bluuebunny/crossref_metadata_2025_split huggingface dataset:
The role of endometrial thickness in predicting ectopic pregnancy after in vitro fertilization and the establishment of a prediction model
Authors: Liu Jing , Kong Hongjiao , Yu Xiaona , Zhou Mengge , Liu Xiaoyang , Liu Xinmi , Zhang Jianrui , Liu Yanli , Wu Shanshan , Guan Yichun 
Published: September 2022

ObjectiveTo explore the risk factors of ectopic pregnancy after in vitro fertilization.MethodsThis retrospective cohort study was conducted at the Reproductive Medical Center of the Third Affiliated Hospital of Zhengzhou University from January 2016 to April 2020. Univariate and multivariate analysis were used to analyze the related factors affecting the occurrence of ectopic pregnancy (EP) and to construct a nomographic prediction model for the incidence of ectopic pregnancy.ResultsA total of 12,766 cycles of 10109 patients were included, comprising 214 cases of EP and 12,552 cases of intrauterine pregnancy (IUP). Multivariate logistic regression analysis showed that the tubal factor was associated with a 2-fold increased risk for EP (aOR = 2.72, 95% CI: 1.69-4.39, P &lt; 0.0001). A stratified analysis showed that women with an endometrial thickness (EMT) between 7.6 to 12.1mm (aOR = 0.57, 95%CI: 0.36-0.90, P = 0.0153) and &gt;12.1mm (aOR = 0.42, 95%CI: 0.24-0.74, P = 0.0026) had a significant reduction of the risk of EP compared to women with an EMT of &lt;7.6mm. Compared to cleavage stage transfer, blastocyst transfer can reduce the risk of ectopic pregnancy (aOR = 0.36, 95%CI: 0.26-0.50, P &lt; 0.0001). The saturation model (full mode) establishes a nomographic prediction model with an AUC = 0.68 and a sensitivity and specificity of 0.67and 0.64, respectively. The nomination model was internally verified by self-sampling method (bootstrap sampling resampling times = 500). The resulting AUC = 0.68 (sensitivity: 0.65; specificity: 0.65) showed that the model was relatively stable.ConclusionsOur findings indicate that EMT is inversely proportional to the risk of EP. Embryo stage, number of embryos transferred were also significantly associated with EP rate. A simple nomogram for the predicting the risk of EP was established in order to reduce the occurrence of EP.
Recovery of soil microbial diversity and functions along a tropical montane forest disturbance gradient
Authors: Sniegocki Renee , Moon Jessica B. , Rutrough Abigail L. , Gireneus Jude , Seelan Jaya Seelan Sathiya , Farmer Michael C. , Weindorf David C. , Naithani Kusum 
Published: September 2022

Logging and forest conversion are occurring at alarming rates in tropical forests. These disturbances alter soil microbial community structure and functions. While direct links between changes in soil properties, such as pH and microbial community structure are well established, the indirect effects of logging and forest conversion on soil microbial community structure and functions are poorly understood. We used a space-for-time substitution to investigate the changes in soil microbial diversity and functions across a forest recovery gradient in the tropical montane forests of northern Borneo. We used surface (top 5 cm) soil to assess soil physicochemical and microbial (next-generation DNA sequencing) properties, and standardized litterbags (Tea Bag Index) to assess litter decomposition and stabilization. Our results show that bacterial and fungal diversity increases with recovery time and reaches pre-disturbance levels between 60- and 80-years post-disturbance. Litter decomposition rate constants increased linearly with increasing bacterial and fungal diversity. Litter stabilization also increased linearly with fungal diversity, but was highest at intermediate levels of bacterial diversity. Our results provide insights on the effects of forest logging and conversion on soils and highlight the tight coupling between soil microbial diversity and soil functions in tropical montane forests.
Urban stream rehabilitation in a densely populated Brazilian metropolis
Authors: Macedo Diego R. , Callisto Marcos , Linares Marden S. , Hughes Robert M. , Romano Bruna M. L. , Rothe-Neves Moana , Silveira Juliana S. 
Published: September 2022

Environmental rehabilitation of urban streams has been widely applied in Global North countries, at least since the 1970s, but it is a recent approach in Global South countries. The objective of this paper is to evaluate whether the rehabilitation experience carried out since 2006 in three urban stream sites in the third-largest Brazilian metropolis (c. 5.5 million inhabitants) was and continues to be effective in terms of socio-environmental improvement after 10 years of interventions. These interventions included the rehabilitation of watercourses (e.g., improvement of water quality through the management of sewage and garbage, stabilization of riverbanks, revegetation of riparian zones, riverbed naturalization, removal of riverbank housing). We evaluated water quality, physical habitat structure, and benthic macroinvertebrate assemblages in three test sites in three sampling periods: pre-intervention (2004–2005), early post-intervention (2008–2011) and late post-intervention (2018–2019). Additionally, three reference-stream sites (2018–2019) were assessed to compare the conditions of the three tested sites versus the reference sites. We also assessed citizen perceptions concerning the interventions through questionnaires given to urban stream residents at the three tested sites in early and late post-rehabilitation (215 in 2008, 180 in 2019). The results of water quality monitoring showed a significant improvement in most parameters used to calculate the Water Quality Index (WQI) in the early intervention phase, and WQI scores have improved since. The physical habitat and macroinvertebrate indicators indicated moderate improvements. The residents indicated increased appreciation of the environmental improvements over 10 years. Given the results in Belo Horizonte, we believe that implementation and evaluation of similar projects and programs aimed at rehabilitating urban streams are technically viable using our approaches throughout the Global South.
Does phosphogypsum application affect salts, nutrients, and trace elements displacement from saline soils?
Authors: Outbakat M Barka , Choukr-Allah Redouane , EL Gharous Mohamed , EL Omari Kamal , Soulaimani Aziz , EL Mejahed Khalil 
Published: September 2022

Salinity and sodicity are the most agricultural challenges in arid and semi-arid regions. A pot experiment was undertaken, to evaluate the effect of Phosphogypsum (PG) and Gypsum (G), to remove salts, nutrients and trace elements in leached water from saline and saline-sodic soils. In order to determine the efficiency and safety of these amendments, as an affordable strategy, for overcoming salinity and sodicity stress. The PG at 0, 15, 30 and 45 t/ha and G at 15 t/ha were mixed with the upper 9 cm soil in the pot before being leached. The soils were collected from Sed El Masjoune and Sidi El Mokhtar areas of morocco with ECe of 140.6 mS/cm and 11.7 mS/cm respectively. The highest doses of PG (≥30 t/ha) removed significant amount of salts and nutrients. Calcium sulfate supplies calcium ions to replace salt ions (sodium, especially). The replaced salts are leached from the soil. The PG was more efficient compared to G in terms of salts leaching. Quantities of trace elements in the leachate, for most analyzed elements, were below the recommended limits of drinking and irrigation water. Because the experiment’s alkaline conditions (basic water and soil) reduce the solubility and mobility of trace elements. The amendment application did not affect saturation index (SI) of the main minerals. However, water passing through the soil increased the SI. which could result in groundwater mineral precipitation.
Ectodermal dysplasias: New perspectives on the treatment of so far immedicable genetic disorders
Authors: Schneider Holm 
Published: September 2022

The past decade has witnessed an expansion of molecular approaches facilitating the differential diagnosis of ectodermal dysplasias, a group of genetic diseases characterized by the lack or malformation of hair, teeth, nails, and certain eccrine glands. Moreover, advances in translational research have increased the therapeutic opportunities for such rare diseases, and new dental, surgical, and ophthalmic treatment options are likely to offer relief to many individuals affected by ectodermal dysplasias. In X-linked hypohidrotic ectodermal dysplasia (XLHED), the genetic deficiency of the signaling molecule ectodysplasin A1 (EDA1) may even be overcome before birth by administration of a recombinant replacement protein. This has been shown at least for the key problem of male subjects with XLHED, the nearly complete absence of sweat glands and perspiration which can lead to life-threatening hyperthermia. Prenatal treatment of six boys by injection of an EDA1 replacement protein into the amniotic fluid consistently induced the development of functional sweat glands. Normal ability to sweat has so far persisted for &gt;5 years in the two oldest boys treated in utero. Thus, timely replacement of a missing protein appears to be a promising therapeutic strategy for the most frequent ectodermal dysplasia and possibly additional congenital disorders.
Comprehensive analysis and validation of novel immune and vascular remodeling related genes signature associated with drug interactions in pulmonary arterial hypertension
Authors: Wang Jie , Uddin Md. Nazim , Wang Rui , Gong Yue-hong , Wu Yun 
Published: September 2022

Background: Previous studies revealed that the gene signatures are associated with the modulation and pathogenesis of pulmonary arterial hypertension (PAH). However, identifying critical transcriptional signatures in the blood of PAH patients remains lacking.Methods: The differentially expressed transcriptional signatures in the blood of PAH patients were identified by a meta-analysis from four microarray datasets. Then we investigated the enrichment of gene ontology and KEGG pathways and identified top hub genes. Besides, we investigated the correlation of crucial hub genes with immune infiltrations, hallmark gene sets, and blood vessel remodeling genes. Furthermore, we investigated the diagnostic efficacy of essential hub genes and their expression validation in an independent cohort of PAH, and we validate the expression level of hub genes in monocrotaline (MCT) induced PAH rats’ model. Finally, we have identified the FDA-approved drugs that target the hub genes and their molecular docking.Results: We found 1,216 differentially expressed genes (DEGs), including 521 up-regulated and 695 down-regulated genes, in the blood of the PAH patients. The up-regulated DEGs are significantly associated with the enrichment of KEGG pathways mainly involved with immune regulation, cellular signaling, and metabolisms. We identified 13 master transcriptional regulators targeting the dysregulated genes in PAH. The STRING-based investigation identified the function of hub genes associated with multiple immune-related pathways in PAH. The expression levels of RPS27A, MAPK1, STAT1, RPS6, FBL, RPS3, RPS2, and GART are positively correlated with ssGSEA scores of various immune cells as positively correlated with the hallmark of oxidative stress. Besides, we found that these hub genes also regulate the vascular remodeling in PAH. Furthermore, the expression levels of identified hub genes showed good diagnostic efficacy in the blood of PAH, and we validated most of the hub genes are consistently dysregulated in an independent PAH cohort. Validation of hub genes expression level in the monocrotaline (MCT)-induced lung tissue of rats with PAH revealed that 5 screened hub genes (MAPK1, STAT1, TLR4, TLR2, GART) are significantly highly expressed in PAH rats, and 4 screened hub genes (RPS6, FBL, RPS3, and RPS2) are substantially lowly expressed in rats with PAH. Finally, we analyzed the interaction of hub proteins and FDA-approved drugs and revealed their molecular docking, and the results showed that MAPK1, TLR4, and GART interact with various drugs with appropriate binding affinity.Conclusion: The identified blood-derived key transcriptional signatures significantly correlate with immune infiltrations, hypoxia, glycolysis, and blood vessel remodeling genes. These findings may provide new insight into the diagnosis and treatment of PAH patients.
Development and validation of a novel cellular senescence-related prognostic signature for predicting the survival and immune landscape in hepatocellular carcinoma
Authors: Sun Rui , Wang Xu , Chen Jiajie , Teng Da , Chan Shixin , Tu Xucan , Wang Zhenglin , Zuo Xiaomin , Wei Xiang , Lin Li , Zhang Qing , Zhang Xiaomin , Tang Kechao , Zhang Huabing , Chen Wei 
Published: September 2022

Background: Cellular senescence is a typical irreversible form of life stagnation, and recent studies have suggested that long non-coding ribonucleic acids (lncRNA) regulate the occurrence and development of various tumors. In the present study, we attempted to construct a novel signature for predicting the survival of patients with hepatocellular carcinoma (HCC) and the associated immune landscape based on senescence-related (sr) lncRNAs.Method: Expression profiles of srlncRNAs in 424 patients with HCC were retrieved from The Cancer Genome Atlas database. Lasso and Cox regression analyses were performed to identify differentially expressed lncRNAs related to senescence. The prediction efficiency of the signature was checked using a receiver operating characteristic (ROC) curve, Kaplan–Meier analysis, Cox regression analyses, nomogram, and calibration. The risk groups of the gene set enrichment analysis, immune analysis, and prediction of the half-maximal inhibitory concentration (IC50) were also analyzed. Quantitative real-time polymerase chain reaction (qPCR) was used to confirm the levels of AC026412.3, AL451069.3, and AL031985.3 in normal hepatic and HCC cell lines.Results: We identified 3 srlncRNAs (AC026412.3, AL451069.3, and AL031985.3) and constructed a new risk model. The results of the ROC curve and Kaplan–Meier analysis suggested that it was concordant with the prediction. Furthermore, a nomogram model was constructed to accurately predict patient prognosis. The risk score also correlated with immune cell infiltration status, immune checkpoint expression, and chemosensitivity. The results of qPCR revealed that AC026412.3 and AL451069.3 were significantly upregulated in hepatoma cell lines.Conclusion: The novel srlncRNA (AC026412.3, AL451069.3, and AL031985.3) signatures may provide insights into new therapies and prognosis predictions for patients with HCC.
Construction and validation of BRAF mutation diagnostic model based on ultrasound examination and clinical features of patients with thyroid nodules
Authors: Xu Chan , Fang Jianqiang , Li Wanying , Sun Chenyu , Li Yaru , Lowe Scott , Bentley Rachel , Chen Shuya , He Cunyu , Li Xinxin , Wang Bing , Yin Chengliang , Li Wenxian , Li Wenle 
Published: September 2022

Introduction: Fine Needle Aspiration (FNA) is currently the most popular method for identifying benign and malignant thyroid nodules. However, its diagnostic sensitivity is sometimes limited, which makes it necessary to apply genetic testing and other modalities as a secondary diagnostic method. The diagnostic accuracy of thyroid nodule can be improved by combining mutations in the B-Raf proto-oncogene serine/threonine kinase (BRAF) with FNA. Thus, this study was conducted to create a nomogram diagnostic model based on the clinical and ultrasonic characteristics of patients with BRAF mutations to aid in the identification of benign and malignant thyroid nodules using FNA.Methods: From April 2018 to December 2021, 275 patients with thyroid nodules who underwent ultrasonography and BRAF gene testing (137 positive and 138 negative) were included from Xianyang Central Hospital. The clinical and ultrasonic characteristics of the patients were used to develop a nomographic, diagnostic model of BRAF gene mutation, and to validate and evaluate the usefulness of the model.Results: Independent risk factors for BRAF mutations included: focal strong echogenicity (microcalcifications, OR = 3.04, 95%CI = 1.41–6.58, p = 0.005), hypoechogenicity (OR = 3.8, 95%CI = 1.14–12.61, p = 0.029), lymph node metastases (OR = 3.54, 95%CI = 1.43–8.75, p = 0.006), margin (lobulated, OR = 3.7, 95%CI = 1.66–8.23, p = 0.001; extrathyroidal invasion, OR = 2.81, 95%CI = 1.11–7.06, p = 0.029), and shape (vertical position, OR = 2.7, 95%CI = 1.11–6.59, p = 0.029). The area under the curve (AUC) of the receiver operating characteristic (ROC) curve of the BRAF mutation diagnostic model constructed on these factors was 0.806 (95% CI = 0.754–0.851), and 39.5% was set as the threshold probability of making a clinical decision. The results of the validation and clinical utility evaluation showed that our model had good predictive performance and clinical application value.Conclusion: Our nomogram diagnostic model based on clinical and ultrasound features of patients accurately predicted the possibility of BRAF gene mutations in patients with thyroid nodules.
Breakthrough infections with the omicron and delta variants of SARS-CoV-2 result in similar re-activation of vaccine-induced immunity
Authors: Søraas Arne , Grødeland Gunnveig , Granerud Beathe Kiland , Ueland Thor , Lind Andreas , Fevang Børre , Murphy Sarah L. , Huse Camilla , Nygaard Anders Benteson , Steffensen Anne Katrine , al-Baldawi Huda , Holberg-Petersen Mona , Andresen Lise Lima , Ågnes Camilla , Ranheim Trine , Schanke Ylva , Istre Mette , Dahl John Arne , Chopra Adity , Dudman Susanne , Kaarbø Mari , Andersen Jan Terje , Vaage Eline Benno , Tran Trung The , Vaage John Torgils , Michelsen Annika E. , Müller Fredrik , Aukrust Pål , Halvorsen Bente , Dahl Tuva B. , Holter Jan Cato , Lund-Johansen Fridtjof 
Published: September 2022

BackgroundResults showing that sera from double vaccinated individuals have minimal neutralizing activity against Omicron have been interpreted as indicating the need for a third vaccine dose for protection. However, there is little information about early immune responses to Omicron infection in double vaccinated individuals.MethodsWe measured inflammatory mediators, antibodies to the SARS-CoV-2 spike and nucleocapsid proteins, and spike peptide-induced release of interferon gamma in whole blood in 51 double-vaccinated individuals infected with Omicron, in 14 infected with Delta, and in 18 healthy controls. The median time points for the first and second samples were 7 and 14 days after symptom onset, respectively.FindingsInfection with Omicron or Delta led to a rapid and similar increase in antibodies to the receptor-binding domain (RBD) of Omicron protein and spike peptide-induced interferon gamma in whole blood. Both the Omicron- and the Delta-infected patients had a mild and transient increase in inflammatory parameters.InterpretationThe results suggest that two vaccine doses are sufficient to mount a rapid and potent immune response upon infection in healthy individuals of with the Omicron variant.FundingThe study was funded by the Oslo University Hospital, and by grants from The Coalition for Epidemic Preparedness Innovations, Research Council of Norway (no 312780, 324272), South-Eastern Norway Regional Health Authority (no 2019067, 2021071, 10357, 2021047, 33612, 2021087, 2017092), EU Horizon 2020 grant no 848099, a philantropic donation from Vivaldi Invest A/S, and The European Virus Archive Global.
IL27 gene expression distinguishes multisystem inflammatory syndrome in children from febrile illness in a South African cohort
Authors: Spracklen Timothy F. , Mendelsohn Simon C. , Butters Claire , Facey-Thomas Heidi , Stander Raphaella , Abrahams Debbie , Erasmus Mzwandile , Baguma Richard , Day Jonathan , Scott Christiaan , Zühlke Liesl J. , Kassiotis George , Scriba Thomas J. , Webb Kate 
Published: September 2022

IntroductionMultisystem inflammatory syndrome in children (MIS-C) is a severe acute inflammatory reaction to SARS-CoV-2 infection in children. There is a lack of data describing differential expression of immune genes in MIS-C compared to healthy children or those with other inflammatory conditions and how expression changes over time. In this study, we investigated expression of immune-related genes in South African MIS-C patients and controls.MethodsThe cohort included 30 pre-treatment MIS-C cases and 54 healthy non-inflammatory paediatric controls. Other controls included 34 patients with juvenile systemic lupus erythematosus, Kawasaki disease or other inflammatory conditions. Longitudinal post-treatment MIS-C specimens were available at various timepoints. Expression of 80 immune-related genes was determined by real-time quantitative PCR.ResultsA total of 29 differentially expressed genes were identified in pre-treatment MIS-C compared to healthy controls. Up-regulated genes were found to be overrepresented in innate immune pathways including interleukin-1 processing and pyroptosis. Post-treatment follow-up data were available for up to 1,200 hours after first treatment. All down-regulated genes and 17/18 up-regulated genes resolved to normal levels in the timeframe, and all patients clinically recovered. When comparing MIS-C to other febrile conditions, only IL27 expression could differentiate these two groups with high sensitivity and specificity.ConclusionsThese data indicate a unique 29-gene signature of MIS-C in South African children. The up-regulation of interleukin-1 and pyroptosis pathway genes highlights the role of the innate immune system in MIS-C. IL-27 is a potent anti-inflammatory and antiviral cytokine that may distinguish MIS-C from other conditions in our setting.