bluuebunny/crossref_metadata_2025_split huggingface dataset:
CAKE: a flexible self-supervised framework for enhancing cell visualization, clustering and rare cell identification
Authors: Liu Jin , Zeng Weixing , Kan Shichao , Li Min , Zheng Ruiqing 
Published: December 2023

Abstract
Single cell sequencing technology has provided unprecedented opportunities for comprehensively deciphering cell heterogeneity. Nevertheless, the high dimensionality and intricate nature of cell heterogeneity have presented substantial challenges to computational methods. Numerous novel clustering methods have been proposed to address this issue. However, none of these methods achieve the consistently better performance under different biological scenarios. In this study, we developed CAKE, a novel and scalable self-supervised clustering method, which consists of a contrastive learning model with a mixture neighborhood augmentation for cell representation learning, and a self-Knowledge Distiller model for the refinement of clustering results. These designs provide more condensed and cluster-friendly cell representations and improve the clustering performance in term of accuracy and robustness. Furthermore, in addition to accurately identifying the major type cells, CAKE could also find more biologically meaningful cell subgroups and rare cell types. The comprehensive experiments on real single-cell RNA sequencing datasets demonstrated the superiority of CAKE in visualization and clustering over other comparison methods, and indicated its extensive application in the field of cell heterogeneity analysis. Contact: Ruiqing Zheng. (rqzheng@csu.edu.cn)
Increased expression of chondroitin sulfate proteoglycans in dentate gyrus and amygdala causes postinfectious seizures
Authors: Patel Dipan C , Swift Nathaniel , Tewari Bhanu P , Browning Jack L , Prim Courtney , Chaunsali Lata , Kimbrough Ian F , Olsen Michelle L , Sontheimer Harald 
Published: December 2023

Abstract
Alterations in the extracellular matrix are common in patients with epilepsy and animal models of epilepsy, yet whether they are the cause or consequence of seizures and epilepsy development is unknown.
Using Theiler’s murine encephalomyelitis virus (TMEV) infection-induced model of acquired epilepsy, we found de novo expression of chondroitin sulfate proteoglycans (CSPGs), a major extracellular matrix component, in dentate gyrus (DG) and amygdala exclusively in mice with acute seizures. Preventing the synthesis of CSPGs specifically in DG and amygdala by deletion of the major CSPG aggrecan reduced seizure burden. Patch-clamp recordings from dentate granule cells revealed enhanced intrinsic and synaptic excitability in seizing mice that was significantly ameliorated by aggrecan deletion. In situ experiments suggested that dentate granule cell hyperexcitability results from negatively charged CSPGs increasing stationary cations on the membrane, thereby depolarizing neurons, increasing their intrinsic and synaptic excitability.
These results show increased expression of CSPGs in the DG and amygdala as one of the causal factors for TMEV-induced acute seizures. We also show identical changes in CSPGs in pilocarpine-induced epilepsy, suggesting that enhanced CSPGs in the DG and amygdala may be a common ictogenic factor and potential therapeutic target.
From Stars to Diamonds: Counting and Listing Almost Complete Subgraphs in Large Networks
Authors: Finocchi Irene , Garcia Renan Leon , Sinaimeri Blerina 
Published: December 2023

Abstract
Listing dense subgraphs is a fundamental task with a variety of network analytics applications. A lot of research has been done focusing on $k$-cliques, i.e. complete subgraphs on $k$ nodes. However, requiring complete connectivity between the nodes of a subgraph may be too restrictive in many real applications. Hence, in this paper, we consider a natural relaxation of cliques, called $k$-diamonds and defined as cliques of size $k$ with one missing edge. We first provide a sequential algorithm that, in $O(nm^{(k-1)/2})$ time, counts and lists all the $k$-diamonds in large graphs, for any constant $k \geq 4$. A parallel extension of the sequential algorithm is then proposed and analyzed in a MapReduce-style model, achieving the same local and total space usage of the state-of-the-art algorithms for $k$-cliques. The running time is optimal on dense graphs and $O(\sqrt{m})$ larger than $k$-clique counting if the graph is sparse. Our algorithms compute induced diamonds by analyzing the structure of directed stars formed by the graph nodes and their neighbors.
Apennine–Pyrenees disjunct distribution: an unusual biogeographic pattern revealed in flea beetles of the Longitarsus candidulus species-group (Coleoptera, Chrysomelidae)
Authors: Berrilli Emanuele , Biondi Maurizio , Garzia Matteo , D’Alessandro Paola , Salvi Daniele 
Published: December 2023

Abstract
European mountain systems have played a crucial role in shaping the distribution of species and of their genetic diversity during the Quaternary climatic changes, with the establishment of allopatric patterns across main mountain ranges. Here we investigated the evolutionary history of flea beetles of the Longitarsus candidulus species-group showing an uncommon disjunct biogeographic pattern across the Apennine and the Pyrenees. We applied a multilocus molecular approach and multispecies coalescent models to establish a phylogenetic and systematic framework for this morphologically homogeneous species-group and to estimate the time of main cladogenetic events underlying the origin of the Apennine-Pyrenees pattern. We found strong support for the monophyly of the candidulus group with a sister relationship between Longitarsus laureolae and L. leonardii endemic to the Apennine and the Pyrenees mountains respectively. The timing of speciation events in the candidulus species-group coincides with 2 major climatic transitions during the Early and Middle Pleistocene which resulted in significant environmental changes in Europe and suggest a scenario of allopatric isolation and divergence on distinct mountain ranges. The split between the thermophilic species L. candidulus and the ancestor of the temperate species L. laureolae and L. leonardii is estimated at ~3 Ma during the transition from Pliocene to Pleistocene and was probably triggered by their segregation in xerophilous and temperate habitats. The speciation between L. laureolae and L. leonardii, estimated at ~1 Ma during the Mid-Pleistocene Transition, can be explained by the establishment of unfavorable conditions in West Alps and Central Massif underlying the onset of the Apennine-Pyrenees disjunct pattern. Finally, the strict association between members of the candidulus group and distinct Thymelaeaceae plants suggests further studies to address the hypothesis that speciation in these flea beetles might have been also associated with Pleistocene range changes of their host plants.
Geographically variable mate preferences shed light on the processes maintaining inversion polymorphism
Authors: Lacoste Pierre , Chouteau Mathieu , Maisonneuve Ludovic , Mauxion Rémi , Joron Mathieu , McClure Melanie 
Published: December 2023

Abstract
An important question in evolution is to understand the mechanisms that maintain phenotypic diversity, despite selection that should drive homogeneity. For example, selection by predators may promote the convergence of colour patterns among defended prey, resulting in the formation of mimetic communities. However, certain aposematic species, such as the Neotropical butterfly Heliconius numata, are polymorphic. In H. numata, wing pattern polymorphism, which is associated with chromosomal inversions, may be maintained via disassortative mating preferences, thought to favour the co-occurrence of individuals with different mimicry phenotypes in Peru. To test whether environmental variation due to geography influences mate choice, here we investigate the occurrence of disassortative mating among the two coexisting forms of H. numata in French Guiana, and its potential role in the maintenance of this polymorphism. Our experimental approach demonstrates that the two forms display weak and slightly asymmetrical disassortative mate preferences. Modelling and simulations suggest that this pattern of mate preference alone is not sufficient to maintain polymorphism, and predict the loss of the choosiest form, unless this form enjoys a survival advantage. In this aposematic species, such an advantage could arise from mimicry, but further studies into the benefits of mimicry and predator generalization are needed to test this hypothesis. More importantly, our results suggest that the balance between selective forces influencing polymorphism may vary across geographical and ecological contexts, and this warrants further study.
Intra-specific correlations between ejaculate traits and competitive fertilization success: a meta-analysis across species and fertilization modes
Authors: Macartney Erin L , Morrison Kyle , Snook Rhonda R , Lagisz Malgorzata , Nakagawa Shinichi 
Published: December 2023

Abstract
Understanding of how selection can act on traits that improve competitiveness and subsequent paternity has advanced, including the idea that internal and external fertilization presents different environments that may select differentially on ejaculate traits. However, no studies have quantitatively synthesized the intra-specific relationships between these traits and paternity. Therefore, we conducted a meta-analysis across 52 papers to determine which ejaculate traits positively correlate with paternity share and how these correlations vary with fertilization mode. Overall, most ejaculate traits were positively associated with paternity, with the notable exception of sperm length. Sub-analyses on sperm number, sperm length, and sperm velocity revealed no statistical differences between fertilization modes in the relationship between traits and paternity when all effect sizes across species were combined. However, in a sub-analysis on fish species only, we found evidence that sperm velocity may be more important in external fertilizers. We also observed differences in the importance of phylogenetic relatedness and some species-specific differences. Our results suggest that while most ejaculate traits should be under positive directional selection in both internal and external fertilizers, sperm length may be subject to more nuanced selection pressures. Overall, we highlight important patterns of intra-specific relationships between ejaculate traits and competitive fertilization success.
‘There should be equality in opinions’: Political Opinion in Intimate Partner Violence Claims
Authors: Anderson Adrienne 
Published: December 2023

ABSTRACT
There is longstanding acceptance that opposition to discrimination against women and/or non-conformity with prevailing gender norms may constitute a political opinion in refugee law. However, courts have not consistently taken an expansive view of political opinion in gender cases. In particular, notwithstanding the global prevalence of intimate partner violence (IPV), there is little jurisprudential and, crucially, academic clarity in relation to the political implications of non-conformity with social mores in the context of IPV. Despite this inhospitable environment, lawyers continue to argue this ground in IPV claims, particularly at jurisprudential crisis points, as occurred recently in the aftermath of a 2018 decision in the United States, overruling previous precedent granting refugee status based on membership in a particular social group.
This article provides an overarching examination of the academic discussion on the desirability and practicability of applying the political opinion ground and the case law considering this ground to date. Using the jurisprudence of appeal tribunals in five common law jurisdictions, the article reveals commonalities in both successful and unsuccessful claims in this context. Notably, it identifies that ‘nexus’ to an opinion is a previously underappreciated barrier to applying the political opinion ground in IPV claims. These observations provide a crucial foundation for further reasoned consideration of the political opinion ground in IPV claims which may arise given this ground’s ongoing invocation at first instance and in lower-level administrative decision making.
In our own eyes: ethical dilemmas and insights encountered by researchers conducting qualitative research in high ambient temperatures in Kilifi, Kenya
Authors: Lusambili A , Chabeda S , Khaemba P 
Published: December 2023

Abstract
We reflect on our fieldwork experience from the Climate Heat Maternal and Neonatal Health Africa (CHAMNHA) project in Kilifi, Kenya, which focused on studying the effects of extreme heat on women during pregnancy, delivery and the post-partum period. We describe the ethical and practical challenges encountered, highlighting valuable lessons learned. We propose potential solutions to address issues concerning the reciprocity of vulnerable participants and the provision of childcare and food for accompanying children. Further, we address challenges related to engaging specific participants, interview cancellations attributed to extreme temperatures and discuss the perpetuation of inequalities by ethics and academic institutions. With the anticipated increase in research at the intersection of climate change–induced heat exposure and its impacts on human populations, research institutions and ethics committees in low- and middle-income countries are responsible for instituting guidelines that account for the risks for the subjects under study and the field researchers.
Patient- and family-centred care transition interventions for adults: a systematic review and meta-analysis of RCTs
Authors: Chartrand Julie , Shea Beverley , Hutton Brian , Dingwall Orvie , Kakkar Anupriya , Chartrand Mariève , Poulin Ariane , Backman Chantal 
Published: December 2023

Abstract
Although patient centredness is part of providing high-quality health care, little is known about the effectiveness of care transition interventions that involve patients and their families on readmissions to the hospital or emergency visits post-discharge. This systematic review (SR) aimed to examine the evidence on patient- and family-centred (PFC) care transition interventions and evaluate their effectiveness on adults’ hospital readmissions and emergency department (ED) visits after discharge. Searches of Medline, CINAHL, and Embase databases were conducted from the earliest available online year of indexing up to and including 14 March 2021. The studies included: (i) were about care transitions (hospital to home) of ≥18-year-old patients; (ii) had components of patient-centred care and care transition frameworks; (iii) reported on one or more outcomes were among hospital readmissions and ED visits after discharge; and (iv) were cluster-, pilot- or randomized-controlled trials published in English or French. Study selection, data extraction, and risk of bias assessment were completed by two independent reviewers. A narrative synthesis was performed, and pooled odd ratios, standardized mean differences, and mean differences were calculated using a random-effects meta-analysis. Of the 10,021 citations screened, 50 trials were included in the SR and 44 were included in the meta-analyses. Care transition intervention types included health assessment, symptom and disease management, medication reconciliation, discharge planning, risk management, complication detection, and emotional support. Results showed that PFC care transition interventions significantly reduced the risk of hospital readmission rates compared to usual care [incident rate ratio (IRR), 0.86; 95% confidence interval (CI), 0.75–0.98; I2 = 73%] regardless of time elapsed since discharge. However, these same interventions had minimal impact on the risk of ED visit rates compared to usual care group regardless of time passed after discharge (IRR, 1.00; 95% CI, 0.85–1.18; I2 = 29%). PFC care transition interventions containing a greater number of patient-centred care (IRR, 0.73; 95% CI, 0.57–0.94; I2 = 59%) and care transition components (IRR, 0.76; 95% CI, 0.64–0.91; I2 = 4%) significantly decreased the risk of patients being readmitted. However, these interventions did not significantly increase the risk of patients visiting the ED after discharge (IRR, 1.54; CI 95%, 0.91–2.61). Future interventions should focus on patients’ and families’ values, beliefs, needs, preferences, race, age, gender, and social determinants of health to improve the quality of adults’ care transitions.
Genomic insight into the insecticidal potential of a new Pseudomonas chlororaphis isolate
Authors: Wang Haitao , Zhang Yali , Dai Dadong , Fu Jinqiu , Sung Kim Dae , Li Shengchun , Zhang Jiang , Wang Yong , Zhang Fengjuan 
Published: December 2023

Abstract
Pseudomonas fluorescens group, such as Pseudomonas protegens and Pseudomonas chlororaphis, can be utilized as insect-killing agents. Most insecticidal Pseudomonas described so far have high toxicity for insects of the order Lepidoptera. In this study, Pseudomonas strain PcR3-3 was isolated from the willow root. It showed a high mortality for the coleopteran species Plagiodera versicolora (Coleoptera: Chrysomelidae), but not for the lepidopteran Helicoverpa armigera. Strain PcR3-3 displayed high colonization ability in the P. versicolora compared with P. chlororaphis PCL1391, indicating that the insecticidal activities correlated with the colonization ability of Pseudomonas strain in the host. Phylogenetic analysis of the genome revealed that PcR3-3 belonged to P. chlororaphis subsp. aureofaciens. Numerous insecticidal protein-encoding genes, typical biosynthetic gene clusters for some insecticidal metabolite and type VI secretion system, known to be involved in insect pathogenicity, were present in the P. chlororaphis PcR3-3 genome. However, the insecticidal toxin Fit-encoding gene which commonly presents in P. chlororaphis, was not found in the P. chlororaphis PcR3-3 genome. Furthermore, there are some divergent insecticidal genes between P. chlororaphis PcR3-3 and P. chlororaphis PCL1391. This finding implies that P. chlororaphis PcR3-3 is a promising biocontrol agent for pest management applications. The P. chlororaphis–P. versicolora association can be used as a model system to study the interaction between Pseudomonas and coleopteran insects.
China’s regulations on new types of unfair competition in the digital age: ‘Internet Provision’ and ‘Data Provision’
Authors: Wang Xuan , Lin Xiuqin 
Published: December 2023

Abstract
This article delves into the emergence of ‘new types of unfair competition’ in China, propelled by the rapid development of the digital economy. It primarily focuses on ‘Internet Provision’ and the proposed ‘Data Provision’. Notably, China’s Anti-Unfair Competition Law, enacted in 1993, underwent its first significant revision after a span of 24 years, leading to the introduction of the ‘Internet Provision’. However, the typology of these provisions presented evident flaws, resulting in the frequent invocation of the ‘catch-all clause’ by the courts since its implementation. This lack of specific categorization for unfair competition in the Internet domain has led to the courts heavily relying on Article 2 of the ‘Anti-Unfair Competition Law’, which is regarded as a general provision. Unfortunately, this approach has given rise to convoluted reasoning, unstable outcomes and excessive judicial intervention in commercial competition matters. To address these issues, the newly proposed ‘data clause’ aims to reestablish clear typification. Nevertheless, it contains semantic ambiguities in its specific expression. More importantly, while the proposed rules consider the cost of public access to information, they do not sufficiently safeguard freedom of information. The lack of well-defined boundaries for data scraping tends to overly favour the original platforms that control the data. Confronting this novel form of unfair competition, it is crucial for codified law countries to endeavour to typify unfair competition acts. However, in designing the legal system, due consideration should be given to the principle of ‘competitive neutrality’ meaning that excessive judicial coercion and interference in the Internet competition landscape should be avoided to ensure a level playing field. The law’s role is to establish clear parameters while allowing for technical solutions to address many of the arising problems. Therefore, it is essential to define a precise and consistent standard. This paper argues against an overly broad recognition of ‘new unfair competition behaviour’, as it may hinder market entry and stifle innovation in the long run.
Persistent NLRP3 inflammasome activation is associated with delayed immunosuppression in septic patients
Authors: Coudereau Rémy , Bodinier Maxime , Lukaszewicz Anne-Claire , Py Bénédicte F , Argaud Laurent , Cour Martin , Bidar Frank , Cerrato Elisabeth , Garnier Lorna , Gossez Morgane , Venet Fabienne , Monneret Guillaume 
Published: December 2023

Abstract
Sepsis triggers a complex response marked by the simultaneous presence of proinflammatory and immunosuppressive elements, disrupting the mechanisms intended to maintain homeostasis. While the NLRP3 inflammasome has been demonstrated to contribute to the inflammatory side, its connection with delayed sepsis-induced immunosuppression remains unexplored. The present objective was to concomitantly and prospectively assess NLRP3 activation (IL-1β, IL-18, and soluble receptors) and features of immune failure (IL-10, mHLA-DR, myeloid-derived suppressor cells) in septic patients. To validate our findings, we conducted a transcriptomic analysis of mRNA of NLRP3-related genes (IL-18R1, IL-1R2) on an additional cohort of 107 patients. Two distinct endotypes were identified. One cluster displayed moderate inflammation rapidly returning to normal values, while the other exhibited a higher inflammatory response persisting until day 28, which was associated with persistent marked immunosuppression and higher 28-d mortality. Identifying endotypes with different pro/anti-inflammatory trajectories could hold important clinical implications for the management of sepsis.