bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ovarian carcinosarcoma is a distinct form of ovarian cancer with poorer survival compared to tubo-ovarian high-grade serous carcinoma
Authors: Hollis Robert L. , Croy Ian , Churchman Michael , Bartos Clare , Rye Tzyvia , Gourley Charlie , Herrington C. Simon 
Published: June 2022

Abstract
Background
Ovarian carcinosarcoma (OCS) is an uncommon, biphasic and highly aggressive ovarian cancer type, which has received relatively little research attention.

Methods
We curated the largest pathologically confirmed OCS cohort to date, performing detailed histopathological characterisation, analysis of features associated with survival and comparison against high-grade serous ovarian carcinoma (HGSOC).

Results
Eighty-two OCS patients were identified; overall survival was poor (median 12.7 months). In all, 79% demonstrated epithelial components of high-grade serous (HGS) type, while 21% were endometrioid. Heterologous elements were common (chondrosarcoma in 32%, rhabdomyosarcoma in 21%, liposarcoma in 2%); chondrosarcoma was more frequent in OCS with endometrioid carcinomatous components. Earlier stage, complete resection and platinum-containing adjuvant chemotherapy were associated with prolonged survival; however, risk of relapse and mortality was high across all patient groups. Histological subclassification did not identify subgroups with distinct survival. Compared to HGSOC, OCS patients were older (P < 0.0001), more likely to be FIGO stage I (P = 0.025), demonstrated lower chemotherapy response rate (P = 0.001) and had significantly poorer survival (P < 0.0001).

Conclusion
OCS represents a distinct, highly lethal form of ovarian cancer for which new treatment strategies are urgently needed. Histological subclassification does not identify patient subgroups with distinct survival. Aggressive adjuvant chemotherapy should be considered for all cases, including those with early-stage disease.
Emerging nanomedical strategies for direct targeting of pediatric and adult diffuse gliomas
Authors: Kolsteeg Christy , Hulleman Esther , Bianco John 
Published: June 2022

AbstractHigh-grade gliomas, in particularly diffuse midline glioma, H3K27-altered in children and glioblastoma in adults, are the most lethal brain tumour with a dismal prognosis. Developments in modern medicine are constantly being applied in the search for a cure, although finding the right strategy remains elusive. Circumventing the blood–brain barrier is one of the biggest challenges when it comes to treating brain tumours. The cat and mouse game of finding the Trojan horse to traverse this barrier and deliver therapeutics to the brain has been a long and hard-fought struggle. Research is ongoing to find new and feasible ways to reach specific targets in the brain, with a special focus on inoperable or recurring brain tumours. Many options and combinations of options have been tested to date and continue to be so in the search to find the most effective and least toxic treatment paradigm. Although improvements are often small and slow, some of these strategies have already shown promise, shining a light of hope that finding the cure is feasible. In this review, we discuss recent findings that elucidate promising but atypical strategies for targeting gliomas and the implications that this work has on developing new treatment regimens.
Identification of an Epi-metabolic dependency on EHMT2/G9a in T-cell acute lymphoblastic leukemia
Authors: Montanaro Anna , Kitara Samuel , Cerretani Elisa , Marchesini Matteo , Rompietti Chiara , Pagliaro Luca , Gherli Andrea , Su Angela , Minchillo Maria Laura , Caputi Mariafrancesca , Fioretzaki Rodanthi , Lorusso Bruno , Ross Linda , Alexe Gabriela , Masselli Elena , Marozzi Marina , Rizzi Federica Maria Angela , La Starza Roberta , Mecucci Cristina , Xiong Yan , Jin Jian , Falco Angela , Knoechel Birgit , Aversa Franco , Candini Olivia , Quaini Federico , Sportoletti Paolo , Stegmaier Kimberly , Roti Giovanni 
Published: June 2022

AbstractGenomic studies have identified recurrent somatic alterations in genes involved in DNA methylation and post-translational histone modifications in acute lymphoblastic leukemia (ALL), suggesting new opportunities for therapeutic interventions. In this study, we identified G9a/EHMT2 as a potential target in T-ALL through the intersection of epigenome-centered shRNA and chemical screens. We subsequently validated G9a with low-throughput CRISPR-Cas9-based studies targeting the catalytic G9a SET-domain and the testing of G9a chemical inhibitors in vitro, 3D, and in vivo T-ALL models. Mechanistically we determined that G9a repression promotes lysosomal biogenesis and autophagic degradation associated with the suppression of sestrin2 (SESN2) and inhibition of glycogen synthase kinase-3 (GSK-3), suggesting that in T-ALL glycolytic dependent pathways are at least in part under epigenetic control. Thus, targeting G9a represents a strategy to exhaust the metabolic requirement of T-ALL cells.
Adipocyte-derived kynurenine promotes obesity and insulin resistance by activating the AhR/STAT3/IL-6 signaling
Authors: Huang Teng , Song Jia , Gao Jia , Cheng Jia , Xie Hao , Zhang Lu , Wang Yu-Han , Gao Zhichao , Wang Yi , Wang Xiaohui , He Jinhan , Liu Shiwei , Yu Qilin , Zhang Shu , Xiong Fei , Zhou Qing , Wang Cong-Yi 
Published: June 2022

AbstractAberrant amino acid metabolism is a common event in obesity. Particularly, subjects with obesity are characterized by the excessive plasma kynurenine (Kyn). However, the primary source of Kyn and its impact on metabolic syndrome are yet to be fully addressed. Herein, we show that the overexpressed indoleamine 2,3-dioxygenase 1 (IDO1) in adipocytes predominantly contributes to the excessive Kyn, indicating a central role of adipocytes in Kyn metabolism. Depletion of Ido1 in adipocytes abrogates Kyn accumulation, protecting mice against obesity. Mechanistically, Kyn impairs lipid homeostasis in adipocytes via activating the aryl hydrocarbon receptor (AhR)/Signal transducer and activator of transcription 3 /interleukin-6 signaling. Genetic ablation of AhR in adipocytes abolishes the effect of Kyn. Moreover, supplementation of vitamin B6 ameliorated Kyn accumulation, protecting mice from obesity. Collectively, our data support that adipocytes are the primary source of increased circulating Kyn, while elimination of accumulated Kyn could be a viable strategy against obesity.
RIViT-seq enables systematic identification of regulons of transcriptional machineries
Authors: Otani Hiroshi , Mouncey Nigel J. 
Published: June 2022

AbstractTranscriptional regulation is a critical process to ensure expression of genes necessary for growth and survival in diverse environments. Transcription is mediated by multiple transcription factors including activators, repressors and sigma factors. Accurate computational prediction of the regulon of target genes for transcription factors is difficult and experimental identification is laborious and not scalable. Here, we demonstrate regulon identification by in vitro transcription-sequencing (RIViT-seq) that enables systematic identification of regulons of transcription factors by combining an in vitro transcription assay and RNA-sequencing. Using this technology, target genes of 11 sigma factors were identified inStreptomyces coelicolorA3(2). The RIViT-seq data expands the transcriptional regulatory network in this bacterium, discovering regulatory cascades and crosstalk between sigma factors. Implementation of RIViT-seq with other transcription factors and in other organisms will improve our understanding of transcriptional regulatory networks across biology.
Context-dependent enhancer function revealed by targeted inter-TAD relocation
Authors: Bolt Christopher Chase , Lopez-Delisle Lucille , Hintermann Aurélie , Mascrez Bénédicte , Rauseo Antonella , Andrey Guillaume , Duboule Denis 
Published: June 2022

AbstractThe expression of some genes depends on large, adjacent regions of the genome that contain multiple enhancers. These regulatory landscapes frequently align with Topologically Associating Domains (TADs), where they integrate the function of multiple similar enhancers to produce a global, TAD-specific regulation. We asked if an individual enhancer could overcome the influence of one of these landscapes, to drive gene transcription. To test this, we transferred an enhancer from its native location, into a nearby TAD with a related yet different functional specificity. We used the biphasic regulation of Hoxd genes during limb development as a paradigm. These genes are first activated in proximal limb cells by enhancers located in one TAD, which is then silenced when the neighboring TAD activates its enhancers in distal limb cells. We transferred a distal limb enhancer into the proximal limb TAD and found that its new context suppresses its normal distal specificity, even though it is bound by HOX13 transcription factors, which are responsible for the distal activity. This activity can be rescued only when a large portion of the surrounding environment is removed. These results indicate that, at least in some cases, the functioning of enhancer elements is subordinated to the host chromatin context, which can exert a dominant control over its activity.
Multifunctional biomimetic tactile system via a stick-slip sensing strategy for human–machine interactions
Authors: Li Yue , Zhao Manjun , Yan Yadong , He Luanxi , Wang Yingyi , Xiong Zuoping , Wang Shuqi , Bai Yuanyuan , Sun Fuqin , Lu Qifeng , Wang Yu , Li Tie , Zhang Ting 
Published: June 2022

AbstractA tactile sensor system enables natural interaction between humans and machines; this interaction is crucial for dexterous robotic hands, interactive entertainment, and other smart scenarios. However, the lack of sliding friction detection significantly limits the accuracy and scope of interactions due to the absence of sophisticated information, such as slippage, material and roughness of held objects. Here, inspired by the stick-slip phenomena in the sliding process, we have developed a multifunctional biomimetic tactile system based on the stick-slip sensing strategy, which is a universal method to detect slippage and estimate the surface properties of objects by sliding. This system consists of a flexible fingertip-inspired tactile sensor, a read-out circuit and a machine-learning module. Based on the stick-slip sensing strategy, our system was endowed with high recognition rates for slippage detection (100.0%), material classification (93.3%) and roughness discrimination (92.8%). Moreover, robotic hand manipulation, interactive games and object classification are demonstrated with this multifunctional system for comprehensive and promising human–machine interactions.
Better force fields start with better data: A data set of cation dipeptide interactions
Authors: Hu Xiaojuan , Lenz-Himmer Maja-Olivia , Baldauf Carsten 
Published: June 2022

AbstractWe present a data set from a first-principles study of amino-methylated and acetylated (capped) dipeptides of the 20 proteinogenic amino acids – including alternative possible side chain protonation states and their interactions with selected divalent cations (Ca2+, Mg2+ and Ba2+). The data covers 21,909 stationary points on the respective potential-energy surfaces in a wide relative energy range of up to 4 eV (390 kJ/mol). Relevant properties of interest, like partial charges, were derived for the conformers. The motivation was to provide a solid data basis for force field parameterization and further applications like machine learning or benchmarking. In particular the process of creating all this data on the same first-principles footing, i.e. density-functional theory calculations employing the generalized gradient approximation with a van der Waals correction, makes this data suitable for first principles data-driven force field development. To make the data accessible across domain borders and to machines, we formalized the metadata in an ontology.
PISCOeo_pm, a reference evapotranspiration gridded database based on FAO Penman-Monteith in Peru
Authors: Huerta Adrian , Bonnesoeur Vivien , Cuadros-Adriazola José , Gutierrez Leonardo , Ochoa-Tocachi Boris F. , Román-Dañobeytia Francisco , Lavado-Casimiro Waldo 
Published: June 2022

AbstractA new FAO Penman-Monteith reference evapotranspiration gridded dataset is introduced, called PISCOeo_pm. PISCOeo_pm has been developed for the 1981–2016 period at ~1 km (0.01°) spatial resolution for the entire continental Peruvian territory. The framework for the development of PISCOeo_pm is based on previously generated gridded data of meteorological subvariables such as air temperature (maximum and minimum), sunshine duration, dew point temperature, and wind speed. Different steps, i.e., (i) quality control, (ii) gap-filling, (iii) homogenization, and (iv) spatial interpolation, were applied to the subvariables. Based on the results of an independent validation, on average, PISCOeo_pm exhibits better precision than three existing gridded products (CRU_TS, TerraClimate, and ERA5-Land) because it presents a predictive capacity above the average observed using daily and monthly data and has a higher spatial resolution. Therefore, PISCOeo_pm is useful for better understanding the terrestrial water and energy balances in Peru as well as for its application in fields such as climatology, hydrology, and agronomy, among others.
A study of triple-mass diffusion species and energy transfer in Carreau–Yasuda material influenced by activation energy and heat source
Authors: Sohail Muhammad , Nazir Umar , El-Zahar Essam R. , Alrabaiah Hussam , Kumam Poom , Mousa Abd Allah A. , Sitthithakerngkiet Kanokwan , Park Choonkil 
Published: June 2022

AbstractThe mechanism of thermal transport can be enhanced by mixing the nanoparticles in the base liquid. This research discusses the utilization of nanoparticles (tri-hybrid) mixture into Carreau–Yasuda material. The flow is assumed to be produced due to the stretching of vertical heated surface. The phenomena of thermal transport are modeled by considering Joule heating and heat generation or absorption involvement. Additionally, activation energy is engaged to enhance heat transfer rate. The mathematical model composing transport of momentum, heat and mass species is developed in Cartesian coordinate system under boundary layer investigation in the form of coupled nonlinear partial differential equations. The complex partial differential equations are converted into coupled nonlinear ordinary differential equations by using the appropriate similarity transformation. The conversion of PDEs into ODEs make the problem easy to handle and it overcome the difficulties to solve the PDEs. The transformed ordinary differential equations are solved with the help of help of finite element scheme. The obtained solution is plotted against numerous involved parameters and comparative study is established for the reliability of method and accuracy of obtained results. An enhancement in fluid temperature is recorded against magnetic parameter and Eckert number. Also, decline in velocity is recorded for Weissenberg number and concentration is controlled against higher values of Schmidt number. Furthermore, it is recommended that the finite element scheme can be implemented to handle complex coupled nonlinear differential equation arising in modeling of several phenomena occurs in mathematical physics.
Mebendazole, an anti-helminth drug, suppresses inflammation, oxidative stress and injury in a mouse model of ulcerative colitis
Authors: Eskandari Moein , Asgharzadeh Fereshteh , Askarnia-faal Mohammad Mostafa , Naimi Hamideh , Avan Amir , Ahadi Mitra , Vossoughinia Hassan , Gharib Masoumeh , Soleimani Atena , Naghibzadeh Niloufar , Ferns Gordon , Ryzhikov Mikhail , Khazaei Majid , Hassanian Seyed Mahdi 
Published: June 2022

AbstractMebendazole (MBZ) is an efficacious anthelmintic with known anti-inflammatory and fibrinolytic properties. In this study, we aimed to explore the protective effects of this FDA-approved drug against DSS-induced colitis in a murine model either alone or in combination with Sulfasalazine (SSZ), a standard therapy for ulcerative colitis. We found that MBZ significantly improved colitis disease activity index as assessed by changes in body weight, degree of stool consistency, rectal bleeding, and prolapse. We also found that MBZ ameliorated the colon histopathological score by attenuating crypt loss, mucosal damage, and inflammation score in colitis tissues. Similarly, DSS-induced colon shortening, colon weight loss, and increase in spleen weight were all abrogated in the presence of MBZ. Moreover, MBZ decreased inflammation, possibly by reducing oxidative stress markers, suppressing inflammatory cell infiltration, and down-regulation of inflammatory genes in colon tissues. Furthermore, MBZ potently reduced fibrosis by decreasing collagen deposition and down-regulating pro-fibrotic genes including Col 1a1 and Col 1a2 in colitis tissue homogenates. In conclusion, our study showed that this broad-spectrum anthelminthic could be repurposed as a novel therapy for ulcerative colitis without any observed side effects, however, regarding the concerns about the potential toxicity of MBZ in UC patients, future experiments on MBZ therapy in other models of UC is needed to completely address the toxicity concerns.
Social capital building interventions and self-reported post-disaster recovery in Ofunato, Japan
Authors: Lee Juheon , Aldrich Daniel P. , Kiyota Emi , Yasuhiro Tanaka , Sawada Yasuyuki 
Published: June 2022

AbstractEvidence shows that communal resources, cohesion, and social infrastructure can mitigate shocks and enhance resilience. However, we know less about how specific social capital building interventions facilitate recovery in post-disaster environments. Using a survey of over 1000 residents of Ofunato, Japan after the 2011 Tohoku earthquake and tsunami, this study demonstrates that the individuals who actively participated in a community center—created for and led by neighborhood elders—reported higher levels of family and neighborhood recovery than similar individuals who did not participate. Results from ordinal logistic regression analyses, propensity score matching (PSM) and coarsened exact matching (CEM) show arguably stronger causal links between bottom-up, microlocal programs to boost connections in post-disaster areas and post-disaster outcomes. Community-based programs that strengthen social ties even among elderly residents can measurably improve their recoveries.
A novel approach GRNTSTE to reconstruct gene regulatory interactions applied to a case study for rat pineal rhythm gene
Authors: Liu Zhenyu , Gao Jing , Li Tao , Jing Yi , Xu Cheng , Zhu Zhengtong , Zuo Dongshi , Chen Junjie 
Published: June 2022

AbstractAccurate inference and prediction of gene regulatory network are very important for understanding dynamic cellular processes. The large-scale time series genomics data are helpful to reveal the molecular dynamics and dynamic biological processes of complex biological systems. Firstly, we collected the time series data of the rat pineal gland tissue in the natural state according to a fixed sampling rate, and performed whole-genome sequencing. The large-scale time-series sequencing data set of rat pineal gland was constructed, which includes 480 time points, the time interval between adjacent time points is 3 min, and the sampling period is 24 h. Then, we proposed a new method of constructing gene expression regulatory network, named the gene regulatory network based on time series data and entropy transfer (GRNTSTE) method. The method is based on transfer entropy and large-scale time-series gene expression data to infer the causal regulatory relationship between genes in a data-driven mode. The comparative experiments prove that GRNTSTE has better performance than dynamical gene network inference with ensemble of trees (dynGENIE3) and SCRIBE, and has similar performance to TENET. Meanwhile, we proved that the performance of GRNTSTE is slightly lower than that of SINCERITIES method and better than other gene regulatory network construction methods in BEELINE framework, which is based on the BEELINE data set. Finally, the rat pineal rhythm gene expression regulatory network was constructed by us based on the GRNTSTE method, which provides an important reference for the study of the pineal rhythm mechanism, and is of great significance to the study of the pineal rhythm mechanism.
Facile in situ construction of a covalent adaptable network polyester vitrimer with advanced performance in repairability, foamability and recyclability
Authors: Li Pengzhi , Lan Bin , Zhang Xutao , Lei Siyuan , Yang Qi , Gong Pengjian , Park Chul B. , Li Guangxian 
Published: June 2022

An environmentally friendly polyester vitrimer was prepared through an efficient one-pot method. The vitrimer possesses advanced recyclability, foamability, creep resistance and self-healing performance.
Construction of a competing endogenous RNA network to analyse glucose-6-phosphate dehydrogenase dysregulation in hepatocellular carcinoma
Authors: Wang Pengyu , Yang Xitong , Liu Dan , Yang Yunhui , Zhang Yuanyuan , Wang Guangming 
Published: June 2022

Abstract
Hepatocellular carcinoma (HCC) is a common malignant tumour with high rates of morbidity and mortality worldwide. Therefore, it is of great significance to find new molecular markers for HCC diagnosis and treatment. G6PD is known to be dysregulated in a variety of tumours. In addition, the ceRNA network plays a crucial role in the occurrence and development of HCC. However, the mechanism by which the ceRNA network regulates G6PD in HCC remains unclear. We used TCGA-LIHC data to analyse the possibility of using G6PD as an independent prognostic marker. Univariate Cox proportional hazards regression, multivariate Cox proportional hazards regression, and receiver operating characteristic curve analysis were used to analyse the influence of G6PD overexpression on the prognosis of HCC patients. We also analysed the biological function of G6PD, its effect on the immune microenvironment, and drug sensitivity. Finally, we constructed a ceRNA network of lncRNAs/miR-122-5p/G6PD to explore the regulatory mechanism of G6PD. G6PD was highly expressed in HCC, was related to pathological stage and poor prognosis, and could be used as an independent prognostic indicator of HCC. The expression of G6PD was closely related to the immune microenvironment of HCC. In addition, the expression of G6PD in HCC could be regulated by the ceRNA network. Therefore, G6PD can be used as an immunotherapy target to improve the survival and prognosis of HCC patients, and the ceRNA regulatory network of G6PD has potential diagnostic and therapeutic value for HCC.