bluuebunny/crossref_metadata_2025_split huggingface dataset:
Loss of function mutation in Ank causes aberrant mineralization and acquisition of osteoblast-like-phenotype by the cells of the intervertebral disc
Authors: Ohnishi Takashi , Tran Victoria , Sao Kimheak , Ramteke Pranay , Querido William , Barve Ruteja A. , van de Wetering Koen , Risbud Makarand V. 
Published: July 2023

AbstractPathological mineralization of intervertebral disc is debilitating and painful and linked to disc degeneration in a subset of human patients. An adenosine triphosphate efflux transporter, progressive ankylosis (ANK) is a regulator of extracellular inorganic pyrophosphate levels and plays an important role in tissue mineralization. However, the function of ANK in intervertebral disc has not been fully explored. Herein we analyzed the spinal phenotype ofAnkmutant mice (ank/ank) with attenuated ANK function. Micro-computed tomography and histological analysis showed that loss of ANK function results in the aberrant annulus fibrosus mineralization and peripheral disc fusions with cranial to caudal progression in the spine. Vertebrae inankmice exhibit elevated cortical bone mass and increased tissue non-specific alkaline phosphatase-positive endplate chondrocytes with decreased subchondral endplate porosity. The acellular dystrophic mineral inclusions in the annulus fibrosus were localized adjacent to apoptotic cells and cells that acquired osteoblast-like phenotype. Fourier transform infrared spectral imaging showed that the apatite mineral in the outer annulus fibrosus had similar chemical composition to that of vertebral bone. Transcriptomic analysis of annulus fibrosus and nucleus pulposus tissues showed changes in several biological themes with a prominent dysregulation of BMAL1/CLOCK circadian regulation. The present study provides new insights into the role of ANK in the disc tissue compartments and highlights the importance of local inorganic pyrophosphate metabolism in inhibiting the mineralization of this important connective tissue.
An open resource combining multi-contrast MRI and microscopy in the macaque brain
Authors: Howard Amy F. D. , Huszar Istvan N. , Smart Adele , Cottaar Michiel , Daubney Greg , Hanayik Taylor , Khrapitchev Alexandre A. , Mars Rogier B. , Mollink Jeroen , Scott Connor , Sibson Nicola R. , Sallet Jerome , Jbabdi Saad , Miller Karla L. 
Published: July 2023

AbstractUnderstanding brain structure and function often requires combining data across different modalities and scales to link microscale cellular structures to macroscale features of whole brain organisation. Here we introduce the BigMac dataset, a resource combining in vivo MRI, extensive postmortem MRI and multi-contrast microscopy for multimodal characterisation of a single whole macaque brain. The data spans modalities (MRI and microscopy), tissue states (in vivo and postmortem), and four orders of spatial magnitude, from microscopy images with micrometre or sub-micrometre resolution, to MRI signals on the order of millimetres. Crucially, the MRI and microscopy images are carefully co-registered together to facilitate quantitative multimodal analyses. Here we detail the acquisition, curation, and first release of the data, that together make BigMac a unique, openly-disseminated resource available to researchers worldwide. Further, we demonstrate example analyses and opportunities afforded by the data, including improvement of connectivity estimates from ultra-high angular resolution diffusion MRI, neuroanatomical insight provided by polarised light imaging and myelin-stained histology, and the joint analysis of MRI and microscopy data for reconstruction of the microscopy-inspired connectome. All data and code are made openly available.
Sequencing trait-associated mutations to clone wheat rust-resistance gene YrNAM
Authors: Ni Fei , Zheng Yanyan , Liu Xiaoke , Yu Yang , Zhang Guangqiang , Epstein Lynn , Mao Xue , Wu Jingzheng , Yuan Cuiling , Lv Bo , Yu Haixia , Li Jinlong , Zhao Qi , Yang Qiyu , Liu Jiajun , Qi Juan , Fu Daolin , Wu Jiajie 
Published: July 2023

AbstractStripe (yellow) rust, caused by Puccinia striiformis f. sp. tritici (Pst), can significantly affect wheat production. Cloning resistance genes is critical for efficient and effective breeding of stripe rust resistant wheat cultivars. One resistance gene (Yr10CG) underlying the Pst resistance locus Yr10 has been cloned. However, following haplotype and linkage analyses indicate the presence of additional Pst resistance gene(s) underlying/near Yr10 locus. Here, we report the cloning of the Pst resistance gene YrNAM in this region using the method of sequencing trait-associated mutations (STAM). YrNAM encodes a non-canonical resistance protein with a NAM domain and a ZnF-BED domain. We show that both domains are required for resistance. Transgenic wheat harboring YrNAM gene driven by its endogenous promoter confers resistance to stripe rust races CYR32 and CYR33. YrNAM is an ancient gene and present in wild wheat species Aegilops longissima and Ae. sharonensis; however, it is absent in most wheat cultivars, which indicates its breeding value.
Nuclear translocation of mitochondrial dehydrogenases as an adaptive cardioprotective mechanism
Authors: Srivastava Shubhi , Gajwani Priyanka , Jousma Jordan , Miyamoto Hiroe , Kwon Youjeong , Jana Arundhati , Toth Peter T. , Yan Gege , Ong Sang-Ging , Rehman Jalees 
Published: July 2023

AbstractChemotherapy-induced cardiac damage remains a leading cause of death amongst cancer survivors. Anthracycline-induced cardiotoxicity is mediated by severe mitochondrial injury, but little is known about the mechanisms by which cardiomyocytes adaptively respond to the injury. We observed the translocation of selected mitochondrial tricarboxylic acid (TCA) cycle dehydrogenases to the nucleus as an adaptive stress response to anthracycline-cardiotoxicity in human induced pluripotent stem cell-derived cardiomyocytes and in vivo. The expression of nuclear-targeted mitochondrial dehydrogenases shifts the nuclear metabolic milieu to maintain their function both in vitro and in vivo. This protective effect is mediated by two parallel pathways: metabolite-induced chromatin accessibility and AMP-kinase (AMPK) signaling. The extent of chemotherapy-induced cardiac damage thus reflects a balance between mitochondrial injury and the protective response initiated by the nuclear pool of mitochondrial dehydrogenases. Our study identifies nuclear translocation of mitochondrial dehydrogenases as an endogenous adaptive mechanism that can be leveraged to attenuate cardiomyocyte injury.
A comparative analysis of the effects of containment policies on the epidemiological manifestation of the COVID-19 pandemic across nine European countries
Authors: Podrecca Chiara , Parimbelli Enea , Pala Daniele , Cheng Cindy , Messerschmidt Luca , Büthe Tim , Bellazzi Riccardo 
Published: July 2023

AbstractThe COVID-19 pandemic has been a catastrophic event that has seriously endangered the world’s population. Governments have largely been unprepared to deal with such an unprecedented calamity, partially due to the lack of sufficient or adequately fine-grained data necessary for forecasting the pandemic’s evolution. To fill this gap, researchers worldwide have been collecting data about different aspects of COVID-19’s evolution and government responses to them so as to provide the foundation for informative models and tools that can be used to mitigate the current pandemic and possibly prevent future ones. Indeed, since the early stages of the pandemic, a number of research initiatives were launched with this goal, including the PERISCOPE (Pan-European Response to the ImpactS of COVID-19 and future Pandemics and Epidemics) Project, funded by the European Commission. PERISCOPE aims to investigate the broad socio-economic and behavioral impacts of the COVID-19 pandemic, with the goal of making Europe more resilient and prepared for future large-scale risks. The purpose of this study, carried out as part of the PERISCOPE project, is to provide a first European-level analysis of the effect of government policies on the spread of the virus. To do so, we assessed the relationship between a novel index, the Policy Intensity Index, and four epidemiological variables collected by the European Centre for Disease Control and Prevention, and then applied a comprehensive Pan-European population model based on Multilevel Vector Autoregression. This model aims at identifying effects that are common to some European countries while treating country-specific policies as covariates, explaining the different evolution of the pandemic in nine selected countries due to data availability: Spain, France, Netherlands, Latvia, Slovenia, Greece, Ireland, Cyprus, Estonia. Results show that specific policies’ effectiveness tend to vary consistently within the different countries, although in general policies related to Health Monitoring and Health Resources are the most effective for all countries.
Revealing the physical properties of chlorine-substituted poly(acetylene)
Authors: Cho Youngsang , Seo Jinwon , Lu Sherilyn J. , Kang Songsu , Kim Yeram , Bielawski Christopher W. 
Published: July 2023

Novel conjugated polymers were synthesized by polymerizing cis-3,4-dichlorocyclobutene followed by elimination.
Unified and pluralistic ideals for data sharing and reuse in biodiversity
Authors: Sterner Beckett , Elliott Steve , Gilbert Edward E , Franz Nico M 
Published: July 2023

Abstract
How should billions of species observations worldwide be shared and made reusable? Many biodiversity scientists assume the ideal solution is to standardize all datasets according to a single, universal classification and aggregate them into a centralized, global repository. This ideal has known practical and theoretical limitations, however, which justifies investigating alternatives. To support better community deliberation and normative evaluation, we develop a novel conceptual framework showing how different organizational models, regulative ideals and heuristic strategies are combined to form shared infrastructures supporting data reuse. The framework is anchored in a general definition of data pooling as an activity of making a taxonomically standardized body of information available for community reuse via digital infrastructure. We describe and illustrate unified and pluralistic ideals for biodiversity data pooling and show how communities may advance toward these ideals using different heuristic strategies. We present evidence for the strengths and limitations of the unification and pluralistic ideals based on systemic relationships of power, responsibility and benefit they establish among stakeholders, and we conclude the pluralistic ideal is better suited for biodiversity data.
The ubiquitin codes in cellular stress responses
Authors: Sheng Xiangpeng , Xia Zhixiong , Yang Hanting , Hu Ronggui 
Published: July 2023

Abstract
Ubiquitination/ubiquitylation, one of the most fundamental post-translational modifications, regulates almost every critical cellular process in eukaryotes. Emerging evidence has shown that essential components of numerous biological processes undergo ubiquitination in mammalian cells upon exposure to diverse stresses, from exogenous factors to cellular reactions, causing a dazzling variety of functional consequences. Various forms of ubiquitin signals generated by ubiquitylation events in specific milieus, known as ubiquitin codes, constitute an intrinsic part of myriad cellular stress responses. These ubiquitination events, leading to proteolytic turnover of the substrates or just switch in functionality, initiate, regulate, or supervise multiple cellular stress-associated responses, supporting adaptation, homeostasis recovery, and survival of the stressed cells. In this review, we attempted to summarize the crucial roles of ubiquitination in response to different environmental and intracellular stresses, while discussing how stresses modulate the ubiquitin system. This review also updates the most recent advances in understanding ubiquitination machinery as well as different stress responses and discusses some important questions that may warrant future investigation.
A novel machine learning algorithm selects proteome signature to specifically identify cancer exosomes
Authors: Li Bingrui , Kugeratski Fernanda G. , Kalluri Raghu 
Published: July 2023

AbstractNon-invasive early cancer diagnosis remains challenging due to the low sensitivity and specificity of current diagnostic approaches. Exosomes are membrane-bound nanovesicles secreted by all cells that contain DNA, RNA, and proteins that are representative of the parent cells. This property, along with the abundance of exosomes in biological fluids makes them compelling candidates as biomarkers. However, a rapid and flexible exosome-based diagnostic method to distinguish human cancers across cancer types in diverse biological fluids is yet to be defined. Here, we describe a novel machine learning-based computational method to distinguish cancers using a panel of proteins associated with exosomes. Employing datasets of exosome proteins from human cell lines, tissue, plasma, serum and urine samples from a variety of cancers, we identify Clathrin Heavy Chain (CLTC), Ezrin, (EZR), Talin-1 (TLN1), Adenylyl cyclase-associated protein 1 (CAP1) and Moesin (MSN) as highly abundant universal biomarkers for exosomes and define three panels of pan-cancer exosome proteins that distinguish cancer exosomes from other exosomes and aid in classifying cancer subtypes employing random forest models. All the models using proteins from plasma, serum, or urine-derived exosomes yield AUROC scores higher than 0.91 and demonstrate superior performance compared to Support Vector Machine, K Nearest Neighbor Classifier and Gaussian Naive Bayes. This study provides a reliable protein biomarker signature associated with cancer exosomes with scalable machine learning capability for a sensitive and specific non-invasive method of cancer diagnosis.
Luxury brands and corporate social responsibility (CSR): exploring the differences between traditional and new luxury
Authors: Kwon Jung Eun , Kim Jongdae , Kim Sang-Hoon 
Published: July 2023

Purpose This study aims to comprehend luxury brands' corporate social responsibility (CSR) strategies. In addition to facing a demand for new CSR strategies (consumer-centric CSR), changes in CSR discourse among luxury brands are observed. This study examines how CSR-related and luxury-related agendas relate in the news media, especially concerning the difference between traditional and new luxury brands.Design/methodology/approach A total of 117,171 fashion-related news articles were collected from January 2016 to December 2020. The word2vec method was used to determine the relationship between CSR and luxury agendas.FindingsThe results indicate that company-centric CSR is more prominent with traditional luxury brands, while consumer-centric CSR is more relevant for new luxury brands. In addition, specific CSR attributes and luxury-related attributes are associated with media discourse, which means that CSR and luxury are compatible.Originality/valueStudies on CSR in the luxury industry are not extensive in the literature. This study addresses this gap through a unique framework that combines agenda-setting theory and existing CSR literature and applies them to the luxury industry. Specifically, this study captures the development of each construct (company-centric CSR to consumer-centric CSR and traditional luxury to new luxury) and identifies the specific relationships between them. This result provides a novel view of the luxury industry indicating that it has evolved to encompass CSR-related values. The empirical results also offer practical implications for luxury marketing.
Over a decade of maqashid sharia studies: a bibliometric analysis and direction for future research
Authors: Tumewang Yunice Karina , Rahmawati Dewi Herlina , Amin Hanudin 
Published: July 2023

Purpose
The purpose of this paper is to build a relationship between the quantitative and structural indicators of maqashid sharia studies produced from bibliometric analysis and the conceptual discussion developed through a thorough review of selected key literature.

Design/methodology/approach
The study uses bibliometric analysis, collecting information drawn from 219 articles published in 68 journals during the period of 2006–2022. This study uses VOSviewer, RStudio, Microsoft Excel, and an examination of research time periods using the Scopus database to illustrate the citation analysis and keyword map. It is also strengthened by content analysis of selected studies.

Findings
The main research theme found in this study is the application of maqashid sharia in Islamic banks, with Islamic banks and Islamic finance among the most frequently used keywords. Meanwhile, the geographical spread of maqashid sharia research has reflected its universal acceptance, as it has spread across both Muslim-dominant and non-Muslim-dominant countries. Besides, maqashid sharia is found to be an extremely important subject for ensuring the ethical dimension of Islamic finance products and services, a more inclusive human development index, and contributing to the international agenda of Sustainable Development Goals. Lastly, future research is expected to broaden it into a multi-dimensional horizon, with several recommendations offered to enrich the understanding of maqashid sharia.

Practical implications
The findings of this study can be beneficial to multiple stakeholders in Islamic finance industry, including the management of Islamic banks, who can enhance the values of maqashid sharia in designing their products/services, and the regulators, who can formulate regulatory frameworks which are reflective of maqashid sharia principles.

Social implications
This study will assist future scholars in this field to formulate and design exciting research ideas and models to address the deficiencies found in the current implementation of maqashid sharia within Islamic finance industry.

Originality/value
The primary contribution of this study is to provide comprehensive review and discussion of selected significant literature on maqashid sharia and give direction for future research. In addition, this study also extends and incorporates the results of bibliometrics using the recent maqashid sharia studies published at the end of 2022.
Draft genome sequence of
Lactiplantibacillus plantarum
subsp.
plantarum
strain HF43, a human gut-associated potential probiotic
Authors: Idrees Maryam , Atiq Naima , Zahra Rabaab , Imran Muhammad , Ghazanfar Shakira 
Published: July 2023

ABSTRACT

Lactiplantibacillus plantarum
adapts to a wide range of ecological niches, including the human gut. Numerous health-promoting benefits have been associated with
L
.
plantarum
strains. Motivated for the development of human-origin target-based probiotics with known genetic markers, we report the draft genome sequence of human gut-associated
Lactiplantibacillus plantarum
subsp.
plantarum
HF43.
Comparative transcriptome profiling of Eimeria tenella in various developmental stages and functional analysis of an ApiAP2 transcription factor exclusively expressed during sporogony
Authors: Chen Linlin , Tang Xinming , Sun Pei , Hu Dandan , Zhang Yuanyuan , Wang Chaoyue , Chen Junmin , Liu Jie , Gao Yang , Hao Zhenkai , Zhang Ning , Chen Wenxuan , Xie Fujie , Suo Xun , Liu Xianyong 
Published: July 2023

Abstract
Background
The apicomplexan parasites Eimeria spp. are the causative agents of coccidiosis, a disease with a significant global impact on the poultry industry. The complex life cycle of Eimeria spp. involves exogenous (sporogony) and endogenous (schizogony and gametogony) stages. Unfortunately, the genetic regulation of these highly dynamic processes, particularly for genes involved in specific developmental phases, is not well understood.

Methods
In this study, we used RNA sequencing (RNA-Seq) analysis to identify expressed genes and differentially expressed genes (DEGs) at seven time points representing different developmental stages of Eimeria tenella. We then performed K-means clustering along with co-expression analysis to identify functionally enriched gene clusters. Additionally, we predicted apicomplexan AP2 transcription factors in E. tenella using bioinformatics methods. Finally, we generated overexpression and knockout strains of ETH2_0411800 to observe its impact on E. tenella development.

Results
In total, we identified 7329 genes that are expressed during various developmental stages, with 3342 genes exhibiting differential expression during development. Using K-means clustering along with co-expression analysis, we identified clusters functionally enriched for oocyte meiosis, cell cycle, and signaling pathway. Among the 53 predicted ApiAP2 transcription factors, ETH2_0411800 was found to be exclusively expressed during sporogony. The ETH2_0411800 overexpression and knockout strains did not exhibit significant differences in oocyst size or output compared to the parental strain, while the resulting ETH2_0411800 knockout parasite showed a relatively small oocyst output.

Conclusions
The findings of our research suggest that ETH2_0411800 is not essential for the growth and development of E. tenella. Our study provides insights into the gene expression dynamics and is a valuable resource for exploring the roles of transcription factor genes in regulating the development of Eimeria parasites.

Graphical Abstract
Seismic-electromagnetic projection attribute: Application in integrating seismic quantitative interpretation and 3D controlled-source electromagnetic-magnetotelluric broadband data inversion for robust ranking and sweet spotting of hydrocarbon prospects in offshore northwest Borneo
Authors: Saleh Ahmad Shahir , Meju Max A. , Mackie Randall L. , Andersen Eric , Ismail Nur Azwin , Nawawi Mohd 
Published: July 2023

We introduce a new seismic-electromagnetic (EM) projection (SEMP) attribute to improve the characterization of pay sands by integrating seismic P impedance and S impedance with electrical resistivity measurements leveraging on the high sensitivity of resistivity to fluid saturation and the capability of seismic data to delineate thin beds. Porosity is predicted using an extended elastic impedance (EEI) approach to reduce the risk of encountering SEMP anomalies related to low porosity. First, we determine the seismic-EM integration concept using well logs from a well that encountered hydrocarbons in a deepwater fold belt in offshore Borneo. The SEMP logs supported by the EEI log successfully delineate the pay zones in the well. Second, we extend the approach in three dimensions and evaluate its effectiveness using large-size seismic controlled-source EM (CSEM) and magnetotelluric (MT) data from the same area. The seismic data are inverted to produce P- and S-impedance volumes. EEI volume calibrated to total porosity also is produced. We then perform 3D anisotropic cross-gradient joint CSEM and MT inversion of a large-size survey comprising 647 receivers with receiver spacing of 1.5–3 km at prospect to regional scale. The SEMP volumes computed using the seismic and CSEM-MT inversion results are then interpreted with the EEI volume to identify possible geobodies of pay sand. Resistive geobodies with low porosity are assigned higher risks because they are likely due to compaction rather than hydrocarbon presence, whereas geobodies with high porosity are assigned lower risks and identified as potential sweet spots. The geobodies need to be corroborated with independent geologic studies to mature them into exploration prospects and assess their associated risk and potential. Although a vertical transverse isotropy approximation is used in our CSEM-MT study, the SEMP concept also is applicable to cases considering tilted transverse isotropy or arbitrary anisotropy where available and operational for such large-size exploration data.