bluuebunny/crossref_metadata_2025_split huggingface dataset:
Selective amide bond formation in redox-active coacervate protocells
Authors: Wang Jiahua , Abbas Manzar , Wang Junyou , Spruijt Evan 
Published: December 2023

AbstractCoacervate droplets are promising protocell models because they sequester a wide range of guest molecules and may catalyze their conversion. However, it remains unclear how life’s building blocks, including peptides, could be synthesized from primitive precursor molecules inside such protocells. Here, we develop a redox-active protocell model formed by phase separation of prebiotically relevant ferricyanide (Fe(CN)63−) molecules and cationic peptides. Their assembly into coacervates can be regulated by redox chemistry and the coacervates act as oxidizing hubs for sequestered metabolites, like NAD(P)H and gluthathione. Interestingly, the oxidizing potential of Fe(CN)63− inside coacervates can be harnessed to drive the formation of new amide bonds between prebiotically relevant amino acids and α-amidothioacids. Aminoacylation is enhanced in Fe(CN)63−/peptide coacervates and selective for amino acids that interact less strongly with the coacervates. We finally use Fe(CN)63−-containing coacervates to spatially control assembly of fibrous networks inside and at the surface of coacervate protocells. These results provide an important step towards the prebiotically relevant integration of redox chemistry in primitive cell-like compartments.
The Cousa objective: a long-working distance air objective for multiphoton imaging in vivo
Authors: Yu Che-Hang , Yu Yiyi , Adsit Liam M. , Chang Jeremy T. , Barchini Jad , Moberly Andrew H. , Benisty Hadas , Kim Jinkyung , Young Brent K. , Heng Kathleen , Farinella Deano M. , Leikvoll Austin , Pavan Rishaab , Vistein Rachel , Nanfito Brandon R. , Hildebrand David G. C. , Otero-Coronel Santiago , Vaziri Alipasha , Goldberg Jeffrey L. , Ricci Anthony J. , Fitzpatrick David , Cardin Jessica A. , Higley Michael J. , Smith Gordon B. , Kara Prakash , Nielsen Kristina J. , Smith Ikuko T. , Smith Spencer LaVere 
Published: December 2023

AbstractMultiphoton microscopy can resolve fluorescent structures and dynamics deep in scattering tissue and has transformed neural imaging, but applying this technique in vivo can be limited by the mechanical and optical constraints of conventional objectives. Short working distance objectives can collide with compact surgical windows or other instrumentation and preclude imaging. Here we present an ultra-long working distance (20 mm) air objective called the Cousa objective. It is optimized for performance across multiphoton imaging wavelengths, offers a more than 4 mm2 field of view with submicrometer lateral resolution and is compatible with commonly used multiphoton imaging systems. A novel mechanical design, wider than typical microscope objectives, enabled this combination of specifications. We share the full optical prescription, and report performance including in vivo two-photon and three-photon imaging in an array of species and preparations, including nonhuman primates. The Cousa objective can enable a range of experiments in neuroscience and beyond.
Continuous solutions of cosmic-rays and waves in astrophysical environments
Authors: Irshad K. , Ramzan B. , Qazi S. N. A. , Areeb F. , Rasheed A. , Jamil M. 
Published: December 2023

AbstractThe propagation of energetic charged particles and cosmic rays in magnetized thermal plasma is focused. We consider a four-fluid system that consists of thermal plasma, cosmic rays, and two opposite propagating Alfvén waves to investigate the dynamics and energy exchange mechanisms of the system. Additionally, cosmic rays diffusion within the plasma is considered along the magnetic field lines whereas neglected the cross field line diffusion effects. This study is important for understanding of pressure gradients and their impact on the feedback in astrophysical environment. Over the last few decades, this problem becomes important when we discuss the interaction of cosmic rays with plasma in space, such as interstellar clouds or interstellar medium.
Rapid and accurate detection of SARS-CoV-2 using the RHAM technology
Authors: Xiao Zhuo , Liu Xiaoli , Kang Xiaolong , Feng Yaoheng , Zheng Lijun , Chen Chong 
Published: December 2023

AbstractRapid and sensitive detection of pathogens is of utmost importance in interrupting the transmission chain of infectious diseases. In recent years, this has proven to be vital during the coronavirus disease (COVID-19) global pandemic that put countless lives at risk. Numerous molecular diagnostic methods were used, including RT-PCR, NASBA, E-SDA, E-RCA, LAMP, and RPA. However, these technologies potentially require primer optimization and complex instruments. Here, we propose the RHAM (RNase Hybridization-Assisted amplification) system as a rapid, specific, and sensitive molecular diagnosis platform. Combining the LAMP and RNase HII-mediated fluorescent reporter, the RHAM system can amplify and visualize the target in one isothermal system with high sensitivity (5 × 102 copies/mL). There was no cross-reactivity with other common respiratory viruses. Analysis of clinical samples revealed the RHAM system to generate positive signals within 15 min without false positive or negative results. The present study shows that RHAM is not only an ideal platform for detecting pathogens, such as SARS-CoV-2 but can be potentially applied in POCT settings.
4D structural changes and pore network model of biomass during pyrolysis
Authors: Edeh Ifeoma Gloria , Masek Ondrej , Fusseis Florian 
Published: December 2023

AbstractBiochar is an engineered carbon-rich substance used for soil improvement, environmental management, and other diverse applications. To date, the understanding of how biomass affects biochar microstructure has been limited due to the complexity of analysis involved in tracing the changes in the physical structure of biomass as it undergoes thermochemical conversion. In this study, we used synchrotron x-ray micro-tomography to visualize changes in the internal structure of biochar from diverse feedstock (miscanthus straw pellets, wheat straw pellets, oilseed rape straw pellets, and rice husk) during pyrolysis by collecting a sequence of 3D scans at 50 °C intervals during progressive heating from 50 °C to 800 °C. The results show a strong dependence of biochar porosity on feedstock as well as pyrolysis temperature, with observed porosity in the range of 7.41–60.56%. Our results show that the porosity, total surface area, pore volume, and equivalent diameter of the largest pore increases with increasing pyrolysis temperature up to about 550 °C. The most dramatic development of pore structure occurred in the temperature range of 350–450 °C. This understanding is pivotal for optimizing biochar’s properties for specific applications in soil improvement, environmental management, and beyond. By elucidating the nuanced variations in biochar’s physical characteristics across different production temperatures and feedstocks, this research advances the practical application of biochar, offering significant benefits in agricultural, environmental, and engineering contexts.
Leveraging machine learning to distinguish between bacterial and viral induced pharyngitis using hematological markers: a retrospective cohort study
Authors: Jin Zhe , Ma Fengmei , Chen Haoyang , Guo Shufan 
Published: December 2023

AbstractAccurate differentiation between bacterial and viral-induced pharyngitis is recognized as essential for personalized treatment and judicious antibiotic use. From a cohort of 693 patients with pharyngitis, data from 197 individuals clearly diagnosed with bacterial or viral infections were meticulously analyzed in this study. By integrating detailed hematological insights with several machine learning algorithms, including Random Forest, Neural Networks, Decision Trees, Support Vector Machine, Naive Bayes, and Lasso Regression, for potential biomarkers were identified, with an emphasis being placed on the diagnostic significance of the Monocyte-to-Lymphocyte Ratio. Distinct inflammatory signatures associated with bacterial infections were spotlighted in this study. An innovation introduced in this research was the adaptation of the high-accuracy Lasso Regression model for the TI-84 calculator, with an AUC (95% CI) of 0.94 (0.925–0.955) being achieved. Using this adaptation, pivotal laboratory parameters can be input on-the-spot and infection probabilities can be computed subsequently. This methodology embodies an improvement in diagnostics, facilitating more effective distinction between bacterial and viral infections while fostering judicious antibiotic use.
Augmenting an electronic Ising machine to effectively solve boolean satisfiability
Authors: Sharma Anshujit , Burns Matthew , Hahn Andrew , Huang Michael 
Published: December 2023

AbstractWith the slowdown of improvement in conventional von Neumann systems, increasing attention is paid to novel paradigms such as Ising machines. They have very different approach to solving combinatorial optimization problems. Ising machines have shown great potential in solving binary optimization problems like MaxCut. In this paper, we present an analysis of these systems in boolean satisfiability (SAT) problems. We demonstrate that, in the case of 3-SAT, a basic architecture fails to produce meaningful acceleration, largely due to the relentless progress made in conventional SAT solvers. Nevertheless, careful analysis attributes part of the failure to the lack of two important components: cubic interactions and efficient randomization heuristics. To overcome these limitations, we add proper architectural support for cubic interaction on a state-of-the-art Ising machine. More importantly, we propose a novel semantic-aware annealing schedule that makes the search-space navigation much more efficient than existing annealing heuristics. Using numerical simulations, we show that such an “Augmented” Ising Machine for SAT is projected to outperform state-of-the-art software-based, GPU-based and conventional hardware SAT solvers by orders of magnitude.
Global birdsong embeddings enable superior transfer learning for bioacoustic classification
Authors: Ghani Burooj , Denton Tom , Kahl Stefan , Klinck Holger 
Published: December 2023

AbstractAutomated bioacoustic analysis aids understanding and protection of both marine and terrestrial animals and their habitats across extensive spatiotemporal scales, and typically involves analyzing vast collections of acoustic data. With the advent of deep learning models, classification of important signals from these datasets has markedly improved. These models power critical data analyses for research and decision-making in biodiversity monitoring, animal behaviour studies, and natural resource management. However, deep learning models are often data-hungry and require a significant amount of labeled training data to perform well. While sufficient training data is available for certain taxonomic groups (e.g., common bird species), many classes (such as rare and endangered species, many non-bird taxa, and call-type) lack enough data to train a robust model from scratch. This study investigates the utility of feature embeddings extracted from audio classification models to identify bioacoustic classes other than the ones these models were originally trained on. We evaluate models on diverse datasets, including different bird calls and dialect types, bat calls, marine mammals calls, and amphibians calls. The embeddings extracted from the models trained on bird vocalization data consistently allowed higher quality classification than the embeddings trained on general audio datasets. The results of this study indicate that high-quality feature embeddings from large-scale acoustic bird classifiers can be harnessed for few-shot transfer learning, enabling the learning of new classes from a limited quantity of training data. Our findings reveal the potential for efficient analyses of novel bioacoustic tasks, even in scenarios where available training data is limited to a few samples.
Ionomic analysis, polyphenols characterization, analgesic, antiinflammatory and antioxidant capacities of Cistus laurifolius leaves: in vitro, in vivo, and in silico investigations
Authors: Zouhri Aziz , Bouddine Toufik , Menyiy Naoual El , Kachkoul Rabie , El-mernissi Yahya , Siddique Farhan , moubachir Rania , Khallouki Farid , Salamatullah Ahmad Mohammad , Wondmie Gezahign Fentahun , Bourhia Mohammed , Hajji Lhoussain 
Published: December 2023

AbstractThis study aims to investigate the chemical and mineral composition, antioxidant, analgesic, and anti-inflammatory effects of the aqueous extract of Cistus laurifolius var. atlanticus Pit. (Cistaceae). Additionally, molecular docking interactions of various ligands with antioxidant protein target urate oxidase (1R4U) and anti-inflammatory protein target cyclooxygenase-2 (3LN1), revealing potential dual activities and highlighting specific residue interactions. The chemical characterization focused at first glance on the mineral composition which showed that C. laurifolius extract is a mineral-rich source of potassium (K), magnesium (Mg), manganese (Mn), sodium (Na), phosphorus (P), and zinc (Zn). We next performed, ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) analysis, the latter showed various polyphenols in C. laurifolius extract including Gallic acid as the predominant polyphenol. Isoquercetin, Taxifolin and Astragalin were also among the major flavonoids detected. The antioxidant capacity of C. laurifolius leaves was tested using 2,2′-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid) (ABTS), 2,2-diphenyl-1- picrylhydrazyl (DPPH) and reducing power (RP) assays. In vitro analysis of the anti-inflammatory property of C. laurifolius leaves was conducted by the albumin denaturation test and the in vivo was assessed in the sequel by carrageenan-induced paw edema test. The analgesic activity was evaluated in vivo using tail flick, acetic acid-induced contortion, and plantar tests. The findings showed that the leave extract had a powerful antioxidant activity with an IC50 values of 2.92 ± 0.03 µg/mL (DPPH) and 2.59 ± 0.09 µg/mL (in RP test). The studied extract strongly abolished the induced inflammation (82%). Albumin denaturation test recorded an IC50 value of 210 µg/mL. Importantly, the oral administration of C. laurifolius extract considerably reduced the nociceptive effect of acetic acid in rats, showing a significant analgesic effect in a dose-related manner. Altogether, our results showed that C. laurifolius can be a promising source of phytochemicals for drug development potential.
Comprehensive analysis of the potential biological significance of cuproptosis-related gene LIPT2 in pan-cancer prognosis and immunotherapy
Authors: Wang Wangbiao , Li Shiang , Huang Yumian , Guo Jun , Sun Lili , Sun Gang 
Published: December 2023

AbstractLipoyltransferase 2 (LIPT2) acts as a key enzyme involved in fatty acid metabolism and cell membrane synthesis. However, the biological function of LIPT2 in various cancer types and its potential significance in prognosis continue to be unresolved. For this analysis, we evaluated the expression levels and the significance of prognosis of LIPT2 gene in all cancers by various bioinformatics methods. The results found that LIPT2 was dramatically overexpressed in the vast majority of cancers. The upregulated LIPT2 was related to bad prognosis in Brain Lower Grade Glioma (LGG), Glioma (GBMLGG), Glioblastoma multiforme (GBM), Kidney Chromophobe (KICH), and High-Risk Wilms Tumor (WT), while it had a favorable prognosis in Kidney renal clear cell carcinoma (KIRC), and Ovarian serous cystadenocarcinoma (OV), Pan-kidney cohort (KIPAN). Furthermore, we assessed the mutation status, methylation levels, and immune status of LIPT2 in pan-cancer. Single-cell sequencing results revealed the correlation of LIPT2 expression with various biological characteristics such as DNA lesion, tumor angiogenesis, cell apoptosis, metastasis, and invasion. Enrichment analysis unveiled potential molecular regulatory mechanisms. In conclusion, our research reveals a detailed key role of LIPT2 in the progression, prognosis, and immune efficacy of various forms of cancer. Therefore, we have reason to believe that LIPT2 has the potential to be a candidate biomarker for tumors.
Tomato maturity recognition with convolutional transformers
Authors: Khan Asim , Hassan Taimur , Shafay Muhammad , Fahmy Israa , Werghi Naoufel , Mudigansalage Seneviratne , Hussain Irfan 
Published: December 2023

AbstractTomatoes are a major crop worldwide, and accurately classifying their maturity is important for many agricultural applications, such as harvesting, grading, and quality control. In this paper, the authors propose a novel method for tomato maturity classification using a convolutional transformer. The convolutional transformer is a hybrid architecture that combines the strengths of convolutional neural networks (CNNs) and transformers. Additionally, this study introduces a new tomato dataset named KUTomaData, explicitly designed to train deep-learning models for tomato segmentation and classification. KUTomaData is a compilation of images sourced from a greenhouse in the UAE, with approximately 700 images available for training and testing. The dataset is prepared under various lighting conditions and viewing perspectives and employs different mobile camera sensors, distinguishing it from existing datasets. The contributions of this paper are threefold: firstly, the authors propose a novel method for tomato maturity classification using a modular convolutional transformer. Secondly, the authors introduce a new tomato image dataset that contains images of tomatoes at different maturity levels. Lastly, the authors show that the convolutional transformer outperforms state-of-the-art methods for tomato maturity classification. The effectiveness of the proposed framework in handling cluttered and occluded tomato instances was evaluated using two additional public datasets, Laboro Tomato and Rob2Pheno Annotated Tomato, as benchmarks. The evaluation results across these three datasets demonstrate the exceptional performance of our proposed framework, surpassing the state-of-the-art by 58.14%, 65.42%, and 66.39% in terms of mean average precision scores for KUTomaData, Laboro Tomato, and Rob2Pheno Annotated Tomato, respectively. This work can potentially improve the efficiency and accuracy of tomato harvesting, grading, and quality control processes.
Hemiarthroplasty through SuperPATH versus hemiarthroplasty through conventional approaches in patients with femoral neck fractures: a systematic review and meta-analysis of randomized controlled trials
Authors: Ramadanov Nikolai , Jóźwiak Katarzyna , Marinova-Kichikova Polina , Lazaru Philip , Dimitrov Dobromir 
Published: December 2023

AbstractThe aim was to conduct a systematic review of literature and meta-analysis of randomized controlled trials (RCTs) comparing short-term outcomes of bipolar hemiarthroplasty (HA) through SuperPATH and bipolar HA through conventional approaches (CAs) in patients with femoral neck fractures. The following PICO question was formulated: In human participants with femoral neck fractures, are the short-term outcomes of SuperPATH HA better than the short-term outcomes of CAs HA? The following databases were searched until 25 August 2023: PubMed, CNKI, CENTRAL of The Cochrane Library, Clinical trials, and Google Scholar. Quality assessment of the RCTs was performed, according to the Cochrane’s Risk of Bias 2 tool and the recommendations of the GRADE system. Furthermore, we evaluated publication bias with funnel plots. Mean differences (MDs) with 95% confidence intervals (CIs) were calculated for continuous variables using the Hartung–Knapp–Sidik–Jonkman method and a random effects model. Nine RCTs with overall 762 patients were included in this meta-analysis. All 9 RCTs were rated with a moderate risk of bias. The quality of evidence of the outcome parameters was rated moderate to very low. The funnel plots were overall broadly symmetrical, possibly indicating low to moderate publication bias. SuperPATH had a longer operation time compared to CAs (MD = 21.79, 95% CI 12.57 to 31.02). SuperPATH decreased incision length (MD = − 4.50; 95% CI − 5.80 to − 3.20), intraoperative blood loss (MD = − 103.96, 95% CI − 150.27 to − 55.66), postoperative drainage volume (MD = − 137.30, 95% CI − 178.74 to − 95.86), time to mobilization (MD = − 3.86; 95% CI − 5.96 to − 1.76), pain VAS ≤ 1 week postoperatively (MD = − 1.81; 95% CI − 2.17 to − 1.45), and hospitalization time (MD = − 4.05; 95% CI − 4.96 to − 3.15). SuperPATH improved HHS ≤ 1 week postoperatively (MD = 11.10; 95% CI 1.65 to 20.54) and HHS 3 months postoperatively (MD = 6.33; 95% CI 3.97 to 8.69). There was no difference in pain VAS 1–3 months postoperatively (MD = − 0.08; 95% CI − 0.22 to 0.05) and HHS 6 months postoperatively (MD = 0.44; 95% CI − 0.11 to 1.00). This is the first meta-analysis comparing SuperPATH HA with CAs HA in patients with femoral neck fractures. SuperPATH HA was superior in the early short-term functional outcome (HHS) compared to CAs HA, reaching minimal clinically important differences. Furthermore, SuperPATH HA showed significantly better results in incision length, blood loss, time to mobilization, pain intensity (VAS), and hospitalization time than CAs HA.
Differences in characteristics between patients from Egypt and Germany presenting with lacunar stroke
Authors: Maged Mohamed , Aref Hany , Nahas Nevine El , Hamid Eman , Fathy Mai , Roushdy Tamer , Schaefer Jan Hendrik , Foerch Christian , Spitzer Daniel 
Published: December 2023

AbstractDespite the enormous health burden of lacunar stroke, data from low- and middle-income countries on lacunar stroke characteristics and its comparison with that of high-income countries are scarce. Thus, we aimed to investigate and compare the variable characteristics and vascular status in patients from Egypt and Germany suffering lacunar stroke. Two cohorts of lacunar stroke patients from Ain Shams University Hospital, Egypt and Goethe University Hospital Frankfurt, Germany were retrospectively collected between January 2019 and December 2020 and analyzed for demographics, risk factors, mode of presentation, neuroimaging features, treatment protocols and outcomes. MRI showed a different distribution pattern of lacunar strokes between cohorts, detecting posterior circulation lacunar infarctions preponderantly in patients from Egypt and anterior circulation lacunar infarctions preponderantly in patients from Germany. Complementary MR/CT angiography revealed a significantly higher proportion of intracranial and combined intracranial and extracranial arterial stenosis in patients from Egypt than in patients from Germany, suggesting differences in pathological processes. Younger age, higher NIHSS on admission, and posterior circulation lacunar infarction were predictors of Egyptian origin, whereas hypertension was a predictor of German origin. Our results support the idea of clinical and neuroimaging phenotype variations in lacunar stroke, including different sources of lacunar stroke in patients of different populations and geographical regions. This implies that guidelines for management of lacunar stroke might be tailored to these differences accordingly.