bluuebunny/crossref_metadata_2025_split huggingface dataset:
Grid Codes versus Multi-Scale, Multi-Field Place Codes for Space
Authors: Dietrich Robin , Waniek Nicolai , Stemmler Martin , Knoll Alois 
Published: June 2023

ABSTRACTRecent work on bats flying over long distances has revealed that single hippocampal cells represent space on many scales, suggesting that these cells simultaneously participate in multiple neuronal networks to yield a multi-scale, multi-field place cell code. While the first theoretical analyses revealed that this code outperforms classical single-scale, single-field place codes, it remains an open question what the performance boundaries of this code are, what functional properties the network responsible for this code has, and how it compares to a highly regular grid code, in which cells form distinct modules, each with its own attractor dynamics on the network.In this paper we address these questions with rigorous analyses of comprehensive simulations. Specifically, we perform an evolutionary optimization of several multi-scale, multi-field place cell networks and compare the results against a single-scale, single-field as well as against a simple grid code. We focus on two main characteristics: the general performance of the code itself and the dynamics of the network generating it. Our simulation experiments show that, under normal conditions, the grid code easily outperforms any multi-scale, multi-field place code with respect to decoding accuracy. However, the latter is more robust to noise and lesions, such as drop-out. The robustness comes at a cost, as the grid code requires a significantly smaller number of neurons and fields per neuron. Further analyses of the network dynamics also revealed that the proposed topology of multi-scale, multi-field place cells does not, in fact, result in a continuous attractor network. More precisely, the simulated networks do not maintain activity bumps without position specific input. The multi-scale, multi-field code, therefore, seems to be a compromise between a place code and a grid code that invokes a trade-off between accurate positional encoding and robustness.
KATPchannel mutation disrupts hippocampal network activity and nocturnal γ shifts
Authors: Burkart Marie-Elisabeth , Kurzke Josephine , Vera Jorge , Ashcroft Frances M. , Eilers Jens , Lippmann Kristina 
Published: June 2023

AbstractATP-sensitive potassium (KATP) channels enable ATP to control the membrane potential and insulin secretion. Humans affected by severe activating mutations in KATPchannels suffer from developmentaldelay,epilepsy andneonataldiabetes (DEND syndrome). While the diabetes in DEND syndrome is well understood, the pathophysiology of the neurological symptoms remains unclear. We hypothesized that parvalbumin-positive interneurons (PV-INs) are key for the pathophysiology and found, by using electrophysiology, that expressing the DEND mutation Kir6.2-V59M selectively in PV-INs reduced intrinsic gamma frequency preference and short-term depression as well as disturbed cognition-associated gamma oscillations and hippocampal sharp waves. Furthermore, risk of seizures is increased and day-night shift in gamma activity disrupted. Thus, PV-INs play a key role in DEND syndrome and this provides a framework for establishing treatment options.One Sentence SummaryOveractive KATPchannels in PV-interneurons disturb cellular behaviour and cognition-associated network oscillations.
The satiety hormone cholecystokinin gates reproduction in fish by controlling gonadotropin secretion
Authors: Hollander Cohen Lian , Cohen Omer , Shulman Miriam , Aiznkot Tomer , Fontanaud Pierre , Revah Omer , Mollard Patrice , Golan Matan , Levavi Sivan Berta 
Published: June 2023

AbstractLife histories of oviparous species dictate high metabolic investment in the process of gonadal development leading to ovulation. In vertebrates, these two distinct processes are controlled by the gonadotropins follicle-stimulating hormone (FSH) and luteinizing hormone (LH), respectively. While it was suggested that a common secretagogue, gonadotropin-releasing hormone (GnRH), oversees both functions, the generation of loss-of-function fish challenged this view. Here, we reveal that the satiety hormone cholecystokinin (CCK) is the primary regulator of this axis in zebrafish. We found that FSH cells express a CCK receptor, and our findings demonstrate that mutating this receptor results in a severe hindrance to ovarian development. Additionally, it causes a complete shutdown of both gonadotropins secretion. Usingin-vivoandex-vivocalcium imaging of gonadotrophs, we show that GnRH predominantly activates LH cells, whereas FSH cells respond to CCK stimulation, designating CCK as the bona fide FSH secretagogue. These findings indicate that the control of gametogenesis in fish was placed under different neural circuits, that are gated by CCK.
The dependence of forecasts on sampling frequency as a guide to optimizing monitoring in community ecology
Authors: Daugaard Uriah , Merkli Stefanie , Merz Ewa , Pomati Francesco , Petchey Owen L. 
Published: June 2023

AbstractFacing climate change and biodiversity loss, it is critical that ecology advances so that processes, such as species interactions and dynamics, can be correctly estimated and skillfully forecasted. As different processes occur on different time scales, the sampling frequency used to record them should intuitively match these scales. Yet, the effect of data sampling frequency on ecological forecasting accuracy is understudied. Using a simple simulated dataset as a baseline and a more complex high-frequency plankton dataset, we tested how different sampling frequencies impacted abundance forecasts of different plankton classes and the estimation of their interactions. We then investigated whether plankton growth rates and body sizes could be used to select the most appropriate sampling frequency. The simple simulated dataset showed that the optimal sampling frequency scaled positively with growth rate. This finding was not repeated in the analyses of the plankton time series, however. There, we found that a reduction in sampling frequency worsened forecasts and led us to both over- and underestimate plankton interactions. This suggests that forecasting can be used to determine the ideal sampling frequency in scientific and monitoring programs. A better study design will improve theoretical understanding of ecology and advance policy measures dealing with current global challenges.Open research statementData and code used for the analyses and figures are available on Zenodo:https://doi.org/10.5281/zenodo.10066786. Environmental (lake) data (Merkli et al. 2022) are available from ERIC:https://doi.org/10.25678/00066D.
Future spinal reflex is embedded in primary motor cortex output
Authors: Umeda Tatsuya , Yokoyama Osamu , Suzuki Michiaki , Kaneshige Miki , Isa Tadashi , Nishimura Yukio 
Published: June 2023

AbstractMammals can execute intended limb movements despite the fact that spinal reflexes involuntarily modulate muscle activity. To generate appropriate muscle activity, the cortical descending motor output must coordinate with spinal reflexes, yet the underlying neural mechanism remains unclear. We simultaneously recorded activities in motor-related cortical areas, afferent neurons, and forelimb muscles of monkeys performing reaching movements. Motor-related cortical areas, primarily the primary motor cortex (M1), encode subsequent afferent activities attributed to forelimb movements. M1 also encodes a subcomponent of muscle activity evoked by these afferent activities, corresponding to spinal reflexes. Furthermore, selective disruption of the afferent pathway specifically reduced this subcomponent of muscle activity, suggesting that M1 output drives muscle activity not only through direct descending pathways but also through the “transafferent” pathway composed of descending plus subsequent spinal reflex pathways. Thus, M1 provides optimal motor output based on an internal forward model that prospectively computes future spinal reflexes.
Insecticidal roof barriers mounted on untreated bednets can be as effective againstAnopheles gambiae s.l.as insecticidal bednets
Authors: Abbott Anthony J. , Matope Agnes , Jones Jeff , Voloshin Vitaly , Towers Cathy , Towers David , McCall Philip J. 
Published: June 2023

ABSTRACTBarrier bednets (BBnets), regular bednets with a vertical insecticidal panel to target mosquitoes above the bednet roof, where activity is highest, have the potential to improve existing Insecticidal Treated Bednets (ITNs), by reducing quantity of insecticide required per net, reducing the toxic risks to those using the net, thus increasing the range of insecticides to choose from. We evaluated performance of different BBnet variants based on the PermaNet 3 (i.e., P3 BBnets with pyrethroid and piperonyl butoxide (PBO) on the roof or barrier; pyrethroid alone on the side walls) in room-scale bioassays, simultaneously video-recorded to track mosquitoes. Experimental results showed the longitudinal P3 barrier (P3L) to be highly effective: P3+P3L were consistently though not significantly more effective than the reference P3 bednet while performance of Ut+P3L was comparable to the reference P3. Comparing contact duration at the treated sections of each variant, the Ut+P3L accumulated 1273 contacts with 1374 seconds duration, all on the barrier, greatly exceeding the 792 seconds duration, from 8049 contacts, accumulated across the entire surface of the PermaNet 3 reference bednet. The BBnet’s potential to augment existing bednets and enhance their performance is considered.
Comprehensive computational analysis of the molecular mechanism of self-incompatibility in Brassicaceae using improved structure prediction
Authors: Sawa Tomoki , Moriwaki Yoshitaka , Jiang Hanting , Murase Kohji , Takayama Seiji , Shimizu Kentaro , Terada Tohru 
Published: June 2023

ABSTRACTPlants employ self-incompatibility (SI) to promote cross-fertilization. In Brassicaceae, this process is regulated by the formation of a complex between the pistil determinantSreceptor kinase (SRK) and the pollen determinantS-locus protein 11 (SP11, also known asS-locus cysteine-rich protein, SCR). In our previous study, we used the crystal structures of two eSRK–SP11 complexes inBrassica rapa S8andS9haplotypes and nine computationally predicted complex models to demonstrate that only the SRK ectodomain (eSRK) and SP11 pairs derived from the sameShaplotype exhibit high binding free energy. However, predicting the eSRK–SP11 complex structures for the other 100+Shaplotypes and genera remains difficult because of SP11 polymorphism in sequence and structure. Although protein structure prediction using AlphaFold2 exhibits considerably high accuracy for most protein monomers and complexes, 46% of the predicted SP11 structures that we tested showed < 75 mean per-residue confidence score (pLDDT). Here, we demonstrate that the use of curated multiple sequence alignment (MSA) for cysteine-rich proteins significantly improved model accuracy for SP11 and eSRK–SP11 complexes. Additionally, we calculated the binding free energies of the predicted eSRK–SP11 complexes using molecular dynamics (MD) simulations and observed that someArabidopsishaplotypes formed a binding mode that was critically different from that ofB. rapa S8andS9. Thus, our computational results provide insights into the haplotype-specific eSRK–SP11 binding modes in Brassicaceae at the residue level. The predicted models are freely available at Zenodo,https://doi.org/10.5281/zenodo.8047768.
Early life adversities affect expected value signaling in the adult brain
Authors: Sacu Seda , Dubois Magda , Aggensteiner Pascal-M. , Monninger Maximilian , Brandeis Daniel , Banaschewski Tobias , Hauser Tobias U. , Holz Nathalie 
Published: June 2023

AbstractBackgroundEarly adverse experiences are assumed to affect fundamental processes of reward learning and decision-making. However, computational neuroimaging studies investigating these circuits are sparse and limited to studies that investigated adversities retrospectively in adolescent samples.MethodsWe used prospective data from a longitudinal birth cohort study (n=156, 87 females, mean age=32.2) to investigate neurocomputational components underlying reinforcement learning in an fMRI-based passive avoidance task. We applied a principal component analysis to capture common variation across seven prenatal and postnatal adversity measures. The resulting adversity factors (factor 1: postnatal psychosocial adversities and prenatal maternal smoking, factor 2: prenatal maternal stress and obstetric adversity, and factor 3: lower maternal stimulation) and single adversity measures were then linked to computational markers of reward learning (i.e. expected value, prediction errors) in the core reward network.ResultsUsing the adversity factors, we found that adversities were linked to lower expected value representation in striatum, ventromedial prefrontal cortex (vmPFC) and anterior cingulate cortex (ACC). Expected value encoding in vmPFC further mediated the relationship between adversities and psychopathology. In terms of specific adversity effects, we found that obstetric adversity was associated with lower prediction error signaling in the vmPFC and ACC, whereas lower maternal stimulation was related to lower expected value encoding in the striatum, vmPFC, and ACC.ConclusionsOur results suggested that adverse experiences have a long-term disruptive effect on reward learning in several important reward-related brain regions, which can be associated with non-optimal decision-making and thereby increase the vulnerability of developing psychopathology.
II. Geometrical framework for thinking about globular proteins: the power of poking
Authors: Škrbić Tatjana , Giacometti Achille , Hoang Trinh X. , Maritan Amos , Banavar Jayanth R. 
Published: June 2023

AbstractRecently, we presented a framework for understanding protein structure based on the idea that simple constructs of holding hands or touching of objects can be used to rationalize the common characteristics of globular proteins. We developed a consistent approach for understanding the formation of the two key common building blocks of helices and sheets as well as the compatible assembly of secondary structures into the tertiary structure through the notion of poking pairwise interactions. Here we benchmark our predictions with a detailed analysis of structural data of over 4000 proteins from the Protein Data Bank. We also present the results of detailed computer simulations of a simplified model demonstrating a pre-sculpted free energy landscape, determined by geometry and symmetry, comprising numerous minima corresponding to putative native state structures. We explore the consequences of our model. Our results suggest that symmetry and geometry are a powerful guide to capture the simplicity underlying protein complexity.Statement for broader audienceA poking interaction in a chain causes two parts of a chain to poke towards each other. We use empirical data to establish a two-way link between geometry and chemistry through poking interactions and hydrogen bonds. We show that our simple and tractable geometrical model, superficially unrelated to proteins, can capture the essential features of a rich and incredibly complex protein molecule.
Building methodological consensus to ensure rigor and reproducibility in zebrafish fertility research
Authors: Kossack ME. , Bowie K. , Tian L. , Plavicki JS. 
Published: June 2023

SummaryZebrafish are an increasingly popular model for studying the genetic and environmental factors that shape male and female fertility; however, the field currently lacks a standardized approach to fertility assessment. The current lack of consensus makes comparisons across studies more challenging and is an obstacle to reproducibility in the fields of reproductive biology and toxicology. Here, we review the diversity of spawning approaches used in zebrafish reproductive toxicology research to asses fertility and provide evidence that spawning parameters can result in meaningful differences in egg production and spawning success.HighlightsZebrafish fertility research lacks methodological consensusMeasures of fertility vary with age and frequency of spawningMethodological consensus will increase reproducibility in toxicology
Defining cat mitogenome variation and accounting for numts via multiplex amplification and Nanopore sequencing
Authors: Patterson Emily , Lall Gurdeep Matharu , Neumann Rita , Ottolini Barbara , Sacchini Federico , Foster Aiden P. , Jobling Mark A. , Wetton Jon H. 
Published: June 2023

AbstractHair shed by domestic cats is a potentially useful source of forensic evidence. Analysable hair DNA is predominantly mitochondrial, but the recent domestication history of cats means that mtDNA diversity is low. A 402-bp control region segment is usually sequenced, defining only a small number of distinct mitotypes in populations. Previously, we used a long-amplicon approach to sequence whole mitogenomes in a sample of blood DNAs from 119 UK cats, greatly increasing observed diversity and reducing random match probabilities. To exploit this variation for forensic analysis, we here describe a multiplex system that amplifies the cat mitogenome in 60 overlapping amplicons of mean length 360 bp, followed by Nanopore sequencing. Variants detected in multiplex sequence data from hair completely mirror those from long-amplicon data from blood from the same individuals. However, applying the multiplex to matched blood DNA reveals additional sequence variants which derive from the major feline nuclear mitochondrial insertion sequence (numt), which covers 7.9 kb of the 17-kb mitogenome and exists in multiple tandem copies. We use long-amplicon Nanopore sequencing to investigate numt variation in a set of cats, together with an analysis of published genome sequences, and show that numt arrays are variable in both structure and sequence, thus providing a potential source of uncertainty when nuclear DNA predominates in a sample. Forensic application of the test was demonstrated by matching hairs from a cat with skeletal remains from its putative mother, both of which shared a globally common mitotype at the control region. The random match probability (RMP) in this case with the CR 402-bp segment was 0.21 and this decreased to 0.03 when considering the whole mitogenome. The developed multiplex and sequencing approach, when applied to cat hair where nuclear DNA is scarce, can provide a reliable and highly discriminating source of forensic genetic evidence. The confounding effect of numt co-amplification in degraded samples where mixed sequences are observed can be mitigated by variant phasing, and by comparison with numt sequence diversity data, such as those presented here.
Need for cognition moderates cognitive effort aversion
Authors: Gheza Davide , Kool Wouter , Pourtois Gilles 
Published: June 2023

AbstractWhen making decisions, humans aim to maximize rewards while minimizing costs. The exertion of mental or physical effort has been proposed to be one those costs, translating into avoidance of behaviors carrying effort demands. This motivational framework also predicts that people should experience positive affect when anticipating demand that is subsequently avoided (i.e., a “relief effect”), but evidence for this prediction is scarce. Here, we follow up on a previous study (1) that provided some initial evidence that people more positively evaluated outcomes if it meant they could avoid performing an additional demanding task. However, the results from this study did not provide evidence that this effect was driven by effort avoidance. Here, we report two experiments that are able to do this. Participants performed a gambling task, and if they did not receive reward they would have to perform an orthogonal effort task. Prior to the gamble, a cue indicated whether this effort task would be easy or hard. We probed hedonic responses to the reward-related feedback, as well as after the subsequent effort task feedback. Participants reported lower hedonic responses for no-reward outcomes when high vs. low effort was anticipated (and later exerted). They also reported higher hedonic responses for reward outcomes when high vs. low effort was anticipated (and avoided). Importantly, this relief effect was smaller in participants with high need for cognition. These results suggest that avoidance of high effort tasks is rewarding, but that the size off this effect depends on the individual disposition to engage with and expend cognitive effort. They also raise the important question of whether this disposition alters the cost of effort per se, or rather offset this cost during cost-benefit analyses.
Frequency modulation increases the specificity of time-resolved connectivity: A resting-state fMRI study
Authors: Faghiri Ashkan , Yang Kun , Ishizuka Koko , Sawa Akira , Adali Tülay , Calhoun Vince 
Published: June 2023

AbstractThe human brain is a highly dynamic system, and the methods we use to analyze the data gathered from this organ should account for this dynamism. One such family of methods that has attracted a lot of attention in the past decades is based on networks. The most well-known method for estimating the connection among these networks uses the sliding window Pearson correlation (SWPC) estimator. Although quite a useful tool, there are some important limitations. One such limitation is that SWPC applies a high pass filter to the activity time series. If we select a small window size (which is desirable to estimate rapid changes in functional connectivity), we will filter out important low-frequency activity information. In this work, we propose an approach based on single sideband modulation (SSB) in communication theory, which aims to solve this issue, allowing us to select smaller window sizes and capture rapid changes in the time-resolved functional connectivity. We use both simulation and real data to demonstrate the superior performance of the proposed method, SSB+SWPC, compared to classical SWPC. In addition, we compare the temporal recurring functional connectivity patterns between individuals with the first episode of psychosis (FEP) and typical controls (TC) and show that FEP stays more in FNC states that show weaker connectivity across the whole brain. A result exclusive to SSB+SWPC is that TC stays more in a state with negative connectivity between sub-cortical and cortical regions. All in all, based on both simulated data and real data, we argue that the proposed method, SSB+SWPC, is more sensitive for capturing temporal variation in functional connectivity.
The songbird lateral habenula projects to dopaminergic midbrain and is important for normal vocal development
Authors: Roeser Andrea , Teoh Han Kheng , Chen Ruidong , Cohen Itai , Goldberg Jesse 
Published: June 2023

AbstractMistakes in performance feel disappointing, suggesting that brain pathways for aversive feedback may play a role in motor learning. Here we tested if the lateral habenula (LHb), an evolutionarily conserved part of the limbic system known in mammals to relay aversive feedback from ventral pallidum (VP) to ventral tegmental area (VTA) dopamine neurons, is involved in birdsong learning and production. By combining viral tract tracing and functional circuit mapping, we discovered that songbird LHb links VP and an auditory cortical area to singing-related DA neurons that signal song errors. As in mammals, VP stimulation activated LHb activity and LHb stimulation suppressed DA firing. To test this pathway’s role in learning we lesioned the LHb in juvenile zebra finches and recorded their songs in adulthood. Birds with the LHb lesioned as juveniles produced highly unusual vocalizations as adults, including prolonged high-pitch notes and species-atypical trills. These findings identify a songbird VP-LHb-VTA pathway with similar functional connectivity as mammals, expand the known territories of vocal learning circuits, and demonstrate that limbic circuits associated with disappointing outcomes are important for motor performance learning.