bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gas6 in chronic liver disease—a novel blood-based biomarker for liver fibrosis
Authors: Staufer Katharina , Huber Heidemarie , Zessner-Spitzenberg Jasmin , Stauber Rudolf , Finkenstedt Armin , Bantel Heike , Weiss Thomas S. , Huber Markus , Starlinger Patrick , Gruenberger Thomas , Reiberger Thomas , Sebens Susanne , McIntyre Gail , Tabibiazar Ray , Giaccia Amato , Zoller Heinz , Trauner Michael , Mikulits Wolfgang 
Published: August 2023

AbstractThe expression of the receptor tyrosine kinase Axl and its cleavage product soluble Axl (sAxl) is increased in liver fibrosis, cirrhosis, and hepatocellular carcinoma (HCC). In this multicenter study, we evaluated the diagnostic value of Gas6, the high-affinity ligand of Axl, in patients with chronic liver disease. Levels of sAxl and Gas6, and their albumin (alb) ratios were analyzed in serum samples of patients with biopsy-proven liver fibrosis, end-stage liver disease, HCC, and healthy controls, and were compared to Fibrosis-4 (FIB-4), enhanced liver fibrosis (ELF™) test, Child-Pugh score (CPS), model of end-stage liver disease (MELD) score, hepatic venous pressure gradient, and α-fetoprotein, respectively. A total of 1111 patients (median age 57.8 y, 67.3% male) was analyzed. Gas6/alb showed high diagnostic accuracy for the detection of significant (≥F2: AUC 0.805) to advanced fibrosis (≥F3: AUC 0.818), and was superior to Fib-4 for the detection of cirrhosis (F4: AUC 0.897 vs. 0.878). In addition, Gas6/alb was highly predictive of liver disease severity (Odds ratios for CPS B/C, MELD ≥ 15, and clinically significant portal hypertension (CSPH) were 16.534, 10.258, and 12.115), and was associated with transplant-free survival (Hazard ratio 1.031). Although Gas6 and Gas6/alb showed high diagnostic accuracy for the detection of HCC in comparison to chronic liver disease patients without cirrhosis (AUC 0.852, 0.868), they failed to discriminate between HCC in cirrhosis versus cirrhosis only. In conclusion, Gas6/alb shows a high accuracy to detect significant to advanced fibrosis and cirrhosis, and predicts severity of liver disease including CSPH.
Lack of apoptosis leads to cellular senescence and tumorigenesis in Drosophila epithelial cells
Authors: Garcia-Arias Juan Manuel , Pinal Noelia , Cristobal-Vargas Sara , Estella Carlos , Morata Ginés 
Published: August 2023

AbstractProgrammed cell death (apoptosis) is a homeostasis program of animal tissues designed to remove cells that are unwanted or are damaged by physiological insults. To assess the functional role of apoptosis, we have studied the consequences of subjecting Drosophila epithelial cells defective in apoptosis to stress or genetic perturbations that normally cause massive cell death. We find that many of those cells acquire persistent activity of the JNK pathway, which drives them into senescent status, characterized by arrest of cell division, cell hypertrophy, Senescent Associated ß-gal activity (SA-ß-gal), reactive oxygen species (ROS) production, Senescent Associated Secretory Phenotype (SASP) and migratory behaviour. We have identified two classes of senescent cells in the wing disc: 1) those that localize to the appendage part of the disc, express the upd, wg and dpp signalling genes and generate tumour overgrowths, and 2) those located in the thoracic region do not express wg and dpp nor they induce tumour overgrowths. Whether to become tumorigenic or non-tumorigenic depends on the original identity of the cell prior to the transformation. We also find that the p53 gene contributes to senescence by enhancing the activity of JNK.
Development of Plasmodium falciparum liver-stages in hepatocytes derived from human fetal liver organoid cultures
Authors: Yang Annie S. P. , Dutta Devanjali , Kretzschmar Kai , Hendriks Delilah , Puschhof Jens , Hu Huili , Boonekamp Kim E. , van Waardenburg Youri , Chuva de Sousa Lopes Susana M. , van Gemert Geert-Jan , de Wilt Johannes H. W. , Bousema Teun , Clevers Hans , Sauerwein Robert W. 
Published: August 2023

AbstractPlasmodium falciparum (Pf) parasite development in liver represents the initial step of the life-cycle in the human host after a Pf-infected mosquito bite. While an attractive stage for life-cycle interruption, understanding of parasite-hepatocyte interaction is inadequate due to limitations of existing in vitro models. We explore the suitability of hepatocyte organoids (HepOrgs) for Pf-development and show that these cells permitted parasite invasion, differentiation and maturation of different Pf strains. Single-cell messenger RNA sequencing (scRNAseq) of Pf-infected HepOrg cells has identified 80 Pf-transcripts upregulated on day 5 post-infection. Transcriptional profile changes are found involving distinct metabolic pathways in hepatocytes with Scavenger Receptor B1 (SR-B1) transcripts highly upregulated. A novel functional involvement in schizont maturation is confirmed in fresh primary hepatocytes. Thus, HepOrgs provide a strong foundation for a versatile in vitro model for Pf liver-stages accommodating basic biological studies and accelerated clinical development of novel tools for malaria control.
Nitroalkanes as thioacyl equivalents to access thioamides and thiopeptides
Authors: Wang Xiaonan , Xu Silong , Tang Yuhai , Lear Martin J. , He Wangxiao , Li Jing 
Published: August 2023

AbstractThioamides are an important, but a largely underexplored class of amide bioisostere in peptides. Replacement of oxoamide units with thioamides in peptide therapeutics is a valuable tactic to improve biological activity and resistance to enzymatic hydrolysis. This tactic, however, has been hampered by insufficient methods to introduce thioamide bonds into peptide or protein backbones in a site-specific and stereo-retentive fashion. In this work, we developed an efficient and mild thioacylation method to react nitroalkanes with amines directly in the presence of elemental sulfur and sodium sulfide to form a diverse range of thioamides in high yields. Notably, this convenient method can be employed for the controlled thioamide coupling of multifunctionalized peptides without epimerization of stereocenters, including the late stage thioacylation of advanced compounds of biological and medicinal interest. Experimental interrogation of postulated mechanisms currently supports the intermediacy of thioacyl species.
A numeric-based machine learning design for detecting organized retail fraud in digital marketplaces
Authors: Mutemi Abed , Bacao Fernando 
Published: August 2023

AbstractOrganized retail crime (ORC) is a significant issue for retailers, marketplace platforms, and consumers. Its prevalence and influence have increased fast in lockstep with the expansion of online commerce, digital devices, and communication platforms. Today, it is a costly affair, wreaking havoc on enterprises’ overall revenues and continually jeopardizing community security. These negative consequences are set to rocket to unprecedented heights as more people and devices connect to the Internet. Detecting and responding to these terrible acts as early as possible is critical for protecting consumers and businesses while also keeping an eye on rising patterns and fraud. The issue of detecting fraud in general has been studied widely, especially in financial services, but studies focusing on organized retail crimes are extremely rare in literature. To contribute to the knowledge base in this area, we present a scalable machine learning strategy for detecting and isolating ORC listings on a prominent marketplace platform by merchants committing organized retail crimes or fraud. We employ a supervised learning approach to classify postings as fraudulent or real based on past data from buyer and seller behaviors and transactions on the platform. The proposed framework combines bespoke data preprocessing procedures, feature selection methods, and state-of-the-art class asymmetry resolution techniques to search for aligned classification algorithms capable of discriminating between fraudulent and legitimate listings in this context. Our best detection model obtains a recall score of 0.97 on the holdout set and 0.94 on the out-of-sample testing data set. We achieve these results based on a select set of 45 features out of 58.
Testing a relational account of search templates in visual foraging
Authors: Grössle Inga M. , Schubö Anna , Tünnermann Jan 
Published: August 2023

AbstractSearch templates guide human visual attention toward relevant targets. Templates are often seen as encoding exact target features, but recent studies suggest that templates rather contain “relational properties” (e.g., they facilitate “redder” stimuli instead of specific hues of red). Such relational guidance seems helpful in naturalistic searches where illumination or perspective renders exact feature values unreliable. So far relational guidance has only been demonstrated in rather artificial single-target search tasks with briefly flashed displays. Here, we investigate whether relational guidance also occurs when humans interact with the search environment for longer durations to collect multiple target elements. In a visual foraging task, participants searched for and collected multiple targets among distractors of different relationships to the target colour. Distractors whose colour differed from the environment in the same direction as the targets reduced foraging efficiency to the same amount as distractors whose colour matched the target colour. Distractors that differed by the same colour distance but in the opposite direction of the target colour did not reduce efficiency. These findings provide evidence that search templates encode relational target features in naturalistic search tasks and suggest that attention guidance based on relational features is a common mode in dynamic, real-world search environments.
Close-kin mark-recapture informs critically endangered terrestrial mammal status
Authors: Lloyd-Jones Luke R. , Bravington Mark V. , Armstrong Kyle N. , Lawrence Emma , Feutry Pierre , Todd Christopher M. , Dorrestein Annabel , Welbergen Justin A. , Martin John M. , Rose Karrie , Hall Jane , Phalen David N. , Peters Isabel , Baylis Shane M. , Macgregor Nicholas A. , Westcott David A. 
Published: August 2023

AbstractReliable information on population size is fundamental to the management of threatened species. For wild species, mark-recapture methods are a cornerstone of abundance estimation. Here, we show the first application of the close-kin mark-recapture (CKMR) method to a terrestrial species of high conservation value; the Christmas Island flying-fox (CIFF). The CIFF is the island's last remaining native terrestrial mammal and was recently listed as critically endangered. CKMR is a powerful tool for estimating the demographic parameters central to CIFF management and circumvents the complications arising from the species’ cryptic nature, mobility, and difficult-to-survey habitat. To this end, we used genetic data from 450 CIFFs captured between 2015 and 2019 to detect kin pairs. We implemented a novel CKMR model that estimates sex-specific abundance, trend, and mortality and accommodates observations from the kin-pair distribution of male reproductive skew and mate persistence. CKMR estimated CIFF total adult female abundance to be approximately 2050 individuals (95% CI (950, 4300)). We showed that on average only 23% of the adult male population contributed to annual reproduction and strong evidence for between-year mate fidelity, an observation not previously quantified for a Pteropus species in the wild. Critically, our population estimates provide the most robust understanding of the status of this critically endangered population, informing immediate and future conservation initiatives.
β-mannanase supplemented in diets saved 85 to 100 kcal of metabolizable energy/kg, supporting growth performance and improving nutrient digestibility in grower pigs
Authors: Genova Jansller Luiz , Azevedo Liliana Bury de , Rupolo Paulo Evaristo , Cordeiro Flávia Beatriz Carvalho , Vilela Hellen Lazarino Oliveira , Careli Pedro Silva , de Castro Fidelis Toledo Damares , Carvalho Silvana Teixeira , Kipper Marcos , Rennó Luciana Navajas , Faveri Juliana Canto , de Oliveira Carvalho Paulo Levi 
Published: August 2023

AbstractThe effects of β-mannanase supplementation in metabolizable energy (ME)-reduced diets containing xylanase-phytase were investigated on growth performance, fecal score, ultra-sounded backfat thickness and loin depth, blood profile, apparent total tract digestibility (ATTD), digesta passage rate, and fecal microbiome in grower pigs (n = 40, 26.09 ± 0.96 kg) randomly assigned within 4 treatments: a control diet containing isolated phytase and xylanase valued at 40 kcal of ME/kg (CD0), CD0 + β-mannanase (0.3 g/kg valued at 30 kcal of ME/kg) (CD70), CD0 + β-mannanase (0.3 g/kg valued at 45 kcal of ME/kg) (CD85), and CD0 + β-mannanase (0.3 g/kg valued at 60 kcal of ME/kg) (CD100). Growth performance was not affected in pigs fed ME-reduced diets containing β-mannanase. Pigs with CD100 had lower serum IL-1β concentration, and higher IL-10 was observed in pigs on CD0 than those fed β-mannanase. Coefficients of ATTD, and ATTD of DM and CP were higher in animals fed CD85 or CD100. Pigs with CD85 had higher alpha diversity richness but lower Firmicutes:Bacteroidota ratio. Acidaminococcaceae and Ruminococcaceae were more abundant in pigs fed CD0, but lower for Christensenellaceae NSJ-63 and NSJ-63 sp014384805. Pigs in CD85 showed higher Bacteroidaceae and Prevotella abundance, and lower for Streptococcaceae and Streptococcus. In conclusion, supplementation of β-mannanase in diets containing xylanase-phytase saved 85 to 100 kcal of ME/kg by supporting growth performance and improving nutrient digestibility in grower pigs.
Optimized sliding mode controller for trajectory tracking of flexible joints three-link manipulator with noise in input and output
Authors: Azeez Muhammad I. , Abdelhaleem A. M. M. , Elnaggar S. , Moustafa Kamal A. F. , Atia Khaled R. 
Published: August 2023

AbstractThe aim of this study is to enhance the performance of a nonlinear three-rigid-link maneuver (RLM) in terms of trajectory tracking, disturbance and noise cancellation, and adaptability to joint flexibility. To achieve this, an optimized sliding mode controller with a proportional integral derivative surface (SMC-PID) is employed for maneuver control. An improved artificial bee colony algorithm with multi-elite guidance (MGABC) is utilized to obtain optimal values for the sliding surface and switching mode gain and attain the best performance for the robot maneuver system. The selection of the MGABC algorithm is based on its efficient exploration and exploitation techniques. The performance of the optimized SMC-PID robotic system is compared against other optimization algorithms found in existing literature, including Particle Swarm Optimization (PSO), Genetic Algorithm (GA), Artificial Bee Colony (ABC), Ant Lion Optimizer (ALO), and Grey Wolf Optimizer (GWO). The implemented controller effectively reduces the tracking error to 0.00691 radians, eliminates chattering phenomena in the control effort, and demonstrates robustness against disturbances and noise. The controller ensures that the objective function (OBJF) is minimized, with 0.954% increase in OBJF under low disturbance and noise conditions and 14.55% under severe disturbance and noise conditions. Moreover, the optimized controller exhibits resilience to variations in payload mass analysis, with the percentage increase in OBJF values ranging from 5.726% under low uncertainty conditions to 18.887% under severe uncertainty conditions. Flexible-link maneuvers (FLM) offer advantages such as improved safety and increased operating speeds in real-world applications. In this study, we investigated the impact of joint flexibility on the performance of the FLM system. Our proposed controller demonstrated superior tracking performance, characterized by minimal vibrations in the movement of the end effector.
Preoperative prediction of sinonasal papilloma by artificial intelligence using nasal video endoscopy: a retrospective study
Authors: Yui Ryosuke , Takahashi Masahiro , Noda Katsuhiko , Yoshida Kaname , Sakurai Rinko , Ohira Shinya , Omura Kazuhiro , Otori Nobuyoshi , Wada Kota , Kojima Hiromi 
Published: August 2023

AbstractSinonasal inverted papilloma (IP) is at risk of recurrence and malignancy, and early diagnosis using nasal endoscopy is essential. We thus developed a diagnostic system using artificial intelligence (AI) to identify nasal sinus papilloma. Endoscopic surgery videos of 53 patients undergoing endoscopic sinus surgery were edited to train and evaluate deep neural network models and then a diagnostic system was developed. The correct diagnosis rate based on visual examination by otolaryngologists was also evaluated using the same videos and compared with that of the AI diagnostic system patients. Main outcomes evaluated included the percentage of correct diagnoses compared to AI diagnosis and the correct diagnosis rate for otolaryngologists based on years of practice experience. The diagnostic system had an area under the curve of 0.874, accuracy of 0.843, false positive rate of 0.124, and false negative rate of 0.191. The average correct diagnosis rate among otolaryngologists was 69.4%, indicating that the AI was highly accurate. Evidently, although the number of cases was small, a highly accurate diagnostic system was created. Future studies with larger samples to improve the accuracy of the system and expand the range of diseases that can be detected for more clinical applications are warranted.
Engineered E. coli Nissle 1917 for delivery of bioactive IL-2 for cancer immunotherapy
Authors: Tumas Sarunas , Meldgaard Trine Sundebo , Vaaben Troels Holger , Suarez Hernandez Sara , Rasmussen Annemette Tengstedt , Vazquez-Uribe Ruben , Hadrup Sine Reker , Sommer Morten O. A. 
Published: August 2023

AbstractIn this study we performed a step-wise optimization of biologically active IL-2 for delivery using E. coli Nissle 1917. Engineering of the strain was coupled with an in vitro cell assay to measure the biological activity of microbially produced IL-2 (mi-IL2). Next, we assessed the immune modulatory potential of mi-IL2 using a 3D tumor spheroid model demonstrating a strong effect on immune cell activation. Finally, we evaluated the anticancer properties of the engineered strain in a murine CT26 tumor model. The engineered strain was injected intravenously and selectively colonized tumors. The treatment was well-tolerated, and tumors of treated mice showed a modest reduction in tumor growth rate, as well as significantly elevated levels of IL-2 in the tumor. This work demonstrates a workflow for researchers interested in engineering E. coli Nissle for a new class of microbial therapy against cancer.
hsa-miR-199b-3p suppresses osteosarcoma progression by targeting CCDC88A, inhibiting epithelial-to-mesenchymal transition, and Wnt/beta-catenin signaling pathway
Authors: Zhu Dongsheng , Qi Han , Zhu Hongqi 
Published: August 2023

AbstractThe present study investigated microRNA (miR)-199b-3p expression in osteosarcoma (OS) and aimed to identify its potential mechanism of action contributing to the development of this disease. Firstly, miR-199b-3p and coiled-coil domain containing 88A (CCDC88A) expression data were evaluated from Gene Expression Profiling Interactive Analysis and Kaplan Meier plotter was used to assess the survival data. By analyzing the GSE65071 dataset from gene expression omnibus, it was found that miR-199b-3p was expressed at a low level. By using reverse transcription-quantitative PCR analysis in OS cells and tissues, CCDC88A was found to be expressed at a high level. Moreover, TargetScan predicted CCDC88A to be a downstream target of miR-199b-3p. Luciferase reporter assays were used to verify this prediction. In vitro overexpression of miR-199b-3p decreased the invasive and proliferative activity of OS cells. Mechanistic studies indicated that decreased miR-199b-3p resulted in increased expression of CCDC88A. Concomitantly, it impeded the Wnt/beta-catenin pathway and the epithelial-to-mesenchymal transition process. Overall, the results of the present study emphasized the pivotal role of the miR-199b-3p in the formation and progression of OS, suggesting that it could be used as a potential tumor biomarker.
Spatial attention-based residual network for human burn identification and classification
Authors: Yadav D. P. , Aljrees Turki , Kumar Deepak , Kumar Ankit , Singh Kamred Udham , Singh Teekam 
Published: August 2023

AbstractDiagnosing burns in humans has become critical, as early identification can save lives. The manual process of burn diagnosis is time-consuming and complex, even for experienced doctors. Machine learning (ML) and deep convolutional neural network (CNN) models have emerged as the standard for medical image diagnosis. The ML-based approach typically requires handcrafted features for training, which may result in suboptimal performance. Conversely, DL-based methods automatically extract features, but designing a robust model is challenging. Additionally, shallow DL methods lack long-range feature dependency, decreasing efficiency in various applications. We implemented several deep CNN models, ResNeXt, VGG16, and AlexNet, for human burn diagnosis. The results obtained from these models were found to be less reliable since shallow deep CNN models need improved attention modules to preserve the feature dependencies. Therefore, in the proposed study, the feature map is divided into several categories, and the channel dependencies between any two channel mappings within a given class are highlighted. A spatial attention map is built by considering the links between features and their locations. Our attention-based model BuRnGANeXt50 kernel and convolutional layers are also optimized for human burn diagnosis. The earlier study classified the burn based on depth of graft and non-graft. We first classified the burn based on the degree. Subsequently, it is classified into graft and non-graft. Furthermore, the proposed model performance is evaluated on Burns_BIP_US_database. The sensitivity of the BuRnGANeXt50 is 97.22% and 99.14%, respectively, for classifying burns based on degree and depth. This model may be used for quick screening of burn patients and can be executed in the cloud or on a local machine. The code of the proposed method can be accessed athttps://github.com/dhirujis02/Journal.gitfor the sake of reproducibility.