bluuebunny/crossref_metadata_2025_split huggingface dataset:
PTPRD-inactivation-induced CXCL8 promotes angiogenesis and metastasis in gastric cancer and is inhibited by metformin
Authors: Bae Won Jung , Ahn Ji Mi , Byeon Hye Eun , Kim Seokwhi , Lee Dakeun 
Published: December 2019

AbstractBackgroundProtein tyrosine phosphatase receptor delta (PTPRD) is frequently inactivated in various types of cancers. Here, we explored the underlying mechanism of PTPRD-loss-induced cancer metastasis and investigated an efficient treatment option for PTPRD-inactivated gastric cancers (GCs).MethodsPTPRD expression was evaluated by immunohistochemistry. Microarray analysis was used to identify differentially expressed genes in PTPRD-inactivated cancer cells. Quantitative reverse transcription (qRT-PCR), western blotting, and/or enzyme-linked immunosorbent assays were used to investigate the PTPRD-CXCL8 axis and the expression of other related genes. An in vitro tube formation assay was performed using HUVECs. The efficacy of metformin was assessed by MTS assay.ResultsPTPRD was frequently downregulated in GCs and the loss of PTPRD expression was associated with advanced stage, worse overall survival, and a higher risk of distant metastasis. Microarray analysis revealed a significant increase in CXCL8 expression upon loss of PTPRD. This was validated in various GC cell lines using transient and stable PTPRD knockdown. PTPRD-loss-induced angiogenesis was mediated by CXCL8, and the increase in CXCL8 expression was mediated by both ERK and STAT3 signaling. Thus, specific inhibitors targeting ERK or STAT3 abrogated the corresponding signaling nodes and inhibited PTPRD-loss-induced angiogenesis. Additionally, metformin was found to efficiently inhibit PTPRD-loss-induced angiogenesis, decrease cell viability in PTPRD-inactivated cancers, and reverse the decrease in PTPRD expression.ConclusionsThus, the PTPRD-CXCL8 axis may serve as a potential therapeutic target, particularly for the suppression of metastasis in PTPRD-inactivated GCs. Hence, we propose that the therapeutic efficacy of metformin in PTPRD-inactivated cancers should be further investigated.
Nonoperative management of splenic injury in closely monitored patients with reduced consciousness is safe and feasible
Authors: Teuben Michel , Spijkerman Roy , Blokhuis Taco , Pfeifer Roman , Teuber Henrik , Pape Hans-Christoph , Leenen Luke 
Published: December 2019

AbstractBackgroundTreatment of blunt splenic injury has changed over the past decades. Nonoperative management (NOM) is the treatment of choice. Adequate patient selection is a prerequisite for successful NOM. Impaired mental status is considered as a relative contra indication for NOM. However, the impact of altered consciousness in well-equipped trauma institutes is unclear. We hypothesized that impaired mental status does not affect outcome in patients with splenic trauma.MethodsOur prospectively composed trauma database was used and adult patients with blunt splenic injury were included during a 14-year time period. Treatment guidelines remained unaltered over time. Patients were grouped based on the presence (Group GCS: < 14) or absence (Group GCS: 14–15) of impaired mental status. Outcome was compared.ResultsA total of 161 patients were included, of whom 82 were selected for NOM. 36% of patients had a GCS-score < 14 (N = 20). The median GCS-score in patients with reduced consciousness was 9 (range 6–12). Groups were comparable except for significantly higher injury severity scores in the impaired mental status group (19 vs. 17,p = 0.007). Length of stay (28 vs. 9 days,p < 0.001) and ICU-stay (8 vs. 0 days,p = 0.005) were longer in patients with decreased GCS-scores. Failure of NOM, total splenectomy rates, complications and mortality did not differ between both study groups.ConclusionThis study shows that NOM for blunt splenic trauma is a viable treatment modality in well-equipped institutions, regardless of the patients mental status. However, the presence of neurologic impairment is associated with prolonged ICU-stay and hospitalization. We recommend, in institutions with adequate monitoring facilities, to attempt nonoperative management for blunt splenic injury, in all hemodynamically stable patients without hollow organ injuries, also in the case of reduced consciousness.
Cortisol total/CRP ratio for the prediction of hospital-acquired pneumonia and initiation of corticosteroid therapy in traumatic brain-injured patients
Authors: Bouras Marwan , Roquilly Antoine , Mahé Pierre-Joachim , Cinotti Raphaël , Vourc’h Mickaël , Perrot Bastien , Bach-Ngohou Kalyane , Masson Damien , Asehnoune Karim 
Published: December 2019

Abstract
Background
To propose a combination of blood biomarkers for the prediction of hospital-acquired pneumonia (HAP) and for the selection of traumatic brain-injured (TBI) patients eligible for corticosteroid therapy for the prevention of HAP.

Methods
This was a sub-study of the CORTI-TC trial, a multicenter, randomized, double-blind, controlled trial evaluating the risk of HAP at day 28 in 336 TBI patients treated or not with corticosteroid therapy. Patients were between 15 and 65 years with severe traumatic brain injury (Glasgow coma scale score ≤ 8 and trauma-associated lesion on brain CT scan) and were enrolled within 24 h of trauma. The blood levels of CRP and cortisoltotal&free, as a surrogate marker of the pro/anti-inflammatory response balance, were measured in samples collected before the treatment initiation. Endpoint was HAP on day 28.

Results
Of the 179 patients with available samples, 89 (49.7%) developed an HAP. Cortisoltotal&free and CRP blood levels upon ICU admission were not significantly different between patients with or without HAP. The cortisoltotal/CRP ratio upon admission was 2.30 [1.25–3.91] in patients without HAP and 3.36 [1.74–5.09] in patients with HAP (p = 0.021). In multivariate analysis, a cortisoltotal/CRP ratio > 3, selected upon the best Youden index on the ROC curve, was independently associated with HAP (OR 2.50, CI95% [1.34–4.64] p = 0.004). The HR for HAP with corticosteroid treatment was 0.59 (CI95% [0.34–1.00], p = 0.005) in patients with a cortisoltotal/CRP ratio > 3, and 0.89 (CI95% [0.49–1.64], p = 0.85) in patients with a ratio < 3.

Conclusion
A cortisoltotal/CRP ratio > 3 upon admission may predict the development of HAP in severe TBI. Among these patients, corticosteroids reduce the occurrence HAP. We suggest that this ratio may select the patients who may benefit from corticosteroid therapy for the prevention of HAP.
Improved spectrophotometric assay for lytic polysaccharide monooxygenase
Authors: Breslmayr Erik , Daly Sarah , Požgajčić Alen , Chang Hucheng , Rezić Tonči , Oostenbrink Chris , Ludwig Roland 
Published: December 2019

Abstract
Background
The availability of a sensitive and robust activity assay is a prerequisite for efficient enzyme production, purification, and characterization. Here we report on a spectrophotometric assay for lytic polysaccharide monooxygenase (LPMO), which is an advancement of the previously published 2,6-dimethoxyphenol (2,6-DMP)-based LPMO assay. The new assay is based on hydrocoerulignone as substrate and hydrogen peroxide as cosubstrate and aims toward a higher sensitivity at acidic pH and a more reliable detection of LPMO in complex matrices like culture media.

Results
An LPMO activity assay following the colorimetric oxidation of hydrocoerulignone to coerulignone was developed. This peroxidase activity of LPMO in the presence of hydrogen peroxide can be detected in various buffers between pH 4–8. By reducing the substrate and cosubstrate concentration, the assay has been optimized for minimal autoxidation and enzyme deactivation while maintaining sensitivity. Finally, the optimized and validated LPMO assay was used to follow the recombinant expression of an LPMO in Pichia pastoris and to screen for interfering substances in fermentation media suppressing the assayed reaction.

Conclusions
The biphenol hydrocoerulignone is a better substrate for LPMO than the monophenol 2,6-DMP, because of a ~ 30 times lower apparent KM value and a 160 mV lower oxidation potential. This greatly increases the measured LPMO activity when using hydrocoerulignone instead of 2,6-DMP under otherwise similar assay conditions. The improved activity allows the adaptation of the LPMO assay toward a higher sensitivity, different buffers and pH values, more stable assay conditions or to overcome low concentrations of inhibiting substances. The developed assay protocol and optimization guidelines increase the adaptability and applicability of the hydrocoerulignone assay for the production, purification, and characterization of LPMOs.
The SMART App: an interactive web application for comprehensive DNA methylation analysis and visualization
Authors: Li Yin , Ge Di , Lu Chunlai 
Published: December 2019

Abstract
Background
Data mining of The Cancer Genome Atlas (TCGA) data has significantly facilitated cancer genome research and provided unprecedented opportunities for cancer researchers. However, existing web applications for DNA methylation analysis does not adequately address the need of experimental biologists, and many additional functions are often required.

Results
To facilitate DNA methylation analysis, we present the SMART (Shiny Methylation Analysis Resource Tool) App, a user-friendly and easy-to-use web application for comprehensively analyzing the DNA methylation data of TCGA project. The SMART App integrates multi-omics and clinical data with DNA methylation and provides key interactive and customized functions including CpG visualization, pan-cancer methylation profile, differential methylation analysis, correlation analysis and survival analysis for users to analyze the DNA methylation in diverse cancer types in a multi-dimensional manner.

Conclusion
The SMART App serves as a new approach for users, especially wet-bench scientists with no programming background, to analyze the scientific big data and facilitate data mining. The SMART App is available at http://www.bioinfo-zs.com/smartapp.
Safety, tolerability, pharmacokinetics, and pharmacodynamics of PF-06650833, a selective interleukin-1 receptor-associated kinase 4 (IRAK4) inhibitor, in single and multiple ascending dose randomized phase 1 studies in healthy subjects
Authors: Danto Spencer I. , Shojaee Negin , Singh Ravi Shankar P. , Li Cheryl , Gilbert Steven A. , Manukyan Zorayr , Kilty Iain 
Published: December 2019

Abstract
Background
PF-06650833 is a potent, selective inhibitor of interleukin-1 receptor-associated kinase 4 (IRAK4). Two randomized, double-blind, sponsor-open phase 1 studies evaluated the safety, pharmacokinetics, and pharmacodynamics of single (SAD) and multiple ascending doses (MAD) of PF-06650833 immediate-release (IR) and modified-release (MR) oral formulations in healthy adult subjects.

Methods
Study 1 (NCT02224651) was a 96-day, placebo-substitution, SAD study of once-daily (QD) oral PF-06650833 IR 1 to 6000 mg and MR 30 to 300 mg in fasted and fed states. Study 2 (NCT02485769) was a 14-day, placebo-controlled, MAD study of PF-06650833 IR 25 to 750 mg twice daily, IR 1000 mg four times per day, IR 330 mg three times per day, and MR 300 mg QD.

Results
PF-06650833 was generally well tolerated, with no dose-limiting treatment-emergent adverse events (TEAEs) identified in either study. TEAEs were generally mild in severity, with headache, gastrointestinal disorders, and acne most commonly reported. No serious AEs or deaths were reported. A maximum tolerated dose was not established in either study. In the SAD study, food intake delayed absorption of IR 30 mg and increased total exposure by 33%. Delayed absorption was achieved with the MR formulation (Tmax of 1 h versus 8 h for IR 100 mg and MR 100 mg formulations, respectively). Food had no effect on total exposure for MR 30 mg, but reduced half-life 1.8-fold and increased Cmax by 62%. In the MAD study, accumulation ranged from 0.9-fold to 1.4-fold for AUCtau and 0.9-fold to 1.3-fold for Cmax. Less than 1% of the dose was recovered unchanged in urine for all dose groups, with renal clearance ranging from 14 to 23 mL/min for IR < 750 mg and MR 300 mg. There was a sustained decrease in serum high-sensitivity C-reactive protein for IR ≥ 250 mg and MR 300 mg. Based on the cholesterol/hydroxycholesterol ratio, no apparent CYP3A induction or inhibition was observed.

Conclusions
PF-06650833, the first IRAK4 inhibitor to enter clinical development, has a favorable safety and pharmacokinetic profile and has shown evidence of pharmacological effect. The data support continued evaluation in human clinical trials for the treatment of rheumatic and autoimmune diseases.

Trial registration
Clinicaltrials.gov, NCT02224651, registered 25 August 2014; NCT02485769, registered 30 June 2015
Point of care testing evaluation of lateral flow immunoassay for diagnosis of cryptococcus meningitis in HIV-positive patients at an urban hospital in Nairobi, Kenya, 2017
Authors: Gitonga Lawrence Kirimi , Boru Waqo Gufu , Kwena Arthur , Maritim Marybeth , Wamicwe Joyce , Ransom James 
Published: December 2019

Abstract
Objectives
The objective of this study was to evaluate the performance of lateral flow immunoassay (LFA) against latex agglutination (LA), India ink and culture in point-of-care diagnosis of cryptococcus meningitis (CM). We conducted cross-sectional study among HIV-positive patients with suspected CM at Mbagathi Hospital, Nairobi, April–July 2017.

Results
Of 124 capillary blood and serum and 99 cerebrospinal fluid (CSF) samples, LFA and LA had a concurrence on serum of 94.4%, kappa (0.88), sensitivity (100%) and specificity (91%). LFA and LA on CSF, was 97.9%, kappa (0.96), sensitivity (100%) and specificity (96%). LFA and India ink was 96.9%, kappa (0.94), sensitivity (100%) and specificity (94.1%). On CSF culture, concurrence was 72.7%, kappa (0.43), sensitivity (100%) and specificity (64%) and of LFA on capillary blood, serum and CSF was 100% with kappa (1.00), sensitivity and specificity of 100%.
Progression to dementia in memory clinic patients with mild cognitive impairment and normal β-amyloid
Authors: Rosenberg Anna , Solomon Alina , Jelic Vesna , Hagman Göran , Bogdanovic Nenad , Kivipelto Miia 
Published: December 2019

Abstract
Background
Determination of β-amyloid (Aβ) positivity and likelihood of underlying Alzheimer’s disease (AD) relies on dichotomous biomarker cut-off values. Individuals with mild cognitive impairment (MCI) and Aβ within the normal range may still have a substantial risk of developing dementia, primarily of Alzheimer type. Their prognosis, as well as predictors of clinical progression, are not fully understood. The aim of this study was to explore the associations of cerebrospinal fluid (CSF) biomarkers (Aβ42, total tau, phosphorylated tau) and other characteristics, including modifiable vascular factors, with the risk of progression to dementia among patients with MCI and normal CSF Aβ42.

Methods
Three hundred eighteen memory clinic patients with CSF and clinical data, and at least 1-year follow-up, were included. Patients had normal CSF Aβ42 levels based on clinical cut-offs. Cox proportional hazard models with age as time scale and adjusted for sex, education, and cognition (Mini-Mental State Examination) were used to investigate predictors of progression to dementia and Alzheimer-type dementia. Potential predictors included CSF biomarkers, cognitive performance (verbal learning and memory), apolipoprotein E (APOE) ε4 genotype, medial temporal lobe atrophy, family history of dementia, depressive symptoms, and vascular factors, including the Cardiovascular Risk Factors, Aging and Dementia (CAIDE) risk score. Predictive performance of patient characteristics was further explored with Harrell C statistic.

Results
Lower normal Aβ42 and higher total tau and phosphorylated tau were associated with higher dementia risk, and the association was not driven by Aβ42 values close to cut-off. Additional predictors included poorer cognition, APOE ε4 genotype, higher systolic blood pressure, and lower body mass index, but not the CAIDE dementia risk score. Aβ42 individually and in combination with other CSF biomarkers improved the risk prediction compared to age and cognition alone. Medial temporal lobe atrophy or vascular factors did not increase the predictive performance.

Conclusions
Possibility of underlying AD pathology and increased dementia risk should not be ruled out among MCI patients with CSF Aβ42 within the normal range. While cut-offs may be useful in clinical practice to identify high-risk individuals, personalized risk prediction tools incorporating continuous biomarkers may be preferable among individuals with intermediate risk. The role of modifiable vascular factors could be explored in this context.
The shift in the balance between osteoblastogenesis and adipogenesis of mesenchymal stem cells mediated by glucocorticoid receptor
Authors: Han Lizhi , Wang Bo , Wang Ruoyu , Gong Song , Chen Guo , Xu Weihua 
Published: December 2019

AbstractMesenchymal stem cells (MSCs) are multipotent cells capable of differentiating into several tissues, such as bone, cartilage, and fat. Glucocorticoids affect a variety of biological processes such as proliferation, differentiation, and apoptosis of various cell types, including osteoblasts, adipocytes, or chondrocytes. Glucocorticoids exert their function by binding to the glucocorticoid receptor (GR). Physiological concentrations of glucocorticoids stimulate osteoblast proliferation and promote osteogenic differentiation of MSCs. However, pharmacological concentrations of glucocorticoids can not only induce apoptosis of osteoblasts and osteocytes but can also reduce proliferation and inhibit the differentiation of osteoprogenitor cells. Several signaling pathways, including the Wnt, TGFβ/BMP superfamily and Notch signaling pathways, transcription factors, post-transcriptional regulators, and other regulators, regulate osteoblastogenesis and adipogenesis of MSCs mediated by GR. These signaling pathways target key transcription factors, such as Runx2 and TAZ for osteogenesis and PPARγ and C/EBPs for adipogenesis. Glucocorticoid-induced osteonecrosis and osteoporosis are caused by various factors including dysfunction of bone marrow MSCs. Transplantation of MSCs is valuable in regenerative medicine for the treatment of osteonecrosis of the femoral head, osteoporosis, osteogenesis imperfecta, and other skeletal disorders. However, the mechanism of inducing MSCs to differentiate toward the osteogenic lineage is the key to an efficient treatment. Thus, a better understanding of the molecular mechanisms behind the imbalance between GR-mediated osteoblastogenesis and adipogenesis of MSCs would not only help us to identify the pathogenic causes of glucocorticoid-induced osteonecrosis and osteoporosis but also promote future clinical applications for stem cell-based tissue engineering and regenerative medicine. Here, we primarily review the signaling mechanisms involved in adipogenesis and osteogenesis mediated by GR and discuss the factors that control the adipo-osteogenic balance.
Aspirin inhibits RANKL-induced osteoclast differentiation in dendritic cells by suppressing NF-κB and NFATc1 activation
Authors: Wu Lili , Luo Zhenhua , Liu Yitong , Jia Lu , Jiang Yiyang , Du Juan , Guo Lijia , Bai Yuxing , Liu Yi 
Published: December 2019

AbstractBackgroundAspirin has been demonstrated to promote osteoblast-mediated bone formation and inhibit osteoclast (OC)-mediated bone resorption. However, it remains unclear whether aspirin influences other immune cells during bone resorption. Dendritic cells (DCs), the most potent antigen-presenting cells, can also transdifferentiate into active OCs in the presence of receptor activator of nuclear factor-κB ligand (RANKL) and macrophage colony-stimulating factor (M-CSF). The effects of aspirin on DC-derived OCs (DDOCs) were investigated in the current study.MethodsFlow cytometry and mixed lymphocyte reaction (MLR) assays were used for DC identification. The proliferative capacity of DCs was determined by BrdU assays. Apoptosis was examined by flow cytometry. The osteoclastic potential of DCs was tested using tartrate-resistant acid phosphatase (TRAP) staining, western blotting, and reverse transcription polymerase chain reaction (RT-PCR). Western blotting was also used to examine signaling pathways. A mandibular bone defect model was established to assess the effect of aspirin on bone resorption.ResultsAspirin had no influence on the surface phenotype, proliferation, or apoptosis of DCs, though aspirin significantly inhibited osteoclast differentiation in RANKL-stimulated DCs. DC osteoclast differentiation was modulated by aspirin via the nuclear factor kappa B (NF-κB)/nuclear factor of activated T cell, cytoplasmic 1 (NFATc1) signaling pathway. Aspirin treatment also had favorable therapeutic effects on bone regeneration in the bone defect model, and the number of osteoclasts was decreased.ConclusionsAspirin inhibited RANKL-induced OC differentiation in DCs via the NF-κB pathway, downregulating expression of NFATc1. Aspirin treatment promoted bone regeneration by inhibiting DDOC activation in the early stages of inflammation in a rat mandibular bone defect model.
HastaLaVista, a web-based user interface for NMR-based untargeted metabolic profiling analysis in biomedical sciences: towards a new publication standard
Authors: Wist Julien 
Published: December 2019

AbstractMetabolic profiling has been shown to be useful to improve our understanding of complex metabolic processes. Shared data are key to the analysis and validation of metabolic profiling and untargeted spectral analysis and may increase the pace of new discovery. Improving the existing portfolio of open software may increase the fraction of shared data by decreasing the amount of effort required to publish them in a manner that is useful to others. However, a weakness of open software, when compared to commercial ones, is the lack of user-friendly graphical interface that may discourage inexperienced researchers. Here, a web-browser-oriented solution is presented and demonstrated for metabolic profiling analysis that combines the power of R for back-end statistical analyses and of JavaScript for front-end visualisations and user interactivity. This unique combination of statistical programming and web-browser visualisation brings enhanced data interoperability and interactivity into the open source realm. It is exemplified by characterizing the extent to which bariatric surgery perturbs the metabolisms of rats, showing the value of the approach in iterative analysis by the end-user to establish a deeper understanding of the system perturbation. HastaLaVista is available at: (https://github.com/jwist/hastaLaVista, 10.5281/zenodo.3544800) under MIT license. The approach described in this manuscript can be extended to connect the interface to other scripting languages such as Python, and to create interfaces for other types of data analysis.