Encouraging responsible reporting practices in the Instructions to Authors of neuroscience and physiology journals: There is room to improve

Journals can substantially influence the quality of research reports by including responsible reporting practices in their Instructions to Authors. We assessed the extent to which 100 journals in neuroscience and physiology required authors to report methods and results in a rigorous and transparent way. For each journal, Instructions to Authors and any referenced reporting guideline or checklist were downloaded from journal websites. Twenty-two questions were developed to assess how journal Instructions to Authors address fundamental aspects of rigor and transparency in five key reporting areas. Journal Instructions to Authors and all referenced external guidelines and checklists were audited against these 22 questions. Of the full sample of 100 Instructions to Authors, 34 did not reference any external reporting guideline or checklist. Reporting whether clinical trial protocols were pre-registered was required by 49 journals and encouraged by 7 others. Making data publicly available was encouraged by 64 journals; making (processing or statistical) code publicly available was encouraged by *30 of the journals. Other responsible reporting practices were mentioned by less than 20 of the journals. Journals can improve the quality of research reports by mandating, or at least encouraging, the responsible reporting practices highlighted here

Research and Education in Computational Science and Engineering

Over the past two decades the field of computational science and engineering (CSE) has penetrated both basic and applied research in academia, industry, and laboratories to advance discovery, optimize systems, support decision-makers, and educate the scientific and engineering workforce. Informed by centuries of theory and experiment, CSE performs computational experiments to answer questions that neither theory nor experiment alone is equipped to answer. CSE provides scientists and engineers of all persuasions with algorithmic inventions and software systems that transcend disciplines and scales. Carried on a wave of digital technology, CSE brings the power of parallelism to bear on troves of data. Mathematics-based advanced computing has become a prevalent means of discovery and innovation in essentially all areas of science, engineering, technology, and society; and the CSE community is at the core of this transformation. However, a combination of disruptive developments---including the architectural complexity of extreme-scale computing, the data revolution that engulfs the planet, and the specialization required to follow the applications to new frontiers---is redefining the scope and reach of the CSE endeavor. This report describes the rapid expansion of CSE and the challenges to sustaining its bold advances. The report also presents strategies and directions for CSE research and education for the next decade.Comment: Major revision, to appear in SIAM Revie

Structure of a highly conserved domain of rock1 required for shroom-mediated regulation of cell morphology

Rho-associated coiled coil containing protein kinase (Rho-kinase or Rock) is a well-defined determinant of actin organization and dynamics in most animal cells characterized to date. One of the primary effectors of Rock is non-muscle myosin II. Activation of Rock results in increased contractility of myosin II and subsequent changes in actin architecture and cell morphology. The regulation of Rock is thought to occur via autoinhibition of the kinase domain via intramolecular interactions between the N-terminus and the C-terminus of the kinase. This autoinhibited state can be relieved via proteolytic cleavage, binding of lipids to a Pleckstrin Homology domain near the C-terminus, or binding of GTP-bound RhoA to the central coiled-coil region of Rock. Recent work has identified the Shroom family of proteins as an additional regulator of Rock either at the level of cellular distribution or catalytic activity or both. The Shroom-Rock complex is conserved in most animals and is essential for the formation of the neural tube, eye, and gut in vertebrates. To address the mechanism by which Shroom and Rock interact, we have solved the structure of the coiled-coil region of Rock that binds to Shroom proteins. Consistent with other observations, the Shroom binding domain is a parallel coiled-coil dimer. Using biochemical approaches, we have identified a large patch of residues that contribute to Shrm binding. Their orientation suggests that there may be two independent Shrm binding sites on opposing faces of the coiled-coil region of Rock. Finally, we show that the binding surface is essential for Rock colocalization with Shroom and for Shroom-mediated changes in cell morphology. © 2013 Mohan et al

How to perceive the width of grasped objects: Insight into the central processes that govern proprioceptive judgements - Data and Code

## Graspolator ***Code and data for the Graspolator manuscript.In the study manuscript, Experiment 1 was conducted by Lovisa, and Experiment 2 was conducted by Kathy.However, Kathy collected data before Lovisa. ### Requirements***- Python >3.7- Package requirements as saved in requirements.txt### Installation***On Mac an Linux:```$cd ../path/to/project/directory$ git clone https://github.com/MartinHeroux/graspolator.git$cd graspolator$ python -m venv venv$source venv/bin/activate$ pip install -r requirements.txt$ python main.py```### Data location***data/### Outputs***The following subdirectories will be created in the project directory:* results: contains text files of numerical outcomes* plots: contains figures from manuscript</p

Effects of horizontal distance and limb crossing on perceived hand spacing and ownership: Differential sensory processing across hand configurations

We have previously shown that, with the hands apart vertically, passively grasping an artificial finger induces a sense of ownership over the artificial finger and coming-together of the hands. The present study investigated this grasp illusion in the horizontal plane. Thirty healthy participants were tested in two conditions (grasp and no grasp) with their hands at different distances apart, either crossed or uncrossed. After 3 min, participants reported perceived spacing between index fingers, perceived index finger location, and, for the grasp condition, perceived ownership over the artificial finger. On average, there was no ownership at any of the hand configurations. With the hands uncrossed 7.5, 15 or 24 cm apart, there was no difference in perceived spacing between the grasp and no grasp conditions. With the hands crossed and 15 cm apart, perceived spacing between index fingers was 3.2 cm [0.7 to 5.7] (mean [95% CI]) smaller during the grasp condition compared to no grasp. Therefore, compared to when the hands are vertically separated, there is an almost complete lack of a grasp illusion in the horizontal plane which indicates the brain may process sensory inputs from the hands differently based on whether the hands are horizontally or vertically apart

Movement of the ribs in supine humans for small and large changes in lung volume

An object-tracking algorithm was used on computed tomography (CT) images of the thorax from six healthy participants and nine participants with chronic obstructive pulmonary disease (COPD) to describe the movement of the ribs between the static lung volumes of functional residual capacity (FRC) and total lung capacity (TLC). The continuous motion of the ribs during tidal breathing was also described using four-dimensional CT datasets from seven participants with thoracic esophageal malignancies. Rib motion was defined relative to a local joint coordinate system where rotations about the axes that predominantly affected the anteroposterior and transverse diameters of the rib cage were referred to as pump-handle and bucket-handle movements, respectively. Between TLC and FRC, pump-handle movements were 1.8 times larger in healthy participants than in participants with COPD, in line with their 1.6 times larger inspiratory capacities. However, when rib motion was normalized to the change in lung volume, pump-handle movements were similar for healthy participants and participants with COPD. We found no differences in bucket-handle movements between participant groups before and after normalization. Pump-handle movement was the dominant rib motion between FRC and TLC, on average four times greater than bucket-handle movement in healthy participants. For expiratory tidal volume, pump-handle movements were 20% smaller than bucket-handle movements. When normalized to tidal volume and compared with inspiratory capacity, pump-handle movements were smaller and bucket-handle movements were larger during tidal breathing. The findings suggest that the pump-handle and bucket-handle components of rib motion vary for small and large changes in lung volume. </p