bluuebunny/crossref_metadata_2025 huggingface dataset:
Terminal Liminality, Life Imprisonment and the Paroled Body
Authors: Vannier Marion , Dagan Netanel
Published: November 2024

Based on an in-depth analysis of parole board hearings in Israel concerning life sentence prisoners who are old or severely ill, we argue that, rather than opening a window onto new beginnings, parole hearings place applicants in a state of terminal liminality that marks a transition from life into death. We uncover how terminal liminality entails constructing a broken paroled body before the parole board, where matters of life and death are performed, detailed, and contextualized. We further lay out a taxonomy to discuss applicants’ negotiation of terminal liminality through fatalism, resilience, resistance and hope, uncovering how they navigate penal and biological ‘clocks’. The performance of the broken paroled body at the back-end of the criminal justice system is revelatory of the punitiveness of the penal system towards the ageing prison population.
Ethics and ontology: comparing Amartya Sen’s ethics and Tony Lawson’s Critical Ethical Naturalism
Authors: Ragkousis Antonis
Published: November 2024

While Sen’s ethics, particularly through his capability approach, are recognised for their critical nature and alignment with certain realist ontological principles, this paper explores the compatibility and potential tensions between Sen’s framework and Critical Ethical Naturalism (CEN), an ethical theory introduced by Tony Lawson. This comparative exercise reveals that Sen’s adoption of realist ontological notions such as openness, relationality and the importance of process and institutions suggests compatibility with CEN—a potential compatibility noted by Lawson himself. However, there is also an important difference between Sen’s moral theory and CEN, which indicates the possibility of further fundamental tensions between them. This difference lies in their divergent orientations regarding the content and relevance of ontology. Sen’s project is shown to be predicated on the irrelevance of ontology to ethical theorising, which contrasts sharply with Lawson’s framework; indeed, the whole point of Lawson’s approach is to develop an ethical theory grounded on an explicit ontological account. Through a detailed examination of Sen’s reluctance to engage with ontology, an exploration of potential sources of this reticence and an analysis of the explicit ontological basis of CEN, the paper highlights fundamental distinctions between Sen’s approach and CEN.
Remote sensing image dehazing method in mountaineering equipment
Authors: Guo Yuanzhao , Zhang Jun
Published: November 2024

With the spread of national sports awareness, more people are fond of outdoor mountaineering. Intelligent mountaineering equipment can provide some safe and convenient services for outdoor mountaineering. However, the positioning accuracy is affected by the ability of remote sensing image recognition in the background. To address the haze interference in remote sensing image positioning, the Retinex algorithm is enhanced using an atmospheric scattering model. This improved Retinex algorithm adopts a multiscale retinal enhancement algorithm with color restoration to enhance images. The Gaussian kernel function plays a filtering role, while the guided filtering is used to improve image texture and details. Test data from background remote sensing images of mountaineering equipment are used to evaluate the algorithm. Results indicate that when the entire test set is used for calculations, the normalized information entropy of I-Retinex, Retinex, generative adversarial networks, and Alex models is 0.92. The median values of normalized mean squared error and mean absolute error are 0.13 and 0.15, respectively, outperforming the contrast defogging model. There is a negative correlation between the normalized peak signal-to-noise ratio and haze noise error in each model. When the entire test set is used, the normalized average gradient of I-Retinex is 0.87, significantly higher than the comparison models. However, the I-Retinex model developed in this study lacks optimal average computation time and memory consumption data. Experimental results demonstrate that the improved haze removal model effectively removes haze from remote sensing images, supporting the remote sensing image-related service functionalities of mountaineering equipment.
Central ligation or partial preservation of the right gastric artery does not seem to affect conduit or anastomotic perfusion during robot-assisted resection of gastroesophageal junction cancer: a randomized clinical trial
Authors: Osterkamp Jens Thomas Fredrik , Nerup Nikolaj , Svendsen Morten Bo S , Strandby Rune B , Svendsen Lars Bo , Aasvang Eske K , Vad Henrik , Plamboeck Astrid , Achiam Michael P
Published: November 2024

The gastric conduit can be created with partial preservation or a central ligation of the right gastric artery. Central ligation may facilitate complete removal of lymph node (LN) station 3; however, whether this influences conduit and anastomotic perfusion is unknown. Hence this study investigated whether a central ligation of the right gastric artery would affect conduit or anastomotic perfusion compared with partial preservation (local standard) during robot-assisted resection of gastroesophageal junction cancer. Patients scheduled for robot-assisted resection of gastroesophageal junction cancer were randomized to either central ligation or partial preservation of the right gastric artery. Perfusion was assessed using quantified indocyanine green angiography: before gastric mobilization, after conduit formation, and after anastomosis. Hemodynamic variables during surgery and surgical outcomes were recorded. We included 70 patients between June 2020 and October 2021, of whom 5 were excluded from the final analysis. The two patient groups did not differ in conduit (0.07 [interquartile range (IQR), 0.05–0.08] vs. 0.07 u [IQR, 0.05–0.08], P = 0.86) or anastomotic perfusion (0.08 [standard deviation (SD), ±0.02] vs. 0.08 u [SD, ±0.02], P = 0.21), nor did they differ in intraoperative blood loss, anastomotic leaks, postoperative complications, or 1-year survival. However, more LNs were resected in the central ligation group (36 [IQR, 30–44] vs. 28 [IQR, 23–43], P = 0.02). Introducing a central ligation of the right gastric artery did not seem to affect conduit or anastomotic perfusion, compared with partial preservation. However, significantly more LNs were resected.
MI5, the Security State and Communist Political Refugees from Nazism in Second World War-Era Britain: The Case of Gustav Beuer, 1938–1946
Authors: Stibbe Matthew
Published: November 2024

This article examines the British Security Service’s monitoring of Gustav Beuer, a Sudeten German communist and former member of the Czechoslovak parliament who arrived in London as a refugee in 1938 and set up home there until 1946. Although from a friendly country, Beuer was placed under continuous surveillance and was interned, together with five of his compatriots, in 1940–41. The article uses this case to challenge previous interpretations of MI5’s role in spying on communist refugees from Central Europe. It does so by taking a model developed by the German political scientist Matthias Lemke for analysing the widely varying levels of threat to democracy posed by exceptional security measures taken by liberal states in closely defined time-frames and applying this to Second-World-War Britain. Far from pursuing a linear strategy based on anti-communist prejudice alone, MI5 was obliged to muddle along in its policy towards Beuer and other communist refugees, assimilating unexpected triggers, shifting legal-bureaucratic frameworks, changes in wartime alliances and public opinion, and instances of ministerial action and inaction. The paradoxical result of this was to inject a certain amount of (unforeseen) pragmatism into MI5’s handling of ‘suspect’ refugees, while at the same time undermining its belief that covert fact-finding alone was enough to establish who was and who was not a threat. The article concludes that the self-doubts and unease within the British security state which are often attributed to intelligence failings and spy scandals in the early Cold War period had deeper roots in the Second World War era.
Brain-body coevolution in incipient versus established primate species—evaluating Simpson’s “most important distinction”
Authors: Bokma Folmer , Tsuboi Masahito , Stenseth Nils Chr
Published: November 2024

Are differences between species the long-term consequence of microevolution within species, or does speciation involve fundamentally different processes? We analyzed the brain and body sizes of present-day primate species using a novel phylogenetic comparative method that decomposes the phenotypic covariance of these traits into speciational and anagenetic components. We estimated that approximately half of speciation events are accompanied by accelerated phenotypic change. Equivalent in magnitude to approximately 7 million years of gradual microevolution, such speciational changes in brain and body size account for about 58% of the phenotypic variation among extant species. Interestingly, speciational changes in brain and body size appear significantly less correlated (r ≈ 0.83) than gradual, microevolutionary changes in these same traits (r ≈ 0.97). This indicates that the strong allometric constraint that dictates microevolution in brain and body sizes is relaxed at speciation events. These results suggest that phenotypic evolution is not only accelerated during speciation but also involves events that seldomly occur at microevolutionary timescales.
A novel method for evaluating earthquake forecast model performance and its implications for refining seismic likelihood model
Authors: Wei Cong-Min , Meng Guo-Jie , Wu Wei-Wei , Chen Xue-Liang , Zhao Guo-Qiang , Dong Zhi-Hua , Yang Yan-Cong , Wang Yu-Fan
Published: November 2024

Utilizing statistical tests to evaluate earthquake forecasting models is crucial to improve forecasting strategies for seismic hazard assessment. We develop a novel evaluation method for alarm-based earthquake forecast, taking into account the magnitude of seismic energy and the impact area of earthquakes, instead of using solely seismic event number and epicentre locations in conventional approaches. First, we derive a scale law of Seismic Area by statistically analysing coseismal maps of past M ≥ 7.0 earthquakes. Second, we proportionally allocate Seismic Moment to surrounding cells based on corresponding seismic area within each cell (SASM-test). Compared to the Molchan test which is conventionally applied for models that forecast the epicentre location, our proposed SASM-test can be applied to the evaluation of forecasting models that focus on the whole earthquake rupture (source area). Third, we apply the SASM-test method to the time-independent probabilistic earthquake forecasting model for the southeastern Tibetan Plateau (RELM-TibetSE) and compare it with other evaluation methods. The retrospective testing shows that the SASM-test demonstrate relatively higher sensitivity, enabling to detect subtle differences between similar models that conventional methods may overlook. Additionally, retrospective test results indicate that: (i) Earthquake forecasting models using Global Navigation Satellite System (GNSS) data performed better in forecasting the ‘source area’ than the ‘epicentre location’; (ii) forecasting models based on principal strain rate outperformed the models based on maximum shear strain rate in forecasting both the epicentre location and the source area and (iii) incorporating spatially varying seismogenic layer thickness and rigidity into seismic forecasting models could improve their ability to forecast the ‘source area’ compared to using uniform seismogenic layer properties. The newly proposed SASM-test method can provide a more sensitive and comprehensive approach for the evaluation of earthquake forecasting models, contributing to the refinement of seismic hazard assessments.
Non–cost-related sources of medication nonadherence in the Medicare population
Authors: Petroski Jason , Strachan Kelly , Schluterman Nicholas , Doss William
Published: November 2024

Significant research and attention to date have focused on cost-related medication nonadherence as rising prescription drug prices worsen affordability and access for many Americans. This study investigated self-reported sources of medication nonadherence, measuring both cost- and non–cost-related medication nonadherence among community-dwelling Medicare Part D beneficiaries in 2022. A total of 13.7% of beneficiaries (4 589 843) reported some type of medication nonadherence; 7.5% reported medication nonadherence related to cost and 6.2% reported for non-cost reasons. Beneficiaries reporting food insecurity, poor functional status, and lack of understanding of the Part D benefit were more likely to report both types of medication nonadherence after adjustment for sociodemographic factors. Beneficiaries receiving the Low-Income Subsidy had lower odds of reporting cost-related but greater odds of reporting non–cost-related medication nonadherence. These findings suggest that non–cost-related sources of medication nonadherence, such as beneficiary preferences or beliefs, understanding of their health situation or insurance coverage, and ability to fill a prescription, are significant contributors to overall nonadherence. Non–cost-related medication nonadherence should be considered alongside recent changes to the Part D benefit and in future Part D Centers for Medicare and Medicaid Services (CMS) Innovation Center models, such as the proposed Medicare $2 Drug List Model, in order to maximize the impact of these initiatives.
Nurse practitioner race and ethnicity and interest in independent primary care practice and serving Medicaid enrollees
Authors: Muench Ulrike , Quan Amy , de Lisser Rosalind , Bates Timothy , Spetz Joanne
Published: November 2024

Nurse practitioners (NPs) are important providers of primary care to underserved populations, particularly in areas with lower physician supply. In 2023, California implemented new regulations aimed at improving access to care, especially primary care services, by providing a pathway for NPs to practice without formal supervision after 3 years of practice and without any physician relationship after 5 years of practice. This study used data from a representative survey of California-licensed NPs fielded in late 2022 to examine NPs' current practice and intentions following implementation of the new regulations. Results indicated notable differences in the characteristics of NPs who are considering establishing an independent primary care practice and who are considering changing their practice to serve more Medicaid enrollees at the advent of expanded scope of practice. The strong association between racial/ethnic identity and greater interest in practice change suggests that after the elimination of physician collaboration requirements, increasing the diversity of the NP workforce may be one of the most important strategies for increasing access to care for Californians and especially for people receiving Medicaid.
Applied potassium negates osmotic stress impacts on plant physiological processes: a meta-analysis
Authors: Zhu Linxing , Sun Yuming , Wang Rongfeng , Zeng Jixing , Li Jia , Huang Mengting , Wang Min , Shen Qirong , Guo Shiwei
Published: November 2024

Potassium (K) availability in plant cells is critical for maintaining plant productivity across many terrestrial ecosystems. Yet, there is no comprehensive assessment of the mechanisms by which plants respond to potassium application in such conditions, despite the global challenge of escalating osmotic stress. Herein, we conducted a meta-analysis using data from 2381 paired observations to investigate plant responses to potassium application across various morphological, physiological, and biochemical parameters under both osmotic and nonosmotic stress. Globally, our results showed the significant effectiveness of potassium application in promoting plant productivity (e.g. +12%~30% in total dry weight), elevating photosynthesis (+12%~30%), and alleviating osmotic damage (e.g. −19%~26% in malonaldehyde), particularly under osmotic stress. Moreover, we found evidence of interactive effects between osmotic stress and potassium on plant traits, which were more pronounced under drought than salt stress, and more evident in C3 than C4 plants. Our synthesis verifies a global potassium control over osmotic stress, and further offers valuable insights into its management and utilization in agriculture and restoration efforts.
VvARF19 represses VvLBD13-mediated cell wall degradation to delay softening of grape berries
Authors: Li Meng , Nie Changjiang , He Shanshan , Xue Zhirui , Li Jiajun , Li Zhiqian , He Chang , Zheng Xianbo , Tan Bin , Cheng Jun , Wang Wei , Li Jidong , Ye Xia , Feng Jiancan
Published: November 2024

Fruit softening directly impacts its storage life, transportability, and customer acceptance. Auxin plays a key role during fruit ripening, but the underlying mechanisms of how auxin regulates fruit softening remain unclear. In this study, we investigated the regulatory roles of auxin on berry cell wall degradation during grape (Vitis vinifera L.) softening. During grape berry development, berry firmness and auxin content both firstly increase and then decrease, and peaks occur 4–6 weeks after full blooming. Exogenous NAA (α-naphthalene acetic acid, a synthetic auxin) treatment inhibits berry softening by delaying propectin, cellulose, and hemicellulose degradation, which maintains cell wall integrity in the grape flesh. Weighted gene co-expression network analysis (WGCNA) showed that VvLBD13, correlated with VvARF19, could be a key gene in this delaying of berry softening, and is involved in auxin signal transduction and cell wall degradation metabolism. Overexpression and transient overexpression of VvLBD13 in tomato or in grape berry indicate that VvLBD13 accelerates hemicellulose degradation by binding the promoters of VvXTH10 (xyloglucan endotransglucosylase/hydrolase 10) and VvEXPLA1 (expansion-like A1), which results in rapid softening after veraison. Collectively, this research furnishes an exhaustive understanding of the auxin-driven regulatory mechanisms of grape berry softening.
Data privacy in China and Europe: individual, collective, subjective, and objective perspectives
Authors: de Jonge Alice
Published: November 2024

This article presents a comparative analysis of personal data governance in the EU and China, using the ‘four quadrants’ framework of Weber’s Integral Theory. Both jurisdictions seek to protect the individual’s right to control personal information. When it comes to the collective aspects of personal information, however, China’s Social Credit System gives the pursual of social objectives a degree of priority over individual rights unacceptable within EU contexts. The value of large-scale, pseudonymized data sets for research and policy-making is recognized in both the EU and China. Facilitating access to valuable data sets while also protecting individual privacy rights remains a key challenge. Similarities can also be found in each jurisdiction’s desire to maintain system integrity and secure digital ecosystems, albeit with different levels of sensitivity surrounding sovereignty and security concerns. The article concludes by proposing a system of international data trusts as a useful tool for facilitating collaborative data sharing and mutual confidence.
U.S. Naval Medical Research Unit SOUTH's Contributions to Strengthening Global Health Security in Peru and Across Latin America
Authors: Marjuki Henju , Hoffman Marshall M , Edgel Kimberly A , Geist Charla C , Schilling Megan A , Pannebaker Danielle L , Moeller Tyler D , Graham W Darnell , Vasquez Gissella M , Lescano A Roxana , Soto Giselle M , Prouty Michael G
Published: November 2024

Infectious diseases (IDs) contribute to major causes of mortality and chronic morbidity in Central and South America. Interest in improving general understanding, prevention, and treatment options motivates the U.S. Department of Defense to establish and run overseas ID institutions to enhance force health protection. One of 6 Department of Defense overseas ID institutions, U.S. Naval Research Medical Unit (NAMRU) SOUTH, has safely and ethically conducted biomedical research, ID surveillance, and medical countermeasure testing and evaluation in Peru and surrounding countries. In its over 40-year history, NAMRU SOUTH medical research collaborations have achieved many milestones leading to critical ID information sharing, funding, services, and education mutually beneficial to the U.S. and regional partners in Latin America.
Web API Usability: A Systematic Mapping Study
Authors: Machini Ariel , Casas Sandra
Published: November 2024

Context

Web APIs play a key role in modern application development, and their usability is crucial for them to be of value. Aim: This systematic mapping study aims to identify and categorize metrics related to web API usability.

Method

We identified four research questions and a set of search terms related to these. We applied inclusion, exclusion, and quality criteria to filter out unrelated articles, and then performed data extraction on the remaining studies.

Results

We found a total of 96 metrics. Most of the usability metrics (40 %) were related to learnability. We also found that only one of the articles proposed metrics in the context of a usability model and that most of the studies obtained values for their metrics automatically.

Conclusions

Our findings highlight a lack of research in the field of web API usability + metrics, with only 14 % of the metrics we identified being explicitly related to web APIs.
Harnessing bacterial antimicrobial peptides: a comprehensive review on properties, mechanisms, applications, and challenges in combating antimicrobial resistance
Authors: Erriah Pirasannah , Puan Sheau Ling , Yahaya Normi Mohd , Kamil Wan Nur Ismah Wan Ahmad , Nordin Syafinaz Amin , Muhamad Azira , Sabri Suriana
Published: November 2024

Antimicrobial resistance (AMR) is a significant global health concern, due to the persistence of pathogens and the emergence of resistance in bacterial infections. Bacterial-derived antimicrobial peptides (BAMPs) have emerged as a promising strategy to combat these challenges. Known for their diversity and multifaceted nature, BAMPs are notable bioactive agents which exhibit potent antimicrobial activities against various pathogens. This review explores the intricate properties and underlying mechanisms of BAMPs, emphasizing their diverse applications in addressing AMR. Additionally, the review investigates the mechanisms, analyses the challenges in utilizing BAMPs effectively, and examines their potential applications and associated deployment challenges providing comprehensive insights into how BAMPs can be harnessed to combat AMR across different domains.
Glucose-1-phosphate thymidylyltransferase promotes the production of 3-O-α-mycarosylerythronolide B in Streptomyces coelicolor
Authors: Gao Hong , Langer Swen , Larson Tony , Gregory Matthew A , Smith Margaret C M
Published: November 2024

Aims

The main objective of this study was to produce erythronolide B (EB) and 3-O-α-mycarosylerythronolide B (MEB) in Streptomyces coelicolor and enhance the MEB production by expressing the glucose-1-phosphate thymidylyltransferase (RfbA).

Methods and results

We expressed eryF and eryB genes (eryBII, eryBIII, eryBIV, eryBV, eryBVI, and eryBVII) to produce EB and MEB. The expression was confirmed by quantitative real-time polymerase chain reaction. Furthermore, the MEB’s production was improved by more than 100-fold by expressing an enzyme, RfbA, which is absent from the erythromycin gene cluster, to promote the biosynthesis of TDP-L-mycarose. We discuss the feasibility of alternative Streptomyces species for erythromycin production based on the presence or absence of RfbA.

Conclusions

The RbfA enzyme from Saccharopolyspora erythraea was expressed in S. coelicolor M1152 along with the MEB biosynthesis pathway, resulting in a large increase in MEB production (>100-fold).
Designing Public Secrecy: Kongfz.com and the Digital Trade in Cultural Revolution Objects
Authors: Inwald Minerva
Published: November 2024

The Chinese e-commerce platform Kongfuzi Second-hand Book Website (Kongfz.com) supports a thriving trade in objects from China’s historically contentious Cultural Revolution (1966–1976) period. This article examines the design of Kongfz.com as a digital artifact to explore how the platform mediates between users and Cultural Revolution objects. Building on the work of Margaret Hillenbrand, I demonstrate that studying Kongfz.com’s design exposes the spectral practices of “public secrecy” that enmesh Cultural Revolution objects. I argue that the design of the platform reminds users that Cultural Revolution objects are more than just commodities, highlighting their status as politically contentious historical artifacts. Outlining the design of the website’s regulatory structures, I show that the platform requires sellers to evaluate the political implications of Cultural Revolution ephemera. Exploring Kongfz.com’s classificatory schema and browsing and search functions, I reveal how ‘obfuscatory tactics’ embedded in the website’s front-end interface complicate the process of finding Cultural Revolution artifacts on the platform, drawing users’ attention to the political sensitivities of these items as they navigate around blockages to discover listings. Through an analysis of how Kongfz.com mediates between users and Cultural Revolution material culture, this article demonstrates that studying digital artifacts can reveal otherwise invisible cultural practices that envelope historical objects.
Clinal variation in autosomal satellite DNA clusters across a contact zone in Barker Frogs
Authors: Souza Lucas Henrique Bonfim , Ferro Juan Martín , Gatto Kaleb Pretto , de Sá Fábio Perin , Haddad Célio Fernando Baptista , Lourenço Luciana Bolsoni
Published: November 2024

Contact zones between genetically divergent lineages offer a unique opportunity to explore gene flow and speciation dynamics. Because satellite DNAs (satDNAs) have high evolutionary rates, they may be useful for comparing related taxa and assessing contact zones. Here, we analysed the distribution of chromosomal clusters of PcP190 satDNA across a contact zone between two distinct genetic lineages of a Neotropical species complex of frogs. The parental lineages, Physalaemus ephippifer and lineage 1B (L1B), exhibited pronounced divergence in the number of PcP190 clusters. We further expanded the geographic scope of this species complex by including two additional Brazilian localities in previously available cytogenetic and mitochondrial DNA datasets. The contact zone exhibited remarkable variation in the chromosomal distribution of PcP190 clusters among the autosomes; the only fixed autosomal site was found on chromosome 3. The highest numbers of PcP190 clusters were observed in specimens collected at sites near (approximately 320 km from) the distribution of L1B, whereas specimens from Dom Eliseu, which is near (approximately 330 km from) the distribution of P. ephippifer, had the lowest numbers of such clusters. Mitochondrial haplotypes also exhibited geographical variation across sites. Our findings expand the known contact zone of these Physalaemus lineages from 1,500 km2 to over 6,200 km2, demonstrating its extensive area, and emphasize the usefulness of satDNAs in studying contact zones.
Development of a Baltimore (MD) population of Calliphora vicina (Diptera: Calliphoridae) reared at several temperatures and estimations of developmental limits and thresholds
Authors: Rivers David B
Published: November 2024

Developmental data for necrophagous Diptera are frequently used in medico-legal investigations to estimate portions of the postmortem interval and interpret periods of insect activity. These applications require baseline developmental data for local populations from geographic locations of interest. For the widely distributed blow fly Calliphora vicina Robineau-Desvoidy (Diptera: Calliphoridae), detailed developmental data does not exist for many locations in the mid-Atlantic region of the United States. This study examined development of C. vicina collected from a large, metropolitan city (Baltimore) in Maryland utilizing 11 ambient temperatures. The developmental threshold and thermal range of growth and tolerance were also estimated, as well as critical thermal minima and maxima based on thermal injury. For this population, linear growth was observed between 10°C and 25°C, whereas flies failed to complete development at temperatures below 7°C or above 28°C. Growth at low temperatures was not curvilinear, which contrasts with other developmental studies using C. vicina and other calliphorids. The lower developmental threshold was estimated to be 5.9°C and corresponds closely with experimental observations. The implications of these result in reference to phenotypic plasticity in populations of C. vicina and applications in forensic entomology are discussed.
Experimental literature and post-critique: reflections on Italo Calvino's Invisible Cities
Authors: Brady Alison M
Published: November 2024

In this article, I begin with Felski and Sedgwick’s diagnosis of the overabundance of critique in education, connecting this to Hodgson, Vlieghe, and Zamojski’s calls for a ‘post-critical pedagogy’. Rather than offering a critique of critique, I aim to think differently about the ‘uses’ of reading, taking my cue from post-critical scholarship as well as from Calvino’s experimental novel, Invisible Cities. First, I discuss how critique and post-critique differ in their orientations when engaging with a text. I argue that, instead of ‘shutting down’ a text to point to its latent assumptions, post-critique opens the text up to the world by cultivating new perceptual and imaginative dimensions in our experience. This partly involves the reader being oriented towards what is worth preserving in a text—an approach that is also central to post-critical pedagogy. Second, I reflect on my own failures with respect to putting a post-critical analysis into words, since it seems that in the context of academic writing, it is difficult to avoid critique. Given this, I argue that it is more fruitful to explore three post-critical pedagogical gestures in Invisible Cities: namely, its tensions (which encourage and resist linear explanations), its fundamental but playful ambiguity (which invites both puzzlement and curiosity), and its transformative potential in relation to the everyday understandings of the cities we inhabit. These gestures encourage readers to surrender themselves to the text in a mood characterized by enchantment rather than suspicion and demonstrate to the educative potential of literature beyond critique.
Biphasic glucose-stimulated insulin secretion over decades: a journey from measurements and modeling to mechanistic insights
Authors: Peng Xiaohong , Wang Kai , Chen Liangyi
Published: November 2024

Glucose-stimulated insulin release from pancreatic β-cells is critical for maintaining blood glucose homeostasis. An abrupt increase in blood glucose concentration evokes a rapid and transient rise in insulin secretion followed by a prolonged, slower phase. A diminished first phase is one of the earliest indicators of β-cell dysfunction in individuals predisposed to develop type 2 diabetes. Consequently, researchers have explored the underlying mechanisms for decades, starting with plasma insulin measurements under physiological conditions and advancing to single-vesicle exocytosis measurements in individual β-cells combined with molecular manipulations. Based on a chain of evidence gathered from genetic manipulation to in vivo mouse phenotyping, a widely accepted theory posits that distinct functional insulin vesicle pools in β-cells regulate biphasic glucose-stimulated insulin secretion (GSIS) via activation of different metabolic signal pathways. Recently, we developed a high-resolution imaging technique to visualize single vesicle exocytosis from β-cells within an intact islet. Our findings reveal that β-cells within the islet exhibit heterogeneity in their secretory capabilities, which also differs from the heterogeneous Ca2+ signals observed in islet β-cells in response to glucose stimulation. Most importantly, we demonstrate that biphasic GSIS emerges from the interactions among α-, β-, and δ-cells within the islet and is driven by a small subset of hypersecretory β-cells. Finally, we propose that a shift from reductionism to holism may be required to fully understand the etiology of complex diseases such as diabetes.
A brief supplement to the Two Oldcastles of London
Authors: Ilsemann Hartmut
Published: November 2024

My previous investigations of the history play Sir John Oldcastle (Ilsemann, 2017) that were carried out with Rolling Delta and Rolling Classify, are viewed again and supplemented by the results of the General Imposters method and the investigations of Lupić in 2018. The Shakespearean character of the play is also supported by Oldcastle n-grams from Rizvi’s data bank which match Much Ado About Nothing (1598), Julius Caesar (1599), Henry V (1599) and As You Like It (1599).
A novel numerical method for mixed-frame multigroup radiation-hydrodynamics with GPU acceleration implemented in the quokka code
Authors: He Chong-Chong , Wibking Benjamin D , Krumholz Mark R
Published: November 2024

Mixed-frame formulations of radiation-hydrodynamics (RHD), where the radiation quantities are computed in an inertial frame but matter quantities are in a comoving frame, are advantageous because they admit algorithms that conserve energy and momentum to machine precision and combine more naturally with adaptive mesh techniques, since unlike pure comoving-frame methods, they do not face the problem that radiation quantities must change frame every time a cell is refined or coarsened. However, implementing multigroup RHD in a mixed-frame formulation presents challenges due to the complexity of handling frequency-dependent interactions and the Doppler shift of radiation boundaries. In this paper, we introduce a novel method for multigroup RHD that integrates a mixed-frame formulation with a piecewise power-law approximation for frequency dependence within groups. This approach ensures the exact conservation of total energy and momentum while effectively managing the Lorentz transformation of group boundaries and evaluation of group-averaged opacities. Our method takes advantage of the locality of matter-radiation coupling, allowing the source term for $N_g$ frequency groups to be handled with simple equations with a sparse Jacobian matrix of size $N_g + 1$, which can be inverted with $O(N_g)$ complexity. This results in a computational complexity that scales linearly with $N_g$ and requires no more communication than a pure hydrodynamics update, making it highly efficient for massively parallel and GPU-based systems. We implement our method in the GPU-accelerated RHD code quokka and demonstrate that it passes a wide range of numerical tests, including preserving the asymptotic diffusion limit. We demonstrate that the piecewise power-law method shows significant advantages over traditional opacity averaging methods for handling rapidly variable opacities with modest frequency resolution.
The enigmatic origin of two dormant BH binaries: Gaia BH1 and Gaia BH2
Authors: Kotko I , Banerjee S , Belczynski K
Published: November 2024

The two systems, namely, Gaia BH1 and Gaia BH2, that have been confirmed as dormant (i.e. no X-ray emission detected) black hole (BH) – low-mass star binaries in the latest Gaia mission data release are intriguing in the context of their formation and evolution. Both systems consist of $\sim 9\, \mathrm{{\rm M}_{\odot }}$ BH and $\sim 1\, \mathrm{{\rm M}_{\odot }}$ star orbiting each other on a wide, eccentric orbit ($e\sim 0.5$). We argue that formation of such Gaia BH-like systems through the isolated binary evolution (IBE) channel, under the standard common envelope assumptions, and from dynamical interactions in young massive and open clusters are equally probable, and that the formation rate of such binaries is of the order of $10^{-7}\, \mathrm{{\rm M}_{\odot }}^{-1}$ for both channels. We estimate that, according to our models, there are at most $\sim 900$ detectable Gaia BH-like binaries in the Milky Way thin disc. What plays an important role in formation of Gaia BH-like systems via the IBE channel is the mutual position of the natal kick velocity vector and the binary angular momentum vector. We find that natal kicks with a median magnitude of $\sim 40$ km s−1 are preferred for the formation of Gaia BH1-like binaries. Approximately 94 per cent of those binaries are formed with the BH spin misaligned to the orbital axis by less than $40^{\circ }$. Gaia BH2-like binaries form if the low-velocity natal kick (of median magnitude $\sim 20$ km s−1) is directed within $15^{\circ }$ about the orbital plane. In addition to natal kick, we also discuss the influence of tidal interaction and the adopted common envelope $\lambda _\mathrm{ce}$ parameter prescription on the evolution of Gaia BH-like binaries. We follow the subsequent evolution of the binaries, once formed as Gaia BH1 and Gaia BH2 systems, to investigate their connection with the low-mass X-ray binary population.
HERB 2.0: an updated database integrating clinical and experimental evidence for traditional Chinese medicine
Authors: Gao Kai , Liu Liu , Lei Shuangshuang , Li Zhinong , Huo Peipei , Wang Zhihao , Dong Lei , Deng Wenxin , Bu Dechao , Zeng Xiaoxi , Li Chun , Zhao Yi , Zhang Wei , Wang Wei , Wu Yang
Published: November 2024

Clinical trials and meta-analyses are considered high-level medical evidence with solid credibility. However, such clinical evidence for traditional Chinese medicine (TCM) is scattered, requiring a unified entrance to navigate all available evaluations on TCM therapies under modern standards. Besides, novel experimental evidence has continuously accumulated for TCM since the publication of HERB 1.0. Therefore, we updated the HERB database to integrate four types of evidence for TCM: (i) we curated 8558 clinical trials and 8032 meta-analyses information for TCM and extracted clear clinical conclusions for 1941 clinical trials and 593 meta-analyses with companion supporting papers. (ii) we updated experimental evidence for TCM, increased the number of high-throughput experiments to 2231, and curated references to 6 644. We newly added high-throughput experiments for 376 diseases and evaluated all pairwise similarities among TCM herbs/ingredients/formulae, modern drugs and diseases. (iii) we provide an automatic analyzing interface for users to upload their gene expression profiles and map them to our curated datasets. (iv) we built knowledge graph representations of HERB entities and relationships to retrieve TCM knowledge better. In summary, HERB 2.0 represents rich data type, content, utilization, and visualization improvements to support TCM research and guide modern drug discovery. It is accessible through http://herb.ac.cn/v2 or http://47.92.70.12.
RADIP technology comprehensively identifies H3K27me3-associated RNA–chromatin interactions
Authors: Shu Xufeng , Kato Masaki , Takizawa Satoshi , Suzuki Yutaka , Carninci Piero
Published: November 2024

Many RNAs associate with chromatin, either directly or indirectly. Several technologies for mapping regions where RNAs interact across the genome have been developed to investigate the function of these RNAs. Obtaining information on the proteins involved in these RNA–chromatin interactions is critical for further analysis. Here, we developed RADIP [RNA and DNA interacting complexes ligated and sequenced (RADICL-seq) with immunoprecipitation], a novel technology that combines RADICL-seq technology with chromatin immunoprecipitation to characterize RNA–chromatin interactions mediated by individual proteins. Building upon the foundational principles of RADICL-seq, RADIP extends its advantages by increasing genomic coverage and unique mapping rate efficiency compared to existing methods. To demonstrate its effectiveness, we applied an anti-H3K27me3 antibody to the RADIP technology and generated libraries from mouse embryonic stem cells (mESCs). We identified a multitude of RNAs, including RNAs from protein-coding genes and non-coding RNAs, that are associated with chromatin via H3K27me3 and that likely facilitate the spread of Polycomb repressive complexes over broad regions of the mammalian genome, thereby affecting gene expression, chromatin structures and pluripotency of mESCs. Our study demonstrates the applicability of RADIP to investigations of the functions of chromatin-associated RNAs.
CAF-1 promotes efficient PrimPol recruitment to nascent DNA for single-stranded DNA gap formation
Authors: Straka Joshua , Khatib Jude B , Pale Lindsey , Nicolae Claudia M , Moldovan George-Lucian
Published: November 2024

Suppression of single-stranded DNA (ssDNA) gap accumulation at replication forks has emerged as a potential determinant of chemosensitivity in homologous recombination (HR)-deficient tumors, as ssDNA gaps are transformed into cytotoxic double-stranded DNA breaks. We have previously shown that the histone chaperone CAF-1’s nucleosome deposition function is vital to preventing degradation of stalled replication forks correlating with HR-deficient cells’ response to genotoxic drugs. Here we report that the CAF-1–ASF1 pathway promotes ssDNA gap accumulation at replication forks in both wild-type and breast cancer (BRCA)-deficient backgrounds. We show that this is independent of CAF-1’s nucleosome deposition function but instead may rely on its proper localization to replication forks. Moreover, we show that the efficient localization to nascent DNA of PrimPol, the enzyme responsible for repriming upon replication stress, is dependent on CAF-1. As PrimPol has been shown to be responsible for generating ssDNA gaps as a byproduct of its repriming function, CAF-1’s role in its recruitment could directly impact ssDNA gap formation. We also show that chemoresistance observed in HR-deficient cells when CAF-1 or ASF1A are lost correlates with suppression of ssDNA gaps rather than protection of stalled replication forks. Overall, this work identifies an unexpected role of CAF-1 in regulating PrimPol recruitment and ssDNA gap generation.
Complex portal 2025: predicted human complexes and enhanced visualisation tools for the comparison of orthologous and paralogous complexes
Authors: Balu Sucharitha , Huget Susie , Medina Reyes Juan Jose , Ragueneau Eliot , Panneerselvam Kalpana , Fischer Samantha N , Claussen Erin R , Kourtis Savvas , Combe Colin W , Meldal Birgit H M , Perfetto Livia , Rappsilber Juri , Kustatscher Georg , Drew Kevin , Orchard Sandra , Hermjakob Henning
Published: November 2024

The Complex Portal (www.ebi.ac.uk/complexportal) is a manually curated reference database for molecular complexes. It is a unifying web resource linking aggregated data on composition, topology and the function of macromolecular complexes from 28 species. In addition to significantly extending the number of manually curated complexes, we have massively extended the coverage of the human complexome through the incorporation of high confidence assemblies predicted by machine-learning algorithms trained on large-scale experimental data. The current content of the portal comprising 2150 human complexes has been augmented by 14 964 machine-learning (ML) predicted complexes from hu.MAP3.0. We have refactored the website to enable easy search and filtering of these different classes of protein complexes and have implemented the Complex Navigator, a visualisation tool to facilitate comparison of related complexes in the context of orthology or paralogy. We have embedded the Rhea reaction visualisation tool into the website to enable users to view the catalytic activity of enzyme complexes.
CAUSALdb2: an updated database for causal variants of complex traits
Authors: Wang Jianhua , Ouyang Liao , You Tianyi , Yang Nianling , Xu Xinran , Zhang Wenwen , Yang Hongxi , Yi Xianfu , Huang Dandan , Zhou Wenhao , Li Mulin Jun
Published: November 2024

Unraveling the causal variants from genome wide association studies (GWASs) is pivotal for understanding genetic underpinnings of complex traits and diseases. Despite continuous efforts, tools to refine and prioritize GWAS signals need enhancement to address the direct causal implications of genetic variations. To overcome challenges related to statistical fine-mapping in identifying causal variants, CAUSALdb has been updated with novel features and comprehensive datasets, morphing into CAUSALdb2. This expanded repository integrates 15 057 updated GWAS summary statistics across 10 839 unique traits and implements both LD-based and LD-free fine-mapping approaches, including innovative applications of approximate Bayes Factor and SuSiE. Additionally, by incorporating larger LD reference panels such as TOPMED and UK Biobank, and integrating functional annotations via PolyFun, CAUSALdb2 enhances the accuracy and context of fine-mapping results. The database now supports interrogation of additional causal signals and offers sophisticated visualizations to aid researchers in deciphering complex genetic architectures. By facilitating a deeper and more precise characterisation of causal variants, CAUSALdb2 serves as a crucial tool for advancing the genetic analysis of complex diseases. Available freely, CAUSALdb2 continues to set benchmarks in the post-GWAS era, fostering the development of targeted diagnostics and therapeutics derived from responsible genetic research. Explore these advancements at http://mulinlab.org/causaldb.
Intrinsically disordered RNA-binding motifs cooperate to catalyze RNA folding and drive phase separation
Authors: Niedner-Boblenz Annika , Monecke Thomas , Hennig Janosch , Klostermann Melina , Hofweber Mario , Davydova Elena , Gerber André P , Anosova Irina , Mayer Wieland , Müller Marisa , Heym Roland Gerhard , Janowski Robert , Paillart Jean-Christophe , Dormann Dorothee , Zarnack Kathi , Sattler Michael , Niessing Dierk
Published: November 2024

RNA-binding proteins are essential for gene regulation and the spatial organization of cells. Here, we report that the yeast ribosome biogenesis factor Loc1p is an intrinsically disordered RNA-binding protein with eight repeating positively charged, unstructured nucleic acid binding (PUN) motifs. While a single of these previously undefined motifs stabilizes folded RNAs, multiple copies strongly cooperate to catalyze RNA folding. In the presence of RNA, these multivalent PUN motifs drive phase separation. Proteome-wide searches in pro- and eukaryotes for proteins with similar arrays of PUN motifs reveal a strong enrichment in RNA-mediated processes and DNA remodeling. Thus, PUN motifs are potentially involved in a large variety of RNA- and DNA-related processes by concentrating them in membraneless organelles. The general function and wide distribution of PUN motifs across species suggest that in an ancient ‘RNA world’ PUN-like motifs may have supported the correct folding of early ribozymes.