bluuebunny/crossref_metadata_2025_split huggingface dataset:
The role of WHO/MMV genotyping in differentiating Plasmodium falciparum recrudescence from re-infections in the POR phase in Sri Lanka
Authors: de A.W.Gunasekera W.M.K.T. , Premaratne Risintha , Handunnetti Shiroma , Weerasena OVDSJ , Premawansa Sunil , Fernando Deepika 
Published: August 2023

Abstract
Background
Sri Lanka after eliminating malaria in 2012, is in the prevention of re-establishment (POR) phase. Being a tropical country with high malariogenic potential, maintaining vigilance is important. All malaria cases are investigated epidemiologically and followed up by integrated drug efficacy surveillance (iDES). Occasionally, that alone is not adequate to differentiate Plasmodium falciparum re-infections from recrudescences. This study evaluated the World Health Organization (WHO) and Medicines for Malaria Venture (MMV) recommended genotyping protocol for merozoite surface proteins (msp1, msp2) and glutamate-rich protein (glurp) to discriminate P. falciparum recrudescence from re-infection in POR phase.
Method
All P. falciparum patients detected from April 2014 to December 2019 were included for this study. Patients were treated and followed up by iDES up to 28 days and were advised to get tested if they develop fever at any time over the following year. Basic socio-demographic information including history of travel was obtained. Details of the malariogenic potential and reactive entomological and parasitological surveillance carried out by the AMC to exclude the possibility of local transmission was also collected. WHO/MMV genotyping was performed for initial and any recurrent infections. Classification of recurrent infections as recrudescence or re-infection was done based on epidemiological findings and was compared with the genotyping outcome.
Results
Among 106 P. falciparum patients, six had recurrent infections. All the initial infections were imported, with a history of travel to malaria endemic countries. In all instances, the reactive entomological and parasitological surveillance had no evidence for local transmission. Five recurrences occurred within 28 days of follow up and were classified as recrudescence. They have not travelled to malaria endemic countries in between the initial and recurrent infections. The other had the recurrent infection after 105 days. It was assumed a re-infection, as he had traveled to the same malaria endemic country in between the two malaria attacks. Genotyping confirmed the recrudescence and the re-infection.
Conclusions
The WHO/MMV genotyping method accurately differentiated re-infections from recrudescence. Since re-infection without a history of travel to a malaria-endemic country would mean local transmission, combining genotyping outcome with epidemiological findings will assist classifying malaria cases without any ambiguity.
Prolonged Door-to-Balloon time leads to glycocalyx damage and endothelial dysfunction in patients with ST-Elevation Myocardial Infarction and cardiogenic shock
Authors: Vahldieck Carl , Fels Benedikt , Löning Samuel , Nickel Laura , Weil Joachim , Kusche-Vihrog Kristina 
Published: August 2023

Abstract
Background
Damage to the endothelial glycocalyx (eGC) and endothelial dysfunction have been reported to develop during cardiac ischemia-and-reperfusion injury (IRI), such as ST-elevation myocardial infarction (STEMI). For patients with acute ischemic syndromes and cardiogenic shock a door-to-balloon time (D2B) < 60 min with rapid revascularization was shown to reduce both mortality and nonfatal complications. Here, we hypothesize that prolonged D2B is associated with an unfavorable outcome for the eGC of patients with STEMI.
Methods
Data of 126 individuals were analyzed in this study. Sixty-three STEMI patients with cardiogenic shock in the event of STEMI were included. All received revascularization through primary percutaneous coronary intervention (PCI). 63 age- and sex-matched healthy volunteers served as controls. After stimulating endothelial cells with patient sera, the nanomechanical properties of the eGC were analyzed using the atomic force microscopy-based nanoindentation technique. Serum levels of eGC components as well as complement anaphylatoxins and angiopoetin-2 were measured via ELISA. Nitric oxide (NO) levels were determined chemiluminescence-based.
Results
eGC height and stiffness (both, p < 0.001) as well as NO concentration (p < 0.001) were reduced after STEMI. Longer D2B led to significantly higher amounts of eGC components (syndecan-1: 35.5 vs. 136.7 ng/ml; p < 0.001 / heparan sulfate: 4.6 vs. 10.8 ng/ml; p < 0.001 / hyaluronic acid: 116.7 vs. 182.9 µg/ml; p < 0.0001) and troponin-t (p < 0.01) in the patient sera. Notably, D2B had a strong impact on patient outcome. D2B > 60 min led to pronounced loss of eGC height and stiffness (both, p < 0.001), activated the complement system (p < 0.001), and prolonged the hospital stay (p < 0.01) compared to D2B ≤ 60 min.
Conclusion
Increased D2B led to severe eGC shedding and endothelial dysfunction in a temporal context. In addition, levels of syndecan-1 and proinflammatory mediators correlated with prolonged D2B, indicating a time-dependent immune reaction during cardiogenic shock with increased IRI to the eGC and prolonged hospitalization. D2B therefore appears to be a crucial factor for endothelial IRI in the case of STEMI with cardiogenic shock. Combining the clinical evaluation of the eGC condition with levels of biomarkers such as syndecan-1 might serve as important predictor for eGC impairment of STEMI patients with cardiogenic shock in the future.
Divya cave - the longest cave in the Perm region (Russia)
Authors: Kazantseva Alena , Krasikov Alexey , Kadebskaya Olga 
Published: August 2023

Abstract
The work is a review of contemporary research carried out in Divya Cave, the longest cave in the Perm region. This is one of the largest and most beautiful limestone caves in the Urals, the first mention of which dates back to the 70s of the 18th century. The cave provides the richest material for geologists, karstologists and speleologists, as it is a relic of an ancient aquifer and it is truly a natural museum, where almost all types of secondary calcite formations found in caves are collected. The remoteness of the cave from roads and settlements has never stopped explorers. The first plan of Divya Cave was drawn up in 1949. Subsequently, many speleologists continued to explore the cave, but not all passages were marked on the latest maps. Hydrogeological and hydrochemical research was done for the first time in 1948, 1956, 1962 and 1967. Numerous springs between the village of Divya and Divya Cave were surveyed, water temperature and flow rates were measured and the hydrochemical indicators of water in the cave lakes were studied. Modern data on the composition of water from surface runoff and the sources flowing from the cave were required. Findings of cryogenic calcite in 1968 prompted further research related to the study of cave deposits, using isotopic analysis methods, taking into account their dating, to determine the migration of permafrost boundaries. Our research was carried out between 2016 and 2020. Significant results obtained during this period include an instrumental and semi-instrumental topographical survey of the cave and surface, followed by the creation of a combined plan, studies of cryogenic mineralization, isotopic studies of water and speleothem and their dating.
Tropical Cyclones in Global High-Resolution Simulations using the IPSL Model
Authors: Bourdin Stella , Fromang Sébastien , Caubel Arnaud , Ghattas Josefine , Meurdesoif Yann , Dubos Thomas 
Published: August 2023

Abstract
Despite many years of extensive research, the evolution of Tropical Cyclone (TC) activity in our changing climate remains uncertain. This is partly because the answer to that question relies primarily on climate simulations with horizontal resolutions of a few tens of kilometers. Such simulations have only recently become accessible for most modeling centers, including the IPSL.
Using recent numerical developments in the IPSL model, we perform a series of historical atmosphericonly simulations that follow the HighResMIP protocol. We assess the impact of increasing the resolution up to 25 km on TC activity. In agreement with previous work, we find a systematic improvement of TC activity with increasing resolution. However, a clear signature of TC frequencies convergence with resolution is still lacking. Cyclogenesis geographical distributions also improve at the scale of individual basins. This is particularly true of the North Atlantic, where the agreement with the observed distribution is impressive at 25 km. In agreement with the observations, TC activity correlates with the large-scale environment and ENSO in that basin. By contrast, TC frequencies remain too small in the Western North Pacific at 25 km, where significant biases of humidity and vorticity are found compared to the reanalysis.
Despite the few minor weaknesses we identified, our results demonstrate that the IPSL model is a suitable tool for studying TCs on climate time scales. This work thus opens the way for further studies contributing to our understanding of TC climatology.
Integrative Bioinformatics and In Vitro Exploration of EVI2A Expression: Unraveling its Immunological and Prognostic Implications in Kidney Renal Clear Cell Carcinoma
Authors: Li Sheng , Xiong Situ , Zheng Fucun , Zhan xiangpeng , Zeng jin , Fu Bin , Xu Songhui , Liu Xiaoqiang 
Published: August 2023

Abstract
Purpose
EVI2A has emerged as a meaningful marker in various diseases, but its biological role and mechanism in kidney renal clear cell carcinoma (KIRC) remain unexplored.
Methods
Utilizing TCGA and GEO databases, we analyzed EVI2A gene expression and conducted pan-cancer analysis. Clinical relevance was assessed through Kaplan-Meier (K-M) analysis, ROC curves, and nomogram. We explored the gene's immune relevance via tumor microenvironment (TME), Tumor Immune Single-cell Hub (TISCH), immune checkpoint, and immunotherapy sensitivity analyses. In vitro, assays validated EVI2A expression and its impact on KIRC behavior.
Results
EVI2A expression was upregulated in KIRC, correlating with tumor grade and T/N/M stage. EVI2A exhibited high diagnostic accuracy (AUC = 0.906) and predicted poor overall and progression-free survival in KIRC patients. EVI2A expression showed significant associations with immunity, including TME scores and specific immune cell types like Tfh cells, CD4 memory T cells, and CD8 + T cells. High EVI2A expression indicated increased sensitivity to PD-1/CTLA-4 and tyrosine kinase inhibitors. In vitro, the knockdown of EVI2A reduced KIRC cell proliferation, invasion, and migration.
Conclusion
Comprehensive analysis highlights EVI2A as a promising biomarker and novel therapeutic target for KIRC intervention. These findings have significant implications for further research and clinical applications.
Landscape of Metabolite-Protein Interaction Networks Reveals Prognostic Subtypes of Ovarian Cancer
Authors: Wu Yong , Chen Siyu , Zhu Jun , Wang Simin , Wu Jiangchun , Ju Xingzhu , Wu Xiaohua , Huang Yan , Chen Xiaojun 
Published: August 2023

Abstract
Background
Metabolic reprogramming, a hallmark of cancer, can promote tumorigenesis and tumour progression through metabolite-protein interactions (MPIs). However, MPI functions and related genes in ovarian cancer (OV) development and treatment remain largely unknown.
Methods
A TCGA-based metabolic heterogeneity analysis of pancancer was used to identify OV-specific metabolic altered genes (MIPros) and classify OV by MPIScore. MPIscores were based on hub genes intersecting the WGCNA module genes and DEGs of the PCA subtype and LASSO Cox regression analysis. A correlation analysis of the MPIscore, clinical features, functional and genomic characteristics, and the immune landscape was performed. The Gene Expression Omnibus (GEO) database was used for validation.
Result
In total, 323 OV-specific MIPros were identified by pancancer analysis and used for PCA. Two subtypes with different survival times, ages, and HRD scores were recognized. Five hub prognosis-related genes were included in the MPIscore, an independent prognostic factor (HR = 4.029, P = 0.0118) of patient survival, and possessed distinct metabolism-related pathways and clinical features. Genomic mutations were distributed diversely among MPIscore subgroups; comutations among frequently mutated were detected. Tumour microenvironment analyses correlated a high MPIscore with greater immune infiltration and TIDE scores, leading to poor responses to immunotherapy. Subtyping was consistent across multiple OV cohorts.
Conclusion
A new OV typing method was developed using specific MIPros, showing differences in metabolism, mutation, immune landscape, and drug response, improving understanding and clinical applications of OV metabolism heterogeneity.
Hawk: An Industrial-strength Multi-label Document Classifier
Authors: Javeed Arshad 
Published: August 2023

Abstract
There are a plethora of methods and algorithms that solve the classical multi-label document classification. However, when it comes to deployment and usage in an industry setting, most, if not all the contemporary approaches fail to address some of the vital aspects or requirements of an ideal solution: i. ability to operate on variable-length texts and rambling documents. ii. catastrophic forgetting problem. iii. modularity when it comes to online learning and updating the model. iv. ability to spotlight relevant text while producing the prediction, i.e. visualizing the predictions. v. ability to operate on imbalanced or skewed datasets. vi. scalability. The paper describes the significance of these problems in detail and proposes a unique neural network architecture that addresses the above problems. The proposed architecture views documents as a sequence of sentences and leverages sentence-level embeddings for input representation. A hydranet-like architecture is designed to have granular control over and improve the modularity, coupled with a weighted loss driving task-specific heads. In particular, two specific mechanisms are compared: Bi-LSTM and Transformer-based. The architecture is benchmarked on some of the popular benchmarking datasets such as Web of Science-5763, Web of Science-11967, BBC Sports, and BBC News datasets. The experimental results reveal that the proposed model outperforms the existing methods by a substantial margin. The ablation study includes comparisons of the impact of the attention mechanism and the application of weighted loss functions to train the task-specific heads in the hydranet.
Long-term effects of ipragliflozin on blood pressure in patients with type 2 diabetes: Insights from the randomized PROTECT study
Authors: Saito Yuichi , Tanaka Atsushi , Imai Takumi , Nakamura Ikuko , Kanda Junji , Matsuhisa Munehide , Uehara Hiroki , Kario Kazuomi , Kobayashi Yoshio , Node Koichi 
Published: August 2023

Abstract
Background/Aims
Although previous reports have shown that sodium-glucose cotransporter-2 (SGLT2) inhibitors have a blood pressure (BP) lowering effect, relevant long-term data is limited. This study aimed to evaluate the effect of the SGLT2 inhibitor ipragliflozin on BP, and associations between BP reduction and changes in cardiometabolic variables in patients with type 2 diabetes.
Methods
This was a sub-analysis of the PROTECT (Prevention of atherosclerosis by SGLT2 inhibitor: multicenter, randomized controlled study) trial, a multicenter, randomized, open-label, blinded-endpoint study to assess if ipragliflozin delays carotid intima-media thickness progression in patients with type 2 diabetes. Participants were randomized to ipragliflozin and control groups. The primary endpoint of the present sub-analysis was the trajectory of systolic BP, which was measured in a routine clinical setting at baseline and at 3, 6, 12 and 24 months. Correlations between systolic BP changes and cardiometabolic variables during the follow-up period were also evaluated.
Results
A total of 232 patients with well-balanced baseline characteristics were included in each study group. During the 24-month follow-up, systolic BP was consistently lower in the ipragliflozin group than the control group. Throughout the 24-month observation period, mean systolic BP was lower in the ipragliflozin group by 3.6 mm Hg (95% confidence interval, 0.7 to 6.5 mm Hg) across several subgroups. Changes in systolic BP correlated significantly with changes in body mass index particularly in the ipragliflozin group, while no significant correlations between changes in systolic BP and carotid intima-media thickness, estimated glomerular filtration rate, or N-terminal pro-B-type natriuretic peptide were observed from baseline to 24 months.
Conclusions
Ipragliflozin treatment was associated with BP reduction throughout the 24-month follow-up period as compared to control treatment. BP reduction correlated with weight loss, which might be a major mechanism for the BP lowering effect of SGLT2 inhibitors.
Trial registration
University Hospital Medical Information Network Clinical Trial Registry; UMIN000018440 and Japan Registry of Clinical Trials; jRCTs071180041 and jRCT1071220089.
Evaluation of biodiversity in farmland restoration project for protection of wetland ecology by planting different crops
Authors: Liu Changqing , Cheng Hai , Wu Yixin , Chen Tianwen , Deng Lina , Zhang Li , Feng Gongneng , Liang Huixing , Li Hongshan 
Published: August 2023

Abstract
The wetland played a crucial role in producing oxygen and purifying the air, so the conservation projects were essential in response to natural and perceived destruction. The farmland restoration project was utilized to repair the southern buffer zone of Jiangsu Yancheng Wetland National Nature Reserve for Rare Birds on the investigation and analysis of migratory birds, soil fauna and crops. In this paper, the five different crops of colza oil, mustard, Chinese cabbage, wheat, barley were planted in the restoration plots, which was eaten by migratory birds overwinter resulting to the low yield of crops. The species and biomass of soil fauna in non-winter (7 species and 98 soil fauna) were more than that in winter (6 species and 54 soil fauna), and the results of restoration plots was more than that in control. The variety and number of migratory birds had a significant improvement (18 species and 164231 migratory birds), which was owed to different crops and soil fauna. This study found that farmland restoration project could significantly improve the ecological environment of wetland, enrich the biodiversity and attract more migratory birds for inhabit.
Immunological and Prognostic Roles of Complement C1q binding protein in Breast Cancer
Authors: Fu Zi-Tong , Chu Yi-Jun , Hao Yi , Ma Jian-Li , Wang Qin , Zhang Xing-Da , Wu Hao 
Published: August 2023

Abstract
Background
Complement C1q binding protein (C1QBP) is upregulated in breast cancer (BRCA) and is involved in cell growth, immunity, and apoptosis. This study explores the potential relationship of C1QBP with the development, prognosis, and immune response of BRCA.
Methods
All original data were downloaded from the The Cancer Genome Atlas (TCGA) database. C1QBP expression was analyzed in normal and cancerous tissues by gepia2. The CIBERSORT algorithm evaluated the relationship between C1QBP expression and immune infiltration through the TCGA dataset. To analyze the mechanisms of C1QBP in BRCA, Gene Set Enrichment Analysis (GSEA), Gene Set Variation Analysis (GSVA), and weighted gene co-expression network (WGCNA) package were used. The analyses of the relevance of C1QBP to cancer drug sensitivity were performed by using the GDSC database.
Results
The expression of C1QBP in BRCA tissues was significantly upregulated and high C1QBP expression in BRCA patients was associated with poor prognosis. The co-expression between C1QBP and immune-related genes such as CXCL16 as well as tumor regulatory genes, such as DGUOK and FXN, existed in BRCA. C1QBP was related to the infiltration of regulatory T cells and other immune cells in BRCA. High expression of C1QBP negatively affected the drug sensitivity of commonly used chemotherapeutic drugs. Finally, we presented a nomogram model that can predict BRCA prognosis.
Conclusion
C1QBP affects the development, immune infiltration, drug treatment effect and prognosis of BRCA through various pathways and may become the potential prognostic and immunologic biomarkers and therapeutic targets for BRCA.
Dynamical analysis of nonlinear smoking mathematical model: Levenberg- Marquardt backpropagated intelligent networks
Authors: Bilal Muhammad , Raja Muhammad Asif Zahoor , Ahmad Iftikhar , Bilal Shafia , Shoaib Muhammad 
Published: August 2023

Abstract
The purpose of this study is to explain the design and analysis of a differential system representing a non-linear smoking mathematical (NSM) model by leveraging the strength of the stochastic method via an artificial Neural Network with Levenberg Marquardt technique (NNs-LMBT), which allows for a more accurate, reliable, and efficient calculation procedure of the dynamics. The NSM model is developed along with experiments that use integer and nonlinear mathematical forms to assign five classes of differential operators to potential smokers, occasional smokers, smokers, smokers who temporarily quit smoking, and smokers who permanently quit smoking. The NSM system is numerically computed using Adams methods, and the results are input into the proposed NNs-LMBT to determine the approximated solution of five distinct examples by incorporating 15% of the data for testing and validation and 85% for training. The given NNs-LMBTs accuracy is demonstrated by comparing the findings from the Adam method's obtained dataset for various scenarios indicating variations in Natural Death frequency. An index of relationships between potential and occasional smokers Index of the relationship between light and heavy smokers, an Index of smoking cessation, The fraction of smokers who effectively quit, and the relationship between smokers and those who temporarily quit but then relapse. In numerical replications of the NNs-LMBTs, the usage of state transitions, error histograms, regression, mean square error, and correlation is also investigated to check their capacity, validity, consistency, correctness, and competence.
Molecular basis of Gabija anti-phage supramolecular assemblies
Authors: Fu Tian-Min , yang Xiao-yuan , Shen Zhangfei , Lin Qingpeng 
Published: August 2023

Abstract
As one of the most prevalent anti-phage defense systems in prokaryotes, Gabija consists of a Gabija protein A (GajA) and a Gabija protein B (GajB). The assembly and function of the Gabija system remain unclear. Here we present cryo-EM structures of GajA and the GajAB complex, revealing tetrameric and octameric assemblies, respectively. In the center of the complex, GajA assembles into a symmetric tetramer, which recruits two sets of GajB dimer at opposite sides of the complex, resulting in a 4:4 GajAB supramolecular complex for anti-phage defense. Further biochemical analysis showed that GajA alone is sufficient to cut double-stranded DNA and plasmid DNA, which can be inhibited by ATP. Unexpectedly, the GajAB displays enhanced activity for plasmid DNA, suggesting a role of substrate selection by GajB. Together, our study defines a framework for understanding anti-phage immune defense by the GajAB complex.