bluuebunny/crossref_metadata_2025_split huggingface dataset:
A neuromorphic model of active vision shows spatio-temporal encoding in lobula neurons can aid pattern recognition in bees
Authors: MaBouDi HaDi , Roper Mark , Guiraud Marie-Genevieve , Chittka Lars , Marshall James A.R. 
Published: June 2023

AbstractBees possess remarkable cognitive abilities in on-the-fly visual learning, making them an ideal model for studying active information acquisition and representation. In this study, we investigated the minimal circuitry required for active vision in bees by considering their flight behaviours during visual pattern scanning. By developing a neural network model inspired by the insect visual system, we examined the influence of scanning behaviour on optic lobe connectivity and neural activity. Through the incorporation of non-associative learning and exposure to diverse natural images, we obtained compelling results that align with neurobiological observations. Our findings reveal that active scanning and non-associative learning dynamically shape the connectivity within the visual lobe, resulting in an efficient representation of visual input. Interestingly, we observed self-organization in orientation-selective neurons in the lobula region, characterized by sparse responses to orthogonal bar movements. These dynamic orientation-selective cells cover various orientations, exhibiting a bias towards the speed and contrast of input sampling. To assess the effectiveness of this spatiotemporal coding for pattern recognition, we integrated our model with the mushroom body circuitry underlying associative learning. Notably, our model demonstrated impressive performance across several pattern recognition tasks, suggesting a similar coding system within the bee visual system. Overall, this study integrates behavioural experiments, neurobiological findings, and computational models to reveal how complex visual features can be condensed through spatiotemporal encoding in the lobula neurons, facilitating efficient sampling of visual cues for identifying rewarding foraging resources. Our findings have broader implications for understanding active vision in diverse animals, including humans, and offer valuable insights for the application of bio-inspired principles in the design of autonomous robots.
Mimicry in motion: A grasshopper species that looks like, and moves like, a sympatric butterfly
Authors: Loeffler-Henry Karl , Kang Changku , Dawson Jeff W. , Sherratt Thomas N. 
Published: June 2023

AbstractFlash displays describe the sudden revealing of a conspicuous signal by an otherwise cryptic animal as it is fleeing from predators. One hypothesis for flash displays is that they have evolved to mislead predators into adopting an inappropriate search strategy following pursuit. Thus, if predators believe that the fleeing prey item will also be conspicuous when settled, then they will tend to give up searching sooner if they fail to find it. Naturally, if this hypothesis is correct then one might expect that the value of the flash display would cease once predators learn the flasher’s true resting appearance. However, even if predators are aware that the resting appearance of the signaller could be cryptic, flash displays will still be selected for if the flasher resembles another species that maintains its conspicuous appearance throughout. Motivated by this insight, we quantified the degree of chromatic and behavioral resemblance between the Carolina grasshopper (Dissosteira carolina) and mourning cloak butterfly (Nymphalis antiopa), a sympatric species with which it is commonly confused. The close similarity in both morphology and flight behavior (in the field and lab) between these distantly related species strongly suggests that they are in a mimetic relationship. It is unclear why this mimicry has evolved. One explanation is that mimicry has arisen through selection to maintain the efficacy of the flash display through search disruption even after predator learning. Another possibility is that the grasshopper has evolved to resemble the butterfly because the latter is harder to catch (evasive mimicry). However, we argue that pursuit and search disruption are entirely complementary explanations for the mimetic resemblance because they interfere with predation at two different stages of the attack sequence.
DesiRNA: structure-based design of RNA sequences with a Monte Carlo approach
Authors: Wirecki Tomasz , Lach Grzegorz , Jaryani Farhang , Badepally Nagendar Goud , Moafinejad S. Naeim , Klaudel Gaja , Bujnicki Janusz M. 
Published: June 2023

ABSTRACTRNA sequences underpin the formation of complex and diverse structures, subsequently governing their respective functional properties. Despite the pivotal role RNA sequences play in cellular mechanisms, creating optimized sequences that can predictably fold into desired structures remains a significant challenge. We have developed DesiRNA, a versatile Python-based software tool for RNA sequence design. This program considers a comprehensive array of constraints, ranging from secondary structures (including pseudoknots) and GC content, to the distribution of dinucleotides emulating natural RNAs. Additionally, it factors in the presence or absence of specific sequence motifs and prevents or promotes oligomerization, thereby ensuring a robust and flexible design process. DesiRNA utilizes the Monte Carlo algorithm for the selection and acceptance of mutation sites. In tests on the EteRNA benchmark, DesiRNA displayed high accuracy and computational efficiency, outperforming most existing RNA design programs.
Brain Templates for Chinese Babies from Newborn to Three Months of Age
Authors: Geng Xiujuan , Chen Peggy HY , Lam Hugh S , Chu Winnie CW , Wong Patrick CM 
Published: June 2023

AbstractThe infant brain develops rapidly and this area of research has great clinical implications. Neurodevelopmental disorders such as autism and developmental delay have their origins, potentially, in abnormal early brain maturation. Searching for potential early neural markers requiresa prioriknowledge about infant brain development and anatomy. One of the most common methods of characterizing brain features requires normalization of individual images into a standard stereotactic space and conduct of group-based analyses in this space. A population representative brain template is critical for these population-based studies. Little research is available on constructing brain templates for typical developing Chinese infants. In the present work, a total of 112 babies from 6 to 98 days of age were included with high resolution structural magnetic resonance imaging scans. T1-weighted and T2-weighted templates were constructed using an unbiased registration approach for babies from newborn to 3 months of age. Age-specific templates were also estimated for babies aged at 0, 1, 2 and 3 months old. Then we conducted a series of evaluations and statistical analyses over whole tissue segmentations and brain parcellations. Compared to the use of population mismatched templates, using our established templates resulted in lower deformation energy to transform individual images into the template space and produced a smaller registration error, i.e., smaller standard deviation of the registered images. Significant volumetric growth was observed across total brain tissues and most of the brain regions within the first three months of age. The total brain tissues exhibited larger volumes in baby boys compared to baby girls. To the best of our knowledge, this is the first study focusing on the construction of Chinese infant brain templates. These templates can be used for investigating birth related conditions such as preterm birth, detecting neural biomarkers for neurological and neurodevelopmental disorders in Chinese populations, and exploring genetic and cultural effects on the brain.
Dual mechanism of kinetochore microtubule detachment
Authors: Conway William , Ha Gloria , Needleman Daniel 
Published: June 2023

SUMMARYDuring eukaryotic cell division, microtubules connect to chromosomes by attaching to the kinetochore via the NDC80 complex (NDC80c). The regulation of kinetochore microtubule (KMT) detachment is crucial for correcting mitotic errors. Here, we investigate the mechanism of KMT detachment by combining photoconversion measurements of KMT detachment rate, FLIM-FRET measurements of NCD80c/KMT binding, and mathematical modeling. Our results support a dual detachment mechanism in which KMTs detach from kinetochores when either 1) all NDC80c spontaneously unbind from the KMT or 2) following KMT catastrophe. We identify kinetochore components that selectively impact these two mechanisms and show that the affinity of NDC80c for KMTs is reduced at low-tension, non-bioriented kinetochores due to centromere-localized Aurora B phosphorylating the NDC80c, resulting in an elevated detachment rate for the associated KMTs. Taken together, this work leads to a biophysical model for the molecular basis of KMT detachments and their regulation during mitotic error correction.
Motion direction is represented as a bimodal probability distribution in the human visual cortex
Authors: Chetverikov Andrey , Jehee Janneke F.M. 
Published: June 2023

AbstractHow do humans infer motion direction from noisy sensory signals? We hypothesized that motion direction is computed not only from velocity but also spatial orientation signals – a ‘streak’ created by moving objects. We implemented this hypothesis in a Bayesian model, which quantifies knowledge with probability distributions, and tested its predictions using psychophysics and fMRI. Using a probabilistic pattern-based analysis, we decoded probability distributions of motion direction from trial-by-trial activity in the human visual cortex. Corroborating the predictions, the decoded distributions had a bimodal shape, with peaks that predicted the direction and magnitude of behavioral errors. Interestingly, we observed similar bimodality in the distribution of the observers’ behavioral responses across trials. Together, these results suggest that observers use spatial orientation signals when estimating motion direction. More broadly, our findings indicate that the cortical representation of low-level visual features, such as motion direction, can reflect a combination of several qualitatively distinct signals.
One thousand samples per day capillary-flow LC/MS/MS for high-speed, high-sensitivity and in-depth proteomics
Authors: Tomioka Ayana , Tomioka Ryota , Mori Issei , Isobe Yosuke , Arita Makoto , Imami Koshi , Kanao Eisuke , Ogata Kosuke , Ishihama Yasushi 
Published: June 2023

AbstractWe developed a capillary-flow LC/MS/MS system with ultrahigh speed, enabling a throughput of 1,000 samples per day while maintaining high sensitivity and depth of analysis. In targeted LC/MS mode, 36 endogenous phosphopeptides in HeLa cells, including EphA2- derived phosphopeptide isomers, were successfully quantified with high selectivity and linearity by combining ion mobility separation. When 500 ng of HeLa cell digest was measured 100 times repeatedly in data-dependent acquisition mode, the coefficient of variation of retention time, peak intensity and number of identified peptides were on average 3.4%, 19.8%, and 6.0%, respectively. In data-independent acquisition mode, this system achieved the identification and quantification of 3,139 protein groups from a 100 ng HeLa cell digest and 2,145 protein groups from a sample of only 10 ng. The coefficient of variation of protein commonly quantified in the triplicate analysis ranged from 12 to 24% for HeLa digest samples ranging from 10 to 1000 ng. Finally, we applied this high-speed system to the spatial proteomics of the mouse brain, and succeeded in capturing the proteome distribution along a 96-sectioned brain structure in 135 minutes. This is the first LC/MS/MS system to achieve both more than 500 samples per day and more than 3000 identified protein groups ID with less than 100 ng human cultured cells simultaneously.
Metabolomic analysis ofDrosophila melanogasterlarvae lacking Pyruvate kinase
Authors: Heidarian Yasaman , Tourigny Jason P. , Fasteen Tess D. , Mahmoudzadeh Nader H. , Hurlburt Alexander J. , Nemkov Travis , Reisz Julie A. , D’Alessandro Angelo , Tennessen Jason M. 
Published: June 2023

ABSTRACTPyruvate kinase (Pyk) is a rate-limiting enzyme that catalyzes the final metabolic reaction in glycolysis. The importance of this enzyme, however, extends far beyond ATP production, as Pyk is also known to regulate tissue growth, cell proliferation, and development. Studies of this enzyme inDrosophila melanogaster, however, are complicated by the fact that the fly genome encodes six Pyk paralogs whose functions remain poorly defined. To address this issue, we used sequence distance and phylogenetic approaches to demonstrate that the genePykencodes the enzyme most similar to the mammalian Pyk orthologs, while the other fiveDrosophilaPyk paralogs have significantly diverged from the canonical enzyme. Consistent with this observation, metabolomic studies of two differentPykmutant backgrounds revealed that larvae lacking Pyk exhibit a severe block in glycolysis, with a buildup of glycolytic intermediates upstream of pyruvate. However, our analysis also unexpectedly reveals that steady state pyruvate levels are unchanged inPykmutants, indicating that larval metabolism maintains pyruvate pool size despite severe metabolic limitations. Consistent with our metabolomic findings, a complementary RNA-seq analysis revealed that genes involved in lipid metabolism and peptidase activity are elevated inPykmutants, again indicating that loss of this glycolytic enzyme induces compensatory changes in other aspects of metabolism. Overall, our study provides both insight into how Drosophila larval metabolism adapts to disruption of glycolytic metabolism as well as immediate clinical relevance, considering that Pyk deficiency is the most common congenital enzymatic defect in humans.
Dopamine alters the effect of brain stimulation on decision-making
Authors: Leow Li-Ann , Marcos Anjeli , Nielsen Esteban , Sewell David K , Ballard Tim , Dux Paul E. , Filmer Hannah L. 
Published: June 2023

AbstractNon-invasive brain stimulation techniques, such as transcranial direct current stimulation (tDCS), show promise in treating cognitive and behavioural impairments in clinical conditions. However, optimisation of such clinical applications requires a better understanding of how tDCS alters cognition and behaviour. Existing evidence implicates dopamine in the way tDCS alters brain activity and plasticity, however, there is as yet no causal evidence for a role of dopamine in tDCS effects on cognition and behaviour. Here, in a preregistered, double-blinded study, we examined how pharmacologically manipulating dopamine altered the effect of tDCS on the speed-accuracy trade-off, which taps ubiquitous strategic cognitive processes. Cathodal tDCS was delivered over the left prefrontal cortex and the superior medial frontal cortex before participants completed a dot-motion task, deciding the direction of moving dots under instructions to emphasize speed, accuracy, or both. We leveraged computational modelling to uncover how our manipulations altered latent decisional processes driving the speed-accuracy tradeoff. We show that dopamine in combination with tDCS (but not tDCS alone, nor dopamine alone) not only impaired decision accuracy, but also impaired discriminability, which suggests that these manipulations altered the encoding or representation of discriminative evidence. This is, to the best of our knowledge, the first direct evidence implicating dopamine in the way tDCS affects cognition and behaviour.Significance statementTranscranial direct current stimulation (tDCS) can improve cognitive and behavioural impairments in clinical conditions, however better understanding of its mechanisms is required to optimise future clinical applications. Here, using a pharmacological approach to manipulate brain dopamine levels in healthy adults, we demonstrate a role for dopamine in the effects of tDCS in the speed-accuracy trade-off, a strategic cognitive process ubiquitous in many contexts. In doing so, we provide direct evidence implicating dopamine in the way tDCS affects cognition and behaviour.
Impaired cerebellar plasticity hypersensitizes sensory reflexes inSCN2A-associated ASD
Authors: Wang Chenyu , Derderian Kimberly D. , Hamada Elizabeth , Zhou Xujia , Nelson Andrew D. , Kyoung Henry , Ahituv Nadav , Bouvier Guy , Bender Kevin J 
Published: June 2023

ABSTRACTChildren diagnosed with autism spectrum disorder (ASD) commonly present with sensory hypersensitivity, or abnormally strong reactions to sensory stimuli. Such hypersensitivity can be overwhelming, causing high levels of distress that contribute markedly to the negative aspects of the disorder. Here, we identify the mechanisms that underlie hypersensitivity in a sensorimotor reflex found to be altered in humans and in mice with loss-of-function in the ASD risk-factor geneSCN2A. The cerebellum-dependent vestibulo-ocular reflex (VOR), which helps maintain one’s gaze during movement, was hypersensitized due to deficits in cerebellar synaptic plasticity. Heterozygous loss ofSCN2A-encoded NaV1.2 sodium channels in granule cells impaired high-frequency transmission to Purkinje cells and long-term potentiation, a form of synaptic plasticity important for modulating VOR gain. VOR plasticity could be rescued in adolescent mice via a CRISPR-activator approach that increasesScn2aexpression, highlighting how evaluation of simple reflexes can be used as quantitative readout of therapeutic interventions.
Genetic factors explaining anthocyanin pigmentation differences
Authors: Recinos Maria F. Marin , Pucker Boas 
Published: June 2023

ABSTRACTBackgroundAnthocyanins represent one of the most abundant coloration factors found in plants. Biological functions of anthocyanins range from reproduction to protection against biotic and abiotic stressors. Owing to a clearly visible phenotype of mutants, the anthocyanin biosynthesis and its sophisticated regulation have been studied in numerous plant species. Genes encoding the anthocyanin biosynthesis enzymes are regulated by a transcription factor complex comprising MYB, bHLH and WD40 proteins.ResultsA systematic comparison of anthocyanin-pigmented vs. non-pigmented varieties across flowering plant species was performed. Literature was screened for cases in which genetic factors causing anthocyanin loss were reported. Additionally, transcriptomic data sets from previous studies were reanalyzed to determine the genes most likely to be responsible for color variation based on their expression pattern. The contribution of different structural and regulatory genes to the pigmentation differences was quantified. Gene expression differences concerning transcription factors are by far the most frequent explanation for pigmentation differences observed between two varieties of the same species. Among the transcription factors in the analyzed cases, MYB genes are substantially more likely to explain pigmentation differences than bHLH or WD40 genes.ConclusionsThese findings support previous assumptions about the plasticity of transcriptional regulation and its importance for the evolution of novel coloration phenotypes. Our findings underline the particular significance of MYBs and their apparent dominant role in the specificity of the MBW complex.
Impact of CoronaVac on Covid-19 outcomes of elderly adults in a large and socially unequal Brazilian city: A target trial emulation study
Authors: Monteiro Higor S. , Lima Neto Antonio S. , Kahn Rebecca , Sousa Geziel S. , Carmona Humberto A. , Andrade José S. , Castro Marcia C. 
Published: June 2023

AbstractBackgroundAlthough CoronaVac was the only Covid-19 vaccine adopted in the first months of the Brazilian vaccination campaign, randomized clinical trials to evaluate its efficacy in elderly adults were limited. In this study, we use routinely collected surveillance and SARS-CoV-2 vaccination and testing data comprising the population of the fifth largest city of Brazil to evaluate the effectiveness of CoronaVac in adults 60+ years old against severe outcomes.MethodsUsing large observational databases on vaccination and surveillance data from the city of Fortaleza, Brazil, we defined a retrospective cohort including 324,302 eligible adults aged ≥ 60 years to evaluate the effectiveness of the CoronaVac vaccine. The cohort included individuals vaccinated between January 21, 2021, and August 31, 2021, who were matched with unvaccinated persons at the time of rollout following a 1:1 ratio according to baseline covariates of age, sex, and Human Development Index of the neighborhood of residence. Only Covid-19-related severe outcomes were included in the analysis: hospitalization, ICU admission, and death. Vaccine effectiveness for each outcome was calculated by using the risk ratio between the two groups, with the risk obtained by the Kaplan-Meier estimator.ResultsWe obtained 62,643 matched pairs for assessing the effectiveness of the two-dose regimen of CoronaVac. The demographic profile of the matched population was statistically representative of the population of Fortaleza. Using the cumulative incidence as the risk associated with each group, starting at day 14 since the receipt of the second dose, we found an 82.3% (95% CI 66.3 - 93.9) effectiveness against Covid-19-related death, 68.4% (95% CI 42.3 - 86.4) against ICU admission, and 55.8% (95% CI 42.7 - 68.3) against hospital admission.ConclusionsOur results show that, despite critical delays in vaccine delivery and limited evidence in efficacy trial estimates, CoronaVac contributed to preventing deaths and severe morbidity due to Covid-19 in elderly adults.
Quality of Systematic Reviews in Dental Journals Published from India: A Methodological Review
Authors: Mathew Rohan Thomas , Babu Anu 
Published: June 2023

AbstractBackgroundEvidence-based medicine (EBM) is a crucial aspect of modern medical practice, emphasizing the use of the best available evidence to inform clinical decision-making. Systematic reviews (SRs) play a key role in EBM by integrating and evaluating findings from multiple studies. However, the methodological quality of SRs can vary, and assessing their quality is essential for accurate interpretation and application of the findings.MethodsThis study aims to analyze the methodological quality of SRs published in dentistry journals from India between 2015 and 2020. A comprehensive search was conducted, resulting in the inclusion of 130 SRs from 21 journals.ResultsThe findings reveal several discrepancies in the methodological quality of the included SRs. Only a small percentage of SRs were registered in the PROSPERO registry, and adherence to PRISMA guidelines was limited. The majority of SRs did not assess scientific quality, such as risk of bias and publication bias, adequately. Furthermore, the study highlights a lack of awareness and support for conducting high-quality SRs, including limited funding and insufficient utilization of standardized guidelines.ConclusionThe authors suggest that increasing awareness among researchers, editors, and funding agencies, as well as adopting standardized guidelines and protocols, can improve the quality and quantity of SRs produced in India. Overall, this study emphasizes the need to enhance the methodological rigor of SRs in dentistry to ensure reliable evidence for clinical decision-making.