bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fusion Neural Network (FusNet) for predicting protein-mediated loops
Authors: Tang Li , Huang Wenjie , Hill Matthew C. , Ellinor Patrick T. , Li Min 
Published: June 2023

AbstractThe organization of the three-dimensional (3D) genome is a complex, and requires a plethora of proteins to ensure the proper formation and regulation of chromatin loops as well as higher order structures. Studying protein-mediated loop regulation can help unravel the intricate interplay between these loops and their crucial roles in modulating gene expression across different cellular contexts. However, current targeted chromatin conformation capture experiments face limitations in capturing protein-mediated loops across various cell types, and existing computational methods fail to predict diverse protein-mediated loops. To address these issues, we propose a fusion neural network (FusNet) designed for predicting protein-mediated loops. FusNet leverages genome sequence information, open chromatin, and ChIP-seq data to efficiently represent and analyze the positions of loop anchors. To extract informative features and reduce the complexity of FusNet, we constructed a convolutional neural network, which compresses the dimensionality of the features while also preserving the most significant ones. To enhance the accuracy and generalization capacity of FusNet, we built a fusion layer by stacking the prediction of fundamental models with a meta-model. FusNet demonstrated its effectiveness in predicting protein-mediated loops, exhibiting high consistency with Hi-C data. Moreover, we find that the loops output from FusNet are highly associated with regulatory functions. Through association analysis with genetic risk variants, FusNet further revealed its potential for unraveling disease-related mechanisms. In conclusion, our study offers a novel computational approach for predicting various protein-mediated chromatin loops, which could substantially enhance research on the functional significance of protein-mediated loop structures in diverse cellular contexts.Significance StatementThe intricate spatial organization of the three-dimensional (3D) genome involves functional proteins critically contributing to chromatin loop formation and regulation. Understanding these protein-mediated loops is vital for elucidating their influence on 3D genome architecture and gene regulation across different cellular types and disease-related contexts. In this study, we propose a Fusion Neural Network (FusNet) for predicting protein-mediated loops. FusNet can concurrently capture and analyze multiple protein-mediated loops in various cell types to advance our understanding of the multitude of protein-mediated loop structures and their functional significance. Importantly, through association analysis with risk variants, FusNet manifests potential in revealing disease-related mechanisms.
The rules of sex and strain: deciphering the chemical language of inbred and wild mouse conspecific scents
Authors: Nagel Maximilian , Niestroj Marco , Bansal Rohini , Fleck David , Lampert Angelika , Stopkova Romana , Stopka Pavel , Ben-Shaul Yoram , Spehr Marc 
Published: June 2023

SummaryIn most mammals, conspecific chemosensory communication relies on semiochemical release within complex bodily secretions and subsequent stimulus detection by the vomeronasal organ (VNO). Urine, a rich source of ethologically relevant chemosignals, conveys detailed information about sex, social hierarchy, health and reproductive state, which becomes accessible to a conspecific via vomeronasal sampling. So far, however, numerous aspects of social chemosignaling along the vomeronasal pathway remain unclear. Moreover, since virtually all research on vomeronasal physiology is based on secretions derived from inbred laboratory mice, it remains uncertain whether such stimuli provide a true representation of potentially more relevant cues found in the wild. Here, we combine a robust low-noise VNO activity assay with comparative molecular profiling of sex- and strain-specific mouse urine samples from two inbred laboratory strains as well as from wild mice. With comprehensive molecular portraits of these secretions, VNO activity analysis now enables us to (i) assess whether and, if so, how much sex- / strain-selective “raw” chemical information in urine is accessible via vomeronasal sampling; (ii) identify which chemicals exhibit sufficient discriminatory power to signal an animal’s sex, strain, or both; (iii) determine the extent to which wild mouse secretions are unique; and (iv) analyze whether vomeronasal response profiles differ between strains. We report both sex- and, in particular, strain-selective VNO representations of chemical information. Within the urinary ‘secretome’, both volatile compounds and proteins exhibit sufficient discriminative power to provide sex- and strain-specific molecular fingerprints. While total protein amount is substantially enriched in male urine, females secrete a larger variety at overall comparatively low concentrations. Surprisingly, the molecular spectrum of wild mouse urine does not dramatically exceed that of inbred strains. Finally, vomeronasal response profiles differ between C57BL/6 and BALB/c animals, with particularly disparate representations of female semiochemicals.
Histone chaperone HIRA, Promyelocytic Leukemia (PML) protein and p62/SQSTM1 coordinate to regulate inflammation during cell senescence
Authors: Dasgupta Nirmalya , Lei Xue , Shi Christina Huan , Arnold Rouven , Teneche Marcos G. , Miller Karl N. , Rajesh Adarsh , Davis Andrew , Anschau Valesca , Campos Alexandre R. , Gilson Rebecca , Havas Aaron , Yin Shanshan , Chua Zong Ming , Liu Tianhui , Proulx Jessica , Alcaraz Michael , Rather Mohammed Iqbal , Baeza Josue , Schultz David C. , Yip Kevin Y. , Berger Shelley L. , Adams Peter D. 
Published: June 2023

SummaryCellular senescence, a stress-induced stable proliferation arrest associated with an inflammatory Senescence-Associated Secretory Phenotype (SASP), is a cause of aging. In senescent cells, Cytoplasmic Chromatin Fragments (CCFs) activate SASP via the anti-viral cGAS/STING pathway. PML protein organizes PML nuclear bodies (NBs), also involved in senescence and anti-viral immunity. The HIRA histone H3.3 chaperone localizes to PML NBs in senescent cells. Here, we show that HIRA and PML are essential for SASP expression, tightly linked to HIRA’s localization to PML NBs. Inactivation of HIRA does not directly block expression of NF-κB target genes. Instead, an H3.3-independent HIRA function activates SASP through a CCF-cGAS-STING-TBK1-NF-κB pathway. HIRA physically interacts with p62/SQSTM1, an autophagy regulator and negative SASP regulator. HIRA and p62 co-localize in PML NBs, linked to their antagonistic regulation of SASP, with PML NBs controlling their spatial configuration. These results outline a role for HIRA and PML in regulation of SASP.
Comparative analysis of N-terminal cysteine dioxygenation and prolyl-hydroxylation as oxygen sensing pathways in mammalian cells
Authors: Tian Ya-Min , Holdship Philip , To Trang Quynh , Ratcliffe Peter J , Keeley Thomas P 
Published: June 2023

AbstractIn animals, adaptation to changes in cellular oxygen levels is coordinated largely by the 2-oxoglutarate dependent prolyl-hydroxylase domain (PHD) dioxygenase family, which regulate the stability of their hypoxia-inducible factor (HIF) substrates to promote expression of genes that adapt cells to hypoxia. Recently, 2-aminoethanethiol dioxygenase (ADO) was identified as a novel O2-sensing enzyme in animals. Through N-terminal cysteine dioxygenation and the N-degron pathway, ADO regulates the stability of a set of non-transcription factor substrates; the regulators of G-protein signalling 4, 5 and 16, and interleukin-32. Here, we set out to compare and contrast thein cellulocharacteristics of ADO and PHD enzymes in an attempt to better understand their co-evolution in animals. We find that ADO operates to regulate the stability of its substrates rapidly and with similar O2-sensitivity to the PHD/HIF pathway. ADO appeared less sensitive to iron chelating agents or transition metal exposure than the PHD enzymes, possibly due to tighter catalytic-site Fe2+coordination. Unlike the PHD/HIF pathway, the ADO/N-degron pathway was not subject to feedback by hypoxic induction of ADO and induction of ADO substrates was well sustained in response to prolonged hypoxia. The data also reveal strong interactions between proteolytic regulation of targets by ADO and transcriptional induction of those targets, that shape integrated cellular responses to hypoxia.
How does China economic policy uncertainty (EPU) impact copper-firms stock returns and copper prices returns?
Authors: Maquieira Carlos , Gahona-Flores Orlando , Espinosa-Méndez Christian 
Published: June 2023

PurposeThis study focuses on how China EPU may impact copper-firms stock returns and also how China EPU mediates between stock returns and copper prices returns.Design/methodology/approachThe sample consists of 44 copper firms from January 2011 to March 2022. The study also considers a subsample of 29 net-exporters countries. Panel data methodology is used, allowing to control for unobservable heterogeneity and endogeneity problems. The equations are estimated through a dynamic panel using the generalized methods of moments (GMM).FindingsChina EPU has a negative and statistically significant relationship with stock returns. Copper price returns are positively associated with stock returns. This research also considers two scenarios: high and low levels of China EPU. For high levels of China EPU states it is reported a negative relationship between stock returns and China EPU and copper price returns show a positive relationship with stock returns.Research limitations/implicationsThere is need to explore other metals for what China exhibits a high demand and observe if China EPU and Global EPU have similar impacts on stock returns. It will be useful to identify main firm's consumers of copper and these other metals to explore the relationship between EPU and stock returns.Originality/valueTo the best of the authors’ knowledge, this is the first paper that analyzes China EPU index and its impact on both copper-firms stocks returns and on changes in copper prices. This is done using all public copper firms worldwide.
Fractal model of thermal contact conductance of micro-segment gear considering friction coefficient
Authors: Sun Xianguang , Xin Xicheng 
Published: June 2023

Purpose
The purpose of this study is to establish a fractal model of thermal contact conductance (TCC) of micro-segment gear considering friction coefficient.

Design/methodology/approach
The influences of friction coefficient, fractal dimension, fractal roughness and contact type on the TCC of the rough surface were studied by using numerical simulation.

Findings
The results show that with the increase of the friction coefficient, the TCC of the rough surface will decrease. As the fractal dimension increases or the fractal roughness decreases, the rough surface becomes smoother and the TCC becomes larger. Under the same load conditions, the TCC of the internal contact type is greater than that of the external contact type. In engineering practice, the desired TCC can be achieved by changing the contact type.

Originality/value
A fractal model of TCC of micro-segment gear considering friction coefficient was established in this study. The achievements of this study provide some theoretical basis for the investigation of the TCC of the gear.
Worker cooperatives in Italy: legislation, prevalence and recent trends
Authors: Lomuscio Marco , Tortia Ermanno Celeste , Cori Andrea 
Published: June 2023

PurposeIn Italy, worker cooperatives (WCs), whose workers hold major control rights over collectively-owned assets, are the leading vehicle for the promotion and development of employee ownership. Worker cooperatives are present in all regions and in most economic sectors, employing about 506,000 workers and generating a turnover of about €22 bn. Despite their history and diffusion, the high prevalence of WCs in Italy is under-researched and -thematised and requires new research.Design/methodology/approachThe paper leverages unpublished primary and secondary data from Centro Studi Legacoop databank, the Aida-Bureau Van Dijk databank and the Cooperative Registry of the Ministry of Economic Development (CRMED) to explain the spread of WCs in Italy.FindingsThis paper reveals descriptive statistics of WCs and investigates their distribution across economic sectors and regions, their economic and financial performance and gives an overview of the relevant legislation. The paper indicates that older small- and medium-sized cooperatives located in central and north-eastern Italy perform best economically. However, in recent years, an increasing number of young cooperatives has emerged in South Italy thanks to favourable legislation, cooperative finance and the diffusion of cooperative know-how. Limitations to such results are reported in the conclusions.Originality/valueThe paper sheds light on past and recent development trends of WCs in Italy, highlights their growth in South Italy and revitalises the debate on the drivers, structures and rationales of employee-owned enterprises in Italy. Findings generate implications for research and practice. Given the tendency of WCs to better protect jobs than investor-owned enterprises, the spread of these enterprises may help workers find better and more stable jobs, counter-cyclically mitigating the dangerous effects of macro- and meso-economic fluctuations and instability.
Improving the performance of a conveyor belt through lean philosophy and Industry 4.0
Authors: Mendes David S.F.T. , Navas Helena V.G. , Charrua-Santos Fernando M.B. 
Published: June 2023

PurposeThe purpose of this study was to develop and implement a new model to improve maintenance management and the production system through the concepts: maintenance, lean philosophy and Industry 4.0.Design/methodology/approachThe methodology employed in this study includes conducting a bibliographic survey of existing models exploring the joint application of the concepts under study, critically analyzing these models, developing a model proposal and subsequently analyzing the results obtained. The model is implemented on a belt conveyor of a feed mill to improve its performance.FindingsThe proposed model contributes to improve maintenance and production system management, proving to be a useful tool to improve real-time decision-making. After its application, it was possible to verify that it increased the performance of the conveyor belt, as well as improved the skills of the operators who operate on it.Research limitations/implicationsLimitation about the distance between the devices that make up the model. The implementation of autonomous maintenance can highlight some challenges within the company. The implementation was only in the belt conveyor, being useful to introduce this in the remaining areas of the factory.Originality/valueThe study presents an innovative, versatile, low-cost and easy-to-apply model to improve maintenance management by combining the three concepts. The model can be easily adapted to monitor condition parameters such as temperature, noise, among others, through the correct choice of devices and proper programming. This work also contributed to help in real-time decision-making for both the maintenance and production departments.
Distribution of N and recently fixed C among a common mycorrhizal network linking an invasive plant, Solidago canadensis, and a native plant, Kummerowia striata
Authors: Awaydul Awagul , Xiao Jing , Chen Xin , Koide Roger , Yuan Yongge , Cheng Lei 
Published: June 2023

Abstract

The invasive plant species, Solidago canadensis, often shares a common mycorrhizal network (CMN) with native plant species in southeast China. We ask whether the transfer of carbon (C) and nitrogen (N) among the invasive S. canadensis, the native Kummerowia striata and their CMN could contribute to the invasiveness of S. canadensis.

We conducted a microcosm experiment in which a CMN was established on S. canadensis and K. striata. We used 13CO2 pulse‐labelling to quantify the relative contribution of recently fixed C from the two host species to the CMN. We also calculated the relative N distribution to each host species from the CMN.

We found that 89% of the recently fixed C in the CMN originated from S. canadensis, while 11% originated from K. striata. We also found that the CMN distributed 77% of the N it absorbed to S. canadensis and 23% to K. striata.

Our results suggest that the unequal distribution of N from a CMN to the invasive and native plant species is related to the unequal contribution of C from the plant species. This mechanism could contribute to invasion of native communities by alien species when there is a stoichiometric exchange of limiting nutrients for C, and when alien species contribute more C to the CMN than natives.

Read the free Plain Language Summary for this article on the Journal blog.
Climate resilience, yield and geographical suitability of sweet potato under the changing climate: A review
Authors: Pushpalatha Raji , Gangadharan Byju 
Published: June 2023

AbstractSweet potato is one of the important tropical tuber crops across the world. This review analyzes the studies on the climate resilience of sweet potato to various environmental parameters, the impact of climate change on its yield, and geographical suitability to exploit more about this crop and find out the knowledge gap in its existing research. Drought tolerance studies indicate the suitability of sweet potato in drought‐prone areas in terms of their survival rate, and their leaves can tolerate up to a wilting point of −1.3 MPa. The optimum night and daytime temperatures for sweet potato are 18°C and 28°C. There are 82 crop varieties available globally with heat‐stress tolerance without compromising the yield. The elevated atmospheric CO2 enhanced the growth and yield of sweet potato and increased the water use efficiency. The salinity tolerance of sweet potato is observed as 11 dS m−1, and it is superior to other major food crops. Sweet potato's ozone tolerance is higher than other crops (59 ppb). The impact studies on crop yield and geographical suitability also recommend its superiority to other major food crops with similar crop duration. As an outcome of this study, further research is needed to explore this crop as sweet potato can substitute for major food grain crops in developing countries regarding food, feed, medicine, and fuel. Research on value‐added products and their marketing is another area that needs immediate attention. Studies must exploit sweet potato leaves to ensure nutritional security in developing countries. The researchers also need to focus on developing climate‐resilient varieties to ensure a continuous supply of planting materials to needy people to ensure food security. This review also demands more studies on the modeling of sweet potato worldwide to issue crop yield forecasts and monitor the spatial distribution of its major pests worldwide.
Odorant‐binding protein 19 in Monochamus alternatus involved in the recognition of a volatile strongly emitted from ovipositing host pines
Authors: Yang Ruinan , Li Dongzhen , Yi Shancheng , Wei Yi , Wang Manqun 
Published: June 2023

AbstractMonochamus alternatus is the primary carrier of pine wood nematodes, which pose a serious threat to Pinus spp. in many countries. Newly emerging M. alternatus adults feed on heathy host pines, while matured adults transfer to stressed host pines for mating and oviposition. Several odorant‐binding proteins (OBPs) of M. alternatus have been proved to aid in the complex process of host location. To clarify the corresponding relations between OBPs and pine volatiles, more OBPs need to be studied. In this research, MaltOBP19 showed a specific expression in the antennae and mouthparts of M. alternatus, and it was marked in 4 types of antenna sensilla by immunolocalization. Fluorescence binding assays demonstrated the high binding affinity of MaltOBP19 with camphene and myrcene in vitro. In Y‐tube olfactory experiments, M. alternatus adults were attracted by camphene and RNAi of OBP19 via microinjection significantly decreased their attraction index. Myrcene induced phobotaxis, but RNAi had no significant effect on this behavior. Further, we found that ingesting dsOBP19 produced by a bacteria‐expressed system with a newly constructed vector could lead to the knockdown of MaltOBP19. These results suggest that MaltOBP19 may play a role in the process of host conversion via the recognition of camphene, which has been identified to be strongly released in stressed host pines. In addition, it is proved that knockdown of OBP can be achieved by oral administration of bacteria‐expressed double‐stranded RNA in M. alternatus adults, providing a new perspective in the control of M. alternatus.
Deficiency for scavenger receptors Stabilin‐1 and Stabilin‐2 leads to age‐dependent renal and hepatic depositions of fasciclin domain proteins TGFBI and Periostin in mice
Authors: Leibing Thomas , Riedel Anna , Xi Yannick , Adrian Monica , Krzistetzko Jessica , Kirkamm Christof , Dormann Christof , Schledzewski Kai , Goerdt Sergij , Géraud Cyrill 
Published: June 2023

AbstractStabilin‐1 (Stab1) and Stabilin‐2 (Stab2) are two major scavenger receptors of liver sinusoidal endothelial cells that mediate removal of diverse molecules from the plasma. Double‐knockout mice (Stab‐DKO) develop impaired kidney function and a decreased lifespan, while single Stabilin deficiency or therapeutic inhibition ameliorates atherosclerosis and Stab1‐inhibition is subject of clinical trials in immuno‐oncology. Although POSTN and TFGBI have recently been described as novel Stabilin ligands, the dynamics and functional implications of these ligands have not been comprehensively studied. Immunofluorescence, Western Blotting and Simple Western™ as well as in situ hybridization (RNAScope™) and qRT‐PCR were used to analyze transcription levels and tissue distribution of POSTN and TGFBI in Stab‐KO mice. Stab‐POSTN‐Triple deficient mice were generated to assess kidney and liver fibrosis and function in young and aged mice. TGFBI and POSTN protein accumulated in liver tissue in Stab‐DKO mice and age‐dependent in glomeruli of Stabilin‐deficient mice despite unchanged transcriptional levels. Stab‐POSTN‐Triple KO mice showed glomerulofibrosis and a reduced lifespan comparable to Stab‐DKO mice. However, alterations of the glomerular diameter and vascular density were partially normalized in Stab‐POSTN‐Triple KO. TGFBI and POSTN are Stabilin‐ligands that are deposited in an age‐dependent manner in the kidneys and liver due to insufficient scavenging in the liver. Functionally, POSTN might partially contribute to the observed renal phenotype in Stab‐DKO mice. This study provides details on downstream effects how Stabilin dysfunction affects organ function on a molecular and functional level.