terminal. Given this deletion involving several genes, the Rab27a/b DKO mouse line should be used with caution or with appropriate back-crossing to other C57BL/6J mouse substrain lines without this deletion.This study was supported by NIH [R56NS115767 (TAY), RF1NS115767-01A1 (TAY), P50NS108675 (TAY), and NINDS/NIA RF1NS078165 (JRM)]