bluuebunny/crossref_metadata_2025_split huggingface dataset:
MiRNA therapeutics based on logic circuits of biological pathways
Authors: Boscaino Valeria , Fiannaca Antonino , La Paglia Laura , La Rosa Massimo , Rizzo Riccardo , Urso Alfonso 
Published: November 2019

Abstract
Background
In silico experiments, with the aid of computer simulation, speed up the process of in vitro or in vivo experiments. Cancer therapy design is often based on signalling pathway. MicroRNAs (miRNA) are small non-coding RNA molecules. In several kinds of diseases, including cancer, hepatitis and cardiovascular diseases, they are often deregulated, acting as oncogenes or tumor suppressors. miRNA therapeutics is based on two main kinds of molecules injection: miRNA mimics, which consists of injection of molecules that mimic the targeted miRNA, and antagomiR, which consists of injection of molecules inhibiting the targeted miRNA. Nowadays, the research is focused on miRNA therapeutics. This paper addresses cancer related signalling pathways to investigate miRNA therapeutics.

Results
In order to prove our approach, we present two different case studies: non-small cell lung cancer and melanoma. KEGG signalling pathways are modelled by a digital circuit. A logic value of 1 is linked to the expression of the corresponding gene. A logic value of 0 is linked to the absence (not expressed) gene. All possible relationships provided by a signalling pathway are modelled by logic gates. Mutations, derived according to the literature, are introduced and modelled as well. The modelling approach and analysis are widely discussed within the paper. MiRNA therapeutics is investigated by the digital circuit analysis. The most effective miRNA and combination of miRNAs, in terms of reduction of pathogenic conditions, are obtained. A discussion of obtained results in comparison with literature data is provided. Results are confirmed by existing data.

Conclusions
The proposed study is based on drug discovery and miRNA therapeutics and uses a digital circuit simulation of a cancer pathway. Using this simulation, the most effective combination of drugs and miRNAs for mutated cancer therapy design are obtained and these results were validated by the literature. The proposed modelling and analysis approach can be applied to each human disease, starting from the corresponding signalling pathway.
Better quality score compression through sequence-based quality smoothing
Authors: Shibuya Yoshihiro , Comin Matteo 
Published: November 2019

Abstract
Motivation
Current NGS techniques are becoming exponentially cheaper. As a result, there is an exponential growth of genomic data unfortunately not followed by an exponential growth of storage, leading to the necessity of compression. Most of the entropy of NGS data lies in the quality values associated to each read. Those values are often more diversified than necessary. Because of that, many tools such as Quartz or GeneCodeq, try to change (smooth) quality scores in order to improve compressibility without altering the important information they carry for downstream analysis like SNP calling.

Results
We use the FM-Index, a type of compressed suffix array, to reduce the storage requirements of a dictionary of k-mers and an effective smoothing algorithm to maintain high precision for SNP calling pipelines, while reducing quality scores entropy.
We present YALFF (Yet Another Lossy Fastq Filter), a tool for quality scores compression by smoothing leading to improved compressibility of FASTQ files. The succinct k-mers dictionary allows YALFF to run on consumer computers with only 5.7 GB of available free RAM. YALFF smoothing algorithm can improve genotyping accuracy while using less resources.

Availability
https://github.com/yhhshb/yalff
In-line filtration of intravenous infusion may reduce organ dysfunction of adult critical patients
Authors: Schmitt Elke , Meybohm Patrick , Herrmann Eva , Ammersbach Karin , Endres Raphaela , Lindau Simone , Helmer Philipp , Zacharowski Kai , Neb Holger 
Published: November 2019

Abstract
Background
The potential harmful effects of particle-contaminated infusions for critically ill adult patients are yet unclear. So far, only significant improved outcome in critically ill children and new-borns was demonstrated when using in-line filters, but for adult patients, evidence is still missing.

Methods
This single-centre, retrospective controlled cohort study assessed the effect of in-line filtration of intravenous fluids with finer 0.2 or 1.2 μm vs 5.0 μm filters in critically ill adult patients. From a total of n = 3215 adult patients, n = 3012 patients were selected by propensity score matching (adjusting for sex, age, and surgery group) and assigned to either a fine filter cohort (with 0.2/1.2 μm filters, n = 1506, time period from February 2013 to January 2014) or a control filter cohort (with 5.0 μm filters, n = 1506, time period from April 2014 to March 2015). The cohorts were compared regarding the occurrence of severe vasoplegia, organ dysfunctions (lung, kidney, and brain), inflammation, in-hospital complications (myocardial infarction, ischemic stroke, pneumonia, and sepsis), in-hospital mortality, and length of ICU and hospital stay.

Results
Comparing fine filter vs control filter cohort, respiratory dysfunction (Horowitz index 206 (119–290) vs 191 (104.75–280); P = 0.04), pneumonia (11.4% vs 14.4%; P = 0.02), sepsis (9.6% vs 12.2%; P = 0.03), interleukin-6 (471.5 (258.8–1062.8) ng/l vs 540.5 (284.5–1147.5) ng/l; P = 0.01), and length of ICU (1.2 (0.6–4.9) vs 1.7 (0.8–6.9) days; P <  0.01) and hospital stay (14.0 (9.2–22.2) vs 14.8 (10.0–26.8) days; P = 0.01) were reduced. Rate of severe vasoplegia (21.0% vs 19.6%; P > 0.20) and acute kidney injury (11.8% vs 13.7%; P = 0.11) was not significantly different between the cohorts.

Conclusions
In-line filtration with finer 0.2 and 1.2 μm filters may be associated with less organ dysfunction and less inflammation in critically ill adult patients.

Trial registration
The study was registered at ClinicalTrials.gov (number: NCT02281604).
Feasibility of Capturing Cancer Treatment Data in the Utah All-Payer Claims Database
Authors: Hashibe Mia , Ou Judy Y. , Herget Kimberly , Bolton Dan , McPherson Jordan , Hawley Charles , Garvin Jennifer , Doherty Jennifer A. , Sweeney Carol 
Published: November 2019

Purpose Incompleteness of treatment data is a recognized limitation of cancer registry data. An all-payer claims database (APCD) is a tool that states use to capture health care information across systems and payer. We linked the Utah Cancer Registry (UCR) records to Utah’s statewide APCD and evaluated how this linkage led to improvements in the capture of cancer treatment information. Methods We linked cancers diagnosed and reported to the UCR with Utah APCD claims for the calendar years 2013 and 2014 using LinkPlus Software. For patients with breast or colorectal cancers, manual abstraction was completed to provide a gold-standard comparison for the treatment data obtained from the claims. Results Among 10,759 reportable cancer occurrences linked to the APCD, the claims identified additional patients with cancer who received therapies that had been unknown to the registry, increasing the proportion treated with chemotherapy from 23.7% to 27.6%, hormone therapy from 14.1% to 18.8%, immunotherapy from 4.3% to 13.2%, and radiation therapy from 24.9% to 27.5%. The APCD increased the sensitivity of treatment variables compared with the abstraction gold standard. Notably, sensitivity of hormonal therapy for breast cancer increased from 78.6% to 95.2% when augmented with APCD claims data. However, the APCD alone did not achieve as high specificity for treatment data as did the data collected through traditional registry methods. Conclusions This is the first study, to our knowledge, showing that linking cancer registry data with a statewide claims database that covers multiple insurance companies improves cancer treatment data collection. Linking of cancer registry and APCD data can improve comprehensiveness of cancer registry treatment data.
Development and Usage of eContour, a Novel, Three-Dimensional, Image-Based Web Site to Facilitate Access to Contouring Guidelines at the Point of Care
Authors: Sherer Michael V. , Lin Diana , Puri Kartikeya , Panjwani Neil , Zhang Zhigang , Murphy James D. , Gillespie Erin F. 
Published: November 2019

PURPOSE Variation in contouring quality by radiation oncologists is common and can have significant clinical consequences. Image-based guidelines can improve contour accuracy but are underused. We sought to develop a free, online, easily accessible contouring resource that allows users to scroll through cases with 3-dimensional images and access relevant evidence-based contouring information. MATERIALS AND METHODS eContour ( http://econtour.org ) was developed using modern Web technologies, primarily HTML5, Python, and JavaScript, to display JPEGs generated from DICOM files from real patient cases. The viewer has standard tools for image manipulation as well as toggling of contours and overlayed images and radiation dose distributions. Brief written content references published guidelines for contour delineation. Mixpanel software was used to collect Web page usage statistics. RESULTS In the first 3 years of operation (March 8, 2016 to March 7, 2019), a total of 13,391 users from 128 countries registered on the Web site, including 2,358 physicians from the United States. High-frequency users were more likely to be physicians ( P < .001) and from the United States ( P < .001). In one 6-month period, there were 68,642 individual case page views, with head-and-neck the most commonly viewed disease site (32%). Users who accessed a head-and-neck case were more likely to be high-frequency users, and 67% of repeat users accessed the same case more than once. CONCLUSION The large, diverse user base and steady growth in Web site traffic over the first 3 years of eContour demonstrate its strong potential to address the unmet need for dissemination and use of evidence-based contouring information at the point of care.
Landscape of Global Oncology Research and Training at National Cancer Institute–Designated Cancer Centers: Results of the 2018 to 2019 Global Oncology Survey
Authors: Abudu Rachel M. , Cira Mishka K. , Pyle Doug H.M. , Duncan Kalina 
Published: November 2019

PURPOSE The National Cancer Institute (NCI)–Designated Cancer Centers (NDCCs) are active in global oncology research and training, leading collaborations to support global cancer control. To better understand global oncology activities led by NDCCs, the NCI Center for Global Health collaborated with ASCO to conduct the 2018/2019 NCI/ASCO Global Oncology Survey of NDCCs. METHODS Seventy NDCCs received a two-part survey that focused on global oncology programs at NDCCs and non–National Institutes of Health (NIH)-funded global oncology projects with an international collaborator led by the NDCCs. Sixty-seven NDCCs responded to the survey. Data were coded and analyzed by NCI-Center for Global Health staff. RESULTS Thirty-three NDCCs (47%) reported having a global oncology program, and 61 (87%) reported a collective total of 613 non–NIH-funded global oncology projects. Of the NDCCs with global oncology programs, 17 reported that trainees completed rotations outside the United States and the same number enrolled trainees from low- and middle-income countries (LMIC). Primary focus areas of non–NIH-funded projects were research (469 [76.5%]) and capacity building or training (197 [32.1%]). Projects included collaborators from 110 countries; 68 of these were LMIC. CONCLUSION This survey shows that there is a substantial amount of global oncology research and training conducted by NDCCs and that much of this is happening in LMIC. Trends in these data reflect those in recent literature: The field of global oncology is growing, advancing scientific knowledge, contributing to building research and training capacity in LMIC, and becoming a recognized career path. Results of the 2018 Global Oncology Survey can be used to foster opportunities for NDCCs to work collaboratively on activities and to share their findings with relevant stakeholders in their LMIC collaborator countries.
Dental stem cells in tooth repair: A systematic review
Authors: Tawfik Tadros Mary Sabry , El-Baz Maha Abd-El Salam , Khairy Mohamed Adel Ezzat Khairy 
Published: November 2019

Background: Dental stem cells (DSCs) are self-renewable teeth cells, which help maintain or develop oral tissues. These cells can differentiate into odontoblasts, adipocytes, cementoblast-like cells, osteoblasts, or chondroblasts and form dentin/pulp. This systematic review aimed to summarize the current evidence regarding the role of these cells in dental pulp regeneration. Methods: We searched the following databases: PubMed, Cochrane Library, MEDLINE, SCOPUS, ScienceDirect, and Web of Science using relevant keywords. Case reports and non-English studies were excluded. We included all studies using dental stem cells in tooth repair whether in vivo or in vitro studies. Results: Dental pulp stem cell (DPSCs) is the most common type of cell. Most stem cells are incorporated and implanted into the root canals in different scaffold forms. Some experiments combine growth factors such as TDM, BMP, and G-CSF with stem cells to improve the results. The transplant of DPSCs and stem cells from apical papilla (SCAPs) was found to be associated with pulp-like recovery, efficient revascularization, enhanced chondrogenesis, and direct vascular supply of regenerated tissue. Conclusion: The current evidence suggests that DPSCs, stem cells from human exfoliated deciduous teeth, and SCAPs are capable of providing sufficient pulp regeneration and vascularization. For the development of the dental repair field, it is important to screen for more effective stem cells, dentine releasing therapies, good biomimicry scaffolds, and good histological markers.
Advancing good governance in data sharing and biobanking - international aspects
Authors: Fernando Buddhika , King Mandella , Sumathipala Athula 
Published: November 2019

Ethical and effective data-sharing among countries can be achieved by considering the interests of all relevant parties: research participants, researchers and funders. Fears of exploitation, however, both of research participants and researchers from low- and middle-income countries (LMIC), can undermine the free flow of data necessary for scientific advancement.In this Open Letter, two case studies presented at the 2018 Global Forum on Bioethics in Research meeting on the Ethics of data sharing and biobanking in Cape Town, South Africa, function as the focal point for a reflection on the attributes of an ideal model of good data governance and how it can help support ethical best practices in biobanking and data sharing.Consideration of the case studies as well as the literature indicate three broad principles that need to be reflected in an ideal data governance framework: (i) collaboration - both among researchers as well as between researchers and participants, (ii) fairness – ensuring that all parties in international collaborations, the data provider, primary data gathering LMIC researcher and the high income country (HIC) institution/funder are treated fairly, and (iii) working towards a level playing field – neither collaboration nor fairness can be effectively achieved with the existing power differential between HIC and LMIC researchers/institutions; it is therefore necessary to work towards achieving a more level playing field between partners in research collaborations.Promoting good governance of data through fair, efficient and accountable governance frameworks can help build trust and ensure continued international data sharing.
Does post-registration palliative care education for nurses improve practice? A systematic review
Authors: Thavaraj Angela , Gillett Karen 
Published: November 2019

Aims:We aimed to answer the question: what is the evidence that post-registration palliative care education for nurses improves practice?Background:The 2008 End of Life Care Strategy emphasised the need for a workforce equipped to provide high-quality end-of-life care for patients and their families. As registered nurses are the healthcare professionals spending most time with patients and families at the end of life, associated policy documents stress the importance of educating nurses to equip them with the necessary knowledge and skills to provide effective care. Despite education being a consistent recommendation, the ability of education to influence nursing practice is uncertain.Methods:We undertook a systematic review of literature using Joanna Briggs Institute Methodology for Mixed Methods by searching the Medline, Embase and CINAHL databases between January 2006 and December 2018.Findings:Ten studies met the inclusion criteria, seven contained quantitative data. Six demonstrated improvements in outcome measures, but not all results were statistically significant. Most quantitative data related to self-reported measures of confidence. Six studies contained qualitative findings that were categorised into themes: confidence, practice change, skills and proactivity.Conclusion:Little research exists exploring the impact of post-registration palliative care education for nurses. Existing outcome measures do not clearly demonstrate changes to end-of-life practice. Research is suggested to establish links between self-reported confidence and improvements to practice. Evaluation of the impact on practice should be an integral component of end-of-life education initiatives.
Implementation of duty of candour within neurosurgery: a national survey and framework for improved application in clinical practice
Authors: Basu S , Marcus HJ , Sayal P , Kitchen N , Ley R , Hutchinson PJ , Thorne L 
Published: November 2019

Introduction Statutory duty of candour was introduced in November 2014 for NHS bodies in England. Contained within the regulation were definitions regarding the threshold for what constitutes a notifiable patient safety incident. However, it can be difficult to determine when the process should be implemented. The aim of this survey was to evaluate the interpretation of these definitions by British neurosurgeons. Materials and methods All full (consultant) members of the Society of British Neurological Surgeons were electronically invited to participate in an online survey. Surgeons were presented with 15 cases and asked to decide in the case of each one whether they would trigger the process of duty of candour. Cases were stratified according to their likelihood and severity. Results In all, 106/357 (29.7%) members participated in the survey. Responses varied widely, with almost no members triggering the process of duty of candour in cases where adverse events were common (greater than 10% likelihood) and required only outpatient follow-up (7/106; 6.6%), and almost all members doing so in cases where adverse events were rare (less than 0.1% likelihood) and resulted in death (102/106; 96.2%). However, there was clear equipoise in triggering the process of duty of candour in cases where adverse events were uncommon (0.1–10% likelihood) and resulted in moderate harm (38/106; 35.8%), severe harm (57/106; 53.8%) or death (49/106; 46.2%). Conclusion There is considerable nationwide variation in the interpretation of definitions regarding the threshold for duty of candour. To this end, we propose a framework for the improved application of duty of candour in clinical practice.
Quality of Life in Families of Young Children With Autism Spectrum Disorder
Authors: Mello Catherine , Rivard Mélina , Terroux Amélie , Mercier Céline 
Published: November 2019

Abstract
The present study investigated family quality of life (FQOL) as experienced by 493 mothers and fathers (295 families) of young children with autism spectrum disorder (ASD) prior to receiving early intervention services in the province of Québec. These families were most satisfied with their physical and material well-being and least satisfied with their family interactions. Children's level of functioning across various standardized and subjective measures were positively associated with parents' FQOL. In both parents, family characteristics associated with financial and personal resources were also linked to FQOL. The child's age and the number of children were associated with mothers' FQOL. Overall, these findings provide a portrait of ASD-related stressors and resources relevant to both parents during the early childhood period.
Unified Extracurricular Activities as a Pathway to Social Inclusion in High Schools
Authors: Siperstein Gary N. , McDowell Emily D. , Jacobs Holly E. , Stokes Jeffrey E. , Cahn Andrea L. 
Published: November 2019

Abstract
The present study examined how a multicomponent intervention embedded in a high school's extracurricular framework impacts students' acceptance of peers with intellectual disability (ID). Data were collected from eight high schools, three of which implemented the Special Olympics Unified Champion Schools (UCS) program involving inclusive sports, clubs, and schoolwide events, and five of which did not. A pretest-posttest survey design was used to measure students' attitudes, perceptions, and interactions (n = 1,230). Lagged dependent variable modeling revealed that UCS participation significantly predicted improved attitudes toward peers with ID and perceptions of school social inclusion, as well as increased social interactions with peers with ID. Unified extracurricular activities may be the next step forward in promoting an inclusive school culture.
Vedolizumab quantitation using high-resolution accurate mass-mass spectrometry middle-up protein subunit: method validation
Authors: Cradic Kendall W. , Ladwig Paula M. , Rivard Ann L. , Katrangi Waddah , Wintgens Karl Florian , Willrich Maria A.V. 
Published: November 2019

Abstract

Background
While quantitation methods for small-molecule and tryptic peptide bottom-up mass spectrometry (MS) have been well defined, quantitation methods for top-down or middle-up MS approaches have not been as well defined. Therapeutic monoclonal antibodies (t-mAbs) are a group of proteins that can be used to both demonstrate the advantages of top-down or middle-up detection methods over classic tryptic peptide bottom-up along with the growing need for robust quantitation strategies/software for these top-down or middle-up methods. Bottom-up proteolytic digest methods for the t-mAbs tend to suffer from challenges such as limited peptide selection due to potential interference from the polyclonal immunoglobulin background, complicated workflows, and inadequate sensitivity and specificity without laborious purification steps, and therefore have prompted the search for new detection and quantitation methods. Time-of-flight along with Orbitrap MS have recently evolved from the research and/or pharmaceutical setting into the clinical laboratory. With their superior mass measurement accuracy, resolution and scanning speeds, these are ideal platforms for top-down or middle-up characterization and quantitation.

Methods
We demonstrate a validated, robust, middle-up protein subunit detection and quantitation method for the IgG1 t-mAb, vedolizumab (VEDO), which takes advantage of the high resolution of the Orbitrap MS detection and quantitation software to increase specificity.

Results
Validated performance characteristics met pre-defined acceptance criteria with simple workflows and rapid turnaround times: characteristics necessary for implementation into a high-volume clinical MS laboratory.

Conclusions
While the extraction method can easily be used with other IgG1 t-mAbs, the detection and quantitation method may become an option for measurement of other proteins.
Menger algebras of k-commutative n-place functions
Authors: Dudek Wieslaw A. , Trokhimenko Valentin S. 
Published: November 2019

Abstract
We prove that the set of all k-commutative n-place functions defined on a fixed set forms a Menger algebra, and characterize such algebras by their densely embedded ideals.
We also describe all automorphisms of such algebras.