bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spatial-Temporal Variation and Correlation Analysis of Ecosystem Service Values and Ecological Risks in Winter Cities: Evidence from Shenyang, China
Authors: Li Yang , Xie Hao 
Published: April 2024

Abstract

Ecosystems in winter cities are complex and fragile, experiencing significant changes due to climate variations and human construction activities. Assessing the ecological status and risk faced by these areas commonly involves using Ecosystem Service Value (ESV) and Ecological Risk Index (ERI). However, limited research has combined these two measures to reveal sptial-temporal trends in urban ecosystem conditions. This study utilizes land use data from 2000, 2010, and 2020 to construct ESV and ERI measurement models using the improved unit area value factor method and landscape pattern index method, respectively. By evaluating the regional and temporal differentiation features of ESV and ERI, in addition to their spatial association, the study identifies priority areas for urban ecological restoration and recommends rationalization solutions. The findings indicate: Between 2000 and 2020, Shenyang's total ESV decreased by 1.31%, from 273.97×108 CNY to 270.38×108 CNY. The ESV per unit area dropped from 21304.50 CNY/hm2 to 21025.33 CNY/hm2. The ecological risk to the study area has increased. The area of ERI high-value, higher-value, and medium-value zones remained relatively stable, while the area of low-value zones decreased by 12.78%, and the area of lower-value zones increased by 13.21%. There is a spatial correlation between ESV and ERI in winter cities. The H-H area is distributed in the northeastern hilly region, which exhibits strong ESV supply capacity while facing severe ecological risks, identifying it as a priority region to pursue ecological rehabilitation. These results offer theoretical justification for urban management and planning, guaranteeing the ecological security and sustainability of winter cities.
NANO.PTML Model for read-across prediction of nanosystems in neurosciences. Computational model and experimental case of study
Authors: He Shan , Nader Karam , Abarrategi Julen Segura , Bediaga Harbil , Nocedo-Mena Deyani , Ascencio Estefania , Casanola-Martin Gerardo M. , Castellanos-Rubio Idoia , Insausti Maite , Rasulev Bakhtiyor , Arrasate Sonia , González-Díaz Humberto 
Published: April 2024

Abstract

Neurodegenerative diseases involve progressive neuronal death. Traditional treatments often struggle due to solubility, bioavailability, and crossing the Blood-Brain Barrier (BBB). Nanoparticles (NPs) in biomedical field are garnering growing attention as neurodegenerative disease drugs (NDDs) carrier to the central nervous system. Here, a specific IFPTML technique was used, which combined Information Fusion (IF) + Perturbation Theory (PT) + Machine Learning (ML) to select the most promising NDDS and NP candidates and to address the few data in the literature. IF-process was carried out between 4403 NDDS assays and 260 cytotoxicity NP assays conducting a dataset of 500000 cases. The optimal IFPTML identified was the DT algorithm, demonstrating satisfactory performance with specificity values of 96.4% and 96.2%, and sensitivity values of 79.3% and 75.7% in the training (375k/75%) and validation (125k/25%) set. Moreover, the DT model obtained AUROC scores of 0.97 and 0.96 in the training and validation series, highlighting its effectiveness in classification tasks. On the other hand, two samples of NPs (Fe3O4_A and Fe3O4_B) were synthesized and structurally characterized by different methods. Additionally, in order to make the as-synthesized hydrophobic NPs (Fe3O4_A and Fe3O4_B) soluble in water the amphiphilic CTAB (hexadecyltrimethylammonium bromide) molecule was employed. Therefore, to conduct a study with a wider range of NP system variants, an experimental illustrative simulation experiment was performed using the IFPTML-DT model. For this, a set of 500000 prediction dataset was created involving n(NP cores)=5 vs. n(cell lines) =53 vs. n(NP shapes) =5 vs. n(NP coats) =16 vs. n(drugs) =123. The outcome of this experiment highlighted certain NANO.PTML systems as promising candidates for further investigation. Specifically, the experiment revealed that the cell line Lycopersicon esculentum showed promise for ecotoxicity studies across various coating systems. In contrast, Danio rerio cell lines (embryos, juveniles, and adults) showed lower predictive values, suggesting less favorable candidates. MacGowan volume was notably relevant for CTAB, PS, and PEG as coating agents, excluding PVA. The NANO.PTML approach holds potential to accelerate experimental investigations and offer initial insights into various NP and NDDS compounds, serving as an efficient alternative to time-consuming trial-and-error procedures.
The shared genetic landscape of polycystic ovary syndrome and breast cancer: convergence on ER+ breast cancer but not ER- breast cancer
Authors: Bi Kaixin , Chen Miaoran , Zhao Qianru , Yang Tongtong , Xie Wenjia , Ma Wenqi , Jia Hongyan 
Published: April 2024

Abstract

Background: The clinically high co-morbidity of polycystic ovary syndrome(PCOS) and breast cancer(BC) has been widely reported, but little is known about their shared genetic basis and mechanisms.
Method: Using summary statistics from the largest GWASs to date, we performed a large-scale genome-wide cross-trait analysis of PCOS and BC with multiple genetic statistical methods to unlock potential shared genetic causes.
Results: The study found some genetic overlap between the three trait pairs, and after dividing the entire genome into 2,495 independent regions, we observed chr8: 75,011,700- 76,295,483, and chr17: 6,305,079- 7,264,458 to be loci with significant localized genetic correlations. Pleiotropic analysis under a composite null hypothesis identified 1,183 significant potential pleiotropic SNPs in 3 trait pairs, FUMA mapped 26 pleiotropic loci in which 16q12.2 and 6q25.1were found to be duplicated across all three pairs of traits and then 3 colocalized loci detected by COLOC. The gene-based analysis identified 23 unique candidate pleiotropy genes, including the FTO locus shared by three trait pairs as well as SER1, RALB, and others. Whereas pathway enrichment analysis further highlighted the biological pathways present between PCOS-BCALL and PCOS-ERPBC that are primarily involved in prostate glandular acinus development, prostate glandular acinus morphogenesis and cellular response to stress. Latent Heritable Confounder Mendelian randomization (LHC-MR) further supports positive causality of PCOS in BCALL and ERPBC but not ERNBC.
Conclusion: In conclusion our genome-wide cross-trait analysis identified a shared genetic basis between PCOS and BC, specific identical genetic mechanisms and causality between PCOS and various BC subtypes, which could better explains the genetics of the co-morbidity of PCOS and ERPBC rather than PCOS and ERNBC. These findings provide new insights into the biological mechanisms underlying the co-morbidity of these two complex diseases, which have important implications for clinical disease intervention, treatment, and improved prognosis.
Impact of Serum Indoxyl Sulfate on One-year Adverse Events in Chronic Kidney Disease Patients with Heart Failure
Authors: Iwasaki Keiichiro , Miyoshi Toru , Urabe Chikara , Sakuragi Satoru , Kawai Yusuke , Fuke Soichiro , Doi Masayuki , Takaishi Atsushi , Oka Takefumi , Tokunaga Naoto , Ito Hiroshi 
Published: April 2024

Abstract

Indoxyl sulfate (IS), a uremic toxin, is associated with mortality and cardiovascular events in patients with chronic kidney disease (CKD). This study aimed to evaluate the prognostic implications of serum IS levels in patients with heart failure and CKD. This was a prospective multicentre observational study. Overall, 300 patients with chronic heart failure with a previous history of hospitalisation and an estimated glomerular filtration rate of 45 mL/min/1.73 m2 or less without dialysis were analysed. The primary outcome assessed was a composite of all-cause death, hospitalisation for heart failure, nonfatal myocardial infarction, and nonfatal stroke. Clinical events were followed up to one year the measurement of IS. The median patient age was 75 years, and 57% of the patients were male. We divided the cohort into low and high IS categories according to a median value of 9.63 mg/mL. The primary outcome occurred in 27 of 150 patients in the low IS group and 27 of 150 patients in the high IS group (hazard ratio, 1.00; 95% confidence interval, 0.58 to 1.70). The results were consistent across various subgroups. Among heart failure patients with CKD, serum IS concentrations were not significantly associated with the subsequent occurrence of cardiovascular events.
Association between TyG-related parameters and non-alcoholic fatty liver disease risk in non-obese individuals: a cross-sectional study based Japanese population
Authors: Wang Xiuli , Liu Jie , Yu Ke , Huang Zhenhua , Liu Hanxiong , Li Xiang 
Published: April 2024

Abstract

The incidence of non-alcoholic fatty liver disease (NAFLD) in non-obese populations is also on the rise but is often overlooked. Therefore, this study aims to investigate the relationship between triglyceride-glucose (TyG) related parameters (TyG-BMI, TyG-WC, TyG-WHtR) and NAFLD in non-obese individuals to enhance early detection and intervention for NAFLD in this population. We conducted a cross-sectional analysis using data from the NAGALA database, covering 11,987 participants who underwent health examinations between 2004 and 2015. Logistic regression models were employed to assess the relationship between TyG-related parameters and NAFLD risk, incorporating cubic spline functions and smooth curve fitting to explore potential nonlinear relationships between TyG-related parameters and NAFLD risk. ROC curve analysis was performed to evaluate their predictive performance. After adjusting for confounding variables, the incidence of NAFLD in non-obese individuals increased with higher TyG-related parameters. Moreover, we identified nonlinear relationships between TyG index and its related parameters with NAFLD risk, along with critical inflection points. Additionally, the area under the ROC curve for TyG index and its related parameters were 0.7984, 0.8553, 0.8584, and 0.8353, respectively, with a more pronounced effect observed in the female population. There exists a nonlinear relationship between TyG-related parameters and the risk of NAFLD occurrence, revealing various turning points associated with NAFLD risk. Notably, TyG-related parameters outperform the TyG index in predicting NAFLD, especially in females. These findings establish crucial theoretical foundations for future research in NAFLD prevention and treatment for non-obese population.
Oysters, a sustainable bluefood?
Authors: Domech Paula Costa , Cooney Ronan , Tahar Alexandre , Kennedy Alan , Wan Alex H L , Clifford Eoghan 
Published: April 2024

Abstract

Sustainable food production that meets consumer demands while reducing environmental impacts is a critical societal challenge. The seafood industry, including shellfish aquaculture, is considered a key segment for future protein supplies. Like all food production sectors, environmental impacts of the "blue food” sector are a key consideration. The present study demonstrated that Irish Pacific oyster (Magallana gigas) farming has relatively low environmental impacts (i.e., 100-year global warming potential of 373.86 kg CO2 eq. tonne-1; acidification potential of 1.33 kg SO2 eq. tonne-1; and eutrophication potential of 0.39 kg PO4 eq. tonne-1) compared to other seafood and terrestrial animal sectors. Using ecosystem services metrics, one tonne of fresh harvested oysters can remove, on average, 3.05 tonnes of nitrogen, 0.35 tonnes of phosphorus, and sequester 70.52 tonnes of carbon from the environment, thus potentially acting as a nutrient remediator and a potential short-term carbon sink. These findings show how oysters can offer a sustainable food source and provide local environmental benefits. The study also points to future work which could further improve ecosystem services modelling for this food source.
In Vitro Anti-Inflammatory, Anticancer Effects and Phytochemical Characterization of Organic Extracts from Aristolochia olivieri Colleg. Ex Boiss
Authors: Abdullah Fuad O. 
Published: April 2024

Abstract

Organic extract plays a crucial role in our lives, providing food and pharmaceuticals. Extracts from plants showed anti-inflammatory potential in an in vitro macrophage model, and their anticancer activities were assessed using real-time PCR and MTT assays. Major compounds in the n-hexane (AR-H) and the ethyl acetate (AR-E) Aristolochia olivieri extracts was n-hexadecanoic acid, and the major component of the methanol extract (AR-M) was pentacosane. The AR-M extract had a strong ability to induce mRNA expression of an inflammatory cytokine, IL-6, as an M1-like macrophage subset compared to the negative control (DMSO-treated cells). In contrast, AR-E treatment showed strong anti-inflammatory activity against macrophages. The AR-H extract had a moderate inflammatory effect against macrophages. The IC50 results of the anticancer assays ranged from 58.29 to 451.03 µg/mL for the three extracts. The anticancer action of the AR-E extract against U-87MG cells was higher (58.29 µg/mL) than that of AR-H and AR-M (156.38 and 196.14 µg/mL, respectively). The greater cytotoxicity effect observed with the AR-E extract against U-87MG can be linked to its high content of hexadecanoic acid (32.49%) and linolenic acid (12.90%). In this study to fully understand the therapeutic potential and uses as food to confirm safety.
BRCAIndica: a Resource for ACMG/AMP classified BRCA1 and BRCA2 Variants
Authors: Vatsyayan Aastha , RI Anu , Mathur Prerika , Uchil Divya , Joshi Ashish , Dwivedi Aradhana , Sirohi Bhawna , Mathew Aju , Damodaran Dileep , Panda Soumya Surath , Kolluri Spoorthy , Ayillath Shaji K. , Amalnath Deepak , Shankar Gomathi , Pandhare Kavita , Scaria Vinod 
Published: April 2024

Abstract

Purpose: As genetic testing becomes increasingly accessible and affordable, the uniform and accurate interpretation of genetic variants becomes essential. The ACMG/AMP joint guidelines provide the basis for systematic and uniform interpretation of pathogenicity of genetic variants. However, the application of these in routine clinical interpretation at-scale has largely been limited by the lack of resources providing harmonized data especially at a population-scale. Here we describe BRCAIndica, a resource for BRCA1 and BRCA2 variants conforming to the ACMG & AMP joint guidelines to aid uniform clinical interpretation of genetic tests with a specific focus on variants reported in the Indian population.
Methods: Variants were collected and harmonized from across several resources including population-scale datasets, literature survey and other variant datasets. They were then classified according to the ACMG/AMP guidelines.
Results: We have collected a total of 10,490 unique variants, of which 2261 Pathogenic and 43 Likely Pathogenic variants belong to BRCA1 and 2694 Pathogenic and 20 Likely Pathogenic variants to BRCA2 respectively.
BRCAIndica can be accessed at: https://clingen.igib.res.in/brcaindica/
Conclusion: BRCAIndica is a powerful resource that offers researchers and clinicians with ACMG/AMP annotated BRCA variants.
Manually operated microtube automatic capper/decapper system for clinical laboratory and biological laboratory personnel
Authors: Jinno Makoto , Nonoyama Ryosuke , SAKURAI Yasuteru , YOSHIKWA Rokusuke , KINOSHITA Takaaki , YASUDA Jiro 
Published: April 2024

Abstract

Polymerase chain reaction (PCR) is an effective method for diagnosing infectious diseases and has been the primary method throughout the novel coronavirus disease (COVID-19) pandemic. PCR tests (from specimen collection to result acquisition) involve sample pretreatment, nucleic acid extraction, and PCR procedure. Automating the pretreatment process is crucial to mitigate the risk of infection for workers and to reduce the likelihood of sample contamination-triggered misdiagnosis, particularly when handling centrifuge tubes, cryopreservation tubes, and microtubes. Robotic systems have been engineered to automate cell culture and PCR-based diagnosis , predominantly designed for use with screw-capped containers. However, this leaves a notable gap in automation solutions for microtubes equipped with press-type caps. To address this gap, we developed a versatile microtube capper/decapper system. On the other hand, many tasks of manual operation using microtubes, which are routinely conducted in clinical tests and biological experiments, were performed. Despite the risks of contamination and infection derived from the manual handling of microtube caps, which can compromise diagnosis/experiment accuracy and worker safety, devices for manually opening and closing microtube caps without direct contact remain lacking. Therefore, leveraging the technology from the developed versatile microtube capper/decapper system for laboratory automation, we created a manually operated microtube equipped with an automatic capper/decapper system tailored for personnel in clinical and biological laboratories.
In this study, we first examined the required specifications and prerequisites for a manual microtube capper/decapper and clarified the operating methods, operating procedures, operation environment, device size, accompanying functions, etc. Based on the required specifications and preconditions, we proceeded with the mechanical and control design of the conceptual model, manufactured a prototype, and confirmed its basic functions and performance. The compliant to the required specifications and preconditions and the usefulness of the proposed manual microtube capper/decapper were validated through various experiments and demonstrations. Because microtubes are used in various clinical tests and biological experiments, we believe that the proposed system can markedly reduce the workload for personnel across numerous clinical and biological laboratories.
METTL3 silencing suppresses cardiac fibrosis via m6A modification of SMOC2
Authors: He Yanru , Pan Xiaodong , Tao Zaixiao , Chen Zhongpu , Ma genshan , Ling Sunkai 
Published: April 2024

Abstract

Cardiac fibrosis leads to decreased cardiac compliance, impaired systolic and diastolic function, resulting in heart failure. M6A methylation plays a role in fibrosis development. However, its underlying mechanism remain poorly understood. This study explores the role and molecular mechanisms of m6A methylation in regulating cardiac fibrosis after myocardial infarction (MI). A mouse myocardial fibrosis model post-MI was established by ligating the left coronary artery. Corresponding gene knockdown was achieved in vitro or in vivo using short hairpin RNA or fibroblast-specific AAV9 virus. Echocardiography assessed cardiac function in mice, while Masson staining determined the degree of collagen deposition post-MI. The meRIP-Seq kit detected mRNA methylation levels in myocardial tissue and hypoxia-treated cardiac fibroblasts. Expression of RNA methylation-related enzymes, fibrosis-related proteins, and SMOC2 expression in the myocardial tissue or cardiac fibroblasts was detected using western blotting. Actinomycin D assessed SMOC2 mRNA stability. Results demonstrated increased levels of m6A methylation and METTL3 expression in myocardial fibrosis tissue post-MI and in hypoxia-treated cardiac fibroblasts. In vivo METTL3 downregulation reduced the fibrotic area and improved cardiac function, while METTL3 downregulation in vitro can alleviate cardiac fibroblast proliferation and differentiation after hypoxia. Per bioinformatic analysis, SMOC2 may be differentially expressed, regulated by RNA methylation during cardiac fibroblast proliferation and differentiation. SMOC2 is significantly elevated in myocardial fibrotic tissue post-MI and hypoxia-induced cardiac fibroblasts. SMOC2 downregulation alleviates cardiac fibroblast proliferation and differentiation. Mechanistically, METTL3 promoted SMOC2 mRNA stability by increasing its m6A methylation level, thereby regulating cardiac fibroblast proliferation and differentiation. Conclusively, METTL3 participates in cardiac fibroblasts proliferation and differentiation post-MI by increasing the m6A methylation level of SMOC2 mRNA, thereby promoting its stability.
Transforming Handwritten Answer Assessment: A Multi-Modal Approach Combining Text Detection, Handwriting Recognition, and Language Models
Authors: Hiremath Aditya , Irabatti Nipun , Desai Akhilesh , Dhondge Prabhuraj , Sheikh Shagufta 
Published: April 2024

Abstract

This paper proposes an automated system for grading handwritten subjective answers, leveraging advanced computer vision, natural language processing, and large language model techniques. Although time-consuming, the system presents a promising theoretical approach by employing CRAFT for text detection, TrOCR for handwritten text recognition, and a fine-tuned language model for answer evaluation. Experimental results demonstrate the system's potential accuracy in transcribing handwritten text and consistency in grading answers compared to human raters. The proposed methodology offers a scalable and efficient solution to automate the traditionally labor-intensive task of grading handwritten responses, with the potential to transform education assessment practices. The system's performance, limitations, and future research directions to improve efficiency are discussed.
Extraction of pentosan from corn cob
Authors: Zuo Jinlong , Jiang Shan , Ma Xuewei , Li Junsheng , Tan Chong , Xia Zhi 
Published: April 2024

Abstract

Corn is an important food crop, but its production often generates a large amount of corn cobs as waste. However, corn cobs contain rich polysaccharides, among which xylan is particularly noteworthy due to its various biological activities and wide potential applications. To improve the utilization rate of corn cobs, xylan is extracted from corn cobs using water extraction, examining the effects of three factors: extraction temperature, extraction time, and liquid-to-solid ratio on the extraction yield of xylan. Through response surface methodology, the optimal extraction conditions are obtained. The structure of the extract is analyzed using SEM, FTIR, and UV-VIS characterization techniques.
Determination of Quality of Drinking Water in Larkana based on the SPI model
Authors: Ali Niaz 
Published: April 2024

Abstract

In light of growing concerns over water contamination, particularly in regions like Sindh, Pakistan, this research aimed to evaluate and map the groundwater quality in Taluka Larkana for both drinking and irrigation applications, addressing the expressed worries of the local community. A total of forty groundwater samples were collected from various sources such as hand pumps, taps, and tube wells. These samples underwent comprehensive analysis encompassing parameters including color, odor, taste, turbidity, pH, total hardness (TH), electrical conductivity (EC), and total dissolved solids (TDS), with comparisons drawn against WHO guidelines.
Results indicated that taste, color, odor, and turbidity of the groundwater samples generally fell within acceptable ranges. However, EC levels varied from moderately elevated to excessively high. Notably, a significant proportion of samples (84% EC, 21% Cl, 30% Ca, 37% Mg, 22% TH, and 84% TDS) exceeded WHO-recommended thresholds.
Assessment via the SPI model classified approximately 16% of samples as moderately contaminated, while 65% were deemed highly contaminated, and 19% were found unsuitable for drinking purposes. These findings underscore the pressing need for concerted efforts to address water quality issues in the region.