bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

Abstract
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

Abstract
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

Abstract
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

Abstract

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

Abstract
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

Abstract

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 (&gt;100-fold).
Designing Public Secrecy: Kongfz.com and the Digital Trade in Cultural Revolution Objects
Authors: Inwald Minerva 
Published: November 2024

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

ABSTRACT
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

ABSTRACT
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

Abstract
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.