bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nano-spectroscopy of excitons in atomically thin transition metal dichalcogenides
Authors: Zhang Shuai , Li Baichang , Chen Xinzhong , Ruta Francesco L. , Shao Yinming , Sternbach Aaron J. , McLeod A. S. , Sun Zhiyuan , Xiong Lin , Moore S. L. , Xu Xinyi , Wu Wenjing , Shabani Sara , Zhou Lin , Wang Zhiying , Mooshammer Fabian , Ray Essance , Wilson Nathan , Schuck P. J. , Dean C. R. , Pasupathy A. N. , Lipson Michal , Xu Xiaodong , Zhu Xiaoyang , Millis A. J. , Liu Mengkun , Hone James C. , Basov D. N. 
Published: January 2022

AbstractExcitons play a dominant role in the optoelectronic properties of atomically thin van der Waals (vdW) semiconductors. These excitons are amenable to on-demand engineering with diverse control knobs, including dielectric screening, interlayer hybridization, and moiré potentials. However, external stimuli frequently yield heterogeneous excitonic responses at the nano- and meso-scales, making their spatial characterization with conventional diffraction-limited optics a formidable task. Here, we use a scattering-type scanning near-field optical microscope (s-SNOM) to acquire exciton spectra in atomically thin transition metal dichalcogenide microcrystals with previously unattainable 20 nm resolution. Our nano-optical data revealed material- and stacking-dependent exciton spectra of MoSe2, WSe2, and their heterostructures. Furthermore, we extracted the complex dielectric function of these prototypical vdW semiconductors. s-SNOM hyperspectral images uncovered how the dielectric screening modifies excitons at length scales as short as few nanometers. This work paves the way towards understanding and manipulation of excitons in atomically thin layers at the nanoscale.
Galectin-9 restricts hepatitis B virus replication via p62/SQSTM1-mediated selective autophagy of viral core proteins
Authors: Miyakawa Kei , Nishi Mayuko , Ogawa Michinaga , Matsunaga Satoko , Sugiyama Masaya , Nishitsuji Hironori , Kimura Hirokazu , Ohnishi Makoto , Watashi Koichi , Shimotohno Kunitada , Wakita Takaji , Ryo Akihide 
Published: January 2022

AbstractAutophagy has been linked to a wide range of functions, including a degradative process that defends host cells against pathogens. Although the involvement of autophagy in HBV infection has become apparent, it remains unknown whether selective autophagy plays a critical role in HBV restriction. Here, we report that a member of the galectin family, GAL9, directs the autophagic degradation of HBV HBc. BRET screening revealed that GAL9 interacts with HBc in living cells. Ectopic expression of GAL9 induces the formation of HBc-containing cytoplasmic puncta through interaction with another antiviral factor viperin, which co-localized with the autophagosome marker LC3. Mechanistically, GAL9 associates with HBc via viperin at the cytoplasmic puncta and enhanced the auto-ubiquitination of RNF13, resulting in p62 recruitment to form LC3-positive autophagosomes. Notably, both GAL9 and viperin are type I IFN-stimulated genes that act synergistically for the IFN-dependent proteolysis of HBc in HBV-infected hepatocytes. Collectively, these results reveal a previously undescribed antiviral mechanism against HBV in infected cells and a form of crosstalk between the innate immune system and selective autophagy in viral infection.
Relative infectiousness of SARS-CoV-2 vaccine breakthrough infections, reinfections, and primary infections
Authors: Abu-Raddad Laith J. , Chemaitelly Hiam , Ayoub Houssein H. , Tang Patrick , Coyle Peter , Hasan Mohammad R. , Yassine Hadi M. , Benslimane Fatiha M. , Al-Khatib Hebah A. , Al-Kanaani Zaina , Al-Kuwari Einas , Jeremijenko Andrew , Kaleeckal Anvar Hassan , Latif Ali Nizar , Shaik Riyazuddin Mohammad , Abdul-Rahim Hanan F. , Nasrallah Gheyath K. , Al-Kuwari Mohamed Ghaith , Butt Adeel A. , Al-Romaihi Hamad Eid , Al-Khal Abdullatif , Al-Thani Mohametabd H. , Bertollini Roberto 
Published: January 2022

AbstractSARS-CoV-2 breakthrough infections in vaccinated individuals and in those who had a prior infection have been observed globally, but the transmission potential of these infections is unknown. The RT-qPCR cycle threshold (Ct) value is inversely correlated with viral load and culturable virus. Here, we investigate differences in RT-qPCR Ct values across Qatar’s national cohorts of primary infections, reinfections, BNT162b2 (Pfizer-BioNTech) breakthrough infections, and mRNA-1273 (Moderna) breakthrough infections. Our matched-cohort analyses of the randomly diagnosed infections show higher mean Ct value in all cohorts of breakthrough infections compared to the cohort of primary infections in unvaccinated individuals. The Ct value is 1.3 (95% CI: 0.9–1.8) cycles higher for BNT162b2 breakthrough infections, 3.2 (95% CI: 1.9–4.5) cycles higher for mRNA-1273 breakthrough infections, and 4.0 (95% CI: 3.5–4.5) cycles higher for reinfections in unvaccinated individuals. Since Ct value correlates inversely with SARS-CoV-2 infectiousness, these differences imply that vaccine breakthrough infections and reinfections are less infectious than primary infections in unvaccinated individuals. Public health benefits of vaccination may have been underestimated, as COVID-19 vaccines not only protect against acquisition of infection, but also appear to protect against transmission of infection.
Circularly polarised luminescence laser scanning confocal microscopy to study live cell chiral molecular interactions
Authors: Stachelek Patrycja , MacKenzie Lewis , Parker David , Pal Robert 
Published: January 2022

AbstractThe molecular machinery of life is founded on chiral building blocks, but no experimental technique is currently available to distinguish or monitor chiral systems in live cell bio-imaging studies. Luminescent chiral molecules encode a unique optical fingerprint within emitted circularly polarized light (CPL) carrying information about the molecular environment, conformation, and binding state. Here, we present a CPL Laser Scanning Confocal Microscope (CPL-LSCM) capable of simultaneous chiroptical contrast based live-cell imaging of endogenous and engineered CPL-active cellular probes. Further, we demonstrate that CPL-active probes can be activated using two-photon excitation, with complete CPL spectrum recovery. The combination of these two milestone results empowers the multidisciplinary imaging community, allowing the study of chiral interactions on a sub-cellular level in a new (chiral) light.
Confocal imaging dataset to assess endothelial cell orientation during extreme glucose conditions
Authors: Porras Hernández Ana María , Barbe Laurent , Pohlit Hannah , Tenje Maria , Antfolk Maria 
Published: January 2022

AbstractConfocal microscopy offers a mean to extract quantitative data on spatially confined subcellular structures. Here, we provide an imaging dataset of confocal z-stacks on endothelial cells spatially confined on lines with different widths, visualizing the nucleus, F-actin, and zonula occludens-1 (ZO-1), as well as the lines. This dataset also includes confocal images of spatially confined endothelial cells challenged with different glucose conditions. We have validated the image quality by established analytical means using the MeasureImageQuality module of the CellProfilerTM software. We envision that this dataset could be used to extract data on both a population and a single cell level, as well as a learning set for the development of new image analysis tools.
Frequencies and characteristics of genome-wide recombination in Streptococcus agalactiae, Streptococcus pyogenes, and Streptococcus suis
Authors: Lee Isaiah Paolo A. , Andam Cheryl P. 
Published: January 2022

AbstractStreptococcus consists of ecologically diverse species, some of which are important pathogens of humans and animals. We sought to quantify and compare the frequencies and characteristics of within-species recombination in the pan-genomes of Streptococcus agalactiae, Streptococcus pyogenes and Streptococcus suis. We used 1081, 1813 and 1204 publicly available genome sequences of each species, respectively. Based on their core genomes, S. agalactiae had the highest relative rate of recombination to mutation (11.5743) compared to S. pyogenes (1.03) and S. suis (0.57). The proportion of the species pan-genome that have had a history of recombination was 12.85%, 24.18% and 20.50% of the pan-genomes of each species, respectively. The composition of recombining genes varied among the three species, and some of the most frequently recombining genes are implicated in adhesion, colonization, oxidative stress response and biofilm formation. For each species, a total of 22.75%, 29.28% and 18.75% of the recombining genes were associated with prophages. The cargo genes of integrative conjugative elements and integrative and mobilizable elements contained genes associated with antimicrobial resistance and virulence. Homologous recombination and mobilizable pan-genomes enable the creation of novel combinations of genes and sequence variants, and the potential for high-risk clones to emerge.
Viral immune evasins impact antigen presentation by allele-specific trapping of MHC I at the peptide-loading complex
Authors: Sethumadhavan Sunesh , Barth Marie , Spaapen Robbert M. , Schmidt Carla , Trowitzsch Simon , Tampé Robert 
Published: January 2022

AbstractMajor histocompatibility complex class I (MHC I) molecules present antigenic peptides to cytotoxic T cells to eliminate infected or cancerous cells. The transporter associated with antigen processing (TAP) shuttles proteasomally generated peptides into the ER for MHC I loading. As central part of the peptide-loading complex (PLC), TAP is targeted by viral factors, which inhibit peptide supply and thereby impact MHC I-mediated immune responses. However, it is still poorly understood how antigen presentation via different MHC I allotypes is affected by TAP inhibition. Here, we show that conditional expression of herpes simplex viral ICP47 suppresses surface presentation of HLA-A and HLA-C, but not of HLA-B, while the human cytomegaloviral US6 reduces surface levels of all MHC I allotypes. This marked difference in HLA-B antigen presentation is echoed by an enrichment of HLA-B allomorphs at US6-arrested PLC in comparison to ICP47-PLC. Although both viral factors prevent TAP-mediated peptide supply, our data imply that MHC I allomorphs favor different conformationally arrested states of the PLC, leading to differential downregulation of MHC I surface presentation. These findings will help understand MHC I biology in general and will even advance the targeted treatment of infections depending on patients’ allotypes.
Formulating a multi-layered framework for automobile architecture
Authors: Chandra Sushil 
Published: January 2022

AbstractProduct architecture is defined as allocation of components to functions and their interfaces. But what makes this formulation insufficient for automobile architecture is their multi-layered allocation of components and the visual aspect of the architecture. This paper suggests, through an empirical study of two-wheeler models being manufactured by a prominent manufacturer, a multi-tiered framework along with a visual template for two-wheeler architecture which includes their visual schema as well. This paper investigates and demonstrates that this framework and template satisfy the requirements of product architecture by using examples from the domain of motorcycle design. Further, this paper investigates the utility of this framework for platforming strategy, innovation, adoption of new technology and standardization.
Age-related changes in oral sensitivity, taste and smell
Authors: Braun Tobias , Doerr Johanna M. , Peters Laura , Viard Maxime , Reuter Iris , Prosiegel Mario , Weber Susanne , Yeniguen Mesut , Tschernatsch Marlene , Gerriets Tibo , Juenemann Martin , Huttner Hagen B. , Hamzic Samra 
Published: January 2022

AbstractOropharyngeal sensitivity plays a vital role in the initiation of the swallowing reflex and is thought to decline as part of the aging-process. Taste and smell functions appear to decline with age as well. The aim of our study was to generate data of oral sensitivity in healthy participants for future studies and to analyse age-related changes and their interdependence by measuring oral sensitivity, taste, and smell function. The experiment involved 30 participants younger than and 30 participants older than 60. Sensitivity threshold as a surrogate of oral sensitivity was measured at the anterior faucial pillar by electrical stimulation using commercially available pudendal electrode mounted on a gloved finger. Smell and taste were evaluated using commercially available test kits. Mean sensitivity was lower in young participants compared to older participants (1.9 ± 0.59 mA vs. 2.42 ± 1.03 mA;p = 0.021). Young participants also performed better in smell (Score 11.13 ± 0.86 vs 9.3 ± 1.93;p < 0.001) and taste examinations (Score 11.83 ± 1.86 vs 8.53 ± 3.18;p < 0.001). ANCOVA revealed a statistical association between sensitivity and smell (p = 0.08) that was moderated by age (p = 0.044). Electrical threshold testing at the anterior faucial pillar is a simple, safe, and accurate diagnostic measure of oral sensitivity. We detected a decline of oral sensitivity, taste, and smell in older adults.Trial registration:Clinicaltrials.gov, NCT03240965. Registered 7th August 2017—https://clinicaltrials.gov/ct2/show/NCT03240965.
Forecasting asylum-related migration flows with machine learning and data at scale
Authors: Carammia Marcello , Iacus Stefano Maria , Wilkin Teddy 
Published: January 2022

AbstractThe sudden and unexpected migration flows that reached Europe during the so-called ‘refugee crisis’ of 2015–2016 left governments unprepared, exposing significant shortcomings in the field of migration forecasting. Forecasting asylum-related migration is indeed problematic. Migration is a complex system, drivers are composite, measurement incorporates uncertainty, and most migration theories are either under-specified or hardly actionable. As a result, approaches to forecasting generally focus on specific migration flows, and the results are often inconsistent and difficult to generalise. Here we present an adaptive machine learning algorithm that integrates administrative statistics and non-traditional data sources at scale to effectively forecast asylum-related migration flows. We focus on asylum applications lodged in countries of the European Union (EU) by nationals of all countries of origin worldwide, but the same approach can be applied in any context provided adequate migration or asylum data are available. Uniquely, our approach (a) monitors drivers in countries of origin and destination to detect early onset change; (b) models individual country-to-country migration flows separately and on moving time windows; (c) estimates the effects of individual drivers, including lagged effects; (d) delivers forecasts of asylum applications up to four weeks ahead; (e) assesses how patterns of drivers shift over time to describe the functioning and change of migration systems. Our approach draws on migration theory and modelling, international protection, and data science to deliver what is, to our knowledge, the first comprehensive system for forecasting asylum applications based on adaptive models and data at scale. Importantly, this approach can be extended to forecast other social processes.
Oriental freshwater mussels arose in East Gondwana and arrived to Asia on the Indian Plate and Burma Terrane
Authors: Bolotov Ivan N. , Pasupuleti Rajeev , Subba Rao Nalluri V. , Unnikrishnan Suresh Kumar , Chan Nyein , Lunn Zau , Win Than , Gofarov Mikhail Y. , Kondakov Alexander V. , Konopleva Ekaterina S. , Lyubas Artyom A. , Tomilova Alena A. , Vikhrev Ilya V. , Pfenninger Markus , Düwel Sophie S. , Feldmeyer Barbara , Nesemann Hasko F. , Nagel Karl-Otto 
Published: January 2022

AbstractFreshwater mussels cannot spread through oceanic barriers and represent a suitable model to test the continental drift patterns. Here, we reconstruct the diversification of Oriental freshwater mussels (Unionidae) and revise their taxonomy. We show that the Indian Subcontinent harbors a rather taxonomically poor fauna, containing 25 freshwater mussel species from one subfamily (Parreysiinae). This subfamily most likely originated in East Gondwana in the Jurassic and its representatives arrived to Asia on two Gondwanan fragments (Indian Plate and Burma Terrane). We propose that the Burma Terrane was connected with the Indian Plate through the Greater India up to the terminal Cretaceous. Later on, during the entire Paleogene epoch, these blocks have served as isolated evolutionary hotspots for freshwater mussels. The Burma Terrane collided with mainland Asia in the Late Eocene, leading to the origin of the Mekong’s Indochinellini radiation. Our findings indicate that the Burma Terrane had played a major role as a Gondwanan “biotic ferry” alongside with the Indian Plate.
CD97 is associated with mitogenic pathway activation, metabolic reprogramming, and immune microenvironment changes in glioblastoma
Authors: Safaee Michael M. , Wang Elaina J. , Jain Saket , Chen Jia-Shu , Gill Sabraj , Zheng Allison C. , Garcia Joseph H. , Beniwal Angad S. , Tran Y. , Nguyen Alan T. , Trieu Melissa , Leung Kevin , Wells Jim , Maclean James M. , Wycoff Keith , Aghi Manish K. 
Published: January 2022

AbstractGlioblastoma (GBM) is the most common primary brain tumor with a median survival under two years. Using in silico and in vitro techniques, we demonstrate heterogeneous expression of CD97, a leukocyte adhesion marker, in human GBM. Beyond its previous demonstrated role in tumor invasion, we show that CD97 is also associated with upregulation of the mitogen-activated protein kinase/extracellular signal-regulated kinase (MAPK/Erk) and phosphatidylinositol 3-kinase/protein kinase B (PI3K/Akt) pathways in GBM. While CD97 knockout decreased Akt activation, CD97 targeting did not alter MAPK/Erk activation, did not slow GBM cell proliferation in culture, and increased levels of glycolytic and oxidative phosphorylation metabolites. Treatment with a soluble CD97 inhibitor did not alter activation of the MAPK/Erk and PI3K/Akt pathways. Tumors with high CD97 expression were associated with immune microenvironment changes including increased naïve macrophages, regulatory T cells, and resting natural killer (NK) cells. These data suggest that, while CD97 expression is associated with conflicting effects on tumor cell proliferative and metabolic pathways that overall do not affect tumor cell proliferation, CD97 exerts pro-tumoral effects on the tumor immune microenvironment, which along with the pro-invasive effects of CD97 we previously demonstrated, provides impetus to continue exploring CD97 as a therapeutic target in GBM.
Identification of potential edible mushroom as SARS-CoV-2 main protease inhibitor using rational drug designing approach
Authors: Sen Debanjan , Debnath Bimal , Debnath Pradip , Debnath Sudhan , Zaki Magdi E. A. , Masand Vijay H. 
Published: January 2022

AbstractSevere Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is highly pathogenic to humans and has created health care threats worldwide. This urgent situation has focused the researchers worldwide towards the development of novel vaccine or small molecule therapeutics for SARS-CoV-2. Although several vaccines have already been discovered and are in use for the masses, no therapeutic medication has yet been approved by FDA for the treatment of COVID-19. Keeping this in view, in the present study, we have identified promising hits against the main protease (Mpro) of SARS-CoV-2 from edible mushrooms. Structure-based virtual screening (VS) of 2433 compounds derived from mushrooms was performed with Mpro protein (6LU7). Four promising hits, namely, Kynapcin-12 (M_78), Kynapcin-28 (M_82), Kynapcin-24 (M_83), and Neonambiterphenyls-A (M_366) were identified based on the result of docking, Lipinski’s rule, 100 ns molecular dynamics (MD) simulation and MM/PBSA binding free energy calculations. Finally, the inhibitory properties of these hits were compared with three known inhibitors, baicalein (1), baicalin (2), and biflavonoid (3). Data indicated that M_78, M_82 and M_83 compounds present in edible mushroom Polyozellus multiplex were potent inhibitors of Mproprotein (6LU7). It could be concluded that edible mushroom Polyozellus multiplex has potential activity against SARS-CoV-2 infection and identified molecules could be further explored as therapeutic inhibitors against SARS-CoV-2.
The impact of melt versus mechanical wear on the formation of pseudotachylyte veins in accretionary complexes
Authors: Moris-Muttoni B. , Raimbourg H. , Augier R. , Champallier R. , Le Trong E. 
Published: January 2022

AbstractWhether seismic rupture propagates over large distances to generate mega-earthquakes or is rapidly aborted mainly depends on the slip processes within the fault core, including particularly frictional melting or intense grain-size reduction and amorphization. The record of seismic slip in exhumed fault zones consists in many instances in Black Faults Rocks, dark and glass-like-filled aphanitic veins that have been interpreted as resulting from the quenching of frictional melts, i.e. pseudotachylytes. Such interpretation has nevertheless been questioned as similar macro to nano-microstructures have been observed either on intensely comminuted natural fault rocks or on slow creep experiments conducted on crustal rocks, where melting is absent. Here, we report a new dataset of Raman Spectroscopy of Carbonaceous Material analyses, aimed at discriminating the slip weakening processes operating in the fault core during slip. Using high spatial resolution profiles on natural Black Fault Rocks from exhumed accretionary complexes and an experimentally calibrated modelling of Raman intensity ratio evolution with temperature, we assessed different scenarios of temperature evolution during fault slip. None of them is able to account for the distribution of Raman signal, so that in the three studied Black Fault Rocks interpreted so far as natural pseudotachylytes, Raman Spectroscopy of Carbonaceous Material rather reflects the effect of intense and localized strain during fault slip. Furthermore, the absence of thermal imprint on Raman signal puts upper bounds on the temperature reached within the fault zone. If one cannot rule out the occurrence of high and short-lived temperature increase due to friction, the latter was not high enough as to melt the large quartz fraction of the fault zone rocks.