bluuebunny/crossref_metadata_2025_split huggingface dataset:
Remote Forcing of Tasman Sea Marine Heatwaves
Authors: Li Zeya , Holbrook Neil J. , Zhang Xuebin , Oliver Eric C. J. , Cougnon Eva A. 
Published: April 2020

AbstractRecent marine heatwave (MHW) events in the Tasman Sea have had dramatic impacts on the ecosystems, fisheries, and aquaculture off Tasmania’s east coast. However, our understanding of the large-scale drivers (forcing) and potential predictability of MHW events in this region off southeast Australia is still in its infancy. Here, we investigate the role of oceanic Rossby waves forced in the interior South Pacific on observed MHW occurrences off southeast Australia from 1994 to 2016, including the extreme 2015/16 MHW event. First, we used an upper-ocean heat budget analysis to show that 51% of these historical Tasman Sea MHWs were primarily due to increased East Australian Current (EAC) Extension poleward transports through the region. Second, we used lagged correlation analysis to empirically connect the EAC Extension intensification to incoming westward-propagating sea surface height (SSH) anomalies from the interior South Pacific. Third, we dynamically analyzed these SSH anomalies using simple process-based baroclinic and barotropic Rossby wave models forced by wind stress curl changes across the South Pacific. Finally, we show that associated monthly SSH changes around New Zealand may be a useful index of western Tasman Sea MHW predictability, with a lead time of 2–3 years. In conclusion, our findings demonstrate that there is potential predictability of advection-dominated MHW event likelihoods in the EAC Extension region up to several years in advance, due to the deterministic contribution from baroclinic and barotropic Rossby waves in modulating the EAC Extension transports.
An Evaluation of a Hybrid, Terrain-Following Vertical Coordinate in the WRF-Based RAP and HRRR Models
Authors: Beck Jeffrey , Brown John , Dudhia Jimy , Gill David , Hertneky Tracy , Klemp Joseph , Wang Wei , Williams Christopher , Hu Ming , James Eric , Kenyon Jaymes , Smirnova Tanya , Kim Jung-Hoon 
Published: April 2020

Abstract
A new hybrid, sigma-pressure vertical coordinate was recently added to the Weather Research and Forecasting (WRF) Model in an effort to reduce numerical noise in the model equations near complex terrain. Testing of this hybrid, terrain-following coordinate was undertaken in the WRF-based Rapid Refresh (RAP) and High-Resolution Rapid Refresh (HRRR) models to assess impacts on retrospective and real-time simulations. Initial cold-start simulations indicated that the majority of differences between the hybrid and traditional sigma coordinate were confined to regions downstream of mountainous terrain and focused in the upper levels. Week-long retrospective simulations generally resulted in small improvements for the RAP, and a neutral impact in the HRRR when the hybrid coordinate was used. However, one possibility is that the inclusion of data assimilation in the experiments may have minimized differences between the vertical coordinates. Finally, analysis of turbulence forecasts with the new hybrid coordinate indicate a significant reduction in spurious vertical motion over the full length of the Rocky Mountains. Overall, the results indicate a potential to improve forecast metrics through implementation of the hybrid coordinate, particularly at upper levels, and downstream of complex terrain.
Impact of Sustained Cardiac Tachyarrhythmias Recorded in Coronary Intensive Care Unit on Short- and Long-Term Mortality and Duration of Hospitalization
Authors: Papakonstantinou Panteleimon E. , Malliou Angelliki , Chlouverakis Gregory , Kallergis Eleftherios , Mavrakis Hercules , Parthenakis Frangiskos , Vardas Panos E. , Simantirakis Emmanuel N. 
Published: April 2020

Background: Studies conducted in coronary intensive care units (CICUs) have demonstrated that tachyarrhythmias are associated with increased mortality after acute coronary syndromes (ACSs). However, the data for tachyarrhythmias occurred in CICUs due to a variety of cardiovascular disorders are limited. Methods: We conducted a single-center prospective observational study, which included consecutive CICU patients (January 1, 2014 to May 31, 2018). We recorded the ventricular arrhythmias (VAs), supraventricular tachycardias (SVTs), and days of CICU hospitalization. The patients were followed up for 6 months after CICU discharge. Results: A total of 943 patients (age: 66.37 ±15.4 years; 673 males [71.4%]) were included. Patients with tachyarrhythmias had higher in-CICU mortality (8.0% vs 4.1%, P = .029, odds ratio [OR]: 2.04, 95% confidence interval [CI]: 1.08-3.86) and higher 6-month all-cause mortality (12.8% vs 6.1%, P = .002, OR: 2.27, 95% CI: 1.35-3.83) than those who did not develop tachyarrhythmias. Ventricular arrhythmias was significantly associated with higher all-cause mortality than no tachyarrhythmia (15.4% vs 6.1%; P = .001) or SVTs (15.4% vs 7.0%; P = .001). The mean duration of hospitalization for the patients with tachyarrhythmias was 3.89 ± 4.90 days, while for the patients without was 2.79 ± 3.31 days ( P < .001). Patients without ACS had higher short- and long-term mortality compared to patients with ACS (9.2% vs 2.9%, P < .001 and 12.9% vs 4.9%, P < .001). Conclusions: Tachyarrhythmias were associated with prolonged CICU hospitalization, while non-ACS cardiovascular disorders and the occurrence of VAs were associated with increased short- and long-term mortality.
E2A-PBX1 functions as a coactivator for RUNX1 in acute lymphoblastic leukemia
Authors: Pi Wen-Chieh , Wang Jun , Shimada Miho , Lin Jia-Wei , Geng Huimin , Lee Yu-Ling , Lu Rui , Li Dongxu , Wang Gang Greg , Roeder Robert G. , Chen Wei-Yi 
Published: April 2020

Abstract
E2A, a basic helix-loop-helix transcription factor, plays a crucial role in determining tissue-specific cell fate, including differentiation of B-cell lineages. In 5% of childhood acute lymphoblastic leukemia (ALL), the t(1,19) chromosomal translocation specifically targets the E2A gene and produces an oncogenic E2A-PBX1 fusion protein. Although previous studies have shown the oncogenic functions of E2A-PBX1 in cell and animal models, the E2A-PBX1–enforced cistrome, the E2A-PBX1 interactome, and related mechanisms underlying leukemogenesis remain unclear. Here, by unbiased genomic profiling approaches, we identify the direct target sites of E2A-PBX1 in t(1,19)–positive pre-B ALL cells and show that, compared with normal E2A, E2A-PBX1 preferentially binds to a subset of gene loci cobound by RUNX1 and gene-activating machineries (p300, MED1, and H3K27 acetylation). Using biochemical analyses, we further document a direct interaction of E2A-PBX1, through a region spanning the PBX1 homeodomain, with RUNX1. Our results also show that E2A-PBX1 binding to gene enhancers is dependent on the RUNX1 interaction but not the DNA-binding activity harbored within the PBX1 homeodomain of E2A-PBX1. Transcriptome analyses and cell transformation assays further establish a significant RUNX1 requirement for E2A-PBX1–mediated target gene activation and leukemogenesis. Notably, the RUNX1 locus itself is also directly activated by E2A-PBX1, indicating a multilayered interplay between E2A-PBX1 and RUNX1. Collectively, our study provides the first unbiased profiling of the E2A-PBX1 cistrome in pre-B ALL cells and reveals a previously unappreciated pathway in which E2A-PBX1 acts in concert with RUNX1 to enforce transcriptome alterations for the development of pre-B ALL.
GOMCL: a toolkit to cluster, evaluate, and extract non-redundant associations of Gene Ontology-based functions
Authors: Wang Guannan , Oh Dong-Ha , Dassanayake Maheshi 
Published: April 2020

Abstract
Background
Functional enrichment of genes and pathways based on Gene Ontology (GO) has been widely used to describe the results of various -omics analyses. GO terms statistically overrepresented within a set of a large number of genes are typically used to describe the main functional attributes of the gene set. However, these lists of overrepresented GO terms are often too large and contains redundant overlapping GO terms hindering informative functional interpretations.

Results
We developed GOMCL to reduce redundancy and summarize lists of GO terms effectively and informatively. This lightweight python toolkit efficiently identifies clusters within a list of GO terms using the Markov Clustering (MCL) algorithm, based on the overlap of gene members between GO terms. GOMCL facilitates biological interpretation of a large number of GO terms by condensing them into GO clusters representing non-overlapping functional themes. It enables visualizing GO clusters as a heatmap, networks based on either overlap of members or hierarchy among GO terms, and tables with depth and cluster information for each GO term. Each GO cluster generated by GOMCL can be evaluated and further divided into non-overlapping sub-clusters using the GOMCL-sub module. The outputs from both GOMCL and GOMCL-sub can be imported to Cytoscape for additional visualization effects.

Conclusions
GOMCL is a convenient toolkit to cluster, evaluate, and extract non-redundant associations of Gene Ontology-based functions. GOMCL helps researchers to reduce time spent on manual curation of large lists of GO terms, minimize biases introduced by redundant GO terms in data interpretation, and batch processing of multiple GO enrichment datasets. A user guide, a test dataset, and the source code of GOMCL are available at https://github.com/Guannan-Wang/GOMCL and www.lsugenomics.org.
Increased Interleukin-35 suppresses peripheral CD14+ monocytes function in patients with Kawasaki disease
Authors: Xing Haijian , Tian Gang 
Published: April 2020

Abstract
Background
Interleukin-35 (IL-35) is a newly identified IL-12 cytokine family member, which regulates the activity of immune cells in infectious diseases and autoimmune disorders. However, the regulatory function of IL-35 in Kawasaki disease is not well elucidated.

Methods
Thirty-three patients with Kawasaki disease and seventeen healthy controls were studied. Peripheral IL-35 concentration was measured by enzyme linked immunosorbent assay. CD14+ monocytes were purified, and mRNA expression of IL-35 receptor (IL-12Rβ2 and gp130) was semi-quantified by real-time polymerase chain reaction. CD14+ monocytes were stimulated with recombinant IL-35. The modulatory role of IL-35 treated CD14+ monocytes to naïve CD4+ T cell activation was investigated by flow cytometry. The influence of IL-35 to cytotoxicity of CD14+ monocytes was assessed by measuring target cell death, cytokine and granzyme secretion.

Results
Plasma IL-35 concentration was elevated in patients with Kawasaki disease. There was no significant differences of either IL-12Rβ2 or gp130 mRNA expression in CD14+ monocytes between Kawasaki disease patients and controls. IL-35 suppressed CD14+ monocytes induced naïve CD4+ T cell activation in Kawasaki disease, and this process required direct cell-to-cell contact. IL-35 also inhibited tumor necrosis factor-α and granzyme B secretion by CD14+ monocytes from patients with Kawasaki disease, however, only granzyme B was responsible for the cytotoxicity of CD14+ monocytes.

Conclusions
IL-35 played an important immunosuppressive role to CD14+ monocytes function in Kawasaki disease.
Identification of cholesterol-assimilating actinomycetes strain and application of statistical modeling approaches for improvement of cholesterol oxidase production by Streptomyces anulatus strain NEAE-94
Authors: El-Naggar Noura El-Ahmady , El-Shweihy Nancy M. 
Published: April 2020

AbstractBackgroundCholesterol oxidase biosensors have been used to determine the level of cholesterol in different serum and food samples. Due to a wide range of industrial and clinical applications of microbial cholesterol oxidase, isolation and identification of a new microbial source (s) of cholesterol oxidase are very important.ResultsThe local isolateStreptomycessp. strain NEAE-94 is a promising source of cholesterol oxidase. It was identified based on cultural, morphological and physiological characteristics; in addition to the 16S rRNA sequence. The sequencing product had been deposited in the GenBank database under the accession number KC354803. Cholesterol oxidase production byStreptomyces anulatusstrain NEAE-94 in shake flasks was optimized using surface response methodology. The different process parameters were first screened using a Plackett-Burman design and the parameters with significant effects on the production of cholesterol oxidase were identified. Out of the 15 factors screened, agitation speed, cholesterol and yeast extract concentrations had the most significant positive effects on the production of cholesterol oxidase. The optimal levels of these variables and the effects of their mutual interactions on cholesterol oxidase production were determined using Box-Behnken design. Cholesterol oxidase production byStreptomyces anulatusstrain NEAE-94 was 11.03, 27.31 U/mL after Plackett-Burman Design and Box-Behnken design; respectively, with a fold of increase of 6.06 times compared to the production before applying the Plackett-Burman design (4.51 U/mL).ConclusionsMaximum cholesterol oxidase activity was obtained at the following fermentation conditions: g/L (cholesterol 4, yeast extract 5, NaCl 0.5, K2HPO41, FeSO4.7H2O 0.01, MgSO4.7H2O 0.5), pH 7, inoculum size 4% (v/v), temperature 37°C, agitation speed of 150 rpm, medium volume 50 mL and incubation time 5 days.
Salt adaptability in a halophytic soybean (Glycine soja) involves photosystems coordination
Authors: Yan Kun , He Wenjun , Bian Lanxing , Zhang Zishan , Tang Xiaoli , An Mengxin , Li Lixia , Han Guangxuan 
Published: April 2020

Abstract
Background
Glycine soja is a halophytic soybean native to saline soil in Yellow River Delta, China. Photosystem I (PSI) performance and the interaction between photosystem II (PSII) and PSI remain unclear in Glycine soja under salt stress. This study aimed to explore salt adaptability in Glycine soja in terms of photosystems coordination.

Results
Potted Glycine soja was exposed to 300 mM NaCl for 9 days with a cultivated soybean, Glycine max, as control. Under salt stress, the maximal photochemical efficiency of PSII (Fv/Fm) and PSI (△MR/MR0) were significantly decreased with the loss of PSI and PSII reaction center proteins in Glycine max, and greater PSI vulnerability was suggested by earlier decrease in △MR/MR0 than Fv/Fm and depressed PSI oxidation in modulated 820 nm reflection transients. Inversely, PSI stability was defined in Glycine soja, as △MR/MR0 and PSI reaction center protein abundance were not affected by salt stress. Consistently, chloroplast ultrastructure and leaf lipid peroxidation were not affected in Glycine soja under salt stress. Inhibition on electron flow at PSII acceptor side helped protect PSI by restricting electron flow to PSI and seemed as a positive response in Glycine soja due to its rapid recovery after salt stress. Reciprocally, PSI stability aided in preventing PSII photoinhibition, as the simulated feedback inhibition by PSI inactivation induced great decrease in Fv/Fm under salt stress. In contrast, PSI inactivation elevated PSII excitation pressure through inhibition on PSII acceptor side and accelerated PSII photoinhibition in Glycine max, according to the positive and negative correlation of △MR/MR0 with efficiency that an electron moves beyond primary quinone and PSII excitation pressure respectively.

Conclusion
Therefore, photosystems coordination depending on PSI stability and rapid response of PSII acceptor side contributed to defending salt-induced oxidative stress on photosynthetic apparatus in Glycine soja. Photosystems interaction should be considered as one of the salt adaptable mechanisms in this halophytic soybean.
25(OH) D3 alleviate liver NK cytotoxicity in acute but not in chronic fibrosis model of BALB/c mice due to modulations in vitamin D receptor
Authors: Salhab Ahmad , Amer Johnny , Yinying Lu , Safadi Rifaat 
Published: April 2020

Abstract
Background
Low 25-Hydroxy-vitamin-D; “25(OH)-D3” serum and vitamin D receptor (VDR) levels were recently correlated to advanced fibrosis. However, VDR mechanism in liver fibrosis modulations is not well understood. In this study, we aimed to evaluate changes in liver NK cells cytotoxicity due to modulations in VDR in CCl4 fibrosis model following 25(OH) D3 injections.

Methods
Carbon-tetrachloride (CCl4) hepatic-fibrosis was induced in BALB/c mice for 1 and 4 weeks as an acute and chronic fibrosis model, respectively. Along 1th to 4th weeks, vitamin D were i.p injected/2x week. Liver were assessed histologically and for proteins quantification for VDR and αSMA expressions. In vitro, potential killing of NK cells were evaluated following co-culture with primary-hepatic-stellate-cells (pHSCs) obtained from BALB/c WT-mice.

Results
Systemic inflammation and hepatic-fibrosis increased along 4 weeks of CCl4 as indicated by serum ALT and αSMA expressions (P < 0.02) as well as histological assessments, respectively. These results were associated with increased NK1.1 activations and hypercalcemia. While vitamin D administrations delayed fibrosis of early stages, vitamin D worsen hepatic-fibrosis of late stages of CCl4. In week 4, no further activations of NK cells were seen following vitamin D injections and were associated with down-expressions of VDR (1.7 Fold, P < 0.004) indicating the inability of vitamin D to ameliorate hepatic fibrosis. In vitro, NK cells from the chronic model of CCl4 did not affect pHSCs killing and fail to reduce fibrosis.

Conclusion
Vitamin D alleviate liver NK cytotoxicity in acute but not in chronic fibrosis model due to modulations in vitamin D receptor and calcium. Hypercalcemia associated with late fibrosis may inhibited VDR levels, however, may not explain the profibrogenic effects of vitamin D.
Gray-matter structure in long-term abstinent methamphetamine users
Authors: Nie Lili , Zhao Zeyong , Wen Xiantao , Luo Wei , Ju Tao , Ren Anlian , Wu Binbin , Li Jing 
Published: April 2020

Abstract
Background
Previous studies of brain structure in methamphetamine users have yielded inconsistent findings, possibly reflecting small sample size and inconsistencies in duration of methamphetamine abstinence as well as sampling and analyses methods. Here we report on a relatively large sample of abstinent methamphetamine users at various stages of long-term abstinence.

Methods
Chronic methamphetamine users (n = 99), abstinent from the drug ranging from 12 to 621 days, and healthy controls (n = 86) received T1-weighted structural magnetic resonance imaging brain scans. Subcortical and cortical gray-matter volumes and cortical thickness were measured and the effects of group, duration of abstinence, duration of methamphetamine use and onset age of methamphetamine use were investigated using the Freesurfer software package.

Results
Methamphetamine users did not differ from controls in gray-matter volumes, except for a cluster in the right lateral occipital cortex where gray-matter volume was smaller, and for regions mainly in the bilateral superior frontal gyrui where thickness was greater. Duration of abstinence correlated positively with gray-matter volumes in whole brain, bilateral accumbens nuclei and insulae clusters, and right hippocampus; and with thickness in a right insula cluster. Duration of methamphetamine use correlated negatively with gray-matter volume and cortical thickness of a cluster in the right lingual and pericalcarine cortex.

Conclusions
Chronic methamphetamine use induces hard-to-recover cortical thickening in bilateral superior frontal gyri and recoverable volumetric reduction in right hippocampus, bilateral accumbens nuclei and bilateral cortical regions around insulae. These alternations might contribute to methamphetamine-induced neurocognitive disfunctions and reflect a regional specific response of the brain to methamphetamine.
Relationships among cyberbullying, parental attitudes, self-harm and suicidal behavior among adolescents: results from a school-based survey in Vietnam
Authors: Nguyen Hoang Thuy Linh , Nakamura Keiko , Seino Kaoruko , Vo Van Thang 
Published: April 2020

Abstract
Background
The rapid and widespread development of social networking sites has created a venue for an increase in cyberbullying among adolescents. Protective mechanisms and actions must be considered, such as how proximal family factors can prevent self-harm and suicidal behaviors among adolescents exposed to cyberbullying. The present study examined the associations among cyberbullying, parental attitudes, self-harm, and suicidal behaviors after adjusting for confounding factors.

Methods
Data were obtained from a school-based survey of randomly selected grade 6 students (11 years old) performed in Hue City, Vietnam, in 2018. A total of 648 students were interviewed face-to-face using a structured questionnaire based on the Global School-based Student Health Survey (GSHS). Univariate, multivariable logistic regression analyses were performed at 95% confidence level.

Results
After adjusting for gender, perceived academic pressure, unhealthy behaviors, use of Internet devices, school bullying, and family living situation, a significantly higher risk of self-harm was detected among those who had experienced cyberbullying (adjusted odd ratio [AOR] = 2.97; 95% CI, 1.32–6.71). Parental acceptance retained a significant association with self-harm and suicidal behavior (P < 0.05) while parental concentration did not exhibit a significant association in a multivariable logistic regression model. In addition, suicidal ideation and suicidal planning were associated with an interaction effect between cyberbullying and parental concentration (AOR = 0.37; 95% CI, 0.15–0.94 and AOR = 0.23; 95% CI, 0.06–0.87, respectively).

Conclusion
Cyberbullying has become an important phenomenon associated with self-harm among young adolescents in developing countries, and parental acceptance in proxy of parental attitude was positively related with severe mental health issues among adolescents. Thus, sufficient attention in efforts to promote adolescent health should be focused on family factors in the digital era of developing countries.