Software Citation Implementation Challenges

The main output of the FORCE11 Software Citation working group (https://www.force11.org/group/software-citation-working-group) was a paper on software citation principles (https://doi.org/10.7717/peerj-cs.86) published in September 2016. This paper laid out a set of six high-level principles for software citation (importance, credit and attribution, unique identification, persistence, accessibility, and specificity) and discussed how they could be used to implement software citation in the scholarly community. In a series of talks and other activities, we have promoted software citation using these increasingly accepted principles. At the time the initial paper was published, we also provided guidance and examples on how to make software citable, though we now realize there are unresolved problems with that guidance. The purpose of this document is to provide an explanation of current issues impacting scholarly attribution of research software, organize updated implementation guidance, and identify where best practices and solutions are still needed

Race, Slavery, and the Expression of Sexual Violence in Louisa Picquet, The Octoroon

Historically, victims of sexual violence have rarely left written accounts of their abuse, so while sexual violence has long been associated with slavery in the United States, historians have few accounts from formerly enslaved people who experienced it first-hand. Through a close reading of the narrative of Louisa Picquet, a survivor of sexual violence in Georgia and Louisiana, this article reflects on the recovery of evidence of sexual violence under slavery through amanuensis-recorded testimony, the unintended evidence of survival within the violent archive of female slavery, and the expression of “race” as an authorial device through which to demonstrate the multigenerational nature of sexual victimhood

The Novel μ-Opioid Receptor Antagonist GSK1521498 Decreases Both Alcohol Seeking and Drinking: Evidence from a New Preclinical Model of Alcohol Seeking.

Distinct environmental and conditioned stimuli influencing ethanol-associated appetitive and consummatory behaviors may jointly contribute to alcohol addiction. To develop an effective translational animal model that illuminates this interaction, daily seeking responses, maintained by alcohol-associated conditioned stimuli (CSs), need to be dissociated from alcohol drinking behavior. For this, we established a procedure whereby alcohol seeking maintained by alcohol-associated CSs is followed by a period during which rats have the opportunity to drink alcohol. This cue-controlled alcohol-seeking procedure was used to compare the effects of naltrexone and GSK1521498, a novel selective μ-opioid receptor antagonist, on both voluntary alcohol-intake and alcohol-seeking behaviors. Rederived alcohol-preferring, alcohol-nonpreferring, and high-alcohol-drinking replicate 1 line of rats (Indiana University) first received 18 sessions of 24 h home cage access to 10% alcohol and water under a 2-bottle choice procedure. They were trained subsequently to respond instrumentally for access to 15% alcohol under a second-order schedule of reinforcement, in which a prolonged period of alcohol-seeking behavior was maintained by contingent presentations of an alcohol-associated CS acting as a conditioned reinforcer. This seeking period was terminated by 20 min of free alcohol drinking access that achieved significant blood alcohol concentrations. The influence of pretreatment with either naltrexone (0.1-1-3 mg/kg) or GSK1521498 (0.1-1-3 mg/kg) before instrumental sessions was measured on both seeking and drinking behaviors, as well as on drinking in the 2-bottle choice procedure. Naltrexone and GSK1521498 dose-dependently reduced both cue-controlled alcohol seeking and alcohol intake in the instrumental context as well as alcohol intake in the choice procedure. However, GSK1521498 showed significantly greater effectiveness than naltrexone, supporting its potential use for promoting abstinence and preventing relapse in alcohol addiction.The present study was funded by Medical Research Council Programme Grant (no. G1002231) and by GlaxoSmithKline (GSK), which has a commercial interest in GSK1521498. Charles R. Goodlett was funded by a grant from the IUPUI International Development Fund, which supported his sabbatical leave at the University of Cambridge. Maria Pilar Garcia-Pardo was funded by Val+id para investigadores en formación (Conselleria de educacion, Generalitat Valenciana), which also supported her stay at the University of Cambridge (January-April 2014) as a Visiting Student.This is the accepted manuscript. The final version is available from NPG at http://dx.doi.org/10.1038/npp.2015.15

The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases

The SIB Swiss Institute of Bioinformatics (www.isb-sib.ch) provides world-class bioinformatics databases, software tools, services and training to the international life science community in academia and industry. These solutions allow life scientists to turn the exponentially growing amount of data into knowledge. Here, we provide an overview of SIB's resources and competence areas, with a strong focus on curated databases and SIB's most popular and widely used resources. In particular, SIB's Bioinformatics resource portal ExPASy features over 150 resources, including UniProtKB/Swiss-Prot, ENZYME, PROSITE, neXtProt, STRING, UniCarbKB, SugarBindDB, SwissRegulon, EPD, arrayMap, Bgee, SWISS-MODEL Repository, OMA, OrthoDB and other databases, which are briefly described in this article

Autonomous Professional Learning through Practitioner Inquiry: A Study of Growth Plan System Experiences

The need for quality science education has long been established, but despite reform after reform, it remains a current concern. What we know as good teaching is not happening, perhaps because there is an increase in science teachers using alternative certification programs to enter the field. This lack of formal training causes teachers to have a reliance on professional learning opportunities to learn about reform-based science education. Unfortunately, traditional forms of professional learning are often inadequate, so newer professional learning designs have been established. Some of these newer designs, such as practitioner inquiry, offer teachers autonomy over how they assess and try to improve their practice. It is worthwhile to study these models, but it is not enough to solely look at these models externally; it is necessary to understand what happens within the professional learning itself. The problem is we cannot achieve that understanding until we know what the teachers actually experience as they engage in professional learning. How teachers conceptualize their professional learning experience is a critical voice. The purpose of this qualitative multiple case study was to uncover this critical voice of secondary science engaging in the Wilcox Science Education Fellowship (SEF), a professional learning program that provides an opportunity for teachers to rethink their practice and become leaders in their education community. In the second year of this program, fellows engage in autonomous practitioner inquiry through the design and implementation of a Growth Plan System (GPS) project. This study addressed one major research question regarding how Wilcox SEF fellows understand their experience designing and implementing their GPS project. Three subquestions were also answered regarding understanding how the fellows came to identify and articulate their GPS goals, what barriers prevented the fellows from investigating their GPS goals prior, and how their processes designing and implementing their GPS work contributed to an understanding of their work as practitioner inquiry. Addressing these research questions resulted in nine assertions. Each assertion was discussed in relation to the theoretical framework, existing literature, and implications

Software Citation Implementation Challenges

The main output of the FORCE11 Software Citation working group (https://www.force11.org/group/software-citation-working-group) was a paper on software citation principles (https://doi.org/10.7717/peerj-cs.86) published in September 2016. This paper laid out a set of six high-level principles for software citation (importance, credit and attribution, unique identification, persistence, accessibility, and specificity) and discussed how they could be used to implement software citation in the scholarly community. In a series of talks and other activities, we have promoted software citation using these increasingly accepted principles. At the time the initial paper was published, we also provided guidance and examples on how to make software citable, though we now realize there are unresolved problems with that guidance. The purpose of this document is to provide an explanation of current issues impacting scholarly attribution of research software, organize updated implementation guidance, and identify where best practices and solutions are still needed