ALBERT

Description: Software is a critical part of modern research and yet there is little support across the scholarly ecosystem for its acknowledgement and citation. Inspired by the activities of the FORCE11 working group focused on data citation, this document summarizes the recommendations of the FORCE11 Software Citation Working Group and its activities between June 2015 and April 2016. Based on a review of existing community practices, the goal of the working group was to produce a consolidated set of citation principles that may encourage broad adoption of a consistent policy for software citation across disciplines and venues. Our work is presented here as a set of software citation principles, a discussion of the motivations for developing the principles, reviews of existing community practice, and a discussion of the requirements these principles would place upon different stakeholders. Working examples and possible technical solutions for how these principles can be implemented will be discussed in a separate paper.

Description: This article describes the motivation, design, and progress of the Journal of Open Source Software (JOSS). JOSS is a free and open-access journal that publishes articles describing research software. It has the dual goals of improving the quality of the software submitted and providing a mechanism for research software developers to receive credit. While designed to work within the current merit system of science, JOSS addresses the dearth of rewards for key contributions to science made in the form of software. JOSS publishes articles that encapsulate scholarship contained in the software itself, and its rigorous peer review targets the software components: functionality, documentation, tests, continuous integration, and the license. A JOSS article contains an abstract describing the purpose and functionality of the software, references, and a link to the software archive. The article is the entry point of a JOSS submission, which encompasses the full set of software artifacts. Submission and review proceed in the open, on GitHub. Editors, reviewers, and authors work collaboratively and openly. Unlike other journals, JOSS does not reject articles requiring major revision; while not yet accepted, articles remain visible and under review until the authors make adequate changes (or withdraw, if unable to meet requirements). Once an article is accepted, JOSS gives it a digital object identifier (DOI), deposits its metadata in Crossref, and the article can begin collecting citations on indexers like Google Scholar and other services. Authors retain copyright of their JOSS article, releasing it under a Creative Commons Attribution 4.0 International License. In its first year, starting in May 2016, JOSS published 111 articles, with more than 40 additional articles under review. JOSS is a sponsored project of the nonprofit organization NumFOCUS and is an affiliate of the Open Source Initiative (OSI).

Description: Background Inflammatory bowel disease (IBD) is a family of debilitating disorders that affects more than 1 million people in the United States. Many animal studies of IBD use a dextran sulfate sodium (DSS) mouse model of colitis that induces rapid and severe colitis symptoms. Although the typical seven-day DSS model is appropriate for many studies, it destroys intestinal barrier function and results in intestinal permeability that is substantially higher than what is typically observed in patients. As such, therapies that enhance or restore barrier integrity are difficult or impossible to evaluate. Methods We identify administration conditions that result in more physiologically relevant intestinal damage by systematically varying the duration of DSS administration. We administered 3.0% DSS for four to seven days and assessed disease metrics including weight, fecal consistency, intestinal permeability, spleen weight, and colon length. Histology was performed to assess the structural integrity of the intestinal epithelium. Results Extended exposure (seven days) to DSS resulted in substantial, unrecoverable loss of intestinal structure and intestinal permeability increases of greater than 600-fold. Attenuated DSS administration durations (four days) produced less severe symptoms by all metrics. Intestinal permeability increased only 8-fold compared to healthy mice, better recapitulating the 2–18 fold increases in permeability observed in patients. The attenuated model retains the hallmark properties of colitis against which to compare therapeutic candidates. Our results demonstrate that an attenuated DSS colitis model obtains clinically relevant increases in intestinal permeability, enabling the effective evaluation of therapeutic candidates that promote barrier function.

Description: Background Weighted-baseball training programs are used at the high school, collegiate, and professional levels of baseball. The purpose of this study was to evaluate the effects of a six-week training period consisting of weighted implements, manual therapy, weightlifting, and other modalities on shoulder external rotation, elbow valgus stress, pitching velocity, and kinematics. Hypothesis A six-week training program that includes weighted implements will increase pitching velocity along with concomitant increases in arm angular velocities, joint kinetics, and shoulder external rotation. Methods Seventeen collegiate and professional baseball pitchers (age range 18–23, average: 19.9 ± 1.3) training at Driveline Baseball were evaluated via a combination of an eight-camera motion-capture system, range-of-motion measurements and radar- and pitch-tracking equipment, both before and after a six-week training period. Each participant received individualized training programs, with significant overlap in training methods for all athletes. Twenty-eight biomechanical parameters were computed for each bullpen trial, four arm range-of-motion measurements were taken, and pitching velocities were recorded before and after the training period. Pre- and post-training period data were compared via post-hoc paired t tests. Results There was no change in pitching velocity across the seventeen subjects. Four biomechanical parameters for the holistic group were significantly changed after the training period: internal rotational velocity was higher (from 4,527 ± 470 to 4,759 ± 542 degrees/second), shoulder abduction was lower at ball release (96 ± 7.6 to 93 ± 5.4°), the shoulder was less externally rotated at ball release (95 ± 15 to 86 ± 18°) and shoulder adduction torque was higher (from 103 ± 39 to 138 ± 53 N-m). Among the arm range of motion measurements, four were significantly different after the training period: the shoulder internal rotation range of motion and total range of motion for both the dominant and non-dominant arm. When the group was divided into those who gained pitching velocity and those who did not, neither group showed a significant increase in shoulder external rotation, or elbow valgus stress. Conclusions Following a six-week weighted implement program, pitchers did not show a significant change in velocity, joint kinetics, or shoulder external rotation range of motion. When comparing pitchers who gained velocity versus pitchers who did not, no statistically significant changes were seen in joint kinetics and shoulder range of motion.

Description: Background Improvements in data processing, increased understanding of the biomechanical background behind kinetics and kinematics, and technological advancements in inertial measurement unit (IMU) sensors have enabled high precision in the measurement of joint angles and acceleration on human subjects. This has resulted in new devices that reportedly measure joint angles, arm speed, and stresses to the pitching arms of baseball players. This study seeks to validate one such sensor, the MotusBASEBALL unit, with a marker-based motion capture laboratory. Hypothesis We hypothesize that the joint angle measurements (“arm slot” and “shoulder rotation”) of the MotusBASEBALL device will hold a statistically significant level of reliability and accuracy, but that the “arm speed” and “stress” metrics will not be accurate due to limitations in IMU technology. Methods A total of 10 healthy subjects threw five to seven fastballs followed by five to seven breaking pitches (slider or curveball) in the motion capture lab. Subjects wore retroreflective markers and the MotusBASEBALL sensor simultaneously. Results It was found that the arm slot (R = 0.975, P 〈 0.001), shoulder rotation (R = 0.749, P 〈 0.001), and stress (R = 0.667, P = 0.001 when compared to elbow torque; R = 0.653, P = 0.002 when compared to shoulder torque) measurements were all significantly correlated with the results from the motion capture lab. Arm speed showed significant correlations to shoulder internal rotation speed (R = 0.668, P = 0.001) and shoulder velocity magnitude (R = 0.659, P = 0.002). For the entire sample, arm slot and shoulder rotation measurements were on a similar scale, or within 5–15% in absolute value, of magnitude to measurements from the motion capture test, averaging eight degrees less (12.9% relative differences) and nine degrees (5.4%) less, respectively. Arm speed had a much larger difference, averaging 3,745 deg/s (80.2%) lower than shoulder internal rotation velocity, and 3,891 deg/s (80.8%) less than the shoulder velocity magnitude. The stress metric was found to be 41 Newton meter (Nm; 38.7%) less when compared to elbow torque, and 42 Nm (39.3%) less when compared to shoulder torque. Despite the differences in magnitude, the correlations were extremely strong, indicating that the MotusBASEBALL sensor had high reliability for casual use. Conclusion This study attempts to validate the use of the MotusBASEBALL for future studies that look at the arm slot, shoulder rotation, arm speed, and stress measurements from the MotusBASEBALL sensor. Excepting elbow extension velocity, all metrics from the MotusBASEBALL unit showed significant correlations to their corresponding metrics from motion capture and while some magnitudes differ substantially and therefore fall short in validity, the link between the metrics is strong enough to indicate reliable casual use. Further research should be done to further investigate the validity and reliability of the arm speed metric.