bluuebunny/crossref_metadata_2025_split huggingface dataset:
Asymmetrizing an icosahedral virus capsid by hierarchical assembly of subunits with designed asymmetry
Authors: Zhao Zhongchao , Wang Joseph Che-Yen , Zhang Mi , Lyktey Nicholas A. , Jarrold Martin F. , Jacobson Stephen C. , Zlotnick Adam 
Published: January 2021

AbstractSymmetrical protein complexes are ubiquitous in biology. Many have been re-engineered for chemical and medical applications. Viral capsids and their assembly are frequent platforms for these investigations. A means to create asymmetric capsids may expand applications. Here, starting with homodimeric Hepatitis B Virus capsid protein, we develop a heterodimer, design a hierarchical assembly pathway, and produce asymmetric capsids. In the heterodimer, the two halves have different growth potentials and assemble into hexamers. These preformed hexamers can nucleate co-assembly with other dimers, leading to Janus-like capsids with a small discrete hexamer patch. We can remove the patch specifically and observe asymmetric holey capsids by cryo-EM reconstruction. The resulting hole in the surface can be refilled with fluorescently labeled dimers to regenerate an intact capsid. In this study, we show how an asymmetric subunit can be used to generate an asymmetric particle, creating the potential for a capsid with different surface chemistries.
Strong geometry dependence of the Casimir force between interpenetrated rectangular gratings
Authors: Wang Mingkang , Tang L. , Ng C. Y. , Messina Riccardo , Guizal Brahim , Crosse J. A. , Antezza Mauro , Chan C. T. , Chan H. B. 
Published: January 2021

AbstractQuantum fluctuations give rise to Casimir forces between two parallel conducting plates, the magnitude of which increases monotonically as the separation decreases. By introducing nanoscale gratings to the surfaces, recent advances have opened opportunities for controlling the Casimir force in complex geometries. Here, we measure the Casimir force between two rectangular silicon gratings. Using an on-chip detection platform, we achieve accurate alignment between the two gratings so that they interpenetrate as the separation is reduced. Just before interpenetration occurs, the measured Casimir force is found to have a geometry dependence that is much stronger than previous experiments, with deviations from the proximity force approximation reaching a factor of ~500. After the gratings interpenetrate each other, the Casimir force becomes non-zero and independent of displacement. This work shows that the presence of gratings can strongly modify the Casimir force to control the interaction between nanomechanical components.
A non-invasive multimodal foetal ECG–Doppler dataset for antenatal cardiology research
Authors: Sulas Eleonora , Urru Monica , Tumbarello Roberto , Raffo Luigi , Sameni Reza , Pani Danilo 
Published: January 2021

AbstractNon-invasive foetal electrocardiography (fECG) continues to be an open topic for research. The development of standard algorithms for the extraction of the fECG from the maternal electrophysiological interference is limited by the lack of publicly available reference datasets that could be used to benchmark different algorithms while providing a ground truth for foetal heart activity when an invasive scalp lead is unavailable. In this work, we present the Non-Invasive Multimodal Foetal ECG-Doppler Dataset for Antenatal Cardiology Research (NInFEA), the first open-access multimodal early-pregnancy dataset in the field that features simultaneous non-invasive electrophysiological recordings and foetal pulsed-wave Doppler (PWD). The dataset is mainly conceived for researchers working on fECG signal processing algorithms. The dataset includes 60 entries from 39 pregnant women, between the 21st and 27th week of gestation. Each dataset entry comprises 27 electrophysiological channels (2048 Hz, 22 bits), a maternal respiration signal, synchronised foetal trans-abdominal PWD and clinical annotations provided by expert clinicians during signal acquisition. MATLAB snippets for data processing are also provided.
High-pH reversed-phase fractionated neural retina proteome of normal growing C57BL/6 mouse
Authors: Sze Ying Hon , Zhao Qian , Cheung Jimmy Ka Wai , Li King Kit , Tse Dennis Yan Yin , To Chi Ho , Lam Thomas Chuen 
Published: January 2021

AbstractThe retina is a key sensory tissue composed of multiple layers of cell populations that work coherently to process and decode visual information. Mass spectrometry-based proteomics approach has allowed high-throughput, untargeted protein identification, demonstrating the presence of these proteins in the retina and their involvement in biological signalling cascades. The comprehensive wild-type mouse retina proteome was prepared using a novel sample preparation approach, the suspension trapping (S-Trap) filter, and further fractionated with high-pH reversed phase chromatography involving a total of 28 injections. This data-dependent acquisition (DDA) approach using a Sciex TripleTOF 6600 mass spectrometer identified a total of 7,122 unique proteins (1% FDR), and generated a spectral library of 5,950 proteins in the normal C57BL/6 mouse retina. Data-independent acquisition (DIA) approach relies on a large and high-quality spectral library to analyse chromatograms, this spectral library would enable access to SWATH-MS acquisition to provide unbiased, multiplexed, and quantification of proteins in the mouse retina, acting as the most extensive reference library to investigate retinal diseases using the C57BL/6 mouse model.
Next-generation sequencing for identification of actionable gene mutations in intestinal-type sinonasal adenocarcinoma
Authors: Sánchez-Fernández Paula , Riobello Cristina , Costales María , Vivanco Blanca , Cabal Virginia N. , García-Marín Rocío , Suárez-Fernández Laura , López Fernando , Cabanillas Rubén , Hermsen Mario A. , Llorente José Luis 
Published: January 2021

AbstractIntestinal-type sinonasal adenocarcinoma (ITAC) is a rare tumor carrying poor prognosis and needing new treatment options. The aim of this study was to identify actionable gene mutations that can guide new personalized target-specific therapies in ITAC patients. A series of 48 tumor and 27 corresponding germline DNA samples were analyzed by next generation sequencing using a panel of 120 genes. In total, 223 sequence variants were found in 70 genes. Matched tumor/germline comparison in 27 cases revealed that 57% were in fact germline variants. In 20 of these 27 cases, 58 somatic variants in 33 different genes were identified, the most frequent being PIK3CA (5 cases), APC and ATM (4 cases), and KRAS, NF1, LRP1B and BRCA1 (3 cases). Many of the somatic gene variants affected PI3K, MAPK/ERK, WNT and DNA repair signaling pathways, although not in a mutually exclusive manner. None of the alterations were related to histological ITAC subtype, tumor stage or survival. Our data showed that thorough interpretation of somatic mutations requires sequencing analysis of the corresponding germline DNA. Potentially actionable somatic mutations were found in 20 of 27 cases, 8 of which being biomarkers of FDA-approved targeted therapies. Our data implicate new possibilities for personalized treatment of ITAC patients.
Impact of PET data driven respiratory motion correction and BSREM reconstruction of 68Ga-DOTATATE PET/CT for differentiating neuroendocrine tumors (NET) and intrapancreatic accessory spleens (IPAS)
Authors: Liberini Virginia , Kotasidis Fotis , Treyer Valerie , Messerli Michael , Orita Erika , Engel-Bicik Ivette , Siebenhüner Alexander , Huellner Martin W. 
Published: January 2021

AbstractTo evaluate whether quantitative PET parameters of motion-corrected 68Ga-DOTATATE PET/CT can differentiate between intrapancreatic accessory spleens (IPAS) and pancreatic neuroendocrine tumor (pNET). A total of 498 consecutive patients with neuroendocrine tumors (NET) who underwent 68Ga-DOTATATE PET/CT between March 2017 and July 2019 were retrospectively analyzed. Subjects with accessory spleens (n = 43, thereof 7 IPAS) and pNET (n = 9) were included, resulting in a total of 45 scans. PET images were reconstructed using ordered-subsets expectation maximization (OSEM) and a fully convergent iterative image reconstruction algorithm with β-values of 1000 (BSREM1000). A data-driven gating (DDG) technique (MOTIONFREE, GE Healthcare) was applied to extract respiratory triggers and use them for PET motion correction within both reconstructions. PET parameters among different samples were compared using non-parametric tests. Receiver operating characteristics (ROC) analyzed the ability of PET parameters to differentiate IPAS and pNETs. SUVmax was able to distinguish pNET from accessory spleens and IPAs in BSREM1000 reconstructions (p < 0.05). This result was more reliable using DDG-based motion correction (p < 0.003) and was achieved in both OSEM and BSREM1000 reconstructions. For differentiating accessory spleens and pNETs with specificity 100%, the ROC analysis yielded an AUC of 0.742 (sensitivity 56%)/0.765 (sensitivity 56%)/0.846 (sensitivity 62%)/0.840 (sensitivity 63%) for SUVmax 36.7/41.9/36.9/41.7 in OSEM/BSREM1000/OSEM + DDG/BSREM1000 + DDG, respectively. BSREM1000 + DDG can accurately differentiate pNET from accessory spleen. Both BSREM1000 and DDG lead to a significant SUV increase compared to OSEM and non-motion-corrected data.
Higher-order structure of polymer melt described by persistent homology
Authors: Shimizu Yohei , Kurokawa Takanori , Arai Hirokazu , Washizu Hitoshi 
Published: January 2021

AbstractThe optimal method of the polymer Materials Informatics (MI) has not been developed because the amorphous nature of the higher-order structure affects these properties. We have now tried to develop the polymer MI’s descriptor of the higher-order structure using persistent homology as the topological method. We have experimentally studied the influence of the MD simulation cell size as the higher-order structure of the polymer on its electrical properties important for a soft material sensor or actuator device. The all-atom MD simulation of the polymer has been calculated and the obtained atomic coordinate has been analyzed by the persistent homology. The change in the higher-order structure by different cell size simulations affects the dielectric constant, although these changes are not described by a radial distribution function (RDF). On the other hand, using the 2nd order persistent diagram (PD), it was found that when the cell size is small, the island-shaped distribution become smoother as the cell size increased. There is the same tendency for the condition of change in the monomer ratio, the polymer chain length or temperature. As a result, the persistent homology may express the higher-order structure generated by the MD simulation as a descriptor of the polymer MI.
Simultaneous mapping of EMCD signals and crystal orientations in a transmission electron microscope
Authors: Ali Hasan , Rusz Jan , Warnatz Tobias , Hjörvarsson Björgvin , Leifer Klaus 
Published: January 2021

AbstractWhen magnetic properties are analysed in a transmission electron microscope using the technique of electron magnetic circular dichroism (EMCD), one of the critical parameters is the sample orientation. Since small orientation changes can have a strong impact on the measurement of the EMCD signal and such measurements need two separate measurements of conjugate EELS spectra, it is experimentally non-trivial to measure the EMCD signal as a function of sample orientation. Here, we have developed a methodology to simultaneously map the quantitative EMCD signals and the local orientation of the crystal. We analyse, both experimentally and by simulations, how the measured magnetic signals evolve with a change in the crystal tilt. Based on this analysis, we establish an accurate relationship between the crystal orientations and the EMCD signals. Our results demonstrate that a small variation in crystal tilt can significantly alter the strength of the EMCD signal. From an optimisation of the crystal orientation, we obtain quantitative EMCD measurements.
Heterosexual, gay, and lesbian people’s reactivity to virtual caresses on their embodied avatars’ taboo zones
Authors: Fusaro Martina , Lisi Matteo P. , Tieri Gaetano , Aglioti Salvatore Maria 
Published: January 2021

AbstractEmbodying an artificial agent through immersive virtual reality (IVR) may lead to feeling vicariously somatosensory stimuli on one’s body which are in fact never delivered. To explore whether vicarious touch in IVR reflects the basic individual and social features of real-life interpersonal interactions we tested heterosexual men/women and gay men/lesbian women reacting subjectively and physiologically to the observation of a gender-matched virtual body being touched on intimate taboo zones (like genitalia) by male and female avatars. All participants rated as most erogenous caresses on their embodied avatar taboo zones. Crucially, heterosexual men/women and gay men/lesbian women rated as most erogenous taboo touches delivered by their opposite and same gender avatar, respectively. Skin conductance was maximal when taboo touches were delivered by female avatars. Our study shows that IVR may trigger realistic experiences and ultimately allow the direct exploration of sensitive societal and individual issues that can otherwise be explored only through imagination.
Formulation, optimization and characterization of allantoin-loaded chitosan nanoparticles to alleviate ethanol-induced gastric ulcer: in-vitro and in-vivo studies
Authors: Aman Reham Mokhtar , Zaghloul Randa A. , El-Dahhan Marwa S. 
Published: January 2021

AbstractAllantoin (ALL) is a phytochemical possessing an impressive array of biological activities. Nonetheless, developing a nanostructured delivery system targeted to augment the gastric antiulcerogenic activity of ALL has not been so far investigated. Consequently, in this survey, ALL-loaded chitosan/sodium tripolyphosphate nanoparticles (ALL-loaded CS/STPP NPs) were prepared by ionotropic gelation technique and thoroughly characterized. A full 24factorial design was adopted using four independently controlled parameters (ICPs). Comprehensive characterization, in vitro evaluations as well as antiulcerogenic activity study against ethanol-induced gastric ulcer in rats of the optimized NPs formula were conducted. The optimized NPs formula, (CS (1.5% w/v), STPP (0.3% w/v), CS:STPP volume ratio (5:1), ALL amount (13 mg)), was the most convenient one with drug content of 6.26 mg, drug entrapment efficiency % of 48.12%, particle size of 508.3 nm, polydispersity index 0.29 and ζ-potential of + 35.70 mV. It displayed a sustained in vitro release profile and mucoadhesive strength of 45.55%. ALL-loaded CS/STPP NPs (F-9) provoked remarkable antiulcerogenic activity against ethanol-induced gastric ulceration in rats, which was accentuated by histopathological, immunohistochemical (IHC) and biochemical studies. In conclusion, the prepared ALL-loaded CS/STPP NPs could be presented to the phytomedicine field as an auspicious oral delivery system for gastric ulceration management.
Color-tunable bioluminescence imaging portfolio for cell imaging
Authors: Tamaki Shota , Kitada Nobuo , Kiyama Masahiro , Fujii Rika , Hirano Takashi , Kim Sung Bae , Maki Shojiro 
Published: January 2021

AbstractThe present study describes a color-tunable imaging portfolio together with twelve novel coelenterazine (CTZ) analogues. The three groups of CTZ analogues create diverse hues of bioluminescence (BL) ranging from blue to far red with marine luciferases. We found that the hue completes the whole color palette in the visible region and shows red-shifted BL with a marine luciferase: for example, Renilla luciferase 8 (RLuc8) and Artificial Luciferase 16 (ALuc16) show 187 nm- and 105 nm-redshifted spectra, respectively, by simply replacing the substrate CTZ with 1d. The optical properties of the new CTZ analogues were investigated such as the kinetic parameters, dose dependency, and luciferase specificity. The 2-series CTZ analogues interestingly have specificity to ALucs and are completely dark with RLuc derivatives, and 3d is highly specific to only NanoLuc. We further determined the theoretical background of the red-shifted BL maximum wavelengths (λBL) values according to the extended π conjugation of the CTZ backbone using Density Functional Theory (DFT) calculations. This color-tunable BL imaging system provides a useful multicolor imaging portfolio that efficiently images molecular events in mammalian cells.
Corals regulate the distribution and abundance of Symbiodiniaceae and biomolecules in response to changing water depth and sea surface temperature
Authors: Sivaguru Mayandi , Todorov Lauren G. , Miller Carly A. H. , Fouke Courtney E. , Munro Cara M. O. , Fouke Kyle W. , Fouke Kaitlyn E. , Baughman Melinda E. , Fouke Bruce W. 
Published: January 2021

AbstractThe Scleractinian corals Orbicella annularis and O. faveolata have survived by acclimatizing to environmental changes in water depth and sea surface temperature (SST). However, the complex physiological mechanisms by which this is achieved remain only partially understood, limiting the accurate prediction of coral response to future climate change. This study quantitatively tracks spatial and temporal changes in Symbiodiniaceae and biomolecule (chromatophores, calmodulin, carbonic anhydrase and mucus) abundance that are essential to the processes of acclimatization and biomineralization. Decalcified tissues from intact healthy Orbicella biopsies, collected across water depths and seasonal SST changes on Curaçao, were analyzed with novel autofluorescence and immunofluorescence histology techniques that included the use of custom antibodies. O. annularis at 5 m water depth exhibited decreased Symbiodiniaceae and increased chromatophore abundances, while O. faveolata at 12 m water depth exhibited inverse relationships. Analysis of seasonal acclimatization of the O. faveolata holobiont in this study, combined with previous reports, suggests that biomolecules are differentially modulated during transition from cooler to warmer SST. Warmer SST was also accompanied by decreased mucus production and decreased Symbiodiniaceae abundance, which is compensated by increased photosynthetic activity enhanced calcification. These interacting processes have facilitated the remarkable resiliency of the corals through geological time.
Absence of S100A4 in the mouse lens induces an aberrant retina-specific differentiation program and cataract
Authors: Maddala Rupalatha , Gao Junyuan , Mathias Richard T. , Lewis Tylor R. , Arshavsky Vadim Y. , Levine Adriana , Backer Jonathan M. , Bresnick Anne R. , Rao Ponugoti V. 
Published: January 2021

AbstractS100A4, a member of the S100 family of multifunctional calcium-binding proteins, participates in several physiological and pathological processes. In this study, we demonstrate that S100A4 expression is robustly induced in differentiating fiber cells of the ocular lens and that S100A4(−/−) knockout mice develop late-onset cortical cataracts. Transcriptome profiling of lenses from S100A4(−/−) mice revealed a robust increase in the expression of multiple photoreceptor- and Müller glia-specific genes, as well as the olfactory sensory neuron-specific gene, S100A5. This aberrant transcriptional profile is characterized by corresponding increases in the levels of proteins encoded by the aberrantly upregulated genes. Ingenuity pathway network and curated pathway analyses of differentially expressed genes in S100A4(−/−) lenses identified Crx and Nrl transcription factors as the most significant upstream regulators, and revealed that many of the upregulated genes possess promoters containing a high-density of CpG islands bearing trimethylation marks at histone H3K27 and/or H3K4, respectively. In support of this finding, we further documented that S100A4(−/−) knockout lenses have altered levels of trimethylated H3K27 and H3K4. Taken together, our findings suggest that S100A4 suppresses the expression of retinal genes during lens differentiation plausibly via a mechanism involving changes in histone methylation.
Motor cortical excitability predicts cognitive phenotypes in amyotrophic lateral sclerosis
Authors: Agarwal Smriti , Highton-Williamson Elizabeth , Caga Jashelle , Howells James , Dharmadasa Thanuja , Matamala José M. , Ma Yan , Shibuya Kazumoto , Hodges John R. , Ahmed Rebekah M. , Vucic Steve , Kiernan Matthew C. 
Published: January 2021

AbstractAmyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) are well-recognised as an extended disease spectrum. This study hypothesised that cortical hyperexcitability, an early pathophysiological abnormality in ALS, would distinguish cognitive phenotypes, as a surrogate marker of pathological disease burden. 61 patients with ALS, matched for disease duration (pure motor ALS, n = 39; ALS with coexistent FTD, ALS-FTD, n = 12; ALS with cognitive/behavioural abnormalities not meeting FTD criteria, ALS-Cog, n = 10) and 30 age-matched healthy controls. Cognitive function on the Addenbrooke’s cognitive examination (ACE) scale, behavioural function on the motor neuron disease behavior scale (MiND-B) and cortical excitability using transcranial magnetic stimulation (TMS) were documented. Cortical resting motor threshold (RMT), lower threshold indicating hyperexcitability, was lower in ALS-FTD (50.2 ± 6.9) compared to controls (64.3 ± 12.6, p < 0.005), while ALS-Cog (63.3 ± 12.7) and ALS (60.8 ± 13.9, not significant) were similar to controls. Short interval intracortical inhibition (SICI) was reduced across all ALS groups compared to controls, indicating hyperexcitability. On receiver operating characteristic curve analysis, RMT differentiated ALS-FTD from ALS (area under the curve AUC = 0.745, p = 0.011). The present study has identified a distinct pattern of cortical excitability across cognitive phenotypes in ALS. As such, assessment of cortical physiology may provide more precise clinical prognostication in ALS.
Direct current stimulation enhances neuronal alpha-synuclein degradation in vitro
Authors: Sala Gessica , Bocci Tommaso , Borzì Valentina , Parazzini Marta , Priori Alberto , Ferrarese Carlo 
Published: January 2021

AbstractDespite transcranial Direct Current Stimulation (DCS) is currently proposed as a symptomatic treatment in Parkinson’s disease, the intracellular and molecular mechanisms elicited by this technique are still unknown, and its disease-modifying potential unexplored. Aim of this study was to elucidate the on-line and off-line effects of DCS on the expression, aggregation and degradation of alpha-synuclein (asyn) in a human neuroblastoma cell line under basal conditions and in presence of pharmachologically-induced increased asyn levels. Following DCS, gene and protein expression of asyn and its main autophagic catabolic pathways were assessed by real-time PCR and Western blot, extracellular asyn levels by Dot blot. We found that, under standard conditions, DCS increased monomeric and reduced oligomeric asyn forms, with a concomitant down-regulation of both macroautophagy and chaperone-mediated autophagy. Differently, in presence of rotenone-induced increased asyn, DCS efficiently counteracted asyn accumulation, not acting on its gene transcription, but potentiating its degradation. DCS also reduced intracellular and extracellular asyn levels, increased following lysosomal inhibition, independently from autophagic degradation, suggesting that other mechanisms are also involved. Collectively, these findings suggest that DCS exerts on-line and off-line effects on the expression, aggregation and autophagic degradation of asyn, indicating a till unknown neuroprotective role of tDCS.