bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optimization of non-coding regions for a non-modified mRNA COVID-19 vaccine
Authors: Gebre Makda S. , Rauch Susanne , Roth Nicole , Yu Jingyou , Chandrashekar Abishek , Mercado Noe B. , He Xuan , Liu Jinyan , McMahan Katherine , Martinot Amanda , Martinez David R. , Giffin Victoria , Hope David , Patel Shivani , Sellers Daniel , Sanborn Owen , Barrett Julia , Liu Xiaowen , Cole Andrew C. , Pessaint Laurent , Valentin Daniel , Flinchbaugh Zack , Yalley-Ogunro Jake , Muench Jeanne , Brown Renita , Cook Anthony , Teow Elyse , Andersen Hanne , Lewis Mark G. , Boon Adrianus C. M. , Baric Ralph S. , Mueller Stefan O. , Petsch Benjamin , Barouch Dan H. 
Published: November 2021

AbstractThe CVnCoV (CureVac) mRNA vaccine for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) was recently evaluated in a phase 2b/3 efficacy trial in humans1. CV2CoV is a second-generation mRNA vaccine containing non-modified nucleosides but with optimized non-coding regions and enhanced antigen expression. Here we report the results of a head-to-head comparison of the immunogenicity and protective efficacy of CVnCoV and CV2CoV in non-human primates. We immunized 18 cynomolgus macaques with two doses of 12 μg lipid nanoparticle-formulated CVnCoV or CV2CoV or with sham (n = 6 per group). Compared with CVnCoV, CV2CoV induced substantially higher titres of binding and neutralizing antibodies, memory B cell responses and T cell responses as well as more potent neutralizing antibody responses against SARS-CoV-2 variants, including the Delta variant. Moreover, CV2CoV was found to be comparably immunogenic to the BNT162b2 (Pfizer) vaccine in macaques. Although CVnCoV provided partial protection against SARS-CoV-2 challenge, CV2CoV afforded more robust protection with markedly lower viral loads in the upper and lower respiratory tracts. Binding and neutralizing antibody titres were correlated with protective efficacy. These data demonstrate that optimization of non-coding regions can greatly improve the immunogenicity and protective efficacy of a non-modified mRNA SARS-CoV-2 vaccine in non-human primates.
Community psychological and behavioural responses to coronavirus disease 2019 over one year of the pandemic in 2020 in Hong Kong
Authors: Liao Qiuyan , Xiao Jingyi , Cheung Justin , Ng Tiffany W. Y. , Lam Wendy W. T. , Ni Michael Y. , Cowling Benjamin J. 
Published: November 2021

AbstractMonitoring community psychological and behavioural responses to coronavirus disease 2019 (COVID-19) is important for informing policy making and risk communication to sustain public compliance with challenging precautionary behaviours and mitigating the psychological impacts. Monthly telephone-based cross-sectional surveys in January–April 2020 and then weekly surveys from May through December 2020 were conducted to monitor changes in public risk perception of COVID-19, personal efficacy in self-protection, confidence in government’s ability to control the pandemic, precautionary behaviours, perceived impact of precautionary behaviours, psychological fatigue and distress in Hong Kong, and examine their inter-relationships. While worry about contracting COVID-19 increased, personal efficacy and confidence in government declined as the community incidence of COVID-19 increased. The public maintained high compliance with most precautionary behaviours throughout but relaxed behaviours that were more challenging when disease incidence declined. Public confidence in government was persistently low throughout, of which, a lower level was associated with more psychological fatigue, lower compliance with precautionary behaviours and greater psychological distress. Perceived greater negative impact of precautionary behaviours was also associated with more psychological fatigue which in turn was associated with relaxation of precautionary behaviours. Female, younger and unemployed individuals reported greater psychological distress throughout different stages of the pandemic. Risk communication should focus on promoting confidence in self-protection and pandemic control to avoid helplessness to act when the pandemic resurges. Policy making should prioritize building public trust, enhancing support for sustaining precautionary behaviours, and helping vulnerable groups to adapt to the stress during the pandemic.
Thermal and optical properties of PMMA films reinforced with Nb2O5 nanoparticles
Authors: Hajduk B. , Bednarski H. , Jarka P. , Janeczek H. , Godzierz M. , Tański T. 
Published: November 2021

AbstractThe article presents the thermal and physical properties of PMMA composite films with the addition of Nb2O5 nanoparticles. The addition of nanoparticles to PMMA mainly influenced the optical transmission and glass transition temperature of composite films compared to pure PMMA. It is clearly visible in the results of the conducted ellipsometric and differential scanning calorimetry tests. X-ray studies showed that the heat treatment of the samples resulted in the ordering of the polymer structure (flattening of the polymer chains). Examining the surface of the samples with scanning electron microscopy, it can be seen that Nb2O5 nanoparticles formed unusual, branched formations resembling "snowflakes".
Social stress drives the multi-wave dynamics of COVID-19 outbreaks
Authors: Kastalskiy Innokentiy A. , Pankratova Evgeniya V. , Mirkes Evgeny M. , Kazantsev Victor B. , Gorban Alexander N. 
Published: November 2021

AbstractThe dynamics of epidemics depend on how people's behavior changes during an outbreak. At the beginning of the epidemic, people do not know about the virus, then, after the outbreak of epidemics and alarm, they begin to comply with the restrictions and the spreading of epidemics may decline. Over time, some people get tired/frustrated by the restrictions and stop following them (exhaustion), especially if the number of new cases drops down. After resting for a while, they can follow the restrictions again. But during this pause the second wave can come and become even stronger then the first one. Studies based on SIR models do not predict the observed quick exit from the first wave of epidemics. Social dynamics should be considered. The appearance of the second wave also depends on social factors. Many generalizations of the SIR model have been developed that take into account the weakening of immunity over time, the evolution of the virus, vaccination and other medical and biological details. However, these more sophisticated models do not explain the apparent differences in outbreak profiles between countries with different intrinsic socio-cultural features. In our work, a system of models of the COVID-19 pandemic is proposed, combining the dynamics of social stress with classical epidemic models. Social stress is described by the tools of sociophysics. The combination of a dynamic SIR-type model with the classical triad of stages of the general adaptation syndrome, alarm-resistance-exhaustion, makes it possible to describe with high accuracy the available statistical data for 13 countries. The sets of kinetic constants corresponding to optimal fit of model to data were found. These constants characterize the ability of society to mobilize efforts against epidemics and maintain this concentration over time and can further help in the development of management strategies specific to a particular society.
Requirement of direct contact between chondrocytes and macrophages for the maturation of regenerative cartilage
Authors: Kanda Kengo , Asawa Yukiyo , Inaki Ryoko , Fujihara Yuko , Hoshi Kazuto , Hikita Atsuhiko 
Published: November 2021

AbstractRegenerative cartilage prepared from cultured chondrocytes is generally immature in vitro and matures after transplantation. Although many factors, including host cells and humoral factors, have been shown to affect cartilage maturation in vivo, the requirement of direct cell–cell contact between host and donor cells remains to be verified. In this study, we examined the host cells that promote cartilage maturation via cell–cell contact. Based on analysis of the transplanted chondrocytes, we examined the contribution of endothelial cells and macrophages. Using a semiclosed device that is permeable to tissue fluids while blocking host cells, we selectively transplanted chondrocytes and HUVECs or untreated/M1-polarized/M2-polarized RAW264.7 cells. As a result, untreated RAW264.7 cells induced cartilage regeneration. Furthermore, an in vitro coculture assay indicated communication between chondrocytes and RAW264.7 cells mediated by RNA, suggesting the involvement of extracellular vesicles in this process. These findings provide insights for establishing a method of in vitro cartilage regeneration.
Interploidy gene flow involving the sexual-asexual cycle facilitates the diversification of gynogenetic triploid Carassius fish
Authors: Mishina Tappei , Takeshima Hirohiko , Takada Mikumi , Iguchi Kei’ichiro , Zhang Chunguang , Zhao Yahui , Kawahara-Miki Ryouka , Hashiguchi Yasuyuki , Tabata Ryoichi , Sasaki Takeshi , Nishida Mutsumi , Watanabe Katsutoshi 
Published: November 2021

AbstractAsexual vertebrates are rare and at risk of extinction due to their restricted adaptability through the loss of genetic recombination. We explore the mechanisms behind the generation and maintenance of genetic diversity in triploid asexual (gynogenetic) Carassius auratus fish, which is widespread in East Asian fresh waters and exhibits one of the most extensive distribution among asexual vertebrates despite its dependence on host sperm. Our analyses of genetic composition using dozens of genetic markers and genome-wide transcriptome sequencing uncover admixed genetic composition of Japanese asexual triploid Carassius consisting of both the diverged Japanese and Eurasian alleles, suggesting the involvement of Eurasian lineages in its origin. However, coexisting sexual diploid relatives and asexual triploids in Japan show regional genetic similarity in both mitochondrial and nuclear markers. These results are attributed to a unique unidirectional gene flow from diploids to sympatric triploids, with the involvement of occasional sexual reproduction. Additionally, the asexual triploid shows a weaker population structure than the sexual diploid, and multiple triploid lineages coexist in most Japanese rivers. The generated diversity via repeated interploidy gene flow as well as an increased establishment of immigrants is assumed to offset the cost of asexual reproduction and might contribute to the successful broad distribution of this asexual vertebrate.
Spatial and temporal patterns of genetic diversity in Bombus terrestris populations of the Iberian Peninsula and their conservation implications
Authors: Cejas Diego , De la Rúa Pilar , Ornosa Concepción , Michez Denis , Muñoz Irene 
Published: November 2021

AbstractThe bumblebee Bombus terrestris is used worldwide for crop pollination. Despite its positive impact on crop yield, it has become a widespread threat to biodiversity due to its interactions with local bumblebee populations. Commercial subspecies introduced to the Iberian Peninsula since the 1990s without any regulation have colonized the environment, with evidence of naturalization and introgression with the endemic subspecies Bombus terrestris lusitanicus. We have used mitochondrial and nuclear genetic data to describe the current genetic diversity of the Iberian population and to estimate the expansion of commercial bumblebees. Samples from the natural distribution range of the commercial subspecies, the natural intergradation area between the two subspecies and from a period prior to the use of commercial colonies (i.e., before the 1990s) have been used for comparison. Our results show that the mitochondrial haplotype of the commercial breeds has spread throughout the territory, which, together with subtle changes observed in the nuclear genetic diversity of the populations, indicates that hybridization and consequent introgression are occurring in most of the peninsula. It is, therefore, necessary to improve the existing legislation concerning the management and exportation of commercial bumblebees to conserve locally adapted populations.
Portable, open-source solutions for estimating wrist position during reaching in people with stroke
Authors: Nie Jeffrey Z. , Nie James W. , Hung Na-Teng , Cotton R. James , Slutzky Marc W. 
Published: November 2021

AbstractArm movement kinematics may provide a more sensitive way to assess neurorehabilitation outcomes than existing metrics. However, measuring arm kinematics in people with stroke can be challenging for traditional optical tracking systems due to non-ideal environments, expense, and difficulty performing required calibration. Here, we present two open-source methods, one using inertial measurement units (IMUs) and another using virtual reality (Vive) sensors, for accurate measurements of wrist position with respect to the shoulder during reaching movements in people with stroke. We assessed the accuracy of each method during a 3D reaching task. We also demonstrated each method’s ability to track two metrics derived from kinematics-sweep area and smoothness-in people with chronic stroke. We computed correlation coefficients between the kinematics estimated by each method when appropriate. Compared to a traditional optical tracking system, both methods accurately tracked the wrist during reaching, with mean signed errors of 0.09 ± 1.81 cm and 0.48 ± 1.58 cm for the IMUs and Vive, respectively. Furthermore, both methods’ estimated kinematics were highly correlated with each other (p < 0.01). By using relatively inexpensive wearable sensors, these methods may be useful for developing kinematic metrics to evaluate stroke rehabilitation outcomes in both laboratory and clinical environments.
Efficiency of cell-type specific and generic promoters in transducing oxytocin neurons and monitoring their neural activity during lactation
Authors: Thirtamara Rajamani Keerthi , Leithead Amanda B. , Kim Michelle , Barbier Marie , Peruggia Michael , Niblo Kristi , Barteczko Lara , Lefevre Arthur , Grinevich Valery , Harony-Nicolas Hala 
Published: November 2021

AbstractHypothalamic oxytocin (OXT) and arginine-vasopressin (AVP) neurons have been at the center of several physiological and behavioral studies. Advances in viral vector biology and the development of transgenic rodent models have allowed for targeted gene expression to study the functions of specific cell populations and brain circuits. In this study, we compared the efficiency of various adeno-associated viral vectors in these cell populations and demonstrated that none of the widely used promoters were, on their own, effective at driving expression of a down-stream fluorescent protein in OXT or AVP neurons. As anticipated, the OXT promoter could efficiently drive gene expression in OXT neurons and this efficiency is solely attributed to the promoter and not the viral serotype. We also report that a dual virus approach using an OXT promoter driven Cre recombinase significantly improved the efficiency of viral transduction in OXT neurons. Finally, we demonstrate the utility of the OXT promoter for conducting functional studies on OXT neurons by using an OXT specific viral system to record neural activity of OXT neurons in lactating female rats across time. We conclude that extreme caution is needed when employing non-neuron-specific viral approaches/promoters to study neural populations within the paraventricular nucleus of the hypothalamus.
Exploring the potential of machine learning for simulations of urban ozone variability
Authors: Ojha Narendra , Girach Imran , Sharma Kiran , Sharma Amit , Singh Narendra , Gunthe Sachin S. 
Published: November 2021

AbstractMachine learning (ML) has emerged as a powerful technique in the Earth system science, nevertheless, its potential to model complex atmospheric chemistry remains largely unexplored. Here, we applied ML to simulate the variability in urban ozone (O3) over Doon valley of the Himalaya. The ML model, trained with past variations in O3 and meteorological conditions, successfully reproduced the independent O3 data (r2 ~ 0.7). Model performance is found to be similar when the variation in major precursors (CO and NOx) were included in the model, instead of the meteorology. Further the inclusion of both precursors and meteorology improved the performance significantly (r2 = 0.86) and the model could also capture the outliers, which are crucial for air quality assessments. We suggest that in absence of high-resolution measurements, ML modeling has profound implications for unraveling the feedback between pollution and meteorology in the fragile Himalayan ecosystem.
Microfluidic active pressure and flow stabiliser
Authors: Södergren Simon , Svensson Karolina , Hjort Klas 
Published: November 2021

AbstractIn microfluidics, a well-known challenge is to obtain reproducible results, often constrained by unstable pressures or flow rates. Today, there are existing stabilisers made for low-pressure microfluidics or high-pressure macrofluidics, often consisting of passive membranes, which cannot stabilise long-term fluctuations. In this work, a novel stabilisation method that is able to handle high pressures in microfluidics is presented. It is based on upstream flow capacitance and thermal control of the fluid’s viscosity through a PID controlled restrictor-chip. The stabiliser consists of a high-pressure-resistant microfluidic glass chip with integrated thin films, used for resistive heating. Thereby, the stabiliser has no moving parts. The quality of the stabilisation was evaluated with an ISCO pump, an HPLC pump, and a Harvard pump. The stability was greatly improved for all three pumps, with the ISCO reaching the highest relative precision of 0.035% and the best accuracy of 8.0 ppm. Poor accuracy of a pump was compensated for in the control algorithm, as it otherwise reduced the capacity to stabilise longer times. As the dead volume of the stabiliser was only 16 nL, it can be integrated into micro-total-analysis- or other lab-on-a-chip-systems. By this work, a new approach to improve the control of microfluidic systems has been achieved.
Characterization of aerosol particles during a high pollution episode over Mexico City
Authors: Carabali Giovanni , Villanueva-Macias José , Ladino Luis A. , Álvarez-Ospina Harry , Raga Graciela B. , Andraca-Ayala Gema , Miranda Javier , Grutter Michel , Silva Ma. Montserrat , Riveros-Rosas David 
Published: November 2021

AbstractMore than 7 thousand wildfires were recorded over Mexico in 2019, affecting almost 640 thousand hectares. Most of these fires occurred during the spring season generating dense smoke plumes, impacting urban areas in the central part of the Mexican plateau. From May 10 to 17, 2019, biomass burning (BB) plumes affected Mexico City (MC) and diffused across the basin, producing PM2.5 levels ~ 2 times higher than the nation's air quality standards. Average PM2.5 concentrations increased sharply from 29.4 ± 7.2 µg m−3 to 65.1 ± 13.6 µg m−3 when the dense smoke plumes were detected. The higher particle concentration impacted the aerosol optical depth (AOD) as values ~ 3 times greater than the annual mean (0.32 ± 0.12) were measured, which resulted in a 17% loss of global horizontal irradiation (GHI). Under these severe pollution conditions, the visibility (Va) was reduced by ~ 80%. The high incidence of strong absorbent particles, such as soot and tarballs was revealed through electron microscopy and X-ray fluorescence (XRF) analysis. These techniques show chemical similarities between MC aerosols and those from the high-altitude (~ 4010 m. a. g. l.) Altzomoni Atmospheric Observatory, evidencing a strong influence of the BB emissions, suggesting a regional transport of these pollutants.
CD8-positive T cells and CD204-positive M2-like macrophages predict postoperative prognosis of very high-risk prostate cancer
Authors: Yanai Yoshinori , Kosaka Takeo , Mikami Shuji , Hongo Hiroshi , Yasumizu Yota , Takeda Toshikazu , Matsumoto Kazuhiro , Miyauchi Jun , Kitano Shigehisa , Oya Mototsugu 
Published: November 2021

AbstractTo stratify the heterogeneity of prostate cancer (PCa) with seminal vesicle invasion (SVI) immunologically after radical prostatectomy focusing on the tumor microenvironment. We retrospectively reviewed the clinicopathological data of 71 PCa patients with SVI, which is known as a factor of very high-risk PCa. Preoperative clinical variables and postoperative pathological variables were evaluated as predictors of biochemical recurrence (BCR) with a multivariate logistic regression. Immune cell infiltration including the CD8-positive cell (CD8+ cell) and CD204-positive M2-like macrophage (CD204+ cell) was investigated by immunohistochemistry. The cumulative incidence and risk of BCR were assessed with a Kaplan–Meier analysis and competing risks regression. A higher CD8+ cell count in the SVI area significantly indicated a favorable prognosis for cancers with SVI (p = 0.004). A lower CD204+ cell count in the SVI area also significantly indicated a favorable prognosis for cancers with SVI (p = 0.004). Furthermore, the combination of the CD8+ and CD204+ cell infiltration ratio of the SVI area to the main tumor area was a significant factor for BCR in the patients with the PCa with SVI (p = 0.001). In PCa patients with SVI, the combination of CD8+ and CD204+ cell infiltration is useful to predict the prognosis.
De novo transcriptome and tissue specific expression analysis of genes associated with biosynthesis of secondary metabolites in Operculina turpethum (L.)
Authors: Biswal Bhagyashree , Jena Biswajit , Giri Alok Kumar , Acharya Laxmikanta 
Published: November 2021

AbstractThis study reported the first-ever de novo transcriptome analysis of Operculina turpethum, a high valued endangered medicinal plant, using the Illumina HiSeq 2500 platform. The de novo assembly generated a total of 64,259 unigenes and 20,870 CDS (coding sequence) with a mean length of 449 bp and 571 bp respectively. Further, 20,218 and 16,458 unigenes showed significant similarity with identified proteins of NR (non-redundant) and UniProt database respectively. The homology search carried out against publicly available database found the best match with Ipomoea nil sequences (82.6%). The KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis identified 6538 unigenes functionally assigned to 378 modules with phenylpropanoid biosynthesis pathway as the most enriched among the secondary metabolite biosynthesis pathway followed by terpenoid biosynthesis. A total of 17,444 DEGs were identified among which majority of the DEGs (Differentially Expressed Gene) involved in secondary metabolite biosynthesis were found to be significantly upregulated in stem as compared to root tissues. The qRT-PCR validation of 9 unigenes involved in phenylpropanoid and terpenoid biosynthesis also showed a similar expression pattern. This finding suggests that stem tissues, rather than root tissues, could be used to prevent uprooting of O. turpethum in the wild, paving the way for the plant's effective conservation. Moreover, the study formed a valuable repository of genetic information which will provide a baseline for further molecular research.