bluuebunny/crossref_metadata_2025_split huggingface dataset:
Machine learning analyses of methylation profiles uncovers tissue‐specific gene expression patterns in wheat
Authors: N'Diaye Amidou , Byrns Brook , Cory Aron T. , Nilsen Kirby T. , Walkowiak Sean , Sharpe Andrew , Robinson Stephen J. , Pozniak Curtis J. 
Published: June 2020

AbstractDNA methylation is a mechanism of epigenetic modification in eukaryotic organisms. Generally, methylation within genes promoter inhibits regulatory protein binding and represses transcription, whereas gene body methylation is associated with actively transcribed genes. However, it remains unclear whether there is interaction between methylation levels across genic regions and which site has the biggest impact on gene regulation. We investigated and used the methylation patterns of the bread wheat cultivar Chinese Spring to uncover differentially expressed genes (DEGs) between roots and leaves, using six machine learning algorithms and a deep neural network. As anticipated, genes with higher expression in leaves were mainly involved in photosynthesis and pigment biosynthesis processes whereas genes that were not differentially expressed between roots and leaves were involved in protein processes and membrane structures. Methylation occurred preponderantly (60%) in the CG context, whereas 35 and 5% of methylation occurred in CHG and CHH contexts, respectively. Methylation levels were highly correlated (r = 0.7 to 0.9) between all genic regions, except within the promoter (r = 0.4 to 0.5). Machine learning models gave a high (0.81) prediction accuracy of DEGs. There was a strong correlation (p‐value = 9.20×10−10) between all features and gene expression, suggesting that methylation across all genic regions contribute to gene regulation. However, the methylation of the promoter, the CDS and the exon in CG context was the most impactful. Our study provides more insights into the interplay between DNA methylation and gene expression and paves the way for identifying tissue‐specific genes using methylation profiles.
Enhanced electrokinetic remediation (EKR) for heavy metal‐contaminated sediments focusing on treatment of generated effluents from EKR and recovery of EDTA
Authors: Ayyanar Arulpoomalai , Thatikonda Shashidhar 
Published: June 2020

AbstractElectrokinetic remediation (EKR) is one of the most successful remediation techniques to treat the sediments contaminated with heavy metals. EDTA is the most widely used enhancing agent to improve the transport process in EKR. But often the generated effluents from EKR contains a high concentration of heavy metals, which cannot be disposed of without treatment. The major objective of this study includes the estimation of optimal concentration of chelating agent EDTA, followed by treatment of contaminated sediments by EKR technique for heavy metal removal. The effluents generated from EKR were further studied for recovery and reuse of EDTA and for safe discharge of heavy metals. The optimum concentration of EDTA was found as 0.05 M with a solid‐to‐liquid ratio as 1:10. When fresh EDTA was used as enhancing agent the average removal of heavy metals obtained as 74.8% with EKR, whereas the application of recovered EDTA in treatment process in first, second, and third cycle showed the slight reduction of heavy metals of about 71.1%, 63.5%, and 52.1%, respectively. The heavy metal removal by recovered EDTA was effective in reduction of heavy metals up to three cycles of re‐use while reducing the ecological risk in sediments.Practitioner points

Treatment of contaminated sediments with heavy metals achieved by electrokinetic remediation (EKR) technique enhanced with EDTA.

The recovery of EDTA and heavy metal reduction from the generated effluents during EKR treatment were performed by the addition of FeCl3 and Na2PO4, and optimized concentration was evaluated.

This study found that the use of recovered EDTA in EKR treatment has effectively reduced the risk associated with heavy metals.
Children’s perceptions of social robots: a study of the robots Pepper, AV1 and Tessa at Norwegian research fairs
Authors: Søraa Roger Andre , Nyvoll Pernille Søderholm , Grønvik Karoline Blix , Serrano J Artur 
Published: June 2020

AbstractThis article studies perceptual differences of three social robots by elementary school children of ages 6–13 years (n = 107) at research fairs. The autonomous humanoid robot Pepper, an advanced social robot primarily designed as a personal assistant with movement and mobility, is compared to the teleoperated AV1 robot—designed to help elementary school children who cannot attend school to have a telepresence through the robot—and the flowerpot robot Tessa, used in the eWare system as an avatar for a home sensor system and dedicated to people with dementia living alone. These three robots were shown at the Norwegian national research fair, held in every major Norwegian city annually, where children were able to interact with the robots. Our analysis is based on quantitative survey data of the school children concerning the robots and qualitative discussions with them. By comparing three different types of social robots, we found that presence can be differently understood and conceptualized with different robots, especially relating to their function and “aliveness.” Additionally, we found a strong difference when relating robots to personal relations to one’s own grandparents versus older adults in general. We found children’s perceptions of robots to be relatively positive, curious and exploratory and that they were quite reflective on their own grandparent having a robot.
The role of perception and action on the use of allocentric information in a large-scale virtual environment
Authors: Karimpur Harun , Kurz Johannes , Fiehler Katja 
Published: June 2020

AbstractIn everyday life, our brain constantly builds spatial representations of the objects surrounding us. Many studies have investigated the nature of these spatial representations. It is well established that we use allocentric information in real-time and memory-guided movements. Most studies relied on small-scale and static experiments, leaving it unclear whether similar paradigms yield the same results on a larger scale using dynamic objects. We created a virtual reality task that required participants to encode the landing position of a virtual ball thrown by an avatar. Encoding differed in the nature of the task in that it was either purely perceptual (“view where the ball landed while standing still”—Experiment 1) or involved an action (“intercept the ball with the foot just before it lands”—Experiment 2). After encoding, participants were asked to place a real ball at the remembered landing position in the virtual scene. In some trials, we subtly shifted either the thrower or the midfield line on a soccer field to manipulate allocentric coding of the ball’s landing position. In both experiments, we were able to replicate classic findings from small-scale experiments and to generalize these results to different encoding tasks (perception vs. action) and response modes (reaching vs. walking-and-placing). Moreover, we found that participants preferably encoded the ball relative to the thrower when they had to intercept the ball, suggesting that the use of allocentric information is determined by the encoding task by enhancing task-relevant allocentric information. Our findings indicate that results previously obtained from memory-guided reaching are not restricted to small-scale movements, but generalize to whole-body movements in large-scale dynamic scenes.
Masur–Veech volumes and intersection theory on moduli spaces of Abelian differentials
Authors: Chen Dawei , Möller Martin , Sauvaget Adrien , Zagier Don 
Published: June 2020

AbstractWe show that the Masur–Veech volumes and area Siegel–Veech constants can be obtained using intersection theory on strata of Abelian differentials with prescribed orders of zeros. As applications, we evaluate their large genus limits and compute the saddle connection Siegel–Veech constants for all strata. We also show that the same results hold for the spin and hyperelliptic components of the strata.
Microplastics provide new microbial niches in aquatic environments
Authors: Yang Yuyi , Liu Wenzhi , Zhang Zulin , Grossart Hans-Peter , Gadd Geoffrey Michael 
Published: June 2020

AbstractMicroplastics in the biosphere are currently of great environmental concern because of their potential toxicity for aquatic biota and human health and association with pathogenic microbiota. Microplastics can occur in high abundance in all aquatic environments, including oceans, rivers and lakes. Recent findings have highlighted the role of microplastics as important vectors for microorganisms, which can form fully developed biofilms on this artificial substrate. Microplastics therefore provide new microbial niches in the aquatic environment, and the developing biofilms may significantly differ in microbial composition compared to natural free-living or particle-associated microbial populations in the surrounding water. In this article, we discuss the composition and ecological function of the microbial communities found in microplastic biofilms. The potential factors that influence the richness and diversity of such microbial microplastic communities are also evaluated. Microbe-microbe and microbe-substrate interactions in microplastic biofilms have been little studied and are not well understood. Multiomics tools together with morphological, physiological and biochemical analyses should be combined to provide a more comprehensive overview on the ecological role of microplastic biofilms. These new microbial niches have so far unknown consequences for microbial ecology and environmental processes in aquatic ecosystems. More knowledge is required on the microbial community composition of microplastic biofilms and their ecological functions in order to better evaluate consequences for the environment and animal health, including humans, especially since the worldwide abundance of microplastics is predicted to dramatically increase.Key Points• Bacteria are mainly studied in community analyses: fungi are neglected.• Microbial colonization of microplastics depends on substrate, location and time.• Community ecology is a promising approach to investigate microbial colonization.• Biodegradable plastics, and ecological roles of microplastic biofilms, need analysis.
Exploratory open-label clinical study to determine the S-588410 cancer peptide vaccine-induced tumor-infiltrating lymphocytes and changes in the tumor microenvironment in esophageal cancer patients
Authors: Daiko H. , Marafioti T. , Fujiwara T. , Shirakawa Y. , Nakatsura T. , Kato K. , Puccio I. , Hikichi T. , Yoshimura S. , Nakagawa T. , Furukawa M. , Stoeber K. , Nagira M. , Ide N. , Kojima T. 
Published: June 2020

AbstractCancer vaccines induce cancer-specific T-cells capable of eradicating cancer cells. The impact of cancer peptide vaccines (CPV) on the tumor microenvironment (TME) remains unclear. S-588410 is a CPV comprising five human leukocyte antigen (HLA)-A*24:02-restricted peptides derived from five cancer testis antigens, DEPDC1, MPHOSPH1, URLC10, CDCA1 and KOC1, which are overexpressed in esophageal cancer. This exploratory study investigated the immunologic mechanism of action of subcutaneous S-588410 emulsified with MONTANIDE ISA51VG adjuvant (median: 5 doses) by analyzing the expression of immune-related molecules, cytotoxic T-lymphocyte (CTL) response and T-lymphocytes bearing peptide-specific T-cell receptor (TCR) sequencing in tumor tissue or blood samples from 15 participants with HLA-A*24:02-positive esophageal cancer. Densities of CD8+, CD8+ Granzyme B+, CD8+ programmed death-1-positive (PD-1+) and programmed death-ligand 1-positive (PD-L1+) cells were higher in post- versus pre-vaccination tumor tissue. CTL response was induced in all patients for at least one of five peptides. The same sequences of peptide-specific TCRs were identified in post-vaccination T-lymphocytes derived from both tumor tissue and blood, suggesting that functional peptide-specific CTLs infiltrate tumor tissue after vaccination. Twelve (80%) participants had treatment-related adverse events (AEs). Injection site reaction was the most frequently reported AE (grade 1, n = 1; grade 2, n = 11). In conclusion, S-588410 induces a tumor immune response in esophageal cancer. Induction of CD8+ PD-1+ tumor-infiltrating lymphocytes and PD-L1 expression in the TME by vaccination suggests S-588410 in combination with anti-PD-(L)1 antibodies may offer a clinically useful therapy.Trial registration UMIN-CTR registration identifier: UMIN000023324.
The association between patellar tendon stiffness measured with shear-wave elastography and patellar tendinopathy—a case-control study
Authors: Breda Stephan J. , van der Vlist Arco , de Vos Robert-Jan , Krestin Gabriel P. , Oei Edwin H. G. 
Published: June 2020

Abstract
Objectives
(1) To determine the association between patellar tendon stiffness and the presence of patellar tendinopathy (PT). (2) To evaluate the reliability of shear-wave elastography (SWE).

Methods
Participants were consecutively enrolled between January 2017 and June 2019. PT was diagnosed clinically and confirmed by either grayscale US or power Doppler US, or both. Controls had no history of anterior knee pain and no clinical signs of PT. Patellar tendon stiffness (kilopascal, kPa) was assessed using SWE. Logistic regression was used to estimate adjusted odds ratios (ORs) and 95% confidence intervals (CIs). Reliability analyses included coefficients-of-variation (CV), coefficients-of-repeatability (CR), intraclass correlation coefficient (ICC) for intraobserver and interobserver reliability, and Bland-Altman analysis.

Results
In total, 76 participants with PT (58 men, mean age 24.4 ± 3.8 years) and 35 asymptomatic controls (16 men, mean age 21.5 ± 3.8 years) were included. Univariate analyses (OR 1.094, 95% CI 1.061–1.128, p < .001) and adjusted multivariate analyses (OR 1.294, 95% CI 1.044–1.605, p = .018) showed that athletes with PT had significantly increased patellar tendon stiffness. ICC for intraobserver reliability was 0.95 (95% CI 0.92–0.97), CR (CV) 12 kPa (10%) and 0.79 (95% CI 0.65–0.88), CR (CV) 18 kPa (21%) for interobserver reliability. Mean differences from Bland-Altman analysis were 5.6 kPa (95% CI 3.1–8.1, p < .001) for intraobserver reliability and 4.6 kPa (95% CI 1.9–7.2, p < .001) for interobserver reliability.

Conclusions
PT is associated with significantly higher patellar tendon stiffness. SWE measurements demonstrate excellent intraobserver reliability and good interobserver reliability. Therefore, SWE is a promising tool to implement in longitudinal studies and future studies should evaluate its prognostic value and utility as a monitoring tool in athletes with PT.

Key Points
• Patellar tendon stiffness measured with shear-wave elastography (SWE) is higher in athletes with patellar tendinopathy than in healthy controls, also after adjusting for potential confounders.
• Excellent intraobserver reliability and good interobserver reliability were found for the quantitative assessment of patellar tendon stiffness using SWE.
Outcome prediction of head and neck squamous cell carcinoma by MRI radiomic signatures
Authors: Mes Steven W. , van Velden Floris H. P. , Peltenburg Boris , Peeters Carel F. W. , te Beest Dennis E. , van de Wiel Mark A. , Mekke Joost , Mulder Doriene C. , Martens Roland M. , Castelijns Jonas A. , Pameijer Frank A. , de Bree Remco , Boellaard Ronald , Leemans C. René , Brakenhoff Ruud H. , de Graaf Pim 
Published: June 2020

Abstract
Objectives
Head and neck squamous cell carcinoma (HNSCC) shows a remarkable heterogeneity between tumors, which may be captured by a variety of quantitative features extracted from diagnostic images, termed radiomics. The aim of this study was to develop and validate MRI-based radiomic prognostic models in oral and oropharyngeal cancer.

Materials and Methods
Native T1-weighted images of four independent, retrospective (2005–2013), patient cohorts (n = 102, n = 76, n = 89, and n = 56) were used to delineate primary tumors, and to extract 545 quantitative features from. Subsequently, redundancy filtering and factor analysis were performed to handle collinearity in the data. Next, radiomic prognostic models were trained and validated to predict overall survival (OS) and relapse-free survival (RFS). Radiomic features were compared to and combined with prognostic models based on standard clinical parameters. Performance was assessed by integrated area under the curve (iAUC).

Results
In oral cancer, the radiomic model showed an iAUC of 0.69 (OS) and 0.70 (RFS) in the validation cohort, whereas the iAUC in the oropharyngeal cancer validation cohort was 0.71 (OS) and 0.74 (RFS). By integration of radiomic and clinical variables, the most accurate models were defined (iAUC oral cavity, 0.72 (OS) and 0.74 (RFS); iAUC oropharynx, 0.81 (OS) and 0.78 (RFS)), and these combined models outperformed prognostic models based on standard clinical variables only (p < 0.001).

Conclusions
MRI radiomics is feasible in HNSCC despite the known variability in MRI vendors and acquisition protocols, and radiomic features added information to prognostic models based on clinical parameters.

Key Points
• MRI radiomics can predict overall survival and relapse-free survival in oral and HPV-negative oropharyngeal cancer.
• MRI radiomics provides additional prognostic information to known clinical variables, with the best performance of the combined models.
• Variation in MRI vendors and acquisition protocols did not influence performance of radiomic prognostic models.
Chance or challenge, spoilt for choice? New recommendations on diagnostic and therapeutic considerations in hereditary transthyretin amyloidosis with polyneuropathy: the German/Austrian position and review of the literature
Authors: Dohrn Maike F. , Auer-Grumbach Michaela , Baron Ralf , Birklein Frank , Escolano-Lozano Fabiola , Geber Christian , Grether Nicolai , Hagenacker Tim , Hund Ernst , Sachau Juliane , Schilling Matthias , Schmidt Jens , Schulte-Mattler Wilhelm , Sommer Claudia , Weiler Markus , Wunderlich Gilbert , Hahn Katrin 
Published: June 2020

AbstractHereditary transthyretin amyloidosis is caused by pathogenic variants (ATTRv) in the TTR gene. Alongside cardiac dysfunction, the disease typically manifests with a severely progressive sensorimotor and autonomic polyneuropathy. Three different drugs, tafamidis, patisiran, and inotersen, are approved in several countries, including the European Union and the United States of America. By stabilizing the TTR protein or degrading its mRNA, all types of treatment aim at preventing amyloid deposition and stopping the otherwise fatal course. Therefore, it is of utmost importance to recognize both onset and progression of neuropathy as early as possible. To establish recommendations for diagnostic and therapeutic procedures in the follow-up of both pre-symptomatic mutation carriers and patients with manifest ATTRv amyloidosis with polyneuropathy, German and Austrian experts elaborated a harmonized position. This paper is further based on a systematic review of the literature. Potential challenges in the early recognition of disease onset and progression are the clinical heterogeneity and the subjectivity of sensory and autonomic symptoms. Progression cannot be defined by a single test or score alone but has to be evaluated considering various disease aspects and their dynamics over time. The first-line therapy should be chosen based on individual symptom constellations and contra-indications. If symptoms worsen, this should promptly implicate to consider optimizing treatment. Due to the rareness and variability of ATTRv amyloidosis, the clinical course is most importantly directive in doubtful cases. Therefore, a systematic follow-up at an experienced center is crucial to identify progression and reassure patients and carriers.
Emulsified silicone oil is taken up by and induces pro-inflammatory response in primary retinal microglia
Authors: Klettner Alexa , Harms Antonia , Waetzig Vicki , Tode Jan , Purtskhvanidze Konstantine , Roider Johann 
Published: June 2020

Abstract
Purpose
Silicone oil is used as endotamponade in combination with vitrectomy. Thinning of retinal layers and loss of retinal cells under silicone oil use have been found. Here, we investigate the influence of silicone oil on primary microglia cells.

Methods
Primary microglia cells were prepared from the porcine retina. Microglia identity was assessed with Iba1 staining. Silicone oil was emulsified by sonification. Cell morphology and silicone oil uptake were evaluated by light microscopy after Coomassie blue staining. Cytokine secretion was evaluated with ELISA. Toxicity of silicone oil on microglia and toxic effect of silicone oil–treated microglia on neuronal cell line PC12 were evaluated by MTT or WST assay, respectively.

Results
Microglia took up silicone oil droplets after 72 h of incubation. Silicone oil induced no toxicity but increased the metabolism in microglial cells. In addition, the secretion of IL-6 and IL-8, but not of IL-1ß or TNF-α, was induced. Silicone oil–treated microglia did not exert any neurotoxic effect on differentiated PC12 cells but induced an increase in metabolism.

Conclusion
Emulsified silicone oil changes the activity level of microglia and induces the secretion of IL-6 and IL-8. Neurotoxicity is not induced. Further experiments are required to investigate the long-term effect of silicone oil on microglia and their consequent effect on neuronal cells.
The patient needs assessment in cancer care: identifying barriers and facilitators to implementation in the UK and Canada
Authors: Williamson Susan , Hack Thomas F. , Bangee Munirah , Benedetto Valerio , Beaver Kinta 
Published: June 2020

Abstract
Purpose
Personalised information and support can be provided to cancer survivors using a structured approach. Needs assessment tools such as the Holistic Needs Assessment (HNA) in the UK and the Comprehensive Problem and Symptom Screening (COMPASS) questionnaire in Canada are recommended for use in practice; however, they are not widely embedded into practice. The study aimed to determine the extent to which nurses working in cancer care in the UK and Manitoba value NA and identify any barriers and facilitators they experience.

Method
Oncology nurses involved in the care of cancer patients in the UK (n = 110) and Manitoba (n = 221) were emailed a link to an online survey by lead cancer nurses in the participating institutions. A snowball technique was used to increase participation across the UK resulting in 306 oncology nurses completing the survey in the UK and 116 in Canada.

Results
Participants expressed concerns that these assessments were becoming bureaucratic “tick-box exercises” which did not meet patients’ needs. Barriers to completion were time, staff shortages, lack of confidence, privacy, and resources. Facilitators were privacy for confidential discussions, training, confidence in knowledge and skills, and referral to resources.

Conclusion
Many busy oncology nurses completed this survey demonstrating the importance they attach to HNAs and COMPASS. The challenges faced with implementing these assessments into everyday practice require training, time, support services, and an appropriate environment. It is vital that the HNA and COMPASS are conducted at optimum times for patients to fully utilise time and resources.