bluuebunny/crossref_metadata_2025_split huggingface dataset:
The effect of taxonomic classification by full-length 16S rRNA sequencing with a synthetic long-read technology
Authors: Jeong Jinuk , Yun Kyeongeui , Mun Seyoung , Chung Won-Hyong , Choi Song-Yi , Nam Young-do , Lim Mi Young , Hong Chang Pyo , Park ChanHyeok , Ahn Yong Ju , Han Kyudong 
Published: January 2021

AbstractCharacterizing the microbial communities inhabiting specimens is one of the primary objectives of microbiome studies. A short-read sequencing platform for reading partial regions of the 16S rRNA gene is most commonly used by reducing the cost burden of next-generation sequencing (NGS), but misclassification at the species level due to its length being too short to consider sequence similarity remains a challenge. Loop Genomics recently proposed a new 16S full-length-based synthetic long-read sequencing technology (sFL16S). We compared a 16S full-length-based synthetic long-read (sFL16S) and V3-V4 short-read (V3V4) methods using 24 human GUT microbiota samples. Our comparison analyses of sFL16S and V3V4 sequencing data showed that they were highly similar at all classification resolutions except the species level. At the species level, we confirmed that sFL16S showed better resolutions than V3V4 in analyses of alpha-diversity, relative abundance frequency and identification accuracy. Furthermore, we demonstrated that sFL16S could overcome the microbial misidentification caused by different sequence similarity in each 16S variable region through comparison the identification accuracy of Bifidobacterium, Bacteroides, and Alistipes strains classified from both methods. Therefore, this study suggests that the new sFL16S method is a suitable tool to overcome the weakness of the V3V4 method.
Deep learning-Based 3D inpainting of brain MR images
Authors: Kang Seung Kwan , Shin Seong A. , Seo Seongho , Byun Min Soo , Lee Dong Young , Kim Yu Kyeong , Lee Dong Soo , Lee Jae Sung 
Published: January 2021

AbstractThe detailed anatomical information of the brain provided by 3D magnetic resonance imaging (MRI) enables various neuroscience research. However, due to the long scan time for 3D MR images, 2D images are mainly obtained in clinical environments. The purpose of this study is to generate 3D images from a sparsely sampled 2D images using an inpainting deep neural network that has a U-net-like structure and DenseNet sub-blocks. To train the network, not only fidelity loss but also perceptual loss based on the VGG network were considered. Various methods were used to assess the overall similarity between the inpainted and original 3D data. In addition, morphological analyzes were performed to investigate whether the inpainted data produced local features similar to the original 3D data. The diagnostic ability using the inpainted data was also evaluated by investigating the pattern of morphological changes in disease groups. Brain anatomy details were efficiently recovered by the proposed neural network. In voxel-based analysis to assess gray matter volume and cortical thickness, differences between the inpainted data and the original 3D data were observed only in small clusters. The proposed method will be useful for utilizing advanced neuroimaging techniques with 2D MRI data.
Phytoplankton consortia as a blueprint for mutually beneficial eukaryote-bacteria ecosystems based on the biocoenosis of Botryococcus consortia
Authors: Blifernez-Klassen Olga , Klassen Viktor , Wibberg Daniel , Cebeci Enis , Henke Christian , Rückert Christian , Chaudhari Swapnil , Rupp Oliver , Blom Jochen , Winkler Anika , Al-Dilaimi Arwa , Goesmann Alexander , Sczyrba Alexander , Kalinowski Jörn , Bräutigam Andrea , Kruse Olaf 
Published: January 2021

AbstractBacteria occupy all major ecosystems and maintain an intensive relationship to the eukaryotes, developing together into complex biomes (i.e., phycosphere and rhizosphere). Interactions between eukaryotes and bacteria range from cooperative to competitive, with the associated microorganisms affecting their host`s development, growth and health. Since the advent of non-culture dependent analytical techniques such as metagenome sequencing, consortia have been described at the phylogenetic level but rarely functionally. Multifaceted analysis of the microbial consortium of the ancient phytoplankton Botryococcus as an attractive model food web revealed that its all abundant bacterial members belong to a niche of biotin auxotrophs, essentially depending on the microalga. In addition, hydrocarbonoclastic bacteria without vitamin auxotrophies seem adversely to affect the algal cell morphology. Synthetic rearrangement of a minimal community consisting of an alga, a mutualistic and a parasitic bacteria underpins the model of a eukaryote that maintains its own mutualistic microbial community to control its surrounding biosphere. This model of coexistence, potentially useful for defense against invaders by a eukaryotic host could represent ecologically relevant interactions that cross species boundaries. Metabolic and system reconstruction is an opportunity to unravel the relationships within the consortia and provide a blueprint for the construction of mutually beneficial synthetic ecosystems.
Ultra-broadband axicon transducer for optoacoustic endoscopy
Authors: Ali Zakiullah , Zakian Christian , Ntziachristos Vasilis 
Published: January 2021

AbstractImage performance in optoacoustic endoscopy depends markedly on the design of the transducer employed. Ideally, high-resolution performance is required over an expanded depth of focus. Current optoacoustic focused transducers achieve lateral resolutions in the range of tens of microns in the mesoscopic regime, but their depth of focus is limited to hundreds of microns by the nature of their spherical geometry. We designed an ultra-broadband axicon detector with a 2 mm central aperture and investigated whether the imaging characteristics exceeded those of a spherical detector of similar size. We show a previously undocumented ability to achieve a broadband elongated pencil-beam optoacoustic sensitivity with an axicon detection geometry, providing approximately 40 μm-lateral resolution maintained over a depth of focus of 950 μm—3.8 times that of the reference spherical detector. This performance could potentially lead to optoacoustic endoscopes that can visualize optical absorption deeper and with higher resolution than any other optical endoscope today.
Integrated analysis of lncRNA and mRNA transcriptomes reveals the potential regulatory role of lncRNA in kiwifruit ripening and softening
Authors: Chen Yiting , Cheng Chunzhen , Feng Xin , Lai Ruilian , Gao Minxia , Chen Wenguang , Wu Rujian 
Published: January 2021

AbstractKiwifruit has gained increasing attention worldwide for its unique flavor and high nutritional value. Rapid softening after harvest greatly shortens its shelf-life and reduces the commercial value. Therefore, it is imperative and urgent to identify and clarify its softening mechanism. This study aimed to analyze and compare the long noncoding RNA (lncRNA) and mRNA expression patterns in ABA-treated (ABA) and room temperature (RT)-stored fruits with those in freshly harvested fruits (CK) as control. A total of 697 differentially expressed genes (DEGs) and 81 differentially expressed lncRNAs (DELs) were identified while comparing ABA with CK, and 458 DEGs and 143 DELs were detected while comparing RT with CK. The Kyoto Encyclopedia of Genes and Genomes analysis of the identified DEGs and the target genes of DELs revealed that genes involved in starch and sucrose metabolism, brassinosteroid biosynthesis, plant hormone signal transduction, and flavonoid biosynthesis accounted for a large part. The co-localization networks, including 38 DEGs and 31 DELs in ABA vs. CK, and 25 DEGs and 25 DELs in RT vs. CK, were also performed. Genes related to fruit ripening, such as genes encoding β-galactosidase, mannan endo-1,4-β-mannosidase, pectinesterase/pectinesterase inhibitor, and NAC transcription factor, were present in the co-localization network, suggesting that lncRNAs were involved in regulating kiwifruit ripening. Notably, several ethylene biosynthesis- and signaling-related genes, including one 1-aminocyclopropane-1-carboxylic acid oxidase gene and three ethylene response factor genes, were found in the co-localization network of ABA vs. CK, suggesting that the promoting effect of ABA on ethylene biosynthesis and fruit softening might be embodied by increasing the expression of these lncRNAs. These results may help understand the regulatory mechanism of lncRNAs in ripening and ABA-induced fruit softening of kiwifruit.
Graphene oxide loaded with tumor-targeted peptide and anti-cancer drugs for cancer target therapy
Authors: Li Ran , Wang Yimei , Du Jie , Wang Xiangyu , Duan Ailin , Gao Ruifang , Liu Junyu , Li Bing 
Published: January 2021

AbstractIn the present work, we constructed nanoscale graphene oxide (NGO) as a drug nanocarrier to improve the process of tumor-targeted drug releases, promote cellular uptake and accumulation of chemotherapy drugs in tumor tissues, and reduce the toxic effects of chemotherapy drugs on normal cells. Hence, great stability was obtained in the biological solution. Moreover, we designed an effective nanoparticle system for the doxorubicin (DOX) delivery targeting the oral squamous cell carcinoma (OSCC) by mediating the HN-1 (TSPLNIHNGQKL) through hydrogen and π–π bonds. DOX@NGO-PEG-HN-1 showed significantly higher cellular uptakes and cytotoxicity in OSCC cells (CAL-27 and SCC-25), compared to free DOX. Moreover, HN-1 showed considerable tumor-targeting and competition inhibition phenomenon. As we expected, the nanocarrier showed pH-responsive drug release. In total, our study represented a good technique to construct OSCC-targeted delivery of nanoparticles and improve the anticancer medicines’ efficiency.
Bisphenol A, S or F mother’s dermal impregnation impairs offspring immune responses in a dose and sex-specific manner in mice
Authors: Malaisé Yann , Lencina Corinne , Cartier Christel , Olier Maïwenn , Ménard Sandrine , Guzylack-Piriou Laurence 
Published: January 2021

AbstractBisphenol (BP)A is an endocrine disruptor (ED) widely used in thermal papers. Regulatory restrictions have been established to prevent risks for human health, leading to BPA substitution by structural analogues, like BPS and BPF. We previously demonstrated that oral perinatal exposure to BPA had long-term consequences on immune responses later in life. It appears now essential to enhance our understanding on immune impact of different routes of BP exposure. In this study, we aimed at comparing the impact of mother dermal exposure to BPs on offspring immune system at adulthood. Gravid mice were dermally exposed to BPA, BPS or BPF at 5 or 50 μg/kg of body weight (BW)/day (d) from gestation day 15 to weaning of pups at post-natal day (PND)21. In offspring, BPs dermal impregnation of mothers led to adverse effects on immune response at intestinal and systemic levels that was dependent on the BP, the dose and offspring sex. These findings provide, for the first time, results on long-term consequences of dermal perinatal BPs exposure on immune responses in offspring. This work warns that it is mandatory to consider immune markers, dose exposure as well as sex in risk assessment associated with new BPA’s alternatives.
An optimised method for intact nuclei isolation from diatoms
Authors: Annunziata Rossella , Balestra Cecilia , Marotta Pina , Ruggiero Antonella , Manfellotto Francesco , Benvenuto Giovanna , Biffali Elio , Ferrante Maria Immacolata 
Published: January 2021

AbstractDue to their abundance in the oceans, their extraordinary biodiversity and the increasing use for biotech applications, the study of diatom biology is receiving more and more attention in the recent years. One of the limitations in developing molecular tools for diatoms lies in the peculiar nature of their cell wall, that is made of silica and organic molecules and that hinders the application of standard methods for cell lysis required, for example, to extract organelles. In this study we present a protocol for intact nuclei isolation from diatoms that was successfully applied to three different species: two pennates, Pseudo-nitzschia multistriata and Phaeodactylum tricornutum, and one centric diatom species, Chaetoceros diadema. Intact nuclei were extracted by treatment with acidified NH4F solution combined to low intensity sonication pulses and separated from cell debris via FAC-sorting upon incubation with SYBR Green. Microscopy observations confirmed the integrity of isolated nuclei and high sensitivity DNA electrophoresis showed that genomic DNA extracted from isolated nuclei has low degree of fragmentation. This protocol has proved to be a flexible and versatile method to obtain intact nuclei preparations from different diatom species and it has the potential to speed up applications such as epigenetic explorations as well as single cell (“single nuclei”) genomics, transcriptomics and proteomics in different diatom species.
Radiolysis generates a complex organosynthetic chemical network
Authors: Adam Zachary R. , Fahrenbach Albert C. , Jacobson Sofia M. , Kacar Betul , Zubarev Dmitry Yu. 
Published: January 2021

AbstractThe architectural features of cellular life and its ecologies at larger scales are built upon foundational networks of reactions between molecules that avoid a collapse to equilibrium. The search for life’s origins is, in some respects, a search for biotic network attributes in abiotic chemical systems. Radiation chemistry has long been employed to model prebiotic reaction networks, and here we report network-level analyses carried out on a compiled database of radiolysis reactions, acquired by the scientific community over decades of research. The resulting network shows robust connections between abundant geochemical reservoirs and the production of carboxylic acids, amino acids, and ribonucleotide precursors—the chemistry of which is predominantly dependent on radicals. Moreover, the network exhibits the following measurable attributes associated with biological systems: (1) the species connectivity histogram exhibits a heterogeneous (heavy-tailed) distribution, (2) overlapping families of closed-loop cycles, and (3) a hierarchical arrangement of chemical species with a bottom-heavy energy-size spectrum. The latter attribute is implicated with stability and entropy production in complex systems, notably in ecology where it is known as a trophic pyramid. Radiolysis is implicated as a driver of abiotic chemical organization and could provide insights about the complex and perhaps radical-dependent mechanisms associated with life’s origins.
The interaction of Ag2O nanoparticles with Escherichia coli: inhibition–sterilization process
Authors: Li Danqing , Chen Shuai , Zhang Ke , Gao Nan , Zhang Miao , Albasher Gadah , Shi Jiangfan , Wang Chuanyi 
Published: January 2021

AbstractSilver-based antibacterial agents have obtained wide attention due to the fact that bacteria in the environment is ubiquitous, which has become one of the most difficult problems for human health. However, the antibacterial mechanism and process are still inconclusive. Here, Ag2O nanoparticles (NPs) with uniform spherical morphology and small size (around 30 nm) were prepared. The as-prepared Ag2O NPs induced high antibacterial activity (100% inhibition ratio) against E. coli. A two-step antibacterial process was proposed and confirmed, which divided into inhibition and sterilization steps. The optical density measurement, malondialdehyde concentration detection, morphologic imaging with electronic microscopy and Fourier transform infrared spectroscopic analysis unveiled the interaction of Ag2O NPs with E. coli, which verified the inhibition–sterilization process we proposed.
Perinatal SSRI exposure affects brain functional activity associated with whisker stimulation in adolescent and adult rats
Authors: Van der Knaap Noortje , Wiedermann Dirk , Schubert Dirk , Hoehn Mathias , Homberg Judith R. 
Published: January 2021

AbstractSelective serotonin reuptake inhibitors (SSRI), such as fluoxetine, are used as first-line antidepressant medication during pregnancy. Since SSRIs cross the placenta the unborn child is exposed to the maternal SSRI medication, resulting in, amongst others, increased risk for autism in offspring. This likely results from developmental changes in brain function. Studies employing rats lacking the serotonin transporter have shown that elevations in serotonin levels particularly affect the development of the whisker related part of the primary somatosensory (barrel) cortex. Therefore, we hypothesized that serotonin level disturbances during development alter brain activity related to whisker stimulation. We treated female dams with fluoxetine or vehicle from gestational day 11 onwards for 21 days. We investigated offspring’s brain activity during whisker stimulation using functional magnetic resonance imaging (fMRI) at adolescence and adulthood. Our results indicate that adolescent offspring displayed increased activity in hippocampal subareas and the mammillary body in the thalamus. Adult offspring exhibited increased functional activation of areas associated with (higher) sensory processing and memory such as the hippocampus, perirhinal and entorhinal cortex, retrospinal granular cortex, piriform cortex and secondary visual cortex. Our data imply that perinatal SSRI exposure leads to complex alterations in brain networks involved in sensory perception and processing.
Complex networks of marine heatwaves reveal abrupt transitions in the global ocean
Authors: Benedetti-Cecchi Lisandro 
Published: January 2021

AbstractUnderstanding how marine heatwaves (MHWs) unfold in space and time under anthropogenic climate change is key to anticipate future impacts on ecosystems and society. Yet, our knowledge of the spatiotemporal dynamics of MHWs is very limited. Here, I combine network theory with topological data analysis and event synchronization to high-resolution satellite data and to a set of Earth System Model simulations to reveal the dynamical organization of complex MHW networks. The analysis reveals that MHWs have already crossed a tipping point separating highly synchronized preindustrial MHWs from the more extreme, but less coherent warming events we experience today. This loose spatiotemporal organization persists under a reduced RCP 2.6 emission scenario, whereas a second abrupt transition towards a permanent state of highly synchronized MHWs is foreseen by 2075 under a business-as-usual RCP 8.5 scenario. These results highlight the risks of abrupt ocean transitions, which may dramatically affect marine life and humanity by eroding valuable time for adaptation to climate change.
Efficacy of therapies and interventions for repeated embryo implantation failure: a systematic review and meta-analysis
Authors: Busnelli Andrea , Somigliana Edgardo , Cirillo Federico , Baggiani Annamaria , Levi-Setti Paolo Emanuele 
Published: January 2021

AbstractThe aim of the present systematic review and meta-analysis was to assess the effect of the different therapeutic options for repeated embryo implantation failure (RIF) on a subsequent IVF cycle outcome. Twenty-two RCTs and nineteen observational studies were included. Pooling of results showed a beneficial effect of intrauterine PBMC infusion on both CPR (RR 2.18; 95% CI 1.58–3.00; p < 0.00001; OR 2.03; 95% CI 1.22–3.36; p = 0.006) and LBR (RR 2.41; 95% CI 1.40–4.16; p = 0.002; OR 3.73; 95% CI 1.13–12.29; p = 0.03), of subcutaneous G-CSF administration on CPR (RR 2.29; 95% CI 1.58–3.31; p < 0.0001) and of intrauterine PRP infusion on CPR (RR 2.45; 95% CI 1.55–3.86; p = 0.0001). Observational studies also demonstrated a positive effect of IVIG and intrauterine hCG infusion on both CPR and LBR and of atosiban on CPR. Studies investigating intrauterine G-CSF infusion, LMWH, intravenous intralipid, hysteroscopy, blastocyst-stage ET, ZIFT, PGT-A and AH failed to observe an impact on IVF outcome. The quality of the evidence that emerged from RCTs focused on intrauterine PBMC infusion and subcutaneous G-CSF administration was moderate. For all other therapies/interventions it varied from low to very low. In conclusion, intrauterine PBMC infusion and subcutaneous G-CSF administration are the most promising therapeutic options for RIF. However, further well conducted RCTs are necessary before their introduction into clinical practice.
Simulated atmospheric nitrogen deposition inhibited the leaf litter decomposition of Cinnamomum migao H. W. Li in Southwest China
Authors: Huang Xiao-Long , Chen Jing-Zhong , Wang Deng , Deng Ming-Ming , Wu Meng-Yao , Tong Bing-Li , Liu Ji-Ming 
Published: January 2021

AbstractAtmospheric nitrogen (N) deposition could affect various ecological processes in forest ecosystems, including plant litter decomposition and nutrient cycling. However, the mechanism of underlying litter decomposition and nutrient cycling of Cinnamomum migao under N deposition remains unclear. Therefore, we conducted a simulated N deposition experiment including four onsite treatments to assess the effects of N input on C. migao leaf litter decomposition, nutrient release, and soil enzyme activity. The results showed that simulated N deposition significantly increased the amount of total residual mass and lignin and cellulose, decreased the decomposition rate, and suppressed net nutrient release. N input increased C, N, and P ratios as decomposition progressed, and the proportion of mass remaining was positively correlated with the proportions of lignin and cellulose remaining at the later stage of decomposition. The differences in soil enzyme activity were primarily due to enzyme type and sampling time. We conclude that simulated N deposition significantly suppressed the leaf litter decomposition of C. migao by mainly altering the chemical properties and suppressing the decomposition of the organic matter in leaf litter. Lignin might have played an important role in the loss of leaf litter biomass at the later stage of decomposition.
Understanding adherence to reactive treatment of asymptomatic malaria infections in The Gambia
Authors: Jaiteh Fatou , Okebe Joseph , Masunaga Yoriko , D’Alessandro Umberto , Achan Jane , Gryseels Charlotte , de Vries Daniel , Ribera Joan Muela , Grietens Koen Peeters 
Published: January 2021

AbstractThe impact of different types of reactive case detection and/or treatment strategies for malaria elimination depends on high coverage and participants’ adherence. However, strategies to optimise adherence are limited, particularly for people with asymptomatic or no infections. As part of a cluster-randomized trial to evaluate the effect of reactive treatment in The Gambia, all residents in the compound of a diagnosed clinical malaria patient received dihydro-artemisinin–piperaquine (DP). Using a mixed method approach, we assessed which factors contribute to adherence among the contacts of malaria cases that showed no symptoms. Adherence was defined as the proportion of compound members that (1) returned all medicine bags empty and (2) self-reported (3-day) treatment completion. Among the 273 individuals from 14 compounds who received DP, 227 (83.1%) were available for and willing to participate in the survey; 85.3% (233/273) returned empty medicine bags and 91.6% (208/227) self-reported treatment completion. Although clinical malaria was not considered a major health problem, reported adherence was high. The drivers of adherence were the strong sense of responsibility towards protecting the individual, compound and the village. Adherence can be optimised through a transdisciplinary implementation research process of engaging communities to bridge the gap between research goals and social realities.