bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deciphering tumour microenvironment and elucidating the origin of cancer cells in ovarian clear cell carcinoma
Authors: Kamaraj Uma S , Gautam Pradeep , Cheng Terence , Chin Tham Su , Tay Sun Kuie , Ho Tew Hong , Nadarajah Ravichandran , Goh Ronald Chin Hong , Wong Shing Lih , Mantoo Sangeeta , Busmanis Inny , Li Hu , Le Minh TN , Li Qi-Jing , Lim Elaine Hsuen , Loh Yuin-Han 
Published: August 2024

AbstractOvarian clear cell carcinoma (CCC) has an East Asian preponderance. It is associated with endometriosis, a benign condition where endometrial (inner lining of the uterus) tissue is found outside the uterus and on the peritoneal surface, in the abdominal or pelvic space. CCC is relatively more resistant to conventional chemotherapy compared to other ovarian cancer subtypes and is associated with a poorer prognosis. In this study, we recruited and obtained tumour tissues from seven patients across the four stages of CCC. The tumour and the tumour microenvironment (TME) from 7 CCC patients spanning clinical stages 1-4 were transcriptionally profiled using high-resolution scRNA-seq to gain insight into CCC’s biological mechanisms. Firstly, we built a scRNA-seq resource for the CCC tumour microenvironment (TME). Secondly, we identified the different cell type proportions and found high levels of immune infiltration in CCC. Thirdly, since CCC is associated with endometriosis, we compared CCC with two publicly available endometriosis scRNA-seq datasets. The CCC malignant cells showed similarities with glandular secretory and ciliated epithelial cells found in endometriosis. Finally, we determined the differences in cell-cell communication between various cell types present in CCC TME and endometriosis conditions to gain insights into the transformations in CCC.
Optics-free reconstruction of 2D images via DNA barcode proximity graphs
Authors: Liao Hanna , Kottapalli Sanjay , Huang Yuqi , Chaw Matthew , Gehring Jase , Waltner Olivia , Phung-Rojas Melissa , Daza Riza M. , Matsen Frederick A. , Trapnell Cole , Shendure Jay , Srivatsan Sanjay 
Published: August 2024

AbstractSpatial genomic technologies include imaging- and sequencing-based methods (1–3). An emerging subcategory of sequencing-based methods relies on a surface coated with coordinate-associated DNA barcodes, which are leveraged to tag endogenous nucleic acids or cells in an overlaid tissue section (4–7). However, the physical registration of DNA barcodes to spatial coordinates is challenging, necessitating either high density printing of coordinate-specific oligonucleotides orin situsequencing/probing of randomly deposited, oligonucleotide-bearing beads. As a consequence, the surface areas available to sequencing-based spatial genomic methods are constrained by the time, labor, cost, and instrumentation required to either print, synthesize or decode a coordinate-tagged surface. To address this challenge, we developed SCOPE (Spatial reConstruction via Oligonucleotide Proximity Encoding), an optics-free, DNA microscopy (8) inspired method. With SCOPE, the relative positions of randomly deposited beads on a 2D surface are inferred from theex situsequencing of chimeric molecules formed from diffusing “sender” and tethered “receiver” oligonucleotides. As a first proof-of-concept, we apply SCOPE to reconstruct an asymmetric “swoosh” shape resembling the Nike logo (16.75 × 9.25 mm). Next, we use a microarray printer to encode a “color” version of the Snellen eye chart for visual acuity (17.18 × 40.97 mm), and apply SCOPE to achieve optics-free reconstruction of individual letters. Although these are early demonstrations of the concept and much work remains to be done, we envision that the optics-free, sequencing-based quantitation of the molecular proximities of DNA barcodes will enable spatial genomics in constant experimental time, across fields of view and at resolutions that are determined by sequencing depth, bead size, and diffusion kinetics, rather than the limitations of optical instruments or microarray printers.
Gut microbiome shifts in chronic systolic heart failure are associated with disease severity and clinical improvement
Authors: Mamic Petra , Shi Handuo , Zhou Wenyu , Bararpour Nasim , Contrepois Kevin , Park Heyjun , Avina Monika , Rose Sophia Miryam Schüssler-Fiorenza , Heidenreich Paul A. , Khush Kiran Kaur , Fowler Michael B. , Tang W. H. Wilson , Sallam Karim , Sonnenburg Justin , Huang Kerwyn Casey , Snyder Michael P. 
Published: August 2024

ABSTRACTChronic systolic heart failure (HF) is a prevalent and morbid disease with marked variability in its progression and response to therapies. The gut microbiome may play a role in pathophysiology and progression of chronic HF, but clinical studies investigating relationships between the two are lacking. We analyzed the gut microbiome in a cohort of adults with chronic systolic HF caused by non-ischemic cardiomyopathy (n=59) using multi-omics profiling and, in some cases, longitudinal sampling. We identified microbiome differences compared to healthy subjects (n=50) and associated these differences with host metabolites, inflammatory markers and physiology. We found depletion of the anti-inflammatory probioticBifidobacteriumand the associated short chain fatty acid producing and formaldehyde detoxifying pathways in the chronic HF cohort. We also discovered HF-specific microbiome-host immunome interactions. In addition to identifying several taxa and microbial pathways broadly associated with HF disease severity, we found significant links betweenBifidobacteriumand clinical HF improvement over time. Gut microbiome-host multi-omic data integration revealed a close association betweenBifidobacteriumand circulating metabolites previously implicated in cardiovascular physiology (e.g., malonic acid), thus pointing to potential mechanisms through whichBifidobacteriummay affect chronic HF physiology. Our results suggest thatBifidobacteriummay serve as a biomarker for chronic HF trajectory as well as suggest potential novel therapeutic interventions strategies.
MMINT: a Metabolic Model Interactive Network Tool for the exploration and comparative visualisation of metabolic networks
Authors: Molina Ortiz Juan P. , Morgan Matthew J. , Paten Amy M. , Warden Andrew C. , Kilby Philip 
Published: August 2024

AbstractGenome-scale metabolic models (GEMs) are essential tools in systems and synthetic biology, enabling the mathematical simulation of metabolic pathways encoded in genomes to predict phenotypes. The complexity of GEMs, however, can often limit the interpretation and comparison of their outputs. Here, we present MMINT (Metabolic Modelling Interactive Network Tool), designed to facilitate the exploration and comparison of metabolic networks. MMINT employs GEM networks and flux solutions derived from Constraint Based Analysis (e.g. Flux Balance Analysis) to create interactive visualizations. This tool allows for seamless toggling of source and target metabolites, network decluttering, enabling exploration and comparison of flux solutions by highlighting similarities and differences between metabolic states, which enhances the identification of mechanistic drivers of phenotypes. We demonstrate MMINT’s capabilities using thePyrococcus furiosusGEM, showcasing its application in distinguishing the metabolic drivers of acetate- and ethanol-producing phenotypes. By providing an intuitive and responsive model-exploration experience, MMINT addresses the need for a tool that simplifies the interpretation of GEM outputs and supports the discovery of novel metabolic engineering strategies. MMINT is available athttps://doi.org/10.6084/m9.figshare.26409328Graphical abstractMMINT functionalities provide an intuitive and responsive model-exploration experience, enabling flux solution comparison and the identification of metabolic drivers of phenotypes
Evaluation of resistant starch from teff (Eragrostis tef) grain as a film coating material for colon-targeted drug delivery
Authors: Teshome Yohannes , Belete Anteneh , Gebre-Mariam Tsige 
Published: August 2024

AbstractTeff (Eragrostis tef, family Poaceae) is a native cereal crop widely grown in Ethiopia, containing approximately 73% carbohydrates, of which about 30% is resistant starch. This study evaluates resistant starch extracted from teff grain as a film coating material for colon-targeted delivery of metronidazole, used as a model drug. Starch was extracted from teff and resistant starch was isolated from the total starch. Metronidazole core tablets were prepared by wet granulation, compressed, and coated with a resistant starch-based film. The physicochemical properties of the tablets were evaluatedin vitro. To prevent premature film disruption caused by the swelling of amylose, a dominant component of resistant starch, a water-insoluble polymer, ethylcellulose, was added. Various proportions of amylose and ethylcellulose were used as film coating materials and evaluated in simulated conditions to determine the optimal combination for drug release in the colon, but not in the upper gastrointestinal tract. The results of the dissolution and fermentation studies indicated the best film coating proportions of amylose to ethylcellulose and the corresponding thicknesses in percentage of total weight gain were: 1:1 ratio at 6% thickness, 1:2 ratio at 4% and 6% thickness, and 1:3 ratio at 2% and 4% thickness. The targeted drug release of the film material is attributed to bacterial enzyme digestion of the resistant starch component in the colon. The digestion of resistant starch creates pores in the ethylcellulose film scaffold, leading to the disruption of the film and release of the drug exclusively in the colon, where the bacterial microflora reside. Based on these results, resistant starch from teff grain shows potential as a colon-targeting excipient.
Paraptosome: A Novel Pathological Feature in Paraptotic Cell Death
Authors: Cui Xiang , Zheng Hongda , Li Haoming , Zhang Fang , Yang Liao , Ni Jiayu , Wang Dengfeng , Zhang Huali , Tang Pan , Li Ru , Zhang Qi , Cui Min 
Published: August 2024

AbstractParaptosis is a novel form of programmed cell death characterized by distinct morphological features such as swelling of the endoplasmic reticulum and mitochondria, and cytoplasmic vacuolation. Unlike apoptosis, paraptosis does not involve the activation of caspases or DNA fragmentation. These unique features make paraptosis an intriguing target for cancer therapy, particularly against apoptosis-resistant cells. Here, we report a novel morphological feature of paraptosis: the formation of high-density spherical structure, which we tentatively term “paraptosome.” We found that these putative paraptosomes originate from the Golgi apparatus, appearing as high-density formations under light microscopy and colocalizing with the trans-Golgi marker β4GALT1-RFP. Time-lapse confocal microscopy and immunostaining demonstrated that putative paraptosomes form due to Golgi stress or disintegration, leading to severe disruption of Golgi function. Furthermore, we show that paraptosis inducers such as glabridin, morusin, and honokiol can cause significant alterations in the endoplasmic reticulum, mitochondria, autophagosomes, and lysosomes in U251MG glioblastoma cells; however, the formation of putative paraptosomes is not induced by isolated stress inducers. Collectively, these findings suggest that the putative paraptosome may be a novel characteristic structure of paraptosis. The discovery of paraptosomes provides a unique marker for defining paraptotic cell death and offers new insights into the characteristic pathological phenomena associated with multiple organelle dysfunction. This finding broadens the scope of cell biology research by introducing a new structural paradigm linked to paraptosis and may have implications for developing targeted therapies against apoptosis-resistant cancers.
Microsaccade direction reveals the variation in auditory selective attention processes
Authors: Yamagishi Shimpei , Furukawa Shigeto 
Published: August 2024

AbstractSelective spatial attention plays a critical role in perception in the daily environment where multiple sensory stimuli exist. Even covertly directing attention to a specific location facilitates the brain’s information processing of stimuli at the attended location. Previous behavioral and neurophysiological studies have shown that microsaccades, tiny involuntary saccadic eye movements, reflect such a process in terms of visual space and can be a marker of spatial attention. However, it is unclear whether auditory spatial attention processes that are supposed to interact with visual attention processes influence microsaccades and vice versa. Here, we examine the relationship between microsaccade direction and auditory spatial attention during dichotic oddball sound detection tasks. The results showed that the microsaccade direction was generally biased contralateral to the ear to which the oddball sound was presented or that to which sustained auditory attention was directed. The post-oddball modulation of microsaccade direction was associated with the behavioral performance of the detection task. The results suggest that the inhibition of stimulus-directed microsaccade occurs to reduce erroneous orientation of ocular responses during selective detection tasks. We also found that the correlation between microsaccade direction and neural response to the tone originated from the auditory brainstem (frequency-following response: FFR). Overall, the present study suggests that microsaccades can be a marker of auditory spatial attention and that the auditory neural activity fluctuates over time with the states of attention and the oculomotor system, also involving the auditory subcortical processes.Significant statementMicrosaccades, tiny involuntary saccadic eye movements, reflect covert visual attention and influence neural activity in the visual pathway depending on the attention states. However, we lack convincing evidence of whether and how microsaccades reflect auditory spatial attention and/or neural activity along the auditory pathway. Intriguingly, we showed that the microsaccade direction exhibited systematic stimulus-related change and correlated with auditory brainstem frequency-following response (FFR) during the dichotic selective attention task. These results suggest that microsaccades are associated with general spatial attention processes, not restricted to the visual domain, and can be a good tool for accessing fluctuating neural activity that may covary with the attention states.
Selective deletion ofTsc1from mouse cerebellar Purkinje neurons drives sex-specific behavioral impairments linked to autism
Authors: Lawson Ryan J. , Lipovsek Nicholas J. , Brown Samuel P. , Jena Achintya K. , Osko Joanna J. , Ransdell Joseph L. 
Published: August 2024

AbstractThere is a striking sex bias in the prevalence and severity of autism spectrum disorder (ASD) with 80% of diagnoses occurring in males. Because the molecular etiology of ASD is likely combinatorial, including interactions across multiple genetic and environmental factors, it is difficult to investigate the physiological mechanisms driving sex-specific differences. Loss of function mutations inTSC1result in dysregulated mTORC1 signaling and underlie a multi-system disorder known as tuberous sclerosis (TSC). Interestingly, more than 50% of individuals diagnosed with TSC are also diagnosed with ASD, making TSC mutations one of the most prevalent monogenic causes of ASD. Mice harboring targeted deletion ofTsc1selectively in cerebellar Purkinje neurons, referred to here asTsc1mut/mut, have multiple ASD-linked behavioral impairments, including deficits in social interactions, motor coordination, and vocalizations. However, these ASD-linked behavioral deficits have only been investigated using maleTsc1mut/mutanimals. Here, we used cohorts of male and femaleTsc1mut/mutanimals to determine if behavioral impairments, previously identified in this model, are similar across sex. Specifically, we measured balance and motor coordination and social interaction behaviors in two age groups across sex. Wedetermined balance and motor coordination deficits are similar in male and femaleTsc1mut/mutmice, and that deficits in the firing ofTsc1mut/mutPurkinje neurons located in the cerebellar vermis are also similar across sex. However, impairments in social approach behavior were found to be significantly more severe inTsc1mut/mutmales compared to females. These results indicate the selective deletion ofTsc1in Purkinje neurons differentially impairs cerebellar circuits based on sex.
ER-phagy drives age-onset remodeling of endoplasmic reticulum structure-function and lifespan
Authors: Donahue EKF , Hepowit NL , Keuchel B , Mulligan AG , Johnson DJ , Ellisman M , Arrojo e Drigo R , MacGurn J , Burkewitz K 
Published: August 2024

AbstractThe endoplasmic reticulum (ER) comprises an array of structurally distinct subdomains, each with characteristic functions. While altered ER-associated processes are linked to age-onset pathogenesis, whether shifts in ER morphology underlie these functional changes is unclear. We report that ER remodeling is a conserved feature of the aging process in models ranging from yeast toC. elegansand mammals. Focusing onC. elegansas an exemplar of metazoan aging, we find that as animals age, ER mass declines in virtually all tissues and ER morphology shifts from rough sheets to tubular ER. The accompanying large-scale shifts in proteomic composition correspond to the ER turning from protein synthesis to lipid metabolism. To drive this substantial remodeling, ER-phagy is activated early in adulthood, promoting turnover of rough ER in response to rises in luminal protein-folding burden and reduced global protein synthesis. Surprisingly, ER remodeling is a pro-active and protective response during aging, as ER-phagy impairment limits lifespan in yeast and diverse lifespan-extending paradigms promote profound remodeling of ER morphology even in young animals. Altogether our results reveal ER-phagy and ER morphological dynamics as pronounced, underappreciated mechanisms of both normal aging and enhanced longevity.
Cr-Cr distance and magnetism in the phase diagram of triangular lattice antiferromagnets: A systematic comparative study
Authors: Nocerino E. , Sugiyama J. , Forslund O. K. , Umegaki I. , Kobayashi S. , Yoshimura K. , Sassa Y. , Månsson M. 
Published: August 2024

In this study, we investigate the influence of Cr-Cr distances on the magnetic properties of triangular lattice antiferromagnets through the lens of the recently synthesized Cr compounds LiCrSe2, LiCrTe2, and NaCrTe2. Our comprehensive analysis integrates existing magnetic structure data and new insights from muon spin rotation measurements, revealing a striking mutual influence between strongly correlated electrons and structural degrees of freedom in systems possessing very different magnetic properties despite having the same crystal symmetry. In particular, we delineate how Cr-Cr distances specifically dictate the magnetic behaviors of the triangular lattice antiferromagnets LiCrSe2, LiCrTe2, and NaCrTe2. By crafting phase diagrams based on these distances, we establish a clear correlation between the structural parameters and the magnetic ground states of these materials together with a wide variety of trivalent Cr triangular lattice layered magnets. Our analysis uncovers a transition range for in-plane and out-of-plane Cr-Cr distances that demarcates distinct magnetic behaviors, highlighting the nuanced role of lattice geometry in the spin-lattice interaction and electron correlation dynamics.

Published by the American Physical Society
2024
Islam in business ethics research: a bibliometric analysis and future research agenda
Authors: Sofyan Andi Syathir , Rusanti Ega , Nurmiati Nurmiati , Sofyan Syaakir , Kurniawan Robert , Caraka Rezzy Eko 
Published: August 2024

Purpose
This study aims to determine research performance in Islamic business ethics and explore future research directions from leading articles and scholars.

Design/methodology/approach
This paper used bibliometric and content analysis to analyze 250 articles from reputable Scopus and Web of Sciences journals.

Findings
To date, the normative style still dominates Islamic business ethics research. Asian countries such as Malaysia and Indonesia are the center of discussion on Islamic business ethics. This study also suggests that researchers and academics study aspects of the economy that Islamic values have not touched, such as the theme of art, artificial intelligence for labor relations, workers' rights and language.

Research limitations/implications
This research aims to contribute knowledge to Muslims as a reference guide for ethical business behavior. Non-Muslim managers can use this paper as a guide in forming a global company that is pluralistic and respectful of religious communities.

Originality/value
This research makes a scholarly contribution by providing a comprehensive exploration and detailed future research directions in each subtheme of Islamic business ethics.
Perception about sustainable development goals among Erasmus students in a Spanish university
Authors: Picatoste Xose , Tirca Diana Mihaela , Novo-Corti Isabel 
Published: August 2024

Purpose
This study aims to analyse the positioning of young people in the face of the challenges posed by the Sustainable Development Goals (SDGs). It focuses on the case of Erasmus+ students at a Spanish university and tries to evaluate the importance of each of the SDGs for them.

Design/methodology/approach
Based on primary data obtained through a survey of more than 300 young people, factor analysis was applied to evaluate the importance assigned to each SDG and quantify the degree of concern assigned to each of them.

Findings
Results show a high degree of concern for all the SDGs among Erasmus students, although they have done so with different levels of intensity. College students especially value education. Women are more concerned about socioeconomic problems. Furthermore, surprising results have been found in terms of gender equality, which indicates the need to deepen this analysis.

Originality/value
This work contributes to the academic literature, still limited but growing, on how Erasmus students perceive the SDGs and to what level they feel committed to these objectives. Furthermore, it can be helpful for public policy managers regarding a specific group of young university students and a hot topic such as sustainability.