bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spike protein mutations and structural insights of pangolin lineage B.1.1.25 with implications for viral pathogenicity and ACE2 binding affinity
Authors: Akter Shahina , Oliveira Jonas Ivan Nobre , Barton Carl , Sarkar Murshed Hasan , Shahab Muhammad , Banu Tanjina Akhtar , Goswami Barna , Osman Eshrar , Uzzaman Mohammad Samir , Nafisa Tasnim , Molla Maruf Ahmed , Yeasmin Mahmuda , Farzana Maisha , Habib Ahashan , Shaikh Aftab Ali , Khan Salim 
Published: August 2023

AbstractSevere Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the causative agent of COVID -19, is constantly evolving, requiring continuous genomic surveillance. In this study, we used whole-genome sequencing to investigate the genetic epidemiology of SARS-CoV-2 in Bangladesh, with particular emphasis on identifying dominant variants and associated mutations. We used high-throughput next-generation sequencing (NGS) to obtain DNA sequences from COVID-19 patient samples and compared these sequences to the Wuhan SARS-CoV-2 reference genome using the Global Initiative for Sharing All Influenza Data (GISAID). Our phylogenetic and mutational analyzes revealed that the majority (88%) of the samples belonged to the pangolin lineage B.1.1.25, whereas the remaining 11% were assigned to the parental lineage B.1.1. Two main mutations, D614G and P681R, were identified in the spike protein sequences of the samples. The D614G mutation, which is the most common, decreases S1 domain flexibility, whereas the P681R mutation may increase the severity of viral infections by increasing the binding affinity between the spike protein and the ACE2 receptor. We employed molecular modeling techniques, including protein modeling, molecular docking, and quantum mechanics/molecular mechanics (QM/MM) geometry optimization, to build and validate three-dimensional models of the S_D614G-ACE2 and S_P681R-ACE2 complexes from the predominant strains. The description of the binding mode and intermolecular contacts of the referenced systems suggests that the P681R mutation may be associated with increased viral pathogenicity in Bangladeshi patients due to enhanced electrostatic interactions between the mutant spike protein and the human ACE2 receptor, underscoring the importance of continuous genomic surveillance in the fight against COVID -19. Finally, the binding profile of the S_D614G-ACE2 and S_P681R-ACE2 complexes offer valuable insights to deeply understand the binding site characteristics that could help to develop antiviral therapeutics that inhibit protein–protein interactions between SARS-CoV-2 spike protein and human ACE2 receptor.
Harmonization service and global library of models to support country-driven global information on salt-affected soils
Authors: Omuto C. T. , Scherstjanoi M. , Kader M. A. , Musana B. , Barman A. , Fantappiè M. , Jiménez L. S. , Jimenez W. A. , Figueredo H. , Balta R. , Santander K. , Malatji A. , Nahar A. , Kairat A. , Ahmadzai H. , Morisson J. , Stone S. , Roopnarine R. , Eudoxie G. , Khat P. , Phy C. , Seng V. , Janjirawuttikul N. , Tina M. , Farradas M. , Alferihat M. , Desire K. , Jayeoba O. J. , Loum M. , Ahmad W. , Al Rasbi A. S. , Matolo N. 
Published: August 2023

AbstractGlobal distribution of salt-affected soils (SAS) has remained at about 1 billion hectares in the literature over the years despite changes in climate, sea levels, and land use patterns which influence the distribution. Lack of periodic update of input soil data, data gaps, and inconsistency are part of the reasons for constant SAS distribution in the literature. This paper proposes harmonization as a suitable alternative for managing inconsistent data and minimizing data gaps. It developed a new harmonization service for supporting country-driven global SAS information update. The service contains a global library of harmonization models for harmonizing inconsistent soil data. It also contains models for identifying gaps in SAS database and for showing global distribution where harmonization of available data is needed. The service can be used by countries to develop national SAS information and update global SAS distribution. Its data availability index is useful in identifying countries without SAS data in the global database, which is a convenient way to identify countries to mobilize when updating global SAS information. Its application in 27 countries showed that the countries have more SAS data than they currently share with the global databases and that most of their data require SAS harmonization.
Depth and direction effects in the prediction of static and shifted reaching goals from kinematics
Authors: Bosco A. , Filippini M. , Borra D. , Kirchner E. A. , Fattori P. 
Published: August 2023

AbstractThe kinematic parameters of reach-to-grasp movements are modulated by action intentions. However, when an unexpected change in visual target goal during reaching execution occurs, it is still unknown whether the action intention changes with target goal modification and which is the temporal structure of the target goal prediction. We recorded the kinematics of the pointing finger and wrist during the execution of reaching movements in 23 naïve volunteers where the targets could be located at different directions and depths with respect to the body. During the movement execution, the targets could remain static for the entire duration of movement or shifted, with different timings, to another position. We performed temporal decoding of the final goals and of the intermediate trajectory from the past kinematics exploiting a recurrent neural network. We observed a progressive increase of the classification performance from the onset to the end of movement in both horizontal and sagittal dimensions, as well as in decoding shifted targets. The classification accuracy in decoding horizontal targets was higher than the classification accuracy of sagittal targets. These results are useful for establishing how human and artificial agents could take advantage from the observed kinematics to optimize their cooperation in three-dimensional space.
An artificial intelligence method using FDG PET to predict treatment outcome in diffuse large B cell lymphoma patients
Authors: Ferrández Maria C. , Golla Sandeep S. V. , Eertink Jakoba J. , de Vries Bart M. , Lugtenburg Pieternella J. , Wiegers Sanne E. , Zwezerijnen Gerben J. C. , Pieplenbosch Simone , Kurch Lars , Hüttmann Andreas , Hanoun Christine , Dührsen Ulrich , de Vet Henrica C. W. ,   PETRA, Hoekstra Otto S. , Burggraaff Coreline N. , Bes Annelies , Heymans Martijn W. , Jauw Yvonne W. S. , Chamuleau Martine E. D. , Barrington Sally F. , Mikhaeel George , Zucca Emanuele , Ceriani Luca , Carr Robert , Györke Tamás , Czibor Sándor , Fanti Stefano , Kostakoglu Lale , Loft Annika , Hutchings Martin , Lee Sze Ting , Zijlstra Josée M. , Boellaard Ronald 
Published: August 2023

AbstractConvolutional neural networks (CNNs) may improve response prediction in diffuse large B-cell lymphoma (DLBCL). The aim of this study was to investigate the feasibility of a CNN using maximum intensity projection (MIP) images from 18F-fluorodeoxyglucose (18F-FDG) positron emission tomography (PET) baseline scans to predict the probability of time-to-progression (TTP) within 2 years and compare it with the International Prognostic Index (IPI), i.e. a clinically used score. 296 DLBCL 18F-FDG PET/CT baseline scans collected from a prospective clinical trial (HOVON-84) were analysed. Cross-validation was performed using coronal and sagittal MIPs. An external dataset (340 DLBCL patients) was used to validate the model. Association between the probabilities, metabolic tumour volume and Dmaxbulk was assessed. Probabilities for PET scans with synthetically removed tumors were also assessed. The CNN provided a 2-year TTP prediction with an area under the curve (AUC) of 0.74, outperforming the IPI-based model (AUC = 0.68). Furthermore, high probabilities (> 0.6) of the original MIPs were considerably decreased after removing the tumours (< 0.4, generally). These findings suggest that MIP-based CNNs are able to predict treatment outcome in DLBCL.
Nanoporous carbons based on coordinate organic polymers as an efficient and eco-friendly nano-sorbent for adsorption of phenol from wastewater
Authors: Sharafinia Soheila , Rashidi Alimorad , Babaei Behnam , Orooji Yasin 
Published: August 2023

AbstractThe major part of water pollutants includes of organic such as phenolic pollutant, thus there are every hazardous to environment. Present work is a comparative onto surface chemistry and adsorptive characteristics of coordinate organic polymer (Cop-150) and nanoporous carbon (NPC) prepared using solvothermal method. New NPC was successfully synthesized to remove of phenol. FT-IR, XRD, XPS, SEM, TGA, and BET techniques have been used to characterization and confirm physicochemical variation during preparing Cop-150 and NPC. Box–Behnken response surface methodology (BBRSM) was used to optimize four important factors of the pH (2–10), contact time (1–40 min), temperature (25–60 °C), and initial concentration of phenol (5–50 mg L−1). To analyze the data obtained from the adsorption of phenol by synthesized adsorbents, four linear, 2FI, quadratic and cubic models were examined, which the quadratic model was recognized as the best model. To the NPC the equal adsorption capacity 500 mg g−1 is achieved at the initial concentration of phenol = 49.252 mg L−1, contact time = 15.738 min, temperature = 28.3 °C, and pH 7.042. On the other hand, the adsorption capacity for Cop-150 in pH 4.638, the contact time = 19.695 min, the temperature = 56.8 °C, and the initial concentration of phenol = 6.902 mg L−1 was equal to 50 mg g−1. The experimental data at different conditions were investigated by some famous kinetic and isotherm models, which among them, were corresponded to the pseudo-second-order kinetic model and the Langmuir isotherm. Moreover, based to result of thermodynamics to the both Cop-150 and NPC, the adsorption process is exothermic and spontaneous. According to results the Cop-150 and NPC could be used for up to four and five cycles without significantly reducing their performance, respectively.
Towards data-driven biopsychosocial classification of non-specific chronic low back pain: a pilot study
Authors: Tagliaferri Scott D. , Owen Patrick J. , Miller Clint T. , Angelova Maia , Fitzgibbon Bernadette M. , Wilkin Tim , Masse-Alarie Hugo , Van Oosterwijck Jessica , Trudel Guy , Connell David , Taylor Anna , Belavy Daniel L. 
Published: August 2023

AbstractThe classification of non-specific chronic low back pain (CLBP) according to multidimensional data could guide clinical management; yet recent systematic reviews show this has not been attempted. This was a prospective cross-sectional study of participants with CLBP (n = 21) and age-, sex- and height-matched pain-free controls (n = 21). Nervous system, lumbar spinal tissue and psychosocial factors were collected. Dimensionality reduction was followed by fuzzy c-means clustering to determine sub-groups. Machine learning models (Support Vector Machine, k-Nearest Neighbour, Naïve Bayes and Random Forest) were used to determine the accuracy of classification to sub-groups. The primary analysis showed that four factors (cognitive function, depressive symptoms, general self-efficacy and anxiety symptoms) and two clusters (normal versus impaired psychosocial profiles) optimally classified participants. The error rates in classification models ranged from 4.2 to 14.2% when only CLBP patients were considered and increased to 24.2 to 37.5% when pain-free controls were added. This data-driven pilot study classified participants with CLBP into sub-groups, primarily based on psychosocial factors. This contributes to the literature as it was the first study to evaluate data-driven machine learning CLBP classification based on nervous system, lumbar spinal tissue and psychosocial factors. Future studies with larger sample sizes should validate these findings.
Potential immunosuppressive clonal hematopoietic mutations in tumor infiltrating immune cells in breast invasive carcinoma
Authors: Anandakrishnan Ramu , Zyvoloski Ian J. , Zyvoloski Lucas R. , Opoku Nana K. , Dai Andrew , Antony Veneeth 
Published: August 2023

AbstractA hallmark of cancer is a tumor cell’s ability to evade immune destruction. Somatic mutations in tumor cells that prevent immune destruction have been extensively studied. However, somatic mutations in tumor infiltrating immune (TII) cells, to our knowledge, have not been previously studied. Understandably so since normal hematopoiesis prevents the accumulation of somatic mutations in immune cells. However, clonal hematopoiesis does result in the accumulation of somatic mutations in immune cells. These mutations cannot “drive” tumor growth, however, they may “facilitate” it by inhibiting an effective anti-tumor immune response. To identify potential immunosuppressive clonal hematopoietic (CH) mutations in TII cells, we analyzed exome and RNA sequencing data from matched tumor and normal blood samples, and single-cell RNA sequencing data, from breast cancer patients. We selected mutations that were somatic, present in TII cells, clonally expanded, potentially pathogenic, expressed in TII cells, unlikely to be a passenger mutation, and in immune response associated genes. We identified eight potential immunosuppressive CH mutations in TII cells. This work is a first step towards determining if immunosuppressive CH mutations in TII cells can affect the progression of solid tumors. Subsequent experimental confirmation could represent a new paradigm in the etiology of cancer.
The healing capacity and osteogenesis pattern of demineralized dentin matrix (DDM)-fibrin glue (FG) compound
Authors: Bao Jibo , Fu Xunan , Wu Yirong , Yang Shengyin , Ren Xiaobin , Fang Xingchen , Yuan Quan , Xie Zhigang , Seriwatanachai Dutmanee 
Published: August 2023

AbstractDemineralized dentin matrix (DDM) is an osteoconductive and osteoinductive material that has been successfully used in sinus floor augmentation and alveolar ridge augmentation in clinical applications. It releases bone morphogenetic proteins (BMPs) and other growth factors, making DDM a suitable grafting material. However, the granular particle of DDM makes it difficult to anchor into the bone defect area. The aim of this study was to investigate the biological effects and osteoinductivity of the combination of DDM and Fibrin Glue (FG) at an optimal ratio on bone healing from a critical bone defect in an animal model. The mouse osteoblastic cell line (MC3T3-E1) was co-cultured with various ratios of DDM and FG to examine their effects on osteoblast proliferation and differentiation, as indicated by alkaline phosphatase (ALP) activity, osteocalcin (OC) production and mineralized nodules formation. The optimal ratio was then chosen for further study with a rabbit calvarial defective model, in which they were implanted with DDM or DDM-FG1 (1 g: 0.1 ml) and DDM-FG2 (1 g: 0.5 ml) compounds, or left blank for 2, 4, 8 and 12 weeks to investigate soft tissue and new bone regeneration. Micro-CT and histology analysis were used to evaluate the total grafting properties according to the different healing periods. The result from in vitro studies demonstrated that the ratio of 1:0.1 induced more ALP activity and mineralized nodules, while the ratio of 1: 0.5 (DDM-FG combined) induced more osteocalcin (OC) at specific time points. In the animal model, the 3D new bone volume in all DDM-FG treatment groups was significantly greater than that in the blank group at 2, 4, 8 and 12 weeks. Furthermore, the new bone volume was greater in DDM-FG2 when compared to the other groups during the early weeks of the healing period. In histological analysis, clusters of osteoblasts were formed adjacent to the DDM particles, and newly formed bone was observed in all groups, suggesting an osteoinductive property of DDM. Moreover, the greater new collagen synthesis observed at 4 weeks suggested that early bone healing was induced in the DDM-FG2 group. This study demonstrated that at an optimal ratio, the DDM-FG compound enhances osteogenic activities and bone regeneration.
A novel polysaccharide/zein conjugate as an alternative green plastic
Authors: Tallawi Marwa , Amrein Danial , Gemmecker Gerd , Aifantis Katerina E. , Drechsler Klaus 
Published: August 2023

AbstractThe flax seed cake is a waste product from flax oil extraction. Adding value to this wasted material aligns with the concept of circularity. In this study, we explored zein protein conjugation with flax mucilage for packaging material development. Although both flax mucilage and zein have excellent film-forming properties, they lack the required mechanical properties for industrial processing and are sensitive to high humidity. We present a simple and non-toxic one-pot method for developing the novel flax mucilage/zein conjugate. Where the flax mucilage undergoes oxidation to form aldehyde groups, which then react with zein's amino groups in a glycation process. The conjugates were analyzed using different techniques. The flax mucilage conjugate had a water-holding capacity of 87–62%. Increasing the zein content improved the surface smoothness of the films. On the other hand, higher levels of zein led to a significant decrease in film solubility (p < 0.05). The flax mucilage conjugate exhibited thermoplastic and elastic properties; revealing Young's modulus of 1–3 GPa, glass transition temperature between 49 °C and 103 °C and excellent processability with various industrial techniques. Showing its potential as a sustainable alternative to traditional plastics.
Pearl shape classification using deep convolutional neural networks from Tahitian pearl rotation in Pinctada margaritifera
Authors: Edeline Paul-Emmanuel , Leclercq Mickaël , Le Luyer Jérémy , Chabrier Sébastien , Droit Arnaud 
Published: August 2023

AbstractTahitian pearls, artificially cultivated from the black-lipped pearl oyster Pinctada margaritifera, are renowned for their unique color and large size, making the pearl industry vital for the French Polynesian economy. Understanding the mechanisms of pearl formation is essential for enabling quality and sustainable production. In this paper, we explore the process of pearl formation by studying pearl rotation. Here we show, using a deep convolutional neural network, a direct link between the rotation of the pearl during its formation in the oyster and its final shape. We propose a new method for non-invasive pearl monitoring and a model for predicting the final shape of the pearl from rotation data with 81.9% accuracy. These novel resources provide a fresh perspective to study and enhance our comprehension of the overall mechanism of pearl formation, with potential long-term applications for improving pearl production and quality control in the industry.
Alteration effects of karstification and hydrothermalism on middle Permian Qixia formation at the Wulong section, South China
Authors: Shang Junxin , Feng Mingyou , Wang Xingzhi , Zhang Benjian , Xu Liang , Liu Xiaohong 
Published: August 2023

AbstractMiddle Permian Qixia Formation in the southwestern region of Sichuan (SW China) has experienced multiphase fluidisation, resulting in an unclear understanding of the reservoir reconstruction effect. In this study, a systematic analysis of the Qi2 member in Wulong Town was carried out by combining field outcrop petrology and geochemistry. The results demonstrated that multiple sets of crystalline dolomite-bioclastic limestone cycles were stacked vertically in the Qi2 member, accompanied by the development of fractures and karst channels. The dolomite was mainly composed of silty-fine dolomite (D1) and recrystallised dolomite (D2). Furthermore, obvious multiphase dolomitic cements (Cd1-Cd2) were present in the fractures and pores. Early karst is known to have lithologic mutation surface development and karst channel development at the top of several secondary cycles. The vadose silt dolomites (Cd1) having karst channels developed dull luminescence under cathode luminescence (CL). Both the geochemical indicators of elements and rare earth element (REE) content indicated dysoxic-oxic environmental conditions. The hydrothermal solution displayed tectonic carniole characteristics in the strata burial stage. Fractures and pores were filled with hydrothermal minerals such as coarse dolomites-saddle dolomites (Cd2, with some caused by recrystallisation of the Cd1 hydrothermal solution) and fluorites. Coarse dolomites-saddle dolomites developed dull-red luminescence with a bright-red rim under CL and their δ18OVPDB values were more negative than those of middle Permian limestone samples. Both the geochemical indicators of elements and REE content indicated the suboxic-anoxic environmental conditions. Karstification had minor constructive impact on the reservoir of the Qi2 member in Baoxing in southwestern Sichuan. Most products of karstification were distributed as fillings in channels. Aside from creating certain networked fractures, the hydrothermal solution was mainly filled with hydrothermal minerals along the fractures, pores and early karst channels. Karst and the hydrothermal solution mainly damaged the middle and upper parts of the middle Permian Qixia Formation in Southwest Sichuan. The impact of episodic fluid on the restoration of the carbonate reservoir was mainly restricted by channels for fluid migration and thickness differences among the reservoir. However, certain thick-layered and massive crystalline dolomite may hold promise for exploration.