bluuebunny/crossref_metadata_2025_split huggingface dataset:
Uncovering the genomic potential of the Amazon River microbiome to degrade rainforest organic matter
Authors: Júnior Célio Dias Santos , Sarmento Hugo , de Miranda Fernando Pellon , Henrique-Silva Flávio , Logares Ramiro 
Published: May 2020

Abstract
Background The Amazon River is one of the largest in the world and receives huge amounts of terrestrial organic matter (TeOM) from the surrounding rainforest. Despite this TeOM is typically recalcitrant (i.e. resistant to degradation), only a small fraction of it reaches the ocean, pointing to a substantial TeOM degradation by the river microbiome. Yet, microbial genes involved in TeOM degradation in the Amazon River were barely known. Here, we examined the Amazon River microbiome by analyzing 106 metagenomes from 30 sampling points distributed along the river.Results We constructed the Amazon River basin Microbial non-redundant Gene Catalogue (AMnrGC) that includes ~ 3.7 million non-redundant genes, affiliating mostly to bacteria. We found that the Amazon River microbiome contains a substantial gene-novelty compared to other relevant known environments (rivers and rainforest soil). Genes encoding for proteins potentially involved in lignin degradation pathways were correlated to tripartite tricarboxylates transporters and hemicellulose degradation machinery, pointing to a possible priming effect. Based on this, we propose a model on how the degradation of recalcitrant TeOM could be modulated by labile compounds in the Amazon River waters. Our results also suggest changes of the microbial community and its genomic potential along the river course.Conclusions Our work contributes to expand significantly our comprehension of the world’s largest river microbiome and its potential metabolism related to TeOM degradation. Furthermore, the produced gene catalogue (AMnrGC) represents an important resource for future research in tropical rivers.
Pediatric NTRK fusion sarcomas
Authors: Kang Jeongwan , Park Jin Woo , Won Jae-Kyung , Bae Jeong Mo , Yun Hongseok , Kim Seung-Ki , Choi Jung Yoon , Kang Hyoung Jin , Shin Joo Heon , Park Sung-Hye 
Published: May 2020

Abstract
Background
While ETV6-NTRK3 fusion is common in infantile fibrosarcoma, NTRK1 fusion in pediatric sarcoma is extremely rare and consequently not well known. Herein, we evaluated NTRK1 fusion pediatric sarcomas to determine their clinicopathological nature and differential diagnosis from classic ETV6-NTRK3 fusion infantile fibrosarcoma.
Methods
We retrieved and reviewed eight NTRK-fusion pediatric sarcomas confirmed by fluorescence in situ hybridization and/or next-generation sequencing from Seoul National University Hospital between 2002 and 2019.
Results
The NTRK1 fusion-positive tumors included one case of TPR-NTRK1 fusion in a 12-year-old boy with an intracranial extra-axial high-grade undifferentiated sarcoma and an LMNA-NTRK1 fusion in a 3-year-old boy with a low-grade infantile fibrosarcoma of the forehead. Six cases of infantile fibrosarcoma with ETV6-NTRK3 fusion were identified (median age: 2.6 months, range: 1.6–5.6 months, M: F = 5:1). The TPR-NTRK1 fusion sarcoma showed nuclear Trk expression, robust CD34/nestin expression (S100 protein-negative), and high mitoses. The LMNA-NTRK1 fusion sarcoma showed nuclear membrane Trk expression, CD34/S100 protein/nestin/CD10 coexpression, and a low mitotic rate. The six cases of infantile fibrosarcoma with ETV6-NTRK3 fusion showed S100 protein (3/6)/nestin(6/6)/CD10 (4/5) coexpression and both cytoplasmic and nuclear Trk expression but were CD34-negative.
Conclusions
All cases of NTRK1 and NTRK3 fusion-positive pediatric sarcomas robustly expressed the Trk protein. A Trk immunopositive pattern and CD34/S100/nestin/CD10 immunohistochemical profile may suggest NTRK fusion partner genes. TPR-NTRK1 and LMNA-NTRK1 fusions might be surrogate markers for pediatric mesenchymal tumors, while LMNA-NTRK1 fusion sarcoma might be a low-grade infantile fibrosarcoma subtype. More than half of the infantile fibrosarcoma cases were S100 protein and CD10-positive. The cases of infantile fibrosarcoma showed good prognoses regardless of tumor cellularity, Ki-67 index, and mitoses.
A novel magnetic field generating machine with a wide range of tunable parameters to study in vitro cells
Authors: Nezamtaheri Maryam sadat , Shariatpanahi Seyed Peyman , Goliaei Bahram , Ansari Alireza Madjid 
Published: May 2020

Abstract
Background Extremely low-frequency magnetic field (ELF-MF) significantly induces apoptosis in cancer cells. To study the biological effects of the ELF-MF on tumor cells, we have designed and constructed a new exposure system that provides a uniform magnetic field with negligible temperature fluctuations during the exposure. Additionally, it provides ideal physiological conditions for live cells inside the incubator. This ELF-MF exposure system eliminates several limitations and disadvantages of other low frequency magnetic field systems; it generates a magnetic field with a frequency of 0 to 70 Hz with a maximum magnetic flux density of 150 mT. Methods The capabilities of the setup were examined using a 1 Hz, 100 mT magnetic field, at various exposure times, to induce apoptosis-mediated cell death in the MC4-L2 cell line. After exposure, apoptosis was assessed by flow cytometry. Results A biphasic response was observed in cells exposed to ELF-MF: at first a decreasing apoptotic rate during 2-12 hours exposure time was detected, after which apoptosis gradually increased during 24-120 hours of exposure. Conclusions We show that ELF-MF exposure with a frequency of 1 Hz and intensity of 100 mT induces apoptosis in MC4-L2 cancer cells in a time-dependent manner. These results show the significance of the long term studies of the ELF exposure effects.
Optimal cumulative dose of cisplatin for concurrent chemoradiotherapy among patients with locally advanced nasopharyngeal carcinoma: a multicenter analysis in Thailand
Authors: Ngamphaiboon Nuttapong , Dechaphunkul Arunee , Setakornnukul Jiraporn , Dechaphunkul Tanadech , Jiratrachu Rungarun , Suktitipat Bhoom , Jiarpinitnun Chuleeporn , Pattaranutaporn Poompis , Danchaivijitr Pongwut 
Published: May 2020

Abstract
IntroductionChemoradiotherapy (CRT) with high cumulative doses (CDs) of cisplatin has been considered the standard of care for locally advanced nasopharyngeal carcinoma (LA-NPC). However, given most patients’ inability to tolerate high CDs due to cisplatin-related toxicities, the optimal CD of cisplatin during CRT remains undetermined.MethodsPatients with LA-NPC who received CRT with cisplatin between 2007 and 2017 were identified through the Thai head and neck cancer multicenter database and then categorized according to cisplatin CD (mg/m2) received. All complications and cisplatin-related toxicities during CRT were recorded.ResultsWe identified 779 LA-NPC patients receiving low (£150; n=97), intermediate (151–250; n=411), and high (>250; n=271) CDs of cisplatin. Low CD patients had significantly lower mean actual radiation dose (p<0.001) and more radiotherapy delay (p=0.010), while intermediate CD patients had the least hospitalization (p<0.001). Overall, 39.3% of the patients experienced cisplatin-related toxicity, which was associated with poor overall survival (OS) (p=0.001). Acute kidney injury was observed in 7% in all patients, which was highest among low CD patients (15.5%; p=0.002). Intermediate CD patients had significantly longer median OS than the low and high groups (64 vs. 49.8 vs. 53.2, respectively; p=0.015). Univariate, but not multivariate, analysis showed that CD of cisplatin was significantly associated with OS.ConclusionCD of cisplatin during CRT was not an independent prognostic factor for OS. An intermediate CD induced minimal toxicity without compromising survival and should be considered the optimal CD. Nonetheless, a randomized phase 3 study evaluating the optimal CD of cisplatin is warranted.
Somatic mutation detection efficiency in EGFR: A comparison between High Resolution Melting Analysis and Sanger Sequencing
Authors: Joy Reenu Anne , Thelakkattusserry Sukrishna Kamalasanan , Vikkath Narendranath , Bhaskaran Renjitha , Vasudevan Damodaran , Krishnan Sajitha , Ariyannur Prasanth S. 
Published: May 2020

Abstract
Background: The current study focuses on comparing the mutation detection efficiency of High-Resolution Melt Analysis (HRM) with Sanger Sequencing in EGFR gene.Methods: The minor allele frequency of somatic mutations was titrated against total DNA concentration using Sanger sequencing and HRM. Somatic mutation detection efficiency, for exons 19 & 21 of the EGFR gene, was compared in 116 formalin fixed paraffin embedded tumor tissues, after screening 275 tumor tissues by Sanger sequencing.Results: The limit of detection of minor allele fraction of exon 19 mutation was 1% with Sequencing, and 0.25% with HRM, whereas for exon 21 mutation, 0.25% MAF was detected using both methods. Mutation positive samples detected by Sanger sequencing, and wild-type samples detected by HRM were corresponding to each other. About 28% cases in exon 19 and 40% in exon 21, detected as mutated in HRM, was not detected by sequencing. Overall, sensitivity and specificity of HRM were found to be 100% and 67% respectively, and the negative predictive value was 100%, while positive predictive value was 80%.Conclusion: The comparative series study suggests that HRM is a modest initial screening test for somatic mutation detection of EGFR, which must further be confirmed by Sanger sequencing.
Association between serum bone biomarker levels and ultrasonographic response in abatacept-treated rheumatoid arthritis patients
Authors: Kawashiri Shin-Ya , Endo Yushiro , Nishino Ayako , Okamoto Momoko , Tsuji Sosuke , Takatani Ayuko , Shimizu Toshimasa , Sumiyoshi Remi , Koga Tomohiro , Iwamoto Naoki , Ichinose Kunihiro , Tamai Mami , Nakamura Hideki , Origuchi Tomoki , Aramaki Toshiyuki , Ueki Yukitaka , Yoshitama Tamami , Eiraku Nobutaka , Matsuoka Naoki , Okada Akitomo , Fujikawa Keita , Hamada Hiroaki , Nagano Shuji , Tada Yoshifumi , Maeda Takahiro , Kawakami Atsushi 
Published: May 2020

Abstract
Background

To evaluate the effect of treatment on bone biomarkers and explore whether bone biomarkers are associated with therapeutic response in rheumatoid arthritis (RA) patients treated with abatacept.
Methods

We enrolled 59 RA patients treated with abatacept from a multicenter prospective ultrasound cohort study of patients who received biologic or targeted synthetic disease-modifying antirheumatic drug (DMARD) therapy. We evaluated the patients' clinical disease activity and musculoskeletal ultrasound (MSUS) scores. The serum concentrations of five bone biomarkers were evaluated (dickkopf-1 [Dkk-1], sclerostin [SOST], osteocalcin [OC], osteopontin [OPN], and osteoprotegerin [OPG]) by multiplex bead assays at baseline, 3, and 6 months: the change over 6 months was defined as the Δ value. 'Power Doppler (PD) responder' was defined as a patient whose Δtotal PD score over 6 months was greater than the median change.
Results

Abatacept significantly improved clinical disease activity as well as the MSUS score over 6 months. Serum OPG was significantly elevated at 6 months after the introduction of abatacept (p = 0.016). The ΔSOST and ΔOPG values were negatively correlated with the Δtotal PD score (rs = − 0.31, p < 0.05 and rs = − 0.34, p < 0.01, respectively). The serum Dkk-1 at baseline was significantly lower in the PD responders (n = 30) compared to the non-PD responders (n = 29) (p = 0.026). A multivariate logistic regression analysis showed that the serum Dkk-1 at baseline (odds ratio 0.50, p = 0.043) was an independent predictor of PD responder status.
Conclusion

Serum levels of bone biomarkers may be useful for predicting RA patients' ultrasonographic response to abatacept.
Medical students’ perceptions of nutrition in medical education and future practice
Authors: Fenwick Peri , Colborne Alyson , Theou Olga , Cahill Leah 
Published: May 2020

Abstract
Background: Physicians are relied upon as knowledgeable sources of nutrition information; however, many report low nutrition knowledge.Objective: The present study assessed first and second-year medical students’ perceptions of nutrition education within the medical curriculum, in terms of their attitudes, learned body of knowledge, and satisfaction.Methods: An online questionnaire was administered to Dalhousie University medical students completing their first or second years (N=125). Mann-Whitney U tests compared the responses of first-year to second-year students and those with and without previous nutrition education.Results: 97.6% of respondents agreed that nutritional counselling can positively influence patient outcomes, with 91.2% agreeing that physicians play a key role in nutritional counselling. Compared to second-year students, first-year students had greater self-perceived knowledge of basic nutrition concepts (p<0.001) and nutrition in the treatment of disease (p=0.005), as did students with previous nutrition education compared to those without (p=0.019 and 0.018 respectively). Satisfaction was <30% agreement, with first-year students more satisfied with their nutrition education than second-year students (p<0.05).Conclusions: First and second-year medical students regard nutrition as an important component of medical practice that can positively impact patient outcomes. However, low satisfaction with their nutrition education suggests that additional nutrition curriculum would better prepare them for future practice.
Increased salt tolerance in Zymomonas mobilis strain generated by adaptative evolution
Authors: Fuchino Katsuya , Bruheim Per 
Published: May 2020

Abstract
BackgroundEthanologenic alphaproteobacterium Zymomonas mobilis has been acknowledged as a promising biofuel producer. There have been numerous efforts to engineer this species applicable for an industrial-scale bioethanol production. Although Z. mobilis is robustly resilient to certain abiotic stress such as ethanol, the species is known to be sensitive to saline stress at a mild concentration, which hampers its industrial use as an efficient biocatalyst. To overcome this issue, we implemented laboratory adaptive evolution approach to obtain salt tolerant Z. mobilis strain.ResultsDuring an adaptive evolution, we biased selection by cell morphology to exclude stressed cells. The evolved strains significantly improved growth and ethanol production in the medium supplemented with 0.225 M NaCl. Furthermore, comparative metabolomics revealed that the evolved strains did not accumulate prototypical osmolytes, such as proline, to counter the stress during their growth. The sequenced genomes of the studied strains suggest that disruption of ZZ6_1149 encoding carboxyl peptidase was likely responsible for the improved phenotype.ConclusionsThe present work successfully generated the strains able to grow and ferment glucose under saline condition that severely perturbs parental strain physiology. Our approach to generate strains, cell shape-based diagnosis and selection, might be applicable to other kind of strain engineering in Z. mobilis.
Source model for the Mw 6.0 earthquake in Jiashi, China on 19 January 2020 from Sentinel-1A InSAR data
Authors: Yu Pengfei , Qiao Xuejun , Xiong Wei , Chen Wei , Nie Zhaosheng , Wang Dijin , Jia Zhige , Li Jie 
Published: May 2020

Abstract
On January 19, 2020, an Mw 6.0 earthquake occurred in Jiashi, Western China. The epicenter was located at the basin-mountain boundary between the southern Tian Shan and the Tarim Basin. Many strong earthquakes occurred in this region, such as the 1997 Jiashi strong earthquake swarm. In this study, Interferometric Synthetic Aperture Radar (InSAR) was used to obtain the coseismic deformation field from the ascending and descending Sentinel-1A satellite data of the European Space Agency. The results showed that the coseismic deformation was distributed along the Kalpingtag fault and the Ozgertaou fault. The earthquake produced significant deformation over an area of approximately 40 km by 30 km. The long axis of the deformation was near the east-west direction. The maximum and minimal displacements along the line of sight (LOS) were 5.3 cm, 7.2 cm and -4.2 cm, -3 cm for the ascending and descending interferograms, respectively. The slip model inverted by the steepest descent method demonstrated that the rupture process of this earthquake is dominated by a thrust fault. The slips were concentrated in a depth of 3.5 ~ 6.5 km. The maximum slip was 0.29 m. The estimated total seismic moment was 1.728×1018 Nm, corresponding to a magnitude of Mw 6.09. The inversion revealed that the coseismic rupture was located at the transition zone between the shallow high-dip fault and the deep detachment fault. The geometry of the coseismic rupture is direct evidence of the deep attitude of the Kalping fault, indicating the possibility of independent earthquakes at the shallow ramp-to-flat transition zone of an orogenic belt. The coseismic Coulomb stress changes have enhanced the stress on the deep margin of the Jiashi earthquake rupture area, indicating that there is still the possibility of another strong earthquake in this region in the future.
The Effect of Cognitive Behavioral Therapy for Insomnia in People with Type 2 Diabetes Mellitus, Pilot RCT Part II: Diabetes Health Outcomes
Authors: Alshehri Mohammed , Alothman Shaima A. , Alenazi Aqeel M. , Rucker Jason L. , Phadnis Milind A. , Miles John M. , Siengsukon Catherine F. , Kluding Patricia M. 
Published: May 2020

Abstract
Background: Previous studies have shown the negative impact of sleep disturbances, specifically insomnia symptoms, on glucose metabolism for people with type 2 diabetes (T2D). People with insomnia symptoms are at risk of poor glycemic control and suboptimal diabetes self-care behavior (DSCB). Investigating the impact of a safe and effective intervention for individuals with T2D and insomnia symptoms on diabetes health outcomes is needed. Therefore, the aim of this exploratory study is to examine the effect of Cognitive Behavioral Therapy for Insomnia (CBT-I) on glycemic control, DSCB, and fatigue. Methods: Twenty-eight participants with T2D and insomnia symptoms after passing an eligibility criteria at a medical research center were randomly assigned to CBT-I (n=14) or Health Education (HE; n=14). The CBT-I and HE groups received 6 weekly one-hour sessions. This Randomized Controlled Trial (RCT) will be using a non-inferiority framework to test the effectiveness of CBT-I. Validated assessments were administered at baseline and post-intervention to assess glycemic control, DSCB, and fatigue. A Wilcoxon signed-rank test was utilized to compare within-group changes from baseline to post-intervention. A Mann-Whitney test was utilized to measure the between-group differences. Linear regression was used to assess the association between blood glucose level and number of days in the CBT-I group. Results: The recruitment duration was from October 2018 to May 2019. A total of 13 participants completed the interventions in each group and included in the final analysis. No adverse events due to being a part of this RCT were reported. CBT-I participants showed significantly greater improvement in glycemic control, DSCB, and fatigue. There significant association between the number of days in the CBT-I intervention with blood glucose level before bedtime (B=-0.56, p=.009) and after awakening in the morning (B=-0.57, p=.007). Conclusions: This study demonstrated a clinically meaningful effect of CBT-I on glycemic control in people with T2D and insomnia symptoms. Also, CBT-I positively impacted daytime functioning, including DSCB and fatigue. Future research is needed to investigate the long-term effect of CBT-I on laboratory tests of glycemic control and to understand the underlying mechanisms of any improvements.Trial registration: Clinical Trials Registry (NCT03713996). Registered 22 October 2018, https://clinicaltrials.gov/ct2/show/NCT03713996
Transcriptome profilings reveal the candidate genes, pathways and transcription factors related to nitrogen utilization and excessive nitrogen stress in perennial ryegrass.
Authors: Li Yinruizhi , Wang Mengdi , Teng Ke , Dong Di , Liu Zhuocheng , Zhang Tiejun , Chao Yuehui , Han Liebao 
Published: May 2020

Abstract
Background：Lolium perenne L. is a kind of high quality forage grass, which can provide a good nutritional basis for herbivorous livestock. However, how to improve the nitrogen utilization rate of ryegrass and avoid the nitrate toxicity caused by excessive nitrogen has been troubling people for a long time. Up to now, the molecular response mechanism of ryegrass to nitrogen is not clear, especially under the condition of excessive nitrogen. Based on this, we tried to obtain a new insight into molecular response of ryegrass in nitrogen utilization and excessive nitrogen stress, providing the molecular theoretical basis for solving this problem.Results: In this study, the transcription of perennial ryegrass at different nitrogen levels was identified by high-throughput next-generation DNA sequencing. Phenotypic characterizations investigated that ryegrass in treatment N0.5 has a better growth state than the other three groups. The treatment N1 and N10 contained excessive nitrogen, which had a stress effect on plant growth. Analysis of differentially expressed genes indicated that 345, 105 genes are considered to involve in the regulation of nitrogen utilization and excessive nitrogen stress, respectively. GO enrichment analysis revealed that plant response to nitrogen mainly enrich in two categories, including “biological process” and “molecular function”. KEGG enrichment analysis suggested that “Photosynthesis-antenna proteins” may respond positively to nitrogen under appropriate nitrogen conditions, whereas “steroid biosynthesis”, “carotenoid biosynthesis” and “C5-branched dibasic acid metabolism” had been identified as top significant enrichment pathways response to excessive nitrogen. Transcription factors analysis showed that 21 TFs related to nitrogen utilization were classified into 10 transcription factor families, especially AP2-EREBP and MYB TF families. 4 TFs related to excessive nitrogen stress were identified, which belonged to 4 transcription factor families including LOB, NAC, AP2-EREBP and HB. The expression patterns of these selected genes above were also analyzed. Conclusions: These results made a contribution to comprehend the molecular mechanism of perennial ryegrass response to nitrogen. It provides new ideas for guiding the production practice and variety improvement of forage and even food crops from the perspective of molecular biology.