bluuebunny/crossref_metadata_2025_split huggingface dataset:
Geochemical markers of paleoenvironments, weathering, and provenance in Permian–Triassic terrestrial sediments
Authors: Galán-Abellán Ana-Belén , Barrenechea José F. , de La Horra Raúl , Alonso-Azcárate Jacinto , Luque Javier F. , Borruel-Abadía Violeta , López-Gómez José 
Published: September 2020

ABSTRACTThis study compares several geochemical factors (major and minor rare earth elements, Ti/Al ratios, and chemical index of alteration, CIA, values) in the Early Triassic Cañizar Formation (Fm) (Buntsandtein facies) of E Iberia with those of adjacent Middle Permian and Middle Triassic units (Alcotas and Eslida fms, respectively). According to significant differences detected, it seems that most geochemical perturbation occurred during the Early Triassic. Variations in Ti/Al ratios suggest changes in source areas between the studied units and even within the Cañizar Fm. These provenance changes correlate with successive tectonic pulses during the opening and development of the Iberian Basin, as they can be linked to major sedimentary surfaces and unconformities, as well as major sedimentological variations. Ti enrichment in the lower and middle part of the Cañizar Fm, together with high Sr and P concentrations, may be indicative of environmental alterations related to acid meteoric waters. Moreover, this acid alteration took place under arid conditions as reflected by CIA values, indicating that during the deposition of the Cañizar Fm, variable but predominantly physical weathering prevailed in contrast to the chemical weathering that took place when the Alcotas and Eslida formations were deposited. Our data along with the known fossil record of the study area indicate that during the Middle–Late Permian and Early Triassic, conditions in this tectonically active area changed from humid to arid-acid, hampering biotic recovery. Then, during late Early–Middle Triassic times, the return of more humid and less acid environments promoted biotic development. Geochemical markers emerged as useful tools complementary to sedimentological, paleontological, and tectonic data for unveiling paleoenvironmental events, especially in a setting of significant regional change.
Photosynthesis, biomass and fine root growth dynamics of soybean in walnut-soybean agroforestry system
Authors: Liu Bin , Gao Pengxiang , Zhang Shuoxin 
Published: September 2020

Abstract
Background:Agroforestry system is regarded as a promising practice in sustainable agricultural management. However, the effects of long-term tree-based intercropping on crop remain poorly understood, especially in the Loess Plateau. In this study, the impacts of photosynthetic and respiration rate were determined by the portable photosynthesis system (Li-6400), and the effects of the root growth dynamics of soybean in walnut-soybean intercropping system were measured by soil auger and WinRHIZO root analysis system, in the Loess Plateau. Results:The results showed that soybean reached the highest net photosynthetic rate during flowering period, with the net photosynthetic rate of intercropped soybean, which was 20.40µmol·m-2·s-1, significantly higher than that of its monocropped counterpart. Soybean biomass reached the maximum during the pod-bearing period, with intercropped soybean biomass being 25.49g, significantly higher than that of its monocropped counterpart. The mean diameter and increased density of soybean fine roots reduced along with increased soil depth. Both the diameter (0.43mm) and increased density (930cm/dm3) of intercropped soybean fine roots were evidently higher than those of monocropped soybean(0.35mm, 780cm/dm3). With increasing cropping years, fine roots of intercropped soybean tended to be mainly distributed in soil at a depth between 0 and 20cm from the fifth year. Conclusion:Collectively, compared with soybean monoculture, walnut soybean agroforestry system is more conducive to soybean growth in the Loess Plateau.
Transcriptomic analysis of s-methoprene resistance in the lesser grain borer, Rhyzopertha dominica, and evaluation of piperonyl butoxide as a resistance breaker
Authors: SAKKA MARIA , Riga Maria , Ioannidis Panagiotis , Baliota Georgia V , Tselika Martha , Jagadeesan Rajeswaran , Nayak Manoj K. , Vontas John , Athanassiou Christos 
Published: September 2020

Abstract
Background: The lesser grain borer, Rhyzopertha dominica is a serious pest of stored grains. Fumigation and contact insecticides play a major role in managing this pest globally. While insects are developing genetic resistance to chemicals, hormonal analogues such as s-methoprene play a key role in reducing general pest pressure as well as managing pest populations that are resistant to fumigants and neurotoxic contact insecticides. However, resistance to s-methoprene has been reported in R. dominica with some reports showing a remarkable high resistance, questioning the use of this compound and other related analogues in grain protection. The current study attempts to identify possible molecular mechanisms that contribute in resistance to s-methoprene in R. dominica. Results: Transcriptome analysis of resistant and susceptible strains of this pest species identified a set of differentially expressed genes related to cytochrome P450s, indicating their potential role in resistance to s-methoprene. Laboratory bioassays were performed with s-methoprene treated wheat grains in presence and absence of piperonyl butoxide (PBO), a cytochrome P450 inhibitor. The results indicate that PBO, when applied alone, at least at the concentration tested here, had no effect on R. dominica adult emergence, but has a clear synergistic effect to s-methoprene. The number of produced progeny decreased in presence of the inhibitor, especially in the resistant strain. In addition, we also identified CYP complement (CYPome) of R. dominica, annotated and analysed phylogenetically, to understand the evolutionary relationships with other species.Conclusions: The information generated in current study suggest that PBO can effectively be used to break resistance to s-methoprene in R. dominica.
Disability-adjusted Life Years for respiratory syncytial virus in children under 2 years
Authors: buendia jefferson , Polack Fernando , Villamil Juana Patricia Sanchez 
Published: September 2020

Abstract
BACKGROUND: Respiratory syncytial virus infection is the leading cause of bronchiolitis in Colombia. There is growing evidence about the impact of Respiratory syncytial virus on society in terms of years of life lost due to this condition. The objective of the present study is to determine the Disability-Adjusted Life Years for respiratory syncytial virus in children under 2 years in ColombiaMETHODS: Data from the national epidemiological surveillance system were used to estimate DALYs, calculated from the sum of years of life lost and years lived with disability due to RSV infection in Colombia. A bootstrapped method with 10000 iterations was used to estimate each statistical parameter using the package DALY calculator in R. RESULTS: In 2019, 260 873 years of life (CI95% 208 180- 347 023) were lost due to RSV bronchiolitis in Colombian children under 2 years. The estimated rate was 20 DALYs / 1000 person-year (95% CI 16 – 27).CONCLUSION: This is the first report estimating the impact of RSV bronchiolitis morbidity and mortality in Colombia. The findings of the present study suggest that the actual burden and cost of bronchiolitis due to RSV is high. Prevention strategies, such as RSV vaccination, to reduce morbidity associated with RSV infection should be encouraged in our country.
Rapid optimisation of cellulolytic enzymes ratios in Saccharomyces cerevisiae using in vitro SCRaMbLE
Authors: Wightman Elizabeth L. I. , Kroukamp Heinrich , Pretorius Isak S. , Paulsen Ian T. , Nevalainen Helena K. M. 
Published: September 2020

Abstract
Background: For the economic production of biofuels and other valuable products from lignocellulosic waste material, a consolidated bioprocessing (CBP) organism is required. With efficient fermentation capability and attractive industrial qualities, Saccharomyces cerevisiae is a preferred candidate and has been engineered to produce enzymes that hydrolyze cellulosic biomass. Efficient cellulose hydrolysis requires the synergistic action of several enzymes; with the optimum combined activity ratio dependent on the composition of the substrate. Results: In vitro SCRaMbLE generated a library of plasmids containing different ratios of a β-glucosidase gene (CEL3A) from Saccharomycopsis fibuligera and an endoglucanase gene (CEL5A) from Trichoderma reesei. S. cerevisiae, transformed with the plasmid library, displayed a range of individual enzyme activities and synergistic capabilities. Furthermore, we show for the first time that 4,6-O-(3-Ketobutylidene)-4-nitrophenyl-β-D-cellopentaoside (BPNPG5) is a suitable substrate to determine synergistic Cel3A and Cel5A action and an accurate predictive model for this synergistic action was devised. Strains with highest BPNPG5 activity had an average CEL3A and CEL5A gene cassette copy number of 1.3 ± 0.6 and 0.8 ± 0.2 respectively (ratio of 1.6:1). Conclusions: Here we describe a synthetic biology approach to rapidly optimize gene copy numbers to achieve efficient synergistic substrate hydrolysis. This study demonstrates how in vitro SCRaMbLE can be applied to rapidly combine gene constructs in various ratios to allow screening of synergistic enzyme activities for efficient substrate hydrolysis.
Comorbidities associated with nontuberculous mycobacterial disease in Japanese adults: A claims-data analysis
Authors: Uno Shunsuke , Aasakura Takanori , Morimoto Kozo , Yoshimura Kimio , Uwamino Yoshifumi , Nishimura Tomoyasu , Hoshino Yoshihiko , Hasegawa Naoki 
Published: September 2020

Abstract
Background: Nontuberculous mycobacterial (NTM) lung disease is one of a growing number of chronic health problems that is difficult to cure in aging societies. While it is important to be vigilant about associated comorbidities in order to provide better patient care, data on the prevalence of comorbidities stratified by country or region are scarce. We aimed to elucidate the comorbidities associated with NTM disease based on Japanese health insurance claims data. Methods: Cross-sectional analyses were performed using the claims data for 2014 provided by the Japan Medical Data Center Co., Ltd. Patients aged 20–75 years with ≥3 claims associated with NTM disease were identified and matched to 10 sex-and-age-matched controls that had never made a claim for NTM disease. Thirty-one comorbidities previously suspected to be associated with NTM disease were selected, and the prevalence of these comorbidities compared between cases and controls. Result: Overall, 419 NTM patients (134 males and 285 females) and 4190 non-NTM controls were selected from the JMDC database. Aspergillosis, asthma, bronchiectasis, chronic heart failure, diffuse panbronchiolitis, gastroesophageal reflux, interstitial pneumonia, lung cancer, cancer other than breast, lung, ovary, or prostate cancer, and rheumatic arthritis were associated with NTM disease in both males and females. Chronic obstructive pulmonary disease was associated with NTM in males while chronic kidney disease, osteoporosis, and Sjögren syndrome were associated with NTM in females. Conclusion: NTM disease was associated with multiple comorbidities that should be considered when providing medical care to individuals with NTM disease.
Study on the community structure and function of symbiotic bacteria from different growth and developmental stages of Hypsizygus marmoreus
Authors: sun shujing , Li Fan , Xu Xin , Liu Yunchao , Kong Xuqiang , Chen Jianqiu , Liu Ting , Chen Liding 
Published: September 2020

Abstract
Background: The symbiotic bacteria associated with edible fungi are valuable microbial resources worthy of in-depth exploration. It is important to analyze the community structure and succession of symbiotic bacteria in mushrooms. This can assist in the isolation of growth-promoting strains that have an essential relationship with the cultivation cycle as well as the agronomic traits and yields of fruiting bodies.Results: In all of the samples from cultivation bags of Hypsizygus marmoreus, 34 bacterial phyla were detected. Firmicutes was the most abundant bacterial phylum (78.85%). The genus Serratia showed an exponential increase in abundance in samples collected from the cultivation bags in the mature period, reaching a peak abundance of 55.74% and the dominant symbiotic flora. The most predominant strain was Serratia odorifera HZSO-1, and its abundance increased with the amount of hyphae of H. marmoreus. Serratia odorifera HZSO-1 could reside in the hyphae of H. marmoreus, promote growth and development, shorten the fruiting cycle by 3-4 days, and further increase the fruiting body yield by 12%. Conclusions: This study is a pioneering demonstration of the community structure of the symbiotic microbiota and bacteria-mushroom interaction in the growth and development of edible fungi. This work lays a theoretical foundation to improve the industrial production of mushrooms with symbiotic bacteria as assisting agents.
Malaria parasites in macaques in Thailand: stump-tailed macaques (Macaca arctoides) are new natural hosts for Plasmodium knowlesi, Plasmodium inui, Plasmodium coatneyi and Plasmodium fieldi
Authors: Fungfuang Wirasak , Udom Chanya , Tongthainan Daraka , Kadir Khamisah Abdul , Singh Balbir 
Published: September 2020

Abstract
Background: Certain species of macaques are natural hosts of Plasmodium knowlesi and Plasmodium cynomolgi, which can both cause malaria in humans, and Plasmodium inui, which can be experimentally transmitted to humans. A significant number of zoonotic malaria cases have been reported in humans throughout Southeast Asia, including Thailand. There have been only two studies undertaken in Thailand to identify malaria parasites in non-human primates in 6 provinces. The objective of this study was to determine the prevalence of P. knowlesi, P. cynomolgi, P. inui, Plasmodium coatneyi and Plasmodium fieldi in non-human primates from 4 new locations in Thailand.Methods: A total of 93 blood samples from Macaca fascicularis, Macaca leonina and Macaca arctoides were collected from four locations in Thailand: 32 were captive M. fascicularis from Chachoengsao Province (CHA), 4 were wild M. fascicularis from Ranong Province (RAN), 32 were wild M. arctoides from Prachuap Kiri Khan Province (PRA), and 25 were wild M. leonina from Nakornratchasima Province (NAK). DNA was extracted from these samples and analysed by nested PCR assays to detect Plasmodium, and subsequently to detect P. knowlesi, P. coatneyi, P. cynomolgi, P. inui and P. fieldi.Results: Twenty-seven of the 93 (29%) samples were Plasmodium-positive by nested PCR assays. Among wild macaques, all 4 M. fascicularis at RAN were infected with malaria parasites followed by 50% of 32 M. arctoides at PRA and 20% of 25 M. leonina at NAK. Only 2 (6.3%) of the 32 captive M. fascicularis at CHA were malaria-positive. All 5 species of Plasmodium were detected and 16 (59.3%) of the 27 macaques had single infections, 9 had double and 2 had triple infections. The composition of Plasmodium species in macaques at each sampling site was different. Macaca arctoides from PRA were infected with P. knowlesi, P. coatneyi, P. cynomolgi, P. inui and P. fieldi.Conclusions: The prevalence and species of Plasmodium varied among the wild and captive macaques, and between macaques at 4 sampling sites in Thailand. Macaca arctoides is a new natural host for P. knowlesi, P. inui, P. coatneyi and P. fieldi.
Connecting METTL3 and intratumoural CD33+ MDSCs in predicting clinical outcome in cervical cancer
Authors: Ni Huan-he , Zhang Lin , Huang He , Dai Shu-qin , Li Jiang 
Published: September 2020

Abstract
Background: Methyltransferase-like 3 (METTL3) is a member of the m6A methyltransferase family and acts as an oncogene in cancers. Recent studies suggest that host innate immunity is regulated by the enzymes controlling m6A epitranscriptomic changes. Here, we aim to explore the associations between the levels of METTL3 and CD33+ myeloid-derived suppressor cells (MDSCs) in tumour tissues and the survival of patients with cervical cancer (CC).Methods: Specimens of paraffin embedded tumour from 197 CC patients were collected. The expression levels of METTL3 and CD33 were measured by immunohistochemical (IHC) staining. The clinical associations of the IHC variants were analysed by Pearson's or Spearman's chi-square tests. Overall survival (OS) and disease-free survival (DFS) were estimated by the Kaplan-Meier method and log-rank test. Hazard ratios (HRs) and independent significance were obtained via Cox proportional hazards models for multivariate analyses. METTL3 in CD33+ cells or CC-derived cells was knocked down by METTL3-specific siRNA, and MDSC induction in vitro was performed in a co-culture system in the presence of METTL3-siRNA and METTL3-knockdown-CC-derived cells compared with that of the corresponding controls.Results: We found that tumour tissues displayed increased levels of METTL3 and CD33+ MDSCs compared with tumour-adjacent tissues from the same CC patients. Importantly, METTL3 expression was positively related to the density of CD33+ cells in tumour tissues (P = 0.011). We further found that the direct CD33+CD11b+HLA-DR- MDSC induction and tumour-derived MDSC induction in vitro were decreased in the absence of METTL3. The level of METTL3 in tumour microenvironments was significantly related to advanced tumour stage. The levels of METTL3 and CD33+ MDSCs in tumour tissues were notably associated with reduced DFS or OS. Cox model analysis revealed that the level of METTL3 in tumour cells was an independent factor for patient survival, specifically for DFS (HR = 3.157, P = 0.022) and OS (HR = 3.271, P = 0.012), while the CD33+ MDSC number was an independent predictor for DFS (HR: 3.958, P = 0.031). Interestingly, in patients with advanced-disease stages (II-IV), METTL3 in tumour cells was an independent factor for DFS (HR = 6.725, P= 0.010) and OS (HR = 5.140, P= 0.021), while CD33+ MDSC density was an independent factor for OS (HR = 8.802, P = 0.037).Conclusion: Our findings suggest that CD33+ MDSC expansion is linked to high levels of METTL3 and that METTL3 and CD33+ MDSCs are independent prognostic factors in CC.
Incomplete Staging in Apparent Early Stage Ovarian Cancer; Guidelines Versus Daily Practice
Authors: Beltman Jogchum , Laven P , Bense JE , Aa Maaike van der , Vos MC , Boll D , Arts HGJ , Reesink N , Trimbos JB , Kruitwagen RFPM 
Published: September 2020

Abstract
Background: Incomplete surgical staging of patients with early stage epithelial ovarian cancer (EOC) has been reported in up to 85% of cases, when based on the International Federation of Obstetrics and Gynaecology (FIGO) staging procedure. The aim of the present retrospective study was to clarify the reasons for incomplete staging.Methods: The PRISMA (Prevention Recovery Information System for Monitoring and Analysis) technique was used to evaluate cases with FIGO I-IIa EOC based on incomplete staging from five gynecologic oncologic center hospitals in the Netherlands in the period 2010-2014.Results: Fifty cases with an incomplete surgical staging of EOC according to national guidelines were included. The most common reasons for incomplete staging were insufficient random biopsies of the peritoneum (n=34, 68%), and less than ten lymph nodes being resected and/or found at pathology (n=16, 32%). The most mentioned reasons for not performing biopsies were forgetting to do so, and believing that after careful inspection and palpation, taking biopsies is irrelevant and/or already are being taken while performing a hysterectomy (peritoneum of cul-de-sac, bladder). The value of contralateral pelvic lymph node dissection in case of a unilateral ovarian malignancy was also doubted, influencing the number of lymph nodes resected.Conclusions: The most important reasons for incomplete staging in EOC are, besides omitting elements by accident, questioning the importance of obligatory elements of the staging procedure. A structured list of staging steps during surgery and more evidence based consensus concerning these obligatory elements might increase the number of complete staging procedures in EOC.
SPAD Value Varies With Age and Leaf of Maize Plant and its Relationship With Grain Yield
Authors: Kandel Bishnu 
Published: September 2020

Abstract
Objectives: A field experiment was conducted to evaluate Soil Plant Analysis Development (SPAD) value in different age and leaf of maize hybrid and correlating with grain yield. Ten maize hybrids were replicated thricely under Randomized Complete Block Design (RCBD) during winter of 2018. SPAD value was measured by SPAD 502 Plus meter. At 30 days interval during vegetative stage SPAD measurement were taken from T1 (top most leaf) and T3 (3rd leaf from top leaf) leaves of five randomly selected plants from one plot and they were averaged. For reproductive phase data taken from eo (leaf attached to ear) and e2 (2nd leaf from eo leaf) leaves at 10 days intervals. Same leaves were used for entire data collection.Results: Significantly different SPAD value was observed for different age and leaves of maize during pre and post anthesis. SPAD value increase with increase in age and decrease at the time of maturity. During vegetative phase T3 leaves has more SPAD value than T1. During reproductive stage eo leaves had more SPAD than e2 leaves, so center leaf of maize contributes more to grain yield. Correlation showed that there is strong positive correlation between different stage of SPAD with grain yield.
Identification of key genes unique to the luminal A and basal-like breast cancer subtypes via bioinformatic analysis
Authors: Jia Rong , Li Zhongxian , Liang Wei , Ji Yucheng , Weng Yujie , Liang Ying , Ning Pengfei 
Published: September 2020

Abstract
Background: Breast cancer subtypes are statistically associated with prognosis. The search for markers of breast tumor heterogeneity and the development of precision medicine for patients are the current focuses of the field.Methods: We used a bioinformatic approach to identify key disease-causing genes unique to the luminal A and basal-like subtypes of breast cancer. First, we retrieved gene expression data for luminal A breast cancer, basal-like breast cancer, and normal breast tissue samples from The Cancer Genome Atlas database. The differentially expressed genes unique to the 2 breast cancer subtypes were identified and subjected to Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses. We constructed protein–protein interaction networks of the differentially expressed genes. Finally, we analyzed the key modules of the networks, which we combined with survival data to identify the unique cancer genes associated with each breast cancer subtype.Results: We identified 1,114 differentially expressed genes in luminal A breast cancer and 1,042 differentially expressed genes in basal-like breast cancer, of which the subtypes shared 500. We observed 614 and 542 differentially expressed genes unique to luminal A and basal-like breast cancer, respectively. Through enrichment analyses, protein–protein interaction network analysis, and module mining, we identified 8 key differentially expressed genes unique to each subtype. Analysis of the gene expression data in the context of the survival data revealed that high expression of NMUR1 and NCAM1 in luminal A breast cancer statistically correlated with poor prognosis, whereas the low expression levels of CDC7, KIF18A, STIL, and CKS2 in basal-like breast cancer statistically correlated with poor prognosis.Conclusions: NMUR1 and NCAM1 are novel key disease-causing genes for luminal A breast cancer, and STIL is a novel key disease-causing gene for basal-like breast cancer. These genes are potential targets for clinical treatment.