ArrayPlex: distributed, interactive and programmatic access to genome sequence, annotation, ontology, and analytical toolsets

ArrayPlex is a software package that centrally provides a large number of flexible toolsets useful for functional genomics

A study to define a scatterometer data preprocessing system Final report

Analysis of scatterometer data preprocessing syste

The Longhorn Array Database (LAD): An Open-Source, MIAME compliant implementation of the Stanford Microarray Database (SMD)

BACKGROUND: The power of microarray analysis can be realized only if data is systematically archived and linked to biological annotations as well as analysis algorithms. DESCRIPTION: The Longhorn Array Database (LAD) is a MIAME compliant microarray database that operates on PostgreSQL and Linux. It is a fully open source version of the Stanford Microarray Database (SMD), one of the largest microarray databases. LAD is available at CONCLUSIONS: Our development of LAD provides a simple, free, open, reliable and proven solution for storage and analysis of two-color microarray data

An RNAi Screen for Genes Required for Growth of Drosophila Wing Tissue

Cell division and tissue growth must be coordinated with development. Defects in these processes are the basis for a number of diseases, including developmental malformations and cancer. We have conducted an unbiased RNAi screen for genes that are required for growth in the Drosophila wing, using GAL4-inducible short hairpin RNA (shRNA) fly strains made by the Drosophila RNAi Screening Center. shRNA expression down the center of the larval wing disc using dpp-GAL4, and the central region of the adult wing was then scored for tissue growth and wing hair morphology. Out of 4,753 shRNA crosses that survived to adulthood, 18 had impaired wing growth. FlyBase and the new Alliance of Genome Resources knowledgebases were used to determine the known or predicted functions of these genes and the association of their human orthologs with disease. The function of eight of the genes identified has not been previously defined in Drosophila The genes identified included those with known or predicted functions in cell cycle, chromosome segregation, morphogenesis, metabolism, steroid processing, transcription, and translation. All but one of the genes are similar to those in humans, and many are associated with disease. Knockdown of lin-52, a subunit of the Myb-MuvB transcription factor, or βNACtes6, a gene involved in protein folding and trafficking, resulted in a switch from cell proliferation to an endoreplication growth program through which wing tissue grew by an increase in cell size (hypertrophy). It is anticipated that further analysis of the genes that we have identified will reveal new mechanisms that regulate tissue growth during development

Integration of professional judgement and decision-making in high-level adventure sports coaching practice

This study examined the integration of professional judgement and decision-making processes in adventure sports coaching. The study utilised a thematic analysis approach to investigate the decision-making practices of a sample of high-level adventure sports coaches over a series of sessions. Results revealed that, in order to make judgements and decisions in practice, expert coaches employ a range of practical and pedagogic management strategies to create and opportunistically use time for decision-making. These approaches include span of control and time management strategies to facilitate the decision-making process regarding risk management, venue selection, aims, objectives, session content, and differentiation of the coaching process. The implication for coaches, coach education, and accreditation is the recognition and training of the approaches that“create time” for the judgements in practice, namely“creating space to think”. The paper concludes by offering a template for a more expertise-focused progression in adventure sports coachin

CUREs in Biochemistry—Where We Are and Where We Should Go

Integration of research experience into classroom is an important and vital experience for all undergraduates. These course-based undergraduate research experiences (CUREs) have grown from independent instructor lead projects to large consortium driven experiences. The impact and importance of CUREs on students at all levels in biochemistry was the focus of a National Science Foundation funded think tank. The state of biochemistry CUREs and suggestions for moving biochemistry forward as well as a practical guide (supplementary material) are reported here

Imperfect Tests, Pervasive Pathogens, and Variable Demographic Performance: Thoughts on Managing Bighorn Sheep Respiratory Disease

Respiratory disease (pneumonia) has been a persistent challenge for bighorn sheep (Ovis canadensis) conservation and its cause has been attributed to numerous bacteria including Mycoplasma ovipneumoniae and several Pasteurellaceae family species. This study sought to investigate efficacy of diagnostic protocols in detecting Pasteurellaceae and Mycoplasma ovipneumoniae, generate sampling recommendations for different protocols, assess the distribution of these disease agents among 17 bighorn sheep populations in Montana and Wyoming, and evaluate what associations existed between detection of these agents and demographic performance of bighorn sheep populations. Analysis of replicate samples from individual bighorn sheep revealed that detection probability for regularlyused diagnostic protocols was generally low (<50%) for Pasteurellaceae and was high (>70%) for Mycoplasma ovipneumoniae, suggesting that routine pathogen sampling likely mischaracterizes respiratory pathogen communities. Power analyses found that most pathogen species could be detected with 80% confidence at the population-level by conducting regularly-used protocols multiple times per animal. Each pathogen species was detected in over half of the study populations, but after accounting for detection probability there was low confidence in negative test results for populations where Pasteurellaceae species were not detected. Seventy-six percent of study populations hosted both Mycoplasma ovipneumoniae and Pasteurellaceae pathogens, yet a number of these populations were estimated to have positive population growth rates and recruitment rates greater than 30%. Overall, the results of this work suggest that bighorn sheep respiratory disease may be mitigated by manipulating population characteristics and respiratory disease epizootics could be caused by pathogens already resident in bighorn sheep population

The just-noticeable difference in speech-to-noise ratio

Just-noticeable differences (JNDs) have been measured for various features of sounds, but despite its importance to communication, there is no benchmark for what is a just-noticeable—and possibly meaningful—difference in speech-to-noise ratio (SNR). SNR plays a crucial role in speech communication for normal-hearing and hearing-impaired listeners. Difficulty hearing speech in background noise—a poor SNR—often leads to dissatisfaction with hearing-assistance devices. While such devices attempt through various strategies to address this problem, it is not currently known how much improvement in SNR is needed to provide a noticeable benefit. To investigate what is a noticeable benefit, we measured the JND in SNR for both normal-hearing and hearing-impaired listeners. Here, we report the SNR JNDs of 69 participants of varying hearing ability, estimated using either an adaptive or fixed-level procedure. The task was to judge which of the two intervals containing a sentence in speech-spectrum noise presented over headphones was clearer. The level of each interval was roved to reduce the influence of absolute level cues. The results of both procedures showed an average SNR JND of 3 dB that was independent of hearing ability. Further experiments using a subset of normal-hearing listeners showed that level roving does elevate threshold. These results suggest that noise reduction schemes may need to achieve a benefit greater than 3 dB to be reliably discriminable

Tackling the Monday Morning Quarterback: Applications of Hindsight Bias in Decision-Making Settings

Extant research has focused largely on what causes hindsight distortion. In contrast, this work examines applied aspects related to the bias in decision-making environments. A conceptual framework is provided and recent real–world examples are presented to outline how decision makers—and those who observe them—show hindsight effects. Then, both negative and positive consequences of the bias are outlined. Strategies are presented to reduce negative effects that occur when decision makers show hindsight distortion. Finally, because it is often not possible to avoid or to correct others\u27 hindsight–tainted evaluations, suggestions for coping with the bias are discussed