bluuebunny/crossref_metadata_2025_split huggingface dataset:
Costs and economic evaluations of Quality Improvement Collaboratives in healthcare: a systematic review
Authors: de la Perrelle Lenore , Radisic Gorjana , Cations Monica , Kaambwa Billingsley , Barbery Gaery , Laver Kate 
Published: March 2020

AbstractBackgroundIn increasingly constrained healthcare budgets worldwide, efforts to improve quality and reduce costs are vital. Quality Improvement Collaboratives (QICs) are often used in healthcare settings to implement proven clinical interventions within local and national programs. The cost of this method of implementation, however, is cited as a barrier to use. This systematic review aims to identify and describe studies reporting on costs and cost-effectiveness of QICs when used to implement clinical guidelines in healthcare.MethodsMultiple databases (CINAHL, MEDLINE, PsycINFO, EMBASE, EconLit and ProQuest) were searched for economic evaluations or cost studies of QICs in healthcare. Studies were included if they reported on economic evaluations or costs of QICs. Two authors independently reviewed citations and full text papers. Key characteristics of eligible studies were extracted, and their quality assessed against the Consolidated Health Economic Evaluation Reporting Standards (CHEERS). Evers CHEC-List was used for full economic evaluations. Cost-effectiveness findings were interpreted through the Johanna Briggs Institute ‘three by three dominance matrix tool’ to guide conclusions. Currencies were converted to United States dollars for 2018 using OECD and World Bank databases.ResultsFew studies reported on costs or economic evaluations of QICs despite their use in healthcare. Eight studies across multiple healthcare settings in acute and long-term care, community addiction treatment and chronic disease management were included. Five were considered good quality and favoured the establishment of QICs as cost-effective implementation methods. The cost savings to the healthcare setting identified in these studies outweighed the cost of the collaborative itself.ConclusionsPotential cost savings to the health care system in both acute and chronic conditions may be possible by applying QICs at scale. However, variations in effectiveness, costs and elements of the method within studies, indicated that caution is needed. Consistent identification of costs and description of the elements applied in QICs would better inform decisions for their use and may reduce perceived barriers. Lack of studies with negative findings may have been due to publication bias. Future research should include economic evaluations with societal perspectives of costs and savings and the cost-effectiveness of elements of QICs.Trial registrationPROSPERO registration number:CRD42018107417.
Patient satisfaction and survey response in 717 hospital surveys in Switzerland: a cross-sectional study
Authors: Perneger Thomas V. , Peytremann-Bridevaux Isabelle , Combescure Christophe 
Published: March 2020

Abstract
Background
The association between patient satisfaction and survey response is only partly understood. In this study, we describe the association between average satisfaction and survey response rate across hospital surveys, and model the association between satisfaction and propensity to respond for individual patients.

Methods
Secondary analysis of patient responses (166′014 respondents) and of average satisfaction scores and response rates obtained in 717 annual patient satisfaction surveys conducted between 2011 and 2015 at 164 Swiss hospitals. The satisfaction score was the average of 5 items scored between 0 and 10. The association between satisfaction and response propensity in individuals was modeled as the function that predicted best the observed response rates across surveys.

Results
Among the 717 surveys, response rates ranged from 16.1 to 80.0% (pooled average 49.8%), and average satisfaction scores ranged from 8.36 to 9.79 (pooled mean 9.15). At the survey level, the mean satisfaction score and response rate were correlated (r = 0.61). This correlation held for all subgroups of surveys, except for the 5 large university hospitals. The estimated individual response propensity function was “J-shaped”: the probability of responding was lowest (around 20%) for satisfaction scores between 3 and 7, increased sharply to about 70% for those maximally satisfied, and increased slightly for the least satisfied. Average satisfaction scores projected for 100% participation were lower than observed average scores.

Conclusions
The most satisfied patients were the most likely to participate in a post-hospitalization satisfaction survey. This tendency produces an upward bias in observed satisfaction scores, and a positive correlation between average satisfaction and response rate across surveys.
Contaminant DNA in bacterial sequencing experiments is a major source of false genetic variability
Authors: Goig Galo A. , Blanco Silvia , Garcia-Basteiro Alberto L. , Comas Iñaki 
Published: March 2020

Abstract
Background
Contaminant DNA is a well-known confounding factor in molecular biology and in genomic repositories. Strikingly, analysis workflows for whole-genome sequencing (WGS) data commonly do not account for errors potentially introduced by contamination, which could lead to the wrong assessment of allele frequency both in basic and clinical research.

Results
We used a taxonomic filter to remove contaminant reads from more than 4000 bacterial samples from 20 different studies and performed a comprehensive evaluation of the extent and impact of contaminant DNA in WGS. We found that contamination is pervasive and can introduce large biases in variant analysis. We showed that these biases can result in hundreds of false positive and negative SNPs, even for samples with slight contamination. Studies investigating complex biological traits from sequencing data can be completely biased if contamination is neglected during the bioinformatic analysis, and we demonstrate that removing contaminant reads with a taxonomic classifier permits more accurate variant calling. We used both real and simulated data to evaluate and implement reliable, contamination-aware analysis pipelines.

Conclusion
As sequencing technologies consolidate as precision tools that are increasingly adopted in the research and clinical context, our results urge for the implementation of contamination-aware analysis pipelines. Taxonomic classifiers are a powerful tool to implement such pipelines.
Epigenetic regulation of epithelial-mesenchymal transition: focusing on hypoxia and TGF-β signaling
Authors: Lin Yueh-Te , Wu Kou-Juey 
Published: March 2020

AbstractEpithelial-mesenchymal transition (EMT) is an important process triggered during cancer metastasis. Regulation of EMT is mostly initiated by outside signalling, including TGF-β, growth factors, Notch ligand, Wnt, and hypoxia. Many signalling pathways have been delineated to explain the molecular mechanisms of EMT. In this review, we will focus on the epigenetic regulation of two critical EMT signalling pathways: hypoxia and TGF-β. For hypoxia, hypoxia-induced EMT is mediated by the interplay between chromatin modifiers histone deacetylase 3 (HDAC3) and WDR5 coupled with the presence of histone 3 lysine 4 acetylation (H3K4Ac) mark that labels the promoter regions of various traditional EMT marker genes (e.g. CDH1, VIM). Recently identified new hypoxia-induced EMT markers belong to transcription factors (e.g. SMO, GLI1) that mediate EMT themselves. For TGF-β-induced ΕΜΤ, global chromatin changes, removal of a histone variant (H2A.Z), and new chromatin modifiers (e.g. UTX, Rad21, PRMT5, RbBP5, etc) are identified to be crucial for the regulation of both EMT transcription factors (EMT-TFs) and EMT markers (EMT-Ms). The epigenetic mechanisms utilized in these two pathways may serve as good model systems for other signalling pathways and also provide new potential therapeutic targets.
Engrailed 2 (EN2) acts as a glioma suppressor by inhibiting tumor proliferation/invasion and enhancing sensitivity to temozolomide
Authors: Li Tengfei , Yang Wanchun , Li Mao , Zhang Shuxin , Zhou Xingwang , Zuo Mingrong , Yuan Qiuyun , Chen Mina , Liu Yanhui 
Published: March 2020

Abstract
Background
Glioma is one of the most malignant brain tumors and accounts for the majority of brain cancer related death. Despite progress on mechanistic studies, current understandings of the initiation and progression of glioma are still incomplete. Previous studies demonstrate that Engrailed-2 (EN2), a homeobox-containing transcription factor, is associated with tumorigenesis in a range of cancers heterogeneously, however, the profiles of EN2 expression and its potential functions in gliomas remain unclear.

Methods
Real-time PCR was used to identify the expression of EN2 in glioma tissues. To study the biological function of EN2 in glioma, we compared the cell viability and proliferation profiles between EN2 overexpressed and control cells using cell counting kit-8 (CCK8) assay, EdU incorporation assay and colony formation assay. Flow cytometry and Hoechst staining assays were performed to investigate the role of EN2 on glioma cell death. Finally, wound healing and transwell assays were carried out to investigate the role of EN2 on glioma cell invasion.

Results
We identified that EN2 was downregulated in human gliomas compared with paired adjacent normal tissues and negatively associated with glioma malignancy. Elevated EN2 expression inhibits cell proliferation, enhances glioma sensitivity to temozolomide and inhibits migration/invasion of glioma cells.

Conclusions
Our data identify a novel function of EN2 in glioma suppression and provide potential therapeutic targets for glioma therapy.
Clinical outcomes of chondroblastoma treated using synthetic bone substitute: risk factors for developing radiographic joint degeneration
Authors: Outani Hidetatsu , Kakunaga Shigeki , Hamada Kenichiro , Takenaka Satoshi , Nakai Sho , Yasuda Naohiro , Imura Yoshinori , Naka Norifumi , Araki Nobuhito , Ueda Takafumi , Yoshikawa Hideki 
Published: March 2020

Abstract
Background
Chondroblastoma (CB) is a rare locally aggressive bone tumor that commonly occurs in the epiphysis or apophysis of long bones. Although surgical treatment of CB carries potential risk for physeal or articular cartilage damage, risk factors for joint degeneration have not been well described. In addition, we have mainly used synthetic bone substitute (SBS) to fill the bone defect after intralesional curettage as treatment for CB. This study thus aimed to evaluate the incidence of and risk factors for adjacent-joint radiographic degeneration after SBS treatment for CB.

Methods
We retrospectively reviewed 48 patients treated for CB at our institutions between 1996 and 2017. Clinical data, radiographic images, treatments, and local recurrence were analyzed.

Results
We identified 40 patients [29 males and 11 females with a mean age of 19 years (range, 8–35 years)] who received SBS to fill the defect after curettage with a minimum follow-up of 1 year. The mean follow-up period was 71 months (range, 13–239 months). A total of 8 patients (20%) developed local recurrence. Radiographic analysis showed that 5 patients (16.7%) developed radiographic joint degeneration. Joint degeneration was significantly associated with the affected joint (p = 0.004).

Conclusions
Curettage and SBS filling had been found to be a reasonable treatment method for CB, which commonly occurs in the epiphysis or apophysis. Radiographic joint degeneration was not uncommon after CB treatment, especially in the talus and proximal humerus.
Tissue microRNAs in non-small cell lung cancer detected with a new kind of liquid bead array detection system
Authors: Zheng Yuan-Yuan , Fei Yun , Wang Zheng , Chen Yue , Qiu Cheng , Li Fu-Rong 
Published: March 2020

Abstract
Background
Commonly used miRNA detection methods cannot be applied for high-throughput analyses. However, this study was aimed to performed a liquid bead array detection system (LBAS) to detect tissue 6 miRNAs in non-small cell lung cancer (NSCLC).

Methods
In this study, evaluation of LBAS was performed to observe the precision, specificity, limitation and stability. Then, a total of 52 primary NSCLC patients who received resection operation without preoperative radiotherapy and chemotherapy between June 2013 and March 2014 were selected, and then the total RNA of the tissues were extracted. We prepared six NSCLC-related miRNAs for LBAS. After optimization and evaluation, LBAS was verified by detecting the relative expression levels of 6 microRNAs in the pathological tissues and corresponding normal tissues of 52 NSCLC patients.

Results
The results of evaluation of LBAS showed that the Mean Fluorescence Intensity (MFI) of the reaction only added with chimeric probes and beads showed no significant change after 180 days (P > 0.05). And the intra-assay Coefficient of Variation (CV) was between 1.57 and 3.5%, while the inter-assay CV was between 4.24 and 11.27%, indicating this system was ideal for diagnostic reagents. In addition, only the beads corresponding to the additional miRNAs showed high MFIs from 8426 to 18,769, whereas the fluorescence values of the other beads were under background levels (MFIs = 20 to 55) in each reaction, indicating no cross reactivity among the miRNAs. The limit of detection of miR-21, miR-210, miR-125b, miR-155, miR-375, and miR-31 were 5.27, 1.39, 1.85, 2.01, 1.34, and 2.73 amol/μL, respectively, showing that the lowest detection limit of miRNA by this system was under pM level. Then, the relative expression levels of miR-21, miR-210, miR-125b, miR-155, miR-375, and miR-31 by using this system were significantly correlated with NSCLC (P < 0.05). And the results of AUC method indicated that specific of the LBAS system was 94.2%.

Conclusions
Our findings suggest that LBAS was simple, high-throughput, and freely combined with absolute quantification. Thus, this system could be applied for tumor miRNAs detection.
Design, synthesis, and biological evaluation of a multifunctional neuropeptide-Y conjugate for selective nuclear delivery of radiolanthanides
Authors: Chastel Adrien , Worm Dennis J. , Alves Isabel D. , Vimont Delphine , Petrel Melina , Fernandez Samantha , Garrigue Philippe , Fernandez Philippe , Hindié Elif , Beck-Sickinger Annette G. , Morgat Clément 
Published: March 2020

Abstract
Background
Targeting G protein-coupled receptors on the surface of cancer cells with peptide ligands is a promising concept for the selective tumor delivery of therapeutically active cargos, including radiometals for targeted radionuclide therapy (TRT). Recently, the radiolanthanide terbium-161 (161Tb) gained significant interest for TRT application, since it decays with medium-energy β-radiation but also emits a significant amount of conversion and Auger electrons with short tissue penetration range. The therapeutic efficiency of radiometals emitting Auger electrons, like 161Tb, can therefore be highly boosted by an additional subcellular delivery into the nucleus, in order to facilitate maximum dose deposition to the DNA. In this study, we describe the design of a multifunctional, radiolabeled neuropeptide-Y (NPY) conjugate, to address radiolanthanides to the nucleus of cells naturally overexpressing the human Y1 receptor (hY1R).
By using solid-phase peptide synthesis, the hY1R-preferring [F7,P34]-NPY was modified with a fatty acid, a cathepsin B-cleavable linker, followed by a nuclear localization sequence (NLS), and a DOTA chelator (compound pb12). In this proof-of-concept study, labeling was performed with either native terbium-159 (natTb), as surrogate for 161Tb, or with indium-111 (111In).

Results
[natTb]Tb-pb12 showed a preserved high binding affinity to endogenous hY1R on MCF-7 cells and was able to induce receptor activation and internalization similar to the hY1R-preferring [F7,P34]-NPY. Specific internalization of the 111In-labeled conjugate into MCF-7 cells was observed, and importantly, time-dependent nuclear uptake of 111In was demonstrated. Study of metabolic stability showed that the peptide is insufficiently stable in human plasma. This was confirmed by injection of [111In]In-pb12 in nude mice bearing MCF-7 xenograft which showed specific uptake only at very early time point.

Conclusion
The multifunctional NPY conjugate with a releasable DOTA-NLS unit represents a promising concept for enhanced TRT with Auger electron-emitting radiolanthanides. Our research is now focusing on improving the reported concept with respect to the poor plasmatic stability of this promising radiopeptide.
Modelling movement and stage-specific habitat preferences of a polyphagous insect pest
Authors: Garcia Adriano G. , Godoy Wesley A. C. , Cônsoli Fernando L. , Ferreira Claudia P. 
Published: March 2020

Abstract
Background
The feeding preferences of Diabrotica speciosa (Coleoptera: Chrysomelidae) cause a parent-offspring conflict, as providing the best host for the offspring development is detrimental to adult survival and fecundity. Understanding the implications of this conflict could help entomologists to implement pest-management programs. With this in mind, the foraging behaviour of D. speciosa was investigated using an individual-based model in two distinct scenarios.

Methods
In an intercropping scenario, parent-offspring conflict was simulated when adult insects exploit two crops (corn and soybean) that provide different nutritional advantages for each insect stage. First, we compared three hypothetical types of adult dispersal, considering a continuous oviposition over time: diffusion, attracted to a fixed host and alternating the preference between hosts with frequency $\frac {1}{\tau }$1τ, where τ is the time in days spent foraging for each host. We also simulated two principles: “mother knows best” (adult females foraging for corn during the oviposition period) and “optimal bad motherhood” (adult females remain foraging for soybean to maximise their own fitness during the oviposition period), but considering the existence of a pre-oviposition period. In a landscape scenario, we investigated the population dynamics in an area composed by 4 crop plots that change over time.

Results
Among dispersal types considering continuous oviposition, the crop-alternating movement a-3 performed best, when close to an optimal τ. Additionally, τ was predicted to be influenced mainly by the width of crop rows. We also verified that the “mother knows best” strategy is better for the population growth than the “optimal bad motherhood”. In the landscape scenario, we observed that including fallow periods in the crop calendar and adopting a more-heterogeneous arrangement of crop plots reduced the density of this insect.

Conclusion
Both the continuous and sequential oviposition simulations indicate that foraging involving switching of target crop benefits population fitness. In the landscape scenario, arranging crop plots more heterogeneously and avoiding vast areas of soybean can help farmers to control this insect pest. Additionally, fallow periods can also reduce significantly D. speciosa populations.
Effect of crocin on antioxidant gene expression, fibrinolytic parameters, redox status and blood biochemistry in nicotinamide-streptozotocin-induced diabetic rats
Authors: Margaritis Ioannis , Angelopoulou Katerina , Lavrentiadou Sophia , Mavrovouniotis Ilias C. , Tsantarliotou Maria , Taitzoglou Ioannis , Theodoridis Alexandros , Veskoukis Aristidis , Kerasioti Efthalia , Kouretas Dimitrios , Zervos Ioannis 
Published: March 2020

Abstract
Background
Diabetes is regarded as an epidemiological threat for the twenty-first century. Phytochemicals with known pharmaceutical properties have gained interest in the field of alleviating secondary complications of diseases. Such a substance is crocin, a basic constituent of saffron (Crocus sativus). The present study aimed at examining the beneficial effects of per os crocin administration on the antioxidant status, blood biochemical profile, hepatic gene expression and plasminogen activator inhibitor-1 activity (PAI-1) in the liver, kidney and plasma (an important marker of pre-diabetic status and major factor of thrombosis in diabetes) of healthy rats, as well as of rats with nicotinamide-streptozotocin-induced diabetes.

Results
Diabetes disrupted the oxidation-antioxidation balance, while crocin improved the antioxidant state in the liver by significantly affecting SOD1 gene expression and/or by restoring SOD and total antioxidant capacity (TAC) levels. In the kidney, crocin improved hydrogen peroxide decomposing activity and TAC. In blood, hepatic transaminases ALT and AST decreased significantly, while there was a trend of decrease regarding blood urea nitrogen (BUN) levels. The expression of PAI-1 gene was affected in the liver by the dose of 50 mg kg−1.

Conclusions
Crocin treatment contributed in restoring some parameters after diabetes induction, primarily by affecting significantly hepatic transaminases ALT and AST, SOD1 and PAI-1 gene expression and nephric H2O2 decomposing activity. In conclusion, crocin did contribute to the alleviation of some complications of diabetes.
Impact of process temperature and organic loading rate on cellulolytic / hydrolytic biofilm microbiomes during biomethanation of ryegrass silage revealed by genome-centered metagenomics and metatranscriptomics
Authors: Maus Irena , Klocke Michael , Derenkó Jaqueline , Stolze Yvonne , Beckstette Michael , Jost Carsten , Wibberg Daniel , Blom Jochen , Henke Christian , Willenbücher Katharina , Rumming Madis , Rademacher Antje , Pühler Alfred , Sczyrba Alexander , Schlüter Andreas 
Published: March 2020

Abstract
Background
Anaerobic digestion (AD) of protein-rich grass silage was performed in experimental two-stage two-phase biogas reactor systems at low vs. increased organic loading rates (OLRs) under mesophilic (37 °C) and thermophilic (55 °C) temperatures. To follow the adaptive response of the biomass-attached cellulolytic/hydrolytic biofilms at increasing ammonium/ammonia contents, genome-centered metagenomics and transcriptional profiling based on metagenome assembled genomes (MAGs) were conducted.

Results
In total, 78 bacterial and archaeal MAGs representing the most abundant members of the communities, and featuring defined quality criteria were selected and characterized in detail. Determination of MAG abundances under the tested conditions by mapping of the obtained metagenome sequence reads to the MAGs revealed that MAG abundance profiles were mainly shaped by the temperature but also by the OLR. However, the OLR effect was more pronounced for the mesophilic systems as compared to the thermophilic ones. In contrast, metatranscriptome mapping to MAGs subsequently normalized to MAG abundances showed that under thermophilic conditions, MAGs respond to increased OLRs by shifting their transcriptional activities mainly without adjusting their proliferation rates. This is a clear difference compared to the behavior of the microbiome under mesophilic conditions. Here, the response to increased OLRs involved adjusting of proliferation rates and corresponding transcriptional activities. The analysis led to the identification of MAGs positively responding to increased OLRs. The most outstanding MAGs in this regard, obviously well adapted to higher OLRs and/or associated conditions, were assigned to the order Clostridiales (Acetivibrio sp.) for the mesophilic biofilm and the orders Bacteroidales (Prevotella sp. and an unknown species), Lachnospirales (Herbinix sp. and Kineothrix sp.) and Clostridiales (Clostridium sp.) for the thermophilic biofilm. Genome-based metabolic reconstruction and transcriptional profiling revealed that positively responding MAGs mainly are involved in hydrolysis of grass silage, acidogenesis and / or acetogenesis.

Conclusions
An integrated -omics approach enabled the identification of new AD biofilm keystone species featuring outstanding performance under stress conditions such as increased OLRs. Genome-based knowledge on the metabolic potential and transcriptional activity of responsive microbiome members will contribute to the development of improved microbiological AD management strategies for biomethanation of renewable biomass.