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1. Systematic analysis of proximal midgut‐ and anorectal‐originating contractions in larval zebrafish using event feature detection and supervised machine learning algorithms

   https://doi.org/10.1111/nmo.14675  

   Cassidy, Ryan M. ; Flores, Erika M. ; Trinh Nguyen, Anh K. ; Cheruvu, Sai S. ; Uribe, Rosa A. ; Krachler, Anne Marie ; Odem, Max A. ( September 2023 , Neurogastroenterology & Motility)

   Zebrafish larvae are translucent, allowing in vivo analysis of gut development and physiology, including gut motility. While recent progress has been made in measuring gut motility in larvae, challenges remain which can influence results, such as how data are interpreted, opportunities for technical user error, and inconsistencies in methods.

   To overcome these challenges, we noninvasively introduced Nile Red fluorescent dye to fill the intraluminal gut space in zebrafish larvae and collected serial confocal microscopic images of gut fluorescence. We automated the detection of fluorescent‐contrasted contraction events against the median‐subtracted signal and compared it to manually annotated gut contraction events across anatomically defined gut regions. Supervised machine learning (multiple logistic regression) was then used to discriminate between true contraction events and noise. To demonstrate, we analyzed motility in larvae under control and reserpine‐treated conditions. We also used automated event detection analysis to compare unfed and fed larvae.

   Automated analysis retained event features for proximal midgut‐originating retrograde and anterograde contractions and anorectal‐originating retrograde contractions. While manual annotation showed reserpine disrupted gut motility, machine learning only achieved equivalent contraction discrimination in controls and failed to accurately identify contractions after reserpine due to insufficient intraluminal fluorescence. Automated analysis also showed feeding had no effect on the frequency of anorectal‐originating contractions.

   Automated event detection analysis rapidly and accurately annotated contraction events, including the previously neglected phenomenon of anorectal contractions. However, challenges remain to discriminate contraction events based on intraluminal fluorescence under treatment conditions that disrupt functional motility.

    

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2. Bridging the gap between movement data and connectivity analysis using the Time-Explicit Habitat Selection (TEHS) model

   https://doi.org/10.1186/s40462-024-00461-1  

   Valle, Denis ; Attias, Nina ; Cullen, Joshua A. ; Hooten, Mevin B. ; Giroux, Aline ; Oliveira-Santos, Luiz Gustavo R. ; Desbiez, Arnaud L. J. ; Fletcher, Jr., Robert J. ( March 2024 , Movement Ecology)

   Understanding how to connect habitat remnants to facilitate the movement of species is a critical task in an increasingly fragmented world impacted by human activities. The identification of dispersal routes and corridors through connectivity analysis requires measures of landscape resistance but there has been no consensus on how to calculate resistance from habitat characteristics, potentially leading to very different connectivity outcomes.

   We propose a new model, called the Time-Explicit Habitat Selection (TEHS) model, that can be directly used for connectivity analysis. The TEHS model decomposes the movement process in a principled approach into a time and a selection component, providing complementary information regarding space use by separately assessing the drivers of time to traverse the landscape and the drivers of habitat selection. These models are illustrated using GPS-tracking data from giant anteaters (Myrmecophaga tridactyla) in the Pantanal wetlands of Brazil.

   The time model revealed that the fastest movements tended to occur between 8 p.m. and 5 a.m., suggesting a crepuscular/nocturnal behavior. Giant anteaters moved faster over wetlands while moving much slower over forests and savannas, in comparison to grasslands. We also found that wetlands were consistently avoided whereas forest and savannas tended to be selected. Importantly, this model revealed that selection for forest increased with temperature, suggesting that forests may act as important thermal shelters when temperatures are high. Finally, using the spatial absorbing Markov chain framework, we show that the TEHS model results can be used to simulate movement and connectivity within a fragmented landscape, revealing that giant anteaters will often not use the shortest-distance path to the destination patch due to avoidance of certain habitats.

   The proposed approach can be used to characterize how landscape features are perceived by individuals through the decomposition of movement patterns into a time and a habitat selection component. Additionally, this framework can help bridge the gap between movement-based models and connectivity analysis, enabling the generation of time-explicit connectivity results.

    

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3. Micromagnetic stimulation (µMS) dose-response of the rat sciatic nerve

   https://doi.org/10.1088/1741-2552/acd582  

   Saha, Renata ; Sanger, Zachary ; Bloom, Robert P. ; Benally, Onri J. ; Wu, Kai ; Tonini, Denis ; Low, Walter C. ; Keirstead, Susan A. ; Netoff, Theoden I. ; Wang, Jian-Ping ( May 2023 , Journal of Neural Engineering)

   Objective.The objective of this study was to investigate the effects of micromagnetic stimuli strength and frequency from theMagneticPen(MagPen) on the rat right sciatic nerve. The nerve’s response was measured by recording muscle activity and movement of the right hind limb.Approach.The MagPen was custom-built to be stably held over the sciatic nerve. Rat leg muscle twitches were captured on video, and movements were extracted using image processing algorithms. EMG recordings were also used to measure muscle activity.Main results.The MagPen prototype, when driven by an alternating current, generates a time-varying magnetic field, which, according to Faraday’s law of electromagnetic induction, induces an electric field for neuromodulation. The orientation-dependent spatial contour maps of the induced electric field from the MagPen prototype have been numerically simulated. Furthermore, in thisin vivowork onµMS, a dose-response relationship has been reported by experimentally studying how varying the amplitude (Range: 25 mV_p-pthrough 6V_p-p) and frequency (range: 100 Hz through 5 kHz) of the MagPen stimuli alters hind limb movement. The primary highlight of this dose-response relationship (repeated overnrats, wheren= 7) is that for aµMS stimuli of higher frequency, significantly smaller amplitudes can trigger hind limb muscle twitch. This frequency-dependent activation can be justified by Faraday’s Law, which states that the magnitude of the induced electric field is directly proportional to the frequency.Significance.This work reports thatµMS can successfully activate the sciatic nerve in a dose-dependent manner. The impact of this dose-response curve addresses the controversy in this research community about whether the stimulation from theseμcoils arise from a thermal effect or micromagnetic stimulation. MagPen probes do not have a direct electrochemical interface with tissue and therefore do not experience electrode degradation, biofouling, and irreversible redox reactions like traditional direct contact electrodes. Magnetic fields from theμcoils create more precise activation than electrodes because they apply more focused and localized stimulation. Finally, unique features ofµMS, such as the orientation dependence, directionality, and spatial specificity, have been discussed.

    

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4. Frugivoria: A trait database for birds and mammals exhibiting frugivory across contiguous Neotropical moist forests

   https://doi.org/10.1111/geb.13716  

   Gerstner, Beth E. ; Bills, Patrick ; Zarnetske, Phoebe L. ( June 2023 , Global Ecology and Biogeography)

   Biodiversity in many areas is rapidly declining because of global change. As such, there is an urgent need for new tools and strategies to help identify, monitor and conserve biodiversity hotspots. This is especially true for frugivores, species consuming fruit, because of their important role in seed dispersal and maintenance of forest structure and health. One way to identify these areas is by quantifying functional diversity, which measures the unique roles of species within a community and is valuable for conservation because of its relationship with ecosystem functioning. Unfortunately, the functional trait information required for these studies can be sparse for certain taxa and specific traits and difficult to harmonize across disparate data sources, especially in biodiversity hotspots. To help fill this need, we compiled Frugivoria, a trait database containing ecological, life‐history, morphological and geographical traits for mammals and birds exhibiting frugivory. Frugivoria encompasses species in contiguous moist montane forests and adjacent moist lowland forests of Central and South America—the latter specifically focusing on the Andean states. Compared with existing trait databases, Frugivoria harmonizes existing trait databases, adds new traits, extends traits originally only available for mammals to birds also and fills gaps in trait categories from other databases. Furthermore, we create a cross‐taxa subset of shared traits to aid in analysis of mammals and birds. In total, Frugivoria adds 8662 new trait values for mammals and 14,999 for birds and includes a total of 45,216 trait entries with only 11.37% being imputed. Frugivoria also contains an open workflow that harmonizes trait and taxonomic data from disparate sources and enables users to analyse traits in space. As such, this open‐access database, which aligns with FAIR data principles, fills a major knowledge gap, enabling more comprehensive trait‐based studies of species in this ecologically important region.

   Ecological, life‐history, morphological and geographical traits.

   Neotropical countries (Mexico, Guatemala, Costa Rica, Panama, El Salvador, Belize, Nicaragua, Ecuador, Colombia, Peru, Bolivia, Argentina, Venezuela and Chile) with contiguous montane regions.

   IUCN spatial data: obtained February 2023, spanning range maps collated from 1998 to 2022. IUCN species data: obtained June 2019–September 2022. Newly included traits: span 1924 to 2023.

   Classes Mammalia and Aves; 40,074 species‐level traits; 5142 imputed traits for 1733 species (mammals: 582; birds: 1147) and 16 sub‐species (mammals).

   .csv; R.

    

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5. Improved 3D real‐time MRI of speech production

   https://doi.org/10.1002/mrm.28651  

   Zhao, Ziwei ; Lim, Yongwan ; Byrd, Dani ; Narayanan, Shrikanth ; Nayak, Krishna S. ( January 2021 , Magnetic Resonance in Medicine)

   To provide 3D real‐time MRI of speech production with improved spatio‐temporal sharpness using randomized, variable‐density, stack‐of‐spiral sampling combined with a 3D spatio‐temporally constrained reconstruction.

   We evaluated five candidate (k,t) sampling strategies using a previously proposed gradient‐echo stack‐of‐spiral sequence and a 3D constrained reconstruction with spatial and temporal penalties. Regularization parameters were chosen by expert readers based on qualitative assessment. We experimentally determined the effect of spiral angle increment andk_ztemporal order. The strategy yielding highest image quality was chosen as the proposed method. We evaluated the proposed and original 3D real‐time MRI methods in 2 healthy subjects performing speech production tasks that invoke rapid movements of articulators seen in multiple planes, using interleaved 2D real‐time MRI as the reference. We quantitatively evaluated tongue boundary sharpness in three locations at two speech rates.

   The proposed data‐sampling scheme uses a golden‐angle spiral increment in thek_x−k_yplane and variable‐density, randomized encoding alongk_z. It provided a statistically significant improvement in tongue boundary sharpness score (P < .001) in the blade, body, and root of the tongue during normal and 1.5‐times speeded speech. Qualitative improvements were substantial during natural speech tasks of alternating high, low tongue postures during vowels. The proposed method was also able to capture complex tongue shapes during fast alveolar consonant segments. Furthermore, the proposed scheme allows flexible retrospective selection of temporal resolution.

   We have demonstrated improved 3D real‐time MRI of speech production using randomized, variable‐density, stack‐of‐spiral sampling with a 3D spatio‐temporally constrained reconstruction.

    

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