bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of spatial transcriptomics technologies across six cancer types
Authors: Cervilla Sergi , Grases Daniela , Perez Elena , Real Francisco X. , Musulen Eva , Esteller Manel , Porta-Pardo Eduard 
Published: May 2024

AbstractSpatial biology experiments integrate the molecular and histological landscape of tissues to provide a previously inaccessible view of tissue biology, unlocking the architecture of complex multicellular tissues. Within spatial biology, spatial transcriptomics platforms are among the most advanced, allowing researchers to characterize the expression of thousands of genes across space. These new technologies are transforming our understanding of how cells are organized in space and communicate with each other to determine emergent phenotypes with unprecedented granularity. This is particularly important in cancer research, as it is becoming evident that tumor evolution is shaped not only by the genetic properties of cancer cells but also by how they interact with the tumor microenvironment and their spatial organization. While many platforms can generate spatial transcriptomics profiles, it is still unclear in which context each platform better suits the needs of its users. Here we compare the results obtained using 4 different spatial transcriptomics (VISIUM, VISIUM CytAssist, Xenium and CosMx) and one spatial proteomics (VISIUM CytAssist) platforms across serial sections of 6 FFPE samples from primary human tumors covering some of the most common forms of the disease (lung, breast, colorectal, bladder, lymphoma and ovary). We observed that the VISIUM platform with CytAssist chemistry yielded superior data quality. Xenium consistently produced more reliable results for in situ platforms, with better gene clustering and fewer false positives than CosMx. Interestingly, these platform-based variations didn’t significantly affect cell type identification. Finally, by comparing VISIUM protein profiles with the spatial transcriptomics data from all four platforms on each sample, we identified several genes with mismatched RNA and protein expression patterns, highlighting the importance of multi-omics profiling to reveal the true biology of human tumors.
Facial expression recognition is modulated by approach–avoidance behavior
Authors: Kobayashi Yugo , Tamura Hideki , Nakauchi Shigeki , Minami Tetsuto 
Published: May 2024

AbstractFacial expression recognition influences approach–avoidance behaviors, but do approach–avoidance behaviors affect facial expression recognition? We conducted psychophysical experiments to this end, indicating a reverse causal relationship. In a virtual reality space, 3D face stimulus facial expressions varied on seven levels—from happy to angry in Experiments 1 and 3 and from happy to fearful in Experiment 2. Participants were asked to perform according to one of the following conditions in response to the stimulus. Participants 1) approached (one-meter forward), 2) avoided (one-meter backward), 3) were approached by, or 4) were avoided by the 3D model. Then, participants selected facial expressions. Experiment 1 revealed that participants recognized the face as angrier when they avoided it rather than when it avoided them. Experiment 2 showed that participants recognized the face as happy when approaching and fearful when avoiding, irrespective of who acted. Experiment 3 revealed that participants recognized the face as angrier when the face approached them rather than when they approached if both parties were physically close. Accordingly, approach–avoidance behavior changes facial expression recognition, indicating a reverse causal relationship. We posit that unconscious learning rooted in biological instincts creates this connection.
Targeting DBS to the centrolateral thalamic nucleus improves movement in a lesion-based model of acquired cerebellar dystonia in mice
Authors: Nguyen Megan X. , Brown Amanda M. , Lin Tao , Sillitoe Roy V. , Gill Jason S. 
Published: May 2024

AbstractDystonia is the third most common movement disorder and an incapacitating co-morbidity in a variety of neurologic conditions. Dystonia can be caused by genetic, degenerative, idiopathic, and acquired etiologies, which are hypothesized to converge on a “dystonia network” consisting of the basal ganglia, thalamus, cerebellum, and cerebral cortex. In acquired dystonia, focal lesions to subcortical areas in the network – the basal ganglia, thalamus, and cerebellum – lead to a dystonia that can be difficult to manage with canonical treatments, including deep brain stimulation (DBS). While studies in animal models have begun to parse the contribution of individual nodes in the dystonia network, how acquired injury to the cerebellar outflow tracts instigates dystonia; and how network modulation interacts with symptom latency remain as unexplored questions. Here, we present an electrolytic lesioning paradigm that bilaterally targets the cerebellar outflow tracts. We found that lesioning these tracts, at the junction of the superior cerebellar peduncles and the medial and intermediate cerebellar nuclei, resulted in acute, severe dystonia. We observed that dystonia is reduced with one hour of DBS of the centrolateral thalamic nucleus, a first order node in the network downstream of the cerebellar nuclei. In contrast, one hour of stimulation at a second order node in the short latency, disynaptic projection from the cerebellar nuclei, the striatum, did not modulate the dystonia in the short-term. Our study introduces a robust paradigm for inducing acute, severe dystonia, and demonstrates that targeted modulation based on network principles powerfully rescues motor behavior. These data inspire the identification of therapeutic targets for difficult to manage acquired dystonia.
Characterization of a major QTL for sodium accumulation in tomato shoot
Authors: Héreil A. , Guillaume M. , Duboscq R. , Carretero Y. , Pelpoir E. , Bitton F. , Giraud C. , Karlova R. , Testerink C. , Stevens R. , Causse M. 
Published: May 2024

AbstractSoil salinity is a serious concern for tomato culture, affecting both yield and quality parameters. Although some genes involved in tomato salt tolerance have been identified, their genetic diversity has been rarely studied. In the present study, we assessed salt tolerance-related traits at juvenile and adult stages in a large core collection and identified salt tolerance QTLs by genome-wide association study (GWAS). The results suggested that a major QTL is involved in leaf sodium accumulation at both physiological stages. We were able to identify the underlying candidate gene, a well-known sodium transporter, called SlHKT1.2. We showed that an eQTL for the expression of this gene colocalized with the sodium content QTL. A polymorphism putatively responsible for its variation was identified in the gene promoter. Finally, to extend the applicability of these results, we carried out the same analysis on a test-cross panel composed of the core collection crossed with a distant line. The results indicated that the identified QTL retained its functional impact even in a hybrid genetic context: this paves the way for its use in breeding programs aimed at improving salinity tolerance in tomato cultivars.Summary statementThe genetic diversity of sodium accumulation in tomato shoot under salt stress is associated with an expression QTL ofSlHKT1.2. This gene, already identified as involved in tomato salinity tolerance, has been differentially selected during domestication and is of interest for the development of salinity-tolerant varieties.
Multi-omics reveals AKR1B1-regulated galactose metabolic as a driver of gastrointestinal stromal tumor progression
Authors: Yin Xiaonan , Yang Hongxin , Liu Baike , Liu Qinghong , Zhu Dan , Li Xiaofen , Chen Ye , Zhang Bo , Dai Lei , Yin Yuan 
Published: May 2024

AbstractThe underlying mechanism of malignant progression in gastrointestinal stromal tumors (GISTs) is not fully understood. Despite recent advancements, a comprehensive profile of metabolome, transcriptome, and proteome of GISTs is lacking. This study conducted an integrated multi-omics analysis of GISTs across different risk classifications. By integrating metabolomics, transcriptomics, and proteomics, we identify distinct metabolic patterns and associated biological pathways implicated in the malignant progression of GISTs. Moreover, we identified galactose metabolism and the pivotal rate-limiting enzyme AKR1B1 is dysregulated in GISTs progression. AKR1B1 was upregulated and predicted poor prognosis in GISTs. In addition, AKR1B1 knockdown resulted in trehalose accumulation in GIST cells, thereby inhibiting cell proliferation and mitosis. These findings not only enhance our comprehension of the underlying mechanisms governing GIST progression from a metabolic reprogramming standpoint but also furnish prognostic biomarkers and potential therapeutic targets for GISTs.
Pannotator integrated with Medpipe provides immunological and subcellular location features using a microservice
Authors: Gonçalves Rafael , Santos Anderson 
Published: May 2024

AbstractGenome sequencing and assembly are trivial tasks nowadays. After assembling contigs and scaffolds from a genome, the subsequent step is annotation. An annotation evidencing the expected features, like rRNA, tRNA, and CDS, is a signal of the quality of our sequencing and assembly. Different techniques to obtain and reproduce DNA samples, as well as sequencing and assembly of genomes, can impact the quality of a genome’s expected features. The Pannotator tool was conceived as an aid annotation tool focusing on the differences between assembling and its reference genome. Some of the key features for bacterial genome annotations are the subcellular location and immunological potential of a CDS. Instead of reimplementing the prediction of these features in Pannotator, we leveraged the capabilities of our microservice to provide them. In the end, Medpipe software was not modified, and Pannotator underwent minor changes to incorporate the subcellular location and immunological potential of all exported proteins annotated by the tool. Moreover, our Medpipe microservice can also be incorporated into other software. The Medpipe microservice is open to anyone, not only to our Pannotator tool. The successful integration of Medpipe to Pannotator, powered by the Medpipe microservice, offers a powerful approach to advanced genomic analysis. The Medpipe microservice, built on Kotlin with the Spring Boot framework, is instrumental in the automation of Medpipe processing. It achieves this using REST endpoints, such as the execution of Medpipe in an asynchronous manner, status retrieval, and prediction generation, which enhance the modularity and scalability of the microservice. The availability of endpoint documentation, detailed request examples, and logs make our microservice user-friendly. The results of this integration demonstrate the value of the information provided by Medpipe, enriching genomic annotation with additional details, such as the density of mature epitopes (MED) and protein subcellular location classification. The Pannotator has evolved beyond basic function annotation and now provides data on immunological potential, structure, and subcellular location after being integrated with our microservice. The Medpipe microservice is available athttps://github.com/santosardr/medpipe-ms.git.
Critical therapeutic landscape design elements for cognitive impairments in the Royal Talbot rehabilitation centre
Authors: Beh Jing Han , Yew Ming Kun , Tan Kok Hong , Rayner John Patrick 
Published: May 2024

PurposeTherapeutic landscapes can be beneficial for patients recovering from cognitive and behavioural impairments. The therapeutic garden in the Royal Talbot rehabilitation centre (RTRC) located in Kew, Melbourne is a precedent for its nature design outdoor spaces and horticultural therapy (HT) program for patients with cognitive impairments due to brain and spinal cord injuries. There have been no studies into the physical design of the RTRC therapeutic garden.Design/methodology/approachThis case study unveils the critical design themes, and dominant physical elements of the RTRC therapeutic garden through site observation and analysis over the course of two months, a semi-structured interview with a key staff, and graphical representations using integrated photography and collaborative digital tools of AutoCAD and Adobe Photoshop.FindingsSeven critical design themes are identified for the RTRC garden: (1) space layout and organization, (2) physical and visual access, (3) pathway and facility, (4) multisensory vegetation, (5) amenity, wayfinding and seasonal interest, (6) cognitive stimulation, (7) utility and HT. Qualitative and quantitative data analysed in visual and descriptive format reveal multisensory vegetation, amenity, wayfinding and seasonal interest, and utility and HT are the top three most pivotal critical design themes in the RTRC therapeutic garden.Research limitations/implicationsThe findings of this case study can be used to impart knowledge about the design of therapeutic landscape settings for cognitive impairments to design professionals and the public.Originality/valueThere is no case study has been conducted for this precedent of therapeutic garden in the Royal Talbot rehabilitation centre that targets for cognitive impairment patients. With the increasing awareness in medical and healthcare environments, this case study would help to inject mutual understanding, generate knowledge and design awareness among design professionals and public, and to cultivate more good quality healthcare settings.
Design of safety warnings and risk perception inducement: a comparative study between safety signs and safety comics in construction workplaces
Authors: Ouyang Yewei , Huang Guoqing , He Shiyi 
Published: May 2024

PurposeSafety warnings remind construction workers about dangers and guide them to take necessary actions to avoid potential injuries, which could encourage their safe behavior. Workers’ behavior compliance with the safety warnings would be impacted by the risk perception levels induced by the warnings. This study aims to examine whether the design of safety warnings would impact the induced risk perception of workersDesign/methodology/approachThis study compared the risk perception levels of construction workers when processing two forms of safety warnings, i.e., safety signs and safety comics, which are commonly used in construction workplaces. Construction workers (n = 20) volunteered for an experiment with an implicit paradigm to probe how they perceive these safety warnings, using event-related potentials (ERPs) features collected by an electroencephalogram (EEG) sensor to indicate the risk perception levelFindingsThe results demonstrated that the design of safety warnings would impact the induced risk perception. The safety signs and safety comics performed differently in inducing the workers’ risk perception. The safety signs representing prohibition and caution warnings induced significantly higher risk perception than the comics, and there were no significant differences regarding direction warningsOriginality/valueThis is the first study to compare the risk perception levels between various forms of safety warnings presenting safety information in different ways. The findings would help to expand the knowledge of the relationship between the design of safety warnings and workers’ safety behavioral compliance
Development and evaluation of a modular smart garment framework
Authors: Lin Albert , Kao Cindy , Park Heeju 
Published: May 2024

PurposeThis study aims to develop and evaluate a modular smart garment design framework that simplifies the technical content associated with smart garment design.Design/methodology/approachSmart garment design challenges were first identified through literature review and interviews. Then, a modular framework and toolkit was created to address these challenges. Finally, workshops were held to evaluate the modular toolkit.FindingsInterviews highlighted the need for easier attachment of hard devices to soft textile materials, simpler electrical connection creation and straightforward device selection. A modular framework was proposed and divided into four elements: (1) the Central Computation Module, (2) Peripheral Electrical Modules, (3) Securely Attaching Modules with Substrates and (4) Managing Intra-garment Connections. Workshops showed the modular framework had statistically significant improvements in function and certain ease ratings when compared to non-modular components.Originality/valueThis research identified specific technical challenges faced by smart garment designers and alleviated them through a modular smart garment framework that in workshops outperformed non-modular components in key function and ease ratings.
E-learning's influence on academic performance, learning outcomes and creativity
Authors: Gupta Shweta , Pandey Shriram , Sahoo Sidhartha , Pandey Chandra Shekhar 
Published: May 2024

PurposeThe study examined the relationship between e-learning usage, creativity, e-learning utility and academic performance among undergraduate (UG) and postgraduate (PG) students at Banaras Hindu University (BHU), India.Design/methodology/approachThe data from 480 students were collected using a cross-sectional survey design. Pearson correlation analysis was performed in order to investigate the association between the variables.FindingsThe results revealed a significant positive correlation between time of use and academic performance (r = 0.294, p < 0.01). However, there was no significant correlation between time of use and the usability of e-learning in the attainment of learning outcomes. Furthermore, there was a negative correlation between time of use and creativity (r = −0.170, p < 0.01).Practical implicationsThe results indicate that educators ought to promote consistent utilization of e-learning platforms to enhance scholarly achievements. However, learners should exercise prudence in their usage, as an over-reliance on these platforms may impede their creativity.Originality/valueThis study contributes to the existing body of knowledge regarding the impacts of e-learning on students' academic performance and creativity. Additionally, it offers instructing professionals and students who make use of e-learning platforms information that might be helpful to them.
Effects of ethnic and global identities on home country brand perceptions: an identity theory perspective
Authors: Ewing Douglas , Zolfagharian Mohammadali , Heingraj Sasawan 
Published: May 2024

PurposeThis study links ethnic identity and global identity with perceptions of brand globalness (BG) and brand local iconness (BLI) regarding home country brands. Identity Theory considers consumer behavior as driven by multiple identities concurrently and interactively.Design/methodology/approachSamples from two populations, Mexicans living in Mexico and Mexican Americans in the United States, were exposed to eight randomly presented real-world Mexican brands, followed by existing measures for several constructs. Comparing such populations is uniquely appealing for studies of immigrants’ home country brands. Data is analyzed via linear regression.FindingsEthnic and global identities have an interactive effect on BG, BLI, and purchase intention even after controlling for ethnocentrism and cosmopolitanism. With the interaction term between ethnic identity and global identity included in the model, (a) global identity exhibits more efficacy than ethnic identity in explaining purchase intention; and (b) relationships involving BLI grow stronger while those involving BG become weaker. The direction of the effect of global identity depends on whether BG or BLI serves as the mediator. Ethnic identity has a significant effect on purchase intention through BLI among Mexican Americans.Originality/valueSimultaneous focus on two interacting identities is novel in the international branding space. This approach is useful for illuminating the effects of brand attributes including BG and BLI as well as studying branding effects where self-symbolizing is of interest.
Modelling physical ergonomics and student performance in higher education: the mediating effect of student motivation
Authors: Abdul Latip Muhammad Safuan , Abdul Latip Siti Nur Nadhirah , Tamrin Masliana , Rahim Faizatul Akmal 
Published: May 2024

PurposeThe study aims to explore factors that influence students’ academic performance in the context of physical ergonomics and assess the mediating effect of motivation between lighting, noise, temperature, chair design and students’ performance from the student’s perspective.Design/methodology/approachThe research was categorised as a correlational study and employed non-contrived and cross-sectional methods to achieve its objectives. The target population was university students aged 18 years old and above enrolled in Malaysia’s higher education institutions. Due to the inaccessibility of the sample frame, convenience sampling, a type of non-probability sampling, was utilised. Data collection was conducted through an online survey primarily distributed among student groups.FindingsThe study’s findings reveal that only two exogenous variables, lighting and noise, directly influence students' performance. Additionally, motivation is a potent and significant factor in shaping students' performance. Motivation is also identified as a mediator in the complex relationship between lighting, noise, temperature and student performance. Surprisingly, although temperature does not directly influence student performance, it indirectly influences performance through motivation.Originality/valueThis study is an original exploration into the intricate factors shaping students' academic performance within the domain of physical ergonomics from a student perspective. The research uniquely investigates the mediating impact of motivation on the relationships between lighting, noise, temperature, seating arrangements and academic outcomes. The findings will contribute novel insights to the existing body of knowledge, offering a distinct perspective on the complex dynamics that influence student learning experiences and performance in educational settings.
Delivering lessons with the CTCA and the lecture method: which one enhances learning in Ghana’s undergraduate human resource management curriculum?
Authors: Awaah Fred , Abdulai Munkaila , Attiogbe Esther Julia Korkor 
Published: May 2024

PurposeThe study investigates the comparative efficacy of the culturo-techno-contextual approach (CTCA) and the lecture method in students’ understanding of the human resource management (HRM) curriculum in Ghana.Design/methodology/approachA quasi-experimental design is employed to gather data from 245 4th-year undergraduate students studying HRM at a Ghanaian public university. The experimental group with a population of 115 students was taught with CTCA, whilst the control group with a population of 130 students was taught using the lecture method. The data was collected using the HRM achievement test (HRMAT). The data were analysed using the descriptive analysis of covariance technique with pre-test scores added as a covariate.FindingsThe findings reveal that the experimental group significantly outperformed the control group in the study of HRM, affirming the effectiveness of the CTCA over the lecture method.Originality/valueThis study is novel because it is the first paper to apply the CTCA to the study of HRM in the Ghanaian higher education space. It will, therefore, benefit HRM education in the country when educational stakeholders adopt a sequential and methodical approach to teaching and learning HRM using the CTCA.