bluuebunny/crossref_metadata_2025_split huggingface dataset:
Significance of m6A Regulators in the Diagnosis and Subtype Classification of Preeclampsia Using the Gene Expression Omnibus Database
Authors: Hou Ying , Zhao Guoqiang , Zhao Jian , Qi Shihong , Du Yichen , Xu Hualin 
Published: July 2022

Abstract
Background: Preeclampsia(PE) is a common obstetric complication, it increases maternal and perinatal mortality. N6-methyladenosine (m6A) is the most common modification in eukaryotic mRNA, and this study aimed to investigate the role of m6A regulators in the diagnosis and subtype classification of PE.Methods: The mRNA profiles of GSE48424 and GSE75010 were downloaded from the Gene Expression Omnibus database. Differential expression analysis of m6A regulators was performed on the blood samples using the limma package of R, and significant results were obtained. A random forest model was used to predict PE. The expression of m6A regulators was also evaluated. Candidate genes were identified, and a nomogram was drawn. Principal component analysis was used to verify the classification of PE patients using a consensus clustering method based on m6A regulators found in serum samples. Infiltrating immune cells in blood samples were evaluated and quantified according to m6A scores. We compared the correlations of different m6A patterns with early-onset preeclampsia (EOPE) and severe preeclampsia (SPE).Results: We screened for the differential expression of three m6A regulators (YTHDF3, HNRNPA2B1, and CBLL1) in serum samples from women with PE and controls. In women with PE, the expression of YTHDF3 and HNRNPA2B1 in placenta and serum was significantly lower than in normal controls. PE can be predicted using a nomogram based on these two genes. Based on m6A regulators, GSE48424 PE patients can be separated into two subgroups (Clusters A and B). Seven immune cell subtypes showed varying degrees of infiltration. Higher m6A scores were found in Cluster A than in Cluster B. PE patients in Cluster B were more likely to have SPE. EOPE and SPE were more likely to occur in PE patients in Cluster A with high m6A scores. Women with SPE or EOPE exhibit high levels of YTHDF3.Conclusions: This study shows that m6A regulators are differentially expressed in serum samples from PE patients and that they have potential diagnostic and typing value. Further research on PE subgroups may lead to more precise prevention and treatment methods.
Hypertension arising after 20 weeks of gestation: gestational hypertension or masked chronic hypertension?
Authors: Espeche Walter , Salazar Martin , Minetto Julian , Sisnieguez Carlos Leiva , Cerri Gustavo , Balbin Eduardo , Stavile Rodolfo , Ramos Patricia Carrera , Soria Adelaida , Santillan Claudia , Grassi Florencia , Torres Soledad , Carbajal Horacio 
Published: July 2022

Abstract
Objectives
the aims were 1- to evaluate the prevalence of masked chronic hypertension in pregnant women classified as gestational hypertension 2- to compare the risks of developing preeclampsia in true gestational hypertension vs those women classified as having gestational hypertension but who had had masked hypertension in the first half of pregnancy.
Methods
We conducted a cohort study in consecutive high-risk pregnancies who were evaluated before 20 weeks of gestation. Women who developed hypertension (office BP ≥ 140/90 mmHg and/or antihypertensive treatment) after 20 weeks of gestation was classified, according to the ABPM performed before 20 weeks of gestation, as having “true” gestational hypertension (if their ABPM before 20 weeks of gestation was normal) or “pseudo” gestational hypertension (if they had masked chronic hypertension). Risks for preeclampsia (PE) were estimated and compared with normotensive women.
Results
Before 20 weeks of gestation, 227 were analyzed (age 32 ± 6 years, median gestation age 15 weeks); 67 had chronic hypertension (29.5%). Of the remaining 160, 39 developed gestational hypertension (16 had true gestational and 23 pseudo gestational hypertension, because they had masked hypertension in the first half of pregnancy). Compared with normotensive pregnant women, true gestational hypertension did not increase the risk of developing PE (OR = 0.76, 95%CI = 0.16–6.65). Conversely, pseudo gestational hypertension increased the risk of PE more than 4 times (0R = 4.47 CI = 1.16–12.63). Risk estimation did not change substantially after the adjustment for multiple possible confounders.
Conclusion
59% of women diagnosed as gestational hypertensives had indeed masked chronic hypertension and a high risk of developing PE.
Examination of a Novel Expression-Based Gene-SNP Annotation Strategy to Identify Tissue-Specific Contributions to Heritability in Multiple Traits
Authors: Mize Travis , Evans Luke 
Published: July 2022

Abstract
Complex traits show clear patterns of tissue-specific expression influenced by single-nucleotide polymorphisms (SNPs), yet current strategies aggregate SNP effects to genes by employing simple physical proximity-based windows. Here, we examined whether incorporating only those SNPs with effects on tissue-specific cis-expression would improve our ability to detect trait-relevant tissues across 31 complex traits using stratified linkage disequilibrium score regression (S-LDSC). We found that a physical proximity annotation produced more significant tissue enrichments and larger S-LDSC regression coefficients, as compared to an expression-based annotation. Furthermore, we showed that our expression-based annotation did not outperform an annotation strategy in which an equal number of randomly chosen SNPs were annotated to genes within the same genomic window, suggesting extensive redundancy among SNP effect estimates due to linkage disequilibrium. That said, current sample sizes limit estimation of cis-genetic SNP effects; therefore, we recommend reexamination of the expression-based annotation when larger tissue-specific expression datasets become available. Finally, we report new and updated tissue enrichment estimates across 31 complex traits, such as significant heritability enrichment of the frontal cortex for cognitive performance, educational attainment, and intelligence, providing further evidence of this structure’s importance in higher cognitive function.
A FRET biosensor, SMART, monitors necroptosis in renal tubular epithelial cells in a cisplatin-induced kidney injury model
Authors: Murai Shin , Takakura Kanako , Sumiyama Kenta , Moriwaki Kenta , Terai Kenta , Komazawa-Sakon Sachiko , Yamaguchi Yoshifumi , Mikami Tetuo , Araki Kimi , Ohmuraya Masaki , Matsuda Michiyuki , Nakano Hiroyasu 
Published: July 2022

Abstract
Necroptosis is a regulated form of cell death involved in various pathological conditions, including ischemic reperfusion injuries, virus infections, and drug-induced tissue injuries. However, it is not fully understood when and where necroptosis occurs in vivo. We previously generated a Forster resonance energy transfer (FRET) biosensor, termed SMART (the sensor for MLKL activation based on FRET), which specifically monitored necroptosis in human and murine cell lines in vitro. Here, we generated transgenic (Tg) mice that expressed the SMART biosensor in various tissues. SMART monitored necroptosis, but not apoptosis or pyroptosis, in primary cells, including peritoneal macrophages and embryonic fibroblasts. Moreover, the FRET signal was elevated in renal tubular cells of cisplatin-treated SMART Tg mice compared to untreated SMART Tg mice. Together, SMART Tg mice may provide a valuable tool for monitoring necroptosis in different types of cells in vitro and in vivo.
Knowledge Domain and Emerging Trends in Internet-based diagnosis and treatment services：A Scientometric Review Based on CiteSpace V Analysis
Authors: Sheng Mengfei , Zhou Jiangping , Song BaoXiang , Wang Enjun 
Published: July 2022

Abstract
Background
In the fight against the COVID-19 epidemic, internet-based diagnosis and treatment services are a promising technology that can be used effectively in health care.
Objective
The goal of this study was to examine the research state and show the hotspots and frontiers of Internet-based diagnosis and therapy using CiteSpace V.
Methods
From 2001 to 2020, we searched the Web of Science Core Collection (WoSCC) for papers on Internet-based diagnosis and therapy. CiteSpace V was used to produce network maps of author, country, and institution collaborations, revealing hotspots and frontiers of Internet-based diagnosis and treatment.
Results
The Web of Science Core Collection (WoSCC) yielded a total of 1067 studies linked to Internet-based diagnosis and therapy. The most prolific author was Gerhard Andersson (16 articles). The United States and Karolinska Institutet were the leading nations and institutions in this discipline, with 590 and 57 publications, respectively. There was active collaboration among the writers, nations, and institutions. Hot subjects included artificial intelligence, health-related quality, and breast cancer.
Conclusions
Based on the findings of CiteSpace V, the present study encourages active collaboration among authors, nations, and institutions. Major continuing research themes include cancer diagnosis and treatment based on artificial intelligence or Internet emphasis, as well as the interplay between Internet-based diagnostic and treatment services and health-related quality.
EDLMPPI: Learning the Protein Language of Proteome-wide Protein-protein Binding Sites via Explainable Ensemble Deep Learning
Authors: Li Xiangtao , Hou Zilong , Yang Yuning , Ma Zhiqiang , Wong Ka-Chun 
Published: July 2022

Abstract
Protein-protein interactions (PPIs) govern cellular pathways and processes, by significantly influencing the functional expression of proteins. Therefore, accurate identification of protein-protein interaction binding sites has become a key step in the functional analysis of proteins. We develop an ensemble deep learning model (EDLMPPI)-based protein-protein interaction site identification method. In particular, we propose to apply a transformer structure-based dynamic word embedding model (ProtT5) to extract potential associations between protein primary structures, capturing their functional and structural properties from readily available sequence data alone. After that, EDLMPPI is based on BiLSTM in order to sufficiently learn the contextual associations between features and to preserve the contextual information through a capsule network to further improve the generalization performance. To address the unbalanced dataset, we employ ensemble learning to train multiple models and then integrate them to further enhance the performance of the algorithm. Evaluation results show that EDLMPPI can achieve the best results on all datasets. Meanwhile, we compared EDLMPPI with other PPI site prediction models and observed that EDLMPPI outperformed the state-of-the-art models by nearly 10% in terms of average accuracy. In addition, the biological and interpretable analyses provide new insights into proteins binding site identification and characterization mechanisms from different perspectives.
Determination of ciprofloxacin using the Ziziphus mauritania derived fluorescent carbon dots based optical sensor
Authors: Chaudhry Navneet , Verma Damini , Yadav Amit K , Sharma Jai Gopal , Solanki Pratima 
Published: July 2022

Abstract
The rapid determination and sensitive monitoring of antibiotics residues are critical challenges and highly essential for the protection of human and environment. Hence, in the present work, facile green synthesis of fluorescent carbon quantum dots (CDs) has been done using one step hydrothermal treatment of fruit exact of Ziziphus mauritiana for the first time, acting as natural source of carbon for optical determination of ciprofloxacin (CIP). These prepared CDs was used to selectively detect CIP, exhibiting high quantum yield of 30% at excitation wavelength of 340 nm. After the optimal parameters, the sensor gave the linear detection range from 20 to 100 µM along with limit of detection of 9.20 µM. The current work depicts the potential to effectively and rapidly determine other forthcoming environmental pollutants.
Zr isotopes reveal long storage timescales of Archean magmas
Authors: Li Zhen-Xin , Zhang Shao-Bing , Zheng Yong-Fei , Antonelli Michael , Zhang Wen , Zhang Liang , Sun Fang-Yuan , Liang Ting 
Published: July 2022

Abstract
The storage timescales and thermal states of magma during the Archean are important factors affecting the growth and evolution of the continental crust. However, few reliable estimates exist for these parameters in ancient magmatic systems. Here, we constrain Archean magma storage timescales by using in-situ Zr isotope (δ94Zr) measurements in zircon (3.4 to 2.5 Ga) paired with disequilibrium crystal growth models. Our calculations suggest that fractional crystallization of zircon at isotopic equilibrium leads to small δ94Zr variations (< 0.4‰), indicating that the observed variations (-0.6 to + 0.4‰) are likely caused by disequilibrium crystal growth. The extents of isotopic disequilibrium require zircon growth rates of 0.0007–0.0415 µm/yr, which in turn yield (minimum) magma storage timescales of 5-193 kyr. Combined with evidence for zircon crystallization at high temperatures (730–910 ℃), these long timescales imply protracted periods of “warm storage” for Archean magmas, in stark contrast with predominantly shorter “cold storage” conditions observed in modern systems. Our results serve as independent evidence for higher geothermal gradients throughout the Archean, and the unique magmatic systems have cascading implications for the growth/emergence of continental crust, volcanic activity, and evolution of the Archean atmosphere.
A chromosome-scale genome sequence of sudangrass (Sorghum sudanense) highlights the genome evolution and regulation of dhurrin biosynthesis
Authors: Li Jieqin , Wang Lihua , Bible Paul W. , Tu Wenmiao , Zheng Jian , Jin Peng , Liu Yanlong , Du Junli , Zheng Jiacheng , Wang Yi-Hong , Zhan Qiuwen 
Published: July 2022

Abstract
Sudangrass [ Sorghum sudanense (Piper) Stapf] is a hybrid between grain sorghum and its wild relative S. bicolor ssp. verticilliflorum and is grown as a forage crop due to its high biomass production and low dhurrin content compared to sorghum. In this study, we sequenced the sudangrass genome and showed that the assembled genome was 715.95 Mb with 35,243 protein-coding genes. Phylogenetic analysis with whole genome proteomes demonstrated that the sudangrass genome was more similar to US commercial sorghums than to its wild relatives and cultivated sorghums from Africa. We confirmed that at seedling stage, sudangrass accessions contained significantly lower dhurrin as measured by hydrocyanic acid potential (HCN-p) than cultivated sorghum accessions. Genome-wide association study identified a QTL most tightly associated with HCN-p and the linked SNPs were located in the 3’ UTR of Sobic.001G012300 which encodes CYP79A1, the enzyme that catalyzes the first step of dhurrin biosynthesis. As in other grasses such as maize and rice, we also found that copia/gypsy long terminal repeat retrotransposons were more abundant in cultivated than in wild sorghums, implying that crop domestication in the grasses was accompanied by increased copia/gypsy LTR retrotransposon insertions in the genomes.
Determination of Optimum Height/Width Ratios of Slender Buildings on Different Soils Against Overturning During Earthquakes
Authors: KALAYLI MEHMET ALİ , DOĞAN ORHAN , ÖZTÜRK BAKİ , YÖRÜBULUT SERAP , KOÇ HALE NUREFŞAN 
Published: July 2022

Abstract
In many parts of the world, it has been observed that many narrow-fronted and high (slender) buildings overturn in one piece without any structural damage during earthquakes. The reason for this overturning is the increase in relative story displacements and second-order moments due to the rotation of foundation which is known as differential settlement that will occur at the base of the building as a result of exceeding the soil bearing capacity and elastic bearing coefficient depending on the earthquake load. In this study, a reference building with the smallest H/B ratio of 1.80 among the buildings overturned in the 1999 Kocaeli earthquake in the Adapazarı city center was modeled together with the soil using the ETABS 18.1.1 program. The linear analysis of the building was carried out according to the finite element method for 20 different soils and earthquake zones, with the approach that the ground does not resist tension. In order to stay on the safe side, considering the peak displacements for the H/B ratio of 1.50, the H/B ratios against overturning depending on the K of the soil and the PGA of the earthquake were determined with 99% regression for 20 different conditions, and a reasonable linear correlation was also obtained.
Mobilization of Monocytic Myeloid-Derived Suppressor Cells is Regulated by PTH1R Activation in Bone Marrow Stromal Cells
Authors: Park Serk In , Lee Kyoung Jin , Lee Eun Jung , Jung Seungpil , Park Kyong Hwa 
Published: July 2022

Abstract
Myeloid-derived suppressor cells (MDSC) originate in the bone marrow and suppress anti-tumoral T cells in the tumor microenvironment (TME). Contrary to the critical functions and regulation in the TME, mechanism of MDSC mobilization from the bone marrow remains unclear. We have previously reported that tumor-derived parathyroid hormone-related peptide (PTHrP) levels correlate with MDSC. Because PTHrP is a potent osteoblast-stimulating factor, we hypothesized that PTHrP regulates MDSC in the bone marrow via osteoblasts. Continuous infusion of PTHrP (amino acids 1–34, a receptor-binding fragment) in mice increased monocytic subtype MDSC (M-MDSC), but not granulocytic MDSC (G-MDSC) in the circulation. M-MDSC was mobilized by PTHrP(1–34) or PTH(1–34), both functional ligands of PTH1R, but not by hematopoietic mobilizing agents, AMD-3100 or GM-CSF, suggesting that activation of osteoblasts is essential to M-MDSC mobilization. Subsequently, our in vitro cell binding assays demonstrated that α4β1 integrin and vascular cell adhesion molecule (VCAM)-1, expressed on M-MDSC and osteoblasts, respectively, are key to M-MDSC binding to osteoblasts. Neutralizing antibodies to VCAM-1 or β1 integrin suppressed M-MDSC binding to osteoblasts. PTH1R activation increased VEGF-A and interleukin-6 expression in osteoblast, leading to activation of Src family kinase in M-MDSCs. Indeed, Src inhibitors suppressed PTHrP-induced MDSC release in vitro and in vivo. Furthermore, activation of Src in M-MDSC increased expression of two proteases, ADAM-17 and MMP7, leading to VCAM-1 shedding and subsequent disruption of M-MDSC tethering to osteoblasts. Collectively, tumor-derived PTHrP stimulates osteoblasts via PTH1R, leading to cytokine expression in osteoblasts and Src-dependent expression of ADAM-17 and MMP-7, leading to M-MDSC mobilization.
The incidence and risk factors of meconium amniotic fluid in singleton pregnancies: An experience of a tertiary hospital in Iran
Authors: Shekari Mitra , Jahromi Malihe Shirzadfard , Ranjbar Amene , Mehrnoush Vahid , Darsareh Fatemeh , Roozbeh Nsibeh 
Published: July 2022

Abstract
Background: Several common maternal or neonatal risk factors have been linked to MAF development; however, the results were contradictory, depending on the study. This study aimed to assess the prevalence and risk factors of MAF in singleton pregnancies.Methods: We retrospectively assessed singleton pregnant mothers who gave birth at Khaleej-e-Fars Hospital (a tertiary hospital) in Bandar Abbas, Iran, between January 1st, 2020, and January 1st, 2022. Mothers were divided into two groups: 1) those diagnosed with meconium amniotic fluid and 2) those diagnosed with clear amniotic fluid. Mothers with bloody amniotic fluid were excluded. Demographic factors (age, educational level, residency place, medical insurance, access to prenatal care facilities, smoking status), obstetrical factors (gestational age, parity, newborn sex, oligohydramnios, preeclampsia, gestational diabetes mellitus (GDM), abnormal placentation, placenta abruption, chorioamnionitis, intrauterine growth restriction (IUGR), and intrauterine fetal death (IUFD)) and maternal comorbidities (overt diabetes mellitus, chronic hypertension, cardiovascular disease, thyroid dysfunction, drug addiction, hepatitis, anemia, infertility, and COVID-19 at the time of admission) were extracted from electronic data of each mother. The Chi-square test was used to compare differences between the groups for categorical variables. Logistic regression models were used to assess meconium amniotic fluid risk factors.Results: Of 8888 singleton deliveries during the study period, 1085 (12.2%) were MAF. MAF was more common in adolescents, mothers with post-term pregnancy, and primiparous mothers, and it was less common in mothers with GDM and overt diabetes. The odds of having MAF in adolescents were three times more than mothers of 20-34 years old (aOR: 3.07, 95%CI: 1.87–4.98). Likewise, the odds of the presence of MAF in mothers with post-date pregnancy (40+1-41 weeks) were (aOR: 5.12, 95%CI: 2.76–8.94), and mothers with post-term pregnancy (more than 41 weeks) were (aOR: 7.09, 95%CI: 3.92–9.80). Primiparous women were also more likely than multiparous mothers to have MAF (aOR: 3.41, 95%CI: 2.11–4.99).Conclusions: Adolescents, primiparous mothers, and mothers with post-term pregnancies had a higher risk of MAF. Maternal comorbidities resulting in early termination of pregnancy can reduce the incidence of MAF.
Therapeutic efficacy of dose-reduced adjuvant chemotherapy with S-1 in patients with pancreatic cancer: a retrospective study
Authors: Kobayashi Kazuki , Einama Takahiro , Takihata Yasuhiro , Yonamine Naoto , Fujinuma Ibuki , Tsunenari Takazumi , Kouzu Keita , Nakazawa Akiko , Iwasaki Toshimitsu , Ueno Hideki , Kishi Yoji 
Published: July 2022

Abstract
BackgroundS-1 adjuvant chemotherapy is the standard treatment for resectable pancreatic ductal adenocarcinoma. The relative dose intensity of adjuvant chemotherapy influences survival in pancreatic cancer, but does not precisely reflect treatment schedule modifications. We investigated the effects of total dose intensity of S-1 adjuvant chemotherapy on the survival of patients with pancreatic cancer and the permissible dose reduction.MethodsWe enrolled patients who underwent surgical resection between 2011 and 2019 for pancreatic cancer. We determined the total dose intensity cut-off value that predicted tumor recurrence within 2 years post-operatively using receiver operating characteristic curves, and compared the outcomes between the high and low total dose intensity groups.ResultsPatients with a total dose intensity ≥62.5% (n = 53) showed significantly better overall survival than those with a total dose intensity <62.5% (n = 16) (median survival time: 53.3 vs. 20.2 months, P <0.001). The median survival of patients without adjuvant chemotherapy (total dose intensity = 0, n = 28) was 24.8 months. Univariate analysis identified lymphatic involvement (P = 0.035), lymph node metastasis (P = 0.034), and total dose intensity (P <0.001) as significant factors associated with survival. In a multivariate analysis, total dose intensity (P <0.001) was an independent predictor of worse survival.ConclusionsMaintaining a total dose intensity of at least 60% in S-1 adjuvant chemotherapy is important in achieving favorable long-term post-operative survival in patients with pancreatic cancer.