bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hagfish genome illuminates vertebrate whole genome duplications and their evolutionary consequences
Authors: Pascual-Anaya Juan , Yu Daqi , Ren Yandong , Uesaka Masahiro , Beavan Alan , Muffato Matthieu , Shen Jieyu , Li Yongxin , Sato Iori , Wan Wenting , Clark James , Keating Joseph , Carlisle Emily , Dearden Richard , Giles Sam , Randle Emma , Sansom Robert , Feuda Roberto , Fleming James , Sugahara Fumiaki , Cummins Carla , Patricio Mateus , Akanni Wasiu , D'Aniello Salvatore , Bertolucci Cristiano , Irie Naoki , Alev Cantas , Sheng Guojun , de Mendoza Alex , Maeso Ignacio , Irimia Manuel , Fromm Bastian , Peterson Kevin , Das Sabyasachi , Hirano Masayuki , Rast Jonathan , Cooper Max , Paps Jordi , Pisani Davide , Kuratani Shigeru , Martin Fergal , Wang Wen , Donoghue Philip , Zhang Yong 
Published: April 2023

Abstract
Whole genome duplications (WGDs) are major events that drastically reshape genome architecture and are causally associated with organismal innovations and radiations1. The 2R Hypothesis suggests that two WGD events (1R and 2R) occurred during early vertebrate evolution2,3. However, the veracity and timing of the 2R event relative to the divergence of gnathostomes (jawed vertebrates) and cyclostomes (jawless hagfishes and lampreys) is unresolved4-6 and whether these WGD events underlie vertebrate phenotypic diversification remains elusive7. Here we present the genome of the inshore hagfish, Eptatretus burgeri. Through comparative analysis with lamprey and gnathostome genomes, we reconstruct the early events in cyclostome genome evolution, leveraging insights into the ancestral vertebrate genome. Genome-wide synteny and phylogenetic analyses support a scenario in which 1R occurred in the vertebrate stem-lineage during the early Cambrian, and the 2R event occurred in the gnathostome stem-lineage in the late Cambrian after its divergence from cyclostomes. We find that the genome of stem-cyclostomes experienced two additional, independent genome duplications (herein CR1 and CR2). Functional genomic and morphospace analyses demonstrate that WGD events generally contribute to developmental evolution with similar changes in the regulatory genome of both vertebrate groups. However, appreciable morphological diversification occurred only after the 2R event, questioning the general expectation that WGDs lead to leaps of morphological complexity7.
Clonal MDS/AML cells with enhanced TWIST1 expression reprogram the differentiation of bone marrow MSCs
Authors: Li Xiang , Li Hongjiao , Wang Yi , Yang Fenfang , Feng Shuang , Chang Kaijing , Yu Xinwen , Guan Feng 
Published: April 2023

Abstract
Bone marrow-derived mesenchymal stem cells (BMMSCs) have the ability to differentiate into osteoblasts and adipocytes, and have been found to promote disease progression of myeloid malignancies like myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML). MDS/AML patient-derived BMMSCs often show a shift in the balance between osteoblastogenesis and adipogenesis, indicating that BMMSCs may be reprogrammed or educated. However, the results of reprogrammed differentiation have been inconclusive. In this study, we found that clonal MDS/AML cells promote adipogenic differentiation and inhibit osteogenic differentiation of BMMSCs, which in turn promotes MDS expansion. Mechanistically, highly expressed transcription factor TWIST1 in clonal MDS/AML cells plays a vital role in the MDS/AML cell-mediated BMMSCs reprogramming differentiation. Enhanced TWIST1 expression induces MDS/AML cells to secrete more IFN-γ, which can induce oxidative stress through STAT1-depenent manner, ultimately causing enhanced adipogenic differentiation and inhibited osteogenic differentiation in BMMSCs. Overall, our findings suggest that targeting the driving oncogenes in malignant clonal cells, such as TWIST1, may offer new therapeutic strategies by remodeling the surrounding bone marrow microenvironment in the treatment of MDS/AML and other hematopoietic malignancies.
A Knowledge Enhanced Graph Convolutional Network for Aspect-based Sentiment Analysis
Authors: Zhang Ping , Liu Peiyu , Chen Xianlin , Cong Guoquan , Li Xinjin 
Published: April 2023

Abstract
Recently, PLMs (pre-trained language models) and syntax-based GCNs (graph convolutional neural networks) have been widely and deeply applied in aspect-based sentiment analysis, effectively promoting the development of this field. However, these methods rarely make use of external knowledge, such as knowledge of high-quality sentiment lexicons, which can be a powerful complement to these methods if the prior knowledge can be effectively used. In this paper, to use external knowledge, we propose a Knowledge Enhanced Graph Convolutional Network for aspect-based sentiment analysis (KEGCN). KEGCN automatically calculates the sentiment eigenvalue of each word and extracts strong sentiment words, then retrains the PLM representations of strong sentiment words to integrate external sentiment knowledge into our model. Experimental results on several benchmark datasets demonstrate the effectiveness of our model, which outperforms previous baseline models in terms of both accuracy and macro-F1.
“But why??” Evaluation of user-suggested synonyms in the Thesaurus of Modern Slovene
Authors: Gapsa Magdalena 
Published: April 2023

Abstract
Various language resources employ user participation in creating a dictionary or evaluating data. An example is Thesaurus of Modern Slovene, which incorporates user participation by allowing users to suggest new synonyms and evaluate existing ones. The aim of this paper was to establish what users of the Thesaurus consider relevant synonymous data and to investigate whether users perceive synonymy differently from lexicographers and, if so, how these differences can be used to improve it. To investigate this, an evaluation of nearly 1,000 user-suggested synonyms was conducted by 42 evaluators representing 7 user groups. The focus was on cross-group analysis of the evaluation. The results showed that users evaluated synonymy differently from experts. The differences were evident in the evaluators’ comments, which gave an insight into user needs. I discussed the findings, e.g. the uneven distribution of reported issues, the need to include evaluators from different regions and age groups, or the similarities between Lexicographers and Students groups. I also addressed possible limitations and presented potential applications of the results. In conclusion, the results demonstrated both the success of the responsive model and user participation, as well as the continuing need for user studies for optimal further development of responsive dictionaries.
Value of adding CT delayed-phase images to Gd-EOB-DTPA in the diagnosis of hepatocellular carcinoma based on LI-RADS
Authors: qing Zhang , yuan Huang , hao Xiong , jie Peng 
Published: April 2023

Abstract
Objective: To explore the potential value of Gadolinium-ethoxybenzyl-diethylenetriamine pentaacetic acid (Gd-EOB-DTPA) in the diagnosis of hepatocellular carcinoma by adding computed tomography (CT) delayed images based on the Liver Imaging Reporting And Data System (LI-RADS).
Methods: The differences in clinical and imaging characteristics between hepatocellular carcinoma (HCC) and non-HCC were compared, and logistic regression was used to analyze the imaging risk factors for the diagnosis of HCC. Based onthe main and HCC-specific auxiliary features of Gd-EOB-DTPA MRI, the HCC diagnostic model 1 was established and the diagnostic efficacy was analyzed. Based on model 1, delayed phase CT images were added to establish model 2 to find reliable predictors of HCC diagnosis. Receiver operating characteristic (ROC) analysis and the DeLong test were used to compare the two models.
Results: There was a significant difference in serum AFP between HCC and non-HCC (p=0.005). Based on main and HCC-specific auxiliary features of Gd-EOB-DTPA MRI, enhancing capsule (OR=0.197, 95%CI=0.06–0.595, p=0.005) and washout (OR=10.345, 95%CI=3.460–30.930, p<0.001) were independent risk factors in Model 1. After adding CT delayed-phase images to build model 2, enhancing capsule (OR=0.132, 95%CI=0.139–0.449, p=0.001) and MRI and (or) CT washout (OR=0.052, 95%CI=0.016–0.172, p<0.001) were reliable predictors of HCC diagnosis. The AUC of model 1 was 0.808, sensitivity was 63.46%, and specificity was 85.00%. The AUC of model 2 was 0.854, the sensitivity was 71.20%, and the specificity was 85.00%. DeLong test (p=0.040) demonstrated the diagnostic efficacy of model 2 significantly superior than model 1.
Conclusion: Tumor washout and enhanced capsule are reliable factors for the diagnosis of HCC. Gd-EOB-DTPA with delayed phase CT images can improve the sensitivity and diagnostic efficiency of HCC on the premise of maintaining high specificity. CT delayed phase images and Gd-EOB-DTPA MRI may be integrated into a single accepted diagnostic algorithm to improve diagnostic performance based on LI-RADS.
Preference of acromegaly patients for treatment attributes in Spain
Authors: Díaz Marcos , Fajardo Carmen , Álvarez-Escola Cristina , Biagetti Betina , Garcia-Centeno Rogelio , Ciriza Raquel , Sánchez-Cenizo Laura 
Published: April 2023

Abstract
Objective Acromegaly is a rare disease caused by increased growth hormone secretion and a subsequent increase in insulin-like growth factor I (IGF-I) levels. Patients display multiple comorbidities that affect their quality of life (QoL). Treatment aims to maintain good biochemical control, tumour control, and reduce the risk of comorbidities; however, their impact on QoL has been overlooked until recently. We interviewed patients to explore their preferences with regard to treatment attributes.
Design Cross-sectional study based on interviews and a discrete choice experiment (DCE) in a Spanish cohort.
Methods Adult patients diagnosed with acromegaly ≥1 year before the start of the study and under treatment were included. Treatment attributes were collected from patient testimony during face-to-face interviews. Then, a DCE was performed to elicit patient preferences for certain treatment attributes.
Results Sixty-seven patients completed the study. QoL improvement was the most important treatment attribute (37%), followed by IGF-I control (20%), blood sugar control (17%), and tumour control (13%). Secondary attributes were pain associated with the route of administration (7%), diarrhoea (2%), administration method (2%), and storage conditions (2%). We then calculated the theoretical share of preference for existing treatments, based on the individual preference utility for each attribute and level. Pegvisomant obtained the highest share of preference overall, and the highest preference as a second-line treatment (53% and 95%, respectively).
Conclusions QoL greatly influences patient treatment preference. Since acromegaly patients are informed and aware of their disease, treatment choice should always be shared with patients.
Mature T-cell Leukemia Primarily Involving Blood and Bone Marrow without TCL1 or MTCP1 Rearrangement: A Subtype of T-Prolymphocytic Leukemia or a Distinct Entity?
Authors: Fang Hong , Beird Hannah , Wang Sa , Ibrahim Andrew , Tang Zhenya , Tang Guilin , You M. James , Hu Shimin , Xu Jie , Li Shaoying , Yin C. Cameron , Hussein Siba El , Le Nhi , Futreal Andrew , Bueso-Ramos Carlos , Thakral Beenu , Kadia Tapan , Thornton Rebecca , Little Latasha , Gumbs Curtis , Song Xingzhi , Medeiros L. , Wang Wei 
Published: April 2023

Abstract
T-prolymphocytic leukemia (T-PLL) is a rare mature T-cell neoplasm defined by rearrangements involving TCL1 or MTCP1. Cases showing some overlapping features with T-PLL but lacking TCL1 and MTCP1 rearrangements have been rarely reported but are not well characterized. Whether these neoplasms belong within the category of T-PLL or represent a distinct entity is unknown. Here, we fully characterize 20 such cases. The median survival for this cohort was 34.7 months. Clinically, 40% of patients were diagnosed incidentally and 65% of patients presents with an indolent phase that was associated with a better survival. Leukemic cells were small to medium sized with a mature morphology. They were CD4-positive with TCRαβ subtype and maintained the expression of other pan-T antigens. A complex karyotype, 11q22.3/ATM deletion and chromosome 8q abnormalities were common, present in 70%, 45% and 35% of patients, respectively. The most common mutations involved ATM and JAK/STAT pathway genes, identified in 40% and 38% of patients, respectively. When this cohort was compared to 42 cases of prototypical T-PLL, they shared many overlapping clinicopathological features and had a similarly poor prognosis. We therefore propose that the neoplasms in this cohort are best classified as TCL1-family negative T-PLL.
Application of a low-cost material for uranium removal: experimental variables and study of concomitants
Authors: Cabranes Malena , Martín Silvana G. , Leyva Ana G. , Babay Paola A. 
Published: April 2023

Abstract
In the present work, the extent in which the presence of concomitant ions affects the removal capacity of uranyl ion by the natural mineral perlite was studied. By using synthetic solutions of uranyl nitrate in batch systems, the variables affecting the process, namely sorbent dose, contact time, pH and initial UO22+ concentration, were firstly investigated. The zeta potential and the sorption capacity of perlite, as well as relevant kinetics and thermodynamic parameters were measured.
Removals up to 90 % were achieved for a dose of 45 g of Pava L-1 and a concentration of U of 100 µg U L-1, of 74 % when the concentration was 1 mg U L-1, 60 % for 10 mg U L-1 and 25 % for a concentration of 50 mg U L-1. The best linear correlations in the adsorption isotherms were achieved by applying the Langmuir and Dubinin-Radushkevich models with adsorption energy of 8.72 kJ mol-1. The thermodynamic variables indicated the feasible, spontaneous and exothermic nature of the sorption of UO22+ by perlite.
The influence of concomitant ions, in decreasing order, was: Cs+ > Ba2+ > Mg2+ > K+ ~ Na+ > NH4+ > Ca2 +. The results of these investigations will allow determining the best treatment, weather the solution is an effluent from a nuclear plant or in case of environmental contamination.
Left ventricle size correlates with peak exercise capacity in pediatric cancer survivors exposed to anthracycline chemotherapy
Authors: Masood Imran , Rezvan Panteha Hayati , Lee Kyuwan , Vervaet Helena , Kuo Christopher , Loss Karla , Menteer JonDavid , Souza Andrew , Freyer David , Su Jennifer 
Published: April 2023

Abstract
Cancer survivors exposed to anthracycline chemotherapy are at risk for developing cardiomyopathy, which may have delayed clinical manifestation. In a retrospective cross-sectional study, we evaluated the utility of cardiopulmonary exercise testing (CPET) for detecting early cardiac disease in 35 pediatric cancer survivors by examining the associations between peak exercise capacity (measured via percent predicted peak VO2) and resting left ventricular (LV) function on echocardiography and cardiac magnetic resonance imaging (cMRI). We additionally assessed the relationships between LV size on resting echocardiography or cMRI and percent predicted peak VO2 since LV growth arrest can occur in anthracycline-exposed patients prior to changes in LV systolic function. We found reduced exercise capacity in this cohort, with low percent predicted peak VO2 (62%, IQR: [53% – 75%]). While most patients in our pediatric cohort had normal LV systolic function, we observed associations between percent predicted peak VO2 and echocardiographic and cMRI measures of LV size. These findings indicate that CPET may be more sensitive in manifesting early anthracycline-induced cardiomyopathy than echocardiography in pediatric cancer survivors. Our study also highlights the importance of assessing LV size in addition to function in pediatric cancer survivors exposed to anthracyclines.
Expert Identification Using Topic Models in Semantic based Genealogical Graphs
Authors: S Aarthy , GS Mahalakshmi , KS Easwarakumar , S Sendhilkumar 
Published: April 2023

Abstract

In scientometrics, semantically closer research articles tend to form a genealogical graph pattern which is used to derive explicit semantic lineage. The assumption of classic research article is that; the article has a high influence factor among the genealogy neighborhood. The candidates for identifying experts in each genealogical graph are chosen by finding one or more classic research articles from that graph and extracting the authors of those classic research articles. This paper proposes machine learning based approaches for mining the genealogical research paths which facilitate the inclusion of implicit citation/reference edges as well as indirectly linked citation lineage edges which are otherwise non-citing, to contribute effectively towards expert identification and ranking.
WITHDRAWN: Combination Low-Concentration Atropine and Contact Lenses for Myopia Control
Authors: Erdinest Nir , Atar-Vardi Maya , Lavy Itay , London Naomi , Landau David , Levinger Nadav , Pras Eran , Morad Yair 
Published: April 2023

Abstract
Purpose: To ascertain the effectivity of 0.01% atropine (A0.01%) treatment to inhibit myopia progression and the possible additive potency with peripheral defocus contact lenses over three years and the rebound effect one year after cessation of treatment.
Methods: This prospective study included 127 children aged 8–15 years, divided into three treatment groups: A0.01% and single vision (SV) spectacles (At, n=36), A0.01% and peripheral defocus contact lens (At+PDCL, n=30), 0.01%At and dual focus (At+DF, n=25) and a control group prescribed SV spectacles (n=36). Cycloplegic spherical equivalence refraction (SER) was measured every six months during three years of treatment and one year after cessation.
Results: Myopia progression decreased over three years of treatment, more during the second and third years than the first, to a statistically significant degree in the A0.01% monotherapy group(P<0.01): In the first, second, and third years respectively in the At group -0.42±0.34D, -0.19±0.18, -0.22±0.19D, in the At+PDCL group -0.26±0.21D, -0.14±0.37D and -0.15±0.31D, in the At+DF group -0.22±0.15D, -0.15±0.22D, and -0.11±0.14D. Myopia progressed one year after cessation of treatment: -0.29±0.28D in the At group, -0.13±0.28D in the At+PDCL group, and -0.09±0.18D in the At+DF group. After three years, there was no statistically significant difference in myopia progression between groups At and At+PDCL or At+DF (P<0.05).
Conclusions: Low-dose atropine has been substantiated in this cohort as an effective treatment to decelerate myopia progression over three years, more effective in the second and third years of treatment. The combination treatment did not exhibit a statistically significant advantage over monotherapy in this cohort. The dual-focus lens group exhibited a statistically lower rebound effect than the monotherapy group.
Silymarin enhances the response to oxytetracycline treatment in Nile tilapia experimentally infected with Aeromonas hydrophila
Authors: Sherif Ahmed H. , Toulan Adel E. , El-kalamwi Naglaa , Mahmoud Abeer E. , Farag Enas A.H. 
Published: April 2023

Abstract
Many governments have approved the use of oxytetracycline as an antibiotic additive to food fish, with oxytetracycline now routinely used in many nations. However, oxytetracycline is known to have immunological and antioxidant suppression. We therefore evaluated the histopathological, immunosuppressive, and genotoxic effects of a diet containing silymarin (100 mg/kg fish feed) in Nile tilapia at 0, 2, 4, 6, and 8 weeks. The protective effects of silymarin against Aeromonas hydrophila (A. hydrophila) infection were also evaluated. Blood parameters (erythrocyte count, white blood cell count, hemoglobin, and packed cell volume) improved over time in fish fed a silymarin-supplemented diet. Serum levels of alanine aminotransferase, a marker of liver injury, were lower in fish fed diets containing silymarin, whereas serum levels of aspartate transferase and alkaline phosphatase were unchanged. Silymarin supplementation affected serum lipid profiles including decreases in serum triglyceride and low-density lipoprotein cholesterol levels and trend toward lower cholesterol levels, whereas serum high-density lipoprotein cholesterol levels were increased compared to fish fed the control diet. Silymarin supplementation increased serum total protein levels and globulin fractions. Significant and progressive increases in catalase and glutathione peroxidase levels were observed after six weeks of feeding with a silymarin-supplemented diet before returning to control levels at the end of the experimental period. In fish fed a diet containing silymarin, interleukin-1, and fish tumor necrosis factor-alpha were upregulated in liver tissues; however, interleukin-10 levels decreased to comparable levels to controls after eight weeks. Fish infected with A. hydrophila displayed signs of septicemia (opaque eye, hemorrhagic ulcers, dentated fins, hepatomegaly, and splenomegaly). Reduced mortality was observed in Nile tilapia infected with A. hydrophila and fed a diet containing silymarin, indicating that silymarin improves fish responses to oxytetracycline with a 37% reduction in mortality.
Association of asthma and lung cancer risk: A pool of cohort studies and Mendelian randomization analysis
Authors: Huang Qinyao , Huang Yunxia , Xu Senkai , Liu Xinqi , Yuan Xiaojun , Chen Zisheng 
Published: April 2023

Abstract
Background
Over the past two decades, population-based studies have shown an increased association between asthma and the risk of lung cancer. However, the causal links between these two conditions remain poorly understood.
Methods
We conducted a comprehensive search of various databases, including PubMed, Embase, Web of Science, and Cochrane Library, up until October 01, 2022. Only articles published in English were included in our study. We performed a meta-analysis using random-effects models to calculate the odds ratio (OR) and corresponding 95% confidence interval (CI). Subgroup analyses were conducted based on study design, gender, and histologic types. We also conducted a two-sample Mendelian randomization (MR) using published genome-wide association study summary data from UK Biobank (376,358 individuals), FinnGen (213,293 individuals), and TAGC (127,669 individuals). We used the fixed effects meta-analysis method to combine estimates from various databases. We used inverse variance weighting (IVW) for the meta-analysis to determine the odds ratio (OR) and corresponding 95% CI.
Results
Our meta-analysis reviewed 21 population-based cohort studies involving 712,418 patients, revealing that asthma is significantly associated with an increased risk of lung cancer (OR = 1.29, 95% CI 1.19–1.40) in all individuals. Subgroup analysis showed a significantly higher risk of lung cancer in females with asthma (OR = 1.23, 95% CI 1.01–1.49). We found no significant association between asthma and lung adenocarcinoma (LUAD) (OR = 0.76, 95% CI 0.54–1.05), lung squamous carcinomas (LUSC) (OR = 1.09, 95% CI 0.79–1.50), or small-cell lung cancer (SCLC) (OR = 1.00, 95% CI 0.68–1.49). However, our MR meta-analysis supported a decreasing causality between asthma and lung cancer (OR = 0.94, 95% CI 0.91–0.98, P = 0.001), specifically with a decreased risk of LUSC (OR = 0.87, 95% CI 0.82–0.92, P < 0.0001).
Conclusions
Through meta-analysis, our study confirms that patients with asthma have a higher risk of developing lung cancer. Our MR study, however, discovered evidence suggesting a declining causal relationship between asthma and the risk of lung cancer, particularly in LUSC. Future studies examining the link between asthma and the risk of developing lung cancer should consider the bias of controlled and uncontrolled asthma.