Leveraging open hardware to alleviate the burden of COVID-19 on global health systems.

With the current rapid spread of COVID-19, global health systems are increasingly overburdened by the sheer number of people that need diagnosis, isolation and treatment. Shortcomings are evident across the board, from staffing, facilities for rapid and reliable testing to availability of hospital beds and key medical-grade equipment. The scale and breadth of the problem calls for an equally substantive response not only from frontline workers such as medical staff and scientists, but from skilled members of the public who have the time, facilities and knowledge to meaningfully contribute to a consolidated global response. Here, we summarise community-driven approaches based on Free and Open Source scientific and medical Hardware (FOSH) as well as personal protective equipment (PPE) currently being developed and deployed to support the global response for COVID-19 prevention, patient treatment and diagnostics

Open labware: 3-D printing your own lab equipment

The introduction of affordable, consumer-oriented 3-D printers is a milestone in the current “maker movement,” which has been heralded as the next industrial revolution. Combined with free and open sharing of detailed design blueprints and accessible development tools, rapid prototypes of complex products can now be assembled in one’s own garage—a game-changer reminiscent of the early days of personal computing. At the same time, 3-D printing has also allowed the scientific and engineering community to build the “little things” that help a lab get up and running much faster and easier than ever before

Photography-based taxonomy is inadequate, unnecessary, and potentially harmful for biological sciences

The question whether taxonomic descriptions naming new animal species without type specimen(s) deposited in collections should be accepted for publication by scientific journals and allowed by the Code has already been discussed in Zootaxa (Dubois & Nemésio 2007; Donegan 2008, 2009; Nemésio 2009a–b; Dubois 2009; Gentile & Snell 2009; Minelli 2009; Cianferoni & Bartolozzi 2016; Amorim et al. 2016). This question was again raised in a letter supported by 35 signatories published in the journal Nature (Pape et al. 2016) on 15 September 2016. On 25 September 2016, the following rebuttal (strictly limited to 300 words as per the editorial rules of Nature) was submitted to Nature, which on 18 October 2016 refused to publish it. As we think this problem is a very important one for zoological taxonomy, this text is published here exactly as submitted to Nature, followed by the list of the 493 taxonomists and collection-based researchers who signed it in the short time span from 20 September to 6 October 2016

Rationale, study design, and analysis plan of the Alveolar Recruitment for ARDS Trial (ART): Study protocol for a randomized controlled trial

Background: Acute respiratory distress syndrome (ARDS) is associated with high in-hospital mortality. Alveolar recruitment followed by ventilation at optimal titrated PEEP may reduce ventilator-induced lung injury and improve oxygenation in patients with ARDS, but the effects on mortality and other clinical outcomes remain unknown. This article reports the rationale, study design, and analysis plan of the Alveolar Recruitment for ARDS Trial (ART). Methods/Design: ART is a pragmatic, multicenter, randomized (concealed), controlled trial, which aims to determine if maximum stepwise alveolar recruitment associated with PEEP titration is able to increase 28-day survival in patients with ARDS compared to conventional treatment (ARDSNet strategy). We will enroll adult patients with ARDS of less than 72 h duration. The intervention group will receive an alveolar recruitment maneuver, with stepwise increases of PEEP achieving 45 cmH(2)O and peak pressure of 60 cmH2O, followed by ventilation with optimal PEEP titrated according to the static compliance of the respiratory system. In the control group, mechanical ventilation will follow a conventional protocol (ARDSNet). In both groups, we will use controlled volume mode with low tidal volumes (4 to 6 mL/kg of predicted body weight) and targeting plateau pressure <= 30 cmH2O. The primary outcome is 28-day survival, and the secondary outcomes are: length of ICU stay; length of hospital stay; pneumothorax requiring chest tube during first 7 days; barotrauma during first 7 days; mechanical ventilation-free days from days 1 to 28; ICU, in-hospital, and 6-month survival. ART is an event-guided trial planned to last until 520 events (deaths within 28 days) are observed. These events allow detection of a hazard ratio of 0.75, with 90% power and two-tailed type I error of 5%. All analysis will follow the intention-to-treat principle. Discussion: If the ART strategy with maximum recruitment and PEEP titration improves 28-day survival, this will represent a notable advance to the care of ARDS patients. Conversely, if the ART strategy is similar or inferior to the current evidence-based strategy (ARDSNet), this should also change current practice as many institutions routinely employ recruitment maneuvers and set PEEP levels according to some titration method.Hospital do Coracao (HCor) as part of the Program 'Hospitais de Excelencia a Servico do SUS (PROADI-SUS)'Brazilian Ministry of Healt

Haves and Have nots must find a better way: The case for Open Scientific Hardware

Although many efforts are being made to make science more open and accessible, they are mostly concentrated on issues that appear before and after experiments are performed: Open access journals, open databases for data and code sharing, and many other tools to increase replicability of science and access to information. While great, these initiatives do not directly increase the access to the scientific equipment necessary to perform experiments and to generate new data. Unfortunately, their availability has always been uneven around the world, mostly due to monetary constraints and affecting mostly low income countries and institutions. In this paper a case is made for the use of free/open source hardware in research and education even in countries and institutions where funds were never a problem

Posner test using Arduino and Python

<p>This fileset contains all information to run a Posner's test (exogenous cues), using an Arduino and Python.</p> <p>Data is generated using Arduino (measurement of reaction times) and fed via USB to a computer running Python to read in and record the data.</p

Nose poke device using 3d printed parts and Arduino

<p>This is a small project that contains all the necessary parts to establish a nose poke device to train rats</p

Building and hacking open source hardware

The first edition of the Aspects of Neuroscience Brainhack took place at the Department of Physics at University of Warsaw, Poland between November 17th and 19th 2017. This hackathon was one of the satellite events of the Aspects of Neuroscience conference, it was organized by the Brainhack organization to promote interaction between researchers, encouraging open (neuro)science and collaborations on projects related to the study of the nervous system. The event had a total of nine projects on many different topics including functional connectivity research, white matter tractography, classification of brain-ageing biomarkers through machine learning, presentation of a portable one channel EEG registration device and a do it yourself 3D-printed neurobiology lab. The latter is highlighted in this paper

Optogenetics.

<p><b>A</b>. Experimental configuration suitable for optogenetic stimulation of an individual zebrafish larva suspended in a drop of E3 (Methods). <b>B</b>. Spectrum and peak power of the three light-emitting diodes (LEDs) embedded at each ring position. Spectral filters can be used to limit excitation light reaching the camera (Rosco Supergel No. 19, ‘Fire’). <b>C</b>. Zebrafish larva (3 days postfertilisation [<i>dpf</i>]) expressing ChR2 broadly in neurons (<i>Et(E1b</i>:<i>Gal4)s1101t</i>, <i>Tg(UAS</i>::<i>Cr</i>.<i>ChR2_H134R-mCherry)s1985t</i>, <i>nacre-/-</i>). <b>D</b>. The animal exhibits pectoral fin burst motor patterns upon activation of blue LEDs (cf. <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2002702#pbio.2002702.s010" target="_blank">S8 Video</a>). <b>E, F</b>. <i>Drosophila</i> larvae expressing ChR2 in all neurons (elav-GAL4/+; UAS-shibre^ts; UAS-ChR2/+; UAS-ChR2/+) crawling on ink-stained agar reliably contract when blue LEDs are active. <b>G</b>, <b>H</b>. Proboscis extension reflex (PER) in adult <i>Drosophila</i> expressing CsChrimson in the gustatory circuit (w; +; GMR86A08-GAL4/UAS-CSChrimson; the GMR86A08-GAL4 is part of the Janelia Farm Flightlight collection [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2002702#pbio.2002702.ref032" target="_blank">32</a>]; its effect on PER is a personal communication from Olivia Schwarz and Jan Pielage, University of Kaiserslautern, Germany, who observed this phenotype as part of behavioural screen [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2002702#pbio.2002702.ref033" target="_blank">33</a>]) is reliably elicited by activation of red LEDs.</p

Thermogenetics.

<p><b>A</b>. The 4 cm x 4 cm Peltier element embedded in the FlyPi base, with the Thermistor clamped into one corner. <b>B</b>. Side view with FlyPi propped up on a set of 3D-printed feet to allow air dissipation beneath the base. The central processing unit (CPU) fan is positioned directly beneath the Peltier. <b>C</b>. Performance of the Peltier-thermistor feedback loop. Command 15°C and 35°C indicated by blue and red shading, switching every 5 minutes; room temperature 19°C (no shading).</p