bluuebunny/crossref_metadata_2025 huggingface dataset:
Design Creativity
Authors: Jun Gyuchan Thomas , Hignett Sue , Clarkson P. John
Published: June 2024

Design creativity describes the process by which needs are explored and translated into requirements for change. This Element examines the role of design creativity within the context of healthcare improvement. It begins by outlining the characteristics of design thinking, and the key status of the Double Diamond Model. It provides practical tools to support design creativity, including ethnographic/observational studies, personas and scenarios, and needs identification and requirements analysis. It also covers brainstorming, Disney, and six thinking hats techniques, the nine windows technique, morphological charts and product architecting, and concept evaluation. The tools, covering all stages of the Double Diamond model, are supported by examples of their use in healthcare improvement. The Element concludes with a critique of design creativity and the evidence for its application in healthcare improvement. This title is also available as Open Access on Cambridge Core.
Rethinking Water Governance in the Saskatchewan River Delta Through Indigenous Relational Worldviews
Authors: Acharibasam John Bosco , Riley Kathryn , Datta Ranjan , McKenzie Elder Denise , Favel Elder Veronica
Published: June 2024

This study critically examines the implications of integrating Indigenous relational worldviews into the water governance framework of the Saskatchewan River Delta. Using a relational theoretical framework and community-based participatory research methodology, both Indigenous community members and non-Indigenous researchers collectively examine the negative impacts of Western water governance policies and practices on the Métis community residing in Cumberland House, located in northeast Saskatchewan, Canada. Through Indigenous traditional water story-sharing methods with Indigenous Elders and Knowledge Keepers, our focus centres on Indigenous interpretations and ways of knowing the Delta. The community highlighted the pervasive influence of power dynamics and political agendas in the governance of the Delta. As such, we emphasise the necessity of challenging settler colonial systems and structures and reinvigorating Indigenous worldviews for water governance. By doing so, we advocate for the advancement of Indigenous sovereignty and self-determination in their relationship with land and water, thereby promoting the meaningful implications of the Truth and Reconciliation Commission Calls to Action.
Fair Play Externalism and the Obligation to Relinquish
Authors: FRIGAULT JOSEPH
Published: June 2024

Abstract

This essay defends a new account of wrongful benefiting based on the principle of fair play. In particular, I argue that certain structurally-conferred group-based benefits or privileges can ground obligations on the part of innocent beneficiaries to relinquish specific gains for purposes of redistribution regardless of whether their receipt is sourced in wrongdoing or involves the imposition of harm upon relevant others. I call this approach to fair play reasoning externalist insofar as it turns on a novel conception of free-riding that eschews necessary appeal to beneficiaries’ mental states or volition. After presenting an empirical example to help illustrate the sort of benefiting at issue and distinguishing my account from arguments rooted in the notion of structural injustice, I defend it via what I call the extension argument, respond to two salient objections, and close by suggesting its potential political utility in the American context specifically.
Building Epistemically Healthier Platforms
Authors: Amico-Korby Dallas , Harrell Maralee , Danks David
Published: June 2024

When thinking about designing social media platforms, we often focus on factors such as usability, functionality, aesthetics, ethics, and so forth. Epistemic considerations have rarely been given the same level of attention in design discussions. This paper aims to rectify this neglect. We begin by arguing that there are epistemic norms that govern environments, including social media environments. Next, we provide a framework for applying these norms to the question of platform design. We then apply this framework to the real-world case of long-form informational content platforms. We argue that many current long-form informational content platforms are epistemically unhealthy. The good news? We provide concrete advice on how to take steps toward improving their health! Specifically, we argue that they should change how they verify and authenticate content creators and how this information is displayed to content consumers. We conclude by connecting this guidance to broader issues about the epistemic health of platforms.
Victims and diplomats: European white stork conservation efforts, animal representations, and images of expertise in postwar ornithology
Authors: Schleper Simone
Published: June 2024

Argument

This article discusses two approaches to save the European white stork populations from extinction that emerged after 1980. Despite the shared objective to devise transnational, science-based conservation measures, the two approaches’ geographical focus was radically different. Projects by the World Wildlife Fund and the International Council for Bird Preservation focused firmly on the stork’s wintering areas on the African continent. Interventions by a second group of ornithologists at the Max Planck Institute for Ornithology in Radolfzell concentrated on the Middle East as a migration bottleneck. Based on archival research, interviews and correspondence with involved ornithologists, the article examines stork representations as an important lens for investigating the professional politics of ecology and conservation. It shows that representations of white storks, the birds’ ecology, and derived conservation hotspots became part of the boundary work used by European ornithologists in the creation of changing scientific and institutional identities.
Precise mode control of laser-written waveguides for broadband, low-dispersion 3D integrated optics
Authors: Wang Yuying , Zhong Lijing , Lau Kuen Yao , Han Xuhu , Yang Yi , Hu Jiacheng , Firstov Sergei , Chen Zhi , Ma Zhijun , Tong Limin , Chiang Kin Seng , Tan Dezhi , Qiu Jianrong
Published: June 2024

Three-dimensional (3D) glass chips are promising waveguide platforms for building hybrid 3D photonic circuits due to their 3D topological capabilities, large transparent windows, and low coupling dispersion. At present, the key challenge in scaling down a benchtop optical system to a glass chip is the lack of precise methods for controlling the mode field and optical coupling of 3D waveguide circuits. Here, we propose an overlap-controlled multi-scan (OCMS) method based on laser-direct lithography that allows customizing the refractive index profile of 3D waveguides with high spatial precision in a variety of glasses. On the basis of this method, we achieve variable mode-field distribution, robust and broadband coupling, and thereby demonstrate dispersionless LP21-mode conversion of supercontinuum pulses with the largest deviation of <0.1 dB in coupling ratios on 210 nm broadband. This approach provides a route to achieve ultra-broadband and low-dispersion coupling in 3D photonic circuits, with overwhelming advantages over conventional planar waveguide-optic platforms for on-chip transmission and manipulation of ultrashort laser pulses and broadband supercontinuum.
Molecular and structural basis of an ATPase-nuclease dual-enzyme anti-phage defense complex
Authors: An Qiyin , Wang Yong , Tian Zhenhua , Han Jie , Li Jinyue , Liao Fumeng , Yu Feiyang , Zhao Haiyan , Wen Yancheng , Zhang Heng , Deng Zengqin
Published: June 2024

Coupling distinct enzymatic effectors emerges as an efficient strategy for defense against phage infection in bacterial immune responses, such as the widely studied nuclease and cyclase activities in the type III CRISPR-Cas system. However, concerted enzymatic activities in other bacterial defense systems are poorly understood. Here, we biochemically and structurally characterize a two-component defense system DUF4297–HerA, demonstrating that DUF4297–HerA confers resistance against phage infection by cooperatively cleaving dsDNA and hydrolyzing ATP. DUF4297 alone forms a dimer, and HerA alone exists as a nonplanar split spiral hexamer, both of which exhibit extremely low enzymatic activity. Interestingly, DUF4297 and HerA assemble into an approximately 1 MDa supramolecular complex, where two layers of DUF4297 (6 DUF4297 molecules per layer) linked via inter-layer dimerization of neighboring DUF4297 molecules are stacked on top of the HerA hexamer. Importantly, the complex assembly promotes dimerization of DUF4297 molecules in the upper layer and enables a transition of HerA from a nonplanar hexamer to a planar hexamer, thus activating their respective enzymatic activities to abrogate phage infection. Together, our findings not only characterize a novel dual-enzyme anti-phage defense system, but also reveal a unique activation mechanism by cooperative complex assembly in bacterial immunity.
An implantable piezoelectric ultrasound stimulator (ImPULS) for deep brain activation
Authors: Hou Jason F. , Nayeem Md Osman Goni , Caplan Kian A. , Ruesch Evan A. , Caban-Murillo Albit , Criado-Hidalgo Ernesto , Ornellas Sarah B. , Williams Brandon , Pearce Ayeilla A. , Dagdeviren Huseyin E. , Surets Michelle , White John A. , Shapiro Mikhail G. , Wang Fan , Ramirez Steve , Dagdeviren Canan
Published: June 2024

Precise neurostimulation can revolutionize therapies for neurological disorders. Electrode-based stimulation devices face challenges in achieving precise and consistent targeting due to the immune response and the limited penetration of electrical fields. Ultrasound can aid in energy propagation, but transcranial ultrasound stimulation in the deep brain has limited spatial resolution caused by bone and tissue scattering. Here, we report an implantable piezoelectric ultrasound stimulator (ImPULS) that generates an ultrasonic focal pressure of 100 kPa to modulate the activity of neurons. ImPULS is a fully-encapsulated, flexible piezoelectric micromachined ultrasound transducer that incorporates a biocompatible piezoceramic, potassium sodium niobate [(K,Na)NbO3]. The absence of electrochemically active elements poses a new strategy for achieving long-term stability. We demonstrated that ImPULS can i) excite neurons in a mouse hippocampal slice ex vivo, ii) activate cells in the hippocampus of an anesthetized mouse to induce expression of activity-dependent gene c-Fos, and iii) stimulate dopaminergic neurons in the substantia nigra pars compacta to elicit time-locked modulation of nigrostriatal dopamine release. This work introduces a non-genetic ultrasound platform for spatially-localized neural stimulation and exploration of basic functions in the deep brain.
Downregulation of rhodopsin is an effective therapeutic strategy in ameliorating peripherin-2-associated inherited retinal disorders
Authors: Rutan Woods Christian T. , Makia Mustafa S. , Lewis Tylor R. , Crane Ryan , Zeibak Stephanie , Yu Paul , Kakakhel Mashal , Castillo Carson M. , Arshavsky Vadim Y. , Naash Muna I. , Al-Ubaidi Muayyad R.
Published: June 2024

Given the absence of approved treatments for pathogenic variants in Peripherin-2 (PRPH2), it is imperative to identify a universally effective therapeutic target for PRPH2 pathogenic variants. To test the hypothesis that formation of the elongated discs in presence of PRPH2 pathogenic variants is due to the presence of the full complement of rhodopsin in absence of the required amounts of functional PRPH2. Here we demonstrate the therapeutic potential of reducing rhodopsin levels in ameliorating disease phenotype in knockin models for p.Lys154del (c.458-460del) and p.Tyr141Cys (c.422 A > G) in PRPH2. Reducing rhodopsin levels improves physiological function, mitigates the severity of disc abnormalities, and decreases retinal gliosis. Additionally, intravitreal injections of a rhodopsin-specific antisense oligonucleotide successfully enhance the physiological function of photoreceptors and improves the ultrastructure of discs in mutant mice. Presented findings shows that reducing rhodopsin levels is an effective therapeutic strategy for the treatment of inherited retinal degeneration associated with PRPH2 pathogenic variants.
Sphingosine d18:1 promotes nonalcoholic steatohepatitis by inhibiting macrophage HIF-2α
Authors: Xia Jialin , Chen Hong , Wang Xiaoxiao , Chen Weixuan , Lin Jun , Xu Feng , Nie Qixing , Ye Chuan , Zhong Bitao , Zhao Min , Yun Chuyu , Zeng Guangyi , Mao Yuejian , Wen Yongping , Zhang Xuguang , Yan Sen , Wang Xuemei , Sun Lulu , Liu Feng , Zhong Chao , Xia Pengyan , Jiang Changtao , Rao Huiying , Pang Yanli
Published: June 2024

Non-alcoholic steatohepatitis (NASH) is a severe type of the non-alcoholic fatty liver disease (NAFLD). NASH is a growing global health concern due to its increasing morbidity, lack of well-defined biomarkers and lack of clinically effective treatments. Using metabolomic analysis, the most significantly changed active lipid sphingosine d18:1 [So(d18:1)] is selected from NASH patients. So(d18:1) inhibits macrophage HIF-2α as a direct inhibitor and promotes the inflammatory factors secretion. Male macrophage-specific HIF-2α knockout and overexpression mice verified the protective effect of HIF-2α on NASH progression. Importantly, the HIF-2α stabilizer FG-4592 alleviates liver inflammation and fibrosis in NASH, which indicated that macrophage HIF-2α is a potential drug target for NASH treatment. Overall, this study confirms that So(d18:1) promotes NASH and clarifies that So(d18:1) inhibits the transcriptional activity of HIF-2α in liver macrophages by suppressing the interaction of HIF-2α with ARNT, suggesting that macrophage HIF-2α may be a potential target for the treatment of NASH.
Control of a gene transfer agent cluster in Caulobacter crescentus by transcriptional activation and anti-termination
Authors: Tran Ngat T. , Le Tung B. K.
Published: June 2024

Gene Transfer Agents (GTAs) are phage-like particles that cannot self-multiply and be infectious. Caulobacter crescentus, a bacterium best known as a model organism to study bacterial cell biology and cell cycle regulation, has recently been demonstrated to produce bona fide GTA particles (CcGTA). Since C. crescentus ultimately die to release GTA particles, the production of GTA particles must be tightly regulated and integrated with the host physiology to prevent a collapse in cell population. Two direct activators of the CcGTA biosynthetic gene cluster, GafY and GafZ, have been identified, however, it is unknown how GafYZ controls transcription or how they coordinate gene expression of the CcGTA gene cluster with other accessory genes elsewhere on the genome for complete CcGTA production. Here, we show that the CcGTA gene cluster is transcriptionally co-activated by GafY, integration host factor (IHF), and by GafZ-mediated transcription anti-termination. We present evidence that GafZ is a transcription anti-terminator that likely forms an anti-termination complex with RNA polymerase, NusA, NusG, and NusE to bypass transcription terminators within the 14 kb CcGTA cluster. Overall, we reveal a two-tier regulation that coordinates the synthesis of GTA particles in C. crescentus.
Charge redistribution of a spatially differentiated ferroelectric Bi4Ti3O12 single crystal for photocatalytic overall water splitting
Authors: Jia Guangri , Sun Fusai , Zhou Tao , Wang Ying , Cui Xiaoqiang , Guo Zhengxiao , Fan Fengtao , Yu Jimmy C.
Published: June 2024

Artificial photosynthesis is a promising approach to produce clean fuels via renewable solar energy. However, it is practically constrained by two issues of slow photogenerated carrier migration and rapid electron/hole recombination. It is also a challenge to achieve a 2:1 ratio of H2 and O2 for overall water splitting. Here we report a rational design of spatially differentiated two-dimensional Bi4Ti3O12 nanosheets to enhance overall water splitting. Such a spatially differentiated structure overcomes the limitation of charge transfer across different crystal planes in a single crystal semiconductor. The experimental results show a redistribution of charge within a crystal plane. The resulting photocatalyst produces 40.3 μmol h–1 of hydrogen and 20.1 μmol h–1 of oxygen at a near stoichiometric ratio of 2:1 and a solar-to-hydrogen efficiency of 0.1% under simulated solar light.
Asymmetric magma plumbing system beneath Axial Seamount based on full waveform inversion of seismic data
Authors: Yang Jidong , Zhu Hejun , Zhao Zeyu , Huang Jianping , Lumley David , Stern Robert J. , Dunn Robert A. , Arnulf Adrien F. , Ma Jianwei
Published: June 2024

The architecture of magma plumbing systems plays a fundamental role in volcano eruption and evolution. However, the precise configuration of crustal magma reservoirs and conduits responsible for supplying eruptions are difficult to explore across most active volcanic systems. Consequently, our understanding of their correlation with eruption dynamics is limited. Axial Seamount is an active submarine volcano located along the Juan de Fuca Ridge, with known eruptions in 1998, 2011, and 2015. Here we present high-resolution images of P-wave velocity, attenuation, and estimates of temperature and partial melt beneath the summit of Axial Seamount, derived from multi-parameter full waveform inversion of a 2D multi-channel seismic line. Multiple magma reservoirs, including a newly discovered western magma reservoir, are identified in the upper crust, with the maximum melt fraction of ~15–32% in the upper main magma reservoir (MMR) and lower fractions of 10% to 26% in other satellite reservoirs. In addition, a feeding conduit below the MMR with a melt fraction of ~4–11% and a low-velocity throat beneath the eastern caldera wall connecting the MMR roof with eruptive fissures are imaged. These findings delineate an asymmetric shallow plumbing system beneath Axial Seamount, providing insights into the magma pathways that fed recent eruptions.
Real-time outage management in active distribution networks using reinforcement learning over graphs
Authors: Jacob Roshni Anna , Paul Steve , Chowdhury Souma , Gel Yulia R. , Zhang Jie
Published: June 2024

Self-healing smart grids are characterized by fast-acting, intelligent control mechanisms that minimize power disruptions during outages. The corrective actions adopted during outages in power distribution networks include reconfiguration through switching control and emergency load shedding. The conventional decision-making models for outage mitigation are, however, not suitable for smart grids due to their slow response and computational inefficiency. Here, we present a graph reinforcement learning model for outage management in the distribution network to enhance its resilience. The distinctive characteristic of our approach is that it explicitly accounts for the underlying network topology and its variations with switching control, while also capturing the complex interdependencies between state variables (along nodes and edges) by modeling the task as a graph learning problem. Our model learns the optimal control policy for power restoration using a Capsule-based graph neural network. We validate our model on three test networks, namely the 13, 34, and 123-bus modified IEEE networks where it is shown to achieve near-optimal, real-time performance. The resilience improvement of our model in terms of loss of energy is 607.45 kWs and 596.52 kWs for 13 and 34 buses, respectively. Our model also demonstrates generalizability across a broad range of outage scenarios.
Dose dense doxorubicin plus cyclophosphamide in a modified KEYNOTE522 regimen for triple negative breast cancer
Authors: Mai Nicholas , Myers Sara , Shen Sherry , Downs-Canner Stephanie , Robson Mark , Norton Larry , Chen Yuan , Traina Tiffany , Abuhadra Nour
Published: June 2024

The KEYNOTE-522 (KN522) regimen for neoadjuvant treatment of triple negative breast cancer (TNBC) utilized q3week dosing for doxorubicin plus cyclophosphamide (AC); however, dose-dense AC (ddAC) has demonstrated superior overall survival (OS) compared to q3week AC in anthracycline and taxane-based regimens. We performed a retrospective analysis assessing the use of ddAC in KN522 and the impact of sequencing ddAC before or after carboplatin/paclitaxel (CbT) plus pembrolizumab on multiple outcomes. 128 patients with TNBC were included. Overall pathologic complete response (pCR) rate of 56%. Sequencing of ddAC vs CbT first showed no difference in pCR rate (ddAC 55% vs. CbT 58%, p = 0.77). However, ddAC first compared to CbT first correlated with a significant increase in the incidence of overall treatment delays (ddAC 70% vs. CbT 51%, p = 0.03), with cytopenias most frequent (ddAC 59% vs. CbT 31%, p = 0.001). ddAC in a modified KN522 regimen is safe, tolerable, and effective. Efficacy is comparable regardless of chemotherapy sequencing, but ddAC first is significantly associated with higher rates of treatment delays and cytopenias.
Disease progression in proposed brain-first and body-first Parkinson’s disease subtypes
Authors: Xu Zhiheng , Hu Tianyu , Xu Chenqin , Liang Xiaoniu , Li Shiyu , Sun Yimin , Liu Fengtao , Wang Jian , Tang Yilin
Published: June 2024

A new Parkinson’s disease (PD) subtyping model has been recently proposed based on the initial location of α-synuclein inclusions, which divides PD patients into the brain-first subtype and the body-first subtype. Premotor RBD has proven to be a predictive marker of the body-first subtype. We found compared to PD patients without possible RBD (PDpRBD–, representing the brain-first subtype), PD patients with possible premotor RBD (PDpRBD+, representing the body-first subtype) had lower Movement Disorders Society Unified Parkinson’s Disease Rating Scale part III (MDS UPDRS-III) score (p = 0.022) at baseline but presented a faster progression rate (p = 0.009) in MDS UPDRS-III score longitudinally. The above finding indicates the body-first subtype exhibited a faster disease progression in motor impairments compared to the brain-first subtype and further validates the proposed subtyping model.
Low-frequency ERK and Akt activity dynamics are predictive of stochastic cell division events
Authors: Bennett Jamie J. R. , Stern Alan D. , Zhang Xiang , Birtwistle Marc R. , Pandey Gaurav
Published: June 2024

Understanding the dynamics of intracellular signaling pathways, such as ERK1/2 (ERK) and Akt1/2 (Akt), in the context of cell fate decisions is important for advancing our knowledge of cellular processes and diseases, particularly cancer. While previous studies have established associations between ERK and Akt activities and proliferative cell fate, the heterogeneity of single-cell responses adds complexity to this understanding. This study employed a data-driven approach to address this challenge, developing machine learning models trained on a dataset of growth factor-induced ERK and Akt activity time courses in single cells, to predict cell division events. The most predictive models were developed by applying discrete wavelet transforms (DWTs) to extract low-frequency features from the time courses, followed by using Ensemble Integration, a data integration and predictive modeling framework. The results demonstrated that these models effectively predicted cell division events in MCF10A cells (F-measure=0.524, AUC=0.726). ERK dynamics were found to be more predictive than Akt, but the combination of both measurements further enhanced predictive performance. The ERK model`s performance also generalized to predicting division events in RPE cells, indicating the potential applicability of these models and our data-driven methodology for predicting cell division across different biological contexts. Interpretation of these models suggested that ERK dynamics throughout the cell cycle, rather than immediately after growth factor stimulation, were associated with the likelihood of cell division. Overall, this work contributes insights into the predictive power of intra-cellular signaling dynamics for cell fate decisions, and highlights the potential of machine learning approaches in unraveling complex cellular behaviors.
Effects and avoidance of photoconversion-induced artifacts in confocal and STED microscopy
Authors: Dasgupta Anindita , Koerfer Agnes , Kokot Boštjan , Urbančič Iztok , Eggeling Christian , Carravilla Pablo
Published: June 2024

Fluorescence microscopy is limited by photoconversion due to continuous illumination, which results in not only photobleaching but also conversion of fluorescent molecules into species of different spectral properties through photoblueing. Here, we determined different fluorescence parameters of photoconverted products for various fluorophores under standard confocal and stimulated emission depletion (STED) microscopy conditions. We observed changes in both fluorescence spectra and lifetimes that can cause artifacts in quantitative measurements, which can be avoided by using exchangeable dyes.
Ensemble of global climate simulations for temperature in historical, 1.5 °C and 2.0 °C scenarios from HadAM4
Authors: Lizana Jesús , Miranda Nicole D. , Sparrow Sarah N. , Watson Peter A. G. , Zachau Walker Miriam , Wallom David C. H. , McCulloch Malcolm D.
Published: June 2024

Large ensembles of global temperature are provided for three climate scenarios: historical (2006–16), 1.5 °C and 2.0 °C above pre-industrial levels. Each scenario has 700 members (70 simulations per year for ten years) of 6-hourly mean temperatures at a resolution of 0.833° ´ 0.556° (longitude ´ latitude) over the land surface. The data was generated using the climateprediction.net (CPDN) climate simulation environment, to run HadAM4 Atmosphere-only General Circulation Model (AGCM) from the UK Met Office Hadley Centre. Biases in simulated temperature were identified and corrected using quantile mapping with reference temperature data from ERA5. The data is stored within the UK Natural and Environmental Research Council Centre for Environmental Data Analysis repository as NetCDF V4 files.
Single chamber Mg/Ca analyses of Globigerinoides ruber for paleo-proxy calibration using femtosecond LA-ICP-MS
Authors: Fischer Alexa , Schiebel Ralf , Jochum Klaus Peter , Heins Lena , Arns Anthea I. , Aardema Hedy M. , Slagter Hans , Calleja Maria Ll. , Levy Noy , Stoll Brigitte , Walter David , Weis Ulrike , Repschläger Janne , Haug Gerald H.
Published: June 2024

Mg/Ca is an independent proxy in paleoceanography to reconstruct past seawater temperature. Femtosecond Laser Ablation Inductively Coupled Plasma Mass Spectrometry (fs-LA-ICP-MS) was employed to determine the Mg/Ca composition of tests (shells) of the planktic foraminifer species Globigerinoides ruber albus (white chromotype) and G. ruber ruber (red/pink chromotype) sampled alive from the temperate to subtropical eastern North Atlantic with the research sailing yacht Eugen Seibold. Mg/Ca data are compared to (i) the measured in-situ temperature of ambient seawater, (ii) average mixed layer temperature, and (iii) sea surface temperature (SST). The pooled mean chamber Mg/Ca from each plankton tow site exhibits a positive relationship with SST. Two chamber-specific calibrations are derived, which are consistent with previous calibration equations for comparable paleo-archives. The results confirm fs-LA-ICP-MS as reliable method for determining Mg/Ca in G. ruber, and both the penultimate and antepenultimate chambers of adult specimens may provide comprehensible Mg/Ca temperatures of the surface ocean.
Publication, funding, and experimental data in support of Human Reference Atlas construction and usage
Authors: Kong Yongxin , Börner Katy
Published: June 2024

Experts from 18 consortia are collaborating on the Human Reference Atlas (HRA) which aims to map the 37 trillion cells in the healthy human body. Information relevant for HRA construction and usage is held by experts, published in scholarly papers, and captured in experimental data. However, these data sources use different metadata schemas and cannot be cross-searched efficiently. This paper documents the compilation of a dataset, named HRAlit, that links the 136 HRA v1.4 digital objects (31 organs with 4,279 anatomical structures, 1,210 cell types, 2,089 biomarkers) to 583,117 experts; 7,103,180 publications; 896,680 funded projects, and 1,816 experimental datasets. The resulting HRAlit has 22 tables with 20,939,937 records including 6 junction tables with 13,170,651 relationships. The HRAlit can be mined to identify leading experts, major papers, funding trends, or alignment with existing ontologies in support of systematic HRA construction and usage.
Chromosome-level genome assembly of the western flower thrips Frankliniella occidentalis
Authors: Song Wei , Cao Li-Jun , Chen Jin-Cui , Bao Wen-Xue , Wei Shu-Jun
Published: June 2024

The western flower thrips Frankliniella occidentalis (Thysanoptera: Thripidae) is a global invasive species that causes increasing damage by direct feeding on crops and transmission of plant viruses. Here, we assemble a previously published scaffold-level genome into a chromosomal level using Hi-C sequencing technology. The assembled genome has a size of 302.58 Mb, with a contig N50 of 1533 bp, scaffold N50 of 19.071 Mb, and BUSCO completeness of 97.8%. All contigs are anchored on 15 chromosomes. A total of 16,312 protein-coding genes are annotated in the genome with a BUSCO completeness of 95.2%. The genome contains 492 non-coding RNA, and 0.41% of interspersed repeats. In conclusion, this high-quality genome provides a convenient and high-quality resource for understanding the ecology, genetics, and evolution of thrips.
A finite element model for predicting impact-induced damage to a skin simulant
Authors: Imam Syed A. , Hughes Angus C. , Carré Matt , Driscoll Heather , Winwood Keith , Venkatraman Prabhuraj , Allen Tom
Published: June 2024

A finite element model was developed for assessing the efficacy of rugby body padding in reducing the risk of sustaining cuts and abrasions. The model was developed to predict the onset of damage to a soft tissue simulant from concentrated impact loading (i.e., stud impact) and compared against a corresponding experiment. The damage modelling techniques involved defining an element deletion criterion, whereby those on the surface of the surrogate were deleted if their maximum principal stress reached a predefined value. Candidate maximum principal stress values for element deletion criteria were identified independently from puncture test simulations on the soft tissue simulant. Experimental impacts with a stud were carried out at three energies (2, 4 and 6 J), at three angular orientations (0°, 15° and 30°) and compared to corresponding simulations. Suitable maximum principal stress values for element deletion criteria settings were first identified for the 4 J impact, selecting the candidates that best matched the experimental results. The same element deletion settings were then applied in simulations at 2 and 6 J and the validity of the model was further assessed (difference < 15% for the force at tear and < 30% for time to tear). The damage modelling techniques presented here could be applied to other skin simulants to assess the onset of skin injuries and the ability of padding to prevent them.
Sinomenine treats rheumatoid arthritis by inhibiting MMP9 and inflammatory cytokines expression: bioinformatics analysis and experimental validation
Authors: Luo Jinfang , Zhu Yi , Yu Yang , Chen Yujie , He Kang , Liu Jianxin
Published: June 2024

Rheumatoid arthritis (RA) is a chronic systemic autoimmune disease marked by inflammatory cell infiltration and joint damage. The Chinese government has approved the prescription medication sinomenine (SIN), an effective anti-inflammation drug, for treating RA. This study evaluated the possible anti-inflammatory actions of SIN in RA based on bioinformatics analysis and experiments. Six microarray datasets were acquired from the gene expression omnibus (GEO) database. We used R software to identify differentially expressed genes (DEGs) and perform function evaluations. The CIBERSORT was used to calculate the abundance of 22 infiltrating immune cells. The weighted gene co-expression network analysis (WGCNA) was used to discover genes associated with M1 macrophages. Four public datasets were used to predict the genes of SIN. Following that, function enrichment analysis for hub genes was performed. The cytoHubba and least absolute shrinkage and selection operator (LASSO) were employed to select hub genes, and their diagnostic effectiveness was predicted using the receiver operator characteristic (ROC) curve. Molecular docking was undertaken to confirm the affinity between the SIN and hub gene. Furthermore, the therapeutic efficacy of SIN was validated in LPS-induced RAW264.7 cells line using Western blot and Enzyme-linked immunosorbent assay (ELISA). The matrix metalloproteinase 9 (MMP9) was identified as the hub M1 macrophages-related biomarker in RA using bioinformatic analysis and molecular docking. Our study indicated that MMP9 took part in IL-17 and TNF signaling pathways. Furthermore, we found that SIN suppresses the MMP9 protein overexpression and pro-inflammatory cytokines, including tumor necrosis factor-α (TNF-α) and interleukin-6 (IL-6) in the LPS-induced RAW264.7 cell line. In conclusion, our work sheds new light on the pathophysiology of RA and identifies MMP9 as a possible RA key gene. In conclusion, the above findings demonstrate that SIN, from an emerging research perspective, might be a potential cost-effective anti-inflammatory medication for treating RA.
Binary quantum random number generator based on value indefinite observables
Authors: Calude Cristian S. , Svozil Karl
Published: June 2024

All quantum random number generators based on measuring value indefinite observables are at least three-dimensional because the Kochen–Specker Theorem and the Located Kochen–Specker Theorem are false in dimension two. In this article, we construct quantum random number generators based on measuring a three-dimensional value indefinite observable that generates binary quantum random outputs with the same randomness qualities as the ternary ones: the outputs are maximally unpredictable.
The hemostatic and anti-inflammatory effects of intravenous single-dose of tranexamic acid in double-segment posterior lumbar interbody fusion: a case control study
Authors: Hao Shenshen , Luo Shiying , Zhao Zhan , Dong Shengli , Liu Shuai , Li Hongke , Li Binbin , Cao Xinhao
Published: June 2024

This study aims to observe the hemostatic and anti-inflammatory effects of intravenous administration of tranexamic acid (TXA) in dual segment posterior lumbar interbody fusion (PLIF). The data of 53 patients with lumbar disease treated with double-segment PLIF were included in this study. The observation group was received a single-dose intravenous of TXA (1 g/100 mL) 15 min before skin incision after general anesthesia. The control group was not received TXA. The observation indicators included postoperative activated partial prothrombin time (APTT), thrombin time (PT), thrombin time (TT), fibrinogen (FIB), platelets (PLT), and postoperative deep vein thrombosis in the lower limbs, surgical time, intraoperative bleeding volume, postoperative drainage volume, transfusion rate, postoperative hospital stay, red blood cell (RBC), hemoglobin (HB), hematocrit (HCT), C-reactive protein (CRP), and erythrocyte sedimentation rate (ESR) on the 1st, 4th, 7th, and last tested day after surgery. All patients successfully completed the operation, and there was no deep vein thrombosis after operation. There was no statistically significant difference in postoperative APTT, PT, TT, FIB, PLT, surgical time, and postoperative hospital stay between the two groups (p > 0.05). The intraoperative bleeding volume, postoperative drainage volume, and transfusion rate in the observation group were lower than those in the control group, and the differences were statistically significant (p < 0.05). There was no statistically significant difference in RBC, HB, HCT, CRP, and ESR between the two groups on the 1st, 4th, 7th, and last tested day after surgery (p > 0.05). Intravenous administration of TXA in dual segment PLIF does not affect coagulation function and can reduce bleeding volume, postoperative drainage volume, and transfusion rate. Moreover, it does not affect the postoperative inflammatory response.
Impact of copper and cobalt-based metal-organic framework materials on the performance and stability of hole-transfer layer (HTL)-free perovskite solar cells and carbon-based
Authors: Arjmand Faezeh , Rashidi Ranjbar Zohreh
Published: June 2024

This article investigates the impact of metal-organic frameworks (MOFs) on the performance and stability of perovskite solar cells (PSCs), specifically focusing on the type of metal and the morphology of the MOF. Two types of MOFs, copper-benzene-1,3,5-tricarboxylate (Cu-BTC MOF) with spherical morphology and cobalt-benzene-1,3,5-tricarboxylate (Co-BTC MOF) with rod morphology, are synthesized and spin-coated on TiO2 substrates to form FTO/TiO2/MOF/CH3NH3PbI3/C-paste PSCs. The morphology and size of the MOFs are characterized by scanning electron microscopy (SEM), and the crystallinity and residual PbI2 of the perovskite films are analyzed by X-ray diffraction (XRD). The results show that the Co-BTC MOF PSC exhibits the highest power conversion efficiency (PCE) of 10.4% and the best stability, retaining 82% of its initial PCE after 264 h of storage in ambient air. The improved performance and stability are attributed to the enhanced crystallinity and reduced residual PbI2 of the perovskite film after Co-BTC MOF modification. The paper showcases the immense potential of MOF-based interlayers to revolutionize PSC technology, offering a path toward next-generation solar cells with enhanced performance and longevity.
Spatiotemporal organization of ant foraging from a complex systems perspective
Authors: Cristín Javier , Fernández-López Pol , Lloret-Cabot Roger , Genovart Meritxell , Méndez Viçenc , Bartumeus Frederic , Campos Daniel
Published: June 2024

We use complex systems science to explore the emergent behavioral patterns that typify eusocial species, using collective ant foraging as a paradigmatic example. Our particular aim is to provide a methodology to quantify how the collective orchestration of foraging provides functional advantages to ant colonies. For this, we combine (i) a purpose-built experimental arena replicating ant foraging across realistic spatial and temporal scales, and (ii) a set of analytical tools, grounded in information theory and spin-glass approaches, to explore the resulting data. This combined approach yields computational replicas of the colonies; these are high-dimensional models that store the experimental foraging patterns through a training process, and are then able to generate statistically similar patterns, in an analogous way to machine learning tools. These in silico models are then used to explore the colony performance under different resource availability scenarios. Our findings highlight how replicas of the colonies trained under constant and predictable experimental food conditions exhibit heightened foraging efficiencies, manifested in reduced times for food discovery and gathering, and accelerated transmission of information under similar conditions. However, these same replicas demonstrate a lack of resilience when faced with new foraging conditions. Conversely, replicas of colonies trained under fluctuating and uncertain food conditions reveal lower efficiencies at specific environments but increased resilience to shifts in food location.
ECG autoencoder based on low-rank attention
Authors: Zhang Shilin , Fang Yixian , Ren Yuwei
Published: June 2024

The prevalence of cardiovascular disease (CVD) has surged in recent years, making it the foremost cause of mortality among humans. The Electrocardiogram (ECG), being one of the pivotal diagnostic tools for cardiovascular diseases, is increasingly gaining prominence in the field of machine learning. However, prevailing neural network models frequently disregard the spatial dimension features inherent in ECG signals. In this paper, we propose an ECG autoencoder network architecture incorporating low-rank attention (LRA-autoencoder). It is designed to capture potential spatial features of ECG signals by interpreting the signals from a spatial perspective and extracting correlations between different signal points. Additionally, the low-rank attention block (LRA-block) obtains spatial features of electrocardiogram signals through singular value decomposition, and then assigns these spatial features as weights to the electrocardiogram signals, thereby enhancing the differentiation of features among different categories. Finally, we utilize the ResNet-18 network classifier to assess the performance of the LRA-autoencoder on both the MIT-BIH Arrhythmia and PhysioNet Challenge 2017 datasets. The experimental results reveal that the proposed method demonstrates superior classification performance. The mean accuracy on the MIT-BIH Arrhythmia dataset is as high as 0.997, and the mean accuracy and $$F_1$$

F
1

-score on the PhysioNet Challenge 2017 dataset are 0.850 and 0.843.
In silico predicted compound targeting the IQGAP1-GRD domain selectively inhibits growth of human acute myeloid leukemia
Authors: Sahasrabudhe Deepak M. , Liesveld Jane L. , Minhajuddin Mohammad , Singh Niloy A. , Nath Subhangi , Kumar Vishuwes Muthu , Balys Marlene , Evans Andrew G. , Azadniv Mitra , Hansen Jeanne N. , Becker Michael W. , Sharon Ashoke , Thomas V. Kaye , Moore Richard G. , Khera Manoj K. , Jordan Craig T. , Singh Rakesh K.
Published: June 2024

Acute myeloid leukemia (AML) is fatal in the majority of adults. Identification of new therapeutic targets and their pharmacologic modulators are needed to improve outcomes. Previous studies had shown that immunization of rabbits with normal peripheral WBCs that had been incubated with fluorodinitrobenzene elicited high titer antibodies that bound to a spectrum of human leukemias. We report that proteomic analyses of immunoaffinity-purified lysates of primary AML cells showed enrichment of scaffolding protein IQGAP1. Immunohistochemistry and gene-expression analyses confirmed IQGAP1 mRNA overexpression in various cytogenetic subtypes of primary human AML compared to normal hematopoietic cells. shRNA knockdown of IQGAP1 blocked proliferation and clonogenicity of human leukemia cell-lines. To develop small molecules targeting IQGAP1 we performed in-silico screening of 212,966 compounds, selected 4 hits targeting the IQGAP1-GRD domain, and conducted SAR of the ‘fittest hit’ to identify UR778Br, a prototypical agent targeting IQGAP1. UR778Br inhibited proliferation, induced apoptosis, resulted in G2/M arrest, and inhibited colony formation by leukemia cell-lines and primary-AML while sparing normal marrow cells. UR778Br exhibited favorable ADME/T profiles and drug-likeness to treat AML. In summary, AML shows response to IQGAP1 inhibition, and UR778Br, identified through in-silico studies, selectively targeted AML cells while sparing normal marrow.
Facile and scalable preparation of superhydrophobic brass mesh for efficient and rapid separation of oil and water
Authors: Asjadi Fatemeh , Yaghoobi Maliheh
Published: June 2024

A facile method for preparing superhydrophobic brass mesh is proposed based on electrochemical etching and surface modification. The impact of processing time and the electric potential of the electrochemical etching were studied on the contact angle (CA) of the mesh. The samples were examined using scanning electron microscopy, Energy-dispersive X-ray spectroscopy analysis, X-ray diffraction, and Fourier-transform infrared spectroscopy. The electrochemical etching process caused the decrement of wires’ thickness and imposed roughness. Results showed more dissolution of zinc than copper under 3 V of the electric potential and the processing times of 3 and 6 min. The optimum condition of electrochemical etching was obtained under the electric voltage of 3 V for a processing time of 6 min, which led to a CA of 155.5 ± 3.2°. The thickness of the mesh wires decreased by 17.7% due to electrochemical etching in this sample. This sample also showed low adhesion for a water drop. The efficiency of oil/water separation was above 95 for the xylene and ethyl acetate in a batch system. The effect of the flow rate of the oil–water mixture on separation efficiency was also examined. The optimum flow rate was 0.8 ml s−1 with a high separation efficiency of 96.8% for xylene/oil separation.
Palaeoproteomic identification of the original binder and modern contaminants in distemper paints from Uvdal stave church, Norway
Authors: Haghighi Zahra , Mackie Meaghan , Apalnes Ørnhøi Anne , Ramsøe Abigail , Olstad Tone Marie , Armitage Simon James , Henshilwood Christopher Stuart , Cappellini Enrico
Published: June 2024

Two distemper paint samples taken from decorative boards in Uvdal stave church, Norway, were analysed using palaeoproteomics, with an aim of identifying their binder and possible contaminants. The results point at the use of calfskin to produce hide glue as the original paint binder, and are consistent with the instructions of binder production and resource allocation in the historical records of Norway. Although we did not observe any evidence of prior restoration treatments using protein-based materials, we found abundant traces of human saliva proteins, as well as a few oats and barley peptides, likely deposited together on the boards during their discovery in the 1970s. This work illustrates the need to fully consider contamination sources in palaeoproteomics and to inform those working with such objects about the potential for their contamination.
Convergent reductive evolution of cyanobacteria in symbiosis with Dinophysiales dinoflagellates
Authors: Nakayama Takuro , Nomura Mami , Yabuki Akinori , Shiba Kogiku , Inaba Kazuo , Inagaki Yuji
Published: June 2024

The diversity of marine cyanobacteria has been extensively studied due to their vital roles in ocean primary production. However, little is understood about the diversity of cyanobacterial species involved in symbiotic relationships. In this study, we successfully sequenced the complete genome of a cyanobacterium in symbiosis with Citharistes regius, a dinoflagellate species thriving in the open ocean. A phylogenomic analysis revealed that the cyanobacterium (CregCyn) belongs to the marine picocyanobacterial lineage, akin to another cyanobacterial symbiont (OmCyn) of a different dinoflagellate closely related to Citharistes. Nevertheless, these two symbionts are representing distinct lineages, suggesting independent origins of their symbiotic lifestyles. Despite the distinct origins, the genome analyses of CregCyn revealed shared characteristics with OmCyn, including an obligate symbiotic relationship with the host dinoflagellates and a degree of genome reduction. In contrast, a detailed analysis of genome subregions unveiled that the CregCyn genome carries genomic islands that are not found in the OmCyn genome. The presence of the genomic islands implies that exogenous genes have been integrated into the CregCyn genome at some point in its evolution. This study contributes to our understanding of the complex history of the symbiosis between dinoflagellates and cyanobacteria, as well as the genomic diversity of marine picocyanobacteria.