bluuebunny/crossref_metadata_2025_split huggingface dataset:
First tracking of the oceanic spawning migrations of Australasian short-finned eels (Anguilla australis)
Authors: Koster Wayne M. , Aarestrup Kim , Birnie-Gauvin Kim , Church Ben , Dawson David , Lyon Jarod , O’Connor Justin , Righton David , Rose Denis , Westerberg Håkan , Stuart Ivor 
Published: November 2021

AbstractAnguillid eel populations have declined dramatically over the last 50 years in many regions of the world, and numerous species are now under threat. A critical life-history phase is migration from freshwater to distant oceans, culminating in a single life-time spawning event. For many anguillids, especially those in the southern hemisphere, mystery still shrouds their oceanic spawning migrations. We investigated the oceanic spawning migrations of the Australasian short-finned eel (Anguilla australis) using pop-up satellite archival tags. Eels were collected from river estuaries (38° S, 142° E) in south-eastern temperate Australia. In 2019, 16 eels were tracked for up to about 5 months, ~ 2620 km from release, and as far north as the tropical Coral Sea (22° S, 155° E) off the north-east coast of Australia. Eels from southern Australia appeared to access deep water off the Australian coast via two main routes: (i) directly east via Bass Strait, or (ii) south-east around Tasmania, which is the shortest route to deep water. Tagged eels exhibited strong diel vertical migrations, alternating between the warm euphotic zone (~ 100–300 m, 15–20 °C) at night and the mesopelagic zone (~ 700–900 m, 6–8 °C) during the day. Marine predators, probably lamnid sharks, tuna, or marine mammals, ended many eel migrations (at least ~ 30%), largely before the eels had left the Australian continental shelf. The long and risky marine migrations of Australasian eels highlight the need for better information on the processes contributing to eel mortality throughout the life cycle, including the impacts of future changes to oceanic currents, predator abundance and direct anthropogenic disturbances.
Cluster analysis and profiling of airway fluid metabolites in pediatric acute hypoxemic respiratory failure
Authors: Grunwell Jocelyn R. , Rad Milad G. , Stephenson Susan T. , Mohammad Ahmad F. , Opolka Cydney , Fitzpatrick Anne M. , Kamaleswaran Rishikesan 
Published: November 2021

AbstractHierarchal clustering of amino acid metabolites may identify a metabolic signature in children with pediatric acute hypoxemic respiratory failure. Seventy-four immunocompetent children, 41 (55.4%) with pediatric acute respiratory distress syndrome (PARDS), who were between 2 days to 18 years of age and within 72 h of intubation for acute hypoxemic respiratory failure, were enrolled. We used hierarchal clustering and partial least squares-discriminant analysis to profile the tracheal aspirate airway fluid using quantitative LC–MS/MS to explore clusters of metabolites that correlated with acute hypoxemia severity and ventilator-free days. Three clusters of children that differed by severity of hypoxemia and ventilator-free days were identified. Quantitative pathway enrichment analysis showed that cysteine and methionine metabolism, selenocompound metabolism, glycine, serine and threonine metabolism, arginine biosynthesis, and valine, leucine, and isoleucine biosynthesis were the top five enriched, impactful pathways. We identified three clusters of amino acid metabolites found in the airway fluid of intubated children important to acute hypoxemia severity that correlated with ventilator-free days < 21 days. Further studies are needed to validate our findings and to test our models.
Mapping the electrostatic potential of the nucleosome acidic patch
Authors: Zhang Heyi , Eerland Jelmer , Horn Velten , Schellevis Raymond , van Ingen Hugo 
Published: November 2021

AbstractThe nucleosome surface contains an area with negative electrostatic potential known as the acidic patch, which functions as a binding platform for various proteins to regulate chromatin biology. The dense clustering of acidic residues may impact their effective pKa and thus the electronegativity of the acidic patch, which in turn could influence nucleosome-protein interactions. We here set out to determine the pKa values of residues in and around the acidic patch in the free H2A-H2B dimer using NMR spectroscopy. We present a refined solution structure of the H2A-H2B dimer based on intermolecular distance restraints, displaying a well-defined histone-fold core. We show that the conserved histidines H2B H46 and H106 that line the acidic patch have pKa of 5.9 and 6.5, respectively, and that most acidic patch carboxyl groups have pKa values well below 5.0. For H2A D89 we find strong evidence for an elevated pKa of 5.3. Our data establish that the acidic patch is highly negatively charged at physiological pH, while protonation of H2B H106 and H2B H46 at slightly acidic pH will reduce electronegativity. These results will be valuable to understand the impact of pH changes on nucleosome-protein interactions in vitro, in silico or in vivo.
Curcumin derivative ST09 modulates the miR-199a-5p/DDR1 axis and regulates proliferation and migration in ovarian cancer cells
Authors: Ravindran Febina , Koroth Jinsha , Manjunath Meghana , Narayan Suchitra , Choudhary Bibha 
Published: November 2021

AbstractOvarian cancers are among the fatal malignancies affecting women globally, mainly due to their metastatic and chemoresistant nature. In this study, we report a potent curcumin derivative ST09 effective against ovarian cancers. Prior in-vitro studies with ST09 drug showed cytotoxicity in tumorigenic cells compared to normal cells and in-vivo, significant tumor reduction was observed with least systemic toxicity. ST09 induced cytotoxicity in the ovarian cancer cells triggering mitochondria-mediated intrinsic apoptotic pathway. Delving deeper to understand the underlying molecular mechanisms involved in ovarian cancer pathogenesis, we identified an inverse correlation of miR-199a-5p with DDR1, a collagen receptor with receptor tyrosine kinase activity. The ST09 treatment in ovarian cancer cell lines resulted in the deregulation of the miR-199a-5p/DDR1 axis, conferring tumor-suppressive functions. We established DDR1 to be a direct target of miR-199a-5p and that ST09-induced DDR1 loss in these ovarian cancer cells resulted in the inactivation of its downstream MMP activation, migration, EMT, and prosurvival NF-κB pathway. Overall this study demonstrates ST09, a potent drug candidate for ovarian cancer treatment which exhibits anti-invasive and migrastatic properties.
Long noncoding RNAs associated with nonalcoholic fatty liver disease in a high cholesterol diet adult zebrafish model
Authors: An Hyo Jung , Lee Yoon Jung , Choe Chong Pyo , Cho Hyun-Kyung , Song Dae Hyun 
Published: November 2021

AbstractThe mechanism of nonalcoholic fatty liver disease (NAFLD) has not been completely revealed. In this study, we investigated the association of liver histological changes and long noncoding RNAs (lncRNAs) in the NAFLD zebrafish model. Forty zebrafish were fed a high-cholesterol diet (1.5 g per day) for 8 weeks. We measured fatty liver changes in the zebrafish liver using oil red O staining and divided them into two groups based on high and low scores. We pooled each group of zebrafish livers and identified lncRNAs, miRNAs, and mRNAs using Next-generation sequencing. Human homologs of lncRNAs were identified using ZFLNC, Ensembl, and NONCODE. We found several significant genes, including 32 lncRNAs, 5 miRNA genes, and 8 protein-coding genes, that were associated with liver metabolism and NAFLD-related functions in zebrafish. In particular, eight conserved human homologs of lncRNAs were found. We discovered the human homologs of eight lncRNA candidates from fatty liver zebrafish for the first time. The spectrum of biological mechanisms by which lncRNAs mediate their functional roles in NAFLD in a high cholesterol diet adult zebrafish model remains to be uncovered.
A deep learning model for identifying diabetic retinopathy using optical coherence tomography angiography
Authors: Ryu Gahyung , Lee Kyungmin , Park Donggeun , Park Sang Hyun , Sagong Min 
Published: November 2021

AbstractAs the prevalence of diabetes increases, millions of people need to be screened for diabetic retinopathy (DR). Remarkable advances in technology have made it possible to use artificial intelligence to screen DR from retinal images with high accuracy and reliability, resulting in reducing human labor by processing large amounts of data in a shorter time. We developed a fully automated classification algorithm to diagnose DR and identify referable status using optical coherence tomography angiography (OCTA) images with convolutional neural network (CNN) model and verified its feasibility by comparing its performance with that of conventional machine learning model. Ground truths for classifications were made based on ultra-widefield fluorescein angiography to increase the accuracy of data annotation. The proposed CNN classifier achieved an accuracy of 91–98%, a sensitivity of 86–97%, a specificity of 94–99%, and an area under the curve of 0.919–0.976. In the external validation, overall similar performances were also achieved. The results were similar regardless of the size and depth of the OCTA images, indicating that DR could be satisfactorily classified even with images comprising narrow area of the macular region and a single image slab of retina. The CNN-based classification using OCTA is expected to create a novel diagnostic workflow for DR detection and referral.
Using explainable machine learning to characterise data drift and detect emergent health risks for emergency department admissions during COVID-19
Authors: Duckworth Christopher , Chmiel Francis P. , Burns Dan K. , Zlatev Zlatko D. , White Neil M. , Daniels Thomas W. V. , Kiuber Michael , Boniface Michael J. 
Published: November 2021

AbstractA key task of emergency departments is to promptly identify patients who require hospital admission. Early identification ensures patient safety and aids organisational planning. Supervised machine learning algorithms can use data describing historical episodes to make ahead-of-time predictions of clinical outcomes. Despite this, clinical settings are dynamic environments and the underlying data distributions characterising episodes can change with time (data drift), and so can the relationship between episode characteristics and associated clinical outcomes (concept drift). Practically this means deployed algorithms must be monitored to ensure their safety. We demonstrate how explainable machine learning can be used to monitor data drift, using the COVID-19 pandemic as a severe example. We present a machine learning classifier trained using (pre-COVID-19) data, to identify patients at high risk of admission during an emergency department attendance. We then evaluate our model’s performance on attendances occurring pre-pandemic (AUROC of 0.856 with 95%CI [0.852, 0.859]) and during the COVID-19 pandemic (AUROC of 0.826 with 95%CI [0.814, 0.837]). We demonstrate two benefits of explainable machine learning (SHAP) for models deployed in healthcare settings: (1) By tracking the variation in a feature’s SHAP value relative to its global importance, a complimentary measure of data drift is found which highlights the need to retrain a predictive model. (2) By observing the relative changes in feature importance emergent health risks can be identified.
Quantification of contrast agent uptake in the hepatobiliary phase helps to differentiate hepatocellular carcinoma grade
Authors: Haimerl Michael , Utpatel Kirsten , Götz Andrea , Zeman Florian , Fellner Claudia , Nickel Dominik , Luerken Lukas , Brennfleck Frank , Stroszczynski Christian , Scheiter Alexander , Verloh Niklas 
Published: November 2021

AbstractThis study aimed to assess the degree of differentiation of hepatocellular carcinoma (HCC) using Gd-EOB-DTPA-assisted magnetic resonance imaging (MRI) with T1 relaxometry. Thirty-three solitary HCC lesions were included in this retrospective study. This study's inclusion criteria were preoperative Gd-EOB-DTPA-assisted MRI of the liver and a histopathological evaluation after hepatic tumor resection. T1 maps of the liver were evaluated to determine the T1 relaxation time and reduction rate between the native phase and hepatobiliary phase (HBP) in liver lesions. These findings were correlated with the histopathologically determined degree of HCC differentiation (G1, well-differentiated; G2, moderately differentiated; G3, poorly differentiated). There was no significant difference between well-differentiated (950.2 ± 140.2 ms) and moderately/poorly differentiated (1009.4 ± 202.0 ms) HCCs in the native T1 maps. After contrast medium administration, a significant difference (p ≤ 0.001) in the mean T1 relaxation time in the HBP was found between well-differentiated (555.4 ± 140.2 ms) and moderately/poorly differentiated (750.9 ± 146.4 ms) HCCs. For well-differentiated HCCs, the reduction rate in the T1 time was significantly higher at 0.40 ± 0.15 than for moderately/poorly differentiated HCCs (0.25 ± 0.07; p = 0.006). In conclusion this study suggests that the uptake of Gd-EOB-DTPA in HCCs is correlated with tumor grade. Thus, Gd-EOB-DTPA-assisted T1 relaxometry can help to further differentiation of HCC.
Simulation studies on the boot shape injection of a giant magnetostrictive injector
Authors: Xue Guangming , Ge Jitao , Ning Peng , Zhou Jun , Wang Ke , Cheng Ziyang , Pei Guoxu 
Published: November 2021

AbstractGiant magnetostrictive injector using giant magnetostrictive material acting an electronic controlled injector may be one new promising injector to acquire adjustable injection rates while maintaining large injection quantity. An electronic controlled injector driven by a giant magnetostrictive actuator was designed through combining the driving requirement and output characteristics of the material. To promote responding speed of the coil current, the driving voltage with open-hold-fall type waveform was employed just like using in an electromagnetic injector. Simulation model for the injection characteristic of the injector was established using AMEsim software and verified using experimental results collected by the single injection meter. From simulation and experimental results, designed giant magnetostrictive injector showed good performances as maximum spray rate of 4.5 L/min and minimum spray pulse width of 0.21 ms, and realized the boot shape injection when generated by the designed voltage wave. Furthermore, duration time and amplitude of the pilot spray part in a boot shape injection were respectively adjusted through changing the dwell time and opening time. The boot shape injection reached by the giant magnetostrictive injector can reach quite accurate control of fuel injection and then promote fuel efficiency effectively.
The role of cardiovascular risk factors in maternal cardiovascular disease according to offspring birth characteristics in the HUNT study
Authors: Haug Eirin B. , Markovitz Amanda R. , Fraser Abigail , Dalen Håvard , Romundstad Pål R. , Åsvold Bjørn O. , Rich-Edwards Janet W. , Horn Julie 
Published: November 2021

AbstractA history of preterm or small (SGA) or large (LGA) for gestational age offspring is associated with smoking and unfavorable levels of BMI, blood pressure, glucose and lipids. Whether and to what extent the excess cardiovascular risk observed in women with these pregnancy complications is explained by conventional cardiovascular risk factors (CVRFs) is not known. We examined the association between a history of SGA, LGA or preterm birth and cardiovascular disease among 23,284 parous women and quantified the contribution of individual CVRFs to the excess cardiovascular risk using an inverse odds weighting approach. The hazard ratios (HR) between SGA and LGA offspring and CVD were 1.30 (95% confidence interval (CI) 1.15, 1.48) and 0.89 (95% CI 0.76, 1.03), respectively. Smoking explained 49% and blood pressure may have explained ≈12% of the excess cardiovascular risk in women with SGA offspring. Women with preterm birth had a 24% increased risk of CVD (HR 1.24, 95% CI 1.06, 1.45), but we found no evidence for CVRFs explaining any of this excess cardiovascular risk. While smoking explains a substantial proportion of excess cardiovascular risk in women with SGA offspring and blood pressure may explain a small proportion in these women, we found no evidence that conventional CVRFs explain any of the excess cardiovascular risk in women with preterm birth.
Phonon-assisted electronic states modulation of few-layer PdSe2 at terahertz frequencies
Authors: Li Ziqi , Peng Bo , Lin Miao-Ling , Leng Yu-Chen , Zhang Bin , Pang Chi , Tan Ping-Heng , Monserrat Bartomeu , Chen Feng 
Published: November 2021

AbstractInformation technology demands high-speed optoelectronic devices, but going beyond the one terahertz (THz) barrier is challenging due to the difficulties associated with generating, detecting, and processing high-frequency signals. Here, we show that femtosecond-laser-driven phonons can be utilized to coherently manipulate the excitonic properties of semiconductors at THz frequencies. The precise control of the pump and subsequent time-delayed broadband probe pulses enables the simultaneous generation and detection processes of both periodic lattice vibrations and their couplings with electronic states. Combining ultralow frequency Raman spectroscopy with first-principles calculations, we identify the unique phonon mode-selective and probe-energy dependent features of electron–phonon interactions in layered PdSe2. Two distinctive types of coherent phonon excitations could couple preferentially to different types of electronic excitations: the intralayer (4.3 THz) mode to carriers and the interlayer (0.35 THz) mode to excitons. This work provides new insights to understand the excited-state phonon interactions of 2D materials and to achieve future applications of optoelectronic devices operating at THz frequencies.
Mass action model of solution activity via speciation by solvation and ion pairing equilibria
Authors: Wilson Aaron D. , Lee Hyeonseok , Stetson Caleb 
Published: November 2021

AbstractSolutes and their concentrations influence many natural and anthropogenic solution processes. Electrolyte and solution models are used to quantify and predict such behavior. Here we present a mechanistic solution model based on mass action equilibria. Solvation and ion pairing are used to model speciated solute and solvent concentrations such that they correlate to a solution’s vapor pressure (solvent activity) according to Raoult’s law from dilute conditions to saturation. This model introduces a hydration equilibrium constant (Kha) that is used with either an ion dissociation constant (Kid) or a hydration modifier (m) with an experimentally determined ion dissociation constant, as adjustable parameters to fit vapor–liquid equilibrium data. The modeled solvation equilibria are accompanied by molecular dynamics (MD) studies that support a decline in the observed degree of solvation with increased concentration. MD calculations indicate this finding is a combination of a solvent that solvates multiple solutes, and changes in a solute’s solvation sphere, with the dominant factor changing with concentration. This speciation-based solution model is lateral to established electrostatics-based electrolyte theories. With its basis in mass action, the model can directly relate experimental data to the modeled solute and solvent speciated concentrations and structures.
Angle-dependent interferences in electron emission accompanying stimulated Compton scattering from molecules
Authors: Sopena Arturo , Palacios Alicia , Catoire Fabrice , Bachau Henri , Martín Fernando 
Published: November 2021

AbstractThe high brilliance of ultrashort X-ray pulses recently generated in free electron lasers will soon open the way to the investigation of non-linear processes that still remain inaccessible due to the smallness of the corresponding cross sections. One of them is stimulated Compton scattering from molecules. In this work, we investigate stimulated Compton scattering from fixed-in-space H2 molecules in the few-hundred eV photon energy range, where both dipole and non-dipole transitions are important. We show that the interference between dipole and non-dipole transitions leads to pronounced asymmetries in the electron angular distributions. These asymmetries strongly depend on molecular orientation, to the point that they can lead to electron emission in either the forward or the backward directions with respect to the propagation axis, or in both directions, or even in the orthogonal direction. This is in contrast with Compton scattering from free electrons or atomic targets.
Generation of spin currents by a temperature gradient in a two-terminal device
Authors: Barfknecht Rafael E. , Foerster Angela , Zinner Nikolaj T. , Volosniev Artem G. 
Published: November 2021

AbstractTheoretical and experimental studies of the interaction between spins and temperature are vital for the development of spin caloritronics, as they dictate the design of future devices. In this work, we propose a two-terminal cold-atom simulator to study that interaction. The proposed quantum simulator consists of strongly interacting atoms that occupy two temperature reservoirs connected by a one-dimensional link. First, we argue that the dynamics in the link can be described using an inhomogeneous Heisenberg spin chain whose couplings are defined by the local temperature. Second, we show the existence of a spin current in a system with a temperature difference by studying the dynamics that follows the spin-flip of an atom in the link. A temperature gradient accelerates the impurity in one direction more than in the other, leading to an overall spin current similar to the spin Seebeck effect.
Increased biomass and carbon burial 2 billion years ago triggered mountain building
Authors: Parnell John , Brolly Connor 
Published: November 2021

AbstractThe geological record following the c. 2.3 billion years old Great Oxidation Event includes evidence for anomalously high burial of organic carbon and the emergence of widespread mountain building. Both carbon burial and orogeny occurred globally over the period 2.1 to 1.8 billion years ago. Prolific cyanobacteria were preserved as peak black shale sedimentation and abundant graphite. In numerous orogens, the exceptionally carbonaceous sediments were strongly deformed by thrusting, folding, and shearing. Here an assessment of the timing of Palaeoproterozoic carbon burial and peak deformation/metamorphism in 20 orogens shows that orogeny consistently occurred less than 200 million years after sedimentation, in a time frame comparable to that of orogens through the Phanerozoic. This implies that the high carbon burial played a critical role in reducing frictional strength and lubricating compressive deformation, which allowed crustal thickening to build Palaeoproterozoic mountain belts. Further, this episode left a legacy of weakening and deformation in 2 billion year-old crust which has supported subsequent orogenies up to the building of the Himalayas today. The link between Palaeoproterozoic biomass and long-term deformation of the Earth’s crust demonstrates the integral relationship between biosphere and lithosphere.