bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metagenomic analysis of bacterial species in tongue microbiome of current and never smokers
Authors: Sato Noriaki , Kakuta Masanori , Hasegawa Takanori , Yamaguchi Rui , Uchino Eiichiro , Kobayashi Wataru , Sawada Kaori , Tamura Yoshihiro , Tokuda Itoyo , Murashita Koichi , Nakaji Shigeyuki , Imoto Seiya , Yanagita Motoko , Okuno Yasushi 
Published: March 2020

AbstractCigarette smoking affects the oral microbiome, which is related to various systemic diseases. While studies that investigated the relationship between smoking and the oral microbiome by 16S rRNA amplicon sequencing have been performed, investigations involving metagenomic sequences are rare. We investigated the bacterial species composition in the tongue microbiome, as well as single-nucleotide variant (SNV) profiles and gene content of these species, in never and current smokers by utilizing metagenomic sequences. Among 234 never smokers and 52 current smokers, beta diversity, as assessed by weighted UniFrac measure, differed between never and current smokers (pseudo-F = 8.44,R2 = 0.028,p = 0.001). Among the 26 species that had sufficient coverage, the SNV profiles ofActinomyces graevenitzii,Megasphaera micronuciformis,Rothia mucilaginosa,Veillonella dispar, and oneVeillonella sp.were significantly different between never and current smokers. Analysis of gene and pathway content revealed that genes related to the lipopolysaccharide biosynthesis pathway inVeillonella disparwere present more frequently in current smokers. We found that species-level tongue microbiome differed between never and current smokers, and 5 species from never and current smokers likely harbor different strains, as suggested by the difference in SNV frequency.
Magnetic and superconducting phase diagrams and transition temperatures predicted using text mining and machine learning
Authors: Court Callum J. , Cole Jacqueline M. 
Published: March 2020

AbstractPredicting the properties of materials prior to their synthesis is of great importance in materials science. Magnetic and superconducting materials exhibit a number of unique properties that make them useful in a wide variety of applications, including solid oxide fuel cells, solid-state refrigerants, photon detectors and metrology devices. In all these applications, phase transitions play an important role in determining the feasibility of the materials in question. Here, we present a pipeline for fully integrating data extracted from the scientific literature into machine-learning tools for property prediction and materials discovery. Using advanced natural language processing (NLP) and machine-learning techniques, we successfully reconstruct the phase diagrams of well-known magnetic and superconducting compounds, and demonstrate that it is possible to predict the phase-transition temperatures of compounds not present in the database. We provide the tool as an online open-source platform, forming the basis for further research into magnetic and superconducting materials discovery for potential device applications.
Towards a widespread adoption of metabolic modeling tools in biopharmaceutical industry: a process systems biology engineering perspective
Authors: Richelle Anne , David Blandine , Demaegd Didier , Dewerchin Marianne , Kinet Romain , Morreale Angelo , Portela Rui , Zune Quentin , von Stosch Moritz 
Published: March 2020

AbstractIn biotechnology, the emergence of high-throughput technologies challenges the interpretation of large datasets. One way to identify meaningful outcomes impacting process and product attributes from large datasets is using systems biology tools such as metabolic models. However, these tools are still not fully exploited for this purpose in industrial context due to gaps in our knowledge and technical limitations. In this paper, key aspects restraining the routine implementation of these tools are highlighted in three research fields: monitoring, network science and hybrid modeling. Advances in these fields could expand the current state of systems biology applications in biopharmaceutical industry to address existing challenges in bioprocess development and improvement.
Fabrication of microfluidic device for Aflatoxin M1 detection in milk samples with specific aptamers
Authors: Kasoju Aruna , Shahdeo Deepshikha , Khan Azmat Ali , Shrikrishna Narlawar Sagar , Mahari Subhasis , Alanazi Amer M. , Bhat Mashooq Ahmad , Giri Jyotsnendu , Gandhi Sonu 
Published: March 2020

AbstractThis study describes the colorimetric detection of aflatoxin M1 (Afl M1) in milk samples using a microfluidic paper-based analytical device (µPAD). Fabrication of µPADs was done using a simple and quick approach. Each μPAD contained a detection zone and a sample zone interconnected by microchannels. The colorimetric assay was developed using unmodified AuNPs as a probe and 21-mer aptamer as a recognition molecule. The free aptamers were adsorbed onto the surface of AuNPs in absence of Afl M1, even at high salt concentrations. The salt induced aggregation of specific aptamers occurred in presence of Afl M1. Under optimum conditions, the analytical linear range was found to be 1 µM to 1 pM with limit of detection 3 pM and 10 nM in standard buffer and spiked milk samples respectively. The proposed aptamer based colorimetric assay was repeatable, quick, selective, and can be used for on-site detection of other toxins in milk and meat samples.
Genome-wide identification of miRNAs and their targets during early somatic embryogenesis in Dimocarpus longan Lour.
Authors: Xu Xiaoping , Chen Xiaohui , Chen Yan , Zhang Qinglin , Su Liyao , Chen Xu , Chen Yukun , Zhang Zihao , Lin Yuling , Lai Zhongxiong 
Published: March 2020

AbstractmiRNAs are endogenous regulatory factors that play pivotal roles in post-transcriptional regulation. However, their specific roles in early somatic embryogenesis (SE) remain unclear. Study of the SE system is fundamental for clarifying the molecular mechanisms in Dimocarpus longan. We identified 289 known miRNAs from 106 different miRNA families and 1087 novel miRNAs during early longan SE, including embryogenic callus (EC), incomplete pro-embryogenic culture (ICpEC), globular embryo (GE), and non-embryogenic callus (NEC). The abundances of known miRNAs were concentrated in GE. The differentially expression (DE) miRNAs showed five expression patterns during early SE. Largely miRNAs were expressed highly and specially in EC, ICpEC, and GE, respectively. Some miRNAs and putative target genes were enriched in lignin metabolism. Most potential targets were related to the pathways of plant hormone signal transduction, alternative splicing, tyrosine metabolism and sulfur metabolism in early longan SE. The regulatory relationships between dlo-miR166a-3p and DlHD-zip8, dlo-miR397a and DlLAC7, dlo-miR408-3p and DlLAC12 were confirmed by RNA ligase-mediated rapid amplification of cDNA ends. The expression patterns of eight DE miRNAs detected by qRT-PCR were consistent with RNA-seq. Finally, the miRNA regulatory network in early SE was constructed, which provided new insight into molecular mechanism of early SE in longan.
Super-resolution photoacoustic and ultrasound imaging with sparse arrays
Authors: Vilov Sergey , Arnal Bastien , Hojman Eliel , Eldar Yonina C. , Katz Ori , Bossy Emmanuel 
Published: March 2020

AbstractIt has previously been demonstrated that model-based reconstruction methods relying on a priori knowledge of the imaging point spread function (PSF) coupled to sparsity priors on the object to image can provide super-resolution in photoacoustic (PA) or in ultrasound (US) imaging. Here, we experimentally show that such reconstruction also leads to super-resolution in both PA and US imaging with arrays having much less elements than used conventionally (sparse arrays). As a proof of concept, we obtained super-resolution PA and US cross-sectional images of microfluidic channels with only 8 elements of a 128-elements linear array using a reconstruction approach based on a linear propagation forward model and assuming sparsity of the imaged structure. Although the microchannels appear indistinguishable in the conventional delay-and-sum images obtained with all the 128 transducer elements, the applied sparsity-constrained model-based reconstruction provides super-resolution with down to only 8 elements. We also report simulation results showing that the minimal number of transducer elements required to obtain a correct reconstruction is fundamentally limited by the signal-to-noise ratio. The proposed method can be straigthforwardly applied to any transducer geometry, including 2D sparse arrays for 3D super-resolution PA and US imaging.
A single polyploidization event at the origin of the tetraploid genome of Coffea arabica is responsible for the extremely low genetic variation in wild and cultivated germplasm
Authors: Scalabrin Simone , Toniutti Lucile , Di Gaspero Gabriele , Scaglione Davide , Magris Gabriele , Vidotto Michele , Pinosio Sara , Cattonaro Federica , Magni Federica , Jurman Irena , Cerutti Mario , Suggi Liverani Furio , Navarini Luciano , Del Terra Lorenzo , Pellegrino Gloria , Ruosi Manuela Rosanna , Vitulo Nicola , Valle Giorgio , Pallavicini Alberto , Graziosi Giorgio , Klein Patricia E. , Bentley Nolan , Murray Seth , Solano William , Al Hakimi Amin , Schilling Timothy , Montagnon Christophe , Morgante Michele , Bertrand Benoit 
Published: March 2020

AbstractThe genome of the allotetraploid species Coffea arabica L. was sequenced to assemble independently the two component subgenomes (putatively deriving from C. canephora and C. eugenioides) and to perform a genome-wide analysis of the genetic diversity in cultivated coffee germplasm and in wild populations growing in the center of origin of the species. We assembled a total length of 1.536 Gbp, 444 Mb and 527 Mb of which were assigned to the canephora and eugenioides subgenomes, respectively, and predicted 46,562 gene models, 21,254 and 22,888 of which were assigned to the canephora and to the eugeniodes subgenome, respectively. Through a genome-wide SNP genotyping of 736 C. arabica accessions, we analyzed the genetic diversity in the species and its relationship with geographic distribution and historical records. We observed a weak population structure due to low-frequency derived alleles and highly negative values of Taijma’s D, suggesting a recent and severe bottleneck, most likely resulting from a single event of polyploidization, not only for the cultivated germplasm but also for the entire species. This conclusion is strongly supported by forward simulations of mutation accumulation. However, PCA revealed a cline of genetic diversity reflecting a west-to-east geographical distribution from the center of origin in East Africa to the Arabian Peninsula. The extremely low levels of variation observed in the species, as a consequence of the polyploidization event, make the exploitation of diversity within the species for breeding purposes less interesting than in most crop species and stress the need for introgression of new variability from the diploid progenitors.
Novel HDAC11 inhibitors suppress lung adenocarcinoma stem cell self-renewal and overcome drug resistance by suppressing Sox2
Authors: Bora-Singhal Namrata , Mohankumar Durairaj , Saha Biswarup , Colin Christelle M. , Lee Jennifer Y. , Martin Matthew W. , Zheng Xiaozhang , Coppola Domenico , Chellappan Srikumar 
Published: March 2020

AbstractNon-small cell lung cancer (NSCLC) is known to have poor patient outcomes due to development of resistance to chemotherapy agents and the EGFR inhibitors, which results in recurrence of highly aggressive lung tumors. Even with recent success in immunotherapy using the checkpoint inhibitors, additional investigations are essential to identify novel therapeutic strategies for efficacious treatment for NSCLC. Our finding that high levels of histone deacetylase 11 (HDAC11) in human lung tumor tissues correlate with poor patient outcome and that depletion or inhibition of HDAC11 not only significantly reduces self-renewal of cancer stem cells (CSCs) from NSCLC but also decreases Sox2 expression that is essential for maintenance of CSCs, indicates that HDAC11 is a potential target to combat NSCLC. We find that HDAC11 suppresses Sox2 expression through the mediation of Gli1, the Hedgehog pathway transcription factor. In addition, we have used highly selective HDAC11 inhibitors that not only target stemness and adherence independent growth of lung cancer cells but these inhibitors could also efficiently ablate the growth of drug-insensitive stem-like cells as well as therapy resistant lung cancer cells. These inhibitors were found to be efficacious even in presence of cancer associated fibroblasts which have been shown to contribute in therapy resistance. Our study presents a novel role of HDAC11 in lung adenocarcinoma progression and the potential use of highly selective inhibitors of HDAC11 in combating lung cancers.
Improved performance of a rainbow trout selected strain is associated with protein digestion rates and synchronization of amino acid absorption
Authors: Brezas Andreas , Hardy Ronald W. 
Published: March 2020

AbstractReplacement of fishmeal in feeds is critical for sustainable aquaculture growth. However, replacement with plant protein concentrates reduces fish performance. A rainbow trout strain selected for high performance on a plant protein diet was compared to a non-selected strain to identify physiological mechanisms associated with improved performance. Nutrient digestibility in fishmeal and plant protein diets was assessed and no strain differences were found. Levels of amino acids in the hepatic portal vein and caudal vein were measured at intervals after a single force-feeding of fishmeal, four plant protein concentrates, and a mixture of the concentrates with or without supplementation of three limiting amino acids. Each ingredient affected plasma amino acid levels in a singular manner when fed individually but without predictable additive effects when fed as a mixture. Amino acid supplementation altered uptake and plasma concentrations of all the essential amino acids. The selected trout strain fed the plant protein mixture with amino acids showed a synchronous and homogenous pattern for essential amino acids over time in the hepatic portal vein in contrast to that of the non-selected strain. The results demonstrate that selection favorably altered temporal dynamics of plant protein digestion.
Immunosuppression response to the neonicotinoid insecticide thiacloprid in females and males of the red mason bee Osmia bicornis L.
Authors: Brandt Annely , Hohnheiser Birgitta , Sgolastra Fabio , Bosch Jordi , Meixner Marina Doris , Büchler Ralph 
Published: March 2020

AbstractSolitary bees are frequently exposed to pesticides, which are considered as one of the main stress factors that may lead to population declines. A strong immune defence is vital for the fitness of bees. However, the immune system can be weakened by environmental factors that may render bees more vulnerable to parasites and pathogens. Here we demonstrate for the first time that field-realistic concentrations of the commonly used neonicotinoid insecticide thiacloprid can severely affect the immunocompetence of Osmia bicornis. In detail, males exposed to thiacloprid solutions of 200 and 555 µg/kg showed a reduction in hemocyte density. Moreover, functional aspects of the immune defence - the antimicrobial activity of the hemolymph - were impaired in males. In females, however, only a concentration of 555 µg/kg elicited similar immunosuppressive effects. Although males are smaller than females, they consumed more food solution. This leads to a 2.77 times higher exposure in males, probably explaining the different concentration thresholds observed between the sexes. In contrast to honeybees, dietary exposure to thiacloprid did not affect melanisation or wound healing in O. bicornis. Our results demonstrate that neonicotinoid insecticides can negatively affect the immunocompetence of O. bicornis, possibly leading to an impaired disease resistance capacity.
CT Lung Screening in Patients with Laryngeal Cancer
Authors: Piersiala Krzysztof , Akst Lee M. , Hillel Alexander T. , Best Simon R. 
Published: March 2020

AbstractLaryngeal cancer (LC) patients who meet the age and smoking criteria of the U.S. Preventive Services Task Force (USPSTF) for annual CT lung screening were analysed for pulmonary nodules (PN) detection and secondary lung cancer (SLC) diagnosis. This is a retrospective chart review of LC patients treated at Johns Hopkins Hospital from January 2010 to December 2017. The study population included patients who met USPSTF criteria by age and smoking history for annual chest screening and were followed for at least 3 consecutive years. A total of 998 LC patients’ records were reviewed, of which 151 met the inclusion criteria. Inadequate follow-up period (37% of excluded cases) was the most common reason for exclusion, followed by not meeting USPSTF age criteria (27% excluded cases). In seventy-eight patients (n = 78, 52% of analysed patients) PN were reported. Nine individuals (6% of analysed patients) were diagnosed with SLC. Age over 70 (p = 0.003) was an independent predictor of malignancy. White race and smoking history over 40 pack-years were positively associated with a pulmonary nodule detection (p = 0.037 and p = 0.044, respectively). The incidence of PN and SLC in patients with LC is high. Many patients with laryngeal cancer meet the formal guidelines for USPSTF screening, and should be screened annually according to evidence-based medicine for the early detection of secondary lung cancers.
Joint influence of genetic origin and climate on the growth of Masson pine (Pinus massoniana Lamb.) in China
Authors: Zhang Zhen , Jin Guoqing , Feng Zhongping , Sun Linshan , Zhou Zhichun , Zheng Yi , Yuan Chengzhi 
Published: March 2020

AbstractAdaptive of trees and its correlation with the climatic are causing changes in tree species performance and distribution, which will change breeding programs and influence forest productivity. To further evaluate the joint influence of climatic factors and provenance on the ring width (RW) and ring density (RD) of Masson pine. We selected 18 provenances at Chun’an (CA) and Taizi Mountain (TZS) test site, which representing four different breeding regions, including the south, west, north and east-central regions. The results showed that the provenance effects were significantly for the RW and RD. The provenances from high temperature and low latitude regions had greater mean RW compared to species from local and cold sources. The geographical genetic variation in wood traits is generally weak. The correlation between RW of Masson pine and precipitation was stronger in the relatively arid TZS site compared with that in relatively wet CA site, as well as the effect of temperature and precipitation on RD was earlier than that in CA test site. The response relationship between establishing the width of tree rings and the environmental variables of provenance indicated that during the transition from the northern and western breeding regions to the eastern and southern breeding regions, the response of RW to climate factors changed from being temperature-based to being precipitation-based. In addition, the response of provenance to the climate of seed sources origin showed their own variation characteristics in each breeding area. Therefore, genetic improvement of big diameter wood and wood density can be gain through selection of provenance and analysis of adaptability.
A universal opportunity model for human mobility
Authors: Liu Er-Jian , Yan Xiao-Yong 
Published: March 2020

AbstractPredicting human mobility between locations has practical applications in transportation science, spatial economics, sociology and many other fields. For more than 100 years, many human mobility prediction models have been proposed, among which the gravity model analogous to Newton’s law of gravitation is widely used. Another classical model is the intervening opportunity (IO) model, which indicates that an individual selecting a destination is related to both the destination’s opportunities and the intervening opportunities between the origin and the destination. The IO model established from the perspective of individual selection behavior has recently triggered the establishment of many new IO class models. Although these IO class models can achieve accurate prediction at specific spatiotemporal scales, an IO class model that can describe an individual’s destination selection behavior at different spatiotemporal scales is still lacking. Here, we develop a universal opportunity model that considers two human behavioral tendencies: one is the exploratory tendency, and the other is the cautious tendency. Our model establishes a new framework in IO class models and covers the classical radiation model and opportunity priority selection model. Furthermore, we use various mobility data to demonstrate our model’s predictive ability. The results show that our model can better predict human mobility than previous IO class models. Moreover, this model can help us better understand the underlying mechanism of the individual’s destination selection behavior in different types of human mobility.
Effects of Conservation Tillage on Soil Physicochemical Properties and Crop Yield in an Arid Loess Plateau, China
Authors: Li Juan , Wang Yi-ke , Guo Zhen , Li Jin-bin , Tian Chang , Hua Dong-wen , Shi Chen-di , Wang Huan-yuan , Han Ji-chang , Xu Yan 
Published: March 2020

AbstractConservation tillage can improve soil physical structure and water storage, protect moisture, and increase crop yield. However, the long-term adoption of a single tillage method may have some adverse effects on soil and ecological environment, although crop yields have increased. Through informed allocation of soil tillage techniques, the combination and configuration of soil tillage measures, such as rotary tillage, subsoiling, and no tillage may reduce the shortcomings of traditional long-term farming. To explore the long-term production mode suitable for production of maize in the loess dryland area, a long-term experiment was conducted in Fuping County, Shaanxi Province, from 2013 to 2018. Six farming modes were used in the experiment: no tillage/subsoiling (N ↔ S), subsoiling/rotary tillage (S ↔ R), rotary tillage/no tillage (R ↔ N), continuous no tillage (N ↔ N), continuous subsoiling (S ↔ S), and continuous rotary tillage (R ↔ R). The changes in soil physical and chemical properties, soil water use patterns, soil water storage, conservation effects during the fallow and growth period, and the effects on farmland yield increase were analyzed. The results showed that rotary tillage can effectively improved soil structure and reduced soil bulk density, where N ↔ S treatment soil bulk density is low and in 0–60 cm soil layer averaged 1.31 g/cm3. Different tillage treatments could be used during the fallow period to store additional soil moisture: the N ↔ S treatment showed good water storage effect. Compared to traditional tillage, different tillage methods provided better soil moisture conditions for crops during the growth period, where N ↔ S treatment showed good soil moisture status during the growth period of spring maize. Among all the treatments, N ↔ S treatment effectively increased the organic carbon storage in the 0–60 cm soil layer, which was 54.3 t/hm2. Compared with traditional tillage, different tillage treatments effectively increased plant height and dry matter accumulation of spring maize, where N ↔ S treatment was found to be the best. Compared with the traditional rotary tillage model, the N ↔ S treatment significantly increased crop yield and water use efficiency (WUE) in continuous cropping fields of corn, the average yield of spring corn was 9340.2 kg/hm2, and the average WUE was 22.9 kg/(hm2·mm). In summary, for long-term sustainable development, the N ↔ S model is the best rotational tillage mode for continuous maize cropping in loess soil.