bluuebunny/crossref_metadata_2025_split huggingface dataset:
Texture features from computed tomography correlate with markers of severity in acute alcohol-associated hepatitis
Authors: Tana Michele M. , McCoy David , Lee Briton , Patel Roshan , Lin Joseph , Ohliger Michael A. 
Published: October 2020

AbstractThe aim of this study was to use texture analysis to establish quantitative CT-based imaging features to predict clinical severity in patients with acute alcohol-associated hepatitis (AAH). A secondary aim was to compare the performance of texture analysis to deep learning. In this study, mathematical texture features were extracted from CT slices of the liver for 34 patients with a diagnosis of AAH and 35 control patients. Recursive feature elimination using random forest (RFE-RF) was used to identify the best combination of features to distinguish AAH from controls. These features were subsequently used as predictors to determine associated clinical values. To compare machine learning with deep learning approaches, a 2D dense convolutional neural network (CNN) was implemented and trained for the classification task of AAH. RFE-RF identified 23 top features used to classify AAH images, and the subsequent model demonstrated an accuracy of 82.4% in the test set. The deep learning CNN demonstrated an accuracy of 70% in the test set. We show that texture features of the liver are unique in AAH and are candidate quantitative biomarkers that can be used in prospective studies to predict the severity and outcomes of patients with AAH.
The transboundary nature of the world’s exploited marine species
Authors: Palacios-Abrantes Juliano , Reygondeau Gabriel , Wabnitz Colette C. C. , Cheung William W. L. 
Published: October 2020

AbstractRegulatory boundaries and species distributions often do not align. This is especially the case for marine species crossing multiple Exclusive Economic Zones (EEZs). Such movements represent a challenge for fisheries management, as policies tend to focus at the national level, yet international collaborations are needed to maximize long-term ecological, social and economic benefits of shared marine species. Here, we combined species distributions and the spatial delineation of EEZs at the global level to identify the number of commercially exploited marine species that are shared between neighboring nations. We found that 67% of the species analyzed are transboundary (n = 633). Between 2005 and 2014, fisheries targeting these species within global-EEZs caught on average 48 million tonnes per year, equivalent to an average of USD 77 billion in annual fishing revenue. For select countries, over 90% of their catch and economic benefits were attributable to a few shared resources. Our analysis suggests that catches from transboundary species are declining more than those from non-transboundary species. Our study has direct implications for managing fisheries targeting transboundary species, highlighting the need for strengthened effective and equitable international cooperation.
Design of CMOS-compatible metal–insulator–metal metasurfaces via extended equivalent-circuit analysis
Authors: Dorodnyy Alexander , Koepfli Stefan M. , Lochbaum Alexander , Leuthold Juerg 
Published: October 2020

AbstractPhotonic metasurfaces compatible with large-scale production such as CMOS are of importance because they promise cointegration of electronics with photonics for detection, communication and sensing. The main challenges on the way of designing such metasurfaces are: (1) large variety of possible geometrical shapes of metasurface elements that makes finding the most appropriate shape difficult; (2) poor compatibility of available electronic layer stacks with photonics. In this paper we show how to address both of these challenges utilizing extended equivalent-circuit analysis. In a first step we classify the behavior of different metasurfaces using the equivalent circuit. We discover that metasurfaces that use inverted-dipole resonator type exhibit higher tolerance to dielectric spacer thickness, higher angular stability and have similar resonance quality-factor as other types. In the second step we utilize the equivalent-circuit scheme to efficiently optimize the parameters of inverted-dipole based metasurfaces for a layer stack such as given in a CMOS process. Finally, as an example we demonstrate how an inverted-cross structure can be adapted to a commercial 110 nm CMOS process with Al metal layers. We measured peak absorption above 90% at center wavelength around 4 µm with quality factor of approximately 5 and angular stability larger than 60°.
The transformer-2 and fruitless characterisation with developmental expression profiles of sex-determining genes in Bactrocera dorsalis and B. correcta
Authors: Laohakieat Kamoltip , Isasawin Siriwan , Thanaphum Sujinda 
Published: October 2020

AbstractSex determination in tephritid fruit flies involves a signaling cascade of alternatively spliced genes. The Transformer (TRA) and Transformer-2 (TRA-2) complex establishes an autoregulatory loop switching sex-specific splicing of tra pre-mRNA in females. The TRA/TRA-2 complex also regulates the sex-specific splicing of downstream effector genes, doublesex (dsx) and fruitless (fru). In Ceratitis capitata, a Maleness-on the-Y (MoY) gene modulates sex-specifically spliced Cctra pre-mRNA and results in the breakdown of the Cctra autoregulatory loop in males. In this study, the tra-2 and fru genes were characterised in two key pests, Bactrocera dorsalis and B. correcta. The tra-2 genes showed high degrees of conservation among tephritids. The complex gene organisation for each of Bdfru and Bcfru were identified. There are sex-specific and non sex-specific transcripts generated by alternative promoters as found in Drosophila melanogaster and other insects. RNAi knockdown of Bdtra transcripts showed that BdTRA controls the sex-specific splicing of Bddsx and Bdfru pre-mRNAs. Developmental expression analysis shows that multiple splice variants of Bdtra and Bctra RNAs are present before and during cellular blastoderm formation and that the mature sex-specific variants become fixed later in embryogenesis. Furthermore, the BddsxM splice variants are found in early embryos at the beginning of gastulation, but BdfruM does not appear until the larval stage. We proposed that the zygotic tra loop is initiated in both female and male embryos before becoming automatised or abolished by MoY, respectively.
Inhibiting the two-component system GraXRS with verteporfin to combat Staphylococcus aureus infections
Authors: Prieto Juana María , Rapún-Araiz Beatriz , Gil Carmen , Penadés José R. , Lasa Iñigo , Latasa Cristina 
Published: October 2020

AbstractInfections caused by Staphylococcus aureus pose a serious and sometimes fatal health issue. With the aim of exploring a novel therapeutic approach, we chose GraXRS, a Two-Component System (TCS) that determines bacterial resilience against host innate immune barriers, as an alternative target to disarm S. aureus. Following a drug repurposing methodology, and taking advantage of a singular staphylococcal strain that lacks the whole TCS machinery but the target one, we screened 1.280 off-patent FDA-approved drug for GraXRS inhibition. Reinforcing the connection between this signaling pathway and redox sensing, we found that antioxidant and redox-active molecules were capable of reducing the expression of the GraXRS regulon. Among all the compounds, verteporfin (VER) was really efficient in enhancing PMN-mediated bacterial killing, while topical administration of such drug in a murine model of surgical wound infection significantly reduced the bacterial load. Experiments relying on the chemical mimicry existing between VER and heme group suggest that redox active residue C227 of GraS participates in the inhibition exerted by this FDA-approved drug. Based on these results, we propose VER as a promising candidate for sensitizing S. aureus that could be helpful to combat persistent or antibiotic-resistant infections.
Reassessment of the role of CaCO3 in n-butanol production from pretreated lignocellulosic biomass by Clostridium acetobutylicum
Authors: Su Zengping , Wang Fengqin , Xie Yaohuan , Xie Hui , Mao Guotao , Zhang Hongsen , Song Andong , Zhang Zhanying 
Published: October 2020

AbstractIn this study, the role of CaCO3 in n-butanol production was further investigated using corn straw hydrolysate (CSH) media by Clostridium acetobutylicum CICC 8016. CaCO3 addition stimulated sugars utilization and butanol production. Further study showed that calcium salts addition to CSH media led to the increase in Ca2+ concentration both intracellularly and extracellularly. Interestingly, without calcium salts addition, intracellular Ca2+ concentration in the synthetic P2 medium was much higher than that in the CSH medium despite the lower extracellular Ca2+ concentrations in the P2 medium. These results indicated that without additional calcium salts, Ca2+ uptake by C. acetobutylicum CICC 8016 in the CSH medium may be inhibited by non-sugar biomass degradation compounds, such as furans, phenolics and organic acids. Comparative proteomics analysis results showed that most enzymes involved in glycolysis, redox balance and amino acids metabolism were up-regulated with CaCO3 addition. This study provides further insights into the role of CaCO3 in n-butanol production using real biomass hydrolysate.
Reconstructing the hydraulics of the world’s first industrial complex, the second century CE Barbegal watermills, France
Authors: Passchier Cees W. , Bourgeois Marcel , Viollet Pierre-Louis , Sürmelihindi Gül , Bernard Vincent , Leveau Philippe , Spötl Christoph 
Published: October 2020

AbstractThe Barbegal watermill complex, a unique cluster of 16 waterwheels in southern France, was the first known attempt in Europe to set up an industrial-scale complex of machines during the culmination of Roman Civilization in the second century CE. Little is known about the state of technological advance in this period, especially in hydraulics and the contemporary diffusion of knowledge. Since the upper part of the Barbegal mill complex has been destroyed and no traces of the wooden machinery survived, the mode of operation of these mills has long remained elusive. Carbonate incrustations that formed on the woodwork of the mills were used to reconstruct its structure and function, revealing a sophisticated hydraulic setup unique in the history of water mills. The lower mills used an elbow shaped flume to bring water onto overshot millwheels. This flume was specially adapted to the small water basins and serial arrangement of the mills on the slope. Carbonate deposits from ancient water systems are therefore a powerful tool in archaeological reconstructions and provide tantalizing insights into the skills of Roman engineers during a period of history that is the direct predecessor of our modern civilization.
Dynamic changes in nocturnal blood glucose levels are associated with sleep-related features in patients with obstructive sleep apnea
Authors: Byun Jung-Ick , Cha Kwang Su , Jun Ji Eun , Kim Tae-Joon , Jung Ki-Young , Jeong In-Kyung , Shin Won Chul 
Published: October 2020

AbstractObstructive sleep apnea (OSA) has a bidirectional relationship with insulin resistance conditions; however, the mechanism remains unclear. This study aimed to compare dynamic nocturnal glucose changes among patients with OSA of varying levels of severity and evaluate temporal changes associated with the cardinal features of OSA (sympathetic hyperactivation, intermittent hypoxemia, and sleep fragmentation) in nondiabetic subjects. Nocturnal glucose was measured with a continuous glucose monitoring device every 5 min during polysomnography (PSG). The OSA features were evaluated using heart rate variability (HRV), minimum saturation, and electroencephalography. Eleven subjects with moderate to severe OSA and 12 subjects with no or mild OSA were evaluated. Those with moderate to severe OSA showed an increasing trend in blood glucose levels after sleep onset, whereas those without or with mild OSA showed a decreasing trend (F = 8.933, p < 0.001). Delta band power also showed different trends during sleep between the two groups (F = 2.991, p = 0.009), and minimum saturation remained lower in the moderate to severe OSA group than in the no or mild OSA group. High degrees of coupling between nocturnal glucose levels and each OSA feature were observed. Altered trends in nocturnal glucose in moderate to severe OSA may reflect glucose intolerance and result in metabolic consequences. Managing the features of sleep-related OSA may have implications for metabolic management in the future.
Vertical fluxes of nutrients enhanced by strong turbulence and phytoplankton bloom around the ocean ridge in the Luzon Strait
Authors: Tsutsumi Eisuke , Matsuno Takeshi , Itoh Sachihiko , Zhang Jing , Senjyu Tomoharu , Sakai Akie , Lee Keunjong , Yanagimoto Daigo , Yasuda Ichiro , Ogawa Hiroshi , Villanoy Cesar 
Published: October 2020

AbstractSteep oceanic ridges and tidal currents in the Luzon Strait generate some of the world’s strongest turbulent mixing. To evaluate the impacts of the turbulence intensity on the marine ecosystem, we carried out measurements of microstructure turbulence and biogeochemical hydrography along 21°N in the Luzon Strait during the R/V Hakuho Maru cruise, KH-17-5-2, in November 2017. We found a turbulent kinetic energy dissipation rate exceeding O(10−7) W kg−1 and vertical eddy diffusivity exceeding O(10−3) m2 s−1, two orders of magnitude larger than those in the open ocean, above a shallow sub-ridge on the eastern ridge of the Luzon Strait. In addition, a clear chlorophyll a bloom was identified in the surface layer above the sub-ridge from in situ measurements and satellite observations. High values of nitrate (4.7 mmol N m−2 d−1) and phosphate (0.33 mmol P m−2 d−1) fluxes estimated near the base of the surface chlorophyll a bloom strongly suggest that enhanced turbulent mixing promotes nutrient supply to the euphotic zone and generates new production within the surface layer, contributing to the formation of a quasi-permanent local chlorophyll a bloom north of Itbayat Island on the eastern ridge.
Electroporation and genetic supply of Cas9 increase the generation efficiency of CRISPR/Cas9 knock-in alleles in C57BL/6J mouse zygotes
Authors: Alghadban Samy , Bouchareb Amine , Hinch Robert , Hernandez-Pliego Polinka , Biggs Daniel , Preece Chris , Davies Benjamin 
Published: October 2020

AbstractCRISPR/Cas9 machinery delivered as ribonucleoprotein (RNP) to the zygote has become a standard tool for the development of genetically modified mouse models. In recent years, a number of reports have demonstrated the effective delivery of CRISPR/Cas9 machinery via zygote electroporation as an alternative to the conventional delivery method of microinjection. In this study, we have performed side-by-side comparisons of the two RNP delivery methods across multiple gene loci and conclude that electroporation compares very favourably with conventional pronuclear microinjection, and report an improvement in mutagenesis efficiency when delivering CRISPR via electroporation for the generation of simple knock-in alleles using single-stranded oligodeoxynucleotide (ssODN) repair templates. In addition, we show that the efficiency of knock-in mutagenesis can be further increased by electroporation of embryos derived from Cas9-expressing donor females. The maternal supply of Cas9 to the zygote avoids the necessity to deliver the relatively large Cas9 protein, and high efficiency generation of both indel and knock-in allele can be achieved by electroporation of small single-guide RNAs and ssODN repair templates alone. Furthermore, electroporation, compared to microinjection, results in a higher rate of embryo survival and development. The method thus has the potential to reduce the number of animals used in the production of genetically modified mouse models.
Metampicillin is a cyclic aminal produced by reaction of ampicillin with formaldehyde
Authors: Reinbold Raphael , John Tobias , Spingardi Paolo , Kawamura Akane , Schofield Christopher J. , Hopkinson Richard J. 
Published: October 2020

AbstractMetampicillin is a β-lactam antibiotic that is prepared by the reaction of ampicillin with formaldehyde. Although metampicillin has been studied for treatment of infections in animals and humans, its structure has been unclear. We report NMR studies revealing that metampicillin contains a formaldehyde-derived cyclic aminal. NMR time-course experiments with excess formaldehyde in solution show formation of another product with an additional exocyclic hemiaminal group formed by reaction with the cyclic aminal nitrogen. The exocyclic hemiaminal group is readily removed by reaction with the formaldehyde scavenger 1,3-cyclohexanedione, whereas the cyclic aminal methylene exhibits greater stability. The overall results assign the structure of metampicillin as containing a cyclic aminal and further reveal the potential for complexity in the reaction of formaldehyde with biomedicinally relevant molecules.
Seq-SymRF: a random forest model predicts potential miRNA-disease associations based on information of sequences and clinical symptoms
Authors: Li Jinlong , Chen Xingyu , Huang Qixing , Wang Yang , Xie Yun , Dai Zong , Zou Xiaoyong , Li Zhanchao 
Published: October 2020

AbstractIncreasing evidence indicates that miRNAs play a vital role in biological processes and are closely related to various human diseases. Research on miRNA-disease associations is helpful not only for disease prevention, diagnosis and treatment, but also for new drug identification and lead compound discovery. A novel sequence- and symptom-based random forest algorithm model (Seq-SymRF) was developed to identify potential associations between miRNA and disease. Features derived from sequence information and clinical symptoms were utilized to characterize miRNA and disease, respectively. Moreover, the clustering method by calculating the Euclidean distance was adopted to construct reliable negative samples. Based on the fivefold cross-validation, Seq-SymRF achieved the accuracy of 98.00%, specificity of 99.43%, sensitivity of 96.58%, precision of 99.40% and Matthews correlation coefficient of 0.9604, respectively. The areas under the receiver operating characteristic curve and precision recall curve were 0.9967 and 0.9975, respectively. Additionally, case studies were implemented with leukemia, breast neoplasms and hsa-mir-21. Most of the top-25 predicted disease-related miRNAs (19/25 for leukemia; 20/25 for breast neoplasms) and 15 of top-25 predicted miRNA-related diseases were verified by literature and dbDEMC database. It is anticipated that Seq-SymRF could be regarded as a powerful high-throughput virtual screening tool for drug research and development. All source codes can be downloaded from https://github.com/LeeKamlong/Seq-SymRF.
Sphingosine-1-phosphate in anti-neutrophil cytoplasmic antibody-associated vasculitis: coagulation-related clinical indicators and complications
Authors: Wu Kai-Li , Liang Qing-Hui , Ding Na , Li Bo-Wei , Hao Jian 
Published: October 2020

Abstract
Background: Sphingosine-1-phosphate (S1P) plays a significant role in anti-neutrophil cytoplasmic antibody (ANCA)-associated vasculitis (AAV).
Methods: We collected the plasma samples from 40 patients with AAV and 10 healthy volunteers. The plasma levels of S1P were tested by enzyme-linked immunosorbent assay (ELISA). The levels of serum creatinine (Scr) were tested by rate method, and then the estimated glomerular filtration rate (eGFR) of the patients was calculated from the Scr, age, and gender. Prothrombin time (PT), partial thromboplastin time (APTT), thrombin time (TT), fibrinogen (FIB), fibrinogen reduction product (FDP), D-dimer and C-reactive protein (CRP) were tested by turbidimetric inhibition immunoassays. Platelets (PLTs) were tested by fluorescently labeled electrical impedance method.
Results: The plasma levels of S1P were significantly higher in AAV patients than in healthy volunteers. Correlation analysis showed that plasma levels of S1P were negatively correlated with glomerular filtration (P=0.022, r = −0.306), and positively correlated with circulating levels of Birmingham vasculitis activity score (BVAS), PLT and D-dimer, (P=0.004, r = 0.443; P&lt;0.001, r = 0.654; P=0.006, r = 0.427). The 40 patients with AAV were classified into three groups: the thromboembolism group (with complications of cerebral infarction and myocardial infarction, n=6), cerebral ischemia group (n=4), and cerebral hemorrhage group (n=2). The plasma levels of S1P were highest in the thromboembolism group and lowest in the cerebral hemorrhage group (P=0.003).
Conclusions: Plasma levels of S1P were associated with circulating levels of D-dimer, PLT and BVAS in the patients with AAV. Hence, plasma S1P level can be used as a biomarker to predict coagulation-related complications in AAV.
Constraining the accretion flow density profile near Sgr A* using theL′-band emission of the S2 star
Authors: Hosseini S. Elaheh , Zajaček Michal , Eckart Andreas , Sabha Nadeen B. , Labadie Lucas 
Published: October 2020

Context.The density of the ambient medium around a supermassive black hole (SMBH) and the way it varies with distance plays an important role in our understanding of the inflow-outflow mechanisms in the Galactic centre (GC). This dependence is often fitted by spherical power-law profiles based on observations in the X-ray, infrared (IR), submillimetre (submm), and radio domains.Aims.Nevertheless, the density profile is poorly constrained at the intermediate scales of 1000 Schwarzschild radii (Rs). Here we independently constrain the spherical density profile using the stellar bow shock of the star S2 which orbits the SMBH at the GC with the pericentre distance of 14.4 mas (∼1500 Rs).Methods.Assuming an elliptical orbit, we apply celestial mechanics and the theory of bow shocks that are at ram pressure equilibrium. We analyse the measured IR flux density and magnitudes of S2 in theL′-band (3.8 micron) obtained over seven epochs in the years between 2004–2018. We put an upper limit on the emission from S2’s associated putative bow shock and constrain the density profile of the ambient medium.Results.We detect no significant change in S2 flux density until the recent periapse in May 2018. The intrinsic flux variability of S2 is at the level of 2–3%. Based on the dust-extinction model, the upper limit on the number density at the S2 periapse is ∼1.87  ×  109 cm−3, which yields a density slope of at most 3.20. Using the synchrotron bow-shock emission, we obtain the ambient density of ≲1.01  ×  105 cm−3and a slope of ≲1.47. These values are consistent with a wide variety of media from hot accretion flows to potentially colder and denser media comparable in properties to broad-line-region clouds. However, a standard thin disc can be excluded at the distance of S2’s pericentre.Conclusions.With the current photometry sensitivity of 0.01 mag, we are not able to make stringent constraints on the density of the ambient medium in the GC using S2-star observations. We can distinguish between hot accretion flows and thin, cold discs, where the latter can be excluded at the scale of the S2 periapse. Future observations of stars in the S cluster using instruments such as Mid-IR Extremely Large Telescope Imager and Spectrograph at Extremely Large Telescope with the photometric sensitivity of as much as 10−3mag will allow the GC medium to be probed at intermediate scales at densities as low as ∼700 cm−3in case of non-thermal bow-shock emission. The new instrumentation, in combination with discoveries of stars with smaller pericentre distances, will help to independently constrain the density profile around Sagittarius A* (Sgr A*).