bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic profile of MYCN non-amplified neuroblastoma and potential for immunotherapeutic strategies in neuroblastoma
Authors: Lee Eunjin , Lee Ji Won , Lee Boram , Park Kyunghee , Shim Joonho , Yoo Keon Hee , Koo Hong Hoe , Sung Ki Woong , Park Woong-Yang 
Published: October 2020

Abstract
Background: MYCN amplification is the most important genomic feature in neuroblastoma (NB). However, limited studies have been conducted on the MYCN non-amplified NB including low- and intermediate-risk NB. Here, the genomic characteristics of MYCN non-amplified NB were studied to allow for the identification of biomarkers for molecular stratification.

Methods: Fifty-eight whole exome sequencing (WES) and 48 whole transcriptome sequencing (WTS) samples of MYCN non-amplified NB were analysed. Forty-one patients harboured WES and WTS pairs .

Results: In the MYCN non-amplified NB WES data, maximum recurrent mutations were found in MUC4 (26%), followed by RBMXL3 (19%), ALB (17%), and MUC16 and SEPD8 (14% each). Two gene fusions, CCDC32 - CBX3 (10%) and SAMD5 - SASH1 (6%), were recurrent in WTS analysis, and these fusions were detected mostly in non-high-risk patients with ganglioneuroblastoma histology. Analysis of risk-group-specific biomarkers showed that several genes and gene sets were differentially expressed between the risk groups, and some immune-related pathways tended to be activated in the high-risk group. Mutational signatures 6 and 18, which represent DNA mismatch repair (MMR) associated mutations, were commonly detected in 60% of the patients. In the tumour mutation burden (TMB) analysis, four patients showed high TMB (> 3 mutations/Mb), and had mutations in genes related to either MMR or homologous recombination. Excluding four outlier samples with TMB > 3 Mb, high-risk patients had significantly higher levels of TMB compared with the non-high-risk patients.

Conclusions: This study provides novel insights into the genomic background of MYCN non-amplified NB. Activation of immune-related pathways in the high-risk group and the results of TMB and mutational signature analyses collectively suggest the need for further investigation to discover potential immunotherapeutic strategies for NB.
Transcriptomic and metabolomic profiling reveals the effect of LED light quality on morphological traits, and phenylpropanoid-derived compounds accumulation in Sarcandra glabra seedlings
Authors: Xie Dejin , Chen Lingyan , Zhou Chengcheng , Tarin Muhammad Waqqas Khan , Yang Deming , Ren Ke , He Tianyou , Rong Jundong , Zheng Yushan 
Published: October 2020

Abstract
Background: Sarcandra glabra is an evergreen and traditional Chinese herb with anti-oxidant, anti-bacterial, anti-inflammatory, and anti-tumor effects. Light is one of the most influential factor affecting the growth and quality of herbs. In recent times, the introduction of Light Emission Diode (LED) technology has been widely used for plants in greenhouse. However, the impact of such lights on plant growth and the regulatory mechanism of phenylpropanoid-derived compounds in S. glabra remain unclear. Results: The red LED light (RL) substantially increased the plant height and decreased the stem diameter and leaf area relative to the white LED light (WL), while the blue LED light (BL) significantly reduced the height and leaf area of S. glabra. According to transcriptomic profiling, 861, 378, 47, 10,033, 7917, and 6379 differentially expressed genes (DEGs) were identified among the groups of leaf tissue under BL (BY) vs. leaf tissue under RL (RY), BY vs. leaf tissue under WL (WY), RY vs. WY, root tissue under WL (WG) vs. WY, stem tissue under WL (WJ) vs. WG, and WJ vs. WY, respectively. We identified 46 genes encoding for almost all known enzymes involved in phenylpropanoid biosynthesis, e.g., phenylalanine ammonia lyase (PAL), chalcone synthase (CHS), and flavonol synthase (FLS). We found 53 genes encoding R2R3-MYB proteins and bHLH proteins, respectively, where several were related to flavonoids biosynthesis. A total of 454 metabolites were identified based on metabolomic profiling, of which 44, 87, and 296 compounds were differentially produced in WY vs. RY, WY vs. BY, and WY vs. WG. In BY there was a substantial reduction in the production of esculetin, caffeic acid, isofraxidin, and fraxidin, while the yields of quercitrin and kaempferol were significantly up-regulated. In RY, the contents of cryptochlorogenic acid, cinnamic acid, and kaempferol decreased significantly. Besides, in WG, the production of metabolites (e.g. chlorogenic acid, cryptochlorogenic acid, and scopolin) declined, while their yields increased significantly (e.g. esculetin, fraxetin, isofraxidin, and fraxidin).Conclusion: These results provide further insight into the regulatory mechanism of accumulation patterns of phenylpropanoid-derived compounds in S. glabra under various light conditions, allowing optimum breeding conditions to be developed for this plant.
Determinants of participation in a post-hospitalization physical exercise program for older adults
Authors: Urquiza Miriam , Echeverria Iñaki , Besga Ariadna , Amasene Maria , Labayen Idoia , Rodriguez Ana , Barroso Julia , Aldamiz Mikel , Irazusta Jon 
Published: October 2020

Abstract
BACKGROUND: Older patients often experience a decline in physical function and cognitive status after hospitalization. Although interventions involving physical exercise are effective in improving functional performance, participation in physical exercise interventions among older individuals is low. We aimed to identify factors that contribute to exercise refusal among post-hospitalized older patients.METHODS: A cross-sectional study of recruitment data from a randomized controlled trial was conducted involving 495 hospitalized people ≥70 years old. Sociodemographic and clinical data were obtained from the Basque Public Health System database. We determined physical function with the Short Physical Performance Battery (SPPB), nutritional status with the Mini-Nutritional Assessment, frailty according to the Fried phenotype criteria, and cognitive function with the Short Portable Mental Status Questionnaire (SPMSQ). Student’s t, Mann-Whitney U, or chi-squared tests were applied for bivariate analysis. Parameters significantly associated with participation were introduced in a logistic multivariate regression model.RESULTS: Among the analyzed patients, 88.8% declined participation in the physical exercise program. Multivariate regression revealed that older age (OR: 1.13; 95% CI: 1.07 - 1.19), poor nutritional status (OR: 0.81; 95% CI: 0.69 - 0.95), and reduced home accessibility (OR: 0.27; 95% CI: 0.08 - 0.94) were predictors of participation refusal. Moreover, patients who declined participation had worse performance on the SPPB (P < 0.05) and its tests of balance, leg strength, and walking speed (P < 0.05). No differences were found between groups in other variables. CONCLUSIONS: This study confirms low participation of older adults in a post-hospitalization physical exercise program. Non-participation was associated with increased age, poor nutritional status, and reduced home accessibility. Our findings support the need for intervention design that accounts for these factors to increase older patient participation in beneficial exercise programs.TRIAL REGISTRATION: ACTRN12619000093189 (retrospectively registered): Registered January 22, 2019.
Multilevel modelling of the risk of malaria among children aged under five years in Nigeria
Authors: Oguoma Victor M , Anyasodor Anayochukwu E , Adeleye Adeniyi O , Eneanya Obiora A , Mbanefo Evaristus C 
Published: October 2020

Abstract
Background:Malaria is still a major cause of morbidity and mortality among children under five (U5) years. This study assessed individual, household, and community risk factors for malaria in Nigerian children U5 years of age.Methods:Data from the Nigerian Malaria Health Indicator Survey 2015 were pooled for analyses. This comprised of national survey of 329 clusters. Children aged 6-59 months who were tested for malaria using microscopy were retained. Multilevel logit model accounting for sampling design was used to assess individual, household and community factors associated with malaria parasitaemia. Results:A total of 5742 children were assessed for malaria parasitaemia with overall prevalence of 27% (95% CI 26-28%). Plasmodium falciparum constituted 98% of the Plasmodium species. There was no significant difference in parasitaemia between older children, and those ≤12 months. In adjusted analyses, rural living, Northwest region, household size of >7, dependence on river and rain water as primary water source were associated with higher odds of parasitaemia; while higher wealth index, all U5s who slept under bed net and dependence on packaged water were associated with lower odds of parasitaemia.Conclusion:Despite sustained investment in malaria control and prevention, a quarter of the overall study population of U5s suffer from malaria. Across the six geopolitical zones, the highest burden was in children living in poorest rural households.
The impact of COL1A1 and COL6A1 expression on hypospadias and penile curvature severity
Authors: yuri prahara , Gunadi . , Lestari Rahmadani Puji , Fardilla Firly Putri , Setyaningsih Wiwit Ananda Wahyu , Arfian Nur , Dachlan Ishandono 
Published: October 2020

Abstract
Background : Hypospadias, the most frequent congenital male external genitalia abnormality, is usually associated with curvature of the ventral penis, i.e. chordee. Abnormality of darto tissue has been suggested as the pathophysiology of chordees. Collagen is one of the most abundant fibrous proteins within the extracellular matrix. In this study, we determined the expression of collagen 1 (COL1A1) and COL6A1 in patients with hypospadias and associated them with the severity of penile curvature.
Methods : We included 60 children <18 years old, consisting of 20 distal hypospadias, 20 proximal hypospadias patients, and 20 controls in our institution from 2017 – 2020. The expression of COL1A1 and COL6A1 in darto tissue was determined by reverse-transcriptase polymerase chain reaction (qPCR). The penile curvature severity was classified as mild (<30 degrees), moderate (30-60 degrees), and severe (>60degrees).
Results : qPCR showed that COL1A1 and COL6A1 expression was significantly downregulated in the distal (0.88 (0.38-2.53) and 0.54 (0.16-4.35), respectively) and proximal 0.76 (0.33-2.57) and 0.57 (0.18-1.38), respectively) hypospadias groups compared to controls (1.85 (0.24-4.61) and 0.93 (0.17-4.06), respectively) with p -values of 0.024 and 0.018, respectively. Furthermore, there was a moderate correlation between COL1A1 and COL6A1 expression ( r= 0.458, p< 0.0001). Interestingly, COL1A1 and COL6A1 were also significantly downregulated in the moderate and severe chordee groups compared to the mild chordee groups, with p -values of 0.003 and 0.037, respectively.
Conclusions : Aberrant COL1A1 and COL6A1 expression might affect abnormalities in darto tissue and penile curvature severity in hypospadias patients.
Keywords: chordee; COL1A1 ; COL6A1 ; expressions; hypospadias; penile curvature severity; qPCR
The Impact of Dementia and Language on Hospitalizations. A Retrospective Cohort of Long-Term Care Residents.
Authors: Riad Karine , Webber Colleen , Batista Ricardo , Reaume Michael , Rhodes Emily , Knight Braden , Prud’homme Denis , Tanuseputro Peter 
Published: October 2020

Abstract
Background: Hospitalizations carry considerable risks for frail, elderly patients; this is especially true for patients with dementia, who are more likely to experience delirium, falls, functional decline, iatrogenic complications, and infections when compared to their peers without dementia. Since up to two thirds of patients in long-term care (LTC) facilities have dementia, there is interest in identifying factors associated with transitions from LTC to hospitals. The purpose of this study was to investigate the association between dementia status and incidence of hospitalization among residents in LTC in Ontario, Canada, and to determine whether this association is modified by linguistic factors.
Methods: We used linked administrative databases to establish a prevalent cohort of 81,188 residents in 628 LTC facilities from April 1 st 2014 to March 31, 2017. Diagnoses of dementia were identified with a previously validated algorithm; all other patient characteristics were obtained from in-person assessments. Residents’ primary language was coded as English or French; facility language (English or French) was determined using language designation status according to the French Language Services Act . We identified all hospitalizations within 3 months of the first assessment performed after April 1 st 2014. We performed multivariate logistic regression analyses to determine the impact of dementia and resident language on the incidence of hospitalization; we considered interactions between dementia and both resident language and resident-facility language discordance.

Results: The odds of hospitalization were 39% lower for residents with dementia compared to residents without dementia (OR 0.61, 95% CI 0.57–0.65). Francophones had lower odds of hospitalization than Anglophones, but this difference was not statistically significant (OR 0.91, 95% CI 0.81 – 1.03). However, Francophones without dementia were significantly less likely to be hospitalized compared to Anglophones without dementia (OR 0.71, 95% CI 0.53 – 0.94). Resident-facility language discordance did not significantly affect hospitalizations.

Conclusions: Residents in LTC facilities were generally less likely to be hospitalized if they had dementia, or if their primary language was French and they did not have dementia. These findings could be explained by differences in end-of-life care goals; however, they could also be the result of poor patient-provider communication.
Knowledge among the rural parents about the vaccinations and vaccination coverage of children in the first year of life in Papua New Guinea – analysis of data provided by Christian Health Services.
Authors: Gowin Ewelina , Kuzma Jerzy , Januszkiewicz-Lewandowska Danuta 
Published: October 2020

Abstract
Background: This analysis aimed to assess rural parents' knowledge about the diseases prevented by vaccinations and establish vaccination coverage in PNG. Methods: Knowledge on vaccinations was checked through a standard questionnaire (five open questions). We analyzed data on vaccination coverage from 2016 to 2018 from all Catholic health facilities. Analyzed vaccinations were the pentavalent vaccine (DTaP-HiB-HepB) and measles vaccine given in the first year of life. Coverage was calculated based on the number of vaccines used compared to the number of eligible children. Results: 56 parents, including 52 mothers and four fathers, participated in the interview. The majority of parents (46%) understood that the vaccine prevents the child from the sick. During the analyzed period, a total of 25,502 doses of measles vaccine was given, 31,428 children were vaccinated with the pentavalent vaccine. In 2016, the coverage rate for the measles vaccine was 26.6% and 33.4% for the pentavalent vaccine. In 2017, the coverage rate for measles and pentavalent vaccines was 12.5% and 16.6%, respectively. There were significant differences in immunization coverage between provinces. A decreasing trend in the number of administered vaccinations was observed. Conclusion: The results of this analysis demonstrate that in PNG, the majority of children are not fully immunized. There are big differences in vaccination coverage between provinces. The problem is the lack of public understanding of the need for vaccinations. Lack of patient vaccination records makes it difficult to establish individual vaccination history.
Natural hybridization between two butterfly bushes in Tibet: dominance of F1 hybrids promotes strong reproductive isolation &nbsp;&nbsp;
Authors: Liao Rongli , Sun Weibang , Ma Yongpeng 
Published: October 2020

Abstract
Background: F1 hybrids acting as a bridgehead for producing later generation hybrids can have evolutionary significance through strengthening reproductive isolation or facilitating gene flow between parental species, depending on whether backcrossing can occur. It had been suggested that the Tibetan plant Buddleja wardii was a hybrid species between B. alternifolia and B. crispa based on their sympatric distributions and the morphological characters in last century. Till now however, we still have limited evidence to prove key issues to B. wardii, like if it is of hybrid origin indeed and whether it is currently a true hybrid species already.Results: In the present study, two sympatric populations of these three taxa were examined and compared using four nuclear genes and three chloroplast intergenic spacers, as well as with 10 morphological characters. Our results suggest that at both sites B. × wardii was likely to be a hybrids between B. alternifolia and B. crispa, and moreover, most of the hybrids present were confirmed to be F1s. This was further supported by morphology as no transgressive characters were detected. B. crispa was found to be the maternal parent in one population (BH), while in the second population (TJ), it was difficult to distinguish the hybridization direction due to shared haplotypes of cpDNA between B. alternifolia and B. crispa. Conclusions: These results provide evidence that the natural hybrids between B. alternifolia and B. crispa mainly comprise F1 hybrids, which have subsequently been given the name B. wardii. The F1 hybrids have also contributed to strong reproductive isolation between parental species.
Degradation and sorption of the herbicides 2,4-D and quizalofop-P-ethyl and their metabolites in soils from railway tracks
Authors: Buerge Ignaz J , Pavlova Pavlina , Hanke Irene , Bächli Astrid , Poiger Thomas 
Published: October 2020

Abstract
Background Broad spectrum of activity and low potential for leaching to groundwater are important arguments for the application of the herbicide glyphosate on railway tracks. Nevertheless, certain weeds are insufficiently controlled or develop resistance, and there is also an ongoing controversial discussion about possible carcinogenicity of glyphosate. Alternatives are thus strongly desired. 2,4-D and quizalofop-P-ethyl (QE) are two selective herbicides with a complementary spectrum of activity. When used in agriculture, the compounds and their metabolites exhibit low groundwater contamination potential. Uses on railway tracks may, however, be more critical since degradation likely is slower and mobility higher than in agricultural soils. In this study, we investigated degradation and sorption of the two active substances as well as five metabolites in three soils collected from railway tracks and in a crushed sand, used for construction works.Results In these railway materials, the compounds were indeed degraded slower than in agricultural soils (mean half-lives differed by a factor of 1.4-26, depending on the substance) and mobility was higher (mean sorption coefficients differed by a factor of 3-19). Half-lives and sorption coefficients were also estimated by extrapolation of data from agricultural soils, considering the organic carbon content of railway soils and agricultural soils. Estimated values were more conservative than measured values. Conclusions Based on our experimental data, possible leaching to groundwater is predicted to be highest for 2,4-D and quizalofop-acid, the primary metabolite of QE, moderate for 2,4-dichlorophenol, the primary metabolite of 2,4-D, but low for QE. Secondary and tertiary metabolites were formed in only low quantities. For herbicides, for which no measured parameters are available for railway soils, estimated values may also be a viable alternative for a first tier groundwater assessment.
Reductive dissolution of biogenic magnetite
Authors: Yamazaki Toshitsugu 
Published: October 2020

Abstract
Reductive dissolution of magnetite is known to occur below the Fe-redox boundary in sediments. In this study detailed processes associated with biogenic magnetite dissolution are documented. A sediment core from the Japan Sea was used for this purpose, in which reductive dissolution of magnetic minerals is known to start at depths of about 1.15 m and is mostly complete within a depth interval of about 0.35 m. Using first-order reversal curve diagrams, preferential dissolution of biogenic magnetite within this interval is estimated from the observation that a narrow peak that extends along the coercivity axis (central ridge), which is indicative of biogenic magnetite, diminishes downcore. Transmission electron microscopy is used to demonstrate that the sediments contain three magnetofossil morpho-types: octahedra, hexagonal prisms, and bullet-shaped forms. Within the reductive dissolution zone, partially etched crystals are commonly observed. With progressive dissolution, the proportion of bullet-shaped magnetofossils decreases, whereas hexagonal prisms become more dominant. This observation can be explained by the differences in resistance to dissolution among crystal planes of magnetite and the differences in surface area to volume ratios. Magnetofossil morphology may reflect the preference of magnetotactic bacterial lineages for inhabiting specific chemical environments in sediments. However, it could also reflect alteration of the original morphological compositions during reductive diagenesis, which should be considered when using magnetofossil morphology as a paleoenvironmental proxy.
Long interspersed nuclear element 1 hypomethylation has novel prognostic value and potential utility in liquid biopsy for oral cavity cancer
Authors: Misawa Kiyoshi , Yamada Satoshi , Mima Masato , Nakagawa Takuya , Kurokawa Tomoya , Imai Atsushi , Mochizuki Daiki , Shinmura Daichi , Yamada Taiki , Kita Junya , Ishikawa Ryuji , Yamaguchi Yuki , Misawa Yuki , Kanazawa Takeharu , Kawasaki Hideya , Mineta Hiroyuki 
Published: October 2020

Abstract
Background: New biomarkers are urgently needed to improve personalized treatment approaches for head and neck squamous cell carcinoma (HNSCC). Global DNA hypomethylation has wide-ranging functions in multistep carcinogenesis, and the hypomethylation of long interspersed nucleotide element-1 (LINE-1) has been generally considered to be related with increased retrotransposon activity and induced genome instability. However, little information is available regarding LINE-1 hypomethylation and its prognostic implications in HNSCC. Methods: In this study, we analyzed LINE-1 hypomethylation levels in a well-characterized dataset of 317 matched pairs of HNSCC tissues and oral cavity cancer (OCC) circulating tumor DNA (ctDNA) using quantitative real-time methylation and unmethylation PCR. This analysis was performed according to various clinical characteristics and prognostic implications. Results: Our results demonstrated that LINE-1 hypomethylation levels were significantly higher in HNSCC tissues than in corresponding normal tissues from the same individuals (P < 0.001). Univariate analysis revealed that high levels of LINE-1 hypomethylation were correlated with poor disease-free survival (DFS; log-rank test, P = 0.038), whereas multivariate analysis demonstrated that it is a significant independent prognostic factor for DFS (hazard ratio: 2.10, 95% confidence interval: 1.02–4.36; P = 0.045). Moreover, patients with high LINE-1 hypomethylation levels exhibited the greatest decrease in 5-hydroxymethylcytosine (5-hmC) levels and increase in tumor-suppressor gene methylation index (P = 0.006 and P < 0.001, respectively). Further ctDNA studies also showed that LINE-1 hypomethylation had high predictive ability for OCC. Conclusions: LINE-1 hypomethylation is associated with a higher risk of early OCC relapse, and is hence, a potential predictive biomarker for OCC. Furthermore, 5-hmC levels also exhibited predictive potential in OCC, based on its inverse correlation with LINE-1 hypomethylation levels. LINE-1 hypomethylation analysis, therefore, has applications in determining patient prognosis and real-time surveillance for disease recurrence, and could serve as an alternative method for OCC screening.