bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nonlinear Riparian Interactions Drive Changes in Headwater Streamflow
Authors: Newcomb Sarah K. , Godsey Sarah E. 
Published: August 2023

AbstractAs drought and wildfire frequency increase across the western United States, our ability to predict how water resources will respond to these disturbances depends on our understanding of the feedbacks that maintain watershed function and streamflow. Previous studies of non‐perennial headwater streams have ranked drivers of low‐flow conditions; however, there is a limited understanding of the interactions between these drivers and the processes through which these interactions affect streamflow. Here, we use stream water level, soil moisture, sap flow, and vapor pressure deficit data to investigate ecohydrological interactions along a mountainous headwater stream. Correlation and cross‐correlation analyses of these variables show that ecohydrological interactions are (a) nonlinear and (b) interconnected, suggesting that analyses assuming linearity and independence of each driver are inadequate for quantifying these interactions. To account for these issues and investigate causal linkages, we use convergent cross‐mapping (CCM) to characterize the feedbacks that influence non‐perennial streamflow. CCM is a nonlinear, dynamic method that has only recently been applied to hydrologic systems. CCM results reveal that atmospheric losses associated with local sap flow and vapor pressure deficit are driving changes in soil moisture and streamflow (p < 0.01) and that atmospheric losses influence stream water more directly than shallow soil moisture. These results also demonstrate that riparian processes continue to affect subsurface flows in the channel corridor even after stream drying. This study proposes a nonlinear framework for quantifying the ecohydrologic interactions that may determine how headwater streams respond to disturbance.
Thermalization and relaxation mediated by phonon management in tin-lead perovskites
Authors: Dai Linjie , Ye Junzhi , Greenham Neil C. 
Published: August 2023

AbstractUnderstanding and control of ultrafast non-equilibrium processes in semiconductors is key to making use of the full photon energy before relaxation, leading to new ways to break efficiency limits for solar energy conversion. In this work, we demonstrate the observation and modulation of slow relaxation in uniformly mixed tin-lead perovskites (MASnxPb1-xI3 and CsSnxPb1-xI3 nanocrystals). Transient absorption measurements reveal that slow cooling mediated by a hot phonon bottleneck effect appears at carrier densities above ~1018 cm−3 for tin-lead alloy nanocrystals, and tin addition is found to give rise to suppressed cooling. Within the alloy nanoparticles, the combination of a newly introduced high-energy band, screened Fröhlich interaction, suppressed Klemens decay and reduced thermal conductivity (acoustic phonon transport) with increased tin content contributes to the slowed relaxation. For inorganic nanocrystals where defect states couple strongly with carriers, sodium doping has been confirmed to benefit in maintaining hot carriers by decoupling them from deep defects, leading to a decreased energy-loss rate during thermalization and an enhanced hot phonon bottleneck effect. The slow cooling we observe uncovers the intrinsic photophysics of perovskite nanocrystals, with implications for photovoltaic applications where suppressed cooling could lead to hot-carrier solar cells.
High-order femtosecond vortices up to the 30th order generated from a powerful mode-locked Hermite-Gaussian laser
Authors: Liu Hongyu , Yan Lisong , Chen Hongshan , Liu Xin , Liu Heyan , Chew Soo Hoon , Gliserin Alexander , Wang Qing , Zhang Jinwei 
Published: August 2023

AbstractFemtosecond vortex beams are of great scientific and practical interest because of their unique phase properties in both the longitudinal and transverse modes, enabling multi-dimensional quantum control of light fields. Until now, generating femtosecond vortex beams for applications that simultaneously require ultrashort pulse duration, high power, high vortex order, and a low cost and compact laser source has been very challenging due to the limitations of available generation methods. Here, we present a compact apparatus that generates powerful high-order femtosecond vortex pulses via astigmatic mode conversion from a mode-locked Hermite-Gaussian Yb:KGW laser oscillator in a hybrid scheme using both the translation-based off-axis pumping and the angle-based non-collinear pumping techniques. This hybrid scheme enables the generation of femtosecond vortices with a continuously tunable vortex order from the 1st up to the 30th order, which is the highest order obtained from any femtosecond vortex laser source based on a mode-locked oscillator. The average powers and pulse durations of all resulting vortex pulses are several hundred milliwatts and <650 fs, respectively. In particular, 424-fs 11th-order vortex pulses have been achieved with an average power of 1.6 W, several times more powerful than state-of-the-art oscillator-based femtosecond vortex sources.
NPM promotes hepatotoxin-induced fibrosis by inhibiting ROS-induced apoptosis of hepatic stellate cells and upregulating lncMIAT-induced TGF-β2
Authors: Ding Xue , Zhu Xin-Le , Xu Dong-Hui , Li Shuang , Yang Qiong , Feng Xian , Wei Yong-Gui , Li Huan , Yang Ling , Zhang Yu-Jun , Deng Xiao-Ling , Liu Kuan-Can , Shi Song-Lin 
Published: August 2023

AbstractLiver fibrosis is caused by a variety of chronic liver injuries and has caused significant morbidity and mortality in the world with increasing tendency. Elucidation of the molecular mechanism of liver fibrosis is the basis for intervention of this pathological process and drug development. Nucleophosmin (NPM) is a widely expressed nucleolar phosphorylated protein, which is particularly important for cell proliferation, differentiation and survival. The biological role of NPM in liver fibrosis remains unknown. Here we show that NPM promotes liver fibrosis through multiple pathways. Our study found that NPM was up-regulated in cirrhosis tissues and activated in hepatic stellate cells (HSCs). NPM inhibition reduced liver fibrosis markers expression in HSCs and inhibited the HSCs proliferation and migration. In mice model, NPM knockdown in HSCs or application of specific NPM inhibitor can remarkably attenuate hepatic fibrosis. Mechanistic analysis showed that NPM promotes hepatic fibrosis by inhibiting HSCs apoptosis through Akt/ROS pathway and by upregulating TGF-β2 through Akt-induced lncMIAT. LncMIAT up-regulated TGF-β2 mRNA by competitively sponging miR-16-5p. In response to liver injury, hepatocytes, Kupffer cells and HSCs up-regulated NPM to increase TGF-β2 secretion to activate HSCs in a paracrine or autocrine manner, leading to increased liver fibrosis. Our study demonstrated that NPM regulated hepatotoxin-induced fibrosis through Akt/ROS-induced apoptosis of HSCs and via the Akt/lncMIAT-up-regulated TGF-β2. Inhibition of NPM or application of NPM inhibitor CIGB300 remarkably attenuated liver fibrosis. NPM serves a potential new drug target for liver fibrosis.
Ficolin B secreted by alveolar macrophage exosomes exacerbates bleomycin-induced lung injury via ferroptosis through the cGAS-STING signaling pathway
Authors: Wu Xu , Jiang Yixia , Li Rong , Xia Yezhou , Li Feifan , Zhao Meiyun , Li Guoqing , Tan Xiaowu 
Published: August 2023

AbstractPathogenesis exploration and timely intervention of lung injury is quite necessary as it has harmed human health worldwide for years. Ficolin B (Fcn B) is a recognition molecule that can recognize a variety of ligands and play an important role in mediating the cell cycle, immune response, and tissue homeostasis in the lung. However, the role of Fcn B in bleomycin (BLM)-induced lung injury is obscure. This study aims to investigate the sources of Fcn B and its mechanism in BLM-induced lung injury. WT, Fcna-/-, and Fcnb-/- mice were selected to construct the BLM-induced lung injury model. Lung epithelial cells were utilized to construct the BLM-induced cell model. Exosomes that were secreted from alveolar macrophages (AMs) were applied for intervention by transporting Fcn B. Clinical data suggested M-ficolin (homologous of Fcn B) was raised in plasma of interstitial lung disease (ILD) patients. In the mouse model, macrophage-derived Fcn B aggravated BLM-induced lung injury and fibrosis. Fcn B further promoted the development of autophagy and ferroptosis. Remarkably, cell experiment results revealed that Fcn B transported by BLM-induced AMs exosomes accelerated autophagy and ferroptosis in lung epithelial cells through the activation of the cGAS-STING pathway. In contrast, the application of 3-Methyladenine (3-MA) reversed the promotion effect of Fcn B from BLM-induced AMs exosomes on lung epithelial cell damage by inhibiting autophagy-dependent ferroptosis. Meanwhile, in the BLM-induced mice model, the intervention of Fcn B secreted from BLM-induced AMs exosomes facilitated lung injury and fibrosis via ferroptosis. In summary, this study demonstrated that Fcn B transported by exosomes from AMs exacerbated BLM-induced lung injury by promoting lung epithelial cells ferroptosis through the cGAS-STING signaling pathway.
Hardware-aware training for large-scale and diverse deep learning inference workloads using in-memory computing-based accelerators
Authors: Rasch Malte J. , Mackin Charles , Le Gallo Manuel , Chen An , Fasoli Andrea , Odermatt Frédéric , Li Ning , Nandakumar S. R. , Narayanan Pritish , Tsai Hsinyu , Burr Geoffrey W. , Sebastian Abu , Narayanan Vijay 
Published: August 2023

AbstractAnalog in-memory computing—a promising approach for energy-efficient acceleration of deep learning workloads—computes matrix-vector multiplications but only approximately, due to nonidealities that often are non-deterministic or nonlinear. This can adversely impact the achievable inference accuracy. Here, we develop an hardware-aware retraining approach to systematically examine the accuracy of analog in-memory computing across multiple network topologies, and investigate sensitivity and robustness to a broad set of nonidealities. By introducing a realistic crossbar model, we improve significantly on earlier retraining approaches. We show that many larger-scale deep neural networks—including convnets, recurrent networks, and transformers—can in fact be successfully retrained to show iso-accuracy with the floating point implementation. Our results further suggest that nonidealities that add noise to the inputs or outputs, not the weights, have the largest impact on accuracy, and that recurrent networks are particularly robust to all nonidealities.
Heterogeneous receptor expression underlies non-uniform peptidergic modulation of olfaction in Drosophila
Authors: Sizemore Tyler R. , Jonaitis Julius , Dacks Andrew M. 
Published: August 2023

AbstractSensory systems are dynamically adjusted according to the animal’s ongoing needs by neuromodulators, such as neuropeptides. Neuropeptides are often widely-distributed throughout sensory networks, but it is unclear whether such neuropeptides uniformly modulate network activity. Here, we leverage the Drosophila antennal lobe (AL) to resolve whether myoinhibitory peptide (MIP) uniformly modulates AL processing. Despite being uniformly distributed across the AL, MIP decreases olfactory input to some glomeruli, while increasing olfactory input to other glomeruli. We reveal that a heterogeneous ensemble of local interneurons (LNs) are the sole source of AL MIP, and show that differential expression of the inhibitory MIP receptor across glomeruli allows MIP to act on distinct intraglomerular substrates. Our findings demonstrate how even a seemingly simple case of modulation can have complex consequences on network processing by acting non-uniformly within different components of the overall network.
Reversal of cell, circuit and seizure phenotypes in a mouse model of DNM1 epileptic encephalopathy
Authors: Bonnycastle Katherine , Dobson Katharine L. , Blumrich Eva-Maria , Gajbhiye Akshada , Davenport Elizabeth C. , Pronot Marie , Steinruecke Moritz , Trost Matthias , Gonzalez-Sulser Alfredo , Cousin Michael A. 
Published: August 2023

AbstractDynamin-1 is a large GTPase with an obligatory role in synaptic vesicle endocytosis at mammalian nerve terminals. Heterozygous missense mutations in the dynamin-1 gene (DNM1) cause a novel form of epileptic encephalopathy, with pathogenic mutations clustering within regions required for its essential GTPase activity. We reveal the most prevalent pathogenic DNM1 mutation, R237W, disrupts dynamin-1 enzyme activity and endocytosis when overexpressed in central neurons. To determine how this mutation impacted cell, circuit and behavioural function, we generated a mouse carrying the R237W mutation. Neurons from heterozygous mice display dysfunctional endocytosis, in addition to altered excitatory neurotransmission and seizure-like phenotypes. Importantly, these phenotypes are corrected at the cell, circuit and in vivo level by the drug, BMS-204352, which accelerates endocytosis. Here, we demonstrate a credible link between dysfunctional endocytosis and epileptic encephalopathy, and importantly reveal that synaptic vesicle recycling may be a viable therapeutic target for monogenic intractable epilepsies.
Deep learning model improves tumor-infiltrating lymphocyte evaluation and therapeutic response prediction in breast cancer
Authors: Choi Sangjoon , Cho Soo Ick , Jung Wonkyung , Lee Taebum , Choi Su Jin , Song Sanghoon , Park Gahee , Park Seonwook , Ma Minuk , Pereira Sérgio , Yoo Donggeun , Shin Seunghwan , Ock Chan-Young , Kim Seokhwi 
Published: August 2023

AbstractTumor-infiltrating lymphocytes (TILs) have been recognized as key players in the tumor microenvironment of breast cancer, but substantial interobserver variability among pathologists has impeded its utility as a biomarker. We developed a deep learning (DL)-based TIL analyzer to evaluate stromal TILs (sTILs) in breast cancer. Three pathologists evaluated 402 whole slide images of breast cancer and interpreted the sTIL scores. A standalone performance of the DL model was evaluated in the 210 cases (52.2%) exhibiting sTIL score differences of less than 10 percentage points, yielding a concordance correlation coefficient of 0.755 (95% confidence interval [CI], 0.693–0.805) in comparison to the pathologists’ scores. For the 226 slides (56.2%) showing a 10 percentage points or greater variance between pathologists and the DL model, revisions were made. The number of discordant cases was reduced to 116 (28.9%) with the DL assistance (p < 0.001). The DL assistance also increased the concordance correlation coefficient of the sTIL score among every two pathologists. In triple-negative and human epidermal growth factor receptor 2 (HER2)-positive breast cancer patients who underwent the neoadjuvant chemotherapy, the DL-assisted revision notably accentuated higher sTIL scores in responders (26.8 ± 19.6 vs. 19.0 ± 16.4, p = 0.003). Furthermore, the DL-assistant revision disclosed the correlation of sTIL-high tumors (sTIL ≥ 50) with the chemotherapeutic response (odd ratio 1.28 [95% confidence interval, 1.01–1.63], p = 0.039). Through enhancing inter-pathologist concordance in sTIL interpretation and predicting neoadjuvant chemotherapy response, here we report the utility of the DL-based tool as a reference for sTIL scoring in breast cancer assessment.
Egyptian mandarin peel oil's anti-scabies potential via downregulation-of-inflammatory/immune-cross-talk: GC–MS and PPI network studies
Authors: Elmaidomy Abeer H. , Abdel-Maqsoud Nehad M. Reda , Tammam Omar. Y. , Abdel-Rahman Islam M. , Elrehany Mahmoud A. , Bakhsh Hussain T. , Altemani Faisal H. , Algehainy Naseh A. , Alzubaidi Mubarak A. , Alsenani Faisal , Sayed Ahmed M. , Abdelmohsen Usama Ramadan , Zahran Eman Maher 
Published: August 2023

AbstractThe current study investigated the scabicidal potential of Egyptian mandarin peel oil (Citrus reticulata Blanco, F. Rutaceae) against sarcoptic mange-in-rabbits. Analysis of the oil's GC–MS identified a total of 20 compounds, accounting for 98.91% of all compounds found. Mandarin peel oil topical application improved all signs of infection, causing a scabicidal effect three days later, whereas in vitro application caused complete mite mortality one day later. In comparison to ivermectin, histopathological analysis showed that the epidermis' inflammatory-infiltration/hyperkeratosis-had disappeared. In addition to TIMP-1, the results of the mRNA gene expression analysis showed upregulation of I-CAM-1-and-KGF and downregulation of ILs-1, 6, 10, VEGF, MMP-9, and MCP-1. The scabies network was constructed and subjected to a comprehensive bioinformatic evaluation. TNF-, IL-1B, and IL-6, the top three hub protein-coding genes, have been identified as key therapeutic targets for scabies. From molecular docking data, compounds 15 and 16 acquired sufficient affinity towards the three screened proteins, particularly both possessing higher affinity towards the IL-6 receptor. Interestingly, it achieved a higher binding energy score than the ligand of the docked protein rather than displaying proper binding interactions like those of the ligand. Meanwhile, geraniol (15) showed the highest affinity towards the GST protein, suggesting its contribution to the acaricidal effect of the extract. The subsequent, MD simulations revealed that geraniol can achieve stable binding inside the binding site of both GST and IL-6. Our findings collectively revealed the scabicidal ability of mandarin peel extract for the first time, paving the way for an efficient, economical, and environmentally friendly herbal alternative for treating rabbits with Sarcoptes mange.
High gravity material extrusion system and extruded polylactic acid performance enhancement
Authors: Jiang Xin , Koike Ryo 
Published: August 2023

AbstractAdditive manufacturing (AM) has gained significant attention in recent years owing to its ability to quickly and easily fabricate complex shapes and geometries that are difficult or impossible to achieve with traditional manufacturing methods. This study presents the development of a high-gravity material extrusion (HG-MEX) system, which generates a high-gravity field through centrifugal acceleration. In this process, the material is dissolved by heating the nozzle and subsequently deposited on the construction platform. The primary objective of this research is to evaluate the positive effects of gravity on material extrusion (MEX), which is a key aspect of AM. To accomplish this, a combined machine comprising a MEX unit and centrifuge is constructed. This HG-MEX system is used to analyze and reflect the influence of gravity on the material extrusion. The experimental evaluations demonstrate that the application of high gravity is a promising approach to improve the shape accuracy and performance of the parts fabricated through MEX. Notably, our results confirm the feasibility of utilizing MEX under high gravity to enhance performance in AM processes.
Trajectory of hiPSCs derived neural progenitor cells differentiation into dermal papilla-like cells and their characteristics
Authors: Riabinin Andrei , Kalabusheva Ekaterina , Khrustaleva Anastasia , Akulinin Mikhail , Tyakht Alexander , Osidak Egor , Chermnykh Elina , Vasiliev Andrey , Vorotelyak Ekaterina 
Published: August 2023

AbstractDermal papilla cells (DPCs) play roles in key functions of the epidermis such as hair generation. The use of human induced pluripotent cells (hiPSCs) makes it possible to obtain DP-like cells and study the molecular mechanisms of DPC development during embryogenesis. In this work, we studied the phenotypic trajectory of hiPSCs during their differentiation into DP-like cells and evaluated the epithelial-mesenchymal interaction potential of the resulting cell line. Specifically, we differentiated hiPSCs into neural progenitor cells (NPCs) and subsequently into DP-like cells. Analysis of bulk RNA-seq data during this process enabled us to observe gene expression dynamics during five stages of dermal differentiation. Furthermore, functional assays (organoids in both collagen gels and hanging drop cultures and tubulogenesis assays) revealed that the dermal cell lines we generated could interact with epidermal cells.
A comparative assessment between Globorisk and WHO cardiovascular disease risk scores: a population-based study
Authors: Dehghan Azizallah , Rezaei Fatemeh , Aune Dagfinn 
Published: August 2023

AbstractThe Globorisk and WHO cardiovascular risk prediction models are country-specific and region-specific, respectively. The goal of this study was to assess the agreement and correlation between the WHO and Globorisk 10-year cardiovascular disease risk prediction models. The baseline data of 6796 individuals aged 40–74 years who participated in the Fasa cohort study without a history of cardiovascular disease or stroke at baseline were included. In the WHO and Globorisk models scores were calculated using age, sex, systolic blood pressure (SBP), current smoking, diabetes, and total cholesterol for laboratory-based risk and age, sex, SBP, current smoking, and body mass index (BMI) for non-laboratory-based risk (office-based or BMI-based). In Globorisk and WHO risk agreement across risk categories (low, moderate, and high) was examined using the kappa statistic. Also, Pearson correlation coefficients and scatter plots were used to assess the correlation between Globorisk and WHO models. Bland–Altman plots were presented for determination agreement between Globorisk and WHO risk scores in individual’s level. In laboratory-based models, agreement across categories was substantial in the overall population (kappa values: 0.75) and also for females (kappa values: 0.74) and males (kappa values: 0.76), when evaluated separately. In non-laboratory-based models, agreement across categories was substantial for the whole population (kappa values: 0.78), and almost perfect for among males (kappa values: 0.82) and substantial for females (kappa values: 0.73). The results showed a very strong positive correlation (r ≥ 0.95) between WHO and Globorisk laboratory-based scores for the whole population, males, and females and also a very strong positive correlation (r > 0.95) between WHO and Globorisk non-laboratory-based scores for the whole population, males, and females. In the laboratory-based models, the limit of agreements was better in males (95%CI 2.1 to − 4.2%) than females (95%CI 4.3 to − 7.3%). Also, in the non-laboratory-based models, the limit of agreements was better in males (95%CI 2.9 to − 4.0%) than females (95%CI 3.2 to − 6.1%). There was a good agreement between both the laboratory-based and the non-laboratory-based WHO models and the Globorisk models. The correlation between two models was very strongly positive. However, in the Globorisk models, more people were in high-risk group than in the WHO models. The scatter plots and Bland–Altman plots showed systematic differences between the two scores that vary according to the level of risk. So, for these models may be necessary to modify the cut points of risk groups. The validity of these models must be determined for this population.