bluuebunny/crossref_metadata_2025_split huggingface dataset:
Replicability of neural responses to speech accent is driven by study design and analytical parameters
Authors: Strauber C. Benjamin , Ali Lestat R. , Fujioka Takako , Thille Candace , McCandliss Bruce D. 
Published: February 2021

AbstractRecent studies have reported evidence that listeners' brains process meaning differently in speech with an in-group as compared to an out-group accent. However, among studies that have used electroencephalography (EEG) to examine neural correlates of semantic processing of speech in different accents, the details of findings are often in conflict, potentially reflecting critical variations in experimental design and/or data analysis parameters. To determine which of these factors might be driving inconsistencies in results across studies, we systematically investigate how analysis parameter sets from several of these studies impact results obtained from our own EEG data set. Data were collected from forty-nine monolingual North American English listeners in an event-related potential (ERP) paradigm as they listened to semantically congruent and incongruent sentences spoken in an American accent and an Indian accent. Several key effects of in-group as compared to out-group accent were robust across the range of parameters found in the literature, including more negative scalp-wide responses to incongruence in the N400 range, more positive posterior responses to congruence in the N400 range, and more positive posterior responses to incongruence in the P600 range. These findings, however, are not fully consistent with the reported observations of the studies whose parameters we used, indicating variation in experimental design may be at play. Other reported effects only emerged under a subset of the analytical parameters tested, suggesting that analytical parameters also drive differences. We hope this spurs discussion of analytical parameters and investigation of the contributions of individual study design variables in this growing field.
Investigation of biological activity of soil fungal extracts and LC/MS-QTOF based metabolite profiling
Authors: Mohammed Afrah E. , Sonbol Hana , Alwakeel Suaad Saleh , Alotaibi Modhi O. , Alotaibi Sohailah , Alothman Nouf , Suliman Rasha Saad , Ahmedah Hanadi Talal , Ali Rizwan 
Published: February 2021

AbstractSoil is considered an extensively explored ecological niche for microorganisms that produce useful biologically active natural products suitable for pharmaceutical applications. The current study aimed at investigating biological activities and metabolic profiles of three fungal strains identified from different desert sites in Saudi Arabia. Soil fungal isolates were collected from AlQasab, Tabuk, and Almuzahimiyah in Saudi Arabia and identified. Furthermore, their antibacterial activity was investigated against Staphylococcus aureus, Enterococcus faecalis, Klebsiella pneumonia, and Escherichia coli in blood, nutrient, and Sabouraud dextrose agars. Moreover, fungal extracts were evaluated on cell viability/proliferation against human breast carcinoma and colorectal adenocarcinoma cells. To identify the biomolecules of the fungal extracts, High-performance liquid chromatography HPLC–DAD coupled to analytical LC–QTOF-MS method was employed for fungal ethyl acetate crude extract. Identified fungal isolates, Chaetomium sp. Bipolaris sp. and Fusarium venenatum showed varied inhibitory activity against tested microbes in relation to crude extract, microbial strain tested, and growth media. F. venenatum showed higher anticancer activity compared to Chaetomium sp. and Bipolaris sp. extracts against four of the tested cancer cell lines. Screening by HPLC and LC/MS-QTOF identified nine compounds from Chaetomium sp. and three from Bipolaris sp. however, for F. venenatum extracts compounds were not fully identified. In light of the present findings, some biological activities of fungal extracts were approved in vitro, suggesting that such extracts could be a useful starting point to find compounds that possess promising agents for medical applications. Further investigations to identify exact biomolecules from F. venenatum extracts are needed.
Insight into the surface activity of defect structure in α-MnO2 nanorod: first-principles research
Authors: Zhao Pengsen , Li Guifa , Zheng Haizhong , Lu Shiqiang , Peng Ping 
Published: February 2021

AbstractThe contribution of defect structure to the catalytic property of α-MnO2 nanorod still keeps mysterious right now. Using microfacet models representing defect structure and bulk models with high Miller index, several parameters, such as cohesive energy, surface energy, density of state, electrostatic potential, et al., have been used to investigate the internal mechanism of their chemical activities by first-principles calculation. The results show that the trend in surface energies of microfacet models follows as Esurface[(112 × 211)] > Esurface[(110 × 211)] > Esurface[(100 × 211)] > Esurface[(111 × 211)] > Esurface[(112 × 112)] > Esurface[(111 × 112)], wherein all of them are larger than that of bulk models. So the chemical activity of defect structure is much more powerful than that of bulk surface. Deep researches on electronic structure show that the excellent chemical activity of microfacet structure has larger value in dipole moments and electrostatic potential than that of bulk surface layer. And the microfacet models possess much more peaks of valent electrons in deformantion electronic density and molecular orbital. Density of state indicates that the excellent chemical activity of defect structure comes from their proper hybridization in p and d orbitals.
Native and invasive ants affect floral visits of pollinating honey bees in pumpkin flowers (Cucurbita maxima)
Authors: Unni Anjana Pisharody , Mir Sajad Hussain , Rajesh T. P. , Ballullaya U. Prashanth , Jose Thomas , Sinu Palatty Allesh 
Published: February 2021

AbstractGlobal pollinator decline is a major concern. Several factors—climate change, land-use change, the reduction of flowers, pesticide use, and invasive species—have been suggested as the reasons. Despite being a potential reason, the effect of ants on flowers received less attention. The consequences of ants being attracted to nectar sources in plants vary depending upon factors like the nectar source's position, ants' identity, and other mutualists interacting with the plants. We studied the interaction between flower-visiting ants and pollinators in Cucurbita maxima and compared the competition exerted by native and invasive ants on its pollinators to examine the hypothesis that the invasive ants exacerbate more interference competition to pollinators than the native ants. We assessed the pollinator's choice, visitation rate, and time spent/visit on the flowers. Regardless of species and nativity, ants negatively influenced all the pollinator visitation traits, such as visitation rate and duration spent on flowers. The invasive ants exerted a higher interference competition on the pollinators than the native ants did. Despite performing pollination in flowers with generalist pollination syndrome, ants can threaten plant-pollinator mutualism in specialist plants like monoecious plants. A better understanding of factors influencing pollination will help in implementing better management practices.
Development and validation of a real-time PCR assay to detect Cannabis sativa in food
Authors: Weck Sandra , Peterseil Verena , Mayer Helmut K. , Hochegger Rupert 
Published: February 2021

AbstractRegarding the prospective investigation of food authenticity and adulteration the aim of the present study was the development and validation of a real-time PCR assay to identify hemp (Cannabis sativa) which has gained increasing importance as a valuable food ingredient. The assay targets a specific spacer DNA sequence in Cannabis sativa chloroplasts and detects 1.5 pg hemp DNA, which is equivalent to 18 copies/µL. Corresponding to the very low LOD (0.00031 ng/µL) the method allows the detection of hemp even in the infinitesimal concentration of contaminants. Due to a SNP in position 603, hemp can be identified unequivocally and discriminated from its closest relative hops (Humulus lupulus). The PCR method shows no cross-reactivity with 39 of 46 tested plant species. Low cross-reactivity with mulberry, stinging nettle, lavender, cornflower, wine, figs and hops can be neglected, because the Δ Ct-values are > 14, and the obtained Ct-values are beyond the cut-off for a positive assessment (Ct-values ≤ 33). Moreover, the suitability of the method to identify hemp as a food ingredient was proved by analysing diverse food products such as chocolate or cookies.
The σ54 system directly regulates bacterial natural product genes
Authors: Ma Muqing , Welch Roy D. , Garza Anthony G. 
Published: February 2021

AbstractBacterial-derived polyketide and non-ribosomal peptide natural products are crucial sources of therapeutics and yet little is known about the conditions that favor activation of natural product genes or the regulatory machinery controlling their transcription. Recent findings suggest that the σ54 system, which includes σ54-loaded RNA polymerase and transcriptional activators called enhancer binding proteins (EBPs), might be a common regulator of natural product genes. Here, we explored this idea by analyzing a selected group of putative σ54 promoters identified in Myxococcus xanthus natural product gene clusters. We show that mutations in putative σ54-RNA polymerase binding regions and in putative Nla28 EBP binding sites dramatically reduce in vivo promoter activities in growing and developing cells. We also show in vivo promoter activities are reduced in a nla28 mutant, that Nla28 binds to wild-type fragments of these promoters in vitro, and that in vitro binding is lost when the Nla28 binding sites are mutated. Together, our results indicate that M. xanthus uses σ54 promoters for transcription of at least some of its natural product genes. Interestingly, the vast majority of experimentally confirmed and putative σ54 promoters in M. xanthus natural product loci are located within genes and not in intergenic sequences.
Diversity of Avian leukosis virus subgroup J in local chickens, Jiangxi, China
Authors: Li Haiqin , Tan Meifang , Zhang Fanfan , Ji Huayuan , Zeng Yanbing , Yang Qun , Tan Jia , Huang Jiangnan , Su Qi , Huang Yu , Kang Zhaofeng 
Published: February 2021

AbstractAvian leukosis caused by avian leukosis virus (ALV) is one of the most severe diseases endangering the poultry industry. When the eradication measures performed in commercial broilers and layers have achieved excellent results, ALV in some local chickens has gradually attracted attention. Since late 2018, following the re-outbreak of ALV-J in white feather broilers in China, AL-like symptoms also suddenly broke out in some local flocks, leading to great economic losses. In this study, a systematic epidemiological survey was carried out in eight local chicken flocks in Jiangxi Province, China, and 71 strains were finally isolated from 560 samples, with the env sequences of them being successfully sequenced. All of those new isolates belong to subgroup J but they have different molecular features and were very different from the strains that emerged in white feature broilers recently, with some strains being highly consistent with those previously isolated from commercial broilers, layers and other flocks or even isolated from USA and Russian, suggesting these local chickens have been acted as reservoirs to accumulate various ALV-J strains for a long time. More seriously, phylogenetic analysis shows that there were also many novel strains emerging and in a separate evolutionary branch, indicating several new mutated ALVs are being bred in local chickens. Besides, ALV-J strains isolated in this study can be further divided into ten groups, while there were more or fewer groups in different chickens, revealing that ALV may cross propagate in those flocks. The above analyses explain the complex background and future evolution trend of ALV-J in Chinese local chickens, providing theoretical support for the establishment of corresponding prevention and control measures.
An immortalized porcine macrophage cell line competent for the isolation of African swine fever virus
Authors: Masujin Kentaro , Kitamura Tomoya , Kameyama Ken -ichiro , Okadera Kota , Nishi Tatsuya , Takenouchi Takato , Kitani Hiroshi , Kokuho Takehiro 
Published: February 2021

AbstractAfrican swine fever virus (ASFV) is the etiological agent of African swine fever (ASF), a fatal hemorrhagic disease of domestic pigs and wild boar. The virus primarily infects macrophage and monocyte host cells, these do not grow in vitro. Many attempts have been made to establish sustainable ASFV-sensitive cell lines, but which supported only low viral replication levels of limited, mostly artificially attenuated strains of ASFV. Here, we examined the competence of a novel cell line of immortalized porcine kidney macrophages (IPKM) for ASFV infection. We demonstrated that IPKM cells can facilitate high levels (> 107.0 TCID50/mL) of viral replication of ASFV, and hemadsorption reactions and cytopathic effects were observed as with porcine alveolar macrophages when inoculated with virulent field isolates: Armenia07, Kenya05/Tk-1, and Espana75. These results suggested that IPKM may be a valuable tool for the isolation, replication, and genetic manipulation of ASFV in both basic and applied ASF research.
Prediction accuracy of standard and total keratometry by swept-source optical biometer for multifocal intraocular lens power calculation
Authors: Lee Hun , Chung Jae Lim , Kim Young Jun , Kim Jae Yong , Tchah Hungwon 
Published: February 2021

AbstractWe aimed to compare the refractive outcomes of cataract surgery with diffractive multifocal intraocular lenses (IOLs) using standard keratometry (K) and total keratometry (TK). In this retrospective observational case series study, a total of 302 patients who underwent cataract surgery with multifocal IOL implantation were included. Predicted refractive outcomes were calculated based on the current standard formulas and a new formula developed for TK using K and TK, which were obtained from a swept-source optical biometer. At 2-month postoperatively, median absolute prediction errors (MedAEs) and proportion of eyes within ± 0.50 diopters (D) of predicted postoperative spherical equivalent (SE) refraction were analyzed. There was no significant difference between MedAEs or proportion of eyes within ± 0.50D of predicted refraction from K and TK in each formula. In TFNT00 and 839MP IOL cases, there was no difference between MedAEs from K and TK using any formula. In 829MP IOL cases, MedAE from TK was significantly larger than that from K in Barrett Universal II/Barrett TK Universal II (P = 0.033). In 677MY IOL cases, MedAE from TK was significantly larger than that from K in Haigis (P = 0.020) and Holladay 2 (P = 0.006) formulas. In the subgroup analysis for IOL, there was no difference between the proportion of eyes within ± 0.50 D of predicted refraction from K and TK using any formula. TFNT00 and 839MP IOLs were favorable with TK, with 677MY IOL with K and 829MP IOL being in a neutral position, which necessitates the study that investigates the accuracy of the new TK technology.
Homologies between SARS-CoV-2 and allergen proteins may direct T cell-mediated heterologous immune responses
Authors: Balz Kathrin , Kaushik Abhinav , Chen Meng , Cemic Franz , Heger Vanessa , Renz Harald , Nadeau Kari , Skevaki Chrysanthi 
Published: February 2021

AbstractThe outbreak of the new severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is a public health emergency. Asthma does not represent a risk factor for COVID-19 in several published cohorts. We hypothesized that the SARS-CoV-2 proteome contains T cell epitopes, which are potentially cross-reactive to allergen epitopes. We aimed at identifying homologous peptide sequences by means of two distinct complementary bioinformatics approaches. Pipeline 1 included prediction of MHC Class I and Class II epitopes contained in the SARS-CoV-2 proteome and allergens along with alignment and elaborate ranking approaches. Pipeline 2 involved alignment of SARS-CoV-2 overlapping peptides with known allergen-derived T cell epitopes. Our results indicate a large number of MHC Class I epitope pairs including known as well as de novo predicted allergen T cell epitopes with high probability for cross-reactivity. Allergen sources, such as Aspergillus fumigatus, Phleum pratense and Dermatophagoides species are of particular interest due to their association with multiple cross-reactive candidate peptides, independently of the applied bioinformatic approach. In contrast, peptides derived from food allergens, as well as MHC class II epitopes did not achieve high in silico ranking and were therefore not further investigated. Our findings warrant further experimental confirmation along with examination of the functional importance of such cross-reactive responses.
An alternative food source for metabolism and longevity studies in Caenorhabditis elegans
Authors: Beydoun Safa , Choi Hyo Sub , Dela-Cruz Gabrielle , Kruempel Joseph , Huang Shijiao , Bazopoulou Daphne , Miller Hillary A. , Schaller Megan L. , Evans Charles R. , Leiser Scott F. 
Published: February 2021

AbstractCaenorhabditis elegans is an instrumental research model used to advance our knowledge in areas including development, metabolism, and aging. However, research on metabolism and/or other measures of health/aging are confounded by the nematode’s food source in the lab, live E. coli bacteria. Commonly used treatments, including ultraviolet irradiation and antibiotics, are successful in preventing bacterial replication, but the bacteria can remain metabolically active. The purpose of this study is to develop a metabolically inactive food source for the worms that will allow us to minimize the confounding effects of bacterial metabolism on worm metabolism and aging. Our strategy is to use a paraformaldehyde (PFA) treated E. coli food source and to determine its effects on worm health, metabolism and longevity. We initially determine the lowest possible concentrations of PFA necessary to rapidly and reproducibly kill bacteria. We then measure various aspects of worm behavior, healthspan and longevity, including growth rate, food attraction, brood size, lifespan and metabolic assessments, such as oxygen consumption and metabolomics. Our resulting data show that worms eat and grow well on these bacteria and support the use of 0.5% PFA-killed bacteria as a nematode food source for metabolic, drug, and longevity experiments.
The cancer glycocalyx mediates intravascular adhesion and extravasation during metastatic dissemination
Authors: Offeddu Giovanni S. , Hajal Cynthia , Foley Colleen R. , Wan Zhengpeng , Ibrahim Lina , Coughlin Mark F. , Kamm Roger D. 
Published: February 2021

AbstractThe glycocalyx on tumor cells has been recently identified as an important driver for cancer progression, possibly providing critical opportunities for treatment. Metastasis, in particular, is often the limiting step in the survival to cancer, yet our understanding of how tumor cells escape the vascular system to initiate metastatic sites remains limited. Using an in vitro model of the human microvasculature, we assess here the importance of the tumor and vascular glycocalyces during tumor cell extravasation. Through selective manipulation of individual components of the glycocalyx, we reveal a mechanism whereby tumor cells prepare an adhesive vascular niche by depositing components of the glycocalyx along the endothelium. Accumulated hyaluronic acid shed by tumor cells subsequently mediates adhesion to the endothelium via the glycoprotein CD44. Trans-endothelial migration and invasion into the stroma occurs through binding of the isoform CD44v to components of the sub-endothelial extra-cellular matrix. Targeting of the hyaluronic acid-CD44 glycocalyx complex results in significant reduction in the extravasation of tumor cells. These studies provide evidence of tumor cells repurposing the glycocalyx to promote adhesive interactions leading to cancer progression. Such glycocalyx-mediated mechanisms may be therapeutically targeted to hinder metastasis and improve patient survival.
Enhanced NRT1.1/NPF6.3 expression in shoots improves growth under nitrogen deficiency stress in Arabidopsis
Authors: Sakuraba Yasuhito , Chaganzhana  , Mabuchi Atsushi , Iba Koh , Yanagisawa Shuichi 
Published: February 2021

AbstractIdentification of genes and their alleles capable of improving plant growth under low nitrogen (N) conditions is key for developing sustainable agriculture. Here, we show that a genome-wide association study using Arabidopsis thaliana accessions suggested an association between different magnitudes of N deficiency responses and diversity in NRT1.1/NPF6.3 that encodes a dual-affinity nitrate transporter involved in nitrate uptake by roots. Various analyses using accessions exhibiting reduced N deficiency responses revealed that enhanced NRT1.1 expression in shoots rather than in roots is responsible for better growth of Arabidopsis seedlings under N deficient conditions. Furthermore, polymorphisms that increased NRT1.1 promoter activity were identified in the NRT1.1 promoter sequences of the accessions analyzed. Hence, our data indicated that polymorphism-dependent activation of the NRT1.1 promoter in shoots could serve as a tool in molecular breeding programs for improving plant growth in low N environments.
Identification of a conserved virion-stabilizing network inside the interprotomer pocket of enteroviruses
Authors: Flatt Justin W. , Domanska Aušra , Seppälä Alma L. , Butcher Sarah J. 
Published: February 2021

AbstractEnteroviruses pose a persistent and widespread threat to human physical health, with no specific treatments available. Small molecule capsid binders have the potential to be developed as antivirals that prevent virus attachment and entry into host cells. To aid with broad-range drug development, we report here structures of coxsackieviruses B3 and B4 bound to different interprotomer-targeting capsid binders using single-particle cryo-EM. The EM density maps are beyond 3 Å resolution, providing detailed information about interactions in the ligand-binding pocket. Comparative analysis revealed the residues that form a conserved virion-stabilizing network at the interprotomer site, and showed the small molecule properties that allow anchoring in the pocket to inhibit virus disassembly.
Alkanes increase the stability of early life membrane models under extreme pressure and temperature conditions
Authors: Misuraca Loreto , Demé Bruno , Oger Philippe , Peters Judith 
Published: February 2021

AbstractTerrestrial life appeared on our planet within a time window of [4.4–3.5] billion years ago. During that time, it is suggested that the first proto-cellular forms developed in the surrounding of deep-sea hydrothermal vents, oceanic crust fractures that are still present nowadays. However, these environments are characterized by extreme temperature and pressure conditions that question the early membrane compartment’s capability to endure a stable structural state. Recent studies proposed an adaptive strategy employed by present-day extremophiles: the use of apolar molecules as structural membrane components in order to tune the bilayer dynamic response when needed. Here we extend this hypothesis on early life protomembrane models, using linear and branched alkanes as apolar stabilizing molecules of prebiotic relevance. The structural ordering and chain dynamics of these systems have been investigated as a function of temperature and pressure. We found that both types of alkanes studied, even the simplest linear ones, impact highly the multilamellar vesicle ordering and chain dynamics. Our data show that alkane-enriched membranes have a lower multilamellar vesicle swelling induced by the temperature increase and are significantly less affected by pressure variation as compared to alkane-free samples, suggesting a possible survival strategy for the first living forms.