bluuebunny/crossref_metadata_2025_split huggingface dataset:
Silencing lncRNA ZFAS1 or elevated microRNA-135a represses proliferation, migration, invasion and resistance to apoptosis of osteosarcoma cells
Authors: Zhao Zilong , Lin Xiafei , Tong Yunhui , Li Wenxia 
Published: December 2019

Abstract
Background
Osteosarcoma (OS) is still a disease with high mortality from malignant tumors in children and adolescents. Due to its poor treatment, this study explored the involvement of lncRNA ZFAS1/microRNA-135a (miR-135a)/apurinic/apyrimidinic exonuclease 1 (APEX1) axis in the regulation of OS growth and metastasis.

Methods
ZFAS1, miR-135a and APEX1 expression in OS tissues and cells were tested by RT-qPCR and western blot analysis. MG63 cells were transfected with sh-ZFAS1, miR-135a mimic or their controls to unearth theirs functions in the proliferation, colony formation, migration, invasion, cycle entry and apoptosis of MG63 cells by MTT and EdU, colony formation assays, flow cytometry, and Transwell assay, severally. The proliferation related factor (Ki-67, CyclinD1), apoptosis related factor (Bax, Bcl-2) and migration related factor (MMP2, MMP9) protein levels were tested. Tumor volume and weight were detected by subcutaneous tumor xenograft in nude mice.

Results
Overexpressed ZFAS1 and APEX1, and down-regulated miR-135a existed in OS tissues and cells. Silenced ZFAS1 or elevated miR-135a inhibited colony formation and proliferation, cycle progression, migration and invasion while promoted apoptosis of MG63 cells. Silenced ZFAS1 or elevated miR-135a suppressed tumor volume and weight of OS in vivo. LncRNA ZFAS1 promoted APEX1 expression by competitively binding with miR-135a.

Conclusion
This study indicates that silenced ZFAS1 or up-regulated miR-135a restrained migration, proliferation and invasion and promoted apoptosis of OS MG63 cells. This study provides a possible theoretical basis for studying the regulatory mechanism of ZFAS1/miR-135a/APEX1 signaling axis on the growth and metastasis of OS.
Silencing of microRNA-146a alleviates the neural damage in temporal lobe epilepsy by down-regulating Notch-1
Authors: Huang Hui , Cui Guiyun , Tang Hai , Kong Lingwen , Wang Xiaopeng , Cui Chenchen , Xiao Qihua , Ji Huiming 
Published: December 2019

AbstractThis study aimed to evaluate the specific regulatory roles of microRNA-146a (miRNA-146a) in temporal lobe epilepsy (TLE) and explore the related regulatory mechanisms. A rat model of TLE was established by intraperitoneal injection of lithium chloride-pilocarpine. These model rats were injected intracerebroventricularly with an miRNA-146a inhibitor and Notch-1 siRNA. Then, neuronal damage and cell apoptosis in the cornu ammonis (CA) 1 and 3 regions of the hippocampus were assessed. SOD and MDA levels in the hippocampus were detected by chromatometry, and IL-1β, IL-6, and IL-18 levels were detected by ELISA. Then, we evaluated the expression levels of caspase-9, GFAP, Notch-1, and Hes-1 in the hippocampus. The interaction between Notch-1 and miRNA-146a was assessed by a dual luciferase reporter gene assay. A rat model of TLE was successfully established, which exhibited significantly increased miRNA-146a expression in the hippocampus. Silencing of miRNA-146a significantly alleviated the neuronal damage and cell apoptosis in the CA1 and CA3 regions of the hippocampus in TLE rats and decreased MDA, IL-1β, IL-6, and IL-18 levels and increased SOD levels in the hippocampus of TLE rats. In addition, silencing of miRNA-146a significantly decreased the expression levels of caspase-9, GFAP, Notch-1, and Hes-1 in the hippocampus of TLE rats. Notch-1 was identified as a target of miRNA-146a and silencing of Notch-1 aggravated the neuronal damage in the CA1 and CA3 regions. Silencing of miRNA-146a alleviated the neuronal damage in the hippocampus of TLE rats by down-regulating Notch-1.
Acute pain management in children: a survey of Italian pediatricians
Authors: Marseglia Gian Luigi , Alessio Maria , Da Dalt Liviana , Giuliano Maria , Ravelli Angelo , Marchisio Paola 
Published: December 2019

AbstractBackgroundCurrent guidelines recommend assessing and relieving pain in all children and in all instances; yet, in clinical practice, management is frequently suboptimal. We investigated the attitude of Italian family pediatricians towards the evaluation and treatment of different types of acute pain in children aged 7–12 years.MethodsThis is a cross-sectional study based on a 17-question survey accessible online from October 2017 to October 2018. Responders had to describe cases of children suffering from any type of acute pain among headache, sore throat, musculoskeletal/post-traumatic pain, and earache. Children’s characteristics, pain assessment modalities and therapeutic approaches were queried. The following tests were used: Z-proportion to evaluate the distribution of categorical data; chi-squared and Kruskall-Wallis to explore data heterogeneity across groups; Mann-Whitney for head-to-head comparisons.ResultsOverall, 929 pediatricians presented 6335 cases uniformly distributed across the types examined. Pain was more frequently of moderate intensity (42.2%,P < 0.001) and short duration (within some days: 98.4%,P < 0.001). Only 50.1% of responders used an algometric scale to measure pain and 60.5% always prescribed a treatment. In children with mild-moderate pain (N = 4438), the most commonly used first-line non-opioids were ibuprofen (53.3%) and acetaminophen (44.4%). Importantly, a non-recommended dosage was prescribed in only 5.3% of acetaminophen-treated cases (overdosing). Among the misconceptions emerged, there were the following: i) ibuprofen and acetaminophen have different efficacy and safety profiles (when choosing the non-opioid, effectiveness weighted more for ibuprofen [79.7% vs 74.3%,P < 0.001] and tolerability for acetaminophen [74.0% vs 55.4%,P < 0.001]); ii) ibuprofen must be taken after meals to prevent gastric toxicities (52.5%); ibuprofen and acetaminophen can be used combined/alternated for persisting mild-moderate pain (16.1%). In case of moderate-severe pain not completely controlled by opioids, ibuprofen and acetaminophen were the most used add-on medications, with ibuprofen being much more prescribed than acetaminophen (65.2% vs 23.7%, respectively) overall and in all pain types.ConclusionsSeveral gaps exist between the current practice of pain assessment and treatment and recommendations. Further efforts are needed to raise awareness and improve education on the possible exposure of the child to short- and long-term consequences in case of suboptimal pain management.
NSABP FB-7: a phase II randomized neoadjuvant trial with paclitaxel + trastuzumab and/or neratinib followed by chemotherapy and postoperative trastuzumab in HER2+ breast cancer
Authors: Jacobs Samuel A. , Robidoux André , Abraham Jame , Pérez-Garcia José Manuel , La Verde Nicla , Orcutt James M. , Cazzaniga Marina E. , Piette Fanny , Antolín Silvia , Aguirre Elena , Cortes Javier , Llombart-Cussac Antonio , Di Cosimo Serena , Kim Rim S. , Feng Huichen , Lipchik Corey , Lucas Peter C. , Srinivasan Ashok , Wang Ying , Song Nan , Gavin Patrick G. , Balousek April D. , Paik Soonmyung , Allegra Carmen J. , Wolmark Norman , Pogue-Geile Katherine L. 
Published: December 2019

AbstractPurposeThe primary aim of NSABP FB-7 was to determine the pathologic complete response (pCR) rate in locally advanced HER2-positive (HER2+) breast cancer patients treated with neoadjuvant trastuzumab or neratinib or the combination and weekly paclitaxel followed by standard doxorubicin plus cyclophosphamide. The secondary aims include biomarker analyses.Experimental designpCR was tested for association with treatment, gene expression, and a single nucleotide polymorphism (SNP) in the Fc fragment of the IgG receptor IIIa-158V/F (FCGR3A). Pre-treatment biopsies and residual tumors were also compared to identify molecular changes.ResultsThe numerical pCR rate in the trastuzumab plus neratinib arm (50% [95%CI 34–66%]) was greater than that for single-targeted therapies with trastuzumab (38% [95%CI 24–54]) or neratinib (33% [95%CI 20–50]) in the overall cohort but was not statistically significant. Hormone receptor-negative (HR−) tumors had a higher pCR rate than HR+tumors in all three treatment arms, with the highest pCR rate in the combination arm. Diarrhea was the most frequent adverse event and occurred in virtually all patients who received neratinib-based therapy. Grade 3 diarrhea was reported in 31% of patients; there were no grade 4 events. Our 8-gene signature, previously validated for trastuzumab benefit in two different clinical trials in theadjuvantsetting, was correlated with pCR across all arms of NSABP FB-7. Specifically, patientspredictedto receive no trastuzumab benefit had a significantly lower pCR rate than did patientspredictedto receive the most benefit (P = 0.03). FCGR genotyping showed that patients who were homozygous for the Fc low-binding phenylalanine (F) allele forFCGR3A-158V/Fwere less likely to achieve pCR.ConclusionsCombining trastuzumab plus neratinib with paclitaxel increased the absolute pCR rate in the overall cohort and in HR−patients. The 8-gene signature, which is validated for predicting trastuzumab benefit in the adjuvant setting, was associated with pCR in the neoadjuvant setting, but remains to be validated as a predictive marker in a larger neoadjuvant clinical trial. HR status, and theFCGR3A-158V/Fgenotype, also warrant further investigation to identify HER2+patients who may benefit from additional anti-HER2 therapies beyond trastuzumab. All of these markers will require further validation in the neoadjuvant setting.Trials registrationClinicalTrials.gov,NCT01008150. Retrospectively registered on October 5, 2010.
Improvement in catalytic activity and thermostability of a GH10 xylanase and its synergistic degradation of biomass with cellulase
Authors: You Shuai , Xie Chen , Ma Rui , Huang Huo-qing , Herman Richard Ansah , Su Xiao-yun , Ge Yan , Cai Hui-yi , Yao Bin , Wang Jun , Luo Hui-ying 
Published: December 2019

Abstract
Background
Xylanase is one of the most extensively used biocatalysts for biomass degradation. However, its low catalytic efficiency and poor thermostability limit its applications. Therefore, improving the properties of xylanases to enable synergistic degradation of lignocellulosic biomass with cellulase is of considerable significance in the field of bioenergy.

Results
Using fragment replacement, we improved the catalytic performance and thermostability of a GH10 xylanase, XylE. Of the ten hybrid enzymes obtained, seven showed xylanase activity. Substitution of fragments, M3, M6, M9, and their combinations enhanced the catalytic efficiency (by 2.4- to fourfold) as well as the specific activity (by 1.2- to 3.3-fold) of XylE. The hybrids, XylE-M3, XylE-M3/M6, XylE-M3/M9, and XylE-M3/M6/M9, showed enhanced thermostability, as observed by the increase in the T50 (3–4.7 °C) and Tm (1.1–4.7 °C), and extended t1/2 (by 1.8–2.3 h). In addition, the synergistic effect of the mutant xylanase and cellulase on the degradation of mulberry bark showed that treatment with both XylE-M3/M6 and cellulase exhibited the highest synergistic effect. In this case, the degree of synergy reached 1.3, and the reducing sugar production and dry matter reduction increased by 148% and 185%, respectively, compared to treatment with only cellulase.

Conclusions
This study provides a successful strategy to improve the catalytic properties and thermostability of enzymes. We identified several xylanase candidates for applications in bioenergy and biorefinery. Synergistic degradation experiments elucidated a possible mechanism of cellulase inhibition by xylan and xylo-oligomers.
Mutational signatures in colon cancer
Authors: Pandey Priyatama , Yang Zhi , Shibata Darryl , Marjoram Paul , Siegmund Kimberly D. 
Published: December 2019

Abstract
Objective
Recently, many tumor sequencing studies have inferred and reported on mutational signatures, short nucleotide patterns at which particular somatic base substitutions appear more often. A number of signatures reflect biological processes in the patient and factors associated with cancer risk. Our goal is to infer mutational signatures appearing in colon cancer, a cancer for which environmental risk factors vary by cancer subtype, and compare the signatures to those in adult stem cells from normal colon. We also compare the mutational signatures to others in the literature.

Results
We apply a probabilistic mutation signature model to somatic mutations previously reported for six adult normal colon stem cells and 431 colon adenocarcinomas. We infer six mutational signatures in colon cancer, four being specific to tumors with hypermutation. Just two signatures explained the majority of mutations in the small number of normal aging colon samples. All six signatures are independently identified in a series of 295 Chinese colorectal cancers.
Cisplatin treatment of testicular cancer patients introduces long-term changes in the epigenome
Authors: Bucher-Johannessen Cecilie , Page Christian M. , Haugen Trine B. , Wojewodzic Marcin W. , Fosså Sophie D. , Grotmol Tom , Haugnes Hege S. , Rounge Trine B. 
Published: December 2019

AbstractBackgroundCisplatin-based chemotherapy (CBCT) is part of standard treatment of several cancers. In testicular cancer (TC) survivors, an increased risk of developing metabolic syndrome (MetS) is observed. In this epigenome-wide association study, we investigated if CBCT relates to epigenetic changes (DNA methylation) and if epigenetic changes render individuals susceptible for developing MetS later in life. We analyzed methylation profiles, using the MethylationEPIC BeadChip, in samples collected ~ 16 years after treatment from 279 Norwegian TC survivors with known MetS status. Among the CBCT treated (n= 176) and non-treated (n= 103), 61 and 34 developed MetS, respectively. We used two linear regression models to identify if (i) CBCT results in epigenetic changes and (ii) epigenetic changes play a role in development of MetS. Then we investigated if these changes in (i) and (ii) links to genes, functional networks, and pathways related to MetS symptoms.ResultsWe identified 35 sites that were differentially methylated when comparing CBCT treated and untreated TC survivors. The PTK6–RAS–MAPk pathway was significantly enriched with these sites and infers a gene network of 13 genes withCACNA1D(involved in insulin release) as a network hub.We found nominal MetS-associations and a functional gene network withABCG1andNCF2as network hubs.ConclusionOur results suggest that CBCT has long-term effects on the epigenome. We could not directly link the CBCT effects to the risk of developing MetS. Nevertheless, since we identified differential methylation occurring in genes associated with conditions pertaining to MetS, we hypothesize that epigenomic changes may also play a role in the development of MetS in TC survivors. Further studies are needed to validate this hypothesis.
A de novo molecular generation method using latent vector based generative adversarial network
Authors: Prykhodko Oleksii , Johansson Simon Viet , Kotsias Panagiotis-Christos , Arús-Pous Josep , Bjerrum Esben Jannik , Engkvist Ola , Chen Hongming 
Published: December 2019

AbstractDeep learning methods applied to drug discovery have been used to generate novel structures. In this study, we propose a new deep learning architecture, LatentGAN, which combines an autoencoder and a generative adversarial neural network for de novo molecular design. We applied the method in two scenarios: one to generate random drug-like compounds and another to generate target-biased compounds. Our results show that the method works well in both cases. Sampled compounds from the trained model can largely occupy the same chemical space as the training set and also generate a substantial fraction of novel compounds. Moreover, the drug-likeness score of compounds sampled from LatentGAN is also similar to that of the training set. Lastly, generated compounds differ from those obtained with a Recurrent Neural Network-based generative model approach, indicating that both methods can be used complementarily.
IgM-enriched immunoglobulins (Pentaglobin) may improve the microcirculation in sepsis: a pilot randomized trial
Authors: Domizi Roberta , Adrario Erica , Damiani Elisa , Scorcella Claudia , Carsetti Andrea , Giaccaglia Paolo , Casarotta Erika , Gabbanelli Vincenzo , Pantanetti Simona , Lamura Elena , Ciucani Silvia , Donati Abele 
Published: December 2019

Abstract
Background
Polyclonal or IgM-enriched immunoglobulins may be beneficial during sepsis as an adjuvant immunomodulatory therapy. We aimed to test whether the infusion of IgM-enriched immunoglobulins improves microvascular perfusion during sepsis.

Methods
Single-centre, randomized, double-blind, placebo-controlled phase II trial including adult patients with a diagnosis of sepsis or septic shock for less than 24 h. Patients received an intravenous infusion of 250 mg/kg (5 mL/kg) per day of IgM-enriched immunoglobulins (Pentaglobin, n = 10) for 72 h or placebo (NaCl 0.9%, n = 9). At baseline and after 24 and 72 h of infusion, the sublingual microcirculation was assessed with Incident Dark Field videomicroscopy. Thenar near-infrared spectroscopy (NIRS) was applied with a vascular occlusion test to assess tissue oxygenation and microvascular reactivity. Levels of interleukin (IL) 1-beta, IL-6, IL-8, IL-10 and tumour necrosis factor alpha were measured in the serum.

Results
The perfused vessel density (PVD) for small vessels (diameter < 20 micron) increased in the Pentaglobin group (from 21.7 ± 4.7 to 25.5 ± 5.1 mm/mm2) and decreased in the placebo group (from 25 ± 5.8 to 20.7 ± 4.1 mm/mm2, p for interaction < 0.001, two-way analysis of variance). The absolute between-group difference at 72 h was 4.77 (standard error 2.34), p = 0.140. The microvascular flow index for small vessels increased at 24 h in the Pentaglobin group (from 2.68 [2.38–2.78] to 2.93 [2.82–3], p < 0.01) and decreased at 72 h in the placebo group (from 2.83 [2.60–2.97] to 2.67 [2.48–2.73], p < 0.05). Changes in general parameters, cytokines and NIRS-derived parameters were similar between the two groups, except for IL-6 and IL-10 that significantly decreased at 72 h only in the Pentaglobin group.

Conclusions
A 72-h infusion of IgM-enriched immunoglobulins (Pentaglobin) in patients with sepsis or septic shock may be associated with an increase in sublingual microvascular perfusion. Further studies are needed to confirm our findings.
Trial registration NCT02655133, www.ClinicalTrials.gov, date of registration 7th January 2016, https://www.clinicaltrials.gov/ct2/show/NCT02655133.
Clinical outcomes of hospitalised patients with catheter-associated urinary tract infection in countries with a high rate of multidrug-resistance: the COMBACTE-MAGNET RESCUING study
Authors:   on behalf of RESCUING Study Group and Study Sites, Gomila Aina , Carratalà Jordi , Eliakim-Raz Noa , Shaw Evelyn , Tebé Cristian , Wolkewitz Martin , Wiegand Irith , Grier Sally , Vank Christiane , Cuperus Nienke , Van den Heuvel Leonard , Vuong Cuong , MacGowan Alasdair , Leibovici Leonard , Addy Ibironke , Pujol Miquel 
Published: December 2019

Abstract
Background
Although catheter-associated urinary tract infection (CA-UTI) is a major healthcare-related problem worldwide, there is a scarcity of current data from countries with high antimicrobial resistance rates. We aimed to determine the clinical outcomes of patients with CA-UTI compared to those of patients with other sources of complicated urinary tract infection (cUTI), and to assess the impact of antimicrobial resistance. We also aimed to identify the factors influencing 30-day mortality among patients with CA-UTI.

Methods
This was a multicentre, multinational retrospective cohort study including hospitalised adults with cUTI between January 2013 and December 2014 in twenty hospitals from eight countries from southern Europe, Turkey and Israel. The primary endpoint was 30-day mortality. The secondary endpoints were length of hospital stay, symptom improvement after 7 days’ treatment, symptom recurrence at 30 days and readmission 60 days after hospital discharge.

Results
Of the 807 cUTI episodes, 341 (42.2%) were CA-UTIs. The time from catheter insertion to cUTI diagnosis was less than 2 weeks in 44.6% of cases. Overall, 74.5% of cases had hospital or healthcare-acquired CA-UTI. Compared to patients with other cUTI aetiologies, those with CA-UTI had the following characteristics: they were more frequently males, older, admitted for a reason other than cUTI and admitted from a long-term care facility; had higher Charlson’s comorbidity index; and more frequently had polymicrobial infections and multidrug-resistant Gram-negative bacteria (MDR-GNB). Patients with CA-UTI also had significantly higher 30-day mortality rates (15.2% vs 6%) and longer hospital stay (median 14 [interquartile range -IQR- 7-27] days vs 8 [IQR 5–14] days) than patients with cUTI of other sources. After adjusting for confounders, CA-UTI was not independently associated with an increased risk of mortality (odds ratio, 1.40; 95% confidence interval, 0.77–2.54), and neither was the presence of MDR-GNB.

Conclusions
CA-UTI was the most frequent source of cUTI, affecting mainly frail patients. The mortality of patients with CA-UTI was high, though this was not directly related to the infection.