bluuebunny/crossref_metadata_2025_split huggingface dataset:
Changes of urinary proteomic before and after QIV and COVID-19 vaccination
Authors: Pan Xuanzhen , Liu Yongtao , Bao Yijin , Wei Lilong , Gao Youhe 
Published: March 2022

AbstractWe first collected a young people’s urine samples cohort of quadrivalent influenza vaccine. Urine protein at 24 hours after vaccination was enriched in immune-related pathways, though the specific pathways varied. Perhaps because different people may be in a previous life encountered some of the viruses in the vaccine, the second immunization was triggered. Or everyone has a different constitution, exposure to the same virus triggering different immunity. We then collected urine samples from several uninfected SARS-CoV-2 young people before and after the first, second, and third doses of the COVID-19 vaccine. We found that the differential protein compared between after the second dose (24h) and before the second dose enriched pathways were involved in regulated exocytosis and immune-related pathways, indicating not first exposure to antigen. Surprisingly, the urine differential protein-enriched pathways before and after the first dose were similar to those before and after the second dose. We assume that although the volunteers have not been infected with SARS-CoV-2, they might have been exposed to other coimmunogenic coronaviruses. 2~4h after the third vaccination, the differentially expressed protein also enriched regulated exocytosis and immune-related pathways, indicating that the body has triggered the immune response in a very short time after vaccination, and urine proteome is a good window to monitor the changes of human immune function.
Neural Correlates of Linguistic Collocations During Continuous Speech Perception
Authors: Garibyan Armine , Schilling Achim , Boehm Claudia , Zankl Alexandra , Krauss Patrick 
Published: March 2022

AbstractLanguage is fundamentally predictable, both on a higher schematic level as well as low-level lexical items. Regarding predictability on a lexical level, collocations are frequent co-occurrences of words that are often characterized by high strength of association. So far, psycho-and neurolin guistic studies have mostly employed highly artificial experimental paradigms in the investigation of collocations by focusing on the processing of single words or isolated sentences. In contrast, here we analyze EEG brain responses recorded during stimulation with continuous speech, i.e. audio books. We find that the N400 response to collocations is significantly different from that of non-collocations, whereas the effect varies with respect to cortical region (anterior/ posterior) and laterality (left/right). Our results are in line with studies using continuous speech, and they mostly contradict those using artificial paradigms and stimuli. To the best of our knowledge, this is the first neurolinguistic study on collocations using continuous speech stimulation.
Influence of residual microbial nucleic acid in instruments for hip joint arthroplasty on false-positive results of metagenomic sequencing
Authors: Yin Han , Wang Chengtan , Xu Duliang , Xu Mingtao , Ha Chengzhi , Li Wei , Pang Feng , Wang Dawei 
Published: March 2022

AbstractThe purpose of this study was to analyze the effect of residual microbial nucleic acid in instruments for hip joint arthroplasty on false-positive sequencing results. Samples were taken from 3 different acetabular reamer for hip arthroplasty in 7 different hospitals. The whole process was strictly aseptic, metagenomic next-generation sequencing (mNGS) was performed according to standard operating procedures. The sterility of instruments was confirmed by culture method. The sequencing results of specimens from different hospitals were compared to analyze the difference of background bacteria. Bioinformatics analysis and visualization were presented through R language. A total of 26 samples were processed by mNGS, including 24 instrument swab samples, 1 blank swab control, and 1 blank water control. 254,314,707 reads were sequenced in all samples. The results showed that 1.13% of Clean Reads can be matched to pathogenic microorganism genomes, of which bacterial sequences account for 87.48%, fungal sequences account for 11.18%, parasite sequences account for 1.26%, and virus sequences account for 0.06%. The results of PCA (Principal Component Analysis) demonstrated that the distribution of bacteria on the surface of instruments was significantly different between medical institutions. Through the Venn diagram, it was found that 465 species of bacteria in all region hospitals, Liaocheng People’s Hospital had a maximum of 340 species of bacteria, followed by Guanxian County People’s Hospital with 169 species. The clustering heat map illustrated that the distribution of bacterial groups in three different instrument samples in the same hospital was basically the same, and the bacterial genera varied significantly among hospitals. The residual microbial nucleic acid fragments are mainly bacterial DNA and represent differences in different medical institutions, The establishment of independent background bacterial libraries in different medical institutions can effectively improve the accuracy of mNGS diagnosis and help to exclude background microorganisms interference.
Dynamics in vertical transmission of viruses in naturally selected and traditionally managed honey bee colonies across Europe
Authors: Claeys Bouuaert David , De Smet Lina , Brunain Marleen , Dahle Bjørn , Blacquière Tjeerd , Dalmon Anne , Dezmirean Daniel , Elen Dylan , Filipi Janja , Giurgiu Alexandru , Gregorc Aleš , Kefuss John , Locke Barbara , de Miranda Joachim R. , Oddie Melissa , Panziera Delphine , Parejo Melanie , Pinto M. Alice , de Graaf Dirk C. 
Published: March 2022

AbstractThe ‘suppressed in-ovo virus infection’ trait (SOV) was the first trait applied in honey bee breeding programs aimed to increase resilience to virus infections, a major threat for colony survival. By screening drone eggs for viruses, the SOV trait scores the antiviral resistance of queens and its implications for vertical transmission. In this study, queens from both naturally surviving and traditionally managed colonies from across Europe were screened using a two-fold improved SOV phenotyping protocol. First, a gel-based RT-PCR was replaced by a RT-qPCR. This not only allowed quantification of the infection load but also increased the test sensitivity. Second, a genotype specific primer set was replaced by a primer set that covered all known deformed wing virus (DWV) genotypes, which resulted in higher virus loads and fewer false negative results. It was demonstrated that incidences of vertical transmission of DWV were more frequent in naturally surviving populations than in traditionally managed colonies, although the virus load in the eggs remained the same. Dynamics in vertical transmission were further emphasized when comparing virus infections with queen age. Interestingly, older queens showed significantly lower infection loads of DWV in both traditionally managed and naturally surviving colonies, as well as reduced DWV infection frequencies in traditionally managed colonies when compared with younger queens. Seasonal variation in vertical transmission was found with lower infection frequencies in spring compared to summer for DWV and black queen cell virus. Together, these patterns in vertical transmission suggest an adaptive antiviral response of queens aimed at reducing vertical transmission over time.
The effects of antibiotic combination treatments onPseudomonas aeruginosatolerance evolution and coexistence withStenotrophomonas maltophilia
Authors: Law Jack P. , Wood A. Jamie , Friman Ville-Petri 
Published: March 2022

AbstractPseudomonas aeruginosabacterium is a common pathogen of Cystic Fibrosis (CF) patients due to its ability to evolve resistance to antibiotics during treatments. WhileP. aeruginosaresistance evolution is well characterised in monocultures, it is less well understood in polymicrobial CF infections. Here, we investigated how exposure to ciprofloxacin, colistin, or tobramycin antibiotics, administered at sub-MIC doses alone and in combination, shaped the tolerance evolution ofP. aeruginosa(PAO1 lab and clinical CF LESB58 strains) in the absence and presence of a commonly co-occurring species,Stenotrophomonas maltophilia. Increases in antibiotic tolerances were primarily driven by the presence of that antibiotic in the treatment. We observed a reciprocal cross-tolerance between ciprofloxacin and tobramycin, and when combined these antibiotics selected increased MICs for all antibiotics. Though the presence ofS. maltophiliadid not affect the tolerance or the MIC evolution, it droveP. aeruginosainto extinction more frequently in the presence of tobramycin due to its relatively greater innate tobramycin tolerance. In contrast,P. aeruginosadominated and droveS. maltophiliaextinct in most other treatments. Together, our findings suggest that besides driving high-level antibiotic tolerance evolution, sub-MIC antibiotic exposure can alter competitive bacterial interactions, leading to target pathogen extinctions in multi-species communities.
Evidence for the role of music on the growth and signal response in duckweed
Authors: Ye Zi , Yang Rui , Xue Ying , Chen Xinglin , Xu Ziyi , Ren Qiuting , Sun Jinge , Ma Xu , Yang Lin 
Published: March 2022

AbstractSound vibration, an external mechanical force, has been proved to modulate plant growth and development like rain, wind, and vibration. However, the role of music on plants, especially on signal response, has been usually neglected in research. Herein, we investigated the growth state, gene expression, and signal response in duckweed treated with soft music. The protein content in duckweed after music treatment for 7 days was about 1.6 times that in duckweed without music treatment. Additionally, Fv/Fm in duckweed treated with music was 0.78, which was significantly higher in comparison with the control group (P < 0.01). Interestingly, music promoted the Glu and Ca signaling response. To further explore the global molecular mechanism, we performed transcriptome analysis. A total of 1296 DEGs were found for all these investigated genes in duckweed treated with music compared to the control group. Among these, up-regulation of the expression of metabolism-related genes related to glycolysis, cell wall biosynthesis, oxidative phosphorylation, and pentose phosphate pathways were found. Overall, these results provided a molecular basis to music-triggered signal response, transcriptomic, and growth changes in duckweed, which also highlighted the potential of music as an environmentally friendly stimulus to promote improved protein production in duckweed.
Cardio PyMEA: A user-friendly, open-source Python application for cardiomyocyte microelectrode array analysis
Authors: Dunham Christopher S. , Mackenzie Madelynn E. , Nakano Haruko , Kim Alexis R. , Nakano Atsushi , Stieg Adam Z. , Gimzewski James K. 
Published: March 2022

AbstractOpen source analytical software for the analysis of electrophysiological cardiomyocyte data offers a variety of new functionalities to complement closed-source, proprietary tools. Here, we present the Cardio PyMEA application, a free, modifiable, and open source program for the analysis of microelectrode array (MEA) data obtained from cardiomyocyte cultures. Cardio PyMEA was written entirely in Python 3 to provide an accessible, integrated workflow that possesses a user-friendly graphical user interface (GUI) written in PyQt5 to allow for performant, cross-platform utilization. This application makes use of object-oriented programming (OOP) principles to facilitate the relatively straightforward incorporation of custom functionalities, e.g. power law analysis, that suit the needs of the user. Cardio PyMEA is available as an open source application under the terms of the GNU General Public License (GPL). The source code for Cardio PyMEA can be downloaded from Github at the following repository: https://github.com/csdunhamUC/cardio_pymea.
Efficient rescue of a newly classified Ebinur lake orthobunyavirus with GFP reporter and its application in rapid antiviral screening
Authors: Ren Nanjie , Wang Fei , Zhao Lu , Wang Shunlong , Zhang Guilin , Li Jiaqi , Zhang Bo , Bergeron Eric , Yuan Zhiming , Xia Han 
Published: March 2022

AbstractOrthobunyaviruses have been reported to cause severe diseases in humans or animals, posing a threat to human health and social economy. Ebinur lake virus (EBIV) is a newly classified orthobunyavirus, which needs further intensive study and therapies to cope with its potential infection risk to human and animals. Here, through the reverse genetics system, the recombinant EBIV of wild type (rEBIV/WT) and NP-conjugated-eGFP (rEBIV/eGFP/S) were rescued for the application of the rapid antiviral drug screening. The eGFP fluorescence signal of the rEBIV/eGFP/S was stable in the process of successive passage in BHK-21 cells (over 10 passages) and this recombinant virus could replicate in various cell lines. Compared to the wild type EBIV, the rEBIV/eGFP/S caused the smaller plaques and its peak titers were lower, suggesting attenuation due to the eGFP insertion. Through the high-content screening (HCS) system, ribavirin showed an inhibitory effect on the rEBIV/eGFP/S with an EC50 of 21.91 μM, while favipiravir did not inhibit, even at high concentrations. In addition, five of ninety-six natural compounds had antiviral against EBIV. The robust reverse genetics system for EBIV will facilitate investigation into replication and assembly mechanisms and assist drug and vaccine development.
Individual behavioral trajectories shape whole-brain connectivity in mice
Authors: Lopes Jadna Bogado , Senko Anna N. , Bahnsen Klaas , Geisler Daniel , Kim Eugene , Bernanos Michel , Cash Diana , Ehrlich Stefan , Vernon Anthony C. , Kempermann Gerd 
Published: March 2022

AbstractIt is widely assumed that our actions shape our brains and that the resulting connections determine who we are. To test this idea in a reductionist setting, in which genes and environment are controlled, we investigated differences in neuroanatomy and structural covariance by ex vivo structural magnetic resonance imaging (MRI) in mice whose behavioral activity was continuously tracked for 3 months in a large, enriched environment. We confirmed that environmental enrichment increases mouse hippocampal volumes. Stratifying the enriched group according to individual longitudinal behavioral trajectories, however, revealed striking differences in mouse brain structural covariance in continuously highly active mice compared to those whose trajectories showed signs of habituating activity. Network-based statistics identified distinct sub-networks of murine structural covariance underlying these differences in behavioral activity. Together, these results reveal that differentiated behavioral trajectories of mice in an enriched environment are associated with differences in brain connectivity.
Production of a functionally active recombinant SARS-CoV-2 (COVID-19) 3C-Like protease and a soluble inactive 3C-like protease-RBD chimeric in a prokaryotic expression system
Authors: De Marco Verissimo Carolina , Lopez-Corrales Jesus , Dorey Amber L. , Cwiklinski Krystyna , Lalor Richard , Calvani Nichola Eliza Davies , Jewhurst Heather L. , Doyle Sean , Dalton John P. 
Published: March 2022

SUMMARYDuring the SARS-CoV-2 intracellular life-cycle, two large polyproteins, pp1a and pp1ab, are produced. Processing of these by viral cysteine proteases, the papain-like protease (PLpro) and the chymotrypsin-like 3C-like protease (3CL-pro) release non-structural proteins necessary for the establishment of the viral replication and transcription complex (RTC), crucial for viral replication. Hence, these proteases are considered prime targets against which anti-COVID-19 drugs could be developed. Here, we describe the expression of a highly soluble and functionally active recombinant 3CL-pro using Escherichia coli BL21 cells. In addition, we assessed the ability of our 3CL-pro to function as a carrier for the Receptor Binding Domain (RBD) of the Spike protein. The co-expressed chimeric protein, 3CLpro-RBD, did not exhibit 3CL-pro activity, but its enhanced solubility made purification easier and improved RBD antigenicity when tested against serum from vaccinated individuals in ELISAs. When used to immunise mice, the 3CLpro-RBD chimer elicited antibodies mainly to the 3CL-pro portion of the molecule indicating that a different chimeric composition (i.e., RBD/full Spike-3CLpro) or expression system (i.e., mammalian cells), might be required to produce and deliver a RBD with immunogenicity similar to the native protein. Chimeric proteins containing the 3CL-pro could represent an innovative approach to developing new COVID-19 vaccines.
Differential Hebbian learning with time-continuous signals for active noise reduction
Authors: Möller Konstantin , Kappel David , Tamosiunaite Minija , Tetzlaff Christian , Porr Bernd , Wörgötter Florentin 
Published: March 2022

AbstractSpike timing-dependent plasticity, related to differential Hebb-rules, has become a leading paradigm in neuronal learning, because weights can grow or shrink depending on the timing of pre- and post-synaptic signals. Here we use this paradigm to reduce unwanted (acoustic) noise. Our system relies on heterosynaptic differential Hebbian learning and we show that it can efficiently eliminate noise by up to −140 dB in multi-microphone setups under various conditions. The system quickly learns, most often within a few seconds, and it is robust with respect to different geometrical microphone configurations, too. Hence, this theoretical study demonstrates that it is possible to successfully transfer differential Hebbian learning, derived from the neurosciences, into a technical domain.
Passionately attached or properly matched? The effect of self-congruence on grocery store loyalty
Authors: Liu Hao , Mu Yu , Fu Xinhong , Liu Yuying 
Published: March 2022

PurposeFresh products' homogeneity makes it difficult for grocery stores to differentiate themselves by improving product or service quality. This study analysed grocery store loyalty from the perspective of self-congruence and compared the relative importance of affective attachment and lifestyle matching, which acts as a mediating mechanism in influencing customer loyalty.Design/methodology/approachIndividuals in Shanghai, Guangzhou, Chengdu, Beijing and Xi'an; representative cities of China's east, south, west, north and central regions, responded to questionnaires. Altogether, 282 valid responses were obtained; structural equation modelling (SEM) was used to test the hypotheses.FindingsThe findings show that lifestyle congruence has a greater mediating effect than emotional attachment in the relationship between store-self congruence and grocery store loyalty. Furthermore, social self-congruence was the dominant dimension of store-self congruence that affects grocery store loyalty.Research limitations/implicationsThe first important academic contribution of this study is the provision of knowledge on the issue of whether to focus on generating grocery store loyalty via the mediating effect of emotional attachment or lifestyle congruence. Furthermore, the empirical findings further clarify the boundary of brand attachment theory, demonstrating the limitation of this theory in explaining the mediating mechanism for self-congruence on loyalty in a context that sells low-involvement products in a collectivistic culture. Another academic contribution focuses on the examination of dominant dimensions of self-congruence.Practical implicationsThis study provides a new strategy for grocery store managers to avoid the trap of homogeneous competition, namely, to clearly define consumers' social rather than personal identity. Additionally, grocery stores should focus on matching their image with target customers' lifestyles when building customer loyalty.Social implicationsThis study's findings also shed light on public policy. Some implications could be increasing the layout rationality of retail commercial outlets to facilitate the interaction between grocery stores and community consumers and promoting the matching of grocery stores and consumer lifestyles. Such policies may boost grocery sales, which in turn would boost farmers' incomes.Originality/valueCompared to previous studies, this study analysed the customer loyalty of grocery stores from the perspective of self-congruence, analysed the mechanisms by which self-congruence influences customer loyalty via the mediating effects of emotional attachment and lifestyle congruence and compared the relative significance of these two paths. Furthermore, this study clarified the relative importance of self-congruence dimensions in influencing grocery store loyalty.
Evaluating logistics outsourcing: a survey conducted with Brazilian industries
Authors: Doratiotto Kaique , Vidal Vieira Jose Geraldo , da Silva Lucas Eric , Fávero Luiz Paulo 
Published: March 2022

PurposeThis research aims to evaluate the factors that influence logistics outsourcing, including the impact of logistics outsourcing on measuring companies' logistics performance. This research provides interactions among the various factors (constructs) such as “financial”, “collaboration and process characteristics”, “external influencer”, and “logistics performance”.Design/methodology/approachTo investigate the interaction between the constructs, structural equation modelling is proposed to understand what the relevant criteria are while outsourcing logistics. Data were acquired from surveys conducted with 129 managers from Brazilian companies in the industry sector.FindingsThe factor “collaboration and process characteristics” is what most influences the “logistics performance” of companies, highlighting the importance of managing contractors; and the “financial” factor also contributes to the logistic outsourcing decision.Research limitations/implicationsSome limitations of this study need to be clarified. First, the model could test the moderate and mediate aspects by using variables inspired on RBV and TCE. Second, the sample is relatively small and restricted to the Brazilian industries' case, although the results may be useful for other countries in the world. Third, the responses represent viewpoints of the people who work in the companies. To address this issue, the authors asked respondents to fill out the questionnaire from the perspective of the organisation.Practical implicationsMost 3PL come from developed countries and find different requirements in Brazil. Then, this new knowledge may help 3L providers better understand the needs of the local or foreign companies that operate in the local market. The measurement model may also help to construct a new organisational process, as it sheds light on the main elements necessary for gathering logistics performance outcomes.Originality/valueTo the best of the authors' knowledge, the literature lacks studies on the interaction among these logistics outsourcing constructs, mainly in emerging markets where significant growth opportunities have led to logistics activities being outsourced. The literature that examines the impact of these constructs on logistics performance is also limited. Therefore, this research contributes to providing a model that measures these impacts according to the company's point of view.