bluuebunny/crossref_metadata_2025_split huggingface dataset:
Extracellular vesicles secreted by cumulus cells contain microRNAs that are potential regulatory factors of mouse oocyte developmental competence
Authors: Fiorentino Giulia , Merico Valeria , Zanoni Mario , Comincini Sergio , Sproviero Daisy , Garofalo Maria , Gagliardi Stella , Cereda Cristina , Lin Chih-Jen , Innocenti Federica , Taggi Marilena , Vaiarelli Alberto , Ubaldi Filippo Maria , Rienzi Laura , Cimadomo Danilo , Garagna Silvia , Zuccotti Maurizio 
Published: May 2024

Abstract
The role of cumulus cells (CCs) in the acquisition of oocyte developmental competence is not yet fully understood. In a previous study, we matured cumulus-denuded fully-grown mouse oocytes to metaphase II (MII) on a feeder layer of CCs (FL-CCs) isolated from developmentally competent (FL-SN-CCs) or incompetent (FL-NSN-CCs) SN (surrounded nucleolus) or NSN (not surrounding nucleolus) oocytes, respectively. We observed that oocytes cultured on the former could develop into blastocysts, while those matured on the latter arrested at the 2-cell stage. To investigate the CC factors contributing to oocyte developmental competence, here we focused on the CCs' release into the medium of extracellular vesicles (EVs) and on their miRNA content. We found that, during the 15-h transition to MII, both FL-SN-CCs and FL-NSN-CCs release EVs that can be detected, by confocal microscopy, inside the zona pellucida (ZP) or the ooplasm. The majority of EVs are &lt;200 nm in size, which is compatible with their ability to cross the ZP. Next-generation sequencing of the miRNome of FL-SN-CC versus FL-NSN-CC EVs highlighted 74 differentially expressed miRNAs, with 43 up- and 31 down-regulated. Although most of these miRNAs do not have known roles in the ovary, in silico functional analysis showed that seven of these miRNAs regulate 71 target genes with specific roles in meiosis resumption (N = 24), follicle growth (N = 23), fertilization (N = 1), and the acquisition of oocyte developmental competence (N = 23). Overall, our results indicate CC EVs as emerging candidates of the CC-to-oocyte communication axis and uncover a group of miRNAs as potential regulatory factors.
TEENA: an integrated web server for transposable element enrichment analysis in various model and non-model organisms
Authors: Li Yuzhuo , Lyu Renzhe , Chen Shuai , Wang Yejun , Sun Ming-an 
Published: May 2024

Abstract
Transposable elements (TEs) are abundant in the genomes of various eukaryote organisms. Increasing evidence suggests that TEs can play crucial regulatory roles—usually by creating cis-elements (e.g. enhancers and promoters) bound by distinct transcription factors (TFs). TE-derived cis-elements have gained unprecedented attentions recently, and one key step toward their understanding is to identify the enriched TEs in distinct genomic intervals (e.g. a set of enhancers or TF binding sites) as candidates for further study. Nevertheless, such analysis remains challenging for researchers unfamiliar with TEs or lack strong bioinformatic skills. Here, we present TEENA (Transposable Element ENrichment Analyzer) to streamline TE enrichment analysis in various organisms. It implements an optimized pipeline, hosts the genome/gene/TE annotations of almost one hundred species, and provides multiple parameters to enable its flexibility. Taking genomic interval data as the only user-supplied file, it can automatically retrieve the corresponding annotations and finish a routine analysis in a couple minutes. Multiple case studies demonstrate that it can produce highly reliable results matching previous knowledge. TEENA can be freely accessed at: https://sun-lab.yzu.edu.cn/TEENA. Due to its easy-to-use design, we expect it to facilitate the studies of the regulatory function of TEs in various model and non-model organisms.
Neural-net-based cell deconvolution from DNA methylation reveals tumor microenvironment associated with cancer prognosis
Authors: Yasumizu Yoshiaki , Hagiwara Masaki , Umezu Yuto , Fuji Hiroaki , Iwaisako Keiko , Asagiri Masataka , Uemoto Shinji , Nakamura Yamami , Thul Sophia , Ueyama Azumi , Yokoi Kazunori , Tanemura Atsushi , Nose Yohei , Saito Takuro , Wada Hisashi , Kakuda Mamoru , Kohara Masaharu , Nojima Satoshi , Morii Eiichi , Doki Yuichiro , Sakaguchi Shimon , Ohkura Naganari 
Published: May 2024

Abstract
DNA methylation is a pivotal epigenetic modification that defines cellular identity. While cell deconvolution utilizing this information is considered useful for clinical practice, current methods for deconvolution are limited in their accuracy and resolution. In this study, we collected DNA methylation data from 945 human samples derived from various tissues and tumor-infiltrating immune cells and trained a neural network model with them. The model, termed MEnet, predicted abundance of cell population together with the detailed immune cell status from bulk DNA methylation data, and showed consistency to those of flow cytometry and histochemistry. MEnet was superior to the existing methods in the accuracy, speed, and detectable cell diversity, and could be applicable for peripheral blood, tumors, cell-free DNA, and formalin-fixed paraffin-embedded sections. Furthermore, by applying MEnet to 72 intrahepatic cholangiocarcinoma samples, we identified immune cell profiles associated with cancer prognosis. We believe that cell deconvolution by MEnet has the potential for use in clinical settings.
Reducing Commercial Tobacco Sales to Youth On and Around California Tribal Reservations With a Reward and Reminder Retail Intervention
Authors: Kornacki Chase , Rodriguez Joseph , Rodriguez Justin , Calac Alec J , Calac Daniel , Lee Juliet P , Moore Roland S , Brucks Lisa , Jacques Isabella , Yang Maxine , Almodovar Veronica , Berber Samantha-Starr 
Published: May 2024

Abstract

Introduction
High prevalence of commercial tobacco product (CTP) use among American Indian and Alaska Native (AI/AN) youth is a public health crisis. A multi-level Tribal-community-based participatory research project under Tribal public health authority implemented a retailer-focused intervention to reduce AI/AN youth CTP use.

Aims and Methods
We sought resolutions in support of a retailer-focused CTP intervention from Tribal Nations organized by a Tribally directed research program. We identified tobacco retail outlets operating on and within five miles of nine Tribal reservations, and CTP products sold at these outlets. We conducted a four-wave Reward and Reminder intervention with apparent minor buyers. Clerks who complied with the law received a modest reward and commendation in social media posts to the local Tribal communities, while clerks who sold without age verification were reminded of the laws.

Results
Of 18 retail outlets selling CTP, eight sold e-cigarettes, and all sold combustible cigarettes. The Reward and Reminder intervention showed an approximate 25% reduction in sales of CTP to apparent minors, with a 33% baseline CTP sales rate without age verification and an 8% intervention CTP sales rate without age verification.

Conclusions
The intervention increased awareness of laws prohibiting CTP sales to minors and mandating age verification for young adults seeking to buy CTP. The intervention, which had support from all governing Tribal Nations, builds the evidence base of effective practices which Tribal public health authorities may utilize to reduce youth access to CTP on and around Tribal reservations.

Implications
Sovereign Tribes have authority over commercial businesses operating on their lands. Tobacco 21 laws aiming to restrict commercial tobacco availability to youth are supported by Tribes. A retailer intervention in which apparent minors attempt commercial tobacco purchases can offer accountability feedback to retailers both on and near Tribal reservations. Obtaining Tribal support and publicizing the interventions helps mobilize Tribal communities to support commercial tobacco prevention and promote healthy youth.
Classifying LEO satellite platforms with boosted decision trees
Authors: Shrive Billy , Pollacco Don , Chote Paul , Blake James A , Cooke Benjamin F , McCormac James , West Richard , Airey Robert , MacManus Alex , Allen Phineas 
Published: May 2024

Abstract
As the cost of reaching LEO (low Earth orbit) has diminished we expect, over the next decade, an almost exponential increase in the numbers of LEO spacecraft from established and potentially new agents. Remote characterization of these and the increasing numbers of decommissioned/debris satellites are thus becoming more important, along with identifying unannounced changes in megaconstellations. In this paper we examine the light curves of known LEO platforms with a boosted tree algorithm in order to determine whether spacecraft properties were discernible. A priori we expected little correlation as we expected the large variations in sight-line geometries would mask signs from the spacecraft. Using large numbers of light curves from the MMT-9 data base, we find that this is not the case and most platforms are statistically identifiable in most sight-lines and tentatively associate this correlation with the differences and similarities between downward facing instruments. Pairs of satellite platforms can be distinguished 86.13 per cent ($N=15\, 600$) of the time using this method. Evolutionary changes to the Starlink satellite platform are also distinguished.
Trade unions and the partisan preferences of their members: Sweden 1986–2021
Authors: Ray Ari A , Pontusson Jonas G 
Published: May 2024

Abstract
Focusing on the effects of union membership on partisan preferences, this article explores how changes in Swedish industrial relations and trade-union politics have affected electoral support for Left parties since the mid-1980s. Our analysis shows that unionization among blue-collar workers has declined sharply since the mid-1990 and that this development has contributed to the decline of electoral support for the Social Democrats and for the Swedish Left as a whole. In addition, we find that the association between union membership and voting for Left parties has declined among white-collar employees without tertiary education as well as blue-collar workers over the same period. We argue that sectoral blue-collar and white-collar unions alike have responded to membership losses and intensified competition between unions by engaging in practices that render the partisan preferences of union members less distinctive than what they used to be (less Left-leaning relative to non-unionized counterparts).
‘The Needs of New Communities’: Social Development, the New Towns, and the Case of Milton Keynes, c. 1962–87
Authors: Fair Alistair 
Published: May 2024

Abstract
This article contributes to the emerging history of ‘community’ in post-war Britain by considering what was known as ‘social development’ in Britain’s new towns, with particular reference to Milton Keynes between the late 1960s and the early 1980s. This article traces the roots of social development in the activities and ideas of the voluntary sector during the 1920s and 1930s and notes how they were co-opted by the state during the 1940s and 1950s. The ‘mark 1’ new towns of that period in some cases took steps to promote social development, understood in terms of an active community life and civic engagement, but the practice was particularly promoted in 1967 by a government committee, which called for new towns to be based on clear social plans as well as physical land-use proposals. In making this argument, the committee reflected a wider train of thought, which had already informed the likes of the Parker Morris report on housing; in essence, they scaled up Parker Morris’ approach from the home to the urban level. These ideas were especially influential in Milton Keynes, whose planners and administrators took a broad, even philosophical view of their role. This article considers the extent to which social development was as much about individual aspiration and opportunity as communal activity and also explores the role of the voluntary sector. In so doing, it makes observations about the nature of the post-war state as an enabler, rather than a universal provider.
RPGRIP1L as a new biomarker for prognosis and tumor immune of breast cancer
Authors: Yi Jianing , Liu Luyao , Chen Yongzhi , Ding Tianjinhao , Fan Peizhi , Yu Jie , Zeng Jie 
Published: May 2024

AbstractThe Retinitis pigmentosa GTPase regulator interacting protein 1‐like (RPGRIP1L) gene encodes an important protein that performs various physiological functions. Variants of RPGRIP1L are related to a number of diseases. However, it is currently unknown whether RPGRIP1L is correlated with breast invasive carcinoma (BRCA). In BRCA tissue specimens, the expression of RPGRIP1L was found to be elevated in comparison to its levels in normal breast tissue. A notable decline in survival rates was associated with patients exhibiting heightened RPGRIP1L gene expression. Consistent with these findings, our data also show the above results. Furthermore, elevated expression of RPGRIP1L corresponded with a spectrum of unfavorable clinicopathological features, including the presence of human epidermal growth factor receptor 2 (HER2) positive, estrogen receptor (ER) positive, over 60 years old, T2, N0, and N3. At the same time, our research indicated that 50 genes and 15 proteins were positively related to RPGRIP1L, and that these proteins and genes were mostly involved in T cell proliferation, immune response, cytokine activity, and metabolic regulation. In addition, in the present study, there was a significant correlation between RPGRIP1L expression and immune cell infiltration. Finally, we found that four Chemicals could downregulate the expression of RPGRIP1L. Altogether, our results strongly indicated that RPGRIP1L might serve as a new prognostic biomarker for BRCA.
Impact of heparanase‐2 (Hpa2) on cancer and inflammation: Advances and paradigms
Authors: Vlodavsky Israel , Hilwi Maram , Kayal Yasmin , Soboh Soaad , Ilan Neta 
Published: May 2024

AbstractHPSE2, the gene‐encoding heparanase 2 (Hpa2), is mutated in urofacial syndrome (UFS), a rare autosomal recessive congenital disease attributed to peripheral neuropathy. Hpa2 lacks intrinsic heparan sulfate (HS)‐degrading activity, the hallmark of heparanase (Hpa1), yet it exhibits a high affinity toward HS, thereby inhibiting Hpa1 enzymatic activity. Hpa2 regulates selected genes that promote normal differentiation, tissue homeostasis, and endoplasmic reticulum (ER) stress, resulting in antitumor, antiangiogenic, and anti‐inflammatory effects. Importantly, stress conditions induce the expression of Hpa2, thus establishing a feedback loop, where Hpa2 enhances ER stress which, in turn, induces Hpa2 expression. In most cases, cancer patients who retain high levels of Hpa2 survive longer than patients bearing Hpa2‐low tumors. Experimentally, overexpression of Hpa2 attenuates the growth of tumor xenografts, whereas Hpa2 gene silencing results in aggressive tumors. Studies applying conditional Hpa2 knockout (cHpa2‐KO) mice revealed an essential involvement of Hpa2 contributed by the host in protecting against cancer and inflammation. This was best reflected by the distorted morphology of the Hpa2‐null pancreas, including massive infiltration of immune cells, acinar to adipocyte trans‐differentiation, and acinar to ductal metaplasia. Moreover, orthotopic inoculation of pancreatic ductal adenocarcinoma (PDAC) cells into the pancreas of Hpa2‐null vs. wild‐type mice yielded tumors that were by far more aggressive. Likewise, intravenous inoculation of cancer cells into cHpa2‐KO mice resulted in a dramatically increased lung colonization reflecting the involvement of Hpa2 in restricting the formation of a premetastatic niche. Elucidating Hpa2 structure–activity‐relationships is expected to support the development of Hpa2‐based therapies against cancer and inflammation.
Interaction of age and CYP2C19 genotypes on voriconazole steady-state trough concentration in Chinese patients
Authors: Du Yin-Xiao , Zhu Ying-Xia , Li Liang , Yang Jing , Chen Xiao-Ping 
Published: May 2024

Objectives
Both age and CYP2C19 genotypes affect voriconazole plasma concentration; the interaction of age and CYP2C19 genotypes on voriconazole plasma concentration remains unknown. This study aims to investigate the combined effects of age and CYP2C19 genotypes on voriconazole plasma concentration in Chinese patients.

Methods
A total of 480 patients who received voriconazole treatment were recruited. CYP2C19*2 (rs4244285) and CYP2C19*3 (rs4986893) polymorphisms were genotyped. Patients were divided into the young and the elderly groups by age of 60 years old. Influence of CYP2C19 genotype on steady-state trough concentration (Css-min) in overall patients and in age subgroups was analyzed.

Results
Voriconazole Css-min correlated positively with age, and mean voriconazole Css-min was significantly higher in the elderly group (P < 0.001). CYP2C19 poor metabolizers showed significantly increased mean voriconazole Css-min in the young but not the elderly group. The percentage of patients with subtherapeutic voriconazole Css-min (<1.0 mg/l) was higher in the young group and that of supratherapeutic voriconazole Css-min (>5.5 mg/l) was higher in the elderly patients. When the average Css-min in the CYP2C19 normal metabolizer genotype was regarded as a reference, CYP2C19 genotypes showed greater impact on voriconazole Css-min in the young group, while the influence of age on voriconazole Css-min exceeded CYP2C19 genotypes in the elderly.

Conclusion

CYP2C19 genotypes affects voriconazole exposure is age dependent. Influence of CYP2C19 poor metabolizer genotype on increased voriconazoleexposure is prominent in the young, while age is a more important determinant factor for increased voriconazole exposure in the elderly patients.
Careful Where You Cut: Strategies for Successful Nerve-preserving Mastectomy
Authors: Coopey Suzanne , Keleher Angela , Daniele Karla , Peled Anne Warren , Gomez Janette , Julian Thomas , Moreira Andrea A. 
Published: May 2024

Summary:
Breast neurotization represents an evolving technique that is not widely practiced in most centers specializing in breast cancer treatment. Recognizing the limited educational resources available for breast and plastic surgeons concerning mastectomy techniques that emphasize nerve preservation, our study sought to bridge this gap. Specifically, we aimed to provide a comprehensive exploration of the surgical applied anatomy of breast sensory innervation and a detailed, step-by-step guide for incorporating nerve-sparing mastectomy and breast neurotization into clinical practice. The significance of this work lies in its potential to enhance the understanding and implementation of nerve-preserving techniques in mastectomy procedures, contributing to improved patient outcomes and quality of life post surgery. We hope that by familiarizing breast and reconstructive surgeons with this procedure, we can gain momentum in our research efforts and ultimately enhance the care provided to mastectomy patients.
Research on the academic thought of distinguished veteran doctors of traditional Chinese medicine based on Mendelian randomization: a case study of the causation between Sjögren’s syndrome and rheumatoid arthritis
Authors: Li Haotian , Hu Sile , Xia Congmin , Liu Yanjun 
Published: May 2024

Aim:
This study investigated the causation between Sjögren’s syndrome (SS) and rheumatoid arthritis (RA) based on Mendelian randomization (MR), with the purpose of promoting research on the academic thought of distinguished veteran doctors of traditional Chinese medicine (TCM) via bioinformatics with information technology and providing new basis for better inheriting and carrying forward the valuable experience of a National Master of TCM, Zhizheng Lu.

Methods:
The causation between RA and SS in TCM was inferred from the perspective of coordination between dryness and dampness. For further assessment, MR was performed based on the summary data of genome-wide association studies (GWAS), with genetic loci closely related to SS(instrumental variables (IVs)), RA(research outcome), inverse-variance weighted (IVW) and MR-Egger regression and weighted median (WME) ( main MR methods). Heterogeneity was evaluated by Cochran Q test, pleiotropy by MR-Egger regression, and robustness by the Leave-One-Out method.

Results:
Except for MR-Egger, all other methods showed a clear statistical significance in the association between SS and RA (P<0.05).

Conclusion:
This study, based on the academic thought of distinguished TCM veteran doctor and the thought “moistening dryness” of National Master of TCM, Zhizheng Lu, speculated that there may be a potential association between SS and RA. MR results demonstrated the clear genetic causation between SS and RA, and the guiding role of the academic thought of distinguished TCM veteran doctor in clinical practice genetically.
Associations of serum glucocorticoid levels on hypertension and blood pressure-related indicators: a nested case–control study in rural China
Authors: Chen Zhiwei , Wei Dandan , Zhao Mengzhen , Shi Jiayu , Ma Cuicui , Zhang Caiyun , Lin Hualiang , Huo Wenqian , Wang Chongjian , Fan Caini , Mao Zhenxing 
Published: May 2024

Background:
The relationship between glucocorticoids and hypertension has shown inconsistent findings in previous studies. To address this, our study employed a nested case–control design in rural areas to further investigate the association between serum glucocorticoid levels and hypertension, and blood pressure-related indicators.

Methods:
This study employed a nested case–control design, involving 560 pairs of hypertensive cases and matched controls. The concentrations of serum cortisol (F), cortisone (E) and 11-deoxycortisol (S) were determined using liquid chromatography-tandem mass spectrometry. We employed various methods, including generalized linear model (GLM), conditional logistic regression model, restricted cubic spline regression, subgroup analysis, interaction, and joint effects, with adjustments for multiple covariates to analyze the relationships between glucocorticoids, hypertension, and blood pressure-related indicators.

Results:
After multivariable adjustments, ln-F, ln-F/E, and ln-S were positively associated with SBP, DBP, pulse pressure (PP), and mean arterial pressure (MAP), while ln-E was negatively associated with DBP and MAP (P < 0.05). Interestingly, ln-S showed no statistically significant association with hypertension prevalence (P > 0.05), whereas ln-F and ln-F/E were positively associated with it (P < 0.05). The adjusted odds ratios (ORs) and 95% confidence intervals (CIs) were 1.153 (1.011–1.315) for ln-F and 2.072 (1.622–2.645) for ln-F/E, respectively. In contrast, ln-E exhibited a negative association with hypertension prevalence (adjusted OR = 0.837, 95% CI 0.714–0.982). Moreover, a significant association was observed between the combined use of high-dose F/E and high-dose S with hypertension prevalence (adjusted OR = 3.273, 95% CI 2.013–5.321). Blood pressure indicators and hypertension prevalence significantly increased with elevated serum F and F/E concentrations (P < 0.05). Interaction analysis further revealed that among women, the positive association between F/E and hypertension prevalence was more pronounced than in men (P < 0.05), and S exhibited a more significant positive association with hypertension prevalence in the overweight population (P < 0.05).

Conclusion:
Serum F/E and S levels demonstrated positive associations with hypertension and blood pressure-related indicators, and their combined influence exhibited a synergistic effect on hypertension. Notably, F, F/E, and S were associated with heightened hypertension risk, warranting particular attention in women and overweight populations.