bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractPrecise 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

AbstractGiven 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

AbstractNon-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

AbstractGene 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

AbstractArtificial 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

AbstractThe 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

AbstractSelf-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

AbstractThe 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

AbstractA 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

AbstractUnderstanding 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

AbstractFluorescence 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

AbstractLarge 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

AbstractMg/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

AbstractExperts 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

AbstractThe 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

AbstractA 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.