A unified open-source platform for multimodal neural recording and perturbation during naturalistic behavior

Behavioral neuroscience faces two conflicting demands: long-duration recordings from large neural populations and unimpeded animal behavior. To meet this challenge, we developed ONIX, an open-source data acquisition system with high data throughput (2GB/sec) and low closed-loop latencies (<1ms) that uses a novel 0.3 mm thin tether to minimize behavioral impact. Head position and rotation are tracked in 3D and used to drive active commutation without torque measurements. ONIX can acquire from combinations of passive electrodes, Neuropixels probes, head-mounted microscopes, cameras, 3D-trackers, and other data sources. We used ONIX to perform uninterrupted, long (~7 hours) neural recordings in mice as they traversed complex 3-dimensional terrain. ONIX allowed exploration with similar mobility as non-implanted animals, in contrast to conventional tethered systems which restricted movement. By combining long recordings with full mobility, our technology will enable new progress on questions that require high-quality neural recordings during ethologically grounded behaviors.

Open-source tool for real-time and automated analysis of droplet-based microfluidic

Droplet-based microfluidic technology is a powerful tool for generating large numbers of monodispersed nanoliter-sized droplets for ultra-high throughput screening of molecules or single cells. Yet further progress in the development of methods for the real-time detection and measurement of passing droplets is needed for achieving fully automated systems and ultimately scalability. Existing droplet monitoring technologies are either difficult to implement by non-experts or require complex experimentation setups. Moreover, commercially available monitoring equipment is expensive and therefore limited to a few laboratories worldwide. In this work, we validated for the first time an easy-to-use, open-source Bonsai visual programming language to accurately measure in real-time droplets generated in a microfluidic device. With this method, droplets are found and characterized from bright-field images with high processing speed. We used off-the-shelf components to achieve an optical system that allows sensitive image-based, label-free, and cost-effective monitoring. As a test of its use we present the results, in terms of droplet radius, circulation speed and production frequency, of our method and compared its performance with that of the widely-used ImageJ software. Moreover, we show that similar results are obtained regardless of the degree of expertise. Finally, our goal is to provide a robust, simple to integrate, and user-friendly tool for monitoring droplets, capable of helping researchers to get started in the laboratory immediately, even without programming experience, enabling analysis and reporting of droplet data in real-time and closed-loop experiments.

Enhanced passive surveillance for early detection of African and classical swine fevers

African swine fever (ASF) and classical swine fever (CSF) are transboundary animal diseases (TADs) of pigs. Much effort and resources are regularly put into preventing these diseases' introduction in free areas. Passive surveillance activities bring the highest chances for the early detection of TAD incursions because they are routinely and widely conducted at farms, and because these activities focus on the time between introduction and when the first sample is sent for diagnostic testing. The authors proposed the implementation of an enhanced passive surveillance (EPS) protocol based on collecting data through participatory surveillance actions using an objective and adaptable scoring system to aid the early detection of ASF or CSF at the farm level. The protocol was applied in two commercial pig farms for ten weeks in the Dominican Republic, which is a CSF- and ASF-infected country. This study was a proof of concept, based on the EPS protocol to aid detection of substantial variations in the risk score triggering testing. One of the followed farms had score variation, which triggered testing of the animals, although the test results were negative. The study enables assessment of some of the weaknesses associated with passive surveillance and provides lessons applicable to the problem. Results demonstrate the potential for overcoming some issues preventing the broad application of EPS protocols and suggest that standardised approaches may contribute to the early detection of CSF and ASF introductions.

A robust role for motor cortex

The role of motor cortex in non-primate mammals remains unclear. More than a century of stimulation, anatomical and electrophysiological studies has implicated neural activity in this region with all kinds of movement. However, following the removal of motor cortex, rats retain most of their adaptive behaviors, including previously learned skilled movements. Here we revisit these two conflicting views of motor cortex and present a new behavior assay, challenging animals to respond to unexpected situations while navigating a dynamic obstacle course. Surprisingly, rats with motor cortical lesions show clear impairments facing an unexpected collapse of the obstacles, while showing no impairment with repeated trials in many motor and cognitive metrics of performance. We propose a new role for motor cortex: extending the robustness of sub-cortical movement systems, specifically to unexpected situations demanding rapid motor responses adapted to environmental context. The implications of this idea for current and future research are discussed.

Associations of tissue tumor mutational burden and mutational status with clinical outcomes in KEYNOTE-042: pembrolizumab versus chemotherapy for advanced PD-L1-positive NSCLC

BACKGROUND

We evaluated whether tissue tumor mutational burden (tTMB) and STK11, KEAP1, and KRAS mutations have clinical utility as biomarkers for pembrolizumab monotherapy versus platinum-based chemotherapy in patients with programmed death ligand- 1 (PD-L1)-positive (tumor proportion score ≥1%) advanced/metastatic non-small-cell lung cancer (NSCLC) without EGFR/ALK alterations in the phase III KEYNOTE-042 trial.

PATIENTS AND METHODS

This retrospective exploratory analysis assessed prevalence of tTMB and STK11, KEAP1, and KRAS mutations determined by whole-exome sequencing of tumor tissue and matched normal DNA and their associations with outcomes in KEYNOTE-042. Clinical utility of tTMB was assessed using a prespecified cut point of 175 mutations/exome.

RESULTS

Of 793 patients, 345 (43.5%) had tTMB ≥175 mutations/exome and 448 patients (56.5%) had tTMB <175 mutations/exome. No association was observed between PD-L1 expression and tTMB. Continuous tTMB score was associated with improved overall survival (OS) and progression-free survival among patients receiving pembrolizumab (Wald test, one-sided P < 0.001) but not those receiving chemotherapy (Wald test, two-sided P > 0.05). tTMB ≥175 mutations/exome was associated with improved outcomes for pembrolizumab versus chemotherapy, whereas tTMB <175 mutations/exome was not {OS: hazard ratio, 0.62 [95% confidence interval (CI) 0.48-0.80] and 1.09 (95% CI 0.88-1.36); progression-free survival: 0.75 (0.59-0.95) and 1.27 (1.04-1.55), respectively}. Improved OS [hazard ratio (95% CI)] for pembrolizumab versus chemotherapy was observed regardless of STK11 [STK11 mutant (n = 33): 0.37 (0.16-0.86), STK11 wild-type (n = 396): 0.83 (0.65-1.05)]; KEAP1 [KEAP1 mutant (n = 64): 0.75 (0.42-1.35), KEAP1 wild-type (n = 365): 0.78 (0.61-0.99)], or KRAS [KRAS mutant (n = 69): 0.42 (0.22-0.81); KRAS wild-type (n = 232): 0.86 (0.63-1.18)] mutation status.

CONCLUSION

tTMB with a cut point of ≥175 mutations/exome is a potential predictive biomarker for pembrolizumab monotherapy for advanced/metastatic PD-L1 tumor proportion score ≥1% NSCLC. Pembrolizumab is a standard first-line treatment in this setting regardless of STK11, KEAP1, or KRAS mutation status.

Bilayer conducting salts with polymeric anions

Five new salts of 5-cyanobenzene-ethylenedithio-tetrathiafulvalene (CNB-EDT-TTF), with general formula (CNB-EDT-TTF)4A, and anions A= Ag(CN)2 (1), Ag(CN)2•H2O (2), Ag2(CN)3 (3), Ag(SCN)2 (4) and Hg2(SCN)5 (5), were prepared by electrocrystallisation and characterised...

C–H⋯NC hydrogen bonding in cyanobenzene-ethylenedithio-tetrathiafulvalene compounds

The importance of C–H⋯NC interactions, which although generally considered weak, are effective in the self-assembly of crystal structures.

Color difference between the vita classical shade guide and composite veneers using the dual-layer technique

Background

The purpose of this in vitro study was to evaluate the color difference between the Vita Classical Shade Guide and composite veneers using the dual-layer technique.

Material and Methods

Thirty samples were fabricated using a custom-made mold (Easy Layering Shade Guide Kit, 3M) using two resin composites: Filtek Supreme Ultra (3M); and Estelite Omega (Tokuyama) (n=3). The composite veneers were made by layering the different enamel and body or dentin shades from each composite. The color measurements were taken using a spectrophotometer (Vita Easyshade V®, Vita Zahnfabrik). The ΔE00 between the Vita Classical Shade Guide (Vita Zahnfabrik) and the composite veneers were calculated using the CIEDE2000 formula.

Results

For the composite veneers using Filtek Supreme Ultra, the best match for A1 Vita shade was achieved layering either EA1 with DA2 or DA3; EA2 with DA1 or DA2 (ΔE00= 1.53 ~ 1.96 ± 0.4). For A2 Vita shade the best match would be EA3 with DA3 or EA3 with DA2 (ΔE00= 1.40 ~ 1.85 ± 0.1); or for A3 Vita shade the best match would be EA3 with DA2 2.50±(0.6). For the composite veneers using Estelite Omega, the were no best match for neither A1, A2 or A3 Vita shade (ΔE00> 2.5).

Conclusions

The combination of enamel and dentin shades from Filtek Supreme Ultra provided acceptable color match for A1, A2 and A3 shades from the Vita Shade Guide, while Estelite Omega did not provide acceptable color match for any of the Vita Shade Guide standard shades tested.

Key words:Color, color matching, optical properties, resin composite, layering.

Effect of Gammulin supplementation during the first 24 d of life on health, growth, and first-lactation performance of Holstein cows

Development and health during calfhood are paramount for the success of dairy operations because they are associated with longevity and productivity later in life. Thus, provision of nutritional supplements has been explored as an alternative to improve growth of preweaned calves. Holstein calves (female = 472, male = 46) from 2 dairies located in the San Joaquin Valley were assigned randomly to receive 25 g/d of Gammulin (APC Inc.) from 2 to 24 d of age (GAM = 263) or to receive no supplementation (control = 255). Calves were fed a mixture of waste milk and milk replacer (3.79 L/d), and study personnel added the supplement to the bottles of calves in the GAM treatment daily. Study personnel monitored calves 6 d/wk and recorded starter intake, fecal score (1 = firm, 4 = watery), and attitude score (1 = alert and responsive, 4 = recumbent). Blood samples were collected (4, 7, 14, 26, 44, 56, and 68 d of age) to determine concentrations of total protein, glucose (n = 64), nonesterified fatty acids (n = 64), β-hydroxybutyrate (n = 171), and hematocrit (n = 518). Calves (n = 64) were treated with 0.5 mg of ovalbumin at 3, 21, and 42 d of age, and concentration of anti-ovalbumin IgG was measured. The percentage of polymorphonuclear leukocytes positive for phagocytosis and oxidative burst after the ex vivo exposure to an enteropathogenic Escherichia coli was evaluated (n = 64). We followed the female calves through the end of the first lactation or until they left the herd to evaluate the effect of treatment on first-lactation performance. Treatment did not affect metabolic and immune responses. During the supplementation (1 to 24 d of age), starter intake did not differ between treatments, but the GAM treatment reduced starter intake (638.5 ± 1.1 vs. 696.6 ± 1.1 g/d; mean ± standard error of the mean) from 25 to 60 d of age and average daily gain (798.8 ± 15.4 and 749.5 ± 15.2) from 23 to 60 d of age, resulting in reduced body weight at 60 d of age (68.4 ± 0.4 vs. 69.8 ± 0.5 kg). From 1 to 24 d of age, GAM treatment reduced the number of days calves had fecal score = 4 (ratio of number of days = 0.92; 95% confidence interval = 0.84-1.00) and it reduced the number of electrolyte treatments calves received (ratio of number of treatments = 0.92; 95% confidence interval = 0.85-0.99). Treatment did not affect the hazard of first calving and first-lactation 305-d milk yield, but the adjusted hazard ratio (0.82; 95% confidence interval = 0.65, 1.04) of pregnancy in the first lactation tended to be reduced for the GAM treatment. In the conditions of this experiment, supplementation with 25 g/d of GAM to the liquid feed from 2 to 24 d of age did not improve calfhood health and performance.

Creating and controlling visual environments using BonVision

Real-time rendering of closed-loop visual environments is important for next-generation understanding of brain function and behaviour, but is often prohibitively difficult for non-experts to implement and is limited to few laboratories worldwide. We developed BonVision as an easy-to-use open-source software for the display of virtual or augmented reality, as well as standard visual stimuli. BonVision has been tested on humans and mice, and is capable of supporting new experimental designs in other animal models of vision. As the architecture is based on the open-source Bonsai graphical programming language, BonVision benefits from native integration with experimental hardware. BonVision therefore enables easy implementation of closed-loop experiments, including real-time interaction with deep neural networks, and communication with behavioural and physiological measurement and manipulation devices.

New Open-Source Tools: Using Bonsai for Behavioral Tracking and Closed-Loop Experiments

The ability to dynamically control a behavioral task based on real-time animal behavior is an important feature for experimental neuroscientists. However, designing automated boxes for behavioral studies requires a coordinated combination of mechanical, electronic, and software design skills which can challenge even the best engineers, and for that reason used to be out of reach for the majority of experimental neurobiology and behavioral pharmacology researchers. Due to parallel advances in open-source hardware and software developed for neuroscience researchers, by neuroscience researchers, the landscape has now changed significantly. Here, we discuss powerful approaches to the study of behavior using examples and tutorials in the Bonsai visual programming language, towards designing simple neuroscience experiments that can help researchers immediately get started. This language makes it easy for researchers, even without programming experience, to combine the operation of several open-source devices in parallel and design their own integrated custom solutions, enabling unique and flexible approaches to the study of behavior, including video tracking of behavior and closed-loop electrophysiology.

Real-time, low-latency closed-loop feedback using markerless posture tracking

The ability to control a behavioral task or stimulate neural activity based on animal behavior in real-time is an important tool for experimental neuroscientists. Ideally, such tools are noninvasive, low-latency, and provide interfaces to trigger external hardware based on posture. Recent advances in pose estimation with deep learning allows researchers to train deep neural networks to accurately quantify a wide variety of animal behaviors. Here, we provide a new DeepLabCut-Live! package that achieves low-latency real-time pose estimation (within 15 ms, >100 FPS), with an additional forward-prediction module that achieves zero-latency feedback, and a dynamic-cropping mode that allows for higher inference speeds. We also provide three options for using this tool with ease: (1) a stand-alone GUI (called DLC-Live! GUI), and integration into (2) Bonsai, and (3) AutoPilot. Lastly, we benchmarked performance on a wide range of systems so that experimentalists can easily decide what hardware is required for their needs.

Electronic nicotine delivery systems (ECs) and COVID-19: the perfect storm for young consumers

The COVID-19 pandemic caused a change in our society and put health systems in crisis worldwide. Different risk factors and comorbidities have been found that increase the risk of mortality when acquiring this infection. The use of alternative devices to the cigarette like the electronic cigarettes, the vapers have been studied widely and generators of great controversy since it has been discovered that they also produce different pulmonary affections. When developing the SARS-CoV2 infection, different theories have been generated about the greater predisposition to a worse prognosis of people who use electronic cigarettes; however, the information on this continues in discovery. A group of experts made up of oncologists, infectologists, pulmonologists, and epidemiologists met to review the literature and then generate theories about the impact of electronic cigarettes on SARS-CoV2 infection.