bluuebunny/crossref_metadata_2025_split huggingface dataset:
Feedback processing in attack and defense conflicts: a neurophysiological study
Authors: Paiva Tiago O. , Coelho Rui C. , Pasion Rita , Dias-Oliveira Eva , De Dreu Carsten K. W. , Barbosa Fernando 
Published: June 2021

AbstractDespite being extensively modelled to explore decision making processes in economic tasks, there are no studies exploring the neurophysiological correlates of the Predator-Prey Game, a game theory paradigm designed to operationalize attack and defence conflicts. In the present study, we explored the relationship between the ERP components associated with feedback, namely feedback-related negativity (FRN) and feedback -elated P3b, and investment in an adapted version of the Predator-Prey Game (PPG), operationalizing attack and defence. Forty-seven (28 female) community-dwelling volunteers without history of neurological disease were recruited. Participants played the PPG game both as attackers and defenders while EEG signal was recorded with a 128 channels sensor net. Behavioural results showed that individuals tend to invest more and decide faster when playing in defence, rather than in attack. Electrophysiological data showed FRN to be sensitive to the valence of feedback, with increased amplitudes of FRN loss feedbacks. On the other hand, the P3b amplitudes were sensitive to the role, with increased amplitude for attack when compared with defence. The integration of the behavioural and ERP findings supports the theoretical model positing that attack elicits more deliberate and less automatic brain processes than defence.
Fast 3D Clear: A Fast, Aqueous, Reversible Three-Day Tissue Clearing Method for Adult and Embryonic Mouse Brain and Whole Body
Authors: Kosmidis Stylianos , Negrean Adrian , Dranovsky Alex , Losonczy Attila , Kandel Eric R. 
Published: June 2021

AbstractTo date, a variety of optical clearing methods have emerged that serve as powerful tools to study intact organs and neuronal circuits. Here we describe a newly developed, aqueous clearing protocol named “Fast 3D Clear”, which relies on tetrahydrofuran (THF) for tissue delipidation, and iohexol (Histodenz) for clearing, such that tissues can be imaged under immersion oil in light sheet imaging systems. Fast 3D Clear requires three days to achieve high transparency of adult and embryonic mouse tissues, while maintaining their anatomical integrity, and preserving a vast array of transgenic and viral/dye fluorophores, such as GCaMP3/6, tdTomato, Fast Blue, and IRF670. A unique advantage of Fast 3D Clear is its complete reversibility and thus compatibility with tissue sectioning and immunohistochemistry. Fast 3D Clear can be easily and quickly applied to a wide range of biomedical studies, thereby greatly facilitating the acquisition of high-resolution, two - and three -dimensional images.
On Improving an Already Competitive Segmentation Algorithm for the Cell Tracking Challenge - Lessons Learned
Authors: Scherr Tim , Löffler Katharina , Neumann Oliver , Mikut Ralf 
Published: June 2021

AbstractThe virtually error-free segmentation and tracking of densely packed cells and cell nuclei is still a challenging task. Especially in low-resolution and low signal-to-noise-ratio microscopy images erroneously merged and missing cells are common segmentation errors making the subsequent cell tracking even more difficult. In 2020, we successfully participated as team KIT-Sch-GE (1) in the 5th edition of the ISBI Cell Tracking Challenge. With our deep learning-based distance map regression segmentation and our graph-based cell tracking, we achieved multiple top 3 rankings on the diverse data sets. In this manuscript, we show how our approach can be further improved by using another optimizer and by fine-tuning training data augmentation parameters, learning rate schedules, and the training data representation. The fine-tuned segmentation in combination with an improved tracking enabled to further improve our performance in the 6th edition of the Cell Tracking Challenge 2021 as team KIT-Sch-GE (2).
Relaxin/insulin-like family peptide receptor 4 (Rxfp4) expressing hypothalamic neurons modulate food intake and preference in mice
Authors: Lewis Jo E , Woodward Orla RM , Nuzzaci Danaé , Smith Christopher A , Adriaenssens Alice E , Billing Lawrence , Brighton Cheryl , Phillips Benjamin U , Tadross John A , Kinston Sarah J , Ciabatti Ernesto , Göttgens Berthold , Tripodi Marco , Hornigold David , Baker David , Gribble Fiona M , Reimann Frank 
Published: June 2021

AbstractRelaxin/insulin-like-family peptide receptor-4 (RXFP4), the cognate receptor for insulin-like peptide 5 (INSL5), has been implicated in feeding behaviour as Rxfp4 knockout mice display shorter meal durations and reduced high fat diet (HFD) intake. Here, we generated transgenic Rxfp4-Cre mice to explore Rxfp4 expression and physiology. Using this model, we identified Rxfp4 expression in the central nervous system, including in the ventromedial hypothalamus (VMH). Intra-VMH infusion of INSL5 increased HFD and highly palatable liquid meal intake (HPM) of ad libitum fed wildtype mice. Single-cell RNA-sequencing of VMH Rxfp4-expressing cells (RXFP4VMH) defined a cluster of Rxfp4-labelled neurons expressing Esr1, Tac1 and Oxtr, alongside known appetite-modulating neuropeptide receptors (Mc4r, Cckar and Nmur2). Viral tracing demonstrated RXFP4VMH neural projections to the bed nucleus of the stria terminalis, paraventricular hypothalamus, paraventricular thalamus and central nucleus of the amygdala. Utilising designer receptors exclusively activated by designer drugs (DREADDs), we found that whole body chemogenetic inhibition (Di) of Rxfp4-expressing cells, mimicking native INSL5-RXFP4 signalling, increased intake of HFD and HPM, whilst activation (Dq), either at whole body level or specifically within the VMH, reduced HFD and HPM intake and altered food preference. Ablating VMH Rxfp4-expressing cells recapitulated the lower HFD intake phenotype of Rxfp4 knockout mice, resulting in reduced body weight. These findings identify a discrete Rxfp4-expressing neuronal population as a key regulator of food intake and preference and reveal hypothalamic RXFP4 signalling as a target for feeding behaviour manipulation.
Predicting and interpreting large scale mutagenesis data using analyses of protein stability and conservation
Authors: Høie Magnus H. , Cagiada Matteo , Frederiksen Anders Haagen Beck , Stein Amelie , Lindorff-Larsen Kresten 
Published: June 2021

AbstractUnderstanding and predicting the functional consequences of single amino acid is central in many areas of protein science. Here we collected and analysed experimental measurements of effects of >150,000 variants in 29 proteins. We used biophysical calculations to predict changes in stability for each variant, and assessed them in light of sequence conservation. We find that the sequence analyses give more accurate prediction of variant effects than predictions of stability, and that about half of the variants that show loss of function do so due to stability effects. We construct a machine learning model to predict variant effects from protein structure and sequence alignments, and show how the two sources of information are able to support one another. Together our results show how one can leverage large-scale experimental assessments of variant effects to gain deeper and general insights into the mechanisms that cause loss of function.
Macroscale structural changes of thylakoid architecture during high light acclimation in Chlamydomonas reinhardtii
Authors: Broderson Mimi , Niyogi Krishna K. , Iwai Masakazu 
Published: June 2021

ABSTRACTPhotoprotection mechanisms are ubiquitous among photosynthetic organisms. The photoprotection capacity of the green alga Chlamydomonas reinhardtii is correlated with protein levels of stress-related light-harvesting complex (LHCSR) proteins, which are strongly induced by high light (HL). However, the dynamic response of overall thylakoid structure during acclimation to growth in HL has not been characterized. Here, we combined live-cell super-resolution microscopy and analytical membrane subfractionation to investigate macroscale structural changes of thylakoid membranes during HL acclimation in C. reinhardtii. Subdiffraction-resolution bioimaging revealed that overall thylakoid structures became thinned and shrunken during HL acclimation. The stromal space around the pyrenoid also became enlarged. Analytical density-dependent membrane fractionation indicated that the structural changes were partly a consequence of membrane unstacking. The analysis of both an LHCSR loss-of-function mutant, npq4 lhcsr1, and a regulatory mutant that over-expresses LHCSR, spa1-1, showed that structural changes occurred independently of LHCSR protein levels, demonstrating that LHCSR was neither necessary nor sufficient to induce the thylakoid structural changes associated with HL acclimation. In contrast, stt7-9, a mutant lacking a kinase of major light-harvesting antenna proteins, had a distinct thylakoid structural response during HL acclimation relative to all other lines tested. Thus, while LHCSR and the antenna protein phosphorylation are core features of HL acclimation, it appears that only the latter acts as a determinant for thylakoid structural rearrangements. These results indicate that two independent mechanisms occur simultaneously to cope with HL conditions. Possible scenarios for HL-induced thylakoid structural changes are discussed.
Evaluation of Host Defense Peptide (CaD23)-Antibiotic Interaction and Mechanism of Action: Insights from Experimental and Molecular Dynamics Simulations Studies
Authors: Ting Darren Shu Jeng , Li Jianguo , Verma Chandra S. , Goh Eunice T. L. , Nubile Mario , Mastropasqua Leonardo , Said Dalia G. , Beuerman Roger W. , Lakshminarayanan Rajamani , Mohammed Imran , Dua Harminder S. 
Published: June 2021

ABSTRACTBackground/aimHost defense peptides (HDPs) have the potential to provide a novel solution to antimicrobial resistance (AMR) in view of their unique and broad-spectrum antimicrobial activities. We had recently developed a novel hybrid HDP based on LL-37 and human beta-defensin-2, named CaD23, which was shown to exhibit good in vivo antimicrobial efficacy against Staphylococcus aureus in a bacterial keratitis murine model. This study aimed to examine the potential CaD23-antibiotic synergism and to evaluate the underlying mechanism of action of CaD23.MethodsAntimicrobial efficacy was determined using minimum inhibitory concentration (MIC) assay with broth microdilution method. Peptide-antibiotic interaction was evaluated against S. aureus, methicillin-resistant S. aureus (MRSA), and Pseudomonas aeruginosa using established checkerboard assay and time-kill kinetics assay. Fractional inhibitory concentration index (FICI) was calculated and interpreted as synergistic (FICI<0.5), additive (FICI between 0.5-1.0), indifferent (FICI between >1.0 and ≤4), or antagonistic (FICI>4). SYTOX green uptake assay was performed to determine the membrane-permeabilising action of CaD23. Molecular dynamics (MD) simulations were performed to evaluate the interaction of CaD23 with bacterial and mammalian mimetic membranes.ResultsCaD23-amikacin and CaD23-levofloxacin combination treatment exhibited a strong additive effect against S. aureus SH1000 (FICI=0.56) and MRSA43300 (FICI=0.56) but a borderline additive-to-indifferent effect against P. aeruginosa (FIC=1.0-2.0). CaD23 (at 25 μg/ml; 2x MIC) was able to achieve complete killing of S. aureus within 30 mins. When used at sub-MIC concentration (3.1 μg/ml; 0.25x MIC), it was able to expedite the antimicrobial action of amikacin against S. aureus by 50%. The rapid antimicrobial action of CaD23 was attributed to the underlying membrane-permeabilising mechanism of action, evidenced by the SYTOX green uptake assay and MD simulations studies. MD simulations revealed that cationicity, alpha-helicity, amphiphilicity and hydrophobicity (related to the Trp residue at C-terminal) play important roles in the antimicrobial action of CaD23.ConclusionsCaD23 is a novel membrane-active synthetic HDP that can enhance and expedite the antimicrobial action of antibiotics against Gram-positive bacteria when used in combination. MD simulation serves as a useful tool in dissecting the mechanism of action and guiding the design and optimisation of HDPs.
Multiple reproductive females in family groups of smooth-coated otters
Authors: Bungum Haaken Zhong , Yee Mei-Mei Tan Heng , Borker Atul , Hsu Chia Da , Johns Philip 
Published: June 2021

AbstractSmooth-coated otters (Lutrogale perspicillata) are inhabitants of the waterways of India and Singapore. Otter families typically consist of a single mating pair with mature, nonbreeding siblings living in family groups, or “romps”. We note here the presence of multiple reproductive female otters within some romps, as well as the possible existence of simultaneous litters by different mothers. This phenomenon has not been recorded amongL. perspicillatabefore. Here we address possible influences leading to multiple reproductive females within romps of smooth-coated otters, including inclusive fitness, incomplete suppression of reproduction, and existing in an urban environment. The numerous, recurring observations of multiple reproductive females warrant further investigation; while uncommon, this phenomenon is not as rare as once thought.
In Vivo Simultaneous Nonlinear Absorption Raman and Fluorescence (SNARF) Imaging of Mouse Brain Cortical Structures
Authors: Francis Andrew T. , Manifold Bryce , Thomas Elena C. , Hu Ruoqian , Hill Andrew H. , Men Shuaiqian , Fu Dan 
Published: June 2021

AbstractTwo-photon excited fluorescence (TPEF) microscopy is a widely used optical imaging technique that has revolutionized neurophotonics through a diverse palette of dyes, specialized transgenic models, easy implementation, and straightforward data analysis. However, in vivo TPEF imaging is often limited in the number of contrasts available to distinguish different cells, structures, or functions. We propose using two label-free multiphoton microscopy techniques – stimulated Raman scattering (SRS) microscopy and transient absorption microscopy (TAM) – as complementary and orthogonal imaging modalities to TPEF for in vivo brain imaging. In this study, we construct a simultaneous nonlinear absorption, Raman, and fluorescence (SNARF) microscope and image several cortical structures up to 250-300 μm below the pial surface, the highest reported in vivo imaging depth for SRS or TAM. We further demonstrate the capabilities of our SNARF microscope through the quantification of age-dependent myelination, hemodynamics, vessel structure, cell density, and cell identity in vivo. Using machine learning, we report the use of label-free SRS and TAM features to predict capillary-lining cell identities with 90% accuracy. The SNARF microscope and methodology outlined herein provide a powerful platform to study several research topics, including neurovascular coupling, blood-brain barrier, neuronal and axonal degeneration in aging, and neurodegenerative diseases.
The role of temporal coherence and temporal predictability in the build-up of auditory grouping
Authors: Sollini Joseph , Poole Katarina C , Blauth-Muszkowski Dominic , Bizley Jennifer K. 
Published: June 2021

AbstractThe cochlea decomposes sounds into separate frequency channels, from which the auditory brain must reconstruct the auditory scene. To do this the auditory system must make decisions about which frequency information should be grouped together, and which should remain distinct. Two key cues for grouping are temporal coherence, resulting from coherent changes in power across frequency, and temporal predictability, resulting from regular or predictable changes over time. To test how these cues contribute to the construction of a sound scene we present listeners with a range of precursor sounds, which act to prime the auditory system by providing information about each sounds structure, followed by a fixed masker in which participants were required to detect the presence of an embedded tone. By manipulating temporal coherence and/or temporal predictability in the precursor we assess how prior sound exposure influences subsequent auditory grouping. In Experiment 1, we measure the contribution of temporal predictability by presenting temporally regular or jittered precursors, and temporal coherence by using either narrow or broadband sounds, demonstrating that both independently contribute to masking/unmasking. In Experiment 2, we measure the relative impact of temporal coherence and temporal predictability and ask whether the influence of each in the precursor signifies an enhancement or disruption of unmasking. We observed that interfering precursors produced the largest changes to thresholds.
Cryo-EM structures of human TMEM120A and TMEM120B
Authors: Ke Meng , Yu Yue , Zhao Changjian , Lai Shirong , Su Qiang , Yuan Weidan , Yang Lina , Deng Dong , Wu Kun , Zeng Weizheng , Geng Jia , Wu Jianping , Yan Zhen 
Published: June 2021

AbstractTMEM120A (Transmembrane protein 120A) was recently identified as a mechanical pain sensing ion channel named as TACAN, while its homologue TMEM120B has no mechanosensing property1. Here, we report the cryo-EM structures of both human TMEM120A and TMEM120B. The two structures share the same dimeric assembly, mediated by extensive interactions through the transmembrane domain (TMD) and the N-terminal coiled coil domain (CCD). However, the nearly identical structures cannot provide clues for the difference in mechanosensing between TMEM120A and TMEM120B. Although TMEM120A could mediate conducting currents in a bilayer system, it does not mediate mechanical-induced currents in a heterologous expression system, suggesting TMEM120A is unlikely a mechanosensing channel. Instead, the TMDs of TMEM120A and TMEM120B resemble the structure of a fatty acid elongase, ELOVL7, indicating their potential role of an enzyme in lipid metabolism.
A universal probabilistic spike count model reveals ongoing modulation of neural variability
Authors: Liu David , Lengyel Máté 
Published: June 2021

AbstractNeural responses are variable: even under identical experimental conditions, single neuron and population responses typically differ from trial to trial and across time. Recent work has demonstrated that this variability has predictable structure, can be modulated by sensory input and behaviour, and bears critical signatures of the underlying network dynamics and computations. However, current methods for characterising neural variability are primarily geared towards sensory coding in the laboratory: they require trials with repeatable experimental stimuli and behavioural covariates. In addition, they make strong assumptions about the parametric form of variability, rely on assumption-free but data-inefficient histogram-based approaches, or are altogether ill-suited for capturing variability modulation by covariates. Here we present a universal probabilistic spike count model that eliminates these shortcomings. Our method builds on sparse Gaussian processes and can model arbitrary spike count distributions (SCDs) with flexible dependence on observed as well as latent covariates, using scalable variational inference to jointly infer the covariate-to-SCD mappings and latent trajectories in a data efficient way. Without requiring repeatable trials, it can flexibly capture covariate-dependent joint SCDs, and provide interpretable latent causes underlying the statistical dependencies between neurons. We apply the model to recordings from a canonical non-sensory neural population: head direction cells in the mouse. We find that variability in these cells defies a simple parametric relationship with mean spike count as assumed in standard models, its modulation by external covariates can be comparably strong to that of the mean firing rate, and slow low-dimensional latent factors explain away neural correlations. Our approach paves the way to understanding the mechanisms and computations underlying neural variability under naturalistic conditions, beyond the realm of sensory coding with repeatable stimuli.
Candida albicans Isolates 529L and CHN1 Exhibit Stable Colonization of the Murine Gastrointestinal Tract
Authors: McDonough Liam , Mishra Animesh Anand , Tosini Nicholas , Kakade Pallavi , Penumutchu Swathi , Liang Shen-Huan , Maufrais Corrine , Zhai Bing , Taur Ying , Belenky Peter , Bennett Richard J. , Hohl Tobias M. , Koh Andrew Y. , Ene Iuliana V. 
Published: June 2021

ABSTRACTCandida albicans is a pathobiont that colonizes multiple niches in the body including the gastrointestinal (GI) tract, but is also responsible for both mucosal and systemic infections. Despite its prevalence as a human commensal, the murine GI tract is generally refractory to colonization with the C. albicans reference isolate SC5314. Here, we identify two C. albicans isolates, 529L and CHN1, that stably colonize the murine GI tract in three different animal facilities under conditions where SC5314 is lost from this niche. Analysis of the bacterial microbiota did not show notable differences between mice colonized with the three C. albicans strains. We compared the genotypes and phenotypes of these three strains and identified thousands of SNPs and multiple phenotypic differences, including their ability to grow and filament in response to nutritional cues. Despite striking filamentation differences under laboratory conditions, however, analysis of cell morphology in the GI tract revealed that the three isolates exhibited similar filamentation properties in this in vivo niche. Notably, we found that SC5314 is more sensitive to the antimicrobial peptide CRAMP, and the use of CRAMP-deficient mice increased the ability of SC5314 to colonize the GI tract relative to CHN1 and 529L. These studies provide new insights into how strain-specific differences impact C. albicans traits in the host and advance CHN1 and 529L as relevant strains to study C. albicans pathobiology in its natural host niche.IMPORTANCEUnderstanding how fungi colonize the GI tract is increasingly recognized as highly relevant to human health. The animal models used to study Candida albicans commensalism commonly rely on altering the host microbiome (via antibiotic treatment or defined diets) to establish successful GI colonization by the C. albicans reference isolate SC5314. Here, we characterize two C. albicans isolates that can colonize the murine GI tract without antibiotic treatment and can therefore be used as tools for studying fungal commensalism. Importantly, experiments were replicated in three different animal facilities and utilized three different mouse strains. Differential colonization between fungal isolates was not associated with alterations in the bacterial microbiome but rather with distinct responses to CRAMP, a host antimicrobial peptide. This work emphasizes the importance of C. albicans intra-species variation as well as host anti-microbial defense mechanisms in defining commensal interactions.