bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptome Dysregulation in Hepatoblastoma: The Pivotal Role of Noncoding Rnas and Changes in Lipid Metabolism
Authors: Rivas Maria Prates , Aguiar Talita Ferreira Marques , de Andrade Edson Mario , Pires Sara Ferreira , Defelicibus Alexandre , Barros Bruna , Novak Estela , Cristofani Lilian Maria , Odone Vicente , Cypriano Monica , de Toledo Silvia Regina Caminada , Cunha Isabela Werneck da , Costa Cecilia Maria Lima da , Carraro Dirce Maria , Tojal Israel , Mendes Tiago Antônio de Oliveira , Krepischi Ana Cristina Victorino 
Published: April 2022

Abstract

Hepatoblastoma, the most common liver tumor in children and exhibited the lowest mutational burden among solid cancers, pointing to chromosomal and epigenetic changes as the main drivers of tumorigenesis. Previous studies explored hepatoblastoma transcriptomes focusing on risk stratification, but no consensual molecular signature emerged. We performed whole-transcriptome analysis with total RNA sequencing using 14 hepatoblastomas compared with control liver samples. A set of 1,492 differentially expressed genes (DEGs) was detected, 1,031 upregulated and 461 downregulated, comprising 920 protein-coding genes (62%). A strong dysregulation of non-coding RNA genes (ncRNAs) was revealed, mostly upregulated. Among the top 50 genes with the highest expression, 42% of them were ncRNAs, and three (MAGED4, SNO144-16, and RP11-431J24.2) were exclusively expressed by hepatoblastomas. Upregulated biological processes were linked to cell differentiation, communication and signaling pathways, as well as embryonic and developmental processes. Enriched biological processes in downregulated genes included mainly negative regulation of oxidation and metabolism inhibition, affecting amine, nicotinamide, and lipids. An integrative analysis between miRNA-mRNA and protein-protein interaction networks highlighted major biological processes associated with metabolism and oxidation reactions of lipids and carbohydrates, methylation-dependent chromatin silencing, and DNA methylation. Four upregulated miRNAs (miR-186, miR-214, miR-377, and miR-494) were disclosed, potentially targeting more than 10 protein-coding transcripts, which suggested a possible role in their negative regulation. In conclusion, the RNASeq analysis revealed the disruption of metabolic pathways, including lipids, amines, and nicotinamides, and disclosed a robust ncRNA transcriptome perturbation, highlighting a new epigenetic player in the control of hepatoblastoma gene expression, along with DNA methylation.
Acid-base balance, osmoregulation and hematological changes in tilapia (Oreochromis niloticus) after sublethal cadmium exposure
Authors: Soegianto Agoes , Yulianto Bambang , Payus Carolyn Melissa , Affandi Moch , Mukholladun Wildanun , Indriyasari Khudrotul Nisa , Marchellina Ary , Rahmatin Nailul Muthiati 
Published: April 2022

Abstract
Tilapia exposed to two different Cd concentrations in freshwater had varying levels of Cd in their gills, with fish exposed to 2 mg/L of Cd having a higher Cd level than fish exposed to 1 mg/L of Cd. The higher Cd level exposure caused considerable metabolic acidosis (lower pH and higher pCO2) and inhibited gill carbonic anhydrase. Fish exposed to higher Cd levels had lower osmolality, levels of plasma Cl− and K+ but constant levels of Na+. All hematological parameters tested in this study, including red blood cells, hemoglobin, hematocrit, and mean cellular hemoglobin concentration hematocrit, decreased as a result of increased Cd exposure. This is consistent with the pO2 measurement, which indicates that fish exposed to greater levels of Cd had a considerable reduction in pO2.
Intelli-NGS: Intelligent NGS, a deep neural network-based artificial intelligence to delineate good and bad variant calls from IonTorrent sequencer data
Authors: Singh Aditya , Bhatia Prateek 
Published: April 2022

Abstract
Ion Torrent is a second-generation sequencing platform with smaller capital costs than Illumina but is also prone to higher machine error than latter (0.5-2% Vs. 0/01 − 0/05%). Limited software tools or pipelines are available for Ion Torrent data filtering and most of them have limitations or take time for analysis. Given to the unexplored possibilities that machine learning could uncover, we explored it to address this issue of solving quality variants from Ion torrent data. The artificial intelligence was developed from scratch in Python 3 using TensorFlow fully connected dense layers. The model takes VCF files as input and solves each variant based on the thirty-five parameters given by the Ion Torrent platform, including the flow-space information which is missed by variant callers other than the default torrent variant caller. The final trained model was able to achieve an accuracy of 93.08% and a ROC-AUC of 0.95 with GIAB validation data. The additional program that was written to run the model annotates each variant using online databases such as dbSNP, ClinVar and others. A probability score for each outcome for each variant is also provided to aid in decision making. The model and running code are available for free at https://www.github.com/aditya-88/intelli-ngs.
The Evaluation of the epigenetics related genes expression (DNMT, HDAC1) in Iranian patients with Systemic Lupus Erythematosus
Authors: Abbasifard Mitra , Mohammadiranjbar Fahimeh , Mohammad-Sadeghipour Maryam , Mahmoodi Mehdi , Hassanshahi Gholamhossein , Swann Jennifer , Hosseiniara Reza , Hajizadeh Mohammad Reza 
Published: April 2022

Abstract
Background: Systemic Lupus Erythematosus (SLE) is an autoimmune disease in which the immune system abnormally reacts against cells and tissues leading to inflammation. Epigenetic alterations, including DNA methylation and histone modification, have critical effects on autoimmune disease and SLE pathogenesis via dysregulation of critical genes. Aims: The purpose of this study was to evaluate the epigenetic-related gene expression of DNA methyltransferase (DNMT) and Histone Deacetylase 1 (HDAC1) in Iranian patients with SLE. Methods: This matched case-control study included 16 people with SLE and 16 healthy people who were referred to the Rafsanjan rheumatology clinic, in the southeast of Iran. The expression of DNMT and HDAC1 genes was measured through a Real-time PCR assay of blood samples. Results: DNMT gene expression did not differ significantly between SLE and healthy groups (P=0.21). In contrast, HDAC1 gene expression was enhanced in the SLE group, but this enhancement failed to reach statistical significance (P=0.94). Conclusion: The results of this study suggest that overexpression of HDAC1 could serve as a diagnostic for SLE disease. Additional studies with larger sample sizes are required to confirm our findings. Evaluation of other genes are related to SLE disease is essential and may help to form an accurate diagnosis of the disease.
A 3-Player Game with Bounded Rationality Concerning Ecology Compensation and Environmental Tax Policies
Authors: Chen Xiaozhu , Zhang Jixiang 
Published: April 2022

Abstract
In the face of environmental hazards caused by low nitrogen utilization efficiency, this paper constructed a 3-player game model which contains local governments, peasant households, and polluting enterprises with bounded rationality, all of which take part in the nitrogen cascade in the watersheds. The Nash equilibrium points and local stability of the dynamical systems were investigated. Complex dynamics i.e. bifurcation and chaos arise from the variation of some parameters of the model, including the adjustment speed of decision-making of a boundedly rational player. Numerical simulations were rendered to manifest bifurcation, chaos, maximal Lyapunov exponent, strange attractor, and sensitive dependence on initial conditions. Chaos control of the dynamic systems was discussed using the delayed feedback scheme. Research results indicate that whereas the adjustment speed of players has a destabilizing effect, a proper increment of the ecological compensation or environmental tax rate will restore the local stability of the system. Moreover, while the excessive adjustment speed has caused the system to behave chaotically, an increase of the feedback controller can eliminate chaos and achieve a stable market.
Ribosomal RNA-depletion provides an efficient method for successful dual RNA-Seq expression profiling of a marine sponge holobiont
Authors: Xiang Xueyan , Poli Davide , Degnan Bernard M. , Degnan Sandie M. 
Published: April 2022

Abstract
Investigations of host-symbiont interactions can benefit enormously from a complete and reliable holobiont gene expression profiling. The most efficient way to acquire holobiont transcriptomes is to perform RNA-Seq on both host and symbionts simultaneously. However, optimal methods for capturing both host and symbiont mRNAs are still under development, particularly when the host is a eukaryote and the symbionts are bacteria or archaea. Traditionally, poly(A)-enriched libraries have been used to capture eukaryotic mRNA, but the ability of this method to adequately capture bacterial mRNAs is unclear because of the short half-life of the bacterial transcripts. To determine the optimal RNA-Seq approach for animal host–bacterial symbiont analysis, we compared transcriptome bias, depth and coverage achieved by two different mRNA capture and sequencing strategies applied to the marine demosponge Amphimedon queenslandica holobiont, for which genomes of the animal host and three most abundant bacterial symbionts are available. The two strategies were: (i) poly(A) captured mRNA-Seq (Poly(A)-RNA-Seq); and (ii) ribosomal RNA depleted RNA-Seq (rRNA-depleted-RNA-Seq). For the host sponge, we find no significant difference in transcriptomes generated by the two different mRNA capture methods. However, for the symbiont transcriptomes, we confirm the expectation that the rRNA-depleted-RNA-Seq performs much better than the Poly(A)-RNA-Seq. Importantly, the availability of all genomes allowed us to accurately assess the nature of the Poly(A) bias compared to the rRNA-depleted transcriptomes. This comparison demonstrates that RNA-Seq by ribosomal RNA depletion is an effective and reliable method to analyse holobiont transcriptomes.
Clinical Target Volume Automatic Segmentation Based on Lymph Node Stations for Lung Cancer with Bulky Lump Lymph Nodes
Authors: Di Mingyi , Shen Jing , Wang Shaobin , Chen Qi , Chen Yu , Liu Zhikai , Lian Xin , Ma Jiabin , Pang Yantian , Dong Tingting , Wang Bei , Guan Qiu , He Lei , Zhang Yue , Liang Hao , Shen Jie , Zhang Fuquan 
Published: April 2022

Abstract
The lack of standardized delineation of lymph node station in lung cancer radiotherapy leads to nonstandard clinical target volume (CTV) contouring, especially in patients with bulky lump gross target volume lymph nodes (GTVnd). Therefore, this study defines lymph node region boundaries in radiotherapy for lung cancer and automatically contours lymph node stations based on the International Association for the Study of Lung Cancer (IASLC) lymph node map. Computed tomography (CT) scans of 200 patients with small cell lung cancer are collected. The lymph node zone boundaries are defined based on the IASLC lymph node map, with adjustments to meet radiotherapy requirements. Contours of lymph node stations are confirmed by two experienced oncologists. A model (DiUNet) is constructed by incorporating the contours of GTVnd to precisely contour the boundaries. Quantitative evaluation metrics and clinical evaluations are conducted. This is the first study to propose a method that automatically contours lymph node regions station by station based on the IASLC lymph node map with bulky lump GTVnd. Delineation of lymph node stations based on the DiUNet model is a promising strategy to obtain accuracy, consistency, and efficiency for CTV delineation in lung cancer patients, especially for bulky lump GTVnd.
Geochemistry of Neogene Nansatsu volcanic rocks and its implications on the evolution of Au province in South Kyushu
Authors: Ishida Mizuki , Murakami Shunpei , Machida Shiki , Fujinaga Koichiro , Yasukawa Kazutaka , Ishikawa Tsuyoshi , Nagaishi Kazuya , Tajiri Rie , Nakamura Kentaro , Kato Yasuhiro 
Published: April 2022

Abstract
In South Kyushu, Japan, epithermal Au deposits are associated with volcanic rocks younger than 7.5 Ma, whereas Sn and W deposits are associated with middle Miocene (17–12 Ma) Outer Zone granitoids. As magma chemistry often controls the type and size of a mineral deposit, the geochemistry of igneous rocks in this area can provide valuable information about the evolution of metallogenic provinces. In this study, we reported the whole-rock major and trace element and Sr–Nd–Pb isotopic compositions of volcanic rocks from the Nansatsu area in South Kyushu, where several high-sulfidation Au deposits are located. We analyzed samples from the Oldest stage (middle Miocene), Older stage (late Miocene), and Middle stage (early Pliocene) Nansatsu volcanic rocks, which were andesite to dacite in composition, with an island-arc trace element signature. Their elemental compositions largely overlapped with both Outer Zone granitoids and volcanic rocks younger than 7.5 Ma in South Kyushu. Isotopic characteristics suggested that the Oldest stage volcanic rocks had magma sources similar to Outer Zone granitoids, whereas the sources for the Older and Middle stage magmas were similar to those of basalts formed <7.5 Ma in South Kyushu. The Oldest stage rocks (as well as Outer Zone granitoids) incorporated a substantial amount of organic-carbon-rich sedimentary rocks (Shimanto Supergroup), which resulted in reduced magma and consequently, lack of Au mineralization. In contrast, it is likely that the magmas that produced the Older and Middle stage rocks did not contaminate as much Shimanto Supergroup, thus avoiding reduction and early sulfide saturation. Effective transportation of mantle-derived magma, without significant crustal contamination, may have been an important factor for Au mineralization after 7.5 Ma in South Kyushu.
Ownership and Use of Long-lasting Insecticidal Nets Three Months after a Mass Distribution Campaign in Uganda, 2021
Authors: Kwiringira Andrew , Nanziri Carol , Nsubuga Edirisa Juniour , Migamba Stella Martha , Ntono Vivian , Atuhaire Immaculate , Ahirirwe Sherry Rita , Asio Alice , Senyange Shaban , Nakamya Petranilla , Masanja Veronicah , Elayeete Sarah , Komakech Allan , Nansikombi Hilda T. , Mwine Patience , Nampeera Rose , Ndyabakira Alex , Okello Paul , Migisha Richard , Bulage Lilian , Kwesiga Benon , Kadobera Daniel , Rutazana Damian , Harris Julie R. , Ario Alex R. 
Published: April 2022

Abstract
Background: Uganda conducted its third mass Long-Lasting Insecticide-treated Net (LLIN) distribution campaign in 2021. The target of the campaign was to ensure that 100% of households own at least 1 LLIN per 2 persons and to achieve 85% use of distributed LLINs. We assessed LLIN ownership, use, and associated factors 3 months after the campaign.Methods: We conducted a cross-sectional household survey in 14 districts during April 13-30, 2021. We selected households using multistage sampling. We asked about LLIN ownership, use, duration since received until the time of interview, and visually verified the presence of LLINs. Outcomes were having at least one LLIN per 2 household members, and individual LLIN use. We used modified Poisson regression to assess associations between exposures and outcomes.Results: In total, 5,529 households with 27,585 residents and 15,426 LLINs were included in the analysis. Overall, 95% of households owned ≥1 LLIN, 92% of the households owned ≥1 LLIN <3 months old, 81% of households owned ≥1 LLIN per 2 persons in the household, and 69% of residents slept under an LLIN the previous night. Factors associated with LLIN ownership included believing that LLINs are protective against malaria (aPR=1.13; 95% CI=1.04-1.24). Reported use of mosquito repellents was negatively associated with ownership of LLINs (aPR=0.96; 95% CI=0.95-0.98). The prevalence of LLIN use was 9% higher among persons who had LLINs 3-12 months old (aPR=1.09; 95% CI=1.06-1.11) and 10% higher among those who had LLINs 13-24 months old (aPR=1.10; 95% CI=1.06-1.14) than those who had LLINs <3 months old. Of 3,859 LLINs identified in the households but not used for sleeping the previous night, 3,250 (84%) were <3 months old. Among these 3,250, 41% were not used because owners were using old LLINs, 16% were not used because of lack of space for hanging them, 11% were not used because of fear of chemicals in the net, 5% were not used because of dislike of the smell of the nets, and 27% were not used because of other reasons.Conclusion: Three months after a LLIN distribution campaign, both LLIN ownership and use remained well below targets. The government should consider distributing additional LLINs to achieve and sustain a target of ≥1 LLIN for 2 household members and behavior change communication before the distribution of LLINs to counter misconceptions about new LLINs.
Spring Test for Automatic Measuring of Signal Complexity
Authors: Cheng Jie , Huang Haiyong , Li Wenshi 
Published: April 2022

Abstract
In order to automatically measure the complexity of time series, we invented 3S plot, and the embedded spring is a one-dimensional manifold. Three automatic statistical indexes are defined by self-similarity measure, extreme value search acceleration and neighborhood rotation phase, respectively. The above three new metrics and another two comparison standards, Lyapunov exponent and spectral entropy complexity, can pass the benchmark system test of unified equation. Under the guidance of visualization of bifurcation diagram, three probability measuring methods with relatively weak independent recognition abilities and one phase measuring method with relatively sensitive detection ability can easily identify the order and chaos states following Chua's equation. Finally, five main measuring tools are used to successfully characterize the new 555 timer-based chaotic signals.
One-Step Acid Bleachable Pretreatment with a Recyclable Acid Hydrotrope and Chlorate for Biomass Valorization
Authors: Zhang Zhen , Shi Xuehui , Tao Furong , Ji Hairui , Ji Xingxiang , Tian Zhongjian , Chen Jiachuan 
Published: April 2022

Abstract
Pretreatment is a necessary step to converting lignocellulosic biomass from its native form into a more accessible form for the value-added utilization of its main components. Herein, we developed a one-step acid bleachable pretreatment method using a recyclable acid hydrotrope (p-toluenesulfonic acid, p-TsOH) and chlorate to achieve the fibers bleaching and lignin extraction simultaneously. Under a mild condition (C80T80t45), 84.33% of hemicellulose and 76.79% of lignin were dissolved out. The obtained dispersed fibers with a high whiteness of 60.13% ISO can be used for papermaking or ethanol production. The results from quasi-simultaneous enzymatic saccharification and combined fermentation (Q-SSF) of the pretreated substrate indicated that the ethanol concentration and yield reached to 39.30 ± 0.57 g/L and 82.36 ± 1.15%, respectively. What’s more, according to the results of lignin characterization, the aromatic rings in extracted lignin were opened forming dicarboxylic acids as well as derivatives due to the oxidation of chlorate, which is beneficial for its catalytic upgrading and composites preparation. Therefore, this study is important to valorization of lignocellulosic biomass.
The Interactions of Adding Polymer and Waste Plastic Fibers to Reinforced Concrete Beams' Flexural Behavior
Authors: Al-Hadithi Abdulkader I. , Al-Waysi Shahd Yonus , Al-Gburi Majid 
Published: April 2022

Abstract
This research was conducted to study the effect of adding waste plastic fibers (WPFs) on the flexural behaviour of polymer-modified reinforced concrete (PMRC) beams. Fifteen simply supported RC beams with a cross section of (100 × 150) mm and a clear span of 1100 mm were tested under two-point loads until failure. Reinforced concrete beams are classified into five groups, each containing three beams with a different area steel ratio (ρ) value. The first group was made up of the normal concrete mix. The second group was made with SBR modified concrete, while the three remaining groups were made of polymer modified concrete PMC containing (WPFs) with volumetric ratios of equal to (0.75, 1.25, and 1.75%). Test results established that the adding of WPFs, in addition, to decreasing the danger of PET wastes to the environment, leads to an increase in the maximum applied load, causing ultimate failure, an increment in ductility index, and transformation of the mode of failure of the tested beams into a more ductile one for all beams containing such kinds of fibers.
Patients’ and clinicians’ perspectives towards primary care consultations for shoulder pain: qualitative findings from the Prognostic And Diagnostic Assessment of the Shoulder programme
Authors: Saunders Benjamin , Burton Claire , Windt Danielle Van Der , Myers Helen , Chester Rachel , Pincus Tamar , Wynne-Jones Gwenllian 
Published: April 2022

Abstract
Background
Clinical management of musculoskeletal shoulder pain can be challenging due to diagnostic uncertainty, variable prognosis and limited evidence for long-term treatment benefits. The UK-based PANDA-S programme (Prognostic And Diagnostic Assessment of the Shoulder) is investigating short and long-term shoulder pain outcomes. This paper reports linked qualitative research exploring patients’ and clinicians’ views towards primary care consultations for shoulder pain.
Methods
Semi-structured interviews were conducted with 24 patients and 15 primary care clinicians. Twenty-two interviews (11 patients, 11 clinicians) were conducted as matched patient-clinician ‘dyads’. Data were analysed thematically.
Results
Clinicians reported attempts to involve patients in management decisions; however, there was variation in whether patients preferred treatment choice, or for decisions to be clinician-led. Some patients felt uncertain about the decisions made, due to a lack of discussion about available management options. Many GPs expressed a lack of confidence in diagnosing shoulder pain. Patients reported either not being given a diagnosis, or receiving different diagnoses from different professionals, resulting in confusion. Whilst clinicians reported routinely discussing prognosis of shoulder pain, patients reported that prognosis was not raised. Patients also expressed concern that their shoulder pain could be caused by serious pathology; however, clinicians felt that this was not a common concern for patients.
Conclusions
Findings showed disparities between patients’ and clinicians’ views towards shoulder pain consultations, indicating a need for improved patient-clinician communication. Findings will inform the design of an intervention to support treatment and referral decisions for shoulder pain that will be tested in a randomised controlled trial.