bluuebunny/crossref_metadata_2025 huggingface dataset:
Predicting Global Marine Sediment Density Using the Random Forest Regressor Machine Learning Algorithm
Authors: Graw J. H. , Wood W. T. , Phrampus B. J.
Published: December 2020

Marine sediment density is of vital importance due to its influence on many geoacoustic and nongeoacoustic parameters, including but not limited to: acoustic impedance, sediment grain size, sediment attenuation, gravity, and isostatic and dynamic responses of oceanic crust. Additionally, it plays a fundamental role on geomechanical behavior which is important for pore pressure generation, seafloor slope stability, and seafloor infrastructure. Subsurface drilling from the Deep Sea Drilling Project, Ocean Drilling Program, International Ocean Discovery Program, a myriad of scientific research cruises, and a number of petroleum companies have amassed large quantities of invaluable seafloor geologic parameters. These point sampling location data yield accurate vertical constraints at a given location, but extrapolating that information away from the location is very difficult. To address this, we have taken a machine learning approach (the random forest regressor [RFR] in this instance) to predict global seafloor density and its associated uncertainty, both at a 5 × 5‐arc minute resolution. The RFR algorithm accepts a sparsely sampled observational data set with densely gridded relatable predictors and predicts statistically optimal estimates where no physical measurements have been made. The final prediction has median, mean, and root‐mean‐square errors of 0.058, 0.076, and 0.1009 g/cm3, respectively. Results show density predictions that coincide with expected lateral density variation (albeit at a very coarse spatial scale) with respect to ocean depth and uncertainties that are low for most of the seafloor. Finally, a parametric isolation indicates locations where additional samples are needed to improve the overall prediction.
Imaging Strong Lateral Heterogeneities Across the Contiguous US Using Body‐To‐Surface Wave Scattering
Authors: Yu Chunquan , Castellanos Jorge C. , Zhan Zhongwen
Published: December 2020

Body‐to‐surface wave scattering, originated from strong lateral heterogeneity, has been observed and modeled for decades. Compared to body waves, scattered surface waves propagate along the Earth's surface with less energy loss and, thus, can be observed over a wider distance range. In this study, we utilize surface waves converted from teleseismic SH or Sdiff wave incidence to map strong lateral heterogeneities across the entire contiguous United States. We apply array‐based phase coherence analysis to broadband waveforms recorded by the USArray Transportable Array and other permanent/temporary networks to detect coherent signals that are associated with body‐to‐surface wave scattering. We then locate the source of the scattering by back‐propagating the beamformed energy using both straight‐ray and curved‐ray approximations. Our results show that the distribution of scatterers correlates well with known geological features across the contiguous United States. Topographic/bathymetric relief along the continental slope off the Pacific Border is the major source of scattering in the western United States. On the other hand, sedimentary basins, especially their margins, are the dominant scatterers in the central United States. Moho offsets, such as the one around the periphery of the Colorado Plateau, are also a strong contributor to scattering, but isolating their effect from that of other near‐surface structures without any additional constraints can be complicated. Finally, we demonstrate the possibility of using scattered surface waves to constrain subsurface velocity structures, as complementary to conventional earthquake‐ or ambient noise‐based surface wave tomography.
Ejecta Thickness Distribution of the Schrödinger Basin on the Moon
Authors: Xu Luyuan , Xie Minggang
Published: December 2020

Thickness distribution of impact ejecta gives insights into the processes of impact cratering, the stratigraphy of planetary crust, future sampling site selection, and the source of lunar samples. In this study, we conduct detailed measurements of ejecta deposit thicknesses for the Schrödinger basin, the second youngest and the best‐preserved peak‐ring impact basin on the Moon. Based on Lunar Reconnaissance Orbiter Camera Wide Angle Camera, Kaguya Terrain Camera, and the Lunar Orbiter Laser Altimeter data, the thicknesses of ejecta deposits are estimated from the measurements of partially filled pre‐Schrödinger craters by using crater morphometry, and the effect of crater degradation is taken into considerations. The thickness distribution of ejecta is derived from the measured thicknesses of ejecta deposits using an updated ballistic sedimentation model. Our measurements yield an ejecta thickness of ∼704 m at the current Schrödinger basin rim under the decay with a power‐law index of −3.0. Based on these measurements, we find that the model of Pike (1974, https://doi.org/10.1016/0012-821x(74)90114-9) provides the best estimates of transient cavity rim radius of 95.5 km and excavation depth of 19.6 km for the Schrödinger basin, whereas the widely used model of McGetchin et al. (1973, https://doi.org/10.1016/0012-821x(73)90162-3) significantly underestimate the ejecta thickness of Schrödinger basin. In addition, our results indicate that the Schrödinger basin‐forming impact does not penetrate through the lunar crust.
Evidence for an Ancient Near‐Equatorial Lunar Dipole From Higher Precision Inversions of Crustal Magnetization
Authors: Maxwell R. E. , Garrick‐Bethell I.
Published: December 2020

Studies of lunar paleopoles have been used to make a variety of inferences about past episodes of true polar wander and the orientation of the ancient dynamo field. However, the large and variable uncertainties commonly reported for such studies make robust conclusions difficult. To make further progress, we used synthetic magnetic anomalies to assess a common method to estimate magnetization direction uncertainty. We find that with this method, magnetic anomalies with higher inclinations have systematically higher uncertainties than lower inclination anomalies. We call this effect inclination bias. A similar effect is found for declination, but it is weaker. We also find that this method often produces overly conservative uncertainty estimates. To avoid these effects, we use Monte Carlo methods to determine magnetization direction uncertainty. We apply our methods to five lunar magnetic anomalies with a wide range of reported magnetization directions and paleopole locations. We find that inclination bias partly explains the previously reported anomalously high and low direction uncertainties for two of these anomalies: Reiner Gamma and Airy. Our more robust uncertainties allow us to conclude that four paleopoles are located near the equator. Such low latitudes cannot be explained by true polar wander inferred from other independent datasets, such as the lunar gravity field and the polar hydrogen distribution. This in turn implies that the dynamo axis was once offset from the spin axis.
Enhanced Rainfall‐Induced Shallow Landslide Activity Following Seismic Disturbance—From Triggering to Healing
Authors: Leshchinsky Ben , Lehmann Peter , Or Dani
Published: December 2020

Evidence suggests that following earthquakes, landslide activity, and susceptibility remain elevated for months to years after cessation of shaking. In landslides constrained within the soil mantle, enhanced post‐seismic activity may be attributed to persistence of progressive failure surface development that results in delayed triggering. With subsequent post‐seismic hydrologic disturbance, a commensurate decay in activity over time reflects evacuation of damaged hillslope materials and mechanical healing of colluvial media and vegetation recovery. In this study, we propose a hydromechanical model for representing the interplay of these processes including trends in timing and magnitude of post‐seismic shallow landslide activity. The hydromechanical model considers seismic or hydrologic disturbances as drivers for failure surface development in the soil mantle over a hillslope with commensurate weakening through accumulation of internal compression, shear softening, and loss of root strength. In the absence of well‐instrumented post‐seismic landslide measurement of evolving stress conditions and deformation, predictions were made against a unique field case study where hydrologically induced hillslope failure kinematics and internal compression were measured. The model accounts for seismic disturbances, demonstrating that certain peak ground accelerations directly reduce subsequent rainfall‐induced landslide‐triggering thresholds relative to undisturbed hillslopes. The model framework can be used to describe progressive, post‐seismic landslide activity, demonstrating that consideration of root or soil healing may suppress subsequent landslide triggering and contribute toward recovery to pre‐seismic disturbance levels of strength. Factors such as shear softening, vegetation, and healing are explored in the context of the temporal evolution of landslide rates after a seismic event. The results of this paper show mechanistically how (1) progressive development or cessation of a failure surface in active, post‐seismic landslides may describe elevated post‐seismic landslide rates and (2) that hillslope healing plays a modest role in the magnitude and timescale of attenuated landslide activity.
Controls on Interactions Between Surface Water, Groundwater, and Riverine Vegetation Along Intermittent Rivers and Ephemeral Streams in Arid Regions
Authors: Schilling Oliver S. , Cook Peter G. , Grierson Pauline F. , Dogramaci Shawan , Simmons Craig T.
Published: December 2020

Intermittent rivers and ephemeral streams (IRES) make up the majority of waterways in arid and semi‐arid regions. While the physical underpinnings of surface water‐groundwater (SW‐GW) flow systems are well understood, how ephemerality, hydraulic properties and vegetation interact along IRES is not clear, posing severe challenges to their sustainable management. This study sought to identify the controls for SW‐GW‐vegetation interactions along IRES. To this end, numerical experiments on a quasi‐hypothetical IRES cross‐section with an integrated surface‐subsurface hydrological model were undertaken. The influence of different degrees of ephemerality on infiltration and riverine transpiration was tested by varying the duration of no‐flow periods. The influence of hydraulic conductivity (K), moisture retention capacity, root density, and local rainfall was also explored. Experiments showed that infiltration is controlled by ephemerality and K, with infiltration decreasing rapidly with increasing ephemerality and decreasing K. Transpiration is influenced by a complex interplay between ephemerality, hydraulic properties, and vegetation. While transpiration is strongly controlled by the degree of ephemerality, the capacity of the subsurface to maintain variably saturated conditions can strongly attenuate the effects of ephemerality. A large moisture retention capacity of the subsurface can partly compensate for the reduced infiltration under increasing ephemerality. Transpiration can be as large under ephemeral as under perennial conditions, especially where water table fluctuations exhibit large amplitudes within the zone of high root density. Overall, the results provide important insights into the complex dynamics of IRES and highlight how changes in flow dynamics can have significant impacts beyond instream processes.
Merkel cell carcinoma-derived exosome-shuttle miR-375 induces fibroblast polarization by inhibition of RBPJ and p53
Authors: Fan Kaiji , Spassova Ivelina , Gravemeyer Jan , Ritter Cathrin , Horny Kai , Lange Anja , Gambichler Thilo , Ødum Niels , Schrama David , Schadendorf Dirk , Ugurel Selma , Becker Jürgen C.
Published: December 2020

Merkel cell carcinoma (MCC) is a highly invasive and metastatic skin cancer. While high expression of miR-375 is a characteristic of MCC, it seems not to contribute to the malignant phenotype of MCC cells. miR-375 enrichment in MCC-derived extracellular vesicles suggests its intercellular signaling function. Here, we demonstrate that horizontally transferred miR-375 causes fibroblast polarization toward cancer-associated fibroblasts (CAFs). The polarization is evidenced by phenotypic changes and induction ofα-SMA,CXCL2, andIL-1β. Fibroblast polarization is inhibited by specific antagomirs and mimicked by experimental miR-375 expression. Mechanistically, miR-375 downregulatesRBPJandp53, two key players regulating fibroblast polarization. In clinical MCC samples, in situ hybridization located miR-375 in CAFs, which correlated with high α-SMA protein and lowRBPJandTP53expression; single-cell RNAseq revealed a disparate fibroblast polarization negatively correlating with p53 pathway-related gene expression. Thus, the functional role of miR-375 in MCC is to generate a pro-tumorigenic microenvironment by inducing fibroblast polarization.
Ubiquitination of RIPK1 regulates its activation mediated by TNFR1 and TLRs signaling in distinct manners
Authors: Li Xingyan , Zhang Mengmeng , Huang Xinyue , Liang Wei , Li Ganquan , Lu Xiaojuan , Li Yanxia , Pan Heling , Shi Linyu , Zhu Hong , Qian Lihui , Shan Bing , Yuan Junying
Published: December 2020

RIPK1 is a death-domain (DD) containing kinase involved in regulating apoptosis, necroptosis and inflammation. RIPK1 activation is known to be regulated by its DD-mediated interaction and ubiquitination, though underlying mechanisms remain incompletely understood. Here we show that K627 in human RIPK1-DD and its equivalent K612 in murine RIPK1-DD is a key ubiquitination site that regulates the overall ubiquitination pattern of RIPK1 and its DD-mediated interactions with other DD-containing proteins. K627R/K612R mutation inhibits the activation of RIPK1 and blocks both apoptosis and necroptosis mediated by TNFR1 signaling. However,Ripk1K612R/K612Rmutation sensitizes cells to necroptosis and caspase-1 activation in response to TLRs signaling.Ripk1K612R/K612Rmice are viable, but develop age-dependent reduction of RIPK1 expression, spontaneous intestinal inflammation and splenomegaly, which can be rescued by antibiotic treatment and partially byRipk3deficiency. Furthermore, we show that the interaction of RIPK1 with FADD contributes to suppressing the activation of RIPK3 mediated by TLRs signaling. Our study demonstrates the distinct roles of K612 ubiquitination in mRIPK1/K627 ubiquitination in hRIPK1 in regulating its pro-death kinase activity in response to TNFα and pro-survival activity in response to TLRs signaling.
Uncertainty quantification and composition optimization for alloy additive manufacturing through a CALPHAD-based ICME framework
Authors: Wang Xin , Xiong Wei
Published: December 2020

During powder production, the pre-alloyed powder composition often deviates from the target composition leading to undesirable properties of additive manufacturing (AM) components. Therefore, we developed a method to perform high-throughput calculation and uncertainty quantification by using a CALPHAD-based ICME framework (CALPHAD: calculations of phase diagrams, ICME: integrated computational materials engineering) to optimize the composition, and took the high-strength low-alloy steel (HSLA) as a case study. We analyzed the process–structure–property relationships for 450,000 compositions around the nominal composition of HSLA-115. Properties that are critical for the performance, such as yield strength, impact transition temperature, and weldability, were evaluated to optimize the composition. With the same uncertainty as to the initial composition, and optimized average composition has been determined, which increased the probability of achieving successful AM builds by 44.7%. The present strategy is general and can be applied to other alloy composition optimization to expand the choices of alloy for additive manufacturing. Such a method also calls for high-quality CALPHAD databases and predictive ICME models.
All inkjet-printed perovskite-based bolometers
Authors: Trudeau Charles , Beaupré Patrick , Bolduc Martin , Cloutier Sylvain G.
Published: December 2020

We show flexible bolometer devices produced entirely using digital inkjet printing on polymer substrates. The bolometers consist of a silver interdigital electrode thermistor covered with a methylammonium lead trihalide perovskite absorber layer which shows good absorber characteristics at visible wavelengths. Both the standalone thermistor and the complete bolometer devices show polymer PTC thermistor-like behavior over a temperature range of 17 to 36 °C, with a change in resistance up-to six orders of magnitude over this temperature range. The addition of the perovskite absorber to the thermistor structure provides the illumination-dependent behavior proper to bolometers.
Insights into the mechanisms controlling the residual corrosion rate of borosilicate glasses
Authors: Gin Stephane , Guo Xiaolei , Delaye Jean-Marc , Angeli Frédéric , Damodaran Kamalesh , Testud Véronique , Du Jincheng , Kerisit Sebastien , Kim Seong H.
Published: December 2020

Borosilicate glasses are widely used to confine high-level radioactive wastes. The lifetime of these materials could reach hundreds of thousands of years if leaching of the glass into groundwater enables the formation of a passivating gel layer. Even in this regime, the glass will never stop corroding as thermodynamic equilibrium between glass and solution cannot be achieved. Therefore, accurate predictions of glass durability including passivation, require a deep understanding of the mechanisms controlling the so-called residual rate. However, despite tremendous efforts, these mechanisms remain poorly understood. Here, focusing on the behavior of the soluble elements of the International Simple Glass (B, Na, and Ca), we show that the residual rate is controlled by the behavior of B, a glass former supposed to dissolve instantaneously when in contact with water and thus widely considered as an ideal tracer. We then demonstrate that B release is controlled by multiple processes highly dependent on the pH. At the beginning of the passivating layer formation, the hydrolysis of B-O-Si linkages is rate-limiting and has an activation energy of ∼60 kJ mol−1, a value slightly lower than that for breaking Si-O-Si linkages. Once the fraction of closed pores resulting from gel restructuring is high enough, then diffusion of both reactants (water molecules) and some products (mainly Baq, Caaq) through the growing gel layer becomes rate-limiting. Consequently, B and Ca accumulate in an inner layer referred to as the active zone, with potential feedback on the B-O-Si hydrolysis. A new paradigm, including B as a key element of the system, is proposed to develop a comprehensive model for the corrosion of borosilicate glass.
Comparative proteomic analysis highlights metabolic dysfunction in α-synucleinopathy
Authors: Sarkar Souvarish , Murphy Michael A. , Dammer Eric B. , Olsen Abby L. , Rangaraju Srikant , Fraenkel Ernest , Feany Mel B.
Published: December 2020

The synaptic protein α-synuclein is linked through genetics and neuropathology to the pathogenesis of Parkinson’s disease and related disorders. However, the mechanisms by which α-synuclein influences disease onset and progression are incompletely understood. To identify pathogenic pathways and therapeutic targets we performed proteomic analysis in a highly penetrant new Drosophila model of α-synucleinopathy. We identified 476 significantly upregulated and 563 significantly downregulated proteins in heads from α-synucleinopathy model flies compared to controls. We then used multiple complementary analyses to identify and prioritize genes and pathways within the large set of differentially expressed proteins for functional studies. We performed Gene Ontology enrichment analysis, integrated our proteomic changes with human Parkinson’s disease genetic studies, and compared the α-synucleinopathy proteome with that of tauopathy model flies, which are relevant to Alzheimer’s disease and related disorders. These approaches identified GTP cyclohydrolase (GCH1) and folate metabolism as candidate mediators of α-synuclein neurotoxicity. In functional validation studies, we found that the knockdown of Drosophila Gch1 enhanced locomotor deficits in α-synuclein transgenic flies, while folate supplementation protected from α-synuclein toxicity. Our integrative analysis suggested that mitochondrial dysfunction was a common downstream mediator of neurodegeneration. Accordingly, Gch1 knockdown enhanced metabolic dysfunction in α-synuclein transgenic fly brains while folate supplementation partially normalized brain bioenergetics. Here we outline and implement an integrative approach to identify and validate potential therapeutic pathways using comparative proteomics and genetics and capitalizing on the facile genetic and pharmacological tools available in Drosophila.
Automatic recognition of murmurs of ventricular septal defect using convolutional recurrent neural networks with temporal attentive pooling
Authors: Wang Jou-Kou , Chang Yun-Fan , Tsai Kun-Hsi , Wang Wei-Chien , Tsai Chang-Yen , Cheng Chui-Hsuan , Tsao Yu
Published: December 2020

Recognizing specific heart sound patterns is important for the diagnosis of structural heart diseases. However, the correct recognition of heart murmur depends largely on clinical experience. Accurately identifying abnormal heart sound patterns is challenging for young and inexperienced clinicians. This study is aimed at the development of a novel algorithm that can automatically recognize systolic murmurs in patients with ventricular septal defects (VSDs). Heart sounds from 51 subjects with VSDs and 25 subjects without a significant heart malformation were obtained in this study. Subsequently, the soundtracks were divided into different training and testing sets to establish the recognition system and evaluate the performance. The automatic murmur recognition system was based on a novel temporal attentive pooling-convolutional recurrent neural network (TAP-CRNN) model. On analyzing the performance using the test data that comprised 178 VSD heart sounds and 60 normal heart sounds, a sensitivity rate of 96.0% was obtained along with a specificity of 96.7%. When analyzing the heart sounds recorded in the second aortic and tricuspid areas, both the sensitivity and specificity were 100%. We demonstrated that the proposed TAP-CRNN system can accurately recognize the systolic murmurs of VSD patients, showing promising potential for the development of software for classifying the heart murmurs of several other structural heart diseases.
Characterization, biological evaluation and molecular docking of mulberry fruit pectin
Authors: Kumar R. Venkatesh , Srivastava Devika , Singh Vandana , Kumar Umesh , Vishvakarma Vijay Kumar , Singh Prashant , Kumar Dinesh , Kumar Rajesh
Published: December 2020

Contemplating the exemplary benefits of pectin on human health, we precisely characterized and evaluated the antibacterial and anticancer activities from purified Mulberry Fruit Pectins (MFP). Here, we tested BR-2 and S-13 varieties of mulberry fruit pectins against six bacterial strains and two human cancer cell lines (HT-29 and Hep G-2), using MIC and an in vitro cell-based assay respectively. The BR-2 mulberry fruit pectin performs superior to S-13 by inhibiting strong bacterial growth (MIC = 500–1000 μg/mL) against tested bacterial strains and cytotoxic activities at the lowest concentration (10 µg/ml) against the Hep G-2 cell line. However, both tested drugs failed to exhibit cytotoxicity on the human colon cancer cell line (HT-29). Based on molecular interaction through docking, pectin binds effectively with the receptors (1e3g, 3t0c, 5czz, 6j7l, 6v40, 5ibs, 5zsy, and 6ggb) and proven to be a promising antimicrobial and anti-cancer agents. The pursuit of unexploited drugs from mulberry fruit pectin will potentially combat against bacterial and cancer diseases. Finally, future perspectives of MFP for the treatment of many chronic diseases will help immensely due to their therapeutic properties.
Improving wear resistance of plasma-sprayed calcia and magnesia-stabilized zirconia mixed coating: roles of phase stability and microstructure
Authors: Hafez Mohamed Abd-Elsattar , Akila Sameh Ahmed , Khedr Mohamed Atta , Khalil Ali Saeid
Published: December 2020

The phase stability and microstructure of ZrO2–5CaO and ZrO2–24MgO mixed coating (wt%) by air plasma spraying on 304 stainless steel substrates were investigated. A Ni–5Al (wt%) metallic bond coating was firstly sprayed between the substrate and the ceramic top layer. The results were compared with the individual coatings of ZrO2–5CaO and ZrO2–24MgO for a better understanding of the correlation between their microstructures and mechanical properties. Mixed zirconia coating was found to have a mixture of cubic and tetragonal phases that stabilized under different plasma spray conditions. Microscopic observations and elemental composition analysis of as-sprayed mixed coating showed that modified ceramic-matrix grains had been formed. Microsized ZrO2–5CaO particles were embedded in the matrix grain creating an intragranular microstructure. Results indicated that ceramic-matrix grains provided a diffusion barrier for the growth of oxides induced stress near and onto the bond layer that reduced cracks, thereby overcoming the top delamination of the ceramic coating. Moreover, disparity in wear resistance and microhardness behavior of the coatings was influenced by initial feedstock powder and matrix microstructures. Improvement in the wear resistance of the mixed zirconia coating was attributed to a decrease in oxide content, which resulted in an increase in intersplat cohesive strength.
Fully automated detection and segmentation of intracranial aneurysms in subarachnoid hemorrhage on CTA using deep learning
Authors: Shahzad Rahil , Pennig Lenhard , Goertz Lukas , Thiele Frank , Kabbasch Christoph , Schlamann Marc , Krischek Boris , Maintz David , Perkuhn Michael , Borggrefe Jan
Published: December 2020

In aneurysmal subarachnoid hemorrhage (aSAH), accurate diagnosis of aneurysm is essential for subsequent treatment to prevent rebleeding. However, aneurysm detection proves to be challenging and time-consuming. The purpose of this study was to develop and evaluate a deep learning model (DLM) to automatically detect and segment aneurysms in patients with aSAH on computed tomography angiography. In this retrospective single-center study, three different DLMs were trained on 68 patients with 79 aneurysms treated for aSAH (2016–2017) using five-fold-cross-validation. Their outputs were combined to a single DLM via ensemble-learning. The DLM was evaluated on an independent test set consisting of 185 patients with 215 aneurysms (2010–2015). Independent manual segmentations of aneurysms in a 3D voxel-wise manner by two readers (neurosurgeon, radiologist) provided the reference standard. For aneurysms > 30 mm3 (mean diameter of ~ 4 mm) on the test set, the DLM provided a detection sensitivity of 87% with false positives (FPs)/scan of 0.42. Automatic segmentations achieved a median dice similarity coefficient (DSC) of 0.80 compared to the reference standard. Aneurysm location (anterior vs. posterior circulation; P = .07) and bleeding severity (Fisher grade ≤ 3 vs. 4; P = .33) did not impede detection sensitivity or segmentation performance. For aneurysms > 100 mm3 (mean diameter of ~ 6 mm), a sensitivity of 96% with DSC of 0.87 and FPs/scan of 0.14 were obtained. In the present study, we demonstrate that the proposed DLM detects and segments aneurysms > 30 mm3 in patients with aSAH with high sensitivity independent of cerebral circulation and bleeding severity while producing FP findings of less than one per scan. Hence, the DLM can potentially assist treating physicians in aSAH by providing automated detection and segmentations of aneurysms.
Prevalence of Ascaris lumbricoides in contaminated faecal samples of children residing in urban areas of Lahore, Pakistan
Authors: Ali Shahida Azhar , Niaz Sadaf , Aguilar-Marcelino Liliana , Ali Wajid , Ali Majid , Khan Adil , Amir Sohail , Nasreen  , Alanazi Abdullah D. , Cossio-Bayugar Raquel , Amaro-Estrada Itzel
Published: December 2020

Ascariasis is a common public health problem of preschool and primary school children in developing countries like Pakistan. The aim of the present study was to determine the prevalence and pattern of Ascaris lumbericoides (A. lumbricoides) infection among children residing in urban areas of Lahore, to provide information on ascariasis to promote awareness and prevention programs between the participants specially on the months or season of higher prevalence. To investigate the prevalence of Ascaris Lumbricoides in the contaminated faecal samples of children residing in urban areas of Lahore, a study was conducted from November 2010 to October 2012 and we collected 3600 stratified faecal samples from six urban study areas. Overall 32/3600 (0.88%) prevalence of fecal samples was found positive for eggs of Ascaris lumbricoides. Area wise highest presence positivity 1.67% was observed in Allama Iqbal Town followed by 1.17% in Samanabad, 1.00% in Wapda Town, 1.00% in Gulberg, 0.50% in Cantt, and the lowest 0.00% in Valencia Town respectively (p < 0.001) The highest month wise positivity prevalence 3/300 (3.33%) (p < 0.001) was observed in the month of September that gradually declined up to 0/300 (0.00%) in the month of March. The results reveal that urban areas of Lahore are susceptible to Ascaris Lubricoides infection and the highest prevalence were observed autumn on the month of September.
Automatic seizure detection based on imaged-EEG signals through fully convolutional networks
Authors: Gómez Catalina , Arbeláez Pablo , Navarrete Miguel , Alvarado-Rojas Catalina , Le Van Quyen Michel , Valderrama Mario
Published: December 2020

Seizure detection is a routine process in epilepsy units requiring manual intervention of well-trained specialists. This process could be extensive, inefficient and time-consuming, especially for long term recordings. We proposed an automatic method to detect epileptic seizures using an imaged-EEG representation of brain signals. To accomplish this, we analyzed EEG signals from two different datasets: the CHB-MIT Scalp EEG database and the EPILEPSIAE project that includes scalp and intracranial recordings. We used fully convolutional neural networks to automatically detect seizures. For our best model, we reached average accuracy and specificity values of 99.3% and 99.6%, respectively, for the CHB-MIT dataset, and corresponding values of 98.0% and 98.3% for the EPILEPSIAE patients. For these patients, the inclusion of intracranial electrodes together with scalp ones increased the average accuracy and specificity values to 99.6% and 58.3%, respectively. Regarding the other metrics, our best model reached average precision of 62.7%, recall of 58.3%, F-measure of 59.0% and AP of 54.5% on the CHB-MIT recordings, and comparatively lowers performances for the EPILEPSIAE dataset. For both databases, the number of false alarms per hour reached values less than 0.5/h for 92% of the CHB-MIT patients and less than 1.0/h for 80% of the EPILEPSIAE patients. Compared to recent studies, our lightweight approach does not need any estimation of pre-selected features and demonstrates high performances with promising possibilities for the introduction of such automatic methods in the clinical practice.
Genome-wide association identifies several QTLs controlling cysteine and methionine content in soybean seed including some promising candidate genes
Authors: Malle Sidiki , Eskandari Milad , Morrison Malcolm , Belzile François
Published: December 2020

Soybean is an important source of protein, oil and carbohydrates, as well as other beneficial nutrients. A major function of proteins in nutrition is to supply adequate amounts of amino acids. Although they are essential for human nutrition, the sulfur-containing amino acids cysteine (Cys) and methionine (Met) are often limited and the genetic control of their content in soybean seeds is poorly characterized. This study aimed to characterize the phenotypic variation and identify quantitative trait loci (QTL) associated with Cys and Met content in a core set of 137 soybean lines, representative of the genetic diversity among Canadian short-season soybean, spanning maturity groups 000-II (MG000-II). Significant phenotypic differences were found among these lines for Cys, Met and Cys + Met content. Using both a mixed linear model and six multi-locus methods with a catalogue of 2.18 M SNPs, we report a total of nine QTLs and seventeen QTNs of which seven comprise promising candidate genes. This work allowed us to reproducibly detect multiple novel loci associated with sulfur-containing amino acid content. The markers and genes identified in this study may be useful for soybean genetic improvement aiming to increase Cys and Met content.
Proteomic profile of extracellular vesicles released by Lactiplantibacillus plantarum BGAN8 and their internalization by non-polarized HT29 cell line
Authors: Bajic Svetlana Sokovic , Cañas Maria-Alexandra , Tolinacki Maja , Badia Josefa , Sánchez Borja , Golic Natasa , Margolles Abelardo , Baldomá Laura , Ruas-Madiedo Patricia
Published: December 2020

In recent years the role of extracellular vesicles (EVs) of Gram-positive bacteria in host-microbe cross-talk has become increasingly appreciated, although the knowledge of their biogenesis, release and host-uptake is still limited. The aim of this study was to characterize the EVs released by the dairy isolate Lactiplantibacillus plantarum BGAN8 and to gain an insight into the putative mechanism of EVs uptake by intestinal epithelial cells. The cryo-TEM observation undoubtedly demonstrated the release of EVs (20 to 140 nm) from the surface of BGAN8, with exopolysaccharides seems to be part of EVs surface. The proteomic analysis revealed that the EVs are enriched in enzymes involved in central metabolic pathways, such as glycolysis, and in membrane components with the most abundant proteins belonging to amino acid/peptide ABC transporters. Putative internalization pathways were evaluated in time-course internalization experiments with non-polarized HT29 cells in the presence of inhibitors of endocytic pathways: chlorpromazine and dynasore (inhibitors of clathrin-mediated endocytosis—CME) and filipin III and nystatin (disrupting lipid rafts). For the first time, our results revealed that the internalization was specifically inhibited by dynasore and chlorpromazine but not by filipin III and nystatin implying that one of the entries of L. plantarum vesicles was through CME pathway.
Unveiling giant hidden Rashba effects in two-dimensional Si2Bi2
Authors: Lee Seungjun , Kwon Young-Kyun
Published: December 2020

Recently, it has been known that the hidden Rashba (R-2) effect in two-dimensional materials gives rise to a physical phenomenon called spin-layer locking (SLL). However, not only its underlying fundamental mechanism has been unclear, but also there are only a few materials exhibiting weak SLL. Here, through the first-principles density functional theory and model Hamiltonian calculation, we reveal that the R-2 SLL can be determined by the competition between the sublayer–sublayer interaction and the spin–orbit coupling, which is related to the Rashba strength. In addition, the orbital angular momentum distribution is another crucial point to realize the strong R-2 SLL. We propose that a 2D material Si2Bi2 possesses an ideal condition for the strong R-2 SLL, whose Rashba strength is evaluated to be 2.16 eVÅ, which is the greatest value ever observed in 2D R-2 materials to the best of our knowledge. Furthermore, we reveal that the interlayer interaction in a bilayer structure ensures R-2 states spatially farther apart, implying a potential application in spintronics.
Differential longitudinal establishment of human fecal bacterial communities in germ-free porcine and murine models
Authors: Aluthge Nirosh D. , Tom Wesley A. , Bartenslager Alison C. , Burkey Thomas E. , Miller Phillip S. , Heath Kelly D. , Kreikemeier-Bower Craig , Kittana Hatem , Schmaltz Robert J. , Ramer-Tait Amanda E. , Fernando Samodha C.
Published: December 2020

The majority of microbiome studies focused on understanding mechanistic relationships between the host and the microbiota have used mice and other rodents as the model of choice. However, the domestic pig is a relevant model that is currently underutilized for human microbiome investigations. In this study, we performed a direct comparison of the engraftment of fecal bacterial communities from human donors between human microbiota-associated (HMA) piglet and mouse models under identical dietary conditions. Analysis of 16S rRNA genes using amplicon sequence variants (ASVs) revealed that with the exception of early microbiota from infants, the more mature microbiotas tested established better in the HMA piglets compared to HMA mice. Of interest was the greater transplantation success of members belonging to phylum Firmicutes in the HMA piglets compared to the HMA mice. Together, these results provide evidence for the HMA piglet model potentially being more broadly applicable for donors with more mature microbiotas while the HMA mouse model might be more relevant for developing microbiotas such as those of infants. This study also emphasizes the necessity to exercise caution in extrapolating findings from HMA animals to humans, since up to 28% of taxa from some donors failed to colonize either model.
The human primary somatosensory cortex encodes imagined movement in the absence of sensory information
Authors: Jafari Matiar , Aflalo Tyson , Chivukula Srinivas , Kellis Spencer Sterling , Salas Michelle Armenta , Norman Sumner Lee , Pejsa Kelsie , Liu Charles Yu , Andersen Richard Alan
Published: December 2020

Classical systems neuroscience positions primary sensory areas as early feed-forward processing stations for refining incoming sensory information. This view may oversimplify their role given extensive bi-directional connectivity with multimodal cortical and subcortical regions. Here we show that single units in human primary somatosensory cortex encode imagined reaches in a cognitive motor task, but not other sensory–motor variables such as movement plans or imagined arm position. A population reference-frame analysis demonstrates coding relative to the cued starting hand location suggesting that imagined reaching movements are encoded relative to imagined limb position. These results imply a potential role for primary somatosensory cortex in cognitive imagery, engagement during motor production in the absence of sensation or expected sensation, and suggest that somatosensory cortex can provide control signals for future neural prosthetic systems.
Instantaneous generation of protein hydration properties from static structures
Authors: Ghanbarpour Ahmadreza , Mahmoud Amr H. , Lill Markus A.
Published: December 2020

Complex molecular simulation methods are typically required to calculate the thermodynamic properties of biochemical systems. One example thereof is the thermodynamic profiling of (de)solvation of proteins, which is an essential driving force for protein-ligand and protein-protein binding. The thermodynamic state of water molecules depends on its enthalpic and entropic components; the latter is governed by dynamic properties of the molecule. Here, we developed, to the best of our knowledge, two novel machine learning methods based on deep neural networks that are able to generate the converged thermodynamic state of dynamic water molecules in the heterogeneous protein environment based solely on the information of the static protein structure. The applicability of our machine learning methods to predict the hydration information is demonstrated in two different studies, the qualitative analysis and quantitative prediction of structure-activity relationships, and the prediction of protein-ligand binding modes.
Detection of Disease-associated Mutations and Biomarkers Using Next-generation Sequencing
Authors: Yan Jian , Wang Xi
Published: December 2020

Next-generation sequencing is a fast-developing field that accelerates the pace of functional genomics. In precision medicine, it enables quick and precise identification of causal mutations and dramatically improves clinical outcome. In this chapter, we will review the next-generation-sequencing-based technologies and strategies for detection of disease-associated mutations and identification of novel biomarkers that can be used in precision medicine. We will cover topics in detection of genomic mutations in protein coding regions and non-coding regulatory elements, detection of circulating tumor DNA, and studies of human and microbiome interactions, as well as applications of bioinformatics in biomarker detection and identification.
Immunological Detection Methods for Biomarkers
Authors: Lim King Hoo , Dotse Eunice , Chow Kwan T.
Published: December 2020

Immunological detection methods play an important role in identifying specific biomarkers for disease diagnosis, prognosis, and treatment in precision medicine. With the recent attention shifted towards personalized treatments, immunological detection methods provide a platform for acquiring precise and accurate information using immunoassays. These assays operate on the principle of antigen–antibody interaction to identify disease-specific biomarkers in clinical application. In immunoassays, the antibody–antigen complex is detected through end-reaction outputs that can be analyzed both qualitatively and quantitatively. This book chapter discusses common immunoassays employed in clinical and research settings, emphasizing specificity and accuracy of each method. The chapter will also highlight some recent advancements in immunoassay technology.
Droplet Microfluidics for Precision Medicine
Authors: Lai Sze Nga , Ouyang Xiaofei , Zheng Bo
Published: December 2020

In recent years, droplet microfluidics has become an important tool for the development of precision medicine. Droplets are uniformly and efficiently produced in microfluidic devices on the scale of picoliters to nanoliters. The droplets act as individual microreactors and facilitate high throughput and quantitative analysis, thus providing an attractive platform for the analysis of biomolecules or single cells in precision medicine. In this chapter, we will review the principles and techniques of droplet microfluidics, and the important applications of droplet microfluidics for precision medicine.
Highly sensitive electrochemical determination of methotrexate based on a N-doped hollow nanocarbon sphere modified electrode
Authors: Li Jiafeng , Chen Dongdong , Zhang Tao , Chen Guolong
Published: December 2020

A simple and highly sensitive electrochemical sensor for methotrexate was developed by preparing N-doped hollow nanocarbon spheres.
One-pot crystallization of two 1,4-cyclohexanedicarboxylate-based tetranuclear Cu(ii) compounds and their DNA binding affinities
Authors: Akhtaruzzaman  , Mohammad Mukti , Khan Samim , Dutta Basudeb , Maity Suvendu , Naaz Sanobar , Alam Seikh Mafiz , Ghosh Prasanta , Islam Md. Maidul , Mir Mohammad Hedayetullah
Published: December 2020

Two new tetranuclear Cu(ii) compounds have been synthesized using flexible linker 1,4-cyclohexanedicarboxylic acid in an one-pot crystallization which exhibit dissimilar affinities to DNA binding.
Pulsed neutron imaging for differentiation of ice and liquid water towards fuel cell vehicle applications
Authors: Higuchi Yuki , Setoyama Daigo , Isegawa Kazuhisa , Tsuchikawa Yusuke , Matsumoto Yoshihiro , Parker Joseph Don , Shinohara Takenao , Nagai Yasutaka
Published: December 2020

Water/ice identification images throughout the thawing process of ice in a metal capillary by using a pulsed neutron source.
A new method of isotope enrichment and separation: preferential embedding of heavier isotopes of Xe into amorphous solid water
Authors: Gibson K. D. , Sibener S. J.
Published: December 2020

Schematic representation of isotope embedding and capture in a cryogenic matrix. Preferential capture has been demonstrated for heavier isotopes as compared to lighter ones.
Lipophilic Re(CO)3pyca complexes for Mid-IR imaging applications
Authors: Schrage Briana R. , Frisinger Baylee R. , Schmidtke Sobeck Sarah J. , Ziegler Christopher J.
Published: December 2020

The one pot reaction of Re(CO)3X, pyridine-2-carboxyaldehyde, and primary aliphatic amines results in the formation of lipophilic Re(CO)3 compounds that could be used as IR dyes.
Interactive transgenerational effects of polystyrene nanoplastics and ethylhexyl salicylate on zebrafish
Authors: Zhou Ranran , Lu Guanghua , Yan Zhenhua , Jiang Runren , Sun Yu , Zhang Peng
Published: December 2020

Effects of PS-NPs on bioaccumulation and transgenerational toxicity of EHS to zebrafish.
Time-resolved pump–probe spectroscopy with spectral domain ghost imaging
Authors: Li Siqi , Driver Taran , Alexander Oliver , Cooper Bridgette , Garratt Douglas , Marinelli Agostino , Cryan James P. , Marangos Jonathan P.
Published: December 2020

We show that spectral ghost imaging can be applied to time-resolved pump–probe measurements.
Correction: A novel green emitting NaGdF4:Dy3+,Ho3+ phosphor with tunable photoluminescence
Authors: Guan Hongxia , Li Yunfei , Liu Guixia
Published: December 2020

Correction for ‘A novel green emitting NaGdF4:Dy3+,Ho3+ phosphor with tunable photoluminescence’ by Hongxia Guan et al., New J. Chem., 2020, 44, 16211–16217, DOI: 10.1039/D0NJ03030A.
Correction: Circumvention of common labelling artefacts using secondary nanobodies
Authors: Sograte-Idrissi Shama , Schlichthaerle Thomas , Duque-Afonso Carlos J. , Alevra Mihai , Strauss Sebastian , Moser Tobias , Jungmann Ralf , Rizzoli Silvio O. , Opazo Felipe
Published: December 2020

Correction for ‘Circumvention of common labelling artefacts using secondary nanobodies’ by Shama Sograte-Idrissi et al., Nanoscale, 2020, 12, 10226–10239, DOI: 10.1039/D0NR00227E.
Copper catalysts for photo- and electro-catalytic hydrogen production
Authors: Abudayyeh Abdullah M. , Schott Olivier , Feltham Humphrey L. C. , Hanan Garry S. , Brooker Sally
Published: December 2020

Square planar1, square pyramidal2and trigonal bipyramidal3copper complexes are poor catalysts for hydrogen evolution (HER) under photocatalytic conditions, whereas1is, or forms, a good and enduring electrocatalyst for HER, but2and3do not.
A generalized tube model of rubber elasticity
Authors: Darabi Ehsan , Itskov Mikhail
Published: December 2020

A new type of micro-mechanically motivated chain network model for rubber-like materials is proposed. The model demonstrates how the local molecular constraints modify under deformation and shows the impact of these changes on the macroscopic elasticity of the material.
Mitochondria and lysosome-targetable fluorescent probes for hydrogen peroxide
Authors: Wei Yongchun , Liu Yuanyuan , He Yongqi , Wang Yanfeng
Published: December 2020

This paper reviews the fluorescent probes used for H2O2 detection in mitochondria and lysosomes and discusses the design methods, response mechanisms and applications.