bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reversal of freshening trend of Antarctic Bottom Water in the Australian-Antarctic Basin during 2010s
Authors: Aoki S. , Yamazaki K. , Hirano D. , Katsumata K. , Shimada K. , Kitade Y. , Sasaki H. , Murase H. 
Published: September 2020

AbstractThe Antarctic continental margin supplies the densest bottom water to the global abyss. From the late twentieth century, an acceleration in the long-term freshening of Antarctic Bottom Waters (AABW) has been detected in the Australian-Antarctic Basin. Our latest hydrographic observations reveal that, in the late 2010s, the freshening trend has reversed broadly over the continental slope. Near-bottom salinities in 2018–2019 were higher than during 2011–2015. Along 170° E, the salinity increase between 2011 and 2018 was greater than that observed in the west. The layer thickness of the densest AABW increased during the 2010s, suggesting that the Ross Sea Bottom Water intensification was a major source of the salinity increase. Freshwater content on the continental slope decreased at a rate of 58 ± 37 Gt/a in the near-bottom layer. The decadal change is very likely due to changes in Ross Sea shelf water attributable to a decrease in meltwater from West Antarctic ice shelves for the corresponding period.
Automatic detection of non-perfusion areas in diabetic macular edema from fundus fluorescein angiography for decision making using deep learning
Authors: Jin Kai , Pan Xiangji , You Kun , Wu Jian , Liu Zhifang , Cao Jing , Lou Lixia , Xu Yufeng , Su Zhaoan , Yao Ke , Ye Juan 
Published: September 2020

AbstractVision loss caused by diabetic macular edema (DME) can be prevented by early detection and laser photocoagulation. As there is no comprehensive detection technique to recognize NPA, we proposed an automatic detection method of NPA on fundus fluorescein angiography (FFA) in DME. The study included 3,014 FFA images of 221 patients with DME. We use 3 convolutional neural networks (CNNs), including DenseNet, ResNet50, and VGG16, to identify non-perfusion regions (NP), microaneurysms, and leakages in FFA images. The NPA was segmented using attention U-net. To validate its performance, we applied our detection algorithm on 249 FFA images in which the NPA areas were manually delineated by 3 ophthalmologists. For DR lesion classification, area under the curve is 0.8855 for NP regions, 0.9782 for microaneurysms, and 0.9765 for leakage classifier. The average precision of NP region overlap ratio is 0.643. NP regions of DME in FFA images are identified based a new automated deep learning algorithm. This study is an in-depth study from computer-aided diagnosis to treatment, and will be the theoretical basis for the application of intelligent guided laser.
Using behavioral rhythms and multi-task learning to predict fine-grained symptoms of schizophrenia
Authors: Tseng Vincent W.-S. , Sano Akane , Ben-Zeev Dror , Brian Rachel , Campbell Andrew T. , Hauser Marta , Kane John M. , Scherer Emily A. , Wang Rui , Wang Weichen , Wen Hongyi , Choudhury Tanzeem 
Published: September 2020

AbstractSchizophrenia is a severe and complex psychiatric disorder with heterogeneous and dynamic multi-dimensional symptoms. Behavioral rhythms, such as sleep rhythm, are usually disrupted in people with schizophrenia. As such, behavioral rhythm sensing with smartphones and machine learning can help better understand and predict their symptoms. Our goal is to predict fine-grained symptom changes with interpretable models. We computed rhythm-based features from 61 participants with 6,132 days of data and used multi-task learning to predict their ecological momentary assessment scores for 10 different symptom items. By taking into account both the similarities and differences between different participants and symptoms, our multi-task learning models perform statistically significantly better than the models trained with single-task learning for predicting patients’ individual symptom trajectories, such as feeling depressed, social, and calm and hearing voices. We also found different subtypes for each of the symptoms by applying unsupervised clustering to the feature weights in the models. Taken together, compared to the features used in the previous studies, our rhythm features not only improved models’ prediction accuracy but also provided better interpretability for how patients’ behavioral rhythms and the rhythms of their environments influence their symptom conditions. This will enable both the patients and clinicians to monitor how these factors affect a patient’s condition and how to mitigate the influence of these factors. As such, we envision that our solution allows early detection and early intervention before a patient’s condition starts deteriorating without requiring extra effort from patients and clinicians.
Genomic profiling of bacterial and fungal communities and their predictive functionality during pulque fermentation by whole-genome shotgun sequencing
Authors: Chacón-Vargas Katherine , Torres Julian , Giles-Gómez Martha , Escalante Adelfo , Gibbons John G. 
Published: September 2020

AbstractPulque is a culturally important 4,000-year-old traditional Mexican fermented drink. Pulque is produced by adding fresh aguamiel (agave sap) to mature pulque, resulting in a mixture of microbial communities and chemical compositions. We performed shotgun metagenomic sequencing of five stages of pulque fermentation to characterize organismal and functional diversity. We identified 6 genera (Acinetobacter, Lactobacillus, Lactococcus, Leuconostoc, Saccharomyces and Zymomonas) and 10 species (Acinetobacter boissieri, Acinetobacter nectaris, Lactobacillus sanfranciscensis, Lactococcus lactis, Lactococcus piscium, Lactococcus plantarum, Leuconostoc citreum, Leuconostoc gelidum, Zymomonas mobilis and Saccharomyces cerevisiae) that were present ≥ 1% in at least one stage of pulque fermentation. The abundance of genera and species changed during fermentation and was associated with a decrease in sucrose and increases in ethanol and lactic acid, suggesting that resource competition shapes organismal diversity. We also predicted functional profiles, based on organismal gene content, for each fermentation stage and identified an abundance of genes associated with the biosynthesis of folate, an essential B-vitamin. Additionally, we investigated the evolutionary relationships of S. cerevisiae and Z. mobilis, two of the major microbial species found in pulque. For S. cerevisiae, we used a metagenomics assembly approach to identify S. cerevisiae scaffolds from pulque, and performed phylogenetic analysis of these sequences along with a collection of 158 S. cerevisiae strains. This analysis suggests that S. cerevisiae from pulque is most closely related to Asian strains isolated from sake and bioethanol. Lastly, we isolated and sequenced the whole-genomes of three strains of Z. mobilis from pulque and compared their relationship to seven previously sequenced isolates. Our results suggest pulque strains may represent a distinct lineage of Z. mobilis.
Satellite DNA-like repeats are dispersed throughout the genome of the Pacific oyster Crassostrea gigas carried by Helentron non-autonomous mobile elements
Authors: Vojvoda Zeljko Tanja , Pavlek Martina , Meštrović Nevenka , Plohl Miroslav 
Published: September 2020

AbstractSatellite DNAs (satDNAs) are long arrays of tandem repeats typically located in heterochromatin and span the centromeres of eukaryotic chromosomes. Despite the wealth of knowledge about satDNAs, little is known about a fraction of short, satDNA-like arrays dispersed throughout the genome. Our survey of the Pacific oysterCrassostrea gigassequenced genome revealed genome assembly replete with satDNA-like tandem repeats. We focused on the most abundant arrays, grouped according to sequence similarity into 13 clusters, and explored their flanking sequences. Structural analysis showed that arrays of all 13 clusters represent central repeats of 11 non-autonomous elements namedCg_HINE,which are classified into theHelentronsuperfamily of DNA transposons. Each of the described elements is formed by a unique combination of flanking sequences and satDNA-like central repeats, coming from one, exceptionally two clusters in a consecutive order. While some of the detectedCg_HINEelements are related according to sequence similarities in flanking and repetitive modules, others evidently arose in independent events. In addition, some of theCg_HINE’s central repeats are related to the classicalC. gigassatDNA, interconnecting mobile elements and satDNAs. Genome-wide distribution ofCg_HINEimplies non-autonomousHelentronsas a dynamic system prone to efficiently propagate tandem repeats in theC. gigasgenome.
Local management and landscape structure determine the assemblage patterns of spiders in vegetable fields
Authors: Saqib Hafiz Sohaib Ahmed , Chen Junhui , Chen Wei , Pozsgai Gabor , Akutse Komivi Senyo , Ashraf Muhammad Furqan , You Minsheng , Gurr Geoff M. 
Published: September 2020

AbstractBoth field- and landscape-scale factors can influence the predator communities of agricultural pests, but the relative importance and interactions between these scales are poorly understood. Focusing on spiders, an important taxon for providing biological control, we tested the influence of field- and landscape-scale factors on structuring the spider communities in a highly dynamic brassica agroecosystem. We found that local factors (pesticide-use and crop type) and forested landscape significantly influenced the abundance and species richness of spiders, whilst grassland patches significantly affected the spider species richness. Correlation results demonstrated that assemblage patterns of most spider families positively responded to the interplay between local factors and forest patches in the landscape. The spiders abundance was greatest in cauliflower crops surrounded with forest and grassland patches in landscape. Similarly, ordination analyses revealed that organic fields of cauliflower in forested landscapes had a strong positive association with the abundance and species richness of spiders. In contrast, insecticide and synthetic fertilizer-treated fields of Chinese cabbage in landscapes with little non-crop habitat reduced the abundance and species richness of spiders. Our results highlight the extent of interaction between local- and landscape-scale factors, help explain recently reported inconsistent effects of landscape factors on conservation biological control.
Modulation of contractions in the small intestine indicate desynchronization via supercritical Andronov–Hopf bifurcation
Authors: Parsons Sean P. , Huizinga Jan D. 
Published: September 2020

AbstractThe small intestine is covered by a network of coupled oscillators, the interstitial cells of Cajal (ICC). These oscillators synchronize to generate rhythmic phase waves of contraction. At points of low coupling, oscillations desynchronise, frequency steps occur and every few waves terminates as a dislocation. The amplitude of contractions is modulated at frequency steps. The phase difference between contractions at a frequency step and a proximal reference point increased slowly at first and then, just at the dislocation, increased rapidly. Simultaneous frequency and amplitude modulation (AM/FM) results in a Fourier frequency spectrum with a lower sideband, a so called Lashinsky spectrum, and this was also seen in the small intestine. A model of the small intestine consisting of a chain of coupled Van der Pol oscillators, also demonstrated simultaneous AM/FM at frequency steps along with a Lashinsky spectrum. Simultaneous AM/FM, together with a Lashinsky spectrum, are predicted to occur when periodically-forced or mutually-coupled oscillators desynchronise via a supercritical Andronov–Hopf bifurcation and have been observed before in other physical systems of forced or coupled oscillators in plasma physics and electrical engineering. Thus motility patterns in the intestine can be understood from the viewpoint of very general dynamical principles.
Influence of host genetics in shaping the rumen bacterial community in beef cattle
Authors: Abbas Waseem , Howard Jeremy T. , Paz Henry A. , Hales Kristin E. , Wells James E. , Kuehn Larry A. , Erickson Galen E. , Spangler Matthew L. , Fernando Samodha C. 
Published: September 2020

AbstractIn light of recent host-microbial association studies, a consensus is evolving that species composition of the gastrointestinal microbiota is a polygenic trait governed by interactions between host genetic factors and the environment. Here, we investigated the effect of host genetic factors in shaping the bacterial species composition in the rumen by performing a genome-wide association study. Using a common set of 61,974 single-nucleotide polymorphisms found in cattle genomes (n = 586) and corresponding rumen bacterial community composition, we identified operational taxonomic units (OTUs), Families and Phyla with high heritability. The top associations (1-Mb windows) were located on 7 chromosomes. These regions were associated with the rumen microbiota in multiple ways; some (chromosome 19; position 3.0–4.0 Mb) are associated with closely related taxa (Prevotellaceae, Paraprevotellaceae, and RF16), some (chromosome 27; position 3.0–4.0 Mb) are associated with distantly related taxa (Prevotellaceae, Fibrobacteraceae, RF16, RFP12, S24-7, Lentisphaerae, and Tenericutes) and others (chromosome 23; position 0.0–1.0) associated with both related and unrelated taxa. The annotated genes associated with identified genomic regions suggest the associations observed are directed toward selective absorption of volatile fatty acids from the rumen to increase energy availability to the host. This study demonstrates that host genetics affects rumen bacterial community composition.
Structure-based inhibitors targeting the alpha-helical domain of the Spiroplasma melliferum histone-like HU protein
Authors: Agapova Yuliya K. , Altukhov Dmitry A. , Timofeev Vladimir I. , Stroylov Victor S. , Mityanov Vitaly S. , Korzhenevskiy Dmitry A. , Vlaskina Anna V. , Smirnova Eugenia V. , Bocharov Eduard V. , Rakitina Tatiana V. 
Published: September 2020

AbstractHere we report bisphenol derivatives of fluorene (BDFs) as a new type of chemical probes targeting a histone-like HU protein, a global regulator of bacterial nucleoids, via its dimerization interface perturbation. BDFs were identified by virtual screening and molecular docking that targeted the core of DNA-binding β-saddle-like domain of the HU protein from Spiroplasma melliferum. However, NMR spectroscopy, complemented with molecular dynamics and site-directed mutagenesis, indicated that the actual site of the inhibitors’ intervention consists of residues from the α-helical domain of one monomer and the side portion of the DNA-binding domain of another monomer. BDFs inhibited DNA-binding properties of HU proteins from mycoplasmas S. melliferum, Mycoplasma gallicepticum and Escherichia coli with half-maximum inhibitory concentrations in the range between 5 and 10 µM. In addition, BDFs demonstrated antimicrobial activity against mycoplasma species, but not against E. coli, which is consistent with the compensatory role of other nucleoid-associated proteins in the higher bacteria. Further evaluation of antimicrobial effects of BDFs against various bacteria and viruses will reveal their pharmacological potential, and the allosteric inhibition mode reported here, which avoids direct competition for the binding site with DNA, should be considered in the development of small molecule inhibitors of nucleoid-associated proteins as well as other types of DNA-binding multimeric proteins.
Monitoring of heat-induced carcinogenic compounds (3-monochloropropane-1,2-diol esters and glycidyl esters) in fries
Authors: Wong Yu Hua , Goh Kok Ming , Nyam Kar Lin , Cheong Ling Zhi , Wang Yong , Nehdi Imededdine Arbi , Mansour Lamjed , Tan Chin Ping 
Published: September 2020

Abstract3-Monochloropropane-1,2-diol (3-MCPD) esters and glycidyl esters (GE) are heat-induced contaminants which form during oil refining process, particularly at the high temperature deodorization stage. It is worth to investigate the content of 3-MCPD and GE in fries which also involved high temperature. The content of 3-MCPD esters and GE were monitored in fries. The factors that been chosen were temperature and duration of frying, and different concentration of salt (NaCl). The results in our study showed that the effect was in the order of concentration of sodium chloride < frying duration < frying temperature. The content of 3-MCPD esters was significantly increased whereas GE was significantly decreased, when prolong the frying duration. A high temperature results in a high 3-MCPD ester level but a low GE level in fries. The present of salt had contributed significant influence to the generation of 3-MCPD. The soaking of potato chips in salt showed no significant effect on the level of GE during the frying. The oil oxidation tests showed that all the fries were below the safety limit. Hence, the frying cycle, temperature and the added salt to carbohydrate-based food during frying should be monitored.
Planktonic foraminifera genomic variations reflect paleoceanographic changes in the Arctic: evidence from sedimentary ancient DNA
Authors: Pawłowska Joanna , Wollenburg Jutta E. , Zajączkowski Marek , Pawlowski Jan 
Published: September 2020

AbstractDeciphering the evolution of marine plankton is typically based on the study of microfossil groups. Cryptic speciation is common in these groups, and large intragenomic variations occur in ribosomal RNA genes of many morphospecies. In this study, we correlated the distribution of ribosomal amplicon sequence variants (ASVs) with paleoceanographic changes by analyzing the high-throughput sequence data assigned to Neogloboquadrina pachyderma in a 140,000-year-old sediment core from the Arctic Ocean. The sedimentary ancient DNA demonstrated the occurrence of various N. pachyderma ASVs whose occurrence and dominance varied through time. Most remarkable was the striking appearance of ASV18, which was nearly absent in older sediments but became dominant during the last glacial maximum and continues to persist today. Although the molecular ecology of planktonic foraminifera is still poorly known, the analysis of their intragenomic variations through time has the potential to provide new insight into the evolution of marine biodiversity and may lead to the development of new and important paleoceanographic proxies.
Poly(ADP-ribose) Polymerase 1 (PARP1) restrains MyoD-dependent gene expression during muscle differentiation
Authors: Matteini Francesca , Andresini Oriella , Petrai Stefano , Battistelli Cecilia , Rossi Marianna Nicoletta , Maione Rossella 
Published: September 2020

AbstractThe myogenic factor MyoD regulates skeletal muscle differentiation by interacting with a variety of chromatin-modifying complexes. Although MyoD can induce and maintain chromatin accessibility at its target genes, its binding and trans-activation ability can be limited by some types of not fully characterized epigenetic constraints. In this work we analysed the role of PARP1 in regulating MyoD-dependent gene expression. PARP1 is a chromatin-associated enzyme, playing a well recognized role in DNA repair and that is implicated in transcriptional regulation. PARP1 affects gene expression through multiple mechanisms, often involving the Poly(ADP-ribosyl)ation of chromatin proteins. In line with PARP1 down-regulation during differentiation, we observed that PARP1 depletion boosts the up-regulation of MyoD targets, such as p57, myogenin, Mef2C and p21, while its re-expression reverts this effect. We also found that PARP1 interacts with some MyoD-binding regions and that its presence, independently of the enzymatic activity, interferes with MyoD recruitment and gene induction. We finally suggest a relationship between the binding of PARP1 and the loss of the activating histone modification H3K4me3 at MyoD-binding regions. This work highlights not only a novel player in the epigenetic control of myogenesis, but also a repressive and catalytic-independent mechanisms by which PARP1 regulates transcription.
A serial multiparametric quantitative magnetic resonance imaging study to assess proteoglycan depletion of human articular cartilage and its effects on functionality
Authors: Hafner Tobias , Schock Justus , Post Manuel , Abrar Daniel Benjamin , Sewerin Philipp , Linka Kevin , Knobe Matthias , Kuhl Christiane , Truhn Daniel , Nebelung Sven 
Published: September 2020

AbstractWater, collagen, and proteoglycans determine articular cartilage functionality. If altered, susceptibility to premature degeneration is increased. This study investigated the effects of enzymatic proteoglycan depletion on cartilage functionality as assessed by advanced Magnetic Resonance Imaging (MRI) techniques under standardized loading. Lateral femoral condylar cartilage-bone samples from patients undergoing knee replacement (n = 29) were serially imaged by Proton Density-weighted and T1, T1ρ, T2, and T2* mapping sequences on a clinical 3.0 T MRI scanner (Achieva, Philips). Using pressure-controlled indentation loading, samples were imaged unloaded and quasi-statically loaded to 15.1 N and 28.6 N, and both before and after exposure to low-concentrated (LT, 0.1 mg/mL, n = 10) or high-concentrated trypsin (HT, 1.0 mg/mL, n = 10). Controls were not treated (n = 9). Responses to loading were assessed for the entire sample and regionally, i.e. sub- and peri-pistonally, and zonally, i.e. upper and lower sample halves. Trypsin effects were quantified as relative changes (Δ), analysed using appropriate statistical tests, and referenced histologically. Histological proteoglycan depletion was reflected by significant sub-pistonal decreases in T1 (p = 0.003) and T2 (p = 0.008) after HT exposure. Loading-induced changes in T1ρ and T2* were not related. In conclusion, proteoglycan depletion alters cartilage functionality and may be assessed using serial T1 and T2 mapping under loading.
Metagenome analysis using serum extracellular vesicles identified distinct microbiota in asthmatics
Authors: Lee Ji-Hyang , Choi Jun-Pyo , Yang Jinho , Won Ha-Kyeong , Park Chan Sun , Song Woo-Jung , Kwon Hyouk-Soo , Kim Tae-Bum , Kim Yoon-Keun , Park Hae-Sim , Cho You Sook 
Published: September 2020

AbstractDifferent patterns of bacterial communities have been reported in the airways and gastrointestinal tract of asthmatics when compared to healthy controls. However, the blood microbiome of asthmatics is yet to be investigated. Therefore, we aimed to determine whether a distinct serum microbiome is observed in asthmatics by metagenomic analysis of serum extracellular vesicles (EVs). We obtained serum from 190 adults with asthma and 260 healthy controls, from which EVs were isolated and analyzed. The bacterial composition of asthmatics was significantly different from that of healthy controls. Chao 1 index was significantly higher in the asthma group, while Shannon and Simpson indices were higher in the control group. At the phylum level, Bacteroidetes was more abundant in asthmatics, while Actinobacter, Verrucomicrobia, and Cyanobacteria were more abundant in healthy controls. At the genus level, 24 bacterial genera showed differences in relative abundance between asthmatics and controls, with linear discriminant analysis scores greater than 3. Further, in a diagnostic model based on these differences, a high predictive value with a sensitivity of 0.92 and a specificity of 0.93 was observed. In conclusion, we demonstrated distinct blood microbiome in asthma indicating the role of microbiome as a potential diagnostic marker of asthma.