bluuebunny/crossref_metadata_2025_split huggingface dataset:
Malignant Progression of an Ancestral Bone Marrow Clone Harboring aCIC-NUTM2AFusion in Isolated Myeloid Sarcoma
Authors: Kamens Jennifer L. , Dang Jinjun , Shaw Timothy I. , Gout Alexander M. , Newman Scott , Hagiwara Kohei , Smith Amelia M.R. , Obermayer Alyssa N. , Aldridge Sarah , Ma Jing , Zhang Yang , Wu Gang , Leventaki Vasiliki , Santiago Teresa , Raimondi Susana , Nakitandwe Joy , Pappo Alberto , Li Chunliang , Zhang Jinghui , Gruber Tanja A. 
Published: January 2023

AbstractMyeloid sarcoma is a rare condition consisting of extramedullary myeloid blasts found in association with acute myeloid leukemia or, in the absence of bone marrow involvement. We identified an infant with isolated myeloid sarcoma whose bone marrow was negative for involvement by flow cytometry. Sequencing revealed the fusion oncogene CIC-NUTM2A and identified the sarcoma to be clonally evolved from the bone marrow, which carried the fusion despite the absence of pathology. Murine modeling confirmed the ability of the fusion to transform hematopoietic cells and identified receptor tyrosine kinase (RTK) signaling activation consistent with disruption of the CIC transcriptional repressor. These findings extend the definition of CIC-rearranged malignancies to include hematologic disease, provide insight into the mechanism of oncogenesis, and demonstrate the importance of molecular analysis and tracking of bone marrow involvement over the course of treatment in myeloid sarcoma, including patients that lack flow cytometric evidence of leukemia at diagnosis.Implications:This study illustrates molecular involvement of phenotypically normal bone marrow in myeloid sarcoma, which has significant implications in clinical care. Further, it extends the definition of CIC-rearrangements to include hematologic malignancies and shows evidence of RTK activation that may be exploited therapeutically in cancer(s) driven by these fusions.
Toll-Like Receptor 4-Dependent Platelet-Related Thrombosis in SARS-CoV-2 Infection
Authors: Carnevale Roberto , Cammisotto Vittoria , Bartimoccia Simona , Nocella Cristina , Castellani Valentina , Bufano Marianna , Loffredo Lorenzo , Sciarretta Sebastiano , Frati Giacomo , Coluccia Antonio , Silvestri Romano , Ceccarelli Giancarlo , Oliva Alessandra , Venditti Mario , Pugliese Francesco , Maria Mastroianni Claudio , Turriziani Ombretta , Leopizzi Martina , D’Amati Giulia , Pignatelli Pasquale , Violi Francesco 
Published: January 2023

Background:
SARS-CoV-2 is associated with an increased risk of venous and arterial thrombosis, but the underlying mechanism is still unclear.

Methods:

We performed a cross-sectional analysis of platelet function in 25 SARS-CoV-2 and 10 healthy subjects by measuring Nox2 (NADPH oxidase 2)-derived oxidative stress and thromboxane B
2
, and investigated if administration of monoclonal antibodies against the S protein (Spike protein) of SARS-CoV-2 affects platelet activation. Furthermore, we investigated in vitro if the S protein of SARS-CoV-2 or plasma from SARS-CoV-2 enhanced platelet activation.

Results:

Ex vivo studies showed enhanced platelet Nox2-derived oxidative stress and thromboxane B
2
biosynthesis and under laminar flow platelet-dependent thrombus growth in SARS-CoV-2 compared with controls; both effects were lowered by Nox2 and TLR4 (Toll-like receptor 4) inhibitors. Two hours after administration of monoclonal antibodies, a significant inhibition of platelet activation was observed in patients with SARS-CoV-2 compared with untreated ones. In vitro study showed that S protein per se did not elicit platelet activation but amplified the platelet response to subthreshold concentrations of agonists and functionally interacted with platelet TLR4. A docking simulation analysis suggested that TLR4 binds to S protein via three receptor-binding domains; furthermore, immunoprecipitation and immunofluorescence showed S protein-TLR4 colocalization in platelets from SARS-CoV-2. Plasma from patients with SARS-CoV-2 enhanced platelet activation and Nox2-related oxidative stress, an effect blunted by TNF (tumor necrosis factor) α inhibitor; this effect was recapitulated by an in vitro study documenting that TNFα alone promoted platelet activation and amplified the platelet response to S protein via p47phox (phagocyte oxidase) upregulation.

Conclusions:
The study identifies 2 TLR4-dependent and independent pathways promoting platelet-dependent thrombus growth and suggests inhibition of TLR4. or p47phox as a tool to counteract thrombosis in SARS-CoV-2.
The Emergence of the Bissau-Guinean Fula Cernos
Authors: Boiro Hamadou , Einarsdóttir Jónína 
Published: January 2023

Abstract
International agencies and non-governmental organisations classify Quranic schoolboys who beg on behalf of their teachers as victims of child trafficking. The aim here is to understand why no Bissau-Guinean Fula religious leader, referred to as cerno, has been sentenced to prison, despite accusations of child trafficking. The findings show that community members hold religious leaders in high esteem for their role within the spiritual, educative, and social spheres. Community members, entrenched in complex discriminatory relations within their ethnic group and beyond, perceive them as their saviours, while politicians, high-ranking officers and traders compete for their endorsement. Criminalising the cernos is unsuccessful; to safeguard the interests of children, the children and their community members, including the cernos, should be put at the heart of the safeguarding measures. Despite complex layers of coloniality, the religious leaders are the masters of the game, and their imprisonment is challenging.
Integration and Special Rights
Authors: Malloy Tove H. 
Published: January 2023

Abstract
For almost 25 years, the Council of Europe and the Danish authorities have entertained a fruitless and stalled dialogue on an option to apply the Council’s Framework Convention for the Protection of National Minorities in the societal integration of Greenlanders living in Denmark. So far, the Danish authorities have not been willing to award the Greenlanders any special rights citing their individual and universal rights to non-discrimination and equal civil rights as sufficient for integration. The refusal is based on the authorities’ specific interpretation of the status of Greenland and Greenlanders under international conventions. A review of the dialogue from 1999 till today set against a short Nordic-Canadian perspective reveals that a combination of special rights and universal equal civil rights puts the view of the Danish authorities in question. This seems, therefore, to indicate an unwillingness on behalf of the authorities to consider feasible alternatives.
Macao’s Split Labour Market
Authors: Kerswell Timothy , Hang Leong Sin , Chan William 
Published: January 2023

Abstract
Edna Bonacich’s split labour market states that socio-political factors generate differential outcomes for workers in a region, generally as the result of ethnic antagonism. This ethnic antagonism, Bonacich argues, does not require open violence or even verbal confrontation but can operate through exclusion movements and “caste” systems. In this paper, we use Bonacich’s framework to analyse the production of a split labour market in the Macao, Special Administrative Region of China. Macao depends on an abundant supply of low-skilled migrant workers to remunerate the workforce. While many migrant workers are foreigners, most are ‘internal’ migrants from Mainland China, meaning that a conventional explanation of ethnic differences is insufficient. Bonacich had observed that “exclusion attempts and caste-like arrangements are found among national groupings within a racial category” giving the example of ‘whites’ in the United States excluding other ‘whites’ from different parts of Europe. However, Macao as a part of China constitutes a unique example in that an exclusion attempt and caste-like arrangement is to be found within the same national grouping of the same racial category in the same country. As this research considers how ethnic and quasi-ethnic differences are produced and sustained in Macao through government policy; social attitudes and the social practices of workers and businesses, we find that permanent Macao id card holders, which gives out numerous benefits and rights, is as a form of exclusion movement. Moreover, local workers act as a labour aristocracy: they extract concessions from businesses and suppress migrant workers economically, politically and socially. Edna Bonacich’s split labour market helps explain how a labour aristocracy is maintained subtly at the interest of local workers through concessions from the businesses.
Breaching Protocol and Flouting Norms on the European Parliament Floor
Authors: Bendazzoli Claudio 
Published: January 2023

Abstract
In the plenary sittings of the European Parliament (EP), institutional discourse is regulated by pre-established procedures and multilingualism is guaranteed thanks to simultaneous interpreting into each official EU language. In this setting, political leaders speak in their native language when addressing other Members of the EP and are allowed to hold the floor for a specific amount of time. What happens when such rules and procedures are disrupted? This study analyses a particular breach of protocol, which triggered a number of reactions at different levels of re-contextualisation. These are discussed by considering both the micro- and the macro-context, including the interpreters’ output in 21 different languages along with the official verbatim report of proceedings and its translation into English. The results point to variability in terms of editing standards in the verbatim reports and professional practices among the interpreting booths, with potential differences in accessibility by target recipients.
CYGNSS Storm-Centric Tropical Cyclone Gridded Wind Speed Product
Authors: Mayers David R. , Ruf Christopher S. , Warnock April M. 
Published: January 2023

Abstract
The Cyclone Global Navigation Satellite System (CYGNSS) mission has generated several new ocean surface data products. Because of its high overpass rate and ability to measure surface wind speeds through weather, these data products are typically higher temporal resolution than traditional satellite tropical cyclone (TC) data products. However, the nature of the Global Navigation Satellite Systems reflectometry (GNSS-R) signal, which is essentially a single pixelwide measurement along the CYGNSS specular point (SP) track on the ground, necessitates aggregating the wind speed data over a period of time to accurately characterize TCs in terms of intensity and structure. The standard CYGNSS level 3 (L3) wind products are averaged over 1 h, which typically is not sufficient to produce an accurate characterization. A new L3 storm-centric gridded (SCG) wind speed product is presented here. It has been developed to improve upon the standard L3 algorithm for the purpose of providing better characterization of TC wind fields over their storm life cycle. This paper describes the L3 SCG algorithm, provides examples of L3 SCG wind fields, and discusses the potential uses and limitations of the new data product.
Review: mountain lakes as freshwater resources at risk from chemical pollution
Authors: Machate Oliver , Schmeller Dirk S. , Schulze Tobias , Brack Werner 
Published: January 2023

AbstractBackgroundChemical pollution forms a severe threat for human and environmental health. While the risks for European lowland water bodies are well known, there is little knowledge on remote aquatic ecosystems and particularly mountain lakes, despite their importance for the provision of freshwater. Here, we critically review the current knowledge on the exposure and risk by chemical pollution for mountain lakes and present a tiered approach on how to advance effectively our understanding in the future.ResultsGenerally, pollutant monitoring data are currently incomplete, with many regions and substances having been only poorly investigated. More reliable data exist only for persistent organic pollutants (POPs). However, there is increasing evidence that even remote mountain lakes are exposed to a wide range of organic pollutants. Among them potent pesticides currently used in agricultural and biocidal applications, such as diazinon and permethrin. The exposure of mountain lakes to pollutants follows a complex pattern. Pollutants are introduced into mountain lakes via the atmospheric deposition and run-off from the watershed, but also local sources, like tourism and pastoralism. Our risk assessment and recent biomonitoring studies suggest that there are widespread chronic toxic risks on crustacean in mountain ranges. If mountain ranges are exposed to tourism and pastoralism, even acute toxic effects on crustacean are possible. Thereby, the vulnerability of mountain lakes to toxic effects has to be expected to be particularly high due to the harsh environmental conditions at high altitudes, the organism’s traits, the insular position of mountain lakes and a lower species richness with increasing altitudes. Furthermore, there is little knowledge on the biological processes leading to the degradation of chemical pollutants under the environmental and ecological conditions of mountain ecosystems.ConclusionWhile the exposure and sensitivity of mountain aquatic ecosystems is currently poorly investigated, the existing data suggest that it is very likely that also water bodies as remote as mountain lakes do suffer from pollution-induced toxicity. To verify this suggestion and expand the existing knowledge, it is necessary that future studies combine a more holistic pollution monitoring with exposure modelling and links to biological effects. Only then will it be possible to obtain a more reliable understanding of the impact of chemical pollution on aquatic mountain ecosystems and to protect these fragile ecosystems.
Novel delivery system with a dual–trigger release of savory essential oil by mesoporous silica nanospheres and its possible targets in leukemia cancer cells: in vitro study
Authors: AbouAitah Khaled , Hassan Heba A. , Ammar Naglaa M. , Abou Baker Doha H. , Higazy Imane M. , Shaker Olfat G. , Elsayed Ahmed A. A. , Hassan Abeer M. E. 
Published: January 2023

Abstract
Introduction
Essential oils (EOs) are complex structures and possess several pharmacological effects. Nanomedicine offers a solution for their major limitations, including poor solubility, volatility, and non–controlled release, preventing their clinical use.

Methods
Here, we developed a novel delivery system by nanoformulations that were prepared by impregnating savory essential oil (SA) into mesoporous silica nanoparticles (MSNs). The nanoformulations were characterized and examined for their anticancer activities on cancer cells (HepG2 liver and HL60 leukemia cells) and MRC5 normal cells. We further tested the mechanisms of action and possible molecular targets against HL60 cells.

Results
The results demonstrated that SA was governed by nanoformulations under the dual–trigger release of pH/glutathione, and it typically fit the Korsmeyer–Peppas kinetic model. The nanoformulations enhanced the anticancer effect against HepG2 cells and HL60 cells compared to SA but were less cytotoxic to MRC5 normal cells and regulated various molecular pathways of apoptosis. Most importantly, new results were obtained on the genetic regulation principle through the high inhibition of long noncoding RNAs (HOTAIR, HULC, CCAT1, and H19) and matrix metalloproteinases (MMP–2 and MMP–9), providing a novel leukemia target.

Conclusions
These results suggest potential impacts for nanoformulations composed of SA with a sustained release pattern controlled by dual–trigger release of pH/GSH that enhanced anticancer cells. This approach may offer a new route for using EOs as new targets for cancers and open the door for deep preclinical investigations.
Predicting the impact of genotype-by-genotype interaction on the purebred–crossbred genetic correlation from phenotype and genotype marker data of parental lines
Authors: Duenk Pascal , Wientjes Yvonne C. J. , Bijma Piter , Iversen Maja W. , Lopes Marcos S. , Calus Mario P. L. 
Published: January 2023

Abstract
Background
The genetic correlation between purebred (PB) and crossbred (CB) performances ($${r}_{pc}$$

r

pc

) partially determines the response in CB when selection is on PB performance in the parental lines. An earlier study has derived expressions for an upper and lower bound of $${r}_{pc}$$

r

pc

, using the variance components of the parental purebred lines, including e.g. the additive genetic variance in the sire line for the trait expressed in one of the dam lines. How to estimate these variance components is not obvious, because animals from one parental line do not have phenotypes for the trait expressed in the other line. Thus, the aim of this study was to propose and compare three methods for approximating the required variance components. The first two methods are based on (co)variances of genomic estimated breeding values (GEBV) in the line of interest, either accounting for shrinkage (VCGEBV-S) or not (VCGEBV). The third method uses restricted maximum likelihood (REML) estimates directly from univariate and bivariate analyses (VCREML) by ignoring that the variance components should refer to the line of interest, rather than to the line in which the trait is expressed. We validated these methods by comparing the resulting predicted bounds of $${r}_{pc}$$

r

pc

with the $${r}_{pc}$$

r

pc

estimated from PB and CB data for five traits in a three-way cross in pigs.

Results
With both VCGEBV and VCREML, the estimated $${r}_{pc}$$

r

pc

(plus or minus one standard error) was between the upper and lower bounds in 14 out of 15 cases. However, the range between the bounds was much smaller with VCREML (0.15–0.22) than with VCGEBV (0.44–0.57). With VCGEBV-S, the estimated $${r}_{pc}$$

r

pc

was between the upper and lower bounds in only six out of 15 cases, with the bounds ranging from 0.21 to 0.44.

Conclusions
We conclude that using REML estimates of variance components within and between parental lines to predict the bounds of $${r}_{pc}$$

r

pc

resulted in better predictions than methods based on GEBV. Thus, we recommend that the studies that estimate $${r}_{pc}$$

r

pc

with genotype data also report estimated genetic variance components within and between the parental lines.
Reporter gene assays and chromatin-level assays define substantially non-overlapping sets of enhancer sequences
Authors: Lindhorst Daniel , Halfon Marc S. 
Published: January 2023

Abstract
Background
Transcriptional enhancers are essential for gene regulation, but how these regulatory elements are best defined remains a significant unresolved question. Traditional definitions rely on activity-based criteria such as reporter gene assays, while more recently, biochemical assays based on chromatin-level phenomena such as chromatin accessibility, histone modifications, and localized RNA transcription have gained prominence.

Results
We examine here whether these two types of definitions, activity-based and chromatin-based, effectively identify the same sets of sequences. We find that, concerningly, the overlap between the two groups is strikingly limited. Few of the data sets we compared displayed statistically significant overlap, and even for those, the degree of overlap was typically small (below 40% of sequences). Moreover, a substantial batch effect was observed in which experiment set rather than experimental method was a primary driver of whether or not chromatin-defined enhancers showed a strong overlap with reporter gene-defined enhancers.

Conclusions
Our results raise important questions as to the appropriateness of both old and new enhancer definitions, and suggest that new approaches are required to reconcile the poor agreement among existing methods for defining enhancers.
Genome-wide identification and systematic analysis of the HD-Zip gene family and its roles in response to pH in Panax ginseng Meyer
Authors: Li Li , Lv Boxin , Zang Kaiyou , Jiang Yue , Wang Chaofan , Wang Yanfang , Wang Kangyu , Zhao Mingzhu , Chen Ping , Lei Jun , Wang Yi , Zhang Meiping 
Published: January 2023

Abstract
Background
Ginseng, Panax ginseng Meyer, is a traditional herb that is immensely valuable both for human health and medicine and for medicinal plant research. The homeodomain leucine zipper (HD-Zip) gene family is a plant-specific transcription factor gene family indispensable in the regulation of plant growth and development and plant response to environmental stresses.

Results
We identified 117 HD-Zip transcripts from the transcriptome of ginseng cv. Damaya that is widely grown in Jilin, China where approximately 60% of the world’s ginseng is produced. These transcripts were positioned to 64 loci in the ginseng genome and the ginseng HD-Zip genes were designated as PgHDZ genes. Identification of 82 and 83 PgHDZ genes from the ginseng acc. IR826 and cv. ChP genomes, respectively, indicated that the PgHDZ gene family consists of approximately 80 PgHDZ genes. Phylogenetic analysis showed that the gene family originated after Angiosperm split from Gymnosperm and before Dicots split from Monocots. The gene family was classified into four subfamilies and has dramatically diverged not only in gene structure and functionality but also in expression characteristics. Nevertheless, co-expression network analysis showed that the activities of the genes in the family remain significantly correlated, suggesting their functional correlation. Five hub PgHDZ genes were identified that might have central functions in ginseng biological processes and four of them were shown to be actively involved in plant response to environmental pH stress in ginseng.

Conclusions
The PgHDZ gene family was identified from ginseng and analyzed systematically. Five potential hub genes were identified and four of them were shown to be involved in ginseng response to environmental pH stress. The results provide new insights into the characteristics, diversity, evolution, and functionality of the PgHDZ gene family in ginseng and lay a foundation for comprehensive research of the gene family in plants.