bluuebunny/crossref_metadata_2025_split huggingface dataset:
Purification of HCC-specific extracellular vesicles on nanosubstrates for early HCC detection by digital scoring
Authors: Sun Na , Lee Yi-Te , Zhang Ryan Y. , Kao Rueihung , Teng Pai-Chi , Yang Yingying , Yang Peng , Wang Jasmine J. , Smalley Matthew , Chen Pin-Jung , Kim Minhyung , Chou Shih-Jie , Bao Lirong , Wang Jing , Zhang Xinyue , Qi Dongping , Palomique Juvelyn , Nissen Nicolas , Han Steven-Huy B. , Sadeghi Saeed , Finn Richard S. , Saab Sammy , Busuttil Ronald W. , Markovic Daniela , Elashoff David , Yu Hsiao-hua , Li Huiying , Heaney Anthony P. , Posadas Edwin , You Sungyong , Yang Ju Dong , Pei Renjun , Agopian Vatche G. , Tseng Hsian-Rong , Zhu Yazhen 
Published: September 2020

AbstractWe report a covalent chemistry-based hepatocellular carcinoma (HCC)-specific extracellular vesicle (EV) purification system for early detection of HCC by performing digital scoring on the purified EVs. Earlier detection of HCC creates more opportunities for curative therapeutic interventions. EVs are present in circulation at relatively early stages of disease, providing potential opportunities for HCC early detection. We develop an HCC EV purification system (i.e., EV Click Chips) by synergistically integrating covalent chemistry-mediated EV capture/release, multimarker antibody cocktails, nanostructured substrates, and microfluidic chaotic mixers. We then explore the translational potential of EV Click Chips using 158 plasma samples of HCC patients and control cohorts. The purified HCC EVs are subjected to reverse-transcription droplet digital PCR for quantification of 10 HCC-specific mRNA markers and computation of digital scoring. The HCC EV-derived molecular signatures exhibit great potential for noninvasive early detection of HCC from at-risk cirrhotic patients with an area under receiver operator characteristic curve of 0.93 (95% CI, 0.86 to 1.00; sensitivity = 94.4%, specificity = 88.5%).
Single pulse all-optical toggle switching of magnetization without gadolinium in the ferrimagnet Mn2RuxGa
Authors: Banerjee C. , Teichert N. , Siewierska K. E. , Gercsi Z. , Atcheson G. Y. P. , Stamenov P. , Rode K. , Coey J. M. D. , Besbas J. 
Published: September 2020

AbstractEnergy-efficient control of magnetization without the help of a magnetic field is a key goal of spintronics. Purely heat-induced single-pulse all-optical toggle switching has been demonstrated, but so far only in Gd-based amorphous ferrimagnet films. In this work, we demonstrate toggle switching in films of the half-metallic ferrimagnetic Heusler alloys Mn2RuxGa, which have two crystallographically-inequivalent Mn sublattices. Moreover, we observe the switching at room temperature in samples that are immune to external magnetic fields in excess of 1 T, provided they exhibit a compensation point above room temperature. Observation of the effect in compensated ferrimagnets without Gd challenges our understanding of all-optical switching. The dynamic behavior indicates that Mn2RuxGa switches in 2 ps or less. Our findings widen the basis for fast optical switching of magnetization and break new ground for engineered materials that can be used for nonvolatile ultrafast switches using ultrashort pulses of light.
Incorporation of biologic factors for the staging of de novo stage IV breast cancer
Authors: He Zhen-Yu , Lian Chen-Lu , Wang Jun , Lei Jian , Hua Li , Zhou Juan , Wu San-Gang 
Published: September 2020

AbstractThis study aimed to investigate the prognostic value of biological factors, including histological grade, estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor-2 (HER2) status in de novo stage IV breast cancer. Based on eligibility, patient data deposited between 2010 and 2014 were collected from the surveillance, epidemiology, and end results database. The receiver operating characteristics curve, Kaplan–Meier analysis, and Cox proportional hazard analysis were used for analysis. We included 8725 patients with a median 3-year breast cancer-specific survival (BCSS) of 52.6%. Higher histologic grade, HER2-negative, ER-negative, and PR-negative disease were significantly associated with lower BCSS in the multivariate prognostic analysis. A risk score staging system separated patients into four risk groups. The risk score was assigned according to a point system: 1 point for grade 3, 1 point if hormone receptor-negative, and 1 point if HER2-negative. The 3-year BCSS was 76.3%, 64.5%, 48.5%, and 23.7% in patients with 0, 1, 2, and 3 points, respectively, with a median BCSS of 72, 52, 35, and 16 months, respectively (P < 0.001). The multivariate prognostic analysis showed that the risk score staging system was an independent prognostic factor associated with BCSS. Patients with a higher risk score had a lower BCSS. Sensitivity analyses replicated similar findings after stratification according to tumor stage, nodal stage, the sites of distant metastasis, and the number of distant metastasis. In conclusion, our risk score staging system shows promise for the prognostic stratification of de novo stage IV breast cancer.
Interplay between $$k$$-core and community structure in complex networks
Authors: Malvestio Irene , Cardillo Alessio , Masuda Naoki 
Published: September 2020

AbstractThe organisation of a network in a maximal set of nodes having at least k neighbours within the set, known as $$k$$
k
-core decomposition, has been used for studying various phenomena. It has been shown that nodes in the innermost $$k$$
k
-shells play a crucial role in contagion processes, emergence of consensus, and resilience of the system. It is known that the $$k$$
k
-core decomposition of many empirical networks cannot be explained by the degree of each node alone,
or equivalently, random graph models that preserve the degree of each node (i.e., configuration model). Here we study the $$k$$
k
-core decomposition of some empirical networks as well as that of some randomised counterparts, and examine the extent to which the $$k$$
k
-shell structure of the networks can be accounted for by the community structure.
We find that preserving the community structure in the randomisation process is crucial for generating networks whose $$k$$
k
-core decomposition is close to the empirical one. We also highlight the existence, in some networks, of a concentration of the nodes in the innermost $$k$$
k
-shells into a small number of communities.
Computational fluid dynamics model and flow resistance characteristics of Jatropha curcas L xylem vessel
Authors: Xu Tianyu , Zhang Lixiang , Li Ze 
Published: September 2020

AbstractXylem vessels are the channels used for water transport inJatropha curcasL. Vessel complexity has a great influence on water transport. Therefore, using anatomical experiments and numerical simulations, the water transport characteristics ofJ. curcasL xylem vessels with perforation plate and secondary wall thickening (pit structures) were analyzed. The results showed that the xylem vessel inJ. curcasprovided a low resistance path. The xylem vessel resistance was composed of three elements: smooth vessels, secondary wall thickening and perforation plate. The proportion of smooth vessel resistance was the largest, accounting for 66.20% of the total resistance. Then the secondary wall thickening resistance accounted for 30.20% of the total resistance, and finally the perforation plate resistance accounted for 3.60% of the total resistance. The total resistance of the vessel model was positively correlated with the pit depth, perforation plate height and perforation plate width and negatively correlated with the vessel inner diameter and pit membrane permeability. The vessel inner diameter and the pit depth had a great influence on the total resistance. The total resistance of the vessel inner diameter of 52 µm was 89.15% higher than that of 61 µm, the total resistance of the pit depth of 5.6 µm was 21.98% higher than that of 2.6 µm. The pit structure in the secondary wall thickening caused the vessel to be transported radially, and the radial transmission efficiency of the vessel was positively correlated with the pit depth and pit membrane permeability and negatively correlated with the vessel inner diameter. The pit membrane permeability had the greatest influence on the radial transmission efficiency, and its radial transmission efficiency was 0–5.09%.
Long-term effects of western diet consumption in male and female mice
Authors: Hasegawa Yu , Chen Shin-Yu , Sheng Lili , Jena Prasant Kumar , Kalanetra Karen M. , Mills David A. , Wan Yu-Jui Yvonne , Slupsky Carolyn M. 
Published: September 2020

AbstractLong-term consumption of a diet with excessive fat and sucrose (Western diet, WD) leads to an elevated risk of obesity and metabolic syndrome in both males and females. However, there are sexual dimorphisms in metabolism which are apparent when considering the prevalence of complications of metabolic syndrome, such as non-alcoholic fatty liver disease. This study aimed to elucidate the impact of a WD on the metabolome and the gut microbiota of male and female mice at 5, 10, and 15 months to capture the dynamic and comprehensive changes brought about by diet at different stages of life. Here we show that there are important considerations of age and sex that should be considered when assessing the impact of diet on the gut microbiome and health.
Quantitative proteomic analysis of the tizoxanide effect in vero cells
Authors: Yamamoto K. A. , Blackburn K. , Migowski E. , Goshe M. B. , Brown D. T. , Ferreira D. F. , Soares M. R. 
Published: September 2020

AbstractNitazoxanide (NTZ) is effective against helminths and numerous microorganisms, including bacteria and viruses. In vivo, NTZ is metabolized into Tizoxanide (TIZ), which is the active circulating metabolite. With the emergence of SARS-Cov-2 as a Pandemic agent, NTZ became one of the molecules already approved for human use to engage clinical trials, due to results in vitro showing that NTZ was highly effective against the SARS-Cov-2, agent of COVID-19. There are currently several ongoing clinical trials mainly in the USA and Brazil involving NTZ due not only to the in vitro results, but also for its long-known safety. Here, we study the response of Vero cells to TIZ treatment and unveil possible mechanisms for its antimicrobial effect, using a label-free proteomic approach (LC/MS/MS) analysis to compare the proteomic profile between untreated- and TIZ-treated cells. Fifteen differentially expressed proteins were observed related to various biological processes, including translation, intracellular trafficking, RNA processing and modification, and signal transduction. The broad antimicrobial range of TIZ points towards its overall effect in lowering cell metabolism and RNA processing and modification. The decreased levels of FASN, HNRNPH and HNRNPK with the treatment appear to be important for antiviral activity.
TRPV6 calcium channel directs homeostasis of the mammary epithelial sheets and controls epithelial mesenchymal transition
Authors: Kärki Tytti , Rajakylä Eeva Kaisa , Acheva Anna , Tojkander Sari 
Published: September 2020

AbstractEpithelial integrity is lost upon cancer progression as cancer cells detach from the primary tumor site and start to invade to the surrounding tissues. Invasive cancers of epithelial origin often express altered levels of TRP-family cation channels. Upregulation of TRPV6 Ca2+-channel has been associated with a number of human malignancies and its high expression in breast cancer has been linked to both proliferation and invasive disease. The mechanisms behind the potential of TRPV6 to induce invasive progression have, however, not been well elucidated. Here we show that TRPV6 is connected to both E-cadherin-based adherens junctions and intracellular cytoskeletal structures. Loss of TRPV6 from normal mammary epithelial cells led to disruption of epithelial integrity and abnormal 3D-mammo sphere morphology. Furthermore, expression level of TRPV6 was tightly linked to the levels of common EMT markers, suggesting that TRPV6 may have a role in the mesenchymal invasion of breast cancer cells. Thus, either too low or too high TRPV6 levels compromise homeostasis of the mammary epithelial sheets and may promote the progression of pathophysiological conditions.
Optimizing a quantum reservoir computer for time series prediction
Authors: Kutvonen Aki , Fujii Keisuke , Sagawa Takahiro 
Published: September 2020

AbstractQuantum computing and neural networks show great promise for the future of information processing. In this paper we study a quantum reservoir computer (QRC), a framework harnessing quantum dynamics and designed for fast and efficient solving of temporal machine learning tasks such as speech recognition, time series prediction and natural language processing. Specifically, we study memory capacity and accuracy of a quantum reservoir computer based on the fully connected transverse field Ising model by investigating different forms of inter-spin interactions and computing timescales. We show that variation in inter-spin interactions leads to a better memory capacity in general, by engineering the type of interactions the capacity can be greatly enhanced and there exists an optimal timescale at which the capacity is maximized. To connect computational capabilities to physical properties of the underlaying system, we also study the out-of-time-ordered correlator and find that its faster decay implies a more accurate memory. Furthermore, as an example application on real world data, we use QRC to predict stock values.
Reliability of fNIRS for noninvasive monitoring of brain function and emotion in sheep
Authors: Chincarini Matteo , Dalla Costa Emanuela , Qiu Lina , Spinelli Lorenzo , Cannas Simona , Palestrini Clara , Canali Elisabetta , Minero Michela , Cozzi Bruno , Ferri Nicola , Ancora Daniele , De Pasquale Francesco , Vignola Giorgio , Torricelli Alessandro 
Published: September 2020

AbstractThe aim of this work was to critically assess if functional near infrared spectroscopy (fNIRS) can be profitably used as a tool for noninvasive recording of brain functions and emotions in sheep. We considered an experimental design including advances in instrumentation (customized wireless multi-distance fNIRS system), more accurate physical modelling (two-layer model for photon diffusion and 3D Monte Carlo simulations), support from neuroanatomical tools (positioning of the fNIRS probe by MRI and DTI data of the very same animals), and rigorous protocols (motor task, startling test) for testing the behavioral response of freely moving sheep. Almost no hemodynamic response was found in the extra-cerebral region in both the motor task and the startling test. In the motor task, as expected we found a canonical hemodynamic response in the cerebral region when sheep were walking. In the startling test, the measured hemodynamic response in the cerebral region was mainly from movement. Overall, these results indicate that with the current setup and probe positioning we are primarily measuring the motor area of the sheep brain, and not probing the too deeply located cortical areas related to processing of emotions.
High-resolution proteomics reveals differences in the proteome of spelt and bread wheat flour representing targets for research on wheat sensitivities
Authors: Afzal Muhammad , Pfannstiel Jens , Zimmermann Julia , Bischoff Stephan C. , Würschum Tobias , Longin C. Friedrich H. 
Published: September 2020

AbstractWheat consumption can trigger celiac disease, allergic reactions and non-celiac wheat sensitivity (NCWS) in humans. Some people with NCWS symptoms claim a better tolerability of spelt compared to bread wheat products. We therefore investigated potential differences in the proteomes of spelt and bread wheat flour using nano LC–ESI–MS/MS on a set of 15 representative varieties for each of the two species. Based on the bread wheat reference, we detected 3,050 proteins in total and for most of them the expression was mainly affected by the environment. By contrast, 274 and 409 proteins in spelt and bread wheat, respectively, had a heritability ≥ 0.4 highlighting the potential to influence their expression level by varietal choice. We found 84 and 193 unique proteins for spelt and bread wheat, respectively, and 396 joint proteins, which expression differed significantly (p ≤ 0.05) when comparing both species. Thus, about one third of proteins differed significantly between spelt and bread wheat. Of them, we identified 81 proteins with high heritability, which therefore might be interesting candidates for future research on wheat hypersensitivities.
Clinical assessment of adenosine stress and rest cardiac magnetic resonance T1 mapping for detecting ischemic and infarcted myocardium
Authors: Yimcharoen Sirilak , Zhang Shuo , Kaolawanich Yodying , Tanapibunpon Prajak , Krittayaphong Rungroj 
Published: September 2020

AbstractCardiac magnetic resonance (CMR) spin-lattice relaxation time (T1) may be influenced by pathologic conditions due to changes in myocardial water content. We aimed to validate the principle and investigate T1 mapping at rest and adenosine stress to differentiate ischemic and infarcted myocardium from controls. Patients with suspected coronary artery disease who underwent CMR were prospectively recruited. Native rest and adenosine stress T1 maps were obtained using standard modified Look-Locker Inversion-Recovery technique. Among 181 patients included, T1 values were measured from three groups. In the control group, 72 patients showed myocardium with a T1 profile of 1,039 ± 75 ms at rest and a significant increase during stress (4.79 ± 3.14%, p < 0.001). While the ischemic (51 patients) and infarcted (58 patients) groups showed elevated resting T1 compared to controls (1,040 ± 90 ms for ischemic; 1,239 ± 121 ms for infarcted, p < 0.001), neither of which presented significant T1 reactivity (1.38 ± 3.02% for ischemic; 1.55 ± 5.25% for infarcted). We concluded that adenosine stress and rest T1 mapping may be useful to differentiate normal, ischemic and infarcted myocardium.
Intensified ambulatory cardiology care: effects on mortality and hospitalisation—a comparative observational study
Authors: Sawicki Olga A. , Mueller Angelina , Glushan Anastasiya , Breitkreuz Thorben , Wicke Felix S. , Karimova Kateryna , Gerlach Ferdinand M. , Wensing Michel , Smetak Norbert , Bosch Ralph F. , Beyer Martin 
Published: September 2020

AbstractSince 2010, an intensified ambulatory cardiology care programme has been implemented in southern Germany. To improve patient management, the structure of cardiac disease management was improved, guideline-recommended care was supported, new ambulatory medical services and a morbidity-adapted reimbursement system were set up. Our aim was to determine the effects of this programme on the mortality and hospitalisation of enrolled patients with cardiac disorders. We conducted a comparative observational study in 2015 and 2016, based on insurance claims data. Overall, 13,404 enrolled patients with chronic heart failure (CHF) and 19,537 with coronary artery disease (CAD) were compared, respectively, to 8,776 and 16,696 patients that were receiving usual ambulatory cardiology care. Compared to the control group, patients enrolled in the programme had lower mortality (Hazard Ratio: 0.84; 95% CI: 0.77–0.91) and fewer all-cause hospitalisations (Rate Ratio: 0.94; 95% CI: 0.90–0.97). CHF-related hospitalisations in patients with CHF were also reduced (Rate Ratio: 0.76; 95% CI: 0.69–0.84). CAD patients showed a similar reduction in mortality rates (Hazard Ratio: 0.81; 95% CI: 0.76–0.88) and all-cause hospitalisation (Rate Ratio: 0.94; 95% CI: 0.91–0.97), but there was no effect on CAD-related hospitalisation. We conclude that intensified ambulatory care reduced mortality and hospitalisation in cardiology patients.
Functional groups of rotifers and an exotic species in a tropical shallow lake
Authors: Arcifa Marlene Sofia , de Souza Bruno Barretto , de Morais-Junior Cláudio Simões , Bruno Cyntia Goulart Corrêa 
Published: September 2020

AbstractIn freshwater environments the rotifer group may be divided into microphagous and raptorial species regarding their feeding patterns, and such guilds differently interact with other community components. Here, we analyzed the influence of cladocerans, cyclopoid nauplii, temperature, food resources and an exotic species on rotifer guilds, based on weekly samplings for 1 year. We have identified rotifer species and their trophi types in order to separate them into the raptorial and microphagous functional groups. The ratio raptorial:microphagous rotifers (Guild ratio, GR) was used in interaction analyses with cladocerans, nauplii, temperature, food resources and the exotic speciesKellicottia bostoniensis. Correlations between total rotifers and food (phytoplankton carbon) and temperature were negative and significant, therefore, these factors did not lead to the increase of rotifer community. On the other hand, microphagous rotifers had opposing relation to cladoceran densities, as GR values showed that they became predominant when cladoceran populations declined. The use of density-based GR was adequate, with similar results compared to biomass-based studies regarding interactions with other organisms. Furthermore, we have found no invasive characteristics for the exotic microphagous rotifer,Kellicottia bostoniensis, and it seems to be outcompeted by the native microphagous species.
Dissipative particle dynamics model of homogalacturonan based on molecular dynamics simulations
Authors: Pieczywek P. M. , Płaziński W. , Zdunek A. 
Published: September 2020

AbstractIn this study we present an alternative dissipative particle dynamics (DPD) parametrization strategy based on data extracted from the united-atom molecular simulations. The model of the homogalacturonan was designed to test the ability of the formation of large-scale structures via hydrogen bonding in water. The extraction of coarse-grained parameters from atomistic molecular dynamics was achieved by means of the proposed molecule aggregation algorithm based on an iterative nearest neighbour search. A novel approach to a time-scale calibration scheme based on matching the average velocities of coarse-grained particles enabled the DPD forcefield to reproduce essential structural features of homogalacturonan molecular chains. The successful application of the proposed parametrization method allowed for the reproduction of the shapes of radial distribution functions, particle velocities and diffusivity of the atomistic molecular dynamics model using DPD force field. The structure of polygalacturonic acid molecules was mapped into the DPD force field by means of the distance and angular bond characteristics, which closely matched the MD results. The resulting DPD trajectories showed that randomly dispersed homogalacturonan chains had a tendency to aggregate into highly organized 3D structures. The final structure resembled a three-dimensional network created by tightly associated homogalacturonan chains organized into thick fibres.