bluuebunny/crossref_metadata_2025_split huggingface dataset:
Atomistic Line Graph Neural Network for improved materials property predictions
Authors: Choudhary Kamal , DeCost Brian 
Published: November 2021

AbstractGraph neural networks (GNN) have been shown to provide substantial performance improvements for atomistic material representation and modeling compared with descriptor-based machine learning models. While most existing GNN models for atomistic predictions are based on atomic distance information, they do not explicitly incorporate bond angles, which are critical for distinguishing many atomic structures. Furthermore, many material properties are known to be sensitive to slight changes in bond angles. We present an Atomistic Line Graph Neural Network (ALIGNN), a GNN architecture that performs message passing on both the interatomic bond graph and its line graph corresponding to bond angles. We demonstrate that angle information can be explicitly and efficiently included, leading to improved performance on multiple atomistic prediction tasks. We ALIGNN models for predicting 52 solid-state and molecular properties available in the JARVIS-DFT, Materials project, and QM9 databases. ALIGNN can outperform some previously reported GNN models on atomistic prediction tasks with better or comparable model training speed.
Revisiting decompression sickness risk and mobility in the context of the SmartSuit, a hybrid planetary spacesuit
Authors: Kluis Logan , Diaz-Artiles Ana 
Published: November 2021

AbstractGas pressurized spacesuits are cumbersome, cause injuries, and are metabolically expensive. Decreasing the gas pressure of the spacesuit is an effective method for improving mobility, but reduction in the total spacesuit pressure also results in a higher risk for decompression sickness (DCS). The risk of DCS is currently mitigated by breathing pure oxygen before the extravehicular activity (EVA) for up to 4 h to remove inert gases from body tissues, but this has a negative operational impact due to the time needed to perform the prebreathe. In this paper, we review and quantify these important trade-offs between spacesuit pressure, mobility, prebreathe time (or risk of DCS), and space habitat/station atmospheric conditions in the context of future planetary EVAs. In addition, we explore these trade-offs in the context of the SmartSuit architecture, a hybrid spacesuit with a soft-robotic layer that, not only increases mobility with assistive actuators in the lower body, but it also applies some level of mechanical counterpressure (MCP). The additional MCP in hybrid spacesuits can be used to supplement the gas pressure (i.e., increasing the total spacesuit pressure), therefore reducing the risk of DCS (or reduce prebreathe time). Alternatively, the MCP can be used to reduce the gas pressure (i.e., maintaining the same total spacesuit pressure), therefore increasing mobility. Finally, we propose a variable pressure concept of operations for the SmartSuit spacesuit. Our framework quantifies critical spacesuit and habitat trade-offs for future planetary exploration and contributes to the assessment of human health and performance during future planetary EVAs.
Diagnostic value of skin RT-QuIC in Parkinson’s disease: a two-laboratory study
Authors: Kuzkina Anastasia , Bargar Connor , Schmitt Daniela , Rößle Jonas , Wang Wen , Schubert Anna-Lena , Tatsuoka Curtis , Gunzler Steven A. , Zou Wen-Quan , Volkmann Jens , Sommer Claudia , Doppler Kathrin , Chen Shu G. 
Published: November 2021

AbstractSkin α-synuclein deposition is considered a potential biomarker for Parkinson’s disease (PD). Real-time quaking-induced conversion (RT-QuIC) is a novel, ultrasensitive, and efficient seeding assay that enables the detection of minute amounts of α-synuclein aggregates. We aimed to determine the diagnostic accuracy, reliability, and reproducibility of α-synuclein RT-QuIC assay of skin biopsy for diagnosing PD and to explore its correlation with clinical markers of PD in a two-center inter-laboratory comparison study. Patients with clinically diagnosed PD (n = 34), as well as control subjects (n = 30), underwent skin punch biopsy at multiple sites (neck, lower back, thigh, and lower leg). The skin biopsy samples (198 in total) were divided in half to be analyzed by RT-QuIC assay in two independent laboratories. The α-synuclein RT-QuIC assay of multiple skin biopsies supported the clinical diagnosis of PD with a diagnostic accuracy of 88.9% and showed a high degree of inter-rater agreement between the two laboratories (92.2%). Higher α-synuclein seeding activity in RT-QuIC was shown in patients with longer disease duration and more advanced disease stage and correlated with the presence of REM sleep behavior disorder, cognitive impairment, and constipation. The α-synuclein RT-QuIC assay of minimally invasive skin punch biopsy is a reliable and reproducible biomarker for Parkinson’s disease. Moreover, α-synuclein RT-QuIC seeding activity in the skin may serve as a potential indicator of progression as it correlates with the disease stage and certain non-motor symptoms.
Comprehensive study of α-terpineol-loaded oil-in-water (O/W) nanoemulsion: interfacial property, formulation, physical and chemical stability
Authors: de Oliveira Felipe Lorena , Bicas Juliano Lemos , Bouhoute Meryem , Nakajima Mitsutoshi , Neves Marcos A. 
Published: November 2021

AbstractIn this study, the interfacial ability of α-terpineol (α-TOH) was reported, followed by its trapping into oil-in-water (O/W) nanoemulsion as active-ingredient and the long-term observation of this nanosystem influenced by the storage-time (410-days) and temperature (5, 25, 50 °C). The results indicated that the α-TOH can reduce the interfacial tension on the liquid-liquid interface (ΔG°m = −1.81 KJ mol−1; surface density = 8.19 × 10−6 mol m−2; polar head group area = 20.29 Å2), in the absence or presence of surfactant. The O/W nanoemulsion loaded with a high amount of α-TOH (90 mg mL−1; 9α-TOH-NE) into the oil phase was successfully formulated. Among the physical parameters, the mean droplet diameter (MDD) showed a great thermal dependence influenced by the storage-temperature, where the Ostwald ripening (OR) was identified as the main destabilizing phenomena that was taking place on 9α-TOH-NE at 5 and 25 °C along with time. Despite of the physical instability, the integrity of both nanoemulsion at 5 °C and 25 °C was fully preserved up to 410th day, displaying a homogeneous and comparable appearance by visual observation. On contrary, a non-thermal dependence was found for chemical stability, where over 88% of the initial amount of the α-TOH nanoemulsified remained in both 9α-TOH-NE at 5 and 25 °C, up to 410th day. Beyond the key data reported for α-TOH, the importance of this research relies on the long-term tracking of a nanostructured system which can be useful for scientific community as a model for a robust evaluation of nanoemulsion loaded with flavor oils.
Lipid profile migration during the tilapia muscle steaming process revealed by a transactional analysis between MS data and lipidomics data
Authors: Sun Rui , Wu Tingting , Guo Hao , Xu Jiamin , Chen Jiahui , Tao Ningping , Wang Xichang , Zhong Jian 
Published: November 2021

AbstractIn this work, lipid profile migration from muscle to juice during the tilapia muscle steaming process was revealed by a transactional analysis of data from ultra-high-performance liquid chromatography coupled with Q Exactive (UHPLC-QE) Orbitrap mass spectrometry (MS) and lipidomics. Firstly, the lipids in tilapia muscles and juices at different steaming time points were extracted and examined by UHPLC-QE Orbitrap mass spectrometry. Secondly, a transactional analysis procedure was developed to analyze the data from UHPLC-QE Orbitrap MS and lipidomics. Finally, the corrected lipidomics data and the normalized MS data were used for lipid migration analysis. The results suggested that the transactional analysis procedure was efficient to significantly decrease UHPLC-QE Orbitrap MS workloads and delete the false-positive data (22.4–36.7%) in lipidomics data, which compensated the disadvantages of the current lipidomics method. The lipid changes could be disappearance, full migration into juice, appearance in juice, appearance in muscle, appearance in both muscle and juice, and retention in the muscle. Moreover, the results showed 9 (compared with 52), 5 (compared with 116), and 10 (compared with 178) of lipid class (compared with individual lipid) variables showed significant differences among the different steaming times (0, 10, 30, and 60 min) in all the muscles, juices, and muscle-juice systems, respectively. These results showed significant lipid profile migration from muscle to juice during the tilapia steaming process.
Sensitive identification of neoantigens and cognate TCRs in human solid tumors
Authors: Arnaud Marion , Chiffelle Johanna , Genolet Raphael , Navarro Rodrigo Blanca , Perez Marta A. S. , Huber Florian , Magnin Morgane , Nguyen-Ngoc Tu , Guillaume Philippe , Baumgaertner Petra , Chong Chloe , Stevenson Brian J. , Gfeller David , Irving Melita , Speiser Daniel E. , Schmidt Julien , Zoete Vincent , Kandalaft Lana E. , Bassani-Sternberg Michal , Bobisse Sara , Coukos George , Harari Alexandre 
Published: November 2021

AbstractThe identification of patient-specific tumor antigens is complicated by the low frequency of T cells specific for each tumor antigen. Here we describe NeoScreen, a method that enables the sensitive identification of rare tumor (neo)antigens and of cognate T cell receptors (TCRs) expressed by tumor-infiltrating lymphocytes. T cells transduced with tumor antigen-specific TCRs identified by NeoScreen mediate regression of established tumors in patient-derived xenograft mice.
Association between immunologic markers and cirrhosis in individuals with chronic hepatitis B
Authors: Argirion Ilona , Pfeiffer Ruth M. , Lam Tram Kim , O’Brien Thomas R. , Yu Kelly , McGlynn Katherine A. , Petrick Jessica L. , Pinto Ligia , Chen Chien-Jen , Lee Mei-Hsuan , Hildesheim Allan , Yang Hwai-I , Koshiol Jill 
Published: November 2021

AbstractHost immune response and chronic inflammation associated with chronic hepatitis B virus (HBV) infection play a key role in the pathogenesis of liver diseases such as cirrhosis and hepatocellular carcinoma (HCC). We sampled 175 HCC, 117 cirrhotic and 165 non-cirrhotic controls from a prospective cohort study of chronically HBV-infected individuals. Multivariable polytomous logistic regression and canonical discriminant analysis (CDA) were used to compare baseline plasma levels for 102 markers in individuals who developed cirrhosis vs. controls and those who developed HCC vs. cirrhosis. Leave-one-out cross validation was used to generate receiver operating characteristic curves to compare the predictive ability of marker groups. After multivariable adjustment, HGF (Q4v1OR: 3.74; p-trend = 0.0001), SLAMF1 (Q4v1OR: 4.07; p-trend = 0.0001), CSF1 (Q4v1OR: 3.00; p-trend = 0.002), uPA (Q4v1OR: 3.36; p-trend = 0.002), IL-8 (Q4v1OR: 2.83; p-trend = 0.004), and OPG (Q4v1OR: 2.44; p-trend = 0.005) were all found to be associated with cirrhosis development compared to controls; these markers predicted cirrhosis with 69% accuracy. CDA analysis identified a nine marker model capable of predicting cirrhosis development with 79% accuracy. No markers were significantly different between HCC and cirrhotic participants. In this study, we assessed immunologic markers in relation to liver disease in chronically-HBV infected individuals. While validation in required, these findings highlight the importance of immunologic processes in HBV-related cirrhosis.
Refining the mandibular osteoradionecrosis rat model by in vivo longitudinal µCT analysis
Authors: Dos Santos Morgane , Demarquay Christelle , Ermeneux Louis , Aberkane Fazia , Bléry Pauline , Weiss Pierre , Milliat Fabien , Mathieu Noëlle 
Published: November 2021

AbstractOsteoradionecrosis (ORN) is one of the most feared side effects of radiotherapy following cancers of the upper aero-digestive tract and leading to severe functional defects in patients. Today, our lack of knowledge about the physiopathology restricts the development of new treatments. In this study, we refined the ORN rat model and quantitatively studied the progression of the disease. We tested the impact of radiation doses from 20 to 40 Gy, delivered with incident 4MV X-ray beams on the left mandible of the inbred Lewis Rat. We used micro-computed tomography (µCT) to obtain in vivo images for longitudinal bone imaging and ex vivo images after animal perfusion with barium sulphate contrast agent for vessel imaging. We compared quantification methods by analyzing 3D images and 2D measurements to determine the most appropriate and precise method according to the degree of damage. We defined 25 Gy as the minimum irradiation dose combined with the median molar extraction necessary to develop non-regenerative bone necrosis. µCT image analyses were correlated with clinical and histological analyses. This refined model and accurate methods for bone and vessel quantification will improve our knowledge of the progression of ORN pathology and allow us to test the efficacy of new regenerative medicine procedures.
Sarcopenia risk and associated factors among Chinese community-dwelling older adults living alone
Authors: Cheng Li , Sit Janet W. H. , Chan Helen Y. L. , Choi Kai Chow , Cheung Regina K. Y. , Wong Martin M. H. , Li Francis Y. K. , Lee Tin Yan , Fung Elina S. M. , Tai Keen Man , So Winnie K. W. 
Published: November 2021

AbstractSarcopenia, defined as a progressive loss of muscle mass and reduced muscle strength and functional capacity, is common among older adults. This study aimed to assess the proportion of people at risk of sarcopenia and probable sarcopenia among Chinese community-dwelling older adults living alone and to identify the associated factors. A total of 390 older adults were included in this study. Sarcopenia and probable sarcopenia were defined according to the criteria of the Asian Working Group for Sarcopenia 2019. Data on socio-demographic characteristics, health status, health behaviours and lifestyle characteristics, nutritional status, physical activity level, and depressive symptoms were collected. The association between these characteristics and sarcopenia risk was analysed using a multivariate ordinal logistic regression. The proportion of subjects at risk of sarcopenia and probable sarcopenia was found to be 57.7% and 30%, respectively. Older age, being malnourished and being at risk of malnutrition were significantly associated with sarcopenia risk. Being educated to secondary level or above, being overweight or obese and higher physical activity level were associated with decreased sarcopenia risk. Our results showed that older adults living alone were at high risk of developing sarcopenia and probable sarcopenia. These results emphasise the urgent need to initiate aggressive screening and holistic lifestyle therapeutic intervention strategies for this high-risk population.
Primary central nervous system lymphomas express immunohistochemical factors of autophagy
Authors: Karpathiou Georgia , Babiuc Silvia-Maria , Camy Florian , Ferrand Elise , Papoudou-Bai Alexandra , Dumollard Jean Marc , Cornillon Jerome , Peoc’h Michel 
Published: November 2021

AbstractPrimary central nervous system lymphoma (PCNSL) is an aggressive and rare disease. Autophagy is a catabolic mechanism boosting various tumors, including lymphomas; its inhibition is thus a promising therapeutic target. Its presence has never been studied in PCNSLs. We conducted a retrospective immunohistochemical study of 25 PCNSLs for LC3B, p62, and M6PR, comparing it with clinicopathological characteristics. Fourteen (56%) and eleven (44%) PCNSLs were of low and high LC3B expression, respectively. p62 expression was present in most tumors (n = 21, 84%). M6PR was present in all tumors, with 14 (56%) and 11 (44%) cases being of low and high M6PR expression, respectively. LC3B expression was correlated with the performance status (PS) (p = 0.04). No association was found with other clinical parameters, such as deep structure invasion, multiple lesions, complete response, and recurrence after response. p62 showed a strong positive association with MUM1 expression (p = 0.0005). M6PR expression showed a positive correlation (p = 0.04) with PD-L1 expression. No association was found with p53, Ki67, CD8, BCL2, BCL6, or double MYC/BLC2 co-expressors. No association of LC3B, p62, and M6PR expression with survival was found. Our findings provide evidence for the possible presence of autophagic markers in PCNSLs and, thus, for possible treatment targets.
Interaction of Spike protein and lipid membrane of SARS-CoV-2 with Ursodeoxycholic acid, an in-silico analysis
Authors: Rodal Canales Francisco Javier , Pérez-Campos Mayoral Laura , Hernández-Huerta María Teresa , Sánchez Navarro Luis Manuel , Matias-Cervantes Carlos Alberto , Martínez Cruz Margarito , Cruz Parada Eli , Zenteno Edgar , Ramos-Martínez Edgar Gustavo , Pérez-Campos Mayoral Eduardo , Romero Díaz Carlos , Pérez-Campos Eduardo 
Published: November 2021

AbstractNumerous repositioned drugs have been sought to decrease the severity of SARS-CoV-2 infection. It is known that among its physicochemical properties, Ursodeoxycholic Acid (UDCA) has a reduction in surface tension and cholesterol solubilization, it has also been used to treat cholesterol gallstones and viral hepatitis. In this study, molecular docking was performed with the SARS-CoV-2 Spike protein and UDCA. In order to confirm this interaction, we used Molecular Dynamics (MD) in “SARS-CoV-2 Spike protein-UDCA”. Using another system, we also simulated MD with six UDCA residues around the Spike protein at random, naming this “SARS-CoV-2 Spike protein-6UDCA”. Finally, we evaluated the possible interaction between UDCA and different types of membranes, considering the possible membrane conformation of SARS-CoV-2, this was named “SARS-CoV-2 membrane-UDCA”. In the “SARS-CoV-2 Spike protein-UDCA”, we found that UDCA exhibits affinity towards the central region of the Spike protein structure of − 386.35 kcal/mol, in a region with 3 alpha helices, which comprises residues from K986 to C1032 of each monomer. MD confirmed that UDCA remains attached and occasionally forms hydrogen bonds with residues R995 and T998. In the presence of UDCA, we observed that the distances between residues atoms OG1 and CG2 of T998 in the monomers A, B, and C in the prefusion state do not change and remain at 5.93 ± 0.62 and 7.78 ± 0.51 Å, respectively, compared to the post-fusion state. Next, in “SARS-CoV-2 Spike protein-6UDCA”, the three UDCA showed affinity towards different regions of the Spike protein, but only one of them remained bound to the region between the region's heptad repeat 1 and heptad repeat 2 (HR1 and HR2) for 375 ps of the trajectory. The RMSD of monomer C was the smallest of the three monomers with a value of 2.89 ± 0.32, likewise, the smallest RMSF was also of the monomer C (2.25 ± 056). In addition, in the simulation of “SARS-CoV-2 membrane-UDCA”, UDCA had a higher affinity toward the virion-like membrane; where three of the four residues remained attached once they were close (5 Å, to the centre of mass) to the membrane by 30 ns. However, only one of them remained attached to the plasma-like membrane and this was in a cluster of cholesterol molecules. We have shown that UDCA interacts in two distinct regions of Spike protein sequences. In addition, UDCA tends to stay bound to the membrane, which could potentially reduce the internalization of SARS-CoV-2 in the host cell.
The Framing of machine learning risk prediction models illustrated by evaluation of sepsis in general wards
Authors: Lauritsen Simon Meyer , Thiesson Bo , Jørgensen Marianne Johansson , Riis Anders Hammerich , Espelund Ulrick Skipper , Weile Jesper Bo , Lange Jeppe 
Published: November 2021

AbstractProblem framing is critical to developing risk prediction models because all subsequent development work and evaluation takes place within the context of how a problem has been framed and explicit documentation of framing choices makes it easier to compare evaluation metrics between published studies. In this work, we introduce the basic concepts of framing, including prediction windows, observation windows, window shifts and event-triggers for a prediction that strongly affects the risk of clinician fatigue caused by false positives. Building on this, we apply four different framing structures to the same generic dataset, using a sepsis risk prediction model as an example, and evaluate how framing affects model performance and learning. Our results show that an apparently good model with strong evaluation results in both discrimination and calibration is not necessarily clinically usable. Therefore, it is important to assess the results of objective evaluations within the context of more subjective evaluations of how a model is framed.
Genetic loci for lung function in Japanese adults with adjustment for exhaled nitric oxide levels as airway inflammation indicator
Authors: Yamada Mitsuhiro , Motoike Ikuko N. , Kojima Kaname , Fuse Nobuo , Hozawa Atsushi , Kuriyama Shinichi , Katsuoka Fumiki , Tadaka Shu , Shirota Matsuyuki , Sakurai Miyuki , Nakamura Tomohiro , Hamanaka Yohei , Suzuki Kichiya , Sugawara Junichi , Ogishima Soichi , Uruno Akira , Kodama Eiichi N. , Fujino Naoya , Numakura Tadahisa , Ichikawa Tomohiro , Mitsune Ayumi , Ohe Takashi , Kinoshita Kengo , Ichinose Masakazu , Sugiura Hisatoshi , Yamamoto Masayuki 
Published: November 2021

AbstractLung function reflects the ability of the respiratory system and is utilized for the assessment of respiratory diseases. Because type 2 airway inflammation influences lung function, genome wide association studies (GWAS) for lung function would be improved by adjustment with an indicator of the inflammation. Here, we performed a GWAS for lung function with adjustment for exhaled nitric oxide (FeNO) levels in two independent Japanese populations. Our GWAS with genotype imputations revealed that the RNF5/AGER locus including AGER rs2070600 SNP, which introduces a G82S substitution of AGER, was the most significantly associated with FEV1/FVC. Three other rare missense variants of AGER were further identified. We also found genetic loci with three candidate genes (NOS2, SPSB2 and RIPOR2) associated with FeNO levels. Analyses with the BioBank-Japan GWAS resource revealed genetic links of FeNO and asthma-related traits, and existence of common genetic background for allergic diseases and their biomarkers. Our study identified the genetic locus most strongly associated with airway obstruction in the Japanese population and three genetic loci associated with FeNO, an indicator of type 2 airway inflammation in adults.