bluuebunny/crossref_metadata_2025_split huggingface dataset:
Probing the Link Between Vision and Language in Material Perception Using Psychophysics and Unsupervised Learning
Authors: Liao Chenxi , Sawayama Masataka , Xiao Bei 
Published: January 2024

AbstractWe can visually discriminate and recognize a wide range of materials. Meanwhile, we use language to express our subjective understanding of visual input and communicate relevant information about the materials. Here, we investigate the relationship between visual judgment and language expression in material perception to understand how visual features relate to semantic representations. We use deep generative networks to construct an expandable image space to systematically create materials of well-defined and ambiguous categories. From such a space, we sampled diverse stimuli and compared the representations of materials from two behavioral tasks: visual material similarity judgments and free-form verbal descriptions. Our findings reveal a moderate but significant correlation between vision and language on a categorical level. However, analyzing the representations with an unsupervised alignment method, we discover structural differences that arise at the image-to-image level, especially among materials morphed between known categories. Moreover, visual judgments exhibit more individual differences compared to verbal descriptions. Our results show that while verbal descriptions capture material qualities on the coarse level, they may not fully convey the visual features that characterize the material’s optical properties. Analyzing the image representation of materials obtained from various pre-trained data-rich deep neural networks, we find that human visual judgments’ similarity structures align more closely with those of the text-guided visual-semantic model than purely vision-based models. Our findings suggest that while semantic representations facilitate material categorization, non-semantic visual features also play a significant role in discriminating materials at a finer level. This work illustrates the need to consider the vision-language relationship in building a comprehensive model for material perception. Moreover, we propose a novel framework for quantitatively evaluating the alignment and misalignment between representations from different modalities, leveraging information from human behaviors and computational models.
Exposure to epoxiconazole induces hyperlocomotion in adult zebrafish
Authors: Reis Carlos G. , Chitolina Rafael , Bastos Leonardo M. , Portela Stefani M. , Stahlhofer-Buss Thailana , Piato Angelo 
Published: January 2024

AbstractGlobal agricultural production is sustained by an elevated use of pesticides. Their application in crops results in environmental contamination, which is demonstrated by widespread detections of these chemicals in aquatic ecosystems. This presence poses a risk to non-target organisms and ecological balance since the effects of potential exposure are misunderstood. Epoxiconazole (EPX) is a widely employed triazole fungicide, which has been frequently reported as a contaminant in superficial waters. However, the behavioral effects of EPX exposure in non-target organisms such as fish remain unexplored. We aimed to investigate the effects of EPX exposure on behavioral and biochemical outcomes, using zebrafish as a model organism. For this purpose, a static system was set with concentrations (24, 144, 240 μg/L) based on the fungicide environmental detection. The novel tank test (NTT) was performed after 96 h of exposure. The social preference test (SPT) was executed after 120 h, as well as the biochemical assays. In the NTT, the animals increased distance traveled, crossings, entries in the top area, and mean speed, indicating hyperlocomotion. No significant effects were observed in the SPT and the biochemical analyses. We suggest that the increased locomotion is related to the stimulant properties of EPX. Our results contribute to an in-depth understanding of this fungicide effects in zebrafish, which is essential for environmental contamination monitoring and management.
Dual effects ofARXpoly-alanine mutations in human cortical and interneuron development
Authors: Nieto-Estevez Vanesa , Varma Parul , Mirsadeghi Sara , Caballero Jimena , Gamero-Alameda Sergio , Hosseini Ali , Silvosa Marc J. , Thodeson Drew M. , Lybrand Zane R. , Giugliano Michele , Navara Christopher , Hsieh Jenny 
Published: January 2024

AbstractInfantile spasms, with an incidence of 1.6 to 4.5 per 10,000 live births, are a relentless and devastating childhood epilepsy marked by severe seizures but also leads to lifelong intellectual disability. Alarmingly, up to 5% of males with this condition carry a mutation in theAristaless-related homeobox(ARX) gene. Our current lack of human-specific models for developmental epilepsy, coupled with discrepancies between animal studies and human data, underscores the gap in knowledge and urgent need for innovative human models, organoids being one of the best available. Here, we used human neural organoid models, cortical organoids (CO) and ganglionic eminences organoids (GEO) which mimic cortical and interneuron development respectively, to study the consequences of PAE mutations, one of the most prevalent mutation inARX. ARXPAEproduces a decrease expression ofARXin GEOs, and an enhancement in interneuron migration. That accelerated migration is cell autonomously driven, and it can be rescued by inhibiting CXCR4. We also found that PAE mutations result in an early increase in radial glia cells and intermediate progenitor cells, followed by a subsequent loss of cortical neurons at later timepoints. Moreover,ARXexpression is upregulated in COs derived from patients at 30 DIV and is associated with alterations in the expression ofCDKN1C. Furthermore, ARXPAEassembloids had hyperactivity which were evident at early stages of development. With effective treatments for infantile spasms and developmental epilepsies still elusive, delving into the role of ARXPAEmutations in human brain organoids represents a pivotal step toward uncovering groundbreaking therapeutic strategies.
Oscillatory Hypoxia Induced Unfolded Protein Folding Response Gene Expression Predicts Low Survival in Human Breast Cancer Patients
Authors: Suhail Yasir , Liu Yamin , Du Wenqiang , Afzal Junaid , Qiu Xihua , Atiq Amina , Vera-Licona Paola , Agmon Eran , Kshitiz  
Published: January 2024

AbstractHypoxia is one of the key factors in the tumor microenvironment regulating nearly all steps in the metastatic cascade in many cancers, including in breast cancer. The hypoxic regions can however be dynamic with the availability of oxygen fluctuating or oscillating. The canonical response to hypoxia is relayed by transcription factor HIF-1, which is stabilized in hypoxia and acts as the master regulator of a large number of downstream genes. However, HIF-1 transcriptional activity can also fluctuate either due to unstable hypoxia, or by lactate mediated non-canonical degradation of HIF-1. Our understanding of how oscillatory hypoxia or HIF-1 activity specifically influence cancer malignancy is very limited. Here, using MDA-MB-231 cells as a model of triple negative breast cancer characterized by severe hypoxia, we measured the gene expression changes induced specifically by oscillatory hypoxia. We found that oscillatory hypoxia can specifically regulate gene expression differently, and at times opposite to stable hypoxia. Using The Cancer Genome Atlas (TCGA) RNAseq data of human cancer samples, we show that the oscillatory specific gene expression signature in MDA-MB-231 is enriched in most human cancers, and prognosticate low survival in breast cancer patients. In particular, we found that oscillatory hypoxia, unlike stable hypoxia, induces unfolded protein folding response (UPR) in cells resulting in gene expression predicting reduced survival.
Adult-Onset Deletion ofATP13A2in Mice Induces Progressive Nigrostriatal Pathway Dopaminergic Degeneration and Lysosomal Abnormalities
Authors: Erb Madalynn L. , Sipple Kayla , Levine Nathan , Chen Xi , Moore Darren J. 
Published: January 2024

AbstractAlthough most cases of Parkinson’s disease (PD) are sporadic, mutations in over 20 genes are known to cause heritable forms of PD. A surprising number of familial PD-linked genes and PD risk genes are involved in intracellular trafficking and protein degradation. Recessive loss-of-function mutations inATP13A2, a lysosomal transmembrane P5B-type ATPase and polyamine exporter, can cause early-onset familial PD. FamilialATP13A2mutations are also linked to related neurodegenerative diseases, including Kufor-Rakeb syndrome (KRS), hereditary spastic paraplegias (HSPs), neuronal ceroid lipofuscinosis, and amyotrophic lateral sclerosis (ALS). Given the severe effects ofATP13A2mutations in humans, it is surprising thatATP13A2knockout (KO) mice fail to exhibit neurodegeneration even at advanced ages. This discrepancy between human subjects and rodents makes it challenging to study the neuropathological effects of ATP13A2 lossin vivo. Germline deletion ofATP13A2in rodents may trigger the upregulation of compensatory pathways during embryonic development that mask the full neurotoxic effects of ATP13A2 loss in the brain. To explore this idea, we selectively deletedATP13A2in the adult mouse brain by the unilateral delivery of an AAV-Cre vector into the substantia nigra of young adult mice carrying conditionalloxP-flankedATP13A2KO alleles. We observe a progressive loss of striatal dopaminergic nerve terminals at 3 and 10 months after AAV-Cre delivery. Cre-injected mice also exhibit robust dopaminergic neuronal degeneration in the substantia nigra at 10 months. Adult-onsetATP13A2KO also recreates many of the phenotypes observed in aged germlineATP13A2KO mice, including lysosomal abnormalities, p62-positive inclusions, and neuroinflammation. Our study demonstrates that the adult-onset homozygous deletion ofATP13A2in the nigrostriatal pathway produces robust and progressive dopaminergic neurodegeneration that serves as a usefulin vivomodel ofATP13A2-related neurodegenerative diseases.
Vagus nerve stimulation (VNS) modulates synaptic plasticity in the rat infralimbic cortex via Trk-B receptor activation to reduce drug-seeking
Authors: Driskill Christopher M. , Childs Jessica E. , Phensy Aarron J. , Rodriguez Sierra R. , O’Brien John T. , Lindquist Kathy L. , Naderi Aurian , Bordieanu Bogdan , McGinty Jacqueline F. , Kroener Sven 
Published: January 2024

AbstractDrugs of abuse cause changes in the prefrontal cortex (PFC) and associated regions that impair inhibitory control over drug-seeking. Breaking the contingencies between drug-associated cues and the delivery of the reward during extinction learning reduces relapse. Vagus nerve stimulation (VNS) has previously been shown to enhance extinction learning and reduce drug-seeking. Here we determined the effects of VNS-mediated release of brain-derived neurotrophic factor (BDNF) on extinction and cue-induced reinstatement in rats trained to self-administer cocaine. Pairing 10 days of extinction training with VNS facilitated extinction and reduced drug-seeking behavior during reinstatement. Rats that received a single extinction session with VNS showed elevated BDNF levels in the medial PFC as determined via an enzyme-linked immunosorbent assay (ELISA). Systemic blockade of Tropomyosin receptor kinase B (TrkB) receptors during extinction, via the TrkB antagonist ANA-12, decreased the effects of VNS on extinction and reinstatement. Whole-cell recordings in brain slices showed that cocaine self-administration induced alterations in the ratio of AMPA and NMDA receptor-mediated currents in layer 5 pyramidal neurons of the infralimbic cortex (IL). Pairing extinction with VNS reversed cocaine-induced changes in glutamatergic transmission by enhancing AMPAR currents, and this effect was blocked by ANA-12. Our study suggests that VNS consolidates extinction of drug-seeking behavior by reversing drug-induced changes in synaptic AMPA receptors in the IL, and this effect is abolished by blocking TrkB receptors during extinction, highlighting a potential mechanism for the therapeutic effects of VNS in addiction.Significance StatementExtinction training can reverse maladaptive neuroplasticity induced by drugs of abuse, but adjunct treatments are sought that can facilitate the process and consolidate the newly formed memories. Pairing extinction training with vagus nerve stimulation (VNS) facilitates extinction and reduces drug-seeking behavior during reinstatement. Here, we show that rats receiving a single extinction session with VNS exhibit elevated brain-derived neurotrophic factor (BDNF) levels in the medial prefrontal cortex (mPFC). We also demonstrate that VNS consolidates the extinction of drug-seeking behavior by reversing cocaine-induced changes in synaptic AMPA receptors in the infralimbic cortex (IL) of the mPFC. This effect is blocked by the TrkB antagonist ANA-12, emphasizing the role of BDNF and TrkB receptors in the therapeutic effects of VNS in addiction.
Beav: A bacterial genome and mobile element annotation pipeline
Authors: Jung Jewell M. , Rahman Arafat , Schiffer Andrea M. , Weisberg Alexandra J. 
Published: January 2024

AbstractComprehensive and accurate genome annotation is crucial for inferring the predicted functions of an organism. Numerous tools exist to annotate genes, gene clusters, mobile genetic elements, and other diverse features. However, these tools and pipelines can be difficult to install and run, be specialized for a particular element or feature, or lack annotations for larger elements that provide important genomic context. Integrating results across analyses is also important for understanding gene function. To address these challenges, we present the Beav annotation pipeline. Beav is a command-line tool that automates the annotation of bacterial genome sequences, mobile genetic elements, molecular systems and gene clusters, key regulatory features, and other elements. Beav uses existing tools in addition to custom models, scripts, and databases to annotate diverse elements, systems, and sequence features. Custom databases for plant-associated microbes are incorporated to improve annotation of key virulence and symbiosis genes in agriculturally important pathogens and mutualists. Beav includes an optionalAgrobacterium-specific pipeline that identifies and classifies oncogenic plasmids and annotates plasmid-specific features. Following the completion of all analyses, annotations are consolidated to produce a single comprehensive output. Finally, Beav generates publication-quality genome and plasmid maps. Beav is on Bioconda and is available for download athttps://github.com/weisberglab/beav.
Axion Dark Matter eXperiment: Run 1A analysis details
Authors: Boutan C. , LaRoque B. H. , Lentz E. , Oblath N. S. , Taubman M. S. , Tedeschi J. , Yang J. , Jones A. M. , Braine T. , Crisosto N. , Rosenberg L. J. , Rybka G. , Will D. , Zhang D. , Kimes S. , Ottens R. , Bartram C. , Bowring D. , Cervantes R. , Chou A. S. , Knirck S. , Mitchell D. V. , Sonnenschein A. , Wester W. , Khatiwada R. , Carosi G. , Du N. , Durham S. , O’Kelley S. R. , Woollett N. , Duffy L. D. , Bradley R. , Clarke J. , Siddiqi I. , Agrawal A. , Dixit A. V. , Gleason J. R. , Hipp A. T. , Jois S. , Sikivie P. , Sullivan N. S. , Tanner D. B. , Buckley J. H. , Gaikwad C. , Henriksen E. A. , Hoffman J. , Murch K. W. , Harrington P. M. , Daw E. J. , Perry M. G. , Hilton G. C. ,   ADMX Collaboration
Published: January 2024

The ADMX Collaboration gathered data for its Run 1A axion dark matter search from January 2017 to June 2017, scanning with an axion haloscope over the frequency range 645–680 MHz (2.66–2.81  μeV in axion mass) at Dine-Fischler-Srednicki-Zhitnitskii (DFSZ) sensitivity. The resulting axion search found no axionlike signals comprising all the dark matter in the form of a virialized galactic halo over the entire frequency range, implying lower bound exclusion limits at or below DFSZ coupling at the 90% confidence level. This paper presents expanded details of the axion search analysis of Run 1A, including review of relevant experimental systems, data-taking operations, preparation and interpretation of raw data, axion search methodology, candidate handling, and final axion limits.

Published by the American Physical Society
2024
Sustainability reporting, institutional pressures and universities: evidence from the Spanish setting
Authors: Andrades Javier , Martinez-Martinez Domingo , Larrán Manuel 
Published: January 2024

Purpose
Relying on institutional theory and Oliver’s (1991) strategic responses framework, the purpose of this paper is to investigate the different strategies adopted by Spanish public universities to respond to institutional pressures for sustainability reporting.

Design/methodology/approach
Data were collected from a variety of sources, such as a series of email-structured interviews with key personnel from universities, a qualitative analysis of sustainability reports and a consultation of the website of each Spanish public university.

Findings
The findings reveal that Spanish public universities have responded to institutional pressures for sustainability reporting by adopting acquiescence, compromise, avoidance and defiance strategies. The variety of strategic responses adopted by Spanish public universities suggests that these organizations have not fully adhered to institutional pressures.

Practical implications
The results of this paper would be useful for practitioners since it tries to demonstrate whether universities, which are facing increasing institutional pressures and demands from stakeholders, have been developing sustainability reporting practices.

Social implications
Universities have a remarkable social impact that could be used to promote sustainability practices. This paper investigates how these organizations can contribute to sustainability reporting as they should reproduce social norms.

Originality/value
The sustainability reporting context is in a phase of change. This paper tries to contribute to the accounting research by analyzing the extent to which universities are engaged in sustainability reporting. Relying on these premises, Oliver’s (1991) framework might be an insightful theoretical perspective to examine the responses provided by universities to institutional pressures.
The discovery and global distribution of hyperaccumulator plants: A personal account
Authors: Reeves Roger D. 
Published: January 2024

AbstractAn instance of extreme accumulation of Zn by a plant species was found in the 19th century, and observations of unusually high concentrations of other elements (Cu, Co, Ni, Cd, Pb, As, Se) were recorded between the 1920s and 1970s. Of relevance to the study of ultramafic areas and their floras is the occurrence of extreme Ni accumulation. The term “hyperaccumulator” was introduced in 1976 to signify a species exhibiting a concentration that can be hundreds or thousands of times greater than that usually found in plants on most common soils. Concentration criteria that allow a species to be regarded as a hyperaccumulator have been defined and refined from time to time. The following account details my own involvement in the discovery of new examples of metal hyperaccumulation, with particular emphasis on Ni accumulation by plants of ultramafic floras worldwide. The interest in hyperaccumulators has prompted investigations into different aspects of the biota of metalliferous soils. The search for new examples of hyperaccumulation continues, aided in part by non‐destructive X‐ray fluorescence scanning of herbarium specimens, which previously served as a resource providing small fragments for sensitive but destructive analysis. Identification of species as hyperaccumulators must be supported by further field exploration to understand the factors governing the level of metal uptake, and to stimulate further work on plant systematics, biochemistry, genetics, and molecular biology. Applications to phytoremediation and agromining are worth pursuing in some cases. Conservation issues are important because many hyperaccumulators are rare and restricted in their distribution.
Scaling circular economy business models: A capability perspective
Authors: Acquier Aurélien , Carbone Valentina , Ezvan Cécile 
Published: January 2024

AbstractIn a context of growing environmental challenges, circular economy (CE) business models appear necessary for business to contribute positively to the ecological transition. While platform business models have been identified as a new and promising model in CE, we still lack a fine‐grained understanding of the critical capabilities involved in developing and scaling them. To fill this gap, we build on a single case study of Phenix, a French‐based fast‐growing start‐up in the food industry, tackling the issue of food waste. We identify three core managerial capabilities involved in the successful scaling of Phenix's business model. In addition to ecosystem orchestration capabilities, we identify two types of ambidextrous capabilities – forms of ambidexterity operating both at the organizational and at the institutional level. Our analysis highlights the importance of considering these capabilities in a bundle as they collectively contribute to the performance and scaling potential of the business model. We also call for an increased consideration of the role of institutional factors in shaping opportunities to design and scale profitable business models.
Stiffness promotes cell migration, invasion, and invadopodia in nasopharyngeal carcinoma by regulating the WT‐CTTN level
Authors: Bao Lili , Zhong Ming , Zhang Zixiang , Yu Xiangqing , You Bo , You Yiwen , Gu Miao , Zhang Qicheng , Chen Wenhui , Lei Wei , Hu Songqun 
Published: January 2024

AbstractMatrix stiffness potently promotes the malignant phenotype in various biological contexts. Therefore, identification of gene expression to participate in mechanical force signals transduced into downstream biochemical signaling will contribute substantially to the advances in nasopharyngeal carcinoma (NPC) treatment. In the present study, we detected that cortactin (CTTN) played an indispensable role in matrix stiffness‐induced cell migration, invasion, and invadopodia formation. Advances in cancer research have highlighted that dysregulated alternative splicing contributes to cancer progression as an oncogenic driver. However, whether WT‐CTTN or splice variants (SV1‐CTTN or SV2‐CTTN) regulate matrix stiffness‐induced malignant phenotype is largely unknown. We proved that alteration of WT‐CTTN expression modulated matrix stiffness‐induced cell migration, invasion, and invadopodia formation. Considering that splicing factors might drive cancer progression through positive feedback loops, we analyzed and showed how the splicing factor PTBP2 and TIA1 modulated the production of WT‐CTTN. Moreover, we determined that high stiffness activated PTBP2 expression. Taken together, our findings showed that the PTBP2‐WT‐CTTN level increases upon stiffening and then promotes cell migration, invasion, and invadopodia formation in NPC.
Is Margaret Cavendish a naïve realist?
Authors: Whiting Daniel 
Published: January 2024

AbstractPerception plays a central and wide‐ranging role in the philosophy of Margaret Cavendish. In this paper, I argue that Cavendish holds a naïve realist theory of perception. The case draws on what Cavendish has to say about perceptual presentation, the role of sympathy in experience, the natures of hallucination and of illusion, and the individuation of kinds. While Cavendish takes perception to have representational content, I explain how this is consistent with naïve realism. In closing, I address challenges to the interpretation, one of which turns on whether Cavendish allows for action at a distance. I argue that she does.