bluuebunny/crossref_metadata_2025_split huggingface dataset:
Response of bacterial and fungal communities to high petroleum pollution in different soils
Authors: Galitskaya Polina , Biktasheva Liliya , Blagodatsky Sergey , Selivanovskaya Svetlana 
Published: January 2021

AbstractPetroleum pollution of soils is a major environmental problem. Soil microorganisms can decompose a significant fraction of petroleum hydrocarbons in soil at low concentrations (1–5%). This characteristic can be used for soil remediation after oil pollution. Microbial community dynamics and functions are well studied in cases of moderate petroleum pollution, while cases with heavy soil pollution have received much less attention. We studied bacterial and fungal successions in three different soils with high petroleum contents (6 and 25%) in a laboratory experiment. The proportion of aliphatic and aromatic compounds decreased by 4–7% in samples with 6% pollution after 120 days of incubation but remained unchanged in samples with 25% hydrocarbons. The composition of the microbial community changed significantly in all cases. Oil pollution led to an increase in the relative abundance of bacteria such as Actinobacteria and the candidate TM7 phylum (Saccaribacteria) and to a decrease in that of Bacteroidetes. The gene abundance (number of OTUs) of oil-degrading bacteria (Rhodococcus sp., candidate class TM7-3 representative) became dominant in all soil samples, irrespective of the petroleum pollution level and soil type. The fungal communities in unpolluted soil samples differed more significantly than the bacterial communities. Nonmetric multidimensional scaling revealed that in the polluted soil, successions of fungal communities differed between soils, in contrast to bacterial communities. However, these successions showed similar trends: fungi capable of lignin and cellulose decomposition, e.g., from the genera Fusarium and Mortierella, were dominant during the incubation period.
Potential use of molecular and structural characterization of the gut bacterial community for postmortem interval estimation in Sprague Dawley rats
Authors: Li Huan , Zhang Siruo , Liu Ruina , Yuan Lu , Wu Di , Yang E. , Yang Han , Ullah Shakir , Ishaq Hafiz Muhammad , Liu Hailong , Wang Zhenyuan , Xu Jiru 
Published: January 2021

AbstractOnce the body dies, the indigenous microbes of the host begin to break down the body from the inside and play a key role thereafter. This study aimed to investigate the probable shift in the composition of the rectal microbiota at different time intervals up to 15 days after death and to explore bacterial taxa important for estimating the time since death. At the phylum level, Proteobacteria and Firmicutes showed major shifts when checked at 11 different intervals and emerged at most of the postmortem intervals. At the species level, Enterococcus faecalis and Proteus mirabilis showed a downward and upward trend, respectively, after day 5 postmortem. The phylum-, family-, genus-, and species-taxon richness decreased initially and then increased considerably. The turning point occurred on day 9, when the genus, rather than the phylum, family, or species, provided the most information for estimating the time since death. We constructed a prediction model using genus-level data from high-throughput sequencing, and seven bacterial taxa, namely, Enterococcus, Proteus, Lactobacillus, unidentified Clostridiales, Vagococcus, unidentified Corynebacteriaceae, and unidentified Enterobacteriaceae, were included in this model. The abovementioned bacteria showed potential for estimating the shortest time since death.
Highly efficient self-powered perovskite photodiode with an electron-blocking hole-transport NiOx layer
Authors: Afzal Amir Muhammad , Bae In-Gon , Aggarwal Yushika , Park Jaewoo , Jeong Hye-Ryeon , Choi Eun Ha , Park Byoungchoo 
Published: January 2021

AbstractHybrid organic–inorganic perovskite materials provide noteworthy compact systems that could offer ground-breaking architectures for dynamic operations and advanced engineering in high-performance energy-harvesting optoelectronic devices. Here, we demonstrate a highly effective self-powered perovskite-based photodiode with an electron-blocking hole-transport layer (NiOx). A high value of responsivity (R = 360 mA W−1) with good detectivity (D = 2.1 × 1011 Jones) and external quantum efficiency (EQE = 76.5%) is achieved due to the excellent interface quality and suppression of the dark current at zero bias voltage owing to the NiOx layer, providing outcomes one order of magnitude higher than values currently in the literature. Meanwhile, the value of R is progressively increased to 428 mA W−1 with D = 3.6 × 1011 Jones and EQE = 77% at a bias voltage of − 1.0 V. With a diode model, we also attained a high value of the built-in potential with the NiOx layer, which is a direct signature of the improvement of the charge-selecting characteristics of the NiOx layer. We also observed fast rise and decay times of approximately 0.9 and 1.8 ms, respectively, at zero bias voltage. Hence, these astonishing results based on the perovskite active layer together with the charge-selective NiOx layer provide a platform on which to realise high-performance self-powered photodiode as well as energy-harvesting devices in the field of optoelectronics.
Particulate matter emission sources and meteorological parameters combine to shape the airborne bacteria communities in the Ligurian coast, Italy
Authors: Palladino Giorgia , Morozzi Pietro , Biagi Elena , Brattich Erika , Turroni Silvia , Rampelli Simone , Tositti Laura , Candela Marco 
Published: January 2021

AbstractAim of the present study is to explore how the chemical composition of particulate matter (PM) and meteorological conditions combine in shaping the air microbiome in Savona (Italy), a medium-size, heavily inhabited urban settlement, hosting a wide range of industrial activities. In particular, the air microbiome and PM10 were monitored over six months in 2012. During that time, the air microbiome was highly dynamic, fluctuating between different compositional states, likely resulting from the aerosolization of different microbiomes emission sources. According to our findings, this dynamic process depends on the combination of local meteorological parameters and particle emission sources, which may affect the prevalent aerosolized microbiomes, thus representing further fundamental tools for source apportionment in a holistic approach encompassing chemical as well as microbiological pollution. In particular, we showed that, in the investigated area, industrial emissions and winds blowing from the inlands combine with an airborne microbiome which include faecal microbiomes components, suggesting multiple citizens’ exposure to both chemicals and microorganisms of faecal origin, as related to landscape exploitation and population density. In conclusion, our findings support the need to include monitoring of the air microbiome compositional structure as a relevant factor for the final assessment of local air quality.
LAMP-based foldable microdevice platform for the rapid detection of Magnaporthe oryzae and Sarocladium oryzae in rice seed
Authors: Prasannakumar M. K. , Parivallal P. Buela , Pramesh Devanna , Mahesh H. B. , Raj Edwin 
Published: January 2021

AbstractRice blast (caused by Magnaporthe oryzae) and sheath rot diseases (caused by Sarocladium oryzae) are the most predominant seed-borne pathogens of rice. The detection of both pathogens in rice seed is essential to avoid production losses. In the present study, a microdevice platform was designed, which works on the principles of loop-mediated isothermal amplification (LAMP) to detect M. oryzae and S. oryzae in rice seeds. Initially, a LAMP, polymerase chain reaction (PCR), quantitative PCR (qPCR), and helicase dependent amplification (HDA) assays were developed with primers, specifically targeting M. oryzae and S. oryzae genome. The LAMP assay was highly efficient and could detect the presence of M. oryzae and S. oryzae genome at a concentration down to 100 fg within 20 min at 60 °C. Further, the sensitivity of the LAMP, HDA, PCR, and qPCR assays were compared wherein; the LAMP assay was highly sensitive up to 100 fg of template DNA. Using the optimized LAMP assay conditions, a portable foldable microdevice platform was developed to detect M. oryzae and S. oryzae in rice seeds. The foldable microdevice assay was similar to that of conventional LAMP assay with respect to its sensitivity (up to 100 fg), rapidity (30 min), and specificity. This platform could serve as a prototype for developing on-field diagnostic kits to be used at the point of care centers for the rapid diagnosis of M. oryzae and S. oryzae in rice seeds. This is the first study to report a LAMP-based foldable microdevice platform to detect any plant pathogens.
Chlamydia trachomatis intra-bacterial and total plasmid copy number in clinical urogenital samples
Authors: Dirks J. A. M. C. , Janssen K. , Hoebe C. J. P. A. , Geelen T. H. B. , Lucchesi M. , Dukers-Muijrers N. H. T. M. , Wolffs P. F. G. 
Published: January 2021

AbstractChlamydia trachomatis (CT) increases its plasmid numbers when stressed, as occurs in clinical trachoma samples. Most CT tests target the plasmid to increase the test sensitivity, but some only target the chromosome. We investigated clinical urogenital samples for total plasmid copy numbers to assess its diagnostic value and intra-bacterial plasmid copy numbers to assess its natural variation. Both plasmid and chromosome copies were quantified using qPCR, and the plasmid:chromosome ratio (PCr) calculated in two cohorts: (1) 383 urogenital samples for the total PCR (tPCr), and (2) 42 vaginal swabs, with one half treated with propium-monoazide (PMA) to prevent the quantification of extracellular DNA and the other half untreated to allow for both tPCr and intra-bacterial PCr (iPCr) quantification. Mann–Whitney U tests compared PCr between samples, in relation to age and gender. Cohort 1: tPCr varied greatly (1–677, median 16). Median tPCr was significantly higher in urines than vaginal swabs (32 vs. 11, p < 0.001). Cohort 2: iPCr was more stable than tPCr (range 0.1–3 vs. 1–11). To conclude, tPCr in urogenital samples was much more variable than previously described. Transport time and temperature influences DNA degradation, impacting chromosomal DNA more than plasmids and urine more than vaginal samples. Data supports a plasmid target in CT screening assays to increase clinical sensitivity.
An experimental validation of partial discharge localization using electromagnetic time reversal
Authors: Karami Hamidreza , Azadifar Mohammad , Rubinstein Marcos , Rachidi Farhad 
Published: January 2021

AbstractThe localization of partial discharge (PD) sources is of importance for the monitoring and maintenance of power transformers. Time difference of arrival (TDoA) based methods are widely adopted in the literature for the localization of PDs. Recently, time reversal (TR) was suggested as an efficient means to locate PD sources. As opposed to TDoA, which needs at least 4 sensors, TR is able to locate PD sources in power transformers with only one sensor. Moreover, it needs neither line-of-sight wave propagation from the PD sources to the sensor nor time synchronization. In this study, we present for the first time an experimental demonstration of the ability of the TR process to locate PD sources. A typical TR process includes three steps: (1) recording the PD-emitted field by a sensor, (2) time reversing and back injecting the signal into the medium, (3) using a proper criterion to obtain the focusing point which corresponds to the location of the PD source. In this work, we present a laboratory setup in which steps one and two are performed experimentally, both in the frequency and in the time domain. The obtained peak electric field value is used as a criterion in the third step. It is found that the accuracy of the proposed method is better than 2.5 cm in a transformer tank model with dimensions 73 × 73 × 103 cm3. The effects of the presence of scatterers such as transformer windings are also investigated experimentally and found not to affect the location accuracy of the method.
Identification of a novel QTL and candidate gene associated with grain size using chromosome segment substitution lines in rice
Authors: Wang Dianwen , Sun Wenqiang , Yuan Zhiyang , Sun Qiang , Fan Kai , Zhang Chaopu , Yu Sibin 
Published: January 2021

AbstractRice is one of the staple crops in the world. Grain size is an important determinant of rice grain yield, but the genetic basis of the grain size remains unclear. Here, we report a set of chromosome segment substitution lines (CSSL) developed in the genetic background of the genome-sequenced indica cultivar Zhenshan 97. Genotyping of the CSSLs by single nucleotide polymorphism array shows that most carry only one or two segments introduced from the genome-sequenced japonica cultivar Nipponbare. Using this population and the high-density markers, a total of 43 quantitative trait loci were identified for seven panicle- and grain-related traits. Among these loci, the novel locus qGL11 for grain length and thousand-grain weight was validated in a CSSL-derived segregating population and finely mapped to a 25-kb region that contains an IAA-amido synthetase gene OsGH3.13, This gene exhibited a significant expression difference in the young panicle between the near-isogenic lines that carry the contrasting Zhenshan 97 and Nipponbare alleles at qGL11. Expression and sequence analyses suggest that this gene is the most likely candidate for qGL11. Furthermore, several OsGH3.13 mutants induced by a CRISPR/Cas9 approach in either japonica or indica exhibit an increased grain length and thousand-grain weight, thus enhancing the final grain yield per plant. These findings provide insights into the genetic basis of grain size for the improvement of yield potential in rice breeding programs.
Platelet CXCL4 mediates neutrophil extracellular traps formation in ANCA-associated vasculitis
Authors: Matsumoto Kotaro , Yasuoka Hidekata , Yoshimoto Keiko , Suzuki Katsuya , Takeuchi Tsutomu 
Published: January 2021

AbstractNeutrophils form neutrophil extracellular traps (NETs), which are involved in the pathogenesis of ANCA-associated vasculitis (AAV). Recent reports suggest that platelets stimulated via toll-like receptor (TLR) pathways can induce NETs formation. However, the mechanism underlying the involvement of platelets in NETs formation in AAV is unknown. We investigated the role of platelets in the pathogenesis of AAV. Platelets from AAV patients and healthy controls (HCs) were co-cultured with peripheral neutrophils, and NETs formation was visualized and quantified. The expression levels of TLRs on platelets were examined by flow cytometry. Platelets were treated with a TLR agonist, platelet-derived humoral factor, CXCL4 (platelet factor 4: PF4), and/or anti-CXCL4 antibody to investigate the effects of TLR–CXCL4 signaling on NETs formation. Platelets from AAV significantly upregulated NETs formation in vitro. Flow cytometric analysis revealed that the proportion of TLR9 positive platelets was significantly higher in AAV than HCs. CXCL4 released from TLR9 agonist-stimulated platelets was significantly enhanced in AAV, which subsequently increased NETs formation. Further, neutralizing anti-CXCL4 antibody significantly inhibited NETs formation enhanced by platelets from AAV. TLR9 signaling and CXCL4 release underlie the key role that platelets play in NETs formation in the pathogenesis of AAV.
Elevated temperatures diminish the effects of a highly resistant rice variety on the brown planthopper
Authors: Horgan Finbarr G. , Arida Arriza , Ardestani Goli , Almazan Maria Liberty P. 
Published: January 2021

AbstractThis study compares the effects of temperature (constant at 15, 20, 25, 30 and 35 °C) on adult longevity, oviposition, and nymph development of the brown planthopper, Nilaparvata lugens, on susceptible and resistant rice varieties. The resistant variety contained the BPH32 gene. In our experiments, nymphs failed to develop to adults at 15, 20 and 35 °C on either variety. Host resistance had its greatest effect in reducing adult survival at 20–25 °C and its greatest effect in reducing nymph weight gain at 25 °C. This corresponded with optimal temperatures for adult survival (20–25 °C) and nymph development (25–30 °C). At 25 and 30 °C, adult females achieved up to three oviposition cycles on the susceptible variety, but only one cycle on the resistant variety. Maximum egg-laying occurred at 30 °C due to larger numbers of egg batches produced during the first oviposition cycle on both the susceptible and resistant varieties, and larger batches during the second and third oviposition cycles on the susceptible variety; however, resistance had its greatest effect in reducing fecundity at 25 °C. This revealed a mismatch between the optimal temperatures for resistance and for egg production in immigrating females. Increasing global temperatures could reduce the effectiveness of anti-herbivore resistance in rice and other crops where such mismatches occur.
Discrimination of standing postures between young and elderly people based on center of pressure
Authors: Fujio Kimiya , Takeuchi Yahiko 
Published: January 2021

AbstractPosturography is utilized to assess the influence of aging on postural control. Although this measurement is advantageous for finding group-level differences between the young and the elderly, it is unclear whether it has the potential to differentiate elderly individuals who are affected by various impacts of aging. The purpose of this study was to determine the utility of posturography to discriminate elderly individuals from young adults. We investigated the performances of the random forest classifiers constructed from center of pressure (COP) indices for discriminating standing postures between healthy elderly and young people. Postural sways in 19 young and 31 community-dwelling elderly participants were measured using force plates in 4 standing conditions: bipedal standing, standing on a narrow base, standing on foam rubber, and standing with eyes closed. We further verified the informative predictors that contributed to the prediction model. As the results, the classifier based on the COP indices for standing on foam rubber showed the best performance (accuracy: 93.4%, sensitivity: 94.4%, specificity: 93.6%, area under the curve of receiving operator characteristics: 0.95), followed by the classifier for standing with eyes closed. The informative predictors varied depending on the postural conditions. Our findings demonstrated the potential of posturography for identifying elderly postures. The evaluation of sensory re-weighting using the appropriate COP indices would be a useful clinical tool for detecting the progress of aging on postural control.
A study on the bio-applicability of aqueous-dispersed van der Waals 1-D material Nb2Se9 using poloxamer
Authors: Chae Sudong , Oh Seungbae , Choi Kyung Hwan , Lee Jin Woong , Jeon Jiho , Liu Zhixiang , Wang Cong , Lim Changmo , Dong Xue , Woo Chaeheon , Asghar Ghulam , Shi Liyi , Kang Joohoon , Kim Sung Jae , Song Si Young , Lee Jung Heon , Yu Hak Ki , Choi Jae-Young 
Published: January 2021

AbstractIn this research, dispersion of a new type of one-dimensional inorganic material Nb2Se9, composed of van der Waals bonds, in aqueous solution for bio-application study were studied. To disperse Nb2Se9, which exhibits hydrophobic properties in water, experiments were carried out using a block copolymer (poloxamer) as a dispersant. It was confirmed that PPO, the hydrophobic portion of Poloxamer, was adsorbed onto the surface of Nb2Se9, and PEO, the hydrophilic portion, induced steric hinderance to disperse Nb2Se9 to a size of 10 nm or less. To confirm the adaptability of muscle cells C2C12 to the dispersed Nb2Se9 using poloxamer 188 as dispersant, a MTT assay and a live/dead assay were performed, demonstrating improvement in the viability and proliferation of C2C12 cells.
Elastic flow instabilities and macroscopic textures in graphene oxide lyotropic liquid crystals
Authors: Wychowaniec Jacek K. , Iliut Maria , Borek Bartłomiej , Muryn Christopher , Mykhaylyk Oleksandr O. , Edmondson Steve , Vijayaraghavan Aravind 
Published: January 2021

AbstractGraphene oxide (GO) forms a well-aligned lyotropic liquid crystal (LC) phase in aqueous dispersions at relatively low concentrations. Under a remarkably wide range of shear rates, we report hitherto unobserved shear-induced polarized light image patterns, a Maltese cross combined with shear banding, recorded in real time and in situ during rheological measurements. This is shown to be a result of elastic flow instabilities that manifest as a helical flow in alternating bands of left- and right-handed helices, arising from a combination of shear flow and Taylor-type vortex flow. The instability is observed for LCs formed from large aspect ratio GO particles owing to their unique viscoelastic properties, but not for smaller aspect ratio particles. This phenomenon coincides with rheopecty and anomalous small-angle X-ray scattering patterns under shear flow, which confirm the instabilities. The results presented here could lead to advanced control over macroscopic periodic alignment in technologically relevant dispersions of two-dimensional material particles.
Deep learning-enabled medical computer vision
Authors: Esteva Andre , Chou Katherine , Yeung Serena , Naik Nikhil , Madani Ali , Mottaghi Ali , Liu Yun , Topol Eric , Dean Jeff , Socher Richard 
Published: January 2021

AbstractA decade of unprecedented progress in artificial intelligence (AI) has demonstrated the potential for many fields—including medicine—to benefit from the insights that AI techniques can extract from data. Here we survey recent progress in the development of modern computer vision techniques—powered by deep learning—for medical applications, focusing on medical imaging, medical video, and clinical deployment. We start by briefly summarizing a decade of progress in convolutional neural networks, including the vision tasks they enable, in the context of healthcare. Next, we discuss several example medical imaging applications that stand to benefit—including cardiology, pathology, dermatology, ophthalmology–and propose new avenues for continued work. We then expand into general medical video, highlighting ways in which clinical workflows can integrate computer vision to enhance care. Finally, we discuss the challenges and hurdles required for real-world clinical deployment of these technologies.