bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pan-cancer Proteomics Analysis to Identify Tumor-Enriched and Highly Expressed Cell Surface Antigens as Potential Targets for Cancer Therapeutics
Authors: Wang Jixin , Yu Wen , D’Anna Rachel , Przybyla Anna , Wilson Matt , Sung Matthew , Bullen John , Hurt Elaine , DAngelo Gina , Sidders Ben , Lai Zhongwu , Zhong Wenyan 
Published: January 2023

ABSTRACTThe National Cancer Institute’s Clinical Proteomic Tumor Analysis Consortium (CPTAC) provides unique opportunities for cancer target discovery using protein expression. Proteomics data from CPTAC tumor types have been primarily generated using a multiplex tandem mass tag (TMT) approach, which is designed to provide protein quantification relative to reference samples. However, relative protein expression data is suboptimal for prioritization of targets within a tissue type, which requires additional reprocessing of the original proteomics data to derive absolute quantitation estimation. We evaluated the feasibility of using differential protein analysis coupled with intensity-based absolute quantification (iBAQ) to identify tumor-enriched and highly expressed cell surface antigens, employing tandem mass tag (TMT) proteomics data from CPTAC. Absolute quantification derived from TMT proteomics data was highly correlated with that of label-free proteomics data from the CPTAC colon adenocarcinoma cohort, which contains proteomics data measured by both approaches. We validated the TMT-iBAQ approach by comparing the iBAQ value to the receptor density value of HER2 and TROP2 measured by flow cytometry in about 30 selected breast and lung cancer cell lines from the Cancer Cell Line Encyclopedia. Collections of these tumor-enriched and highly expressed cell surface antigens could serve as a valuable resource for the development of cancer therapeutics, including antibody-drug conjugates and immunotherapeutic agents.
White matter microstructure is associated with the precision of visual working memory
Authors: Li Xuqian , Rangelov Dragan , Mattingley Jason B. , Oestreich Lena , Lévy-Bencheton Delphine , O’Sullivan Michael J. 
Published: January 2023

AbstractVisual working memory is critical for goal-directed behaviour as it maintains continuity between previous and current visual input. Functional neuroimaging studies have shown that visual working memory relies on communication between distributed brain regions, which implies an important role for long-range white matter connections in visual working memory performance. Here, we characterised the relationship between the microstructure of white matter association tracts and the precision of visual working memory representations. To that purpose, we devised a delayed estimation task which required participants to reproduce visual features along a continuous scale. A sample of 80 healthy adults performed the task and underwent diffusion-weighted MRI. We applied mixture distribution modelling to quantify the precision of working memory representations and guess rates, both of which contribute to observed responses. Latent components of tract-specific microstructural indices were identified by principal component analysis. Higher working memory precision was associated with lower bulk diffusion across ten tracts of interest and higher directionality of diffusion in a group of frontoparietal-occipital tracts. Importantly, there was no association between guess rates and any of the structural components. Our findings suggest that microstructural properties of white matter tracts connecting posterior and frontal brain regions mediate, in a functionally specific manner, the precision of visual working memory.
RIPK3 promotes brain region-specific interferon signaling and restriction of tick-borne flavivirus infection
Authors: Lindman Marissa , Angel Juan P , Estevez Irving , Chang Nydia P , Chou Tsui-Wen , McCourt Micheal , Atkins Colm , Daniels Brian P. 
Published: January 2023

AbstractInnate immune signaling in the central nervous system (CNS) exhibits many remarkable specializations that vary across cell types and CNS regions. In the setting of neuroinvasive flavivirus infection, neurons employ the immunologic kinase receptor-interacting kinase 3 (RIPK3) to promote an antiviral transcriptional program, independently of the traditional function of this enzyme in promoting necroptotic cell death. However, while recent work has established roles for neuronal RIPK3 signaling in controlling mosquito-borne flavivirus infections, including West Nile virus and Zika virus, functions for RIPK3 signaling in the CNS during tick-borne flavivirus infection have not yet been explored. Here, we use a model of Langat virus (LGTV) encephalitis to show that RIPK3 signaling is specifically required in neurons of the cerebellum to control LGTV replication and restrict disease pathogenesis. This effect did not require the necroptotic executioner molecule mixed lineage kinase domain like protein (MLKL), a finding similar to previous observations in models of mosquito-borne flavivirus infection. However, control of LGTV infection required a unique, region-specific dependence on RIPK3 to promote expression of key antiviral interferon-stimulated genes (ISG) in the cerebellum. This RIPK3- mediated potentiation of ISG expression was associated with robust cell-intrinsic restriction of LGTV replication in cerebellar granule cell neurons. These findings further illuminate the complex roles of RIPK3 signaling in the coordination of neuroimmune responses to viral infection, as well as provide new insight into the mechanisms of region-specific innate immune signaling in the CNS.ImportanceInteractions between the nervous and immune systems are very carefully orchestrated in order to protect the brain and spinal cord from immune-mediated damage, while still maintaining protective defenses against infection. These specialized neuro-immune interactions have been shown to vary significantly across regions of the brain, with innate antiviral signaling being particularly strong in the cerebellum, although the reasons for this are poorly understood. Here, we show a specialized adaptation of programmed cell death signaling that uniquely protects the cerebellum from tick-borne flavivirus infection. These findings provide important new insight into the molecular mechanisms that promote the uniquely robust antiviral immunity of the cerebellum. They also provide new clues into the pathogenesis of tick-borne encephalitis, a zoonosis of significant global concern.
A transcriptional and regulatory map of mouse somitogenesis
Authors: Ibarra-Soria Ximena , Thierion Elodie , Mok Gi Fay , Münsterberg Andrea E. , Odom Duncan T. , Marioni John C. 
Published: January 2023

ABSTRACTThe mammalian body plan is shaped by rhythmic segmentation of mesoderm into somites, which are transient embryonic structures consisting of hundreds of cells that form down each side of the neural tube. We have systematically analysed the genome-wide transcriptional and chromatin dynamics occurring within nascent somites, from early inception of somitogenesis to the latest stages of body plan establishment. We created matched gene expression and open chromatin maps for the three leading pairs of somites at six time points during embryonic development. Here we show that the rate of somite differentiation accelerates as development progresses. We identified a conserved maturation programme followed by all somites after segmentation, but somites from more developed embryos concomitantly switch on differentiation programmes from derivative cell lineages soon after segmentation. Integrated analysis of the somitic transcriptional and chromatin activities revealed opposing regulatory modules controlling the onset of differentiation. We identified transcription factors expressed during early development that inhibit the activity of proteins required for commitment and differentiation of skeletal cell populations. Our results provide a powerful, high-resolution view of the molecular genetics underlying somitic development in mammals.
Caf1 regulates Ash1 histone methyltransferase activity via sensing unmodified histone H3
Authors: Yoon Eojin , Song Ji-Joon 
Published: January 2023

AbstractHistone modifications are one of key mechanisms to regulate gene expression. Ash1 is a histone H3K36 methyltransferase and involved in gene activation. Ash1 forms a large complex with Mrg15 and Caf1/p55/Nurf55/RbAp48 (AMC complex). Ash1 subunit alone has very low activity due to the auto-inhibition and the binding of Mrg15 releases the auto-inhibition. Caf1 is a scaffolding protein commonly found in several chromatin modifying complexes. Caf1 has an ability to sense unmodified histone H3K4 residue. However, the role of Caf1 in AMC complex has not been investigated. Here, we dissected the interaction among the AMC complex subunits, revealing that Caf1 uses the histone H4 binding pocket to interact with Ash1 near the histone binding module cluster. Furthermore, we show that H3K4 methylation inhibits AMC HMTase activity via Caf1 sensing unmodified histone H3K4 to regulate the activity in an inter-nucleosomal manner, suggesting that there is a crosstalk between H3K4 and H3K36 methylations. Our work reveals a delicate regulatory mechanism of AMC histone H3K36 methyltransferase complex.
Early maturation of sound duration processing in the infant brain
Authors: Polver Silvia , Tóth Brigitta , Háden Gábor P. , Bulf Hermann , Winkler István 
Published: January 2023

AbstractThe ability to process sound duration is crucial already at a very early age for laying the foundation for the main functions of auditory perception, such as object perception and music and language acquisition. With the availability of age-appropriate structural anatomical templates, we can reconstruct EEG source activity with much-improved reliability. The current study capitalized on this possibility by reconstructing the sources of event-related potential (ERP) waveforms sensitive to sound duration in four- and nine-month-old infants. Infants were presented with short (200 ms) and long (300 ms) sounds equiprobably delivered in random order. Two temporally separate ERP waveforms were found to be modulated by sound duration. Generators of these waveforms were mainly located in primary and secondary auditory area and other language-related regions, such as the superior temporal and the inferior frontal gyri. The results show marked developmental changes between four and nine months, partly reflected by scalp-recorded ERPs, but appearing in the underlying generators in a far more nuanced way. The results also confirm the feasibility of the application of anatomical templates in developmental populations.
A multidimensional atlas of human glioblastoma organoids reveals highly coordinated molecular networks and effective drugs
Authors: Wang Changwen , Sun Meng , Shao Chunxuan , Schlicker Lisa , Zhuo Yue , Harim Yassin , Peng Tianping , Tian Weili , Stöffler Nadja , Schneider Martin , Helm Dominic , Mallm Jan-Philipp , Wu Yonghe , Schulze Almut , Liu Hai-Kun 
Published: January 2023

AbstractRecent advances in the genomics of glioblastoma (GBM) led to the introduction of molecular neuropathology but failed to translate into treatment improvement. This is largely attributed to the genetic and phenotypic heterogeneity of GBM, which are considered the major obstacle to GBM therapy. Here, we use advanced human GBM organoid (LEGO:LaboratoryEngineeredGlioblastomaOrganoid) and provide an unprecedented comprehensive characterization of LEGO models using single-cell transcriptome, DNA methylome, metabolome, lipidome, proteome, and phospho-proteome analysis. We discovered that genetic heterogeneity dictates functional heterogeneity across molecular layers and demonstrates thatNF1mutation drives mesenchymal signature. Most importantly, we found that glycerol lipid reprogramming is a hallmark of GBM, and several targets and drugs were discovered along this line. We also provide a genotype-based drug reference map using LEGO-based drug screen. This study provides novel human GBM models and a research path toward effective GBM therapy.
Cell Instance Segmentation Via Multi-Scale Non-Local Correlation
Authors: Duan Bin , Cao Jianfeng , Wang Wei , Cai Dawen , Yan Yan 
Published: January 2023

ABSTRACTFor cell instance segmentation on Electron Microscopy (EM) images, state-of-the-art methods either conduct pixel-wise classification or follow a detection and segmentation manner. However, both approaches suffer from the enormous cell instances of EM images where cells are tightly close to each other and show inconsistent morphological properties and/or homogeneous appearances. This fact can easily lead to over-segmentation and under-segmentation problems for model prediction,i.e., falsely splitting and merging adjacent instances. In this paper, we propose a novel approach incorporating non-local correlation in the embedding space to make pixel features distinct or similar to their neighbors and thus address the over- and under-segmentation problems. We perform experiments on five different EM datasets where our proposed method yields better results than several strong baselines. More importantly, by using non-local correlation, we observe fewer false separations within one cell and fewer false fusions between cells.
Microsaccades are directed towards the midpoint between targets in a variably cued attention task
Authors: Willett Shawn M. , Mayo J. Patrick 
Published: January 2023

AbstractReliable, non-invasive biomarkers that reveal the internal state of a subject are an invaluable tool for neurological diagnoses. Small fixational eye movements, called microsaccades, are a candidate biomarker thought to reflect a subject’s focus of attention (1, 2). The linkage between the direction of microsaccades and attention has mainly been demonstrated using explicit and unambiguous attentional cues. However, the natural world is seldom predictable and rarely provides unambiguous information. Thus, a useful biomarker must be robust to such changes in environmental statistics. To determine how well microsaccades reveal visual-spatial attention across behavioral contexts, we analyzed these fixational eye movements in monkeys performing a conventional change detection task. The task included two stimulus locations and variable cue validities across blocks of trials. Subjects were adept at the task, showing precise and graded modulations of visual attention for subtle target changes and performing better and faster when the cue was more reliable (3). However, over tens of thousands of microsaccades, we found no difference in microsaccade direction between cued locations when cue variability was high nor between hit and miss trials. Instead, microsaccades were made towards the midpoint of the two target locations, not towards individual targets. Our results suggest that the direction of microsaccades should be interpreted with caution and may not be a reliable measure of covert spatial attention in more complex viewing conditions.Significance StatementSmall fixational eye movements called microsaccades are thought to “point” towards a location that is being attended in the visual periphery. This phenomenon has largely been studied using visual cues that unambiguously indicate the location of the upcoming stimulus change. Because the natural world is rarely unambiguous, we studied the relationship between microsaccade direction and spatial attention using less reliable cues. We found that monkeys’ microsaccade directions in a standard visuospatial attention task did not indicate the animals’ focus of attention, despite behavioral and neuronal evidence of spatial attention. Instead, microsaccades were made towards the midpoint between the target locations in both animals, suggesting a more complex relationship between microsaccades and attention in naturalistic settings.
An artificial neural network (ANN) model for publication bias: a machine learning-based study on PubMed meta-analyses
Authors: Motahari-Nezhad Hossein 
Published: January 2023

PurposeNo study has investigated the effects of different parameters on publication bias in meta-analyses using a machine learning approach. Therefore, this study aims to evaluate the impact of various factors on publication bias in meta-analyses.Design/methodology/approachAn electronic questionnaire was created according to some factors extracted from the Cochrane Handbook and AMSTAR-2 tool to identify factors affecting publication bias. Twelve experts were consulted to determine their opinion on the importance of each factor. Each component was evaluated based on its content validity ratio (CVR). In total, 616 meta-analyses comprising 1893 outcomes from PubMed that assessed the presence of publication bias in their reported outcomes were randomly selected to extract their data. The multilayer perceptron (MLP) technique was used in IBM SPSS Modeler 18.0 to construct a prediction model. 70, 15 and 15% of the data were used for the model's training, testing and validation partitions.FindingsThere was a publication bias in 968 (51.14%) outcomes. The established model had an accuracy rate of 86.1%, and all pre-selected nine variables were included in the model. The results showed that the number of databases searched was the most important predictive variable (0.26), followed by the number of searches in the grey literature (0.24), search in Medline (0.17) and advanced search with numerous operators (0.13).Practical implicationsThe results of this study can help clinical researchers minimize publication bias in their studies, leading to improved evidence-based medicine.Originality/valueTo the best of the author’s knowledge, this is the first study to model publication bias using machine learning.
Fuzzy ISM–DEMATEL modeling for the sustainable development hindrances in the renewable energy supply chain
Authors: Ghasemian Sahebi Iman , Toufighi Seyed Pendar , Azzavi Mahdi , Masoomi Behzad , Maleki Mohammad Hasan 
Published: January 2023

Purpose
By replacing traditional fossil fuels, renewable energy (RE) has the potential to become an outstanding sustainable energy supply. However, owing to technological, economic, social and legal constraints, RE is still in its early stages of development. Hence, this paper aims to analyze the sustainable development hindrances in the RE supply chain (RESC).

Design/methodology/approach
Twenty-three hindrances to the sustainable development of the RE industry were investigated in this research, which included a review of the expert opinion and literature. Then, a mutual relationship between the hindrances by integrating interpretive structural modeling and decision-making trial and evaluation laboratory in fuzzy environment was established. Furthermore, using the cross-impact matrix multiplication applied to a classification analysis, these hindrances were grouped.

Findings
The findings show that the important hindrances are “lack of standards for the RESC (H19), lack of entrepreneurship support (H21), lack of incentives/subsidies to encourage RE producers to compete (H30) and lack of governmental support for sustainable supply chain solutions (H31).

Originality/value
This research provides unique insights into the area of sustainability in RESC. To the best of the authors’ knowledge, this is the first paper to analyze the sustainability hindrances in the RESC.
Effect of employees' CSR perceptions on affective commitment: exploring multiple mediation mechanisms
Authors: Maqbool Shafat , Nazir Nazir A. 
Published: January 2023

PurposeThis study aims to empirically examine how corporate social responsibility (CSR) facilitates the employee's affective commitment in the hospitality sector.Design/methodology/approachA total of 408 questionnaires were distributed among the employees of the selected 13 hotels in Delhi-National capital region (NCR). Structural equation modeling (SEM) was employed to test the proposed hypotheses.FindingsThe study results confirm that CSR has a positive influence on the employees' affective commitment. Further, this study demonstrates that CSR facilitates work meaningfulness and trust among employees and consequently enhances employees' commitment.Originality/valueThis study enhances the understanding of the CSR-affective commitment link in the hospitality sector. This will add a new perspective to the literature, especially in the context of micro-foundation factors of “work meaningfulness” and “organizational trust.”
Assessment of the Sharīʿah requirements in the Malaysian Islamic Financial Services Act 2013 from the managerialism and Maqāṣid al-Sharīʿah perspectives
Authors: Alam Md. Mahmudul , Hoque Muhammad Nazmul , Muda Ruhaini 
Published: January 2023

Purpose
The Maqāṣid (objective) hierarchy is a triple-tiered conceptualisation of individual and social needs that is grounded in the five objectives of Sharīʿah (Islamic Law). Managerialism is the ideological representation of human interaction based on managerial doctrines and practices. This paper aims to explore the tension between the Maqāṣid hierarchy and managerialism by evaluating the Sharīʿah requirements in the Islamic Financial Services Act (IFSA) 2013 of Malaysia from the Maqāṣid al-Sharīʿah perspective.

Design/methodology/approach
This qualitative study uses an inductive approach to review the sources of Sharīʿah and classical literature of Islamic jurists to present Sharīʿah rulings on managerialism and Maqāṣid al-Sharīʿah.

Findings
The Maqāṣid hierarchy promotes a vision of human life that is the opposite of managerialism. In the case of IFSA 2013, the Maqāṣid hierarchy, which is supposed to be the bedrock for Islamic finance, is replaced by a managerial hierarchy closer to Maslow’s hierarchy than it is to Imam Shatibi’s concept of human life. A process of fitting the Maqāṣid hierarchy into a narrow managerial mould occurs in IFSA 2013, meaning that many of the unique aspects of the Maqāṣid al-Sharīʿah are lost.

Social implications
This study will assist Sharīʿah scholars, policymakers and Islamic financial institutions to develop the financial system and to implement the Maqāṣid al-Sharīʿah to improve macro policy and shaping Islamic institutions.

Originality/value
This is a pioneer study that develops a bridge between the Islamic Maqāṣid and conventional managerial hierarchies, which will encourage academics and practitioners to enrich the literature by conducting more in-depth studies on this topic.
Mapping and visualizing flexible manufacturing system in business and management: a systematic review and future agenda
Authors: Priyadarshini Jaya , Gupta Amit Kumar 
Published: January 2023

Purpose
A flexible manufacturing system (FMS) helps improve the system’s performance, thus increasing its overall competitiveness. FMS is an essential component of Industry 4.0 (I4.0), which has revolutionized the way firms manufacture their products. This study aims to investigate the diverse focus of the research being published over the years and the direction of scholarly work in applying FMSs in business and management.

Design/methodology/approach
A total of 1,096 bibliometric data were extracted from the Scopus database from the years 2001 to 2021. A systematic review and bibliometric analysis were performed on the data and related articles for performance measurement and scientific mapping on the FMS themes.

Findings
Based on co-keyword, the study reveals four major themes in the FMS field: mathematical models and quantitative techniques, scheduling and optimization techniques, cellular manufacturing and decision-making in FMSs. Based on bibliometric coupling on 2018–2021 bibliometric data, four themes emerged for future research: scheduling problems in FMS, manufacturing cell formation problem, interplay of FMS with other latest technologies and I4.0 and FMS.

Originality/value
The originality lies in answering the following research questions: What are the most highlighting themes in FMS, and how have they evolved over the past 20 years (2001–2021)? What topics have been at the forefront of research in FMS in the past five years (2016–2021)? What are the promising avenues of research in FMS?