bluuebunny/crossref_metadata_2025_split huggingface dataset:
In situ population dynamics of Aurelia coerulea polyps in Tokyo Bay
Authors: Nagatsuka Sarasa , Ishii Haruto , Morimitsu Ryo , Yasuda Akira 
Published: April 2024

Abstract

Long-term changes in the abundance, occurrence period and distribution of Aurelia coerulea polyps were monitored in the innermost (35°37.2′ N, 139°46.4′ E) and mouth regions (35°8.2′ N, 139°37.4′ E) of Tokyo Bay, Japan. The monitoring was performed from January to September 2010 and from January to December 2011, respectively. In the innermost of the bay, the population of A. coerulea polyps was maintained from January to April. However, it rapidly declined in May; by June, it had completely disappeared, losing its attachment space to other sessile organisms such as mussels. Strobilae were observed from January to April, with a peak in March. In contrast, the population of A. coerulea polyps was maintained throughout the year in the mouth of the bay. Strobilae were observed from February to May, with the highest abundance in April The ephyra liberation time was longer in the mouth part than in the innermost of the bay. However, the total number of liberated ephyrae was larger in the innermost part than in the mouth of the bay. These differences were attributed to the substantial variability in water temperature and salinity at the innermost of the bay. The scale of ephyra liberation seems to have been determined by the instability of the water temperature, salinity in the area and the degree of invasion of other sessile organisms in the area. This might be related to the observed medusae blooms in the innermost of the bay.
Mesoporous activated carbon prepared from waste fibers and their application on removing iron (II) ions from aqueous solution: Adsorption isotherm, kinetics, and thermodynamic studies
Authors: azizi Mohamed , azizi Mohamed 
Published: April 2024

Abstract
In this work, a new mesoporous activated carbon from waste corrugated fiberboard (WCF) and waste paper (WP) were prepared via chemical activation impregnation with zinc chloride at different temperatures as a low cost, eco-friendly, and effective biosorbent for elimination of Fe(II) from the aqueous solution. The morphology and surface properties of ACWCF and ACWP were characterized by, scanning electron microscopy (SEM), Boehm's titration, specific surface area (BET), and Fourier transform infrared spectrometer (FTIR). The results showed that the ACWCF and ACWP had a high surface area of 1110.99 m2/g and 298.59 m2/g, respectively. Batch experiments tested the influence of pH, initial Fe(II) concentration, adsorbent mass, contact time, and temperature on the adsorption process. The adsorption kinetics could be expressed well by the PSO model. The adsorptions of Fe(II) onto ACWCF and ACWP were fitted best using the Langmuir and Dubinin- Radushkevich isotherm models with maximum capacities of 66.66 mg/g and 41.67 mg/g at 55°C, respectively. The adsorption process on ACWCF and ACWP may be controlled for both electrostatic interaction mechanisms. Based on the above results, it can be concluded that the ACWCF is effective adsorbent for the elimination of Fe(II) from aqueous solutions
Characteristics and transcriptional regulators of spontaneous epithelial–mesenchymal transition in real-world genetically unperturbed non-spindle breast carcinoma
Authors: Lien Huang-Chun , Yu Hui-Chieh , Yu Wen-Hsuan , Lin Su-Fang , Chen Tom Wei-Wu , Chen I-Chun , Hsiao Li-Ping , Yeh Ling-Chun , Li Yu-Chia , Lo Chiao , Lu Yen-Shen 
Published: April 2024

Abstract

Background
Although epithelial–mesenchymal transition (EMT) has been well-characterized in experimental models, convincing histopathological evidence of EMT in primary carcinomas has only been obtained for rare spindle carcinomas. The existence, characteristics, and transcriptional regulators of spontaneous EMT in real-world, genetically unperturbed non-spindle carcinoma remain underexplored.
Methods
We used primary culture combined with RNA sequencing (RNA-seq), single-cell RNA-seq (scRNA-seq), and in situ RNA-seq to explore the characteristics and transcription factors (TFs) associated with potential spontaneous EMT in non-spindle breast carcinoma.
Results
Our primary culture revealed carcinoma cells expressing diverse epithelial–mesenchymal traits, consistent with epithelial–mesenchymal plasticity. Importantly, carcinoma cells undergoing spontaneous EMT did not necessarily exhibit spindle morphology, even when undergoing complete EMT. EMT was a favored process, whereas mesenchymal–epithelial transition appeared to be crucial for secondary tumor growth. Through scRNA-seq, we identified TFs that were sequentially and significantly upregulated as carcinoma cells progressed through the EMT process, which correlated with increasing VIM expression. Once upregulated, the TFs remained active throughout the EMT process. ZEB1 was a key initiator and sustainer of EMT, as indicated by its earliest significant upregulation in the EMT process, its exact correlation with VIM expression, and the reversal of EMT and downregulation of EMT-upregulated TFs upon ZEB1 knockdown. The correlation between ZEB1 and vimentin expression in triple-negative breast cancer and metaplastic breast carcinoma tumor cohorts further highlighted its role. The immediate upregulation of ZEB2 following that of ZEB1 suggested their functional cooperation in EMT. This finding, together with that of a lack of correlation of SNAI1, SNAI2, and TWIST1 expression with the mesenchymal phenotype, indicated EMT-TFs have a context-dependent role in EMT. Upregulation of EMT-related gene signatures during EMT correlated with poor patient outcomes, highlighting the biological importance of the model. Elevated EMT gene signatures and increased ZEB1 and ZEB2 expression in vimentin-positive compared to vimentin-negative carcinoma cells within the corresponding primary tumor tissue confirmed ZEB1 and ZEB2 as intrinsic, instead of microenvironmentally-induced, EMT regulators, and vimentin as an in vivo indicator of EMT.
Conclusions
Our findings provide insights into the characteristics and transcriptional regulators of spontaneous EMT in non-spindle carcinoma in real-world scenarios.
A molecular subtype model of ccRCC based on immune-related genes for predicting immunotherapy response
Authors: Li Song , Pan Yang , Hao Xuexue , Liu Xiaoqiang 
Published: April 2024

Abstract

Purpose
To construct a molecular subtype based on immunotherapy response in renal clear cell carcinoma (ccRCC) and explore the regulatory molecular mechanisms of the immune microenvironment between the subtype.
Methods
RNA-seq data related to immune checkpoint blockade (ICB) therapy for ccRCC-related from GSE67501 dataset and clinical information were collected from GEO and TCGA datasets. Differentially expressed genes (DEGs) were identified using the 'limma' R package. GO and KEGG pathways analysis of the DEGs were performed using 'clusterProfiler' R-package. The 'Immuneconv' package was used to assess potential ICB response and tumor mutational burden (TMB) score in different subgroups. ROC curve and survival analysis were conducted for the High-group and Low-group based on the stromal, immune, ESTIMATE scores using 'surviva' and 'survivalROC' packages. Single-cell transcriptome profiling data for ccRCC (GSE121636) was obtained from the GEO database. Immunohistochemistry was used to detect the expression of MALs in human histology. Western blot was used to detect the stable knockdown of MALs cell lines. MACS magnetic bead sorting technology was used to sort CD8+cells. Transwell and flow cytometry were used to detect the proportion of chemotactic CD8+T cell infiltration.
Results
A total of 311 DEGs were identified with ICB response and non-response. The renal carcinoma samples were classified into two subgroups (C1 group and C2 group) through consistency cluster analysis. A nomogram was developed based on stage, grade, immune score, and subgroup, with an area under the ROC curve of 0.732. The TIDE score of the C2 group was significantly higher than that of the C1 group, and the immune infiltration levels of B cells, neutrophils, macrophages and myeloid dendritic cells were significantly higher in group C1 compared to group C2. The immune score in the C2 group was significantly higher than that in the C1 group. The expression of MAL gene was negatively correlated with TBM score and was highly expressed in CD8+T cell group of both peripheral blood and tumor tissues. Furthermore, The immunohistochemical results showed that the expression of MAL was significantly lower in renal cancer tissues compared to adjacent tissues. Flow cytometry showed that the proportion of CD8+T cells tending towards si-MAL cells was only 13.35%, while the control group had a chemotactic proportion of 38.09%.
Conclusion
This study identified a correlation between the distribution of infiltrating immune cells and ccRCC subtypes, which could help clinicians to predict the efficacy of ICB. Moreover, MAL gene may play a role in the diagnosis and prognosis of ccRCC by regulating CD8+ T cells infiltration.
Obesity is associated with adverse outcomes in primary immune thrombocytopenia- A retrospective single-center study
Authors: Xiao Zhengrui , He Zhiqiang , Nguyen Hieu Liem Le , Thakur Rahul , Hammami M Bakri , Narvel Hiba , Vegivinti Charan , Townsend Noelle , Billett Henny , Murakhovskaya Irina 
Published: April 2024

Abstract

The pathophysiology of immune thrombocytopenia (ITP) involves immune-mediated platelet destruction. The presence of adipose tissue in obese individuals creates an inflammatory environment that could potentially impact the clinical course and outcomes of ITP. However the relationship between obesity and ITP outcomes has not been well described. We evaluated ITP outcomes in 275 patients diagnosed with primary ITP from 2012 to 2022. Patients were categorized into four groups based on their body mass index (BMI) at diagnosis. Female gender was associated with a lower platelet count at the time of diagnosis at any BMI. Patients with high BMI had lower platelet counts at diagnosis and at platelet nadir (p < 0.001), an increased likelihood of requiring therapy (p < 0.001) and requiring multiple lines of therapy (p = 0.032). Non-obese patients who required corticosteroid treatment experienced a longer remission duration compared to obese patients (p = 0.009) and were less likely to be steroid-dependent (p = 0.048). Our findings suggest that obesity may be a significant risk factor for developing ITP and for ITP prognosis. Future studies are needed to evaluate the role of weight loss intervention in improving ITP outcomes.
Polarised human alveolar epithelia enable identification of dichloroacetate as an effective drug against respiratory viruses
Authors: de Iturrate Paula Martínez , Hernáez Bruno , Santos Patricia de los , García-Gómez Alba , Sánchez-Cruz Alonso , Hernández-Sánchez Catalina , Rivas Luis , Val Margarita del , Rial Eduardo 
Published: April 2024

Abstract

Respiratory viral infections are a significant cause of morbidity and mortality worldwide. The COVID-19 pandemic has highlighted the lack of chemotherapeutic tools available for fighting emerging viruses and the need to focus on preclinical models that better recapitulate human disease. We performed a comparative analysis of inhibitors of the PI3K/AKT/mTOR pathway, which is involved in virus-induced metabolic reprogramming, since strategies aimed at identifying cellular targets could serve to combat diverse viruses and hamper the development of resistance. Tests were performed in two human cell lines, MRC5 lung fibroblasts and Huh7 hepatoma cells, and the results showed that the inhibitors had markedly different effects on energy metabolism and antiviral activity. Thus, dichloroacetate (DCA) has potent antiviral activity against HCoV-229E in MRC5 cells but not in Huh7 cells, suggesting that the screening model is more critical than previously assumed. DCA was then tested in polarized human alveolar epithelia in air-liquid interface, a 3D model used to study respiratory infections. DCA reduced the viral progeny of HCoV-229E, SARS-CoV-2 and respiratory syncytial virus by 2-3 orders of magnitude, and it was effective even when applied once infection had been established. Although DCA has previously been shown to be effective against other viruses, suggesting that it could be a broad-spectrum antiviral, our experiments reinforce the need to use physiologically appropriate disease models to screen antiviral compound.
WARIO: Weighted families of contact maps to characterize conformational ensembles of (highly-)flexible proteins
Authors: González-Delgado Javier , Bernadó Pau , Neuvial Pierre , Cortés Juan 
Published: April 2024

Abstract
Characterizing the structure of flexible proteins, particularly within the realm of intrinsic disorder, presents a formidable challenge due to their high conformational variability. Currently, their structural representation relies on (possibly large) conformational ensembles derived from a combination of experimental and computational methods. The detailed structural analysis of these ensembles is a difficult task, for which existing tools have limited effectiveness. This study proposes an innovative extension of the concept of contact maps to the ensemble framework, incorporating the intrinsic probabilistic nature of disordered proteins. Within this framework, a conformational ensemble is characterized through a weighted family of contact maps. To achieve this, conformations are first described using a refined definition of contact that appropriately accounts for the geometry of the inter-residue interactions and the sequence context. Representative structural features of the ensemble naturally emerge from the subsequent clustering of the resulting contact-based descriptors. Importantly, transiently-populated structural features are readily identified within large ensembles. The performance of the method is illustrated by several use cases and compared with other existing approaches, highlighting its superiority in capturing relevant structural features of highly flexible proteins. An open-source implementation of the method is provided together with an easy-to-use Jupyter notebook, available at https://gitlab.laas.fr/moma/WARIO.
Can Cell-Free DNA Testing Suffice for Isolated Fetal Nuchal Translucency Between the 95th – 99th Centile? A Retrospective Analysis in A Centre in North India
Authors: Sethi Neha , Kaul Anita , Gupta Rachna , Prabhu Akshatha 
Published: April 2024

Abstract

All pregnancies with increased nuchal translucency (NT) > 95th percentile are traditionally offered invasive testing. This study aimed to determine whether cell-free DNA (cfDNA) could suffice in patients with an isolated increased NT between the 95th – 99th centile. A retrospectively analyzed prospective study was conducted in the Fetal Medicine Unit, Indraprastha Apollo Hospitals, New Delhi, between 2007 and 2021. Study criteria were singletons with increased NT between 95th – 99th centile without soft markers or structural abnormalities. cfDNA/follow-up was offered if patients declined invasive tests. Karyotyping was the primary genetic testing from 2007 to 2015, while microarray ± exome began thereafter. All outcomes were obtained over the phone or through patient records. There were 213 pregnancies with isolated findings of NT 95th – 99th centile. All were offered invasive testing, and 17 were lost to follow-up. In 196 cases with outcomes available, 7 (3.5%) had an abnormal genetic diagnosis. Four fetuses had trisomy 21, one trisomy 18, and two fetuses (1%) had other cytogenetic abnormalities. Five fetuses (2.5%) with chromosomal aneuploidy could be potentially detected with cfDNA. cfDNA may be a viable substitution to detect common aneuploidies in this clinical population. However, in 1% of cases, microdeletions may still be missed.
Sarcopenia is Associated with Aortic Arch Calcification on Chest X-ray in Unselected Middle- and Older-Aged Patients
Authors: Erkan Merve , OZCAN Seray Gizem GUR , BEKIRCAVUSOGLU Ayse Füsun , CATALKAYA Sibel 
Published: April 2024

Abstract

Purpose
Sarcopenia is the presence of low skeletal muscle quantity or quality. It is associated with increased morbidity and mortality. Aortic arch calcification (AAC) is a type of vascular calcification that can be easily detected using chest X-rays. AAC and sarcopenia share common risk factors such as aging, inflammation, diabetes mellitus, and chronic kidney disease. In this study, we investigated the relationship between AAC and sarcopenia to evaluate whether chest X-rays can be used to predict sarcopenia in daily clinical practice.
Methods
AAC was assessed via a simple chest X-ray. Sarcopenia was evaluated using chest computed tomography imaging, which allows for the calculation of skeletal mass area (SMA) and skeletal mass index (SMI). Correlation analysis and multivariable models were used to assess the relationship between AAC and sarcopenia.
Results
A total of 340 patients were included in this study (122 with AAC, and 218 without AAC). Sarcopenia was more frequent in patients with AAC than those without (38.5% vs 16.5%, p < 0.001). SMI was also negatively correlated with the severity of AAC (r: -0.246, p < 0.001). In the multivariable model, AAC was independently related to age, glomerular filtration rate, and sarcopenia [(OR = 1.077, 95% CI 1.034–1.120, p < 0.001), (OR = 0.985, 95% CI 0.975–0.996, p = 0.008), and (OR = 1.812, 95% CI 1.030–3.188, p = 0.03), respectively)].
Conclusion
AAC detected by simple chest X-rays is independently related to sarcopenia. It might be used to predict patients with sarcopenia in this population.
Interface Potential Induced Natural Antioxidant Mimic System for the Treatment of Alzheimer's Disease
Authors: Gao Nan , Liu Kangning , Ding Qi , Cao Doudou , Xi Enpeng , Zhao Yun , Yuan Ye 
Published: April 2024

Abstract

Although the pathogenesis of Alzheimer's disease (AD) is still unknown, the molecular biology of its pathological phenomena is indeed clear, mainly due to mitochondrial dysfunction and central nervous system inflammation caused by imbalanced antioxidant capacity in nerve cells, as well as subsequent synaptic dysfunction, so antioxidant therapy is still the preferred treatment for AD in clinical practice. However, although antioxidant enzymes have high catalytic efficiency, the substrate spectrum is narrow (just targeting specific types of substrates); Antioxidants have a wider range of effects, but their efficiency is low. Therefore, the antioxidant system in organisms is composed of both antioxidant enzymes and antioxidants, which is also the key to using simulated antioxidant systems for AD treatment. Since the antioxidant defense system in high-grade organisms is composed of both enzymatic and non-enzymatic systems, therefore we synthesized a metal-organic framework (MOF) with superoxide dismutase activity, and then depending on the interface potential effect, curcumin (non-enzymatic antioxidant capacity) was loaded into MOF to construct a synergistic antioxidant AD treatment system. This system demonstrates both good antioxidant activity and efficient β-amyloid plaque scavenging ability, which slowed down the cognitive dysfunction in the brain of AD mice.
Role of immune cells in mediating the effect of phosphatidylcholine (17:0_18:2) on liver cirrhosis
Authors: Lin Weiye , Han Ning , Qu Yiqian , Hong Qianran , Li Jiayang , He Yuting , Qiu Shengliang 
Published: April 2024

Abstract

Liver cirrhosis (LC) is the terminal stage of various chronic liver diseases, with complications of decompensated liver cirrhosis being the primary cause of death. Recent studies have shown that lipid metabolic disorders and chronic inflammatory responses within the liver, leading to fibrosis and inflammation, are associated with the development of liver cirrhosis. This study investigated the causal relationship between phosphatidylcholine (17:0_18:2) (PC) and LC, as well as the mediating role of immune cells. Utilizing summary data from genome-wide association studies (GWAS) and information from the Finnish database, single nucleotide polymorphisms (SNPs) were selected as instrumental variables (IVs) for a two-step Mendelian randomization (MR) analysis of gene-predicted LC (including 1266 cases and 407,801 controls). The results indicate a negative causal relationship between genetically predicted PC levels and LC (OR 0.819, 95% CI 0.693–0.967; P = 0.019, IVW method). Immune cells, specifically CD33 on CD33dim HLA DR- (with a mediation effect ratio of 7.027%) and CD33 on Im MDSC (with a mediation effect ratio of 5.763%), play a reverse mediating role in the causal relationship between PC and LC. This study provides a new perspective on the prevention and treatment strategies for liver cirrhosis involving lipid metabolism and immune regulation.
Polyphasic identification of Fusarium species associated with sunflower seed-borne diseases in Brazil
Authors: de Farias Otília Ricardo , Veloso Josiene Silva , Barbosa Paulo Roberto Ramos , Cruz José Manoel Ferreira de Lima , Xavier Lucimere Maria da Silva , Materatski Patrick , Varanda Carla Marisa Reis , Oliveira Mônica Danielly de Mello , Nascimento Luciana Cordeiro do 
Published: April 2024

Abstract

Fusarium spp. are among the most common fungal species associated with diseases both on wild and cultivated plants, including sunflowers. They infect all plant tissues causing damage to roots, bundle vessels, stems, leaves, and seeds, often causing significant yield losses. Because contaminated seeds can spread diseases into new areas and transmit them to growing plants, the quality and sanitary status of the seeds are the key to limit the spread of the disease. This study aimed to identify and determine the prevalence of Fusarium species associated with sunflower seeds and access their transmission to growing plants. A set of 49 Fusarium isolates was collected from seeds of eight sunflower cultivars. They were characterized through morphological, cultural, and genetic features. Genetic diversity was estimated through amplification of the elongation factor gene (EF-1 α), which also served to select representative isolates to perform amplification of the β-tubulin 2 gene (TUB2). There were identified four species of Fusarium (i.e., F. fabacearum, F. proliferatum, F. pseudocircinatum and F. verticillioides) that caused seed rot, vascular darkening, withering, malformation, and stunting of growing sunflower plants. Among them, F. proliferatum was the most prevalent species. Our results highlight that various species of Fusarium are associated with damage on sunflower seeds and all of them can be transmitted through infected seeds and cause disease in growing plants.
The Survival Benefit of Neo-adjuvant Therapy Among Women Undergoing Breast Reconstruction Surgery: A Real World Study
Authors: Ni Peng , Yang Zejian , Qiu Pei , Cheng Yuan , Wang Yu , Wang Jichang , Li Juan , Niu Ligang , Yan Yu , Ge Guanqun , Ma Yunfeng , Zhou Can 
Published: April 2024

Abstract

As a crucial therapeutic regimen, the popularity of breast reconstruction surgery (BRS) has partly been driven by the rise in the utilization of neo-adjuvant therapy (Neo-AT). However, few studies have specifically examined the survival outcome for patients underwent BRS after Neo-AT. This study aimed to investigate and elucidate the survival benefit of neo-adjuvant therapy (Neo-AT) and adjuvant therapy (AT) among the women who underwent BRS. A total of 18919 patients were obtained from the Surveillance, Epidemiology, and End Results (SEER) database between 2007 and 2020. Kaplan-Meier, Cox regression model, and propensity score matching (PSM) analyses were employed to identify the predictors associated with the survival. A nomogram was developed using the variables selected by multivariable Cox analysis to predict short and long-term probabilities of BCSS. In this study, the administration of Neo-AT was founded to be associated with a worse prognosis in comparison with AT. This model is anticipated to offer precise and personalized prediction in BCSS, aiding in treatment decision-making.