bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nonlinear Singular Value Decomposition Beamforming for Ultrasound Imaging of Gas Vesicles
Authors: Zhang Ge , Vert Mathis , Nouhoum Mohamed , Rivera Esteban , Haidour Nabil , Jimenez Anatole , Deffieux Thomas , Barral Simon , Hersen Pascal , Rabut Claire , Shapiro Mikhail , Tanter Mickael 
Published: October 2024

AbstractUltrasound imaging holds significant promise for the observation of molecular and cellular phenomena through the utilization of acoustic contrast agents and acoustic reporter genes. Optimizing imaging methodologies for enhanced detection represents an imperative advancement in this field. Most advanced techniques relying on amplitude modulation scheme such as cross amplitude modulation (xAM) and ultrafast amplitude modulation (uAM) combined with Hadamard encoded multiplane wave transmissions have shown efficacy in capturing acoustic signals of gas vesicles (GVs). Nonetheless, uAM sequence requires odd- or even-element transmissions leading to imprecise amplitude modulation emitting scheme, and the complex multiplane wave transmission scheme inherently yields overlong pulse durations. xAM sequence is limited in terms of field of view and imaging depth. To overcome these limitations, we introduce an innovative ultrafast imaging sequence called nonlinear singular value decomposition (SVD) beamforming. Our method demonstrated a contrast imaging sensitivity comparable to the current gold-standard xAM and uAM, while requiring 4.8 times less pulse transmissions. With similar number of transmit pulses, nonlinear SVD beamforming outperforms xAM and uAM in terms of an improvement in signal-to-background ratio of + 4.78 ± 0.35 dB and + 8.29 ± 3.52 dB respectively. Additionally, our method provides a higher flexibility in terms of the selection of acoustic pressure amplitude compared to the other methods. Furthermore, it shows a significant potential for application in the realm of ultrasound localization microscopy (ULM), where it stands poised to facilitate the more precise extraction of nonlinear signatures originating from contrast agents.
TRENDY: Gene Regulatory Network Inference Enhanced by Transformer
Authors: Tian Xueying , Patel Yash , Wang Yue 
Published: October 2024

AbstractGene regulatory networks (GRNs) play a crucial role in the control of cellular functions. Numerous methods have been developed to infer GRNs from gene expression data, including mechanism-based approaches, information-based approaches, and more recent deep learning techniques, the last of which often overlooks the underlying gene expression mechanisms. In this work, we introduce TRENDY, a novel GRN inference method that integrates transformer models to enhance the mechanism-based WENDY approach. Through testing on both simulated and experimental datasets, TRENDY demonstrates superior performance compared to existing methods. Furthermore, we apply this transformer-based approach to three additional inference methods, showcasing its broad potential to enhance GRN inference.
Chronic obesity does not alter cancer survival inTp53R270H/+mice
Authors: Panzeri Ilaria , Madaj Zachary , Fagnocchi Luca , Apostle Stefanos , Tompkins Megan , Hostetter Galen , Andrew Pospisilik J. 
Published: October 2024

AbstractObesity is a complex chronic disease characterized by excessive adiposity and associations with numerous co-morbidities, including cancer. Despite extensive research, we have limited understanding of the mechanisms coupling obesity to cancer risk, and, of the contexts in which obesity does or does not exacerbate disease. Here, we show that chronic high-fat diet (HFD)-induced obesity has no significant effect on theTp53R270H/+mouse, a model of human Li-Fraumeni multi-cancer syndrome. Surprisingly, despite inducing rapid and highly penetrant obesity and long-term differences in metabolic and adiposity, greater than one year of HFD had no significant effect on survival or tumor burden. These findings were replicated in two separate cohorts and thus provide important negative data for the field. Given strong publication bias against negative data in the literature, this large cohort study represents a clear case where chronic diet-induced obesity does not accelerate or aggravate cancer outcomes. The data thus carry high impact for researchers, funders, and policymakers alike.
Pan-cistrome analysis of the leaf accessible chromatin regions of 214 maize inbred lines
Authors: Zhu Yongli , Ngan Heiyuen , Zhu Tao , Nan Lili , Li Wenqiang , Xiao Yingjie , Zhuo Lin , Chen Dijun , Tu Xiaoyu , Gao Kang , Yan Jianbing , Zhong Silin , Yang Ning 
Published: October 2024

ABSTRACTCharacterizing the noncoding regions of the genome, particularly the cis-regulatory elements (CREs) located in accessible chromatin regions (ACRs) in gene promoters, is crucial for understanding how gene expression is regulated and how genotype contributes to phenotypic diversity in plants.In this study, we used ATAC-seq to resequence and map the ACRs of 214 maize inbred lines. We identified 82,174 ACRs and reported that 39.55% of them exhibited significant variation across the population. Next, we used the accessibility of ACRs as a quantitative feature and performed a chromatin associability GWAS (caGWAS), resulting in 27,004 caQTLs. Among them, 2,463 were predicted to disrupt the cis-regulatory elements that TF binds in these ACRs, suggesting that TF binding affects chromatin accessibility. Specifically, we identified two caACRs that regulate the expression offad7, which encodes a fatty acid desaturase and affects the linolenic acid content.Our findings highlight the dynamic nature of maize ACRs and demonstrate that chromatin accessibility information could be used for GWASs, offering key insights into the genetic and regulatory mechanisms of chromatin accessibility and its impact on complex traits in plants.
Genomic Discovery of EF-24 Targets Unveils Antitumorigenic Mechanisms in Leukemia Cells
Authors: Singh Ajeet P. , Wax Noah , Duncan James , Fernandes Ana , Jacobs Jonathan L. 
Published: October 2024

AbstractCurcumin, a polyphenolic compound derived from the plantCurcuma longaL., has demonstrated a wide range of therapeutic properties, including potential anticancer effects. However, its clinical efficacy is limited due to poor bioavailability and stability. To overcome these challenges, curcumin analogs like EF-24 have been developed with improved pharmacological properties. In this study, we used whole-transcriptome profiling to identify the genome-wide functional impacts of EF-24 treatment in leukemia cells to improve our understanding of its potential mechanisms of action. This approach allowed us to establish a model system for associating druggable genes with clinical disease targets. We used the chronic myeloid leukemia (CML) cell line K-562 and acute myeloid leukemia (AML) cell lines HL-60, Kasumi-1, and THP-1 to conduct EF-24 treatment studies. Cell viability was significantly decreased in the EF-24–treated cells as compared to the untreated controls. We discovered that the genes ATF3, CLU, HSPA6, OSGIN1, ZFAND2A, and CXCL8, which are associated with reduced cell viability and proliferation, were consistently upregulated in all EF-24–treated cell lines. Further analysis of the tested cell lines revealed the activation of various signaling pathways, including the STAT1 regulated S100 family signaling pathway, that controlled downstream gene expression in response to EF-24 treatment. Our results elucidate the molecular mechanisms underlying EF-24’s antitumor efficacy against leukemia, highlighting its multifaceted impact on signaling pathways and gene networks that regulate cell survival, proliferation, and immune responses in myeloid leukemia cells.SignificanceThis study reveals how EF-24, a curcumin analog, disrupts key signaling pathways in chronic and acute myeloid leukemia cell lines, offering insights to enhance targeted therapies and provide new targets for investigation.Conflict of Interest StatementThe authors declare no potential conflicts of interest.
Information transfer from spatial to social distance in rats: implications for the role of the posterior parietal cortex in spatial-social integration
Authors: Wise Taylor B. , Templer Victoria , Burwell Rebecca D. 
Published: October 2024

ABSTRACTHumans and other social animals can represent and navigate complex networks of social relationships in ways that are suggestive of representation and navigation in space. There is some evidence that cortical regions initially required for processing space have been adapted to include processing of social information. One candidate region for supporting both spatial and social information processing is the posterior parietal cortex (PPC). We examined the hypothesis that rats can transfer or generalize distance information across spatial and social domains and that this phenomenon requires the PPC. In a novel apparatus, rats learned to discriminate two conspecifics positioned at different spatial distances (near vs. far) in a goal-driven paradigm.Following spatial learning, subjects were tested on probe trials in which spatial distance was replaced with social distance (cagemate vs. less familiar conspecific). The PPC was chemogenetically inactivated during a subset of probe sessions. We predicted that, in control probe trials, subjects would select conspecifics whose social distance matched the previously learned spatial distance. That is, if trained on the near distance, the rat would choose the highly familiar cagemate, and if trained on the far distance, the rat would choose the less familiar conspecific. Subjects learned to discriminate conspecifics based on spatial distance in our goal-driven paradigm. Moreover, choice for the appropriate social distance in the first probe session was significantly higher than chance. This result suggests that rats transferred learned spatial information to social contexts. Contrary to our predictions, PPC inactivation did not impair spatial to social information transfer. Possible reasons are discussed. To our knowledge, this is the first study to provide evidence that spatial and social distance are processed by shared cognitive mechanisms in the rat model.
PUBLIC ATTITUDES TOWARDS FOOD TAXES FOR HEALTHY EATING IN THE UNITED KINGDOM
Authors: Martínez-Jiménez Mario , Brinsden Hannah , Sassi Franco 
Published: October 2024

AbstractIntroductionAppropriately designed food taxes can improve diet quality and health. Fiscal levers are used in several countries to combat the rise in obesity and diet-related diseases. This study aims to investigate public attitudes, knowledge, and policy preferences regarding food taxes for promoting healthy eating in the UK.MethodsA survey was administered through YouGov Plc to a nationally representative sample of 2,125 adults, gathering information on: acceptability and support for different types of food taxes, awareness and knowledge of existing taxes, and preferences for the characteristics of possible new taxes.ResultsOverall, 48% of respondents support higher taxes on unhealthy foods, rising to 72% if taxes made healthy foods more affordable. Respondents with high socio-economic status and those living in London showed the highest support. Respondents had limited awareness of existing food and beverage taxes, and prioritised discretionary items such as cakes and crisps for possible increased taxation.ConclusionsThe survey shows a high level of support for taxing unhealthy foods, as well as concern for the affordability of healthy foods. A carefully designed holistic approach to food taxation can be part of a wider public health strategy and can be favourably met by the general population in the UK.
Perceptual Expertise and Attention: An Exploration using Deep Neural Networks
Authors: Das Soukhin , Mangun G.R. , Ding Mingzhou 
Published: October 2024

AbstractPerceptual expertise and attention are two important factors that enable superior object recognition and task performance. While expertise enhances knowledge and provides a holistic understanding of the environment, attention allows us to selectively focus on task-related information and suppress distraction. It has been suggested that attention operates differently in experts and in novices, but much remains unknown. This study investigates the relationship between perceptual expertise and attention using convolutional neural networks (CNNs), which are shown to be good models of primate visual pathways. Two CNN models were trained to become experts in either face or scene recognition, and the effect of attention on performance was evaluated in tasks involving complex stimuli, such as superimposed images containing superimposed faces and scenes. The goal was to explore how feature-based attention (FBA) influences recognition within and outside the domain of expertise of the models. We found that each model performed better in its area of expertise—and that FBA further enhanced task performance, but only within the domain of expertise, increasing performance by up to 35% in scene recognition, and 15% in face recognition. However, attention had reduced or negative effects when applied outside the models’ expertise domain. Neural unit-level analysis revealed that expertise led to stronger tuning towards category-specific features and sharper tuning curves, as reflected in greater representational dissimilarity between targets and distractors, which, in line with the biased competition model of attention, leads to enhanced performance by reducing competition. These findings highlight the critical role of neural tuning at single as well as network level neural in distinguishing the effects of attention in experts and in novices and demonstrate that CNNs can be used fruitfully as computational models for addressing neuroscience questions not practical with the empirical methods.
Disrupted Hippocampal-Prefrontal Networks in a Rat Model of Fragile X Syndrome: A Study Linking Neural Dynamics to Autism-Like Behavioral Impairments
Authors: Ouardouz Mohamed , Jasinski Patrick , Khalife Mohamed , Mahoney J Matthew , Hernan Amanda E , Scott Rod C 
Published: October 2024

ABSTRACTFragile X Syndrome (FXS) is associated with autism spectrum disorder (ASD) symptoms that are associated with cognitive, learning, and behavioral challenges. We investigated how known molecular disruptions in the Fmr1 knockout (FMR-KO) rat model of FXS negatively impact hippocampal-prefrontal cortex (H-PFC) neural network activity and consequent behavior.MethodsFMR-KO and control rats underwent a battery of behavioral tests assessing sociability, memory, and anxiety. Single-unit electrophysiology recordings were then conducted to measure patterns of neural activity in H-PFC circuit. Advanced mathematical models were used to characterize the patterns that were then compared between groups using generalized linear mixed models.ResultsFMR-KO rats demonstrated significant behavioral deficits in sociability, spatial learning, and anxiety, aligning with symptoms of ASD. At the neural level, these rats exhibited abnormal firing patterns in the H-PFC circuit that is critical for learning, memory, and social behavior. The neural networks in FMR-KO rats were also less densely connected and more fragmented, particularly in hippocampal-PFC correlated firing. These findings suggest that disruptions in neural network dynamics underlie the observed behavioral impairments in FMR-KO rats.ConclusionFMR-KO significantly disrupts several characteristics of action potential firing in the H-PFC network, leading to deficits in social behavior, memory, and anxiety, as seen in FXS. This disruption is characterized by less organized and less resilient hippocampal-PFC networks. These findings suggest that therapeutic strategies aimed at normalizing neural dynamics, such as with brain stimulation, could potentially improve behavior and cognitive functions in autistic individuals.HIGHLIGHTSFragile X Syndrome is associated with autism, cognitive challenges and anxietyThe loss of Fmr1 protein disrupts processes involved in building neural networksThe consequence is abnormal neural dynamics in hippocampal-prefrontal cortex networksNormalization of dynamics could improve outcomes in FXS and ASD
Implied motion guides neither gaze following nor intention attribution
Authors: Görner Marius , Shafiei Masih , Thier Peter 
Published: October 2024

AbstractThe “gaze beam hypothesis (GBH)” of gaze following posits that the other’s eyes emit imaginary beams of moving energy travelling to the other’s object of attention (1), drawing the observer’s attention to the same object. This idea was initially supported by behavioral experiments showing a motion aftereffect (MAE), indicated by longer reaction times in detecting motion direction after viewing a cartoon face looking at an object in the same direction (2). However, this effect could also be expected if the observer used gaze direction to assume an intentional link between the looker and the object, envisioning directed actions toward the latter (3). To critically compare the two hypotheses, we tested whether an MAE could be induced by having human subjects detect motion direction after viewing various cue images, designed to differentiate the explanatory power of the two. Cues either suggested a connection between an agent and an object through the agent’s gaze or an object-oriented intention by the presence of equipment in the agent’s hand, without the agent directly looking at the object. Using Bayesian statistics, our findings provided strong evidence against both hypotheses at the population level, as reaction time modulations did not align with the MAE, leading us to reject motion adaptation as the underlying mechanism for gaze following but also intention attribution. As on an individual level we observed highly diverse effects, with some compatible with one or the other hypothesis, we assume that individual subjects may resort to different perceptual strategies based on different scene interpretations.
A Cortical Site that Encodes Vocal Expression and Reception
Authors: Pomberger Thomas , Kaplan Katherine S , Carter Rene , Harmon Thomas C , Mooney Richard 
Published: October 2024

AbstractSocially effective vocal communication requires brain regions that encode expressive and receptive aspects of vocal communication in a social context-dependent manner. Here, we combined a novel behavioral assay with microendoscopy to interrogate neuronal activity in the posterior insula (pIns) in socially interacting mice as they switched rapidly between states of vocal expression and reception. We found that distinct but spatially intermingled subsets of pIns neurons were active during vocal expression and reception. Notably, pIns activity during vocal expression increased prior to vocal onset and was also detected in congenitally deaf mice, pointing to a motor signal. Furthermore, receptive pIns activity depended strongly on social cues, including female odorants. Lastly, tracing experiments reveal that deep layer neurons in the pIns directly bridge the auditory thalamus to a midbrain vocal gating region. Therefore, the pIns is a site that encodes vocal expression and reception in a manner that depends on social context.
Whistle variability and social acoustic interactions in bottlenose dolphins
Authors: Mustun Faadil , Semenzin Chiara , Rance Dean , Marachlian Emiliano , Guillerm Zohria-Lys , Mancini Agathe , Bouaziz Inès , Fleck Elisabeth , Shashar Nadav , de Polavieja Gonzalo G. , Sumbre Germán 
Published: October 2024

AbstractBottlenose dolphins exhibit a sophisticated social structure, known as a fission-fusion society. To sustain this complex system, dolphins rely on a rich vocal repertoire: clicks exclusively used for echolocation, burst-pulse sounds associated with emotions during social interactions, and whistles, including signature whistles that serve as individual-specific identifiers (‘names’).How dolphins maintain their complex social structure based only on a limited repertoire of sounds remains elusive. Previous studies suggest that contextual information can be transferred by the modulation of the whistles.Here, we investigated the whistle variability using a comprehensive computational approach, and studied the structure of the interactions between the whistle variants. Using a unique large dataset, acquired in a natural environment, we observed that signature whistles exhibit variations in their frequency contours. Unsupervised clustering revealed that signature whistles could be classified into sub-categories (signature whistle variants). The existence of these categories, and their independence on the emitter dolphin, indicate that these variations are not random. Analysis of pairwise interactions between sub-categories revealed a clustered structure similar to that of their social hierarchy. Network analysis of this structure showed that whistle sub-categories had different functional roles: some acted as hubs, others as bridges, and certain were used for turn-taking between the main whistle categories. We also found that the dolphins emit signature whistles of their deceased mothers, a phenomenon only observed in human language.Overall, these findings suggest that dolphins modulate signature whistles to transmit additional information beyond individual identity, and that they engage in "dialogue-like" acoustic interactions.
Study of Plasma Adiponectin Levels in Patients with Metabolic Syndrome and Therapeutic Indication in Bangladesh
Authors: Parul Salina Shaheen , Ahmmed Reaz , Hasan Md. Taohid , Islam Ariful , Rahman Md. Motiar , Manirujjaman M. , Bari Md. Wasim , Ahmed Md. Sakil , Hasan Md. Sohel , Islam Mohammad Amirul 
Published: October 2024

AbstractBackgroundThe metabolic syndrome (Met-S) is a cluster of some interrelated common clinical disorders, including central obesity, dyslipidemia, hypertension, and glucose intolerance. Central obesity, accompanied by insulin resistance, is a key factor for the development of metabolic syndrome. Adiponectin is an adipose-specific plasma protein, secreted from adipocyte with anti-atherogenic and insulin-sensitizing activities.PurposeThis study aimed to investigate the relationship of plasma adiponectin levels with metabolic syndrome, related disorders and its drug repurposing through in silico approach.Materials and MethodsFor this study, 269 individuals were recruited with written consent. The participants were selected based on their full medical history, clinical examination, and laboratory reports. Anthropometric measurements as well as blood pressure was measured before sample collection. Fasting blood samples were collected for the estimation of lipid profile, blood glucose, and serum adiponectin levels.ResultsOur results show that the adiponectin levels in the subjects with Met-S were significantly lower than those of without Met-S (p <0.0001). Among the metabolic syndrome risk factors, adiponectin levels were associated with hypertriglyceridemia and reduced HDL-cholesterol (p<0.0001). Three drugs (Saquinavir, Candesartan and Glimepiride) were suggested to control the plasma adiponectin level in the subjects with Met-S.ConclusionsSince the plasma adiponectin levels are significantly lower in patients with Met-S, it might be used as diagnostic & prognostic marker for Met-S disorder and adiponectin targeted drugs might be minimize the Met-S of the subjects.