bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of an early survival prognostic gene signature for localized osteosarcoma patients
Authors: Patel Tajhal D. , Grimm Sandra L. , Kanchi Rupa S. , Gandhi Tanmay , Koirala Amrit , Yustein Jason T. , Coarfa Cristian 
Published: March 2024

AbstractOsteosarcoma is the most prevalent bone tumor in pediatric patients. Neoadjuvant chemotherapy has improved osteosarcoma patient survival, however the 5-year survival rate for localized osteosarcoma is 75% with a 30–50% recurrence rate. We, therefore, sought to identify a prognostic gene signature which could predict poor prognosis in localized osteosarcoma patients. Using the TARGET osteosarcoma transcriptomic dataset, we identified a 13-hub gene signature associated with overall survival and time to death of localized osteosarcoma patients, with the high-risk group showing a 22% and the low-risk group showing 100% overall survival. Furthermore, network analysis identified five modules of co-expressed genes that significantly correlated with survival, and identified 65 pathways enriched across 3 modules, including Hedgehog signaling, which includes 2 of the 13 genes, IHH and GLI1. Subsequently, we demonstrated that GLI antagonists inhibited growth of a recurrent localized PDX-derived cell line with elevated IHH and GLI1 expression, but not a non-relapsed cell line with low pathway activation. Finally, we show that our signature outperforms previously reported signatures in predicting poor prognosis and death within 3 years in patients with localized osteosarcoma.
A novel multi-variate immunological approach, reveals immune variation associated with environmental conditions, and co-infection in the koala (Phascolarctos cinereus)
Authors: Fernandez Cristina M. , Krockenberger Mark B. , Valentina  , Mella S. A. , Wright Belinda R. , Crowther Mathew S. , Higgins Damien P. 
Published: March 2024

AbstractExternal signs of disease are frequently used as indicators of disease susceptibility. However, immune profiling can be a more effective indicator to understand how host responses to infection may be shaped by host, pathogen and environmental factors. To better inform wildlife health assessment and research directions, we investigated the utility of a novel multivariate immunophenotyping approach examining innate and adaptive immune responses in differing climatic, pathogen co-infection and demographic contexts across two koala (Phascolarctos cinereus) populations in New South Wales: the Liverpool Plains (LP), and Southern Highlands to South-west Sydney (SHSWS). Relative to the comparatively healthy SHSWS, the LP had greater and more variable innate immune gene expression (IL-1β, IL-6), and KoRV transcription. During extreme heat and drought, koalas from the LP displayed upregulation of a stress pathway gene and reduced adaptive immune genes expression, haematocrit and plasma protein, suggesting the possibility of environmental impacts through multiple pathways. In those koalas, KoRV transcription status, Chlamydia pecorum infection loads, and visible urogenital inflammation were not associated with immune variation, suggesting that immune markers were more sensitive indicators of real-time impacts than observed disease outcomes.
Biosynthesis and assessment of antibacterial and antioxidant activities of silver nanoparticles utilizing Cassia occidentalis L. seed
Authors: Arya Arvind , Tyagi Pankaj Kumar , Bhatnagar Sachin , Bachheti Rakesh Kumar , Bachheti Archana , Ghorbanpour Mansour 
Published: March 2024

AbstractThis research explores the eco-friendly synthesis of silver nanoparticles (AgNPs) using Cassia occidentalis L. seed extract. Various analytical techniques, including UV–visible spectroscopy, transmission electron microscopy (TEM), scanning electron microscopy (SEM), X-ray diffraction (XRD), and energy dispersive X-ray spectroscopy (EDX), were employed for comprehensive characterization. The UV–visible spectra revealed a distinct peak at 425 nm, while the seed extract exhibited peaks at 220 and 248 nm, indicating the presence of polyphenols and phytochemicals. High-resolution TEM unveiled spherical and oval-shaped AgNPs with diameters ranging from 6.44 to 28.50 nm. The SEM exhibiting a spherical shape and a polydisperse nature, thus providing insights into the morphology of the AgNPs. EDX analysis confirmed the presence of silver atoms at 10.01% in the sample. XRD results unequivocally confirm the crystalline nature of the AgNPs suspension, thereby providing valuable insights into their structural characteristics and purity. The antioxidant properties of AgNPs, C. occidentalis seed extract, and butylated hydroxytoluene (BHT) were assessed, revealing IC50 values of 345, 500, and 434 μg/mL, respectively. Antibacterial evaluation against Bacillus subtilis, Staphylococcus aureus, and Escherichia coli demonstrated heightened sensitivity of bacteria to AgNPs compared to AgNO3. Standard antibiotics, tetracycline, and ciprofloxacin, acting as positive controls, exhibited substantial antibacterial efficacy. The green-synthesized AgNPs displayed potent antibacterial activity, suggesting their potential as a viable alternative to conventional antibiotics for combating pathogenic bacterial infections. Furthermore, potential biomedical applications of AgNPs were thoroughly discussed.
Clinical outcomes of interstitial lung abnormalities: a systematic review and meta-analysis
Authors: Seok Jinwoo , Park Shinhee , Yoon Eun Chong , Yoon Hee-Young 
Published: March 2024

AbstractInterstitial lung abnormalities (ILA), incidental findings on computed tomography scans, have raised concerns due to their association with worse clinical outcomes. Our meta-analysis, which included studies up to April 2023 from PubMed/MEDLINE, Embase, and Cochrane Library, aimed to clarify the impact of ILA on mortality, lung cancer development, and complications from lung cancer treatments. Risk ratios (RR) with 95% confidence intervals (CI) were calculated for outcomes. Analyzing 10 studies on ILA prognosis and 9 on cancer treatment complications, we found that ILA significantly increases the risk of overall mortality (RR 2.62, 95% CI 1.94–3.54; I2 = 90%) and lung cancer development (RR 3.85, 95% CI 2.64–5.62; I2 = 22%). Additionally, cancer patients with ILA had higher risks of grade 2 radiation pneumonitis (RR 2.28, 95% CI 1.71–3.03; I2 = 0%) and immune checkpoint inhibitor-related interstitial lung disease (RR 3.05, 95% CI 1.37–6.77; I2 = 83%) compared with those without ILA. In conclusion, ILA significantly associates with increased mortality, lung cancer risk, and cancer treatment-related complications, highlighting the necessity for vigilant patient management and monitoring.
Exploring the relationship across autonomous motivation, affects, and anxiety among gym practitioners during the second COVID-19 lockdown
Authors: Antunes Raúl , Rodrigues Filipe , Jacinto Miguel , Amaro Nuno , Matos Rui , Monteiro Diogo 
Published: March 2024

AbstractThe present study explores the association of autonomous motivation and the relationship of positive and negative affect on anxiety levels among individuals engaged in gym practitioners during the second COVID-19 lockdown. A total of 196 exercisers (29.17 ± 10.77) were enrolled in the present study, of which 112 (57.1%) were women and 84 (42.9%) were men. The survey included sociodemographic data, as well as validated instruments measuring autonomous motivation, positive and negative affect, and anxiety states related to the COVID-19 pandemic. The results revealed a positive association between autonomous motivation and positive affect (β = 0.36, CI 0.12, 0.37; p < 0.001), and a negative association between autonomous motivation and negative affect (β = − 0.17, CI − 0.31, − 0.01; p = 0.03). Moreover positive, and negative affect are negatively (β = − 0.33, CI − 0.43, − 0.24; p < 0.001) and positively (β = 0.72, CI 0.57, 0.82; p < 0.001) associated to anxiety, respectively. Thus, this study appears to emphasize the association of autonomous motivation on affect as a potential buffer against anxiety levels, particularly in a context where practitioners found themselves restricted in their usual gym practices.
Obesity differentially effects the somatosensory cortex and striatum of TgF344-AD rats
Authors: Ahmed Minhal , Lai Aaron Y. , Hill Mary E. , Ribeiro Jessica A. , Amiraslani Ashley , McLaurin JoAnne 
Published: March 2024

AbstractLifestyle choices leading to obesity, hypertension and diabetes in mid-life contribute directly to the risk of late-life Alzheimer’s disease (AD). However, in late-life or in late-stage AD conditions, obesity reduces the risk of AD and disease progression. To examine the mechanisms underlying this paradox, TgF344-AD rats were fed a varied high-carbohydrate, high-fat (HCHF) diet to induce obesity from nine months of age representing early stages of AD to twelve months of age in which rats exhibit the full spectrum of AD symptomology. We hypothesized regions primarily composed of gray matter, such as the somatosensory cortex (SSC), would be differentially affected compared to regions primarily composed of white matter, such as the striatum. We found increased myelin and oligodendrocytes in the somatosensory cortex of rats fed the HCHF diet with an absence of neuronal loss. We observed decreased inflammation in the somatosensory cortex despite increased AD pathology. Compared to the somatosensory cortex, the striatum had fewer changes. Overall, our results suggest that the interaction between diet and AD progression affects myelination in a brain region specific manner such that regions with a lower density of white matter are preferentially affected. Our results offer a possible mechanistic explanation for the obesity paradox.
Employing deep learning and transfer learning for accurate brain tumor detection
Authors: Mathivanan Sandeep Kumar , Sonaimuthu Sridevi , Murugesan Sankar , Rajadurai Hariharan , Shivahare Basu Dev , Shah Mohd Asif 
Published: March 2024

AbstractArtificial intelligence-powered deep learning methods are being used to diagnose brain tumors with high accuracy, owing to their ability to process large amounts of data. Magnetic resonance imaging stands as the gold standard for brain tumor diagnosis using machine vision, surpassing computed tomography, ultrasound, and X-ray imaging in its effectiveness. Despite this, brain tumor diagnosis remains a challenging endeavour due to the intricate structure of the brain. This study delves into the potential of deep transfer learning architectures to elevate the accuracy of brain tumor diagnosis. Transfer learning is a machine learning technique that allows us to repurpose pre-trained models on new tasks. This can be particularly useful for medical imaging tasks, where labelled data is often scarce. Four distinct transfer learning architectures were assessed in this study: ResNet152, VGG19, DenseNet169, and MobileNetv3. The models were trained and validated on a dataset from benchmark database: Kaggle. Five-fold cross validation was adopted for training and testing. To enhance the balance of the dataset and improve the performance of the models, image enhancement techniques were applied to the data for the four categories: pituitary, normal, meningioma, and glioma. MobileNetv3 achieved the highest accuracy of 99.75%, significantly outperforming other existing methods. This demonstrates the potential of deep transfer learning architectures to revolutionize the field of brain tumor diagnosis.
Impact of 24 h shifts on urinary catecholamine in emergency physicians: a cross-over randomized trial
Authors: Dutheil Frédéric , Fournier Alicia , Perrier Christophe , Richard Damien , Trousselard Marion , Mnatzaganian George , Baker Julien S. , Bagheri Reza , Mermillod Martial , Clinchamps Maelys , Schmidt Jeannot , Bouillon-Minois Jean-Baptiste 
Published: March 2024

Abstract24-h shift (24 hS) exposed emergency physicians to a higher stress level than 14-h night shift (14 hS), with an impact spreading on several days. Catecholamines are supposed to be chronic stress biomarker. However, no study has used catecholamines to assess short-term residual stress or measured them over multiple shifts. A shift-randomized trial was conducted to study urinary catecholamines levels of 17 emergency physicians during a control day (clerical work on return from leave) and two working day (14 hS and 24 hS). The Wilcoxon matched-pairs test was utilized to compare the mean catecholamine levels. Additionally, a multivariable generalized estimating equations model was employed to further analyze the independent relationships between key factors such as shifts (compared to control day), perceived stress, and age with catecholamine levels. Dopamine levels were lower during 24 hS than 14 hS and the control day. Norepinephrine levels increased two-fold during both night shifts. Epinephrine levels were higher during the day period of both shifts than on the control day. Despite having a rest day, the dopamine levels did not return to their normal values by the end of the third day after the 24 hS. The generalized estimating equations model confirmed relationships of catecholamines with workload and fatigue. To conclude, urinary catecholamine biomarkers are a convenient and non-invasive strong measure of stress during night shifts, both acutely and over time. Dopamine levels are the strongest biomarker with a prolonged alteration of its circadian rhythm. Due to the relation between increased catecholamine levels and both adverse psychological effects and cardiovascular disease, we suggest that emergency physicians restrict their exposure to 24 hS to mitigate these risks.
Validation of reference gene stability for normalization of RT-qPCR in Phytophthora capsici Leonian during its interaction with Piper nigrum L.
Authors: Vijayakumar Saranya , Sakuntala Manjula 
Published: March 2024

AbstractThe selection of stable reference genes for the normalization of reverse transcription quantitative real-time PCR (RT-qPCR) is generally overlooked despite being the crucial element in determining the accuracy of the relative expression of genes. In the present study, the stability of seven candidate reference genes: actin (act), α-tubulin (atub), β-tubulin (btub), translation elongation factor 1-α (ef1), elongation factor 2 (ef2), ubiquitin-conjugating enzyme (ubc) and 40S ribosomal protein S3A (ws21) inPhytophthora capsicihas been validated. The validation was performed at six infection time points during its interaction with its susceptible hostPiper nigrum, two developmental stages, and for the combined dataset. Four algorithms: geNorm, NormFinder, BestKeeper, and the ΔCt method were compared, and a comprehensive ranking order was produced using RefFinder. The overall analysis revealed thatef1,ws21, andubcwere identified as the three most stable genes in the combined dataset,ef1,ws21, andactwere the most stable at the infection stages, and,ef1,btub, andubcwere most stable during the developmental stages. These findings were further corroborated by validating theP. capsicipathogenesis geneNPP1expression. The findings are significant as this is the first study addressing the stability of reference genes forP. capsici–P. nigruminteraction studies.
Wetting and evaporation behavior of dilute sodium dodecyl sulfate droplets on soft substrates under a direct current electric field
Authors: Jiang Biao , Xu Shuai , Lu Yingfa , Yu Yingsong 
Published: March 2024

AbstractWetting and evaporation behavior of dilute sodium dodecyl sulfate (SDS) droplets on planar polydimethylsiloxane (PDMS) surfaces under a direct current (DC) electric field were experimentally investigated. Two characteristic voltages—actuation voltage and saturation voltage were observed in the electrowetting of dilute SDS droplets on PDMS surfaces. It was found that for dilute SDS droplets with a fixed SDS concentration substrate elasticity has an obvious influence on actuation voltage, and saturation voltage increased with the increase of mass ratio of PDMS surfaces. SDS concentration was also found to obviously influence actuation voltage and saturation voltage when SDS concentration was in a certain range. For the case of evaporation of sessile dilute SDS droplets on PDMS surfaces with the application of a DC electric field, substrate elasticity, SDS concentration and the magnitude of applied voltage were all found to have an influence on the duration of CCR stage. Moreover, contact angle hysteresis for dilute SDS droplets on a planar PDMS 10:1 surface under different applied voltage was measured and it was found that the magnitude of applied voltage greatly influenced contact angle hysteresis, which also depends on SDS concentration and KCl concentration.
Artificial intelligence-based assessment of PD-L1 expression in diffuse large B cell lymphoma
Authors: Yan Fang , Da Qian , Yi Hongmei , Deng Shijie , Zhu Lifeng , Zhou Mu , Liu Yingting , Feng Ming , Wang Jing , Wang Xuan , Zhang Yuxiu , Zhang Wenjing , Zhang Xiaofan , Lin Jingsheng , Zhang Shaoting , Wang Chaofu 
Published: March 2024

AbstractDiffuse large B cell lymphoma (DLBCL) is an aggressive blood cancer known for its rapid progression and high incidence. The growing use of immunohistochemistry (IHC) has significantly contributed to the detailed cell characterization, thereby playing a crucial role in guiding treatment strategies for DLBCL. In this study, we developed an AI-based image analysis approach for assessing PD-L1 expression in DLBCL patients. PD-L1 expression represents as a major biomarker for screening patients who can benefit from targeted immunotherapy interventions. In particular, we performed large-scale cell annotations in IHC slides, encompassing over 5101 tissue regions and 146,439 live cells. Extensive experiments in primary and validation cohorts demonstrated the defined quantitative rule helped overcome the difficulty of identifying specific cell types. In assessing data obtained from fine needle biopsies, experiments revealed that there was a higher level of agreement in the quantitative results between Artificial Intelligence (AI) algorithms and pathologists, as well as among pathologists themselves, in comparison to the data obtained from surgical specimens. We highlight that the AI-enabled analytics enhance the objectivity and interpretability of PD-L1 quantification to improve the targeted immunotherapy development in DLBCL patients.
Graphene oxide-based membranes for water desalination and purification
Authors: Tiwary Saurabh Kr , Singh Maninderjeet , Chavan Shubham Vasant , Karim Alamgir 
Published: March 2024

AbstractMillions of people across the globe are severely afflicted because of water potability issues, and to proffer a solution to this crisis, efficient and cost-effective desalination techniques are necessitated. Membranes, in particular Graphene-derived membranes, have emerged as a potential answer to this grave problem because of their tunable ionic and molecular sieving capability, thin structure, and customizable microstructure. Among graphene-derived membranes, Graphene Oxide membranes have been the most promising, given the replete presence of oxygen-containing functional groups on its surface. However, the prospects of commercial applicability of these membranes are currently plagued by uneven stacking, crossflow delamination, flawed pores, screening and pH effects, and horizontal defects in the membrane. In addition, due to the selectivity–permeability trade-off that commonly exists in all membranes, the separation efficiency is negatively influenced. This review, while studying these challenges, aims to outline the most recent ground-breaking developments in graphene-based membrane technology, encompassing their separation mechanism, selectivity, adjustable mechanical characteristics, and uses. Additionally, we have covered in detail how several process variables such as temperature, total oxygen concentration, and functional groups affect the effectiveness of membrane separation with the focal point tilted toward studying the currently used intercalation techniques and effective nanomaterial graphene oxide membranes for water desalination
Enhancing dielectric passivation on monolayer WS2 via a sacrificial graphene oxide seeding layer
Authors: Wyndaele P.-J. , de Marneffe J.-F. , Sergeant S. , de la Rosa C. J. L. , Brems S. , Caro A. M. , De Gendt S. 
Published: March 2024

AbstractThe full utilization of two-dimensional transition metal dichalcogenides (2D TMDCs) faces several challenges, among which is realizing uniform material deposition on the 2D surface. Typical strategies to enable material growth lead to a poor interface quality, degrading the 2D TMDC’s properties. In this work, a sacrificial, graphene oxide-based seeding layer is used (1) as passivation layer, protecting the underlying 2D TMDC and (2) as nucleation layer, enabling uniform material growth. Graphene is transferred on monolayer WS2, establishing a high-quality van der Waals interface. After transfer, the polymeric residues on graphene are cleaned via a combination of wet- and dry treatments and functionalized via dry UV/O3 oxidation. The rate of graphene oxidation is shown to be substrate dependent, which is explained by UV light-induced ultrafast charge transfer between the graphene and WS2 monolayer. The carbon-oxygen functionalities serve as nucleation sites in a subsequent HfO2 ALD process, achieving more uniform dielectric growth and faster layer closure compared to direct deposition. The graphene-based nucleation- / passivation approach offers adaptability, allowing for tailored surface chemistry to enable any alternative material growth, while maintaining a prefect van der Waals interface.
TRPM5 activation depends on a synergistic effect of calcium and PKC phosphorylation
Authors: Nmarneh Alaa , Priel Avi 
Published: March 2024

AbstractTransient receptor potential melastatin 5 (TRPM5) is a calcium-activated monovalent-specific ion channel involved in insulin secretion and taste transduction, making it an attractive target for drug development in various pathologies. While TRPM5 activation involves ligand binding to Gq/G-protein coupled receptors (GPCR) and subsequent elevation of intracellular calcium levels, recent reports suggest the need for additional molecular determinants. Hence, the mechanism of TRPM5 activation remains to be elucidated. Here, we show that PKC phosphorylation and the elevation of intracellular Ca2+ levels are required for TRPM5 activation, with PKC phosphorylation being crucial for channel-evoked currents, primarily at physiological membrane potentials. In contrast, physiological relevant calcium levels alone only induce TRPM5 activation at positive voltages. Our findings highlight the necessity of coordinated intracellular calcium release and PKC phosphorylation for TRPM5 activation. Thus, our results suggest that regulation of PKC activity could be a promising therapeutic target for diseases associated with TRPM5 modulation.