bluuebunny/crossref_metadata_2025_split huggingface dataset:
High alkaline phosphatase and low intact parathyroid hormone associate with worse clinical outcome in peritoneal dialysis patients
Authors: Chen Zhimin , Zhang Xiaohui , Han Fei , Xie Xishao , Hua Zhou , Huang Xiaohan , Lindholm Bengt , Haarhaus Mathias , Stenvinkel Peter , Qureshi Abdul Rashid , Chen Jianghua 
Published: May 2020

Objective: Alkaline phosphatase (ALP) is used as a biomarker to monitor the chronic kidney disease–mineral bone disorder (CKD-MBD) and high levels of parathyroid hormone (PTH) that were reported to be related to increased mortality in CKD patients. Therefore, we conducted this longitudinal cohort study to evaluate the relations between ALP and intact PTH (iPTH) and the associations with all-cause and cardiovascular mortality in peritoneal dialysis (PD) patients. Methods: In 1276 incident PD patients (median age 50 years, 56% males), baseline serum ALP, iPTH, and metabolic biomarkers potentially linked to CKD-MBD were analyzed in relation to mortality during follow-up period of up to 60 months. All-cause and cardiovascular mortality risk of ALP and iPTH were analyzed with competing-risks regression models with transplantation as competing risk adjusting for all covariates. Results: After adjustments for confounders by logistic regression model, older age, higher change level to levels of iPTH, S-albumin, calcium, alanine transaminase (ALT), and lower level of phosphorus were associated with higher ALP level (>79 U/L), and female gender, non-diabetes mellitus, younger age, lower calcium, higher ALT, total bilirubin, phosphorus, and ALP were associated with higher iPTH level (>300 pg/mL). During 60 months (median 44 months) of follow-up, the all-cause mortality rate was 16%, and 91 (46%) of the 199 deaths were caused by cardiovascular disease. In competing-risks regression analysis, “high ALP + low iPTH” was independently associated with all-cause and cardiovascular mortality after adjustment for age, gender, presence of diabetes, and cardiovascular disease, the calendar year of recruitment and vitamin D therapy in PD patients. The subhazard ratio (sHR) of group “high ALP + low iPTH” was 1.96 times and 3.35 times higher than sHR of group “low ALP + high iPTH” for all-cause mortality and cardiovascular mortality, respectively. Conclusions: The combination of high ALP and low iPTH was independently associated with increased all-cause and cardiovascular mortality in PD patients, suggesting that ALP and iPTH have the potential to predict clinical outcomes and might be useful risk assessment tools in PD patients. Further studies exploring the observed association between combination of ALP with iPTH and mortality are warranted.
Oral manifestations associated with antimalarial therapy in patients with systemic lupus erythematosus
Authors: Chacón-Dulcey Verónica , López-Labady Jeaneth , Villarroel-Dorrego Mariana , Frías Jennifer , Tirado Wirman , González Nieves , Pérez Alfonzo Ricardo 
Published: May 2020

Introduction Lupus erythematosus (LE) is an autoimmune disease often treated with antimalarial drugs. The prolonged use of chloroquine and hydroxychloroquine can cause hyperpigmentation in the skin, oral mucosa and retinal pigment epithelium, which in turn can trigger toxicity in this epithelium, which in some cases causes vision loss. The objective of the present work was to establish the association between the presence of oral pigmented macules by antimalarial and secondary retinal toxicity. Methods A total of 105 patients diagnosed with LE being treated with chloroquine/hydroxychloroquine were evaluated. All patients were ophthalmologically evaluated for retinopathy screening. When the patient showed oral hyperpigmented maculae, an incisional biopsy was performed with the corresponding histopathological study with informed consent. The variables were compared using the chi-square test for quantitative variables and the non-parametric Mann–Whitney U-test for categorical variables. The confidence level was established at 95%, and p-values of ≤0.005 were considered statistically significant. Results Only 9.5% of the patients showed oral brown spots. Histopathologically, 100% of the oral macules showed characteristics of oral pigmentation by drug and 100% ophthalmological parameters of normality. Two patients presented with a diagnosis of pre-retinopathy, but none showed oral lesions. Conclusion Hyperpigmented macules in the buccal mucosa in lupus patients receiving antimalarial treatment are not frequent and do not represent a predictive finding of toxicity of the drug.
Understanding why healthcare workers refuse the flu vaccine
Authors: Ferragut Mariano Jose , Barry Deborah , Cummins Martina 
Published: May 2020

Background: Vaccination is one of the most effective interventions used to reduce infections. Nonetheless, concerns and misconceptions about vaccines have resulted in an increased rate of refusal of vaccination among healthcare workers (HCWs) and within the general population. Aim/ Objective: To understand the factors that underlie vaccination-refusal. Methods: A questionnaire was given to the HCWs in the inpatient area of an acute London hospital during May 2019. The sample was one of convenience, i.e. the wards where the principle investigator covered. All staff were approached: 306 in total completed the questionnaire. Findings/results: In total, 212 (69.28%) healthcare professionals had the flu vaccine during the 2018–2019 campaign, 94 (30.62%) did not have the flu vaccine and 37 (39.36%) of the HCWs that did not receive the flu vaccine reported they had previously a bad reaction following administration of the vaccine. Discussion: This report will provide the Trust and other healthcare settings with information integrating the disconnection between misconceptions and vaccination knowledge, which may inform practical interventions to address the challenges of vaccination in future campaigns. Increasing HCWs’ knowledge of flu vaccine side effects could address this and may increase rates of vaccination compliance.
Spatial clusters and temporal trends of malignant melanoma mortality in Ecuador
Authors: Núñez-González Solange , Bedoya Estefania , Simancas-Racines Daniel , Gault Christopher 
Published: May 2020

Objective: The aim of this study is two fold. First, it describes the temporal trends of malignant melanoma mortality from 2000 to 2016 in Ecuador. Second, it analyzes the spatial clusters of high mortality rates due to malignant melanoma in the country, from 2011 to 2016. Methods: This is an ecological study; we included all death certificates of malignant melanoma from the National Institute of Statistics and Census database in Ecuador from 2000 to 2016. We calculated crude mortality rates and age-standardized mortality rates, all rates are expressed as deaths per 100,000 population. In order to assess the trend of malignant melanoma rates, we obtained average annual percent changes through Joinpoint regression analysis. Spatial scan statistics were used to identify high-risk clusters and the spatial autocorrelation was evaluated through a global Moran index. Results: In Ecuador, between 2000 and 2016, malignant melanoma caused a total of 958 deaths. Crude mortality rates increased significantly (annual percent change = 4.8%; 95% confidence interval: 2.6–7.0), the age-standardized mortality rate also increased (annual percent change: 2.9%; 95% confidence interval: 0.5–5.4). The most likely cluster included 19 cantons and the second most likely cluster included 10 cantons, located in the Highlands region. The Global Moran I index for the study period shows a positive spatial autocorrelation (0.32; p = 0.001). Conclusion: Mortality due to malignant melanoma in Ecuador significantly increased over the 17-year study period; the spatial analysis and spatial autocorrelation indicates the presence of high-risk occurrence clusters in the Highlands region of the country.
Significant Loss of ACL Graft Force With Tibial-Sided Soft Tissue Interference Screw Fixation Over 24 Hours: A Biomechanical Study
Authors: Kruppa Philipp , Flies Anne , Wulsten Dag , Collette Robert , Duda Georg N. , Schaser Klaus-Dieter , Becker Roland , Kopf Sebastian 
Published: May 2020

Background: Tibial-sided graft fixation is thought to be critical for the success of anterior cruciate ligament (ACL) reconstruction. Nevertheless, little is known about the graft force after fixation during the first 24 hours after surgery or the influence of screw diameter and length during this time. Purpose: To investigate the force, over the course of 24 hours, in soft tissue grafts secured with a tibial interference screw and to evaluate the effect of different screw diameters (7, 8, and 9 mm) and lengths (25 and 30 mm) on the force in these grafts. Study Design: Controlled laboratory study. Methods: Quadruple-strand flexor tendon grafts were fixed with bioabsorbable interference screws in 60 porcine tibiae. Grafts were pretensioned at 80 N over 10 minutes, and screws were inserted outside-in while a preload force of 80 N was applied. Different screw lengths (25 and 30 mm) and diameters (7, 8, and 9 mm), resulting in 6 groups with 10 specimens each, were tested. After release of the preload, graft force was recorded over 24 hours. Results: A significant decrease in graft force progressed in all groups over the 24-hour period. In total, a median loss of 75 N (IQR, 68-79 N) compared with the initial loading force was observed. Compared with the loading force of 80 N, this corresponded to a median loss of 91%. No significant differences in the remaining graft force could be found among the 6 different screw length and diameter groups after 10 minutes, 100 minutes, or 24 hours. Conclusion: Graft force in soft tissue grafts secured with a tibial interference screw decreased substantially over the first 24 hours after fixation. Neither the screw diameter nor the screw length affected the decrease in graft force. This raises substantial questions regarding the remaining fixation strength in vivo. Clinical Relevance: It should not be expected that ACL reconstruction can mechanically restabilize an injured knee as would an intact ACL. Reconstructed knees should be protected from mechanical overload in the early postoperative period.
Induction of blood-circulating bile acids supports recovery from myelosuppressive chemotherapy
Authors: Sigurdsson Valgardur , Haga Youichi , Takei Hajime , Mansell Els , Okamatsu-Haga Chizuko , Suzuki Mitsuyoshi , Radulovic Visnja , van der Garde Mark , Koide Shuhei , Soboleva Svetlana , Gåfvels Mats , Nittono Hiroshi , Ohara Akira , Miharada Kenichi 
Published: May 2020

AbstractChemotherapeutic agents can reduce bone marrow (BM) activity, causing myelosuppression, a common life-threatening complication of cancer treatment. It is challenging to predict the patients in whom prolonged myelosuppression will occur, resulting in a delay or discontinuation of the treatment protocol. An early indicator of recovery from myelosuppression would thus be highly beneficial in clinical settings. In this study, bile acids (BAs) were highly increased in the systemic circulation as a natural response during recovery from myelosuppression, supporting regeneration of BM cells. BA levels in the blood of pediatric cancer patients and mice treated with chemotherapeutic agents were increased, in synchrony with early proliferation of BM cells and recovery from myelosuppression. In a mouse model of altered BA composition, Cyp8b1 knockout mice, a subset of mice recovered poorly after chemotherapy. The poor recovery correlated with low levels and changes in composition of BAs in the liver and systemic circulation. Conversely, BA supplementation in chemotherapy-treated wild-type mice resulted in significantly improved recovery. The results suggest that part of the mechanism by which BAs support recovery is the suppression of endoplasmic reticulum stress pathways in expanding and recovering hematopoietic cells. The findings propose a novel role of BAs as early markers of recovery and active components of the recovery process after chemotherapy.
Strain Engineering on the Electronic and Optical Properties of WSSe Bilayer
Authors: Guo Jian , Ke Congming , Wu Yaping , Kang Junyong 
Published: May 2020

AbstractControllable optical properties are important for optoelectronic applications. Based on the unique properties and potential applications of two-dimensional Janus WSSe, we systematically investigate the strain-modulated electronic and optical properties of WSSe bilayer through the first-principle calculations. The preferred stacking configurations and chalcogen orders are determined by the binding energies. The bandgap of all the stable structures are found sensitive to the external stress and could be tailored from semiconductor to metallicity under appropriate compressive strains. Atomic orbital projected energy bands reveal a positive correlation between the degeneracy and the structural symmetry, which explains the bandgap evolutions. Dipole transition preference is tuned by the biaxial strain. A controllable transformation between anisotropic and isotropic optical properties is achieved under an around − 6%~− 4% critical strain. The strain controllable electronic and optical properties of the WSSe bilayer may open up an important path for exploring next-generation optoelectronic applications.
Prediction model construction of mouse stem cell pluripotency using CpG and non-CpG DNA methylation markers
Authors: Joe Soobok , Nam Hojung 
Published: May 2020

AbstractBackgroundGenome-wide studies of DNA methylation across the epigenetic landscape provide insights into the heterogeneity of pluripotent embryonic stem cells (ESCs). Differentiating into embryonic somatic and germ cells, ESCs exhibit varying degrees of pluripotency, and epigenetic changes occurring in this process have emerged as important factors explaining stem cell pluripotency.ResultsHere, using paired scBS-seq and scRNA-seq data of mice, we constructed a machine learning model that predicts degrees of pluripotency for mouse ESCs. Since the biological activities of non-CpG markers have yet to be clarified, we tested the predictive power of CpG and non-CpG markers, as well as a combination thereof, in the model. Through rigorous performance evaluation with both internal and external validation, we discovered that a model using both CpG and non-CpG markers predicted the pluripotency of ESCs with the highest prediction performance (0.956 AUC, external test). The prediction model consisted of 16 CpG and 33 non-CpG markers. The CpG and most of the non-CpG markers targeted depletions of methylation and were indicative of cell pluripotency, whereas only a few non-CpG markers reflected accumulations of methylation. Additionally, we confirmed that there exists the differing pluripotency between individual developmental stages, such as E3.5 and E6.5, as well as between induced mouse pluripotent stem cell (iPSC) and somatic cell.ConclusionsIn this study, we investigated CpG and non-CpG methylation in relation to mouse stem cell pluripotency and developed a model thereon that successfully predicts the pluripotency of mouse ESCs.
Blast2Fish: a reference-based annotation web tool for transcriptome analysis of non-model teleost fish
Authors: Tso Chun-Hsi , Wu Jen-Leih , Lu Ming-Wei 
Published: May 2020

Abstract
Background
Transcriptome analysis by next-generation sequencing has become a popular technique in recent years. This approach is quite suitable for non-model organism study, as de novo assembly is independent of prior genomic sequences of organisms. De novo sequencing has benefited many studies on commercially important fish species. However, to understand the functions of these assembled sequences, they still need to be annotated with existing sequence databases. By combining Basic Local Alignment Search Tool (BLAST) and Gene Ontology analysis, we were able to identify homologous sequences of assembled sequences and describe their characteristics using pre-defined tags for each gene, though the above conventional annotation results obtained for non-model assembled sequences was still associated with a lack of pre-defined tags and poorly documented records in the database.

Results
We introduced Blast2Fish, a novel approach for performing functional enrichment analysis on non-model teleost fish transcriptome data. The Blast2Fish pipeline was designed to be a reference-based enrichment method. Instead of annotating the BLAST single top hit by a pre-defined gene-to-tag database, we included 500 hits to search related PubMed articles and parse biological terms. These descriptive terms were then sorted and recorded as annotations for the query. The results showed that Blast2Fish was capable of providing meaningful annotations on immunology topics for non-model fish transcriptome analysis.

Conclusion
Blast2Fish provides a novel approach for annotating sequences of non-model fish. The reference-based strategy allows annotation to be performed without pre-defined tags for each gene. This method strongly benefits non-model teleost fish studies for gene functional enrichment analysis.
Casparian strip membrane domain proteins in Gossypium arboreum: genome-wide identification and negative regulation of lateral root growth
Authors: Wang Xiaoyang , Zhang Yuanming , Wang Liyuan , Pan Zhaoe , He Shoupu , Gao Qiong , Chen Baojun , Gong Wenfang , Du Xiongming 
Published: May 2020

Abstract
Background
Root systems are critical for plant growth and development. The Casparian strip in root systems is involved in stress resistance and maintaining homeostasis. Casparian strip membrane domain proteins (CASPs) are responsible for the formation of Casparian strips.

Results
To investigate the function of CASPs in cotton, we identified and characterized 48, 54, 91 and 94 CASPs from Gossypium arboreum, Gossypium raimondii, Gossypium barbadense and Gossypium hirsutum, respectively, at the genome-wide level. However, only 29 common homologous CASP genes were detected in the four Gossypium species. A collinearity analysis revealed that whole genome duplication (WGD) was the primary reason for the expansion of the genes of the CASP family in the four cotton species. However, dispersed duplication could also contribute to the expansion of the GaCASPs gene family in the ancestors of G. arboreum. Phylogenetic analysis was used to cluster a total of 85 CASP genes from G. arboreum and Arabidopsis into six distinct groups, while the genetic structure and motifs of CASPs were conserved in the same group. Most GaCASPs were expressed in diverse tissues, with the exception of that five GaCASPs (Ga08G0113, Ga08G0114, Ga08G0116, Ga08G0117 and Ga08G0118) that were highly expressed in root tissues. Analyses of the tissue and subcellular localization suggested that GaCASP27 genes (Ga08G0117) are membrane protein genes located in the root. In the GaCASP27 silenced plants and the Arabidopsis mutants, the lateral root number significantly increased. Furthermore, GaMYB36, which is related to root development was found to regulate lateral root growth by targeting GaCASP27.

Conclusions
This study provides a fundamental understanding of the CASP gene family in cotton and demonstrates the regulatory role of GaCASP27 on lateral root growth and development.
The metabolome as a link in the genotype-phenotype map for peroxide resistance in the fruit fly, Drosophila melanogaster
Authors: Harrison Benjamin R. , Wang Lu , Gajda Erika , Hoffman Elise V. , Chung Brian Y. , Pletcher Scott D. , Raftery Daniel , Promislow Daniel E. L. 
Published: May 2020

AbstractBackgroundGenetic association studies that seek to explain the inheritance of complex traits typically fail to explain a majority of the heritability of the trait under study. Thus, we are left with a gap in the map from genotype to phenotype. Several approaches have been used to fill this gap, including those that attempt to map endophenotype such as the transcriptome, proteome or metabolome, that underlie complex traits. Here we used metabolomics to explore the nature of genetic variation for hydrogen peroxide (H2O2) resistance in the sequenced inbredDrosophilaGenetic Reference Panel (DGRP).ResultsWe first studied genetic variation for H2O2resistance in 179 DGRP lines and along with identifying the insulin signaling modulatoru-shapedand several regulators of feeding behavior, we estimate that a substantial amount of phenotypic variation can be explained by a polygenic model of genetic variation. We then profiled a portion of the aqueous metabolome in subsets of eight ‘high resistance’ lines and eight ‘low resistance’ lines. We used these lines to represent collections of genotypes that were either resistant or sensitive to the stressor, effectively modeling a discrete trait. Across the range of genotypes in both populations, flies exhibited surprising consistency in their metabolomic signature of resistance. Importantly, the resistance phenotype of these flies was more easily distinguished by their metabolome profiles than by their genotypes. Furthermore, we found a metabolic response to H2O2in sensitive, but not in resistant genotypes. Metabolomic data further implicated at least two pathways, glycogen and folate metabolism, as determinants of sensitivity to H2O2. We also discovered a confounding effect of feeding behavior on assays involving supplemented food.ConclusionsThis work suggests that the metabolome can be a point of convergence for genetic variation influencing complex traits, and can efficiently elucidate mechanisms underlying trait variation.
Transcriptome analysis reveals rapid defence responses in wheat induced by phytotoxic aphid Schizaphis graminum feeding
Authors: Zhang Yong , Fu Yu , Wang Qian , Liu Xiaobei , Li Qian , Chen Julian 
Published: May 2020

Abstract
Background
Schizaphis graminum is one of the most important and devastating cereal aphids worldwide, and its feeding can cause chlorosis and necrosis in wheat. However, little information is available on the wheat defence responses triggered by S. graminum feeding at the molecular level.

Results
Here, we collected and analysed transcriptome sequencing data from leaf tissues of wheat infested with S. graminum at 2, 6, 12, 24 and 48 hpi (hours post infestation). A total of 44,835 genes were either up- or downregulated and differed significantly in response to aphid feeding. The expression levels of a number of genes (9761 genes) were significantly altered within 2 hpi and continued to change during the entire 48 h experiment. Gene Ontology analysis showed that the downregulated DEGs were mainly enriched in photosynthesis and light harvesting, and the total chlorophyll content in wheat leaves was also significantly reduced after S. graminum infestation at 24 and 48 hpi. However, a number of related genes of the salicylic acid (SA)-mediated defence signalling pathway and MAPK-WRKY pathway were significantly upregulated at early feeding time points (2 and 6 hpi). In addition, the gene expression and activity of antioxidant enzymes, such as peroxidase and superoxide dismutase, were rapidly increased at 2, 6 and 12 hpi. DAB staining results showed that S. graminum feeding induced hydrogen peroxide (H2O2) accumulation at the feeding sites at 2 hpi, and increased H2O2 production was detected with the increases in aphid feeding time. Pretreatment with diphenylene iodonium, an NADPH oxidase inhibitor, repressed the H2O2 accumulation and expression levels of SA-associated defence genes in wheat.

Conclusions
Our transcriptomic analysis revealed that defence-related pathways and oxidative stress in wheat were rapidly induced within hours after the initiation of aphid feeding. Additionally, NADPH oxidase plays an important role in aphid-induced defence responses and H2O2 accumulation in wheat. These results provide valuable insight into the dynamic transcriptomic responses of wheat leaves to phytotoxic aphid feeding and the molecular mechanisms of aphid-plant interactions.