bluuebunny/crossref_metadata_2025_split huggingface dataset:
Symbol ungrounding: what the successes (and failures) of large language models reveal about human cognition
Authors: Dove Guy 
Published: August 2024

Large language models can handle sophisticated natural language processing tasks. This raises the question of how their understanding of semantic meaning compares to that of human beings. Supporters of embodied cognition often point out that because these models are trained solely on text, their representations of semantic content are not grounded in sensorimotor experience. This paper contends that human cognition exhibits capabilities that fit with both the embodied and artificial intelligence approaches. Evidence suggests that semantic memory is partially grounded in sensorimotor systems and dependent on language-specific learning. From this perspective, large language models demonstrate the richness of language as a source of semantic information. They show how our experience with language might scaffold and extend our capacity to make sense of the world. In the context of an embodied mind, language provides access to a valuable form of ungrounded cognition.
This article is part of the theme issue ‘Minds in movement: embodied cognition in the age of artificial intelligence’.
Skill building in freediving as an example of embodied culture
Authors: Downey Greg 
Published: August 2024

Skilled activity is a complex mix of automatized action, changed attention patterns, cognitive strategies and physiological adaptations developed within a community of practice. Drawing on physiological and ethnographic research on freediving, this article argues that skill acquisition demonstrates the variety of mechanisms that link biological and cultural processes to produce culturally shaped forms of embodiment. In particular, apneists alter phenotypic expression through patterned practices that canalize development, exaggerating the dive response, developing resistance to elevated carbon dioxide levels (hypercapnia) and accommodating hydrostatic pressure at depth. The community of divers provides technical advice and helps to orient individuals’ motivations. Some biological processes are phenomenologically accessible, but others are sub-aware and must be accessed indirectly through behaviour or altered interactions with the environment. The close analysis of embodied skills like freediving illustrates how phenotypic plasticity is inflected by culturally patterned behaviours. Divers do developmental work on bodily traits like the dive response to achieve more dramatic performance, even if they cannot directly control all elements of the neurological and physiological responses. The example of expert freediving illustrates the imbrication of biology and culture in embodiment.
This article is part of the theme issue ‘Minds in movement: embodied cognition in the age of artificial intelligence’.
Gestures can help children learn mathematics: how researchers can work with teachers to make gesture studies applicable to classrooms
Authors: Seccia Amanda , Goldin-Meadow Susan 
Published: August 2024

The gestures we produce serve a variety of functions—they affect our communication, guide our attention and help us think and change the way we think. Gestures can consequently also help us learn, generalize what we learn and retain that knowledge over time. The effects of gesture-based instruction in mathematics have been well studied. However, few of these studies are directly applicable to classroom environments. Here, we review literature that highlights the benefits of producing and observing gestures when teaching and learning mathematics, and we provide suggestions for designing research studies with an eye towards how gestures can feasibly be applied to classroom learning.
This article is part of the theme issue ‘Minds in movement: embodied cognition in the age of artificial intelligence’.
Peripersonal space: why so last-second?
Authors: de Vignemont Frédérique , Farnè Alessandro 
Published: August 2024

A vast range of neurophysiological, neuropsychological and behavioural results in monkeys and humans have shown that the immediate surroundings of the body, also known as peripersonal space (PPS), are processed in a unique way. Three roles have been ascribed to PPS mechanisms: to react to threats, to avoid obstacles and to act on objects. However, in many circumstances, one does not wait for objects or agents to enter PPS to plan these behaviours. Typically, one has more chances to survive if one starts running away from the lion when one sees it in the distance than if it is a few steps away. PPS makes sense in shortsighted creatures but we are not such creatures. The crucial question is thus twofold: (i) why are these adaptive processes triggered only at the last second or even milliseconds? And (ii) what is their exact contribution, especially for defensive and navigational behaviours? Here, we propose that PPS mechanisms correspond to a plan B, useful in unpredictable situations or when other anticipatory mechanisms have failed. Furthermore, we argue that there are energetic, cognitive and behavioural costs to PPS mechanisms, which explain why this plan B is triggered only at the last second.
This article is part of the theme issue ‘Minds in movement: embodied cognition in the age of artificial intelligence’.
Boundary conditions for synaptic homeodynamics during the sleep-wake cycle
Authors: Kinoshita Fukuaki L. , Yamada Rikuhiro G. , Ode Koji L. , Ueda Hiroki R. 
Published: August 2024

AbstractUnderstanding synaptic dynamics during the sleep-wake cycle is crucial yet remains controversial. The synaptic homeostasis hypothesis (SHY) suggests synaptic depression during non-rapid eye movement (NREM) sleep, while other studies report synaptic potentiation or synaptic changes during NREM sleep depending on activities in wakefulness. To find boundary conditions between these contradictory observations, we focused on learning rules and firing patterns that contribute to the synaptic dynamics. Using computational models, we found that under Hebbian and spike-timing dependent plasticity (STDP), wake-like firing patterns decrease synaptic weights, while sleep-like patterns strengthen synaptic weights. We refer to this tendency as Wake Inhibition and Sleep Excitation (WISE). Conversely, under Anti-Hebbian and Anti-STDP, synaptic depression during NREM sleep was observed, aligning with the conventional synaptic homeostasis hypothesis. Moreover, synaptic changes depended on firing rate differences between NREM sleep and wakefulness. We provide a unified framework that could explain synaptic homeodynamics under the sleep-wake cycle.
SUV39H1 Preserves Cancer Stem Cell Chromatin State and Properties in Glioblastoma
Authors: Li Chunying , Xie Qiqi , Ghosh Sugata , Cao Bihui , Du Yuanning , Vo Giau Van , Huang Timothy Y. , Spruck Charles , Wang Y. Alan , Nephew Kenneth P. , Shen Jia 
Published: August 2024

AbstractOf the more than 100 types of brain cancer, glioblastoma (GBM) is the deadliest. As GBM stem cells (GSCs) are considered to be responsible for therapeutic resistance and tumor recurrence, effective targeting and elimination of GSCs could hold promise for preventing GBM recurrence and achieving potential cures. We show here thatSUV39H1, which encodes a histone-3, lysine-9 methyltransferase, plays a critical role in GSC maintenance and GBM progression. Upregulation of SUV39H1 was observed in GBM samples compared to normal brain tissues, and knockdown of SUV39H1 in patient-derived GSCs impaired their proliferation and stemness. Single-cell RNA-seq analysis demonstrated restricted expression of SUV39H1 is in GSCs relative to non-stem GBM cells, likely due to super-enhancer-mediated transcriptional activation, while whole cell RNA-seq analysis revealed that SUV39H1 regulates G2/M cell cycle progression, stem cell maintenance, and cell death pathways in GSCs. By integrating the RNA-seq data with ATAC-seq (assay for transposase-accessible chromatin followed by sequencing), we further demonstrated altered chromatin accessibility in key genes associated with these pathways following SUV39H1 knockdown. Treatment with chaetocin, a SUV39H1 inhibitor, mimicked the functional effects of SUV39H1 knockdown in GSCs and sensitized GSCs to the GBM chemotherapy drug temozolomide. Furthermore, targeting SUV39H1 in vivo using a patient-derived xenograft model for GBM inhibited GSC-driven tumor formation. This is the first report demonstrating a critical role for SUV39H1 in GSC maintenance. SUV39H1-mediated targeting of GSCs could enhance the efficacy of existing chemotherapy, presenting a promising strategy for improving GBM treatment and patient outcomes.HighlightsSUV39H1 is upregulated in GBM, especially GSCsTargeting SUV39H1 disrupts GSC maintenance and sensitizes GSCs to TMZTargeting SUV39H1 alters chromatin accessibility at cell cycle and stemness genesTargeting SUV39H1 suppresses GSC-driven tumors in a patient-derived xenograft model
De-biased sparse canonical correlation for identifying cancer-related trans-regulated genes
Authors: Huey Nathan , Dutta Diptavo , Laha Nilanjana 
Published: August 2024

SummaryIn cancer multi-omic studies, identifying the effects of somatic copy number aberrations (CNA) on physically distal gene expressions (trans-associations) can potentially uncover genes critical for cancer pathogenesis. Sparse canonical correlation analysis (SCCA) has emerged as a promising method for identifying associations in high-dimensional settings, owing to its ability to aggregate weaker associations and its improved interpretability. Traditional SCCA lacks hypothesis testing capabilities, which are critical for controlling false discoveries. This limitation has recently been addressed through a bias correction technique that enables calibrated hypothesis testing. In this article, we leverage the theoretical advancements in de-biased SCCA to present a computationally efficient pipeline for multi-omics analysis. This pipeline identifies and tests associations between multi-omics data modalities in biomedical settings, such as the trans-effects of CNA on gene expression. We propose a detailed algorithm to choose the tuning parameters of de-biased SCCA. Applying this pipeline to data on estrogen receptor (ER)-associated CNAs and 10,756 gene expressions from 1,904 breast cancer patients in the METABRIC study, we identified 456 CNAs trans-associated with 256 genes. Among these, 5 genes were identified only through de-biased SCCA and not by the standard pairwise regression approach. Downstream analysis with the 256 genes revealed that these genes were overrepresented in pathways relevant to breast cancer.
Mutualisms within light microhabitats drive sensory convergence in a mimetic butterfly community
Authors: Wainwright J. Benito , Loupasaki Theodora , Ramírez Francisco , Penry Williams Iestyn L. , England Sam J. , Barker Annalie , Meier Joana I. , How Martin J. , Roberts Nicholas W. , Troscianko Jolyon , Montgomery Stephen H. 
Published: August 2024

AbstractNiche partitioning within variable habitats can expose species to distinct sensory information. Vision is the primary sensory modality used by many animals to interact with their habitat. However, within diurnal terrestrial ecosystems, little is known if, and how, variation in light environments impact species assemblages and visual system evolution. By studying a diverse, sympatric community of mimetic butterflies, we demonstrate that forest architecture creates a mosaic of light microhabitats that drive adaptive sensory convergence and divergence in both peripheral and central sensory systems. Our study provides insights into the dynamic response of visual systems when confronted with similar ecological challenges, and illustrates the wide-reaching consequences of interspecific mutualisms, such as mimicry, on organismal evolution.
Dialogues in colour and behaviour - Integration of complex signalling traits and physiology
Authors: Patro Subhasmita , Saravanan Thejaswini , Parag Ayush , Thaker Maria 
Published: August 2024

AbstractAnimal communication can be complex, often involving multiple static and dynamic traits. The extent to which these traits are correlated can elucidate their function as either redundant or multiple messages. Using the agamid lizard,Psammophilus dorsalis, as a model system we examined patterns of trait expression and the role of steroid hormones in mediating these traits during social interactions. We staged male-male interactions in the lab and measured the repertoire of display behaviour and colours, which change dynamically in the visible and ultraviolet ranges in different body regions. Additionally, we measured testosterone and corticosterone levels before and after the social trials.Our results show that within behaviour and colour trait categories, components were strongly correlated within individuals, suggesting either a shared physiological pathway or redundant information content. However, across trait categories, correlation patterns varied. The chromatic contrast of the (yellow) dorsal region of lizards was correlated with both body size and level of aggression, whereas the size of UV patches was correlated with body size only. We also found a negative association between baseline corticosterone levels, body size and dorsal yellow chromatic contrast, suggesting a mechanistic link between these traits. However, social interaction induced testosterone and corticosterone levels were uncorrelated with the expression of the dynamic behavioural and colour displays during the social interactions itself. Notably, the intensity of colour and behavioural displays of males were matched by their opponents. Overall, our results suggest that multiple signalling traits can ensure both redundancy as well as provide multiple messages to receivers, thus improving the robustness of information transfer, particularly during competitions which have high fitness consequences.
4-week GLP immunotoxicity assessment of lactoferrin alpha produced byKomagataella phaffiiin Sprague Dawley rats
Authors: Peterson Ross , Crawford Robert B. , Blevins Lance K. , Kaminski Norbert E. , Clark Anthony J. , Malinczak Carrie-Anne 
Published: August 2024

ABSTRACTOral toxicity and toxicokinetic properties of human lactoferrin (LF) alpha produced inKomagataella Phaffii(effera™) were investigated in adult Sprague-Dawley rats over a 28-day period under good laboratory practice conditions. Main study dosing used groups of 10 rats/sex/dose, and a secondary study evaluating toxicokinetic parameters used 6 rats/sex/dose. The vehicle control group received sodium citrate buffer, test groups received daily doses of 200, 600, and 2000 mg of effera™ per kg body weight, and the comparative control group received 2000 mg bovine LF (bLF)/kg body weight per day. T-cell dependent antibody response against keyhole limpet hemocyanin and immunophenotyping of the spleen were performed as measures of immunotoxicity. Clinical observations, body weight, hematology, coagulation, clinical chemistry, urinalysis, immunotoxicity, gross necropsy, and histopathology were assessed. Toxicokinetic parameters were analyzed as an indication of LF bioavailability, and anti-LF antibody assays were conducted to detect antibodies produced against LF to measure immunogenicity. No treatment related toxicologically significant changes were observed. Based on the absence of toxicologically relevant changes, effera™ is well tolerated in rats at doses up to 2000 mg rhLF/kg/day, an amount ∼400 times that of the estimated daily intake at the 90th percentile proposed for human adult use.
Immunojanus Particles for low-volume and isolation-free unlabeled characterization of small Extracellular Vesicle in biofluids: Characterization of disease type by surface marker profiling
Authors: Kumar Sonu , Sinclair John Alex , Shi Tiger , Chuang Han-Sheng , Senapati Satyajyoti , Chang Hsueh-Chia 
Published: August 2024

AbstractSmall extracellular vesicles (sEVs) are vital for cellular communication and serve as critical biomarker carriers for diseases such as cancer. However, quantifying and profiling sEV surface markers presents significant challenges due to the low concentration of specific sEV-bound proteins and interference by more abundant dispersed proteins. This paper presents Immunojanus Particles (IJPs), a new method that enables the direct detection of sEVs in less than an hour without isolation. The design of IJPs incorporates fluorescent and non-fluorescent halves, utilizing rotational Brownian motion to detect captured sEVs through the change in the blinking rate, without interference from the smaller dispersed proteins. We demonstrate a detection limit of 2E5 sEVs/mL with low sample volumes and the capability to characterize sEVs directly from plasma, serum, cell culture media, and urine. In a small pilot study involving 87 subjects, including individuals with colorectal cancer, pancreatic ductal adenocarcinoma, glioblastoma, Alzheimer’s disease, and healthy controls, our method accurately identified the type of disease with high 0.90-0.99 AUC in a blind setting. Compared with an orthogonal ultracentrifugation plus surface plasmon resonance (UC+SPR) method that requires about 24 hours, the sensitivity and dynamic range of IJP are better by 2 logs.
Attention and working memory investigated through the P300 component in children practicing Karate at different stages of biological maturation
Authors: Nicoliche Eduardo , Vasconcelos Alexandre , Machado Marcos , Tanaka Guaraci , Vicente Renan , Marques Adriana , Costa Élida , Gongora Mariana , Di Giacomo Jessé , Nobre Marcelo , Teixeira Silmar , Bastos Victor Hugo , Cagy Mauricio , Fernandes Isabelle , Machado Caroline , Ribeiro Pedro , Gupta Daya S. , Velasques Bruna , Budde Henning 
Published: August 2024

AbstractAimTo investigate attention and working memory, comparing children practice Karate and non-Karate practitioners at different stages of biological maturation through the amplitude and latency of the P300 component during the execution of a Go/No-Go paradigm.Material and MethodsThe P300 was analyzed for Fz, Cz, and Pz electrodes in 80 participants separated in two groups: an Karate practitioners group comprising Karate practitioners and comprising non-Karate practitioners. Each group was further subdivided according to the biological maturation range defined by Peak Height Velocity. In addition, the participants performed a Go/No-Go paradigm to measure amplitude and latency.ResultsThe EEG analysis showed Ffr electrodes Pz and Cz, an interaction was found between group and Peak Height Velocity for the amplitude variable (respectively: F = 45.858; d = 0.38; p < 0.001 / F = 10.411; d = 0.17; p = 0.004). For the Fz electrode, a main effect was found between group and Peak Height Velocity (respectively: F = 40.330; d = 0.34; p = 0.010 / F = 36.730; d = 0.30; p = 0.012) for the variable amplitude and latency. main effect between group and Peak Height Velocity (respectively: F = 7.719; d = 0.14; p = 0.012 / F = 38.370; d = 0.31; p = 0.010).ConclusionsIn general, it is possible to conclude that participants in the Karate practitioners group exhibited electrocortical measures corresponding to greater efficiency in decision-making and attention processes, motor planning, working memory, attention allocation, motor execution, and greater attentional engagement. It was also demonstrated that, despite the children being at very close chronological ages, their biological maturation differed.
Automated Navigation of the lncRNA Transcriptome: A comprehensive SnakeMake based computational Pipeline for robust Identification of lncRNAs and their putative targets
Authors: Kandpal Manu , Mukherjee Chitranjan , Rami Bhadresh 
Published: August 2024

ABSTRACTBackgroundLong non-coding RNAs (lncRNAs) have emerged as potent regulatory elements in cellular processes. The substantial increase in transcriptomic data resulting from high-throughput RNA sequencing necessitates effective approaches for the identification and functional annotation of lncRNAs.MethodTo address this need, we have developed a SnakeMake-based pipeline. Our pipeline automates and integrates several key steps: 1) RNA-seq analysis using Hisat2 and stringTie, (2) lncRNA identification using inhouse python scripts and tools CPC2 and BLASTX, (3) prediction ofcis-andtrans-gene targets of lncRNAs, and (4) KEGG pathway enrichment to obtain biological insights. Importantly, the pipeline allows users to customize parameters for each step through a user-friendly configuration file (config.yaml), enhancing flexibility and ease of use. One of the distinctive features of our approach is its single command execution, facilitating multiple runs without the need for extensive user intervention. This not only enhances user convenience but also ensures reproducibility of analyses across different studies.ResultWe applied our pipeline on rice, sorghum, and human RNA-seq data, to identify (1) List of all differentially expressed transcripts., (2) List of differentially expressed lncRNAs, (3) lncRNA target genes, (4) Enriched pathways to which target genes belong and (5) Obtain a visualization output in the form of a bubble plot that depicts the enriched pathways. Our approach can help researchers obtain valuable biological insights into how lncRNAs contribute to various biological functions.ConclusionThe distinctive features of our SnakeMake-based automation pipeline position it as a versatile asset for researchers seeking a user-friendly, adaptable, robust, and reproducible solution for pan species lncRNA analysis. By efficiently uncovering the regulatory roles of lncRNAs in cellular processes, this pipeline has the potential to shed light on various biological phenomena, such as developmental biology, disease progression, and cellular response to external stimuli.GRAPHICAL ABSTRACTThis study presents a SnakeMake-based pipeline for identifying and annotating long non-coding RNAs (IncRNAs) from RNA sequencing data. It integrates RNA-seq analysis, IncRNA identification, gene target prediction, and pathway enrichment, with customizable parameters through a user-friendly configuration file. The pipeline’s single command execution enhances convenience and reproducibility. (The bubble chart in the figure is a representative chart and provided as an example.)
Development of Machine Learning-based QSAR Models for the Designing of Novel Anti-cancer Therapeutics Against Malignant Glioma
Authors: Asaad Fareed , Zaka Mehreen , Durdağı Serdar 
Published: August 2024

AbstractIn the early drug design and discovery phase, virtual screening of diverse small molecule libraries is crucial. Machine learning (ML)-based algorithms have made this process easier and faster. In this study, we have applied ML-based algorithms to generate the QSAR models for virtual screening. The aim of study is to design the statistically significant models for the screening of small molecule libraries to identify the novel hits against IDH1 mutant receptor crucial for glioblastoma multiforme (GBM). To construct the models, we have used both cell lines data (U87 and U251 cells) and the inhibitors of IDH1 mutant reported in the literature and used the pIC50activity data to train our models. Furthermore, ligand-based 3D QSAR models and structure-based pharmacophore models were also constructed and validated.