bluuebunny/crossref_metadata_2025_split huggingface dataset:
CRISPR-Cas9-mediated knockout of SPRY2 in human hepatocytes leads to increased glucose uptake and lipid droplet accumulation
Authors: Cook Naomi L. , Pjanic Milos , Emmerich Andrew G. , Rao Abhiram S. , Hetty Susanne , Knowles Joshua W. , Quertermous Thomas , Castillejo-López Casimiro , Ingelsson Erik 
Published: October 2019

Abstract

Background
The prevalence of obesity and its comorbidities, including type 2 diabetes mellitus (T2DM), is dramatically increasing throughout the world; however, the underlying aetiology is incompletely understood. Genome-wide association studies (GWAS) have identified hundreds of genec susceptibility loci for obesity and T2DM, although the causal genes and mechanisms are largely unknown. SPRY2 is a candidate gene identified in GWAS of body fat percentage and T2DM, and has recently been linked to insulin production in pancreatic β-cells. In the present study, we aimed to further understand SPRY2 via functional characterisation in HepG2 cells, an in vitro model of human hepatocytes widely used to investigate T2DM and insulin resistance.

Methods
CRISPR-Cas9 genome editing was used to target SPRY2 in HepG2 cells, and the functional consequences of SPRY2 knockout (KO) and overexpression subsequently assessed using glucose uptake and lipid droplet assays, measurement of protein kinase phosphorylation and RNA sequencing.

Results
The major functional consequence of SPRY2 KO was a significant increase in glucose uptake, along with elevated lipid droplet accumulation. These changes were attenuated, but not reversed, in cells overexpressing SPRY2. Phosphorylation of protein kinases across key signalling pathways (including Akt and mitogen activated protein kinases) was not altered after SPRY2 KO. Transcriptome profiling in SPRY2 KO and mock (control) cells revealed a number of differentially expressed genes related to cholesterol biosynthesis, cell cycle regulation and cellular signalling pathways. Phospholipase A2 group IIA (PLA2G2A) mRNA level was subsequently validated as significantly upregulated following SPRY2 KO, highlighting this as a potential mediator downstream of SPRY2.

Conclusion
These findings suggest a role for SPRY2 in glucose and lipid metabolism in hepatocytes and contribute to clarifying the function of this gene in the context of metabolic diseases.
Neutrophils from severe asthmatic patients induce epithelial to mesenchymal transition in healthy bronchial epithelial cells
Authors: Haddad Alexandre , Gaudet Mellissa , Plesa Maria , Allakhverdi Zoulfia , Mogas Andrea K. , Audusseau Severine , Baglole Carolyn J. , Eidelman David H. , Olivenstein Ronald , Ludwig Mara S. , Hamid Qutayba 
Published: October 2019

Abstract

Background
Asthma is a heterogenous disease characterized by chronic inflammation and airway remodeling. An increase in the severity of airway remodeling is associated with a more severe form of asthma. There is increasing interest in the epithelial to mesenchymal transition process and mechanisms involved in the differentiation and repair of the airway epithelium, especially as they apply to severe asthma. Growing evidence suggests that Epithelial-Mesenchymal transition (EMT) could contribute to airway remodeling and fibrosis in asthma. Severe asthmatic patients with remodeled airways have a neutrophil driven inflammation. Neutrophils are an important source of TGF-β1, which plays a role in recruitment and activation of inflammatory cells, extracellular matrix (ECM) production and fibrosis development, and is a potent inducer of EMT.

Objective
As there is little data examining the contribution of neutrophils and/or their mediators to the induction of EMT in airway epithelial cells, the objective of this study was to better understand the potential role of neutrophils in severe asthma in regards to EMT.

Methods
We used an in vitro system to investigate the neutrophil-epithelial cell interaction. We obtained peripheral blood neutrophils from severe asthmatic patients and control subjects and examined for their ability to induce EMT in primary airway epithelial cells.

Results
Our data indicate that neutrophils from severe asthmatic patients induce changes in morphology and EMT marker expression in bronchial epithelial cells consistent with the EMT process when co-cultured. TGF-β1 levels in the culture medium of severe asthmatic patients were increased compared to that from co-cultures of non-asthmatic neutrophils and epithelial cells.

Conclusions and clinical relevance
As an inducer of EMT and an important source of TGF-β1, neutrophils may play a significant role in the development of airway remodeling and fibrosis in severe asthmatic airways.
Barriers to equitable maternal health in Aotearoa New Zealand: an integrative review
Authors: Dawson Pauline , Jaye Chrys , Gauld Robin , Hay-Smith Jean 
Published: October 2019

AbstractBackgroundThe purpose of this review was to examine the literature for themes of underlying social contributors to inequity in maternal health outcomes and experiences in the high resource setting of Aotearoa New Zealand. These ‘causes of the causes’ were explored and compared with the international context to identify similarities and New Zealand-specific differences.MethodA structured integrative review methodology was employed to enable a complex cross disciplinary analysis of data from a variety of published sources. This method enabled incorporation of diverse research methodologies and theoretical approaches found in the literature to form a unified overall of the topic.ResultsSix integrated factors – Physical Access, Political Context, Maternity Care System, Acceptability, Colonialism, and Cultural factors – were identified as barriers to equitable maternal health in Aotearoa New Zealand. The structure of the maternal health system in New Zealand, which includes free maternity care and a woman centred continuity of care structure, should help to ameliorate inequity in maternal health and yet does not appear to. A complex set of underlying structural and systemic factors, such as institutionalised racism, serve to act as barriers to equitable maternity outcomes and experiences. Initiatives that appear to be working are adapted to the local context and involve self-determination in research, clinical outreach and community programmes.ConclusionsThe combination of six social determinants identified in this review that contribute to maternal health inequity is specific to New Zealand, although individually these factors can be identified elsewhere; this creates a unique set of challenges in addressing inequity. Due to the specific social determinants in Aotearoa New Zealand, localised solutions have potential to further maternal health equity.
CircMYO10 promotes osteosarcoma progression by regulating miR-370-3p/RUVBL1 axis to enhance the transcriptional activity of β-catenin/LEF1 complex via effects on chromatin remodeling
Authors: Chen Junxin , Liu Gang , Wu Yizheng , Ma Jianjun , Wu Hongfei , Xie Ziang , Chen Shuai , Yang Yute , Wang Shengyu , Shen Panyang , Fang Yifan , Fan Shunwu , Shen Shuying , Fang Xiangqian 
Published: October 2019

Abstract

Background
CircMYO10 is a circular RNA generated by back-splicing of gene MYO10 and is upregulated in osteosarcoma cell lines, but its functional role in osteosarcoma is still unknown. This study aimed to clarify the mechanism of circMYO10 in osteosarcoma.

Methods
CircMYO10 expression in 10 paired osteosarcoma and chondroma tissues was assessed by quantitative reverse transcription polymerase chain reaction (PCR). The function of circMYO10/miR-370-3p/RUVBL1 axis was assessed regarding two key characteristics: proliferation and endothelial–mesenchymal transition (EMT). Bioinformatics analysis, western blotting, real-time PCR, fluorescence in situ hybridization, immunoprecipitation, RNA pull-down assays, luciferase reporter assays, chromatin immunoprecipitation, and rescue experiments were used to evaluate the mechanism. Stably transfected MG63 cells were injected via tail vein or subcutaneously into nude mice to assess the role of circMYO10 in vivo.

Results
CircMYO10 was significantly upregulated, while miR-370-3p was downregulated, in osteosarcoma cell lines and human osteosarcoma samples. Silencing circMYO10 inhibited cell proliferation and EMT in vivo and in vitro. Mechanistic investigations revealed that miR-370-3p targets RUVBL1 directly, and inhibits the interaction between RUVBL1 and β-catenin/LEF1 complex while circMYO10 showed a contrary effect via the inhibition of miR-370-3p. RUVBL1 was found to be complexed with chromatin remodeling and histone-modifying factor TIP60, and lymphoid enhancer factor-1 (LEF1) to promote histone H4K16 acetylation (H4K16Ac) in the vicinity of the promoter region of gene C-myc. Chromatin immunoprecipitation methods showed that miR-370-3p sponge promotes H4K16Ac in the indicated region, which is partially abrogated by RUVBL1 small hairpin RNA (shRNA) while circMYO10 showed a contrary result via the inhibition of miR-370-3p. Either miR-370-3p sponge or ShRUVBL1 attenuated circMYO10-induced phenotypes in osteosarcoma cell lines. MiR-370-3p inhibition abrogated the inhibition of proliferation, EMT of osteosarcoma cells in vitro and in vivo seen upon circMYO10 suppression via Wnt/β-catenin signaling.

Conclusions
CircMYO10 promotes osteosarcoma progression by regulating miR-370-3p/RUVBL1 axis to promote chromatin remodeling and thus enhances the transcriptional activity of β-catenin/LEF1 complex, which indicates that circMYO10 may be a potential therapeutic target for osteosarcoma treatment.
Clinical significance of PD-L1 expression in serum-derived exosomes in NSCLC patients
Authors: Li Chuling , Li Chuwei , Zhi Chunchun , Liang Wenjun , Wang Xuan , Chen Xi , Lv Tangfeng , Shen Qin , Song Yong , Lin Dang , Liu Hongbing 
Published: October 2019

Abstract

Background
Exosomes are 50–150 nm endocytic vesicles secreted by almost all type of cells that carry bioactive molecules from host. These small vesicles are considered to be novel cross-talk circuits established by tumor cells and tumor microenvironment. Previous studies have shown certain biological influence of exosomal programmed cell-death ligand 1 (Exo-PD-L1) on immune suppression and dysfunction. The aim of the current study was to investigate the impact of Exo-PD-L1 and soluble PD-L1 (sPD-L1) on non-small cell lung cancer (NSCLC) and explore the concordance between Exo-PD-L1 and PD-L1 expression in matched tumor tissues in NSCLC patients.

Methods
85 consecutive patients from April 2017 to December 2017 at General Hospital of Eastern Command Theatre who were primarily diagnosed with NSCLC and 27 healthy individuals were enrolled in this study. Two milliliters of whole blood samples were collected from each participant and further centrifuged. Exosomes were derived from serum using the commercial kit (Total Exosome Isolation Kit), which was further identified by Western blotting analysis (CD63/TSG101), transmission electron microscope analysis (TEM) and nanoparticle tracking analysis (NTA). Exosomes were next solubilized for Exo-PD-L1 detection by enzyme-linked immuno-sorbent assay (ELISA). PD-L1 expression in matched tissue were assessed by PD-L1 immunohistochemistry (IHC) (clone 28-8) assay. Tumor proportion score (TPS) ≥ 1% was deemed as “positive” in this study and TPS < 1% was deemed as “negative”. Written informed consent were obtained before acquisition of all data and biological sample. Data were analyzed using SPSS 20.0 and Graphpad Prism 5 software. Chi square test was conducted to estimate the correlation between Exo-PD-L1 levels, sPD-L1 levels, PD-L1 IHC profiles and clinicopathological features. For all analysis, a two-sided p < 0.05 was considered significant statistically.

Results
Exo-PD-L1 levels were higher in NSCLC patients with advanced tumor stage, larger tumor size (> 2.5 cm) (p < 0.001), positive lymph node status (p < 0.05) and distant metastasis (p < 0.05). In contrast, sPD-L1 levels were not different between NSCLC patients and healthy donors, it was not correlated with any clinicopathologic features except for tumor size (> 2.5 cm) (p < 0.05). In addition, Exo-PD-L1 levels showed slight correlation with sPD-L1 levels (Spearman’s correlation at r = 0.3, p = 0.0027) while no correlation with PD-L1 IHC profiles was detected.

Conclusions
In conclusion, Exo-PD-L1, but not sPD-L1, was correlated with NSCLC disease progression, including tumor size, lymph node status, metastasis and TNM stage. However, Exo-PD-L1 was not associated with PD-L1 IHC status.
RapidPlan knowledge based planning: iterative learning process and model ability to steer planning strategies
Authors: Fogliata A. , Cozzi L. , Reggiori G. , Stravato A. , Lobefalo F. , Franzese C. , Franceschini D. , Tomatis S. , Scorsetti M. 
Published: October 2019

Abstract

Purpose
To determine if the performance of a knowledge based RapidPlan (RP) planning model could be improved with an iterative learning process, i.e. if plans generated by an RP model could be used as new input to re-train the model and achieve better performance.

Methods
Clinical VMAT plans from 83 patients presenting with head and neck cancer were selected to train an RP model, CL-1. With this model, new plans on the same patients were generated, and subsequently used as input to train a novel model, CL-2. Both models were validated on a cohort of 20 patients and dosimetric results compared. Another set of 83 plans was realised on the same patients with different planning criteria, by using a simple template with no attempt to manually improve the plan quality. Those plans were employed to train another model, TP-1. The differences between the plans generated by CL-1 and TP-1 for the validation cohort of patients were compared with respect to the differences between the original plans used to build the two models.

Results
The CL-2 model presented an improvement relative to CL-1, with higher R2 values and better regression plots. The mean doses to parallel organs decreased with CL-2, while D1% to serial organs increased (but not significantly). The different models CL-1 and TP-1 were able to yield plans according to each original strategy.

Conclusion
A refined RP model allowed the generation of plans with improved quality, mostly for parallel organs at risk and, possibly, also the intrinsic model quality.
Sequence characterization of RET in 117 Chinese Hirschsprung disease families identifies a large burden of de novo and parental mosaic mutations
Authors: Jiang Qian , Wang Yang , Li Qi , Zhang Zhen , Xiao Ping , Wang Hui , Liu Na , Wu Jian , Zhang Feng , Chakravarti Aravinda , Cai Wei , Li Long 
Published: October 2019

Abstract

Background
Hirschsprung disease (HSCR) is an inherited congenital disorder characterized by the absence of enteric ganglia in the distal part of the gut. RET is the major causative gene and contains > 80% of all known disease-causing mutations.

Results
To determine the incidence of RET pathogenic variants, be they Mendelian inherited, mosaic in parents or true de novo variants (DNVs) in 117 Chinese families, we used high-coverage NGS and droplet digital polymerase chain reaction (ddPCR) to identify 15 (12.8%) unique RET coding variants (7 are novel); one was inherited from a heterozygous unaffected mother, 11 were DNVs (73.3%), and 3 full heterozygotes were inherited from parental mosaicism (2 paternal, 1 maternal): two clinically unaffected parents were identified by NGS and confirmed by ddPCR, with mutant allele frequency (13–27%) that was the highest in hair, lowest in urine and similar in blood and saliva. An extremely low-level paternal mosaicism (0.03%) was detected by ddPCR in blood. Six positive-controls were examined to compare the mosaicism detection limit and sensitivity of NGS, amplicon-based deep sequencing and ddPCR.

Conclusion
Our findings expand the clinical and molecular spectrum of RET variants in HSCR and reveal a high frequency of RET DNVs in the Chinese population.
Correlation between end-tidal carbon dioxide and the degree of compression of heart cavities measured by transthoracic echocardiography during cardiopulmonary resuscitation for out-of-hospital cardiac arrest
Authors: Skulec Roman , Vojtisek Petr , Cerny Vladimir 
Published: October 2019

Abstract

Background
The concept of personalized cardiopulmonary resuscitation (CPR) requires a parameter that reflects its hemodynamic efficiency. While intra-arrest ultrasound is increasingly implemented into the advanced life support, we realized a pre-hospital clinical study to evaluate whether the degree of compression of the right ventricle (RV) and left ventricle (LV) induced by chest compressions during CPR for out-of-hospital cardiac arrest (OHCA) and measured by transthoracic echocardiography correlates with the levels of end-tidal carbon dioxide (EtCO2) measured at the time of echocardiographic investigation.

Methods
Thirty consecutive patients resuscitated for OHCA were included in the study. Transthoracic echocardiography was performed from a subcostal view during ongoing chest compressions in all of them. This was repeated three times during CPR in each patient, and EtCO2 levels were registered. From each investigation, a video loop was recorded. Afterwards, maximal and minimal diameters of LV and RV were obtained from the recorded loops and the compression index of LV (LVCI) and RV (RVCI) was calculated as (maximal − minimal/maximal diameter) × 100. Maximal compression index (CImax) defined as the value of LVCI or RVCI, whichever was greater was also assessed. Correlations between EtCO2 and LVCI, RVCI, and CImax were expressed as Spearman’s correlation coefficient (r).

Results
Evaluable echocardiographic records were found in 18 patients, and a total of 52 measurements of all parameters were obtained. Chest compressions induced significant compressions of all observed cardiac cavities (LVCI = 20.6 ± 13.8%, RVCI = 34.5 ± 21.6%, CImax = 37.4 ± 20.2%). We identified positive correlation of EtCO2 with LVCI (r = 0.672, p < 0.001) and RVCI (r = 0.778, p < 0.001). The strongest correlation was between EtCO2 and CImax (r = 0.859, p < 0.001). We identified that a CImax cut-off level of 17.35% predicted to reach an EtCO2 level > 20 mmHg with 100% sensitivity and specificity.

Conclusions
Evaluable echocardiographic records were reached in most of the patients. EtCO2 positively correlated with all parameters under consideration, while the strongest correlation was found between CImax and EtCO2. Therefore, CImax is a candidate parameter for the guidance of hemodynamic-directed CPR.

Trial registration
ClinicalTrial.gov, NCT03852225. Registered 21 February 2019 - Retrospectively registered.
Preparing intensive care for the next pandemic influenza
Authors: Kain Taylor , Fowler Robert 
Published: October 2019

Abstract
Few viruses have shaped the course of human history more than influenza viruses. A century since the 1918–1919 Spanish influenza pandemic—the largest and deadliest influenza pandemic in recorded history—we have learned much about pandemic influenza and the origins of antigenic drift among influenza A viruses. Despite this knowledge, we remain largely underprepared for when the next major pandemic occurs.
While emergency departments are likely to care for the first cases of pandemic influenza, intensive care units (ICUs) will certainly see the sickest and will likely have the most complex issues regarding resource allocation. Intensivists must therefore be prepared for the next pandemic influenza virus. Preparation requires multiple steps, including careful surveillance for new pandemics, a scalable response system to respond to surge capacity, vaccine production mechanisms, coordinated communication strategies, and stream-lined research plans for timely initiation during a pandemic. Conservative models of a large-scale influenza pandemic predict more than 170% utilization of ICU-level resources. When faced with pandemic influenza, ICUs must have a strategy for resource allocation as strain increases on the system.
There are several current threats, including avian influenza A(H5N1) and A(H7N9) viruses. As humans continue to live in closer proximity to each other, travel more extensively, and interact with greater numbers of birds and livestock, the risk of emergence of the next pandemic influenza virus mounts. Now is the time to prepare and coordinate local, national, and global efforts.
Fingerprinting cities: differentiating subway microbiome functionality
Authors: Zhu Chengsheng , Miller Maximilian , Lusskin Nick , Mahlich Yannick , Wang Yanran , Zeng Zishuo , Bromberg Yana 
Published: October 2019

Abstract

Background
Accumulating evidence suggests that the human microbiome impacts individual and public health. City subway systems are human-dense environments, where passengers often exchange microbes. The MetaSUB project participants collected samples from subway surfaces in different cities and performed metagenomic sequencing. Previous studies focused on taxonomic composition of these microbiomes and no explicit functional analysis had been done till now.

Results
As a part of the 2018 CAMDA challenge, we functionally profiled the available ~ 400 subway metagenomes and built predictor for city origin. In cross-validation, our model reached 81% accuracy when only the top-ranked city assignment was considered and 95% accuracy if the second city was taken into account as well. Notably, this performance was only achievable if the similarity of distribution of cities in the training and testing sets was similar. To assure that our methods are applicable without such biased assumptions we balanced our training data to account for all represented cities equally well. After balancing, the performance of our method was slightly lower (76/94%, respectively, for one or two top ranked cities), but still consistently high. Here we attained an added benefit of independence of training set city representation. In testing, our unbalanced model thus reached (an over-estimated) performance of 90/97%, while our balanced model was at a more reliable 63/90% accuracy. While, by definition of our model, we were not able to predict the microbiome origins previously unseen, our balanced model correctly judged them to be NOT-from-training-cities over 80% of the time.
Our function-based outlook on microbiomes also allowed us to note similarities between both regionally close and far-away cities. Curiously, we identified the depletion in mycobacterial functions as a signature of cities in New Zealand, while photosynthesis related functions fingerprinted New York, Porto and Tokyo.

Conclusions
We demonstrated the power of our high-speed function annotation method, mi-faser, by analysing ~ 400 shotgun metagenomes in 2 days, with the results recapitulating functional signals of different city subway microbiomes. We also showed the importance of balanced data in avoiding over-estimated performance. Our results revealed similarities between both geographically close (Ofa and Ilorin) and distant (Boston and Porto, Lisbon and New York) city subway microbiomes. The photosynthesis related functional signatures of NYC were previously unseen in taxonomy studies, highlighting the strength of functional analysis.