bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unravelling horizontal direct effect in EU law: the case of the fundamental right to paid annual leave between ‘myth’ and ‘practice’
Authors: Cecchetti Lorenzo 
Published: December 2023

Abstract
It is rather trendy to talk about the ‘horizontal effect’ of fundamental rights in a society where the dividing line between public and private power is increasingly blurred. However, as soon as one tries to define the exact meaning of horizontal effect and its conditions, several issues swiftly arise. This article explores the past, the present, and the future of the horizontal direct effect in the European Union (EU) legal order, by focusing on the application of this doctrine to the fundamental labour rights today protected in the Charter of fundamental rights. Most notably, with the approaching of the fifth birthday of Bauer and Max-Planck, by looking at the case of the fundamental right to paid annual leave under Article 31(2) of the Charter, this article aims at unravelling the actual meaning of the conditions for the horizontal direct effect of the EU fundamental rights and the actual perimeter of this direct effect. Although the effectiveness of minimum labour rights mandatorily enhanced by this case law should be welcomed, it is argued that the doctrine of the horizontal direct effect of EU fundamental rights seems still stuck between being a proper constitutional doctrine and a mere type of direct effect. It is also claimed, first, that horizontal direct effect is not a unitary phenomenon in EU law. In spite of the continuity in the ECJ’s technical reasoning, there is indeed a striking contrast between the language of ‘perfect equalisation’ of the Charter to the treaties and its actual approach to the assessment of the horizontal direct effect of fundamental (labour) rights. The ECJ’s case law analysis on the fundamental right to paid annual leave will prove this point. Secondly, it is suggested that horizontal direct effect can be defined as a sui generis, on-call, subsidiary, corollary, and ‘amputee’ doctrine, and we will offer some considerations on each of these features by reference to the Court’s practice under investigation. Thirdly, we suggest that the horizontal direct effect of fundamental (labour) rights relies more on the history and trajectory of the EU regulation of that specific right in the EU legal order rather than on the wording of the Charter’s provision or other technicalities.
The species problem in Artemia Leach, 1819 (Crustacea: Anostraca), a genus with sexual species and obligate parthenogenetic lineages
Authors: Asem Alireza , Gajardo Gonzalo , Hontoria Francisco , Yang Chaojie , Shen Chun-Yang , Rastegar-Pouyani Nasrullah , Padhye Sameer M , Sorgeloos Patrick 
Published: December 2023

Abstract
Parthenogenesis is an asexual reproduction mode characterized by the development of a female oocyte without fertilization. From an evolutionary perspective, parthenogenesis seems less successful than the predominant sexual mode, though there are groups in which both reproductive types exist, an example of which is the genus Artemia Leach, 1819. This salt-tolerant crustacean inhabiting hypersaline environments contains regionally endemic sexual species and obligate parthenogenetic groups with different ploidy levels, collectively referred to as Artemia parthenogenetica. Here, we discuss the difficulties of using a common species concept in Artemia Leach, 1819. While sexual species are widespread and fit the Biological Species Concept (BSC), which emphasizes reproductive isolation to maintain species genetic integrity or cohesiveness, it does not apply to uniparental organisms originating from sexual species with major meiotic changes. We show that different ploidy levels of parthenogenetic Artemia groups with uniform nuclear gene pools are maternally independent genetic entities (or cohesive), collectively and wrongly referred to as Artemia parthenogenetica. Thus, we conclude that ‘Artemia parthenogenetica’ is an invalid nominal specific name. Additionally, parthenogenetic Artemia groups cannot be considered a form of Artemia species (A. urmiana and/or A. sinica). In conclusion, we recommend using the term ‘parthenogenetic lineage(s)’ instead of ‘parthenogenetic population(s)’ to describe asexual Artemia group(s), because in modern population genetics and systematics, the term ‘population’ refers to interbreeding individuals with sexual reproduction. Furthermore, it clarifies that parthenogenetic lineages of Artemia are native to Mediterranean biodiversity.
68Ga-Citrate PET/CT Imaging in the Diagnosis of Skull Base Osteomyelitis and Its Usefulness in the Assessment of Treatment Response
Authors: Johnson Hanna Elizabeth , Sunny Saumya Sara , Hephzibah Julie , Thomas Regi , Sundaresan Rajan 
Published: December 2023

Purpose

68Ga-citrate PET/CT imaging in the diagnosis of skull base osteomyelitis (SBO) and its usefulness in the assessment of treatment response.

Methods
Eighteen patients underwent 68Ga-citrate PET/CT scans for suspected SBO for diagnosis/assessment of treatment response.

Results
Of 18 patients, 16 patients had a positive study for SBO, and 2 patients had a negative study. Scan findings were correlated with clinical, biochemical, microbiological, and radiological parameters.

Conclusion

68Ga-citrate PET/CT is a promising tool in the diagnosis and management of skull base osteomyelitis.
Transformation From Atypical to Anaplastic Metastatic Meningioma
Authors: Morcet-Delattre Robin , Meneret Pierre , Coue Olivier , Vauleon Elodie , Prigent Kevin 
Published: December 2023

Abstract
World Health Organization (WHO) grade III anaplastic meningioma is scarce. In this way, most studies compared WHO grade I and II. Otherwise, some authors are uncertain about using 18F-FDG as a diagnostic tool to estimate the WHO grade, especially high. We report the case from a man with a grading tumor evolution from WHO grade II atypical to grade III anaplastic metastatic meningioma. This turning point was imaged using 68Ga-DOTATOC and 18F-FDG. Diagnostic was confirmed by histology. The case underlines the unparalleled power of molecular imaging characterized by high sensitivity staging and spectacular avidity changing relationship with grading tumor evolution.
Autophagy Restricts Tomato Fruit Ripening Via a General Role in Ethylene Repression
Authors: Kumaran Girishkumar , Pathak Pradeep Kumar , Quandoh Ebenezer , Mursalimov Sergey , Devi Jyoti , Alkalai-Tuvia Sharon , Leong Jia Xuan , Schenstnyi Kyrylo , Levin Elena , Üstün Suayib , Michaeli Simon 
Published: December 2023

ABSTRACTAutophagy, a cellular degradation pathway, and the phytohormone ethylene function in plant development, senescence, and stress responses. However, the manner of their interaction is mostly unknown. We reasoned that this may be revealed by studying autophagy in a climacteric fruit ripening context, for which ethylene is crucial. During ripening, fruits undergo softening, color change, toxic compound degradation, volatile production, and sugar assembly by fine-tuning synthesis and degradation of their cellular content. For autophagy activity assessment, we analyzed autophagy-related 8 (ATG8) lipidation and GFP-ATG8-labeled autophagosome flux in tomato fruit cells. Autophagy activity increased sharply from ripening initiation, climaxed at its middle stage, and declined towards its end, resembling ethylene production dynamics. Silencing the core-autophagy genesSlATG2,SlATG7, andSlATG4separately in mature fruits resulted in early ethylene production and ripening onset, which was abrogated by 1-methylcyclopropene (1-MCP), an ethylene signaling inhibitor. Beyond ripening, Arabidopsisatg5andatg7mutant seedlings exhibited elevated ethylene production and sensitivity to 1-Aminocyclopropane 1-carboxylic acid (ACC), ethylenès precursor, which induces autophagy. This research demonstrates that autophagy limits tomato fruit ripening via a general role in ethylene restriction, opening the path for a mechanistic understanding of autophagy-ethylene crosstalk and harnessing autophagy for fruit shelf-life extension.
Use of phase plate cryo-EM reveals conformation diversity of therapeutic IgG with 50 kDa Fab fragment resolved below 6 Å
Authors: Lin Hsin-Hung , Wang Chun-Hsiung , Wu Yi-Min , Huang Shih-Hsin , Lin Sam Song-Yao , Kato Takayuki , Namba Keiichi , Hosogi Naoki , Song Chihong , Murata Kazuyoshi , Yen Ching-Hsuan , Hsu Tsui-Ling , Wong Chi-Huey , Tu I-Ping , Chang Wei-Hau 
Published: December 2023

AbstractWhile cryogenic electron microscopy (cryo-EM) is fruitfully used for harvesting high-resolution structures of sizable macromolecules, its application to small or flexible proteins composed of domains like immunoglobulin (IgG) remain challenging. Here, we applied single particle cryo-EM to Rituximab, a therapeutic IgG mediating cancer cell toxicity, to explore its solution conformations. We found Rituximab molecules exhibited aggregates in cryo-EM specimens contrary to its solution behavior, and utilized a non-ionic detergent to successfully disperse them as isolated particles amenable to single particle analysis. As the detergent adversely reduced the protein-to-solvent contrast, we employed phase plate contrast to mitigate the impaired protein visibility. Assisted by phase plate imaging, we obtained a canonical three-arm IgG structure with other structures displaying variable arm densities co-existing in solution, affirming high flexibility of arm-connecting linkers. Furthermore, we showed phase plate imaging enables reliable structure determination of Fab to sub-nanometer resolution from ab initio, yielding a characteristic two-lobe structure that could be unambiguously docked with crystal structure. Our findings revealed conformation diversity of IgG and demonstrated phase plate was viable for cryo-EM analysis of small proteins without symmetry. This work helps extend cryo-EM boundaries, providing a valuable imaging and structural analysis framework for macromolecules with similar challenging features.
A suicidal and extensively disordered luciferase with a bright luminescence
Authors: Dijkema Fenne Marjolein , Escarpizo-Lorenzana Marta Iglesia , Nordentoft Matilde Knapkøien , Rabe Hanna Christin , Sahin Cagla , Landreh Michael , Branca Rui Mamede , Sørensen Esben Skipper , Christensen Brian Søndergaard , Prestel Andreas , Teilum Kaare , Winther Jakob Rahr 
Published: December 2023

AbstractGaussia luciferase (GLuc) is one of the most luminescent luciferases known and is widely used as a reporter in biochemistry and cell biology. During catalysis GLuc undergoes inactivation by irreversible covalent modification. The mechanism by which GLuc generates luminescence and how it becomes inactivated are however not known. Here we show that GLuc unlike other enzymes has an extensively disordered structure with a minimal hydrophobic core and no apparent binding pocket for the main substrate, coelenterazine. From an alanine scan, we identified two Arg residues required for light production. These residues separated with an average of about 22 Å and a major structural rearrangement is required if they are to interact with the substrate simultaneously. We furthermore show that in addition to coelenterazine, GLuc also can oxidize furimazine, however, in this case without production of light. Both substrates result in the formation of adducts with the enzyme, which eventually leads to enzyme inactivation. Our results demonstrate that a rigid protein structure and substrate binding site are no prerequisites for high enzymatic activity and specificity. In addition to the increased understanding of enzymes in general, the findings will facilitate future improvement of GLuc as a reporter luciferase.Significance statementEnzymes are typically characterized by an overall globular structure with a hydrophobic core and a defined cavity for binding of substrate, containing the active site amino acid residues. Gaussia Luciferase is a widely used luminescent reporter with a very strong, albeit short-lived, flash of light due to rapid auto-inactivation. We show, using solution NMR, that while this luciferase shows some secondary structure elements held together by disulfide bonds this highly unusual enzyme is extensively disordered with essentially no hydrophobic core. Although the enzymatic mechanism remains unknown, we have identified two essential arginine residues but, in the structure, these do not point into a common active site. In spite of this, the enzyme has high substrate specificity suggesting that it undergoes major structural rearrangements upon binding of substrate.
CDC20 determines the sensitivity to spindle assembly checkpoint (SAC) inhibitors
Authors: Zheng Siqi , Raz Linoy , Zhou Lin , Cohen-Sharir Yael , Tian Ruifang , Wardenaar Rene , Broekhuis Mathilde , Rodriguez Maria Suarez Peredo , Wobben Soraya , van den Brink Anouk , Bakker Petra , Foijer Floris , David Uri-Ben 
Published: December 2023

AbstractSpindle assembly checkpoint (SAC) inhibitors are a recently developed class of drugs that perturb the regulation of chromosome segregation during division, induce chromosomal instability (CIN), and eventually lead to cell death. While they are currently in clinical trials for solid cancers, biomarkers to predict the response to SAC inhibitors are still lacking. We recently reported that aneuploid cancer cells are preferentially sensitive to SAC inhibition. Here, we investigated the molecular determinants of the response to SAC inhibition that underlies the differential sensitivity of aneuploid cells to these drugs. We found that this response was largely driven by the expression of CDC20, a main activator of the anaphase-promoting complex (APC/C), rather than by APC/C itself. Mechanistically, we discovered that CDC20 depletion prolonged metaphase duration, diminished mitotic errors, and reduced sensitivity to SAC inhibition. Aneuploid cells expressed high levels of CDC20 and experienced shorter metaphases and multiple mitotic errors, resulting in increased long-term sensitivity to SAC inhibition. Our findings propose high CDC20 expression as a favorable biomarker for SAC inhibition therapy and as an aneuploidy-induced therapeutic vulnerability.
The pattern of genetic variability in a core collection of 2,021 cowpea accessions
Authors: Fiscus Christopher J. , Herniter Ira A. , Tchamba Marimagne , Paliwal Rajneesh , Muñoz-Amatriaín María , Roberts Philip A. , Abberton Michael , Alaba Oluwafemi , Close Timothy J. , Oyatomi Olaniyi , Koenig Daniel 
Published: December 2023

AbstractCowpea is a highly drought-adapted leguminous crop with great promise for improving agricultural sustainability and food security. Here, we report analyses derived from array-based genotyping of 2,021 accessions constituting a core subset of the world’s largest cowpea collection, held at the International Institute of Tropical Agriculture (IITA) in Ibadan, Nigeria. We used this dataset to examine genetic variation and population structure in worldwide cowpea. We confirm that the primary pattern of population structure is two geographically defined subpopulations origining in West and East Africa, respectively, and that population structure is associated with shifts in phenotypic distribution. Furthermore, we establish the cowpea core collection as a resource for genome-wide association studies by mapping the genetic basis of several phenotypes, with a focus on seed coat pigmentation patterning and color. We anticipate that the genotyped IITA cowpea core collection will serve as a powerful tool for mapping complex traits, facilitating the acceleration of breeding programs to enhance the resilience of this crop in the face of rapid global climate change.
Assessing tissue-specific gene expression of essential genes from human and mouse
Authors: Zheng Huiwen , Fard Atefeh Taherian , Mar Jessica C 
Published: December 2023

AbstractA gene satisfies the definition of essentiality when the loss of its function compromises an organism’s viability. Identifying essential genes is useful for understanding the core components that regulate a biological system and ensure its survival. Advances in gene editing techniques like CRISPR-Cas9 generate the capacity to comprehensively interrogate a genome to elucidate what genes are essential. However, these techniques are often applied in the context of a single cell line and even when studies have collated essential gene sets across multiple cell lines, this information is rarely probed at a level that incorporates multiple cell and tissue types. The recent availability of large-scale single-cell RNA-sequencing (scRNA-seq) atlases provides an unprecedented opportunity to investigate the distribution of essential gene expression in cell and tissue types.Here, we leverage information contained in benchmarking datasets, single cell tissue atlases, and databases of essential genes, and develop a computational method, scEssentials, which uses a statistical framework to report on the robustness and specificity of essential genes in human and mouse across multiple cell types. Using scEssentials, both mouse and human models showed consistently high in expression and exhibit limited variably across more than 60 cell types. We also demonstrate a substantial number of significantly correlated gene pairs within scEssentials, which produce densely connected co-expression networks with functional annotation. Furthermore, we showed high frequencies of scEssentials across 200 pathways. Finally, we develop a score to quantify the relative essentiality of genes within scEssentials, which further validates with significant association with gene mutation frequency and chromatin accessibility.Using the heterogeneous ageing process, we demonstrate the application of scEssentials and their robust gene expression profile. Only one-fifth of scEssentials showed significant ageing-related differential expression among three age groups, occurring primarily in muscle satellite cells of varying tissue origins and highly interacting brain cells. Collectively, the robustness of scEssentials serves as a reference for analysing scRNA-seq data and provides insight into the heterogeneous nature of biological processes such as ageing.
Resource-efficient nitrogen removal from source separated urine with partial nitritation/anammox in a membrane aerated biofilm reactor
Authors: Timmer Marijn J. , De Paepe Jolien , Van Winckel Tim , Spiller Marc , Spacova Irina , De Paepe Kim , Pintelon Isabel , Lebeer Sarah , De Vos Winnok H. , Lasseur Christophe , Ganigué Ramon , Udert Kai M. , Vlaeminck Siegfried E. 
Published: December 2023

AbstractSource separation and decentralized urine treatment can cut costs in centralized wastewater treatment by diverting 80% of the nitrogen load in sewage. One promising approach for nitrogen removal in this context is partial nitritation/anammox (PN/A), reducing the aeration demand by 67% and organics dosage by 100% compared to nitrification/denitrification. Whilst previous studies with suspended biomass have encountered stability issues during PN/A treatment of urine, a PN/A biofilm was hypothesized to be more resilient. Its use for urine treatment was pioneered here for maximum rates and efficiencies in the energy efficient membrane-aerated biofilm reactor (MABR). Nitrogen removal rates of 1.0 g N L-1d-1and removal efficiencies of 80-95% were achieved during a 335-day stable operation at 28°C on stabilized (pH>11), diluted urine (10%). A balance between N2and NO3-formation was observed whilst optimizing the supply of O2and was rate limiting for the conversion towards N2. Short-term operation on less- and undiluted urine yielded N removal rates of 0.6-0.8 g N L-1d-1and removal efficiencies of 93% on 66% urine and 85% on undiluted urine. Metataxonomic analysis and fluorescencein-situhybridization confirmed the presence of biofilms consisting of nitrifiers (Nitrosomonas, Nitrospira) at the membrane side and anammox bacteria (“CandidatusBrocadia”) at the anoxic bulk side. The findings suggest that a biofilm approach to PN/A treatment of urine overcomes stability issues, and a PN/A-MABR has significant potential for resource efficient decentralized treatment. In human long-duration deep-space missions, this gravity-independent technology could produce N2to compensate artificial atmosphere losses whilst facilitating water recovery from urine.[GRAPHICAL ABSTRACT, COLOR]
Connecting Hippo pathway and cytoophidia inDrosophilaposterior follicle cells
Authors: Weng Rui-Yu , Zhang Lei , Liu Ji-Long 
Published: December 2023

AbstractCTP synthase (CTPS), the rate-limiting enzyme inde novosynthesis of CTP, assembles into filamentous structures termed cytoophidia. Here we study the impact of Hippo pathway on the posterior follicle cells (PFCs) inDrosophilaegg chambers. We find that the inactivation of Hippo pathway correlates with a reduction in cytoophidium length and number within PFCs. During the overexpression of CTPS, the presence of Hippo mutations also reduces the length of cytoophidia in PFCs. In addition, we observe that knocking down CTPS mitigateshpo(Hippo)-associated over-proliferation. In summary, our results suggest a connection between the Hippo pathway and the nucleotide biosynthesis enzyme CTPS in PFCs.
Systems genetics uncover new loci containing functional gene candidates inMycobacterium tuberculosis-infected Diversity Outbred mice
Authors: Gatti DM , Tyler AL , Mahoney JM , Churchill GA , Yener B , Koyuncu D , Gurcan MN , Niazi MKK , Tavolara T , Gower AC , Dayao D , McGlone E , Ginese ML , Specht A , Alsharaydeh A , Tessier PA , Kurtz SL , Elkins K , Kramnik I , Beamer G 
Published: December 2023

ABSTRACTMycobacterium tuberculosis,the bacillus that causes tuberculosis (TB), infects 2 billion people across the globe, and results in 8-9 million new TB cases and 1-1.5 million deaths each year. Most patients have no known genetic basis that predisposes them to disease. We investigated the complex genetic basis of pulmonary TB by modelling human genetic diversity with the Diversity Outbred mouse population. When infected withM. tuberculosis, one-third develop early onset, rapidly progressive, necrotizing granulomas and succumb within 60 days. The remaining develop non-necrotizing granulomas and survive longer than 60 days. Genetic mapping using clinical indicators of disease, granuloma histopathological features, and immune response traits identified five new loci on mouse chromosomes 1, 2, 4, 16 and three previously identified loci on chromosomes 3 and 17. Quantitative trait loci (QTLs) on chromosomes 1, 16, and 17, associated with multiple correlated traits and had similar patterns of allele effects, suggesting these QTLs contain important genetic regulators of responses toM. tuberculosis. To narrow the list of candidate genes in QTLs, we used a machine learning strategy that integrated gene expression signatures from lungs ofM. tuberculosis-infected Diversity Outbred mice with gene interaction networks, generating functional scores. The scores were then used to rank candidates for each mapped trait in each locus, resulting in 11 candidates:Ncf2, Fam20b, S100a8, S100a9, Itgb5, Fstl1, Zbtb20, Ddr1, Ier3, Vegfa,andZfp318. Importantly, all 11 candidates have roles in infection, inflammation, cell migration, extracellular matrix remodeling, or intracellular signaling. Further, all candidates contain single nucleotide polymorphisms (SNPs), and some but not all SNPs were predicted to have deleterious consequences on protein functions. Multiple methods were used for validation including (i) a statistical method that showed Diversity Outbred mice carrying PWH/PhJ alleles on chromosome 17 QTL have shorter survival; (ii) quantification of S100A8 protein levels, confirming predicted allele effects; and (iii) infection of C57BL/6 mice deficient for theS100a8gene. Overall, this work demonstrates that systems genetics using Diversity Outbred mice can identify new (and known) QTLs and new functionally relevant gene candidates that may be major regulators of granuloma necrosis and acute inflammation in pulmonary TB.