Miracle-dz/UniFAR-FTUs huggingface dataset:
Two-photon light-sheet microscopy for high-speed whole-brain functional imaging of zebrafish neuronal physiology and pathology

We present the development of a custom-made two-photon light-sheet microscope optimized for high-speed (5 Hz) volumetric imaging of zebrafish larval brain for the analysis of neuronal physiological and pathological activity. High-speed volumetric two-photon light-sheet microscopy is challenging to achieve, due to constrains on the signal-to-noise ratio. To maximize this parameter, we optimized our setup for high peak power of excitation light, while finely controlling its polarization, and we implemented remote scanning of the focal plane to record without disturbing the sample. Two-photon illumination is advantageous for zebrafish larva studies since infra-red excitation does not induce a visual response, that otherwise would affect the neuronal activity. In particular, we were able to record whole-brain neuronal activity of the larva with high temporal- and spatial-resolution during the nocturnal period without affecting the circadian rhythm. Analyzing the spatially resolved power spectra of GCaMP signal, we found significant differences for several frequency bands between the day/night phases in various brain regions. Moreover, we studied the fast dynamics that characterize the acutely induced pathological epileptic activity of the larvae, identifying the brain structures that are more susceptible to the action of the epileptogenic drug. In conclusion, the high speed two-photon light-sheet microscope that we developed is proving to be an important tool to study both the physiological and the pathological activity of the zebrafish larval brain without undesired visual stimulation.
Comparative Sequence Analysis of Historic and Current Porcine Rotavirus C Strains and Their Pathogenesis in 3-Day-Old and 3-Week-Old Piglets

The increased prevalence of porcine group C rotavirus (PRVC) in suckling piglets and the emergence of new genetically distinct PRVC strains are concerning due to the associated significant economic losses they cause to the swine industry. We sequenced and analyzed two new PRVC strains, RV0104 (G3), and RV0143 (G6) and compared their pathogenesis with that of the historic strain Cowden (G1) in gnotobiotic (Gn) pigs. Near complete genome sequence analysis confirmed that these two strains were distinct from one another and the Cowden strain. VP1, VP2, VP6, NSP1-NSP3, and NSP5 genes were more similar between Cowden and RV0143, whereas VP3, VP7, and NSP4 shared higher nucleotide identity between Cowden and RV0104. Three-day-old and 3-week-old Gn piglets were inoculated with 105 FFU/piglet of Cowden, RV0104 or RV0143, or mock. All 3-day-old piglets developed severe diarrhea, anorexia, and lethargy, with mean PRVC fecal shedding titers peaking and numerically higher in RV0104 and RV0143 piglets on post infection day (PID) 2. Histopathological examination of the small intestine revealed that the 3-day-old Cowden and RV0104 inoculated piglets were mildly affected, while significant destruction of small intestinal villi was observed in the RV0143 inoculated piglets. Consistent with the highest degree of pathological changes in the small intestines, the RV0143 inoculated piglets had numerically higher levels of serum IL-17 and IFN-α cytokines and numerically lower PRVC IgA geometric mean antibody titers. Milder pathological changes and overall higher titers of PRVC IgA antibodies were observed in 3-week-old vs. 3-day-old piglets. Additionally, diarrhea was only observed in RV0104 and RV0143 (but not Cowden) inoculated 3-week-old piglets, while levels of serum IL-10 and PRVC IgA antibodies were higher in Cowden inoculated pigs, consistent with the lack of diarrhea. Thus, we confirmed that these current, genetically heterogeneous PRVC strains possess distinct pathobiological characteristics that may contribute to the increased prevalence of PRVC diarrhea in neonatal suckling piglets.
Military participation in health security: analysis of Joint External Evaluation mission reports and National Action Plans for Health Security

Militaries across the world play an important but at times poorly defined and underappreciated role in global health security. For example, they are often called upon to support civilian authorities in humanitarian crises and to provide routine healthcare for civilians. Furthermore, military personnel are a unique population in a health security context, as they are highly mobile and often deploy to austere settings domestically and internationally, which may increase exposure to infectious diseases. Despite the role of militaries, few studies have systematically evaluated the involvement of militaries in global health security activities, including the Global Health Security Agenda (GHSA). To address this shortcoming, we analyzed Joint External Evaluation (JEE) mission reports (n=91) and National Action Plans for Health Security (n=11) that had been completed as of October 2019 (n=91) to determine the extent to which military organizations have been involved in the evaluation process, country military contributions to health security are accounted for, and specific recommendations are provided for the country's military. For JEE reports, military involvement was highest for the "Respond" core area (73%) but much lower for the Prevent (36%) and Detect (30%) core areas. Similarly, 73% of NAPHS documents mentioned military involvement in the Respond core area, compared to 27% and 36% for Prevent and Detect, respectively. Additionally, only 26% of JEE reports provide recommendations for the military in any of the core areas. Our results indicate the need to more fully incorporate military roles and contributions into the GHSA framework and other health security activities in order to improve national capabilities to prevent, detect, and respond to infectious disease threats.
Effects of Growth Medium and Water Stress on Soybean [Glycine max (L.) Merr.] Growth, Soil Water Extraction and Rooting Profiles by Depth in 1-m Rooting Columns

The pattern of soil water availability in frequently watered small pots is different from field environments. In small pots, volumetric soil water content (VSWC) is relatively high throughout the rooting zone due to a lack of suction to remove water from large and midsize capillaries. This necessitates the use of growing media with large pore space to avoid anaerobic conditions and so prohibits the use of field soil (FS) in small pots. We hypothesized that in 1-m rooting columns, the 0.01-MPa gravitational potential difference between top and bottom may permit the use of lightly-amended FS as a growing medium and provide for realistic VSWC and rooting profiles by depth. This study aimed to investigate the effects of amending a typical sand-based potting mix with different proportions of FS on soybean growth [dry matter (DM) accumulation], water use, VSWC and rooting profiles by depth under control and water stress conditions, in 1-m rooting columns (polyvinyl chloride tubes having an inside diameter of 10 cm and length of 1 m). We tested three growth media (0, 50, and 67% FS mixes), watered daily to either 100% of the maximum soil water holding capacity (SWHC; control) or 75% SWHC (stress). VSWC was calculated from time-domain reflectometry measurements. Compared to all growth media, the 67% FS mix resulted in the highest DM accumulation, water use, water use efficiency (WUE), and also produced realistic VSWC and rooting profiles by depth similar to those reported in the literature under field conditions. Compared to the control, the water stress treatment reduced shoot DM by 24%, root DM by 13%, whole-plant DM by 22%, and water use by 25%, but increased root-to-shoot DM ratio by 18% and WUE by 6%. Of the three growth media tested, the 67% FS mix was the most suitable growth medium for controlled environment phenotyping studies of root functional traits affecting drought tolerance in soybean. This study provides novel phenotyping tools to select for root function and yield formation traits that could increase soybean yield under soil water deficit conditions.
Impact of cannabis mass gathering events on mental health and health service utilization

Background: The Canadian government has legalized and regulated access to cannabis as of October 2018. In this context, there is a need to analyze data that may provide insights on the effects of increased accessibility and tolerance for cannabis use. One source of data is the phenomenon known as 4/20, a decades-old yearly mass gathering event supporting the legalization of cannabis. These events offer naturalistic epidemiologic data to ascertain specific impacts of cannabis consumption in a context of increased tolerance on health service utilization. Our study assessed the association between cannabis mass gathering events and health service utilization related to mental illness and substance use disorders at the nearest local emergency department. Methods: Emergency department service utilization data (2005-2015) was used. The sample analyzed consists of emergency department visits due to mental and substance use disorders. A multiple linear regression model was used to predict the number of daily visits with year, month, day of the week, and day of income assistance distribution as independent variables. Daily residuals were averaged, and residuals for the days with the highest number of visits were compared with the mean residual number of visits. Also, correlation of number of visits with attendance to mass gathering events was explored. Results: The residual number of visits for mental health and substance use disorder was the highest on April 20th 2015 (n=51.0, z-score=11.0, p<0.001), and on days associated with subsequent cannabis mass gathering events. Moreover, this number of visits is positively correlated with the number of attendees at the 4/20 event (Pearson's correlation coefficient: 0.76, 95% CI: 0.19 to 0.956, p=0.002), and increased over time. Conclusion: Cannabis mass gathering events were associated with an increased number of emergency visits for patients with mental health and substance use diagnoses at the nearest local emergency department. In the context of legalization and regulation of cannabis use, these specific gatherings will not necessarily be discontinued. Indeed, as per news reports the recent post-legalization 4/20 drew tens of thousands of people in Vancouver. Also, in the new context other non-specific mass gatherings may also lead to foreseeable episodic surges in ER utilization. In light of this and from a public health perspective, services need to be prepared to care for predictably larger numbers of people suffering cannabis intoxication during mass gatherings, as well as to make provisions to provide all other services that are regularly needed for other emergency conditions. Also, educational campaigns about responsible use during these events will become particularly important, as well as offering on-site support, triage and basic services. This will allow for specific care to be provided in a non-stigmatizing manner, proportional to need, and without overcrowding general emergency services.
Metabolic shift underlies recovery in reversible infantile respiratory chain deficiency

Reversible infantile respiratory chain deficiency (RIRCD) is a rare mitochondrial myopathy leading to severe metabolic disturbances in infants, which recover spontaneously after 6‐months of age. RIRCD is associated with the homoplasmic m.14674T>C mitochondrial DNA mutation; however, only ~ 1/100 carriers develop the disease. We studied 27 affected and 15 unaffected individuals from 19 families and found additional heterozygous mutations in nuclear genes interacting with mt‐tRNAGlu including EARS2 and TRMU in the majority of affected individuals, but not in healthy carriers of m.14674T>C, supporting a digenic inheritance. Our transcriptomic and proteomic analysis of patient muscle suggests a stepwise mechanism where first, the integrated stress response associated with increased FGF21 and GDF15 expression enhances the metabolism modulated by serine biosynthesis, one carbon metabolism, TCA lipid oxidation and amino acid availability, while in the second step mTOR activation leads to increased mitochondrial biogenesis. Our data suggest that the spontaneous recovery in infants with digenic mutations may be modulated by the above described changes. Similar mechanisms may explain the variable penetrance and tissue specificity of other mtDNA mutations and highlight the potential role of amino acids in improving mitochondrial disease.
Social Attention in Autism: Neural Sensitivity to Speech Over Background Noise Predicts Encoding of Social Information

Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by lack of attention to social cues in the environment, including speech. Hypersensitivity to sensory stimuli, such as loud noises, is also extremely common in youth with ASD. While a link between sensory hypersensitivity and impaired social functioning has been hypothesized, very little is known about the neural mechanisms whereby exposure to distracting sensory stimuli may interfere with the ability to direct attention to socially-relevant information. Here, we used functional magnetic resonance imaging (fMRI) in youth with and without ASD (N=54, age range 8–18 years) to (1) examine brain responses during presentation of brief social interactions (i.e., two-people conversations) shrouded in ecologically-valid environmental noises, and (2) assess how brain activity during encoding might relate to later accuracy in identifying what was heard. During exposure to conversation-in-noise (vs. conversation or noise alone), both neurotypical youth and youth with ASD showed robust activation of canonical language networks. However, the extent to which youth with ASD activated temporal language regions, including voice-selective cortex (i.e., posterior superior temporal sulcus), predicted later discriminative accuracy in identifying what was heard. Further, relative to neurotypical youth, ASD youth showed significantly greater activity in left-hemisphere speech-processing cortex (i.e., angular gyrus) while listening to conversation-in-noise (vs. conversation or noise alone). Notably, in youth with ASD, increased activity in this region was associated with higher social motivation and better social cognition measures. This heightened activity in voice-selective/speech-processing regions may serve as a compensatory mechanism allowing youth with ASD to hone in on the conversations they heard in the context of non-social distracting stimuli. These findings further suggest that focusing on social and non-social stimuli simultaneously may be more challenging for youth with ASD requiring the recruitment of additional neural resources to encode socially-relevant information.
Population modeling of early COVID-19 epidemic dynamics in French regions and estimation of the lockdown impact on infection rate

We propose a population approach to model the beginning of the French COVID-19 epidemic at the regional level. We rely on an extended Susceptible-Exposed-Infectious-Recovered (SEIR) mechanistic model, a simplified representation of the average epidemic process. Combining several French public datasets on the early dynamics of the epidemic, we estimate region-specific key parameters conditionally on this mechanistic model through Stochastic Approximation Expectation Maximization (SAEM) optimization using Monolix software. We thus estimate basic reproductive numbers by region before isolation (between 2.4 and 3.1), the percentage of infected people over time (between 2.0 and 5.9% as of May 11th, 2020) and the impact of nationwide household confinement on the infection rate (decreasing the transmission rate by 72% toward a Re ranging from 0.7 to 0.9). We conclude that a lifting of the lockdown should be accompanied by further interventions to avoid an epidemic rebound.
The spinal nerves that constitute the plexus lumbosacrales of the red squirrel (Sciurus vulgaris)

This study was aimed at investigating the lumbosacral plexus of squirrels (Sciurus vulgaris ). Ten squirrels were used in this work. The animals were carefully dissected and the spinal nerves that constitute the lumbosacral plexus were examined. It was discovered that the lumbosacral plexus was formed by L6, L7, S1, S2 in nine animals and in the one remaining animal in addition to these branches rami ventralis of L4 and L5 were forming the plexus. The common root forming the last part of the lumbosacral plexus and giving branches dis - persing to the hind limb was formed by the rami ventralis of L6, L7, S1, S2. Thus, in squirrels, the spinal nerves forming the lumbosacral plexus and the joining of these spinal nerves to each other differs from other rodents and mammals.
Characterization of Amphetamine, Methylphenidate, Nicotine, and Atomoxetine on Measures of Attention, Impulsive Action, and Motivation in the Rat: Implications for Translational Research

Amphetamine (AMP), methylphenidate (MPH), and atomoxetine (ATX) are approved treatments for ADHD, and together with nicotine (NIC), represent pharmacological agents widely studied on cognitive domains including attention and impulsive action in humans. These agents thus represent opportunities for clinical observation to be reinvestigated in the preclinical setting, i.e., reverse translation. The present study investigated each drug in male, Long Evans rats trained to perform either (1) the five-choice serial reaction time task (5-CSRTT), (2) Go/NoGo task, or (3) a progressive ratio (PR) task, for the purpose of studying each drug on attention, impulsive action and motivation. Specific challenges were adopted in the 5-CSRTT designed to tax attention and impulsivity, i.e., high frequency of stimulus presentation (sITI), variable reduction in stimulus duration (sSD), and extended delay to stimulus presentation (10-s ITI). Initially, performance of a large (> 80) cohort of rats in each task variant was conducted to examine performance stability over repeated challenge sessions, and to identify subgroups of “high” and “low” attentive rats (sITI and sSD schedules), and “high” and “low” impulsives (10-s ITI). Using an adaptive sequential study design, the effects of AMP, MPH, ATX, and NIC were examined and contrasting profiles noted across the tests. Both AMP (0.03–0.3 mg/kg) and MPH (1–6 mg/kg) improved attentional performance in the sITI but not sSD or 10-s ITI condition, NIC (0.05–0.2 mg/kg) improved accuracy across all conditions. ATX (0.1–1 mg/kg) detrimentally affected performance in the sITI and sSD condition, notably in “high” performers. In tests of impulsive action, ATX reduced premature responses notably in the 10-s ITI condition, and also reduced false alarms in Go/NoGo. Both AMP and NIC increased premature responses in all task variants, although AMP reduced false alarms highlighting differences between these two measures of impulsive action. The effect of MPH was mixed and appeared baseline dependent. ATX reduced break point for food reinforcement suggesting a detrimental effect on motivation for primary reward. Taken together these studies highlight differences between AMP, MPH, and ATX which may translate to their clinical profiles. NIC had the most reliable effect on attentional accuracy, whereas ATX was reliably effective against all tests of impulsive action.
Cellular Plasticity in Breast Cancer Progression and Therapy

With the exception of non-melanoma skin cancer, breast cancer is the most frequently diagnosed malignant disease among women, with the majority of mortality being attributable to metastatic disease. Thus, even with improved early screening and more targeted treatments which may enable better detection and control of early disease progression, metastatic disease remains a significant problem. While targeted therapies exist for breast cancer patients with particular subtypes of the disease (Her2+ and ER/PR+), even in these subtypes the therapies are often not efficacious once the patient's tumor metastasizes. Increases in stemness or epithelial-to-mesenchymal transition (EMT) in primary breast cancer cells lead to enhanced plasticity, enabling tumor progression, therapeutic resistance, and distant metastatic spread. Numerous signaling pathways, including MAPK, PI3K, STAT3, Wnt, Hedgehog, and Notch, amongst others, play a critical role in maintaining cell plasticity in breast cancer. Understanding the cellular and molecular mechanisms that regulate breast cancer cell plasticity is essential for understanding the biology of breast cancer progression and for developing novel and more effective therapeutic strategies for targeting metastatic disease. In this review we summarize relevant literature on mechanisms associated with breast cancer plasticity, tumor progression, and drug resistance.
Necrostatin-1 Ameliorates Neutrophilic Inflammation in Asthma by Suppressing MLKL Phosphorylation to Inhibiting NETs Release

Neutrophilic inflammation occurs during asthma exacerbation, and especially, in patients with steroid-refractory asthma, but the underlying mechanisms are poorly understood. Recently, a significant accumulation of neutrophil extracellular traps (NETs) in the airways of neutrophilic asthma has been documented, suggesting that NETs may play an important role in the pathogenesis. In this study, we firstly demonstrated that NETs could induce human airway epithelial cell damage in vitro. In a mouse asthmatic model of neutrophil-dominated airway inflammation, we found that NETs were markedly increased in bronchoalveolar lavage (BAL), and the formation of NETs exacerbated the airway inflammation. Additionally, a small-molecule drug necrostatin-1 (Nec-1) shown to inhibit NETs formation was found to alleviate the neutrophil-dominated airway inflammation. Nec-1 reduced total protein concentration, myeloperoxidase activity, and the levels of inflammatory cytokines in BAL. Finally, further experiments proved that the inhibition of Nec-1 on NETs formation might be related to its ability to inhibiting mixed lineage kinase domain-like (MLKL) phosphorylation and perforation. Together, these results document that NETs are closely associated with the pathogenesis of neutrophilic asthma and inhibition of the formation of NETs by Nec-1 may be a new therapeutic strategy to ameliorate neutrophil-dominated airway inflammation.